D-I-TASSER A6NDP7

D-I-TASSER results for A6NDP7

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

Summary of the Protein

Uniprot ID: A6NDP7
Protein Name: Myeloid-associated differentiation marker-like protein 2
Gene Name: MYADML2

Input Sequence in FASTA format

>A6NDP7 (307 residues)
MGSTMEPPGGAYLHLGAVTSPVGTARVLQLAFGCTTFSLVAHRGGFAGVQGTFCMAAWGF
CFAVSALVVACEFTRLHGCLRLSWGNFTAAFAMLATLLCATAAVLYPLYFARRECSPEPA
GCAARDFRLAASVFAGLLFLAYAVEVALTRARPGQVSSYMATVSGLLKIVQAFVACIIFG
ALVHDSRYGRYVATQWCVAVYSLCFLATVAVVALSVMGHTGGLGCPFDRLVVVYTFLAVL
LYLSAAVIWPVFCFDPKYGEPKRPPNCARGSCPWDSQLVVAIFTYVNLLLYVVDLAYSQR
IRFVPSL

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	A6NDP7-D1	1-155	155		MGSTMEPPGGAYLHLGAVTSPVGTARVLQLAFGCTTFSLVAHRGGFAGVQGTFCMAAWGFCFAVSALVVACEFTRLHGCLRLSWGNFTAAFAMLATLLCATAAVLYPLYFARRECSPEPAGCAARDFRLAASVFAGLLFLAYAVEVALTRARPGQ
2	A6NDP7-D2	156-307	152		VSSYMATVSGLLKIVQAFVACIIFGALVHDSRYGRYVATQWCVAVYSLCFLATVAVVALSVMGHTGGLGCPFDRLVVVYTFLAVLLYLSAAVIWPVFCFDPKYGEPKRPPNCARGSCPWDSQLVVAIFTYVNLLLYVVDLAYSQRIRFVPSL

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.82

(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	6r9tA	0.53	5.37	0.059	0.775	model1_6r9tA.pdb.gz
2	7mpeA	0.50	5.39	0.039	0.723	model1_7mpeA.pdb.gz
3	1ki1D	0.48	4.84	0.048	0.668	model1_1ki1D.pdb.gz
4	1st6A	0.47	6.11	0.028	0.756	model1_1st6A.pdb.gz
5	5hziA	0.47	5.93	0.033	0.723	model1_5hziA.pdb.gz
6	3ksyA	0.47	4.99	0.042	0.658	model1_3ksyA.pdb.gz
7	4yonA	0.46	4.49	0.059	0.635	model1_4yonA.pdb.gz
8	1foeA	0.46	5.66	0.071	0.684	model1_1foeA.pdb.gz
9	2jbsC	0.46	4.84	0.062	0.648	model1_2jbsC.pdb.gz
10	4a01A	0.46	5.60	0.074	0.710	model1_4a01A.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:0098772	0.60	molecular function regulator
GO:0005088	0.53	Ras guanyl-nucleotide exchange factor 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:0044699	0.95	single-organism process
GO:0065007	0.94	biological regulation
GO:0009987	0.94	cellular process
GO:0050789	0.92	regulation of biological process
GO:0050794	0.91	regulation of cellular process
GO:0044763	0.91	single-organism cellular process
GO:0051179	0.89	localization
GO:0009966	0.87	regulation of signal transduction
GO:1902531	0.85	regulation of intracellular signal transduction
GO:0006810	0.85	transport
GO:0032502	0.84	developmental process
GO:0051641	0.83	cellular localization
GO:0008104	0.83	protein localization
GO:1902578	0.80	single-organism localization
GO:0071702	0.80	organic substance transport
GO:0048856	0.80	anatomical structure development
GO:0048522	0.80	positive regulation of cellular process
GO:0044767	0.80	single-organism developmental process
GO:0016043	0.80	cellular component organization
GO:1902580	0.79	single-organism cellular localization
GO:0065008	0.79	regulation of biological quality
GO:0051128	0.79	regulation of cellular component organization
GO:0048869	0.79	cellular developmental process
GO:0031579	0.79	membrane raft organization
GO:0006886	0.79	intracellular protein transport
GO:0032879	0.78	regulation of localization
GO:0048519	0.77	negative regulation of biological process
GO:0051239	0.76	regulation of multicellular organismal process
GO:0048523	0.76	negative regulation of cellular process
GO:0045785	0.76	positive regulation of cell adhesion
GO:0044765	0.76	single-organism transport
GO:0001932	0.76	regulation of protein phosphorylation
GO:1900026	0.75	positive regulation of substrate adhesion-dependent cell spreading
GO:0090038	0.75	negative regulation of protein kinase C signaling
GO:0072661	0.75	protein targeting to plasma membrane
GO:0061028	0.75	establishment of endothelial barrier
GO:0034115	0.75	negative regulation of heterotypic cell-cell adhesion
GO:0030837	0.75	negative regulation of actin filament polymerization
GO:0030335	0.75	positive regulation of cell migration
GO:0010629	0.75	negative regulation of gene expression
GO:0001933	0.75	negative regulation of protein phosphorylation

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:0005737	0.71	cytoplasm
GO:0044444	0.57	cytoplasmic part
GO:0043226	0.53	organelle
GO:0043229	0.51	intracellular 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	2ix6A	0.424	5.30	0.060	0.622	1.3.3.6	NA
2	0.060	1jqnA	0.420	6.01	0.049	0.674	4.1.1.31	NA
3	0.060	2vsfA	0.421	5.92	0.058	0.674	3.6.4.12	NA
4	0.060	1jqiA	0.422	5.11	0.066	0.606	1.3.99.2	NA
5	0.060	2iukB	0.394	6.13	0.063	0.642	1.13.11.12	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	0.01	2ibfA	0.262	3.91	0.033	0.332	0.58	III	complex1.pdb.gz	23,24,26,27,29,33,36,37,59
2	0.01	2jbtA	0.463	4.73	0.062	0.645	0.40	4HP	complex2.pdb.gz	33,37,135
3	0.01	3tj5A	0.265	3.43	0.044	0.326	0.44	III	complex3.pdb.gz	48,54,57,58,60,61,64,65,132,135,139,143,146
4	0.01	2rfqC	0.452	5.21	0.054	0.674	0.62	1PS	complex4.pdb.gz	107,132,136,137
5	0.01	3s90A	0.291	5.48	0.066	0.430	0.41	III	complex5.pdb.gz	29,32,58,88,92,95,96,99
6	0.01	3rf3A	0.262	4.08	0.014	0.336	0.49	III	complex6.pdb.gz	21,22,25,26,29,30,32,33,35,36,37,39,54,88,92,95,96,99,102,103,106
7	0.01	2gdcA	0.266	3.60	0.047	0.329	0.41	III	complex7.pdb.gz	21,22,25,26,29,32,58,89
8	0.01	2ibfA	0.262	3.91	0.033	0.332	0.40	III	complex8.pdb.gz	22,25,28,29,32,33,36,58,85,88,92,96,99,100,103
9	0.01	1azs1	0.191	4.53	0.022	0.261	0.45	III	complex9.pdb.gz	33,54,60,61,63,67,72
10	0.01	2rfqD	0.462	5.05	0.049	0.658	0.53	1PS	complex10.pdb.gz	53,54,132,135,136,139

	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.