* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
Download MIBiG Annotation Form
Genetic engineering wikipedia , lookup
Public health genomics wikipedia , lookup
Protein moonlighting wikipedia , lookup
Copy-number variation wikipedia , lookup
Pathogenomics wikipedia , lookup
Epigenetics of diabetes Type 2 wikipedia , lookup
Saethre–Chotzen syndrome wikipedia , lookup
Genome evolution wikipedia , lookup
Genome (book) wikipedia , lookup
Gene therapy of the human retina wikipedia , lookup
Neuronal ceroid lipofuscinosis wikipedia , lookup
Nutriepigenomics wikipedia , lookup
Vectors in gene therapy wikipedia , lookup
Gene therapy wikipedia , lookup
Genome editing wikipedia , lookup
Gene expression programming wikipedia , lookup
Point mutation wikipedia , lookup
Gene desert wikipedia , lookup
Gene expression profiling wikipedia , lookup
Mir-92 microRNA precursor family wikipedia , lookup
Site-specific recombinase technology wikipedia , lookup
Helitron (biology) wikipedia , lookup
Microevolution wikipedia , lookup
Gene nomenclature wikipedia , lookup
Therapeutic gene modulation wikipedia , lookup
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