Release 7.0 of the NCBI Hidden Markov models (HMM), used by the Prokaryotic Genome Annotation Pipeline (PGAP), is now available for download. You can search this collection against your favorite prokaryotic proteins to identify their function using the HMMER sequence analysis package.
Figure 1. Recently added HMM-based Protein Family Model for the histidine-histamine antiporter family (NF040512), with GO terms (framed in red).
Release 7.0 contains 15,346 models, including 111 that are new since 6.0. We have added better names, EC numbers, GO terms or gene symbols to over 2,500 existing HMMs. You can search and view the details for these in the Protein Family Model collection (Figure 1). Each record in the Protein Family Model collection, which also includes conserved domain architectures and BlastRules models in addition to HMMs, shows the RefSeq proteins that are named by the model.