D-I-TASSER A6NCI4

D-I-TASSER results for A6NCI4

[Click result.zip to download all results on this page]

Summary of the Protein

Uniprot ID: A6NCI4
Protein Name: von Willebrand factor A domain-containing protein 3A
Gene Name: VWA3A

Input Sequence in FASTA format

>A6NCI4 (1184 residues)
MKKYRKISIGCFAMATQTSHVFHGQENMFLENHCIRRNTGRDSKKPLKQKNMNGLGQNSD
NGLLVTHVNQTQDLLRLQGSETQSSDWEDSEDWLSAHSLKCQKLTLADLISQGTEVLEEG
TNVVQKICFSTQIIRHFESKLSDTIEVYQERIQWLTENSKKAFGLIKGARVSILIDVSAI
SSGPQKEEFQKDLMSLIDEQLSHKEKLFVLSFGTNAGSLWPDPMEVSASTLQELKLWVKT
LQPDGGSNLLQALKKIFTLKGLDSLVAIMRSCPDQPSEILSDYIQQSTMGRDLIIHFITY
RCDDQMPPAVLKNLAEAVRGYYHCYSPKMEHYTSRDMDELLAEIQKAQSLLSHVQALQHS
SPCEALTCTMEEISTEITNGPLISLLPKPPKHDAPLTIEFPNLDKTSAEWLKVNGLKAKK
LSLYQVLAPNAFSPVEEFVPILQKTVSSTIHEKAMIQFEWHDGTVKNIHVDPPFLYKYQQ
QLSRAMRMYERRIEWLSLASRRIWGTVCEKRVVVLLDISATNSMYIIHIQHSLRLLLEEQ
LSNKDCFNLIAFGSTIESWRPEMVPVSHNNLQSAWRWALNLRCRGSRNVLSALRKAVEVD
FKDKDKHQSQGIYLFTGGIPDQDMPTLSAYMAEACGGCDLQLNVCLFYVGEPKMDTTPPA
RYASHTDTAAAYKEVTRAAGGRFHWFGDTGIYESDDINSIMSEMEKALNYSQKCAFLMAS
LKNHSGKVLGSSALPKEKPKTLQLRSQPKKLCPPRPTVPLGARMSIKDDPDREKSPPLKS
LKWRPLSSRVGISPAAAQPTKEGMMELRRKTKSREAETSLLLFYTEKGNDVGSVYKKYPQ
GRGLRRTSSSIDLPRKDTVCSSQEWVAKYGLKKLKLEISRCMGPNCTHQKSGQRSASAKH
CSIFPSVEIHGVVRHIQWTPREMEVYIRHLEKVLRRYVQRLQWLLSGSRRLFGTVLESKV
CILLDTSGSMGPYLQQVKTELVLLIWEQLRKCCDSFNLLSFAESFQSWQDTLVETTDAAC
HEAMQWVTHLQAQGSTSILQALLKAFSFHDLEGLYLLTDGKPDTSCSLVLNEVQKLREKR
DVKVHTISLNCSDRAAVEFLRKLASFTGGRYHCPVGEDTLSKIHSLLTKGFINEKDPTLP
PFEGDDLRILAQEITKARSFLWQAQSFRSQLQKKNDAEPKVTLS

Predicted Contact and Distance Map Used in D-I-TASSER simulation

Contact Map

Distance Map

D-I-TASSER simulation is guided by the consensus contact map (left figure) and distance map (right figure) derived based on confidence scores of AttentionPotential. In the contact, distance map and hydrogen bond networks, the axes mark the residue index along the sequence. For the contact map, each dot represents a residue pair with predicted contact, while for the distance map and hydrogen bond network, a color scale represents a distance of 1-20+ angstroms or a angle of 0-180 degree.

Information of Domain

No. of Domain	Domain	Domain Boundary	Length of Domain	Models of Domain	Sequence
1	A6NCI4-D1	1-1184	1184		MKKYRKISIGCFAMATQTSHVFHGQENMFLENHCIRRNTGRDSKKPLKQKNMNGLGQNSDNGLLVTHVNQTQDLLRLQGSETQSSDWEDSEDWLSAHSLKCQKLTLADLISQGTEVLEEGTNVVQKICFSTQIIRHFESKLSDTIEVYQERIQWLTENSKKAFGLIKGARVSILIDVSAISSGPQKEEFQKDLMSLIDEQLSHKEKLFVLSFGTNAGSLWPDPMEVSASTLQELKLWVKTLQPDGGSNLLQALKKIFTLKGLDSLVAIMRSCPDQPSEILSDYIQQSTMGRDLIIHFITYRCDDQMPPAVLKNLAEAVRGYYHCYSPKMEHYTSRDMDELLAEIQKAQSLLSHVQALQHSSPCEALTCTMEEISTEITNGPLISLLPKPPKHDAPLTIEFPNLDKTSAEWLKVNGLKAKKLSLYQVLAPNAFSPVEEFVPILQKTVSSTIHEKAMIQFEWHDGTVKNIHVDPPFLYKYQQQLSRAMRMYERRIEWLSLASRRIWGTVCEKRVVVLLDISATNSMYIIHIQHSLRLLLEEQLSNKDCFNLIAFGSTIESWRPEMVPVSHNNLQSAWRWALNLRCRGSRNVLSALRKAVEVDFKDKDKHQSQGIYLFTGGIPDQDMPTLSAYMAEACGGCDLQLNVCLFYVGEPKMDTTPPARYASHTDTAAAYKEVTRAAGGRFHWFGDTGIYESDDINSIMSEMEKALNYSQKCAFLMASLKNHSGKVLGSSALPKEKPKTLQLRSQPKKLCPPRPTVPLGARMSIKDDPDREKSPPLKSLKWRPLSSRVGISPAAAQPTKEGMMELRRKTKSREAETSLLLFYTEKGNDVGSVYKKYPQGRGLRRTSSSIDLPRKDTVCSSQEWVAKYGLKKLKLEISRCMGPNCTHQKSGQRSASAKHCSIFPSVEIHGVVRHIQWTPREMEVYIRHLEKVLRRYVQRLQWLLSGSRRLFGTVLESKVCILLDTSGSMGPYLQQVKTELVLLIWEQLRKCCDSFNLLSFAESFQSWQDTLVETTDAACHEAMQWVTHLQAQGSTSILQALLKAFSFHDLEGLYLLTDGKPDTSCSLVLNEVQKLREKRDVKVHTISLNCSDRAAVEFLRKLASFTGGRYHCPVGEDTLSKIHSLLTKGFINEKDPTLPPFEGDDLRILAQEITKARSFLWQAQSFRSQLQKKNDAEPKVTLS

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.5916

(a)

D-I-TASSER simulations generate a large ensemble of structural conformations, i.e. decoys. These decoys are clustered by SPICKER based on pairwise structure similarity to report up to five final models from the five largest clusters. Models are ranked in descending order of cluster size. If the simulations converge well, it is possible to have less than 5 models generated, which is usually an indication of good model quality.

(b)

The model confidence is quantitatified by estimated TM-score (eTM-score), calculated based on significance of threading template alignments, contact map satisfaction rate, mean absolute error between distance of model and distance of AttentionPotential, and convergence of D-I-TASSER simulations. eTM-score is typically in the range of [0, 1], with higher eTM-score signifies higher model confidence.

Proteins with similar structure

Top 10 structural analogs in PDB (as identified by TM-align)

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Alignment
1	6z2wE	0.31	9.44	0.043	0.483	model1_6z2wE.pdb.gz
2	5x6oC	0.30	9.72	0.039	0.484	model1_5x6oC.pdb.gz
3	6reyc	0.29	9.02	0.034	0.439	model1_6reyc.pdb.gz
4	6jxaA	0.29	9.65	0.045	0.454	model1_6jxaA.pdb.gz
5	6emkA	0.29	8.61	0.036	0.420	model1_6emkA.pdb.gz
6	4bedA	0.28	9.35	0.030	0.438	model1_4bedA.pdb.gz
7	5fvmA	0.28	8.56	0.042	0.406	model1_5fvmA.pdb.gz
8	6ez8A	0.28	10.19	0.043	0.457	model1_6ez8A.pdb.gz
9	4i43B	0.28	9.94	0.041	0.451	model1_4i43B.pdb.gz
10	6bcuA	0.28	9.03	0.029	0.413	model1_6bcuA.pdb.gz

(a)	Query structure is shown in cartoon, while the structural analog is displayed using backbone trace.
(b)	Ranking of proteins is based on TM-score of the structural alignment between the query structure and known structures in the PDB library.
(c)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(e)	Cov. represents the coverage of the alignment by TM-align and is equal to the number of structurally aligned residues divided by length of the query protein.

Predicted Gene Ontology (GO) Terms

Molecular Function (MF)

GO term	Cscore^GO	Name
GO:0097367	0.75	carbohydrate derivative binding
GO:0035639	0.74	purine ribonucleoside triphosphate binding
GO:0032559	0.74	adenyl ribonucleotide binding
GO:0032550	0.74	purine ribonucleoside binding
GO:0098772	0.66	molecular function regulator
GO:0003824	0.57	catalytic activity
GO:0016740	0.55	transferase activity
GO:0052813	0.52	phosphatidylinositol bisphosphate kinase activity
GO:0052742	0.52	phosphatidylinositol kinase activity
GO:0035004	0.52	phosphatidylinositol 3-kinase activity
GO:0016307	0.52	phosphatidylinositol phosphate kinase activity

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Molecular Function. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Biological Process (BP)

GO term	Cscore^GO	Name
GO:0009987	0.90	cellular process
GO:0065007	0.78	biological regulation
GO:0050789	0.78	regulation of biological process
GO:0044699	0.77	single-organism process
GO:0044763	0.75	single-organism cellular process
GO:0051179	0.70	localization
GO:0051234	0.69	establishment of localization
GO:0006810	0.68	transport
GO:0016043	0.64	cellular component organization
GO:0050794	0.62	regulation of cellular process
GO:0006996	0.62	organelle organization
GO:0007165	0.60	signal transduction
GO:0006811	0.59	ion transport
GO:0071704	0.55	organic substance metabolic process
GO:0044710	0.54	single-organism metabolic process
GO:0044238	0.54	primary metabolic process
GO:0044237	0.54	cellular metabolic process
GO:1901576	0.53	organic substance biosynthetic process
GO:0044711	0.53	single-organism biosynthetic process
GO:0044249	0.53	cellular biosynthetic process
GO:0046834	0.52	lipid phosphorylation
GO:0006661	0.52	phosphatidylinositol biosynthetic process

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Biological Process. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Cellular Component (CC)

GO term	Cscore^GO	Name
GO:0044424	1.00	intracellular part
GO:0016020	1.00	membrane
GO:0044425	0.96	membrane part
GO:0005886	0.91	plasma membrane
GO:0098796	0.90	membrane protein complex
GO:0005942	0.86	phosphatidylinositol 3-kinase complex
GO:0043227	0.78	membrane-bounded organelle
GO:0043231	0.75	intracellular membrane-bounded organelle
GO:0005737	0.74	cytoplasm
GO:0044459	0.70	plasma membrane part
GO:0044444	0.65	cytoplasmic part
GO:0005634	0.65	nucleus
GO:0005829	0.62	cytosol

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Cellular Component. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Predicted Enzyme Commission (EC) Numbers

Top 5 enzyme homologs in PDB

Rank	Cscore^EC	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	EC Number	Predicted Active Site Residues
1	0.060	1ofdA	0.259	9.52	0.041	0.404	1.4.7.1	NA
2	0.060	3b8eA	0.210	8.84	0.054	0.315	3.6.3.9	NA
3	0.060	2vz8A	0.229	9.67	0.032	0.363	2.3.1.85	NA
4	0.060	3btaA	0.221	9.32	0.028	0.341	3.4.24.69	NA
5	0.060	1xc6A	0.215	9.42	0.029	0.335	3.2.1.23	172

	Click on the radio buttons to visualize predicted active site residues.
(a)	Cscore^EC is the confidence score for the Enzyme Commission (EC) number prediction. Cscore^EC values range in between [0-1]; where a higher score indicates a more reliable EC number prediction.
(b)	TM-score is a measure of global structural similarity between query and template protein.
(c)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(e)	Cov. represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.

Predicted Ligand Binding Sites

Template proteins with similar binding site:

Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
1	0.01	3b9jC	0.171	8.47	0.041	0.252	0.11	UUU	complex1.pdb.gz	167,588,629
2	0.01	3eubC	0.157	8.65	0.032	0.231	0.12	UUU	complex2.pdb.gz	291,292,293,294,319
3	0.01	3eubL	0.169	8.18	0.028	0.242	0.16	XAN	complex3.pdb.gz	168,320,628
4	0.01	3b9jB	0.096	6.63	0.029	0.122	0.11	FAD	complex4.pdb.gz	167,168,169,170,171,263,264
5	0.01	2ckjD	0.228	9.04	0.035	0.343	0.35	FES	complex5.pdb.gz	166,168,635,642
6	0.01	1v97A	0.232	9.10	0.040	0.351	0.28	FES	complex6.pdb.gz	167,168,170,612
7	0.01	3cmvC	0.244	9.71	0.022	0.389	0.10	ANP	complex7.pdb.gz	168,169,170
8	0.01	3eubL	0.169	8.18	0.028	0.242	0.18	UUU	complex8.pdb.gz	167,319,589,629
9	0.01	3nvvC	0.170	8.23	0.026	0.244	0.18	UUU	complex9.pdb.gz	320,322,589,628,629
10	0.01	1vdvA	0.213	9.81	0.028	0.343	0.13	YSH	complex10.pdb.gz	297,321,590,592,593

	Click on the radio buttons to visualize predicted binding site and residues.
(a)	Cscore^LB is the confidence score of predicted binding site. Cscore^LB values range in between [0-1]; where a higher score indicates a more reliable ligand-binding site prediction.
(b)	BS-score is a measure of local similarity (sequence & structure) between template binding site and predicted binding site in the query structure. Based on large scale benchmarking analysis, we have observed that a BS-score >1 reflects a significant local match between the predicted and template binding site.
(c)	TM-score is a measure of global structural similarity between query and template protein.
(d)	RMSD^a the RMSD between residues that are structurally aligned by TM-align.
(e)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(f)	Cov. represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.

[Click result.zip to download all results on this page]

References:
1.	Wei Zheng, Chengxin Zhang, Yang Li, Robin Pearce, Eric W. Bell, Yang Zhang. Folding non-homology proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. In preparation, 2020.