D-I-TASSER Q9H816

D-I-TASSER results for Q9H816

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

Summary of the Protein

Uniprot ID: Q9H816
Protein Name: 5' exonuclease Apollo
Gene Name: DCLRE1B

Input Sequence in FASTA format

>Q9H816 (532 residues)
MNGVLIPHTPIAVDFWSLRRAGTARLFFLSHMHSDHTVGLSSTWARPLYCSPITAHLLHR
HLQVSKQWIQALEVGESHVLPLDEIGQETMTVTLLDANHCPGSVMFLFEGYFGTILYTGD
FRYTPSMLKEPALTLGKQIHTLYLDNTNCNPALVLPSRQEAAHQIVQLIRKHPQHNIKIG
LYSLGKESLLEQLALEFQTWVVLSPRRLELVQLLGLADVFTVEEKAGRIHAVDHMEICHS
NMLRWNQTHPTIAILPTSRKIHSSHPDIHVIPYSDHSSYSELRAFVAALKPCQVVPIVSR
RPCGGFQDSLSPRISVPLIPDSVQQYMSSSSRKPSLLWLLERRLKRPRTQGVVFESPEES
ADQSQADRDSKKAKKEKLSPWPADLEKQPSHHPLRIKKQLFPDLYSKEWNKAVPFCESQK
RVTMLTAPLGFSVHLRSTDEEFISQKTREEIGLGSPLVPMGDDDGGPEATGNQSAWMGHG
SPLSHSSKGTPLLATEFRGLALKYLLTPVNFFQAGYSSRRFDQQVEKYHKPC

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	Q9H816-D1	1-532	532		MNGVLIPHTPIAVDFWSLRRAGTARLFFLSHMHSDHTVGLSSTWARPLYCSPITAHLLHRHLQVSKQWIQALEVGESHVLPLDEIGQETMTVTLLDANHCPGSVMFLFEGYFGTILYTGDFRYTPSMLKEPALTLGKQIHTLYLDNTNCNPALVLPSRQEAAHQIVQLIRKHPQHNIKIGLYSLGKESLLEQLALEFQTWVVLSPRRLELVQLLGLADVFTVEEKAGRIHAVDHMEICHSNMLRWNQTHPTIAILPTSRKIHSSHPDIHVIPYSDHSSYSELRAFVAALKPCQVVPIVSRRPCGGFQDSLSPRISVPLIPDSVQQYMSSSSRKPSLLWLLERRLKRPRTQGVVFESPEESADQSQADRDSKKAKKEKLSPWPADLEKQPSHHPLRIKKQLFPDLYSKEWNKAVPFCESQKRVTMLTAPLGFSVHLRSTDEEFISQKTREEIGLGSPLVPMGDDDGGPEATGNQSAWMGHGSPLSHSSKGTPLLATEFRGLALKYLLTPVNFFQAGYSSRRFDQQVEKYHKPC

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.63

(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	4xwtA	0.74	2.70	0.147	0.808	model1_4xwtA.pdb.gz
2	3zq4A	0.74	3.02	0.143	0.816	model1_3zq4A.pdb.gz
3	3bk1A	0.70	3.56	0.143	0.803	model1_3bk1A.pdb.gz
4	5a0tA	0.61	2.09	0.170	0.643	model1_5a0tA.pdb.gz
5	6k6sA	0.60	2.32	0.143	0.643	model1_6k6sA.pdb.gz
6	6k6wA	0.60	2.37	0.132	0.641	model1_6k6wA.pdb.gz
7	5haaA	0.57	2.42	0.164	0.609	model1_5haaA.pdb.gz
8	6v4xI	0.55	3.16	0.134	0.617	model1_6v4xI.pdb.gz
9	3af5A	0.54	3.07	0.171	0.605	model1_3af5A.pdb.gz
10	2ycbA	0.54	3.16	0.196	0.605	model1_2ycbA.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:0003824	0.99	catalytic activity
GO:1901363	0.97	heterocyclic compound binding
GO:0097159	0.97	organic cyclic compound binding
GO:0004518	0.97	nuclease activity
GO:0008409	0.96	5'-3' exonuclease activity
GO:0003676	0.96	nucleic acid binding
GO:0003684	0.95	damaged DNA binding
GO:0035312	0.94	5'-3' exodeoxyribonuclease 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:0071704	1.00	organic substance metabolic process
GO:0044238	1.00	primary metabolic process
GO:0044237	1.00	cellular metabolic process
GO:0006259	0.99	DNA metabolic process
GO:0065007	0.98	biological regulation
GO:0006996	0.97	organelle organization
GO:0006974	0.97	cellular response to DNA damage stimulus
GO:0031848	0.96	protection from non-homologous end joining at telomere
GO:0006281	0.95	DNA repair
GO:0036297	0.94	interstrand cross-link repair
GO:0006303	0.94	double-strand break repair via nonhomologous end joining

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:0044446	0.97	intracellular organelle part
GO:0000781	0.96	chromosome, telomeric region
GO:0044428	0.95	nuclear part
GO:0000784	0.94	nuclear chromosome, telomeric region

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	0.067	2dkfA	0.532	3.06	0.156	0.590	3.1.-.-	NA
2	0.067	2i7vA	0.530	3.29	0.156	0.602	3.1.27.-	NA
3	0.066	2i7tA	0.501	3.10	0.155	0.566	3.1.27.-	103,277
4	0.060	3b9jC	0.283	7.80	0.020	0.468	1.17.3.2 1.17.1.4	NA
5	0.060	1pg3B	0.345	6.66	0.041	0.515	6.2.1.1	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	0.05	3bk2A	0.709	3.52	0.142	0.808	0.11	U5P	complex1.pdb.gz	103,104,118
2	0.03	3ielB	0.532	3.11	0.156	0.590	0.11	U5P	complex2.pdb.gz	119,120,183,186
3	0.02	3iemC	0.534	2.99	0.152	0.590	0.30	SSU	complex3.pdb.gz	28,29,36,119
4	0.02	3ie1A	0.533	3.13	0.152	0.592	0.30	RQA	complex4.pdb.gz	33,34,35,182,183,184,204,205
5	0.01	3ho8C	0.285	7.14	0.035	0.438	0.11	COA	complex5.pdb.gz	14,99,103,104
6	0.01	3ho8D	0.292	7.20	0.062	0.457	0.16	COA	complex6.pdb.gz	14,102,103,119
7	0.01	3bg5C	0.371	7.80	0.038	0.630	0.13	PYR	complex7.pdb.gz	30,31,186,214
8	0.01	3ho8B	0.318	7.10	0.053	0.500	0.22	COA	complex8.pdb.gz	94,95,96,97,275

	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.