NCGR_LOCUS27674 encodes a predicted 714-amino acid protein annotated as UMP-CMP kinase (EC 2.7.4.14) in Miscanthus lutarioriparius, a C4 perennial grass. However, this gene model is almost certainly a chimeric artifact resulting from the incorrect fusion of at least two separate genes during genome annotation: an N-terminal UMP-CMP kinase (adenylate kinase family, Pfam PF00406) and a C-terminal chalcone isomerase-fold fatty acid-binding protein (Pfam PF16035, positions 555-650). At 714 AA, the protein is 2-3.5x larger than any characterized UMP-CMP kinase (e.g. Arabidopsis 202 AA [PMID:9576794], rice YL2 351 AA [PMID:29392476]). The conflicting automated annotations - kinase activities from the ADK domain and fatty acid binding / intramolecular lyase from the CHI-fold domain - are explained by this fusion. The M. lutarioriparius genome has 68,328 predicted gene models [PMID:33911077], unusually high even for an allotetraploid, consistent with gene model artifacts from the EVidenceModeler pipeline. All 13 GO annotations are IEA with no experimental evidence. The annotations pertaining to the UMP-CMP kinase portion (N-terminal domain) are likely correct for that domain, while annotations from the CHI-fold domain (fatty acid binding, intramolecular lyase activity) are artifacts of the chimeric model.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005504 fatty acid binding | IEA GO_REF:0000118 | REMOVE | Summary: This annotation derives from TreeGrafter matching the C-terminal chalcone isomerase-fold domain (Pfam PF16035, Chalcone_2, positions 555-650) to PANTHER family PTHR47284 (FATTY-ACID-BINDING PROTEIN 2). The CHI-fold superfamily includes non-catalytic fatty acid-binding proteins (FAPs) that localize to plastids and participate in de novo fatty acid biosynthesis [PMID:22622584]. However, this annotation reflects a domain from what is almost certainly a chimeric gene model, not the true function of the UMP-CMP kinase that constitutes the N-terminal portion of this protein. The 714 AA size is 2-3.5x larger than any known UMP-CMP kinase, and no natural ADK-CHI domain fusion has been reported in any organism. Reason: This annotation is an artifact of a chimeric gene model. The fatty acid binding function derives from the C-terminal CHI-fold/FAP domain (positions 555-650), which is a separate gene incorrectly fused with the N-terminal UMP-CMP kinase during genome annotation of M. lutarioriparius [PMID:33911077]. FAP proteins in the CHI superfamily do bind fatty acids [PMID:22622584], but this activity belongs to a distinct gene product, not a UMP-CMP kinase. Supporting Evidence: PMID:22622584 These three CHI-fold proteins localize to plastids, the site of de novo fatty-acid biosynthesis in plant cells. Furthermore, their expression profiles correlate with those of core fatty-acid biosynthetic enzymes PMID:33911077 A total of 68,328 gene models were predicted, with an average CDS length of 1215 bp file:9POAL/NCGR_LOCUS27674/NCGR_LOCUS27674-notes.md This protein is almost certainly a chimeric gene model artifact resulting from incorrect fusion of two separate genes during genome annotation. |
| GO:0005524 ATP binding | IEA GO_REF:0000002 | ACCEPT | Summary: ATP binding is assigned via InterPro match to IPR000850 (Adenylate/UMP-CMP kinase). UMP-CMP kinases catalyze the phosphorylation of pyrimidine nucleoside monophosphates at the expense of ATP, so ATP binding is an inherent part of their catalytic mechanism. The UniProt record confirms ATP binding sites at positions 36-41, 149, and 192 via HAMAP-Rule MF_03172. This annotation is consistent with the N-terminal UMP-CMP kinase domain of this protein. Reason: ATP binding is a core requirement for UMP-CMP kinase activity. The protein contains a P-loop NTPase domain with conserved ATP binding residues identified by HAMAP and InterPro. All characterized UMP-CMP kinases require ATP as the phosphate donor [PMID:9576794]. Supporting Evidence: file:9POAL/NCGR_LOCUS27674/NCGR_LOCUS27674-uniprot.txt Catalyzes the phosphorylation of pyrimidine nucleoside monophosphates at the expense of ATP. PMID:9576794 the UMP/CMP kinase preferentially uses ATP file:9POAL/NCGR_LOCUS27674/NCGR_LOCUS27674-deep-research-manual.md Core function: phosphorylation of UMP, CMP, and dCMP to their diphosphate forms using ATP as the phosphate donor. |
| GO:0016776 phosphotransferase activity, phosphate group as acceptor | IEA GO_REF:0000002 | ACCEPT | Summary: Assigned via InterPro match to IPR006266 (UMP-CMP kinase). GO:0016776 is an ancestor of GO:0033862 (UMP kinase activity) in the GO hierarchy, so this is a broader but valid annotation for a UMP-CMP kinase. UMP-CMP kinases transfer a phosphate group from ATP to nucleoside monophosphate substrates (UMP, CMP, dCMP), which already carry a phosphate group, making them phosphotransferases with phosphate group as acceptor. Reason: This is a valid parent term of the more specific UMP/CMP/dCMP kinase activities also annotated to this protein. While broader than the specific kinase activities (GO:0033862, GO:0036430, GO:0036431), it correctly captures the biochemical mechanism. The InterPro match to IPR006266 (UMP-CMP kinase family) is appropriate for the N-terminal domain. Supporting Evidence: file:9POAL/NCGR_LOCUS27674/NCGR_LOCUS27674-uniprot.txt Reaction=CMP + ATP = CDP + ADP |
| GO:0016872 intramolecular lyase activity | IEA GO_REF:0000002 | REMOVE | Summary: This annotation derives from InterPro match to IPR036298 (Chalcone isomerase superfamily), which is mapped to GO:0016872 via InterPro2GO. Chalcone isomerases catalyze intramolecular cyclization of chalcones to flavanones. However, this annotation is inappropriate for two reasons: (1) the CHI-fold domain in this protein likely belongs to the non-catalytic FAP (fatty acid-binding) subfamily, which lacks the catalytic residues for isomerase activity [PMID:22622584]; and (2) this domain is part of a chimeric gene model and belongs to a separate gene product. The InterPro2GO mapping from IPR036298 to GO:0016872 is overly broad, applying catalytic function to the entire superfamily including non-catalytic members. Reason: This is a doubly erroneous annotation: the intramolecular lyase activity derives from the CHI superfamily InterPro match, but the CHI-fold domain in this protein is likely a FAP subfamily member that is non-catalytic. Furthermore, the CHI-fold domain (positions 555-650) belongs to a separate gene that was incorrectly fused with the UMP-CMP kinase in this chimeric gene model. A UMP-CMP kinase has no intramolecular lyase activity. Supporting Evidence: PMID:22622584 the FAP discovery defines the adaptive evolution of a stereospecific and catalytically 'perfected' enzyme from a non-enzymatic ancestor over a defined period of plant evolution. file:9POAL/NCGR_LOCUS27674/NCGR_LOCUS27674-notes.md C-terminal (positions 555-650) Chalcone isomerase domain (Pfam PF16035, Chalcone_2) - functionally unrelated to the N-terminal UMP-CMP kinase domain. |
| GO:0019205 nucleobase-containing compound kinase activity | IEA GO_REF:0000002 | ACCEPT | Summary: Assigned via InterPro match to IPR000850 (Adenylate/UMP-CMP kinase). GO:0019205 is an ancestor of GO:0033862 (UMP kinase activity) in the GO hierarchy. UMP-CMP kinases phosphorylate nucleoside monophosphates (nucleobase-containing compounds), so this broader annotation is valid. Reason: This is a valid broader term for UMP-CMP kinase activity. The protein's N-terminal domain belongs to the adenylate kinase family UMP-CMP kinase subfamily, which phosphorylates nucleobase-containing compounds (UMP, CMP, dCMP). While less specific than GO:0033862/GO:0036430/GO:0036431, it is not incorrect. Supporting Evidence: PMID:9576794 both UMP (Km = 153 microM) and CMP (Km = 266 microM) were equally acceptable as the phosphate acceptor. |
| GO:0033862 UMP kinase activity | IEA GO_REF:0000104 | ACCEPT | Summary: Assigned via UniRule UR000111469 based on shared sequence features with characterized UMP-CMP kinases. UMP kinase activity (catalysis of UMP + ATP = UDP + ADP) is a core function of the UMP-CMP kinase family. The UniProt record explicitly lists this catalytic activity with EC 2.7.4.14. This annotation applies to the N-terminal adenylate kinase domain. Reason: UMP kinase activity is the primary molecular function of UMP-CMP kinases. The protein contains the conserved ADK domain (PF00406) and matches HAMAP rule MF_03172 for the UMP-CMP kinase subfamily. Confirmed in the rice ortholog YL2 [PMID:29392476] and Arabidopsis [PMID:9576794]. Supporting Evidence: file:9POAL/NCGR_LOCUS27674/NCGR_LOCUS27674-uniprot.txt Reaction=UMP + ATP = UDP + ADP PMID:29392476 Prokaryotic UMP kinase activity was subsequently confirmed, with YL2 deficiency causing a significant reduction in chlorophyll accumulation and photochemical efficiency. file:9POAL/NCGR_LOCUS27674/NCGR_LOCUS27674-deep-research-manual.md Plant UMP-CMP kinases catalyze the phosphorylation of pyrimidine nucleoside monophosphates (UMP, CMP, dCMP) using ATP. |
| GO:0036430 dCMP kinase activity | IEA GO_REF:0000104 | ACCEPT | Summary: Assigned via UniRule UR000111469. dCMP kinase activity (catalysis of dCMP + ATP = dCDP + ADP) is a known activity of UMP-CMP kinases. The UniProt record explicitly lists this catalytic reaction. Reason: dCMP kinase activity is a well-characterized function of the UMP-CMP kinase family. The catalytic reaction is explicitly listed in the UniProt record. This applies to the N-terminal kinase domain. Supporting Evidence: file:9POAL/NCGR_LOCUS27674/NCGR_LOCUS27674-uniprot.txt Reaction=dCMP + ATP = dCDP + ADP |
| GO:0036431 CMP kinase activity | IEA GO_REF:0000104 | ACCEPT | Summary: Assigned via UniRule UR000111469. CMP kinase activity (catalysis of CMP + ATP = CDP + ADP) is a core function of UMP-CMP kinases. The UniProt record explicitly lists this catalytic reaction. Reason: CMP kinase activity is a core function of the UMP-CMP kinase family. Arabidopsis UMP/CMP kinase accepts both UMP and CMP as phosphate acceptors [PMID:9576794]. Supporting Evidence: file:9POAL/NCGR_LOCUS27674/NCGR_LOCUS27674-uniprot.txt Reaction=CMP + ATP = CDP + ADP PMID:9576794 both UMP (Km = 153 microM) and CMP (Km = 266 microM) were equally acceptable as the phosphate acceptor. |
| GO:0006207 'de novo' pyrimidine nucleobase biosynthetic process | IEA GO_REF:0000002 | MODIFY | Summary: Assigned via InterPro match to IPR006266 (UMP-CMP kinase). UMP-CMP kinases play an important role in de novo pyrimidine nucleotide biosynthesis by phosphorylating UMP to UDP. However, GO:0006207 specifically refers to pyrimidine nucleobase biosynthesis (the base itself), whereas UMP-CMP kinases act on nucleotides (nucleobase + sugar + phosphate). The more appropriate term is GO:0006221 (pyrimidine nucleotide biosynthetic process), which is already annotated. Reason: UMP-CMP kinases act on pyrimidine nucleotides, not nucleobases. GO:0006207 is technically not the correct process for a nucleoside monophosphate kinase. GO:0006221 (pyrimidine nucleotide biosynthetic process) is more appropriate and already annotated. Proposed replacements: pyrimidine nucleotide biosynthetic process Supporting Evidence: file:9POAL/NCGR_LOCUS27674/NCGR_LOCUS27674-uniprot.txt Plays an important role in de novo pyrimidine nucleotide biosynthesis. Has preference for UMP and CMP as phosphate acceptors. |
| GO:0006221 pyrimidine nucleotide biosynthetic process | IEA GO_REF:0000120 | ACCEPT | Summary: Assigned via combined automated annotation (InterPro IPR006266 + UniRule UR000111469). UMP-CMP kinases participate in pyrimidine nucleotide biosynthesis by catalyzing the phosphorylation of pyrimidine nucleoside monophosphates (UMP, CMP) to their diphosphate forms (UDP, CDP). The UniProt record explicitly states the protein plays an important role in de novo pyrimidine nucleotide biosynthesis. Reason: Pyrimidine nucleotide biosynthesis is a core biological process for UMP-CMP kinases. The phosphorylation of UMP to UDP and CMP to CDP are essential steps in maintaining the pyrimidine nucleotide pool. Confirmed in rice YL2 [PMID:29392476] and Arabidopsis PUMPKIN [PMID:30409856]. Supporting Evidence: file:9POAL/NCGR_LOCUS27674/NCGR_LOCUS27674-uniprot.txt Plays an important role in de novo pyrimidine nucleotide biosynthesis. PMID:29392476 our results suggest that UMP kinase activity plays an essential role in chloroplast development and regulating cpATPase biogenesis in rice. |
| GO:0005634 nucleus | IEA GO_REF:0000120 | UNDECIDED | Summary: Assigned via combined automated annotation (UniProtKB-SubCell SL-0191 + UniRule UR000111469). The UniProt record states nuclear localization based on HAMAP rule MF_03172. However, for plant UMP-CMP kinases, characterized orthologs are predominantly cytosolic (Arabidopsis UMK) or plastid-localized (rice YL2, Arabidopsis PUMPKIN) [PMID:29392476, PMID:30409856]. Nuclear localization is not well-established for plant UMKs. Reason: Nuclear localization is inferred from homology to animal UMP-CMP kinases via the HAMAP rule, but characterized plant orthologs localize to the cytoplasm or plastids rather than the nucleus. Without direct experimental evidence in plants, the nuclear localization annotation should be treated with caution. Supporting Evidence: file:9POAL/NCGR_LOCUS27674/NCGR_LOCUS27674-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm. Nucleus. PMID:30409856 the sole plastid UMP kinase (PUMPKIN) in Arabidopsis (Arabidopsis thaliana) |
| GO:0005737 cytoplasm | IEA GO_REF:0000120 | ACCEPT | Summary: Assigned via combined automated annotation (UniProtKB-SubCell SL-0086 + UniRule UR000111469). Cytoplasmic localization is consistent with the known localization of several plant UMP-CMP kinase isoforms. The Arabidopsis UMP/CMP kinase characterized by Zhou et al. was expressed and purified as a cytosolic protein [PMID:9576794]. Reason: Cytoplasmic localization is well-supported for plant UMP-CMP kinases. Arabidopsis has cytosolic UMK isoforms alongside the plastid-localized PUMPKIN. Even if this particular gene model is chimeric, the UMP-CMP kinase portion would likely localize to the cytoplasm or plastids. Supporting Evidence: file:9POAL/NCGR_LOCUS27674/NCGR_LOCUS27674-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm. PMID:9576794 A cDNA encoding the Arabidopsis thaliana uridine 5'-monophosphate (UMP)/cytidine 5'-monophosphate (CMP) kinase was isolated by complementation of a Saccharomyces cerevisiae ura6 mutant. |
| GO:0009570 chloroplast stroma | IEA GO_REF:0000118 | UNDECIDED | Summary: Assigned via TreeGrafter matching to PANTHER PTN009208978. Chloroplast localization is plausible for plant UMP-CMP kinases - rice YL2 and Arabidopsis PUMPKIN are chloroplast-localized UMKs [PMID:29392476, PMID:30409856]. However, the specific sub-compartment is questionable: rice YL2 localizes to thylakoid membranes, not the stroma [PMID:29392476]. Additionally, the TreeGrafter match may be influenced by the chimeric gene model, as CHI-fold FAP proteins also localize to plastids [PMID:22622584]. Reason: While chloroplast localization is plausible for a plant UMP-CMP kinase, the specific annotation to chloroplast stroma (GO:0009570) is uncertain. The closest characterized ortholog, rice YL2, is a thylakoid membrane-localized protein [PMID:29392476]. Furthermore, the TreeGrafter PANTHER match could reflect either the UMK domain or the CHI-fold FAP domain, both of which can be plastid-targeted. Supporting Evidence: PMID:29392476 YL2 encodes a thylakoid membrane-localized protein with significant sequence similarity to UMP kinase proteins in prokaryotes and eukaryotes. PMID:22622584 These three CHI-fold proteins localize to plastids, the site of de novo fatty-acid biosynthesis in plant cells. |
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