D-I-TASSER Q12913-D3

D-I-TASSER results for Q12913-D3

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

Input Sequence in FASTA format

>Q12913 (73 residues)
DVTAVNISATSLTLIWKVSDNESSSNYTYKIHVAGETDSSNLNVSEPRAVIPGLRSSTFY
NITVCPVLGDIEG

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| DVTAVNISATSLTLIWKVSDNESSSNYTYKIHVAGETDSSNLNVSEPRAVIPGLRSSTFYNITVCPVLGDIEG
Prediction	CCSSSSSSCCSSSSSSSSCCCCCCCSSSSSSSSSCCCCCCCSSSCCCSSSSSCCCCCCSSSSSSSSSSCCCCC
Confidence	9269985166589999818999850489999993588741123245179971679863788999886257789
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| DVTAVNISATSLTLIWKVSDNESSSNYTYKIHVAGETDSSNLNVSEPRAVIPGLRSSTFYNITVCPVLGDIEG
Prediction	8354362444414030425565433312030213474543434364341304414443323030202256478
	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

CCSSSSSSCCSSSSSSSSCCCCCCCSSSSSSSSSCCCCCCCSSSCCCSSSSSCCCCCCSSSSSSSSSSCCCCC
DVTAVNISATSLTLIWKVSDNESSSNYTYKIHVAGETDSSNLNVSEPRAVIPGLRSSTFYNITVCPVLGDIEG

1fnfA

0.18

5.78

1.33

DEthreader

TLRFTNIGPDTMRVTWAPPPSI-D-LTNFLVRYSPNEDVAELSISDNAVVLTNLLPGTEYVVSVSSVYEQHES

5e52A1

0.15

5.07

1.45

SPARKS-K

IVIVEEITESTATLSWSPAADNHSPISSYNLQARSPFSLGIITGDMESAMAVDLNPWVEYEFRVVATNPTGDP

2n1kA

0.24

0.23

7.25

0.39

MapAlign

PPTVDQVDDTSIVVRWSRP---QAPITGYRIVYSPEGSSTELNLEANSVTLSDLQPGVQYNITIYAVEENQES

5fn8A

0.19

6.18

0.26

CEthreader

GMKTSRASDNSINVTCNSPYEINGPEARYILEVKSGGLVKTFNQSTCKFVVDNLYYSTDYEFLVYFYNGEYLG

2dleA

1.00

28.00

1.12

MUSTER

DVTAVNISATSLTLIWKVSDNESSSNYTYKIHVAGETDSSNLNVSEPRAVIPGLRSSTFYNITVCPVLGDIEG

4bk4A

0.21

6.55

0.83

HHsearch

LVQAKEVTRYSVALAWLEPDRPNGVILEYEVKYYEKDQSYIVRTAARNTDIKGLNPLTSYVFHVRARTAAGYG

2jllA2

0.10

3.59

1.32

FFAS-3D

SIHGQPSSGKSFKLSITKQDDGGAPILEYIVKYRSQWLEKKVQGNKDHIILEHLQWTMGYEVQITAANRLGYS

7ndgB3

0.19

6.18

0.37

EigenThreader

DVTVVSKKPRTIIVNWQPPSEANGKITGYIIYYSTDHDWVIEPVNRLTHQIQELTLDTPYYFKIQARNSKGMG

2dleA

1.00

28.00

1.26

CNFpred

DVTAVNISATSLTLIWKVSDNESSSNYTYKIHVAGETDSSNLNVSEPRAVIPGLRSSTFYNITVCPVLGDIEG

1fnfA3

0.18

5.78

1.33

DEthreader

TLRFTNIGPDTMRVTWAPPPSI-D-LTNFLVRYSPNEDVAELSISDNAVVLTNLLPGTEYVVSVSSVYEQHES

(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	0.84

(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	5dftA	0.87	1.16	0.129	0.959	model1_5dftA.pdb.gz
2	2rb8A	0.87	1.25	0.143	0.959	model1_2rb8A.pdb.gz
3	5fn8A	0.87	1.56	0.192	1.000	model1_5fn8A.pdb.gz
4	1fnfA	0.87	1.39	0.197	0.973	model1_1fnfA.pdb.gz
5	4gh7B	0.86	1.47	0.197	0.973	model1_4gh7B.pdb.gz
6	6gvkA	0.86	1.58	0.192	1.000	model1_6gvkA.pdb.gz
7	5fmvA2	0.86	1.60	0.178	1.000	model1_5fmvA2.pdb.gz
8	1wfoA	0.85	1.42	0.151	1.000	model1_1wfoA.pdb.gz
9	1qr4A2	0.85	1.25	0.186	0.959	model1_1qr4A2.pdb.gz
10	1x5hA	0.84	1.54	0.205	1.000	model1_1x5hA.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	0.84	catalytic activity
GO:0016791	0.80	phosphatase activity
GO:0004721	0.67	phosphoprotein phosphatase activity
GO:0004725	0.66	protein tyrosine phosphatase activity
GO:0005102	0.65	receptor binding
GO:0019899	0.64	enzyme binding
GO:0045295	0.63	gamma-catenin binding
GO:0019901	0.63	protein kinase binding
GO:0005161	0.63	platelet-derived growth factor receptor binding
GO:0070097	0.62	delta-catenin binding
GO:0051019	0.62	mitogen-activated protein kinase binding
GO:0008013	0.62	beta-catenin 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:0051898	1.00	negative regulation of protein kinase B signaling
GO:0051894	1.00	positive regulation of focal adhesion assembly
GO:0050860	1.00	negative regulation of T cell receptor signaling pathway
GO:0048008	1.00	platelet-derived growth factor receptor signaling pathway
GO:0043407	1.00	negative regulation of MAP kinase activity
GO:0042059	1.00	negative regulation of epidermal growth factor receptor signaling pathway
GO:0009987	0.87	cellular process
GO:0044699	0.86	single-organism process
GO:0008152	0.85	metabolic process
GO:0044763	0.84	single-organism cellular process
GO:0044238	0.84	primary metabolic process
GO:0044237	0.84	cellular metabolic process
GO:0043170	0.84	macromolecule metabolic process
GO:0006464	0.83	cellular protein modification process
GO:0065008	0.82	regulation of biological quality
GO:0048584	0.82	positive regulation of response to stimulus
GO:0035335	0.82	peptidyl-tyrosine dephosphorylation
GO:0032879	0.82	regulation of localization
GO:0023056	0.82	positive regulation of signaling
GO:0010647	0.82	positive regulation of cell communication
GO:0002684	0.82	positive regulation of immune system process
GO:0051897	0.81	positive regulation of protein kinase B signaling
GO:0050918	0.81	positive chemotaxis
GO:0043116	0.81	negative regulation of vascular permeability
GO:0030336	0.81	negative regulation of cell migration
GO:0030308	0.81	negative regulation of cell growth
GO:0010642	0.81	negative regulation of platelet-derived growth factor receptor signaling pathway
GO:0008285	0.81	negative regulation of cell proliferation
GO:0002376	0.55	immune system process
GO:0002757	0.53	immune response-activating signal transduction
GO:0060242	0.52	contact inhibition
GO:0050852	0.52	T cell receptor signaling pathway

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:0005911	1.00	cell-cell junction
GO:0005886	1.00	plasma membrane
GO:0043226	0.86	organelle
GO:0043227	0.85	membrane-bounded organelle
GO:0044425	0.84	membrane part
GO:0044459	0.82	plasma membrane part
GO:0070062	0.81	extracellular exosome
GO:0009986	0.81	cell surface
GO:0001772	0.81	immunological synapse
GO:0044424	0.56	intracellular part
GO:0016021	0.55	integral component of membrane
GO:0005887	0.53	integral component of plasma 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	0.117	1k85A	0.747	1.93	0.217	0.945	3.2.1.14	NA
2	0.080	2dlhA	0.818	1.91	0.192	1.000	3.1.3.48	NA
3	0.067	1zvhA	0.654	2.97	0.099	0.973	3.2.1.17	NA
4	0.067	2hvbB	0.674	2.33	0.043	0.945	1.15.1.2	NA
5	0.067	1zvyA	0.634	3.09	0.085	0.973	3.2.1.17	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	0.04	3dgcR	0.784	1.79	0.181	0.986	1.06	UUU	complex1.pdb.gz	35,36,38,53,55,60

	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.