D-I-TASSER P38567

D-I-TASSER results for P38567

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

Summary of the Protein

Uniprot ID: P38567
Protein Name: Hyaluronidase PH-20
Gene Name: SPAM1

Input Sequence in FASTA format

>P38567 (509 residues)
MGVLKFKHIFFRSFVKSSGVSQIVFTFLLIPCCLTLNFRAPPVIPNVPFLWAWNAPSEFC
LGKFDEPLDMSLFSFIGSPRINATGQGVTIFYVDRLGYYPYIDSITGVTVNGGIPQKISL
QDHLDKAKKDITFYMPVDNLGMAVIDWEEWRPTWARNWKPKDVYKNRSIELVQQQNVQLS
LTEATEKAKQEFEKAGKDFLVETIKLGKLLRPNHLWGYYLFPDCYNHHYKKPGYNGSCFN
VEIKRNDDLSWLWNESTALYPSIYLNTQQSPVAATLYVRNRVREAIRVSKIPDAKSPLPV
FAYTRIVFTDQVLKFLSQDELVYTFGETVALGASGIVIWGTLSIMRSMKSCLLLDNYMET
ILNPYIINVTLAAKMCSQVLCQEQGVCIRKNWNSSDYLHLNPDNFAIQLEKGGKFTVRGK
PTLEDLEQFSEKFYCSCYSTLSCKEKADVKDTDAVDVCIADGVCIDAFLKPPMETEEPQI
FYNASPSTLSATMFIVSILFLIISSVASL

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	P38567-D1	1-80,217-509	373		MGVLKFKHIFFRSFVKSSGVSQIVFTFLLIPCCLTLNFRAPPVIPNVPFLWAWNAPSEFCLGKFDEPLDMSLFSFIGSPRGYYLFPDCYNHHYKKPGYNGSCFNVEIKRNDDLSWLWNESTALYPSIYLNTQQSPVAATLYVRNRVREAIRVSKIPDAKSPLPVFAYTRIVFTDQVLKFLSQDELVYTFGETVALGASGIVIWGTLSIMRSMKSCLLLDNYMETILNPYIINVTLAAKMCSQVLCQEQGVCIRKNWNSSDYLHLNPDNFAIQLEKGGKFTVRGKPTLEDLEQFSEKFYCSCYSTLSCKEKADVKDTDAVDVCIADGVCIDAFLKPPMETEEPQIFYNASPSTLSATMFIVSILFLIISSVASL
2	P38567-D2	81-216	136		INATGQGVTIFYVDRLGYYPYIDSITGVTVNGGIPQKISLQDHLDKAKKDITFYMPVDNLGMAVIDWEEWRPTWARNWKPKDVYKNRSIELVQQQNVQLSLTEATEKAKQEFEKAGKDFLVETIKLGKLLRPNHLW

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	2pe4A	0.79	1.23	0.399	0.805	model1_2pe4A.pdb.gz
2	2atmA	0.59	2.05	0.323	0.621	model1_2atmA.pdb.gz
3	1fcvA	0.59	2.18	0.293	0.621	model1_1fcvA.pdb.gz
4	5gsmA	0.58	5.91	0.059	0.792	model1_5gsmA.pdb.gz
5	5gslA	0.57	5.87	0.061	0.780	model1_5gslA.pdb.gz
6	3tonA	0.56	6.52	0.051	0.829	model1_3tonA.pdb.gz
7	2x2hA	0.56	6.57	0.081	0.825	model1_2x2hA.pdb.gz
8	6jr6A	0.56	6.36	0.071	0.805	model1_6jr6A.pdb.gz
9	5kzwA	0.56	6.29	0.066	0.798	model1_5kzwA.pdb.gz
10	4b9yA	0.55	6.23	0.073	0.792	model1_4b9yA.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	1.00	catalytic activity
GO:0015929	0.98	hexosaminidase activity
GO:0004415	0.96	hyalurononglucosaminidase activity
GO:0004872	0.88	receptor activity
GO:0001618	0.75	virus receptor activity
GO:0038023	0.50	signaling receptor 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:0071704	0.94	organic substance metabolic process
GO:1901564	0.83	organonitrogen compound metabolic process
GO:1901135	0.83	carbohydrate derivative metabolic process
GO:1901575	0.82	organic substance catabolic process
GO:0043170	0.82	macromolecule metabolic process
GO:0009987	0.82	cellular process
GO:0030203	0.81	glycosaminoglycan metabolic process
GO:0009057	0.80	macromolecule catabolic process
GO:0006027	0.79	glycosaminoglycan catabolic process
GO:1903510	0.76	mucopolysaccharide metabolic process
GO:0051704	0.76	multi-organism process
GO:0050794	0.76	regulation of cellular process
GO:0009605	0.74	response to external stimulus
GO:0009416	0.74	response to light stimulus
GO:0044699	0.73	single-organism process
GO:0030212	0.72	hyaluronan metabolic process
GO:0048523	0.70	negative regulation of cellular process
GO:0030214	0.70	hyaluronan catabolic process
GO:0071493	0.69	cellular response to UV-B
GO:0071347	0.69	cellular response to interleukin-1
GO:0009615	0.69	response to virus
GO:0006950	0.69	response to stress
GO:0051216	0.67	cartilage development
GO:0071495	0.65	cellular response to endogenous stimulus
GO:0071363	0.65	cellular response to growth factor stimulus
GO:0051240	0.65	positive regulation of multicellular organismal process
GO:0048522	0.65	positive regulation of cellular process
GO:0030334	0.65	regulation of cell migration
GO:0030308	0.65	negative regulation of cell growth
GO:0000302	0.65	response to reactive oxygen species
GO:0044238	0.52	primary metabolic process
GO:0032501	0.51	multicellular organismal 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	0.99	cell part
GO:0043226	0.91	organelle
GO:0043231	0.89	intracellular membrane-bounded organelle
GO:0031410	0.89	cytoplasmic vesicle
GO:0005764	0.78	lysosome
GO:0016020	0.72	membrane
GO:0044459	0.59	plasma membrane part
GO:0031988	0.54	membrane-bounded vesicle
GO:0042995	0.51	cell projection
GO:0016023	0.50	cytoplasmic, membrane-bounded vesicle

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	0.185	2pe4A	0.791	1.23	0.399	0.805	3.2.1.35	NA
2	0.124	1fcuA	0.589	2.20	0.293	0.621	3.2.1.35	NA
3	0.062	1uokA	0.473	5.53	0.047	0.638	3.2.1.10	359
4	0.060	1b1yA	0.501	5.42	0.072	0.656	3.2.1.2	170
5	0.060	1xc6A	0.524	6.07	0.049	0.733	3.2.1.23	77

	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	2x2iA	0.559	6.59	0.074	0.823	0.26	QPS	complex1.pdb.gz	50,74,75,76
2	0.01	2x2iC	0.555	6.54	0.073	0.815	0.28	QPS	complex2.pdb.gz	85,89,131,212,213,214
3	0.01	1vepA	0.520	6.03	0.068	0.723	0.15	GLC	complex3.pdb.gz	43,53,87,142
4	0.01	2qmjA	0.551	6.30	0.064	0.790	0.16	ACR	complex4.pdb.gz	88,141,143,144,216
5	0.01	1vepA	0.520	6.03	0.068	0.723	0.16	UUU	complex5.pdb.gz	81,142,144
6	0.01	2x2iD	0.555	6.56	0.065	0.815	0.12	QPS	complex6.pdb.gz	58,62,89,336,338,339
7	0.01	2f2hF	0.534	6.26	0.066	0.764	0.33	XTG	complex7.pdb.gz	53,141,142,143
8	0.01	2x2iB	0.555	6.20	0.052	0.798	0.14	QPS	complex8.pdb.gz	43,217,335
9	0.01	3lppB	0.550	6.25	0.048	0.788	0.13	KTL	complex9.pdb.gz	302,335,337
10	0.01	3l4tA	0.547	6.32	0.062	0.788	0.20	BJ1	complex10.pdb.gz	87,141,143,144,216,259,301,335

	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.