YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|118479292, gi...
Organism:	Bacillus thuringiensis str. Al Hakam
Length:	296 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|118479292, gi....

Description	E-value	Query Range	Subject Range
gi\|153167810, gi... - gi\|153167810\|ref\|ZP_01927895.1\| tyrosine recombinase XerD [Listeria monocytogenes FSL N1-017], gi\|13... gi\|254992940 - gi\|254992940\|ref\|ZP_05275130.1\| integrase/recombinase [Listeria monocytogenes FSL J2-064] gi\|153202948, gi... - gi\|254931873\|ref\|ZP_05265232.1\| integrase/recombinase [Listeria monocytogenes HPB2262], gi\|153202948... gi\|254877926 - gi\|254877926\|ref\|ZP_05250636.1\| integrase/recombinase [Listeria monocytogenes FSL J2-071] gi\|255520096 - gi\|255520096\|ref\|ZP_05387333.1\| integrase/recombinase [Listeria monocytogenes FSL J1-175] XERD_LISMF - Tyrosine recombinase XerD OS=Listeria monocytogenes serotype 4b (strain F2365) GN=xerD PE=3 SV=1 gi\|47093384, gi\|... - gi\|47093384\|ref\|ZP_00231151.1\| integrase/recombinase XerD [Listeria monocytogenes str. 4b H7858], gi... gi\|226224560, gi... - gi\|226224560\|ref\|YP_002758667.1\| integrase/recombinase [Listeria monocytogenes Clip81459], gi\|225877... gi\|254852857 - gi\|254852857\|ref\|ZP_05242205.1\| integrase/recombinase [Listeria monocytogenes FSL R2-503] gi\|254825549 - gi\|254825549\|ref\|ZP_05230550.1\| integrase/recombinase [Listeria monocytogenes FSL J1-194]	1.0E-63	[1..296]	[1..297]
gi\|98662087 - gi\|98662087\|dbj\|GAA00976.1\| unnamed protein product [Pelotomaculum thermopropionicum SI]	1.0E-63	[1..296]	[47..341]
gi\|228625631, gi... - gi\|229157674\|ref\|ZP_04285749.1\| Tyrosine recombinase xerD [Bacillus cereus ATCC 4342], gi\|228625631\|... gi\|228987282, gi... - gi\|228987282\|ref\|ZP_04147403.1\| Tyrosine recombinase xerD [Bacillus thuringiensis serovar tochigiens... gi\|51974871, gi\|... - gi\|52141402\|ref\|YP_085426.1\| site-specific tyrosine recombinase XerD [Bacillus cereus E33L], gi\|5197...	3.0E-63	[1..296]	[1..296]
gi\|228671946, gi... - gi\|229111564\|ref\|ZP_04241115.1\| Tyrosine recombinase xerD [Bacillus cereus Rock1-15], gi\|228671946\|g... gi\|229081347, gi... - gi\|229081347\|ref\|ZP_04213850.1\| Tyrosine recombinase xerD [Bacillus cereus Rock4-2], gi\|228701969\|gb... gi\|228711531, gi... - gi\|229071595\|ref\|ZP_04204813.1\| Tyrosine recombinase xerD [Bacillus cereus F65185], gi\|228711531\|gb\|... gi\|229047783, gi... - gi\|229047783\|ref\|ZP_04193363.1\| Tyrosine recombinase xerD [Bacillus cereus AH676], gi\|228723575\|gb\|E... gi\|229180370, gi... - gi\|229180370\|ref\|ZP_04307713.1\| Tyrosine recombinase xerD [Bacillus cereus 172560W], gi\|228603117\|gb... gi\|228631254, gi... - gi\|229152292\|ref\|ZP_04280485.1\| Tyrosine recombinase xerD [Bacillus cereus m1550], gi\|228631254\|gb\|E... gi\|228636835, gi... - gi\|229146665\|ref\|ZP_04275032.1\| Tyrosine recombinase xerD [Bacillus cereus BDRD-ST24], gi\|228636835\|... gi\|228653975, gi... - gi\|229129370\|ref\|ZP_04258341.1\| Tyrosine recombinase xerD [Bacillus cereus BDRD-Cer4], gi\|228653975\|... gi\|29897733, gi\|... - gi\|30022176\|ref\|NP_833807.1\| site-specific tyrosine recombinase XerD [Bacillus cereus ATCC 14579], g... gi\|228941242, gi... - gi\|228941242\|ref\|ZP_04103795.1\| Tyrosine recombinase xerD [Bacillus thuringiensis serovar berliner A... gi\|228909920, gi... - gi\|228909920\|ref\|ZP_04073741.1\| Tyrosine recombinase xerD [Bacillus thuringiensis IBL 200], gi\|22884... gi\|228857041, gi... - gi\|228902600\|ref\|ZP_04066751.1\| Tyrosine recombinase xerD [Bacillus thuringiensis IBL 4222], gi\|2288... gi\|218543889, gi... - gi\|218899252\|ref\|YP_002447663.1\| integrase/recombinase XerD [Bacillus cereus G9842], gi\|218543889\|gb... gi\|228778934, gi... - gi\|228980765\|ref\|ZP_04141070.1\| Tyrosine recombinase xerD [Bacillus thuringiensis Bt407], gi\|2287789... gi\|228974174, gi... - gi\|228974174\|ref\|ZP_04134744.1\| Tyrosine recombinase xerD [Bacillus thuringiensis serovar thuringien... gi\|206734005, gi... - gi\|206971233\|ref\|ZP_03232184.1\| integrase/recombinase XerD [Bacillus cereus AH1134], gi\|206734005\|gb... gi\|228799379, gi... - gi\|228960355\|ref\|ZP_04122008.1\| Tyrosine recombinase xerD [Bacillus thuringiensis serovar pakistani ... gi\|218235095, gi... - gi\|218235095\|ref\|YP_002368894.1\| integrase/recombinase XerD [Bacillus cereus B4264], gi\|218163052\|gb... gi\|228954374, gi... - gi\|228954374\|ref\|ZP_04116400.1\| Tyrosine recombinase xerD [Bacillus thuringiensis serovar kurstaki s...	3.0E-63	[1..296]	[1..296]
gi\|217961583, gi... - gi\|217961583\|ref\|YP_002340153.1\| integrase/recombinase XerD [Bacillus cereus AH187], gi\|217064224\|gb... gi\|206976263, gi... - gi\|206976263\|ref\|ZP_03237171.1\| integrase/recombinase XerD [Bacillus cereus H3081.97], gi\|206745459\|... gi\|228585232, gi... - gi\|229198213\|ref\|ZP_04324921.1\| Tyrosine recombinase xerD [Bacillus cereus m1293], gi\|228585232\|gb\|E... gi\|229140825, gi... - gi\|229140825\|ref\|ZP_04269370.1\| Tyrosine recombinase xerD [Bacillus cereus BDRD-ST26], gi\|228642615\|... gi\|42783204, gi\|... - gi\|42783204\|ref\|NP_980451.1\| site-specific tyrosine recombinase XerD [Bacillus cereus ATCC 10987], g...	3.0E-63	[1..296]	[1..296]
XERD_LISIN - Tyrosine recombinase xerD OS=Listeria innocua GN=xerD PE=3 SV=1 XERD_LISIN - Tyrosine recombinase XerD OS=Listeria innocua serovar 6a (strain CLIP 11262) GN=xerD PE=3 SV=1	8.0E-63	[1..296]	[1..297]
gi\|254912513, gi... - gi\|254912513\|ref\|ZP_05262525.1\| hypothetical protein LmonJ2_06931 [Listeria monocytogenes J2818], gi... gi\|133729635, gi... - gi\|254827160\|ref\|ZP_05231847.1\| hypothetical protein LmonocytogeFSL_01770 [Listeria monocytogenes FS... XERD_LISMO - Tyrosine recombinase xerD OS=Listeria monocytogenes GN=xerD PE=3 SV=1 gi\|254936840 - gi\|254936840\|ref\|ZP_05268537.1\| hypothetical protein LmonF6_06921 [Listeria monocytogenes F6900] gi\|47097098, gi\|... - gi\|47097098\|ref\|ZP_00234668.1\| integrase/recombinase XerD [Listeria monocytogenes str. 1/2a F6854], ... gi\|255028942 - gi\|255028942\|ref\|ZP_05300893.1\| hypothetical protein LmonL_06711 [Listeria monocytogenes LO28] XERD_LISMO - Tyrosine recombinase XerD OS=Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e) GN=xe... gi\|224498595 - gi\|224498595\|ref\|ZP_03666944.1\| hypothetical protein LmonF1_02414 [Listeria monocytogenes Finland 19... gi\|224501245 - gi\|224501245\|ref\|ZP_03669552.1\| hypothetical protein LmonFR_01770 [Listeria monocytogenes FSL R2-561... gi\|254899348, gi... - gi\|254899348\|ref\|ZP_05259272.1\| hypothetical protein LmonJ_06029 [Listeria monocytogenes J0161], gi\|...	9.0E-63	[1..296]	[1..297]
gi\|51892959, gi\|... - gi\|51892959\|ref\|YP_075650.1\| recombinase [Symbiobacterium thermophilum IAM 14863], gi\|51856648\|dbj\|B...	1.0E-62	[1..296]	[1..294]
gi\|163864029, gi... - gi\|89207375\|ref\|ZP_01185918.1\| Tyrosine recombinase XerD [Bacillus weihenstephanensis KBAB4], gi\|891... gi\|228748067, gi... - gi\|229013300\|ref\|ZP_04170441.1\| Tyrosine recombinase xerD [Bacillus mycoides DSM 2048], gi\|228748067... gi\|229061763, gi... - gi\|229061763\|ref\|ZP_04199096.1\| Tyrosine recombinase xerD [Bacillus cereus AH603], gi\|228717509\|gb\|E...	1.0E-62	[1..296]	[1..296]
gi\|83573258, gi\|... - gi\|83590344\|ref\|YP_430353.1\| tyrosine recombinase XerD subunit [Moorella thermoacetica ATCC 39073], ...	2.0E-62	[1..296]	[1..295]

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Predicted Domain #1

Region A:
Residues: [1-296]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MEDQLKDFIH YMVVEKGLAK NTVVSYERDL KSYVKYLQKV EQAKSFHEVT RLHIVNFLQH  60
   61 LKENGKSSKT LARHIASIRS FHQFLLRERA VEHDPSVHIE TPQGERKLPK VLSVDEVEAL 120
  121 LQTPKMTSAF GVRDKAMLEL LYATGLRVSE LIALNLEDVH LTMGFVRCVG KGNKERIIPL 180
  181 GSLATEAIQK YIEKGRRELM GKKVVDALFL NHHGNRLSRQ GFWKILKRLA KEANIEKELT 240
  241 PHTLRHSFAT HLLENGADLR AVQEMLGHAD ISTTQIYTHV SKTRLKDVYK QFHPRA

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	55.045757
Match:	1a0pA
Description:	SITE-SPECIFIC RECOMBINASE, XERD
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
site-specific recombinase activity	4.99325011803106	bayes_pls_golite062009
integrase activity	3.60695091575172	bayes_pls_golite062009
catalytic activity	2.22520758916604	bayes_pls_golite062009
structure-specific DNA binding	0.11292854906722	bayes_pls_golite062009
DNA binding	0.10970863758177	bayes_pls_golite062009
nucleic acid binding	0.06580979261817	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: