ARBA00026799 NAD+ kinase activity (GO:0003951)

View original ARBA rule on UniProt

Type: ARBA
Status: COMPLETE
Action: ACCEPT
Confidence: 0.75

Description

Assigns GO:0003951 (NAD+ kinase activity) from five alternative condition sets: one InterPro and PANTHER conjunction for the NAD kinase family, and four CATH FunFams each limited to a taxon.

Analysis Summary

Condition-set counts describe the sets recorded in this review, which may omit the full rule.

0
Domain Pairs Analyzed
5
Recorded condition sets
0
Subset Relationships
0
Redundant Annotations

No domain overlap table is shown: the cached overlap analysis for this version of the review is not available. Run just analyze-rule ARBA00026799 and re-render to add it.

Review Summary

All five condition sets of the rule as served on 2026-11-10 were turned into UniProtKB queries. In every set the reviewed matches are NAD kinases by curated EC number (698 of 704 across the sets), and sets 1 and 5 include members with experimental GO:0003951 annotations. The one soft spot is in set 1, which also matches the mitochondrial NADH kinase POS5 and its S. pombe ortholog; these are curated as NADH kinases (EC 2.7.1.86), and NAD+ kinase activity is not annotated for POS5.

Action Rationale

Each condition set selects the NAD kinase family, and the consequent is the family's defining activity. The NADH kinase members of set 1 are few (3 of 541 reviewed matches), belong to the same family, and are not shown to lack NAD+ kinase activity, so they do not justify a change. The counts are from reviewed entries, which the rule was derived from; unreviewed matches were counted, not inspected.

GO Annotations

GO:0003951 - NAD+ kinase activity
Aspect: MF

Annotation Assessments

CORRECT GO_TERM GO:0003951 - NAD+ kinase activity
Matched proteins: 31532; incorrect:
Correct examples: O95544, P0A7B3, P21373, P32622, Q4G0N4

matched_protein_count is the sum of the five set counts and may count an entry twice. Correct examples with experimental GO:0003951: O95544 (IDA PMID:11594753), P0A7B3 (IDA PMID:11488932), P21373 (IDA PMID:11425472), P32622 (IDA PMID:15978040), Q4G0N4 (IDA PMID:23212377). Not listed as incorrect: Q06892 (POS5), annotated to GO:0042736 only; the rule does not put GO:0003951 on it in QuickGO.

Rule Definition

Condition Sets

Condition Set 1

3 condition(s)
Notes:

UniProtKB 2026_04: 27,802 entries, 541 reviewed. 535 of the reviewed entries carry EC 2.7.1.23. The other six are NADH kinases (EC 2.7.1.86: P32622 YEF1, Q06892 POS5, Q9UT98 S. pombe pos5) and three uncharacterized S. pombe kinases (Q9P7K3, Q6LA56, O13863). YEF1 has GO:0003951 IDA PMID:15978040 (SGD). POS5 (Q06892) is annotated only to GO:0042736 NADH kinase activity (IDA PMID:12727869, SGD), so for POS5-like members NAD+ kinase activity is unconfirmed. Experimental GO:0003951 on set members: human NADK O95544 IDA PMID:11594753; E. coli nadK P0A7B3 IDA PMID:11488932; yeast UTR1 P21373 IDA PMID:11425472.

Condition Set 2

2 condition(s)
Notes:

UniProtKB 2026_04: 1,600 entries, 106 reviewed, all 106 with EC 2.7.1.23.

Condition Set 3

2 condition(s)
Notes:

UniProtKB 2026_04: 1,073 entries, 52 reviewed, all 52 with EC 2.7.1.23.

Condition Set 4

2 condition(s)
Notes:

UniProtKB 2026_04: 669 entries, 2 reviewed, both with EC 2.7.1.23.

Condition Set 5

2 condition(s)
Notes:

UniProtKB 2026_04: 388 entries, 3 reviewed, all 3 with EC 2.7.1.23. Human NADK2 Q4G0N4 has GO:0003951 IDA PMID:23212377.

Assessments

APPROPRIATE

GO:0003951 (NAD+ kinase activity) is the activity named by EC 2.7.1.23, which the reviewed matches carry. GO:0042736 (NADH kinase activity) is a separate term for the EC 2.7.1.86 reaction.

Raw YAML

View Source YAML 
id: ARBA00026799
description: 'Assigns GO:0003951 (NAD+ kinase activity) from five alternative condition sets: one InterPro
  and PANTHER conjunction for the NAD kinase family, and four CATH FunFams each limited to a taxon.'
status: COMPLETE
rule_type: ARBA
rule:
  rule_id: ARBA00026799
  condition_sets:
  - number: 1
    conditions:
    - condition_type: INTERPRO
      value: IPR002504
      label: NAD kinase
    - condition_type: INTERPRO
      value: IPR016064
      label: NAD kinase/diacylglycerol kinase-like domain superfamily
    - condition_type: PANTHER
      value: PTHR20275:SF0
      label: NAD KINASE
    notes: 'UniProtKB 2026_04: 27,802 entries, 541 reviewed. 535 of the reviewed entries carry EC 2.7.1.23.
      The other six are NADH kinases (EC 2.7.1.86: P32622 YEF1, Q06892 POS5, Q9UT98 S. pombe pos5) and
      three uncharacterized S. pombe kinases (Q9P7K3, Q6LA56, O13863). YEF1 has GO:0003951 IDA PMID:15978040
      (SGD). POS5 (Q06892) is annotated only to GO:0042736 NADH kinase activity (IDA PMID:12727869, SGD),
      so for POS5-like members NAD+ kinase activity is unconfirmed. Experimental GO:0003951 on set members:
      human NADK O95544 IDA PMID:11594753; E. coli nadK P0A7B3 IDA PMID:11488932; yeast UTR1 P21373 IDA
      PMID:11425472.'
  - number: 2
    conditions:
    - condition_type: FUNFAM
      value: 2.60.200.30:FF:000001
      label: NAD kinase
    - condition_type: TAXON
      value: Bacteria
      label: Bacteria
      curie: NCBITaxon:2
    notes: 'UniProtKB 2026_04: 1,600 entries, 106 reviewed, all 106 with EC 2.7.1.23.'
  - number: 3
    conditions:
    - condition_type: FUNFAM
      value: 2.60.200.30:FF:000002
      label: NAD kinase
    - condition_type: TAXON
      value: Bacillati
      label: Bacillati
      curie: NCBITaxon:1783272
    notes: 'UniProtKB 2026_04: 1,073 entries, 52 reviewed, all 52 with EC 2.7.1.23.'
  - number: 4
    conditions:
    - condition_type: FUNFAM
      value: 3.40.50.10330:FF:000014
      label: NAD kinase a
    - condition_type: TAXON
      value: Eukaryota
      label: Eukaryota
      curie: NCBITaxon:2759
    notes: 'UniProtKB 2026_04: 669 entries, 2 reviewed, both with EC 2.7.1.23.'
  - number: 5
    conditions:
    - condition_type: FUNFAM
      value: 3.40.50.10330:FF:000021
      label: NAD kinase 2, mitochondrial
    - condition_type: TAXON
      value: Metazoa
      label: Metazoa
      curie: NCBITaxon:33208
    notes: 'UniProtKB 2026_04: 388 entries, 3 reviewed, all 3 with EC 2.7.1.23. Human NADK2 Q4G0N4 has
      GO:0003951 IDA PMID:23212377.'
  go_annotations:
  - go_id: GO:0003951
    go_label: NAD+ kinase activity
    aspect: MF
  entries: []
  created_date: '2021-10-20'
  modified_date: '2026-07-18'
  retrieved_date: '2026-11-10'
  source_condition_set_count: 5
review_summary: All five condition sets of the rule as served on 2026-11-10 were turned into UniProtKB
  queries. In every set the reviewed matches are NAD kinases by curated EC number (698 of 704 across the
  sets), and sets 1 and 5 include members with experimental GO:0003951 annotations. The one soft spot
  is in set 1, which also matches the mitochondrial NADH kinase POS5 and its S. pombe ortholog; these
  are curated as NADH kinases (EC 2.7.1.86), and NAD+ kinase activity is not annotated for POS5.
action: ACCEPT
action_rationale: Each condition set selects the NAD kinase family, and the consequent is the family's
  defining activity. The NADH kinase members of set 1 are few (3 of 541 reviewed matches), belong to the
  same family, and are not shown to lack NAD+ kinase activity, so they do not justify a change. The counts
  are from reviewed entries, which the rule was derived from; unreviewed matches were counted, not inspected.
go_specificity:
  assessment: APPROPRIATE
  notes: GO:0003951 (NAD+ kinase activity) is the activity named by EC 2.7.1.23, which the reviewed matches
    carry. GO:0042736 (NADH kinase activity) is a separate term for the EC 2.7.1.86 reaction.
annotation_assessments:
- annotation_kind: GO_TERM
  value: GO:0003951
  label: NAD+ kinase activity
  assessment: CORRECT
  matched_protein_count: 31532
  correct_examples:
  - O95544
  - P0A7B3
  - P21373
  - P32622
  - Q4G0N4
  notes: 'matched_protein_count is the sum of the five set counts and may count an entry twice. Correct
    examples with experimental GO:0003951: O95544 (IDA PMID:11594753), P0A7B3 (IDA PMID:11488932), P21373
    (IDA PMID:11425472), P32622 (IDA PMID:15978040), Q4G0N4 (IDA PMID:23212377). Not listed as incorrect:
    Q06892 (POS5), annotated to GO:0042736 only; the rule does not put GO:0003951 on it in QuickGO.'
confidence: 0.75
corrections:
- date: '2026-11-10'
  withdrawn_claim: literature_support STRONG, supported by a quotation from the review's own deep-research-manual
    file; condition_overlap supported by a quotation from ARBA00026799.enriched.json.
  correction: The literature assessment cited no publication and is removed until one is cited. The enriched.json
    file is not in the repository, so that quotation cannot be checked and is removed.
  error_type: UNSUPPORTED_SOURCE
  evidence:
  - rules/arba/ARBA00026799/ contains no ARBA00026799.enriched.json (checked 2026-11-10)
- date: '2026-11-10'
  withdrawn_claim: ACCEPT at 0.85 with six recorded condition sets, no rule snapshot, and go_specificity,
    taxonomic_scope and the overall verdict supported only by quotations from the review's own deep-research-manual
    file.
  correction: 'The recorded sets were not the live rule: UniProt served five sets on 2026-11-10, and three
    of the six recorded sets (two-FunFam conjunctions and an unrestricted FunFam) are not among them.
    The review was redone against the live rule with UniProtKB counts and QuickGO annotations; the citations
    to the notes file are removed.'
  error_type: STALE_RULE_VERSION
  evidence:
  - 'https://rest.uniprot.org/arba/ARBA00026799 on 2026-11-10: 5 condition sets, modifiedDate 2026-07-18'
  - 'Set 1 query (xref:interpro-IPR002504) AND (xref:interpro-IPR016064) AND (xref:panther-PTHR20275)
    AND (reviewed:true): 541; with (ec:2.7.1.23): 535 (UniProtKB 2026_04)'