Journal: Journal of structural biology

Article Title: The insertion domain 1 of class IIA dimeric glycyl-tRNA synthetase is a rubredoxin-like zinc ribbon.

doi: 10.1016/j.jsb.2015.02.004

Figure Lengend Snippet: Fig.3. Structure-based multiple sequence alignment of representative sequences of a2GRS ID1. Gene identification (gi) number/PDBid, organism name abbreviation, the first and the last residue numbers of the regions depicted in the alignment are indicated for each sequence. The secondary structural elements of the zinc ribbon are indicated above the alignment. Long insertions are not shown and the numbers of omitted residues are represented by numbers boxed in violet. Potential metal-binding ligands are boxed in black and non-metal-binding residues at the same position are boxed in red. Secondary zinc binding sites are boxed in blue. Uncharged residues (all aminoacids except Asp, Glu, Lys and Arg) in mostly hydrophobic sites are highlighted yellow and conserved aromatic residues are highlighted cyan. The conserved residues involved in interaction with Ap4A are indicated by an asterisk sign (*). Gi’s and organism name of protein sequences from archaea, bacteria and eukaryotes are colored in red, black and green respectively. The organism abbreviations are: Ob – Oceanospirillales bacterium SCGC AAA298-N10, Sb – SAR86 cluster bacterium SAR86B, Mb – Microgenomates bacterium SCGC AAA040-P11, Mi – Microgenomates bacterium SCGC AAA011-J08, Tp – Treponema pallidum subsp. pallidum str. Chicago, Sa – Spirochaeta africana DSM 8902, Bb – Bdellovibrio bacteriovorus HD100, Me – Methylacidiphilum infernorum V4, Ub – uncultured bacterium, Mg – Mycoplasma genitalium G37, Cp – Corynebacterium pyruviciproducens, Cd – candidate division YNPFFA, Tv – Thermoplasma volcanium GSS1, Mj – Methanocaldococcus jannaschii DSM 2661, Mo – Methanothermococcus okinawensis IH1, Ta – Thermosphaera aggregans DSM 11486, Cs – Cenarchaeum symbiosum A, My – Mycoplasma arthritidis 158L3-1, Fs – Fibrobacter succinogenes subsp. succinogenes S85, Ht – Halorhabdus tiamatea SARL4B, Ca – Candidatus Micrarchaeum acidiphilum ARMAN-2, Nc – Nosema ceranae BRL01, Dp – Desulfobacter postgatei, Pm – Perkinsus marinus ATCC 50983, Ns – Nematocida sp. 1 ERTm2, Mr – Melioribacter roseus P3M-2, Hs – Homo sapiens, Tt – Thermus thermophilus, Sr – Salinibacter ruber DSM 13855, To – Thermus oshimai, Pa – Blattabacterium sp. (Periplaneta americana) str. BPLAN, Pp – Plesiocystis pacifica, Cy – Cyanidioschyzon merolae strain 10D, Ma – Marinimicrobia bacterium JGI 0000039-D08, Cm – Cordyceps militaris CM01, Ia – Ignavibacterium album JCM 16511, Py – Plasmodium yoelii 17X, Cb – candidate division SR1 bacterium RAAC1_SR1_1, Pt – Phaeodactylum tricornutum CCAP 1055/1, Cf – Chthoniobacter flavus, Nv – Nematostella vectensis, Sc – Saccharomyces cerevisiae, Pl – Planctomyces maris, Th – Theileria parva strain Muguga, Ce – Candidatus Entotheonella sp. TSY1, Pf – Plasmodium falciparum Palo Alto/Uganda.

Article Snippet: Chicago, Sa – Spirochaeta africana DSM 8902, Bb – Bdellovibrio bacteriovorus HD100, Me – Methylacidiphilum infernorum V4, Ub – uncultured bacterium, Mg – Mycoplasma genitalium G37, Cp – Corynebacterium pyruviciproducens, Cd – candidate division YNPFFA, Tv – Thermoplasma volcanium GSS1, Mj – Methanocaldococcus jannaschii DSM 2661, Mo – Methanothermococcus okinawensis IH1, Ta – Thermosphaera aggregans DSM 11486, Cs – Cenarchaeum symbiosum A, My – Mycoplasma arthritidis 158L3-1, Fs – Fibrobacter succinogenes subsp. succinogenes S85, Ht – Halorhabdus tiamatea SARL4B, Ca – Candidatus Micrarchaeum acidiphilum ARMAN-2, Nc – Nosema ceranae BRL01, Dp – Desulfobacter postgatei, Pm – Perkinsus marinus ATCC 50983, Ns – Nematocida sp. 1 ERTm2, Mr – Melioribacter roseus P3M-2, Hs – Homo sapiens, Tt – Thermus thermophilus, Sr – Salinibacter ruber DSM 13855, To – Thermus oshimai, Pa – Blattabacterium sp. (Periplaneta americana) str.

Techniques: Sequencing, Residue, Binding Assay, Bacteria

Journal: Standards in Genomic Sciences

Article Title: Phylogeny-driven target selection for large-scale genome-sequencing (and other) projects

doi: 10.4056/sigs.3446951

Figure Lengend Snippet: Selection results for the 20 LTP strains with the highest bRPD scores.

Article Snippet: Fibrobacter intestinalis , AJ496284 , Fibrobacteres , 0.1358 , 0.1341 , Not at DSMZ.

Techniques: Selection