Protein Info for HER17_RS10875 in Pectobacterium carotovorum WPP14

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 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 800 866 PF01751: Toprim" amino acids 5 to 143 (139 residues), 72 bits, see alignment E=9.2e-24 TIGR01051: DNA topoisomerase I" amino acids 5 to 635 (631 residues), 848.6 bits, see alignment E=2.3e-259 PF01131: Topoisom_bac" amino acids 158 to 565 (408 residues), 433.1 bits, see alignment E=3.1e-133 PF01396: zf-C4_Topoisom" amino acids 598 to 623 (26 residues), 22.6 bits, see alignment (E = 1.8e-08) amino acids 710 to 746 (37 residues), 39.9 bits, see alignment (E = 7.5e-14) PF21372: TOP1_ZnF" amino acids 652 to 696 (45 residues), 99.5 bits, see alignment 1.7e-32 PF08272: Topo_Zn_Ribbon" amino acids 759 to 794 (36 residues), 44.7 bits, see alignment (E = 2.2e-15) amino acids 825 to 863 (39 residues), 77.2 bits, see alignment (E = 1.5e-25)

Best Hits

Swiss-Prot: 86% 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 aat:D11S_1336)

MetaCyc: 86% 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

Find the best match in UniProt

Protein Sequence (866 amino acids)

>HER17_RS10875 type I DNA topoisomerase (Pectobacterium carotovorum WPP14)
MGKALVIVESPAKAKTINKYLGNDYVVKSSVGHVRDLPTSGSVSKKSADSTTKDKTKKKV
KKDEKSALVNRMGVDPYHGWKANYEILPGKEKVVSELKTLAENADHIYLATDLDREGEAI
AWHLREIIGGDDQRFSRVVFNEITKNAIKQAFEKPDTLNIDRVNAQQARRFMDRVVGYMV
SPLLWKKIARGLSAGRVQSVAVRLIVDREREIKAFVPEEYWELHADLLAGSDIQLQMQVT
HHNSKPFKPVNKEQTHAAVSLLENARYVVADREDKPTSSKPGAPFITSTLQQAASTRLGF
GVKKTMMMAQRLYEAGYITYMRTDSTNLSQDALTMVRGYIGEEFGKRYLPESANLYSSKE
NSQEAHEAIRPSDVGVLADSLKDMEADAQKLYQLIWRQFVACQMTPAQYDSTTLIVEAAD
YQLRAKGRTLRFDGWTKVMPALRKNDEDRTLPTVAVGEVLSLQKLLPGQHFTKPPARYSD
ASLVKELEKRGIGRPSTYASIISTIQDRGYVRVENRRFYAEKMGEIVTDRLEENFRELMN
YDFTARMESRLDQVANNQAEWKAVLDEFFNEFSQQLEKAEQDPEEGGMRPNAMVLTSIDC
PTCSRQMGIRTASTGVFLGCSGYALPPKERCKTTINLIPETEVLNVLEGDDAETNALRAR
RRCEKCGTAMDSYLIDNQRKLHVCGNNPACDGYEIEAGEFRIKGYDGPIVECEKCGSEMH
LKMGRFGKYMACTSETCSNTRKILRNGDVAPPKEDPVPLPELPCEKSDAYFVLRDGAAGV
FLAANTFPKSRETRAPLVEELVRFKDRLPEKLRYLADAPVADNDGNKTQVRFSRKTKQQY
VSSEKDGKATGWSAFYIDGKWVEGKK