Recherche:Les clusters de gènes tRNA et rRNA chez les procaryotes/Fiche/Bacteroidetes
Fiche mémoire sur Bacteroidetes
Bacteroidetes
modifierbactero blocs
modifier- Lien tableur: bactero blocs
- Légende:
- - 23s': possible 23S ribosomal RNA but does not have good blast hits on one or both of the ends.
- - 23s°: 23S ribosomal RNA rRNA prediction is too short
- - 16s': possible 16S ribosomal RNA but does not have good blast hits on one or both of the ends.
- - 16s°: 16S ribosomal RNA rRNA prediction is too short
lien | blocs | 16s | total aas | avec | sans | total page | bac001-46 | Notes | ||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
bac001 | 2*16atcgca235 | 2 | 38 | 4 | 34 | 16s23s5s | 16-atcgca-35 | 16-atc-35 | avant | |||
bac002 | 2*16s23s5s | 3 | 41 | 2 | 39 | sans | 16 | 32 | 0 | 1 | 1-3 | |
16atcgca235 | 1-3 | 1 | 16atcgca235-tca | |||||||||
bac003 | 16s23s5s | 2 | 53 | 2 | 51 | 50 | total | 16 | 33 | 0 | 1 | avant |
16atcgca235 | cgt-16s23s5s | |||||||||||
bac005 | 2*16s23s5s | 3 | 38 | 2 | 36 | incomplets | ||||||
16atcgca | 2*16atcgca | |||||||||||
23s5s | 16s-atc-gaa-cds-agg | |||||||||||
16s-gca | ||||||||||||
bac007 | 6*16atcgca235 | 6 | 73 | 12 | 61 | |||||||
bac011 | 5*16atcgca235 | 5 | 68 | 10 | 58 | autres incomplets | ||||||
bac014 | 6*16atcgca235 | 7 | 85 | 14 | 71 | 3*23s5s | ||||||
16atcgca235-5s | ||||||||||||
5s de trop | ||||||||||||
bac016 | 4*16atcgca235 | 5 | 62 | 11 | 51 | 16atcgca235-5s | ||||||
16atcgca235-tca | ||||||||||||
bac017 | 2*16s23s5s | 4 | 40 | 3 | 37 | |||||||
cgt-16s23s5s | ||||||||||||
16atcgca235 | ||||||||||||
bac018 | 16atcgca235 | 1 | 33 | 2 | 31 | |||||||
bac027 | 16atcgca | 2 | 38 | 5 | 33 | |||||||
23s5s | ||||||||||||
16s-atc-gaa-cds-agg | ||||||||||||
bac038 | 3*16atcgca235 | 3 | 46 | 6 | 40 | |||||||
bac041 | 5*16s23s5s | 5 | 45 | 0 | 45 | |||||||
bac046 | 4*16s23s5s | 6 | 79 | 3 | 76 | |||||||
16atcgca235 | ||||||||||||
16s-gca | ||||||||||||
23s5s | 54 | |||||||||||
lien | blocs | 16s | total aas | avec | sans | total page | bac047-138 | Notes | ||||
bac047 | 6*16atcgca235 | 6 | 86 | 12 | 74 | 16s23s5s | 16-atcgca-35 | 16-atc-35 | avant | |||
3 | sans | 1 | 67 | 2 | 1 | 1-3 | ||||||
bac060 | 2*16atcgca235 | 74 | 4 | 70 | 1-3 | 1 | 16atcgca235-cca | |||||
16s23s5s | ||||||||||||
72 | total | 1 | 68 | 2 | 1 | avant | ||||||
bac063 | 5*16atcgca235 | 5 | 75 | 10 | 65 | aac-16atcgca235 | ||||||
bac066 | 6*16atcgca235 | 6 | 49 | 12 | 37 | |||||||
5s de trop | ||||||||||||
bac095 | 4*16atcgca235 | 5 | 104 | 11 | 93 | 16atcgca235-5s | ||||||
aac-16atcgca235 | ||||||||||||
bac096 | 8*16atcgca235 | 8 | 107 | 16 | 91 | |||||||
bac105 | 3*16atcgca235 | 3 | 53 | 6 | 47 | |||||||
bac106 | 7*16atcgca235 | 7 | 83 | 14 | 69 | |||||||
bac113 | 4*16atcgca235 | 4 | 53 | 8 | 45 | |||||||
bac117 | 5*16atcgca235 | 5 | 61 | 10 | 51 | |||||||
bac124 | 16atcgca235 | 1 | 46 | 2 | 44 | |||||||
bac127 | 3*16atcgca235 | 3 | 41 | 6 | 35 | |||||||
bac137 | 4*16atcgca235 | 4 | 62 | 8 | 54 | |||||||
bac138 | 2*16atcgca235 | 4 | 56 | 6 | 50 | |||||||
2*16-atc-235 | ||||||||||||
bac139 | 6*16atcgca235 | 8 | 88 | 17 | 71 | |||||||
16atcgca235-cca | ||||||||||||
16atcgca235-5s | ||||||||||||
72 | ||||||||||||
lien | blocs | 16s | total aas | avec | sans | total page | Total | Notes | ||||
29 | 16s23s5s | 16-atcgca-35 | 16-atc-35 | avant | ||||||||
sans | 17 | 99 | 2 | 2 | 1-3 | |||||||
Moyenne | 61 | 8 | 54 | 1-3 | 0 | 2 | 0 | 0 | 16atcgca235-tca | |||
ecartype | 21 | 5 | 17 | 16atcgca235-cca | ||||||||
max | 107 | 17 | 93 | 122 | total | 17 | 101 | 2 | 2 | |||
min | 33 | 0 | 31 | avant | ||||||||
cgt-16s23s5s | ||||||||||||
aac-16atcgca235 | ||||||||||||
incomplets | ||||||||||||
2*16atcgca | ||||||||||||
blocs | 126 | 16s-atc-gaa-cds-agg | ||||||||||
génomes | 29 | 16s-gca | ||||||||||
cds incomplet | 1 | |||||||||||
16s23s5s | 15% | autres incomplets | ||||||||||
16atcgca235 | 84% | 3*23s5s | ||||||||||
5s de trop | ||||||||||||
2*16atcgca235-5s |
bactero notes
modifier- Lien tableur: bactero notes
- Les aas en dehors des blocs: Il y a très peu de tRNAs avant ou après les blocs, tca cca après et cgt aac avant.
- Sur 126 blocs il y a à peine un cds incomplet 16s-atc-gaa-cds-agg.
bactero typage
modifier- Lien tableur: bactero typage
- Les bacteroidites ont des blocs solides et quasiment uniformes sur un total de 126:
- - 16atcgca235 81%
- - 16s23s5s 14%
- - incomplets 3%
bactero type 16-y-235 après 16s
modifier- Typpe
type tableau avant 16s total % 16s23s5s 17 1 18 15 atcgca 101 1 102 84 atc 2 2 2 total 120 2 122
bactero type 16235-z après 5s
modifier- Type
type tableau % sans 120 98 cca 1 1 tca 1 1 total 122
bactero type x-16235 avant 16s
modifier- Type
type tableau cgt 1 aac 1
Tableau des noms bactero
modifier- Lien tableur: bactero noms
- Prélèvement: fait vers le 20.8.19 et mise en forme le 4.9.19 Paris.
- Légende:
- - rRNAs, 666 ou "10,10,10", sous la forme indiquée par NCBI, (5S, 16S, 23S).
- - rupture, sélection des génomes sur les 2 premiers attributs
- - fait, dans génomes bactero
- - code, utilisé dans les génomes "fait"
- - tRNAs, nombre de tRNAs tel qu'il est déduit de la de la construction des noms.
- - notes
- - 80+84, à partir de gtRNAdb et la méthode de construction de la liste des noms, le même noms peut regrouper quelques échantillons ayant le même nombre de tRNAs.
tRNAs total 7181 génomes ruptures faits total 82 29 146
- Construction de la liste des noms
ruptures | notes | rRNAs | fait | code | tRNAs | génomes |
---|---|---|---|---|---|---|
1 | 222 | 1 | bac001 | 38 | Aequorivita sublithincola DSM 14238 | |
1 | 333 | 1 | bac002 | 41 | Algoriphagus machipongonensis PR1 | |
1 | 222 | 1 | bac003 | 53 | Alistipes finegoldii DSM 17242 | |
bac004 | 45 | Alistipes shahii WAL 8301 | ||||
1 | 333 | 1 | bac005 | 38 | Bacteroidales bacterium CF | |
1 | 80+84 | bac006 | 164 | Bacteroides dorei | ||
1 | 666 | 1 | bac007 | 73 | Bacteroides fragilis 638R | |
bac008 | 71 | Bacteroides fragilis BOB25 | ||||
bac009 | 73 | Bacteroides fragilis NCTC 9343 | ||||
bac010 | 74 | Bacteroides fragilis YCH46 | ||||
1 | 555 | 1 | bac011 | 68 | Bacteroides helcogenes P 36-108 | |
1 | bac012 | 82 | Bacteroides salanitronis DSM 18170 | |||
1 | bac013 | 71 | Bacteroides thetaiotaomicron VPI-5482 | |||
1 | 877 | 1 | bac014 | 85 | Bacteroides vulgatus ATCC 8482 | |
1 | bac015 | 59 | Bacteroides xylanisolvens XB1A | |||
1 | 555 | 1 | bac016 | 62 | Barnesiella viscericola DSM 18177 C46 DSM 18177 | |
1 | 444 | 1 | bac017 | 40 | Belliella baltica DSM 15883 | |
1 | 111 | 1 | bac018 | 33 | Blattabacterium sp. Blaberus giganteus BGIGA | |
bac019 | 34 | Blattabacterium sp. Blatta orientalis str. Tarazona | ||||
bac020 | 34 | Blattabacterium sp. Blattella germanica str. Bge | ||||
bac021 | 32 | Blattabacterium sp. Cryptocercus punctulatus str. Cpu | ||||
bac022 | 34 | Blattabacterium sp. Mastotermes darwiniensis str. MADAR | ||||
bac023 | 34 | Blattabacterium sp. Nauphoeta cinerea | ||||
bac024 | 34 | Blattabacterium sp. Panesthia angustipennis spadica str. BPAA | ||||
bac025 | 34 | Blattabacterium sp. Periplaneta americana str. BPLAN | ||||
1 | bac026 | 35 | Candidatus Amoebophilus asiaticus 5a2 | |||
1 | 121 | 1 | bac027 | 38 | Candidatus Azobacteroides pseudotrichonymphae genomovar. CFP2 | |
1 | bac028 | 31 | Candidatus Sulcia muelleri BGSS | |||
bac029 | 30 | Candidatus Sulcia muelleri CARI | ||||
bac030 | 31 | Candidatus Sulcia muelleri DMIN | ||||
bac031 | 31 | Candidatus Sulcia muelleri GWSS | ||||
bac032 | 30 | Candidatus Sulcia muelleri ML | ||||
bac033 | 30 | Candidatus Sulcia muelleri PSPU | ||||
bac034 | 28 | Candidatus Sulcia muelleri SMDSEM | ||||
bac035 | 30 | Candidatus Sulcia muelleri str. Sulcia-ALF | ||||
bac036 | 30 | Candidatus Sulcia muelleri TETUND | ||||
1 | bac037 | 32 | Candidatus Uzinura diaspidicola str. ASNER | |||
1 | 333 | 1 | bac038 | 46 | Capnocytophaga canimorsus Cc5 | |
bac039 | 47 | Capnocytophaga ochracea DSM 7271 | ||||
1 | bac040 | 37 | Cardinium endosymbiont cEper1 of Encarsia pergandiella | |||
1 | 555 | 1 | bac041 | 45 | Cellulophaga algicola DSM 14237 | |
bac042 | 43 | Cellulophaga baltica 18 | ||||
bac043 | 44 | Cellulophaga baltica NN016038 | ||||
bac044 | 40 | Cellulophaga lytica DSM 7489 | ||||
bac045 | 40 | Cellulophaga lytica HI1 | ||||
1 | 666 | 1 | bac046 | 79 | Chitinophaga pinensis DSM 2588 | |
1 | 666 | 1 | bac047 | 86 | Chryseobacterium sp. StRB126 | |
1 | bac048 | 37 | Croceibacter atlanticus HTCC2559 | |||
1 | bac049 | 46 | Cyclobacterium marinum DSM 745 | |||
1 | bac050 | 41 | Cytophaga hutchinsonii ATCC 33406 | |||
1 | bac051 | 43 | Dokdonia sp. 4H-3-7-5 | |||
bac052 | 42 | Dokdonia sp. MED134 | ||||
1 | bac053 | 46 | Draconibacterium orientale FH5T | |||
1 | bac054 | 39 | Dyadobacter fermentans DSM 18053 | |||
1 | bac055 | 49 | Echinicola vietnamensis DSM 17526 | |||
1 | bac056 | 52 | Elizabethkingia anophelis NUHP1 | |||
bac057 | 58 | Elizabethkingia sp. BM10 | ||||
1 | bac058 | 42 | Emticicia oligotrophica DSM 17448 | |||
1 | bac059 | 35 | endosymbiont of Llaveia axin axin | |||
1 | 333 | 1 | bac060 | 74 | Fibrella aestuarina BUZ 2 | |
1 | bac061 | 42 | Flavobacteriaceae bacterium 3519-10 | |||
bac062 | 44 | Flavobacterium branchiophilum FL-15 | ||||
555 | 1 | bac063 | 75 | Flavobacterium columnare ATCC 49512 | ||
bac064 | 63 | Flavobacterium indicum GPTSA100-9 DSM 17447 | ||||
bac065 | 62 | Flavobacterium johnsoniae UW101 ATCC 17061 | ||||
1 | 666 | 1 | bac066 | 49 | Flavobacterium psychrophilum 3 | |
bac067 | 37 | Flavobacterium psychrophilum 4 | ||||
bac068 | 49 | Flavobacterium psychrophilum 5 | ||||
bac069 | 38 | Flavobacterium psychrophilum 950106-1/1 | ||||
bac070 | 50 | Flavobacterium psychrophilum CSF259-93 | ||||
bac071 | 50 | Flavobacterium psychrophilum FPG101 | ||||
bac072 | 49 | Flavobacterium psychrophilum FPG3 | ||||
bac073 | 49 | Flavobacterium psychrophilum JIP02/86 | ||||
bac074 | 49 | Flavobacterium psychrophilum MH1 | ||||
bac075 | 49 | Flavobacterium psychrophilum PG2 | ||||
bac076 | 39 | Flavobacterium psychrophilum V3-5 | ||||
bac077 | 38 | Flavobacterium psychrophilum V4-24 | ||||
bac078 | 39 | Flavobacterium psychrophilum v4-33 | ||||
bac079 | 49 | Flavobacterium psychrophilum VQ50 | ||||
1 | bac080 | 50 | Flexibacter litoralis DSM 6794 | |||
1 | bac081 | 45 | Fluviicola taffensis DSM 16823 | |||
1 | bac082 | 45 | Formosa agariphila KMM 3901 | |||
1 | bac083 | 45 | Gramella forsetii KT0803 | |||
1 | bac084 | 53 | Haliscomenobacter hydrossis DSM 1100 | |||
1 | bac085 | 47 | Hymenobacter sp. APR13 | |||
bac086 | 44 | Hymenobacter sp. DG25B | ||||
bac087 | 48 | Hymenobacter swuensis DY53 | ||||
1 | bac088 | 36 | Lacinutrix sp. 5H-3-7-4 | |||
1 | bac089 | 42 | Leadbetterella byssophila DSM 17132 | |||
1 | bac090 | 40 | Maribacter sp. HTCC2170 | |||
1 | bac091 | 41 | Marivirga tractuosa DSM 4126 | |||
1 | bac092 | 39 | Mucinivorans hirudinis | |||
1 | bac093 | 40 | Muricauda lutaonensis CC-HSB-11 | |||
bac094 | 38 | Muricauda ruestringensis DSM 13258 | ||||
1 | 555 | 1 | bac095 | 104 | Myroides profundi D25 | |
1 | 888 | 1 | bac096 | 107 | Myroides sp. A21 | |
1 | bac097 | 41 | Niabella soli DSM 19437 JS13-8 | |||
1 | bac098 | 67 | Niastella koreensis GR20-10 | |||
1 | bac099 | 42 | Nonlabens dokdonensis DSW-6 | |||
bac100 | 37 | Nonlabens marinus S1-08 | ||||
1 | bac101 | 61 | Odoribacter splanchnicus DSM 20712 DSM 220712 | |||
1 | bac102 | 43 | Ornithobacterium rhinotracheale DSM 15997 | |||
bac103 | 43 | Ornithobacterium rhinotracheale ORT-UMN 88 | ||||
1 | bac104 | 38 | Owenweeksia hongkongensis DSM 17368 | |||
1 | 333 | 1 | bac105 | 53 | Paludibacter propionicigenes WB4 | |
1 | 777 | 1 | bac106 | 83 | Parabacteroides distasonis ATCC 8503 | |
1 | bac107 | 47 | Pedobacter heparinus DSM 2366 | |||
bac108 | 55 | Pedobacter saltans DSM 12145 | ||||
1 | bac109 | 35 | Polaribacter sp. MED152 | |||
1 | bac110 | 49 | Pontibacter korlensis X14-1T | |||
1 | bac111 | 46 | Porphyromonadaceae bacterium ING2-E5B | |||
1 | bac112 | 47 | Porphyromonas asaccharolytica DSM 20707 | |||
444 | 1 | bac113 | 53 | Porphyromonas gingivalis ATCC 33277 | ||
bac114 | 53 | Porphyromonas gingivalis HG66 | ||||
bac115 | 53 | Porphyromonas gingivalis TDC60 | ||||
bac116 | 53 | Porphyromonas gingivalis W83 | ||||
1 | 555 | 1 | bac117 | 61 | Prevotella dentalis DSM 3688 | |
bac118 | 50 | Prevotella denticola F0289 | ||||
bac119 | 50 | Prevotella intermedia 17 | ||||
bac120 | 49 | Prevotella melaninogenica ATCC 25845 | ||||
bac121 | 54 | Prevotella ruminicola 23 Bryant 23 | ||||
bac122 | 49 | Prevotella sp. oral taxon 299 str. F0039 | ||||
1 | bac123 | 38 | Psychroflexus torquis ATCC 700755 | |||
1 | 111 | 1 | bac124 | 46 | Rhodothermus marinus DSM 4252 | |
bac125 | 47 | Rhodothermus marinus SG0.5JP17-172 | ||||
1 | bac126 | 77 | Riemerella anatipestifer ATCC 11845 DSM 15868 | |||
1 | 333 | 1 | bac127 | 41 | Riemerella anatipestifer CH3 | |
bac128 | 41 | Riemerella anatipestifer RA-CH-1 | ||||
bac129 | 41 | Riemerella anatipestifer RA-CH-2 | ||||
bac130 | 40 | Riemerella anatipestifer RA-GD | ||||
1 | bac131 | 41 | Robiginitalea biformata HTCC2501 | |||
1 | bac132 | 44 | Runella slithyformis DSM 19594 | |||
1 | bac133 | 46 | Salinibacter ruber DSM 13855 M31 | |||
bac134 | 47 | Salinibacter ruber M8 | ||||
1 | bac135 | 48 | Saprospira grandis str. Lewin | |||
1 | bac136 | 44 | Siansivirga zeaxanthinifaciens CC-SAMT-1 | |||
1 | 444 | 1 | bac137 | 62 | Solitalea canadensis DSM 3403 | |
1 | 444 | 1 | bac138 | 56 | Sphingobacterium sp. 21 | |
1 | 988 | 1 | bac139 | 88 | Sphingobacterium sp. ML3W | |
1 | bac140 | 52 | Spirosoma linguale DSM 74 | |||
bac141 | 42 | Spirosoma radiotolerans DG5A | ||||
1 | bac142 | 46 | Tannerella forsythia 92A2 | |||
1 | bac143 | 59 | Weeksella virosa DSM 16922 | |||
1 | bac144 | 57 | Winogradskyella sp. PG-2 | |||
1 | bac145 | 40 | Zobellia galactanivorans DsiJT | |||
1 | bac146 | 49 | Zunongwangia profunda SM-A87 SMA-87 | |||
82 | 29 |