D-I-TASSER Q02153-D1

D-I-TASSER results for Q02153-D1

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

Input Sequence in FASTA format

>Q02153 (70 residues)
MYGFVNHALELLVIRNYGPEVWEDIKKEAQLDEEGQFLVRIIYDDSKTYDLVAAASKVLN
LNAGEILQMF

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| MYGFVNHALELLVIRNYGPEVWEDIKKEAQLDEEGQFLVRIIYDDSKTYDLVAAASKVLNLNAGEILQMF
Prediction	CCHHHHHHHHHHHHHHHCHHHHHHHHHHHCCCCCCSSSSSCCCCHHHHHHHHHHHHHHHCCCHHHHHHHC
Confidence	9317999999999998069999999999199998757530253869999999999999896999999739
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| MYGFVNHALELLVIRNYGPEVWEDIKKEAQLDEEGQFLVRIIYDDSKTYDLVAAASKVLNLNAGEILQMF
Prediction	6312014003410475215620550274171746432333331436203500420163273426402754
	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

                   |                   |                   |

SS
Seq

CCHHHHHHHHHHHHHHHCHHHHHHHHHHHCCCCCCSSSSSCCCCHHHHHHHHHHHHHHHCCCHHHHHHHC
MYGFVNHALELLVIRNYGPEVWEDIKKEAQLDEEGQFLVRIIYDDSKTYDLVAAASKVLNLNAGEILQMF

2o0cA

0.43

12.56

1.50

DEthreader

MYGLVNKAIQDMISKHHGEDTWEAIKQKAGLDID-FFVGMEAYSDDVTYHLVGAASEVLGKPAEELLIAF

6bddA1

0.23

0.20

6.27

1.85

SPARKS-K

MKGIIFTEFLDLVEDKFGLEMVDKIITQSELESEGVYTSIGTYRFSEMLQLLQNLSANTDV---------

2o0cA

0.41

12.19

1.34

MapAlign

MYGLVNKAIQDMISKHHGEDTWEAIKQKAGLEDIDFFVGMEAYSDDVTYHLVGAASEVLGKPAEELLIAF

2o0cA

0.41

12.19

1.15

CEthreader

MYGLVNKAIQDMISKHHGEDTWEAIKQKAGLEDIDFFVGMEAYSDDVTYHLVGAASEVLGKPAEELLIAF

5mnwA

1.00

28.00

1.44

MUSTER

MYGFVNHALELLVIRNYGPEVWEDIKKEAQLDEEGQFLVRIIYDDSKTYDLVAAASKVLNLNAGEILQMF

5mnwA

1.00

28.00

1.60

HHsearch

MYGFVNHALELLVIRNYGPEVWEDIKKEAQLDEEGQFLVRIIYDDSKTYDLVAAASKVLNLNAGEILQMF

6bddA

0.21

6.79

1.25

FFAS-3D

MKGIIFTEFLDLVEDKFGLEMVDKIITQSELESEGVYTSIGTYRFSEMLQLLQNLSANTDVSIDDLLLTY

6ocvA

0.26

7.94

1.00

EigenThreader

MMGMVFTGLMELIEDEFGYETLDTLLESCELQSEGIYTSVGSYDHQELLQLVVKLSEVSSVPVTELVRLF

5mnwA

1.00

28.00

1.03

CNFpred

MYGFVNHALELLVIRNYGPEVWEDIKKEAQLDEEGQFLVRIIYDDSKTYDLVAAASKVLNLNAGEILQMF

5mnwA

1.00

28.00

1.50

DEthreader

MYGFVNHALELLVIRNYGPEVWEDIKKEAQLDEEGQFLVRIIYDDSKTYDLVAAASKVLNLNAGEILQMF

(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	0.833

(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	6jt0B1	0.96	0.60	1.000	1.000	model1_6jt0B1.pdb.gz
2	2o0cA	0.95	0.69	0.414	1.000	model1_2o0cA.pdb.gz
3	6bddA	0.89	1.56	0.214	1.000	model1_6bddA.pdb.gz
4	6pasB1	0.86	1.31	0.557	1.000	model1_6pasB1.pdb.gz
5	6ocvA	0.83	1.44	0.235	0.971	model1_6ocvA.pdb.gz
6	1xbnA1	0.75	1.62	0.179	0.957	model1_1xbnA1.pdb.gz
7	2kilA	0.73	2.03	0.188	0.957	model1_2kilA.pdb.gz
8	4oltA2	0.66	2.98	0.106	0.886	model1_4oltA2.pdb.gz
9	4ilyB	0.65	2.73	0.106	0.857	model1_4ilyB.pdb.gz
10	1chkA2	0.65	2.74	0.104	0.843	model1_1chkA2.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:0004383	0.99	guanylate cyclase activity
GO:0004016	0.98	adenylate cyclase 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:0050794	0.99	regulation of cellular process
GO:0007165	0.98	signal transduction
GO:0009987	0.73	cellular process
GO:0044699	0.67	single-organism process
GO:0008152	0.67	metabolic process
GO:0071704	0.65	organic substance metabolic process
GO:0044238	0.65	primary metabolic process
GO:0044237	0.65	cellular metabolic process
GO:0044763	0.63	single-organism cellular process
GO:0006807	0.63	nitrogen compound metabolic process
GO:0006139	0.62	nucleobase-containing compound metabolic process
GO:0044249	0.61	cellular biosynthetic process
GO:0034654	0.60	nucleobase-containing compound biosynthetic process
GO:0044710	0.59	single-organism metabolic process
GO:0044281	0.58	small molecule metabolic process
GO:0006796	0.58	phosphate-containing compound metabolic process
GO:1901564	0.57	organonitrogen compound metabolic process
GO:0055086	0.57	nucleobase-containing small molecule metabolic process
GO:0019637	0.57	organophosphate metabolic process
GO:0044711	0.56	single-organism biosynthetic process
GO:0009150	0.56	purine ribonucleotide metabolic process
GO:0009187	0.55	cyclic nucleotide metabolic process
GO:0009152	0.55	purine ribonucleotide biosynthetic process
GO:0052652	0.54	cyclic purine nucleotide metabolic process
GO:0006182	0.53	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:0044424	0.99	intracellular part
GO:0044444	0.97	cytoplasmic part
GO:0016020	0.97	membrane
GO:0043234	0.96	protein complex
GO:0005886	0.96	plasma membrane
GO:0008074	0.95	guanylate cyclase complex, soluble

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	3no9A	0.527	3.48	0.123	0.929	4.2.1.2	63
2	0.060	2z6bA	0.535	3.63	0.034	0.843	3.2.1.17	45
3	0.060	1z1wA	0.530	2.95	0.098	0.800	3.4.11.-	NA
4	0.060	1kanA	0.528	3.35	0.015	0.843	2.7.7.-	NA
5	0.060	2i5oA	0.289	2.68	0.000	0.414	2.7.7.7	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	0.43	2o0gA	0.958	0.64	0.414	1.000	0.12	UUU	complex1.pdb.gz	2,6,9,10,17,18,35
2	0.33	3l6jA	0.953	0.69	0.414	1.000	0.16	Z90	complex2.pdb.gz	9,10,13,17,21,23
3	0.33	2o09A	0.955	0.68	0.414	1.000	0.13	HEM	complex3.pdb.gz	45,57,59,62,65
4	0.13	3eeeD	0.804	1.86	0.186	1.000	0.19	UUU	complex4.pdb.gz	19,44,48,51,54,55
5	0.12	3sj5B	0.807	1.87	0.186	1.000	0.15	HEM	complex5.pdb.gz	5,17,23,25,28,45
6	0.11	1u55B	0.807	1.86	0.186	1.000	0.14	UUU	complex6.pdb.gz	4,8,12,15,18,19,29,30
7	0.11	2kilA	0.729	2.03	0.188	0.957	0.15	UUU	complex7.pdb.gz	5,18,21,22,25,26,29
8	0.06	3nvuA	0.810	1.85	0.186	1.000	0.19	UUU	complex8.pdb.gz	4,9,18,53,56,60,62,65,66
9	0.03	3laiB	0.786	1.92	0.186	1.000	0.14	UUU	complex9.pdb.gz	4,8,12
10	0.03	3ebiA	0.578	2.41	0.115	0.800	0.13	BEY	complex10.pdb.gz	18,21,22,55,61

	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.