D-I-TASSER Q9Y2S2-D2

D-I-TASSER results for Q9Y2S2-D2

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

Input Sequence in FASTA format

>Q9Y2S2 (126 residues)
VLNRLQYAIISEAWRLVEEGIVSPSDLDLVMSEGLGMRYAFIGPLETMHLNAEGMLSYCD
RYSEGIKHVLQTFGPIPEFSRATAEKVNQDMCMKVPDDPEHLAARRQWRDECLMRLAKLK
SQVQPQ

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| VLNRLQYAIISEAWRLVEEGIVSPSDLDLVMSEGLGMRYAFIGPLETMHLNAEGMLSYCDRYSEGIKHVLQTFGPIPEFSRATAEKVNQDMCMKVPDDPEHLAARRQWRDECLMRLAKLKSQVQPQ
Prediction	CHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCC
Confidence	543899999999999999289999999999995678654455727876530534899999997889989886189987779999999999985268972039999999999999999999983889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| VLNRLQYAIISEAWRLVEEGIVSPSDLDLVMSEGLGMRYAFIGPLETMHLNAEGMLSYCDRYSEGIKHVLQTFGPIPEFSRATAEKVNQDMCMKVPDDPEHLAARRQWRDECLMRLAKLKSQVQPQ
Prediction	742021301330013005532031630140024034332332112233231122033204423520450176245365145402530253147434643641551254015202401512573688
	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

                   |                   |                   |                   |                   |                   |

SS
Seq

CHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCC
VLNRLQYAIISEAWRLVEEGIVSPSDLDLVMSEGLGMRYAFIGPLETMHLNAEGMLSYCDRYSEGIKHVLQTFGPIPEFSRATAEKVNQDMCMKVPDDPEHLAARRQWRDECLMRLAKLKSQVQPQ

3a97A2

0.88

0.86

24.12

1.21

SPARKS-K

VLNRLQYAIISEAWRLVEEGIVSPSDLDLVMSDGLGMRYAFIGPLETMHLNAEGMLSYCDRYSEGMKRVLKSFGSIPEFSGATVEKVNQAMCKKVPADPEHLAARREWRDECLKRLAKLKRQM---

3a97A2

0.88

0.86

24.12

1.69

MUSTER

VLNRLQYAIISEAWRLVEEGIVSPSDLDLVMSDGLGMRYAFIGPLETMHLNAEGMLSYCDRYSEGMKRVLKSFGSIPEFSGATVEKVNQAMCKKVPADPEHLAARREWRDECLKRLAKLKRQM---

3a97A2

0.88

0.86

24.12

1.99

HHsearch

VLNRLQYAIISEAWRLVEEGIVSPSDLDLVMSDGLGMRYAFIGPLETMHLNAEGMLSYCDRYSEGMKRVLKSFGSIPEFSGATVEKVNQAMCKKVPADPEHLAARREWRDECLKRLAKLKRQM---

3a97A2

0.88

0.86

24.12

2.04

FFAS-3D

VLNRLQYAIISEAWRLVEEGIVSPSDLDLVMSDGLGMRYAFIGPLETMHLNAEGMLSYCDRYSEGMKRVLKSFGSIPEFSGATVEKVNQAMCKKVPADPEHLAARREWRDECLKRLAKLKRQM---

3a97A

0.75

0.52

14.84

1.00

DEthreader

VLNRLQYAIISEAWRLVEEGIVSPSDLDLVMSDLGMRYA-----------------------------------FGSIPESATVEKVNQAMCKKVPADPEHLAARREWRDECLKRLAKLKRQM---

6tnmA3

0.15

0.13

4.56

1.09

SPARKS-K

FVNRVLFPYFAGFSQLLRDG-ADFRKIDKVMEKQFGWP---MGPAYLLDVVG------IDTAHHAQAVMAAGFPQYRDAIDALFDAGQKNGLGFWRYKEDSKGKPKKEEDAAVEDLLAEVSQPKRD

1zcjA

0.20

0.14

4.57

0.71

MapAlign

-LERCLYSLINEAFRILEEGMARPEHIDVIYLHGYGWPRHKGGPMFYAASV------GLPTVLEKLQKYYRQQLEPSDYLRRLVAQGSPPLKEWQSL-----------------------------

2wtbA3

0.17

0.12

3.92

0.57

CEthreader

IIEMTFFPVVNEACRVFAEGIAKAADLDIAGIMGMGFPPYRGGIMFWADSIG------SKYIYSRLDEWSKAYGKPCAFLAERGSKGVLLSAPVK-------------------------------

4om8A2

0.22

0.21

6.75

1.32

MUSTER

VENRVLYALLREAVDLVERGVIDPEDLDTCVSWGIGYKIAVIGPMALLDMAGLDIYKSVSSFLNADL---SNRDDVAPMVLEKTSAGIKSGEGMFCYTPEQTKALQAERARKLVAVRRILEGRE--

4om8A2

0.23

0.22

6.96

1.88

HHsearch

VENRVLYALLREAVDLVERGVIDPEDLDTCVSWGIGYKIAVIGPMALLDMAGLDIYKSVSS---FLNADLSNRDDVAPMVLEKTSASKKSGEGMFCYTPEQTKALQAERARKLVAVRRILEGRE--

(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	0.7025

(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	3a97A	0.66	1.96	0.642	0.714	model1_3a97A.pdb.gz
2	4pzcA2	0.56	2.42	0.221	0.675	model1_4pzcA2.pdb.gz
3	6hrdA	0.56	2.44	0.247	0.667	model1_6hrdA.pdb.gz
4	6tnmA3	0.56	3.08	0.097	0.730	model1_6tnmA3.pdb.gz
5	2x58A4	0.56	2.49	0.211	0.667	model1_2x58A4.pdb.gz
6	2wtbA	0.55	2.35	0.153	0.651	model1_2wtbA.pdb.gz
7	4om8A	0.55	3.40	0.233	0.698	model1_4om8A.pdb.gz
8	4kueA	0.55	2.63	0.214	0.667	model1_4kueA.pdb.gz
9	6jufB	0.55	4.32	0.050	0.921	model1_6jufB.pdb.gz
10	1wdlA3	0.55	3.44	0.130	0.754	model1_1wdlA3.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:0051287	1.00	NAD binding
GO:0016616	1.00	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
GO:0070403	0.96	NAD+ binding
GO:0050104	0.96	L-gulonate 3-dehydrogenase 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	0.95	single-organism process
GO:0008152	0.82	metabolic process
GO:0009987	0.76	cellular process
GO:0071704	0.73	organic substance metabolic process
GO:0044710	0.73	single-organism metabolic process
GO:0044237	0.71	cellular metabolic process
GO:0044763	0.65	single-organism cellular process
GO:0044281	0.65	small molecule metabolic process
GO:1901575	0.58	organic substance catabolic process
GO:0044248	0.57	cellular catabolic process
GO:0006082	0.52	organic acid metabolic process
GO:0019752	0.50	carboxylic acid 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:0044424	1.00	intracellular part
GO:0044444	0.99	cytoplasmic part
GO:0005829	0.77	cytosol
GO:0044446	0.64	intracellular organelle part
GO:0043226	0.64	organelle
GO:0043229	0.62	intracellular organelle
GO:0043227	0.61	membrane-bounded organelle
GO:0043231	0.60	intracellular membrane-bounded organelle
GO:0016020	0.54	membrane
GO:0005634	0.51	nucleus
GO:0005737	0.50	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	0.060	3ckeD	0.458	4.11	0.064	0.738	4.2.3.9	NA
2	0.060	2hivA	0.485	4.54	0.068	0.833	6.5.1.1	NA
3	0.060	1rqiA	0.522	4.00	0.037	0.849	2.5.1.10	NA
4	0.060	1e9yB	0.512	4.05	0.047	0.833	3.5.1.5	NA
5	0.060	2j1pB	0.374	5.05	0.089	0.682	2.5.1.1 2.5.1.10 2.5.1.29	38

	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	0.03	1f140	0.541	2.75	0.247	0.667	0.50	III	complex1.pdb.gz	1,2,4,5,9,12,13,16,20,21,22,26,27,29,30,33,34,36,39,40,75

	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.