Protein Info for Sama_0823 in Shewanella amazonensis SB2B

Annotation: RNA polymerase sigma-70 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 50 100 150 200 250 300 350 400 450 500 550 620 PF03979: Sigma70_r1_1" amino acids 8 to 84 (77 residues), 107.1 bits, see alignment E=1.1e-34 PF00140: Sigma70_r1_2" amino acids 99 to 129 (31 residues), 45.7 bits, see alignment (E = 1.6e-15) PF04546: Sigma70_ner" amino acids 140 to 355 (216 residues), 244.4 bits, see alignment E=3.3e-76 TIGR02937: RNA polymerase sigma factor, sigma-70 family" amino acids 382 to 607 (226 residues), 125.5 bits, see alignment E=1.6e-40 TIGR02393: RNA polymerase sigma factor RpoD" amino acids 382 to 618 (237 residues), 401.7 bits, see alignment E=1.1e-124 PF04542: Sigma70_r2" amino acids 386 to 456 (71 residues), 82.8 bits, see alignment E=3.5e-27 PF04539: Sigma70_r3" amino acids 465 to 540 (76 residues), 102.3 bits, see alignment E=3.9e-33 PF04545: Sigma70_r4" amino acids 554 to 607 (54 residues), 66.1 bits, see alignment 4.6e-22

Best Hits

Swiss-Prot: 83% identical to RPOD_SHEVD: RNA polymerase sigma factor RpoD (rpoD) from Shewanella violacea (strain JCM 10179 / CIP 106290 / LMG 19151 / DSS12)

KEGG orthology group: K03086, RNA polymerase primary sigma factor (inferred from 100% identity to saz:Sama_0823)

MetaCyc: 79% identical to RNA polymerase sigma factor RpoD (Escherichia coli K-12 substr. MG1655)

Predicted SEED Role

"RNA polymerase sigma factor RpoD" in subsystem Flagellum or Macromolecular synthesis operon or Transcription factors cyanobacterial RpoD-like sigma factors or 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 A1S3S4 at UniProt or InterPro

Protein Sequence (620 amino acids)

>Sama_0823 RNA polymerase sigma-70 factor (RefSeq) (Shewanella amazonensis SB2B)
MISMDHTPQSQLKMLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVYE
EAPDADEMMMSEDNTDEDAAEEAAAALATVESELGRTTDPVRMYMREMGTVELLTREGEI
VIAKRIEEGINTVQSSVAEYPQAISMILEQFDQFEADAIRLSDIISGFVDPNEEDVGPTA
THIGSELSEEELEDEDDMDEDEEEDEDGDSSDDDGAKGPDPEVARERFAALRAAYDNALK
VIEVKGRAHPESTRALFELGEIFKEFRLVPKQFDRLVKSMREMMDKVRVQERLIMKLCVE
QAKMPKKNFVKLFTGNETDLTWFNKEIEAGRPYSADLKLVDEDVQRCRAKLEAIEVETGL
SIESIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM
KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQE
MGREPSPEELAERMAMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLD
SATSESLKQATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAK
ALRKLRHPSRSEILKSFLDD