D-I-TASSER Q9UDR5-D2

D-I-TASSER results for Q9UDR5-D2

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

Input Sequence in FASTA format

>Q9UDR5 (155 residues)
AFGQWAGVAGMINILHGMGLRLLALGHHTPFMHIGMAHNYRNSSQAVQAVRDAGYEISLG
LMPKSIGPLTFVFTGTGNVSKGAQAIFNELPCEYVEPHELKEVSQTGDLRKVYGTVLSRH
HHLVRKTDAVYDPAEYDKHPERYISRFNTDIAPYT

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| AFGQWAGVAGMINILHGMGLRLLALGHHTPFMHIGMAHNYRNSSQAVQAVRDAGYEISLGLMPKSIGPLTFVFTGTGNVSKGAQAIFNELPCEYVEPHELKEVSQTGDLRKVYGTVLSRHHHLVRKTDAVYDPAEYDKHPERYISRFNTDIAPYT
Prediction	CCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCSSSSSSCCCCHHHHHHHHHHHCCCSSSCHHHHHHHHHCCCCCSSSSSSSCHHHHCSCCCCCCCCHHHHHHCHHHCCCCCCCCCCCCC
Confidence	96202357779999999999999717788877788512389999999999999999995499877998799996687344789999997698586599999999639997499999336782230799999989986093215556113468999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| AFGQWAGVAGMINILHGMGLRLLALGHHTPFMHIGMAHNYRNSSQAVQAVRDAGYEISLGLMPKSIGPLTFVFTGTGNVSKGAQAIFNELPCEYVEPHELKEVSQTGDLRKVYGTVLSRHHHLVRKTDAVYDPAEYDKHPERYISRFNTDIAPYT
Prediction	74232012000210021203312534342322414433525316402510450053056451477221010000032311400320075062640317304511753744301002032531143356761347303731650434036422437
	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

CCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCSSSSSSCCCCHHHHHHHHHHHCCCSSSCHHHHHHHHHCCCCCSSSSSSSCHHHHCSCCCCCCCCHHHHHHCHHHCCCCCCCCCCCCC
AFGQWAGVAGMINILHGMGLRLLALGHHTPFMHIGMAHNYRNSSQAVQAVRDAGYEISLGLMPKSIGPLTFVFTGTGNVSKGAQAIFNELPCEYVEPHELKEVSQTGDLRKVYGTVLSRHHHLVRKTDAVYDPAEYDKHPERYISRFNTDIAPYT

2qrlA1

0.12

0.11

3.86

1.10

SPARKS-K

-FGFYAGFAGAALGVRDWAFKQTHSDDE----DLPAVSPYPNEKALVKDVTKDYKEALAT---GARKPTVLIIGALGRCGSGAIDLLHKVGIPDANILKWIKETSRGGPDIFINCIYLS-------KPIATNMEKLNNPNRRLRTVVDVSADTTN

2qrlA1

0.14

0.13

4.43

3.00

HHsearch

-FGFYAGFAGAALGVRDWAFKQTHSD-DED---LPAVSPYPNEKALVKDVTKDYKEALA-TG--ARKPTVLIIGALGRCGSGAIDLLHKVGIPDANILKWKETSRGFQADIFINCIFTNMEKLNNRDTNPHNPIPIYTVATVFNKPTV-LVPTSL

2qrlA1

0.16

0.13

4.28

1.08

FFAS-3D

-FGFYAGFAGAALGVRDWAFKQTHSDDED----LPAVSPYPNEKALVKDVTKDYKEALA---TGARKPTVLIIGALGRCGSGAIDLLHKVGIPDILKWDIKETSRGGPFDEIFINCI----YLSKPIAPFTNMEKL-------------------

2qrlA

0.18

0.12

3.99

0.83

DEthreader

AFGFYAGFAGAALGVRDWAFKQTHSD-----L--PAVSPYPNEKALVKDVTKDY-KE--ALATG-ARKPTVLIIGLGRCGSGAIDLLHKVGIPDA-----------------NILKWDIKETSR--------------------GG-PFDEIPQA

2qrlA

0.13

0.12

4.05

0.95

SPARKS-K

AFGFYAGFAGAALGVRDWAFKQTHSDDE----DLPAVSPYPNEKALVKDVTKDYKEALATGAR---KPTVLIIGALGRCGSGAIDLLHKVGIPDANILKWIKETSRGGPFIFINCIYLS-------KPIATNMEKLNNPNRRLRTVVDVSADTTN

3mosA

0.11

3.94

0.66

MapAlign

-QQKLQALKDTANRLRISSIQTTAGSGHPSCCAAMAVRFVLSKGHAAPILYAVWAAMAF-ASIYKLDVAILDINRLQHQMDIYQKRCEAWHAIIVDGEELCKAFGQAKQPTAIIAKTFKRIIALDKNSTFS-EIFKKEHPDRFIPFCSTFAAFFT

2qrlA1

0.12

0.11

3.91

0.79

CEthreader

-FGFYAGFAGAALGVRDWAFKQTHSDDE----DLPAVSPYPNEKALVKDVTKDYKEALATGAR---KPTVLIIGALGRCGSGAIDLLHKVGIPDANILKWDIKETSIPQADIFINCIYLSKPIAPFTTNPHNPIPIYTVATVFNKPTVLVPTTAG

2qrlA

0.19

0.17

5.61

0.95

MUSTER

AFGFYAGFAGAALGVRDWAFKQTHSD-DEDL---PAVSPYPNEKALVKDVTKDYKEALATGAR---KPTVLIIGALGRCGSGAIDLLHKVGIPDILKWDIKETSRGGPFDEIPQADI----IYLSKPIAPFTNMEKLNNPNR-TNPHNP--IPIY

2qrlA

0.13

0.12

4.26

2.33

HHsearch

AFGFYAGFAGAALGVRDWAFKQTHSD-DED---LPAVSPYPNEKALVKDVTKDYKEALATG---ARKPTVLIIGALGRCGSGAIDLLHKVGIPDANILKWDIKETRGQADIFINCIFTNMEKLNNNDTNPHNPIPIYTVATVFNKPTV-LVPTSL

2qrlA

0.14

0.11

3.77

0.61

FFAS-3D

AFGFYAGFAGAALGVRDWAFKQTHSDDED----LPAVSPYPNEKAL---VKDVTKDYKEALATGARKPTVLIIGALGRCGSGAIDLLHKVGIPDANILKWDIKETSRGGADIFINCI----YLSKPIAPFTNMEKL-------------------

(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	0.7775

(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	2qrlA	0.54	3.75	0.147	0.742	model1_2qrlA.pdb.gz
2	5fgnA	0.52	3.93	0.040	0.806	model1_5fgnA.pdb.gz
3	6l30A	0.51	4.72	0.033	0.832	model1_6l30A.pdb.gz
4	4kayA	0.51	4.02	0.040	0.787	model1_4kayA.pdb.gz
5	5n6yB	0.50	4.17	0.067	0.774	model1_5n6yB.pdb.gz
6	4tn0A	0.50	4.04	0.089	0.774	model1_4tn0A.pdb.gz
7	2wpnB	0.50	5.19	0.049	0.852	model1_2wpnB.pdb.gz
8	6bncA	0.50	4.25	0.040	0.793	model1_6bncA.pdb.gz
9	5k4pA	0.50	4.18	0.040	0.781	model1_5k4pA.pdb.gz
10	6ksiA2	0.49	4.36	0.074	0.755	model1_6ksiA2.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:0004753	1.00	saccharopine dehydrogenase activity
GO:0047131	0.90	saccharopine dehydrogenase (NAD+, L-glutamate-forming) activity
GO:0047130	0.52	saccharopine dehydrogenase (NADP+, L-lysine-forming) 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:0044238	1.00	primary metabolic process
GO:0044237	1.00	cellular metabolic process
GO:0044699	0.93	single-organism process
GO:0044710	0.91	single-organism metabolic process
GO:0044281	0.90	small molecule metabolic process
GO:0044763	0.88	single-organism cellular process
GO:0006807	0.87	nitrogen compound metabolic process
GO:1901564	0.86	organonitrogen compound metabolic process
GO:0019752	0.86	carboxylic acid metabolic process
GO:1901606	0.85	alpha-amino acid catabolic process
GO:0009066	0.85	aspartate family amino acid metabolic process
GO:0009063	0.85	cellular amino acid catabolic process
GO:0006554	0.84	lysine catabolic process
GO:0019477	0.52	L-lysine 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:0044444	1.00	cytoplasmic part
GO:0043231	0.91	intracellular membrane-bounded organelle
GO:0005739	0.80	mitochondrion

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	1np2A	0.471	4.72	0.043	0.768	3.2.1.21	NA
2	0.060	2pbgA	0.481	4.46	0.042	0.774	3.2.1.85	NA
3	0.060	1n2cA	0.431	5.49	0.062	0.806	1.18.6.1	3,6,10
4	0.060	1h1lB	0.399	5.76	0.075	0.806	1.18.6.1	8
5	0.060	2zktB	0.472	4.08	0.098	0.697	5.4.2.1	81

	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	0.02	2qrkA	0.545	3.72	0.147	0.742	0.63	AMP	complex1.pdb.gz	74,75,77,78,79,118,119,122
2	0.01	3aekD	0.470	4.62	0.037	0.787	1.03	PMR	complex2.pdb.gz	7,10,11,14,15
3	0.01	3aekB	0.484	4.34	0.039	0.781	0.55	PMR	complex3.pdb.gz	76,77,79,82
4	0.01	3aekB	0.484	4.34	0.039	0.781	0.56	SF4	complex4.pdb.gz	3,4,5,6
5	0.01	3aetB	0.482	4.37	0.039	0.774	0.58	SF4	complex5.pdb.gz	8,10,11,84
6	0.01	3aeqB	0.482	4.41	0.039	0.781	0.57	SF4	complex6.pdb.gz	8,10,11,86

	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.