D-I-TASSER O15197-D1

D-I-TASSER results for O15197-D1

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

Input Sequence in FASTA format

>O15197 (73 residues)
MATEGAAQLGNRVAGMVCSLWVLLLVSSVLALEEVLLDTTGETSEIGWLTYPPGGWDEVS
VLDDQRRLTRTFE

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| MATEGAAQLGNRVAGMVCSLWVLLLVSSVLALEEVLLDTTGETSEIGWLTYPPGGWDEVSVLDDQRRLTRTFE
Prediction	CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCSSSSSCCCCCCCCCCCSSCCCCCCSSSSCCCCCCCCSSCCC
Confidence	9866767764222417999999999501232125751364210002314379999335211157898201159
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| MATEGAAQLGNRVAGMVCSLWVLLLVSSVLALEEVLLDTTGETSEIGWLTYPPGGWDEVSVLDDQRRLTRTFE
Prediction	7446466542530131112010212133344432312214434442313433773153034336754434438
	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

                   |                   |                   |

SS
Seq

CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCSSSSSCCCCCCCCCCCSSCCCCCCSSSSCCCCCCCCSSCCC
MATEGAAQLGNRVAGMVCSLWVLLLVSSVLALEEVLLDTTGETSEIGWLTYPPGGWDEVSVLDDQRRLTRTFE

7k7jA

1.00

0.56

15.73

1.15

SPARKS-K

--------------------------------EEVLLDTTGETSEIGWLTYPPGGWDEVSVLDDQRRLTRTFE

3lifA

0.03

1.71

1.17

DEthreader

DK-IAQSETE-RNLSHSLAEHATHTFQGADVVLDDIVSFWRPHPSPVFERRADNLSDVAILAHRKFFGVVVAT

3etpA

0.40

0.26

7.68

1.07

MUSTER

-------------------------AMAISDPEETLMDSTTATAELGWMVHPPSGWEEVSGYDENMNTIRTYQ

4bk4A

0.41

0.25

7.26

2.72

HHsearch

-----------------------------PANEVTLLDSRSVQGELGWIASPLGGWEEVSIMDEKNTPIRTYQ

3etpA

0.40

0.26

7.68

1.13

SPARKS-K

-------------------------AMAISDPEETLMDSTTATAELGWMVHPPSGWEEVSGYDENMNTIRTYQ

3lifA1

0.03

1.71

1.17

DEthreader

DK-IAQSETE-RNLSHSLAEHATHTFQGADVVLDDIVSFWRPHPSPVFERRADNLSDVAILAHRKFFGVVVAT

7k7jA

1.00

0.56

15.73

2.60

HHsearch

--------------------------------EEVLLDTTGETSEIGWLTYPPGGWDEVSVLDDQRRLTRTFE

2hleA

0.37

0.25

7.33

1.08

SPARKS-K

------------------------AGHHHHHHEETLLNTKLETADLKWVTFPQVQWEELSGLDEEQHSVRTYE

3t4jA

0.03

1.73

1.17

DEthreader

DD-ANRREEVLVSMCDQRARMLQDQFSVSVNHVHALAILSYHSIDQETEYARTAFSGVAYAEILRTAGYLGGA

7k7jA1

1.00

0.56

15.73

2.29

HHsearch

--------------------------------EEVLLDTTGETSEIGWLTYPPGGWDEVSVLDDQRRLTRTFE

(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	0.554

(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	3e4oA	0.66	2.76	0.130	0.945	model1_3e4oA.pdb.gz
2	6mniA	0.65	2.87	0.041	0.986	model1_6mniA.pdb.gz
3	3lifA	0.64	3.10	0.056	0.986	model1_3lifA.pdb.gz
4	3by9A	0.64	2.84	0.041	0.973	model1_3by9A.pdb.gz
5	5mtvA	0.63	2.66	0.059	0.877	model1_5mtvA.pdb.gz
6	3fosA	0.63	2.81	0.042	0.959	model1_3fosA.pdb.gz
7	2p7jB	0.62	3.13	0.027	0.986	model1_2p7jB.pdb.gz
8	1ciiA2	0.51	3.33	0.018	0.740	model1_1ciiA2.pdb.gz
9	2onkC	0.50	3.65	0.028	0.849	model1_2onkC.pdb.gz
10	3a8rB	0.45	2.98	0.118	0.630	model1_3a8rB.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:0003824	0.92	catalytic activity
GO:0016740	0.91	transferase activity
GO:0016301	0.90	kinase activity
GO:0004672	0.88	protein kinase activity
GO:0005003	0.74	ephrin receptor 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:0065007	0.98	biological regulation
GO:0050789	0.96	regulation of biological process
GO:0009987	0.91	cellular process
GO:0050794	0.87	regulation of cellular process
GO:0044699	0.79	single-organism process
GO:0007165	0.75	signal transduction
GO:0008152	0.73	metabolic process
GO:0007166	0.73	cell surface receptor signaling pathway
GO:0048013	0.72	ephrin receptor signaling pathway
GO:0044237	0.71	cellular metabolic process
GO:0071704	0.67	organic substance metabolic process
GO:0044763	0.67	single-organism cellular process
GO:0044238	0.66	primary metabolic process
GO:0043170	0.65	macromolecule metabolic process
GO:0044260	0.64	cellular macromolecule metabolic process
GO:0032502	0.64	developmental process
GO:0048518	0.63	positive regulation of biological process
GO:0044767	0.62	single-organism developmental process
GO:0006796	0.57	phosphate-containing compound metabolic process
GO:0065009	0.55	regulation of molecular function
GO:0016310	0.55	phosphorylation
GO:0006928	0.55	movement of cell or subcellular component
GO:0006464	0.50	cellular protein modification process

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:0044464	1.00	cell part
GO:0044424	0.90	intracellular part
GO:0044425	0.62	membrane part
GO:0016020	0.62	membrane
GO:0044459	0.58	plasma membrane part
GO:0044444	0.58	cytoplasmic part
GO:0043226	0.58	organelle
GO:0031224	0.57	intrinsic component of membrane
GO:0043227	0.56	membrane-bounded organelle
GO:0016021	0.56	integral component of membrane
GO:0005887	0.54	integral component of plasma membrane

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	2rgrA	0.605	3.42	0.069	0.931	5.99.1.3	NA
2	0.060	1flcD	0.533	2.44	0.067	0.699	3.1.1.53	NA
3	0.060	3fofA	0.541	3.57	0.042	0.877	5.99.1.-	NA
4	0.060	1fd9A	0.537	3.14	0.028	0.794	5.2.1.8	NA
5	0.060	2p4qA	0.537	3.51	0.056	0.863	1.1.1.44	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	3i7bA	0.578	3.30	0.138	0.877	0.15	BK1	complex1.pdb.gz	55,59,60
2	0.02	3nyvA	0.567	3.57	0.108	0.890	0.16	DTQ	complex2.pdb.gz	35,48,52
3	0.02	3t4jB	0.650	2.95	0.068	0.986	0.20	ZIP	complex3.pdb.gz	35,37,54,56
4	0.02	3t4sA	0.616	3.31	0.071	0.931	0.22	H35	complex4.pdb.gz	51,58,70,72
5	0.02	2xctU	0.565	3.12	0.127	0.877	0.12	QNA	complex5.pdb.gz	48,49,50,53
6	0.01	3t4kA	0.615	3.31	0.071	0.931	0.15	EMU	complex6.pdb.gz	36,54,56
7	0.01	1ay2A	0.571	3.47	0.070	0.959	0.34	UUU	complex7.pdb.gz	48,50,51
8	0.01	1mc0A	0.433	3.92	0.081	0.849	0.25	PCG	complex8.pdb.gz	33,34,47,55,57,70
9	0.01	3i7cA	0.501	4.16	0.056	0.890	0.16	BK2	complex9.pdb.gz	36,49,51,70

	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, Qiqige Wuyun, Yang Li, Quancheng Liu, Xiaogen Zhou, Yiheng Zhu, P. Lydia Freddolino, Yang Zhang. Integrating deep learning potentials with I-TASSER for single- and multi-domain protein structure prediction. Submitted. 2023.