D-I-TASSER Q02763-D1

D-I-TASSER results for Q02763-D1

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

Input Sequence in FASTA format

>Q02763 (43 residues)
MDSLASLVLCGVSLLLSGTVEGAMDLILINSLPLVSDAETSLT

Predicted Secondary Structure

Sequence	20 40 \| \| MDSLASLVLCGVSLLLSGTVEGAMDLILINSLPLVSDAETSLT
Prediction	CCHHHHHHHHHHHSSSSCCCCSSSSSSSSSCCCCCCCCCCCCC
Confidence	9626776975410235321111455777724544225633349
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 \| \| MDSLASLVLCGVSLLLSGTVEGAMDLILINSLPLVSDAETSLT
Prediction	8543332333333233323143313122133133334564638
	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

                   |                   |

SS
Seq

CCHHHHHHHHHHHSSSSCCCCSSSSSSSSSCCCCCCCCCCCCC
MDSLASLVLCGVSLLLSGTVEGAMDLILINSLPLVSDAETSLT

5xtcV

0.08

0.07

2.79

1.17

DEthreader

QRKAYSTTSIASVAGLAVYTFTAAAVGAVFGAGTLGTHN----

1griA1

0.02

1.63

0.64

CEthreader

QRHDGAFLIRFSLSVKFGNDVQHFKVLRDGAGKYFLWVVKFNS

7cq5C2

0.09

3.51

0.57

EigenThreader

FIPSLLIGAAWGRLFGGKYALMGAAAQLGGIVRLVLMTAKIVG

3iyeP1

0.27

0.26

7.86

0.20

FFAS-3D

-EKLAEIIVEAVSAVVDDEGKVDKDLIKIEKKSGASIDDTEL-

2v5iA2

0.25

0.23

7.21

0.73

SPARKS-K

---ISGTVLPDEGVLDINTMSLYLDLWALIRLPDGSKTRMKLS

4xmmE

0.17

0.12

3.84

0.49

CNFpred

DGFTSIISLESLHQLLSIHYRITLQVLLTF-------------

3lsnA2

0.05

2.12

1.00

DEthreader

VKTGALIEASVILGALAEELKALQTYAQAIARAALRP------

4cvbA

0.07

2.81

0.84

MapAlign

-LGAAKRSIASSGPIVVDGVVIAGSTCQFSGFGCYVWMTGA--

3dl8C

0.20

0.16

5.21

0.81

MUSTER

--KATISVI-IFSLAIGVYL-WILDLTFTKIISFI----LSLR

2gy5A1

1.00

0.49

13.67

0.44

HHsearch

----------------------AMDLILINSLPLVSDAETSLT

(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	0.6182

(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	5x6sA	0.59	2.90	0.070	0.954	model1_5x6sA.pdb.gz
2	6ksuA1	0.59	2.87	0.140	1.000	model1_6ksuA1.pdb.gz
3	2vp8B	0.58	2.42	0.024	0.954	model1_2vp8B.pdb.gz
4	4ffvA	0.58	2.89	0.119	0.954	model1_4ffvA.pdb.gz
5	3blvC2	0.58	2.85	0.023	0.954	model1_3blvC2.pdb.gz
6	3g0bB	0.57	2.84	0.095	0.954	model1_3g0bB.pdb.gz
7	3m4rA	0.57	2.34	0.093	0.977	model1_3m4rA.pdb.gz
8	1pb3A2	0.56	2.80	0.070	0.954	model1_1pb3A2.pdb.gz
9	1hqsA2	0.56	2.82	0.070	0.954	model1_1hqsA2.pdb.gz
10	1ve6A	0.56	2.80	0.143	0.954	model1_1ve6A.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:0004713	1.00	protein tyrosine kinase activity
GO:0004872	0.53	receptor activity
GO:0004871	0.53	signal transducer 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:0048869	1.00	cellular developmental process
GO:0048014	1.00	Tie signaling pathway
GO:0045766	1.00	positive regulation of angiogenesis
GO:0008152	0.83	metabolic process
GO:0071704	0.82	organic substance metabolic process
GO:0044238	0.82	primary metabolic process
GO:0044237	0.82	cellular metabolic process
GO:0044260	0.81	cellular macromolecule metabolic process
GO:0080090	0.79	regulation of primary metabolic process
GO:0060255	0.79	regulation of macromolecule metabolic process
GO:0031323	0.79	regulation of cellular metabolic process
GO:0048522	0.78	positive regulation of cellular process
GO:0032502	0.78	developmental process
GO:0048856	0.77	anatomical structure development
GO:0048583	0.77	regulation of response to stimulus
GO:0048523	0.77	negative regulation of cellular process
GO:0044767	0.77	single-organism developmental process
GO:0032501	0.77	multicellular organismal process
GO:0031399	0.77	regulation of protein modification process
GO:0031325	0.77	positive regulation of cellular metabolic process
GO:0023051	0.77	regulation of signaling
GO:0019220	0.77	regulation of phosphate metabolic process
GO:0016043	0.77	cellular component organization
GO:0010646	0.77	regulation of cell communication
GO:0010604	0.77	positive regulation of macromolecule metabolic process
GO:2000352	0.76	negative regulation of endothelial cell apoptotic process
GO:0070374	0.76	positive regulation of ERK1 and ERK2 cascade
GO:0060347	0.76	heart trabecula formation
GO:0051897	0.76	positive regulation of protein kinase B signaling
GO:0051894	0.76	positive regulation of focal adhesion assembly
GO:0046777	0.76	protein autophosphorylation
GO:0043552	0.76	positive regulation of phosphatidylinositol 3-kinase activity
GO:0034446	0.76	substrate adhesion-dependent cell spreading
GO:0032878	0.76	regulation of establishment or maintenance of cell polarity
GO:0018108	0.76	peptidyl-tyrosine phosphorylation
GO:0016525	0.76	negative regulation of angiogenesis
GO:0014068	0.76	positive regulation of phosphatidylinositol 3-kinase signaling
GO:0010595	0.76	positive regulation of endothelial cell migration
GO:0007507	0.76	heart development
GO:0002040	0.76	sprouting angiogenesis
GO:0001935	0.76	endothelial cell proliferation
GO:0035556	0.53	intracellular signal transduction
GO:0050896	0.52	response to stimulus
GO:0042127	0.52	regulation of cell proliferation
GO:0006928	0.52	movement of cell or subcellular component
GO:0002376	0.52	immune system process
GO:2000251	0.51	positive regulation of actin cytoskeleton reorganization
GO:0051259	0.51	protein oligomerization
GO:0050900	0.51	leukocyte migration
GO:0044707	0.51	single-multicellular organism process
GO:0042221	0.51	response to chemical
GO:0030097	0.51	hemopoiesis
GO:0001936	0.51	regulation of endothelial cell proliferation
GO:1901700	0.50	response to oxygen-containing compound
GO:0030154	0.50	cell differentiation
GO:0010033	0.50	response to organic substance

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:0045121	1.00	membrane raft
GO:0016324	1.00	apical plasma membrane
GO:0016323	1.00	basolateral plasma membrane
GO:0009986	1.00	cell surface
GO:0009925	1.00	basal plasma membrane
GO:0005911	1.00	cell-cell junction
GO:0005902	1.00	microvillus
GO:0005887	1.00	integral component of plasma membrane
GO:0005886	1.00	plasma membrane
GO:0005884	1.00	actin filament
GO:0001725	1.00	stress fiber
GO:0044444	0.61	cytoplasmic 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	0.060	3blvH	0.447	2.58	0.182	0.767	1.1.1.41	NA
2	0.060	2ebnA	0.545	2.58	0.048	0.861	3.2.1.96	37,39
3	0.060	3g0bB	0.574	2.84	0.095	0.954	3.4.14.5	NA
4	0.060	2veoB	0.564	3.08	0.048	0.977	3.1.1.3	NA
5	0.060	1s3tA	0.551	2.84	0.071	0.977	3.5.1.5	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:

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	3blwC	0.446	3.04	0.152	0.767	0.31	AMP	complex1.pdb.gz	12,18,22,23,24
2	0.02	3blwO	0.446	3.04	0.152	0.767	0.16	AMP	complex2.pdb.gz	19,20,21,26
3	0.01	1u8eA	0.541	2.90	0.095	0.954	0.18	UUU	complex3.pdb.gz	13,19,21
4	0.01	2bgn0	0.555	2.91	0.095	0.954	0.14	III	complex4.pdb.gz	19,35,38
5	0.01	2h640	0.265	3.80	0.079	0.698	0.31	III	complex5.pdb.gz	12,18,19,20,21,36,37,38,39
6	0.01	2h642	0.265	3.80	0.079	0.698	0.23	III	complex6.pdb.gz	13,14,29

	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.