D-I-TASSER O75439

D-I-TASSER results for O75439

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

Summary of the Protein

Uniprot ID: O75439
Protein Name: Mitochondrial-processing peptidase subunit beta
Gene Name: PMPCB

Input Sequence in FASTA format

>O75439 (489 residues)
MAAAAARVVLSSAARRRLWGFSESLLIRGAAGRSLYFGENRLRSTQAATQVVLNVPETRV
TCLESGLRVASEDSGLSTCTVGLWIDAGSRYENEKNNGTAHFLEHMAFKGTKKRSQLDLE
LEIENMGAHLNAYTSREQTVYYAKAFSKDLPRAVEILADIIQNSTLGEAEIERERGVILR
EMQEVETNLQEVVFDYLHATAYQNTALGRTILGPTENIKSISRKDLVDYITTHYKGPRIV
LAAAGGVSHDELLDLAKFHFGDSLCTHKGEIPALPPCKFTGSEIRVRDDKMPLAHLAIAV
EAVGWAHPDTICLMVANTLIGNWDRSFGGGMNLSSKLAQLTCHGNLCHSFQSFNTSYTDT
GLWGLYMVCESSTVADMLHVVQKEWMRLCTSVTESEVARARNLLKTNMLLQLDGSTPICE
DIGRQMLCYNRRIPIPELEARIDAVNAETIREVCTKYIYNRSPAIAAVGPIKQLPDFKQI
RSNMCWLRD

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	O75439-D1	1-54,278-489	266		MAAAAARVVLSSAARRRLWGFSESLLIRGAAGRSLYFGENRLRSTQAATQVVLNKFTGSEIRVRDDKMPLAHLAIAVEAVGWAHPDTICLMVANTLIGNWDRSFGGGMNLSSKLAQLTCHGNLCHSFQSFNTSYTDTGLWGLYMVCESSTVADMLHVVQKEWMRLCTSVTESEVARARNLLKTNMLLQLDGSTPICEDIGRQMLCYNRRIPIPELEARIDAVNAETIREVCTKYIYNRSPAIAAVGPIKQLPDFKQIRSNMCWLRD
2	O75439-D2	55-277	223		VPETRVTCLESGLRVASEDSGLSTCTVGLWIDAGSRYENEKNNGTAHFLEHMAFKGTKKRSQLDLELEIENMGAHLNAYTSREQTVYYAKAFSKDLPRAVEILADIIQNSTLGEAEIERERGVILREMQEVETNLQEVVFDYLHATAYQNTALGRTILGPTENIKSISRKDLVDYITTHYKGPRIVLAAAGGVSHDELLDLAKFHFGDSLCTHKGEIPALPPC

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.89

(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	1hr6D	0.85	1.55	0.451	0.881	model1_1hr6D.pdb.gz
2	7jrgA	0.84	2.03	0.483	0.881	model1_7jrgA.pdb.gz
3	1hr6A	0.84	2.04	0.265	0.881	model1_1hr6A.pdb.gz
4	1be3A	0.84	2.15	0.553	0.879	model1_1be3A.pdb.gz
5	7jrgB	0.83	1.87	0.278	0.869	model1_7jrgB.pdb.gz
6	2ibzA	0.80	2.48	0.253	0.861	model1_2ibzA.pdb.gz
7	3hdiA	0.79	2.29	0.278	0.838	model1_3hdiA.pdb.gz
8	3eoqB	0.77	2.01	0.246	0.806	model1_3eoqB.pdb.gz
9	4nnzA	0.73	2.35	0.227	0.785	model1_4nnzA.pdb.gz
10	2g47B	0.72	3.90	0.135	0.859	model1_2g47B.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:0008233	1.00	peptidase activity
GO:0046872	0.99	metal ion binding
GO:0004222	0.99	metalloendopeptidase activity
GO:0008270	0.98	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:0071704	1.00	organic substance metabolic process
GO:0016485	0.99	protein processing
GO:0009987	0.86	cellular process
GO:0044237	0.83	cellular metabolic process
GO:0044699	0.79	single-organism process
GO:0044710	0.72	single-organism metabolic process
GO:0044763	0.63	single-organism cellular process
GO:0006091	0.56	generation of precursor metabolites and energy
GO:0055114	0.54	oxidation-reduction process
GO:0022904	0.53	respiratory electron transport chain
GO:0009060	0.52	aerobic respiration
GO:0006122	0.52	mitochondrial electron transport, ubiquinol to cytochrome c

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	0.99	cytoplasmic part
GO:0044446	0.95	intracellular organelle part
GO:0044429	0.93	mitochondrial part
GO:0032991	0.73	macromolecular complex
GO:0044425	0.72	membrane part
GO:0043234	0.72	protein complex
GO:0098798	0.70	mitochondrial protein complex
GO:0044455	0.69	mitochondrial membrane part
GO:1902494	0.68	catalytic complex
GO:0098800	0.68	inner mitochondrial membrane protein complex
GO:1990204	0.67	oxidoreductase complex
GO:0098803	0.67	respiratory chain complex
GO:0005750	0.66	mitochondrial respiratory chain complex III

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	0.585	3eoqB	0.783	2.01	0.246	0.824	3.4.24.56	104
2	0.417	2fyuA	0.842	2.04	0.563	0.879	1.10.2.2	105,108,130,132,142,160,416,420,424
3	0.277	1hr6D	0.854	1.55	0.451	0.881	3.4.24.64	104
4	0.209	1hr9F	0.853	1.57	0.448	0.881	3.4.24.64	181
5	0.194	1be3A	0.837	2.15	0.553	0.879	1.10.2.2	104

	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	0.36	1hr8B	0.853	1.58	0.452	0.881	1.05	III	complex1.pdb.gz	101,104,105,108,131,132,133,134,135,136,185,191,211,212,305,310,314,318,322,354,355,356,404
2	0.34	1hr9B	0.852	1.60	0.452	0.881	0.72	III	complex2.pdb.gz	101,104,105,133,134,135,212,354,420
3	0.27	1hr61	0.852	1.59	0.455	0.881	1.36	III	complex3.pdb.gz	72,78,108,117,120,121,124,125,126,127,128,129,130,131,144,145,146,398,399,402,405,406,409,410,413,415,435,436,439
4	0.22	3hdiB	0.790	2.18	0.278	0.838	0.73	III	complex4.pdb.gz	104,105,131,132,133,134,138,142,211,415,420,424

	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.