The three genes for the L, M and H subunit.
| Name | Accession | Start | Stop | Strand | GeneID | Locus | Locus tag | Protein product | Length | Protein name |
|---|---|---|---|---|---|---|---|---|---|---|
| Un | NZ_JTHE01000129.1 | 1447 | 2301 | + | - | - | QQ91_RS05655 | WP_039723522.1 | 284 | photosynthetic reaction center subunit L |
| Un | NZ_JTHE01000129.1 | 2315 | 3298 | + | - | - | QQ91_RS05660 | WP_039723523.1 | 327 | photosynthetic reaction center subunit M |
| Un | NZ_JTHE01000254.1 | 3008 | 3799 | - | - | - | QQ91_RS10590 | WP_039724487.1 | 263 | photosynthetic reaction center subunit H |
1. The best hit for the L subunit was to:
Photosynthetic reaction center subunit L [Oceanibaculum indicum]
ref|WP_008944428.1|
| Score | Expect | Method | Identities | Positives | Gaps |
|---|---|---|---|---|---|
| 442 bits(1137) | 2e-153 | Compositional matrix adjust. | 222/280(79%) | 240/280(85%) | 1/280(0%) |
2. The best hit for the M subunit was to:
Photosynthetic reaction center subunit M [Ahrensia sp. R2A130]
ref|WP_009758337.1|
| Score | Expect | Method | Identities | Positives | Gaps | |||
|---|---|---|---|---|---|---|---|---|
| 457 bits(1175) | 5e-158 | Compositional matrix adjust. | 221/308(72%) | 260/308(84%) | 2/308(0%) |
3. The best hit for the H subunit was to:
Photosynthetic reaction centre, H-chain [Hoeflea phototrophica]
ref|WP_007196606.1|
| Score | Expect | Method | Identities | Positives | Gaps |
|---|---|---|---|---|---|
| 282 bits(721) | 5e-91 | Compositional matrix adjust. | 139/258(54%) | 175/258(67%) | 2/258(0%) |
What is going on?
When I BLASTed the BchZ subunit of chlorophyllide a reductase from Rhodobacter sphaeroides, which makes bacteriochlorophyllide a from chlorophyllide a... the best hit was to this same strain of cyanobacteria: but it seems it is a fragment only (see image below, never mind the annotation). A close homologous to BchY did not retrieve anything out of the ordinary, the same for BchX. So this cyanobacterium cannot really make bacteriochlorophyll... I wonder if the anoxygenic Type II reaction center in this strain could be active using chlorophyll a along side PSII and PSI.
The fact that the best hits to the reaction center proteins are below 80% means that the alphaproteobacterium that donated this genes represents at least a new genus or something.
UPDATE: It turned out after all to be contamination. It might be that the cultures used were not completely axenic. It's a pity.
