Table 2.
Automatic distribution of protein functions, based on the COG classification, between Helicobacter strains
| 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% | ||||||||||
*The CDSs were manually curated in the MaGe system for the elimination of artifacts.