YRC Public Data Repository - Protein Structure Prediction

Protein:	CCA1
Organism:	Saccharomyces cerevisiae
Length:	546 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 CCA1.

Description	E-value	Query Range	Subject Range
gi\|151944885 - gi\|151944885\|gb\|EDN63144.1\| tRNA nucleotidyltransferase [Saccharomyces cerevisiae YJM789] CCA1_YEAST - CCA tRNA nucleotidyltransferase, mitochondrial OS=Saccharomyces cerevisiae (strain ATCC 204508 / S28... CCA1 - ATP (CTP):tRNA-specific tRNA nucleotidyltransferase; different forms targeted to the nucleus, cytoso... gi\|207345792 - gi\|207345792\|gb\|EDZ72498.1\| YER168Cp-like protein [Saccharomyces cerevisiae AWRI1631] gi\|190405724 - gi\|190405724\|gb\|EDV08991.1\| tRNA nucleotidyltransferase [Saccharomyces cerevisiae RM11-1a]	0.0	[1..546]	[1..546]
gi\|8698608 - gi\|8698608\|gb\|AAF78448.1\|AF098803_1 tRNA nucleotidyltransferase [Candida glabrata]	0.0	[22..546]	[7..530]
gi\|9836828 - gi\|9836828\|gb\|AAG00316.1\|AF207744_1 tRNA nucleotidyltransferase [Kluyveromyces lactis]	0.0	[23..542]	[2..486]
gi\|23198306, gi\|... - gi\|23198306\|gb\|AAN15680.1\| tRNA adenylyltransferase-like protein [Arabidopsis thaliana], gi\|15219925...	0.0	[4..544]	[59..600]
SPCC645.10 - ATP(CTP) tRNA nucleotidyltransferase CCA2_SCHPO - Putative CCA tRNA nucleotidyltransferase 2 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN...	0.0	[28..542]	[3..483]
gi\|15829401, gi\|... - gi\|15829401\|ref\|NP_308174.1\| poly(A) polymerase I [Escherichia coli O157:H7 str. Sakai], gi\|13359603... gi\|227884943, gi... - gi\|227884943\|ref\|ZP_04002748.1\| polynucleotide adenylyltransferase [Escherichia coli 83972], gi\|2278... gi\|1786336, gi\|1... - gb\|AAC73254.1\| poly(A) polymerase I [Escherichia coli K12], gi\|16128136\|ref\|NP_414685.1\| poly(A) po... gi\|117622430, gi... - gi\|117622430\|ref\|YP_851343.1\| poly(A) polymerase I [Escherichia coli APEC O1], gi\|115511554\|gb\|ABI99... gi\|209746094, gi... - pir\|\|G64737 polynucleotide adenylyltransferase (EC 2.7.7.19) I pcnB [validated] - Escherichia coli (... gi\|188014580, gi... - gi\|188014580\|gb\|EDU52702.1\| poly(A) polymerase [Escherichia coli O157:H7 str. EC4113], gi\|168751363\|... gi\|15829401, gi\|... - gi\|15829401\|ref\|NP_308174.1\| poly(A) polymerase I [Escherichia coli O157:H7], gi\|13359603\|dbj\|BAB335... gi\|168764713, gi... - gi\|189365327\|gb\|EDU83743.1\| poly(A) polymerase [Escherichia coli O157:H7 str. EC4501], gi\|168764713\|... gi\|168755755, gi... - gi\|189356985\|gb\|EDU75404.1\| poly(A) polymerase [Escherichia coli O157:H7 str. EC4401], gi\|168755755\|... gi\|189000464, gi... - gi\|189000464\|gb\|EDU69450.1\| poly(A) polymerase [Escherichia coli O157:H7 str. EC4076], gi\|168782034\|... gi\|189360734, gi... - gi\|189360734\|gb\|EDU79153.1\| poly(A) polymerase [Escherichia coli O157:H7 str. EC4486], gi\|168770386\|... gi\|191166336, gi... - gi\|75230494\|ref\|ZP_00716975.1\| COG0617: tRNA nucleotidyltransferase/poly(A) polymerase [Escherichia ... gi\|190906921, gi... - gi\|75240266\|ref\|ZP_00724213.1\| COG0617: tRNA nucleotidyltransferase/poly(A) polymerase [Escherichia ... gi\|187428215, gi... - gi\|75176511\|ref\|ZP_00696648.1\| COG0617: tRNA nucleotidyltransferase/poly(A) polymerase [Shigella boy... gi\|194413654, gi... - gi\|75210468\|ref\|ZP_00710619.1\| COG0617: tRNA nucleotidyltransferase/poly(A) polymerase [Escherichia ... gi\|74310764, gi\|... - gi\|74310764\|ref\|YP_309183.1\| poly(A) polymerase I [Shigella sonnei Ss046], gi\|73854241\|gb\|AAZ86948.1... gi\|75258866, gi\|... - gi\|75258866\|ref\|ZP_00730256.1\| COG0617: tRNA nucleotidyltransferase/poly(A) polymerase [Escherichia ... gi\|188493474, gi... - gi\|75512019\|ref\|ZP_00734614.1\| COG0617: tRNA nucleotidyltransferase/poly(A) polymerase [Escherichia ... gi\|217322438, gi... - gi\|217326217\|ref\|ZP_03442301.1\| poly(A) polymerase [Escherichia coli O157:H7 str. TW14588], gi\|21732... gi\|215263375, gi... - gi\|215485303\|ref\|YP_002327734.1\| poly(A) polymerase I [Escherichia coli O127:H6 str. E2348/69], gi\|2... gi\|194433394, gi... - gi\|83569724\|ref\|ZP_00921174.1\| COG0617: tRNA nucleotidyltransferase/poly(A) polymerase [Shigella dys... gi\|168801481, gi... - gi\|189376394\|gb\|EDU94810.1\| poly(A) polymerase [Escherichia coli O157:H7 str. EC508], gi\|168801481\|r... gi\|168789251, gi... - gi\|189371104\|gb\|EDU89520.1\| poly(A) polymerase [Escherichia coli O157:H7 str. EC869], gi\|168789251\|r... gi\|195938175 - gi\|195938175\|ref\|ZP_03083557.1\| poly(A) polymerase I [Escherichia coli O157:H7 str. EC4024] gi\|170680324, gi... - gi\|170680324\|ref\|YP_001742271.1\| poly(A) polymerase [Escherichia coli SMS-3-5], gi\|170518042\|gb\|ACB1... gi\|208735864, gi... - gi\|208814587\|ref\|ZP_03255916.1\| poly(A) polymerase [Escherichia coli O157:H7 str. EC4045], gi\|208735... gi\|208807142, gi... - gi\|208807142\|ref\|ZP_03249479.1\| poly(A) polymerase [Escherichia coli O157:H7 str. EC4206], gi\|208726... gi\|209398537, gi... - gi\|209398537\|ref\|YP_002268752.1\| poly(A) polymerase [Escherichia coli O157:H7 str. EC4115], gi\|20915... gi\|208741461, gi... - gi\|208821338\|ref\|ZP_03261658.1\| poly(A) polymerase [Escherichia coli O157:H7 str. EC4042], gi\|208741...	7.0E-98	[27..443]	[15..412]
gi\|25497051 - gi\|25497051\|pir\|\|C85498 poly(A) polymerase I [imported] - Escherichia coli (strain O157:H7, substrai... gi\|15799827, gi\|... - gi\|15799827\|ref\|NP_285839.1\| poly(A) polymerase I [Escherichia coli O157:H7 EDL933], gi\|12512861\|gb\|...	2.0E-97	[27..443]	[15..412]
gi\|7507776 - gi\|7507776\|pir\|\|T16867 probable cytochrome P450 T13C5.1 [similarity] - Caenorhabditis elegans	3.0E-97	[25..529]	[62..552]
gi\|16763574, gi\|... - gi\|16763574\|ref\|NP_459189.1\| poly(A) polymerase I [Salmonella typhimurium LT2], gi\|16418686\|gb\|AAL19... lcl\|NC_016856.1_... - [gene=pcnB] [protein=poly(A) polymerase I] [protein_id=YP_005235849.1] [location=complement(214578..... PCNB_SALTY - (Q8ZRQ8) Poly(A) polymerase (EC 2.7.7.19) (PAP) (Plasmid copy number protein)	4.0E-97	[27..445]	[33..432]
gi\|62391931, gi\|... - gi\|62391931\|ref\|YP_227333.1\| polyA polymerase [Corynebacterium glutamicum ATCC 13032], gi\|41223078\|e...	7.0E-97	[10..540]	[1..486]

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Predicted Domain #1

Region A:
Residues: [1-123]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MLRSTISLLM NSAAQKTMTN SNFVLNAPKI TLTKVEQNIC NLLNDYTDLY NQKYHNKPEP  60
   61 LTLRITGGWV RDKLLGQGSH DLDIAINVMS GEQFATGLNE YLQQHYAKYG AKPHNIHKID 120
  121 KNP

[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	SCOP Match	SCOP Description
View	Download	0.546	c.95.1	Thiolase-like
View	Download	0.636	d.80.1	Tautomerase/MIF
View	Download	0.616	d.52.3	Prokaryotic type KH domain (KH-domain type II)
View	Download	0.651	d.58.41	SEA domain
View	Download	0.597	d.50.2	Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain
View	Download	0.523	c.95.1	Thiolase-like
View	Download	0.520	a.45.1	Glutathione S-transferase (GST), C-terminal domain
View	Download	0.493	d.58.5	GlnB-like
View	Download	0.477	c.2.1	NAD(P)-binding Rossmann-fold domains
View	Download	0.472	c.17.1	Caspase-like
View	Download	0.470	d.204.1	Ribosome binding protein Y (YfiA homologue)
View	Download	0.470	c.47.1	Thioredoxin-like
View	Download	0.465	c.58.1	Aminoacid dehydrogenase-like, N-terminal domain
View	Download	0.442	a.24.16	Nucleotidyltransferase substrate binding subunit/domain
View	Download	0.436	c.47.1	Thioredoxin-like
View	Download	0.425	c.23.5	Flavoproteins
View	Download	0.422	f.36.1	Neurotransmitter-gated ion-channel pransmembrane pore
View	Download	0.413	a.24.17	Group V grass pollen allergen
View	Download	0.405	c.26.1	Nucleotidylyl transferase
View	Download	0.403	d.52.4	YhbC-like, N-terminal domain
View	Download	0.392	a.1.1	Globin-like
View	Download	0.391	d.58.49	YajQ-like
View	Download	0.383	a.25.1	Ferritin-like
View	Download	0.379	a.24.11	Bacterial GAP domain
View	Download	0.379	d.58.19	Bacterial exopeptidase dimerisation domain
View	Download	0.375	a.66.1	Transducin (alpha subunit), insertion domain
View	Download	0.368	a.27.1	Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
View	Download	0.345	a.24.3	Cytochromes
View	Download	0.343	a.24.9	alpha-catenin/vinculin
View	Download	0.339	c.80.1	SIS domain
View	Download	0.337	a.24.4	Hemerythrin
View	Download	0.336	d.227.1	OsmC-like
View	Download	0.331	c.30.1	PreATP-grasp domain
View	Download	0.330	d.110.4	SNARE-like
View	Download	0.328	c.49.1	Pyruvate kinase, C-terminal domain
View	Download	0.325	a.24.15	FAD-dependent thiol oxidase
View	Download	0.322	d.38.1	Thioesterase/thiol ester dehydrase-isomerase
View	Download	0.319	d.58.12	eEF-1beta-like
View	Download	0.308	d.16.1	FAD-linked reductases, C-terminal domain
View	Download	0.307	c.23.4	Succinyl-CoA synthetase domains
View	Download	0.303	d.58.47	Hypothetical protein VC0424
View	Download	0.300	c.50.1	Macro domain-like
View	Download	0.299	a.7.6	Ribosomal protein S20
View	Download	0.289	d.58.4	Dimeric alpha+beta barrel
View	Download	0.287	d.108.1	Acyl-CoA N-acyltransferases (Nat)
View	Download	0.282	c.30.1	PreATP-grasp domain
View	Download	0.280	d.122.1	ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
View	Download	0.278	d.110.4	SNARE-like
View	Download	0.278	d.52.6	BolA-like
View	Download	0.277	d.79.5	2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF
View	Download	0.269	c.25.1	Ferredoxin reductase-like, C-terminal NADP-linked domain
View	Download	0.266	b.60.1	Lipocalins
View	Download	0.264	c.32.1	Tubulin/Dihydroxyacetone kinase nucleotide-binding domain
View	Download	0.264	c.26.2	Adenine nucleotide alpha hydrolases-like
View	Download	0.259	d.92.2	beta-N-acetylhexosaminidase-like domain
View	Download	0.259	a.83.1	Guanido kinase N-terminal domain
View	Download	0.258	a.84.1	Scaffolding protein gpD of bacteriophage procapsid
View	Download	0.257	d.58.43	Mechanosensitive channel protein MscS (YggB), C-terminal domain
View	Download	0.256	d.109.1	Actin depolymerizing proteins
View	Download	0.254	d.129.1	TATA-box binding protein-like
View	Download	0.252	c.23.6	Cobalamin (vitamin B12)-binding domain
View	Download	0.249	d.58.18	Regulatory domain in the aminoacid metabolism
View	Download	0.249	c.47.1	Thioredoxin-like
View	Download	0.246	d.129.2	Phosphoglucomutase, C-terminal domain
View	Download	0.244	d.52.7	Ribosome-binding factor A, RbfA
View	Download	0.240	d.58.10	Acylphosphatase-like
View	Download	0.240	c.16.1	Lumazine synthase
View	Download	0.238	a.26.1	4-helical cytokines
View	Download	0.237	b.55.1	PH domain-like
View	Download	0.236	d.56.1	GroEL-intermediate domain like
View	Download	0.235	a.74.1	Cyclin-like
View	Download	0.235	c.2.1	NAD(P)-binding Rossmann-fold domains
View	Download	0.227	c.78.1	Aspartate/ornithine carbamoyltransferase
View	Download	0.225	a.74.1	Cyclin-like
View	Download	0.222	c.26.2	Adenine nucleotide alpha hydrolases-like
View	Download	0.219	c.9.1	Barstar (barnase inhibitor)
View	Download	0.218	a.118.9	ENTH/VHS domain
View	Download	0.214	c.37.1	P-loop containing nucleoside triphosphate hydrolases
View	Download	0.214	a.22.1	Histone-fold
View	Download	0.211	a.63.1	Apolipophorin-III
View	Download	0.205	d.58.44	Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains
View	Download	0.204	d.58.7	RNA-binding domain, RBD
View	Download	0.204	c.56.1	HybD-like

Predicted functions:

Term	Confidence	Notes
transferase activity, transferring phosphorus-containing groups	2.63905617158862	bayes_pls_golite062009
transferase activity	2.28535908015265	bayes_pls_golite062009
nucleotidyltransferase activity	2.17198033243932	bayes_pls_golite062009
tRNA binding	1.96218336722441	bayes_pls_golite062009
RNA binding	1.77578561123536	bayes_pls_golite062009
nucleic acid binding	1.43322212500405	bayes_pls_golite062009
polynucleotide adenylyltransferase activity	1.24026612395993	bayes_pls_golite062009
tRNA nucleotidyltransferase activity	1.05100814747368	bayes_pls_golite062009
DNA binding	0.920001549206154	bayes_pls_golite062009
binding	0.888087430062829	bayes_pls_golite062009
catalytic activity	0.75232920999699	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [124-350]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 EKSKHLETAT TKLFGVEVDF VNLRSEKYTE LSRIPKVCFG TPEEDALRRD ATLNALFYNI  60
   61 HKGEVEDFTK RGLQDLKDGV LRTPLPAKQT FLDDPLRVLR LIRFASRFNF TIDPEVMAEM 120
  121 GDPQINVAFN SKISRERVGV EMEKILVGPT PLLALQLIQR AHLENVIFFW HNDSSVVKFN 180
  181 EENCQDMDKI NHVYNDNILN SHLKSFIELY PMFLEKLPIL REKIGRS

[Run NCBI BLAST on this sequence.]

Detection Method:	Pfam
Confidence:	77.086186
Match:	PF01743
Description:	Poly A polymerase family

Shown below are all of our structure predictions for this domain.
Click here to view only most confident match.

Found no structure predictions for this domain.

Predicted Domain #3

Region A:
Residues: [351-546]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 PGFQQNFILS AILSPMANLQ IIGNPKKKIN NLVSVTESIV KEGLKLSKND AAVIAKTVDS  60
   61 ICSYEEILAK FADRSQLKKS EIGIFLRNFN GEWETAHFAS LSDAFLKIPK LETKKIELLF 120
  121 QNYNEFYSYI FDNNLNNCHE LKPIVDGKQM AKLLQMKPGP WLGKINNEAI RWQFDNPTGT 180
  181 DQELITHLKA ILPKYL

[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.

Found no structure predictions for this domain.

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: