D-I-TASSER P31930-D3

D-I-TASSER results for P31930-D3

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

Input Sequence in FASTA format

>P31930 (54 residues)
ATESEVARGKNILRNALVSHLDGTTPVCEDIGRSLLTYGRRIPLAEWESRIAEV

Predicted Secondary Structure

Sequence	20 40 \| \| ATESEVARGKNILRNALVSHLDGTTPVCEDIGRSLLTYGRRIPLAEWESRIAEV
Prediction	CCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHCC
Confidence	989999999999999999846684789999999999829989999999998719
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 \| \| ATESEVARGKNILRNALVSHLDGTTPVCEDIGRSLLTYGRRIPLAEWESRIAEV
Prediction	856632640354134322333444443144104311334442316401531577
	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

                   |                   |

SS
Seq

CCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHCC
ATESEVARGKNILRNALVSHLDGTTPVCEDIGRSLLTYGRRIPLAEWESRIAEV

4nnzA

0.13

4.50

1.33

DEthreader

PSAAEIERVRAQMIAGMVYEKDSIAAQASSIGQLESVGLSWKLIDQDLEALKAV

3ivlA1

0.12

0.11

3.96

1.10

SPARKS-K

-SQEELERARSKWLTAWQQTYADPEKVGVALSEAIAS-GDWRLFFLQRDRVRDA

4nnzA2

0.13

4.50

1.33

DEthreader

PSAAEIERVRAQMIAGMVYEKDSIAAQASSIGQLESVGLSWKLIDQDLEALKAV

7jrgB

0.33

10.00

0.92

SPARKS-K

VTQVQLDRAKKSTKSAVLMNLESRMIASEDIGRQILTYGERKPLEQFLKAVDEI

4mvfA

0.22

7.00

0.84

MapAlign

FTEKNAATIMKQIFSAIFYLHSLKYDKKCDIWSKLLTPNERCTIEEALNHITQM

3ivlA

0.11

3.98

0.56

CEthreader

FSQEELERARSKWLTAWQQTYADPEKVGVALSEAIAS-GDWRLFFLQRDRVRDA

1hr6A

0.41

12.00

0.93

MUSTER

LTEDEVSRAKNQLKSSLLMNLESKLVELEDMGRQVLMHGRKIPVNEMISKIEDL

3ivlA1

0.12

0.11

3.96

0.79

HHsearch

-SQEELERARSKWLTAWQQTYADPEKVGVALSEAIAS-GDWRLFFLQRDRVRDA

3ivlA1

0.12

0.11

3.96

0.99

FFAS-3D

-SQEELERARSKWLTAWQQTYADPEKVGVALSEAIA-SGDWRLFFLQRDRVRDA

3hdiA2

0.28

8.50

0.72

EigenThreader

LTEKELENGKEQLKGSLMLSLESTNSRMSRNGKNELLLKKHRSLDEMIEQINAV

(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	0.6934

(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	3hdiA2	0.87	0.98	0.278	1.000	model1_3hdiA2.pdb.gz
2	5hxkA2	0.86	1.04	0.315	1.000	model1_5hxkA2.pdb.gz
3	7jrgA	0.86	1.01	0.574	1.000	model1_7jrgA.pdb.gz
4	4nnzA2	0.86	1.27	0.130	1.000	model1_4nnzA2.pdb.gz
5	1hr6A2	0.85	1.11	0.407	1.000	model1_1hr6A2.pdb.gz
6	1be3A2	0.83	1.21	0.963	1.000	model1_1be3A2.pdb.gz
7	3h1kB	0.82	1.22	0.222	1.000	model1_3h1kB.pdb.gz
8	2ibzA2	0.80	1.32	0.241	1.000	model1_2ibzA2.pdb.gz
9	3amiA	0.78	1.72	0.185	1.000	model1_3amiA.pdb.gz
10	3d3yA2	0.76	1.61	0.275	0.944	model1_3d3yA2.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:0016787	1.00	hydrolase activity
GO:0004222	0.99	metalloendopeptidase activity
GO:0008270	0.98	zinc 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:0008152	1.00	metabolic process
GO:0006508	0.99	proteolysis
GO:0009987	0.98	cellular process
GO:0044237	0.97	cellular metabolic process
GO:0016485	0.97	protein processing
GO:0044699	0.92	single-organism process
GO:0044710	0.90	single-organism metabolic process
GO:0044763	0.84	single-organism cellular process
GO:0055114	0.82	oxidation-reduction process
GO:0006091	0.82	generation of precursor metabolites and energy
GO:0022904	0.80	respiratory electron transport chain
GO:0009060	0.79	aerobic respiration
GO:0006122	0.79	mitochondrial electron transport, ubiquinol to cytochrome c

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:0044444	1.00	cytoplasmic part
GO:0044429	0.99	mitochondrial part
GO:0032991	0.87	macromolecular complex
GO:0044425	0.86	membrane part
GO:0043234	0.86	protein complex
GO:0098798	0.85	mitochondrial protein complex
GO:0044455	0.84	mitochondrial membrane part
GO:1990204	0.83	oxidoreductase complex
GO:0098803	0.83	respiratory chain complex
GO:0098800	0.83	inner mitochondrial membrane protein complex
GO:0005750	0.80	mitochondrial respiratory chain complex III

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	1hr6A	0.853	1.11	0.407	1.000	3.4.24.64	NA
2	0.060	2hk5A	0.611	3.04	0.020	0.944	2.7.10.2	NA
3	0.060	2ofvA	0.586	3.04	0.039	0.889	2.7.10.2	NA
4	0.060	2reiA	0.581	2.66	0.100	0.870	2.7.10.1	NA
5	0.060	1hr7A	0.854	1.11	0.407	1.000	3.4.24.64	34

	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	0.14	1ppjA	0.878	0.93	0.963	1.000	0.39	AZI	complex1.pdb.gz	10,51,52,53
2	0.07	2i6sA	0.653	1.93	0.083	0.852	0.17	UUU	complex2.pdb.gz	26,27,29,30
3	0.02	3q60A	0.632	2.08	0.146	0.889	0.18	ATP	complex3.pdb.gz	25,36,37
4	0.02	2i6qA	0.657	2.10	0.080	0.870	0.22	UUU	complex4.pdb.gz	22,23,24,32
5	0.02	3kntA	0.612	2.35	0.113	0.963	0.13	UUU	complex5.pdb.gz	24,27,33,44,45,46,47,49
6	0.02	3kntA	0.612	2.35	0.113	0.963	0.11	QNA	complex6.pdb.gz	26,27,28,29
7	0.01	2rfsA	0.621	2.81	0.078	0.907	0.15	AM8	complex7.pdb.gz	18,27,28,29,31
8	0.01	3plsA	0.635	2.45	0.078	0.944	0.16	ANP	complex8.pdb.gz	21,23,32
9	0.01	3q6wA	0.641	2.97	0.059	0.944	0.16	Q6W	complex9.pdb.gz	18,25,26,29,41
10	0.01	3f66B	0.622	2.54	0.059	0.889	0.23	GBL	complex10.pdb.gz	29,30,34

	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.