D-I-TASSER Q9BXU9

D-I-TASSER results for Q9BXU9

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

Summary of the Protein

Uniprot ID: Q9BXU9
Protein Name: Calcium-binding protein 8
Gene Name: CALN1

Input Sequence in FASTA format

>Q9BXU9 (219 residues)
MPFHHVTAGLLYKGNYLNRSLSAGSDSEQLANISVEELDEIREAFRVLDRDGNGFISKQE
LGMAMRSLGYMPSEVELAIIMQRLDMDGDGQVDFDEFMTILGPKLVSSEGRDGFLGNTID
SIFWQFDMQRITLEELKHILYHAFRDHLTMKDIENIIINEEESLNETSGNCQTEFEGVHS
QKQNRQTCVRKSLICAFAMAFIISVMLIAANQILRSGME

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	Q9BXU9-D1	1-219	219		MPFHHVTAGLLYKGNYLNRSLSAGSDSEQLANISVEELDEIREAFRVLDRDGNGFISKQELGMAMRSLGYMPSEVELAIIMQRLDMDGDGQVDFDEFMTILGPKLVSSEGRDGFLGNTIDSIFWQFDMQRITLEELKHILYHAFRDHLTMKDIENIIINEEESLNETSGNCQTEFEGVHSQKQNRQTCVRKSLICAFAMAFIISVMLIAANQILRSGME

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.5465

(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	6xw2A	0.72	2.95	0.236	0.831	model1_6xw2A.pdb.gz
2	4i2yA	0.63	2.52	0.274	0.712	model1_4i2yA.pdb.gz
3	3evuA	0.60	1.83	0.268	0.648	model1_3evuA.pdb.gz
4	6xyrA2	0.59	2.42	0.280	0.657	model1_6xyrA2.pdb.gz
5	3u0kA	0.58	3.07	0.286	0.690	model1_3u0kA.pdb.gz
6	6u2mA	0.54	3.33	0.244	0.680	model1_6u2mA.pdb.gz
7	4gowD	0.53	2.67	0.317	0.635	model1_4gowD.pdb.gz
8	4nqgA	0.53	4.08	0.112	0.703	model1_4nqgA.pdb.gz
9	1uhiA	0.53	3.92	0.129	0.694	model1_1uhiA.pdb.gz
10	1dtlA	0.53	3.19	0.278	0.653	model1_1dtlA.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:0046872	0.65	metal ion binding
GO:0005509	0.58	calcium ion binding
GO:1901363	0.52	heterocyclic compound binding
GO:0097159	0.52	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:0009987	0.97	cellular process
GO:0008152	0.93	metabolic process
GO:0071704	0.90	organic substance metabolic process
GO:0044237	0.90	cellular metabolic process
GO:0065007	0.89	biological regulation
GO:0044238	0.89	primary metabolic process
GO:0043170	0.89	macromolecule metabolic process
GO:0050789	0.88	regulation of biological process
GO:0044260	0.86	cellular macromolecule metabolic process
GO:0050794	0.85	regulation of cellular process
GO:0019538	0.84	protein metabolic process
GO:0044267	0.80	cellular protein metabolic process
GO:0044699	0.78	single-organism process
GO:0006464	0.77	cellular protein modification process
GO:0007165	0.73	signal transduction
GO:0035556	0.71	intracellular signal transduction
GO:0006796	0.69	phosphate-containing compound metabolic process
GO:0044767	0.68	single-organism developmental process
GO:0008218	0.68	bioluminescence
GO:0006468	0.68	protein phosphorylation
GO:0048856	0.67	anatomical structure development
GO:0050896	0.64	response to stimulus
GO:0048518	0.64	positive regulation of biological process
GO:0044763	0.64	single-organism cellular process
GO:0051239	0.63	regulation of multicellular organismal process
GO:0048522	0.63	positive regulation of cellular process
GO:0031323	0.63	regulation of cellular metabolic process
GO:0080090	0.62	regulation of primary metabolic process
GO:0065008	0.62	regulation of biological quality
GO:0060255	0.62	regulation of macromolecule metabolic process
GO:0044057	0.62	regulation of system process
GO:0065009	0.61	regulation of molecular function
GO:0051049	0.61	regulation of transport
GO:0042221	0.61	response to chemical
GO:0031326	0.61	regulation of cellular biosynthetic process
GO:0031325	0.61	positive regulation of cellular metabolic process
GO:0019219	0.61	regulation of nucleobase-containing compound metabolic process
GO:0009966	0.61	regulation of signal transduction
GO:1902531	0.60	regulation of intracellular signal transduction
GO:0060341	0.60	regulation of cellular localization
GO:0051246	0.60	regulation of protein metabolic process
GO:0050790	0.60	regulation of catalytic activity
GO:0048584	0.60	positive regulation of response to stimulus
GO:0045935	0.60	positive regulation of nucleobase-containing compound metabolic process
GO:0043269	0.60	regulation of ion transport
GO:0031328	0.60	positive regulation of cellular biosynthetic process
GO:0022402	0.60	cell cycle process
GO:0010604	0.60	positive regulation of macromolecule metabolic process
GO:2001257	0.59	regulation of cation channel activity
GO:1904064	0.59	positive regulation of cation transmembrane transport
GO:1903047	0.59	mitotic cell cycle process
GO:1902533	0.59	positive regulation of intracellular signal transduction
GO:1901700	0.59	response to oxygen-containing compound
GO:0051592	0.59	response to calcium ion
GO:0051336	0.59	regulation of hydrolase activity
GO:0051279	0.59	regulation of release of sequestered calcium ion into cytosol
GO:0045937	0.59	positive regulation of phosphate metabolic process
GO:0043085	0.59	positive regulation of catalytic activity
GO:0033993	0.59	response to lipid
GO:0031401	0.59	positive regulation of protein modification process
GO:0014070	0.59	response to organic cyclic compound
GO:0010564	0.59	regulation of cell cycle process
GO:0009719	0.59	response to endogenous stimulus
GO:1901841	0.58	regulation of high voltage-gated calcium channel activity
GO:0060316	0.58	positive regulation of ryanodine-sensitive calcium-release channel activity
GO:0051412	0.58	response to corticosterone
GO:0051343	0.58	positive regulation of cyclic-nucleotide phosphodiesterase activity
GO:0051000	0.58	positive regulation of nitric-oxide synthase activity
GO:0043388	0.58	positive regulation of DNA binding
GO:0032516	0.58	positive regulation of phosphoprotein phosphatase activity
GO:0032465	0.58	regulation of cytokinesis
GO:0021762	0.58	substantia nigra development
GO:0018298	0.58	protein-chromophore linkage
GO:0007190	0.58	activation of adenylate cyclase activity
GO:0005513	0.58	detection of calcium ion
GO:0002027	0.58	regulation of heart rate
GO:0001975	0.58	response to amphetamine
GO:0000086	0.58	G2/M transition of mitotic cell cycle
GO:0051179	0.51	localization
GO:0051234	0.50	establishment of localization

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:0043226	0.84	organelle
GO:0043229	0.81	intracellular organelle
GO:0043227	0.72	membrane-bounded organelle
GO:0043231	0.68	intracellular membrane-bounded organelle
GO:0005634	0.63	nucleus
GO:0044444	0.57	cytoplasmic part
GO:0016020	0.54	membrane
GO:0044422	0.52	organelle part
GO:0005737	0.52	cytoplasm
GO:0044446	0.51	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	0.060	2odoA	0.300	6.11	0.034	0.543	5.1.1.1	NA
2	0.060	1ua4A	0.412	5.80	0.063	0.712	2.7.1.147	194
3	0.060	1gpeB	0.423	5.72	0.062	0.744	1.1.3.4	131
4	0.060	3fimB	0.430	5.82	0.064	0.749	1.1.3.7	NA
5	0.060	1vfsA	0.411	5.64	0.072	0.699	5.1.1.1	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	0.46	1dtlA	0.526	3.19	0.278	0.653	1.58	CA	complex1.pdb.gz	49,51,53,55,60
	2	0.45	3ek8A	0.635	3.44	0.291	0.758	1.58	CA	complex2.pdb.gz	85,87,88,89,91,93,96

	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.