Protein Info for Atu1304 in Agrobacterium fabrum C58

Annotation: DNA topoisomerase I

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 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 800 850 892 PF01751: Toprim" amino acids 3 to 114 (112 residues), 64.1 bits, see alignment E=2.3e-21 TIGR01051: DNA topoisomerase I" amino acids 4 to 641 (638 residues), 770.5 bits, see alignment E=9.7e-236 PF01131: Topoisom_bac" amino acids 130 to 561 (432 residues), 397.2 bits, see alignment E=1.8e-122 PF01396: Zn_ribbon_Top1" amino acids 607 to 642 (36 residues), 50 bits, see alignment (E = 4.2e-17) PF13368: Toprim_C_rpt" amino acids 662 to 716 (55 residues), 45.5 bits, see alignment 1.1e-15 amino acids 720 to 774 (55 residues), 60.2 bits, see alignment 2.9e-20 amino acids 788 to 840 (53 residues), 68 bits, see alignment 1.1e-22

Best Hits

Swiss-Prot: 50% identical to TOP1_RICFE: DNA topoisomerase 1 (topA) from Rickettsia felis (strain ATCC VR-1525 / URRWXCal2)

KEGG orthology group: K03168, DNA topoisomerase I [EC: 5.99.1.2] (inferred from 100% identity to atu:Atu1304)

Predicted SEED Role

"DNA topoisomerase I (EC 5.99.1.2)" in subsystem Conserved gene cluster associated with Met-tRNA formyltransferase or DNA topoisomerases, Type I, ATP-independent or pVir Plasmid of Campylobacter (EC 5.99.1.2)

Isozymes

Compare fitness of predicted isozymes for: 5.99.1.2

Use Curated BLAST to search for 5.99.1.2

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 A9CJ93 at UniProt or InterPro

Protein Sequence (892 amino acids)

>Atu1304 DNA topoisomerase I (Agrobacterium fabrum C58)
MNVVVVESPAKAKTINKYLGSGYKVLASFGHVRDLPAKDGSVLPDQDFEMSWEVDSASAK
RMKDIADAVKSSDGLFLATDPDREGEAISWHVLDLLKKKRVLGDKPVKRVVFNAITKKAV
LDAMANPRDIDVPLVDAYLARRALDYLVGFNLSPVLWRKLPGARSAGRVQSVALRLVCDR
ESEIERFVSEEYWNISALLKTPRGDEFEAKLVSADGKRLQSRGIKTGEDANRLKALLEGA
TYVVDTVEAKPVKRNPGPPFTTSTLQQAASSRMGFGASRTMQVAQKLYEGIDIGGETVGL
ITYMRTDGVQIAPEAIDAARLAIGEQFGERYVPEKARFYSTKAKNAQEAHEAIRPTDFTR
TPDQVKRYLDADQLRLYDLIWKRGIASQMASAEIERTTVEILADKNGEKAGLRAVGSVIR
FDGFIAAYTDQKEDGEQSDDGDDEGRLPQINARENLAKQKINASQHFTEPPPRYSEASLI
KKMEELGIGRPSTYAATLKTLSDREYIVIDKRKLIPHSRGRLVTAFLESFFTKYVEYDFT
AALEEKLDRISAGELDWKQVLRDFWKDFFAQIEDTKELRVTNVLDALNEVLAPLVFPKRE
DGSDPRICQVCGTGNLSLKLGKYGAFVGCSNYPECNYTRQLTSDGAEADAAASNEPKALG
ADPMTGEELTLRSGRFGPYIQRGDGKEAKRSSLPKGWKPEDIDHEKALALINLPRDIGKH
PETGKMISAGLGRYGPFLLHDGSYANLESIEDVFSIGLNRAVTVIAEKQAKGPGRSGTPA
ALKELGDHPDGGAITVRDGRYGAYVNWGKVNATIPKGQDPASVTLDESLVLIAERIAKTG
TGGKPAKAKKTTAKKADGEAAAKPKATKAKAATKSKAAAKPKAAAKTKKAAE