Protein Info for Sama_0016 in Shewanella amazonensis SB2B

Annotation: DNA topoisomerase (ATP-hydrolyzing) (RefSeq)

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 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 805 TIGR01059: DNA gyrase, B subunit" amino acids 6 to 805 (800 residues), 1014.7 bits, see alignment E=0 PF02518: HATPase_c" amino acids 33 to 173 (141 residues), 65.9 bits, see alignment E=1.3e-21 PF00204: DNA_gyraseB" amino acids 221 to 391 (171 residues), 202 bits, see alignment E=1.6e-63 PF01751: Toprim" amino acids 420 to 532 (113 residues), 65.8 bits, see alignment E=9.9e-22 PF21249: GyrB_hook" amino acids 534 to 561 (28 residues), 41.4 bits, see alignment (E = 2.5e-14) PF18053: GyrB_insert" amino acids 565 to 730 (166 residues), 174.1 bits, see alignment E=7.3e-55 PF00986: DNA_gyraseB_C" amino acids 733 to 794 (62 residues), 109.7 bits, see alignment 1.9e-35

Best Hits

Swiss-Prot: 74% identical to GYRB_VIBCH: DNA gyrase subunit B (gyrB) from Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)

KEGG orthology group: K02470, DNA gyrase subunit B [EC: 5.99.1.3] (inferred from 76% identity to amc:MADE_00006)

MetaCyc: 73% identical to DNA gyrase subunit B (Escherichia coli K-12 substr. MG1655)
5.99.1.3-RXN [EC: 5.6.2.2]

Predicted SEED Role

"DNA gyrase subunit B (EC 5.99.1.3)" in subsystem DNA topoisomerases, Type II, ATP-dependent or Resistance to fluoroquinolones (EC 5.99.1.3)

Isozymes

Compare fitness of predicted isozymes for: 5.99.1.3

Use Curated BLAST to search for 5.6.2.2 or 5.99.1.3

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 A1S1H2 at UniProt or InterPro

Protein Sequence (805 amino acids)

>Sama_0016 DNA topoisomerase (ATP-hydrolyzing) (RefSeq) (Shewanella amazonensis SB2B)
MSENTYDSSSIKVLKGLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNSIDEALAGHCSEI
TITIHVDGSVSVKDDGRGIPVAIHPEEGVSAAEVIMTVLHAGGKFDDNSYKVSGGLHGVG
VSVVNALSKKLQLTIRRDGKVHEQFYTHGVPDAPIKVVGDATKTGTEVRFWPSEETFSDT
LFHFDILAKRVRELSFLNSGVGIRLVDERDNKDEFFKYEGGISAFVEYLNRNKTPVNKDI
FHFAQEREDGITVEVAMQWNDGFQENIYCFTNNIPQRDGGTHLAGFRGALTRNLNNYMEA
EGYNKKNKTNATGDDAREGLTAVISVKVPDPKFSSQTKDKLVSSEVKSAVEQTMGEKLGD
YLLENPGDAKLIVGKIIDAARAREAARKAREMTRRKGALDLGGLPGKLADCQEKDPGLSE
IYIVEGDSAGGSAKQGRNRKNQAILPLKGKILNVEKARFDKMLSSQEVATLITALGCGIG
RDEYDPDKTRYHYIIIMTDADVDGSHIRTLLLTFFFRQMPELIERGYVYIAQPPLYKVKK
GKHEQYLKDDPALTEFLTTGALDGASIHPSQGAPGMSGEPLEKLVNQYREVEGIIARLDL
RYPEVLTDRMLYHPVLSNDILADQAKVQAWCDAFVADLVERESSGVLYNAVAEHDPERQV
YVPKVTLRRHGIDHEYLFSYDFFQSSDYRKMGALANALDGLIEEGGYVQRGEKVKPVTSF
IEALDWLVGESKRGLYIQRYKGLGEMNPEQLWETTMDPESRRMLQVTIEDAIAADQLFTC
LMGDQVEPRRDFIEANALNVANLDV