Protein Info for Xcc-8004.4729.1 in Xanthomonas campestris pv. campestris strain 8004

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 50 100 150 200 250 300 350 400 450 500 550 624 PF03979: Sigma70_r1_1" amino acids 8 to 87 (80 residues), 100.9 bits, see alignment E=9.3e-33 PF00140: Sigma70_r1_2" amino acids 104 to 135 (32 residues), 47.9 bits, see alignment (E = 3.2e-16) PF04546: Sigma70_ner" amino acids 145 to 358 (214 residues), 184.2 bits, see alignment E=9.2e-58 TIGR02393: RNA polymerase sigma factor RpoD" amino acids 385 to 621 (237 residues), 403 bits, see alignment E=4.5e-125 TIGR02937: RNA polymerase sigma factor, sigma-70 family" amino acids 385 to 610 (226 residues), 133.2 bits, see alignment E=6.7e-43 PF04542: Sigma70_r2" amino acids 389 to 459 (71 residues), 82.8 bits, see alignment E=3.5e-27 PF04539: Sigma70_r3" amino acids 468 to 543 (76 residues), 106.9 bits, see alignment E=1.4e-34 PF04545: Sigma70_r4" amino acids 557 to 610 (54 residues), 68.6 bits, see alignment 8e-23

Best Hits

Swiss-Prot: 100% identical to RPOD_XANCP: RNA polymerase sigma factor RpoD (rpoD) from Xanthomonas campestris pv. campestris (strain ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25)

KEGG orthology group: K03086, RNA polymerase primary sigma factor (inferred from 100% identity to xcc:XCC3736)

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 A0A0H2XBP7 at UniProt or InterPro

Protein Sequence (624 amino acids)

>Xcc-8004.4729.1 RNA polymerase sigma factor RpoD (Xanthomonas campestris pv. campestris strain 8004)
MANERPAQQSDIKLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHE
VAPDAETLLLNDGNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLT
REGEIAIAKRIEEGLSQVQAALGTFPLSTELLLSDYEAHKEGKKRLAEIVVGFNDLIEEA
DAAAAALAAAGPVAVDEDAVDEDADEDGDDDAAEEEAGPTGPDPVEVATRMENLANEYAK
FKKAYVKYGAEHKNVAKAREDMAAIFTTLKLPLPLTDALVTQLRGVVNGIKDHERKVLHL
ATTVARMPRKDFIRSWEGNQTNLEWVEDALKRKQKWSSALRDVKDQIVSEQQGSIEMEKA
NYLTLAEIKDISRAMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNI
GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQM
LQQFGREATPEELAKEMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVES
PIDNTTNINLSETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQI
EAKALRKLRHPSRSEQLRSFLDID