Protein Info for Shew_2956 in Shewanella loihica PV-4

Annotation: ECF subfamily RNA polymerase sigma-24 factor (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 50 100 150 190 TIGR02937: RNA polymerase sigma factor, sigma-70 family" amino acids 42 to 189 (148 residues), 84.6 bits, see alignment E=3.1e-28 PF04542: Sigma70_r2" amino acids 46 to 112 (67 residues), 62.1 bits, see alignment E=6.9e-21 PF08281: Sigma70_r4_2" amino acids 136 to 186 (51 residues), 57.2 bits, see alignment E=2.1e-19 PF04545: Sigma70_r4" amino acids 140 to 184 (45 residues), 24.7 bits, see alignment 2.6e-09

Best Hits

KEGG orthology group: K03088, RNA polymerase sigma-70 factor, ECF subfamily (inferred from 100% identity to slo:Shew_2956)

Predicted SEED Role

"RNA polymerase sigma factor RpoE" in subsystem Transcription initiation, bacterial sigma factors

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 A3QH74 at UniProt or InterPro

Protein Sequence (190 amino acids)

>Shew_2956 ECF subfamily RNA polymerase sigma-24 factor (RefSeq) (Shewanella loihica PV-4)
MSNRYCSLTGKTDLSALTSPDDAHQLLDAVLVQRAKQGDKTAFRQLYDQHHRRVYALCFR
LAGQTELAEEATQETFVRLWQKLPLFDGKSQFTTWLHSLTVNQALSCIKKHKSFWARFMP
SEETHAAAIDFDYQGVDKLLLRLPERARIVFVLYALEGYQHDEIAKRLNIAPGTSKAQYH
RAKKLLQEMI