Protein Info for PP_0013 in Pseudomonas putida KT2440

Annotation: DNA gyrase subunit B

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 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 806 TIGR01059: DNA gyrase, B subunit" amino acids 7 to 805 (799 residues), 1003.3 bits, see alignment E=2.5e-306 PF02518: HATPase_c" amino acids 34 to 173 (140 residues), 62.5 bits, see alignment E=1.5e-20 PF00204: DNA_gyraseB" amino acids 222 to 392 (171 residues), 194.2 bits, see alignment E=3.7e-61 PF01751: Toprim" amino acids 421 to 533 (113 residues), 65.5 bits, see alignment E=1.3e-21 PF21249: GyrB_hook" amino acids 535 to 563 (29 residues), 58.6 bits, see alignment (E = 1.1e-19) PF18053: GyrB_insert" amino acids 566 to 731 (166 residues), 178.6 bits, see alignment E=2.9e-56 PF00986: DNA_gyraseB_C" amino acids 734 to 795 (62 residues), 106.7 bits, see alignment 1.6e-34

Best Hits

Swiss-Prot: 99% identical to GYRB_PSEPU: DNA gyrase subunit B (gyrB) from Pseudomonas putida

KEGG orthology group: K02470, DNA gyrase subunit B [EC: 5.99.1.3] (inferred from 86% identity to avn:Avin_00040)

MetaCyc: 68% 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 Q88RW6 at UniProt or InterPro

Protein Sequence (806 amino acids)

>PP_0013 DNA gyrase subunit B (Pseudomonas putida KT2440)
MSENQTYDSSSIKVLKGLDAVRKRPGMYIGDTDDGSGLHHMVFEVVDNSIDEALAGHCDD
ITVIIHPDESISVRDNGRGIPVDVHKEEGVSAAEVIMTVLHAGGKFDDNSYKVSGGLHGV
GVSVVNALSEKLVLTVRRSGKIWEQTYVHGVPQAPMAVVGDSETTGTHIHFKPSAETFKN
IHFSWDILAKRIRELSFLNSGVGILLKDERSGKEEFFKYEGGLRAFVEYLNTNKTPVNSQ
VFHFNVQRDDGVGVEVALQWNDSFNENLLCFTNNIPQRDGGTHLVGFRSSLTRSLNSYIE
QEGLAKKNKVATTGDDAREGLTAIISVKVPDPKFSSQTKDKLVSSEVKTAVEQEMNKYFA
DFLLENPNEAKAVVGKMIDAARAREAARKAREMTRRKGALDIAGLPGKLADCQEKDPALS
ELYLVEGDSAGGSAKQGRNRRTQAILPLKGKILNVEKARFDKMISSQEVGTLITALGCGI
GREEYNIDKLRYHNIIIMTDADVDGSHIRTLLLTFFFRQLPELVERGYIYIAQPPLYKVK
RGKQEQYIKDDEAMEEYMTQSALEDASLHLDESAPAVSGVQLEALVNEFRSVMKTLKRLS
RLYPEELTEHFVYLPEVTLEQLGDHAVMQAWLAQFQARLNSSQKSGLAYNASLREDKERN
VWLPEVEITSHGLASYITFNRDFFGSNDYRTVVNIGAKLSSLLGEGAYVQRGERRKAIVE
FKEGLDWLMNETTKRHTIQRYKGLGEMNPDQLWETTMDPTVRRMLKVTIEDAIAADQIFN
TLMGDAVEPRRDFIESNALSVSNLDF