EmZ medical microbiology and classification.pptx

1. ..‫الله‬ ‫رسول‬ ‫علي‬ ‫والسالم‬ ‫والصالة‬ ‫الله‬ ‫بسم‬
،‫يعلم‬ ‫لم‬ ‫ما‬ ‫اإلنسان‬ ‫علم‬ ،‫بالقلم‬ ‫علم‬ ‫الذي‬ ‫لله‬ ‫الحمد‬
‫محمد‬ ‫الخير‬ ‫الناس‬ ‫معلم‬ ‫خير‬ ‫علي‬ ‫والسالم‬ ‫والصالة‬
‫وسلم‬ ‫عليه‬ ‫الله‬ ‫صلي‬

2. BIOINFORMATICS APPLICATIONS IN EVOLUTIONARY HISTORY AND
DIAGNOSTICS OF FUNGUS SPECIES GROUP INCLUDING ROSACEAE
PATHOTYPES
EMAN ZAKARIA MOHAMED FARAG
FACULTY OF SCIENCE, MENOUFIA UNIVERSITY.
2018
University of Sadat City
Genetic Engineering and Biotechnology Research Institute (GEBRI)
Bioinformatics Department

3. SUPERVISION COMMITTEE:
• Prof. Dr. El-Sayed Abd El-Khalk El-Absawy
Emeritus Professor of Plant breeding, Bioinformatics Department, Genetic Engineering and
Biotechnology Research Institute (GEBRI), University of Sadat City.
• Dr. Waleed Mahmoud Ead
Associate Professor of Information Systems, Faculty of Computers and Artificial Intelligence,
Beni-Suef University.
University of Sadat City
Genetic Engineering and Biotechnology Research Institute (GEBRI)
Bioinformatics Department

4. APPROVAL COMMITTEE
• Prof. Dr. El-Shawadfi Mansour Mousa
Emeritus Professor of Nematode Plant Pathology, Advisor to the Minister of Higher Education, Plant
Pathology Department, Faculty of Agriculture, Menoufia University.
• Prof. Dr. Abd El-Fattah Mondy Zanaty
Emeritus Professor of Genetics, Genetics Department, Faculty of Agriculture, Menoufia University.
University of Sadat City
Genetic Engineering and Biotechnology Research Institute (GEBRI)
Bioinformatics Department

5. OUTLINES
•Introduction
•Aim of Study
•Materials &Methods
•Results
•Conclusion

6. INTRODUCTION..

7. Apple (Malus demostica)
Highly Productive Fruit.
Cultivated in temperate regions worldwide.
Rich in Fiber, Vitamins, Minerals, and
Antioxidants.
Fire blight
Alternaria blotch

8. Alternaria Blotch Disease..
small, circular, dark brown to black lesions
Irregular spots

9. Alternaria alternata apple
pathotype
produces
HSTs (AM-Toxins) Alternaria Blotch
causes
AM-BAC-14
BAC Clones are used for sequencing of toxin gene cluster regions from three apple pathotype isolates

10. Although the level of susceptibility of apple cultivars to Alternaria blotch varies, the cutivars
‘Delicious,’ ‘Indo,’ and their sports and descendants are particularly susceptible.

11. Bioinformatics is an interdisciplinary field of science that
develops methods and software tools for understanding
biological data, especially when the data sets are large
and complex.
Bioinformatics uses biology, chemistry, physics, computer
science, computer programming, information engineering,
mathematics and statistics to analyze and interpret
biological data.

12. AIM OF STUDY

13. 1. Perform genome organization and
characterization using bioinformatics
software and servers
To identify the functional
genes of resistance/
susceptibility in “Starking
Delicious” BAC clones.
To identify and characterize
the virulence genes in
Alternaria alternata isolate
(AM-BAC-14).
2. Construct the 3D structure of proteins
for the integration and correlation of the
structural and functional analysis of target
genes and proteins using bioinformatics
approaches.
3. Identify the key functional motifs
and active sites of these target
proteins for inhibition their functions .

14. MATERIALS
AND
METHODS

15. THE METHODS EMPLOYED FOR THIS STUDY INVOLVE
TWO CONSIDERABLE LEVELS OF ANALYSIS.

16. Bioinformatics Approaches and Tools for Genome Analysis
In-silico Gene Prediction
and Characterization
Multiple Sequence
Alignment and Prediction of
Conserved Regions
Molecular Evolution and
Phylogenetic Analysis
Domain Separation
FGENESH
GeneMark
ORF Finder
GeneID
BLASTp
BioEdit
Clustal
Omega
MEGA 11
MAFFT
InterProDB
NCBI-CDD

17. Bioinformatics Approaches and Tools For Proteome Analysis
Three-Dimensional
(3D) Structure
Prediction
Model
Refinement
Model
Evaluation
Conserved Motifs Prediction
Structural Classification of
Protein
I-TASSER
Alphafold
Swiss-Model
Robetta
GalaxyWeb
ModRefiner
TM-score
TM-align
Structure
Assessment
QMEAN
ERRAT
MotifFinder
SMART
ScanProsite SCOP
CATH

18. RESULTS..

19. Genome and Proteome Analysis of Apple BAC clones
(SD-178_L15 and SD-241_O01)

20. IN SILICO GENE PREDICTION
AND CHARACTERIZATION..

21. BAC Clone Genes
Transcription
start (bp)
Transcription
end (bp)
Deduced
amino acid
length (aa)
Strand Homologous protein (Species) E-value Accession Number
SD-178_L15
SD_A*1 2852 10772 1674 + predicted putative disease resistance RPP13-like protein 1 [Malus domestica] 0.0 BBC44083.1
SD_A2 13365 14113 - - No significant similarity found - -
SD_A3 15030 15923 200 - predicted hypothetical protein [Malus domestica] 3e-43 BBC44084.1
SD_A4 16208 28015 1411 + Predicted putative disease resistance RPP13-like protein 1 [Malus domestica] 0.0 BBC44085.1
SD_A5 30109 36250 830 + predicted putative disease resistance protein RGA3 isoform X2 [Malus domestica] 0.0 BBC44088.1
SD_A6 41351 55514 1405 + putative disease resistance RPP13-like protein 1 [Malus domestica] 0.0 XP_028943762.1
SD_A7 56185 57351 304 + uncharacterized protein [Malus domestica] 0.0 BDX99459.1
SD_A8 58456 60591 1079 + hypothetical protein C1H46_000541 [Malus baccata] 0.0 TQE13910.1
SD_A9 63835 66217 115 + predicted uncharacterized protein 103967858 isoform X1 [Malus domestica] 2e-56 BBC44097.1
SD_A10 70209 70907 - + No significant similarity found - -
SD_A11 71821 74184 650 + WEB family protein At5g55860 [Malus domestica] 0.0 XP_008384579.3
SD-241_O01
SD_a*1 1138 5438 1446 + Seven transmembrane MLO family protein [Prunus dulcis] 0.0 BBH03633.1
SD_a2 11018 15235 1405 + putative disease resistance RPP13-like protein 1 [Malus domestica] 0.0 XP_028943762.1
SD_a3 15918 16886 322 + Predicted uncharacterized protein LOC110755101 [Malus domestica] 0.0 BBC44096.1
SD_a4 18191 20326 923 + hypothetical protein C1H46_000541 [Malus baccata] 0.0 TQE13910.1
SD_a5 23629 24682 115 + predicted uncharacterized protein 103967858 isoform X1 [Malus domestica] 1e-40 BBC44097.1
SD_a6 26518 27177 177 + hypothetical protein C1H46_010219 [Malus baccata] 9e-102 TQE04225.1
SD_a7 29180 30589 - + No significant similarity found - -
SD_a8 31512 33879 650 + WEB family protein At5g55860 [Malus domestica] 0.0 XP_008384579.3
SD_a9 34876 38180 469 + predicted uncharacterized protein LOC103447176 [Malus domestica] 0.0 BBC44099.1
SD_a10 39961 44294 323 -
predicted phosphatidylinositol/phosphatidylcholine transfer protein SFH1-like [Malus
domestica]
0.0 BBC44100.1
SD_a11 49599 49822 - + No significant similarity found. - -
SD_a12 50024 50925 161 - hypothetical protein DVH24_041908 [Malus domestica] 7e-61 RXH85140.1
SD_a13 51902 52822 69 + predicted kinesin-like protein KIf1C [Malus domestica] 2e-26 BBC44101.1
SD_a14 55214 57550 611 - serine/threonine-protein kinase D6PK-like [Malus domestica] 0.0 XP_008358895.2
SD_a15 61247 64083 187 + pre-rRNA-processing protein TSR2-like [Malus domestica] 2e-120 BDX99460.1
SD_a16 65070 69437 347 -
predicted DNA-directed RNA polymerases I and III subunit rpac1-like [Malus
domestica]
0.0 BBC44104.1
SD_a17 70743 71722 1416 - putative disease resistance RPP13-like protein 1 [Malus domestica] 0.0 XP_008384580.2
Identification of putative genes in BAC clones using FGENESH.

22. MULTIPLE SEQUENCE
ALIGNMENT AND PREDICTION
OF CONSERVED REGIONS..

23. High similarity
(Resistance Proteins)
High similarity
(Defense Related Protein)

24. High similarity
(Resistance Proteins)
High similarity
(Defense Related Protein)

25. Amino acid sequence alignment of predicted genes of SD_A4,
SD_A6 and SD_a2. Alignment was performed using Clustal omega

26. Amino acid sequence alignment of predicted genes of SD_A9 and SD_a5. Alignment
was performed using Clustal omega
an essential regulator of plant defense pathways

27. MOLECULAR EVOLUTION AND
PHYLOGENETIC ANALYSIS..

28. Phylogenetic tree analysis including genes from
two BAC clones (SD-178_L15 and SD-
241_O01)
R Proteins
Defense related
Prot

29. DOMAIN
SEPARATION AND
MOTIFS ANALYSIS..

30. Identification of functional domains
using NCBI-CDD. (a); target proteins of
BAC clone SD-178_L15. (b); target
proteins of BAC clone SD-241_O01

31. STRUCTURAL CLASSIFICATION OF TARGET
PROTEINS

32. BAC Clone Genes Name Match position (aa) E-value
SD-178_L15
SD_A4
P-loop containing nucleoside triphosphate
hydrolases
165-434 7.52e-62
L domain-like
496-717, 759-901, 913-1165,
1181-1392
1.06e-34, 1.06e-34, 2.01e-16,
2.07e-19
Ribonuclease H-like (Family: Retroviral
integrase, catalytic domain)
1508-1635 3.87e-22
SD_A5
RNI-like 120-251 2.50e-06
L domain-like 254-563 1.71e-30
F-box domain 633-683 1.39e-12
SD_A6
P-loop containing nucleoside triphosphate
hydrolases
406-671 1.46e-63
L domain-like
733-959, 992-1140, 1151-1399,
1361-1639
2.75e-34, 2.75e-34, 6.95e-16,
9.64e-31
SD_A7 Cysteine alpha-hairpin motif 169-202 7.03e-03
SD_A8
DNA/RNA polymerases (Family: Reverse
transcriptase)
163-544 3.95e-33
SD-241_O01
SD_a1
Ribonuclease H-like (Family: Retroviral
integrase, catalytic domain)
509-680 1.42e-43
DNA/RNA polymerases (Family: Reverse
transcriptase)
882-1060,1089-1270 2.30e-29
SD_a2
P-loop containing nucleoside triphosphate
hydrolases
161-425 1.40e-63
L domain-like
487-713,746-894, 5.86e-17,
1.10e-31
1.83e-34, 1.83e-34, 905-1178,
1113-1393
SD_a3 Cysteine alpha-hairpin motif 248-275 2.34e-02
SD_a4
DNA/RNA polymerases (Family: Reverse
transcriptase)
175-542 2.15e-36
Structural classification of target proteins in the Alt region using Superfamily Server.

33. BAC clone Gene level CATH Code Description Match E-value
SD-178_L15
SD_A4
Class 3 Alpha Beta
Probable disease resistance protein At5g66900
(3.80.10.10/FF/1050)
1.5e-28
Architecture 3.80 Alpha-Beta Horseshoe
Topology 3.80.10
Leucine-rich repeat, LRR (right-handed beta-
alpha superhelix)
Homologous
Superfamily
3.80.10.10 Ribonuclease Inhibitor
SD_A5
Class 3 Alpha Beta
Disease resistance-like protein DSC1
(3.80.10.10/FF/1394)
4.0e-16
Architecture 3.80 Alpha-Beta Horseshoe
Topology 3.80.10
Leucine-rich repeat, LRR (right-handed beta-
alpha superhelix)
Homologous
Superfamily
3.80.10.10 Ribonuclease Inhibitor
SD_A6
Class 3 Alpha Beta
Probable disease resistance protein At5g66900
(3.80.10.10/FF/1050)
6.2e-31
Architecture 3.80 Alpha-Beta Horseshoe
Topology 3.80.10
Leucine-rich repeat, LRR (right-handed beta-
alpha superhelix)
Homologous
Superfamily
3.80.10.10 Ribonuclease Inhibitor
SD-241_O01
SD_a1
Class 3 Alpha Beta
Retrovirus-related Pol polyprotein from transposon
297-like Protein (3.30.420.10/FF/32)
4.2e-16
Architecture 3.30 2-Layer Sandwich
Topology 3.30.420 Nucleotidyltransferase; domain 5
Homologous
Superfamily
3.30.420.10
Ribonuclease H-like superfamily/Ribonuclease
H
SD_a2
Class 3 Alpha Beta
Probable disease resistance protein At5g66900
(3.80.10.10/FF/1050)
2.8e-31
Architecture 3.80 Alpha-Beta Horseshoe
Topology 3.80.10
Leucine-rich repeat, LRR (right-handed beta-
alpha superhelix)
Homologous
Superfamily
3.80.10.10 Ribonuclease Inhibitor
Structural classification of target proteins in the Alt region using CATH.

34. Genome And Proteome Analysis of Alternaria alternata
(AM-BAC-14)

35. IN SILICO GENE PREDICTION
AND CHARACTERIZATION..

36. BAC Clone Gene
Transcription
start (bp)
Transcription
end (bp)
Strand Homologus Protein E-value
Accession
Number
AM-BAC-14
AMT1 25795 38886 -
RecName: Full=AM-toxin synthetase AMT1; AltName: Full=Cyclic peptide
synthetase AMT; AltName: Full=Nonribosomal peptide synthetase AMT1;
Short=NRPS AMT1 [Alternaria alternata]
0.0 C9K7B5.1
AMT2 45870 47123 -
RecName: Full=Aldo-keto reductase AMT2; AltName: Full=AM-toxin
biosynthesis protein 2 [Alternaria alternata]
0.0 Q75ZG2.1
AMT3 39935 41495 +
RecName: Full=Cytochrome P450 monooxygenase AMT3; AltName: Full=AM-
toxin biosynthesis protein 3 [Alternaria alternata]
0.0 A7VMU4.2
AMT4 57089 58001 +
RecName: Full=Thioesterase AMT4; AltName: Full=AM-toxin biosynthesis protein
4 [Alternaria alternata]
0.0 A7VMU5.1
AMT5 47664 48886 -
RecName: Full=Transaminase AMT5; AltName: Full=AM-toxin biosynthesis
protein 5 [Alternaria alternata]
0.0 C9K7B6.1
AMT6 49187 50589 +
RecName: Full=3-isopropylmalate dehydrogenase AMT6; AltName: Full=AM-
toxin biosynthesis protein 6 [Alternaria alternata]
0.0 C9K7B7.1
AMT7 51305 53101 -
RecName: Full=Isopropyl malate synthase AMT7; AltName: Full=AM-toxin
biosynthesis protein 7 [Alternaria alternata]
0.0 C9K7B8.1
AMT8 53635 56463 +
RecName: Full=Aconitase AMT8; AltName: Full=AM-toxin biosynthesis protein 8
[Alternaria alternata]
0.0 C9K7B9.1
AMT9 60160 61570 -
RecName: Full=O-methyltransferase AMT9; AltName: Full=AM-toxin
biosynthesis protein 9 [Alternaria alternata]
0.0 C9K7C0.1
AMT10 63243 65945 +
RecName: Full=Nonribosomal peptide synthetase AMT10; AltName: Full=AM-
toxin biosynthesis protein 10 [Alternaria alternata]
0.0 C9K7C1.1
AMTR1 70749 73209 -
RecName: Full=Transcription activator AMTR1; AltName: Full=AM-toxin
biosynthesis regulator 1 [Alternaria alternata]
0.0 C9K7C2.1
Identification of putative genes in BAC clone (AM-BAC-14) using FGENESH.

37. MULTIPLE SEQUENCE
ALIGNMENT AND
PHYLOGENETIC ANALYSIS..

38. Phylogenetic tree analysis including 17 submitted genes from Alternaria alternata isolate (AM-BAC-14)

39. DOMAIN
SEPARATION AND
MOTIFS ANALYSIS..

40. Identification of Functional domains and
Key Motif of target proteins using
MotifFinder. (c); target protein of BAC
clone AM-BAC-14

41. THREE-DIMENSIONAL (3-D)
STRUCTURE PREDICTION..

42. FIRST: CONSTRUCTION OF
INITIAL MODEL USING TARGET-
TEMPLATE ALIGNMENT.
SECOND: REDUCED-LEVEL
STRUCTURE ASSEMBLY AND
REFINEMENT SIMULATIONS.
THIRD: MODEL EVALUATION
AND SELECTION

43. Target protein Servers RMSD TM-Score GDT-TS GDT-HA QMEANDisCo Overall Quality Mol Probity Clash Score Ramachandram Favoured
A-AM
Modrefiner
I-TASSER 2.18 0.9903 0.7471 0.5351 0.59 67.6626 3.36 92.95 83.30%
Alphafold2 2.20 0.9954 0.6462 0.4323 0.64 84.3478 2.27 44.97 97.25%
Robetta 3.50 0.9974 0.5156 0.3523 0.63 79.0941 2.38 53.02 96.90%
Swiss-model 3.11 0.9968 0.6277 0.4211 0.63 83.6331 2.25 45.10 97.36%
Galaxy Web
I-TASSER 2.12 0.94231 0.7515 0.9400 0.62 86.3874 2.579 15.55 87.1%
Alphafold2 2.13 0.90308 0.6555 0.9876 0.65 97.6786 1.641 7.38 99.14%
Robetta 3.57 0.73780 0.5356 0.9910 0.65 95.9578 1.736 8.61 98.5 %
Swiss-model 2.95 0.87896 0.6360 0.9939 0.65 96.7093 1.532 5.25 99.12%
trRosetta
I-TASSER 2.09 0.90873 0.6623 0.4503 0.65 94.3942 1.18 2.18 96.90%
Alphafold2 2.09 0.951 0.6686 0.4576 0.66 92.9204 1.29 2.53 96.21
Robetta 2.11 0.91298 0.6647 0.4537 0.66 92.7817 1.08 1.95 97.42%
Swiss-model 2.06 0.947 0.6540 0.4488 0.66 94.6619 1.06 2.46 97.89%
B-AM
Modrefiner
I-TASSER 1.95 0.9906 0.5195 0.3565 0.60 76.7824 2.83 62.44 90.28%
Alphafold2 2.14 0.9939 0.6051 0.3940 0.65 86.6906 2.29 45.99 97.17%
Robetta 3.40 0.9957 0.4781 0.3142 0.65 79.8198 2.41 54.44 96.82%
Swiss-model 4.25 0.9932 0.5136 0.3361 0.62 67.9417 2.64 64.87 94.88%
Galaxy Web
I-TASSER 1.86 0.72166 0.5321 0.9467 0.63 87.1087 2.141 8.34 92.8%
Alphafold2 2.13 0.88387 0.6182 0.9930 0.67 96.7033 1.512 4.29 99.3%
Robetta 3.44 0.72460 0.4927 0.9969 0.66 94.6886 1.704 8.45 98.4%
Swiss-model 4.32 0.74951 0.5170 0.9780 0.65 88.3549 1.837 8.80 97.2%
trRosetta
I-TASSER 2.07 0.947 0.6547 0.4416 0.67 95.0276 1.30 3.33 97.00%
Alphafold2 2.09 0.944 0.6625 0.4509 0.69 94.7467 0.99 2.14 98.59%
Robetta 2.75 0.946 0.6639 0.4538 0.65 77.1739 2.61 48.63 92.93%
Swiss-model 2.77 0.943 0.6649 0.4528 0.68 94.8435 1.25 3.09 97.17%
C-AM
Modrefiner
I-TASSER 1.81 0.9896, 0.5418 0.3857 0.60 75.6184 3.10 71.57 89.60%
Alphafold2 2.22 0.9957 0.6503 0.4363 0.63 87.4113 2.23 40.52 97.23%
Robetta 2.10 0.9956 0.5068 0.3439 0.61 84.5884 2.44 49.18 96.01%
Swiss-model 2.14 0.9909 0.4966 0.3273 0.61 87.8319 2.05 37.26 98.52%
Galaxy Web
I-TASSER 1.81 0.72692 0.5418 0.9555 0.62 90.6977 2.184 11.59 94.11%
Alphafold2 2.14 0.90324 0.6566 0.9909, 0.64 95.1699 1.558 5.51 99.83
Robetta 3.38 0.73404 0.5146 0.9870 0.63 95.8929 1.766 6.19 97.40%
Swiss-model 3.39 0.77177 0.4976 0.9879 0.62 97.0917 1.551 5.75 98.94%
trRosetta
I-TASSER 2.10 0.91416 0.6717 0.4601 0.65 95.5516 1.18 2.56 97.23%
Alphafold2 2.13 0.91394 0.6654 0.4562 0.65 97.1581 1.20 2.21 96.71%
Robetta 2.79 0.91424 0.6727 0.4650 0.65 95.9507 1.22 2.68 97.05%
Swiss-model 3.04 0.78630 0.0520 0.0302 0.62 91.17 1.33 2.83 96.19%
D-AM
Modrefiner
I-TASSER 2.04 0.9663 0.5704 0.3668 0.54 70.4981 3.03 77.22 89.14%
Alphafold2 2.45 0.9911 0.4027 0.2769 0.55 84.6743 2.02 34.43 98.13%
Robetta 2.89 0.9956 0.5210 0.3129 0.54 83.908 2.52 38.97 92.88%
Swiss-model 2.51 0.9902 0.4102 0.2904 0.55 81.6 2.03 35.14 98.13%
Galaxy Web
I-TASSER 2.65 0.6589 0.5808 0.9117 0.56 82.8794 2.462 13.86 89.14%
Alphafold2 2.34 0.52982 0.4072 0.9833 0.57 98.4375 1.398 2.87 100.00%
Robetta 2.91 0.71457 0.5135 0.9888 0.56 95.7692 1.695 4.06 97.00%
Swiss-model 2.38 0.53326 0.4117 0.9805 0.58 99.5781 1.273 2.15 99.63%
trRosetta
I-TASSER 2.20 0.757 0.4087 0.2665 0.56 93.0502 1.62 3.95 93.26%
Alphafold2 2.78 0.75623 0.5704 0.3548 0.59 91.5663 1.05 1.73 97.38%
Robetta 2.82 0.776, 0.5704 0.3563 0.59 93.0612 1.21 2.96 97.38%
Swiss-model 2.84 0.75801 0.5704 0.3578 0.59 96.4567 1.11 2.71 97.75%

44. Target protein Servers RMSD TM-Score GDT-TS GDT-HA QMEAN Overall Quality Mol Probity Clash Score
Ramachandram
Favoured
AMT2
Modrefiner
I-TASSER 1.34 0.9883 0.9105 0.7751 0.63 81.8942 3.21 75.48 88.22%
AlphaFold2 1.99 0.9944 0.8286 0.6388 0.67 87.1866 2.07 35.15 97.81%
Robetta 1.74 0.9879 0.8261 0.6129 0.65 93.0362 2.31 45.32 96.99%
Swiss-model 1.85 0.9859 0.8445 0.6547 0.67 91.8994 2.28 42.19 96.98%
GalaxyWeb
I-TASSER 1.23 0.97226 0.9256 0.9414 0.65 82.4513 2.528 15.85 87.7%
Alphafold2 1.37 0.93687 0.8294 0.9966 0.68 93.2394 1.573 6.20 98.90%
Robetta 1.73 0.94215 0.8319 0.9877 0.66 89.3855 1.611 7.06 98.1%
Swiss-model 1.41 0.93645 0.8269 0.9904 0.68 96.0784 1.544 5.88 98.9%
trRosetta
I-TASSER 1.17 0.94939 0.8754 0.6856 0.69 93.9655 1.16 2.15 96.99%
Alphafold2 1.21 0.94926 0.8788 0.6948 0.68 93.8375 1.37 3.22 96.16%
Robetta 1.84 0.94801 0.8721 0.6865 0.69 92.6761 1.03 2.15 97.81%
Swiss-model 1.84 0.94787 0.4406 0.2099 0.69 91.8079 1.35 3.23 96.43%
AMT3
Modrefiner
I-TASSER 2.33 0.9581 0.7355 0.5151 0.53 79.5833 2.83 78.41 92.61%
Alphafold2 2.43 0.9944 0.6038 0.3800 0.56 94.5946 2.12 43.49 98.15%
Robetta 2.86 0.9969 0.6189 0.3890 0.57 89.8129 2.38 55.77 97.54
Swiss-model 2.97 0.9861 0.6010 0.3772 0.56 92.6931 2.07 39.15 98.77%
GalaxyWeb
I-TASSER 2.34 0.93007 0.7349 0.9315 0.55 83.3333 2.581 14.32 88.71%
Alphafold2 2.46 0.87253 0.5982 0.9918 0.57 96.875 1.500 3.71 99.0%
Robetta 2.86 0.88483 0.6155 0.9944 0.58 95.2183 1.775 6.52 97.95%
Swiss-model 2.96 0.87496 0.6021 0.9923 0.57 94.9896 1.422 3.84 99.0%
trRosetta
I-TASSER 2.27 0.942 0.6267 0.4018 0.59 95.8159 1.22 3.73 97.74%
Alphafold2 2.30 0.944 0.6306 0.4029 0.59 95.8159 1.11 3.20 98.36%
Robetta 2.73 0.88945 0.6300 0.4063 0.59 96.0417 1.17 3.86 98.56%
Swiss-model 2.28 0.89024 0.6283 0.4018 0.59 96.6667 1.20 3.99 97.95%
AMT4
Modrefiner
I-TASSER 2.13 0.9848 0.8145 0.6222 0.55 77.7778 2.80 64.69 91.12%
AlphaFold2 2.73 0.9879 0.6923 0.5090 0.58 91.2351 1.97 30.59 98.84%
Robetta 2.60 0.9858 0.6867 0.4955 0.58 86.9565 2.51 48.92 97.5%
Swiss-model 2.69 0.9916 0.7002 0.5181 0.57 91.4286 1.99 32.11 98.84%
GalaxyWeb
I-TASSER 2.23 0.91031 0.8326 0.9502 0.56 88.8 2.334 12.03 91.12%
Alphafold2 2.74 0.85828 0.6968 0.9693 0.59 94.3775 1.682 5.52 98.84%
Robetta 1.95 , 0.85553 0.6957 0.9722 0.59 95.6522 2.165 9.78 93.44%
Swiss-model 2.75 0.85716 0.7014 0.9828 0.59 97.541 1.514 4.51 99.23%
trRosetta
I-TASSER 2.61 0.927 0.7070 0.5215 0.60 90.4382 1.24 2.33 96.53%
Alphafold2 2.56 0.927 0.7206 0.5260 0.60 92.0635 1.26 1.81 95.37%
Robetta 1.86 0.918 0.7240 0.5362 0.60 94.8617 1.33 2.07 94.98%
Swiss-model 2.58 0.923 0.7115 0.5147 0.59 96.0317 1.50 2.85 93.44%

45. The best predicted three-dimensional structure
of catalytic domains (A-AM, B-AM, C-AM and
D-AM) of AMT1 protein.

46. The best predicted three-dimensional
structure of AMT2, AMT3 and AMT4 proteins.

47. CONCLUSION..

48. * Through in silico analysis of BAC clones SD-178_L15 and SD-241_O0, we
identified several candidate genes within the Alt region on chromosome 11,
which may contribute to the plant’s response to the pathogen.
* The identification of CC-NB-LRR class R proteins (SD_A4, SD_A5, SD_A6, SD_a2) within
the Alt candidate region supports their potential involvement in recognizing pathogen
effectors and triggering a hypersensitive response (HR). Additionally, the presence of RIN4
(SD_A9, SD_a5) indicates its potential role in plant defense against the Alternaria
alternata apple pathotype.

49. * Additionally, the constructed 3D structural models provide a graphical
illustration of the key motifs involved in AM-toxin production,
establishing the basis for future research on the pathogenicity pathways
of A. alternata and for the inhibition of these proteins.
*Our results will be useful for developing improved disease
management measures, as well as improving our understanding of the
co-evolution of plant defense mechanisms and fungal pathogenicity.

50. ACKNOWLEDGEMENT

51.  Prof. Dr. El-Shawadfi Mansour Mousa
 Prof. Dr. Abd El-Fattah Mondy Zanaty
 Prof. Dr. El-Sayed Abd El-Khalk El-Absawy
 Dr. Waleed Mahmoud Ead
 Dr. Mohamed El-Sayed Mohamed Hasan
 Bioinformatics Department

52. THANK YOU..