mobileOG-db (for mobile orthologous groups) is a manually curated database of protein families mediating the integration/excision, replication/recombination/repair, stability/defense, or transfer of bacterial mobile genetic elements and phages as well as the associated transcriptional regulators of these processes. mobileOG-db was created in a process involving more than 15,000 unique manual curation events, with 1,558 references and 2,444 unique manual functional annotations at present.
Thanks to Dr. Jason Grant for his work getting mobileOG-db available on https://proksee.ca/
Try mobileOG-pl, a pipeline to detect and categorize bacterial mobile genetic elements from contigs or long reads.
https://github.com/clb21565/mobileOG-db/blob/main/mobileOG-pl/UsageGuidance.md
The current version of the database can be browsed accessed through its website: https://mobileogdb.flsi.cloud.vt.edu/
[email protected], [email protected]
Brown CL, Mullet J, Hindi F, Stoll JE, Gupta S, Choi M, Keenum I, Vikesland P, Pruden A, Zhang L. mobileOG-db: a Manually Curated Database of Protein Families Mediating the Life Cycle of Bacterial Mobile Genetic Elements. Appl Environ Microbiol. 2022 Aug 29:e0099122. doi: 10.1128/aem.00991-22. Epub ahead of print. PMID: 36036594.
To create mobileOG-db, we analyzed 10,776,212 proteins derived from 8 different databases of complete MGE sequences. The references to these databases are below.
1. ICEBerg (ICEs, AICEs, CIMEs, IMEs):
Meng Liu, Xiaobin Li, Yingzhou Xie, Dexi Bi, Jingyong Sun, Jun Li, Cui Tai, Zixin Deng, Hong-Yu Ou, ICEberg 2.0: an updated database of bacterial integrative and conjugative elements, Nucleic Acids Research, Volume 47, Issue D1, 08 January 2019, Pages D660–D665, https://doi.org/10.1093/nar/gky1123
2. ACLAME (various):
Leplae R, Lima-Mendez G, Toussaint A. ACLAME: a CLAssification of Mobile genetic Elements, update 2010. Nucleic Acids Res. 2010 Jan;38(Database issue):D57-61. doi: 10.1093/nar/gkp938. Epub 2009 Nov 23. PMID: 19933762; PMCID: PMC2808911.
3. GutPhage Database (Bacteriophages derived from human gut metagenomes):
Camarillo-Guerrero LF, Almeida A, Rangel-Pineros G, Finn RD, Lawley TD. Massive expansion of human gut bacteriophage diversity. Cell. 2021 Feb 18;184(4):1098-1109.e9. doi: 10.1016/j.cell.2021.01.029. PMID: 33606979; PMCID: PMC7895897.
4. Prokaryotic viral orthologous groups (pVOG) (a collection of prokaryotic virus protein HMMs):
Grazziotin AL, Koonin EV, Kristensen DM. Prokaryotic Virus Orthologous Groups (pVOGs): a resource for comparative genomics and protein family annotation. Nucleic Acids Res. 2017;45(D1):D491-D498. doi:10.1093/nar/gkw975
5. COMPASS (plasmids):
Douarre PE, Mallet L, Radomski N, Felten A, Mistou MY. Analysis of COMPASS, a New Comprehensive Plasmid Database Revealed Prevalence of Multireplicon and Extensive Diversity of IncF Plasmids. Front Microbiol. 2020;11:483. Published 2020 Mar 24. doi:10.3389/fmicb.2020.00483
6. NCBI Plasmid RefSeq (plasmids):
O'Leary NA, Wright MW, Brister JR, et al. Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. Nucleic Acids Res. 2016;44(D1):D733-D745. doi:10.1093/nar/gkv1189
7. immedb (integrative elements):
Jiang,X., Hall,A.B., Xavier,R.J. and Alm,E.J. (2019) Comprehensive analysis of chromosomal mobile genetic elements in the gut microbiome reveals phylum-level niche-adaptive gene pools. PLoS One, 14, e0223680.
8. ISfinder (insertion sequences):
Siguier P, Perochon J, Lestrade L, Mahillon J, Chandler M. ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D32-6. doi: 10.1093/nar/gkj014. PMID: 16381877; PMCID: PMC1347377.