D-I-TASSER Q8WX39

D-I-TASSER results for Q8WX39

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

Summary of the Protein

Uniprot ID: Q8WX39
Protein Name: Epididymal-specific lipocalin-9
Gene Name: LCN9

Input Sequence in FASTA format

>Q8WX39 (176 residues)
MALLLLSLGLSLIAAQEFDPHTVMQRNYNVARVSGVWYSIFMASDDLNRIKENGDLRVFV
RNIEHLKNGSLIFDFEYMVQGECVAVVVVCEKTEKNGEYSINYEGQNTVAVSETDYRLFI
TFHLQNFRNGTETHTLALYETCEKYGLGSQNIIDLTNKDPCYSKHYRSPPRPPMRW

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	Q8WX39-D1	1-176	176		MALLLLSLGLSLIAAQEFDPHTVMQRNYNVARVSGVWYSIFMASDDLNRIKENGDLRVFVRNIEHLKNGSLIFDFEYMVQGECVAVVVVCEKTEKNGEYSINYEGQNTVAVSETDYRLFITFHLQNFRNGTETHTLALYETCEKYGLGSQNIIDLTNKDPCYSKHYRSPPRPPMRW

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.6997

(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	1gm6A	0.75	1.79	0.371	0.812	model1_1gm6A.pdb.gz
2	5nghA	0.75	1.67	0.408	0.812	model1_5nghA.pdb.gz
3	1epbB	0.74	2.19	0.162	0.830	model1_1epbB.pdb.gz
4	2l5pA	0.74	2.85	0.130	0.875	model1_2l5pA.pdb.gz
5	2qosC	0.73	2.61	0.131	0.858	model1_2qosC.pdb.gz
6	1ew3A	0.73	2.06	0.378	0.812	model1_1ew3A.pdb.gz
7	3zq3A	0.73	1.87	0.382	0.801	model1_3zq3A.pdb.gz
8	1df3A	0.70	2.16	0.359	0.795	model1_1df3A.pdb.gz
9	2xstA	0.67	1.77	0.229	0.744	model1_2xstA.pdb.gz
10	1hqpA	0.66	2.07	0.273	0.750	model1_1hqpA.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:0005549	0.67	odorant binding
GO:0003824	0.66	catalytic activity
GO:0005550	0.60	pheromone binding
GO:0097159	0.59	organic cyclic compound binding
GO:0005215	0.57	transporter activity
GO:0004714	0.56	transmembrane receptor protein tyrosine kinase activity
GO:0008289	0.50	lipid 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	0.97	single-organism process
GO:0009987	0.94	cellular process
GO:0044763	0.91	single-organism cellular process
GO:0008152	0.89	metabolic process
GO:0065007	0.88	biological regulation
GO:0050896	0.88	response to stimulus
GO:0050789	0.86	regulation of biological process
GO:0044710	0.86	single-organism metabolic process
GO:0050794	0.82	regulation of cellular process
GO:0042221	0.80	response to chemical
GO:0032502	0.80	developmental process
GO:0044767	0.79	single-organism developmental process
GO:0044237	0.79	cellular metabolic process
GO:0051716	0.76	cellular response to stimulus
GO:0048523	0.76	negative regulation of cellular process
GO:0051049	0.75	regulation of transport
GO:0016043	0.75	cellular component organization
GO:0051223	0.74	regulation of protein transport
GO:0032501	0.74	multicellular organismal process
GO:0065008	0.73	regulation of biological quality
GO:0060255	0.73	regulation of macromolecule metabolic process
GO:0023051	0.73	regulation of signaling
GO:0010646	0.73	regulation of cell communication
GO:0080090	0.72	regulation of primary metabolic process
GO:0048583	0.72	regulation of response to stimulus
GO:0060341	0.71	regulation of cellular localization
GO:0051224	0.71	negative regulation of protein transport
GO:0048585	0.71	negative regulation of response to stimulus
GO:0048522	0.71	positive regulation of cellular process
GO:0045833	0.71	negative regulation of lipid metabolic process
GO:0031324	0.71	negative regulation of cellular metabolic process
GO:0023057	0.71	negative regulation of signaling
GO:0010648	0.71	negative regulation of cell communication
GO:0010605	0.71	negative regulation of macromolecule metabolic process
GO:0010033	0.71	response to organic substance
GO:0009966	0.71	regulation of signal transduction
GO:0042592	0.70	homeostatic process
GO:0033993	0.69	response to lipid
GO:0070887	0.68	cellular response to chemical stimulus
GO:0048878	0.68	chemical homeostasis
GO:0044707	0.68	single-multicellular organism process
GO:0006950	0.67	response to stress
GO:0071396	0.66	cellular response to lipid
GO:0050708	0.66	regulation of protein secretion
GO:0010817	0.66	regulation of hormone levels
GO:0009653	0.66	anatomical structure morphogenesis
GO:0007610	0.66	behavior
GO:0050796	0.65	regulation of insulin secretion
GO:0048869	0.65	cellular developmental process
GO:0032844	0.65	regulation of homeostatic process
GO:0023056	0.65	positive regulation of signaling
GO:0010647	0.65	positive regulation of cell communication
GO:2000113	0.64	negative regulation of cellular macromolecule biosynthetic process
GO:1903507	0.64	negative regulation of nucleic acid-templated transcription
GO:1902589	0.64	single-organism organelle organization
GO:1902533	0.64	positive regulation of intracellular signal transduction
GO:0061178	0.64	regulation of insulin secretion involved in cellular response to glucose stimulus
GO:0051896	0.64	regulation of protein kinase B signaling
GO:0048512	0.64	circadian behavior
GO:0046890	0.64	regulation of lipid biosynthetic process
GO:0046676	0.64	negative regulation of insulin secretion
GO:0045333	0.64	cellular respiration
GO:0032990	0.64	cell part morphogenesis
GO:0032845	0.64	negative regulation of homeostatic process
GO:0010883	0.64	regulation of lipid storage
GO:0010677	0.64	negative regulation of cellular carbohydrate metabolic process
GO:0010676	0.64	positive regulation of cellular carbohydrate metabolic process
GO:0010629	0.64	negative regulation of gene expression
GO:0010604	0.64	positive regulation of macromolecule metabolic process
GO:0007626	0.64	locomotory behavior
GO:0007005	0.64	mitochondrion organization
GO:0006355	0.64	regulation of transcription, DNA-templated
GO:0006111	0.64	regulation of gluconeogenesis
GO:0001659	0.64	temperature homeostasis
GO:0006952	0.57	defense response
GO:1901700	0.55	response to oxygen-containing compound
GO:0002376	0.52	immune system process
GO:0006955	0.51	immune response
GO:0006810	0.50	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:0005576	1.00	extracellular region
GO:0044421	0.97	extracellular region part
GO:0005615	0.95	extracellular space
GO:0044464	0.91	cell part
GO:0043226	0.91	organelle
GO:0043227	0.89	membrane-bounded organelle
GO:0044424	0.86	intracellular part
GO:0044444	0.77	cytoplasmic part
GO:0043231	0.73	intracellular membrane-bounded organelle
GO:0070062	0.55	extracellular exosome
GO:0005634	0.50	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	0.086	2e4jA	0.652	3.19	0.170	0.818	5.3.99.2	25,38,99,113
2	0.060	1i78A	0.425	5.15	0.059	0.682	3.4.23.49	NA
3	0.060	1t09B	0.384	5.57	0.050	0.710	1.1.1.42	36
4	0.060	1gwhA	0.474	3.97	0.050	0.670	1.11.1.6	118
5	0.060	1lwdA	0.404	5.41	0.037	0.710	1.1.1.42	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	0.10	3uexA	0.693	2.50	0.203	0.801	0.65	STE	complex1.pdb.gz	30,63,71,88,101,109,111,122,124
2	0.05	1epbB	0.741	2.19	0.162	0.830	0.59	REA	complex2.pdb.gz	28,30,33,37,107,111,120,122,124,137
3	0.04	1felA	0.657	2.83	0.162	0.784	0.54	FEN	complex3.pdb.gz	72,74,88,92,99,111
4	0.04	2gj5A	0.698	2.41	0.203	0.807	0.51	VD3	complex4.pdb.gz	30,33,34,64,72
5	0.02	1obq0	0.653	3.50	0.102	0.835	0.53	III	complex5.pdb.gz	86,87,88,105,107
6	0.02	1gkaA	0.648	3.53	0.096	0.835	0.51	AXT	complex6.pdb.gz	92,98,100,106,107,108,109

	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.