D-I-TASSER P39023-D2

D-I-TASSER results for P39023-D2

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

Input Sequence in FASTA format

>P39023 (123 residues)
PPMVVVGIVGYVETPRGLRTFKTVFAEHISDECKRRFYKNWHKSKKKAFTKYCKKWQDED
GKKQLEKDFSSMKKYCQVIRVIAHTQMRLLPLRQKKAHLMEIQVNGGTVAEKLDWARERL
EQQ

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| PPMVVVGIVGYVETPRGLRTFKTVFAEHISDECKRRFYKNWHKSKKKAFTKYCKKWQDEDGKKQLEKDFSSMKKYCQVIRVIAHTQMRLLPLRQKKAHLMEIQVNGGTVAEKLDWARERLEQQ
Prediction	CCSSSSSSSSSSSCCCCCSSSSSSSCCCCCHHHHHHCCCCCHHCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCSSSSSSSSCCHHHCCCCCCCCCSSSSSCCCCCHHHHHHHHHHHHCCC
Confidence	985999999998679984676777412265578762155301011112444421345425799999999984254618999996161224788886315898517999999999999985579
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| PPMVVVGIVGYVETPRGLRTFKTVFAEHISDECKRRFYKNWHKSKKKAFTKYCKKWQDEDGKKQLEKDFSSMKKYCQVIRVIAHTQMRLLPLRQKKAHLMEIQVNGGTVAEKLDWARERLEQQ
Prediction	640300000013434623321030216414750443044435445654355335426576335414531661463032010001022443725543130251315254165215203732678
	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                  60                  80                 100                 120

                   |                   |                   |                   |                   |                   |

SS
Seq

CCSSSSSSSSSSSCCCCCSSSSSSSCCCCCHHHHHHCCCCCHHCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCSSSSSSSSCCHHHCCCCCCCCCSSSSSCCCCCHHHHHHHHHHHHCCC
PPMVVVGIVGYVETPRGLRTFKTVFAEHISDECKRRFYKNWHKSKKKAFTKYCKKWQDEDGKKQLEKDFSSMKKYCQVIRVIAHTQMRLLPLRQKKAHLMEIQVNGGTVAEKLDWARERLEQQ

3j39B

0.61

0.57

16.29

1.33

DEthreader

PPMIVVGAVGYIETPFGLRALVNVWAQHLSEECRRRFYKN-----KA-FTKASKKW-TDDLGKSIENDFRKMLRYCKVIRVIAHSQIRL--IKQQKAHVMEIQLNGGSIEDKVKWAREHLEKP

3j39B2

0.64

0.63

17.88

3.99

SPARKS-K

---IVVGAVGYIETPFGLRALVNVWAQHLSEECRRRFYKNWYKSKKKAFTKASKKWTDDLGKKSIENDFRKMLRYCKVIRVIAHSQIRLIKQRQKKAHVMEIQLNGGSIEDKVKWAREHLEKP

4a17B

0.55

0.53

15.24

1.42

MapAlign

PPMTIVGVVGYIDTPRGLRALTTVWAKTIDNNTKKRFYKNWANSNKKAFTHHEKNF----DQKAQDLLLKRIEKYCSVVRVIAHTNMSKLNLRQKKNHILEIQVNGGKVAEKVAFAKSLLEKE

4a17B

0.55

0.53

15.24

1.23

CEthreader

PPMTIVGVVGYIDTPRGLRALTTVWAKTIDNNTKKRFYKNWANSNKKAFTHHEKN----FDQKAQDLLLKRIEKYCSVVRVIAHTNMSKLNLRQKKNHILEIQVNGGKVAEKVAFAKSLLEKE

3j39B2

0.64

0.63

17.88

3.35

MUSTER

---IVVGAVGYIETPFGLRALVNVWAQHLSEECRRRFYKNWYKSKKKAFTKASKKWTDDLGKKSIENDFRKMLRYCKVIRVIAHSQIRLIKQRQKKAHVMEIQLNGGSIEDKVKWAREHLEKP

3j39B2

0.64

0.63

17.88

3.43

HHsearch

---IVVGAVGYIETPFGLRALVNVWAQHLSEECRRRFYKNWYKSKKKAFTKASKKWTDDLGKKSIENDFRKMLRYCKVIRVIAHSQIRLIKQRQKKAHVMEIQLNGGSIEDKVKWAREHLEKP

3j39B2

0.64

0.63

17.88

2.22

FFAS-3D

---IVVGAVGYIETPFGLRALVNVWAQHLSEECRRRFYKNWYKSKKKAFTKASKKWTDDLGKKSIENDFRKMLRYCKVIRVIAHSQIRLIKQRQKKAHVMEIQLNGGSIEDKVKWAREHLEKP

3j39B2

0.64

0.63

17.88

1.32

EigenThreader

---IVVGAVGYIETPFGLRALVNVWAQHLSEECRRRFYKNWYKSKKKAFTKASKKWTDDLGKKSIENDFRKMLRYCKVIRVIAHSQIRLIKQRQKKAHVMEIQLNGGSIEDKVKWAREHLEKP

3j3bB

1.00

28.00

2.47

CNFpred

PPMVVVGIVGYVETPRGLRTFKTVFAEHISDECKRRFYKNWHKSKKKAFTKYCKKWQDEDGKKQLEKDFSSMKKYCQVIRVIAHTQMRLLPLRQKKAHLMEIQVNGGTVAEKLDWARERLEQQ

4a17B

0.50

0.45

12.98

1.33

DEthreader

PPMTIVGVVGYIDTPRGLRALTTVWAKTIDNNTKKRFYK------KA-FTHHEKNF----DQKAQDLLLKRIEKYCSVVRVIAHTNMSK-LNLRQKNHILEIQVNGGKVAEKVAFAKSLLEKE

(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	0.8696

(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	3j39B	0.95	0.99	0.648	0.992	model1_3j39B.pdb.gz
2	3jctB	0.94	0.90	0.653	0.984	model1_3jctB.pdb.gz
3	4a17B	0.94	0.78	0.546	0.968	model1_4a17B.pdb.gz
4	1vx7E	0.93	0.72	0.551	0.959	model1_1vx7E.pdb.gz
5	5xy3B	0.88	1.68	0.471	0.968	model1_5xy3B.pdb.gz
6	3zf7f1	0.88	1.74	0.488	1.000	model1_3zf7f1.pdb.gz
7	5an9A	0.86	2.01	0.442	0.976	model1_5an9A.pdb.gz
8	3iz5C	0.84	1.75	0.504	0.968	model1_3iz5C.pdb.gz
9	2zkrb	0.75	2.03	0.688	0.886	model1_2zkrb.pdb.gz
10	3j21C	0.75	2.08	0.250	0.878	model1_3j21C.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:0003735	1.00	structural constituent of ribosome
GO:1901363	0.63	heterocyclic compound binding
GO:0097159	0.63	organic cyclic compound 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:0009987	1.00	cellular process
GO:0006412	0.99	translation
GO:0000027	0.98	ribosomal large subunit assembly

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:0044446	0.99	intracellular organelle part
GO:0044444	0.97	cytoplasmic part
GO:0032991	0.96	macromolecular complex
GO:0030529	0.95	intracellular ribonucleoprotein complex
GO:0022625	0.94	cytosolic large ribosomal subunit

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	1fbaA	0.401	4.80	0.051	0.740	4.1.2.13	NA
2	0.060	1xdmB	0.424	4.09	0.068	0.699	4.1.2.13	NA
3	0.060	2z3uA	0.442	4.36	0.009	0.756	1.-.-.-	NA
4	0.060	1wz2A	0.429	4.37	0.077	0.691	6.1.1.4	NA
5	0.060	2fr7A	0.433	4.72	0.042	0.789	1.14.-.-	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	1jffB	0.421	4.04	0.031	0.667	0.17	TA1	complex1.pdb.gz	4,5,25
2	0.01	1sa0D	0.428	3.92	0.052	0.675	0.22	CN2	complex2.pdb.gz	8,22,69,112,118
3	0.01	3hkdD	0.430	3.70	0.072	0.667	0.16	N16	complex3.pdb.gz	25,109,112
4	0.01	3lplB	0.443	4.43	0.070	0.764	0.18	TDP	complex4.pdb.gz	8,80,103,105
5	0.01	2g25A	0.439	4.38	0.052	0.756	0.16	TDK	complex5.pdb.gz	5,7,107
6	0.01	3hkbB	0.426	4.62	0.080	0.740	0.17	GDP	complex6.pdb.gz	10,12,14,72
7	0.01	3lplA	0.446	4.50	0.070	0.772	0.25	TDP	complex7.pdb.gz	105,107,108,109
8	0.01	2g25B	0.443	4.43	0.070	0.764	0.15	TDK	complex8.pdb.gz	20,101,104,105
9	0.01	2qtcB	0.442	4.44	0.070	0.764	0.17	TDK	complex9.pdb.gz	80,102,104,105,106,109
10	0.01	2hldY	0.334	4.75	0.056	0.585	0.38	III	complex10.pdb.gz	104,105,106,115

	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.