D-I-TASSER O75781

D-I-TASSER results for O75781

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

Summary of the Protein

Uniprot ID: O75781
Protein Name: Paralemmin-1
Gene Name: PALM

Input Sequence in FASTA format

>O75781 (387 residues)
MEVLAAETTSQQERLQAIAEKRKRQAEIENKRRQLEDERRQLQHLKSKALRERWLLEGTP
SSASEGDEDLRRQMQDDEQKTRLLEDSVSRLEKEIEVLERGDSAPATAKENAAAPSPVRA
PAPSPAKEERKTEVVMNSQQTPVGTPKDKRVSNTPLRTVDGSPMMKAAMYSVEITVEKDK
VTGETRVLSSTTLLPRQPLPLGIKVYEDETKVVHAVDGTAENGIHPLSSSEVDELIHKAD
EVTLSEAGSTAGAAETRGAVEGAARTTPSRREITGVQAQPGEATSGPPGIQPGQEPPVTM
IFMGYQNVEDEAETKKVLGLQDTITAELVVIEDAAEPKEPAPPNGSAAEPPTEAASREEN
QAGPEATTSDPQDLDMKKHRCKCCSIM

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	O75781-D1	1-387	387		MEVLAAETTSQQERLQAIAEKRKRQAEIENKRRQLEDERRQLQHLKSKALRERWLLEGTPSSASEGDEDLRRQMQDDEQKTRLLEDSVSRLEKEIEVLERGDSAPATAKENAAAPSPVRAPAPSPAKEERKTEVVMNSQQTPVGTPKDKRVSNTPLRTVDGSPMMKAAMYSVEITVEKDKVTGETRVLSSTTLLPRQPLPLGIKVYEDETKVVHAVDGTAENGIHPLSSSEVDELIHKADEVTLSEAGSTAGAAETRGAVEGAARTTPSRREITGVQAQPGEATSGPPGIQPGQEPPVTMIFMGYQNVEDEAETKKVLGLQDTITAELVVIEDAAEPKEPAPPNGSAAEPPTEAASREENQAGPEATTSDPQDLDMKKHRCKCCSIM

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.3704

(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	3ecqB	0.43	6.56	0.040	0.695	model1_3ecqB.pdb.gz
2	4av3A	0.43	6.27	0.038	0.641	model1_4av3A.pdb.gz
3	4a01A	0.43	6.38	0.039	0.643	model1_4a01A.pdb.gz
4	6ljaA	0.41	6.59	0.042	0.651	model1_6ljaA.pdb.gz
5	1st6A	0.40	6.97	0.080	0.674	model1_1st6A.pdb.gz
6	6elhA	0.40	6.60	0.023	0.633	model1_6elhA.pdb.gz
7	3ayfA	0.40	6.31	0.059	0.615	model1_3ayfA.pdb.gz
8	1jb0A	0.40	6.99	0.048	0.682	model1_1jb0A.pdb.gz
9	3mk7A	0.38	6.63	0.029	0.594	model1_3mk7A.pdb.gz
10	1kyzE	0.25	6.98	0.036	0.426	model1_1kyzE.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:0005102	0.56	receptor binding
GO:0001664	0.53	G-protein coupled receptor binding
GO:0031750	0.52	D3 dopamine receptor 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:0048523	1.00	negative regulation of cellular process
GO:0044699	0.96	single-organism process
GO:0009987	0.96	cellular process
GO:0080090	0.95	regulation of primary metabolic process
GO:0050790	0.95	regulation of catalytic activity
GO:0044763	0.95	single-organism cellular process
GO:0031326	0.95	regulation of cellular biosynthetic process
GO:0051128	0.94	regulation of cellular component organization
GO:0007194	0.94	negative regulation of adenylate cyclase activity
GO:0048583	0.78	regulation of response to stimulus
GO:0009966	0.77	regulation of signal transduction
GO:0009968	0.76	negative regulation of signal transduction
GO:0048518	0.75	positive regulation of biological process
GO:0048522	0.74	positive regulation of cellular process
GO:0060160	0.70	negative regulation of dopamine receptor signaling pathway
GO:0051491	0.70	positive regulation of filopodium assembly
GO:0050896	0.63	response to stimulus
GO:0051179	0.62	localization
GO:0016043	0.61	cellular component organization
GO:0006810	0.60	transport
GO:1902578	0.59	single-organism localization
GO:0065008	0.59	regulation of biological quality
GO:0044802	0.59	single-organism membrane organization
GO:0008104	0.59	protein localization
GO:0051649	0.58	establishment of localization in cell
GO:0051641	0.58	cellular localization
GO:0044765	0.58	single-organism transport
GO:0015031	0.58	protein transport
GO:0050793	0.57	regulation of developmental process
GO:0044767	0.57	single-organism developmental process
GO:0006996	0.57	organelle organization
GO:0006886	0.57	intracellular protein transport
GO:0072657	0.56	protein localization to membrane
GO:0051716	0.56	cellular response to stimulus
GO:0008360	0.56	regulation of cell shape
GO:0007010	0.56	cytoskeleton organization
GO:0006605	0.56	protein targeting
GO:0072661	0.55	protein targeting to plasma membrane
GO:0071257	0.55	cellular response to electrical stimulus
GO:0060074	0.55	synapse maturation

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	1.00	cell part
GO:0016020	0.94	membrane
GO:0044424	0.93	intracellular part
GO:0005886	0.92	plasma membrane
GO:0044446	0.84	intracellular organelle part
GO:0043229	0.72	intracellular organelle
GO:0043231	0.70	intracellular membrane-bounded organelle
GO:0044428	0.69	nuclear part
GO:0005654	0.68	nucleoplasm
GO:0005634	0.68	nucleus
GO:0044444	0.53	cytoplasmic part
GO:0044463	0.52	cell projection part
GO:0044425	0.51	membrane part

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	2e1qA	0.305	7.24	0.040	0.532	1.17.3.2 1.17.1.4	NA
2	0.060	3ecqB	0.430	6.56	0.040	0.695	3.2.1.97	NA
3	0.060	2pffA	0.368	7.04	0.034	0.620	2.3.1.41 2.3.1.86	NA
4	0.060	3b9jI	0.166	5.39	0.070	0.238	1.17.1.4 1.17.3.2	NA
5	0.060	1vlbA	0.381	7.02	0.035	0.651	1.2.99.7	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:

No Binding sites was predicted

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

	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.