YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|46581622, gi\|...
Organism:	Desulfovibrio vulgaris str. Hildenborough
Length:	459 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|46581622, gi|....

Description	E-value	Query Range	Subject Range
gi\|120601219, gi... - gi\|120601219\|ref\|YP_965619.1\| two component, sigma54 specific, Fis family transcriptional regulator ...	437.0	[0..1]	[459..1]
gi\|158320115, gi... - gi\|158320115\|ref\|YP_001512622.1\| two component, sigma54 specific, Fis family transcriptional regulat...	431.0	[0..1]	[456..1]
gi\|77545639, gi\|... - gi\|77919556\|ref\|YP_357371.1\| response regulator transcription factor [Pelobacter carbinolicus DSM 23...	431.0	[0..1]	[456..12]
gi\|134299175, gi... - gi\|88944680\|ref\|ZP_01147905.1\| Helix-turn-helix, Fis-type [Desulfotomaculum reducens MI-1], gi\|88925...	430.0	[0..4]	[456..3]
gi\|94731568, gi\|... - gi\|94987319\|ref\|YP_595252.1\| response regulator [Lawsonia intracellularis PHE/MN1-00], gi\|94731568\|e...	428.0	[0..4]	[459..2]
gi\|77639083, gi\|... - gi\|77685113\|ref\|ZP_00800523.1\| Helix-turn-helix, Fis-type [Alkaliphilus metalliredigenes QYMF], gi\|7...	428.0	[0..6]	[456..3]
gi\|78194911, gi\|... - gi\|78223656\|ref\|YP_385403.1\| two component, sigma54 specific, Fis family transcriptional regulator [...	426.0	[0..3]	[457..7]
gi\|146398219, gi... - gi\|88934576\|ref\|ZP_01140218.1\| Helix-turn-helix, Fis-type [Geobacter uraniumreducens Rf4], gi\|889187...	426.0	[0..1]	[456..1]
gi\|75243036, gi\|... - gi\|75243036\|ref\|ZP_00726742.1\| COG2204: Response regulator containing CheY-like receiver, AAA-type A... gi\|91211514, gi\|... - gi\|91211514\|ref\|YP_541500.1\| acetoacetate metabolism regulatory protein AtoC [Escherichia coli UTI89... gi\|218559138, gi... - gi\|218559138\|ref\|YP_002392051.1\| acetoacetate metabolism regulatory protein AtoC [Escherichia coli S... gi\|110344022, gi... - gi\|110642430\|ref\|YP_670160.1\| acetoacetate metabolism regulatory protein AtoC [Escherichia coli 536]... gi\|218427947, gi... - gi\|218690383\|ref\|YP_002398595.1\| acetoacetate metabolism regulatory protein AtoC [Escherichia coli E... gi\|115513538, gi... - gi\|117624414\|ref\|YP_853327.1\| acetoacetate metabolism regulatory protein AtoC [Escherichia coli APEC... gi\|237704695, gi... - gi\|237704695\|ref\|ZP_04535176.1\| acetoacetate metabolism regulatory protein AtoC [Escherichia sp. 3_2... gi\|227835628, gi... - gi\|227887278\|ref\|ZP_04005083.1\| acetoacetate metabolism regulatory protein AtoC [Escherichia coli 83... gi\|26109014, gi\|... - gi\|26248609\|ref\|NP_754649.1\| acetoacetate metabolism regulatory protein AtoC [Escherichia coli CFT07...	426.0	[0..1]	[456..1]

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Predicted Domain #1

Region A:
Residues: [1-390]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSETTHILVI DDEKNYLLVL EALLTDAGYA VTALNDPETA LAFLEESEVD VVITDMKMPR  60
   61 VTGREVLERV KKTWPHIPVC IMTAFGSIEG AVDVMKYGAF DYITKPFSND ELLLSVQNAA 120
  121 ELSRVHRQYR ALRANLEERY GTHQIIGRSK AIREVLDMVD RAAPSRSTVL ITGESGTGKE 180
  181 LVARAIHFSS PRNSGPFVSV NCMALNPGVL ESELFGHEKG SFTGAMAMRR GRFEQADGGT 240
  241 LFLDEIGELT PELQVKLLRV LQERRFERVG GGDEIEVDIR VVAATNKDLQ KEVENGTFRE 300
  301 DLYYRLNVVH VALPPLRERR EDIPLLVGHF VEKLARDNGM KPKTFTPEAH DYLTGYEWPG 360
  361 NIRQLQNVVE RCLVLVASDT VGVDDLPPEI

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	95.0
Match:	1ny5A
Description:	Crystal structure of sigm54 activator (AAA+ ATPase) in the inactive state
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
protein histidine kinase activity	2.35011582062573	bayes_pls_golite062009
two-component sensor activity	2.32303301074957	bayes_pls_golite062009
phosphotransferase activity, nitrogenous group as acceptor	2.28838869071567	bayes_pls_golite062009
nucleoside-triphosphatase activity	1.95073642969863	bayes_pls_golite062009
pyrophosphatase activity	1.91141407779641	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides	1.9017593265179	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides	1.90014393273511	bayes_pls_golite062009
carboxylic acid transmembrane transporter activity	1.82370030183942	bayes_pls_golite062009
organic acid transmembrane transporter activity	1.79922369980544	bayes_pls_golite062009
transporter activity	1.55572428045529	bayes_pls_golite062009
amino acid transmembrane transporter activity	1.52217781539459	bayes_pls_golite062009
ATPase activity	1.48474288797022	bayes_pls_golite062009
two-component response regulator activity	1.45919623810582	bayes_pls_golite062009
amine transmembrane transporter activity	1.4031990658196	bayes_pls_golite062009
transmembrane transporter activity	1.38483976298883	bayes_pls_golite062009
ATPase activity, coupled	1.37457738689583	bayes_pls_golite062009
catalytic activity	1.37148167194523	bayes_pls_golite062009
binding	1.30574971150356	bayes_pls_golite062009
active transmembrane transporter activity	1.24278046928678	bayes_pls_golite062009
P-P-bond-hydrolysis-driven transmembrane transporter activity	1.2014318795788	bayes_pls_golite062009
primary active transmembrane transporter activity	1.19670408144267	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances	1.17063957238561	bayes_pls_golite062009
ATPase activity, coupled to movement of substances	1.16918853509059	bayes_pls_golite062009
ATPase activity, coupled to transmembrane movement of substances	1.16885789920943	bayes_pls_golite062009
hydrolase activity	1.09839981963412	bayes_pls_golite062009
nucleic acid binding	0.900561861643259	bayes_pls_golite062009
transcription regulator activity	0.530058973650498	bayes_pls_golite062009
purine ribonucleotide binding	0.5127850474754	bayes_pls_golite062009
ribonucleotide binding	0.51230334374838	bayes_pls_golite062009
purine nucleotide binding	0.50688037036449	bayes_pls_golite062009
protein binding	0.502813311049029	bayes_pls_golite062009
nucleotide binding	0.49473184426584	bayes_pls_golite062009
DNA binding	0.460315660888175	bayes_pls_golite062009
branched-chain aliphatic amino acid transmembrane transporter activity	0.32754685224555	bayes_pls_golite062009
amine-transporting ATPase activity	0.128277449580549	bayes_pls_golite062009
amino acid-transporting ATPase activity	0.109938795198381	bayes_pls_golite062009
substrate-specific transporter activity	0.0838665746103899	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [391-459]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 RDEESQLKSA VDLLPVRLDL ADTLEKIEAA LIRRALVRAE FVQVKAAELL GISKSLLQYK  60
   61 LKKYGITGH

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	86.221849
Match:	1ojlA
Description:	Crystal structure of a sigma54-activator suggests the mechanism for the conformational switch necessary for sigma54 binding
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: