;  SAM: prettyalign v3.5 (May 1, 2004) compiled 07/27/04_17:12:31
;  (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        50        60  
                 |         |         |         |         |         |  
T0247 ..MAQQTPLYEQHTLCGARMVDFHGWMMPLHYGSQIDEHHAVRTDAGMFDVSHMTIVDLRGSRT
1nrkA gsHMAFTPFPPR--------QPTASA----------------RLPLTLMTLDDWALATITGADS


            70        80        90       100       110       120      
             |         |         |         |         |         |      
T0247 REFLRYLLANDVAKLTKSGKALYSGMLNASGGVIDDLIVYYFTEDFFRLVVNSATREKDLSWIT
1nrkA EKYMQGQVTADVSQM-AEDQHLLAAHCDAKGKMWSNLRLFRD-GDGFAWIERRSVREPQLTELK


       130       140       150       160       170       180       190
         |         |         |         |         |         |         |
T0247 QHAEPFGIEITVRDDLSMIAVQGPNAQAKAATLFNDAQRQAVEGMKPFFGVQAGDLFIATTGYT
1nrkA KYAVFSKVTIAPDDERVLLGVAGFQARAALANLFSELPSKEKQ----V--VKEGATTLLWFEHP


             200       210       220       230       240       250    
               |         |         |         |         |         |    
T0247 GEAGYEIALPNEKAADFWRALVEAGVKPCGLGARDTLRLEAGMNLYGQEMDETISPLAANMGWT
1nrkA AE-RFLIVTDEATANMLTDKLRG-EAELNNSQQWLALNIEAGFPVIDAANSGQFIPQATNLQAL


         260       270         280       290       300       310      
           |         |           |         |         |         |      
T0247 IAWEPADRDFIGREALEVQREHGT..EKLVGLVMTEKGVLRNELPVRFTDAQGNQHEGIITSGT
1nrkA GGISFKKGCYTGQEMVARAKFRGAnkRALWLLAGSASRLPEAGEDLELKMGENWRRTGTVLAAV


       320       330       340       350       360    
         |         |         |         |         |    
T0247 FSPTLGYSIALARVPEGIGETAIVQIRNREMPVKVTKPVFVRNGKAVA
1nrkA K-LEDGQVVVQVVMNNDMEPDSIFRVRDDANTLHIEPLPYSLE-----