TABLE 1. — Functional classification of genes in the Amalthea mahilanii F.P.Cabrera & A.R.Sherwood, sp. nov. chloroplast genome. Categories for classification follow Ohta et al. (2003).
| Genetic system |
Number |
Genes |
| Maintenance |
2 |
dnaB |
rne |
|
|
|
|
|
|
| RNA Polymerase |
4 |
rpoA |
rpoB |
rpoC1 |
rpoC2 |
rpoZ |
|
|
|
| Transcription factors |
4 |
ntcA |
ompR |
rbcR |
ycf29 |
|
|
|
|
| Translation |
4 |
infB |
infC |
tsf |
tufA |
|
|
|
|
| Ribosomal proteins |
| Large subunit |
28 |
rpl1 |
rpl2 |
rpl3 |
rpl4 |
rpl5 |
rpl6 |
rpl9 |
rpl11 |
| rpl12 |
rpl13 |
rpl14 |
rpl16 |
rpl18 |
rpl19 |
rpl20 |
rpl21 |
| rpl22 |
rpl23 |
rpl24 |
rpl27 |
rpl28 |
rpl29 |
rpl311 |
rpl32 |
| rpl33 |
rpl34 |
rpl35 |
rpl36 |
|
|
|
|
| 18 |
rps1 |
rps2 |
rps3 |
rps4 |
rps5 |
rps6 |
rps7 |
rps8 |
| Small subunit |
|
rps9 rps18 |
rps10 rps19 |
rps11 |
rps12 |
rps13 |
rps14 |
rps16 |
rps17 |
| TRNA processing |
1 |
tilS |
|
|
|
|
|
|
|
| Protein quality control |
4 |
clpc |
dnak |
ftsH |
groEL |
|
|
|
|
| Photosystems |
| Phycobilisomes |
11 |
apcA cpeA |
apcB cpeB |
apcD nblA |
apcE |
apcF |
cpcA |
cpcB |
cpcG |
| Photosystem I |
13 |
psaA |
psaB |
psaC |
psaD |
psaE |
psaF |
psaI |
psaJ |
| psaK |
psaL |
psaM |
ycf3 |
ycf4 |
|
|
|
| 19 |
psbA |
psbB |
psbC |
psbD |
psbE |
psbF |
psbH |
psbI |
| Photosystem II |
|
psbJ psbY |
psbK psbZ |
psbL Psb30 |
psbN |
psbT |
psbV |
psbW |
psbX |
| Cytochrome complex |
11 |
ccs1 petL |
ccsA petM |
petA petN |
petB |
petD |
petF |
petG |
petJ |
| Redox system |
7 |
acsF |
bas1 |
dsbD |
ftrB |
grx |
pbsA |
trxA |
|
| ATP synthesis |
| ATP synthase |
9 |
atpA |
atpB |
atpD |
atpE |
atpF |
atpG |
atpH |
atpl |
| clpC |
sufB |
sufC |
|
|
|
|
|
| Metabolism |
| Carbohydrates |
5 |
odpA |
odpB |
pgmA |
rbcL |
rbcS |
cbbx |
|
|
| Lipids |
5 |
accA |
accB |
accD |
acpP |
fabH |
|
|
|
| Nucleotides |
2 |
carA |
upp |
|
|
|
|
|
|
| Amino acids |
8 |
argB |
gltB |
ilvB |
ilvH |
syfB |
syh |
trpA |
trpG |
| Cofactors |
6 |
chll |
mоеB |
preA |
thiG |
thiS |
dfr |
|
|
| Transport |
| Transport |
7 |
cemA |
secA |
secG |
secY |
ycf38 |
ycf63 |
tatC |
|
| Unknown |
|
31 |
ORF58 |
ORF83 |
ORF745 |
ORF101 |
ORF152 |
ycf17 |
ycf19 |
ycf20 |
| Conserved ORFs |
|
ycf21 |
ycf22 |
ycf23 |
ycf33 |
ycf34 |
ycf35 |
ycf36 |
ycf37 |
|
ycf39 |
ycf41 |
ycf45 |
ycf46 |
ycf52 |
ycf53 |
ycf54 |
ycf55 |
|
ycf58 |
ycf60 |
ycf62 |
ycf65 |
ycf80 |
ycf86 |
ycf92 |
|
| RNA genes |
| rRNAs |
3 |
rrn5 |
rrn23 |
rrn16 |
|
|
|
|
|
| 29 |
trnA-UGC |
trnC-GCA |
trnD-GUC |
trnE-UUC |
trnF-GAA |
trnG-GCC |
trnG-UCC |
trnH-GUG |
| tRNAs |
|
trnI-GAU |
trnK-UUU |
trnL-CAA |
trnL-UAA |
trnL-UAG |
trnM-CAU |
trnM-CAU |
trnM-CAU |
|
trnN-GUU |
trnP-UGG |
trnQ-UUG |
trnR-ACG |
trnR-CCG |
trnR-UCU |
trnS-GCU |
trnS-UGA |
|
trnT-GGU |
trnT-UGU |
trnV-GAC |
trnW-CCA |
trnY-GUA |
|
|
|
| Miscellaneous RNAs |
1 |
rnpB |
|
|
|
|
|
|
|