D-I-TASSER A4D256-D1

D-I-TASSER results for A4D256-D1

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

Input Sequence in FASTA format

>A4D256 (132 residues)
MRSSTLQDPRRRDPQDDVYVDITDRLRFAILYSRPKSASNVHYFSIDNELEYENFSEDFG
PLNLAMVYRYCCKINKKLKSITMLRKKIVHFTGSDQRKQANAAFLVGCYMVIYLGRTPEA
AYRILIFGDTPY

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MRSSTLQDPRRRDPQDDVYVDITDRLRFAILYSRPKSASNVHYFSIDNELEYENFSEDFGPLNLAMVYRYCCKINKKLKSITMLRKKIVHFTGSDQRKQANAAFLVGCYMVIYLGRTPEAAYRILIFGDTPY
Prediction	CCCCCCCCCCCCCCCCCSSSSSCCCSSSSSCCCCCCCCCCCSSSSSCCSSSSCCCCCCCCCCHHHHHHHHHHHHHHHHHCHHHCCCSSSSSCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCC
Confidence	985221351125666763799699289998267999999817997188388603211248841789999999999998073435985999769983477999999999999983999999999998379999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MRSSTLQDPRRRDPQDDVYVDITDRLRFAILYSRPKSASNVHYFSIDNELEYENFSEDFGPLNLAMVYRYCCKINKKLKSITMLRKKIVHFTGSDQRKQANAAFLVGCYMVIYLGRTPEAAYRILIFGDTPY
Prediction	855555554666543530141045200000034417746411000023413033114121021011012003302620654646622000001444532010000000100021623053004204746458
	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

CCCCCCCCCCCCCCCCCSSSSSCCCSSSSSCCCCCCCCCCCSSSSSCCSSSSCCCCCCCCCCHHHHHHHHHHHHHHHHHCHHHCCCSSSSSCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCC
MRSSTLQDPRRRDPQDDVYVDITDRLRFAILYSRPKSASNVHYFSIDNELEYENFSEDFGPLNLAMVYRYCCKINKKLKSITMLRKKIVHFTGSDQRKQANAAFLVGCYMVIYLGRTPEAAYRILIFGDTPY

5xw4A

0.25

0.23

7.06

1.33

DEthreader

--RS--V-Y-----LDNTIEFLRGRVYLGAYDYTPEDTDELVFFTVEDAIFYNSFHLDFGPMNIGHLYRFAVIFHEILNDPENANKAVVFYSSASTRQRANAACMLCCYMILVQAWTPHQVLQPLAQVDPPF

5xw4A1

0.23

7.34

3.38

SPARKS-K

ENLYFQGSMRRSVYLDNTIEFLRGRVYLGAYDYTPEDTDELVFFTVEDAIFYNSFHLDFGPMNIGHLYRFAVIFHEILNDPENANKAVVFYSSASTRQRANAACMLCCYMILVQAWTPHQVLQPLAQVDPPF

1oheA

0.94

0.85

23.81

0.89

MapAlign

-------------PQDDVYLDITDRLCFAILYSRPKSASNVHYFSIDNELEYENFYADFGPLNLAMVYRYCCKINKKLKSITMLRKKIVHFTGSDQRKQANAAFLVGCYMVIYLGRTPEEAYRILIFGETSY

1oheA1

0.94

0.86

24.23

0.90

CEthreader

-----------RDPQDDVYLDITDRLCFAILYSRPKSASNVHYFSIDNELEYENFYADFGPLNLAMVYRYCCKINKKLKSITMLRKKIVHFTGSDQRKQANAAFLVGCYMVIYLGRTPEEAYRILIFGETSY

5xw4A1

0.23

7.34

2.48

MUSTER

ENLYFQGSMRRSVYLDNTIEFLRGRVYLGAYDYTPEDTDELVFFTVEDAIFYNSFHLDFGPMNIGHLYRFAVIFHEILNDPENANKAVVFYSSASTRQRANAACMLCCYMILVQAWTPHQVLQPLAQVDPPF

1oheA1

0.94

0.86

24.23

4.43

HHsearch

-----------RDPQDDVYLDITDRLCFAILYSRPKSASNVHYFSIDNELEYENFYADFGPLNLAMVYRYCCKINKKLKSITMLRKKIVHFTGSDQRKQANAAFLVGCYMVIYLGRTPEEAYRILIFGETSY

1oheA1

0.94

0.86

24.23

2.33

FFAS-3D

-----------RDPQDDVYLDITDRLCFAILYSRPKSASNVHYFSIDNELEYENFYADFGPLNLAMVYRYCCKINKKLKSITMLRKKIVHFTGSDQRKQANAAFLVGCYMVIYLGRTPEEAYRILIFGETSY

5xw4A1

0.23

7.34

1.08

EigenThreader

ENLYFQGSMRRSVYLDNTIEFLRGRVYLGAYDYTPEDTDELVFFTVEDAIFYNSFHLDFGPMNIGHLYRFAVIFHEILNDPENANKAVVFYSSASTRQRANAACMLCCYMILVQAWTPHQVLQPLAQVDPPF

1ohcA

0.94

0.86

24.23

1.63

CNFpred

-----------RDPQDDVYLDITDRLCFAILYSRPKSASNVHYFSIDNELEYENFYADFGPLNLAMVYRYCCKINKKLKSITMLRKKIVHFTGSDQRKQANAAFLVGCYMVIYLGRTPEEAYRILIFGETSY

5xw4A1

0.25

0.23

7.06

1.33

DEthreader

--RS--V-Y-----LDNTIEFLRGRVYLGAYDYTPEDTDELVFFTVEDAIFYNSFHLDFGPMNIGHLYRFAVIFHEILNDPENANKAVVFYSSASTRQRANAACMLCCYMILVQAWTPHQVLQPLAQVDPPF

(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	0.8528

(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	5xw4A1	0.89	1.62	0.237	0.992	model1_5xw4A1.pdb.gz
2	1oheA	0.86	1.28	0.917	0.894	model1_1oheA.pdb.gz
3	1yn9B	0.68	2.28	0.094	0.811	model1_1yn9B.pdb.gz
4	4mbbA	0.67	2.55	0.089	0.826	model1_4mbbA.pdb.gz
5	1larA	0.67	3.13	0.056	0.909	model1_1larA.pdb.gz
6	1jlnA	0.67	2.84	0.040	0.871	model1_1jlnA.pdb.gz
7	2jjdF	0.67	3.18	0.073	0.917	model1_2jjdF.pdb.gz
8	2c46B	0.66	2.33	0.099	0.803	model1_2c46B.pdb.gz
9	2pa5A	0.66	3.21	0.031	0.901	model1_2pa5A.pdb.gz
10	2qdpA	0.65	2.92	0.056	0.864	model1_2qdpA.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:0004721	1.00	phosphoprotein phosphatase activity
GO:0004725	0.99	protein tyrosine phosphatase activity
GO:0004722	0.89	protein serine/threonine phosphatase 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	0.92	regulation of cellular process
GO:0009987	0.92	cellular process
GO:0044260	0.69	cellular macromolecule metabolic process
GO:0044238	0.69	primary metabolic process
GO:0006996	0.65	organelle organization
GO:0006351	0.64	transcription, DNA-templated
GO:0022402	0.63	cell cycle process
GO:0044763	0.62	single-organism cellular process
GO:0042384	0.61	cilium assembly
GO:1903047	0.58	mitotic cell cycle process
GO:0048523	0.58	negative regulation of cellular process
GO:1901987	0.57	regulation of cell cycle phase transition
GO:0071850	0.54	mitotic cell cycle arrest
GO:0051256	0.54	mitotic spindle midzone assembly
GO:0007096	0.54	regulation of exit from mitosis

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:0043229	0.99	intracellular organelle
GO:0005634	0.97	nucleus
GO:0005737	0.88	cytoplasm
GO:0044446	0.61	intracellular organelle part
GO:0043232	0.59	intracellular non-membrane-bounded organelle
GO:0005819	0.54	spindle
GO:0005813	0.54	centrosome

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	0.067	2hxpA	0.637	2.57	0.104	0.803	3.1.3.48 3.1.3.16	126
2	0.067	2nt2B	0.631	2.65	0.124	0.795	3.1.3.16 3.1.3.48	73
3	0.067	2e0tA	0.618	2.74	0.123	0.788	3.1.3.16 3.1.3.48	100
4	0.067	2j17B	0.602	2.85	0.102	0.788	3.1.3.48	NA
5	0.067	1yz4A	0.621	2.99	0.063	0.818	3.1.3.16 3.1.3.48	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	0.03	2imgA	0.638	2.73	0.128	0.818	0.62	MLT	complex1.pdb.gz	71,106,107,108
2	0.03	2wgpA	0.634	2.72	0.103	0.811	0.72	PO4	complex2.pdb.gz	47,93,94,95,96,97,98
3	0.03	1yn9A	0.677	2.37	0.094	0.818	0.58	PO4	complex3.pdb.gz	93,99,100,101
4	0.02	3f81A	0.635	2.73	0.090	0.811	0.51	STT	complex4.pdb.gz	47,100,101,102
5	0.02	2i42A	0.639	3.30	0.062	0.894	0.41	I42	complex5.pdb.gz	60,97,100,101
6	0.02	1g1gA	0.622	3.21	0.064	0.864	0.44	III	complex6.pdb.gz	93,95,99,100,101
7	0.01	2hy3A	0.639	2.88	0.057	0.849	0.42	VO4	complex7.pdb.gz	103,105,106,107,108,110

	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.