D-I-TASSER Q6UWL2-D2

D-I-TASSER results for Q6UWL2-D2

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

Input Sequence in FASTA format

>Q6UWL2 (77 residues)
CLEGYRATNNNKTFIPNDGTFCTDIDECEVSGLCRHGGRCVNTHGSFECYCMDGYLPRNG
PEPFHPTTDATSCTEID

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| CLEGYRATNNNKTFIPNDGTFCTDIDECEVSGLCRHGGRCVNTHGSFECYCMDGYLPRNGPEPFHPTTDATSCTEID
Prediction	CCCCCSSSCCCCCSSCCCCCCCCSCCCCCCCCCCCCCCSSSSCCCCSSSSCCCCCSCCCCCCCCCCCCCCCSSSCCC
Confidence	98983724599828789999401416779999889987828579948986489820479876652578997526089
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| CLEGYRATNNNKTFIPNDGTFCTDIDECEVSGLCRHGGRCVNTHGSFECYCMDGYLPRNGPEPFHPTTDATSCTEID
Prediction	86752404147324347645303311135575414753434423422423446314257475425317556446538
	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

CCCCCSSSCCCCCSSCCCCCCCCSCCCCCCCCCCCCCCSSSSCCCCSSSSCCCCCSCCCCCCCCCCCCCCCSSSCCC
CLEGYRATNNNKTFIPNDGTFCTDIDECEVSGLCRHGGRCVNTHGSFECYCMDGYLPRNGPEPFHPTTDATSCTEID

2bo2A

0.35

0.32

9.69

2.13

SPARKS-K

CSPGYEPVSGAKTFKNESENTCQDVDECSSGQHCDSSTVCFNTVGSYSCRCRPGWKPRHGIPNNQK---DTVCE---

2bo2A

0.32

0.30

9.01

1.48

MUSTER

CNPGFSS---FSEIITTPMETCDDINECATLVSCGKFSDCWNTEGSYDCVCSPGYEPVSGAKTFKNE-SENTCQDVD

4xbmB

0.25

7.65

1.21

HHsearch

CRPGYTGATCELGIDEFYGKICESAMTCA-DGPCFNGGRCSDSPDGYSCRCPVGYSGFNCEKKSSPCSNGAKCVDLG

2bo2A

0.32

0.30

9.01

2.47

CNFpred

CNPGFSSFS---EIITTPMETCDDINECATKVSCGKFSDCWNTEGSYDCVCSPGYEPVSGAKTFK-NESENTCQDVD

6polB

0.37

0.29

8.48

0.83

DEthreader

CKSGYISVQ----GDS---AYCEDIDECAMHYCHANT-VCVNLPGLYRCDCVPGYIRV-------D---DFSCTEHD

6pogB1

0.42

0.36

10.68

1.83

SPARKS-K

CMENSICRNLNDRALREDNAYCEDIDECAERHYCRENTMCVNTPGSFMCICKTGYIRIDD----------YSCTEH-

1nziB

0.28

0.23

7.16

0.66

MapAlign

VPEGYGIHLVEEFQVPYNKLVATDINECTDDVPCS--HFCNNFIGGYFCSCPPEYFLH---------DDMKNCGVN-

2bo2A

0.32

0.30

9.01

0.56

CEthreader

CNPGFSSF---SEIITTPMETCDDINECATLSKCGKFSDCWNTEGSYDCVCSPGYEPVSGAKTFK-NESENTCQDVD

4xbmB3

0.29

0.27

8.31

1.28

MUSTER

CQQPWQCNCQEGWG----GLFCNDLNYCTHHKPCKNGATCTNTGGSYTCSCRPGYTGATCELGISPCKNGGSCTDLE

5b4xB

0.35

0.26

7.75

1.21

HHsearch

CPAGFQLL---------DQKTCGDIDECKDPDACSQ--ICVNYKGYFKCECYPGYEMD---------LLTKNCKAAA

(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	0.4898

(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	2bo2A	0.66	2.43	0.232	0.896	model1_2bo2A.pdb.gz
2	4lmfA	0.66	2.38	0.242	0.857	model1_4lmfA.pdb.gz
3	1nziB	0.65	2.30	0.246	0.844	model1_1nziB.pdb.gz
4	3demA	0.64	2.30	0.231	0.844	model1_3demA.pdb.gz
5	6polB	0.64	1.84	0.367	0.779	model1_6polB.pdb.gz
6	6pogB	0.63	1.97	0.467	0.779	model1_6pogB.pdb.gz
7	1nt0A	0.62	2.39	0.226	0.805	model1_1nt0A.pdb.gz
8	6f1cA	0.62	2.48	0.258	0.857	model1_6f1cA.pdb.gz
9	1yo8A	0.59	2.37	0.339	0.805	model1_1yo8A.pdb.gz
10	1uzjA	0.58	1.99	0.429	0.727	model1_1uzjA.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:0046872	0.91	metal ion binding
GO:0005509	0.85	calcium ion binding
GO:0005198	0.67	structural molecule activity
GO:0003824	0.67	catalytic activity
GO:0005201	0.64	extracellular matrix structural constituent
GO:0005102	0.60	receptor binding
GO:0044877	0.58	macromolecular complex binding
GO:0032403	0.56	protein complex binding
GO:0005178	0.55	integrin binding
GO:0030023	0.54	extracellular matrix constituent conferring elasticity
GO:0005179	0.54	hormone activity
GO:0008233	0.52	peptidase activity
GO:0070011	0.51	peptidase activity, acting on L-amino acid peptides

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:0065007	0.90	biological regulation
GO:0050789	0.88	regulation of biological process
GO:0050794	0.86	regulation of cellular process
GO:0009987	0.85	cellular process
GO:0044699	0.84	single-organism process
GO:0032502	0.79	developmental process
GO:0044763	0.76	single-organism cellular process
GO:0008152	0.76	metabolic process
GO:0071704	0.75	organic substance metabolic process
GO:0044238	0.75	primary metabolic process
GO:0044767	0.74	single-organism developmental process
GO:0007165	0.73	signal transduction
GO:0048518	0.72	positive regulation of biological process
GO:0048856	0.71	anatomical structure development
GO:0048583	0.70	regulation of response to stimulus
GO:0009653	0.69	anatomical structure morphogenesis
GO:0043170	0.68	macromolecule metabolic process
GO:0048522	0.66	positive regulation of cellular process
GO:0031323	0.66	regulation of cellular metabolic process
GO:0016043	0.66	cellular component organization
GO:0080090	0.64	regulation of primary metabolic process
GO:0060255	0.64	regulation of macromolecule metabolic process
GO:0031326	0.64	regulation of cellular biosynthetic process
GO:2000112	0.63	regulation of cellular macromolecule biosynthetic process
GO:0051179	0.63	localization
GO:0051171	0.63	regulation of nitrogen compound metabolic process
GO:0048519	0.63	negative regulation of biological process
GO:0048513	0.63	animal organ development
GO:0010468	0.63	regulation of gene expression
GO:0050896	0.62	response to stimulus
GO:0048523	0.62	negative regulation of cellular process
GO:0031325	0.62	positive regulation of cellular metabolic process
GO:0019219	0.62	regulation of nucleobase-containing compound metabolic process
GO:0090287	0.61	regulation of cellular response to growth factor stimulus
GO:0006355	0.61	regulation of transcription, DNA-templated
GO:0065008	0.60	regulation of biological quality
GO:0044710	0.60	single-organism metabolic process
GO:0019538	0.60	protein metabolic process
GO:0010604	0.60	positive regulation of macromolecule metabolic process
GO:0009966	0.60	regulation of signal transduction
GO:0065009	0.59	regulation of molecular function
GO:0051246	0.59	regulation of protein metabolic process
GO:0048731	0.59	system development
GO:0048584	0.59	positive regulation of response to stimulus
GO:0002376	0.59	immune system process
GO:0048585	0.58	negative regulation of response to stimulus
GO:0043062	0.58	extracellular structure organization
GO:0032268	0.58	regulation of cellular protein metabolic process
GO:0044281	0.57	small molecule metabolic process
GO:0030198	0.57	extracellular matrix organization
GO:0019220	0.57	regulation of phosphate metabolic process
GO:0009968	0.57	negative regulation of signal transduction
GO:0009887	0.57	organ morphogenesis
GO:0006357	0.57	regulation of transcription from RNA polymerase II promoter
GO:1901700	0.56	response to oxygen-containing compound
GO:0090092	0.56	regulation of transmembrane receptor protein serine/threonine kinase signaling pathway
GO:0071310	0.56	cellular response to organic substance
GO:0048598	0.56	embryonic morphogenesis
GO:0043549	0.56	regulation of kinase activity
GO:0043085	0.56	positive regulation of catalytic activity
GO:0042592	0.56	homeostatic process
GO:0035556	0.56	intracellular signal transduction
GO:0009886	0.56	post-embryonic morphogenesis
GO:0002682	0.56	regulation of immune system process
GO:0001934	0.56	positive regulation of protein phosphorylation
GO:0001822	0.56	kidney development
GO:0001501	0.56	skeletal system development
GO:1990314	0.55	cellular response to insulin-like growth factor stimulus
GO:0048050	0.55	post-embryonic eye morphogenesis
GO:0048048	0.55	embryonic eye morphogenesis
GO:0043010	0.55	camera-type eye development
GO:0042593	0.55	glucose homeostasis
GO:0035583	0.55	sequestering of TGFbeta in extracellular matrix
GO:0035582	0.55	sequestering of BMP in extracellular matrix
GO:0034199	0.55	activation of protein kinase A activity
GO:0022617	0.55	extracellular matrix disassembly
GO:0010737	0.55	protein kinase A signaling
GO:0007507	0.55	heart development
GO:0006006	0.55	glucose metabolic process
GO:0002684	0.55	positive regulation of immune system process
GO:0001656	0.55	metanephros development
GO:0006508	0.54	proteolysis
GO:0002253	0.54	activation of immune response
GO:0006955	0.52	immune response

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	0.95	cell part
GO:0043226	0.82	organelle
GO:0043227	0.81	membrane-bounded organelle
GO:0044424	0.79	intracellular part
GO:0044421	0.73	extracellular region part
GO:0016020	0.69	membrane
GO:0005576	0.67	extracellular region
GO:0043229	0.60	intracellular organelle
GO:0043231	0.57	intracellular membrane-bounded organelle
GO:0005886	0.57	plasma membrane
GO:0031982	0.54	vesicle
GO:0031988	0.53	membrane-bounded vesicle
GO:0044444	0.52	cytoplasmic 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	1dtyA	0.459	3.40	0.051	0.766	2.6.1.62	NA
2	0.060	1uw8A	0.456	4.05	0.105	0.818	4.1.1.2	NA
3	0.060	1nt0A	0.618	2.39	0.226	0.805	3.4.21.104	34,67
4	0.060	1apqA	0.435	2.36	0.341	0.571	3.4.21.41 3.4.21.42	26,72
5	0.060	1nb7A	0.453	3.92	0.013	0.831	3.4.21.98	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	0.88	2w86A	0.550	2.18	0.509	0.714	1.70	CA	complex1.pdb.gz	24,25,27,42,43,45,46

	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.