HMM length of domain: 55 aa

c-Evalue (conditional Evalue): It is an attempt to measure the statistical significance of each domain, given that we’ve already decided that the target sequence is a true homolog. It is the expected number of additional domains we’d find with a domain score this big in the set of sequences reported in the top hits list, if those sequences consisted only of random nonhomologous sequence outside the region that sufficed to define them as homologs.
i-Evalue (independent Evalue): The significance of the sequence in the whole database search, if this were the only domain we had identified. 
Domain annotation for each sequence:
#	score	bias	c-Evalue	i-Evalue	hmmfrom	hmm to	alifrom	ali to
--	-----	----	--------	--------	-------	------	-------	------
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
1	57.8	0.9	2e-18	7.1e-16	1	54	48	98
2	4.8	0.1	0.072	25	7	29	183	205
3	-1.9	0.0	9.3	3.3e+03	44	55	285	296

  Alignments for each domain:
  == domain 1  score: 57.8 bits;  conditional E-value: 2e-18
                   CHHHHHHHHHHHHHHHHHHHHHHHHCSCCCH.TTSS-STHHHHHHHHHHHHHHH CS
           bHLH  1 rRtahnerErrRRdriNdafeeLrellPkaskakskKlsKaeiLekAveYIkqL 54
                   rR+ +n +ErrR+++iN +f+ Lr+llP     +++KlsKa+iL+++ eYI  L
  KWMTBOMO07379 48 RREIANSNERRRMQSINAGFQALRTLLPRH---EGEKLSKAAILQQTAEYIYNL 98
                   79999************************9...9*****************887 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.072
                    HHHHHHHHHHHHHHHHHHHCSCC CS
           bHLH   7 erErrRRdriNdafeeLrellPk 29 
                    e Err R+ + ++f+ L + + +
  KWMTBOMO07379 183 EQERRLRRLLAERFNALETQVYP 205
                    78***************998866 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 9.3
                    HHHHHHHHHHHH CS
           bHLH  44 LekAveYIkqLq 55 
                    Le  ve I++L+
  KWMTBOMO07379 285 LETIVEAIRHLE 296
                    788899999995 PP