D-I-TASSER Q9Y223-D2

D-I-TASSER results for Q9Y223-D2

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

Input Sequence in FASTA format

>Q9Y223 (182 residues)
CPSYDKLLSAKNKDYMSIIRMWLGDDVKSKDYIVALQHPVTTDIKHSIKMFELTLDALIS
FNKRTLVLFPNIDAGSKEMVRVMRKKGIEHHPNFRAVKHVPFDQFIQLVAHAGCMIGNSS
CGVREVGAFGTPVINLGTRQIGRETGENVLHVRDADTQDKILQALHLQFGKQYPCSKIYG
DG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| CPSYDKLLSAKNKDYMSIIRMWLGDDVKSKDYIVALQHPVTTDIKHSIKMFELTLDALISFNKRTLVLFPNIDAGSKEMVRVMRKKGIEHHPNFRAVKHVPFDQFIQLVAHAGCMIGNSSCGVREVGAFGTPVINLGTRQIGRETGENVLHVRDADTQDKILQALHLQFGKQYPCSKIYGDG
Prediction	CCCHHHHHCCCCCCHHHHHHHHHCCCCCCCCSSSSSSCCCCCCCCCHHHHHHHHHHHHHHCCCCSSSSSCCCCCCCHHHHHHHHHHHHHCCCCSSSSCCCCHHHHHHHHHHCCSSSSCCCCCSSSSCCCCCCSSSCCCCCCCCSCCCCSSSCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCC
Confidence	98578887166677456899973789888978999977874678888999999999999739979998289998724899999999983899689967798689999999696899728702377321699678517996652447726715850139999999999998741688999999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| CPSYDKLLSAKNKDYMSIIRMWLGDDVKSKDYIVALQHPVTTDIKHSIKMFELTLDALISFNKRTLVLFPNIDAGSKEMVRVMRKKGIEHHPNFRAVKHVPFDQFIQLVAHAGCMIGNSSCGVREVGAFGTPVINLGTRQIGRETGENVLHVRDADTQDKILQALHLQFGKQYPCSKIYGDG
Prediction	54313312536356255315523717156430000000021355653351042005004717440000002324435401530462147436202004415353012003303000013300020012141000102524511441530040447632620250045315762636223378
	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

                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCHHHHHCCCCCCHHHHHHHHHCCCCCCCCSSSSSSCCCCCCCCCHHHHHHHHHHHHHHCCCCSSSSSCCCCCCCHHHHHHHHHHHHHCCCCSSSSCCCCHHHHHHHHHHCCSSSSCCCCCSSSSCCCCCCSSSCCCCCCCCSCCCCSSSCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCC
CPSYDKLLSAKNKDYMSIIRMWLGDDVKSKDYIVALQHPVTTDIKHSIKMFELTLDALISFNKRTLVLFPNIDAGSKEMVRVMRKKGIEHHPNFRAVKHVPFDQFIQLVAHAGCMIGNSSCGVREVGAFGTPVINLGTRQIGRETGENVLHVRDADTQDKILQALHLQFGKQYPCSKIYGDG

6vlbA

0.12

4.07

1.33

DEthreader

KTVIDALMVLELKIIKKQMEQAFPFIQDNSKVILITAHRR--E--NHGEGIKNIGLSILELKPTFSFVIPLHLN--PNVRKPIQDL-LSSVHNVHLIEPQEYLPFVYLMSKSHIILSDSGGIQEEAPSLGKPVLVLRTTERPEAAAGTVKLVG-SE-TQNIIESFTQLIPYEANIENPYGIA

3dzcA2

0.19

0.18

5.86

1.10

SPARKS-K

NTVIDALLAVTDMDLQATLESQFPMLDASKKLILVTGHRR-ESFGGGFERICQALITTAEQHPECQILYPVHLN--PNVREPVNKLL-KGVSNIVLIEPQQYLPFVYLMDRAHIILTDSGGIQEEAPSLGKPVLVMRERPEAVAAGTVKLVGT---NQQQICDALSLLLTDPSQAHNPYGDG

3c4qA2

0.16

0.14

4.76

0.47

MapAlign

-ADVELYS-PGNDRATERSRREL--GILHTKVVAFVGRL------QPFKGPQVLIKAVAALFRNLRVIICGG----PTYRHMAEELGVE--KRIRFLDPRPPSELVAVYRAADIVAVPSGLVAMEAQASGTPVIAARGLPIAVAEGETGLLVDGH-SPHAWADALATLLIRMGEAVEHARTF

3c4qA2

0.17

0.16

5.22

0.41

CEthreader

-GADVELYSPGNDRATERSRRELGIP-LHTKVVAFVGRLQ------PFKGPQVLIKAVAALFRNLRVIICGGPT----YRHMAEELGV--EKRIRFLDPRPPSELVAVYRAADIVAVPSGLVAMEAQASGTPVIAARGLPIAVAEGETGLLVD-GHSPHAWADALATLLDDDETRIRMGEDA

4zhtA

0.92

0.89

25.00

1.09

MUSTER

CPSYDKLLSAKNKDYS--IIRWLGDDVKSKDYIVALQHPVTTDIK-HSIKFELTLDALISFNKRTLVLFPNIDAGSK--EVRVRKKGIEHHPNFRAVKHVPFDQFIQLVAHAGCIGN-SSCGVREVGAFGTPVINLGTRQIGRETGENVLHVRDADTQDKILQALHLQFGKQYPCSKIYGDG

5xvsA

0.24

0.21

6.50

1.10

HHsearch

ALGLDHIQRTTFKSISE-LSELYDFD-FSKPYFLITYHPEN------V---APLFDALKQI-NDVNFIFS-YPNTVKAMLDLKAQ----LPDRVLLVKSFGIQNYLSVLKNALAMVGNSSSGLSEAPALQVPTVNIGDRQKGRLRCESIDVRL---DENEIVEALQKAINF-----PPLGLG

5xvsA1

0.25

0.20

6.13

1.52

FFAS-3D

-----------TFKSISELSELYDFDFS-KPYFLITYHPEN---------VAPLFDALKQINDVNFIFSYPN----TNIVKAMLDLKAQLPDRVLLVKSFGIQNYLSVLKNALAMVGNSSSGLSEAPALQVPTVNIGDRQKGRLRCESILDV--RLDENEIVEALQKAIN------------

3dzcA2

0.16

5.27

0.60

EigenThreader

NTVIDALLAVREKIHTDTLESQFPMLDASKKLILVTGHRRESFGGGFERICQALITTAEQHPECQILYPVHLNPNVREPVNKLL----KGVSNIVLIEPQQYLPFVYLMDRAHIILTDSGGIQEEAPSLGKPVLVMRTERPEAVAAGTVKLV--GTNQQQICDALSLLLTDQAHNPYGDGKA

4zhtA

1.00

28.00

1.67

CNFpred

CPSYDKLLSAKNKDYMSIIRMWLGDDVKSKDYIVALQHPVTTDIKHSIKMFELTLDALISFNKRTLVLFPNIDAGSKEMVRVMRKKGIEHHPNFRAVKHVPFDQFIQLVAHAGCMIGNSSCGVREVGAFGTPVINLGTRQIGRETGENVLHVRDADTQDKILQALHLQFGKQYPCSKIYGDG

6vlbA2

0.12

4.06

1.33

DEthreader

NTVIDALMVLELKIIKKQMEQAFPFIQDNSKVILITAHRR--E--NHGEGIKNIGLSILELKPTFSFVIPLHLN--PNVRKPIQDL-LSSVHNVHLIEPQEYLPFVYLMSKSHIILSDSGGIQEEAPSLGKPVLVLRTTERPAVAGTV-KLVG-SE-TQNIIESFTQLIPYEMNIENPYGIA

(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	0.8496

(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	6vlbA	0.84	2.14	0.116	0.951	model1_6vlbA.pdb.gz
2	5enzA	0.82	2.00	0.160	0.929	model1_5enzA.pdb.gz
3	3dzcA	0.82	2.33	0.214	0.951	model1_3dzcA.pdb.gz
4	5dldA	0.82	2.27	0.167	0.956	model1_5dldA.pdb.gz
5	3ot5A2	0.81	2.09	0.130	0.929	model1_3ot5A2.pdb.gz
6	3beoA2	0.81	2.07	0.142	0.929	model1_3beoA2.pdb.gz
7	4zhtA	0.81	2.36	0.896	0.951	model1_4zhtA.pdb.gz
8	1f6dA2	0.81	2.56	0.178	0.956	model1_1f6dA2.pdb.gz
9	4neqA2	0.79	2.73	0.126	0.956	model1_4neqA2.pdb.gz
10	1o6cB2	0.77	2.00	0.165	0.868	model1_1o6cB2.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	1.00	catalytic activity
GO:0016853	0.80	isomerase activity
GO:0008761	0.79	UDP-N-acetylglucosamine 2-epimerase 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:0044699	1.00	single-organism process
GO:0009987	0.96	cellular process
GO:0044763	0.95	single-organism cellular process
GO:0008152	0.79	metabolic process
GO:0071704	0.75	organic substance metabolic process
GO:0044710	0.69	single-organism metabolic process
GO:0044237	0.65	cellular metabolic process
GO:0044281	0.59	small molecule metabolic process
GO:0044767	0.52	single-organism developmental process
GO:0048856	0.51	anatomical structure development
GO:0044707	0.51	single-multicellular organism process
GO:0048747	0.50	muscle fiber development
GO:0043009	0.50	chordate embryonic development
GO:0040011	0.50	locomotion

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:0005829	1.00	cytosol
GO:0005737	0.53	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	0.197	2o6lB	0.648	2.79	0.144	0.797	2.4.1.17	68,104,122
2	0.067	2jzcA	0.619	3.25	0.094	0.813	2.4.1.141	116
3	0.066	3ewiB	0.528	3.78	0.066	0.731	2.7.7.43	118,125
4	0.066	2q4dA	0.549	3.09	0.083	0.703	3.2.2.-	125
5	0.066	1qzuC	0.519	2.91	0.093	0.643	4.1.1.36	53,122

	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	0.35	1f6dB	0.815	2.35	0.197	0.951	0.66	UDP	complex1.pdb.gz	37,101,105,118,119,120,125
2	0.17	3beoA	0.814	2.07	0.142	0.929	0.52	UDP	complex2.pdb.gz	70,100,102,105,106,118,119,122,126
3	0.14	3s29B	0.761	3.11	0.131	0.962	0.52	UDP	complex3.pdb.gz	36,70,99,100,105,120,121,122,125
4	0.13	3okcA	0.759	2.82	0.149	0.923	0.53	GDP	complex4.pdb.gz	38,100,121,122,125
5	0.10	1p2dA	0.734	3.42	0.084	0.978	0.52	GLC	complex5.pdb.gz	124,125,127,128,145
6	0.10	1exvA	0.758	3.08	0.080	0.962	0.54	700	complex6.pdb.gz	116,125,129
7	0.03	2qn8A	0.735	3.40	0.084	0.978	0.50	NBY	complex7.pdb.gz	122,125,126,129
8	0.03	1gfzA	0.735	3.40	0.084	0.978	0.71	CFF	complex8.pdb.gz	7,128,180,182
9	0.03	1l5qA	0.739	3.42	0.079	0.978	0.65	CFF	complex9.pdb.gz	3,8,127,182
10	0.03	3bd7A	0.735	3.41	0.084	0.978	0.60	CKB	complex10.pdb.gz	137,139,140

	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.