YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|24375751, gi\|...
Organism:	Shewanella oneidensis MR-1
Length:	1188 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|24375751, 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	424.0	[0..5]	[1186..13]
gi\|213428390 - gi\|213428390\|ref\|ZP_03361140.1\| type I restriction enzyme EcoKI subunit R [Salmonella enterica subsp... gi\|29140449, gi\|... - gi\|29144810\|ref\|NP_808152.1\| type I restriction enzyme EcoKI subunit R [Salmonella enterica subsp. e... gi\|213864870 - gi\|213864870\|ref\|ZP_03386989.1\| type I restriction enzyme EcoKI subunit R [Salmonella enterica subsp... gi\|25289195, gi\|... - gi\|25289195\|pir\|\|AD1069 type 1 site-specific deoxyribonuclease (EC 3.1.21.3) - Salmonella enterica s... gi\|16763332 - gi\|16763332\|ref\|NP_458949.1\| type I restriction enzyme EcoKI subunit R [Salmonella enterica subsp. e...	414.0	[0..12]	[1186..1]
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...	414.0	[0..12]	[1186..1]
gi\|58427678, gi\|... - gi\|58583084\|ref\|YP_202100.1\| type I restriction enzyme EcoKI subunit R [Xanthomonas oryzae pv. oryza...	413.0	[0..15]	[1186..31]
gi\|16423093, gi\|... - gi\|16767770\|ref\|NP_463385.1\| type I restriction enzyme EcoKI subunit R [Salmonella typhimurium LT2],...	410.0	[0..12]	[1186..1]
gi\|78685297, gi\|... - gi\|78685297\|ref\|ZP_00850076.1\| Helicase, C-terminal:DEAD/DEAH box helicase, N-terminal [Shewanella s...	410.0	[0..14]	[1186..7]
gi\|115515786, gi... - gi\|117626662\|ref\|YP_859985.1\| type I restriction enzyme EcoKI subunit R [Escherichia coli APEC O1], ...	410.0	[0..11]	[1186..1]
gi\|84624923, gi\|... - gi\|84624923\|ref\|YP_452295.1\| type I restriction enzyme EcoKI subunit R [Xanthomonas oryzae pv. oryza...	409.0	[0..15]	[1186..31]
gi\|91075575, gi\|... - gi\|91214001\|ref\|YP_543987.1\| type I restriction enzyme EcoKI subunit R [Escherichia coli UTI89], gi\|...	408.0	[0..12]	[1186..1]
gi\|32476613, gi\|... - gi\|32476613\|ref\|NP_869607.1\| type I restriction enzyme EcoKI subunit R [Rhodopirellula baltica SH 1]...	403.0	[0..5]	[1186..2]

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Predicted Domain #1

Region A:
Residues: [1-1003]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MALDTQGQST EKDSANFSFL KPYDPIFIDL ACSAERAFTS DPNTTLIKLR QLGEAMAQDI  60
   61 AARCGIEFDD KTTQADLLFK INRELTLEPV VRQLFHALRI EGNKATHQFR TQHKEALEGL 120
  121 KLARSLAIWF HHTFGDQKTA FKAGPFVPPE DPSKQLQELQ TQIELLRSEL NDNHQQLADN 180
  181 QQLTTLLARE KEEYAVLAEQ MDAEARALSK LAAQHEQALV AQKHQFELRI KALQAELVQL 240
  241 AQVDNQAATK NKKQLSQQAS KAGNHIELNE ELTRVLIDQQ LIEAGWIADS QRLDFRKGTR 300
  301 PEKGKNLAIA EWITWHKGKK GRADYVLFCG LIPVAVVEAK KENTHVAGKI SQAERYSKGY 360
  361 KLIAPQQGAW EIEGRTVAWA DDADGHYHIP FVYSCNGREF NKQLAELSGT WFRDTRKPSN 420
  421 TKRALQQFHS PDGLLDKLKR SREAAEQTLQ QEGFDYLGLR DYQQKAIAAV ESALAQDNTQ 480
  481 CLLAMATGTG KTRTIIGLMY RFLKAERFRR ILFLVDRTAL GEQACDSFDE AKLEQNKVLS 540
  541 SIYNIAELGD MKSEAETRIQ VATVQAMVKR IFMSDNPPPL DEFDCIIVDE AHRGYALDQQ 600
  601 MTEGELATRD ASQYLSSYRR VLDYFDAVRI GLTATPAKHT SEIFGKPVYT YSYREAVAGD 660
  661 WLIDHEPPIR YETLLNKHGI KFEKGETVTS INTQTGEIET ADLEDELKFD VESFNKRVIT 720
  721 ESFNEVICQE LIKELDPFGD EKTMIFCATD VHADMVKRLL DKAFLDMYGD DYNQAAVAKI 780
  781 TGQSDKVSQL IRQYKNERYP NIAITVDLLS TGIDVPKICH LVFLRRVKSR ILYEQMMGRA 840
  841 TRRCDDIGKT AFKIYDPVDI YSALEAVNTM KPIVKDPNIT LEQLVDELTD DTFLERALNT 900
  901 PGEQVGAGAD SHTNSHAHDV LNQLGQKVMR VMRKATKKAE NKPELKAKLE QLEELWGVAP 960
  961 AKLHQHLHQI GPREAAQFFK QHQSLINQLA EVRYLVGSDS MPL

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	79.69897
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: [1004-1188]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 IYEGRDEFIE RQQNYGIHEK PADYLESFSH FIKQNINQSA ALSVVVNRPK DLTRAQLKEV  60
   61 KLLLDEAGYS EAHLQSAWRK NTNQDIAASI IGYIRQAALD EALIPFAQRV NNAMQRIYSE 120
  121 HDWNPNQRKW LDRLAKQLVH EAVIDKAFVN NRFASDGGAK RFNSVLNDQL DTILDELNAY 180
  181 LWQVG

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	69.39794
Match:	1d9xA
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: