Protein Info for Atu1956 in Agrobacterium fabrum C58

Annotation: DNA-directed RNA polymerase beta chain

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 1378 TIGR02013: DNA-directed RNA polymerase, beta subunit" amino acids 12 to 1360 (1349 residues), 1947.4 bits, see alignment E=0 PF04563: RNA_pol_Rpb2_1" amino acids 29 to 507 (479 residues), 87.9 bits, see alignment E=2e-28 PF04561: RNA_pol_Rpb2_2" amino acids 160 to 231 (72 residues), 25 bits, see alignment 4.3e-09 amino acids 357 to 464 (108 residues), 72 bits, see alignment 1.6e-23 PF04565: RNA_pol_Rpb2_3" amino acids 523 to 591 (69 residues), 106.5 bits, see alignment 1.8e-34 PF10385: RNA_pol_Rpb2_45" amino acids 601 to 666 (66 residues), 87.2 bits, see alignment 1.8e-28 PF00562: RNA_pol_Rpb2_6" amino acids 728 to 1285 (558 residues), 462.5 bits, see alignment E=3.4e-142 PF04560: RNA_pol_Rpb2_7" amino acids 1287 to 1361 (75 residues), 96.7 bits, see alignment 2.6e-31

Best Hits

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 Q8UE08 at UniProt or InterPro

Protein Sequence (1378 amino acids)

>Atu1956 DNA-directed RNA polymerase beta chain (Agrobacterium fabrum C58)
MAQTLSFNGRRRVRKFFGKIPEVAEMPNLIEVQKASYDQFLMVDEPKGGRPDEGLNAVFK
SVFPITDFSGASMLEFVSYEFEAPKFDVEECRQRDLTYAAPLKVTLRLIVFDIDEDTGAK
SIKDIKEQSVYMGDMPLMTNNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKSHSSGKLLF
AARVIPYRGSWLDIEFDAKDIVYARIDRRRKLPVTSLLMALGMDGEEILSTFYTKATYER
SGDGWRIPFQPEALKNAKVITDMIDADTGEVVVEGGKKLTPRLIRQLVDKGLKALKATDE
DLYGNYLAEDIVNYSTGEIYLEAGDEIDEKTLGLILQSGFDEIPVLNIDHVNVGAYIRNT
LSADKNQNRQEALFDIYRVMRPGEPPTMDSAEAMFNSLFFDAERYDLSAVGRVKMNMRLD
LDAEDTVRTLRKEDILAVVKMLVELRDGKGEIDDIDNLGNRRVRSVGELMENQYRLGLLR
MERAIKERMSSIEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQVNPLSEITHKRRL
SALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESP
YRKIIDGKVTTDVIYLSAMEEAKYYVAQANAELDGEGAFTEEFVVCRHSGEVMLAPRDNI
NLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLLRAEAPFVGTGMEPIVAR
DSGAAIAARRGGVVDQVDATRIVIRATEDLDAGKSGVDIYRLQKFQRSNQNTCVNQRPLV
SVGDAISKGDIIADGPSTDLGDLALGRNALVAFMPWNGYNYEDSILMSERIVSDDVFTSI
HIEEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVQPGDILVGKITPKG
ESPMTPEEKLLRAIFGEKASDVRDTSMRMPPGTFGTIVEVRVFNRHGVEKDERAMAIERE
EIERLAKDRDDEQAILDRNVYGRLIDMLRGHVSIAGPKGFKKGVELSNAVVSEYPRSQWW
MFAVEDEKAQSELEALRGQYDESKSRLEQRFMDKVEKVQRGDEMPPGVMKMVKVFVAVKR
KIQPGDKMAGRHGNKGVVSRIVPVEDMPFLEDGTHVDICLNPLGVPSRMNVGQILETHLA
WACAGMGKKIGEMLEEYRKTMDISELRSELTEIYASEANDEVQRFDDDSLVKLAEEAKRG
VSIATPVFDGAHEPDVAAMLKKAGLHESGQSVLYDGRTGEPFDRKVTVGYMYMIKLNHLV
DDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVA
GRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLSVELENSKIENQSEDQLPDAAE