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
Bibliographic record
Abstract
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).
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.002 | 0.019 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.001 |
| Bibliometrics | 0.003 | 0.006 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.002 | 0.003 |
| Open science | 0.003 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.848 | 0.154 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".