D-I-TASSER P49005

D-I-TASSER results for P49005

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

Summary of the Protein

Uniprot ID: P49005
Protein Name: DNA polymerase delta subunit 2
Gene Name: POLD2

Input Sequence in FASTA format

>P49005 (469 residues)
MFSEQAAQRAHTLLSPPSANNATFARVPVATYTNSSQPFRLGERSFSRQYAHIYATRLIQ
MRPFLENRAQQHWGSGVGVKKLCELQPEEKCCVVGTLFKAMPLQPSILREVSEEHNLLPQ
PPRSKYIHPDDELVLEDELQRIKLKGTIDVSKLVTGTVLAVFGSVRDDGKFLVEDYCFAD
LAPQKPAPPLDTDRFVLLVSGLGLGGGGGESLLGTQLLVDVVTGQLGDEGEQCSAAHVSR
VILAGNLLSHSTQSRDSINKAKYLTKKTQAASVEAVKMLDEILLQLSASVPVDVMPGEFD
PTNYTLPQQPLHPCMFPLATAYSTLQLVTNPYQATIDGVRFLGTSGQNVSDIFRYSSMED
HLEILEWTLRVRHISPTAPDTLGCYPFYKTDPFIFPECPHVYFCGNTPSFGSKIIRGPED
QTVLLVTVPDFSATQTACLVNLRSLACQPISFSGFGAEDDDLGGLGLGP

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	P49005-D1	1-60,180-469	350		MFSEQAAQRAHTLLSPPSANNATFARVPVATYTNSSQPFRLGERSFSRQYAHIYATRLIQDLAPQKPAPPLDTDRFVLLVSGLGLGGGGGESLLGTQLLVDVVTGQLGDEGEQCSAAHVSRVILAGNLLSHSTQSRDSINKAKYLTKKTQAASVEAVKMLDEILLQLSASVPVDVMPGEFDPTNYTLPQQPLHPCMFPLATAYSTLQLVTNPYQATIDGVRFLGTSGQNVSDIFRYSSMEDHLEILEWTLRVRHISPTAPDTLGCYPFYKTDPFIFPECPHVYFCGNTPSFGSKIIRGPEDQTVLLVTVPDFSATQTACLVNLRSLACQPISFSGFGAEDDDLGGLGLGP
2	P49005-D2	61-179	119		MRPFLENRAQQHWGSGVGVKKLCELQPEEKCCVVGTLFKAMPLQPSILREVSEEHNLLPQPPRSKYIHPDDELVLEDELQRIKLKGTIDVSKLVTGTVLAVFGSVRDDGKFLVEDYCFA

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.69

(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	3e0jA	0.67	1.83	0.818	0.693	model1_3e0jA.pdb.gz
2	6p1hB	0.63	2.34	0.281	0.676	model1_6p1hB.pdb.gz
3	5iheA	0.61	3.28	0.155	0.689	model1_5iheA.pdb.gz
4	6knbA	0.58	3.85	0.138	0.691	model1_6knbA.pdb.gz
5	5vbnA	0.57	3.14	0.139	0.646	model1_5vbnA.pdb.gz
6	3floA	0.57	3.47	0.118	0.652	model1_3floA.pdb.gz
7	4y97A	0.57	3.44	0.157	0.652	model1_4y97A.pdb.gz
8	6hv8B	0.56	3.65	0.105	0.650	model1_6hv8B.pdb.gz
9	2x2hA	0.43	6.77	0.052	0.667	model1_2x2hA.pdb.gz
10	2xvgA	0.43	6.79	0.033	0.667	model1_2xvgA.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:0016772	1.00	transferase activity, transferring phosphorus-containing groups
GO:0003887	0.91	DNA-directed DNA polymerase 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:0009987	1.00	cellular process
GO:0044237	0.95	cellular metabolic process
GO:0071704	0.90	organic substance metabolic process
GO:0044238	0.90	primary metabolic process
GO:0006139	0.89	nucleobase-containing compound metabolic process
GO:0044260	0.88	cellular macromolecule metabolic process
GO:0090304	0.87	nucleic acid metabolic process
GO:0006259	0.86	DNA metabolic process
GO:1901576	0.85	organic substance biosynthetic process
GO:0044249	0.85	cellular biosynthetic process
GO:0034645	0.84	cellular macromolecule biosynthetic process
GO:0006260	0.76	DNA replication

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	0.87	intracellular organelle part
GO:0044428	0.79	nuclear part
GO:0043226	0.63	organelle
GO:0043229	0.62	intracellular organelle
GO:0043227	0.57	membrane-bounded organelle
GO:0043231	0.56	intracellular membrane-bounded organelle
GO:0005654	0.52	nucleoplasm
GO:0005634	0.51	nucleus

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	0.095	3e0jA	0.667	1.83	0.818	0.693	2.7.7.7	138
2	0.060	1rboB	0.359	7.15	0.058	0.584	4.1.1.39	NA
3	0.060	3b9jC	0.283	7.44	0.035	0.473	1.17.3.2 1.17.1.4	NA
4	0.060	3l4uA	0.398	6.91	0.045	0.623	3.2.1.20 3.2.1.3	NA
5	0.060	1qbaA	0.384	6.63	0.051	0.580	3.2.1.52	62

	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	0.01	1kc7A	0.416	6.84	0.047	0.650	0.22	PPR	complex1.pdb.gz	85,143,145,163
2	0.01	2jkeB	0.381	7.40	0.056	0.627	0.15	NOJ	complex2.pdb.gz	82,85,163,174
3	0.01	1ofdA	0.386	6.95	0.045	0.621	0.15	FMN	complex3.pdb.gz	95,169,170
4	0.01	2jkeA	0.378	7.57	0.057	0.635	0.12	NOJ	complex4.pdb.gz	62,66,136,141
5	0.01	2x2jA	0.399	6.84	0.047	0.618	0.11	NOJ	complex5.pdb.gz	153,155,156
6	0.01	1ofdB	0.393	7.00	0.056	0.633	0.24	F3S	complex6.pdb.gz	144,157,158,159
7	0.01	2vdcA	0.381	7.01	0.057	0.610	0.15	FMN	complex7.pdb.gz	134,159,163,164,165

	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.