D-I-TASSER Q7Z2X4

D-I-TASSER results for Q7Z2X4

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

Summary of the Protein

Uniprot ID: Q7Z2X4
Protein Name: PTB-containing, cubilin and LRP1-interacting protein
Gene Name: PID1

Input Sequence in FASTA format

>Q7Z2X4 (250 residues)
MFSLPLSLPLCEDTAFLPSKCCSSHKTIKQARTLIMIFLASGTHFQTMLKSKLNVLTLKK
EPLPAVIFHEPEAIELCTTTPLMKTRTHSGCKVTYLGKVSTTGMQFLSGCTEKPVIELWK
KHTLAREDVFPANALLEIRPFQVWLHHLDHKGEATVHMDTFQVARIAYCTADHNVSPNIF
AWVYREINDDLSYQMDCHAVECESKLEAKKLAHAMMEAFRKTFHSMKSDGRIHSNSSSEE
VSQELESDDG

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	Q7Z2X4-D1	1-250	250		MFSLPLSLPLCEDTAFLPSKCCSSHKTIKQARTLIMIFLASGTHFQTMLKSKLNVLTLKKEPLPAVIFHEPEAIELCTTTPLMKTRTHSGCKVTYLGKVSTTGMQFLSGCTEKPVIELWKKHTLAREDVFPANALLEIRPFQVWLHHLDHKGEATVHMDTFQVARIAYCTADHNVSPNIFAWVYREINDDLSYQMDCHAVECESKLEAKKLAHAMMEAFRKTFHSMKSDGRIHSNSSSEEVSQELESDDG

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.618

(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	6ituA	0.50	2.56	0.146	0.556	model1_6ituA.pdb.gz
2	3so6A	0.50	2.18	0.175	0.540	model1_3so6A.pdb.gz
3	1ntvA	0.49	2.92	0.117	0.556	model1_1ntvA.pdb.gz
4	1m7eA	0.48	2.87	0.125	0.552	model1_1m7eA.pdb.gz
5	3suzA	0.48	3.73	0.151	0.576	model1_3suzA.pdb.gz
6	3dxdA	0.48	2.10	0.145	0.516	model1_3dxdA.pdb.gz
7	1wj1A	0.46	3.11	0.148	0.536	model1_1wj1A.pdb.gz
8	2m38A	0.45	2.35	0.128	0.504	model1_2m38A.pdb.gz
9	3d8dA	0.45	2.44	0.194	0.504	model1_3d8dA.pdb.gz
10	2yszA	0.44	2.82	0.116	0.496	model1_2yszA.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:0035615	0.13	clathrin adaptor activity
GO:0035612	0.13	AP-2 adaptor complex binding
GO:0005546	0.13	phosphatidylinositol-4,5-bisphosphate binding
GO:0001540	0.13	beta-amyloid 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:0007155	0.99	cell adhesion
GO:0045944	0.86	positive regulation of transcription from RNA polymerase II promoter
GO:0001933	0.86	negative regulation of protein phosphorylation
GO:0032502	0.81	developmental process
GO:2001274	0.67	negative regulation of glucose import in response to insulin stimulus
GO:2001171	0.67	positive regulation of ATP biosynthetic process
GO:2001170	0.67	negative regulation of ATP biosynthetic process
GO:2000379	0.67	positive regulation of reactive oxygen species metabolic process
GO:2000045	0.67	regulation of G1/S transition of mitotic cell cycle
GO:0090298	0.67	negative regulation of mitochondrial DNA replication
GO:0090005	0.67	negative regulation of establishment of protein localization to plasma membrane
GO:0071398	0.67	cellular response to fatty acid
GO:0071356	0.67	cellular response to tumor necrosis factor
GO:0071354	0.67	cellular response to interleukin-6
GO:0070584	0.67	mitochondrion morphogenesis
GO:0070346	0.67	positive regulation of fat cell proliferation
GO:0051881	0.67	regulation of mitochondrial membrane potential
GO:0046627	0.67	negative regulation of insulin 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:0005654	1.00	nucleoplasm
GO:0031225	0.99	anchored component of membrane
GO:0005737	0.78	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	1bakA	0.347	3.35	0.092	0.432	2.7.11.15	90,144
2	0.060	1p6sA	0.322	3.24	0.095	0.396	2.7.11.1	NA
3	0.060	2nq5A	0.336	5.68	0.050	0.552	2.1.1.14	182
4	0.060	1ynnD	0.239	6.66	0.037	0.456	2.7.7.6	NA
5	0.060	2hg4C	0.347	5.99	0.026	0.588	2.3.1.94	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	2l1cA	0.433	3.57	0.133	0.536	0.16	III	complex1.pdb.gz	185,195,215
2	0.01	2jkqA	0.234	5.63	0.086	0.384	0.30	VG8	complex2.pdb.gz	134,136,137,144
3	0.01	3bz3A	0.243	6.46	0.011	0.428	0.24	YAM	complex3.pdb.gz	96,136,143,145,160
4	0.01	2j0lA	0.244	5.67	0.049	0.392	0.20	ANP	complex4.pdb.gz	137,138,172,198
5	0.01	2ijmA	0.234	5.71	0.075	0.388	0.29	ATP	complex5.pdb.gz	103,104,105,166,168,186,187
6	0.01	3pvuA	0.369	3.45	0.075	0.448	0.19	QRW	complex6.pdb.gz	97,133,204,211
7	0.01	3krwA	0.366	3.66	0.074	0.448	0.21	BA1	complex7.pdb.gz	185,186,187
8	0.01	3pvwA	0.369	3.45	0.075	0.448	0.13	QRX	complex8.pdb.gz	96,97,98,99,118

	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.