D-I-TASSER Q6NUN0-D3

D-I-TASSER results for Q6NUN0-D3

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

Input Sequence in FASTA format

>Q6NUN0 (107 residues)
DVINSSSYRIGPVEVESALAEHPAVLESAVVSSPDPIRGEVVKAFIVLTPAYSSHDPEAL
TRELQEHVKRVTAPYKYPRKVAFVSELPKTVSGKIQRSKLRSQEWGK

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| DVINSSSYRIGPVEVESALAEHPAVLESAVVSSPDPIRGEVVKAFIVLTPAYSSHDPEALTRELQEHVKRVTAPYKYPRKVAFVSELPKTVSGKIQRSKLRSQEWGK
Prediction	CSSSSCCCSSCHHHHHHHHHHCCCSSSSSSSCCCCCCCCCSSSSSSSSCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCSSSSCCCCCCCCCHHHHHHHHHHHHHCC
Confidence	91787681027489999997382423573545777678966999999589989991899999999999997077668838998289999972567999999999569
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| DVINSSSYRIGPVEVESALAEHPAVLESAVVSSPDPIRGEVVKAFIVLTPAYSSHDPEALTRELQEHVKRVTAPYKYPRKVAFVSELPKTVSGKIQRSKLRSQEWGK
Prediction	83330243323232003003614301100003332634232010000035436365463026203610374114232244032267144343342223303542578
	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 AttentionPotential. 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

                   |                   |                   |                   |                   |

SS
Seq

CSSSSCCCSSCHHHHHHHHHHCCCSSSSSSSCCCCCCCCCSSSSSSSSCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCSSSSCCCCCCCCCHHHHHHHHHHHHHCC
DVINSSSYRIGPVEVESALAEHPAVLESAVVSSPDPIRGEVVKAFIVLTPAYSSHDPEALTRELQEHVKRVTAPYKYPRKVAFVSELPKTVSGKIQRSKLRSQEWGK

5gxdA

0.30

9.07

1.50

DEthreader

DVINVAGHRLSTGAMEEVLASHPDVAECAVIGVSDTLKGQMPLGFLCLSAGV-NRPHDEIAKECVKLVREKIGPVAAFKLACVVDRLPKTRSGKILRGTMVNIADGP

3b7wA2

0.74

0.73

20.67

3.27

SPARKS-K

DIINSSGYRIGPSEVENALMEHPAVVETAVISSPDPVRGEVVKAFVVLASQFLSHDPEQLTKELQQHVKSVTAPYKYPRKIEFVLNLPKTVTGKIQRAKLRDKEWK-

3b7wA

0.74

0.73

20.66

0.76

MapAlign

DIINSSGYRIGPSEVENALMEHPAVVETAVISSPDPVRGEVVKAFVVLASQFLSHDPEQLTKELQQHVKSVTAPYKYPRKIEFVLNLPKTVTGKIQRAKLRDKEW--

3b7wA2

0.74

0.73

20.67

0.52

CEthreader

DIINSSGYRIGPSEVENALMEHPAVVETAVISSPDPVRGEVVKAFVVLASQFLSHDPEQLTKELQQHVKSVTAPYKYPRKIEFVLNLPKTVTGKIQRAKLRDKEWK-

3b7wA2

0.74

0.73

20.67

2.68

MUSTER

DIINSSGYRIGPSEVENALMEHPAVVETAVISSPDPVRGEVVKAFVVLASQFLSHDPEQLTKELQQHVKSVTAPYKYPRKIEFVLNLPKTVTGKIQRAKLRDKEWK-

7kdsA1

0.40

0.38

11.31

1.27

HHsearch

DVVNVSGHRLSTAEIEAALIEDKKVSEAAVVGIHDDITGQAVIAYVALKEED----SEGLRKELVLQVRKTIGPFAAPKSVIIVQDLPKTRSGKIMRRILRKVSSNE

3b7wA2

0.74

0.73

20.66

2.24

FFAS-3D

DIINSSGYRIGPSEVENALMEHPAVVETAVISSPDPVRGEVVKAFVVLASQFLSHDPEQLTKELQQHVKSVTAPYKYPRKIEFVLNLPKTVTGKIQRAKLRDKEW--

3fccA3

0.25

0.24

7.54

0.90

EigenThreader

FQIKLHGYRMELEEIEHHLRACSYVEGAVIVPIKKGEKYDYLLAVVVPG-EHSFEKEFKLTSAIKKELNERLPNYMIPRKFMYQSSIPMTPNGKVDRKKLLSEVTA-

2vzeA

0.74

0.73

20.67

1.83

CNFpred

DIINSSGYRIGPSEVENALMEHPAVVETAVISSPDPVRGEVVKAFVVLASQFLSHDPEQLTKELQQHVKSVTAPYKYPRKIEFVLNLPKTVTGKIQRAKLRDKEWK-

5gxdA2

0.30

9.07

1.50

DEthreader

DVINVAGHRLSTGAMEEVLASHPDVAECAVIGVSDTLKGQMPLGFLCLSAGV-NRPHDEIAKECVKLVREKIGPVAAFKLACVVDRLPKTRSGKILRGTMVNIADGP

(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	0.8934

(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 AttentionPotential, 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	3b7wA2	0.94	0.96	0.736	0.991	model1_3b7wA2.pdb.gz
2	5u2aA	0.94	0.94	0.571	0.981	model1_5u2aA.pdb.gz
3	1pg3B	0.92	1.21	0.371	0.981	model1_1pg3B.pdb.gz
4	5gxdA	0.91	1.19	0.302	0.991	model1_5gxdA.pdb.gz
5	5ifiA	0.91	1.34	0.430	1.000	model1_5ifiA.pdb.gz
6	7kdsA	0.90	1.13	0.408	0.963	model1_7kdsA.pdb.gz
7	4wv3A2	0.89	1.42	0.476	0.981	model1_4wv3A2.pdb.gz
8	3a9uA	0.87	1.30	0.314	0.953	model1_3a9uA.pdb.gz
9	6eqoA	0.86	1.66	0.295	0.981	model1_6eqoA.pdb.gz
10	1ultA	0.86	1.44	0.347	0.944	model1_1ultA.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:0003824	0.99	catalytic activity
GO:0016874	0.90	ligase activity
GO:0016877	0.86	ligase activity, forming carbon-sulfur bonds
GO:0016878	0.73	acid-thiol ligase activity
GO:0016405	0.64	CoA-ligase 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:0008152	0.97	metabolic process
GO:0044699	0.94	single-organism process
GO:0009987	0.93	cellular process
GO:0071704	0.91	organic substance metabolic process
GO:0044237	0.91	cellular metabolic process
GO:0044710	0.90	single-organism metabolic process
GO:0044763	0.82	single-organism cellular process
GO:0044281	0.79	small molecule metabolic process
GO:0044238	0.65	primary metabolic process
GO:0009058	0.65	biosynthetic process
GO:0006082	0.63	organic acid metabolic process
GO:1901576	0.62	organic substance biosynthetic process
GO:0043436	0.62	oxoacid metabolic process
GO:0044249	0.61	cellular biosynthetic process
GO:0019752	0.61	carboxylic acid metabolic process
GO:0032787	0.56	monocarboxylic acid metabolic process
GO:0044711	0.53	single-organism biosynthetic process
GO:0006629	0.52	lipid metabolic 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	0.99	cell part
GO:0044424	0.98	intracellular part
GO:0044444	0.93	cytoplasmic part
GO:0043226	0.79	organelle
GO:0043227	0.78	membrane-bounded organelle
GO:0043229	0.76	intracellular organelle
GO:0043231	0.75	intracellular membrane-bounded organelle
GO:0044422	0.52	organelle part
GO:0044446	0.51	intracellular organelle part

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	3imlD	0.556	4.21	0.096	0.841	2.5.1.6	NA
2	0.060	1bpxA	0.525	3.93	0.071	0.832	2.7.7.7	NA
3	0.060	1ry2A	0.839	1.77	0.390	0.935	6.2.1.1	NA
4	0.060	3etcB	0.777	0.94	0.621	0.813	6.2.1.-	NA
5	0.060	2gv9B	0.543	3.56	0.102	0.813	2.7.7.7	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	0.17	1pg3A	0.915	1.18	0.371	0.981	0.12	PRX	complex1.pdb.gz	32,33,34
2	0.13	3gpcB	0.951	0.80	0.736	0.991	0.11	COA	complex2.pdb.gz	17,92,94
3	0.11	3eq6A	0.939	0.93	0.736	0.991	0.36	BCO	complex3.pdb.gz	6,7,8,38,69,74,75,77,79
4	0.11	3eq6B	0.939	0.92	0.736	0.991	0.11	AMP	complex4.pdb.gz	4,76,79
5	0.10	1mdbA	0.861	1.35	0.366	0.944	0.11	UUU	complex5.pdb.gz	7,8,42
6	0.06	3a9vA	0.828	1.37	0.316	0.916	0.10	AMP	complex6.pdb.gz	1,11,12,13,94,98
7	0.05	3qovC	0.662	2.79	0.162	0.906	0.25	COA	complex7.pdb.gz	9,10,11,12
8	0.04	1amuA	0.784	2.12	0.245	0.916	0.10	AMP	complex8.pdb.gz	11,12,13
9	0.03	2y4oA	0.643	3.12	0.118	0.935	0.11	DLL	complex9.pdb.gz	34,40,97

	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, Chengxin Zhang, Yang Li, Robin Pearce, Eric W. Bell, Yang Zhang. Folding non-homology proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. In preparation, 2020.