D-I-TASSER P10266

D-I-TASSER results for P10266

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

Summary of the Protein

Uniprot ID: P10266
Protein Name: Endogenous retrovirus group K member 10 Pol protein
Gene Name: ERVK-10

Input Sequence in FASTA format

>P10266 (1014 residues)
NKSRKRRNRVSFLGAVTVEPPKPIPLTWKTEKPVWVNQWPLPKQKLEALHLLANEQLEKG
HIEPSFSPWNSPVFVIQKKSGKWHTLTDLRAVNAVIQPMGPLQPGLPSPAMIPKDWPLII
IDLKDCFFTIPLAEQDCEKFAFTIPAINNKEPATRFQWKVLPQGMLNSPTICQTFVGRAL
QPVREKFSDCYIIHYIDDILCAAETKDKLIDCYTFLQAEVANAGLAIASDKIQTSTPFHY
LGMQIENRKIKPQKIEIRKDTLKTLNDFQKLLGDINWIRPTLGIPTYAMSNLFSILRGDS
DLNSQRILTPEATKEIKLVEEKIQSAQINRIDPLAPLQLLIFATAHSPTGIIIQNTDLVE
WSFLPHSTVKTFTLYLDQIATLIGQTRLRITKLCGNDPDKIVVPLTKEQVRQAFINSGAW
QIGLANFVGLIDNHYPKTKIFQFLKLTTWILPKITRREPLENALTVFTDGSSNGKAAYTG
PKERVIKTPYQSAQRDELVAVITVLQDFDQPINIISDSAYVVQATRDVETALIKYSMDDQ
LNQLFNLLQQTVRKRNFPFYITYIRAHTNLPGPLTKANEQADLLVSSALIKAQELHALTH
VNAAGLKNKFDVTWKQAKDIVQHCTQCQVLHLPTQEAGVNPRGLCPNALWQMDVTHVPSF
GRLSYVHVTVDTYSHFIWATCQTGESTSHVKKHLLSCFAVMGVPEKIKTDNGPGYCSKAF
QKFLSQWKISHTTGIPYNSQGQAIVERTNRTLKTQLVKQKEGGDSKECTTPQMQLNLALY
TLNFLNIYRNQTTTSAEQHLTGKKNSPHEGKLIWWKDNKNKTWEIGKVITWGRGFACVSP
GENQLPVWLPTRHLKFYNEPIGDAKKRASTEMVTPVTWMDNPIEVYVNDSIWVPGPIDDR
CPAKPEEEGMMINISIGYRYPPICLGRAPGCLMPAVQNWLVEVPTVSPISRFTYHMVSGM
SLRPRVNYLQDFSYQRSLKFRPKGKPCPKEIPKESKNTEVLVWEECVANSAVIL

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 DeepPotential. 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	P10266-D1	1-105,131-162,587-646	197		NKSRKRRNRVSFLGAVTVEPPKPIPLTWKTEKPVWVNQWPLPKQKLEALHLLANEQLEKGHIEPSFSPWNSPVFVIQKKSGKWHTLTDLRAVNAVIQPMGPLQPGPLAEQDCEKFAFTIPAINNKEPATRFQWKVLPSALIKAQELHALTHVNAAGLKNKFDVTWKQAKDIVQHCTQCQVLHLPTQEAGVNPRGLCP
2	P10266-D2	106-130,163-368,446-586,864-906	415		LPSPAMIPKDWPLIIIDLKDCFFTIQGMLNSPTICQTFVGRALQPVREKFSDCYIIHYIDDILCAAETKDKLIDCYTFLQAEVANAGLAIASDKIQTSTPFHYLGMQIENRKIKPQKIEIRKDTLKTLNDFQKLLGDINWIRPTLGIPTYAMSNLFSILRGDSDLNSQRILTPEATKEIKLVEEKIQSAQINRIDPLAPLQLLIFATAHSPTGIIIQNTDLVEWSFLPHSTLTTWILPKITRREPLENALTVFTDGSSNGKAAYTGPKERVIKTPYQSAQRDELVAVITVLQDFDQPINIISDSAYVVQATRDVETALIKYSMDDQLNQLFNLLQQTVRKRNFPFYITYIRAHTNLPGPLTKANEQADLLVSAKKRASTEMVTPVTWMDNPIEVYVNDSIWVPGPIDDRCPAKPE
3	P10266-D3	369-445,907-1014	185		VKTFTLYLDQIATLIGQTRLRITKLCGNDPDKIVVPLTKEQVRQAFINSGAWQIGLANFVGLIDNHYPKTKIFQFLKEEGMMINISIGYRYPPICLGRAPGCLMPAVQNWLVEVPTVSPISRFTYHMVSGMSLRPRVNYLQDFSYQRSLKFRPKGKPCPKEIPKESKNTEVLVWEECVANSAVIL
4	P10266-D4	647-754	108		NALWQMDVTHVPSFGRLSYVHVTVDTYSHFIWATCQTGESTSHVKKHLLSCFAVMGVPEKIKTDNGPGYCSKAFQKFLSQWKISHTTGIPYNSQGQAIVERTNRTLKT
5	P10266-D5	755-863	109		QLVKQKEGGDSKECTTPQMQLNLALYTLNFLNIYRNQTTTSAEQHLTGKKNSPHEGKLIWWKDNKNKTWEIGKVITWGRGFACVSPGENQLPVWLPTRHLKFYNEPIGD

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.46

(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 DeepPotential, 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	5ovnA	0.38	4.94	0.177	0.441	model1_5ovnA.pdb.gz
2	1mu2A	0.38	5.07	0.204	0.439	model1_1mu2A.pdb.gz
3	3drrA	0.34	6.04	0.141	0.416	model1_3drrA.pdb.gz
4	6r9tA	0.32	9.44	0.043	0.515	model1_6r9tA.pdb.gz
5	5ganA	0.30	9.29	0.052	0.485	model1_5ganA.pdb.gz
6	6um1A	0.30	8.79	0.034	0.460	model1_6um1A.pdb.gz
7	3qmzA	0.30	9.12	0.038	0.472	model1_3qmzA.pdb.gz
8	6uebA	0.30	9.08	0.038	0.464	model1_6uebA.pdb.gz
9	3ecqB	0.30	9.12	0.036	0.472	model1_3ecqB.pdb.gz
10	7o0gA	0.30	7.68	0.097	0.412	model1_7o0gA.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	0.73	catalytic activity
GO:0004518	0.62	nuclease activity
GO:0034061	0.59	DNA polymerase activity
GO:0008233	0.59	peptidase activity
GO:0004540	0.59	ribonuclease activity
GO:0016891	0.58	endoribonuclease activity, producing 5'-phosphomonoesters

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:0006139	0.98	nucleobase-containing compound metabolic process
GO:0006259	0.97	DNA metabolic process
GO:0034654	0.83	nucleobase-containing compound biosynthetic process
GO:0071897	0.82	DNA biosynthetic process
GO:0030260	0.82	entry into host cell
GO:0019043	0.82	establishment of viral latency
GO:0051169	0.79	nuclear transport
GO:0022607	0.76	cellular component assembly
GO:0075713	0.66	establishment of integrated proviral latency
GO:0019072	0.66	viral genome packaging
GO:0019068	0.66	virion assembly
GO:0019064	0.66	fusion of virus membrane with host plasma membrane
GO:0019061	0.66	uncoating of virus
GO:0019058	0.66	viral life cycle
GO:0006278	0.66	RNA-dependent DNA biosynthetic 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:0044464	1.00	cell part
GO:0044424	0.91	intracellular part
GO:0016020	0.79	membrane
GO:0044428	0.76	nuclear part
GO:0044444	0.71	cytoplasmic part
GO:0005829	0.70	cytosol
GO:0005654	0.65	nucleoplasm
GO:0005886	0.64	plasma membrane
GO:0005576	0.63	extracellular 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	0.060	1bglA	0.277	9.23	0.046	0.440	3.2.1.23	NA
2	0.060	1llwA	0.284	9.30	0.033	0.455	1.4.7.1	NA
3	0.060	2vdcF	0.290	9.14	0.040	0.456	1.4.1.13	NA
4	0.060	3b9jI	0.093	5.17	0.065	0.111	1.17.1.4 1.17.3.2	132
5	0.060	2vkzG	0.266	9.12	0.032	0.422	2.3.1.38 3.1.2.14	15

	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	0.14	3lakA	0.334	5.60	0.154	0.397	0.20	KR1	complex1.pdb.gz	26,27,100,162,164
2	0.13	1tvrA	0.333	5.96	0.163	0.407	0.16	TB9	complex2.pdb.gz	25,27,162
3	0.13	3dm2A	0.321	5.58	0.155	0.382	0.31	GWE	complex3.pdb.gz	100,103,104,128,130,132,160,161,162
4	0.12	1jlcA	0.321	5.52	0.154	0.381	0.19	FTC	complex4.pdb.gz	26,27,97,160
5	0.12	1fkoA	0.325	5.57	0.157	0.386	0.23	EFZ	complex5.pdb.gz	26,105,129,161
6	0.12	2ic3A	0.338	5.83	0.155	0.410	0.24	HBY	complex6.pdb.gz	25,26,98,100,104,105
7	0.12	3drsA	0.335	5.94	0.148	0.405	0.22	R8D	complex7.pdb.gz	25,26,100,102,163
8	0.12	1sv5A	0.338	5.68	0.152	0.405	0.18	65B	complex8.pdb.gz	26,27,28,29,98,105,162
9	0.01	1bqnA	0.340	6.08	0.168	0.419	0.18	HBY	complex9.pdb.gz	26,27,98
10	0.01	3medA	0.331	5.77	0.154	0.396	0.18	65B	complex10.pdb.gz	98,100,104

	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, Qiqige Wuyun, Yang Li, Quancheng Liu, Xiaogen Zhou, Yiheng Zhu, P. Lydia Freddolino, Yang Zhang. Integrating deep learning potentials with I-TASSER for single- and multi-domain protein structure prediction. Submitted. 2023.