Protein families database of alignments and HMMs   Trigger_N

Accession number: PF05697 Previous identifiers: Trigger; Bacterial trigger factor protein (TF) In the E. coli cytosol, a fraction of the newly synthesised proteins requires the activity of molecular chaperones for folding to the native state. The major chaperones implicated in this folding process are the ribosome-associated Trigger Factor (TF), and the DnaK and GroEL chaperones with their respective co-chaperones. Trigger Factor is an ATP-independent chaperone and displays chaperone and peptidyl-prolyl-cis-trans-isomerase (PPIase) activities in vitro. It is composed of at least three domains, an N-terminal domain which mediates association with the large ribosomal subunit, a central substrate binding and PPIase domain with homology to FKBP proteins, and a C-terminal domain of unknown function. The positioning of TF at the peptide exit channel, together with its ability to interact with nascent chains as short as 57 residues renders TF a prime candidate for being the first chaperone that binds to the nascent polypeptide chains [1]. This family represents the N-terminal region of the protein. INTERPRO description (entry IPR008881) In the Escherichia coli cytosol, a fraction of the newly synthesised proteins requires the activity of molecular chaperones for folding to the native state. The major chaperones implicated in this folding process are the ribosome-associated Trigger Factor (TF), and the DnaK and GroEL chaperones with their respective co-chaperones. Trigger Factor is an ATP-independent chaperone and displays chaperone and peptidyl-prolyl-cis-trans-isomerase (PPIase) activities in vitro. It is composed of at least three domains, an N-terminal domain which mediates association with the large ribosomal subunit, a central substrate binding and PPIase domain with homology to FKBP proteins, and a C-terminal domain of unknown function. The positioning of TF at the peptide exit channel, together with its ability to interact with nascent chains as short as 57 residues renders TF a prime candidate for being the first chaperone that binds to the nascent polypeptide chains MEDLINE:22493129. This group of sequences contain the ribosomal subunit association domain. QuickGO PROCESS : protein transport (GO:0015031)

Alignment	Domain organisation
Seed (52)  Full (121) Format Coloured alignment Plain Pfam format Plain Stockholm format Fasta format (with gaps) MSF format Belvu (unix only) Belvu (old version unix only) Jalview (Java) Further alignment options here Help relating to Pfam alignments here	Seed (52)  Full (121) As a Graphic As a Tree Zoom pixels/aa. Bootstrap tree To find out about the NIFAS tree-viewer, click here
Species Distribution	Phylogenetic tree
View alignments & domain organisation by species Tree depth : Show all levels 1 level 2 levels 3 levels 4 levels 5 levels	Seed (52)  Full (121) The trees were generated using Quicktree To find out more about ATV phylogenetic tree-viewer click here

Database References
SYSTERS	Trigger_N
PANDIT	Trigger_N

Literature References 1. Trigger Factor and DnaK possess overlapping substrate pools and binding specificities. Deuerling E, Patzelt H, Vorderwulbecke S, Rauch T, Kramer G, Schaffitzel E, Mogk A, Schulze-Specking A, Langen H, Bukau B; Mol Microbiol 2003;47:1317-1328.

Pfam specific information Author of entry Moxon SJ Type definition Family Alignment method of seed Clustalw Source of seed members Pfam-B_8447 (release 8.0) Average Length 152.4 Average %id 25 Average Coverage 34.60% HMMER build information   Pfam_ls  [Download HMM] Pfam_fs  [Download HMM] Gathering cutoff 25.0 25.0; 50.0 50.0 Trusted cutoff 32.6 32.6; 50.8 50.8 Noise cutoff -12.5 -12.5; 46.4 37.0 Build method of HMM hmmbuild -F HMM_ls SEED hmmcalibrate --seed 0 HMM_ls hmmbuild -f -F HMM_fs SEED hmmcalibrate --seed 0 HMM_fs

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