Protein Info for DDA3937_RS10535 in Dickeya dadantii 3937

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 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 800 867 TIGR01051: DNA topoisomerase I" amino acids 5 to 636 (632 residues), 847.4 bits, see alignment E=5e-259 PF01751: Toprim" amino acids 5 to 144 (140 residues), 72.7 bits, see alignment E=5.9e-24 PF01131: Topoisom_bac" amino acids 159 to 566 (408 residues), 432.1 bits, see alignment E=6.1e-133 PF01396: zf-C4_Topoisom" amino acids 599 to 624 (26 residues), 25.3 bits, see alignment (E = 2.6e-09) amino acids 710 to 747 (38 residues), 39.1 bits, see alignment (E = 1.3e-13) PF21372: TOP1_ZnF" amino acids 653 to 697 (45 residues), 99.9 bits, see alignment 1.3e-32 PF08272: Topo_Zn_Ribbon" amino acids 760 to 795 (36 residues), 44.5 bits, see alignment (E = 2.5e-15) amino acids 826 to 864 (39 residues), 78.7 bits, see alignment (E = 5.2e-26)

Best Hits

Swiss-Prot: 85% identical to TOP1_ECOLI: DNA topoisomerase 1 (topA) from Escherichia coli (strain K12)

KEGG orthology group: K03168, DNA topoisomerase I [EC: 5.99.1.2] (inferred from 71% identity to avr:B565_1038)

MetaCyc: 85% identical to DNA topoisomerase I (Escherichia coli K-12 substr. MG1655)
5.99.1.2-RXN [EC: 5.6.2.1]

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 5.6.2.1 or 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

See E0SBX6 at UniProt or InterPro

Protein Sequence (867 amino acids)

>DDA3937_RS10535 type I DNA topoisomerase (Dickeya dadantii 3937)
MGKALVIVESPAKAKTINKYLGNDFVVKSSVGHVRDLPTSGSGSASKKSAEANGEKAKKA
VKKDEKTALVNRMGVDPYRGWQANYEILPGKEKVVSELKTLAQNADHVYLATDLDREGEA
IAWHLREIIGGDDKRFSRVVFNEITKNAIRQAFENPGELNINRVNAQQARRFMDRVVGYM
VSPLLWKKIARGLSAGRVQSVAVRLVVEREREIKAFVPEEFWELHADLLANPDIALQMQV
THHNGKPFRPVNQAQTQAAVSLLEKASYVVAEREDKPTSSKPGAPFITSTLQQAASTRLG
FGVKKTMMMAQRLYEAGHITYMRTDSTNLSQDALAMARDYIQDEFGKRYLPEAPNLYTSK
ENSQEAHEAIRPSDVKVLADQLKDMEADAQKLYQLIWRQFVACQMMPAQYDSTTLVVSAG
DYQLRAKGRTLRFDGWTKVMPALRKGDEDRTLPAIDVGQSLSLEKLLPSQHFTKPPARYS
EASLVKELEKRGIGRPSTYAAIISTIQDRGYVRVENRRFYAEKMGEIVTDRLEDNFRELM
NYDFTARMENSLDLVANSQAEWKAVLDEFFAEFSKQLETAEQEPDEGGMKPNQMVLTSID
CPTCGRKMGIRTASTGVFLGCSGYALPPKERCKTTINLIPEAEVLNVLEGDEAETNALRA
RRRCSKCGTAMDSYLIDNQRKLHVCGNNPSCDGYEIEQGEFRLKGYDGPVVECEKCSSEM
HLKMGRFGKYMACTNESCGNTRKILRNGEVAPPKEDPVPLPELACEKSDAYFVLRDGAAG
VFLAANTFPKSRETRAPLVEELVRFRDRLPEKLRYLAEAPVTDPEGNKTLVRFSRKTKQQ
YVSSEKEGKATGWSAFYVDGKWVESSR