batch4

.claude/agents/annotation-reviewer.md

@@ -53,12 +53,15 @@ You should make use of:
    - **MODIFY**: Essence is sound but better terms exist (provide proposed_replacement_terms). Use this if the term is too deep or too shallow
    - **MARK_AS_OVER_ANNOTATED**: Not wrong but likely over-annotation
    - **UNDECIDED**: Unclear annotation requiring more evidence (always use if unable to access relevant publications)
+   - **NEW**: ONLY use this to suggest completely new annotations not in the set already provided by GO. You will need to come up with the evidence and reference
 
 Note that duplicates (i.e exact same GO ID) are perfectly fine, there is no need to favor one evidence code over another.
 
 It may also be OK for IEAs to be broader than what is determined by IBA or literature, you can just mark these as accept,
 unless you think the mapping is too general.
 
+
+
 5. **Detailed Justification**: For each annotation, provide:
    - Clear rationale for the assigned action
    - Specific evidence supporting your decision

app/schema.js

@@ -50,6 +50,12 @@ window.searchSchema = {
       "type": "string",
       "sortBy": "count"
     },
+    {
+      "field": "term_label",
+      "label": "Term",
+      "type": "string",
+      "sortBy": "count"
+    },
     {
       "field": "negated",
       "label": "Negated",

genes/AZOVI/nifA/nifA-ai-review.yaml

@@ -125,11 +125,11 @@ references:
   title: 'UniProt entry for NifA from Azotobacter vinelandii'
   findings:
     - statement: 'Required for activation of most nif operons involved in nitrogen fixation'
-      supporting_text: 'Central role in nitrogen fixation gene regulation'
+      supporting_text: 'FUNCTION: Required for activation of most nif operons, which are directly involved in nitrogen fixation'
     - statement: 'Interacts with sigma-54'
-      supporting_text: 'Evidence for sigma-54-dependent transcriptional activation'
+      supporting_text: 'SUBUNIT: Interacts with sigma-54'
     - statement: 'Contains GAF domain (37-178), sigma-54 interaction domain (211-439), and HTH DNA-binding domain (494-513)'
-      supporting_text: 'Domain architecture supporting NifA functions'
+      supporting_text: 'DOMAIN 37..178 /note="GAF" ... DOMAIN 211..439 /note="Sigma-54 factor interaction" ... DNA_BIND 494..513 /note="H-T-H motif"'
 - id: GO_REF:0000002
   title: Gene Ontology annotation through association of InterPro records with GO terms.
   findings: []

genes/BPZF4/ACA2/ACA2-ai-review.yaml

@@ -0,0 +1,123 @@
+id: H9C180
+gene_symbol: H9C180
+taxon:
+  id: NCBITaxon:1127516
+  label: Pectobacterium phage ZF40
+description: >-
+  Aca2 repressor from bacteriophage ZF40 that functions as a dual transcriptional and translational
+  repressor of the acrIF8-aca2 operon. This 116 amino acid protein forms homodimers and uses its
+  N-terminal helix-turn-helix domain to bind specific DNA inverted repeats in the operon promoter,
+  blocking RNA polymerase access. Additionally, Aca2 binds conserved RNA stem-loops in the mRNA to
+  inhibit ribosome access. This dual regulatory mechanism ensures tight control of anti-CRISPR (AcrIF8)
+  expression during phage infection, preventing toxic overexpression while allowing sufficient production
+  to evade host CRISPR-Cas immunity. The protein is essential for phage viability, as uncontrolled AcrIF8
+  expression is detrimental to both phage replication and host cell fitness.
+existing_annotations:
+- term:
+    id: GO:0003677
+    label: DNA binding
+  evidence_type: IEA
+  original_reference_id: GO_REF:0000120
+  review:
+    summary: >-
+      This annotation is correct but too general. Aca2 is specifically a sequence-specific DNA-binding
+      transcription factor that recognizes inverted repeat operator sequences in the acrIF8-aca2 promoter
+      through its N-terminal HTH domain. The protein binds as a homodimer to regulate transcription.
+    action: MODIFY
+    proposed_replacement_terms:
+    - id: GO:0003700
+      label: DNA-binding transcription factor activity
+    supported_by:
+    - reference_id: PMID:31428783
+      supporting_text: >-
+        Aca2 is a dimer that represses the expression of the acrIF8–aca2 operon, and that this autoregulation is mediated through binding to inverted repeats in the promoter region
+- term:
+    id: GO:0003723
+    label: RNA binding
+  evidence_type: IEA
+  original_reference_id: GO_REF:0000043
+  review:
+    summary: >-
+      Correct annotation supported by experimental evidence. Aca2 binds conserved RNA stem-loops
+      on the acrIF8-aca2 mRNA to block ribosome access and inhibit translation. This RNA-binding
+      function, mediated by the same HTH domain that binds DNA, provides a second layer of
+      regulatory control beyond transcriptional repression.
+    action: ACCEPT
+    supported_by:
+    - reference_id: PMID:38987591
+      supporting_text: >-
+        Phage anti-CRISPR control by an RNA- and DNA-binding helix-turn-helix protein
+- term:
+    id: GO:0046872
+    label: metal ion binding
+  evidence_type: IEA
+  original_reference_id: GO_REF:0000043
+  review:
+    summary: >-
+      This annotation has minimal support. While crystallographic structures show Mg2+ bound at
+      position 92, this appears to be a crystallization artifact rather than a functionally
+      relevant metal-binding site. There is no evidence that metal binding is required for
+      Aca2's repressor function.
+    action: REMOVE
+references:
+- id: GO_REF:0000043
+  title: Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping
+  findings: []
+- id: GO_REF:0000120
+  title: Combined Automated Annotation using Multiple IEA Methods.
+  findings: []
+- id: PMID:31428783
+  title: The autoregulator Aca2 mediates anti-CRISPR repression
+  findings: []
+- id: PMID:34756887
+  title: Structural basis for anti-CRISPR repression mediated by bacterial operon proteins Aca1 and Aca2
+  findings: []
+- id: PMID:34116143
+  title: Crystal structure of the anti-CRISPR repressor Aca2
+  findings: []
+- id: PMID:38987591
+  title: Phage anti-CRISPR control by an RNA- and DNA-binding helix-turn-helix protein
+  findings: []
+core_functions:
+- description: >-
+    Functions as a dual DNA/RNA-binding transcriptional and translational repressor of the
+    acrIF8-aca2 operon, controlling anti-CRISPR gene expression during phage infection
+  molecular_function:
+    id: GO:0003700
+    label: DNA-binding transcription factor activity
+  directly_involved_in:
+    - id: GO:0045892
+      label: negative regulation of DNA-templated transcription
+    - id: GO:0017148
+      label: negative regulation of translation
+  supported_by:
+    - reference_id: PMID:31428783
+      supporting_text: Aca2 forms dimers and binds two inverted repeat sequences in the operon's promoter to repress its transcription
+    - reference_id: PMID:38987591
+      supporting_text: Aca2 not only represses transcription of acrIF8, but also binds to the acrIF8–aca2 mRNA to inhibit its translation
+- description: >-
+    Binds conserved RNA stem-loops in the acrIF8-aca2 mRNA to block ribosome access and
+    inhibit translation as a second layer of regulatory control
+  molecular_function:
+    id: GO:0003723
+    label: RNA binding
+  directly_involved_in:
+    - id: GO:0017148
+      label: negative regulation of translation
+  supported_by:
+    - reference_id: PMID:38987591
+      supporting_text: Phage anti-CRISPR control by an RNA- and DNA-binding helix-turn-helix protein
+- description: >-
+    Forms homodimers essential for DNA binding and repressor function through C-terminal
+    domain interactions
+  molecular_function:
+    id: GO:0042803
+    label: protein homodimerization activity
+  directly_involved_in:
+    - id: GO:0045892
+      label: negative regulation of DNA-templated transcription
+  supported_by:
+    - reference_id: PMID:34116143
+      supporting_text: Crystal structure reveals Aca2's operator overlaps the –35/–10 promoter elements
+    - reference_id: PMID:34756887
+      supporting_text: Each Aca2 dimer binds one IR1 site without bending the DNA significantly