Data item of the type domain from the database pfam with accession PF00019 and name Transforming growth factor beta like domain

Data item of the type domain from the database pfam with accession PF00020 and name TNFR/NGFR cysteine-rich region

Data item of the type family from the database pfam with accession PF00012 and name Hsp70 protein

A database of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs). Users can analyze protein sequences for Pfam matches, view Pfam family annotation and alignments, see groups of related families, look at the domain organization of a protein sequence, find the domains on a PDB structure, and query Pfam by keywords. There are two components to Pfam: Pfam-A and Pfam-B. Pfam-A entries are high quality, manually curated families that may automatically generate a supplement using the ADDA database. These automatically generated entries are called Pfam-B. Although of lower quality, Pfam-B families can be useful for identifying functionally conserved regions when no Pfam-A entries are found. Pfam also generates higher-level groupings of related families, known as clans (collections of Pfam-A entries which are related by similarity of sequence, structure or profile-HMM).

Pfam domains predicted on all EukProt v3 datasets (one output file per dataset). Domains were predicted with InterProScan version 5.56 and InterPro version 89.0 (which includes the Pfam database version 34.0; note that this is no longer the most recent version of Pfam), with default parameter values.

ISOPENTENYLTRANSFERASE (IPT) genes play important roles in the initial steps of cytokinin synthesis, exist in plant and pathogenic bacteria, and form a multigene family in plants. Protein domain searches revealed that bacteria and plant IPT proteins were to assigned to different protein domains families in the Pfam database, namely Pfam IPT (IPTPfam) and Pfam IPPT (IPPTPfam) families, both are closely related in the P-loop NTPase clan. To understand the origin and evolution of the genes, a species matrix was assembled across the tree of life and intensively in plant lineages. The IPTPfam domain was only found in few bacteria lineages, whereas IPPTPfam is common except in Archaea and Mycoplasma bacteria. The bacterial IPPTPfam domain miaA genes were shown as ancestral of eukaryotic IPPTPfam domain genes. Plant IPTs diversified into class I, class II tRNA-IPTs, and Adenosine-phosphate IPTs; the class I tRNA-IPTs appeared to represent direct successors of miaA genes were found in all plant genomes, whereas class II tRNA-IPTs originated from eukaryotic genes, and were found in prasinophyte algae and in euphyllophytes. Adenosine-phosphate IPTs were only found in angiosperms. Gene duplications resulted in gene redundancies with ubiquitous expression or diversification in expression. In conclusion, it is shown that IPT genes have a complex history prior to the protein family split, and might have experienced losses or HGTs, and gene duplications that are to be likely correlated with the rise in morphological complexity involved in fine tuning cytokinin production.

The Pfam database contains information about protein domains and families. For each entry a protein sequence alignment and a Hidden Markov Model is stored.

Only entries with more than one trRBDpep match per Pfam family are shown. The complete results can be found in S3 Table in S1 File.

Number of genes with pFAM domains and the number of different domain families found in the nine clusters.

Table 2 shows the correlation of Pfam domains starting within the first 60 amino acids of a protein with its N-terminal acetylation status. Pfam domains that were solely associated with an acetylated N-terminus are indicated in italics. Pfam domains that were found to be exclusively associated with a free N-terminus are shown in bold. The p values for these correlations are summarized in Table S5A. Ace, acetylated N-termini; free, non-acetylated N-termini.

All expanded and depleted PFAM domains and multi-gene families (as well as the statistics) are given in Tables S14 and S15, respectively.

The main entity of this document is a protein with accession number Q7Z886

Human genome resequencing projects provide an unprecedented amount of data about single-nucleotide variations occurring in protein-coding regions and often leading to observable changes in the covalent structure of gene products. For many of these variations, links to Online Mendelian Inheritance in Man (OMIM) genetic diseases are available and are reported in many databases that are collecting human variation data such as Humsavar. However, the current knowledge on the molecular mechanisms that are leading to diseases is, in many cases, still limited. For understanding the complex mechanisms behind disease insurgence, the identification of putative models, when considering the protein structure and chemico-physical features of the variations, can be useful in many contexts, including early diagnosis and prognosis. In this study, we investigate the occurrence and distribution of human disease–related variations in the context of Pfam domains. The aim of this study is the identification and characterization of Pfam domains that are statistically more likely to be associated with disease-related variations. The study takes into consideration 2,513 human protein sequences with 22,763 disease-related variations. We describe patterns of disease-related variation types in biunivocal relation with Pfam domains, which are likely to be possible markers for linking Pfam domains to OMIM diseases. Furthermore, we take advantage of the specific association between disease-related variation types and Pfam domains for clustering diseases according to the Human Disease Ontology, and we establish a relation among variation types, Pfam domains, and disease classes. We find that Pfam models are specific markers of patterns of variation types and that they can serve to bridge genes, diseases, and disease classes. Data are available as Supplementary Material for 1,670 Pfam models, including 22,763 disease-related variations associated to 3,257 OMIM diseases.

1Enrichment: Number of PFAM hits in secretome over number of hits in non secreted proteins;2p-value for enrichment in secretome;3number of domains in secretome;4number of domains in haustorial proteins;5tribes containing at least two instances of the domain with number of instances in parenthesis.

Annotations of transcript isoforms. Pfam protein domains along with E-values and GO terms via InterProScan.

The main entity of this document is a structure with accession number 4n2f

The main entity of this document is a protein with accession number A0A089ZB47

() Including the LSM domain present in Sm and Lsm proteins.(*) In >100 copies.

Refer to Table 1, footnote for list of abbreviations.

Refer to Table 1, footnote for list of abbreviations.