snapshot_type: uniprot_record_evidence_extract
archive:
  repository: https://github.com/ai4curation/uniprot-orphan-analysis
  commit: f6a331cb47f61256ad070bbaa75567094ef64e8a
extraction: Original source line ranges with two context lines; not complete records. Structured fields
  are selected from the same archived snapshots. Sequence values are replaced by lengths and SHA-256 digests.
sources:
- url: https://rest.uniprot.org/uniprotkb/P0A434.json
  retrieved_at: '2026-10-18T23:39:09.123417+00:00'
  uniprot_release: '2026_03'
- url: https://rest.uniprot.org/proteomes/UP000596117.json
  retrieved_at: '2026-10-18T23:39:09.282256+00:00'
  uniprot_release: '2026_03'
- url: https://rest.uniprot.org/unisave/P0A434?format=txt&versions=74
  retrieved_at: '2026-10-18T23:39:09.555094+00:00'
  uniprot_release: '2026_03'
- url: https://rest.uniprot.org/unisave/P0A434?format=txt&versions=93
  retrieved_at: '2026-10-18T23:39:12.341560+00:00'
  uniprot_release: '2026_03'
- url: https://rest.uniprot.org/unisave/P0A434?format=txt&versions=105
  retrieved_at: '2026-10-18T23:39:14.454653+00:00'
  uniprot_release: '2026_03'
observations:
  primary_accession: P0A434
  alternative_accession: null
  sequence_identical: null
  primary_sequence_length: 365
  alternative_sequence_length: null
  shared_uniparc_id: null
  same_taxon: null
  reference_proteome: UP000596117
  proteome_is_reference: true
  proteome_taxon_matches: true
  primary_in_reference_proteome: false
  alternative_in_reference_proteome: null
  searched_reference_proteomes:
  - UP000596117
  primary_in_any_reference_proteome: false
  sampled_history_versions:
  - 74
  - 93
  - 105
  sampled_versions_with_proteome_links: []
current_records:
- primaryAccession: P0A434
  entryType: UniProtKB reviewed (Swiss-Prot)
  entryAudit:
    firstPublicDate: '2005-03-15'
    lastAnnotationUpdateDate: '2026-09-02'
    lastSequenceUpdateDate: '2005-03-15'
    entryVersion: 110
    sequenceVersion: 1
  genes:
  - geneName:
      value: opd
  geneLocations:
  - value: pCMS1
    geneEncodingType: Plasmid
  organism:
    scientificName: Brevundimonas diminuta
    taxonId: 293
  sequence:
    length: 365
    sha256: 9d1278b38575c3f1a16a62725fe17a7ffef89237170c7d531862d63d7f4ab501
  uniProtKBCrossReferences: []
reference_proteomes:
- id: UP000596117
  proteomeType: Reference proteome
  taxonomy:
    scientificName: Brevundimonas diminuta
    synonyms:
    - Pseudomonas diminuta
    taxonId: 293
    mnemonic: BREDI
unisave_records:
- entry_version: 74
  url: https://rest.uniprot.org/unisave/P0A434?format=txt&versions=74
  entry_date: 11-NOV-2015, entry version 74.
  proteomes: []
  reference_proteome_keyword: false
  record_text: ''
- entry_version: 93
  url: https://rest.uniprot.org/unisave/P0A434?format=txt&versions=93
  entry_date: 12-AUG-2020, entry version 93.
  proteomes: []
  reference_proteome_keyword: false
  record_text: ''
- entry_version: 105
  url: https://rest.uniprot.org/unisave/P0A434?format=txt&versions=105
  entry_date: 27-NOV-2024, entry version 105.
  proteomes: []
  reference_proteome_keyword: false
  record_text: ''
archived_sources:
- path: genes/BREDI/opd/opd-record-evidence.yaml
  url: https://github.com/ai4curation/uniprot-orphan-analysis/blob/f6a331cb47f61256ad070bbaa75567094ef64e8a/genes/BREDI/opd/opd-record-evidence.yaml
  sha256: cb082c93d0beeef4518104ca2831927882f5b9ca3b6d5c3b61498f72229d8f3f
  excerpts:
  - start_line: 31
    end_line: 35
    text: |2
        searched_reference_proteomes:
        - UP000596117
        primary_in_any_reference_proteome: false
        sampled_history_versions:
        - 74
  - start_line: 1120
    end_line: 1124
    text: |2
        geneLocations:
        - value: pCMS1
          geneEncodingType: Plasmid
        keywords:
        - id: KW-0002
  - start_line: 2442
    end_line: 2447
    text: |
      - entry_version: 74
        url: https://rest.uniprot.org/unisave/P0A434?format=txt&versions=74
        entry_date: 11-NOV-2015, entry version 74.
        proteomes: []
        reference_proteome_keyword: false
        record_text: |
  - start_line: 2758
    end_line: 2763
    text: |
      - entry_version: 93
        url: https://rest.uniprot.org/unisave/P0A434?format=txt&versions=93
        entry_date: 12-AUG-2020, entry version 93.
        proteomes: []
        reference_proteome_keyword: false
        record_text: |
  - start_line: 3146
    end_line: 3151
    text: |
      - entry_version: 105
        url: https://rest.uniprot.org/unisave/P0A434?format=txt&versions=105
        entry_date: 27-NOV-2024, entry version 105.
        proteomes: []
        reference_proteome_keyword: false
        record_text: |
- path: genes/BREDI/opd/opd-bioinformatics/reference-counterparts/comparison.yaml
  url: https://github.com/ai4curation/uniprot-orphan-analysis/blob/f6a331cb47f61256ad070bbaa75567094ef64e8a/genes/BREDI/opd/opd-bioinformatics/reference-counterparts/comparison.yaml
  sha256: d9b61dc9b43eb6b929440ae3d21b3ba198fe8cdca58ab8d7e0abfc30195b306b
  excerpts:
  - start_line: 25
    end_line: 29
    text: |2
        - -v
        - '1'
        target_sequence_count: 3387
        query_sha256: ea44562b3e62a235e7fd017800eccac1006e4b50cb04c02b29c9984898f97e4f
        targets_sha256: 5ab347579c8adc3c90421c97da8b1c580d43bdff0613c29e0d4ead2417831c0d
  - start_line: 44
    end_line: 47
    text: |2
          sha256: 5ab347579c8adc3c90421c97da8b1c580d43bdff0613c29e0d4ead2417831c0d
        detailed_alignment_limit: 10
      candidate_count: 0
      candidates: []
comparison:
  provenance:
    query_accession: P0A434
    run_at: '2026-10-18T23:34:32.106266+00:00'
    biopython_version: '1.85'
    mmseqs_version: 18-8cc5c
    command:
    - mmseqs
    - easy-search
    - genes/BREDI/opd/opd-bioinformatics/reference-counterparts/query.fasta
    - .cache/orphan-curated/UP000596117.fasta
    - genes/BREDI/opd/opd-bioinformatics/reference-counterparts/search.tsv
    - genes/BREDI/opd/opd-bioinformatics/reference-counterparts/tmp
    - --threads
    - '4'
    - -s
    - '7.5'
    - -e
    - 1e-5
    - --max-seqs
    - '1000'
    - --format-output
    - query,target,pident,alnlen,qstart,qend,qlen,tstart,tend,tlen,evalue,bits
    - --remove-tmp-files
    - '1'
    - -v
    - '1'
    target_sequence_count: 3387
    query_sha256: ea44562b3e62a235e7fd017800eccac1006e4b50cb04c02b29c9984898f97e4f
    targets_sha256: 5ab347579c8adc3c90421c97da8b1c580d43bdff0613c29e0d4ead2417831c0d
    global_alignment:
      mode: global
      matrix: BLOSUM62
      open_gap: -10
      extend_gap: -0.5
      terminal_gaps_penalized: true
    identity_denominator: All global alignment columns, including gaps
    coverage_denominator: Full query/target length; numerator is paired nongap residues
    limitation: MMseqs2 heuristic search; no guarantee of exhaustive retrieval or locus equivalence
    target_source:
      url: https://rest.uniprot.org/uniprotkb/stream?query=proteome%3AUP000596117&format=fasta
      retrieved_at: '2026-10-18T23:32:34.408702+00:00'
      uniprot_release: '2026_03'
      sequence_count: 3387
      sha256: 5ab347579c8adc3c90421c97da8b1c580d43bdff0613c29e0d4ead2417831c0d
    detailed_alignment_limit: 10
  candidate_count: 0
  retained_alignment_count: 0
  candidates: []