Bacteriophage Genome Curation & Pathway Hole Filling

SCOPING BIOLOGY_DOMAINPIPELINE

Species: BPT4, 9CAUD, BPZF4, BPBPP, BPPHT, BPD31, ENTM13, ENTPH, SIRV1

Bacteriophage Genome Curation & Pathway Hole Filling

Bottom line: Bacteriophages are an unusually strong proving ground for combining end-to-end whole-genome annotation review with module-based pathway satisfiability and hole filling (PATHWAY_SATISFIABILITY.md). Phage genomes are compact (4 to ~290 genes), organized into syntenic functional operons, and phenotypically constrained: every plaque-forming phage must execute host attachment, genome entry, replication/transcription, virion assembly, and host release—either via phage-encoded proteins, non-orthologous displacements hidden in "viral dark matter," or explicit hijacking of host machinery. Moreover, unlike cellular metabolic pathways where a missing step is almost always an annotation gap, phage lifecycles provide true negatives by biology (for example, the temperate latency/integration module is genuinely absent in obligately lytic phages like T7, T4, φX174, and MS2) and mutually exclusive variant branches (four distinct release mechanisms, three tail-ejection mechanisms, four packaging mechanisms), making them ideal for calibrating evaluate() and abduce() in src/ai_gene_review/module_logic.py.

The repository already holds 61 phage and archaeal-virus gene folders across 9 taxon codes (49 in T4 BPT4—46 COMPLETE and 3 DRAFT (DAM, E, frd) curated with Falcon deep research from SPKW/SPKW-BPT4.md—plus 12 reviewed genes across 9CAUD, BPZF4, BPBPP, BPPHT, BPD31, ENTM13, ENTPH, and SIRV1) alongside two viral modules (MODULE:viral_factory and MODULE:anti_crispr_suppression). A focused 5-genome core reference set (λ, φX174, MS2, T7, and M13/φ6/PRD1, totaling ~160 genes—roughly the cost of half of T4) covers every branch of every core phage module.

Why Phages for Module Satisfiability & Pathway Hole Filling?

Our module engine in src/ai_gene_review/module_logic.py treats variant_sets as OR and required parts as AND, using gene-product annotation presence as the oracle and abduce(expr, env) to propose minimal sets of missing steps ("pathway holes"). Phages test this architecture in five ways that cellular genomes cannot:

  1. Mutually exclusive variant_sets grounded in virion & envelope biology:
  2. Release / Lysis module: Four distinct routes—canonical 3-step holin + endolysin + spanin (λ, T7, T4), 2-step holin + endolysin without spanin (Gram-positive phages like φ29, SPO1; or mycolate-cleaving Lysin A + Lysin B in Mycobacteriophage L5), single-gene lysis (Sgl) inhibiting peptidoglycan biosynthesis (GO:0039640 in φX174 E and Qβ A2, or membrane-lesion L in MS2), and non-lytic chronic filamentous extrusion (GO:0099045 in M13). Each reference genome should satisfy exactly one branch; a module definition that lets M13 satisfy the holin route is wrong.
  3. Genome ejection module: Three mutually exclusive mechanism children exist in GO (GO:0099000 contractile tail, GO:0099001 long flexible tail, GO:0099002 short tail), plus pilus-retraction (M13, MS2), DNA pilot tube (φX174), and membrane-fusion/spike (φ6, PRD1) routes.
  4. Genome packaging module: GO:0098006 headful packaging (T4, P22, P1) vs. GO:0098037 5'-extended cos packaging (λ, P2) vs. terminal-protein (gp3)/pRNA-primed packaging (φ29) vs. vertex ATPase packaging without a canonical terminase (PRD1, φ6).
  5. True negatives for calibrating abduction false-discovery rates:
  6. In cellular central metabolism (e.g. E. coli or P. putida glycolysis), an unsatisfied module step is nearly always a curation or homology gap. In phages, the temperate latency module (GO:0098689 latency-replication decision, GO:0075713 proviral integration, GO:0032359 provirus excision) is biologically absent in obligately lytic genomes (T4, T7, φX174, MS2, φ29). Running abduce() across lytic vs. temperate phages measures the false-gap rate of abductive hole-filling leads.
  7. Multi-functional single genes mapping to multiple modules:
  8. Micro-phages compress multiple module roles into single polypeptides—for example, Qβ maturation protein A2 both mediates pilus attachment/RNA protection (GO:0039666) and executes single-gene lysis (GO:0039640) by inhibiting host MurA (UDP-GlcNAc enolpyruvyl transferase), while MS2 coat protein cp is both the icosahedral capsid subunit (GO:0019030) and the translational operator repressor of the replicase gene.
  9. Cross-genome helper/satellite satisfiability (P2 + P4):
  10. Satellite phage P4 (BPP4, 13 genes) encodes its own replication and size-determination scaffold (Sid, which redirects helper P2 capsid protein gpN from $T=7$ to smaller $T=4$ heads) plus polarity suppressor (Psu), but lacks head, tail, and lysis structural genes. P4's morphogenetic and release modules are unsatisfiable in BPP4 alone and become satisfiable only over the composite proteome BPP4 ∪ BPP2.
  11. Synteny-constrained resolution of "viral dark matter":
  12. Sequence similarity decays rapidly across phages, leaving 30–70% of ORFs unannotated even in model clades. Because phage genes are tightly ordered into co-directional operons (e.g., terminase small → terminase large → portal → prohead protease → scaffold → major capsid, or holin → endolysin → i-spanin / +1 overlapping o-spanin), an unsatisfied leaf predicate from abduce() points directly to a specific genomic slot.

Candidate Phage Genomes (with Verified UniProt Taxon & Proteome Counts)

To avoid strain/host taxon fragmentation in UniProt (several phages such as λ, Mu, P1, P2, and T5 have multiple taxon IDs across isolates), gene folders should pin the canonical UniProt Taxon IDs and mnemonics listed below. Counts reflect current UniProt proteomes (Reviewed = Swiss-Prot curated entries; Total = Swiss-Prot + TrEMBL entries, which may include a few variant or fragment records).

Tier 1: Small Genomes — Tractable 100% End-to-End Curation (4–28 Genes)

Phage UniProt Taxon Mnemonic Reviewed / Total Lifestyle & Virion Role in End-to-End Curation & Module Testing
φX174 (Sinsheimervirus phiX174) 1217068 (also 10847) BPPHS (BPPHX) 10 / 10 Lytic ssDNA circular microvirus ($T=1$, tailless, 5.39 kb, 11 genes) 100% Swiss-Prot reviewed minimal DNA genome: Overlapping ORFs (A, A*, B, C, D, E, F, G, H, J, K). Defines rolling-circle ssDNA replication (gpA, GO:0039683), internal/external scaffolding (gpB, gpD), DNA pilot tube (gpH), and single-gene lysis via MraY inhibition (gpE, GO:0039640).
MS2 (Emesvirus zinderi) 12022 BPMS2 4 / 33 Lytic (+)ssRNA levivirus ($T=3$, tailless, 3.57 kb, 4 genes) Complete viral lifecycle in 4 proteins: Maturation/adhesin (mat, F-pilus attachment GO:0039666), coat/translational repressor (cp), single-gene lysis (lys/L — membrane lesion without PG-biosynthesis inhibition), and RdRp $\beta$-subunit (rep, GO:0003968, which hijacks host EF-Tu, EF-Ts, and ribosomal S1).
Qβ (Qbetavirus qbeta) 39803 BPQBE 4 / 92 Lytic (+)ssRNA levivirus ($T=3$, 4.22 kb, 4 genes) Dual-module single protein (A2) + readthrough coat (A1): A2 serves as both the F-pilus maturation/attachment protein (GO:0039666) and the single-gene lysis effector (GO:0039640) by inhibiting host MurA.
M13 (Inovirus M13) 1977402 BPM13 (ENTM13 / ENTPH) 9 / 19 Chronic ssDNA filamentous phage (6.41 kb, ~10–11 genes) Non-lytic chronic extrusion (GO:0099045): Already has gpI (P03656) reviewed in genes/ENTM13/ and genes/ENTPH/. Curating the remaining 9 genes (gpII–gpX, including F-pilus tip adhesin gpIII and outer-membrane secretin gpIV) covers the sole non-lytic extrusion branch.
φ6 (Cystovirus phi6) 2928686 (also 10879) BPPH6 13 / 13 Lytic enveloped segmented dsRNA phage (P. syringae, 13.4 kb, 13 genes) 100% reviewed enveloped dsRNA phage: Exercises GO:0019031 (viral envelope), type IV pilus attachment (P3/P6), membrane fusion (P6), virion peptidoglycan endopeptidase (P5), hexameric packaging NTPase (P4), and intra-capsid RdRp (P2, GO:0039694).
PRD1 (Alphatectivirus PRD1) 10658 BPPRD 25 / 30 Lytic dsDNA tectivirus with internal lipid membrane (14.9 kb, ~25–30 genes) Internal viral membrane (GO:0039641) & terminase-independent ATPase packaging: Structurally related to adenoviruses; uses a lipid vesicle inside the icosahedral capsid that transforms into a tail-like tube for DNA ejection, plus protein-primed replication (gp8 TP + gp1 Pol) and vertex packaging ATPase (gp9).
φ29 (Salasvirus phi29) 2884424 (also 10756) BPPH2 25 / 28 Lytic Gram-positive podovirus (B. subtilis, 19.3 kb, ~25 genes) Gram-positive comparator + protein-primed replication: Pairs with BACSU.md. Defines protein-primed replication (gp2 Pol + gp3 TP), pRNA-assisted packaging motor (gp16), and 2-step Gram-positive lysis (holin gp14 + lysozyme gp15, no spanin).

Tier 2: Canonical Tailed Phages (Caudoviricetes) — Core Module Satisfiability Benchmarks

Phage UniProt Taxon Mnemonic Reviewed / Total Lifestyle & Virion Role in End-to-End Curation & Module Testing
λ (Lambda) (Lambdavirus lambda) 2681611 (also 10710) LAMBD 62 / 67 Temperate siphovirus (E. coli, 48.5 kb, ~70 genes) Primary recommended starting genome: >90% Swiss-Prot reviewed and literature-dense. Populates every core module simultaneously: cos 5'-extended packaging (Nu1/A, GO:0098037), head-tail joining (GO:0098005), long flexible tail ejection (gpJ/gpH, GO:0099001), canonical holin/endolysin/spanin lysis (S/R/Rz/Rz1), proviral integration/excision (Int/Xis, GO:0075713/GO:0032359), transcription antitermination (N/Q, GO:0031564), and the CI–Cro–CII–CIII latency-replication switch (GO:0098689).
T7 (Teseptimavirus T7) 10760 BPT7 57 / 157 Obligately lytic podovirus (E. coli, 39.9 kb, ~57 genes) Lytic tailed contrast to λ: Short-tail ejection (GO:0099002) with internal core proteins (gp14/gp15/gp16), anti-R-M DNA mimic Ocr (gp0.3, GO:0099018), host RNAP shutoff (gp0.7, gp2, GO:0039653), autonomous single-subunit RNAP (gp1), minimal 4-protein replisome (gp5 Pol + host trxA, gp4, gp2.5), and amidase endolysin (gp3.5, GO:0008745).
P22 (Lederbergvirus P22) 10754 BPP22 65 / 142 Temperate podovirus (S. enterica, 41.7 kb, ~65 genes) Temperate podovirus contrast to λ & T7: Combines λ-like lysogeny (c2, int, xis, plus antirepressor Ant and superinfection exclusion sieA/sieB) with podovirus morphology, LPS-cleaving tailspike (gp9, GO:0039638), non-proteolytic scaffold recycling (gp8), and headful pac packaging (gp3/gp2, GO:0098006).
Mu (Muvirus mu) 2681603 (also 10677) BPMU 56 / 74 Temperate transposable myovirus (36.7 kb, ~56 genes) Transposition-driven replication & integration: Replaces standard replication/integration with MuA/MuB transposase (GO:0004803), includes the Gin invertible G-segment tail-fiber switch (S/U vs. S'/U') and Mom DNA carbamoylmethyltransferase (GO:0099018).
P2 + Satellite P4 2905681 (P2) / 10680 (P4) BPP2 / BPP4 39 / 43 (P2) & 13 / 13 (P4) Temperate contractile myovirus + capsid-pirating satellite Compact myovirus + cross-genome helper dependency: P2 (43 genes) is the most compact autonomous myovirus for curating a complete contractile tail/baseplate; P4 (13/13 reviewed) tests multi-genome satisfiability where P4's assembly/lysis modules require P2 helper proteins.
Mycobacteriophage L5 (L5virus L5) 31757 BPML5 84 / 90 Temperate siphovirus (Mycobacterium, 52.3 kb, ~85 genes) Non-proteobacterial / mycolata envelope benchmark: >90% reviewed in Swiss-Prot; tests how the mycolic-acid outer membrane reshapes the entry and lysis modules (requiring both peptidoglycan-cleaving Lysin A and mycolylarabinogalactan-cleaving Lysin B esterase).
T4 (Tequatrovirus T4) 10665 BPT4 269 / 288 Obligately lytic myovirus (E. coli, 168.9 kb, ~288 genes) Curated in genes/BPT4/ (46 COMPLETE, 3 DRAFT): The richest model myovirus—contractile tail ejection (GO:0099000), 28-protein baseplate/tail assembly, dCMP $\to$ 5-hmC $\to$ ghmdC DNA hypermodification, ADP-ribosylation & sigma-factor takeover (Alt, ModA/B, AsiA, gp55), and lysis inhibition (rI, GO:0039639). All 46 Falcon-seeded genes are now COMPLETE (DAM, E, and frd remain DRAFT), providing full myovirus structural and counter-defense coverage without making all ~288 genes a prerequisite for the module library.

Tier 3: Large / Jumbo & Specialized Counter-Defense Phages (Targeted Module Cohorts)

Phage UniProt Taxon Mnemonic Existing Repo Footprint Strategic Module Value
Punavirus P1 10678 BPP1 / 9CAUD darB (Q9XJG2, DRAFT) Episomal plasmid latency (GO:0075720): ParA/ParB partition, Cre-loxP recombinase, pinholin (lydA) + SAR-endolysin (lyz), and capsid-injected DarA/DarB antirestriction.
Bacillus phage phi3T / SPβ 10736 BPPHT AimP (P0DOE2, DRAFT) Arbitrium quorum-sensing latency switch (GO:0098689): AimP hexapeptide + AimR receptor TF + aimX non-coding RNA regulator.
Bordetella phage BPP-1 2885909 BPBPP brt (Q775D8, DRAFT) Diversity-Generating Retroelement (DGR): Mutagenic reverse transcription (brt + avd + TR) hypermutating the mtd tail-fiber receptor-binding protein.
Anti-CRISPR phages (JBD5, D3112, ZF40, LP-101, SIRV1) 1223261, 2907964, 1127516, 1458856, 157898 9CAUD, BPD31, BPZF4, SIRV1 acrIF3, orf30, AcrF8, ACA2, acrIIA2, orf114 (all COMPLETE) Counter-defense islands (MODULE:anti_crispr_suppression): Benchmarks for GO:0098672 and Aca autoregulatory operons.
Pseudomonas jumbo phages 201φ2-1 & ΦKZ 536053, 169683 BPFKZ MODULE:viral_factory (chmA shell) Phage nucleus compartmentalization: Chimallin (chmA) protein shell, PhuZ tubulin spindle, and virion/non-virion multisubunit RNAPs.

Existing Phage & Viral Footprint in the Repository

Taxon Code Organism NCBITaxon Reviewed (COMPLETE / DRAFT) Seeded (INITIALIZED w/ Deep Research) Key Genes & Biology Covered
BPT4 Tequatrovirus T4 NCBITaxon:10665 49 (46 COMPLETE, 3 DRAFT) 0 Prior DRAFT reviews: DAM (P04392, DNA adenine MTase / R-M evasion GO:0099018), E (P00720, endolysin muramidase GO:0003796 / cytolytic release GO:0044659), frd (P04382, DHFR GO:0004146). Completed (COMPLETE) with Falcon deep research: 28 structural/tail/baseplate/capsid genes (gp5, gp6–gp12, gp18–gp20, gp23, gp25–gp29, gp35–gp38, gp48, gp51, gp53, gp54, gp57, soc, wac), 10 counter-defense/host-takeover genes (gp2, adfA, agt, arn, bgt, stp, ndd, gp46, gp47, denA), and 8 replication/lysis/caution genes (ac, gp41, dda, uvsW, rI, t, y13J, y13K). See SPKW/SPKW-BPT4.md.
9CAUD Caudoviricetes (JBD5, LP-101, P1, phiNIT1, phiR8-01) Various 5 (3 COMPLETE, 2 DRAFT) 0 acrIF3 (L7P7R7), acrIIA2 (A0A059T5F6), darB (Q9XJG2), dfrP (D0VXF2), g022 (I7J3R9).
BPZF4 Pectobacterium phage ZF40 NCBITaxon:1127516 2 (COMPLETE) 0 AcrF8 (H9C181) and ACA2 (H9C180).
BPD31 Pseudomonas phage D3112 NCBITaxon:2907964 1 (COMPLETE) 0 orf30 (Q6TM72, AcrIF2 DNA-mimic anti-CRISPR).
BPBPP Bordetella phage BPP-1 NCBITaxon:2885909 1 (DRAFT) 0 brt (Q775D8, DGR reverse transcriptase).
BPPHT Bacillus phage phi3T NCBITaxon:10736 1 (DRAFT) 0 AimP (P0DOE2, arbitrium quorum-sensing peptide).
ENTM13 / ENTPH Inovirus M13 NCBITaxon:1977402 2 (COMPLETE) 0 I (P03656, G1P/G11P assembly/extrusion ATPase).
SIRV1 Sulfolobus islandicus rod-shaped virus 1 NCBITaxon:157898 1 (COMPLETE) 0 orf114 (Q8QL27, AcrIII-1 $\text{cA}_4$ ring nuclease).

Module-Route Matrix Across the Core Reference Genomes

Each reference phage takes a specific, testable path through the modular lifecycle. Satisfiability evaluation (evaluate()) should verify that each genome satisfies its active variant branch while rejecting alternative branches (and leaving the temperate module unsatisfied in obligately lytic phages):

Lifecycle Module λ (LAMBD) T7 (BPT7) T4 (BPT4) φX174 (BPPHS) MS2 / Qβ (BPMS2 / BPQBE) M13 (BPM13) φ29 (BPPH2) P2 + P4 (BPP2 + BPP4)
1. Attachment (GO:0019062) gpJ $\to$ LamB (GO:0098670) gp17 $\to$ LPS (GO:0039638) gp37 (GO:0098671) $\to$ gp12 (GO:0098670) gpF/gpG $\to$ LPS mat / A2 $\to$ F-pilus (GO:0039666) gpIII $\to$ F-pilus (GO:0039666) + TolA gp12 $\to$ wall teichoic acid P2 tail fibers gpH/gpG
2. Genome Ejection (GO:0039678) Long flexible tail (GO:0099001, gpH) Short tail + internal core (GO:0099002, gp14/15/16) Contractile tail + spike lysozyme (GO:0099000, gp18/19/5) DNA pilot tube (gpH) Pilus retraction RNA entry (mat/A2) Pilus retraction + TolQRA import Short tail + peptidoglycan hydrolase (gp13) Contractile tail (GO:0099000, P2 FI/FII)
3. Temperate Latency (GO:0019042) SATISFIED: CI/Cro/CII/CIII (GO:0098689) + Int/Xis (GO:0075713, GO:0032359) Unsatisfied (True Negative — obligately lytic) Unsatisfied (True Negative — obligately lytic) Unsatisfied (True Negative — obligately lytic) Unsatisfied (True Negative — obligately lytic) Unsatisfied (Chronic persistent episome) Unsatisfied (True Negative — obligately lytic) SATISFIED: C/Cox + Int
4. Transcription (GO:0019083) Host RNAP + N/Q antitermination (GO:0031564) Host RNAP early $\to$ phage RNAP (gp1) + host shutoff (gp2, GO:0039653) Host RNAP remodeled via Alt/ModA/B, MotA/AsiA, gp55/gp33 Host RNAP None (ssRNA genome is directly translated) Host RNAP Host RNAP + viral TF gp4 Host RNAP + P2 Ogr / P4 PSU antiterminator
5. Genome Replication (GO:0039693 / GO:0039694) O/P recruit host DnaB/Pol III ($\theta \to \sigma$ GO:0039686 $\to$ GO:0039683) + Red (exo/bet) Autonomous replisome (gp5 Pol + host trxA, gp4, gp2.5) Autonomous replisome + RDR (gp43, gp44/62, gp45, gp41/61, gp32, uvsX/Y) + ghmdC pathway Rolling-circle (gpA nickase + host Pol III/Rep, GO:0039683) Viral RdRp (rep + host EF-Tu/EF-Ts/S1, GO:0039694) Rolling-circle (gpII nickase + gpV SSB + host Pol III, GO:0039683) Protein-primed (gp2 Pol + gp3 TP + gp5/gp6) Rolling-circle (gpA in P2; α primase-helicase in P4)
6. Capsid & Packaging (GO:0019069, GO:0019073) cos 5' packaging (Nu1/A, GO:0098037), gpB portal, gpC protease, gpE coat, gpD decoration Headful/concatemer packaging (gp18/gp19), gp8 portal, gp9 scaffold, gp10 coat Headful packaging (gp16/gp17, GO:0098006), gp20 portal, gp21 protease, gp22 scaffold, gp23 coat, Hoc/Soc gpB/gpD scaffolds, gpF coat, gpG spike, gpJ DNA-condensing protein Co-replicative RNA encapsidation by cp coat dimers (GO:0019030) Coupled membrane assembly/coat replacement (gpV $\to$ gpVIII/gpIII/gpVI/gpVII/gpIX) gp7 scaffold, gp8 coat, gp10 portal + gp16 ATPase/pRNA motor P4 pirates P2 gpN/gpO/gpQ via P4 Sid external scaffold ($T=7 \to T=4$)
7. Virion Release (GO:0019076) 3-step cytolysis (GO:0044659): Holin S (GO:0044660) + endolysin R + spanin Rz/Rz1 3-step cytolysis (GO:0044659): Holin gp17.5 + amidase gp3.5 (GO:0008745) + spanin gp18.5/gp18.7 3-step cytolysis + LIN: Holin t + lysozyme E (GO:0003796) + spanin pseT.3/pseT.2 + LIN rI (GO:0039639) Single-gene lysis (GO:0039640): E inhibits host MraY Single-gene lysis: Qβ A2 inhibits MurA (GO:0039640); MS2 L membrane pore Non-lytic extrusion (GO:0099045): gpI/gpXI IM ATPase + gpIV OM secretin 2-step Gram+ cytolysis: Holin gp14 + lysozyme gp15 (no spanin) P2 holin Y + endolysin K + LysA/LysB/LysC

Reference Phage GO Term Catalog (Verified Against Current OLS)

Every GO ID and label below has been verified against the current Gene Ontology in OLS (none obsolete). Curators and automated module definitions should draw from this vocabulary rather than generic roots (GO:0016032 viral process, GO:0019058 viral life cycle, GO:0044423 virion component) or eukaryote-centric immune terms (GO:0052170, GO:0042742).

1. Lifecycle — Biological Process (BP)

Adsorption and Entry

Stage GO Term Typical Phage Examples
Attachment (general) GO:0019062 virion attachment to host cell All phages (use when receptor class is unknown)
Reversible binding GO:0098671 adhesion receptor-mediated virion attachment to host cell T4 long tail fibers (gp37) binding LPS or OmpC
Irreversible binding GO:0098670 entry receptor-mediated virion attachment to host cell λ gpJ binding LamB; T5 binding FhuA; T4 short tail fibers (gp12)
To lipopolysaccharide GO:0039638 lipopolysaccharide-mediated virion attachment to host cell P22 tailspike (gp9), T7 tail fiber (gp17)
To pilus GO:0039666 virion attachment to host cell pilus M13 pIII on F-pilus; MS2 mat / Qβ A2 on F-pilus; φ6 P3 on type IV pilus
To flagellum GO:0098931 virion attachment to host cell flagellum Flagellotropic phage χ (chi)
Entry (general) GO:0046718 symbiont entry into host cell General parent (prefer specific ejection/disruption child when known)
Genome ejection (parent) GO:0039678 symbiont genome ejection through host cell envelope General ejection across bacterial envelope
— Contractile tail GO:0099000 symbiont genome ejection through host cell envelope, contractile tail mechanism T4 (gp18/gp19/gp5), P2, Mu (myoviruses)
— Long flexible tail GO:0099001 symbiont genome ejection through host cell envelope, long flexible tail mechanism λ (gpH/gpJ), T5, L5 (siphoviruses)
— Short tail GO:0099002 symbiont genome ejection through host cell envelope, short tail mechanism T7 (gp14/gp15/gp16), P22, φ29 (podoviruses)
Cell wall degradation during entry GO:0098932 symbiont entry into host cell via disruption of host cell wall peptidoglycan T4 baseplate central spike lysozyme (gp5); T7 internal core (gp16); φ6 P5
Inner membrane crossing GO:0099008 symbiont entry into host cell via permeabilization of inner membrane Ejectosome / pilot-protein inner-membrane channels

Host Takeover and Counter-Defence

Genome Replication

Assembly and Packaging

Virion Release and Lysis

Mode GO Term Typical Phage Examples
General GO:0019076 viral release from host cell Root release term
Lysis (dsDNA phages) GO:0044659 viral release from host cell by cytolysis λ (R/S/Rz/Rz1), T4 (E/t), T7 (gp3.5/gp17.5), φ29 (gp15)
Holin pore formation GO:0044660 viral release via pore formation in host cell membrane λ S, T4 t, T7 gp17.5, φ29 gp14
Single-gene lysis (PG synthesis inhibition) GO:0039640 viral release via suppression of host peptidoglycan biosynthetic process φX174 E (inhibits MraY), Qβ A2 (inhibits MurA). (Note: Not MS2 L, which lyses without inhibiting PG synthesis.)
Lysis inhibition (LIN) GO:0039639 suppression by virus of host cell lysis in response to superinfection T4 rI, rIII
Non-lytic extrusion GO:0099045 viral extrusion M13 (gpI/gpIV) and other filamentous inoviruses

Temperate Decisions (Lysogeny / Viral Latency)

2. Cellular Components (CC)

Structure GO Terms
Root GO:0044423 virion component (avoid as final core term when a specific substructure term below applies)
Head / Capsid GO:0019028 viral capsid; GO:0019030 icosahedral viral capsid; GO:0039621 T=13 icosahedral viral capsid (T4 gp23)
Decoration proteins GO:0098021 viral capsid, decoration (λ gpD, T4 Hoc/Soc)
Precursor head GO:0046729 viral procapsid; GO:0046806 viral scaffold (T4 gp22, P22 gp8, φ29 gp7)
Portal GO:0046798 viral portal complex (T4 gp20, λ gpB, T7 gp8, φ29 gp10)
Packaging motor GO:0043493 viral terminase complex; GO:0098009 viral terminase, large subunit; GO:0097710 viral terminase, small subunit
Tail & Substructures GO:0098015 virus tail · GO:0098026 virus tail, tube · GO:0098027 virus tail, sheath · GO:0098025 virus tail, baseplate · GO:0098024 virus tail, fiber · GO:0098023 virus tail, tip (λ gpJ)
Viral Membranes GO:0019031 viral envelope (φ6); GO:0039641 viral inner membrane (PRD1); GO:0055036 virion membrane
Host Subcellular Locations GO:0020002 host cell plasma membrane (holins, M13 gpI assembly complex); GO:0044229 host cell periplasmic space (spanins, active endolysins); GO:0039662 host cell outer membrane (Rz1 o-spanin, M13 gpIV secretin); GO:0030430 host cell cytoplasm

3. High-Frequency Molecular Functions (MF)

4. Known Ontology Gaps (proposed_new_terms Targets)

Synteny & Domain Rules for Resolving Phage Pathway Holes

When abduce() flags an unsatisfied step in a phage module (and the step is not excluded by a lytic/morphotype variant or fulfilled by a host protein), curators can locate the missing gene in the phage genome using conserved operon synteny and biophysical/structural signatures:

Missing Module Step (Abduction Lead) Expected Syntenic Slot Structural / Biophysical Resolution Signature
Outer-membrane o-spanin (Rz1) Embedded in the +1 reading frame of i-spanin (Rz), overlapping its 3' end, or immediately adjacent downstream of endolysin Small (40–70 aa) proline-rich polypeptide with an N-terminal Signal Peptidase II lipobox ([LVI][ASTVI][GAS]C); routinely missed by ORF callers and absent from many UniProt proteomes.
Inner-membrane i-spanin (Rz) or u-spanin (gp11) Immediately downstream of endolysin (R) i-spanin: N-terminal transmembrane helix (TMD) + periplasmic $\alpha$-helical coiled-coil. u-spanin: N-terminal OM lipobox + periplasmic domain + C-terminal IM TMD.
Holin / Pinholin (S, t, gp17.5) Immediately upstream of (or adjacent to) endolysin Small (60–150 aa) protein with 1–4 TMDs and a hydrophilic, positively charged C-terminal cytoplasmic tail (>50 sequence-unrelated families).
Small terminase subunit (terS, Nu1, gp16) Immediately upstream of terL (large terminase GO:0098009) 15–25 kDa oligomer (8–12-mer ring) with an N-terminal HTH/winged-HTH DNA-binding domain and central coiled-coil oligomerization bundle.
Prohead scaffold (gp22, gp8, gp7) Between portal/prohead_protease and major_capsid (or fused as an N-terminal $\Delta$-domain on the major capsid protein, as in HK97) Charged, $\alpha$-helical coiled-coil / intrinsically disordered protein (20–35 kDa).
Head-tail neck adaptors (gpW/gpFII, gp13/gp14) Immediately downstream of major_capsid Small (10–20 kDa) dodecameric/hexameric rings identifiable via AlphaFold/Foldseek (STRUCTURAL_REASONING.md) even below 15% sequence identity.
Tail assembly frameshift chaperone (gpG/gpGT) Between major_tail_protein (gpV) and tape_measure_protein (gpH) in siphoviruses and myoviruses Overlapping $-1$ programmed ribosomal frameshift cassette producing a shorter (gpG) and longer (gpGT) isoform at ~30:1 stoichiometry.
Prophage excisionase (xis) Immediately adjacent to prophage integrase (int) Tiny (50–90 aa) basic winged-HTH DNA architectural protein required for GO:0032359 provirus excision.
dCTPase/dUTPase sanitation enzyme (T4 gp56) Co-inherited in phages encoding a pyrimidine hydroxymethylase (T4 gp42 dCMP HMase or SPO1 dUMP HMase) or PurZ Pyrophosphohydrolase that purges canonical dCTP/dTTP/dATP so the viral polymerase incorporates only the modified nucleotide.

Concrete Execution Plan (5-Genome Core Reference Set $\approx$ 160 Genes)

Rather than attempting all ~288 genes of T4 upfront, we can cover every branch of every phage lifecycle module in roughly 160 genes across 5 core reference genomes (plus targeted completion of the already-seeded T4 and specialty phage genes):

Step 1: Start with Phage λ (LAMBD, Taxon 2681611 — 62/67 Reviewed)

Step 2: Add Micro-Genomes φX174 (BPPHS, 10/10), MS2 (BPMS2, 4/33), and Qβ (BPQBE, 4/92)

Step 3: Curate Phage T7 (BPT7, Taxon 10760 — 57/157 Reviewed)

Step 4: Completed the 46 Falcon-Seeded T4 Genes (BPT4, Taxon 10665 — 46/49 Curated; 269/288 Swiss-Prot Reviewed in Proteome)

Step 5: Expand to Morphotype & Envelope Outliers (BPM13, BPPH6, BPPRD, BPPH2, BPP2/BPP4, BPML5)