Protein Info for DDA3937_RS17260 in Dickeya dadantii 3937

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 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 800 829 TIGR02063: ribonuclease R" amino acids 19 to 722 (704 residues), 921.5 bits, see alignment E=3.5e-281 PF08461: HTH_12" amino acids 22 to 85 (64 residues), 65.2 bits, see alignment 1.1e-21 TIGR00358: VacB and RNase II family 3'-5' exoribonucleases" amino acids 67 to 721 (655 residues), 894.4 bits, see alignment E=4.2e-273 PF08206: OB_RNB" amino acids 87 to 144 (58 residues), 78.5 bits, see alignment 6e-26 PF17876: CSD2" amino acids 164 to 238 (75 residues), 82.3 bits, see alignment E=5.5e-27 PF00773: RNB" amino acids 260 to 587 (328 residues), 370.8 bits, see alignment E=1.7e-114 PF00575: S1" amino acids 639 to 720 (82 residues), 51.2 bits, see alignment E=3.4e-17

Best Hits

Swiss-Prot: 77% identical to RNR_ECOLI: Ribonuclease R (rnr) from Escherichia coli (strain K12)

KEGG orthology group: K12573, ribonuclease R [EC: 3.1.-.-] (inferred from 100% identity to ddd:Dda3937_02609)

MetaCyc: 77% 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

See E0SEE7 at UniProt or InterPro

Protein Sequence (829 amino acids)

>DDA3937_RS17260 ribonuclease R (Dickeya dadantii 3937)
MSQDPFLEREAEKYEFPIPSREYILEHLAKRDTPISREELASDLQLTNDEQLEALRRRLR
AMERDGQLVFTRRQCYALPEKLDLLRGTVLGHRDGYGFLRVEGRKDDLYLSAEQMKTVIH
GDVVLAQPLGEDRRGRREGRIVRILEPRTSQIVGRYFTEAGTGFVVPDDSRLSFDILIPP
EFIAGARMGSVVVVELTQRATRRTKAIGKIVEILGDNMGTGLAVDIALRTHEIPHSWPPK
VEEQVGDLADEVPEDAKKGRVDLRSLPLVTIDGEDARDFDDAVYCEKKRGGGWRLWVAIA
DVSYYVRPGTALDHEARARGTSVYFPSQVVPMLPEVLSNGLCSLNPQVDRLCMVCEMTVS
TQGKLSGYKFYEAVMSSHARLTYTKVWSILQGDEVLREHYQPLVAPLEELHRLYKVLDHA
REVRGGIAFETEEAKFIFNAERRIERVEAVVRNDAHKLIEECMILANISAAKFVEKSEEP
ALFRVHDQPSEDHVLALRSVLGELGLTLKGGMKPQPKDYAELMDSIADRPDHEMLQTMLL
RSMKQAVYDPENRGHFGLALTSYAHFTSPIRRYPDLSLHRAIKYLLSDRKARWTHSGGWH
SDFNEMLQLGEHCSMTERRADEATRDVADWLKCDFMQDHVGEAFTGIISSVTGFGFFVRL
NDLFIDGLVHVSTLDNDYYRYDNVGQRLIGESRGQVYRLGDEVQIRVEAVHMDERKIDFA
LLSSTRKVRGEGKTARDRAKKGGEADAKPPRRRRSGQRANFEPDSAFRSEGDGKRQPAGA
GKGKDKDKAKTGGRKKTAKPQKNAEKTRKIAAATRAKRASKKKKPAEPA