D-I-TASSER Q8ND23-D1

D-I-TASSER results for Q8ND23-D1

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

Input Sequence in FASTA format

>Q8ND23 (123 residues)
MAKPSVELTRELQDSIRRCLSQGAVLQQHHVKLETKPKKFEDRVLALTSWRLHLFLLKVP
AKVESSFNVLEIRAFNTLSQNQILVETERGMVSMRLPSAESVDQVTRHVSSALSKVCPGP
GCL

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MAKPSVELTRELQDSIRRCLSQGAVLQQHHVKLETKPKKFEDRVLALTSWRLHLFLLKVPAKVESSFNVLEIRAFNTLSQNQILVETERGMVSMRLPSAESVDQVTRHVSSALSKVCPGPGCL
Prediction	CCCCCCHHCHHHHHHHHHHHCCCSSSSSSSSSSSCCCCCCCCSSSSSSCCSSSSSSCCCCCSSSSSSSSSSSSSSSSCCCCSSSSSSCCCSSSSSSCCHHHHHHHHHHHHHHHHHHCCCCCCC
Confidence	997731222899999999848662788876885134786344399996426799854786268876547888988525898699998792489982785459999999999999858999999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MAKPSVELTRELQDSIRRCLSQGAVLQQHHVKLETKPKKFEDRVLALTSWRLHLFLLKVPAKVESSFNVLEIRAFNTLSQNQILVETERGMVSMRLPSAESVDQVTRHVSSALSKVCPGPGCL
Prediction	855545603540353046214552332334242545675444200001332010022423440434032020441534544301030564413141444640440042023103421444668
	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

                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCHHCHHHHHHHHHHHCCCSSSSSSSSSSSCCCCCCCCSSSSSSCCSSSSSSCCCCCSSSSSSSSSSSSSSSSCCCCSSSSSSCCCSSSSSSCCHHHHHHHHHHHHHHHHHHCCCCCCC
MAKPSVELTRELQDSIRRCLSQGAVLQQHHVKLETKPKKFEDRVLALTSWRLHLFLLKVPAKVESSFNVLEIRAFNTLSQNQILVETERGMVSMRLPSAESVDQVTRHVSSALSKVCPGPGCL

3a58A

0.09

3.37

1.17

DEthreader

-AEQYERDRKAIINCCFRPDPPNNYITHV-RIIEDSLEKKK-RLLILSAIQIHKARENSFQIGR-TWQLTELVRVEKDISEGFILT--SKKYYWETNSAKERTVFIKSLITLYIQTFEHVSYA

4k17A1

0.33

0.29

8.80

1.53

SPARKS-K

---------PRELESIKDVIGRKIISVKKKVKLEVKGDRVENKVLVLTSCRAFLLSARIPSKLELTFSYLEIHGVICHKPAQ-VVETEKCNSK---VSPEDVSEVLAHIGTCLRRIFPGLSPL

6bcbA

0.14

0.12

4.16

0.61

MapAlign

---------DQRLKEIAAKMQQRQLHLEGALCWKSTSGRLKDVLAVLLTDVLLLLQEYVFASVPPVISLQKLI-VREVEEKAMFLISAPEMYEMYTSSKEDRNIWMAHIRRAVESCP------

1b55A

0.16

0.13

4.33

0.48

CEthreader

----------------------AAVILESIFLKRSQQKNFKKRLFLLTVHKLSYYEYGRRGSKKGSIDVEKITCVETVVPYPFQVVYDEGPLYVFSPTEELRKRWIHQLKNVIRYNSDLVQKY

4k17A1

0.33

0.29

8.80

1.42

MUSTER

---------PRELESIKDVIGRKKISVKKKVKLEVKGDRVENKVLVLTSCRAFLLSARIPSKLELTFSYLEIHGVICHKPAQ-VVETEKCNSK---VSPEDVSEVLAHIGTCLRRIFPGLSPL

4k17A1

0.33

0.29

8.80

4.59

HHsearch

---------PRELESIKDVIGRKKISVKKKVKLEVKGDRVENKVLVLTSCRAFLLSARIPSKLELTFSYLEIHGVICHKPAQ-VVETEKCNSK---VSPEDVSEVLAHIGTCLRRIFPGLSPL

4k17A1

0.29

0.25

7.68

1.50

FFAS-3D

----------RELESIKDVIGRKIKIVKKKVKLEVKGDRVENKVLVLTSCRAFLLSARIPSKLELTFSYLEIHGVICHKPAQVVETEKCN----SKVSPEDVSEVLAHIGTCLRRIFPGLSP-

1w1hB

0.13

4.49

0.68

EigenThreader

LQFSEDEKRLLLEKQWHQFVENNLILKMGPVDKRKGL-FARRRQLLLTGPHLYYVDPVNKVLKGEIPWSQELRPEAKNF-KTFFVHTPNRTYYLMDPSGN-AHKWCRKIQEVWRQRYQSHPDA

4k17A

0.36

0.33

9.93

1.78

CNFpred

--------PRELMESIKDVIGKIKISVKKKVKLEVKGDRVENKVLVLTSCRAFLLSARIPSKLELTFSYLEIHGVICHKPAQMVVETEKCNMSMKMVSPEDVSEVLAHIGTCLRRIFPGLSPL

1w1hB

0.10

0.09

3.31

1.17

DEthreader

IDLD-SNS---GNP-WHQFVEN-NLILKMGPVDKRKLFARR-RQLLLTEPHLYYVDPVNKVLKG-EIPWSQELRPEAKNFKTFFVHTPNRTYYLMDPSG-NAHKWCRKIQEVWRQRYQS----

(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	0.6967

(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	4k17A1	0.82	1.31	0.364	0.894	model1_4k17A1.pdb.gz
2	1w1hB	0.77	2.37	0.101	0.911	model1_1w1hB.pdb.gz
3	3a58A	0.76	2.49	0.101	0.951	model1_3a58A.pdb.gz
4	4d0nB	0.76	2.34	0.126	0.886	model1_4d0nB.pdb.gz
5	1x86A2	0.76	2.30	0.080	0.894	model1_1x86A2.pdb.gz
6	1xcgE	0.75	2.55	0.070	0.878	model1_1xcgE.pdb.gz
7	1kz7A	0.73	2.65	0.129	0.911	model1_1kz7A.pdb.gz
8	1foeA	0.73	2.93	0.104	0.911	model1_1foeA.pdb.gz
9	3odoA2	0.72	2.11	0.058	0.846	model1_3odoA2.pdb.gz
10	2lg1A	0.71	2.74	0.100	0.886	model1_2lg1A.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:0044877	0.85	macromolecular complex binding
GO:0032403	0.78	protein complex 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:0050794	1.00	regulation of cellular process
GO:0044763	1.00	single-organism cellular process
GO:0048523	0.96	negative regulation of cellular process
GO:0016043	0.95	cellular component organization
GO:0030031	0.80	cell projection assembly
GO:0048583	0.79	regulation of response to stimulus
GO:1902531	0.74	regulation of intracellular signal transduction
GO:0048522	0.72	positive regulation of cellular process
GO:0051128	0.71	regulation of cellular component organization
GO:0032879	0.70	regulation of localization
GO:0031344	0.68	regulation of cell projection organization
GO:0030334	0.68	regulation of cell migration
GO:0071704	0.67	organic substance metabolic process
GO:0051495	0.65	positive regulation of cytoskeleton organization
GO:0044237	0.65	cellular metabolic process
GO:0032273	0.65	positive regulation of protein polymerization
GO:0030833	0.65	regulation of actin filament polymerization
GO:0050793	0.64	regulation of developmental process
GO:0045595	0.64	regulation of cell differentiation
GO:2000812	0.62	regulation of barbed-end actin filament capping
GO:2000147	0.62	positive regulation of cell motility
GO:1902743	0.62	regulation of lamellipodium organization
GO:0051234	0.62	establishment of localization
GO:0031346	0.62	positive regulation of cell projection organization
GO:0030836	0.62	positive regulation of actin filament depolymerization
GO:0032502	0.59	developmental process
GO:0051094	0.58	positive regulation of developmental process
GO:0045785	0.58	positive regulation of cell adhesion
GO:0045597	0.58	positive regulation of cell differentiation
GO:0044767	0.58	single-organism developmental process
GO:0010769	0.57	regulation of cell morphogenesis involved in differentiation
GO:0044710	0.56	single-organism metabolic process
GO:0006810	0.56	transport
GO:0040011	0.55	locomotion
GO:0006928	0.55	movement of cell or subcellular component
GO:0044281	0.54	small molecule metabolic process
GO:0006897	0.54	endocytosis
GO:0002376	0.54	immune system process
GO:0050776	0.53	regulation of immune response
GO:0006907	0.53	pinocytosis
GO:1902532	0.52	negative regulation of intracellular signal transduction
GO:0006082	0.52	organic acid metabolic process
GO:1900024	0.51	regulation of substrate adhesion-dependent cell spreading
GO:0051695	0.51	actin filament uncapping
GO:0051492	0.51	regulation of stress fiber assembly
GO:0048584	0.51	positive regulation of response to stimulus
GO:0032233	0.51	positive regulation of actin filament bundle assembly
GO:0010811	0.51	positive regulation of cell-substrate adhesion
GO:0010770	0.51	positive regulation of cell morphogenesis involved in differentiation

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	0.96	cell part
GO:0016020	0.85	membrane
GO:0005886	0.83	plasma membrane
GO:0044424	0.73	intracellular 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	0.084	2dynA	0.631	2.28	0.096	0.764	3.6.5.5	NA
2	0.075	2ys1A	0.605	2.76	0.103	0.772	3.6.5.5	NA
3	0.067	2oqbB	0.587	2.54	0.088	0.724	2.1.1.125	NA
4	0.066	2yt2A	0.627	2.84	0.123	0.780	2.7.10.1	NA
5	0.060	1tu5A	0.519	3.96	0.086	0.821	1.4.3.21	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:

No Binding sites was predicted

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

	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.