D-I-TASSER Q86SS6-D2

D-I-TASSER results for Q86SS6-D2

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

Input Sequence in FASTA format

>Q86SS6 (141 residues)
VDLGELMFSLCYLPTAGRLTITIIKARNLKAMDITGASDPYVKVSLMCDGRRLKKRKTST
KRNTLNPVYNEAIVFDVPPENIDQIHLSIAVMDYDRVGHNEIIGVCQVGNEAERLGRDHW
SEMLSYPRKPIAHWHSLVEKR

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| VDLGELMFSLCYLPTAGRLTITIIKARNLKAMDITGASDPYVKVSLMCDGRRLKKRKTSTKRNTLNPVYNEAIVFDVPPENIDQIHLSIAVMDYDRVGHNEIIGVCQVGNEAERLGRDHWSEMLSYPRKPIAHWHSLVEKR
Prediction	CCCSSSSSSSSSSCCCCSSSSSSSSSCCCCCCCCCCCCCSSSSSSSSCCCCSSSSSSCCSSCCCCCCCCCSSSSSSSCHHHCCCCSSSSSSSSCCCCCCCCSSSSSSSCCCCCCCHHHHHHHHHHCCCCSSSSSSSCCCCC
Confidence	941389999999289997999999951999878898989079999974991452684224619999643526999836553688589999994899888754479998450066237899999967998341425377899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| VDLGELMFSLCYLPTAGRLTITIIKARNLKAMDITGASDPYVKVSLMCDGRRLKKRKTSTKRNTLNPVYNEAIVFDVPPENIDQIHLSIAVMDYDRVGHNEIIGVCQVGNEAERLGRDHWSEMLSYPRKPIAHWHSLVEKR
Prediction	773440201021337544330201204444446675311010102024676434434032345322041344040404474167243301011334144522012020317536443610340174564434552544578
	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                 140

                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCSSSSSSSSSSCCCCSSSSSSSSSCCCCCCCCCCCCCSSSSSSSSCCCCSSSSSSCCSSCCCCCCCCCSSSSSSSCHHHCCCCSSSSSSSSCCCCCCCCSSSSSSSCCCCCCCHHHHHHHHHHCCCCSSSSSSSCCCCC
VDLGELMFSLCYLPTAGRLTITIIKARNLKAMDITGASDPYVKVSLMCDGRRLKKRKTSTKRNTLNPVYNEAIVFDVPPENIDQIHLSIAVMDYDRVGHNEIIGVCQVGNEAERLGRDHWSEMLSYPRKPIAHWHSLVEKR

2r83A

0.51

14.79

1.50

DEthreader

EKLGDICFSLRYVPTAGKLTVVILEAKNLKKMDVGGLSDPYVKIHLMQNGKRLKKKKTTIKKNTLNPYYNESFSFEVPFEQIQKVQVVVTVLDYDKIGKNDAIGKVFVGYNSTGAELRHWSDMLANPRRPIAQWHTLQVEE

3n5aA

0.46

0.45

13.23

2.38

SPARKS-K

-SRGELLLSLCYNPSANSIIVNIIKARNLKAMDIGGTSDPYVKVWLMYKDKRVEKKKTVTKKRNLNPIFNESFAFDIPTEKLRETTIIITVMDKDKLSRNDVIGKIYLSWKSGPGEVKHWKDMIARPRQPVAQWHQLKA--

2r83A

0.52

0.51

14.77

1.03

MapAlign

-KLGDICFSLRYVPTAGKLTVVILEAKNLKKMDVGGLSDPYVKIHLMQNGKRLKKKKTTIKKNTLNPYYNESFSFEVPFEQIQKVQVVVTVLDYDKIGKNDAIGKVFVGYNSTGAELRHWSDMLANPRRPIAQWHTLQVE-

2r83A

0.51

14.79

0.67

CEthreader

EKLGDICFSLRYVPTAGKLTVVILEAKNLKKMDVGGLSDPYVKIHLMQNGKRLKKKKTTIKKNTLNPYYNESFSFEVPFEQIQKVQVVVTVLDYDKIGKNDAIGKVFVGYNSTGAELRHWSDMLANPRRPIAQWHTLQVEE

2r83A2

0.51

14.79

1.86

MUSTER

EKLGDICFSLRYVPTAGKLTVVILEAKNLKKMDVGGLSDPYVKIHLMQNGKRLKKKKTTIKKNTLNPYYNESFSFEVPFEQIQKVQVVVTVLDYDKIGKNDAIGKVFVGYNSTGAELRHWSDMLANPRRPIAQWHTLQVEE

2r83A

0.51

14.79

1.76

HHsearch

EKLGDICFSLRYVPTAGKLTVVILEAKNLKKMDVGGLSDPYVKIHLMQNGKRLKKKKTTIKKNTLNPYYNESFSFEVPFEQIQKVQVVVTVLDYDKIGKNDAIGKVFVGYNSTGAELRHWSDMLANPRRPIAQWHTLQVEE

3n5aA

0.46

0.45

13.23

2.39

FFAS-3D

-SRGELLLSLCYNPSANSIIVNIIKARNLKAMDIGGTSDPYVKVWLMYKDKRVEKKKTVTKKRNLNPIFNESFAFDIPTEKLRETTIIITVMDKDKLSRNDVIGKIYLSWKSGPGEVKHWKDMIARPRQPVAQWHQLKA--

2r83A2

0.51

14.79

0.95

EigenThreader

EKLGDICFSLRYVPTAGKLTVVILEAKNLKKMDVGGLSDPYVKIHLMQNGKRLKKKKTTIKKNTLNPYYNESFSFEVPFEQIQKVQVVVTVLDYDKIGKNDAIGKVFVGYNSTGAELRHWSDMLANPRRPIAQWHTLQVEE

5ccjA

0.50

14.60

2.35

CNFpred

EKLGDICFSLAYVPTAGKLTVVILAAKNLKKMDVGGLSDPYVKIHLMQNGKRLKKKKTTIKKNTLNPWYNESFSFEVPFEQIQKVQVVVTVLDYDKIGKNDAIGKVFVGYNSTGAELRHWSDMLANPAAPIAQWHTLQVEE

2r83A2

0.51

14.79

1.50

DEthreader

EKLGDICFSLRYVPTAGKLTVVILEAKNLKKMDVGGLSDPYVKIHLMQNGKRLKKKKTTIKKNTLNPYYNESFSFEVPFEQIQKVQVVVTVLDYDKIGKNDAIGKVFVGYNSTGAELRHWSDMLANPRRPIAQWHTLQVEE

(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	0.9306

(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	2r83A2	0.99	0.54	0.511	1.000	model1_2r83A2.pdb.gz
2	3n5aA	0.96	0.67	0.464	0.979	model1_3n5aA.pdb.gz
3	3hn8A	0.95	1.16	0.716	1.000	model1_3hn8A.pdb.gz
4	6ankA	0.95	0.96	0.464	0.979	model1_6ankA.pdb.gz
5	2cm6A	0.91	1.42	0.380	0.972	model1_2cm6A.pdb.gz
6	1w15A	0.90	1.03	0.447	0.936	model1_1w15A.pdb.gz
7	5h4yA	0.83	1.43	0.357	0.894	model1_5h4yA.pdb.gz
8	2d8kA	0.80	1.80	0.354	0.901	model1_2d8kA.pdb.gz
9	3fdwA	0.79	2.04	0.302	0.894	model1_3fdwA.pdb.gz
10	4ts6A	0.79	1.76	0.260	0.872	model1_4ts6A.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:0046872	0.83	metal ion binding
GO:0008289	0.83	lipid binding
GO:0005543	0.82	phospholipid binding
GO:0005509	0.82	calcium ion binding
GO:0005544	0.81	calcium-dependent phospholipid binding
GO:0000149	0.75	SNARE binding
GO:0019905	0.74	syntaxin binding
GO:0030276	0.73	clathrin 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:0065007	0.96	biological regulation
GO:0050789	0.94	regulation of biological process
GO:0044699	0.94	single-organism process
GO:0050794	0.93	regulation of cellular process
GO:0044763	0.92	single-organism cellular process
GO:0006810	0.89	transport
GO:1902578	0.87	single-organism localization
GO:0044765	0.86	single-organism transport
GO:0032940	0.84	secretion by cell
GO:0016192	0.84	vesicle-mediated transport
GO:0016043	0.84	cellular component organization
GO:0099531	0.83	presynaptic process involved in chemical synaptic transmission
GO:0051649	0.83	establishment of localization in cell
GO:0023061	0.83	signal release
GO:1902580	0.82	single-organism cellular localization
GO:0099643	0.82	signal release from synapse
GO:0045055	0.82	regulated exocytosis
GO:0032879	0.82	regulation of localization
GO:0051049	0.81	regulation of transport
GO:0016079	0.81	synaptic vesicle exocytosis
GO:1903530	0.80	regulation of secretion by cell
GO:0060627	0.80	regulation of vesicle-mediated transport
GO:0044802	0.79	single-organism membrane organization
GO:0017157	0.79	regulation of exocytosis
GO:0017158	0.78	regulation of calcium ion-dependent exocytosis
GO:0006996	0.78	organelle organization
GO:1902589	0.77	single-organism organelle organization
GO:0061025	0.77	membrane fusion
GO:0048791	0.77	calcium ion-regulated exocytosis of neurotransmitter
GO:0006906	0.76	vesicle fusion

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:0016020	0.85	membrane
GO:0005886	0.80	plasma membrane
GO:0044424	0.79	intracellular part
GO:0044444	0.66	cytoplasmic part
GO:0043226	0.56	organelle
GO:0043229	0.54	intracellular organelle
GO:0043227	0.52	membrane-bounded organelle
GO:0043231	0.50	intracellular membrane-bounded organelle

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	0.177	2b3rB	0.776	1.89	0.270	0.865	2.7.1.154	61,66
2	0.066	2hvbB	0.504	3.39	0.031	0.674	1.15.1.2	NA
3	0.060	2q0zX	0.504	3.62	0.029	0.709	3.6.4.13	36,38
4	0.060	3hhsB	0.507	3.97	0.017	0.787	1.14.18.1	NA
5	0.060	1bdyB	0.559	2.87	0.158	0.702	2.7.11.13	41

	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:

Click to view	Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
	1	0.20	1dsyA	0.780	2.07	0.306	0.879	1.46	PSF	complex1.pdb.gz	33,34,35,39,62,94,95,96,97
	2	0.06	1a250	0.776	2.19	0.288	0.886	1.14	III	complex2.pdb.gz	2,3,28,29,30,31,32,33,95,101,139

	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.