D-I-TASSER O95786-D5

D-I-TASSER results for O95786-D5

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

Input Sequence in FASTA format

>O95786 (141 residues)
RISDKFKYIIAQLMRDTESLAKRICKDLENLSQIQNREFGTQKYEQWIVTVQKACMVFQM
PDKDEESRICKALFLYTSHLRKYNDALIISEHARMKDALDYLKDFFSNVRAAGFDEIEQD
LTQRFEEKLQELESVSRDPSN

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| RISDKFKYIIAQLMRDTESLAKRICKDLENLSQIQNREFGTQKYEQWIVTVQKACMVFQMPDKDEESRICKALFLYTSHLRKYNDALIISEHARMKDALDYLKDFFSNVRAAGFDEIEQDLTQRFEEKLQELESVSRDPSN
Prediction	CCCCCHHHHHHHHHHHHHHHHHHCHHCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHCCCC
Confidence	999947999999999999999850010221045554679984046899999998888626420367799999999999999999998773478999999999999999984489869999999999999999999818899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| RISDKFKYIIAQLMRDTESLAKRICKDLENLSQIQNREFGTQKYEQWIVTVQKACMVFQMPDKDEESRICKALFLYTSHLRKYNDALIISEHARMKDALDYLKDFFSNVRAAGFDEIEQDLTQRFEEKLQELESVSRDPSN
Prediction	867441452045006403620552355156135356672333513320141454144252665555441143023004103512400302420203201420550155347553550143025205633630462076688
	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                 140

                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCHHHHHHHHHHHHHHHHHHCHHCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHCCCC
RISDKFKYIIAQLMRDTESLAKRICKDLENLSQIQNREFGTQKYEQWIVTVQKACMVFQMPDKDEESRICKALFLYTSHLRKYNDALIISEHARMKDALDYLKDFFSNVRAAGFDEIEQDLTQRFEEKLQELESVSRDPSN

6kyvB1

0.91

0.87

24.31

1.33

DEthreader

RISDKFKYIIAQLMRDTESLAKRICK---D-LENSQNREFTQKYEQWIVTVQKACMVFQMPDKDEESRICKALFLYTSHLRKYNDALIISEHARMKDALDYLKDFFSNVRA-D-E-IEQDLTQRFEEKLQELESVSRDPSN

6kyvB1

1.00

0.98

27.40

2.03

SPARKS-K

RISDKFKYIIAQLMRDTESLAKRICKDLENLSQIQNREFGTQKYEQWIVTVQKACMVFQMPDKDEESRICKALFLYTSHLRKYNDALIISEHARMKDALDYLKDFFSNVRA---DEIEQDLTQRFEEKLQELESVSRDPSN

6kyvB

0.99

0.97

27.21

1.08

MapAlign

RISDKFKYIIAQLMRDTESLAKRICKDLENLSQIQNREFGTQKYEQWIVTVQKACMVFQMPDKDEESRICKALFLYTSHLRKYNDALIISEHARMKDALDYLKDFFSNVR---ADEIEQDLTQRFEEKLQELESVSRDPSN

6kyvB1

0.99

0.97

27.21

1.00

CEthreader

RISDKFKYIIAQLMRDTESLAKRICKDLENLSQIQNREFGTQKYEQWIVTVQKACMVFQMPDKDEESRICKALFLYTSHLRKYNDALIISEHARMKDALDYLKDFFSNVR---ADEIEQDLTQRFEEKLQELESVSRDPSN

4a2pA2

0.55

0.50

14.50

1.31

MUSTER

RIHNPFAAIISNLMSETEALMRTIY----------SKDFGTQNYEHWIVVTQRKCRLL---DKEEESRICRALFICTEHLRKYNDALIISEDARIIDALSYLTEFFTNVKNGPYTELEQHLTAKFQEKEPELIALSKDETN

6kyvB1

0.98

0.96

26.83

3.93

HHsearch

RISDKFKYIIAQLMRDTESLAKRICKDLENLSQIQNREFGTQKYEQWIVTVQKACMVFQMPDKDEESRICKALFLYTSHLRKYNDALIISEHARMKDALDYLKDFFSN--V-RADEIEQDLTQRFEEKLQELESVSRDPSN

6kyvB1

0.99

0.97

27.21

2.48

FFAS-3D

RISDKFKYIIAQLMRDTESLAKRICKDLENLSQIQNREFGTQKYEQWIVTVQKACMVFQMPDKDEESRICKALFLYTSHLRKYNDALIISEHARMKDALDYLKDFFSNVR---ADEIEQDLTQRFEEKLQELESVSRDPSN

6kyvB1

0.98

0.96

26.83

1.33

EigenThreader

RISDKFKYIIAQLMRDTESLAKRICKDLENLSQIQNREFGTQKYEQWIVTVQKACMVFQMPDKDEESRICKALFLYTSHLRKYNDALIISEHARMKDALDYLKDFFSNVRADEI---EQDLTQRFEEKLQELESVSRDPSN

2ykgA

1.00

0.96

26.81

1.01

CNFpred

RISDKFKYIIAQLMRDTESLAKRICKDLENLSQIQNREFGTQKYEQWIVTVQKACMV------DEESRICKALFLYTSHLRKYNDALIISEHARMKDALDYLKDFFSNVRAAGFDEIEQDLTQRFEEKLQELESVSRDPSN

6kyvB

0.91

0.87

24.31

1.33

DEthreader

RISDKFKYIIAQLMRDTESLAKRICK---D-LENSQNREFTQKYEQWIVTVQKACMVFQMPDKDEESRICKALFLYTSHLRKYNDALIISEHARMKDALDYLKDFFSNVRA-D-E-IEQDLTQRFEEKLQELESVSRDPSN

(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	0.8213

(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	6kyvB1	0.93	1.31	1.000	0.979	model1_6kyvB1.pdb.gz
2	7jl1A	0.89	1.40	0.985	0.950	model1_7jl1A.pdb.gz
3	4a2pA	0.88	0.92	0.555	0.908	model1_4a2pA.pdb.gz
4	5jc3A	0.79	1.59	0.306	0.858	model1_5jc3A.pdb.gz
5	3ts9A	0.77	1.62	0.261	0.844	model1_3ts9A.pdb.gz
6	5jajA	0.77	1.57	0.316	0.830	model1_5jajA.pdb.gz
7	4gl2A	0.75	1.93	0.286	0.837	model1_4gl2A.pdb.gz
8	1wp9A	0.65	3.06	0.113	0.879	model1_1wp9A.pdb.gz
9	1qz2A	0.45	4.36	0.055	0.702	model1_1qz2A.pdb.gz
10	4rz9A	0.40	5.06	0.108	0.716	model1_4rz9A.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:1901363	0.94	heterocyclic compound binding
GO:0097159	0.94	organic cyclic compound binding
GO:0003676	0.93	nucleic acid binding
GO:0003723	0.92	RNA binding
GO:0003725	0.91	double-stranded RNA binding
GO:0043167	0.70	ion binding
GO:0046872	0.69	metal ion binding
GO:0008270	0.68	zinc ion binding
GO:0003727	0.67	single-stranded RNA 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:0065007	0.92	biological regulation
GO:0050789	0.91	regulation of biological process
GO:0050896	0.90	response to stimulus
GO:0050794	0.90	regulation of cellular process
GO:0009987	0.86	cellular process
GO:0048518	0.83	positive regulation of biological process
GO:0006950	0.83	response to stress
GO:0002376	0.83	immune system process
GO:0006952	0.82	defense response
GO:0048583	0.75	regulation of response to stimulus
GO:0001817	0.75	regulation of cytokine production
GO:0080134	0.74	regulation of response to stress
GO:0050776	0.74	regulation of immune response
GO:0048584	0.74	positive regulation of response to stimulus
GO:0016032	0.74	viral process
GO:0001819	0.74	positive regulation of cytokine production
GO:0045088	0.73	regulation of innate immune response
GO:0031349	0.73	positive regulation of defense response
GO:0009615	0.73	response to virus
GO:0002684	0.73	positive regulation of immune system process
GO:0007165	0.71	signal transduction
GO:0035556	0.67	intracellular signal transduction
GO:0002221	0.67	pattern recognition receptor signaling pathway
GO:0039528	0.66	cytoplasmic pattern recognition receptor signaling pathway in response to virus
GO:0039529	0.61	RIG-I signaling pathway
GO:0006955	0.53	immune response
GO:0045087	0.52	innate immune response

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	0.78	cytoplasmic part
GO:0043226	0.68	organelle
GO:0043229	0.67	intracellular organelle
GO:0005829	0.64	cytosol

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	2zdxA	0.594	3.68	0.062	0.816	2.7.11.2	NA
2	0.060	2occN	0.542	4.78	0.043	0.901	1.9.3.1	NA
3	0.060	1cc1L	0.510	4.36	0.061	0.801	1.12.99.6	NA
4	0.060	1h2aL	0.507	4.40	0.043	0.794	1.12.2.1	NA
5	0.060	1yqwR	0.429	4.83	0.085	0.731	1.12.2.1	18

	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	2zdxB	0.612	3.51	0.068	0.823	0.22	P4A	complex1.pdb.gz	44,85,87,89
2	0.01	2e0aB	0.601	3.47	0.069	0.808	0.24	ANP	complex2.pdb.gz	7,10,11,90,91,92
3	0.01	1yuz0	0.575	3.67	0.066	0.801	0.22	III	complex3.pdb.gz	8,40,70,74,75,77,78,83
4	0.01	1jm6B	0.533	3.82	0.061	0.766	0.29	ADP	complex4.pdb.gz	14,17,18,82,86,87
5	0.01	1jm6A	0.530	3.60	0.061	0.752	0.27	ADP	complex5.pdb.gz	85,88,89

	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.