D-I-TASSER Q6NXR0-D1

D-I-TASSER results for Q6NXR0-D1

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

Input Sequence in FASTA format

>Q6NXR0 (247 residues)
MATSKLPVVPGEEENTILMAKERLEALRTAFESGDLPQAASHLQELLASTESIRLEVGVT
GESGAGKSSLINALRGLEAEDPGAALTGVMETTMQPSPYPHPQFPDVTLWDLPGAGSPGC
PADKYLKQVDFSRYDFFLLVSPRRCGAVETRLAAEILCQGKKFYFVRTKVDEDLAATRTQ
RPSGFREAAVLQEIRDHCAERLREAGVADPRIFLVSNLSPARYDFPTLVSTWEHDLPSHR
RHAGLLS

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 \| \| \| \| \| \| \| \| \| \| \| \| MATSKLPVVPGEEENTILMAKERLEALRTAFESGDLPQAASHLQELLASTESIRLEVGVTGESGAGKSSLINALRGLEAEDPGAALTGVMETTMQPSPYPHPQFPDVTLWDLPGAGSPGCPADKYLKQVDFSRYDFFLLVSPRRCGAVETRLAAEILCQGKKFYFVRTKVDEDLAATRTQRPSGFREAAVLQEIRDHCAERLREAGVADPRIFLVSNLSPARYDFPTLVSTWEHDLPSHRRHAGLLS
Prediction	CCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHCCCCSSSSSSCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCSSSSSCCCCCCSSSSSCCCCCCCCCCHHHHHHHHHHCCCSSSSSSCCCCCCHHHHHHHHHHHHHCCCSSSSSSCCCCCCHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCCCSSSSSCCCCCCCCHHHHHHHHHHHCHHHHHHHHCCC
Confidence	9853243322114542237989999999999957989999999999987304873899986999968899999958876665456899998645306886379996099988999987865899999986418719999448998789999999999829978999847744315777642543138999999999999999971999994899754431359979999999998079876553169
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 \| \| \| \| \| \| \| \| \| \| \| \| MATSKLPVVPGEEENTILMAKERLEALRTAFESGDLPQAASHLQELLASTESIRLEVGVTGESGAGKSSLINALRGLEAEDPGAALTGVMETTMQPSPYPHPQFPDVTLWDLPGAGSPGCPADKYLKQVDFSRYDFFLLVSPRRCGAVETRLAAEILCQGKKFYFVRTKVDEDLAATRTQRPSGFREAAVLQEIRDHCAERLREAGVADPRIFLVSNLSPARYDFPTLVSTWEHDLPSHRRHAGLLS
Prediction	6545326303645535222455306403510675406501630462066167340200000345112000000023343545522344344224422303247344100000013334624244204423043000000004440343024004203736120000000223335644563456153640054026302630573607413001023343551314302520273037333330317
	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                 240

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHCCCCSSSSSSCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCSSSSSCCCCCCSSSSSCCCCCCCCCCHHHHHHHHHHCCCSSSSSSCCCCCCHHHHHHHHHHHHHCCCSSSSSSCCCCCCHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCCCSSSSSCCCCCCCCHHHHHHHHHHHCHHHHHHHHCCC
MATSKLPVVPGEEENTILMAKERLEALRTAFESGDLPQAASHLQELLASTESIRLEVGVTGESGAGKSSLINALRGLEAEDPGAALTGVMETTMQPSPYPHPQFPDVTLWDLPGAGSPGCPADKYLKQVDFSRYDFFLLVSPRRCGAVETRLAAEILCQGKKFYFVRTKVDEDLAATRTQRPSGFREAAVLQEIRDHCAERLREAGVADPRIFLVSNLSPARYDFPTLVSTWEHDLPSHRRHAGLLS

1tq6A

0.40

0.36

10.75

1.17

DEthreader

-------------------SQEILNLIELRMRKGNIQLTNSAISDALKEIDSSVLNVAVTGETGSGKSSFINTLRGIGNEEEGA-AKTGVVETMERHPYKHPNIPNVVFWDLPGIGSTNFPPDTYLEKMKFYEYDFFIIISATRFKKNDIDIAKAISAMKKEFYFVRTKVDSDITNEADGEPQTFDKEKVLQDIRLNCVNTFREGIAE-PPIFLLSNKNVCHYDFPVLMDKLISDLPIYKRHNFQRL

1tq6A1

0.40

11.82

1.76

SPARKS-K

LPSSFTGYFKKFNTGRKIISQEILNLIELRMRKGNIQLTNSAISDALKEIDSSVLNVAVTGETGSGKSSFINTLRGIGNEEEGAAKTGVVEVTMERHPYKHPNIPNVVFWDLPGIGSTNFPPDTYLEKMKFYEYDFFIIISATRFKKNDIDIAKAISAMKKEFYFVRTKVDSDITNEADGEPQTFDKEKVLQDIRLNCVNTFRENGIAEPPIFLLSNKNVCHYDFPVLMDKLISDLPIYKRHNFMVS

6j72A1

0.18

0.15

4.87

0.61

MapAlign

-----------------VIVELIDHTSAIAAAKDRADLVERLRAAKAR-ISDPQIRVVIAGQLKQGKSQLLNSLLNIP-----VARVGDDESTVLATVVSYSLKGGLAFVDTPGVGGGQPHLSATLG-L-LPDADAMLMISDTEFTEPEMKFIRQALEI-CVAAIVATKTDLY---------------PHWRQIVDANIAHLQRAGLN-VPVIPASSVLREESNFPAIVKFLSEHVLSRQNDRIRDQ

1tq6A1

0.40

11.82

0.52

CEthreader

LPSSFTGYFKKFNTGRKIISQEILNLIELRMRKGNIQLTNSAISDALKEIDSSVLNVAVTGETGSGKSSFINTLRGIGNEEEGAAKTGVVEVTMERHPYKHPNIPNVVFWDLPGIGSTNFPPDTYLEKMKFYEYDFFIIISATRFKKNDIDIAKAISAMKKEFYFVRTKVDSDITNEADGEPQTFDKEKVLQDIRLNCVNTFRENGIAEPPIFLLSNKNVCHYDFPVLMDKLISDLPIYKRHNFMVS

1tq6A1

0.40

11.82

1.58

MUSTER

LPSSFTGYFKKFNTGRKIISQEILNLIELRMRKGNIQLTNSAISDALKEIDSSVLNVAVTGETGSGKSSFINTLRGIGNEEEGAAKTGVVEVTMERHPYKHPNIPNVVFWDLPGIGSTNFPPDTYLEKMKFYEYDFFIIISATRFKKNDIDIAKAISAMKKEFYFVRTKVDSDITNEADGEPQTFDKEKVLQDIRLNCVNTFRENGIAEPPIFLLSNKNVCHYDFPVLMDKLISDLPIYKRHNFMVS

1tq6A

0.40

11.82

1.63

HHsearch

LPSSFTGYFKKFNTGRKIISQEILNLIELRMRKGNIQLTNSAISDALKEIDSSVLNVAVTGETGSGKSSFINTLRGIGNEEEGAAKTGVVEVTMERHPYKHPNIPNVVFWDLPGIGSTNFPPDTYLEKMKFYEYDFFIIISATRFKKNDIDIAKAISAMKKEFYFVRTKVDSDITNEADGEPQTFDKEKVLQDIRLNCVNTFRENGIAEPPIFLLSNKNVCHYDFPVLMDKLISDLPIYKRHNFMVS

1tq6A1

0.42

0.40

11.66

2.26

FFAS-3D

------------NTGRKIISQEILNLIELRMRKGNIQLTNSAISDALKEIDSSVLNVAVTGETGSGKSSFINTLRGIGNEEEGAAKTGVVEVTMERHPYKHPNIPNVVFWDLPGIGSTNFPPDTYLEKMKFYEYDFFIIISATRFKKNDIDIAKAISAMKKEFYFVRTKVDSDITNEADGEPQTFDKEKVLQDIRLNCVNTFRENGIAEPPIFLLSNKNVCHYDFPVLMDKLISDLPIYKRHNFMVS

1tq6A1

0.40

0.39

11.59

0.90

EigenThreader

ENNDFKKFNTGRKIISQEILNLIELRMRKG----NIQLTNSAISDALKEIDSSVLNVAVTGETGSGKSSFINTLRGIGNEEEGAAKTGVVEVTMERHPYKHPNIPNVVFWDLPGIGSTNFPPDTYLEKMKFYEYDFFIIISATRFKKNDIDIAKAISAMKKEFYFVRTKVDSDITNEADGEPQTFDKEKVLQDIRLNCVNTFRENGIAEPPIFLLSNKNVCHYDFPVLMDKLISDLPIYKRHNFMVS

4lv5B

0.42

0.39

11.54

1.97

CNFpred

----------------KIISQEILNLIELRMRKGNIQLTNSAISDALKEIDSSVLNVAVTGETGSGKSSFINTLRGIGNEEEGAAKTGVVEVTMERHPYKHPNIPNVVFWDLPGIGSTNFPPNTYLEKMKFYEYDFFIIISATRFKKNDIDIAKAISMMKKEFYFVRTKVDSDITNEADGKPQTFDKEKVLQDIRLNCVNTFRENGIAEPPIFLLSNKNVCHYDFPVLMDKLISDLPIYKRHNFMVS

1tq6A1

0.40

0.36

10.75

1.17

DEthreader

-------------------SQEILNLIELRMRKGNIQLTNSAISDALKEIDSSVLNVAVTGETGSGKSSFINTLRGIGNEEEGA-AKTGVVETMERHPYKHPNIPNVVFWDLPGIGSTNFPPDTYLEKMKFYEYDFFIIISATRFKKNDIDIAKAISAMKKEFYFVRTKVDSDITNEADGEPQTFDKEKVLQDIRLNCVNTFREGIAE-PPIFLLSNKNVCHYDFPVLMDKLISDLPIYKRHNFQRL

(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	0.806

(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	1tq6A	0.78	3.12	0.397	0.923	model1_1tq6A.pdb.gz
2	7c3kA1	0.73	2.98	0.378	0.846	model1_7c3kA1.pdb.gz
3	7vesA1	0.65	3.18	0.386	0.781	model1_7vesA1.pdb.gz
4	2j69A	0.65	3.87	0.144	0.814	model1_2j69A.pdb.gz
5	6j72A1	0.64	3.40	0.189	0.773	model1_6j72A1.pdb.gz
6	6jfkA	0.64	3.59	0.147	0.789	model1_6jfkA.pdb.gz
7	5gnrA	0.63	3.59	0.146	0.777	model1_5gnrA.pdb.gz
8	5owvA	0.63	3.81	0.163	0.789	model1_5owvA.pdb.gz
9	5mtvA	0.61	4.03	0.129	0.777	model1_5mtvA.pdb.gz
10	2qptA	0.61	3.64	0.168	0.757	model1_2qptA.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:0003924	0.99	GTPase activity
GO:1901363	0.92	heterocyclic compound binding
GO:0097367	0.92	carbohydrate derivative binding
GO:0097159	0.92	organic cyclic compound binding
GO:0005525	0.91	GTP binding
GO:0042802	0.56	identical protein binding
GO:0019003	0.54	GDP binding
GO:0046872	0.50	metal ion 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	0.92	cellular process
GO:0050896	0.80	response to stimulus
GO:0065007	0.69	biological regulation
GO:0050789	0.69	regulation of biological process
GO:0050794	0.66	regulation of cellular process
GO:0010033	0.66	response to organic substance
GO:0051716	0.65	cellular response to stimulus
GO:0034097	0.65	response to cytokine
GO:0044699	0.64	single-organism process
GO:0035458	0.64	cellular response to interferon-beta
GO:0006950	0.63	response to stress
GO:0051707	0.62	response to other organism
GO:0006952	0.62	defense response
GO:0002376	0.61	immune system process
GO:0006955	0.60	immune response
GO:0007165	0.57	signal transduction
GO:0044763	0.54	single-organism cellular process
GO:0042832	0.54	defense response to protozoan
GO:0042742	0.54	defense response to bacterium
GO:0050829	0.53	defense response to Gram-negative bacterium
GO:0019221	0.53	cytokine-mediated signaling pathway
GO:0010506	0.53	regulation of autophagy
GO:0045087	0.51	innate immune response

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:0044424	0.98	intracellular part
GO:0044444	0.83	cytoplasmic part
GO:0043226	0.69	organelle
GO:0043229	0.67	intracellular organelle
GO:0043227	0.57	membrane-bounded organelle
GO:0043231	0.54	intracellular membrane-bounded organelle
GO:0005737	0.51	cytoplasm

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	0.070	1m2oB	0.513	2.86	0.142	0.599	3.6.5.-	NA
2	0.067	2atxA	0.522	3.82	0.126	0.664	3.6.5.2	NA
3	0.067	1aa9A	0.508	3.47	0.151	0.632	3.6.5.-	NA
4	0.067	1e0sA	0.510	3.10	0.086	0.607	3.6.1.47	NA
5	0.066	1rflA	0.459	3.81	0.171	0.603	3.6.-.-	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:

Click to view	Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
	1	0.85	1tq2B	0.765	3.01	0.410	0.887	1.60	GNP	complex1.pdb.gz	63,64,66,67,68,69,87,88,169,171,172,216,217,218

	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.