D-I-TASSER Q8NEN0-D3

D-I-TASSER results for Q8NEN0-D3

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

Input Sequence in FASTA format

>Q8NEN0 (117 residues)
SRKNLLNVCKLIFKISRNEKNDSLIQNDSILESLLEVLRSEDLQTNMEAFLYCMGSIKFI
SGNLGFLNEMISKGAVEILINLIKQINENIKKCGTFLPNSGHLLVQVTATLRNLVDS

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| SRKNLLNVCKLIFKISRNEKNDSLIQNDSILESLLEVLRSEDLQTNMEAFLYCMGSIKFISGNLGFLNEMISKGAVEILINLIKQINENIKKCGTFLPNSGHLLVQVTATLRNLVDS
Prediction	CCCHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHCCC
Confidence	942399999999999634532588860886999999984437777727999999889871389799999998293999999999999865413555532777999999999986379
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| SRKNLLNVCKLIFKISRNEKNDSLIQNDSILESLLEVLRSEDLQTNMEAFLYCMGSIKFISGNLGFLNEMISKGAVEILINLIKQINENIKKCGTFLPNSGHLLVQVTATLRNLVDS
Prediction	845302200200030045562121146561041014104444346413000001100110143560253026440141014104412642565654356112001100110122378
	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

                   |                   |                   |                   |                   |

SS
Seq

CCCHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHCCC
SRKNLLNVCKLIFKISRNEKNDSLIQNDSILESLLEVLRSEDLQTNMEAFLYCMGSIKFISGNLGFLNEMISKGAVEILINLIKQINENIKKCGTFLPNSGHLLVQVTATLRNLVDS

4k6jA

0.11

4.00

1.33

DEthreader

VEDCMRAIIGVLLNLTNNEWGSTKTGEQGLIGTALNCVLQPKLPQRFDIRVLGLGLLINLVESARNRHCLVNMHAVQALVQLFLERERAAQLAETAHMEDCIVASYTALLLGCLCES

4gmnA1

0.11

0.10

3.73

1.10

FFAS-3D

--KSRTTAAGAIANIVQDAKCRKLLLREQVVHIVLTETLTDN---NIDSRAAGWEILKVLAEEADFCVHLYRLDVLTAIEHAAKAVLETLTTSEPPFSKVWDITGSLLVLIGLLALA

4r0zA

0.12

0.11

3.96

1.33

DEthreader

VEEVTEPALCALRHCTAAEEAQSELRFCQAFPVILDQLETL-R---TPVIKAALGVIRNSALLQTNLIELTQETAVSLTMDILRRAITAIEE-NPDIAPMWGVIEGAVSALHQLANH

4r0zA3

0.10

0.09

3.18

0.87

SPARKS-K

NDGMTACACGTLSNLTCNTRNKQTVCSHGGIDALVTAIRRL--PEVEEVTEPALCALRHCTLAEEAQSELRFCQAFPVILDQLE-------------TLRTPVIKAALGVIRNSALL

4r0zA

0.12

4.19

0.58

MapAlign

-EEVTEPALCALRHCTAAEEAQSELRFCQAFPVILDQLET--L--RTPVIKAALGVIRNSALLQTNLIELTQETAVSLTMDILRRAITAIEENPDIDGVMWGVIEGAVSALHQLANH

4hxtA1

0.15

0.13

4.32

0.34

CEthreader

DSETQKEAARDLAEIAGPASAIKAIVDAGGVEVLVKLLTST----DSEVQKEAARALANIASGDEAIKAIVDAGGVEVLVKLL-------------TSTDSEVQKEAARALANIASG

3l6xA

0.19

0.17

5.54

0.81

MUSTER

KKEVHLGACGALKNISRDQDNKIAIKNCDGVPALVRLLRKAR---DMDLTEVITGTLWNLSSHDSIKMEIVDHA-LHALTDEVIIPHSG-----WEHIEWESVLTNTAGCLRNVSSE

1xm9A

0.16

0.15

5.12

0.94

HHsearch

DEKYQAIGAYYIQHTCQDESAKQQVYQLGGICKLVDLLRSP----NQNVQQAAAGALRNLVRSTTNKLETRRQNGIREAVSLLRRTNAEIQSTDEVCVVDPEVFFNATGCLRNLSSA

2z6gA3

0.12

0.10

3.61

0.94

FFAS-3D

--EIVEACTGALHILARDIHNRIVIRGLNTIPLFVQLLYSPI----ENIQRVAAGVLCELAQDKEAAEAIEAEGATAPLTELLH-------------SRNEGVATYAAAVLFRMSED

5mqiA1

0.15

4.89

0.75

EigenThreader

TYPDCLESVKDLIRYLRHEDVRQQLGAAQILQSDLPILTQHH--QDKPLFDAVIRLMVNLTQVLTYLQAYKEAFAFGVLSETLYEL--LQLGWEERQEEDNLLIERILLLVRNILHV

(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	0.8061

(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	4k6jA	0.85	1.66	0.125	0.957	model1_4k6jA.pdb.gz
2	2z6gA	0.84	1.99	0.105	0.974	model1_2z6gA.pdb.gz
3	6nmgA	0.83	2.50	0.094	0.992	model1_6nmgA.pdb.gz
4	3c2hB	0.83	1.87	0.155	0.940	model1_3c2hB.pdb.gz
5	3l6xA3	0.83	1.74	0.139	0.923	model1_3l6xA3.pdb.gz
6	4gmnA1	0.83	1.87	0.105	0.974	model1_4gmnA1.pdb.gz
7	3tt9A	0.81	1.09	0.158	0.863	model1_3tt9A.pdb.gz
8	1xm9A1	0.81	1.12	0.158	0.863	model1_1xm9A1.pdb.gz
9	4r0zA3	0.80	1.31	0.098	0.872	model1_4r0zA3.pdb.gz
10	2ynsA	0.79	1.31	0.149	0.863	model1_2ynsA.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:0046983	0.38	protein dimerization activity
GO:0042802	0.37	identical protein binding
GO:0005198	0.36	structural molecule activity
GO:0086080	0.35	protein binding involved in heterotypic cell-cell adhesion
GO:0050839	0.35	cell adhesion molecule binding
GO:0019902	0.35	phosphatase binding
GO:0019900	0.35	kinase 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	0.91	single-organism process
GO:0009987	0.91	cellular process
GO:0065007	0.88	biological regulation
GO:0050789	0.88	regulation of biological process
GO:0044763	0.88	single-organism cellular process
GO:0050794	0.87	regulation of cellular process
GO:0080090	0.84	regulation of primary metabolic process
GO:0060255	0.84	regulation of macromolecule metabolic process
GO:0048583	0.84	regulation of response to stimulus
GO:0048518	0.84	positive regulation of biological process
GO:0023051	0.84	regulation of signaling
GO:0010646	0.84	regulation of cell communication
GO:0060828	0.83	regulation of canonical Wnt signaling pathway
GO:0048870	0.83	cell motility
GO:0044707	0.83	single-multicellular organism process
GO:0008283	0.83	cell proliferation
GO:0010604	0.82	positive regulation of macromolecule metabolic process
GO:0007389	0.82	pattern specification process
GO:0048869	0.76	cellular developmental process
GO:0048523	0.75	negative regulation of cellular process
GO:0090090	0.74	negative regulation of canonical Wnt signaling pathway
GO:0045732	0.74	positive regulation of protein catabolic process
GO:0045595	0.74	regulation of cell differentiation
GO:0016477	0.74	cell migration
GO:0007026	0.74	negative regulation of microtubule depolymerization
GO:0001708	0.74	cell fate specification

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:0005634	1.00	nucleus
GO:0044446	0.92	intracellular organelle part
GO:0005737	0.91	cytoplasm
GO:0044444	0.88	cytoplasmic part
GO:0044428	0.75	nuclear part
GO:0005829	0.74	cytosol
GO:0005654	0.65	nucleoplasm
GO:0044430	0.54	cytoskeletal part
GO:0016020	0.52	membrane
GO:0043234	0.50	protein complex

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	1h54B	0.613	3.79	0.062	0.966	2.4.1.8	NA
2	0.060	1h12A	0.588	3.57	0.018	0.880	3.2.1.8	NA
3	0.060	2gtqA	0.532	3.06	0.090	0.761	3.4.11.2	NA
4	0.060	1ks8A	0.594	3.61	0.057	0.880	3.2.1.4	NA
5	0.060	1fp3A	0.615	3.84	0.088	0.966	5.1.3.8	72

	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	0.19	1bk6B	0.789	1.22	0.150	0.855	0.97	III	complex1.pdb.gz	16,17,18,22,55,59,106,109,113
2	0.18	3kndA	0.794	1.98	0.162	0.897	0.71	III	complex2.pdb.gz	6,10,14,16,17,18,22,52,55,59,62,63,109,113,116
3	0.01	1qgk1	0.248	2.69	0.071	0.308	0.73	III	complex3.pdb.gz	66,68,69,71,76,77,80,81,84,87,88,89,92

	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.