D-I-TASSER Q8WU10

D-I-TASSER results for Q8WU10

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

Summary of the Protein

Uniprot ID: Q8WU10
Protein Name: Pyridine nucleotide-disulfide oxidoreductase domain-containing protein 1
Gene Name: PYROXD1

Input Sequence in FASTA format

>Q8WU10 (500 residues)
MEAARPPPTAGKFVVVGGGIAGVTCAEQLATHFPSEDILLVTASPVIKAVTNFKQISKIL
EEFDVEEQSSTMLGKRFPNIKVIESGVKQLKSEEHCIVTEDGNQHVYKKLCLCAGAKPKL
ICEGNPYVLGIRDTDSAQEFQKQLTKAKRIMIIGNGGIALELVYEIEGCEVIWAIKDKAI
GNTFFDAGAAEFLTSKLIAEKSEAKIAHKRTRYTTEGRKKEARSKSKADNVGSALGPDWH
EGLNLKGTKEFSHKIHLETMCEVKKIYLQDEFRILKKKSFTFPRDHKSVTADTEMWPVYV
ELTNEKIYGCDFIVSATGVTPNVEPFLHGNSFDLGEDGGLKVDDHMHTSLPDIYAAGDIC
TTSWQLSPVWQQMRLWTQARQMGWYAAKCMAAASSGDSIDMDFSFELFAHVTKFFNYKVV
LLGKYNAQGLGSDHELMLRCTKGREYIKVVMQNGRMMGAVLIGETDLEETFENLILNQMN
LSSYGEDLLDPNIDIEDYFD

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	Q8WU10-D1	1-115,321-404	199		MEAARPPPTAGKFVVVGGGIAGVTCAEQLATHFPSEDILLVTASPVIKAVTNFKQISKILEEFDVEEQSSTMLGKRFPNIKVIESGVKQLKSEEHCIVTEDGNQHVYKKLCLCAGPNVEPFLHGNSFDLGEDGGLKVDDHMHTSLPDIYAAGDICTTSWQLSPVWQQMRLWTQARQMGWYAAKCMAAASSGDSIDMDFS
2	Q8WU10-D2	116-177,254-320	129		AKPKLICEGNPYVLGIRDTDSAQEFQKQLTKAKRIMIIGNGGIALELVYEIEGCEVIWAIKDKIHLETMCEVKKIYLQDEFRILKKKSFTFPRDHKSVTADTEMWPVYVELTNEKIYGCDFIVSATGVT
3	Q8WU10-D3	178-253,405-500	172		KAIGNTFFDAGAAEFLTSKLIAEKSEAKIAHKRTRYTTEGRKKEARSKSKADNVGSALGPDWHEGLNLKGTKEFSHFELFAHVTKFFNYKVVLLGKYNAQGLGSDHELMLRCTKGREYIKVVMQNGRMMGAVLIGETDLEETFENLILNQMNLSSYGEDLLDPNIDIEDYFD

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.82

(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	1nhqA	0.71	3.10	0.192	0.796	model1_1nhqA.pdb.gz
2	2bc0A	0.71	3.54	0.154	0.810	model1_2bc0A.pdb.gz
3	3fg2P	0.70	3.26	0.180	0.790	model1_3fg2P.pdb.gz
4	5er0A	0.69	3.46	0.180	0.798	model1_5er0A.pdb.gz
5	3ef6A	0.69	3.01	0.154	0.776	model1_3ef6A.pdb.gz
6	6pfzD	0.69	3.49	0.190	0.798	model1_6pfzD.pdb.gz
7	3cgcA	0.69	3.52	0.160	0.796	model1_3cgcA.pdb.gz
8	2gr3A	0.69	3.16	0.183	0.776	model1_2gr3A.pdb.gz
9	3ictA	0.69	3.48	0.192	0.788	model1_3ictA.pdb.gz
10	2cduA	0.68	3.59	0.175	0.798	model1_2cduA.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:0003824	0.76	catalytic activity
GO:0016491	0.72	oxidoreductase activity
GO:1901363	0.70	heterocyclic compound binding
GO:0097159	0.70	organic cyclic compound binding
GO:0003676	0.65	nucleic acid binding
GO:0016651	0.62	oxidoreductase activity, acting on NAD(P)H
GO:0036094	0.61	small molecule binding
GO:0003677	0.60	DNA binding
GO:0000166	0.60	nucleotide binding
GO:0016667	0.58	oxidoreductase activity, acting on a sulfur group of donors
GO:0009055	0.56	electron carrier activity
GO:0016860	0.55	intramolecular oxidoreductase activity
GO:0071949	0.54	FAD binding
GO:0046983	0.54	protein dimerization activity
GO:0016174	0.54	NAD(P)H oxidase activity
GO:0016864	0.53	intramolecular oxidoreductase activity, transposing S-S bonds
GO:0016668	0.53	oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor
GO:0016684	0.51	oxidoreductase activity, acting on peroxide as acceptor
GO:0016209	0.51	antioxidant 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:0044699	0.98	single-organism process
GO:0008152	0.98	metabolic process
GO:0044710	0.97	single-organism metabolic process
GO:0009987	0.97	cellular process
GO:0044763	0.95	single-organism cellular process
GO:0050794	0.88	regulation of cellular process
GO:0055114	0.86	oxidation-reduction process
GO:0065008	0.82	regulation of biological quality
GO:0045454	0.81	cell redox homeostasis
GO:0044237	0.74	cellular metabolic process
GO:0071704	0.69	organic substance metabolic process
GO:0050896	0.63	response to stimulus
GO:0031323	0.63	regulation of cellular metabolic process
GO:0080090	0.62	regulation of primary metabolic process
GO:0048518	0.62	positive regulation of biological process
GO:0060255	0.61	regulation of macromolecule metabolic process
GO:0042221	0.61	response to chemical
GO:1901700	0.60	response to oxygen-containing compound
GO:0048522	0.60	positive regulation of cellular process
GO:0019219	0.60	regulation of nucleobase-containing compound metabolic process
GO:0007165	0.60	signal transduction
GO:0044238	0.59	primary metabolic process
GO:0031325	0.59	positive regulation of cellular metabolic process
GO:0010604	0.59	positive regulation of macromolecule metabolic process
GO:0010035	0.59	response to inorganic substance
GO:1901698	0.58	response to nitrogen compound
GO:0016043	0.58	cellular component organization
GO:0009725	0.58	response to hormone
GO:0044281	0.57	small molecule metabolic process
GO:0035556	0.57	intracellular signal transduction
GO:0010243	0.57	response to organonitrogen compound
GO:0009605	0.57	response to external stimulus
GO:0006950	0.57	response to stress
GO:0071241	0.56	cellular response to inorganic substance
GO:0051128	0.56	regulation of cellular component organization
GO:0050790	0.56	regulation of catalytic activity
GO:0032270	0.56	positive regulation of cellular protein metabolic process
GO:0022607	0.56	cellular component assembly
GO:0009628	0.56	response to abiotic stimulus
GO:0071732	0.55	cellular response to nitric oxide
GO:0051336	0.55	regulation of hydrolase activity
GO:0048869	0.55	cellular developmental process
GO:0045862	0.55	positive regulation of proteolysis
GO:0042981	0.55	regulation of apoptotic process
GO:0042542	0.55	response to hydrogen peroxide
GO:0034622	0.55	cellular macromolecular complex assembly
GO:0030261	0.55	chromosome condensation
GO:0006807	0.55	nitrogen compound metabolic process
GO:0006461	0.55	protein complex assembly
GO:1904045	0.54	cellular response to aldosterone
GO:1902510	0.54	regulation of apoptotic DNA fragmentation
GO:1902065	0.54	response to L-glutamate
GO:0090650	0.54	cellular response to oxygen-glucose deprivation
GO:0071392	0.54	cellular response to estradiol stimulus
GO:0070301	0.54	cellular response to hydrogen peroxide
GO:0070059	0.54	intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress
GO:0043525	0.54	positive regulation of neuron apoptotic process
GO:0032981	0.54	mitochondrial respiratory chain complex I assembly
GO:0030182	0.54	neuron differentiation
GO:0006919	0.54	activation of cysteine-type endopeptidase activity involved in apoptotic process
GO:0002931	0.54	response to ischemia
GO:1990748	0.51	cellular detoxification

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:0044464	0.99	cell part
GO:0044424	0.97	intracellular part
GO:0005737	0.71	cytoplasm
GO:0044444	0.60	cytoplasmic part
GO:0005623	0.56	cell
GO:0043226	0.54	organelle
GO:0043229	0.51	intracellular organelle
GO:0043227	0.51	membrane-bounded organelle

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	0.292	1zdlA	0.663	3.54	0.146	0.762	1.8.1.9	468
2	0.291	1bzlA	0.678	3.44	0.134	0.772	1.8.1.12	468
3	0.288	2wbaA	0.673	3.31	0.150	0.764	1.8.1.12	468
4	0.282	1feaA	0.672	3.43	0.142	0.768	1.8.1.12	468
5	0.282	1dxlA	0.667	3.32	0.142	0.758	1.8.1.4	25

	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	0.55	3icrA	0.701	3.45	0.196	0.804	0.98	FAD	complex1.pdb.gz	17,19,20,21,42,43,50,51,85,86,87,113,114,115,133,134,239,326,357,358,374,375,376,379
2	0.23	2gr0A	0.688	3.09	0.183	0.774	0.83	ADP	complex2.pdb.gz	16,17,18,22,24,41,42,43,44,49,113,114
3	0.04	3icsB	0.697	3.52	0.196	0.802	1.13	COA	complex3.pdb.gz	19,20,23,24,27,28,31,49,52,77,375,380,384

	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.