YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|16505640, gi\|...
Organism:	Salmonella enterica subsp. enterica serovar Typhi
Length:	462 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|16505640, gi|....

Description	E-value	Query Range	Subject Range
gi\|117626660, gi... - gi\|117626660\|ref\|YP_859983.1\| specificity determinant for hsdM and hsdR [Escherichia coli APEC O1], ... gi\|91075572, gi\|... - gi\|91213998\|ref\|YP_543984.1\| specificity determinant for hsdM and hsdR [Escherichia coli UTI89], gi\|...	1.0E-72	[1..462]	[1..455]
gi\|89111057, gi\|... - gi\|89111057\|ref\|AP_004837.1\| specificity determinant for hsdM and hsdR [Escherichia coli str. K-12 s... EG10460 - specificity determinant for hsdM and hsdR / Specificity determinant for HsdM and HsdR T1SK_ECOLI - Type I restriction enzyme EcoKI specificity protein (S protein) (S.EcoKI) - Escherichia coli EG10460 - specificity determinant for hsdM and hsdR / Specificity determinant for HsdM and HsdR gi\|238863570, gi... - gi\|238903436\|ref\|YP_002929232.1\| specificity determinant for hsdM and hsdR [Escherichia coli BW2952]...	4.0E-70	[1..462]	[1..464]
gi\|197240292, gi... - gi\|197262037\|ref\|ZP_03162111.1\| type I restriction enzyme StySJI specificity protein [Salmonella ent... T1S_SALTY - Type-1 restriction enzyme StySJI specificity protein OS=Salmonella typhimurium GN=hsdS PE=3 SV=1 T1S_SALTY - Type-1 restriction enzyme StySJI specificity protein OS=Salmonella typhimurium GN=hsdS PE=3 SV=1 T1S_SALTY - Type-1 restriction enzyme StySJI specificity protein OS=Salmonella typhimurium (strain LT2 / SGSC141... gi\|205330268, gi... - gi\|205330268\|gb\|EDZ17032.1\| type I restriction enzyme StySJI specificity protein [Salmonella enteric... lcl\|NC_016856.1_... - [gene=hsdS] [protein=type I restriction enzyme specificity protein] [protein_id=YP_005240863.1] [loc... gi\|205337035, gi... - gi\|205337035\|gb\|EDZ23799.1\| type I restriction enzyme StySJI specificity protein [Salmonella enteric... gi\|194449649, gi... - gi\|194449649\|ref\|YP_002048547.1\| type I restriction enzyme StySJI specificity protein [Salmonella en...	5.0E-70	[1..462]	[1..469]
gi\|21228805, gi\|... - gi\|21228805\|ref\|NP_634727.1\| type I restriction-modification system specificity subunit [Methanosarc...	2.0E-69	[5..451]	[6..440]
gi\|25397750 - pir\|\|B87326 hypothetical protein CC0621 [imported] - Caulobacter crescentus gi\|16124874, gi\|... - gi\|16124874\|ref\|NP_419438.1\| type I restriction-modification system, S subunit [Caulobacter crescent... gi\|221233594, gi... - gi\|221233594\|ref\|YP_002516030.1\| type I restriction-modification system specificity subunit [Cauloba...	5.0E-68	[4..422]	[18..440]
T1S_SALPO - Type-1 restriction enzyme StySPI specificity protein OS=Salmonella potsdam GN=hsdS PE=3 SV=1 gi\|79033 - gi\|79033\|pir\|\|A26652 type I site-specific deoxyribonuclease (EC 3.1.21.3) - Salmonella sp	7.0E-68	[1..462]	[1..463]
gi\|58427681, gi\|... - gi\|58583087\|ref\|YP_202103.1\| Type I restriction enzyme StySPI specificity protein [Xanthomonas oryza...	3.0E-67	[5..462]	[8..462]
gi\|72397880, gi\|... - gi\|73670718\|ref\|YP_306733.1\| type I restriction-modification system specificity subunit [Methanosarc...	1.0E-65	[5..452]	[17..492]
gi\|24371978, gi\|... - gi\|24371978\|ref\|NP_716020.1\| type I restriction-modification system, S subunit [Shewanella oneidensi... SO0382 - type I restriction-modification system S subunit	1.0E-64	[4..427]	[10..436]
gi\|57019896, gi\|... - gi\|57168615\|ref\|ZP_00367747.1\| HsdS [Campylobacter coli RM2228], gi\|57019896\|gb\|EAL56576.1\| HsdS [Ca...	1.0E-64	[3..420]	[1..408]

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Predicted Domain #1

Region A:
Residues: [1-462]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSGGKLPEGW VTTHLSEICS KPQYGYTTKS SSMGDVKFLR TTDITKGAVD WSSVPYCMDA  60
   61 PEDVSKYQLQ DRDIVISRAG SVGFSFLVQN PPSQVVFASY LIRFKPVNYF SEYYLKRFLE 120
  121 SSDYWNQLSL MSAGNAVQNV NAQKLSTLTV PIPPIAEQKI IAEKLDTLLA QVDSTKARLE 180
  181 QIPQILKRFR QAVLAAAVSG LLIGSNKRNH HPLCSEWQWP DLPSTWSVHK YSELVDSRLG 240
  241 KMLDKAKNFG SATKYLGNIN VRWFSFDLEN LQDILISDIE RRELSLKLGD VLICEGGEPG 300
  301 RCAIWSEPQD IPVIFQKALH RARVKDKIIP EWLVYNLKND SNNISLSQLF TGTTIKHLTG 360
  361 KALANYPIRV PPLEEQHEIV RRVEQLFAWA DTIEKQVNNA LNRVNSLTQS ILAKAFRGEL 420
  421 TAQWRAENPS LISGENSAAA LLEKIKAERA ASGGKKTSRK KA

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	54.69897
Match:	1yf2A
Description:	Three-dimensional structure of DNA sequence specificity (S) subunit of a type I restriction-modification enzyme and its functional implications
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
nucleic acid binding	1.4210145112553	bayes_pls_golite062009
DNA binding	1.41179209561821	bayes_pls_golite062009
binding	1.33040179592624	bayes_pls_golite062009
endodeoxyribonuclease activity	0.80284978967783	bayes_pls_golite062009
deoxyribonuclease activity	0.63913609426399	bayes_pls_golite062009
catalytic activity	0.316629025709297	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: