D-I-TASSER Q8IYB8

D-I-TASSER results for Q8IYB8

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

Summary of the Protein

Uniprot ID: Q8IYB8
Protein Name: ATP-dependent RNA helicase SUPV3L1, mitochondrial
Gene Name: SUPV3L1

Input Sequence in FASTA format

>Q8IYB8 (786 residues)
MSFSRALLWARLPAGRQAGHRAAICSALRPHFGPFPGVLGQVSVLATASSSASGGSKIPN
TSLFVPLTVKPQGPSADGDVGAELTRPLDKNEVKKVLDKFYKRKEIQKLGADYGLDARLF
HQAFISFRNYIMQSHSLDVDIHIVLNDICFGAAHADDLFPFFLRHAKQIFPVLDCKDDLR
KISDLRIPPNWYPDARAMQRKIIFHSGPTNSGKTYHAIQKYFSAKSGVYCGPLKLLAHEI
FEKSNAAGVPCDLVTGEERVTVQPNGKQASHVSCTVEMCSVTTPYEVAVIDEIQMIRDPA
RGWAWTRALLGLCAEEVHLCGEPAAIDLVMELMYTTGEEVEVRDYKRLTPISVLDHALES
LDNLRPGDCIVCFSKNDIYSVSRQIEIRGLESAVIYGSLPPGTKLAQAKKFNDPNDPCKI
LVATDAIGMGLNLSIRRIIFYSLIKPSINEKGERELEPITTSQALQIAGRAGRFSSRFKE
GEVTTMNHEDLSLLKEILKRPVDPIRAAGLHPTAEQIEMFAYHLPDATLSNLIDIFVDFS
QVDGQYFVCNMDDFKFSAELIQHIPLSLRVRYVFCTAPINKKQPFVCSSLLQFARQYSRN
EPLTFAWLRRYIKWPLLPPKNIKDLMDLEAVHDVLDLYLWLSYRFMDMFPDASLIRDLQK
ELDGIIQDGVHNITKLIKMSETHKLLNLEGFPSGSQSRLSGTLKSQARRTRGTKALGSKA
TEPPSPDAGELSLASRLVQQGLLTPDMLKQLEKEWMTQQTEHNKEKTESGTHPKGTRRKK
KEPDSD

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	Q8IYB8-D1	1-59	59		MSFSRALLWARLPAGRQAGHRAAICSALRPHFGPFPGVLGQVSVLATASSSASGGSKIP
2	Q8IYB8-D2	60-173	114		NTSLFVPLTVKPQGPSADGDVGAELTRPLDKNEVKKVLDKFYKRKEIQKLGADYGLDARLFHQAFISFRNYIMQSHSLDVDIHIVLNDICFGAAHADDLFPFFLRHAKQIFPVL
3	Q8IYB8-D3	174-786	613		DCKDDLRKISDLRIPPNWYPDARAMQRKIIFHSGPTNSGKTYHAIQKYFSAKSGVYCGPLKLLAHEIFEKSNAAGVPCDLVTGEERVTVQPNGKQASHVSCTVEMCSVTTPYEVAVIDEIQMIRDPARGWAWTRALLGLCAEEVHLCGEPAAIDLVMELMYTTGEEVEVRDYKRLTPISVLDHALESLDNLRPGDCIVCFSKNDIYSVSRQIEIRGLESAVIYGSLPPGTKLAQAKKFNDPNDPCKILVATDAIGMGLNLSIRRIIFYSLIKPSINEKGERELEPITTSQALQIAGRAGRFSSRFKEGEVTTMNHEDLSLLKEILKRPVDPIRAAGLHPTAEQIEMFAYHLPDATLSNLIDIFVDFSQVDGQYFVCNMDDFKFSAELIQHIPLSLRVRYVFCTAPINKKQPFVCSSLLQFARQYSRNEPLTFAWLRRYIKWPLLPPKNIKDLMDLEAVHDVLDLYLWLSYRFMDMFPDASLIRDLQKELDGIIQDGVHNITKLIKMSETHKLLNLEGFPSGSQSRLSGTLKSQARRTRGTKALGSKATEPPSPDAGELSLASRLVQQGLLTPDMLKQLEKEWMTQQTEHNKEKTESGTHPKGTRRKKKEPDSD

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.47

(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	3rc3A	0.66	3.40	0.824	0.710	model1_3rc3A.pdb.gz
2	6f4aB	0.53	1.89	0.283	0.543	model1_6f4aB.pdb.gz
3	5aorA	0.52	6.06	0.100	0.663	model1_5aorA.pdb.gz
4	5n8rA	0.49	5.78	0.087	0.622	model1_5n8rA.pdb.gz
5	5vhaA	0.48	5.13	0.107	0.579	model1_5vhaA.pdb.gz
6	6zm2A	0.48	5.22	0.112	0.587	model1_6zm2A.pdb.gz
7	3kx2B	0.48	5.95	0.099	0.611	model1_3kx2B.pdb.gz
8	6o16A	0.47	5.59	0.115	0.597	model1_6o16A.pdb.gz
9	4xgtA	0.47	5.02	0.159	0.558	model1_4xgtA.pdb.gz
10	6c90A	0.47	5.15	0.160	0.560	model1_6c90A.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:0004386	1.00	helicase activity
GO:1901363	0.91	heterocyclic compound binding
GO:0097159	0.91	organic cyclic compound binding
GO:0003678	0.87	DNA helicase activity
GO:0003676	0.87	nucleic acid binding
GO:0003677	0.81	DNA binding
GO:0016887	0.74	ATPase activity
GO:0003724	0.73	RNA helicase activity
GO:0003723	0.68	RNA binding
GO:0008026	0.67	ATP-dependent helicase activity
GO:0004004	0.65	ATP-dependent RNA helicase activity
GO:0034458	0.54	3'-5' RNA helicase activity
GO:0003725	0.54	double-stranded RNA 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	0.97	cellular process
GO:0008152	0.90	metabolic process
GO:0044237	0.87	cellular metabolic process
GO:0071704	0.86	organic substance metabolic process
GO:0044238	0.86	primary metabolic process
GO:0044260	0.85	cellular macromolecule metabolic process
GO:0034641	0.85	cellular nitrogen compound metabolic process
GO:0090304	0.84	nucleic acid metabolic process
GO:0016070	0.82	RNA metabolic process
GO:0006996	0.80	organelle organization
GO:0032508	0.76	DNA duplex unwinding
GO:0065007	0.75	biological regulation
GO:0050789	0.74	regulation of biological process
GO:0044699	0.73	single-organism process
GO:0050794	0.71	regulation of cellular process
GO:0006396	0.69	RNA processing
GO:0048518	0.68	positive regulation of biological process
GO:0016071	0.68	mRNA metabolic process
GO:0048522	0.67	positive regulation of cellular process
GO:0006401	0.67	RNA catabolic process
GO:0044763	0.66	single-organism cellular process
GO:0000959	0.66	mitochondrial RNA metabolic process
GO:0080090	0.63	regulation of primary metabolic process
GO:0060255	0.63	regulation of macromolecule metabolic process
GO:0051171	0.63	regulation of nitrogen compound metabolic process
GO:0031323	0.63	regulation of cellular metabolic process
GO:0000965	0.62	mitochondrial RNA 3'-end processing
GO:0051173	0.60	positive regulation of nitrogen compound metabolic process
GO:0044767	0.60	single-organism developmental process
GO:0031325	0.60	positive regulation of cellular metabolic process
GO:0010604	0.60	positive regulation of macromolecule metabolic process
GO:0006402	0.60	mRNA catabolic process
GO:0051128	0.59	regulation of cellular component organization
GO:0006259	0.58	DNA metabolic process
GO:0048869	0.56	cellular developmental process
GO:0000957	0.56	mitochondrial RNA catabolic process
GO:0051252	0.55	regulation of RNA metabolic process
GO:0048519	0.55	negative regulation of biological process
GO:0040008	0.55	regulation of growth
GO:0048523	0.54	negative regulation of cellular process
GO:0043933	0.54	macromolecular complex subunit organization
GO:0006310	0.54	DNA recombination
GO:0051254	0.53	positive regulation of RNA metabolic process
GO:0043066	0.53	negative regulation of apoptotic process
GO:0009653	0.53	anatomical structure morphogenesis
GO:0006325	0.53	chromatin organization
GO:0070827	0.52	chromatin maintenance
GO:0070584	0.52	mitochondrion morphogenesis
GO:0035946	0.52	mitochondrial mRNA surveillance
GO:0035945	0.52	mitochondrial ncRNA surveillance
GO:0030307	0.52	positive regulation of cell growth
GO:0000962	0.52	positive regulation of mitochondrial RNA catabolic process
GO:0000958	0.52	mitochondrial mRNA catabolic 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:0044424	1.00	intracellular part
GO:0044444	0.98	cytoplasmic part
GO:0044446	0.95	intracellular organelle part
GO:0044429	0.93	mitochondrial part
GO:0005759	0.88	mitochondrial matrix
GO:0043229	0.87	intracellular organelle
GO:0043231	0.82	intracellular membrane-bounded organelle
GO:0005739	0.75	mitochondrion
GO:0032991	0.74	macromolecular complex
GO:0043234	0.70	protein complex
GO:0005634	0.67	nucleus
GO:0000178	0.66	exosome (RNase complex)
GO:0098798	0.65	mitochondrial protein complex
GO:0000177	0.64	cytoplasmic exosome (RNase complex)
GO:0045025	0.63	mitochondrial degradosome

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	2vdcA	0.295	8.72	0.026	0.480	1.4.1.13	NA
2	0.060	3kx2B	0.476	5.95	0.099	0.611	3.6.4.13	NA
3	0.060	2bhrA	0.374	5.04	0.116	0.447	3.4.21.91	NA
4	0.060	2db3A	0.321	3.61	0.129	0.359	3.6.4.13	633
5	0.060	1w36D	0.312	6.15	0.073	0.408	3.1.11.5	591

	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	2oc7A	0.096	6.00	0.053	0.127	0.12	III	complex1.pdb.gz	21,24,46
2	0.01	1ns3B	0.110	5.86	0.087	0.142	0.11	III	complex2.pdb.gz	1,2,3,41,429
3	0.01	2gvfC	0.089	5.89	0.034	0.116	0.11	III	complex3.pdb.gz	5,6,7,722
4	0.01	2gvfA	0.108	5.43	0.051	0.137	0.12	III	complex4.pdb.gz	21,22,23,591
5	0.01	1rgqB	0.107	5.85	0.023	0.140	0.12	III	complex5.pdb.gz	23,27,46,580,581,582
6	0.01	3keeA	0.107	5.47	0.072	0.136	0.10	III	complex6.pdb.gz	3,29,30,54
7	0.01	1jxpA	0.105	5.43	0.073	0.132	0.10	III	complex7.pdb.gz	513,514,517
8	0.01	2a4gA	0.102	6.38	0.019	0.139	0.11	III	complex8.pdb.gz	43,44,45,46,47,48,49
9	0.01	2vbcA	0.382	5.73	0.084	0.476	0.12	III	complex9.pdb.gz	445,447,453,455,457
10	0.01	1dy9A	0.097	6.09	0.039	0.129	0.12	III	complex10.pdb.gz	397,398,457

	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.