Protein Info for Psest_3682 in Pseudomonas stutzeri RCH2

Annotation: RNA polymerase sigma factor, sigma-70 family

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 50 100 150 200 250 300 350 400 450 500 550 617 PF03979: Sigma70_r1_1" amino acids 6 to 83 (78 residues), 101 bits, see alignment E=8.9e-33 PF00140: Sigma70_r1_2" amino acids 98 to 128 (31 residues), 48.4 bits, see alignment (E = 2.1e-16) PF04546: Sigma70_ner" amino acids 139 to 352 (214 residues), 224.7 bits, see alignment E=3.9e-70 TIGR02393: RNA polymerase sigma factor RpoD" amino acids 379 to 615 (237 residues), 402.7 bits, see alignment E=5.2e-125 TIGR02937: RNA polymerase sigma factor, sigma-70 family" amino acids 379 to 604 (226 residues), 123.8 bits, see alignment E=5.2e-40 PF04542: Sigma70_r2" amino acids 383 to 453 (71 residues), 82.9 bits, see alignment E=3.5e-27 PF04539: Sigma70_r3" amino acids 462 to 537 (76 residues), 102.1 bits, see alignment E=4.4e-33 PF04545: Sigma70_r4" amino acids 551 to 604 (54 residues), 66 bits, see alignment 5.1e-22

Best Hits

Swiss-Prot: 86% identical to RPOD_PSEPH: RNA polymerase sigma factor RpoD (rpoD) from Pseudomonas protegens (strain DSM 19095 / LMG 27888 / CHA0)

KEGG orthology group: K03086, RNA polymerase primary sigma factor (inferred from 97% identity to psa:PST_0712)

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

See L0GRZ4 at UniProt or InterPro

Protein Sequence (617 amino acids)

>Psest_3682 RNA polymerase sigma factor, sigma-70 family (Pseudomonas stutzeri RCH2)
MSGKAQQQSRLKELIQRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFEV
APDADALLLAEADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIE
IAKRIEEGIREVMSAIAHFPGTVDSILADYERVTTEGGRLSDILSGYIDPDDDGAAAPQE
VEPEAPQTAAKPAADDKDDEDEEDSDTEEEEGDGGPDPEVARLRFGAVAEQLEKANKALK
KHGRASQQAVEELEALAILFMPIKLVPKQYDALVERVRNALNQIRAQERAIMQLCVRDAR
MPRADFLRQFPSNETNLDWAEQLASGKGKYAEAIGNRKEDIQRCQQMLIELEQECSLAIA
DIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV
DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR
EPTPEELGERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSAMQSPIDVAT
VESLKEATREVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR
KLRHPTRSEHLRSFLDE