D-I-TASSER O96017-D1

D-I-TASSER results for O96017-D1

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

Input Sequence in FASTA format

>O96017 (67 residues)
MSRESDVEAQQSHGSSACSQPHGSVTQSQGSSSQSQGISSSSTSTMPNSSQSSHSSSGTL
SSLETVS

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| MSRESDVEAQQSHGSSACSQPHGSVTQSQGSSSQSQGISSSSTSTMPNSSQSSHSSSGTLSSLETVS
Prediction	CCCCCCHHHHHCCCCCCCCCCCCCSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSCC
Confidence	9744414666414877545788871013464456787444666778776655656776301213259
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| MSRESDVEAQQSHGSSACSQPHGSVTQSQGSSSQSQGISSSSTSTMPNSSQSSHSSSGTLSSLETVS
Prediction	8655575635654455435544442455544446444244644443445555454453315426538
	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

                   |                   |                   |

SS
Seq

CCCCCCHHHHHCCCCCCCCCCCCCSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSCC
MSRESDVEAQQSHGSSACSQPHGSVTQSQGSSSQSQGISSSSTSTMPNSSQSSHSSSGTLSSLETVS

1smpI

0.08

0.07

3.00

0.61

CEthreader

AEQHCDIRLNTDVLDGTTWKLAGVGWRPTPDGLTLTQADGSAVAFFSRNRYEHKLVDGSVRTLKKK-

6fec23

0.03

1.81

0.53

EigenThreader

ENEGEDSAVLMERLCKYIYAKDRTDRIRTCAILCHIYHHYLHSRWYQARDLMTMVQLGICAFRQGLT

2hgqE2

0.19

0.12

3.87

0.22

FFAS-3D

MKRWNFAGGPDSHGAHKIHRHPGSIGNRKTPGRVYKGKKMAGH------------------------

5jcss

0.12

4.22

0.95

SPARKS-K

VSIDDGIKKIEPDMSIPLKHYVPSYLSRPCIFAQVHDILLLSDEEPIEESLAAVIPISHLGEVGKWA

5il9A

0.36

0.07

2.22

0.55

CNFpred

-----------------------------------------------------SVTSGVVSRMEILS

4he8N

0.03

1.72

0.83

DEthreader

WVGLVPTPVLKLAYSSHATAFA-VLQSP-D-RVPALRGLYDPLLAFAMYLGA--EETPFR-PGRVAA

1md6A

0.06

2.55

0.82

MapAlign

RMKDSALKVLYLHNNQLLAGGLHAEKVIKGEEISPVILGVQGGSQCLSCGTEKGPILKLEPVN----

5w3nA

0.36

0.30

8.88

0.87

MUSTER

QSTDTSGYGQSSYSSYGQSQNTGY-----GTQSTPQGYGSTGGYGSSQSSQSSY---GQQSSY----

3wsxA5

0.10

0.07

2.75

0.33

HHsearch

ATDALGVPCTSPSDGNECLLGHKTVFKRRTPHATCFNGE---DFDRPVVVSN---------------

3v47C2

0.03

1.76

0.54

CEthreader

FKNVTGYDTYAAGADKYRVDINSGAVVTDAVAPDKVYVNAANGQLT---TDDAENNTKTKNESAKLS

(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	0.6004

(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	1hvcA	0.44	3.98	0.031	0.955	model1_1hvcA.pdb.gz
2	6k52A1	0.43	4.19	0.015	0.895	model1_6k52A1.pdb.gz
3	1r21A	0.43	3.59	0.018	0.761	model1_1r21A.pdb.gz
4	3fm8A	0.42	3.90	0.091	0.791	model1_3fm8A.pdb.gz
5	1j83A	0.42	3.78	0.051	0.746	model1_1j83A.pdb.gz
6	3gqsB	0.42	3.60	0.091	0.776	model1_3gqsB.pdb.gz
7	2ff4A2	0.42	3.57	0.109	0.761	model1_2ff4A2.pdb.gz
8	2kfuA	0.42	4.17	0.068	0.806	model1_2kfuA.pdb.gz
9	5djoA	0.42	3.65	0.109	0.776	model1_5djoA.pdb.gz
10	2eh0A	0.41	3.96	0.068	0.806	model1_2eh0A.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:0042803	1.00	protein homodimerization activity
GO:0031625	1.00	ubiquitin protein ligase binding
GO:0019901	1.00	protein kinase binding
GO:0004674	1.00	protein serine/threonine kinase 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:1901796	1.00	regulation of signal transduction by p53 class mediator
GO:0090399	1.00	replicative senescence
GO:0090307	1.00	mitotic spindle assembly
GO:0072428	1.00	signal transduction involved in intra-S DNA damage checkpoint
GO:0050821	1.00	protein stabilization
GO:0046777	1.00	protein autophosphorylation
GO:0045893	1.00	positive regulation of transcription, DNA-templated
GO:0044257	1.00	cellular protein catabolic process
GO:0042176	1.00	regulation of protein catabolic process
GO:0008630	1.00	intrinsic apoptotic signaling pathway in response to DNA damage
GO:0006977	1.00	DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest
GO:0006975	1.00	DNA damage induced protein phosphorylation
GO:0006302	1.00	double-strand break repair
GO:0001302	1.00	replicative cell aging
GO:0000086	1.00	G2/M transition of mitotic cell cycle
GO:0000077	1.00	DNA damage checkpoint

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:0005794	1.00	Golgi apparatus
GO:0005654	1.00	nucleoplasm

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	2wkgA	0.391	3.62	0.100	0.746	3.2.1.54	NA
2	0.060	3gguA	0.321	3.67	0.024	0.627	3.4.23.16	NA
3	0.060	1rpiA	0.275	4.47	0.044	0.627	3.4.23.16	NA
4	0.060	1j83A	0.421	3.78	0.051	0.746	3.2.1.4	NA
5	0.060	2o40A	0.442	3.86	0.033	0.910	3.4.23.16	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	0.10	2pqzA	0.276	4.59	0.109	0.627	0.56	G0G	complex1.pdb.gz	10,12,22,23,24,38
2	0.09	3nuoA	0.277	4.66	0.107	0.642	0.55	478	complex2.pdb.gz	11,22,23,36
3	0.08	1t7jA	0.273	4.75	0.074	0.627	0.52	478	complex3.pdb.gz	10,11,13,37
4	0.07	2bpwB	0.279	4.58	0.091	0.642	0.54	1IN	complex4.pdb.gz	8,9,10,21,38
5	0.01	1mrxA	0.276	4.71	0.109	0.627	0.56	K57	complex5.pdb.gz	8,9,21,22,36,37
6	0.01	3h5bB	0.325	3.58	0.048	0.627	0.51	031	complex6.pdb.gz	10,23,34,37
7	0.01	3i8wA	0.278	4.81	0.036	0.642	0.52	CB5	complex7.pdb.gz	25,38,39
8	0.01	1n49A	0.274	4.72	0.071	0.642	0.52	RIT	complex8.pdb.gz	9,10,20,21,22,35
9	0.01	1z1hA	0.274	4.71	0.056	0.627	0.50	HBB	complex9.pdb.gz	3,5,35,37,38
10	0.01	2r5qB	0.281	4.73	0.073	0.642	0.52	1UN	complex10.pdb.gz	10,11,22,23,24,35,36

	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.