This repo contains the latest version of the HMMs and system models used by PADLOC. The latest version of this database can be downloaded by running padloc --db-update.
The following document describes each field of hmm_meta.txt and sys_meta.txt, and how you can use your own HMMs and system models with PADLOC.
If you use PADLOC or PADLOC-DB please cite:
Payne, L.J., Todeschini, T.C., Wu, Y., Perry, B.J., Ronson, C.W., Fineran, P.C., Nobrega, F.L., Jackson, S.A. (2021) Identification and classification of antiviral defence systems in bacteria and archaea with PADLOC reveals new system types. Nucleic Acids Research, 49, 10868-10878. doi: https://doi.org/10/gzgh
The HMMs in PADLOC-DB were built/curated using data from various sources, we encourage you to also give credit to these groups by citing them too.
System models are written using YAML syntax:
---
maximum_separation: 4 <- Number of unrelated genes allowed to separate each component.
minimum_core: 4 <- Number of core genes that need to be present.
minimum_total: 5 <- Number of total genes that need to be present.
core_genes: <- Genes that are generally considered essential.
- GenA
- GenB
- GenC
- GenD
optional_genes: <- Genes that are not always present.
- GenX
- GenY
prohibited_genes: <- Genes that cannot be present.
- GenZ
...These fields must be filled out for use with PADLOC.
| Field | Example | Description |
|---|---|---|
hmm.accession |
PDLC00001 | A unique identifier for each padlocDB HMM. |
hmm.name |
GajA_6 | Another unique identifier for each HMM. If the HMM is from an external database, the original ID from that database is preferred. |
hmm.description |
Predicted ATPase | A one line description of the HMM e.g. describing protein function or domains. |
protein.name |
PemK|MazF | The name of the protein that the HMM represents. Multiple protein names are separated by '|'. Capitalisation of the first letter is preferred. These are the names that are referenced in the system models. |
e.value.threshold |
1e-05 | The minimum E-value allowed when reporting hits. |
hmm.coverage.threshold |
0.3 | The proportion of the HMM that must contribute to the HMM/target alignment when reporting hits. |
target.coverage.threshold |
0.3 | The proportion of the target that must contribute to the HMM/target alignment when reporting hits. |
comment |
NA | Other information that is relevant. This may include comments from the original database where applicable. |
These fields are for reference only, and are not strictly required by PADLOC.
| Field | Example | Description |
|---|---|---|
secondary.name |
CRISPR-accessory | A secondary identifier that can be referred to in the system definition for groups of proteins rather than individual protein names |
system |
DISARM, RESTRICTION MODIFICATION | The category of defence system to which the HMM belongs. Multiple system names are separated by ', '. The full system name is used where reasonable. |
author |
Payne LJ, Jackson SA | Author(s) of the entry. If the HMM is from an external database, crediting the original author is preferred. If the HMM is from a study where an author was not explicity credited, authorship is attributed to the first author of the study. Multiple authors are separated by ', '. |
hmm.nseq |
49 | The number of sequences that contribute to the HMM. |
hmm.length |
120 | The length of the the HMM. |
literature.ref |
10/f2wkj3 | The DOI for the literature that implies that the HMM or underlying proteins belong to the protein/defence system. Multiple references are separated by ', '. DOIs can be resolved at doi.org. |
database.ref |
PFAM; PF06527 | Reference to the original accession of the alignment/HMM if it was taken from an external database, e.g. PFAM, COG, etc. Includes the name of the database and the identifier separated by '; '. |
| Field | Example | Description |
|---|---|---|
yaml.name |
druantia_type_I | The exact name of the yaml file that corresponds with the system type (without the .yaml extension) |
search |
T | Set to TRUE or FALSE (or T / F) to determine whether the system is searched or not. |
comment |
NA | Other information that is relevant. |
| Field | Example | Description |
|---|---|---|
system.name |
Druantia | The name of the system |
type |
type I | The subtype of the system. |
Additional HMMs and system models can be added directly to your copy of this database, or a separate database can be set up in the same way as this one.
Additional HMMs can be added to the hmm/ directory, hmm_meta.txt also needs to be updated to include metadata for the new HMMs. When using with PADLOC, these HMMs need to be concatenated into a single file in the hmm/ directory called padlocdb.hmm.
Additional system models can be added to the sys/ directory, sys_meta.txt should also be updated to include metadata for the new models.
The HMMs in PADLOC-DB were built/curated using data from various sources, we encourage you to also give credit to these groups by citing them too:
Doron, S., Melamed, S., Ofir, G., Leavitt, A., Lopatina, A., Keren, M., Amitai, G. and Sorek, R. (2018) Systematic discovery of antiphage defense systems in the microbial pangenome. Science, 359, eaar4120. doi: 10/ggqhzm
Millman, A., Melamed, S., Amitai, G. and Sorek, R. (2020) Diversity and classification of cyclic-oligonucleotide-based anti-phage signalling systems. Nature Microbiology, 5, 1608–1615. doi: 10/gg84nk
Couvin, D., Bernheim, A., Toffano-Nioche, C., Touchon, M., Michalik, J., Néron, B., Rocha, E. P. C., Vergnaud, G., Gautheret, D. and Pourcel, C. (2018) CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins. Nucleic Acids Res, 46, W246–W251. doi: 10/ggdjdf
Makarova, K. S., Wolf, Y. I., Iranzo, J., Shmakov, S. A., Alkhnbashi, O. S., Brouns, S. J. J., Charpentier, E., Cheng, D., Haft, D. H., Horvath, P., et al. (2020) Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants. Nat Rev Microbiol, 18, 67–83. doi: 10/ggkfgj
Shah, S. A., Alkhnbashi, O. S., Behler, J., Han, W., She, Q., Hess, W. R., Garrett, R. A. and Backofen, R. (2019) Comprehensive search for accessory proteins encoded with archaeal and bacterial type III CRISPR-cas gene cassettes reveals 39 new cas gene families. RNA Biology, 16, 530–542. doi: 10/ggqv9p
Shmakov, S. A., Makarova, K. S., Wolf, Y. I., Severinov, K. V. and Koonin, E. V. (2018) Systematic prediction of genes functionally linked to CRISPR-Cas systems by gene neighborhood analysis. PNAS, 115, E5307–E5316. doi: 10/gdpqwq
Russel, J., Pinilla-Redondo, R., Mayo-Muñoz, D., Shah, S. A. and Sørensen, S. J. (2020) CRISPRCasTyper: Automated Identification, Annotation, and Classification of CRISPR-Cas Loci. The CRISPR Journal, 3, 462–469. doi: 10/gshm
Gao, L., Altae-Tran, H., Böhning, F., Makarova, K. S., Segel, M., Schmid-Burgk, J. L., Koob, J., Wolf, Y. I., Koonin, E. V. and Zhang, F. (2020) Diverse enzymatic activities mediate antiviral immunity in prokaryotes. Science, 369, 1077–1084. doi: 10/gpsx
Makarova, K. S., Timinskas, A., Wolf, Y. I., Gussow, A. B., Siksnys, V., Venclovas, Č. and Koonin, E. V. (2020) Evolutionary and functional classification of the CARF domain superfamily, key sensors in prokaryotic antivirus defense. Nucleic Acids Res, 48, 8828–8847. doi: 10/gg7qx6
Bouchard, J. D., Dion, E., Bissonnette, F. and Moineau, S. (2002) Characterization of the Two-Component Abortive Phage Infection Mechanism AbiT from Lactococcus lactis. Journal of Bacteriology, 184, 6325–6332. doi: 10/btq97w
Parma, D. H., Snyder, M., Sobolevski, S., Nawroz, M., Brody, E. and Gold, L. (1992) The Rex system of bacteriophage lambda: tolerance and altruistic cell death. Genes Dev., 6, 497–510. doi: 10/b9xpsb
Jabbar, M. A. and Snyder, L. (1984) Genetic and physiological studies of an Escherichia coli locus that restricts polynucleotide kinase- and RNA ligase-deficient mutants of bacteriophage T4. Journal of Virology, 51, 522–529. doi: 10/gndc4t
Cram, D., Ray, A. and Skurray, R. (1984) Molecular analysis of F plasmid pif region specifying abortive infection of T7 phage. Mol Gen Genet, 197, 137–142. doi: 10/fg7s8g
Smith, H. S., Pizer, L. I., Pylkas, L. and Lederberg, S. (1969) Abortive Infection of Shigella dysenteriae P2 by T2 Bacteriophage. Journal of Virology, 4, 162–168. doi: 10/gndc4r
Dai, G., Su, P., Allison, G. E., Geller, B. L., Zhu, P., Kim, W. S. and Dunn, N. W. (2001) Molecular Characterization of a New Abortive Infection System (AbiU) from Lactococcus lactisLL51-1. Applied and Environmental Microbiology, 67, 5225–5232. doi: 10/cwbxdg
Lindahl, G., Sironi, G., Bialy, H. and Calendar, R. (1970) Bacteriophage Lambda; Abortive Infection of Bacteria Lysogenic for Phage P2. PNAS, 66, 587–594. doi: 10/fkgq7x
Bergsland, K. J., Kao, C., Yu, Y. T. N., Gulati, R. and Snyder, L. (1990) A site in the T4 bacteriophage major head protein gene that can promote the inhibition of all translation in Escherichia coli. Journal of Molecular Biology, 213, 477–494. doi: 10/fv36tb
Durmaz, E. and Klaenhammer, T. R. (2007) Abortive Phage Resistance Mechanism AbiZ Speeds the Lysis Clock To Cause Premature Lysis of Phage-Infected Lactococcus lactis. Journal of Bacteriology, 189, 1417–1425. doi: 10/dnndhw
Haaber, J., Moineau, S., Fortier, L. C. and Hammer, K. (2008) AbiV, a Novel Antiphage Abortive Infection Mechanism on the Chromosome of Lactococcus lactis subsp. cremoris MG1363. Applied and Environmental Microbiology, 74, 6528–6537. doi: 10/cnwcq7
Emond, E., Dion, E., Walker, S. A., Vedamuthu, E.R., Kondo, J.K. and Moineau, S. (1998) AbiQ, an Abortive Infection Mechanism fromLactococcus lactis. Applied and Environmental Microbiology, 64, 4748–4756. doi: 10/gndc4p
Domingues, S., Chopin, A., Ehrlich, S. D. and Chopin, M. C. (2004) The Lactococcal Abortive Phage Infection System AbiP Prevents both Phage DNA Replication and Temporal Transcription Switch. Journal of Bacteriology, 186, 713–721. doi: 10/bjjwc6
Prevots, F. and Ritzenthaler, P. (1998) Complete Sequence of the New Lactococcal Abortive Phage Resistance Gene abiO. Journal of Dairy Science, 81, 1483–1485. doi: 10/cg69rg
Prévots, F., Tolou, S., Delpech, B., Kaghad, M. and Daloyau, M. (1998) Nucleotide sequence and analysis of the new chromosomal abortive infection gene abiN of Lactococcus lactis subsp. cremoris S114. FEMS Microbiology Letters, 159, 331–336. doi: 10/c94sd6
Deng, Y. M., Liu, C. Q. and W. Dunn, N. (1999) Genetic organization and functional analysis of a novel phage abortive infection system, AbiL, from Lactococcus lactis. Journal of Biotechnology, 67, 135–149. doi: 10/bwc9k8
Emond, E., Holler, B. J., Boucher, I., Vandenbergh, P. A., Vedamuthu, E. R., Kondo, J. K. and Moineau, S. (1997) Phenotypic and genetic characterization of the bacteriophage abortive infection mechanism AbiK from Lactococcus lactis. Applied and Environmental Microbiology, 63, 1274–1283. doi: 10/gndc4n
Deng, Y. M., Harvey, M. L., Liu, C. Q. and Dunn, N. W. (1997) A novel plasmid-encoded phage abortive infection system from Lactococcus lactis biovar. diacetylactis. FEMS Microbiology Letters, 146, 149–154. doi: 10/d24tcq
Su, P., Harvey, M., Im, H. J. and Dunn, N. W. (1997) Isolation, cloning and characterisation of the abiI gene from Lactococcus lactis subsp. lactis M138 encoding abortive phage infection. Journal of Biotechnology, 54, 95–104. doi: 10/ckwmpp
Prévots, F., Daloyau, M., Bonin, O., Dumont, X. and Tolou, S. (1996) Cloning and sequencing of the novel abortive infection gene abiH of Lactococcus lactis ssp. lactis biovar. diacetylactis S94. FEMS Microbiology Letters, 142, 295–299. doi: 10/dvjcb5
O’Connor, L., Coffey, A., Daly, C. and Fitzgerald, G. F. (1996) AbiG, a genotypically novel abortive infection mechanism encoded by plasmid pCI750 of Lactococcus lactis subsp. cremoris UC653. Applied and Environmental Microbiology, 62, 3075–3082. doi: 10/gndc4m
Garvey, P., Fitzgerald, G. F. and Hill, C. (1995) Cloning and DNA sequence analysis of two abortive infection phage resistance determinants from the lactococcal plasmid pNP40. Applied and Environmental Microbiology, 61, 4321–4328. doi: 10/gndc3x
Dy, R. L., Przybilski, R., Semeijn, K., Salmond, G. P. C. and Fineran, P. C. (2014) A widespread bacteriophage abortive infection system functions through a Type IV toxin–antitoxin mechanism. Nucleic Acids Research, 42, 4590–4605. doi: 10/f5zkmw
McLandsborough, L.A., Kolaetis, K. M., Requena, T. and McKay, L. L. (1995) Cloning and characterization of the abortive infection genetic determinant abiD isolated from pBF61 of Lactococcus lactis subsp. lactis KR5. Applied and Environmental Microbiology, 61, 2023–2026. doi: 10/gndc4j
Garvey, P., Fitzgerald, G. F. and Hill, C. (1995) Cloning and DNA sequence analysis of two abortive infection phage resistance determinants from the lactococcal plasmid pNP40. Applied and Environmental Microbiology, 61, 4321–4328. doi: 10/gndc3x
Anba, J., Bidnenko, E., Hillier, A., Ehrlich, D. and Chopin, M. C. (1995) Characterization of the lactococcal abiD1 gene coding for phage abortive infection. Journal of Bacteriology, 177, 3818–3823. doi: 10/gndc3w
Durmaz, E., Higgins, D. L. and Klaenhammer, T. R. (1992) Molecular characterization of a second abortive phage resistance gene present in Lactococcus lactis subsp. lactis ME2. Journal of Bacteriology, 174, 7463–7469. doi: 10/gndc3v
Parreira, R., Ehrlich, S. D. and Chopin, M. C. (1996) Dramatic decay of phage transcripts in lactococcal cells carrying the abortive infection determinant AbiB. Molecular Microbiology, 19, 221–230. doi: 10/b835bf
Cluzel, P. J., Chopin, A., Ehrlich, S. D. and Chopin, M. C. (1991) Phage abortive infection mechanism from Lactococcus lactis subsp. lactis, expression of which is mediated by an Iso-ISS1 element. Applied and Environmental Microbiology, 57, 3547–3551. doi: 10/gndc3t
Dinsmore, P. K. and Klaenhammer, T. R. (1994) Phenotypic Consequences of Altering the Copy Number of abiA, a Gene Responsible for Aborting Bacteriophage Infections in Lactococcus lactis. Applied and Environmental Microbiology, 60, 1129–1136. doi: 10/gndc3s
Owen, S. V., Wenner, N., Dulberger, C. L., Rodwell, E. V., Bowers-Barnard, A., Quinones-Olvera, N., Rigden, D. J., Rubin, E. J., Garner, E. C., Baym, M., et al. (2021) Prophages encode phage-defense systems with cognate self-immunity. Cell Host & Microbe, 29, 1620-1633. doi: 10/g29b
Bari, S. M. N., Chou-Zheng, L., Howell, O., Cater, K., Dandu, V. S., Thomas, A., Aslan, B., and Hatoum-Aslan, A. (2021). A unique mode of nucleic acid immunity performed by a single multifunctional enzyme. bioRxiv. doi: 10/gkw6wr
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Mestre, M. R., González-Delgado, A., Gutiérrez-Rus, L. I., Martínez-Abarca, F., and Toro, N. (2020). Systematic prediction of genes functionally associated with bacterial retrons and classification of the encoded tripartite systems. Nucleic Acids Research, 48, 12632–12647. doi: 10/fzk3
Millman, A., Bernheim, A., Stokar-Avihail, A., Fedorenko, T., Voichek, M., Leavitt, A., Oppenheimer-Shaanan, Y., and Sorek, R. (2020). Bacterial Retrons Function In Anti-Phage Defense. Cell, 183, 1551-1561.e12. doi: 10/ghjct3
Bernheim, A., Millman, A., Ofir, G., Meitav, G., Avraham, C., Shomar, H., Rosenberg, M. M., Tal, N., Melamed, S., Amitai, G., et al. (2021). Prokaryotic viperins produce diverse antiviral molecules. Nature, 589, 120–124. doi: 10/d9ss
Goldfarb, T., Sberro, H., Weinstock, E., Cohen, O., Doron, S., Charpak‐Amikam, Y., Afik, S., Ofir, G., and Sorek, R. (2015). BREX is a novel phage resistance system widespread in microbial genomes. EMBO J, 34, 169–183. doi: 10/f2wkj3
Ofir, G., Melamed, S., Sberro, H., Mukamel, Z., Silverman, S., Yaakov, G., Doron, S., and Sorek, R. (2018). DISARM is a widespread bacterial defence system with broad anti-phage activities. Nat Microbiol, 3, 90–98. doi: 10/ggnszb
Yuan, Y., Hutinet, G., Valera, J. G., Hu, J., Hillebrand, R., Gustafson, A., Iwata-Reuyl, D., Dedon, P. C., and de Crécy-Lagard, V. (2018). Identification of the minimal bacterial 2′-deoxy-7-amido-7-deazaguanine synthesis machinery. Molecular Microbiology, 110, 469–483. doi: 10/gfft6b
Thiaville, J. J., Kellner, S. M., Yuan, Y., Hutinet, G., Thiaville, P. C., Jumpathong, W., Mohapatra, S., Brochier-Armanet, C., Letarov, A. V., Hillebrand, R., et al. (2016). Novel genomic island modifies DNA with 7-deazaguanine derivatives. Proc Natl Acad Sci USA, 113, E1452–E1459. doi: 10/ggr4f7
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The relevant refences for individual HMMs can be found by inspecting the hmm_meta.txt file provided with PADLOC-DB.
This software and data is available as open source under the terms of the MIT License.