D-I-TASSER Q15334-D2

D-I-TASSER results for Q15334-D2

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

Input Sequence in FASTA format

>Q15334 (151 residues)
RLGVQKVALCKYTAQMVVAGTAGQVLVLELSDVPVEQAVSVAIIDLLQDREGFTWKGHER
LSPRTGPLPWPAGFQPRVLVQCLPPAAVTAVTLHTEWSLVAFGTSHGFGLFDYQRKSPVL
ARCTLHPNDSLAMEGPLSRVKSLKKSLRQSF

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| RLGVQKVALCKYTAQMVVAGTAGQVLVLELSDVPVEQAVSVAIIDLLQDREGFTWKGHERLSPRTGPLPWPAGFQPRVLVQCLPPAAVTAVTLHTEWSLVAFGTSHGFGLFDYQRKSPVLARCTLHPNDSLAMEGPLSRVKSLKKSLRQSF
Prediction	CCSSSSSSSCCCCCSSSSSCCCCSSSSSSSCCCCCCCCSSSSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSSCCCCCSSSSSSSCCCCSSSSSCCCCSSSSSCCCCSSSSSSCCCCHHHHCCCCCCCCCCCCCCCHHHHCC
Confidence	9305899984788959997664669999932786655415899861356666533787555555786446998671599981599233677861557859996499179998147869998446884550557896425554431334229
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| RLGVQKVALCKYTAQMVVAGTAGQVLVLELSDVPVEQAVSVAIIDLLQDREGFTWKGHERLSPRTGPLPWPAGFQPRVLVQCLPPAAVTAVTLHTEWSLVAFGTSHGFGLFDYQRKSPVLARCTLHPNDSLAMEGPLSRVKSLKKSLRQSF
Prediction	7310320201351320000220010000203546355504323041356475243762640524755253434010300010332330100013361200001143000000134431001313143623434753343355345434748
	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

CCSSSSSSSCCCCCSSSSSCCCCSSSSSSSCCCCCCCCSSSSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSSCCCCCSSSSSSSCCCCSSSSSCCCCSSSSSCCCCSSSSSSCCCCHHHHCCCCCCCCCCCCCCCHHHHCC
RLGVQKVALCKYTAQMVVAGTAGQVLVLELSDVPVEQAVSVAIIDLLQDREGFTWKGHERLSPRTGPLPWPAGFQPRVLVQCLPPAAVTAVTLHTEWSLVAFGTSHGFGLFDYQRKSPVLARCTLHPNDSLAMEGPLSRVKSLKKSLRQSF

6n8pA

0.62

0.55

15.73

1.17

DEthreader

RLGIQKIFLCKYSGYLAVAGTAGQVLVLELNDEAAEQAVEQVEADLLQDQEGYRWKGHERLAARSGPVRFEPGFQPFVLVQCQPPAVVTSLALHSEWRLVAFGTSHGFGLFDHQQRRQVFVKCTLH--PSD-------FTGF---N-----

6n8pA

0.58

16.74

1.67

SPARKS-K

RLGIQKIFLCKYSGYLAVAGTAGQVLVLELNDEAAEQAVEQVEADLLQDQEGYRWKGHERLAARSGPVRFEPGFQPFVLVQCQPPAVVTSLALHSEWRLVAFGTSHGFGLFDHQQRRQVFVKCTLHPSDQLSFTGFVRTLYFADTYLKDSS

6n8pA

0.60

0.57

16.33

1.21

MapAlign

RLGIQKIFLCKYSGYLAVAGTAGQVLVLELNDEAAEQAVEQVEADLLQDQEGYRWKGHERLAARSGPVRFEPGFQPFVLVQCQPPAVVTSLALHSEWRLVAFGTSHGFGLFDHQQRRQVFVKCTLHPSDQLSFTGFVRTLYFAD-------

6n8pA

0.58

16.74

0.89

CEthreader

RLGIQKIFLCKYSGYLAVAGTAGQVLVLELNDEAAEQAVEQVEADLLQDQEGYRWKGHERLAARSGPVRFEPGFQPFVLVQCQPPAVVTSLALHSEWRLVAFGTSHGFGLFDHQQRRQVFVKCTLHPSDQLSFTGFVRTLYFADTYLKDSS

6n8pA

0.61

0.58

16.69

1.31

MUSTER

RLGIQKIFLCKYSGYLAVAGTAGQVLVLELNDEAAEQAVEQVEADLLQDQEGYRWKGHERLAARSGPVRFEPGFQPFVLVQCQPPAVVTSLALHSEWRLVAFGTSHGFGLFDHQQRRQVFVKCTLHPSDQLSFTGFVR-------YLKDSS

6n8pA

0.58

16.56

0.76

HHsearch

RLGIQKIFLCKYSGYLAVAGTAGQVLVLELNDEAAEQAVEQVEADLLQDQEGYRWKGHERLAARSGPVRFEPGFQPFVLVQCQPPAVVTSLALHSEWRLVAFGTSHGFGLFDHQQRRQVFVKCTLHPSDQLSFTGFVAYFSVPPAERRAEQ

6n8pA

0.59

0.58

16.73

1.02

FFAS-3D

RLGIQKIFLCKYSGYLAVAGTAGQVLVLELNDEAAEQAVEQVEADLLQDQEGYRWKGHERLAARSGPVRFEPGFQPFVLVQCQPPAVVTSLALHSEWRLVAFGTSHGFGLFDHQQRRQVFVKCTLHPSDQLSFTGFVRTLYFADTYLKDS-

5vh9B2

0.11

0.09

3.10

0.62

EigenThreader

EFPIEKVKFIWGMQYCVSASRDRTIKIWEIP--LPTLMAH----------------------RAPIPNPTDSNFRCVLTLKG-HLSWVRDISIR--GQYLFSCADKSVRCWDLNTGQCLHVWEKLHF-----DSNVTPRQMMVT--GGLDC

6n8pA

0.65

0.56

16.07

2.46

CNFpred

RLGIQKIFLCKYSGYLAVAGTAGQVLVLELNDEAAEQAVEQVEADLLQDQEGYRWKGHERLAARSGPVRFEPGFQPFVLVQCQPPAVVTSLALHSEWRLVAFGTSHGFGLFDHQQRRQVFVKCTLHPSDQL--------------------

2oajA

0.15

0.11

3.79

1.00

DEthreader

ELAVDKISFAAETLELAVSIETGDVVLFKYE-VNQF-F-LTNGV----------------L-VDVRDRAPVQGFMPSTAVHANK-GKTSAINNSNI-GFVGIAYAASLMLIDRRGPAIIYMENIREI-S------GA-QSAC---D-----

(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	0.7488

(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	6n8pA	0.96	1.05	0.576	0.993	model1_6n8pA.pdb.gz
2	2oajA	0.66	3.17	0.125	0.815	model1_2oajA.pdb.gz
3	6hqaB	0.61	2.62	0.079	0.742	model1_6hqaB.pdb.gz
4	1sq9A	0.61	2.35	0.111	0.702	model1_1sq9A.pdb.gz
5	4zovA	0.60	2.45	0.091	0.722	model1_4zovA.pdb.gz
6	3iytA	0.59	2.78	0.055	0.722	model1_3iytA.pdb.gz
7	4jspD	0.59	2.85	0.087	0.722	model1_4jspD.pdb.gz
8	5k19A	0.59	3.60	0.082	0.795	model1_5k19A.pdb.gz
9	1u2vC	0.59	2.32	0.105	0.695	model1_1u2vC.pdb.gz
10	5oqlA4	0.59	3.77	0.107	0.808	model1_5oqlA4.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:0000149	1.00	SNARE binding
GO:0019905	0.99	syntaxin binding
GO:0017137	0.99	Rab GTPase binding
GO:0005096	0.99	GTPase activator 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	1.00	regulation of cellular process
GO:0050708	0.95	regulation of protein secretion
GO:0017157	0.95	regulation of exocytosis
GO:0044699	0.91	single-organism process
GO:0009987	0.88	cellular process
GO:0044763	0.86	single-organism cellular process
GO:0023051	0.86	regulation of signaling
GO:0010646	0.86	regulation of cell communication
GO:0048583	0.85	regulation of response to stimulus
GO:0051234	0.84	establishment of localization
GO:0009966	0.84	regulation of signal transduction
GO:0016043	0.83	cellular component organization
GO:0008593	0.83	regulation of Notch signaling pathway
GO:1902578	0.82	single-organism localization
GO:0051649	0.82	establishment of localization in cell
GO:0051641	0.82	cellular localization
GO:0048869	0.82	cellular developmental process
GO:1902580	0.81	single-organism cellular localization
GO:0051656	0.81	establishment of organelle localization
GO:0030029	0.80	actin filament-based process
GO:0006996	0.80	organelle organization
GO:0051294	0.79	establishment of spindle orientation
GO:0032878	0.79	regulation of establishment or maintenance of cell polarity
GO:0030866	0.79	cortical actin cytoskeleton organization
GO:0030154	0.78	cell differentiation
GO:0022008	0.77	neurogenesis

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:0044424	0.98	intracellular part
GO:0043229	0.97	intracellular organelle
GO:0016020	0.97	membrane
GO:0044444	0.96	cytoplasmic part
GO:0005886	0.91	plasma membrane
GO:0044422	0.83	organelle part
GO:0044446	0.82	intracellular organelle part
GO:0044430	0.79	cytoskeletal part
GO:0043232	0.79	intracellular non-membrane-bounded organelle
GO:0030864	0.78	cortical actin cytoskeleton

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	3fw0A	0.544	3.19	0.101	0.702	4.3.2.5	NA
2	0.060	1v0eA	0.509	3.90	0.061	0.748	3.2.1.129	NA
3	0.060	1kv9A	0.539	3.76	0.081	0.768	1.1.99.-	NA
4	0.060	2gc7A	0.523	3.74	0.109	0.722	1.4.99.3	7,25
5	0.060	1kitA	0.513	3.74	0.027	0.729	3.2.1.18	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:

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	0.02	3mksD	0.572	2.06	0.081	0.649	0.64	C1C	complex1.pdb.gz	81,82,118,120,121
	2	0.01	3k71E	0.576	2.77	0.083	0.715	0.43	UUU	complex2.pdb.gz	18,20,22

	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.