Protein Family Models

The thrombospondin repeat is a short aspartate rich repeat which binds to calcium ions. The repeat was initially identified in thrombospondin proteins that contained 7 of these repeats [1]. The repeat lacks defined secondary structure [2]. [1]. 2430973. The structure of human thrombospondin, an adhesive glycoprotein. with multiple calcium-binding sites and homologies with several. different proteins.. Lawler J, Hynes RO;. J Cell Biol 1986;103:1635-1648.. [2]. 15014436. Structure of a thrombospondin C-terminal fragment reveals a. novel calcium core in the type 3 repeats.. Kvansakul M, Adams JC, Hohenester E;. EMBO J. 2004;23:1223-1233. (from Pfam)

Date:

2024-08-14

This model describes MYXO-CTERM, a C-terminal putative protein sorting domain, analogous to LPXTG (TIGR01167) and PEP-CTERM (TIGR02595). It is restricted to the Myxococcales, a division of the Deltaproteobacteria, with over 60 members occurring in Plesiocystis pacifica SIR-1. An example protein is TraA, involved in outer membrane exchange (lipids and proteins) through which one strain of Myxococcus can repair a mobility defect in another. Users of this model should be aware that the short length, great diversity, and lineage-specific differences in the protein regions recognized by this model guarantee that this model has some false-positive hits (e.g. anything in the Firmicutes) and many false-negatives. Researchers interested in getting a full census of MYXO-CTERM in any member of the Myxococcales are advised to use this model to find lineage-specific sequences and the improve the model iteratively.

Date:

2024-10-03

This model largely duplicates TIGR03901, but differs somewhat in coverage. The domain described here, now called MYXO-CTERM, is small (about 30 amino acids), hydrophobic, only moderately conserved, and similar to numerous other transmembrane helix-containing sequence regions from convergent evolution. The trusted cutoff for the HMM therefore must be set fairly high. This domain is found, once per protein but in many proteins per genome in several bacteria of the order Myxococcales. It begins with a signature Gly-Cys motif. Its other features, including a hydrophobic transmembrane helix, Arg-rich cluster, and location at the protein C-terminus, resemble the PEP-CTERM proposed protein targeting domain. MYXO-CTERM domains occur in species with the processing endopeptidase myxosortase. It is likely that lipid is attached to the Cys side chain prior to a cleavage of the sorting domain distal to the GC site.

Date:

2023-07-12