D-I-TASSER P38606

D-I-TASSER results for P38606

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

Summary of the Protein

Uniprot ID: P38606
Protein Name: V-type proton ATPase catalytic subunit A
Gene Name: ATP6V1A

Input Sequence in FASTA format

>P38606 (617 residues)
MDFSKLPKILDEDKESTFGYVHGVSGPVVTACDMAGAAMYELVRVGHSELVGEIIRLEGD
MATIQVYEETSGVSVGDPVLRTGKPLSVELGPGIMGAIFDGIQRPLSDISSQTQSIYIPR
GVNVSALSRDIKWDFTPCKNLRVGSHITGGDIYGIVSENSLIKHKIMLPPRNRGTVTYIA
PPGNYDTSDVVLELEFEGVKEKFTMVQVWPVRQVRPVTEKLPANHPLLTGQRVLDALFPC
VQGGTTAIPGAFGCGKTVISQSLSKYSNSDVIIYVGCGERGNEMSEVLRDFPELTMEVDG
KVESIMKRTALVANTSNMPVAAREASIYTGITLSEYFRDMGYHVSMMADSTSRWAEALRE
ISGRLAEMPADSGYPAYLGARLASFYERAGRVKCLGNPEREGSVSIVGAVSPPGGDFSDP
VTSATLGIVQVFWGLDKKLAQRKHFPSVNWLISYSKYMRALDEYYDKHFTEFVPLRTKAK
EILQEEEDLAEIVQLVGKASLAETDKITLEVAKLIKDDFLQQNGYTPYDRFCPFYKTVGM
LSNMIAFYDMARRAVETTAQSDNKITWSIIREHMGDILYKLSSMKFKDPLKDGEAKIKSD
YAQLLEDMQNAFRSLED

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	P38606-D1	1-87	87		MDFSKLPKILDEDKESTFGYVHGVSGPVVTACDMAGAAMYELVRVGHSELVGEIIRLEGDMATIQVYEETSGVSVGDPVLRTGKPLS
2	P38606-D2	88-127,207-501	335		VELGPGIMGAIFDGIQRPLSDISSQTQSIYIPRGVNVSALQVWPVRQVRPVTEKLPANHPLLTGQRVLDALFPCVQGGTTAIPGAFGCGKTVISQSLSKYSNSDVIIYVGCGERGNEMSEVLRDFPELTMEVDGKVESIMKRTALVANTSNMPVAAREASIYTGITLSEYFRDMGYHVSMMADSTSRWAEALREISGRLAEMPADSGYPAYLGARLASFYERAGRVKCLGNPEREGSVSIVGAVSPPGGDFSDPVTSATLGIVQVFWGLDKKLAQRKHFPSVNWLISYSKYMRALDEYYDKHFTEFVPLRTKAKEILQEEEDLAEIVQLVGKASL
3	P38606-D3	128-206	79		SRDIKWDFTPCKNLRVGSHITGGDIYGIVSENSLIKHKIMLPPRNRGTVTYIAPPGNYDTSDVVLELEFEGVKEKFTMV
4	P38606-D4	502-617	116		AETDKITLEVAKLIKDDFLQQNGYTPYDRFCPFYKTVGMLSNMIAFYDMARRAVETTAQSDNKITWSIIREHMGDILYKLSSMKFKDPLKDGEAKIKSDYAQLLEDMQNAFRSLED

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.842

(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	6vq6A	0.96	1.01	0.978	0.972	model1_6vq6A.pdb.gz
2	5ze9A	0.92	1.65	0.488	0.950	model1_5ze9A.pdb.gz
3	3j9tA	0.91	2.15	0.662	0.960	model1_3j9tA.pdb.gz
4	5bn3A	0.88	1.89	0.453	0.912	model1_5bn3A.pdb.gz
5	3a5cA	0.86	1.93	0.495	0.904	model1_3a5cA.pdb.gz
6	3i4lA	0.78	2.49	0.474	0.823	model1_3i4lA.pdb.gz
7	7p2yA	0.70	2.99	0.222	0.754	model1_7p2yA.pdb.gz
8	8dbsA	0.69	2.91	0.213	0.747	model1_8dbsA.pdb.gz
9	7jg5A	0.69	2.96	0.174	0.747	model1_7jg5A.pdb.gz
10	2wssA	0.69	2.90	0.194	0.744	model1_2wssA.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:0022857	0.65	transmembrane transporter activity
GO:0015075	0.64	ion transmembrane transporter activity
GO:0015078	0.63	hydrogen ion transmembrane transporter activity
GO:0003824	0.62	catalytic activity
GO:0016787	0.58	hydrolase activity
GO:0017111	0.55	nucleoside-triphosphatase activity
GO:0016887	0.54	ATPase activity

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:0044699	0.91	single-organism process
GO:0009987	0.87	cellular process
GO:0044763	0.78	single-organism cellular process
GO:0065007	0.70	biological regulation
GO:0006810	0.68	transport
GO:0065008	0.59	regulation of biological quality
GO:0042592	0.56	homeostatic process
GO:0048878	0.55	chemical homeostasis
GO:0055067	0.51	monovalent inorganic cation homeostasis
GO:0006812	0.51	cation 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:0016020	0.87	membrane
GO:0044424	0.82	intracellular part
GO:0044425	0.79	membrane part
GO:0044444	0.70	cytoplasmic part
GO:0044459	0.63	plasma membrane part
GO:0016324	0.56	apical plasma membrane
GO:0044446	0.50	intracellular organelle part

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	0.224	3gqbA	0.897	1.86	0.510	0.935	3.6.3.14	NA
2	0.176	1fx0B	0.658	2.90	0.253	0.712	3.6.3.14	NA
3	0.173	3i4lA	0.775	2.49	0.474	0.823	3.6.3.14	249,274,277,280,282,284,313,316,323,348,351,409
4	0.147	1skyB	0.682	2.91	0.202	0.737	3.6.3.14	NA
5	0.143	2qe7A	0.670	3.25	0.192	0.737	3.6.1.34	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	0.11	3i73A	0.766	2.37	0.470	0.810	0.24	ADP	complex1.pdb.gz	327,330,331,332,348
2	0.09	2hldX	0.656	3.16	0.264	0.720	0.15	ANP	complex2.pdb.gz	26,28,29
3	0.07	3i4lA	0.775	2.49	0.474	0.823	0.19	ANP	complex3.pdb.gz	53,67,101,102,326
4	0.06	2wssK	0.668	2.97	0.196	0.726	0.28	ANP	complex4.pdb.gz	324,325,326,352
5	0.06	1h8eE	0.649	3.05	0.266	0.712	0.17	ADP	complex5.pdb.gz	326,327,328,329
6	0.04	3fksO	0.653	3.31	0.263	0.720	0.30	PO4	complex6.pdb.gz	72,75,76,77,78
7	0.04	1cowE	0.640	3.46	0.257	0.723	0.13	AUR	complex7.pdb.gz	28,50,77
8	0.04	1bmfD	0.651	3.11	0.252	0.713	0.21	ADP	complex8.pdb.gz	101,337,338
9	0.04	2wpdB	0.690	2.89	0.207	0.744	0.25	ATP	complex9.pdb.gz	101,102,103,104

	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.