Protein Info for Psyr_4641 in Pseudomonas syringae pv. syringae B728a ΔmexB

Annotation: RNA polymerase, sigma 70 subunit, 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 50 100 150 200 250 300 350 400 450 500 550 616 PF03979: Sigma70_r1_1" amino acids 6 to 83 (78 residues), 100.5 bits, see alignment E=1.3e-32 PF00140: Sigma70_r1_2" amino acids 98 to 128 (31 residues), 48.6 bits, see alignment (E = 1.9e-16) PF04546: Sigma70_ner" amino acids 139 to 351 (213 residues), 206.3 bits, see alignment E=1.6e-64 TIGR02393: RNA polymerase sigma factor RpoD" amino acids 378 to 614 (237 residues), 402.7 bits, see alignment E=5.3e-125 TIGR02937: RNA polymerase sigma factor, sigma-70 family" amino acids 378 to 603 (226 residues), 124.2 bits, see alignment E=4e-40 PF04542: Sigma70_r2" amino acids 382 to 452 (71 residues), 82.9 bits, see alignment E=3.5e-27 PF04539: Sigma70_r3" amino acids 461 to 536 (76 residues), 102.9 bits, see alignment E=2.5e-33 PF04545: Sigma70_r4" amino acids 550 to 603 (54 residues), 65.6 bits, see alignment 6.6e-22

Best Hits

Swiss-Prot: 93% identical to RPOD_PSEPH: RNA polymerase sigma factor RpoD (rpoD) from Pseudomonas protegens (strain DSM 19095 / LMG 27888 / CHA0)

KEGG orthology group: K03086, RNA polymerase primary sigma factor (inferred from 100% identity to psb:Psyr_4641)

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 Q4ZMF1 at UniProt or InterPro

Protein Sequence (616 amino acids)

>Psyr_4641 RNA polymerase, sigma 70 subunit, RpoD (Pseudomonas syringae pv. syringae B728a ΔmexB)
MSGKAQQQSRIKELITLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHES
APDADALMLADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIE
IAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVLSGYIDPDDGIAPPAEV
PPPVDPKAVKAEGADDDEEESADASDEEDEVESGPDPVIAQQRFGAVSDQMEITRKALKK
FGRDDKHAIAEMVALAELFMPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARM
PRADFLRQFPGNEVDESWTDALAKGKSKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAE
IKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD
KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGRE
PTPEELGERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATV
ESLKEATREVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRK
LRHPTRSEHLRSFLDE