D-I-TASSER Q8NET4

D-I-TASSER results for Q8NET4

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

Summary of the Protein

Uniprot ID: Q8NET4
Protein Name: Retrotransposon Gag-like protein 9
Gene Name: RTL9

Input Sequence in FASTA format

>Q8NET4 (1388 residues)
MSIPLHSLRFNNTMREENVEPQNKQMAFCRPMTETRADVQILHSHVQLPIVSTSASDPGG
TSTQLMTSPVFDTMSAPLMGVPNSGALSPPLMPASDSGALSPLLMPASDSGALSPLLMPA
LDSGTLSPLLSTSEYGVMSPGMMTIPDFGTMSATLMVAPDSAEISPLAMPAPSSGVVCTP
IMSTSSSEAMSTPLMLAPDSGELSPILMQDMNPGVMSTQPVPAPSSEAMSPLQITDEDTE
AMSKVLMTALASGEISSLLMSGTDSEAISSLIMSAVASGGTSPQPTSTQNSGGIPTPLMS
DLDSGIMSSLLMSSPGSEVMSTPLLSVPDAGEMSTLPKPAPDAEAMSPALMTALPSGVMP
TQTMPAPGSGAMSPWSTQNVDSEMMSNPPVRATASGVMSAPPVRALDSGAMSTPLMGAPA
SGNMSTLQKTVPASGAMTTSLMTVPSSGVMSTEQMSATASRVMSAQLTMAKTSGAMPTGS
MKAVAKQYKRATASGKMSTPLRRAPTSGAMSTQPVTATASETMSMPQLTVPASGSMSMLQ
MRAPVSEAMSMPQMRTMASGLTSAAQMKAMTSGAMSTPLMTAQTSGSTSTLLMRDTASGV
MSCPQMRSLASGALSKPLMTPKASGTMFTEKMTTTASEAMPTLLMRDTVSGALSMPQMTD
TASGGLSASLMRDTASGAMSTSQMTATVSGGMSMPLMRAQDPGVMPASLMRAKVSGKMLS
QPMSTQDPGGMSMSPMKSMTAGGMQMNSPTSDVMSTPTVRAWTSETMSTPLMRTSDPGER
PSLLTRASSSGEMSLPLMRAPASGEIATPLRSPAYGAMSAPQMTATASGMMSSMPQVKAP
ISGAMSMPLTRSTASGGMSMPLMRAPDSRVTSTSQMMPTASGDMCTLPVRAPASGGVSSP
LVRAPASGTMSTPLRRPSACETVSTELMRASASGHMSTAQTTAMVSGGMSKPLMRAPASG
TMPMPLMSAMASGEMSMPLMETMASGATSTLQTSVANSRSMSLSQTTYTVSGRMATAPIR
ASASGARSTSFMRASVSGSMPMPLPRATASGCGMGMSMPQMTATDSRGMSTPLMRASGPG
TMSTPQTAFGVMSTPEIKATDSGEASTSHINITASGSKPTSHMTATTPETAKPPPKEVPS
FGMLTPALCYLLEEQEAARGSCSVEEEMEIDEEKQMKGFLDDSERMAFLVSLHLGAAERW
FILQMEVGEPLSHENKSFLRRSQGIYDSLSEIDILSAVLCHPKQGQKSVRQYATDFLLLA
RHLSWSDAILRTRFLEGLSEAVTTKMGRIFLKVAGSLKELIDRSLYTECQLAEEKDSPGN
SSQVLPTACKRNNEEAMGNELSSQQQTEEHQHVSKRCYYLKEHGDPQEGLHDHLGQSTGH
HQKAHTNK

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	Q8NET4-D1	1-729,811-1099	1018		MSIPLHSLRFNNTMREENVEPQNKQMAFCRPMTETRADVQILHSHVQLPIVSTSASDPGGTSTQLMTSPVFDTMSAPLMGVPNSGALSPPLMPASDSGALSPLLMPASDSGALSPLLMPALDSGTLSPLLSTSEYGVMSPGMMTIPDFGTMSATLMVAPDSAEISPLAMPAPSSGVVCTPIMSTSSSEAMSTPLMLAPDSGELSPILMQDMNPGVMSTQPVPAPSSEAMSPLQITDEDTEAMSKVLMTALASGEISSLLMSGTDSEAISSLIMSAVASGGTSPQPTSTQNSGGIPTPLMSDLDSGIMSSLLMSSPGSEVMSTPLLSVPDAGEMSTLPKPAPDAEAMSPALMTALPSGVMPTQTMPAPGSGAMSPWSTQNVDSEMMSNPPVRATASGVMSAPPVRALDSGAMSTPLMGAPASGNMSTLQKTVPASGAMTTSLMTVPSSGVMSTEQMSATASRVMSAQLTMAKTSGAMPTGSMKAVAKQYKRATASGKMSTPLRRAPTSGAMSTQPVTATASETMSMPQLTVPASGSMSMLQMRAPVSEAMSMPQMRTMASGLTSAAQMKAMTSGAMSTPLMTAQTSGSTSTLLMRDTASGVMSCPQMRSLASGALSKPLMTPKASGTMFTEKMTTTASEAMPTLLMRDTVSGALSMPQMTDTASGGLSASLMRDTASGAMSTSQMTATVSGGMSMPLMRAQDPGVMPASLMRAKVSGKMLSQPMSTQDPGRSPAYGAMSAPQMTATASGMMSSMPQVKAPISGAMSMPLTRSTASGGMSMPLMRAPDSRVTSTSQMMPTASGDMCTLPVRAPASGGVSSPLVRAPASGTMSTPLRRPSACETVSTELMRASASGHMSTAQTTAMVSGGMSKPLMRAPASGTMPMPLMSAMASGEMSMPLMETMASGATSTLQTSVANSRSMSLSQTTYTVSGRMATAPIRASASGARSTSFMRASVSGSMPMPLPRATASGCGMGMSMPQMTATDSRGMSTPLMRASGPGTMSTPQTAFGVMSTPEIKA
2	Q8NET4-D2	730-810,1100-1137	119		GMSMSPMKSMTAGGMQMNSPTSDVMSTPTVRAWTSETMSTPLMRTSDPGERPSLLTRASSSGEMSLPLMRAPASGEIATPLTDSGEASTSHINITASGSKPTSHMTATTPETAKPPPKE
3	Q8NET4-D3	1138-1194	57		VPSFGMLTPALCYLLEEQEAARGSCSVEEEMEIDEEKQMKGFLDDSERMAFLVSLHL
4	Q8NET4-D4	1195-1388	194		GAAERWFILQMEVGEPLSHENKSFLRRSQGIYDSLSEIDILSAVLCHPKQGQKSVRQYATDFLLLARHLSWSDAILRTRFLEGLSEAVTTKMGRIFLKVAGSLKELIDRSLYTECQLAEEKDSPGNSSQVLPTACKRNNEEAMGNELSSQQQTEEHQHVSKRCYYLKEHGDPQEGLHDHLGQSTGHHQKAHTNK

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.41

(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	7abhE	0.70	3.00	0.074	0.728	model1_7abhE.pdb.gz
2	5hy7A	0.65	3.95	0.067	0.710	model1_5hy7A.pdb.gz
3	5lqwX	0.59	5.07	0.073	0.678	model1_5lqwX.pdb.gz
4	5nrlP	0.59	5.91	0.066	0.699	model1_5nrlP.pdb.gz
5	3ei2A	0.57	5.76	0.073	0.668	model1_3ei2A.pdb.gz
6	6eojA	0.54	6.38	0.060	0.649	model1_6eojA.pdb.gz
7	6bllA	0.53	6.05	0.065	0.623	model1_6bllA.pdb.gz
8	6jp6A	0.36	7.79	0.046	0.480	model1_6jp6A.pdb.gz
9	5wlcLQ	0.35	4.62	0.042	0.392	model1_5wlcLQ.pdb.gz
10	6p2kA	0.34	5.65	0.057	0.408	model1_6p2kA.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:1901363	0.79	heterocyclic compound binding
GO:0097159	0.79	organic cyclic compound binding
GO:0003676	0.72	nucleic acid binding

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	0.95	cellular process
GO:0065007	0.87	biological regulation
GO:0044699	0.87	single-organism process
GO:0044763	0.81	single-organism cellular process
GO:0050789	0.80	regulation of biological process
GO:0008152	0.79	metabolic process
GO:0050794	0.78	regulation of cellular process
GO:0071704	0.77	organic substance metabolic process
GO:0044238	0.77	primary metabolic process
GO:0044237	0.77	cellular metabolic process
GO:0044260	0.76	cellular macromolecule metabolic process
GO:0016043	0.70	cellular component organization
GO:0065008	0.69	regulation of biological quality
GO:0006139	0.69	nucleobase-containing compound metabolic process
GO:0090304	0.68	nucleic acid metabolic process
GO:0048518	0.66	positive regulation of biological process
GO:0019538	0.65	protein metabolic process
GO:0050896	0.64	response to stimulus
GO:0048522	0.64	positive regulation of cellular process
GO:0048519	0.64	negative regulation of biological process
GO:0006464	0.64	cellular protein modification process
GO:0048523	0.63	negative regulation of cellular process
GO:0051128	0.62	regulation of cellular component organization
GO:0043933	0.62	macromolecular complex subunit organization
GO:0007267	0.62	cell-cell signaling
GO:0007165	0.62	signal transduction
GO:0006996	0.61	organelle organization
GO:0022607	0.60	cellular component assembly
GO:0006950	0.60	response to stress
GO:0006325	0.59	chromatin organization
GO:1903047	0.58	mitotic cell cycle process
GO:0065003	0.58	macromolecular complex assembly
GO:0051726	0.58	regulation of cell cycle
GO:0051716	0.58	cellular response to stimulus
GO:0016567	0.58	protein ubiquitination
GO:0051130	0.57	positive regulation of cellular component organization
GO:0044087	0.57	regulation of cellular component biogenesis
GO:0042592	0.57	homeostatic process
GO:0034622	0.57	cellular macromolecular complex assembly
GO:1901987	0.56	regulation of cell cycle phase transition
GO:0071214	0.56	cellular response to abiotic stimulus
GO:0065004	0.56	protein-DNA complex assembly
GO:0044089	0.56	positive regulation of cellular component biogenesis
GO:0033554	0.56	cellular response to stress
GO:0016570	0.56	histone modification
GO:0010941	0.56	regulation of cell death
GO:0007346	0.56	regulation of mitotic cell cycle
GO:0007166	0.56	cell surface receptor signaling pathway
GO:0006259	0.56	DNA metabolic process
GO:0051603	0.55	proteolysis involved in cellular protein catabolic process
GO:0051276	0.55	chromosome organization
GO:0048878	0.55	chemical homeostasis
GO:0048524	0.55	positive regulation of viral process
GO:0044770	0.55	cell cycle phase transition
GO:0044265	0.55	cellular macromolecule catabolic process
GO:0043069	0.55	negative regulation of programmed cell death
GO:0042981	0.55	regulation of apoptotic process
GO:0034644	0.55	cellular response to UV
GO:0031334	0.55	positive regulation of protein complex assembly
GO:0006281	0.55	DNA repair
GO:1905114	0.54	cell surface receptor signaling pathway involved in cell-cell signaling
GO:1903902	0.54	positive regulation of viral life cycle
GO:1902186	0.54	regulation of viral release from host cell
GO:0198738	0.54	cell-cell signaling by wnt
GO:0090305	0.54	nucleic acid phosphodiester bond hydrolysis
GO:0051606	0.54	detection of stimulus
GO:0046719	0.54	regulation by virus of viral protein levels in host cell
GO:0045069	0.54	regulation of viral genome replication
GO:0044772	0.54	mitotic cell cycle phase transition
GO:0033522	0.54	histone H2A ubiquitination
GO:0032508	0.54	DNA duplex unwinding
GO:0010498	0.54	proteasomal protein catabolic process
GO:0010390	0.54	histone monoubiquitination
GO:0006511	0.54	ubiquitin-dependent protein catabolic process
GO:0006289	0.54	nucleotide-excision repair

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	0.99	cell part
GO:0044424	0.97	intracellular part
GO:0043226	0.95	organelle
GO:0043229	0.85	intracellular organelle
GO:0044422	0.84	organelle part
GO:0043227	0.84	membrane-bounded organelle
GO:0044446	0.83	intracellular organelle part
GO:0044421	0.82	extracellular region part
GO:0043231	0.82	intracellular membrane-bounded organelle
GO:0032991	0.80	macromolecular complex
GO:0005634	0.80	nucleus
GO:0043234	0.78	protein complex
GO:0043230	0.78	extracellular organelle
GO:0044428	0.76	nuclear part
GO:0005737	0.69	cytoplasm
GO:0005654	0.61	nucleoplasm
GO:1990234	0.59	transferase complex
GO:0044427	0.59	chromosomal part
GO:0031988	0.59	membrane-bounded vesicle
GO:0070062	0.58	extracellular exosome

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	1e5tA	0.270	6.47	0.049	0.332	3.4.21.26	NA
2	0.060	2gbcA	0.256	7.14	0.046	0.328	3.4.14.5 3.4.15.5	NA
3	0.060	2vz8A	0.278	10.15	0.045	0.437	2.3.1.85	NA
4	0.060	3eqlM	0.231	9.60	0.033	0.352	2.7.7.6	NA
5	0.060	2ckjA	0.264	9.77	0.027	0.405	1.17.1.4 1.17.3.2	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:

No Binding sites was predicted

Click to view	Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues

	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.