αr45 is a family of bacterial small non-coding RNAs with representatives in a broad group of α-proteobacteria from the order Hyphomicrobiales. The first member of this family (Smr45C) was found in a Sinorhizobium meliloti 1021 locus located in the chromosome (C). Further homology and structure conservation analysis identified homologs in several nitrogen-fixing symbiotic rhizobia (i.e. S. medicae, S. fredii, Rhizobium 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), in Bartonella species (i.e. B. henselae, B. clarridgeiae, B. tribocorum, B. quintana, B. bacilliformis, B. grahamii), in several members of the Xanthobactereacea family (i.e. Azorhizobium caulinodans, Starkey novella, Xhantobacter autotrophicus), and in some representatives of the Beijerinckiaceae family (i.e. Methylocella silvestris, Beijerinckia indica subsp. indica). αr45C RNA species are 147-153 nt long (Table 1) and share a well defined common secondary structure (Figure 1). All of the αr45 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).
Discovery and Structure
editSmr45C sRNA was 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) . Northern hybridization experiments confirmed that the predicted smr45C locus did express a single transcript of 130-179 nt length, which accumulated differentially in free-living and endosymbiotic bacteria. TAP-based 5’-RACE experiments mapped the transcription start site (TSS) of the full-length Smr45C transcript to the 3,105,445 nt position in the S. meliloti 1021 genome (http://iant.toulouse.inra.fr/bacteria/annotation/cgi/rhime.cgi) whereas the 3’-end was initially assumed to be located at the 3,105,265 nt position matching the last residue of a short stretch of Us (Figure 2) of a putative, but low-rated, Rho-independent terminator. Recent deep sequencing-based characterization of the small RNA fraction (50-350 nt) of S. meliloti 2011 further confirmed the expression of Smr45C (here referred to as SmelC706), and mapped the full-length transcript to the same 5’ end and to the 3' end position 3,105,298.[2]
The nucleotide sequence of Smr45C was initially used as query to search against the Rfam database (version 10.0; http://www.sanger.ac.uk/Software/Rfam). This homology search rendered no matches to known bacterial sRNA in this database. Smr45C 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)[3] (Figure 2). This CM was used in a further search for new members of the αr45 family in the existing bacterial genomic databases.
| CM model | Name | GI accession number | begin | end | strand | %GC | length | Organism |
|---|---|---|---|---|---|---|---|---|
| αr45 | Smr45C | gi|15963753|ref|NC_003047.1| | 3105265 | 3105445 | - | 59 | 148 | Sinorhizobium meliloti 1021 |
| αr45 | Smedr45C | gi|150395228|ref|NC_009636.1| | 2892729 | 2892909 | - | 59 | 148 | Sinorhizobium medicae WSM419 chromosome |
| αr45 | Sfr45C | gi|227820587|ref|NC_012587.1| | 3069095 | 3069275 | - | 59 | 148 | Sinorhizobium fredii NGR234 chromosome |
| αr45 | Atr45C | gi|159185562|ref|NC_003063.2| | 205601 | 205782 | - | 57 | 148 | Agrobacterium tumefaciens str. C58 chromosome linear |
| αr45 | ReCIATr45C | gi|190889639|ref|NC_010994.1| | 3953756 | 3953936 | - | 59 | 148 | Rhizobium etli CIAT 652 |
| αr45 | Arr45CI | gi|222084201|ref|NC_011985.1| | 3124263 | 3124442 | - | 57 | 147 | Agrobacterium radiobacter K84 chromosome 1 |
| αr45 | Rlt2304r45C | gi|209547612|ref|NC_011369.1| | 3504209 | 3504389 | - | 59 | 148 | Rhizobium leguminosarum bv. trifolii WSM2304 |
| αr45 | Avr45CI | gi|222147015|ref|NC_011989.1| | 3166967 | 3167147 | - | 59 | 148 | Agrobacterium vitis S4 chromosome 1 |
| αr45 | Rlvr45C | gi|116249766|ref|NC_008380.1| | 4405210 | 4405390 | - | 59 | 148 | Rhizobium leguminosarum bv. viciae 3841 |
| αr45 | Rlt1325r45C | gi|241202755|ref|NC_012850.1| | 3739371 | 3739551 | - | 59 | 148 | Rhizobium leguminosarum bv. trifolii WSM1325 |
| αr45 | ReCFNr45C | gi|86355669|ref|NC_007761.1| | 3840978 | 3841158 | - | 59 | 148 | Rhizobium etli CFN 42 |
| αr45 | Mlr45C | gi|57165207|ref|NC_002678.2| | 2390687 | 2390867 | - | 62 | 147 | Mesorhizobium loti MAFF303099 chromosome |
| αr45 | Mcr45C | gi|319779749|ref|NC_014923.1| | 1999110 | 1999290 | + | 63 | 147 | Mesorhizobium ciceri biovar biserrulae WSM1271 chromosome |
| αr45 | Bcr45CII | gi|161620094|ref|NC_010104.1| | 97148 | 97326 | + | 60 | 143 | Brucella canis ATCC 23365 chromosome II |
| αr45 | Bs23445r45CII | gi|163844199|ref|NC_010167.1| | 97254 | 97432 | + | 60 | 146 | Brucella suis ATCC 23445 chromosome II |
| αr45 | Bm16Mr45CII | gi|17988344|ref|NC_003318.1| | 1172651 | 1172829 | - | 60 | 146 | Brucella melitensis bv. 1 str. 16M chromosome II |
| αr45 | BaS19r45CII | gi|189022234|ref|NC_010740.1| | 96948 | 97126 | + | 60 | 146 | Brucella abortus S19 chromosome 2 |
| αr45 | Bm23457r45CII | gi|225685871|ref|NC_012442.1| | 97129 | 97307 | + | 60 | 146 | Brucella melitensis ATCC 23457 chromosome II |
| αr45 | Bs1330r45CII | gi|56968493|ref|NC_004311.2| | 97128 | 97306 | + | 60 | 146 | Brucella suis 1330 chromosome II |
| αr45 | Ba19941r45CII | gi|62316961|ref|NC_006933.1| | 96885 | 97063 | + | 60 | 146 | Brucella abortus bv. 1 str. 9-941 chromosome II |
| αr45 | Bmar45CII | gi|83268957|ref|NC_007624.1| | 96950 | 97128 | + | 60 | 146 | Brucella melitensis biovar Abortus 2308 chromosome II |
| αr45 | Bor45CII | gi|148557829|ref|NC_009504.1| | 96814 | 96992 | + | 60 | 146 | Brucella ovis ATCC 25840 chromosome II |
| αr45 | Bmir45CII | gi|256014795|ref|NC_013118.1| | 97102 | 97280 | + | 60 | 146 | Brucella microti CCM 4915 chromosome 2 |
| αr45 | Oar45CII | gi|153010078|ref|NC_009668.1| | 1673505 | 1673683 | - | 60 | 146 | Brucella anthropi ATCC 49188 chromosome 2 |
| αr45 | MsBNCr45C | gi|110632362|ref|NC_008254.1| | 2952752 | 2952930 | + | 60 | 146 | Mesorhizobium sp. BNC1 |
| αr45 | Bahr45C | gi|49474831|ref|NC_005956.1| | 1421835 | 1422014 | - | 54 | 147 | Bartonella henselae str. Houston-1 |
| αr45 | Bacr45C | gi|319898193|ref|NC_014932.1| | 1277567 | 1277776 | - | 54 | 147 | Bartonella clarridgeiae 73 |
| αr45 | Batr45C | gi|163867306|ref|NC_010161.1| | 1865843 | 1866022 | - | 54 | 147 | Bartonella tribocorum CIP 105476 |
| αr45 | Baqr45C | gi|49473688|ref|NC_005955.1| | 1185140 | 1185319 | - | 53 | 147 | Bartonella quintana str. Toulouse |
| αr45 | Babr45C | gi|121601635|ref|NC_008783.1| | 1120052 | 1120229 | - | 56 | 147 | Bartonella bacilliformis KC583 |
| αr45 | Bagr45C | gi|240849682|ref|NC_012846.1| | 1761390 | 1761567 | - | 53 | 147 | Bartonella grahamii as4aup |
| αr45 | Acr45C | gi|158421624|ref|NC_009937.1| | 385443 | 385629 | - | 64 | 154 | Azorhizobium caulinodans ORS 571 |
| αr45 | Stnr45C | gi|298290017|ref|NC_014217.1| | 4175745 | 4175703 | + | 65 | 156 | Starkeya novella DSM 506 chromosome |
| αr45 | Xar45C | gi|154243958|ref|NC_009720.1| | 2404335 | 2404523 | - | 63 | 156 | Xanthobacter autotrophicus Py2 chromosome |
| αr45 | Mesr45C | gi|217976200|ref|NC_011666.1| | 1244610 | 1244795 | - | 64 | 155 | Methylocella silvestris BL2 chromosome |
| αr45 | Beir45C | gi|182677002|ref|NC_010581.1| | 1241316 | 1241498 | - | 61 | 153 | Beijerinckia indica subsp. indica ATCC 9039 chromosome |
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[4] with very similar predictions. The manual inspection of the sequences found with the CM using Infernal allowed finding 39 closer homolog sequences, all of them present as single chromosomal copies in the α-proteobacterial genomes. The rhizobial species encoding these homologs to Smr45C were: S. medicae and S. fredii, two R. leguminosarum trifolii strains (WSM304 and WSM35), 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, Brucella species (B. ovis, B. canis, B. abortus, B. microtis, and several biobars of B. melitensis), Brucella anthropi, the Mesorhizobium species loti, M. ciceri and M. BNC., Bartonella species (i.e. B. henselae, B. clarridgeiae, B. tribocorum, B. quintana, B. bacilliformis, B. grahamii). All these sequences showed significant Infernal E-values (8.93E-40 – 6.12E-36) and bit-scores. The rest of the sequences found with the model showed high E-values between (3.28E-06 and 4.56E-04) but lower bit-scores and are encoded by several members of the Xanthobactereacea family (i.e. A. caulinodans, Sa. novella, X. autotrophicus), Me. silvestris, and Be. indica subsp. indica.
Expression information
editThe expression of Smr45C in S. meliloti 1021 was assessed 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] The expression of Smr45C in free-living bacteria was found to be growth-dependent, being the gene strongly down-regulated when bacteria entered the stationary phase. However, luteolin moderately stimulated the expression of Smr45C (2-fold) but the gene was not detectable in endosymbiotic bacteria.
Recent co-inmuno precipitation experiments[7] corroborate that Smr45C, does bind the bacterial protein Hfq for efficient target binding.
Promoter Analysis
editAll the promoter regions of the αr45 family members examined so far are very conserved in a sequence stretch extending up to 80 bp upstream of the transcription start site of the sRNA. All closest homolog loci have recognizable σ70-dependent promoters showing a -35/-10 consensus motif CTTAGAC-n17-CTATAT, which has been previously shown to be widely conserved among several other genera in the α-subgroup of proteobacteria.[8] To identify binding sites for other known transcription factors we used the fasta sequences provided by RegPredict[9](http://regpredict.lbl.gov/regpredict/help.html), and used those position weight matrices (PSWM) provided by RegulonDB[10] (http://regulondb.ccg.unam.mx). We built PSWM for each transcription factor from the RegPredict sequences using the Consensus/Patser program, choosing the best final matrix for motif lengths between 14 and 30 bps a threshold average E-value < 10E-10 for each matrix was established, (see "Thresholded consensus" in http://gps-tools2.its.yale.edu). Moreover, we searched for conserved unknown motifs using MEME[11] (http://meme.sdsc.edu/meme4_6_1/intro.html) and used relaxed regular expressions (i.e. pattern matching) over all Smr45C homologs promoters.
This study predicts differences in the regulation of the expression of the αr45 representatives in the different α-proteobacterial species. The Sinorhizobium, Rhizobium, and Agrobacterium groups presented a very well conserved motif that matches the consensus sequence recognized by the maltose repressor Mall. Furthermore, the promoters of the αr45 members of the . Furthermore, the promoters of the αr45 members of the Sinorhizobium group presented an additional conserved region between positions -60 and -85 (boxed in orange in Figure 4), with significant similarity to the matrix SMb21598_Rhizobiales from Reg_Predict. This binding site corresponds to a transcriptional regulator of the LacI family. The Rhizobium group, presented also a well conserved motif in this region for which no significant similarity could be found (marked in green in Figure 4). This analysis also revealed an extended conserved sequence stretch among the promoters of the Brucella and Bartonella αr45 sRNA loci, but no known transcription factor binding sites were recognizable in these motifs.
Genomic Context
editAll members of the αr45 family are trans-encoded sRNAs transcribed from independent promoters in chromosomal IGRs. Most of the neighboring genes of the seed alignment's members were not annotated and thus were further manually curated.[12][13][14] The genomic regions of the αr45 sRNAs from Sinorhizobium, Rhizobium, A. vitis and A. radiobacter exhibited a great degree of conservation including the upstream and downstream genes which have been predicted to code for a LysR family transcriptional regulator and an ornithine descarboxilase, respectively (solo como aclaración, upstream and downstream se refieren al sentido de transcripción). Partial synteny of the αr45 genomic regions was observed in the Mesorhizobium and Brucella species where instead of aLysR family transcriptional regulator' gene an amidase coding gene was found. In Bartonella species the αr45 upstream gene was always found to code for a protein containing a rhodanase domain. In the genomic regions of the αr45 homologs in more distantly related α-proteobacteria (e.g. Starkeya, Metthylocella or Xanthobacter species) synteny was restricted to the downstream ornithine descarboxylase gene.
| Family | Feature | Name | Strand | Begin | End | Protein name | Annotation | Organism |
|---|---|---|---|---|---|---|---|---|
| αr45 | gene | SMc02983 | R | 3103912 | 3105051 | NP_386981.1 | Ornithine or Arginine decarboxylase | Sinorhizobium meliloti 1021 (NC_003047) |
| αr45 | sRNA | Smr45C | R | 3105265 | 3105445 | - | - | Sinorhizobium meliloti 1021 (NC_003047) |
| αr45 | gene | SMc02984 | D | 3105638 | 3106531 | NP_386982.1 | LysR family transcriptional regulator | Sinorhizobium meliloti 1021 (NC_003047) |
| αr45 | gene | Smed_2772 | R | 2891376 | 2892509 | YP_001328437.1 | Ornithine decarboxylase | Sinorhizobium medicae WSM419 chromosome (NC_009636) |
| αr45 | sRNA | Smedr45C | R | 2892729 | 2892909 | - | - | Sinorhizobium medicae WSM419 chromosome (NC_009636) |
| αr45 | gene | Smed_2773 | D | 2893045 | 2893959 | YP_001328438.1 | LysR family transcriptional regulator | Sinorhizobium medicae WSM419 chromosome (NC_009636) |
| αr45 | gene | NGR_c29260 | R | 3067740 | 3068873 | YP_002827423.1 | Ornithine decarboxylase | Sinorhizobium fredii NGR234 chromosome(NC_012587) |
| αr45 | sRNA | Sfr45C | R | 3069095 | 3069275 | - | - | Sinorhizobium fredii NGR234 chromosome (NC_012587) |
| αr45 | gene | NGR_c29280 | D | 3069481 | 3070374 | YP_002827424.1 | LysR family transcriptional regulator | Sinorhizobium fredii NGR234 chromosome (NC_012587) |
| αr45 | gene | RL4156 | R | 4403850 | 4404983 | YP_769731.1 | Lisine-Ornithine decarboxylase | Rhizobium leguminosarum bv viciae 3841 (NC_008380) |
| αr45 | sRNA | Rlvr45C | R | 4405210 | 4405390 | - | - | Rhizobium leguminosarum bv viciae 3841 (NC_008380) |
| αr45 | gene | RL4157 | D | 4405512 | 4406405 | YP_769732.1 | LysR family transcriptional regulator | Rhizobium leguminosarum bv viciae 3841 (NC_008380) |
| αr45 | gene | RHECIAT_CH0003899 | R | 3952396 | 3953529 | YP_001980014.1 | Ornithine decarboxylase | Rhizobium etli CIAT 652 (NC_010994) |
| αr45 | sRNA | ReCIATr45C | R | 3953756 | 3953936 | - | - | Rhizobium etli CIAT 652 (NC_010994) |
| αr45 | gene | RHECIAT_CH0003900 | D | 3954059 | 3954952 | YP_001980015.1 | LysR family transcriptional regulator | Rhizobium etli CIAT 652 (NC_010994) |
| αr45 | gene | Rleg2_3390 | R | 3502850 | 3503983 | YP_002282883.1 | Ornithine decarboxylase | Rhizobium leguminosarum bv trifolii WSM2304 (NC_011369) |
| αr45 | sRNA | Rlt2304r45C | R | 3504209 | 3504389 | - | - | Rhizobium leguminosarum bv trifolii WSM2304 (NC_011369) |
| αr45 | gene | Rleg2_3391 | D | 3504512 | 3505405 | YP_002282884.1 | LysR family transcriptional regulator | Rhizobium leguminosarum bv trifolii WSM2304 (NC_011369) |
| αr45 | gene | Rleg_3689 | R | 3738011 | 3739144 | YP_002977471.1 | Ornithine decarboxylase | Rhizobium leguminosarum bv trifolii WSM1325 (NC_012850) |
| αr45 | sRNA | Rlt1325r45C | R | 3739371 | 3739551 | - | - | Rhizobium leguminosarum bv trifolii WSM1325 (NC_012850) |
| αr45 | gene | Rleg_3690 | D | 3739671 | 3740564 | YP_002977472.1 | LysR family transcriptional regulator | Rhizobium leguminosarum bv trifolii WSM1325 (NC_012850) |
| αr45 | gene | RHE_CH03628 | R | 3838931 | 3839521 | YP_471110.1 | acetyltransferase | Rhizobium etli CFN 42 (NC_007761) |
| αr45 | sRNA | ReCFNr45C | R | 3840978 | 3841158 | - | - | Rhizobium etli CFN 42 (NC_007761) |
| αr45 | gene | RHE_CH03631 | D | 3842303 | 3842944 | YP_471113.1 | DUF1007 | Rhizobium etli CFN 42 (NC_007761) |
| αr45 | gene | Avi_3806 | R | 3165600 | 3166733 | YP_002550752.1 | Ornithine decarboxylase | Agrobacterium vitis S4 chromosome 1 (NC_011989) |
| αr45 | sRNA | Avr45CI | R | 3166967 | 3167147 | - | - | Agrobacterium vitis S4 chromosome 1 (NC_011989) |
| αr45 | gene | Avi_3808 | D | 3167282 | 3168211 | YP_002550753.1 | LysR family transcriptional regulator | Agrobacterium vitis S4 chromosome 1 (NC_011989) |
| αr45 | gene | Arad_3911 | R | 3122903 | 3124036 | YP_002545680.1 | Ornithine decarboxylase | Agrobacterium radiobacter K84 chromosome 1 (NC_011985) |
| αr45 | sRNA | Arr45CI | R | 3124263 | 3124442 | - | - | Agrobacterium radiobacter K84 chromosome 1 (NC_011985) |
| αr45 | gene | Arad_3912 | D | 3124569 | 3125462 | YP_002545681.1 | LysR family transcriptional regulator | Agrobacterium radiobacter K84 chromosome 1 (NC_011985) |
| αr45 | gene | Atu3196 | R | 204249 | 205382 | NP_357406.2 | Ornithine decarboxylase | Agrobacterium tumefaciens str. C58 chromosome linear (NC_003063) |
| αr45 | sRNA | Atr45C | R | 205601 | 205782 | - | - | Agrobacterium tumefaciens str. C58 chromosome linear (NC_003063) |
| αr45 | gene | Atu3197 | D | 205919 | 206812 | NP_357405.2 | LysR family transcriptional regulator | Agrobacterium tumefaciens str. C58 chromosome linear (NC_003063) |
| αr45 | gene | Meso_2714 | R | 2951455 | 2952642 | YP_675256.1 | amidase | Mesorhizobium sp. BNC1 (NC_008254) |
| αr45 | sRNA | MsBNCr45C | D | 2952752 | 2952930 | - | - | Mesorhizobium sp. BNC1 (NC_008254) |
| αr45 | gene | Meso_2715 | D | 2953176 | 2954309 | YP_675257.1 | Ornithine decarboxylase | Mesorhizobium sp. BNC1 (NC_008254) |
| αr45 | gene | Oant_4245 | R | 1672055 | 1673188 | YP_001372774.1 | Ornithine decarboxylase | Brucella anthropi ATCC 49188 chromosome 2 (NC_009668) |
| αr45 | sRNA | Oar45CII | R | 1673505 | 1673683 | - | - | Brucella anthropi ATCC 49188 chromosome 2 (NC_009668) |
| αr45 | gene | Oant_4246 | D | 1673866 | 1675053 | YP_001372775.1 | amidase | Brucella anthropi ATCC 49188 chromosome 2 (NC_009668) |
| αr45 | gene | BOV_A0091 | R | 94529 | 95420 | A5VTL3 | amidase | Brucella ovis ATCC 25840 chromosome II (NC_009504) |
| αr45 | sRNA | Bor45CII | D | 96814 | 96992 | - | - | Brucella ovis ATCC 25840 chromosome II (NC_009504) |
| αr45 | gene | BOV_A0092 | D | 97214 | 98347 | YP_001257169.1 | Ornithine decarboxylase | Brucella ovis ATCC 25840 chromosome II (NC_009504) |
| αr45 | sRNA | Bcr45CII | D | 97148 | 97326 | - | - | Brucella canis ATCC 23365 chromosome II (NC_010104) |
| αr45 | gene | BCAN_B0102 | R | 95758 | 96963 | YP_001594073.1 | amidase | Brucella canis ATCC 23365 chromosome II (NC_010104) |
| αr45 | gene | BCAN_B0104 | D | 97548 | 98681 | YP_001594074.1 | Lisine-Ornithine decarboxylase | Brucella canis ATCC 23365 chromosome II (NC_010104) |
| αr45I | sRNA | Bs23445r45CII | D | 97254 | 97432 | - | - | Brucella suis ATCC 23445 chromosome II (NC_010167) |
| αr45 | gene | BSUIS_B0104 | R | 95864 | 97069 | YP_001621952.1 | amidase | Brucella suis ATCC 23445 chromosome II (NC_010167) |
| αr45 | gene | BSUIS_B0106 | D | 97654 | 98787 | YP_001621953.1 | Lisine-Ornithine decarboxylase | Brucella suis ATCC 23445 chromosome II (NC_010167) |
| αr45 | sRNA | Bm16Mr45CII | R | 1172651 | 1172829 | - | - | Brucella melitensis bv. 1 str. 16M chromosome II (NC_003318) |
| αr45 | gene | BMEII1133 | R | 1171296 | 1172429 | NP_542111.1 | Ornithine decarboxylase | Brucella melitensis bv. 1 str. 16M chromosome II (NC_003318) |
| αr45 | gene | BMEII1134 | D | 1173014 | 1174219 | NP_542112.1 | amidase | Brucella melitensis bv. 1 str. 16M chromosome II (NC_003318) |
| αr45 | sRNA | BaS19r45CII | D | 96948 | 97126 | - | - | Brucella abortus S19 chromosome 2 (NC_010740) |
| αr45 | gene | BAbS19_II00900 | R | 95559 | 96764 | YP_001932063.1 | amidase | Brucella abortus S19 chromosome 2 (NC_010740) |
| αr45 | gene | BAbS19_II00910 | D | 97348 | 98481 | YP_001932064.1 | Ornithine decarboxylase | Brucella abortus S19 chromosome 2 (NC_010740) |
| αr45 | sRNA | Bm23457r45CII | D | 97129 | 97307 | - | - | Brucella melitensis ATCC 23457 chromosome II (NC_012442) |
| αr45 | gene | BMEA_B0101 | R | 95739 | 96944 | YP_002733935.1 | amidase | Brucella melitensis ATCC 23457 chromosome II (NC_012442) |
| αr45 | gene | BMEA_B0103 | D | 97529 | 98662 | YP_002733936.1 | Lisine-Ornithine decarboxylase | Brucella melitensis ATCC 23457 chromosome II (NC_012442) |
| αr45 | sRNA | Bmir45CII | D | 97102 | 97280 | - | - | Brucella microti CCM 4915 chromosome 2 (NC_013118) |
| αr45 | gene | BMI_II99 | R | 95713 | 96918 | YP_003104900.1 | amidase | Brucella microti CCM 4915 chromosome 2 (NC_013118) |
| αr45 | gene | BMI_II100 | D | 97502 | 98635 | YP_003104901.1 | Ornithine decarboxylase | Brucella microti CCM 4915 chromosome 2 (NC_013118) |
| αr45 | sRNA | Bs1330r45CII | D | 97128 | 97306 | - | - | Brucella suis 1330 chromosome II (NC_004311) |
| αr45 | gene | BRA0099 | R | 95738 | 96943 | NP_699304.1 | amidase | Brucella suis 1330 chromosome II (NC_004311) |
| αr45 | gene | BRA0100 | D | 97528 | 98661 | NP_699305.1 | Ornithine Arginine decarboxylase | Brucella suis 1330 chromosome II (NC_004311) |
| αr45 | sRNA | Ba19941r45CII | D | 96885 | 97063 | - | - | Brucella abortus bv. 1 str. 9-941 chromosome II (NC_006933) |
| αr45 | gene | BruAb2_0098 | R | 95495 | 96700 | YP_222910.1 | amidase | Brucella abortus bv. 1 str. 9-941 chromosome II (NC_006933) |
| αr45 | gene | BruAb2_0099 | D | 97285 | 98418 | YP_222911.1 | Ornithine Arginine decarboxylase | Brucella abortus bv. 1 str. 9-941 chromosome II (NC_006933) |
| αr45 | sRNA | Bmar45CII | D | 96950 | 97128 | - | - | Brucella melitensis biovar Abortus 2308 chromosome II (NC_007624) |
| αr45 | gene | BAB2_0097 | R | 95560 | 96765 | YP_418341.1 | amidase | Brucella melitensis biovar Abortus 2308 chromosome II (NC_007624) |
| αr45 | gene | BAB2_0098 | D | 97350 | 98483 | YP_418342.1 | Ornithine Arginine decarboxylase | Brucella melitensis biovar Abortus 2308 chromosome II (NC_007624) |
| αr45 | gene | Mesci_1912 | R | 1997804 | 1999000 | YP_004141115.1 | amidase | Mesorhizobium ciceri biovar biserrulae WSM1271 chromosome (NC_014923) |
| αr45 | sRNA | Mcr45C | D | 1999110 | 1999290 | - | - | Mesorhizobium ciceri biovar biserrulae WSM1271 chromosome (NC_014923) |
| αr45 | gene | Mesci_1913 | D | 1999541 | 2000674 | YP_004141116.1 | Ornithine decarboxylase | Mesorhizobium ciceri biovar biserrulae WSM1271 chromosome (NC_014923) |
| αr45 | gene | mll2974 | R | 2389301 | 2390434 | NP_104188.1 | Ornithine decarboxylase | Mesorhizobium loti MAFF303099 chromosome (NC_002678) |
| αr45 | sRNA | Mlr45C | R | 2390687 | 2390867 | - | - | Mesorhizobium loti MAFF303099 chromosome (NC_002678) |
| αr45 | gene | mlr2975 | D | 2390977 | 2392173 | NP_104189.1 | amidase | Mesorhizobium loti MAFF303099 chromosome (NC_002678) |
| αr45 | gene | BH12730 | R | 1420457 | 1421590 | YP_034014.1 | Ornithine decarboxylase | Bartonella henselae str. Houston-1 (NC_005956) |
| αr45 | sRNA | Bahr45C | R | 1421835 | 1422014 | - | - | Bartonella henselae str. Houston-1 (NC_005956) |
| αr45 | gene | BH12750 | D | 1422471 | 1423014 | Pseudogen | Bartonella henselae str. Houston-1 (NC_005956) | |
| αr45 | gene | BARCL_1139 | R | 1276216 | 1277577 | YP_004159385.1 | Lisine-Ornithine decarboxylase | Bartonella clarridgeiae 73 (NC_014932) |
| αr45 | sRNA | Bacr45C | R | 1277597 | 1277776 | - | - | Bartonella clarridgeiae 73 (NC_014932) |
| αr45 | gene | BARCL_1140 | R | 1278001 | 1278918 | YP_004159386.1 | rhodanese domain. | Bartonella clarridgeiae 73 (NC_014932) |
| αr45 | gene | Btr_1749 | R | 1864467 | 1865600 | YP_001610035.1 | Lisine-Ornithine decarboxylase | Bartonella tribocorum CIP 105476 (NC_010161) |
| αr45 | sRNA | Batr45C | R | 1865843 | 1866022 | - | - | Bartonella tribocorum CIP 105476 (NC_010161) |
| αr45 | gene | Btr_1751 | R | 1867923 | 1868852 | YP_001610036.1 | rhodanese domain. | Bartonella tribocorum CIP 105476 (NC_010161) |
| αr45 | gene | BQ10050 | R | 1183759 | 1184892 | YP_032587.1 | Ornithine decarboxylase | Bartonella quintana str. Toulouse (NC_005955) |
| αr45 | sRNA | Baqr45C | R | 1185140 | 1185319 | - | - | Bartonella quintana str. Toulouse (NC_005955) |
| αr45 | gene | BQ10070 | R | 1186001 | 1186915 | YP_032589.1 | rhodanese domain. | Bartonella quintana str. Toulouse (NC_005955) |
| αr45 | sRNA | Babr45C | R | 1120052 | 1120229 | - | - | Bartonella bacilliformis KC583 (NC_008783) |
| αr45 | gene | BARBAKC583_1090 | R | 1118676 | 1119809 | YP_989352.1 | pyridoxal-dependent decarboxylas | Bartonella bacilliformis KC583 (NC_008783) |
| αr45 | gene | BARBAKC583_1091 | R | 1120463 | 1121380 | YP_989353.1 | rhodanese domain. | Bartonella bacilliformis KC583 (NC_008783) |
| αr45 | sRNA | Bagr45C | R | 1761390 | 1761567 | - | - | Bartonella grahamii as4aup (NC_012846) |
| αr45 | gene | Bgr_15560 | R | 1760016 | 1761149 | YP_002972413.1 | Ornithine decarboxylase | Bartonella grahamii as4aup (NC_012846) |
| αr45 | gene | Bgr_15590 | D | 1763885 | 1764550 | YP_002972415.1 | 2-dehydro-3-deoxyphosphogluconate aldolase | Bartonella grahamii as4aup (NC_012846) |
| αr45 | gene | AZC_0333 | R | 384008 | 385138 | YP_001523249.1 | Ornithine decarboxylase | Azorhizobium caulinodans ORS 571 (NC_009937) |
| αr45 | sRNA | Acr45C | R | 385443 | 385629 | - | - | Azorhizobium caulinodans ORS 571 (NC_009937) |
| αr45 | gene | AZC_0334 | D | 386047 | 387324 | YP_001523250.1 | 5-aminolevulinate synthase | Azorhizobium caulinodans ORS 571 (NC_009937) |
| αr45 | gene | Snov_3938 | D | 4175011 | 4175250 | YP_003695827.1 | hypothetical protein | Starkeya novella DSM 506 chromosome (NC_014217) |
| αr45 | sRNA | Stnr45C | D | 4175515 | 4175703 | - | - | Starkeya novella DSM 506 chromosome (NC_014217) |
| αr45 | gene | Snov_3939 | D | 4175960 | 4177090 | YP_003695828.1 | Ornithine decarboxylase | Starkeya novella DSM 506 chromosome (NC_014217) |
| αr45 | gene | Xaut_2140 | R | 2402902 | 2404032 | YP_001417041.1 | Ornithine decarboxylase | Xanthobacter autotrophicus Py2 chromosome (NC_009720) |
| αr45 | sRNA | Xar45C | R | 2404335 | 2404523 | - | - | Xanthobacter autotrophicus Py2 chromosome (NC_009720) |
| αr45 | gene | Xaut_2141 | D | 2404953 | 2405258 | YP_001417042.1 | hypothetical protein | Xanthobacter autotrophicus Py2 chromosome (NC_009720) |
| αr45 | gene | Msil_1157 | R | 1243178 | 1244308 | YP_002361488.1 | Ornithine decarboxylase | Methylocella silvestris BL2 chromosome (NC_011666) |
| αr45 | sRNA | Mesr45C | R | 1244610 | 1244795 | - | - | Methylocella silvestris BL2 chromosome (NC_011666) |
| αr45 | gene | Msil_1158 | D | 1245160 | 1246743 | YP_002361489.1 | glucan biosynthesis protein | Methylocella silvestris BL2 chromosome (NC_011666) |
| αr45 | gene | Bind_1080 | R | 1239883 | 1241013 | YP_001832212.1 | Ornithine decarboxylase | Beijerinckia indica subsp. indica ATCC 9039 chromosome (NC_010581) |
| αr45 | sRNA | Beir45C | R | 1241316 | 1241498 | - | - | Beijerinckia indica subsp. indica ATCC 9039 chromosome (NC_010581) |
| αr45 | gene | Bind_1081 | D | 1242373 | 1243974 | YP_001832213.1 | glucan biosynthesis protein | Beijerinckia indica subsp. indica ATCC 9039 chromosome (NC_010581) |
| αr45 | gene | RPE_4802 | R | 5380582 | 5381724 | YP_783701.1 | Ornithine decarboxylase | Rhodopseudomonas palustris BisA53 chromosome (NC_008435) |
| αr45 | sRNA | Rhpr45C | R | 5381912 | 5382109 | - | - | Rhodopseudomonas palustris BisA53 chromosome (NC_008435) |
| αr45 | gene | RPE_4803 | R | 5382436 | 5382696 | YP_783702.1 | hypothetical protein | Rhodopseudomonas palustris BisA53 chromosome (NC_008435) |
References
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