D-I-TASSER Q008S8

D-I-TASSER results for Q008S8

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

Summary of the Protein

Uniprot ID: Q008S8
Protein Name: Epithelial cell-transforming sequence 2 oncogene-like
Gene Name: ECT2L

Input Sequence in FASTA format

>Q008S8 (904 residues)
MESFHTRFSAWTPFSNKSLNRQLFQERVALISHWFDLWTNKQRQEFLFAIFLRCTKSQLR
FVQDWFSERMQVAKVDFSTVLPRFISLYIFSFLSPKDLCAAAQVSWPWKFLTEQDCLWMP
KCVKFGWFLPYTPTDNEYGAWKRHYIACVSHLDWLTPREAAATYGTLNEPKTEDEELLER
QREKCLRKRIWEKIALRKKELFKVRPPWVSGTCCSSVLKPRCQPRLSQTVRERVGLHEAL
EKQLVLTSLETLPKRSNISGSHSYPLLSKKNWHGVHKNDDRSSYALRPHFMLISSRIPAY
EMVMESVKAGVVSVVYEHSVTLESLLYLIEKALDGQKAQSIGIFSDGDSREINLLQGYKI
GVKNLLRPEVRDFWEKLGSYVATEEEGGHVDFFVPLGASEAGIEVLSQLSQLTGTFFTAP
TGIATGSYQHILSDWLGSQWGKAPSSIYFCESKLQTWSSFTDFLEETLKTVRKQLYPFFK
ELQKSISGRMIGQFMFDTMGMTNILNNQDTAQALADGLMELSKEDSERNVVEDNSWDTKS
RLSKNDLNFEALINLERILQKDSAEKRARVVRELLQSERKYVQILEIVRDVYVAPLKAAL
SSNRAILSAANIQIIFCDILQILSLNRQFLDNLRDRLQEWGPAHCVGEIVTKFGSQLNTY
TNFFNNYPVILKTIEKCREMIPAFRTFLKRHDKTIVTKMLSLPELLLYPSRRFEEYLNLL
YAVRLHTPAEHVDRGDLTTAIDQIKKYKGYIDQMKQNITMKDHLSDIQRIIWGCPTLSEV
NRYLIRVQDVAQLHCCDEEISFSLRLYEHIHDLSLFLFNDALLVSSRGTSHTPFERTSKT
TYQFIASVALHRLLIENIPDSKYVKNAFILQGPKYKWICATEIEDDKFLWLSVLRNAIKS
SMEK

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	Q008S8-D1	1-417	417		MESFHTRFSAWTPFSNKSLNRQLFQERVALISHWFDLWTNKQRQEFLFAIFLRCTKSQLRFVQDWFSERMQVAKVDFSTVLPRFISLYIFSFLSPKDLCAAAQVSWPWKFLTEQDCLWMPKCVKFGWFLPYTPTDNEYGAWKRHYIACVSHLDWLTPREAAATYGTLNEPKTEDEELLERQREKCLRKRIWEKIALRKKELFKVRPPWVSGTCCSSVLKPRCQPRLSQTVRERVGLHEALEKQLVLTSLETLPKRSNISGSHSYPLLSKKNWHGVHKNDDRSSYALRPHFMLISSRIPAYEMVMESVKAGVVSVVYEHSVTLESLLYLIEKALDGQKAQSIGIFSDGDSREINLLQGYKIGVKNLLRPEVRDFWEKLGSYVATEEEGGHVDFFVPLGASEAGIEVLSQLSQLTGTFF
2	Q008S8-D2	418-777	360		TAPTGIATGSYQHILSDWLGSQWGKAPSSIYFCESKLQTWSSFTDFLEETLKTVRKQLYPFFKELQKSISGRMIGQFMFDTMGMTNILNNQDTAQALADGLMELSKEDSERNVVEDNSWDTKSRLSKNDLNFEALINLERILQKDSAEKRARVVRELLQSERKYVQILEIVRDVYVAPLKAALSSNRAILSAANIQIIFCDILQILSLNRQFLDNLRDRLQEWGPAHCVGEIVTKFGSQLNTYTNFFNNYPVILKTIEKCREMIPAFRTFLKRHDKTIVTKMLSLPELLLYPSRRFEEYLNLLYAVRLHTPAEHVDRGDLTTAIDQIKKYKGYIDQMKQNITMKDHLSDIQRIIWGCPTL
3	Q008S8-D3	778-904	127		SEVNRYLIRVQDVAQLHCCDEEISFSLRLYEHIHDLSLFLFNDALLVSSRGTSHTPFERTSKTTYQFIASVALHRLLIENIPDSKYVKNAFILQGPKYKWICATEIEDDKFLWLSVLRNAIKSSMEK

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.45

(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	3ky9B	0.30	4.21	0.112	0.339	model1_3ky9B.pdb.gz
2	7mpeA	0.29	8.63	0.066	0.458	model1_7mpeA.pdb.gz
3	5tsiA	0.29	8.60	0.038	0.457	model1_5tsiA.pdb.gz
4	6bcuA	0.29	9.06	0.028	0.469	model1_6bcuA.pdb.gz
5	5twvB	0.29	9.03	0.027	0.462	model1_5twvB.pdb.gz
6	2uvcG	0.28	7.81	0.052	0.414	model1_2uvcG.pdb.gz
7	7bdiB	0.28	8.37	0.042	0.429	model1_7bdiB.pdb.gz
8	6r9tA	0.28	8.59	0.032	0.441	model1_6r9tA.pdb.gz
9	5u71A	0.28	8.71	0.040	0.445	model1_5u71A.pdb.gz
10	7bc4B	0.28	8.00	0.048	0.416	model1_7bc4B.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:0098772	0.83	molecular function regulator
GO:0005085	0.77	guanyl-nucleotide exchange factor activity
GO:0005088	0.72	Ras guanyl-nucleotide exchange factor activity
GO:0003824	0.51	catalytic 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	0.87	biological regulation
GO:0009987	0.85	cellular process
GO:0050794	0.84	regulation of cellular process
GO:0048583	0.69	regulation of response to stimulus
GO:0009966	0.68	regulation of signal transduction
GO:1902531	0.66	regulation of intracellular signal transduction
GO:0065009	0.64	regulation of molecular function
GO:0048518	0.64	positive regulation of biological process
GO:0007165	0.64	signal transduction
GO:0050790	0.63	regulation of catalytic activity
GO:0048522	0.63	positive regulation of cellular process
GO:0051336	0.62	regulation of hydrolase activity
GO:0051056	0.62	regulation of small GTPase mediated signal transduction
GO:0008152	0.62	metabolic process
GO:0071704	0.61	organic substance metabolic process
GO:0044699	0.60	single-organism process
GO:0044093	0.60	positive regulation of molecular function
GO:0043087	0.60	regulation of GTPase activity
GO:0043085	0.59	positive regulation of catalytic activity
GO:0046578	0.58	regulation of Ras protein signal transduction
GO:0044238	0.58	primary metabolic process
GO:0035556	0.58	intracellular signal transduction
GO:0051345	0.57	positive regulation of hydrolase activity
GO:0044237	0.56	cellular metabolic process
GO:0043170	0.55	macromolecule metabolic process
GO:0007264	0.55	small GTPase mediated signal transduction
GO:0019538	0.53	protein metabolic process
GO:0007265	0.53	Ras protein signal transduction
GO:0044260	0.52	cellular macromolecule metabolic process
GO:0007266	0.52	Rho protein signal transduction

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:0044444	0.97	cytoplasmic part
GO:0005829	0.87	cytosol
GO:0043226	0.86	organelle
GO:0016020	0.86	membrane
GO:0043229	0.80	intracellular organelle
GO:0043227	0.80	membrane-bounded organelle
GO:0005737	0.75	cytoplasm
GO:0005886	0.71	plasma membrane
GO:0043231	0.66	intracellular membrane-bounded organelle
GO:0032991	0.59	macromolecular complex
GO:0043234	0.53	protein complex

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	2uv8G	0.275	8.13	0.037	0.410	2.3.1.86	NA
2	0.060	3ffzA	0.256	8.79	0.053	0.398	3.4.24.69	NA
3	0.060	2dqmA	0.233	7.92	0.040	0.342	3.4.11.2	NA
4	0.060	1t7lA	0.250	8.50	0.051	0.388	2.1.1.14	NA
5	0.060	1fa9A	0.236	8.48	0.025	0.365	2.4.1.1	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:

No Binding sites was predicted

Click to view	Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues

	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.