D-I-TASSER O00165

D-I-TASSER results for O00165

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Summary of the Protein

Uniprot ID: O00165
Protein Name: HCLS1-associated protein X-1
Gene Name: HAX1

Input Sequence in FASTA format

>O00165 (279 residues)
MSLFDLFRGFFGFPGPRSHRDPFFGGMTRDEDDDEEEEEEGGSWGRGNPRFHSPQHPPEE
FGFGFSFSPGGGIRFHDNFGFDDLVRDFNSIFSDMGAWTLPSHPPELPGPESETPGERLR
EGQTLRDSMLKYPDSHQPRIFGGVLESDARSESPQPAPDWGSQRPFHRFDDVWPMDPHPR
TREDNDLDSQVSQEGLGPVLQPQPKSYFKSISVTKITKPDGIVEERRTVVDSEGRTETTV
TRHEADSSPRGDPESPRPPALDDAFSILDLFLGRWFRSR

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	O00165-D1	1-279	279		MSLFDLFRGFFGFPGPRSHRDPFFGGMTRDEDDDEEEEEEGGSWGRGNPRFHSPQHPPEEFGFGFSFSPGGGIRFHDNFGFDDLVRDFNSIFSDMGAWTLPSHPPELPGPESETPGERLREGQTLRDSMLKYPDSHQPRIFGGVLESDARSESPQPAPDWGSQRPFHRFDDVWPMDPHPRTREDNDLDSQVSQEGLGPVLQPQPKSYFKSISVTKITKPDGIVEERRTVVDSEGRTETTVTRHEADSSPRGDPESPRPPALDDAFSILDLFLGRWFRSR

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.4064

(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	3gwjA	0.42	6.25	0.054	0.728	model1_3gwjA.pdb.gz
2	4l37A	0.41	6.27	0.057	0.724	model1_4l37A.pdb.gz
3	3hhsB	0.41	6.51	0.051	0.735	model1_3hhsB.pdb.gz
4	1qhbA	0.41	6.60	0.065	0.731	model1_1qhbA.pdb.gz
5	1wqlA	0.40	6.31	0.033	0.692	model1_1wqlA.pdb.gz
6	1hcyA2	0.35	6.19	0.056	0.599	model1_1hcyA2.pdb.gz
7	3ixvM2	0.30	6.45	0.028	0.523	model1_3ixvM2.pdb.gz
8	2p3xA	0.29	6.56	0.037	0.516	model1_2p3xA.pdb.gz
9	3wecA	0.29	6.81	0.071	0.527	model1_3wecA.pdb.gz
10	3ba1A	0.28	6.63	0.073	0.512	model1_3ba1A.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:0047485	0.63	protein N-terminus binding
GO:0019966	0.63	interleukin-1 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	1.00	cellular process
GO:0065007	0.92	biological regulation
GO:0050789	0.92	regulation of biological process
GO:0050794	0.91	regulation of cellular process
GO:0044699	0.91	single-organism process
GO:0044763	0.90	single-organism cellular process
GO:0080090	0.89	regulation of primary metabolic process
GO:0060255	0.89	regulation of macromolecule metabolic process
GO:0050896	0.89	response to stimulus
GO:0048518	0.89	positive regulation of biological process
GO:0031323	0.89	regulation of cellular metabolic process
GO:0065008	0.88	regulation of biological quality
GO:0051716	0.88	cellular response to stimulus
GO:0051247	0.88	positive regulation of protein metabolic process
GO:0051240	0.88	positive regulation of multicellular organismal process
GO:0048584	0.88	positive regulation of response to stimulus
GO:0048523	0.88	negative regulation of cellular process
GO:0045595	0.88	regulation of cell differentiation
GO:0042981	0.88	regulation of apoptotic process
GO:0031399	0.88	regulation of protein modification process
GO:0031325	0.88	positive regulation of cellular metabolic process
GO:0019220	0.88	regulation of phosphate metabolic process
GO:0016043	0.88	cellular component organization
GO:0009966	0.88	regulation of signal transduction
GO:0006355	0.88	regulation of transcription, DNA-templated
GO:0002684	0.88	positive regulation of immune system process
GO:2000251	0.87	positive regulation of actin cytoskeleton reorganization
GO:0071345	0.87	cellular response to cytokine stimulus
GO:0051897	0.87	positive regulation of protein kinase B signaling
GO:0050731	0.87	positive regulation of peptidyl-tyrosine phosphorylation
GO:0045944	0.87	positive regulation of transcription from RNA polymerase II promoter
GO:0043066	0.87	negative regulation of apoptotic process
GO:0033138	0.87	positive regulation of peptidyl-serine phosphorylation
GO:0030854	0.87	positive regulation of granulocyte differentiation
GO:0030833	0.87	regulation of actin filament polymerization
GO:0014068	0.87	positive regulation of phosphatidylinositol 3-kinase signaling
GO:0006996	0.50	organelle organization

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:0044444	1.00	cytoplasmic part
GO:0043229	0.93	intracellular organelle
GO:0043227	0.93	membrane-bounded organelle
GO:0016020	0.93	membrane
GO:0043231	0.92	intracellular membrane-bounded organelle
GO:0005783	0.91	endoplasmic reticulum
GO:0044422	0.80	organelle part
GO:0044446	0.79	intracellular organelle part
GO:0032991	0.75	macromolecular complex
GO:0043234	0.74	protein complex
GO:0031090	0.66	organelle membrane
GO:0098805	0.65	whole membrane
GO:0098588	0.65	bounding membrane of organelle
GO:0044429	0.65	mitochondrial part
GO:0031966	0.64	mitochondrial membrane
GO:0005758	0.64	mitochondrial intermembrane space
GO:0070013	0.63	intracellular organelle lumen
GO:0030027	0.63	lamellipodium
GO:0015629	0.63	actin cytoskeleton
GO:0005741	0.63	mitochondrial outer membrane
GO:0005739	0.63	mitochondrion
GO:0005667	0.63	transcription factor complex
GO:0016529	0.57	sarcoplasmic reticulum

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	1izjA	0.373	5.81	0.042	0.595	3.2.1.135 3.2.1.1	NA
2	0.060	3fedA	0.372	6.41	0.024	0.645	3.4.17.21	NA
3	0.060	2zoxA	0.360	6.42	0.051	0.634	3.2.1.21	70
4	0.060	3nqbA	0.390	6.36	0.055	0.681	3.5.4.2	NA
5	0.060	2dgaA	0.373	6.19	0.065	0.638	3.2.1.21	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:

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
	1	0.01	2xshG	0.393	6.02	0.040	0.674	0.55	FES	complex1.pdb.gz	208,230,232,233,234
	2	0.01	2gbwC	0.397	6.33	0.042	0.685	0.70	FES	complex2.pdb.gz	230,232,233

	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.