D-I-TASSER Q12929

D-I-TASSER results for Q12929

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

Summary of the Protein

Uniprot ID: Q12929
Protein Name: Epidermal growth factor receptor kinase substrate 8
Gene Name: EPS8

Input Sequence in FASTA format

>Q12929 (822 residues)
MNGHISNHPSSFGMYPSQMNGYGSSPTFSQTDREHGSKTSAKALYEQRKNYARDSVSSVS
DISQYRVEHLTTFVLDRKDAMITVDDGIRKLKLLDAKGKVWTQDMILQVDDRAVSLIDLE
SKNELENFPLNTIQHCQAVMHSCSYDSVLALVCKEPTQNKPDLHLFQCDEVKANLISEDI
ESAISDSKGGKQKRRPDALRMISNADPSIPPPPRAPAPAPPGTVTQVDVRSRVAAWSAWA
ADQGDFEKPRQYHEQEETPEMMAARIDRDVQILNHILDDIEFFITKLQKAAEAFSELSKR
KKNKKGKRKGPGEGVLTLRAKPPPPDEFLDCFQKFKHGFNLLAKLKSHIQNPSAADLVHF
LFTPLNMVVQATGGPELASSVLSPLLNKDTIDFLNYTVNGDERQLWMSLGGTWMKARAEW
PKEQFIPPYVPRFRNGWEPPMLNFMGATMEQDLYQLAESVANVAEHQRKQEIKRLSTEHS
SVSEYHPADGYAFSSNIYTRGSHLDQGEAAVAFKPTSNRHIDRNYEPLKTQPKKYAKSKY
DFVARNNSELSVLKDDILEILDDRKQWWKVRNASGDSGFVPNNILDIVRPPESGLGRADP
PYTHTIQKQRMEYGPRPADTPPAPSPPPTPAPVPVPLPPSTPAPVPVSKVPANITRQNSS
SSDSGGSIVRDSQRHKQLPVDRRKSQMEEVQDELIHRLTIGRSAAQKKFHVPRQNVPVIN
ITYDSTPEDVKTWLQSKGFNPVTVNSLGVLNGAQLFSLNKDELRTVCPEGARVYSQITVQ
KAALEDSSGSSELQEIMRRRQEKISAAASDSGVESFDEGSSH

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	Q12929-D1	1-822	822		MNGHISNHPSSFGMYPSQMNGYGSSPTFSQTDREHGSKTSAKALYEQRKNYARDSVSSVSDISQYRVEHLTTFVLDRKDAMITVDDGIRKLKLLDAKGKVWTQDMILQVDDRAVSLIDLESKNELENFPLNTIQHCQAVMHSCSYDSVLALVCKEPTQNKPDLHLFQCDEVKANLISEDIESAISDSKGGKQKRRPDALRMISNADPSIPPPPRAPAPAPPGTVTQVDVRSRVAAWSAWAADQGDFEKPRQYHEQEETPEMMAARIDRDVQILNHILDDIEFFITKLQKAAEAFSELSKRKKNKKGKRKGPGEGVLTLRAKPPPPDEFLDCFQKFKHGFNLLAKLKSHIQNPSAADLVHFLFTPLNMVVQATGGPELASSVLSPLLNKDTIDFLNYTVNGDERQLWMSLGGTWMKARAEWPKEQFIPPYVPRFRNGWEPPMLNFMGATMEQDLYQLAESVANVAEHQRKQEIKRLSTEHSSVSEYHPADGYAFSSNIYTRGSHLDQGEAAVAFKPTSNRHIDRNYEPLKTQPKKYAKSKYDFVARNNSELSVLKDDILEILDDRKQWWKVRNASGDSGFVPNNILDIVRPPESGLGRADPPYTHTIQKQRMEYGPRPADTPPAPSPPPTPAPVPVPLPPSTPAPVPVSKVPANITRQNSSSSDSGGSIVRDSQRHKQLPVDRRKSQMEEVQDELIHRLTIGRSAAQKKFHVPRQNVPVINITYDSTPEDVKTWLQSKGFNPVTVNSLGVLNGAQLFSLNKDELRTVCPEGARVYSQITVQKAALEDSSGSSELQEIMRRRQEKISAAASDSGVESFDEGSSH

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.4662

(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	6sytA	0.32	8.59	0.032	0.518	model1_6sytA.pdb.gz
2	6edoA	0.30	8.68	0.039	0.478	model1_6edoA.pdb.gz
3	6z2wE	0.30	8.36	0.030	0.464	model1_6z2wE.pdb.gz
4	3s4wA	0.29	8.30	0.037	0.454	model1_3s4wA.pdb.gz
5	5h64A	0.29	8.30	0.046	0.453	model1_5h64A.pdb.gz
6	7dxjA	0.29	8.43	0.029	0.453	model1_7dxjA.pdb.gz
7	5cskA	0.29	7.94	0.047	0.428	model1_5cskA.pdb.gz
8	6ar6A	0.29	8.59	0.034	0.456	model1_6ar6A.pdb.gz
9	6tnfB	0.28	8.04	0.044	0.439	model1_6tnfB.pdb.gz
10	4bedA	0.28	9.01	0.023	0.471	model1_4bedA.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:0008092	0.76	cytoskeletal protein binding
GO:0003779	0.74	actin binding
GO:0019899	0.54	enzyme 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:0065007	0.91	biological regulation
GO:0050794	0.88	regulation of cellular process
GO:0044699	0.81	single-organism process
GO:0051128	0.77	regulation of cellular component organization
GO:0009987	0.77	cellular process
GO:0044087	0.74	regulation of cellular component biogenesis
GO:0007165	0.73	signal transduction
GO:0044763	0.71	single-organism cellular process
GO:0016043	0.65	cellular component organization
GO:0065008	0.63	regulation of biological quality
GO:0035556	0.63	intracellular signal transduction
GO:0048523	0.61	negative regulation of cellular process
GO:0007264	0.61	small GTPase mediated signal transduction
GO:0033043	0.60	regulation of organelle organization
GO:0007265	0.60	Ras protein signal transduction
GO:0032956	0.59	regulation of actin cytoskeleton organization
GO:0043254	0.58	regulation of protein complex assembly
GO:0030833	0.57	regulation of actin filament polymerization
GO:0022607	0.56	cellular component assembly
GO:0051129	0.55	negative regulation of cellular component organization
GO:0007015	0.53	actin filament organization
GO:0051017	0.52	actin filament bundle assembly
GO:0051016	0.52	barbed-end actin filament capping
GO:0016601	0.52	Rac protein signal transduction
GO:0002376	0.51	immune system process
GO:0050793	0.50	regulation of developmental 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	0.98	cell part
GO:0044424	0.92	intracellular part
GO:0044444	0.76	cytoplasmic part
GO:0016020	0.70	membrane
GO:0005737	0.68	cytoplasm
GO:0044425	0.67	membrane part
GO:0044459	0.65	plasma membrane part
GO:0044422	0.63	organelle part
GO:0098590	0.60	plasma membrane region
GO:0032587	0.59	ruffle membrane
GO:0043226	0.57	organelle
GO:0043227	0.55	membrane-bounded organelle
GO:0042995	0.52	cell projection

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	3lxuX	0.232	8.52	0.038	0.366	3.4.14.10	NA
2	0.060	2vdcF	0.220	8.51	0.035	0.348	1.4.1.13	NA
3	0.060	2vkzG	0.206	8.68	0.020	0.325	2.3.1.38 3.1.2.14	NA
4	0.060	2pffD	0.226	8.88	0.013	0.370	2.3.1.86	NA
5	0.060	1z0hB	0.151	7.32	0.029	0.219	3.4.24.69	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	0.01	2p9i2	0.122	6.42	0.057	0.164	0.12	III	complex1.pdb.gz	559,575,576,577,578,579
2	0.01	1ynjC	0.250	8.81	0.035	0.407	0.20	SRN	complex2.pdb.gz	571,575,577
3	0.01	3mdjA	0.240	8.74	0.046	0.391	0.23	UUU	complex3.pdb.gz	277,280,436
4	0.01	1ynnC	0.244	8.50	0.050	0.384	0.22	RFP	complex4.pdb.gz	566,568,569,571,572
5	0.01	3cmvC	0.177	8.69	0.025	0.283	0.15	ANP	complex5.pdb.gz	554,555,556,575
6	0.01	3mdjA	0.240	8.74	0.046	0.391	0.16	BES	complex6.pdb.gz	557,558,559,575,579

	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.