Protein Info for EX28DRAFT_3102 in Enterobacter asburiae PDN3

Annotation: RNA polymerase, sigma 70 subunit, RpoD

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 50 100 150 200 250 300 350 400 450 500 550 600 660 PF03979: Sigma70_r1_1" amino acids 49 to 126 (78 residues), 103.6 bits, see alignment E=1.3e-33 PF00140: Sigma70_r1_2" amino acids 143 to 173 (31 residues), 46.4 bits, see alignment (E = 9.3e-16) PF04546: Sigma70_ner" amino acids 184 to 395 (212 residues), 253.6 bits, see alignment E=5.3e-79 TIGR02393: RNA polymerase sigma factor RpoD" amino acids 422 to 658 (237 residues), 399 bits, see alignment E=7e-124 TIGR02937: RNA polymerase sigma factor, sigma-70 family" amino acids 422 to 647 (226 residues), 128.6 bits, see alignment E=1.8e-41 PF04542: Sigma70_r2" amino acids 426 to 496 (71 residues), 82.7 bits, see alignment E=3.8e-27 PF04539: Sigma70_r3" amino acids 505 to 580 (76 residues), 101.1 bits, see alignment E=8.7e-33 PF04545: Sigma70_r4" amino acids 594 to 647 (54 residues), 66.4 bits, see alignment 3.9e-22

Best Hits

Swiss-Prot: 97% identical to RPOD_SALTI: RNA polymerase sigma factor RpoD (rpoD) from Salmonella typhi

KEGG orthology group: K03086, RNA polymerase primary sigma factor (inferred from 100% identity to enc:ECL_04399)

MetaCyc: 91% 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)

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

Find the best match in UniProt

Protein Sequence (660 amino acids)

>EX28DRAFT_3102 RNA polymerase, sigma 70 subunit, RpoD (Enterobacter asburiae PDN3)
MPNIDREAPGSRTERQRQKYKYALALKVGSPIADTNQTNKCGYRLMEQNPQSQLKLLVQR
GKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLLLAETSNNTD
EDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQCS
VAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDMAPTATHVGSELSQEEMDDD
EDEDEEESDDDTADDDNSIDPELAREKFAELRTQYEVTRDTIKAKGRSHAAAQEEILKLS
EVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERIIMKLCVEQCKMPKKNFITLFTGNETSE
TWFNAAIAMNKPWSEKLHDVKDDVHRGLQKLHQIEEETGLTIEQVKDINRRMSIGEAKAR
RAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW
WIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDK
IRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTA
REAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLDD