D-I-TASSER O14656-D2

D-I-TASSER results for O14656-D2

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

Input Sequence in FASTA format

>O14656 (63 residues)
LPLEYKHLKMCIRVEMQSRGYEIDEDIVSRVAEEMTFFPKEERVFSDKGCKTVFTKLDYY
YDD

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| LPLEYKHLKMCIRVEMQSRGYEIDEDIVSRVAEEMTFFPKEERVFSDKGCKTVFTKLDYYYDD
Prediction	CCCCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCSSCCCCCSSSCCCCCSHHHHHHHHHCC
Confidence	986389999999999999199989999999998470235998545102894399998876169
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| LPLEYKHLKMCIRVEMQSRGYEIDEDIVSRVAEEMTFFPKEERVFSDKGCKTVFTKLDYYYDD
Prediction	774445203400351047473624562044016304222774420044203414530532368
	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

                   |                   |                   |

SS
Seq

CCCCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCSSCCCCCSSSCCCCCSHHHHHHHHHCC
LPLEYKHLKMCIRVEMQSRGYEIDEDIVSRVAEEMTFFPKEERVFSDKGCKTVFTKLDYYYDD

5j1sA

1.00

0.97

27.11

1.33

DEthreader

LPLEYKHLKMCIRVEMQSRGYEIDEDIVSRVAEEMTFFPKE-RVFSDKGCKTVFTKLDYYYD-

5j1sA2

1.00

0.97

27.11

2.81

SPARKS-K

-PLEYKHLKMCIRVEMQSRGYEIDEDIVSRVAEEMTFFPKEERVFSDKGCKTVFTKLDYYYD-

5j1sA2

1.00

0.95

26.67

1.05

MapAlign

-PLEYKHLKMCIRVEMQSRGYEIDEDIVSRVAEEMTFFPKEERVFSDKGCKTVFTKLDYYY--

5j1sA2

1.00

0.97

27.11

1.16

CEthreader

-PLEYKHLKMCIRVEMQSRGYEIDEDIVSRVAEEMTFFPKEERVFSDKGCKTVFTKLDYYYD-

5j1sA2

1.00

0.97

27.11

2.87

MUSTER

-PLEYKHLKMCIRVEMQSRGYEIDEDIVSRVAEEMTFFPKEERVFSDKGCKTVFTKLDYYYD-

5j1sA2

1.00

0.97

27.11

2.44

HHsearch

-PLEYKHLKMCIRVEMQSRGYEIDEDIVSRVAEEMTFFPKEERVFSDKGCKTVFTKLDYYYD-

5j1sA2

1.00

0.97

27.11

1.49

FFAS-3D

-PLEYKHLKMCIRVEMQSRGYEIDEDIVSRVAEEMTFFPKEERVFSDKGCKTVFTKLDYYYD-

5j1sA2

1.00

0.97

27.11

0.82

EigenThreader

-PLEYKHLKMCIRVEMQSRGYEIDEDIVSRVAEEMTFFPKEERVFSDKGCKTVFTKLDYYY-D

5j1sA

1.00

0.98

27.56

1.00

CNFpred

LPLEYKHLKMCIRVEMQSRGYEIDEDIVSRVAEEMTFFPKEERVFSDKGCKTVFTKLDYYYD-

5j1sA2

0.98

0.94

26.24

1.33

DEthreader

P-LEYKHLKMCIRVEMQSRGYEIDEDIVSRVAEEMTFFPKE-RVFSDKGCKTVFTKLDYYYD-

(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	0.8358

(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	5j1sA	0.94	0.59	1.000	0.984	model1_5j1sA.pdb.gz
2	6blbA	0.68	1.36	0.154	0.825	model1_6blbA.pdb.gz
3	1fnnA3	0.68	2.16	0.121	0.921	model1_1fnnA3.pdb.gz
4	1qvrA2	0.67	2.04	0.109	0.873	model1_1qvrA2.pdb.gz
5	1j7kA	0.67	1.45	0.173	0.825	model1_1j7kA.pdb.gz
6	1w5tB	0.67	2.27	0.052	0.921	model1_1w5tB.pdb.gz
7	1iqpA	0.64	1.70	0.135	0.825	model1_1iqpA.pdb.gz
8	2qbyA1	0.64	2.13	0.091	0.873	model1_2qbyA1.pdb.gz
9	2v1uA1	0.64	2.01	0.127	0.873	model1_2v1uA1.pdb.gz
10	2chvA	0.63	1.83	0.115	0.825	model1_2chvA.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	0.96	catalytic activity
GO:0016887	0.95	ATPase 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:0009987	1.00	cellular process
GO:0051260	0.91	protein homooligomerization
GO:0006996	0.81	organelle organization
GO:0065007	0.80	biological regulation
GO:0044699	0.80	single-organism process
GO:0050789	0.77	regulation of biological process
GO:0044763	0.77	single-organism cellular process
GO:0050794	0.75	regulation of cellular process
GO:0071763	0.72	nuclear membrane organization
GO:0008152	0.71	metabolic process
GO:0071704	0.70	organic substance metabolic process
GO:0044238	0.69	primary metabolic process
GO:0044237	0.68	cellular metabolic process
GO:0043170	0.68	macromolecule metabolic process
GO:0048518	0.67	positive regulation of biological process
GO:0044260	0.67	cellular macromolecule metabolic process
GO:0048522	0.66	positive regulation of cellular process
GO:0019538	0.66	protein metabolic process
GO:0065008	0.65	regulation of biological quality
GO:0006508	0.65	proteolysis
GO:0006464	0.65	cellular protein modification process
GO:0070646	0.64	protein modification by small protein removal
GO:0051128	0.64	regulation of cellular component organization
GO:0051049	0.64	regulation of transport
GO:0044765	0.64	single-organism transport
GO:0023051	0.64	regulation of signaling
GO:0010646	0.64	regulation of cell communication
GO:0007155	0.64	cell adhesion
GO:0006457	0.64	protein folding
GO:2000008	0.63	regulation of protein localization to cell surface
GO:1900244	0.63	positive regulation of synaptic vesicle endocytosis
GO:0072321	0.63	chaperone-mediated protein transport
GO:0071712	0.63	ER-associated misfolded protein catabolic process
GO:0061077	0.63	chaperone-mediated protein folding
GO:0051584	0.63	regulation of dopamine uptake involved in synaptic transmission
GO:0048489	0.63	synaptic vesicle transport
GO:0045104	0.63	intermediate filament cytoskeleton organization
GO:0044319	0.63	wound healing, spreading of cells
GO:0034504	0.63	protein localization to nucleus
GO:0031175	0.63	neuron projection development
GO:0006998	0.63	nuclear envelope organization
GO:0000338	0.63	protein deneddylation

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:0044444	1.00	cytoplasmic part
GO:0044446	0.97	intracellular organelle part
GO:0043226	0.86	organelle
GO:0043229	0.85	intracellular organelle
GO:0043227	0.85	membrane-bounded organelle
GO:0043231	0.84	intracellular membrane-bounded organelle
GO:0005788	0.82	endoplasmic reticulum lumen
GO:0044428	0.78	nuclear part
GO:0005635	0.76	nuclear envelope
GO:0031988	0.75	membrane-bounded vesicle
GO:0016020	0.65	membrane
GO:0044425	0.59	membrane part
GO:0031090	0.54	organelle membrane
GO:0097458	0.53	neuron part
GO:0044463	0.53	cell projection part
GO:0042406	0.52	extrinsic component of endoplasmic reticulum membrane
GO:0030659	0.52	cytoplasmic vesicle membrane
GO:0030426	0.52	growth cone
GO:0030141	0.52	secretory granule
GO:0008021	0.52	synaptic vesicle
GO:0005783	0.52	endoplasmic reticulum

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	2hcsA	0.388	3.38	0.075	0.714	2.7.7.48 3.4.21.91	NA
2	0.060	2peyB	0.335	3.75	0.000	0.540	2.7.1.25 2.7.7.4	NA
3	0.060	3letA	0.616	2.64	0.053	0.905	2.7.7.-	NA
4	0.060	1wmdA	0.599	2.80	0.068	0.936	3.4.21.-	NA
5	0.060	3lxuX	0.616	2.49	0.066	0.968	3.4.14.10	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	1xxiB	0.661	1.48	0.058	0.825	0.47	ADP	complex1.pdb.gz	13,15,49,50,51,52,53
	2	0.01	2awb6	0.249	4.18	0.049	0.571	0.60	III	complex2.pdb.gz	34,36,48,49,50

	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.