D-I-TASSER Q96J94-D2

D-I-TASSER results for Q96J94-D2

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

Input Sequence in FASTA format

>Q96J94 (71 residues)
YQYHIDYNPLMEARRLRSALLFQHEDLIGKCHAFDGTILFLPKRLQQKVTEVFSKTRNGE
DVRITITLTNE

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| YQYHIDYNPLMEARRLRSALLFQHEDLIGKCHAFDGTILFLPKRLQQKVTEVFSKTRNGEDVRITITLTNE
Prediction	CCSSSSSCCCCCCHHHHHHHHHHHHHHHCCCSSSCCSSSSCCCCCCCCSSSSSSSCCCCCSSSSSSSSSCC
Confidence	91577504854687999999999898719956744604533651799528999991799879999999569
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| YQYHIDYNPLMEARRLRSALLFQHEDLIGKCHAFDGTILFLPKRLQQKVTEVFSKTRNGEDVRITITLTNE
Prediction	76242525173625412441055147324633022112121354157533423144576440303042478
	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 AttentionPotential. 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

CCSSSSSCCCCCCHHHHHHHHHHHHHHHCCCSSSCCSSSSCCCCCCCCSSSSSSSCCCCCSSSSSSSSSCC
YQYHIDYNPLMEARRLRSALLFQHEDLIGKCHAFDGTILFLPKRLQQKVTEVFSKTRNGEDVRITITLTNE

5guhA

0.37

10.87

1.33

DEthreader

YQYHVDISPEEDSTGVRKALMRVHSKTL-GGYLFDGTVLYTVNRLHPDPMELYSDRKTNERMRILIKLTCE

5guhA

0.39

0.38

11.25

1.54

SPARKS-K

YQYHVDISPEEDSTGVRKALMRVHSKTLG-GYLFDGTVLYTVNRLHPDPMELYSDRKTNERMRILIKLTCE

5guhA1

0.39

0.38

11.25

1.26

MapAlign

YQYHVDISPEEDSTGVRKALMRVHSKTLGG-YLFDGTVLYTVNRLHPDPMELYSDRKDNERMRILIKLTCE

5guhA1

0.39

0.38

11.25

1.18

CEthreader

YQYHVDISPEEDSTGVRKALMRVHSKTLGG-YLFDGTVLYTVNRLHPDPMELYSDRKDNERMRILIKLTCE

6kr6A

0.28

8.61

1.66

MUSTER

VHYHVEFEPSIENPRVRMGVLSNHANLLGSGYLFDGLQLFTTRKFEQEITVLSGKSKLDIEYKISIKFVGF

5guhA1

0.39

0.38

11.25

2.07

HHsearch

YQYHVDISPEEDSTGVRKALMRVHSKTLGG-YLFDGTVLYTVNRLHPDPMELYSRKTDNERMRILIKLTCE

6kr6A

0.28

8.61

1.11

FFAS-3D

VHYHVEFEPSIENPRVRMGVLSNHANLLGSGYLFDGLQLFTTRKFEQEITVLSGKSKLDIEYKISIKFVGF

2f8tA3

0.09

0.08

3.23

0.58

EigenThreader

TFTVFKPTHEIQ-KEKLNKVRWRVFLQTGLPTFRRDEFWCAG---KVEKDTLYLTLSNGEIVELKRVGEEE

5guhA

0.39

0.38

11.25

1.35

CNFpred

YQYHVDISPEEDSTGVRKALMRVHSKTLG-GYLFDGTVLYTVNRLHPDPMELYSDRKDNERMRILIKLTCE

5guhA1

0.37

10.87

1.33

DEthreader

YQYHVDISPEEDSTGVRKALMRVHSKTL-GGYLFDGTVLYTVNRLHPDPMELYSDRKTNERMRILIKLTCE

(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	0.8314

(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 AttentionPotential, 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	5guhA	0.94	0.72	0.371	0.986	model1_5guhA.pdb.gz
2	6kr6A	0.87	1.12	0.261	0.972	model1_6kr6A.pdb.gz
3	4ei1A2	0.80	1.51	0.206	0.958	model1_4ei1A2.pdb.gz
4	3wz0C	0.71	2.35	0.058	0.958	model1_3wz0C.pdb.gz
5	2av5A	0.70	2.58	0.057	0.972	model1_2av5A.pdb.gz
6	3f73A2	0.70	2.55	0.132	0.958	model1_3f73A2.pdb.gz
7	2f8tA	0.64	2.33	0.090	0.944	model1_2f8tA.pdb.gz
8	5i4aA	0.46	3.20	0.036	0.761	model1_5i4aA.pdb.gz
9	1mkyA3	0.45	3.93	0.045	0.859	model1_1mkyA3.pdb.gz
10	2j9oD	0.45	3.82	0.050	0.789	model1_2j9oD.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:0003723	1.00	RNA binding
GO:0034584	0.94	piRNA 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:0065007	1.00	biological regulation
GO:0050789	1.00	regulation of biological process
GO:0044763	1.00	single-organism cellular process
GO:0031047	0.97	gene silencing by RNA
GO:0044702	0.96	single organism reproductive process
GO:0071704	0.78	organic substance metabolic process
GO:0044260	0.77	cellular macromolecule metabolic process
GO:0044238	0.77	primary metabolic process
GO:0034641	0.77	cellular nitrogen compound metabolic process
GO:0090304	0.76	nucleic acid metabolic process
GO:0044767	0.76	single-organism developmental process
GO:0016070	0.75	RNA metabolic process
GO:0007276	0.70	gamete generation
GO:0050794	0.67	regulation of cellular process
GO:0034660	0.65	ncRNA metabolic process
GO:0022412	0.64	cellular process involved in reproduction in multicellular organism
GO:0048869	0.62	cellular developmental process
GO:0003006	0.62	developmental process involved in reproduction
GO:0048856	0.61	anatomical structure development
GO:0034587	0.61	piRNA metabolic process
GO:0007281	0.58	germ cell development
GO:0080090	0.56	regulation of primary metabolic process
GO:0051171	0.56	regulation of nitrogen compound metabolic process
GO:0031323	0.56	regulation of cellular metabolic process
GO:0010608	0.54	posttranscriptional regulation of gene expression
GO:2000112	0.52	regulation of cellular macromolecule biosynthetic 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:0044464	1.00	cell part
GO:0032991	1.00	macromolecular complex
GO:0044424	0.99	intracellular part
GO:0044444	0.97	cytoplasmic part
GO:0043229	0.97	intracellular organelle
GO:0043232	0.96	intracellular non-membrane-bounded organelle
GO:0036464	0.93	cytoplasmic ribonucleoprotein granule
GO:0005737	0.93	cytoplasm
GO:0043186	0.92	P granule
GO:0043231	0.57	intracellular membrane-bounded organelle
GO:0005634	0.51	nucleus

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	0.067	1fvqA	0.544	2.79	0.066	0.859	3.6.3.4	27
2	0.066	1spbP	0.523	2.80	0.054	0.775	3.4.21.62	NA
3	0.066	3cjkA	0.568	2.67	0.083	0.845	3.6.3.4	19
4	0.066	1fwpA	0.500	2.88	0.169	0.817	2.7.13.3	21,25,66
5	0.060	2ausA	0.613	2.53	0.077	0.915	5.4.99.-	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	0.15	3f73B	0.708	2.54	0.132	0.958	0.12	QNA	complex1.pdb.gz	38,40,62,64
2	0.03	3dlhA	0.716	2.48	0.132	0.958	0.19	QNA	complex2.pdb.gz	40,62,64
3	0.02	3ho1A	0.697	2.55	0.132	0.958	0.14	QNA	complex3.pdb.gz	4,17,18
4	0.01	2qe2A	0.627	2.59	0.016	0.901	0.19	452	complex4.pdb.gz	21,22,38,39
5	0.01	3golB	0.641	2.37	0.015	0.915	0.17	XND	complex5.pdb.gz	21,22,38,39
6	0.01	2whoB	0.641	2.60	0.015	0.930	0.20	VGI	complex6.pdb.gz	29,30,32,34
7	0.01	3skeA	0.649	2.38	0.015	0.915	0.14	054	complex7.pdb.gz	18,21,22,38,39
8	0.01	2hwhA	0.651	2.36	0.015	0.915	0.23	RNA	complex8.pdb.gz	29,35,54
9	0.01	3skhA	0.641	2.42	0.015	0.915	0.12	058	complex9.pdb.gz	25,36,40
10	0.01	3csoA	0.645	2.58	0.015	0.930	0.12	XNI	complex10.pdb.gz	23,24,25,36,40

	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, Chengxin Zhang, Yang Li, Robin Pearce, Eric W. Bell, Yang Zhang. Folding non-homology proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. In preparation, 2020.