D-I-TASSER Q9UNU6-D2

D-I-TASSER results for Q9UNU6-D2

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

Input Sequence in FASTA format

>Q9UNU6 (140 residues)
GQYAKKLVLKVFGYRSVQGDHEMIHSASTKHLRFTAGYLSLFGYTKDKEQDLLQAGELFM
EFRKFDLLFPRFVYSLLWPREWLEVGRLQRLFHKMLSVSHSQEKEGISNWLGNMLQFLRE
QGVPSAMQDKFNFMMLWASQ

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| GQYAKKLVLKVFGYRSVQGDHEMIHSASTKHLRFTAGYLSLFGYTKDKEQDLLQAGELFMEFRKFDLLFPRFVYSLLWPREWLEVGRLQRLFHKMLSVSHSQEKEGISNWLGNMLQFLREQGVPSAMQDKFNFMMLWASQ
Prediction	CCHHHHHHHHHHCCCCCCCHHHHHHHHCCCSSSSSSSHHHHSCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCC
Confidence	81799999998445566431444445311225655110011057842346799999999999999999999998169999999999999999997087764212474189999999999739998999899999886139
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| GQYAKKLVLKVFGYRSVQGDHEMIHSASTKHLRFTAGYLSLFGYTKDKEQDLLQAGELFMEFRKFDLLFPRFVYSLLWPREWLEVGRLQRLFHKMLSVSHSQEKEGISNWLGNMLQFLREQGVPSAMQDKFNFMMLWASQ
Prediction	86214400330232433743341043344430203101010113467555334404500630351033012202230446225304402530263032640474742251044124315746247613431100202238
	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

                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCHHHHHHHHHHCCCCCCCHHHHHHHHCCCSSSSSSSHHHHSCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCC
GQYAKKLVLKVFGYRSVQGDHEMIHSASTKHLRFTAGYLSLFGYTKDKEQDLLQAGELFMEFRKFDLLFPRFVYSLLWPREWLEVGRLQRLFHKMLSVSHSQEKEGISNWLGNMLQFLREQGVPSAMQDKFNFMMLWASQ

2iagA

0.26

7.93

1.33

DEthreader

FHYAIFLMERIFDVQLPHYSPSEKARMKTLL-LLRAGYLTLYGIEASQAQDRVHSADVFHTFRQLDRLLPKLARGSLSVGDKDHMCSVKSRLWKLLSARL-ARRAHRSKWLESYLLHLEEMGVSEEMQARALVLQLWATG

3daxA1

0.24

0.18

5.58

1.21

SPARKS-K

---------------------------------FEAGYLTIFGRDLTRRTQKAHILNNLDNFKQFDKVFPALVAGLP-IHMFRTAHNAREKLAESLRHENLQKRESISELISLRMFLNDTLTFDDLEKAKTHLVVLWASQ

2iagA

0.27

8.33

0.92

MapAlign

HAYAIFLMERIFDVQLPHYSPQALTEAMYTNLLLRAGYLTLYGIEESQAQDRVHSADVFHTFRQLDRLLPKLARGSLSVGDKDHMCSVKSRLWKLLSPARLARRAHRSKWLESYLLHLEEMGVSEEMQARALVLQLWATQ

2iagA

0.27

8.33

0.77

CEthreader

MYTNLHAVLLGDATEAGSGWHEMGLLDFSYSFLLRAGYLTLYGIEALPAQDRVHSADVFHTFRQLDRLLPKLARGSLSVGDKDHMCSVKSRLWKLLSPARLARRAHRSKWLESYLLHLEEMGVSEEMQARALVLQLWATQ

3daxA1

0.24

0.18

5.58

1.34

MUSTER

---------------------------------FEAGYLTIFGRDLTRRTQKAHILNNLDNFKQFDKVFPALVAGLP-IHMFRTAHNAREKLAESLRHENLQKRESISELISLRMFLNDTLTFDDLEKAKTHLVVLWASQ

3daxA1

0.24

0.18

5.58

3.17

HHsearch

---------------------------------FEAGYLTIFGRDLTRDTQKAHILNNLDNFKQFDKVFPALVAGLP-IHMFRTAHNAREKLAESLRHENLQKRESISELISLRMFLDTLSTFDDLEKAKTHLVVLWASQ

3daxA1

0.24

0.18

5.58

1.68

FFAS-3D

---------------------------------FEAGYLTIFGRDTRRDTQKAHILNNLDNFKQFDKVFPALVAG-LPIHMFRTAHNAREKLAESLRHENLQKRESISELISLRMFLNDTSTFDDLEKAKTHLVVLWASQ

2iagA

0.26

7.94

1.35

EigenThreader

HAYAIFLMERIFDVQLPHYSPSDEKARMKLTFLLRAGYLTLYGIEALPAQDRVHSADVFHTFRQLDRLLPKLARGSLSVGDKDHMCSVKSRLWKLLSPARLARRAHRSKWLESYLLHLEEMGVSEEMQARALVLQLWATQ

3b6hA

0.27

0.26

8.12

0.92

CNFpred

YTNLHAVLLGDATEAG--GWHEMGLLDFSYSFLLRAGYLTLYGIEASQAQDRVHSADVFHTFRQLDRLLPKLARGSLSVGDKDHMCSVKSRLWKLLSPARLARRAHRSKWLESYLLHLEEMGVSEEMQARALVLQLWATQ

3daxA

0.20

0.19

6.19

1.33

DEthreader

WKFHFATSAKAFHIDPTTENINDTFIKTLLL-MFEAGYLTIFGRDLRRDTQKAHILNNLDNFKQFDKVFPALVAGLPIHMF-RTAHNAREKLAESLRENL-QKRESISELISLRMFLNDTLSFDDLEKAKTHLVVLWASQ

(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	0.94

(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	7lyxA2	0.97	0.57	1.000	0.986	model1_7lyxA2.pdb.gz
2	2iagA	0.93	1.35	0.264	1.000	model1_2iagA.pdb.gz
3	3b98A	0.86	2.25	0.248	0.979	model1_3b98A.pdb.gz
4	3daxA	0.86	2.06	0.209	0.993	model1_3daxA.pdb.gz
5	4l40A	0.70	3.23	0.076	0.943	model1_4l40A.pdb.gz
6	2q9fA	0.69	3.23	0.098	0.950	model1_2q9fA.pdb.gz
7	5fsaA	0.69	3.22	0.127	0.957	model1_5fsaA.pdb.gz
8	7x2qA	0.69	3.80	0.044	0.971	model1_7x2qA.pdb.gz
9	2ve3A	0.69	3.35	0.169	0.929	model1_2ve3A.pdb.gz
10	7ry8A	0.69	3.35	0.113	0.950	model1_7ry8A.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:0016491	0.75	oxidoreductase activity
GO:0016705	0.70	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
GO:0004497	0.70	monooxygenase activity
GO:0008397	0.68	sterol 12-alpha-hydroxylase 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:0072330	1.00	monocarboxylic acid biosynthetic process
GO:0008610	1.00	lipid biosynthetic process
GO:0065007	0.88	biological regulation
GO:0050789	0.88	regulation of biological process
GO:0050794	0.87	regulation of cellular process
GO:0044255	0.87	cellular lipid metabolic process
GO:0006631	0.86	fatty acid metabolic process
GO:0042981	0.85	regulation of apoptotic process
GO:0001516	0.85	prostaglandin biosynthetic process
GO:0080090	0.64	regulation of primary metabolic process
GO:0060255	0.63	regulation of macromolecule metabolic process
GO:0050896	0.63	response to stimulus
GO:0048522	0.63	positive regulation of cellular process
GO:0031323	0.63	regulation of cellular metabolic process
GO:0051171	0.62	regulation of nitrogen compound metabolic process
GO:0048583	0.62	regulation of response to stimulus
GO:0048519	0.62	negative regulation of biological process
GO:0042221	0.62	response to chemical
GO:0010556	0.62	regulation of macromolecule biosynthetic process
GO:2000026	0.61	regulation of multicellular organismal development
GO:0071310	0.61	cellular response to organic substance
GO:0032102	0.61	negative regulation of response to external stimulus
GO:0031347	0.61	regulation of defense response
GO:0031324	0.61	negative regulation of cellular metabolic process
GO:0022603	0.61	regulation of anatomical structure morphogenesis
GO:0009967	0.61	positive regulation of signal transduction
GO:0006950	0.61	response to stress
GO:0006355	0.61	regulation of transcription, DNA-templated
GO:1900119	0.60	positive regulation of execution phase of apoptosis
GO:0071456	0.60	cellular response to hypoxia
GO:0071354	0.60	cellular response to interleukin-6
GO:0071347	0.60	cellular response to interleukin-1
GO:0050728	0.60	negative regulation of inflammatory response
GO:0045766	0.60	positive regulation of angiogenesis
GO:0045019	0.60	negative regulation of nitric oxide biosynthetic process
GO:0035360	0.60	positive regulation of peroxisome proliferator activated receptor signaling pathway
GO:0032088	0.60	negative regulation of NF-kappaB transcription factor 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 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:0044444	1.00	cytoplasmic part
GO:0044425	1.00	membrane part
GO:0016020	1.00	membrane
GO:0043231	0.84	intracellular membrane-bounded organelle
GO:0044459	0.81	plasma membrane part
GO:0044421	0.81	extracellular region part
GO:0005634	0.81	nucleus
GO:0005901	0.80	caveola
GO:0005783	0.80	endoplasmic reticulum
GO:0005615	0.80	extracellular space
GO:0044446	0.54	intracellular organelle 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

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	2ve3A	0.687	3.35	0.169	0.929	1.14.-.-	NA
2	0.060	3k9vA	0.650	3.61	0.065	0.929	1.14.13.-	NA
3	0.060	1jpzB	0.640	4.15	0.088	0.979	1.14.14.1 1.6.2.4	NA
4	0.060	2d09A	0.599	3.75	0.073	0.879	1.14.-.-	NA
5	0.060	2wuzA	0.653	3.70	0.147	0.964	1.14.13.70	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	0.05	3sn5A	0.834	2.15	0.235	0.971	0.50	UNX	complex1.pdb.gz	38,106,107

	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.