OMPdb

[…] in , last column, and comparisons between TCDB and Pfam are discussed in the text as well as in reference 131. It is apparent that many of the families in TCDB often correlate with those in Pfam and OMPdb, and some of the TC families found within a single superfamily are also found in single clans in Pfam.While Pfam, HHomp and OMPdb are based substantially on HMMs as noted above, TCDB is based la […]

[…] of β-barrel prediction was based on a Profile Hidden Markov Model (pHMM)-approach using the program HMMer (Eddy, ). We used the Protein Family (Pfam) database (Finn et al., ), OPM (Lomize et al., ), OMPdb (Tsirigos et al., ), which provide information on domain architecture and structures of β-barrel OMPs to build HMM profiles for each known β-barrel OMP family. These profiles were used to search […]

[…] rrucomicrobia available in GenBank, plus the recently published genome of “Candidatus Scalindua profunda” (van de Vossenberg et al., ). Additionally, we have used the outer membrane protein database (OMPdb; Tsirigos et al., ) and BOMP (Berven et al., ) to determine the number of predicted OMPs in these genomes. To ascertain that the identified genes are not remnants of a no longer existing structu […]

[…] nd the presence of the C-terminal OMP signature sequence was predicted by comparing the last 15 amino acids of XatA to the last 15 amino acids of both the E. coli and X. fastidiosa OMPs listed in the OMPdb database (. Secondary structure predictions for the XatA passenger domain were obtained using PsiPred (. Further analysis of this domain was conducted using HHrepID, a method for the de novo ide […]