D-I-TASSER Q6ZUJ8

D-I-TASSER results for Q6ZUJ8

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

Summary of the Protein

Uniprot ID: Q6ZUJ8
Protein Name: Phosphoinositide 3-kinase adapter protein 1
Gene Name: PIK3AP1

Input Sequence in FASTA format

>Q6ZUJ8 (805 residues)
MAASGVPRGCDILIVYSPDAEEWCQYLQTLFLSSRQVRSQKILTHRLGPEASFSAEDLSL
FLSTRCVVVLLSAELVQHFHKPALLPLLQRAFHPPHRVVRLLCGVRDSEEFLDFFPDWAH
WQELTCDDEPETYVAAVKKAISEDSGCDSVTDTEPEDEKVVSYSKQQNLPTVTSPGNLMV
VQPDRIRCGAETTVYVIVRCKLDDRVATEAEFSPEDSPSVRMEAKVENEYTISVKAPNLS
SGNVSLKIYSGDLVVCETVISYYTDMEEIGNLLSNAANPVEFMCQAFKIVPYNTETLDKL
LTESLKNNIPASGLHLFGINQLEEEDMMTNQRDEELPTLLHFAAKYGLKNLTALLLTCPG
ALQAYSVANKHGHYPNTIAEKHGFRDLRQFIDEYVETVDMLKSHIKEELMHGEEADAVYE
SMAHLSTDLLMKCSLNPGCDEDLYESMAAFVPAATEDLYVEMLQASTSNPIPGDGFSRAT
KDSMIRKFLEGNSMGMTNLERDQCHLGQEEDVYHTVDDDEAFSVDLASRPPVPVPRPETT
APGAHQLPDNEPYIFKVFAEKSQERPGNFYVSSESIRKGPPVRPWRDRPQSSIYDPFAGM
KTPGQRQLITLQEQVKLGIVNVDEAVLHFKEWQLNQKKRSESFRFQQENLKRLRDSITRR
QREKQKSGKQTDLEITVPIRHSQHLPAKVEFGVYESGPRKSVIPPRTELRRGDWKTDSTS
STASSTSNRSSTRSLLSVSSGMEGDNEDNEVPEVTRSRSPGPPQVDGTPTMSLERPPRVP
PRAASQRPPTRETFHPPPPVPPRGR

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	Q6ZUJ8-D1	1-163	163		MAASGVPRGCDILIVYSPDAEEWCQYLQTLFLSSRQVRSQKILTHRLGPEASFSAEDLSLFLSTRCVVVLLSAELVQHFHKPALLPLLQRAFHPPHRVVRLLCGVRDSEEFLDFFPDWAHWQELTCDDEPETYVAAVKKAISEDSGCDSVTDTEPEDEKVVSY
2	Q6ZUJ8-D2	164-275	112		SKQQNLPTVTSPGNLMVVQPDRIRCGAETTVYVIVRCKLDDRVATEAEFSPEDSPSVRMEAKVENEYTISVKAPNLSSGNVSLKIYSGDLVVCETVISYYTDMEEIGNLLSN
3	Q6ZUJ8-D3	276-492,762-805	261		AANPVEFMCQAFKIVPYNTETLDKLLTESLKNNIPASGLHLFGINQLEEEDMMTNQRDEELPTLLHFAAKYGLKNLTALLLTCPGALQAYSVANKHGHYPNTIAEKHGFRDLRQFIDEYVETVDMLKSHIKEELMHGEEADAVYESMAHLSTDLLMKCSLNPGCDEDLYESMAAFVPAATEDLYVEMLQASTSNPIPGDGFSRATKDSMIRKFLEGNPPQVDGTPTMSLERPPRVPPRAASQRPPTRETFHPPPPVPPRGR
4	Q6ZUJ8-D4	493-761	269		SMGMTNLERDQCHLGQEEDVYHTVDDDEAFSVDLASRPPVPVPRPETTAPGAHQLPDNEPYIFKVFAEKSQERPGNFYVSSESIRKGPPVRPWRDRPQSSIYDPFAGMKTPGQRQLITLQEQVKLGIVNVDEAVLHFKEWQLNQKKRSESFRFQQENLKRLRDSITRRQREKQKSGKQTDLEITVPIRHSQHLPAKVEFGVYESGPRKSVIPPRTELRRGDWKTDSTSSTASSTSNRSSTRSLLSVSSGMEGDNEDNEVPEVTRSRSPG

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	5cskA	0.36	8.44	0.034	0.559	model1_5cskA.pdb.gz
2	5u1sA	0.35	8.65	0.039	0.575	model1_5u1sA.pdb.gz
3	6g2dC	0.34	8.53	0.044	0.545	model1_6g2dC.pdb.gz
4	6um1A	0.34	8.54	0.037	0.537	model1_6um1A.pdb.gz
5	4m5dA	0.33	8.23	0.033	0.511	model1_4m5dA.pdb.gz
6	7cpxA	0.33	8.56	0.053	0.519	model1_7cpxA.pdb.gz
7	6z2wE	0.32	8.09	0.053	0.487	model1_6z2wE.pdb.gz
8	5yz0A	0.31	8.56	0.027	0.501	model1_5yz0A.pdb.gz
9	5fvmA	0.31	8.52	0.031	0.497	model1_5fvmA.pdb.gz
10	4bujB	0.31	8.69	0.033	0.502	model1_4bujB.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:0036312	0.88	phosphatidylinositol 3-kinase regulatory subunit 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:0050794	1.00	regulation of cellular process
GO:0007165	0.97	signal transduction
GO:0048518	0.82	positive regulation of biological process
GO:0048522	0.81	positive regulation of cellular process
GO:0048583	0.80	regulation of response to stimulus
GO:0048584	0.79	positive regulation of response to stimulus
GO:0009966	0.79	regulation of signal transduction
GO:1902533	0.78	positive regulation of intracellular signal transduction
GO:0002682	0.76	regulation of immune system process
GO:0050776	0.73	regulation of immune response
GO:0002376	0.73	immune system process
GO:0050778	0.72	positive regulation of immune response
GO:0002764	0.72	immune response-regulating signaling pathway
GO:0014068	0.71	positive regulation of phosphatidylinositol 3-kinase signaling
GO:0002224	0.71	toll-like receptor signaling pathway
GO:0050727	0.70	regulation of inflammatory response
GO:0034162	0.70	toll-like receptor 9 signaling pathway
GO:0034154	0.70	toll-like receptor 7 signaling pathway
GO:0034142	0.70	toll-like receptor 4 signaling pathway
GO:0034134	0.70	toll-like receptor 2 signaling pathway
GO:0009987	0.58	cellular process
GO:0031323	0.55	regulation of cellular metabolic process
GO:0019220	0.52	regulation of phosphate metabolic process
GO:0042325	0.51	regulation of 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:0044424	1.00	intracellular part
GO:0044444	0.84	cytoplasmic part
GO:0005829	0.81	cytosol
GO:0016020	0.80	membrane
GO:0005886	0.58	plasma membrane
GO:0005737	0.52	cytoplasm

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	3eqlD	0.262	9.02	0.026	0.441	2.7.7.6	NA
2	0.060	1ug9A	0.232	8.39	0.049	0.365	3.2.1.70	NA
3	0.060	2vumA	0.254	8.62	0.023	0.407	2.7.7.6	NA
4	0.060	2e9bA	0.283	8.65	0.044	0.461	3.2.1.41	NA
5	0.060	1bf2A	0.283	7.98	0.036	0.426	3.2.1.68	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	3cmvA	0.255	8.60	0.031	0.412	0.21	ANP	complex1.pdb.gz	335,336,350
2	0.01	1xmvA	0.138	7.20	0.043	0.200	0.13	ADP	complex2.pdb.gz	342,343,344,360
3	0.01	3cmvD	0.283	8.71	0.034	0.462	0.22	ANP	complex3.pdb.gz	301,302,304,305,350,363
4	0.01	3cmvB	0.248	8.87	0.034	0.409	0.19	ANP	complex4.pdb.gz	338,340,341,344
5	0.01	3cmvA	0.255	8.60	0.031	0.412	0.20	ANP	complex5.pdb.gz	336,337,360

	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.