Protein Info for GFF2912 in Sphingobium sp. HT1-2

Annotation: DNA-directed RNA polymerase 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 1418 PF04997: RNA_pol_Rpb1_1" amino acids 15 to 343 (329 residues), 286.8 bits, see alignment E=7.1e-89 TIGR02386: DNA-directed RNA polymerase, beta' subunit" amino acids 19 to 1014 (996 residues), 1485.2 bits, see alignment E=0 PF00623: RNA_pol_Rpb1_2" amino acids 345 to 486 (142 residues), 121.6 bits, see alignment E=1.3e-38 PF04983: RNA_pol_Rpb1_3" amino acids 490 to 643 (154 residues), 101.2 bits, see alignment E=1.7e-32 PF05000: RNA_pol_Rpb1_4" amino acids 672 to 759 (88 residues), 72.3 bits, see alignment 8.6e-24 PF04998: RNA_pol_Rpb1_5" amino acids 762 to 1301 (540 residues), 252.8 bits, see alignment E=1.3e-78

Best Hits

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

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

Find the best match in UniProt

Protein Sequence (1418 amino acids)

>GFF2912 DNA-directed RNA polymerase beta (Sphingobium sp. HT1-2)
MNELTNFANPIQKPETFDQIQIGLASPERIRSWSFGEIKKPETINYRTFKPERDGLFCAR
IFGPIKDYECLCGKYKRMKYKGIVCEKCGVEVTVSKVRRERMGHIELAAPVAHIWFLKSL
PSRIGLLLDMQLKQLERVLYFESYIVTEPGLTPLEKYQLLTEDELLDAQDEYGEDAFSAG
IGAEAVKQMLMDLDLEGEKQALLDELAVTKSELKPKKIIKRLKVVESFLESGNRPEWMIL
DVVPVIPPELRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLMELRAPDIIVRNEKRML
QEAVDALFDNGRRGRVITGANKRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVTGP
ELKLHQCGLPKKMALELFKPFIYARLDAKGLSMTLKQAKKWVEKERKEVWDILDEVIREH
PVMLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCSAFNADFDGDQMAVHVPLSLEAQLE
ARVLMMSTNNILSPANGKPIIVPSQDMVLGIYYLSMEREGEPGEGMLLSDMQEVHQALYA
KAVTLHSKIISRVPQTDENGQQYMKRFETTPGRMLLGECLPKSHKVPFDVVNRLLTKKEI
GDVIDQVYRHTGQKDTVLFADAIMSLGFRHAFQAGISFGKDDMVIPDSKVTMVDETKALV
ADYEQQYQDGLITQQEKYNKVIDAWSRCGDQVANAMMDEIRAQPKDPKTGRLAPINSIYM
MAHSGARGSQAQMKQLAGMRGLMAKPSGEIIETPIISNFKEGLTVLEYFNSTHGARKGLA
DTALKTANSGYLTRRLVDVSQDCTIVEDDCGTEKALEMKAIVQGGSVIASLGERILGRTT
AQDIVDSKDGTVIIPIGTLLDEAMITQIEAIGTQAVKIRSPLICESRMGVCGKCYGRDLA
RGTPVNIGEAVGVIAAQSIGEPGTQLTMRTFHIGGAANFNETSNLEALSDGTIELRDMPT
ITDKNGRRLSLARNGEVAIIDSEGRERETHRLPYGATILFADGDAVKKGDRFAEWDPFTM
PVITEKPGIVKYVDLIDNKTLTEQTDEATGIAQRVVIEHRGAARTKEDLRPRLTLMDDNS
GEAARYMLAVGATLSVDDGAEVQAGDVLARVSREAAKTRDITGGLPRVAELFEARKPKDN
AIIAKVSGRVQFLKDYKAKRKIAINPEDGGEPVEYLIPKSKVIDVQEGDYVKRGDNLIGG
SPDPHDILEVLGIEPLAEYLVAEIQEVYRLQGVKINDKHIETIVRQMLQKVEIIESGDTT
LLVGEQVDREEMDEINSKLQPGFAPAAGKPVLLGITKASLQTRSFISAASFQETTRVLTE
AAVQGKKDTLVGLKENVIVGRLIPAGTGAGMNRLRVAASSRDAAMRAALRASAQVDLIAP
KSAAEEHAAELAQGPEAAIGDDPLGAVQGDDFTTQDMD