E/F clan: subclan 2
Description
Most phycobilin lyase-isomerases of the E/F subclan 2 have been biochemically characterized. They do not seem to form heteroduplexes, thus members of this group might be monomers or homodimers. This group also contains several enzymes that have been characterized but are not phycobilin lyases (CpeZ, IaiH, NblB, etc.) and numerous homologs with unknown function.
References
- Alvey et al., 2011. Attachment of noncognate chromophores to CpcA of Synechocystis sp. PCC 6803 and Synechococcus sp. PCC 7002 by heterologous expression in Escherichia coli Biochemistry, 50, 4890-4902.
- Humily et al., 2013. A gene island with two possible configurations is involved in chromatic acclimation in marine Synechococcus PLoS One, 8, e84459.
- Mahmoud et al., 2017. Adaptation to blue light in marine Synechococcus requires MpeU, an enzyme with similarity to phycoerythrobilin lyase isomerases Front Microbiol, 8, 243.
- Shukla et al., 2012. Phycoerythrin-specific bilin lyase-isomerase controls blue-green chromatic acclimation in marine Synechococcus Proc Natl Acad Sci USA, 49, 20136-20141.
- 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 |
|---|---|---|---|---|---|---|---|---|---|
| CpeF family | Tery_0978 | YP_720832.1 | Trichodesmium erythraeum | IMS101 | PC+PEI | N-term shortened (24 aa removed) | 310 | 08-30-2012 | |
| CpeF family | Tery_0987 | YP_720840.1 | Trichodesmium erythraeum | IMS101 | PC+PEI | Best BlastP hit on CpeF (but lower than Tery_0978) | 285 | 08-30-2012 | |
| CpeF family | S7335_4282 | ZP_05037842.1 | Synechococcus sp. | PCC7335 | PC+PEI | CA3 | Low blast and protomatch score. | 332 | 01-02-2012 |
| CpeF family | CWATWH0003_5310t4 | EHJ09925.1 | Crocosphaera watsonii | WH0003 | PC+PEI | incomplete n-term (start of contig) | 262 | 02-22-2012 | |
| CpeY family | CwatDRAFT_0665 | ZP_00518425.1 | Crocosphaera watsonii | WH8501 | PC+PEI | There is another partial CpeY sequence in this genome almost 100% identical to this one (possibly an assembly error). | 419 | 08-27-2012 | |
| CpeY family | CwatDRAFT_5980 | ZP_00514215.1 | Crocosphaera watsonii | WH8501 | PC+PEI | Sequence incomplete. N-term extended (35 aa added) but still incomplete. | 282 | 08-27-2012 | |
| CpeZ family | Tery_0980 | YP_720834.1 | Trichodesmium erythraeum | IMS101 | PC+PEI | Blastp hit on cpeZ (but lower than >Tery_0995) | 219 | 09-26-2011 | |
| CpeZ family | CAJ73184.1| | CAJ73184.1 | Guillardia theta | CCMP2712 | Cr-PE 545 | n.a. | Low protoscan score | 229 | 10-28-2011 |
| CpeZ family | CwatDRAFT_0406 | ZP_00518848.1 | Crocosphaera watsonii | WH8501 | PC+PEI | Low score, similar to Tery_0980 (IMS101) | 219 | 12-02-2011 | |
| CpeZ family | CWATWH0003_5315a1 | EHJ09924.1 | Crocosphaera watsonii | WH0003 | PC+PEI | Incomplete, 2nd copy? | 186 | 02-22-2012 | |
| L8106_11777 homologs family | AplaP_010100002137 | ZP_06380464.1 | Arthrospira (Spirulina) platensis | Paraca | PC | 1 | Incomplete n-term (end of contig). Almost identical to homologs in other Arthrospira species. | 179 | 08-27-2012 |
| L8106_22089 homologs family | IPF_5551 | CAO86824.1 | Microcystis aeruginosa | PCC7806 | PC | 1 | Incomplete sequence. Another chunk is in IPF_6118 (CAO87604.1) | 325 | 01-10-2012 |
| L8106_22089 homologs family | CwatDRAFT_0171 | ZP_00519405.1 | Crocosphaera watsonii | WH8501 | PC+PEI | split between 3 different contigs: ZP_00517336.1 (CwatDRAFT_2581), ZP_00513741.1 (CwatDRAFT_6637) and ZP_00519405.1 (CwatDRAFT_0171) | 107 | 08-29-2012 | |
| L8106_22089 homologs family | IPF_6118 | CAO87604.1 | Microcystis aeruginosa | PCC7806 | PC | 1 | Shorter than other L8106_22089 homologs | 251 | 04-24-2013 |
| MC7420_3535 homologs family | OSCI_440025 | ZP_07108865.1 | Oscillatoria sp. | PCC6506 (PCC9029/ATCC29081 /UTEX 1547) | PC | 1 | 992 | 12-07-2011 | |
| MC7420_3535 homologs family | alr2986 | NP_487026.1 | Anabaena (Nostoc) sp. | PCC7120 | PC+PEC | 885 | 12-07-2011 | ||
| MC7420_3535 homologs family | IPF_2635 | CAO90934.1 | Microcystis aeruginosa | PCC7806 | PC | 1 | Much shorter than other MC7420_3535 homologs | 263 | 12-07-2011 |
| MC7420_3535 homologs family | L8106_24365 | ZP_01619849.1 | Lyngbya aestuarii | CCY9616 (PCC8106/CCY8106) | PC | 1 | 1044 | 12-07-2011 | |
| MC7420_3535 homologs family | PCC7424_1763 | YP_002377065.1 | Cyanothece sp. | PCC7424 | PC+PEI | 2 | 1475 | 12-07-2011 | |
| MC7420_3535 homologs family | MC7420_2915 | ZP_05024179.1 | Microcoleus chthonoplastes | PCC7420 | PC+PEC | 1355 | 12-07-2011 | ||
| MC7420_3535 homologs family | LYNGBM3L_40770 | ZP_08429450.1 | Lyngbya majuscula | 3L | PC+PEI | 2 | 1273 | 12-07-2011 | |
| MC7420_3535 homologs family | AmaxDRAFT_0188 | ZP_03271372.1 | Arthrospira (Spirulina) maxima | CS-328 | PC | 1 | 786 | 12-07-2011 | |
| MC7420_3535 homologs family | PCC8801_0753 | YP_002370992.1 | Cyanothece sp. | PCC8801 | PC+PEI | 2 | 838 | 12-07-2011 | |
| MC7420_4701 homologs family | MC7420_1061 | ZP_05028540.1 | Microcoleus chthonoplastes | PCC7420 | PC+PEC | This sequence has a much shorter N-term than others. But not a frameshift. | 173 | 09-11-2012 | |
| CotB homologs 1 family | Cyan7425_3615 | YP_002484296.1 | Cyanothece sp. | PCC7425 | PC | 1 | 221 | 09-26-2011 | |
| CotB homologs 1 family | Synpcc7942_2325 | YP_401342.1 | Synechococcus elongatus | PCC7942 | PC | 1 | N-term shortened (30 aa removed : MASAIAKLSAAPASVTPCGSVKDERLSCAS) | 225 | 08-28-2012 |
| CotB homologs 1 family | syc1777_d | YP_172487.1 | Synechococcus elongatus | PCC6301 (ATCC 27144) | PC | 1 | 225 | 09-26-2011 | |
| CotB homologs 2 family | gvip128 | NP_923927.1 | Gloeobacter violaceus | PCC7421 | PC+PEI | 2 | 233 | 11-24-2011 | |
| CotB homologs 2 family | gvip219 | NP_924521.1 | Gloeobacter violaceus | PCC7421 | PC+PEI | 2 | 234 | 11-24-2011 | |
| CotB homologs 2 family | AM1_0043 | YP_001514445.1 | Acaryochloris marina | MBIC11017 (AM1) | PC | 1 | 221 | 09-26-2011 | |
| CotB homologs 2 family | CMS328C | Cyanidioschyzon merolae | 10D | PC | 1 | on contig c19f0009, found by tblastn | 332 | 02-21-2012 | |
| CotB homologs 2 family | CMM226C | Cyanidioschyzon merolae | 10D | PC | 1 | on contig c13f0002, found by tblastn | 420 | 02-21-2012 | |
| CotB homologs 2 family | AplaP_010100006817 | ZP_06381377.1 | Arthrospira (Spirulina) platensis | Paraca | PC | 1 | Incomplete - lacks C-term (end of contig) | 154 | 09-13-2012 |
| CotB homologs 2 family | ACCM5_010100026572 | ZP_09250884.1 | Acaryochloris sp. | CCMEE5410 | APC only | 221 | 01-24-2012 |
Model strains, Marine strains
Last update: 21 Apr 2023 7:50:29
