Protein Family Models

This entry represents a conserved region found in bacteriophage pre-tape measure proteins, located just upstream of the tape measure protein. The region is typically around 140-160 amino acids in length. In some phages the pre-tape measure protein is produced by a programmed translational frameshift. (from Pfam)

Date:

2025-02-22

Ribosomal_L26 is a family of the 50S and the 60S ribosomal proteins from eukaryotes - L26 - and archaea - L25. [1][1]. 2243110422431104. Frameshift mutation in p53 regulator RPL26 is associated withFrameshift mutation in p53 regulator RPL26 is associated with multiple physical abnormalities and a specific pre-ribosomal RNAmultiple physical abnormalities and a specific pre-ribosomal RNA processing defect in diamond-blackfan anemia.processing defect in diamond-blackfan anemia. Gazda HT, Preti M, Sheen MR, O'Donohue MF, Vlachos A, Davies SM,Gazda HT, Preti M, Sheen MR, O'Donohue MF, Vlachos A, Davies SM, Kattamis A, Doherty L, Landowski M, Buros C, Ghazvinian R, SieffKattamis A, Doherty L, Landowski M, Buros C, Ghazvinian R, Sieff CA, Newburger PE, Niewiadomska E, Matysiak M, Glader B,CA, Newburger PE, Niewiadomska E, Matysiak M, Glader B, Atsidaftos E, Lipton JM, Gleizes PE, Beggs AH;Atsidaftos E, Lipton JM, Gleizes PE, Beggs AH;. Hum Mutat. 2012;33:1037-1044.Hum Mutat. 2012;33:1037-1044. (from Pfam)

Date:

2025-02-20

This domain is found Bacteriophage lambda minor tail protein G and related sequences [1]. The construction of phage tails involves a stage of tail-tube formation, and tail-tube polymerisation requires two additional proteins, gpG and gpGT. The open reading frames, ORFs, for gpG and gpGT are overlapping and are related by a programmed translational frameshift. During virion morphogenesis, gpG is expressed in large amounts, and about 3.5% of the time, a -1 translational frameshift leads to the production of the larger fusion protein, gpGT. The correct ratio of gpG to gpGT, as determined by the frequency of frameshifting, is crucial for tail assembly. Since gpG accumulates to high levels during a lambda infection and yet is not found in mature phage particles it is believed to act as a chaperone [2]. [1][1]. 82301928230192. A programmed translational frameshift is required for theA programmed translational frameshift is required for the synthesis of a bacteriophage lambda tail assembly protein.synthesis of a bacteriophage lambda tail assembly protein. Levin ME, Hendrix RW, Casjens SR;Levin ME, Hendrix RW, Casjens SR;. J Mol Biol 1993;234:124-139.J Mol Biol 1993;234:124-139. [2][2]. 2354234423542344. A conserved spiral structure for highly diverged phage tailA conserved spiral structure for highly diverged phage tail assembly chaperones.assembly chaperones. Pell LG, Cumby N, Clark TE, Tuite A, Battaile KP, Edwards AM,Pell LG, Cumby N, Clark TE, Tuite A, Battaile KP, Edwards AM, Chirgadze NY, Davidson AR, Maxwell KL;Chirgadze NY, Davidson AR, Maxwell KL;. J Mol Biol. 2013;425:2436-2449.J Mol Biol. 2013;425:2436-2449. (from Pfam)

Date:

2025-02-20

The prominins are an emerging family of proteins that among the multispan membrane proteins display a novel topology. Mouse prominin and human prominin (mouse)-like 1 (PROML1) are predicted to contain five membrane spanning domains, with an N-terminal domain exposed to the extracellular space followed by four, alternating small cytoplasmic and large extracellular, loops and a cytoplasmic C-terminal domain [1]. The exact function of prominin is unknown although in humans defects in PROM1, the gene coding for prominin, cause retinal degeneration [2]. [1][1]. 1146784211467842. Rat prominin, like its mouse and human orthologues, is aRat prominin, like its mouse and human orthologues, is a pentaspan membrane glycoprotein.pentaspan membrane glycoprotein. Corbeil D, Fargeas CA, Huttner WB;Corbeil D, Fargeas CA, Huttner WB;. Biochem Biophys Res Commun 2001;285:939-944.Biochem Biophys Res Commun 2001;285:939-944. [2][2]. 1058757510587575. A frameshift mutation in prominin (mouse)-like 1 causes humanA frameshift mutation in prominin (mouse)-like 1 causes human retinal degeneration.retinal degeneration. Maw MA, Corbeil D, Koch J, Hellwig A, Wilson-Wheeler JC, BridgesMaw MA, Corbeil D, Koch J, Hellwig A, Wilson-Wheeler JC, Bridges RJ, Kumaramanickavel G, John S, Nancarrow D, Roper K, WeigmannRJ, Kumaramanickavel G, John S, Nancarrow D, Roper K, Weigmann A, Huttner WB, Denton MJ;A, Huttner WB, Denton MJ;. Hum Mol Genet 2000;9:27-34.Hum Mol Genet 2000;9:27-34. (from Pfam)

Date:

2025-02-20

This family consists of several bacterial and phage proteins of around 130 residues in length which seem to be related to the bacteriophage P2 GpU protein (Swiss:O64315) which is thought to be involved in tail assembly [1]. [1][1]. 1242634012426340. Programmed translational frameshift in the bacteriophage P2Programmed translational frameshift in the bacteriophage P2 FETUD tail gene operon.FETUD tail gene operon. Christie GE, Temple LM, Bartlett BA, Goodwin TS;Christie GE, Temple LM, Bartlett BA, Goodwin TS;. J Bacteriol 2002;184:6522-6531.J Bacteriol 2002;184:6522-6531. (from Pfam)

Date:

2025-02-20

Transcripts harbouring premature signals for translation termination are recognised and rapidly degraded by eukaryotic cells through a pathway known as nonsense-mediated mRNA decay. In Saccharomyces cerevisiae, three trans-acting factors (Upf1 to Upf3) are required for nonsense-mediated mRNA decay [1]. [1][1]. 1107399411073994. Novel Upf2p orthologues suggest a functional link betweenNovel Upf2p orthologues suggest a functional link between translation initiation and nonsense surveillance complexes.translation initiation and nonsense surveillance complexes. Mendell JT, Medghalchi SM, Lake RG, Noensie EN, Dietz HC;Mendell JT, Medghalchi SM, Lake RG, Noensie EN, Dietz HC;. Mol Cell Biol 2000;20:8944-8957.Mol Cell Biol 2000;20:8944-8957. (from Pfam)

Date:

2025-02-20

This family consists of several phage and bacterial proteins which are closely related to the GpE tail protein from Phage P2. [1][1]. 1242634012426340. Programmed translational frameshift in the bacteriophage P2Programmed translational frameshift in the bacteriophage P2 FETUD tail gene operon.FETUD tail gene operon. Christie GE, Temple LM, Bartlett BA, Goodwin TS;Christie GE, Temple LM, Bartlett BA, Goodwin TS;. J Bacteriol 2002;184:6522-6531.J Bacteriol 2002;184:6522-6531. (from Pfam)

Date:

2025-02-20

Colony stimulating factor 1 (CSF-1) is a homodimeric polypeptide growth factor whose primary function is to regulate the survival, proliferation, differentiation, and function of cells of the mononuclear phagocytic lineage. This lineage includes mononuclear phagocytic precursors, blood monocytes, tissue macrophages, osteoclasts, and microglia of the brain, all of which possess cell surface receptors for CSF-1. The protein has also been linked with male fertility [1] and mutations in the Csf-1 gene have been found to cause osteopetrosis and failure of tooth eruption [2]. Structurally these are short-chain 4-helical cytokines. [1][1]. 1189769811897698. Colony-stimulating factor 1 regulation of neuroendocrineColony-stimulating factor 1 regulation of neuroendocrine pathways that control gonadal function in mice.pathways that control gonadal function in mice. Cohen PE, Zhu L, Nishimura K, Pollard JW;Cohen PE, Zhu L, Nishimura K, Pollard JW;. Endocrinology 2002;143:1413-1422.Endocrinology 2002;143:1413-1422. [2][2]. 1237974212379742. The osteopetrotic mutation toothless (tl) is a loss-of-functionThe osteopetrotic mutation toothless (tl) is a loss-of-function frameshift mutation in the rat Csf1 gene: Evidence of a crucialframeshift mutation in the rat Csf1 gene: Evidence of a crucial role for CSF-1 in osteoclastogenesis and endochondralrole for CSF-1 in osteoclastogenesis and endochondral ossification.ossification. Van Wesenbeeck L, Odgren PR, MacKay CA, D'Angelo M, Safadi FF,Van Wesenbeeck L, Odgren PR, MacKay CA, D'Angelo M, Safadi FF, Popoff SN, Van Hul W, Marks SC Jr;Popoff SN, Van Hul W, Marks SC Jr;. Proc Natl Acad Sci U S . TRUNCATED at 1650 bytes (from Pfam)

Date:

2025-02-20

A common motif in phage that rely on a tape measure protein to control the length of the tail tube is to have two tandem ORFs, with protein biosynthesis that makes the upstream protein, but a small percentage of the time undergoes a -1 frameshift at a slippery site near the C-terminus and then continues through the downstream ORF to make a long version of the protein. The short form is referred to as gpG, and the long form as gpGT. This HMM represents the coding region C-terminal to that frameshift, present in gpGT but not in gpG. However, a number of member proteins, such as WP_311056037.1, represent the long form, gpGT, encoded with no frameshift. The region upstream of the frameshift is represented by NF047360.

Gene:

gpGT

Date:

2024-08-07

Analogous to gpG from phage lambda, but not obviously homologous, members of this family are tail assembly chaperone proteins, required for a scaffold function during tail assembly but not a part of mature phage. It appears that this protein behaves the same as lambda gpG, with a -1 frameshift site near its C-terminus that enables about 1 in 20 translations be synthesized in a longer form. The region downstream of the frameshift is represented by NF047426.

Gene:

gpG

Date:

2024-08-06

PilC, as found in Neisseria meningitidis and Neisseria gonorrhoeae, is the tip adhesin of the type IV pilus. It also occurs in the bacterial outer membrane, and contributes to pilus biogenesis and to competence for transformation. Typically two paralogs are found, PilC1 and PilC2, and this HMM does not distinguish between them. PilC genes are phase-variable because of expression is controlled by frameshift mutations in a run of G residues in DNA encoding the signal peptide region.

Gene:

pilC

Date:

2022-04-12

The bacterial peptide chain release factor 2 (RF-2), product of the prfB gene, recognizes the stop codons UGA and UAA during protein translation, and it is the only release factor to recognize UGA. In about 80 percent of known bacterial species, a +1 frameshift must occur at a UGA stop codon about 25 amino acids from the N-terminus, or translation is aborted by a premature termination. RF-2 can therefore regulate its own production by readthrough only when RF-2 is insufficient.

Gene:

prfB

Date:

2024-05-30

YjhR is a putative DNA helicase, found as an apparent pseudogene in the KpLE2 phage-like element of Escherichia coli str. K-12 substr. MG1655. Compared to WP_176259710.1 , the full-length homolog used to define this BlastRule, YjhR in the reference strain is 97 percent identical in regions that align, but lacks the first 758 amino acids and additionally has a frameshift at position 828. This BlastRule assigns the name YjhR to full-length proteins with a high level of amino acid sequence identity to WP_176259710.1. Note that a more distantly related protein, STM4489 from Salmonella enterica reference strain LT2, is identical in length while being only 63 percent identical in sequence.

Gene:

yjhR

Date:

2021-02-16

ElpA (ER-localizing protein A), as found in Coxiella burnetii, is a type IVB secretion system effector, oddly present in virtually all strains but disrupted by a frameshift in the Nine Mile reference isolate. CBUD_1884 is an example of a strain-specific locus of ElpA.

Gene:

elpA

Date:

2019-08-23

QacE is an SMR family efflux transporter for quaternary ammonium compounds, which are used as antibacterial compounds. QacE ends with the sequence VSGVVVLNLLSKASAH. QacEdelta1 ends with the sequence AFLLARSPSWKSLRRPTPW, and is therefore slightly longer. The forms differ by a frameshift, and both forms are active.

Gene:

qacE

Date:

2018-12-14

This HMM describes a family of bacteriophage proteins including G of phage lambda. This protein has been described as undergoing a translational frameshift at a Gly-Lys dipeptide near the C-terminus of protein G from phage lambda, with about 4 % efficiency, to produce the longer tail assembly protein G-T. The Lys of the Gly-Lys pair is the conserved second-to-last residue of seed alignment for this family. Subsequent work has shown that apparent -1 frameshift motifs are a regular feature the overlap regions of analogous gpG and gpGT tail assembly protein gene pairs found in the region between the phage major tail protein (V) and the phage tail tape measure protein (H).

Gene:

gpG

Date:

2024-07-23

This HMM represents a translation of the T gene in phage lambda and related phage. A translational frameshift from the upstream gene G into the frame of T produces a minor protein gpG-T, essential in tail assembly but not found in the mature virion.

Date:

2019-09-10

This model represents the well-conserved first ~ 365 amino acids of the translation of the dnaX gene. The full-length product of the dnaX gene in the model bacterium E. coli is the DNA polymerase III tau subunit. A translational frameshift leads to early termination and a truncated protein subunit gamma, about 1/3 shorter than tau and present in roughly equal amounts. This frameshift mechanism is not necessarily universal for species with DNA polymerase III but appears conserved in the exterme thermophile Thermus thermophilis.

Gene:

dnaX

Date:

2024-05-30

Members of this family of trimethoprim-resistant dihydrofolate reductases include DfrA12, DfrA21, DfrA22, and DfrA33 (recently split from DfrA22). DfrA13, seen only once, differs from DfrA21 mostly by a double frameshift and is now thought to represent a sequencing artifact rather than natural variation.

Gene:

dfrA

Date:

2024-03-21

Proteins of this family are DDE transposases encoded by the IS1 family elements usually through a translational frameshift mechanism.

Date:

2022-03-28