YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|24345828, gi\|...
Organism:	Shewanella oneidensis MR-1
Length:	1033 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|24345828, gi|....

Description	E-value	Query Range	Subject Range
gi\|207088276 - gi\|207088276\|gb\|EDZ65548.1\| type I site-specific deoxyribonuclease, HsdR family, putative [Nitrosoco... gi\|224408622, gi... - gi\|254435165\|ref\|ZP_05048672.1\| type I site-specific deoxyribonuclease, HsdR family, putative [Nitro... gi\|77166360, gi\|... - gi\|77166360\|ref\|YP_344885.1\| Type I site-specific deoxyribonuclease HsdR [Nitrosococcus oceani ATCC ...	433.0	[0..3]	[1030..25]
gi\|77955756, gi\|... - gi\|77955756\|ref\|ZP_00820100.1\| Type I site-specific deoxyribonuclease HsdR [Marinobacter aquaeolei V...	431.0	[0..1]	[1031..1]
gi\|67529292, gi\|... - gi\|67549404\|ref\|ZP_00427268.1\| Type I site-specific deoxyribonuclease HsdR [Burkholderia vietnamiens...	420.0	[0..1]	[1024..1]
gi\|11362801 - pir\|\|A82522 type I restriction-modification system endonuclease XF2739 [imported] - Xylella fastidio... gi\|15839328, gi\|... - gi\|9107977\|gb\|AAF85524.1\|AE004080_6 type I restriction-modification system endonuclease [Xylella fas...	417.0	[0..1]	[1024..15]
gi\|78686855, gi\|... - gi\|78686855\|ref\|ZP_00851616.1\| Type I site-specific deoxyribonuclease HsdR [Shewanella sp. ANA-3], g...	408.0	[0..1]	[1030..1]
gi\|120597152, gi... - gi\|82741285\|ref\|ZP_00904010.1\| Type I site-specific deoxyribonuclease HsdR [Shewanella sp. W3-18-1],...	406.0	[0..1]	[1030..1]
gi\|87300619, gi\|... - gi\|87300619\|ref\|ZP_01083461.1\| type I restriction-modification system endonuclease [Synechococcus sp...	406.0	[0..6]	[1024..5]
gi\|66796591, gi\|... - gi\|94986111\|ref\|YP_605475.1\| HsdR family type I site-specific deoxyribonuclease [Deinococcus geother...	404.0	[0..1]	[1024..1]
gi\|86145624, gi\|... - gi\|86145624\|ref\|ZP_01063954.1\| type I restriction-modification system, R subunit [Vibrio sp. MED222]...	403.0	[0..1]	[1030..1]

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Predicted Domain #1

Region A:
Residues: [1-884]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MDQDELHKVE LPAIAQLSLL GWQYVAGAKL TPEYHERPYL RDVVLVGRLE AAIKRINPWI  60
   61 NDENLRKVCR DITHPNFVGL MEYNQAIYQT LVNYLSVEQD VGKGRKGQTV KLIDFDNLAA 120
  121 NEFICTSQFK VEGVNQNIIP DIVCFINGLP LAVIECKSPY ISAPISEGIN QLRRYANLRN 180
  181 SVDDEGAQRL FWYNQLMVST CRDQAKVGTI SSNASHYADW KDAYPFTDTT LSEQNLSQAF 240
  241 SRNSLDDMQV NDNPALYTAT SSNYDAITAV TAQQRLIAGI FSPASFLDIL QNFIIFEPVE 300
  301 GKLIKKVARY QQYRAVNKVI ERLKTGQDRK EKSGVVWHTQ GSGKSLTMVM LAVKMRRDPV 360
  361 LKQYKLVFIT DRTQLDEQLS STFRAAQGET IYNAGSVAEL KALLKKDSSD LVTAMVQKFL 420
  421 DLEKELSTNN ENEGFINLNP SDKIIVLADE AHRTQFGGLA MTINAALPNA PKIGFTGTPL 480
  481 LKTQKMDKAF GGYIDEYKIN QAVDDGATVR ILYEGRQVKT EVAGESLDKL FEAYFGSYSK 540
  541 EEQREIKQKY GVERAVREAP ARIRWVCMDL LEHYRKHIQP DGFKAMIVVG SRHAATIFKK 600
  601 TLDELGAPPS EVIISGYHND EAYIAVHTDK TKQKKIIQDF TKPLSENPVA FLIVKDMLLT 660
  661 GFDAPIAQVM YIDRKLQDHT LMQAIARVNR TYAKKECGFI VDYFGLSNHL IEAMEMFSSD 720
  721 DVEGTYQSLK DEIPKLKATH TLAISFFRHI KNKDVDSYVL ALKEETVRAQ FDMAFKRFAK 780
  781 QMNIVLPDVA AAPFLADMKL LGKVHNSARN QYRDAGLDMT DIGAKVRKLV DEHILSTGVD 840
  841 PKIPPIDLLA ANFKESIRPE KSAESKASEI ESAIKHHITV KLEE

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	60.69897
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 #2

Region A:
Residues: [885-1033]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 DPEYYKSLSL RLRDIIEKTA GQWEQQLELL LAMVDTIEID RRRAAKDAGL SETEFAFYNI  60
   61 LTAEVTQTSD IEVIDEHQLI EIKTITQNLV AMFDEATQIV DFFNKGDEIK RLKKEIKRAV 120
  121 IDASFSNVEL ISNLQDRFME LAKHKFNKQ

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	51.045757
Match:	1t5lA
Description:	Crystal structure of the DNA repair protein UvrB point mutant Y96A revealing a novel fold for domain 2
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: