;  SAM: /projects/compbio/programs/hmm-server-2.0/bin/i686/prettyalign v3.2.1 (Noverber 14, 2000) compiled 11/17/00_00:59:04
;  (c) 1992-2000 Regents of the University of California, Santa Cruz
;
;          Sequence Alignment and Modeling Software System
;         http://www.cse.ucsc.edu/research/compbio/sam.html
;
; ----------------- Citations (SAM, SAM-T99, HMMs) --------------------
; R. Hughey, A. Krogh, Hidden Markov models for sequence analysis:
;  Extension and analysis of the basic method, CABIOS 12:95-107, 1996.
; K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting
;  remote protein homologies, Bioinformatics 14(10):846-856, 1999.
; A. Krogh et al., Hidden Markov models in computational biology:
;  Applications to protein modeling, JMB 235:1501-1531, Feb 1994.
; ---------------------------------------------------------------------
; Sequences correspond to the following labels:
; 1 T0197
; 2 1gm6A
; 3 1ew3A
                 10        20        30         40             50      
                 |         |         |          |              |      
   1 ahhHHHHGSEVEIK---FKIKLEDFLHTLNTFNPEFvRYEEQEDVYFEVPrpkllRIRGVHNLkK
   2 ...HKEAGQDVVTSNFDASKIAGEWYSILLASDAKE.NIEENGSMRVFVE.....HIRVLDNS.S
   3 ...-------VAIRNFDISKISGEWYSIFLASDVKE.KIEENGSMRVFVD.....VIRALDNS.S


         60        70         80        90        100            110   
         |         |          |         |          |              |   
   1 YYLTFKEILDENNEEFYEVEFEI.GDFEKAVEVFKRLGFKIQaTIKKKRWVYkl6vtLEVNRVEG
   2 LAFKFQRKVNGECTDFYAVCDKV.GDGVYTVAYYGENKFRLL.EVNYSDYVI.....LHLVDVNG
   3 LYAEYQTKVNGECTEFPMVFDKTeEDGVYSLNYDGYNVFRIS.EFENDEHII.....LYLVNFDK


          120       130       140       150       160       170      
           |         |         |         |         |         |      
   1 IGDFVDIEVISDSPE---EAKEKIWEVAKMLGLKEEDV----EPRLYLELINELSGRSS....
   2 DKTFQLMEFYGRKPDVEPKLKDKFVEICQQYGIIKENIIDLTKIDRCFQLRGSGGVQESsae.
   3 DRPFQLFEFYAREPDVSPEIKEEFVKIVQKRGIVKENIIDLTKIDRCFQLRG-------....