D-I-TASSER A8MVJ9

D-I-TASSER results for A8MVJ9

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

Summary of the Protein

Uniprot ID: A8MVJ9
Protein Name: Putative histone PARylation factor 1-like
Gene Name: HPDL

Input Sequence in FASTA format

>A8MVJ9 (347 residues)
MVGGGWKRRPGAGAGPQCEKTVDVKKSKFCEADVSSDLRKEVENHYTLSLPEDFYHFWKF
CEELDSEKPADPLSASLGLQLVDPYNILAGKHKMKKKSTVPNFNLHWRFYYDPPEFQTII
IRDKLSATWGISDRDSPDELPVYVGINEAKKNCIIVPNGDNVFAAVKLYLMKKLKEVTDK
KKTNLFKNVDEKLTETARELGYSLEQRTMKMKQRDKKVVTKTFHGTGLVPPVDKNVVGYR
ELPETDADLKRICKTIVEAASDDERRKAFAPIQEMMTFVQFANDECDYGMGLELGMDLFC
YGSHYFHKVAGQLLPLAYNLLKRNLFAEIMKDHLANRRKENIDQFAA

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	A8MVJ9-D1	1-228	228		MVGGGWKRRPGAGAGPQCEKTVDVKKSKFCEADVSSDLRKEVENHYTLSLPEDFYHFWKFCEELDSEKPADPLSASLGLQLVDPYNILAGKHKMKKKSTVPNFNLHWRFYYDPPEFQTIIIRDKLSATWGISDRDSPDELPVYVGINEAKKNCIIVPNGDNVFAAVKLYLMKKLKEVTDKKKTNLFKNVDEKLTETARELGYSLEQRTMKMKQRDKKVVTKTFHGTGL
2	A8MVJ9-D2	229-347	119		VPPVDKNVVGYRELPETDADLKRICKTIVEAASDDERRKAFAPIQEMMTFVQFANDECDYGMGLELGMDLFCYGSHYFHKVAGQLLPLAYNLLKRNLFAEIMKDHLANRRKENIDQFAA

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.81

(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	6x0lO	0.86	1.06	0.869	0.879	model1_6x0lO.pdb.gz
2	6tvhA	0.81	1.54	0.478	0.839	model1_6tvhA.pdb.gz
3	3pyaA	0.43	6.13	0.052	0.669	model1_3pyaA.pdb.gz
4	3p5pA	0.43	6.04	0.056	0.669	model1_3p5pA.pdb.gz
5	3s9vA	0.42	6.25	0.062	0.671	model1_3s9vA.pdb.gz
6	3n0fA	0.42	5.97	0.043	0.654	model1_3n0fA.pdb.gz
7	3saeA	0.42	6.15	0.057	0.671	model1_3saeA.pdb.gz
8	5xq3A	0.42	6.63	0.054	0.697	model1_5xq3A.pdb.gz
9	6i33A	0.42	7.10	0.045	0.741	model1_6i33A.pdb.gz
10	3c68A	0.42	6.65	0.041	0.715	model1_3c68A.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:0042393	0.73	histone binding
GO:0003824	0.65	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:0010835	1.00	regulation of protein ADP-ribosylation
GO:0006974	1.00	cellular response to DNA damage stimulus
GO:0044763	0.96	single-organism cellular process
GO:0071704	0.54	organic substance metabolic process
GO:0044281	0.54	small molecule metabolic process
GO:0044238	0.54	primary metabolic process
GO:0044237	0.54	cellular metabolic process
GO:0006531	0.53	aspartate 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:0005634	1.00	nucleus
GO:0044444	0.77	cytoplasmic part

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	2o1xB	0.388	6.80	0.044	0.663	2.2.1.7	NA
2	0.060	1vpeA	0.383	6.52	0.066	0.614	2.7.2.3	NA
3	0.060	1e6vA	0.386	6.57	0.052	0.637	2.8.4.1	NA
4	0.060	2j5cB	0.417	5.93	0.082	0.640	4.2.3.-	58
5	0.060	3bg3A	0.392	6.81	0.032	0.660	6.4.1.1	135

	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	2cqsA	0.420	6.02	0.058	0.651	0.35	BGC	complex1.pdb.gz	112,113,302
2	0.01	3qg0B	0.418	6.02	0.052	0.651	0.15	UUU	complex2.pdb.gz	110,111,112,296,303
3	0.01	1n1zA	0.414	6.29	0.070	0.660	0.29	POP	complex3.pdb.gz	116,289,292,296,300
4	0.01	3g4fB	0.412	6.14	0.075	0.657	0.17	FPF	complex4.pdb.gz	295,296,298,310
5	0.01	1n20B	0.418	5.74	0.039	0.628	0.17	3AG	complex5.pdb.gz	148,224,296,297,303,337
6	0.01	2cfzA	0.407	6.79	0.045	0.700	0.21	1DO	complex6.pdb.gz	158,160,226
7	0.01	3p5rB	0.427	6.04	0.056	0.660	0.24	FGG	complex7.pdb.gz	296,297,300
8	0.01	3n0gA	0.412	6.29	0.045	0.663	0.19	DST	complex8.pdb.gz	296,297,300
9	0.01	1n24B	0.416	6.19	0.036	0.651	0.17	BP2	complex9.pdb.gz	49,160,211,214
10	0.01	1n21A	0.418	6.27	0.057	0.663	0.14	3AG	complex10.pdb.gz	296,297,299,333

	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.