Protein Info for DVU2929 in Desulfovibrio vulgaris Hildenborough JW710

Name: rpoC
Annotation: DNA-directed RNA polymerase, beta prime subunit (TIGR)

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

1 100 200 300 400 500 600 700 800 900 1000 1100 1200 1300 1385 PF04997: RNA_pol_Rpb1_1" amino acids 20 to 348 (329 residues), 296.3 bits, see alignment E=1.1e-91 TIGR02386: DNA-directed RNA polymerase, beta' subunit" amino acids 25 to 1354 (1330 residues), 1767.8 bits, see alignment E=0 PF00623: RNA_pol_Rpb1_2" amino acids 350 to 403 (54 residues), 34.9 bits, see alignment (E = 6.4e-12) amino acids 397 to 491 (95 residues), 92.7 bits, see alignment 1.2e-29 PF04983: RNA_pol_Rpb1_3" amino acids 495 to 638 (144 residues), 96.5 bits, see alignment E=5.6e-31 PF05000: RNA_pol_Rpb1_4" amino acids 667 to 759 (93 residues), 75.7 bits, see alignment 9.3e-25 PF04998: RNA_pol_Rpb1_5" amino acids 761 to 1296 (536 residues), 241.7 bits, see alignment E=3.6e-75

Best Hits

KEGG orthology group: K03046, DNA-directed RNA polymerase subunit beta' [EC: 2.7.7.6] (inferred from 59% identity to aap:NT05HA_1812)

MetaCyc: 60% identical to RNA polymerase subunit beta' (Escherichia coli K-12 substr. MG1655)
DNA-directed RNA polymerase. [EC: 2.7.7.6]

Predicted SEED Role

"DNA-directed RNA polymerase beta' 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 Q727C6 at UniProt or InterPro

Protein Sequence (1385 amino acids)

>DVU2929 DNA-directed RNA polymerase, beta prime subunit (TIGR) (Desulfovibrio vulgaris Hildenborough JW710)
MTLDDLFTVRGSAANIANIRNLKAIQITIASPENIREWSYGEVKKPETINYRTFKPERDG
LFCAKIFGPVKDYECNCGKYKRMKHRGIVCEKCGVEVIASKVRRERMGHIELAAPVAHIW
FLKTLPSKIGTLLDMTMADLEKVLYFDSYIVLDPGSTNLTKMQVISEDQYLQVIDHYGED
ALTVGMGAEAVRSLLEELNLEELRVQLREESQATKSQTKKKKLTKRLKIVEAFLESNNKP
EWMVMEVIPVIPPELRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLMELGAPDIIIRN
EKRMLQEAVDALFDNGRRGRAITGTNGRPLKSLSDMIKGKQGRFRQNLLGKRVDYSGRSV
IVVGPKLKLHQCGLPKKMALELFKPFIYSELEKRGLASTIKSAKKMVEREELVVWDILEE
VVREYPIMLNRAPTLHRLGIQSFEPLLVEGKAIQLHPLVCSAYNADFDGDQMAVHVPLSV
EAQIECRVLMMSTNNILSPANGSPVIVPSQDIVLGLYYMTVDRSFEKGENMSFCAPWEVV
AAYDAGVVALHARINVRMEDGKVVRTTVGRILVWELLPHCVPFSMVNTTLTKKNIARLVS
TAYRDAGTKATVILCDRLKDVGYEYATRAGVTIAVKDLTIPSTKKGLIETAQNEVDDIER
QYRDGIITRTEKYNKVVDVWTKATQDVSNEMIREISSDIVEDPRTGAKEANSSFNSIYMM
STSGARGNQDQMRQLAGMRGLMAKPSGEIIETPITSSFREGLSVLQYFTSTHGARKGLAD
TALKTANSGYLTRRLVDVVQDVIVSEHDCGTVDGIELTHIKEGGEIKIPLADRALGRVLL
YPVYDPETRDLLFPENTLVDENVAKVLVEREVSSVMIRSALTCQSDRGICTLCYGRDLAR
GHIVNIGETVGIIAAQSIGEPGTQLTMRTFHIGGTASREIERSSFEAQHPGRVILSRVKA
VRNRDGQYMVMGKSGQLAIVDDQGREREKYTLPNGSRLLVTEGEEIRKGQILAEWDPFNE
PFVSEVDGVIRFSDIVEGKTFQEKMDEATRMTTQTIIEYRTTNFRPSISICDEHGEVKMR
GNNIPATYSLPVGAIIMVKNGQDLQAGDIIARKPRETSKTKDIVGGLPRVAELFEVRKPK
DMAVVSEIAGIVTYAGETKGKRKLVVTPEIGEAKEYLVPKGKHITVTDGDFVEAGDLLTE
GHPELHDILRTRGEKYLARYLTDEIQEVYRFQGVAIDDKHIEVIVRQMLKKVTVLDPGGT
TFLVGEQVDKGEFRVENTRAMGEGRTPATAEPLVLGITQASLTTSSFISAASFQETTKVL
TEASLRGKMDYLRGLKENVIVGRLIPAGTGYREYVNTDILVPEQRERPDKFLEDLEENPL
LVDIY