D-I-TASSER Q9Y4W6-D1

D-I-TASSER results for Q9Y4W6-D1

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

Input Sequence in FASTA format

>Q9Y4W6 (287 residues)
MAHRCLRLWGRGGCWPRGLQQLLVPGGVGPGEQPCLRTLYRFVTTQARASRNSLLTDIIA
AYQRFCSRPPKGFEKYFPNGKNGKKASEPKEVMGEKKESKPAATTRSSGGGGGGGGKRGG
KKDDSHWWSRFQKGDIPWDDKDFRMFFLWTALFWGGVMFYLLLKRSGREITWKDFVNNYL
SKGVVDRLEVVNKRFVRVTFTPGKTPVDGQYVWFNIGSVDTFERNLETLQQELGIEGENR
VPVVYIAESDGSFLLSMLPTVLIIAFLLYTIRRGPAGIGRTGRGMGG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 280 \| \| \| \| \| \| \| \| \| \| \| \| \| \| MAHRCLRLWGRGGCWPRGLQQLLVPGGVGPGEQPCLRTLYRFVTTQARASRNSLLTDIIAAYQRFCSRPPKGFEKYFPNGKNGKKASEPKEVMGEKKESKPAATTRSSGGGGGGGGKRGGKKDDSHWWSRFQKGDIPWDDKDFRMFFLWTALFWGGVMFYLLLKRSGREITWKDFVNNYLSKGVVDRLEVVNKRFVRVTFTPGKTPVDGQYVWFNIGSVDTFERNLETLQQELGIEGENRVPVVYIAESDGSFLLSMLPTVLIIAFLLYTIRRGPAGIGRTGRGMGG
Prediction	CCHHHHHHHHCCCCCCCCCCCSCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCCCCSSSSSSCCCSSSSSSCCCCCCCCCCSSSSSCCCHHHHHHHHHHHHHHHCCCCCCCCCSSSSSCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCC
Confidence	94245566531565556654110467667664124555655542211335451578899999999716997601136444454432222334442223555456677778887766567777776421135678888873679999999999999999996268898757999999999741993289998497899998378766677659996289899999999999993999323542599624648999999999999999999998523568888888899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 280 \| \| \| \| \| \| \| \| \| \| \| \| \| \| MAHRCLRLWGRGGCWPRGLQQLLVPGGVGPGEQPCLRTLYRFVTTQARASRNSLLTDIIAAYQRFCSRPPKGFEKYFPNGKNGKKASEPKEVMGEKKESKPAATTRSSGGGGGGGGKRGGKKDDSHWWSRFQKGDIPWDDKDFRMFFLWTALFWGGVMFYLLLKRSGREITWKDFVNNYLSKGVVDRLEVVNKRFVRVTFTPGKTPVDGQYVWFNIGSVDTFERNLETLQQELGIEGENRVPVVYIAESDGSFLLSMLPTVLIIAFLLYTIRRGPAGIGRTGRGMGG
Prediction	60230031144341344414432344334543430132034323344425444215402510330074026315511575665555656565655656566665666766667665565567666653563665744454440211223323333333211134464441325402540176430520202146303020345454544420204113264036305501762705575403040446431320333333323323332312123335445456468
	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 AttentionPotential. 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

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

SS
Seq

CCHHHHHHHHCCCCCCCCCCCSCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCCCCSSSSSSCCCSSSSSSCCCCCCCCCCSSSSSCCCHHHHHHHHHHHHHHHCCCCCCCCCSSSSSCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCC
MAHRCLRLWGRGGCWPRGLQQLLVPGGVGPGEQPCLRTLYRFVTTQARASRNSLLTDIIAAYQRFCSRPPKGFEKYFPNGKNGKKASEPKEVMGEKKESKPAATTRSSGGGGGGGGKRGGKKDDSHWWSRFQKGDIPWDDKDFRMFFLWTALFWGGVMFYLLLKRSGREITWKDFVNNYLSKGVVDRLEVVNKRFVRVTFTPGKTPVDGQYVWFNIGSVDTFERNLETLQQELGIEGENRVPVVYIAESDGSFLLSMLPTVLIIAFLLYTIRRGPAGIGRTGRGMGG

2lnaA

1.00

0.31

8.59

1.21

FFAS-3D

-------------------------------------------------------------------------------------------------------------------------------------------------------------------KRSGREITWKDFVNNYLSKGVVDRLEVVNKRFVRVTFTPGKTPVDGQYVWFNIGSVDTFERNLETLQQELGIEGENRVPVVYIAESDG------------------------------------

2lnaA

0.89

0.31

8.62

1.22

SPARKS-K

--------------------------------------------------------------------------------------------------------------------------------------------------------MGHHHHHHSHMKRSGREITWKDFVNNYLSKGVVDRLEVVNKRFVRVTFTPGKTPVDGQYVWFNIGSVDTFERNLETLQQELGIEGENRVPVVYIAESDG------------------------------------

2lnaA

0.91

0.31

8.71

4.16

HHsearch

---------------------------------------------------------------------------------------------------------------------------------------------------------MGHHHHHSHMKRSGREITWKDFVNNYLSKGVVDRLEVVNKRFVRVTFTPGKTPVDGQYVWFNIGSVDTFERNLETLQQELGIEGENRVPVVYIAESDG------------------------------------

1vt4I3

0.14

4.76

0.51

CEthreader

GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG

3v8vA

0.08

0.07

2.93

0.57

EigenThreader

MNSLF---ASTARGLEELLKTELENLGATRLVYQSLMWSRLASRDRAGIAPIKETLAAAIVMRSGWQPGTPLLDP--MCGSGRWGFSGWA---QHDKDVAQLTNPLPKGPPYGDSEPALIALHSLLGRIMKNQFGGWMVAEDYTNRLRKNLKKFEKWARQEGTDYLDTGLFLDHRIARRMLGQMSKDFLNLFSYTGSATVHAGLG--GARSTTTVDMSRTYLEWAERNLRLN---GLTGRAHRLIQADCLAWLREARDHLALMKDLKRDGLAKLITQKTLSNRQIHN

2wwbA2

0.12

0.10

3.57

0.49

FFAS-3D

-----ISLFIATNICETIVWKAFSPTTVNTGRGMEIALFHLLATRTDKVRALRFVFAVVIYFQGFRVDLPIKSARYRGQYNTYPIKLFYTSNIPARFSGNLLVSLLGTWSDTSSGGPARAYPVGGLCHYLSPPESFGSVLEDPVHAVVYIVFMLGSCAFFSKTWIEVSGSSAKDVAKQLKEQQMV---------------MRGHRETS---------MVHELNRYIPTAAAFGGL---------------CIGALSVLAILLAVTIIYQYFEIFVKEQSEVG-SMG-

5khnB

0.08

0.07

2.84

0.68

SPARKS-K

PHSESMSTLLAKDSPEAAVNDVTLLAPSLADALPEVGRTTTLSTFIPAPEKRAAIATAASTLLPALT------------QPPAPPATDAQRVAALKRASDLLGYAAEDHPG------PGAAQHLSQSLAKLAAADSATRDRAERAFADTLRIALNQLAALLQPQEITRTLP-PPLVRDWVAPD----------GKALVQISPKVPKGVDP------NDDTMLRHFATAVKAAE----PGAIGGPISILHSANTIISAFLHAALWSIISITILLWITLRRFGDVLRTL

2lnaA

1.00

0.31

8.59

0.92

CNFpred

-------------------------------------------------------------------------------------------------------------------------------------------------------------------KRSGREITWKDFVNNYLSKGVVDRLEVVNKRFVRVTFTPGKTPVDGQYVWFNIGSVDTFERNLETLQQELGIEGENRVPVVYIAESDG------------------------------------

4ui9I

0.04

0.03

1.42

0.67

DEthreader

---------------------IALANTAGE--WSFPPNENTGESSNTSKIFHSALLIGSLLYHLSELKGSWKKYEGLDAAGIEEAITAGFILKANELLQVIDSSMKNFADTFV----------------QWYLFPYYPKLFVKRRMENIIDQCLQKPADVIGKSMNQAICIP--------------NLHYLLFCILRRHT------D-ISQSV--GLIAIYQFTGTYST-------------PTR-M--YVAGNSCVVFEMDIDDEWEL-D----------------

6tzvA

0.08

3.25

0.71

MapAlign

DPLLRLSNFFDDGSVERDRSGVLAAAGTVNGVRTIAFCTDGTVMGGAMGVEGCTHIVNAYDTAIESGGARLAEGVRALHAVGQVFEAMIRASGYIPQISVVVGFAAGGAAYGPALTDVVVMAPESRVFVSGVCHIVADDELDAYDRGRRLVGLFRSKAEALPESSRRAYDVRPIVTAILDADTPFDEFQAWAPSMVVGLGRLSG---RTVGVLANNCLNSESAEKAARFVRLCDAFGIPLLPGVDQEWGGVVRRGAKLLHAFGEQLAAEHERIAGGVDSALDIGVVD

(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	0.5987

(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 AttentionPotential, 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	6r9tA	0.42	6.22	0.037	0.690	model1_6r9tA.pdb.gz
2	4ui9I	0.41	6.10	0.057	0.665	model1_4ui9I.pdb.gz
3	6h02A	0.40	6.21	0.041	0.669	model1_6h02A.pdb.gz
4	6rw8A	0.40	6.39	0.026	0.690	model1_6rw8A.pdb.gz
5	7dxjA	0.40	5.99	0.053	0.645	model1_7dxjA.pdb.gz
6	6yejA	0.40	5.94	0.053	0.641	model1_6yejA.pdb.gz
7	4uhwA	0.39	6.30	0.049	0.665	model1_4uhwA.pdb.gz
8	7duwA	0.39	6.13	0.051	0.665	model1_7duwA.pdb.gz
9	4fhmB	0.39	6.41	0.059	0.679	model1_4fhmB.pdb.gz
10	2dfsA	0.39	5.72	0.035	0.627	model1_2dfsA.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:0008237	1.00	metallopeptidase activity
GO:0004176	1.00	ATP-dependent peptidase 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:0071704	1.00	organic substance metabolic process
GO:0044238	1.00	primary metabolic process
GO:0009987	1.00	cellular process
GO:0007005	0.99	mitochondrion organization
GO:0006508	0.99	proteolysis
GO:0044699	0.95	single-organism process
GO:0044763	0.94	single-organism cellular process
GO:0044237	0.94	cellular metabolic process
GO:0044260	0.92	cellular macromolecule metabolic process
GO:0006810	0.92	transport
GO:1902582	0.91	single-organism intracellular transport
GO:0044267	0.91	cellular protein metabolic process
GO:0015031	0.91	protein transport
GO:0045041	0.90	protein import into mitochondrial intermembrane space
GO:0042407	0.90	cristae formation
GO:0034982	0.90	mitochondrial protein processing
GO:0008053	0.90	mitochondrial fusion
GO:0006461	0.90	protein complex assembly
GO:0032502	0.52	developmental process
GO:0048856	0.51	anatomical structure 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:0044444	1.00	cytoplasmic part
GO:0044446	0.94	intracellular organelle part
GO:0044429	0.93	mitochondrial part
GO:0016020	0.85	membrane
GO:0005743	0.82	mitochondrial inner 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	0.060	2azdB	0.349	5.76	0.024	0.547	2.4.1.1	NA
2	0.060	2e1qA	0.391	6.59	0.037	0.690	1.17.3.2 1.17.1.4	NA
3	0.060	2pdaA	0.347	6.26	0.042	0.571	1.2.7.1	NA
4	0.060	2vumA	0.363	6.24	0.058	0.596	2.7.7.6	234
5	0.060	1qe0B	0.339	6.24	0.051	0.578	6.1.1.21	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:

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	1w7i0	0.360	5.90	0.056	0.561	0.50	III	complex1.pdb.gz	218,219,220,222,223,224,225,227,228,231,235
	2	0.01	1o6pB	0.224	5.97	0.022	0.369	0.57	III	complex2.pdb.gz	177,181,229

	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, Chengxin Zhang, Yang Li, Robin Pearce, Eric W. Bell, Yang Zhang. Folding non-homology proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. In preparation, 2020.