Protein Info for Synpcc7942_1746 in Synechococcus elongatus PCC 7942

Name: rpoD2
Annotation: group2 RNA polymerase sigma factor SigB

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 50 100 150 200 250 320 TIGR02997: RNA polymerase sigma factor, cyanobacterial RpoD-like family" amino acids 11 to 308 (298 residues), 462.4 bits, see alignment E=6.4e-143 PF00140: Sigma70_r1_2" amino acids 11 to 42 (32 residues), 40.7 bits, see alignment 3.6e-14 TIGR02937: RNA polymerase sigma factor, sigma-70 family" amino acids 85 to 309 (225 residues), 127.9 bits, see alignment E=3e-41 PF04542: Sigma70_r2" amino acids 89 to 159 (71 residues), 84 bits, see alignment E=1e-27 PF04539: Sigma70_r3" amino acids 168 to 243 (76 residues), 92.8 bits, see alignment E=2.3e-30 PF04545: Sigma70_r4" amino acids 256 to 308 (53 residues), 59 bits, see alignment 5.3e-20

Best Hits

Swiss-Prot: 100% identical to SIGA2_SYNE7: RNA polymerase sigma factor SigA2 (sigA2) from Synechococcus elongatus (strain PCC 7942)

KEGG orthology group: K03087, RNA polymerase nonessential primary-like sigma factor (inferred from 100% identity to syc:syc2345_d)

Predicted SEED Role

"Cyanobacteria-specific RpoD-like sigma factor, type-3 @ Group 2 RNA polymerase sigma factor"

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 Q31ME3 at UniProt or InterPro

Protein Sequence (320 amino acids)

>Synpcc7942_1746 group2 RNA polymerase sigma factor SigB (Synechococcus elongatus PCC 7942)
MSTSSAQYSPDLVRAYLQEIGRVRLLTAEEELCFGRQVQRLMMLLDAQTELRDRLGHEPS
KEEWAAAVDLNLEDLDRQIEQGQRAKRKMIEANLRLVVSIAKKYQKRHMEFLDLIQEGTL
GLERGVEKFDPSKGYKFSTYAYWWIRQAITRAIAQQSRTIRLPIHITEKLNKLKKTQREL
SQQLGRSATASELAEVLELPLEQVREYIQMNRQPVSLDVKVGDSQDTELQELLEDEQSSP
SDYVEQESLRRDLRNLMAELTPQQQAVIALRYGLDEGDSLSLAKVGERLNISRERVRKLE
RQAMDHLRRRSRLLAEYAAS