D-I-TASSER Q96DR5

D-I-TASSER results for Q96DR5

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

Summary of the Protein

Uniprot ID: Q96DR5
Protein Name: BPI fold-containing family A member 2
Gene Name: BPIFA2

Input Sequence in FASTA format

>Q96DR5 (249 residues)
MLQLWKLVLLCGVLTGTSESLLDNLGNDLSNVVDKLEPVLHEGLETVDNTLKGILEKLKV
DLGVLQKSSAWQLAKQKAQEAEKLLNNVISKLLPTNTDIFGLKISNSLILDVKAEPIDDG
KGLNLSFPVTANVTVAGPIIGQIINLKASLDLLTAVTIETDPQTHQPVAVLGECASDPTS
ISLSLLDKHSQIINKFVNSVINTLKSTVSSLLQKEICPLIRIFIHSLDVNVIQQVVDNPQ
HKTQLQTLI

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	Q96DR5-D1	1-249	249		MLQLWKLVLLCGVLTGTSESLLDNLGNDLSNVVDKLEPVLHEGLETVDNTLKGILEKLKVDLGVLQKSSAWQLAKQKAQEAEKLLNNVISKLLPTNTDIFGLKISNSLILDVKAEPIDDGKGLNLSFPVTANVTVAGPIIGQIINLKASLDLLTAVTIETDPQTHQPVAVLGECASDPTSISLSLLDKHSQIINKFVNSVINTLKSTVSSLLQKEICPLIRIFIHSLDVNVIQQVVDNPQHKTQLQTLI

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.581

(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	4kghB	0.53	3.84	0.189	0.655	model1_4kghB.pdb.gz
2	3zpmA	0.50	3.82	0.139	0.651	model1_3zpmA.pdb.gz
3	5wd6A	0.49	4.38	0.259	0.667	model1_5wd6A.pdb.gz
4	8bgmB	0.49	4.46	0.054	0.675	model1_8bgmB.pdb.gz
5	4m4dA	0.47	4.80	0.109	0.667	model1_4m4dA.pdb.gz
6	1bp1A	0.47	4.77	0.082	0.663	model1_1bp1A.pdb.gz
7	2obdA1	0.41	3.89	0.145	0.542	model1_2obdA1.pdb.gz
8	4kp1A	0.28	6.07	0.044	0.486	model1_4kp1A.pdb.gz
9	3ksyA3	0.25	4.41	0.037	0.341	model1_3ksyA3.pdb.gz
10	1tnzL2	0.23	5.94	0.060	0.394	model1_1tnzL2.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:0008289	0.95	lipid binding
GO:0001530	0.90	lipopolysaccharide 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:0065007	0.99	biological regulation
GO:0050789	0.96	regulation of biological process
GO:0050896	0.94	response to stimulus
GO:0002376	0.94	immune system process
GO:0050794	0.93	regulation of cellular process
GO:0048519	0.93	negative regulation of biological process
GO:0006955	0.92	immune response
GO:0048523	0.90	negative regulation of cellular process
GO:0045087	0.90	innate immune response
GO:0044699	0.86	single-organism process
GO:0042592	0.79	homeostatic process
GO:0048871	0.78	multicellular organismal homeostasis
GO:0043207	0.78	response to external biotic stimulus
GO:0043903	0.76	regulation of symbiosis, encompassing mutualism through parasitism
GO:0043901	0.76	negative regulation of multi-organism process
GO:1900228	0.75	regulation of single-species biofilm formation in or on host organism
GO:1900191	0.75	negative regulation of single-species biofilm formation
GO:0051707	0.75	response to other organism
GO:0032879	0.75	regulation of localization
GO:1904062	0.74	regulation of cation transmembrane transport
GO:0050878	0.74	regulation of body fluid levels
GO:0030104	0.74	water homeostasis
GO:0019730	0.74	antimicrobial humoral response
GO:0002028	0.74	regulation of sodium ion transport
GO:0050828	0.71	regulation of liquid surface tension
GO:0042742	0.67	defense response to bacterium
GO:1900229	0.56	negative regulation of single-species biofilm formation in or on host organism
GO:1902305	0.54	regulation of sodium ion transmembrane transport
GO:0050891	0.54	multicellular organismal water homeostasis
GO:0019731	0.54	antibacterial humoral response
GO:0009987	0.53	cellular process
GO:0044763	0.51	single-organism cellular process

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	0.93	extracellular region part
GO:0005576	0.92	extracellular region
GO:0043227	0.78	membrane-bounded organelle
GO:0031988	0.77	membrane-bounded vesicle
GO:0070062	0.69	extracellular exosome

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	1n6bA	0.388	5.81	0.056	0.651	1.14.14.1	NA
2	0.060	1vlbA	0.415	5.70	0.065	0.703	1.2.99.7	NA
3	0.060	3i3kA	0.361	5.72	0.050	0.582	1.14.13.70	NA
4	0.060	3b6hB	0.396	5.65	0.060	0.651	5.3.99.4	138,204,208
5	0.060	2ve3A	0.390	5.87	0.063	0.651	1.14.-.-	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	0.01	2ckjC	0.441	5.73	0.062	0.731	0.54	FES	complex1.pdb.gz	121,122,156,169
	2	0.01	2ckjA	0.414	5.97	0.049	0.703	0.53	FES	complex2.pdb.gz	101,134,135,136,137

	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, Qiqige Wuyun, Yang Li, Quancheng Liu, Xiaogen Zhou, Yiheng Zhu, P. Lydia Freddolino, Yang Zhang. Integrating deep learning potentials with I-TASSER for single- and multi-domain protein structure prediction. Submitted. 2023.