D-I-TASSER Q9BYD9

D-I-TASSER results for Q9BYD9

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

Summary of the Protein

Uniprot ID: Q9BYD9
Protein Name: Actin-related protein T3
Gene Name: ACTRT3

Input Sequence in FASTA format

>Q9BYD9 (372 residues)
MNHCQLPVVIDNGSGMIKAGVAGCREPQFIYPNIIGRAKGQSRAAQGGLELCVGDQAQDW
RSSLFISYPVERGLITSWEDMEIMWKHIYDYNLKLKPCDGPVLITEPALNPLANRQQITE
MFFEHLGVPAFYMSIQAVLALFAAGFTTGLVLNSGAGVTQSVPIFEGYCLPHGVQQLDLA
GLDLTNYLMVLMKNHGIMLLSASDRKIVEDIKESFCYVAMNYEEEMAKKPDCLEKVYQLP
DGKVIQLHDQLFSCPEALFSPCHMNLEAPGIDKICFSSIMKCDTGLRNSFFSNIILAGGS
TSFPGLDKRLVKDIAKVAPANTAVQVIAPPERKISVWMGGSILASLSAFQDMWITAAEFK
EVGPNIVHQRCF

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	Q9BYD9-D1	1-144,328-372	189		MNHCQLPVVIDNGSGMIKAGVAGCREPQFIYPNIIGRAKGQSRAAQGGLELCVGDQAQDWRSSLFISYPVERGLITSWEDMEIMWKHIYDYNLKLKPCDGPVLITEPALNPLANRQQITEMFFEHLGVPAFYMSIQAVLALFAAAPPERKISVWMGGSILASLSAFQDMWITAAEFKEVGPNIVHQRCF
2	Q9BYD9-D2	145-327	183		GFTTGLVLNSGAGVTQSVPIFEGYCLPHGVQQLDLAGLDLTNYLMVLMKNHGIMLLSASDRKIVEDIKESFCYVAMNYEEEMAKKPDCLEKVYQLPDGKVIQLHDQLFSCPEALFSPCHMNLEAPGIDKICFSSIMKCDTGLRNSFFSNIILAGGSTSFPGLDKRLVKDIAKVAPANTAVQVI

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.89

(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	3eksA	0.98	0.93	0.491	0.997	model1_3eksA.pdb.gz
2	4eahD	0.92	1.50	0.503	0.952	model1_4eahD.pdb.gz
3	3qb0A	0.90	2.32	0.261	0.976	model1_3qb0A.pdb.gz
4	4fo0A	0.90	2.25	0.228	0.970	model1_4fo0A.pdb.gz
5	5aftA	0.89	2.53	0.418	0.981	model1_5aftA.pdb.gz
6	4am6A	0.89	2.45	0.229	0.962	model1_4am6A.pdb.gz
7	6gejR	0.89	2.32	0.249	0.960	model1_6gejR.pdb.gz
8	6kw5f	0.88	2.27	0.228	0.952	model1_6kw5f.pdb.gz
9	6w17B	0.88	2.08	0.366	0.941	model1_6w17B.pdb.gz
10	1u2vA	0.87	2.78	0.310	0.981	model1_1u2vA.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:1901363	0.95	heterocyclic compound binding
GO:0097159	0.95	organic cyclic compound binding
GO:0035639	0.93	purine ribonucleoside triphosphate binding
GO:0032555	0.93	purine ribonucleotide binding
GO:0032550	0.93	purine ribonucleoside binding
GO:0005524	0.92	ATP binding
GO:0005200	0.84	structural constituent of cytoskeleton
GO:0003824	0.52	catalytic activity
GO:0008092	0.50	cytoskeletal protein 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:0044699	0.96	single-organism process
GO:0065007	0.91	biological regulation
GO:0050789	0.90	regulation of biological process
GO:0048518	0.86	positive regulation of biological process
GO:0032501	0.84	multicellular organismal process
GO:0010468	0.84	regulation of gene expression
GO:0044707	0.83	single-multicellular organism process
GO:0090131	0.82	mesenchyme migration
GO:0010628	0.82	positive regulation of gene expression
GO:0009987	0.81	cellular process
GO:0008152	0.62	metabolic process
GO:0071704	0.60	organic substance metabolic process
GO:0044763	0.60	single-organism cellular process
GO:0044238	0.60	primary metabolic process
GO:0044237	0.60	cellular metabolic process
GO:0043170	0.59	macromolecule metabolic process
GO:0044260	0.58	cellular macromolecule metabolic process
GO:0016043	0.57	cellular component organization
GO:0034641	0.56	cellular nitrogen compound metabolic process
GO:0090304	0.55	nucleic acid metabolic process
GO:0032502	0.52	developmental process
GO:0044767	0.50	single-organism developmental 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:0043229	1.00	intracellular organelle
GO:0044444	0.65	cytoplasmic part
GO:0043232	0.60	intracellular non-membrane-bounded organelle
GO:0044446	0.59	intracellular organelle part
GO:0005856	0.56	cytoskeleton
GO:0005737	0.55	cytoplasm
GO:0043227	0.54	membrane-bounded organelle
GO:0016020	0.53	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	0.121	2aa4A	0.533	3.70	0.119	0.656	2.7.1.60	NA
2	0.120	3eo3A	0.530	3.91	0.109	0.653	5.1.3.14 2.7.1.60	NA
3	0.110	2hoeA	0.574	3.43	0.091	0.677	2.7.1.59	NA
4	0.110	3htvA	0.507	4.29	0.128	0.650	2.7.1.55	NA
5	0.110	1xc3A	0.529	3.30	0.116	0.624	2.7.1.4	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	0.62	2yjeC	0.908	0.99	0.510	0.922	1.67	ATP	complex1.pdb.gz	13,14,15,16,18,155,156,157,158,181,209,212,213,299,302,303,333
2	0.58	3buzB	0.933	1.37	0.500	0.962	1.17	LAR	complex2.pdb.gz	16,32,58,68,156,182,185,208,209,212
3	0.39	2vcpA	0.959	1.44	0.495	0.989	1.57	III	complex3.pdb.gz	23,24,25,142,147,168,341,345,346,348,352,372
4	0.35	3tpqB	0.930	1.30	0.503	0.957	1.32	CA	complex4.pdb.gz	13,18,136,154
5	0.32	1d4x0	0.961	1.27	0.497	0.984	1.63	III	complex5.pdb.gz	23,24,25,142,147,166,167,168,331,338,342,343,345,346,347,348,351
6	0.32	1qz6A	0.945	1.06	0.503	0.962	1.63	JAS	complex6.pdb.gz	23,24,25,138,142,167,168,331,338,341,342,343,345,352
7	0.31	2q0rA	0.944	1.11	0.506	0.962	1.54	PXT	complex7.pdb.gz	74,106,108,109,110,111,115,171,172,174,175,176,281
8	0.31	1h1v0	0.958	1.31	0.495	0.984	1.58	III	complex8.pdb.gz	142,147,166,168,220,308,311,312,323,331,342,343,345,346,347,352,372
9	0.31	1ma91	0.930	1.18	0.503	0.952	1.55	III	complex9.pdb.gz	112,142,147,165,166,168,170,172,276,277,280,281,283,284,285,287,288,292,325,342,348,368
10	0.31	2a410	0.947	1.55	0.495	0.981	1.54	III	complex10.pdb.gz	16,23,24,25,26,27,28,30,55,59,92,142,147,166,167,168,203,206,207,209,210,240,333,334,341,342,343,345,346,348,349,351,352

	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.