Protein Info for Shew_0003 in Shewanella loihica PV-4

Annotation: DNA replication and repair protein RecF (RefSeq)

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 50 100 150 200 250 300 360 TIGR00611: DNA replication and repair protein RecF" amino acids 1 to 355 (355 residues), 361.3 bits, see alignment E=3e-112 PF13514: AAA_27" amino acids 1 to 126 (126 residues), 32.1 bits, see alignment E=2.2e-11 PF13175: AAA_15" amino acids 1 to 71 (71 residues), 39.8 bits, see alignment E=1e-13 PF02463: SMC_N" amino acids 3 to 355 (353 residues), 133.3 bits, see alignment E=2.2e-42 PF13476: AAA_23" amino acids 5 to 176 (172 residues), 51 bits, see alignment E=7.5e-17

Best Hits

Swiss-Prot: 100% identical to RECF_SHELP: DNA replication and repair protein RecF (recF) from Shewanella loihica (strain ATCC BAA-1088 / PV-4)

KEGG orthology group: K03629, DNA replication and repair protein RecF (inferred from 100% identity to slo:Shew_0003)

MetaCyc: 46% identical to recombination mediator protein RecF (Escherichia coli K-12 substr. MG1655)
RXN0-2606

Predicted SEED Role

"DNA recombination and repair protein RecF" in subsystem DNA repair, bacterial RecFOR pathway

Sequence Analysis Tools

PaperBLAST (search for papers about homologs of this protein)

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

Compare to protein 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 A3Q8S8 at UniProt or InterPro

Protein Sequence (360 amino acids)

>Shew_0003 DNA replication and repair protein RecF (RefSeq) (Shewanella loihica PV-4)
MSLSRLHIDSFRNIASAQLQLGDGLNLIYGQNGSGKTSILEAIFFLGMGRSFRSHLSQRV
IQNDQDKLTLFAQLEQGEQETKIGLRRYRSGETEVKMNGEKVKRLSTLAETLPIQVITPE
SFSLLFEGPKSRRQFIDWGAFHTDKSFYTAWANVRRILKHRNQMLKSETPYQQIQFWDKE
LVRYAEIVTEIRKRYVGSLNERLKGIIEEFLPQVDVKVSFTRGWDSKTDYQTLLQAQYPR
DLAAGHTASGPHKADLRLRVGTLPVQDALSRGQLKLLVCALRIAQGKLLKQQIDKNSIYL
VDDLPSELDARHRQLLLQQLSDTGAQVFVTAIEPAAIMDSLNTPPVKVFHVEQGRVTVIE