D-I-TASSER P51449-D2

D-I-TASSER results for P51449-D2

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

Input Sequence in FASTA format

>P51449 (119 residues)
GADTLTYTLGLPDGQLPLGSSPDLPEASACPPGLLKASGSGPSYSNNLAKAGLNGASCHL
EYSPERGKAEGRESFYSTGSQLTPDRCGLRFEEHRHPGLGELGQGPDSYGSPSFRSTPE

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| GADTLTYTLGLPDGQLPLGSSPDLPEASACPPGLLKASGSGPSYSNNLAKAGLNGASCHLEYSPERGKAEGRESFYSTGSQLTPDRCGLRFEEHRHPGLGELGQGPDSYGSPSFRSTPE
Prediction	CCCCCCCSCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCHHHHCCCCCCSSSCCCCCHHHCHHCCCCCCCCCCCCCCCCCCSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Confidence	99876301247888666789999864357995562489999886321333156873243245821200010144114677547885411037888988888787887777865345899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| GADTLTYTLGLPDGQLPLGSSPDLPEASACPPGLLKASGSGPSYSNNLAKAGLNGASCHLEYSPERGKAEGRESFYSTGSQLTPDRCGLRFEEHRHPGLGELGQGPDSYGSPSFRSTPE
Prediction	86543413141463414346447246254134221434354452444145342542423362447424353463123344513474241326645344255365146432344246458
	Values range from 0 (buried residue) to 8 (highly exposed residue)

Predicted Contact, Hydrogen and Distance Map Used in D-I-TASSER simulation

Contact Map

Distance Map

Hydrogen bond networks

D-I-TASSER simulation is guided by the consensus contact map (left figure), distance map (middle figure) and Hydrogen bond network (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.

Top 10 threading templates used by D-I-TASSER

Rank

PDB
hit

ID1

ID2

Cov

Norm.
Zscore

Download
alignment

                  20                  40                  60                  80                 100

                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCSCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCHHHHCCCCCCSSSCCCCCHHHCHHCCCCCCCCCCCCCCCCCCSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
GADTLTYTLGLPDGQLPLGSSPDLPEASACPPGLLKASGSGPSYSNNLAKAGLNGASCHLEYSPERGKAEGRESFYSTGSQLTPDRCGLRFEEHRHPGLGELGQGPDSYGSPSFRSTPE

3nvqA3

0.06

0.04

1.83

0.59

CEthreader

------------------------------------HTVLFHEPGSSSVWVGGRGKVYLFDFPEGKNASVRKGSCLDKRDCENYITLLERRSEGLLACGTNARHPSCWNLVNGTVVPLG

3r67A

0.07

2.79

0.52

EigenThreader

EGINPIVSPDTTTVWESSNSAVGIGS---RTSRLGDGLHFNRTVPVFPRVAVTEDGLYVLAFAEFSKSASIVYWYWGEKFVNVATKVITPREGKFDSDGDTLYTANSYIPGQYPAGTVF

3o2zI

0.13

0.12

4.08

0.36

FFAS-3D

--KTHSYR-GVDLEKLLEMSTEDFVK--------LAPARVRRRFARGMTSKPAGFMKKLRAAKLAAPENEKPARTHMRNMIIVPEMIGSVVGIYNGKAFNQVEIRPEMLGHYEFSITYT

7jjvA

0.14

4.85

1.33

SPARKS-K

GADGTSNGQAGASGL-AGGPNCNGGKGGKGAPGVGTAGGAGGVGGAGGTGNTNGGAGGSGGNSDVAAGGAGAAGGAAGGAGTGGTGGNGGAGKPGGAPGAGGAGTPAGSAGSPGQTTVL

3zs3A

0.21

0.05

1.60

0.54

CNFpred

-------------------------ETADCGSGQVACNGAGAVPPATLVEITI------------------------------------------------------------------

6f2pA4

0.04

0.03

1.82

0.83

DEthreader

----------AFGLSMFSSRIDKSWAGMESWFMFEIVAVISILENSAQAVKETQLNVTGINFWRKASVMTKEFEISVIYIDVNKSATGLI-SKDNEITVIQTMKFKVNVNSGGKSYKVK

1vt4I3

0.15

0.14

4.82

0.95

MapAlign

-----GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG

3cesA

0.18

5.75

0.76

MUSTER

GSIPLSRRLPLRVGRLKTGTPPRIDARTIDFSVLAQQHGDNPMPVFSFMGNHPQQVPCYITHTNEKTHDVIRSNLDRSPSI--EDKVMRFADRNQHQIFLEPEGSNEIYPNGISTSLPF

6e1rA2

0.22

0.13

4.25

0.60

HHsearch

GSSVGVASLSHPS--------------------ISGASYGGRAI-FGTTAAGTNSAVYELLVTSVGT----A-----------KYI--SQIGS---AGLTSG----AAASHPSFTWSIN

6tmrA

0.10

3.72

0.52

CEthreader

VAACRDAYNWKVSGDPRYEDSSGSRTVTTTKESLLIISPSIVEMDRTLHSPMFPSGVCSNVYPSVPSCETNHDYTLWLPEDPSLSLVCDIFTSSNGKKAMNGSRICGFKDERGFYRSLK

(a)	ID1 is the number of template residues identical to query divided by number of aligned residues.
(b)	ID2 is the number of template residues identical to query divided by query sequence length.
(c)	Cov is equal the number of aligned template residues divided by query sequence length.
(d)	Norm. Zscore is the normalized Z-score of the threading alignments. A Normalized Z-score >1 means a good alignment and is highlighted in bold.
(e)	Download alignment lists the threading program used to identify the template, and provide the 3D structure of aligned regions of threading templates (threading[1-10].pdb.gz).
(f)	Template residues identical to query sequence are highlighted in color.

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.5444

(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	6oqqA	0.46	4.83	0.036	0.849	model1_6oqqA.pdb.gz
2	5vobA	0.45	4.80	0.052	0.824	model1_5vobA.pdb.gz
3	3m1cA	0.44	5.02	0.089	0.815	model1_3m1cA.pdb.gz
4	4neiA	0.44	4.45	0.036	0.748	model1_4neiA.pdb.gz
5	5wylA	0.44	4.88	0.009	0.798	model1_5wylA.pdb.gz
6	1ve5A1	0.44	4.30	0.100	0.765	model1_1ve5A1.pdb.gz
7	4r1dA	0.44	4.40	0.106	0.773	model1_4r1dA.pdb.gz
8	3hmkB	0.44	4.51	0.034	0.765	model1_3hmkB.pdb.gz
9	2zr8A	0.42	5.04	0.052	0.815	model1_2zr8A.pdb.gz
10	4xhjA	0.42	5.07	0.065	0.798	model1_4xhjA.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:0003700	1.00	transcription factor activity, sequence-specific DNA binding
GO:1901363	0.69	heterocyclic compound binding
GO:0097159	0.69	organic cyclic compound binding
GO:0003676	0.68	nucleic acid binding
GO:0003677	0.67	DNA binding
GO:0098531	0.66	transcription factor activity, direct ligand regulated sequence-specific DNA binding
GO:0043565	0.66	sequence-specific DNA binding
GO:0008289	0.65	lipid binding
GO:0008142	0.64	oxysterol 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:0007623	1.00	circadian rhythm
GO:0065007	0.90	biological regulation
GO:0050789	0.89	regulation of biological process
GO:0050794	0.87	regulation of cellular process
GO:0009987	0.86	cellular process
GO:0048518	0.84	positive regulation of biological process
GO:0044699	0.84	single-organism process
GO:0080090	0.83	regulation of primary metabolic process
GO:0060255	0.83	regulation of macromolecule metabolic process
GO:0031323	0.83	regulation of cellular metabolic process
GO:0008152	0.83	metabolic process
GO:0048522	0.82	positive regulation of cellular process
GO:0044763	0.82	single-organism cellular process
GO:0044237	0.82	cellular metabolic process
GO:0009893	0.82	positive regulation of metabolic process
GO:0006355	0.82	regulation of transcription, DNA-templated
GO:0048856	0.81	anatomical structure development
GO:0045893	0.81	positive regulation of transcription, DNA-templated
GO:0044767	0.81	single-organism developmental process
GO:0048513	0.80	animal organ development
GO:0045595	0.80	regulation of cell differentiation
GO:0044707	0.80	single-multicellular organism process
GO:0042752	0.80	regulation of circadian rhythm
GO:0030154	0.80	cell differentiation
GO:0022610	0.80	biological adhesion
GO:0009888	0.80	tissue development
GO:0006357	0.80	regulation of transcription from RNA polymerase II promoter
GO:0002252	0.80	immune effector process
GO:0001775	0.80	cell activation
GO:0072539	0.79	T-helper 17 cell differentiation
GO:0060850	0.79	regulation of transcription involved in cell fate commitment
GO:0060612	0.79	adipose tissue development
GO:0048541	0.79	Peyer's patch development
GO:0048535	0.79	lymph node development
GO:0045598	0.79	regulation of fat cell differentiation
GO:0042753	0.79	positive regulation of circadian rhythm
GO:0032922	0.79	circadian regulation of gene expression
GO:0019218	0.79	regulation of steroid metabolic process
GO:0010906	0.79	regulation of glucose metabolic process
GO:0006805	0.79	xenobiotic metabolic process
GO:0071704	0.59	organic substance metabolic process
GO:0044238	0.59	primary metabolic process
GO:0043170	0.58	macromolecule metabolic process
GO:0044260	0.57	cellular macromolecule metabolic process
GO:0050896	0.56	response to stimulus
GO:0048519	0.55	negative regulation of biological process
GO:0048523	0.54	negative regulation of cellular process
GO:0010033	0.53	response to organic substance
GO:1901700	0.52	response to oxygen-containing compound
GO:0071310	0.52	cellular response to organic substance
GO:0033993	0.52	response to lipid
GO:0014070	0.52	response to organic cyclic compound
GO:0070244	0.51	negative regulation of thymocyte apoptotic process
GO:0036315	0.51	cellular response to sterol

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:0043231	1.00	intracellular membrane-bounded organelle
GO:0044446	0.89	intracellular organelle part
GO:0044428	0.88	nuclear part
GO:0043232	0.86	intracellular non-membrane-bounded organelle
GO:0005730	0.85	nucleolus
GO:0005634	0.50	nucleus

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	9cgtA	0.421	4.91	0.037	0.790	2.4.1.19	43
2	0.060	1dgjA	0.416	4.90	0.046	0.790	1.2.-.-	NA
3	0.060	1v8zB	0.423	5.12	0.044	0.824	4.2.1.20	NA
4	0.060	1lpaB	0.415	5.13	0.043	0.832	3.1.1.3	NA
5	0.060	1eg7A	0.420	4.78	0.020	0.765	6.3.4.3	68

	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	3gdpA	0.389	4.60	0.062	0.723	0.45	UUU	complex1.pdb.gz	36,37,39

	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.