D-I-TASSER Q9P0U3

D-I-TASSER results for Q9P0U3

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

Summary of the Protein

Uniprot ID: Q9P0U3
Protein Name: Sentrin-specific protease 1
Gene Name: SENP1

Input Sequence in FASTA format

>Q9P0U3 (644 residues)
MDDIADRMRMDAGEVTLVNHNSVFKTHLLPQTGFPEDQLSLSDQQILSSRQGHLDRSFTC
STRSAAYNPSYYSDNPSSDSFLGSGDLRTFGQSANGQWRNSTPSSSSSLQKSRNSRSLYL
ETRKTSSGLSNSFAGKSNHHCHVSAYEKSFPIKPVPSPSWSGSCRRSLLSPKKTQRRHVS
TAEETVQEEEREIYRQLLQMVTGKQFTIAKPTTHFPLHLSRCLSSSKNTLKDSLFKNGNS
CASQIIGSDTSSSGSASILTNQEQLSHSVYSLSSYTPDVAFGSKDSGTLHHPHHHHSVPH
QPDNLAASNTQSEGSDSVILLKVKDSQTPTPSSTFFQAELWIKELTSVYDSRARERLRQI
EEQKALALQLQNQRLQEREHSVHDSVELHLRVPLEKEIPVTVVQETQKKGHKLTDSEDEF
PEITEEMEKEIKNVFRNGNQDEVLSEAFRLTITRKDIQTLNHLNWLNDEIINFYMNMLME
RSKEKGLPSVHAFNTFFFTKLKTAGYQAVKRWTKKVDVFSVDILLVPIHLGVHWCLAVVD
FRKKNITYYDSMGGINNEACRILLQYLKQESIDKKRKEFDTNGWQLFSKKSQEIPQQMNG
SDCGMFACKYADCITKDRPINFTQQHMPYFRKRMVWEILHRKLL

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	Q9P0U3-D1	1-644	644		MDDIADRMRMDAGEVTLVNHNSVFKTHLLPQTGFPEDQLSLSDQQILSSRQGHLDRSFTCSTRSAAYNPSYYSDNPSSDSFLGSGDLRTFGQSANGQWRNSTPSSSSSLQKSRNSRSLYLETRKTSSGLSNSFAGKSNHHCHVSAYEKSFPIKPVPSPSWSGSCRRSLLSPKKTQRRHVSTAEETVQEEEREIYRQLLQMVTGKQFTIAKPTTHFPLHLSRCLSSSKNTLKDSLFKNGNSCASQIIGSDTSSSGSASILTNQEQLSHSVYSLSSYTPDVAFGSKDSGTLHHPHHHHSVPHQPDNLAASNTQSEGSDSVILLKVKDSQTPTPSSTFFQAELWIKELTSVYDSRARERLRQIEEQKALALQLQNQRLQEREHSVHDSVELHLRVPLEKEIPVTVVQETQKKGHKLTDSEDEFPEITEEMEKEIKNVFRNGNQDEVLSEAFRLTITRKDIQTLNHLNWLNDEIINFYMNMLMERSKEKGLPSVHAFNTFFFTKLKTAGYQAVKRWTKKVDVFSVDILLVPIHLGVHWCLAVVDFRKKNITYYDSMGGINNEACRILLQYLKQESIDKKRKEFDTNGWQLFSKKSQEIPQQMNGSDCGMFACKYADCITKDRPINFTQQHMPYFRKRMVWEILHRKLL

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.5877

(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	5yz0A	0.35	8.22	0.042	0.590	model1_5yz0A.pdb.gz
2	5ijoJ	0.32	8.21	0.031	0.528	model1_5ijoJ.pdb.gz
3	6rw9A	0.31	7.86	0.014	0.491	model1_6rw9A.pdb.gz
4	5ganA	0.31	7.78	0.030	0.480	model1_5ganA.pdb.gz
5	7cpxA	0.30	7.83	0.040	0.480	model1_7cpxA.pdb.gz
6	2uvcG	0.30	7.85	0.031	0.472	model1_2uvcG.pdb.gz
7	2pffB	0.29	8.60	0.033	0.500	model1_2pffB.pdb.gz
8	6yejA	0.29	8.06	0.036	0.466	model1_6yejA.pdb.gz
9	6emkA	0.28	8.08	0.032	0.460	model1_6emkA.pdb.gz
10	4w8jA	0.28	7.94	0.044	0.453	model1_4w8jA.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:0070011	0.99	peptidase activity, acting on L-amino acid peptides
GO:0019783	0.98	ubiquitin-like protein-specific protease activity
GO:0016929	0.97	SUMO-specific protease activity
GO:0004175	0.89	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:0008152	1.00	metabolic process
GO:0044260	0.99	cellular macromolecule metabolic process
GO:0006508	0.99	proteolysis
GO:0070646	0.98	protein modification by small protein removal
GO:0018205	0.98	peptidyl-lysine modification
GO:0016926	0.97	protein desumoylation

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:0044424	1.00	intracellular part
GO:0043229	0.99	intracellular organelle
GO:0005634	0.98	nucleus

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	2vkzG	0.257	7.75	0.035	0.407	2.3.1.38 3.1.2.14	NA
2	0.060	2e1qA	0.235	7.79	0.063	0.376	1.17.3.2 1.17.1.4	NA
3	0.060	1vlbA	0.233	7.73	0.041	0.360	1.2.99.7	NA
4	0.060	3b9jI	0.105	5.31	0.056	0.134	1.17.1.4 1.17.3.2	497,499
5	0.060	3hmjA	0.259	8.12	0.025	0.430	2.3.1.86	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	0.02	2vdcB	0.274	7.40	0.046	0.416	0.25	OMT	complex1.pdb.gz	470,505,529,530
2	0.01	1ofeA	0.249	8.07	0.039	0.404	0.25	ONL	complex2.pdb.gz	466,467,505
3	0.01	1d0xA	0.184	8.70	0.027	0.318	0.25	MNQ	complex3.pdb.gz	464,467,468,469,501,502,529
4	0.01	1ofdB	0.250	8.07	0.041	0.410	0.24	F3S	complex4.pdb.gz	499,501,509
5	0.01	1fmwA	0.201	8.31	0.051	0.334	0.10	ATP	complex5.pdb.gz	461,502,505,506
6	0.01	2y8iX	0.217	6.96	0.037	0.317	0.16	ADP	complex6.pdb.gz	464,467,469,503,505
7	0.01	1w9kA	0.179	8.18	0.038	0.295	0.12	UUU	complex7.pdb.gz	467,468,471,472,502,503,505,506,507
8	0.01	1mneA	0.178	8.13	0.044	0.289	0.35	POP	complex8.pdb.gz	500,502,530,531
9	0.01	3cf4A	0.254	7.83	0.030	0.404	0.28	SF4	complex9.pdb.gz	470,474,505
10	0.01	1mmdA	0.199	8.25	0.021	0.323	0.14	UUU	complex10.pdb.gz	464,467,468,469,470,503,504,505,506

	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.