D-I-TASSER O60565

D-I-TASSER results for O60565

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

Summary of the Protein

Uniprot ID: O60565
Protein Name: Gremlin-1
Gene Name: GREM1

Input Sequence in FASTA format

>O60565 (184 residues)
MSRTAYTVGALLLLLGTLLPAAEGKKKGSQGAIPPPDKAQHNDSEQTQSPQQPGSRNRGR
GQGRGTAMPGEEVLESSQEALHVTERKYLKRDWCKTQPLKQTIHEEGCNSRTIINRFCYG
QCNSFYIPRHIRKEEGSFQSCSFCKPKKFTTMMVTLNCPELQPPTKKKRVTRVKQCRCIS
IDLD

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	O60565-D1	1-184	184		MSRTAYTVGALLLLLGTLLPAAEGKKKGSQGAIPPPDKAQHNDSEQTQSPQQPGSRNRGRGQGRGTAMPGEEVLESSQEALHVTERKYLKRDWCKTQPLKQTIHEEGCNSRTIINRFCYGQCNSFYIPRHIRKEEGSFQSCSFCKPKKFTTMMVTLNCPELQPPTKKKRVTRVKQCRCISIDLD

Top 1 final models from D-I-TASSER

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Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.552

(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

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Top 10 structural analogs in PDB (as identified by TM-align)

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Alignment
1	6x99A	0.47	5.39	0.049	0.815	model1_6x99A.pdb.gz
2	6ovbA	0.45	5.30	0.043	0.739	model1_6ovbA.pdb.gz
3	2oitA	0.45	4.93	0.052	0.766	model1_2oitA.pdb.gz
4	3v4pA	0.44	5.29	0.047	0.772	model1_3v4pA.pdb.gz
5	3k7dA	0.44	5.11	0.063	0.734	model1_3k7dA.pdb.gz
6	5mz9A	0.44	5.55	0.056	0.799	model1_5mz9A.pdb.gz
7	4g1eA	0.44	5.31	0.051	0.761	model1_4g1eA.pdb.gz
8	6jt5A	0.44	5.26	0.073	0.739	model1_6jt5A.pdb.gz
9	1xipA	0.44	5.08	0.046	0.739	model1_1xipA.pdb.gz
10	3vi3A1	0.44	5.33	0.038	0.766	model1_3vi3A1.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:0016015	0.68	morphogen 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:0050794	0.98	regulation of cellular process
GO:0044699	0.96	single-organism process
GO:0048523	0.84	negative regulation of cellular process
GO:0080090	0.81	regulation of primary metabolic process
GO:0060255	0.81	regulation of macromolecule metabolic process
GO:0031323	0.81	regulation of cellular metabolic process
GO:0006355	0.79	regulation of transcription, DNA-templated
GO:0006357	0.78	regulation of transcription from RNA polymerase II promoter
GO:0048583	0.73	regulation of response to stimulus
GO:0048585	0.72	negative regulation of response to stimulus
GO:0051239	0.69	regulation of multicellular organismal process
GO:0050793	0.69	regulation of developmental process
GO:0007165	0.69	signal transduction
GO:2000026	0.68	regulation of multicellular organismal development
GO:0044707	0.66	single-multicellular organism process
GO:0032502	0.66	developmental process
GO:0009966	0.66	regulation of signal transduction
GO:0090092	0.65	regulation of transmembrane receptor protein serine/threonine kinase signaling pathway
GO:0009968	0.65	negative regulation of signal transduction
GO:0090101	0.64	negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway
GO:0044767	0.64	single-organism developmental process
GO:0007389	0.64	pattern specification process
GO:0090288	0.62	negative regulation of cellular response to growth factor stimulus
GO:0030514	0.61	negative regulation of BMP signaling pathway
GO:0051093	0.58	negative regulation of developmental process
GO:0051241	0.57	negative regulation of multicellular organismal process
GO:0048856	0.56	anatomical structure development
GO:0009987	0.54	cellular process
GO:0009653	0.50	anatomical structure morphogenesis

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:0005615	0.95	extracellular space
GO:0044464	0.65	cell part

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

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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	3kf5A	0.417	5.66	0.063	0.766	3.2.1.26	NA
2	0.060	1utwF	0.412	5.56	0.034	0.739	3.2.1.26	NA
3	0.060	1vb3A	0.404	5.69	0.032	0.739	4.2.3.1	NA
4	0.060	2uvkB	0.414	5.33	0.048	0.728	5.1.3.-	NA
5	0.060	1kl7A	0.349	5.94	0.026	0.658	4.2.3.1	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

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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	2yftA	0.435	5.64	0.036	0.783	0.11	DQR	complex1.pdb.gz	91,92,145
2	0.01	1jofH	0.397	5.36	0.027	0.668	0.23	PIN	complex2.pdb.gz	142,144,177
3	0.01	2iahA	0.422	5.43	0.068	0.728	0.24	PVE	complex3.pdb.gz	120,124,126

	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.