D-I-TASSER Q6UWW8

D-I-TASSER results for Q6UWW8

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

Summary of the Protein

Uniprot ID: Q6UWW8
Protein Name: Carboxylesterase 3
Gene Name: CES3

Input Sequence in FASTA format

>Q6UWW8 (571 residues)
MERAVRVESGVLVGVVCLLLACPATATGPEVAQPEVDTTLGRVRGRQVGVKGTDRLVNVF
LGIPFAQPPLGPDRFSAPHPAQPWEGVRDASTAPPMCLQDVESMNSSRFVLNGKQQIFSV
SEDCLVLNVYSPAEVPAGSGRPVMVWVHGGALITGAATSYDGSALAAYGDVVVVTVQYRL
GVLGFFSTGDEHAPGNQGFLDVVAALRWVQENIAPFGGDLNCVTVFGGSAGGSIISGLVL
SPVAAGLFHRAITQSGVITTPGIIDSHPWPLAQKIANTLACSSSSPAEMVQCLQQKEGEE
LVLSKKLKNTIYPLTVDGTVFPKSPKELLKEKPFHSVPFLMGVNNHEFSWLIPRGWGLLD
TMEQMSREDMLAISTPVLTSLDVPPEMMPTVIDEYLGSNSDAQAKCQAFQEFMGDVFINV
PTVSFSRYLRDSGSPVFFYEFQHRPSSFAKIKPAWVKADHGAEGAFVFGGPFLMDESSRL
AFPEATEEEKQLSLTMMAQWTHFARTGDPNSKALPPWPQFNQAEQYLEINPVPRAGQKFR
EAWMQFWSETLPSKIQQWHQKQKNRKAQEDL

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	Q6UWW8-D1	1-347,418-539	469		MERAVRVESGVLVGVVCLLLACPATATGPEVAQPEVDTTLGRVRGRQVGVKGTDRLVNVFLGIPFAQPPLGPDRFSAPHPAQPWEGVRDASTAPPMCLQDVESMNSSRFVLNGKQQIFSVSEDCLVLNVYSPAEVPAGSGRPVMVWVHGGALITGAATSYDGSALAAYGDVVVVTVQYRLGVLGFFSTGDEHAPGNQGFLDVVAALRWVQENIAPFGGDLNCVTVFGGSAGGSIISGLVLSPVAAGLFHRAITQSGVITTPGIIDSHPWPLAQKIANTLACSSSSPAEMVQCLQQKEGEELVLSKKLKNTIYPLTVDGTVFPKSPKELLKEKPFHSVPFLMGVNNHEINVPTVSFSRYLRDSGSPVFFYEFQHRPSSFAKIKPAWVKADHGAEGAFVFGGPFLMDESSRLAFPEATEEEKQLSLTMMAQWTHFARTGDPNSKALPPWPQFNQAEQYLEINPVPRAGQKF
2	Q6UWW8-D2	348-417,540-571	102		FSWLIPRGWGLLDTMEQMSREDMLAISTPVLTSLDVPPEMMPTVIDEYLGSNSDAQAKCQAFQEFMGDVFREAWMQFWSETLPSKIQQWHQKQKNRKAQEDL

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.81

(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	2wqzA	0.85	2.63	0.318	0.904	model1_2wqzA.pdb.gz
2	5x61B	0.84	2.26	0.323	0.883	model1_5x61B.pdb.gz
3	1q83A	0.84	2.43	0.327	0.888	model1_1q83A.pdb.gz
4	3i6mA	0.83	2.43	0.320	0.883	model1_3i6mA.pdb.gz
5	6cqtA	0.83	2.50	0.339	0.884	model1_6cqtA.pdb.gz
6	1mx9D	0.83	2.78	0.447	0.888	model1_1mx9D.pdb.gz
7	2pm8A	0.83	2.28	0.318	0.872	model1_2pm8A.pdb.gz
8	4qwwA	0.82	2.54	0.322	0.881	model1_4qwwA.pdb.gz
9	1qo9A	0.82	2.29	0.287	0.870	model1_1qo9A.pdb.gz
10	1aknA	0.79	2.94	0.301	0.860	model1_1aknA.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:0052689	1.00	carboxylic ester hydrolase 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:0044699	0.99	single-organism process
GO:0009987	0.98	cellular process
GO:0044763	0.97	single-organism cellular process
GO:0065007	0.96	biological regulation
GO:0050789	0.88	regulation of biological process
GO:0050794	0.87	regulation of cellular process
GO:0022607	0.85	cellular component assembly
GO:0050804	0.84	modulation of synaptic transmission
GO:0007155	0.84	cell adhesion
GO:0007158	0.83	neuron cell-cell adhesion
GO:0008152	0.77	metabolic process
GO:0065008	0.67	regulation of biological quality
GO:0050808	0.66	synapse organization
GO:0044710	0.66	single-organism metabolic process
GO:0071704	0.65	organic substance metabolic process
GO:0044237	0.65	cellular metabolic process
GO:0007416	0.65	synapse assembly
GO:0001505	0.63	regulation of neurotransmitter levels
GO:0032501	0.58	multicellular organismal process
GO:0051179	0.57	localization
GO:0048583	0.56	regulation of response to stimulus
GO:0048523	0.56	negative regulation of cellular process
GO:0048518	0.56	positive regulation of biological process
GO:0006810	0.56	transport
GO:1902578	0.55	single-organism localization
GO:0051239	0.55	regulation of multicellular organismal process
GO:0048522	0.55	positive regulation of cellular process
GO:0032879	0.55	regulation of localization
GO:0009966	0.55	regulation of signal transduction
GO:0003008	0.55	system process
GO:0098815	0.54	modulation of excitatory postsynaptic potential
GO:0071709	0.54	membrane assembly
GO:0065009	0.54	regulation of molecular function
GO:0051962	0.54	positive regulation of nervous system development
GO:0051130	0.54	positive regulation of cellular component organization
GO:0051050	0.54	positive regulation of transport
GO:0050877	0.54	neurological system process
GO:0050807	0.54	regulation of synapse organization
GO:0048584	0.54	positive regulation of response to stimulus
GO:0045595	0.54	regulation of cell differentiation
GO:0034613	0.54	cellular protein localization
GO:2000463	0.53	positive regulation of excitatory postsynaptic potential
GO:2000311	0.53	regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity
GO:2000310	0.53	regulation of N-methyl-D-aspartate selective glutamate receptor activity
GO:1903532	0.53	positive regulation of secretion by cell
GO:1902531	0.53	regulation of intracellular signal transduction
GO:1902474	0.53	positive regulation of protein localization to synapse
GO:0097119	0.53	postsynaptic density protein 95 clustering
GO:0097104	0.53	postsynaptic membrane assembly
GO:0072553	0.53	terminal button organization
GO:0065003	0.53	macromolecular complex assembly
GO:0061002	0.53	negative regulation of dendritic spine morphogenesis
GO:0060999	0.53	positive regulation of dendritic spine development
GO:0060341	0.53	regulation of cellular localization
GO:0060080	0.53	inhibitory postsynaptic potential
GO:0051968	0.53	positive regulation of synaptic transmission, glutamatergic
GO:0051965	0.53	positive regulation of synapse assembly
GO:0035418	0.53	protein localization to synapse
GO:0032230	0.53	positive regulation of synaptic transmission, GABAergic
GO:0015031	0.53	protein transport
GO:0006996	0.53	organelle organization
GO:0002087	0.53	regulation of respiratory gaseous exchange by neurological system process
GO:2000809	0.52	positive regulation of synaptic vesicle clustering
GO:2000302	0.52	positive regulation of synaptic vesicle exocytosis
GO:1902533	0.52	positive regulation of intracellular signal transduction
GO:1900244	0.52	positive regulation of synaptic vesicle endocytosis
GO:1900029	0.52	positive regulation of ruffle assembly
GO:0097120	0.52	receptor localization to synapse
GO:0097115	0.52	neurexin clustering involved in presynaptic membrane assembly
GO:0097114	0.52	NMDA glutamate receptor clustering
GO:0097113	0.52	AMPA glutamate receptor clustering
GO:0060291	0.52	long-term synaptic potentiation
GO:0051491	0.52	positive regulation of filopodium assembly
GO:0051290	0.52	protein heterotetramerization
GO:0051260	0.52	protein homooligomerization
GO:0048789	0.52	cytoskeletal matrix organization at active zone
GO:0045161	0.52	neuronal ion channel clustering
GO:0016339	0.52	calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules
GO:0016080	0.52	synaptic vesicle targeting
GO:0010841	0.52	positive regulation of circadian sleep/wake cycle, wakefulness
GO:0007157	0.52	heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules
GO:0006605	0.52	protein targeting
GO:0044238	0.50	primary metabolic process
GO:0009056	0.50	catabolic process
GO:0006807	0.50	nitrogen compound 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:0005615	0.98	extracellular space
GO:0044464	0.82	cell part
GO:0044424	0.63	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	0.431	1lpsA	0.748	3.31	0.225	0.827	3.1.1.3	220
2	0.195	1maaD	0.833	2.47	0.331	0.886	3.1.1.7	NA
3	0.193	1b41A	0.831	2.34	0.335	0.879	3.1.1.7	NA
4	0.190	1mx9D	0.826	2.78	0.447	0.888	3.1.1.1	NA
5	0.185	2pm8A	0.826	2.28	0.318	0.872	3.1.1.8	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	0.37	2ha0A	0.831	2.47	0.331	0.884	0.20	NWA	complex1.pdb.gz	41,63,126,127
2	0.27	4a23A	0.832	2.46	0.330	0.884	0.17	C56	complex2.pdb.gz	41,60,61,63
3	0.24	2c0qB	0.830	2.45	0.334	0.881	0.16	NTJ	complex3.pdb.gz	128,129,212
4	0.24	2ha6B	0.829	2.40	0.329	0.879	0.19	SCK	complex4.pdb.gz	45,61,63,64,128,163
5	0.24	1maaB	0.831	2.45	0.332	0.883	0.15	DME	complex5.pdb.gz	41,63,205
6	0.24	2xuiB	0.830	2.42	0.332	0.881	0.14	TZ5	complex6.pdb.gz	41,60,204,205
7	0.24	2jeyB	0.826	2.47	0.334	0.881	0.11	HLO	complex7.pdb.gz	62,63,202,205
8	0.21	2xufA	0.833	2.41	0.331	0.884	0.10	TZ4	complex8.pdb.gz	37,45,140,141
9	0.11	2ha7A	0.833	2.46	0.327	0.886	0.13	BUA	complex9.pdb.gz	44,62,63
10	0.06	1maaD	0.833	2.47	0.331	0.886	0.34	UUU	complex10.pdb.gz	43,45,63,82

	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.