D-I-TASSER Q9NY64-D2

D-I-TASSER results for Q9NY64-D2

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

Input Sequence in FASTA format

>Q9NY64 (238 residues)
EQSFHLALLRQPGIYKPFIIGVSLMAFQQLSGVNAVMFYAETIFEEAKFKDSSLASVVVG
VIQVLFTAVAALIMDRAGRRLLLVLSGVVMVFSTSAFGAYFKLTQGGPGNSSHVAISAPV
SAQPVDASVGLAWLAVGSMCLFIAGFAVGWGPIPWLLMSEIFPLHVKGVATGICVLTNWL
MAFLVTKEFSSLMEVLRPYGAFWLASAFCIFSVLFTLFCVPETKGKTLEQITAHFEGR

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| EQSFHLALLRQPGIYKPFIIGVSLMAFQQLSGVNAVMFYAETIFEEAKFKDSSLASVVVGVIQVLFTAVAALIMDRAGRRLLLVLSGVVMVFSTSAFGAYFKLTQGGPGNSSHVAISAPVSAQPVDASVGLAWLAVGSMCLFIAGFAVGWGPIPWLLMSEIFPLHVKGVATGICVLTNWLMAFLVTKEFSSLMEVLRPYGAFWLASAFCIFSVLFTLFCVPETKGKTLEQITAHFEGR
Prediction	CCCCHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCSSSSCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHCC
Confidence	9861367865974179999999999999864533344333899999599904799999999999999999999973176689999999999999999999996147877654332233444555433202599999999999999723201447776662168223578999999999999999999999999984742589999999999999999624579999999999998149
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| EQSFHLALLRQPGIYKPFIIGVSLMAFQQLSGVNAVMFYAETIFEEAKFKDSSLASVVVGVIQVLFTAVAALIMDRAGRRLLLVLSGVVMVFSTSAFGAYFKLTQGGPGNSSHVAISAPVSAQPVDASVGLAWLAVGSMCLFIAGFAVGWGPIPWLLMSEIFPLHVKGVATGICVLTNWLMAFLVTKEFSSLMEVLRPYGAFWLASAFCIFSVLFTLFCVPETKGKTLEQITAHFEGR
Prediction	8552404203445112000000311330231330022010030044141643230012213303311331223013332230033013212300220011010243444444334443444444344341100000321321131113232311102000120340213010000100331023113011300433333311221022022223323311200372315202631778
	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                 180                 200                 220

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCSSSSCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHCC
EQSFHLALLRQPGIYKPFIIGVSLMAFQQLSGVNAVMFYAETIFEEAKFKDSSLASVVVGVIQVLFTAVAALIMDRAGRRLLLVLSGVVMVFSTSAFGAYFKLTQGGPGNSSHVAISAPVSAQPVDASVGLAWLAVGSMCLFIAGFAVGWGPIPWLLMSEIFPLHVKGVATGICVLTNWLMAFLVTKEFSSLMEVLRPYGAFWLASAFCIFSVLFTLFCVPETKGKTLEQITAHFEGR

7crzA

0.33

0.30

9.08

1.33

DEthreader

NRKQVTVELRVSSYRQPIIISIVLQLSQQLSGINAVFYYSTGIFKDAGVQEPIYATIGAGVVNTIFTVVSLFLVERAGRRTLHMIGLGGMAFCSTLMTVSLLLKD-N---------------Y---N--GMSFVCIGAILVFVAFFEIGPGPIPWFIVAELFSQGPRPAAMAVAGCSNWTSNFLVGLLFPSAAHYLG-AYVFIIFTGFLITFLAFTFFKVPETRGRTFEDITRAFEAH

6h7dA2

0.28

0.26

7.85

2.35

SPARKS-K

--ENPWKNIMESKYRPALIFCSAIPFFQQITGINVIMFYAPVLFKTLGFGAALMSAVITGVVNMLSTFVSIYAVDRYGRRLLFLEGGIQMFICQLLVGSFIGARFGTSGTGTLTP--------------ATADWILAFICVYVAGFAWSWGPLGWLVPSEICPLEIRPAGQAINVSVNMFFTFLIGQFFLTMLCHMKFG-LFYFFASMVAIMTVFIYFLLPETKGVPIEEMGRVWKQH

7crzA

0.35

0.31

9.29

0.71

MapAlign

---VTVLELRVSSYRQPIIISIVLQLSQQLSGINAVFYYSTGIFKDAGVQEPIYATIGAGVVNTIFTVVSLFLVERAGRRTLHMIGLGGMAFCSTLMTVSLLLK---------------------DNYNGMSFVCIGAILVFVAFFEIGPGPIPWFIVAELFSQGPRPAAMAVAGCSNWTSNFLVGLLFPSAAHYL-GAYVFIIFTGFLITFLAFTFFKVPETRGRTFEDITRAFEGQ

7crzA

0.35

0.32

9.42

0.46

CEthreader

KQVTVLELFRVSSYRQPIIISIVLQLSQQLSGINAVFYYSTGIFKDAGVQEPIYATIGAGVVNTIFTVVSLFLVERAGRRTLHMIGLGGMAFCSTLMTVSLLLKDNYNG---------------------MSFVCIGAILVFVAFFEIGPGPIPWFIVAELFSQGPRPAAMAVAGCSNWTSNFLVGLLFPSAAHYL-GAYVFIIFTGFLITFLAFTFFKVPETRGRTFEDITRAFEGQ

6h7dA

0.28

0.26

7.97

1.44

MUSTER

KVENPWKNIMESKYRPALIFCSAIPFFQQITGINVIMFYAPVLFKTLGFGAALMSAVITGVVNMLSTFVSIYAVDRYGRRLLFLEGGIQMFICQLLVGSFIGARFGTSGTGTL--------------TPATADWILAFICVYVAGFAWSWGPLGWLVPSEICPLEIRPAGQAINVSVNMFFTFLIGQFFLTMLCHMK-FGLFYFFASMVAIMTVFIYFLLPETKGVPIEEMGRVWKQH

6h7dA

0.28

0.26

8.08

1.66

HHsearch

KVENPWKNIMESKYRPALIFCSAIPFFQQITGINVIMFYAPVLFKTLGFGDDLMSAVITGVVNMLSTFVSIYAVDRYGRRLLFLEGGIQMFICQLLVGSFIGARFGTSG--------------TGTLTPATADWILAFICVYVAGFAWSWGPLGWLVPSEICPLEIRPAGQAINVSVNMFFTFLIGQFFLTMLCHMKF-GLFYFFASMVAIMTVFIYFLLPETKGVPIEEMGRVWKQH

5c65A2

0.36

0.31

9.27

3.20

FFAS-3D

KQVTVLELFRVSSYRQPIIISIVLQLSQQLSGINAVFYYSTGIFKDAP----IYATIGAGVVNTIFTVVSLFLVERAGRRTLHMIGLGGMAFCSTLMTVSLLLKDM-------------------------SFVCIGAILVFVAFFEIGPGPIPWFIVAELFSQGPRPAAMAVAGCSNWTSNFLVGLLFPSAAHYL-GAYVFIIFTGFLITFLAFTFFKVPETRGRTFEDITRAFEGQ

6h7dA2

0.28

0.26

7.96

1.23

EigenThreader

--ENPWKNIMESKYRPALIFCSAIPFFQQITGINVIMFYAPVLFKTLGFGAALMSAVITGVVNMLSTFVSIYAVDRYGRRLLFLEGGIQMFICQLLVGSFIGARFGTSGTGTL--------------TPATADWILAFICVYVAGFAWSWGPLGWLVPSEICPLEIRPAGQAINVSVNMFFTFLIGQFFLTMLCHM-KFGLFYFFASMVAIMTVFIYFLLPETKGVPIEEMGRVWKQH

4zw9A

0.34

0.31

9.19

1.60

CNFpred

EKQVTVLELFRSSYRQPIIISIVLQLSQQLSGINAVFYYSTGIFKDAGVQEPIYATIGAGVVNTIFTVVSLFLVERAGRRTLHMIGLGGMAFCSTLMTVSLLLKDNY---------------------NGMSFVCIGAILVFVAFFEIGPGPIPWFIVAELFSQGPRPAAMAVAGCSNWTSNFLVGLLFPSAAHYLG-AYVFIIFTGFLITFLAFTFFKVPETRGRTFEDITRAFEGQ

6h7dA

0.28

0.26

7.97

1.33

DEthreader

KVENPWKNIMESKYRPALIFCSAIPFFQQITGINVIMFYAPVLFKTLGFGAALMSAVITGVVNMLSTFVSIYAVDRYGRRLLFLEGGIQMFICQLLVGSFIGARFGTSGTG------------TL--TPATADWILAFICVYVAGFAWSWGPLGWLVPSEICPLEIRPAGQAINVSVNMFFTFLIGQFFLTMLCH-MKFGLFYFFASMVAIMTVFIYFLLPETKGVPIEEMGRKYIPE

(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	0.7967

(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	7crzA	0.87	1.23	0.338	0.908	model1_7crzA.pdb.gz
2	6h7dA	0.87	1.85	0.278	0.937	model1_6h7dA.pdb.gz
3	4ybqA	0.86	1.44	0.273	0.908	model1_4ybqA.pdb.gz
4	6m2lA	0.81	2.32	0.242	0.903	model1_6m2lA.pdb.gz
5	6thaA2	0.79	1.57	0.308	0.845	model1_6thaA2.pdb.gz
6	4pypA	0.79	1.60	0.308	0.845	model1_4pypA.pdb.gz
7	4gbyA2	0.78	2.02	0.343	0.857	model1_4gbyA2.pdb.gz
8	4ldsA2	0.76	1.89	0.303	0.832	model1_4ldsA2.pdb.gz
9	4zowA1	0.64	2.99	0.148	0.777	model1_4zowA1.pdb.gz
10	1z6aA	0.31	6.02	0.044	0.550	model1_1z6aA.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:0022891	1.00	substrate-specific transmembrane transporter activity
GO:0051119	0.99	sugar transmembrane transporter activity
GO:0015149	0.95	hexose transmembrane transporter activity
GO:0005355	0.94	glucose transmembrane transporter activity
GO:0015293	0.93	symporter activity
GO:0008324	0.93	cation transmembrane transporter activity
GO:0005351	0.92	sugar:proton symporter 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	0.99	single-organism process
GO:0044765	0.98	single-organism transport
GO:0071702	0.97	organic substance transport
GO:0008643	0.96	carbohydrate transport
GO:0008645	0.94	hexose transport
GO:0015758	0.93	glucose transport
GO:0055085	0.92	transmembrane transport
GO:0046323	0.90	glucose import
GO:0035428	0.88	hexose transmembrane transport

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:0044425	0.96	membrane part
GO:0044459	0.95	plasma membrane part
GO:0016021	0.95	integral component of membrane
GO:0005887	0.94	integral component of plasma membrane
GO:0016020	0.55	membrane

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	2pffD	0.411	6.15	0.017	0.710	2.3.1.86	29,153
2	0.060	3fieA	0.419	4.77	0.051	0.618	3.4.24.69	NA
3	0.060	2p0mA	0.432	4.91	0.058	0.630	1.13.11.33	NA
4	0.060	2np0A	0.423	4.78	0.056	0.626	3.4.24.69	NA
5	0.060	3fg3A	0.430	4.59	0.059	0.622	4.2.1.92 1.13.11.40	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	0.02	3s8gA	0.440	3.87	0.065	0.584	0.93	OLC	complex1.pdb.gz	83,87,149,150,151
2	0.01	3gjcA	0.456	5.86	0.067	0.769	0.75	NA	complex2.pdb.gz	145,146,147,148,149
3	0.01	1ppj1	0.452	4.88	0.070	0.651	0.82	III	complex3.pdb.gz	28,29,30,31,143,144,146,147,151,152
4	0.01	3h1jC	0.444	5.03	0.063	0.668	0.77	CDL	complex4.pdb.gz	149,153,156,157
5	0.01	1pp9P	0.446	5.15	0.058	0.672	0.73	HEM	complex5.pdb.gz	23,24,27,28,30,31,83,84,87,88,90,149,150,154

	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.