D-I-TASSER Q9BYE2

D-I-TASSER results for Q9BYE2

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

Summary of the Protein

Uniprot ID: Q9BYE2
Protein Name: Transmembrane protease serine 13
Gene Name: TMPRSS13

Input Sequence in FASTA format

>Q9BYE2 (586 residues)
MERDSHGNASPARTPSAGASPAQASPAGTPPGRASPAQASPAQASPAGTPPGRASPAQAS
PAGTPPGRASPGRASPAQASPAQASPARASPALASLSRSSSGRSSSARSASVTTSPTRVY
LVRATPVGAVPIRSSPARSAPATRATRESPGTSLPKFTWREGQKQLPLIGCVLLLIALVV
SLIILFQFWQGHTGIRYKEQRESCPKHAVRCDGVVDCKLKSDELGCVRFDWDKSLLKIYS
GSSHQWLPICSSNWNDSYSEKTCQQLGFESAHRTTEVAHRDFANSFSILRYNSTIQESLH
RSECPSQRYISLQCSHCGLRAMTGRIVGGALASDSKWPWQVSLHFGTTHICGGTLIDAQW
VLTAAHCFFVTREKVLEGWKVYAGTSNLHQLPEAASIAEIIINSNYTDEEDDYDIALMRL
SKPLTLSAHIHPACLPMHGQTFSLNETCWITGFGKTRETDDKTSPFLREVQVNLIDFKKC
NDYLVYDSYLTPRMMCAGDLRGGRDSCQGDSGGPLVCEQNNRWYLAGVTSWGTGCGQRNK
PGVYTKVTEVLPWIYSKMEVRSLQQDTAPSRLGTSSGGDPGGAPRL

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 DeepPotential. 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	Q9BYE2-D1	1-586	586		MERDSHGNASPARTPSAGASPAQASPAGTPPGRASPAQASPAQASPAGTPPGRASPAQASPAGTPPGRASPGRASPAQASPAQASPARASPALASLSRSSSGRSSSARSASVTTSPTRVYLVRATPVGAVPIRSSPARSAPATRATRESPGTSLPKFTWREGQKQLPLIGCVLLLIALVVSLIILFQFWQGHTGIRYKEQRESCPKHAVRCDGVVDCKLKSDELGCVRFDWDKSLLKIYSGSSHQWLPICSSNWNDSYSEKTCQQLGFESAHRTTEVAHRDFANSFSILRYNSTIQESLHRSECPSQRYISLQCSHCGLRAMTGRIVGGALASDSKWPWQVSLHFGTTHICGGTLIDAQWVLTAAHCFFVTREKVLEGWKVYAGTSNLHQLPEAASIAEIIINSNYTDEEDDYDIALMRLSKPLTLSAHIHPACLPMHGQTFSLNETCWITGFGKTRETDDKTSPFLREVQVNLIDFKKCNDYLVYDSYLTPRMMCAGDLRGGRDSCQGDSGGPLVCEQNNRWYLAGVTSWGTGCGQRNKPGVYTKVTEVLPWIYSKMEVRSLQQDTAPSRLGTSSGGDPGGAPRL

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.4042

(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 DeepPotential, 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	6esoA	0.66	4.25	0.257	0.783	model1_6esoA.pdb.gz
2	2f83A	0.46	6.30	0.204	0.625	model1_2f83A.pdb.gz
3	2i6qA	0.41	5.09	0.135	0.514	model1_2i6qA.pdb.gz
4	1zjkA	0.41	4.59	0.250	0.490	model1_1zjkA.pdb.gz
5	4kkdA	0.41	4.56	0.210	0.488	model1_4kkdA.pdb.gz
6	4igdA	0.41	4.91	0.215	0.495	model1_4igdA.pdb.gz
7	1z8gA	0.41	4.17	0.302	0.473	model1_1z8gA.pdb.gz
8	1elvA	0.40	4.42	0.256	0.469	model1_1elvA.pdb.gz
9	2ok5A	0.40	5.78	0.128	0.522	model1_2ok5A.pdb.gz
10	4durA	0.39	5.77	0.212	0.517	model1_4durA.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:0043621	0.97	protein self-association
GO:0008233	0.97	peptidase activity
GO:0070011	0.95	peptidase activity, acting on L-amino acid peptides
GO:0008236	0.92	serine-type peptidase activity
GO:0004175	0.82	endopeptidase activity
GO:0004252	0.79	serine-type endopeptidase 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:0065007	0.98	biological regulation
GO:0071704	0.75	organic substance metabolic process
GO:0044238	0.74	primary metabolic process
GO:0043170	0.74	macromolecule metabolic process
GO:0019538	0.73	protein metabolic process
GO:0050789	0.69	regulation of biological process
GO:0032501	0.69	multicellular organismal process
GO:0006508	0.67	proteolysis
GO:0050794	0.66	regulation of cellular process
GO:0065008	0.65	regulation of biological quality
GO:0003008	0.62	system process
GO:0042981	0.60	regulation of apoptotic process
GO:0003081	0.50	regulation of systemic arterial blood pressure by renin-angiotensin

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	0.75	cell part
GO:0044421	0.75	extracellular region part
GO:0005615	0.72	extracellular space
GO:0044424	0.68	intracellular part
GO:0043227	0.61	membrane-bounded organelle
GO:0043231	0.56	intracellular membrane-bounded organelle
GO:0044444	0.54	cytoplasmic 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

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	0.160	1kdqA	0.193	2.53	0.325	0.206	3.4.21.1	366,414
2	0.137	1ab9B	0.194	2.54	0.368	0.208	3.4.21.1	366,414
3	0.060	1gj5H	0.344	2.82	0.359	0.375	3.4.21.5	NA
4	0.060	1ekbB	0.354	2.75	0.371	0.386	3.4.21.9	366
5	0.060	2puxB	0.361	2.89	0.332	0.396	3.4.21.5	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	0.43	3pmaB	0.344	2.86	0.357	0.377	0.86	III	complex1.pdb.gz	333,334,335,336,338,339,428,429,431,432,434,447,449,499,518,521,522,523
2	0.06	1etrH	0.360	2.93	0.343	0.396	0.83	MIT	complex2.pdb.gz	366,505,506,507,511,529,531,532,534,535
3	0.04	1sb1H	0.358	2.78	0.345	0.391	0.97	NA	complex3.pdb.gz	340,352,451,452,513
4	0.04	3p70B	0.360	2.83	0.342	0.394	0.98	NA	complex4.pdb.gz	353,354,362,363,512,513,514,525
5	0.04	1abiH	0.360	2.81	0.346	0.394	0.81	III	complex5.pdb.gz	344,348,349,350,351,366,393,505,506,507,511,529,530,531,532,534,542
6	0.04	1tbr0	0.362	2.87	0.343	0.398	0.80	III	complex6.pdb.gz	344,348,350,351,366,380,382,394,509,510,511,530,531,532

	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, Qiqige Wuyun, Yang Li, Quancheng Liu, Xiaogen Zhou, Yiheng Zhu, P. Lydia Freddolino, Yang Zhang. Integrating deep learning potentials with I-TASSER for single- and multi-domain protein structure prediction. Submitted. 2023.