D-I-TASSER Q9UJ72-D2

D-I-TASSER results for Q9UJ72-D2

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

Input Sequence in FASTA format

>Q9UJ72 (74 residues)
PPPLYDAHELWHAMKGVGTDENCLIEILASRTNGEIFQMREAYCLQYSNNLQEDIYSETS
GHFRDTLMNLVQGT

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| PPPLYDAHELWHAMKGVGTDENCLIEILASRTNGEIFQMREAYCLQYSNNLQEDIYSETSGHFRDTLMNLVQGT
Prediction	CCHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCHHHHHHHHCCHHHHHHHHHHHCCC
Confidence	96499999999998435997789988885599999999999999997989899988627838999999997249
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| PPPLYDAHELWHAMKGVGTDENCLIEILASRTNGEIFQMREAYCLQYSNNLQEDIYSETSGHFRDTLMNLVQGT
Prediction	75453205202500443335441002001323452153026204742755026104741344134002201648
	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

                   |                   |                   |

SS
Seq

CCHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCHHHHHHHHCCHHHHHHHHHHHCCC
PPPLYDAHELWHAMKGVGTDENCLIEILASRTNGEIFQMREAYCLQYSNNLQEDIYSETSGHFRDTLMNLVQGT

1axnA1

0.46

13.41

1.67

DEthreader

PPAVFDAKQLKKSMKGAGTNEDALIEILTTRTSRQMKDISQAYYTVYKKSLGDDISSETSGDFRKALLTLADGR

1dm5A3

0.42

12.31

2.18

SPARKS-K

KPDEFLAEQLHAAMKGLGTDKNALIDILCTQSNAQIHAIKAAFKLLYKEDLEKEIISETSGNFQRLLVSMLQGG

6t58A

0.47

13.77

0.87

MapAlign

TPAQYDASELKASMKGLGTDEDSLIEIICSRTNQELQEINRVYKEMYKTDLEKDIISDTSGDFRKLMVALAKGR

6t58A5

0.47

13.77

0.56

CEthreader

TPAQYDASELKASMKGLGTDEDSLIEIICSRTNQELQEINRVYKEMYKTDLEKDIISDTSGDFRKLMVALAKGR

1dm5A3

0.42

12.31

2.32

MUSTER

KPDEFLAEQLHAAMKGLGTDKNALIDILCTQSNAQIHAIKAAFKLLYKEDLEKEIISETSGNFQRLLVSMLQGG

2zhjA2

0.53

15.23

1.23

HHsearch

PTVLYDVQELRRAMKGAGTDEGCLIEILASRNPEEIRRINQTYQQQYGRSLEEDICSDTSFMFQRVLVSLTAGG

1axnA1

0.46

13.41

1.41

FFAS-3D

PPAVFDAKQLKKSMKGAGTNEDALIEILTTRTSRQMKDISQAYYTVYKKSLGDDISSETSGDFRKALLTLADGR

1n00A

0.26

7.93

0.88

EigenThreader

PSVSEDCEQLRKAFSGWGTNEGLIIDILGHRNAEQRNLIRKTYAETYGEDLLKALDKELSNDFERLVLLWALDP

5lpxA

0.47

13.77

0.99

CNFpred

TPAQYDASELKASMKGLGTDEDSLIEIICSRTNQELQEINRVYKEMYKTDLEKDIISDTSGDFRKLMVALAKGR

1axnA

0.46

13.41

1.67

DEthreader

PPAVFDAKQLKKSMKGAGTNEDALIEILTTRTSRQMKDISQAYYTVYKKSLGDDISSETSGDFRKALLTLADGR

(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	0.8833

(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	6t58A5	0.98	0.38	0.473	1.000	model1_6t58A5.pdb.gz
2	1axnA1	0.98	0.39	0.459	1.000	model1_1axnA1.pdb.gz
3	1xjlA	0.98	0.48	0.473	1.000	model1_1xjlA.pdb.gz
4	1m9iA	0.97	0.51	0.527	1.000	model1_1m9iA.pdb.gz
5	6tu2A	0.96	0.65	0.500	1.000	model1_6tu2A.pdb.gz
6	2zhjA	0.96	0.68	0.527	1.000	model1_2zhjA.pdb.gz
7	1hm6A	0.96	0.70	0.473	1.000	model1_1hm6A.pdb.gz
8	1bc0A1	0.95	0.71	0.479	0.987	model1_1bc0A1.pdb.gz
9	1dm5A2	0.92	1.08	0.333	0.973	model1_1dm5A2.pdb.gz
10	1n00A1	0.92	1.41	0.270	0.987	model1_1n00A1.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:0005543	0.66	phospholipid binding
GO:0043169	0.58	cation binding
GO:0046872	0.57	metal ion binding
GO:0005544	0.53	calcium-dependent phospholipid 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:0044699	0.96	single-organism process
GO:0009987	0.95	cellular process
GO:0044763	0.90	single-organism cellular process
GO:0065007	0.86	biological regulation
GO:0050789	0.85	regulation of biological process
GO:0006810	0.85	transport
GO:0050794	0.84	regulation of cellular process
GO:0044765	0.82	single-organism transport
GO:0016043	0.80	cellular component organization
GO:0050896	0.77	response to stimulus
GO:0034220	0.75	ion transmembrane transport
GO:0070588	0.74	calcium ion transmembrane transport
GO:0048519	0.74	negative regulation of biological process
GO:0032879	0.73	regulation of localization
GO:0065008	0.72	regulation of biological quality
GO:0051239	0.72	regulation of multicellular organismal process
GO:0048523	0.72	negative regulation of cellular process
GO:0048518	0.72	positive regulation of biological process
GO:0042221	0.72	response to chemical
GO:0048522	0.71	positive regulation of cellular process
GO:0048583	0.70	regulation of response to stimulus
GO:2000145	0.69	regulation of cell motility
GO:0051049	0.69	regulation of transport
GO:0010033	0.69	response to organic substance
GO:0051241	0.68	negative regulation of multicellular organismal process
GO:0051051	0.68	negative regulation of transport
GO:0032101	0.68	regulation of response to external stimulus
GO:0023051	0.68	regulation of signaling
GO:0010646	0.68	regulation of cell communication
GO:0080134	0.67	regulation of response to stress
GO:0051716	0.67	cellular response to stimulus
GO:0009725	0.67	response to hormone
GO:1903531	0.66	negative regulation of secretion by cell
GO:0061041	0.66	regulation of wound healing
GO:0048585	0.66	negative regulation of response to stimulus
GO:0046883	0.65	regulation of hormone secretion
GO:0032870	0.65	cellular response to hormone stimulus
GO:0010035	0.64	response to inorganic substance
GO:1901700	0.63	response to oxygen-containing compound
GO:0065009	0.63	regulation of molecular function
GO:0042981	0.63	regulation of apoptotic process
GO:0022607	0.63	cellular component assembly
GO:0050709	0.62	negative regulation of protein secretion
GO:0044092	0.62	negative regulation of molecular function
GO:0051592	0.61	response to calcium ion
GO:0051259	0.61	protein oligomerization
GO:0050878	0.61	regulation of body fluid levels
GO:0043066	0.61	negative regulation of apoptotic process
GO:1901701	0.60	cellular response to oxygen-containing compound
GO:0051260	0.60	protein homooligomerization
GO:0050790	0.60	regulation of catalytic activity
GO:0043434	0.60	response to peptide hormone
GO:0043065	0.60	positive regulation of apoptotic process
GO:0030193	0.60	regulation of blood coagulation
GO:1902721	0.59	negative regulation of prolactin secretion
GO:1901317	0.59	regulation of sperm motility
GO:0097211	0.59	cellular response to gonadotropin-releasing hormone
GO:0097066	0.59	response to thyroid hormone
GO:0071284	0.59	cellular response to lead ion
GO:0043086	0.59	negative regulation of catalytic activity
GO:0030195	0.59	negative regulation of blood coagulation
GO:0019222	0.52	regulation of metabolic process
GO:0007165	0.51	signal transduction
GO:0060255	0.50	regulation of macromolecule metabolic process
GO:0006996	0.50	organelle organization

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	0.93	intracellular part
GO:0043226	0.83	organelle
GO:0043227	0.77	membrane-bounded organelle
GO:0016020	0.74	membrane
GO:0044444	0.73	cytoplasmic part
GO:0044422	0.67	organelle part
GO:0031982	0.65	vesicle
GO:0044446	0.64	intracellular organelle part
GO:0044421	0.60	extracellular region part
GO:0031988	0.59	membrane-bounded vesicle
GO:0043229	0.57	intracellular organelle
GO:0005737	0.54	cytoplasm
GO:0043230	0.53	extracellular organelle
GO:0070062	0.51	extracellular exosome

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	2vvnA	0.612	3.10	0.059	0.919	3.2.1.52	NA
2	0.060	1fmiA	0.548	3.36	0.072	0.932	3.2.1.113	NA
3	0.060	1e6bA	0.566	3.33	0.043	0.905	2.5.1.18	NA
4	0.060	2qezF	0.565	3.40	0.062	0.851	4.3.1.7	13
5	0.060	2vo4A	0.593	3.14	0.058	0.932	2.5.1.18	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	0.92	2zocA	0.975	0.50	0.527	1.000	1.74	CA	complex1.pdb.gz	14,16,17,18,58
2	0.10	1g5nA	0.950	0.78	0.473	1.000	1.24	UUU	complex2.pdb.gz	11,15,16,17,56,57
3	0.09	2hyvA	0.952	0.81	0.473	1.000	1.24	UUU	complex3.pdb.gz	17,18,58,59,60,61

	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.