Protein Info for ABID97_RS10535 in Variovorax sp. OAS795

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 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 784 PF03979: Sigma70_r1_1" amino acids 168 to 247 (80 residues), 84.2 bits, see alignment E=1.5e-27 PF00140: Sigma70_r1_2" amino acids 264 to 295 (32 residues), 45.5 bits, see alignment (E = 1.7e-15) PF04546: Sigma70_ner" amino acids 306 to 518 (213 residues), 189.9 bits, see alignment E=1.7e-59 TIGR02937: RNA polymerase sigma factor, sigma-70 family" amino acids 545 to 770 (226 residues), 137.2 bits, see alignment E=4.2e-44 TIGR02393: RNA polymerase sigma factor RpoD" amino acids 545 to 781 (237 residues), 390.1 bits, see alignment E=3.9e-121 PF04542: Sigma70_r2" amino acids 549 to 619 (71 residues), 82.2 bits, see alignment E=5.6e-27 PF04539: Sigma70_r3" amino acids 628 to 703 (76 residues), 78.1 bits, see alignment E=1.3e-25 PF04545: Sigma70_r4" amino acids 718 to 770 (53 residues), 64.4 bits, see alignment 1.6e-21

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 (784 amino acids)

>ABID97_RS10535 RNA polymerase sigma factor RpoD (Variovorax sp. OAS795)
MPSSKKPAPSLAKGAAAKPVAEKPLKAGAMPATKTGAAASKSAAATKVKTVSTKSTPIDD
PKKAAAKTVATAPAAKKVGRPPKAAGAAAPATGAKRGRKPKAGNDAPESDIDLSDIEEDL
AGDEPAVASTTEEKVKPLRMKISKAKERALMKEFGLDETVLSEEDLAKRRSRLKTLITLG
KTRGYLTHGEISDHLPDKLVDAETMEVVVTMLNDMGVAVYEQTPDAETLLLNNTAPTATT
VEEAEEEAEAALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEGGLMAMME
AISASPATIAEILRLAADIREGKVVISTVVDGFSNPNEADDYVAEEDFDEFDEEDDDDGK
GGSKALTKKLEELKRDALERFDRIASMFEKVHKIYDKEGYGTPAYQKAQQALSEELMTIR
FTAKTIEKLCDLVRTQVDDVRKKERELRRIIVDKCGFPQDEFIRDFSGYDKNGNRIPSNL
LNLKWVEKQAAAGKPWSAVLARNIPPVQELQQKLTDIQSRVVVPLTQLKEINKRMNEGES
SSRDAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY
ATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQEFGFEPDAGILAAKMEIP
EDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDSSNTAPIEAAMQAGLRDVVKDILDS
LTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLKHPSRSDKLRSF
IDTL