Reading FASTA files
KHAB17.fasta was obtained from Supplemental Information of Kacar et al. (2017) and is provided in the extdata/fasta directory of canprot. Use read_fasta() to read the file and return a data frame of amino acid composition.
fasta_file <- system.file("extdata/fasta/KHAB17.fasta", package = "canprot")
aa <- read_fasta(fasta_file)## read_fasta: reading KHAB17.fasta ... 57 lines ... 6 sequencesThe result is small enough that we can look at it here. The data frame has four columns for identifying information (protein, organism, ref, and abbrv); the first two are filled by read_fasta(). The chains column is the number of polypeptide chains.
## protein organism ref abbrv chains Ala Cys Asp Glu Phe Gly His Ile Lys
## 1 Anc_I/II/III KHAB17 NA NA 1 42 4 26 46 14 42 15 30 28
## 2 Anc_I/III KHAB17 NA NA 1 42 2 26 45 14 41 16 30 29
## 3 Anc_I/III' KHAB17 NA NA 1 42 1 25 44 15 42 14 32 30
## 4 Anc_I KHAB17 NA NA 1 52 1 28 32 18 40 9 18 28
## 5 Anc_IA/B KHAB17 NA NA 1 48 7 28 33 23 43 14 20 24
## 6 Anc_IB KHAB17 NA NA 1 46 7 27 31 23 44 15 20 24
## Leu Met Asn Pro Gln Arg Ser Thr Val Trp Tyr
## 1 42 10 8 21 4 22 13 19 29 5 13
## 2 39 13 9 22 6 22 15 17 29 5 13
## 3 41 11 8 23 7 22 18 17 29 4 14
## 4 42 12 13 24 13 31 16 29 37 10 17
## 5 43 12 14 21 11 30 17 32 30 10 15
## 6 44 12 15 22 13 29 16 31 28 9 16None of the first five columns is necessary for the calculation of chemical metrics. They are provided for compatibility with CHNOSZ, and if you don’t plan to use CHNOSZ, you can put any information here that you want, including NA values, or remove the columns completely. The columns that do matter for the calculation of chemical metrics are the last 20 columns, which are named with the 3-letter abbreviations of the amino acids.
These particular sequences are ancestral sequences of Rubisco. A geochemical biology hypothesis is that proteins are oxidized when the environment is oxidizing. Is this what happens? Plot the carbon oxidation state (ZC) to find out. Note the use of pre-formatted plot labels for chemical metrics available in cplab.
xlab <- "Ancestral sequences (older to younger)"
plot(Zc(aa), type = "b", xaxt = "n", xlab = xlab, ylab = cplab$Zc)
names <- gsub(".*_", "", aa$protein)
axis(1, at = 1:6, names)
abline(v = 3.5, lty = 2, col = 2)
axis(3, at = 3.5, "GOE (proposed)")
The vertical line denotes the proposed timing of the Great Oxidation Event (GOE) between Anc. I/III and Anc. I (Kacar et al., 2017). This analysis shows that reconstructed ancestral Rubiscos become more oxidized around the proposed timing of GOE.
