E/F subclan 1 - Phycobilin lyases
Description
All members of this subclan form heterodimers (E/F or Y/Z). CpcE/F are found in C-PC-containing strains (which has PCB chromophores at all binding sites) and RpcE/F in strains possessing R-PC (Ong and Glazer 1987, Six et al., 2007). CpcE/F and RpcE/F are mutually exclusive. CpeY/Z are present only in PE-containing strains.
References
- Chen et al., 2006. Diverse and unique picocyanobacteria in Chesapeake Bay, revealed by 16S-23S rRNA internal transcribed spacer sequences Appl Environ Microbiol, 72, 2239-2243.
- Ong et al., 1987. R-phycocyanin II, a new phycocyanin occurring in marine Synechococcus species J Biol Chem, 262, 6323-6327.
- Schluchter et al., 2010. Phycobiliprotein Biosynthesis in Cyanobacteria: Structure and Function of Enzymes Involved in Post-translational Modification Adv Exp Med Biol, 675, 211-228.
- Six et al., 2007. Diversity and evolution of phycobilisomes in marine Synechococcus spp.: a comparative genomics study Genome Biol, 8, R259.
Showing only unsure genes
| Gene | Locus tag | Genbank | Species | Strain | PBP in rods | Pigment type | Remark | Length | Last change |
|---|---|---|---|---|---|---|---|---|---|
| CpcE/RpcE family | WH7805_06756 | ZP_01123351.1 | Synechococcus sp. | WH7805 | PC+PEI | 2 | The R-PC-III present in this strain has a PCB:PEB ratio of 2:1 (Sidler, 1994). It is unclear whether WH7805 has CpcE/F or RpcE/F but the presence of CpcT (and not RpcT) however argues for the following pigmentation: alpha-84=PEB; beta-84=PCB; beta-155=PCB. | 265 | 09-19-2012 |
| CpcE/RpcE family | SynRCC307_2066 | YP_001228322.1 | Synechococcus sp. | RCC307 | PC+PEI+PEII | 3eA | Unclear whether this strain has CpcE/F or RpcE/F | 274 | 12-06-2011 |
| CpcE/RpcE family | S7335_2363 | ZP_05035931.1 | Synechococcus sp. | PCC7335 | PC+PEI | CA3 | CpcEII or RpcE | 274 | 12-06-2011 |
| CpcE-I subfamily | N9414_13270 | ZP_01632751.1 | Nodularia spumigena | CCY9414 | PC | 1 | Sequence incomplete: lacks C-term (end of contig) | 158 | 01-10-2012 |
| CpcE-I subfamily | CYB_2736 | YP_478924.1 | Synechococcus sp. | JA-2-3B'a(2-13) | PC | 1 | This is a second copy of cpcE (cpcE-2) NOT associated with a cpcF | 276 | 12-06-2011 |
| CpcE-I subfamily | CYA_2040 | YP_475443.1 | Synechococcus sp. | JA-3-3Ab | PC | 1 | This is a second copy of cpcE (cpcE-2) NOT associated with a cpcF | 275 | 12-06-2011 |
| CpcE-I subfamily | CMJ043C | Cyanidioschyzon merolae | 10D | PC | 1 | Distantly related to cyanobacterial CpcE : many insertions in matching sequences and much longer N-term, found by tblastn | 516 | 02-21-2012 | |
| CpcE-I subfamily | CWATWH0003_3128t1 | EHJ12159.1 | Crocosphaera watsonii | WH0003 | PC+PEI | Incomplete (end of contig) | 212 | 02-22-2012 | |
| CpcE-I subfamily | Pse7367_3924 | YP_007083576.1 | Pseudanabaena sp. | PCC7367 | PC+PEI | 2 copies? | 303 | 06-20-2013 | |
| CpcE-I subfamily | ZP_18907676 | ZP_18907676.1 | Leptolyngbya sp. | PCC7375 | PC+PEI | 2 | Low protomatch score | 279 | 06-20-2013 |
| CpcE-I subfamily | Pse7367_2387 | YP_007103076.1 | Pseudanabaena sp. | PCC7367 | PC+PEI | 2 copies? | 273 | 06-20-2013 | |
| CpcF/RpcF family | WH7805_06761 | ZP_01123352.1 | Synechococcus sp. | WH7805 | PC+PEI | 2 | Unclear whether this strain has CpcE/F or RpcE/F. Two possibilities: a-84 and b-84 = PCB; b-155 = PEB a-84 = PEB,b-84 and b-155 = PCB |
212 | 12-06-2011 |
| CpcF/RpcF family | SynRCC307_2067 | YP_001228323.1 | Synechococcus sp. | RCC307 | PC+PEI+PEII | 3eA | Unclear whether this strain has CpcE/F or RpcE/F | 218 | 12-06-2011 |
| CpcF/RpcF family | S7335_4405 | ZP_05037964.1 | Synechococcus sp. | PCC7335 | PC+PEI | CA3 | CpcFII or RpcF | 225 | 12-06-2011 |
| CpcF-I subfamily | CMJ044C | Cyanidioschyzon merolae | 10D | PC | 1 | found by tblastn | 312 | 02-21-2012 |
Model strains, Marine strains
Last update: 06 Jun 2013 9:03:39
