D-I-TASSER P05090

D-I-TASSER results for P05090

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

Summary of the Protein

Uniprot ID: P05090
Protein Name: Apolipoprotein D
Gene Name: APOD

Input Sequence in FASTA format

>P05090 (189 residues)
MVMLLLLLSALAGLFGAAEGQAFHLGKCPNPPVQENFDVNKYLGRWYEIEKIPTTFENGR
CIQANYSLMENGKIKVLNQELRADGTVNQIEGEATPVNLTEPAKLEVKFSWFMPSAPYWI
LATDYENYALVYSCTCIIQLFHVDFAWILARNPNLPPETVDSLKNILTSNNIDVKKMTVT
DQVNCPKLS

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	P05090-D1	1-189	189		MVMLLLLLSALAGLFGAAEGQAFHLGKCPNPPVQENFDVNKYLGRWYEIEKIPTTFENGRCIQANYSLMENGKIKVLNQELRADGTVNQIEGEATPVNLTEPAKLEVKFSWFMPSAPYWILATDYENYALVYSCTCIIQLFHVDFAWILARNPNLPPETVDSLKNILTSNNIDVKKMTVTDQVNCPKLS

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.751

(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	5ez2A	0.86	1.17	0.395	0.884	model1_5ez2A.pdb.gz
2	1gkaB	0.83	1.85	0.251	0.905	model1_1gkaB.pdb.gz
3	1i4uA	0.81	1.96	0.254	0.894	model1_1i4uA.pdb.gz
4	2hzqA	0.81	1.64	0.957	0.862	model1_2hzqA.pdb.gz
5	1z24A	0.78	2.29	0.305	0.878	model1_1z24A.pdb.gz
6	2acoA	0.74	1.98	0.285	0.799	model1_2acoA.pdb.gz
7	1aqbA	0.73	2.41	0.228	0.841	model1_1aqbA.pdb.gz
8	1qabE	0.72	2.71	0.211	0.852	model1_1qabE.pdb.gz
9	3qkgA	0.71	2.77	0.140	0.825	model1_3qkgA.pdb.gz
10	1t0vA	0.70	2.94	0.248	0.857	model1_1t0vA.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:0043178	1.00	alcohol binding
GO:0008289	1.00	lipid binding
GO:0097159	0.94	organic cyclic compound binding
GO:0015485	0.93	cholesterol 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:0050896	0.95	response to stimulus
GO:0065007	0.92	biological regulation
GO:0042221	0.89	response to chemical
GO:0009987	0.89	cellular process
GO:0050789	0.87	regulation of biological process
GO:0044763	0.87	single-organism cellular process
GO:0006950	0.87	response to stress
GO:0032502	0.86	developmental process
GO:1901700	0.84	response to oxygen-containing compound
GO:0050794	0.84	regulation of cellular process
GO:0044767	0.84	single-organism developmental process
GO:0008152	0.84	metabolic process
GO:0006979	0.84	response to oxidative stress
GO:0048856	0.83	anatomical structure development
GO:0044710	0.83	single-organism metabolic process
GO:0071704	0.82	organic substance metabolic process
GO:0044281	0.82	small molecule metabolic process
GO:0044238	0.81	primary metabolic process
GO:0048519	0.80	negative regulation of biological process
GO:0048513	0.80	animal organ development
GO:0033554	0.80	cellular response to stress
GO:0006629	0.80	lipid metabolic process
GO:0048523	0.79	negative regulation of cellular process
GO:0051239	0.78	regulation of multicellular organismal process
GO:0051223	0.78	regulation of protein transport
GO:0023051	0.78	regulation of signaling
GO:0019222	0.78	regulation of metabolic process
GO:0010646	0.78	regulation of cell communication
GO:0006006	0.78	glucose metabolic process
GO:0080090	0.77	regulation of primary metabolic process
GO:0051241	0.77	negative regulation of multicellular organismal process
GO:0048583	0.77	regulation of response to stimulus
GO:0031323	0.77	regulation of cellular metabolic process
GO:0009888	0.77	tissue development
GO:0008285	0.77	negative regulation of cell proliferation
GO:0002682	0.77	regulation of immune system process
GO:0080134	0.76	regulation of response to stress
GO:0060255	0.76	regulation of macromolecule metabolic process
GO:0031324	0.76	negative regulation of cellular metabolic process
GO:0016043	0.76	cellular component organization
GO:0048589	0.75	developmental growth
GO:0045833	0.75	negative regulation of lipid metabolic process
GO:0010605	0.75	negative regulation of macromolecule metabolic process
GO:2000405	0.74	negative regulation of T cell migration
GO:2000098	0.74	negative regulation of smooth muscle cell-matrix adhesion
GO:1900016	0.74	negative regulation of cytokine production involved in inflammatory response
GO:0071638	0.74	negative regulation of monocyte chemotactic protein-1 production
GO:0060588	0.74	negative regulation of lipoprotein lipid oxidation
GO:0051895	0.74	negative regulation of focal adhesion assembly
GO:0048662	0.74	negative regulation of smooth muscle cell proliferation
GO:0042493	0.74	response to drug
GO:0042308	0.74	negative regulation of protein import into nucleus
GO:0042246	0.74	tissue regeneration
GO:0014012	0.74	peripheral nervous system axon regeneration
GO:0010642	0.74	negative regulation of platelet-derived growth factor receptor signaling pathway
GO:0007568	0.74	aging
GO:0007420	0.74	brain development
GO:0000302	0.74	response to reactive oxygen species

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:0044421	0.97	extracellular region part
GO:0005615	0.96	extracellular space
GO:0044464	0.93	cell part
GO:0044424	0.91	intracellular part
GO:0044444	0.89	cytoplasmic part
GO:0043226	0.85	organelle
GO:0043227	0.84	membrane-bounded organelle
GO:0043231	0.81	intracellular membrane-bounded organelle
GO:0032991	0.77	macromolecular complex
GO:0005783	0.75	endoplasmic reticulum
GO:0043232	0.74	intracellular non-membrane-bounded organelle
GO:0043025	0.74	neuronal cell body
GO:0030529	0.74	intracellular ribonucleoprotein complex
GO:0048471	0.73	perinuclear region of cytoplasm
GO:0030425	0.73	dendrite
GO:0022626	0.73	cytosolic ribosome

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	2zj7A	0.405	4.92	0.052	0.645	3.1.1.3	NA
2	0.060	1crkA	0.433	4.54	0.053	0.651	2.7.3.2	NA
3	0.060	2j2mA	0.426	4.05	0.043	0.609	1.11.1.6	NA
4	0.060	1cb7B	0.419	5.30	0.042	0.693	5.4.99.1	NA
5	0.060	1kdgB	0.412	4.55	0.024	0.609	1.1.99.18	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	0.29	1n0sA	0.747	2.46	0.274	0.857	0.95	FLU	complex1.pdb.gz	42,48,66,78,90,107,116,118,147
2	0.26	1bbpA	0.762	2.36	0.297	0.868	0.88	BLV	complex2.pdb.gz	48,55,56,63,64,78,79,80,90,118,133,145,147,149
3	0.24	2wq9A	0.726	2.45	0.230	0.836	0.83	OLA	complex3.pdb.gz	56,57,66,76,78,90,91,92,107,109,118,131,147,149
4	0.18	1epbA	0.661	2.79	0.208	0.778	0.90	REA	complex4.pdb.gz	39,42,46,77,116,118,120,129,131,133,147,149
5	0.05	1gkaA	0.804	1.96	0.256	0.889	0.96	AXT	complex5.pdb.gz	23,56,57,64,79,107,109,116,133,141,145,147,149
6	0.05	1obq0	0.810	1.99	0.254	0.894	0.84	III	complex6.pdb.gz	54,55,56,57,91,92,93,108,109,110,111,112,113,115,117,135

	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.