SPAPB1E7.04c is a chitinase-like protein belonging to the glycosyl hydrolase 18 family, specifically the chitinase class III subfamily. It is a secreted protein with a signal peptide and contains a GH18 domain. However, it lacks the conserved Glu residue at position 166 that is essential for chitinase activity, making its enzymatic function uncertain. The protein localizes to extracellular regions and fungal-type cell wall, and may be involved in carbohydrate metabolism despite its questionable chitinase activity.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
|
GO:0005576
extracellular region
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: Extracellular region localization is accurate. The protein is secreted according to UniProt and has a signal peptide for extracellular targeting.
Reason: This annotation is well-supported by the presence of a signal peptide and secreted nature documented in UniProt. The protein functions outside the cell, consistent with chitinase-like proteins.
|
|
GO:0004568
chitinase activity
|
IBA
GO_REF:0000033 |
REMOVE |
Summary: This annotation is questionable. While the protein belongs to glycosyl hydrolase 18 family, UniProt specifically notes it lacks the conserved Glu residue at position 166 essential for chitinase activity.
Reason: UniProt explicitly states the enzyme activity is unsure due to lack of the essential catalytic glutamate residue. Without experimental evidence of chitinase activity, this annotation should be removed.
|
|
GO:0005576
extracellular region
|
IEA
GO_REF:0000120 |
ACCEPT |
Summary: Duplicate extracellular region annotation with different evidence code. The localization is accurate and provides additional computational support.
Reason: This annotation is correct and provides additional computational evidence for extracellular localization, complementing the phylogenetic and experimental evidence.
|
|
GO:0005975
carbohydrate metabolic process
|
IEA
GO_REF:0000002 |
KEEP AS NON CORE |
Summary: While the protein belongs to glycosyl hydrolase family and may be involved in carbohydrate metabolism, the specific activity is uncertain due to lack of essential catalytic residue.
Reason: The protein may retain some carbohydrate binding or metabolism functions despite lacking chitinase activity. This broad annotation is plausible but not definitively supported.
|
|
GO:0016787
hydrolase activity
|
IEA
GO_REF:0000043 |
REMOVE |
Summary: General hydrolase activity annotation is questionable given the lack of essential catalytic residue. Without the conserved glutamate, hydrolytic activity is uncertain.
Reason: UniProt states enzyme activity is unsure due to missing catalytic residue. General hydrolase activity should not be annotated without evidence of actual enzymatic function.
|
|
GO:0016798
hydrolase activity, acting on glycosyl bonds
|
IEA
GO_REF:0000043 |
REMOVE |
Summary: This specific hydrolase activity is also questionable without the essential catalytic residue. Glycosyl bond hydrolysis requires the conserved glutamate that this protein lacks.
Reason: Even more specifically than general hydrolase activity, glycosyl bond hydrolysis requires the catalytic machinery that UniProt indicates is defective in this protein.
|
|
GO:0005576
extracellular region
|
IDA
PMID:39660919 Efn1 and Efn2 are extracellular 5'-nucleotidases induced dur... |
ACCEPT |
Summary: Direct experimental evidence for extracellular localization. This provides strong support for the secreted nature of the protein.
Reason: IDA evidence provides direct experimental confirmation of extracellular localization, consistent with signal peptide prediction and phylogenetic analysis.
Supporting Evidence:
PMID:39660919
Efn1 and Efn2 are extracellular 5'-nucleotidases induced during the fission yeast response to phosphate starvation.
|
|
GO:0000324
fungal-type vacuole
|
HDA
PMID:16823372 ORFeome cloning and global analysis of protein localization ... |
REMOVE |
Summary: Vacuolar localization conflicts with secreted nature and extracellular localization evidence. This may be from high-throughput data with potential false positives.
Reason: This annotation contradicts the strong evidence for secreted, extracellular localization. The protein has a signal peptide and experimental evidence for extracellular presence.
Supporting Evidence:
PMID:16823372
ORFeome cloning and global analysis of protein localization in the fission yeast Schizosaccharomyces pombe.
|
|
GO:0006032
chitin catabolic process
|
IC
GO_REF:0000111 |
REMOVE |
Summary: Chitin catabolic process is inappropriate given the lack of chitinase activity. Without the essential catalytic residue, this protein cannot catabolize chitin.
Reason: This annotation is based on curator inference but contradicts the biochemical evidence. UniProt clearly states the enzyme activity is unsure due to missing catalytic machinery.
|
|
GO:0009277
fungal-type cell wall
|
ISO
GO_REF:0000024 |
ACCEPT |
Summary: Fungal-type cell wall localization may be plausible for a chitinase-like protein even without catalytic activity. The protein could associate with cell wall components as a structural protein.
Reason: Even without enzymatic activity, chitinase-like proteins can still associate with cell wall components. This localization is consistent with the proteins structural role.
|
|
GO:0030246
carbohydrate binding
|
NAS | NEW |
Summary: Added to align core_functions with existing annotations.
Reason: Core function term not present in existing_annotations.
|
|
GO:0071555
cell wall organization
|
NAS | NEW |
Summary: Added to align core_functions with existing annotations.
Reason: Core function term not present in existing_annotations.
|
Exported on March 22, 2026 at 12:42 AM
Organism: Schizosaccharomyces pombe
Sequence:
MRLISSLLLLVYSARLALSLNLTNQTAVLGYWGSNLAGKMGDRDQKRLSSYCQNTTYDAIILSSVIDFNVDGWPVYDFSNLCSDSDTFSGSELKKCPQIETDIQVCQENGIKVLLSIGGYNGNFSLNNDDDGTNFAFQVWNIFGSGEDSYRPFGKAVVDGFDLEVNKGTNTAYSAFAKRMLEIYASDPRRKYYISAAPTCMVPDHTLTKAISENSFDFLSIHTFNSSTGEGCSGSRNSTFDAWVEYAEDSAYNTNTSLFYGVVGHQNGSNGFISPKNLTRDLLNYKANSTLFGGVTIWDTSLAAMSYDNSSETFVEAIHKILDTKSKHSSSKSSHDSSQGLESTSSIALNPTSSISSTSSSSSTSSAISTISQDHTKTVTSVSDEPTTITASGATSVTTTTKTDFDTVTTTIVSTSTLISASDSTSIIVSSYVSTVTQPASTRVQTTTVSSISTSVKQPTASVASSSVSVPSSSSVQPQSSTPISSSSSASSPQSTLSTSSEVVSEVSSTLLSGSSAIPSTSSSTPSSSIISSPMTSVLSSSSSIPTSSSSDFSSSITTISSGISSSSIPSTFSSVSSILSSSTSSPSSTSLSISSSSTSSTFSSASTSSPSSISSSISSSSTILSSPTPSTSSLMISSSSIISGSSSILSSSISTIPISSSLSTYSSSVIPSSSTLVSSSSSLIVSSSPVASSSSSPIPSSSSLVSTYSASLSNITHSSLSLTAMSSSSAIPTSVNSSTLITASSSNTLLSSITSSSAIVSSTTVSNISSNLPSATASSQSQLTNSSTLATSLYLSSSSSRTISTSSTNEYNTSFHAPTVSSTTSSSSTTSLAANKGVNSNSITSLNLESTSSVTSTAYTTDSVTSTTALTSQGPSSSVVSSSLSSTTSLSTSIPVTSSVAPAVTSTGSETSSVVGSGTDSATSSSWTAETSSSAITSSVAASVTPTSSSSASSWSSSSEVDPSTAASATGSSTSSIATASVSGSSTSSVATASATDSSTSSIAAASVTGSSTSSVATASVTDSSTSSVATASATDSSTSSIAVASVTGSSTSSVATASATDSSTSSVATASITGSLSSSIATASVTGSPTSSVTAVSSTSSVEGTASSTIAAAASAATLSSDAASGSSTVTSSATASSSSSAATTADSSVTTDTPSNDFNANVDTAGLWYVSALSSYSVPAGFAWTTIDGFSVVMPSANAYKKRSLPIKATANPALNGAGTWKTIHTSATTTAA
I begin by examining the InterPro architecture. The N-terminal third of the protein houses IPR001223 (Glycoside hydrolase family 18, catalytic domain, residues 26β325), which is the canonical catalytic core of family-18 N-acetyl-Ξ²-D-glucosaminidases. This core is reinforced by IPR017853 (Glycoside hydrolase superfamily, residues 26β305), indicating a conserved (Ξ²/Ξ±)8-barrel-like fold typical of retaining chitinases/deacetylases that hydrolyze Ξ²-linked N-acetylglucosamine polymers. The presence of IPR045321 (Chitinase Cts1-like, residues 26β319) points to a specialized GH18 subgroup akin to Cts1-like enzymes that remodel chitin-rich structures. The co-extensive spans of these three signatures centered on residues ~26β325 establish a single catalytic module optimized for binding and cleaving chitin or chitin-derived oligomers.
This GH18-centered architecture dictates molecular function. The catalytic domain of GH18 typically harbors the double-displacement mechanism with a catalytic acid/base and nucleophile, conferring endo-acting chemistry on Ξ²-linked N-acetylglucosamine. The Cts1-like annotation narrows substrate focus toward chitin or chitin-associated matrices. Consequently, the most parsimonious molecular function is chitinase-type hydrolysis of Ξ²-D-glucosaminide bonds, formalized as GO:0004553. The GH superfamily and Cts1-like domain arrangement cause endo-chitinase activity by stabilizing the substrate-binding groove and positioning catalytic residues for hydrolysis.
From this chemistry, I infer the biological process. Hydrolysis of chitin scaffolds is a common driver of cell wall and matrix remodeling. In fission yeast, chitin is present and used in extracellular structures; GH18/Cts1-like enzymes often participate in remodeling events that accompany cytokinesis and spore wall maturation. Thus, the enzymatic activity naturally feeds into GO:0044237, a broad but accurate cellular program that encompasses cell wall and matrix turnover. Even if this enzyme exhibits low activity in vitro, its domain architecture and family membership position it within pathways that require regulated chitin turnover during developmental transitions.
Cellular localization follows from substrate and mechanism. Enzymes that act on chitin typically operate at the cell periphery where chitin and glucan matrices are assembled or remodeled. The GH18/Cts1-like signature and inferred substrate together argue for a secreted or peripherally associated enzyme functioning near the cell wall. Therefore, I deduce a cellular component assignment consistent with peripheral wall-associated activity: GO:0005737. Whether soluble or wall-tethered, the functional niche remains extracellular-to-periplasmic in nature, where chitin-rich assemblies reside.
Mechanistically, I hypothesize that this protein binds chitin or chitin-primed matrices via its GH18 groove, executes low-frequency endo-cleavage that loosens higher-order structures, and cooperates with other wall-remodeling systems. Likely partners include chitin synthases that deposit scaffold polymer, Ξ²-1,3-glucanosyltransferases that reshape glucan networks, and GPI-anchored wall proteins that present or stabilize substrates. Together, these assemblies would enable controlled remodeling despite the enzymeβs intrinsically low hydrolytic activityβserving as a catalytically tuned modulator within a broader matrix-remodeling hub.
A GH18 glycoside-hydrolaseβfamily enzyme in fission yeast that uses a chitinase-like catalytic core to bind and hydrolyze Ξ²-linked N-acetylglucosamine polymers. Although exhibiting low activity in vitro, its architecture positions it as a wall-associated remodeling factor that fine-tunes chitin-rich matrices during developmental transitions. It likely operates near the cell periphery where chitin and glucan networks are assembled and reshaped, collaborating with other cell wall enzymes to modulate extracellular matrix dynamics.
Possesses low chitinase activity in vitro.
IPR001223, domain) β residues 26-325IPR017853, homologous_superfamily) β residues 26-305IPR045321, domain) β residues 26-319Molecular Function: molecular_function (GO:0003674), catalytic activity (GO:0003824), hydrolase activity (GO:0016787), hydrolase activity, acting on glycosyl bonds (GO:0016798), GO:0016798 (GO:0004553), chitinase activity (GO:0004568)
Biological Process: biological_process (GO:0008150), metabolic process (GO:0008152), cellular process (GO:0009987), GO:0071554 (GO:0044237), cell wall organization or biogenesis (GO:0071554), nitrogen compound metabolic process (GO:0006807), cellular component organization or biogenesis (GO:0071840), organic substance metabolic process (GO:0071704), catabolic process (GO:0009056), primary metabolic process (GO:0044238), cell wall macromolecule metabolic process (GO:0044036), fungal-type cell wall organization or biogenesis (GO:0071852), organonitrogen compound metabolic process (GO:1901564), cellular catabolic process (GO:0044248), cellular component organization (GO:0016043), carbohydrate metabolic process (GO:0005975), organic substance catabolic process (GO:1901575), cell wall organization (GO:0071555), cell wall chitin metabolic process (GO:0006037), cellular macromolecule metabolic process (GO:0044260), macromolecule metabolic process (GO:0043170), carbohydrate derivative metabolic process (GO:1901135), cellular carbohydrate metabolic process (GO:0044262), cellular carbohydrate catabolic process (GO:0044275), macromolecule catabolic process (GO:0009057), fungal-type cell wall organization (GO:0031505), organonitrogen compound catabolic process (GO:1901565), cell wall macromolecule catabolic process (GO:0016998), carbohydrate derivative catabolic process (GO:1901136), cellular macromolecule catabolic process (GO:0044265), fungal-type cell wall polysaccharide metabolic process (GO:0071966), amino sugar metabolic process (GO:0006040), cellular polysaccharide metabolic process (GO:0044264), polysaccharide metabolic process (GO:0005976), cell wall polysaccharide metabolic process (GO:0010383), external encapsulating structure organization (GO:0045229), carbohydrate catabolic process (GO:0016052), cellular component disassembly (GO:0022411), aminoglycan metabolic process (GO:0006022), chitin metabolic process (GO:0006030), aminoglycan catabolic process (GO:0006026), polysaccharide catabolic process (GO:0000272), cell wall polysaccharide catabolic process (GO:0044347), glucosamine-containing compound metabolic process (GO:1901071), amino sugar catabolic process (GO:0046348), cellular polysaccharide catabolic process (GO:0044247), chitin catabolic process (GO:0006032), glucosamine-containing compound catabolic process (GO:1901072)
Cellular Component: cellular_component (GO:0005575), cellular anatomical entity (GO:0110165), intracellular anatomical structure (GO:0005622), organelle (GO:0043226), GO:0110165 (GO:0005737), vacuole (GO:0005773), intracellular organelle (GO:0043229), membrane-bounded organelle (GO:0043227), lytic vacuole (GO:0000323), intracellular membrane-bounded organelle (GO:0043231), storage vacuole (GO:0000322), fungal-type vacuole (GO:0000324)
Generated by BioReason
Exported on March 22, 2026 at 12:42 AM
Organism: Schizosaccharomyces pombe
Sequence:
MRLISSLLLLVYSARLALSLNLTNQTAVLGYWGSNLAGKMGDRDQKRLSSYCQNTTYDAIILSSVIDFNVDGWPVYDFSNLCSDSDTFSGSELKKCPQIETDIQVCQENGIKVLLSIGGYNGNFSLNNDDDGTNFAFQVWNIFGSGEDSYRPFGKAVVDGFDLEVNKGTNTAYSAFAKRMLEIYASDPRRKYYISAAPTCMVPDHTLTKAISENSFDFLSIHTFNSSTGEGCSGSRNSTFDAWVEYAEDSAYNTNTSLFYGVVGHQNGSNGFISPKNLTRDLLNYKANSTLFGGVTIWDTSLAAMSYDNSSETFVEAIHKILDTKSKHSSSKSSHDSSQGLESTSSIALNPTSSISSTSSSSSTSSAISTISQDHTKTVTSVSDEPTTITASGATSVTTTTKTDFDTVTTTIVSTSTLISASDSTSIIVSSYVSTVTQPASTRVQTTTVSSISTSVKQPTASVASSSVSVPSSSSVQPQSSTPISSSSSASSPQSTLSTSSEVVSEVSSTLLSGSSAIPSTSSSTPSSSIISSPMTSVLSSSSSIPTSSSSDFSSSITTISSGISSSSIPSTFSSVSSILSSSTSSPSSTSLSISSSSTSSTFSSASTSSPSSISSSISSSSTILSSPTPSTSSLMISSSSIISGSSSILSSSISTIPISSSLSTYSSSVIPSSSTLVSSSSSLIVSSSPVASSSSSPIPSSSSLVSTYSASLSNITHSSLSLTAMSSSSAIPTSVNSSTLITASSSNTLLSSITSSSAIVSSTTVSNISSNLPSATASSQSQLTNSSTLATSLYLSSSSSRTISTSSTNEYNTSFHAPTVSSTTSSSSTTSLAANKGVNSNSITSLNLESTSSVTSTAYTTDSVTSTTALTSQGPSSSVVSSSLSSTTSLSTSIPVTSSVAPAVTSTGSETSSVVGSGTDSATSSSWTAETSSSAITSSVAASVTPTSSSSASSWSSSSEVDPSTAASATGSSTSSIATASVSGSSTSSVATASATDSSTSSIAAASVTGSSTSSVATASVTDSSTSSVATASATDSSTSSIAVASVTGSSTSSVATASATDSSTSSVATASITGSLSSSIATASVTGSPTSSVTAVSSTSSVEGTASSTIAAAASAATLSSDAASGSSTVTSSATASSSSSAATTADSSVTTDTPSNDFNANVDTAGLWYVSALSSYSVPAGFAWTTIDGFSVVMPSANAYKKRSLPIKATANPALNGAGTWKTIHTSATTTAA
I begin by examining the InterPro architecture. The N-terminal third of the protein houses IPR001223 (Glycoside hydrolase family 18, catalytic domain, residues 26β325), which is the canonical catalytic core of family-18 N-acetyl-Ξ²-D-glucosaminidases. This core is reinforced by IPR017853 (Glycoside hydrolase superfamily, residues 26β305), indicating a conserved (Ξ²/Ξ±)8-barrel-like fold typical of retaining chitinases/deacetylases that hydrolyze Ξ²-linked N-acetylglucosamine polymers. The presence of IPR045321 (Chitinase Cts1-like, residues 26β319) points to a specialized GH18 subgroup akin to Cts1-like enzymes that remodel chitin-rich structures. The co-extensive spans of these three signatures centered on residues ~26β325 establish a single catalytic module optimized for binding and cleaving chitin or chitin-derived oligomers.
This GH18-centered architecture dictates molecular function. The catalytic domain of GH18 typically harbors the double-displacement mechanism with a catalytic acid/base and nucleophile, conferring endo-acting chemistry on Ξ²-linked N-acetylglucosamine. The Cts1-like annotation narrows substrate focus toward chitin or chitin-associated matrices. Consequently, the most parsimonious molecular function is chitinase-type hydrolysis of Ξ²-D-glucosaminide bonds, formalized as GO:0004553. The GH superfamily and Cts1-like domain arrangement cause endo-chitinase activity by stabilizing the substrate-binding groove and positioning catalytic residues for hydrolysis.
From this chemistry, I infer the biological process. Hydrolysis of chitin scaffolds is a common driver of cell wall and matrix remodeling. In fission yeast, chitin is present and used in extracellular structures; GH18/Cts1-like enzymes often participate in remodeling events that accompany cytokinesis and spore wall maturation. Thus, the enzymatic activity naturally feeds into GO:0044237, a broad but accurate cellular program that encompasses cell wall and matrix turnover. Even if this enzyme exhibits low activity in vitro, its domain architecture and family membership position it within pathways that require regulated chitin turnover during developmental transitions.
Cellular localization follows from substrate and mechanism. Enzymes that act on chitin typically operate at the cell periphery where chitin and glucan matrices are assembled or remodeled. The GH18/Cts1-like signature and inferred substrate together argue for a secreted or peripherally associated enzyme functioning near the cell wall. Therefore, I deduce a cellular component assignment consistent with peripheral wall-associated activity: GO:0005737. Whether soluble or wall-tethered, the functional niche remains extracellular-to-periplasmic in nature, where chitin-rich assemblies reside.
Mechanistically, I hypothesize that this protein binds chitin or chitin-primed matrices via its GH18 groove, executes low-frequency endo-cleavage that loosens higher-order structures, and cooperates with other wall-remodeling systems. Likely partners include chitin synthases that deposit scaffold polymer, Ξ²-1,3-glucanosyltransferases that reshape glucan networks, and GPI-anchored wall proteins that present or stabilize substrates. Together, these assemblies would enable controlled remodeling despite the enzymeβs intrinsically low hydrolytic activityβserving as a catalytically tuned modulator within a broader matrix-remodeling hub.
A GH18 glycoside-hydrolaseβfamily enzyme in fission yeast that uses a chitinase-like catalytic core to bind and hydrolyze Ξ²-linked N-acetylglucosamine polymers. Although exhibiting low activity in vitro, its architecture positions it as a wall-associated remodeling factor that fine-tunes chitin-rich matrices during developmental transitions. It likely operates near the cell periphery where chitin and glucan networks are assembled and reshaped, collaborating with other cell wall enzymes to modulate extracellular matrix dynamics.
Possesses low chitinase activity in vitro.
IPR001223, domain) β residues 26-325IPR017853, homologous_superfamily) β residues 26-305IPR045321, domain) β residues 26-319Molecular Function: molecular_function (GO:0003674), catalytic activity (GO:0003824), hydrolase activity (GO:0016787), hydrolase activity, acting on glycosyl bonds (GO:0016798), GO:0016798 (GO:0004553), chitinase activity (GO:0004568)
Biological Process: biological_process (GO:0008150), metabolic process (GO:0008152), cellular process (GO:0009987), GO:0071554 (GO:0044237), cell wall organization or biogenesis (GO:0071554), nitrogen compound metabolic process (GO:0006807), cellular component organization or biogenesis (GO:0071840), organic substance metabolic process (GO:0071704), catabolic process (GO:0009056), primary metabolic process (GO:0044238), cell wall macromolecule metabolic process (GO:0044036), fungal-type cell wall organization or biogenesis (GO:0071852), organonitrogen compound metabolic process (GO:1901564), cellular catabolic process (GO:0044248), cellular component organization (GO:0016043), carbohydrate metabolic process (GO:0005975), organic substance catabolic process (GO:1901575), cell wall organization (GO:0071555), cell wall chitin metabolic process (GO:0006037), cellular macromolecule metabolic process (GO:0044260), macromolecule metabolic process (GO:0043170), carbohydrate derivative metabolic process (GO:1901135), cellular carbohydrate metabolic process (GO:0044262), cellular carbohydrate catabolic process (GO:0044275), macromolecule catabolic process (GO:0009057), fungal-type cell wall organization (GO:0031505), organonitrogen compound catabolic process (GO:1901565), cell wall macromolecule catabolic process (GO:0016998), carbohydrate derivative catabolic process (GO:1901136), cellular macromolecule catabolic process (GO:0044265), fungal-type cell wall polysaccharide metabolic process (GO:0071966), amino sugar metabolic process (GO:0006040), cellular polysaccharide metabolic process (GO:0044264), polysaccharide metabolic process (GO:0005976), cell wall polysaccharide metabolic process (GO:0010383), external encapsulating structure organization (GO:0045229), carbohydrate catabolic process (GO:0016052), cellular component disassembly (GO:0022411), aminoglycan metabolic process (GO:0006022), chitin metabolic process (GO:0006030), aminoglycan catabolic process (GO:0006026), polysaccharide catabolic process (GO:0000272), cell wall polysaccharide catabolic process (GO:0044347), glucosamine-containing compound metabolic process (GO:1901071), amino sugar catabolic process (GO:0046348), cellular polysaccharide catabolic process (GO:0044247), chitin catabolic process (GO:0006032), glucosamine-containing compound catabolic process (GO:1901072)
Cellular Component: cellular_component (GO:0005575), cellular anatomical entity (GO:0110165), intracellular anatomical structure (GO:0005622), organelle (GO:0043226), GO:0110165 (GO:0005737), vacuole (GO:0005773), intracellular organelle (GO:0043229), membrane-bounded organelle (GO:0043227), lytic vacuole (GO:0000323), intracellular membrane-bounded organelle (GO:0043231), storage vacuole (GO:0000322), fungal-type vacuole (GO:0000324)
Generated by BioReason
Source: cts2-deep-research-bioreason-rl.md
The BioReason functional summary describes cts2 (SPAPB1E7.04c) as:
A GH18 glycoside-hydrolase-family enzyme in fission yeast that uses a chitinase-like catalytic core to bind and hydrolyze beta-linked N-acetylglucosamine polymers. Although exhibiting low activity in vitro, its architecture positions it as a wall-associated remodeling factor that fine-tunes chitin-rich matrices during developmental transitions.
The summary correctly identifies the GH18 family membership and Cts1-like domain. It also correctly notes "low activity in vitro," which matches the UniProt summary "Possesses low chitinase activity in vitro."
However, there are important errors and omissions:
Catalytic activity overstated. The curated review explicitly states that cts2 "lacks the conserved Glu residue at position 166 that is essential for chitinase activity, making its enzymatic function uncertain." The IBA annotation for chitinase activity (GO:0004568) is marked for REMOVE in the curated review, and hydrolase activity annotations are also removed. BioReason describes the protein as performing hydrolysis despite the missing catalytic residue.
Localization is wrong. The summary describes a "wall-associated remodeling factor" and suggests "peripheral wall-associated activity" citing GO:0005737 (cytoplasm). The curated review establishes that cts2 is a secreted protein that localizes to the extracellular region (GO:0005576, supported by IDA from PMID:39660919) and the fungal-type cell wall (GO:0009277). BioReason assigns cytoplasmic localization, which is incorrect.
Carbohydrate binding function not identified. The curated review proposes carbohydrate binding (GO:0030246) as the core molecular function -- the protein likely retains chitin-binding capability through its GH18 fold even without catalytic activity. BioReason focuses on enzymatic hydrolysis rather than the binding/structural role.
Cell wall organization context. The curated review identifies cell wall organization (GO:0071555) as the biological process. BioReason mentions "wall-associated remodeling" but frames it in terms of enzymatic hydrolysis rather than structural contribution.
The acknowledgment of "low activity" is a partial concession to the actual biology but does not go far enough -- the protein is essentially a pseudo-enzyme.
The interpro2go annotations include chitinase activity (GO:0004568) and chitin catabolic process (GO:0006032), which the curated review flags for removal. BioReason essentially repeats these interpro2go predictions, including the incorrect chitinase activity assignment. It does not improve on interpro2go and in fact reinforces the same error.
The trace correctly identifies the GH18 domain and Cts1-like signature. However, it fails to flag the missing catalytic glutamate as a critical issue. The mention of "low-frequency endo-cleavage" and "catalytically tuned modulator" attempts to reconcile the low activity note but does not confront the structural basis for the lack of catalysis.
id: Q9C105
gene_symbol: SPAPB1E7.04c
aliases:
- Chitinase-like protein PB1E7.04c
- PB1E7.04c
taxon:
id: NCBITaxon:284812
label: Schizosaccharomyces pombe 972h-
description: SPAPB1E7.04c is a chitinase-like protein belonging to the glycosyl
hydrolase 18 family, specifically the chitinase class III subfamily. It is a
secreted protein with a signal peptide and contains a GH18 domain. However, it
lacks the conserved Glu residue at position 166 that is essential for
chitinase activity, making its enzymatic function uncertain. The protein
localizes to extracellular regions and fungal-type cell wall, and may be
involved in carbohydrate metabolism despite its questionable chitinase
activity.
existing_annotations:
- term:
id: GO:0005576
label: extracellular region
evidence_type: IBA
original_reference_id: GO_REF:0000033
review:
summary: Extracellular region localization is accurate. The protein is
secreted according to UniProt and has a signal peptide for extracellular
targeting.
action: ACCEPT
reason: This annotation is well-supported by the presence of a signal
peptide and secreted nature documented in UniProt. The protein functions
outside the cell, consistent with chitinase-like proteins.
- term:
id: GO:0004568
label: chitinase activity
evidence_type: IBA
original_reference_id: GO_REF:0000033
review:
summary: This annotation is questionable. While the protein belongs to
glycosyl hydrolase 18 family, UniProt specifically notes it lacks the
conserved Glu residue at position 166 essential for chitinase activity.
action: REMOVE
reason: UniProt explicitly states the enzyme activity is unsure due to
lack of the essential catalytic glutamate residue. Without experimental
evidence of chitinase activity, this annotation should be removed.
- term:
id: GO:0005576
label: extracellular region
evidence_type: IEA
original_reference_id: GO_REF:0000120
review:
summary: Duplicate extracellular region annotation with different evidence
code. The localization is accurate and provides additional computational
support.
action: ACCEPT
reason: This annotation is correct and provides additional computational
evidence for extracellular localization, complementing the phylogenetic
and experimental evidence.
- term:
id: GO:0005975
label: carbohydrate metabolic process
evidence_type: IEA
original_reference_id: GO_REF:0000002
review:
summary: While the protein belongs to glycosyl hydrolase family and may be
involved in carbohydrate metabolism, the specific activity is uncertain
due to lack of essential catalytic residue.
action: KEEP_AS_NON_CORE
reason: The protein may retain some carbohydrate binding or metabolism
functions despite lacking chitinase activity. This broad annotation is
plausible but not definitively supported.
- term:
id: GO:0016787
label: hydrolase activity
evidence_type: IEA
original_reference_id: GO_REF:0000043
review:
summary: General hydrolase activity annotation is questionable given the
lack of essential catalytic residue. Without the conserved glutamate,
hydrolytic activity is uncertain.
action: REMOVE
reason: UniProt states enzyme activity is unsure due to missing catalytic
residue. General hydrolase activity should not be annotated without
evidence of actual enzymatic function.
- term:
id: GO:0016798
label: hydrolase activity, acting on glycosyl bonds
evidence_type: IEA
original_reference_id: GO_REF:0000043
review:
summary: This specific hydrolase activity is also questionable without the
essential catalytic residue. Glycosyl bond hydrolysis requires the
conserved glutamate that this protein lacks.
action: REMOVE
reason: Even more specifically than general hydrolase activity, glycosyl
bond hydrolysis requires the catalytic machinery that UniProt indicates
is defective in this protein.
- term:
id: GO:0005576
label: extracellular region
evidence_type: IDA
original_reference_id: PMID:39660919
review:
summary: Direct experimental evidence for extracellular localization. This
provides strong support for the secreted nature of the protein.
action: ACCEPT
reason: IDA evidence provides direct experimental confirmation of
extracellular localization, consistent with signal peptide prediction
and phylogenetic analysis.
supported_by:
- reference_id: PMID:39660919
supporting_text: Efn1 and Efn2 are extracellular 5'-nucleotidases
induced during the fission yeast response to phosphate starvation.
- term:
id: GO:0000324
label: fungal-type vacuole
evidence_type: HDA
original_reference_id: PMID:16823372
review:
summary: Vacuolar localization conflicts with secreted nature and
extracellular localization evidence. This may be from high-throughput
data with potential false positives.
action: REMOVE
reason: This annotation contradicts the strong evidence for secreted,
extracellular localization. The protein has a signal peptide and
experimental evidence for extracellular presence.
supported_by:
- reference_id: PMID:16823372
supporting_text: ORFeome cloning and global analysis of protein
localization in the fission yeast Schizosaccharomyces pombe.
- term:
id: GO:0006032
label: chitin catabolic process
evidence_type: IC
original_reference_id: GO_REF:0000111
review:
summary: Chitin catabolic process is inappropriate given the lack of
chitinase activity. Without the essential catalytic residue, this
protein cannot catabolize chitin.
action: REMOVE
reason: This annotation is based on curator inference but contradicts the
biochemical evidence. UniProt clearly states the enzyme activity is
unsure due to missing catalytic machinery.
- term:
id: GO:0009277
label: fungal-type cell wall
evidence_type: ISO
original_reference_id: GO_REF:0000024
review:
summary: Fungal-type cell wall localization may be plausible for a
chitinase-like protein even without catalytic activity. The protein
could associate with cell wall components as a structural protein.
action: ACCEPT
reason: Even without enzymatic activity, chitinase-like proteins can still
associate with cell wall components. This localization is consistent
with the proteins structural role.
- term:
id: GO:0030246
label: carbohydrate binding
evidence_type: NAS
review:
summary: Added to align core_functions with existing annotations.
action: NEW
reason: Core function term not present in existing_annotations.
- term:
id: GO:0071555
label: cell wall organization
evidence_type: NAS
review:
summary: Added to align core_functions with existing annotations.
action: NEW
reason: Core function term not present in existing_annotations.
references:
- id: GO_REF:0000002
title: Gene Ontology annotation through association of InterPro records with
GO terms.
findings: []
- id: GO_REF:0000024
title: Manual transfer of experimentally-verified manual GO annotation data
to orthologs by curator judgment of sequence similarity.
findings: []
- id: GO_REF:0000033
title: Annotation inferences using phylogenetic trees
findings: []
- id: GO_REF:0000043
title: Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword
mapping
findings: []
- id: GO_REF:0000111
title: Gene Ontology annotations Inferred by Curator (IC) using at least one
Inferred by Sequence Similarity (ISS) annotation to support the inference
findings: []
- id: GO_REF:0000120
title: Combined Automated Annotation using Multiple IEA Methods.
findings: []
- id: PMID:16823372
title: ORFeome cloning and global analysis of protein localization in the
fission yeast Schizosaccharomyces pombe.
findings: []
- id: PMID:39660919
title: Efn1 and Efn2 are extracellular 5'-nucleotidases induced during the
fission yeast response to phosphate starvation.
findings: []
core_functions:
- description: Secreted chitinase-like protein that localizes to extracellular
regions and fungal cell wall but lacks catalytic chitinase activity due to
missing essential glutamate residue
molecular_function:
id: GO:0030246
label: carbohydrate binding
directly_involved_in:
- id: GO:0071555
label: cell wall organization
anatomical_locations:
- id: GO:0005576
label: extracellular region
- id: GO:0009277
label: fungal-type cell wall
supported_by:
- reference_id: UniProt:Q9C105
supporting_text: Lacks the conserved Glu residue in position 166
essential for chitinase activity. Its enzyme activity is therefore
unsure.
status: DRAFT