YRC Public Data Repository - Protein Structure Prediction

Protein:	PCD1
Organism:	Saccharomyces cerevisiae
Length:	340 amino acids
Reference:	Malmström L, et al. (2007) Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology. PLoS Biol 5(4): e76. doi:10.1371/journal.pbio.0050076

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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 PCD1.

Description	E-value	Query Range	Subject Range
PCD1 - Peroxisomal nudix pyrophosphatase with specificity for coenzyme A and CoA derivatives, may function ... gi\|190406180 - gi\|190406180\|gb\|EDV09447.1\| coenzyme A diphosphatase [Saccharomyces cerevisiae RM11-1a] PCD1_YEAST - Peroxisomal coenzyme A diphosphatase 1, peroxisomal OS=Saccharomyces cerevisiae (strain ATCC 204508 ... gi\|151941313 - gi\|151941313\|gb\|EDN59691.1\| coenzyme A diphosphatase [Saccharomyces cerevisiae YJM789]	0.0	[1..340]	[1..340]
gi\|25522240, gi\|... - pir\|\|AB2853 NTP pyrophosphohydrolase, MutT family [imported] - Agrobacterium tumefaciens (strain C58... gi\|17740724, gi\|... - gi\|17936134\|ref\|NP_532924.1\| NTP pyrophosphohydrolase, MutT family [Agrobacterium tumefaciens str. C...	6.0E-40	[5..225]	[15..209]
gi\|15075386 - gi\|15075386\|emb\|CAC46942.1\| Nudix hydrolase [Sinorhizobium meliloti 1021] gi\|15966116 - gi\|15966116\|ref\|NP_386469.1\| hypothetical protein SMc02701 [Sinorhizobium meliloti 1021]	2.0E-37	[5..225]	[12..209]
gi\|14023181, gi\|... - gi\|14023181\|dbj\|BAB49788.1\| mll2727 [Mesorhizobium loti MAFF303099], gi\|13472435\|ref\|NP_104002.1\| hy...	1.0E-36	[5..225]	[9..203]
gi\|229505112, gi... - gi\|229505112\|ref\|ZP_04394622.1\| hypothetical protein VCF_000318 [Vibrio cholerae BX 330286], gi\|2293... gi\|229345051, gi... - gi\|229518336\|ref\|ZP_04407780.1\| hypothetical protein VCC_002360 [Vibrio cholerae RC9], gi\|229345051\|... gi\|229608116, gi... - gi\|229608116\|ref\|YP_002878764.1\| hypothetical protein VCD_003034 [Vibrio cholerae MJ-1236], gi\|22937... gi\|227117769, gi... - gi\|75826692\|ref\|ZP_00756127.1\| COG0494: NTP pyrophosphohydrolases including oxidative damage repair ... gi\|75816918, gi\|... - gi\|75816918\|ref\|ZP_00747375.1\| COG0494: NTP pyrophosphohydrolases including oxidative damage repair ... gi\|9655791, gi\|1... - gi\|9655791\|gb\|AAF94461.1\| MutT/nudix family protein [Vibrio cholerae O1 biovar El Tor str. N16961], ... gi\|11355715 - pir\|\|A82216 MutT/nudix family protein VC1302 [imported] - Vibrio cholerae (strain N16961 serogroup O... gi\|121586565, gi... - gi\|121586565\|ref\|ZP_01676351.1\| MutT/nudix family protein [Vibrio cholerae 2740-80], gi\|121549244\|gb... gi\|153222934, gi... - gi\|153222934\|ref\|ZP_01953541.1\| MutT/nudix family protein [Vibrio cholerae MAK 757], gi\|124118521\|gb... gi\|126510169, gi... - gi\|153819266\|ref\|ZP_01971933.1\| MutT/nudix family protein [Vibrio cholerae NCTC 8457], gi\|126510169\|... gi\|75829226, gi\|... - gi\|75829226\|ref\|ZP_00758537.1\| COG0494: NTP pyrophosphohydrolases including oxidative damage repair ... gi\|126519570, gi... - gi\|229511218\|ref\|ZP_04400697.1\| hypothetical protein VCE_002625 [Vibrio cholerae B33], gi\|229351183\|... gi\|227009361, gi... - gi\|227081473\|ref\|YP_002810024.1\| MutT/nudix family protein [Vibrio cholerae M66-2], gi\|227009361\|gb\|...	6.0E-35	[9..231]	[1..204]
gi\|25526325 - pir\|\|AH3309 phosphohydrolase (mutT/nudiX family protein) BMEI0462 [imported] - Brucella melitensis (... gi\|17982372, gi\|... - gi\|17986745\|ref\|NP_539379.1\| phosphohydrolase (MUTT/NUDIX family protein) [Brucella melitensis 16M],...	2.0E-33	[13..225]	[20..206]
gi\|25399577 - pir\|\|F87299 MutT/nudix family protein [imported] - Caulobacter crescentus gi\|13421568, gi\|... - gi\|16124662\|ref\|NP_419226.1\| MutT/nudix family protein [Caulobacter crescentus CB15], gi\|13421568\|gb... gi\|220962523, gi... - gi\|221233351\|ref\|YP_002515787.1\| CoA pyrophosphatase [Caulobacter crescentus NA1000], gi\|220962523\|g...	1.0E-32	[13..222]	[22..204]
gi\|17427949 - gi\|17427949\|emb\|CAD14639.1\| putative nucleoside diphosphate hydrolase; protein [Ralstonia solanacear... gi\|17545656 - gi\|17545656\|ref\|NP_519058.1\| hypothetical protein RSc0937 [Ralstonia solanacearum GMI1000]	3.0E-32	[12..225]	[1..201]
gi\|42570219, gi\|... - gi\|79318810\|ref\|NP_001031104.1\| ATNUDX15 (ARABIDOPSIS THALIANA NUDIX HYDROLASE HOMOLOG 15); hydrolas...	2.0E-30	[21..241]	[83..261]
gi\|18859595, gi\|... - gi\|18859595\|ref\|NP_077757.1\| nudix (nucleoside diphosphate linked moiety X)-type motif 7 isoform 1 [...	5.0E-30	[9..218]	[1..189]

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Predicted Domain #1

Region A:
Residues: [1-244]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MILSQRRMLS SKQLIENLIR YKFHKTPYTR SSIWPFKRNS AVIILLFIGM KGELRVLLTK  60
   61 RSRTLRSFSG DVSFPGGKAD YFQETFESVA RREAEEEIGL PHDPEVLHKE FGMKLDNLVM 120
  121 DMPCYLSRTF LSVKPMVCFL YKDKLEKHED KYKVPLDIRK FFGKLNPGET SSLFSVPLND 180
  181 LVIHLLPEAD EDVKSYQAEY FERKEYKLNW GGIKWLIMHY HFHVANNNEM PWLQTIEDLS 240
  241 SSDE

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	14.0
Match:	1f3yA_
Description:	Diadenosine tetraphosphate hydrolase (Ap4A hydrolase)
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
catalytic activity	1.49075808737475	bayes_pls_golite062009
binding	0.219596749019403	bayes_pls_golite062009
hydrolase activity	0.214635043348567	bayes_pls_golite062009
nucleic acid binding	0.0715631252684563	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [245-340]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 DGVDGGIFRF RDLWGLTCKI LFDVSCIANG LMDEKLKGEL GHEDLIVGLH DYGNQMQPNG  60
   61 RSEWEIGMIN GDRNLKYSDV IPEYYMKHLL ECRSLW

[Run NCBI BLAST on this sequence.]

Detection Method:

deduced

Shown below are all of our de novo (Rosetta) predictions for this domain.
Click here to view only most confident match.

		MCM Score	GO Score	GO Term	SCOP Match	SCOP Description
View	Download	0.554	0.035	pyrophosphatase activity	a.77.1	DEATH domain
View	Download	0.541	0.035	pyrophosphatase activity	a.74.1	Cyclin-like
View	Download	0.905	0.035	pyrophosphatase activity	a.158.1	F-box domain
View	Download	0.706	0.035	pyrophosphatase activity	a.68.1	Wiscott-Aldrich syndrome protein, WASP, C-terminal domain
View	Download	0.905	0.035	pyrophosphatase activity	a.158.1	F-box domain
View	Download	0.706	0.035	pyrophosphatase activity	a.68.1	Wiscott-Aldrich syndrome protein, WASP, C-terminal domain
View	Download	0.554	0.035	pyrophosphatase activity	a.77.1	DEATH domain
View	Download	0.541	0.035	pyrophosphatase activity	a.74.1	Cyclin-like
View	Download	0.534	0.035	pyrophosphatase activity	a.74.1	Cyclin-like
View	Download	0.460	0.035	pyrophosphatase activity	a.121.1	Tetracyclin repressor-like, C-terminal domain
View	Download	0.455	0.035	pyrophosphatase activity	b.82.3	cAMP-binding domain-like
View	Download	0.427	0.035	pyrophosphatase activity	a.7.6	Ribosomal protein S20
View	Download	0.402	0.035	pyrophosphatase activity	a.100.1	6-phosphogluconate dehydrogenase C-terminal domain-like
View	Download	0.392	0.035	pyrophosphatase activity	a.24.4	Hemerythrin
View	Download	0.389	0.035	pyrophosphatase activity	a.69.3	1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain
View	Download	0.387	0.035	pyrophosphatase activity	d.54.1	Enolase N-terminal domain-like
View	Download	0.385	0.035	pyrophosphatase activity	a.112.1	Description not found.
View	Download	0.379	0.035	pyrophosphatase activity	a.61.1	Retroviral matrix proteins
View	Download	0.377	0.035	pyrophosphatase activity	a.4.5	"Winged helix" DNA-binding domain
View	Download	0.373	0.035	pyrophosphatase activity	a.3.1	Cytochrome c
View	Download	0.350	0.035	pyrophosphatase activity	a.74.1	Cyclin-like
View	Download	0.349	0.035	pyrophosphatase activity	a.138.1	Multiheme cytochromes
View	Download	0.349	0.035	pyrophosphatase activity	d.198.1	Type III secretory system chaperone
View	Download	0.344	0.035	pyrophosphatase activity	a.24.3	Cytochromes
View	Download	0.342	0.035	pyrophosphatase activity	a.100.1	6-phosphogluconate dehydrogenase C-terminal domain-like
View	Download	0.339	0.035	pyrophosphatase activity	a.36.1	Signal peptide-binding domain
View	Download	0.335	0.035	pyrophosphatase activity	d.74.1	Pterin-4a-carbinolamine dehydratase (PCD)/dimerization cofactor of HNF1 (DCoH)
View	Download	0.334	0.035	pyrophosphatase activity	a.4.5	"Winged helix" DNA-binding domain
View	Download	0.333	0.035	pyrophosphatase activity	d.52.7	Ribosome-binding factor A, RbfA
View	Download	0.327	0.035	pyrophosphatase activity	a.156.1	S13-like H2TH domain
View	Download	0.324	0.035	pyrophosphatase activity	d.2.1	Lysozyme-like
View	Download	0.319	0.035	pyrophosphatase activity	a.58.1	Chemotaxis receptor methyltransferase CheR, N-terminal domain
View	Download	0.312	0.035	pyrophosphatase activity	a.7.7	BAG domain
View	Download	0.310	0.035	pyrophosphatase activity	a.35.1	lambda repressor-like DNA-binding domains
View	Download	0.302	0.035	pyrophosphatase activity	b.40.4	Nucleic acid-binding proteins
View	Download	0.301	0.035	pyrophosphatase activity	a.77.1	DEATH domain
View	Download	0.300	0.035	pyrophosphatase activity	a.149.1	RNase III endonuclease catalytic domain
View	Download	0.291	0.035	pyrophosphatase activity	d.58.36	Sulfite reductase, domains 1 and 3
View	Download	0.283	0.035	pyrophosphatase activity	a.74.1	Cyclin-like
View	Download	0.278	0.035	pyrophosphatase activity	a.3.1	Cytochrome c
View	Download	0.260	0.035	pyrophosphatase activity	d.2.1	Lysozyme-like
View	Download	0.257	0.035	pyrophosphatase activity	a.5.4	Elongation factor TFIIS domain 2
View	Download	0.248	0.035	pyrophosphatase activity	a.69.1	C-terminal domain of alpha and beta subunits of F1 ATP synthase
View	Download	0.240	0.035	pyrophosphatase activity	a.6.1	Putative DNA-binding domain
View	Download	0.235	0.035	pyrophosphatase activity	c.37.1	P-loop containing nucleoside triphosphate hydrolases
View	Download	0.235	0.035	pyrophosphatase activity	a.19.1	Fertilization protein
View	Download	0.230	0.035	pyrophosphatase activity	a.24.13	Domain of the SRP/SRP receptor G-proteins
View	Download	0.228	0.035	pyrophosphatase activity	a.90.1	Transcription factor STAT-4 N-domain
View	Download	0.226	0.035	pyrophosphatase activity	a.60.2	RuvA domain 2-like
View	Download	0.224	0.035	pyrophosphatase activity	a.28.2	Colicin E immunity proteins
View	Download	0.219	0.035	pyrophosphatase activity	a.4.6	C-terminal effector domain of the bipartite response regulators
View	Download	0.211	0.035	pyrophosphatase activity	a.20.1	PGBD-like
View	Download	0.209	0.035	pyrophosphatase activity	a.177.1	Sigma2 domain of RNA polymerase sigma factors
View	Download	0.206	0.035	pyrophosphatase activity	a.133.1	Phospholipase A2, PLA2

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: