Protein Analysis (Beyond BLAST)

1. Protein Analysis (Beyond BLAST) • Basic Protein Data (MW, pI) • Generalized Features • Multiple Sequence Alignments • Fingerprints, Profiles, Domains • Using Structure

2. Multiple Sequence AlignmentsComparison of Methods DIALIGN At         368   LY-------- ---------- --AEVAYHNF APPHVTKNSY FAAILGHNNNPY54             383   AY-------- ---------- --EKWFRTDP RWAKCDEDVF FSELLGHD--VHML             273   HHyqrvshts hgefsfrlpg hlCRIAFHEF RHNGESKAAF RSRVLGHSGGBB003            298   IY-------- ---------- --CKFSYLAF APKNMEMNYW ITKVLGHEPNN15              390   AY-------- ---------- --EMFFRVDP RWKNVDEDVF FMEILGHD--Ecto             304   SH-------- ---------- --RTFk---- --NNCSINIW LTKTLLHE-- At               398   DLETSLSYMT YTL------- ---------- ---------- ----------PY54             411   DPDTQLAYKQ FKL------- ---VNFNPKW TPNISDENPR LAALQELDNDVHML             323   DKSTQNHYEG FELdskveti gvvDMGQNEA DKSYNKQL-- LKHLEQYDATBB003            328   DITTAFHYNR YVL------- ---DNLDDKA DNSLLTLL-- NQRIYTYVRRN15              418   DENTQLHYKQ FKL------- ---ANFSRTW RPEVGDENTR LVALQKLDDEEcto             326   ALDTSIFYSR FRI------- ---DKCStnr gewaf----- ---------- ClustalW PY54 FRTDPRWAKCDEDVFFSELLGHD--DPDTQLAYKQFKLVNFNPKWTPNISDENPRLAALQ 456 N15 FRVDPRWKNVDEDVFFMEILGHD--DENTQLHYKQFKLANFSRTWRPEVGDENTRLVALQ 452 Ecto K------NNCSINIWLTKTLLHE--ALDTSIFYSRFRIDKCS------------------ 342 VHML R-----HNGESKAAFRSRVLGHSGGDKSTQNHYEGFELDSKVETIG-------------- 343 At AP-----PHVTKNSYFAAILGHNNNDLETSLSYMTYTLPEDR------------------ 414 BBB03 AP-----KNMEMNYWITKVLGHEPNDITTAFHYNRYVLDNLD------------------ 344

3. Multiple Sequence Alignments • Method of choice depends upon goal of alignment • FMI – Thompson et al., 1999. Nucleic Acids Research 27:2682-90. A comprehensive comparison of multiple sequence alignment programs.

4. Multiple Sequence Alignment Protein/Position within SequenceSequence YNZ5_YEAST/135-152           RLCYNCNETGHISKDCPKO65639/100-117               SGCYNCGELGHISKDCGIQ94821/1600-1617             KGCFNCGEEGHQSRECTKBYR3_SCHPO/17-34             PRCYNCGENGHQARECTKO44758/570-587               RGCHNCGEEGHISKECDKGLH1_CAEEL/262-279           RGCFNCGEQGHRSNECPNO96068/51-68                 KGCFKCGEEGHMSRECPQHEXP_LEIMA/43-60             TTCFRCGEEGHMSRECPNO46363/5-22                  VTCYKCGEAGHMSRECPKHEXP_LEIMA/196-213           RKCYKCGESGHMSRECPS

5. Pattern Searches Ultimate Goal Atwood, 2000, Int. J. Biochem. Cell Biol. 32:139-55

6. Pattern Searches 3 Levels Atwood, 2000, Int. J. Biochem. Cell Biol. 32:139-55

7. Pattern Searches Hidden Markov Model Atwood, 2000, Int. J. Biochem. Cell Biol. 32:139-55