D-I-TASSER P00519-D4

D-I-TASSER results for P00519-D4

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

Input Sequence in FASTA format

>P00519 (133 residues)
NTLAELVHHHSTVADGLITTLHYPAPKRNKPTVYGVSPNYDKWEMERTDITMKHKGGSGF
RSPHLWKKSSTLTSSRLATGEEEGGGSSSKRFLRSCSASCVPHGAKDTEWRLPHKEEAGK
GSALGTPAAAEPV

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| NTLAELVHHHSTVADGLITTLHYPAPKRNKPTVYGVSPNYDKWEMERTDITMKHKGGSGFRSPHLWKKSSTLTSSRLATGEEEGGGSSSKRFLRSCSASCVPHGAKDTEWRLPHKEEAGKGSALGTPAAAEPV
Prediction	CCHHHHHHHHHHCCCCCCSCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHSSSSSSSCCCCCSSSSSCCSSSSSSSSSSSCCCCCCCCCHHHHHHHHHHHHCCCCCCCCSSSCCCCCCCCCCCCCCCCCCCCCC
Confidence	9699999999863587722378646678998524557774314358677243233378531126856724331589986124768789999999999851446776640234431134654234787766889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| NTLAELVHHHSTVADGLITTLHYPAPKRNKPTVYGVSPNYDKWEMERTDITMKHKGGSGFRSPHLWKKSSTLTSSRLATGEEEGGGSSSKRFLRSCSASCVPHGAKDTEWRLPHKEEAGKGSALGTPAAAEPV
Prediction	8435411510364243012304410355742433424453551514462050253044221120214443613133033441576444363014303441334436534141346264444342545556658
	Values range from 0 (buried residue) to 8 (highly exposed residue)

Predicted Contact, Hydrogen and Distance Map Used in D-I-TASSER simulation

Contact Map

Distance Map

Hydrogen bond networks

D-I-TASSER simulation is guided by the consensus contact map (left figure), distance map (middle figure) and Hydrogen bond network (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.

Top 10 threading templates used by D-I-TASSER

Rank

PDB
hit

ID1

ID2

Cov

Norm.
Zscore

Download
alignment

                  20                  40                  60                  80                 100                 120

                   |                   |                   |                   |                   |                   |

SS
Seq

CCHHHHHHHHHHCCCCCCSCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHSSSSSSSCCCCCSSSSSCCSSSSSSSSSSSCCCCCCCCCHHHHHHHHHHHHCCCCCCCCSSSCCCCCCCCCCCCCCCCCCCCCC
NTLAELVHHHSTVADGLITTLHYPAPKRNKPTVYGVSPNYDKWEMERTDITMKHKGGSGFRSPHLWKKSSTLTSSRLATGEEEGGGSSSKRFLRSCSASCVPHGAKDTEWRLPHKEEAGKGSALGTPAAAEPV

6znpA

0.10

0.08

3.07

0.83

DEthreader

YLFPNPDMLHSAIPHYELFPAISLRSAS-DF-------ANLA-VQL-KVLEIKTKEKSRTSLHYGVTHTSAA-WLEIKTAEDI-GETLEQLLLGISNVLQHI-----P---MCDRNDVHVV-SQIKAA-YDHY

2fo0A

0.58

0.51

14.69

1.90

SPARKS-K

NTLAELVHHHSTVADGLITTLHYPAPKRNKPTVYGVSPNYDKWEMERTDITMKHKLGGGQYGEGVWKKYLTVAVKTLKEDTME-----VEEFLKEAAVMKEI----------KHPNLQLLGVCTREPPFYIIT

1zaoA

0.08

2.95

0.42

MapAlign

IGEEKARNILKYLSDLRVVQNRQKDYEGSTFTFIGLSLYSLHRLVRSGKVDIGKLMKESAVFNCYSEKFGECVVKFHKVGHTKVKEFLAIRSARNEFRALQKLQGLAV-PKVYAWEGNAVLMEL---------

2pziA

0.06

2.60

0.26

CEthreader

PVVPESKRFCWNCGRPVGRSGASEGWCPYCGSPYSFLPQLNPGDIVAGQYEVKGCIALGWIYLALDRNGRPVVLKGLV---HSGDAEAQAMAMAERQFLAEVVHPSIVQIFNFVEHDPVGYIVMEYVGGQSLK

4xi2A

0.23

0.20

6.14

1.19

MUSTER

STIPELINYHQHNSAGLISRLKYPVSKQNKNAPSTAGLGYGSWEIDPKDLTFLKELGTGQFKYGKWRGQYDVAIKMI-----REGSMSEDEFIEEAKVMMNLSEKLVQ----------LYGVCTKQ----RPI

2ozoA

0.19

0.17

5.57

1.29

HHsearch

DTLWQLVEYLKLKADGLIYCLKEACPNMDTSVFSDPELKDKKLFLKRDNLLIDIELGCGNFGQGVYRKQIDVAIKVLKQGTE---KADTEEMMREAQIMH----------QLDNPYIRLIGVCQAEALVMEMA

1qcfA

0.22

0.19

5.92

1.19

FFAS-3D

STLQELVDHYKKGNDGLCQKLSVPCMS----SKPQKPWEKDAWEIPRESLKLEKKLGAGQFGEVWM--ATYNKHTKVAVKTMKPGSMSVEAFLAEANVMKTLQHDKLVKL---------HAVVTKEP------

3c4wB

0.05

2.17

0.58

EigenThreader

LFQQFLRTRAAYLEPQAQLFCSFLSLYFLRFLQWKWLEAQPMGELD----FRVLGRGGFGEVFACQKATGACKKLNKKRLKKRKGYQGAMVEKKILAKVHSRFIVSLAYAFETK---TDLCLVMTIMRDLKPE

1oplA

0.58

0.51

14.69

2.17

CNFpred

NTLAELVHHHSTVADGLITTLHYPAPKRNKPTVYGVSPNYDKWEMERTDITMKHKLGGGEVYEGVWKKSLTVAVKTLKE-----DTMEVEEFLKEAAVMK----------EIKHPNLVLLGVCTREPPFYIIT

7b5cA

0.04

0.03

1.60

0.83

DEthreader

GVFYK--YQPIDLVRKYFVGFAWGYMLASIVGVFGLDNPTVFSVM------AIGVIYRITVNI-----FVSYPIVFKGFVGR----ECAGGCLMELCIQLS---------IIMQLQFVLFVASTSDFVFQV--

(a)	ID1 is the number of template residues identical to query divided by number of aligned residues.
(b)	ID2 is the number of template residues identical to query divided by query sequence length.
(c)	Cov is equal the number of aligned template residues divided by query sequence length.
(d)	Norm. Zscore is the normalized Z-score of the threading alignments. A Normalized Z-score >1 means a good alignment and is highlighted in bold.
(e)	Download alignment lists the threading program used to identify the template, and provide the 3D structure of aligned regions of threading templates (threading[1-10].pdb.gz).
(f)	Template residues identical to query sequence are highlighted in color.

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.4476

(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	3bkbA	0.56	3.61	0.123	0.774	model1_3bkbA.pdb.gz
2	6ty3A	0.52	3.06	0.078	0.699	model1_6ty3A.pdb.gz
3	3ky2A1	0.51	2.96	0.116	0.662	model1_3ky2A1.pdb.gz
4	2fo0A	0.50	3.37	0.261	0.662	model1_2fo0A.pdb.gz
5	2x2kA1	0.50	2.75	0.130	0.617	model1_2x2kA1.pdb.gz
6	6j5tH	0.50	3.58	0.073	0.707	model1_6j5tH.pdb.gz
7	3ewhA1	0.49	2.57	0.152	0.609	model1_3ewhA1.pdb.gz
8	5ek7A	0.49	2.83	0.101	0.609	model1_5ek7A.pdb.gz
9	7bttA	0.48	3.19	0.137	0.609	model1_7bttA.pdb.gz
10	5k5xA	0.48	3.32	0.094	0.632	model1_5k5xA.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	0.97	protein kinase activity
GO:0004713	0.94	protein tyrosine kinase activity
GO:0005102	0.92	receptor binding
GO:0004715	0.91	non-membrane spanning protein tyrosine kinase 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:0050794	0.99	regulation of cellular process
GO:0044699	0.99	single-organism process
GO:0009987	0.99	cellular process
GO:0044763	0.98	single-organism cellular process
GO:0006468	0.98	protein phosphorylation
GO:0050896	0.97	response to stimulus
GO:0046777	0.97	protein autophosphorylation
GO:0018212	0.96	peptidyl-tyrosine modification
GO:0042127	0.95	regulation of cell proliferation
GO:0007169	0.95	transmembrane receptor protein tyrosine kinase signaling pathway
GO:0006950	0.95	response to stress
GO:0038083	0.93	peptidyl-tyrosine autophosphorylation
GO:0002376	0.93	immune system process
GO:0045087	0.92	innate immune response
GO:0048869	0.90	cellular developmental process
GO:0030154	0.86	cell differentiation

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:0044459	1.00	plasma membrane part
GO:0016020	1.00	membrane
GO:0044424	0.98	intracellular part
GO:0031234	0.90	extrinsic component of cytoplasmic side of plasma membrane
GO:0005886	0.82	plasma membrane
GO:0043226	0.63	organelle
GO:0016021	0.63	integral component of membrane
GO:0043227	0.62	membrane-bounded organelle
GO:0044444	0.59	cytoplasmic part
GO:0043229	0.58	intracellular organelle
GO:0043231	0.57	intracellular membrane-bounded organelle
GO:0005887	0.57	integral component of plasma membrane
GO:0005737	0.52	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	0.060	2helA	0.462	2.55	0.141	0.564	2.7.10.1	NA
2	0.060	1k9aB	0.469	3.75	0.077	0.677	2.7.10.2 2.7.1.112	NA
3	0.060	3fxxA	0.481	2.99	0.149	0.617	2.7.10.1	NA
4	0.060	3gvuA	0.476	2.91	0.292	0.602	2.7.10.2	NA
5	0.060	2hz0B	0.455	2.53	0.325	0.556	2.7.10.2	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	0.25	1m52A	0.477	2.47	0.338	0.579	0.49	P17	complex1.pdb.gz	56,57,61,73,74,75,95,99
2	0.12	2g1tA	0.418	3.34	0.291	0.549	0.41	112	complex2.pdb.gz	56,58,59,61,73,75
3	0.07	2pwlB	0.501	2.62	0.174	0.617	0.50	ABG	complex3.pdb.gz	55,56,58,62,73,75,133
4	0.06	3bkbA	0.564	3.61	0.123	0.774	0.41	STU	complex4.pdb.gz	56,57,58,60,74,76,95
5	0.04	2g2iB	0.471	2.29	0.329	0.564	0.44	III	complex5.pdb.gz	59,60,79,81

	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.