D-I-TASSER Q8TDR2

D-I-TASSER results for Q8TDR2

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

Summary of the Protein

Uniprot ID: Q8TDR2
Protein Name: Serine/threonine-protein kinase 35
Gene Name: STK35

Input Sequence in FASTA format

>Q8TDR2 (534 residues)
MGHQESPLARAPAGGAAYVKRLCKGLSWREHVESHGSLGAQASPASAAAAEGSATRRARA
ATSRAARSRRQPGPGADHPQAGAPGGKRAARKWRCAGQVTIQGPAPPRPRAGRRDEAGGA
RAAPLLLPPPPAAMETGKDGARRGTQSPERKRRSPVPRAPSTKLRPAAAARAMDPVAAEA
PGEAFLARRRPEGGGGSARPRYSLLAEIGRGSYGVVYEAVAGRSGARVAVKKIRCDAPEN
VELALAEFWALTSLKRRHQNVVQFEECVLQRNGLAQRMSHGNKSSQLYLRLVETSLKGER
ILGYAEEPCYLWFVMEFCEGGDLNQYVLSRRPDPATNKSFMLQLTSAIAFLHKNHIVHRD
LKPDNILITERSGTPILKVADFGLSKVCAGLAPRGKEGNQDNKNVNVNKYWLSSACGSDF
YMAPEVWEGHYTAKADIFALGIIIWAMIERITFIDSETKKELLGTYIKQGTEIVPVGEAL
LENPKMELHIPQKRRTSMSEGIKQLLKDMLAANPQDRPDAFELETRMDQVTCAA

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 DeepPotential. 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	Q8TDR2-D1	1-186	186		MGHQESPLARAPAGGAAYVKRLCKGLSWREHVESHGSLGAQASPASAAAAEGSATRRARAATSRAARSRRQPGPGADHPQAGAPGGKRAARKWRCAGQVTIQGPAPPRPRAGRRDEAGGARAAPLLLPPPPAAMETGKDGARRGTQSPERKRRSPVPRAPSTKLRPAAAARAMDPVAAEAPGEAFL
2	Q8TDR2-D2	187-317	131		ARRRPEGGGGSARPRYSLLAEIGRGSYGVVYEAVAGRSGARVAVKKIRCDAPENVELALAEFWALTSLKRRHQNVVQFEECVLQRNGLAQRMSHGNKSSQLYLRLVETSLKGERILGYAEEPCYLWFVMEF
3	Q8TDR2-D3	318-534	217		CEGGDLNQYVLSRRPDPATNKSFMLQLTSAIAFLHKNHIVHRDLKPDNILITERSGTPILKVADFGLSKVCAGLAPRGKEGNQDNKNVNVNKYWLSSACGSDFYMAPEVWEGHYTAKADIFALGIIIWAMIERITFIDSETKKELLGTYIKQGTEIVPVGEALLENPKMELHIPQKRRTSMSEGIKQLLKDMLAANPQDRPDAFELETRMDQVTCAA

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.709

(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 DeepPotential, 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	1q99B	0.48	2.95	0.210	0.526	model1_1q99B.pdb.gz
2	4myiA	0.48	3.80	0.156	0.545	model1_4myiA.pdb.gz
3	8ewyA	0.47	3.77	0.123	0.543	model1_8ewyA.pdb.gz
4	6xr4A	0.47	3.94	0.150	0.543	model1_6xr4A.pdb.gz
5	2vx3A	0.47	2.77	0.232	0.509	model1_2vx3A.pdb.gz
6	7rj6A	0.47	2.54	0.214	0.502	model1_7rj6A.pdb.gz
7	8em8A	0.47	3.58	0.168	0.530	model1_8em8A.pdb.gz
8	3kvwA	0.47	2.96	0.196	0.509	model1_3kvwA.pdb.gz
9	2wu6A	0.47	3.15	0.196	0.513	model1_2wu6A.pdb.gz
10	4iw0A	0.47	2.75	0.176	0.509	model1_4iw0A.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:0035639	0.92	purine ribonucleoside triphosphate binding
GO:0032555	0.92	purine ribonucleotide binding
GO:0032550	0.92	purine ribonucleoside binding
GO:0004674	0.92	protein serine/threonine kinase activity
GO:0005524	0.91	ATP binding
GO:0005516	0.77	calmodulin binding
GO:0042802	0.70	identical protein binding
GO:0005525	0.56	GTP binding
GO:0000149	0.56	SNARE binding
GO:0017075	0.55	syntaxin-1 binding
GO:0004871	0.50	signal transducer 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	0.97	cellular process
GO:0071704	0.94	organic substance metabolic process
GO:0044260	0.93	cellular macromolecule metabolic process
GO:0044238	0.93	primary metabolic process
GO:0006796	0.92	phosphate-containing compound metabolic process
GO:0006464	0.92	cellular protein modification process
GO:0065007	0.91	biological regulation
GO:0050789	0.91	regulation of biological process
GO:0006468	0.91	protein phosphorylation
GO:0050794	0.90	regulation of cellular process
GO:0007165	0.82	signal transduction
GO:0046777	0.75	protein autophosphorylation
GO:0035556	0.74	intracellular signal transduction
GO:0044699	0.72	single-organism process
GO:0050896	0.68	response to stimulus
GO:0048518	0.66	positive regulation of biological process
GO:0044763	0.66	single-organism cellular process
GO:0048522	0.64	positive regulation of cellular process
GO:0080090	0.63	regulation of primary metabolic process
GO:0048519	0.63	negative regulation of biological process
GO:0031323	0.63	regulation of cellular metabolic process
GO:0060255	0.62	regulation of macromolecule metabolic process
GO:0048583	0.62	regulation of response to stimulus
GO:0048523	0.62	negative regulation of cellular process
GO:0023051	0.61	regulation of signaling
GO:0010646	0.61	regulation of cell communication
GO:0065009	0.60	regulation of molecular function
GO:0051716	0.60	cellular response to stimulus
GO:0032879	0.60	regulation of localization
GO:0032268	0.60	regulation of cellular protein metabolic process
GO:0031325	0.60	positive regulation of cellular metabolic process
GO:0010604	0.60	positive regulation of macromolecule metabolic process
GO:0009966	0.60	regulation of signal transduction
GO:2000112	0.59	regulation of cellular macromolecule biosynthetic process
GO:0051171	0.59	regulation of nitrogen compound metabolic process
GO:0050790	0.59	regulation of catalytic activity
GO:0042981	0.59	regulation of apoptotic process
GO:0042221	0.59	response to chemical
GO:0010468	0.59	regulation of gene expression
GO:0051049	0.58	regulation of transport
GO:0043085	0.58	positive regulation of catalytic activity
GO:0043066	0.58	negative regulation of apoptotic process
GO:0032270	0.58	positive regulation of cellular protein metabolic process
GO:0010033	0.58	response to organic substance
GO:0071310	0.57	cellular response to organic substance
GO:0032269	0.57	negative regulation of cellular protein metabolic process
GO:0009968	0.57	negative regulation of signal transduction
GO:2001233	0.56	regulation of apoptotic signaling pathway
GO:2000113	0.56	negative regulation of cellular macromolecule biosynthetic process
GO:0051345	0.56	positive regulation of hydrolase activity
GO:0051172	0.56	negative regulation of nitrogen compound metabolic process
GO:0045862	0.56	positive regulation of proteolysis
GO:0043065	0.56	positive regulation of apoptotic process
GO:0034097	0.56	response to cytokine
GO:0032412	0.56	regulation of ion transmembrane transporter activity
GO:0010629	0.56	negative regulation of gene expression
GO:0010506	0.56	regulation of autophagy
GO:0006417	0.56	regulation of translation
GO:2000310	0.55	regulation of N-methyl-D-aspartate selective glutamate receptor activity
GO:1902042	0.55	negative regulation of extrinsic apoptotic signaling pathway via death domain receptors
GO:0071346	0.55	cellular response to interferon-gamma
GO:0043280	0.55	positive regulation of cysteine-type endopeptidase activity involved in apoptotic process
GO:0017148	0.55	negative regulation of translation
GO:0044710	0.51	single-organism metabolic process
GO:1901576	0.50	organic substance biosynthetic process
GO:0044249	0.50	cellular 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:0044464	1.00	cell part
GO:0044424	0.98	intracellular part
GO:0043226	0.84	organelle
GO:0043229	0.82	intracellular organelle
GO:0043227	0.79	membrane-bounded organelle
GO:0005737	0.78	cytoplasm
GO:0043231	0.76	intracellular membrane-bounded organelle
GO:0044444	0.68	cytoplasmic part
GO:0016020	0.66	membrane
GO:0005634	0.65	nucleus
GO:0044422	0.58	organelle part
GO:0044446	0.54	intracellular organelle part
GO:0005886	0.52	plasma membrane

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	0.072	3eqrB	0.451	2.31	0.215	0.481	2.7.10.2	NA
2	0.071	3f69B	0.457	2.95	0.242	0.504	2.7.11.1	NA
3	0.060	2owbA	0.466	2.41	0.225	0.498	2.7.11.21	211
4	0.060	2bujA	0.453	2.61	0.213	0.489	2.7.11.1	NA
5	0.060	2excX	0.428	3.21	0.239	0.477	2.7.11.24 2.7.1.37	212

	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	2wo6B	0.471	2.71	0.233	0.507	1.52	D15	complex1.pdb.gz	208,209,210,211,214,216,229,231,316,317,318,319,321,365,367,381
2	0.50	1vjyA	0.454	3.10	0.244	0.502	1.14	460	complex2.pdb.gz	208,229,231,251,262,313,315,316,317,318,321,367,381
3	0.46	1q99B	0.479	2.95	0.210	0.526	1.35	ANP	complex3.pdb.gz	210,211,212,213,214,216,229,231,262,316,318,381,384
4	0.27	3anqB	0.471	2.81	0.227	0.509	1.21	EHB	complex4.pdb.gz	213,229,231,315,316,318,367,380,381
5	0.27	2rkuA	0.464	2.47	0.225	0.498	1.25	R78	complex5.pdb.gz	206,207,208,210,216,218,230,262,315,316,317,318,319,321,367
6	0.22	2x7gA	0.463	3.07	0.204	0.511	1.05	PVB	complex6.pdb.gz	208,209,210,211,229,315,316,318,321,322,367
7	0.20	1q97B	0.474	2.97	0.209	0.521	0.81	ADN	complex7.pdb.gz	210,216,229,262,319
8	0.20	2x7oA	0.462	3.33	0.210	0.513	0.82	ZOP	complex8.pdb.gz	208,209,216,229,231,247,262,313,315,316,318,319,320,321,325,329,367

	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, Qiqige Wuyun, Yang Li, Quancheng Liu, Xiaogen Zhou, Yiheng Zhu, P. Lydia Freddolino, Yang Zhang. Integrating deep learning potentials with I-TASSER for single- and multi-domain protein structure prediction. Submitted. 2023.