D-I-TASSER P16444

D-I-TASSER results for P16444

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

Summary of the Protein

Uniprot ID: P16444
Protein Name: Dipeptidase 1
Gene Name: DPEP1

Input Sequence in FASTA format

>P16444 (411 residues)
MWSGWWLWPLVAVCTADFFRDEAERIMRDSPVIDGHNDLPWQLLDMFNNRLQDERANLTT
LAGTHTNIPKLRAGFVGGQFWSVYTPCDTQNKDAVRRTLEQMDVVHRMCRMYPETFLYVT
SSAGIRQAFREGKVASLIGVEGGHSIDSSLGVLRALYQLGMRYLTLTHSCNTPWADNWLV
DTGDSEPQSQGLSPFGQRVVKELNRLGVLIDLAHVSVATMKATLQLSRAPVIFSHSSAYS
VCASRRNVPDDVLRLVKQTDSLVMVNFYNNYISCTNKANLSQVADHLDHIKEVAGARAVG
FGGDFDGVPRVPEGLEDVSKYPDLIAELLRRNWTEAEVKGALADNLLRVFEAVEQASNLT
QAPEEEPIPLDQLGGSCRTHYGYSSGASSLHRHWGLLLASLAPLVLCLSLL

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	P16444-D1	1-411	411		MWSGWWLWPLVAVCTADFFRDEAERIMRDSPVIDGHNDLPWQLLDMFNNRLQDERANLTTLAGTHTNIPKLRAGFVGGQFWSVYTPCDTQNKDAVRRTLEQMDVVHRMCRMYPETFLYVTSSAGIRQAFREGKVASLIGVEGGHSIDSSLGVLRALYQLGMRYLTLTHSCNTPWADNWLVDTGDSEPQSQGLSPFGQRVVKELNRLGVLIDLAHVSVATMKATLQLSRAPVIFSHSSAYSVCASRRNVPDDVLRLVKQTDSLVMVNFYNNYISCTNKANLSQVADHLDHIKEVAGARAVGFGGDFDGVPRVPEGLEDVSKYPDLIAELLRRNWTEAEVKGALADNLLRVFEAVEQASNLTQAPEEEPIPLDQLGGSCRTHYGYSSGASSLHRHWGLLLASLAPLVLCLSLL

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.7805

(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	1ituA	0.89	0.42	1.000	0.898	model1_1ituA.pdb.gz
2	5lwzA	0.86	1.62	0.383	0.898	model1_5lwzA.pdb.gz
3	3itcA	0.83	1.34	0.458	0.849	model1_3itcA.pdb.gz
4	6vgoA	0.82	1.59	0.489	0.847	model1_6vgoA.pdb.gz
5	3b40A	0.78	1.90	0.237	0.813	model1_3b40A.pdb.gz
6	2ragA	0.77	1.61	0.241	0.798	model1_2ragA.pdb.gz
7	3fdgB	0.75	2.07	0.276	0.786	model1_3fdgB.pdb.gz
8	3lu2A	0.71	1.56	0.272	0.735	model1_3lu2A.pdb.gz
9	2i5gA	0.68	1.73	0.249	0.713	model1_2i5gA.pdb.gz
10	4dziA	0.52	3.99	0.108	0.633	model1_4dziA.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:0008233	1.00	peptidase activity
GO:0008238	0.98	exopeptidase activity
GO:0008237	0.96	metallopeptidase activity
GO:0070573	0.95	metallodipeptidase activity
GO:0046872	0.93	metal ion binding
GO:0072341	0.92	modified amino acid binding
GO:0043027	0.92	cysteine-type endopeptidase inhibitor activity involved in apoptotic process
GO:0008270	0.92	zinc ion 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:0009987	1.00	cellular process
GO:0008152	0.96	metabolic process
GO:0071704	0.94	organic substance metabolic process
GO:0044237	0.94	cellular metabolic process
GO:0044699	0.93	single-organism process
GO:0065007	0.92	biological regulation
GO:0044763	0.92	single-organism cellular process
GO:0044710	0.92	single-organism metabolic process
GO:0006807	0.92	nitrogen compound metabolic process
GO:0050794	0.91	regulation of cellular process
GO:1901564	0.90	organonitrogen compound metabolic process
GO:0050896	0.90	response to stimulus
GO:0048519	0.90	negative regulation of biological process
GO:0044281	0.90	small molecule metabolic process
GO:0051716	0.89	cellular response to stimulus
GO:0051336	0.89	regulation of hydrolase activity
GO:0044092	0.89	negative regulation of molecular function
GO:0042493	0.89	response to drug
GO:0032879	0.89	regulation of localization
GO:0032269	0.89	negative regulation of cellular protein metabolic process
GO:0010941	0.89	regulation of cell death
GO:0006790	0.89	sulfur compound metabolic process
GO:0006082	0.89	organic acid metabolic process
GO:0050667	0.88	homocysteine metabolic process
GO:0043154	0.88	negative regulation of cysteine-type endopeptidase activity involved in apoptotic process
GO:0035690	0.88	cellular response to drug
GO:0030336	0.88	negative regulation of cell migration
GO:0016999	0.88	antibiotic metabolic 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:0016020	0.97	membrane
GO:0045177	0.94	apical part of cell
GO:0005886	0.94	plasma membrane
GO:0044424	0.64	intracellular 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	0.679	1itqA	0.893	0.62	1.000	0.898	3.4.13.19	168,304
2	0.067	1zzmA	0.495	3.51	0.095	0.586	3.1.21.-	NA
3	0.067	2wjfA	0.454	4.31	0.081	0.567	3.1.3.48	157,162
4	0.060	2v3eA	0.521	5.40	0.064	0.723	3.2.1.45	NA
5	0.060	3dc8A	0.450	6.14	0.063	0.659	3.5.2.2	304

	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	0.77	1ituA	0.895	0.42	1.000	0.898	1.48	CIL	complex1.pdb.gz	38,41,84,168,214,235,246,268,271,304,307,308,309
2	0.26	3nehA	0.723	1.54	0.262	0.752	0.76	L3A	complex2.pdb.gz	36,38,41,214,235,246,304,307
3	0.04	2i5g0	0.681	1.73	0.249	0.713	0.72	III	complex3.pdb.gz	148,149,150,190,191,192,194,195,198,222

	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.