D-I-TASSER O14908

D-I-TASSER results for O14908

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

Summary of the Protein

Uniprot ID: O14908
Protein Name: PDZ domain-containing protein GIPC1
Gene Name: GIPC1

Input Sequence in FASTA format

>O14908 (333 residues)
MPLGLGRRKKAPPLVENEEAEPGRGGLGVGEPGPLGGGGSGGPQMGLPPPPPALRPRLVF
HTQLAHGSPTGRIEGFTNVKELYGKIAEAFRLPTAEVMFCTLNTHKVDMDKLLGGQIGLE
DFIFAHVKGQRKEVEVFKSEDALGLTITDNGAGYAFIKRIKEGSVIDHIHLISVGDMIEA
INGQSLLGCRHYEVARLLKELPRGRTFTLKLTEPRKAFDMISQRSAGGRPGSGPQLGTGR
GTLRLRSRGPATVEDLPSAFEEKAIEKVDDLLESYMGIRDTELAATMVELGKDKRNPDEL
AEALDERLGDFAFPDEFVFDVWGAIGDAKVGRY

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	O14908-D1	1-333	333		MPLGLGRRKKAPPLVENEEAEPGRGGLGVGEPGPLGGGGSGGPQMGLPPPPPALRPRLVFHTQLAHGSPTGRIEGFTNVKELYGKIAEAFRLPTAEVMFCTLNTHKVDMDKLLGGQIGLEDFIFAHVKGQRKEVEVFKSEDALGLTITDNGAGYAFIKRIKEGSVIDHIHLISVGDMIEAINGQSLLGCRHYEVARLLKELPRGRTFTLKLTEPRKAFDMISQRSAGGRPGSGPQLGTGRGTLRLRSRGPATVEDLPSAFEEKAIEKVDDLLESYMGIRDTELAATMVELGKDKRNPDELAEALDERLGDFAFPDEFVFDVWGAIGDAKVGRY

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.5458

(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	5v6bA	0.77	1.29	0.889	0.787	model1_5v6bA.pdb.gz
2	7ky5A	0.44	6.60	0.033	0.724	model1_7ky5A.pdb.gz
3	6lknA1	0.42	6.63	0.047	0.703	model1_6lknA1.pdb.gz
4	2vdcA	0.42	6.92	0.031	0.733	model1_2vdcA.pdb.gz
5	7bspA	0.42	6.08	0.056	0.667	model1_7bspA.pdb.gz
6	6k7gA	0.42	6.17	0.048	0.667	model1_6k7gA.pdb.gz
7	6vdeA	0.41	6.68	0.058	0.700	model1_6vdeA.pdb.gz
8	3ba6A	0.40	6.56	0.067	0.661	model1_3ba6A.pdb.gz
9	6rohA3	0.40	6.58	0.057	0.670	model1_6rohA3.pdb.gz
10	3b8cA2	0.40	6.36	0.049	0.655	model1_3b8cA2.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:0005102	0.38	receptor binding
GO:0046983	0.33	protein dimerization activity
GO:0042802	0.33	identical protein binding
GO:0017022	0.33	myosin binding
GO:0042803	0.31	protein homodimerization activity
GO:0003779	0.30	actin 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:0044699	0.99	single-organism process
GO:0065007	0.84	biological regulation
GO:0050789	0.83	regulation of biological process
GO:0050794	0.82	regulation of cellular process
GO:0009987	0.71	cellular process
GO:0007165	0.71	signal transduction
GO:0044763	0.67	single-organism cellular process
GO:0048518	0.62	positive regulation of biological process
GO:0040011	0.62	locomotion
GO:0080090	0.61	regulation of primary metabolic process
GO:0048519	0.61	negative regulation of biological process
GO:0031323	0.61	regulation of cellular metabolic process
GO:0060255	0.60	regulation of macromolecule metabolic process
GO:0051179	0.60	localization
GO:0048523	0.60	negative regulation of cellular process
GO:0048522	0.60	positive regulation of cellular process
GO:0048583	0.59	regulation of response to stimulus
GO:0032268	0.58	regulation of cellular protein metabolic process
GO:0023051	0.58	regulation of signaling
GO:0010646	0.58	regulation of cell communication
GO:0008104	0.58	protein localization
GO:0009966	0.57	regulation of signal transduction
GO:1902578	0.56	single-organism localization
GO:0090092	0.54	regulation of transmembrane receptor protein serine/threonine kinase signaling pathway
GO:0051726	0.54	regulation of cell cycle
GO:0051641	0.54	cellular localization
GO:0048584	0.54	positive regulation of response to stimulus
GO:0031324	0.54	negative regulation of cellular metabolic process
GO:0006810	0.54	transport
GO:0032502	0.53	developmental process
GO:0032269	0.53	negative regulation of cellular protein metabolic process
GO:0044767	0.52	single-organism developmental process
GO:0044765	0.52	single-organism transport
GO:0009967	0.52	positive regulation of signal transduction
GO:0065008	0.51	regulation of biological quality
GO:0015031	0.51	protein transport
GO:0007186	0.51	G-protein coupled receptor signaling pathway
GO:0006811	0.51	ion transport
GO:0048167	0.50	regulation of synaptic plasticity
GO:0032940	0.50	secretion by cell
GO:0032467	0.50	positive regulation of cytokinesis
GO:0031329	0.50	regulation of cellular catabolic process
GO:0030511	0.50	positive regulation of transforming growth factor beta receptor signaling pathway
GO:0030162	0.50	regulation of proteolysis
GO:0016477	0.50	cell migration
GO:0007268	0.50	chemical synaptic transmission
GO:0006605	0.50	protein targeting

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	0.92	cell part
GO:0043227	0.92	membrane-bounded organelle
GO:0044424	0.85	intracellular part
GO:0031982	0.84	vesicle
GO:0031988	0.76	membrane-bounded vesicle
GO:0044444	0.72	cytoplasmic part
GO:0043229	0.68	intracellular organelle
GO:0016020	0.68	membrane
GO:0043231	0.67	intracellular membrane-bounded organelle
GO:0044421	0.60	extracellular region part
GO:0070062	0.58	extracellular exosome
GO:0005829	0.56	cytosol
GO:0016023	0.54	cytoplasmic, membrane-bounded vesicle
GO:0005737	0.53	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	1fo4A	0.378	6.79	0.071	0.658	1.17.1.4	NA
2	0.060	2hnhA	0.334	7.22	0.052	0.610	2.7.7.7	186,188
3	0.060	1kb0A	0.373	6.04	0.053	0.586	1.1.99.-	NA
4	0.060	1n63B	0.369	7.01	0.058	0.652	1.2.99.2	NA
5	0.060	1eulA	0.323	6.89	0.050	0.562	3.6.3.8	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	1ea0A	0.418	6.88	0.050	0.718	0.55	F3S	complex1.pdb.gz	148,149,150,151,152,187,189
2	0.01	3ar7A	0.356	7.08	0.072	0.658	0.59	PTY	complex2.pdb.gz	145,199,205
3	0.01	2voyK	0.064	2.31	0.031	0.069	0.73	III	complex3.pdb.gz	152,193,200
4	0.01	2agvA	0.369	6.45	0.052	0.613	0.64	PTY	complex4.pdb.gz	142,199,205

	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.