Protein Info for GFF5880 in Variovorax sp. SCN45

Annotation: DNA-directed RNA polymerase beta' 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

1 100 200 300 400 500 600 700 800 900 1000 1100 1200 1300 1411 PF04997: RNA_pol_Rpb1_1" amino acids 16 to 340 (325 residues), 265 bits, see alignment E=3.1e-82 TIGR02386: DNA-directed RNA polymerase, beta' subunit" amino acids 19 to 1365 (1347 residues), 1763.6 bits, see alignment E=0 PF00623: RNA_pol_Rpb1_2" amino acids 342 to 389 (48 residues), 33.2 bits, see alignment (E = 1.9e-11) amino acids 391 to 483 (93 residues), 96.7 bits, see alignment 5.8e-31 PF04983: RNA_pol_Rpb1_3" amino acids 487 to 643 (157 residues), 92.6 bits, see alignment E=7.9e-30 PF05000: RNA_pol_Rpb1_4" amino acids 673 to 763 (91 residues), 75.5 bits, see alignment 8.8e-25 PF04998: RNA_pol_Rpb1_5" amino acids 765 to 1309 (545 residues), 251.5 bits, see alignment E=3e-78

Best Hits

Swiss-Prot: 90% identical to RPOC_ACIAC: DNA-directed RNA polymerase subunit beta' (rpoC) from Acidovorax citrulli (strain AAC00-1)

KEGG orthology group: K03046, DNA-directed RNA polymerase subunit beta' [EC: 2.7.7.6] (inferred from 90% identity to aaa:Acav_4446)

MetaCyc: 66% 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

Find the best match in UniProt

Protein Sequence (1411 amino acids)

>GFF5880 DNA-directed RNA polymerase beta' subunit (EC 2.7.7.6) (Variovorax sp. SCN45)
MKSLLDLFKQFTPDEHFDAIKIGMASPEKIRSWSFGEVKKPETINYRTFKPERDGLFCAK
IFGPIKDYECLCGKYKRLKHRGVICEKCGVEVTQTKVRRERMGHIDLAAPCAHIWFLKSL
PSRLGLVLDMTLRDIERVLYFEAYVITDPGMTPLKKFGIMSEDDYDAKRKEYGDEFIAKM
GAEGIKDLLEGIELDSEIERLRGDLTGSEVKVKKNSKRLKVLEAFRKSGIKPEWMVLDVL
PVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNSRLRRLLELKAPEIIARNEKRMLQEA
VDSLLDNGRRGKAMTGANKRALKSLADMIKGKSGRFRQNLLGKRVDYSGRSVIVVGPTLK
LHQCGLPKLMALELFKPFIFSRLEAMGIATTIKAAKKEVESGTPVVWDILEEVIKEHPVM
LNRAPTLHRLGIQAFEPILIEGKAIQLHPLVCAAFNADFDGDQMAVHVPLSVEAQMEART
LMLASNNVLFPASGEPSIVPSQDVVLGLYYTTRDRINGKGEGLIFSDIGEVQRALDANEV
ELTARVAVRITEYTKNKETGEFTPSTSLVDTTVGRALLSEILPKGLPFSNINKALKKKEI
SKLINVSFRKCGLKETVVFADKLLQNGFRLATKAGISIAIDDMLVPAEKHGIIDRSAKEV
KEIEQQYVSGLVTSGERYNKVVDIWGKAGDEVSKVMMAKLSKQKVIDRHGKEVEQESFNS
IYMMADSGARGSAAQIRQVAGMRGLMAKPDGSIIETPITANFREGLNVLEYFISTHGARK
GLADTALKTANSGYLTRRLVDVTQDLVVTEQDCGTHGGYLMRAIVEGGEVIESLRDRILG
RSAADDVLHPENRSVLLKAGEMFDEDNIEALEAQGVDEVKVRTALTCETRFGICATCYGR
DLGRGGLINIGEAVGVIAAQSIGEPGTQLTMRTFHIGGAASRAAIASSVEAKSNGSIGFN
ATMRYVTNSKGELVVISRSGEIVIHDEHGRERERHKVPYGATLTVKADQQIKAGHVLANW
DPLTRPIITEFAGKTQFENVEEGLTVAKQVDEVTGLSTLVVIDPKRRGAAKVVRPQVKLI
DAQGQEVKIPGTDHSVTIGFPIGALVQIRDGQDVGPGEVLARIPVEGQKTRDITGGLPRV
AELFEARSPKDKGMLAEMTGTVSFGKETKGKIRLQITDPEGTVWEDLVPKEKNILVHEGQ
VVNKGESVVDGPADPQDILRLLGSEELARYIVDEVQDVYRLQGVKINDKHIEVIVRQMLR
RVVVDNIGETGYISGEQVERSEMLNTNDALRAEGKIPATFTNLLLGITKASLSTDSFISA
ASFQETTRVLTEAAIMGKRDELRGLKENVIVGRLIPAGTGMAYHQARKVKDAMDEAERRA
IAESEAAELAGSGDSDAATSTVDASEGAATE