D-I-TASSER Q5TDP6

D-I-TASSER results for Q5TDP6

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

Summary of the Protein

Uniprot ID: Q5TDP6
Protein Name: Lengsin
Gene Name: LGSN

Input Sequence in FASTA format

>Q5TDP6 (509 residues)
MNNEEDLLQEDSTRDEGNETEANSMNTLRRTRKKVTKPYVCSTEVGETDMSNSNDCMRDS
SQILTPPQLSSRMKHIRQAMAKNRLQFVRFEATDLHGVSRSKTIPAHFFQEKVSHGVCMP
RGYLEVIPNPKDNEMNNIRATCFNSDIVLMPELSTFRVLPWADRTARVICDTFTVTGEPL
LTSPRYIAKRQLSHLQASGFSLLSAFIYDFCIFGVPEILNSKIISFPALTFLNNHDQPFM
QELVDGLYHTGANVESFSSSTRPGQMEISFLPEFGISSADNAFTLRTGVKEVARKYNYIA
SFFIETGFCDSGILSHSLWDVDRKKNMFCSTSGTEQLTITGKKWLAGLLKHSAALSCLMA
PSVSCRKRYSKDRKDLKKSVPTTWGYNDNSCIFNIKCHGEKGTRIENKLGSATANPYLVL
AATVAAGLDGLHSSNEVLAGPDESTDFYQVEPSEIPLKLEDALVALEEDQCLRQALGETF
IRYFVAMKKYELENEEIAAERNKFLEYFI

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	Q5TDP6-D1	1-182,477-509	215		MNNEEDLLQEDSTRDEGNETEANSMNTLRRTRKKVTKPYVCSTEVGETDMSNSNDCMRDSSQILTPPQLSSRMKHIRQAMAKNRLQFVRFEATDLHGVSRSKTIPAHFFQEKVSHGVCMPRGYLEVIPNPKDNEMNNIRATCFNSDIVLMPELSTFRVLPWADRTARVICDTFTVTGEPLLTGETFIRYFVAMKKYELENEEIAAERNKFLEYFI
2	Q5TDP6-D2	183-205,314-476	186		SPRYIAKRQLSHLQASGFSLLSALSHSLWDVDRKKNMFCSTSGTEQLTITGKKWLAGLLKHSAALSCLMAPSVSCRKRYSKDRKDLKKSVPTTWGYNDNSCIFNIKCHGEKGTRIENKLGSATANPYLVLAATVAAGLDGLHSSNEVLAGPDESTDFYQVEPSEIPLKLEDALVALEEDQCLRQAL
3	Q5TDP6-D3	206-313	108		FIYDFCIFGVPEILNSKIISFPALTFLNNHDQPFMQELVDGLYHTGANVESFSSSTRPGQMEISFLPEFGISSADNAFTLRTGVKEVARKYNYIASFFIETGFCDSGI

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.79

(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	3qajA	0.64	3.65	0.197	0.731	model1_3qajA.pdb.gz
2	6pewD	0.63	4.24	0.156	0.745	model1_6pewD.pdb.gz
3	5zliA	0.63	4.02	0.151	0.741	model1_5zliA.pdb.gz
4	3ng0A	0.63	4.03	0.172	0.735	model1_3ng0A.pdb.gz
5	1htoX	0.62	4.11	0.162	0.735	model1_1htoX.pdb.gz
6	1f1hL	0.62	3.95	0.184	0.725	model1_1f1hL.pdb.gz
7	7cqlA	0.62	3.80	0.205	0.713	model1_7cqlA.pdb.gz
8	4hppA	0.60	4.16	0.174	0.703	model1_4hppA.pdb.gz
9	4s17A	0.59	3.84	0.186	0.690	model1_4s17A.pdb.gz
10	3o6xA	0.57	4.51	0.099	0.692	model1_3o6xA.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:0003824	0.91	catalytic activity
GO:0016879	0.83	ligase activity, forming carbon-nitrogen bonds
GO:0016880	0.78	acid-ammonia (or amide) ligase activity
GO:0016211	0.72	ammonia ligase activity
GO:1901363	0.67	heterocyclic compound binding
GO:0097159	0.67	organic cyclic compound binding
GO:0000166	0.63	nucleotide binding
GO:0097367	0.62	carbohydrate derivative binding
GO:0017076	0.62	purine nucleotide binding
GO:0035639	0.61	purine ribonucleoside triphosphate binding
GO:0032555	0.61	purine ribonucleotide binding
GO:0032550	0.61	purine ribonucleoside binding
GO:0032559	0.60	adenyl ribonucleotide 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:0009987	0.95	cellular process
GO:0044699	0.90	single-organism process
GO:0008152	0.85	metabolic process
GO:0044763	0.81	single-organism cellular process
GO:0071704	0.80	organic substance metabolic process
GO:0044237	0.77	cellular metabolic process
GO:0006807	0.75	nitrogen compound metabolic process
GO:1901564	0.70	organonitrogen compound metabolic process
GO:0044710	0.70	single-organism metabolic process
GO:0044281	0.69	small molecule metabolic process
GO:0044238	0.65	primary metabolic process
GO:0006082	0.59	organic acid metabolic process
GO:0043436	0.58	oxoacid metabolic process
GO:0019752	0.57	carboxylic acid metabolic process
GO:1901576	0.54	organic substance biosynthetic process
GO:0044249	0.54	cellular biosynthetic process
GO:0006520	0.54	cellular amino acid metabolic process
GO:1901605	0.53	alpha-amino acid metabolic process
GO:0009064	0.52	glutamine family amino acid metabolic process
GO:1901566	0.51	organonitrogen compound biosynthetic process
GO:0044711	0.51	single-organism biosynthetic process
GO:0006541	0.51	glutamine metabolic process
GO:0016053	0.50	organic acid biosynthetic 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:0044464	1.00	cell part
GO:0044424	0.94	intracellular part
GO:0044444	0.66	cytoplasmic part
GO:0044446	0.59	intracellular organelle part
GO:0016020	0.58	membrane

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	0.072	1f1hL	0.624	3.95	0.184	0.725	6.3.1.2	NA
2	0.067	2d3aA	0.505	3.62	0.118	0.587	6.3.1.2	NA
3	0.067	3fkyC	0.516	3.67	0.149	0.601	6.3.1.2	NA
4	0.060	2uu7A	0.521	3.70	0.154	0.607	6.3.1.2	NA
5	0.060	3b9jJ	0.217	7.18	0.039	0.348	1.17.1.4 1.17.3.2	140

	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	0.03	2lgsA	0.597	3.84	0.200	0.690	0.19	GLU	complex1.pdb.gz	115,116,149
2	0.02	2whiE	0.623	4.12	0.167	0.737	0.16	1AZ	complex2.pdb.gz	90,92,97,99
3	0.02	1htqA	0.622	4.20	0.162	0.735	0.18	AMP	complex3.pdb.gz	90,91,92,96,97,98,99
4	0.02	2qc8J	0.511	3.56	0.158	0.593	0.11	ADP	complex4.pdb.gz	93,94,97
5	0.01	2d3aA	0.505	3.62	0.118	0.587	0.16	ADP	complex5.pdb.gz	89,91,93
6	0.01	2d3bD	0.504	3.63	0.118	0.587	0.13	MSL	complex6.pdb.gz	210,211,213
7	0.01	2d3bC	0.504	3.63	0.118	0.587	0.13	UUU	complex7.pdb.gz	116,121,146,148,182,183,416,481
8	0.01	2d3aG	0.504	3.62	0.118	0.587	0.11	ADP	complex8.pdb.gz	117,119,121,122,478
9	0.01	2d3aE	0.505	3.62	0.118	0.587	0.10	ADP	complex9.pdb.gz	91,93,95

	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.