D-I-TASSER P63136

D-I-TASSER results for P63136

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

Summary of the Protein

Uniprot ID: P63136
Protein Name: Endogenous retrovirus group K member 25 Pol protein
Gene Name: ERVK-25

Input Sequence in FASTA format

>P63136 (954 residues)
NKSKKRRNRVSFLGAATVEPPKPIPLTWKTEKPVWVNQWPLPKQKLEALHLLANEQLEKG
HIEPSFSPWNSPVFVIQKKSGKWRMLTDLRAVNAVIQPMGPLQPGLPSPAMIPKDWPLII
IDLKDCFFTIPLAEQDCEKFAFTIPAINNKEPATRFQWKVLPQGMLNSPTICQTFVGRAL
QPVREKFSDCYIIHYIDDILCAAETKDKLIDCYTFLQAEVANAGLAIASDKIQTSTPFHY
LGMQIENRKIKPQKIEIRKDTLKALNDFQKLLGDINWIRPTLGIPTYAMSNLFSILRGDS
DLNSKRMLTPEATKEIKLVEEKIQSAQINRIDPLAPLQLLIFATAHSPTGIIIQNTDLVE
WSFLPHSTVKTFTLYLDQIATLIGQTRLRIIKLCGNDPDKIVVPLTKEQVRQAFINSGAW
QIGLANFVGIIDNHYPKTKIFQFLKLTTWILPKITRREPLENALTVFTDGSSNGKAAYTG
PKERVIKTPYQSAQRAELVAVITVLQDFDINIISDSAYVVQATRDVETALIKYSMDDQLN
QLFNLLQQTVRKRNFPFYITHIRAHTNLPGPLTKANKQADLLVSSALIKAQELHALTHVN
AAGLKNKFDVTWKLAKDIVQHCTQCQVLHLPTQEAGVNPRGLCPNALWQMDVTHVPSFGR
LSYVHVTVDTYSHFIWATCHTGESTSHVKKHLLSCFAVMGVPEKIKTDNGPGYCSKAFQK
FLSQWKISHTTGIPYNSQGQAIVERTNRTLKTQLVKQKEGGDSKECTTPQMQLNLALYTL
NFLNIYRNQTTTSAEQHLTGKKNSPHEGKLIWWKDNKNKTWEIGKVITWGRGFACVSPGE
NQLPVWIPTRHLKFYNEPIRDAKKSTSAETETPQSSTVDSQDEQNGDVRRTDEVAIHQEG
RAANLGTTKEADAVSYKISREHKGDTNPREYAACSLDDCINGGKSPYACRSSCS

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	P63136-D1	1-255	255		NKSKKRRNRVSFLGAATVEPPKPIPLTWKTEKPVWVNQWPLPKQKLEALHLLANEQLEKGHIEPSFSPWNSPVFVIQKKSGKWRMLTDLRAVNAVIQPMGPLQPGLPSPAMIPKDWPLIIIDLKDCFFTIPLAEQDCEKFAFTIPAINNKEPATRFQWKVLPQGMLNSPTICQTFVGRALQPVREKFSDCYIIHYIDDILCAAETKDKLIDCYTFLQAEVANAGLAIASDKIQTSTPFHYLGMQIENRKIKPQKI
2	P63136-D2	256-532	277		EIRKDTLKALNDFQKLLGDINWIRPTLGIPTYAMSNLFSILRGDSDLNSKRMLTPEATKEIKLVEEKIQSAQINRIDPLAPLQLLIFATAHSPTGIIIQNTDLVEWSFLPHSTVKTFTLYLDQIATLIGQTRLRIIKLCGNDPDKIVVPLTKEQVRQAFINSGAWQIGLANFVGIIDNHYPKTKIFQFLKLTTWILPKITRREPLENALTVFTDGSSNGKAAYTGPKERVIKTPYQSAQRAELVAVITVLQDFDINIISDSAYVVQATRDVETALIK
3	P63136-D3	533-773	241		YSMDDQLNQLFNLLQQTVRKRNFPFYITHIRAHTNLPGPLTKANKQADLLVSSALIKAQELHALTHVNAAGLKNKFDVTWKLAKDIVQHCTQCQVLHLPTQEAGVNPRGLCPNALWQMDVTHVPSFGRLSYVHVTVDTYSHFIWATCHTGESTSHVKKHLLSCFAVMGVPEKIKTDNGPGYCSKAFQKFLSQWKISHTTGIPYNSQGQAIVERTNRTLKTQLVKQKEGGDSKECTTPQMQL
4	P63136-D4	774-847	74		NLALYTLNFLNIYRNQTTTSAEQHLTGKKNSPHEGKLIWWKDNKNKTWEIGKVITWGRGFACVSPGENQLPVWI
5	P63136-D5	848-954	107		PTRHLKFYNEPIRDAKKSTSAETETPQSSTVDSQDEQNGDVRRTDEVAIHQEGRAANLGTTKEADAVSYKISREHKGDTNPREYAACSLDDCINGGKSPYACRSSCS

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.45

(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	1rw3A	0.28	3.90	0.170	0.308	model1_1rw3A.pdb.gz
2	7lhtA	0.28	9.20	0.025	0.448	model1_7lhtA.pdb.gz
3	6rc9A	0.28	9.71	0.048	0.471	model1_6rc9A.pdb.gz
4	4o9xA	0.28	9.15	0.042	0.444	model1_4o9xA.pdb.gz
5	2pffB	0.27	8.87	0.030	0.428	model1_2pffB.pdb.gz
6	2uvcG	0.27	8.90	0.027	0.429	model1_2uvcG.pdb.gz
7	7cpxA	0.27	8.89	0.026	0.430	model1_7cpxA.pdb.gz
8	3hmjG	0.27	9.05	0.026	0.427	model1_3hmjG.pdb.gz
9	6u5vB	0.27	9.44	0.044	0.442	model1_6u5vB.pdb.gz
10	3p8cA	0.27	9.26	0.031	0.434	model1_3p8cA.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	0.70	catalytic activity
GO:0004518	0.60	nuclease activity
GO:0016772	0.57	transferase activity, transferring phosphorus-containing groups
GO:0034061	0.56	DNA polymerase activity
GO:0004540	0.56	ribonuclease activity
GO:0016891	0.55	endoribonuclease activity, producing 5'-phosphomonoesters
GO:0008233	0.55	peptidase 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:0044260	0.98	cellular macromolecule metabolic process
GO:0044238	0.98	primary metabolic process
GO:0006259	0.95	DNA metabolic process
GO:0071897	0.76	DNA biosynthetic process
GO:0019058	0.72	viral life cycle
GO:0030260	0.68	entry into host cell
GO:0019043	0.68	establishment of viral latency
GO:0075713	0.55	establishment of integrated proviral latency
GO:0051169	0.55	nuclear transport
GO:0019072	0.55	viral genome packaging
GO:0019068	0.55	virion assembly
GO:0019064	0.55	fusion of virus membrane with host plasma membrane
GO:0019061	0.55	uncoating of virus
GO:0006278	0.55	RNA-dependent DNA biosynthetic process
GO:0019538	0.50	protein 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:0044464	1.00	cell part
GO:0044424	0.91	intracellular part
GO:0016020	0.83	membrane
GO:0044446	0.78	intracellular organelle part
GO:0044444	0.73	cytoplasmic part
GO:0044428	0.70	nuclear part
GO:0005886	0.65	plasma membrane
GO:0005829	0.65	cytosol
GO:0005576	0.64	extracellular region
GO:0005654	0.62	nucleoplasm

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	1bxrA	0.229	9.16	0.031	0.368	6.3.5.5	NA
2	0.060	2pffB	0.194	8.90	0.039	0.308	2.3.1.86	NA
3	0.060	2hvtB	0.189	5.75	0.153	0.236	2.7.7.49	NA
4	0.060	2pffA	0.247	9.05	0.032	0.394	2.3.1.41 2.3.1.86	NA
5	0.060	1t3tA	0.253	8.67	0.020	0.389	6.3.5.3	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	0.01	3lamA	0.263	4.08	0.155	0.292	0.17	KRP	complex1.pdb.gz	16,336,337,338,393
2	0.01	1rtdC	0.252	3.33	0.136	0.270	0.16	QNA	complex2.pdb.gz	297,298,517
3	0.01	3kk1A	0.248	4.49	0.159	0.283	0.14	QNA	complex3.pdb.gz	88,90,93,164,166,169
4	0.01	1c0uA	0.259	4.38	0.157	0.293	0.15	BM5	complex4.pdb.gz	336,337,338,394
5	0.01	3qo9A	0.259	4.42	0.148	0.293	0.16	QO9	complex5.pdb.gz	8,9,60,342,350
6	0.01	1s1uA	0.260	4.19	0.172	0.291	0.19	NVP	complex6.pdb.gz	337,338,339

	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.