;  SAM: prettyalign v3.5 (May 1, 2004) compiled 05/13/04_16:24:56
;  (c) 1992-2001 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-T2K, 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, et al., What is the value added by human intervention in protein
;  structure prediction, Proteins: Stucture, Function, Genetics 45(S5):86--91, 2001.
; A. Krogh et al., Hidden Markov models in computational biology:
;  Applications to protein modeling, JMB 235:1501-1531, Feb 1994.
; ---------------------------------------------------------------------
              10             20                      30        40     
               |              |                       |         |     
T0228 MSEPVIKSLLDTdmykiTMHAAVFTNFPdvtvtykytnrssqLTFNKEAINWLKEQFSYLGNLR
1qpoA GLSDWELAAARA.....AIARGLDEDLR..............YGPDVTTLATVPASATTTASLV


         50        60        70        80                  90       10
          |         |         |         |                   |         
T0228 FTEEEIEYLKQEIPYLPSAYIKYISSSNYKLHPEEQISFTSEEIegkpthyklkILVSGSWKDT
1qpoA TREAGVVAGLDVALLTLNEVLGTNGYRVLDRVEDGARVPPGEAL..........MTLEAQTRGL


      0       110       120                          130       140    
      |         |         |                            |         |    
T0228 ILYEIPLL------SLISEAYFKFVDIdwdyenqleqaekkaetlfDNGIRFSEFGTRRRRSlk
1qpoA LTAERTMLNLVGHLSGIATATAAWVDA...................VRGTKAKIRDTRKTLP..


             150                 160           170       180          
               |                   |             |         |          
T0228 aqDLIMQGIMKAVNGnpdrnkslllGTSNIlfakKYGVKPIGTVAHEWVMGVASISEdylhank
1qpoA ..GLRALQKYAVRTG..........GGVNH....RLGLGDAALIKDNHVAAAGSVVD.......


           190        200         210           220                   
             |          |           |             |                   
T0228 nAMDCWINTFGAkNAGLALTDTFgtDDFLKSFRPpysdAYVGVRQDSGdpveytkkishhyhdv
1qpoA .ALRAVRNAAPD.LPCEVEVDSL..EQLDAVLPE....KPELILLDNF................


                                                                    23
                                                                      
T0228 lklpkfskiicysdslnvekaityshaakengmlatfgigtnftndfrkksepqvksePLNIVI
1qpoA ..........................................................AVWQTQ


      0       240       250            260       270       280      
      |         |         |              |         |         |      
T0228 KLLEVNGNHA----IKISDNLgknmgDPATVKRVKEE------LGYTERSWSGDNEAHRWtz
1qpoA TAVQRRDSRAPTVMLESSGGL.....SLQTAATYAETGVDYLAVGALTHSVRVLDIGLDM..