Protein Info for HMPREF1078_RS11640 in Parabacteroides merdae CL09T00C40

Annotation: type I DNA topoisomerase

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 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 781 PF01751: Toprim" amino acids 5 to 113 (109 residues), 76.6 bits, see alignment E=2.1e-25 TIGR01051: DNA topoisomerase I" amino acids 5 to 484 (480 residues), 622.6 bits, see alignment E=5.8e-191 PF01131: Topoisom_bac" amino acids 128 to 484 (357 residues), 369.7 bits, see alignment E=3.1e-114 PF13368: Toprim_C_rpt" amino acids 595 to 656 (62 residues), 48.7 bits, see alignment 9.2e-17 amino acids 661 to 707 (47 residues), 46.4 bits, see alignment 4.8e-16 amino acids 719 to 769 (51 residues), 48.4 bits, see alignment 1.1e-16

Best Hits

KEGG orthology group: K03168, DNA topoisomerase I [EC: 5.99.1.2] (inferred from 88% identity to pdi:BDI_3599)

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)

Search 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 (781 amino acids)

>HMPREF1078_RS11640 type I DNA topoisomerase (Parabacteroides merdae CL09T00C40)
MQKNLVIVESPAKAKTIEKFLGKDYKVMSSYGHIRDLKTKEFSIDIEHDYAPQYVIPADK
KKLVSELKSEAKSAEQVWLASDEDREGEAISWHLYEVLGLKPENTKRIVFHEITKNAILH
AIETPRDININLVNAQQARRVLDRIVGFELSPILWRKVKPALSAGRVQSVAVRLIVERER
EINEFVSEAAFRVIANFILPDGTTVLKAELNRRLKDKKEVEAFLESCKNASFTIDDITTK
PVKKSPAPPFTTSTLQQEAARKLGYSVSQTMMIAQRLYESGLITYMRTDSVNLSDLALGT
AKEAIFETYGEKYYKFRQYHTKSKGAQEAHEAIRPTYISNVEAGSSSQEKKLYELIRKRT
IACQMADAELERTTISVGISGQTERFVAVGEVISFEGFLQVYMESNDDDTEKEQENGLLP
PVKLHETLSLKDIVATERFTQRPPRYTEASLVRRLEELGIGRPSTYAPTIQTIQNREYVV
KGDKEGVERAYTVVSLSKGKIEEAEKTETVGADRNKLMPTDIGTVVNDFLMEYFPDVLDY
NFTASVEKEFDSVAEGELVWTKAIDKFYKIFHPIVEATAAVKTEHKVGERELGIDPKSGN
PVFVKIGRYGPVVQIGAAHADDKEAPKPQFASLMKGQSIDTITLEEALKLFDLPRTVGEY
EGKVMVAAVGRFGPFIRHDGKFVSIPKDLNPLTITAEEAIALIEGKRVKDEQRFIKKFEE
DPEMEILKGRFGPYISYQKANYRIPKTVTDPTVLTLEDCKKIIAEAGEKPAAKKTTRKKK
A