;  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 1kpf
; 2 1rzyA
; 3 4rhn
; 4 1fit
; 5 2fhi
; 6 1emsA
               10        20        30        40        50        60    
               |         |         |         |         |         |    
   1 xADEIAKAQVARPGGDTIFGKIIRKEIPAKIIF-EDDRCLAFHDISPQAPTHFLVIPKKHISQIS
   2 mADEIAKAQVARPGGDTIFGKIIRKEIPAKIIF-EDDQCLAFHDISPQAPTHFLVIPKKHISQIS
   3 .----------RPGGDTIFGKIIRKEIPAKIIF-EDDQCLAFHDISPQAPTHFLVIPKKHISQIS
   4 .----------------MSFRFGQHLIKPSVVFLKTELSFALVNRKPVVPGHVLVCPLRPVERFH
   5 .----------------MSFRFGQHLIKPSVVFLKTELSFALVNRKPVVPGHVLVCPLRPVERFH
   6 .RSDLYTLHINEKSSETGGLKFARFNIPADHIFYSTPHSFVFVNLKPVTDGHVLVSPKRVVPRLT


          70           80        90       100       110       120      
          |            |         |         |         |         |      
   1 VAEDDDeslLGHLMIVGKKCAADLGLN---KGYRMVVNEGSDGGQSVYHVHLHVLGGRQMHWPPG
   2 AAEDADeslLGHLMIVGKKCAADLGLK---KGYRMVVNEGSDGGQSVYHVHLHVLGGRQMNWPPG
   3 AAEDADeslLGHLMIVGKKCAADLGLK---KGYRMVVNEGSDGGQSVYHVHLHVLGGRQMNWPPG
   4 DLRPDE...VADLFQTTQRVGTVVEKHFHGTSLTFSMQDGPEAGQTVKHVHVHVLPRKAGDFHRN
   5 DLRPDE...VADLFQTTQRVGTVVEKHFHGTSLTFSMQDGPEAGQTVKHVNVHVLPRKAGDFHRN
   6 DLTDAE...TADLFIVAKKVQAMLEKHHNVTSTTICVQDGKDAGQTVPHVHIHILPRRAGDFGDN


        130       140        150       160  
         |         |          |         |  
   1 -.--------------.-------------------..
   2 -.--------------.-------------------..
   3 -.--------------.-------------------..
   4 DsIYEELQKHDKEDFPaSWRSEEEMAAEAAALRVYFq.
   5 DsIYEELQKHDKEDFPaSWRSEEEMAAEAAALRVYFq.
   6 E.IYQKLASHDKEPER.KPRSNEQMAEEAVVYRNLM..