Result : P36675
| Protein Information |
| Information Type | Description |
|---|---|
| Protein name | Alternative ribosome-rescue factor A |
| NCBI Accession ID | L29458.1 |
| Organism | Escherichia coli (strain K12) |
| Left | 408 |
| Right | 626 |
| Strand | - |
| Nucleotide Sequence | ATGAGTCGATATCAGCATACTAAAGGGCAGATAAAGGATAATGCGATAGAAGCATTACTACATGATCCCTTATTCCGACAGCGCGTAGAGAAAAATAAGAAGGGGAAAGGCAGTTACATGCGAAAAGGAAAACATGGCAATCGGGGGAACTGGGAGGCCAGTGGCAAGAAAGTAAATCACTTTTTTACCACTGGTCTTCTGCTTTCAGGCGCTTGTTAA |
| Sequence | MSRYQHTKGQIKDNAIEALLHDPLFRQRVEKNKKGKGSYMRKGKHGNRGNWEASGKKVNHFFTTGLLLSGAC |
| Source of smORF | Swiss-Prot |
| Function | Rescues ribosomes stalled at the 3' end of non-stop mRNAs (Pubmed:21062370, Pubmed:21435036). This activity is crucial when the stalled ribosome cannot be rescued by the SsrA(tmRNA)-SmpB quality control system (Pubmed:21062370, Pubmed:21435036). Binds the 30S subunit, contacting 16S rRNA with the N-terminus near the decoding center and its C-terminus in the mRNA entry channel; contacts change in the presence of release factor 2 (RF2, also named PrfB) (Pubmed:25355516, Pubmed:27906160, Pubmed:27906161, Pubmed:27934701, Pubmed:28077875). Requires RF2/PrfB to hydrolyze stalled peptidyl-tRNA on the ribosome; recruits and probably helps position RF2/PrfB correctly in the ribosomal A site so RF2's GGQ motif can hydrolyze the peptidyl-tRNA bond (Pubmed:22857598, Pubmed:22922063, Pubmed:25355516, Pubmed:27906160, Pubmed:27906161, Pubmed:27934701, Pubmed:28077875). Does not release ribosomes with a programmed pause caused by regulatory chains such as SecM-mediated pausing (Pubmed:22857598). Binds tRNA which may stimulate its ribosome rescue activity (Pubmed:22857598). {ECO:0000269|Pubmed:21062370, ECO:0000269|Pubmed:21435036, ECO:0000269|Pubmed:22857598, ECO:0000269|Pubmed:22922063, ECO:0000269|Pubmed:25355516, ECO:0000269|Pubmed:27906160, ECO:0000269|Pubmed:27906161, ECO:0000269|Pubmed:27934701, ECO:0000269|Pubmed:28077875}. |
| Pubmed ID | 8063098 9278503 16738553 21062370 21435036 21952205 22857598 22922063 25355516 27906160 27906161 27934701 28077875 |
| Domain | CDD:421476 |
| Functional Category | RNA-binding |
| Uniprot ID | P36675 |
| ORF Length (Amino Acid) | 72 |
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| Conservation Analysis |
No. of Species: 86
| Sr.No. | Left Position | Right Position | Strand | NCBI Accession id | Species Name |
|---|---|---|---|---|---|
| 1 | 3438431 | 3438649 | - | NC_000913.3 | Escherichia coli str. K-12 substr. MG1655 |
| 2 | 4173571 | 4173789 | - | NC_002695.2 | Escherichia coli O157:H7 str. Sakai |
| 3 | 386436 | 386654 | + | NZ_CP061527.1 | Shigella dysenteriae |
| 4 | 2359722 | 2359940 | - | NZ_CP057657.1 | Escherichia fergusonii |
| 5 | 1667486 | 1667704 | + | NZ_LT556085.1 | Citrobacter amalonaticus |
| 6 | 3941617 | 3941835 | - | NZ_LR134340.1 | Escherichia marmotae |
| 7 | 14860 | 15078 | - | NZ_CP045205.1 | Citrobacter telavivensis |
| 8 | 3414438 | 3414656 | - | NZ_AP014857.1 | Escherichia albertii |
| 9 | 4336793 | 4337011 | - | NC_009792.1 | Citrobacter koseri ATCC BAA-895 |
| 10 | 4771807 | 4772025 | + | NC_013716.1 | Citrobacter rodentium ICC168 |
| 11 | 2842200 | 2842418 | + | NZ_CP044098.1 | Citrobacter portucalensis |
| 12 | 4166084 | 4166299 | - | NZ_CP012871.1 | [Enterobacter] lignolyticus |
| 13 | 2240455 | 2240673 | - | NZ_CP033744.1 | Citrobacter freundii |
| 14 | 402284 | 402499 | + | NZ_CP054058.1 | Scandinavium goeteborgense |
| 15 | 4296552 | 4296767 | - | NC_015968.1 | Enterobacter soli |
| 16 | 3840588 | 3840797 | + | NZ_CP038469.1 | Citrobacter tructae |
| 17 | 1192357 | 1192572 | + | NZ_CP020388.1 | Pluralibacter gergoviae |
| 18 | 437091 | 437306 | + | NZ_CP050508.1 | Raoultella terrigena |
| 19 | 435526 | 435741 | + | NZ_CP041247.1 | Raoultella electrica |
| 20 | 4263154 | 4263369 | - | NZ_CP027986.1 | Enterobacter sichuanensis |
| 21 | 473864 | 474079 | + | NZ_CP046672.1 | Raoultella ornithinolytica |
| 22 | 2844651 | 2844866 | - | NZ_CP017279.1 | Enterobacter ludwigii |
| 23 | 2015006 | 2015221 | - | NZ_AP019007.1 | Enterobacter oligotrophicus |
| 24 | 1242684 | 1242899 | - | NZ_CP026047.1 | Raoultella planticola |
| 25 | 4189167 | 4189382 | - | NZ_AP022508.1 | Enterobacter bugandensis |
| 26 | 4282090 | 4282305 | - | NZ_CP017184.1 | Enterobacter roggenkampii |
| 27 | 3017520 | 3017762 | + | NZ_CP025034.2 | Enterobacter sp. SGAir0187 |
| 28 | 4618206 | 4618421 | - | NZ_CP043318.1 | Enterobacter chengduensis |
| 29 | 5152262 | 5152477 | + | NZ_CP011602.1 | Phytobacter ursingii |
| 30 | 438760 | 438975 | + | NZ_LR134475.1 | Klebsiella aerogenes |
| 31 | 4386098 | 4386313 | - | NZ_CP009756.1 | Enterobacter cloacae |
| 32 | 463971 | 464183 | + | NZ_CP014007.2 | Kosakonia oryzae |
| 33 | 459760 | 460005 | + | NZ_CP013990.1 | Leclercia adecarboxylata |
| 34 | 991335 | 991550 | + | NZ_CP051548.1 | Phytobacter diazotrophicus |
| 35 | 4064600 | 4064815 | + | NZ_CP045769.1 | Enterobacter cancerogenus |
| 36 | 4860058 | 4860270 | - | NZ_CP015113.1 | Kosakonia radicincitans |
| 37 | 556785 | 557000 | + | NZ_CP036175.1 | Klebsiella huaxiensis |
| 38 | 2683016 | 2683228 | - | NZ_CP016337.1 | Kosakonia sacchari |
| 39 | 2983658 | 2983900 | - | NZ_CP023529.1 | Lelliottia amnigena |
| 40 | 405616 | 405858 | + | NZ_AP023184.1 | Buttiauxella agrestis |
| 41 | 4433076 | 4433288 | - | NZ_CP063425.1 | Kosakonia pseudosacchari |
| 42 | 3571631 | 3571843 | + | NZ_CP045300.1 | Kosakonia arachidis |
| 43 | 2128396 | 2128611 | + | NZ_CP042941.1 | Atlantibacter hermannii |
| 44 | 4087138 | 4087338 | - | NZ_CP048796.1 | Providencia vermicola |
| 45 | 323577 | 323816 | + | NC_017910.1 | Shimwellia blattae DSM 4481 = NBRC 105725 |
| 46 | 702118 | 702357 | - | NZ_CP040428.1 | Jejubacter calystegiae |
| 47 | 327031 | 327240 | + | NZ_CP023567.1 | Erwinia pyrifoliae |
| 48 | 4368455 | 4368655 | - | NZ_CP032487.1 | Yersinia hibernica |
| 49 | 4383441 | 4383653 | - | NZ_CP034938.1 | Pectobacterium odoriferum |
| 50 | 1124711 | 1124923 | - | NZ_CP015750.1 | Pectobacterium wasabiae CFBP 3304 |
| 51 | 2148742 | 2148954 | + | NZ_CP047495.1 | Pectobacterium brasiliense |
| 52 | 3196248 | 3196460 | - | NZ_CP017482.1 | Pectobacterium polaris |
| 53 | 4223001 | 4223213 | - | NZ_CP038498.1 | Pectobacterium punjabense |
| 54 | 1396106 | 1396312 | + | NZ_CP007044.2 | Chania multitudinisentens RB-25 |
| 55 | 4177474 | 4177710 | - | NZ_CP025799.1 | Dickeya zeae |
| 56 | 4060301 | 4060507 | - | NZ_CP016948.1 | Serratia surfactantfaciens |
| 57 | 4832201 | 4832407 | - | NZ_CP038662.1 | Serratia nematodiphila |
| 58 | 4746792 | 4747004 | + | NZ_CP015749.1 | Pectobacterium parmentieri |
| 59 | 350377 | 350583 | + | NZ_CP071320.1 | Serratia ureilytica |
| 60 | 4998978 | 4999184 | - | NC_015567.1 | Serratia plymuthica AS9 |
| 61 | 531932 | 532144 | + | NZ_CP065044.1 | Pectobacterium aroidearum |
| 62 | 1305408 | 1305614 | - | NZ_CP011254.1 | Serratia fonticola |
| 63 | 4882952 | 4883158 | - | NZ_CP048784.1 | Serratia liquefaciens |
| 64 | 390071 | 390295 | + | NC_012912.1 | Dickeya chrysanthemi Ech1591 |
| 65 | 490521 | 490736 | + | NZ_CP051652.1 | Pectobacterium carotovorum |
| 66 | 1105231 | 1105437 | - | NZ_CP065640.1 | Serratia rubidaea |
| 67 | 489872 | 490105 | + | NZ_CP026377.1 | Mixta gaviniae |
| 68 | 4392901 | 4393113 | - | NZ_CP009125.1 | Pectobacterium atrosepticum |
| 69 | 433780 | 433995 | + | NZ_LN907827.1 | Erwinia gerundensis |
| 70 | 498926 | 499171 | + | NZ_CP034036.1 | Brenneria nigrifluens DSM 30175 = ATCC 13028 |
| 71 | 321862 | 322062 | + | NZ_LR134373.1 | Yersinia pseudotuberculosis |
| 72 | 3600352 | 3600585 | - | NZ_CP034148.1 | Pantoea agglomerans |
| 73 | 4354363 | 4354563 | - | NZ_CP043727.1 | Yersinia canariae |
| 74 | 4414290 | 4414493 | - | NZ_CP031560.1 | Dickeya dianthicola |
| 75 | 486802 | 487005 | + | NZ_CP042220.2 | Dickeya poaceiphila |
| 76 | 3471589 | 3471813 | - | NC_013961.1 | Erwinia amylovora CFBP1430 |
| 77 | 3151495 | 3151695 | - | NZ_CP016176.1 | Xenorhabdus hominickii |
| 78 | 1634113 | 1634316 | - | NZ_CP015137.1 | Dickeya solani IPO 2222 |
| 79 | 4052726 | 4052926 | - | NC_013892.1 | Xenorhabdus bovienii SS-2004 |
| 80 | 318702 | 318953 | + | NZ_LR134531.1 | Pragia fontium |
| 81 | 285560 | 285760 | + | NZ_FO704550.1 | Xenorhabdus doucetiae |
| 82 | 4132449 | 4132655 | - | NZ_CP034752.1 | Jinshanibacter zhutongyuii |
| 83 | 3319587 | 3319793 | - | NZ_CP029185.2 | Limnobaculum parvum |
| 84 | 1208572 | 1208826 | - | NZ_LR134327.1 | Aggregatibacter aphrophilus ATCC 33389 |
| 85 | 227270 | 227476 | - | NZ_LS483443.1 | Aggregatibacter segnis ATCC 33393 |
| 86 | 4345934 | 4346137 | + | NZ_CP051883.1 | Aeromonas salmonicida |
| 87 | 2155762 | 2156007 | - | NZ_CP040863.1 | Rodentibacter heylii |
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| Neighborhood Conservation Analysis |
* Arrows marked in Genome Diagram shows ORFs; Multiple PFAMs can be mapped to a single ORF.
* 'Small ORF' represents the entry/query analyzed.
* Image generated using 'gggenes'(R-Package).
Neighborhood Representative Chosen(Species): NC_000913.3
| Sr.No. | Domain | Co-occurrence Frequency | No. of species in which domain occurs with smORF | Median distance b/w smORF and domain bearing ORFs | Orientation relative to smORF | PFAM Information |
|---|---|---|---|---|---|---|
| 1 | PF01327.23 | 0.87 | 75 | 4265.5 | opposite-strand | Polypeptide deformylase |
| 2 | PF00551.21 | 0.92 | 79 | 3296.0 | opposite-strand | Formyl transferase |
| 3 | PF02911.20 | 0.93 | 80 | 3296 | opposite-strand | Formyl transferase, C-terminal domain |
| 4 | PF01189.19 | 0.94 | 81 | 1956.0 | opposite-strand | 16S rRNA methyltransferase RsmB/F |
| 5 | PF01029.20 | 0.94 | 81 | 1956.0 | opposite-strand | NusB family |
| 6 | PF02254.20 | 0.95 | 82 | 554 | opposite-strand | TrkA-N domain |
| 7 | PF02080.23 | 0.94 | 81 | 554 | opposite-strand | TrkA-C domain |
| 8 | PF01741.20 | 0.91 | 78 | 1 | opposite-strand | Large-conductance mechanosensitive channel, MscL |
| 9 | PF13411.8 | 0.76 | 65 | 58.0 | same-strand | MerR HTH family regulatory protein |
| 10 | PF09278.13 | 0.76 | 65 | 58.0 | same-strand | MerR, DNA binding |
| 11 | PF00376.25 | 0.76 | 65 | 58.0 | same-strand | MerR family regulatory protein |
| 12 | PF09350.12 | 0.72 | 62 | 486 | same-strand | Domain of unknown function (DUF1992) |
| 13 | PF01196.21 | 0.95 | 82 | 962 | same-strand | Ribosomal protein L17 |
| 14 | PF03118.17 | 0.95 | 82 | 1388 | same-strand | Bacterial RNA polymerase, alpha chain C terminal domain |
| 15 | PF01000.28 | 0.95 | 82 | 1388 | same-strand | RNA polymerase Rpb3/RpoA insert domain |
| 16 | PF01193.26 | 0.95 | 82 | 1388 | same-strand | RNA polymerase Rpb3/Rpb11 dimerisation domain |
| 17 | PF00163.21 | 0.95 | 82 | 2403 | same-strand | Ribosomal protein S4/S9 N-terminal domain |
| 18 | PF01479.27 | 0.95 | 82 | 2403 | same-strand | S4 domain |
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