YRC Public Data Repository - Protein Structure Prediction

Protein:	PARE_ECOLI
Organism:	Escherichia coli
Length:	630 amino acids
Reference:	Drew K, et al. (2011) The proteome folding project: Proteome-scale prediction of structure and function. Genome Res. 2011 Sep 16

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Top Sequence Alignment Hits

Listed below are up to the top 10 sequence alignment matches, by species, for the PSI-BLAST search against the protein sequence for PARE_ECOLI.

Description	E-value	Query Range	Subject Range
gi\|88951625, gi\|... - gi\|88951625\|ref\|ZP_01154102.1\| DNA gyrase, B subunit [Methanosaeta thermophila PT], gi\|88929302\|gb\|E...	868.0	[0..1]	[630..1]
gi\|147921290, gi... - gi\|147921290\|ref\|YP_684896.1\| type II DNA topoisomerase II (gyrase), subunit B [uncultured methanoge...	862.0	[0..2]	[630..7]
gi\|145408666, gi... - gi\|82499797\|ref\|ZP_00885234.1\| DNA gyrase, B subunit [Caldicellulosiruptor saccharolyticus DSM 8903]...	858.0	[0..2]	[630..8]
gi\|52078497, gi\|... - gi\|52078497\|ref\|YP_077288.1\| DNA gyrase subunit B [Bacillus licheniformis ATCC 14580], gi\|52001708\|g...	854.0	[0..3]	[630..7]
GYRB_BACSU - DNA gyrase subunit B OS=Bacillus subtilis GN=gyrB PE=3 SV=1 gi\|221312137 - gi\|221312137\|ref\|ZP_03593942.1\| DNA gyrase subunit B [Bacillus subtilis subsp. subtilis str. NCIB 36... GYRB_BACSU - DNA gyrase subunit B OS=Bacillus subtilis (strain 168) GN=gyrB PE=3 SV=1 gi\|221317070 - gi\|221317070\|ref\|ZP_03598364.1\| DNA gyrase subunit B [Bacillus subtilis subsp. subtilis str. JH642] gi\|221321333 - gi\|221321333\|ref\|ZP_03602627.1\| DNA gyrase subunit B [Bacillus subtilis subsp. subtilis str. SMY]	852.0	[0..3]	[630..6]
gi\|20806552, gi\|... - gi\|20806552\|ref\|NP_621723.1\| DNA gyrase subunit B [Thermoanaerobacter tengcongensis MB4], gi\|2051499... gi\|20806552 - gi\|20806552\|ref\|NP_621723.1\| DNA gyrase subunit B [Thermoanaerobacter tengcongensis MB4]	852.0	[0..3]	[630..26]
gi\|68560921, gi\|... - gi\|68560921\|ref\|ZP_00600228.1\| DNA gyrase, B subunit [Rubrobacter xylanophilus DSM 9941], gi\|6851286...	851.0	[0..3]	[629..12]
GYRB_BACHD - DNA gyrase subunit B OS=Bacillus halodurans GN=gyrB PE=3 SV=1 gi\|11270951, gi\|... - gi\|2760177\|dbj\|BAA24187.1\| B subunit of DNA gyrase [Bacillus sp.], pir\|\|T46551 DNA topoisomerase (AT... GYRB_BACHD - DNA gyrase subunit B OS=Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 ...	847.0	[0..3]	[630..6]
gi\|56418540, gi\|... - gi\|56418540\|ref\|YP_145858.1\| DNA gyrase subunit B [Geobacillus kaustophilus HTA426], gi\|56378382\|dbj...	844.0	[0..3]	[630..7]

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Predicted Domain #1

Region A:
Residues: [1-395]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MTQTYNADAI EVLTGLEPVR RRPGMYTDTT RPNHLGQEVI DNSVDEALAG HAKRVDVILH  60
   61 ADQSLEVIDD GRGMPVDIHP EEGVPAVELI LCRLHAGGKF SNKNYQFSGG LHGVGISVVN 120
  121 ALSKRVEVNV RRDGQVYNIA FENGEKVQDL QVVGTCGKRN TGTSVHFWPD ETFFDSPRFS 180
  181 VSRLTHVLKA KAVLCPGVEI TFKDEINNTE QRWCYQDGLN DYLAEAVNGL PTLPEKPFIG 240
  241 NFAGDTEAVD WALLWLPEGG ELLTESYVNL IPTMQGGTHV NGLRQGLLDA MREFCEYRNI 300
  301 LPRGVKLSAE DIWDRCAYVL SVKMQDPQFA GQTKERLSSR QCAAFVSGVV KDAFILWLNQ 360
  361 NVQAAELLAE MAISSAQRRM RAAKKVVRKK LTSGP

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	136.0
Match:	1s16A
Description:	Crystal Structure of E. coli Topoisomerase IV ParE 43kDa subunit complexed with ADPNP
Matching Structure (courtesy of the PDB):

Predicted Domain #2

Region A:
Residues: [396-630]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 ALPGKLADCT AQDLNRTELF LVEGDSAGGS AKQARDREYQ AIMPLKGKIL NTWEVSSDEV  60
   61 LASQEVHDIS VAIGIDPDSD DLSQLRYGKI CILADADSDG LHIATLLCAL FVKHFRALVK 120
  121 HGHVYVALPP LYRIDLGKEV YYALTEEEKE GVLEQLKRKK GKPNVQRFKG LGEMNPMQLR 180
  181 ETTLDPNTRR LVQLTIDDED DQRTDAMMDM LLAKKRSEDR RNWLQEKGDM AEIEV

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	51.39794
Match:	1bgwA
Description:	TOPOISOMERASE RESIDUES 410-1202,
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
DNA topoisomerase (ATP-hydrolyzing) activity	2.32279006303682	bayes_pls_golite062009
binding	2.2777380001787	bayes_pls_golite062009
DNA topoisomerase activity	2.1147376780944	bayes_pls_golite062009
nucleic acid binding	2.05731599309128	bayes_pls_golite062009
DNA binding	1.99548954924236	bayes_pls_golite062009
catalytic activity	1.28862988439947	bayes_pls_golite062009
isomerase activity	0.673377410014343	bayes_pls_golite062009

TMHMM	2.0c	PSIPRED	v2.61
SignalP	3.0	COILS	1999
DISOPRED	v0.1	NCBI nr	06/2007
PSI-BLAST	2.2.18	FFAS	ffas03
PDB	06/2007	Pfam	22
HMMER	2.3.2

View Structure Prediction Details

Top Sequence Alignment Hits

Predicted functions: