Protein Info for GFF2879 in Variovorax sp. SCN45

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 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 776 PF03979: Sigma70_r1_1" amino acids 160 to 239 (80 residues), 83.5 bits, see alignment E=2.5e-27 PF00140: Sigma70_r1_2" amino acids 256 to 287 (32 residues), 46 bits, see alignment (E = 1.2e-15) PF04546: Sigma70_ner" amino acids 298 to 510 (213 residues), 186.8 bits, see alignment E=1.6e-58 TIGR02937: RNA polymerase sigma factor, sigma-70 family" amino acids 537 to 762 (226 residues), 137.2 bits, see alignment E=4.1e-44 TIGR02393: RNA polymerase sigma factor RpoD" amino acids 537 to 773 (237 residues), 390.1 bits, see alignment E=3.8e-121 PF04542: Sigma70_r2" amino acids 541 to 611 (71 residues), 82.1 bits, see alignment E=5.8e-27 PF04539: Sigma70_r3" amino acids 620 to 695 (76 residues), 78.1 bits, see alignment E=1.3e-25 PF04545: Sigma70_r4" amino acids 710 to 762 (53 residues), 65.5 bits, see alignment 7.4e-22

Best Hits

KEGG orthology group: K03086, RNA polymerase primary sigma factor (inferred from 96% identity to vpe:Varpa_1936)

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 (776 amino acids)

>GFF2879 RNA polymerase sigma factor RpoD (Variovorax sp. SCN45)
MPSSKKPAPSLAKSVATKPAAEKPLKAGQSPATKTGAAASKSAAATKVKTVPTKSTSLDD
PKKAAAPAAKKVGRPPKAAGAATTGAKRGRKPKADKDAPESDIDLSDIEDDLAGDEPAAT
TTTEEKVKPLRMKISKAKERALMKEFGLDETVLSEEDLAKRRSRLKTLITLGKTRGYLTH
GEISDHLPDKLVDAETMEVVVTMLNDMGVAVYEQTPDAETLLLNNTAPTATTVEEAEEEA
EAALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEGGLMAMMEAISASPAT
IAAILEMAATIREGKVVISTIVDGFSNPNEADDYVAEEDFDEFDEEDDDDGKGGSKALTK
KLEELKRDALERFDRIASLFEKVHKIYDKEGYGTPAYVKAQEAMSEELMTIRFTAKTIEK
LCDLVRTQVDDVRKKERELRRIIVDKCGFPQEEFIRDFSGFDKNGNVVASNLLNLKWVEK
QAAAGKPWSAVLARNIPPVQELQQRLTDIQSRVVVPLTQLKDINKRMNEGESSSRDAKKE
MIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA
ITRSIADQARTIRIPVHMIETINKMNRISRQHLQEFGFEPDAGILAAKMEIPEDKIRKIM
KIAKEPISMETPIGDDDDSHLGDFIEDSSNTAPIEAAMQAGLRDVVKDILDSLTPREAKV
LRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLKHPSRSDKLRSFIDTL