Additional file 1 of Patterns of abundance, chromosomal localization, and domain organization among c-di-GMP-metabolizing genes revealed by comparative genomics of five alphaproteobacterial orders
Notice bibliographique
Résumé
Additional file 1: Figure S1. Numerical relationships between the number of GGDEF and EAL (GGDEF:EAL) sequences by genera. The ratios were calculated per genome and the mean per genus was plotted. Figure S2. Numerical relationships between the number of GGDEF and GGDEF_EAL (GGDEF:GGDEF_EAL) sequences by genera. The ratios were calculated per genome and the mean per genus was plotted. Figure S3. Numerical relationships between the number of GGDEF and HD-GYP (GGDEF:HDGYP) sequences by genera. The ratios were calculated per genome and the mean per genus was plotted. Figure S4. Numbers of c-di-GMP sequences in a phylogenetic context. Phylogenetic relationships are based on RpoB sequences. All alignments were done using MAFFT with LINS-i option. Bootstrap values based on 1000 replicates and hill-climbing nearest-neighbor interchange search were used. A. Rhizobiales. B. Caulobacterales. C. Rhodobacterales. D. Rhodospirillales. E. Sphingomonadales. Figure S5. Relationships between chromosome size and the number of encoded c-di-GMP enzymatic domains. Spearman's rank correlation was used to evaluate the significance. Only the biggest replicon, considered the main chromosome, was included in this analysis. Figure S6. Chromosomal locations of c-di-GMP-associated genes. Cumulative distributions of cdi-GMP-associated genes on the chromosomes, with lengths normalized to 100% where ori is at 0% and 100% and ter is at 50%. The red line indicates the estimate of the kernel density. In this analysis only closed genomes with one unambiguously identified ori were used. Figure S7. Secondary domains that are present along with the different c-di-GMP-associated enzyme groups. A. Shared and individual secondary domains. The c-di-GMP-modulating domains are not included in this analysis. The color code of the Venn diagram represents domain counts from highest(red) to zero (white). B. Number of sequences that have zero, one, or more than one secondary domain. Figure S8. Relationships between protein length and presence of detected auxiliary domains. The sequences with EAL and GGDEF domains were segregated based on the occurrence of auxiliary domains. The minimal amino acid lengths for proteins containing auxiliary domains (left panel) were identified as 375 for EAL proteins and 275 for GGDEF proteins (blue dashed lines). This threshold was then used to calculate the percentage of sequences without identified auxiliary domains that were shorter and longer than these minimal lengths (right panel).
Récupéré en direct depuis OpenAlex et désinversé. Les résumés ne sont pas conservés dans cette base de données : les index inversés représentent 8,6 Go des 9,3 Go de texte de la base, et le serveur dispose de 13 Go libres.
Comment cette classification a été obtenuedéplier
Prédiction distillée sur la base complète
Imitation des enseignantsNi prévalence calibrée, ni vérité terrain. Validation humaine à venir. Apprise à partir de 10 348 étiquettes directes de Codex et de 10 348 étiquettes directes de Gemma. Le mode candidate est l'union des têtes enseignantes seuillées; le consensus est leur intersection. Ces sorties portent le statut machine_predicted_unvalidated et ne sont ni des étiquettes humaines ni des étiquettes directes de modèles de pointe.
Scores Codex et Gemma par catégorie
| Catégorie | Codex | Gemma |
|---|---|---|
| Métarecherche | 0,000 | 0,000 |
| Méta-épidémiologie (sens strict) | 0,000 | 0,000 |
| Méta-épidémiologie (sens large) | 0,000 | 0,000 |
| Bibliométrie | 0,000 | 0,000 |
| Études des sciences et des technologies | 0,000 | 0,000 |
| Communication savante | 0,000 | 0,000 |
| Science ouverte | 0,000 | 0,000 |
| Intégrité de la recherche | 0,000 | 0,000 |
| Charge utile insuffisante (le modèle a refusé de juger) | 0,298 | 0,000 |
Scores machine (provisoires)
Les deux têtes enseignantes du modèle étudiant, lues sur ce travail. Un score ordonne la base pour la relecture; il n'affirme jamais une catégorie, et le statut de validation accompagne chaque rangée tel quel.
Scores de référence d'un modèle non mature (critères de maturité non atteints, 7 itérations). Un score ordonne; il n'affirme jamais une catégorie.
score_only:v0-immature-baseline · tel quel depuis la passe de notation : score_only signifie que le nombre peut ordonner les travaux, et qu'aucune étiquette de catégorie n'en découleClassification
machine, non validéePrédiction automatique; un appel candidat d’une seule tête enseignante, pas un consensus.
Le détail, modèle par modèle et score par score, se trouve en fin de page sous « Comment cette classification a été obtenue ».