D-I-TASSER A6NGN9-D3

D-I-TASSER results for A6NGN9-D3

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

Input Sequence in FASTA format

>A6NGN9 (121 residues)
YPPTITDVTSARTALGRAALLRCEAMAVPPADFQWYKDDRLLSSGTAEGLKVQTERTRSM
LLFANVSARHYGNYTCRAANRLGASSASMRLLRPGSLENSAPRPPGLLALLSALGWLWWR
M

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| YPPTITDVTSARTALGRAALLRCEAMAVPPADFQWYKDDRLLSSGTAEGLKVQTERTRSMLLFANVSARHYGNYTCRAANRLGASSASMRLLRPGSLENSAPRPPGLLALLSALGWLWWRM
Prediction	CCCSSSCCCCSSSCCCCSSSSSSSSSSSCCCSSSSSSCCSSCCCCCCSSSSSSSCCCSSSSSSCCCCHHHCSSSSSSSSSCCCSSSSSSSSSSCCCCCCCCCCCCCHHHSCCCSSSSSSSC
Confidence	9972556774698389319999999961798899998999958999715999975988999985688356779999999479638999999982798788998984110113306889969
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| YPPTITDVTSARTALGRAALLRCEAMAVPPADFQWYKDDRLLSSGTAEGLKVQTERTRSMLLFANVSARHYGNYTCRAANRLGASSASMRLLRPGSLENSAPRPPGLLALLSALGWLWWRM
Prediction	7444245265341434661456250454354404623574405757444131446644120304504562465433404153343414040304453666436244335324233233234
	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

                   |                   |                   |                   |                   |                   |

SS
Seq

CCCSSSCCCCSSSCCCCSSSSSSSSSSSCCCSSSSSSCCSSCCCCCCSSSSSSSCCCSSSSSSCCCCHHHCSSSSSSSSSCCCSSSSSSSSSSCCCCCCCCCCCCCHHHSCCCSSSSSSSC
YPPTITDVTSARTALGRAALLRCEAMAVPPADFQWYKDDRLLSSGTAEGLKVQTERTRSMLLFANVSARHYGNYTCRAANRLGASSASMRLLRPGSLENSAPRPPGLLALLSALGWLWWRM

1qgc4

0.18

0.17

5.64

1.33

DEthreader

-DIVLTQSPSLAVSLGQRATISCRASESVDSFMHWYQQPKLLINLGPDRFSGSGSRTDFTLTIDPVEADDVATYYCQQSNEVPLTFGGTKLDLKRADAAP-TVSICF-K-KI-DGSTCEAT

2wwmD

0.19

0.15

4.81

1.18

SPARKS-K

IPPKIEAPSDISIDEGKVLTVACAFTGEPTPEVTWSCGGRKIHSQEQGRFHIENTDDLTTLIIMDVQKQDGGLYTLSLGNEFGSDSATVNIHIRSI-------------------------

3pxjA

0.26

7.89

0.55

MapAlign

HPPEIIRPQNQGVRVGGVASFYCAARGDPPPSIVWRKNGKKV-SGTQSRYTVLEQGGISILRIEPVRARDDAPYECVAENGVGAVSADATLTIYEGDKTPAGFPVITQGPGMTCKAIGN--

2va4A

0.24

0.19

5.91

0.38

CEthreader

VQPHIIQLKNETTYENGQVTLVCDAEGEPIPEITWKRAVDTFTEGDKSRIEVKGQHGSSSLHIKDVKLSDSGRYDCEAASRIGGHQKSMYLDIE---------------------------

5uv6A3

0.42

0.34

9.96

1.19

MUSTER

YPPYISKAKNTGVSVGQKGILSCEASAVPMAEFQWFKEETRLATG-LDGMRIENKGRMSTLTFFNVSEKDYGNYTCVATNKLGNTNASITLYGPGAALV----------------------

2jllA

0.19

0.18

5.88

0.41

HHsearch

-QPHIIQLKNETTYENGQVTLVCDAEGEPIPEITWKRAVDGFTFSLDGRIEVKGQHGSSSLHIKDVKLSDSGRYDCEAASRIGGHQKSMYLDIEYAPKFISN--QTIYYSGNPINISCDVK

3mtrA1

0.30

0.23

7.02

1.62

FFAS-3D

YAPKLQGPVAVYTWEGNQVNITCEVFAYPSATISWFRDGQLLPSSNYSNIKIYNTPSASYLEVTPDSENDFGNYNCTAVNRIGQESLEFILVQA---------------------------

6a69B

0.17

5.45

0.43

EigenThreader

AAPDIGHKRSENKNEGQDATMYCKSVGYPHPDWIWRKKGMPIVNT-SGRFFIINKENYTELNIVNLQIEDPGEYECNATNAIGSASVVTVLRVSHLAPLWPFLGILAEIIILVVIIVVYEK

2rikA

0.22

0.21

6.79

1.78

CNFpred

APPFFDLKPSVDLALGESGTFKCHVTGTAPIKITWAKDNREIRP--GGNYKMTLVENTATLTVLKVTKGDAGQYTCYASNVAGKDSCSAQLGVQEPPRFIKKLPSRIVKQDEHTRYECKIG

2rcjT

0.15

5.00

1.33

DEthreader

-ESVLTQPPSASGTPGQRVTISCTGTSSGSITVNWYQQPKLLIMRVPTRFSGSKSGTSASLAISGLEAEDESDYYCASWNSNSYVFGGTKVTVLGQPKAN-PTVLCIVAWKADGSPSCQVH

(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	0.776

(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	3pxjA	0.76	1.75	0.254	0.860	model1_3pxjA.pdb.gz
2	2nziA	0.76	1.83	0.161	0.851	model1_2nziA.pdb.gz
3	2jllA	0.75	1.79	0.200	0.843	model1_2jllA.pdb.gz
4	3pxhA	0.75	2.18	0.172	0.860	model1_3pxhA.pdb.gz
5	6iaaA	0.75	2.51	0.190	0.901	model1_6iaaA.pdb.gz
6	2wwmD	0.74	1.46	0.188	0.793	model1_2wwmD.pdb.gz
7	6ywcB	0.74	2.72	0.136	0.909	model1_6ywcB.pdb.gz
8	5i99A	0.74	1.67	0.181	0.826	model1_5i99A.pdb.gz
9	3b43A	0.74	1.95	0.227	0.843	model1_3b43A.pdb.gz
10	1ya5A1	0.73	1.29	0.219	0.793	model1_1ya5A1.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:1901363	0.71	heterocyclic compound binding
GO:0097159	0.71	organic cyclic compound binding
GO:0043167	0.69	ion binding
GO:0046872	0.67	metal ion binding
GO:0097367	0.64	carbohydrate derivative binding
GO:0035639	0.62	purine ribonucleoside triphosphate binding
GO:0032555	0.62	purine ribonucleotide binding
GO:0032550	0.62	purine ribonucleoside binding
GO:0005524	0.61	ATP binding
GO:0005516	0.59	calmodulin binding
GO:0008092	0.51	cytoskeletal protein 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:0009987	0.94	cellular process
GO:0044699	0.91	single-organism process
GO:0044763	0.86	single-organism cellular process
GO:0065007	0.77	biological regulation
GO:0032502	0.77	developmental process
GO:0050789	0.75	regulation of biological process
GO:0050794	0.74	regulation of cellular process
GO:0044767	0.72	single-organism developmental process
GO:0016043	0.69	cellular component organization
GO:0048869	0.66	cellular developmental process
GO:0044260	0.65	cellular macromolecule metabolic process
GO:0044238	0.65	primary metabolic process
GO:0048856	0.62	anatomical structure development
GO:0009653	0.62	anatomical structure morphogenesis
GO:0032501	0.58	multicellular organismal process
GO:0006928	0.55	movement of cell or subcellular component
GO:1902589	0.54	single-organism organelle organization
GO:0006914	0.52	autophagy
GO:0080090	0.50	regulation of primary metabolic process
GO:0050896	0.50	response to stimulus
GO:0031323	0.50	regulation of cellular metabolic process
GO:0022411	0.50	cellular component disassembly

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	1.00	cell part
GO:0044424	0.88	intracellular part
GO:0043226	0.76	organelle
GO:0016020	0.71	membrane
GO:0043229	0.70	intracellular organelle
GO:0043227	0.69	membrane-bounded organelle
GO:0044425	0.67	membrane part
GO:0005886	0.62	plasma membrane
GO:0031224	0.61	intrinsic component of membrane
GO:0044444	0.59	cytoplasmic part
GO:0043231	0.59	intracellular membrane-bounded organelle
GO:0016021	0.59	integral component of membrane
GO:0044422	0.57	organelle part
GO:0005634	0.55	nucleus
GO:0044459	0.54	plasma membrane 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	0.282	2eo1A	0.637	2.04	0.239	0.736	2.7.11.1	36,38,42,44,88,90
2	0.261	2bk8A	0.704	1.69	0.177	0.793	2.7.11.1	36,40
3	0.260	2dm7A	0.641	2.03	0.208	0.744	2.7.11.1	NA
4	0.169	2edrA	0.622	2.15	0.179	0.736	2.7.11.1	23,88
5	0.166	1tnnA	0.594	2.67	0.242	0.752	2.7.11.1	73

	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	0.04	1rivL	0.724	2.61	0.138	0.893	0.55	OBE	complex1.pdb.gz	16,66,67,71
2	0.03	1tetL	0.729	2.53	0.164	0.893	0.51	III	complex2.pdb.gz	15,17,19,74
3	0.03	1q72H	0.693	2.83	0.128	0.893	0.81	COC	complex3.pdb.gz	30,32,79,80,83
4	0.03	1riuL	0.724	2.61	0.138	0.893	0.55	RBE	complex4.pdb.gz	16,66,71
5	0.03	2z93D	0.718	2.61	0.103	0.893	0.84	END	complex5.pdb.gz	36,40,77,79,85,87
6	0.03	1vpoH	0.686	2.82	0.092	0.884	0.52	TES	complex6.pdb.gz	37,71,74,89
7	0.03	1wcbA	0.714	2.46	0.105	0.884	0.52	PE1	complex7.pdb.gz	20,22,71,73
8	0.02	1cbvH	0.676	2.86	0.087	0.876	0.52	QNA	complex8.pdb.gz	30,31,32,78,79,80,82,83,84

	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.