Slide 1

Visualise conservationEMBO Workshop, Cape Town, 2014Colour -> BLOSUM621.

1Reduce redundancyEdit-> Remove Redundancy1.PICK 80%2.

2EMBO Workshop, Cape Town, 2014

3Edit-> Remove Empty Columns1.EMBO Workshop, Cape Town, 2014

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EMBO Workshop, Cape Town, 2014Define boundaries5Define boundariesColour -> Hydrophobicity1.

EMBO Workshop, Cape Town, 20146

TUM, January 20132KX7 model 1

EEVTESER7

CLICK on residue number bar to select column1.Edit -> Remove right2.EMBO Workshop, Cape Town, 2014Trim alignment8

EMBO Workshop, Cape Town, 2014Trim alignmentCLICK on residue number bar to select column1.Edit -> Remove left2.9

Save SEED alignmentFile -> Save as RcsD-ABL-SEED-ali.fasta 1.EMBO Workshop, Cape Town, 201410

Create HMM and run against database(s)EMBO Workshop, Cape Town, 2014CLICK on Start1.11

Create HMM and run against database(s)EMBO Workshop, Cape Town, 2014CLICK on Choose File1.Choose RcsD-ABL-SEED-ali.fasta 2.12

First run against RP75 to see if anything has changedEMBO Workshop, Cape Town, 2014CLICK on rp751.13First run against RP75 to see if anything has changed

BEFORE

NOW14

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Now we run against UniProtKBEMBO Workshop, Cape Town, 201417Check ScoresEMBO Workshop, Cape Town, 2014

18Check Low ScoresEMBO Workshop, Cape Town, 2014

19Define significance thresholdEMBO Workshop, Cape Town, 2014

20Check taxonomic distributionEMBO Workshop, Cape Town, 2014

21Check taxonomic distributionEMBO Workshop, Cape Town, 2014

22Check architectures

23Save HMMEMBO Workshop, Cape Town, 2014

24EMBO Workshop, Cape Town, 2014Job done?25

TUM, January 2013

2KX7Pick a target regionEMBO Workshop, Cape Town, 2014Schme et al. Structure 2011 26

TUM, January 2013

2KX7Pick a target regionEMBO Workshop, Cape Town, 2014RcsD_ABL (PF16359)Schme et al. Structure 2011 27

TUM, January 2013

2KX7Pick a target regionEMBO Workshop, Cape Town, 2014RcsD_ABL (PF16359)Schme et al. Structure 2011 28EMBO Workshop, Cape Town, 2014

Schme et al. Structure 2011 2KX7Job done?2AYY29EMBO Workshop, Cape Town, 2014Job done?

30EMBO Workshop, Cape Town, 2014ExerciseRun the UNIPROT ID: Q820A8with the hmmer website (2 iterations) and observe results31EMBO Workshop, Cape Town, 2014ExerciseRun the UNIPROT ID: Q820A8with the hmmer website (2 iterations) and observe results

Run the Q820A8-PASTA-domain.fastawith the hmmer website (2 iterations) and observe results32EMBO Workshop, Cape Town, 2014ExerciseRun the UNIPROT ID: Q820A8with the hmmer website (2 iterations) and observe results

Run the this portion of the Q820A8 sequenceVTLSDYSGISYDNAVSRLIALGIPESQIKRVDEESDKVEKDTVISQEPASGTAVDPKNDTITLHVSKwith the hmmer website (2 iterations) and observe results33EMBO Workshop, Cape Town, 2014AcknowledgementsRob Finn (Protein Family Team Leader)

The Pfam Team:Penny CoggillRuth EberhardtJaina MistryJohn TateIlias Lavidas

Alex Bateman (Protein sequence resources cluster)Sean Eddy -> HMMER3 (Janelia Farm)Erik Sonnhammer (Stockholm University)

All organisers of the EMBO course, trainers and trainees

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