D-I-TASSER A0A1B0GU29

D-I-TASSER results for A0A1B0GU29

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

Summary of the Protein

Uniprot ID: A0A1B0GU29
Protein Name: Small integral membrane protein 28
Gene Name: SMIM28

Input Sequence in FASTA format

>A0A1B0GU29 (152 residues)
MRGLLGSSWKKFGHAGRGTYEWLTSEPGLPLLETQLQGTQGVSSTQEDVEPFLCILLPAT
ILLFLAFLLLFLYRRCKSPPPQGQVFSIDLPEHPPAGEVTDLLPGLAWSSEDFPYSPLPP
EATLPSQCLPPSYEEATRNPPGEEAQGCSPSV

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	A0A1B0GU29-D1	1-152	152		MRGLLGSSWKKFGHAGRGTYEWLTSEPGLPLLETQLQGTQGVSSTQEDVEPFLCILLPATILLFLAFLLLFLYRRCKSPPPQGQVFSIDLPEHPPAGEVTDLLPGLAWSSEDFPYSPLPPEATLPSQCLPPSYEEATRNPPGEEAQGCSPSV

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.4391

(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	1jskC	0.55	3.87	0.071	0.822	model1_1jskC.pdb.gz
2	1a6zA	0.55	4.19	0.053	0.822	model1_1a6zA.pdb.gz
3	4s0uC	0.55	3.86	0.077	0.809	model1_4s0uC.pdb.gz
4	2h26A1	0.55	4.06	0.047	0.822	model1_2h26A1.pdb.gz
5	6v7yA1	0.54	4.11	0.047	0.816	model1_6v7yA1.pdb.gz
6	1lqvB	0.54	4.43	0.108	0.849	model1_1lqvB.pdb.gz
7	3d2uE	0.53	4.27	0.044	0.822	model1_3d2uE.pdb.gz
8	4f7cA	0.53	4.25	0.070	0.829	model1_4f7cA.pdb.gz
9	3jvgB1	0.53	4.29	0.069	0.836	model1_3jvgB1.pdb.gz
10	1kcgC	0.53	4.35	0.078	0.822	model1_1kcgC.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

./A0A1B0GU29-D1/GOsearchresult_final_MF.svg

Molecular Function (MF)

GO term	Cscore^GO	Name
GO:0042277	0.49	peptide binding
GO:0042287	0.39	MHC protein binding
GO:0030881	0.39	beta-2-microglobulin binding
GO:0030882	0.37	lipid antigen 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]

./A0A1B0GU29-D1/GOsearchresult_final_BP.svg

Biological Process (BP)

GO term	Cscore^GO	Name
GO:0071346	0.49	cellular response to interferon-gamma
GO:0042742	0.49	defense response to bacterium
GO:0042590	0.49	antigen processing and presentation of exogenous peptide antigen via MHC class I
GO:0019730	0.49	antimicrobial humoral response
GO:0019221	0.49	cytokine-mediated signaling pathway
GO:0002711	0.49	positive regulation of T cell mediated immunity
GO:0001914	0.49	regulation of T cell mediated cytotoxicity
GO:0001912	0.49	positive regulation of leukocyte mediated cytotoxicity
GO:2001187	0.39	positive regulation of CD8-positive, alpha-beta T cell activation
GO:2000564	0.39	regulation of CD8-positive, alpha-beta T cell proliferation
GO:1903557	0.39	positive regulation of tumor necrosis factor superfamily cytokine production
GO:0071357	0.39	cellular response to type I interferon
GO:0051023	0.39	regulation of immunoglobulin secretion
GO:0050714	0.39	positive regulation of protein secretion
GO:0046641	0.39	positive regulation of alpha-beta T cell proliferation
GO:0045953	0.39	negative regulation of natural killer cell mediated cytotoxicity
GO:0045089	0.39	positive regulation of innate immune response
GO:0032680	0.39	regulation of tumor necrosis factor production
GO:0032679	0.39	regulation of TRAIL production
GO:0032673	0.39	regulation of interleukin-4 production
GO:0032656	0.39	regulation of interleukin-13 production
GO:0002639	0.39	positive regulation of immunoglobulin production
GO:0002483	0.39	antigen processing and presentation of endogenous peptide antigen
GO:0002428	0.39	antigen processing and presentation of peptide antigen via MHC class Ib
GO:0048003	0.37	antigen processing and presentation of lipid antigen via MHC class Ib

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]

./A0A1B0GU29-D1/GOsearchresult_final_CC.svg

Cellular Component (CC)

GO term	Cscore^GO	Name
GO:0031224	1.00	intrinsic component of membrane
GO:0016020	1.00	membrane
GO:0044464	0.95	cell part
GO:0016021	0.84	integral component of membrane
GO:0044459	0.68	plasma membrane part
GO:0005886	0.68	plasma membrane
GO:0042612	0.53	MHC class I protein complex

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	2occN	0.486	4.42	0.069	0.757	1.9.3.1	27
2	0.060	1gqfA	0.471	4.37	0.042	0.763	3.4.22.60	NA
3	0.060	1iduA	0.515	4.06	0.058	0.763	1.11.1.10	NA
4	0.060	1shjB	0.426	4.20	0.057	0.678	3.4.22.60 3.4.22.-	NA
5	0.060	1eulA	0.502	4.30	0.046	0.763	3.6.3.8	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	0.02	3ta3A	0.521	4.33	0.078	0.816	0.76	UUU	complex1.pdb.gz	8,26,27,28,67
2	0.02	3o9wA	0.531	4.37	0.070	0.829	0.72	UUU	complex2.pdb.gz	5,6,13,24
3	0.01	1zhnA	0.527	4.31	0.063	0.822	0.67	UUU	complex3.pdb.gz	26,27,28,29,63,64
4	0.01	1n368	0.238	4.66	0.030	0.382	0.79	III	complex4.pdb.gz	8,12,13,32

	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.