D-I-TASSER Q8NCU1-D1

D-I-TASSER results for Q8NCU1-D1

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

Input Sequence in FASTA format

>Q8NCU1 (143 residues)
MAAMDTGQRADPSNPGDKEGDLQGLWQELYQLQAKQKKLKREVEKHKLFEDYLIKVLEKI
PEGCTGWEEPEEVLVEATVKHYGKLFTASQDTQKRLEAFCQMIQAVHRSLESLEEDHRAL
IASRSGCVSCRRSATASRSSGGS

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MAAMDTGQRADPSNPGDKEGDLQGLWQELYQLQAKQKKLKREVEKHKLFEDYLIKVLEKIPEGCTGWEEPEEVLVEATVKHYGKLFTASQDTQKRLEAFCQMIQAVHRSLESLEEDHRALIASRSGCVSCRRSATASRSSGGS
Prediction	CCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCSSHHHCCCCCCCCCC
Confidence	97533455689999874036899999999999999999999999962159999999998110014545614569999999999998833999999999999789999999999999987412335540000000002345899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MAAMDTGQRADPSNPGDKEGDLQGLWQELYQLQAKQKKLKREVEKHKLFEDYLIKVLEKIPEGCTGWEEPEEVLVEATVKHYGKLFTASQDTQKRLEAFCQMIQAVHRSLESLEEDHRALIASRSGCVSCRRSATASRSSGGS
Prediction	74324554735374465544414300530462545454156426635224610240053036424537434432043005314403333551353153125445534541551465241213445213413443445456668
	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

CCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCSSHHHCCCCCCCCCC
MAAMDTGQRADPSNPGDKEGDLQGLWQELYQLQAKQKKLKREVEKHKLFEDYLIKVLEKIPEGCTGWEEPEEVLVEATVKHYGKLFTASQDTQKRLEAFCQMIQAVHRSLESLEEDHRALIASRSGCVSCRRSATASRSSGGS

6djlB

0.07

0.06

2.27

1.00

DEthreader

VD-PRIQGELEKLNQSTDDINRRETELEDARQKFRSVLVEATVKLDELVKKIG-------------------------------K--AVEDSK-PYWEARRVARQAQLEAQKATQDFQRATEVLRAAKETISLAEQRLLEDDK

6z9lA4

0.08

3.08

0.51

CEthreader

LANKQKEEAKAKDQKTKDDQAVADQQTVVTTSQEKVTDAKADTAAKQADLTAKENALKDKQAATKQAQNTAQQAESDAQQARSASQQALNTAKTTQATAEKELSVHKATLANLQAVATKSTTNYEEKVRQTATAEKSLQQTKD

3j4aA

0.08

3.08

0.53

EigenThreader

MAEKRTGLAEDGAKSVYERLKNDRAQNCAQYTIGARGLNNLASKLMLALFPMQTWMRLTISEAKQLLSDPDGLAKVDEGLSMVERIIMNIEEYLGDLRSLENLQEAIVKMSMIPLVRVLLKQDKLERCVTAWRIANAIGIDTS

5lpnB

0.08

0.07

2.72

0.98

FFAS-3D

-----------------KEEEMKRF-CKAQTIQRRLNEIEAALRELEAEGVKLELALRRQSSSPEQQKKLWVGQLLQLVDKKNSLVAEEAELTVQELNLEEKQWQLDQELRGYRQAEDQVLRKLVDLVNQRDALIRF------

6egcA

0.09

0.08

3.21

0.88

SPARKS-K

--TRTEIIRELERSLREQEELAKRLKELLRELERLQREVRELLREIKELVEEIEKLAREQKYLVEELKRQGNEIIRELERSLREQEELAKRLKELLRELERLQREVRELLREIKELVEEIEKLAREQKYLVEELKRQ------

5xg2A

0.09

0.08

3.16

0.65

CNFpred

---------------KRAEEEKERLKAEILTGEARLPGLRERAENLRRLVEEKRAEISELERRLSSISFELRIKLSDLEKELELARKDLEKVLAEERAVREEIEVAKRRINELDTLIERERGELAKLRGRIERLERKRDKLKK

7d6dA

0.05

0.03

1.66

1.00

DEthreader

---------------------------------TDPEVY-S-SAEF-----KLALNTALFASLMLLSRALSQLAEVEEKIEQLHQEQANNDFFLLAELLSDYIRLLAIVRAAFDQRMKTWQRWQDAQATLQKKRESEARLLWA

6gy6A

0.07

2.89

0.79

MapAlign

LKLIGGELSDGTIAQGLQPQISSKKKLLSTTIKDLQSKIDEKNKEIDQFQKDYNKYVGLAFSGMVGGIISWAITGGIFGDKAEKARKQKNKLIDEVKDLQSQVKDKSALQTSVQNLSLSFAGIHTSMVDAEEALNHLDFMWNT

3na7A

0.11

4.01

0.75

MUSTER

IDSLEPLIREKRKDLDKALNDKEAKNKAILNLEEEKLALKLQVSKNEQTLQDTNAKIASIQKKMSEIKSERE--LRSLNIEEDIAKERSNQANREIENLQNEIKRKSEKQEDLKKEMLELEKLALELESLVENEVKNIKETQQ

4ll8E

0.10

0.08

2.81

0.69

HHsearch

----EHMESKLLEIFERKNKKLKELEKDYSELSNRYNEQKEKMDQLSKLAKNSSAIEQSCSE-----------KLQNMEVNYNSLLESQNLYRDH---YSDEISKLNEKIGLLELELSNQNLN--------------------

(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	0.5494

(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	6ewyA	0.85	2.18	0.156	0.986	model1_6ewyA.pdb.gz
2	6yvuB	0.81	2.53	0.077	1.000	model1_6yvuB.pdb.gz
3	6z9lA	0.81	2.57	0.105	0.993	model1_6z9lA.pdb.gz
4	2b5uA3	0.81	2.36	0.080	0.965	model1_2b5uA3.pdb.gz
5	4tkoB	0.80	2.62	0.085	0.986	model1_4tkoB.pdb.gz
6	6z6fD	0.78	2.72	0.091	0.993	model1_6z6fD.pdb.gz
7	6z6fC	0.77	2.44	0.082	0.937	model1_6z6fC.pdb.gz
8	1ciiA2	0.76	2.91	0.085	0.986	model1_1ciiA2.pdb.gz
9	3l4qC	0.76	2.99	0.079	0.972	model1_3l4qC.pdb.gz
10	6gy6B	0.75	2.94	0.092	0.979	model1_6gy6B.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:0052813	0.60	phosphatidylinositol bisphosphate kinase activity
GO:0035591	0.60	signaling adaptor activity
GO:0032403	0.60	protein complex binding
GO:0030971	0.60	receptor tyrosine kinase binding
GO:0030674	0.60	protein binding, bridging
GO:0019902	0.60	phosphatase binding
GO:0017046	0.60	peptide hormone binding
GO:0005167	0.60	neurotrophin TRK receptor binding
GO:0004871	0.60	signal transducer 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:2000147	0.60	positive regulation of cell motility
GO:1903557	0.60	positive regulation of tumor necrosis factor superfamily cytokine production
GO:1903078	0.60	positive regulation of protein localization to plasma membrane
GO:1902531	0.60	regulation of intracellular signal transduction
GO:1900101	0.60	regulation of endoplasmic reticulum unfolded protein response
GO:0097193	0.60	intrinsic apoptotic signaling pathway
GO:0097191	0.60	extrinsic apoptotic signaling pathway
GO:0071482	0.60	cellular response to light stimulus
GO:0071378	0.60	cellular response to growth hormone stimulus
GO:0050870	0.60	positive regulation of T cell activation
GO:0050851	0.60	antigen receptor-mediated signaling pathway
GO:0045670	0.60	regulation of osteoclast differentiation
GO:0044764	0.60	multi-organism cellular process
GO:0044403	0.60	symbiosis, encompassing mutualism through parasitism
GO:0043484	0.60	regulation of RNA splicing
GO:0043069	0.60	negative regulation of programmed cell death
GO:0042981	0.60	regulation of apoptotic process
GO:0042113	0.60	B cell activation
GO:0038127	0.60	ERBB signaling pathway
GO:0038094	0.60	Fc-gamma receptor signaling pathway
GO:0032680	0.60	regulation of tumor necrosis factor production
GO:0031647	0.60	regulation of protein stability
GO:0031294	0.60	lymphocyte costimulation
GO:0030334	0.60	regulation of cell migration
GO:0030098	0.60	lymphocyte differentiation
GO:0010812	0.60	negative regulation of cell-substrate adhesion
GO:0009967	0.60	positive regulation of signal transduction
GO:0009411	0.60	response to UV
GO:0007596	0.60	blood coagulation
GO:0006974	0.60	cellular response to DNA damage stimulus
GO:0006464	0.60	cellular protein modification process
GO:0002762	0.60	negative regulation of myeloid leukocyte differentiation
GO:0002433	0.60	immune response-regulating cell surface receptor signaling pathway involved in phagocytosis
GO:0002431	0.60	Fc receptor mediated stimulatory signaling pathway
GO:0001952	0.60	regulation of cell-matrix adhesion

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	0.84	cell part
GO:0016020	0.74	membrane
GO:0044425	0.63	membrane part
GO:0044424	0.58	intracellular part
GO:0005886	0.58	plasma 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	0.060	2qb0B	0.262	5.44	0.027	0.482	3.2.1.17	28
2	0.060	1rr8C	0.332	4.47	0.079	0.552	5.99.1.2	NA
3	0.060	1dofA	0.476	3.47	0.068	0.643	4.3.2.2	65
4	0.060	1sesA	0.491	4.11	0.085	0.755	6.1.1.11	NA
5	0.060	2zr3B	0.534	4.13	0.072	0.790	6.1.1.11	65

	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	0.03	1jch0	0.812	2.44	0.077	0.972	0.54	III	complex1.pdb.gz	17,24,27,28,62,71,76,80,83,84,87,94,98,102
2	0.02	1g730	0.667	2.48	0.058	0.790	0.66	III	complex2.pdb.gz	79,80,82,83,86,87,90
3	0.01	2hdi1	0.264	3.86	0.105	0.371	0.41	III	complex3.pdb.gz	58,79,82,83,86

	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, 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.