D-I-TASSER O75381

D-I-TASSER results for O75381

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

Summary of the Protein

Uniprot ID: O75381
Protein Name: Peroxisomal membrane protein PEX14
Gene Name: PEX14

Input Sequence in FASTA format

>O75381 (377 residues)
MASSEQAEQPSQPSSTPGSENVLPREPLIATAVKFLQNSRVRQSPLATRRAFLKKKGLTD
EEIDMAFQQSGTAADEPSSLGPATQVVPVQPPHLISQPYSPAGSRWRDYGALAIIMAGIA
FGFHQLYKKYLLPLILGGREDRKQLERMEAGLSELSGSVAQTVTQLQTTLASVQELLIQQ
QQKIQELAHELAAAKATTSTNWILESQNINELKSEINSLKGLLLNRRQFPPSPSAPKIPS
WQIPVKSPSPSSPAAVNHHSSSDISPVSNESTSSSPGKEGHSPEGSTVTYHLLGPQEEGE
GVVDVKGQVRMEVQGEEEKREDKEDEEDEEDDDVSHVDEEDCLGVQREDRRGGDGQINEQ
VEKLRRPEGASNESERD

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	O75381-D1	1-377	377		MASSEQAEQPSQPSSTPGSENVLPREPLIATAVKFLQNSRVRQSPLATRRAFLKKKGLTDEEIDMAFQQSGTAADEPSSLGPATQVVPVQPPHLISQPYSPAGSRWRDYGALAIIMAGIAFGFHQLYKKYLLPLILGGREDRKQLERMEAGLSELSGSVAQTVTQLQTTLASVQELLIQQQQKIQELAHELAAAKATTSTNWILESQNINELKSEINSLKGLLLNRRQFPPSPSAPKIPSWQIPVKSPSPSSPAAVNHHSSSDISPVSNESTSSSPGKEGHSPEGSTVTYHLLGPQEEGEGVVDVKGQVRMEVQGEEEKREDKEDEEDEEDDDVSHVDEEDCLGVQREDRRGGDGQINEQVEKLRRPEGASNESERD

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.4868

(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	3btaA	0.42	6.80	0.039	0.711	model1_3btaA.pdb.gz
2	3ffzA	0.42	7.14	0.042	0.722	model1_3ffzA.pdb.gz
3	4knhA	0.41	5.96	0.059	0.618	model1_4knhA.pdb.gz
4	1f31A1	0.31	7.25	0.048	0.552	model1_1f31A1.pdb.gz
5	4g56A	0.31	7.26	0.059	0.552	model1_4g56A.pdb.gz
6	1z7hA	0.29	7.20	0.039	0.512	model1_1z7hA.pdb.gz
7	2fpqA	0.29	7.04	0.028	0.485	model1_2fpqA.pdb.gz
8	1zb7A	0.28	6.83	0.031	0.472	model1_1zb7A.pdb.gz
9	1n1zA	0.28	6.70	0.026	0.464	model1_1n1zA.pdb.gz
10	2ongA2	0.27	6.49	0.065	0.424	model1_2ongA2.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:0047485	0.79	protein N-terminus binding
GO:0003714	0.79	transcription corepressor 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:0009987	0.99	cellular process
GO:0044699	0.88	single-organism process
GO:0006996	0.85	organelle organization
GO:0044763	0.84	single-organism cellular process
GO:0007031	0.84	peroxisome organization
GO:0051179	0.74	localization
GO:0006810	0.73	transport
GO:0006886	0.72	intracellular protein transport
GO:0072594	0.71	establishment of protein localization to organelle
GO:0033365	0.71	protein localization to organelle
GO:0006605	0.71	protein targeting
GO:0065007	0.68	biological regulation
GO:0006625	0.68	protein targeting to peroxisome
GO:0050789	0.67	regulation of biological process
GO:0050794	0.66	regulation of cellular process
GO:1902578	0.64	single-organism localization
GO:0055085	0.63	transmembrane transport
GO:0019222	0.63	regulation of metabolic process
GO:1902589	0.62	single-organism organelle organization
GO:0080090	0.62	regulation of primary metabolic process
GO:0065002	0.62	intracellular protein transmembrane transport
GO:0060255	0.62	regulation of macromolecule metabolic process
GO:0031323	0.62	regulation of cellular metabolic process
GO:2000112	0.61	regulation of cellular macromolecule biosynthetic process
GO:0065009	0.61	regulation of molecular function
GO:0044743	0.61	intracellular protein transmembrane import
GO:0031324	0.61	negative regulation of cellular metabolic process
GO:0019219	0.61	regulation of nucleobase-containing compound metabolic process
GO:0010605	0.61	negative regulation of macromolecule metabolic process
GO:0010468	0.61	regulation of gene expression
GO:0006461	0.61	protein complex assembly
GO:0051260	0.60	protein homooligomerization
GO:0045892	0.60	negative regulation of transcription, DNA-templated
GO:0043433	0.60	negative regulation of sequence-specific DNA binding transcription factor activity
GO:0016558	0.60	protein import into peroxisome matrix

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:0042579	1.00	microbody
GO:0005777	0.83	peroxisome
GO:0044446	0.79	intracellular organelle part
GO:0016020	0.76	membrane
GO:0098588	0.72	bounding membrane of organelle
GO:0005778	0.71	peroxisomal membrane
GO:0032991	0.55	macromolecular complex
GO:0043234	0.54	protein complex

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	3gtgB	0.371	7.08	0.045	0.639	2.7.7.6	NA
2	0.060	1m53A	0.356	6.51	0.053	0.573	5.4.99.12	175
3	0.060	2uxwA	0.355	6.26	0.052	0.536	1.3.99.-	154
4	0.060	2vuaA	0.284	6.92	0.037	0.467	3.4.24.69	170
5	0.060	1rw9A	0.358	6.76	0.051	0.594	4.2.2.5	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	1i1eA	0.398	7.25	0.068	0.708	0.40	DM2	complex1.pdb.gz	57,58,119,125

	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.