D-I-TASSER Q6ZVD7

D-I-TASSER results for Q6ZVD7

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

Summary of the Protein

Uniprot ID: Q6ZVD7
Protein Name: Storkhead-box protein 1
Gene Name: STOX1

Input Sequence in FASTA format

>Q6ZVD7 (989 residues)
MARPVQLAPGSLALVLCRLEAQKAAGAAEEPGGRAVFRAFRRANARCFWNARLARAASRL
AFQGWLRRGVLLVRAPPACLQVLRDAWRRRALRPPRGFRIRAVGDVFPVQMNPITQSQFV
PLGEVLCCAISDMNTAQIVVTQESLLERLMKHYPGIAIPSEDILYTTLGTLIKERKIYHT
GEGYFIVTPQTYFITNTTTQENKRMLPSDESRLMPASMTYLVSMESCAESAQENAAPISH
CQSCQCFRDMHTQDVQEAPVAAEVTRKSHRGLGESVSWVQNGAVSVSAEHHICESTKPLP
YTRDKEKGKKFGFSLLWRSLSRKEKPKTEHSSFSAQFPPEEWPVRDEDDLDNIPRDVEHE
IIKRINPILTVDNLIKHTVLMQKYEEQKKYNSQGTSTDMLTIGHKYPSKEGVKKRQGLSA
KPQGQGHSRRDRHKARNQGSEFQPGSIRLEKHPKLPATQPIPRIKSPNEMVGQKPLGEIT
TVLGSHLIYKKRISNPFQGLSHRGSTISKGHKIQKTSDLKPSQTGPKEKPFQKPRSLDSS
RIFDGKAKEPYAEQPNDKMEAESIYINDPTVKPINDDFRGHLFSHPQQSMLQNDGKCCPF
MESMLRYEVYGGENEVIPEVLRKSHSHFDKLGETKQTPHSLPSRGASFSDRTPSACRLVD
NTIHQFQNLGLLDYPVGVNPLRQAARQDKDSEELLRKGFVQDAETTSLENEQLSNDDQAL
YQNEVEDDDGACSSLYLEEDDISENDDLRQMLPGHSQYSFTGGSQGNHLGKQKVIERSLT
EYNSTMERVESQVLKRNECYKPTGLHATPGESQEPNLSAESCGLNSGAQFGFNYEEEPSV
AKCVQASAPADERIFDYYSARKASFEAEVIQDTIGDTGKKPASWSQSPQNQEMRKHFPQK
FQLFNTSHMPVLAQDVQYEHSHLEGTENHSMAGDSGIDSPRTQSLGSNNSVILDGLKRRQ
NFLQNVEGTKSSQPLTSNSLLPLTPVINV

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	Q6ZVD7-D1	1-178,396-491	274		MARPVQLAPGSLALVLCRLEAQKAAGAAEEPGGRAVFRAFRRANARCFWNARLARAASRLAFQGWLRRGVLLVRAPPACLQVLRDAWRRRALRPPRGFRIRAVGDVFPVQMNPITQSQFVPLGEVLCCAISDMNTAQIVVTQESLLERLMKHYPGIAIPSEDILYTTLGTLIKERKIYSTDMLTIGHKYPSKEGVKKRQGLSAKPQGQGHSRRDRHKARNQGSEFQPGSIRLEKHPKLPATQPIPRIKSPNEMVGQKPLGEITTVLGSHLIYKK
2	Q6ZVD7-D2	179-270	92		HTGEGYFIVTPQTYFITNTTTQENKRMLPSDESRLMPASMTYLVSMESCAESAQENAAPISHCQSCQCFRDMHTQDVQEAPVAAEVTRKSHR
3	Q6ZVD7-D3	271-395	125		GLGESVSWVQNGAVSVSAEHHICESTKPLPYTRDKEKGKKFGFSLLWRSLSRKEKPKTEHSSFSAQFPPEEWPVRDEDDLDNIPRDVEHEIIKRINPILTVDNLIKHTVLMQKYEEQKKYNSQGT
4	Q6ZVD7-D4	492-989	498		RISNPFQGLSHRGSTISKGHKIQKTSDLKPSQTGPKEKPFQKPRSLDSSRIFDGKAKEPYAEQPNDKMEAESIYINDPTVKPINDDFRGHLFSHPQQSMLQNDGKCCPFMESMLRYEVYGGENEVIPEVLRKSHSHFDKLGETKQTPHSLPSRGASFSDRTPSACRLVDNTIHQFQNLGLLDYPVGVNPLRQAARQDKDSEELLRKGFVQDAETTSLENEQLSNDDQALYQNEVEDDDGACSSLYLEEDDISENDDLRQMLPGHSQYSFTGGSQGNHLGKQKVIERSLTEYNSTMERVESQVLKRNECYKPTGLHATPGESQEPNLSAESCGLNSGAQFGFNYEEEPSVAKCVQASAPADERIFDYYSARKASFEAEVIQDTIGDTGKKPASWSQSPQNQEMRKHFPQKFQLFNTSHMPVLAQDVQYEHSHLEGTENHSMAGDSGIDSPRTQSLGSNNSVILDGLKRRQNFLQNVEGTKSSQPLTSNSLLPLTPVINV

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.35

(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	6um1A	0.28	9.34	0.019	0.459	model1_6um1A.pdb.gz
2	6g2dC	0.27	8.96	0.027	0.427	model1_6g2dC.pdb.gz
3	6yejA	0.27	8.62	0.037	0.407	model1_6yejA.pdb.gz
4	5cskA	0.27	8.98	0.034	0.421	model1_5cskA.pdb.gz
5	5yz0A	0.27	8.90	0.024	0.418	model1_5yz0A.pdb.gz
6	5xjyA	0.27	9.35	0.031	0.431	model1_5xjyA.pdb.gz
7	6z2wE	0.27	8.70	0.019	0.406	model1_6z2wE.pdb.gz
8	2uvcG	0.27	8.88	0.039	0.417	model1_2uvcG.pdb.gz
9	6bq1A	0.26	8.94	0.031	0.412	model1_6bq1A.pdb.gz
10	7d3eA	0.26	9.28	0.033	0.421	model1_7d3eA.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:0000977	0.97	RNA polymerase II regulatory region sequence-specific DNA binding

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	0.78	single-organism process
GO:0009987	0.78	cellular process
GO:0065007	0.77	biological regulation
GO:0050789	0.75	regulation of biological process
GO:0050794	0.73	regulation of cellular process
GO:0080090	0.68	regulation of primary metabolic process
GO:0060255	0.68	regulation of macromolecule metabolic process
GO:0048518	0.68	positive regulation of biological process
GO:0031323	0.68	regulation of cellular metabolic process
GO:0051171	0.66	regulation of nitrogen compound metabolic process
GO:0048522	0.66	positive regulation of cellular process
GO:0031325	0.65	positive regulation of cellular metabolic process
GO:0010604	0.65	positive regulation of macromolecule metabolic process
GO:0006355	0.65	regulation of transcription, DNA-templated
GO:0065008	0.64	regulation of biological quality
GO:0051246	0.64	regulation of protein metabolic process
GO:0048583	0.64	regulation of response to stimulus
GO:0006357	0.64	regulation of transcription from RNA polymerase II promoter
GO:0050896	0.63	response to stimulus
GO:0048519	0.63	negative regulation of biological process
GO:0032268	0.63	regulation of cellular protein metabolic process
GO:0010628	0.63	positive regulation of gene expression
GO:0080134	0.62	regulation of response to stress
GO:0051247	0.62	positive regulation of protein metabolic process
GO:0010605	0.62	negative regulation of macromolecule metabolic process
GO:0001932	0.62	regulation of protein phosphorylation
GO:1904031	0.61	positive regulation of cyclin-dependent protein kinase activity
GO:1902882	0.61	regulation of response to oxidative stress
GO:1901858	0.61	regulation of mitochondrial DNA metabolic process
GO:0071500	0.61	cellular response to nitrosative stress
GO:0061418	0.61	regulation of transcription from RNA polymerase II promoter in response to hypoxia
GO:0051881	0.61	regulation of mitochondrial membrane potential
GO:0033138	0.61	positive regulation of peptidyl-serine phosphorylation
GO:0010971	0.61	positive regulation of G2/M transition of mitotic cell cycle
GO:0010800	0.61	positive regulation of peptidyl-threonine phosphorylation
GO:0010629	0.61	negative regulation of gene expression
GO:0008284	0.61	positive regulation of cell proliferation
GO:0032502	0.59	developmental process
GO:0044767	0.58	single-organism developmental process
GO:0048856	0.56	anatomical structure development

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:0005737	1.00	cytoplasm
GO:0005634	1.00	nucleus
GO:0005813	0.97	centrosome
GO:0005730	0.97	nucleolus
GO:0005654	0.97	nucleoplasm
GO:0044444	0.59	cytoplasmic part

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	1eulA	0.173	9.77	0.035	0.293	3.6.3.8	NA
2	0.060	1ug9A	0.207	8.78	0.046	0.320	3.2.1.70	NA
3	0.060	2cseW	0.222	8.95	0.039	0.350	3.6.4.13	NA
4	0.060	2vz8A	0.223	9.03	0.033	0.347	2.3.1.85	NA
5	0.060	2zxqA	0.224	8.74	0.037	0.343	3.2.1.97	NA

	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:

No Binding sites was predicted

Click to view	Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues

	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.