Protein Info for PS417_07590 in Pseudomonas simiae WCS417

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 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 800 873 PF01751: Toprim" amino acids 5 to 149 (145 residues), 75.5 bits, see alignment E=7.6e-25 TIGR01051: DNA topoisomerase I" amino acids 5 to 639 (635 residues), 826.3 bits, see alignment E=1.2e-252 PF01131: Topoisom_bac" amino acids 164 to 571 (408 residues), 425.6 bits, see alignment E=5.6e-131 PF01396: Zn_ribbon_Top1" amino acids 603 to 627 (25 residues), 21.7 bits, see alignment (E = 3.5e-08) amino acids 714 to 748 (35 residues), 45 bits, see alignment (E = 1.9e-15) PF21372: Zn_ribbon_bTOP1" amino acids 656 to 699 (44 residues), 85.4 bits, see alignment 4.3e-28 PF08272: Zn_Ribbon_Topo" amino acids 761 to 797 (37 residues), 43.3 bits, see alignment (E = 6.2e-15) amino acids 828 to 867 (40 residues), 72.2 bits, see alignment 5.8e-24

Best Hits

Swiss-Prot: 87% identical to TOP1_PSEAE: DNA topoisomerase 1 (topA) from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)

KEGG orthology group: K03168, DNA topoisomerase I [EC: 5.99.1.2] (inferred from 66% identity to aha:AHA_3104)

MetaCyc: 67% 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)

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 A0A1N7TVT7 at UniProt or InterPro

Protein Sequence (873 amino acids)

>PS417_07590 DNA topoisomerase I (Pseudomonas simiae WCS417)
MGKSLVIVESPAKAKTINKYLGNEYVVKSSIGHIRDLPTSGSASASKEPAAKRGKAAAGE
GPVLTPKEKARKQLVSRMGVDPDHGWKAKYEILPGKEKVIEELRRLAKDADTIYLATDLD
REGEAIAWHLREAIGGDDSRYKRVVFNEITKKAIQEAFSKPGELDIDRVNAQQARRFLDR
VVGYMVSPLLWAKIARGLSAGRVQSVAVKLVVEREREIRAFIPEEYWEVHADLGTAKGAN
VRFEVAREKGEAFKPLNEAQAMAALEKLKSSSYSIVKREDKPTSSKPSAPFITSTLQQAA
SNRLGFGVKKTMMMAQRLYEAGYITYMRTDSTNLSVDAVAMARTYIEEEFGKKYLPEKPN
VYSSKEGAQEAHEAIRPSDANTTPAKLSGMERDAERLYELIWRQFLACQMLPAQYLSTTV
TVAASDFELRAKGRILKFDGYTRVMPQIAKPGDDDVLPDMAQGDTLKLITLDPSQHFTKP
PARYSEASLVKEMEKRGIGRPSTYAAIISTIQDRGYVALHNRRFYSEKMGDIVTERLSES
FSNLMDYGFTAGMEENLDDVAQGERDWKNVLDEFYGDFKKKLEVAESPESGMRANQPVMT
DIPCQTCGRPMQIRTASTGVFLGCSGYSLPPKERCKATVNLVPGDEIAADDEGESESLVL
RGKHRCPICSTAMDAYLLDEKHKLHICGNNPDCNGYEIEEGTYRIKGYEGPSLECDKCGS
EMQLKTGRFGKFFGCTNPTCKNTRKLLKSGDAAPPKMDPVKMPELKCEKVNDTYILRDGA
SGLFLAASQFPKNRETRAPLVLEIVPHKDEIDPKYHFLCEAPKKDPDGRPAVIRYSRKTK
EQYVQTEVDGKPTGWKAFYDGGKWKVEDKRQGA