D-I-TASSER Q14940-D3

D-I-TASSER results for Q14940-D3

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

Input Sequence in FASTA format

>Q14940 (85 residues)
LTCLPPHPRGTEEPQVPLHLPSDPRSSFAFPPSLAKAGRSRSESSADLPQQQELQPLMGH
KDHTHLSPGTATSHWCIQFNRGSRL

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| LTCLPPHPRGTEEPQVPLHLPSDPRSSFAFPPSLAKAGRSRSESSADLPQQQELQPLMGHKDHTHLSPGTATSHWCIQFNRGSRL
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCSSSSSCCCCCC
Confidence	9878999887678766556899998764578334222445444678861223311112665667668888896168885366779
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| LTCLPPHPRGTEEPQVPLHLPSDPRSSFAFPPSLAKAGRSRSESSADLPQQQELQPLMGHKDHTHLSPGTATSHWCIQFNRGSRL
Prediction	7543453444375444346336554432423441364345456645644555514423346744414454443301021455667
	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

                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCSSSSSCCCCCC
LTCLPPHPRGTEEPQVPLHLPSDPRSSFAFPPSLAKAGRSRSESSADLPQQQELQPLMGHKDHTHLSPGTATSHWCIQFNRGSRL

5ig1A1

0.05

2.14

0.52

CEthreader

KRSVIGKGAFSTVHRCVNKRTGEVCAVKVIALKSLRSSEIN-------KIKREIGICSSLQHESMRRAFRDESHFYLVFEY----

6tdwB1

0.02

1.60

0.58

EigenThreader

TALGERLAKFEPLSSTGMVNAEDNENPTGALLAASNLLTALGHEAEAKKIAAAVAKAYTT---DRILPKELPGGKADLEAFIDAV

7kwzA

0.17

0.16

5.40

0.33

FFAS-3D

FGAFSINPAMMAAAQAALQSSWGMMGMLA--SQQNQSGPSGNNQNQGNMQREPNQAFGSGNNSYSGSNSGAAIGWGSASNAGS--

2nbiA2

0.16

5.45

0.97

SPARKS-K

GPQPSSQPSECADELCPYDTCFLPFDDSSRPPDCTDPSVNRPDCDAIDFTCPTCCPTQCRPDNPMFSPSPGSPPVCSPTMMPSPL

5imuA

0.21

0.08

2.62

0.59

CNFpred

-----------------------------------------GAVSARAAEQQRLQRIVDAVA------QEPRISWAAGLRD----

3s1sA

0.04

1.85

0.83

DEthreader

SSSTRRL--KPVVSQISPIVVGN----STNLVDILENRK--DNSTSWHQALVVAGYEYIRG-VLRGDLSSLNDLGELLIDIATFL

1trjA

0.07

0.06

2.46

0.84

MapAlign

-----------VQDCTLTADGAYALSASWDKTLRLWDVATGETYQRFVGHKSDVMSVDIDKKASMIISGSRDKTIKVWTIKGQCL

2mk0A

0.18

5.76

0.86

MUSTER

EPSSQPSDCGEVIEECPIDACFLPKSDSARPPDCTAVGRPDCNVLPFPNNIPSCCPFECSPDNPMFTPSPGSPPNCSPTMLPSPS

3pcrA

0.20

0.13

4.14

0.75

HHsearch

----------------------ES--C---AEKLFSFGLWNPTYS--RSERQSFQELLTVLEPVYPLPNELG-RVSARFSDGSSL

3k1qA2

0.06

2.51

0.46

CEthreader

LITTHGFCVTGFFGVPDDGTSDLGIDAVRLFDPMF-------SDAVANLPSNALASLVSRVVPSSIMFTRVPVSTTIYGKRTFLS

(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	0.571

(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	3bt7A	0.50	3.48	0.047	0.812	model1_3bt7A.pdb.gz
2	2btdA	0.49	3.59	0.038	0.776	model1_2btdA.pdb.gz
3	2uvcG	0.49	3.53	0.015	0.788	model1_2uvcG.pdb.gz
4	3hwcA1	0.49	2.96	0.051	0.694	model1_3hwcA1.pdb.gz
5	4g5eA1	0.49	2.96	0.051	0.694	model1_4g5eA1.pdb.gz
6	2c2nA1	0.46	3.64	0.121	0.741	model1_2c2nA1.pdb.gz
7	1u8vA	0.42	4.54	0.026	0.776	model1_1u8vA.pdb.gz
8	3cr3A	0.42	3.87	0.063	0.753	model1_3cr3A.pdb.gz
9	1j36A	0.42	4.20	0.024	0.741	model1_1j36A.pdb.gz
10	3fmwC	0.40	4.25	0.053	0.706	model1_3fmwC.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:0015385	1.00	sodium:proton antiporter activity
GO:0015079	0.81	potassium ion transmembrane transporter activity
GO:0015386	0.79	potassium:proton antiporter 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:0006814	1.00	sodium ion transport
GO:0009987	0.89	cellular process
GO:0044763	0.87	single-organism cellular process
GO:0065007	0.84	biological regulation
GO:0055085	0.83	transmembrane transport
GO:0065008	0.80	regulation of biological quality
GO:0098719	0.79	sodium ion import across plasma membrane
GO:0071805	0.79	potassium ion transmembrane transport
GO:0051453	0.79	regulation of intracellular pH

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:0005886	1.00	plasma membrane

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	1e5dA	0.460	3.63	0.066	0.741	1.-.-.-	NA
2	0.060	2wz1A	0.466	3.83	0.027	0.776	4.6.1.2	NA
3	0.060	1bibA	0.479	3.50	0.053	0.776	6.3.4.15	NA
4	0.060	2ohhA	0.473	3.55	0.039	0.776	1.-.-.-	62
5	0.060	1wc4A	0.463	3.74	0.055	0.765	4.6.1.1	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	1p0bA	0.462	3.67	0.024	0.788	0.28	PQ0	complex1.pdb.gz	54,58,70,71
2	0.01	2uvaG	0.476	3.69	0.000	0.776	0.12	FMN	complex2.pdb.gz	9,10,37,38
3	0.01	1q63A	0.465	3.88	0.047	0.788	0.16	AIQ	complex3.pdb.gz	4,38,39,79,84
4	0.01	2ohhA	0.473	3.55	0.039	0.776	0.34	FMN	complex4.pdb.gz	14,15,16,27,28,78,79,80,82,83,84
5	0.01	3bldA	0.423	4.05	0.037	0.753	0.25	PRF	complex5.pdb.gz	11,38,39,40
6	0.01	2uvcG	0.492	3.53	0.015	0.788	0.12	FMN	complex6.pdb.gz	38,79,80
7	0.01	1q2rA	0.465	3.70	0.060	0.776	0.24	9DG	complex7.pdb.gz	26,28,66,69
8	0.01	1pxgA	0.467	3.76	0.060	0.776	0.20	PRF	complex8.pdb.gz	8,10,38
9	0.01	3eouA	0.423	4.12	0.037	0.765	0.33	PK3	complex9.pdb.gz	3,7,29,31,84
10	0.01	1bc20	0.471	3.53	0.031	0.741	0.38	III	complex10.pdb.gz	11,12,13,53,54,55

	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.