D-I-TASSER Q9NQS3-D1

D-I-TASSER results for Q9NQS3-D1

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

Input Sequence in FASTA format

>Q9NQS3 (167 residues)
MARTLRPSPLCPGGGKAQLSSASLLGAGLLLQPPTPPPLLLLLFPLLLFSRLCGALAGPI
IVEPHVTAVWGKNVSLKCLIEVNETITQISWEKIHGKSSQTVAVHHPQYGFSVQGEYQGR
VLFKNYSLNDATITLHNIGFSDSGKYICKAVTFPLGNAQSSTTVTVL

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MARTLRPSPLCPGGGKAQLSSASLLGAGLLLQPPTPPPLLLLLFPLLLFSRLCGALAGPIIVEPHVTAVWGKNVSLKCLIEVNETITQISWEKIHGKSSQTVAVHHPQYGFSVQGEYQGRVLFKNYSLNDATITLHNIGFSDSGKYICKAVTFPLGNAQSSTTVTVL
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCSCCCCCCCHHHHHHHHHHHHHHHHCCSSSSSSSCCSSSSSCCCCSSSSSSSCCCCCSSSSSSSSSCCCCCCSSSSSSCCCCCSCCCCCCCCSSSSCCCCCSSSSSSSCCCHHHCSSSSSSSSSCCCCCSSSSSSSSSC
Confidence	99898887446788887555445666621037998852999999999999851432589993991899848548999996799965799999967999719999959988531876678389846999747999904893544899999995799847878999989
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MARTLRPSPLCPGGGKAQLSSASLLGAGLLLQPPTPPPLLLLLFPLLLFSRLCGALAGPIIVEPHVTAVWGKNVSLKCLIEVNETITQISWEKIHGKSSQTVAVHHPQYGFSVQGEYQGRVLFKNYSLNDATITLHNIGFSDSGKYICKAVTFPLGNAQSSTTVTVL
Prediction	87443524231344442425442444331223334313202322333322111333324133475040433750544040446541340352345685431000004543453475143113035464420101035033414243333031346344524040304
	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                 160

                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCSCCCCCCCHHHHHHHHHHHHHHHHCCSSSSSSSCCSSSSSCCCCSSSSSSSCCCCCSSSSSSSSSCCCCCCSSSSSSCCCCCSCCCCCCCCSSSSCCCCCSSSSSSSCCCHHHCSSSSSSSSSCCCCCSSSSSSSSSC
MARTLRPSPLCPGGGKAQLSSASLLGAGLLLQPPTPPPLLLLLFPLLLFSRLCGALAGPIIVEPHVTAVWGKNVSLKCLIEVNETITQISWEKIHGKSSQTVAVHHPQYGFSVQGEYQGRVLFKNYSLNDATITLHNIGFSDSGKYICKAVTFPLGNAQSSTTVTVL

6wznA

0.14

0.12

4.06

1.17

DEthreader

-----------------------------STTSVIPYATKYPDIPPDAYSGSSSGTQVQLVESGGGLVQPGGSLRLSCAASGLTSNYAMNWVRQAGKGLEWVSSISSRGTTYYADSVKGRFTISRDNSSTLYLQMNSLRAEDAAVYYCARLRNSMDVWGPGTTVTVS

4fomA1

1.00

0.66

18.44

1.14

SPARKS-K

---------------------------------------------------------GPIIVEPHVTAVWGKNVSLKCLIEVNETITQISWEKIHGKSSQTVAVHHPQYGFSVQGEYQGRVLFKNYSLNDATITLHNIGFSDSGKYICKAVTFPLGNAQSSTTVTVL

4frwA

0.32

0.21

6.32

0.53

MapAlign

---------------------------------------------------------GELETSDVVTVVLGQDAKLPCFYRGDEQVGQVAWARVDGEGAQELALLHSKYGLHVSPAYEGRVEQPPRNPLDGSVLLRNAVQADEGEYECRVSTFPAGSFQARLRLRVL

4frwA

0.31

0.20

6.16

0.41

CEthreader

---------------------------------------------------------GELETSDVVTVVLGQDAKLPCFYRGDEQVGQVAWARVDAGGAQELALLHSKYGLHVSPAYEGRVEQPPRNPLDGSVLLRNAVQADEGEYECRVSTFPAGSFQARLRLRVL

4fomA1

1.00

0.66

18.44

1.07

MUSTER

---------------------------------------------------------GPIIVEPHVTAVWGKNVSLKCLIEVNETITQISWEKIHGKSSQTVAVHHPQYGFSVQGEYQGRVLFKNYSLNDATITLHNIGFSDSGKYICKAVTFPLGNAQSSTTVTVL

2ch8A1

0.18

0.11

3.51

0.44

HHsearch

-----------------------------------------------------------------VTAFLGERVTLTSYWRRVGPEIEVSWFKLGPGEEQVLIGRMHHDVIFIEWPFRGFFDIHR-SANTFFLVVTAANISHDGNYLCRMKLG-ETEVTKQEHLSVV

4fomA1

1.00

0.65

18.28

1.69

FFAS-3D

----------------------------------------------------------PIIVEPHVTAVWGKNVSLKCLIEVNETITQISWEKIHGKSSQTVAVHHPQYGFSVQGEYQGRVLFKNYSLNDATITLHNIGFSDSGKYICKAVTFPLGNAQSSTTVTVL

1lmkA

0.15

0.13

4.43

0.42

EigenThreader

PGHGGGDKFKGKSSNIAYMQLSSLTSEDYYAYWYVLDG---------------GGSDIELTQSPLSLPVSGDQASISCRSSQSLVHTSLHWYLKKPGQSPKLLIYKVS-TRFSG--VPDRFSGGT----DFTLKISRVEAEDLGVYFCSQSTHVPFTFGSGTKLELK

4fomA

1.00

0.66

18.44

1.46

CNFpred

---------------------------------------------------------GPIIVEPHVTAVWGKNVSLKCLIEVNETITQISWEKIHGKSSQTVAVHHPQYGFSVQGEYQGRVLFKNYSLNDATITLHNIGFSDSGKYICKAVTFPLGNAQSSTTVTVL

5fhxH

0.14

0.11

3.70

1.17

DEthreader

-----------------------------------ETRLNQRFQGRARSPTSESSSEVQLKESGPGLVAPGGSLSITCTVSGFSTDSSINWVRQPGKGLEWLGMIWGDGRIDYADALKSRLSISKDSSSQVFLEMTSLRTDDTATYYCARDGYFYMDFWGGTSVTVS

(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	0.6945

(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	3f8uD	0.66	3.61	0.094	0.838	model1_3f8uD.pdb.gz
2	5opiC	0.65	3.49	0.142	0.802	model1_5opiC.pdb.gz
3	2ocwA	0.64	3.54	0.130	0.832	model1_2ocwA.pdb.gz
4	2fboJ	0.64	3.28	0.162	0.790	model1_2fboJ.pdb.gz
5	4fomA1	0.63	1.08	0.991	0.659	model1_4fomA1.pdb.gz
6	3mj6A	0.62	3.37	0.149	0.772	model1_3mj6A.pdb.gz
7	3r0nA	0.62	1.67	0.304	0.671	model1_3r0nA.pdb.gz
8	6igoC	0.61	1.51	0.182	0.659	model1_6igoC.pdb.gz
9	4bfiB1	0.61	1.35	0.193	0.653	model1_4bfiB1.pdb.gz
10	4frwA	0.61	1.53	0.309	0.659	model1_4frwA.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:0004872	0.84	receptor activity
GO:0042802	0.83	identical protein binding
GO:0005102	0.83	receptor binding
GO:0050839	0.82	cell adhesion molecule binding
GO:0046983	0.82	protein dimerization activity
GO:0042803	0.81	protein homodimerization 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	0.92	single-organism process
GO:0009987	0.91	cellular process
GO:0044763	0.90	single-organism cellular process
GO:0007155	0.88	cell adhesion
GO:0098609	0.82	cell-cell adhesion
GO:0008037	0.80	cell recognition
GO:0007157	0.80	heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules
GO:0007156	0.80	homophilic cell adhesion via plasma membrane adhesion molecules
GO:0065007	0.54	biological regulation
GO:0050789	0.53	regulation of biological 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	0.98	cell part
GO:0044425	0.85	membrane part
GO:0030054	0.85	cell junction
GO:0070161	0.84	anchoring junction
GO:0016021	0.84	integral component of membrane
GO:0005911	0.84	cell-cell junction
GO:0005912	0.83	adherens junction
GO:0005887	0.83	integral component of plasma membrane
GO:0005913	0.82	cell-cell adherens junction

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	0.190	2edrA	0.456	2.22	0.165	0.521	2.7.11.1	78,161,163
2	0.175	2dm7A	0.451	2.17	0.217	0.515	2.7.11.1	101,161,163
3	0.173	2edtA	0.458	2.01	0.174	0.515	2.7.11.1	161,163
4	0.135	1zv5A	0.559	2.56	0.182	0.647	3.2.1.17	NA
5	0.131	2edwA	0.459	2.10	0.183	0.515	2.7.11.1	74,92

	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	0.10	1yegH	0.589	2.25	0.189	0.665	0.65	BPN	complex1.pdb.gz	95,145,147,163
2	0.09	2pcpD	0.577	2.24	0.198	0.653	0.74	1PC	complex2.pdb.gz	93,95,98,146,148,160,161
3	0.09	1a0qH	0.578	2.17	0.174	0.653	0.52	HEP	complex3.pdb.gz	94,145,148,160,163
4	0.07	1a6vJ	0.582	2.34	0.189	0.665	0.55	NPC	complex4.pdb.gz	93,95,146,148
5	0.05	1mh5B	0.587	2.12	0.191	0.659	0.52	HAL	complex5.pdb.gz	94,145,164,166
6	0.04	1p6a1	0.572	1.96	0.252	0.641	0.99	III	complex6.pdb.gz	88,90,101,104,106,111,112,113,114,149,151,152,153
7	0.04	1eaj0	0.596	2.14	0.241	0.671	0.91	III	complex7.pdb.gz	88,90,104,106,109,113,115,149,151,153,154
8	0.03	1oaz3	0.579	2.38	0.171	0.659	0.54	III	complex8.pdb.gz	58,83,87,89,149
9	0.03	2x6mA	0.568	2.37	0.173	0.653	0.53	III	complex9.pdb.gz	72,73,74,75,140,142,144

	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.