Αr14 RNA

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

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αr14  | Smr14C1  | gi|15963753|ref|NC_003047.1| | 206862  | 206980  | \-  | 63  | 119  | Sinorhizobium meliloti 1021
αr14  | Smr14C2  | gi|15963753|ref|NC_003047.1| | 1667491  | 1667613  | \-  | 65  | 123  | Sinorhizobium meliloti 1021
αr14  | Smr14C3  | gi|15963753|ref|NC_003047.1| | 1667769  | 1667891  | \-  | 62  | 123  | Sinorhizobium meliloti 1021
αr14  | Smr14A1  | gi|16262453|ref|NC_003037.1| | 1220690  | 1220808  | \+  | 62  | 119  | Sinorhizobium meliloti 1021 plasmid pSymA
αr14  | Smr14A2  | gi|16262453|ref|NC_003037.1| | 1328176  | 1328301  | \-  | 60  | 126  | Sinorhizobium meliloti 1021 plasmid pSymA
αr14  | Smr14B  | gi|16263748|ref|NC_003078.1| | 1605826  | 1605943  | \+  | 64  | 118  | Sinorhizobium meliloti 1021 plasmid pSymB
αr14  | Smedr14C1  | gi|150395228|ref|NC_009636.1| | 1258038  | 1258160  | \-  | 63  | 123  | Sinorhizobium medicae WSM419 chromosome
αr14  | Smedr14C2  | gi|150395228|ref|NC_009636.1| | 1258311  | 1258431  | \-  | 65  | 121  | Sinorhizobium medicae WSM419 chromosome
αr14  | Smedr14C3  | gi|150395228|ref|NC_009636.1| | 3590299  | 3590417  | \-  | 63  | 119  | Sinorhizobium medicae WSM419 chromosome
αr14  | Smedr14p01  | gi|150375726|ref|NC_009620.1| | 679043  | 679160  | \-  | 66  | 118  | Sinorhizobium medicae WSM419 plasmid pSMED01
αr14  | Smedr14p021  | gi|150377168|ref|NC_009621.1| | 316304  | 316428  | \+  | 64  | 125  | Sinorhizobium medicae WSM419 plasmid pSMED02
αr14  | Smedr14p022  | gi|150377168|ref|NC_009622.1| | 338866  | 338990  | \+  | 63  | 125  | Sinorhizobium medicae WSM419 plasmid pSMED02
αr14  | Sfr14C1  | gi|227820587|ref|NC_012587.1| | 1434171  | 1434293  | \-  | 64  | 123  | Sinorhizobium fredii NGR234 chromosome
αr14  | Sfr14C2  | gi|227820587|ref|NC_012587.1| | 1434463  | 1434586  | \-  | 60  | 124  | Sinorhizobium fredii NGR234 chromosome
αr14  | Sfr14C3  | gi|227820587|ref|NC_012587.1| | 3720579  | 3720700  | \+  | 66  | 122  | Sinorhizobium fredii NGR234 chromosome
αr14  | Sfr14b  | gi|227818258|ref|NC_012586.1| | 2205311  | 2205428  | \+  | 64  | 118  | Sinorhizobium fredii NGR234 plasmid pNGR234b
αr14  | Atr14C1  | gi|159184118|ref|NC_003062.2| | 109473  | 109601  | \+  | 59  | 129  | Agrobacterium tumefaciens str. C58 chromosome circular
αr14  | Atr14C2  | gi|159185562|ref|NC_003063.2| | 1230297  | 1230426  | \+  | 60  | 130  | Agrobacterium tumefaciens str. C58 chromosome linear
αr14  | Atr14C3  | gi|159185562|ref|NC_003063.2| | 1831483  | 1831614  | \+  | 57  | 132  | Agrobacterium tumefaciens str. C58 chromosome linear
αr14  | AH13r14C1  | gi|325291453|ref|NC_015183.1| | 109372  | 109501  | \+  | 58  | 130  | Agrobacterium sp. H13-3 chromosome
αr14  | ReCIATr14C1  | gi|190889639|ref|NC_010994.1| | 513993  | 514114  | \+  | 60  | 122  | Rhizobium etli CIAT 652
αr14  | ReCIATr14C2  | gi|190889639|ref|NC_010994.1| | 1173512  | 1173639  | \+  | 59  | 128  | Rhizobium etli CIAT 652
αr14  | ReCIATr14C3  | gi|190889639|ref|NC_010994.1| | 1912478  | 1912597  | \-  | 64  | 120  | Rhizobium etli CIAT 652
αr14  | ReCIATr14C4  | gi|190889639|ref|NC_010994.1| | 4444894  | 4445016  | \-  | 55  | 123  | Rhizobium etli CIAT 652
αr14  | ReCIATr14A  | gi|190895317|ref|NC_010998.1| | 345900  | 346021  | \-  | 63  | 122  | Rhizobium etli CIAT 652 plasmid pA
αr14  | ReCIATr14B  | gi|190893983|ref|NC_010996.1| | 112292  | 112425  | \+  | 61  | 134  | Rhizobium etli CIAT 652 plasmid pB
αr14  | Arr14CI1  | gi|222084201|ref|NC_011985.1| | 597903  | 598030  | \+  | 61  | 128  | Agrobacterium radiobacter K84 chromosome 1
αr14  | Arr14CI2  | gi|222084201|ref|NC_011985.1| | 1693278  | 1693409  | \-  | 60  | 132  | Agrobacterium radiobacter K84 chromosome 1
αr14  | Arr14CI3  | gi|222084201|ref|NC_011985.1| | 3945511  | 3945639  | \-  | 59  | 129  | Agrobacterium radiobacter K84 chromosome 1
αr14  | Arr14CII1  | gi|222080781|ref|NC_011983.1| | 957687  | 957817  | \+  | 58  | 131  | Agrobacterium radiobacter K84 chromosome 2
αr14  | Arr14CII2  | gi|222080781|ref|NC_011983.1| | 1921110  | 1921242  | \-  | 61  | 133  | Agrobacterium radiobacter K84 chromosome 2
αr14  | Arr14Atc  | gi|222101962|ref|NC_011987.1| | 138495  | 138625  | \-  | 60  | 131  | Agrobacterium radiobacter K84 plasmid pAtK84c
αr14  | Rlt2304r14C1  | gi|209547612|ref|NC_011369.1| | 98050  | 98171  | \+  | 60  | 122  | Rhizobium leguminosarum bv. trifolii WSM2304 chromosome
αr14  | Rlt2304r14C2  | gi|209547612|ref|NC_011369.1| | 1534501  | 1534621  | \-  | 63  | 121  | Rhizobium leguminosarum bv. trifolii WSM2304 chromosome
αr14  | Rlt2304r14C3  | gi|209547612|ref|NC_011369.1| | 4019326  | 4019446  | \-  | 57  | 121  | Rhizobium leguminosarum bv. trifolii WSM2304 chromosome
αr14  | Rlt2304r14p011  | gi|209546450|ref|NC_011368.1| | 306339  | 306454  | \-  | 70  | 116  | Rhizobium leguminosarum bv trifolii WSM2304 plasmid pRLG201
αr14  | Rlt2304r14p012  | gi|209546450|ref|NC_011368.1| | 607636  | 607759  | \+  | 62  | 124  | Rhizobium leguminosarum bv trifolii WSM2304 plasmid pRLG201
αr14  | Rlt2304r14p02  | gi|209545999|ref|NC_011366.1| | 50814  | 50936  | \+  | 63  | 123  | Rhizobium leguminosarum bv trifolii WSM2304 plasmid pRLG202
αr14  | Avr14CI1  | gi|222147015|ref|NC_011989.1| | 115126  | 115257  | \+  | 58  | 132  | Agrobacterium vitis S4 chromosome 1
αr14  | Avr14CI2  | gi|222147015|ref|NC_011989.1| | 2043913  | 2044044  | \-  | 64  | 132  | Agrobacterium vitis S4 chromosome 1
αr14  | Avr14CI3  | gi|222147015|ref|NC_011989.1| | 2793803  | 2793939  | \+  | 63  | 137  | Agrobacterium vitis S4 chromosome 1
αr14  | Avr14CII1  | gi|222106127|ref|NC_011988.1| | 598426  | 598556  | \+  | 62  | 131  | Agrobacterium vitis S4 chromosome 2
αr14  | Avr14CII2  | gi|222106127|ref|NC_011988.1| | 901035  | 901159  | \-  | 63  | 125  | Agrobacterium vitis S4 chromosome 2
αr14  | Avr14Atc  | gi|222083145|ref|NC_011984.1| | 7318  | 7444  | \+  | 61  | 127  | Agrobacterium vitis S4 plasmid pAtS4c
αr14  | Rlvr14C1  | gi|116249766|ref|NC_008380.1| | 512658  | 512779  | \+  | 59  | 122  | Rhizobium leguminosarum bv. viciae 3841
αr14  | Rlvr14C2  | gi|116249766|ref|NC_008380.1| | 2174956  | 2175074  | \-  | 65  | 119  | Rhizobium leguminosarum bv. viciae 3841
αr14  | Rlvr14C3  | gi|116249766|ref|NC_008380.1| | 4988030  | 4988158  | \-  | 58  | 129  | Rhizobium leguminosarum bv. viciae 3841
αr14  | Rlvr14p11  | gi|116255200|ref|NC_008384.1| | 574471  | 574593  | \-  | 59  | 123  | Rhizobium leguminosarum bv. viciae 384 plasmid pRL11
αr14  | Rlvr14p12  | gi|116248676|ref|NC_008378.1| | 407202  | 407316  | \+  | 65  | 115  | Rhizobium leguminosarum bv. viciae 384 plasmid pRL12
αr14  | Rlt1325r14C1  | gi|241202755|ref|NC_012850.1| | 107063  | 107184  | \+  | 58  | 122  | Rhizobium leguminosarum bv. trifolii WSM1325
αr14  | Rlt1325r14C2  | gi|241202755|ref|NC_012850.1| | 1697038  | 1697156  | \-  | 63  | 119  | Rhizobium leguminosarum bv. trifolii WSM1325
αr14  | Rlt1325r14C3  | gi|241202755|ref|NC_012850.1| | 4296632  | 4296749  | \-  | 58  | 118  | Rhizobium leguminosarum bv. trifolii WSM1325
αr14  | Rlt1325r14p012  | gi|241113003|ref|NC_012848.1| | 265945  | 266069  | \+  | 62  | 125  | Rhizobium leguminosarum bv. trifolii WSM1325 plasmid pR132501
αr14  | Rlt1325r14p011  | gi|241113003|ref|NC_012848.1| | 112604  | 112728  | \+  | 66  | 125  | Rhizobium leguminosarum bv. trifolii WSM1325 plasmid pR132501
αr14  | Rlt1325r14p02  | gi|241666492|ref|NC_012858.1| | 28646  | 28767  | \+  | 60  | 122  | Rhizobium leguminosarum bv. trifolii WSM1325 plasmid pR132502
αr14  | Rlt1325r14p04  | gi|241258599|ref|NC_012852.1| | 119314  | 119443  | \+  | 59  | 130  | Rhizobium leguminosarum bv. trifolii WSM1325 plasmid pR132504
αr14  | Rlt1325r14p05  | gi|241554070|ref|NC_012854.1| | 2286  | 2409  | \-  | 65  | 124  | Rhizobium leguminosarum bv. trifolii WSM1325 plasmid pR132505
αr14  | ReCFNr14C1  | gi|86355669|ref|NC_007761.1| | 462566  | 462687  | \-  | 58  | 122  | Rhizobium etli CFN 42
αr14  | ReCFNr14C2  | gi|86355669|ref|NC_007761.1| | 1926239  | 1926358  | \+  | 65  | 120  | Rhizobium etli CFN 42
αr14  | ReCFNr14C3  | gi|86355669|ref|NC_007761.1| | 4314384  | 4314505  | \+  | 58  | 122  | Rhizobium etli CFN 42
αr14  | ReCFNr14e  | gi|86360278|ref|NC_007765.1| | 443001  | 443129  | \+  | 64  | 129  | Rhizobium etli CFN 42 plasmid p42e
αr14  | ReCFNr14f  | gi|86360734|ref|NC_007766.1| | 22818  | 22935  | \-  | 64  | 118  | Rhizobium etli CFN 42 plasmid p42f
αr14  | ReCFNr14d  | gi|89255298|ref|NC_004041.2| | 77668  | 77794  | \-  | 61  | 127  | Rhizobium etli CFN 42 symbiotic plasmid p42d
αr14  | Mlr14C1  | gi|57165207|ref|NC_002678.2| | 890582  | 890702  | \+  | 68  | 121  | Mesorhizobium loti MAFF303099 chromosome
αr14  | Mlr14C2  | gi|57165207|ref|NC_002678.2| | 890760  | 890880  | \+  | 64  | 121  | Mesorhizobium loti MAFF303099 chromosome
αr14  | Mlr14C3  | gi|57165207|ref|NC_002678.2| | 890941  | 891061  | \+  | 63  | 121  | Mesorhizobium loti MAFF303099 chromosome
αr14  | Mlr14C4  | gi|57165207|ref|NC_002678.2| | 5350767  | 5350882  | \+  | 65  | 116  | Mesorhizobium loti MAFF303099 chromosome
αr14  | Mlr14C5  | gi|57165207|ref|NC_002678.2| | 6092423  | 6092540  | \-  | 64  | 118  | Mesorhizobium loti MAFF303099 chromosome
αr14  | Mcr14C1  | gi|319779749|ref|NC_014923.1| | 3674843  | 3674963  | \-  | 64  | 121  | Mesorhizobium ciceri biovar biserrulae WSM1271 chromosome
αr14  | Mcr14C2  | gi|319779749|ref|NC_014923.1| | 3675022  | 3675142  | \-  | 67  | 121  | Mesorhizobium ciceri biovar biserrulae WSM1271 chromosome
αr14  | Mcr14C3  | gi|319779749|ref|NC_014923.1| | 3675197  | 3675318  | \-  | 65  | 122  | Mesorhizobium ciceri biovar biserrulae WSM1271 chromosome
αr14  | Mcr14C4  | gi|319779749|ref|NC_014923.1| | 2545673  | 2545788  | \+  | 64  | 116  | Mesorhizobium ciceri biovar biserrulae WSM1271 chromosome
αr14  | Mcr14C5  | gi|319779749|ref|NC_014923.1| | 5265891  | 5266009  | \+  | 63  | 119  | Mesorhizobium ciceri biovar biserrulae WSM1271 chromosome
αr14  | Mcr14p01  | gi|319777789|ref|NC_014918.1| | 241412  | 241531  | \-  | 63  | 120  | Mesorhizobium ciceri biovar biserrulae WSM1271 plasmid pMESCI01
αr14  | Bcr14CI1  | gi|161617991|ref|NC_010103.1| | 338021  | 338128  | \+  | 56  | 108  | Brucella canis ATCC 23365 chromosome I
αr14  | Bcr14CI2  | gi|161617991|ref|NC_010103.1| | 867217  | 867335  | \-  | 60  | 119  | Brucella canis ATCC 23365 chromosome I
αr14  | Bs23445r14CI1  | gi|163842277|ref|NC_010169.1| | 355557  | 355664  | \+  | 57  | 108  | Brucella suis ATCC 23445 chromosome I
αr14  | Bs23445r14CI2  | gi|163842277|ref|NC_010169.1| | 888713  | 888831  | \-  | 60  | 119  | Brucella suis ATCC 23445 chromosome I
αr14  | Bm16Mr14CI1  | gi|17986284|ref|NC_003317.1| | 1116661  | 1116787  | \+  | 59  | 127  | Brucella melitensis bv. 1 str. 16M chromosome
αr14  | Bm16Mr14CI2  | gi|17986284|ref|NC_003317.1| | 1644167  | 1644273  | \-  | 56  | 107  | Brucella melitensis bv. 1 str. 16M chromosome
αr14  | BaS19r14CI1  | gi|189023268|ref|NC_010742.1| | 358310  | 358417  | \+  | 56  | 108  | Brucella abortus S19 chromosome 1
αr14  | BaS19r14CI2  | gi|189023268|ref|NC_010742.1| | 888877  | 888995  | \-  | 59  | 119  | Brucella abortus S19 chromosome 1
αr14  | Bm23457r14CI2  | gi|225851546|ref|NC_012441.1| | 890343  | 890461  | \-  | 59  | 119  | Brucella melitensis ATCC 23457 chromosome I
αr14  | Bm23457r14CI1  | gi|225851546|ref|NC_012441.1| | 358976  | 359082  | \+  | 56  | 107  | Brucella melitensis ATCC 23457 chromosome I
αr14  | Bs1330r14CI1  | gi|56968325|ref|NC_004310.3| | 338032  | 338139  | \+  | 56  | 108  | Brucella suis 1330 chromosome I
αr14  | Bs1330r14CI2  | gi|56968325|ref|NC_004310.3| | 868847  | 868965  | \-  | 60  | 119  | Brucella suis 1330 chromosome I
αr14  | Ba19941r14CI1  | gi|62288991|ref|NC_006932.1| | 359925  | 360032  | \+  | 56  | 108  | Brucella abortus bv. 1 str. 9-941 chromosome I
αr14  | Ba19941r14CI2  | gi|62288991|ref|NC_006932.1| | 890576  | 890694  | \-  | 59  | 119  | Brucella abortus bv. 1 str. 9-941 chromosome I
αr14  | Bmar14CI2  | gi|82698932|ref|NC_007618.1| | 886854  | 886972  | \-  | 59  | 119  | Brucella melitensis biovar Abortus 2308 chromosome I
αr14  | Bmar14CI1  | gi|82698932|ref|NC_007618.1| | 356293  | 356400  | \+  | 56  | 108  | Brucella melitensis biovar Abortus 2308 chromosome I
αr14  | Bor14CI1  | gi|148558820|ref|NC_009505.1| | 359682  | 359789  | \+  | 56  | 108  | Brucella ovis ATCC 25840 chromosome I
αr14  | Bor14CI2  | gi|148558820|ref|NC_009505.1| | 895749  | 895867  | \-  | 60  | 119  | Brucella ovis ATCC 25840 chromosome I
αr14  | Bmir14CI1  | gi|256368465|ref|NC_013119.1| | 339699  | 339806  | \+  | 57  | 108  | Brucella microti CCM 4915 chromosome 1
αr14  | Bmir14CI2  | gi|256368465|ref|NC_013119.1| | 873049  | 873167  | \-  | 60  | 119  | Brucella microti CCM 4915 chromosome 1
αr14  | Oar14CII1  | gi|153010078|ref|NC_009668.1| | 274684  | 274807  | \+  | 55  | 124  | Brucella anthropi ATCC 49188 chromosome 2
αr14  | Oar14CII2  | gi|153010078|ref|NC_009668.1| | 1275649  | 1275772  | \+  | 58  | 124  | Brucella anthropi ATCC 49188 chromosome 2
αr14  | Oar14CI1  | gi|153007346|ref|NC_009667.1| | 448505  | 448614  | \+  | 58  | 110  | Brucella anthropi ATCC 49188 chromosome 1
αr14  | Oar14CI2  | gi|153007346|ref|NC_009667.1| | 2453973  | 2454100  | \+  | 56  | 128  | Brucella anthropi ATCC 49188 chromosome 1
αr14  | MsBCNr14C1  | gi|110632362|ref|NC_008254.1| | 1916694  | 1916817  | \+  | 60  | 124  | Mesorhizobium sp. BNC1
αr14  | MsBCNr14C2  | gi|110632362|ref|NC_008254.1| | 3977086  | 3977208  | \-  | 60  | 123  | Mesorhizobium sp. BNC1
αr14  | MsBCNr14p1  | gi|110346917|ref|NC_008242.1| | 135270  | 135386  | \-  | 66  | 117  | Mesorhizobium sp. BNC1 plasmid 1

## Contents

* 1 Discovery and structure
* 2 Expression information
* 3 Promoter analysis
* 4 Genomic context
* 5 References

## 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]

Figure 1: Consensus secondary structure of Smr14C2 and the ar14 family predicted by RNA[6] and RNAalifold.[7] The color scheme represent the base pair probabilities.

The nucleotide sequence of Smr14C2 was initially used as query to search against the Rfam database (version 10.0;https://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)[8] (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 1021  | 3  | 3  | 6
Sinorhizobium medicae WSM419  | 3  | 3  | 6
Sinorhizobium fredii NGR234  | 3  | 3  | 6
Rhizobium etli CIAT 652  | 3  | 3  | 6
Rhizobium etli CFN 42  | 3  | 3  | 6
Rhizobium leguminosarum bv. trifolii WSM2304  | 3  | 2  | 5
Rhizobium leguminosarum bv. trifolii WSM1325  | 3  | 5  | 8
Rhizobium leguminosarum bv. viciae 3841  | 4  | 2  | 6
Agrobacterium sp. H13-3  | 2  |

Agrobacterium vitis S4  | 3 CI / 2 CII  | 1  | 6
Agrobacterium radiobacter K84  | 3 CI / 2 CII  | 1  | 6
Agrobacterium tumefaciens str. C58  | 3  |
| 3
Brucella suis ATCC 23445  | 2  |
| 2
Brucella microti CCM 4915  | 2  |
| 2
Brucella ovis ATCC 25840  | 2  |
| 2
Brucella canis ATCC 23365  | 2  |
| 2
Brucella melitensis ATCC 23457  | 2  |
| 2
Brucella abortus S19  | 2  |
| 2
Brucella abortus bv 1 str 9-941  | 2  |
| 2
Brucella melitensis biovar Abortus 2308  | 2  |
| 2
Brucella suis 1330  | 2  |
| 2
Mesorhizobium loti MAFF303099  | 5  |
| 5
Mesorhizobium sp. BNC1  | 2  | 1  | 3
Mesorhizobium ciceri biovar biserrulae WSM127  | 4  | 1  | 5
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[9] 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:

* Smr14C3 referred as: sra38,[3] Sm7[4] or SmelC398[5]
* Smr14A1 referred as: sma8[4] or SmelA075[5]
* Smr14A2 referred as: SmelA099[5]
* Smr14B referred as: SmelB161[5]

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

Figure 2: Covariance Model in stockholm format showing the consensus structure for the αr15 family. Each of the stems represented by the structure line #=GC SS_cons is in a different color, corresponding the red one to the rho independent terminator stem. Covariance Model in stockholm format can be downloaded here. Figure 3: Phylogenetic distribution of known and predicted αr14 genes. Gene numbers are based on computational analysis using the program Infernal. Shadowed in red are the closer homologs with high Infernal E-values and bit scores. Legend: αr14_Smr14C2 = Sinorhizobium meliloti 1021 (NC_003047) (NC_010994), αr14_Smr14C3 = Sinorhizobium meliloti 1021 (NC_003047) (NC_011985), αr14_Smedr14C1 = Sinorhizobium medicae WSM419 chromosome (NC_009636) (NC_011983), αr14_Smedr14C2 = Sinorhizobium medicae WSM419 chromosome (NC_009636) (NC_011369), αr14_ReCIATr14C3 = Rhizobium etli CIAT 652 (NC_010994) (NC_012850), αr14_Atr14C2 = Agrobacterium tumefaciens str. C58 chromosome linear (NC_003063) (NC_007761), αr14_Rlt1325r14C2 = Rhizobium leguminosarum bv. trifolii WSM1325 (NC_012850) (NC_012441), αr14_ReCFNr14C2 = Rhizobium etli CFN 42 (NC_007761) (NC_010994), αr14_Rlt2304r14C2 = Rhizobium leguminosarum bv. trifolii WSM2304 chromosome (NC_011369) (NC_011985), αr14_AH13r14C1 = Agrobacterium sp. H13-3 chromosome (NC_015183) (NC_011983), αr14_Sfr14C2 = Sinorhizobium fredii NGR234 chromosome (NC_012587) (NC_011369), αr14_Sfr14C1 = Sinorhizobium fredii NGR234 chromosome (NC_012587) (NC_012850), αr14_Rlt2304r14C1 = Rhizobium leguminosarum bv. trifolii WSM2304 chromosome (NC_011369) (NC_007761), αr14_Atr14C1 = Agrobacterium tumefaciens str. C58 chromosome circular (NC_003062) (NC_012441), αr14_ReCIATr14C1 = Rhizobium etli CIAT 652 (NC_010994) (NC_010994), αr14_Rlvr14C1 = Rhizobium leguminosarum bv. viciae 3841 (NC_008380) (NC_011985), αr14_ReCFNr14C1 = Rhizobium etli CFN 42 (NC_007761) (NC_011983), αr14_Avr14CI1 = Agrobacterium vitis S4 chromosome 1 chromosome 1 (NC_011989) (NC_011369), αr14_Arr14CI2 = Agrobacterium radiobacter K84 chromosome 1 (NC_011985) (NC_012850), αr14_ReCIATr14C4 = Rhizobium etli CIAT 652 (NC_010994) (NC_007761), αr14_Rlt1325r14C1 = Rhizobium leguminosarum bv. trifolii WSM1325 (NC_012850) (NC_012441), αr14_Avr14CI2 = Agrobacterium vitis S4 chromosome 1 chromosome 1 (NC_011989) (NC_010994), αr14_Sfr14b = Sinorhizobium fredii NGR234 plasmid pNGR234b (NC_012586) (NC_011985), αr14_Arr14CI3 = Agrobacterium radiobacter K84 chromosome 1 (NC_011985) (NC_011983), αr14_ReCFNr14C3 = Rhizobium etli CFN 42 (NC_007761) (NC_011369), αr14_Rlt1325r14C3 = Rhizobium leguminosarum bv. trifolii WSM1325 (NC_012850) (NC_012850), αr14_Rlvr14C3 = Rhizobium leguminosarum bv. viciae 3841 (NC_008380) (NC_007761), αr14_Rlt2304r14C3 = Rhizobium leguminosarum bv. trifolii WSM2304 chromosome (NC_011369) (NC_012441), αr14_Arr14Atc = Agrobacterium radiobacter K84 plasmid pAtK84c (NC_011987) (NC_010994), αr14_Arr14CII1 = Agrobacterium radiobacter K84 chromosome 2 (NC_011983) (NC_011985), αr14_Smr14B = Sinorhizobium meliloti 1021 plasmid pSymB (NC_003078) (NC_011983), αr14_Avr14CII1 = Agrobacterium vitis S4 chromosome 2 (NC_011988) (NC_011369), αr14_Smedr14p01 = Sinorhizobium medicae WSM419 plasmid pSMED01 (NC_009620) (NC_012850), αr14_Rlt1325r14p05 = Rhizobium leguminosarum bv. trifolii WSM1325 plasmid pR132505 (NC_012854) (NC_007761), αr14_Rlt1325r14p02 = Rhizobium leguminosarum bv. trifolii WSM1325 plasmid pR132502(NC_012858) (NC_012441), αr14_Smedr14p022 = Sinorhizobium medicae WSM419 plasmid pSMED02 (NC_009621) (NC_010994), αr14_Rlvr14p11 = Rhizobium leguminosarum bv. viciae 3841 plasmid pRL11 (NC_008384) (NC_011985), αr14_Arr14CII2 = Agrobacterium radiobacter K84 chromosome 2 (NC_011983) (NC_011983), αr14_Arr14CI1 = Agrobacterium radiobacter K84 chromosome 1 (NC_011985) (NC_011369), αr14_ReCFNr14e = Rhizobium etli CFN 42 plasmid p42e (NC_007765) (NC_012850), αr14_Rlt1325r14p012 = Rhizobium leguminosarum bv. trifolii WSM1325 plasmid pR132501 (NC_012848) (NC_007761), αr14_Rlt2304r14p02 = Rhizobium leguminosarum bv. trifolii WSM2304 plasmid pR132501 (NC_011366) (NC_012441), αr14_Rlt2304r14p012 = Rhizobium leguminosarum bv. trifolii WSM2304 plasmid pR132501 (NC_011368) (NC_010994), αr14_Rlt1325r14p04 = Rhizobium leguminosarum bv. trifolii WSM1325 plasmid pR132504 (NC_012852) (NC_011985), αr14_Avr14CI3 = Agrobacterium vitis S4 chromosome 1 (NC_011989) (NC_011983), αr14_ReCIATr14A = Rhizobium etli CIAT 652 plasmid pA (NC_010998) (NC_011369), αr14_MsBCNr14C1 = Mesorhizobium sp. BNC1 (NC_008254) (NC_012850), αr14_Avr14CII2 = Agrobacterium vitis S4 chromosome 2 (NC_011988) (NC_007761), αr14_Avr14Atc = Agrobacterium vitis S4 plasmid pAtS4c (NC_011984) (NC_012441), αr14_ReCIATr14C2 = Rhizobium etli CIAT 652 (NC_010994) (NC_010994), αr14_Atr14C3 = Agrobacterium tumefaciens str. C58 chromosome linear (NC_003063) (NC_011985), αr14_ReCIATr14B = Rhizobium etli CIAT 652 plasmid pB (NC_010996) (NC_011983), αr14_ReCFNr14d = Rhizobium etli CFN 42 symbiotic plasmid p42d (NC_004041) (NC_011369), αr14_Sfr14C3 = Sinorhizobium fredii NGR234 chromosome (NC_012587) (NC_012850), αr14_Smedr14C3 = Sinorhizobium medicae WSM419 chromosome (NC_009636) (NC_007761), αr14_Smr14C1 = Sinorhizobium meliloti 1021 (NC_003047) (NC_012441), αr14_Mlr14C1 = Mesorhizobium loti MAFF303099 chromosome (NC_002678) (NC_010994), αr14_Mlr14C2 = Mesorhizobium loti MAFF303099 chromosome (NC_002678) (NC_011985), αr14_Smr14A1 = Sinorhizobium meliloti 1021 plasmid pSymA (NC_003037) (NC_011983), αr14_Rlvr14p12 = Rhizobium leguminosarum bv. viciae 3841 plasmid pRL12 (NC_008378) (NC_011369), αr14_Mcr14C1 = Mesorhizobium ciceri biovar biserrulae WSM1271 chromosome (NC_014923) (NC_012850), αr14_Mcr14C2 = Mesorhizobium ciceri biovar biserrulae WSM1271 chromosome (NC_014923) (NC_007761), αr14_Oar14CI1 = Brucella anthropi ATCC 49188 chromosome 1 (NC_009667) (NC_012441), αr14_Oar14CII1 = Brucella anthropi ATCC 49188 chromosome 2 (NC_009668) (NC_010994), αr14_Smr14A2 = Sinorhizobium meliloti 1021 plasmid pSymA (NC_003037) (NC_011985), αr14_Oar14CI2 = Brucella anthropi ATCC 49188 chromosome 1 (NC_009667) (NC_011983), αr14_Rlt1325r14p011 = Rhizobium leguminosarum bv. trifolii WSM1325 plasmid pR132501 (NC_012848) (NC_011369), αr14_MsBCNr14C2 = Mesorhizobium sp. BNC1 (NC_008254) (NC_012850), αr14_Bs23445r14CI1 = Brucella suis ATCC 23445 chromosome I (NC_010169) (NC_007761), αr14_Bmir14CI1 = Brucella microti CCM 4915 chromosome I (NC_013119) (NC_012441), αr14_Bor14CI1 = Brucella ovis ATCC 25840 chromosome I (NC_009505) (NC_010994), αr14_Bcr14CI1 = Brucella canis ATCC 23365 chromosome I (NC_010103) (NC_011985), αr14_Bm23457r14CI1 = Brucella melitensis ATCC 23457 chromosome I (NC_012441) (NC_011983), αr14_BaS19r14CI1 = Brucella abortus S19 chromosome I (NC_010742) (NC_011369), αr14_Ba19941r14CI1 = Brucella abortus bv. 1 str. 9-941 chromosome I (NC_006932) (NC_012850), αr14_Bmar14CI1 = Brucella melitensis biovar Abortus 2308 chromosome I (NC_007618) (NC_007761), αr14_Bs1330r14CI1 = Brucella suis 1330 chromosome I (NC_004310) (NC_012441), αr14_Smedr14p021 = Sinorhizobium medicae WSM419 plasmid pSMED02 (NC_009621) (NC_010994), αr14_ReCFNr14f = Rhizobium etli CFN 42 plasmid p42f (NC_007766) (NC_011985), αr14_Oar14CII2 = Brucella anthropi ATCC 49188 chromosome 2 (NC_009668) (NC_011983), αr14_Rlt2304r14p011 = Rhizobium leguminosarum bv. trifolii WSM2304 plasmid pRLG201 (NC_011368) (NC_011369), αr14_Mcr14p01 = Mesorhizobium ciceri biovar biserrulae WSM1271 chromosome I (NC_014918) (NC_012850), αr14_Mcr14CI4 = Mesorhizobium ciceri biovar biserrulae WSM1271 chromosome I (NC_014923) (NC_007761), αr14_Mcr14CI5 = Mesorhizobium ciceri biovar biserrulae WSM1271 chromosome I (NC_014923) (NC_012441), αr14_Bor14CI2 = Brucella ovis ATCC 25840 chromosome I (NC_009505) (NC_010994), αr14_Bcr14CI2 = Brucella canis ATCC 23365 chromosome I (NC_010103) (NC_011985), αr14_Bs23445r14CI2 = Brucella suis ATCC 23445 chromosome I (NC_010169) (NC_011983), αr14_Bmir14CI2 = Brucella microti CCM 4915 chromosome 1 (NC_013119) (NC_011369), αr14_Bs1330r14CI2 = Brucella suis 1330 chromosome I (NC_004310) (NC_012850), αr14_Mlr14C5 = Mesorhizobium loti MAFF303099 chromosome (NC_002678) (NC_007761), αr14_Bm16Mr14CI1 = Brucella melitensis bv. 1 str. 16M chromosome (NC_003317) (NC_012441), αr14_BaS19r14CI2 = Brucella abortus S19 chromosome 1 (NC_010742) (NC_010994), αr14_Bm23457r14CI2 = Brucella melitensis ATCC 23457 chromosome I (NC_012441) (NC_011985), αr14_Ba19941r14CI2 = Brucella abortus bv. 1 str. 9-941 chromosome I (NC_006932) (NC_011983), αr14_Bmar14CI2 = Brucella melitensis biovar Abortus 2308 chromosome I (NC_007618) (NC_011369), αr14_MsBCNr14p1 = Mesorhizobium sp. BNC1 plasmid 1 (NC_008242) (NC_012850), αr14_Mlr14C4 = Mesorhizobium loti MAFF303099 chromosome (NC_002678) (NC_007761), αr14_Rlvr14C2 = Rhizobium leguminosarum bv. viciae 3841 (NC_008380) (NC_012441).

## 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)[2] and high salt stress, oxidative stress and cold and hot shock stresses.[4] 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.[2] Recent deep sequencing data[5] 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.[10] 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 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.

Figure 5: Graphic representation of the αr14 seed members' promoter region. All members presented putative σ70 promoters with -30 and -10 boxes marked in green and red respectively. Figure 6: Graphic representation of the αr14 further related members' promoter region.

## 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.[14][15][16] 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.

Figure 5: Group I according to the genomic context of the αr14 family.. The αr14 RNA genes are represented by red arrows and the flanking ORFs by arrows on different colors depending on their product function (legend). Numbers indicate the αr14 RNA gene's and flanking ORFs coordinates in each organism genome database. The gene strand is represented with the file direction. On the left of the figure identification names are used which correspond to a certain organism: αr14_Smedr14C1 = Sinorhizobium medicae WSM419 chromosome (NC_009636), αr14_Smr14C2 = Sinorhizobium meliloti 1021 (NC_003047), αr14_Sfr14C1 = Sinorhizobium fredii NGR234 chromosome (NC_012587), αr14_ReCIATr14A = Rhizobium etli CIAT 65 plasmid pA (NC_010998), αr14_Rlt2304r14p02 = Rhizobium leguminosarum bv trifolii WSM2304 plasmid pRLG202 (NC_011366), αr14_Rlvr14p11 = Rhizobium leguminosarum bv viciae 384 plasmid pRL11 (NC_008384), αr14_Rlt1325r14p02 = Rhizobium leguminosarum bv trifolii WSM1325 plasmid pR132502 (NC_012858). Figure 6: Group II according to the genomic context of the αr14 family.. The αr14 RNA genes are represented by red arrows and the flanking ORFs by arrows on different colors depending on their product function (legend). Numbers indicate the αr14 RNA gene's and flanking ORFs coordinates in each organism genome database. The gene strand is represented with the file direction. On the left of the figure identification names are used which correspond to a certain organism: αr14_Arr14CI3 = Agrobacterium radiobacter K84 chromosome 1 (NC_011985), αr14_Rlt2304r14C3 = Rhizobium leguminosarum bv trifolii WSM2304 (NC_011369), αr14_Rlvr14C3 = Rhizobium leguminosarum bv viciae 3841 (NC_008380), αr14_Rlt1325r14C3 = Rhizobium leguminosarum bv trifolii WSM1325 (NC_012850), αr14_ReCFNr14C3 = Rhizobium etli CFN 42 (NC_007761). Figure 7: Group III according to the genomic context of the αr14 family. The αr14 RNA genes are represented by red arrows and the flanking ORFs by arrows on different colors depending on their product function (legend). Numbers indicate the αr14 RNA gene's and flanking ORFs coordinates in each organism genome database. The gene strand is represented with the file direction. On the left of the figure identification names are used which correspond to a certain organism: αr14_Rlvr14C2 = Rhizobium leguminosarum bv viciae 3841 (NC_008380), αr14_Mlr14C1 = Mesorhizobium loti MAFF303099 chromosome (NC_002678), αr14_Mcr14C1 = Mesorhizobium ciceri biovar biserrulae WSM127 chromosome (NC_014923), αr14_Bcr14CI2 = Brucella canis ATCC 23365 chromosome I (NC_010103), αr14_Bs23445r14CI2 = Brucella suis ATCC 23445 chromosome I (NC_010169), αr14_Bm16Mr14CI1 = Brucella melitensis bv str 16M chromosome I (NC_003317), αr14_BaS19r14CI2 = Brucella abortus S19 chromosome 2 (NC_010742), αr14_Bm23457r14CI1 = Brucella melitensis ATCC 23457 chromosome II (NC_012441), αr14_Bs1330r14CI2 = Brucella suis 1330 chromosome I (NC_004310), αr14_Ba19941r14CI2 = Brucella abortus bv str 9-94chromosome I (NC_006932), αr14_Bmar14CI2 = Brucella melitensis biovar Abortus 2308 chromosome I (NC_007618), αr14_Bor14CI2 = Brucella ovis ATCC 25840 chromosome I (NC_009505), αr14_Bmir14CI2 = Brucella microti CCM 4915 chromosome 2 (NC_013119), αr14_Oar14CI2 = Brucella anthropi ATCC 49188 chromosome 1 (NC_009667). Figure 8: Group IV according to the genomic context of the αr14 family.. The αr14 RNA genes are represented by red arrows and the flanking ORFs by arrows on different colors depending on their product function (legend). Numbers indicate the αr14 RNA gene's and flanking ORFs coordinates in each organism genome database. The gene strand is represented with the file direction. On the left of the figure identification names are used which correspond to a certain organism: αr14_Bcr14CI1 = Brucella canis ATCC 23365 chromosome I (NC_010103), αr14_Bs23445r14CI1 = Brucella suis ATCC 23445 chromosome I (NC_010169), αr14_BaS19r14CI1 = Brucella abortus S19 chromosome 1 (NC_010742), αr14_Bs1330r14CI1 = Brucella suis 1330 chromosome I (NC_004310), αr14_Ba19941r14CI1 = Brucella abortus bv str 9-94chromosome I (NC_006932), αr14_Bor14CI1 = Brucella ovis ATCC 25840 chromosome I (NC_009505), αr14_Bmir14CI1 = Brucella microti CCM 4915 chromosome 1 (NC_013119).

Additional files:

* Additional file 1
* Additional file 2
* Additional file 3
* Additional file 4
* Additional file 5
* Additional file 6
* Additional file 7
* Additional file 8
* Additional file 9
* Additional file 10
* Additional file 11

Table 3: Detailed Genomic context information of the α14 sRNA seed members. Family | Feature | Name | Strand | Begin | End | Protein name | Annotation | Organism

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αr14  | gene  | SMc02051  | R  | 1666735  | 1666878  | NP_385651.1  | DUF1127  | Sinorhizobium meliloti 1021 (NC_003047)
αr14  | sRNA  | Smr14C2  | R  | 1667491  | 1667613  | \-  | sRNA  | Sinorhizobium meliloti 1021 (NC_003047)
αr14  | sRNA  | Smr14C3  | R  | 1667769  | 1667891  | \-  | sRNA  | Sinorhizobium meliloti 1021 (NC_003047)
αr14  | gene  | SMc02050  | D  | 1668357  | 1668441  | YP_001326866.1  | trigger factor  | Sinorhizobium meliloti 1021 (NC_003047)
αr14  | gene  | Smed_1180  | R  | 1257614  | 1257814  | YP_001326866.1  | DUF1127  | Sinorhizobium medicae WSM419 (NC_009636)
αr14  | sRNA  | Smedr14C1  | R  | 1258038  | 1258160  | \-  | sRNA  | Sinorhizobium medicae WSM419 chromosome (NC_009636)
αr14  | sRNA  | Smedr14C2  | R  | 1258311  | 1258431  | \-  | sRNA  | Sinorhizobium medicae WSM419 chromosome (NC_009636)
αr14  | gene  | Smed_1181  | D  | 1258759  | 1258843  | YP_001326867.1  | trigger factor  | Sinorhizobium medicae WSM419 chromosome (NC_009636)
αr14  | gene  | RHECIAT_CH0001925  | D  | 1911937  | 1912446  | YP_001978070.1  | hypothetical protein  | Rhizobium etli CIAT 652 (NC_010994)
αr14  | sRNA  | ReCIATr14C3  | R  | 1912478  | 1912597  | \-  | sRNA  | Rhizobium etli CIAT 652 (NC_010994)
αr14  | gene  | RHECIAT_CH0001926  | D  | 1912923  | 1914026  | YP_001978071.1  | membrane protein  | Rhizobium etli CIAT 652 (NC_010994)
αr14  | gene  | Atu4110  | D  | 1229427  | 1230176  | NP_356536.1  | serine dehydrogenase  | Agrobacterium tumefaciens str. C58 chromosome linear (NC_003063)
αr14  | sRNA  | Atr14C2  | D  | 1230297  | 1230426  | \-  | sRNA  | Agrobacterium tumefaciens str. C58 chromosome linear (NC_003063)
αr14  | gene  | Atu4112  | D  | 1230719  | 1231906  | NP_356534.2  | proline dipeptidase-metalloexopeptidase  | Agrobacterium tumefaciens str. C58 chromosome linear (NC_003063)
αr14  | gene  | Rleg_1700  | R  | 1696657  | 1696803  | YP_002975526.1  | DUF1127  | Rhizobium leguminosarum bv. trifolii WSM1325 (NC_012850)
αr14  | sRNA  | Rlt1325r14C2  | R  | 1697038  | 1697156  | \-  | sRNA  | Rhizobium leguminosarum bv. trifolii WSM1325 (NC_012850)
αr14  | gene  | Rleg_1701  | D  | 1697482  | 1698585  | YP_002975527.1  | membrane protein  | Rhizobium leguminosarum bv. trifolii WSM1325 (NC_012850)
αr14  | gene  | RHE_CH01838  | D  | 1925699  | 1926187  | YP_469358.1  | hypothetical protein  | Rhizobium etli CFN 42 (NC_007761)
αr14  | sRNA  | ReCFNr14C2  | R  | 1926239  | 1926358  | \-  | sRNA  | Rhizobium etli CFN 42 (NC_007761)
αr14  | gene  | RHE_CH01839  | D  | 1926684  | 1927778  | YP_469359.1  | membrane protein  | Rhizobium etli CFN 42 (NC_007761)
αr14  | gene  | Rleg2_1502  | R  | 1533929  | 1534075  | YP_002281020.1  | DUF1127  | Rhizobium leguminosarum bv. trifolii WSM2304 chromosome (NC_011369)
αr14  | sRNA  | Rlt2304r14C2  | R  | 1534501  | 1534621  | \-  | sRNA  | Rhizobium leguminosarum bv. trifolii WSM2304 chromosome (NC_011369)
αr14  | gene  | Rleg2_1503  | D  | 1534947  | 1536050  | YP_002281021.1  | membrane protein  | Rhizobium leguminosarum bv. trifolii WSM2304 chromosome (NC_011369)
αr14  | gene  | AGROH133_02958  | R  | 108794  | 109252  | YP_004277412.1  | aminoacyl-tRNA ligase  | Agrobacterium sp. H13-3 chromosome (NC_015183)
αr14  | sRNA  | AH13r14C1  | D  | 109372  | 109501  | \-  | sRNA  | Agrobacterium sp. H13-3 chromosome (NC_015183)
αr14  | gene  | AGROH133_02961  | D  | 109733  | 109942  | YP_004277414.1  | cold shock protein  | Agrobacterium sp. H13-3 chromosome (NC_015183)
αr14  | gene  | NGR_c13890  | R  | 1433785  | 1433985  | YP_002825922.1  | DUF1127  | Sinorhizobium fredii NGR234 chromosome (NC_012587)
αr14  | sRNA  | Sfr14C2  | R  | 1434463  | 1434586  | \-  | sRNA  | Sinorhizobium fredii NGR234 chromosome (NC_012587)
αr14  | sRNA  | Sfr14C1  | R  | 1434171  | 1434293  | \-  | sRNA  | Sinorhizobium fredii NGR234 chromosome (NC_012587)
αr14  | gene  | NGR_c13920  | R  | 1434843  | 1434925  | YP_002825924.1  | trigger factor  | Sinorhizobium fredii NGR234 chromosome (NC_012587)
αr14  | gene  | Rleg2_0104  | D  | 96796  | 97677  | YP_002279632.1  | aldo/keto reductase  | Rhizobium leguminosarum bv. trifolii WSM2304 chromosome (NC_011369)
αr14  | sRNA  | Rlt2304r14C1  | D  | 98050  | 98171  | \-  | sRNA  | Rhizobium leguminosarum bv. trifolii WSM2304 chromosome (NC_011369)
αr14  | gene  | Rleg2_0105  | D  | 98282  | 99559  | YP_002279633.1  | DUF900, alpha/beta hydrolase  | Rhizobium leguminosarum bv. trifolii WSM2304 chromosome (NC_011369)
αr14  | gene  | Atu0104  | R  | 108895  | 109353  | NP_353139.1  | aminoacyl-tRNA ligase  | Agrobacterium tumefaciens str. C58 chromosome circular (NC_003062)
αr14  | sRNA  | Atr14C1  | D  | 109473  | 109601  | \-  | sRNA  | Agrobacterium tumefaciens str. C58 chromosome circular (NC_003062)
αr14  | gene  | Atu0106  | D  | 109823  | 110032  | NP_353140.2  | cold shock protein  | Agrobacterium tumefaciens str. C58 chromosome circular (NC_003062)
αr14  | gene  | RHECIAT_CH0000515  | D  | 512732  | 513613  | YP_001976686.1  | oxidoreductase  | Rhizobium etli CIAT 652 (NC_010994)
αr14  | sRNA  | ReCIATr14C1  | D  | 513993  | 514114  | \-  | sRNA  | Rhizobium etli CIAT 652 (NC_010994)
αr14  | gene  | RHECIAT_CH0000517  | D  | 514221  | 515498  | YP_001976688.1  | DUF900, alpha/beta hydrolase  | Rhizobium etli CIAT 652 (NC_010994)
αr14  | gene  | RL0474  | D  | 511376  | 512272  | YP_766083.1  | aldo/keto reductase  | Rhizobium leguminosarum bv. viciae 3841 (NC_008380)
αr14  | sRNA  | Rlvr14C1  | D  | 512658  | 512779  | \-  | sRNA  | Rhizobium leguminosarum bv. viciae 3841 (NC_008380)
αr14  | gene  | RL0475  | R  | 512816  | 513202  | YP_766084.1  | hypothetical protein  | Rhizobium leguminosarum bv. viciae 3841 (NC_008380)
αr14  | gene  | RHE_CH00449  | D  | 461301  | 462182  | YP_467997.1  | oxidoreductase  | Rhizobium etli CFN 42 (NC_007761)
αr14  | sRNA  | ReCFNr14C1  | D  | 462566  | 462687  | \-  | sRNA  | Rhizobium etli CFN 42 (NC_007761)
αr14  | gene  | RHE_CH00450  | D  | 462794  | 464071  | YP_467998.1  | DUF900, alpha/beta hydrolase  | Rhizobium etli CFN 42 (NC_007761)
αr14  | gene  | Avi_0122  | R  | 113190  | 114716  | YP_002548072.1  | sulfatase  | Agrobacterium vitis S4 chromosome 1 chromosome 1 (NC_011989)
αr14  | sRNA  | Avr14CI1  | D  | 115126  | 115257  | \-  | sRNA  | Agrobacterium vitis S4 chromosome 1 chromosome 1 (NC_011989)
αr14  | gene  | Avi_0126  | D  | 115395  | 116840  | YP_002548074.1  | phosphomannomutase  | Agrobacterium vitis S4 chromosome 1 chromosome 1 (NC_011989)
αr14  | gene  | Arad_2144  | R  | 1692677  | 1692823  | YP_002544330.1  | DUF1127  | Agrobacterium radiobacter K84 chromosome 1 (NC_011985)
αr14  | sRNA  | Arr14CI2  | R  | 1693278  | 1693409  | \-  | sRNA  | Agrobacterium radiobacter K84 chromosome 1 (NC_011985)
αr14  | gene  | Arad_2145  | D  | 1693731  | 1694870  | YP_002544331.1  | membrane protein  | Agrobacterium radiobacter K84 chromosome 1 (NC_011985)
αr14  | gene  | RHECIAT_CH0004359  | D  | 4444289  | 4444867  | YP_001980464.1  | nicotinic acid mononucleotide adenylyltransferase  | Rhizobium etli CIAT 652 (NC_010994)
αr14  | sRNA  | ReCIATr14C4  | R  | 4444894  | 4445016  | \-  | sRNA  | Rhizobium etli CIAT 652 (NC_010994)
αr14  | gene  | RHECIAT_CH0004360  | R  | 4445118  | 4445327  | YP_001980465.1  | hypothetical protein  | Rhizobium etli CIAT 652 (NC_010994)
αr14  | gene  | Rleg_0114  | D  | 105825  | 106706  | YP_002973964.1  | aldo/keto reductase  | Rhizobium leguminosarum bv. trifolii WSM1325 (NC_012850)
αr14  | sRNA  | Rlt1325r14C1  | D  | 107063  | 107184  | \-  | sRNA  | Rhizobium leguminosarum bv. trifolii WSM1325 (NC_012850)
αr14  | gene  | Rleg_0115  | D  | 107377  | 108654  | YP_002973965.1  | DUF900, alpha/beta hydrolase  | Rhizobium leguminosarum bv. trifolii WSM1325 (NC_012850)
αr14  | gene  | Avi_2480  | R  | 2042548  | 2043660  | YP_002549780.1  | membrane protein  | Agrobacterium vitis S4 chromosome 1 chromosome 1 (NC_011989)
αr14  | sRNA  | Avr14CI2  | D  | 2043913  | 2044044  | \-  | sRNA  | Agrobacterium vitis S4 chromosome 1 chromosome 1 (NC_011989)
αr14  | gene  | Avi_2481  | D  | 2044292  | 2044441  | YP_002549781.1  | DUF1127  | Agrobacterium vitis S4 chromosome 1 chromosome 1 (NC_011989)
αr14  | gene  | NGR_b21490  | R  | 2204845  | 2205168  | YP_002824347.1  | acylphosphatase  | Sinorhizobium fredii NGR234 plasmid pNGR234b (NC_012586)
αr14  | sRNA  | Sfr14b  | D  | 2205311  | 2205428  | \-  | sRNA  | Sinorhizobium fredii NGR234 plasmid pNGR234b (NC_012586)
αr14  | gene  | NGR_b21500  | D  | 2205588  | 2206316  | YP_002824348.1  | RNA polymerase sigma factor  | Sinorhizobium fredii NGR234 plasmid pNGR234b (NC_012586)
αr14  | gene  | Arad_4880  | D  | 3944888  | 3945469  | YP_002546417.1  | nicotinic acid mononucleotide adenylyltransferase  | Agrobacterium radiobacter K84 chromosome 1 (NC_011985)
αr14  | sRNA  | Arr14CI3  | R  | 3945511  | 3945639  | \-  | sRNA  | Agrobacterium radiobacter K84 chromosome 1 (NC_011985)
αr14  | gene  | Arad_4883  | D  | 3946044  | 3946844  | YP_002546419.1  | molybdenum ABC transporter  | Agrobacterium radiobacter K84 chromosome 1 (NC_011985)
αr14  | gene  | RHE_CH04070  | D  | 4313781  | 4314359  | YP_471540.1  | nicotinic acid mononucleotide adenylyltransferase  | Rhizobium etli CFN 42 (NC_007761)
αr14  | sRNA  | ReCFNr14C3  | R  | 4314384  | 4314505  | \-  | sRNA  | Rhizobium etli CFN 42 (NC_007761)
αr14  | gene  | RHE_CH04071  | D  | 4314798  | 4315589  | YP_471541.1  | molybdenum ABC transporter  | Rhizobium etli CFN 42 (NC_007761)
αr14  | gene  | Rleg_4201  | D  | 4295976  | 4296575  | YP_002977981.1  | nicotinic acid mononucleotide adenylyltransferase  | Rhizobium leguminosarum bv. trifolii WSM1325 (NC_012850)
αr14  | sRNA  | Rlt1325r14C3  | R  | 4296632  | 4296749  | \-  | sRNA  | Rhizobium leguminosarum bv. trifolii WSM1325 (NC_012850)
αr14  | gene  | Rleg_4202  | D  | 4297098  | 4297889  | YP_002977982.1  | molybdenum ABC transporter  | Rhizobium leguminosarum bv. trifolii WSM1325 (NC_012850)
αr14  | gene  | RL4684  | D  | 4987413  | 4988012  | YP_770246.1  | nicotinic acid mononucleotide adenylyltransferase  | Rhizobium leguminosarum bv. viciae 3841 (NC_008380)
αr14  | sRNA  | Rlvr14C3  | R  | 4988030  | 4988158  | \-  | sRNA  | Rhizobium leguminosarum bv. viciae 3841 (NC_008380)
αr14  | gene  | RL4685  | D  | 4988507  | 4989298  | YP_770247.1  | molybdenum ABC transporter  | Rhizobium leguminosarum bv. viciae 3841 (NC_008380)
αr14  | gene  | Rleg2_3877  | D  | 4018721  | 4019299  | YP_002283365.1  | nicotinic acid mononucleotide adenylyltransferase  | Rhizobium leguminosarum bv. trifolii WSM2304 chromosome (NC_011369)
αr14  | sRNA  | Rlt2304r14C3  | R  | 4019326  | 4019446  | \-  | sRNA  | Rhizobium leguminosarum bv. trifolii WSM2304 chromosome (NC_011369)
αr14  | gene  | Rleg2_3878  | D  | 4019781  | 4020572  | YP_002283366.1  | molybdenum ABC transporter  | Rhizobium leguminosarum bv. trifolii WSM2304 chromosome (NC_011369)
αr14  | gene  | Arad_12190  | D  | 137950  | 138255  | YP_002546688.1  | FAD dependent oxidoreductase  | Agrobacterium radiobacter K84 plasmid pAtK84c (NC_011987)
αr14  | sRNA  | Arr14Atc  | R  | 138495  | 138625  | \-  | sRNA  | Agrobacterium radiobacter K84 plasmid pAtK84c (NC_011987)
αr14  | gene  | Arad_12193  | R  | 139226  | 140683  | YP_002546689.1  | Cytochrome c2C mono- and diheme oxidoreductase  | Agrobacterium radiobacter K84 plasmid pAtK84c (NC_011987)
αr14  | gene  | Arad_8084  | D  | 957315  | 957461  | YP_002541036.1  | DUF1127  | Agrobacterium radiobacter K84 chromosome 2 (NC_011983)
αr14  | sRNA  | Arr14CII1  | D  | 957686  | 957817  | \-  | sRNA  | Agrobacterium radiobacter K84 chromosome 2 (NC_011983)
αr14  | gene  | Arad_8086  | R  | 957909  | 958754  | YP_002541037.1  | DUF900, alpha/beta hydrolase  | Agrobacterium radiobacter K84 chromosome 2 (NC_011983)
αr14  | gene  | SM_b20590  | R  | 1605382  | 1605705  | NP_438042.1  | acylphosphatase  | Sinorhizobium meliloti 1021 plasmid pSymB (NC_003078)
αr14  | sRNA  | Smr14B  | D  | 1605826  | 1605943  | \-  | sRNA  | Sinorhizobium meliloti 1021 plasmid pSymB (NC_003078)
αr14  | gene  | SM_b20592  | D  | 1606089  | 1606772  | NP_438044.1  | RNA polymerase sigma factor  | Sinorhizobium meliloti 1021 plasmid pSymB (NC_003078)
αr14  | gene  | Avi_5586  | D  | 597555  | 598229  | YP_002547399.1  | hypothetical protein  | Agrobacterium vitis S4 chromosome 2 (NC_011988)
αr14  | sRNA  | Avr14CII1  | R  | 598426  | 598556  | \-  | sRNA  | Agrobacterium vitis S4 chromosome 2 (NC_011988)
αr14  | gene  | Avi_5587  | R  | 598779  | 598925  | YP_002547400.1  | DUF1127  | Agrobacterium vitis S4 chromosome 2 (NC_011988)
αr14  | gene  | Smed_4197  | R  | 678214  | 678885  | YP_001312935.1  | RNA polymerase sigma factor  | Sinorhizobium medicae WSM419 plasmid pSMED01 (NC_009620)
αr14  | sRNA  | Smedr14p01  | R  | 679043  | 679160  | \-  | sRNA  | Sinorhizobium medicae WSM419 plasmid pSMED01 (NC_009620)
αr14  | gene  | Smed_4198  | D  | 679315  | 679599  | YP_001312936.1  | acylphosphatase  | Sinorhizobium medicae WSM419 plasmid pSMED01 (NC_009620)
αr14  | gene  | Rleg_6288  | D  | 1484  | 2256  | YP_002979285.1  | hypothetical protein  | Rhizobium leguminosarum bv. trifolii WSM1325 plasmid pR132505 (NC_012854)
αr14  | sRNA  | Rlt1325r14p05  | R  | 2286  | 2409  | \-  | sRNA  | Rhizobium leguminosarum bv. trifolii WSM1325 plasmid pR132505 (NC_012854)
αr14  | gene  | Rleg_6290  | D  | 3237  | 3734  | YP_002979286.1  | hypothetical protein  | Rhizobium leguminosarum bv. trifolii WSM1325 plasmid pR132505 (NC_012854)
αr14  | gene  | Rleg_6602  | D  | 28280  | 28426  | YP_002984605.1  | DUF1127  | Rhizobium leguminosarum bv. trifolii WSM1325 plasmid pR132502 (NC_012858)
αr14  | sRNA  | Rlt1325r14p02  | D  | 28646  | 28767  | \-  | sRNA  | Rhizobium leguminosarum bv. trifolii WSM1325 plasmid pR132502(NC_012858)
αr14  | gene  | Rleg_6603  | D  | 29055  | 29891  | YP_002984606.1  | 5-keto-4-deoxyuronate isomerase  | Rhizobium leguminosarum bv. trifolii WSM1325 plasmid pR132502 (NC_012858)
αr14  | gene  | Smed_5370  | D  | 338535  | 338681  | YP_001314073.1  | DUF1127  | Sinorhizobium medicae WSM419 plasmid pSMED02 (NC_009621)
αr14  | sRNA  | Smedr14p022  | D  | 338866  | 338990  | \-  | sRNA  | Sinorhizobium medicae WSM419 plasmid pSMED02 (NC_009621)
αr14  | gene  | Smed_5371  | R  | 339017  | 339226  | YP_001314074.1  | hypothetical protein  | Sinorhizobium medicae WSM419 plasmid pSMED02 (NC_009621)
αr14  | gene  | pRL110530  | R  | 573348  | 574184  | YP_771564.1  | 5-keto-4-deoxyuronate isomerase  | Rhizobium leguminosarum bv. viciae 3841 plasmid pRL11 (NC_008384)
αr14  | sRNA  | Rlvr14p11  | R  | 574471  | 574593  | \-  | sRNA  | Rhizobium leguminosarum bv. viciae 3841 plasmid pRL11 (NC_008384)
αr14  | gene  | pRL110532  | R  | 574811  | 574957  | YP_771566.1  | DUF1127  | Rhizobium leguminosarum bv. viciae 3841 plasmid pRL11 (NC_008384)
αr14  | gene  | Arad_9216  | R  | 1920052  | 1920927  | YP_002541901.1  | glutathione S-transferase Ygh  | Agrobacterium radiobacter K84 chromosome 2 (NC_011983)
αr14  | sRNA  | Arr14CII2  | R  | 1921110  | 1921242  | \-  | sRNA  | Agrobacterium radiobacter K84 chromosome 2 (NC_011983)
αr14  | gene  | Arad_9217  | R  | 1921485  | 1921631  | YP_002541902.1  | DUF1127  | Agrobacterium radiobacter K84 chromosome 2 (NC_011983)
αr14  | gene  | Arad_0725  | D  | 596785  | 597666  | YP_002543276.1  | oxidoreductase  | Agrobacterium radiobacter K84 chromosome 1 (NC_011985)
αr14  | sRNA  | Arr14CI1  | D  | 597903  | 598030  | \-  | sRNA  | Agrobacterium radiobacter K84 chromosome 1 (NC_011985)
αr14  | gene  | Arad_0727  | D  | 598187  | 599503  | YP_002543277.1  | DUF900, alpha/beta hydrolase  | Agrobacterium radiobacter K84 chromosome 1 (NC_011985)
αr14  | gene  | RHE_PE00400  | R  | 441962  | 442798  | YP_472562.1  | 5-keto-4-deoxyuronate isomerase  | Rhizobium etli CFN 42 plasmid p42e (NC_007765)
αr14  | sRNA  | ReCFNr14e  | R  | 443001  | 443129  | \-  | sRNA  | Rhizobium etli CFN 42 plasmid p42e (NC_007765)
αr14  | gene  | RHE_PE00401  | R  | 443336  | 443482  | YP_472563.1  | hypothetical protein  | Rhizobium etli CFN 42 plasmid p42e (NC_007765)
αr14  | gene  | Rleg_4483  | D  | 265481  | 265806  | \-  | pseudogen  | Rhizobium leguminosarum bv. trifolii WSM1325 plasmid pR132501 (NC_012848)
αr14  | sRNA  | Rlt1325r14p012  | D  | 265945  | 266069  | \-  | sRNA  | Rhizobium leguminosarum bv. trifolii WSM1325 plasmid pR132501 (NC_012848)
αr14  | gene  | Rleg_4484  | R  | 266933  | 267917  | \-  | pseudogen  | Rhizobium leguminosarum bv. trifolii WSM1325 plasmid pR132501 (NC_012848)
αr14  | gene  | Rleg2_5661  | D  | 50447  | 50593  | YP_002277936.1  | DUF1127  | Rhizobium leguminosarum bv. trifolii WSM2304 plasmid pR132501 (NC_011366)
αr14  | sRNA  | Rlt2304r14p02  | D  | 50814  | 50936  | \-  | sRNA  | Rhizobium leguminosarum bv. trifolii WSM2304 plasmid pR132501 (NC_011366)
αr14  | gene  | Rleg2_5662  | D  | 51199  | 52035  | YP_002277937.1  | 5-keto-4-deoxyuronate isomerase  | Rhizobium leguminosarum bv. trifolii WSM2304 plasmid pR132501 (NC_011366)
αr14  | gene  | Rleg2_4962  | R  | 606812  | 607117  | YP_002278931.1  | hypothetical protein  | Rhizobium leguminosarum bv. trifolii WSM2304 plasmid pR132501 (NC_011368)
αr14  | sRNA  | Rlt2304r14p012  | D  | 607636  | 607759  | \-  | sRNA  | Rhizobium leguminosarum bv. trifolii WSM2304 plasmid pR132501 (NC_011368)
αr14  | gene  | Rleg2_4963  | R  | 607786  | 608067  | \-  | pseudogen  | Rhizobium leguminosarum bv. trifolii WSM2304 plasmid pR132501 (NC_011368)
αr14  | gene  | Rleg_6084  | D  | 118943  | 119089  | YP_002978590.1  | DUF1127  | Rhizobium leguminosarum bv. trifolii WSM1325 plasmid pR132504 (NC_012852)
αr14  | sRNA  | Rlt1325r14p04  | D  | 119314  | 119443  | \-  | sRNA  | Rhizobium leguminosarum bv. trifolii WSM1325 plasmid pR132504 (NC_012852)
αr14  | gene  | Rleg_6085  | R  | 119664  | 120056  | YP_002978591.1  | Cell wall assembly/cell proliferation coordinating protein, KNR4-like  | Rhizobium leguminosarum bv. trifolii WSM1325 plasmid pR132504 (NC_012852)
αr14  | gene  | Avi_3374  | D  | 2792636  | 2793793  | YP_002550427.1  | DNA polymerase I  | Agrobacterium vitis S4 chromosome 1 (NC_011989)
αr14  | sRNA  | Avr14CI3  | R  | 2793803  | 2793939  | \-  | sRNA  | Agrobacterium vitis S4 chromosome 1 (NC_011989)
αr14  | gene  | Avi_3375  | R  | 2794154  | 2794300  | YP_002550428.1  | DUF1127  | Agrobacterium vitis S4 chromosome 1 (NC_011989)
αr14  | gene  | RHECIAT_PA0000319  | R  | 344808  | 345644  | YP_001985926.1  | 5-keto-4-deoxyuronate isomerase  | Rhizobium etli CIAT 652 plasmid pA (NC_010998)
αr14  | sRNA  | ReCIATr14A  | R  | 345900  | 346021  | \-  | sRNA  | Rhizobium etli CIAT 652 plasmid pA (NC_010998)
αr14  | gene  | RHECIAT_PA0000320  | R  | 346130  | 346366  | YP_001985927.1  | DUF1127  | Rhizobium etli CIAT 652 plasmid pA (NC_010998)
αr14  | gene  | Meso_1791  | D  | 1916546  | 1916686  | YP_674350.1  | DUF1127  | Mesorhizobium sp. BNC1 (NC_008254)
αr14  | sRNA  | MsBCNr14C1  | D  | 1916694  | 1916817  | \-  | sRNA  | Mesorhizobium sp. BNC1 (NC_008254)
αr14  | gene  | Meso_1793  | R  | 1918307  | 1920064  | YP_674352.1  | hypothetical protein  | Mesorhizobium sp. BNC1 (NC_008254)
αr14  | gene  | Avi_5890  | D  | 899428  | 900909  | YP_002547646.1  | sulfate permease  | Agrobacterium vitis S4 chromosome 2 (NC_011988)
αr14  | sRNA  | Avr14CII2  | D  | 901035  | 901159  | \-  | sRNA  | Agrobacterium vitis S4 chromosome 2 (NC_011988)
αr14  | gene  | Avi_5891  | R  | 901178  | 902659  | YP_002547647.1  | siroheme synthase  | Agrobacterium vitis S4 chromosome 2 (NC_011988)
αr14  | gene  | Avi_9007  | D  | 6113  | 7192  | YP_002542553.1  | two component sensor kinase  | Agrobacterium vitis S4 plasmid pAtS4c (NC_011984)
αr14  | sRNA  | Avr14Atc  | D  | 7318  | 7444  | \-  | sRNA  | Agrobacterium vitis S4 plasmid pAtS4c (NC_011984)
αr14  | gene  | Avi_9008  | R  | 7500  | 8633  | YP_002542554.1  | phage integrase family protein  | Agrobacterium vitis S4 plasmid pAtS4c (NC_011984)
αr14  | gene  | RHECIAT_CH0001166  | R  | 1172125  | 1173279  | YP_001977325.1  | polyhydroxybutyrate depolymerase protein  | Rhizobium etli CIAT 652 (NC_010994)
αr14  | sRNA  | ReCIATr14C2  | D  | 1173512  | 1173639  | \-  | sRNA  | Rhizobium etli CIAT 652 (NC_010994)
αr14  | gene  | RHECIAT_CH0001168  | D  | 1173948  | 1174214  | YP_001977327.1  | DUF2277  | Rhizobium etli CIAT 652 (NC_010994)
αr14  | gene  | Atu4670  | R  | 1831052  | 1831294  | NP_535148.1  | hypothetical protein  | Agrobacterium tumefaciens str. C58 chromosome linear (NC_003063)
αr14  | sRNA  | Atr14C3  | D  | 1831483  | 1831614  | \-  | sRNA  | Agrobacterium tumefaciens str. C58 chromosome linear (NC_003063)
αr14  | gene  | Atu4671  | R  | 1831642  | 1832085  | NP_355992.2  | response regulator  | Agrobacterium tumefaciens str. C58 chromosome linear (NC_003063)
αr14  | gene  | RHECIAT_PB0000101  | R  | 111975  | 112217  | YP_001984364.1  | hypothetical protein  | Rhizobium etli CIAT 652 plasmid pB (NC_010996)
αr14  | sRNA  | ReCIATr14B  | D  | 112292  | 112425  | \-  | sRNA  | Rhizobium etli CIAT 652 plasmid pB (NC_010996)
αr14  | gene  | RHECIAT_PB0000102  | D  | 112536  | 113108  | YP_001984365.1  | hypothetical protein  | Rhizobium etli CIAT 652 plasmid pB (NC_010996)
αr14  | gene  | RHE_PD00068  | D  | 76637  | 77354  | NP_659968.2  | hypothetical protein  | Rhizobium etli CFN 42 symbiotic plasmid p42d (NC_004041)
αr14  | sRNA  | ReCFNr14d  | D  | 77668  | 77794  | \-  | sRNA  | Rhizobium etli CFN 42 symbiotic plasmid p42d (NC_004041)
αr14  | gene  | RHE_PD00069  | D  | 77912  | 78484  | NP_659967.1  | hydrolase  | Rhizobium etli CFN 42 symbiotic plasmid p42d (NC_004041)
αr14  | gene  | NGR_c35080  | R  | 3718015  | 3720336  | YP_002827985.1  | penicillin-binding  | Sinorhizobium fredii NGR234 chromosome (NC_012587)
αr14  | sRNA  | Sfr14C3  | D  | 3720579  | 3720700  | \-  | sRNA  | Sinorhizobium fredii NGR234 chromosome (NC_012587)
αr14  | gene  | NGR_c35100  | D  | 3721900  | 3722382  | YP_002827987.1  | hypothetical protein  | Sinorhizobium fredii NGR234 chromosome (NC_012587)
αr14  | gene  | Smed_3386  | R  | 3589318  | 3590205  | YP_001329042.1  | membrane protein  | Sinorhizobium medicae WSM419 chromosome (NC_009636)
αr14  | sRNA  | Smedr14C3  | R  | 3590299  | 3590417  | \-  | sRNA  | Sinorhizobium medicae WSM419 chromosome (NC_009636)
αr14  | gene  | Smed_3387  | R  | 3590494  | 3590925  | YP_001329043.1  | pyrimidine dimer DNA glycosylase  | Sinorhizobium medicae WSM419 chromosome (NC_009636)
αr14  | gene  | SMc02855  | R  | 205860  | 206783  | NP_384286.1  | membrane protein  | Sinorhizobium meliloti 1021 (NC_003047)
αr14  | sRNA  | Smr14C1  | R  | 206862  | 206980  | \-  | sRNA  | Sinorhizobium meliloti 1021 (NC_003047)
αr14  | gene  | SMc02856  | D  | 207244  | 209547  | NP_384287.1  | penicillin-binding protein  | Sinorhizobium meliloti 1021 (NC_003047)
αr14  | gene  | msr1062  | D  | 890180  | 890389  | NP_102735.1  | DUF1127  | Mesorhizobium loti MAFF303099 chromosome (NC_002678)
αr14  | sRNA  | Mlr14C1  | D  | 890582  | 890702  | \-  | sRNA  | Mesorhizobium loti MAFF303099 chromosome (NC_002678)
αr14  | sRNA  | Mlr14C2  | D  | 890760  | 890880  | \-  | sRNA  | Mesorhizobium loti MAFF303099 chromosome (NC_002678)
αr14  | gene  | mlr1064  | D  | 891150  | 892568  | NP_102736.1  | tRNA (uracil-5-)-methyltransferase  | Mesorhizobium loti MAFF303099 chromosome (NC_002678)
αr14  | gene  | SMa2165  | D  | 1219615  | 1220355  | NP_436422.1  | oxidoreductase  | Sinorhizobium meliloti 1021 plasmid pSymA (NC_003037)
αr14  | sRNA  | Smr14A1  | D  | 1220690  | 1220808  | \-  | sRNA  | Sinorhizobium meliloti 1021 plasmid pSymA (NC_003037)
αr14  | gene  | SMa2167  | D  | 1221480  | 1221947  | NP_436423.1  | transcription factor regulator  | Sinorhizobium meliloti 1021 plasmid pSymA (NC_003037)
αr14  | gene  | pRL120374  | R  | 403573  | 404652  | YP_764884.1  | ribonuclease domain-containing protein  | Rhizobium leguminosarum bv. viciae 3841 plasmid pRL12 (NC_008378)
αr14  | sRNA  | Rlvr14p12  | D  | 407202  | 407316  | \-  | sRNA  | Rhizobium leguminosarum bv. viciae 3841 plasmid pRL12 (NC_008378)
αr14  | gene  | pRL120378  | R  | 408099  | 409010  | YP_764885.1  | L-isoaspartate O-methyltransferase  | Rhizobium leguminosarum bv. viciae 3841 plasmid pRL12 (NC_008378)
αr14  | gene  | Mesci_3513  | R  | 3673344  | 3674753  | YP_004142683.1  | tRNA (uracil-5-)-methyltransferase  | Mesorhizobium ciceri biovar biserrulae WSM1271 chromosome (NC_014923)
αr14  | sRNA  | Mcr14C1  | R  | 3674843  | 3674963  | \-  | sRNA  | Mesorhizobium ciceri biovar biserrulae WSM1271 chromosome (NC_014923)
αr14  | sRNA  | Mcr14C2  | R  | 3675022  | 3675142  | \-  | sRNA  | Mesorhizobium ciceri biovar biserrulae WSM1271 chromosome (NC_014923)
αr14  | gene  | Mesci_3514  | R  | 3675321  | 3675461  | YP_004142684.1  | DUF1127  | Mesorhizobium ciceri biovar biserrulae WSM1271 chromosome (NC_014923)
αr14  | gene  | Oant_0422  | D  | 447656  | 448351  | YP_001368982.1  | LrgB membrane protein /hydrolase  | Brucella anthropi ATCC 49188 chromosome 1 (NC_009667)
αr14  | sRNA  | Oar14CI1  | D  | 448505  | 448614  | \-  | sRNA  | Brucella anthropi ATCC 49188 chromosome 1 (NC_009667)
αr14  | gene  | Oant_0423  | D  | 448748  | 450301  | YP_001368983.1  | glyoxalase bleomycin resistance protein dioxygenase/hydrolase  | Brucella anthropi ATCC 49188 chromosome 1 (NC_009667)
αr14  | gene  | Oant_2969  | R  | 272174  | 273850  | YP_001371506.1  | hypothetical protein  | Brucella anthropi ATCC 49188 chromosome 2 (NC_009668)
αr14  | sRNA  | Oar14CII1  | D  | 274684  | 274807  | \-  | sRNA  | Brucella anthropi ATCC 49188 chromosome 2 (NC_009668)
αr14  | gene  | Oant_2970  | D  | 275652  | 276380  | YP_001371507.1  | septum formation inhibitor  | Brucella anthropi ATCC 49188 chromosome 2 (NC_009668)
αr14  | gene  | SMa2355  | D  | 1327042  | 1328151  | NP_436520.4  | DNA polymerase I  | Sinorhizobium meliloti 1021 plasmid pSymA (NC_003037)
αr14  | sRNA  | Smr14A2  | R  | 1328176  | 1328301  | \-  | sRNA  | Sinorhizobium meliloti 1021 plasmid pSymA (NC_003037)
αr14  | gene  | SMa2357  | D  | 1329978  | 1330670  | NP_436521.2  | adenylate guanylate cyclase  | Sinorhizobium meliloti 1021 plasmid pSymA (NC_003037)
αr14  | gene  | Oant_2332  | D  | 2453758  | 2453904  | YP_001370875.1  | DUF1127  | Brucella anthropi ATCC 49188 chromosome 1 (NC_009667)
αr14  | sRNA  | Oar14CI2  | D  | 2453973  | 2454100  | \-  | sRNA  | Brucella anthropi ATCC 49188 chromosome 1 (NC_009667)
αr14  | gene  | Oant_2333  | D  | 2454171  | 2455601  | YP_001370876.1  | tRNA (uracil-5-)-methyltransferase  | Brucella anthropi ATCC 49188 chromosome 1 (NC_009667)
αr14  | gene  | Rleg_4742  | D  | 111695  | 112336  | YP_002972933.1  | hypothetical protein  | Rhizobium leguminosarum bv. trifolii WSM1325 plasmid pR132501 (NC_012848)
αr14  | sRNA  | Rlt1325r14p011  | D  | 112604  | 112728  | \-  | sRNA  | Rhizobium leguminosarum bv. trifolii WSM1325 plasmid pR132501 (NC_012848)
αr14  | gene  | Rleg_4743  | R  | 112925  | 113309  | \-  | hypothetical protein  | Rhizobium leguminosarum bv. trifolii WSM1325 plasmid pR132501 (NC_012848)
αr14  | gene  | Meso_3687  | R  | 3975340  | 3976962  | YP_676220.1  | alpha amylase-C hydrolase  | Mesorhizobium sp. BNC1 (NC_008254)
αr14  | sRNA  | MsBCNr14C2  | R  | 3977086  | 3977208  | \-  | sRNA  | Mesorhizobium sp. BNC1 (NC_008254)
αr14  | gene  | Meso_3688  | D  | 3977363  | 3978682  | YP_676221.1  | homoserine dehydrogenase-C NAD-binding  | Mesorhizobium sp. BNC1 (NC_008254)
αr14  | gene  | BSUIS_A0355  | D  | 354629  | 355336  | YP_001627017.1  | LrgB membrane protein /hydrolase  | Brucella suis ATCC 23445 chromosome I (NC_010169)
αr14  | sRNA  | Bs23445r14CI1  | D  | 355557  | 355664  | \-  | sRNA  | Brucella suis ATCC 23445 chromosome I (NC_010169)
αr14  | gene  | BSUIS_A0356  | D  | 355877  | 357124  | YP_001627018.1  | hypothetical protein  | Brucella suis ATCC 23445 chromosome I (NC_010169)
αr14  | gene  | BMI_I332  | D  | 338771  | 339478  | YP_003106291.1  | LrgB membrane protein /hydrolase  | Brucella microti CCM 4915 chromosome I (NC_013119)
αr14  | sRNA  | Bmir14CI1  | D  | 339699  | 339806  | \-  | sRNA  | Brucella microti CCM 4915 chromosome I (NC_013119)
αr14  | gene  | BMI_I334  | D  | 340025  | 341266  | YP_003106293.1  | DUF900, alpha/beta hydrolase  | Brucella microti CCM 4915 chromosome I (NC_013119)
αr14  | gene  | BOV_0342  | D  | 358754  | 359461  | YP_001258364.1  | hydrolase  | Brucella ovis ATCC 25840 chromosome I (NC_009505)
αr14  | sRNA  | Bor14CI1  | D  | 359682  | 359789  | \-  | sRNA  | Brucella ovis ATCC 25840 chromosome I (NC_009505)
αr14  | gene  | BOV_0343  | D  | 360008  | 361250  | \-  | pseudogen  | Brucella ovis ATCC 25840 chromosome I (NC_009505)
αr14  | gene  | BCAN_A0335  | D  | 337093  | 337800  | YP_001592196.1  | LrgB membrane protein /hydrolase  | Brucella canis ATCC 23365 chromosome I (NC_010103)
αr14  | sRNA  | Bcr14CI1  | D  | 338021  | 338128  | \-  | sRNA  | Brucella canis ATCC 23365 chromosome I (NC_010103)
αr14  | gene  | BCAN_A0337  | D  | 338347  | 339588  | YP_001592198.1  | DUF900, alpha/beta hydrolase  | Brucella canis ATCC 23365 chromosome I (NC_010103)
αr14  | gene  | BMEA_A0364  | D  | 358048  | 358755  | YP_002732104.1  | LrgB membrane protein /hydrolase  | Brucella melitensis ATCC 23457 chromosome I (NC_012441)
αr14  | sRNA  | Bm23457r14CI1  | D  | 358976  | 359082  | \-  | sRNA  | Brucella melitensis ATCC 23457 chromosome I (NC_012441)
αr14  | gene  | BMEA_A0366  | D  | 359302  | 360543  | YP_002732106.1  | DUF900, alpha/beta hydrolase  | Brucella melitensis ATCC 23457 chromosome I (NC_012441)
αr14  | gene  | BAbS19_I03260  | D  | 357382  | 358089  | YP_001934341.1  | LrgB membrane protein /hydrolase  | Brucella abortus S19 chromosome I (NC_010742)
αr14  | sRNA  | BaS19r14CI1  | D  | 358310  | 358417  | \-  | sRNA  | Brucella abortus S19 chromosome I (NC_010742)
αr14  | gene  | BAbS19_I03270  | D  | 358635  | 359876  | YP_001934342.1  | DUF900, alpha/beta hydrolase  | Brucella abortus S19 chromosome I (NC_010742)
αr14  | gene  | BruAb1_0352  | D  | 358997  | 359704  | YP_221113.1  | membrane protein  | Brucella abortus bv. 1 str. 9-941 chromosome I (NC_006932)
αr14  | sRNA  | Ba19941r14CI1  | D  | 359925  | 360032  | \-  | sRNA  | Brucella abortus bv. 1 str. 9-941 chromosome I (NC_006932)
αr14  | gene  | BruAb1_0355  | D  | 361578  | 362459  | YP_221115.1  | pantoate—beta-alanine ligase  | Brucella abortus bv. 1 str. 9-941 chromosome I (NC_006932)
αr14  | gene  | BAB1_0356  | D  | 355365  | 356072  | YP_413824.1  | LrgB membrane protein /hydrolase  | Brucella melitensis biovar Abortus 2308 chromosome I (NC_007618)
αr14  | sRNA  | Bmar14CI1  | D  | 356293  | 356400  | \-  | sRNA  | Brucella melitensis biovar Abortus 2308 chromosome I (NC_007618)
αr14  | gene  | BAB1_0358  | D  | 356618  | 357859  | YP_413825.1  | DUF900, alpha/beta hydrolase  | Brucella melitensis biovar Abortus 2308 chromosome I (NC_007618)
αr14  | gene  | BR0326  | D  | 337104  | 337811  | NP_697360.1  | DUF900, alpha/beta hydrolase  | Brucella suis 1330 chromosome I (NC_004310)
αr14  | sRNA  | Bs1330r14CI1  | D  | 338032  | 338139  | \-  | sRNA  | Brucella suis 1330 chromosome I (NC_004310)
αr14  | gene  | BR0328  | D  | 338358  | 339599  | NP_697362.1  | tRNA (uracil-5-)-methyltransferase  | Brucella suis 1330 chromosome I (NC_004310)
αr14  | gene  | Smed_5352  | R  | 313859  | 314596  | YP_001314057.1  | adenylate guanylate cyclase  | Sinorhizobium medicae WSM419 plasmid pSMED02 (NC_009621)
αr14  | sRNA  | Smedr14p021  | D  | 316304  | 316428  | \-  | sRNA  | Sinorhizobium medicae WSM419 plasmid pSMED02 (NC_009621)
αr14  | gene  | Smed_5353  | R  | 316485  | 317621  | YP_001314058.1  | DNA polymerase I  | Sinorhizobium medicae WSM419 plasmid pSMED02 (NC_009621)
αr14  | gene  | RHE_PF00022  | R  | 22159  | 22494  | YP_472643.1  | hypothetical protein  | Rhizobium etli CFN 42 plasmid p42f (NC_007766)
αr14  | sRNA  | ReCFNr14f  | D  | 22818  | 22935  | \-  | sRNA  | Rhizobium etli CFN 42 plasmid p42f (NC_007766)
αr14  | gene  | RHE_PF00023  | D  | 23286  | 23726  | YP_472644.1  | carbon-sulfur lyase  | Rhizobium etli CFN 42 plasmid p42f (NC_007766)
αr14  | gene  | Oant_3865  | D  | 1275426  | 1275572  | YP_001372399.1  | DUF1127  | Brucella anthropi ATCC 49188 chromosome 2 (NC_009668)
αr14  | sRNA  | Oar14CII2  | D  | 1275649  | 1275772  | \-  | sRNA  | Brucella anthropi ATCC 49188 chromosome 2 (NC_009668)
αr14  | gene  | Oant_3866  | R  | 1275787  | 1277010  | YP_001372400.1  | membrane protein  | Brucella anthropi ATCC 49188 chromosome 2 (NC_009668)
αr14  | gene  | Rleg2_4668  | D  | 305380  | 306273  | YP_002278660.1  | L-isoaspartate O-methyltransferase  | Rhizobium leguminosarum bv. trifolii WSM2304 plasmid pRLG201 (NC_011368)
αr14  | sRNA  | Rlt2304r14p011  | R  | 306339  | 306454  | \-  | sRNA  | Rhizobium leguminosarum bv. trifolii WSM2304 plasmid pRLG201 (NC_011368)
αr14  | gene  | Rleg2_4670  | R  | 306976  | 307923  | YP_002278662.1  | transposase IS110 family protein  | Rhizobium leguminosarum bv. trifolii WSM2304 plasmid pRLG201 (NC_011368)
αr14  | gene  | Mesci_6302  | D  | 240660  | 240910  | YP_004134462.1  | hypothetical protein  | Mesorhizobium ciceri biovar biserrulae WSM1271 chromosome I (NC_014918)
αr14  | sRNA  | Mcr14p01  | R  | 241412  | 241531  | \-  | sRNA  | Mesorhizobium ciceri biovar biserrulae WSM1271 chromosome I (NC_014918)
αr14  | gene  | Mesci_6303  | R  | 241784  | 242047  | YP_004134463.1  | hypothetical protein  | Mesorhizobium ciceri biovar biserrulae WSM1271 chromosome I (NC_014918)
αr14  | gene  | Mesci_2426  | D  | 2545134  | 2545592  | YP_004141622.1  | phasin  | Mesorhizobium ciceri biovar biserrulae WSM1271 chromosome I (NC_014923)
αr14  | sRNA  | Mcr14CI4  | D  | 2545673  | 2545788  | \-  | sRNA  | Mesorhizobium ciceri biovar biserrulae WSM1271 chromosome I (NC_014923)
αr14  | gene  | Mesci_2427  | D  | 2545962  | 2546038  | YP_004141623  | FAD dependent oxidoreductase  | Mesorhizobium ciceri biovar biserrulae WSM1271 chromosome I (NC_014923)
αr14  | gene  | Mesci_5119  | D  | 5264750  | 5265772  | YP_004144269.1  | LacI family transcription regulator  | Mesorhizobium ciceri biovar biserrulae WSM1271 chromosome I (NC_014923)
αr14  | sRNA  | Mcr14CI5  | D  | 5265891  | 5266009  | \-  | sRNA  | Mesorhizobium ciceri biovar biserrulae WSM1271 chromosome I (NC_014923)
αr14  | gene  | Mesci_5121  | R  | 5266103  | 5266693  | YP_004144271.1  | TetR family transcription regulator  | Mesorhizobium ciceri biovar biserrulae WSM1271 chromosome I (NC_014923)
αr14  | gene  | BOV_0890  | R  | 894271  | 895671  | YP_001258873.1  | tRNA (uracil-5-)-methyltransferase  | Brucella ovis ATCC 25840 chromosome I (NC_009505)
αr14  | sRNA  | Bor14CI2  | R  | 895749  | 895867  | \-  | sRNA  | Brucella ovis ATCC 25840 chromosome I (NC_009505)
αr14  | gene  | BOV_0891  | R  | 895931  | 896077  | YP_001258874.1  | DUF1127  | Brucella ovis ATCC 25840 chromosome I (NC_009505)
αr14  | gene  | BCAN_A0908  | R  | 865739  | 867139  | YP_001592741.1  | tRNA (uracil-5-)-methyltransferase  | Brucella canis ATCC 23365 chromosome I (NC_010103)
αr14  | sRNA  | Bcr14CI2  | R  | 867217  | 867335  | \-  | sRNA  | Brucella canis ATCC 23365 chromosome I (NC_010103)
αr14  | gene  | BCAN_A0909  | R  | 867399  | 867545  | YP_001592742.1  | DUF1127  | Brucella canis ATCC 23365 chromosome I (NC_010103)
αr14  | gene  | BSUIS_A0933  | R  | 887235  | 888635  | YP_001627570.1  | tRNA (uracil-5-)-methyltransferase  | Brucella suis ATCC 23445 chromosome I (NC_010169)
αr14  | sRNA  | Bs23445r14CI2  | R  | 888713  | 888831  | \-  | sRNA  | Brucella suis ATCC 23445 chromosome I (NC_010169)
αr14  | gene  | BSUIS_A0934  | R  | 888895  | 889041  | YP_001627571.1  | hypothetical protein  | Brucella suis ATCC 23445 chromosome I (NC_010169)
αr14  | gene  | BMI_I892  | R  | 871571  | 872971  | YP_003106830.1  | tRNA (uracil-5-)-methyltransferase  | Brucella microti CCM 4915 chromosome 1 (NC_013119)
αr14  | sRNA  | Bmir14CI2  | R  | 873049  | 873167  | \-  | sRNA  | Brucella microti CCM 4915 chromosome 1 (NC_013119)
αr14  | gene  | BMI_I893  | R  | 873231  | 873377  | YP_003106831.1  | DUF1127  | Brucella microti CCM 4915 chromosome 1 (NC_013119)
αr14  | gene  | BR0894  | R  | 867369  | 868769  | NP_697907.1  | tRNA (uracil-5-)-methyltransferase  | Brucella suis 1330 chromosome I (NC_004310)
αr14  | sRNA  | Bs1330r14CI2  | R  | 868847  | 868965  | \-  | sRNA  | Brucella suis 1330 chromosome I (NC_004310)
αr14  | gene  | BR0895  | R  | 869029  | 869175  | NP_697908.1  | DUF1127  | Brucella suis 1330 chromosome I (NC_004310)
αr14  | gene  | mlr7359  | D  | 6091731  | 6092324  | NP_107697.1  | transcription factor regulator  | Mesorhizobium loti MAFF303099 chromosome (NC_002678)
αr14  | sRNA  | Mlr14C5  | R  | 6092423  | 6092540  | \-  | sRNA  | Mesorhizobium loti MAFF303099 chromosome (NC_002678)
αr14  | gene  | mll7360  | R  | 6092659  | 6093681  | NP_107698.1  | transcription factor regulator  | Mesorhizobium loti MAFF303099 chromosome (NC_002678)
αr14  | gene  | BMEI1072  | D  | 1116469  | 1116615  | NP_539989.1  | DUF1127  | Brucella melitensis bv. 1 str. 16M chromosome (NC_003317)
αr14  | sRNA  | Bm16Mr14CI1  | D  | 1116661  | 1116787  | \-  | sRNA  | Brucella melitensis bv. 1 str. 16M chromosome (NC_003317)
αr14  | gene  | BMEI1073  | D  | 1116821  | 1118257  | NP_539990.1  | tRNA (uracil-5-)-methyltransferase  | Brucella melitensis bv. 1 str. 16M chromosome (NC_003317)
αr14  | gene  | BAbS19_I08530  | R  | 887399  | 888799  | YP_001934848.1  | tRNA (uracil-5-)-methyltransferase  | Brucella abortus S19 chromosome 1 (NC_010742)
αr14  | sRNA  | BaS19r14CI2  | R  | 888877  | 888995  | \-  | sRNA  | Brucella abortus S19 chromosome 1 (NC_010742)
αr14  | gene  | BAbS19_I08540  | R  | 889041  | 889187  | YP_001934849.1  | DUF1127  | Brucella abortus S19 chromosome 1 (NC_010742)
αr14  | gene  | BMEA_A0933  | R  | 888865  | 890265  | YP_002732640.1  | tRNA (uracil-5-)-methyltransferase  | Brucella melitensis ATCC 23457 chromosome I (NC_012441)
αr14  | sRNA  | Bm23457r14CI2  | R  | 890343  | 890461  | \-  | sRNA  | Brucella melitensis ATCC 23457 chromosome I (NC_012441)
αr14  | gene  | BMEA_A0934  | R  | 890507  | 890653  | YP_002732641.1  | DUF1127  | Brucella melitensis ATCC 23457 chromosome I (NC_012441)
αr14  | gene  | BruAb1_0906  | R  | 889098  | 890498  | YP_221632.1  | tRNA (uracil-5-)-methyltransferase  | Brucella abortus bv. 1 str. 9-941 chromosome I (NC_006932)
αr14  | sRNA  | Ba19941r14CI2  | R  | 890576  | 890694  | \-  | sRNA  | Brucella abortus bv. 1 str. 9-941 chromosome I (NC_006932)
αr14  | gene  | BruAb1_0907  | R  | 890740  | 890886  | YP_221633.1  | DUF1127  | Brucella abortus bv. 1 str. 9-941 chromosome I (NC_006932)
αr14  | gene  | BAB1_0913  | R  | 885376  | 886776  | YP_414338.1  | tRNA (uracil-5-)-methyltransferase  | Brucella melitensis biovar Abortus 2308 chromosome I (NC_007618)
αr14  | sRNA  | Bmar14CI2  | R  | 886854  | 886972  | \-  | sRNA  | Brucella melitensis biovar Abortus 2308 chromosome I (NC_007618)
αr14  | gene  | BAB1_0914  | R  | 887018  | 887164  | YP_414339.1  | oxidoreductase  | Brucella melitensis biovar Abortus 2308 chromosome I (NC_007618)
αr14  | gene  | Meso_4235  | R  | 134555  | 135097  | YP_665858.1  | hypothetical protein  | Mesorhizobium sp. BNC1 plasmid 1 (NC_008242)
αr14  | sRNA  | MsBCNr14p1  | R  | 135270  | 135386  | \-  | sRNA  | Mesorhizobium sp. BNC1 plasmid 1 (NC_008242)
αr14  | gene  | Meso_4236  | R  | 135539  | 136099  | YP_665859.1  | hypothetical protein  | Mesorhizobium sp. BNC1 plasmid 1 (NC_008242)
αr14  | gene  | mlr6541  | D  | 5350228  | 5350686  | NP_107027.1  | phasin  | Mesorhizobium loti MAFF303099 chromosome (NC_002678)
αr14  | sRNA  | Mlr14C4  | D  | 5350767  | 5350882  | \-  | sRNA  | Mesorhizobium loti MAFF303099 chromosome (NC_002678)
αr14  | gene  | mlr6543  | D  | 5351042  | 5351115  | \-  | two component regulator  | Mesorhizobium loti MAFF303099 chromosome (NC_002678)
αr14  | gene  | RL2059  | R  | 2172416  | 2173849  | YP_767657.1  | tRNA (uracil-5-)-methyltransferase  | Rhizobium leguminosarum bv. viciae 3841 (NC_008380)
αr14  | sRNA  | Rlvr14C2  | R  | 2174956  | 2175074  | \-  | sRNA  | Rhizobium leguminosarum bv. viciae 3841 (NC_008380)
αr14  | gene  | RL2060  | D  | 2175400  | 2176503  | YP_767658.1  | membrane protein  | Rhizobium leguminosarum bv. viciae 3841 (NC_008380)

## References

1. ↑ "A conserved α-proteobacterial small RNA contributes to osmoadaptation and symbiotic efficiency of rhizobia on legume roots". Environmental Microbiology 19 (7): 2661–2680. July 2017. doi:10.1111/1462-2920.13757. PMID 28401641. Bibcode: 2017EnvMi..19.2661R.
2. ↑ 2.0 2.1 2.2 "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. doi:10.1111/j.1365-2958.2007.05978.x. PMID 17971083.
3. ↑ 3.0 3.1 "Identification of chromosomal alpha-proteobacterial small RNAs by comparative genome analysis and detection in Sinorhizobium meliloti strain 1021". BMC Genomics 8 (467). December 2007. doi:10.1186/1471-2164-8-467. PMID 18093320.
4. ↑ 4.0 4.1 4.2 4.3 "Prediction of Sinorhizobium meliloti sRNA genes and experimental detection in strain 2011". BMC Genomics 9 (406): 416. September 2008. doi:10.1186/1471-2164-9-416. PMID 18793445.
5. ↑ 5.0 5.1 5.2 5.3 5.4 5.5 5.6 5.7 "Integration of physical and genetic maps of common bean through BAC-derived microsatellite markers". BMC Genomics 11 (245). July 2010. doi:10.1186/1471-2164-11-436. PMID 20637113.
6. ↑ I. L. Hofacker; W. Fontana; P. F. Stadler; L. S. Bonhoeffer; M. Tacker; P. Schuster (1994). "Fast folding and comparison of RNA secondary structures". Monatshefte für Chemie 125 (2): 167–188. doi:10.1007/BF00818163.
7. ↑ "RNAalifold: improved consensus structure prediction for RNA alignments". BMC Bioinformatics 9 (474). November 2008. doi:10.1186/1471-2105-9-474. PMID 19014431.
8. ↑ "Infernal 1.0: inference of RNA alignments". Bioinformatics 25 (10): 1335–7. May 2009. doi:10.1093/bioinformatics/btp157. PMID 19307242.
9. ↑ "Inferring Noncoding RNA Families and Classes by Means of Genome-Scale Structure-Based Clustering". PLOS Comput Biol 4 (65): e65. 2007. doi:10.1371/journal.pcbi.0030065. PMID 17432929. Bibcode: 2007PLSCB...3...65W.
10. ↑ "Promoter prediction in the rhizobia". Microbiology 152 (Pt 6): 1751–63. June 2006. doi:10.1099/mic.0.28743-0. PMID 16735738.
11. ↑ "RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach". Nucleic Acids Research 38 (Web Server issue): W299–307. July 2010. doi:10.1093/nar/gkq531. PMID 20542910.
12. ↑ "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. doi:10.1093/nar/gkq1110. PMID 21051347.
13. ↑ "Fitting a mixture model by expectation maximization to discover motifs in biopolymers". Proceedings. International Conference on Intelligent Systems for Molecular Biology (AAAI Press, Menlo Park, California) 2: 28–36. 1994. PMID 7584402.
14. ↑ "GOPET: a tool for automated predictions of Gene Ontology terms". BMC Bioinformatics 7. March 2006. doi:10.1186/1471-2105-7-161. PMID 16549020.
15. ↑ "Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research". Bioinformatics 21 (18): 3674–6. September 2005. doi:10.1093/bioinformatics/bti610. PMID 16081474. https://hal.archives-ouvertes.fr/hal-01238282/file/Rokitta_2014_BMC Genomics.pdf.
16. ↑ "ProtSweep, 2Dsweep and DomainSweep: protein analysis suite at DKFZ". Nucleic Acids Research 35 (Web Server issue): W444–50. July 2007. doi:10.1093/nar/gkm364. PMID 17526514.

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