D-I-TASSER Q86X24

D-I-TASSER results for Q86X24

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

Summary of the Protein

Uniprot ID: Q86X24
Protein Name: HORMA domain-containing protein 1
Gene Name: HORMAD1

Input Sequence in FASTA format

>Q86X24 (394 residues)
MATAQLQRTPMSALVFPNKISTEHQSLVLVKRLLAVSVSCITYLRGIFPECAYGTRYLDD
LCVKILREDKNCPGSTQLVKWMLGCYDALQKKYLRMVVLAVYTNPEDPQTISECYQFKFK
YTNNGPLMDFISKNQSNESSMLSTDTKKASILLIRKIYILMQNLGPLPNDVCLTMKLFYY
DEVTPPDYQPPGFKDGDCEGVIFEGEPMYLNVGEVSTPFHIFKVKVTTERERMENIDSTI
LSPKQIKTPFQKILRDKDVEDEQEHYTSDDLDIETKMEEQEKNPASSELEEPSLVCEEDE
IMRSKESPDLSISHSQVEQLVNKTSELDMSESKTRSGKVFQNKMANGNQPVKSSKENRKR
SQHESGRIVLHHFDSSSQESVPKRRKFSEPKEHI

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	Q86X24-D1	1-394	394		MATAQLQRTPMSALVFPNKISTEHQSLVLVKRLLAVSVSCITYLRGIFPECAYGTRYLDDLCVKILREDKNCPGSTQLVKWMLGCYDALQKKYLRMVVLAVYTNPEDPQTISECYQFKFKYTNNGPLMDFISKNQSNESSMLSTDTKKASILLIRKIYILMQNLGPLPNDVCLTMKLFYYDEVTPPDYQPPGFKDGDCEGVIFEGEPMYLNVGEVSTPFHIFKVKVTTERERMENIDSTILSPKQIKTPFQKILRDKDVEDEQEHYTSDDLDIETKMEEQEKNPASSELEEPSLVCEEDEIMRSKESPDLSISHSQVEQLVNKTSELDMSESKTRSGKVFQNKMANGNQPVKSSKENRKRSQHESGRIVLHHFDSSSQESVPKRRKFSEPKEHI

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.571

(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	4tzlA	0.54	1.69	0.171	0.564	model1_4tzlA.pdb.gz
2	4trkA	0.53	2.13	0.202	0.558	model1_4trkA.pdb.gz
3	2v64A	0.44	3.00	0.135	0.500	model1_2v64A.pdb.gz
4	4aezB	0.42	2.27	0.161	0.452	model1_4aezB.pdb.gz
5	3abeC	0.42	3.26	0.141	0.480	model1_3abeC.pdb.gz
6	6f91A	0.40	6.90	0.052	0.680	model1_6f91A.pdb.gz
7	4wz9A	0.40	7.32	0.048	0.703	model1_4wz9A.pdb.gz
8	4kx7A	0.40	7.09	0.043	0.680	model1_4kx7A.pdb.gz
9	1ry2A	0.40	6.37	0.052	0.634	model1_1ry2A.pdb.gz
10	6x99A	0.40	7.22	0.053	0.703	model1_6x99A.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	0.64	heterocyclic compound binding
GO:0097159	0.64	organic cyclic compound 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:0070192	1.00	chromosome organization involved in meiotic cell cycle
GO:0007126	0.93	meiotic nuclear division
GO:0007062	0.93	sister chromatid cohesion
GO:0051177	0.92	meiotic sister chromatid cohesion
GO:0044699	0.85	single-organism process
GO:0065007	0.84	biological regulation
GO:0050789	0.84	regulation of biological process
GO:0022607	0.84	cellular component assembly
GO:0050794	0.83	regulation of cellular process
GO:0044763	0.83	single-organism cellular process
GO:0007130	0.82	synaptonemal complex assembly
GO:0044702	0.81	single organism reproductive process
GO:0008152	0.81	metabolic process
GO:0048856	0.80	anatomical structure development
GO:0044767	0.80	single-organism developmental process
GO:0044238	0.80	primary metabolic process
GO:0044237	0.80	cellular metabolic process
GO:0043170	0.80	macromolecule metabolic process
GO:0048869	0.79	cellular developmental process
GO:0045786	0.79	negative regulation of cell cycle
GO:0010564	0.79	regulation of cell cycle process
GO:0006139	0.79	nucleobase-containing compound metabolic process
GO:0000075	0.79	cell cycle checkpoint
GO:0090304	0.78	nucleic acid metabolic process
GO:0051598	0.78	meiotic recombination checkpoint
GO:0003006	0.78	developmental process involved in reproduction
GO:0060629	0.76	regulation of homologous chromosome segregation
GO:0048477	0.76	oogenesis
GO:0042138	0.76	meiotic DNA double-strand break formation
GO:0007283	0.76	spermatogenesis
GO:0001824	0.66	blastocyst development

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:0005694	1.00	chromosome
GO:0005634	0.98	nucleus

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	3ej6A	0.356	7.37	0.040	0.634	1.11.1.6	NA
2	0.060	9cgtA	0.357	6.99	0.043	0.586	2.4.1.19	NA
3	0.060	1cdgA	0.291	7.41	0.029	0.515	2.4.1.19	NA
4	0.060	1n1hA	0.323	7.60	0.047	0.589	2.7.7.48	NA
5	0.060	1h54B	0.372	7.32	0.045	0.652	2.4.1.8	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	2qyfA	0.436	2.59	0.142	0.480	1.04	III	complex1.pdb.gz	47,48,73,77,81,96,98,114,173,174,175,176,177,178,179,186,189,194,195,196,200
2	0.08	3abdB	0.418	2.88	0.141	0.469	0.78	III	complex2.pdb.gz	46,48,49,75,78,174,176,177,178,179,180,195,196
3	0.08	3abeC	0.417	3.26	0.141	0.480	0.75	III	complex3.pdb.gz	46,47,48,51,52,68,81,171,172,174,176,177,178,181,191,201

	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.