Protein Info for CSW01_13155 in Vibrio cholerae E7946 ATCC 55056

Annotation: ribonuclease R

These analyses and tools can help you predict a protein's function, but be skeptical. For enzymes, over 10% of annotations from KEGG or SEED are probably incorrect. For other types of proteins, the error rates may be much higher. MetaCyc and Swiss-Prot have low error rates, but the best hits in these databases are often quite distant, so this protein's function may not be the same. TIGRFam has low error rates. Finally, many experimentally-characterized proteins are not in any of these databases. To find relevant papers, use PaperBLAST.

Protein Families and Features

1 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 821 TIGR02063: ribonuclease R" amino acids 23 to 734 (712 residues), 906.9 bits, see alignment E=9.3e-277 PF08461: HTH_12" amino acids 26 to 88 (63 residues), 43.8 bits, see alignment 5.1e-15 TIGR00358: VacB and RNase II family 3'-5' exoribonucleases" amino acids 71 to 733 (663 residues), 846.6 bits, see alignment E=1.2e-258 PF08206: OB_RNB" amino acids 91 to 151 (61 residues), 71.8 bits, see alignment 7.5e-24 PF17876: CSD2" amino acids 171 to 245 (75 residues), 90.8 bits, see alignment E=1.2e-29 PF00773: RNB" amino acids 267 to 593 (327 residues), 382.4 bits, see alignment E=5.1e-118 PF00575: S1" amino acids 650 to 731 (82 residues), 49.8 bits, see alignment E=9e-17

Best Hits

Swiss-Prot: 100% identical to RNR_VIBCH: Ribonuclease R (rnr) from Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)

KEGG orthology group: K12573, ribonuclease R [EC: 3.1.-.-] (inferred from 100% identity to vcm:VCM66_2519)

MetaCyc: 67% identical to RNase R (Escherichia coli K-12 substr. MG1655)
3.1.13.-

Predicted SEED Role

"3'-to-5' exoribonuclease RNase R" in subsystem RNA processing and degradation, bacterial

Isozymes

Compare fitness of predicted isozymes for: 3.1.-.-

Use Curated BLAST to search for 3.1.-.-

Sequence Analysis Tools

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Search structures

Predict protein localization: PSORTb (Gram-negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the current SEED with FIGfam search

Find homologs in fast.genomics or the ENIGMA genome browser

Find the best match in UniProt

Protein Sequence (821 amino acids)

>CSW01_13155 ribonuclease R (Vibrio cholerae E7946 ATCC 55056)
MSDTTHLDPFADREADNYDNPIPSREYILEFLTQANVPMNRNDLFEALKLEGEEQYEGLR
RRLRAMERDGQLVFTRRQCYALPEKLEMVKGYVIGHKDGHGWVRPEGSLNKEGDILLPHH
QMRTLIHGDFVLVQPSGTDKRGRKEGRLVRILEERNGQIVGRFFFEYGYSYVVPDDSRIH
HDILIPNDLRAGARMGNVVVIEITDRGTRNRGMMGKVVEVLGENMAPGMETQIAIRTHQI
PHEWPAEVEQQVAGLTEEVPEEAKQGRVDLRALPLVTIDGEDARDFDDAVYCEAKKGGGW
RLWVAIADVSYYVRPDTALDKEAINRGNSVYFPSQVVPMLPEVLSNGLCSLNPQVDRLCM
VCEMTVSETGKLSGYKHYEAVMNSHARLTYTKVHEILEGDEELRERYKALVPHLEELHKM
YQVLKSARDERGAIEFETVETKFIFNAQRKIESIEPVVRNDAHKLIEECMILANIASASL
VEKAKEAALYRVHEPPGEERLTGFRDFLGELGLDLSGGLEPSPTDYANLMKQIGERPDKE
LIQTMLLRSMKQAVYNADNAGHFGLALKRYAHFTSPIRRYPDLLLHRAIKYLIAKQEGRN
QDRWTPTGGYHYSFDDMDFYGEQCSMTERRADDATREVSDWLKCEYMQDHVGEELEGVVA
NVTSFGFFVRLTELHIDGLVHISTLANDYYHYDPIGQRLVGESFGAIYRLGDAVKVKVLA
VNLDDRQIDFELVETSRKLRGQGKTAKKRADEARAKAQGKKEAATKGACGKSPTKSELKP
QVEATRRPDSEGRSKPKKTKAPKKRKDQARKKSGKVRDKTK