Nitrosopumilus maritimus genome reveals unique - de la Torre ...

Supplemental Table 1: Number and genomic density of genes grouped as clusters of orthologous genes (COGs).
Nitrosopumilus
maritimus SCM1
Nitrosococcus oceani
ATCC 19707
Nitrosomonas
europaea ATCC 19718
Nitrosomonas
eutropha C71
Nitrosospira
multiformis ATCC
25196
Pelagibacter ubique
HTCC1062
Procholoroccus
species
Synechococcus
species
Archaeoglobus
fulgidus DSM 4304
Halobacterium sp.
NRC-1
Methanococcus
maripaludis S2
Thermoplasma
acidophilum DSM 1728
Genome size (Mb) 1.65 3.52 2.81 2.78 3.23 1.31 1.64-2.68 2.22-3.05 2.18 2.57 1.66 1.56 1.74-1.91 2.23-2.99
ORFs 1,997 3,186 2,628 2,578 2,827 1,.389 1,901 - 3,152 2,580 - 3,401 2,471 2,674 1,772 1,548 1,879 - 2,229 2,305 - 3,031
COG Genes 1,131 2,290 1,995 1,952 2,102 1,131 1,157-1,540 1,459-1,968 1,918 1,812 1,417 1,201 1,421-1,575 1,563-2,105
# #/Mb # #/Mb # #/Mb # #/Mb # #/Mb # #/Mb # #/Mb # #/Mb # #/Mb # #/Mb # #/Mb # #/Mb # #/Mb # #/Mb
Amino acid transport &
141-
114-
150metabolism
109 66 180 51 139 49 141 51 154 48 182 139 121-152 57-76 178 57-65 149 68 151 59 125 75 130 83 159 66-83 202 63-68
Carbohydrate transport &
88metabolism
46 28 105 30 73 26 81 29 94 29 64 49 62-94 34-41 86-108 29-46 54 25 60 23 50 30 92 59 80-93 45-49 128 37-43
Cell cycle control, cell division 11 7 31 9 39 14 32 12 31 10 13 10 15-18 6-10 18-33 7-11 23 11 31 12 16 10 8 5 18-21 9-12 8-15 4-5
Cell motility 6 4 75 21 82 29 75 27 64 20 12 9 1-20 1-7 4-28 2-10 21 10 45 18 27 16 14 9 13-27 7-16 10-14 4-5
Cell wall/membrane/envelope
113biogenesis
49 30 186 53 167 59 152 55 194 60 99 76 86-136 47-60 137 38-60 60 28 59 23 38 23 41 26 46-61 26-32 51-79 19-26
Coenzyme transport &
122-
102metabolism
95 58 114 32 102 36 99 36 108 33 77 59 106-122 45-66 143 47-56 114 52 109 42 126 76 86 55 70-89 40-47 110 37-49
Defense mechanisms 13 8 59 17 49 17 41 15 31 10 11 8 14-33 8-14 23-37 9-14 18 8 22 9 11 7 12 8 16-29 9-15 17-22 7-8
Energy production &
110-
104-
144conservation
100 61 182 52 122 43 142 51 160 49 99 76 82-106 40-52 139 43-51 227 104 130 51 151 91 103 66 128 60-68 176 59-65
140-
189- 99- 147-
Function unknown 86 52 235 67 172 61 149 54 197 61 78 60 85-145 48-56 179 55-67 259 119 187 73 219 132 116 74 197 113 187 59-69
171-
262- 144- 272- 116-
General function prediction only
Inorganic ion tranport &
152 92 282 80 221 79 196 70 228 70 112 86 141-189 70-91 270 77-98 331 152 276 107 207 125 186 119 287 162 346 122
metabolism
Intracellular trafficking &
63 38 135 38 164 58 115 41 105 32 40 31 55-77 27-38 72-148 32-49 91 42 128 50 77 46 51 33 78-99 45-56 63-85 25-28
secretion 11 7 91 26 91 32 107 38 96 30 38 29 20-52 12-21 27-47 12-17 25 11 23 9 21 13 20 13 20-21 10-12 14-21 5-7
Lipid transport & metabolism
Nucleotide transport &
30 18 72 20 65 23 63 23 78 24 51 39 37-49 18-26 35-51 12-20 109 50 56 22 16 10 56 36 19-25 11-13 70-89 26-40
metabolism 45 27 56 16 50 18 54 19 54 17 46 35 48-52 18-31 52-63 18-24 51 23 63 25 51 31 50 32 47-52 27-28 62-66 21-28
Posttranslational modifications 74 45 130 37 103 37 127 46 129 40 61 47 70-95 35-48 90-119 36-42 69 32 105 41 53 32 49 31 51-55 29-30 67-88 27-33
Replication, recombination &
67-
84- 38repair
Secondary metabolites
56 34 202 57 170 60 225 81 182 56 54 41 62-84 31-40 78-207 31-70 98 45 169 66 58 35 67 43 109 38-57 326 109
biosynthesis & transport 15 9 44 12 36 13 49 18 59 18 37 28 19-46 11-17 27-47 9-18 33 15 26 10 5 3 22 14 10-12 6-7 35-53 13-24
Singal transduction mechanisms 47 29 121 34 126 45 86 31 124 38 34 26 23-49 14-20 42-116 19-42 71 33 76 30 35 21 9 6 19-33 10-19 23-28
95-
8-10
Transcription 76 46 96 27 113 40 92 33 99 31 42 32 36-63 21-26 60-93 24-34 97 45 122 47 75 45 71 45 80-85 42-49 107 34-43
Translation, ribosomal structure
137-
160-
165-
& biogenesis 136 83 149 42 154 55 152 55 151 47 113 86 128-146 54-80 144 45-64 160 73 148 58 155 93 136 87 166 87-92 166 55-74
Pyrococcus
species
Sulfolobus
species