D-I-TASSER A6NHM9-D2

D-I-TASSER results for A6NHM9-D2

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

Input Sequence in FASTA format

>A6NHM9 (162 residues)
LQVVHPDDLDVPEDTIIHDLEITNFLIPEDDTTYACTFLPLPIVSEKHHIYKFEPKLVYH
NETTVHHILVYACGNASVLPTGISDCYGADPAFSLCSQVIVGSAVGGTSYQFPDDVGVSI
GTPLDPQWILEIHYSNFNNLPGVYDSSGIRVYYTSQLCKYDT

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| LQVVHPDDLDVPEDTIIHDLEITNFLIPEDDTTYACTFLPLPIVSEKHHIYKFEPKLVYHNETTVHHILVYACGNASVLPTGISDCYGADPAFSLCSQVIVGSAVGGTSYQFPDDVGVSIGTPLDPQWILEIHYSNFNNLPGVYDSSGIRVYYTSQLCKYDT
Prediction	CCCCCCCCCCCCCCCCSSSSSSCCCCCCCCCCSSSSSSSSCCCCCCCSSSSSSSSSSCCCCCCCSSSSSSSSSCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSSCCCCCCCCCCCCSSSSCCCCCCSSSSSSCSCCCCCCCCCCCCCCSSSSSCCCCCCCCC
Confidence	966689999999875289998079636999963889999689998742699875355169967315999984089998888888889999754558426999956998751898721773899998699998218976689998887429998399898999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| LQVVHPDDLDVPEDTIIHDLEITNFLIPEDDTTYACTFLPLPIVSEKHHIYKFEPKLVYHNETTVHHILVYACGNASVLPTGISDCYGADPAFSLCSQVIVGSAVGGTSYQFPDDVGVSIGTPLDPQWILEIHYSNFNNLPGVYDSSGIRVYYTSQLCKYDT
Prediction	644342764623750431403166151376612020232514635453203413230346245200000001045444355442414444542442330010003336424025400030247633200000002226447634120101022076347468
	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

CCCCCCCCCCCCCCCCSSSSSSCCCCCCCCCCSSSSSSSSCCCCCCCSSSSSSSSSSCCCCCCCSSSSSSSSSCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSSCCCCCCCCCCCCSSSSCCCCCCSSSSSSCSCCCCCCCCCCCCCCSSSSSCCCCCCCCC
LQVVHPDDLDVPEDTIIHDLEITNFLIPEDDTTYACTFLPLPIVSEKHHIYKFEPKLVYHNETTVHHILVYACGNASVLPTGISDCYGADPAFSLCSQVIVGSAVGGTSYQFPDDVGVSIGTPLDPQWILEIHYSNFNNLPGVYDSSGIRVYYTSQLCKYDT

4zelA

0.32

0.31

9.29

1.33

DEthreader

-------EPELPSDACTMEVQAPNIQIPSQETTYWCYIKELPKGFSRHHIIKYEPIVTKGNEALVHHMEVFQCAPMDSVPHFSGPCDSKPDRLNYCRHVLAAWALGAKAFYYPEEAGLAFGGPGSRYLRLEVHYHNPLVIEGRNDSSGIRLYYTAKLRRFNA

4zelA2

0.32

0.31

9.29

3.28

SPARKS-K

-----IPEPELPSDACTMEVQAPNIQIPSQETTYWCYIKELPKGFSRHHIIKYEPIVTKGNEALVHHMEVFQCAPMDSVPHFSGPCDSKMKPLNYCRHVLAAWALGAKAFYYPEEAGLAFGGPSSRYLRLEVHYHNPLVIEGRNDSSGIRLYYTAKLRRF--

4zelA

0.33

0.31

9.27

2.03

MapAlign

----------LPSDACTMEVQAPNIQIPSQETTYWCYIKELPKGFSRHHIIKYEPIVTKGNEALVHHMEVFQCAPMDSVPHFSGPCDMKPDRLNYCRHVLAAWALGAKAFYYPEEAGLAFGGPGSSYLRLEVHYHNPLVIEGRNDSSGIRLYYTAKLRRFNA

4zelA

0.31

9.50

1.52

CEthreader

LLKPNIPEPELPSDACTMEVQAPNIQIPSQETTYWCYIKELPKGFSRHHIIKYEPIVTKGNEALVHHMEVFQCAPMDSVPHFSGPCDSKMKPLNYCRHVLAAWALGAKAFYYPEEAGLAFGGPGSSYLRLEVHYHNPLVIEGRNDSSGIRLYYTAKLRRFNA

4zelA

0.32

9.67

2.00

MUSTER

VQLLKPPEPELPSDACTMEVQAPNIQIPSQETTYWCYIKELPKGFSRHHIIKYEPIVTKGNEALVHHMEVFQCAPEMDVPHFSGPCDSKMKPLNYCRHVLAAWALGAKAFYYPEEAGLAFGGPGSSYLRLEVHYHNPLVIEGRNDSSGIRLYYTAKLRRFNA

4zelA

0.32

9.67

5.04

HHsearch

VQLLKPNIPELPSDACTMEVQAPNIQIPSQETTYWCYIKELPKGFSRHHIIKYEPIVTKGNEALVHHMEVFQCAPEMDVPHFSGPCDSKMKPLNYCRHVLAAWALGAKAFYYPEEAGLAFGGPGSSRYLLEVHYHNPLVIEGRNDSSGIRLYYTAKLRRFNA

4zelA2

0.32

0.30

9.12

2.28

FFAS-3D

------PEPELPSDACTMEVQAPNIQIPSQETTYWCYIKELPKGFSRHHIIKYEPIVTKGNEALVHHMEVFQCAPEMDSVPHPCDSKMKPDRLNYCRHVLAAWALGAKAFYYPEEAGLAFGGPGSRYLRLEVHYHNPLVIEGRNDSSGIRLYYTAKLRRF--

4zelA2

0.31

0.30

8.96

1.17

EigenThreader

-----IPEPELPSDACTMEVQAPNIQIPSQETTYWCYIKELPKGFSRHHIIKYEPIVTKGNEALVHHMEVFQCAPEMDSVPHFCDSKMKPDRLNYCRHVLAAWALGAKAFYYPEEAGLAFGPGSSRYLRLEVHYHNPLVIEGRNDSSGIRLYYTAKLRRF--

4zelA

0.31

0.30

9.14

2.97

CNFpred

-----IPEPELPSDACTMEVQAPNIQIPSQETTYWCYIKELPKGFSRHHIIKYEPIVTKGNEALVHHMEVFQCAPEMDSVHFSGPCDSKMKPLNYCRHVLAAWALGAKAFYYPEEAGLAFGGPSSRYLRLEVHYHNPLVIEGRNDSSGIRLYYTAKLRRFNA

4zelA2

0.33

0.31

9.28

1.33

DEthreader

-------EPELPSDACTMEVQAPNIQIPSQETTYWCYIKELPKGFSRHHIIKYEPIVTKGNEALVHHMEVFQCAPMDSVPHFSGPCDSKPDRLNYCRHVLAAWALGAKAFYYPEEAGLAFGGPGSRYLRLEVHYHNPLVIEGRNDSSGIRLYYTAKLRRF--

(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	0.8702

(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	4zelA	0.93	1.34	0.309	0.982	model1_4zelA.pdb.gz
2	6nckA	0.75	2.62	0.201	0.889	model1_6nckA.pdb.gz
3	5jzgC	0.60	4.19	0.058	0.926	model1_5jzgC.pdb.gz
4	4nuyA	0.59	3.71	0.036	0.827	model1_4nuyA.pdb.gz
5	1pov0	0.59	4.22	0.033	0.907	model1_1pov0.pdb.gz
6	1sva1	0.58	4.18	0.077	0.870	model1_1sva1.pdb.gz
7	3cjiC	0.58	4.31	0.059	0.895	model1_3cjiC.pdb.gz
8	1k5mB	0.58	4.45	0.045	0.901	model1_1k5mB.pdb.gz
9	4mbxA	0.57	4.06	0.077	0.852	model1_4mbxA.pdb.gz
10	1d4m2	0.57	4.45	0.032	0.895	model1_1d4m2.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:0046872	0.94	metal ion binding
GO:0016491	0.92	oxidoreductase activity
GO:0016715	0.86	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced ascorbate as one donor, and incorporation of one atom of oxygen
GO:0046914	0.80	transition metal ion binding
GO:0005507	0.73	copper ion binding
GO:0005509	0.71	calcium ion binding
GO:0004500	0.56	dopamine beta-monooxygenase 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:0050896	0.99	response to stimulus
GO:0050877	0.99	neurological system process
GO:0044707	0.99	single-multicellular organism process
GO:0007610	0.99	behavior
GO:0008306	0.98	associative learning
GO:0007632	0.98	visual behavior
GO:0008542	0.97	visual learning
GO:1901564	0.96	organonitrogen compound metabolic process
GO:0044237	0.96	cellular metabolic process
GO:1901362	0.86	organic cyclic compound biosynthetic process
GO:0019438	0.86	aromatic compound biosynthetic process
GO:1901566	0.85	organonitrogen compound biosynthetic process
GO:0046189	0.85	phenol-containing compound biosynthetic process
GO:0044763	0.72	single-organism cellular process
GO:0042424	0.72	catecholamine catabolic process
GO:0042417	0.72	dopamine metabolic process
GO:0042415	0.72	norepinephrine metabolic process
GO:0009713	0.72	catechol-containing compound biosynthetic process
GO:0065008	0.69	regulation of biological quality
GO:0034641	0.65	cellular nitrogen compound metabolic process
GO:0044281	0.59	small molecule metabolic process
GO:0042421	0.59	norepinephrine biosynthetic process
GO:0042420	0.59	dopamine catabolic process
GO:0051704	0.53	multi-organism process
GO:0050794	0.53	regulation of cellular process
GO:0048609	0.53	multicellular organismal reproductive process
GO:0010033	0.53	response to organic substance
GO:0009719	0.53	response to endogenous stimulus
GO:0006950	0.50	response to stress

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:0043227	0.99	membrane-bounded organelle
GO:0005634	0.98	nucleus
GO:0044444	0.82	cytoplasmic part
GO:0016020	0.81	membrane
GO:0044446	0.77	intracellular organelle part
GO:0044421	0.76	extracellular region part
GO:0005615	0.63	extracellular space
GO:0030667	0.54	secretory granule 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	1c8m1	0.557	4.02	0.068	0.815	3.4.22.28	53,122
2	0.060	3c8xA	0.501	3.78	0.059	0.728	2.7.10.1	127,129
3	0.060	2g8eA	0.352	4.89	0.052	0.611	3.4.22.52	NA
4	0.060	1pnfA	0.534	3.97	0.070	0.772	3.5.1.52	NA
5	0.060	1qxpB	0.562	3.98	0.050	0.821	3.4.22.53 3.4.22.52	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	0.04	3mihA	0.746	2.73	0.201	0.889	0.47	AZI	complex1.pdb.gz	55,102,104
2	0.04	1opmA	0.745	2.73	0.201	0.889	0.47	IYG	complex2.pdb.gz	52,54,150,151,152
3	0.02	1qjx1	0.557	4.03	0.068	0.815	0.50	W02	complex3.pdb.gz	39,41,53,70,103,110,122,127,130
4	0.02	1c8m1	0.557	4.02	0.068	0.815	0.48	W11	complex4.pdb.gz	19,41,53,55,68,69,70,103,122,125,127,130
5	0.02	1qju1	0.557	4.03	0.068	0.815	0.42	W01	complex5.pdb.gz	17,52,54,70,72,99,128
6	0.01	2hwd1	0.559	3.84	0.047	0.802	0.57	W91	complex6.pdb.gz	42,51,53,71,126
7	0.01	1sidE	0.561	4.44	0.058	0.883	0.41	UUU	complex7.pdb.gz	112,118,119,120,155
8	0.01	2nqaB	0.349	5.02	0.063	0.617	0.45	CA	complex8.pdb.gz	68,102,106

	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.