D-I-TASSER Q9BRQ0

D-I-TASSER results for Q9BRQ0

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

Summary of the Protein

Uniprot ID: Q9BRQ0
Protein Name: Pygopus homolog 2
Gene Name: PYGO2

Input Sequence in FASTA format

>Q9BRQ0 (406 residues)
MAASAPPPPDKLEGGGGPAPPPAPPSTGRKQGKAGLQMKSPEKKRRKSNTQGPAYSHLTE
FAPPPTPMVDHLVASNPFEDDFGAPKVGVAAPPFLGSPVPFGGFRVQGGMAGQVPPGYST
GGGGGPQPLRRQPPPFPPNPMGPAFNMPPQGPGYPPPGNMNFPSQPFNQPLGQNFSPPSG
QMMPGPVGGFGPMISPTMGQPPRAELGPPSLSQRFAQPGAPFGPSPLQRPGQGLPSLPPN
TSPFPGPDPGFPGPGGEDGGKPLNPPASTAFPQEPHSGSPAAAVNGNQPSFPPNSSGRGG
GTPDANSLAPPGKAGGGSGPQPPPGLVYPCGACRSEVNDDQDAILCEASCQKWFHRECTG
MTESAYGLLTTEASAVWACDLCLKTKEIQSVYIREGMGQLVAANDG

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	Q9BRQ0-D1	1-406	406		MAASAPPPPDKLEGGGGPAPPPAPPSTGRKQGKAGLQMKSPEKKRRKSNTQGPAYSHLTEFAPPPTPMVDHLVASNPFEDDFGAPKVGVAAPPFLGSPVPFGGFRVQGGMAGQVPPGYSTGGGGGPQPLRRQPPPFPPNPMGPAFNMPPQGPGYPPPGNMNFPSQPFNQPLGQNFSPPSGQMMPGPVGGFGPMISPTMGQPPRAELGPPSLSQRFAQPGAPFGPSPLQRPGQGLPSLPPNTSPFPGPDPGFPGPGGEDGGKPLNPPASTAFPQEPHSGSPAAAVNGNQPSFPPNSSGRGGGTPDANSLAPPGKAGGGSGPQPPPGLVYPCGACRSEVNDDQDAILCEASCQKWFHRECTGMTESAYGLLTTEASAVWACDLCLKTKEIQSVYIREGMGQLVAANDG

Top 1 final models from D-I-TASSER

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Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.5582

(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

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

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Alignment
1	6w2jA	0.45	6.99	0.035	0.761	model1_6w2jA.pdb.gz
2	1st6A	0.40	6.62	0.036	0.633	model1_1st6A.pdb.gz
3	5yz0A	0.40	7.37	0.042	0.692	model1_5yz0A.pdb.gz
4	6h02A	0.39	7.10	0.045	0.658	model1_6h02A.pdb.gz
5	1bxrA	0.39	7.42	0.063	0.687	model1_1bxrA.pdb.gz
6	3ecqB	0.38	7.14	0.035	0.658	model1_3ecqB.pdb.gz
7	5a22A	0.38	6.77	0.049	0.613	model1_5a22A.pdb.gz
8	4xwhA	0.38	6.73	0.053	0.611	model1_4xwhA.pdb.gz
9	1kjiA	0.26	6.81	0.055	0.429	model1_1kjiA.pdb.gz
10	4nuyA	0.24	7.03	0.043	0.409	model1_4nuyA.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:0003682	0.62	chromatin binding
GO:0042393	0.61	histone binding
GO:0030234	0.60	enzyme regulator activity
GO:0035034	0.59	histone acetyltransferase regulator 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:0016043	1.00	cellular component organization
GO:0065007	0.81	biological regulation
GO:0050789	0.81	regulation of biological process
GO:0050794	0.79	regulation of cellular process
GO:0044699	0.79	single-organism process
GO:0032502	0.76	developmental process
GO:0044767	0.75	single-organism developmental process
GO:0044763	0.75	single-organism cellular process
GO:0019222	0.75	regulation of metabolic process
GO:0080090	0.74	regulation of primary metabolic process
GO:0060255	0.74	regulation of macromolecule metabolic process
GO:0031323	0.74	regulation of cellular metabolic process
GO:0048856	0.73	anatomical structure development
GO:0048869	0.71	cellular developmental process
GO:0044707	0.71	single-multicellular organism process
GO:0007165	0.71	signal transduction
GO:0048513	0.70	animal organ development
GO:0016055	0.70	Wnt signaling pathway
GO:0048468	0.69	cell development
GO:0022412	0.69	cellular process involved in reproduction in multicellular organism
GO:0003006	0.69	developmental process involved in reproduction
GO:0009791	0.68	post-embryonic development
GO:0007289	0.68	spermatid nucleus differentiation
GO:0007286	0.68	spermatid development
GO:0001822	0.68	kidney development
GO:0048589	0.62	developmental growth
GO:2000026	0.61	regulation of multicellular organismal development
GO:0032268	0.61	regulation of cellular protein metabolic process
GO:0007275	0.61	multicellular organism development
GO:0051099	0.60	positive regulation of binding
GO:0033043	0.60	regulation of organelle organization
GO:0060070	0.59	canonical Wnt signaling pathway
GO:0060021	0.59	palate development
GO:0051569	0.59	regulation of histone H3-K4 methylation
GO:0035563	0.59	positive regulation of chromatin binding
GO:0033599	0.59	regulation of mammary gland epithelial cell proliferation
GO:0030879	0.59	mammary gland development
GO:0007420	0.59	brain development
GO:0002088	0.59	lens development in camera-type eye
GO:0001701	0.59	in utero embryonic 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:0044424	1.00	intracellular part
GO:0043229	0.80	intracellular organelle
GO:0043231	0.78	intracellular membrane-bounded organelle
GO:0005634	0.75	nucleus
GO:0044446	0.50	intracellular organelle 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

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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	1r9mB	0.333	7.29	0.054	0.576	3.4.14.5	NA
2	0.060	2fgeA	0.279	7.35	0.043	0.488	3.4.24.-	NA
3	0.060	2c4mC	0.333	6.66	0.030	0.534	2.4.1.1	NA
4	0.060	1jqnA	0.362	7.17	0.045	0.623	4.1.1.31	NA
5	0.060	2np0A	0.331	6.80	0.036	0.537	3.4.24.69	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

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Template proteins with similar binding site:

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
	1	0.01	2c3oA	0.370	7.48	0.042	0.660	0.41	SF4	complex1.pdb.gz	114,115,116,117,118,119,120,126,127

	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.