D-I-TASSER P55083

D-I-TASSER results for P55083

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

Summary of the Protein

Uniprot ID: P55083
Protein Name: Microfibril-associated glycoprotein 4
Gene Name: MFAP4

Input Sequence in FASTA format

>P55083 (255 residues)
MKALLALPLLLLLSTPPCAPQVSGIRGDALERFCLQQPLDCDDIYAQGYQSDGVYLIYPS
GPSVPVPVFCDMTTEGGKWTVFQKRFNGSVSFFRGWNDYKLGFGRADGEYWLGLQNMHLL
TLKQKYELRVDLEDFENNTAYAKYADFSISPNAVSAEEDGYTLFVAGFEDGGAGDSLSYH
SGQKFSTFDRDQDLFVQNCAALSSGAFWFRSCHFANLNGFYLGGSHLSYANGINWAQWKG
FYYSLKRTEMKIRRA

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	P55083-D1	1-255	255		MKALLALPLLLLLSTPPCAPQVSGIRGDALERFCLQQPLDCDDIYAQGYQSDGVYLIYPSGPSVPVPVFCDMTTEGGKWTVFQKRFNGSVSFFRGWNDYKLGFGRADGEYWLGLQNMHLLTLKQKYELRVDLEDFENNTAYAKYADFSISPNAVSAEEDGYTLFVAGFEDGGAGDSLSYHSGQKFSTFDRDQDLFVQNCAALSSGAFWFRSCHFANLNGFYLGGSHLSYANGINWAQWKGFYYSLKRTEMKIRRA

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.8205

(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	3ghgI	0.92	1.38	0.387	0.953	model1_3ghgI.pdb.gz
2	1n73C	0.90	1.72	0.377	0.957	model1_1n73C.pdb.gz
3	1ei3C	0.89	1.73	0.391	0.953	model1_1ei3C.pdb.gz
4	4m7fA	0.85	0.58	0.553	0.859	model1_4m7fA.pdb.gz
5	1m1jE	0.84	1.34	0.350	0.871	model1_1m1jE.pdb.gz
6	3ghgK	0.84	1.42	0.346	0.871	model1_3ghgK.pdb.gz
7	1lwuE	0.83	1.53	0.370	0.871	model1_1lwuE.pdb.gz
8	2j3uB	0.83	1.29	0.495	0.851	model1_2j3uB.pdb.gz
9	1jc9A	0.82	0.91	0.460	0.835	model1_1jc9A.pdb.gz
10	2j60A	0.81	1.26	0.451	0.835	model1_2j60A.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	0.81	catalytic activity
GO:0043167	0.78	ion binding
GO:0046872	0.74	metal ion binding
GO:0005102	0.74	receptor binding
GO:0030971	0.57	receptor tyrosine kinase binding
GO:0016787	0.56	hydrolase activity
GO:0097367	0.55	carbohydrate derivative binding
GO:0008233	0.55	peptidase activity
GO:0004252	0.53	serine-type endopeptidase activity
GO:0016829	0.51	lyase 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	0.88	cellular process
GO:0044699	0.83	single-organism process
GO:0071704	0.77	organic substance metabolic process
GO:0044238	0.70	primary metabolic process
GO:0044763	0.69	single-organism cellular process
GO:0065007	0.64	biological regulation
GO:0050789	0.59	regulation of biological process
GO:0044237	0.56	cellular metabolic process
GO:0050794	0.52	regulation of cellular 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	0.91	cell part
GO:0044424	0.81	intracellular part
GO:0044421	0.71	extracellular region part
GO:0016020	0.50	membrane
GO:0044446	0.46	intracellular organelle part
GO:0043226	0.43	organelle
GO:0005737	0.41	cytoplasm
GO:0005615	0.40	extracellular space
GO:0043234	0.39	protein complex
GO:0043227	0.39	membrane-bounded organelle
GO:0044425	0.37	membrane part
GO:0070062	0.34	extracellular exosome
GO:0005576	0.34	extracellular region

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	3b9jI	0.227	6.16	0.033	0.396	1.17.1.4 1.17.3.2	101,219
2	0.060	1i8qA	0.381	6.55	0.053	0.710	4.2.2.1	71
3	0.060	1qlmA	0.396	5.61	0.044	0.639	3.5.4.27	NA
4	0.060	3eifA	0.398	5.47	0.067	0.643	3.4.21.110	NA
5	0.060	2ckjA	0.316	6.73	0.071	0.600	1.17.1.4 1.17.3.2	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	0.29	2j2pC	0.814	0.90	0.500	0.831	1.64	SC2	complex1.pdb.gz	89,105,107,108,109
2	0.12	2j1gF	0.823	1.45	0.498	0.851	1.27	SC2	complex2.pdb.gz	52,53,69,70,71,73,83,249
3	0.11	2j3uF	0.822	1.50	0.498	0.851	1.13	GLA	complex3.pdb.gz	52,71,73,249,251
4	0.09	2j0yF	0.821	1.05	0.498	0.843	1.64	BGC	complex4.pdb.gz	91,93,94,95,188
5	0.09	2j0yC	0.821	1.05	0.498	0.843	1.38	BGC	complex5.pdb.gz	95,96,97,98,190
6	0.09	2j2pE	0.827	1.32	0.495	0.851	1.04	SC2	complex6.pdb.gz	91,94,95,98
7	0.08	1fzc2	0.896	1.71	0.387	0.953	1.08	III	complex7.pdb.gz	12,15,19,20,21,22,23,25,56,65,67,97,98,101,102,103,104,105,106,107,110,111,112,116
8	0.08	1fic0	0.830	1.27	0.425	0.859	0.95	III	complex8.pdb.gz	136,138,238,239,240
9	0.07	1m1jC	0.904	1.59	0.391	0.953	0.82	CA	complex9.pdb.gz	185,193,200,201,205
10	0.07	1fzc1	0.838	1.41	0.346	0.871	1.02	III	complex10.pdb.gz	27,29,47,48,53,58,65,91,94,104,105

	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.