| [B] Corynebacterium diphtheriae | CORDI01486 | RIMM_CORDI | Similar to Mycobacterium leprae probable 16S rRNA processing protein RimM or ML1616 or MLCB250.34 SW:RIMM_MYCLE (O33016) (179 aa) fasta scores: E(): 1.4e-23, 47.12% id in 174 aa, and to Bacillus halodurans probable 16S rRNA processing protein RimM or BH2480 SW:RIMM_BACHD (Q9KA14) (173 aa) fasta scores: E(): 2.3e-12, 34.5% id in 171 aa Putative 16s rRNA processing protein |
| [B] Corynebacterium efficiens | COREF01905 | RIMM_COREF | similar to AP001515-214|BAB06199.1| percent identity: 31 in 168 aa putative 16S rRNA processing protein |
| [B] Corynebacterium glutamicum | CORGL02562 | RIMM_CORGL | Ribosome maturation factor rimM |
| [B] Corynebacterium glutamicum (strain R) | CORGB01972 | RIMM_CORGB | Hypothetical protein |
| [B] Mycobacterium abscessus (strain ATCC 19977 / DSM 44196) | MYCA903198 | RIMM_MYCA9 | Probable 16S rRNA processing protein RimM |
| [B] Mycobacterium avium (strain 104) | MYCA103550 | RIMM_MYCA1 | 16S rRNA processing protein RimM identified by match to protein family HMM PF01782; match to protein family HMM PF05239; match to protein family HMM TIGR02273 |
| [B] Mycobacterium paratuberculosis | MYCPA02945 | RIMM_MYCPA | RimM |
| [B] Mycobacterium gilvum (strain PYR-GCK) | MYCGI04072 | RIMM_MYCGI | 16S rRNA processing protein RimM TIGRFAM: 16S rRNA processing protein RimM PFAM: RimM protein; PRC-barrel domain protein KEGG: mva:Mvan_2189 16S rRNA processing protein RimM |
| [B] Mycobacterium leprae | MYCLE01609 | RIMM_MYCLE | Highly similar to many 16s rRNA processing proteins including: Escherichia coli SW:RIMM_ECOLI (P21504) (182 aa); Fasta score E(): 2.8e-10, 30.6% identity in 183 aa overlap and Mycobacterium tuberculosis RV2907C SW:RIMM_MYCTU (Q10824) (176 aa); Fasta score E(): 0, 73.1% identity in 175 aa overlap. Contains Pfam match to entry PF01782 RimM, RimM. 16S rRNA processing protein |
| [B] Mycobacterium leprae (strain Br4923) | MYCLB01601 | RIMM_MYCLB | 16S rRNA processing protein |
| [B] Mycobacterium marinum (strain ATCC BAA-535 / M) | MYCMM01761 | RIMM_MYCMM | 16S rRNA processing protein RimM |
| [B] Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) | MYCS202267 | RIMM_MYCS2 | 16S rRNA processing protein RimM |
| [B] Mycobacterium sp. (strain JLS) | MYCSJ01905 | RIMM_MYCSJ | 16S rRNA processing protein RimM TIGRFAM: 16S rRNA processing protein RimM PFAM: RimM protein; PRC-barrel domain protein KEGG: mmc:Mmcs_1967 16S rRNA processing protein RimM |
| [B] Mycobacterium sp. (strain KMS) | MYCSK01947 | RIMM_MYCSK | 16S rRNA processing protein RimM TIGRFAM: 16S rRNA processing protein RimM PFAM: RimM protein; PRC-barrel domain protein KEGG: mmc:Mmcs_1967 16S rRNA processing protein RimM |
| [B] Mycobacterium sp. (strain MCS) | MYCSS01935 | RIMM_MYCSS | 16S rRNA processing protein RimM |
| [B] Mycobacterium bovis | MYCBO02922 | RIMM_MYCBO | Mb2931c, rimM, len: 176 aa. Equivalent to Rv2907c, len: 176 aa, from Mycobacterium tuberculosis strain H37Rv, (100.0% identity in 176 aa overlap). Probable rimM, 16S rRNA processing protein, equivalent to O33016|RIMM_MYCLE PROBABLE 16S RRNA PROCESSING protein from Mycobacterium leprae (179 aa), FASTA scores: opt: 797, E(): 2.4e-46, (73.15% identity in 175 aa overlap). Also highly similar to others e.g. O69881|RIMM_STRCO from Streptomyces coelicolor (188 aa), FASTA scores: opt: 485, E(): 2.3e-25, (48.85% identity in 176 aa overlap); Q9KA14|RIMM_BACHD from Bacillus halodurans (173 aa), FASTA scores: opt: 289, E(): 3.2e-12, (30.65% identity in 173 aa overlap); P21504|RIMM_ECOLI|RIMM|B2608 from Escherichia coli strain K12 (182 aa), FASTA scores: opt: 237, E(): 1e-08, (29.4% identity in 177 aa overlap). BELONGS TO THE RIMM FAMILY. PROBABLE 16S RRNA PROCESSING PROTEIN RIMM |
| [B] Mycobacterium bovis (strain BCG / Paris 1173P2) | MYCBP02902 | RIMM_MYCBP | Probable 16S rRNA processing protein rimM |
| [B] Mycobacterium tuberculosis | MYCTU04033 | RIMM_MYCTU | Ribosome maturation factor rimM |
| [B] Mycobacterium tuberculosis (strain ATCC 25177 / H37Ra) | MYCTA02959 | RIMM_MYCTA | 16S rRNA-processing protein |
| [B] Mycobacterium tuberculosis (strain F11) | MYCTF02838 | A5WRF9 | 16S rRNA processing protein rimM Mapped to H37Rv Rv2907c |
| [B] Mycobacterium ulcerans (strain Agy99) | MYCUA01679 | RIMM_MYCUA | 16S rRNA processing protein RimM cytoplasmic protein essential for efficient processing of 16S rRNA. probably part of the 30S subunit prior to or during the final step in the processing of 16S free 30S ribosomal subunits. it could be some accessory protein needed for efficient assembly of the 30S subunit. RimM is needed in a step prior to RbfA during the maturation of 16S rRNA. has affinity for free ribosomal 30S subunits but not for 70S ribosomes. |
| [B] Mycobacterium vanbaalenii (strain DSM 7251 / PYR-1) | MYCVP02100 | RIMM_MYCVP | 16S rRNA processing protein RimM TIGRFAM: 16S rRNA processing protein RimM PFAM: RimM protein; PRC-barrel domain protein KEGG: mmc:Mmcs_1967 16S rRNA processing protein RimM |
| [B] Nocardia farcinica | NOCFA04159 | RIMM_NOCFA | putative 16S rRNA processing protein |
| [B] Rhodococcus erythropolis (strain PR4 / NBRC 100887) | RHOE402440 | RIMM_RHOE4 | Probable 16S rRNA processing protein RimM |
| [B] Rhodococcus opacus (strain B4) | RHOOB06584 | RIMM_RHOOB | Putative 16S rRNA processing protein RimM |
| [B] Rhodococcus sp. (strain RHA1) | RHOSR06445 | RIMM_RHOSR | 16S rRNA processing protein |
| [B] Acidothermus cellulolyticus (strain ATCC 43068 / 11B) | ACIC101555 | RIMM_ACIC1 | 16S rRNA processing protein RimM TIGRFAM: 16S rRNA processing protein RimM PFAM: RimM protein; PRC-barrel domain protein KEGG: sco:SCO5593 putative 16S rRNA processing protein |
| [B] Frankia alni (strain ACN14a) | FRAAA05657 | RIMM_FRAAA | 16S rRNA processing protein rimM Evidence 2b : Function of strongly homologous gene; Product type e : enzyme |
| [B] Frankia sp. (strain CcI3) | FRASC03482 | RIMM_FRASC | 16S rRNA processing protein RimM |
| [B] Kineococcus radiotolerans (strain ATCC BAA-149 / DSM 14245 / SRS30216) | KINRD01396 | RIMM_KINRD | 16S rRNA processing protein RimM |
| [B] Arthrobacter aurescens (strain TC1) | ARTAT02335 | ABM08221.1 | 16S rRNA processing protein RimM |
| [B] Arthrobacter chlorophenolicus (strain A6 / ATCC 700700 / DSM 12829 / JCM 12360) | ARTCA02182 | B8HA95 | 16S rRNA processing protein RimM |
| [B] Arthrobacter sp. (strain FB24) | ARTS202454 | RIMM_ARTS2 | 16S rRNA processing protein RimM TIGRFAM: 16S rRNA processing protein RimM PFAM: RimM protein; PRC-barrel domain protein KEGG: sma:SAV2642 putative 16S rRNA processing protein |
| [B] Nocardioides sp. (strain BAA-499 / JS614) | NOCSJ03188 | RIMM_NOCSJ | 16S rRNA processing protein RimM |
| [B] Propionibacterium acnes | PROAC01423 | RIMM_PROAC | probable 16S rRNA processing protein RimM |
| [B] Saccharopolyspora erythraea (strain NRRL 23338) | SACEN05819 | RIMM_SACEN | 16S rRNA processing protein |
| [B] Phytoplasma sp. (strain STRAWB1) | STRAW02641 | RIMM_STRAW | Ribosome maturation factor rimM |
| [B] Streptomyces coelicolor | STRCO05562 | RIMM_STRCO | SC2E1.10, probable 16S rRNA processing protein, len: 188 aa; similar to hypothetical proteins from many organisms e.g. YX38_MYCTU MTCY274.38c (176 aa), fasta scores; opt: 479 z-score: 693.1 E(): 2.3e-31, 48.3% identity in 176 aa overlap. Also some similarity to RIMM_HAEIN 16S rRNA processing protein rimM (178 aa), fasta scores; opt: 210 z-score: 174.2 E(): 0.018, 27.6% identity in 170 aa overlap and to SW:RIMM_ECOLI (EMBL:X01818) Escherichia coli 16S rRNA processing protein RimM or B2608, 182 aa; fasta scores: opt: 216 Z-score: 258.0 E(): 9.8e-07; 24.561% identity in 171 aa overlap putative 16S rRNA processing protein |
| [B] Streptomyces griseus subsp. griseus (strain JCM 4626 / NBRC 13350) | STRGG01760 | RIMM_STRGG | Putative 16S rRNA processing protein |
| [B] Thermobifida fusca (strain YX) | THEFY00662 | RIMM_THEFY | 16S rRNA processing protein RimM |
| [B] Rubrobacter xylanophilus (strain DSM 9941 / NBRC 16129) | RUBXD01366 | RIMM_RUBXD | 16S rRNA processing protein RimM TIGRFAM: 16S rRNA processing protein RimM PFAM: RimM protein PRC-barrel KEGG: sth:STH1469 16S rRNA processing protein |
| [B] Herpetosiphon aurantiacus (strain ATCC 23779 / DSM 785) | HERA204577 | RIMM_HERA2 | 16S rRNA processing protein RimM |
| [B] Thermomicrobium roseum (strain ATCC 27502 / DSM 5159 / P-2) | THERP00110 | B9KXC6 | 16S rRNA processing protein RimM |
| [B] Staphylococcus aureus (strain COL) | STAAC01223 | RIMM_STAAC | identified by match to protein family HMM PF01782; match to protein family HMM PF05239; match to protein family HMM TIGR02273 16S rRNA processing protein RimM |
| [B] Staphylococcus aureus (strain JH1) | STAA201287 | RIMM_STAA2 | 16S rRNA processing protein RimM TIGRFAM: 16S rRNA processing protein RimM PFAM: RimM protein; PRC-barrel domain protein KEGG: saa:SAUSA300_1132 16S rRNA processing protein RimM |
| [B] Staphylococcus aureus (strain JH9) | STAA901263 | RIMM_STAA9 | 16S rRNA processing protein RimM TIGRFAM: 16S rRNA processing protein RimM PFAM: RimM protein; PRC-barrel domain protein |
| [B] Staphylococcus aureus (strain MRSA252) | STAAR01177 | RIMM_STAAR | Similar to Escherichia coli 16S rRNA processing protein RimM SW:RIMM_ECOLI (P21504) (182 aa) fasta scores: E(): 3.8e-07, 25.153% id in 163 aa, and to Bacillus subtilis probable 16S rRNA processing protein RimM SW:RIMM_BACSU (O31740) (174 aa) fasta scores: E(): 1.2e-25, 49.102% id in 167 aa 16S rRNA processing protein |
| [B] Staphylococcus aureus (strain MSSA476) | STAAS01178 | RIMM_STAAS | Ortholog of S. aureus MRSA252 (BX571856) SAR1215 16S rRNA processing protein |
| [B] Staphylococcus aureus (strain MW2) | STAAW01122 | RIMM_STAAW | probable 16S rRNA processing protein |
| [B] Staphylococcus aureus (strain Mu3 / ATCC 700698) | STAA101214 | RIMM_STAA1 | Probable 16S rRNA processing protein |
| [B] Staphylococcus aureus (strain Mu50 / ATCC 700699) | STAAM01233 | RIMM_STAAM | probable 16S rRNA processing protein |
| [B] Staphylococcus aureus (strain N315) | STAAN01106 | RIMM_STAAN | probable 16S rRNA processing protein |
| [B] Staphylococcus aureus (strain NCTC 8325) | STAA801138 | RIMM_STAA8 | conserved hypothetical protein |
| [B] Staphylococcus aureus (strain Newman) | STAAE01107 | RIMM_STAAE | 16S rRNA processing protein |
| [B] Staphylococcus aureus (strain USA300) | STAA301105 | RIMM_STAA3 | 16S rRNA processing protein RimM identified by match to protein family HMM PF01782; match to protein family HMM PF05239; match to protein family HMM TIGR02273 |
| [B] Staphylococcus aureus (strain bovine RF122) | STAAB01097 | RIMM_STAAB | 16S rRNA processing protein |
| [B] Bartonella bacilliformis (strain ATCC 35685 / KC583) | BARBK00084 | RIMM_BARBK | 16S rRNA processing protein RimM |
| [B] Bartonella henselae | BARHE01492 | RIMM_BARHE | 16s rRNA processing protein rimM |
| [B] Bartonella quintana | BARQU01219 | RIMM_BARQU | 16s rRNA processing protein rimM |
| [B] Bartonella tribocorum (strain CIP 105476 / IBS 506) | BART101805 | RIMM_BART1 | 16S rRNA processing protein hypothetical protein |
| [B] Methylocella silvestris (strain BL2 / DSM 15510 / NCIMB 13906) | METSB02816 | B8ETG1 | 16S rRNA processing protein RimM |
| [B] Bradyrhizobium japonicum | BRAJA00481 | RIMM_BRAJA | Ribosome maturation factor rimM |
| [B] Bradyrhizobium sp. (strain BTAi1 / ATCC BAA-1182) | BRASB00346 | RIMM_BRASB | 16S rRNA processing protein, putative function |
| [B] Bradyrhizobium sp. (strain ORS278) | BRASO00348 | RIMM_BRASO | 16S rRNA processing protein, putative function |
| [B] Nitrobacter hamburgensis (strain X14 / DSM 10229) | NITHX03345 | RIMM_NITHX | 16S rRNA processing protein RimM |
| [B] Nitrobacter winogradskyi (strain Nb-255 / ATCC 25391) | NITWN02630 | RIMM_NITWN | 16S rRNA processing protein RimM |
| [B] Oligotropha carboxidovorans (strain ATCC 49405 / DSM 1227 / OM5) | OLICO00266 | B6JAQ5 | 16S rRNA processing protein RimM |
| [B] Rhodopseudomonas palustris | RHOPA00243 | RIMM_RHOPA | observed by proteomics Citation: Proteomics from VerBerkmoes et al. (2003) unpublished putative 16S rRNA processing protein. |
| [B] Rhodopseudomonas palustris (strain BisA53) | RHOP500326 | RIMM_RHOP5 | 16S rRNA processing protein RimM TIGRFAM: 16S rRNA processing protein RimM PFAM: RimM protein; PRC-barrel domain protein KEGG: rpc:RPC_0223 16S rRNA processing protein RimM |
| [B] Rhodopseudomonas palustris (strain BisB18) | RHOPB00219 | RIMM_RHOPB | 16S rRNA processing protein RimM |
| [B] Rhodopseudomonas palustris (strain BisB5) | RHOPS00503 | RIMM_RHOPS | 16S rRNA processing protein RimM |
| [B] Rhodopseudomonas palustris (strain HaA2) | RHOP200350 | RIMM_RHOP2 | 16S rRNA processing protein RimM |
| [B] Rhodopseudomonas palustris (strain TIE-1) | RHOPT00242 | RIMM_RHOPT | 16S rRNA processing protein RimM |
| [B] Brucella abortus | BRUAB01768 | RIMM_BRUAB | similar to BR1915, 16S rRNA processing protein RimM RimM, 16S rRNA processing protein |
| [B] Brucella abortus (strain 2308) | BRUA201900 | RIMM_BRUA2 | ATP/GTP-binding site motif A (P-loop):RimM protein |
| [B] Brucella abortus (strain S19) | BRUA101706 | RIMM_BRUA1 | RimM protein |
| [B] Brucella canis (strain ATCC 23365 / NCTC 10854) | BRUC201829 | RIMM_BRUC2 | 16S rRNA processing protein RimM |
| [B] Brucella melitensis | BRUME00148 | RIMM_BRUME | Probable 16S rRNA-processing protein rimM |
| [B] Brucella ovis (strain ATCC 25840 / 63/290 / NCTC 10512) | BRUO201640 | RIMM_BRUO2 | 16S rRNA processing protein RimM |
| [B] Brucella suis | BRUSU01836 | RIMM_BRUSU | similar to GP:15157914, and SP:P21504; identified by sequence similarity; putative 16S rRNA processing protein RimM |
| [B] Brucella suis (strain ATCC 23445 / NCTC 10510) | BRUSI01643 | RIMM_BRUSI | 16S rRNA processing protein RimM GO_function: RNA binding [GO ID 0003723]; GO_process: rRNA processing [GO ID 0006364] |
| [B] Ochrobactrum anthropi (strain ATCC 49188 / DSM 6882 / NCTC 12168) | OCHA400926 | RIMM_OCHA4 | 16S rRNA processing protein RimM |
| [B] Methylobacterium chloromethanicum (strain CM4 / NCIMB 13688) | METC400613 | RIMM_METC4 | 16S rRNA processing protein RimM TIGRFAM: 16S rRNA processing protein RimM; PFAM: RimM protein; PRC-barrel domain protein; KEGG: mex:Mext_0654 16S rRNA processing protein RimM |
| [B] Methylobacterium extorquens (strain PA1) | METEP00635 | RIMM_METEP | 16S rRNA processing protein RimM |
| [B] Mesorhizobium sp. (strain BNC1) | MESSB03407 | RIMM_MESSB | 16S rRNA processing protein RimM TIGRFAM: 16S rRNA processing protein RimM PFAM: RimM protein PRC-barrel KEGG: mlo:mll4288 putative 16S rRNA processing protein |
| [B] Rhizobium loti | RHILO03294 | RIMM_RHILO | putative 16S rRNA processing protein |
| [B] Parvibaculum lavamentivorans (strain DS-1 / DSM 13023 / NCIMB 13966) | PARL101362 | RIMM_PARL1 | 16S rRNA processing protein RimM |
| [B] Agrobacterium tumefaciens (strain C58 / ATCC 33970) | AGRT502626 | RIMM_AGRT5 | Ribosome maturation factor rimM |
| [B] Rhizobium etli (strain CIAT 652) | RHIE604181 | RIMM_RHIE6 | 16S rRNA processing protein |
| [B] Rhizobium leguminosarum bv. trifolii (strain WSM2304) | RHILW03704 | RIMM_RHILW | Ribosome maturation factor rimM |
| [B] Rhizobium leguminosarum bv. viciae (strain 3841) | RHIL304534 | CAK10034.1 | putative 16S rRNA processing protein similarity:fasta; with=UniProt:RIMM_ECOLI (EMBL:AE016764); Shigella flexneri.; rimM; 16S rRNA processing protein rimM (21K).; length=182; id 25.000; 168 aa overlap; query 10-168; subject 12-177 similarity:fasta; with=UniProt:RIMM_RHIME (EMBL:SME591793); Rhizobium meliloti (Sinorhizobium meliloti).; rimM; Probable 16S rRNA processing protein rimM.; length=187; id 80.000; 185 aa overlap; query 5-189; subject 1-181 |
| [B] Rhizobium meliloti | RHIME03201 | RIMM_RHIME | Product confidence : probable Gene name confidence : probable predicted by Codon_usage predicted by Homology predicted by FrameD PROBABLE 16S RRNA PROCESSING PROTEIN |
| [B] Sinorhizobium medicae (strain WSM419) | SINMW03040 | ABR61924.1 | 16S rRNA processing protein RimM |
| [B] Azorhizobium caulinodans (strain ATCC 43989 / DSM 5975 / ORS 571) | AZOC503942 | RIMM_AZOC5 | 16S rRNA processing protein |
| [B] Xanthobacter autotrophicus (strain ATCC BAA-1158 / Py2) | XANP202440 | RIMM_XANP2 | 16S rRNA processing protein RimM |
| [B] Paracoccus denitrificans (strain Pd 1222) | PARDP03770 | RIMM_PARDP | 16S rRNA processing protein RimM TIGRFAM: 16S rRNA processing protein RimM PFAM: RimM protein; PRC-barrel domain protein KEGG: rsp:RSP_1047 putative 16S rRNA processing protein |
| [B] Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158) | RHOS402660 | RIMM_RHOS4 | putative 16S rRNA processing protein |
| [B] Rhodobacter sphaeroides (strain ATCC 17025 / ATH 2.4.3) | RHOS500174 | RIMM_RHOS5 | 16S rRNA processing protein RimM |
| [B] Rhodobacter sphaeroides (strain ATCC 17029 / ATH 2.4.9) | RHOS102671 | RIMM_RHOS1 | 16S rRNA processing protein RimM TIGRFAM: 16S rRNA processing protein RimM PFAM: RimM protein; PRC-barrel domain protein KEGG: rsp:RSP_1047 putative 16S rRNA processing protein |
| [B] Rhodobacter sphaeroides (strain KD131 / KCTC 12085) | RHOSK02419 | B9KNX9 | 16S rRNA-processing protein rimM |
| [B] Roseobacter denitrificans (strain ATCC 33942 / OCh 114) | ROSDO01212 | RIMM_ROSDO | 16S rRNA processing protein RimM |
| [B] Rhodospirillum centenum (strain ATCC 51521 / SW) | RHOCS02142 | RIMM_RHOCS | 16S rRNA processing protein RimM, putative |
| [B] Rhodospirillum rubrum (strain ATCC 11170 / NCIB 8255) | RHORT01180 | RIMM_RHORT | 16S rRNA processing protein RimM |
| [B] Myxococcus xanthus (strain DK 1622) | MYXXD03402 | RIMM_MYXXD | 16S rRNA processing protein RimM identified by similarity to SP:P21504; match to protein family HMM PF01782; match to protein family HMM PF05239; match to protein family HMM TIGR02273 |