D-I-TASSER Q8TD43-D2

D-I-TASSER results for Q8TD43-D2

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

Input Sequence in FASTA format

>Q8TD43 (90 residues)
LLLIDGDEKMLTRIENATQAQLPCLLVAGSGGAADCLAETLEDTLAPGSGGARQGEARDR
IRRFFPKGDLEVLQAQVERIMTRKELLTVY

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| LLLIDGDEKMLTRIENATQAQLPCLLVAGSGGAADCLAETLEDTLAPGSGGARQGEARDRIRRFFPKGDLEVLQAQVERIMTRKELLTVY
Prediction	CSSSCCCHHHHHHHHHHHHCCCCSSSSSCCCCHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCSSSC
Confidence	878719877999999997418988999379718999999996212457761268999999997699122999999999998277725529
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| LLLIDGDEKMLTRIENATQAQLPCLLVAGSGGAADCLAETLEDTLAPGSGGARQGEARDRIRRFFPKGDLEVLQAQVERIMTRKELLTVY
Prediction	431143446205302521545120000133431041014116444444566244541462057403773144015304502735311334
	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

                   |                   |                   |                   |

SS
Seq

CSSSCCCHHHHHHHHHHHHCCCCSSSSSCCCCHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCSSSC
LLLIDGDEKMLTRIENATQAQLPCLLVAGSGGAADCLAETLEDTLAPGSGGARQGEARDRIRRFFPKGDLEVLQAQVERIMTRKELLTVY

6co7A

0.14

0.13

4.58

1.33

DEthreader

LLVLEGGPNTVATMYELIKKKVPAVVIDGSGRAASVVGFAYNH-TIKRIDPQEDEVRAKVVEV-FGAKGADKTYSMIKDVLEDEKMISVY

6co7A

0.16

5.19

1.17

SPARKS-K

LLVLEGGPNTVATMYELIKKKVPAVVIDGSGRAASVVGFAYNHTIKRNVDGQEDEVRAKVVEVF-GAKGADKTYSMIKDVLEDEKMISVY

6co7A1

0.15

0.14

4.89

1.26

MapAlign

LLVLEGGPNTVATMYELIKKKVPAVVIDGSGRAASVVGFAYNKRNVDGQTINVIEVRAKVVE-VFGAKGADKTYSMIKDVLEDEKMISVY

6co7A

0.17

5.50

1.03

CEthreader

LLVLEGGPNTVATMYELIKKKVPAVVIDGSGRAASVVGFAYNHTIKRNTINVIDPEVRAKVVEVFGAKGADKTYSMIKDVLEDEKMISVY

6drjA

0.20

6.40

1.24

MUSTER

CVVLDGGPGTLNTIYNSMLNHTPCVVLEGSGRLADVIAHVASVPVSKVTMALINRLLKRFFMQEYKNLQIIEWTKKIQDILRMPHLLTVF

6drjA

0.24

0.23

7.26

2.08

HHsearch

CVVLDGGPGTLNTIYNSMLNHTPCVVLEGSGRLADVIAHVASVPVSKV----TMALINRLLKRFFMQEQIIEWTKKIQDILRMPHLLTVF

6co7A1

0.17

5.49

1.03

FFAS-3D

-LVLEGGPNTVATMYELIKKKVPAVVIDGSGRAASVVGFAYNHTIKRNVDGQTEDEVRAKVVEVFGAKGADKTYSMIKDVLEDEKMISVY

6co7A1

0.14

4.90

1.07

EigenThreader

AGVLEGGPNTVATMYELIKKKVPAVVIDGSGRAASVVGFAYNHTIKRNVDINVIDEVRAKVVEVFGAKGADKTYSMIKDVLEDEKMISVY

6drjA

0.25

0.23

7.24

0.91

CNFpred

CVVLDGGPGTLNTIYNSMLNHTPCVVLEGSGRLADVIAHVASVPVSK----VTMALINRLLKRFFM-LQIIEWTKKIQDILRMPHLLTVF

6co7A1

0.14

0.13

4.58

1.33

DEthreader

LLVLEGGPNTVATMYELIKKKVPAVVIDGSGRAASVVGFAYNH-TIKRIDPQEDEVRAKVVEV-FGAKGADKTYSMIKDVLEDEKMISVY

(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	0.7786

(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	8si7C1	0.86	1.65	0.256	0.967	model1_8si7C1.pdb.gz
2	6co7A1	0.83	1.94	0.146	0.967	model1_6co7A1.pdb.gz
3	8si2A	0.82	1.95	0.244	0.967	model1_8si2A.pdb.gz
4	7mbpA	0.81	1.81	0.274	0.933	model1_7mbpA.pdb.gz
5	5wp6A	0.80	1.14	0.633	0.878	model1_5wp6A.pdb.gz
6	8e4lA	0.78	1.74	0.232	0.911	model1_8e4lA.pdb.gz
7	6drjA	0.77	2.07	0.202	0.933	model1_6drjA.pdb.gz
8	6mixA1	0.77	2.00	0.268	0.911	model1_6mixA1.pdb.gz
9	7vq1A	0.76	2.02	0.271	0.933	model1_7vq1A.pdb.gz
10	8ddqA1	0.76	2.09	0.215	0.878	model1_8ddqA1.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:0005261	1.00	cation channel activity
GO:0022836	0.93	gated channel activity
GO:0005227	0.92	calcium activated cation channel activity
GO:0046873	0.79	metal ion transmembrane transporter activity
GO:0015077	0.54	monovalent inorganic cation transmembrane transporter 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:0044699	0.91	single-organism process
GO:0009987	0.90	cellular process
GO:0065007	0.88	biological regulation
GO:0044763	0.88	single-organism cellular process
GO:0050789	0.87	regulation of biological process
GO:0050794	0.86	regulation of cellular process
GO:0008152	0.84	metabolic process
GO:0065008	0.83	regulation of biological quality
GO:0048518	0.83	positive regulation of biological process
GO:0032501	0.83	multicellular organismal process
GO:0051049	0.82	regulation of transport
GO:0048878	0.82	chemical homeostasis
GO:0048583	0.82	regulation of response to stimulus
GO:0048522	0.82	positive regulation of cellular process
GO:0048519	0.82	negative regulation of biological process
GO:0044260	0.82	cellular macromolecule metabolic process
GO:0019538	0.82	protein metabolic process
GO:0008016	0.82	regulation of heart contraction
GO:1904199	0.81	positive regulation of regulation of vascular smooth muscle cell membrane depolarization
GO:1904179	0.81	positive regulation of adipose tissue development
GO:1903949	0.81	positive regulation of atrial cardiac muscle cell action potential
GO:0090263	0.81	positive regulation of canonical Wnt signaling pathway
GO:0045907	0.81	positive regulation of vasoconstriction
GO:0045668	0.81	negative regulation of osteoblast differentiation
GO:0045600	0.81	positive regulation of fat cell differentiation
GO:0035774	0.81	positive regulation of insulin secretion involved in cellular response to glucose stimulus
GO:0030502	0.81	negative regulation of bone mineralization
GO:0016925	0.81	protein sumoylation
GO:0010460	0.81	positive regulation of heart rate
GO:0008284	0.81	positive regulation of cell proliferation
GO:0007204	0.81	positive regulation of cytosolic calcium ion concentration
GO:0002724	0.81	regulation of T cell cytokine production
GO:0002407	0.81	dendritic cell chemotaxis
GO:0006810	0.79	transport
GO:0006811	0.76	ion transport
GO:0006816	0.66	calcium ion transport
GO:0055085	0.56	transmembrane transport
GO:0034220	0.51	ion transmembrane transport

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	0.97	membrane
GO:0005886	0.96	plasma membrane
GO:0043025	0.91	neuronal cell body
GO:0044424	0.90	intracellular part
GO:0044444	0.88	cytoplasmic part
GO:0043231	0.87	intracellular membrane-bounded organelle
GO:0005829	0.86	cytosol
GO:0005794	0.85	Golgi apparatus
GO:0005783	0.85	endoplasmic reticulum
GO:0044422	0.64	organelle part
GO:0044446	0.63	intracellular organelle part
GO:0044428	0.59	nuclear part
GO:0005654	0.58	nucleoplasm

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	1mc8A	0.547	3.44	0.117	0.800	3.1.-.-	NA
2	0.060	2bijA	0.519	4.15	0.108	0.867	3.1.3.48	NA
3	0.060	2fh7A	0.520	3.97	0.095	0.867	3.1.3.48	NA
4	0.060	1n1eA	0.530	3.24	0.045	0.867	1.1.1.8	NA
5	0.060	2oc3A	0.531	3.66	0.037	0.867	3.1.3.48	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	4a21D	0.539	3.60	0.085	0.867	0.64	SO4	complex1.pdb.gz	4,6,27,35
2	0.01	1q6tB	0.539	3.84	0.046	0.900	0.69	600	complex2.pdb.gz	34,37,38
3	0.01	1q6nB	0.539	3.84	0.046	0.900	0.52	P90	complex3.pdb.gz	35,38,39
4	0.01	1q6pB	0.538	3.68	0.047	0.878	0.52	213	complex4.pdb.gz	31,34,35,37
5	0.01	1q6nA	0.539	3.84	0.046	0.900	0.52	P90	complex5.pdb.gz	29,32,33

	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.