D-I-TASSER C9JTQ0

D-I-TASSER results for C9JTQ0

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

Summary of the Protein

Uniprot ID: C9JTQ0
Protein Name: Ankyrin repeat domain-containing protein 63
Gene Name: ANKRD63

Input Sequence in FASTA format

>C9JTQ0 (380 residues)
MLKPKDLCPRAGTRTFLEAMQAGKVHLARFVLDALDRSIIDCRAEQGRTPLMVAVGLPDP
ALRARFVRLLLEQGAAVNLRDERGRTALSLACERGHLDAVQLLVQFSGDPEAADSAGNSP
VMWAAACGHGAVLEFLVRSFRRLGLRLDRTNRAGLTALQLAAARGHGTCVQALTGPWGRA
AAAAAARGSNSDSPPGRPAPAASPEHRRPSPRRLPRPLLARFARAAGGHGGEAGSAGKNS
GRHRAQGSERPELGRSMSLALGAVTEEEAARLRAGALMALPNSPQSSGTGRWRSQEVLEG
APPTLAQAPIGLSPHPEGGPGSGRLGLRRRSTAPDIPSLVGEAPGPESGPELEANALSVS
VPGPNPWQAGTEAVVLRAQR

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	C9JTQ0-D1	1-215	215		MLKPKDLCPRAGTRTFLEAMQAGKVHLARFVLDALDRSIIDCRAEQGRTPLMVAVGLPDPALRARFVRLLLEQGAAVNLRDERGRTALSLACERGHLDAVQLLVQFSGDPEAADSAGNSPVMWAAACGHGAVLEFLVRSFRRLGLRLDRTNRAGLTALQLAAARGHGTCVQALTGPWGRAAAAAAARGSNSDSPPGRPAPAASPEHRRPSPRRLP
2	C9JTQ0-D2	216-380	165		RPLLARFARAAGGHGGEAGSAGKNSGRHRAQGSERPELGRSMSLALGAVTEEEAARLRAGALMALPNSPQSSGTGRWRSQEVLEGAPPTLAQAPIGLSPHPEGGPGSGRLGLRRRSTAPDIPSLVGEAPGPESGPELEANALSVSVPGPNPWQAGTEAVVLRAQR

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.564

(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	6aunA	0.49	4.26	0.138	0.584	model1_6aunA.pdb.gz
2	8c4aA	0.46	5.88	0.068	0.695	model1_8c4aA.pdb.gz
3	7xj0B	0.45	4.04	0.144	0.537	model1_7xj0B.pdb.gz
4	5le2A	0.45	2.68	0.199	0.497	model1_5le2A.pdb.gz
5	7ykrA	0.45	2.72	0.142	0.495	model1_7ykrA.pdb.gz
6	7lqyA	0.45	3.72	0.152	0.532	model1_7lqyA.pdb.gz
7	7uzuA	0.45	3.64	0.132	0.508	model1_7uzuA.pdb.gz
8	3j5pB	0.45	3.86	0.155	0.526	model1_3j5pB.pdb.gz
9	8fc7A	0.44	3.69	0.133	0.518	model1_8fc7A.pdb.gz
10	8h8xA	0.44	3.07	0.146	0.495	model1_8h8xA.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:0097159	0.59	organic cyclic compound binding
GO:1901363	0.58	heterocyclic compound binding
GO:0008092	0.54	cytoskeletal protein binding
GO:0003824	0.53	catalytic 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	0.85	biological regulation
GO:0009987	0.84	cellular process
GO:0050789	0.80	regulation of biological process
GO:0050794	0.79	regulation of cellular process
GO:0044699	0.79	single-organism process
GO:0044763	0.70	single-organism cellular process
GO:0016043	0.62	cellular component organization
GO:0051179	0.59	localization
GO:0006810	0.58	transport
GO:0007165	0.55	signal transduction
GO:1902578	0.53	single-organism localization
GO:0060255	0.52	regulation of macromolecule metabolic process
GO:0051649	0.52	establishment of localization in cell
GO:0051641	0.52	cellular localization
GO:0044765	0.52	single-organism transport
GO:0080090	0.51	regulation of primary metabolic process
GO:0071702	0.51	organic substance transport
GO:0048518	0.51	positive regulation of biological process
GO:0046907	0.51	intracellular transport
GO:0031323	0.51	regulation of cellular metabolic process
GO:0008104	0.51	protein localization
GO:1902580	0.50	single-organism cellular localization
GO:0044802	0.50	single-organism membrane organization
GO:0034613	0.50	cellular protein localization
GO:0006886	0.50	intracellular protein transport

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:0043226	0.90	organelle
GO:0043229	0.89	intracellular organelle
GO:0043231	0.85	intracellular membrane-bounded organelle
GO:0044444	0.76	cytoplasmic part
GO:0005737	0.76	cytoplasm
GO:0005634	0.76	nucleus
GO:0016020	0.75	membrane
GO:0005886	0.61	plasma membrane
GO:0044425	0.59	membrane part
GO:0044422	0.57	organelle part
GO:0032991	0.56	macromolecular complex
GO:0044459	0.55	plasma membrane part
GO:0043234	0.54	protein complex
GO:0005829	0.52	cytosol

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	2x38A	0.318	6.24	0.048	0.508	2.7.1.153	108
2	0.060	2x6fA	0.330	6.28	0.034	0.526	2.7.1.137 2.7.1.153 2.7.1.154	NA
3	0.060	1dceA	0.338	5.98	0.050	0.508	2.5.1.60	NA
4	0.060	3ffzA	0.344	6.89	0.021	0.574	3.4.24.69	NA
5	0.060	1dioA	0.324	6.38	0.058	0.518	4.2.1.28	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	0.10	3twsA	0.389	1.69	0.310	0.408	1.05	III	complex1.pdb.gz	18,21,23,48,53,57,63,81,83,85,90,116
2	0.08	2nyjA	0.413	3.53	0.190	0.484	0.84	ATP	complex2.pdb.gz	48,53,56,57,85,94
3	0.07	3twtB	0.388	1.63	0.303	0.405	1.25	III	complex3.pdb.gz	46,48,53,56,85,90,93,94,96,114,116,118,123,129
4	0.04	1bi81	0.381	1.91	0.312	0.405	1.10	III	complex4.pdb.gz	26,44,48,53,54,57,81,82,90,93,94,96,98
5	0.04	2bkk1	0.387	1.73	0.277	0.408	1.28	III	complex5.pdb.gz	14,18,46,48,52,56,57,81,82,83,85,90,93,94,123
6	0.04	1svx0	0.393	1.71	0.287	0.413	1.02	III	complex6.pdb.gz	46,48,53,56,57,81,94,96
7	0.03	2dvw0	0.422	2.54	0.208	0.455	0.90	III	complex7.pdb.gz	21,48,56,57,63,82,83,85,90,93,94,116,123,126,127,153,160,164,166

	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.