D-I-TASSER Q9Y6Q6-D2

D-I-TASSER results for Q9Y6Q6-D2

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

Input Sequence in FASTA format

>Q9Y6Q6 (350 residues)
RKPPNEPHVYLPGLIILLLFASVALVAAIIFGVCYRKKGKALTANLWHWINEACGRLSGD
KESSGDSCVSTHTANFGQQGACEGVLLLTLEEKTFPEDMCYPDQGGVCQGTCVGGGPYAQ
GEDARMLSLVSKTEIEEDSFRQMPTEDEYMDRPSQPTDQLLFLTEPGSKSTPPFSEPLEV
GENDSLSQCFTGTQSTVGSESCNCTEPLCRTDWTPMSSENYLQKEVDSGHCPHWAASPSP
NWADVCTGCRNPPGEDCEPLVGSPKRGPLPQCAYGMGLPPEEEASRTEARDQPEDGADGR
LPSSARAGAGSGSSPGGQSPASGNVTGNSNSTFISSGQVMNFKGDIIVVY

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 280 300 320 340 \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| RKPPNEPHVYLPGLIILLLFASVALVAAIIFGVCYRKKGKALTANLWHWINEACGRLSGDKESSGDSCVSTHTANFGQQGACEGVLLLTLEEKTFPEDMCYPDQGGVCQGTCVGGGPYAQGEDARMLSLVSKTEIEEDSFRQMPTEDEYMDRPSQPTDQLLFLTEPGSKSTPPFSEPLEVGENDSLSQCFTGTQSTVGSESCNCTEPLCRTDWTPMSSENYLQKEVDSGHCPHWAASPSPNWADVCTGCRNPPGEDCEPLVGSPKRGPLPQCAYGMGLPPEEEASRTEARDQPEDGADGRLPSSARAGAGSGSSPGGQSPASGNVTGNSNSTFISSGQVMNFKGDIIVVY
Prediction	CCCCCCCCSCCCHHHHHHHHHHHHHHHHHHSSSSSCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCSSSSCCCCCCCCCCCCSSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSCCCCSSCCCCCSSSSC
Confidence	98998864013048999999999999986202466157861336788888877754258877888864133126787765334436520256568866656788876677667888766776665034312334578755678875455678999988774323799998999888666788875234667888766788777878998888765674435677788999874002689763346456789988889886678888789863347889964444423457898887666578765577777899899999876313688850440461652335368869
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 280 300 320 340 \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| RKPPNEPHVYLPGLIILLLFASVALVAAIIFGVCYRKKGKALTANLWHWINEACGRLSGDKESSGDSCVSTHTANFGQQGACEGVLLLTLEEKTFPEDMCYPDQGGVCQGTCVGGGPYAQGEDARMLSLVSKTEIEEDSFRQMPTEDEYMDRPSQPTDQLLFLTEPGSKSTPPFSEPLEVGENDSLSQCFTGTQSTVGSESCNCTEPLCRTDWTPMSSENYLQKEVDSGHCPHWAASPSPNWADVCTGCRNPPGEDCEPLVGSPKRGPLPQCAYGMGLPPEEEASRTEARDQPEDGADGRLPSSARAGAGSGSSPGGQSPASGNVTGNSNSTFISSGQVMNFKGDIIVVY
Prediction	86457413210100011211311132011000000244144001301200240044033545454321112314434344103100001156421475222244332145213231323435514211103434466451451335552365425464112214327546342155316334463144114235334637334154142625113223452255327536124244463443541141044134644521333373231131121242246532555535433333662534455544442544366441442403234321101321202043200003
	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                 300                 320                 340

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

SS
Seq

CCCCCCCCSCCCHHHHHHHHHHHHHHHHHHSSSSSCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCSSSSCCCCCCCCCCCCSSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSCCCCSSCCCCCSSSSC
RKPPNEPHVYLPGLIILLLFASVALVAAIIFGVCYRKKGKALTANLWHWINEACGRLSGDKESSGDSCVSTHTANFGQQGACEGVLLLTLEEKTFPEDMCYPDQGGVCQGTCVGGGPYAQGEDARMLSLVSKTEIEEDSFRQMPTEDEYMDRPSQPTDQLLFLTEPGSKSTPPFSEPLEVGENDSLSQCFTGTQSTVGSESCNCTEPLCRTDWTPMSSENYLQKEVDSGHCPHWAASPSPNWADVCTGCRNPPGEDCEPLVGSPKRGPLPQCAYGMGLPPEEEASRTEARDQPEDGADGRLPSSARAGAGSGSSPGGQSPASGNVTGNSNSTFISSGQVMNFKGDIIVVY

2pffB

0.09

3.39

1.16

MapAlign

-TPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGTFAGHSLGEYAALASLADVMSIESLVEVVFYRGMTMQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVVERVGKRTGWLVEIVNYNVENQQYVAA-

2pffB

0.21

0.19

5.92

1.20

HHsearch

PEPTEADDEPTTPAELVGKFLYVVLNLCLEFEYLEGNDIHALAAKLLQEKNYITARIMAKRKKSNSALFRAVGEGNA-----QLVAIFGGQGN--TDDYFEELRD-LY-----QTYHVLV-GDLIKFSEIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLIGVFTPGELKGATGHSQGLAETDSWESFFVSVCYEAYPNTSLPPSILEDSLEN-NEGVPSPMLSIS-NLTQEQDYVNSHLPAGKQVEIAKNLVVSG-PPQSLYGLNLTLRKAKA-------PSGLDQSRIPFSERKLK---FSNRFLPVASPFHSVKNNVSF-------NAKDIQIPVY

1mhsA

0.07

2.77

0.54

CEthreader

QMKEEKENHFLKFLGFFVGPIQFVMEGAAVLAAGLEDWVDFGVICGLLLLNAVVGFVQEFQAGSIVDELKKTLALKAVVLRDGTLKEIEAPEVVPEGTIIPADGRIVKGDQVFASSAVKRGEAFVVITATGDNTFVGRAAALVNAASGGSGHFTEVLNGIGTILLILVIFTLLIVWVSSFYRSNPIVQILEFTLAIT-IIGVPVGLPAVVTTTMAVGAAYLAKKKAIVQKLSAHDPYTVAGVDPEDLMLTACLAASRKKKGIDAIDKAFLKSLKYYPRAKSVLSKYKVLQFHPFDPVSKKVVAVVESPQGERITCVKGAPLFVLKTVEEDHPIPEEVDQAYKNKVAEFAT

6cc4A

0.07

0.06

2.61

0.65

EigenThreader

PKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEG-KVKEAQAAAEQLKTTRNAYIQKYLKSAAPWVIMVTAPGFADTAD--------KFALTSQLLKITFNISMIGFALFAAPYFNPPVLALAWAVT--VGGVLQLVYQLPHLKKIGMLVLPRINFALPSAVALGILSGPLTVSLFQYGKFTAFDALMTQRALIAYSVGLIGLIVVKVLQDIKTPVKIAIVTLILTQLMNLAFIGPLKHAGLSLSIGLAACLNASLLYWQLRKQKIFTPQPGVMSGVLLGMLHIMPEWSLGTMPWRLLRLMAVVLAGIAAYFAALAVLGFKVKEFA---------------------

6ezoI

0.10

3.58

0.55

FFAS-3D

-LPKDQPRVLLPLALIDYTLEFLTATGVQETFVFCCWKAAQIKEHLLK-----------SKWCRPTSLNVVRIITSELYRSLGDVLRDVDAKALVRSDFLLVYGDVISNINITRALLRRKLEKNVSVMTMIFKESSPSHPTRCHEDNVVVAVDSTTNRVLHFQKTQSSDGVEVRYDLLDCHDYQTRDDFVRGLLVNEEILGNQIHMHVTAKEYGARVSNLHMYSAVCADVIRRWVYPLTPEANSCTHSRHNIYRGPEVSLGHGSILEENVLLGSGTVIGSNCFITNSVIGPGCHIGDNVVLDQTQGVRVAAGAQIHQSLLCDNAEVKERPRSVLTSQVVVGPNITL----

6ybt2

0.09

0.07

2.74

0.97

SPARKS-K

-----------------------------------MKPILLQGHERSITQIKYNREGDLLFTVAKDPIVNVYSVNGERLGTYMAVWCVDADWDTWDCETGKQLALLKTNSAVRTCGFDFGGNIIMFSTFVSFFDLRDPSQIDNNEPYMKIPCNDSKITSAVWGPLGEC---------IIAGHESGELNQYSAKSGEVLVNVKEHSRQ--INDIQLSRDMTMF---VTASKDNTAKLFDSTTLEHQKTFRTERPVNSA----ALSPNYDHVVLGGGQEAMDVTTTSTRIGKARFFHLAFEEEFGRVKGHFGPINSVAFHPDGKSYSSGGEDGYVRIH--------------

3g68A

0.12

0.03

0.90

0.56

CNFpred

----------KGYYCTKLNLMLLGLQIAREKGIISSEKYNEEINKILDAINRFEAVYKLSKQWIER--------NKEKLVNSKEIRIIGHS-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

3fahA

0.07

0.05

2.00

0.67

DEthreader

-KMPADGRIWSKYPRPTAVAKVTGTLDYADLGLKM--PAGT--LHLA-MVQAKV-ANIKGHKKNRILDCHLYMIAPGVG-LEPDQ-----------GYKFSP-------YNYQQQQQ-------YTGKRSPWE-M-NVKFMIGAGYNIPNIRGLGRT-GSAFRYGPQSMFASEMLRYKPIDQ-RPKYQ---GISIGVY-----HGQG-----SGGSRQQVMTGNAIR-V-ACENL-------KITG-NWTASGATKFVVYM-----Y-GVFMAMTLMATDGQIYG--A---G-SVG-PFIKQIPDKLD----I----VYVNH----------------------------

3ixzA

0.06

2.54

0.97

MapAlign

ARQLAGGLQCLMWVAAAICLIALRAMVFFMAIVVAYVPELATVTVCLSLTAKRLASKNCVVKNLKRIVIGDASETALLKFSELTLGNAMGYRERFPKVCEIPFNSTNKFQLSIHTLEDPRDPRHVLVMKGAPERVLERCSSILIKGQELPLTGDHPITAKAIAASVGIISEGSETVEDRLRVPVDQVNRKDARACVINGMQLKDPEMVFARTSPQQKLVIVESCQRLGAIVAVTGDLKKADIGVAMGIAGSAKNAADMILLDDNFASIVTGVEQGRLIFDNLKKSIAAAYSYFQIGAIQSFAGFTDYFTAMAQEGWFPLLCVGLRPQWENHHLQDLQDSYGQEWTFGQR-

6fmlG

0.13

0.12

4.19

0.73

MUSTER

VKGDIEIDVFCE-----LSYRQRAMYQSLRNQISIMDLDSATLMNLVMQFRKVCN-DLFERADTSSPFFCGHFAETGSFLVALGYSTRSLVEYRLPRLIWCDGGRLDKPGPGNLVAGFRSKYLNHMMNIWTPENIRSSLEGIENFTWLRFVDTSLQEAYRASHTDVFARAVDLASKQNRLGHMQIVYDEPEDKKWTPVHALFQICERENPKAVAEITTEGVLRDLMNIARVKYRELGLCRLEKAARPRASAPPIESRSAVIERENIMFHPAMRKALFGPTPSEIKEASFGPRPVTLYPPRALLPAPDHDKQRFTNITVPSMARFVT--------DSGAKL--GGHRVLLY

(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	0.3996

(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	3vsmA	0.44	6.20	0.048	0.703	model1_3vsmA.pdb.gz
2	1hmwA	0.43	6.65	0.047	0.729	model1_1hmwA.pdb.gz
3	6f2pA	0.43	6.77	0.071	0.740	model1_6f2pA.pdb.gz
4	6jp4A	0.43	6.68	0.036	0.726	model1_6jp4A.pdb.gz
5	1llwA	0.43	6.65	0.049	0.723	model1_1llwA.pdb.gz
6	1j0nA	0.43	6.18	0.047	0.689	model1_1j0nA.pdb.gz
7	2wdaA	0.43	6.70	0.045	0.729	model1_2wdaA.pdb.gz
8	3ob8A	0.42	6.95	0.034	0.731	model1_3ob8A.pdb.gz
9	1hn0A	0.42	6.49	0.060	0.703	model1_1hn0A.pdb.gz
10	6mixA	0.42	6.62	0.052	0.697	model1_6mixA.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:0005031	1.00	tumor necrosis factor-activated receptor 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:0097190	1.00	apoptotic signaling pathway
GO:0044707	1.00	single-multicellular organism process
GO:0043410	1.00	positive regulation of MAPK cascade
GO:0042981	1.00	regulation of apoptotic process
GO:0042127	1.00	regulation of cell proliferation
GO:0032496	1.00	response to lipopolysaccharide
GO:0006955	1.00	immune response
GO:0006954	0.93	inflammatory response
GO:0048856	0.89	anatomical structure development
GO:0044767	0.89	single-organism developmental process
GO:0007275	0.88	multicellular organism 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:0005887	1.00	integral component of plasma membrane
GO:0044424	0.56	intracellular 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	1larA	0.369	6.41	0.028	0.611	3.1.3.48	272
2	0.060	1lf6A	0.367	6.80	0.069	0.617	3.2.1.3	NA
3	0.060	1ojnA	0.428	6.78	0.051	0.726	4.2.2.1	NA
4	0.060	1h54B	0.375	6.75	0.057	0.637	2.4.1.8	NA
5	0.060	3ig5A	0.403	6.63	0.042	0.666	6.3.2.2	213

	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	0.01	1jyxA	0.415	6.79	0.034	0.711	0.22	IPT	complex1.pdb.gz	104,181,184,316
2	0.01	1ofdA	0.355	6.80	0.053	0.600	0.12	AKG	complex2.pdb.gz	176,193,277
3	0.01	1ofdA	0.355	6.80	0.053	0.600	0.15	FMN	complex3.pdb.gz	192,213,272,273,276
4	0.01	1llwA	0.430	6.65	0.049	0.723	0.14	FMN	complex4.pdb.gz	275,312,313,314,319
5	0.01	1lm1A	0.382	7.39	0.034	0.691	0.15	FMN	complex5.pdb.gz	271,322,323
6	0.01	1ofdB	0.356	6.38	0.042	0.571	0.34	F3S	complex6.pdb.gz	149,150,171,197,198
7	0.01	1llzA	0.371	6.48	0.035	0.600	0.15	FMN	complex7.pdb.gz	179,275,313,314
8	0.01	1ofeA	0.355	6.47	0.042	0.577	0.27	ONL	complex8.pdb.gz	191,203,204,205,206
9	0.01	1jyxD	0.415	6.79	0.038	0.711	0.14	IPT	complex9.pdb.gz	273,277,333
10	0.01	1llwA	0.430	6.65	0.049	0.723	0.12	AKG	complex10.pdb.gz	203,271,276

	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.