From: Phylogenetic Analysis of the ING Family of PHD Finger Proteins FIG. 3.— Amino acid sequence alignments of INGs from human, cow, mouse, rat, frogs, fish, mosquito, fruit fly, worms, fungi, and plants. The multiple sequence alignment was done using T-COFFEE. The alignment was then visualized by the multiple sequence alignment editor, GENEDOC. Shading is based on conservation, with the darkest shading representing 100% conservation and the lightest less than 60%. Four conserved regions are indicated. The characteristic signature motif of PHD domains, C4-H-C3, is the most highly conserved region across all sequences. The boxes outline the signature motifs on both the PCR and PIM. These motifs are characteristic for the corresponding ING subfamily. LZL, leucine zipper–like motif; PCR, potential chromatin regulatory domain; PHD, plant homeodomain; PIM, peptide-interacting motif. From: Phylogenetic Analysis of the ING Family of PHD Finger Proteins Mol Biol Evol. 2004;22(1):104-116. doi:10.1093/molbev/msh256 Mol Biol Evol | Molecular Biology and Evolution vol. 22 no. 1 © Society for Molecular Biology and Evolution 2005; all rights reserved.
From: Phylogenetic Analysis of the ING Family of PHD Finger Proteins FIG. 1.— Chromosomal localization of the inhibitor of growth (ING) genes in Homo sapiens. Chromosome number and the approximate chromosomal length (in Mbp) are indicated. Cytogenetic positions of the ING genes are shown. The chromosomal localization of INGs and several flanking genes are listed with the approximate chromosomal start positions in kbp. The distance to telomeres was estimated by calculating the distance between the ING positions to the end of the chromosome, where the telomere/subtelomere region is located. In the case of ING<sub>X</sub>, the distance to the centromere was calculated. The centromeric regions are indicated as constrictions. The gene positions and the identities of the flanking genes are available at http://www.ncbi.nlm.nih.gov/genome/guide/human/. From: Phylogenetic Analysis of the ING Family of PHD Finger Proteins Mol Biol Evol. 2004;22(1):104-116. doi:10.1093/molbev/msh256 Mol Biol Evol | Molecular Biology and Evolution vol. 22 no. 1 © Society for Molecular Biology and Evolution 2005; all rights reserved.
From: Phylogenetic Analysis of the ING Family of PHD Finger Proteins FIG. 2.— Structure of the inhibitor of growth (ING) proteins in Homo sapiens. (A) Amino acid sequence alignment of the ING protein members, including the four ING1 splicing variants. Different conserved domains are indicated by different colored boxes, including a proliferating cell nuclear antigen (PCNA)-interacting protein (PIP) domain on p33<sup>ING1b</sup>; a leucine zipper–like motif (LZL) on ING2, ING3, ING4, and ING5; the nuclear localization sequence (NLS, within which are three nucleolar targeting signals [NTS]); and a plant homeodomain (PHD) conserved in all members except ING<sub>X</sub>, which only has a partial PHD, a phosphorylation-dependent interacting motif (PDIM), and a peptide-interacting motif (PIM) only found on ING1 and ING2. A potential chromatin regulatory (PCR) domain is also shown (pink box) that may link ING proteins to HAT and HDAC complexes. p47<sup>ING1a</sup> and ING3 have additional inserted sequences that are unique and are indicated by the black lines protruding out of the sequence alignment. (B) A diagrammatic representation of the major structural features of the ING proteins. From: Phylogenetic Analysis of the ING Family of PHD Finger Proteins Mol Biol Evol. 2004;22(1):104-116. doi:10.1093/molbev/msh256 Mol Biol Evol | Molecular Biology and Evolution vol. 22 no. 1 © Society for Molecular Biology and Evolution 2005; all rights reserved.
From: Phylogenetic Analysis of the ING Family of PHD Finger Proteins FIG. 4.— The phylogenetic trees of the ING protein family. The tree on the left is derived by neighbor-joining distance analysis, whereas the tree on the right is derived by parsimony analysis. The statistical reliability of the inferred tree topology was assessed by the bootstrap test. The bootstrap values, which show as a percentage calculated form 1,000 data sets, are shown at the nodes. The distinct groups of ING proteins are also indicated. Phylogenetic analyses of PHD only and of the four conserved regions gave similar results. These results and the percent identity values are available from the authors upon request. From: Phylogenetic Analysis of the ING Family of PHD Finger Proteins Mol Biol Evol. 2004;22(1):104-116. doi:10.1093/molbev/msh256 Mol Biol Evol | Molecular Biology and Evolution vol. 22 no. 1 © Society for Molecular Biology and Evolution 2005; all rights reserved.
From: Phylogenetic Analysis of the ING Family of PHD Finger Proteins FIG. 5.— The composite tree of the ING protein family. Branch positions were determined by neighbor-joining analysis of the 60 ING/ING-like sequences compiled in table 1. The five major ING groups are color coded and indicated in brackets. From: Phylogenetic Analysis of the ING Family of PHD Finger Proteins Mol Biol Evol. 2004;22(1):104-116. doi:10.1093/molbev/msh256 Mol Biol Evol | Molecular Biology and Evolution vol. 22 no. 1 © Society for Molecular Biology and Evolution 2005; all rights reserved.