Protein Info for GFF934 in Xanthobacter sp. DMC5

Annotation: DNA topoisomerase 1

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 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 800 850 907 PF01751: Toprim" amino acids 15 to 127 (113 residues), 73.6 bits, see alignment E=2.5e-24 TIGR01051: DNA topoisomerase I" amino acids 16 to 650 (635 residues), 769.6 bits, see alignment E=1.8e-235 PF01131: Topoisom_bac" amino acids 142 to 570 (429 residues), 410.9 bits, see alignment E=1.3e-126 PF01396: Zn_ribbon_Top1" amino acids 616 to 650 (35 residues), 55 bits, see alignment (E = 1.1e-18) PF13368: Toprim_C_rpt" amino acids 667 to 723 (57 residues), 48.2 bits, see alignment 1.7e-16 amino acids 728 to 783 (56 residues), 72.2 bits, see alignment 5.4e-24 amino acids 796 to 847 (52 residues), 77 bits, see alignment 1.7e-25

Best Hits

KEGG orthology group: K03168, DNA topoisomerase I [EC: 5.99.1.2] (inferred from 82% identity to azc:AZC_1861)

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

Find the best match in UniProt

Protein Sequence (907 amino acids)

>GFF934 DNA topoisomerase 1 (Xanthobacter sp. DMC5)
MGRRPLIETRFVMQVVIVESPAKAKTINKYLGPGYEVIASYGHVRDLPSKDGSVDPDADF
RMLWDVDPKAQKRLNEIAAAVKGADGLILATDPDREGEAISWHVLEVLRQKKALKSQKVE
RVVFNAITKQAVLEAMKSPRAIDSALVDAYLARRALDYLVGFTLSPVLWRKLPGARSAGR
VQSVALRLVCDREREIETFVRKEYWSILAKLATPRNEEFEARLSGADGKKITRLSVGTAE
EARAFREALDSAAFRVRSVEAKPMKRHPQPPFTTSTLQQEASRKLGLAPARTMQIAQRLY
EGVDVGGETVGLITYMRTDGVDMAPEAVAATRDAIGKQFGQKYLPGVPRKYTTKAKNAQE
AHEAIRPTDPSRHPRDVARYLDGEQAKLYELIWIRTVASQMESAELERTTADIEAKAGAR
TLDLTATGTVVKFDGFLTLYREGKDDEDDDEEGRRLPAMSANEALAKRDISTTQHFTEPP
PRYSEASLVKRMEELGIGRPSTYAAVLAVLRDREYVKLDKKKLVPEDKGRLVTAFLESFF
KRYVEYDFTADLEEKLDEVSAAELDWKEVLRAFWQDFHAAIEATKDLRVSQVLDALDEML
TAHIFPPREDGTDPRLCPTCGTGRLSLKMGKFGAFIGCSNYPECRHTRPLTGDNPQEGDG
TRVLGLDPDSGEEVTIRSGRFGTYLQLGEGKEGEKPKRSSLPKGLAPADVDLETALKLLS
LPREIGLHPEDREPILAGIGRYGPYVQHGRTYANIEDGDDILAIGLNRAVALIAEKQSKG
RGGRGGTPAGRVVGDHPTLGGPITVRPGRFGPYVNHGKVNATLPKSTDPEALTLEQAVQL
IDAKAASSPAKPARGARKAAAGDDGEKAAPKKAAAKKPAAKKTATKAAAPKKPAAKKAAA
SKPDAAE