D-I-TASSER P52701-D3

D-I-TASSER results for P52701-D3

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

Input Sequence in FASTA format

>P52701 (139 residues)
RKSSRKETPSATKQATSISSETKNIITKGTQTYSVLEGDPSENYSKYLLSLKEKEEDSSG
HTRAYGVCFVDTSLGKFFIGQFSDDRHCSRFRTLVAHYPPVQVLFEKGNLSKETKTILKS
SLSCSLQEGLIPGSQFWDA

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| RKSSRKETPSATKQATSISSETKNIITKGTQTYSVLEGDPSENYSKYLLSLKEKEEDSSGHTRAYGVCFVDTSLGKFFIGQFSDDRHCSRFRTLVAHYPPVQVLFEKGNLSKETKTILKSSLSCSLQEGLIPGSQFWDA
Prediction	CHHHHCCCCCCCCCCCCSSSSSSSSSCCCSCSCCCCCCCCCCCCCCSSSSSSSSCCCCCCCCCSSSSSSSSCCCCSSSSSSSCCCCHHHHHHHHHHHCCCSSSSSCCCCCCHHHHHHHHHCCCCCCSCCCCCCCCCCCC
Confidence	9145412733367886078715999879822443324555788786799999841677788757999999867780999996386269999999985598199983998999999999850797611045874223689
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| RKSSRKETPSATKQATSISSETKNIITKGTQTYSVLEGDPSENYSKYLLSLKEKEEDSSGHTRAYGVCFVDTSLGKFFIGQFSDDRHCSRFRTLVAHYPPVQVLFEKGNLSKETKTILKSSLSCSLQEGLIPGSQFWDA
Prediction	8555457456655564104130020113111113433742557312000001133566445432000000002333021230424532540351046140200013574136402510443243233440446451378
	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

CHHHHCCCCCCCCCCCCSSSSSSSSSCCCSCSCCCCCCCCCCCCCCSSSSSSSSCCCCCCCCCSSSSSSSSCCCCSSSSSSSCCCCHHHHHHHHHHHCCCSSSSSCCCCCCHHHHHHHHHCCCCCCSCCCCCCCCCCCC
RKSSRKETPSATKQATSISSETKNIITKGTQTYSVLEGDPSENYSKYLLSLKEKEEDSSGHTRAYGVCFVDTSLGKFFIGQFSDDRHCSRFRTLVAHYPPVQVLFEKGNLSKETKTILKSSLSCSLQEGLIPGSQFWDA

2o8cB1

0.73

0.65

18.58

1.17

DEthreader

----------PTVWYNWHSGFEFGSDIKTQTYSV-EGDP-SENYSKYLLSLKEKEE-D-SSTRAYGVCFVDTSLGKFFIGQFSDDRHCSRFRTLVAHYPPVQVLFEKGNLSKETKTILKSSLSCSLQEGLIPSQFFYKD

2o8cB

0.83

0.82

23.14

2.40

SPARKS-K

MEARCRKMAHISKYDRVVRREICRIITKGTQTYSVLEGDPSENYSKYLLSLKEKEE-DSSHTRAYGVCFVDTSLGKFFIGQFSDDRHCSRFRTLVAHYPPVQVLFEKGNLSKETKTILKSSLSCSLQEGLIPGSQFWDA

2o8cB

0.98

0.80

22.37

0.87

MapAlign

------------------------IITKGTQTYSVLEGDPSENYSKYLLSLKEKEE-DSSHTRAYGVCFVDTSLGKFFIGQFSDDRHCSRFRTLVAHYPPVQVLFEKGNLSKETKTILKSSLSCSLQEGLIPGSQFWD-

2o8cB1

0.84

0.83

23.53

0.92

CEthreader

MEARCRKMAHISKYDRVVRREICRIITKGTQTYSVLEGDPSENYSKYLLSLKEKEEDSS-HTRAYGVCFVDTSLGKFFIGQFSDDRHCSRFRTLVAHYPPVQVLFEKGNLSKETKTILKSSLSCSLQEGLIPGSQFWDA

2o8cB

0.83

23.33

1.92

MUSTER

MEARCRKMAHISKYDRVVRREICRIITKGTQTYSVLEGDPSENYSKYLLSLKEKEED-SSHTRAYGVCFVDTSLGKFFIGQFSDDRHCSRFRTLVAHYPPVQVLFEKGNLSKETKTILKSSLSCSLQEGLIPGSQFWDA

2o8cB1

0.83

23.33

3.41

HHsearch

KVARVEQTETPEMYDRVVRREICRIITKGTQTYSVLEGDPSENYSKYLLSLKEKEED-SSHTRAYGVCFVDTSLGKFFIGQFSDDRHCSRFRTLVAHYPPVQVLFEKGNLSKETKTILKSSLSCSLQEGLIPGSQFWDA

2o8cB1

0.82

0.81

22.73

1.28

FFAS-3D

-EARCRKMAHISKYDRVVRREICRIITKGTQTYSVLEGDPSENYSKYLLSLKEKE-EDSSHTRAYGVCFVDTSLGKFFIGQFSDDRHCSRFRTLVAHYPPVQVLFEKGNLSKETKTILKSSLSCSLQEGLIPGSQFWD-

2o8cB1

0.52

0.51

14.77

1.00

EigenThreader

KGNAFGRYSDSLVQKGYKVARVEQTETPEMMEARCRKMDRVVRYSKYLLSLKEKEEDS--SHTRAYGVCFVDLGKFFIGQFSDDRHC-SRFRTLVAHYPPVQVLFEKGNLSKETKTILKSSLSCSLQEGLIPGSQFWDA

2o8bB

0.84

0.83

23.53

1.83

CNFpred

MEARCRKMAHISKYDRVVRREICRIITKGTQTYSVLEGDPSENYSKYLLSLKEKEEDSS-HTRAYGVCFVDTSLGKFFIGQFSDDRHCSRFRTLVAHYPPVQVLFEKGNLSKETKTILKSSLSCSLQEGLIPGSQFWDA

2o8cB

0.73

0.65

18.58

1.17

DEthreader

----------PTVWYNWHSGFEFGSDIKTQTYSV-EGDP-SENYSKYLLSLKEKEE-D-SSTRAYGVCFVDTSLGKFFIGQFSDDRHCSRFRTLVAHYPPVQVLFEKGNLSKETKTILKSSLSCSLQEGLIPSQFFYKD

(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	0.8027

(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	2o8cB1	0.92	1.42	0.826	0.993	model1_2o8cB1.pdb.gz
2	3thwB	0.77	3.01	0.187	0.957	model1_3thwB.pdb.gz
3	1e3mA	0.67	1.92	0.140	0.770	model1_1e3mA.pdb.gz
4	1nneA	0.65	2.27	0.167	0.777	model1_1nneA.pdb.gz
5	2o8fA2	0.54	2.08	0.186	0.619	model1_2o8fA2.pdb.gz
6	1nktA1	0.43	4.60	0.023	0.655	model1_1nktA1.pdb.gz
7	1iy8A	0.41	3.86	0.082	0.590	model1_1iy8A.pdb.gz
8	1qi6A1	0.37	3.84	0.048	0.540	model1_1qi6A1.pdb.gz
9	1vl5A	0.36	4.53	0.066	0.619	model1_1vl5A.pdb.gz
10	1tilD	0.36	4.15	0.065	0.532	model1_1tilD.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:0030983	1.00	mismatched DNA binding
GO:0003684	0.94	damaged DNA binding
GO:0032137	0.84	guanine/thymine mispair binding
GO:0032138	0.77	single base insertion or deletion binding
GO:0000400	0.76	four-way junction DNA 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:0006259	1.00	DNA metabolic process
GO:0006281	0.95	DNA repair
GO:0000710	0.94	meiotic mismatch repair
GO:0007131	0.93	reciprocal meiotic recombination
GO:0043570	0.83	maintenance of DNA repeat elements
GO:0051053	0.77	negative regulation of DNA metabolic process
GO:0045910	0.76	negative regulation of DNA recombination
GO:0009416	0.75	response to light stimulus
GO:0009411	0.73	response to UV

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:0043229	1.00	intracellular organelle
GO:0044428	0.99	nuclear part
GO:0032300	0.99	mismatch repair complex
GO:0000228	0.96	nuclear chromosome
GO:0032301	0.82	MutSalpha complex

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	2jlzB	0.408	5.03	0.039	0.698	3.4.21.91	80
2	0.060	7reqB	0.495	4.51	0.069	0.820	5.4.99.2	NA
3	0.060	1x3mA	0.501	2.68	0.057	0.633	2.7.2.15 2.7.2.-	NA
4	0.060	3iayA	0.530	3.81	0.067	0.727	2.7.7.7	NA
5	0.060	1hjrC	0.513	2.18	0.071	0.604	3.1.22.4	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	1e3mA	0.689	1.91	0.138	0.784	0.14	ADP	complex1.pdb.gz	30,68,69
2	0.03	2o8cA	0.615	3.21	0.127	0.799	0.15	ADP	complex2.pdb.gz	48,51,77
3	0.03	2o8fA	0.621	3.00	0.135	0.791	0.16	ADP	complex3.pdb.gz	28,29,69,70
4	0.03	1ewqA	0.648	2.34	0.165	0.784	0.17	QNA	complex4.pdb.gz	100,101,102
5	0.02	1oh5A	0.687	1.92	0.138	0.784	0.18	QNA	complex5.pdb.gz	27,28,29
6	0.02	2wtuB	0.608	2.12	0.151	0.705	0.32	QNA	complex6.pdb.gz	73,74,77
7	0.02	1oh8B	0.624	2.13	0.128	0.712	0.37	QNA	complex7.pdb.gz	26,28,32
8	0.02	1oh6B	0.624	2.12	0.120	0.712	0.27	QNA	complex8.pdb.gz	65,67,74
9	0.02	1w7aB	0.618	2.05	0.128	0.705	0.13	ATP	complex9.pdb.gz	37,40,70,71,75,76

	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.