Αr15 RNA explained

αr15 is a family of bacterial small non-coding RNAs with representatives in a broad group of α-proteobacteria from the order Rhizobiales. The first members of this family (smr15C1 and smrC15C2) were found tandemly arranged in the same intergenic region (IGR) of the Sinorhizobium meliloti 1021 chromosome (C).[1] Further homology and structure conservation analysis have identified full-length Smr15C1 and Smr15C2 homologs 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). The Smr15C1 (115 nt) and Smr15C2 (121 nt) homologs are also encoded in tandem within the same IGR region of Rhizobium and Agrobacterium species, whereas in Brucella species the αr15C loci are spread in the IGRs of Chromosome I. Moreover, this analysis also identified a third αr15 loci in extrachromosomal replicons of the mentioned nitrogen-fixing α-proteobacteria and in the Chromosome II of Brucella species. αr15 RNA species are 99-121 nt long (Table 1) and share a well defined common secondary structure consisting of three stem loops (Figure 1). The transcripts of the αr15 family can be catalogued as trans-acting sRNAs encoded by independent transcription units with recognizable promoter and transcription termination signatures within intergenic regions (IGRs) of the α-proteobacterial genomes (Figure 5).

Discovery and structure

Smr15C1 y Smr15C2 sRNAs were described by del Val et al.,[1] as a result of a computational comparative genomic approach in the intergenic regions (IGRs) of the reference S. meliloti 1021 strain (http://iant.toulouse.inra.fr/bacteria/annotation/cgi/rhime.cgi). Although the primary nucleotide sequence of Smr15C1 y Smr15C2 showed high similarity (84% identity), specific probes for each sRNA could be designed which detected transcripts of different size and expression profiles.[1]

TAP-based 5’-RACE experiments mapped the Smr15C1 and Smr15C2 transcription start sites (TSS) in the S. meliloti 1021 genome (http://iant.toulouse.inra.fr/bacteria/annotation/cgi/rhime.cgi). The Smr15C1 TSS was mapped to the chromosomal position 1698731 nt and the TSS of Smr15C2 to the nt 1698937. The 3’-ends were assumed to be located at the 1698617 nt and 1698817 nt respectively, matching the last residue of the consecutive Us stretch of a bona fide Rho-independent terminator (Figure 5). Parallel and later studies,[2] [3] in which Smr15C1 and Smr15C2 transcripts are referred to as two copies of sra41 or Sm3/Sm3', independently confirmed the expression of these sRNAs 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 also revealed the expression of Smr15C1 and Smr15C2, here referred to as SmelC411 and SmelC412 respectively, mapping the 5’- and 3´-ends of the full-length transcripts to essentially the same positions as del Val et al. in the S. meliloti 1021 chromosome. However, this study identified an additional TSS for Smr15C2 at position 1698948.[4]

The nucleotide sequences of Smr15C1 and Smr15C2 were initially used as query to search against the Rfam database (version 10.0; http://rfam.xfam.org). This search revealed partial homology of both transcripts, restricted to the second hairpin and the Rho-independent terminator, to the RF00519 family of RNAs known as suhB (http://rfam.xfam.org/family/RF00519). However, no structural homologs of the full-length sRNAs were found in this database.

Both S.melilloti αr15 sRNAs were also 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)[5] (Figure 2). This CM was used in a further search for new members of the αr15 family in the existing bacterial genomic databases.

Table 1: Smr15C1 and Smr15C2 homologs in other symbionts and pathogens
CM model Name GI accession number begin end strand %GC length Organism
class=cellinside αr15class=cellinside Smr15C1class=cellinside gi|15963753|ref|NC_003047.1|class=cellinside 1698617class=cellinside 1698731class=cellinside -class=cellinside 54class=cellinside 115class=cellinside Sinorhizobium meliloti 1021
class=cellinside αr15class=cellinside Smr15C2class=cellinside gi|15963753|ref|NC_003047.1|class=cellinside 1698817class=cellinside 1698937class=cellinside -class=cellinside 50class=cellinside 121class=cellinside Sinorhizobium meliloti 1021
class=cellinside αr15class=cellinside Smr15Aclass=cellinside gi|16262453|ref|NC_003037.1|class=cellinside 552873class=cellinside 552984class=cellinside +class=cellinside 51class=cellinside 112class=cellinside Sinorhizobium meliloti 1021 plasmid pSymA
class=cellinside αr15class=cellinside Smedr15C1class=cellinside gi|150395228|ref|NC_009636.1|class=cellinside 1337011class=cellinside 1337126class=cellinside -class=cellinside 53class=cellinside 116class=cellinside Sinorhizobium medicae WSM419 chromosome
class=cellinside αr15class=cellinside Smedr15C2class=cellinside gi|150395228|ref|NC_009636.1|class=cellinside 1337212class=cellinside 1337331class=cellinside -class=cellinside 50class=cellinside 120class=cellinside Sinorhizobium medicae WSM419 chromosome
class=cellinside αr15class=cellinside Smedr15p03class=cellinside gi|150378263|ref|NC_009622.1|class=cellinside 40054class=cellinside 40165class=cellinside -class=cellinside 52class=cellinside 112class=cellinside Sinorhizobium medicae WSM419 plasmid pSMED03
class=cellinside αr15class=cellinside Sfr15C1class=cellinside gi|227820587|ref|NC_012587.1|class=cellinside 1612511class=cellinside 1612626class=cellinside -class=cellinside 59class=cellinside 116class=cellinside Sinorhizobium fredii NGR234 chromosome
class=cellinside αr15class=cellinside Sfr15C2class=cellinside gi|227820587|ref|NC_012587.1|class=cellinside 1612711class=cellinside 1612830class=cellinside -class=cellinside 51class=cellinside 120class=cellinside Sinorhizobium fredii NGR234 chromosome
class=cellinside αr15class=cellinside Sfr15bclass=cellinside gi|227818258|ref|NC_012586.1|class=cellinside 134078class=cellinside 134190class=cellinside -class=cellinside 55class=cellinside 113class=cellinside Sinorhizobium fredii NGR234 plasmid pNGR234b
class=cellinside αr15class=cellinside Atr15C1class=cellinside gi|159184118|ref|NC_003062.2|class=cellinside 2163254class=cellinside 2163370class=cellinside +class=cellinside 53class=cellinside 117class=cellinside Agrobacterium tumefaciens str. C58 chromosome circular
class=cellinside αr15class=cellinside Atr15C2class=cellinside gi|159184118|ref|NC_003062.2|class=cellinside 2163454class=cellinside 2163554class=cellinside +class=cellinside 57class=cellinside 101class=cellinside Agrobacterium tumefaciens str. C58 chromosome circular
class=cellinside αr15class=cellinside AH13r15C1class=cellinside gi|325291453|ref|NC_015183.1|class=cellinside 2112823class=cellinside 2112939class=cellinside +class=cellinside 52class=cellinside 117class=cellinside Agrobacterium sp. H13-3 chromosome
class=cellinside αr15class=cellinside AH13r15C2class=cellinside gi|325291453|ref|NC_015183.1|class=cellinside 2113023class=cellinside 2113121class=cellinside +class=cellinside 54class=cellinside 99class=cellinside Agrobacterium sp. H13-3 chromosome
class=cellinside αr15class=cellinside AH13r15aclass=cellinside gi|325168279|ref|NC_015184.1|class=cellinside 211698class=cellinside 211807class=cellinside -class=cellinside 53class=cellinside 110class=cellinside Agrobacterium sp. H13-3 plasmid pAspH13-3a
class=cellinside αr15class=cellinside ReCIATr15C1class=cellinside gi|190889639|ref|NC_010994.1|class=cellinside 3155217class=cellinside 3155332class=cellinside +class=cellinside 51class=cellinside 116class=cellinside Rhizobium etli CIAT 652
class=cellinside αr15class=cellinside ReCIATr15C2class=cellinside gi|190889639|ref|NC_010994.1|class=cellinside 3155440class=cellinside 3155555class=cellinside +class=cellinside 48class=cellinside 116class=cellinside Rhizobium etli CIAT 652
class=cellinside αr15class=cellinside ReCIATr15pCclass=cellinside gi|190894340|ref|NC_010997.1|class=cellinside 941345class=cellinside 941452class=cellinside +class=cellinside 53class=cellinside 108class=cellinside Rhizobium etli CIAT 652 plasmid pC
class=cellinside αr15class=cellinside ReCIATr15Bclass=cellinside gi|190893983|ref|NC_010996.1|class=cellinside 187927class=cellinside 188041class=cellinside -class=cellinside 50class=cellinside 115class=cellinside Rhizobium etli CIAT 652 plasmid pB
class=cellinside αr15class=cellinside Arr15CI1class=cellinside gi|222084201|ref|NC_011985.1|class=cellinside 2506215class=cellinside 2506331class=cellinside +class=cellinside 52class=cellinside 117class=cellinside Agrobacterium radiobacter K84 chromosome 1
class=cellinside αr15class=cellinside Arr15CI2class=cellinside gi|222084201|ref|NC_011985.1|class=cellinside 2506418class=cellinside 2506534class=cellinside +class=cellinside 54class=cellinside 117class=cellinside Agrobacterium radiobacter K84 chromosome 1
class=cellinside αr15class=cellinside Arr15CIIclass=cellinside gi|222080781|ref|NC_011983.1|class=cellinside 1011511class=cellinside 1011624class=cellinside -class=cellinside 57class=cellinside 114class=cellinside Agrobacterium radiobacter K84 chromosome 2
class=cellinside αr15class=cellinside Rlt2304r15C1class=cellinside gi|209547612|ref|NC_011369.1|class=cellinside 2770612class=cellinside 2770727class=cellinside +class=cellinside 50class=cellinside 116class=cellinside Rhizobium leguminosarum bv. trifolii WSM2304 chromosome
class=cellinside αr15class=cellinside Rlt2304r15C2class=cellinside gi|209547612|ref|NC_011369.1|class=cellinside 2770835class=cellinside 2770949class=cellinside +class=cellinside 50class=cellinside 115class=cellinside Rhizobium leguminosarum bv. trifolii WSM2304 chromosome
class=cellinside αr15class=cellinside Avr15CI1class=cellinside gi|222147015|ref|NC_011989.1|class=cellinside 2608532class=cellinside 2608647class=cellinside +class=cellinside 54class=cellinside 116class=cellinside Agrobacterium vitis S4 chromosome 1
class=cellinside αr15class=cellinside Avr15CI2class=cellinside gi|222147015|ref|NC_011989.1|class=cellinside 2608739class=cellinside 2608839class=cellinside +class=cellinside 46class=cellinside 101class=cellinside Agrobacterium vitis S4 chromosome 1
class=cellinside αr15class=cellinside Avr15Atcclass=cellinside gi|222083145|ref|NC_011984.1|class=cellinside 122624class=cellinside 122736class=cellinside -class=cellinside 50class=cellinside 113class=cellinside Agrobacterium vitis S4 plasmid pAtS4c
class=cellinside αr15class=cellinside Avr15Ateclass=cellinside gi|222102412|ref|NC_011981.1|class=cellinside 198928class=cellinside 199039class=cellinside +class=cellinside 51class=cellinside 112class=cellinside Agrobacterium vitis S4 plasmid pAtS4e
class=cellinside αr15class=cellinside Avr15Ticlass=cellinside gi|222080117|ref|NC_011982.1|class=cellinside 52286class=cellinside 52397class=cellinside -class=cellinside 57class=cellinside 112class=cellinside Agrobacterium vitis S4 plasmid pTiS4
class=cellinside αr15class=cellinside Rlvr15C1class=cellinside gi|116249766|ref|NC_008380.1|class=cellinside 3605490class=cellinside 3605605class=cellinside +class=cellinside 51class=cellinside 116class=cellinside Rhizobium leguminosarum bv. viciae 3841
class=cellinside αr15class=cellinside Rlvr15C2class=cellinside gi|116249766|ref|NC_008380.1|class=cellinside 3605714class=cellinside 3605829class=cellinside +class=cellinside 48class=cellinside 116class=cellinside Rhizobium leguminosarum bv. viciae 3841
class=cellinside αr15class=cellinside Rlvr15p10class=cellinside gi|116254467|ref|NC_008381.1|class=cellinside 138799class=cellinside 138912class=cellinside +class=cellinside 56class=cellinside 114class=cellinside Rhizobium leguminosarum bv. viciae 3841 plasmid pRL10
class=cellinside αr15class=cellinside Rlvr15p11class=cellinside gi|116255200|ref|NC_008384.1|class=cellinside 567053class=cellinside 567166class=cellinside -class=cellinside 53class=cellinside 114class=cellinside Rhizobium leguminosarum bv. viciae 3841 plasmid pRL11
class=cellinside αr15class=cellinside Rlt1325r15C1class=cellinside gi|241202755|ref|NC_012850.1|class=cellinside 2981275class=cellinside 2981390class=cellinside +class=cellinside 50class=cellinside 116class=cellinside Rhizobium leguminosarum bv. trifolii WSM1325
class=cellinside αr15class=cellinside Rlt1325r15C2class=cellinside gi|241202755|ref|NC_012850.1|class=cellinside 2981499class=cellinside 2981613class=cellinside +class=cellinside 50class=cellinside 115class=cellinside Rhizobium leguminosarum bv. trifolii WSM1325
class=cellinside αr15class=cellinside Rlt1325r15p02class=cellinside gi|241666492|ref|NC_012858.1|class=cellinside 36176class=cellinside 36289class=cellinside +class=cellinside 51class=cellinside 114class=cellinside Rhizobium leguminosarum bv. trifolii WSM1325 plasmid pR132502
class=cellinside αr15class=cellinside ReCFNr15C1class=cellinside gi|86355669|ref|NC_007761.1|class=cellinside 3117667class=cellinside 3117782class=cellinside +class=cellinside 50class=cellinside 116class=cellinside Rhizobium etli CFN 42
class=cellinside αr15class=cellinside ReCFNr15C2class=cellinside gi|86355669|ref|NC_007761.1|class=cellinside 3117890class=cellinside 3118004class=cellinside +class=cellinside 50class=cellinside 115class=cellinside Rhizobium etli CFN 42
class=cellinside αr15class=cellinside ReCFNr15dclass=cellinside gi|89255298|ref|NC_004041.2|class=cellinside 172760class=cellinside 172874class=cellinside -class=cellinside 50class=cellinside 115class=cellinside Rhizobium etli CFN 42 symbiotic plasmid p42d
class=cellinside αr15class=cellinside ReCFNr15aclass=cellinside gi|86359705|ref|NC_007762.1|class=cellinside 157296class=cellinside 157409class=cellinside +class=cellinside 56class=cellinside 114class=cellinside Rhizobium etli CFN 42 plasmid p42a
class=cellinside αr15class=cellinside Mlr15aclass=cellinside gi|13488050|ref|NC_002679.1|class=cellinside 65044class=cellinside 65154class=cellinside -class=cellinside 51class=cellinside 111class=cellinside Mesorhizobium loti MAFF303099 plasmid pMLa
class=cellinside αr15class=cellinside Bcr15CIIclass=cellinside gi|161620094|ref|NC_010104.1|class=cellinside 707465class=cellinside 707572class=cellinside +class=cellinside 56class=cellinside 108class=cellinside Brucella canis ATCC 23365 chromosome II
class=cellinside αr15class=cellinside Bcr15CI1class=cellinside gi|161617991|ref|NC_010103.1|class=cellinside 1379297class=cellinside 1379398class=cellinside -class=cellinside 51class=cellinside 102class=cellinside Brucella canis ATCC 23365 chromosome I
class=cellinside αr15class=cellinside Bcr15CI2class=cellinside gi|161617991|ref|NC_010103.1|class=cellinside 1451969class=cellinside 1452087class=cellinside -class=cellinside 50class=cellinside 119class=cellinside Brucella canis ATCC 23365 chromosome I
class=cellinside αr15class=cellinside Bs23445r15CI1class=cellinside gi|163842277|ref|NC_010169.1|class=cellinside 1401085class=cellinside 1401186class=cellinside -class=cellinside 51class=cellinside 102class=cellinside Brucella suis ATCC 23445 chromosome I
class=cellinside αr15class=cellinside Bs23445r15CI2class=cellinside gi|163842277|ref|NC_010169.1|class=cellinside 1473791class=cellinside 1473909class=cellinside -class=cellinside 50class=cellinside 119class=cellinside Brucella suis ATCC 23445 chromosome I
class=cellinside αr15class=cellinside Bs23445r15CIIclass=cellinside gi|163844199|ref|NC_010167.1|class=cellinside 696081class=cellinside 696188class=cellinside +class=cellinside 56class=cellinside 108class=cellinside Brucella suis ATCC 23445 chromosome II
class=cellinside αr15class=cellinside Bm16Mr15CIclass=cellinside gi|17986284|ref|NC_003317.1|class=cellinside 607684class=cellinside 607785class=cellinside +class=cellinside 51class=cellinside 102class=cellinside Brucella melitensis bv. 1 str. 16M chromosome I
class=cellinside αr15class=cellinside Bm16Mr15CIIclass=cellinside gi|17988344|ref|NC_003318.1|class=cellinside 589501class=cellinside 589608class=cellinside -class=cellinside 56class=cellinside 108class=cellinside Brucella melitensis bv. 1 str. 16M chromosome II
class=cellinside αr15class=cellinside BaS19r15CIIclass=cellinside gi|189022234|ref|NC_010740.1|class=cellinside 508055class=cellinside 508162class=cellinside -class=cellinside 56class=cellinside 108class=cellinside Brucella abortus S19 chromosome 2
class=cellinside αr15class=cellinside BaS19r15CI1class=cellinside gi|189023268|ref|NC_010742.1|class=cellinside 1396794class=cellinside 1396895class=cellinside -class=cellinside 51class=cellinside 102class=cellinside Brucella abortus S19 chromosome 1
class=cellinside αr15class=cellinside BaS19r15CI2class=cellinside gi|189023268|ref|NC_010742.1|class=cellinside 1469407class=cellinside 1469525class=cellinside -class=cellinside 50class=cellinside 119class=cellinside Brucella abortus S19 chromosome 1
class=cellinside αr15class=cellinside Bm23457r15CIIclass=cellinside gi|225685871|ref|NC_012442.1|class=cellinside 687290class=cellinside 687397class=cellinside +class=cellinside 56class=cellinside 108class=cellinside Brucella melitensis ATCC 23457 chromosome II
class=cellinside αr15class=cellinside Bm23457r15CIclass=cellinside gi|225851546|ref|NC_012441.1|class=cellinside 1400641class=cellinside 1400742class=cellinside -class=cellinside 51class=cellinside 102class=cellinside Brucella melitensis ATCC 23457 chromosome I
class=cellinside αr15class=cellinside Bs1330r15CIIclass=cellinside gi|56968493|ref|NC_004311.2|class=cellinside 708185class=cellinside 708292class=cellinside +class=cellinside 56class=cellinside 108class=cellinside Brucella suis 1330 chromosome II
class=cellinside αr15class=cellinside Bs1330r15CI1class=cellinside gi|56968325|ref|NC_004310.3|class=cellinside 1380381class=cellinside 1380482class=cellinside -class=cellinside 51class=cellinside 102class=cellinside Brucella suis 1330 chromosome I
class=cellinside αr15class=cellinside Bs1330r15CI2class=cellinside gi|56968325|ref|NC_004310.3|class=cellinside 1453011class=cellinside 1453129class=cellinside -class=cellinside 50class=cellinside 119class=cellinside Brucella suis 1330 chromosome I
class=cellinside αr15class=cellinside Ba19941r15CI1class=cellinside gi|62288991|ref|NC_006932.1|class=cellinside 1398464class=cellinside 1398565class=cellinside -class=cellinside 51class=cellinside 102class=cellinside Brucella abortus bv. 1 str. 9-941 chromosome I
class=cellinside αr15class=cellinside Ba19941r15CI2class=cellinside gi|62288991|ref|NC_006932.1|class=cellinside 1471073class=cellinside 1471191class=cellinside -class=cellinside 50class=cellinside 119class=cellinside Brucella abortus bv. 1 str. 9-941 chromosome I
class=cellinside αr15class=cellinside Ba19941r15CIIclass=cellinside gi|62316961|ref|NC_006933.1|class=cellinside 508851class=cellinside 508958class=cellinside -class=cellinside 56class=cellinside 108class=cellinside Brucella abortus bv. 1 str. 9-941 chromosome II
class=cellinside αr15class=cellinside Bmar15CIIclass=cellinside gi|83268957|ref|NC_007624.1|class=cellinside 508839class=cellinside 508946class=cellinside -class=cellinside 56class=cellinside 108class=cellinside Brucella melitensis biovar Abortus 2308 chromosome II
class=cellinside αr15class=cellinside Bmar15CI1class=cellinside gi|82698932|ref|NC_007618.1|class=cellinside 1395614class=cellinside 1395715class=cellinside -class=cellinside 51class=cellinside 102class=cellinside Brucella melitensis biovar Abortus 2308 chromosome I
class=cellinside αr15class=cellinside Bmar15CI2class=cellinside gi|82698932|ref|NC_007618.1|class=cellinside 1468227class=cellinside 1468345class=cellinside -class=cellinside 50class=cellinside 119class=cellinside Brucella melitensis biovar Abortus 2308 chromosome I
class=cellinside αr15class=cellinside Bor15CI1class=cellinside gi|148558820|ref|NC_009505.1|class=cellinside 1387928class=cellinside 1388029class=cellinside -class=cellinside 50class=cellinside 102class=cellinside Brucella ovis ATCC 25840 chromosome I
class=cellinside αr15class=cellinside Bor15CI2class=cellinside gi|148558820|ref|NC_009505.1|class=cellinside 1460506class=cellinside 1460624class=cellinside -class=cellinside 50class=cellinside 119class=cellinside Brucella ovis ATCC 25840 chromosome I
class=cellinside αr15class=cellinside Bor15CIIclass=cellinside gi|148557829|ref|NC_009504.1|class=cellinside 709415class=cellinside 709524class=cellinside +class=cellinside 54class=cellinside 110class=cellinside Brucella ovis ATCC 25840 chromosome II
class=cellinside αr15class=cellinside Bmir15CIIclass=cellinside gi|256014795|ref|NC_013118.1|class=cellinside 709102class=cellinside 709209class=cellinside +class=cellinside 56class=cellinside 108class=cellinside Brucella microti CCM 4915 chromosome 2
class=cellinside αr15class=cellinside Bmir15CI1class=cellinside gi|256368465|ref|NC_013119.1|class=cellinside 1387776class=cellinside 1387877class=cellinside -class=cellinside 51class=cellinside 102class=cellinside Brucella microti CCM 4915 chromosome 1
class=cellinside αr15class=cellinside Bmir15CI2class=cellinside gi|256368465|ref|NC_013119.1|class=cellinside 1461298class=cellinside 1461416class=cellinside -class=cellinside 50class=cellinside 119class=cellinside Brucella microti CCM 4915 chromosome 1
class=cellinside αr15class=cellinside Oar15CIclass=cellinside gi|153007346|ref|NC_009667.1|class=cellinside 1751482class=cellinside 1751598class=cellinside +class=cellinside 49class=cellinside 117class=cellinside Brucella anthropi ATCC 49188 chromosome 1
class=cellinside αr15class=cellinside Oar15CIIclass=cellinside gi|153010078|ref|NC_009668.1|class=cellinside 1270083class=cellinside 1270191class=cellinside +class=cellinside 56class=cellinside 109class=cellinside Brucella anthropi ATCC 49188 chromosome 2
class=cellinside αr15class=cellinside Oar15p02class=cellinside gi|153011934|ref|NC_009670.1|class=cellinside 22208class=cellinside 22320class=cellinside +class=cellinside 54class=cellinside 113class=cellinside Brucella anthropi ATCC 49188 plasmid pOANT02

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[6] comparing the obtained predictions. The manual inspection of the sequences found with the CM using Infernal allowed finding 38 true homologues in phylogenetically related α-proteobacterial genomes. The 26 closest αr15 family members were found as tandem in the same chromosomal IGRs for the following species besides S. melilloti:

All these sequences showed significant bit scores and Infernal E-values (1.71e-28 - 2.03e-20). However, the plasmidic copies of all mentioned α-proteobacterial genomes and those αr15 members encoded by Brucella species (B. ovis, B. canis, B. abortus, B. microtis, and several biovars of B. melitensis), Brucella anthropi and Mesorhizobium lotishowed high E-values between (1e-19 and 8e-03) but very low bit-scores.

Expression and functional information

Several studies have assessed Smr15C1 and Smr15C2 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),[1] high salt stress, oxidative stress and cold and hot shock stresses. The results showed different expression profiles for both sRNAs,[1] which is consistent with their organization in independent and differentially regulated transcription units within the same IGR (Figure 4 and Figure 5).

The expression of Smr15C1 and Smr15C2 in free-living bacteria was found to be growth-dependent but in an opposite manner. While Smr15C1 is accumulated in the stationary phase Smr15C2 is The expression of Smr15C1 and Smr15C2 in free-living bacteria was found to be growth-dependent but in an opposite manner. While Smr15C1 is accumulated in the stationary phase, Smr15C2 is preferentially expressed in log bacterial cultures.[1] Additionally, Schlüter et al. recently described the up-regulation of Smr15C2 under cold shock stress, while no effects of a temperature downshift were observed in the expression of Smr15C1. The growth-dependent opposite expression profiles of Smr15C1 and Smr15C2, have not been observed in their Agrobacterium tumefaciens counterparts referred to as AbcR1 and AbcR2, respectively, by Wilms et al. (Atr15C1 and Atr15C2 in this work). AbcR1 and AbcR2 are induced simultaneously and both accumulate in stationary phase.[7] This behavior agrees with the fact that AbcR1 and AbcR2 have identical promoter-like sequences, being these very similar to the one of Smr15C2, but not to the promoter sequence of Smr15C1 (see Promoter Analysis). Furthermore, a first approach to the function of the AbcR genes revealed that these sRNAs silence the GABA uptake system through the down-regulation of the corresponding ABC transporter genes in an Hfq-dependent manner.[7] GABA is one of the plants signals recognized by rhizobacteria in some plant-bacteria interactions. Thus, these results, point to the shutting off synthesis of the GABA uptake system as a way used by A. tumefaciens to subvert the plant defense mechanism.

Recent co-immunoprecipitation experiment[8] showed that both, Smr15C1 and Smr15C2, do bind the S. meliloti RNA chaperone Hfq, supporting also a role for these transcripts in this bacterium as trans-acting antisense riboregulators.They were also shown to fine-tune nutrient uptake.[9]

Promoter analysis

All αr15 loci have recognizable σ70-dependent promoters showing a -35/-10 consensus motif CTTGAC-n17-CTATAT, which has been previously shown to be widely conserved among several other genera in the α-subgroup of proteobacteria.[10] A multiple sequence alignment of these promoter regions revealed a conserved sequence stretch extending up to 80 bp upstream of the transcription start site in all the αr15 loci with the only exceptions of the S. meliloti, S.fredii and S. medicae αr15C1 promoters.

To identify binding sites for other known transcription factors we used the fasta sequences provided by RegPredict[11] (http://regpredict.lbl.gov/regpredict/help.html), and used those position weight matrices (PSWM) provided by RegulonDB[12] (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[13] (http://meme.sdsc.edu/meme4_6_1/intro.html) and used relaxed regular expressions (i.e. pattern matching) over all αr15 homologs promoters.

These studies revealed a difference in regulation between S. melilloti, S.fredii and S. medicae αr15C1 sRNAs and the rest of the αr15 family members independently of their group of origin (Rhizobium or Agrobacterium) and genomic location (αr15C1, αr15C2, αr15plasmid) (Figure 4).

The rest of the family members presented a very well conserved 30 bp long region between positions -36 and -75. This conserved region, was used to query databases of known transcription factor motifs with TomTom,[14] the best matching motif was SMb20667_Rhizobiales, motif belonging to RegTransBase (http://regtransbase.lbl.gov/cgi-bin/regtransbase?page=main). The Smb20667 correspond to the binding site for a dicarboxylate metabolism regulator in Rhizobiales that belongs to the LacI family. This motif was identified clustering genes of tartrate dehydrogenase, succinate semialdehyde dehydrogenase, 3-hydroxyisobutyrate dehydrogenase and hydroxypyruvate isomerase in S. meliloti, and several Rhizobiums and it is marked in the promoter alignment figure (Figure 5) with an orange box. Moreover, another conserved sequence was found using MEME in the promoter region of the Sinorhizobium species αr15C1. This conserved region was used to query databases of known transcription factor motifs with TomTom, and the best matching motif was SMb20537_Rhizobiales (Figure 5 in red), that identifies the binding site for a sugar utilization regulator in Rhizobiales from the LacI family as well.

Genomic context

Most of the αr15 family members are trans-encoded sRNAs transcribed from independent promoters in chromosomal IGRs. Many of the αr15 members neighboring genes were not annotated, and thus they were further manually curated.[15] [16] [17] As a result, we could classify the members of the family in four subgroups according to their genomic context. In the first group are the tandem αr15C1 and αr15C2 loci of the Rhizobium, Sinorhizobium and Agrobacterium species. They exhibited a great degree of conservation in the up and downstream genes, which have been predicted to code for a LysR transcriptional regulator and an AsR transcriptional regulator protein respectively (Figure 5). The only exception in this group was found for S. fredii that presented a very different genomic context. The second group includes the αr15CI1 loci in the Brucella species (additional file 2), which presented a very well conserved genomic context (Aspartate amino transferase and LysR/unknown transcriptional regulator) with partial synteny to the first group. A very different genomic context, not even partially conserved in most cases, was present in all plasmid-borne αr15 loci (additional file 1), which integrates the defined group three, where the flanking genes corresponded to ABC transporter proteins, excisonase or transposase among others. The αr15CI2 loci in the Brucella species (additional file 3) conform the group four and presented an up and downstream conserved genomic context, coding all regions for UDP-3-O-hydroxymyristoyl N-acetylglucosamine deacetylase and GTPAse cell division protein FtsZ. To the last group correspond the αr15CII loci in the Brucella group (additional file 4) where only one of the genes could be annotated always as a glycine deshidrogenase, the other sRNA flanking position was mostly coped by a hypothetical protein conserved in the Brucella group to which no domain, motif or GO functional annotation could be assigned.

Additional Files:

Table 2: Detailed Genomic context information of the αr15 sRNA seed members.! Family !! Feature type !! Feature name !! Strand !! Begin !! End !! Protein name !! Annotation !! Organism
class=cellinside αr15_Smr15Cclass=cellinside geneclass=cellinside SMc01226class=cellinside Rclass=cellinside 1698201class=cellinside 1698491class=cellinside NP_385671.1class=cellinside transcription regulator proteinclass=cellinside Sinorhizobium meliloti 1021 (NC_003047)
class=cellinside αr15_Smr15Cclass=cellinside sRNAclass=cellinside Smr15C1class=cellinside Rclass=cellinside 1698617class=cellinside 1698731class=cellinside -class=cellinside sRNAclass=cellinside Sinorhizobium meliloti 1021 (NC_003047)
class=cellinside αr15_Smr15Cclass=cellinside sRNAclass=cellinside Smr15C2class=cellinside Rclass=cellinside 1698817class=cellinside 1698937class=cellinside -class=cellinside sRNAclass=cellinside Sinorhizobium meliloti 1021 (NC_003047)
class=cellinside αr15_Smr15Cclass=cellinside geneclass=cellinside SMc01225class=cellinside Rclass=cellinside 1699144class=cellinside 1700052class=cellinside NP_385672.1class=cellinside transcription regulator proteinclass=cellinside Sinorhizobium meliloti 1021 (NC_003047)
class=cellinside αr15_Smed15Cclass=cellinside geneclass=cellinside Smed_1246class=cellinside Rclass=cellinside 1336608class=cellinside 1336898class=cellinside YP_001326931.1class=cellinside ArsR family transcriptional regulatorclass=cellinside Sinorhizobium medicae WSM419 chromosome (NC_009636)
class=cellinside αr15_Smed15Cclass=cellinside sRNAclass=cellinside Smedr15C1class=cellinside Rclass=cellinside 1337011class=cellinside 1337126class=cellinside -class=cellinside sRNAclass=cellinside Sinorhizobium medicae WSM419 chromosome (NC_009636)
class=cellinside αr15_Smed15Cclass=cellinside sRNAclass=cellinside Smedr15C2class=cellinside Rclass=cellinside 1337212class=cellinside 1337331class=cellinside -class=cellinside sRNAclass=cellinside Sinorhizobium medicae WSM419 chromosome (NC_009636)
class=cellinside αr15_Smed15Cclass=cellinside geneclass=cellinside Smed_1247class=cellinside Rclass=cellinside 1337537class=cellinside 1338433class=cellinside YP_001326932.1class=cellinside LysR family transcriptional regulatorclass=cellinside Sinorhizobium medicae WSM419 chromosome (NC_009636)
class=cellinside αr15_Rlt2304r15Cclass=cellinside geneclass=cellinside Rleg2_2722class=cellinside Dclass=cellinside 2769491class=cellinside 2770402class=cellinside YP_002282219.1class=cellinside LysR family transcriptional regulatorclass=cellinside Rhizobium leguminosarum bv. trifolii WSM2304 chromosome (NC_011369)
class=cellinside αr15_Rlt2304r15Cclass=cellinside sRNAclass=cellinside Rlt2304r15C1class=cellinside Dclass=cellinside 2770612class=cellinside 2770727class=cellinside -class=cellinside sRNAclass=cellinside Rhizobium leguminosarum bv. trifolii WSM2304 chromosome (NC_011369)
class=cellinside αr15_Rlt2304r15Cclass=cellinside sRNAclass=cellinside Rlt2304r15C2class=cellinside Dclass=cellinside 2770835class=cellinside 2770949class=cellinside -class=cellinside sRNAclass=cellinside Rhizobium leguminosarum bv. trifolii WSM2304 chromosome (NC_011369)
class=cellinside αr15_Rlt2304r15Cclass=cellinside geneclass=cellinside Rleg2_2723class=cellinside Dclass=cellinside 2771064class=cellinside 2771357class=cellinside YP_002282220.1class=cellinside ArsR family transcriptional regulatorclass=cellinside Rhizobium leguminosarum bv. trifolii WSM2304 chromosome (NC_011369)
class=cellinside αr15_Rlt1325r15Cclass=cellinside geneclass=cellinside Rleg_2983class=cellinside Dclass=cellinside 2980263class=cellinside 2981174class=cellinside YP_002976781.1class=cellinside LysR family transcriptional regulatorclass=cellinside Rhizobium leguminosarum bv. trifolii WSM1325 (NC_012850)
class=cellinside αr15_Rlt1325r15Cclass=cellinside sRNAclass=cellinside Rlt1325r15C1class=cellinside Dclass=cellinside 2981275class=cellinside 2981390class=cellinside -class=cellinside sRNAclass=cellinside Rhizobium leguminosarum bv. trifolii WSM1325 (NC_012850)
class=cellinside αr15_Rlt1325r15Cclass=cellinside sRNAclass=cellinside Rlt1325r15C2class=cellinside Dclass=cellinside 2981499class=cellinside 2981613class=cellinside -class=cellinside sRNAclass=cellinside Rhizobium leguminosarum bv. trifolii WSM1325 (NC_012850)
class=cellinside αr15_Rlt1325r15Cclass=cellinside geneclass=cellinside Rleg_2984class=cellinside Dclass=cellinside 2981728class=cellinside 2982021class=cellinside YP_002976782.1class=cellinside ArsR family transcriptional regulatorclass=cellinside Rhizobium leguminosarum bv. trifolii WSM1325 (NC_012850)
class=cellinside αr15_ReCFNr15Cclass=cellinside geneclass=cellinside RHE_CH02976class=cellinside Dclass=cellinside 3116670class=cellinside 3117566class=cellinside YP_470470.1class=cellinside LysR family transcriptional regulatorclass=cellinside Rhizobium etli CFN 42 (NC_007761)
class=cellinside αr15_ReCFNr15Cclass=cellinside sRNAclass=cellinside ReCFNr15C1class=cellinside Dclass=cellinside 3117667class=cellinside 3117782class=cellinside -class=cellinside sRNAclass=cellinside Rhizobium etli CFN 42 (NC_007761)
class=cellinside αr15_ReCFNr15Cclass=cellinside sRNAclass=cellinside ReCFNr15C2class=cellinside Dclass=cellinside 3117890class=cellinside 3118004class=cellinside -class=cellinside sRNAclass=cellinside Rhizobium etli CFN 42 (NC_007761)
class=cellinside αr15_ReCFNr15Cclass=cellinside geneclass=cellinside RHE_CH02977class=cellinside Dclass=cellinside 3118119class=cellinside 3118412class=cellinside YP_470471.1class=cellinside ArsR family transcriptional regulatorclass=cellinside Rhizobium etli CFN 42 (NC_007761)
class=cellinside αr15_ReCIATr15Cclass=cellinside geneclass=cellinside RHECIAT_CH0003143class=cellinside Dclass=cellinside 3154220class=cellinside 3155116class=cellinside YP_001979269.1class=cellinside LysR family transcriptional regulatorclass=cellinside Rhizobium etli CIAT 652 (NC_010994)
class=cellinside αr15_ReCIATr15Cclass=cellinside sRNAclass=cellinside ReCIATr15C1class=cellinside Dclass=cellinside 3155217class=cellinside 3155332class=cellinside -class=cellinside sRNAclass=cellinside Rhizobium etli CIAT 652 (NC_010994)
class=cellinside αr15_ReCIATr15Cclass=cellinside sRNAclass=cellinside ReCIATr15C2class=cellinside Dclass=cellinside 3155440class=cellinside 3155555class=cellinside -class=cellinside sRNAclass=cellinside Rhizobium etli CIAT 652 (NC_010994)
class=cellinside αr15_ReCIATr15Cclass=cellinside geneclass=cellinside RHECIAT_CH0003144class=cellinside Dclass=cellinside 3155652class=cellinside 3155963class=cellinside YP_001979270.1class=cellinside ArsR family transcriptional regulatorclass=cellinside Rhizobium etli CIAT 652 (NC_010994)
class=cellinside αr15_Rlvr15Cclass=cellinside geneclass=cellinside RL3429class=cellinside Dclass=cellinside 3604478class=cellinside 3605389class=cellinside YP_769009.1class=cellinside LysR family transcriptional regulatorclass=cellinside Rhizobium leguminosarum bv. viciae 3841 (NC_008380)
class=cellinside αr15_Rlvr15Cclass=cellinside sRNAclass=cellinside Rlvr15C1class=cellinside Dclass=cellinside 3605490class=cellinside 3605605class=cellinside -class=cellinside sRNAclass=cellinside Rhizobium leguminosarum bv. viciae 3841 (NC_008380)
class=cellinside αr15_Rlvr15Cclass=cellinside sRNAclass=cellinside Rlvr15C2class=cellinside Dclass=cellinside 3605714class=cellinside 3605829class=cellinside -class=cellinside sRNAclass=cellinside Rhizobium leguminosarum bv. viciae 3841 (NC_008380)
class=cellinside αr15_Rlvr15Cclass=cellinside geneclass=cellinside RL3430class=cellinside Dclass=cellinside 3605944class=cellinside 3606237class=cellinside YP_769010.1class=cellinside ArsR family transcriptional regulatorclass=cellinside Rhizobium leguminosarum bv. viciae 3841 (NC_008380)
class=cellinside αr15_Sfr15Cclass=cellinside geneclass=cellinside NGR_c15610class=cellinside Rclass=cellinside 1611431class=cellinside 1612354class=cellinside YP_002826082.1class=cellinside lytic transglycosylase catalyticclass=cellinside Sinorhizobium fredii NGR234 chromosome (NC_012587)
class=cellinside αr15_Sfr15Cclass=cellinside sRNAclass=cellinside Sfr15C1class=cellinside Rclass=cellinside 1612511class=cellinside 1612626class=cellinside -class=cellinside sRNAclass=cellinside Sinorhizobium fredii NGR234 chromosome (NC_012587)
class=cellinside αr15_Sfr15Cclass=cellinside sRNAclass=cellinside Sfr15C2class=cellinside Rclass=cellinside 1612711class=cellinside 1612830class=cellinside -class=cellinside sRNAclass=cellinside Sinorhizobium fredii NGR234 chromosome (NC_012587)
class=cellinside αr15_Sfr15Cclass=cellinside geneclass=cellinside NGR_c15640class=cellinside Rclass=cellinside 1612866class=cellinside 1612961class=cellinside YP_002826083.1class=cellinside hypothetical proteinclass=cellinside Sinorhizobium fredii NGR234 chromosome (NC_012587)
class=cellinside αr15_Arr15CIclass=cellinside geneclass=cellinside Arad_3145class=cellinside Dclass=cellinside 2505179class=cellinside 2506090class=cellinside YP_002545096.1class=cellinside transcription regulator proteinclass=cellinside Agrobacterium radiobacter K84 chromosome 1 (NC_011985)
class=cellinside αr15_Arr15CIclass=cellinside sRNAclass=cellinside Arr15CI1class=cellinside Dclass=cellinside 2506215class=cellinside 2506331class=cellinside -class=cellinside sRNAclass=cellinside Agrobacterium radiobacter K84 chromosome 1 (NC_011985)
class=cellinside αr15_Arr15CIclass=cellinside sRNAclass=cellinside Arr15CI2class=cellinside Dclass=cellinside 2506418class=cellinside 2506534class=cellinside -class=cellinside sRNAclass=cellinside Agrobacterium radiobacter K84 chromosome 1 (NC_011985)
class=cellinside αr15_Arr15CIclass=cellinside geneclass=cellinside Arad_3147class=cellinside Dclass=cellinside 2506657class=cellinside 2506950class=cellinside YP_002545097.1class=cellinside transcription regulator proteinclass=cellinside Agrobacterium radiobacter K84 chromosome 1 (NC_011985)
class=cellinside αr15_AH13r15Cclass=cellinside geneclass=cellinside AGROH133_07649class=cellinside Dclass=cellinside 2111723class=cellinside 2112625class=cellinside YP_004279410.1class=cellinside LysR family transcriptional regulatorclass=cellinside Agrobacterium sp. H13-3 chromosome (NC_015183)
class=cellinside αr15_AH13r15Cclass=cellinside sRNAclass=cellinside AH13r15C1class=cellinside Dclass=cellinside 2112823class=cellinside 2112939class=cellinside -class=cellinside sRNAclass=cellinside Agrobacterium sp. H13-3 chromosome (NC_015183)
class=cellinside αr15_AH13r15Cclass=cellinside sRNAclass=cellinside AH13r15C2class=cellinside Dclass=cellinside 2113023class=cellinside 2113121class=cellinside -class=cellinside sRNAclass=cellinside Agrobacterium sp. H13-3 chromosome (NC_015183)
class=cellinside αr15_AH13r15Cclass=cellinside geneclass=cellinside AGROH133_07651class=cellinside Dclass=cellinside 2113201class=cellinside 2113515class=cellinside YP_004279411.1class=cellinside LysR family transcriptional regulatorclass=cellinside Agrobacterium sp. H13-3 chromosome (NC_015183)
class=cellinside αr15_Atr15Cclass=cellinside geneclass=cellinside Atu2186class=cellinside Dclass=cellinside 2162154class=cellinside 2163056class=cellinside NP_355147.1class=cellinside LysR family transcriptional regulatorclass=cellinside Agrobacterium tumefaciens C58 chromosome circular (NC_003062)
class=cellinside αr15_Atr15Cclass=cellinside sRNAclass=cellinside Atr15C1class=cellinside Dclass=cellinside 2163254class=cellinside 2163370class=cellinside -class=cellinside sRNAclass=cellinside Agrobacterium tumefaciens C58 chromosome circular (NC_003062)
class=cellinside αr15_Atr15Cclass=cellinside sRNAclass=cellinside Atr15C2class=cellinside Dclass=cellinside 2163454class=cellinside 2163554class=cellinside -class=cellinside sRNAclass=cellinside Agrobacterium tumefaciens C58 chromosome circular (NC_003062)
class=cellinside αr15_Atr15Cclass=cellinside geneclass=cellinside Atu2187class=cellinside Dclass=cellinside 2163657class=cellinside 2163947class=cellinside NP_355148.2class=cellinside ArsR family transcriptional regulatorclass=cellinside Agrobacterium tumefaciens C58 chromosome circular (NC_003062)
class=cellinside αr15_Avr15CIclass=cellinside geneclass=cellinside Avi_3141class=cellinside Dclass=cellinside 2607436class=cellinside 2608350class=cellinside YP_002550262.1class=cellinside LysR family transcriptional regulatorclass=cellinside Agrobacterium vitis S4 chromosome 1 (NC_011989)
class=cellinside αr15_Avr15CIclass=cellinside sRNAclass=cellinside Avr15CI1class=cellinside Dclass=cellinside 2608532class=cellinside 2608647class=cellinside -class=cellinside sRNAclass=cellinside Agrobacterium vitis S4 chromosome 1 (NC_011989)
class=cellinside αr15_Avr15CIclass=cellinside sRNAclass=cellinside Avr15CI2class=cellinside Dclass=cellinside 2608739class=cellinside 2608839class=cellinside -class=cellinside sRNAclass=cellinside Agrobacterium vitis S4 chromosome 1 (NC_011989)
class=cellinside αr15_Avr15CIclass=cellinside geneclass=cellinside Avi_3142class=cellinside Dclass=cellinside 2608951class=cellinside 2609238class=cellinside YP_002550263.1class=cellinside ArsR family transcriptional regulatorclass=cellinside Agrobacterium vitis S4 chromosome 1 (NC_011989)
class=cellinside αr15_ReCFNr15aclass=cellinside geneclass=cellinside RHE_PA00141class=cellinside Dclass=cellinside 152078class=cellinside 157177class=cellinside YP_471730.1class=cellinside n-6 DNA methylaseclass=cellinside Rhizobium etli CFN 42 plasmid p42a (NC_007762)
class=cellinside αr15_ReCFNr15aclass=cellinside sRNAclass=cellinside ReCFNr15aclass=cellinside Dclass=cellinside 157296class=cellinside 157409class=cellinside -class=cellinside sRNAclass=cellinside Rhizobium etli CFN 42 plasmid p42a (NC_007762)
class=cellinside αr15_ReCFNr15aclass=cellinside geneclass=cellinside RHE_PA00143class=cellinside Dclass=cellinside 157744class=cellinside 159486class=cellinside YP_471732.1class=cellinside plasmid partitioning proteinclass=cellinside Rhizobium etli CFN 42 plasmid p42a (NC_007762)
class=cellinside αr15_ReCIATr15Bclass=cellinside geneclass=cellinside RHECIAT_PB0000171class=cellinside Rclass=cellinside 187267class=cellinside 187788class=cellinside YP_001984434.1class=cellinside excisonase proteinclass=cellinside Rhizobium etli CIAT 652 plasmid pB (NC_010996)
class=cellinside αr15_ReCIATr15Bclass=cellinside sRNAclass=cellinside ReCIATr15Bclass=cellinside Rclass=cellinside 187927class=cellinside 188041class=cellinside -class=cellinside sRNAclass=cellinside Rhizobium etli CIAT 652 plasmid pB (NC_010996)
class=cellinside αr15_ReCIATr15Bclass=cellinside geneclass=cellinside RHECIAT_PB0000172class=cellinside Rclass=cellinside 188226class=cellinside 189416class=cellinside YP_001984435.1class=cellinside hypothetical proteinclass=cellinside Rhizobium etli CIAT 652 plasmid pB (NC_010996)
class=cellinside αr15_Avr15Atcclass=cellinside geneclass=cellinside Avi_9155class=cellinside Dclass=cellinside 121509class=cellinside 122600class=cellinside YP_002542647.1class=cellinside DNA polymerase III alpha chainclass=cellinside Agrobacterium vitis S4 plasmid pAtS4c (NC_011984)
class=cellinside αr15_Avr15Atcclass=cellinside sRNAclass=cellinside Avr15Atcclass=cellinside Rclass=cellinside 122624class=cellinside 122736class=cellinside -class=cellinside sRNAclass=cellinside Agrobacterium vitis S4 plasmid pAtS4c (NC_011984)
class=cellinside αr15_Avr15Atcclass=cellinside geneclass=cellinside Avi_9156class=cellinside Dclass=cellinside 123011class=cellinside 123358class=cellinside YP_002542648.1class=cellinside helicase subunit of the DNA excision repair complexclass=cellinside Agrobacterium vitis S4 plasmid pAtS4c (NC_011984)
class=cellinside αr15_ReCFNr15dclass=cellinside geneclass=cellinside RHE_PD00155class=cellinside Rclass=cellinside 172105class=cellinside 172731class=cellinside NP_659882.1class=cellinside excisonase proteinclass=cellinside Rhizobium etli CFN 42 symbiotic plasmid p42d (NC_004041)
class=cellinside αr15_ReCFNr15dclass=cellinside sRNAclass=cellinside ReCFNr15dclass=cellinside Rclass=cellinside 172760class=cellinside 172874class=cellinside -class=cellinside sRNAclass=cellinside Rhizobium etli CFN 42 symbiotic plasmid p42d (NC_004041)
class=cellinside αr15_ReCFNr15dclass=cellinside geneclass=cellinside RHE_PD00156class=cellinside Rclass=cellinside 173058class=cellinside 174248class=cellinside NP_659881.2class=cellinside hypothetical proteinclass=cellinside Rhizobium etli CFN 42 symbiotic plasmid p42d (NC_004041)
class=cellinside αr15_Avr15Ateclass=cellinside geneclass=cellinside Avi_7235class=cellinside Dclass=cellinside 198046class=cellinside 198699class=cellinside YP_002539630.1class=cellinside ABC transporter membrane spanning proteinclass=cellinside Agrobacterium vitis S4 plasmid pAtS4e (NC_011981)
class=cellinside αr15_Avr15Ateclass=cellinside sRNAclass=cellinside Avr15Ateclass=cellinside Dclass=cellinside 198928class=cellinside 199039class=cellinside -class=cellinside sRNAclass=cellinside Agrobacterium vitis S4 plasmid pAtS4e (NC_011981)
class=cellinside αr15_Avr15Ateclass=cellinside geneclass=cellinside Avi_7237class=cellinside Dclass=cellinside 199739class=cellinside 200020class=cellinside YP_002539631.1class=cellinside transposaseclass=cellinside Agrobacterium vitis S4 plasmid pAtS4e (NC_011981)
class=cellinside αr15_AH13r15aclass=cellinside geneclass=cellinside AGROH133_14527class=cellinside Rclass=cellinside 210807class=cellinside 211133class=cellinside YP_004280311.1class=cellinside XRE family transcriptional regulatorclass=cellinside Agrobacterium sp. H13-3 plasmid pAspH13-3a (NC_015184)
class=cellinside αr15_AH13r15aclass=cellinside geneclass=cellinside AGROH133_14529class=cellinside Rclass=cellinside 211195class=cellinside 211713class=cellinside -class=cellinside addiction module toxinclass=cellinside Agrobacterium sp. H13-3 plasmid pAspH13-3a (NC_015184)
class=cellinside αr15_AH13r15aclass=cellinside sRNAclass=cellinside AH13r15aclass=cellinside Rclass=cellinside 211698class=cellinside 211807class=cellinside -class=cellinside sRNAclass=cellinside Agrobacterium sp. H13-3 plasmid pAspH13-3a (NC_015184)
class=cellinside αr15_AH13r15aclass=cellinside geneclass=cellinside AGROH133_14530class=cellinside Rclass=cellinside 211828class=cellinside 212286class=cellinside YP_004280313.1class=cellinside hypothetical proteinclass=cellinside Agrobacterium sp. H13-3 plasmid pAspH13-3a (NC_015184)
class=cellinside αr15_Smedr15p03class=cellinside geneclass=cellinside Smed_6375class=cellinside Rclass=cellinside 39464class=cellinside 39784class=cellinside YP_001314894.1class=cellinside XRE family transcriptional regulatorclass=cellinside Sinorhizobium medicae WSM419 plasmid pSMED03 (NC_009622)
class=cellinside αr15_Smedr15p03class=cellinside sRNAclass=cellinside Smedr15p03class=cellinside Rclass=cellinside 40054class=cellinside 40165class=cellinside -class=cellinside sRNAclass=cellinside Sinorhizobium medicae WSM419 plasmid pSMED03 (NC_009622)
class=cellinside αr15_Smedr15p03class=cellinside geneclass=cellinside Smed_6376class=cellinside Dclass=cellinside 40123class=cellinside 40425class=cellinside -class=cellinside hypothetical proteinclass=cellinside Sinorhizobium medicae WSM419 plasmid pSMED03 (NC_009622)
class=cellinside αr15_Avr15Ticlass=cellinside geneclass=cellinside Avi_8074class=cellinside Rclass=cellinside 51395class=cellinside 51682class=cellinside YP_002540018.1class=cellinside XRE family transcriptional regulatorclass=cellinside Agrobacterium vitis S4 plasmid pTiS4 (NC_011982)
class=cellinside αr15_Avr15Ticlass=cellinside sRNAclass=cellinside Avr15Ticlass=cellinside Rclass=cellinside 52286class=cellinside 52397class=cellinside -class=cellinside sRNAclass=cellinside Agrobacterium vitis S4 plasmid pTiS4 (NC_011982)
class=cellinside αr15_Avr15Ticlass=cellinside geneclass=cellinside Avi_8076class=cellinside Dclass=cellinside 52672class=cellinside 53013class=cellinside YP_002540020.1class=cellinside helicase subunit of the DNA excision repair complexclass=cellinside Agrobacterium vitis S4 plasmid pTiS4 (NC_011982)
class=cellinside αr15_Rlt1325r15p02class=cellinside geneclass=cellinside Rleg_6607class=cellinside Dclass=cellinside 35260class=cellinside 35928class=cellinside YP_002984610.1class=cellinside hypothetical proteinclass=cellinside Rhizobium leguminosarum bv. trifolii WSM1325 plasmid pRt132502 (NC_012858)
class=cellinside αr15_Rlt1325r15p02class=cellinside sRNAclass=cellinside Rlt1325r15p02class=cellinside Dclass=cellinside 36176class=cellinside 36289class=cellinside -class=cellinside sRNAclass=cellinside Rhizobium leguminosarum bv. trifolii WSM1325 plasmid pRt132502 (NC_012858)
class=cellinside αr15_Rlt1325r15p02class=cellinside geneclass=cellinside Rleg_6608class=cellinside Dclass=cellinside 36740class=cellinside 37528class=cellinside YP_002984611.1class=cellinside Exonuclease RNase T and DNA polymerase IIclass=cellinside Rhizobium leguminosarum bv. trifolii WSM1325 plasmid pRt132502 (NC_012858)
class=cellinside αr15_Sfr15bclass=cellinside geneclass=cellinside NGR_b01430class=cellinside Dclass=cellinside 133718class=cellinside 133900class=cellinside YP_002822362.1class=cellinside hypothetical proteinclass=cellinside Sinorhizobium fredii NGR234 plasmid pNGR234b (NC_012586)
class=cellinside αr15_Sfr15bclass=cellinside sRNAclass=cellinside Sfr15bclass=cellinside Rclass=cellinside 134078class=cellinside 134190class=cellinside -class=cellinside sRNAclass=cellinside Sinorhizobium fredii NGR234 plasmid pNGR234b (NC_012586)
class=cellinside αr15_Sfr15bclass=cellinside geneclass=cellinside NGR_b01450class=cellinside Rclass=cellinside 134349class=cellinside 136811class=cellinside YP_002822364.1class=cellinside diguanylate cyclase phosphodiesterase with pas pac sensorclass=cellinside Sinorhizobium fredii NGR234 plasmid pNGR234b (NC_012586)
class=cellinside αr15_Rlvr15p11class=cellinside geneclass=cellinside pRL110525class=cellinside Rclass=cellinside 566752class=cellinside 566955class=cellinside YP_771559.1class=cellinside hypothetical proteinclass=cellinside Rhizobium leguminosarum bv. viciae 3841 plasmid pRL11 (NC_008384)
class=cellinside αr15_Rlvr15p11class=cellinside sRNAclass=cellinside Rlvr15p11class=cellinside Rclass=cellinside 567053class=cellinside 567166class=cellinside -class=cellinside sRNAclass=cellinside Rhizobium leguminosarum bv. viciae 3841 plasmid pRL11 (NC_008384)
class=cellinside αr15_Rlvr15p11class=cellinside geneclass=cellinside pRL110526class=cellinside Rclass=cellinside 567397class=cellinside 568065class=cellinside YP_771560.1class=cellinside hypothetical proteinclass=cellinside Rhizobium leguminosarum bv. viciae 3841 plasmid pRL11 (NC_008384)
class=cellinside αr15_Oar15p02class=cellinside geneclass=cellinside Oant_4749class=cellinside Dclass=cellinside 21546class=cellinside 21971class=cellinside YP_001373166.1class=cellinside PilT domain-containing proteinclass=cellinside Brucella anthropi ATCC 49188 plasmid pOANT02 (NC_009670)
class=cellinside αr15_Oar15p02class=cellinside sRNAclass=cellinside Oar15p02class=cellinside Dclass=cellinside 22208class=cellinside 22320class=cellinside -class=cellinside sRNAclass=cellinside Brucella anthropi ATCC 49188 plasmid pOANT02 (NC_009670)
class=cellinside αr15_Oar15p02class=cellinside geneclass=cellinside Oant_4750class=cellinside Dclass=cellinside 22661class=cellinside 24454class=cellinside YP_001373167.1class=cellinside plasmid partitioning proteinclass=cellinside Brucella anthropi ATCC 49188 plasmid pOANT02 (NC_009670)
class=cellinside αr15_Mlr15aclass=cellinside geneclass=cellinside msl9071class=cellinside Rclass=cellinside 64650class=cellinside 64817class=cellinside NP_085644.1class=cellinside hypothetical proteinclass=cellinside Mesorhizobium loti MAFF303099 plasmid pMLa (NC_002679)
class=cellinside αr15_Mlr15aclass=cellinside sRNAclass=cellinside Mlr15aclass=cellinside Rclass=cellinside 65044class=cellinside 65154class=cellinside -class=cellinside sRNAclass=cellinside Mesorhizobium loti MAFF303099 plasmid pMLa (NC_002679)
class=cellinside αr15_Mlr15aclass=cellinside geneclass=cellinside msl9074class=cellinside Rclass=cellinside 65712class=cellinside 66008class=cellinside NP_085645.1class=cellinside hypothetical proteinclass=cellinside Mesorhizobium loti MAFF303099 plasmid pMLa (NC_002679)
class=cellinside αr15_Smr15Aclass=cellinside geneclass=cellinside SMa0995class=cellinside Rclass=cellinside 551249class=cellinside 552481class=cellinside NP_435782.1class=cellinside transposaseclass=cellinside Sinorhizobium meliloti 1021 plasmid pSymA (NC_003037)
class=cellinside αr15_Smr15Aclass=cellinside sRNAclass=cellinside Smr15Aclass=cellinside Dclass=cellinside 552873class=cellinside 552984class=cellinside -class=cellinside sRNAclass=cellinside Sinorhizobium meliloti 1021 plasmid pSymA (NC_003037)
class=cellinside αr15_Smr15Aclass=cellinside geneclass=cellinside SMa0997class=cellinside Dclass=cellinside 553196class=cellinside 553492class=cellinside NP_435783.1class=cellinside transposaseclass=cellinside Sinorhizobium meliloti 1021 plasmid pSymA (NC_003037)
class=cellinside αr15_Arr15CIIclass=cellinside geneclass=cellinside Arad_8155class=cellinside Dclass=cellinside 1010459class=cellinside 1011472class=cellinside YP_002541089.1class=cellinside hypothetical proteinclass=cellinside Agrobacterium radiobacter K84 chromosome 2 (NC_011983)
class=cellinside αr15_Arr15CIIclass=cellinside sRNAclass=cellinside Arr15CIIclass=cellinside Rclass=cellinside 1011511class=cellinside 1011624class=cellinside -class=cellinside sRNAclass=cellinside Agrobacterium radiobacter K84 chromosome 2 (NC_011983)
class=cellinside αr15_Arr15CIIclass=cellinside geneclass=cellinside Arad_8157class=cellinside Dclass=cellinside 1012367class=cellinside 1013791class=cellinside YP_002541091.1class=cellinside monooxygenase proteinclass=cellinside Agrobacterium radiobacter K84 chromosome 2 (NC_011983)
class=cellinside αr15_Oar15CIclass=cellinside geneclass=cellinside Oant_1670class=cellinside Rclass=cellinside 1750252class=cellinside 1751097class=cellinside YP_001370215.1class=cellinside metallophosphoesteraseclass=cellinside Brucella anthropi ATCC 49188 chromosome 1 (NC_009667)
class=cellinside αr15_Oar15CIclass=cellinside sRNAclass=cellinside Oar15CIclass=cellinside Dclass=cellinside 1751482class=cellinside 1751598class=cellinside -class=cellinside sRNAclass=cellinside Brucella anthropi ATCC 49188 chromosome 1 (NC_009667)
class=cellinside αr15_Oar15CIclass=cellinside geneclass=cellinside Oant_1671class=cellinside Dclass=cellinside 1752063class=cellinside 1753466class=cellinside YP_001370216.1class=cellinside RNA-directed DNA polymeraseclass=cellinside Brucella anthropi ATCC 49188 chromosome 1 (NC_009667)
class=cellinside αr15_ReCIATr15pCclass=cellinside geneclass=cellinside RHECIAT_PC0000855class=cellinside Rclass=cellinside 938497class=cellinside 939639class=cellinside YP_001985475.1class=cellinside acyltransferase 3class=cellinside Rhizobium etli CIAT 652 plasmid pC (NC_010997)
class=cellinside αr15_ReCIATr15pCclass=cellinside sRNAclass=cellinside ReCIATr15pCclass=cellinside Dclass=cellinside 941345class=cellinside 941452class=cellinside -class=cellinside sRNAclass=cellinside Rhizobium etli CIAT 652 plasmid pC (NC_010997)
class=cellinside αr15_ReCIATr15pCclass=cellinside geneclass=cellinside RHECIAT_PC0000856class=cellinside Rclass=cellinside 941811class=cellinside 945572class=cellinside YP_001985476.1class=cellinside hemolysin-type calcium-binding proteinclass=cellinside Rhizobium etli CIAT 652 plasmid pC (NC_010997)
class=cellinside αr15_Oar15CIIclass=cellinside geneclass=cellinside Oant_3861class=cellinside Rclass=cellinside 1269354class=cellinside 1269818class=cellinside YP_001372395.1class=cellinside hypothetical proteinclass=cellinside Brucella anthropi ATCC 49188 chromosome 2 (NC_009668)
class=cellinside αr15_Oar15CIIclass=cellinside sRNAclass=cellinside Oar15CIIclass=cellinside Dclass=cellinside 1270083class=cellinside 1270191class=cellinside -class=cellinside sRNAclass=cellinside Brucella anthropi ATCC 49188 chromosome 2 (NC_009668)
class=cellinside αr15_Oar15CIIclass=cellinside geneclass=cellinside Oant_3862class=cellinside Rclass=cellinside 1270409class=cellinside 1273222class=cellinside YP_001372396.1class=cellinside glycine dehydrogenaseclass=cellinside Brucella anthropi ATCC 49188 chromosome 2 (NC_009668)
class=cellinside αr15_Bm23445r15CIIclass=cellinside geneclass=cellinside BSUIS_B0713class=cellinside Rclass=cellinside 695738class=cellinside 695851class=cellinside YP_001622510.1class=cellinside hypothetical proteinclass=cellinside Brucella suis ATCC 23445 chromosome II (NC_010167)
class=cellinside αr15_Bm23445r15CIIclass=cellinside sRNAclass=cellinside Bm23445r15CIIclass=cellinside Dclass=cellinside 696081class=cellinside 696188class=cellinside -class=cellinside sRNAclass=cellinside Brucella suis ATCC 23445 chromosome II (NC_010167)
class=cellinside αr15_Bm23445r15CIIclass=cellinside geneclass=cellinside BSUIS_B0714class=cellinside Dclass=cellinside 696129class=cellinside 696196class=cellinside -class=cellinside unknownclass=cellinside Brucella suis ATCC 23445 chromosome II (NC_010167)
class=cellinside αr15_Bm23445r15CIIclass=cellinside geneclass=cellinside BSUIS_B0715class=cellinside Rclass=cellinside 696787class=cellinside 699585class=cellinside YP_001622511.1class=cellinside glycine dehydrogenaseclass=cellinside Brucella suis ATCC 23445 chromosome II (NC_010167)
class=cellinside αr15_Bm16Mr15CIIclass=cellinside geneclass=cellinside BMEII0561class=cellinside Dclass=cellinside 586104class=cellinside 588902class=cellinside NP_541539.1class=cellinside glycine dehydrogenaseclass=cellinside Brucella melitensis bv. 1 str. 16M chromosome II (NC_003318)
class=cellinside αr15_Bm16Mr15CIIclass=cellinside sRNAclass=cellinside Bm16Mr15CIIclass=cellinside Rclass=cellinside 589501class=cellinside 589608class=cellinside -class=cellinside sRNAclass=cellinside Brucella melitensis bv. 1 str. 16M chromosome II (NC_003318)
class=cellinside αr15_Bm16Mr15CIIclass=cellinside geneclass=cellinside BMEII0562class=cellinside Dclass=cellinside 589690class=cellinside 589950class=cellinside NP_541540.1class=cellinside hypothetical proteinclass=cellinside Brucella melitensis bv. 1 str. 16M chromosome II (NC_003318)
class=cellinside αr15_BaS19r15CIIclass=cellinside geneclass=cellinside BAbS19_II04850class=cellinside Dclass=cellinside 504658class=cellinside 507456class=cellinside YP_001932428.1class=cellinside glycine dehydrogenaseclass=cellinside Brucella abortus S19 chromosome 2 (NC_010740)
class=cellinside αr15_BaS19r15CIIclass=cellinside sRNAclass=cellinside BaS19r15CIIclass=cellinside Rclass=cellinside 508055class=cellinside 508162class=cellinside -class=cellinside sRNAclass=cellinside Brucella abortus S19 chromosome 2 (NC_010740)
class=cellinside αr15_BaS19r15CIIclass=cellinside geneclass=cellinside BAbS19_II04860class=cellinside Dclass=cellinside 508392class=cellinside 508505class=cellinside YP_001932429.1class=cellinside hypothetical proteinclass=cellinside Brucella abortus S19 chromosome 2 (NC_010740)
class=cellinside αr15_Bm23457r15CIIclass=cellinside geneclass=cellinside BMEA_B0698class=cellinside Dclass=cellinside 686472class=cellinside 686966class=cellinside YP_002734467.1class=cellinside proline dehydrogenase transcriptional activatorclass=cellinside Brucella melitensis ATCC 23457 chromosome II (NC_012442)
class=cellinside αr15_Bm23457r15CIIclass=cellinside sRNAclass=cellinside Bm23457r15CIIclass=cellinside Dclass=cellinside 687290class=cellinside 687397class=cellinside -class=cellinside sRNAclass=cellinside Brucella melitensis ATCC 23457 chromosome II (NC_012442)
class=cellinside αr15_Bm23457r15CIIclass=cellinside geneclass=cellinside BMEA_B0701class=cellinside Rclass=cellinside 687996class=cellinside 690794class=cellinside YP_002734468.1class=cellinside glycine dehydrogenaseclass=cellinside Brucella melitensis ATCC 23457 chromosome II (NC_012442)
class=cellinside αr15_Bmir15CIIclass=cellinside geneclass=cellinside BMI_II717class=cellinside Rclass=cellinside 708784class=cellinside 709020class=cellinside YP_003105497.1class=cellinside hypothetical proteinclass=cellinside Brucella microti CCM 4915 chromosome 2 (NC_013118)
class=cellinside αr15_Bmir15CIIclass=cellinside sRNAclass=cellinside Bmir15CIIclass=cellinside Dclass=cellinside 709102class=cellinside 709209class=cellinside -class=cellinside sRNAclass=cellinside Brucella microti CCM 4915 chromosome 2 (NC_013118)
class=cellinside αr15_Bmir15CIIclass=cellinside geneclass=cellinside BMI_II718class=cellinside Rclass=cellinside 709832class=cellinside 712630class=cellinside YP_003105498.1class=cellinside glycine dehydrogenaseclass=cellinside Brucella microti CCM 4915 chromosome 2 (NC_013118)
class=cellinside αr15_Bs1330r15CIIclass=cellinside geneclass=cellinside BRA0724class=cellinside Rclass=cellinside 707842class=cellinside 707955class=cellinside NP_699901.1class=cellinside hypothetical proteinclass=cellinside Brucella suis 1330 chromosome II (NC_004311)
class=cellinside αr15_Bs1330r15CIIclass=cellinside sRNAclass=cellinside Bs1330r15CIIclass=cellinside Dclass=cellinside 708185class=cellinside 708292class=cellinside -class=cellinside sRNAclass=cellinside Brucella suis 1330 chromosome II (NC_004311)
class=cellinside αr15_Bs1330r15CIIclass=cellinside geneclass=cellinside BRA0725class=cellinside Rclass=cellinside 708891class=cellinside 711689class=cellinside NP_699902.1class=cellinside glycine dehydrogenaseclass=cellinside Brucella suis 1330 chromosome II (NC_004311)
class=cellinside αr15_Ba19941r15CIIclass=cellinside geneclass=cellinside BruAb2_0506class=cellinside Dclass=cellinside 505454class=cellinside 508252class=cellinside YP_223286.1class=cellinside glycine dehydrogenaseclass=cellinside Brucella abortus bv. 1 str. 9-941 chromosome II (NC_006933)
class=cellinside αr15_Ba19941r15CIIclass=cellinside sRNAclass=cellinside Ba19941r15CIIclass=cellinside Rclass=cellinside 508851class=cellinside 508958class=cellinside -class=cellinside sRNAclass=cellinside Brucella abortus bv. 1 str. 9-941 chromosome II (NC_006933)
class=cellinside αr15_Ba19941r15CIIclass=cellinside geneclass=cellinside BruAb2_0507class=cellinside Dclass=cellinside 509188class=cellinside 509301class=cellinside YP_223287.1class=cellinside hypothetical proteinclass=cellinside Brucella abortus bv. 1 str. 9-941 chromosome II (NC_006933)
class=cellinside αr15_Bmαr15CIIclass=cellinside geneclass=cellinside BAB2_0515class=cellinside Dclass=cellinside 505442class=cellinside 508240class=cellinside YP_418705.1class=cellinside glycine dehydrogenaseclass=cellinside Brucella melitensis biovar Abortus 2308 chromosome II (NC_007624)
class=cellinside αr15_Bmαr15CIIclass=cellinside sRNAclass=cellinside Bmαr15CIIclass=cellinside Rclass=cellinside 508839class=cellinside 508946class=cellinside -class=cellinside sRNAclass=cellinside Brucella melitensis biovar Abortus 2308 chromosome II (NC_007624)
class=cellinside αr15_Bmαr15CIIclass=cellinside geneclass=cellinside BAB2_0516class=cellinside Dclass=cellinside 509028class=cellinside 509264class=cellinside YP_418706.1class=cellinside hypothetical proteinclass=cellinside Brucella melitensis biovar Abortus 2308 chromosome II (NC_007624)
class=cellinside αr15_Bcr15CIIclass=cellinside geneclass=cellinside BCAN_B0729class=cellinside Dclass=cellinside 706646class=cellinside 707140class=cellinside YP_001594668.1class=cellinside proline dehydrogenase transcriptional activatorclass=cellinside Brucella canis ATCC 23365 chromosome II (NC_010104)
class=cellinside αr15_Bcr15CIIclass=cellinside sRNAclass=cellinside Bcr15CIIclass=cellinside Dclass=cellinside 707465class=cellinside 707572class=cellinside -class=cellinside sRNAclass=cellinside Brucella canis ATCC 23365 chromosome II (NC_010104)
class=cellinside αr15_Bcr15CIIclass=cellinside geneclass=cellinside BCAN_B0730class=cellinside Rclass=cellinside 708171class=cellinside 710969class=cellinside YP_001594669.1class=cellinside glycine dehydrogenaseclass=cellinside Brucella canis ATCC 23365 chromosome II (NC_010104)
class=cellinside αr15_Bor15CI2class=cellinside geneclass=cellinside BOV_1448class=cellinside Dclass=cellinside 1459218class=cellinside 1460420class=cellinside YP_001259376.1class=cellinside aspartate aminotransferaseclass=cellinside Brucella ovis ATCC 25840 chromosome I (NC_009505)
class=cellinside αr15_Bor15CI2class=cellinside sRNAclass=cellinside Bor15CI2class=cellinside Rclass=cellinside 1460506class=cellinside 1460624class=cellinside -class=cellinside sRNAclass=cellinside Brucella ovis ATCC 25840 chromosome I (NC_009505)
class=cellinside αr15_Bor15CI2class=cellinside geneclass=cellinside BOV_1449class=cellinside Rclass=cellinside 1460890class=cellinside 1461795class=cellinside YP_001259377.1class=cellinside LysR family transcriptional regulatorclass=cellinside Brucella ovis ATCC 25840 chromosome I (NC_009505)
class=cellinside αr15_Bcr15CI2class=cellinside geneclass=cellinside BCAN_A1532class=cellinside Dclass=cellinside 1450681class=cellinside 1451883class=cellinside YP_001593329.1class=cellinside aspartate aminotransferaseclass=cellinside Brucella canis ATCC 23365 chromosome I (NC_010103)
class=cellinside αr15_Bcr15CI2class=cellinside sRNAclass=cellinside Bcr15CI2class=cellinside Rclass=cellinside 1451969class=cellinside 1452087class=cellinside -class=cellinside sRNAclass=cellinside Brucella canis ATCC 23365 chromosome I (NC_010103)
class=cellinside αr15_Bcr15CI2class=cellinside geneclass=cellinside BCAN_A1535class=cellinside Rclass=cellinside 1452353class=cellinside 1453258class=cellinside YP_001593332.1class=cellinside transcription regulator proteinclass=cellinside Brucella canis ATCC 23365 chromosome I (NC_010103)
class=cellinside αr15_Bmir15CI2class=cellinside geneclass=cellinside BMI_I1510class=cellinside Dclass=cellinside 1460010class=cellinside 1461212class=cellinside YP_003107423.1class=cellinside aspartate aminotransferaseclass=cellinside Brucella microti CCM 4915 chromosome 1 (NC_013119)
class=cellinside αr15_Bmir15CI2class=cellinside sRNAclass=cellinside Bmir15CI2class=cellinside Rclass=cellinside 1461298class=cellinside 1461416class=cellinside -class=cellinside sRNAclass=cellinside Brucella microti CCM 4915 chromosome 1 (NC_013119)
class=cellinside αr15_Bmir15CI2class=cellinside geneclass=cellinside BMI_I1512class=cellinside Rclass=cellinside 1461682class=cellinside 1462587class=cellinside YP_003107425.1class=cellinside LysR family transcriptional regulatorclass=cellinside Brucella microti CCM 4915 chromosome 1 (NC_013119)
class=cellinside αr15_Bs1330r15CI2class=cellinside geneclass=cellinside BR1495class=cellinside Dclass=cellinside 1451723class=cellinside 1452925class=cellinside NP_698491.1class=cellinside aspartate aminotransferaseclass=cellinside Brucella suis 1330 chromosome I (NC_004310)
class=cellinside αr15_Bs1330r15CI2class=cellinside sRNAclass=cellinside Bs1330r15CI2class=cellinside Rclass=cellinside 1453011class=cellinside 1453129class=cellinside -class=cellinside sRNAclass=cellinside Brucella suis 1330 chromosome I (NC_004310)
class=cellinside αr15_Bs1330r15CI2class=cellinside geneclass=cellinside BR1498class=cellinside Rclass=cellinside 1453395class=cellinside 1454300class=cellinside NP_698494.1class=cellinside LysR family transcriptional regulatorclass=cellinside Brucella suis 1330 chromosome I (NC_004310)
class=cellinside αr15_Bor15CIIclass=cellinside sRNAclass=cellinside Bor15CIIclass=cellinside Dclass=cellinside 709415class=cellinside 709524class=cellinside -class=cellinside sRNAclass=cellinside Brucella ovis ATCC 25840 chromosome II (NC_009504)
class=cellinside αr15_Bor15CIIclass=cellinside geneclass=cellinside BOV_A0677class=cellinside Rclass=cellinside 704750class=cellinside 708432class=cellinside -class=cellinside proline dehydrogenase transcriptional activatorclass=cellinside Brucella ovis ATCC 25840 chromosome II (NC_009504)
class=cellinside αr15_Bor15CIIclass=cellinside geneclass=cellinside BOV_A0679class=cellinside Rclass=cellinside 710122class=cellinside 712920class=cellinside YP_001257680.1class=cellinside glycine dehydrogenaseclass=cellinside Brucella ovis ATCC 25840 chromosome II (NC_009504)
class=cellinside αr15_Bm23445r15CI2class=cellinside geneclass=cellinside BSUIS_A1552class=cellinside Dclass=cellinside 1472504class=cellinside 1473706class=cellinside YP_001628154.1class=cellinside aspartate aminotransferaseclass=cellinside Brucella suis ATCC 23445 chromosome I (NC_010169)
class=cellinside αr15_Bm23445r15CI2class=cellinside sRNAclass=cellinside Bm23445r15CI2class=cellinside Rclass=cellinside 1473791class=cellinside 1473909class=cellinside -class=cellinside sRNAclass=cellinside Brucella suis ATCC 23445 chromosome I (NC_010169)
class=cellinside αr15_Bm23445r15CI2class=cellinside geneclass=cellinside BSUIS_A1554class=cellinside Rclass=cellinside 1474175class=cellinside 1475080class=cellinside YP_001628156.1class=cellinside hypothetical proteinclass=cellinside Brucella suis ATCC 23445 chromosome I (NC_010169)
class=cellinside αr15_BaS19r15CI2class=cellinside geneclass=cellinside BAbS19_I14120class=cellinside Dclass=cellinside 1468120class=cellinside 1469322class=cellinside YP_001935379.1class=cellinside aspartate aminotransferaseclass=cellinside Brucella abortus S19 chromosome 1 (NC_010742)
class=cellinside αr15_BaS19r15CI2class=cellinside sRNAclass=cellinside BaS19r15CI2class=cellinside Rclass=cellinside 1469407class=cellinside 1469525class=cellinside -class=cellinside sRNAclass=cellinside Brucella abortus S19 chromosome 1 (NC_010742)
class=cellinside αr15_BaS19r15CI2class=cellinside geneclass=cellinside BAbS19_I14130class=cellinside Dclass=cellinside 1469632class=cellinside 1469739class=cellinside YP_001935380.1class=cellinside hypothetical proteinclass=cellinside Brucella abortus S19 chromosome 1 (NC_010742)
class=cellinside αr15_Ba19941r15CI2class=cellinside geneclass=cellinside BruAb1_1488class=cellinside Dclass=cellinside 1469786class=cellinside 1470988class=cellinside YP_222177.1class=cellinside aspartate aminotransferaseclass=cellinside Brucella abortus bv. 1 str. 9-941 chromosome I (NC_006932)
class=cellinside αr15_Ba19941r15CI2class=cellinside sRNAclass=cellinside Ba19941r15CI2class=cellinside Rclass=cellinside 1471073class=cellinside 1471191class=cellinside -class=cellinside sRNAclass=cellinside Brucella abortus bv. 1 str. 9-941 chromosome I (NC_006932)
class=cellinside αr15_Ba19941r15CI2class=cellinside geneclass=cellinside BruAb1_1490class=cellinside Dclass=cellinside 1471190class=cellinside 1471405class=cellinside YP_222179.1class=cellinside hypothetical proteinclass=cellinside Brucella abortus bv. 1 str. 9-941 chromosome I (NC_006932)
class=cellinside αr15_Bmαr15CI2class=cellinside geneclass=cellinside BAB1_1514class=cellinside Dclass=cellinside 1466940class=cellinside 1468142class=cellinside YP_414880.1class=cellinside aspartate aminotransferaseclass=cellinside Brucella melitensis biovar Abortus 2308 chromosome I (NC_007618)
class=cellinside αr15_Bmαr15CI2class=cellinside sRNAclass=cellinside Bmαr15CI2class=cellinside Rclass=cellinside 1468227class=cellinside 1468345class=cellinside -class=cellinside sRNAclass=cellinside Brucella melitensis biovar Abortus 2308 chromosome I (NC_007618)
class=cellinside αr15_Bmαr15CI2class=cellinside geneclass=cellinside BAB1_1516class=cellinside Dclass=cellinside 1468344class=cellinside 1468559class=cellinside YP_414882.1class=cellinside hypothetical proteinclass=cellinside Brucella melitensis biovar Abortus 2308 chromosome I (NC_007618)
class=cellinside αr15_Bcr15CI1class=cellinside geneclass=cellinside BCAN_A1457class=cellinside Rclass=cellinside 1377955class=cellinside 1378815class=cellinside YP_001593259.1class=cellinside UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylaseclass=cellinside Brucella canis ATCC 23365 chromosome I (NC_010103)
class=cellinside αr15_Bcr15CI1class=cellinside sRNAclass=cellinside Bcr15CI1class=cellinside Rclass=cellinside 1379297class=cellinside 1379398class=cellinside -class=cellinside sRNAclass=cellinside Brucella canis ATCC 23365 chromosome I (NC_010103)
class=cellinside αr15_Bcr15CI1class=cellinside sRNAclass=cellinside BCAN_A1458class=cellinside Rclass=cellinside 1379355class=cellinside 1381055class=cellinside YP_001593260.1class=cellinside cell division protein Ftsclass=cellinside Brucella canis ATCC 23365 chromosome I (NC_010103)
class=cellinside αr15_Bcr15CI1class=cellinside geneclass=cellinside BCAN_A1459class=cellinside Rclass=cellinside 1381152class=cellinside 1382474class=cellinside YP_001593261.1class=cellinside cell division protein Ftsclass=cellinside Brucella canis ATCC 23365 chromosome I (NC_010103)
class=cellinside αr15_Bm23445r15CI1class=cellinside geneclass=cellinside BSUIS_A1476class=cellinside Dclass=cellinside 1400706class=cellinside 1400831class=cellinside YP_001628084.1class=cellinside hypothetical proteinclass=cellinside Brucella suis ATCC 23445 chromosome I (NC_010169)
class=cellinside αr15_Bm23445r15CI1class=cellinside sRNAclass=cellinside Bm23445r15CI1class=cellinside Rclass=cellinside 1401085class=cellinside 1401186class=cellinside -class=cellinside sRNAclass=cellinside Brucella suis ATCC 23445 chromosome I (NC_010169)
class=cellinside αr15_Bm23445r15CI1class=cellinside geneclass=cellinside BSUIS_A1477class=cellinside Rclass=cellinside 1401143class=cellinside 1402843class=cellinside YP_001628085.1class=cellinside cell division protein Ftsclass=cellinside Brucella suis ATCC 23445 chromosome I (NC_010169)
class=cellinside αr15_Bm23445r15CI1class=cellinside geneclass=cellinside BSUIS_A1478class=cellinside Rclass=cellinside 1402940class=cellinside 1404262class=cellinside YP_001628086.1class=cellinside cell division protein Ftsclass=cellinside Brucella suis ATCC 23445 chromosome I (NC_010169)
class=cellinside αr15_Bm16Mr15CIclass=cellinside geneclass=cellinside BMEI0585class=cellinside Dclass=cellinside 606025class=cellinside 607641class=cellinside NP_539502.1class=cellinside cell division protein Ftsclass=cellinside Brucella melitensis bv. 1 str. 16M chromosome I (NC_003317)
class=cellinside αr15_Bm16Mr15CIclass=cellinside sRNAclass=cellinside Bm16Mr15CIclass=cellinside Dclass=cellinside 607684class=cellinside 607785class=cellinside -class=cellinside sRNAclass=cellinside Brucella melitensis bv. 1 str. 16M chromosome I (NC_003317)
class=cellinside αr15_Bm16Mr15CIclass=cellinside geneclass=cellinside BMEI0586class=cellinside Dclass=cellinside 608267class=cellinside 609127class=cellinside NP_539503.1class=cellinside UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylaseclass=cellinside Brucella melitensis bv. 1 str. 16M chromosome I (NC_003317)
class=cellinside αr15_BaS19r15CI1class=cellinside geneclass=cellinside BAbS19_I13490class=cellinside Rclass=cellinside 1395452class=cellinside 1396312class=cellinside YP_001935318.1class=cellinside UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylaseclass=cellinside Brucella abortus S19 chromosome 1 (NC_010742)
class=cellinside αr15_BaS19r15CI1class=cellinside geneclass=cellinside BAbS19_I13500class=cellinside Rclass=cellinside 1396852class=cellinside 1398552class=cellinside YP_001935319.1class=cellinside cell division protein Ftsclass=cellinside Brucella abortus S19 chromosome 1 (NC_010742)
class=cellinside αr15_BaS19r15CI1class=cellinside sRNAclass=cellinside BaS19r15CI1class=cellinside Rclass=cellinside 1396794class=cellinside 1396895class=cellinside -class=cellinside sRNAclass=cellinside Brucella abortus S19 chromosome 1 (NC_010742)
class=cellinside αr15_BaS19r15CI1class=cellinside geneclass=cellinside BAbS19_I13510class=cellinside Rclass=cellinside 1398649class=cellinside 1399971class=cellinside YP_001935320.1class=cellinside heat shock protein Hsp7class=cellinside Brucella abortus S19 chromosome 1 (NC_010742)
class=cellinside αr15_Bm23457r15CIclass=cellinside geneclass=cellinside BMEA_A1472class=cellinside Rclass=cellinside 1399299class=cellinside 1400159class=cellinside YP_002733139.1class=cellinside UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylaseclass=cellinside Brucella melitensis ATCC 23457 chromosome I (NC_012441)
class=cellinside αr15_Bm23457r15CIclass=cellinside sRNAclass=cellinside Bm23457r15CIclass=cellinside Rclass=cellinside 1400641class=cellinside 1400742class=cellinside -class=cellinside sRNAclass=cellinside Brucella melitensis ATCC 23457 chromosome I (NC_012441)
class=cellinside αr15_Bm23457r15CIclass=cellinside geneclass=cellinside BMEA_A1473class=cellinside Rclass=cellinside 1400699class=cellinside 1402399class=cellinside YP_002733140.1class=cellinside cell division protein Ftsclass=cellinside Brucella melitensis ATCC 23457 chromosome I (NC_012441)
class=cellinside αr15_Bm23457r15CIclass=cellinside geneclass=cellinside BMEA_A1474class=cellinside Rclass=cellinside 1402496class=cellinside 1403818class=cellinside YP_002733141.1class=cellinside cell division protein Ftsclass=cellinside Brucella melitensis ATCC 23457 chromosome I (NC_012441)
class=cellinside αr15_Bmir15CI1class=cellinside geneclass=cellinside BMI_I1436class=cellinside Rclass=cellinside 1386434class=cellinside 1387294class=cellinside YP_003107351.1class=cellinside UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylaseclass=cellinside Brucella microti CCM 4915 chromosome 1 (NC_013119)
class=cellinside αr15_Bmir15CI1class=cellinside sRNAclass=cellinside Bmir15CI1class=cellinside Rclass=cellinside 1387776class=cellinside 1387877class=cellinside -class=cellinside sRNAclass=cellinside Brucella microti CCM 4915 chromosome 1 (NC_013119)
class=cellinside αr15_Bmir15CI1class=cellinside geneclass=cellinside BMI_I1437class=cellinside Rclass=cellinside 1387834class=cellinside 1389534class=cellinside YP_003107352.1class=cellinside cell division protein Ftsclass=cellinside Brucella microti CCM 4915 chromosome 1 (NC_013119)
class=cellinside αr15_Bmir15CI1class=cellinside geneclass=cellinside BMI_I1438class=cellinside Rclass=cellinside 1389631class=cellinside 1390953class=cellinside YP_003107353.1class=cellinside cell division protein Ftsclass=cellinside Brucella microti CCM 4915 chromosome 1 (NC_013119)
class=cellinside αr15_Bs1330r15CI1class=cellinside geneclass=cellinside BR1424class=cellinside Rclass=cellinside 1379039class=cellinside 1379899class=cellinside NP_698422.1class=cellinside UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylaseclass=cellinside Brucella suis 1330 chromosome I (NC_004310)
class=cellinside αr15_Bs1330r15CI1class=cellinside sRNAclass=cellinside Bs1330r15CI1class=cellinside Rclass=cellinside 1380381class=cellinside 1380482class=cellinside -class=cellinside sRNAclass=cellinside Brucella suis 1330 chromosome I (NC_004310)
class=cellinside αr15_Bs1330r15CI1class=cellinside geneclass=cellinside BR1425class=cellinside Rclass=cellinside 1380439class=cellinside 1382139class=cellinside NP_698423.1class=cellinside cell division protein Ftsclass=cellinside Brucella suis 1330 chromosome I (NC_004310)
class=cellinside αr15_Bs1330r15CI1class=cellinside geneclass=cellinside BR1426class=cellinside Rclass=cellinside 1382236class=cellinside 1383558class=cellinside NP_698424.1class=cellinside cell division protein Ftsclass=cellinside Brucella suis 1330 chromosome I (NC_004310)
class=cellinside αr15_Ba19941r15CI1class=cellinside geneclass=cellinside BruAb1_1419class=cellinside Rclass=cellinside 1397122class=cellinside 1397982class=cellinside YP_222110.1class=cellinside UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylaseclass=cellinside Brucella abortus bv. 1 str. 9-941 chromosome I (NC_006932)
class=cellinside αr15_Ba19941r15CI1class=cellinside sRNAclass=cellinside Ba19941r15CI1class=cellinside Rclass=cellinside 1398464class=cellinside 1398565class=cellinside -class=cellinside sRNAclass=cellinside Brucella abortus bv. 1 str. 9-941 chromosome I (NC_006932)
class=cellinside αr15_Ba19941r15CI1class=cellinside geneclass=cellinside BruAb1_1420class=cellinside Rclass=cellinside 1398522class=cellinside 1400222class=cellinside YP_222111.1class=cellinside cell division protein Ftsclass=cellinside Brucella abortus bv. 1 str. 9-941 chromosome I (NC_006932)
class=cellinside αr15_Ba19941r15CI1class=cellinside geneclass=cellinside BruAb1_1421class=cellinside Rclass=cellinside 1400319class=cellinside 1401641class=cellinside YP_222112.1class=cellinside cell division protein Ftsclass=cellinside Brucella abortus bv. 1 str. 9-941 chromosome I (NC_006932)
class=cellinside αr15_Bmαr15CI1class=cellinside geneclass=cellinside BAB1_1443class=cellinside Rclass=cellinside 1394272class=cellinside 1395132class=cellinside YP_414815.1class=cellinside UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylaseclass=cellinside Brucella melitensis biovar Abortus 2308 chromosome I (NC_007618)
class=cellinside αr15_Bmαr15CI1class=cellinside sRNAclass=cellinside Bmαr15CI1class=cellinside Rclass=cellinside 1395614class=cellinside 1395715class=cellinside -class=cellinside sRNAclass=cellinside Brucella melitensis biovar Abortus 2308 chromosome I (NC_007618)
class=cellinside αr15_Bmαr15CI1class=cellinside geneclass=cellinside BAB1_1444class=cellinside Rclass=cellinside 1395672class=cellinside 1397372class=cellinside YP_414816.1class=cellinside cell division protein Ftsclass=cellinside Brucella melitensis biovar Abortus 2308 chromosome I (NC_007618)
class=cellinside αr15_Bmαr15CI1class=cellinside geneclass=cellinside BAB1_1445class=cellinside Rclass=cellinside 1397469class=cellinside 1398791class=cellinside YP_414817.1class=cellinside heat shock protein Hsp7class=cellinside Brucella melitensis biovar Abortus 2308 chromosome I (NC_007618)
class=cellinside αr15_Jspr15Cclass=cellinside geneclass=cellinside mma_2445class=cellinside Rclass=cellinside 2769080class=cellinside 2769601class=cellinside YP_001354135.1class=cellinside phosphinothricin N-acetyltransferasclass=cellinside Janthinobacterium sp. Marseille (NC_009659)
class=cellinside αr15_Jspr15Cclass=cellinside sRNAclass=cellinside Jspr15Cclass=cellinside Rclass=cellinside 2769681class=cellinside 2769776class=cellinside -class=cellinside sRNAclass=cellinside Janthinobacterium sp. Marseille (NC_009659)
class=cellinside αr15_Jspr15Cclass=cellinside geneclass=cellinside mma_2446class=cellinside Rclass=cellinside 2769784class=cellinside 2770767class=cellinside YP_001354136.1class=cellinside tricarboxylate binding receptorclass=cellinside Janthinobacterium sp. Marseille (NC_009659)
class=cellinside αr15_Bor15CI1class=cellinside geneclass=cellinside BOV_1381class=cellinside Dclass=cellinside 1387334class=cellinside 1387726class=cellinside YP_001259317.1class=cellinside transposase Orfclass=cellinside Brucella ovis ATCC 25840 chromosome I (NC_009505)
class=cellinside αr15_Bor15CI1class=cellinside sRNAclass=cellinside Bor15CI1class=cellinside Rclass=cellinside 1387928class=cellinside 1388029class=cellinside -class=cellinside sRNAclass=cellinside Brucella ovis ATCC 25840 chromosome I (NC_009505)
class=cellinside αr15_Bor15CI1class=cellinside geneclass=cellinside BOV_1382class=cellinside Rclass=cellinside 1387986class=cellinside 1389686class=cellinside YP_001259318.1class=cellinside cell division protein Ftsclass=cellinside Brucella ovis ATCC 25840 chromosome I (NC_009505)
class=cellinside αr15_Bor15CI1class=cellinside geneclass=cellinside BOV_1383class=cellinside Rclass=cellinside 1389783class=cellinside 1391105class=cellinside YP_001259319.1class=cellinside cell division protein Ftsclass=cellinside Brucella ovis ATCC 25840 chromosome I (NC_009505)

Notes and References

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  2. 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 .
  3. 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 .
  4. 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 .
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  6. 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 .
  7. Wilms I, Voss B, Hess WR, Leichert LI, Narberhaus F . Small RNA-mediated control of the Agrobacterium tumefaciens GABA binding protein . Molecular Microbiology . 80 . 2 . 492–506 . April 2011 . 21320185 . 10.1111/j.1365-2958.2011.07589.x . free .
  8. Torres-Quesada O, Oruezabal RI, Peregrina A, Jofre E, Lloret J, Rivilla R, Toro N, Jiménez-Zurdo JI . The Sinorhizobium meliloti RNA chaperone Hfq influences central carbon metabolism and the symbiotic interaction with alfalfa . BMC Microbiol. 6. 2010.
  9. Torres-Quesada O, Millán V, Nisa-Martínez R, Bardou F, Crespi M, Toro N, Jiménez-Zurdo JI . Independent activity of the homologous small regulatory RNAs AbcR1 and AbcR2 in the legume symbiont Sinorhizobium meliloti . PLOS ONE . 8 . 7 . e68147 . 2013-07-15 . 23869210 . 3712013 . 10.1371/journal.pone.0068147 . 2013PLoSO...868147T . free .
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  12. 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 .
  13. 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.
  14. John Stamatoyannopoulos . Gupta S, Stamatoyannopoulos JA, Bailey TL, Noble WS . Quantifying similarity between motifs . Genome Biology . 8 . 2 . R24 . 2007 . 17324271 . 1852410 . 10.1186/gb-2007-8-2-r24 . free .
  15. 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 .
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