D-I-TASSER Q8TBC3

D-I-TASSER results for Q8TBC3

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

Summary of the Protein

Uniprot ID: Q8TBC3
Protein Name: SH3KBP1-binding protein 1
Gene Name: SHKBP1

Input Sequence in FASTA format

>Q8TBC3 (707 residues)
MAAAATAAEGVPSRGPPGEVIHLNVGGKRFSTSRQTLTWIPDSFFSSLLSGRISTLKDET
GAIFIDRDPTVFAPILNFLRTKELDPRGVHGSSLLHEAQFYGLTPLVRRLQLREELDRSS
CGNVLFNGYLPPPVFPVKRRNRHSLVGPQQLGGRPAPVRRSNTMPPNLGNAGLLGRMLDE
KTPPSPSGQPEEPGMVRLVCGHHNWIAVAYTQFLVCYRLKEASGWQLVFSSPRLDWPIER
LALTARVHGGALGEHDKMVAAATGSEILLWALQAEGGGSEIGVFHLGVPVEALFFVGNQL
IATSHTGRIGVWNAVTKHWQVQEVQPITSYDAAGSFLLLGCNNGSIYYVDVQKFPLRMKD
NDLLVSELYRDPAEDGVTALSVYLTPKTSDSGNWIEIAYGTSSGGVRVIVQHPETVGSGP
QLFQTFTVHRSPVTKIMLSEKHLISVCADNNHVRTWSVTRFRGMISTQPGSTPLASFKIL
ALESADGHGGCSAGNDIGPYGERDDQQVFIQKVVPSASQLFVRLSSTGQRVCSVRSVDGS
PTTAFTVLECEGSRRLGSRPRRYLLTGQANGSLAMWDLTTAMDGLGQAPAGGLTEQELME
QLEHCELAPPAPSAPSWGCLPSPSPRISLTSLHSASSNTSLSGHRGSPSPPQAEARRRGG
GSFVERCQELVRSGPDLRRPPTPAPWPSSGLGTPLTPPKMKLNETSF

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	Q8TBC3-D1	1-330	330		MAAAATAAEGVPSRGPPGEVIHLNVGGKRFSTSRQTLTWIPDSFFSSLLSGRISTLKDETGAIFIDRDPTVFAPILNFLRTKELDPRGVHGSSLLHEAQFYGLTPLVRRLQLREELDRSSCGNVLFNGYLPPPVFPVKRRNRHSLVGPQQLGGRPAPVRRSNTMPPNLGNAGLLGRMLDEKTPPSPSGQPEEPGMVRLVCGHHNWIAVAYTQFLVCYRLKEASGWQLVFSSPRLDWPIERLALTARVHGGALGEHDKMVAAATGSEILLWALQAEGGGSEIGVFHLGVPVEALFFVGNQLIATSHTGRIGVWNAVTKHWQVQEVQPITSY
2	Q8TBC3-D2	331-430	100		DAAGSFLLLGCNNGSIYYVDVQKFPLRMKDNDLLVSELYRDPAEDGVTALSVYLTPKTSDSGNWIEIAYGTSSGGVRVIVQHPETVGSGPQLFQTFTVHR
3	Q8TBC3-D3	431-707	277		SPVTKIMLSEKHLISVCADNNHVRTWSVTRFRGMISTQPGSTPLASFKILALESADGHGGCSAGNDIGPYGERDDQQVFIQKVVPSASQLFVRLSSTGQRVCSVRSVDGSPTTAFTVLECEGSRRLGSRPRRYLLTGQANGSLAMWDLTTAMDGLGQAPAGGLTEQELMEQLEHCELAPPAPSAPSWGCLPSPSPRISLTSLHSASSNTSLSGHRGSPSPPQAEARRRGGGSFVERCQELVRSGPDLRRPPTPAPWPSSGLGTPLTPPKMKLNETSF

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.44

(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	6um1A	0.40	7.94	0.041	0.627	model1_6um1A.pdb.gz
2	6xjaP	0.38	8.28	0.045	0.614	model1_6xjaP.pdb.gz
3	7boys	0.37	7.16	0.036	0.532	model1_7boys.pdb.gz
4	6uebA	0.37	7.91	0.047	0.573	model1_6uebA.pdb.gz
5	3cmuA	0.36	8.76	0.044	0.618	model1_3cmuA.pdb.gz
6	5u1sA	0.36	8.22	0.048	0.579	model1_5u1sA.pdb.gz
7	5a5uB	0.36	6.69	0.046	0.498	model1_5a5uB.pdb.gz
8	4xqkA	0.36	8.55	0.039	0.591	model1_4xqkA.pdb.gz
9	4fhmB	0.36	7.11	0.069	0.518	model1_4fhmB.pdb.gz
10	6zu9p	0.35	6.66	0.039	0.489	model1_6zu9p.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:0005215	0.64	transporter activity
GO:0015267	0.63	channel activity
GO:0015075	0.63	ion transmembrane transporter activity
GO:0022843	0.62	voltage-gated cation channel activity
GO:0005249	0.61	voltage-gated potassium channel activity
GO:0005251	0.58	delayed rectifier potassium channel 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	0.94	biological regulation
GO:0050789	0.92	regulation of biological process
GO:0050794	0.90	regulation of cellular process
GO:0010646	0.79	regulation of cell communication
GO:0048583	0.78	regulation of response to stimulus
GO:0048518	0.78	positive regulation of biological process
GO:0023051	0.78	regulation of signaling
GO:0048522	0.77	positive regulation of cellular process
GO:0009966	0.77	regulation of signal transduction
GO:0048584	0.72	positive regulation of response to stimulus
GO:0045742	0.71	positive regulation of epidermal growth factor receptor signaling pathway

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	0.98	intracellular part
GO:0044446	0.82	intracellular organelle part
GO:0032991	0.76	macromolecular complex
GO:0043226	0.70	organelle
GO:0044444	0.69	cytoplasmic part
GO:0044428	0.66	nuclear part
GO:0043227	0.66	membrane-bounded organelle
GO:0043234	0.65	protein complex
GO:0043229	0.65	intracellular organelle
GO:0043231	0.61	intracellular membrane-bounded organelle
GO:0005634	0.56	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	1eurA	0.226	5.94	0.045	0.297	3.2.1.18	NA
2	0.060	1lrwA	0.296	6.09	0.044	0.393	1.1.99.8	NA
3	0.060	1aomB	0.295	6.29	0.053	0.400	1.7.99.1 1.7.2.1	NA
4	0.060	1qksB	0.296	6.33	0.053	0.402	1.7.2.1	63
5	0.060	1hn0A	0.313	8.17	0.035	0.502	4.2.2.20	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	3cmxA	0.316	8.46	0.050	0.520	0.11	ALF	complex1.pdb.gz	25,28,29
2	0.01	2vz9B	0.335	8.30	0.035	0.537	0.10	NAP	complex2.pdb.gz	47,65,66,75
3	0.01	3cmvC	0.283	8.52	0.025	0.472	0.26	ANP	complex3.pdb.gz	54,55,56,57
4	0.01	3cmvB	0.290	8.68	0.037	0.491	0.26	ANP	complex4.pdb.gz	46,51,52,53,54
5	0.01	1xmsA	0.143	6.34	0.036	0.197	0.15	ANP	complex5.pdb.gz	47,48,50,51,52,53,54
6	0.01	1n03A	0.166	6.59	0.058	0.233	0.13	ADP	complex6.pdb.gz	26,28,29
7	0.01	1shy1	0.313	5.78	0.059	0.403	0.22	III	complex7.pdb.gz	25,26,74,75,103
8	0.01	3cmvG	0.298	8.38	0.028	0.487	0.13	ANP	complex8.pdb.gz	51,102,105
9	0.01	3cmvC	0.283	8.52	0.025	0.472	0.14	ANP	complex9.pdb.gz	27,28,29,30

	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.