D-I-TASSER Q13794

D-I-TASSER results for Q13794

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

Summary of the Protein

Uniprot ID: Q13794
Protein Name: Phorbol-12-myristate-13-acetate-induced protein 1
Gene Name: PMAIP1

Input Sequence in FASTA format

>Q13794 (54 residues)
MPGKKARKNAQPSPARAPAELEVECATQLRRFGDKLNFRQKLLNLISKLFCSGT

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 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.

Information of Domain

No. of Domain	Domain	Domain Boundary	Length of Domain	Models of Domain	Sequence
1	Q13794-D1	1-54	54		MPGKKARKNAQPSPARAPAELEVECATQLRRFGDKLNFRQKLLNLISKLFCSGT

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.5044

(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	2jd1A	0.56	2.74	0.118	0.907	model1_2jd1A.pdb.gz
2	2l7nA	0.55	2.73	0.140	0.926	model1_2l7nA.pdb.gz
3	1e0pA	0.55	2.87	0.040	0.926	model1_1e0pA.pdb.gz
4	4xtlA	0.55	2.70	0.040	0.926	model1_4xtlA.pdb.gz
5	6rz6A	0.55	2.60	0.040	0.907	model1_6rz6A.pdb.gz
6	6rz4A1	0.55	2.47	0.063	0.889	model1_6rz4A1.pdb.gz
7	5ys3A	0.55	2.63	0.100	0.926	model1_5ys3A.pdb.gz
8	4jr8A	0.55	2.82	0.080	0.926	model1_4jr8A.pdb.gz
9	4fbzA	0.54	2.75	0.020	0.907	model1_4fbzA.pdb.gz
10	3a7kA	0.52	2.71	0.020	0.907	model1_3a7kA.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:0046983	0.26	protein dimerization activity
GO:1901363	0.25	heterocyclic compound binding
GO:0097159	0.25	organic cyclic compound binding
GO:0046982	0.22	protein heterodimerization activity
GO:0003824	0.20	catalytic activity
GO:0003676	0.14	nucleic acid binding
GO:0036094	0.13	small molecule binding
GO:0000166	0.12	nucleotide binding
GO:0046872	0.11	metal ion binding
GO:0003677	0.11	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:0043065	1.00	positive regulation of apoptotic process
GO:0009987	0.93	cellular process
GO:0044763	0.90	single-organism cellular process
GO:0006915	0.88	apoptotic process
GO:0080090	0.79	regulation of primary metabolic process
GO:0060255	0.79	regulation of macromolecule metabolic process
GO:0031323	0.79	regulation of cellular metabolic process
GO:0032268	0.77	regulation of cellular protein metabolic process
GO:0031325	0.77	positive regulation of cellular metabolic process
GO:0010604	0.77	positive regulation of macromolecule metabolic process
GO:0051345	0.76	positive regulation of hydrolase activity
GO:0051130	0.76	positive regulation of cellular component organization
GO:0045862	0.76	positive regulation of proteolysis
GO:0043281	0.76	regulation of cysteine-type endopeptidase activity involved in apoptotic process
GO:0043280	0.75	positive regulation of cysteine-type endopeptidase activity involved in apoptotic process
GO:0010638	0.75	positive regulation of organelle organization
GO:0050896	0.68	response to stimulus
GO:0048583	0.67	regulation of response to stimulus
GO:0007165	0.67	signal transduction
GO:0009966	0.66	regulation of signal transduction
GO:2001233	0.65	regulation of apoptotic signaling pathway
GO:1902531	0.65	regulation of intracellular signal transduction
GO:0065008	0.65	regulation of biological quality
GO:0051716	0.65	cellular response to stimulus
GO:0009967	0.65	positive regulation of signal transduction
GO:0007005	0.65	mitochondrion organization
GO:0006950	0.65	response to stress
GO:2001235	0.64	positive regulation of apoptotic signaling pathway
GO:1902533	0.64	positive regulation of intracellular signal transduction
GO:0097193	0.64	intrinsic apoptotic signaling pathway
GO:0080134	0.64	regulation of response to stress
GO:0046902	0.64	regulation of mitochondrial membrane permeability
GO:0042592	0.64	homeostatic process
GO:0033554	0.64	cellular response to stress
GO:0002376	0.64	immune system process
GO:1900740	0.63	positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway
GO:0072332	0.63	intrinsic apoptotic signaling pathway by p53 class mediator
GO:0043517	0.63	positive regulation of DNA damage response, signal transduction by p53 class mediator
GO:0043029	0.63	T cell homeostasis
GO:0010917	0.63	negative regulation of mitochondrial membrane potential
GO:0009628	0.63	response to abiotic stimulus
GO:0008152	0.50	metabolic 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:0005739	1.00	mitochondrion

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	1qxyA	0.484	3.00	0.042	0.833	3.4.11.18	NA
2	0.060	1t13A	0.492	3.09	0.067	0.833	2.5.1.9	16
3	0.060	2x58A	0.488	3.16	0.080	0.926	5.3.3.8 4.2.1.17 1.1.1.35	46
4	0.060	1q0lA	0.509	3.20	0.096	0.926	1.1.1.267	NA
5	0.060	3dwfB	0.492	2.68	0.091	0.796	1.1.1.146	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	2h88D	0.519	3.25	0.038	0.944	0.68	UNL	complex1.pdb.gz	19,22,23,49,50

	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.