Amino acid and intergenic alignments and genomic context. (a) Amino acid alignment of Methanothermobacter thermautotrophicus (NP_276465.1) and Methanosarcina acetivorans C2A (NP_616392.1) MsvR proteins. Conserved residues are shaded black. The region of the alignment used to determine protein identity and similarity is underlined in gray. The DNA binding domain and V4R domain are represented by black boxes indicating the residues belonging to each domain. Red boxes indicate residues predicted to be involved directly in DNA binding whilst orange boxes indicate residues predicted to be involved in dimerization in both Ma and Mth MsvR. Residues within a predicted zinc binding domain in both Ma and Mth MsvR are represented by pink boxes . Conserved cysteine residues are represented by blue boxes [pfam 02830, ]. Gray boxes identify additional cysteine residues in MaMsvR. A purple box indicates the CX2CX3H motif in MthMsvR. (b) Alignment of MsvR binding boxes in Ma PmsvR to those previously identified in Mth PmsvR/fpaA. Gray boxes indicate MsvR binding boxes 1, 2, and 3 on Mth PmsvR/fpaA and boxes A and B on Ma PmsvR. Conserved nucleotides are shaded in black. (c) The genomic context of Ma msvR is illustrated (http://img.jgi.doe.gov webcite, NCBI taxon ID 188937). Gray brackets identify intergenic regions and their corresponding lengths (181 bp and 128 bp). Dashed black outset lines identify the sequence of the region just upstream of Ma msvR. Green and turquoise boxes identify the msvR TATA box and B-recognition element, respectively. A bent arrow and the +1 designation indicate the mapped transcription start site of Ma msvR. The position of MsvR binding boxes A and B (solid black lines) in relationship to these two features is illustrated.
Isom et al. BMC Microbiology 2013 13:163 doi:10.1186/1471-2180-13-163