Curated counterpart assessments

Curated counterpart assessments

Generated from the genes declared in ORPHAN_CURATED and their review YAML. Do not edit this report by hand.

Regenerate: just project-counterparts --project projects/ORPHAN_CURATED.md. Add --check to detect stale outputs.

39 gene reviews across 23 species directories; 39 assessment rows. Counts below are rows, so a gene with multiple assessments can contribute more than once. Unassessed genes remain visible.

Assessment Rows
CANDIDATE 8
EQUIVALENT 18
LOCUS_COUNTERPART 3
NO_SUPPORTED_COUNTERPART 10

Equivalence is a curated judgment and need not imply identical sequence. Locus counterparts may differ in function or integrity; candidates remain unresolved. A search with no supported counterpart does not establish gene absence. This report does not transfer GO annotations or change primary IDs.

Primary review Alternative Assessment Reference proteomes Reviewed
STRTR/cas10 · A0A0A7HFE1 A0ACM8UA39 CANDIDATE UP000232434 2026-10-19
OCTVU/DDO · A0A7E6FSU6 None asserted NO_SUPPORTED_COUNTERPART UP001162480 2026-10-19
STAWA/cfr · A2AXI2 None asserted NO_SUPPORTED_COUNTERPART UP000814367 2026-10-19
CHLRE/CP12 · A6Q0K5 A0A2K3DI03 EQUIVALENT UP000006906 2026-10-19
POPTR/PRX2 · A9PCL4 B9ILP9 EQUIVALENT UP000006729 2026-10-19
ORYSJ/PIKM1-TS · B5UBC1 Q2QZF2 CANDIDATE UP000059680 2026-10-19
STECR/nas-8 · D2KBH9 A0A4U8UYW6 EQUIVALENT UP000298663 2026-10-19
ORYSJ/RGA4 · F7J0M4 F7J0M6 LOCUS_COUNTERPART UP000059680 2026-10-19
ORYSJ/RGA5 · F7J0N2 Q2R8L1 CANDIDATE UP000059680 2026-10-19
THLAR/TFP · G1FNI6 A0AAU9R9U8 EQUIVALENT UP000836841 2026-10-19
DERPT/Derp23 · L7N6F8 A0ABQ8JBE4 CANDIDATE UP000887458 2026-10-19
POPTR/CCOAOMT1 · O65862 A0A2K1Z5Q2 EQUIVALENT UP000006729 2026-10-19
POPTR/CCOAOMT2 · O65922 A0A2K2C664 EQUIVALENT UP000006729 2026-10-19
STAHA/lnuA · P06107 None asserted NO_SUPPORTED_COUNTERPART UP000306300 2026-10-19
PSEPK/xylR · P06519 A0A1L7N7J0 CANDIDATE UP000218731 2026-10-19
DERPT/Derp1 · P08176 A0ABQ8JGY3 CANDIDATE UP000887458 2026-10-19
ECOLI/traD · P09130 None asserted NO_SUPPORTED_COUNTERPART UP000000625 2026-10-19
BREDI/opd · P0A434 None asserted NO_SUPPORTED_COUNTERPART UP000596117 2026-10-19
ARATH/FRI · P0DH90 Q67Z93 LOCUS_COUNTERPART UP000006548 2026-10-19
TOXGO/SAG1 · P13664 A0A7J6K396 EQUIVALENT UP000557509 2026-10-19
PENCH/aatA · P15802 A0ABQ8WFJ5 EQUIVALENT UP001220256 2026-10-19
POPTR/WIN6 · P16579 B9HQY4 CANDIDATE UP000006729 2026-10-19
ECOLI/traC · P18004 None asserted NO_SUPPORTED_COUNTERPART UP000000625 2026-10-19
FULFL/AVR9 · P22287 L7YER9 EQUIVALENT UP000756132 2026-10-19
XANAU/dhlA · P22643 None asserted NO_SUPPORTED_COUNTERPART UP001161920, UP001603991 2026-10-19
POPTR/MAOX · P34105 B9ILT5 EQUIVALENT UP000006729 2026-10-19
ECOLI/traB · P41067 None asserted NO_SUPPORTED_COUNTERPART UP000000625 2026-10-19
POPTR/PAL · P45730 A0A2K1XD28 EQUIVALENT UP000006729 2026-10-19
THLAR/CYP71B1 · P49264 A0AAU9RUE5 EQUIVALENT UP000836841 2026-10-19
DERPT/Derp2 · P49278 A0ABQ8J715 EQUIVALENT UP000887458 2026-10-19
FULFL/AVR4 · Q00363 L7YE01 EQUIVALENT UP000756132 2026-10-19
BACAN/ermJ · Q04720 None asserted NO_SUPPORTED_COUNTERPART UP000000427, UP000000594 2026-10-19
MOOTH/acsD · Q07341 A0A1D7XAJ1 EQUIVALENT UP000322283 2026-10-19
DICDI/chlA · Q54FI4 None asserted NO_SUPPORTED_COUNTERPART UP000002195 2026-10-19
MEDTR/DMI1 · Q6RHR6 G7IN96 EQUIVALENT UP000002051 2026-10-19
MEDTR/NORK · Q8L4H4 A9YWR7 EQUIVALENT UP000002051 2026-10-19
NICAT/NaPMT1.1 · Q93XQ5 A0A314LG79 CANDIDATE UP000187609 2026-10-19
ARATH/AOP2 · Q945B5 Q9ZTA2 LOCUS_COUNTERPART UP000006548 2026-10-19
THLAR/matK · Q9GF35 A0A1U9RZH7 EQUIVALENT UP000836841 2026-10-19

Rationale and evidence

STRTR/cas10 — A0A0A7HFE1

CANDIDATE → A0ACM8UA39

Retain A0A0A7HFE1 as the primary Swiss-Prot accession. The full-length Cas10/Csm1 match is strong but nonidentical (94.61% global identity). The characterized protein is from strain DGCC8004. A shared genomic locus or operon correspondence across the source and reference strains has not been established; retain a candidate rather than assuming equivalent CRISPR complexes.

OCTVU/DDO — A0A7E6FSU6

NO_SUPPORTED_COUNTERPART

Retain A0A7E6FSU6 as the primary Swiss-Prot accession. The four returned oxidase-family hits have only about 25-27% global identity and incomplete query coverage. They do not establish a D-aspartate oxidase counterpart; a D-amino-acid oxidase-like label is not evidence of matching substrate specificity. No supported counterpart was identified by this search.

STAWA/cfr — A2AXI2

NO_SUPPORTED_COUNTERPART

Retain A2AXI2 as the primary Swiss-Prot accession. The only hit is the related RlmN methyltransferase A0A2T4Q1F7 (33.69% global identity), not an established Cfr counterpart. Shared radical-SAM/RNA-methyltransferase ancestry does not establish the Cfr resistance activity or gene identity. The source is strain 11562A; no supported reference-strain counterpart was identified.

CHLRE/CP12 — A6Q0K5

EQUIVALENT → A0A2K3DI03

Retain A6Q0K5 as the primary Swiss-Prot accession. All 107 residues of the Swiss-Prot protein align identically to the 131-residue reference protein, which has a 24-residue extension. Both records share RefSeq XP_001694345.2, supporting the counterpart assignment independently of the sequence match. The precursor boundary difference is explicit; the sequences are not literally identical.

POPTR/PRX2 — A9PCL4

EQUIVALENT → B9ILP9

Retain A9PCL4 as the primary Swiss-Prot accession. B9ILP9 at POPTR_018G083500 is the manually assessed reference-proteome counterpart: 161/162 identical residues, full ungapped coverage, and only N117D. The competing POPTR_001G423500 paralog (A0A2K2CCD0) differs at seven residues. The original EF146010 cDNA is explicitly from Nisqually-1, so a different cultivar cannot explain this pair. This is a sequence-supported locus assignment, not a shared primary-record locus cross-reference; the one-residue discrepancy remains unexplained.

ORYSJ/PIKM1-TS — B5UBC1

CANDIDATE → Q2QZF2

Retain B5UBC1 as the primary Swiss-Prot accession. The leading hit is reviewed PIK5-NP, with the synonym PIKM1, but only 58.42% global identity and extensive differences. The source cultivars differ, and the reference record describes Nipponbare lacking AVR-Pik recognition. A related resistance-locus representation is plausible, but copy-number, locus and specificity differences prevent an equivalence assertion.

STECR/nas-8 — D2KBH9

EQUIVALENT → A0A4U8UYW6

Retain D2KBH9 as the primary Swiss-Prot accession. The 418-residue reference protein differs by one residue across full ungapped coverage (99.76% identity), with a large separation from other metallopeptidase hits. This supports a qualified sequence-based counterpart assessment. The source protein is from strain Breton; the origin and biological effect of the single residue difference are not established.

ORYSJ/RGA4 — F7J0M4

LOCUS_COUNTERPART → F7J0M6

Retain F7J0M4 as the primary Swiss-Prot accession. Both reviewed records represent RGA4 in different rice cultivars, and the reference entry is the leading full-length match. UniProt contrasts AVR-Pia recognition in Aichi asahi/Sasanishiki with its absence in Nipponbare. Record this as a reference-cultivar locus counterpart, not equivalent resistance function; loss of recognition by the RGA4/RGA5 system does not establish that RGA4 alone is inactive.

ORYSJ/RGA5 — F7J0N2

CANDIDATE → Q2R8L1

Retain F7J0N2 as the primary Swiss-Prot accession. Q2R8L1 is a plausible reference-proteome counterpart, but the captured evidence does not independently map the Sasanishiki protein to the Nipponbare locus. The target is named RGA5 at Os11g0225300 / LOC_Os11g11810; those identifiers locate the target only. The sequence is substantially divergent (624 identities over 1105 paired residues, with 207 gap columns), and the cultivar-dependent AVR-Pia recognition statement concerns the resistance system. Retain a candidate pending cross-cultivar locus mapping; do not assert equivalent receptor specificity or protein integrity.

THLAR/TFP — G1FNI6

EQUIVALENT → A0AAU9R9U8

Retain G1FNI6 as the primary Swiss-Prot accession. The leading reference sequence has 97.13% global identity, full target coverage and a short terminal difference, and is separated from other specifier-family hits. This supports a qualified sequence-based counterpart. Its generic epithiospecifier annotation does not independently establish thiocyanate-forming specificity, so functional annotation transfer still requires review.

DERPT/Derp23 — L7N6F8

CANDIDATE → A0ABQ8JBE4

Retain L7N6F8 as the primary Swiss-Prot accession. The leading small chitin-binding protein is a plausible Der p 23 counterpart, but global identity is 75.51% with substitutions and indels. Other chitin-binding proteins are present, and no shared source/target locus cross-reference establishes identity. Retain a candidate pending genomic mapping and gene-model assessment.

POPTR/CCOAOMT1 — O65862

EQUIVALENT → A0A2K1Z5Q2

Retain O65862 as the preferred Swiss-Prot accession. A0A2K1Z5Q2 represents the same protein sequence at the corresponding reference-proteome locus, supported by exact sequence identity and a shared Gramene identifier. The source cultivars differ; this relationship does not assert that all GO annotations can be transferred automatically.

POPTR/CCOAOMT2 — O65922

EQUIVALENT → A0A2K2C664

Retain O65922 as the preferred Swiss-Prot accession. A0A2K2C664 represents the same protein sequence at the corresponding reference-proteome locus, supported by exact sequence identity and a shared Gramene identifier. The source cultivars differ; this relationship does not assert that all GO annotations can be transferred automatically.

STAHA/lnuA — P06107

NO_SUPPORTED_COUNTERPART

Retain P06107 as the primary Swiss-Prot accession. The reference-proteome search returned no significant hit to this lincosamide-resistance protein at the documented search settings. This does not establish absence from the species or its accessory genome. No alternative accession is asserted.

PSEPK/xylR — P06519

CANDIDATE → A0A1L7N7J0

Retain P06519 as the primary Swiss-Prot accession. The leading hit is a full-length xyl-upper-pathway transcriptional activator with 66.67% global identity. The source is strain mt-2 and the reference strain differs. Related regulatory function and sequence similarity do not establish the same mobile-element locus or effector specificity; retain a candidate.

DERPT/Derp1 — P08176

CANDIDATE → A0ABQ8JGY3

Retain P08176 as the primary Swiss-Prot accession. The full 320-residue query is represented within a much longer 837-residue reference model: 300 identities over 320 paired residues, but only 35.84% identity when all global-alignment columns are counted. The target is labeled MCM2_2/MCM DNA helicase despite peptidase-C1 family evidence. This is a possible fused or otherwise problematic gene model, not an established intact equivalent; retain a candidate for genomic/model review.

ECOLI/traD — P09130

NO_SUPPORTED_COUNTERPART

Retain P09130 as the primary Swiss-Prot accession. No significant reference-proteome hit was returned. The reviewed entry explicitly derives from F and related plasmids, whereas the selected reference proteome does not provide a supported counterpart in this search. This is compatible with accessory-plasmid content; it is not proof of absence from E. coli K12 generally.

BREDI/opd — P0A434

NO_SUPPORTED_COUNTERPART

Retain P0A434 as the primary Swiss-Prot accession. No significant reference-proteome hit was returned for the characterized parathion hydrolase from strain MG. Strain/accessory-genome differences are plausible context, but the search alone does not establish why UniProt omitted the proteome association or that the gene is absent from the species.

ARATH/FRI — P0DH90

LOCUS_COUNTERPART → Q67Z93

Retain P0DH90 as the primary Swiss-Prot accession. UniProt explicitly links active FRI from cv. H51 to the inactive Columbia allele Q67Z93. The reference protein covers only part of the full active sequence; curated cautions attribute inactivity to loss-of-function mutations. This is a same-locus counterpart, not functional equivalence.

TOXGO/SAG1 — P13664

EQUIVALENT → A0A7J6K396

Retain P13664 as the primary Swiss-Prot accession. The reference SRS29B sequence is exactly identical across all 336 residues to reviewed SAG1. The full-proteome comparison separates it from other SAG-related proteins. This supports an equivalent protein representation while preserving the experimentally curated SAG1 accession.

PENCH/aatA — P15802

EQUIVALENT → A0ABQ8WFJ5

Retain P15802 as the primary Swiss-Prot accession. The 357-residue reference sequence differs at two residues with full ungapped coverage (99.44% identity). The other retrieved hit is distant and structurally dissimilar. This supports a qualified sequence-based counterpart; the source strain is AS-P-78 and no functional neutrality of the two substitutions is assumed.

POPTR/WIN6 — P16579

CANDIDATE → B9HQY4

Retain P16579 as the primary Swiss-Prot accession. B9HQY4 at POPTR_009G141800v4 is the leading candidate, not an established equivalent. It has 317 identical residues across 340 global-alignment columns (16 substitutions and seven gap columns). B9HQZ1 represents a second model of the same locus, while nearby chitinase loci also match strongly. Hybrid H11-11 provenance and the absence of a direct locus cross-reference leave allele, model, and paralog alternatives unresolved. Mapping source genomic record U01661, including flanks, to the reference assembly is needed before promoting this relationship.

ECOLI/traC — P18004

NO_SUPPORTED_COUNTERPART

Retain P18004 as the primary Swiss-Prot accession. No significant reference-proteome hit was returned for TraC. This reviewed protein belongs to the F-plasmid conjugation system, so accessory-replicon coverage is a relevant explanation to investigate rather than replacing it with a chromosomal protein. No supported alternative is asserted.

FULFL/AVR9 — P22287

EQUIVALENT → L7YER9

Retain P22287 as the primary Swiss-Prot accession. The reference Avr9 precursor is exactly identical across all 63 residues and is the sole significant hit. This supports equivalent protein representation. Retain the reviewed race-5 accession and its evidence rather than transferring race-specific claims automatically.

XANAU/dhlA — P22643

NO_SUPPORTED_COUNTERPART

Retain P22643 as the primary Swiss-Prot accession. Both exact-taxon reference proteomes were searched as a deduplicated union. The leading alpha/beta-hydrolase hits are remote (about 25% global identity) and do not establish haloalkane dehalogenase identity or substrate specificity. The source is strain GJ10; no supported counterpart was identified in either reference proteome.

POPTR/MAOX — P34105

EQUIVALENT → B9ILT5

Retain P34105 as the primary Swiss-Prot accession. B9ILT5 at POPTR_018G086700 is the manually assessed reference-proteome counterpart: 584/591 identical residues with full ungapped coverage. Its seven differences are Y53F, H60Q, T84A, I204M, R251K, I413T, and Q457E. It is clearly separated from other malic-enzyme loci in the full-proteome search and global alignments. The original material is hybrid clone 064; sequence equivalence is assessed at the protein/locus level, not as literal identity or proof of parental origin.

ECOLI/traB — P41067

NO_SUPPORTED_COUNTERPART

Retain P41067 as the primary Swiss-Prot accession. No significant reference-proteome hit was returned. The reviewed entry explicitly cites F and ColB2 plasmids, making accessory-replicon differences relevant. The negative result applies to the searched reference proteome, not all E. coli strains or plasmids.

POPTR/PAL — P45730

EQUIVALENT → A0A2K1XD28

Retain P45730 as the primary Swiss-Prot accession. A0A2K1XD28 at POPTR_016G091100 is the manually assessed reference-proteome counterpart: 714/715 identical residues with full ungapped coverage and only R22L. The next full-length family match, A0A2K2A1A8 at POPTR_006G126800, has 32 substitutions and one gap column. The source sequence is from a P. trichocarpa x P. deltoides hybrid; the counterpart assignment is inferred from the sequence comparison and does not establish the parental origin or cause of R22L.

THLAR/CYP71B1 — P49264

EQUIVALENT → A0AAU9RUE5

Retain P49264 as the primary Swiss-Prot accession. The reference sequence is exactly identical across all 496 residues. Other P450 hits are substantially less similar. This supports equivalent protein representation without relying on the broad automatic cytochrome-P450 name to establish substrate specificity.

DERPT/Derp2 — P49278

EQUIVALENT → A0ABQ8J715

Retain P49278 as the primary Swiss-Prot accession. The 146-residue reference sequence differs at three residues with full ungapped coverage (97.95% identity), and is strongly separated from other lipid-transfer-family matches. This supports a qualified sequence-based Der p 2 counterpart; its generic transfer-protein label does not independently establish allergenicity or identical immunological properties.

FULFL/AVR4 — Q00363

EQUIVALENT → L7YE01

Retain Q00363 as the primary Swiss-Prot accession. The reference Avr4 sequence is exactly identical across all 135 residues and is the only significant hit. This supports equivalent protein representation while retaining the reviewed accession and its source-race-specific evidence.

BACAN/ermJ — Q04720

NO_SUPPORTED_COUNTERPART

Retain Q04720 as the primary Swiss-Prot accession. Both exact-taxon reference proteomes were searched. The only hit is RsmA Q81W00 at 27.30% global identity, a distinct ribosomal methyltransferase. Related methyltransferase ancestry does not establish an ErmJ resistance counterpart; no supported alternative was identified.

MOOTH/acsD — Q07341

EQUIVALENT → A0A1D7XAJ1

Retain Q07341 as the primary Swiss-Prot accession. The reference corrinoid/iron-sulfur small-subunit sequence is exactly identical across all 323 residues. The changed organism code in the target entry name is not used as taxonomy evidence; live record/proteome taxon identifiers are checked. Retain the Swiss-Prot accession.

DICDI/chlA — Q54FI4

NO_SUPPORTED_COUNTERPART

Retain Q54FI4 as the primary Swiss-Prot accession. No significant reference-proteome hit was returned for the AX4 chlA sequence. Because the source and reference context are closely related, this is a notable gene-model or proteome-coverage question for UniProt. The negative protein search does not establish genomic absence; investigate its source genomic locus before drawing that conclusion.

MEDTR/DMI1 — Q6RHR6

EQUIVALENT → G7IN96

Retain Q6RHR6 as the primary Swiss-Prot accession. The reference sequence is exactly identical across all 882 residues and is separated from CASTOR-like paralogs. Primary-record genomic cross-references provide additional mapping context. This supports equivalent DMI1 protein representation; the broad pollux-like target label is not a separate functional assertion.

MEDTR/NORK — Q8L4H4

EQUIVALENT → A9YWR7

Retain Q8L4H4 as the primary Swiss-Prot accession. The reference sequence is exactly identical across all 925 residues. G7KGF4 is an additional shorter model with 902 identical residues, but A9YWR7 represents the complete primary sequence. The kinase-family search reached its 1000-hit cap; this does not weaken the observed full-length identity but prevents claiming exhaustive paralog retrieval.

NICAT/NaPMT1.1 — Q93XQ5

CANDIDATE → A0A314LG79

Retain Q93XQ5 as the primary Swiss-Prot accession. The leading sequence differs by one residue across 388 residues, but the reference entry is reviewed PMT3 whereas the primary is PMT1. Near identity is insufficient to collapse duplicated PMT loci or resolve nomenclature. Retain a candidate pending genomic placement and reconciliation of PMT1/PMT3 naming.

ARATH/AOP2 — Q945B5

LOCUS_COUNTERPART → Q9ZTA2

Retain Q945B5 as the primary Swiss-Prot accession. UniProt explicitly identifies Q9ZTA2 as the Columbia AOP2 allele with a 5-bp deletion leading to a non-functional protein, contrasting the functional Cvi allele Q945B5. The observed sequence differences and length loss are consistent with that curated distinction. Record same-locus correspondence, not equivalent catalytic function.

THLAR/matK — Q9GF35

EQUIVALENT → A0A1U9RZH7

Retain Q9GF35 as the primary Swiss-Prot accession. The leading full-length chloroplast maturase-K sequence has 98.21% global identity, eight substitutions and one gap column. Other hits are much shorter maturase fragments. This supports a qualified sequence-based counterpart while preserving the source sequence and documenting the differences.