D-I-TASSER Q96BJ3-D2

D-I-TASSER results for Q96BJ3-D2

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

Input Sequence in FASTA format

>Q96BJ3 (192 residues)
VPLRRILAPGEEENLEFEEDEEEGGAGAGSPDSFPARVPGTLLPRLPSEPGMTLLTIRIE
KIGLKDAGQCIDPYITVSVKDLNGIDLTPVQDTPVASRKEDTYVHFNVDIELQKHVEKLT
KGAAIFFEFKHYKPKKRFTSTKCFAFMEMDEIKPGPIVIELYKKPTDFKRKKLQLLTKKP
LYLHLHQTLHKE

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| VPLRRILAPGEEENLEFEEDEEEGGAGAGSPDSFPARVPGTLLPRLPSEPGMTLLTIRIEKIGLKDAGQCIDPYITVSVKDLNGIDLTPVQDTPVASRKEDTYVHFNVDIELQKHVEKLTKGAAIFFEFKHYKPKKRFTSTKCFAFMEMDEIKPGPIVIELYKKPTDFKRKKLQLLTKKPLYLHLHQTLHKE
Prediction	CCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSSSSSSSSCCHHHCCCCSSSSSSSCCCCCSCCCCCCCCCCCCCCCCSSSSCCSSSSCCCHHHCCCCCSSSSSSSSCCCCCCCSSSSSSSSSSCCCCCCCCSSSSSSCCCCCHHHHHHHHHCCCCCSSSSSSSSSCC
Confidence	973323379996320233543126788888656788899988888766899607999998998568343379759999985999745654458986434698899840699726578789981999999842676662026777877500277884355520489883576665511698438999999659
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| VPLRRILAPGEEENLEFEEDEEEGGAGAGSPDSFPARVPGTLLPRLPSEPGMTLLTIRIEKIGLKDAGQCIDPYITVSVKDLNGIDLTPVQDTPVASRKEDTYVHFNVDIELQKHVEKLTKGAAIFFEFKHYKPKKRFTSTKCFAFMEMDEIKPGPIVIELYKKPTDFKRKKLQLLTKKPLYLHLHQTLHKE
Prediction	641443361745641544555656456544464344546543333247344332010104301054264144020001022364440443472434444643102131303033315614720000010332546664320300020315515733131401432342445325314644130303220468
	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

                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSSSSSSSSCCHHHCCCCSSSSSSSCCCCCSCCCCCCCCCCCCCCCCSSSSCCSSSSCCCHHHCCCCCSSSSSSSSCCCCCCCSSSSSSSSSSCCCCCCCCSSSSSSCCCCCHHHHHHHHHCCCCCSSSSSSSSSCC
VPLRRILAPGEEENLEFEEDEEEGGAGAGSPDSFPARVPGTLLPRLPSEPGMTLLTIRIEKIGLKDAGQCIDPYITVSVKDLNGIDLTPVQDTPVASRKEDTYVHFNVDIELQKHVEKLTKGAAIFFEFKHYKPKKRFTSTKCFAFMEMDEIKPGPIVIELYKKPTDFKRKKLQLLTKKPLYLHLHQTLHKE

2qz5B

0.98

0.79

22.04

1.17

DEthreader

--------VP-----------------------------GTLLPRLPSEPGMTLLTIRIEKIGLKDAGQCIDPYITVSVKDLNGIDLTPVQDTPVASRKEDTYVHFNVDIELQKHVEKLTKGAAIFFEFKHYKPKKRFTSTKCFAFMEMDEIKPGPIVIELYKKPTDFKRKKLQLLTKKPLYLHLHQSLHK-

2qz5B

0.99

0.80

22.32

3.15

SPARKS-K

-------------------------------------VPGTLLPRLPSEPGMTLLTIRIEKIGLKDAGQCIDPYITVSVKDLNGIDLTPVQDTPVASRKEDTYVHFNVDIELQKHVEKLTKGAAIFFEFKHYKPKKRFTSTKCFAFMEMDEIKPGPIVIELYKKPTDFKRKKLQLLTKKPLYLHLHQSLHK-

2qz5B

0.99

0.78

21.73

0.97

MapAlign

-----------------------------------------LLPRLPSEPGMTLLTIRIEKIGLKDAGQCIDPYITVSVKDLNGIDLTPVQDTPVASRKEDTYVHFNVDIELQKHVEKLTKGAAIFFEFKHYKPKKRFTSTKCFAFMEMDEIKPGPIVIELYKKPTDFKRKKLQLLTKKPLYLHLHQSLHK-

2qz5B

0.99

0.80

22.32

0.84

CEthreader

-------------------------------------VPGTLLPRLPSEPGMTLLTIRIEKIGLKDAGQCIDPYITVSVKDLNGIDLTPVQDTPVASRKEDTYVHFNVDIELQKHVEKLTKGAAIFFEFKHYKPKKRFTSTKCFAFMEMDEIKPGPIVIELYKKPTDFKRKKLQLLTKKPLYLHLHQSLHK-

2qz5B

0.99

0.80

22.32

2.40

MUSTER

-------------------------------------VPGTLLPRLPSEPGMTLLTIRIEKIGLKDAGQCIDPYITVSVKDLNGIDLTPVQDTPVASRKEDTYVHFNVDIELQKHVEKLTKGAAIFFEFKHYKPKKRFTSTKCFAFMEMDEIKPGPIVIELYKKPTDFKRKKLQLLTKKPLYLHLHQSLHK-

2qz5B

0.99

0.80

22.32

8.79

HHsearch

-------------------------------------VPGTLLPRLPSEPGMTLLTIRIEKIGLKDAGQCIDPYITVSVKDLNGIDLTPVQDTPVASRKEDTYVHFNVDIELQKHVEKLTKGAAIFFEFKHYKPKKRFTSTKCFAFMEMDEIKPGPIVIELYKKPTDFKRKKLQLLTKKPLYLHLHQSLHK-

2qz5B

0.99

0.80

22.32

2.89

FFAS-3D

-------------------------------------VPGTLLPRLPSEPGMTLLTIRIEKIGLKDAGQCIDPYITVSVKDLNGIDLTPVQDTPVASRKEDTYVHFNVDIELQKHVEKLTKGAAIFFEFKHYKPKKRFTSTKCFAFMEMDEIKPGPIVIELYKKPTDFKRKKLQLLTKKPLYLHLHQSLHK-

2qz5B

0.99

0.80

22.32

1.10

EigenThreader

-------------------------------------VPGTLLPRLPSEPGMTLLTIRIEKIGLKDAGQCIDPYITVSVKDLNGIDLTPVQDTPVASRKEDTYVHFNVDIELQKHVEKLTKGAAIFFEFKHYKPKKRFTSTKCFAFMEMDEIKPGPIVIELYKKPTDFKRKKLQLLTKKPLYLHLHQSLHK-

2qz5A

0.99

0.79

22.03

3.23

CNFpred

---------------------------------------GTLLPRLPSEPGMTLLTIRIEKIGLKDAGQCIDPYITVSVKDLNGIDLTPVQDTPVASRKEDTYVHFNVDIELQKHVEKLTKGAAIFFEFKHYKPKKRFTSTKCFAFMEMDEIKPGPIVIELYKKPTDFKRKKLQLLTKKPLYLHLHQSLHK-

6tgbA

0.09

0.08

2.97

1.00

DEthreader

-----GGGGGGGGGGGGGGG-----------GGGGGGGGGG--------DVRNDIYITLLQGDFKYNTTQRNVEVIMCVCAEDGKTLPNNEYRSVVYYQV-KQPRWMETVKVAVPIEDMQ-RIHLRFMFRHRSESKDKGEKNAMSYVKLKTLHDGFHDLVVLKGDSKEDAAGGLSVSS-RDVFSISTLVSTI

(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	0.7381

(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	2qz5B	0.78	0.86	0.994	0.802	model1_2qz5B.pdb.gz
2	6tgbA1	0.65	4.06	0.086	0.901	model1_6tgbA1.pdb.gz
3	3l4cB	0.60	2.61	0.132	0.708	model1_3l4cB.pdb.gz
4	6nctA3	0.58	3.30	0.090	0.714	model1_6nctA3.pdb.gz
5	6gy0A	0.58	3.04	0.061	0.693	model1_6gy0A.pdb.gz
6	7clxA	0.57	3.22	0.099	0.714	model1_7clxA.pdb.gz
7	3hizA2	0.56	3.57	0.110	0.708	model1_3hizA2.pdb.gz
8	5dfzC	0.55	3.14	0.128	0.688	model1_5dfzC.pdb.gz
9	3b7yB	0.55	3.49	0.125	0.703	model1_3b7yB.pdb.gz
10	6kxkA3	0.55	4.29	0.128	0.781	model1_6kxkA3.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:0035091	1.00	phosphatidylinositol 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:0050794	1.00	regulation of cellular process
GO:0044699	0.94	single-organism process
GO:0007389	0.92	pattern specification process
GO:0009953	0.91	dorsal/ventral pattern formation
GO:0048264	0.76	determination of ventral identity
GO:0007165	0.75	signal transduction
GO:0035556	0.73	intracellular signal transduction

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:0016020	1.00	membrane
GO:0044464	0.73	cell part
GO:0044424	0.64	intracellular part

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	0.066	2b3rB	0.456	2.76	0.103	0.547	2.7.1.154	173
2	0.060	2enqA	0.589	2.96	0.119	0.703	2.7.1.153	NA
3	0.060	2a4zA	0.329	6.18	0.057	0.656	2.7.1.153	152
4	0.060	1oacB	0.401	5.62	0.043	0.714	1.4.3.21 1.4.3.6	NA
5	0.060	1ciuA	0.430	4.79	0.076	0.688	2.4.1.19	122

	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	0.14	3qk0A	0.553	2.90	0.099	0.661	0.22	QK0	complex1.pdb.gz	82,123,125,147,165
2	0.14	1e90A	0.545	3.26	0.096	0.667	0.19	MYC	complex2.pdb.gz	81,123,126
3	0.13	3mjwA	0.539	2.90	0.098	0.646	0.18	WYF	complex3.pdb.gz	84,122,123,125
4	0.13	1e8xA	0.548	2.98	0.096	0.661	0.20	ATP	complex4.pdb.gz	122,124,160,162
5	0.13	3eneA	0.550	3.14	0.103	0.667	0.14	NPZ	complex5.pdb.gz	124,125,126,127
6	0.07	3qarA	0.562	3.27	0.088	0.688	0.12	QAR	complex6.pdb.gz	85,149,150,160
7	0.07	2wxjA	0.575	3.07	0.061	0.693	0.17	RW3	complex7.pdb.gz	54,55,149,150,151
8	0.02	3qjzA	0.535	2.91	0.101	0.641	0.27	QJZ	complex8.pdb.gz	82,122,124,148,150,163
9	0.02	3zw3A	0.536	2.89	0.099	0.641	0.21	ZW3	complex9.pdb.gz	82,122,123,124,125,145
10	0.02	2v4lA	0.545	3.05	0.103	0.667	0.31	ABJ	complex10.pdb.gz	77,126,128,155

	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.