D-I-TASSER Q9NR20

D-I-TASSER results for Q9NR20

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

Summary of the Protein

Uniprot ID: Q9NR20
Protein Name: Dual specificity tyrosine-phosphorylation-regulated kinase 4
Gene Name: DYRK4

Input Sequence in FASTA format

>Q9NR20 (520 residues)
MPASELKASEIPFHPSIKTQDPKAEEKSPKKQKVTLTAAEALKLFKNQLSPYEQSEILGY
AELWFLGLEAKKLDTAPEKFSKTSFDDEHGFYLKVLHDHIAYRYEVLETIGKGSFGQVAK
CLDHKNNELVALKIIRNKKRFHQQALMELKILEALRKKDKDNTYNVVHMKDFFYFRNHFC
ITFELLGINLYELMKNNNFQGFSLSIVRRFTLSVLKCLQMLSVEKIIHCDLKPENIVLYQ
KGQASVKVIDFGSSCYEHQKVYTYIQSRFYRSPEVILGHPYDVAIDMWSLGCITAELYTG
YPLFPGENEVEQLACIMEVLGLPPAGFIQTASRRQTFFDSKGFPKNITNNRGKKRYPDSK
DLTMVLKTYDTSFLDFLRRCLVWEPSLRMTPDQALKHAWIHQSRNLKPQPRPQTLRKSNS
FFPSETRKDKVQGCHHSSRKADEITKETTEKTKDSPTKHVQHSGDQQDCLQHGADTVQLP
QLVDAPKKSEAAVGAEVSMTSPGQSKNFSLKNTNVLPPIV

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	Q9NR20-D1	1-185	185		MPASELKASEIPFHPSIKTQDPKAEEKSPKKQKVTLTAAEALKLFKNQLSPYEQSEILGYAELWFLGLEAKKLDTAPEKFSKTSFDDEHGFYLKVLHDHIAYRYEVLETIGKGSFGQVAKCLDHKNNELVALKIIRNKKRFHQQALMELKILEALRKKDKDNTYNVVHMKDFFYFRNHFCITFEL
2	Q9NR20-D2	186-413	228		LGINLYELMKNNNFQGFSLSIVRRFTLSVLKCLQMLSVEKIIHCDLKPENIVLYQKGQASVKVIDFGSSCYEHQKVYTYIQSRFYRSPEVILGHPYDVAIDMWSLGCITAELYTGYPLFPGENEVEQLACIMEVLGLPPAGFIQTASRRQTFFDSKGFPKNITNNRGKKRYPDSKDLTMVLKTYDTSFLDFLRRCLVWEPSLRMTPDQALKHAWIHQSRNLKPQPRPQ
3	Q9NR20-D3	414-520	107		TLRKSNSFFPSETRKDKVQGCHHSSRKADEITKETTEKTKDSPTKHVQHSGDQQDCLQHGADTVQLPQLVDAPKKSEAAVGAEVSMTSPGQSKNFSLKNTNVLPPIV

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.63

(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	3kvwA	0.73	1.40	0.530	0.748	model1_3kvwA.pdb.gz
2	2wu6A	0.60	2.05	0.343	0.633	model1_2wu6A.pdb.gz
3	2vx3A	0.60	1.64	0.447	0.614	model1_2vx3A.pdb.gz
4	1z57A	0.58	1.95	0.332	0.608	model1_1z57A.pdb.gz
5	1q99B	0.57	2.63	0.283	0.617	model1_1q99B.pdb.gz
6	3lltA	0.57	2.03	0.314	0.598	model1_3lltA.pdb.gz
7	6q2aA	0.57	2.49	0.256	0.606	model1_6q2aA.pdb.gz
8	4ianA	0.56	2.11	0.330	0.590	model1_4ianA.pdb.gz
9	5z33A	0.56	2.95	0.241	0.612	model1_5z33A.pdb.gz
10	3i4bA	0.56	2.81	0.281	0.604	model1_3i4bA.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:0004672	0.99	protein kinase activity
GO:0004674	0.94	protein serine/threonine kinase activity
GO:1901363	0.93	heterocyclic compound binding
GO:0097159	0.93	organic cyclic compound binding
GO:0035639	0.89	purine ribonucleoside triphosphate binding
GO:0032555	0.89	purine ribonucleotide binding
GO:0032550	0.89	purine ribonucleoside binding
GO:0005524	0.88	ATP binding
GO:0005516	0.71	calmodulin binding
GO:0042802	0.67	identical protein binding
GO:0004712	0.60	protein serine/threonine/tyrosine kinase activity
GO:0046872	0.56	metal ion binding
GO:0005525	0.54	GTP binding
GO:0017075	0.51	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	0.96	cellular macromolecule metabolic process
GO:0044238	0.96	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	0.92	protein phosphorylation
GO:0007165	0.79	signal transduction
GO:0035556	0.74	intracellular signal transduction
GO:0018193	0.74	peptidyl-amino acid modification
GO:0046777	0.73	protein autophosphorylation
GO:0048518	0.63	positive regulation of biological process
GO:0019222	0.63	regulation of metabolic process
GO:0080090	0.62	regulation of primary metabolic process
GO:0060255	0.62	regulation of macromolecule metabolic process
GO:0031323	0.62	regulation of cellular metabolic process
GO:0048522	0.61	positive regulation of cellular process
GO:0050896	0.60	response to stimulus
GO:0018108	0.60	peptidyl-tyrosine phosphorylation
GO:2000112	0.58	regulation of cellular macromolecule biosynthetic process
GO:0051171	0.58	regulation of nitrogen compound metabolic process
GO:0048583	0.58	regulation of response to stimulus
GO:0048519	0.58	negative regulation of biological process
GO:0010604	0.58	positive regulation of macromolecule metabolic process
GO:0010468	0.58	regulation of gene expression
GO:0048523	0.57	negative regulation of cellular process
GO:0031325	0.57	positive regulation of cellular metabolic process
GO:0009966	0.57	regulation of signal transduction
GO:0051716	0.56	cellular response to stimulus
GO:0032268	0.56	regulation of cellular protein metabolic process
GO:0018105	0.56	peptidyl-serine phosphorylation
GO:0065009	0.55	regulation of molecular function
GO:0042981	0.55	regulation of apoptotic process
GO:0042221	0.55	response to chemical
GO:0032879	0.55	regulation of localization
GO:0051049	0.54	regulation of transport
GO:0050790	0.54	regulation of catalytic activity
GO:0044093	0.54	positive regulation of molecular function
GO:0032270	0.54	positive regulation of cellular protein metabolic process
GO:0010033	0.54	response to organic substance
GO:0071310	0.53	cellular response to organic substance
GO:0048585	0.53	negative regulation of response to stimulus
GO:0043085	0.53	positive regulation of catalytic activity
GO:0043066	0.53	negative regulation of apoptotic process
GO:0031324	0.53	negative regulation of cellular metabolic process
GO:0023057	0.53	negative regulation of signaling
GO:0010648	0.53	negative regulation of cell communication
GO:0010605	0.53	negative regulation of macromolecule 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:0043269	0.52	regulation of ion transport
GO:0043065	0.52	positive regulation of apoptotic process
GO:0032269	0.52	negative regulation of cellular protein metabolic process
GO:0010629	0.52	negative regulation of gene expression
GO:0009968	0.52	negative regulation of signal transduction
GO:0006417	0.52	regulation of translation
GO:2000310	0.51	regulation of N-methyl-D-aspartate selective glutamate receptor activity
GO:1902042	0.51	negative regulation of extrinsic apoptotic signaling pathway via death domain receptors
GO:0071346	0.51	cellular response to interferon-gamma
GO:0043280	0.51	positive regulation of cysteine-type endopeptidase activity involved in apoptotic process
GO:0017148	0.51	negative regulation of translation
GO:0010506	0.51	regulation of autophagy

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	0.97	intracellular part
GO:0043229	0.79	intracellular organelle
GO:0043227	0.77	membrane-bounded organelle
GO:0043231	0.76	intracellular membrane-bounded organelle
GO:0005634	0.73	nucleus
GO:0005737	0.66	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	0.326	3mtlA	0.495	2.83	0.264	0.538	2.7.11.22	111,113,118,231,251,271,285
2	0.167	3lm0A	0.466	2.54	0.233	0.500	2.7.11.1	NA
3	0.124	2vx3A	0.598	1.65	0.450	0.615	2.7.12.1	NA
4	0.117	1z57A	0.583	1.95	0.332	0.608	2.7.12.1	NA
5	0.096	1vywA	0.522	2.09	0.284	0.550	2.7.11.22 2.7.1.37	112

	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	0.78	3kvwA	0.732	1.40	0.540	0.752	1.60	IRB	complex1.pdb.gz	110,118,131,133,183,185,186,187,237,249,250
2	0.75	2wo6B	0.591	1.50	0.459	0.608	1.62	D15	complex2.pdb.gz	110,111,112,113,116,118,131,133,184,185,186,187,188,235,237,250
3	0.53	3anrA	0.593	1.67	0.458	0.614	1.20	HRM	complex3.pdb.gz	110,131,133,183,184,186,250,251
4	0.38	1q99B	0.571	2.63	0.283	0.617	1.38	ANP	complex4.pdb.gz	112,113,114,115,116,118,131,133,167,184,186,250,253
5	0.35	3f88A	0.542	3.00	0.276	0.592	1.31	2HT	complex5.pdb.gz	111,115,118,234,235,250
6	0.32	1q3wB	0.538	3.06	0.279	0.589	0.99	ATU	complex6.pdb.gz	133,184,186,188,237,249,250
7	0.23	2wo6B	0.591	1.50	0.459	0.608	1.44	III	complex7.pdb.gz	115,140,141,191,230,232,233,234,264,266,267,268,269,270,271,296
8	0.05	1q5k0	0.542	3.06	0.279	0.592	1.18	III	complex8.pdb.gz	114,115,147,262,264,265,266,267,268,276,277,307,308,309,310,311,313,314,338,343

	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.