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/Q93XQ5.json
  retrieved_at: '2026-10-18T23:39:42.050994+00:00'
  uniprot_release: '2026_03'
- url: https://rest.uniprot.org/uniprotkb/A0A314LG79.json
  retrieved_at: '2026-10-18T23:39:42.229220+00:00'
  uniprot_release: '2026_03'
- url: https://rest.uniprot.org/proteomes/UP000187609.json
  retrieved_at: '2026-10-18T23:39:42.401250+00:00'
  uniprot_release: '2026_03'
- url: https://rest.uniprot.org/unisave/Q93XQ5?format=txt&versions=59
  retrieved_at: '2026-10-18T23:39:44.041374+00:00'
  uniprot_release: '2026_03'
- url: https://rest.uniprot.org/unisave/Q93XQ5?format=txt&versions=71
  retrieved_at: '2026-10-18T23:39:44.236157+00:00'
  uniprot_release: '2026_03'
- url: https://rest.uniprot.org/unisave/Q93XQ5?format=txt&versions=81
  retrieved_at: '2026-10-18T23:39:46.831853+00:00'
  uniprot_release: '2026_03'
observations:
  primary_accession: Q93XQ5
  alternative_accession: A0A314LG79
  sequence_identical: false
  primary_sequence_length: 388
  alternative_sequence_length: 388
  shared_uniparc_id: null
  same_taxon: true
  reference_proteome: UP000187609
  proteome_is_reference: true
  proteome_taxon_matches: true
  primary_in_reference_proteome: false
  alternative_in_reference_proteome: true
  searched_reference_proteomes:
  - UP000187609
  primary_in_any_reference_proteome: false
  sampled_history_versions:
  - 59
  - 71
  - 81
  sampled_versions_with_proteome_links: []
current_records:
- primaryAccession: Q93XQ5
  entryType: UniProtKB reviewed (Swiss-Prot)
  entryAudit:
    firstPublicDate: '2022-08-03'
    lastAnnotationUpdateDate: '2026-09-02'
    lastSequenceUpdateDate: '2001-12-01'
    entryVersion: 85
    sequenceVersion: 1
  genes:
  - geneName:
      evidences:
      - evidenceCode: ECO:0000303
        source: PubMed
        id: '11299398'
      value: PMT1
  organism:
    scientificName: Nicotiana attenuata
    taxonId: 49451
  sequence:
    length: 388
    sha256: eb3b72a82af5341a13a3327f43ee4e09b71d5f31860019f1c1f54c8dffe1174c
  uniProtKBCrossReferences: []
- primaryAccession: A0A314LG79
  entryType: UniProtKB reviewed (Swiss-Prot)
  entryAudit:
    firstPublicDate: '2022-08-03'
    lastAnnotationUpdateDate: '2026-09-02'
    lastSequenceUpdateDate: '2018-10-10'
    entryVersion: 25
    sequenceVersion: 1
  genes:
  - geneName:
      evidences:
      - evidenceCode: ECO:0000303
        source: Reference
        id: Ref.1
      value: PMT3
    orfNames:
    - evidences:
      - evidenceCode: ECO:0000312
        source: EMBL
        id: OIT40668.1
      value: A4A49_61142
  organism:
    scientificName: Nicotiana attenuata
    taxonId: 49451
  sequence:
    length: 388
    sha256: debdd406f070a7fbd9f3d0714bd09a5d2ca3b6845f0247a6bd89e215fcd9b394
  uniProtKBCrossReferences:
  - database: Gramene
    id: OIT40668
    properties:
    - key: ProteinId
      value: OIT40668
    - key: GeneId
      value: A4A49_61142
  - database: Proteomes
    id: UP000187609
    properties:
    - key: Component
      value: Unassembled WGS sequence
reference_proteomes:
- id: UP000187609
  proteomeType: Reference proteome
  taxonomy:
    scientificName: Nicotiana attenuata
    commonName: Coyote tobacco
    taxonId: 49451
    mnemonic: NICAT
unisave_records:
- entry_version: 59
  url: https://rest.uniprot.org/unisave/Q93XQ5?format=txt&versions=59
  entry_date: 09-DEC-2015, entry version 59.
  proteomes: []
  reference_proteome_keyword: false
  record_text: ''
- entry_version: 71
  url: https://rest.uniprot.org/unisave/Q93XQ5?format=txt&versions=71
  entry_date: 12-AUG-2020, entry version 71.
  proteomes: []
  reference_proteome_keyword: false
  record_text: ''
- entry_version: 81
  url: https://rest.uniprot.org/unisave/Q93XQ5?format=txt&versions=81
  entry_date: 27-NOV-2024, entry version 81.
  proteomes: []
  reference_proteome_keyword: false
  record_text: ''
archived_sources:
- path: genes/NICAT/NaPMT1.1/NaPMT1.1-record-evidence.yaml
  url: https://github.com/ai4curation/uniprot-orphan-analysis/blob/f6a331cb47f61256ad070bbaa75567094ef64e8a/genes/NICAT/NaPMT1.1/NaPMT1.1-record-evidence.yaml
  sha256: f7bc7b7d8962d099c443dcd56adcd1300fe11f73a751f5bb1b68e857a62a8620
  excerpts:
  - start_line: 26
    end_line: 38
    text: |2
        alternative_sequence_length: 388
        shared_uniparc_id: null
        same_taxon: true
        reference_proteome: UP000187609
        proteome_is_reference: true
        proteome_taxon_matches: true
        primary_in_reference_proteome: false
        alternative_in_reference_proteome: true
        searched_reference_proteomes:
        - UP000187609
        primary_in_any_reference_proteome: false
        sampled_history_versions:
        - 59
  - start_line: 100
    end_line: 104
    text: |2
              source: PubMed
              id: '11299398'
            value: PMT1
        comments:
        - texts:
  - start_line: 905
    end_line: 909
    text: |2
              source: Reference
              id: Ref.1
            value: PMT3
          orfNames:
          - evidences:
  - start_line: 2010
    end_line: 2015
    text: |
      - entry_version: 59
        url: https://rest.uniprot.org/unisave/Q93XQ5?format=txt&versions=59
        entry_date: 09-DEC-2015, entry version 59.
        proteomes: []
        reference_proteome_keyword: false
        record_text: |
  - start_line: 2076
    end_line: 2081
    text: |
      - entry_version: 71
        url: https://rest.uniprot.org/unisave/Q93XQ5?format=txt&versions=71
        entry_date: 12-AUG-2020, entry version 71.
        proteomes: []
        reference_proteome_keyword: false
        record_text: |
  - start_line: 2153
    end_line: 2158
    text: |
      - entry_version: 81
        url: https://rest.uniprot.org/unisave/Q93XQ5?format=txt&versions=81
        entry_date: 27-NOV-2024, entry version 81.
        proteomes: []
        reference_proteome_keyword: false
        record_text: |
- path: genes/NICAT/NaPMT1.1/NaPMT1.1-bioinformatics/reference-counterparts/comparison.yaml
  url: https://github.com/ai4curation/uniprot-orphan-analysis/blob/f6a331cb47f61256ad070bbaa75567094ef64e8a/genes/NICAT/NaPMT1.1/NaPMT1.1-bioinformatics/reference-counterparts/comparison.yaml
  sha256: f4506f466ea18879e30f57f72f257a93cd3ed93bcd940a34cc9caece004f497f
  excerpts:
  - start_line: 25
    end_line: 29
    text: |2
        - -v
        - '1'
        target_sequence_count: 32918
        query_sha256: 9a8a3d4fc974d7154c18660a43596cfd7a67aa831d6b3c23adf34bed98fb5354
        targets_sha256: ff3c425fd8ecd38823462d1a2a9f0f94c67567a12c15fa74071f54e088c7c4bc
  - start_line: 44
    end_line: 48
    text: |2
          sha256: ff3c425fd8ecd38823462d1a2a9f0f94c67567a12c15fa74071f54e088c7c4bc
        detailed_alignment_limit: 10
      candidate_count: 8
      candidates:
      - accession: A0A314LG79
  - start_line: 52
    end_line: 64
    text: |2
        bit_score: 787.0
        global_score: 2047.0
        query_length: 388
        target_length: 388
        alignment_columns: 388
        identities: 387
        mismatches: 1
        gap_columns: 0
        identity_percent: 99.7423
        query_coverage_percent: 100.0
        target_coverage_percent: 100.0
        substitutions:
        - query_position: 369
comparison:
  provenance:
    query_accession: Q93XQ5
    run_at: '2026-10-18T23:35:53.077438+00:00'
    biopython_version: '1.85'
    mmseqs_version: 18-8cc5c
    command:
    - mmseqs
    - easy-search
    - genes/NICAT/NaPMT1.1/NaPMT1.1-bioinformatics/reference-counterparts/query.fasta
    - .cache/orphan-curated/UP000187609.fasta
    - genes/NICAT/NaPMT1.1/NaPMT1.1-bioinformatics/reference-counterparts/search.tsv
    - genes/NICAT/NaPMT1.1/NaPMT1.1-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: 32918
    query_sha256: 9a8a3d4fc974d7154c18660a43596cfd7a67aa831d6b3c23adf34bed98fb5354
    targets_sha256: ff3c425fd8ecd38823462d1a2a9f0f94c67567a12c15fa74071f54e088c7c4bc
    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%3AUP000187609&format=fasta
      retrieved_at: '2026-10-18T23:32:30.193791+00:00'
      uniprot_release: '2026_03'
      sequence_count: 32918
      sha256: ff3c425fd8ecd38823462d1a2a9f0f94c67567a12c15fa74071f54e088c7c4bc
    detailed_alignment_limit: 10
  candidate_count: 8
  retained_alignment_count: 8
  candidates:
  - accession: A0A314LG79
    description: sp|A0A314LG79|PMT3_NICAT Putrescine N-methyltransferase 3 OS=Nicotiana attenuata OX=49451
      GN=PMT3 PE=2 SV=1
    evalue: 3.971e-258
    bit_score: 787.0
    global_score: 2047.0
    query_length: 388
    target_length: 388
    alignment_columns: 388
    identities: 387
    mismatches: 1
    gap_columns: 0
    identity_percent: 99.7423
    query_coverage_percent: 100.0
    target_coverage_percent: 100.0
  - accession: Q93XQ4
    description: sp|Q93XQ4|PMT2_NICAT Putrescine N-methyltransferase 2 OS=Nicotiana attenuata OX=49451
      GN=PMT2 PE=2 SV=1
    evalue: 2.051e-235
    bit_score: 721.0
    global_score: 1872.5
    query_length: 388
    target_length: 371
    alignment_columns: 388
    identities: 359
    mismatches: 12
    gap_columns: 17
    identity_percent: 92.5258
    query_coverage_percent: 95.6186
    target_coverage_percent: 100.0