Article Figures & Data
Figures
- FIG. 1.
Circular map of M. maripaludis genome. First (outer) double ring, top Blastp hits; second double ring, ORFs unique to M. maripaludis; third double ring, functional categories; black single ring, deviation from average mol% G+C; inner ring, GC skew. Top Blast hits are coded as follows: blue, Methanocaldococcus jannaschii; magenta, other methanogens; green, other Archaea; brown, Bacteria and Eukarya. Sectors containing top Blast hits predominately to groups other than Methanocaldococcus jannaschii are shown, with ORF number intervals. Functional categories are coded as follows: red, replication and repair; green, energy metabolism; blue, carbohydrate metabolism; cyan, lipid metabolism; magenta, transcription; yellow, translation; sky blue, cellular processes; orange, amino acid metabolism; pink, metabolism of cofactors; light red, nucleotide metabolism; gray, conserved hypothetical proteins; white, hypothetical proteins; brown, unassigned proteins; black, other; pale green, RNAs.
- FIG. 2.
Map of major metabolic pathways in M. maripaludis. Shown are energy and redox-related pathways (shaded areas), CO2 fixation, the reductive branch of the TCA cycle, nitrogen assimilation, glycolysis and gluconeogenesis, the nonoxidative pentose phosphate pathway, and amino acid biosynthesis. Some reactions and minor substrates and products were omitted. Abbreviations: ASA, aspartate semialdehyde; CHR, chorismate; (CO), enzyme-bound carbon monoxide; CoA, coenzyme A; CoB, coenzyme B; CoM, coenzyme M; E4P, erythrose-4-phosphate; F6P, fructose-6-phosphate; FBP, fructose-bis-phosphate; Fdx, ferredoxin; FUM, fumarate; F420, coenzyme F420; GA3P, glyceraldehyde-3-phosphate; G1P, glucose-1-phosphate; G6P, glucose-6-phosphate; (2H), low-potential hydride on unknown carrier; H+ (ext), proton-motive force; H4MPT, tetrahydromethanopterin; HSE, homoserine; IND, indole-3-glycerol-phosphate; KIV, 2-ketoisovalerate; MAL, malate; mDAP, meso-diaminopimelate; MFR, methanofuran; OAA, oxaloacetate; 2OG, 2-oxoglutarate; PEP, phosphoenolpyruvate; 3PG, 3-phosphoglycerate; PP, pyrophosphate; PPA, prephenate; PRPP, phosphoribosylpyrophosphate; PYR, pyruvate; R5P, ribose-5-phosphate; SDAP, succinyldiaminopimelate; SKA, shikimate; SUCC, succinate; S7P, sedoheptulose-7-phosphate; THDP, tetrahydrodipicolinate; X5P, xylulose-5-phosphate; ?, incomplete knowledge of pathway.
Tables
- TABLE 1.
General features of the M. maripaludis genome
Parameter Value Total no. of bases 1,661,137 No. of protein-coding genes 1,722 No. of predicted transmembrane proteins 350 Gene density (genes/kb) 1.036 Average gene length (bp) 857 Protein-coding percentage 88.9 No. of tRNAs 38 No. of rRNA operons 3 %GC 33.1 - TABLE 2.
Functional categories of proteins encoded by M. maripaludis genome
Functiona No. of ORFs % of ORFs Amino acid biosynthesis 82 4.8 Biosynthesis of cofactors, prosthetic groups, and carriers 68 3.9 Cell envelope 8 0.56 Cellular processes (cell division, chemotaxis, and motility) 30 1.7 Central intermediary metabolism 112 6.5 DNA metabolism 40 2.3 Energy metabolism (methanogenesis, hydrogen metabolism, and ATPase) 81 4.7 Fatty acid and phospholipid metabolism 6 0.35 Hypothetical proteins 102 5.9 Unique proteins of unknown function 27 1.6 Conserved hypothetical proteins 656 38 Protein fate 22 1.3 Protein synthesis 119 6.9 Purines, pyrimidines, nucleosides, and nucleotides 44 2.6 Regulatory functions 38 2.2 Transcription 22 1.3 Transport and binding proteins 86 5.0 Unclassified and unknown function 179 10.4 Total 1,722 100 ↵ a Adapted from The Institute for Genome Research's functional categories.
- TABLE 3.
Phylogenetic distributions and functions of clustered non-Methanocaldococcus jannaschii top Blastp hit categories
ORF intervala (Mmp no.) Predominant group(s)b Represented functions 0345-0371 Other Archaea Conserved hypothetical proteins, carbohydrate metabolism 0483-0536 Other methanogens and Bacteria Conserved hypothetical proteins, Fmd, Mo transport, molybdopterin biosynthesis, metal chelatase, probable cation transport 0709-0734 Bacteria and other methanogens Divalent cation transport, UvrABC 0753-0762 Bacteria Conserved hypothetical proteins 0772-0862 Other methanogens and Bacteria Conserved hypothetical proteins, Vhc 0973-0988 Other methanogens Cdh
