D-I-TASSER Q9UDY8-D4

D-I-TASSER results for Q9UDY8-D4

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

Input Sequence in FASTA format

>Q9UDY8 (217 residues)
QPLAKDKVALLIGNMNYREHPKLKAPLVDVYELTNLLRQLDFKVVSLLDLTEYEMRNAVD
EFLLLLDKGVYGLLYYAGHGYENFGNSFMVPVDAPNPYRSENCLCVQNILKLMQEKETGL
NVFLLDMCRKRNDYDDTIPILDALKVTANIVFGYATCQGAEAFEIQHSGLANGIFMKFLK
DRLLEDKKITVLLDEVAEDMGKCHLTKGKQALEIRSS

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| QPLAKDKVALLIGNMNYREHPKLKAPLVDVYELTNLLRQLDFKVVSLLDLTEYEMRNAVDEFLLLLDKGVYGLLYYAGHGYENFGNSFMVPVDAPNPYRSENCLCVQNILKLMQEKETGLNVFLLDMCRKRNDYDDTIPILDALKVTANIVFGYATCQGAEAFEIQHSGLANGIFMKFLKDRLLEDKKITVLLDEVAEDMGKCHLTKGKQALEIRSS
Prediction	CCCCCCCSSSSSSSCCCCCCCCCCCHHHHHHHHHHHHHHCCCSSSSSCCCCHHHHHHHHHHHHHHCCCCCSSSSSSSCCCCSSCCCCSSSSCCCCCCCCCCCCSSHHHHHHHHHHCCCCCSSSSSSCCCCCCCCCCCCCCCCCCCCCCCSSSSSSCCCCCSSSSSCCCCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCSSCCC
Confidence	9987886799997478999866898699999999999990998999238999999999999997558995899999168606489337995179976555563339999999983899948999978999897555533223445789989999759997676526999857289999999855699999999999999998641489603311269
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| QPLAKDKVALLIGNMNYREHPKLKAPLVDVYELTNLLRQLDFKVVSLLDLTEYEMRNAVDEFLLLLDKGVYGLLYYAGHGYENFGNSFMVPVDAPNPYRSENCLCVQNILKLMQEKETGLNVFLLDMCRKRNDYDDTIPILDALKVTANIVFGYATCQGAEAFEIQHSGLANGIFMKFLKDRLLEDKKITVLLDEVAEDMGKCHLTKGKQALEIRSS
Prediction	7542653202010035077266072034005202500572604022232042620250045115404621100000001023344410000000436445330020330141057365422202340323344365444425526244100000002442401215555442001021105103673404400530252046254474443233558
	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 DeepPotential. 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

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCSSSSSSSCCCCCCCCCCCHHHHHHHHHHHHHHCCCSSSSSCCCCHHHHHHHHHHHHHHCCCCCSSSSSSSCCCCSSCCCCSSSSCCCCCCCCCCCCSSHHHHHHHHHHCCCCCSSSSSSCCCCCCCCCCCCCCCCCCCCCCCSSSSSSCCCCCSSSSSCCCCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCSSCCC
QPLAKDKVALLIGNMNYREHPKLKAPLVDVYELTNLLRQLDFKVVSLLDLTEYEMRNAVDEFLLLLDKGVYGLLYYAGHGYENFGNSFMVPVDAPNPYRSENCLCVQNILKLMQEKETGLNVFLLDMCRKRNDYDDTIPILDALKVTANIVFGYATCQGAEAFEIQHSGLANGIFMKFLKDRLLEDKKITVLLDEVAEDMGKCHLTKGKQALEIRSS

3uo8B1

1.00

0.98

27.49

1.50

DEthreader

-MLAKDKVALLIGNMNYREHPKLKAPLVDVYELTNLLRQLDFKVVSLLDLTEYEMRNAVDEFLLLLDKGVYGLLYYAGHGYENFGNSFMVPVDAPNPYRSENCLCVQNILKLMQEKETGLNVFLLDMCRKRNDY--TIPILDALKVTANIVFGYATCQGAEAFEIQHSGLANGIFMKFLKDRLLEDKKITVLLDEVAEDMGKCHLTKGKQALEIRSS

3uo8B1

1.00

0.99

27.75

2.10

SPARKS-K

-MLAKDKVALLIGNMNYREHPKLKAPLVDVYELTNLLRQLDFKVVSLLDLTEYEMRNAVDEFLLLLDKGVYGLLYYAGHGYENFGNSFMVPVDAPNPYRSENCLCVQNILKLMQEKETGLNVFLLDMCRKRNDYDDTIPILDALKVTANIVFGYATCQGAEAFEIQHSGLANGIFMKFLKDRLLEDKKITVLLDEVAEDMGKCHLTKGKQALEIRSS

3uo8B1

1.00

0.99

27.61

1.13

MapAlign

---AKDKVALLIGNMNYREHPKLKAPLVDVYELTNLLRQLDFKVVSLLDLTEYEMRNAVDEFLLLLDKGVYGLLYYAGHGYENFGNSFMVPVDAPNPYRSENCLCVQNILKLMQEKETGLNVFLLDMCRKRNDYDDTIPILDALKVTANIVFGYATCQGAEAFEIQHSGLANGIFMKFLKDRLLEDKKITVLLDEVAEDMGKCHLTKGKQALEIRSS

3uo8B1

1.00

0.99

27.75

0.85

CEthreader

-MLAKDKVALLIGNMNYREHPKLKAPLVDVYELTNLLRQLDFKVVSLLDLTEYEMRNAVDEFLLLLDKGVYGLLYYAGHGYENFGNSFMVPVDAPNPYRSENCLCVQNILKLMQEKETGLNVFLLDMCRKRNDYDDTIPILDALKVTANIVFGYATCQGAEAFEIQHSGLANGIFMKFLKDRLLEDKKITVLLDEVAEDMGKCHLTKGKQALEIRSS

3uo8B1

1.00

0.99

27.75

1.99

MUSTER

-MLAKDKVALLIGNMNYREHPKLKAPLVDVYELTNLLRQLDFKVVSLLDLTEYEMRNAVDEFLLLLDKGVYGLLYYAGHGYENFGNSFMVPVDAPNPYRSENCLCVQNILKLMQEKETGLNVFLLDMCRKRNDYDDTIPILDALKVTANIVFGYATCQGAEAFEIQHSGLANGIFMKFLKDRLLEDKKITVLLDEVAEDMGKCHLTKGKQALEIRSS

3uo8B

1.00

0.99

27.75

2.43

HHsearch

-MLAKDKVALLIGNMNYREHPKLKAPLVDVYELTNLLRQLDFKVVSLLDLTEYEMRNAVDEFLLLLDKGVYGLLYYAGHGYENFGNSFMVPVDAPNPYRSENCLCVQNILKLMQEKETGLNVFLLDMCRKRNDYDDTIPILDALKVTANIVFGYATCQGAEAFEIQHSGLANGIFMKFLKDRLLEDKKITVLLDEVAEDMGKCHLTKGKQALEIRSS

3uo8B1

1.00

0.99

27.74

2.52

FFAS-3D

--LAKDKVALLIGNMNYREHPKLKAPLVDVYELTNLLRQLDFKVVSLLDLTEYEMRNAVDEFLLLLDKGVYGLLYYAGHGYENFGNSFMVPVDAPNPYRSENCLCVQNILKLMQEKETGLNVFLLDMCRKRNDYDDTIPILDALKVTANIVFGYATCQGAEAFEIQHSGLANGIFMKFLKDRLLEDKKITVLLDEVAEDMGKCHLTKGKQALEIRSS

3uo8B1

1.00

0.99

27.75

1.02

EigenThreader

-MLAKDKVALLIGNMNYREHPKLKAPLVDVYELTNLLRQLDFKVVSLLDLTEYEMRNAVDEFLLLLDKGVYGLLYYAGHGYENFGNSFMVPVDAPNPYRSENCLCVQNILKLMQEKETGLNVFLLDMCRKRNDYDDTIPILDALKVTANIVFGYATCQGAEAFEIQHSGLANGIFMKFLKDRLLEDKKITVLLDEVAEDMGKCHLTKGKQALEIRSS

3uo8B

1.00

0.99

27.75

2.26

CNFpred

-MLAKDKVALLIGNMNYREHPKLKAPLVDVYELTNLLRQLDFKVVSLLDLTEYEMRNAVDEFLLLLDKGVYGLLYYAGHGYENFGNSFMVPVDAPNPYRSENCLCVQNILKLMQEKETGLNVFLLDMCRKRNDYDDTIPILDALKVTANIVFGYATCQGAEAFEIQHSGLANGIFMKFLKDRLLEDKKITVLLDEVAEDMGKCHLTKGKQALEIRSS

3uo8B

1.00

0.98

27.49

1.50

DEthreader

-MLAKDKVALLIGNMNYREHPKLKAPLVDVYELTNLLRQLDFKVVSLLDLTEYEMRNAVDEFLLLLDKGVYGLLYYAGHGYENFGNSFMVPVDAPNPYRSENCLCVQNILKLMQEKETGLNVFLLDMCRKRNDY--TIPILDALKVTANIVFGYATCQGAEAFEIQHSGLANGIFMKFLKDRLLEDKKITVLLDEVAEDMGKCHLTKGKQALEIRSS

(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	0.9092

(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 DeepPotential, 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	3uo8B	0.98	0.60	0.995	0.995	model1_3uo8B.pdb.gz
2	1jxqA	0.81	2.13	0.174	0.894	model1_1jxqA.pdb.gz
3	6w8rA	0.80	2.66	0.158	0.935	model1_6w8rA.pdb.gz
4	2j30A	0.79	2.14	0.173	0.876	model1_2j30A.pdb.gz
5	4m9rA	0.79	2.13	0.194	0.876	model1_4m9rA.pdb.gz
6	3e4cA	0.79	2.67	0.143	0.908	model1_3e4cA.pdb.gz
7	2funB	0.79	2.14	0.153	0.876	model1_2funB.pdb.gz
8	1gqfA	0.78	2.82	0.165	0.912	model1_1gqfA.pdb.gz
9	2nn3D	0.77	2.85	0.151	0.889	model1_2nn3D.pdb.gz
10	3sirA	0.67	3.49	0.187	0.811	model1_3sirA.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	0.79	catalytic activity
GO:0008233	0.76	peptidase activity
GO:0016740	0.72	transferase activity
GO:0004871	0.71	signal transducer activity
GO:0004842	0.71	ubiquitin-protein transferase activity
GO:0043621	0.70	protein self-association
GO:0019207	0.70	kinase regulator activity
GO:0008047	0.70	enzyme activator activity
GO:0019209	0.69	kinase activator 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:0009987	1.00	cellular process
GO:0050896	0.94	response to stimulus
GO:0065007	0.93	biological regulation
GO:0050789	0.93	regulation of biological process
GO:0016043	0.93	cellular component organization
GO:0006950	0.93	response to stress
GO:0050794	0.91	regulation of cellular process
GO:0048518	0.89	positive regulation of biological process
GO:0080090	0.87	regulation of primary metabolic process
GO:0071704	0.87	organic substance metabolic process
GO:0060255	0.87	regulation of macromolecule metabolic process
GO:0048522	0.87	positive regulation of cellular process
GO:0044238	0.87	primary metabolic process
GO:0031323	0.87	regulation of cellular metabolic process
GO:0048584	0.86	positive regulation of response to stimulus
GO:0043170	0.86	macromolecule metabolic process
GO:0031325	0.86	positive regulation of cellular metabolic process
GO:0019219	0.86	regulation of nucleobase-containing compound metabolic process
GO:0010604	0.86	positive regulation of macromolecule metabolic process
GO:0007165	0.86	signal transduction
GO:0002684	0.86	positive regulation of immune system process
GO:0002376	0.86	immune system process
GO:0001817	0.86	regulation of cytokine production
GO:0051347	0.85	positive regulation of transferase activity
GO:0045859	0.85	regulation of protein kinase activity
GO:0043933	0.85	macromolecular complex subunit organization
GO:0043123	0.85	positive regulation of I-kappaB kinase/NF-kappaB signaling
GO:0042981	0.85	regulation of apoptotic process
GO:0038093	0.85	Fc receptor signaling pathway
GO:0022407	0.85	regulation of cell-cell adhesion
GO:0006952	0.85	defense response
GO:0006810	0.85	transport
GO:0006508	0.85	proteolysis
GO:0006355	0.85	regulation of transcription, DNA-templated
GO:0002757	0.85	immune response-activating signal transduction
GO:0002696	0.85	positive regulation of leukocyte activation
GO:0001934	0.85	positive regulation of protein phosphorylation
GO:0001819	0.85	positive regulation of cytokine production
GO:0051259	0.84	protein oligomerization
GO:0051168	0.84	nuclear export
GO:0051092	0.84	positive regulation of NF-kappaB transcription factor activity
GO:0050870	0.84	positive regulation of T cell activation
GO:0050852	0.84	T cell receptor signaling pathway
GO:0038095	0.84	Fc-epsilon receptor signaling pathway
GO:0032743	0.84	positive regulation of interleukin-2 production
GO:0007250	0.84	activation of NF-kappaB-inducing kinase activity
GO:0002726	0.84	positive regulation of T cell cytokine production
GO:0044699	0.65	single-organism process
GO:0044763	0.63	single-organism cellular process
GO:0012501	0.52	programmed cell death

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:0044464	0.97	cell part
GO:0044424	0.94	intracellular part
GO:0043234	0.89	protein complex
GO:0044444	0.87	cytoplasmic part
GO:0044446	0.79	intracellular organelle part
GO:0005829	0.77	cytosol
GO:0005737	0.76	cytoplasm
GO:0043229	0.75	intracellular organelle
GO:0043227	0.75	membrane-bounded organelle
GO:0043231	0.74	intracellular membrane-bounded organelle
GO:0005634	0.73	nucleus
GO:0005730	0.70	nucleolus
GO:0016020	0.51	membrane

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	0.137	1k88A	0.788	2.30	0.156	0.885	3.4.22.60 3.4.22.-	NA
2	0.132	1shjB	0.745	2.48	0.166	0.834	3.4.22.60 3.4.22.-	NA
3	0.126	1i4eB	0.788	2.15	0.153	0.876	3.4.22.61	79,80
4	0.124	2fp3A	0.769	2.74	0.128	0.889	3.4.22.-	NA
5	0.122	2j30A	0.794	2.14	0.173	0.876	3.4.22.56	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:

Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
1	0.50	1nmqA	0.793	2.15	0.173	0.876	0.98	160	complex1.pdb.gz	23,78,79,80,126,128,161,162,163,164,165,174,205
2	0.48	3h0eA	0.791	2.19	0.173	0.876	0.83	H0E	complex2.pdb.gz	79,80,81,128,161,162,163,164
3	0.26	1rwvA	0.529	2.47	0.187	0.599	1.42	5PH	complex3.pdb.gz	23,78,79,80,126,128
4	0.20	1rhqA	0.512	2.23	0.167	0.571	1.09	0ZZ	complex4.pdb.gz	78,79,80,81,91,127,128

	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, Qiqige Wuyun, Yang Li, Quancheng Liu, Xiaogen Zhou, Yiheng Zhu, P. Lydia Freddolino, Yang Zhang. Integrating deep learning potentials with I-TASSER for single- and multi-domain protein structure prediction. Submitted. 2023.