D-I-TASSER P15172

D-I-TASSER results for P15172

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

Summary of the Protein

Uniprot ID: P15172
Protein Name: Myoblast determination protein 1
Gene Name: MYOD1

Input Sequence in FASTA format

>P15172 (320 residues)
MELLSPPLRDVDLTAPDGSLCSFATTDDFYDDPCFDSPDLRFFEDLDPRLMHVGALLKPE
EHSHFPAAVHPAPGAREDEHVRAPSGHHQAGRCLLWACKACKRKTTNADRRKAATMRERR
RLSKVNEAFETLKRCTSSNPNQRLPKVEILRNAIRYIEGLQALLRDQDAAPPGAAAAFYA
PGPLPPGRGGEHYSGDSDASSPRSNCSDGMMDYSGPPSGARRRNCYEGAYYNEAPSEPRP
GKSAAVSSLDCLSSIVERISTESPAAPALLLADVPSESPPRRQEAAAPSEGESSGDPTQS
PDAAPQCPAGANPNPIYQVL

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	P15172-D1	1-320	320		MELLSPPLRDVDLTAPDGSLCSFATTDDFYDDPCFDSPDLRFFEDLDPRLMHVGALLKPEEHSHFPAAVHPAPGAREDEHVRAPSGHHQAGRCLLWACKACKRKTTNADRRKAATMRERRRLSKVNEAFETLKRCTSSNPNQRLPKVEILRNAIRYIEGLQALLRDQDAAPPGAAAAFYAPGPLPPGRGGEHYSGDSDASSPRSNCSDGMMDYSGPPSGARRRNCYEGAYYNEAPSEPRPGKSAAVSSLDCLSSIVERISTESPAAPALLLADVPSESPPRRQEAAAPSEGESSGDPTQSPDAAPQCPAGANPNPIYQVL

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.4601

(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	3eb7A	0.47	5.55	0.042	0.713	model1_3eb7A.pdb.gz
2	6fhjA	0.46	5.96	0.045	0.741	model1_6fhjA.pdb.gz
3	6owkA	0.46	5.65	0.039	0.700	model1_6owkA.pdb.gz
4	6z16A	0.46	6.04	0.045	0.716	model1_6z16A.pdb.gz
5	6wpcA	0.45	5.73	0.042	0.706	model1_6wpcA.pdb.gz
6	4av3A	0.45	6.09	0.064	0.722	model1_4av3A.pdb.gz
7	4w8jA	0.45	5.74	0.055	0.706	model1_4w8jA.pdb.gz
8	6ovbA	0.45	5.85	0.030	0.700	model1_6ovbA.pdb.gz
9	5zi1A	0.45	5.80	0.046	0.697	model1_5zi1A.pdb.gz
10	2c9kA	0.45	6.13	0.065	0.722	model1_2c9kA.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:1901363	0.98	heterocyclic compound binding
GO:0097159	0.98	organic cyclic compound binding
GO:0003677	0.97	DNA binding
GO:0044212	0.93	transcription regulatory region DNA binding
GO:0003700	0.92	transcription factor activity, sequence-specific DNA binding
GO:0000976	0.85	transcription regulatory region sequence-specific DNA binding
GO:0000977	0.84	RNA polymerase II regulatory region sequence-specific DNA binding
GO:0000981	0.76	RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0000978	0.63	RNA polymerase II core promoter proximal region sequence-specific DNA binding
GO:0001228	0.62	transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding
GO:0003705	0.61	transcription factor activity, RNA polymerase II distal enhancer sequence-specific 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:0065007	0.93	biological regulation
GO:0050789	0.93	regulation of biological process
GO:0050794	0.92	regulation of cellular process
GO:0009987	0.88	cellular process
GO:0044699	0.86	single-organism process
GO:0048522	0.80	positive regulation of cellular process
GO:0044763	0.79	single-organism cellular process
GO:0048869	0.76	cellular developmental process
GO:0050793	0.75	regulation of developmental process
GO:0051239	0.72	regulation of multicellular organismal process
GO:2000026	0.71	regulation of multicellular organismal development
GO:0045595	0.71	regulation of cell differentiation
GO:0030154	0.69	cell differentiation
GO:0051094	0.68	positive regulation of developmental process
GO:0060284	0.66	regulation of cell development
GO:0045597	0.65	positive regulation of cell differentiation
GO:0051240	0.63	positive regulation of multicellular organismal process
GO:0051128	0.62	regulation of cellular component organization
GO:0022603	0.62	regulation of anatomical structure morphogenesis
GO:0010720	0.62	positive regulation of cell development
GO:0051130	0.61	positive regulation of cellular component organization
GO:0010830	0.61	regulation of myotube differentiation
GO:1901741	0.60	positive regulation of myoblast fusion
GO:0045663	0.60	positive regulation of myoblast differentiation
GO:0016202	0.59	regulation of striated muscle tissue development
GO:0048641	0.58	regulation of skeletal muscle tissue development
GO:0048743	0.57	positive regulation of skeletal muscle fiber development
GO:0035914	0.57	skeletal muscle cell differentiation
GO:0019222	0.54	regulation of metabolic process
GO:0080090	0.53	regulation of primary metabolic process
GO:0060255	0.53	regulation of macromolecule metabolic process
GO:0031323	0.53	regulation of cellular metabolic process
GO:2000112	0.50	regulation of cellular macromolecule biosynthetic process
GO:0019219	0.50	regulation of nucleobase-containing compound metabolic process
GO:0010468	0.50	regulation of gene expression

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:0043229	0.93	intracellular organelle
GO:0043231	0.90	intracellular membrane-bounded organelle
GO:0005634	0.89	nucleus

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	1m56A	0.392	5.82	0.033	0.603	1.9.3.1	NA
2	0.060	1ojnA	0.407	6.35	0.030	0.678	4.2.2.1	NA
3	0.060	1rw9A	0.411	6.38	0.068	0.684	4.2.2.5	NA
4	0.060	1gu6A	0.393	6.50	0.053	0.669	1.7.2.2	NA
5	0.060	1b0pA	0.344	6.27	0.045	0.569	1.2.7.1	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	2ioaB	0.397	6.13	0.050	0.641	0.11	GGA	complex1.pdb.gz	79,120,121
2	0.01	1zw2A	0.262	5.11	0.046	0.375	0.28	III	complex2.pdb.gz	94,97,98,149,153,156,160,163,167
3	0.01	2ot4A	0.403	6.36	0.058	0.675	0.15	HEC	complex3.pdb.gz	93,121,122,125,128,158,162,163
4	0.01	2ot4A	0.403	6.36	0.058	0.675	0.16	HEC	complex4.pdb.gz	92,97,99,102,120,121,128,129,131,132,133,164
5	0.01	2ioaA	0.397	6.14	0.046	0.641	0.10	GGA	complex5.pdb.gz	92,127,128,157,161
6	0.01	2fonB	0.409	5.96	0.063	0.628	0.33	FAD	complex6.pdb.gz	97,101,117,118,160
7	0.01	2gwwA	0.281	5.30	0.011	0.397	0.22	III	complex7.pdb.gz	93,96,97,111,157,160
8	0.01	2io8A	0.398	6.30	0.062	0.653	0.16	ADP	complex8.pdb.gz	94,99,156,157,163
9	0.01	2hsqA	0.256	6.13	0.058	0.412	0.24	III	complex9.pdb.gz	94,97,146,157,160,161
10	0.01	3ttbA	0.404	6.24	0.069	0.666	0.11	UUU	complex10.pdb.gz	121,158,162,163,179

	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.