D-I-TASSER P16066-D5

D-I-TASSER results for P16066-D5

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

Input Sequence in FASTA format

>P16066 (43 residues)
TIPASFHDGLLLYIQAVTETLAHGGTVTDGENITQRMWNRSFQ

Predicted Secondary Structure

Sequence	20 40 \| \| TIPASFHDGLLLYIQAVTETLAHGGTVTDGENITQRMWNRSFQ
Prediction	CCHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCC
Confidence	9315677999999999999998189998879999998587789
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 \| \| TIPASFHDGLLLYIQAVTETLAHGGTVTDGENITQRMWNRSFQ
Prediction	8431333212202131134116654746404410531364538
	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

CCHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCC
TIPASFHDGLLLYIQAVTETLAHGGTVTDGENITQRMWNRSFQ

1dp4C

0.91

25.49

1.33

DEthreader

IIPASFHDGLLLYVQAVTETLAQGGTVTDGENITQRMWNRSFL

1dp4C1

0.93

26.12

0.97

SPARKS-K

IIPASFHDGLLLYVQAVTETLAQGGTVTDGENITQRMWNRSFQ

3jacA

0.10

0.09

3.49

0.95

MapAlign

GGGGGGGGGGGGGGGGGGGGGGGGGGGG-GGGGGGGGGGGGGG

1jdnA1

0.42

12.30

0.48

CEthreader

MFVEGFHDAILLYVLALHEVLRAGYSKKDGGKIIQQTWNRTFE

1dp4C

0.93

26.12

0.95

MUSTER

IIPASFHDGLLLYVQAVTETLAQGGTVTDGENITQRMWNRSFQ

6n51B

0.07

2.88

0.89

HHsearch

SKMGFVINAIYSMAYGLHNMQMSLMKPIDGRKLLESLMKTNFT

1jdnA1

0.44

0.42

12.26

0.51

FFAS-3D

--VEGFHDAILLYVLALHEVLRAGYSKKDGGKIIQQTWNRTFE

5kcaA

0.14

4.77

0.45

EigenThreader

ISNLYIYDTVLLLANAFHKKLEDRKWHSGGRSMLETIKKGGNP

1dp4A

0.93

26.12

0.76

CNFpred

IIPASFHDGLLLYVQAVTETLAQGGTVTDGENITQRMWNRSFQ

1dp4C1

0.91

25.49

1.33

DEthreader

IIPASFHDGLLLYVQAVTETLAQGGTVTDGENITQRMWNRSFL

(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	0.7067

(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	1dp4C	0.92	0.73	0.930	1.000	model1_1dp4C.pdb.gz
2	1jdnA	0.83	1.00	0.419	1.000	model1_1jdnA.pdb.gz
3	3q41A	0.68	1.65	0.209	1.000	model1_3q41A.pdb.gz
4	4f11A1	0.67	1.72	0.070	1.000	model1_4f11A1.pdb.gz
5	4gnrA1	0.56	2.83	0.103	0.884	model1_4gnrA1.pdb.gz
6	2imsA	0.55	2.23	0.093	0.721	model1_2imsA.pdb.gz
7	4hhxA	0.52	1.77	0.103	0.721	model1_4hhxA.pdb.gz
8	2bz0B	0.51	2.54	0.139	0.767	model1_2bz0B.pdb.gz
9	3lopA1	0.50	2.77	0.077	0.814	model1_3lopA1.pdb.gz
10	2qshA	0.49	3.12	0.029	0.791	model1_2qshA.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:0016849	1.00	phosphorus-oxygen lyase activity
GO:0009975	1.00	cyclase activity
GO:0004016	0.96	adenylate cyclase activity
GO:0004383	0.79	guanylate cyclase activity
GO:0004872	0.74	receptor activity
GO:0001653	0.69	peptide receptor activity
GO:0016941	0.68	natriuretic peptide receptor 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:0071704	0.97	organic substance metabolic process
GO:0050794	0.97	regulation of cellular process
GO:0044699	0.97	single-organism process
GO:0044238	0.97	primary metabolic process
GO:0009987	0.97	cellular process
GO:0044237	0.96	cellular metabolic process
GO:0007165	0.96	signal transduction
GO:0034654	0.95	nucleobase-containing compound biosynthetic process
GO:0006796	0.94	phosphate-containing compound metabolic process
GO:0044711	0.93	single-organism biosynthetic process
GO:0009117	0.93	nucleotide metabolic process
GO:0009190	0.92	cyclic nucleotide biosynthetic process
GO:0052652	0.91	cyclic purine nucleotide metabolic process
GO:0009152	0.91	purine ribonucleotide biosynthetic process
GO:0006182	0.72	cGMP biosynthetic 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	1.00	cell part
GO:0016020	0.99	membrane
GO:0005886	0.98	plasma membrane
GO:0044424	0.94	intracellular part
GO:0044444	0.81	cytoplasmic part
GO:0043234	0.77	protein complex
GO:0008074	0.75	guanylate cyclase complex, soluble
GO:0043226	0.50	organelle

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	0.066	1z8yM	0.456	1.13	0.125	0.558	3.4.21.90	NA
2	0.060	7reqD	0.668	2.22	0.150	0.837	5.4.99.2	21
3	0.060	1h16A	0.699	2.18	0.047	1.000	2.3.1.54	NA
4	0.060	2ewgA	0.667	2.39	0.070	0.977	2.5.1.10	NA
5	0.060	2b0tA	0.754	2.01	0.070	0.977	1.1.1.42	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	0.13	1dp40	0.919	0.73	0.930	1.000	0.23	III	complex1.pdb.gz	11,14,15,18,19
2	0.08	1yk0B	0.849	0.94	0.419	1.000	0.10	III	complex2.pdb.gz	26,29,32,36,40
3	0.02	1cvuB	0.710	1.50	0.049	0.954	0.15	ACD	complex3.pdb.gz	10,13,14,18
4	0.01	3qmoB	0.714	1.61	0.048	0.977	0.14	NS4	complex4.pdb.gz	12,15,16
5	0.01	1ddxA	0.673	2.20	0.048	0.977	0.17	PGX	complex5.pdb.gz	6,11,30,33,34,38
6	0.01	1ddxD	0.674	2.20	0.048	0.977	0.14	PGX	complex6.pdb.gz	32,35,36,38
7	0.01	3ntbA	0.543	2.13	0.073	0.954	0.11	T1N	complex7.pdb.gz	10,30,34,38

	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.