D-I-TASSER Q8WUJ3-D4

D-I-TASSER results for Q8WUJ3-D4

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

Input Sequence in FASTA format

>Q8WUJ3 (153 residues)
YKTSNLRMKIIKNDFPSHPLYLEGALTRSTHYQQYQPVVTLQKGYTIHWDQTAPAELAIW
LINFNKGDWIRVGLCYPRGTTFSILSDVHNRLLKQTSKTGVFVRTLQMDKVEQSYPGRSH
YYWDEDSGLLFLKLKAQNEREKFAFCSMKGCER

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| YKTSNLRMKIIKNDFPSHPLYLEGALTRSTHYQQYQPVVTLQKGYTIHWDQTAPAELAIWLINFNKGDWIRVGLCYPRGTTFSILSDVHNRLLKQTSKTGVFVRTLQMDKVEQSYPGRSHYYWDEDSGLLFLKLKAQNEREKFAFCSMKGCER
Prediction	CCCCCCSSSSSSCCCCCCCSSSSCCCCCCCCCCCSSSSSSSCCCSSSSCCCCCCCCSSSSSSCCCCCCSSSSSSSCCCCCSSSSSSSSSSCCCCCSCCCCSSSSCCCHHHHHCCCCCCCSSSSCCCCCSSSSSSSSCCCCCCCCCCCCCCCCC
Confidence	988985699996378998369982789999843154789834526998399999845999750479976999997599958999997652244412465146644788998447899854787189865899998236888765478778689
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| YKTSNLRMKIIKNDFPSHPLYLEGALTRSTHYQQYQPVVTLQKGYTIHWDQTAPAELAIWLINFNKGDWIRVGLCYPRGTTFSILSDVHNRLLKQTSKTGVFVRTLQMDKVEQSYPGRSHYYWDEDSGLLFLKLKAQNEREKFAFCSMKGCER
Prediction	853741403023342463303041236644534311000134430102063431640302033254431010000014613040234234434443454441331441551465475432000154112000102244626432103553178
	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

CCCCCCSSSSSSCCCCCCCSSSSCCCCCCCCCCCSSSSSSSCCCSSSSCCCCCCCCSSSSSSCCCCCCSSSSSSSCCCCCSSSSSSSSSSCCCCCSCCCCSSSSCCCHHHHHCCCCCCCSSSSCCCCCSSSSSSSSCCCCCCCCCCCCCCCCC
YKTSNLRMKIIKNDFPSHPLYLEGALTRSTHYQQYQPVVTLQKGYTIHWDQTAPAELAIWLINFNKGDWIRVGLCYPRGTTFSILSDVHNRLLKQTSKTGVFVRTLQMDKVEQSYPGRSHYYWDEDSGLLFLKLKAQNEREKFAFCSMKGCER

2x2hA2

0.06

2.50

0.64

CEthreader

TDEDPLVFEVFPLGNNRADGMCYLDDG-GVTTNAEDNGKFSVVKVAAEQDGGTETITFTNDCYEYVFGGPFYVRVRGAQSPSNIHVSSG-----AGSQDMKVSSATSRAALFNDGE-NGDFWVDQETDSLWLKLPNVVLPDAVITIT------

5whzH

0.12

0.10

3.73

0.68

EigenThreader

DFDNAWMTWVRQPPGKGLEWVGRITGPGEGWSVDYAEEMNNVTGYYFCARTYPPGEEYFQDWGRKPGTSVKVSCKAPGNTLLHWVRSVP----GQGLQW-MGWISHEGDKKVIVERFKAKVTIDWSTNTAYLQLSGLTSGD----------TA

6jr6A2

0.07

0.05

2.15

0.46

FFAS-3D

-----------------YPVTFDIFPGNLNK----------ETSFTFYEDDGESVFCKTKITSKASNEEIKITVGEAGPRNFILKIHASNKPKDVFAGGEKLKNVKPHVLEKNIDFTKINWSWNEAENVISVRIPDSGKN-------------

3qd1X1

0.12

0.10

3.43

0.68

SPARKS-K

YHDVKGSVTTSFDD-TSRLLTWTINLTPRQVKSNLGALVSISETRTVTINGAW----NLYTGESVNNNVLRITTQVNDTGKLGLRLVTSDK--KITKT----NLPLEFSQV-AATTNGS-----------WDKAGYNTTIVEK----------

5f7uA

0.13

0.11

3.83

1.04

CNFpred

FAKAGAIIPMNMTD----GYQLGQNVGNDLSYDNLTFRVYPSSEYSFYDDVNGGEMRDISVSEDFANEKVSVDLPAM-ADETTMQVFSTE-PTSVTIDGADVAKADTLDAFNEA---TTGYYYDTVQNLTYVKAAA-----------------

2x2hA

0.10

0.07

2.68

0.83

DEthreader

-----------YRWQLLGGHDR------------GAILPTDDLVFEVFPLGNEQTETITFTNYYVFGGPFYVRVRGA-QSPSNIHVSSG--A---GSQDMKVSSATSRAALFNDGE-NGDFWVDQETDSLWLKLPNVVLP----DAV------

4pfeA

0.08

3.08

0.76

MapAlign

MPEGYVQERTIFKDDGTYKTRAEVKFEGDTLVNRIEIRHNVVQLADHYQQNTPIQLVESGGALVQPGGSLRLSCAASVNYSMRWYRQAPGK----EREWVAGM-SSAGDRSSYEVKGRFTISRDDARNTVYLQMNLKPTAVYYCNVNVGFEYW

4kmqA7

0.16

0.13

4.35

0.51

MUSTER

--------AII-TDGYQLGQN---VGNDLKSYDNLTFRVYPSGEYSFYDVNGG--ERDISVSEDFANEKVSVDLP-AADETTQVFST---EPTSVTIDGADVAKADTLDAFNE---ATTGYYYDTVQNLTYVKAAAKDAKNGVNHA-------

6m76A

0.10

3.59

0.55

HHsearch

TPLWKVPVFV-KDG---SIIPMTNNNPKEIQRDQRSFLIYPNTSFNMYEDGISTSTTKINSQGPKEKGDLTVTIEYKDFDSTTLDLLASEA-PESGGTEVTLKQAANKEEFLAG---TNLYYFDKEQSALSVKLAKQSVTAGFINKGTGGNTT

2x2hA

0.09

0.08

3.21

0.56

CEthreader

TDEDPLVFEVFPLGNNRADGMCYLDDGGVTTNAEDNGKFSVVKVAAEQDGGTETITFTNDCYEYVFGGPFYVRVRGAQSPSNIHVS-------SGAGSQDMKVSSATSRAALFNDGENGDFWVDQETDSLWLKLPNVVLPDAVITIT------

(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	0.6933

(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	2x2hA	0.52	4.08	0.079	0.745	model1_2x2hA.pdb.gz
2	6tzlA	0.51	4.99	0.060	0.856	model1_6tzlA.pdb.gz
3	6m76A	0.50	3.76	0.106	0.712	model1_6m76A.pdb.gz
4	2hc9A	0.49	4.63	0.081	0.837	model1_2hc9A.pdb.gz
5	5nthA2	0.49	4.68	0.092	0.830	model1_5nthA2.pdb.gz
6	5ntfA1	0.49	4.68	0.081	0.830	model1_5ntfA1.pdb.gz
7	6ggyA	0.49	4.47	0.050	0.791	model1_6ggyA.pdb.gz
8	5nz7A	0.49	4.65	0.086	0.817	model1_5nz7A.pdb.gz
9	4efdA	0.49	4.96	0.068	0.843	model1_4efdA.pdb.gz
10	6evuA	0.48	5.02	0.081	0.837	model1_6evuA.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	0.91	catalytic activity
GO:0097367	0.89	carbohydrate derivative binding
GO:0016787	0.89	hydrolase activity
GO:0046923	0.88	ER retention sequence binding
GO:0032050	0.88	clathrin heavy chain binding
GO:0005540	0.88	hyaluronic acid binding
GO:0004415	0.88	hyalurononglucosaminidase 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:0065007	0.86	biological regulation
GO:0050789	0.86	regulation of biological process
GO:0050794	0.85	regulation of cellular process
GO:0008152	0.85	metabolic process
GO:0071704	0.84	organic substance metabolic process
GO:0048518	0.82	positive regulation of biological process
GO:0043170	0.82	macromolecule metabolic process
GO:0006807	0.82	nitrogen compound metabolic process
GO:1901564	0.81	organonitrogen compound metabolic process
GO:0080090	0.81	regulation of primary metabolic process
GO:0065008	0.81	regulation of biological quality
GO:0043270	0.81	positive regulation of ion transport
GO:0031325	0.81	positive regulation of cellular metabolic process
GO:0010604	0.81	positive regulation of macromolecule metabolic process
GO:1900020	0.80	positive regulation of protein kinase C activity
GO:0090314	0.80	positive regulation of protein targeting to membrane
GO:0051281	0.80	positive regulation of release of sequestered calcium ion into cytosol
GO:0030335	0.80	positive regulation of cell migration
GO:0030214	0.80	hyaluronan catabolic process
GO:0010800	0.80	positive regulation of peptidyl-threonine phosphorylation
GO:0050877	0.55	neurological system process
GO:0007600	0.54	sensory perception
GO:0007605	0.53	sensory perception of sound
GO:0009987	0.50	cellular process

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:0043227	1.00	membrane-bounded organelle
GO:0044464	0.92	cell part
GO:0044424	0.88	intracellular part
GO:0016020	0.84	membrane
GO:0044444	0.83	cytoplasmic part
GO:0044446	0.82	intracellular organelle part
GO:0043229	0.81	intracellular organelle
GO:0043231	0.80	intracellular membrane-bounded organelle
GO:0005886	0.80	plasma membrane
GO:0098588	0.79	bounding membrane of organelle
GO:0005737	0.79	cytoplasm
GO:0030665	0.78	clathrin-coated vesicle membrane
GO:0005783	0.78	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	1lf6A	0.469	4.75	0.038	0.771	3.2.1.3	NA
2	0.060	11asA	0.449	4.75	0.044	0.739	6.3.1.1	118
3	0.060	12asA	0.446	4.96	0.037	0.752	6.3.1.1	NA
4	0.060	2hb6A	0.486	4.83	0.067	0.843	3.4.11.1	NA
5	0.060	3ecaA	0.441	4.74	0.068	0.752	3.5.1.1	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	0.01	1d6uA	0.479	4.66	0.048	0.784	0.12	HY1	complex1.pdb.gz	61,71,72
2	0.01	3kzwD	0.474	4.81	0.054	0.817	0.34	NA	complex2.pdb.gz	72,73,128
3	0.01	2x2iB	0.517	3.99	0.079	0.739	0.10	QPS	complex3.pdb.gz	44,45,46
4	0.01	3kr5I	0.485	4.60	0.034	0.817	0.37	CO3	complex4.pdb.gz	67,68,69
5	0.01	3kr4A	0.481	4.65	0.034	0.817	0.15	BES	complex5.pdb.gz	73,131,132,133,134
6	0.01	3kr5F	0.483	4.64	0.020	0.817	0.14	BEY	complex6.pdb.gz	65,68,121
7	0.01	3t8wA	0.482	4.75	0.034	0.824	0.12	DGZ	complex7.pdb.gz	42,47,68,70,138
8	0.01	2x2iC	0.516	4.08	0.079	0.745	0.28	QPS	complex8.pdb.gz	44,60,61,65,66
9	0.01	3kr5J	0.484	4.61	0.034	0.817	0.16	BEY	complex9.pdb.gz	60,71,72,114
10	0.01	2j9aA	0.474	4.70	0.061	0.804	0.21	III	complex10.pdb.gz	43,112,114,116,117

	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.