hmmpfam reads a single sequence from seqfile and compares it against all the HMMs in hmmfile looking for significantly similar sequence matches.hmmfile will be looked for first in the current working directory, then in a directory named by the environment variable HMMERDB. This lets administrators install HMM library(s) such as Pfam in a common location.The output consists of three sections: a ranked list of the best scoring HMMs, a list of the best scoring domains in order of their occurrence in the sequence, and alignments for all the best scoring domains. A sequence score may be higher than a domain score for the same sequence if there is more than one domain in the sequence; the sequence score takes into account all the domains. All sequences scoring above the -E and -T cutoffs are shown in the first list, then every domain found in this list is shown in the second list of domain hits. If desired, E-value and bit score thresholds may also be applied to the domain list using the -domE and -domT options.