D-I-TASSER P15941-D3

D-I-TASSER results for P15941-D3

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

Input Sequence in FASTA format

>P15941 (43 residues)
TAPPAHGVTSAPDTRPAPGSTAPPAHGVTSAPDTRPAPGSTAP

Predicted Secondary Structure

Sequence	20 40 \| \| TAPPAHGVTSAPDTRPAPGSTAPPAHGVTSAPDTRPAPGSTAP
Prediction	CCCCCCCSCCCCCCCCCCCCCCCCCCCSCCCCCCCCCCCCCCC
Confidence	9998652036888888999889984321258888888898899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 \| \| TAPPAHGVTSAPDTRPAPGSTAPPAHGVTSAPDTRPAPGSTAP
Prediction	8544443345346454454644443433453454444556668
	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

CCCCCCCSCCCCCCCCCCCCCCCCCCCSCCCCCCCCCCCCCCC
TAPPAHGVTSAPDTRPAPGSTAPPAHGVTSAPDTRPAPGSTAP

4dt5A

0.14

4.77

0.90

CEthreader

TGRGATARSTSTGRGTATTTATGTASATSNAIGQGTATTTATG

3tiqA2

0.02

1.60

0.80

EigenThreader

-VKGDSIEKEEIFEKERLAPGTGEIESKETKPINELTEYGPET

5yfpH2

0.21

0.14

4.44

0.30

FFAS-3D

--------------RYLQSTQQTPGRENNRSPNKNSMGGSITP

1zvoC2

0.15

0.14

4.72

1.81

SPARKS-K

--GSLAKATTAPATTRNTGRGGEEKKKEKEKEEQEERETKTPE

4q4gX

0.14

0.05

1.58

0.69

CNFpred

-----------------------------SATSAQVTANMGRK

5xi0A

0.08

0.07

2.77

0.67

DEthreader

NVQITKAGPINAPRVLVVGSGLSIT-----AAASTIGVFGNSF

4dt5A

0.10

0.09

3.44

0.84

MapAlign

-GATARSTSTGRGTATTTATGTASATSNAIGQGTATTTATG--

2rrlA

0.21

6.65

0.64

MUSTER

VVAAAATSAKVEVDSPPAPVTHGAAMPTLSSATAQPLPVASAP

6em5r2

0.13

0.05

1.60

0.58

HHsearch

TNEPDRDGCV----------------NAVLL------------

7jjvA

0.21

6.65

0.80

CEthreader

NCNGGKGGKGAPGVGTAGGAGTNGGAGGSGGNSDVAAGGAGAA

(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	0.6445

(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	3szeA5	0.55	2.35	0.024	0.954	model1_3szeA5.pdb.gz
2	4om9A3	0.55	2.37	0.049	0.954	model1_4om9A3.pdb.gz
3	1m6bB	0.55	2.55	0.047	1.000	model1_1m6bB.pdb.gz
4	3i2tA1	0.51	2.62	0.000	1.000	model1_3i2tA1.pdb.gz
5	1wxrA3	0.50	2.39	0.049	0.954	model1_1wxrA3.pdb.gz
6	3h09B	0.48	2.65	0.098	0.954	model1_3h09B.pdb.gz
7	2ahxB2	0.46	2.78	0.047	1.000	model1_2ahxB2.pdb.gz
8	1igrA1	0.45	2.48	0.083	0.837	model1_1igrA1.pdb.gz
9	3syjA4	0.44	3.24	0.049	0.954	model1_3syjA4.pdb.gz
10	1n8yC2	0.44	2.85	0.070	1.000	model1_1n8yC2.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:0003712	1.00	transcription cofactor activity
GO:0002039	1.00	p53 binding
GO:0000978	1.00	RNA polymerase II core promoter proximal region sequence-specific DNA 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:1902166	1.00	negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator
GO:0090240	1.00	positive regulation of histone H4 acetylation
GO:0036003	1.00	positive regulation of transcription from RNA polymerase II promoter in response to stress
GO:0033629	1.00	negative regulation of cell adhesion mediated by integrin
GO:0016266	1.00	O-glycan processing
GO:0010944	1.00	negative regulation of transcription by competitive promoter binding
GO:0006978	1.00	DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator
GO:0006977	1.00	DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest

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:0070062	1.00	extracellular exosome
GO:0005887	1.00	integral component of plasma membrane
GO:0005796	1.00	Golgi lumen
GO:0005615	1.00	extracellular space
GO:0000790	1.00	nuclear chromatin

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	1n8zC	0.558	2.45	0.047	1.000	2.7.10.1	NA
2	0.060	1ru4A	0.480	2.83	0.093	1.000	4.2.2.2	NA
3	0.060	1llwA	0.500	2.65	0.073	0.954	1.4.7.1	NA
4	0.060	2qx3A	0.520	2.70	0.047	1.000	4.2.2.2	NA
5	0.060	3b4nA	0.506	2.70	0.070	1.000	4.2.2.2	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	0.01	3b2uB	0.443	3.23	0.023	1.000	0.32	UUU	complex1.pdb.gz	19,21,24

	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.