D-I-TASSER Q96AX1

D-I-TASSER results for Q96AX1

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

Summary of the Protein

Uniprot ID: Q96AX1
Protein Name: Vacuolar protein sorting-associated protein 33A
Gene Name: VPS33A

Input Sequence in FASTA format

>Q96AX1 (596 residues)
MAAHLSYGRVNLNVLREAVRRELREFLDKCAGSKAIVWDEYLTGPFGLIAQYSLLKEHEV
EKMFTLKGNRLPAADVKNIIFFVRPRLELMDIIAENVLSEDRRGPTRDFHILFVPRRSLL
CEQRLKDLGVLGSFIHREEYSLDLIPFDGDLLSMESEGAFKECYLEGDQTSLYHAAKGLM
TLQALYGTIPQIFGKGECARQVANMMIRMKREFTGSQNSIFPVFDNLLLLDRNVDLLTPL
ATQLTYEGLIDEIYGIQNSYVKLPPEKFAPKKQGDGGKDLPTEAKKLQLNSAEELYAEIR
DKNFNAVGSVLSKKAKIISAAFEERHNAKTVGEIKQFVSQLPHMQAARGSLANHTSIAEL
IKDVTTSEDFFDKLTVEQEFMSGIDTDKVNNYIEDCIAQKHSLIKVLRLVCLQSVCNSGL
KQKVLDYYKREILQTYGYEHILTLHNLEKAGLLKPQTGGRNNYPTIRKTLRLWMDDVNEQ
NPTDISYVYSGYAPLSVRLAQLLSRPGWRSIEEVLRILPGPHFEERQPLPTGLQKKRQPG
ENRVTLIFFLGGVTFAEIAALRFLSQLEDGGTEYVIATTKLMNGTSWIEALMEKPF

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	Q96AX1-D1	1-142	142		MAAHLSYGRVNLNVLREAVRRELREFLDKCAGSKAIVWDEYLTGPFGLIAQYSLLKEHEVEKMFTLKGNRLPAADVKNIIFFVRPRLELMDIIAENVLSEDRRGPTRDFHILFVPRRSLLCEQRLKDLGVLGSFIHREEYSL
2	Q96AX1-D2	143-243,463-596	235		DLIPFDGDLLSMESEGAFKECYLEGDQTSLYHAAKGLMTLQALYGTIPQIFGKGECARQVANMMIRMKREFTGSQNSIFPVFDNLLLLDRNVDLLTPLATQYPTIRKTLRLWMDDVNEQNPTDISYVYSGYAPLSVRLAQLLSRPGWRSIEEVLRILPGPHFEERQPLPTGLQKKRQPGENRVTLIFFLGGVTFAEIAALRFLSQLEDGGTEYVIATTKLMNGTSWIEALMEKPF
3	Q96AX1-D3	244-367	124		LTYEGLIDEIYGIQNSYVKLPPEKFAPKKQGDGGKDLPTEAKKLQLNSAEELYAEIRDKNFNAVGSVLSKKAKIISAAFEERHNAKTVGEIKQFVSQLPHMQAARGSLANHTSIAELIKDVTTS
4	Q96AX1-D4	368-462	95		EDFFDKLTVEQEFMSGIDTDKVNNYIEDCIAQKHSLIKVLRLVCLQSVCNSGLKQKVLDYYKREILQTYGYEHILTLHNLEKAGLLKPQTGGRNN

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.929

(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	4bx8A	0.94	1.19	0.998	0.951	model1_4bx8A.pdb.gz
2	4jc8A	0.88	2.33	0.384	0.926	model1_4jc8A.pdb.gz
3	7zu0D	0.79	3.15	0.208	0.867	model1_7zu0D.pdb.gz
4	3c98A	0.69	4.98	0.144	0.866	model1_3c98A.pdb.gz
5	4ccaA	0.68	4.77	0.155	0.846	model1_4ccaA.pdb.gz
6	2xheA	0.66	5.30	0.130	0.854	model1_2xheA.pdb.gz
7	1epuA	0.65	5.07	0.150	0.826	model1_1epuA.pdb.gz
8	6xjlA	0.63	5.41	0.137	0.814	model1_6xjlA.pdb.gz
9	2pjxA	0.63	5.03	0.129	0.794	model1_2pjxA.pdb.gz
10	1mqsA	0.62	5.51	0.125	0.797	model1_1mqsA.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:0000149	0.50	SNARE binding
GO:0019905	0.39	syntaxin binding
GO:1901363	0.37	heterocyclic compound binding
GO:0097159	0.37	organic cyclic compound binding
GO:0000166	0.31	nucleotide binding
GO:0032555	0.30	purine ribonucleotide binding
GO:0032550	0.30	purine ribonucleoside 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:0051234	0.89	establishment of localization
GO:0006810	0.88	transport
GO:0009987	0.85	cellular process
GO:0044699	0.84	single-organism process
GO:0044763	0.75	single-organism cellular process
GO:0016192	0.70	vesicle-mediated transport
GO:0016043	0.70	cellular component organization
GO:0006996	0.65	organelle organization
GO:0065007	0.64	biological regulation
GO:0051641	0.62	cellular localization
GO:0050789	0.60	regulation of biological process
GO:0051649	0.57	establishment of localization in cell
GO:0046907	0.51	intracellular 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:0044464	0.99	cell part
GO:0044424	0.96	intracellular part
GO:0044444	0.93	cytoplasmic part
GO:0016020	0.76	membrane
GO:0044446	0.70	intracellular organelle part
GO:0043226	0.70	organelle
GO:0043227	0.69	membrane-bounded organelle
GO:0043229	0.62	intracellular organelle
GO:0043231	0.61	intracellular membrane-bounded organelle
GO:0098588	0.57	bounding membrane of organelle
GO:0032991	0.55	macromolecular complex
GO:0044437	0.54	vacuolar part
GO:0044425	0.54	membrane part
GO:0043234	0.54	protein complex
GO:0098805	0.51	whole 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	3g0bB	0.320	7.78	0.023	0.520	3.4.14.5	NA
2	0.060	2hpiA	0.326	7.65	0.040	0.530	2.7.7.7	NA
3	0.060	1ofdA	0.342	7.92	0.043	0.560	1.4.7.1	NA
4	0.060	1bxrA	0.315	8.19	0.030	0.532	6.3.5.5	578
5	0.060	3b9jJ	0.210	6.74	0.052	0.312	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:

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	2dqmA	0.356	7.82	0.050	0.572	0.12	BES	complex1.pdb.gz	48,49,50,64,65
2	0.01	3k30A	0.340	7.64	0.042	0.544	0.13	ADP	complex2.pdb.gz	146,147,258,261
3	0.01	2qkiA	0.245	8.23	0.043	0.414	0.12	III	complex3.pdb.gz	45,46,53,82,83,84,112
4	0.01	3cmxA	0.334	7.65	0.040	0.527	0.18	ALF	complex4.pdb.gz	40,42,47
5	0.01	3k30B	0.339	7.57	0.042	0.542	0.14	FMN	complex5.pdb.gz	46,115,179,182,183

	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.