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Table 2 Automatic distribution of protein functions, based on the COG classification, between Helicobacter strains

From: From array-based hybridization of Helicobacter pylori isolates to the complete genome sequence of an isolate associated with MALT lymphoma

Species and strains   H. p B38 H. p 26695 H. p J99 H. p HPAG1 H. p Shi470 H. p G27 H. p P12 H. acinonychis H. hepaticus
CELLULAR PROCESSES AND SIGNALING
Cell cycle control, cell division, chromosome partitioning D 39 2.55% 39 2.38% 38 2.46% 34 2.21% 38 2.39% 37 2.30% 39 2.38% 37 2.10% 33 1.78%
Cell wall/membrane/envelope biogenesis M 109 7.13% 106 6.48% 105 6.81% 105 6.82% 104 6,53% 108 6.70% 106 6.47% 109 6.20% 134 7.24%
Cell motility N 65 4.26% 58 3.54% 60 3.89% 57 3.70% 55 3.46% 59 3.66% 61 3.72% 57 3.24% 68 3.68%
Posttranslational modification, protein turnover, chaperones O 71 4.65% 74 4.52% 75 4.86% 74 4.81% 77 4.84% 76 4.72% 76 4.64% 73 4.15% 85 4.60%
Signal transduction mechanisms T 54 3.53% 52 3.18% 56 3.63% 47 3.05% 46 2.89% 51 3.17% 57 3.48% 46 2.62% 68 3.68%
Intracellular trafficking, secretion, vesicular transport U 59 3.86% 76 4.64% 73 4.73% 66 4.29% 71 4.46% 74 4.59% 83 5.06% 56 3.18% 60 3.24%
Defense mechanisms V 57 3.73% 52 3.18% 54 3.50% 53 3.44% 51 3.20% 53 3.29% 52 3.17% 42 2.39% 38 2.05%
Extracellular structures W 0 0.00% 0 0.00% 0 0.00% 1 0.07% 1 0.06% 1 0.06% 0 0 0 0% 1 0.05%
Cytoskeleton Z 0 0.00% 0 0.00% 0 0.00% 0 0.00% 0 0.00% 0 0 0 0 0 0% 1 0.05%
INFORMATION STORAGE AND PROCESSING
Chromatin structure and dynamics B 1 0.07% 1 0.06% 0 0 1 0.07% 1 0.06% 1 0.06% 1 0.06% 0 0% 1 0.05%
Translation, ribosomal structure, biogenesis J 134 8.77% 138 8.43% 141 9.14% 137 8.90% 138 8.67% 136 8.44% 139 8.48% 134 7.62% 148 8.00%
Transcription K 53 3.47% 44 2.69% 46 2.98% 48 3.12% 43 2.70% 49 3.04% 49 2.99% 43 2.45% 59 3.19%
Replication, recombination and repair L 154 10.08% 177 10.69% 155 10.05% 149 9.68% 150 9.42% 171 10.62% 163 9.95% 155 8.82% 100 5.41%
METABOLISM                    
Energy prodcution and conversion C 90 5.89% 89 5.44% 87 5.64% 93 6.04% 93 5.84% 92 5.71% 93 5.67% 87 4.95% 118 6.38%
Amino acid transport E 151 9.88% 145 8.86% 152 9.85% 146 9.49% 153 9.61% 150 9.31% 150 9.15% 160 9.10% 200 10.81%
Nucleotide transport F 46 3.01% 45 2.75% 47 3.05% 45 2.92% 44 2.76% 47 2.92% 47 2.87% 47 2.67% 58 3.14%
Carbohydrate transport G 60 3.93% 56 3.42% 57 3.69% 55 3.57% 63 3.96% 55 3.41% 59 3.60% 59 3.35% 76 4.11%
Coenzyme transport H 75 4.91% 73 4.46% 75 4.86% 75 4.87% 75 4.71% 75 4.66% 76 4.64% 67 3.81% 87 4.70%
Lipid transport I 50 3.27% 49 2.99% 49 3.18% 50 3.25% 47 2.95% 51 3.17% 51 3.11% 47 2.67% 54 2.92%
Inorganic ion transport P 97 6.35% 94 5.74% 100 6.48% 94 6.11% 103 6.47% 97 6.02% 98 5.98% 95 5.40% 125 6.76%
Secondary matabolites biosynthesis, transport Q 26 1.70% 25 1.53% 25 1.62% 23 1.50% 23 1.45% 22 1.37% 26 1.59% 24 1.36% 37 2.00%
POORLY CHARACTERIZED
General function prediction only R 174 11.39% 173 10.57% 178 11.54% 160 10.40% 174 10.93% 168 10.43% 175 10.68% 166 9.44% 234 12.65%
Function unknown S 84 5.50% 80 4.89% 71 4.60% 78 5.07% 70 4.40% 84 5.21% 81 4.94% 70 3.98% 113 6.11%
CDS Not Classified to any COG (Number/%)   339/22.2 435/26.6 363/23.5 367/23.9 422/26.5 395/24.5 440/26.9 536/31.6 479/25.9
TOTAL CDS*   1528 1637 1543 1539 1592 1611 1639 1696 1850
%CDS at least in one COG   77.81% 73.43% 76.47% 76.15% 73.49% 75.48% 73.15% 68.40% 74.11%
  1. *The CDSs were manually curated in the MaGe system for the elimination of artifacts.