D-I-TASSER P98082

D-I-TASSER results for P98082

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

Summary of the Protein

Uniprot ID: P98082
Protein Name: Disabled homolog 2
Gene Name: DAB2

Input Sequence in FASTA format

>P98082 (770 residues)
MSNEVETSATNGQPDQQAAPKAPSKKEKKKGPEKTDEYLLARFKGDGVKYKAKLIGIDDV
PDARGDKMSQDSMMKLKGMAAAGRSQGQHKQRIWVNISLSGIKIIDEKTGVIEHEHPVNK
ISFIARDVTDNRAFGYVCGGEGQHQFFAIKTGQQAEPLVVDLKDLFQVIYNVKKKEEEKK
KIEEASKAVENGSEALMILDDQTNKLKSGVDQMDLFGDMSTPPDLNSPTESKDILLVDLN
SEIDTNQNSLRENPFLTNGITSCSLPRPTPQASFLPENAFSANLNFFPTPNPDPFRDDPF
TQPDQSTPSSFDSLKSPDQKKENSSSSSTPLSNGPLNGDVDYFGQQFDQISNRTGKQEAQ
AGPWPFSSSQTQPAVRTQNGVSEREQNGFSVKSSPNPFVGSPPKGLSIQNGVKQDLESSV
QSSPHDSIAIIPPPQSTKPGRGRRTAKSSANDLLASDIFAPPVSEPSGQASPTGQPTALQ
PNPLDLFKTSAPAPVGPLVGLGGVTVTLPQAGPWNTASLVFNQSPSMAPGAMMGGQPSGF
SQPVIFGTSPAVSGWNQPSPFAASTPPPVPVVWGPSASVAPNAWSTTSPLGNPFQSNIFP
APAVSTQPPSMHSSLLVTPPQPPPRAGPPKDISSDAFTALDPLGDKEIKDVKEMFKDFQL
RQPPAVPARKGEQTSSGTLSAFASYFNSKVGIPQENADHDDFDANQLLNKINEPPKPAPR
QVSLPVTKSTDNAFENPFFKDSFGSSQASVASSQPVSSEMYRDPFGNPFA

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	P98082-D1	1-770	770		MSNEVETSATNGQPDQQAAPKAPSKKEKKKGPEKTDEYLLARFKGDGVKYKAKLIGIDDVPDARGDKMSQDSMMKLKGMAAAGRSQGQHKQRIWVNISLSGIKIIDEKTGVIEHEHPVNKISFIARDVTDNRAFGYVCGGEGQHQFFAIKTGQQAEPLVVDLKDLFQVIYNVKKKEEEKKKIEEASKAVENGSEALMILDDQTNKLKSGVDQMDLFGDMSTPPDLNSPTESKDILLVDLNSEIDTNQNSLRENPFLTNGITSCSLPRPTPQASFLPENAFSANLNFFPTPNPDPFRDDPFTQPDQSTPSSFDSLKSPDQKKENSSSSSTPLSNGPLNGDVDYFGQQFDQISNRTGKQEAQAGPWPFSSSQTQPAVRTQNGVSEREQNGFSVKSSPNPFVGSPPKGLSIQNGVKQDLESSVQSSPHDSIAIIPPPQSTKPGRGRRTAKSSANDLLASDIFAPPVSEPSGQASPTGQPTALQPNPLDLFKTSAPAPVGPLVGLGGVTVTLPQAGPWNTASLVFNQSPSMAPGAMMGGQPSGFSQPVIFGTSPAVSGWNQPSPFAASTPPPVPVVWGPSASVAPNAWSTTSPLGNPFQSNIFPAPAVSTQPPSMHSSLLVTPPQPPPRAGPPKDISSDAFTALDPLGDKEIKDVKEMFKDFQLRQPPAVPARKGEQTSSGTLSAFASYFNSKVGIPQENADHDDFDANQLLNKINEPPKPAPRQVSLPVTKSTDNAFENPFFKDSFGSSQASVASSQPVSSEMYRDPFGNPFA

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.3549

(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	5ak1A	0.92	2.71	0.101	0.981	model1_5ak1A.pdb.gz
2	2y8kA	0.53	2.91	0.115	0.574	model1_2y8kA.pdb.gz
3	4v2xA	0.39	6.17	0.056	0.514	model1_4v2xA.pdb.gz
4	5e0cA	0.39	6.20	0.054	0.514	model1_5e0cA.pdb.gz
5	6hqvA	0.38	8.25	0.040	0.600	model1_6hqvA.pdb.gz
6	3og2A	0.38	6.65	0.028	0.513	model1_3og2A.pdb.gz
7	1tg7A	0.38	6.64	0.031	0.512	model1_1tg7A.pdb.gz
8	3czjA	0.37	6.64	0.042	0.508	model1_3czjA.pdb.gz
9	6sd0A	0.37	6.75	0.043	0.509	model1_6sd0A.pdb.gz
10	6hzeA	0.37	7.08	0.042	0.523	model1_6hzeA.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:0030276	0.54	clathrin 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	0.92	biological regulation
GO:0050789	0.91	regulation of biological process
GO:0050794	0.90	regulation of cellular process
GO:0044699	0.88	single-organism process
GO:0009987	0.87	cellular process
GO:0048583	0.72	regulation of response to stimulus
GO:0019222	0.71	regulation of metabolic process
GO:0009966	0.71	regulation of signal transduction
GO:0080090	0.70	regulation of primary metabolic process
GO:0044763	0.70	single-organism cellular process
GO:0060255	0.69	regulation of macromolecule metabolic process
GO:0031323	0.69	regulation of cellular metabolic process
GO:0048518	0.68	positive regulation of biological process
GO:0048522	0.66	positive regulation of cellular process
GO:0031326	0.64	regulation of cellular biosynthetic process
GO:0051128	0.62	regulation of cellular component organization
GO:0032879	0.58	regulation of localization
GO:0032502	0.58	developmental process
GO:0051130	0.57	positive regulation of cellular component organization
GO:0048523	0.57	negative regulation of cellular process
GO:0060627	0.56	regulation of vesicle-mediated transport
GO:0051239	0.56	regulation of multicellular organismal process
GO:2000026	0.55	regulation of multicellular organismal development
GO:0045807	0.55	positive regulation of endocytosis
GO:0045595	0.55	regulation of cell differentiation
GO:0044767	0.55	single-organism developmental process
GO:0051240	0.54	positive regulation of multicellular organismal process
GO:0051179	0.54	localization
GO:0048856	0.54	anatomical structure development
GO:0010720	0.54	positive regulation of cell development
GO:0009968	0.53	negative regulation of signal transduction
GO:0009893	0.53	positive regulation of metabolic process
GO:0032268	0.52	regulation of cellular protein metabolic process
GO:0007165	0.52	signal transduction
GO:0065009	0.51	regulation of molecular function
GO:0051171	0.51	regulation of nitrogen compound metabolic process
GO:0031399	0.51	regulation of protein modification process
GO:0031325	0.51	positive regulation of cellular metabolic process
GO:0022603	0.51	regulation of anatomical structure morphogenesis
GO:0010556	0.51	regulation of macromolecule biosynthetic process
GO:0051234	0.50	establishment of localization
GO:0051129	0.50	negative regulation of cellular component organization
GO:0010769	0.50	regulation of cell morphogenesis involved in differentiation
GO:0006355	0.50	regulation of transcription, DNA-templated
GO:0001932	0.50	regulation of protein phosphorylation

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	1.00	cell part
GO:0044424	0.99	intracellular part
GO:0044422	0.85	organelle part
GO:0044446	0.84	intracellular organelle part
GO:0044444	0.80	cytoplasmic part
GO:0043226	0.78	organelle
GO:0043229	0.77	intracellular organelle
GO:0016020	0.77	membrane
GO:0043227	0.75	membrane-bounded organelle
GO:0043231	0.74	intracellular membrane-bounded organelle
GO:0005886	0.70	plasma membrane
GO:0044428	0.60	nuclear part
GO:0043232	0.60	intracellular non-membrane-bounded organelle
GO:0005730	0.57	nucleolus
GO:0044425	0.52	membrane 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	0.060	1yq2A	0.370	6.93	0.037	0.513	3.2.1.23	NA
2	0.060	2nq5A	0.317	7.18	0.032	0.449	2.1.1.14	NA
3	0.060	3ecqB	0.337	7.26	0.044	0.483	3.2.1.97	NA
4	0.060	1b0pA	0.330	8.39	0.052	0.529	1.2.7.1	NA
5	0.060	1px8A	0.317	5.70	0.045	0.404	3.2.1.37	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.