D-I-TASSER Q8N4H0

D-I-TASSER results for Q8N4H0

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

Summary of the Protein

Uniprot ID: Q8N4H0
Protein Name: Spermatogenesis associated 6-like protein
Gene Name: SPATA6L

Input Sequence in FASTA format

>Q8N4H0 (392 residues)
MPLEVVVELQIRAISCPGVFLPGKQDVYLGVYLMNQYLETNSFPSAFPIMIQESMRFEKV
FESAVDPGAVVDLLEMWDELAYYEENTRDFLFPEPKLTPSHPRRCREVLMKTALGFPGIA
PKIEFSTRTAIRECVFLHRNRFLEERHESRRPLSTSHEPIFPLNTIKMKLKENNLNRLPK
GMQARAPSQYSTRHFFQDQPAQLNLGNNFKISGGSKPPFVVRHVDSAKPFGENISEHHLR
RSRRKSKFSDFPFPTRRASSLDSLAANVKVIKEPDERIVLRSDSSSCLDSSQFGKSSSSK
QGDADFHGKASFATYQHSTSPGPLDQPLLRERFHPGSQSTWKNIHERVCSLLTSHRAQLH
QNKEDSTSEVNYIIERPSYPLKKYSLHEQRYF

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	Q8N4H0-D1	1-392	392		MPLEVVVELQIRAISCPGVFLPGKQDVYLGVYLMNQYLETNSFPSAFPIMIQESMRFEKVFESAVDPGAVVDLLEMWDELAYYEENTRDFLFPEPKLTPSHPRRCREVLMKTALGFPGIAPKIEFSTRTAIRECVFLHRNRFLEERHESRRPLSTSHEPIFPLNTIKMKLKENNLNRLPKGMQARAPSQYSTRHFFQDQPAQLNLGNNFKISGGSKPPFVVRHVDSAKPFGENISEHHLRRSRRKSKFSDFPFPTRRASSLDSLAANVKVIKEPDERIVLRSDSSSCLDSSQFGKSSSSKQGDADFHGKASFATYQHSTSPGPLDQPLLRERFHPGSQSTWKNIHERVCSLLTSHRAQLHQNKEDSTSEVNYIIERPSYPLKKYSLHEQRYF

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.4603

(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	4q2cA2	0.43	6.55	0.065	0.694	model1_4q2cA2.pdb.gz
2	5v9xA	0.42	6.51	0.050	0.673	model1_5v9xA.pdb.gz
3	4f91B2	0.41	6.51	0.037	0.666	model1_4f91B2.pdb.gz
4	5wsge	0.41	6.32	0.034	0.653	model1_5wsge.pdb.gz
5	4qqxA	0.41	6.77	0.049	0.673	model1_4qqxA.pdb.gz
6	6zm2A	0.41	6.46	0.056	0.645	model1_6zm2A.pdb.gz
7	5xjcY	0.41	6.46	0.053	0.643	model1_5xjcY.pdb.gz
8	5vhaA	0.41	6.72	0.050	0.668	model1_5vhaA.pdb.gz
9	7abis	0.40	6.47	0.036	0.643	model1_7abis.pdb.gz
10	3l9oA	0.40	6.94	0.048	0.691	model1_3l9oA.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:0008092	0.43	cytoskeletal protein binding
GO:0032027	0.36	myosin light chain binding
GO:1901363	0.35	heterocyclic compound binding
GO:0097159	0.35	organic cyclic compound 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	0.85	cellular process
GO:0044699	0.76	single-organism process
GO:0044763	0.68	single-organism cellular process
GO:0016043	0.59	cellular component organization
GO:0032502	0.56	developmental process
GO:0044767	0.55	single-organism developmental process
GO:0022414	0.53	reproductive process
GO:0006996	0.52	organelle organization
GO:1902589	0.50	single-organism organelle organization
GO:0048609	0.50	multicellular organismal reproductive process
GO:0044702	0.50	single organism reproductive 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:0044422	0.72	organelle part
GO:0044424	0.59	intracellular part
GO:0016020	0.47	membrane
GO:0097224	0.46	sperm connecting piece
GO:0032991	0.41	macromolecular complex
GO:0043234	0.39	protein complex
GO:0044425	0.34	membrane part
GO:0005886	0.33	plasma membrane

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	1ofdA	0.363	6.89	0.042	0.602	1.4.7.1	NA
2	0.060	2iukB	0.353	6.84	0.059	0.584	1.13.11.12	NA
3	0.060	1yksA	0.361	6.50	0.037	0.579	3.4.21.91	NA
4	0.060	1kqfA	0.372	6.77	0.042	0.610	1.2.1.2	NA
5	0.060	1q16A	0.347	6.96	0.036	0.594	1.7.99.4	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	1t36A	0.371	7.09	0.012	0.628	0.20	U	complex1.pdb.gz	18,19,118
2	0.01	1ea0A	0.387	6.93	0.029	0.643	0.11	AKG	complex2.pdb.gz	17,20,28
3	0.01	2vdcA	0.386	6.72	0.041	0.625	0.11	AKG	complex3.pdb.gz	17,20,28
4	0.01	1ce8C	0.368	6.94	0.044	0.607	0.14	ADP	complex4.pdb.gz	26,45,46,47,119
5	0.01	1m6vC	0.373	6.85	0.039	0.612	0.11	ADP	complex5.pdb.gz	13,15,51,52
6	0.01	1ce8E	0.346	7.46	0.041	0.620	0.22	ADP	complex6.pdb.gz	12,13,14,18,44
7	0.01	1ce8A	0.371	6.69	0.042	0.600	0.19	IMP	complex7.pdb.gz	30,31,38,40,110,117,119
8	0.01	1jdbH	0.370	7.09	0.012	0.625	0.35	GLN	complex8.pdb.gz	18,19,20,44,45
9	0.01	1bxrA	0.373	7.46	0.053	0.658	0.13	ANP	complex9.pdb.gz	21,42,119
10	0.01	2vdcB	0.388	6.65	0.042	0.630	0.12	AKG	complex10.pdb.gz	18,28,118

	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.