Protein Analysis Beyond BLAST Basic Protein Data MW

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

Multiple Sequence Alignments Comparison of Methods DIALIGN At PY 54 VHML BB 003 N 15 Ecto 368 383 273 298 390 304 LY-------AY-------HHyqrvshts IY-------AY-------SH---------hgefsfrlpg -------------- --AEVAYHNF --EKWFRTDP hl. CRIAFHEF --CKFSYLAF --EMFFRVDP -- RTFk---- APPHVTKNSY RWAKCDEDVF RHNGESKAAF APKNMEMNYW RWKNVDEDVF --NNCSINIW FAAILGHNNN FSELLGHD-RSRVLGHSGG ITKVLGHEPN FMEI LGHD-LTKTLLHE-- At PY 54 VHML BB 003 N 15 Ecto 398 411 323 328 418 326 DLE TSLSYMT DPD TQLAYKQ DKS TQNHYEG DIT TAFHYNR DEN TQLHYKQ ALDTSIFYSR YTL------FKL------FELdskveti YVL------FKL------FRI-------VNFNPKW gvv. DMGQNEA ---DNLDDKA ---ANFSRTW ---DKCStnr -----TPNISDENPR DKSYNKQL-DNSLLTLL-RPEVGDENTR gewaf-----LAALQELDND LKHLEQYDAT NQRIYTYVRR LVALQKLDDE ----- Clustal. W PY 54 N 15 Ecto VHML At BBB 03 FRTDPRWAKCDEDVF FSELLGHD--DPDTQLAYKQFKLVNFNPKWTPNISDENPRLAALQ FRVDPRWKNVDEDVF FMEILGHD--DENTQLHYKQFKLANFSRTWRPEVGDENTRLVALQ K------NNCSINIW LTKTLLHE--ALDTSIFYSRFRIDKCS---------R-----HNGESKAAFRSRV LGHSGGDKSTQNHYEGFELDSKVETIG-------AP-----PHVTKNSY FAAILGHNNNDLETSLSYMTYTLPEDR---------AP-----KNMEMNYW ITKVLGHEPNDITTAFHYNRYVLDNLD--------- 456 452 343 414 344

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.

Multiple Sequence Alignment Protein/Position within Sequence YNZ 5_YEAST/135 -152 O 65639/100 -117 Q 94821/1600 -1617 BYR 3_SCHPO/17 -34 O 44758/570 -587 GLH 1_CAEEL/262 -279 O 96068/51 -68 HEXP_LEIMA/43 -60 O 46363/5 -22 HEXP_LEIMA/196 -213 Sequence RLCYNCNETGHISKDCPK SGCYNCGELGHISKDCGI KGCFNCGEEGHQSRECTK PRCYNCGENGHQARECTK RGCHNCGEEGHISKECDK RGCFNCGEQGHRSNECPN KGCFKCGEEGHMSRECPQ TTCFRCGEEGHMSRECPN VTCYKCGEAGHMSRECPK RKCYKCGESGHMSRECPS

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

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

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