| Annotation aspect | Summary for T4 y13K / P39504 | Key citations (year; URL) |
|---|---|---|
| Identifiers | **UniProt:** P39504. **Gene:** **y13K**; synonym **pseT.3**. **Organism:** *Enterobacteria phage T4*. Literature identifies **pseT.3** as the **Rz-equivalent / i-spanin** in the T4 spanin pair, resolving the gene-symbol ambiguity in favor of the T4 lysis protein rather than unrelated genes in other organisms. (pqac-00000007, pqac-00000010) | Summer et al., 2007, https://doi.org/10.1016/j.jmb.2007.08.045; Catalão et al., 2013, https://doi.org/10.1111/1574-6976.12006 |
| Functional role | **Primary function:** inner-membrane spanin (**i-spanin**) subunit of the T4 two-component spanin complex, required for the **final outer-membrane disruption step** of phage lysis after holin/endolysin action. T4 pseT.2/pseT.3 were described as promoting “the last step in cell lysis.” (pqac-00000007, pqac-00000013, pqac-00000016) | Summer et al., 2007, https://doi.org/10.1016/j.jmb.2007.08.045; Burch et al., 2011, https://doi.org/10.1128/JB.00138-11; Cahill & Young, 2019, https://doi.org/10.1016/bs.aivir.2018.09.003 |
| Partner gene / complex organization | y13K/**pseT.3** is paired with **pseT.2**, the **Rz1-equivalent / o-spanin**. T4 is a classic **two-component spanin** system with **separated** gene architecture (distinct coding regions; described as adjacent/head-to-tail, with overlapping stop/start codons in some annotations but not embedded as in λ). (pqac-00000007, pqac-00000008, pqac-00000011) | Summer et al., 2007, https://doi.org/10.1016/j.jmb.2007.08.045; Young, 2014, https://doi.org/10.1007/s12275-014-4087-z |
| Localization / topology | **PseT.3 (y13K)** carries the hallmark **N-terminal transmembrane domain**, consistent with an **inner-membrane anchor** and periplasm-spanning/ periplasm-facing domain; **PseT.2** carries an **outer-membrane lipoprotein signal**, consistent with an **o-spanin** tethered to the OM. Together they form an IM–periplasm–OM bridge. (pqac-00000008, pqac-00000009, pqac-00000010) | Summer et al., 2007, https://doi.org/10.1016/j.jmb.2007.08.045; Catalão et al., 2013, https://doi.org/10.1111/1574-6976.12006 |
| Mechanistic interpretation | By analogy to experimentally dissected spanins and explicitly including T4 in the spanin class, pseT.3/pseT.2 are inferred to act by **inner-membrane–outer-membrane fusion** (or equivalent catastrophic membrane merger) that is **gated by peptidoglycan degradation**: intact PG restrains spanin activation; endolysin-mediated PG removal permits spanin oligomerization/conformational change and OM disruption. (pqac-00000015, pqac-00000017, pqac-00000020) | Rajaure et al., 2015, https://doi.org/10.1073/pnas.1420588112; Young, 2014, https://doi.org/10.1007/s12275-014-4087-z; Cahill & Young, 2019, https://doi.org/10.1016/bs.aivir.2018.09.003 |
| T4-specific experimental evidence | **Direct T4 genetics:** deletion of **Δ(pseT.3 pseT.2)** caused a **classical Mg²⁺-dependent lysis defect**, with infected cells becoming **spherical** rather than lysing normally; recombinant mutants formed **small plaques**. This is the defining T4 evidence that pseT.3/pseT.2 are bona fide spanin (Rz/Rz1-equivalent) genes. (pqac-00000008, pqac-00000012, pqac-00000014) | Summer et al., 2007, https://doi.org/10.1016/j.jmb.2007.08.045 |
| T4 deletion construct details | The T4 deletion analyzed in Summer et al. removed the **pseT.3/pseT.2 region** using a construct spanning **nt 134,678–136,253** with an internal deletion of **nt 135,165–135,726**; recombinant **T4 ΔrI Δ(pseT.3 pseT.2)** phages were confirmed by PCR/sequencing and tested under different Mg²⁺ conditions. (pqac-00000014) | Summer et al., 2007, https://doi.org/10.1016/j.jmb.2007.08.045 |
| Broader spanin definition | **Spanins** are the phage lysis proteins that solve the **third envelope barrier** in Gram-negative bacteria: after holin disrupts the IM and endolysin degrades PG, spanins remove the **OM barrier**. Two-component spanins comprise an **i-spanin** plus **o-spanin**; T4 provides the **separated** architecture exemplar, whereas λ is **embedded** and P2 is **overlapped**. (pqac-00000002, pqac-00000025) | Young, 2014, https://doi.org/10.1007/s12275-014-4087-z; Kongari et al., 2018, https://doi.org/10.1186/s12859-018-2342-8 |
| Diversity / comparative context | Spanins are widespread and diverse. In a 677-genome survey of Gram-negative-host dsDNA phages, **528 two-component spanins** and **58 unimolecular spanins** were identified; two-component architectures included **182 embedded, 228 overlapped, and 118 separated** systems. T4-like spanins are sequence-divergent from λ-like spanins but conserve topology/function; the **T4 family** was the largest listed separated/o-spanin family with **47 members**. (pqac-00000024, pqac-00000026, pqac-00000027) | Kongari et al., 2018, https://doi.org/10.1186/s12859-018-2342-8 |
| Annotation confidence for y13K | Confidence is **high** that UniProt **P39504 = y13K = pseT.3 = T4 i-spanin**: multiple reviews and the primary 2007 discovery paper independently map T4 **pseT.3** to the **i-spanin/Rz-equivalent** role, paired with **pseT.2** as **o-spanin**, and supported by T4 deletion phenotypes. (pqac-00000007, pqac-00000008, pqac-00000011) | Summer et al., 2007, https://doi.org/10.1016/j.jmb.2007.08.045; Young, 2014, https://doi.org/10.1007/s12275-014-4087-z |


*Table: This table summarizes the verified identity, function, topology, mechanism, and T4-specific evidence for bacteriophage T4 gene y13K (UniProt P39504), also known as pseT.3. It is useful as a compact annotation record linking the gene to the two-component spanin system and the experimental lysis phenotype that supports this assignment.*