Protein Info for Psest_3580 in Pseudomonas stutzeri RCH2

Annotation: DNA-directed RNA polymerase, alpha subunit, bacterial and chloroplast-type

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 50 100 150 200 250 300 333 TIGR02027: DNA-directed RNA polymerase, alpha subunit" amino acids 24 to 315 (292 residues), 359.9 bits, see alignment E=5e-112 PF01193: RNA_pol_L" amino acids 29 to 227 (199 residues), 90.8 bits, see alignment E=5.4e-30 PF01000: RNA_pol_A_bac" amino acids 60 to 177 (118 residues), 123 bits, see alignment E=1.2e-39 PF03118: RNA_pol_A_CTD" amino acids 244 to 307 (64 residues), 84.2 bits, see alignment E=6.2e-28

Best Hits

Swiss-Prot: 100% identical to RPOA_PSEU5: DNA-directed RNA polymerase subunit alpha (rpoA) from Pseudomonas stutzeri (strain A1501)

KEGG orthology group: K03040, DNA-directed RNA polymerase subunit alpha [EC: 2.7.7.6] (inferred from 100% identity to psa:PST_0809)

MetaCyc: 73% identical to RNA polymerase subunit alpha (Escherichia coli K-12 substr. MG1655)
DNA-directed RNA polymerase. [EC: 2.7.7.6]

Predicted SEED Role

"DNA-directed RNA polymerase alpha subunit (EC 2.7.7.6)" in subsystem RNA polymerase bacterial (EC 2.7.7.6)

KEGG Metabolic Maps

Isozymes

Compare fitness of predicted isozymes for: 2.7.7.6

Use Curated BLAST to search for 2.7.7.6

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 L0GRY5 at UniProt or InterPro

Protein Sequence (333 amino acids)

>Psest_3580 DNA-directed RNA polymerase, alpha subunit, bacterial and chloroplast-type (Pseudomonas stutzeri RCH2)
MQSSVNEFLTPRHIDVQVVSPTRAKITLEPLERGFGHTLGNALRRILLSSMPGCAVVEAE
IDGVLHEYSAIEGVQEDVIEILLNLKGIAIKLHGRDEVTLSLVKKGAGAVTAADIQLDHD
VEIVNGDHLIANLAANGSLNMKLKVARGRGYEPADARQSDEDESRSIGRLQLDATFSPVR
RVAYVVENARVEQRTNLDKLVIDLETNGTLDPEEAIRRAATILQQQLAAFVDLKGDSEPV
VIEQEDEIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNLGKKSLT
EIKDVLASRGLSLGMRLDNWPPASLKKDDKATA