Protein Info for MIT1002_01705 in Alteromonas macleodii MIT1002

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 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 800 850 884 TIGR01051: DNA topoisomerase I" amino acids 5 to 643 (639 residues), 842.7 bits, see alignment E=1.4e-257 PF01751: Toprim" amino acids 5 to 149 (145 residues), 78.7 bits, see alignment E=7.8e-26 PF01131: Topoisom_bac" amino acids 164 to 572 (409 residues), 443.3 bits, see alignment E=2.4e-136 PF01396: Zn_ribbon_Top1" amino acids 605 to 630 (26 residues), 25.6 bits, see alignment (E = 2.2e-09) amino acids 717 to 753 (37 residues), 37.3 bits, see alignment (E = 4.6e-13) amino acids 771 to 801 (31 residues), 8.3 bits, see alignment (E = 0.00053) PF21372: Zn_ribbon_bTOP1" amino acids 660 to 703 (44 residues), 85.1 bits, see alignment 5.4e-28 PF08272: Zn_Ribbon_Topo" amino acids 766 to 801 (36 residues), 38.8 bits, see alignment (E = 1.5e-13) amino acids 832 to 872 (41 residues), 75.3 bits, see alignment 6e-25

Best Hits

Swiss-Prot: 72% 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 97% identity to amc:MADE_02352)

MetaCyc: 72% 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

Find the best match in UniProt

Protein Sequence (884 amino acids)

>MIT1002_01705 DNA topoisomerase 1 (Alteromonas macleodii MIT1002)
MAKSLVIVESPAKAKTINKYLGKNFIVKSSVGHVRDLPTKALGKVEPKKPAKELKTLSEE
ERQEYLRRHEYLKLVDRMGVDPEKDWKAHYQVLQGKEKVVNELKKLAKDADTIYLATDLD
REGEAIAWHLQELLGKKDKTYQRVVFNEITKNAIQDAFSDPGELNISRVNAQQARRFLDR
VVGFMVSPLLWKKIARGLSAGRVQSVAVRLVVEREREIKAFVPEEFWDVHADLTSQQKAA
LRMLVAKHQGNAFKPKNKAETDKALADLEGANYKVESRESKPTQSRPSAPFITSTLQQAA
STRLGFGVKKTMMMAQRLYEAGYITYMRTDSTNLSQEALDSARAYISDNFGDKYLPDSPN
RYGSKEGAQEAHEAIRPSNVSISAASLGDMERDAQRLYELIWRQFVACQMTPAKYDATTI
KVAAGDYELTAKGRVLKFDGWTRVQPQLRKKGEEELMLPDVQKGDVLDLKALDPKQHFTK
PVARFNEASLVKELEKRGIGRPSTYASIISTIQDRGYVRLENKRFYAEKMGEIVNDRLME
NFDDLMSYDFTANMEQHLDDIAEGKKNWKDVLNDFYSGFYGKLLNAEKDPEEGGMRLNQA
VPAGVECDKCGREMNVRTASTGVFLGCSGYNLPPKERCTNTMNLTPGDEVVKVDDEEELE
TEALRSKKRCPKCGTAMDSYLVDETRKLHVCGNTPTCDGTLVETGTFKIKGYDGPIIECD
KCGSDMELKNGRFGKYFGCTKEECKNTRKLLRNGEAAPPKEDPVDLPELPCEKSDAHFML
RDGASGIFLAAHNFPKSRETRAPKVEELARFRDRISPKFYYLADAPQTDPDGNPAIVRYS
RKTKQQYVMSENDNGKATGWSAWYDNGKWQEQAAKKPATKAKKK