D-I-TASSER P17813-D2

D-I-TASSER results for P17813-D2

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

Input Sequence in FASTA format

>P17813 (130 residues)
CHLEGVAGHKEAHILRVLPGHSAGPRTVTVKVELSCAPGDLDAVLILQGPPYVSWLIDAN
HNMQIWTTGEYSFKIFPEKNIRGFKLPDTPQGLLGEARMLNASIVASFVELPLASIVSLH
ASSCGGRLQT

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| CHLEGVAGHKEAHILRVLPGHSAGPRTVTVKVELSCAPGDLDAVLILQGPPYVSWLIDANHNMQIWTTGEYSFKIFPEKNIRGFKLPDTPQGLLGEARMLNASIVASFVELPLASIVSLHASSCGGRLQT
Prediction	CCCCCCCCCCSSSSSSSSCCCCCCCCSSSSSSSSCCCCCCCCSSSSSSCCCCCSSSSSCCCCSSSSSSCSSSSSSCCCCCCCCCSCCCCHHHHHHHHHHHCCCSSSSSSSCCCCCSSSSSSCCCCCCCCC
Confidence	9113678984589999806999999558999997158899976999818995079996388479999351999974787778732899828999999982993478777524653489981378888789
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| CHLEGVAGHKEAHILRVLPGHSAGPRTVTVKVELSCAPGDLDAVLILQGPPYVSWLIDANHNMQIWTTGEYSFKIFPEKNIRGFKLPDTPQGLLGEARMLNASIVASFVELPLASIVSLHASSCGGRLQT
Prediction	3446426644202003023457652432403030404674441000031364020103243403021334130331355615444147235301530473614212322423333403030453564468
	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

CCCCCCCCCCSSSSSSSSCCCCCCCCSSSSSSSSCCCCCCCCSSSSSSCCCCCSSSSSCCCCSSSSSSCSSSSSSCCCCCCCCCSCCCCHHHHHHHHHHHCCCSSSSSSSCCCCCSSSSSSCCCCCCCCC
CHLEGVAGHKEAHILRVLPGHSAGPRTVTVKVELSCAPGDLDAVLILQGPPYVSWLIDANHNMQIWTTGEYSFKIFPEKNIRGFKLPDTPQGLLGEARMLNASIVASFVELPLASIVSLHASSCGGRLQT

5hzwA

0.83

0.78

21.91

1.33

DEthreader

VRGCHLAGHKEAHILRVLPGHSAGPRTVTVKVELSAPG-DLDAVLILQGPPYVSWLIDANHNMQIWTT-GEYSFKIFP-NIRGFKLPDTPQGLLGEARMLNASIVASFVELPLASIVSLHAS-SC-----

6mznA1

0.29

0.28

8.42

2.19

SPARKS-K

CVLSGPDHEQEVHIIELQAPNSSSAFQVDVIVDLRPLDGDRDVVLLLKCEKSVNWVIKAHKKLEIMTSDTVSLSEDTERLMQVQKLPAGSQALIQWAEENGFNPVTSYTNTPVANHFNLRLRE-------

5hzwA2

1.00

0.94

26.28

1.66

MapAlign

--LEGVAGHKEAHILRVLPGHSAGPRTVTVKVELSCAPGDLDAVLILQGPPYVSWLIDANHNMQIWTTGEYSFKIFPEKNIRGFKLPDTPQGLLGEARMLNASIVASFVELPLASIVSLHASSC------

5hzwA

1.00

0.95

26.71

1.64

CEthreader

CHLEGVAGHKEAHILRVLPGHSAGPRTVTVKVELSCAPGDLDAVLILQGPPYVSWLIDANHNMQIWTTGEYSFKIFPEKNIRGFKLPDTPQGLLGEARMLNASIVASFVELPLASIVSLHASSC------

5hzwA2

1.00

0.95

26.71

1.76

MUSTER

CHLEGVAGHKEAHILRVLPGHSAGPRTVTVKVELSCAPGDLDAVLILQGPPYVSWLIDANHNMQIWTTGEYSFKIFPEKNIRGFKLPDTPQGLLGEARMLNASIVASFVELPLASIVSLHASSC------

5hzwA2

1.00

0.95

26.71

3.53

HHsearch

CHLEGVAGHKEAHILRVLPGHSAGPRTVTVKVELSCAPGDLDAVLILQGPPYVSWLIDANHNMQIWTTGEYSFKIFPEKNIRGFKLPDTPQGLLGEARMLNASIVASFVELPLASIVSLHASSC------

6mznA1

0.29

0.28

8.42

1.83

FFAS-3D

CVLSGPDHEQEVHIIELQAPNSSSAFQVDVIVDLRPLDGDRDVVLLLKCEKSVNWVIKAHKKLEIMTSDTVSLSEDTERLMQKQKLPAGSQALIQWAEENGFNPVTSYTNTPVANHFNLRLRE-------

5hzwA2

0.98

0.93

26.08

1.67

EigenThreader

ALVEGVAGHKEAHILRVLPGHSAGPRTVTVKVELSCAPGDLDAVLILQGPPYVSWLIDANHNMQIWTTGEYSFKIFPEKNIRGFKLPDTPQGLLGEARMLNASIVASFVELPLASIVSLHASSC------

5hzwA

1.00

0.95

26.71

1.87

CNFpred

CHLEGVAGHKEAHILRVLPGHSAGPRTVTVKVELSCAPGDLDAVLILQGPPYVSWLIDANHNMQIWTTGEYSFKIFPEKNIRGFKLPDTPQGLLGEARMLNASIVASFVELPLASIVSLHASSC------

5hzwA2

0.83

0.78

21.91

1.33

DEthreader

VRGCHLAGHKEAHILRVLPGHSAGPRTVTVKVELSAPG-DLDAVLILQGPPYVSWLIDANHNMQIWTT-GEYSFKIFP-NIRGFKLPDTPQGLLGEARMLNASIVASFVELPLASIVSLHAS-SC-----

(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	0.8205

(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	5hzwA2	0.94	0.52	1.000	0.954	model1_5hzwA2.pdb.gz
2	6mznA	0.70	2.84	0.244	0.877	model1_6mznA.pdb.gz
3	7lbgD	0.68	3.05	0.179	0.877	model1_7lbgD.pdb.gz
4	1j0eA	0.53	3.91	0.032	0.839	model1_1j0eA.pdb.gz
5	1tzmC	0.52	3.88	0.033	0.839	model1_1tzmC.pdb.gz
6	1l7nB	0.52	3.74	0.008	0.769	model1_1l7nB.pdb.gz
7	2i2xA	0.52	4.34	0.080	0.862	model1_2i2xA.pdb.gz
8	2no4B	0.51	3.94	0.054	0.785	model1_2no4B.pdb.gz
9	2hszA	0.51	3.85	0.073	0.785	model1_2hszA.pdb.gz
10	1qh9A	0.50	3.40	0.106	0.723	model1_1qh9A.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:0005114	1.00	type II transforming growth factor beta receptor binding
GO:0004871	0.87	signal transducer activity
GO:0003824	0.78	catalytic activity
GO:0038023	0.75	signaling receptor activity
GO:0016740	0.75	transferase activity
GO:0019199	0.74	transmembrane receptor protein kinase activity
GO:0004674	0.74	protein serine/threonine kinase activity
GO:0005024	0.73	transforming growth factor beta-activated receptor activity
GO:0097367	0.63	carbohydrate derivative binding
GO:0005539	0.59	glycosaminoglycan binding
GO:0034713	0.58	type I transforming growth factor beta receptor 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:0050794	1.00	regulation of cellular process
GO:0044699	0.91	single-organism process
GO:0009987	0.91	cellular process
GO:0048518	0.89	positive regulation of biological process
GO:0044763	0.89	single-organism cellular process
GO:0051239	0.88	regulation of multicellular organismal process
GO:0048522	0.88	positive regulation of cellular process
GO:0044767	0.88	single-organism developmental process
GO:0080090	0.84	regulation of primary metabolic process
GO:0060255	0.84	regulation of macromolecule metabolic process
GO:0031323	0.84	regulation of cellular metabolic process
GO:0051240	0.83	positive regulation of multicellular organismal process
GO:0048856	0.83	anatomical structure development
GO:0010628	0.83	positive regulation of gene expression
GO:0010557	0.83	positive regulation of macromolecule biosynthetic process
GO:0009966	0.83	regulation of signal transduction
GO:0001934	0.83	positive regulation of protein phosphorylation
GO:0017015	0.82	regulation of transforming growth factor beta receptor signaling pathway
GO:0050896	0.72	response to stimulus
GO:0009628	0.70	response to abiotic stimulus
GO:0048513	0.66	animal organ development
GO:0007165	0.64	signal transduction
GO:0007179	0.56	transforming growth factor beta receptor signaling pathway
GO:0051179	0.55	localization
GO:0042221	0.55	response to chemical
GO:0051716	0.54	cellular response to stimulus
GO:0044765	0.54	single-organism transport
GO:0010033	0.54	response to organic substance
GO:0009719	0.54	response to endogenous stimulus
GO:0071559	0.53	response to transforming growth factor beta
GO:0071260	0.53	cellular response to mechanical stimulus
GO:0070278	0.53	extracellular matrix constituent secretion
GO:0060348	0.53	bone development
GO:0042493	0.53	response to drug
GO:0032967	0.53	positive regulation of collagen biosynthetic process
GO:0031960	0.53	response to corticosteroid

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:0044424	0.80	intracellular part
GO:0044446	0.67	intracellular organelle part
GO:0044425	0.66	membrane part
GO:0044421	0.65	extracellular region part
GO:0044428	0.63	nuclear part
GO:0005615	0.62	extracellular space
GO:0005737	0.61	cytoplasm
GO:0005654	0.61	nucleoplasm
GO:0009986	0.52	cell surface

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	1od0B	0.499	4.57	0.060	0.823	3.2.1.21	NA
2	0.060	2bneB	0.495	4.13	0.057	0.769	2.7.4.22	15
3	0.060	2vs4A	0.503	3.73	0.026	0.715	2.4.1.87	NA
4	0.060	1judA	0.498	3.56	0.105	0.731	3.8.1.2	NA
5	0.060	2hszA	0.508	3.77	0.081	0.785	3.1.3.18	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	0.01	1o95E	0.511	3.81	0.104	0.769	0.24	AMP	complex1.pdb.gz	28,65,66,67,68
2	0.01	1l7nA	0.520	3.67	0.043	0.761	0.24	AF3	complex2.pdb.gz	48,49,69
3	0.01	2hxvA	0.506	3.75	0.086	0.731	0.22	NDP	complex3.pdb.gz	47,96,107
4	0.01	1g93A	0.503	3.63	0.034	0.708	0.27	GAL	complex4.pdb.gz	27,50,55,68
5	0.01	2d5nB	0.517	3.55	0.076	0.723	0.13	NDP	complex5.pdb.gz	16,17,19,86
6	0.01	2yqhA	0.502	3.88	0.072	0.769	0.11	GN1	complex6.pdb.gz	67,68,112
7	0.01	1gww0	0.505	3.80	0.029	0.739	0.24	III	complex7.pdb.gz	63,64,65,66,96
8	0.01	1j0eA	0.529	3.91	0.032	0.839	0.11	UUU	complex8.pdb.gz	19,20,23,24
9	0.01	1gwwB	0.503	3.74	0.026	0.715	0.16	GLC	complex9.pdb.gz	26,48,70
10	0.01	1j0bB	0.523	3.92	0.057	0.831	0.27	5PA	complex10.pdb.gz	21,24,49,50,51,52,54,112

	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, Qiqige Wuyun, Yang Li, Quancheng Liu, Xiaogen Zhou, Yiheng Zhu, P. Lydia Freddolino, Yang Zhang. Integrating deep learning potentials with I-TASSER for single- and multi-domain protein structure prediction. Submitted. 2023.