D-I-TASSER P46379

D-I-TASSER results for P46379

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

Summary of the Protein

Uniprot ID: P46379
Protein Name: Large proline-rich protein BAG6
Gene Name: BAG6

Input Sequence in FASTA format

>P46379 (1132 residues)
MEPNDSTSTAVEEPDSLEVLVKTLDSQTRTFIVGAQMNVKEFKEHIAASVSIPSEKQRLI
YQGRVLQDDKKLQEYNVGGKVIHLVERAPPQTHLPSGASSGTGSASATHGGGSPPGTRGP
GASVHDRNANSYVMVGTFNLPSDGSAVDVHINMEQAPIQSEPRVRLVMAQHMIRDIQTLL
SRMETLPYLQCRGGPQPQHSQPPPQPPAVTPEPVALSSQTSEPVESEAPPREPMEAEEVE
ERAPAQNPELTPGPAPAGPTPAPETNAPNHPSPAEYVEVLQELQRLESRLQPFLQRYYEV
LGAAATTDYNNNHEGREEDQRLINLVGESLRLLGNTFVALSDLRCNLACTPPRHLHVVRP
MSHYTTPMVLQQAAIPIQINVGTTVTMTGNGTRPPPTPNAEAPPPGPGQASSVAPSSTNV
ESSAEGAPPPGPAPPPATSHPRVIRISHQSVEPVVMMHMNIQDSGTQPGGVPSAPTGPLG
PPGHGQTLGQQVPGFPTAPTRVVIARPTPPQARPSHPGGPPVSGTLQGAGLGTNASLAQM
VSGLVGQLLMQPVLVAQGTPGMAPPPAPATASASAGTTNTATTAGPAPGGPAQPPPTPQP
SMADLQFSQLLGNLLGPAGPGAGGSGVASPTITVAMPGVPAFLQGMTDFLQATQTAPPPP
PPPPPPPPAPEQQTMPPPGSPSGGAGSPGGLGLESLSPEFFTSVVQGVLSSLLGSLGARA
GSSESIAAFIQRLSGSSNIFEPGADGALGFFGALLSLLCQNFSMVDVVMLLHGHFQPLQR
LQPQLRSFFHQHYLGGQEPTPSNIRMATHTLITGLEEYVRESFSLVQVQPGVDIIRTNLE
FLQEQFNSIAAHVLHCTDSGFGARLLELCNQGLFECLALNLHCLGGQQMELAAVINGRIR
RMSRGVNPSLVSWLTTMMGLRLQVVLEHMPVGPDAILRYVRRVGDPPQPLPEEPMEVQGA
ERASPEPQRENASPAPGTTAEEAMSRGPPPAPEGGSRDEQDGASAETEPWAAAVPPEWVP
IIQQDIQSQRKVKPQPPLSDAYLSGMPAKRRKTMQGEGPQLLLSEAVSRAAKAAGARPLT
SPESLSRDLEAPEVQESYRQQLRSDIQKRLQEDPNYSPQRFPNAQRAFADDP

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	P46379-D1	1-220	220		MEPNDSTSTAVEEPDSLEVLVKTLDSQTRTFIVGAQMNVKEFKEHIAASVSIPSEKQRLIYQGRVLQDDKKLQEYNVGGKVIHLVERAPPQTHLPSGASSGTGSASATHGGGSPPGTRGPGASVHDRNANSYVMVGTFNLPSDGSAVDVHINMEQAPIQSEPRVRLVMAQHMIRDIQTLLSRMETLPYLQCRGGPQPQHSQPPPQPPAVTPEPVALSSQT
2	P46379-D2	221-1132	912		SEPVESEAPPREPMEAEEVEERAPAQNPELTPGPAPAGPTPAPETNAPNHPSPAEYVEVLQELQRLESRLQPFLQRYYEVLGAAATTDYNNNHEGREEDQRLINLVGESLRLLGNTFVALSDLRCNLACTPPRHLHVVRPMSHYTTPMVLQQAAIPIQINVGTTVTMTGNGTRPPPTPNAEAPPPGPGQASSVAPSSTNVESSAEGAPPPGPAPPPATSHPRVIRISHQSVEPVVMMHMNIQDSGTQPGGVPSAPTGPLGPPGHGQTLGQQVPGFPTAPTRVVIARPTPPQARPSHPGGPPVSGTLQGAGLGTNASLAQMVSGLVGQLLMQPVLVAQGTPGMAPPPAPATASASAGTTNTATTAGPAPGGPAQPPPTPQPSMADLQFSQLLGNLLGPAGPGAGGSGVASPTITVAMPGVPAFLQGMTDFLQATQTAPPPPPPPPPPPPAPEQQTMPPPGSPSGGAGSPGGLGLESLSPEFFTSVVQGVLSSLLGSLGARAGSSESIAAFIQRLSGSSNIFEPGADGALGFFGALLSLLCQNFSMVDVVMLLHGHFQPLQRLQPQLRSFFHQHYLGGQEPTPSNIRMATHTLITGLEEYVRESFSLVQVQPGVDIIRTNLEFLQEQFNSIAAHVLHCTDSGFGARLLELCNQGLFECLALNLHCLGGQQMELAAVINGRIRRMSRGVNPSLVSWLTTMMGLRLQVVLEHMPVGPDAILRYVRRVGDPPQPLPEEPMEVQGAERASPEPQRENASPAPGTTAEEAMSRGPPPAPEGGSRDEQDGASAETEPWAAAVPPEWVPIIQQDIQSQRKVKPQPPLSDAYLSGMPAKRRKTMQGEGPQLLLSEAVSRAAKAAGARPLTSPESLSRDLEAPEVQESYRQQLRSDIQKRLQEDPNYSPQRFPNAQRAFADDP

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.34

(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	6reyc	0.31	8.81	0.031	0.458	model1_6reyc.pdb.gz
2	6vr4A	0.30	9.69	0.034	0.482	model1_6vr4A.pdb.gz
3	5a22A	0.30	9.67	0.030	0.482	model1_5a22A.pdb.gz
4	6h02A	0.29	8.55	0.044	0.420	model1_6h02A.pdb.gz
5	6yejA	0.28	9.31	0.034	0.436	model1_6yejA.pdb.gz
6	6h3iA	0.28	9.81	0.035	0.457	model1_6h3iA.pdb.gz
7	4o9xA	0.28	9.64	0.051	0.439	model1_4o9xA.pdb.gz
8	7b52A	0.28	9.37	0.027	0.431	model1_7b52A.pdb.gz
9	6jxaA	0.27	9.75	0.030	0.444	model1_6jxaA.pdb.gz
10	6eqoA	0.27	9.47	0.045	0.425	model1_6eqoA.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:0043130	0.87	ubiquitin binding
GO:0031593	0.86	polyubiquitin binding
GO:0044877	0.74	macromolecular complex binding
GO:0070628	0.73	proteasome binding
GO:0043022	0.73	ribosome 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:0065007	0.92	biological regulation
GO:0050789	0.92	regulation of biological process
GO:0009987	0.92	cellular process
GO:0050794	0.91	regulation of cellular process
GO:0008152	0.89	metabolic process
GO:0044238	0.88	primary metabolic process
GO:0044237	0.88	cellular metabolic process
GO:0043170	0.88	macromolecule metabolic process
GO:0044260	0.87	cellular macromolecule metabolic process
GO:0019538	0.84	protein metabolic process
GO:0048519	0.83	negative regulation of biological process
GO:0048523	0.82	negative regulation of cellular process
GO:0044267	0.81	cellular protein metabolic process
GO:0044699	0.80	single-organism process
GO:0006464	0.80	cellular protein modification process
GO:0080090	0.78	regulation of primary metabolic process
GO:0060255	0.78	regulation of macromolecule metabolic process
GO:0050896	0.77	response to stimulus
GO:0031323	0.77	regulation of cellular metabolic process
GO:0044265	0.76	cellular macromolecule catabolic process
GO:0006508	0.76	proteolysis
GO:0051179	0.75	localization
GO:0007165	0.75	signal transduction
GO:0006511	0.75	ubiquitin-dependent protein catabolic process
GO:0051246	0.74	regulation of protein metabolic process
GO:0051234	0.74	establishment of localization
GO:0032502	0.74	developmental process
GO:0016043	0.74	cellular component organization
GO:0006950	0.74	response to stress
GO:0051716	0.73	cellular response to stimulus
GO:0044767	0.73	single-organism developmental process
GO:0042176	0.73	regulation of protein catabolic process
GO:0032268	0.73	regulation of cellular protein metabolic process
GO:1903050	0.72	regulation of proteolysis involved in cellular protein catabolic process
GO:0065008	0.72	regulation of biological quality
GO:0048856	0.72	anatomical structure development
GO:0045184	0.72	establishment of protein localization
GO:0033554	0.72	cellular response to stress
GO:0010605	0.72	negative regulation of macromolecule metabolic process
GO:0071816	0.71	tail-anchored membrane protein insertion into ER membrane
GO:0061136	0.71	regulation of proteasomal protein catabolic process
GO:0044707	0.71	single-multicellular organism process
GO:0031324	0.71	negative regulation of cellular metabolic process
GO:0022607	0.71	cellular component assembly
GO:0022402	0.71	cell cycle process
GO:0006996	0.71	organelle organization
GO:0006974	0.71	cellular response to DNA damage stimulus
GO:0072331	0.70	signal transduction by p53 class mediator
GO:0051276	0.70	chromosome organization
GO:0048513	0.70	animal organ development
GO:0044702	0.70	single organism reproductive process
GO:0032434	0.70	regulation of proteasomal ubiquitin-dependent protein catabolic process
GO:0032269	0.70	negative regulation of cellular protein metabolic process
GO:0070059	0.69	intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress
GO:0050821	0.69	protein stabilization
GO:0042771	0.69	intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator
GO:0032435	0.69	negative regulation of proteasomal ubiquitin-dependent protein catabolic process
GO:0030324	0.69	lung development
GO:0018393	0.69	internal peptidyl-lysine acetylation
GO:0009790	0.69	embryo development
GO:0007420	0.69	brain development
GO:0007283	0.69	spermatogenesis
GO:0007130	0.69	synaptonemal complex assembly
GO:0001822	0.69	kidney development
GO:0042981	0.50	regulation of apoptotic 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:0044424	0.99	intracellular part
GO:0044444	0.93	cytoplasmic part
GO:0005829	0.86	cytosol
GO:0043226	0.85	organelle
GO:0043229	0.84	intracellular organelle
GO:0043227	0.84	membrane-bounded organelle
GO:0043231	0.83	intracellular membrane-bounded organelle
GO:0032991	0.80	macromolecular complex
GO:0005634	0.78	nucleus
GO:0044445	0.73	cytosolic part
GO:0043234	0.73	protein complex
GO:0071818	0.68	BAT3 complex

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	2g49A	0.217	9.10	0.031	0.332	3.4.24.56	731
2	0.060	1bxrA	0.228	9.42	0.039	0.359	6.3.5.5	NA
3	0.060	2uv8G	0.246	9.10	0.029	0.376	2.3.1.86	NA
4	0.060	3hkzJ	0.240	9.62	0.028	0.383	2.7.7.6	NA
5	0.060	3cmmC	0.217	9.57	0.024	0.348	6.3.2.19	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	0.01	1l0l3	0.122	7.16	0.030	0.164	0.45	III	complex1.pdb.gz	90,91,92,329,331,333

	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.