D-I-TASSER O15304

D-I-TASSER results for O15304

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

Summary of the Protein

Uniprot ID: O15304
Protein Name: Apoptosis regulatory protein Siva
Gene Name: SIVA1

Input Sequence in FASTA format

>O15304 (175 residues)
MPKRSCPFADVAPLQLKVRVSQRELSRGVCAERYSQEVFEKTKRLLFLGAQAYLDHVWDE
GCAVVHLPESPKPGPTGAPRAARGQMLIGPDGRLIRSLGQASEADPSGVASIACSSCVRA
VDGKAVCGQCERALCGQCVRTCWGCGSVACTLCGLVDCSDMYEKVLCTSCAMFET

Predicted Contact and Distance Map Used in D-I-TASSER simulation

Contact Map

Distance Map

D-I-TASSER simulation is guided by the consensus contact map (left figure) and distance map (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.

Information of Domain

No. of Domain	Domain	Domain Boundary	Length of Domain	Models of Domain	Sequence
1	O15304-D1	1-175	175		MPKRSCPFADVAPLQLKVRVSQRELSRGVCAERYSQEVFEKTKRLLFLGAQAYLDHVWDEGCAVVHLPESPKPGPTGAPRAARGQMLIGPDGRLIRSLGQASEADPSGVASIACSSCVRAVDGKAVCGQCERALCGQCVRTCWGCGSVACTLCGLVDCSDMYEKVLCTSCAMFET

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.4232

(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	6at7B	0.48	5.14	0.081	0.806	model1_6at7B.pdb.gz
2	1xmeA	0.47	4.61	0.053	0.726	model1_1xmeA.pdb.gz
3	1m56A	0.47	5.19	0.048	0.777	model1_1m56A.pdb.gz
4	6qrjA	0.47	5.23	0.047	0.777	model1_6qrjA.pdb.gz
5	7jroa	0.47	5.20	0.036	0.766	model1_7jroa.pdb.gz
6	3ck9B	0.47	5.59	0.036	0.834	model1_3ck9B.pdb.gz
7	3cu7A	0.47	5.62	0.048	0.851	model1_3cu7A.pdb.gz
8	4xydA	0.46	5.45	0.051	0.806	model1_4xydA.pdb.gz
9	3ihvA	0.44	5.40	0.071	0.789	model1_3ihvA.pdb.gz
10	3o0rB	0.44	5.58	0.069	0.789	model1_3o0rB.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:0005175	1.00	CD27 receptor binding
GO:0001618	1.00	virus receptor activity
GO:0046872	0.64	metal ion binding
GO:0008270	0.60	zinc ion 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:0097191	1.00	extrinsic apoptotic signaling pathway
GO:0009987	0.71	cellular process
GO:0044699	0.68	single-organism process
GO:0048518	0.65	positive regulation of biological process
GO:0080090	0.64	regulation of primary metabolic process
GO:0060255	0.64	regulation of macromolecule metabolic process
GO:0048519	0.64	negative regulation of biological process
GO:0031323	0.64	regulation of cellular metabolic process
GO:0048583	0.63	regulation of response to stimulus
GO:0048522	0.63	positive regulation of cellular process
GO:0044763	0.63	single-organism cellular process
GO:0019219	0.62	regulation of nucleobase-containing compound metabolic process
GO:2000112	0.61	regulation of cellular macromolecule biosynthetic process
GO:0065008	0.61	regulation of biological quality
GO:0048584	0.61	positive regulation of response to stimulus
GO:0006996	0.61	organelle organization
GO:1902589	0.60	single-organism organelle organization
GO:0051128	0.60	regulation of cellular component organization
GO:0051049	0.60	regulation of transport
GO:0044092	0.60	negative regulation of molecular function
GO:0009967	0.60	positive regulation of signal transduction
GO:0007005	0.60	mitochondrion organization
GO:0006355	0.60	regulation of transcription, DNA-templated
GO:0051130	0.59	positive regulation of cellular component organization
GO:0051050	0.59	positive regulation of transport
GO:0046902	0.59	regulation of mitochondrial membrane permeability
GO:0043433	0.59	negative regulation of sequence-specific DNA binding transcription factor activity
GO:0043067	0.59	regulation of programmed cell death
GO:0035556	0.59	intracellular signal transduction
GO:0033043	0.59	regulation of organelle organization
GO:0006915	0.59	apoptotic process
GO:1901030	0.58	positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway
GO:0097193	0.58	intrinsic apoptotic signaling pathway
GO:0032088	0.58	negative regulation of NF-kappaB transcription factor activity
GO:0006924	0.58	activation-induced cell death of T cells

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:0005654	1.00	nucleoplasm
GO:0044444	0.57	cytoplasmic part
GO:0043226	0.57	organelle
GO:0043229	0.55	intracellular organelle
GO:0043227	0.53	membrane-bounded organelle
GO:0043231	0.51	intracellular membrane-bounded organelle

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	2j5wA	0.455	5.53	0.107	0.823	1.16.3.1	NA
2	0.060	1yrqI	0.441	5.40	0.032	0.783	1.12.2.1	NA
3	0.060	2jg0A	0.431	5.43	0.065	0.794	3.2.1.28	53
4	0.060	1ksdA	0.453	5.41	0.041	0.794	3.2.1.4	NA
5	0.060	1ut9A	0.456	5.33	0.036	0.806	3.2.1.4	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:

Click to view	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	3dtuC	0.468	5.17	0.054	0.783	1.04	DXC	complex1.pdb.gz	43,46,47,50,88,93
	2	0.01	3s8gA	0.464	4.87	0.043	0.726	0.79	OLC	complex2.pdb.gz	44,48,92,93

	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.