Αr14 RNA explained

αr14 is a family of bacterial small non-coding RNAs with representatives in a broad group of α-proteobacteria. The first member of this family (Smr14C2) was found in a Sinorhizobium meliloti 1021 locus located in the chromosome (C). It was later renamed NfeR1 (Nodule Formation Efficiency RNA) and shown to be highly expressed in salt stress and during the symbiotic interaction on legume roots.[1] Further homology and structure conservation analysis identified 2 other chromosomal copies and 3 plasmidic ones. Moreover, full-length Smr14C homologs have been identified in several nitrogen-fixing symbiotic rhizobia (i.e. R. leguminosarum bv.viciae, R. leguminosarum bv. trifolii, R. etli, and several Mesorhizobium species), in the plant pathogens belonging to Agrobacterium species (i.e. A. tumefaciens, A. vitis, A. radiobacter, and Agrobacterium H13) as well as in a broad spectrum of Brucella species (B. ovis, B. canis, B. abortus and B. microtis, and several biovars of B. melitensis). αr14C RNA species are 115-125 nt long (Table 1) and share a well defined common secondary structure (Figure 1). Most of the αr14 transcripts can be catalogued as trans-acting sRNAs expressed from well-defined promoter regions of independent transcription units within intergenic regions (IGRs) of the α-proteobacterial genomes (Figure 5).

Table 1: αr14 homologs in other symbionts and pathogens
CM model Name GI accession number begin end strand %GC length Organism
class=cellinside αr14class=cellinside Smr14C1class=cellinside gi|15963753|ref|NC_003047.1|class=cellinside 206862class=cellinside 206980class=cellinside -class=cellinside 63class=cellinside 119class=cellinside Sinorhizobium meliloti 1021
class=cellinside αr14class=cellinside Smr14C2class=cellinside gi|15963753|ref|NC_003047.1|class=cellinside 1667491class=cellinside 1667613class=cellinside -class=cellinside 65class=cellinside 123class=cellinside Sinorhizobium meliloti 1021
class=cellinside αr14class=cellinside Smr14C3class=cellinside gi|15963753|ref|NC_003047.1|class=cellinside 1667769class=cellinside 1667891class=cellinside -class=cellinside 62class=cellinside 123class=cellinside Sinorhizobium meliloti 1021
class=cellinside αr14class=cellinside Smr14A1class=cellinside gi|16262453|ref|NC_003037.1|class=cellinside 1220690class=cellinside 1220808class=cellinside +class=cellinside 62class=cellinside 119class=cellinside Sinorhizobium meliloti 1021 plasmid pSymA
class=cellinside αr14class=cellinside Smr14A2class=cellinside gi|16262453|ref|NC_003037.1|class=cellinside 1328176class=cellinside 1328301class=cellinside -class=cellinside 60class=cellinside 126class=cellinside Sinorhizobium meliloti 1021 plasmid pSymA
class=cellinside αr14class=cellinside Smr14Bclass=cellinside gi|16263748|ref|NC_003078.1|class=cellinside 1605826class=cellinside 1605943class=cellinside +class=cellinside 64class=cellinside 118class=cellinside Sinorhizobium meliloti 1021 plasmid pSymB
class=cellinside αr14class=cellinside Smedr14C1class=cellinside gi|150395228|ref|NC_009636.1|class=cellinside 1258038class=cellinside 1258160class=cellinside -class=cellinside 63class=cellinside 123class=cellinside Sinorhizobium medicae WSM419 chromosome
class=cellinside αr14class=cellinside Smedr14C2class=cellinside gi|150395228|ref|NC_009636.1|class=cellinside 1258311class=cellinside 1258431class=cellinside -class=cellinside 65class=cellinside 121class=cellinside Sinorhizobium medicae WSM419 chromosome
class=cellinside αr14class=cellinside Smedr14C3class=cellinside gi|150395228|ref|NC_009636.1|class=cellinside 3590299class=cellinside 3590417class=cellinside -class=cellinside 63class=cellinside 119class=cellinside Sinorhizobium medicae WSM419 chromosome
class=cellinside αr14class=cellinside Smedr14p01class=cellinside gi|150375726|ref|NC_009620.1|class=cellinside 679043class=cellinside 679160class=cellinside -class=cellinside 66class=cellinside 118class=cellinside Sinorhizobium medicae WSM419 plasmid pSMED01
class=cellinside αr14class=cellinside Smedr14p021class=cellinside gi|150377168|ref|NC_009621.1|class=cellinside 316304class=cellinside 316428class=cellinside +class=cellinside 64class=cellinside 125class=cellinside Sinorhizobium medicae WSM419 plasmid pSMED02
class=cellinside αr14class=cellinside Smedr14p022class=cellinside gi|150377168|ref|NC_009622.1|class=cellinside 338866class=cellinside 338990class=cellinside +class=cellinside 63class=cellinside 125class=cellinside Sinorhizobium medicae WSM419 plasmid pSMED02
class=cellinside αr14class=cellinside Sfr14C1class=cellinside gi|227820587|ref|NC_012587.1|class=cellinside 1434171class=cellinside 1434293class=cellinside -class=cellinside 64class=cellinside 123class=cellinside Sinorhizobium fredii NGR234 chromosome
class=cellinside αr14class=cellinside Sfr14C2class=cellinside gi|227820587|ref|NC_012587.1|class=cellinside 1434463class=cellinside 1434586class=cellinside -class=cellinside 60class=cellinside 124class=cellinside Sinorhizobium fredii NGR234 chromosome
class=cellinside αr14class=cellinside Sfr14C3class=cellinside gi|227820587|ref|NC_012587.1|class=cellinside 3720579class=cellinside 3720700class=cellinside +class=cellinside 66class=cellinside 122class=cellinside Sinorhizobium fredii NGR234 chromosome
class=cellinside αr14class=cellinside Sfr14bclass=cellinside gi|227818258|ref|NC_012586.1|class=cellinside 2205311class=cellinside 2205428class=cellinside +class=cellinside 64class=cellinside 118class=cellinside Sinorhizobium fredii NGR234 plasmid pNGR234b
class=cellinside αr14class=cellinside Atr14C1class=cellinside gi|159184118|ref|NC_003062.2|class=cellinside 109473class=cellinside 109601class=cellinside +class=cellinside 59class=cellinside 129class=cellinside Agrobacterium tumefaciens str. C58 chromosome circular
class=cellinside αr14class=cellinside Atr14C2class=cellinside gi|159185562|ref|NC_003063.2|class=cellinside 1230297class=cellinside 1230426class=cellinside +class=cellinside 60class=cellinside 130class=cellinside Agrobacterium tumefaciens str. C58 chromosome linear
class=cellinside αr14class=cellinside Atr14C3class=cellinside gi|159185562|ref|NC_003063.2|class=cellinside 1831483class=cellinside 1831614class=cellinside +class=cellinside 57class=cellinside 132class=cellinside Agrobacterium tumefaciens str. C58 chromosome linear
class=cellinside αr14class=cellinside AH13r14C1class=cellinside gi|325291453|ref|NC_015183.1|class=cellinside 109372class=cellinside 109501class=cellinside +class=cellinside 58class=cellinside 130class=cellinside Agrobacterium sp. H13-3 chromosome
class=cellinside αr14class=cellinside ReCIATr14C1class=cellinside gi|190889639|ref|NC_010994.1|class=cellinside 513993class=cellinside 514114class=cellinside +class=cellinside 60class=cellinside 122class=cellinside Rhizobium etli CIAT 652
class=cellinside αr14class=cellinside ReCIATr14C2class=cellinside gi|190889639|ref|NC_010994.1|class=cellinside 1173512class=cellinside 1173639class=cellinside +class=cellinside 59class=cellinside 128class=cellinside Rhizobium etli CIAT 652
class=cellinside αr14class=cellinside ReCIATr14C3class=cellinside gi|190889639|ref|NC_010994.1|class=cellinside 1912478class=cellinside 1912597class=cellinside -class=cellinside 64class=cellinside 120class=cellinside Rhizobium etli CIAT 652
class=cellinside αr14class=cellinside ReCIATr14C4class=cellinside gi|190889639|ref|NC_010994.1|class=cellinside 4444894class=cellinside 4445016class=cellinside -class=cellinside 55class=cellinside 123class=cellinside Rhizobium etli CIAT 652
class=cellinside αr14class=cellinside ReCIATr14Aclass=cellinside gi|190895317|ref|NC_010998.1|class=cellinside 345900class=cellinside 346021class=cellinside -class=cellinside 63class=cellinside 122class=cellinside Rhizobium etli CIAT 652 plasmid pA
class=cellinside αr14class=cellinside ReCIATr14Bclass=cellinside gi|190893983|ref|NC_010996.1|class=cellinside 112292class=cellinside 112425class=cellinside +class=cellinside 61class=cellinside 134class=cellinside Rhizobium etli CIAT 652 plasmid pB
class=cellinside αr14class=cellinside Arr14CI1class=cellinside gi|222084201|ref|NC_011985.1|class=cellinside 597903class=cellinside 598030class=cellinside +class=cellinside 61class=cellinside 128class=cellinside Agrobacterium radiobacter K84 chromosome 1
class=cellinside αr14class=cellinside Arr14CI2class=cellinside gi|222084201|ref|NC_011985.1|class=cellinside 1693278class=cellinside 1693409class=cellinside -class=cellinside 60class=cellinside 132class=cellinside Agrobacterium radiobacter K84 chromosome 1
class=cellinside αr14class=cellinside Arr14CI3class=cellinside gi|222084201|ref|NC_011985.1|class=cellinside 3945511class=cellinside 3945639class=cellinside -class=cellinside 59class=cellinside 129class=cellinside Agrobacterium radiobacter K84 chromosome 1
class=cellinside αr14class=cellinside Arr14CII1class=cellinside gi|222080781|ref|NC_011983.1|class=cellinside 957687class=cellinside 957817class=cellinside +class=cellinside 58class=cellinside 131class=cellinside Agrobacterium radiobacter K84 chromosome 2
class=cellinside αr14class=cellinside Arr14CII2class=cellinside gi|222080781|ref|NC_011983.1|class=cellinside 1921110class=cellinside 1921242class=cellinside -class=cellinside 61class=cellinside 133class=cellinside Agrobacterium radiobacter K84 chromosome 2
class=cellinside αr14class=cellinside Arr14Atcclass=cellinside gi|222101962|ref|NC_011987.1|class=cellinside 138495class=cellinside 138625class=cellinside -class=cellinside 60class=cellinside 131class=cellinside Agrobacterium radiobacter K84 plasmid pAtK84c
class=cellinside αr14class=cellinside Rlt2304r14C1class=cellinside gi|209547612|ref|NC_011369.1|class=cellinside 98050class=cellinside 98171class=cellinside +class=cellinside 60class=cellinside 122class=cellinside Rhizobium leguminosarum bv. trifolii WSM2304 chromosome
class=cellinside αr14class=cellinside Rlt2304r14C2class=cellinside gi|209547612|ref|NC_011369.1|class=cellinside 1534501class=cellinside 1534621class=cellinside -class=cellinside 63class=cellinside 121class=cellinside Rhizobium leguminosarum bv. trifolii WSM2304 chromosome
class=cellinside αr14class=cellinside Rlt2304r14C3class=cellinside gi|209547612|ref|NC_011369.1|class=cellinside 4019326class=cellinside 4019446class=cellinside -class=cellinside 57class=cellinside 121class=cellinside Rhizobium leguminosarum bv. trifolii WSM2304 chromosome
class=cellinside αr14class=cellinside Rlt2304r14p011class=cellinside gi|209546450|ref|NC_011368.1|class=cellinside 306339class=cellinside 306454class=cellinside -class=cellinside 70class=cellinside 116class=cellinside Rhizobium leguminosarum bv trifolii WSM2304 plasmid pRLG201
class=cellinside αr14class=cellinside Rlt2304r14p012class=cellinside gi|209546450|ref|NC_011368.1|class=cellinside 607636class=cellinside 607759class=cellinside +class=cellinside 62class=cellinside 124class=cellinside Rhizobium leguminosarum bv trifolii WSM2304 plasmid pRLG201
class=cellinside αr14class=cellinside Rlt2304r14p02class=cellinside gi|209545999|ref|NC_011366.1|class=cellinside 50814class=cellinside 50936class=cellinside +class=cellinside 63class=cellinside 123class=cellinside Rhizobium leguminosarum bv trifolii WSM2304 plasmid pRLG202
class=cellinside αr14class=cellinside Avr14CI1class=cellinside gi|222147015|ref|NC_011989.1|class=cellinside 115126class=cellinside 115257class=cellinside +class=cellinside 58class=cellinside 132class=cellinside Agrobacterium vitis S4 chromosome 1
class=cellinside αr14class=cellinside Avr14CI2class=cellinside gi|222147015|ref|NC_011989.1|class=cellinside 2043913class=cellinside 2044044class=cellinside -class=cellinside 64class=cellinside 132class=cellinside Agrobacterium vitis S4 chromosome 1
class=cellinside αr14class=cellinside Avr14CI3class=cellinside gi|222147015|ref|NC_011989.1|class=cellinside 2793803class=cellinside 2793939class=cellinside +class=cellinside 63class=cellinside 137class=cellinside Agrobacterium vitis S4 chromosome 1
class=cellinside αr14class=cellinside Avr14CII1class=cellinside gi|222106127|ref|NC_011988.1|class=cellinside 598426class=cellinside 598556class=cellinside +class=cellinside 62class=cellinside 131class=cellinside Agrobacterium vitis S4 chromosome 2
class=cellinside αr14class=cellinside Avr14CII2class=cellinside gi|222106127|ref|NC_011988.1|class=cellinside 901035class=cellinside 901159class=cellinside -class=cellinside 63class=cellinside 125class=cellinside Agrobacterium vitis S4 chromosome 2
class=cellinside αr14class=cellinside Avr14Atcclass=cellinside gi|222083145|ref|NC_011984.1|class=cellinside 7318class=cellinside 7444class=cellinside +class=cellinside 61class=cellinside 127class=cellinside Agrobacterium vitis S4 plasmid pAtS4c
class=cellinside αr14class=cellinside Rlvr14C1class=cellinside gi|116249766|ref|NC_008380.1|class=cellinside 512658class=cellinside 512779class=cellinside +class=cellinside 59class=cellinside 122class=cellinside Rhizobium leguminosarum bv. viciae 3841
class=cellinside αr14class=cellinside Rlvr14C2class=cellinside gi|116249766|ref|NC_008380.1|class=cellinside 2174956class=cellinside 2175074class=cellinside -class=cellinside 65class=cellinside 119class=cellinside Rhizobium leguminosarum bv. viciae 3841
class=cellinside αr14class=cellinside Rlvr14C3class=cellinside gi|116249766|ref|NC_008380.1|class=cellinside 4988030class=cellinside 4988158class=cellinside -class=cellinside 58class=cellinside 129class=cellinside Rhizobium leguminosarum bv. viciae 3841
class=cellinside αr14class=cellinside Rlvr14p11class=cellinside gi|116255200|ref|NC_008384.1|class=cellinside 574471class=cellinside 574593class=cellinside -class=cellinside 59class=cellinside 123class=cellinside Rhizobium leguminosarum bv. viciae 384 plasmid pRL11
class=cellinside αr14class=cellinside Rlvr14p12class=cellinside gi|116248676|ref|NC_008378.1|class=cellinside 407202class=cellinside 407316class=cellinside +class=cellinside 65class=cellinside 115class=cellinside Rhizobium leguminosarum bv. viciae 384 plasmid pRL12
class=cellinside αr14class=cellinside Rlt1325r14C1class=cellinside gi|241202755|ref|NC_012850.1|class=cellinside 107063class=cellinside 107184class=cellinside +class=cellinside 58class=cellinside 122class=cellinside Rhizobium leguminosarum bv. trifolii WSM1325
class=cellinside αr14class=cellinside Rlt1325r14C2class=cellinside gi|241202755|ref|NC_012850.1|class=cellinside 1697038class=cellinside 1697156class=cellinside -class=cellinside 63class=cellinside 119class=cellinside Rhizobium leguminosarum bv. trifolii WSM1325
class=cellinside αr14class=cellinside Rlt1325r14C3class=cellinside gi|241202755|ref|NC_012850.1|class=cellinside 4296632class=cellinside 4296749class=cellinside -class=cellinside 58class=cellinside 118class=cellinside Rhizobium leguminosarum bv. trifolii WSM1325
class=cellinside αr14class=cellinside Rlt1325r14p012class=cellinside gi|241113003|ref|NC_012848.1|class=cellinside 265945class=cellinside 266069class=cellinside +class=cellinside 62class=cellinside 125class=cellinside Rhizobium leguminosarum bv. trifolii WSM1325 plasmid pR132501
class=cellinside αr14class=cellinside Rlt1325r14p011class=cellinside gi|241113003|ref|NC_012848.1|class=cellinside 112604class=cellinside 112728class=cellinside +class=cellinside 66class=cellinside 125class=cellinside Rhizobium leguminosarum bv. trifolii WSM1325 plasmid pR132501
class=cellinside αr14class=cellinside Rlt1325r14p02class=cellinside gi|241666492|ref|NC_012858.1|class=cellinside 28646class=cellinside 28767class=cellinside +class=cellinside 60class=cellinside 122class=cellinside Rhizobium leguminosarum bv. trifolii WSM1325 plasmid pR132502
class=cellinside αr14class=cellinside Rlt1325r14p04class=cellinside gi|241258599|ref|NC_012852.1|class=cellinside 119314class=cellinside 119443class=cellinside +class=cellinside 59class=cellinside 130class=cellinside Rhizobium leguminosarum bv. trifolii WSM1325 plasmid pR132504
class=cellinside αr14class=cellinside Rlt1325r14p05class=cellinside gi|241554070|ref|NC_012854.1|class=cellinside 2286class=cellinside 2409class=cellinside -class=cellinside 65class=cellinside 124class=cellinside Rhizobium leguminosarum bv. trifolii WSM1325 plasmid pR132505
class=cellinside αr14class=cellinside ReCFNr14C1class=cellinside gi|86355669|ref|NC_007761.1|class=cellinside 462566class=cellinside 462687class=cellinside -class=cellinside 58class=cellinside 122class=cellinside Rhizobium etli CFN 42
class=cellinside αr14class=cellinside ReCFNr14C2class=cellinside gi|86355669|ref|NC_007761.1|class=cellinside 1926239class=cellinside 1926358class=cellinside +class=cellinside 65class=cellinside 120class=cellinside Rhizobium etli CFN 42
class=cellinside αr14class=cellinside ReCFNr14C3class=cellinside gi|86355669|ref|NC_007761.1|class=cellinside 4314384class=cellinside 4314505class=cellinside +class=cellinside 58class=cellinside 122class=cellinside Rhizobium etli CFN 42
class=cellinside αr14class=cellinside ReCFNr14eclass=cellinside gi|86360278|ref|NC_007765.1|class=cellinside 443001class=cellinside 443129class=cellinside +class=cellinside 64class=cellinside 129class=cellinside Rhizobium etli CFN 42 plasmid p42e
class=cellinside αr14class=cellinside ReCFNr14fclass=cellinside gi|86360734|ref|NC_007766.1|class=cellinside 22818class=cellinside 22935class=cellinside -class=cellinside 64class=cellinside 118class=cellinside Rhizobium etli CFN 42 plasmid p42f
class=cellinside αr14class=cellinside ReCFNr14dclass=cellinside gi|89255298|ref|NC_004041.2|class=cellinside 77668class=cellinside 77794class=cellinside -class=cellinside 61class=cellinside 127class=cellinside Rhizobium etli CFN 42 symbiotic plasmid p42d
class=cellinside αr14class=cellinside Mlr14C1class=cellinside gi|57165207|ref|NC_002678.2|class=cellinside 890582class=cellinside 890702class=cellinside +class=cellinside 68class=cellinside 121class=cellinside Mesorhizobium loti MAFF303099 chromosome
class=cellinside αr14class=cellinside Mlr14C2class=cellinside gi|57165207|ref|NC_002678.2|class=cellinside 890760class=cellinside 890880class=cellinside +class=cellinside 64class=cellinside 121class=cellinside Mesorhizobium loti MAFF303099 chromosome
class=cellinside αr14class=cellinside Mlr14C3class=cellinside gi|57165207|ref|NC_002678.2|class=cellinside 890941class=cellinside 891061class=cellinside +class=cellinside 63class=cellinside 121class=cellinside Mesorhizobium loti MAFF303099 chromosome
class=cellinside αr14class=cellinside Mlr14C4class=cellinside gi|57165207|ref|NC_002678.2|class=cellinside 5350767class=cellinside 5350882class=cellinside +class=cellinside 65class=cellinside 116class=cellinside Mesorhizobium loti MAFF303099 chromosome
class=cellinside αr14class=cellinside Mlr14C5class=cellinside gi|57165207|ref|NC_002678.2|class=cellinside 6092423class=cellinside 6092540class=cellinside -class=cellinside 64class=cellinside 118class=cellinside Mesorhizobium loti MAFF303099 chromosome
class=cellinside αr14class=cellinside Mcr14C1class=cellinside gi|319779749|ref|NC_014923.1|class=cellinside 3674843class=cellinside 3674963class=cellinside -class=cellinside 64class=cellinside 121class=cellinside Mesorhizobium ciceri biovar biserrulae WSM1271 chromosome
class=cellinside αr14class=cellinside Mcr14C2class=cellinside gi|319779749|ref|NC_014923.1|class=cellinside 3675022class=cellinside 3675142class=cellinside -class=cellinside 67class=cellinside 121class=cellinside Mesorhizobium ciceri biovar biserrulae WSM1271 chromosome
class=cellinside αr14class=cellinside Mcr14C3class=cellinside gi|319779749|ref|NC_014923.1|class=cellinside 3675197class=cellinside 3675318class=cellinside -class=cellinside 65class=cellinside 122class=cellinside Mesorhizobium ciceri biovar biserrulae WSM1271 chromosome
class=cellinside αr14class=cellinside Mcr14C4class=cellinside gi|319779749|ref|NC_014923.1|class=cellinside 2545673class=cellinside 2545788class=cellinside +class=cellinside 64class=cellinside 116class=cellinside Mesorhizobium ciceri biovar biserrulae WSM1271 chromosome
class=cellinside αr14class=cellinside Mcr14C5class=cellinside gi|319779749|ref|NC_014923.1|class=cellinside 5265891class=cellinside 5266009class=cellinside +class=cellinside 63class=cellinside 119class=cellinside Mesorhizobium ciceri biovar biserrulae WSM1271 chromosome
class=cellinside αr14class=cellinside Mcr14p01class=cellinside gi|319777789|ref|NC_014918.1|class=cellinside 241412class=cellinside 241531class=cellinside -class=cellinside 63class=cellinside 120class=cellinside Mesorhizobium ciceri biovar biserrulae WSM1271 plasmid pMESCI01
class=cellinside αr14class=cellinside Bcr14CI1class=cellinside gi|161617991|ref|NC_010103.1|class=cellinside 338021class=cellinside 338128class=cellinside +class=cellinside 56class=cellinside 108class=cellinside Brucella canis ATCC 23365 chromosome I
class=cellinside αr14class=cellinside Bcr14CI2class=cellinside gi|161617991|ref|NC_010103.1|class=cellinside 867217class=cellinside 867335class=cellinside -class=cellinside 60class=cellinside 119class=cellinside Brucella canis ATCC 23365 chromosome I
class=cellinside αr14class=cellinside Bs23445r14CI1class=cellinside gi|163842277|ref|NC_010169.1|class=cellinside 355557class=cellinside 355664class=cellinside +class=cellinside 57class=cellinside 108class=cellinside Brucella suis ATCC 23445 chromosome I
class=cellinside αr14class=cellinside Bs23445r14CI2class=cellinside gi|163842277|ref|NC_010169.1|class=cellinside 888713class=cellinside 888831class=cellinside -class=cellinside 60class=cellinside 119class=cellinside Brucella suis ATCC 23445 chromosome I
class=cellinside αr14class=cellinside Bm16Mr14CI1class=cellinside gi|17986284|ref|NC_003317.1|class=cellinside 1116661class=cellinside 1116787class=cellinside +class=cellinside 59class=cellinside 127class=cellinside Brucella melitensis bv. 1 str. 16M chromosome
class=cellinside αr14class=cellinside Bm16Mr14CI2class=cellinside gi|17986284|ref|NC_003317.1|class=cellinside 1644167class=cellinside 1644273class=cellinside -class=cellinside 56class=cellinside 107class=cellinside Brucella melitensis bv. 1 str. 16M chromosome
class=cellinside αr14class=cellinside BaS19r14CI1class=cellinside gi|189023268|ref|NC_010742.1|class=cellinside 358310class=cellinside 358417class=cellinside +class=cellinside 56class=cellinside 108class=cellinside Brucella abortus S19 chromosome 1
class=cellinside αr14class=cellinside BaS19r14CI2class=cellinside gi|189023268|ref|NC_010742.1|class=cellinside 888877class=cellinside 888995class=cellinside -class=cellinside 59class=cellinside 119class=cellinside Brucella abortus S19 chromosome 1
class=cellinside αr14class=cellinside Bm23457r14CI2class=cellinside gi|225851546|ref|NC_012441.1|class=cellinside 890343class=cellinside 890461class=cellinside -class=cellinside 59class=cellinside 119class=cellinside Brucella melitensis ATCC 23457 chromosome I
class=cellinside αr14class=cellinside Bm23457r14CI1class=cellinside gi|225851546|ref|NC_012441.1|class=cellinside 358976class=cellinside 359082class=cellinside +class=cellinside 56class=cellinside 107class=cellinside Brucella melitensis ATCC 23457 chromosome I
class=cellinside αr14class=cellinside Bs1330r14CI1class=cellinside gi|56968325|ref|NC_004310.3|class=cellinside 338032class=cellinside 338139class=cellinside +class=cellinside 56class=cellinside 108class=cellinside Brucella suis 1330 chromosome I
class=cellinside αr14class=cellinside Bs1330r14CI2class=cellinside gi|56968325|ref|NC_004310.3|class=cellinside 868847class=cellinside 868965class=cellinside -class=cellinside 60class=cellinside 119class=cellinside Brucella suis 1330 chromosome I
class=cellinside αr14class=cellinside Ba19941r14CI1class=cellinside gi|62288991|ref|NC_006932.1|class=cellinside 359925class=cellinside 360032class=cellinside +class=cellinside 56class=cellinside 108class=cellinside Brucella abortus bv. 1 str. 9-941 chromosome I
class=cellinside αr14class=cellinside Ba19941r14CI2class=cellinside gi|62288991|ref|NC_006932.1|class=cellinside 890576class=cellinside 890694class=cellinside -class=cellinside 59class=cellinside 119class=cellinside Brucella abortus bv. 1 str. 9-941 chromosome I
class=cellinside αr14class=cellinside Bmar14CI2class=cellinside gi|82698932|ref|NC_007618.1|class=cellinside 886854class=cellinside 886972class=cellinside -class=cellinside 59class=cellinside 119class=cellinside Brucella melitensis biovar Abortus 2308 chromosome I
class=cellinside αr14class=cellinside Bmar14CI1class=cellinside gi|82698932|ref|NC_007618.1|class=cellinside 356293class=cellinside 356400class=cellinside +class=cellinside 56class=cellinside 108class=cellinside Brucella melitensis biovar Abortus 2308 chromosome I
class=cellinside αr14class=cellinside Bor14CI1class=cellinside gi|148558820|ref|NC_009505.1|class=cellinside 359682class=cellinside 359789class=cellinside +class=cellinside 56class=cellinside 108class=cellinside Brucella ovis ATCC 25840 chromosome I
class=cellinside αr14class=cellinside Bor14CI2class=cellinside gi|148558820|ref|NC_009505.1|class=cellinside 895749class=cellinside 895867class=cellinside -class=cellinside 60class=cellinside 119class=cellinside Brucella ovis ATCC 25840 chromosome I
class=cellinside αr14class=cellinside Bmir14CI1class=cellinside gi|256368465|ref|NC_013119.1|class=cellinside 339699class=cellinside 339806class=cellinside +class=cellinside 57class=cellinside 108class=cellinside Brucella microti CCM 4915 chromosome 1
class=cellinside αr14class=cellinside Bmir14CI2class=cellinside gi|256368465|ref|NC_013119.1|class=cellinside 873049class=cellinside 873167class=cellinside -class=cellinside 60class=cellinside 119class=cellinside Brucella microti CCM 4915 chromosome 1
class=cellinside αr14class=cellinside Oar14CII1class=cellinside gi|153010078|ref|NC_009668.1|class=cellinside 274684class=cellinside 274807class=cellinside +class=cellinside 55class=cellinside 124class=cellinside Brucella anthropi ATCC 49188 chromosome 2
class=cellinside αr14class=cellinside Oar14CII2class=cellinside gi|153010078|ref|NC_009668.1|class=cellinside 1275649class=cellinside 1275772class=cellinside +class=cellinside 58class=cellinside 124class=cellinside Brucella anthropi ATCC 49188 chromosome 2
class=cellinside αr14class=cellinside Oar14CI1class=cellinside gi|153007346|ref|NC_009667.1|class=cellinside 448505class=cellinside 448614class=cellinside +class=cellinside 58class=cellinside 110class=cellinside Brucella anthropi ATCC 49188 chromosome 1
class=cellinside αr14class=cellinside Oar14CI2class=cellinside gi|153007346|ref|NC_009667.1|class=cellinside 2453973class=cellinside 2454100class=cellinside +class=cellinside 56class=cellinside 128class=cellinside Brucella anthropi ATCC 49188 chromosome 1
class=cellinside αr14class=cellinside MsBCNr14C1class=cellinside gi|110632362|ref|NC_008254.1|class=cellinside 1916694class=cellinside 1916817class=cellinside +class=cellinside 60class=cellinside 124class=cellinside Mesorhizobium sp. BNC1
class=cellinside αr14class=cellinside MsBCNr14C2class=cellinside gi|110632362|ref|NC_008254.1|class=cellinside 3977086class=cellinside 3977208class=cellinside -class=cellinside 60class=cellinside 123class=cellinside Mesorhizobium sp. BNC1
class=cellinside αr14class=cellinside MsBCNr14p1class=cellinside gi|110346917|ref|NC_008242.1|class=cellinside 135270class=cellinside 135386class=cellinside -class=cellinside 66class=cellinside 117class=cellinside Mesorhizobium sp. BNC1 plasmid 1

Discovery and structure

Smr14C2 sRNA was described by del Val et al.,[2] as a result of a computational comparative genomic approach consisting in the integration of complementary strategies, designed to search for novel sRNA-encoding genes in the intergenic regions (IGRs) of the reference S. meliloti 1021 strain (http://iant.toulouse.inra.fr/bacteria/annotation/cgi/rhime.cgi) . Northern hybridization experiments confirmed that the predicted smr14C2 locus did express a single transcript of the expected size, which accumulated differentially in free-living and endosymbiotic bacteria. TAP-based 5’-RACE experiments mapped the transcription start site (TSS) of the full-length Smr14C transcript to the 1,667,613 nt position in the S. meliloti 1021 genome (http://iant.toulouse.inra.fr/bacteria/annotation/cgi/rhime.cgi) whereas the 3’-end was assumed to be located at the 1,667,491 nt position matching the last residue of the consecutive stretch of Us of a bona fide Rho-independent terminator (Figure 5). Parallel and later studies[3] [4] in which Smr14C2 transcript is referred to as sra38 or Sm7', independently confirmed the expression this sRNA in S. melilloti and in its closely related strain 2011. Recent deep sequencing-based characterization of the small RNA fraction (50-350 nt) of S. meliloti 2011 further confirmed the expression of Smr14C2 (here referred to as SmelC397), and mapped the 5’- and 3´-ends of the full-length transcript to the same position in the S. meliloti 1021 genome.[5]

The nucleotide sequence of Smr14C2 was initially used as query to search against the Rfam database (version 10.0;http://www.sanger.ac.uk/Software/Rfam). This homology search rendered no matches to known bacterial sRNA in this database. Smr14C2 was next BLASTed with default parameters against all the currently available bacterial genomes (1,615 sequences at 20 April 2011; https://www.ncbi.nlm.nih.gov;). The regions exhibiting significant homology to the query sequence (78-89% similarity) were extracted to create a Covariance Model (CM) from a seed alignment using Infernal (version1.0)[6] (Figure 2). This CM was used in a further search for new members of the αr9 family in the existing bacterial genomic databases and resumed in the following Table 2:

Table 2: Number of copies
Organism Nr. of αr14 chromosomal homologs Nr. of αr14 plasmids homologs Total nr Nr. of αr14 copies
Sinorhizobium meliloti 1021336
Sinorhizobium medicae WSM419336
Sinorhizobium fredii NGR234336
Rhizobium etli CIAT 652336
Rhizobium etli CFN 42336
Rhizobium leguminosarum bv. trifolii WSM2304325
Rhizobium leguminosarum bv. trifolii WSM1325358
Rhizobium leguminosarum bv. viciae 3841426
Agrobacterium sp. H13-32

Agrobacterium vitis S4 3 CI / 2 CII16
Agrobacterium radiobacter K843 CI / 2 CII16
Agrobacterium tumefaciens str. C583
3
Brucella suis ATCC 23445 2
2
Brucella microti CCM 49152
2
Brucella ovis ATCC 25840 2
2
Brucella canis ATCC 23365 2
2
Brucella melitensis ATCC 23457 2
2
Brucella abortus S192
2
Brucella abortus bv 1 str 9-9412
2
Brucella melitensis biovar Abortus 23082
2
Brucella suis 13302
2
Mesorhizobium loti MAFF3030995
5
Mesorhizobium sp. BNC1213
Mesorhizobium ciceri biovar biserrulae WSM127415
Brucella anthropi ATCC 49188 2 CI / 2 CII
4

The results were manually inspected to deduce a consensus secondary structure for the family (Figure 1 and Figure 2). The consensus structure was also independently predicted with the program locARNATE[7] with very similar predictions. The manual inspection of the sequences found with the CM using Infernal allowed finding 101 homolog sequences. The rhizobial species encoding the 36 closer homologs to Smr14C2 were: S. medicae and S. fredii, two R. leguminosarum trifolii strains (WSM2304 and WSM1325), two R. etli strains CFN 42 and CIAT 652, the reference R. leguminosarum bv. viciae 3841 strain, and the Agrobacterium species A. vitis,A. tumefaciens, A. radiobacter and A. H13. All these sequences showed significant Infernal E-values (5.63E-29 - 8.16E-18) and bit-scores. The rest of the sequences found with the model showed high E-values between (1.33E-17 and 8.79E-03) but lower bit-scores and are encoded by Brucella species (B. ovis, B. canis, B. abortus, B. microtis, and several biobars of B. melitensis), Brucella anthropi and the Mesorhizobum species loti, M. ciceri and M. BNC.

The model identified five additional copies in the S. meliloti genome, locating two of them in tandem in the same IGR (Smr14C2, Smr14C3). The same results were obtained for S. medicae (Smedr14C1, Smedr14C2), S. fredii (Sfr14C1, Sfr14C2), M. loti (Mlr14C1, Mlr14C2) and M. ciceri (Mcr14C1, Mcr14C2).

Concerning the additional copies found in the S. meliloti genome, the expression of four out of the five copies have been independently confirmed in recent studies:

There are no experimental evidences up to now for the predicted copy Smr14C1.

Expression information

Parallel studies assessed Smr14C expression in S. meliloti 1021 under different biological conditions; i.e. bacterial growth in TY, minimal medium (MM) and luteolin-MM broth and endosymbiotic bacteria (i.e. mature symbiotic alfalfa nodules) and high salt stress, oxidative stress and cold and hot shock stresses. Expression of Smr14C2 in free-living bacteria was found to be growth-dependent, being the gene strongly down-regulated when bacteria entered the stationary phase. Expression of Smr14C2 increased ~5-fold in nodules when compared with free-living bacteria (log phase TY or MM cultures), suggesting the induction of these sRNAs during bacterial infection and/or bacteroid differentiation. Recent deep sequencing data found differential expression of the plasmic copies. Smr14A1 showed differential expression conditions, with a very low expression level in complex medium and in the same medium at decreased temperature. However, it was strongly up-regulated by heat-shock stress.[5] Smr14B showed an increase of its expression in the stationary phase greater that 8 fold. Moreover, also showed a week upregulation (<8 fold) upon acidic, basic and oxidative stress[5]

Promoter analysis

All the promoter regions of the αr14 family members examined so far are very conserved in a sequence stretch extending up to 120 bp upstream of the transcription start site of the sRNA. All closest homolog loci have recognizable σ70-dependent promoters showing a -35/-10 consensus motif CTTAGAC-n17-CTATAT, which has been previously shown to be widely conserved among several other genera in the α-subgroup of proteobacteria.[8] To identify binding sites for other known transcription factors we used the fasta sequences provided by RegPredict[9] (http://regpredict.lbl.gov/regpredict/help.html), and used those position weight matrices (PSWM) provided by RegulonDB[10] (http://regulondb.ccg.unam.mx). We built PSWM for each transcription factor from the RegPredict sequences using the Consensus/Patser program, choosing the best final matrix for motif lengths between 14 and 30 a threshold average E-value < 10E-10 for each matrix was established, (see "Thresholded consensus" in http://gps-tools2.its.yale.edu). Moreover, we searched for conserved unknown motifs using MEME[11] (http://meme.sdsc.edu/meme4_6_1/intro.html) and used relaxed regular expressions (i.e. pattern matching) over all Smr14C2 homologs promoters. This studies revealed two well defined groups of loci, the first one represented by the closest homologs (Figure 5) that presented a 26 bp long region very conserved between positions -40 and -75, marked as conserved MEME motif in (Figure 5), but no significant similarity to known transcription factor binding sites matrices could be established. A group of not so closely related members of the αr14 family constituted the second group of conserved promoters (Figure6). They presented a different promoter region, very well conserved across all members and an additional unknown 20 bp motif.

Genomic context

Most of the members of the αr14 family are trans-encoded sRNAs transcribed from independent promoters in chromosomal IGRs. Many of the neighboring genes of the seed alignment's members were not annotated and thus were further manually curated.[12] [13] [14] The tandem copies in the Sinorhizobium group's genomes (Smr14C2, Smr14C3, Smedr14C1, Smedr14C2, Sfr14C1, Sfr14C2) presented a conserved genomic context. The gene upstream coded for an unknown protein containing the domain DUF1127 and the gene downstream coded for a trigger factor.

Partially conserved genomic context, DUF1127 protein upstream and 5-keto-4-deoxyuronate isomerase downstream, was found for the plasmidic copies of the Rhizobium group Rlt1325r14p02, Rlvr14p11, Rlt2304r14p02, and ReCIATr14A.

A similar case of partial genomic conservation, DUF1127 protein upstream and tRNA (uracil-5-)-methyltransferase downstream, was found in the case of the Mesorhizobium species, which also presented tandem copies M. loti (Mlr14C1, Mlr14C2) and M. ciceri (Mcr14C1, Mcr14C2). The same context was found for the second copy in the chromosome II of Brucella anthropi (Oar14CII2) and the second copy in chromosome I in the Brucella group (Bor14CI2, Bcr14CI2, Bmir14CI2, Bs1330r14CI2, Bm16Mr14CI1, BaS19r14CI2, Bm23457r14CI1, BMEA_A0934, BruAb1_0906, Ba19941r14CI2). In all these cases the sRNAs did appear as single copy in their IGR. Bs23445r14CI2, Bmar14CI2, and Rlvr14C2 shared the gene coding for tRNA (uracil-5-)-methyltransferase downstream, but did not share the genes coding upstream.

The results showed two other well-conserved genomic contexts. One with a gene coding for nicotinic acid mononucleotide adenylyltransferase upstream and a gene coding for a molybdenum ABC transporter downstream, which is shared by the third copy of ar14 family in the A. radiobacter genome (Arr14CI3) and in the Rhizobium group genomes (ReCFNr14C3, Rlt1325r14C3, Rlvr14C3, Rlt2304r14C3). The second group is formed by the first copy in the Chromosome I in the Brucellas genomes that share the gene upstream coding for an LrgB membrane protein and the gene downstream a coding for an alpha/beta hydrolase.

Additional files:

Table 3: Detailed Genomic context information of the α14 sRNA seed members.! Family !! Feature !! Name !! Strand !! Begin !! End !! Protein name !! Annotation !! Organism
class=cellinside αr14class=cellinside geneclass=cellinside SMc02051class=cellinside Rclass=cellinside 1666735class=cellinside 1666878class=cellinside NP_385651.1class=cellinside DUF1127class=cellinside Sinorhizobium meliloti 1021 (NC_003047)
class=cellinside αr14class=cellinside sRNAclass=cellinside Smr14C2class=cellinside Rclass=cellinside 1667491class=cellinside 1667613class=cellinside -class=cellinside sRNAclass=cellinside Sinorhizobium meliloti 1021 (NC_003047)
class=cellinside αr14class=cellinside sRNAclass=cellinside Smr14C3class=cellinside Rclass=cellinside 1667769class=cellinside 1667891class=cellinside -class=cellinside sRNAclass=cellinside Sinorhizobium meliloti 1021 (NC_003047)
class=cellinside αr14class=cellinside geneclass=cellinside SMc02050class=cellinside Dclass=cellinside 1668357class=cellinside 1668441class=cellinside YP_001326866.1class=cellinside trigger factorclass=cellinside Sinorhizobium meliloti 1021 (NC_003047)
class=cellinside αr14class=cellinside geneclass=cellinside Smed_1180class=cellinside Rclass=cellinside 1257614class=cellinside 1257814class=cellinside YP_001326866.1class=cellinside DUF1127class=cellinside Sinorhizobium medicae WSM419 (NC_009636)
class=cellinside αr14class=cellinside sRNAclass=cellinside Smedr14C1class=cellinside Rclass=cellinside 1258038class=cellinside 1258160class=cellinside -class=cellinside sRNAclass=cellinside Sinorhizobium medicae WSM419 chromosome (NC_009636)
class=cellinside αr14class=cellinside sRNAclass=cellinside Smedr14C2class=cellinside Rclass=cellinside 1258311class=cellinside 1258431class=cellinside -class=cellinside sRNAclass=cellinside Sinorhizobium medicae WSM419 chromosome (NC_009636)
class=cellinside αr14class=cellinside geneclass=cellinside Smed_1181class=cellinside Dclass=cellinside 1258759class=cellinside 1258843class=cellinside YP_001326867.1class=cellinside trigger factorclass=cellinside Sinorhizobium medicae WSM419 chromosome (NC_009636)
class=cellinside αr14class=cellinside geneclass=cellinside RHECIAT_CH0001925class=cellinside Dclass=cellinside 1911937class=cellinside 1912446class=cellinside YP_001978070.1class=cellinside hypothetical proteinclass=cellinside Rhizobium etli CIAT 652 (NC_010994)
class=cellinside αr14class=cellinside sRNAclass=cellinside ReCIATr14C3class=cellinside Rclass=cellinside 1912478class=cellinside 1912597class=cellinside -class=cellinside sRNAclass=cellinside Rhizobium etli CIAT 652 (NC_010994)
class=cellinside αr14class=cellinside geneclass=cellinside RHECIAT_CH0001926class=cellinside Dclass=cellinside 1912923class=cellinside 1914026class=cellinside YP_001978071.1class=cellinside membrane proteinclass=cellinside Rhizobium etli CIAT 652 (NC_010994)
class=cellinside αr14class=cellinside geneclass=cellinside Atu4110class=cellinside Dclass=cellinside 1229427class=cellinside 1230176class=cellinside NP_356536.1class=cellinside serine dehydrogenaseclass=cellinside Agrobacterium tumefaciens str. C58 chromosome linear (NC_003063)
class=cellinside αr14class=cellinside sRNAclass=cellinside Atr14C2class=cellinside Dclass=cellinside 1230297class=cellinside 1230426class=cellinside -class=cellinside sRNAclass=cellinside Agrobacterium tumefaciens str. C58 chromosome linear (NC_003063)
class=cellinside αr14class=cellinside geneclass=cellinside Atu4112class=cellinside Dclass=cellinside 1230719class=cellinside 1231906class=cellinside NP_356534.2class=cellinside proline dipeptidase-metalloexopeptidaseclass=cellinside Agrobacterium tumefaciens str. C58 chromosome linear (NC_003063)
class=cellinside αr14class=cellinside geneclass=cellinside Rleg_1700class=cellinside Rclass=cellinside 1696657class=cellinside 1696803class=cellinside YP_002975526.1class=cellinside DUF1127class=cellinside Rhizobium leguminosarum bv. trifolii WSM1325 (NC_012850)
class=cellinside αr14class=cellinside sRNAclass=cellinside Rlt1325r14C2class=cellinside Rclass=cellinside 1697038class=cellinside 1697156class=cellinside -class=cellinside sRNAclass=cellinside Rhizobium leguminosarum bv. trifolii WSM1325 (NC_012850)
class=cellinside αr14class=cellinside geneclass=cellinside Rleg_1701class=cellinside Dclass=cellinside 1697482class=cellinside 1698585class=cellinside YP_002975527.1class=cellinside membrane proteinclass=cellinside Rhizobium leguminosarum bv. trifolii WSM1325 (NC_012850)
class=cellinside αr14class=cellinside geneclass=cellinside RHE_CH01838class=cellinside Dclass=cellinside 1925699class=cellinside 1926187class=cellinside YP_469358.1class=cellinside hypothetical proteinclass=cellinside Rhizobium etli CFN 42 (NC_007761)
class=cellinside αr14class=cellinside sRNAclass=cellinside ReCFNr14C2class=cellinside Rclass=cellinside 1926239class=cellinside 1926358class=cellinside -class=cellinside sRNAclass=cellinside Rhizobium etli CFN 42 (NC_007761)
class=cellinside αr14class=cellinside geneclass=cellinside RHE_CH01839class=cellinside Dclass=cellinside 1926684class=cellinside 1927778class=cellinside YP_469359.1class=cellinside membrane proteinclass=cellinside Rhizobium etli CFN 42 (NC_007761)
class=cellinside αr14class=cellinside geneclass=cellinside Rleg2_1502class=cellinside Rclass=cellinside 1533929class=cellinside 1534075class=cellinside YP_002281020.1class=cellinside DUF1127class=cellinside Rhizobium leguminosarum bv. trifolii WSM2304 chromosome (NC_011369)
class=cellinside αr14class=cellinside sRNAclass=cellinside Rlt2304r14C2class=cellinside Rclass=cellinside 1534501class=cellinside 1534621class=cellinside -class=cellinside sRNAclass=cellinside Rhizobium leguminosarum bv. trifolii WSM2304 chromosome (NC_011369)
class=cellinside αr14class=cellinside geneclass=cellinside Rleg2_1503class=cellinside Dclass=cellinside 1534947class=cellinside 1536050class=cellinside YP_002281021.1class=cellinside membrane proteinclass=cellinside Rhizobium leguminosarum bv. trifolii WSM2304 chromosome (NC_011369)
class=cellinside αr14class=cellinside geneclass=cellinside AGROH133_02958class=cellinside Rclass=cellinside 108794class=cellinside 109252class=cellinside YP_004277412.1class=cellinside aminoacyl-tRNA ligaseclass=cellinside Agrobacterium sp. H13-3 chromosome (NC_015183)
class=cellinside αr14class=cellinside sRNAclass=cellinside AH13r14C1class=cellinside Dclass=cellinside 109372class=cellinside 109501class=cellinside -class=cellinside sRNAclass=cellinside Agrobacterium sp. H13-3 chromosome (NC_015183)
class=cellinside αr14class=cellinside geneclass=cellinside AGROH133_02961class=cellinside Dclass=cellinside 109733class=cellinside 109942class=cellinside YP_004277414.1class=cellinside cold shock proteinclass=cellinside Agrobacterium sp. H13-3 chromosome (NC_015183)
class=cellinside αr14class=cellinside geneclass=cellinside NGR_c13890class=cellinside Rclass=cellinside 1433785class=cellinside 1433985class=cellinside YP_002825922.1class=cellinside DUF1127class=cellinside Sinorhizobium fredii NGR234 chromosome (NC_012587)
class=cellinside αr14class=cellinside sRNAclass=cellinside Sfr14C2class=cellinside Rclass=cellinside 1434463class=cellinside 1434586class=cellinside -class=cellinside sRNAclass=cellinside Sinorhizobium fredii NGR234 chromosome (NC_012587)
class=cellinside αr14class=cellinside sRNAclass=cellinside Sfr14C1class=cellinside Rclass=cellinside 1434171class=cellinside 1434293class=cellinside -class=cellinside sRNAclass=cellinside Sinorhizobium fredii NGR234 chromosome (NC_012587)
class=cellinside αr14class=cellinside geneclass=cellinside NGR_c13920class=cellinside Rclass=cellinside 1434843class=cellinside 1434925class=cellinside YP_002825924.1class=cellinside trigger factorclass=cellinside Sinorhizobium fredii NGR234 chromosome (NC_012587)
class=cellinside αr14class=cellinside geneclass=cellinside Rleg2_0104class=cellinside Dclass=cellinside 96796class=cellinside 97677class=cellinside YP_002279632.1class=cellinside aldo/keto reductaseclass=cellinside Rhizobium leguminosarum bv. trifolii WSM2304 chromosome (NC_011369)
class=cellinside αr14class=cellinside sRNAclass=cellinside Rlt2304r14C1class=cellinside Dclass=cellinside 98050class=cellinside 98171class=cellinside -class=cellinside sRNAclass=cellinside Rhizobium leguminosarum bv. trifolii WSM2304 chromosome (NC_011369)
class=cellinside αr14class=cellinside geneclass=cellinside Rleg2_0105class=cellinside Dclass=cellinside 98282class=cellinside 99559class=cellinside YP_002279633.1class=cellinside DUF900, alpha/beta hydrolaseclass=cellinside Rhizobium leguminosarum bv. trifolii WSM2304 chromosome (NC_011369)
class=cellinside αr14class=cellinside geneclass=cellinside Atu0104class=cellinside Rclass=cellinside 108895class=cellinside 109353class=cellinside NP_353139.1class=cellinside aminoacyl-tRNA ligaseclass=cellinside Agrobacterium tumefaciens str. C58 chromosome circular (NC_003062)
class=cellinside αr14class=cellinside sRNAclass=cellinside Atr14C1class=cellinside Dclass=cellinside 109473class=cellinside 109601class=cellinside -class=cellinside sRNAclass=cellinside Agrobacterium tumefaciens str. C58 chromosome circular (NC_003062)
class=cellinside αr14class=cellinside geneclass=cellinside Atu0106class=cellinside Dclass=cellinside 109823class=cellinside 110032class=cellinside NP_353140.2class=cellinside cold shock proteinclass=cellinside Agrobacterium tumefaciens str. C58 chromosome circular (NC_003062)
class=cellinside αr14class=cellinside geneclass=cellinside RHECIAT_CH0000515class=cellinside Dclass=cellinside 512732class=cellinside 513613class=cellinside YP_001976686.1class=cellinside oxidoreductaseclass=cellinside Rhizobium etli CIAT 652 (NC_010994)
class=cellinside αr14class=cellinside sRNAclass=cellinside ReCIATr14C1class=cellinside Dclass=cellinside 513993class=cellinside 514114class=cellinside -class=cellinside sRNAclass=cellinside Rhizobium etli CIAT 652 (NC_010994)
class=cellinside αr14class=cellinside geneclass=cellinside RHECIAT_CH0000517class=cellinside Dclass=cellinside 514221class=cellinside 515498class=cellinside YP_001976688.1class=cellinside DUF900, alpha/beta hydrolaseclass=cellinside Rhizobium etli CIAT 652 (NC_010994)
class=cellinside αr14class=cellinside geneclass=cellinside RL0474class=cellinside Dclass=cellinside 511376class=cellinside 512272class=cellinside YP_766083.1class=cellinside aldo/keto reductaseclass=cellinside Rhizobium leguminosarum bv. viciae 3841 (NC_008380)
class=cellinside αr14class=cellinside sRNAclass=cellinside Rlvr14C1class=cellinside Dclass=cellinside 512658class=cellinside 512779class=cellinside -class=cellinside sRNAclass=cellinside Rhizobium leguminosarum bv. viciae 3841 (NC_008380)
class=cellinside αr14class=cellinside geneclass=cellinside RL0475class=cellinside Rclass=cellinside 512816class=cellinside 513202class=cellinside YP_766084.1class=cellinside hypothetical proteinclass=cellinside Rhizobium leguminosarum bv. viciae 3841 (NC_008380)
class=cellinside αr14class=cellinside geneclass=cellinside RHE_CH00449class=cellinside Dclass=cellinside 461301class=cellinside 462182class=cellinside YP_467997.1class=cellinside oxidoreductaseclass=cellinside Rhizobium etli CFN 42 (NC_007761)
class=cellinside αr14class=cellinside sRNAclass=cellinside ReCFNr14C1class=cellinside Dclass=cellinside 462566class=cellinside 462687class=cellinside -class=cellinside sRNAclass=cellinside Rhizobium etli CFN 42 (NC_007761)
class=cellinside αr14class=cellinside geneclass=cellinside RHE_CH00450class=cellinside Dclass=cellinside 462794class=cellinside 464071class=cellinside YP_467998.1class=cellinside DUF900, alpha/beta hydrolaseclass=cellinside Rhizobium etli CFN 42 (NC_007761)
class=cellinside αr14class=cellinside geneclass=cellinside Avi_0122class=cellinside Rclass=cellinside 113190class=cellinside 114716class=cellinside YP_002548072.1class=cellinside sulfataseclass=cellinside Agrobacterium vitis S4 chromosome 1 chromosome 1 (NC_011989)
class=cellinside αr14class=cellinside sRNAclass=cellinside Avr14CI1class=cellinside Dclass=cellinside 115126class=cellinside 115257class=cellinside -class=cellinside sRNAclass=cellinside Agrobacterium vitis S4 chromosome 1 chromosome 1 (NC_011989)
class=cellinside αr14class=cellinside geneclass=cellinside Avi_0126class=cellinside Dclass=cellinside 115395class=cellinside 116840class=cellinside YP_002548074.1class=cellinside phosphomannomutaseclass=cellinside Agrobacterium vitis S4 chromosome 1 chromosome 1 (NC_011989)
class=cellinside αr14class=cellinside geneclass=cellinside Arad_2144class=cellinside Rclass=cellinside 1692677class=cellinside 1692823class=cellinside YP_002544330.1class=cellinside DUF1127class=cellinside Agrobacterium radiobacter K84 chromosome 1 (NC_011985)
class=cellinside αr14class=cellinside sRNAclass=cellinside Arr14CI2class=cellinside Rclass=cellinside 1693278class=cellinside 1693409class=cellinside -class=cellinside sRNAclass=cellinside Agrobacterium radiobacter K84 chromosome 1 (NC_011985)
class=cellinside αr14class=cellinside geneclass=cellinside Arad_2145class=cellinside Dclass=cellinside 1693731class=cellinside 1694870class=cellinside YP_002544331.1class=cellinside membrane proteinclass=cellinside Agrobacterium radiobacter K84 chromosome 1 (NC_011985)
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class=cellinside αr14class=cellinside geneclass=cellinside RHECIAT_CH0001168class=cellinside Dclass=cellinside 1173948class=cellinside 1174214class=cellinside YP_001977327.1class=cellinside DUF2277class=cellinside Rhizobium etli CIAT 652 (NC_010994)
class=cellinside αr14class=cellinside geneclass=cellinside Atu4670class=cellinside Rclass=cellinside 1831052class=cellinside 1831294class=cellinside NP_535148.1class=cellinside hypothetical proteinclass=cellinside Agrobacterium tumefaciens str. C58 chromosome linear (NC_003063)
class=cellinside αr14class=cellinside sRNAclass=cellinside Atr14C3class=cellinside Dclass=cellinside 1831483class=cellinside 1831614class=cellinside -class=cellinside sRNAclass=cellinside Agrobacterium tumefaciens str. C58 chromosome linear (NC_003063)
class=cellinside αr14class=cellinside geneclass=cellinside Atu4671class=cellinside Rclass=cellinside 1831642class=cellinside 1832085class=cellinside NP_355992.2class=cellinside response regulatorclass=cellinside Agrobacterium tumefaciens str. C58 chromosome linear (NC_003063)
class=cellinside αr14class=cellinside geneclass=cellinside RHECIAT_PB0000101class=cellinside Rclass=cellinside 111975class=cellinside 112217class=cellinside YP_001984364.1class=cellinside hypothetical proteinclass=cellinside Rhizobium etli CIAT 652 plasmid pB (NC_010996)
class=cellinside αr14class=cellinside sRNAclass=cellinside ReCIATr14Bclass=cellinside Dclass=cellinside 112292class=cellinside 112425class=cellinside -class=cellinside sRNAclass=cellinside Rhizobium etli CIAT 652 plasmid pB (NC_010996)
class=cellinside αr14class=cellinside geneclass=cellinside RHECIAT_PB0000102class=cellinside Dclass=cellinside 112536class=cellinside 113108class=cellinside YP_001984365.1class=cellinside hypothetical proteinclass=cellinside Rhizobium etli CIAT 652 plasmid pB (NC_010996)
class=cellinside αr14class=cellinside geneclass=cellinside RHE_PD00068class=cellinside Dclass=cellinside 76637class=cellinside 77354class=cellinside NP_659968.2class=cellinside hypothetical proteinclass=cellinside Rhizobium etli CFN 42 symbiotic plasmid p42d (NC_004041)
class=cellinside αr14class=cellinside sRNAclass=cellinside ReCFNr14dclass=cellinside Dclass=cellinside 77668class=cellinside 77794class=cellinside -class=cellinside sRNAclass=cellinside Rhizobium etli CFN 42 symbiotic plasmid p42d (NC_004041)
class=cellinside αr14class=cellinside geneclass=cellinside RHE_PD00069class=cellinside Dclass=cellinside 77912class=cellinside 78484class=cellinside NP_659967.1class=cellinside hydrolaseclass=cellinside Rhizobium etli CFN 42 symbiotic plasmid p42d (NC_004041)
class=cellinside αr14class=cellinside geneclass=cellinside NGR_c35080class=cellinside Rclass=cellinside 3718015class=cellinside 3720336class=cellinside YP_002827985.1class=cellinside penicillin-binding class=cellinside Sinorhizobium fredii NGR234 chromosome (NC_012587)
class=cellinside αr14class=cellinside sRNAclass=cellinside Sfr14C3class=cellinside Dclass=cellinside 3720579class=cellinside 3720700class=cellinside -class=cellinside sRNAclass=cellinside Sinorhizobium fredii NGR234 chromosome (NC_012587)
class=cellinside αr14class=cellinside geneclass=cellinside NGR_c35100class=cellinside Dclass=cellinside 3721900class=cellinside 3722382class=cellinside YP_002827987.1class=cellinside hypothetical proteinclass=cellinside Sinorhizobium fredii NGR234 chromosome (NC_012587)
class=cellinside αr14class=cellinside geneclass=cellinside Smed_3386class=cellinside Rclass=cellinside 3589318class=cellinside 3590205class=cellinside YP_001329042.1class=cellinside membrane proteinclass=cellinside Sinorhizobium medicae WSM419 chromosome (NC_009636)
class=cellinside αr14class=cellinside sRNAclass=cellinside Smedr14C3class=cellinside Rclass=cellinside 3590299class=cellinside 3590417class=cellinside -class=cellinside sRNAclass=cellinside Sinorhizobium medicae WSM419 chromosome (NC_009636)
class=cellinside αr14class=cellinside geneclass=cellinside Smed_3387class=cellinside Rclass=cellinside 3590494class=cellinside 3590925class=cellinside YP_001329043.1class=cellinside pyrimidine dimer DNA glycosylaseclass=cellinside Sinorhizobium medicae WSM419 chromosome (NC_009636)
class=cellinside αr14class=cellinside geneclass=cellinside SMc02855class=cellinside Rclass=cellinside 205860class=cellinside 206783class=cellinside NP_384286.1class=cellinside membrane proteinclass=cellinside Sinorhizobium meliloti 1021 (NC_003047)
class=cellinside αr14class=cellinside sRNAclass=cellinside Smr14C1class=cellinside Rclass=cellinside 206862class=cellinside 206980class=cellinside -class=cellinside sRNAclass=cellinside Sinorhizobium meliloti 1021 (NC_003047)
class=cellinside αr14class=cellinside geneclass=cellinside SMc02856class=cellinside Dclass=cellinside 207244class=cellinside 209547class=cellinside NP_384287.1class=cellinside penicillin-binding proteinclass=cellinside Sinorhizobium meliloti 1021 (NC_003047)
class=cellinside αr14class=cellinside geneclass=cellinside msr1062class=cellinside Dclass=cellinside 890180class=cellinside 890389class=cellinside NP_102735.1class=cellinside DUF1127class=cellinside Mesorhizobium loti MAFF303099 chromosome (NC_002678)
class=cellinside αr14class=cellinside sRNAclass=cellinside Mlr14C1class=cellinside Dclass=cellinside 890582class=cellinside 890702class=cellinside -class=cellinside sRNAclass=cellinside Mesorhizobium loti MAFF303099 chromosome (NC_002678)
class=cellinside αr14class=cellinside sRNAclass=cellinside Mlr14C2class=cellinside Dclass=cellinside 890760class=cellinside 890880class=cellinside -class=cellinside sRNAclass=cellinside Mesorhizobium loti MAFF303099 chromosome (NC_002678)
class=cellinside αr14class=cellinside geneclass=cellinside mlr1064class=cellinside Dclass=cellinside 891150class=cellinside 892568class=cellinside NP_102736.1class=cellinside tRNA (uracil-5-)-methyltransferaseclass=cellinside Mesorhizobium loti MAFF303099 chromosome (NC_002678)
class=cellinside αr14class=cellinside geneclass=cellinside SMa2165class=cellinside Dclass=cellinside 1219615class=cellinside 1220355class=cellinside NP_436422.1class=cellinside oxidoreductaseclass=cellinside Sinorhizobium meliloti 1021 plasmid pSymA (NC_003037)
class=cellinside αr14class=cellinside sRNAclass=cellinside Smr14A1class=cellinside Dclass=cellinside 1220690class=cellinside 1220808class=cellinside -class=cellinside sRNAclass=cellinside Sinorhizobium meliloti 1021 plasmid pSymA (NC_003037)
class=cellinside αr14class=cellinside geneclass=cellinside SMa2167class=cellinside Dclass=cellinside 1221480class=cellinside 1221947class=cellinside NP_436423.1class=cellinside transcription factor regulatorclass=cellinside Sinorhizobium meliloti 1021 plasmid pSymA (NC_003037)
class=cellinside αr14class=cellinside geneclass=cellinside pRL120374class=cellinside Rclass=cellinside 403573class=cellinside 404652class=cellinside YP_764884.1class=cellinside ribonuclease domain-containing proteinclass=cellinside Rhizobium leguminosarum bv. viciae 3841 plasmid pRL12 (NC_008378)
class=cellinside αr14class=cellinside sRNAclass=cellinside Rlvr14p12class=cellinside Dclass=cellinside 407202class=cellinside 407316class=cellinside -class=cellinside sRNAclass=cellinside Rhizobium leguminosarum bv. viciae 3841 plasmid pRL12 (NC_008378)
class=cellinside αr14class=cellinside geneclass=cellinside pRL120378class=cellinside Rclass=cellinside 408099class=cellinside 409010class=cellinside YP_764885.1class=cellinside L-isoaspartate O-methyltransferaseclass=cellinside Rhizobium leguminosarum bv. viciae 3841 plasmid pRL12 (NC_008378)
class=cellinside αr14class=cellinside geneclass=cellinside Mesci_3513class=cellinside Rclass=cellinside 3673344class=cellinside 3674753class=cellinside YP_004142683.1class=cellinside tRNA (uracil-5-)-methyltransferaseclass=cellinside Mesorhizobium ciceri biovar biserrulae WSM1271 chromosome (NC_014923)
class=cellinside αr14class=cellinside sRNAclass=cellinside Mcr14C1class=cellinside Rclass=cellinside 3674843class=cellinside 3674963class=cellinside -class=cellinside sRNAclass=cellinside Mesorhizobium ciceri biovar biserrulae WSM1271 chromosome (NC_014923)
class=cellinside αr14class=cellinside sRNAclass=cellinside Mcr14C2class=cellinside Rclass=cellinside 3675022class=cellinside 3675142class=cellinside -class=cellinside sRNAclass=cellinside Mesorhizobium ciceri biovar biserrulae WSM1271 chromosome (NC_014923)
class=cellinside αr14class=cellinside geneclass=cellinside Mesci_3514class=cellinside Rclass=cellinside 3675321class=cellinside 3675461class=cellinside YP_004142684.1class=cellinside DUF1127class=cellinside Mesorhizobium ciceri biovar biserrulae WSM1271 chromosome (NC_014923)
class=cellinside αr14class=cellinside geneclass=cellinside Oant_0422class=cellinside Dclass=cellinside 447656class=cellinside 448351class=cellinside YP_001368982.1class=cellinside LrgB membrane protein /hydrolaseclass=cellinside Brucella anthropi ATCC 49188 chromosome 1 (NC_009667)
class=cellinside αr14class=cellinside sRNAclass=cellinside Oar14CI1class=cellinside Dclass=cellinside 448505class=cellinside 448614class=cellinside -class=cellinside sRNAclass=cellinside Brucella anthropi ATCC 49188 chromosome 1 (NC_009667)
class=cellinside αr14class=cellinside geneclass=cellinside Oant_0423class=cellinside Dclass=cellinside 448748class=cellinside 450301class=cellinside YP_001368983.1class=cellinside glyoxalase bleomycin resistance protein dioxygenase/hydrolaseclass=cellinside Brucella anthropi ATCC 49188 chromosome 1 (NC_009667)
class=cellinside αr14class=cellinside geneclass=cellinside Oant_2969class=cellinside Rclass=cellinside 272174class=cellinside 273850class=cellinside YP_001371506.1class=cellinside hypothetical proteinclass=cellinside Brucella anthropi ATCC 49188 chromosome 2 (NC_009668)
class=cellinside αr14class=cellinside sRNAclass=cellinside Oar14CII1class=cellinside Dclass=cellinside 274684class=cellinside 274807class=cellinside -class=cellinside sRNAclass=cellinside Brucella anthropi ATCC 49188 chromosome 2 (NC_009668)
class=cellinside αr14class=cellinside geneclass=cellinside Oant_2970class=cellinside Dclass=cellinside 275652class=cellinside 276380class=cellinside YP_001371507.1class=cellinside septum formation inhibitorclass=cellinside Brucella anthropi ATCC 49188 chromosome 2 (NC_009668)
class=cellinside αr14class=cellinside geneclass=cellinside SMa2355class=cellinside Dclass=cellinside 1327042class=cellinside 1328151class=cellinside NP_436520.4class=cellinside DNA polymerase Iclass=cellinside Sinorhizobium meliloti 1021 plasmid pSymA (NC_003037)
class=cellinside αr14class=cellinside sRNAclass=cellinside Smr14A2class=cellinside Rclass=cellinside 1328176class=cellinside 1328301class=cellinside -class=cellinside sRNAclass=cellinside Sinorhizobium meliloti 1021 plasmid pSymA (NC_003037)
class=cellinside αr14class=cellinside geneclass=cellinside SMa2357class=cellinside Dclass=cellinside 1329978class=cellinside 1330670class=cellinside NP_436521.2class=cellinside adenylate guanylate cyclaseclass=cellinside Sinorhizobium meliloti 1021 plasmid pSymA (NC_003037)
class=cellinside αr14class=cellinside geneclass=cellinside Oant_2332class=cellinside Dclass=cellinside 2453758class=cellinside 2453904class=cellinside YP_001370875.1class=cellinside DUF1127class=cellinside Brucella anthropi ATCC 49188 chromosome 1 (NC_009667)
class=cellinside αr14class=cellinside sRNAclass=cellinside Oar14CI2class=cellinside Dclass=cellinside 2453973class=cellinside 2454100class=cellinside -class=cellinside sRNAclass=cellinside Brucella anthropi ATCC 49188 chromosome 1 (NC_009667)
class=cellinside αr14class=cellinside geneclass=cellinside Oant_2333class=cellinside Dclass=cellinside 2454171class=cellinside 2455601class=cellinside YP_001370876.1class=cellinside tRNA (uracil-5-)-methyltransferaseclass=cellinside Brucella anthropi ATCC 49188 chromosome 1 (NC_009667)
class=cellinside αr14class=cellinside geneclass=cellinside Rleg_4742class=cellinside Dclass=cellinside 111695class=cellinside 112336class=cellinside YP_002972933.1class=cellinside hypothetical proteinclass=cellinside Rhizobium leguminosarum bv. trifolii WSM1325 plasmid pR132501 (NC_012848)
class=cellinside αr14class=cellinside sRNAclass=cellinside Rlt1325r14p011class=cellinside Dclass=cellinside 112604class=cellinside 112728class=cellinside -class=cellinside sRNAclass=cellinside Rhizobium leguminosarum bv. trifolii WSM1325 plasmid pR132501 (NC_012848)
class=cellinside αr14class=cellinside geneclass=cellinside Rleg_4743class=cellinside Rclass=cellinside 112925class=cellinside 113309class=cellinside -class=cellinside hypothetical proteinclass=cellinside Rhizobium leguminosarum bv. trifolii WSM1325 plasmid pR132501 (NC_012848)
class=cellinside αr14class=cellinside geneclass=cellinside Meso_3687class=cellinside Rclass=cellinside 3975340class=cellinside 3976962class=cellinside YP_676220.1class=cellinside alpha amylase-C hydrolaseclass=cellinside Mesorhizobium sp. BNC1 (NC_008254)
class=cellinside αr14class=cellinside sRNAclass=cellinside MsBCNr14C2class=cellinside Rclass=cellinside 3977086class=cellinside 3977208class=cellinside -class=cellinside sRNAclass=cellinside Mesorhizobium sp. BNC1 (NC_008254)
class=cellinside αr14class=cellinside geneclass=cellinside Meso_3688class=cellinside Dclass=cellinside 3977363class=cellinside 3978682class=cellinside YP_676221.1class=cellinside homoserine dehydrogenase-C NAD-bindingclass=cellinside Mesorhizobium sp. BNC1 (NC_008254)
class=cellinside αr14class=cellinside geneclass=cellinside BSUIS_A0355class=cellinside Dclass=cellinside 354629class=cellinside 355336class=cellinside YP_001627017.1class=cellinside LrgB membrane protein /hydrolaseclass=cellinside Brucella suis ATCC 23445 chromosome I (NC_010169)
class=cellinside αr14class=cellinside sRNAclass=cellinside Bs23445r14CI1class=cellinside Dclass=cellinside 355557class=cellinside 355664class=cellinside -class=cellinside sRNAclass=cellinside Brucella suis ATCC 23445 chromosome I (NC_010169)
class=cellinside αr14class=cellinside geneclass=cellinside BSUIS_A0356class=cellinside Dclass=cellinside 355877class=cellinside 357124class=cellinside YP_001627018.1class=cellinside hypothetical proteinclass=cellinside Brucella suis ATCC 23445 chromosome I (NC_010169)
class=cellinside αr14class=cellinside geneclass=cellinside BMI_I332class=cellinside Dclass=cellinside 338771class=cellinside 339478class=cellinside YP_003106291.1class=cellinside LrgB membrane protein /hydrolaseclass=cellinside Brucella microti CCM 4915 chromosome I (NC_013119)
class=cellinside αr14class=cellinside sRNAclass=cellinside Bmir14CI1class=cellinside Dclass=cellinside 339699class=cellinside 339806class=cellinside -class=cellinside sRNAclass=cellinside Brucella microti CCM 4915 chromosome I (NC_013119)
class=cellinside αr14class=cellinside geneclass=cellinside BMI_I334class=cellinside Dclass=cellinside 340025class=cellinside 341266class=cellinside YP_003106293.1class=cellinside DUF900, alpha/beta hydrolaseclass=cellinside Brucella microti CCM 4915 chromosome I (NC_013119)
class=cellinside αr14class=cellinside geneclass=cellinside BOV_0342class=cellinside Dclass=cellinside 358754class=cellinside 359461class=cellinside YP_001258364.1class=cellinside hydrolaseclass=cellinside Brucella ovis ATCC 25840 chromosome I (NC_009505)
class=cellinside αr14class=cellinside sRNAclass=cellinside Bor14CI1class=cellinside Dclass=cellinside 359682class=cellinside 359789class=cellinside -class=cellinside sRNAclass=cellinside Brucella ovis ATCC 25840 chromosome I (NC_009505)
class=cellinside αr14class=cellinside geneclass=cellinside BOV_0343class=cellinside Dclass=cellinside 360008class=cellinside 361250class=cellinside -class=cellinside pseudogenclass=cellinside Brucella ovis ATCC 25840 chromosome I (NC_009505)
class=cellinside αr14class=cellinside geneclass=cellinside BCAN_A0335class=cellinside Dclass=cellinside 337093class=cellinside 337800class=cellinside YP_001592196.1class=cellinside LrgB membrane protein /hydrolaseclass=cellinside Brucella canis ATCC 23365 chromosome I (NC_010103)
class=cellinside αr14class=cellinside sRNAclass=cellinside Bcr14CI1class=cellinside Dclass=cellinside 338021class=cellinside 338128class=cellinside -class=cellinside sRNAclass=cellinside Brucella canis ATCC 23365 chromosome I (NC_010103)
class=cellinside αr14class=cellinside geneclass=cellinside BCAN_A0337class=cellinside Dclass=cellinside 338347class=cellinside 339588class=cellinside YP_001592198.1class=cellinside DUF900, alpha/beta hydrolaseclass=cellinside Brucella canis ATCC 23365 chromosome I (NC_010103)
class=cellinside αr14class=cellinside geneclass=cellinside BMEA_A0364class=cellinside Dclass=cellinside 358048class=cellinside 358755class=cellinside YP_002732104.1class=cellinside LrgB membrane protein /hydrolaseclass=cellinside Brucella melitensis ATCC 23457 chromosome I (NC_012441)
class=cellinside αr14class=cellinside sRNAclass=cellinside Bm23457r14CI1class=cellinside Dclass=cellinside 358976class=cellinside 359082class=cellinside -class=cellinside sRNAclass=cellinside Brucella melitensis ATCC 23457 chromosome I (NC_012441)
class=cellinside αr14class=cellinside geneclass=cellinside BMEA_A0366class=cellinside Dclass=cellinside 359302class=cellinside 360543class=cellinside YP_002732106.1class=cellinside DUF900, alpha/beta hydrolaseclass=cellinside Brucella melitensis ATCC 23457 chromosome I (NC_012441)
class=cellinside αr14class=cellinside geneclass=cellinside BAbS19_I03260class=cellinside Dclass=cellinside 357382class=cellinside 358089class=cellinside YP_001934341.1class=cellinside LrgB membrane protein /hydrolaseclass=cellinside Brucella abortus S19 chromosome I (NC_010742)
class=cellinside αr14class=cellinside sRNAclass=cellinside BaS19r14CI1class=cellinside Dclass=cellinside 358310class=cellinside 358417class=cellinside -class=cellinside sRNAclass=cellinside Brucella abortus S19 chromosome I (NC_010742)
class=cellinside αr14class=cellinside geneclass=cellinside BAbS19_I03270class=cellinside Dclass=cellinside 358635class=cellinside 359876class=cellinside YP_001934342.1class=cellinside DUF900, alpha/beta hydrolaseclass=cellinside Brucella abortus S19 chromosome I (NC_010742)
class=cellinside αr14class=cellinside geneclass=cellinside BruAb1_0352class=cellinside Dclass=cellinside 358997class=cellinside 359704class=cellinside YP_221113.1class=cellinside membrane proteinclass=cellinside Brucella abortus bv. 1 str. 9-941 chromosome I (NC_006932)
class=cellinside αr14class=cellinside sRNAclass=cellinside Ba19941r14CI1class=cellinside Dclass=cellinside 359925class=cellinside 360032class=cellinside -class=cellinside sRNAclass=cellinside Brucella abortus bv. 1 str. 9-941 chromosome I (NC_006932)
class=cellinside αr14class=cellinside geneclass=cellinside BruAb1_0355class=cellinside Dclass=cellinside 361578class=cellinside 362459class=cellinside YP_221115.1class=cellinside pantoate—beta-alanine ligaseclass=cellinside Brucella abortus bv. 1 str. 9-941 chromosome I (NC_006932)
class=cellinside αr14class=cellinside geneclass=cellinside BAB1_0356class=cellinside Dclass=cellinside 355365class=cellinside 356072class=cellinside YP_413824.1class=cellinside LrgB membrane protein /hydrolaseclass=cellinside Brucella melitensis biovar Abortus 2308 chromosome I (NC_007618)
class=cellinside αr14class=cellinside sRNAclass=cellinside Bmar14CI1class=cellinside Dclass=cellinside 356293class=cellinside 356400class=cellinside -class=cellinside sRNAclass=cellinside Brucella melitensis biovar Abortus 2308 chromosome I (NC_007618)
class=cellinside αr14class=cellinside geneclass=cellinside BAB1_0358class=cellinside Dclass=cellinside 356618class=cellinside 357859class=cellinside YP_413825.1class=cellinside DUF900, alpha/beta hydrolaseclass=cellinside Brucella melitensis biovar Abortus 2308 chromosome I (NC_007618)
class=cellinside αr14class=cellinside geneclass=cellinside BR0326class=cellinside Dclass=cellinside 337104class=cellinside 337811class=cellinside NP_697360.1class=cellinside DUF900, alpha/beta hydrolaseclass=cellinside Brucella suis 1330 chromosome I (NC_004310)
class=cellinside αr14class=cellinside sRNAclass=cellinside Bs1330r14CI1class=cellinside Dclass=cellinside 338032class=cellinside 338139class=cellinside -class=cellinside sRNAclass=cellinside Brucella suis 1330 chromosome I (NC_004310)
class=cellinside αr14class=cellinside geneclass=cellinside BR0328class=cellinside Dclass=cellinside 338358class=cellinside 339599class=cellinside NP_697362.1class=cellinside tRNA (uracil-5-)-methyltransferaseclass=cellinside Brucella suis 1330 chromosome I (NC_004310)
class=cellinside αr14class=cellinside geneclass=cellinside Smed_5352class=cellinside Rclass=cellinside 313859class=cellinside 314596class=cellinside YP_001314057.1class=cellinside adenylate guanylate cyclaseclass=cellinside Sinorhizobium medicae WSM419 plasmid pSMED02 (NC_009621)
class=cellinside αr14class=cellinside sRNAclass=cellinside Smedr14p021class=cellinside Dclass=cellinside 316304class=cellinside 316428class=cellinside -class=cellinside sRNAclass=cellinside Sinorhizobium medicae WSM419 plasmid pSMED02 (NC_009621)
class=cellinside αr14class=cellinside geneclass=cellinside Smed_5353class=cellinside Rclass=cellinside 316485class=cellinside 317621class=cellinside YP_001314058.1class=cellinside DNA polymerase Iclass=cellinside Sinorhizobium medicae WSM419 plasmid pSMED02 (NC_009621)
class=cellinside αr14class=cellinside geneclass=cellinside RHE_PF00022class=cellinside Rclass=cellinside 22159class=cellinside 22494class=cellinside YP_472643.1class=cellinside hypothetical proteinclass=cellinside Rhizobium etli CFN 42 plasmid p42f (NC_007766)
class=cellinside αr14class=cellinside sRNAclass=cellinside ReCFNr14fclass=cellinside Dclass=cellinside 22818class=cellinside 22935class=cellinside -class=cellinside sRNAclass=cellinside Rhizobium etli CFN 42 plasmid p42f (NC_007766)
class=cellinside αr14class=cellinside geneclass=cellinside RHE_PF00023class=cellinside Dclass=cellinside 23286class=cellinside 23726class=cellinside YP_472644.1class=cellinside carbon-sulfur lyaseclass=cellinside Rhizobium etli CFN 42 plasmid p42f (NC_007766)
class=cellinside αr14class=cellinside geneclass=cellinside Oant_3865class=cellinside Dclass=cellinside 1275426class=cellinside 1275572class=cellinside YP_001372399.1class=cellinside DUF1127class=cellinside Brucella anthropi ATCC 49188 chromosome 2 (NC_009668)
class=cellinside αr14class=cellinside sRNAclass=cellinside Oar14CII2class=cellinside Dclass=cellinside 1275649class=cellinside 1275772class=cellinside -class=cellinside sRNAclass=cellinside Brucella anthropi ATCC 49188 chromosome 2 (NC_009668)
class=cellinside αr14class=cellinside geneclass=cellinside Oant_3866class=cellinside Rclass=cellinside 1275787class=cellinside 1277010class=cellinside YP_001372400.1class=cellinside membrane proteinclass=cellinside Brucella anthropi ATCC 49188 chromosome 2 (NC_009668)
class=cellinside αr14class=cellinside geneclass=cellinside Rleg2_4668class=cellinside Dclass=cellinside 305380class=cellinside 306273class=cellinside YP_002278660.1class=cellinside L-isoaspartate O-methyltransferaseclass=cellinside Rhizobium leguminosarum bv. trifolii WSM2304 plasmid pRLG201 (NC_011368)
class=cellinside αr14class=cellinside sRNAclass=cellinside Rlt2304r14p011class=cellinside Rclass=cellinside 306339class=cellinside 306454class=cellinside -class=cellinside sRNAclass=cellinside Rhizobium leguminosarum bv. trifolii WSM2304 plasmid pRLG201 (NC_011368)
class=cellinside αr14class=cellinside geneclass=cellinside Rleg2_4670class=cellinside Rclass=cellinside 306976class=cellinside 307923class=cellinside YP_002278662.1class=cellinside transposase IS110 family proteinclass=cellinside Rhizobium leguminosarum bv. trifolii WSM2304 plasmid pRLG201 (NC_011368)
class=cellinside αr14class=cellinside geneclass=cellinside Mesci_6302class=cellinside Dclass=cellinside 240660class=cellinside 240910class=cellinside YP_004134462.1class=cellinside hypothetical proteinclass=cellinside Mesorhizobium ciceri biovar biserrulae WSM1271 chromosome I (NC_014918)
class=cellinside αr14class=cellinside sRNAclass=cellinside Mcr14p01class=cellinside Rclass=cellinside 241412class=cellinside 241531class=cellinside -class=cellinside sRNAclass=cellinside Mesorhizobium ciceri biovar biserrulae WSM1271 chromosome I (NC_014918)
class=cellinside αr14class=cellinside geneclass=cellinside Mesci_6303class=cellinside Rclass=cellinside 241784class=cellinside 242047class=cellinside YP_004134463.1class=cellinside hypothetical proteinclass=cellinside Mesorhizobium ciceri biovar biserrulae WSM1271 chromosome I (NC_014918)
class=cellinside αr14class=cellinside geneclass=cellinside Mesci_2426class=cellinside Dclass=cellinside 2545134class=cellinside 2545592class=cellinside YP_004141622.1class=cellinside phasinclass=cellinside Mesorhizobium ciceri biovar biserrulae WSM1271 chromosome I (NC_014923)
class=cellinside αr14class=cellinside sRNAclass=cellinside Mcr14CI4class=cellinside Dclass=cellinside 2545673class=cellinside 2545788class=cellinside -class=cellinside sRNAclass=cellinside Mesorhizobium ciceri biovar biserrulae WSM1271 chromosome I (NC_014923)
class=cellinside αr14class=cellinside geneclass=cellinside Mesci_2427class=cellinside Dclass=cellinside 2545962class=cellinside 2546038class=cellinside YP_004141623class=cellinside FAD dependent oxidoreductaseclass=cellinside Mesorhizobium ciceri biovar biserrulae WSM1271 chromosome I (NC_014923)
class=cellinside αr14class=cellinside geneclass=cellinside Mesci_5119class=cellinside Dclass=cellinside 5264750class=cellinside 5265772class=cellinside YP_004144269.1class=cellinside LacI family transcription regulatorclass=cellinside Mesorhizobium ciceri biovar biserrulae WSM1271 chromosome I (NC_014923)
class=cellinside αr14class=cellinside sRNAclass=cellinside Mcr14CI5class=cellinside Dclass=cellinside 5265891class=cellinside 5266009class=cellinside -class=cellinside sRNAclass=cellinside Mesorhizobium ciceri biovar biserrulae WSM1271 chromosome I (NC_014923)
class=cellinside αr14class=cellinside geneclass=cellinside Mesci_5121class=cellinside Rclass=cellinside 5266103class=cellinside 5266693class=cellinside YP_004144271.1class=cellinside TetR family transcription regulatorclass=cellinside Mesorhizobium ciceri biovar biserrulae WSM1271 chromosome I (NC_014923)
class=cellinside αr14class=cellinside geneclass=cellinside BOV_0890class=cellinside Rclass=cellinside 894271class=cellinside 895671class=cellinside YP_001258873.1class=cellinside tRNA (uracil-5-)-methyltransferaseclass=cellinside Brucella ovis ATCC 25840 chromosome I (NC_009505)
class=cellinside αr14class=cellinside sRNAclass=cellinside Bor14CI2class=cellinside Rclass=cellinside 895749class=cellinside 895867class=cellinside -class=cellinside sRNAclass=cellinside Brucella ovis ATCC 25840 chromosome I (NC_009505)
class=cellinside αr14class=cellinside geneclass=cellinside BOV_0891class=cellinside Rclass=cellinside 895931class=cellinside 896077class=cellinside YP_001258874.1class=cellinside DUF1127class=cellinside Brucella ovis ATCC 25840 chromosome I (NC_009505)
class=cellinside αr14class=cellinside geneclass=cellinside BCAN_A0908class=cellinside Rclass=cellinside 865739class=cellinside 867139class=cellinside YP_001592741.1class=cellinside tRNA (uracil-5-)-methyltransferaseclass=cellinside Brucella canis ATCC 23365 chromosome I (NC_010103)
class=cellinside αr14class=cellinside sRNAclass=cellinside Bcr14CI2class=cellinside Rclass=cellinside 867217class=cellinside 867335class=cellinside -class=cellinside sRNAclass=cellinside Brucella canis ATCC 23365 chromosome I (NC_010103)
class=cellinside αr14class=cellinside geneclass=cellinside BCAN_A0909class=cellinside Rclass=cellinside 867399class=cellinside 867545class=cellinside YP_001592742.1class=cellinside DUF1127class=cellinside Brucella canis ATCC 23365 chromosome I (NC_010103)
class=cellinside αr14class=cellinside geneclass=cellinside BSUIS_A0933class=cellinside Rclass=cellinside 887235class=cellinside 888635class=cellinside YP_001627570.1class=cellinside tRNA (uracil-5-)-methyltransferaseclass=cellinside Brucella suis ATCC 23445 chromosome I (NC_010169)
class=cellinside αr14class=cellinside sRNAclass=cellinside Bs23445r14CI2class=cellinside Rclass=cellinside 888713class=cellinside 888831class=cellinside -class=cellinside sRNAclass=cellinside Brucella suis ATCC 23445 chromosome I (NC_010169)
class=cellinside αr14class=cellinside geneclass=cellinside BSUIS_A0934class=cellinside Rclass=cellinside 888895class=cellinside 889041class=cellinside YP_001627571.1class=cellinside hypothetical proteinclass=cellinside Brucella suis ATCC 23445 chromosome I (NC_010169)
class=cellinside αr14class=cellinside geneclass=cellinside BMI_I892class=cellinside Rclass=cellinside 871571class=cellinside 872971class=cellinside YP_003106830.1class=cellinside tRNA (uracil-5-)-methyltransferaseclass=cellinside Brucella microti CCM 4915 chromosome 1 (NC_013119)
class=cellinside αr14class=cellinside sRNAclass=cellinside Bmir14CI2class=cellinside Rclass=cellinside 873049class=cellinside 873167class=cellinside -class=cellinside sRNAclass=cellinside Brucella microti CCM 4915 chromosome 1 (NC_013119)
class=cellinside αr14class=cellinside geneclass=cellinside BMI_I893class=cellinside Rclass=cellinside 873231class=cellinside 873377class=cellinside YP_003106831.1class=cellinside DUF1127class=cellinside Brucella microti CCM 4915 chromosome 1 (NC_013119)
class=cellinside αr14class=cellinside geneclass=cellinside BR0894class=cellinside Rclass=cellinside 867369class=cellinside 868769class=cellinside NP_697907.1class=cellinside tRNA (uracil-5-)-methyltransferaseclass=cellinside Brucella suis 1330 chromosome I (NC_004310)
class=cellinside αr14class=cellinside sRNAclass=cellinside Bs1330r14CI2class=cellinside Rclass=cellinside 868847class=cellinside 868965class=cellinside -class=cellinside sRNAclass=cellinside Brucella suis 1330 chromosome I (NC_004310)
class=cellinside αr14class=cellinside geneclass=cellinside BR0895class=cellinside Rclass=cellinside 869029class=cellinside 869175class=cellinside NP_697908.1class=cellinside DUF1127class=cellinside Brucella suis 1330 chromosome I (NC_004310)
class=cellinside αr14class=cellinside geneclass=cellinside mlr7359class=cellinside Dclass=cellinside 6091731class=cellinside 6092324class=cellinside NP_107697.1class=cellinside transcription factor regulatorclass=cellinside Mesorhizobium loti MAFF303099 chromosome (NC_002678)
class=cellinside αr14class=cellinside sRNAclass=cellinside Mlr14C5class=cellinside Rclass=cellinside 6092423class=cellinside 6092540class=cellinside -class=cellinside sRNAclass=cellinside Mesorhizobium loti MAFF303099 chromosome (NC_002678)
class=cellinside αr14class=cellinside geneclass=cellinside mll7360class=cellinside Rclass=cellinside 6092659class=cellinside 6093681class=cellinside NP_107698.1class=cellinside transcription factor regulatorclass=cellinside Mesorhizobium loti MAFF303099 chromosome (NC_002678)
class=cellinside αr14class=cellinside geneclass=cellinside BMEI1072class=cellinside Dclass=cellinside 1116469class=cellinside 1116615class=cellinside NP_539989.1class=cellinside DUF1127class=cellinside Brucella melitensis bv. 1 str. 16M chromosome (NC_003317)
class=cellinside αr14class=cellinside sRNAclass=cellinside Bm16Mr14CI1class=cellinside Dclass=cellinside 1116661class=cellinside 1116787class=cellinside -class=cellinside sRNAclass=cellinside Brucella melitensis bv. 1 str. 16M chromosome (NC_003317)
class=cellinside αr14class=cellinside geneclass=cellinside BMEI1073class=cellinside Dclass=cellinside 1116821class=cellinside 1118257class=cellinside NP_539990.1class=cellinside tRNA (uracil-5-)-methyltransferaseclass=cellinside Brucella melitensis bv. 1 str. 16M chromosome (NC_003317)
class=cellinside αr14class=cellinside geneclass=cellinside BAbS19_I08530class=cellinside Rclass=cellinside 887399class=cellinside 888799class=cellinside YP_001934848.1class=cellinside tRNA (uracil-5-)-methyltransferaseclass=cellinside Brucella abortus S19 chromosome 1 (NC_010742)
class=cellinside αr14class=cellinside sRNAclass=cellinside BaS19r14CI2class=cellinside Rclass=cellinside 888877class=cellinside 888995class=cellinside -class=cellinside sRNAclass=cellinside Brucella abortus S19 chromosome 1 (NC_010742)
class=cellinside αr14class=cellinside geneclass=cellinside BAbS19_I08540class=cellinside Rclass=cellinside 889041class=cellinside 889187class=cellinside YP_001934849.1class=cellinside DUF1127class=cellinside Brucella abortus S19 chromosome 1 (NC_010742)
class=cellinside αr14class=cellinside geneclass=cellinside BMEA_A0933class=cellinside Rclass=cellinside 888865class=cellinside 890265class=cellinside YP_002732640.1class=cellinside tRNA (uracil-5-)-methyltransferaseclass=cellinside Brucella melitensis ATCC 23457 chromosome I (NC_012441)
class=cellinside αr14class=cellinside sRNAclass=cellinside Bm23457r14CI2class=cellinside Rclass=cellinside 890343class=cellinside 890461class=cellinside -class=cellinside sRNAclass=cellinside Brucella melitensis ATCC 23457 chromosome I (NC_012441)
class=cellinside αr14class=cellinside geneclass=cellinside BMEA_A0934class=cellinside Rclass=cellinside 890507class=cellinside 890653class=cellinside YP_002732641.1class=cellinside DUF1127class=cellinside Brucella melitensis ATCC 23457 chromosome I (NC_012441)
class=cellinside αr14class=cellinside geneclass=cellinside BruAb1_0906class=cellinside Rclass=cellinside 889098class=cellinside 890498class=cellinside YP_221632.1class=cellinside tRNA (uracil-5-)-methyltransferaseclass=cellinside Brucella abortus bv. 1 str. 9-941 chromosome I (NC_006932)
class=cellinside αr14class=cellinside sRNAclass=cellinside Ba19941r14CI2class=cellinside Rclass=cellinside 890576class=cellinside 890694class=cellinside -class=cellinside sRNAclass=cellinside Brucella abortus bv. 1 str. 9-941 chromosome I (NC_006932)
class=cellinside αr14class=cellinside geneclass=cellinside BruAb1_0907class=cellinside Rclass=cellinside 890740class=cellinside 890886class=cellinside YP_221633.1class=cellinside DUF1127class=cellinside Brucella abortus bv. 1 str. 9-941 chromosome I (NC_006932)
class=cellinside αr14class=cellinside geneclass=cellinside BAB1_0913class=cellinside Rclass=cellinside 885376class=cellinside 886776class=cellinside YP_414338.1class=cellinside tRNA (uracil-5-)-methyltransferaseclass=cellinside Brucella melitensis biovar Abortus 2308 chromosome I (NC_007618)
class=cellinside αr14class=cellinside sRNAclass=cellinside Bmar14CI2class=cellinside Rclass=cellinside 886854class=cellinside 886972class=cellinside -class=cellinside sRNAclass=cellinside Brucella melitensis biovar Abortus 2308 chromosome I (NC_007618)
class=cellinside αr14class=cellinside geneclass=cellinside BAB1_0914class=cellinside Rclass=cellinside 887018class=cellinside 887164class=cellinside YP_414339.1class=cellinside oxidoreductaseclass=cellinside Brucella melitensis biovar Abortus 2308 chromosome I (NC_007618)
class=cellinside αr14class=cellinside geneclass=cellinside Meso_4235class=cellinside Rclass=cellinside 134555class=cellinside 135097class=cellinside YP_665858.1class=cellinside hypothetical proteinclass=cellinside Mesorhizobium sp. BNC1 plasmid 1 (NC_008242)
class=cellinside αr14class=cellinside sRNAclass=cellinside MsBCNr14p1class=cellinside Rclass=cellinside 135270class=cellinside 135386class=cellinside -class=cellinside sRNAclass=cellinside Mesorhizobium sp. BNC1 plasmid 1 (NC_008242)
class=cellinside αr14class=cellinside geneclass=cellinside Meso_4236class=cellinside Rclass=cellinside 135539class=cellinside 136099class=cellinside YP_665859.1class=cellinside hypothetical proteinclass=cellinside Mesorhizobium sp. BNC1 plasmid 1 (NC_008242)
class=cellinside αr14class=cellinside geneclass=cellinside mlr6541class=cellinside Dclass=cellinside 5350228class=cellinside 5350686class=cellinside NP_107027.1class=cellinside phasinclass=cellinside Mesorhizobium loti MAFF303099 chromosome (NC_002678)
class=cellinside αr14class=cellinside sRNAclass=cellinside Mlr14C4class=cellinside Dclass=cellinside 5350767class=cellinside 5350882class=cellinside -class=cellinside sRNAclass=cellinside Mesorhizobium loti MAFF303099 chromosome (NC_002678)
class=cellinside αr14class=cellinside geneclass=cellinside mlr6543class=cellinside Dclass=cellinside 5351042class=cellinside 5351115class=cellinside -class=cellinside two component regulatorclass=cellinside Mesorhizobium loti MAFF303099 chromosome (NC_002678)
class=cellinside αr14class=cellinside geneclass=cellinside RL2059class=cellinside Rclass=cellinside 2172416class=cellinside 2173849class=cellinside YP_767657.1class=cellinside tRNA (uracil-5-)-methyltransferaseclass=cellinside Rhizobium leguminosarum bv. viciae 3841 (NC_008380)
class=cellinside αr14class=cellinside sRNAclass=cellinside Rlvr14C2class=cellinside Rclass=cellinside 2174956class=cellinside 2175074class=cellinside -class=cellinside sRNAclass=cellinside Rhizobium leguminosarum bv. viciae 3841 (NC_008380)
class=cellinside αr14class=cellinside geneclass=cellinside RL2060class=cellinside Dclass=cellinside 2175400class=cellinside 2176503class=cellinside YP_767658.1class=cellinside membrane proteinclass=cellinside Rhizobium leguminosarum bv. viciae 3841 (NC_008380)

Notes and References

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  2. del Val C, Rivas E, Torres-Quesada O, Toro N, Jiménez-Zurdo JI . Identification of differentially expressed small non-coding RNAs in the legume endosymbiont Sinorhizobium meliloti by comparative genomics . Molecular Microbiology . 66 . 5 . 1080–91 . December 2007 . 17971083 . 2780559 . 10.1111/j.1365-2958.2007.05978.x .
  3. Ulvé VM, Sevin EW, Chéron A, Barloy-Hubler F . Identification of chromosomal alpha-proteobacterial small RNAs by comparative genome analysis and detection in Sinorhizobium meliloti strain 1021 . BMC Genomics . 8 . 467 . 467 . December 2007 . 18093320 . 2245857 . 10.1186/1471-2164-8-467 . free .
  4. Valverde C, Livny J, Schlüter JP, Reinkensmeier J, Becker A, Parisi G . Prediction of Sinorhizobium meliloti sRNA genes and experimental detection in strain 2011 . BMC Genomics . 9 . 406 . 416 . September 2008 . 18793445 . 2573895 . 10.1186/1471-2164-9-416 . free .
  5. Córdoba JM, Chavarro C, Schlueter JA, Jackson SA, Blair MW . Integration of physical and genetic maps of common bean through BAC-derived microsatellite markers . BMC Genomics . 11 . 245 . 436 . July 2010 . 20637113 . 3091635 . 10.1186/1471-2164-11-436 . free .
  6. Nawrocki EP, Kolbe DL, Eddy SR . Infernal 1.0: inference of RNA alignments . Bioinformatics . 25 . 10 . 1335–7 . May 2009 . 19307242 . 2732312 . 10.1093/bioinformatics/btp157 .
  7. Will S, Reiche K, Hofacker IL, Stadler PF, Backofen R . Inferring Noncoding RNA Families and Classes by Means of Genome-Scale Structure-Based Clustering. PLOS Comput Biol. 4. 65. e65. 10.1371/journal.pcbi.0030065. 17432929. 1851984. 2007. 2007PLSCB...3...65W . free .
  8. MacLellan SR, MacLean AM, Finan TM . Promoter prediction in the rhizobia . Microbiology . 152 . Pt 6 . 1751–63 . June 2006 . 16735738 . 10.1099/mic.0.28743-0 . free .
  9. Novichkov PS, Rodionov DA, Stavrovskaya ED, Novichkova ES, Kazakov AE, Gelfand MS, Arkin AP, Mironov AA, Dubchak I . RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach . Nucleic Acids Research . 38 . Web Server issue . W299–307 . July 2010 . 20542910 . 2896116 . 10.1093/nar/gkq531 .
  10. Gama-Castro S, Salgado H, Peralta-Gil M, Santos-Zavaleta A, Muñiz-Rascado L, Solano-Lira H, Jimenez-Jacinto V, Weiss V, García-Sotelo JS, López-Fuentes A, Porrón-Sotelo L, Alquicira-Hernández S, Medina-Rivera A, Martínez-Flores I, Alquicira-Hernández K, Martínez-Adame R, Bonavides-Martínez C, Miranda-Ríos J, Huerta AM, Mendoza-Vargas A, Collado-Torres L, Taboada B, Vega-Alvarado L, Olvera M, Olvera L, Grande R, Morett E, Collado-Vides J . RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units) . Nucleic Acids Research . 39 . Database issue . D98–105 . January 2011 . 21051347 . 3013702 . 10.1093/nar/gkq1110 .
  11. Bailey TL, Elkan C . Proceedings. International Conference on Intelligent Systems for Molecular Biology . Fitting a mixture model by expectation maximization to discover motifs in biopolymers. 28–36. AAAI Press, Menlo Park, California. 1994. 2. 7584402.
  12. Vinayagam A, del Val C, Schubert F, Eils R, Glatting KH, Suhai S, König R . GOPET: a tool for automated predictions of Gene Ontology terms . BMC Bioinformatics . 7 . 161 . March 2006 . 16549020 . 1434778 . 10.1186/1471-2105-7-161 . free .
  13. Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, Robles M . Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research . Bioinformatics . 21 . 18 . 3674–6 . September 2005 . 16081474 . 10.1093/bioinformatics/bti610 . free .
  14. del Val C, Ernst P, Falkenhahn M, Fladerer C, Glatting KH, Suhai S, Hotz-Wagenblatt A . ProtSweep, 2Dsweep and DomainSweep: protein analysis suite at DKFZ . Nucleic Acids Research . 35 . Web Server issue . W444–50 . July 2007 . 17526514 . 1933246 . 10.1093/nar/gkm364 .

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