D-I-TASSER Q86YV6

D-I-TASSER results for Q86YV6

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

Summary of the Protein

Uniprot ID: Q86YV6
Protein Name: Myosin light chain kinase family member 4
Gene Name: MYLK4

Input Sequence in FASTA format

>Q86YV6 (388 residues)
MLKVKRLEEFNTCYNSNQLEKMAFFQCREEVEKVKCFLEKNSGDQDSRSGHNEAKEVWSN
ADLTERMPVKSKRTSALAVDIPAPPAPFDHRIVTAKQGAVNSFYTVSKTEILGGGRFGQV
HKCEETATGLKLAAKIIKTRGMKDKEEVKNEISVMNQLDHANLIQLYDAFESKNDIVLVM
EYVDGGELFDRIIDESYNLTELDTILFMKQICEGIRHMHQMYILHLDLKPENILCVNRDA
KQIKIIDFGLARRYKPREKLKVNFGTPEFLAPEVVNYDFVSFPTDMWSVGVIAYMLLSGL
SPFLGDNDAETLNNILACRWDLEDEEFQDISEEAKEFISKLLIKEKSWRISASEALKHPW
LSDHKLHSRLNAQKKKNRGSDAQDFVTK

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	Q86YV6-D1	1-182	182		MLKVKRLEEFNTCYNSNQLEKMAFFQCREEVEKVKCFLEKNSGDQDSRSGHNEAKEVWSNADLTERMPVKSKRTSALAVDIPAPPAPFDHRIVTAKQGAVNSFYTVSKTEILGGGRFGQVHKCEETATGLKLAAKIIKTRGMKDKEEVKNEISVMNQLDHANLIQLYDAFESKNDIVLVMEY
2	Q86YV6-D2	183-388	206		VDGGELFDRIIDESYNLTELDTILFMKQICEGIRHMHQMYILHLDLKPENILCVNRDAKQIKIIDFGLARRYKPREKLKVNFGTPEFLAPEVVNYDFVSFPTDMWSVGVIAYMLLSGLSPFLGDNDAETLNNILACRWDLEDEEFQDISEEAKEFISKLLIKEKSWRISASEALKHPWLSDHKLHSRLNAQKKKNRGSDAQDFVTK

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.79

(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	3c4wB	0.68	3.85	0.209	0.794	model1_3c4wB.pdb.gz
2	6pjxA	0.68	3.75	0.213	0.781	model1_6pjxA.pdb.gz
3	3q5iA	0.68	2.10	0.345	0.714	model1_3q5iA.pdb.gz
4	2acxA	0.68	3.47	0.208	0.773	model1_2acxA.pdb.gz
5	4yhjA	0.68	3.85	0.202	0.786	model1_4yhjA.pdb.gz
6	4myiA	0.68	3.53	0.210	0.765	model1_4myiA.pdb.gz
7	3lijA	0.67	2.08	0.328	0.711	model1_3lijA.pdb.gz
8	6c0tA	0.67	3.08	0.258	0.750	model1_6c0tA.pdb.gz
9	3hx4A	0.67	2.18	0.336	0.714	model1_3hx4A.pdb.gz
10	1cdkA	0.67	2.91	0.231	0.737	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:1901363	0.90	heterocyclic compound binding
GO:0097159	0.90	organic cyclic compound binding
GO:0004674	0.89	protein serine/threonine kinase activity
GO:0005524	0.86	ATP binding
GO:0005516	0.76	calmodulin binding
GO:0042802	0.64	identical protein binding
GO:0005525	0.64	GTP binding
GO:0017075	0.63	syntaxin-1 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	0.95	cellular macromolecule metabolic process
GO:0044238	0.95	primary metabolic process
GO:0065007	0.93	biological regulation
GO:0050789	0.93	regulation of biological process
GO:0050794	0.92	regulation of cellular process
GO:0006468	0.91	protein phosphorylation
GO:0007165	0.86	signal transduction
GO:0035556	0.79	intracellular signal transduction
GO:0050896	0.73	response to stimulus
GO:0048518	0.72	positive regulation of biological process
GO:0080090	0.71	regulation of primary metabolic process
GO:0046777	0.71	protein autophosphorylation
GO:0031323	0.71	regulation of cellular metabolic process
GO:0060255	0.70	regulation of macromolecule metabolic process
GO:0048522	0.70	positive regulation of cellular process
GO:2000112	0.68	regulation of cellular macromolecule biosynthetic process
GO:0051171	0.68	regulation of nitrogen compound metabolic process
GO:0048583	0.68	regulation of response to stimulus
GO:0048523	0.68	negative regulation of cellular process
GO:0031325	0.68	positive regulation of cellular metabolic process
GO:0010646	0.68	regulation of cell communication
GO:0010468	0.68	regulation of gene expression
GO:0051246	0.67	regulation of protein metabolic process
GO:0010604	0.67	positive regulation of macromolecule metabolic process
GO:0009966	0.67	regulation of signal transduction
GO:0065009	0.66	regulation of molecular function
GO:0051716	0.66	cellular response to stimulus
GO:0042981	0.66	regulation of apoptotic process
GO:0042221	0.66	response to chemical
GO:0032879	0.66	regulation of localization
GO:0032270	0.66	positive regulation of cellular protein metabolic process
GO:0070887	0.65	cellular response to chemical stimulus
GO:0051049	0.65	regulation of transport
GO:0043085	0.65	positive regulation of catalytic activity
GO:0043066	0.65	negative regulation of apoptotic process
GO:0010033	0.65	response to organic substance
GO:0071310	0.64	cellular response to organic substance
GO:0051336	0.64	regulation of hydrolase activity
GO:0043269	0.64	regulation of ion transport
GO:0043065	0.64	positive regulation of apoptotic process
GO:0032269	0.64	negative regulation of cellular protein metabolic process
GO:0031327	0.64	negative regulation of cellular biosynthetic process
GO:0009968	0.64	negative regulation of signal transduction
GO:2000310	0.63	regulation of N-methyl-D-aspartate selective glutamate receptor activity
GO:1902042	0.63	negative regulation of extrinsic apoptotic signaling pathway via death domain receptors
GO:0071346	0.63	cellular response to interferon-gamma
GO:0043280	0.63	positive regulation of cysteine-type endopeptidase activity involved in apoptotic process
GO:0017148	0.63	negative regulation of translation
GO:0010506	0.63	regulation of autophagy
GO:0044699	0.60	single-organism process
GO:1901576	0.59	organic substance biosynthetic process
GO:0044249	0.58	cellular biosynthetic process
GO:0009059	0.58	macromolecule biosynthetic process
GO:0034645	0.57	cellular macromolecule biosynthetic process
GO:0044763	0.53	single-organism cellular 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	0.95	intracellular part
GO:0043226	0.75	organelle
GO:0043229	0.74	intracellular organelle
GO:0043227	0.72	membrane-bounded organelle
GO:0043231	0.71	intracellular membrane-bounded organelle
GO:0005634	0.68	nucleus
GO:0005737	0.53	cytoplasm

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	0.566	2x4fA	0.653	2.76	0.878	0.719	2.7.11.1	227,229,231,246,250,268,270,288,295
2	0.369	3lm0A	0.639	2.10	0.386	0.683	2.7.11.1	228
3	0.359	2bfyB	0.627	2.41	0.232	0.683	2.7.11.1	112,135,186,234
4	0.249	3db8A	0.595	2.28	0.236	0.642	2.7.11.21	163
5	0.137	1yhvA	0.660	2.56	0.248	0.722	2.7.11.1 2.7.1.37	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	0.41	3hx4A	0.673	2.18	0.336	0.714	0.88	ANP	complex1.pdb.gz	112,120,133,135,181,183,234
2	0.40	3l9mA	0.673	2.77	0.238	0.737	1.28	L9M	complex2.pdb.gz	112,117,120,133,135,164,180,181,183,187,231,232,234,246,247
3	0.37	3nx8A	0.670	2.69	0.241	0.735	1.42	IPH	complex3.pdb.gz	113,114,115,120,187,231,232,246
4	0.35	2f7xE	0.670	2.69	0.241	0.735	1.07	4EA	complex4.pdb.gz	114,115,118,119,120,133,135,137,181,182,183,234,246,247
5	0.34	2uvzA	0.673	2.97	0.235	0.742	1.16	III	complex5.pdb.gz	117,187,189,190,193,229,230,231,250,263,264,265,266,267,268,295,299,300,301,304,305,306,311,321
6	0.34	1szmB	0.646	3.01	0.208	0.729	1.27	BI4	complex6.pdb.gz	112,114,120,133,135,180,181,182,183,184,185
7	0.33	1xh6A	0.669	2.83	0.238	0.737	1.06	R94	complex7.pdb.gz	113,114,115,116,118,119,120,133,135,144,151,180,181,182,183,187,231,232,234,246,247,249,250
8	0.22	3tkuA	0.664	3.10	0.232	0.747	0.92	M77	complex8.pdb.gz	112,113,120,181,182,183,231,232,234
9	0.21	2uvxA	0.672	2.65	0.237	0.735	1.04	GVH	complex9.pdb.gz	112,133,164,180,181,182,183,234,246
10	0.21	2gnfA	0.670	2.70	0.230	0.735	0.89	Y27	complex10.pdb.gz	112,120,181,182,183,233,247

	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.