D-I-TASSER Q96J94-D3

D-I-TASSER results for Q96J94-D3

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

Input Sequence in FASTA format

>Q96J94 (115 residues)
SETVLDFMFNFYHQTEEHKFQEQVSKELIGLVVLTKYNNKTYRVDDIDWDQNPKSTFKKA
DGSEVSFLEYYRKQYNQEITDLKQPVLVSQPKRRRGPGGTLPGPAMLIPELCYLT

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| SETVLDFMFNFYHQTEEHKFQEQVSKELIGLVVLTKYNNKTYRVDDIDWDQNPKSTFKKADGSEVSFLEYYRKQYNQEITDLKQPVLVSQPKRRRGPGGTLPGPAMLIPELCYLT
Prediction	CCCHHHHHHHHHHHCCCHHHHHHHHHHCCCCSSSSCCCCCSSSSSSSCCCCCCCCSSCCCCCCSCCHHHHHHHHCCCSSCCCCCCSSSSSSCCCCCCCCCCCCSSSSCHHHCCCC
Confidence	9339999999998424268999999980994999657991899911337999566401799970239999999809411169985489873244577888774598671323589
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| SETVLDFMFNFYHQTEEHKFQEQVSKELIGLVVLTKYNNKTYRVDDIDWDQNPKSTFKKADGSEVSFLEYYRKQYNQEITDLKQPVLVSQPKRRRGPGGTLPGPAMLIPELCYLT
Prediction	8420241034026555574125303640361001032543202034034734153405477444110230036416140525711001023354657665464201000111547
	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

                   |                   |                   |                   |                   |

SS
Seq

CCCHHHHHHHHHHHCCCHHHHHHHHHHCCCCSSSSCCCCCSSSSSSSCCCCCCCCSSCCCCCCSCCHHHHHHHHCCCSSCCCCCCSSSSSSCCCCCCCCCCCCSSSSCHHHCCCC
SETVLDFMFNFYHQTEEHKFQEQVSKELIGLVVLTKYNNKTYRVDDIDWDQNPKSTFKKADGSEVSFLEYYRKQYNQEITDLKQPVLVSQPKRRRGPGGTLPGPAMLIPELCYLT

3o3iX

0.99

0.90

25.33

1.33

DEthreader

SETVLDFMFNFYHQTEEHKFQEQVSKELIGLVVLTKYNNKTYRVDDIDWDQNPKSTFKKADGSEVSFLEYYRKQYNQEITDLKQPVLVSQP----------KGPAMLIPELCYLT

3o3iX

0.99

0.90

25.33

3.42

SPARKS-K

SETVLDFMFNFYHQTEEHKFQEQVSKELIGLVVLTKYNNKTYRVDDIDWDQNPKSTFKKADGSEVSFLEYYRKQYNQEITDLKQPVLVSQP----------KGPAMLIPELCYLT

5guhA

0.39

0.36

10.55

1.21

MapAlign

LRTVLQMLSEYAA------TKKIFLEDVVGKIVMTDYNKRTYRVDDVA-NVSPKSTFKM-RDENITYIEYYYKKYNLRIQDPGQPLLISRSKPREIRAGLP-ELIYLVPELCRQT

3o3iX

1.00

0.91

25.57

1.18

CEthreader

SETVLDFMFNFYHQTEEHKFQEQVSKELIGLVVLTKYNNKTYRVDDIDWDQNPKSTFKKADGSEVSFLEYYRKQYNQEITDLKQPVLVSQPK----------GPAMLIPELCYLT

3o7xA

0.43

12.50

2.91

MUSTER

NDCVLDVMHAIYQQ-NKEHFQDECTKLLVGNIVITRYNNRTYRIDDVDWNKTPKDSFTMSDGKEITFLEYYSKNYGITVKEEDQPLLIHRPSERQDNHGMLKGEILLLPELSFMT

3o3iX

0.99

0.90

25.33

2.74

HHsearch

SETVLDFMFNFYHQTEEHKFQEQVSKELIGLVVLTKYNNKTYRVDDIDWDQNPKSTFKKADGSEVSFLEYYRKQYNQEITDLKQPVLVSQP----------KGPAMLIPELCYLT

3o7xA

0.43

12.50

2.08

FFAS-3D

NDCVLDVMHAIYQQN-KEHFQDECTKLLVGNIVITRYNNRTYRIDDVDWNKTPKDSFTMSDGKEITFLEYYSKNYGITVKEEDQPLLIHRPSERQDNHGLLKGEILLLPELSFMT

3o7xA

0.39

0.38

11.30

1.47

EigenThreader

CV---LDVMHAIYQQNKEHFQDECTKLLVGNIVITRYNNRTYRIDDVDWNKTPKDSFTMSDGKEITFLEYYSKNYGITVKEEDQPLLIHRPERQDNHGMLLKGEILLLPELSFMT

2l5cA

1.00

28.00

2.49

CNFpred

SETVLDFMFNFYHQTEEHKFQEQVSKELIGLVVLTKYNNKTYRVDDIDWDQNPKSTFKKADGSEVSFLEYYRKQYNQEITDLKQPVLVSQPKRRRGPGGTLPGPAMLIPELCYLT

5guhA

0.40

0.35

10.27

1.33

DEthreader

RDTVLQMLSEYAATK------KIFLEDVVGKIVMTDYNKRTYRVDDVA-NVSPKSTFKMRD-ENITYIEYYYKKYNLRIQDPGQPLLISRS-KP-----REPELIYLVPELCRQT

(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	0.8435

(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	3o3iX	0.85	1.31	0.990	0.913	model1_3o3iX.pdb.gz
2	5guhA	0.83	1.95	0.387	0.913	model1_5guhA.pdb.gz
3	3o7xA	0.75	2.06	0.363	0.852	model1_3o7xA.pdb.gz
4	6kr6A1	0.75	0.73	0.467	0.774	model1_6kr6A1.pdb.gz
5	2fflA	0.73	2.03	0.245	0.835	model1_2fflA.pdb.gz
6	4ei1A	0.72	1.92	0.192	0.844	model1_4ei1A.pdb.gz
7	1r4kA	0.71	2.55	0.190	0.904	model1_1r4kA.pdb.gz
8	1t2rA	0.67	2.69	0.165	0.878	model1_1t2rA.pdb.gz
9	4f1nA4	0.67	2.17	0.176	0.791	model1_4f1nA4.pdb.gz
10	2yhaA2	0.38	4.45	0.073	0.652	model1_2yhaA2.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	0.99	RNA binding
GO:0034584	0.57	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:0009987	1.00	cellular process
GO:0044699	0.84	single-organism process
GO:0065007	0.83	biological regulation
GO:0050789	0.82	regulation of biological process
GO:0044763	0.80	single-organism cellular process
GO:0071704	0.79	organic substance metabolic process
GO:0060255	0.78	regulation of macromolecule metabolic process
GO:0044260	0.78	cellular macromolecule metabolic process
GO:0044238	0.78	primary metabolic process
GO:0034641	0.78	cellular nitrogen compound metabolic process
GO:0090304	0.77	nucleic acid metabolic process
GO:0048519	0.77	negative regulation of biological process
GO:0010468	0.77	regulation of gene expression
GO:0016070	0.76	RNA metabolic process
GO:0010629	0.76	negative regulation of gene expression
GO:0031047	0.75	gene silencing by RNA
GO:0022414	0.65	reproductive process
GO:0044702	0.63	single organism reproductive process
GO:0034660	0.62	ncRNA metabolic process
GO:0032502	0.57	developmental process
GO:0044767	0.56	single-organism developmental process
GO:0050794	0.52	regulation of cellular process
GO:0006396	0.50	RNA processing

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:0044424	1.00	intracellular part
GO:0032991	1.00	macromolecular complex
GO:0043229	0.98	intracellular organelle
GO:0030529	0.94	intracellular ribonucleoprotein complex
GO:0005737	0.94	cytoplasm
GO:0044444	0.81	cytoplasmic part
GO:0043232	0.74	intracellular non-membrane-bounded organelle
GO:0043227	0.70	membrane-bounded organelle
GO:0035770	0.70	ribonucleoprotein granule
GO:0043231	0.69	intracellular membrane-bounded organelle
GO:0036464	0.69	cytoplasmic ribonucleoprotein granule
GO:0043186	0.67	P granule
GO:0005634	0.64	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	0.060	2du3A	0.433	3.97	0.059	0.678	6.1.1.27	NA
2	0.060	1jdbF	0.433	4.70	0.051	0.774	6.3.5.5	NA
3	0.060	1f4rA	0.464	4.36	0.100	0.783	3.2.2.21	NA
4	0.060	1eqrA	0.464	4.55	0.056	0.783	6.1.1.12	43
5	0.060	1nj8D	0.435	4.51	0.048	0.748	6.1.1.15	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	0.06	3dlhA	0.635	2.15	0.138	0.756	0.90	QNA	complex1.pdb.gz	37,40,42,59,70,71,77,103,105,106,107
2	0.04	1si3A	0.735	2.22	0.214	0.878	0.82	RQA	complex2.pdb.gz	36,40,42,43,57,70,71,74,75,105,106,107
3	0.04	1si2A	0.743	2.17	0.214	0.878	0.79	RQA	complex3.pdb.gz	36,40,43,58,60,70,71,75,91,103,104,105,106,107

	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.