D-I-TASSER Q9NQT5-D2

D-I-TASSER results for Q9NQT5-D2

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

Input Sequence in FASTA format

>Q9NQT5 (86 residues)
YVPVKGDHVIGIVTAKSGDIFKVDVGGSEPASLSYLSFEGATKRNRPNVQVGDLIYGQFV
VANKDMEPEMVCIDSCGRANGMGVIG

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| YVPVKGDHVIGIVTAKSGDIFKVDVGGSEPASLSYLSFEGATKRNRPNVQVGDLIYGQFVVANKDMEPEMVCIDSCGRANGMGVIG
Prediction	CCCCCCCSSSSSSSSSSCCSSSSSCCCCCSSSSCHHHCCCCHHHCCCCCCCCCSSSSSSSSCCCCCCSSSSSSCCCCCCCCCCCCC
Confidence	98999957999999982767999838996067544556761121356789981999999971799863899957876433873079
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| YVPVKGDHVIGIVTAKSGDIFKVDVGGSEPASLSYLSFEGATKRNRPNVQVGDLIYGQFVVANKDMEPEMVCIDSCGRANGMGVIG
Prediction	74245713000203444443130203343403023331542366445405423101010241367240303022564467423638
	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

CCCCCCCSSSSSSSSSSCCSSSSSCCCCCSSSSCHHHCCCCHHHCCCCCCCCCSSSSSSSSCCCCCCSSSSSSCCCCCCCCCCCCC
YVPVKGDHVIGIVTAKSGDIFKVDVGGSEPASLSYLSFEGATKRNRPNVQVGDLIYGQFVVANKDMEPEMVCIDSCGRANGMGVIG

2ja9A

0.38

0.36

10.69

1.33

DEthreader

YIPSVNDFVIGVIIGTFSDSYKVSLQNSSSVSLSYMAFPNAKNR-P-TLQVGDLVYARVCTAEKELEAEIECFDGRDA--GFGILE

2ja9A1

0.42

12.29

2.46

SPARKS-K

YIPSVNDFVIGVIIGTFSDSYKVSLQNFSSVSLSYMAFPNASKKNRPTLQVGDLVYARVCTAEKELEAEIECFDSTGRDAGFGIL-

4ifdH2

0.26

0.24

7.52

0.61

MapAlign

YAPETGDHVVGRIAEVGNKRWKVDIGGKQHAVLMLGSVNSDELQMRSFLKEGDLLNAEVQSLFQDGSASLHTRS-----LKYGKL-

4ifdH

0.26

0.24

7.53

0.46

CEthreader

YAPETGDHVVGRIAEVGNKRWKVDIGGKQHAVLMLGSVNSDELQMRSFLKEGDLLNAEVQSLFQDGSASLHTRS-----LKYGKLR

2nn6G2

1.00

0.99

27.67

2.32

MUSTER

YVPVKGDHVIGIVTAKSGDIFKVDVGGSEPASLSYLSFEGATKRNRPNVQVGDLIYGQFVVANKDMEPEMVCIDSCGRANGMGVI-

2ja9A1

0.42

12.29

1.39

HHsearch

YIPSVNDFVIGVIIGTFSDSYKVSLQNFSSVSLSYMAFPNASKKNRPTLQVGDLVYARVCTAEKELEAEIECFDSTGRDAGFGIL-

2nn6G2

1.00

0.99

27.67

1.55

FFAS-3D

YVPVKGDHVIGIVTAKSGDIFKVDVGGSEPASLSYLSFEGATKRNRPNVQVGDLIYGQFVVANKDMEPEMVCIDSCGRANGMGVI-

6fszGG

0.37

11.05

0.75

EigenThreader

YIPSVNDFVIGVIIGTFSDSYKVSLQNFSSVSLSYMAFPNASKKNRPTLQVGDLVYARVCTAEKELEAEIECFDSTTGRDAGFDGM

2nn6G

1.00

28.00

1.26

CNFpred

YVPVKGDHVIGIVTAKSGDIFKVDVGGSEPASLSYLSFEGATKRNRPNVQVGDLIYGQFVVANKDMEPEMVCIDSCGRANGMGVIG

2ja9A1

0.37

0.35

10.36

1.33

DEthreader

YIPSVNDFVIGVIIGTFSDSYKVSLQNSSSVSLSYMAFPNAKNR-P-TLQVGDLVYARVCTAEKELEAEIECFDGRDAG--FGIL-

(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	0.8982

(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	2ja9A	0.92	1.30	0.430	1.000	model1_2ja9A.pdb.gz
2	2nn6G	0.89	1.02	0.867	0.965	model1_2nn6G.pdb.gz
3	6fszGG	0.88	1.45	0.400	0.988	model1_6fszGG.pdb.gz
4	2jeaI	0.83	1.79	0.210	0.942	model1_2jeaI.pdb.gz
5	4ifdH2	0.80	1.95	0.247	0.942	model1_4ifdH2.pdb.gz
6	2z0sA	0.80	2.26	0.309	0.942	model1_2z0sA.pdb.gz
7	2ba0B2	0.80	1.77	0.222	0.942	model1_2ba0B2.pdb.gz
8	4yhbA1	0.45	3.16	0.095	0.651	model1_4yhbA1.pdb.gz
9	1vizA	0.36	4.78	0.070	0.767	model1_1vizA.pdb.gz
10	4l5gA1	0.35	2.58	0.130	0.477	model1_4l5gA1.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

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	0.99	cellular process
GO:0044260	0.98	cellular macromolecule metabolic process
GO:0044238	0.98	primary metabolic process
GO:0034641	0.98	cellular nitrogen compound metabolic process
GO:0016070	0.97	RNA metabolic process
GO:0016071	0.95	mRNA metabolic process
GO:0006364	0.95	rRNA processing
GO:0071051	0.94	polyadenylation-dependent snoRNA 3'-end processing
GO:0071049	0.94	nuclear retention of pre-mRNA with aberrant 3'-ends at the site of transcription
GO:0071038	0.94	nuclear polyadenylation-dependent tRNA catabolic process
GO:0071035	0.94	nuclear polyadenylation-dependent rRNA catabolic process
GO:0071034	0.94	CUT catabolic process
GO:0043928	0.94	exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay
GO:0034475	0.94	U4 snRNA 3'-end processing
GO:0034427	0.94	nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5'
GO:0000467	0.94	exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)

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:0044446	1.00	intracellular organelle part
GO:0000178	1.00	exosome (RNase complex)
GO:0000177	0.99	cytoplasmic exosome (RNase complex)
GO:0000176	0.99	nuclear exosome (RNase complex)

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	3hkzQ	0.765	2.02	0.175	0.930	2.7.7.6	3,26,33
2	0.060	1go3E	0.798	1.72	0.125	0.930	2.7.7.6	21,26,33,60
3	0.060	3iceC	0.556	3.16	0.125	0.837	3.6.1.-	NA
4	0.060	2hivA	0.579	2.80	0.068	0.802	6.5.1.1	NA
5	0.060	1asyA	0.596	3.39	0.077	0.895	6.1.1.12	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	0.08	2ja90	0.916	1.30	0.430	1.000	0.82	III	complex1.pdb.gz	36,39,40,41,42,44,45,77,78,81,85
2	0.05	2c351	0.734	1.98	0.208	0.895	0.65	III	complex2.pdb.gz	2,4,5,6,7,8,9,10,12,24,26,27,52,54,56,81
3	0.04	1y140	0.745	2.24	0.190	0.919	0.64	III	complex3.pdb.gz	15,16,17,18,19,20,22,32,36,37,62
4	0.03	2vrtD	0.722	3.21	0.128	0.954	0.41	RQA	complex4.pdb.gz	7,34,38
5	0.02	2a192	0.668	2.26	0.107	0.837	0.48	III	complex5.pdb.gz	18,19,22,60
6	0.02	3h15A	0.609	3.07	0.115	0.895	0.41	QNA	complex6.pdb.gz	10,54,56
7	0.01	1twh5	0.192	3.77	0.000	0.314	0.45	III	complex7.pdb.gz	9,11,12,13

	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.