CyanoLyase

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 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
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
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 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 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 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 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
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 CMM226C Cyanidioschyzon merolae 10D PC 1 on contig c13f0002, found by tblastn 420 02-21-2012

Model strain Model strains, Marine strains

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