D-I-TASSER Q9Y3R4-D2

D-I-TASSER results for Q9Y3R4-D2

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

Input Sequence in FASTA format

>Q9Y3R4 (186 residues)
QARLDGHRSMNPCPLYDAQTGTLFLFFIAIPGQVTEQQQLQTRANVTRLCQVTSTDHGRT
WSSPRDLTDAAIGPAYREWSTFAVGPGHCLQLHDRARSLVVPAYAYRKLHPIQRPIPSAF
CFLSHDHGRTWARGHFVAQDTLECQVAEVETGEQRVVTLNARSHLRARVQAQSTNDGLDF
QESQLV

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| QARLDGHRSMNPCPLYDAQTGTLFLFFIAIPGQVTEQQQLQTRANVTRLCQVTSTDHGRTWSSPRDLTDAAIGPAYREWSTFAVGPGHCLQLHDRARSLVVPAYAYRKLHPIQRPIPSAFCFLSHDHGRTWARGHFVAQDTLECQVAEVETGEQRVVTLNARSHLRARVQAQSTNDGLDFQESQLV
Prediction	CCCCCCCCSCCCSSSSSCCCCSSSSSSSSSCCCCCCCCCCCCCCCCCSSSSSSSCCCCCCCCCCSSCCCCCCCCCCCCCSSSSCCCCCSSSSSCCCCCSSSSSSSSCCCCCCCCCCCSSSSSSSCCCCCCCSCCCCCCCCCCCCSSSSSCCCCSSSSSSSCCCCCCCSSSSSSCCCCCCCCCCSSC
Confidence	973799970464799969999699999982698772010246888538999993899956789777640115765575137731798479964179818998988616888888875689999879998515266568999840689927997899998565799958999982899388887429
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| QARLDGHRSMNPCPLYDAQTGTLFLFFIAIPGQVTEQQQLQTRANVTRLCQVTSTDHGRTWSSPRDLTDAAIGPAYREWSTFAVGPGHCLQLHDRARSLVVPAYAYRKLHPIQRPIPSAFCFLSHDHGRTWARGHFVAQDTLECQVAEVETGEQRVVTLNARSHLRARVQAQSTNDGLDFQESQLV
Prediction	816377431000000014762200000000123244433234364221000020345146144145036504466354131203032200103345311000000134344444322100000023424304325325764310200114534220000001154421010203142534552546
	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

CCCCCCCCSCCCSSSSSCCCCSSSSSSSSSCCCCCCCCCCCCCCCCCSSSSSSSCCCCCCCCCCSSCCCCCCCCCCCCCSSSSCCCCCSSSSSCCCCCSSSSSSSSCCCCCCCCCCCSSSSSSSCCCCCCCSCCCCCCCCCCCCSSSSSCCCCSSSSSSSCCCCCCCSSSSSSCCCCCCCCCCSSC
QARLDGHRSMNPCPLYDAQTGTLFLFFIAIPGQVTEQQQLQTRANVTRLCQVTSTDHGRTWSSPRDLTDAAIGPAYREWSTFAVGPGHCLQLHDRARSLVVPAYAYRKLHPIQRPIPSAFCFLSHDHGRTWARGHFVAQDTLECQVAEVETGEQRVVTLNARSHLRARVQAQSTNDGLDFQESQLV

2f27B

0.96

26.98

1.50

DEthreader

AQRLDGHRSMNPCPLYDAQTGTLFLFFIAIPGQVTQEQQLQTRANVTRLCQVTSTDHGRTWSSPRDLTDAAIGPAYREWSTFAVGPGHCLQLNDRARSLVVPAYAYRKLHPIQRPIPSAFCFLSHDHGRTWARGHFVAQDTLECQVAEVETGEQRVVTLNARSHLRARVQAQSTNDGLDFQESQVK

2f27B2

0.98

27.56

2.13

SPARKS-K

QARLDGHRSMNPCPLYDAQTGTLFLFFIAIPGQVTQEQQLQTRANVTRLCQVTSTDHGRTWSSPRDLTDAAIGPAYREWSTFAVGPGHCLQLNDRARSLVVPAYAYRKLHPIQRPIPSAFCFLSHDHGRTWARGHFVAQDTLECQVAEVETGEQRVVTLNARSHLRARVQAQSTNDGLDFQESQLV

2f27B2

0.98

0.97

27.11

0.53

MapAlign

---LDGHRSMNPCPLYDAQTGTLFLFFIAIPGQVTQEQQLQTRANVTRLCQVTSTDHGRTWSSPRDLTDAAIGPAYREWSTFAVGPGHCLQLNDRARSLVVPAYAYRKLHPIQRPIPSAFCFLSHDHGRTWARGHFVAQDTLECQVAEVETGEQRVVTLNARSHLRARVQAQSTNDGLDFQESQLV

2f27B2

0.98

27.56

0.52

CEthreader

QARLDGHRSMNPCPLYDAQTGTLFLFFIAIPGQVTQEQQLQTRANVTRLCQVTSTDHGRTWSSPRDLTDAAIGPAYREWSTFAVGPGHCLQLNDRARSLVVPAYAYRKLHPIQRPIPSAFCFLSHDHGRTWARGHFVAQDTLECQVAEVETGEQRVVTLNARSHLRARVQAQSTNDGLDFQESQLV

2f27B2

0.98

27.56

1.86

MUSTER

QARLDGHRSMNPCPLYDAQTGTLFLFFIAIPGQVTQEQQLQTRANVTRLCQVTSTDHGRTWSSPRDLTDAAIGPAYREWSTFAVGPGHCLQLNDRARSLVVPAYAYRKLHPIQRPIPSAFCFLSHDHGRTWARGHFVAQDTLECQVAEVETGEQRVVTLNARSHLRARVQAQSTNDGLDFQESQLV

2f27B2

0.98

27.56

1.69

HHsearch

QARLDGHRSMNPCPLYDAQTGTLFLFFIAIPGQVTQEQQLQTRANVTRLCQVTSTDHGRTWSSPRDLTDAAIGPAYREWSTFAVGPGHCLQLNDRARSLVVPAYAYRKLHPIQRPIPSAFCFLSHDHGRTWARGHFVAQDTLECQVAEVETGEQRVVTLNARSHLRARVQAQSTNDGLDFQESQLV

2f27B2

0.98

27.56

2.17

FFAS-3D

QARLDGHRSMNPCPLYDAQTGTLFLFFIAIPGQVTQEQQLQTRANVTRLCQVTSTDHGRTWSSPRDLTDAAIGPAYREWSTFAVGPGHCLQLNDRARSLVVPAYAYRKLHPIQRPIPSAFCFLSHDHGRTWARGHFVAQDTLECQVAEVETGEQRVVTLNARSHLRARVQAQSTNDGLDFQESQLV

2f27B2

0.94

26.40

0.97

EigenThreader

AQARLDGHSMNPCPLYDAQTGTLFLFFIAIPGQVTQEQQLQTRANVTRLCQVTSTDHGRTWSSPRDLTDAAIGPAYREWSTFAVGPGHCLQLNDRARSLVVPAYAYRKLHPIQRPIPSAFCFLSHDHGRTWARGHFVAQDTLECQVAEVETGEQRVVTLNARSHLRARVQAQSTNDGLDFQESQLV

2f26A

0.98

27.56

2.65

CNFpred

QARLDGHRSMNPCPLYDAQTGTLFLFFIAIPGQVTQEQQLQTRANVTRLCQVTSTDHGRTWSSPRDLTDAAIGPAYREWSTFAVGPGHCLQLNDRARSLVVPAYAYRKLHPIQRPIPSAFCFLSHDHGRTWARGHFVAQDTLECQVAEVETGEQRVVTLNARSHLRARVQAQSTNDGLDFQESQLV

2f27B2

0.96

26.98

1.50

DEthreader

AQRLDGHRSMNPCPLYDAQTGTLFLFFIAIPGQVTQEQQLQTRANVTRLCQVTSTDHGRTWSSPRDLTDAAIGPAYREWSTFAVGPGHCLQLNDRARSLVVPAYAYRKLHPIQRPIPSAFCFLSHDHGRTWARGHFVAQDTLECQVAEVETGEQRVVTLNARSHLRARVQAQSTNDGLDFQESQVK

(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

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Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.8236

(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

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Top 10 structural analogs in PDB (as identified by TM-align)

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Alignment
1	2f27B	0.99	0.43	0.984	1.000	model1_2f27B.pdb.gz
2	6qzhA	0.86	2.29	0.225	0.957	model1_6qzhA.pdb.gz
3	2vk7A1	0.86	1.86	0.214	0.930	model1_2vk7A1.pdb.gz
4	6mnjA2	0.84	1.79	0.287	0.919	model1_6mnjA2.pdb.gz
5	1w8nA1	0.84	2.02	0.279	0.925	model1_1w8nA1.pdb.gz
6	3h71B	0.83	2.25	0.234	0.919	model1_3h71B.pdb.gz
7	1kitA3	0.83	2.02	0.193	0.919	model1_1kitA3.pdb.gz
8	2sliA	0.82	2.00	0.213	0.909	model1_2sliA.pdb.gz
9	4fj6A	0.81	1.99	0.281	0.898	model1_4fj6A.pdb.gz
10	2agsA	0.81	2.26	0.171	0.914	model1_2agsA.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:0004308	1.00	exo-alpha-sialidase 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:0044710	1.00	single-organism metabolic process
GO:0044238	1.00	primary metabolic process
GO:0009987	1.00	cellular process
GO:0001573	0.99	ganglioside metabolic process
GO:0005975	0.94	carbohydrate metabolic process
GO:0009313	0.93	oligosaccharide catabolic process
GO:0006689	0.93	ganglioside catabolic process

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	0.99	intracellular part
GO:0043229	0.95	intracellular organelle
GO:0043227	0.95	membrane-bounded organelle
GO:0043231	0.94	intracellular membrane-bounded organelle
GO:0016020	0.93	membrane
GO:0005737	0.67	cytoplasm
GO:0044444	0.61	cytoplasmic 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

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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	3kf5A	0.701	2.68	0.126	0.855	3.2.1.26	NA
2	0.060	2htrA	0.624	2.80	0.097	0.753	3.2.1.18	NA
3	0.060	1st8A	0.708	2.61	0.107	0.855	3.2.1.80	66
4	0.060	1kb0A	0.653	3.72	0.091	0.882	1.1.99.-	NA
5	0.060	1s0kA	0.809	2.24	0.194	0.914	3.2.1.18	148,150

	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

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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	0.28	2f27B	0.993	0.43	0.984	1.000	0.68	DAN	complex1.pdb.gz	10,11,104,106,142,143,162
2	0.08	2xzkB	0.761	2.16	0.237	0.860	0.67	K99	complex2.pdb.gz	16,17,23,98,128
3	0.05	2xzjB	0.760	2.18	0.237	0.860	0.68	NA	complex3.pdb.gz	15,26,86,87

	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.