The alignment they used to build the HMM is included as supplementary file 8 in the paper you cite:
Multiple amino acid sequence alignment of RNH genes and domains from diverse taxa constructed and used for the phylogenetic reconstruction in the present study. (TXT 45 kb)
So, you can download that alignment and then use a tool like hmmbuild (part of HMMER) to build the HMM profile:
hmmbuild model.hmm 13100_2017_87_MOESM8_ESM.txt
The command above will create the file model.hmm
which contains the HMM built from the alignment in the supplementary file 13100_2017_87_MOESM8_ESM.txt
. I am including the first few lines here (this is not the entire file, don't use this as the model—build it yourself. I only include it to illustrate the format):
HMMER3/f [3.1b2 | February 2015]
NAME 13100_2017_87_MOESM8_ESM
LENG 121
ALPH amino
RF no
MM no
CONS yes
CS no
MAP yes
DATE Mon Dec 11 13:33:29 2017
NSEQ 165
EFFN 5.697556
CKSUM 2893352190
STATS LOCAL MSV -9.8975 0.71332
STATS LOCAL VITERBI -10.6450 0.71332
STATS LOCAL FORWARD -3.9247 0.71332
HMM A C D E F G H I K L M N P Q R S T V W Y
m->m m->i m->d i->m i->i d->m d->d
COMPO 2.34473 4.21240 2.85435 2.69203 3.54228 2.79153 3.54812 3.01140 2.72630 2.48370 3.82225 2.94269 3.49156 3.05882 2.84632 2.63343 2.86306 2.72633 4.27012 3.56181
2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
0.13773 5.45955 2.08419 0.61958 0.77255 0.00000 *
1 2.99488 4.57852 4.44659 3.29307 1.80597 4.16203 3.88788 2.87265 3.75733 2.38594 3.30344 3.33633 4.53284 3.64324 3.69630 2.90350 3.30742 2.83413 4.36991 1.50673 1 y - - -
2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
0.00723 5.32905 6.05140 0.61958 0.77255 0.45275 1.01027
2 2.66602 2.17750 5.01715 4.40788 1.72617 4.29647 4.62737 2.89579 4.21116 2.71668 3.64495 4.43195 4.66188 4.35829 3.99238 3.10363 2.02207 1.89528 5.14692 3.02155 2 f - - -
2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
0.00661 5.41881 6.14115 0.61958 0.77255 0.61842 0.77391