D-I-TASSER A0A3B3IU63

D-I-TASSER results for A0A3B3IU63

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Summary of the Protein

Uniprot ID: A0A3B3IU63
Protein Name: Histone H2A
Gene Name: H2AL1RP

Input Sequence in FASTA format

>A0A3B3IU63 (148 residues)
MAGNKMFCRPRRQRLSHSRRAELQFPVSHLERCLRESQHARHLSSTTPVFLAGVLEYLTA
NILEKVGKEVKNSCRLCITPEHVKRALQKDEQLRWILELEDDTHSQVEEMPQSEEEEEEE
EEKEEEMVVLVVMGGRRRRRRRRRRKDS

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	A0A3B3IU63-D1	1-148	148		MAGNKMFCRPRRQRLSHSRRAELQFPVSHLERCLRESQHARHLSSTTPVFLAGVLEYLTANILEKVGKEVKNSCRLCITPEHVKRALQKDEQLRWILELEDDTHSQVEEMPQSEEEEEEEEEKEEEMVVLVVMGGRRRRRRRRRRKDS

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.5564

(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	1kx5C	0.66	2.43	0.323	0.770	model1_1kx5C.pdb.gz
2	2f8nG	0.62	2.42	0.287	0.703	model1_2f8nG.pdb.gz
3	5z30G	0.61	2.57	0.321	0.710	model1_5z30G.pdb.gz
4	5z23C	0.60	2.10	0.330	0.676	model1_5z23C.pdb.gz
5	6px3C	0.60	2.15	0.319	0.676	model1_6px3C.pdb.gz
6	2jssA	0.55	2.92	0.303	0.676	model1_2jssA.pdb.gz
7	3ksyA	0.54	2.91	0.175	0.649	model1_3ksyA.pdb.gz
8	6a7uA	0.51	1.20	0.396	0.547	model1_6a7uA.pdb.gz
9	4khaA	0.50	3.99	0.089	0.696	model1_4khaA.pdb.gz
10	4g91C	0.48	2.07	0.099	0.561	model1_4g91C.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

./A0A3B3IU63-D1/GOsearchresult_final_MF.svg

Molecular Function (MF)

GO term	Cscore^GO	Name
GO:0003677	0.99	DNA binding
GO:0046982	0.56	protein heterodimerization 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]

./A0A3B3IU63-D1/GOsearchresult_final_BP.svg

Biological Process (BP)

GO term	Cscore^GO	Name
GO:0065007	1.00	biological regulation
GO:0045892	0.97	negative regulation of transcription, DNA-templated
GO:0009987	0.97	cellular process
GO:0040029	0.96	regulation of gene expression, epigenetic
GO:0006325	0.96	chromatin organization
GO:0006342	0.95	chromatin silencing

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]

./A0A3B3IU63-D1/GOsearchresult_final_CC.svg

Cellular Component (CC)

GO term	Cscore^GO	Name
GO:0043229	1.00	intracellular organelle
GO:0044446	0.98	intracellular organelle part
GO:0044428	0.97	nuclear part
GO:0044427	0.97	chromosomal part
GO:0032991	0.97	macromolecular complex
GO:0044454	0.96	nuclear chromosome part
GO:0000790	0.95	nuclear chromatin
GO:0043231	0.69	intracellular membrane-bounded organelle
GO:0005634	0.57	nucleus
GO:0043234	0.50	protein complex
GO:0043232	0.50	intracellular non-membrane-bounded organelle

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	1gytJ	0.419	5.11	0.049	0.757	3.4.11.1	NA
2	0.060	2e5dB	0.445	5.10	0.088	0.750	2.4.2.12	NA
3	0.060	5r1rA	0.393	5.18	0.046	0.730	1.17.4.1	NA
4	0.060	2pywA	0.457	4.81	0.065	0.757	2.7.1.100	102
5	0.060	2excX	0.351	5.37	0.021	0.669	2.7.11.24 2.7.1.37	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	0.21	1zlaG	0.617	2.16	0.349	0.689	1.40	III	complex1.pdb.gz	56,57,60,61,64,90,92
2	0.21	1hio0	0.594	1.43	0.400	0.642	1.44	III	complex2.pdb.gz	17,18,19,20,21,22,23,24,25,26,30,33,39,40,41,42,43,44,46,47,49,50,51,53,54,55,56,57,58,59,60,61,62,63,64,71,76,77,78,83,92,93,95,96,97,106
3	0.01	2voyK	0.205	0.69	0.097	0.209	1.22	III	complex3.pdb.gz	49,53,56,57,64
4	0.01	2agvA	0.423	4.84	0.030	0.750	0.58	PTY	complex4.pdb.gz	46,50,53,54

	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.