D-I-TASSER Q15465

D-I-TASSER results for Q15465

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

Summary of the Protein

Uniprot ID: Q15465
Protein Name: Sonic hedgehog protein
Gene Name: SHH

Input Sequence in FASTA format

>Q15465 (462 residues)
MLLLARCLLLVLVSSLLVCSGLACGPGRGFGKRRHPKKLTPLAYKQFIPNVAEKTLGASG
RYEGKISRNSERFKELTPNYNPDIIFKDEENTGADRLMTQRCKDKLNALAISVMNQWPGV
KLRVTEGWDEDGHHSEESLHYEGRAVDITTSDRDRSKYGMLARLAVEAGFDWVYYESKAH
IHCSVKAENSVAAKSGGCFPGSATVHLEQGGTKLVKDLSPGDRVLAADDQGRLLYSDFLT
FLDRDDGAKKVFYVIETREPRERLLLTAAHLLFVAPHNDSATGEPEASSGSGPPSGGALG
PRALFASRVRPGQRVYVVAERDGDRRLLPAAVHSVTLSEEAAGAYAPLTAQGTILINRVL
ASCYAVIEEHSWAHRAFAPFRLAHALLAALAPARTDRGGDSGGGDRGGGGGRVALTAPGA
ADAPGAGATAGIHWYSQLLYQIGTWLLDSEALHPLGMAVKSS

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	Q15465-D1	1-462	462		MLLLARCLLLVLVSSLLVCSGLACGPGRGFGKRRHPKKLTPLAYKQFIPNVAEKTLGASGRYEGKISRNSERFKELTPNYNPDIIFKDEENTGADRLMTQRCKDKLNALAISVMNQWPGVKLRVTEGWDEDGHHSEESLHYEGRAVDITTSDRDRSKYGMLARLAVEAGFDWVYYESKAHIHCSVKAENSVAAKSGGCFPGSATVHLEQGGTKLVKDLSPGDRVLAADDQGRLLYSDFLTFLDRDDGAKKVFYVIETREPRERLLLTAAHLLFVAPHNDSATGEPEASSGSGPPSGGALGPRALFASRVRPGQRVYVVAERDGDRRLLPAAVHSVTLSEEAAGAYAPLTAQGTILINRVLASCYAVIEEHSWAHRAFAPFRLAHALLAALAPARTDRGGDSGGGDRGGGGGRVALTAPGAADAPGAGATAGIHWYSQLLYQIGTWLLDSEALHPLGMAVKSS

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.5226

(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	6l7iF1	0.39	7.35	0.061	0.643	model1_6l7iF1.pdb.gz
2	4o9xA	0.39	7.34	0.054	0.638	model1_4o9xA.pdb.gz
3	2x2hA	0.37	7.20	0.038	0.597	model1_2x2hA.pdb.gz
4	4aeeA	0.36	7.61	0.032	0.628	model1_4aeeA.pdb.gz
5	4uhwA	0.36	7.67	0.042	0.625	model1_4uhwA.pdb.gz
6	7bwmA	0.36	7.06	0.039	0.578	model1_7bwmA.pdb.gz
7	4u33A	0.36	7.30	0.060	0.597	model1_4u33A.pdb.gz
8	7ky5A	0.36	6.93	0.036	0.561	model1_7ky5A.pdb.gz
9	4aefA	0.36	7.65	0.045	0.613	model1_4aefA.pdb.gz
10	6u5oL	0.36	7.47	0.047	0.606	model1_6u5oL.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:0005509	0.94	calcium ion binding
GO:0008270	0.78	zinc ion binding
GO:0005102	0.75	receptor binding
GO:0005113	0.58	patched 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:0044699	0.98	single-organism process
GO:0009987	0.93	cellular process
GO:0044763	0.91	single-organism cellular process
GO:0065007	0.84	biological regulation
GO:0050789	0.83	regulation of biological process
GO:0050794	0.81	regulation of cellular process
GO:0044707	0.79	single-multicellular organism process
GO:0032502	0.75	developmental process
GO:0044767	0.74	single-organism developmental process
GO:0048856	0.73	anatomical structure development
GO:0048869	0.66	cellular developmental process
GO:0007389	0.66	pattern specification process
GO:0030154	0.65	cell differentiation
GO:0003002	0.63	regionalization
GO:0048518	0.62	positive regulation of biological process
GO:0009653	0.62	anatomical structure morphogenesis
GO:0080090	0.61	regulation of primary metabolic process
GO:0048522	0.61	positive regulation of cellular process
GO:0051239	0.59	regulation of multicellular organismal process
GO:0050793	0.59	regulation of developmental process
GO:0031323	0.59	regulation of cellular metabolic process
GO:0009889	0.59	regulation of biosynthetic process
GO:2000026	0.58	regulation of multicellular organismal development
GO:0060255	0.58	regulation of macromolecule metabolic process
GO:0042127	0.58	regulation of cell proliferation
GO:0048523	0.57	negative regulation of cellular process
GO:0006355	0.56	regulation of transcription, DNA-templated
GO:0009966	0.55	regulation of signal transduction
GO:0045595	0.53	regulation of cell differentiation
GO:0008152	0.53	metabolic process
GO:0031325	0.52	positive regulation of cellular metabolic process
GO:0010604	0.52	positive regulation of macromolecule metabolic process
GO:0051240	0.50	positive regulation of multicellular organismal process
GO:0051094	0.50	positive regulation of developmental process
GO:0048598	0.50	embryonic morphogenesis
GO:0045597	0.50	positive regulation of cell differentiation
GO:0010628	0.50	positive 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:0044464	0.88	cell part
GO:0044424	0.77	intracellular part
GO:0044421	0.69	extracellular region part
GO:0005615	0.62	extracellular space
GO:0043226	0.58	organelle
GO:0043229	0.57	intracellular organelle
GO:0043227	0.57	membrane-bounded organelle
GO:0043231	0.56	intracellular membrane-bounded 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	1peuA	0.329	7.49	0.038	0.556	1.17.4.1	NA
2	0.060	1ea9C	0.354	7.42	0.057	0.606	3.2.1.54	NA
3	0.060	1hi8A	0.329	7.20	0.067	0.545	2.7.7.48	237,241,360
4	0.060	2qllA	0.332	7.47	0.052	0.561	2.4.1.1	223,353
5	0.060	1t3tA	0.343	7.85	0.066	0.606	6.3.5.3	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	1jdbE	0.363	7.70	0.039	0.625	0.42	GLN	complex1.pdb.gz	266,267,268,307
	2	0.01	1ea0A	0.342	7.73	0.055	0.597	0.56	F3S	complex2.pdb.gz	198,199,200,201,202,215,216,346

	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.