Coding sequences for Maryland HMM

[nignatiadis]

We still need to create a HMM for adenylation domains based on (Beer et al., 2014) boundaries and Maryland seed domains.

In order to achieve this, while also extending the database at the same time, we should add the coding sequences of the following adenylation domains to the database. Again, it would be great if someone (non-Ilia) could work on this starting from tomorrow. @nilsigem many of these should already be in the database, could you check which?

• [x] CssA-M2-MeLeu ( cyclosporin synthetase)
• [x] CssA-M8-MeLeu
• [x] CssA-M3-MeLeu
• [x] CssA-M10-MeLeu
• [x] CssA-M1-dAla id: 251
• [x] CssA-M4-MeVal
• [x] CssA-M9-Val
• [x] CssA-M11-Ala
• [x] CssA-M7-MeGly
• [x] CssA-M5-MBmt
• [x] CssA-M6-Avu
• [x] Esyn1-M2-MeVal (enniatin synthetase)
• [x] BacA-M5-Ile (bacitracin synthetase)
• [x] BacC-M1-Ile id:233
• [x] BACA-M1-ILE
• [x] FenB-M1-Ile (fengycin synthetase)
• [x] FenE-M2-Val
• [x] BacB-M2-Orn (bacitracin synthetase) BacB7A
• [x] FenC-M2-Orn (fengycin synthetase)
• [x] AngR-M1-Cys (anguibactin synthetase)
• [x] MbtB-M1-Ser/Thr (mycobactin synthetase)
• [x] FenA-M3-Tyr (fengycin synthetase)
• [x] FenD-M1-Tyr (fengycin synthetase)
• [x] BacC-M3-His (bacitracin synthetase) id:240
• [x] ACMB-M1-THR (actinomycin synthetase)
• [x] Cda1-M2-Thr (calcium-dependent antibiotic) id:560
• [x] FxbC-M2-Thr (exochelin synthetase)
• [x] FenD-M2-Thr (fengycin synthetase)
• [x] ACMB-M2-VAL (actinomycin synthetase)
• [x] Cda1-M6-pHPG (calcium-dependent antibiotic)
• [x] Cda1-M3-Trp id:563
• [x] Cda3-M2-Trp
• [x] BacC-M2-Phe (bacitracin synthetase) id:236
• [x] Cda1-M4-Asp (calcium-dependent antibiotic) id:566
• [x] Cda1-M5-Asp id:569
• [x] Cda2-M1-Asp
• [x] Cda2-M3-pAsn
• [x] Cda3-M1-MeGlu
• [x] FxbC-M1-Orn (exochelin synthetase)
• [x] FxbC-M3-Orn
• [x] Cda1-M1-Ser (calcium-dependent antibiotic)
• [x] FxbC-M4-?? (exochelin synthetase)
• [x] EntF-M1-Ser (enterobactin synthetase)
• [x] FenC-M1-Glu (fengycin synthetase)
• [x] FenE-M1-Glu (fengycin synthetase)
• [x] FenA-M2-Glu (fengycin synthetase)
• [x] FxbB-M1-Orn (exochelin synthetase)
• [x] MbtE-M1-Lys (mycobactin synthetase))
• [x] BacA-M4-Glu (bacitracin synthetase)
• [x] Cda2-M2-Gly
• [x] BacA-M2-Cys
• [x] BacA-M3-Leu
• [x] BacB-M1-Lys id:226
• [x] FenA-M1-Pro
• [x] BacC-M4-Asp -> BacC11A
• [x] BacC-M5-Asn -> BacC12A
• [x] FxbB-M2-bAla
• [x] CmaA-M1-aIle
• [x] Esyn1-M1-dHIV (enniatin synthetase)

Also see the following: http://nrps.igs.umaryland.edu/nrps/instructions.html

[Hetitus]

already in the database: Fen B-E (Fen A is missing) B.subtilis Acm (A-C) - Streptomyces anulatus AngR - Vibrio anguillarum cdaPSI - Streptomyces coelicolor Bac A-C Bacillus licheniformis esyn - Fusarium equiseti fxb B-C Mycobacterium smegmatis

if I checked this correctly we're currently missing CssA (fungus Tolypocladium inflation Gams) ; Mbt (Mycobacterium tuberculosis ); EntF (Escherichia coli); Cma(?) and FenA Let's see if I can find one of the genomes :dart: