D-I-TASSER Q13144-D1

D-I-TASSER results for Q13144-D1

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

Input Sequence in FASTA format

>Q13144 (300 residues)
MAAPVVAPPGVVVSRANKRSGAGPGGSGGGGARGAEEEPPPPLQAVLVADSFDRRFFPIS
KDQPRVLLPLANVALIDYTLEFLTATGVQETFVFCCWKAAQIKEHLLKSKWCRPTSLNVV
RIITSELYRSLGDVLRDVDAKALVRSDFLLVYGDVISNINITRALEEHRLRRKLEKNVSV
MTMIFKESSPSHPTRCHEDNVVVAVDSTTNRVLHFQKTQGLRRFAFPLSLFQGSSDGVEV
RYDLLDCHISICSPQVAQLFTDNFDYQTRDDFVRGLLVNEEILGNQIHMHVTAKEYGARV

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 280 300 \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| MAAPVVAPPGVVVSRANKRSGAGPGGSGGGGARGAEEEPPPPLQAVLVADSFDRRFFPISKDQPRVLLPLANVALIDYTLEFLTATGVQETFVFCCWKAAQIKEHLLKSKWCRPTSLNVVRIITSELYRSLGDVLRDVDAKALVRSDFLLVYGDVISNINITRALEEHRLRRKLEKNVSVMTMIFKESSPSHPTRCHEDNVVVAVDSTTNRVLHFQKTQGLRRFAFPLSLFQGSSDGVEVRYDLLDCHISICSPQVAQLFTDNFDYQTRDDFVRGLLVNEEILGNQIHMHVTAKEYGARV
Prediction	CCCCCCCCCCHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSCCCCCCCCCCCCCCCCCCSSSSCCSSHHHHHHHHHHHHCCCSSSSSCCCCHHHHHHHHHHHHHCCCCCCCSSSSSSCCCCCCCCCHHHHHHHHHCCCCCSSSSSCCSSSCCCHHHHHHHHHHHHHCCCCCCSSSSSSSCCCCCCCCCCCCCCCSSSSSCCCCSSSSSSSCCCCCCCCCCHHHHHCCCCCSSSSCCCSSCSSSSSCHHHHHHHHCCCCCCCHHHHHHHHHHHCHHCCCSSSSSSCCCCCSSCC
Confidence	998866885012222113355677777777766642235666179999089998146321689882026699437999999999909988999917849999999975311256787569999656788844067765555348998899946735548989999999997211468764899986069988654467662899949999799997069987432456776406885588558334436874768987630368877646657788763010388179998288402159
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 280 300 \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| MAAPVVAPPGVVVSRANKRSGAGPGGSGGGGARGAEEEPPPPLQAVLVADSFDRRFFPISKDQPRVLLPLANVALIDYTLEFLTATGVQETFVFCCWKAAQIKEHLLKSKWCRPTSLNVVRIITSELYRSLGDVLRDVDAKALVRSDFLLVYGDVISNINITRALEEHRLRRKLEKNVSVMTMIFKESSPSHPTRCHEDNVVVAVDSTTNRVLHFQKTQGLRRFAFPLSLFQGSSDGVEVRYDLLDCHISICSPQVAQLFTDNFDYQTRDDFVRGLLVNEEILGNQIHMHVTAKEYGARV
Prediction	753343436443454444445545556556456546554652010000002442203210462011001005100011004203714042000001132620351035134444442311102234444302100200204620643000000200011304400530354445553100000002325354424244410000014763201101434736424143520333364140211100000000344015204762516236410340055460363300000057414435
	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                 120                 140                 160                 180                 200                 220                 240                 260                 280                 300

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSCCCCCCCCCCCCCCCCCCSSSSCCSSHHHHHHHHHHHHCCCSSSSSCCCCHHHHHHHHHHHHHCCCCCCCSSSSSSCCCCCCCCCHHHHHHHHHCCCCCSSSSSCCSSSCCCHHHHHHHHHHHHHCCCCCCSSSSSSSCCCCCCCCCCCCCCCSSSSSCCCCSSSSSSSCCCCCCCCCCHHHHHCCCCCSSSSCCCSSCSSSSSCHHHHHHHHCCCCCCCHHHHHHHHHHHCHHCCCSSSSSSCCCCCSSCC
MAAPVVAPPGVVVSRANKRSGAGPGGSGGGGARGAEEEPPPPLQAVLVADSFDRRFFPISKDQPRVLLPLANVALIDYTLEFLTATGVQETFVFCCWKAAQIKEHLLKSKWCRPTSLNVVRIITSELYRSLGDVLRDVDAKALVRSDFLLVYGDVISNINITRALEEHRLRRKLEKNVSVMTMIFKESSPSHPTRCHEDNVVVAVDSTTNRVLHFQKTQGLRRFAFPLSLFQGSSDGVEVRYDLLDCHISICSPQVAQLFTDNFDYQTRDDFVRGLLVNEEILGNQIHMHVTAKEYGARV

5b04I

0.43

0.37

10.76

1.33

DEthreader

---------------------------------------KHALQAIVLSDSYNYRFRPLTLDKPRCLLPLANTPLIEYTFEFLALAGVQEVYVFCCAHAGQIREYIEKSKWNLPSSPFSVNTIVS-RESL-SVGDALRELDQLITSDFILVSGDVVSNVPLNEVLKEHRKRREDD-KNAIMTMVVREASPFHRTRARTESSVFVIDKKTSQCVHYQANERGKHYVSMDPEIFNEHEELEVRNDLIDCQIDICSNDVPALFTENFDYQDRKDFVYGVLTSDLLG-KKIHCHVAKENYAARV

5b04I1

0.46

0.40

11.66

1.82

SPARKS-K

---------------------------------------KHALQAIVLSDSYNYRFRPLTLDKPRCLLPLANTPLIEYTFEFLALAGVQEVYVFCCAHAGQIREYIEKSKWNLPSSPFSVNTIVSRESLSVGDALRELDSKQLITSDFILVSGDVVSNVPLNEVLKEHRKRREDDKN-AIMTMVVREASPFHRTRARTESSVFVIDKKTSQCVHYQANERGKHYVSMDPEIFNEHEELEVRNDLIDCQIDICSNDVPALFTENFDYQDIKDFVYGVLT-SDLLGKKIHCHVAKENYAARV

5b04I1

0.43

0.37

10.85

0.82

MapAlign

---------------------------------------KHALQAIVLSDSYNYRFRPLTLDKPRCLLPLANTPLIEYTFEFLALAGVQEVYVFCCAHAGQIREYIEKSKWNLPSSPFSVNTIVSRES-LSV-GDALRELDSLITSDFILVSGDVVSNVPLNEVLKEHRKRREDD-KNAIMTMVVREASPFHRTRARTESSVFVIDKKTSQCVHYQANERGKHYVSMDPEIFNEHEELEVRNDLIDCQIDICSNDVPALFTENFDYQDIRDFVYGVL-TSDLLGKKIHCHVAKENYAARV

5b04I1

0.46

0.39

11.48

0.57

CEthreader

---------------------------------------KHALQAIVLSDSYNYRFRPLTLDKPRCLLPLANTPLIEYTFEFLALAGVQEVYVFCCAHAGQIREYIEKSKWNLPSSPFSVNTIVSRESLSVGDALRELDSKQLITSDFILVSGDVVSNVPLNEVLKEHRKRREDD-KNAIMTMVVREASPFHRTRARTESSVFVIDKKTSQCVHYQANERGKHYVSMDPEIFNEHEELEVRNDLIDCQIDICSNDVPALFTENFDYQDIRDFVYGVLTSDL-LGKKIHCHVAKENYAARV

6jlwJ1

1.00

0.85

23.80

1.78

MUSTER

----------------------------------------PPLQAVLVADSFDRRFFPISKDQPRVLLPLANVALIDYTLEFLTATGVQETFVFCCWKAAQIKEHLLKSKWCRPTSLNVVRIITSELYRSLGDVLRDVDAKALVRSDFLLVYGDVISNINITRALEEHRLRRKLEKNVSVMTMIFKESSPSHPTRCHEDNVVVAVDSTTNRVLHFQKTQGLRRFAFPLSLFQGSSDGVEVRYDLLDCHISICSPQVAQLFTDNFDYQTRDDFVRGLLVN-----NQIHMHVTAKEYGARV

6jlwJ

1.00

0.85

23.80

2.07

HHsearch

----------------------------------------PPLQAVLVADSFDRRFFPISKDQPRVLLPLANVALIDYTLEFLTATGVQETFVFCCWKAAQIKEHLLKSKWCRPTSLNVVRIITSELYRSLGDVLRDVDAKALVRSDFLLVYGDVISNINITRALEEHRLRRKLEKNVSVMTMIFKESSPSHPTRCHEDNVVVAVDSTTNRVLHFQKTQGLRRFAFPLSLFQGSSDGVEVRYDLLDCHISICSPQVAQLFTDNFDYQTRDDFVRGLLVN-----NQIHMHVTAKEYGARV

6jlwJ1

1.00

0.85

23.80

2.59

FFAS-3D

----------------------------------------PPLQAVLVADSFDRRFFPISKDQPRVLLPLANVALIDYTLEFLTATGVQETFVFCCWKAAQIKEHLLKSKWCRPTSLNVVRIITSELYRSLGDVLRDVDAKALVRSDFLLVYGDVISNINITRALEEHRLRRKLEKNVSVMTMIFKESSPSHPTRCHEDNVVVAVDSTTNRVLHFQKTQGLRRFAFPLSLFQGSSDGVEVRYDLLDCHISICSPQVAQLFTDNFDYQTRDDFVRGLLVN-----NQIHMHVTAKEYGARV

6jlwJ1

1.00

0.84

23.62

1.20

EigenThreader

----------------------------------------PPLQAVLVADSFDRRFFPISKDQPRVLLPLANVALIDYTLEFLTATGVQETFVFCCWKAAQIKEHLLKSKWCRPTSLNVVRIITSELYRSLGDVLRDVDAKALVRSDFLLVYGDVISNINITRALEEHRLRRKLEKNVSVMTMIFKESSPSHPTRCHEDNVVVAVDSTTNRVLHFQKTQGLRRFAFPLSLFQGSSDGVEVRYDLLDCHISICSPQVAQLFTDNFDYQTRDDFVRGLLVN-----NQIHMHVTAKEYGAS-

6cajA

1.00

0.85

23.80

2.71

CNFpred

----------------------------------------PPLQAVLVADSFDRRFFPISKDQPRVLLPLANVALIDYTLEFLTATGVQETFVFCCWKAAQIKEHLLKSKWCRPTSLNVVRIITSELYRSLGDVLRDVDAKALVRSDFLLVYGDVISNINITRALEEHRLRRKLEKNVSVMTMIFKESSPSHPTRCHEDNVVVAVDSTTNRVLHFQKTQGLRRFAFPLSLFQGSSDGVEVRYDLLDCHISICSPQVAQLFTDNFDYQTRDDFVRGLLVN-----NQIHMHVTAKEYGARV

5b04I1

0.43

0.37

10.76

1.33

DEthreader

---------------------------------------KHALQAIVLSDSYNYRFRPLTLDKPRCLLPLANTPLIEYTFEFLALAGVQEVYVFCCAHAGQIREYIEKSKWNLPSSPFSVNTIVS-RESL-SVGDALRELDQLITSDFILVSGDVVSNVPLNEVLKEHRKRREDD-KNAIMTMVVREASPFHRTRARTESSVFVIDKKTSQCVHYQANERGKHYVSMDPEIFNEHEELEVRNDLIDCQIDICSNDVPALFTENFDYQDRKDFVYGVLTSDLLG-KKIHCHVAKENYAARV

(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	0.7498

(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	5b04I	0.84	0.89	0.428	0.857	model1_5b04I.pdb.gz
2	6i3mG	0.80	1.84	0.352	0.853	model1_6i3mG.pdb.gz
3	6jlwJ1	0.78	1.90	0.968	0.843	model1_6jlwJ1.pdb.gz
4	6ezoI	0.78	1.78	0.900	0.833	model1_6ezoI.pdb.gz
5	5b04E1	0.73	2.62	0.159	0.823	model1_5b04E1.pdb.gz
6	1yp3C	0.69	2.91	0.123	0.793	model1_1yp3C.pdb.gz
7	6qg2F	0.69	3.13	0.139	0.813	model1_6qg2F.pdb.gz
8	6ezoE	0.68	2.62	0.161	0.767	model1_6ezoE.pdb.gz
9	5l6sA1	0.67	3.03	0.134	0.770	model1_5l6sA1.pdb.gz
10	2pa4B	0.66	2.61	0.116	0.750	model1_2pa4B.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:0005085	0.97	guanyl-nucleotide exchange factor activity
GO:1901363	0.95	heterocyclic compound binding
GO:0097159	0.95	organic cyclic compound binding
GO:0003676	0.93	nucleic acid binding
GO:0003743	0.92	translation initiation factor activity

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	0.97	cellular process
GO:0008152	0.97	metabolic process
GO:0044237	0.96	cellular metabolic process
GO:0006413	0.91	translational initiation
GO:0044699	0.85	single-organism process
GO:0044763	0.81	single-organism cellular process
GO:0050896	0.75	response to stimulus
GO:0048856	0.75	anatomical structure development
GO:0065007	0.74	biological regulation
GO:0051716	0.74	cellular response to stimulus
GO:0048468	0.74	cell development
GO:0014003	0.73	oligodendrocyte development
GO:0050794	0.72	regulation of cellular process
GO:0006950	0.72	response to stress
GO:0042221	0.71	response to chemical
GO:0034976	0.71	response to endoplasmic reticulum stress
GO:0048708	0.70	astrocyte differentiation
GO:0042552	0.70	myelination
GO:0035690	0.70	cellular response to drug
GO:0014002	0.70	astrocyte development
GO:0009408	0.70	response to heat
GO:0080090	0.69	regulation of primary metabolic process
GO:0031326	0.69	regulation of cellular biosynthetic process
GO:0010468	0.69	regulation of gene expression
GO:0006417	0.68	regulation of translation
GO:0006446	0.67	regulation of translational initiation
GO:0048518	0.62	positive regulation of biological process
GO:1901700	0.60	response to oxygen-containing compound
GO:0051247	0.60	positive regulation of protein metabolic process
GO:0051173	0.60	positive regulation of nitrogen compound metabolic process
GO:0031328	0.60	positive regulation of cellular biosynthetic process
GO:0022414	0.60	reproductive process
GO:0010628	0.60	positive regulation of gene expression
GO:0010557	0.60	positive regulation of macromolecule biosynthetic process
GO:0010033	0.60	response to organic substance
GO:0045948	0.59	positive regulation of translational initiation
GO:0043434	0.59	response to peptide hormone
GO:0009749	0.59	response to glucose
GO:0001541	0.59	ovarian follicle development

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:0044424	1.00	intracellular part
GO:0044444	0.99	cytoplasmic part
GO:0032991	0.94	macromolecular complex
GO:0005851	0.93	eukaryotic translation initiation factor 2B complex
GO:0005737	0.67	cytoplasm

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	0.366	1lvwA	0.639	2.66	0.147	0.727	2.7.7.24	55
2	0.360	2ux8G	0.628	3.35	0.140	0.760	2.7.7.9	55
3	0.348	2ux8A	0.575	2.89	0.141	0.663	2.7.7.9	55
4	0.341	2pa4B	0.657	2.61	0.116	0.750	2.7.7.9	55
5	0.102	1h7tA	0.608	3.16	0.151	0.710	2.7.7.38	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	0.40	1lvwA	0.639	2.66	0.147	0.727	1.07	TYD	complex1.pdb.gz	48,50,65,66,125,152,154
2	0.20	1yp3C	0.695	2.91	0.123	0.793	0.88	ATP	complex2.pdb.gz	48,50,51,94,129,130,131,152,153,154,248,268,269
3	0.20	1hm9A	0.613	2.88	0.150	0.710	0.90	UD1	complex3.pdb.gz	48,49,50,51,55,65,125,128,129,130,131,152,153,154,199,246,247,268,269
4	0.17	3pkpA	0.652	2.50	0.132	0.730	0.85	DTP	complex4.pdb.gz	48,50,51,52,53,54,55,65,66,125,153,154

	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.