Protein Info for GFF3193 in Sphingobium sp. HT1-2

Annotation: DNA-directed RNA polymerase alpha subunit (EC 2.7.7.6)

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 50 100 150 200 250 300 353 TIGR02027: DNA-directed RNA polymerase, alpha subunit" amino acids 29 to 331 (303 residues), 376.6 bits, see alignment E=4.1e-117 PF01193: RNA_pol_L" amino acids 34 to 229 (196 residues), 83.4 bits, see alignment E=1.1e-27 PF01000: RNA_pol_A_bac" amino acids 64 to 179 (116 residues), 115 bits, see alignment E=3.5e-37 PF03118: RNA_pol_A_CTD" amino acids 259 to 322 (64 residues), 89.6 bits, see alignment E=1.3e-29

Best Hits

Swiss-Prot: 88% identical to RPOA_SPHAL: DNA-directed RNA polymerase subunit alpha (rpoA) from Sphingopyxis alaskensis (strain DSM 13593 / LMG 18877 / RB2256)

KEGG orthology group: K03040, DNA-directed RNA polymerase subunit alpha [EC: 2.7.7.6] (inferred from 94% identity to sjp:SJA_C1-05790)

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

Find the best match in UniProt

Protein Sequence (353 amino acids)

>GFF3193 DNA-directed RNA polymerase alpha subunit (EC 2.7.7.6) (Sphingobium sp. HT1-2)
MTVNMKNWQELKKPNALEIKPTGDGKRKATFVAEPLERGFGLTLGNALRRVLLSSLQGAA
VTSIKIENVLHEFSSLAGVREDVTDIVLNIKQVALKMEGEGPKRLQLSATGPAVVKAGDI
AVVGDIEVMNPDLVICHLDQGATLNMELTADIGKGYVPAVANRPADAPIGLIPVDALYSP
VRQVAYKVDNTRVGQELDYDKLSLTLETDGTVTPEDAIAYAARILQDQLQLFVHFEDALP
AAAPAAGHAAAAASEGESDTNQINRYLLKKVDELELSVRSANCLKNDNIIYIGDLVQKTE
AEMLRTPNFGRKSLNEIKEVLSSMGLRLGMDIPGWPPENIEEMAKKLEQELLG