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Hmms building: Sco PriA aa seq

seqs.a2m Alignment editing Elimination of redundancy w0.5 CR filtering

w0.5

a2m

1st hmm

hmmscore

Initial training set: Phylobook sequences: 558 seqs

seqs.a2m

seqs.a2m

Alignment editing Elimination of redundancy w0.5 CR filtering

2nd hmm

a2m

hmmscore

2nd trainig set: 548 seqs

Alignment editing Elimination of redundancy CR filtering

a2m

3rd hmm

‌

hmmscore

3rd trainig set: 538 seqs

w0.5

nth hmm

hmmscore

nth trainig set: seqs

Stop Criteria Top 10 hits Remove hits from training set

Top 10 hits Remove hits from training set

Top 10 hits Remove hits from training set


UniProt database scoring 1st hmm

Top 100 hits using 1st hmm 2nd hmm

Top 100 hits using 2nd hmm

3rd hmm

Top 100 hits using 3rd hmm

4th hmm

Top 100 hits using 4th hmm

5th hmm

Top 100 hits using 5th hmm

6th hmm

calibration

Top 100 hits using 6th hmm

• Each model was calibrated and used to score a subset of the UniProt database (sequences 201-300 aa in length) • The top 100 hits of each scoring were retrieved. • 108 sequences were left in a NR set • The scores for each sequence for each iteration were plotted analyzed `


Actinobacteria

PriA

PriA? & neoHisA


Sequences used for each hmm Ids file model2.ids P16250 Streptomyces coelicolor Q47QS4 Thermobifida fusca Q5YYP5 Nocardia farcinica A1T8W5 Mycobacterium vanbaalenii A6WCU8 Kineococcus radiotolerans A0LTS5 Acidothermus cellulolyticus

Ids file model3.ids P16250 Streptomyces coelicolor Q47QS4 Thermobifida fusca A6WCU8 Kineococcus radiotolerans A0LTS5 Acidothermus cellulolyticus A4FLL9 Saccharopolyspora erythraea B1MBX5 Mycobacterium abscessus Q9CC56 Mycobacterium leprae

Ids file model4.ids P16250 Streptomyces coelicolor Q47QS4 Thermobifida fusca Q2J8L2 Frankia sp A6WCU8 Kineococcus radiotolerans A0LTS5 Acidothermus cellulolyticus A4FLL9 Saccharopolyspora erythraea B1MBX5 Mycobacterium abscessus A0JUZ7 Arthrobacter sp B1VDA6 Rhodococcus erythropolis A8LX58 Salinispora arenicola A1SL57 Nocardioides sp Q4JW54 Corynebacterium jeikeium Q9CC56 Mycobacterium leprae

Ids file model5_cr.ids P16250 Streptomyces coelicolor Q47QS4 Thermobifida fusca Q2J8L2 Frankia sp A6WCU8 Kineococcus radiotolerans A0LTS5 Acidothermus cellulolyticus A4FLL9 Saccharopolyspora erythraea B1MBX5 Mycobacterium abscessus A0JUZ7 Arthrobacter sp B1VDA6 Rhodococcus erythropolis A8LX58 Salinispora arenicola A1SL57 Nocardioides sp A5CSK6 Clavibacter michiganensis A4AHK5 marine actinobacteria B1TVC5 Micrococcus luteus PRIA_ACTNA Actonomyces naeslundi Q4JW54 Corynebacterium jeikeium Q9CC56 Mycobacterium leprae A3TLY4 Janibacter sp Q6AE15 Leifsonia xyli

Ids file model6_cr.ids P16250 Streptomyces coelicolor Q47QS4 Thermobifida fusca Q2J8L2 Frankia sp A6WCU8 Kineococcus radiotolerans A0LTS5 Acidothermus cellulolyticus A4FLL9 Saccharopolyspora erythraea B1MBX5 Mycobacterium abscessus A0JUZ7 Arthrobacter sp B1VDA6 Rhodococcus erythropolis A8LX58 Salinispora arenicola A1SL57 Nocardioides sp A5CSK6 Clavibacter michiganensis A4AHK5 marine actinobacteria B1TVC5 Micrococcus luteus PRIA_ACTNA Actinomyces naeslundi Q4JW54 Corynebacterium jeikeium Q9CC56 Mycobacterium leprae A3TLY4 Janibacter sp Q6AE15 Leifsonia xyli Q8G4S5 Bifidobacterium longum Q6A8L1 Propionibacterium acnes Q7N8D1 Photorhabdus luminescens A7BD07 Actinomyces odontolyticus B1I557 Desulforudis audaxviator Q2RGW1 Moorella thermoacetica

Ids file model7_cr.ids P16250 Streptomyces coelicolor Q47QS4 Thermobifida fusca Q2J8L2 Frankia sp A6WCU8 Kineococcus radiotolerans A0LTS5 Acidothermus cellulolyticus A4FLL9 Saccharopolyspora erythraea B1MBX5 Mycobacterium abscessus A0JUZ7 Arthrobacter sp B1VDA6 Rhodococcus erythropolis A8LX58 Salinispora arenicola A1SL57 Nocardioides sp A5CSK6 Clavibacter michiganensis A4AHK5 marine actinobacteria B1TVC5 Micrococcus luteus PRIA_ACTNA Actinomyces naeslundi Q4JW54 Corynebacterium jeikeium Q9CC56 Mycobacterium leprae A3TLY4 Janibacter sp Q6AE15 Leifsonia xyli Q8G4S5 Bifidobacterium longum Q6A8L1 Propionibacterium acnes Q7N8D1 Photorhabdus luminescens A7BD07 Actinomyces odontolyticus O35006 Bacillus subtilis A5CZ74 Pelotomaculum thermopropionicum B1I557 Desulforudis audaxviator Q2B721 Bacillus sp A4ISR3 Geobacillus thermodenitrificans B0C904 Acaryochloris marina Q2RGW1 Moorella thermoacetica B1SQW0 Geobacillus sp P74561 Synechocystis sp A4J708 Desulfotomaculum reducens B0TDM8 Heliobacterium modesticaldum A0YW53 Lyngbya sp

summary  

test for issuu

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