Protein Info for Shew_1213 in Shewanella loihica PV-4

Annotation: RpoD family RNA polymerase sigma 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 50 100 150 200 250 324 TIGR02394: RNA polymerase sigma factor RpoS" amino acids 40 to 322 (283 residues), 456.5 bits, see alignment E=4e-141 PF00140: Sigma70_r1_2" amino acids 50 to 80 (31 residues), 38.3 bits, see alignment (E = 2.1e-13) TIGR02937: RNA polymerase sigma factor, sigma-70 family" amino acids 84 to 310 (227 residues), 121.1 bits, see alignment E=3.6e-39 PF04542: Sigma70_r2" amino acids 88 to 157 (70 residues), 80.7 bits, see alignment E=1.1e-26 PF04539: Sigma70_r3" amino acids 168 to 241 (74 residues), 73.7 bits, see alignment E=2e-24 PF04545: Sigma70_r4" amino acids 256 to 308 (53 residues), 60.4 bits, see alignment 1.9e-20

Best Hits

Swiss-Prot: 80% identical to RPOS_SALTY: RNA polymerase sigma factor RpoS (rpoS) from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)

KEGG orthology group: K03087, RNA polymerase nonessential primary-like sigma factor (inferred from 100% identity to slo:Shew_1213)

MetaCyc: 80% identical to RNA polymerase sigma factor RpoS (Escherichia coli K-12 substr. MG1655)

Predicted SEED Role

"RNA polymerase sigma factor RpoS" 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)

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 A3QC85 at UniProt or InterPro

Protein Sequence (324 amino acids)

>Shew_1213 RpoD family RNA polymerase sigma factor (RefSeq) (Shewanella loihica PV-4)
MGRKQSTAVAEPLVDLSKNESDLSVTNSKEVLKDAELEQQVQDDLQKNLDATQLYLSEIG
FSPLLSAEEEVYFSRKALKGCEKSRNRMIESNLRLVVKIARRYNNRGLALLDLIEEGNLG
LIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRTARELA
HKLDHEPTAEEIAEQLDLPSSDVSKMLKLNERITSVDTPLGGDNDKALLDVLADDDCVGP
DYKVQDDDMSKSVVRWLDELNSKQREVLARRFGLLGYEPSTLENVGKEIGLTRERVRQIQ
VEALKRLRDLLSAQGLSVEAIFRV