Protein Info for Shewana3_1124 in Shewanella sp. ANA-3

Annotation: RNA polymerase, sigma 38 subunit, RpoS (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 50 100 150 200 250 300 326 TIGR02394: RNA polymerase sigma factor RpoS" amino acids 42 to 324 (283 residues), 452.9 bits, see alignment E=4.9e-140 PF00140: Sigma70_r1_2" amino acids 52 to 82 (31 residues), 36.3 bits, see alignment (E = 8.7e-13) TIGR02937: RNA polymerase sigma factor, sigma-70 family" amino acids 86 to 312 (227 residues), 122.1 bits, see alignment E=1.7e-39 PF04542: Sigma70_r2" amino acids 90 to 159 (70 residues), 80.6 bits, see alignment E=1.1e-26 PF04539: Sigma70_r3" amino acids 170 to 243 (74 residues), 72.4 bits, see alignment E=5.3e-24 PF04545: Sigma70_r4" amino acids 258 to 310 (53 residues), 60.1 bits, see alignment 2.3e-20

Best Hits

Swiss-Prot: 77% identical to RPOS_YEREN: RNA polymerase sigma factor RpoS (rpoS) from Yersinia enterocolitica

KEGG orthology group: K03087, RNA polymerase nonessential primary-like sigma factor (inferred from 100% identity to son:SO_3432)

MetaCyc: 76% 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)

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 A0KU90 at UniProt or InterPro

Protein Sequence (326 amino acids)

>Shewana3_1124 RNA polymerase, sigma 38 subunit, RpoS (RefSeq) (Shewanella sp. ANA-3)
MSRINSTAAEELVDFSVDTAEFDLDKEDIAADLVQELGLEQQVQDDLQKNLDATQLYLGE
IGFSPLLSAEEEVYFSRKALKGCEKSRNRMIESNLRLVVKIARRYNNRGLALLDLIEEGN
LGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRTARE
LAQKLDHEPTAEEIAEKLQVSSVDVSRMLKLNEKITSVDIPLGGDNDKALLDVLADDDNV
GPDYKVQDEDISNSVVKWLNELNTKQREVLARRFGLLGYEPSTLEDVGAEIGLTRERVRQ
IQVEALKRLRDLLGAQGLSVEALFRN