Protein Info for Sama_1044 in Shewanella amazonensis SB2B

Annotation: RNA polymerase sigma-38 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 50 100 150 200 250 300 327 TIGR02394: RNA polymerase sigma factor RpoS" amino acids 43 to 325 (283 residues), 455.6 bits, see alignment E=7.5e-141 PF00140: Sigma70_r1_2" amino acids 53 to 83 (31 residues), 41 bits, see alignment (E = 2.9e-14) TIGR02937: RNA polymerase sigma factor, sigma-70 family" amino acids 87 to 313 (227 residues), 122.1 bits, see alignment E=1.8e-39 PF04542: Sigma70_r2" amino acids 91 to 160 (70 residues), 80.9 bits, see alignment E=9.4e-27 PF04539: Sigma70_r3" amino acids 171 to 244 (74 residues), 69.6 bits, see alignment E=3.9e-23 PF04545: Sigma70_r4" amino acids 259 to 311 (53 residues), 60.4 bits, see alignment 1.9e-20

Best Hits

Swiss-Prot: 79% identical to RPOS_SALDU: RNA polymerase sigma factor RpoS (rpoS) from Salmonella dublin

KEGG orthology group: K03087, RNA polymerase nonessential primary-like sigma factor (inferred from 100% identity to saz:Sama_1044)

MetaCyc: 79% 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 A1S4E5 at UniProt or InterPro

Protein Sequence (327 amino acids)

>Sama_1044 RNA polymerase sigma-38 factor (RefSeq) (Shewanella amazonensis SB2B)
MSLKNNTLVAEKLVDFSGKEADTDTNMDGEEVSLVQDLELEQQVQDDLQRNLDATQLYLS
EIGFSPLLTAEEEVYYSRKALRGCEKSRNRMIESNLRLVVKIARRYNNRGLALLDLIEEG
NLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRTAR
ELAHKLDHEPTAEEIAAKLNLPSVEVSRMLKLNEKITSVDVPLGGDNDKALLDVLPDDDS
VGPDYKVQDEDISNSVVNWLNELNTKQREVLARRFGLLGYEPSTLEDVGAEIGLTRERVR
QIQVEALKRLRDILSAQGLSVEALFRT