hmmpfam - search one or more sequences against HMM database
HMMER 2.3.2 (Oct 2003)
Copyright (C) 1992-2003 HHMI/Washington University School of Medicine
Freely distributed under the GNU General Public License (GPL)
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HMM file:                 /home/genome/SCOP/1.73/Scop1.73.bin
Sequence file:            /home/genome/FASTA/gib_20655.fasta
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Query sequence: AAL64909.1
Accession:      [none]
Description:    paer1 AAL64909.1 GIB00076CH01 "conserved hypothetical protein"

Scores for sequence family classification (score includes all domains):
Model    Description                                    Score    E-value  N 
-------- -----------                                    -----    ------- ---
0039893  alpha/beta knot                                137.8    2.1e-40   1
0039892  Nucleic acid-binding proteins                   28.8    2.1e-11   1

Parsed for domains:
Model    Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
-------- ------- ----- -----    ----- -----      -----  -------
0039893    1/1       2   262 ..     1   192 []   137.8  2.1e-40
0039892    1/1      92   167 ..     1    71 []    28.8  2.1e-11

Alignments of top-scoring domains:
0039893: domain 1 of 1, from 2 to 262: score 137.8, E = 2.1e-40
                   *->lsrktvsvaiPtsildnakslelktylagqiaRaaaiFgvdeiviyd
                           +s+aiP+ +l+++ +   k +++g++aRaaaiF+ ++i+iy+
  AAL64909.1     2    -----FSIAIPHDFLSEIPDEAGKVRKLGYLARAAAIFKAEYIIIYH 43   

                   dd..ledeakllaslleyletPqylrkllfpisnelkfagllppLdilph
                    ++   ++ ++  ++leyl+tP+ylrk +++i n lk+agllppL+i +h
  AAL64909.1    44 YGtpRREDIDFAKTVLEYLVTPPYLRKKVYKIDNRLKLAGLLPPLKIPSH 93   

                   lvidlls..glrealv..................................
                   +v  + ++ ++re++v+  + ++  +++   +++++ + + + +   + +
  AAL64909.1    94 TVPVEPRigEIREGIVerwdgyysliyigggkyakvpkpypigtrllvri 143  

                   ...................................dagvdvligtsedge
                   + ++   +++ ++++  +  ++  +++++   ++  +g+d++i+t  +g+
  AAL64909.1   144 egttsrpdtyraavyrgappdywgykidvrplqnlSEGFDTVILTGKEGK 193  

                   plssakdelatrlrkfrgvlvvfggplgglpevl.......fdlvvntvp
                    +++ak +++      +++lvvfggp++g++e++ ++  + +  ++n++p
  AAL64909.1   194 SICEAKPKIG------KKTLVVFGGPRKGVDEIFreaglepPGELINFAP 237  

                   gqgsrtlRtEeallaalsalnylnkPhhlrkdeklleyreGvvldrsgkgtlvdvGldklvliekklepgtr
                      +h +  +++++e+reG+v +  g  +l+ +G  k + + k  + gtr
  AAL64909.1    92    SHTVPVEPRIGEIREGIVERWDGYYSLIYIGGGKYAKVPKPYPIGTR 138  

                   vtvkl.....lkllkgllvspaePglyWG