ZnF-Prot: Zinc finger motifs in proteome

Pfam library

The HMM profiles corresponding to 31 zinc finger domains was collected from Pfam (protein families) database (http://pfam.xfam.org/). Pfam has a massive collection of protein families represented by multiple sequence alignment (MSA) and HMM profiles and the functional domain information. A total of 288 HMM profiles were collected for 31 zinc finger domains. The HMM profiles corresponding to the zinc finger domains were searched through the keyword "zinc finger" in the keyword search option of the Pfam database. Subsequently, the grouping of the collected HMM profiles corresponding to 31 different zinc finger classes was done as described below. The HMM profiles belonging to a particular ZnF clan in the Pfam database were initially directly assigned under a zinc finger domain HMM profile. For example, the 52 different HMM profiles corresponding to the Pfam clan C2H2-zf (CL0361) were categorized as C2H2 zinc finger HMM profiles. However, categorizing all the HMM profiles corresponding to the 31 different ZnF domains was not straightforward since many HMM profiles were not defined under a particular ZnF clan. Such HMM profiles were assigned under a zinc finger domain based on the “description” or “name” given in the HMM profiles or through the literature survey. For instance, zf-B_box (PF00643) is not categorized under any clan in the Pfam database. However, it was categorized under treble clef zinc finger domain in the local repository based on the HMM profile “description”. The collected HMM profiles corresponding to 31 different zinc finger classes are displayed below.