;  SAM: /projects/compbio/experiments/protein-predict/SAM_T08test/bin_freeze/sam/prettyalign v3.5 (July 15, 2005) compiled 04/12/08_09:06:02
;  (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.
; ---------------------------------------------------------------------
; Sequences correspond to the following labels:
; 1 T0460 PF0246, Pyrococcus furiosus, 111 residues
; 2 gi|18976618|ref|NP_577975.1|_1:103 hypothetical protein PF0246 [Pyrococcus furiosus DSM 3638] >gi|18892185|gb|AAL80370.1| hypothetical protein [Pyrococcus furiosus DSM 3638]
; 3 gi|14521894|ref|NP_127371.1|_1:102 hypothetical protein PAB1233 [Pyrococcus abyssi GE5] >gi|5459114|emb|CAB50600.1| Hypothetical protein [Pyrococcus abyssi GE5]
; 4 gi|57641721|ref|YP_184199.1|_1:102 hypothetical protein TK1786 [Thermococcus kodakarensis KOD1] >gi|57160045|dbj|BAD85975.1| hypothetical protein, conserved [Thermococcus kodakarensis KOD1]
; 5 gi|14591662|ref|NP_143749.1|_1:102 hypothetical protein PH1920 [Pyrococcus horikoshii OT3] >gi|3258362|dbj|BAA31045.1| 102aa long hypothetical protein [Pyrococcus horikoshii OT3]
              10        20        30        40        50        60     
              |         |         |         |         |         |     
   1 MNSEVIKEFLEDIGEDYIELENEIHLKPEVFYEVWKYVGEPELKTYVIEDEIVEPGEYDPPEMKY
   2 MNSEVIKEFLEDIGEDYIELENEIHLKPEVFYEVWKYVGEPELKTYVIEDEIVEPGEYDPPEMKY
   3 MNSEVIKEFLEDIGADYIELEGEIHLEPRVFYEVWKYVGEPELKTYVVEDEVVEPGEYDPPEMKY
   4 MHFEVVKEFLEDIGADWIEIEGEIHLDPEVFYEVWKYVGQPELKTYVIEDEVVEPGSYDPPEMKY
   5 MNSEVIKEFLEDIGADYIELEGEIHLEPKVFYEVWKYVGEPELKTYVIEDEIVEPGEYDPPEMRY


         70        80        90       100       110 
         |         |         |         |         | 
   1 TNVKKVKIKKVYFETLDNVRVVTDYSEFQKILKKRGTKLEHHHHHH
   2 TNVKKVKIKKVYFETLDNVRVVTDYSEFQKILKKRGTK--------
   3 TEARKIKIKKVYFETLDGVKVVTDYSDFQKILKETKA---------
   4 TDVKKVKIKKVYFETLDGKKIVTDYSEFQKLVKEKSA---------
   5 TEAKKIKIKKVYFETLDGVKVVTDHSEFQKIIKEMKS---------