Protein Info for GFF9 in Xanthobacter sp. DMC5

Annotation: DNA-directed RNA polymerase subunit beta'

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 1394 PF04997: RNA_pol_Rpb1_1" amino acids 17 to 344 (328 residues), 287.5 bits, see alignment E=3.5e-89 TIGR02386: DNA-directed RNA polymerase, beta' subunit" amino acids 20 to 1025 (1006 residues), 1490.7 bits, see alignment E=0 PF00623: RNA_pol_Rpb1_2" amino acids 346 to 487 (142 residues), 121.3 bits, see alignment E=1.2e-38 PF04983: RNA_pol_Rpb1_3" amino acids 491 to 644 (154 residues), 92.5 bits, see alignment E=7.1e-30 PF05000: RNA_pol_Rpb1_4" amino acids 673 to 760 (88 residues), 77.5 bits, see alignment 1.8e-25 PF04998: RNA_pol_Rpb1_5" amino acids 763 to 1308 (546 residues), 233.5 bits, see alignment E=8.2e-73

Best Hits

Swiss-Prot: 69% identical to RPOC_ACICJ: DNA-directed RNA polymerase subunit beta' (rpoC) from Acidiphilium cryptum (strain JF-5)

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 (1394 amino acids)

>GFF9 DNA-directed RNA polymerase subunit beta' (Xanthobacter sp. DMC5)
MNQEILNVFNPTVPAPSFNQIRISIASPEKIKSWSYGEIKKPETINYRTFKPERDGLFCA
RIFGPIKDYECLCGKYKRMKYKGIICEKCGVEVTLSRVRRERMGHIELAAPVAHIWFLKS
LPSRIGLLLDMTLKDLERILYFEYFVVIEPGITKLKYRQLLSEDDYLRAQDEYGESSFTA
MIGAEAIRELLRSMDLEKIAADLRQEIAEATTELKPKKLAKRLKIVEAFQLSGNKPEWMI
LTHVPVIPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLIELRAPDIIIRNEKRM
LQEAVDALFDNGRRGRVITGANKRPLKSLADMLKGKQGRFRQNLLGKRVDYSGRSVIVVG
PELKLHQCGLPKKMALELFKPFIYSRLDAKGHSATVKQAKKLVEKERPEVWDILDEVIRE
HPVMLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCSAFNADFDGDQMAVHVPLSLEAQL
EARVLMMSTNNILHPANGQPIIVPSQDIVLGLYYLSIMKEKEPGEGMMFANMAEIDHALN
AKAITLATKIKGRYIGIGPDGKQYSKIYETTPGRMKIGELLPKDPKLSYDVVNKLMTKKE
ISNMIDAVYRHCGQKESVIFCDRIMALGFYNAFRAGISFGKDDMVVPKKKWELVEETRAL
TKEYEQQYNDGLITQGEKYNKVVDAWGKCSDRVAEEMMKEISSVKKDPKTGREKQINSIY
MMSHSGARGSPAQMKQLAGMRGLMAKPSGEIIESPIISNFKEGLTVMEYFNSTHGARKGL
ADTALKTANSGYLTRRLVDVAQDSIITERDCGSEKGIHMRAIIDAGQIVASLASRVLGRT
AAEDIVEPATGDVIVPKGQMIEEPHVERINKSGIQEIKIRSVLTCETRNGVCGTCYGRDL
ARGTPVNMGEAVGVIAAQSIGEPGTQLTMRTFHIGGAATLADSSFVESNFEGTVRIRNRN
VARNSDGDLVVMARNLAVVIVDHDGTERAVNRVQYGARLKVDEGDTIKRGQRIAEWDPYT
RPILSEVDGTVAFEDLMEGSSMNEQVDESTGIAKRVVTDSRSGRGPELRPAILIKGKDGK
IIKLPRGGDARYALPVEAIISVDPNQTLKAGDAVARVPLESAKTRDITGGLPRVAELFEA
RRPKDAAIIAEISGSIRFGRDYKNKRRLSIEPTDGGDPVEYLIPKGKHIHLQDGDVVEKG
DFIVDGNPAPHDILAIKGVEELAAFLVNEIQEVYRLQGVHINDKHIEVIVRNMLQKVEID
DSGETDFLDNEQVDRLEFLEANEKAAEEGKKPATGHPVLLGITKASLQTRSFFSAASFQE
TTRVLTEAAVNGKIDPLEGLKENVIVGRLIPAGTGAQMSRLRTIATNRDDLIVATRDEQG
EGQPLVEGPADAAE