YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|77630961, gi\|...
Organism:	Yersinia pseudotuberculosis IP 31758
Length:	804 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 gi|77630961, gi|....

Description	E-value	Query Range	Subject Range
gi\|1546916 - gi\|1546916\|emb\|CAA69221.1\| subunit B of DNA gyrase [Salmonella typhimurium] gi\|1546916\|emb\|C... - subunit B of DNA gyrase [Salmonella typhimurium]	0.0	[1..804]	[1..804]
gi\|81243376, gi\|... - gi\|82779228\|ref\|YP_405577.1\| DNA gyrase subunit B [Shigella dysenteriae Sd197], gi\|81243376\|gb\|ABB64...	0.0	[1..804]	[1..804]
gi\|218367543, gi... - gi\|218560774\|ref\|YP_002393687.1\| DNA gyrase subunit B [Escherichia coli S88], gi\|218367543\|emb\|CAR05... gi\|218429551, gi... - gi\|218691987\|ref\|YP_002400199.1\| DNA gyrase subunit B [Escherichia coli ED1a], gi\|218429551\|emb\|CAR1... gi\|110644042, gi... - gi\|110644042\|ref\|YP_671772.1\| DNA gyrase subunit B [Escherichia coli 536], gi\|110345634\|gb\|ABG71871.... gi\|227883920, gi... - gi\|227883920\|ref\|ZP_04001725.1\| DNA gyrase subunit B [Escherichia coli 83972], gi\|227839198\|gb\|EEJ49... gi\|190909423, gi... - gi\|75242511\|ref\|ZP_00726255.1\| COG0187: Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV... gi\|115515099, gi... - gi\|117625975\|ref\|YP_859298.1\| DNA gyrase subunit B [Escherichia coli APEC O1], gi\|115515099\|gb\|ABJ03...	0.0	[1..804]	[1..804]
gi\|26110870, gi\|... - gi\|26250440\|ref\|NP_756480.1\| DNA gyrase subunit B [Escherichia coli CFT073], gi\|26110870\|gb\|AAN83054... gi\|91213221, gi\|... - gi\|91213221\|ref\|YP_543207.1\| DNA gyrase subunit B [Escherichia coli UTI89], gi\|91074795\|gb\|ABE09676.... gi\|237703499, gi... - gi\|237703499\|ref\|ZP_04533980.1\| subunit B [Escherichia sp. 3_2_53FAA], gi\|226902763\|gb\|EEH89022.1\| s...	0.0	[1..804]	[2..805]
GYRB_SALTY - DNA gyrase subunit B OS=Salmonella typhimurium GN=gyrB PE=3 SV=2 gi\|224470162, gi... - gi\|224585634\|ref\|YP_002639433.1\| DNA gyrase subunit B [Salmonella enterica subsp. enterica serovar P... gi\|214001463 - gi\|214001463\|ref\|ZP_03412198.1\| DNA gyrase subunit B [Salmonella enterica subsp. enterica serovar Ty... gi\|213424954 - gi\|213424954\|ref\|ZP_03357704.1\| DNA gyrase subunit B [Salmonella enterica subsp. enterica serovar Ty... gi\|207859061, gi... - gi\|207859061\|ref\|YP_002245712.1\| DNA gyrase subunit B [Salmonella enterica subsp. enterica serovar E... GYRB_SALTI - DNA gyrase subunit B OS=Salmonella typhi GN=gyrB PE=3 SV=2 GYRB_SALTY - DNA gyrase subunit B OS=Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) GN=gyrB PE=1 SV... GYRB_SALTI - DNA gyrase subunit B OS=Salmonella typhi GN=gyrB PE=3 SV=2 lcl\|NC_016856.1_... - [gene=gyrB] [protein=DNA gyrase subunit B] [protein_id=YP_005240101.1] [location=complement(4052548.... gi\|29143978, gi\|... - gi\|29143978\|ref\|NP_807320.1\| DNA gyrase subunit B [Salmonella enterica subsp. enterica serovar Typhi... gi\|16762490 - gi\|16762490\|ref\|NP_458107.1\| DNA gyrase subunit B [Salmonella enterica subsp. enterica serovar Typhi... gi\|238913088 - gi\|238913088\|ref\|ZP_04656925.1\| DNA gyrase subunit B [Salmonella enterica subsp. enterica serovar Te... gi\|205325567, gi... - gi\|205325567\|gb\|EDZ13406.1\| DNA gyrase, B subunit [Salmonella enterica subsp. enterica serovar Saint... GYRB_SALTY - DNA gyrase subunit B OS=Salmonella typhimurium GN=gyrB PE=3 SV=2 gi\|161616952, gi... - gi\|161616952\|ref\|YP_001590917.1\| DNA gyrase subunit B [Salmonella enterica subsp. enterica serovar P... gi\|197240529, gi... - gi\|197262274\|ref\|ZP_03162348.1\| DNA gyrase, B subunit [Salmonella enterica subsp. enterica serovar S... gi\|194712574, gi... - gi\|194737072\|ref\|YP_002116779.1\| DNA gyrase, B subunit [Salmonella enterica subsp. enterica serovar ... gi\|194472695, gi... - gi\|194472695\|ref\|ZP_03078679.1\| DNA gyrase, B subunit [Salmonella enterica subsp. enterica serovar K... gi\|194449732, gi... - gi\|194449732\|ref\|YP_002047868.1\| DNA gyrase subunit B [Salmonella enterica subsp. enterica serovar H... gi\|205354578, gi... - gi\|205354578\|ref\|YP_002228379.1\| DNA gyrase subunit B [Salmonella enterica subsp. enterica serovar G... gi\|204322190, gi... - gi\|204928757\|ref\|ZP_03219956.1\| DNA gyrase, B subunit [Salmonella enterica subsp. enterica serovar J... gi\|199604199, gi... - gi\|200387101\|ref\|ZP_03213713.1\| DNA gyrase, B subunit [Salmonella enterica subsp. enterica serovar V... gi\|197938563, gi... - gi\|198244047\|ref\|YP_002217785.1\| DNA gyrase, B subunit [Salmonella enterica subsp. enterica serovar ... gi\|205338996, gi... - gi\|205338996\|gb\|EDZ25760.1\| DNA gyrase, B subunit [Salmonella enterica subsp. enterica serovar Heide... gi\|197291517, gi... - gi\|197291517\|gb\|EDY30869.1\| DNA gyrase, B subunit [Salmonella enterica subsp. enterica serovar Schwa... gi\|168233389, gi... - gi\|205332584\|gb\|EDZ19348.1\| DNA gyrase, B subunit [Salmonella enterica subsp. enterica serovar Kentu... gi\|205329403, gi... - gi\|205329403\|gb\|EDZ16167.1\| DNA gyrase, B subunit [Salmonella enterica subsp. enterica serovar 4,[5]... gi\|194442844, gi... - gi\|194442844\|ref\|YP_002043085.1\| DNA gyrase, B subunit [Salmonella enterica subsp. enterica serovar ... gi\|168818305, gi... - gi\|205344661\|gb\|EDZ31425.1\| DNA gyrase, B subunit [Salmonella enterica subsp. enterica serovar Welte... gi\|195632426, gi... - gi\|195632426\|gb\|EDX50910.1\| DNA gyrase, B subunit [Salmonella enterica subsp. enterica serovar Newpo... gi\|168260381, gi... - gi\|205350152\|gb\|EDZ36783.1\| DNA gyrase, B subunit [Salmonella enterica subsp. enterica serovar Hadar...	0.0	[1..804]	[1..804]
GYRB_SHIFL - DNA gyrase subunit B OS=Shigella flexneri GN=gyrB PE=3 SV=2 GYRB_ECOLI - DNA gyrase subunit B (EC 5.99.1.3) - Escherichia coli gi\|30043268, gi\|... - gi\|30065007\|ref\|NP_839178.1\| DNA gyrase subunit B [Shigella flexneri 2a str. 2457T], gi\|30043268\|gb\|... gi\|157068859, gi... - gi\|75197597\|ref\|ZP_00707667.1\| COG0187: Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV... GYRB_ECO57 - DNA gyrase subunit B OS=Escherichia coli O157:H7 GN=gyrB PE=3 SV=2 gi\|75210689, gi\|... - gi\|75210689\|ref\|ZP_00710830.1\| COG0187: Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV... EG10424 - DNA gyrase, subunit B / DNA gyrase, subunit B; novobiocin, coumermycin resistance gi\|194425377, gi... - gi\|83588435\|ref\|ZP_00927059.1\| COG0187: Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV... gi\|157077909, gi... - gi\|75188456\|ref\|ZP_00701723.1\| COG0187: Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV... gi\|110617159, gi... - gi\|110807611\|ref\|YP_691131.1\| DNA gyrase subunit B [Shigella flexneri 5 str. 8401], gi\|110617159\|gb\|... gi\|168772266, gi... - gi\|187771557\|gb\|EDU35401.1\| DNA gyrase, B subunit [Escherichia coli O157:H7 str. EC4196], gi\|1687722... gi\|189364475, gi... - gi\|189364475\|gb\|EDU82894.1\| DNA gyrase, B subunit [Escherichia coli O157:H7 str. EC4486], gi\|1687661... gi\|189374237, gi... - gi\|189374237\|gb\|EDU92653.1\| DNA gyrase, B subunit [Escherichia coli O157:H7 str. EC869], gi\|16878565... gi\|168779921, gi... - gi\|189002544\|gb\|EDU71530.1\| DNA gyrase, B subunit [Escherichia coli O157:H7 str. EC4076], gi\|1687799... gi\|170018065, gi... - gi\|170018065\|ref\|YP_001723019.1\| DNA gyrase subunit B [Escherichia coli ATCC 8739], gi\|169752993\|gb\|... gi\|168798734, gi... - gi\|189378801\|gb\|EDU97217.1\| DNA gyrase, B subunit [Escherichia coli O157:H7 str. EC508], gi\|16879873... gi\|208728266, gi... - gi\|208808465\|ref\|ZP_03250802.1\| DNA gyrase, B subunit [Escherichia coli O157:H7 str. EC4206], gi\|208... gi\|15833888, gi\|... - gi\|15833888\|ref\|NP_312661.1\| DNA gyrase subunit B [Escherichia coli O157:H7 str. Sakai], gi\|13364109... gi\|195936320 - gi\|195936320\|ref\|ZP_03081702.1\| DNA gyrase subunit B [Escherichia coli O157:H7 str. EC4024] gi\|168748585, gi... - gi\|188016891\|gb\|EDU55013.1\| DNA gyrase, B subunit [Escherichia coli O157:H7 str. EC4113], gi\|1687485... gi\|189369611, gi... - gi\|189369611\|gb\|EDU88027.1\| DNA gyrase, B subunit [Escherichia coli O157:H7 str. EC4501], gi\|1687598... gi\|168753588, gi... - gi\|189359308\|gb\|EDU77727.1\| DNA gyrase, B subunit [Escherichia coli O157:H7 str. EC4401], gi\|1687535... gi\|238860819, gi... - gi\|238902789\|ref\|YP_002928585.1\| DNA gyrase, subunit B [Escherichia coli BW2952], gi\|238860819\|gb\|AC... gi\|251786965, gi... - gi\|251786965\|ref\|YP_003001269.1\| hypothetical protein B21_03526 [Escherichia coli BL21], gi\|24237923... gi\|253979707, gi... - gi\|254290400\|ref\|YP_003056148.1\| DNA gyrase subunit B [Escherichia coli BL21(DE3)], gi\|253979707\|gb\|... gi\|254163650, gi... - gi\|254163650\|ref\|YP_003046758.1\| DNA gyrase subunit B [Escherichia coli B str. REL606], gi\|253975551... gi\|254795702, gi... - gi\|254795702\|ref\|YP_003080539.1\| DNA gyrase, subunit B [Escherichia coli O157:H7 str. TW14359], gi\|2... gi\|208742117, gi... - gi\|208821994\|ref\|ZP_03262314.1\| DNA gyrase, B subunit [Escherichia coli O157:H7 str. EC4042], gi\|208... gi\|208733443, gi... - gi\|208812166\|ref\|ZP_03253495.1\| DNA gyrase, B subunit [Escherichia coli O157:H7 str. EC4045], gi\|208... gi\|218363033, gi... - gi\|218556264\|ref\|YP_002389178.1\| DNA gyrase subunit B [Escherichia coli IAI1], gi\|218363033\|emb\|CAR0... gi\|209921176, gi... - gi\|209921176\|ref\|YP_002295260.1\| DNA gyrase subunit B [Escherichia coli SE11], gi\|209914435\|dbj\|BAG7... gi\|218354153, gi... - gi\|218697421\|ref\|YP_002405088.1\| DNA gyrase subunit B [Escherichia coli 55989], gi\|218354153\|emb\|CAV... EG10424 - DNA gyrase, subunit B / DNA gyrase, subunit B; novobiocin, coumermycin resistance gi\|124529046, gi... - gi\|124529046\|ref\|ZP_01700192.1\| DNA gyrase, B subunit [Escherichia coli B], gi\|124500185\|gb\|EAY47662... gi\|75258239, gi\|... - gi\|75258239\|ref\|ZP_00729687.1\| COG0187: Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV... gi\|75514238, gi\|... - gi\|75514238\|ref\|ZP_00736546.1\| COG0187: Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV... gi\|190904111, gi... - gi\|75231030\|ref\|ZP_00717465.1\| COG0187: Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV... gi\|192957551, gi... - gi\|75236423\|ref\|ZP_00720519.1\| COG0187: Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV... gi\|56480411, gi\|... - gi\|56480411\|ref\|NP_709501.2\| DNA gyrase subunit B [Shigella flexneri 2a str. 301], gi\|56383962\|gb\|AA... gi\|74314013, gi\|... - gi\|74314013\|ref\|YP_312432.1\| DNA gyrase subunit B [Shigella sonnei Ss046], gi\|73857490\|gb\|AAZ90197.1... gi\|89110314, gi\|... - gi\|89110314\|ref\|AP_004094.1\| DNA gyrase, subunit B [Escherichia coli str. K-12 substr. W3110], gi\|85...	0.0	[1..804]	[1..804]
gi\|187428646, gi... - gi\|75177732\|ref\|ZP_00697797.1\| COG0187: Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV... gi\|81247448, gi\|... - gi\|82546037\|ref\|YP_409984.1\| DNA gyrase subunit B [Shigella boydii Sb227], gi\|81247448\|gb\|ABB68156.1...	0.0	[1..804]	[1..804]
gi\|45443725, gi\|... - gi\|45443725\|ref\|NP_995264.1\| DNA gyrase subunit B [Yersinia pestis biovar Microtus str. 91001], gi\|4... gi\|22127978, gi\|... - gi\|22127978\|ref\|NP_671401.1\| DNA gyrase subunit B [Yersinia pestis KIM], gi\|21961123\|gb\|AAM87652.1\|A...	0.0	[1..804]	[2..805]
gi\|56129965, gi\|... - gi\|56415708\|ref\|YP_152783.1\| DNA gyrase subunit B [Salmonella enterica subsp. enterica serovar Parat... gi\|197364636, gi... - gi\|197364636\|ref\|YP_002144273.1\| DNA gyrase subunit B [Salmonella enterica subsp. enterica serovar P...	0.0	[1..804]	[1..804]

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Predicted Domain #1

Region A:
Residues: [1-395]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSNTYDSSSI KVLKGLDAVR KRPGMYIGDT DDGTGLHHMV FEVVDNAIDE ALAGHCKEIL  60
   61 VTIHADNSVS VQDDGRGIPT GMHDEEGVSA AEVIMTVLHA GGKFDDNSYK VSGGLHGVGV 120
  121 SVVNALSEKL ELVIRREGKV HEQTYKMGVP QAPLKVVGET EQTGTTVRFW PSFQTFTNNT 180
  181 EFQYEILAKR LRELSFLNSG VSIKLKDKRN DKEDHFHYEG GIKAFVEYLN KNKNPIHPKV 240
  241 FYFSTMKDDI GVEVALQWND GFQENIYCFT NNIPQRDGGT HLVGFRTAMT RTLNSYMDKE 300
  301 GYSKKAKISA TGDDAREGLI AVVSVKVPDP KFSSQTKDKL VSSEVKTAVE TLMNEKLVEY 360
  361 LLENPTDAKI VVGKIIDAAR AREAARKARE MTRRK

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	164.0
Match:	1ei1A
Description:	DNA gyrase B
Matching Structure (courtesy of the PDB):

Predicted Domain #2

Region A:
Residues: [396-642]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 GALDLAGLPG KLADCQERDP ALSELYLVEG DSAGGSAKQG RNRKNQAILP LKGKILNVEK  60
   61 ARFDKMLSSQ EVATLITALG CGIGRDEYNP DKLRYHNIII MTDADVDGSH IRTLLLTFFY 120
  121 RQMPEIIERG HVFIAQPPLY KVKKGKQEQY IKDDDAMEQY QMTLALDGAA LHTNAHAPAL 180
  181 AGEPLEKLVA EHYSVQKTIA RMERRYPRAL LNNLIYQPTL QEEDLGNKEV VTQWIDSLVV 240
  241 LLNEKEH

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	58.30103
Match:	1bgwA
Description:	TOPOISOMERASE RESIDUES 410-1202,
Matching Structure (courtesy of the PDB):

Predicted Domain #3

Region A:
Residues: [643-804]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 HGSSYSSVVR ENRERQLFEP ILRIRTHGVD TDYDLDFDFI HGGEYRKICL LGDKLRGLIE  60
   61 DGAFVERGER RVPVSSFEEA LDWLVKESRR GLAIQRYKGL GEMNPDQLWE TTMDPESRRM 120
  121 LRVMVKDAIA ADQLFTTLMG DAVEPRRAFI EENALRAANI DI

[Run NCBI BLAST on this sequence.]

Detection Method:	FFAS03
Confidence:	4.49
Match:	1bgwA
Description:	TOPOISOMERASE RESIDUES 410-1202,
Matching Structure (courtesy of the PDB):

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