D-I-TASSER P53396-D3

D-I-TASSER results for P53396-D3

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

Input Sequence in FASTA format

>P53396 (196 residues)
GIKPGCFKIGNTGGMLDNILASKLYRPGSVAYVSRSGGMSNELNNIISRTTDGVYEGVAI
GGDRYPGSTFMDHVLRYQDTPGVKMIVVLGEIGGTEEYKICRGIKEGRLTKPIVCWCIGT
CATMFSSEVQFGHAGACANQASETAVAKNQALKEAGVFVPRSFDELGEIIQSVYEDLVAN
GVIVPAQEVPPPTVPM

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| GIKPGCFKIGNTGGMLDNILASKLYRPGSVAYVSRSGGMSNELNNIISRTTDGVYEGVAIGGDRYPGSTFMDHVLRYQDTPGVKMIVVLGEIGGTEEYKICRGIKEGRLTKPIVCWCIGTCATMFSSEVQFGHAGACANQASETAVAKNQALKEAGVFVPRSFDELGEIIQSVYEDLVANGVIVPAQEVPPPTVPM
Prediction	CCCCCCCSSSCCCCCCCCCCCCCCCCCCCSSSSSCCCHHHHHHHHHHHHHCCCSSSSSSCCCCCCCCCCHHHHHHHHHHCCCCCSSSSSSCCCCCHHHHHHHHHHHHCCCCCSSSSSSCCCCCCCCCCCCCCCCCCSCCCCCCCHHHHHHHHHHCCCSSCCCHHHHHHHHHHHHHHHHHCCCSCCCCCCCCCCCCC
Confidence	9099998314377443334551248996389995771699999999998299878898158971379999999999960999848999950388389999999998499997699971345566875222354332214788899999999999099127999999999999999875528721378999999999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| GIKPGCFKIGNTGGMLDNILASKLYRPGSVAYVSRSGGMSNELNNIISRTTDGVYEGVAIGGDRYPGSTFMDHVLRYQDTPGVKMIVVLGEIGGTEEYKICRGIKEGRLTKPIVCWCIGTCATMFSSEVQFGHAGACANQASETAVAKNQALKEAGVFVPRSFDELGEIIQSVYEDLVANGVIVPAQEVPPPTVPM
Prediction	8244301000214423101122412541100000112310120011147341110101123443010110000031047265030000002323543230030036464522000021444365344343443323324454421520240046030410531530051024005512763313446637437147
	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                 140                 160                 180

                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCSSSCCCCCCCCCCCCCCCCCCCSSSSSCCCHHHHHHHHHHHHHCCCSSSSSSCCCCCCCCCCHHHHHHHHHHCCCCCSSSSSSCCCCCHHHHHHHHHHHHCCCCCSSSSSSCCCCCCCCCCCCCCCCCCSCCCCCCCHHHHHHHHHHCCCSSCCCHHHHHHHHHHHHHHHHHCCCSCCCCCCCCCCCCC
GIKPGCFKIGNTGGMLDNILASKLYRPGSVAYVSRSGGMSNELNNIISRTTDGVYEGVAIGGDRYPGSTFMDHVLRYQDTPGVKMIVVLGEIGGTEEYKICRGIKEGRLTKPIVCWCIGTCATMFSSEVQFGHAGACANQASETAVAKNQALKEAGVFVPRSFDELGEIIQSVYEDLVANGVIVPAQEVPPPTVPM

6hxiB

0.47

0.46

13.53

1.50

DEthreader

IVAVITVGGMTAGAFRIGNGTIISLRPGCVGFVSKSGGMLNEAFNIISRNSDGIYEGVAIGGDRYPGSNMLDHILRYERNPAIKMIACLGELGGEDEYMIIQALKEKKITKPLVAWVTGTCSPYLPASV-QFGAGAKANTEKETAQAKNDAFRQAGAYVPRSFDDYGEMVRQVYDMLLTRGIVQKFDEPEVPRIPT

6hxiB3

0.54

0.52

15.02

2.03

SPARKS-K

------VGGMTAAGTIENIIASKLYRPGCVGFVSKSGGMLNEAFNIISRNSDGIYEGVAIGGDRYPGSNMLDHILRYERNPAIKMIACLGELGGEDEYMIIQALKEKKITKPLVAWVTGTCSPYLPASVQFGHAGAKANTEKETAQAKNDAFRQAGAYVPRSFDDYGEMVRQVYDMLLTRGIVQKFDEPEVPRIPT

1eucA

0.30

0.27

8.20

1.05

MapAlign

LIGPNCPGVINPGECKIGIMPGHIHKKGRIGIVSRSGTLTYEAVHQTTQVGLGQSLCVGIGGDPFNGTDFTDCLEIFLNDPATEGIILIGEIGGNAEENAAEFLKQHNKSKPVVSFIAGLTAPPG---RRMGHAGAIIAGGKGGAKEKITALQSAGVVVSMSPAQLGTTIYKE---FEKRKML-------------

1eucA

0.31

0.28

8.34

0.75

CEthreader

LIGPNCPGVINPGECKIGIMPGHIHKKGRIGIVSRSGTLTYEAVHQTTQVGLGQSLCVGIGGDPFNGTDFTDCLEIFLNDPATEGIILIGEIGGNAEENAAEFLKQHNKSKPVVSFIAGLTA---PPGRRMGHAGAIIAGGKGGAKEKITALQSAGVVVSMSPAQLGTTIYKEFEKRKML----------------

6hxiB3

0.56

16.02

2.05

MUSTER

GMTAGAFRIGNTAGTIENIIASKLYRPGCVGFVSKSGGMLNEAFNIISRNSDGIYEGVAIGGDRYPGSNMLDHILRYERNPAIKMIACLGELGGEDEYMIIQALKEKKITKPLVAWVTGTCSPYLPASVQFGHAGAKANTEKETAQAKNDAFRQAGAYVPRSFDDYGEMVRQVYDMLLTRGIVQKFDEPEVPRIPT

6hxiB

0.51

14.78

2.71

HHsearch

VIGPATVGGMTAGFIGNTAGTIKLYRPGCVGFVSKSGGMLNEAFNIISRNSDGIYEGVAIGGDRYPGSNMLDHILRYERNPAIKMIACLGELGGEDEYMIIQALKEKKITKPLVAWVTGTCSPYLPASVQFGHAGAKANTEKETAQAKNDAFRQAGAYVPRSFDDYGEMVRQVYDMLLTRGIVQKFDEPEVPRIPT

6hxiB3

0.55

15.87

2.35

FFAS-3D

-VGAGAFRIGNTAGTIENIIASKLYRPGCVGFVSKSGGMLNEAFNIISRNSDGIYEGVAIGGDRYPGSNMLDHILRYERNPAIKMIACLGELGGEDEYMIIQALKEKKITKPLVAWVTGTCSPYLPASVQFGHAGAKANTEKETAQAKNDAFRQAGAYVPRSFDDYGEMVRQVYDMLLTRGIVQKFDEPEVPRIPT

6hxiB

0.52

15.05

0.87

EigenThreader

LDKPATVGGMTAGAFRIGNIASKLYRPGCVGFVSKSGGMLNEAFNIISRNSDGIYEGVAIGGDRYPGSNMLDHILRYERNPAIKMIACLGELGGEDEYMIIQALKEKKITKPLVAWVTGTCSPYLPASVQFGHAGAKANTEKETAQAKNDAFRQAGAYVPRSFDDYGEMVRQVYDMLLTRGIVQKFDEPEVPRIPT

5te1A

1.00

0.95

26.57

1.81

CNFpred

GIKPGCFKIGNTGGMLDNILASKLYRPGSVAYVSRSGGMSNELNNIISRTTDGVYEGVAIGGDRYPGSTFMDHVLRYQDTPGVKMIVVLGEIGGTEEYKICRGIKEGRLTKPIVCWCIGTCATMFSSEVQFGHAGACANQASETAVAKNQALKEAGVFVPRSFDELGEIIQSVYEDLVANGVIVPA----------

6hxiB3

0.48

0.46

13.50

1.33

DEthreader

-----V-GGMTAGAFRIGNGTIISLRPGCVGFVSKSGGMLNEAFNIISRNSDGIYEGVAIGGDRYPGSNMLDHILRYERNPAIKMIACLGELGGEDEYMIIQALKEKKITKPLVAWVTGTCSPYLPASV-QFGAGAKANTEKETAQAKNDAFRQAGAYVPRSFDDYGEMVRQVYDMLLTRGIVQKFDEPEVPRIPT

(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	0.8679

(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	6hxiB	0.98	0.76	0.495	1.000	model1_6hxiB.pdb.gz
2	7lj9D	0.92	1.13	0.866	0.954	model1_7lj9D.pdb.gz
3	6hxjB	0.87	1.26	0.311	0.918	model1_6hxjB.pdb.gz
4	3mwdB	0.86	1.04	0.874	0.888	model1_3mwdB.pdb.gz
5	3pffA	0.84	0.93	0.871	0.867	model1_3pffA.pdb.gz
6	1eucA	0.83	1.64	0.305	0.903	model1_1eucA.pdb.gz
7	1scuA2	0.79	1.39	0.352	0.842	model1_1scuA2.pdb.gz
8	1oi7A	0.72	1.60	0.294	0.781	model1_1oi7A.pdb.gz
9	2yv2A2	0.71	1.25	0.313	0.750	model1_2yv2A2.pdb.gz
10	2yv1A	0.71	1.63	0.285	0.770	model1_2yv1A.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:0003824	1.00	catalytic activity
GO:0016878	0.78	acid-thiol ligase activity
GO:0004775	0.77	succinate-CoA ligase (ADP-forming) activity
GO:0004776	0.53	succinate-CoA ligase (GDP-forming) 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:0008152	0.97	metabolic process
GO:0071704	0.95	organic substance metabolic process
GO:0044699	0.94	single-organism process
GO:0009987	0.94	cellular process
GO:0044710	0.92	single-organism metabolic process
GO:0044238	0.92	primary metabolic process
GO:0044237	0.92	cellular metabolic process
GO:1901576	0.91	organic substance biosynthetic process
GO:0044763	0.88	single-organism cellular process
GO:0044281	0.88	small molecule metabolic process
GO:0044249	0.87	cellular biosynthetic process
GO:0044711	0.85	single-organism biosynthetic process
GO:0006637	0.85	acyl-CoA metabolic process
GO:0006082	0.85	organic acid metabolic process
GO:0019752	0.82	carboxylic acid metabolic process
GO:1901360	0.80	organic cyclic compound metabolic process
GO:0043648	0.79	dicarboxylic acid metabolic process
GO:0006807	0.79	nitrogen compound metabolic process
GO:1901362	0.78	organic cyclic compound biosynthetic process
GO:0046483	0.78	heterocycle metabolic process
GO:0034641	0.78	cellular nitrogen compound metabolic process
GO:0006725	0.78	cellular aromatic compound metabolic process
GO:0006139	0.77	nucleobase-containing compound metabolic process
GO:0034654	0.76	nucleobase-containing compound biosynthetic process
GO:0006099	0.76	tricarboxylic acid cycle
GO:0006796	0.74	phosphate-containing compound metabolic process
GO:0009142	0.73	nucleoside triphosphate biosynthetic process
GO:0006105	0.73	succinate metabolic process
GO:0006104	0.73	succinyl-CoA metabolic 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:0044424	1.00	intracellular part
GO:0044444	0.93	cytoplasmic part
GO:0005829	0.84	cytosol
GO:0044446	0.74	intracellular organelle part
GO:0044429	0.60	mitochondrial part
GO:0005759	0.55	mitochondrial matrix
GO:0043226	0.51	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	0.262	1eucA	0.835	1.64	0.305	0.903	6.2.1.4	91,133
2	0.153	2yv2A	0.741	1.25	0.320	0.781	6.2.1.5	91
3	0.133	2yv1A	0.707	1.63	0.285	0.770	6.2.1.5	91
4	0.130	2yxbA	0.503	2.87	0.126	0.622	5.4.99.2	NA
5	0.067	1y80A	0.475	2.93	0.052	0.582	2.1.1.13	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	0.12	2scu1	0.811	1.32	0.357	0.857	1.01	III	complex1.pdb.gz	36,38,39,41,42,45,64,65,92,93,94,99,116,118,119,120,121,131,132,135,162,163,164
2	0.02	1jllE	0.581	2.92	0.111	0.689	0.68	COA	complex2.pdb.gz	33,35,37,40,60,61,62
3	0.02	2nu8E	0.577	2.99	0.111	0.689	0.69	COA	complex3.pdb.gz	90,92,93,95,100
4	0.02	2nu7B	0.590	2.86	0.109	0.699	0.61	COA	complex4.pdb.gz	89,90,93,97,99
5	0.02	1cqiB	0.578	2.84	0.104	0.684	0.69	COA	complex5.pdb.gz	38,42,45
6	0.02	1cqjB	0.577	2.85	0.104	0.684	0.69	COA	complex6.pdb.gz	37,38,39,40,58,60
7	0.02	1gtl2	0.563	3.80	0.071	0.755	0.71	CA	complex7.pdb.gz	12,26,28

	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.