D-I-TASSER Q9Y239-D5

D-I-TASSER results for Q9Y239-D5

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

Input Sequence in FASTA format

>Q9Y239 (144 residues)
GTQELLRFFQEWMPPAGAATTSCYPPFLPFQCLQGSGPAREDLFKNKDHFQFTNLFLCGL
LSKAKQKLLRHLVPAAALRRKRKALWAHLFSSLRGYLKSLPRVQVESFNQVQAMPTFIWM
LRCIYETQSQKVGQLAARGICANY

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| GTQELLRFFQEWMPPAGAATTSCYPPFLPFQCLQGSGPAREDLFKNKDHFQFTNLFLCGLLSKAKQKLLRHLVPAAALRRKRKALWAHLFSSLRGYLKSLPRVQVESFNQVQAMPTFIWMLRCIYETQSQKVGQLAARGICANY
Prediction	CHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCC
Confidence	828999999863477676544222221405542388854234234787534689999987504579999997799999999999999999999999705999997654421026228999999999735899999994356899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| GTQELLRFFQEWMPPAGAATTSCYPPFLPFQCLQGSGPAREDLFKNKDHFQFTNLFLCGLLSKAKQKLLRHLVPAAALRRKRKALWAHLFSSLRGYLKSLPRVQVESFNQVQAMPTFIWMLRCIYETQSQKVGQLAARGICANY
Prediction	845401510352255564334313242033321455555554335545203011111010024534510441245411542242034201520452044134345762541212222110010012145661044004414477
	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

                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCC
GTQELLRFFQEWMPPAGAATTSCYPPFLPFQCLQGSGPAREDLFKNKDHFQFTNLFLCGLLSKAKQKLLRHLVPAAALRRKRKALWAHLFSSLRGYLKSLPRVQVESFNQVQAMPTFIWMLRCIYETQSQKVGQLAARGICANY

5irlA

0.27

0.25

7.67

1.32

SPARKS-K

PLEFLHITFQCFLAAFYLVLSTDVPTASLRYLFNCSTVAALLQKTEPHNLQITAAFLAGLLSREHRDLLAACQSERSLLRRRACARWCLARSLHKHFRSIPA-----------MPGFLWLIRSLYEMQEERLAQEAVRGLNVEH

5irlA4

0.28

0.24

7.43

3.09

HHsearch

DPDDISGFLVQA--P-LEFLHITFQCFLAAFYLVLCSTVAALQKTEPHNLQITAAFLAGLLSREHRDLLAACQASERLR-RRACARWCLARSLHKHFRS-----------IPAMPGFLWLIRSLYEMQEERLAQEAVRGL----

5irlA4

0.28

0.23

7.01

1.31

FFAS-3D

---TFQCFLAAFSTDVPTA--------SLRYLFNCSTVAALLQKTEPHNLQITAAFLAGLLSREHRDLLAACQSERSLLRRRACARWCLARSLHKHFRSIPAM-----------PGFLWLIRSLYEMQEERLAQEAVRGL----

5irlA

0.27

0.23

7.05

1.00

DEthreader

FYIHTFQCFLAAFYL----S-TDVPTASLRYLNCAAL-LQ-KT--EPHNLQITAAFLAGLLSREHRDLLAACQSERSLLRRRACARWCLARSLHKHFRSIP-----------AMPGFLWLIRSLYEMQEERLAQEAVRGLNVEH

5irlA4

0.33

0.24

7.29

1.19

SPARKS-K

PTASLRYLFNCST---------------VAALLQKTE---------PHNLQITAAFLAGLLSREHRDLLAACQASESLLRRRACARWCLARSLHKHFRSIPA-----------MPGFLWLIRSLYEMQEERLAQEAVRGL----

5irlA

0.26

0.23

7.08

0.84

MapAlign

--LALWGLGMCFLAAFYLVLSTDVPTASLRYLFNCSTVAALLQKTEPHNLQITAAFLAGLLSREHRDLLAACQSERSLLRRRACARWCLARSLHKHFR-----------SIPAMPGFLWLIRSLYEMQEERLAQEAVRGLNV--

5irlA

0.28

0.26

7.86

0.85

CEthreader

PLEFLHITFQCFLAAFYLVLSTDVPTASLRYLFNCSTVAALLQKTEPHNLQITAAFLAGLLSREHRDLLAACQASRSLLRRRACARWCLARSLHKHFRSIP-----------AMPGFLWLIRSLYEMQEERLAQEAVRGLNVEH

5irlA4

0.30

0.25

7.60

0.79

MUSTER

QPDDIS-FLVQAP-----LSTDVPTASLRYL-FNCSTVAALLQKTEPHNLQITAAFLAGLLSREHRDLLAACQASRSLLRRRACARWCLARSLHKHFRSIP-----------AMPGFLWLIRSLYEMQEERLAQEAVRGL----

5irlA

0.30

0.28

8.42

2.53

HHsearch

RLPTLLRVFSAQQLQAAQVDPITFQCFLAAFYLVCSTVAALLQKTEPHNLQITAAFLAGLLSREHRDLLAACQASERLLRRRACARWCLARSLHKHFRS-----------IPAMPGFLWLIRSLYEMQEERLAQEAVRGLNVEH

5irlA

0.30

0.22

6.53

0.67

FFAS-3D

-----------------------------RYLFNCSTVAALLQKTEPHNLQITAAFLAGLLSREHRDLLAACQSERSLLRRRACARWCLARSLHKHF-----------RSIPAMPGFLWLIRSLYEMQEERLAQEAVRGLNVEH

(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	0.6947

(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	5irlA	0.71	3.01	0.254	0.896	model1_5irlA.pdb.gz
2	4knhA	0.60	4.07	0.090	0.882	model1_4knhA.pdb.gz
3	6tnfB	0.60	3.82	0.068	0.840	model1_6tnfB.pdb.gz
4	5yz0A	0.59	3.71	0.051	0.840	model1_5yz0A.pdb.gz
5	3s4wA	0.58	3.94	0.045	0.833	model1_3s4wA.pdb.gz
6	3a6pA1	0.58	4.22	0.084	0.896	model1_3a6pA1.pdb.gz
7	2pftA	0.58	3.67	0.055	0.833	model1_2pftA.pdb.gz
8	4fgvA1	0.56	4.41	0.053	0.861	model1_4fgvA1.pdb.gz
9	5ijnD	0.55	4.32	0.058	0.826	model1_5ijnD.pdb.gz
10	3icqT	0.54	4.24	0.090	0.833	model1_3icqT.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:0050700	0.84	CARD domain binding
GO:0097367	0.53	carbohydrate derivative binding

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:0065007	0.89	biological regulation
GO:0050789	0.89	regulation of biological process
GO:0048518	0.83	positive regulation of biological process
GO:0050794	0.78	regulation of cellular process
GO:0050896	0.77	response to stimulus
GO:0048522	0.71	positive regulation of cellular process
GO:0019222	0.71	regulation of metabolic process
GO:0009893	0.70	positive regulation of metabolic process
GO:0006950	0.65	response to stress
GO:0006952	0.64	defense response
GO:0009605	0.63	response to external stimulus
GO:0009987	0.62	cellular process
GO:0065009	0.58	regulation of molecular function
GO:0051704	0.57	multi-organism process
GO:0044093	0.57	positive regulation of molecular function
GO:0098542	0.56	defense response to other organism
GO:0060255	0.56	regulation of macromolecule metabolic process
GO:0051239	0.55	regulation of multicellular organismal process
GO:0042742	0.55	defense response to bacterium
GO:0010604	0.54	positive regulation of macromolecule metabolic process
GO:0001817	0.54	regulation of cytokine production
GO:0051240	0.53	positive regulation of multicellular organismal process
GO:0010468	0.53	regulation of gene expression
GO:0010033	0.52	response to organic substance
GO:0001819	0.52	positive regulation of cytokine production
GO:1901700	0.51	response to oxygen-containing compound
GO:0048583	0.51	regulation of response to stimulus
GO:0010243	0.51	response to organonitrogen compound
GO:0048584	0.50	positive regulation of response to stimulus
GO:0032495	0.50	response to muramyl dipeptide
GO:0002682	0.50	regulation of immune system 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:0005737	1.00	cytoplasm
GO:0016020	0.77	membrane
GO:0044444	0.67	cytoplasmic part
GO:0044425	0.66	membrane part
GO:0044459	0.64	plasma membrane part
GO:0098590	0.63	plasma membrane region
GO:0016323	0.62	basolateral plasma membrane
GO:0005829	0.57	cytosol
GO:0043226	0.51	organelle
GO:0043229	0.50	intracellular organelle
GO:0043227	0.50	membrane-bounded organelle

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	2eabA	0.518	4.27	0.083	0.819	3.2.1.63	NA
2	0.060	1e1eB	0.477	4.84	0.064	0.819	3.2.1.21	NA
3	0.060	3gzkA	0.522	4.40	0.084	0.799	3.2.1.4	NA
4	0.060	1js4A	0.524	4.71	0.083	0.854	3.2.1.4	NA
5	0.060	1ft1B	0.502	4.43	0.092	0.812	2.5.1.58 2.5.1.-	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	2nw8B	0.497	4.64	0.044	0.771	0.42	TRP	complex1.pdb.gz	133,134,137

	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.