D-I-TASSER A0A0B4J2F0

D-I-TASSER results for A0A0B4J2F0

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

Summary of the Protein

Uniprot ID: A0A0B4J2F0
Protein Name: Protein PIGBOS1
Gene Name: PIGBOS1

Input Sequence in FASTA format

>A0A0B4J2F0 (54 residues)
MFRRLTFAQLLFATVLGIAGGVYIFQPVFEQYAKDQKELKEKMQLVQESEEKKS

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	A0A0B4J2F0-D1	1-54	54		MFRRLTFAQLLFATVLGIAGGVYIFQPVFEQYAKDQKELKEKMQLVQESEEKKS

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.4566

(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	1ge9A	0.79	1.41	0.130	1.000	model1_1ge9A.pdb.gz
2	5tw1D1	0.78	1.94	0.111	0.963	model1_5tw1D1.pdb.gz
3	6vvsD	0.78	1.86	0.093	0.963	model1_6vvsD.pdb.gz
4	2yn7A	0.78	1.58	0.037	0.963	model1_2yn7A.pdb.gz
5	1iseA2	0.78	1.64	0.075	0.982	model1_1iseA2.pdb.gz
6	1is1A	0.76	1.70	0.148	1.000	model1_1is1A.pdb.gz
7	4gfqA	0.76	1.82	0.130	1.000	model1_4gfqA.pdb.gz
8	1t1mC	0.76	1.76	0.132	0.982	model1_1t1mC.pdb.gz
9	1wqgA2	0.75	1.72	0.075	0.982	model1_1wqgA2.pdb.gz
10	2v46Y2	0.69	2.14	0.132	0.982	model1_2v46Y2.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

./A0A0B4J2F0-D1/GOsearchresult_final_MF.svg

Molecular Function (MF)

GO term	Cscore^GO	Name
GO:0098811	0.35	transcriptional repressor activity, RNA polymerase II activating transcription factor binding
GO:0044877	0.35	macromolecular complex binding
GO:0001134	0.35	transcription factor activity, transcription factor recruiting
GO:0001083	0.35	transcription factor activity, RNA polymerase II basal transcription factor binding
GO:0001071	0.35	nucleic acid binding transcription factor activity
GO:0000987	0.35	core promoter proximal region sequence-specific DNA binding
GO:0000977	0.35	RNA polymerase II regulatory region sequence-specific DNA 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]

./A0A0B4J2F0-D1/GOsearchresult_final_BP.svg

Biological Process (BP)

GO term	Cscore^GO	Name
GO:2000144	0.35	positive regulation of DNA-templated transcription, initiation
GO:1903832	0.35	regulation of cellular response to amino acid starvation
GO:1901566	0.35	organonitrogen compound biosynthetic process
GO:0090294	0.35	nitrogen catabolite activation of transcription
GO:0046394	0.35	carboxylic acid biosynthetic process
GO:0045944	0.35	positive regulation of transcription from RNA polymerase II promoter
GO:0045898	0.35	regulation of RNA polymerase II transcriptional preinitiation complex assembly
GO:0032109	0.35	positive regulation of response to nutrient levels
GO:0010688	0.35	negative regulation of ribosomal protein gene transcription from RNA polymerase II promoter
GO:0010647	0.35	positive regulation of cell communication
GO:0006520	0.35	cellular amino acid metabolic process
GO:0001079	0.35	nitrogen catabolite regulation of transcription from RNA polymerase II promoter

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]

./A0A0B4J2F0-D1/GOsearchresult_final_CC.svg

Cellular Component (CC)

GO term	Cscore^GO	Name
GO:0044464	0.92	cell part
GO:0044424	0.88	intracellular part
GO:0044428	0.54	nuclear part
GO:0005634	0.54	nucleus
GO:0005667	0.50	transcription factor complex
GO:0000790	0.50	nuclear chromatin

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	0.161	2jwaA	0.518	2.18	0.000	0.667	2.7.10.1	22
2	0.138	1z8yN	0.499	1.60	0.114	0.630	3.4.21.90	22
3	0.132	2wieA	0.647	1.97	0.019	0.944	3.6.3.14	NA
4	0.131	1qleD	0.526	1.80	0.119	0.648	1.9.3.1	12
5	0.127	1xtcC	0.498	1.36	0.121	0.611	2.4.2.36	17

	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	0.04	3iqeC	0.734	1.69	0.075	0.963	0.17	H4M	complex1.pdb.gz	11,12,21,22,30,33
2	0.03	1xcg0	0.714	1.99	0.151	0.982	0.16	III	complex2.pdb.gz	12,16,17,26,29,33,36,37,40,41,44
3	0.02	1fgjA	0.717	1.70	0.093	0.963	0.14	HEC	complex3.pdb.gz	13,14,17,20,27,28,31,32
4	0.02	1seuA	0.714	1.67	0.094	0.963	0.12	QNA	complex4.pdb.gz	19,20,29,32,36
5	0.02	3iqeB	0.739	1.67	0.075	0.963	0.16	H4M	complex5.pdb.gz	15,16,24,29
6	0.01	3ll9A	0.714	2.16	0.019	0.907	0.16	ADP	complex6.pdb.gz	15,21,28,29
7	0.01	1nh3A	0.491	3.39	0.041	0.815	0.11	UUU	complex7.pdb.gz	20,29,32,36

	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.