D-I-TASSER Q9P2X3-D1

D-I-TASSER results for Q9P2X3-D1

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

Input Sequence in FASTA format

>Q9P2X3 (127 residues)
MAEGDAGSDQRQNEEIEAMAAIYGEEWCVIDDCAKIFCIRISDDIDDPKWTLCLQVMLPN
EYPGTAPPIYQLNAPWLKGQERADLSNSLEEIYIQNIGESILYLWVEKIRDVLIQKSQMT
EPGPDVK

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MAEGDAGSDQRQNEEIEAMAAIYGEEWCVIDDCAKIFCIRISDDIDDPKWTLCLQVMLPNEYPGTAPPIYQLNAPWLKGQERADLSNSLEEIYIQNIGESILYLWVEKIRDVLIQKSQMTEPGPDVK
Prediction	CCCCCCCCHHHHHHHHHHHHHHCCCCSSSSCCCCCSSSSSSCCCCCCCCSSSSSSSSSCCCCCCCCCCSSSSSCCCCCHHHHHHHHHHHHHHHHHHCCCSSHHHHHHHHHHHHHHHHCCCCCCCCCC
Confidence	9975421069999999999986799659952899739999768999872369999994899988777458872689999999999999999999829952099999999999998522468886779
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MAEGDAGSDQRQNEEIEAMAAIYGEEWCVIDDCAKIFCIRISDDIDDPKWTLCLQVMLPNEYPGTAPPIYQLNAPWLKGQERADLSNSLEEIYIQNIGESILYLWVEKIRDVLIQKSQMTEPGPDVK
Prediction	6566567346415411400404155414234676430303044647554130202031276355442322214174046631540253045106724413001300430352046337467455648
	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

                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCHHHHHHHHHHHHHHCCCCSSSSCCCCCSSSSSSCCCCCCCCSSSSSSSSSCCCCCCCCCCSSSSSCCCCCHHHHHHHHHHHHHHHHHHCCCSSHHHHHHHHHHHHHHHHCCCCCCCCCC
MAEGDAGSDQRQNEEIEAMAAIYGEEWCVIDDCAKIFCIRISDDIDDPKWTLCLQVMLPNEYPGTAPPIYQLNAPWLKGQERADLSNSLEEIYIQNIGESILYLWVEKIRDVLIQKSQMTEPGPDVK

2ebmA

0.19

0.17

5.61

1.33

DEthreader

----MTDYGEEQRNELEALESIYPDSFTVLSENPPSFTITVTSEAGDETVQTTLKFTYSEKYP-DEAPLYEISQENLEDNDVSDILKLLALQAEENLGMVMIFTLVTAVQEKLNEIVDQIK-T-R--

2ebmA

0.19

0.18

5.86

2.33

SPARKS-K

GSSGMTDYGEEQRNELEALESIYPDSFTVLSENPPSFTITVTSEANDETVQTTLKFTYSEKYPDEAPLYEIFSQENLEDNDVSDILKLLALQAEENLGMVMIFTLVTAVQEKLNEIVDQIKTR----

2ebmA

0.20

0.17

5.56

1.03

MapAlign

-----TDYGEEQRNELEALESIYPDSFTVLSENPPSFTITVTSEENDETVQTTLKFTYSEKYPDE-APLYEIFQENLEDNDVSDILKLLALQAEENLGMVMIFTLVTAVQEKLNEIVD---------

2ebmA

0.18

0.17

5.65

0.87

CEthreader

GSSGMTDYGEEQRNELEALESIYPDSFTVLSENPPSFTITVTSEAGEETVQTTLKFTYSEKYPDEAPLYEIFSQENLEDNDVSDILKLLALQAEENLGMVMIFTLVTAVQEKLNEIVDQIKTR----

2ebmA

0.19

0.18

5.86

2.09

MUSTER

GSSGMTDYGEEQRNELEALESIYPDSFTVLSENPPSFTITVTSEANDETVQTTLKFTYSEKYPDEAPLYEIFSQENLEDNDVSDILKLLALQAEENLGMVMIFTLVTAVQEKLNEIVDQIKTR----

2ebmA

0.19

0.18

5.85

2.49

HHsearch

GSSGMTDYGEEQRNELEALESIYPDSFTVLSENPPSFTITVTSEANDETVQTTLKFTYSEKYPDE-APLYEIFQENLEDNDVSDILKLLALQAEENLGMVMIFTLVTAVQEKLNEIVDQIKTR----

2yz0A

0.19

0.18

5.87

1.84

FFAS-3D

MSLSHDQYYEIQCNELEAIRSIYMDDFTDLTKRKIIFEITLRSVDKEVESSITLHFAMTPMYPYTAPEIEFKNVQNVMDSQLQMLKSEFKKIHNTSRGQEIIFEITSFTQEKLDEFQNVVNTQS---

2daxA

0.15

5.03

1.22

EigenThreader

SSGSSGEQAEAQLAELDLLASMFPGELIVNDSSKVYFTINMNLVSDEKMAMFSLACILPF-KYPAVLPEITVRSVLLSRSQQTQLNTDLTAFLQKHHGDVCILNATEWVREHASGYVSRDTSSSGPS

1ukxA

0.20

6.28

1.27

CNFpred

GSSGMESYSQRQDHELQALEAIYGSDFQDLRPEPPEINLVLYPQGLEVYVQVELRVKCPPTYPDV-VPEIDLKNAGLSNESVNLLKSHLEELAKKQCGEVMIFELAHHVQSFLSEHNKSGPSSG---

2yz0A

0.15

0.14

4.80

1.33

DEthreader

-SLTLDQYYEIQCNELEAIRSIYMDDFTDLTKPQIIFEITLRSVDKEVESSITLHFAMTPMYP-YTAPEIEFKVQNVMDSQLQMLKSEFKKIHNTSRGQEIIFEITSFTQEKLDEFQNVV--NTQSL

(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	0.8169

(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	2ebmA	0.89	1.31	0.189	0.953	model1_2ebmA.pdb.gz
2	2yz0A	0.83	2.25	0.144	0.961	model1_2yz0A.pdb.gz
3	1ukxA	0.80	2.15	0.220	0.913	model1_1ukxA.pdb.gz
4	2dawA	0.79	2.49	0.187	0.945	model1_2dawA.pdb.gz
5	2dmfA	0.79	2.35	0.190	0.905	model1_2dmfA.pdb.gz
6	2daxA	0.79	2.20	0.195	0.921	model1_2daxA.pdb.gz
7	2ebkA	0.74	2.27	0.221	0.874	model1_2ebkA.pdb.gz
8	1cjyA2	0.38	5.15	0.035	0.756	model1_1cjyA2.pdb.gz
9	1we7A	0.36	4.60	0.057	0.622	model1_1we7A.pdb.gz
10	3bpkB	0.35	4.68	0.033	0.630	model1_3bpkB.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	0.93	catalytic activity
GO:0016740	0.91	transferase activity
GO:0061630	0.87	ubiquitin protein ligase activity
GO:0031624	0.84	ubiquitin conjugating enzyme 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:0050794	1.00	regulation of cellular process
GO:0009987	0.99	cellular process
GO:0032270	0.96	positive regulation of cellular protein metabolic process
GO:0044699	0.67	single-organism process
GO:0008152	0.64	metabolic process
GO:0071704	0.61	organic substance metabolic process
GO:0044763	0.61	single-organism cellular process
GO:0044238	0.59	primary metabolic process
GO:0044237	0.59	cellular metabolic process
GO:0043170	0.57	macromolecule metabolic process
GO:0048583	0.55	regulation of response to stimulus
GO:0048519	0.55	negative regulation of biological process
GO:0044260	0.55	cellular macromolecule metabolic process
GO:0050896	0.54	response to stimulus
GO:0048523	0.54	negative regulation of cellular process
GO:0032502	0.53	developmental process
GO:0060548	0.52	negative regulation of cell death
GO:0051716	0.52	cellular response to stimulus
GO:0051171	0.52	regulation of nitrogen compound metabolic process
GO:0044767	0.52	single-organism developmental process
GO:0031326	0.52	regulation of cellular biosynthetic process
GO:0019538	0.52	protein metabolic process
GO:0010556	0.52	regulation of macromolecule biosynthetic process
GO:0010468	0.52	regulation of gene expression
GO:0010033	0.52	response to organic substance
GO:0009719	0.52	response to endogenous stimulus
GO:0009628	0.52	response to abiotic stimulus
GO:0006950	0.52	response to stress
GO:2001141	0.51	regulation of RNA biosynthetic process
GO:2000112	0.51	regulation of cellular macromolecule biosynthetic process
GO:0072755	0.51	cellular response to benomyl
GO:0071468	0.51	cellular response to acidic pH
GO:0070301	0.51	cellular response to hydrogen peroxide
GO:0051239	0.51	regulation of multicellular organismal process
GO:0051173	0.51	positive regulation of nitrogen compound metabolic process
GO:0044267	0.51	cellular protein metabolic process
GO:0034198	0.51	cellular response to amino acid starvation
GO:0031328	0.51	positive regulation of cellular biosynthetic process
GO:0010557	0.51	positive regulation of macromolecule biosynthetic process
GO:2000026	0.50	regulation of multicellular organismal development
GO:0080134	0.50	regulation of response to stress
GO:0060284	0.50	regulation of cell development
GO:0051240	0.50	positive regulation of multicellular organismal process
GO:0051172	0.50	negative regulation of nitrogen compound metabolic process
GO:0051128	0.50	regulation of cellular component organization
GO:0032269	0.50	negative regulation of cellular protein metabolic process
GO:0031327	0.50	negative regulation of cellular biosynthetic process
GO:0010628	0.50	positive regulation of gene expression
GO:0006464	0.50	cellular protein modification process
GO:0006417	0.50	regulation of translation
GO:0006355	0.50	regulation of transcription, DNA-templated
GO:0001932	0.50	regulation of protein phosphorylation

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	1.00	intracellular part
GO:0032991	1.00	macromolecular complex
GO:0043234	0.53	protein complex
GO:0030529	0.53	intracellular ribonucleoprotein complex
GO:0005844	0.51	polysome
GO:0005737	0.50	cytoplasm
GO:0000151	0.50	ubiquitin ligase complex

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	0.093	2c4pB	0.695	3.05	0.136	0.913	6.3.2.19	NA
2	0.091	2gmiA	0.682	3.11	0.127	0.898	6.3.2.19	NA
3	0.090	1yh2A	0.702	3.18	0.126	0.921	6.3.2.19	NA
4	0.084	1e2cC	0.694	3.28	0.098	0.945	6.3.2.19	99
5	0.081	1i7kB	0.684	3.10	0.111	0.913	6.3.2.19	56

	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	0.07	1j7d0	0.683	3.03	0.161	0.921	0.67	III	complex1.pdb.gz	4,5,6,7,9,10,13,16
2	0.03	1fbv1	0.669	3.10	0.104	0.890	0.93	III	complex2.pdb.gz	10,11,13,14,17,20,21,63,65,97,98,99
3	0.03	2c2v4	0.673	3.46	0.131	0.945	0.59	III	complex3.pdb.gz	5,6,7,8,16,17
4	0.03	3eb62	0.684	3.09	0.127	0.905	0.55	III	complex4.pdb.gz	7,10,11,14,15,18,21,65,94
5	0.01	3k1lA	0.555	2.97	0.044	0.740	0.53	MAL	complex5.pdb.gz	98,101,103,105,106

	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.