Download MIBiG Annotation Form

MIBiG Annotation Form
11/11/14 13:59
MIBiG&Community&Annota0on&Submission&Form
MIBiG Submission form
Please fill out this form to submit MIBiG-compliant annotation data on a biosynthetic gene cluster.
1
Personal
Name, E-mail, etc.
2
MIBiG Data
Annotation of the gene cluster
3
Comments
Clarifications, comments, etc.
MIBiG data
MIBiG accession number, if pre-assigned
BGC0000628
Use this field for the community annotation only, for those pathways for which an accession number was provided to you. E.g.,
'BGC0000829'.
Biosynthetic class
NRP
Polyketide
RiPP
Terpene
Saccharide
Alkaloid
Other
Hold ctrl or cmd key to select multiple classes in the case of a hybrid gene cluster. Select all categories that apply: e.g., a
polyketide with sugar monomers attached should be both 'Polyketide' and 'Saccharide'.
Key publications associated with this gene cluster, pathway or molecule
25215495
Publications describing experiments on this pathway. Please input PubMed IDs (PMIDs, not PMCIDs!), separated by commas: e.g.,
'12000953,8843436'. Only enter numeric characters and commas.
Gene cluster sequence information
Specify the gene cluster sequence as deposited/submitted in/to GenBank (or ENA/DDBJ). If the pathway is
split over multiple clusters, add multiple genomic locus entries below. The genome or gene cluster sequence
must be submitted to GenBank/ENA/DDBJ (and an accession number must be received) before this form can
be filled out.
Complete gene cluster sequence?
complete
incomplete
unknown
__ Genomic loci
Genomic locus 1
Genomic locus
GenBank nucleotide accession number
ACGO02000004
http://www.marnixmedema.nl/mibig/form.html
Page 1 of 4
MIBiG Annotation Form
11/11/14 13:59
E.g., AL645882. Only use GenBank accessions, not RefSeq accessions or GI numbers.
MIxS-compliant
Whether the GBK/EMBL/DDBJ is annotated with metadata according to the MIxS standard (Yilmaz et al. Nat Biotechnol 29:
415–420). If unknown, leave unticked.
Start coordinate
9724
Insert numeric characters only. May be left empty if gene cluster covers entire GenBank nucleotide record.
End coordinate
22493
Insert numeric characters only. May be left empty if gene cluster covers entire GenBank nucleotide record.
Evidence of involvement
Knock-out studies
Enzymatic assays
Heterologous expression
Proven expression in natural host
Sequence-based prediction
Other
Type of evidence that shows that this gene cluster is responsible for the biosynthesis of the designated molecules. Hold ctrl
or cmd key for multiple selection.
__ Chemical compound(s)
Add one entry for each molecule produced from this pathway / gene cluster.
Compound 1
Chemical compound
Compound name
Lactocillin
Synonyms for this compound
Synonyms for the compound, separated by commas.
Deposited in a chemical database.
Whether there is an entry for the molecule on PubChem, chEMBL, chEBI or ChemSpider. If there is an entry but this does not
contain the correct chemical structure, please do not tick the box to enable you to input updated data.
Compound structure
O=C(NC(C(O)=O)C)C1=CSC(C2=CSC(C3=NC(C
Mandatory for all structurally characterized compounds except for large ones such as most RiPPs and polysaccharides.
Chemical structure entered as SMILES string, preferentially isomeric. This can be easily acquired with standard software such as
ChemDraw, by, e.g., choosing 'Copy as SMILES'.
Molecular formula
C51H45N13O10S7
Exact molecular mass
1224.15184
Observed exact molecular mass in Daltons. Use a dot as a decimal point, not a comma.
Ion type for this mass
[M+H]+
Molecular activities
http://www.marnixmedema.nl/mibig/form.html
Page 2 of 4
MIBiG Annotation Form
11/11/14 13:59
Unknown
Antibacterial
Antifungal
Antioxidant
Cytotoxic
Inhibitor
Siderophore
Signalling
Surfactant
Other
Hold ctrl or cmd key to select multiple items. Enter only proven activities; always provide the publication IDs where the
evidence was provided under 'Key publications' above.
Molecular targets
Binds to the 50S ribosomal subunit, Protein s
Enter proteins, RNAs or other (macro)molecules targeted by this compound, separated by commas. Enter only proven targets;
always provide the publication IDs where the evidence was provided under 'Key publications' below.
Unusual chemical moieties in this molecule
With 'unusual', it is meant that they are not covered by NRPS/PKS/RiPP/terpene/saccharide biosynthetic
mechanisms. Moieties synthesized by a separate PKS like 6-methylsalicylic acid should also be indicated.
Chemical moiety
Chemical moiety
Other
Specify other chemical moiety
Indole carboxylic acid
Sub-cluster involved in the biosynthesis of this moiety
Note that a sub-cluster may consist of genes dispersed throughout the gene cluster. Enter locus tags, protein IDs or gene
IDs (in this order of preference) exactly as they are specified in the submitted GenBank/ENA/DDBJ entry, separated by
commas.
Genes in this gene cluster
RiPP-specific parameters
RiPP subclass
Thiopeptide
Linear
Cyclic
Internal cyclizations of an amino acid or cyclizations of two adjacent amino acids do not count to define a cyclic compound: a
cyclization should bridge residues that would otherwise not be connected.
Genes in cluster encoding RiPP precursor peptides
RiPP precursor
Gene ID:
hmpref0514_11728
Enter locus tags, protein IDs or gene IDs (in this order of preference) that make up this operon, exactly as they are
specified in the submitted GenBank/ENA/DDBJ entry, separated by commas.
RiPP core peptide amino acid sequence(s)
http://www.marnixmedema.nl/mibig/form.html
Page 3 of 4
MIBiG Annotation Form
11/11/14 13:59
SCTTCTCCCSCCA
Input sequence as single-AA abbreviations, e.g. 'ITSISLCTPGCKTGALMGCNMKTATCHCSIHVSK'. If there are multiple (such as
in the case of cyanobactins), separate by commas.
Length of the leader peptide
45
Length in AA, including N-terminal signal if present.
Length of the follower peptide
13
Amino acid sequence(s) of cleavage recognition site(s), if known. If multiple, separate by
commas.
Recognition motif in leader peptide for modification peptide
E.g., FNLD for certain lanthipeptides.
Peptidase(s) involved in precursor cleavage
Enter locus tags, protein IDs or gene IDs (in this order of preference), exactly as they are used in the submitted
GenBank/ENA/DDBJ entry, separated by commas.
Crosslinks within final peptide
Add Item
Back
http://www.marnixmedema.nl/mibig/form.html
Next
Page 4 of 4