YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|29140449, gi\|...
Organism:	Salmonella enterica subsp. enterica serovar Typhi str. Ty2
Length:	1169 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|29140449, gi|....

Description	E-value	Query Range	Subject Range
gi\|16132171, gi\|... - gi\|1790809\|gb\|AAC77306.1\| endonuclease R [Escherichia coli str. K-12 substr. MG1655], gi\|16132171\|re... gi\|85677090, gi\|... - gi\|89111059\|ref\|AP_004839.1\| endonuclease R [Escherichia coli str. K-12 substr. W3110], gi\|85677090\|... gi\|238861030, gi... - gi\|238903438\|ref\|YP_002929234.1\| endonuclease R [Escherichia coli BW2952], gi\|238861030\|gb\|ACR63028.... gi\|537192\|gb\|AAA... - CG Site No. 620; alternate gene names hs, hsp, hsr, rm; apparent frameshift in GenBank Accession Num... T1RK_ECOLI - Type I restriction enzyme EcoKI R protein (EC 3.1.21.3) (R.EcoKI) - Escherichia coli	0.0	[1..1169]	[20..1188]
gi\|16423093, gi\|... - gi\|16767770\|ref\|NP_463385.1\| type I restriction enzyme EcoKI subunit R [Salmonella typhimurium LT2],...	0.0	[1..1169]	[1..1169]
gi\|197365233, gi... - gi\|197365233\|ref\|YP_002144870.1\| type I restriction enzyme EcoKI subunit R [Salmonella enterica subs... gi\|56130567, gi\|... - gi\|56416310\|ref\|YP_153385.1\| type I restriction enzyme EcoKI subunit R [Salmonella enterica subsp. e...	0.0	[1..1169]	[1..1169]
gi\|115515786, gi... - gi\|117626662\|ref\|YP_859985.1\| type I restriction enzyme EcoKI subunit R [Escherichia coli APEC O1], ...	0.0	[1..1169]	[2..1170]
gi\|91075575, gi\|... - gi\|91214001\|ref\|YP_543987.1\| type I restriction enzyme EcoKI subunit R [Escherichia coli UTI89], gi\|...	0.0	[1..1169]	[1..1169]
gi\|41752 - gi\|41752\|emb\|CAA29791.1\| unnamed protein product [Escherichia coli]	0.0	[1..1066]	[20..1085]
gi\|90329499, gi\|... - gi\|90410146\|ref\|ZP_01218163.1\| endonuclease R, host restriction [Photobacterium profundum 3TCK], gi\|...	0.0	[1..1166]	[1..1172]
SO4267 - type I restriction-modification system R subunit gi\|24375751, gi\|... - gi\|24375751\|ref\|NP_719794.1\| type I restriction enzyme EcoKI subunit R [Shewanella oneidensis MR-1],...	0.0	[2..1166]	[13..1186]
gi\|32476613, gi\|... - gi\|32476613\|ref\|NP_869607.1\| type I restriction enzyme EcoKI subunit R [Rhodopirellula baltica SH 1]...	0.0	[4..1167]	[12..1136]
gi\|186467442, gi... - gi\|23129551\|ref\|ZP_00111377.1\| COG4096: Type I site-specific restriction-modification system, R (res...	0.0	[5..1166]	[6..1102]

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Predicted Domain #1

Region A:
Residues: [1-99]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MNKSNFDFLK GVNDFIYAIA CAAENNYPDD PNTTLIKMRM FGEATAKHLG QLLDIPVCEN  60
   61 QHDLLRELGK IAFIDDSILS VFHKLRRIGN LAVHEFHND

[Run NCBI BLAST on this sequence.]

Detection Method:	FFAS03
Confidence:	1.05
Match:	1ylmA
Description:	Hypothetical cytosolic protein YutE from Bacillus subtilis
Matching Structure (courtesy of the PDB):

Predicted Domain #2

Region A:
Residues: [100-997]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 LDDAQMCLRL GFRLSVWYYR LVTKDYDFPV PMFVLPEHGE NLYHQEVLTL KQQLERQAQE  60
   61 KVQSQAELEA QQQRLVALNG YIAILEGKQQ ETEAQTKARL AALEAQLAAK DAELAKQTEQ 120
  121 ERKAYHKEIT DQAIKRTLNL SEEESRFLID AQLRKAGWQA DSKTLRFAKG ARPEPGVNKA 180
  181 IAEWPTGTDE TGKTGFADYV LFVGLKPIAV VEAKRKNTDV FSKLNESYRY SKYFDNGFLR 240
  241 DTLLEHYAPD EVHDAVPEYE ISWQDTSGKQ RFKIPFCYST NGREYRAAMK TKSGIWYRDV 300
  301 RHTTNMSKAL PEWHRPEELL DMLGSDPQKQ NQWFAENPGM SELGLRYYQE DAVRAVEKAI 360
  361 VNGQQEILLA MATGTGKTRT AIALMFRLIQ SQRFKRVLFL VDRRSLGEQA LGSFEDTRIN 420
  421 GDTFNSIFDI KGLTDKFPED STKIHVATVQ SLVKRTLQSD EPMPVGRYDC IVVDEAHRGY 480
  481 ILDKEQTEGE LQFRSQLDYV SAYRRILDHF DAVKIALTAT PALHTVEIFG EPVYRYTYRT 540
  541 AVIDGYLIDQ DPPIQIVTRN AQDGVYLSEG EQVERLNPQG ELINDTLADD QDFEVADFNR 600
  601 GLVIPAFNRA VCGELTKYLD PIGQQKTLVF CVTNAHADMV VDELRTAFKK KYPQLEHDAI 660
  661 IKITGDADKD AKKVQSMIVR FNKERLPNIV VTVDLLTTGV DIPSICNIVF LRKVKSRILY 720
  721 EQMKGRATRL CPSVGKTSFK IYDCVDIYSS LESVDTMRPV VVRPQVELQT LVNEITDSET 780
  781 YKTIEADGRS FAEHSHEQLV AKLQRIIGLA TYNRDHSETV DKQVRRLDEL CLDAAGVNFG 840
  841 GLASRLREKG PHWSAEIFNK LPGFIARLER LKTDINALRD APIFLDIDDE VVSVKSLY

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	60.0
Match:	2eyqA
Description:	Crystal structure of Escherichia coli transcription-repair coupling factor
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
nucleoside-triphosphatase activity	2.16381244011837	bayes_pls_golite062009
pyrophosphatase activity	2.13284212711072	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides	2.11265775498161	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides	2.11046854230259	bayes_pls_golite062009
hydrolase activity	1.66122526893602	bayes_pls_golite062009
ATPase activity	1.53315090215319	bayes_pls_golite062009
binding	1.41264401383678	bayes_pls_golite062009
DNA-dependent ATPase activity	1.1653223755451	bayes_pls_golite062009
catalytic activity	1.00104173493322	bayes_pls_golite062009
purine ribonucleotide binding	0.923452757551011	bayes_pls_golite062009
ribonucleotide binding	0.923391844349459	bayes_pls_golite062009
purine nucleotide binding	0.920821955769652	bayes_pls_golite062009
nucleotide binding	0.917754212279227	bayes_pls_golite062009
helicase activity	0.895387263223335	bayes_pls_golite062009
DNA helicase activity	0.8104901979223	bayes_pls_golite062009
ATP binding	0.60527666756293	bayes_pls_golite062009
adenyl ribonucleotide binding	0.573214556107072	bayes_pls_golite062009
adenyl nucleotide binding	0.554530910579109	bayes_pls_golite062009
nucleic acid binding	0.216266069700019	bayes_pls_golite062009
ATP-dependent helicase activity	0.156322124775303	bayes_pls_golite062009
purine NTP-dependent helicase activity	0.156322124775303	bayes_pls_golite062009
ATP-dependent DNA helicase activity	0.0398638249772338	bayes_pls_golite062009

Predicted Domain #3

Region A:
Residues: [998-1169]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 GDYDTPQDFL EAFDALVQHA PNAQPALQAV INRPRDLTRK GLVELQEWFD RQHFEESSLR  60
   61 SAWKETRNED IAARLIGHIR RAAVGDALKP FDERVDHALA RIKGENDWSP EQLSWLDRLA 120
  121 QALKEKVVLD DDVFKTGNFH RRGGKSMLQR TFDDNLDSVL DKFSDYIWDE LA

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	71.0
Match:	1d9zA
Description:	Nucleotide excision repair enzyme UvrB
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

Predicted functions: