D-I-TASSER Q9BVQ7

D-I-TASSER results for Q9BVQ7

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

Summary of the Protein

Uniprot ID: Q9BVQ7
Protein Name: Spermatogenesis-associated protein 5-like protein 1
Gene Name: SPATA5L1

Input Sequence in FASTA format

>Q9BVQ7 (753 residues)
MAPDSDPFPEGPLLKLLPLDARDRGTQRCRLGPAALHALGARLGSAVKISLPDGGSCLCT
AWPRRDGADGFVQLDPLCASPGAAVGASRSRRSLSLNRLLLVPCPPLRRVAVWPVLRERA
GAPGARNTAAVLEAAQELLRNRPISLGHVVVAPPGAPGLVAALHIVGGTPSPDPAGLVTP
RTRVSLGGEPPSEAQPQPEVPLGGLSEAADSLRELLRLPLRYPRALTALGLAVPRGVLLA
GPPGVGKTQLVRAVAREAGAELLAVSAPALQGSRPGETEENVRRVFQRARELASRGPSLL
FLDEMDALCPQRGSRAPESRVVAQVLTLLDGASGDREVVVVGATNRPDALDPALRRPGRF
DREVVIGTPTLKQRKEILQVITSKMPISSHVDLGLLAEMTVGYVGADLTALCREAAMHAL
LHSEKNQDNPVIDEIDFLEAFKNIQPSSFRSVIGLMDIKPVDWEEIGGLEDVKLKLKQSI
EWPLKFPWEFVRMGLTQPKGVLLYGPPGCAKTTLVRALATSCHCSFVSVSGADLFSPFVG
DSEKVLSQIFRQARASTPAILFLDEIDSILGARSASKTGCDVQERVLSVLLNELDGVGLK
TIERRGSKSSQQEFQEVFNRSVMIIAATNRPDVLDTALLRPGRLDKIIYIPPPDHKGRLS
ILKVCTKTMPIGPDVSLENLAAETCFFSGADLRNLCTEAALLALQENGLDATTVKQEHFL
KSLKTVKPSLSCKDLALYENLFKKEGFSNVEGI

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	Q9BVQ7-D1	1-101	101		MAPDSDPFPEGPLLKLLPLDARDRGTQRCRLGPAALHALGARLGSAVKISLPDGGSCLCTAWPRRDGADGFVQLDPLCASPGAAVGASRSRRSLSLNRLLL
2	Q9BVQ7-D2	102-192	91		VPCPPLRRVAVWPVLRERAGAPGARNTAAVLEAAQELLRNRPISLGHVVVAPPGAPGLVAALHIVGGTPSPDPAGLVTPRTRVSLGGEPPS
3	Q9BVQ7-D3	193-366	174		EAQPQPEVPLGGLSEAADSLRELLRLPLRYPRALTALGLAVPRGVLLAGPPGVGKTQLVRAVAREAGAELLAVSAPALQGSRPGETEENVRRVFQRARELASRGPSLLFLDEMDALCPQRGSRAPESRVVAQVLTLLDGASGDREVVVVGATNRPDALDPALRRPGRFDREVVI
4	Q9BVQ7-D4	367-446	80		GTPTLKQRKEILQVITSKMPISSHVDLGLLAEMTVGYVGADLTALCREAAMHALLHSEKNQDNPVIDEIDFLEAFKNIQP
5	Q9BVQ7-D5	447-651	205		SSFRSVIGLMDIKPVDWEEIGGLEDVKLKLKQSIEWPLKFPWEFVRMGLTQPKGVLLYGPPGCAKTTLVRALATSCHCSFVSVSGADLFSPFVGDSEKVLSQIFRQARASTPAILFLDEIDSILGARSASKTGCDVQERVLSVLLNELDGVGLKTIERRGSKSSQQEFQEVFNRSVMIIAATNRPDVLDTALLRPGRLDKIIYIP
6	Q9BVQ7-D6	652-753	102		PPDHKGRLSILKVCTKTMPIGPDVSLENLAAETCFFSGADLRNLCTEAALLALQENGLDATTVKQEHFLKSLKTVKPSLSCKDLALYENLFKKEGFSNVEGI

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.83

(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	6matA	0.58	4.44	0.343	0.684	model1_6matA.pdb.gz
2	6mdmB	0.56	5.41	0.188	0.695	model1_6mdmB.pdb.gz
3	1qvrA	0.54	5.42	0.147	0.664	model1_1qvrA.pdb.gz
4	6azyA	0.53	5.14	0.126	0.641	model1_6azyA.pdb.gz
5	6ahfC	0.53	5.42	0.119	0.661	model1_6ahfC.pdb.gz
6	3j94A	0.52	4.52	0.237	0.619	model1_3j94A.pdb.gz
7	5d4wA	0.52	4.29	0.158	0.606	model1_5d4wA.pdb.gz
8	5kneA	0.51	4.46	0.135	0.595	model1_5kneA.pdb.gz
9	6em8A	0.49	5.16	0.119	0.610	model1_6em8A.pdb.gz
10	4ciuA	0.49	5.14	0.128	0.603	model1_4ciuA.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:0016787	0.99	hydrolase activity
GO:0016887	0.98	ATPase activity
GO:0042623	0.89	ATPase activity, coupled
GO:0097159	0.80	organic cyclic compound binding
GO:1901363	0.79	heterocyclic compound binding
GO:0035639	0.76	purine ribonucleoside triphosphate binding
GO:0032555	0.76	purine ribonucleotide binding
GO:0032550	0.76	purine ribonucleoside binding
GO:0005524	0.74	ATP binding
GO:0046872	0.57	metal ion 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	0.96	cellular process
GO:0071704	0.80	organic substance metabolic process
GO:0044238	0.79	primary metabolic process
GO:0043170	0.78	macromolecule metabolic process
GO:0044699	0.77	single-organism process
GO:0019538	0.75	protein metabolic process
GO:0065007	0.73	biological regulation
GO:0044763	0.73	single-organism cellular process
GO:0044237	0.73	cellular metabolic process
GO:0016043	0.72	cellular component organization
GO:0006508	0.72	proteolysis
GO:0050789	0.71	regulation of biological process
GO:0044260	0.71	cellular macromolecule metabolic process
GO:0050794	0.70	regulation of cellular process
GO:0019222	0.66	regulation of metabolic process
GO:0031323	0.65	regulation of cellular metabolic process
GO:0006996	0.65	organelle organization
GO:0080090	0.64	regulation of primary metabolic process
GO:0060255	0.64	regulation of macromolecule metabolic process
GO:0048518	0.61	positive regulation of biological process
GO:0019219	0.61	regulation of nucleobase-containing compound metabolic process
GO:0009057	0.61	macromolecule catabolic process
GO:0048522	0.60	positive regulation of cellular process
GO:0044248	0.60	cellular catabolic process
GO:0030163	0.60	protein catabolic process
GO:1902589	0.59	single-organism organelle organization
GO:0051603	0.59	proteolysis involved in cellular protein catabolic process
GO:0051128	0.59	regulation of cellular component organization
GO:0044265	0.59	cellular macromolecule catabolic process
GO:0031326	0.59	regulation of cellular biosynthetic process
GO:0031325	0.59	positive regulation of cellular metabolic process
GO:0010604	0.59	positive regulation of macromolecule metabolic process
GO:0045935	0.58	positive regulation of nucleobase-containing compound metabolic process
GO:0031328	0.58	positive regulation of cellular biosynthetic process
GO:0006511	0.58	ubiquitin-dependent protein catabolic process
GO:0043161	0.57	proteasome-mediated ubiquitin-dependent protein catabolic process
GO:0030433	0.56	ER-associated ubiquitin-dependent protein catabolic process
GO:0051130	0.55	positive regulation of cellular component organization
GO:0007017	0.55	microtubule-based process
GO:0031334	0.54	positive regulation of protein complex assembly
GO:0000226	0.54	microtubule cytoskeleton organization
GO:0051179	0.51	localization
GO:0006810	0.50	transport

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	0.84	cytoplasmic part
GO:0044446	0.83	intracellular organelle part
GO:0043226	0.81	organelle
GO:0043229	0.80	intracellular organelle
GO:0043227	0.77	membrane-bounded organelle
GO:0043231	0.76	intracellular membrane-bounded organelle
GO:0005634	0.64	nucleus
GO:0005737	0.63	cytoplasm
GO:0032991	0.58	macromolecular complex
GO:0043234	0.57	protein complex
GO:0044428	0.54	nuclear part
GO:0016020	0.51	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	2fhbA	0.282	8.55	0.041	0.461	3.2.1.41	210
2	0.060	2qf7A	0.231	8.62	0.039	0.379	6.4.1.1	NA
3	0.060	1mc0A	0.158	6.67	0.055	0.219	3.1.4.17	206
4	0.060	1bglA	0.285	8.60	0.039	0.471	3.2.1.23	NA
5	0.060	1ixsB	0.288	4.39	0.147	0.333	3.6.4.12	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:

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
	1	0.77	3cf0A	0.341	2.46	0.407	0.360	1.49	ADP	complex1.pdb.gz	201,202,203,205,244,245,246,247,248,249,377,405,406,409

	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.