D-I-TASSER Q9NRN5

D-I-TASSER results for Q9NRN5

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

Summary of the Protein

Uniprot ID: Q9NRN5
Protein Name: Olfactomedin-like protein 3
Gene Name: OLFML3

Input Sequence in FASTA format

>Q9NRN5 (406 residues)
MGPSTPLLILFLLSWSGPLQGQQHHLVEYMERRLAALEERLAQCQDQSSRHAAELRDFKN
KMLPLLEVAEKEREALRTEADTISGRVDRLEREVDYLETQNPALPCVEFDEKVTGGPGTK
GKGRRNEKYDMVTDCGYTISQVRSMKILKRFGGPAGLWTKDPLGQTEKIYVLDGTQNDTA
FVFPRLRDFTLAMAARKASRVRVPFPWVGTGQLVYGGFLYFARRPPGRPGGGGEMENTLQ
LIKFHLANRTVVDSSVFPAEGLIPPYGLTADTYIDLAADEEGLWAVYATREDDRHLCLAK
LDPQTLDTEQQWDTPCPRENAEAAFVICGTLYVVYNTRPASRARIQCSFDASGTLTPERA
ALPYFPRRYGAHASLRYNPRERQLYAWDDGYQIVYKLEMRKKEEEV

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	Q9NRN5-D1	1-104	104		MGPSTPLLILFLLSWSGPLQGQQHHLVEYMERRLAALEERLAQCQDQSSRHAAELRDFKNKMLPLLEVAEKEREALRTEADTISGRVDRLEREVDYLETQNPAL
2	Q9NRN5-D2	105-151,323-406	131		PCVEFDEKVTGGPGTKGKGRRNEKYDMVTDCGYTISQVRSMKILKRFAAFVICGTLYVVYNTRPASRARIQCSFDASGTLTPERAALPYFPRRYGAHASLRYNPRERQLYAWDDGYQIVYKLEMRKKEEEV
3	Q9NRN5-D3	152-256	105		GGPAGLWTKDPLGQTEKIYVLDGTQNDTAFVFPRLRDFTLAMAARKASRVRVPFPWVGTGQLVYGGFLYFARRPPGRPGGGGEMENTLQLIKFHLANRTVVDSSV
4	Q9NRN5-D4	257-322	66		FPAEGLIPPYGLTADTYIDLAADEEGLWAVYATREDDRHLCLAKLDPQTLDTEQQWDTPCPRENAE

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.54

(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	4wxqA	0.54	2.24	0.279	0.576	model1_4wxqA.pdb.gz
2	5afbA	0.53	2.15	0.219	0.562	model1_5afbA.pdb.gz
3	4d77A	0.52	2.34	0.224	0.562	model1_4d77A.pdb.gz
4	5amoA	0.51	2.07	0.296	0.544	model1_5amoA.pdb.gz
5	6qzhA	0.50	5.30	0.057	0.685	model1_6qzhA.pdb.gz
6	3vsrA	0.49	4.64	0.079	0.633	model1_3vsrA.pdb.gz
7	2yfrA	0.42	5.03	0.069	0.562	model1_2yfrA.pdb.gz
8	3lrvA2	0.30	4.23	0.073	0.389	model1_3lrvA2.pdb.gz
9	3dvlA	0.28	6.92	0.076	0.463	model1_3dvlA.pdb.gz
10	1dwfM	0.27	7.48	0.045	0.488	model1_1dwfM.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:0004888	0.48	transmembrane signaling receptor activity
GO:0046872	0.43	metal ion binding
GO:0005102	0.41	receptor binding
GO:0001664	0.39	G-protein coupled receptor binding
GO:0008092	0.38	cytoskeletal protein binding
GO:0017022	0.37	myosin binding
GO:1990782	0.34	protein tyrosine kinase 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	0.95	cellular process
GO:0044699	0.94	single-organism process
GO:0044763	0.92	single-organism cellular process
GO:0065007	0.89	biological regulation
GO:0050789	0.88	regulation of biological process
GO:0050794	0.87	regulation of cellular process
GO:0032502	0.84	developmental process
GO:0016043	0.84	cellular component organization
GO:0048518	0.83	positive regulation of biological process
GO:0044767	0.83	single-organism developmental process
GO:0051094	0.82	positive regulation of developmental process
GO:0048522	0.81	positive regulation of cellular process
GO:0051130	0.78	positive regulation of cellular component organization
GO:0048869	0.78	cellular developmental process
GO:0045597	0.76	positive regulation of cell differentiation
GO:0048519	0.74	negative regulation of biological process
GO:0019222	0.73	regulation of metabolic process
GO:0010770	0.73	positive regulation of cell morphogenesis involved in differentiation
GO:0060255	0.72	regulation of macromolecule metabolic process
GO:2000026	0.67	regulation of multicellular organismal development
GO:0051240	0.67	positive regulation of multicellular organismal process
GO:0048856	0.65	anatomical structure development
GO:0007165	0.64	signal transduction
GO:0008152	0.61	metabolic process
GO:0050896	0.58	response to stimulus
GO:0031323	0.58	regulation of cellular metabolic process
GO:0080090	0.56	regulation of primary metabolic process
GO:0071704	0.56	organic substance metabolic process
GO:0048523	0.56	negative regulation of cellular process
GO:0048513	0.56	animal organ development
GO:0044237	0.56	cellular metabolic process
GO:0032501	0.56	multicellular organismal process
GO:1900024	0.55	regulation of substrate adhesion-dependent cell spreading
GO:0048583	0.55	regulation of response to stimulus
GO:0044238	0.55	primary metabolic process
GO:0044089	0.55	positive regulation of cellular component biogenesis
GO:0030030	0.55	cell projection organization
GO:0023051	0.55	regulation of signaling
GO:0010811	0.55	positive regulation of cell-substrate adhesion
GO:0010646	0.55	regulation of cell communication
GO:0043170	0.54	macromolecule metabolic process
GO:0030334	0.54	regulation of cell migration
GO:0009968	0.54	negative regulation of signal transduction
GO:1902532	0.53	negative regulation of intracellular signal transduction
GO:0065008	0.53	regulation of biological quality
GO:0051246	0.53	regulation of protein metabolic process
GO:0048584	0.53	positive regulation of response to stimulus
GO:0046578	0.53	regulation of Ras protein signal transduction
GO:0044710	0.53	single-organism metabolic process
GO:0019220	0.53	regulation of phosphate metabolic process
GO:0003008	0.53	system process
GO:2000147	0.52	positive regulation of cell motility
GO:1904181	0.52	positive regulation of membrane depolarization
GO:1903393	0.52	positive regulation of adherens junction organization
GO:1902533	0.52	positive regulation of intracellular signal transduction
GO:1901890	0.52	positive regulation of cell junction assembly
GO:0051900	0.52	regulation of mitochondrial depolarization
GO:0051896	0.52	regulation of protein kinase B signaling
GO:0051893	0.52	regulation of focal adhesion assembly
GO:0046580	0.52	negative regulation of Ras protein signal transduction
GO:0044260	0.52	cellular macromolecule metabolic process
GO:0043501	0.52	skeletal muscle adaptation
GO:0042552	0.52	myelination
GO:0038129	0.52	ERBB3 signaling pathway
GO:0038128	0.52	ERBB2 signaling pathway
GO:0038030	0.52	non-canonical Wnt signaling pathway via MAPK cascade
GO:0035023	0.52	regulation of Rho protein signal transduction
GO:0032292	0.52	peripheral nervous system axon ensheathment
GO:0032233	0.52	positive regulation of actin filament bundle assembly
GO:0032232	0.52	negative regulation of actin filament bundle assembly
GO:0014897	0.52	striated muscle hypertrophy
GO:0014066	0.52	regulation of phosphatidylinositol 3-kinase signaling
GO:0010812	0.52	negative regulation of cell-substrate adhesion
GO:0001954	0.52	positive regulation of cell-matrix adhesion
GO:0001932	0.52	regulation of protein phosphorylation
GO:0022607	0.51	cellular component assembly
GO:0035556	0.50	intracellular signal transduction

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	0.80	cell part
GO:0044424	0.68	intracellular part
GO:0043226	0.67	organelle
GO:0043227	0.63	membrane-bounded organelle
GO:0044421	0.56	extracellular region part
GO:0044444	0.52	cytoplasmic part
GO:0043229	0.51	intracellular organelle

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	1s0kA	0.448	4.63	0.058	0.579	3.2.1.18	248
2	0.060	1kitA	0.469	4.69	0.057	0.608	3.2.1.18	NA
3	0.060	1eusA	0.445	4.62	0.071	0.581	3.2.1.18	NA
4	0.060	2aepA	0.429	4.87	0.052	0.574	3.2.1.18	173
5	0.060	2vsmA	0.441	4.68	0.041	0.579	3.2.1.18	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	0.01	1y9mA	0.455	4.51	0.077	0.591	0.58	UUU	complex1.pdb.gz	159,161,170,217
2	0.01	2f0zA	0.449	4.79	0.086	0.591	0.45	ZMR	complex2.pdb.gz	156,157,173,211,286,288
3	0.01	3pijA	0.463	4.71	0.041	0.606	0.41	FRU	complex3.pdb.gz	156,176,209,210,274,275,373,387

	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.