D-I-TASSER Q9Y2T1

D-I-TASSER results for Q9Y2T1

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

Summary of the Protein

Uniprot ID: Q9Y2T1
Protein Name: Axin-2
Gene Name: AXIN2

Input Sequence in FASTA format

>Q9Y2T1 (843 residues)
MSSAMLVTCLPDPSSSFREDAPRPPVPGEEGETPPCQPGVGKGQVTKPMSVSSNTRRNED
GLGEPEGRASPDSPLTRWTKSLHSLLGDQDGAYLFRTFLEREKCVDTLDFWFACNGFRQM
NLKDTKTLRVAKAIYKRYIENNSIVSKQLKPATKTYIRDGIKKQQIDSIMFDQAQTEIQS
VMEENAYQMFLTSDIYLEYVRSGGENTAYMSNGGLGSLKVVCGYLPTLNEEEEWTCADFK
CKLSPTVVGLSSKTLRATASVRSTETVDSGYRSFKRSDPVNPYHIGSGYVFAPATSANDS
EISSDALTDDSMSMTDSSVDGIPPYRVGSKKQLQREMHRSVKANGQVSLPHFPRTHRLPK
EMTPVEPATFAAELISRLEKLKLELESRHSLEERLQQIREDEEREGSELTLNSREGAPTQ
HPLSLLPSGSYEEDPQTILDDHLSRVLKTPGCQSPGVGRYSPRSRSPDHHHHHHSQYHSL
LPPGGKLPPAAASPGACPLLGGKGFVTKQTTKHVHHHYIHHHAVPKTKEEIEAEATQRVH
CFCPGGSEYYCYSKCKSHSKAPETMPSEQFGGSRGSTLPKRNGKGTEPGLALPAREGGAP
GGAGALQLPREEGDRSQDVWQWMLESERQSKPKPHSAQSTKKAYPLESARSSPGERASRH
HLWGGNSGHPRTTPRAHLFTQDPAMPPLTPPNTLAQLEEACRRLAEVSKPPKQRCCVASQ
QRDRNHSATVQTGATPFSNPSLAPEDHKEPKKLAGVHALQASELVVTYFFCGEEIPYRRM
LKAQSLTLGHFKEQLSKKGNYRYYFKKASDEFACGAVFEEIWEDETVLPMYEGRILGKVE
RID

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	Q9Y2T1-D1	1-355	355		MSSAMLVTCLPDPSSSFREDAPRPPVPGEEGETPPCQPGVGKGQVTKPMSVSSNTRRNEDGLGEPEGRASPDSPLTRWTKSLHSLLGDQDGAYLFRTFLEREKCVDTLDFWFACNGFRQMNLKDTKTLRVAKAIYKRYIENNSIVSKQLKPATKTYIRDGIKKQQIDSIMFDQAQTEIQSVMEENAYQMFLTSDIYLEYVRSGGENTAYMSNGGLGSLKVVCGYLPTLNEEEEWTCADFKCKLSPTVVGLSSKTLRATASVRSTETVDSGYRSFKRSDPVNPYHIGSGYVFAPATSANDSEISSDALTDDSMSMTDSSVDGIPPYRVGSKKQLQREMHRSVKANGQVSLPHFPRT
2	Q9Y2T1-D2	356-711	356		HRLPKEMTPVEPATFAAELISRLEKLKLELESRHSLEERLQQIREDEEREGSELTLNSREGAPTQHPLSLLPSGSYEEDPQTILDDHLSRVLKTPGCQSPGVGRYSPRSRSPDHHHHHHSQYHSLLPPGGKLPPAAASPGACPLLGGKGFVTKQTTKHVHHHYIHHHAVPKTKEEIEAEATQRVHCFCPGGSEYYCYSKCKSHSKAPETMPSEQFGGSRGSTLPKRNGKGTEPGLALPAREGGAPGGAGALQLPREEGDRSQDVWQWMLESERQSKPKPHSAQSTKKAYPLESARSSPGERASRHHLWGGNSGHPRTTPRAHLFTQDPAMPPLTPPNTLAQLEEACRRLAEVSKPP
3	Q9Y2T1-D3	712-843	132		KQRCCVASQQRDRNHSATVQTGATPFSNPSLAPEDHKEPKKLAGVHALQASELVVTYFFCGEEIPYRRMLKAQSLTLGHFKEQLSKKGNYRYYFKKASDEFACGAVFEEIWEDETVLPMYEGRILGKVERID

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.41

(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	7c6oA	0.35	8.71	0.039	0.556	model1_7c6oA.pdb.gz
2	4zhjA	0.35	8.58	0.042	0.550	model1_4zhjA.pdb.gz
3	5cskA	0.33	8.78	0.036	0.530	model1_5cskA.pdb.gz
4	4f91B	0.33	8.93	0.039	0.533	model1_4f91B.pdb.gz
5	6g2dC	0.32	8.72	0.043	0.508	model1_6g2dC.pdb.gz
6	7cpxA	0.32	8.46	0.042	0.495	model1_7cpxA.pdb.gz
7	6x99A	0.32	8.65	0.051	0.505	model1_6x99A.pdb.gz
8	5i8iA	0.31	8.41	0.036	0.491	model1_5i8iA.pdb.gz
9	4bgdA	0.31	8.89	0.035	0.509	model1_4bgdA.pdb.gz
10	7b54X	0.31	8.80	0.034	0.497	model1_7b54X.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:0005096	0.93	GTPase activator activity
GO:0019899	0.57	enzyme binding
GO:0019904	0.56	protein domain specific binding
GO:0019901	0.56	protein kinase binding
GO:0008013	0.56	beta-catenin binding
GO:0070016	0.55	armadillo repeat domain 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	0.99	regulation of cellular process
GO:0007165	0.93	signal transduction
GO:0048583	0.90	regulation of response to stimulus
GO:0023051	0.90	regulation of signaling
GO:0010646	0.90	regulation of cell communication
GO:0009987	0.89	cellular process
GO:0009966	0.89	regulation of signal transduction
GO:0044699	0.88	single-organism process
GO:0007166	0.88	cell surface receptor signaling pathway
GO:0016055	0.87	Wnt signaling pathway
GO:0080090	0.85	regulation of primary metabolic process
GO:0060255	0.85	regulation of macromolecule metabolic process
GO:0031323	0.85	regulation of cellular metabolic process
GO:0048523	0.83	negative regulation of cellular process
GO:2000112	0.82	regulation of cellular macromolecule biosynthetic process
GO:0050896	0.82	response to stimulus
GO:0032501	0.82	multicellular organismal process
GO:0030111	0.82	regulation of Wnt signaling pathway
GO:0019219	0.82	regulation of nucleobase-containing compound metabolic process
GO:0010468	0.82	regulation of gene expression
GO:0009968	0.82	negative regulation of signal transduction
GO:0044763	0.81	single-organism cellular process
GO:0044707	0.81	single-multicellular organism process
GO:0006355	0.81	regulation of transcription, DNA-templated
GO:1903827	0.80	regulation of cellular protein localization
GO:0070887	0.80	cellular response to chemical stimulus
GO:0060828	0.80	regulation of canonical Wnt signaling pathway
GO:0030178	0.80	negative regulation of Wnt signaling pathway
GO:0010033	0.80	response to organic substance
GO:0090244	0.79	Wnt signaling pathway involved in somitogenesis
GO:0090090	0.79	negative regulation of canonical Wnt signaling pathway
GO:0071407	0.79	cellular response to organic cyclic compound
GO:0035412	0.79	regulation of catenin import into nucleus
GO:0048869	0.78	cellular developmental process
GO:0007389	0.77	pattern specification process
GO:0009950	0.76	dorsal/ventral axis specification
GO:0008219	0.76	cell death
GO:0045595	0.73	regulation of cell differentiation
GO:0045596	0.72	negative regulation of cell differentiation
GO:0051239	0.54	regulation of multicellular organismal process
GO:0030154	0.52	cell differentiation

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:0005737	0.94	cytoplasm
GO:0016020	0.90	membrane
GO:0005886	0.89	plasma membrane
GO:0044444	0.73	cytoplasmic part
GO:0043226	0.71	organelle
GO:0043229	0.70	intracellular organelle
GO:0043227	0.69	membrane-bounded organelle
GO:0043231	0.68	intracellular membrane-bounded organelle
GO:0044446	0.65	intracellular organelle part
GO:0032991	0.60	macromolecular complex
GO:0044430	0.59	cytoskeletal part
GO:0043234	0.59	protein complex
GO:0043232	0.58	intracellular non-membrane-bounded organelle
GO:0097458	0.56	neuron part
GO:0031410	0.55	cytoplasmic vesicle
GO:0005938	0.55	cell cortex
GO:0005874	0.55	microtubule
GO:0016023	0.54	cytoplasmic, membrane-bounded vesicle
GO:0014069	0.54	postsynaptic density
GO:0005881	0.54	cytoplasmic microtubule
GO:0030877	0.53	beta-catenin destruction complex

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	2vuaA	0.175	7.54	0.036	0.257	3.4.24.69	177,185
2	0.060	3h0gA	0.270	8.84	0.024	0.439	2.7.7.6	NA
3	0.060	2vdcF	0.295	8.71	0.027	0.473	1.4.1.13	91
4	0.060	1gl9B	0.271	8.83	0.042	0.439	5.99.1.3	NA
5	0.060	1mo7A	0.131	5.51	0.054	0.164	3.6.3.9	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	3aohD	0.271	8.54	0.039	0.431	0.54	MG	complex1.pdb.gz	86,88,90
2	0.01	2p9i3	0.084	5.72	0.058	0.108	0.73	III	complex2.pdb.gz	94,95,96,109,112,113,115
3	0.01	2onk2	0.111	5.18	0.023	0.136	0.54	III	complex3.pdb.gz	90,93,94,95,96,97,98,99,100,115

	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.