D-I-TASSER P78352-D4

D-I-TASSER results for P78352-D4

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

Input Sequence in FASTA format

>P78352 (200 residues)
TVTQMEVHYARPIIILGPTKDRANDDLLSEFPDKFGSCVPHTTRPKREYEIDGRDYHFVS
SREKMEKDIQAHKFIEAGQYNSHLYGTSVQSVREVAEQGKHCILDVSANAVRRLQAAHLH
PIAIFIRPRSLENVLEINKRITEEQARKAFDRATKLEQEFTECFSAIVEGDSFEEIYHKV
KRVIEDLSGPYIWVPARERL

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| TVTQMEVHYARPIIILGPTKDRANDDLLSEFPDKFGSCVPHTTRPKREYEIDGRDYHFVSSREKMEKDIQAHKFIEAGQYNSHLYGTSVQSVREVAEQGKHCILDVSANAVRRLQAAHLHPIAIFIRPRSLENVLEINKRITEEQARKAFDRATKLEQEFTECFSAIVEGDSFEEIYHKVKRVIEDLSGPYIWVPARERL
Prediction	CCCCCCCCCCCSSSSSCCCHHHHHHHHHHHCCCCSSSSSCCCCCCCCCCCCCCCCCSSCCCHHHHHHHHHHCCCSSSSSSCCCCCCCCHHHHHHHHHHCCCSSSSSCHHHHHHHHHHCCCCSSSSSCCCCHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCCCCSSSSCCCHHHHHHHHHHHHHHHHCCCCSCCCCCCC
Confidence	98778899997699987992699999998599958865424689999998799643647929999999990994889998694577889999999991991999828999999999589958999659999999986399999999999999999999855639999978879999999999999961898521575779
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| TVTQMEVHYARPIIILGPTKDRANDDLLSEFPDKFGSCVPHTTRPKREYEIDGRDYHFVSSREKMEKDIQAHKFIEAGQYNSHLYGTSVQSVREVAEQGKHCILDVSANAVRRLQAAHLHPIAIFIRPRSLENVLEINKRITEEQARKAFDRATKLEQEFTECFSAIVEGDSFEEIYHKVKRVIEDLSGPYIWVPARERL
Prediction	84562657341000000023430143016525741100000012643761641420210345540461177541021022330200022630451175421000002350043027423400000020132530374375544630450264045203612730110002430450063035005615753101226378
	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 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.

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                 140                 160                 180                 200

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCSSSSSCCCHHHHHHHHHHHCCCCSSSSSCCCCCCCCCCCCCCCCCSSCCCHHHHHHHHHHCCCSSSSSSCCCCCCCCHHHHHHHHHHCCCSSSSSCHHHHHHHHHHCCCCSSSSSCCCCHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCCCCSSSSCCCHHHHHHHHHHHHHHHHCCCCSCCCCCCC
TVTQMEVHYARPIIILGPTKDRANDDLLSEFPDKFGSCVPHTTRPKREYEIDGRDYHFVSSREKMEKDIQAHKFIEAGQYNSHLYGTSVQSVREVAEQGKHCILDVSANAVRRLQAAHLHPIAIFIRPRSLENVLEINKRITEEQARKAFDRATKLEQEFTECFSAIVEGDSFEEIYHKVKRVIEDLSGPYIWVPARERL

7luyA

0.20

0.18

5.92

1.33

DEthreader

-----NQRRGFLFILSSSGKSTLSRLLLK-DG-KLELSISMTTRQKRPSEVDGLHYHFI-SKKEFKRKRDGNEFIEWAEVHGNYYGTLRESVENVLSTGRDMLFDIDYQGTKQLQKKMPDTVSVFILPPSMKELISRLYADSQDIINLRLKNARTEMQHWR-SYDYVIINENLNQSVSLIKSIYLAETVKRER-------

1kjwA

1.00

28.00

2.08

SPARKS-K

TVTQMEVHYARPIIILGPTKDRANDDLLSEFPDKFGSCVPHTTRPKREYEIDGRDYHFVSSREKMEKDIQAHKFIEAGQYNSHLYGTSVQSVREVAEQGKHCILDVSANAVRRLQAAHLHPIAIFIRPRSLENVLEINKRITEEQARKAFDRATKLEQEFTECFSAIVEGDSFEEIYHKVKRVIEDLSGPYIWVPARERL

1kjwA

1.00

0.96

27.02

1.03

MapAlign

-VTQMEVHYARPIIILGPTKDRANDDLLSEFPDKFGSCVPHTTRPKREYEIDGRDYHFVSSREKMEKDIQAHKFIEAGQYNSHLYGTSVQSVREVAEQGKHCILDVSANAVRRLQAAHLHPIAIFIRPRSLENVLEINKRITEEQARKAFDRATKLEQEFTECFSAIVEGDSFEEIYHKVKRVIEDLSGPYIWV------

1kjwA

1.00

28.00

0.82

CEthreader

TVTQMEVHYARPIIILGPTKDRANDDLLSEFPDKFGSCVPHTTRPKREYEIDGRDYHFVSSREKMEKDIQAHKFIEAGQYNSHLYGTSVQSVREVAEQGKHCILDVSANAVRRLQAAHLHPIAIFIRPRSLENVLEINKRITEEQARKAFDRATKLEQEFTECFSAIVEGDSFEEIYHKVKRVIEDLSGPYIWVPARERL

1kjwA

1.00

28.00

2.09

MUSTER

TVTQMEVHYARPIIILGPTKDRANDDLLSEFPDKFGSCVPHTTRPKREYEIDGRDYHFVSSREKMEKDIQAHKFIEAGQYNSHLYGTSVQSVREVAEQGKHCILDVSANAVRRLQAAHLHPIAIFIRPRSLENVLEINKRITEEQARKAFDRATKLEQEFTECFSAIVEGDSFEEIYHKVKRVIEDLSGPYIWVPARERL

1kjwA

1.00

28.00

2.69

HHsearch

TVTQMEVHYARPIIILGPTKDRANDDLLSEFPDKFGSCVPHTTRPKREYEIDGRDYHFVSSREKMEKDIQAHKFIEAGQYNSHLYGTSVQSVREVAEQGKHCILDVSANAVRRLQAAHLHPIAIFIRPRSLENVLEINKRITEEQARKAFDRATKLEQEFTECFSAIVEGDSFEEIYHKVKRVIEDLSGPYIWVPARERL

3tvtA

0.69

0.68

19.20

2.63

FFAS-3D

-VQRLSINYTRPVIILGPLKDRINDDLISEYPDKFGSCVPHTTRPKREYEVDGRDYHFVSSREQMERDIQNHLFIEAGQYNDNLYGTSVASVREVAEKGKHCILDVSGNAIKRLQVAQLYPVAVFIKPKSVDSVMEMNRRMTEEQAKKTYERAIKMEQEFGEYFTGVVQGDTIEEIYSKVKSMIWSQSGPTIWVPS----

4wsiA

0.35

0.34

10.01

1.07

EigenThreader

TYEEQPANRKRPIILIGPQQNELRQRLMNKEKDRFASAVPHTTRSRRDQEVAGRDYHFVS-RQAFEADIAAGKFIEHGEFEKNLYGTSIDSVRQVINSGKICLLSLRTQSLKTLRNSDLKPYIIFIAPPSQERLRALL---ELREIIEKTREMEQNN---GHYFDTAIVNSDLDKAYQELLRLINKLDTEPQWVPSTWLR

5yprA

1.00

0.98

27.58

2.17

CNFpred

TVTQMEVHYARPIIILGPTKDRANDDLLSEFPDKFGSCVPHTTRPKREYEIDGRDYHFVSSREKMEKDIQAHKFIEAGQYNSHLYGTSVQSVREVAEQGKHCILDVSANAVRRLQAAHLHPIAIFIRPRSLENVLEINKRITEEQARKAFDRATKLEQEFTECFSAIVEGDSFEEIYHKVKRVIEDLSGPYIWVPAR---

3tr0A

0.22

0.20

6.30

1.33

DEthreader

-------NKANLFIISASGKTSLVRALVKAL-AEIKISISHTTRPKRPGDQEGVDYFFID-ETRFQA-VKEGAFLEHATIYERHYGTEKDWVLRQLKAGRDVLLEIDWQGARQIRELFPPALSIFILPPSIEALRERLKRDDTAIIEQRLALAREE-AHYK-EFDYLVVNDNFDQAVQNLIHIISAERLQDV--------

(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	0.8058

(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	2xkxA	0.96	1.14	0.995	1.000	model1_2xkxA.pdb.gz
2	1kjwA	0.96	1.14	1.000	1.000	model1_1kjwA.pdb.gz
3	3tvtA	0.94	1.16	0.689	0.980	model1_3tvtA.pdb.gz
4	4wsiA	0.84	2.30	0.337	0.955	model1_4wsiA.pdb.gz
5	1kgdA	0.78	2.07	0.262	0.860	model1_1kgdA.pdb.gz
6	3neyA	0.77	2.60	0.266	0.885	model1_3neyA.pdb.gz
7	1s96A	0.74	2.66	0.215	0.885	model1_1s96A.pdb.gz
8	1z8fA	0.71	2.95	0.217	0.875	model1_1z8fA.pdb.gz
9	3lh5A	0.70	2.61	0.253	0.790	model1_3lh5A.pdb.gz
10	1z6gA	0.66	3.50	0.249	0.860	model1_1z6gA.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	0.86	catalytic activity
GO:0016740	0.85	transferase activity
GO:0016301	0.84	kinase activity
GO:0004385	0.83	guanylate kinase activity
GO:0005102	0.69	receptor binding
GO:0035254	0.66	glutamate receptor binding
GO:0035255	0.65	ionotropic glutamate receptor 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:0044699	0.97	single-organism process
GO:0009987	0.96	cellular process
GO:0044763	0.94	single-organism cellular process
GO:0016043	0.86	cellular component organization
GO:0032502	0.83	developmental process
GO:0051179	0.80	localization
GO:0048856	0.77	anatomical structure development
GO:0008104	0.76	protein localization
GO:0007163	0.74	establishment or maintenance of cell polarity
GO:0045197	0.70	establishment or maintenance of epithelial cell apical/basal polarity
GO:0007267	0.70	cell-cell signaling
GO:0051641	0.67	cellular localization
GO:0034613	0.66	cellular protein localization
GO:1902578	0.65	single-organism localization
GO:1902580	0.63	single-organism cellular localization
GO:0048731	0.63	system development
GO:0044802	0.63	single-organism membrane organization
GO:0097120	0.62	receptor localization to synapse
GO:0043113	0.62	receptor clustering
GO:0007268	0.61	chemical synaptic transmission
GO:0007399	0.58	nervous system development
GO:0065007	0.57	biological regulation
GO:0050789	0.53	regulation of biological 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	0.98	cell part
GO:0044424	0.92	intracellular part
GO:0016020	0.85	membrane
GO:0044425	0.83	membrane part
GO:0044459	0.81	plasma membrane part
GO:0043226	0.78	organelle
GO:0043229	0.76	intracellular organelle
GO:0098590	0.75	plasma membrane region
GO:0032991	0.72	macromolecular complex
GO:0097458	0.71	neuron part
GO:0016323	0.68	basolateral plasma membrane
GO:0043234	0.67	protein complex
GO:0044456	0.66	synapse part
GO:0098796	0.65	membrane protein complex
GO:0098797	0.64	plasma membrane protein complex
GO:0097060	0.64	synaptic membrane
GO:0043232	0.64	intracellular non-membrane-bounded organelle
GO:0008328	0.63	ionotropic glutamate receptor complex
GO:0045211	0.62	postsynaptic membrane
GO:0014069	0.62	postsynaptic density

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	0.176	1z6gA	0.658	3.50	0.249	0.860	2.7.4.8	55
2	0.175	1gkyA	0.654	3.80	0.291	0.880	2.7.4.8	17,85,105
3	0.070	3lncA	0.599	3.84	0.142	0.800	2.7.4.8	168
4	0.068	2j41D	0.598	3.57	0.195	0.800	2.7.4.8	20,80,85
5	0.067	2ancF	0.546	2.76	0.165	0.655	2.7.4.8	17

	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	0.81	1jxmA	0.968	1.00	1.000	1.000	1.36	5GP	complex1.pdb.gz	56,80,85,105
2	0.73	3uatA	0.939	1.24	0.751	0.985	1.85	III	complex2.pdb.gz	40,44,47,50,54,55,56,72,76,77,78,79,80,85,113
3	0.03	1e98A	0.588	4.00	0.126	0.775	0.97	ADP	complex3.pdb.gz	19,20,21,22,171,172,173

	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.