# DSMZ Plasmid Catalogue - Information file
# Version 2023.02.16.1
# Last Updated February 16, 2023
# Author: Domenico Marra & Francesca Piersigilli & Paolo Romano
# (c) CABRI 1999-2023
$DSMZ_PLASMID_RES=$Resource:[
description:
|<p>
|This is the DSMZ Plasmid database.
contact:
|<ADDRESS>
|Leibniz-Institut DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH,<br>
|Inhoffenstr. 7B,<br>
|D-38124 BRAUNSCHWEIG,<br>
|Germany.<br>
|</ADDRESS><P>
www:
|Web: <a href="http://www.dsmz.de/">http://www.dsmz.de/</a><br>
|Email: Dr Christine Rohde <a href=mailto:christine.rohde@dsmz.de>christine.rohde@dsmz.de</a>
email:
|<a href=mailto:help@dsmz.de>help@dsmz.de</a>
fields: {
Name:
|Name of the element<br>
|<b>Input process</b>: name given by the depositor or as published<br>
|<b>Required for</b>: Minimum Data SETo (MDS)<br>
|<b>Indexed by</b>: Single words<br>
|<b>Skipped characters</b>: /.-<br>
|<b>Not indexed characters</b>: )(+%$"\&'?!|#@<<br>
Collection_number:
|Number of the element in the own collection under
|which it is distributed<br>
|<b>Input process</b>: Collection acronym followed by a number
|separated by space<br>
|<b>Required for</b>: Minimum Data SETo (MDS)<br>
|<b>Indexed by</b>: Unique element<br>
|<b>Skipped characters</b>: ,;:.+*<br>
|<b>Not indexed characters</b>: +$"\&'?!|#@<br>
Type:
|Element type<br>
|<b>Input process</b>: Reference list: plasmid, phasmid, cosmid,
|shuttle vector, transposon, minitransposon, IS element<br>
|<b>Required for</b>: Minimum Data SETo (MDS)<br>
|<b>Indexed by</b>: Single words<br>
|<b>Skipped characters</b>: Blank space<br>
|<b>Not indexed characters</b>: )(+$"\'?!=|#@<br>
Class:
|Origin of the element<br>
|<b>Input process</b>: Reference list: non-recombinant, recombinant<br>
|<b>Required for</b>: Minimum Data SETo (MDS)<br>
|<b>Indexed by</b>: Single words<br>
|<b>Skipped characters</b>: Blank space<br>
|<b>Not indexed characters</b>: )(+$"\'?!=|#@<br>
Other_culture_collection_numbers:
|Numbers of the element under which it is distributed by other
|culture<br>
|collections, incl. non-CABRI numbers if possible
|(e.g. ATCC, NCTC, etc.)<br>
|<b>Input process</b>: Automatically generated.
|If the content of this field cannot automatically be generated at
|the main site it will be removed from the MDS for plasmids.<br>
|<b>Required for</b>: Minimum Data SETo (MDS)<br>
|<b>Indexed by</b>: Single words<br>
|<b>Skipped characters</b>: Blank space<br>
|<b>Not indexed characters</b>: )(+$"\'?!=|#@<br>
Host_for_distribution:
|Taxonomic designation and strain designation of the host organism in
|which the element is distributed<br>
|<b>Input process</b>: e.g. Escherichia coli K12 MC1061.
|Reference list: CABRI in house agreed list<br>
|<b>Required for</b>: Minimum Data SETo (MDS)<br>
|<b>Indexed by</b>: Single words<br>
|<b>Skipped characters</b>: Blank space<br>
|<b>Not indexed characters</b>: )(+$"\'?!=|#@<br>
Medium:
|Name or collection number of the medium on which the host organism is
|preferably grown<br>
|<b>Input process</b>: Free text which may be linked to a text file
|describing the recipe for the medium<br>
|<b>Required for</b>: Minimum Data SETo (MDS)<br>
|<b>Indexed by</b>: Single words<br>
|<b>Skipped characters</b>: Blank space<br>
|<b>Not indexed characters</b>: )(+$"\'?!|#@<br>
Restricted_distribution:
|Restrictions for distribution of the element (hazard group, "for
|research purposes only", patent info, import/export regulations,
|etc.)<br>
|<b>Input process</b>: Free text: "No" or the description of the
|appropriate restrictions<br>
|<b>Required for</b>: Minimum Data SETo (MDS)<br>
|<b>Indexed by</b>: Single words<br>
|<b>Skipped characters</b>: Blank space<br>
|<b>Not indexed characters</b>: )(+$"\'?!=|#@<br>
Literature:
|Original publication in which the element is described<br>
|<b>Input process</b>: Free text<br> <u>New entry</u>: Author, Title
|Year';'Volume(iusse)':'beginning page#'-'ending page#<br>
|The title of the journal is abbreviated following international
|standard rules; the abbreviations are without dot
|The title of the article is not mentioned<br>
|<u>Existing entries</u>: Conversion by SRS following
|CABRI agreed standard<br>
|<b>Required for</b>: Minimum Data SETo (MDS)<br>
|<b>Indexed by</b>: Single words<br>
|<b>Skipped characters skipped</b>: Blank space<br>
|<b>Not indexed characters</b>: )(+$"\'?!=|#@<br>
History_of_deposit:
|History of the element from author to depositor, in reverse order<br>
|<b>Input process</b>: Free text. The name of the depositor must be
|entered obligatory; history when known<br>
|<b>Required for</b>: Minimum Data SETo (MDS)<br>
|<b>Indexed by</b>: Single words<br>
|<b>Skipped characters</b>: Blank space<br>
|<b>Not indexed characters</b>: )(+$"\'?!=|#@<br>
Selectable_phenotype:
|Feature encoded by the element enforcing its host strain
|to maintain the
|element in order to survive under
|appropriate cultivation conditions<br>
|<b>Input process</b>: Reference list: CABRI in house agreed list<br>
|<b>Required for</b>: Minimum Data SETo (MDS)<br>
|<b>Indexed by</b>: Single words<br>
|<b>Skipped characters</b>: Blank space<br>
|<b>Not indexed characters</b>: )(+$"\'?!=|#@<br>
Replicon:
|Names of replicon elements<br>
|<b>Input process</b>: Reference list: CABRI in house agreed list<br>
|<b>Required for</b>: Minimum Data SETo (MDS)<br>
|<b>Indexed by</b>: Single words<br>
|<b>Skipped characters</b>: Blank space<br>
|<b>Not indexed characters</b>: )(+$"\'?!=|#@<br>
Host_range:
|Hosts in which the element can be propagated and/or used and, when
|applicable, the peculiar features that are necessary for making use of
|the special characteristics of the element<br>
|<b>Input process</b>: Free text based on the VECAP3 list in
|Vicente et al., World J. Microbiol. and Biotechnol.
|8 (1992), 519-526<br>
|<b>Required for</b>: Minimum Data SETo (MDS)<br>
|<b>Indexed by</b>: Single words<br>
|<b>Skipped characters</b>: Blank space<br>
|<b>Not indexed characters</b>: )(+$"\'?!=|#@<br>
Properties_and_applications:
|Description of the properties of the element, as well as its
|application possibilities<br>
|<b>Input process</b>: Reference list: CABRI in house agreed list
|based on the VECAP4, VECAP5 and VECAP6 lists in Vicente et al.,
|World J. Microbiol. and Biotechnol. 8 (1992), 519-526)<br>
|<b>Required for</b>: Minimum Data SETo (MDS)<br>
|<b>Indexed by</b>: Single words<br>
|<b>Skipped characters</b>: Blank space<br>
|<b>Not indexed characters</b>: )(+$"\'?!=|#@&<br>
Cloned_gene:
|Description of the genetic markers inserted<br>
|<b>Input process</b>: Free text<br>
|<b>Required for</b>: Full Data SETo (FDS)<br>
|<b>Indexed by</b>: Single words<br>
|<b>Skipped characters</b>: Blank space<br>
|<b>Not indexed characters</b>: )(+$"'?!=|#@<br>
Promoter:
|Type of promoters present on the plasmid.
|The promoters controlling expression of the prokaryotic
|antibiotic resistance genes are not indicated<br>
|<b>Input process</b>: Free text<br>
|<b>Required for</b>: Full Data SETo (FDS)<br>
|<b>Indexed by</b>: Single words<br>
|<b>Skipped characters</b>: Blank space<br>
|<b>Not indexed characters</b>: )(+$"'?!=|#@<br>
Ribosome_binding_site:
|Type of ribosome binding sites present on the plasmid.
|The ribosome binding sites upstream of the prokaryotic antibiotic
|resistance genes are not indicated<br>
|<b>Input process</b>: Free text<br>
|<b>Required for</b>: Full Data SETo (FDS)<br>
|<b>Indexed by</b>: Single words<br>
|<b>Skipped characters</b>: Blank space<br>
|<b>Not indexed characters</b>: )(+$"'?!=|#@<br>
Terminator:
|Type of transcription terminators present on the plasmid<br>
|<b>Input process</b>: Free text<br>
|<b>Required for</b>: Full Data SETo (FDS)<br>
|<b>Indexed by</b>: Single words<br>
|<b>Skipped characters</b>: Blank space<br>
|<b>Not indexed characters</b>: )(+$"'?!=|#@<br>
Further_information:
|Description of peculiar features and special functions which are
|not easily fitted into the other sections.<br>
|Remarks on the history, other names and queries about the fine
|structure of the plasmid are also mentioned here<br>
|<b>Input process</b>: Free text<br>
|<b>Required for</b>: Full Data SETo (FDS)<br>
|<b>Indexed by</b>: Single words<br>
|<b>Skipped characters</b>: Blank space<br>
|<b>Not indexed characters</b>: )(+$"'?!=|#@<br>
Restriction_sites:
|The restriction sites are obtained from REBASE version 611
|(Dr R.J. Roberts Enzyme Database; New England Biolabs).<br>
|They are indicated as U-sites (really unique sites) or as E-sites
|(expression sites). In case the expression site is not unique,
|this is mentioned in the field 'Further information'<br>
|<b>Input process</b>: Free text<br>
|<b>Required for</b>: Full Data SETo (FDS)<br>
|<b>Indexed by</b>: Single words<br>
|<b>Skipped characters</b>: Blank space<br>
|<b>Not indexed characters</b>: )(+$"'?!=|#@<br>
Sequence_detail:
|Part of the nucleotide sequence of the plasmid (e.g. a multiple
|cloning site, the result of a mutagenesis) is described in detail<br>
|<b>Input process</b>: Free text<br>
|<b>Required for</b>: Full Data SETo (FDS)<br>
|<b>Indexed by</b>: Single words<br>
|<b>Skipped characters</b>: Blank space<br>
|<b>Not indexed characters</b>: )(+$"'?!=|#@<br>
}
]