D-I-TASSER Q7RTY3-D2

D-I-TASSER results for Q7RTY3-D2

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

Input Sequence in FASTA format

>Q7RTY3 (124 residues)
ICLPEPNFNLKVGTQCWVTGWSQVKQRFSANSMLTPELQEAEVFIMDNKRCDRHYKKSFF
PPVVPLVLGDMICATNYGENLCYGDSGGPLACEVEGRWILAGVLSWEKACVKAQNPGVYT
RITK

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| ICLPEPNFNLKVGTQCWVTGWSQVKQRFSANSMLTPELQEAEVFIMDNKRCDRHYKKSFFPPVVPLVLGDMICATNYGENLCYGDSGGPLACEVEGRWILAGVLSWEKACVKAQNPGVYTRITK
Prediction	CCCCCCCCCCCCCCSSSSSSCCSCCCCCCCCCCCCCCCSSSSSSSCCHHHHHHHHCCCCCCCCCCCCCCCSSSCCCCCCSCCCCCCCCCSSSSSCCSSSSSSSSSCCCCCCCCCCCSSSSSCCC
Confidence	9188999988996389998161224688889987751358874531899986776114676556755888465289996167688999147865998999999870656689998937775469
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| ICLPEPNFNLKVGTQCWVTGWSQVKQRFSANSMLTPELQEAEVFIMDNKRCDRHYKKSFFPPVVPLVLGDMICATNYGENLCYGDSGGPLACEVEGRWILAGVLSWEKACVKAQNPGVYTRITK
Prediction	8441677450554340200031304554547453363034060401447414631564445444540363004026433203145334100044743020000002030114473141414248
	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

CCCCCCCCCCCCCCSSSSSSCCSCCCCCCCCCCCCCCCSSSSSSSCCHHHHHHHHCCCCCCCCCCCCCCCSSSCCCCCCSCCCCCCCCCSSSSSCCSSSSSSSSSCCCCCCCCCCCSSSSSCCC
ICLPEPNFNLKVGTQCWVTGWSQVKQRFSANSMLTPELQEAEVFIMDNKRCDRHYKKSFFPPVVPLVLGDMICATNYGENLCYGDSGGPLACEVEGRWILAGVLSWEKACVKAQNPGVYTRITK

3e0nB

0.39

0.38

11.21

1.33

DEthreader

ISLPAAQASFPNGLHCTVTGWGHVAPSV--SLLTPKPLQQLEVPLISRETCNSLYID-AKPEEPHFVQEDMVCAGYGGKDACQGDSGGPLSCPVEGLWYLTGIVSWGDACGARNRPGVYTLASA

1a0lA

0.39

0.38

11.22

2.19

SPARKS-K

VTLPPASETFPPGMPCWVTGWGDVDNDERLPPPFP--LKQVKVPIMENHICDAKYHLGAYTGDDVRIRDDMLCAGNTRRDSCQGDSGGPLVCKVNGTWLQAGVVSWGEGCAQPNRPGIYTRVTY

2a7jA

0.34

0.31

9.18

0.68

MapAlign

GVLPRAGTILANNSPCYITGWGLT----RTNGQLAQTLQQAYLPTVDYAICSSYWG--------STVKNSMVCAGGDGRSGCQGDSGGPLHCLVNGQYAVHGVTSFVSGCNVTRKPTVFTRVSA

1ekbB

0.38

0.35

10.27

0.51

CEthreader

ICLPEENQVFPPGRICSIAGWGALIYQ----GSTADVLQEADVPLLSNEKCQQQMP-------EYNITENMVCAGYGGVDSCQGDSGGPLMCQENNRWLLAGVTSFGYQCALPNRPGVYARVPR

1a0lA

0.40

11.65

1.92

MUSTER

VTLPPASETFPPGMPCWVTGWGDVDNDE--RLPPPFPLKQVKVPIMENHICDAKYHLAYTGDDVRIVRDDMLCAGNTRRDSCQGDSGGPLVCKVNGTWLQAGVVSWGEGCAQPNRPGIYTRVTY

6esoA

0.38

0.34

10.04

1.97

HHsearch

ICLPSKGDTSTIYTNCWVTGWGFSKEKG----EIQNILQKVNIPLVTNEECQKRYQDY-------KITQRMVCA--GGKDACKGDSGGPLVCKHNGMWRLVGITSWGEGCARREQPGVYTKVAE

1ekbB

0.37

0.34

10.07

1.70

FFAS-3D

ICLPEENQVFPPGRICSIAGWGALIYQGST----ADVLQEADVPLLSNEKCQQQ-----MPEYNITENMVCAGYEAGGVDSCQGDSGGPLMCQENNRWLLAGVTSFGYQCALPNRPGVYARVPR

1a0lA

0.40

11.65

0.95

EigenThreader

VTLPPASETFPPGMPCWVTGWGDVDNDER--LPPPFPLKQVKVPIMENHICDAKYHLGAYTGDVRIVRDDMLCAGNTRRDSCQGDSGGPLVCKVNGTWLQAGVVSWGEGCAQPNRPGIYTRVTY

3e0nB

0.39

0.38

11.22

3.18

CNFpred

ISLPAAQASFPNGLHCTVTGWGHVAPSVSLLT--PKPLQQLEVPLISRETCNSLYNIDAKPEEPHFVQEDMVCAGYVEKDACQGDSGGPLSCPVEGLWYLTGIVSWGDACGARNRPGVYTLASS

1a0lA

0.40

0.39

11.43

1.33

DEthreader

VTLPPASETFPPGMPCWVTGWGDVDNDE--RLPPPFPLKQVKVPIMENHICDAKYHLGAYTGVRIVRD-DMLCAGNTRRDSCQGDSGGPLVCKVNGTWLQAGVVSWGEGCAQPNRPGIYTRVTL

(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	0.8598

(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	3e0nB	0.89	1.42	0.417	0.968	model1_3e0nB.pdb.gz
2	1a0lA	0.87	1.87	0.405	0.968	model1_1a0lA.pdb.gz
3	3elaH	0.86	1.40	0.310	0.935	model1_3elaH.pdb.gz
4	3w94A	0.86	1.11	0.354	0.911	model1_3w94A.pdb.gz
5	2vntC	0.86	1.47	0.330	0.927	model1_2vntC.pdb.gz
6	1ekbB	0.86	1.12	0.381	0.911	model1_1ekbB.pdb.gz
7	6kd5B	0.85	1.52	0.383	0.927	model1_6kd5B.pdb.gz
8	2oq5A	0.85	1.46	0.333	0.919	model1_2oq5A.pdb.gz
9	1yc0A	0.85	1.51	0.357	0.927	model1_1yc0A.pdb.gz
10	3govB	0.85	1.10	0.375	0.903	model1_3govB.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:0008233	0.99	peptidase activity
GO:0070011	0.98	peptidase activity, acting on L-amino acid peptides
GO:0008236	0.96	serine-type peptidase activity
GO:0004175	0.89	endopeptidase activity
GO:0004252	0.88	serine-type endopeptidase activity
GO:0098772	0.51	molecular function regulator

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:0065007	0.99	biological regulation
GO:0044238	0.95	primary metabolic process
GO:0043170	0.95	macromolecule metabolic process
GO:0006508	0.94	proteolysis
GO:0050789	0.74	regulation of biological process
GO:0032501	0.71	multicellular organismal process
GO:0065008	0.68	regulation of biological quality
GO:0044699	0.67	single-organism process
GO:0048518	0.59	positive regulation of biological process
GO:0050794	0.57	regulation of cellular process
GO:0048522	0.56	positive regulation of cellular process
GO:0044707	0.54	single-multicellular organism process
GO:0019222	0.52	regulation of metabolic process
GO:0080090	0.50	regulation of primary metabolic process
GO:0050878	0.50	regulation of body fluid levels

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	0.80	cell part
GO:0044421	0.78	extracellular region part
GO:0005576	0.77	extracellular region
GO:0005615	0.76	extracellular space
GO:0044424	0.55	intracellular part
GO:0016020	0.50	membrane

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	0.430	1npmA	0.797	1.34	0.383	0.863	3.4.21.118	102
2	0.290	2pkaB	0.792	1.57	0.306	0.871	3.4.21.35	16,82,85,102
3	0.246	3beuA	0.817	1.45	0.279	0.895	3.4.21.4	NA
4	0.110	2kaiB	0.795	1.53	0.296	0.871	3.4.21.35 3.4.21.8	NA
5	0.109	2qxhA	0.800	1.30	0.355	0.863	3.4.21.117	84

	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	0.77	3e0pB	0.898	1.41	0.413	0.976	0.94	B3C	complex1.pdb.gz	64,71,81,82,83,84,85,86,104,105,106,107,108,109
2	0.76	2fwwA	0.881	1.80	0.405	0.968	1.47	C1R	complex2.pdb.gz	80,81,82,83,84,85,86,104,106,110,117
3	0.59	2f9pB	0.876	1.85	0.397	0.968	1.05	III	complex3.pdb.gz	81,82,86,105,106,107,108,109,117
4	0.55	3mwiU	0.855	1.48	0.322	0.927	1.54	B25	complex4.pdb.gz	81,83,86,104,106,107,117,118
5	0.51	1gj7B	0.850	1.53	0.330	0.927	0.93	132	complex5.pdb.gz	80,81,82,83,86,104,105,106,107,108,109,110,111,115,117,118,119

	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.