SIDERITE update log

[RuolinHe]

In this conversation, SIDERITE team will record the update of SIDERITE database.

Announce new siderophores will be added into database in advance.

The content is same with Google Group of SIDERITE.

[RuolinHe]

Recently (may April or May in 2024), we will update SIDERITE to cover new siderophores.

As of 2024-3-13, there are 52 new siderophores with unique structures after the first version of SIDERITE.

Here is the list of new siderophore names:

Aeruginaldehyde
Aerugine
Aeruginoic acid
Aeruginol
Avenic acid B
C12 acylated desferrioxamine+200+200+30
C12 acylated desferrioxamine+200+30
C12 acylated desferrioxamine+30
Caribactin A
Caribactin B
Caribactin C
Caribactin D
Caribactin E
Caribactin F
Chlorodactyloferrin
Dactyloferrin
Dihydroaeruginoic acid
Fulvivirgamide A2
Fulvivirgamide B2
Fulvivirgamide B3
Fulvivirgamide B4
Methyl 2-(2-hydroxyphenyl)-4,5-dihydrooxazole-4-carboxylate
Methyl thiazostatin B
Myxochelin B-succinate
N,N′,N′-tris(S-2,3-dihydroxybenzoyl)-O-seryl-O-seryl methoxy serinate
N,N′-bis(S-2,3-dihydroxybenzoyl)-O-seryl methoxy serinate
Nobachelin A
Nobachelin B
Nobachelin C
Pacifibactin-Ser
Pulicatin A
Pulicatin B
Pulicatin C
Pulicatin D
Pulicatin E
Pulicatin F
Pulicatin G
Pulicatin H
Pulicatin I
Pulicatin J
Pyonitrin A
Pyonitrin B
Pyonitrin C
Pyonitrin D
Pyoverdine P482
Serratiochelin D
Spoxazomicin E
Streptochelin A
Thermochelin
Thiazostatin C
Tistrellabactin A
Tistrellabactin B

[RuolinHe]

SIDERITE update log in 20240531

Number change

The number of SIDERITE records = 872 (last time) + 77 (new records) - 4 (4 duplication: NBRI16716A, Amonabactin T789, Amonabactin P750, Pacifibactin-Gly. See "Correct and update records" for more details.) = 945

The number of unique siderophore structures: 649 + 62 (new) - 4 ( 4 duplication: SID00046, SID00047, SID00068, SID00170) = 707

The number of Siderophore clusters: 25 - 1 (Cluster 5) + 2 (Cluster 5 and Cluster 26) = 26

Archive files

SIDERITE_records_20240531.xlsx
contains 945 siderophore records

SIDERITE_unique_structures_20240531.xlsx
contains 707 unique siderophore structures

The same siderophore structures can be found in different species, leading to multiple records. Therefore, the number of siderophore records can exceed the number of unique siderophore structures.

They can be downloaded in zenodo: https://zenodo.org/doi/10.5281/zenodo.11441109

Correct and update records

1. Corrected the structure of Malleobactin A (SID00236) in Burkholderia pseudomallei
2. Corrected name of the second record of Pacifibactin-Gly in Alcanivorax pacificus. It should be Pacifibactin-Ser, rather than Pacifibactin-Gly.
3. Deleted duplicate NBRI16716A of Perisporiopsis melioloides Mer-f16716.
4. Corrected name of Linear trichrisobactin. It should be Linear trichrysobactin.
5. Corrected name of Aeruginic acid. It should be Aeruginoic acid.
6. Merged Amonabactin T789 (SID00204) into Amonabactin T (SID00203). They are same in the structure.
7. Merged Amonabactin P750 (SID00205) into Amonabactin P (SID00206). They are same in the structure.
8. Merged Linear trichrysobactin (SID00217) into Frederiksenibactin (SID00218). They are same in the structure.
9. Merged Legiobactin (SID00126) into Rhizoferrin (SID00127). They are same in the structure.
10. Deleted SID00204, SID00205, SID00217, SID00126 due to mergence.
11. Exchange the main name and other name for SID00046, SID00047, SID00068, SID00170.
    Now main name (the other name) is as follows:
    Gentisic acid(2,5-dihydroxybenzoic acid)
    Protocatechuic acid(3,4-dihydroxybenzoic acid)
    Salicylic acid(2-hydroxybenzoic acid)
    Itoic acid(2,3-dihydroxybenzoylglycine)
12. Update Phylum due to NCBI Taxonomy update: Proteobacteria is replaced by Pseudomonadota. Actinobacteria is replaced by Actinomycetota. Bacteroidetes is replaced by Bacteroidota.
13. Update Class due to NCBI Taxonomy update: Actinomycetia is replaced by Actinomycetes.
14. Update Order due to NCBI Taxonomy update: Streptomycetales is replaced by Kitasatosporales.

Update in excel

SIDERITE_records

1. Removed "IUPAC Name" column because most records don't contain this item.
2. Added new Column Contributor in BI column which records the contributor (except SIDERITE team) for this record.

Note: The pictures of siderophore structures in "structure" column are no longer updated.

SIDERITE_unique_structures

1. Changed Header into Pseudomonadota from Proteobacteria.
2. Changed Header into Actinomycetota from Actinobacteria.
3. Changed Header into Bacteroidota from Bacteroidetes.
4. Changed Header into Siderophore Cluster from Siderophore Large Class.
5. Changed Header into Siderophore Group from Siderophore Class.
6. Changed Header into Siderophore Index from Siderophore Small Id.
7. Added new Column Myxococcota in AM column which is a new bacteria phylum for siderophore producers.
8. Added new Column Contributor in BQ column which records the contributor (except SIDERITE team) for this record.

Update in Siderophore Cluster

Original Cluster 5 (including SID00082, SID00141, SID00602, SID00603, SID00604, SID00605, SID00606, SID00607, SID00632, SID00633, SID00634, SID00635, SID00636, SID00637)is merged into Cluster 1.

New Cluster 5 (including SID00694, SID00695, SID00692, SID00691, SID00690, SID00689, SID00652, SID00650, SID00699, SID00698, SID00700, SID00697) and Cluster 26 (including SID00671) is added.

New siderophroes

As of 2024-5-31, there are 62 new siderophores with unique structures after the last version of SIDERITE.

Here is the list of new siderophore names:

Aeruginaldehyde

Aerugine

Aeruginol

Arthrobactin A

Avenic acid B

C12 acylated desferrioxamine+200+200+30

C12 acylated desferrioxamine+200+30

C12 acylated desferrioxamine+30

Caribactin A

Caribactin B

Caribactin C

Caribactin D

Caribactin E

Caribactin F

Chlorodactyloferrin

Dactyloferrin

Desoxy-desferrioxamine B

Desoxy-desferrioxamine D1

Didesoxy-desferrioxamine B

Didesoxy-desferrioxamine D1

Dihydroaeruginoic acid

Ethylenediamine-disuccinate

Fulvivirgamide A2

Fulvivirgamide B2

Fulvivirgamide B3

Fulvivirgamide B4

Megalochelin

Methyl 2-(2-hydroxyphenyl)-4,5-dihydrooxazole-4-carboxylate

Methyl thiazostatin B

Myxochelin B-succinate

N,N′,N′-tris(S-2,3-dihydroxybenzoyl)-O-seryl-O-seryl methoxy serinate

N,N′-bis(S-2,3-dihydroxybenzoyl)-O-seryl methoxy serinate

N-deoxy arthrobactin A

Nobachelin A

Nobachelin B

Nobachelin C

Pacifibactin-Ser

Pulicatin A

Pulicatin B

Pulicatin C

Pulicatin D

Pulicatin E

Pulicatin F

Pulicatin G

Pulicatin H

Pulicatin I

Pulicatin J

Pyonitrin A

Pyonitrin B

Pyonitrin C

Pyonitrin D

Pyoverdine P482

Serratiochelin D

Spoxazomicin E

Streptochelin A

Thermochelin

Thiazostatin C

Tistrellabactin A

Tistrellabactin B

Variochelin C

Variochelin D

Variochelin E