YRC Public Data Repository - Protein Structure Prediction

Protein:	vps4
Organism:	Schizosaccharomyces pombe
Length:	432 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 vps4.

Description	E-value	Query Range	Subject Range
gi\|58380313, gi\|... - gi\|58380313\|ref\|XP_310453.2\| AGAP000625-PA [Anopheles gambiae str. PEST], gi\|55243167\|gb\|EAA06410.2\|... AGAP000625-PA - vacuolar protein-sorting-associated protein 4\|protein_coding\|X:11264037:11267188:1\|gene:AGAP000625	273.0	[0..1]	[432..1]
gi\|108881599, gi... - gi\|157133092\|ref\|XP_001656171.1\| skd/vacuolar sorting [Aedes aegypti], gi\|157133090\|ref\|XP_001656170...	271.0	[0..1]	[432..1]
gi\|1054845 - gi\|1054845\|emb\|CAA63364.1\| END13 [Saccharomyces cerevisiae]	270.0	[0..1]	[432..1]
gi\|49091474, gi\|... - gi\|67525207\|ref\|XP_660665.1\| hypothetical protein AN3061.2 [Aspergillus nidulans FGSC A4], ref\|XP_40...	270.0	[0..1]	[432..1]
gi\|46442656, gi\|... - gi\|68470534\|ref\|XP_720771.1\| potential vacuolar sorting ATPase [Candida albicans SC5314], gi\|4644265... gi\|238882705 - gi\|238882705\|gb\|EEQ46343.1\| vacuolar protein sorting-associated protein VPS4 [Candida albicans WO-1] orf19.11814 - VPS4 CGDID:CAL0000992 Assembly 19, Contig19-20202 (215915, 217234) CDS, translated using codon table...	269.0	[0..5]	[432..6]
gi\|83766090 - gi\|83766090\|dbj\|BAE56233.1\| unnamed protein product [Aspergillus oryzae] gi\|169767528 - gi\|169767528\|ref\|XP_001818235.1\| hypothetical protein [Aspergillus oryzae RIB40]	268.0	[0..1]	[432..1]
gi\|148222387, gi... - gi\|27503354\|gb\|AAH42286.1\| Vps4b-prov protein [Xenopus laevis], gi\|148222387\|ref\|NP_001080109.1\| vac...	267.0	[0..2]	[432..3]
gi\|49526839, gi\|... - gi\|50290195\|ref\|XP_447529.1\| hypothetical protein CAGL0I06402g [Candida glabrata CBS138], gi\|4952683... gi\|49526839 - gi\|49526839\|emb\|CAG60466.1\| unnamed protein product [Candida glabrata]	267.0	[0..1]	[432..1]

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Predicted Domain #1

Region A:
Residues: [1-368]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSNPDCLSKA ISLVKTAIDN DNAEQYPDAY KYYQSALDYF MMALKYEKNE KSKEIIRSKV  60
   61 IEYLDRAEKL KVYLQEKNNQ ISSKSRVSNG NVEGSNSPTA NEALDSDAKK LRSALTSAIL 120
  121 VEKPNVRWDD IAGLENAKEA LKETVLLPIK LPQLFSHGRK PWSGILLYGP PGTGKSYLAK 180
  181 AVATEAGSTF FSISSSDLVS KWMGESERLV RQLFEMAREQ KPSIIFIDEI DSLCGSRSEG 240
  241 ESESSRRIKT EFLVQMNGVG KDESGVLVLG ATNIPWTLDS AIRRRFEKRI YIPLPNAHAR 300
  301 ARMFELNVGK IPSELTSQDF KELAKMTDGY SGSDISIVVR DAIMEPVRRI HTATHFKEVY 360
  361 DNKSNRTL

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	25.0
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
hydrolase activity	4.71605970197038	bayes_pls_golite062009
hydrogen ion transporting ATP synthase activity, rotational mechanism	4.45975815173802	bayes_pls_golite062009
peptidase activity	3.6994352506738	bayes_pls_golite062009
peptidase activity, acting on L-amino acid peptides	3.52737232558306	bayes_pls_golite062009
endopeptidase activity	3.48761031707503	bayes_pls_golite062009
substrate-specific transmembrane transporter activity	3.4837867129694	bayes_pls_golite062009
ion transmembrane transporter activity	3.35436118751376	bayes_pls_golite062009
transporter activity	3.10463051760206	bayes_pls_golite062009
cation transmembrane transporter activity	3.08390071341252	bayes_pls_golite062009
transmembrane transporter activity	2.95886887664984	bayes_pls_golite062009
nucleoside-triphosphatase activity	2.95079405147356	bayes_pls_golite062009
monovalent inorganic cation transmembrane transporter activity	2.9271291809464	bayes_pls_golite062009
pyrophosphatase activity	2.87427509025394	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides	2.85499564954033	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides	2.85178667290149	bayes_pls_golite062009
binding	2.64537357529343	bayes_pls_golite062009
hydrogen ion transmembrane transporter activity	2.63419811368692	bayes_pls_golite062009
primary active transmembrane transporter activity	2.61775212528604	bayes_pls_golite062009
P-P-bond-hydrolysis-driven transmembrane transporter activity	2.61467977505707	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances	2.57552435627908	bayes_pls_golite062009
ATPase activity, coupled to transmembrane movement of substances	2.57107347424517	bayes_pls_golite062009
ATPase activity, coupled to movement of substances	2.57054427875021	bayes_pls_golite062009
active transmembrane transporter activity	2.50494515048649	bayes_pls_golite062009
ATPase activity, coupled	2.43862163407966	bayes_pls_golite062009
inorganic cation transmembrane transporter activity	2.40292717311506	bayes_pls_golite062009
ATPase activity	2.39535714892224	bayes_pls_golite062009
motor activity	2.32425703346903	bayes_pls_golite062009
metal ion transmembrane transporter activity	2.26365379756656	bayes_pls_golite062009
microtubule motor activity	2.26003723459523	bayes_pls_golite062009
nucleic acid binding	2.11222585187695	bayes_pls_golite062009
alpha-tubulin binding	2.02293807820805	bayes_pls_golite062009
substrate-specific transporter activity	1.91091452720653	bayes_pls_golite062009
voltage-gated cation channel activity	1.8621490001046	bayes_pls_golite062009
potassium channel activity	1.79629698691358	bayes_pls_golite062009
DNA binding	1.7904783386531	bayes_pls_golite062009
voltage-gated ion channel activity	1.74551765217439	bayes_pls_golite062009
voltage-gated channel activity	1.74536227612384	bayes_pls_golite062009
transcription regulator activity	1.68903321260301	bayes_pls_golite062009
syntaxin-13 binding	1.51788105466838	bayes_pls_golite062009
apolipoprotein A-I binding	1.51788105466838	bayes_pls_golite062009
apolipoprotein receptor activity	1.51788105466838	bayes_pls_golite062009
apolipoprotein A-I receptor activity	1.51788105466838	bayes_pls_golite062009
cholesterol transporter activity	1.26047467122235	bayes_pls_golite062009
ATPase activity, coupled to transmembrane movement of ions	1.23799860254751	bayes_pls_golite062009
lipid transporter activity	1.10957173853622	bayes_pls_golite062009
sterol transporter activity	1.00610936344232	bayes_pls_golite062009
catalytic activity	1.00104173493322	bayes_pls_golite062009
purine nucleotide binding	0.929901285538132	bayes_pls_golite062009
nucleotide binding	0.922442819194247	bayes_pls_golite062009
purine ribonucleotide binding	0.920987930180051	bayes_pls_golite062009
ribonucleotide binding	0.920926158369519	bayes_pls_golite062009
structural constituent of ribosome	0.860102064846772	bayes_pls_golite062009
di-, tri-valent inorganic cation transmembrane transporter activity	0.767424210804186	bayes_pls_golite062009
glutathione S-conjugate-exporting ATPase activity	0.719430645205088	bayes_pls_golite062009
inorganic anion transmembrane transporter activity	0.69784475011795	bayes_pls_golite062009
beta-tubulin binding	0.654735466720932	bayes_pls_golite062009
cation channel activity	0.644849120170412	bayes_pls_golite062009
guanyl nucleotide binding	0.640772201693186	bayes_pls_golite062009
guanyl ribonucleotide binding	0.63468044350616	bayes_pls_golite062009
GTP binding	0.621689261700018	bayes_pls_golite062009
transcription factor activity	0.603758349693077	bayes_pls_golite062009
cytoskeletal protein binding	0.568484017802328	bayes_pls_golite062009
anion transmembrane-transporting ATPase activity	0.563503770238611	bayes_pls_golite062009
protein transporter activity	0.498432226280822	bayes_pls_golite062009
microtubule-severing ATPase activity	0.491769258942331	bayes_pls_golite062009
protein transmembrane transporter activity	0.46552249844591	bayes_pls_golite062009
GTPase activity	0.437665353870877	bayes_pls_golite062009
anion transmembrane transporter activity	0.43332053110728	bayes_pls_golite062009
ATP binding	0.41092997612902	bayes_pls_golite062009
adenyl ribonucleotide binding	0.385813421701492	bayes_pls_golite062009
adenyl nucleotide binding	0.377870145186619	bayes_pls_golite062009
tubulin binding	0.326239364039846	bayes_pls_golite062009
signal recognition particle binding	0.29390189699022	bayes_pls_golite062009
translation regulator activity	0.29096092258568	bayes_pls_golite062009
translation factor activity, nucleic acid binding	0.274994961137851	bayes_pls_golite062009
transition metal ion transmembrane transporter activity	0.248918847596573	bayes_pls_golite062009
microtubule binding	0.225323885896927	bayes_pls_golite062009
proton-transporting ATPase activity, rotational mechanism	0.219473333671469	bayes_pls_golite062009
protein binding	0.170837278876362	bayes_pls_golite062009
ion channel activity	0.154779598791225	bayes_pls_golite062009
channel activity	0.134817721656507	bayes_pls_golite062009
passive transmembrane transporter activity	0.134817721656507	bayes_pls_golite062009
substrate-specific channel activity	0.126911677161968	bayes_pls_golite062009
nucleobase, nucleoside, nucleotide kinase activity	0.12351419478929	bayes_pls_golite062009
structural molecule activity	0.11239762372728	bayes_pls_golite062009
helicase activity	0.0775311459068899	bayes_pls_golite062009
cation-transporting ATPase activity	0.0536898657672154	bayes_pls_golite062009
actin binding	0.0206144204131673	bayes_pls_golite062009
macromolecule transmembrane transporter activity	0.00571427458217011	bayes_pls_golite062009
P-P-bond-hydrolysis-driven protein transmembrane transporter activity	0.00571427458217011	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [369-432]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 VTPCSPGDPD AFESSWLEVN PEDIMEPKLT VRDFYSAVRK VKPTLNAGDI EKHTQFTKDF  60
   61 GAEG

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	62.0
Match:	2qp9X
Description:	No description for 2qp9X was found.

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: