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ssd strain

Probable staphyloferrin b siderophore synthesis decarboxylase protein

Annotation score:1 out of 5

The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score cannot be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.

– Protein inferred from homology i

This indicates the type of evidence that supports the existence of the protein. Note that the ‘protein existence’ evidence does not give information on the accuracy or correctness of the sequence(s) displayed.

Select a section on the left to see content.

This section provides any useful information about the protein, mostly biological knowledge.

This subsection of the ‘Function’ section provides information relevant to cofactors. A cofactor is any non-protein substance required for a protein to be catalytically active. Some cofactors are inorganic, such as the metal atoms zinc, iron, and copper in various oxidation states. Others, such as most vitamins, are organic.

Information which has been generated by the UniProtKB automatic annotation system, without manual validation.

Automatic assertion according to rules i

The Gene Ontology (GO) project provides a set of hierarchical controlled vocabulary split into 3 categories:

GO – Molecular function i

  • catalytic activity Source: InterPro
GO – Biological process i
  • polyamine biosynthetic process Source: InterPro
Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.

Names & Taxonomy i

This subsection of the Names and taxonomy section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.

Information which has been imported from another database using automatic procedures.

Automatic assertion inferred from database entries i

This subsection of the Names and taxonomy section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: ‘Name’, ‘Synonyms’, ‘Ordered locus names’ and ‘ORF names’.

Automatic assertion inferred from database entries i

Automatic assertion inferred from database entries i

This subsection of the Names and taxonomy section indicates if the gene coding for the protein originates from the hydrogenosome, the mitochondrion, the nucleomorph, different plastids or a plasmid. The absence of this section means that the gene is located in one of the main chromosomal element(s).

Automatic assertion inferred from database entries i

This subsection of the Names and taxonomy section provides information on the name(s) of the organism that is the source of the protein sequence.

Automatic assertion inferred from database entries i

This subsection of the Names and taxonomy section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the ‘taxonomic identifier’ or ‘taxid’.

This subsection of the Names and taxonomy section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.

This subsection of the Names and taxonomy section is present for entries that are part of a proteome, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.

A UniProt proteome can consist of several components.
The component name refers to the genomic component encoding a set of proteins.

This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.

Protein-protein interaction databases

STRING: functional protein association networks

This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.

Family & Domains i

Domains and Repeats

This subsection of the Family and Domains section describes the position and type of a domain, which is defined as a specific combination of secondary structures organized into a characteristic three-dimensional structure or fold.

Information which has been generated by the UniProtKB automatic annotation system, without manual validation.

Automatic assertion inferred from signature match i

Automatic assertion inferred from signature match i

This subsection of the ‘Family and domains’ section provides information about the sequence similarity with other proteins.

Sequence similarities i

Automatic assertion according to rules i

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

Identification of Orthologs from Complete Genome Data

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

Integrated resource of protein families, domains and functional sites

Pfam protein domain database

Protein Motif fingerprint database; a protein domain database

Superfamily database of structural and functional annotation

PROSITE; a protein domain and family database

This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including length and molecular weight. The information is filed in different subsections. The current subsections and their content are listed below:

This subsection of the Sequence section indicates if the canonical sequence displayed by default in the entry is complete or not.

Sequence status i : Complete.

The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.

It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.

However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).

The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x 64 + x 4 + x 3 + x + 1. The algorithm is described in the ISO 3309 standard.

Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.
Cyclic redundancy and other checksums
Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993))

Checksum: i 57A2CD5348D4B0D4

Sequence databases

EMBL nucleotide sequence database

GenBank nucleotide sequence database

DNA Data Bank of Japan; a nucleotide sequence database

NCBI Reference Sequences

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

Database of genes from NCBI RefSeq genomes

KEGG: Kyoto Encyclopedia of Genes and Genomes

Pathosystems Resource Integration Center (PATRIC)

This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (UniRef).

Similar proteins i

  • 100% Identity
  • 90% Identity
  • 50% Identity

This section is used to point to information related to entries and found in data collections other than UniProtKB.

Sequence databases
3D structure databases

Database of comparative protein structure models

SWISS-MODEL Interactive Workspace

Protein-protein interaction databases
Genome annotation databases
EnsemblBacteria i CAD17575; CAD17575; RSp0424
GeneID i 1222731
KEGG i rso:RSp0424
PATRIC i fig|267608.8.peg.3905
Phylogenomic databases
eggNOG i COG0019, Bacteria
HOGENOM i CLU_026444_0_3_4
OMA i NISHHDF
Enzyme and pathway databases
Family and domain databases

ProtoNet; Automatic hierarchical classification of proteins

MobiDB: a database of protein disorder and mobility annotations

This section provides general information on the entry.

Entry information i

This subsection of the ‘Entry information’ section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.

This subsection of the ‘Entry information’ section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called ‘Primary (citable) accession number’.

This subsection of the ‘Entry information’ section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification (‘Last modified’). The version number for both the entry and the canonical sequence are also displayed.

This subsection of the ‘Entry information’ section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (reviewed) or to the computer-annotated TrEMBL section (unreviewed).

This section contains any relevant information that doesn’t fit in any other defined sections

UniProtKB Keywords constitute a controlled vocabulary with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.

Keywords – Technical term i

Automatic assertion inferred from database entries i

Tools
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Probable staphyloferrin b siderophore synthesis decarboxylase protein Annotation score:1 out of 5 The annotation score provides a heuristic measure of the annotation content of a UniProtKB

Ssd strain

BacDive ID: 17673

Species: Haloplasma contractile

Strain Designation: SSD-17B

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Haloplasma contractile SSD-17B is an anaerobe, mesophilic bacterium that was isolated from anoxic hypersaline brine-sediment interface.

  1. anaerobe
  2. mesophilic
  3. 16S sequence
  4. Bacteria
  5. genome sequence
[Ref.: #7744] Sample type/isolated from anoxic hypersaline brine-sediment interface
[Ref.: #7744] Geographic location (country and/or sea, region) Red Sea, Shaban Deep
[Ref.: #7744] Country Saudi Arabia
[Ref.: #7744] Country ISO 3 Code SAU
[Ref.: #7744] Continent Asia
Isolation sources categories
#Environmental #Aquatic
#Environmental #Aquatic #Sediment
#Condition #Anoxic (anaerobic)
#Condition #Saline
  • References
  • #7744 Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18853
  • #20215 Leibniz Institute DSMZ D.Gleim, M.Kracht, N.Weiss et. al.: Prokaryotic Nomenclature Up-to-date – compilation of all names of Bacteria and Archaea, validly published according to the Bacteriological Code since 1. Jan. 1980, and validly published nomenclatural changes since .
  • #20218 Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 – 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
  • #66792 Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .
  • * These References are textmined

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Metadata on 17673