Protein Info for GFF4921 in Hydrogenophaga sp. GW460-11-11-14-LB1

Annotation: 3'-to-5' exoribonuclease RNase 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 50 100 150 200 250 300 350 400 450 500 550 600 650 722 TIGR00358: VacB and RNase II family 3'-5' exoribonucleases" amino acids 1 to 636 (636 residues), 634.1 bits, see alignment E=2.6e-194 TIGR02063: ribonuclease R" amino acids 2 to 477 (476 residues), 608.9 bits, see alignment E=1.3e-186 PF17876: CSD2" amino acids 48 to 121 (74 residues), 81.3 bits, see alignment E=8.8e-27 PF00773: RNB" amino acids 143 to 474 (332 residues), 365 bits, see alignment E=7.9e-113 PF00575: S1" amino acids 555 to 633 (79 residues), 42.5 bits, see alignment E=1.4e-14

Best Hits

KEGG orthology group: K12573, ribonuclease R [EC: 3.1.-.-] (inferred from 87% identity to pol:Bpro_2700)

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 (722 amino acids)

>GFF4921 3'-to-5' exoribonuclease RNase R (Hydrogenophaga sp. GW460-11-11-14-LB1)
VLHKDRVKARIVRLDRKGRPEGRVTEIVERSDSPIIGRLLQESGVWLVAPEDKRYGQDVL
IPKGATGSAKPGQVVVVQLTEPPALYGQPVGRVKEVLGEIDDPGMEIEIAVRKYGVPHEF
SDAALAQARALPDHVRAADHKHRVDLRDVPLVTIDGEDARDFDDAVYCEPAKVGKGKGWR
LLVAIADVSHYVETGSPIDVDAYDRATSVYFPRRVIPMLPEKLSNGLCSLNPGVERLCMV
CDMLVNAKGEVHAYQFYPAVMFSHARFTYTEVAAILQNTRGPEAAQRKALVPYLLNLHDV
YRALLAARGERGAVDFETTETQIVCDESGRIEKIVPRTRNDAHKLIEEAMLAANVCSADF
IQQGKHTGLFRVHEGPTPEKQEILRNYLKAMGVSQTIGDNPKPGDFQAIANATKDRPEAQ
QIHTMLLRSMQQAIYTPVNSGHFGLAFEAYTHFTSPIRRYPDLLVHRVIKAILARKRYEL
PNLPTPGEAHAKLSKRLASRVRPPVAGEPVKKPSADTLAWQAAGLHCSANERRADEASRD
VEAWLKCKYMREHLGEEFSGVVTAVTSFGLFVTLDAMYVEGLVHITELGGEYFRFDEARQ
ELRGERTGIRYALGTRVKVQVSRVDLDGRRIDFRLVSDNDDLVLRAMRDKTGMSPASDNQ
APPARAGKARRSRSEGAPQGRHAQVPPMEVKAAVRKAAGKKDKGARGGGARGTASPSRKN
RR