YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|24371957, gi\|...
Organism:	Shewanella oneidensis MR-1
Length:	701 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|24371957, gi|....

Description	E-value	Query Range	Subject Range
gi\|20516195, gi\|... - gi\|20807650\|ref\|NP_622821.1\| guanosine polyphosphate pyrophosphohydrolase/synthetase [Thermoanaeroba... gi\|20807650 - gi\|20807650\|ref\|NP_622821.1\| Guanosine polyphosphate pyrophosphohydrolase/synthetase [Thermoanaeroba...	837.0	[0..3]	[700..1]
gi\|10443847 - gi\|10443847\|gb\|AAG17607.1\|AF242653_1 ppGpp synthetase/hydrolase Rel [Geobacillus stearothermophilus]	827.0	[0..5]	[700..10]
gi\|56421113, gi\|... - gi\|56421113\|ref\|YP_148431.1\| GTP pyrophosphokinase (ppGpp synthetase) [Geobacillus kaustophilus HTA4...	826.0	[0..5]	[700..10]
gi\|124546426, gi... - gi\|124546426\|ref\|ZP_01705522.1\| (p)ppGpp synthetase I, SpoT/RelA [Shewanella putrefaciens 200], gi\|1... gi\|120560650, gi... - gi\|120600557\|ref\|YP_965131.1\| bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate... gi\|77811557, gi\|... - gi\|77813466\|ref\|ZP_00812741.1\| RelA/SpoT protein [Shewanella putrefaciens CN-32], gi\|77811557\|gb\|EAO...	818.0	[0..1]	[701..1]
gi\|254824418 - gi\|254824418\|ref\|ZP_05229419.1\| (p)ppGpp synthetase [Listeria monocytogenes FSL J1-194] gi\|226224124, gi... - gi\|226224124\|ref\|YP_002758231.1\| (p)ppGpp synthetase [Listeria monocytogenes Clip81459], gi\|22587658... gi\|254878988 - gi\|254878988\|ref\|ZP_05251698.1\| (p)ppGpp synthetase [Listeria monocytogenes FSL J2-071] gi\|46907751, gi\|... - gi\|46907751\|ref\|YP_014140.1\| GTP pyrophosphokinase [Listeria monocytogenes str. 4b F2365], gi\|468810... gi\|254852146 - gi\|254852146\|ref\|ZP_05241494.1\| (p)ppGpp synthetase [Listeria monocytogenes FSL R2-503] gi\|133735221, gi... - gi\|254931458\|ref\|ZP_05264817.1\| (p)ppGpp synthetase [Listeria monocytogenes HPB2262], gi\|153202446\|r...	818.0	[0..5]	[700..10]
gi\|81243289, gi\|... - gi\|82779141\|ref\|YP_405490.1\| bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate ...	817.0	[0..1]	[701..1]
gi\|124528991, gi... - gi\|124528991\|ref\|ZP_01700137.1\| metal dependent phosphohydrolase [Escherichia coli B], gi\|124500130\|... gi\|24054163, gi\|... - gi\|24114920\|ref\|NP_709430.1\| bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate ... gi\|168779806, gi... - gi\|189002275\|gb\|EDU71261.1\| guanosine-3',5'-bis(diphosphate) 3'-diphosphatase [Escherichia coli O157... SPOT_SHIFL - Guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase OS=Shigella flexneri GN=spoT PE=3 SV=1 gi\|189374284, gi... - gi\|189374284\|gb\|EDU92700.1\| guanosine-3',5'-bis(diphosphate) 3'-diphosphatase [Escherichia coli O157... SPOT_ECO57 - Guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase OS=Escherichia coli O157:H7 GN=spoT PE=3 SV... gi\|168798620, gi... - gi\|189378740\|gb\|EDU97156.1\| guanosine-3',5'-bis(diphosphate) 3'-diphosphatase [Escherichia coli O157... gi\|30043335, gi\|... - gi\|30065074\|ref\|NP_839245.1\| bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate ... gi\|170018120, gi... - gi\|170018120\|ref\|YP_001723074.1\| bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosph... gi\|15804191, gi\|... - gi\|15804191\|ref\|NP_290230.1\| bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate ... gi\|13364000, gi\|... - gi\|15833779\|ref\|NP_312552.1\| bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate ... gi\|170517691, gi... - gi\|170679973\|ref\|YP_001745950.1\| guanosine-3',5'-bis(diphosphate) 3'-diphosphatase [Escherichia coli... EG10966 - bifunctional (p)ppGpp synthetase II / guanosine-3',5'-bis pyrophosphate 3'-pyrophosphohydrolase / ppG... gi\|110617220, gi... - gi\|110807672\|ref\|YP_691192.1\| bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate... gi\|195936211 - gi\|195936211\|ref\|ZP_03081593.1\| bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophospha... gi\|208809066, gi... - gi\|208809066\|ref\|ZP_03251403.1\| guanosine-3',5'-bis(diphosphate) 3'-diphosphatase [Escherichia coli ... gi\|208735324, gi... - gi\|208814047\|ref\|ZP_03255376.1\| guanosine-3',5'-bis(diphosphate) 3'-diphosphatase [Escherichia coli ... gi\|188016940, gi... - gi\|188016940\|gb\|EDU55062.1\| guanosine-3',5'-bis(diphosphate) 3'-diphosphatase [Escherichia coli O157... gi\|189359047, gi... - gi\|189359047\|gb\|EDU77466.1\| guanosine-3',5'-bis(diphosphate) 3'-diphosphatase [Escherichia coli O157... gi\|168759771, gi... - gi\|189369840\|gb\|EDU88256.1\| guanosine-3',5'-bis(diphosphate) 3'-diphosphatase [Escherichia coli O157... gi\|168766071, gi... - gi\|189364357\|gb\|EDU82776.1\| guanosine-3',5'-bis(diphosphate) 3'-diphosphatase [Escherichia coli O157... gi\|168772381, gi... - gi\|187771785\|gb\|EDU35629.1\| guanosine-3',5'-bis(diphosphate) 3'-diphosphatase [Escherichia coli O157... gi\|218434381, gi... - gi\|218707284\|ref\|YP_002414803.1\| bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosph... gi\|254595005, gi... - gi\|254795605\|ref\|YP_003080442.1\| bifunctional (p)ppGpp synthetase II and guanosine-3',5'-bis pyropho... gi\|208740042, gi... - gi\|208819919\|ref\|ZP_03260239.1\| guanosine-3',5'-bis(diphosphate) 3'-diphosphatase [Escherichia coli ... gi\|226838816, gi... - gi\|254038851\|ref\|ZP_04872903.1\| guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase [Escherichi... gi\|209162363, gi... - gi\|209400963\|ref\|YP_002273130.1\| guanosine-3',5'-bis(diphosphate) 3'-diphosphatase [Escherichia coli... gi\|209914382, gi... - gi\|209921123\|ref\|YP_002295207.1\| bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosph... gi\|215488945, gi... - gi\|215488945\|ref\|YP_002331376.1\| bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosph... EG10966 - bifunctional (p)ppGpp synthetase II / guanosine-3',5'-bis pyrophosphate 3'-pyrophosphohydrolase / ppG... gi\|217322802, gi... - gi\|217326581\|ref\|ZP_03442665.1\| guanosine-3',5'-bis(diphosphate) 3'-diphosphatase [Escherichia coli ... gi\|218362981, gi... - gi\|218556213\|ref\|YP_002389126.1\| bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosph... SPOT_ECOLI - Guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase (EC 3.1.7.2) ((ppGpp)ase) (Penta-phosphate ... gi\|218697371, gi... - gi\|218697371\|ref\|YP_002405038.1\| bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosph... gi\|218702419, gi... - gi\|218702419\|ref\|YP_002410048.1\| bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosph... gi\|73857592, gi\|... - gi\|74314115\|ref\|YP_312534.1\| bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate ... gi\|81247492, gi\|... - gi\|82546081\|ref\|YP_410028.1\| bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate ... gi\|75258191, gi\|... - gi\|75258191\|ref\|ZP_00729639.1\| COG0317: Guanosine polyphosphate pyrophosphohydrolases/synthetases [E... gi\|188494223, gi... - gi\|75514287\|ref\|ZP_00736595.1\| COG0317: Guanosine polyphosphate pyrophosphohydrolases/synthetases [E... gi\|85676393, gi\|... - gi\|89110362\|ref\|AP_004142.1\| bifunctional (p)ppGpp synthetase II and guanosine-3',5'-bis pyrophospha... gi\|83588503, gi\|... - gi\|83588503\|ref\|ZP_00927127.1\| COG0317: Guanosine polyphosphate pyrophosphohydrolases/synthetases [E... gi\|75179691, gi\|... - gi\|75179691\|ref\|ZP_00699678.1\| COG0317: Guanosine polyphosphate pyrophosphohydrolases/synthetases [S... gi\|194420599, gi... - gi\|83571437\|ref\|ZP_00922877.1\| COG0317: Guanosine polyphosphate pyrophosphohydrolases/synthetases [S... gi\|190902152, gi... - gi\|75229041\|ref\|ZP_00715625.1\| COG0317: Guanosine polyphosphate pyrophosphohydrolases/synthetases [E... gi\|193070400, gi... - gi\|75234808\|ref\|ZP_00719111.1\| COG0317: Guanosine polyphosphate pyrophosphohydrolases/synthetases [E... gi\|157078900, gi... - gi\|75188408\|ref\|ZP_00701675.1\| COG0317: Guanosine polyphosphate pyrophosphohydrolases/synthetases [E... gi\|75197553, gi\|... - gi\|75197553\|ref\|ZP_00707623.1\| COG0317: Guanosine polyphosphate pyrophosphohydrolases/synthetases [E...	816.0	[0..1]	[701..1]
gi\|91213168, gi\|... - gi\|91213168\|ref\|YP_543154.1\| bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate ... gi\|190909368, gi... - gi\|75242571\|ref\|ZP_00726315.1\| COG0317: Guanosine polyphosphate pyrophosphohydrolases/synthetases [E... gi\|226902708, gi... - gi\|237703444\|ref\|ZP_04533925.1\| guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase [Escherichi... gi\|218367491, gi... - gi\|218560722\|ref\|YP_002393635.1\| bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosph... gi\|110643891, gi... - gi\|110643891\|ref\|YP_671621.1\| bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate... gi\|26110727, gi\|... - gi\|26250297\|ref\|NP_756337.1\| bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate ...	816.0	[0..1]	[701..1]
gi\|241903868, gi... - gi\|241903868\|ref\|ZP_04788584.1\| (p)ppGpp synthetase I, SpoT/RelA [Thermoanaerobacter brockii subsp. ... gi\|76797241, gi\|... - gi\|76797241\|ref\|ZP_00779574.1\| RelA/SpoT protein [Thermoanaerobacter ethanolicus ATCC 33223], gi\|765...	816.0	[0..3]	[700..1]
gi\|254898311, gi... - gi\|254898311\|ref\|ZP_05258235.1\| hypothetical protein LmonJ_00810 [Listeria monocytogenes J0161], gi\|... gi\|127633725, gi... - gi\|254829718\|ref\|ZP_05234373.1\| hypothetical protein Lmon1_00115 [Listeria monocytogenes 10403S], gi... gi\|254936525 - gi\|254936525\|ref\|ZP_05268222.1\| hypothetical protein LmonF6_05310 [Listeria monocytogenes F6900] gi\|127765529, gi... - gi\|254912197\|ref\|ZP_05262209.1\| hypothetical protein LmonJ2_05325 [Listeria monocytogenes J2818], gi... gi\|133729913, gi... - gi\|254828243\|ref\|ZP_05232930.1\| hypothetical protein LmonocytogeFSL_07257 [Listeria monocytogenes FS... gi\|47014602, gi\|... - gi\|47097020\|ref\|ZP_00234593.1\| GTP pyrophosphokinase [Listeria monocytogenes str. 1/2a F6854], gi\|47... gi\|16803563 - gi\|16803563\|ref\|NP_465048.1\| hypothetical protein lmo1523 [Listeria monocytogenes EGD-e] gi\|224499816 - gi\|224499816\|ref\|ZP_03668165.1\| hypothetical protein LmonF1_09074 [Listeria monocytogenes Finland 19... gi\|224501537 - gi\|224501537\|ref\|ZP_03669844.1\| hypothetical protein LmonFR_03302 [Listeria monocytogenes FSL R2-561... gi\|25289077, gi\|... - pir\|\|AC1265 (p)ppGpp synthetase homolog relA [imported] - Listeria monocytogenes (strain EGD-e), gi\|...	816.0	[0..5]	[700..10]

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Predicted Domain #1

Region A:
Residues: [1-386]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MYLFEGLKES ASGYLEPEQV ELLKQAYQVA RDAHEGQMRT SGEPYITHPV AVARILAEMR  60
   61 LDHETLMAAL LHDTIEDTYV TKEDLAERFG ESVAELVEGV SKLDKLKFRD KKEAQAENFR 120
  121 KMMMAMTQDI RVILIKLADR THNMRTLGAL RPDKRRRIAR ETLEIYAPIA NRLGIHNIKT 180
  181 ELEDLGFQAY YPMRYRVLKE VVKAARGNRK ELIQGIEAAV LTRLNDAGIK GKVKGREKNL 240
  241 YSIYNKMQSK ELQFQEVMDI YAFRVIVDSI DTCYRVLGAM HGLYKPRPGR FKDYIAIPKA 300
  301 NGYQSLHTSL FGPHGVPVEI QIRTEDMDQM ADKGVAAHWA YKGGAETGQG TTTQVRARKW 360
  361 MQSLLELQQS ASTSFEFVEN VKTELF

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	129.0
Match:	1vj7A
Description:	Crystal structure of the bifunctional catalytic fragment of RelSeq, the RelA/SpoT homolog from Streptococcus equisimilis.
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
GTP diphosphokinase activity	1.5953523101767	bayes_pls_golite062009
cyclic-nucleotide phosphodiesterase activity	1.53556412385088	bayes_pls_golite062009
3',5'-cyclic-nucleotide phosphodiesterase activity	1.52960140313397	bayes_pls_golite062009
transferase activity, transferring phosphorus-containing groups	1.17940277430091	bayes_pls_golite062009
guanosine-3',5'-bis(diphosphate) 3'-diphosphatase activity	1.1479499593037	bayes_pls_golite062009
diphosphoric monoester hydrolase activity	1.1479499593037	bayes_pls_golite062009
catalytic activity	1.122769147009	bayes_pls_golite062009
nucleotidyltransferase activity	0.92178707322923	bayes_pls_golite062009
hydrolase activity	0.89382287998944	bayes_pls_golite062009
phosphoric diester hydrolase activity	0.874654356902841	bayes_pls_golite062009
transferase activity	0.63270331673446	bayes_pls_golite062009
hydrolase activity, acting on ester bonds	0.262138492248739	bayes_pls_golite062009
phosphoric ester hydrolase activity	0.196287846714023	bayes_pls_golite062009
3',5'-cyclic-AMP phosphodiesterase activity	0.0897894719596	bayes_pls_golite062009
3',5'-cyclic-GMP phosphodiesterase activity	0.0229959143092802	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [387-571]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 PEEIYVFTPE GRILELPVNA TAVDFAYEVH TDVGNTCVGA RVNRQAYPLS QPLISGQTVE  60
   61 IITAKGARPN AAWLNFVVTG KARAKIRQVL KSLKGDDAIA LGRRLLNHAL GKTKLDSIPA 120
  121 EQIEKVVRDT KHASLNALLA DIGLGNAMSI VIAQRLIGDN LENQESRDSH QMPIRGAEGM 180
  181 LVTFA

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	24.30103
Match:	1nyqA
Description:	Structure of Staphylococcus aureus threonyl-tRNA synthetase complexed with an analogue of threonyl adenylate
Matching Structure (courtesy of the PDB):

Predicted Domain #3

Region A:
Residues: [572-701]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 NCCRPIPGDA VIAHVSQGKG LVVHMENCAN IRGYQSEPDK YIPVQWDNVE GVEYQANLRV  60
   61 EIVNHQGALA KITSIIAAEG SNIHNLSTEE RDGRVYLINL RISVKDRIHL ANVMRRIRVL 120
  121 PEVLRTSRNR

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	12.69897
Match:	2f1fA
Description:	Crystal structure of the regulatory subunit of acetohydroxyacid synthase isozyme III from E. coli
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
transferase activity, transferring aldehyde or ketonic groups	1.58611270031811	bayes_pls_golite062009
catalytic activity	1.01569611874813	bayes_pls_golite062009
binding	0.162590183060409	bayes_pls_golite062009
transferase activity	0.07375530569672	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:

Predicted functions: