Protein Info for CCNA_03142 in Caulobacter crescentus NA1000

Annotation: RNA polymerase sigma factor 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 50 100 150 200 250 300 350 400 450 500 550 600 652 PF03979: Sigma70_r1_1" amino acids 25 to 89 (65 residues), 75.8 bits, see alignment E=6.3e-25 PF00140: Sigma70_r1_2" amino acids 113 to 145 (33 residues), 49.9 bits, see alignment (E = 7.7e-17) PF04546: Sigma70_ner" amino acids 157 to 386 (230 residues), 131.8 bits, see alignment E=1e-41 TIGR02393: RNA polymerase sigma factor RpoD" amino acids 414 to 650 (237 residues), 397.7 bits, see alignment E=1.8e-123 TIGR02937: RNA polymerase sigma factor, sigma-70 family" amino acids 414 to 639 (226 residues), 130.6 bits, see alignment E=4.4e-42 PF04542: Sigma70_r2" amino acids 418 to 488 (71 residues), 82.7 bits, see alignment E=3.8e-27 PF04539: Sigma70_r3" amino acids 497 to 572 (76 residues), 102.5 bits, see alignment E=3.2e-33 PF04545: Sigma70_r4" amino acids 586 to 639 (54 residues), 65.2 bits, see alignment 9e-22

Best Hits

Swiss-Prot: 100% identical to RPOD_CAUVC: RNA polymerase sigma factor RpoD (rpoD) from Caulobacter vibrioides (strain ATCC 19089 / CB15)

KEGG orthology group: K03086, RNA polymerase primary sigma factor (inferred from 100% identity to ccs:CCNA_03142)

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 A0A0H3CAV3 at UniProt or InterPro

Protein Sequence (652 amino acids)

>CCNA_03142 RNA polymerase sigma factor rpoD (Caulobacter crescentus NA1000)
MSNNSSAETEAPETTGGDGPLLDLTDAGVKKFIKQAKARGYVTMDELNKVLPSEEVSPDA
IEDTLAMLSEMGVNVVEAEEDAENAEGGEVATRDENTTVIASDKPAAYDRTDDPVRMYLR
EMGSVELLSREGEIAIAKRIEAGRDTMIRGLCESALTFEAIMVWREELGTGRILLREVID
LEGTYAAINGVAAQPAAEDDEGPAEPVDDEAGEAKAEGAEGEDEDDFDDGAGPTVSAMEG
ELREGVMAILDAIASEFEAFRKLQDKLVGSRLKGEDLSDADRKAYEGLSATIIQHLKTLK
LNNNRIEALVEQLYAINKRLIGLEGRLLRLADSYGISRGEFLKAYFGSELNPTWSEQVKA
MGVRWTKFVENDSQSVTDIRSEIAALATETGVPIDDYRRIVQTVQKGEREARQAKKEMVE
ANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITR
SIADQARTIRIPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIA
KEPISLETPIGDEEDSHLGDFIEDKNAILPIDAAIQSNLRETTTRVLASLTPREERVLRM
RFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLDS