D-I-TASSER A6NDA9-D2

D-I-TASSER results for A6NDA9-D2

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

Input Sequence in FASTA format

>A6NDA9 (94 residues)
KPQISTPSANITIRAGQNVTLRCLAQASPSPSIAWTYPLSMWREFDVLTSSTGEDTALSE
LAIPAAHLVDSGNYTCMASNSIGKSNLVISLHVQ

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| KPQISTPSANITIRAGQNVTLRCLAQASPSPSIAWTYPLSMWREFDVLTSSTGEDTALSELAIPAAHLVDSGNYTCMASNSIGKSNLVISLHVQ
Prediction	CCSSSSCCCCSSSCCCCCSSSSSSSSSSCCCSSSSSSCCSSCCCCCCSSSSSSSSCCSSSSSSCCCCHHHCSSSSSSSSSCCCSSSSSSSSSSC
Confidence	9789940884899089429999999750798899998994635676335557875570799996655244879999999288549999999989
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| KPQISTPSANITIRAGQNVTLRCLAQASPSPSIAWTYPLSMWREFDVLTSSTGEDTALSELAIPAAHLVDSGNYTCMASNSIGKSNLVISLHVQ
Prediction	8667455365241445650456340444352434734665515747444444455444145435504554575433404243443314246458
	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

                   |                   |                   |                   |

SS
Seq

CCSSSSCCCCSSSCCCCCSSSSSSSSSSCCCSSSSSSCCSSCCCCCCSSSSSSSSCCSSSSSSCCCCHHHCSSSSSSSSSCCCSSSSSSSSSSC
KPQISTPSANITIRAGQNVTLRCLAQASPSPSIAWTYPLSMWREFDVLTSSTGEDTALSELAIPAAHLVDSGNYTCMASNSIGKSNLVISLHVQ

6efyA

0.22

7.03

1.50

DEthreader

HPVIQVPNQLVGAPLGTDVQIECHVEASPKSINYWIKDTGEMIVTYHVQESSQSMETKMSMIVRKFQKDDVGSYRCIAKNSLGEVDSSIRLYEI

1u2hA

0.27

8.17

1.22

SPARKS-K

PPTFKVSLMDQSVREGQDVIMSIRVQGEPKPVVSWLRNRQPVRPDQRRFAEEA-EGGLCRLRILAAERGDAGFYTCKAVNEYGARQCEARLEVR

6efyA3

0.24

7.61

0.58

MapAlign

HPVIQVPNQLVGAPLGTDVQIECHVEASPKSINYWIKDTGEMGKYHVQESSQSMYETKMSMIVRKFQKDDVGSYRCIAKNSLGEVDSSIRLYEI

3dmkA2

0.28

8.47

0.44

CEthreader

PPVIRQAFQEETMEPGPSVFLKCVAGGNPTPEISWELDGKKIANYQVGQYVTVNGDVVSYLNITSVHANDGGLYKCIAKSKVGVAEHSAKLNVY

1u2hA

0.28

8.46

1.20

MUSTER

PPTFKVSLMDQSVREGQDVIMSIRVQGEPKPVVSWLRNRQPVRPDQRRFAEEAEG-GLCRLRILAAERGDAGFYTCKAVNEYGARQCEARLEVR

6iaaA2

0.24

0.23

7.29

0.41

HHsearch

PPQFVVRPRDQIVAQGRTVTFPCETKGNPQPAVFWQKEGSQNLLFPNSRCSV---SPTGDLTITNIQRSDAGYYICQALTVAGSILAKAQLEVT

3b43A1

0.25

0.24

7.59

1.80

FFAS-3D

PPYFIEPLEHVEAAIGEPITLQCKVDGTPEIRIAWYKEHTKLRSAPAYKMQFKN--NVASLVINKVDHSDVGEYTCKAENSVGAVASSAVLVIK

2dm2A

0.27

8.15

0.30

EigenThreader

APFFEMKLKHYKIFEGMPVTFTCRVAGNPKPKIYWFKDGKQISDHYTIQRDL---DGTCSLHTTASTLDDDGNYTIMAANPQGRISCTGRLMVQ

1u2hA

0.28

8.46

1.64

CNFpred

PPTFKVSLMDQSVREGQDVIMSIRVQGEPKPVVSWLRNRQPVRPDQRRFAEEAE-GGLCRLRILAAERGDAGFYTCKAVNEYGARQCEARLEVR

6efyA3

0.22

7.03

1.50

DEthreader

HPVIQVPNQLVGAPLGTDVQIECHVEASPKSINYWIKDTGEMIVTYHVQESSQSMETKMSMIVRKFQKDDVGSYRCIAKNSLGEVDSSIRLYEI

(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	0.9328

(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	6eg0B3	0.95	0.89	0.255	1.000	model1_6eg0B3.pdb.gz
2	6efyA3	0.93	1.13	0.245	1.000	model1_6efyA3.pdb.gz
3	6efzA3	0.92	1.10	0.258	0.989	model1_6efzA3.pdb.gz
4	3dmkA2	0.91	1.26	0.277	1.000	model1_3dmkA2.pdb.gz
5	1tlkA	0.89	1.12	0.222	0.957	model1_1tlkA.pdb.gz
6	1u2hA	0.89	1.18	0.278	0.957	model1_1u2hA.pdb.gz
7	2e9wB3	0.89	1.27	0.217	0.979	model1_2e9wB3.pdb.gz
8	1g1cA	0.84	1.52	0.211	0.957	model1_1g1cA.pdb.gz
9	1qz1A	0.84	1.44	0.287	0.925	model1_1qz1A.pdb.gz
10	1koaA	0.84	1.34	0.239	0.936	model1_1koaA.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	0.81	heterocyclic compound binding
GO:0097159	0.81	organic cyclic compound binding
GO:0097367	0.79	carbohydrate derivative binding
GO:0032555	0.77	purine ribonucleotide binding
GO:0032550	0.77	purine ribonucleoside binding
GO:0035639	0.76	purine ribonucleoside triphosphate binding
GO:0005524	0.70	ATP binding
GO:0042802	0.64	identical protein binding
GO:0046983	0.59	protein dimerization activity
GO:0042803	0.58	protein homodimerization activity
GO:0043169	0.52	cation binding
GO:0046872	0.51	metal ion binding
GO:0004872	0.51	receptor activity
GO:0003824	0.51	catalytic 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:0044699	0.89	single-organism process
GO:0009987	0.88	cellular process
GO:0065007	0.87	biological regulation
GO:0050789	0.86	regulation of biological process
GO:0050794	0.85	regulation of cellular process
GO:0044763	0.83	single-organism cellular process
GO:0032502	0.76	developmental process
GO:0044767	0.72	single-organism developmental process
GO:0050896	0.61	response to stimulus
GO:0048869	0.61	cellular developmental process
GO:0016043	0.61	cellular component organization
GO:0048518	0.60	positive regulation of biological process
GO:0009653	0.59	anatomical structure morphogenesis
GO:0007165	0.59	signal transduction
GO:0048522	0.58	positive regulation of cellular process
GO:0048856	0.55	anatomical structure development
GO:0006950	0.54	response to stress
GO:0006952	0.53	defense response
GO:0032879	0.52	regulation of localization
GO:0006954	0.52	inflammatory response
GO:2000145	0.50	regulation of cell motility
GO:0008152	0.50	metabolic process
GO:0006928	0.50	movement of cell or subcellular component

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	0.90	intracellular part
GO:0043226	0.75	organelle
GO:0044444	0.74	cytoplasmic part
GO:0016020	0.71	membrane
GO:0044425	0.67	membrane part
GO:0044422	0.63	organelle part
GO:0043229	0.62	intracellular organelle
GO:0031224	0.62	intrinsic component of membrane
GO:0016021	0.61	integral component of membrane
GO:0005886	0.61	plasma membrane
GO:0043227	0.58	membrane-bounded organelle
GO:0044459	0.57	plasma membrane part
GO:0005737	0.50	cytoplasm

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	0.201	2bk8A	0.834	1.40	0.148	0.936	2.7.11.1	37
2	0.122	1rv6Y	0.675	2.61	0.143	0.883	2.7.10.1	19,36
3	0.105	2edrA	0.744	1.85	0.205	0.883	2.7.11.1	20,23,60
4	0.095	1zvyA	0.776	1.90	0.191	0.936	3.2.1.17	NA
5	0.091	2cr6A	0.729	1.96	0.167	0.894	2.7.11.1	71,74

	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	0.06	2fdb1	0.879	1.38	0.275	0.968	0.66	III	complex1.pdb.gz	27,28,29,30,31,32,34,36,38,47,48,49,51,57,59,77,79,80,81,86
2	0.06	2iep0	0.829	1.56	0.253	0.925	1.05	III	complex2.pdb.gz	5,6,9,18,20,22,24,26,60
3	0.05	1tlk0	0.889	1.12	0.222	0.957	0.61	III	complex3.pdb.gz	32,33,34,42
4	0.05	2pyeD	0.833	1.77	0.220	0.968	0.66	III	complex4.pdb.gz	16,69,70,71
5	0.05	2bnqD	0.828	1.75	0.222	0.957	0.62	III	complex5.pdb.gz	17,65,67,68,71,72
6	0.04	2e7lC	0.803	2.09	0.157	0.947	0.61	III	complex6.pdb.gz	30,81,82,83

	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.