D-I-TASSER O14862

D-I-TASSER results for O14862

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

Summary of the Protein

Uniprot ID: O14862
Protein Name: Interferon-inducible protein AIM2
Gene Name: AIM2

Input Sequence in FASTA format

>O14862 (343 residues)
MESKYKEILLLTGLDNITDEELDRFKFFLSDEFNIATGKLHTANRIQVATLMIQNAGAVS
AVMKTIRIFQKLNYMLLAKRLQEEKEKVDKQYKSVTKPKPLSQAEMSPAASAAIRNDVAK
QRAAPKVSPHVKPEQKQMVAQQESIREGFQKRCLPVMVLKAKKPFTFETQEGKQEMFHAT
VATEKEFFFVKVFNTLLKDKFIPKRIIIIARYYRHSGFLEVNSASRVLDAESDQKVNVPL
NIIRKAGETPKINTLQTQPLGTIVNGLFVVQKVTEKKKNILFDLSDNTGKMEVLGVRNED
TMKCKEGDKVRLTFFTLSKNGEKLQLTSGVHSTIKVIKAKKKT

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 AttentionPotential. 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	O14862-D1	1-343	343		MESKYKEILLLTGLDNITDEELDRFKFFLSDEFNIATGKLHTANRIQVATLMIQNAGAVSAVMKTIRIFQKLNYMLLAKRLQEEKEKVDKQYKSVTKPKPLSQAEMSPAASAAIRNDVAKQRAAPKVSPHVKPEQKQMVAQQESIREGFQKRCLPVMVLKAKKPFTFETQEGKQEMFHATVATEKEFFFVKVFNTLLKDKFIPKRIIIIARYYRHSGFLEVNSASRVLDAESDQKVNVPLNIIRKAGETPKINTLQTQPLGTIVNGLFVVQKVTEKKKNILFDLSDNTGKMEVLGVRNEDTMKCKEGDKVRLTFFTLSKNGEKLQLTSGVHSTIKVIKAKKKT

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.6388

(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 AttentionPotential, 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	5z7dA	0.71	3.11	0.264	0.793	model1_5z7dA.pdb.gz
2	5yzpA	0.55	1.17	0.407	0.566	model1_5yzpA.pdb.gz
3	5yzwA	0.53	1.53	0.424	0.554	model1_5yzwA.pdb.gz
4	4jbjA	0.53	1.52	0.384	0.551	model1_4jbjA.pdb.gz
5	3rn2A	0.52	1.79	0.963	0.554	model1_3rn2A.pdb.gz
6	2oq0C	0.52	1.38	0.446	0.542	model1_2oq0C.pdb.gz
7	3b6yA	0.52	1.38	0.465	0.539	model1_3b6yA.pdb.gz
8	2xpyA	0.28	6.89	0.040	0.478	model1_2xpyA.pdb.gz
9	1kfqA	0.27	6.94	0.033	0.475	model1_1kfqA.pdb.gz
10	4jbmA1	0.27	0.91	0.559	0.271	model1_4jbmA1.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:1901363	0.95	heterocyclic compound binding
GO:0097159	0.95	organic cyclic compound binding
GO:0003676	0.94	nucleic acid binding
GO:0003690	0.93	double-stranded DNA binding
GO:0003723	0.61	RNA binding
GO:0003700	0.61	transcription factor activity, sequence-specific DNA binding
GO:0000975	0.61	regulatory region DNA binding
GO:0044822	0.60	poly(A) RNA binding
GO:0001047	0.60	core promoter binding
GO:0000977	0.60	RNA polymerase II regulatory region sequence-specific DNA binding
GO:0008134	0.59	transcription factor binding
GO:0001078	0.59	transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding
GO:0000978	0.59	RNA polymerase II core promoter proximal region sequence-specific DNA 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:0009987	0.96	cellular process
GO:0050896	0.95	response to stimulus
GO:0051716	0.94	cellular response to stimulus
GO:0065007	0.88	biological regulation
GO:0050789	0.88	regulation of biological process
GO:0050794	0.83	regulation of cellular process
GO:0042221	0.77	response to chemical
GO:0070887	0.75	cellular response to chemical stimulus
GO:0048519	0.72	negative regulation of biological process
GO:0048518	0.72	positive regulation of biological process
GO:0002682	0.71	regulation of immune system process
GO:0007165	0.68	signal transduction
GO:0048522	0.66	positive regulation of cellular process
GO:0050776	0.65	regulation of immune response
GO:0080090	0.64	regulation of primary metabolic process
GO:0060255	0.64	regulation of macromolecule metabolic process
GO:0051239	0.64	regulation of multicellular organismal process
GO:0031323	0.64	regulation of cellular metabolic process
GO:0002684	0.64	positive regulation of immune system process
GO:0051240	0.61	positive regulation of multicellular organismal process
GO:0044699	0.61	single-organism process
GO:0002376	0.61	immune system process
GO:0048584	0.59	positive regulation of response to stimulus
GO:0002253	0.58	activation of immune response
GO:0001817	0.58	regulation of cytokine production
GO:0051246	0.57	regulation of protein metabolic process
GO:0009889	0.57	regulation of biosynthetic process
GO:0032268	0.56	regulation of cellular protein metabolic process
GO:0006355	0.56	regulation of transcription, DNA-templated
GO:0050790	0.55	regulation of catalytic activity
GO:0045088	0.55	regulation of innate immune response
GO:0044092	0.55	negative regulation of molecular function
GO:0030162	0.55	regulation of proteolysis
GO:0001819	0.55	positive regulation of cytokine production
GO:2000116	0.54	regulation of cysteine-type endopeptidase activity
GO:0010033	0.54	response to organic substance
GO:0071310	0.52	cellular response to organic substance
GO:0044763	0.52	single-organism cellular process
GO:0071345	0.51	cellular response to cytokine stimulus
GO:0031325	0.51	positive regulation of cellular metabolic process
GO:0010604	0.51	positive regulation of macromolecule metabolic process
GO:0007166	0.51	cell surface receptor signaling pathway
GO:0035458	0.50	cellular response to interferon-beta
GO:0032270	0.50	positive regulation of cellular protein metabolic process

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	0.99	intracellular part
GO:0005737	0.88	cytoplasm
GO:0043226	0.78	organelle
GO:0043227	0.77	membrane-bounded organelle
GO:0044446	0.73	intracellular organelle part
GO:0043229	0.72	intracellular organelle
GO:0043231	0.71	intracellular membrane-bounded organelle
GO:0044444	0.70	cytoplasmic part
GO:0005634	0.68	nucleus
GO:0044428	0.66	nuclear part
GO:0016020	0.66	membrane
GO:0043232	0.60	intracellular non-membrane-bounded organelle
GO:0005730	0.59	nucleolus
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	3kzwA	0.374	6.63	0.066	0.630	3.4.11.1	NA
2	0.060	2fxhA	0.397	6.88	0.042	0.688	1.11.1.7 1.11.1.6	NA
3	0.060	3btaA	0.370	6.59	0.035	0.621	3.4.24.69	NA
4	0.060	2zxqA	0.367	6.80	0.024	0.644	3.2.1.97	NA
5	0.060	2z8yP	0.269	7.50	0.039	0.507	2.3.1.169	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:

No Binding sites was predicted

Click to view	Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues

	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, Chengxin Zhang, Yang Li, Robin Pearce, Eric W. Bell, Yang Zhang. Folding non-homology proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. In preparation, 2020.