Hello,

I am trying to understand the output of HMMSCAN. I went trough the documentation and I understand the lines returned by the program.

In the following example, how can I deduce in which state is the model at each column? For each position in the seq, I would like to extract the probability distribution over the 20 possible AA given by the HMM model, however I don't know whether the model is in a match or insert state.

Query:       d1ux8a_  [L=119]
Description: a.1.1.1 (A:) Protozoan/bacterial hemoglobin {Bacillus subtilis [TaxId: 1423]}
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.9e-32  111.5   0.0    3.2e-32  111.3   0.0    1.0  1  Bac_globin   Bacterial-like globin
    0.00063   19.8   0.0    0.00098   19.2   0.0    1.2  1  Protoglobin  Protoglobin


Domain annotation for each model (and alignments):
>> Bac_globin  Bacterial-like globin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.3   0.0   3.3e-36   3.2e-32       3     120 ..       4     117 ..       2     118 .. 0.94

  Alignments for each domain:
  == domain 1  score: 111.3 bits;  conditional E-value: 3.3e-36
                 HHHHTHHHHHHHHHHHHHHHHHT-CCCCCCGGGTTSSHHHHHHHHHHHHHHHTTSSSHHHHHHSS-.HHHHHTTS--BHHHHHHHHHHHHHHHHHCT-- CS
  Bac_globin   3 ydaiGgeatveelvdrfYervdedeeealseifsgtdlegsreklveFlvqalgGPelYverrGhPrlrkrHapfeitaaerdawlkhlaeAleetgvs 101
                 y+aiG  + + +lvd fYerv++ +   l++if ++dl++   k+ +Fl+q+lgGP+lY+e +GhP+lr+rH+pf+it++ +dawl ++++A++++g +
     d1ux8a_   4 YEAIGE-ELLSQLVDTFYERVASHPL--LKPIF-PSDLTETARKQKQFLTQYLGGPPLYTEEHGHPMLRARHLPFPITNERADAWLSCMKDAMDHVGLE 98
                 999986.99*****************..88887.789999999******************************************************** PP

                 HHHHHHHHHHHHHHHHHHC CS
  Bac_globin 102 sedreeklellealahaaq 120
                  e re  + +le +a ++
     d1ux8a_  99 GEIREFLFGRLELTARHMV 117
                 **99999999999888875 PP