GENOMICS (387)

A phage defense system in which an organism possesses a 6A-MBL locus that can protect bacteria from bacteriophage infection.

A phage defense system in which an organism possesses an ARMADA YprA-like-helicase locus whose Type I and Type II operons share BrxHII-like and PglX-like components with DISARM Class I systems and whose experimentally tested Type II forms protect against a broad range of phages.

A phage defense system in which an organism possesses a locus encoding a STAND-superfamily antiviral ATPase/NTPase that functions as a modular Avs receptor-effector, recognizes conserved bacteriophage proteins, and activates subtype-specific antiphage outputs to inhibit bacteriophage replication.

An abortive infection system in which an organism possesses a single-component Abi-like locus represented by the DefenseFinder Abi2 model namespace and mandatory Abi2__Abi_2/PF07751 profile.

An abortive infection system in which an organism possesses an AbiA-family locus whose copy number or expression modulates Lactococcus lactis resistance to multiple phages and that DefenseFinder represents with AbiA_large or AbiA_small model subrules.

An abortive infection system in which an organism possesses an abi-alpha-family locus represented by the DefenseFinder AbiAlpha__AbiAlpha profile and exemplified by the Enterococcus faecalis V583 prophage 6 abi-alpha determinant, whose encoded DUF4393/PF14337-family activity perturbs the Idefix lytic cycle and causes premature lysis of infected Enterococcus faecalis.

An abortive infection system in which an organism possesses an abiB-family locus represented by the DefenseFinder AbiB__AbiB profile and exemplified by the Lactococcus lactis IL1403 determinant whose AbiB activity blocks sensitive bIL170 phage growth and promotes rapid degradation of sensitive phage transcripts after infection.

An abortive infection system in which an organism possesses an abiC-family locus represented by the DefenseFinder AbiC__AbiC profile and exemplified by the Lactococcus lactis subsp. lactis ME2 pTN20 determinant whose abiC structural gene confers Prf abortive resistance to small isometric-headed phage p2, reducing plaquing, plaque size, and burst size while killing most infected Prf-positive cells.

An abortive infection system in which an organism possesses an abiD-family locus represented by the DefenseFinder AbiD__AbiD profile and exemplified by the Lactococcus lactis subsp. lactis KR5 pBF61 determinant whose abiD open reading frame confers an abortive phage infection phenotype with reduced plating efficiency, plaque size, and c2 phage burst size.

An abortive infection system in which an organism possesses an abiE bicistronic locus whose AbiEii DUF1814-family bacteriostatic toxin and AbiEi COG5340-family antitoxin constitute a non-interacting type IV toxin-antitoxin module that supports phage resistance.

An abortive infection system in which an organism possesses a pNP40-derived abiF locus whose single complete open reading frame encodes a phage-insensitivity determinant that inhibits bacteriophage phi 712 DNA replication.

An abortive infection system in which an organism possesses a two-gene abiG locus with abiGi and abiGii open reading frames, exemplified by the Lactococcus lactis subsp. cremoris UC653 plasmid pCI750 locus that restricts lactococcal phages without blocking phage DNA replication and is represented by the DefenseFinder AbiG__AbiGi and AbiG__AbiGii profiles.

An abortive infection system in which an organism possesses an abiH-family locus represented by the DefenseFinder AbiH__AbiH profile and exemplified by the Lactococcus lactis S94 abiH gene that encodes lactococcal phage abortive-infection resistance.

An abortive infection system in which an organism possesses an abiI-family locus represented by the DefenseFinder AbiI__AbiI profile and exemplified by the Lactococcus lactis M138 pND852 locus whose single abiI open reading frame restricts lactococcal phage propagation by an abortive-infection mechanism.

An abortive infection system in which an organism possesses an AbiJ-family locus represented by the DefenseFinder AbiJ model namespace and mandatory AbiJ__AbiJ profile.

An abortive infection system in which an organism possesses an abiK locus encoding a reverse-transcriptase-related polymerase that uses conserved RT motifs for phage resistance and restricts 936/P335 lactococcal phage propagation.

An abortive infection system in which an organism possesses a two-component AbiL-family locus represented by DefenseFinder as mandatory AbiL__AbiLi and AbiL__AbiLii profiles.

An abortive infection system in which an organism possesses a single-component AbiN-family locus represented by DefenseFinder as a mandatory AbiN__AbiN profile.

An abortive infection system in which an organism possesses a single-component AbiO-family locus represented by DefenseFinder as a mandatory AbiO__AbiO profile.

An abortive infection system in which an organism possesses a single-component AbiP2-family reverse-transcriptase-like locus represented by DefenseFinder as a mandatory AbiP2__AbiP2 profile.

An abortive infection system in which an organism possesses an AbiQ type III toxin-antitoxin locus whose protein endoribonuclease and cognate RNA antitoxin module alter early phage mRNA profiles and restrict phage propagation after adsorption.

An abortive infection system in which an organism possesses a multicomponent AbiR determinant represented by the DefenseFinder AbiR__AbiRa, AbiR__AbiRb, and AbiR__AbiRc profiles and capable of restricting lactococcal phage propagation by an early abortive-infection mechanism that impedes phage DNA replication, as exemplified by the two pKR223 loci from Lactococcus lactis subsp. lactis KR2 separated by the LlaKR2I restriction-modification genes.

An abortive infection system in which an organism possesses the two-gene pED1 abiT locus whose constitutively cotranscribed abiTi and abiTii genes encode an AbiTi-AbiTii phage-resistance module that acts late in the 936/P335 lactococcal phage lytic cycle.

An abortive infection system in which an organism possesses an abiU-family locus represented by the DefenseFinder AbiU__AbiU profile and exemplified by the Lactococcus lactis LL51-1 AbiU determinant, whose abiU1 open reading frame is responsible for phage resistance, whose abiU2 region may downregulate 936/P335 resistance, and whose activity reduces c2, 936, and P335 lactococcal phage plaquing while delaying transcription of phages 712 and c2.

An abortive infection system in which an organism possesses an abiV locus whose encoded AbiV protein can restrict 936-like or c2-like lactococcal phages by interacting with phage-encoded SaV and inhibiting phage protein translation.

An abortive infection system in which an organism possesses an abiZ locus encoding a membrane-associated lactococcal phage-resistance determinant that accelerates infected-cell lysis through AbiZ-enhanced holin/lysin activity and restricts P335 phage propagation.

A phage defense system in which an organism possesses a two-component Aditi locus represented by DitA and DitB profiles that can protect bacteria from bacteriophage infection.

A phage defense system in which an organism possesses a five-gene Ambrosia locus encoding AbrR, AbrA, AbrB, AbrC, and AbrD components that can limit siphophage and myophage propagation.

A phage defense system in which an organism possesses a single-component ApeA locus represented by the DefenseFinder Gao_Ape__ApeA profile, encoding an oligomeric HEPN-domain antiviral ribonuclease whose activation can cleave RNA substrates to restrict bacteriophage infection.

A genomics trait describing possession of an ApsAB anti-plasmid defense locus encoding the nuclease/helicase ApsA and Argonaute-like ApsB proteins that can destabilize high- and low-copy-number plasmids.

A phage defense system in which an organism possesses an Aristaios locus that can restrict bacteriophage infection.

A phage defense system in which an organism possesses an Audmula locus that can restrict bacteriophage infection.

An AVAST system in which an organism possesses a genome-encoded subtype I locus represented by DefenseFinder with Avs1A, Avs1B, and Avs1C profiles.

An AVAST system in which an organism possesses a genome-encoded subtype II locus represented by DefenseFinder with an Avs2A profile.

An AVAST system in which an organism possesses a genome-encoded subtype III locus represented by DefenseFinder with Avs3A and Avs3B profiles.

An AVAST system in which an organism possesses a genome-encoded subtype IV locus represented by DefenseFinder with an Avs4A profile.

An AVAST system in which an organism possesses a genome-encoded subtype V locus represented by DefenseFinder with an Avs5A profile.

A phage defense system in which an organism possesses an Azaca locus represented by ZacA, ZacB, and ZacC profiles that can protect bacteria from bacteriophage infection.

A genomics trait describing possession of a bacteriophage exclusion defense system that uses host DNA methylation to discriminate self from non-self and inhibit phage DNA replication.

A phage defense system in which an organism possesses a Belenos locus represented by a VCA0457 profile that can protect bacteria from bacteriophage infection.

A phage defense system in which an organism possesses a Belisama locus represented by a VCA0458 profile that can protect bacteria from bacteriophage infection.

A phage defense system in which an organism possesses a Bil bacterial ubiquitin-like conjugation locus that can covalently attach a ubiquitin-like protein to the bacteriophage central tail fibre and impair phage infectivity.

A phage defense system in which an organism possesses a Borvo locus represented by BovA profiles that can protect bacteria from bacteriophage infection.

A phage defense system in which an organism possesses a gcu113/Brc113 bacteriophage-resistance integron cassette that supports growth during bacteriophage challenge.

A phage defense system in which an organism possesses a gcu142/Brc142 bacteriophage-resistance integron cassette that supports growth during bacteriophage challenge.

A phage defense system in which an organism possesses a gcu167/Brc167 bacteriophage-resistance integron cassette that supports growth during bacteriophage challenge.

A phage defense system in which an organism possesses a gcu217/Brc217 bacteriophage-resistance integron cassette that supports growth during bacteriophage challenge.

A phage defense system in which an organism possesses a gcu22/Brc22 bacteriophage-resistance integron cassette that supports growth during bacteriophage challenge.

A phage defense system in which an organism possesses a gcu23/Brc23 bacteriophage-resistance integron cassette that supports growth during bacteriophage challenge.

A phage defense system in which an organism possesses a gcu233/Brc233 bacteriophage-resistance integron cassette that supports growth during bacteriophage challenge.

A phage defense system in which an organism possesses a gcu24/Brc24 bacteriophage-resistance integron cassette that supports growth during bacteriophage challenge.

A phage defense system in which an organism possesses a Brc59 bacteriophage-resistance integron cassette that supports growth during bacteriophage challenge.

A phage defense system in which an organism possesses a gcu76/Brc76 bacteriophage-resistance integron cassette that supports growth during bacteriophage challenge.

A phage defense system in which an organism possesses a gcuWGS21/BrcWGS21 bacteriophage-resistance integron cassette that supports growth during bacteriophage challenge.

A phage defense system in which an organism possesses a brig1-family locus whose encoded DNA glycosylase can excise alpha-glucosyl-hydroxymethylcytosine nucleobases from T-even bacteriophage DNA, generate abasic sites, and inhibit viral DNA replication.

A phage defense system in which an organism possesses a Brigantia locus represented by a VCA0419 profile that can protect bacteria from bacteriophage infection.

An abortive infection system in which an organism possesses a BstA-family phage-defense locus whose encoded BstA protein can suppress lytic phage DNA replication and whose cognate anti-BstA aba element can self-immunize the encoding prophage from BstA activity.

A phage defense system in which an organism possesses a two-component Bunzi locus represented by BnzA and BnzB profiles that can protect bacteria from bacteriophage infection.

A phage defense system in which an organism possesses a Butters gp30-gp31 locus that can protect bacteria from bacteriophage infection.

A phage defense system in which an organism possesses a Butters gp57r locus that can protect bacteria from bacteriophage infection.

A CARD-NLR system in which an organism possesses a genome-encoded DefenseFinder CARD_NLR_GasderMIN subtype locus represented by the CARD_NLR_GasderMIN rule row requiring the GasderMIN__bGSDM profile.

A CARD-NLR system in which an organism possesses a genome-encoded DefenseFinder CARD_NLR_Endonuclease subtype locus represented by the CARD_NLR__Endonuclease mandatory rule profile.

A CARD-NLR system in which an organism possesses a genome-encoded DefenseFinder CARD_NLR_Phospho subtype locus represented by the CARD_NLR__Trypsin_Phospho mandatory rule profile.

A CARD-NLR system in which an organism possesses a genome-encoded DefenseFinder CARD_NLR_Subtilase subtype locus represented by the CARD_NLR_Subtilase rule row requiring the CARD_NLR__Subtilase_long_new profile.

A phage defense system in which an organism possesses a CARD-NLR locus represented by the DefenseFinder CARD_NLR model namespace, coupling bacterial CARD-like detector components and NLR-like profiles to subtype-specific GasderMIN, endonuclease, Trypsin_Phospho, or Subtilase effector profiles that can promote cell death after phage recognition.

A CARD-NLR system in which an organism possesses a genome-encoded DefenseFinder CARD_NLR_like subtype locus represented by the CARD_NLR_like rule row requiring two matches from the CARD_NLR__Endonuclease, CARD_NLR__Phospho_Trypsin, CARD_NLR__Subtilase_long_new, and CARD_NLR__Trypsin_Phospho effector-profile set and four genes overall after considering CARD_NLR__CARD_Protease, CARD_NLR__NLR_new, and CARD_NLR__Trypsin accessory profiles.

A genomics trait describing possession of a cyclic-oligonucleotide-based antiphage signaling locus in which an oligonucleotide cyclase produces cyclic oligonucleotide signals during phage infection that activate an effector to inhibit bacteriophage replication.

A genomics trait describing possession of a CRISPR-Cas adaptive immune system that records fragments of invading nucleic acids in CRISPR arrays and uses Cas proteins to recognize and cleave matching sequences.

A phage defense system in which an organism possesses a fused CapRel toxin-antitoxin locus encoding an N-terminal toxSAS toxin domain and a C-terminal antitoxin sensor domain that together can restrict bacteriophage propagation.

A phage defense system in which an organism possesses a Ceres locus that can protect bacteria from bacteriophage infection.

A phage defense system in which an organism possesses a Cernunnos locus represented by a VCA0410 profile that can protect bacteria from bacteriophage infection.

A phage defense system in which an organism possesses a Charlie gp32 locus that can protect bacteria from bacteriophage infection.

A phage defense system in which an organism possesses a Clover anti-phage system whose CloA deoxynucleoside triphosphohydrolase dynamically responds to an activating phage cue and to a CloB-produced inhibitory p3diT nucleotide signal to coordinate nucleotide-pool disruption during antiviral immunity.

An abortive infection system in which an organism possesses a cmdTAC toxin-antitoxin-chaperone locus whose CmdC chaperone senses viral capsid proteins and whose CmdA antitoxin degradation liberates the CmdT ADP-ribosyltransferase to modify messenger RNA, arrest translation, and inhibit bacteriophage replication.

A phage defense system in which an organism possesses a CoCoNuT locus from a coiled-coil nuclease tandem branch of McrBC Type IV restriction systems whose domain and genomic-context architecture predict RNA targeting and, in many CoCoNuTs, DNA targeting via McrC nuclease homologs.

A phage defense system in which an organism possesses a Crouga antiviral locus that is encoded by P4-like phage satellites and can protect bacteria from bacteriophage infection.

A phage defense system in which activated DARNA cleaves a subset of host tRNAs and thereby inhibits phage propagation after activation by single-stranded DNA presented by phage SSB.

A genomics trait describing possession of a Defense Island System Associated with Restriction-Modification locus that uses methyltransferase-associated self/non-self discrimination and DrmAB activation to inhibit bacteriophage DNA replication.

A DISARM system in which an organism possesses a genome-encoded DefenseFinder DISARM_1 subtype locus represented by DISARM_1__drmD, DISARM_1__drmMI, DISARM__drmA, DISARM__drmB, and DISARM__drmC rule profiles.

A DISARM system in which an organism possesses a genome-encoded DefenseFinder DISARM_2 subtype locus represented by DISARM_2__drmE, DISARM_2__drmMII, DISARM__drmA, DISARM__drmB, and DISARM__drmC rule profiles.

A phage defense system in which an organism possesses a defense-associated reverse transcriptase locus whose RT-domain component or components can confer bacteriophage defense and are modeled by DefenseFinder as DRT subtypes.

A DRT system in which an organism possesses a genome-encoded DefenseFinder DRT_1 subtype locus represented by the mandatory DRT_1__drt1a and DRT_1__drt1b profiles.

A DRT system in which an organism possesses a genome-encoded DefenseFinder DRT_2 subtype locus represented by the DRT_2__drt2 profile.

A DRT system in which an organism possesses a genome-encoded DefenseFinder DRT_3 subtype locus represented by the mandatory DRT_3__drt3a and DRT_3__drt3b profiles.

A DRT system in which an organism possesses a genome-encoded DefenseFinder DRT_4 subtype locus represented by the DRT_4__drt4 profile.

A DRT system in which an organism possesses a genome-encoded DefenseFinder DRT_5 subtype locus represented by the DRT_5__drt5 profile.

A DRT system in which an organism possesses a genome-encoded DefenseFinder DRT6 subtype locus represented by the DRT6__DRT6 profile.

A DRT system in which an organism possesses a genome-encoded DefenseFinder DRT7 subtype locus represented by the DRT7__DRT7 or DRT7__DRT7_small profiles.

A DRT system in which an organism possesses a genome-encoded DefenseFinder DRT8 subtype locus represented by a mandatory DRT8__DRT8 profile, optionally accompanied by the DRT8__DRT8b accessory profile.

A DRT system in which an organism possesses a genome-encoded DefenseFinder DRT9 subtype locus represented by a mandatory DRT9__DRT9 profile.

A phage defense system in which an organism possesses the two-gene DefensePredictor-discovered system 1 locus cataloged as working transcriptional unit D390 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 10 locus cataloged as working transcriptional unit ZAPB and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 11 locus cataloged as working transcriptional unit IMPD and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the two-gene DefensePredictor-discovered system 12 locus cataloged as working transcriptional unit PD3A and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses a genome-encoded DefensePredictor-discovered system 13 locus represented in the pinned DefenseFinder model inventory by DS-13A and DS-13B custom HMM profiles.

A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 14 locus cataloged as working transcriptional unit RMOR and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the three-gene DefensePredictor-discovered system 15 locus cataloged as working transcriptional unit AAA1 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the two-gene DefensePredictor-discovered system 16 locus cataloged as working transcriptional unit PLIK and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 17 locus cataloged as working transcriptional unit NUCS and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 18 locus cataloged as working transcriptional unit 6602 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 19 locus cataloged as working transcriptional unit PDP4 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the three-gene DefensePredictor-discovered system 2 locus cataloged as working transcriptional unit DISA and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 20 locus cataloged as working transcriptional unit PDX1 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the three-gene DefensePredictor-discovered system 21 locus cataloged as working transcriptional unit TOXO and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 22 locus cataloged as working transcriptional unit MVB1 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 23 locus cataloged as working transcriptional unit E2DP and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 24 locus cataloged as working transcriptional unit RED2 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses a genome-encoded DefensePredictor-discovered system 25 locus represented in the pinned DefenseFinder model inventory by DS-25A and DS-25B custom HMM profiles.

A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 26 locus cataloged as working transcriptional unit NERD and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 27 locus cataloged as working transcriptional unit SMEK and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the two-gene DefensePredictor-discovered system 28 locus cataloged as working transcriptional unit ANEX and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 29 locus cataloged as working transcriptional unit HEP3 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the one-gene DefensePredictor-discovered system 3 locus cataloged as working transcriptional unit PIN8 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the four-gene DefensePredictor-discovered system 30 locus cataloged as working transcriptional unit ABC3 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 31 locus cataloged as working transcriptional unit RED7 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the two-gene DefensePredictor-discovered system 32 locus cataloged as working transcriptional unit NADR and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the two-gene DefensePredictor-discovered system 33 locus cataloged as working transcriptional unit GNAT and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the two-gene DefensePredictor-discovered system 34 locus cataloged as working transcriptional unit CITO and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 35 locus cataloged as working transcriptional unit RED5 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses a genome-encoded DefensePredictor-discovered system 36 locus represented in the pinned DefenseFinder model inventory by the DS-36 custom HMM profile.

A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 37 locus cataloged as working transcriptional unit SC24 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 38 locus cataloged as working transcriptional unit HEP2 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 39 locus cataloged as working transcriptional unit AAA5 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the five-gene DefensePredictor-discovered system 4 locus cataloged as working transcriptional unit NTTI and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 40 locus cataloged as working transcriptional unit D295 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 41 locus cataloged as working transcriptional unit AAA2 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the three-gene DefensePredictor-discovered system 42 locus cataloged as working transcriptional unit PRO1 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 43 locus cataloged as working transcriptional unit D668 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses a genome-encoded DefensePredictor-discovered system 44 locus represented in the pinned DefenseFinder model inventory by the DS-44 custom HMM profile.

A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 45 locus cataloged as working transcriptional unit 2971 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the two-gene DS-46 locus cataloged as working transcriptional unit RMRT and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the two-gene DefensePredictor-discovered system 5 locus cataloged as working transcriptional unit PN12 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the two-gene DefensePredictor-discovered system 6 locus cataloged with working_id HIPA and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 7 locus cataloged with working_id SVIR and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 8 locus cataloged with working_id MNAC and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the two-gene DefensePredictor-discovered system 9 locus cataloged with working_id MHAD and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses a genome-encoded, DUF262-associated prokaryotic Schlafen nuclease locus.

A phage defense system in which an organism possesses a Dag-family DNA-glycosylase system whose Dag1 or Dag2 effectors selectively target phages carrying modified guanine bases.

A phage defense system in which an organism possesses a Damona locus represented by a VCA0399 profile that can protect bacteria from bacteriophage infection.

A phage defense system in which an organism possesses a DarTG toxin-antitoxin locus whose DarT toxin can be released during bacteriophage infection to ADP-ribosylate viral DNA, block phage genome replication, and prevent production of mature virions.

A phage defense system in which an organism possesses a two-component Dazbog locus encoding DzbA and DzbB components that can protect bacteria from bacteriophage infection.

A genomics trait describing possession of a DdmDE anti-plasmid defense locus encoding the DNA-guided prokaryotic Argonaute DdmE and the helicase-nuclease DdmD, whose DNA recognition and handoff trigger processive plasmid destruction.

A phage defense system in which an organism possesses a Detocs locus represented in DefenseFinder by DtcA and DtcB profiles plus optional DtcC-family profiles, with an ATP nucleosidase output that can degrade ATP and dATP upon phage infection and halt phage propagation.

A phage defense system in which an organism possesses a three-gene Dionysus locus encoding DinA, DinB, and DinC components that can block jumbo-phage infection.

A phage defense system in which an organism possesses a Divona locus represented by a VCA0374 profile that can protect bacteria from bacteriophage infection.

A phosphorothioate defense system in which an organism possesses a Dnd restriction-modification locus that pairs a Dnd-family DNA phosphorothioation module with a DndFGH restriction module to nick invading DNA that lacks phosphorothioate modification.

A phosphorothioate defense system in which an organism possesses a DndCDEA-PbeABCD locus that pairs DndCDEA-mediated host-DNA phosphorothioation with PbeABCD-dependent targeting of non-phosphorothioated viral DNA to inhibit viral DNA replication.

A phage defense system in which an organism possesses a two-component Dodola locus represented by DolA and DolB profiles that can protect bacteria from bacteriophage infection.

A phage defense system in which an organism possesses a Dpd genomic island whose dpdA-K genes install 7-deazaguanine derivatives into DNA and are modeled by DefenseFinder as a multi-profile Dpd system.

A Druantia system in which an organism possesses a genome-encoded DefenseFinder Druantia_III subtype locus represented by the Druantia_III rule row requiring both the Druantia_III__DruH and Druantia__DruE_1 profiles.

A phage defense system in which an organism possesses a Druantia locus encoding a conserved DruE-family core and subtype-specific partner proteins.

A Druantia system in which an organism possesses a locus encoding DruE together with DruB, DruC and DruD, with or without DruA.

A Druantia system in which an organism possesses a locus encoding DruE together with DruM, DruF and DruG.

A Druantia system in which an organism possesses a locus encoding DruE and DruF together with DruL, without the type-II DruM and DruG components.

A phage defense system in which an organism possesses a defense-associated sirtuin locus whose SIR2-domain effector can deplete NAD+ during bacteriophage defense and is modeled by DefenseFinder as Dsr subtypes.

A phage defense system in which an organism possesses an ENDPaCF1 Type IIS restriction endonuclease-like locus with an inactive Endonuclease III sensing domain that can recognize diverse DNA hypermodifications and protect bacteria from hypermodified phages.

A type IV modification-dependent restriction system in which an organism possesses an EcoKMcrA mcrA locus encoding a methylcytosine- and hydroxymethylcytosine-dependent restriction endonuclease whose nuclease active site is required for efficient restriction of DNA modified in the correct sequence context.

A phage defense system in which an organism possesses an Eleos locus represented by LeoA, LeoB, LeoBC, and LeoC profiles that can protect bacteria from bacteriophage infection.

A phage defense system in which an organism possesses an Epona locus represented by a VCA0366 profile that can protect bacteria from bacteriophage infection.

A phage defense system in which an organism possesses an Erebus locus that can protect bacteria from bacteriophage infection.

A phage defense system in which an organism possesses an Esos locus represented by a VCA0450 profile that can protect bacteria from bacteriophage infection.

A phage defense system in which an organism possesses an FS_GIY_YIG locus represented by DefenseFinder as a single-profile model requiring FS_GIY_YIG__GIY_YIG.

A phage defense system in which an organism possesses an FS_HEPN_TM locus represented by DefenseFinder as a two-profile model requiring FS_HEPN_TM__HEPN and FS_HEPN_TM__TM.

A phage defense system in which an organism possesses an FS_HP locus represented by DefenseFinder as a single-profile model requiring FS_HP__HP.

A phage defense system in which an organism possesses an FS_HP_SDH_sah locus represented by DefenseFinder as a two-profile model requiring FS_HP_SDH_sah__HP and FS_HP_SDH_sah__SDH_sah.

A phage defense system in which an organism possesses an FS_HsdR_like locus represented by DefenseFinder as a two-gene model drawing from custom FS_HsdR_like__DUF6731, FS_HsdR_like__HP, and FS_HsdR_like__HdrR profiles.

A phage defense system in which an organism possesses an FS_Sma locus represented by DefenseFinder as a single-profile model requiring FS_Sma__Sma.

A phage defense system in which an organism possesses a two-component Fliodhais locus that can reduce Lactococcus bacteriophage c2 plaque development.

A phage defense system in which an organism possesses a Gamma-Mobile-Trio island-associated GAPS1 locus that can be triggered by a phage capsid protein to induce cell dormancy.

A phage defense system in which an organism possesses a GMT-encoded GAPS2 locus represented by DefenseFinder as a single-profile model, GAPS2__GAPS2, and experimentally linked to P1-vir and lambda-vir protection when expressed in E. coli.

A phage defense system in which an organism possesses a GMT-encoded GAPS4 locus represented by DefenseFinder as a two-profile model, GAPS4__GAPS4a and GAPS4__GAPS4b, and experimentally linked to T7, T4, P1-vir, and lambda-vir protection when expressed in E. coli.

A phage defense system in which an organism possesses a GMT-encoded GAPS6 locus represented by DefenseFinder as a two-profile model, GAPS6__GAPS6a and GAPS6__GAPS6b, and experimentally linked to T7, T4, P1-vir, and lambda-vir protection when expressed in E. coli.

A quality that is describing the percentage of guanine and cytosine nucleotides in genomic DNA, calculated as the ratio of GC base pairs to total base pairs.

A GC-content phenotype with genome-wide GC composition at or below approximately 42.65% (the METPO `GC_<=42.65` bin; note that the upstream label 'high' does not match this numeric threshold, but the synonym is preserved as the authoritative bin definition).

A GC-content phenotype with genome-wide GC composition between approximately 42.65% and 57.0% (the METPO `GC_42.65_57.0` bin; note that the upstream label 'low' does not match this mid-range numeric threshold, but the synonym is preserved as the authoritative bin definition).

A GC-content phenotype with genome-wide GC composition above approximately 66.3% (the METPO `GC_>66.3` bin; note that the upstream label 'mid1' does not match this high-end numeric threshold, but the synonym is preserved as the authoritative bin definition).

A GC-content phenotype with genome-wide GC composition between approximately 57.0% and 66.3% (the METPO `GC_57.0_66.3` bin).

A genome-sequence property describing strand asymmetry in guanine versus cytosine content between the leading and lagging replication strands, commonly used to locate the replication origin and terminus.

A genomics trait describing possession of a Gabija antiphage defense locus whose GajA and GajB proteins assemble into a complex that inhibits bacteriophage replication.

A phage defense system in which an organism possesses a Gao_Her locus represented by DefenseFinder as either a Gao_Her_DUF or Gao_Her_SIR two-profile subsystem.

A phage defense system in which an organism possesses a Gao_Her_DUF locus represented by DefenseFinder as a two-profile model requiring Gao_Her_DUF__DUF4297 and Gao_Her_DUF__HerA_DUF.

A phage defense system in which an organism possesses a Gao_Her_SIR locus represented by DefenseFinder as a two-profile model requiring Gao_Her_SIR__HerA_SIR2 and Gao_Her_SIR__SIR2.

A phage defense system in which an organism possesses a Gao_Hhe locus represented by DefenseFinder as a single-profile model requiring Gao_Hhe__HheA.

A phage defense system in which an organism possesses a Gao_Iet locus represented by DefenseFinder as a two-profile model requiring Gao_Iet__IetA and Gao_Iet__IetS.

A phage defense system in which an organism possesses a Gao_Mza locus represented by DefenseFinder as a five-profile model requiring Gao_Mza__MzaA, Gao_Mza__MzaB, Gao_Mza__MzaC, Gao_Mza__MzaD, and Gao_Mza__MzaE.

A phage defense system in which an organism possesses a Gao_Ppl locus represented by DefenseFinder as a single-profile model requiring Gao_Ppl__PplA.

A phage defense system in which an organism possesses a Gao_Qat locus represented by DefenseFinder as a four-profile model requiring Gao_Qat__QatA, Gao_Qat__QatB, Gao_Qat__QatC, and Gao_Qat__QatD.

A phage defense system in which an organism possesses a Gao_RL locus represented by DefenseFinder as a four-profile model requiring Gao_RL__RL_A, Gao_RL__RL_B, Gao_RL__RL_C, and Gao_RL__RL_D.

A phage defense system in which an organism possesses a Gao_TerY locus represented by DefenseFinder as a three-profile model requiring Gao_TerY__TerYA, Gao_TerY__TerYB, and Gao_TerY__TerYC.

A phage defense system in which an organism possesses a Gao_Tmn locus represented by DefenseFinder as a single-profile model requiring Gao_Tmn__TmnA.

A phage defense system in which an organism possesses a Gao_Upx locus represented by DefenseFinder as a single-profile model requiring Gao_Upx__UpxA.

A phage defense system in which an organism possesses a bacterial gasdermin locus represented by the DefenseFinder GasderMIN__bGSDM profile, whose bGSDM effectors are associated with bacteriophage defense and can be proteolytically activated in characterized bGSDM-protease systems to assemble membrane pores, disrupt membrane integrity, and execute cell death.

A phage defense system in which an organism possesses a Geb locus that can protect bacteria from bacteriophage infection.

A type IV modification-dependent restriction system in which an organism possesses a GmrSD locus encoding either separate GmrS and GmrD proteins or a fused double-domain GmrSD-family protein, that targets glucosylated hydroxymethylcytosine-containing DNA.

A phage defense system in which an organism possesses the two-gene HEC-02 Hma-embedded candidate locus, encoding an ABC ATPase and an associated nuclease-related domain protein, that can reduce bacteriophage plaquing.

A phage defense system in which an organism possesses the two-gene HEC-03 Hma-embedded candidate locus, encoding an ABC ATPase and an associated PilT N-terminal domain protein, that can reduce bacteriophage plaquing.

A phage defense system in which an organism possesses the single-gene HEC-04 Hma-embedded candidate locus, encoding an ABC ATPase fused to a TOPRIM-family nuclease domain, that can reduce bacteriophage plaquing.

A phage defense system in which an organism possesses the single-gene HEC-05 Hma-embedded candidate locus, encoding a GmrSD-like protein closely matching BrxU, that can reduce bacteriophage plaquing.

A phage defense system in which an organism possesses the single-gene HEC-06 Hma-embedded candidate locus, encoding a GmrSD-like protein, that can reduce bacteriophage plaquing.

A phage defense system in which an organism possesses the single-gene HEC-07 Hma-embedded candidate locus, encoding a RelE domain-containing protein, that can reduce bacteriophage plaquing.

A phage defense system in which an organism possesses the single-gene HEC-08 Hma-embedded candidate locus, encoding a higher eukaryotes and prokaryotes nucleotide-binding domain-containing protein, that can reduce bacteriophage plaquing.

A phage defense system in which an organism possesses a Hachiman antiphage locus encoding a HamA/HamB core.

A Hachiman system in which an organism possesses a HamA/HamB locus without a HamC component.

A Hachiman system in which an organism possesses a locus encoding HamA and HamB together with an additional HamC (DUF3223) component.

A phage defense system in which an organism possesses a Hailong locus encoding a HalB NTase DNA-signal enzyme and a HalA membrane effector complex that can be held inactive by HalB-derived oligodeoxyadenylate until viral DNA exonucleases release the primed HalA complex and induce protective host cell growth arrest.

A phage defense system in which an organism possesses a Hesat locus that can restrict bacteriophage infection.

A phage defense system in which an organism possesses a genome-encoded Hma locus with predicted HmaA helicase, HmaB m5c methyltransferase, and HmaC ATPase components.

A phage defense system in which an organism possesses an Hna locus encoding a single SF2 helicase/nuclease effector that protects cells from bacteriophage infection by responding to phage single-stranded DNA-binding protein challenge, shifting toward dysregulated nuclease activation, and triggering abortive infection.

A phage defense system in which an organism possesses a Hypnos locus that can protect bacteria from bacteriophage infection.

A phage defense system in which an organism possesses a genome-encoded prokaryotic Schlafen nuclease fused to an immunoglobulin-like sensor domain that recognizes T5-like phage tail assembly chaperones and activates Schlafen tRNase defense.

A phage defense system in which an organism possesses a two-gene jukAB locus encoding a JukA sensor that binds a PhiKZ-like gp241 early phage protein at the EPI vesicle and directly recruits the pore-forming-toxin-like JukB effector to destabilize the vesicle, suppress early phage gene expression, and prevent phage DNA replication and nucleus assembly.

A phage defense system in which an organism possesses a Kamadhenu locus that can restrict bacteriophage infection.

A phage defense system in which an organism possesses a two-component Kiwa locus encoding the transmembrane sensor KwaA and DNA-binding effector KwaB that assemble into a membrane-associated supercomplex and coordinate phage-attachment sensing with inhibition of phage DNA replication and late transcription.

A phage defense system in which an organism possesses a Kongming locus that uses phage-triggered deoxyinosine triphosphate signaling to activate a KomBC effector complex and mediate NAD depletion-linked death of infected cells.

A Lamassu system in which an organism possesses a defense locus encoding a protease-domain LmuA effector together with a hydrolase-like protein, an SMC-like LmuB sensor, and LmuC.

A phage defense system in which an organism possesses a Lamassu locus built around a conserved SMC-like LmuB sensor paired with a modular LmuA effector and subfamily-specific partner architecture, enabling viral-DNA sensing and effector-mediated antiviral activity.

A Lamassu system in which an organism possesses a locus encoding the LmuA effector and SMC-like LmuB sensor but no LmuC component.

A Lamassu system in which an organism possesses a locus with an additional LmuC component alongside the LmuA effector module and SMC-like LmuB sensor.

A Lamassu system in which an organism possesses a genome-encoded DefenseFinder Lamassu-Amidase subtype locus represented by the Lamassu-Amidase rule row requiring the Lamassu-Fam__LmuA_effector_Amidase and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II profiles.

A Lamassu system in which an organism possesses a genome-encoded DefenseFinder Lamassu-Cap4_nuclease subtype locus represented by the Lamassu-Cap4_nuclease rule row requiring the Lamassu-Fam__LmuA_effector_Cap4_nuclease_II and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II profiles.

A Lamassu system in which an organism possesses a genome-encoded DefenseFinder Lamassu-FMO subtype locus represented by the Lamassu-FMO rule row requiring the Lamassu-Fam__LmuA_effector_FMO and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II profiles.

A Lamassu system in which an organism possesses a locus encoding an HNH-domain LmuA effector, a short-form SMC-like LmuB sensor, and LmuC.

A Lamassu system in which an organism possesses a genome-encoded DefenseFinder Lamassu-Hydrolase subtype locus represented by the Lamassu-Hydrolase rule row requiring the Lamassu-Fam__LmuA_effector_Hydrolase and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II profiles.

A Lamassu system in which an organism possesses a genome-encoded DefenseFinder Lamassu-Lipase subtype locus represented by the Lamassu-Lipase rule row requiring the Lamassu-Fam__LmuA_effector_Lipase and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II profiles.

A Lamassu system in which an organism possesses a genome-encoded DefenseFinder Lamassu-Mrr subtype locus represented by the Lamassu-Mrr rule row requiring the Lamassu-Fam__LmuA_effector_Mrr and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II profiles.

A Lamassu system in which an organism possesses a genome-encoded DefenseFinder Lamassu-PDDEXK subtype locus represented by the Lamassu-PDDEXK rule row requiring the Lamassu-Fam__LmuA_effector_PDDEXK and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II profiles.

A Lamassu system in which an organism possesses a genome-encoded DefenseFinder Lamassu-Protease subtype locus represented by the Lamassu-Protease rule row requiring the Lamassu-Fam__LmuA_effector_Protease and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II profiles.

A Lamassu system in which an organism possesses a locus encoding an LmuA effector with a SMEK domain, an SMC-like LmuB sensor, and LmuC.

A Lamassu system in which an organism possesses a genome-encoded DefenseFinder Lamassu-Sir2 subtype locus represented by the Lamassu-Sir2 rule row requiring the Lamassu-Fam__LmuA_effector_Sir2 and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II profiles.

A phage defense system in which an organism possesses a Lit locus represented by DefenseFinder as a single-profile model requiring Lit__Lit.

A phage defense system in which an organism possesses a Lugos locus represented by a VCA0409 profile that can protect bacteria from bacteriophage infection.

A phage defense system in which an organism possesses a methylation-associated defense system locus whose canonical architecture has mad1 through mad8 genes and whose methylation-coupled self/non-self discrimination can restrict bacteriophage infection.

A phage defense system in which an organism possesses an MMB gp29-gp30 locus that can protect bacteria from bacteriophage infection.

A phage defense system in which an organism possesses a two-component MazEF toxin-antitoxin locus whose MazE antitoxin and MazF endoribonuclease can protect Escherichia coli against RNA phages and that DefenseFinder represents with mandatory MazEF__MazE and MazEF__MazF profiles.

A type IV modification-dependent restriction system in which an organism possesses an mcrBC locus encoding McrB DNA-binding and McrC cleavage-associated subunits that assemble into an McrBC restriction endonuclease complex targeting methylated cytosine-containing DNA.

A phage defense system in which an organism possesses a Menshen locus represented by NsnA, NsnB, and NsnC profile choices that can protect bacteria from bacteriophage infection.

A phage defense system in which an organism possesses a Metis locus that senses phage-mediated host-genome degradation through N6-methyl-deoxyadenosine monophosphate and activates a type-specific toxic effector.

A Wadjet system in which an organism possesses an MksBEFG derivative SMC locus encoding an MksBEF ATPase core and an MksG nuclease that degrades plasmid DNA.

A phage defense system in which an organism possesses a hok/sok toxin-antitoxin locus represented by DefenseFinder as the two-profile Mok_Hok_Sok model and experimentally linked to bacteriophage T4 exclusion by the plasmid R1 hok/sok locus.

A phage defense system in which an organism possesses a Mokosh locus represented by MkoA/MkoB type I or MkoC type II components that can protect bacteria from bacteriophage infection.

A phage defense system in which an organism possesses a tripartite MqsRAC toxin-antitoxin-chaperone locus represented by DefenseFinder as a two-profile model requiring MqsRAC__mqsC and MqsRAC__mqsR.

A type IV modification-dependent restriction system in which an organism possesses an MspJI-family Mrr-like locus encoding a restriction endonuclease that recognizes methylcytosine- or hydroxymethylcytosine-modified DNA and cleaves both strands at a fixed distance from the modified cytosine.

A phage defense system in which an organism possesses an NLR-related bacterial NACHT locus represented by DefenseFinder as an NLR_like_bNACHT01 or NLR_like_bNACHT09 single-profile model, encoding a NACHT-module STAND-family protein that can restrict bacteriophage production.

A phage defense system in which an organism possesses a Nantosuelta locus represented by a VCA0322 profile that can protect bacteria from bacteriophage infection.

A phage defense system in which an organism possesses a Nemetona locus represented by a VCA0441 profile that can protect bacteria from bacteriophage infection.

A phage defense system in which an organism possesses an Nhi-family locus represented by the DefenseFinder Nhi__Nhi profile and exemplified by a single enzyme with nuclease and helicase activities that protects against diverse staphylococcal phages, prevents phage DNA accumulation, and is inferred to target and degrade phage-specific replication intermediates.

A phage defense system in which an organism possesses a NixI-family phage-satellite locus represented by the DefenseFinder NixI__NixI profile and exemplified by a PLE-encoded nicking endonuclease that cleaves ICP1 bacteriophage DNA, inhibits ICP1 genome replication, and reduces progeny production in Vibrio cholerae.

A phage defense system in which an organism possesses an Ogmios locus represented by a VCA0308 profile that can protect bacteria from bacteriophage infection.

A phage defense system in which an organism possesses an Old exonuclease locus represented by DefenseFinder as a single-profile model, Old_exonuclease__Old_exonuclease, and experimentally linked to interference with phage lambda by the bacteriophage P2 Old protein.

A phage defense system in which an organism possesses a two-component Olokun locus represented by OloA and OloB profiles that can protect bacteria from bacteriophage infection.

A phage defense system in which an organism possesses a three-gene Ophion locus encoding OpnA, OpnB, and OpnC components that can block jumbo-phage infection before phage-nucleus formation.

A phage defense system in which an organism possesses an Oshun locus that can protect bacteria from bacteriophage infection.

An abortive infection system in which an organism possesses a phage anti-restriction-induced system locus encoding an AriA ABC ATPase sensor and an AriB TOPRIM-family nuclease whose activation by phage anti-restriction or other foreign proteins releases AriB to inhibit translation through lysine tRNA cleavage and block bacteriophage propagation.

A phage defense system in which an organism possesses a PD-Lambda-1 locus represented by DefenseFinder as a single-profile model, PD-Lambda-1__PD-Lambda-1, and experimentally linked to LambdaVir protection when expressed in E. coli.

A phage defense system in which an organism possesses a PD-Lambda-2 locus represented by DefenseFinder as a model with two mandatory profiles, PD-Lambda-2__PD-Lambda-2_A and PD-Lambda-2__PD-Lambda-2_B, plus the accessory PD-Lambda-2__PD-Lambda-2_C profile.

A phage defense system in which an organism possesses a PD-Lambda-3 locus represented by DefenseFinder as a two-profile model, PD-Lambda-3__PD-Lambda-3_A and PD-Lambda-3__PD-Lambda-3_B, and experimentally linked to LambdaVir protection when expressed in E. coli.

A phage defense system in which an organism possesses a PD-Lambda-4 locus represented by DefenseFinder as a two-profile model, PD-Lambda-4__PD-Lambda-4_A and PD-Lambda-4__PD-Lambda-4_B, and experimentally linked to T4, LambdaVir, SECphi27, and T7 protection when expressed in E. coli.

A phage defense system in which an organism possesses a PD-Lambda-5 locus represented by DefenseFinder as a two-profile model, PD-Lambda-5__PD-Lambda-5_A and PD-Lambda-5__PD-Lambda-5_B, and experimentally linked to T2, T4, T6, LambdaVir, SECphi17, SECphi18, SECphi27, T3, and T7 protection when expressed in E. coli.

A phage defense system in which an organism possesses a PD-Lambda-6 locus represented by DefenseFinder as a single-profile model, PD-Lambda-6__PD-Lambda-6, and experimentally linked to LambdaVir and T5 protection when expressed in E. coli.

A phage defense system in which an organism possesses a two-gene PD-T2-1 operon whose expression was experimentally linked to protection against T2, T6, Bas18, T4, and T5 phages.

A phage defense system in which an organism possesses a PD-T4-1 locus represented by DefenseFinder as a single-profile model, PD-T4-1__PD-T4-1, and experimentally linked to T2, T4, and T6 protection when expressed in E. coli.

An abortive infection system in which an organism possesses a PD-T4-10 locus represented by DefenseFinder as a two-profile model, PD-T4-10__PD-T4-10_A and PD-T4-10__PD-T4-10_B, and experimentally linked to T2, T4, T6, T5, and SECphi27 protection when expressed in E. coli.

A phage defense system in which an organism possesses a PD-T4-2 locus represented by DefenseFinder as a two-profile model requiring PD-T4-2__PD-T4-2_A and PD-T4-2__PD-T4-2_B, and experimentally linked to T2, T4, T6, T5, and SECphi27 protection when expressed in E. coli.

A phage defense system in which an organism possesses a PD-T4-3 locus represented by DefenseFinder as a single-profile model, PD-T4-3__PD-T4-3, and experimentally linked to T2, T4, and T6 protection when expressed in E. coli.

A phage defense system in which an organism possesses a PD-T4-4 locus represented by DefenseFinder as a two-profile model requiring PD-T4-4__PD-T4-4_A and PD-T4-4__PD-T4-4_B, and experimentally linked to T2, T4, T6, and SECphi17 protection when expressed in E. coli.

A phage defense system in which an organism possesses a PD-T4-5 locus represented by DefenseFinder as a single-profile model, PD-T4-5__PD-T4-5, and experimentally linked to T4, T6, LambdaVir, and T5 protection when expressed in E. coli.

A phage defense system in which an organism possesses a PD-T4-6 locus represented by DefenseFinder as a single-profile model, PD-T4-6__PD-T4-6, and experimentally linked to T2, T4, and T6 protection when expressed in E. coli.

An abortive infection system in which an organism possesses a PD-T4-7 locus represented by DefenseFinder as a single-profile model, PD-T4-7__PD-T4-7, and experimentally linked to T2, T4, and T6 protection when expressed in E. coli.

A phage defense system in which an organism possesses a PD-T4-8 locus represented by DefenseFinder as a single-profile model, PD-T4-8__PD-T4-8, and experimentally linked to T2, T4, T6, SECphi18, and SECphi27 protection when expressed in E. coli.

A phage defense system in which an organism possesses a PD-T7-1 locus represented by DefenseFinder as a single-profile model, PD-T7-1__PD-T7-1, and experimentally linked to T7 protection when expressed in E. coli.

A phage defense system in which an organism possesses a PD-T7-2 locus represented by DefenseFinder as a two-profile model, PD-T7-2__PD-T7-2_A and PD-T7-2__PD-T7-2_B, and experimentally linked to T2, T4, T6, LambdaVir, T5, SECphi18, SECphi27, T3, and T7 protection when expressed in E. coli.

A phage defense system in which an organism possesses a PD-T7-3 locus represented by DefenseFinder as a single-profile model, PD-T7-3__PD-T7-3, and experimentally linked to protection against T2, T4, T6, T5, SECphi17, T3, and T7 when expressed in E. coli.

A phage defense system in which an organism possesses a PD-T7-4 locus represented by DefenseFinder as a single-profile model, PD-T7-4__PD-T7-4, and experimentally linked to protection against SECphi18, SECphi27, T3, and T7 when expressed in E. coli.

A phage defense system in which an organism possesses a PD-T7-5 locus represented by DefenseFinder as a single-profile model, PD-T7-5__PD-T7-5, and experimentally linked to SECphi17, T3, and T7 protection when expressed in E. coli.

A phage defense system in which an organism possesses a Panchino gp28 locus that can protect bacteria from bacteriophage infection.

A phage defense system in which an organism possesses a two-gene optSE locus encoding an OptS protein that constitutively produces cyclic dinucleotides and an OptE transmembrane effector that is released from cyclic-dinucleotide repression when phage Acb2-like proteins sequester those signals, leading to inner-membrane disruption.

A phage defense system in which an organism possesses a Pf4 prophage-encoded PfiAT toxin-antitoxin locus represented by DefenseFinder as a two-profile model requiring PfiAT__PfiA and PfiAT__PfiT.

A phage defense system in which an organism possesses a Phrann gp29-gp30 locus that can protect bacteria from bacteriophage infection.

An abortive infection system in which an organism possesses an F-plasmid pif-family locus represented by the DefenseFinder Pif__PifA and Pif__PifC profiles and exemplified by the pif region that specifies abortive infection of T7 phage.

A phage defense system in which an organism possesses a Prithvi locus that can protect bacteria from bacteriophage infection.

A phage defense system in which an organism possesses a Prometheus locus that can protect bacteria from bacteriophage infection.

A phage defense system in which an organism possesses a PrrC locus represented by DefenseFinder as a two-profile model requiring PrrC__EcoprrI and PrrC__PrrC, with type I restriction-modification components accepted as accessory markers.

A phage defense system in which an organism possesses a two-component PsyrTA locus represented by PsyrA and PsyrT profiles that can protect bacteria from bacteriophage infection.

A type IV modification-dependent restriction system in which an organism possesses a PvuRts1I-family locus encoding a restriction endonuclease that recognizes 5-hydroxymethylcytosine or 5-glucosylhydroxymethylcytosine in double-stranded DNA and cleaves both strands on the 3'-side away from the recognized modified cytosine.

A phage defense system in which an organism possesses a Pycsar locus encoding a PycC pyrimidine cyclase and a cognate cyclic-pyrimidine receptor effector whose phage-induced cyclic CMP or cyclic UMP signaling activates antiviral effector outputs that inhibit bacteriophage propagation.

A phage defense system in which an organism possesses a restriction by an adenosine deaminase acting on RNA locus encoding an RdrA AAA+ ATPase and an RdrB adenosine deaminase that assemble into a supramolecular defense complex to modify adenosine-containing substrates and inhibit bacteriophage replication.

A phage defense system in which an organism possesses a locus encoding a RAZR zinc-finger HEPN RNase that can form a phage-triggered higher-order ring complex, cleave RNA broadly, inhibit translation, and restrict phage propagation.

A phage defense system in which an organism possesses a genome-encoded, resolvase- and DUF5677-associated prokaryotic Schlafen nuclease locus.

A phage defense system in which an organism possesses a genome-encoded, resolvase- and KAP NTPase-associated prokaryotic Schlafen nuclease locus.

A phage defense system in which an organism possesses a genome-encoded, resolvase-associated prokaryotic Schlafen nuclease locus.

A phage defense system in which an organism possesses a retron locus encoding a reverse transcriptase, an msr/msd non-coding RNA that yields multicopy single-stranded DNA, and an associated effector whose activation can inhibit bacteriophage propagation through abortive infection.

A phage defense system in which an organism possesses a single-gene Reve antiviral locus that is encoded by P4-like phage satellites and can protect bacteria from bacteriophage infection.

An abortive infection system in which an organism possesses a bacteriophage-lambda Rex-family locus represented by the DefenseFinder RexAB__RexA and RexAB__RexB profiles and exemplified by the rexA and rexB two-component system that aborts lytic growth of bacterial viruses.

A phage defense system in which an organism possesses a Rhea locus that can restrict bacteriophage infection.

A phage defense system in which an organism possesses a genome-encoded RloC locus represented by DefenseFinder as a one-profile model requiring RloC__RloC.

A phage defense system in which an organism possesses a genome-encoded RnlAB toxin-antitoxin locus represented by DefenseFinder as a two-profile model requiring RnlAB__RnlA and RnlAB__RnlB.

A phage defense system in which an organism possesses a two-component RosmerTA locus represented by RmrA and RmrT profiles that can protect bacteria from bacteriophage infection.

A phage defense system in which an organism possesses a P4-like TIR-NLR locus represented by DefenseFinder as the Rst_TIR-NLR single-profile model and experimentally linked to broad virulent-phage and P2-like phage restriction.

A phage defense system in which an organism possesses a P4-like gop-beta-cII locus represented by DefenseFinder as the Rst_gop_beta_cll model and experimentally linked to lambda and P1 phage restriction.

A phage defense system in which an organism possesses a three-protein Rst_2TM_1TM_TIR locus represented by DefenseFinder as a three-profile model requiring Rst_2TM_1TM_TIR__Rst_1TM_TIR, Rst_2TM_1TM_TIR__Rst_2TM_TIR, and Rst_2TM_1TM_TIR__Rst_TIR_tm and experimentally linked to multi-phage protection when expressed in Escherichia coli C.

A phage defense system in which an organism possesses a three-protein Rst_3HP locus represented by DefenseFinder as a three-profile model requiring Rst_3HP__Hp1, Rst_3HP__Hp2, and Rst_3HP__Hp3 and experimentally linked to P1 protection when expressed in Escherichia coli.

A phage defense system in which an organism possesses a single-gene Rst_DUF4238 locus represented by DefenseFinder as an Rst_DUF4238__DUF4238_Pers single-profile model and experimentally linked to strong resistance against phage T7.

A phage defense system in which an organism possesses a two-protein Rst_HelicaseDUF2290 locus represented by DefenseFinder as a two-profile model requiring Rst_HelicaseDUF2290__DUF2290 and Rst_HelicaseDUF2290__Helicase and experimentally linked to T7 protection when expressed in Escherichia coli.

A phage defense system in which an organism possesses a two-protein Rst_Hydrolase-3Tm locus represented by DefenseFinder as a two-profile Rst_Hydrolase-Tm model requiring Rst_Hydrolase-Tm__Hydrolase and Rst_Hydrolase-Tm__Hydrolase-Tm and experimentally linked to T7 protection when expressed in Escherichia coli.

A phage defense system in which an organism possesses a two-protein Rst_RT-nitrilase-Tm locus represented by DefenseFinder as a two-profile Rst_RT-Tm model requiring Rst_RT-Tm__RT and Rst_RT-Tm__RT-Tm and experimentally linked to AL505_P2 protection when expressed in Escherichia coli.

A phage defense system in which an organism possesses a Rugutis locus that can restrict bacteriophage infection.

A phage defense system in which an organism possesses an SDIC1 locus encoding a TIR-domain SDIC1A component and a ubiquitin-ligase-like SDIC1B component that can provide population-wide immunity against bacteriophages.

A phage defense system in which an organism possesses an SDIC3 Serratia defense-island candidate locus that can confer strong protection against several bacteriophages when plasmid expressed.

A phage defense system in which an organism possesses an SDIC4 locus encoding an SDIC4A component and a VasI-like SDIC4B component that can reduce adsorption of invading bacteriophages.

A phage defense system in which an organism possesses a SEFIR locus represented by a bSEFIR profile that can protect bacteria from bacteriophage infection.

A phage defense system in which an organism possesses a SNIPE anti-bacteriophage system that localizes to the bacterial membrane, exploits the spatial organization of phage genome injection, and directly cleaves incoming phage DNA to block siphovirus infection.

A genomics trait describing possession of a short prokaryotic Argonaute TIR-APAZ (SPARTA) locus whose short pAgo and TIR-APAZ proteins form heterodimeric complexes that oligomerize after guide RNA-mediated target DNA binding and unleash TIR domain-mediated NAD(P)ase activity that depletes NAD(P)+ to remove plasmid-invaded cells.

A phage defense system in which an organism possesses a sanaTA toxin-antitoxin locus represented by DefenseFinder as a SanaA/SanaT two-profile model and experimentally linked to resistance against T7 phage mutants lacking gene 4.5 anti-defense activity.

A type IV modification-dependent restriction system in which an organism possesses a ScoMcrA-family locus encoding a sulfur-binding-domain phosphorothioated-DNA restriction endonuclease.

A phage defense system in which an organism possesses a Septu locus encoding PtuA and the HNH endonuclease PtuB, whose PtuAB oligomer confers antiphage immunity through nuclease-mediated phage genome cleavage in standalone systems and can be regulated by retron RT-msDNA complexes in Retron-Septu loci.

A phage defense system in which an organism possesses a Shango locus represented by a mandatory SngA profile and an SngB or SngC profile that can protect bacteria from bacteriophage infection.

A genomics trait describing possession of a Shedu antiphage defense system encoding a single-protein immune nuclease with a conserved nuclease core and regulated sensor domain architecture.

A phage defense system in which an organism possesses a two-component ShosTA locus represented by ShosA and ShosT profiles that can protect bacteria from bacteriophage infection.

A phage defense system in which an organism possesses a Sirona locus represented by a VCA0356 profile that can protect bacteria from bacteriophage infection.

A phage defense system in which an organism possesses a SoFIC locus represented by a SoFic profile that can protect bacteria from bacteriophage infection.

An abortive infection system in which an organism possesses a SpbK-family locus represented by the DefenseFinder SpbK__SpbK profile and exemplified by the ICEBs1 spbK gene whose SPβ-YonE-dependent activity inhibits SPβ production and kills infected cells.

A phosphorothioate defense system in which an organism possesses an SspABCD-SspE locus that pairs an SspABCD single-stranded DNA phosphorothioation module with the SspE restriction enzyme to sense host phosphorothioate marks and nick invading DNA.

A phosphorothioate defense system in which an organism possesses an SspABCD-SspFGH locus that pairs an SspABCD-family single-stranded DNA phosphorothioation module with an SspFGH restriction module to damage non-phosphorothioated phage DNA and suppress phage DNA replication.

An abortive infection system in which an organism possesses a phage-defense locus encoding the Stk2 serine/threonine kinase, which can be activated by a phage protein to phosphorylate host proteins and induce host-cell death that prevents bacteriophage propagation.

A phage defense system in which an organism possesses a Sucellos locus represented by SclA_VCA0367 and SclB_VCA0368 profiles that can protect bacteria from bacteriophage infection.

A phage defense system in which an organism possesses a TIR-I locus, represented in the pinned DefenseFinder HMM inventory by TIR-I__TIR-I_A and TIR-I__TIR-I_B custom profiles, that can inhibit bacteriophage plaquing.

A phage defense system in which an organism possesses a TIR-III locus, represented in the pinned DefenseFinder HMM inventory by TIR-III__TIR-III_A and TIR-III__TIR-III_B custom profiles, that can inhibit bacteriophage plaquing.

A phage defense system in which an organism possesses a TIR-IV locus, represented in the pinned DefenseFinder HMM inventory by TIR-IV__TIR-IV_A and TIR-IV__TIR-IV_B custom profiles, that can inhibit bacteriophage plaquing.

A phage defense system in which an organism possesses a TIR-VII locus, represented in the pinned DefenseFinder HMM inventory by TIR-VII__TIR-VII_A and TIR-VII__TIR-VII_B custom profiles, that can inhibit bacteriophage plaquing.

A phage defense system in which an organism possesses a TIR-VIII locus, represented in the pinned DefenseFinder HMM inventory by TIR-VIII__TIR-VIII_A and TIR-VIII__TIR-VIII_B custom profiles, that can inhibit bacteriophage plaquing.

A phage defense system in which an organism or resident prophage possesses a Tab virion-assembly-inhibition locus that expresses the Tab tail-assembly-blocking protein, blocks assembly of invading phage tails, prevents infectious virion formation, and protects the bacterial community from phage spread.

A type IV modification-dependent restriction system in which an organism possesses a TagI-family locus encoding an SRA-HNH restriction endonuclease that recognizes 5-methylcytosine- or 5-hydroxymethylcytosine-modified DNA.

A phage defense system in which an organism possesses a Taranis locus represented by a VCA0396 profile that can protect bacteria from bacteriophage infection.

A restriction-modification system in which an organism possesses a two-gene TgvAB locus embedded in the Vibrio cholerae VPI-2 type I R-M cluster, encoding TgvA and TgvB modification-dependent restriction proteins related to GmrSD type IV restriction enzymes that restrict glucosylated hmC-containing T-even-like phage DNA.

A phage defense system in which an organism possesses a Tha tail-activated HEPN anti-phage locus that can be activated by incoming-phage minor tail proteins to mediate nonspecific RNase-linked defense.

A genomics trait describing possession of a Thoeris antiphage defense locus in which phage-triggered TIR-domain proteins generate a cyclic-ADP-ribose-like signal that activates a ThsA NADase effector to deplete NAD and inhibit bacteriophage replication.

A phage defense system in which an organism possesses a Tiamat locus represented by a TmtA profile that can protect bacteria from bacteriophage infection.

A phage defense system in which an organism possesses a single-protein Toga antiviral locus that is encoded by P4-like phage satellites and can protect bacteria from bacteriophage infection.

A phage defense system in which an organism possesses a Toutatis locus represented by TutA_VCA0446 and TutB_VCA0447 profiles that can protect bacteria from bacteriophage infection.

An abortive infection system in which an organism possesses a toxIN type III protein-RNA toxin-antitoxin locus whose ToxN toxin and tandem ToxI RNA antitoxins constitute a two-component Abi module that inhibits bacterial growth and restricts phage propagation.

A phage defense system in which an organism possesses a Ukko locus that can protect bacteria from bacteriophage infection.

A phage defense system in which an organism possesses an Uzume locus represented by a UzuA profile that can protect bacteria from bacteriophage infection.

A phage defense system in which an organism possesses a VP1796-family locus represented by the DefenseFinder VP1796__VP1796 custom HMM profile and experimentally linked to reduced bacteriophage plaquing when the cloned Vibrio parahaemolyticus RIMD 2210633 vp1796 cassette is expressed from a VSV105 plasmid.

A phage defense system in which an organism possesses a VP1817-family locus represented by the DefenseFinder VP1817__VP1817 custom HMM profile and experimentally linked to reduced bacteriophage plaquing when the cloned Vibrio parahaemolyticus RIMD 2210633 vp1817 cassette is expressed from a VSV105 plasmid.

A phage defense system in which an organism possesses a VP1823-family locus represented by the DefenseFinder VP1823__VP1823 custom HMM profile and experimentally linked to reduced bacteriophage plaquing when the cloned Vibrio parahaemolyticus RIMD 2210633 vp1823 cassette is expressed from a VSV105 plasmid.

A phage defense system in which an organism possesses a VP1826-family locus represented by the DefenseFinder VP1826__VP1826 custom HMM profile and experimentally linked to reduced bacteriophage plaquing when the cloned Vibrio parahaemolyticus RIMD 2210633 vp1826 cassette is expressed from a VSV105 plasmid.

A phage defense system in which an organism possesses a VP1839-family locus represented by the DefenseFinder VP1839__VP1839 custom HMM profile and experimentally linked to reduced bacteriophage plaquing when the cloned Vibrio parahaemolyticus RIMD 2210633 vp1839 cassette is expressed from a VSV105 plasmid.

A phage defense system in which an organism possesses a VP1840-family locus represented by the DefenseFinder VP1840__VP1840 custom HMM profile and experimentally linked to reduced bacteriophage plaquing when the cloned Vibrio parahaemolyticus RIMD 2210633 vp1840 cassette is expressed from a VSV105 plasmid.

A phage defense system in which an organism possesses a VP1848-family locus represented by the DefenseFinder VP1848__VP1848 custom HMM profile and experimentally linked to reduced bacteriophage plaquing when the cloned Vibrio parahaemolyticus RIMD 2210633 vp1848 cassette is expressed from a VSV105 plasmid.

A phage defense system in which an organism possesses a VP1851-family locus represented by the DefenseFinder VP1851__VP1851 custom HMM profile and experimentally linked to reduced bacteriophage plaquing when the cloned Vibrio parahaemolyticus RIMD 2210633 vp1851 cassette is expressed from a VSV105 plasmid.

A phage defense system in which an organism possesses a VP1853-family locus represented by the DefenseFinder VP1853__VP1853 custom HMM profile and experimentally linked to reduced bacteriophage plaquing when the cloned Vibrio parahaemolyticus RIMD 2210633 vp1853 cassette is expressed from a VSV105 plasmid.

A type IV modification-dependent restriction system in which an organism possesses a VcaM4I-family locus encoding an EVE-HNH restriction endonuclease that recognizes 5-methylcytosine- or 5-hydroxymethylcytosine-modified DNA.

A phage defense system in which an organism possesses a Veles locus that can protect bacteria from bacteriophage infection.

A phage defense system in which an organism possesses a prokaryotic viperin locus represented by a pVip profile that can produce antiviral modified ribonucleotides and protect against phage infection.

A genomics trait describing possession of a Wadjet anti-plasmid defense locus encoding a derivative SMC complex such as JetABCD, MksBEFG, or EptABCD that restricts circular plasmids by ATPase-dependent DNA cleavage.

A genomics trait describing possession of a Zorya antiphage defense locus in which conserved ZorA/ZorB membrane-motor core proteins and subtype-specific effector proteins inhibit bacteriophage propagation.

A Zorya system in which an organism possesses a genome-encoded DefenseFinder Zorya_TypeI subtype locus whose rule row lists Zorya_TypeI__ZorC, Zorya_TypeI__ZorD, Zorya__ZorA, and Zorya__ZorB in its mandatory profile set with 3 mandatory matches and 3 genes required.

A Zorya system in which an organism possesses a genome-encoded DefenseFinder Zorya_TypeII subtype locus represented by Zorya_TypeII__ZorE, Zorya__ZorA2, and Zorya__ZorB rule profiles.

A Zorya system in which an organism possesses a locus encoding ZorA and ZorB together with ZorF and ZorG.

A genomics trait describing possession of a bacteriophage abortive-infection defense system in which phage infection activates a host-encoded growth-arrest or cell-death program that prevents completion of phage replication and protects nearby bacterial cells.

A genome-sequence property describing non-uniform usage of synonymous codons across a genome, shaped by mutational bias and translational selection and correlated with gene expression level.

A phage defense system in which an organism possesses a dCTPdeaminase locus that converts dCTP into deoxy-uracil nucleotides during phage infection, depletes dCTP from the nucleotide pool, and halts phage replication by starving the phage of an essential DNA building block.

A phage defense system in which an organism possesses a dGTPase locus that degrades dGTP into phosphate-free deoxy-guanosine during phage infection, depletes dGTP from the nucleotide pool, and halts phage replication by starving the phage of an essential DNA building block.

A quantitative genomics property describing the total length of an organism's genome (typically expressed in megabase pairs), which varies widely across prokaryotes and reflects lifestyle and evolutionary forces.

A genomics trait describing selective reduction of genome size and gene content in free-living microbes with very large effective population sizes, minimizing the cellular cost of replication and biosynthesis.

A genomics trait describing possession of a genomic island — a horizontally acquired chromosomal region (e.g. a pathogenicity, symbiosis, or metabolic island) that often retains mobility signatures such as flanking repeats and atypical nucleotide composition.

A fungal phenotype characterized by the coexistence of genetically distinct nuclei within a shared cytoplasm.

A genomic island trait in which an organism possesses an integrative and conjugative element, a self-transmissible mobile genetic element that integrates into host DNA, excises under induced expression, and encodes type IV secretion machinery for conjugative transfer to recipient cells.

A phage defense system in which an organism possesses a lanthivirin lanthipeptide biosynthetic gene cluster that can confer anti-phage activity in a native Streptomyces context and after heterologous expression of complete lanthivirin systems.

A Lamassu system in which an organism possesses a locus from the long-LmuB family, characterized by longer coiled-coil regions in its SMC-like LmuB sensor than in short Lamassu systems.

A genomics trait describing possession of DNA segments that can move within or between genomes and mediate horizontal gene transfer, including plasmids, prophages, transposable elements, and genomic islands.

A genomics trait describing the structure of a species' pangenome — the balance of core versus accessory genes and whether the pangenome is open (continually acquiring new genes across genomes) or closed.

A genomics trait describing possession of one or more bacterial or archaeal immune systems that inhibit bacteriophage infection.

A genomics trait describing possession of a DNA phosphorothioation-dependent antiviral locus in which host DNA phosphorothioate modification is paired with a Dnd-, Ssp-, or Pbe-family effector module to restrict invading viral DNA.

A genomics trait describing possession of one or more plasmids — extrachromosomal, typically circular DNA replicons that carry accessory genes such as resistance, virulence, or metabolic functions and can transfer by conjugation.

A genomics trait describing the number of complete genome copies per cell; many bacteria and archaea are polyploid, maintaining many chromosome copies that support survival, repair, and large cell size.

A genomics trait describing possession of a prokaryotic Argonaute-centered defense locus that uses a pAgo protein, alone or with cognate accessory proteins, to defend against plasmids, bacteriophages, or other mobile genetic elements.

A genomics trait describing possession of an integrated (or extrachromosomal) temperate bacteriophage genome (a prophage) maintained in the host during lysogeny, often contributing genes that alter host phenotype.

A quantitative genomics property describing the number of ribosomal RNA (rrn) operons encoded in a genome, which correlates with maximal growth rate and ecological strategy.

A genomics trait describing possession of a restriction-modification system that distinguishes self from non-self DNA through sequence-specific methylation and cleavage of unmethylated DNA by a restriction endonuclease.

A Lamassu system in which an organism possesses a locus from the short-LmuB family, characterized by shorter coiled-coil regions in its SMC-like LmuB sensor than in long Lamassu systems.

A genomics trait describing possession of transposable elements — such as insertion sequences and transposons — that move within the genome and drive genome rearrangement, gene inactivation, and plasticity.

A restriction-modification system in which an organism possesses a Type I R-M locus encoding a pentameric enzyme with HsdR-like restriction, HsdM-like methylation, and HsdS-like DNA sequence-recognition subunits, including RM_Type_I loci represented by DefenseFinder.

A restriction-modification system in which an organism possesses a Type II restriction endonuclease activity paired with cognate methyltransferase self-protection, including conventional RM_Type_II loci represented by DefenseFinder.

A restriction-modification system in which an organism possesses a Type IIG locus centered on a restriction-methyltransferase-specificity fusion gene represented by DefenseFinder as the RM_Type_IIG subsystem.

A restriction-modification system in which an organism possesses a Type III R-M locus encoding Mod-like DNA methyltransferase and Res-like ATP-dependent restriction subunits, including RM_Type_III loci represented by DefenseFinder.

A phage defense system in which an organism possesses a Type IV modification-dependent restriction locus, including DefenseFinder RM_Type_IV loci, whose restriction-enzyme activity cleaves foreign DNA carrying recognized base or backbone modifications rather than the unmodified targets of canonical Type I-III restriction-modification systems.