D-I-TASSER Q96QS6

D-I-TASSER results for Q96QS6

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

Summary of the Protein

Uniprot ID: Q96QS6
Protein Name: Serine/threonine-protein kinase H2
Gene Name: PSKH2

Input Sequence in FASTA format

>Q96QS6 (385 residues)
MGCGASRKVVPGPPALAWAKHEGQNQAGVGGAGPGPEAAAQAAQRIQVARFRAKFDPRVL
ARYDIKALIGTGSFSRVVRVEQKTTKKPFAIKVMETREREGREACVSELSVLRRVSHRYI
VQLMEIFETEDQVYMVMELATGGELFDRLIAQGSFTERDAVRILQMVADGIRYLHALQIT
HRNLKPENLLYYHPGEESKILITDFGLAYSGKKSGDWTMKTLCGTPEYIAPEVLLRKPYT
SAVDMWALGVITYALLSGFLPFDDESQTRLYRKILKGKYNYTGEPWPSISHLAKDFIDKL
LILEAGHRMSAGQALDHPWVITMAAGSSMKNLQRAISRNLMQRASPHSQSPGSAQSSKSH
YSHKSRHMWSKRNLRIVESPLSALL

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	Q96QS6-D1	1-139	139		MGCGASRKVVPGPPALAWAKHEGQNQAGVGGAGPGPEAAAQAAQRIQVARFRAKFDPRVLARYDIKALIGTGSFSRVVRVEQKTTKKPFAIKVMETREREGREACVSELSVLRRVSHRYIVQLMEIFETEDQVYMVMEL
2	Q96QS6-D2	140-385	246		ATGGELFDRLIAQGSFTERDAVRILQMVADGIRYLHALQITHRNLKPENLLYYHPGEESKILITDFGLAYSGKKSGDWTMKTLCGTPEYIAPEVLLRKPYTSAVDMWALGVITYALLSGFLPFDDESQTRLYRKILKGKYNYTGEPWPSISHLAKDFIDKLLILEAGHRMSAGQALDHPWVITMAAGSSMKNLQRAISRNLMQRASPHSQSPGSAQSSKSHYSHKSRHMWSKRNLRIVESPLSALL

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.87

(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	6c9dA	0.71	3.05	0.284	0.782	model1_6c9dA.pdb.gz
2	1u5rA	0.71	2.52	0.223	0.779	model1_1u5rA.pdb.gz
3	3tkuA	0.69	3.48	0.248	0.797	model1_3tkuA.pdb.gz
4	1yhwA	0.69	2.35	0.236	0.748	model1_1yhwA.pdb.gz
5	2f2uA	0.68	3.51	0.226	0.787	model1_2f2uA.pdb.gz
6	3pfqA	0.68	2.48	0.235	0.738	model1_3pfqA.pdb.gz
7	2pmlX	0.68	3.00	0.196	0.769	model1_2pmlX.pdb.gz
8	3a7hB	0.68	2.45	0.246	0.751	model1_3a7hB.pdb.gz
9	2vd5A	0.68	3.41	0.253	0.771	model1_2vd5A.pdb.gz
10	1cdkA	0.68	3.23	0.305	0.769	model1_1cdkA.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	0.98	catalytic activity
GO:0004672	0.97	protein kinase activity
GO:0004674	0.90	protein serine/threonine kinase activity
GO:1901363	0.84	heterocyclic compound binding
GO:0097159	0.84	organic cyclic compound binding
GO:0005524	0.76	ATP binding
GO:0005516	0.57	calmodulin 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:0009987	0.98	cellular process
GO:0044260	0.94	cellular macromolecule metabolic process
GO:0044238	0.94	primary metabolic process
GO:0065007	0.91	biological regulation
GO:0050789	0.91	regulation of biological process
GO:0050794	0.90	regulation of cellular process
GO:0006468	0.88	protein phosphorylation
GO:0007165	0.71	signal transduction
GO:0050896	0.64	response to stimulus
GO:0080090	0.62	regulation of primary metabolic process
GO:0060255	0.62	regulation of macromolecule metabolic process
GO:0046777	0.62	protein autophosphorylation
GO:0031323	0.62	regulation of cellular metabolic process
GO:1901576	0.60	organic substance biosynthetic process
GO:0044249	0.60	cellular biosynthetic process
GO:0035556	0.59	intracellular signal transduction
GO:0034645	0.59	cellular macromolecule biosynthetic process
GO:2000112	0.58	regulation of cellular macromolecule biosynthetic process
GO:0051171	0.58	regulation of nitrogen compound metabolic process
GO:0048523	0.58	negative regulation of cellular process
GO:0010468	0.58	regulation of gene expression
GO:0051716	0.56	cellular response to stimulus
GO:0032268	0.56	regulation of cellular protein metabolic process
GO:0044699	0.55	single-organism process
GO:0042221	0.55	response to chemical
GO:0070887	0.54	cellular response to chemical stimulus
GO:0048518	0.54	positive regulation of biological process
GO:0010033	0.54	response to organic substance
GO:0071310	0.53	cellular response to organic substance
GO:0032269	0.53	negative regulation of cellular protein metabolic process
GO:2000113	0.52	negative regulation of cellular macromolecule biosynthetic process
GO:0051172	0.52	negative regulation of nitrogen compound metabolic process
GO:0034097	0.52	response to cytokine
GO:0010629	0.52	negative regulation of gene expression
GO:0010506	0.52	regulation of autophagy
GO:0006417	0.52	regulation of translation
GO:0071346	0.51	cellular response to interferon-gamma
GO:0048522	0.51	positive regulation of cellular process
GO:0017148	0.51	negative regulation of translation

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	1.00	cell part
GO:0044424	0.99	intracellular part
GO:0043226	0.93	organelle
GO:0043229	0.92	intracellular organelle
GO:0043227	0.91	membrane-bounded organelle
GO:0043231	0.90	intracellular membrane-bounded organelle
GO:0005634	0.86	nucleus
GO:0005737	0.84	cytoplasm
GO:0044444	0.65	cytoplasmic part
GO:0016020	0.59	membrane
GO:0044422	0.55	organelle part
GO:0044446	0.52	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

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	0.330	3lm0A	0.641	2.17	0.306	0.688	2.7.11.1	144,146,185,190,225
2	0.277	3a7hB	0.679	2.45	0.246	0.751	2.7.11.1	69,77,92,190,197
3	0.151	1u5qA	0.710	2.54	0.222	0.782	2.7.11.1	NA
4	0.150	3ckxA	0.664	2.12	0.264	0.717	2.7.11.1	NA
5	0.142	2biyA	0.660	2.19	0.291	0.707	2.7.11.1	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:

Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
1	0.49	2erzE	0.686	3.00	0.305	0.766	1.31	HFS	complex1.pdb.gz	69,71,77,90,121,137,138,139,140,187,188,190,203,204
2	0.43	3pooA	0.684	2.98	0.312	0.764	1.09	S69	complex2.pdb.gz	69,72,73,74,75,76,77,90,92,94,137,138,139,140,190,203,204
3	0.41	2uw8A	0.686	3.01	0.298	0.766	1.09	GVQ	complex3.pdb.gz	69,70,71,76,77,90,144,187,188,203
4	0.39	1szmB	0.656	3.07	0.268	0.738	1.18	BI4	complex4.pdb.gz	69,71,77,90,92,137,138,139,140
5	0.37	3aglB	0.689	2.97	0.301	0.766	1.12	A03	complex5.pdb.gz	71,72,73,74,75,77,90,94,121,138,139,140,144,146,150,186,187,190,203,207,227,254
6	0.36	3mvjE	0.682	3.15	0.305	0.766	0.91	XFE	complex6.pdb.gz	69,70,90,137,138,140,144,190,203
7	0.27	2erzE	0.686	3.00	0.305	0.766	1.18	III	complex7.pdb.gz	144,146,150,185,186,187,207,222,223,224,225,226,227,254,258,259,260,263,264,270
8	0.27	3a7jA	0.679	2.30	0.246	0.740	1.23	ADP	complex8.pdb.gz	69,72,78,90,92,137,138,140,188,190,204
9	0.23	2xikA	0.677	2.53	0.257	0.746	1.01	J60	complex9.pdb.gz	68,69,90,137,138,139,140,141,143,147,190
10	0.22	2pmlX	0.680	3.00	0.196	0.769	1.05	ANP	complex10.pdb.gz	70,75,77,90,92,138,139,140,143,185,187,189,204

	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.