BMC Caller Help

Overview

BMC Caller can be used to assign the type and inventory the contents of Bacterial Microcompartment loci from protein sequences (link to paper describing BMC Caller). For general information on Bacterial Microcompartments (BMCs) see Wikipedia (link) or a recent review (link).

Use

There are two modes for BMC Caller, 1) analysis of BMC protein components (includes the shell, the core enzymes and any other conserved loci-associated proteins) and 2) a BMC shell protein-only mode.

Input: Both modes accept multi-FASTA files as input with a first line marked by ">" followed by the sequence identifier and the following line(s) containing the protein sequence (with no terminator character) and subsequent sequences starting again with a new line and ">" followed by sequence identifier. Also see example link on submission page for a sample input.

For BMC locus analysis:

The order of the sequences should represent the order of the genes from the genome for optimal BMC type assignment but is not needed to identify the individual components. Generally a range of +/- 12 genes from any shell protein gene contains the whole BMC locus and is optimal for BMC type assignment.

For BMC shell protein analysis:

Whole proteomes can be used as input, only shell proteins will be displayed as output. This is a good way to find the best input sequences for BMC locus analysis and might already properly identify all the BMC loci in the proteome/genome.

The following genome / proteome databases can be used as sources of multi-FASTA files:

JGI IMG/M : search for the target genome, download the .faa file and then use the BMC shell protein analysis to find BMC locus sites and/or copy-paste the desired protein sequences for BMC locus analysis.

Uniprot Proteomes: search for genome, then download all entries in uncompressed "FASTA (canonical)" format. BMC locus sites can be identified with the BMC shell protein analysis tool or searching the FASTA file with relevant terms like "microcompartment" or "carboxysome".

NCBI taxonomy: search for the desired organism and follow the links to organism details; click on the Protein/Direct links number in red. Click the "Sent to:" button and choose FASTA format and default order.

Examples
For examples, use the example link above the input field or copy-paste the input from examples below:
locus analysis example, copy and paste
proteome shell protein example, copy and paste

BMC type abbreviations

Abbreviation	Description	Comments / Alternate Nomenclature / Updates
ACI	Acidobacterium microcompartment
ARO	Aromatic substrate microcompartment
BUF	Bacterial microcompartment of unknown function (and no AldDh)	BUF1 is also known as Xau / Xanthine utilization (link)
CsomeACh	Alpha-carboxysome of chemoautotroph bacteria
CsomeACy	Alpha-carboxysome of cyanobacteria
CsomeBCy	Beta-carboxysome of cyanobacteria
ETU	Ethanol utilizing microcompartment
EUT	Ethanolamine utilizing microcompartment
EUT2x	EUT BMC, missing signature enzyme
FRAG	Fragmented type microcompartment
GRM	Glycyl radical enzyme containing microcompartment	GRM1/2 process choline, and are also known as Cut BMCs, GRM 3/4/6 process propanediol, GRM5 fucose/rhamnose
GRM5like	GRM5 BMC with missing signature enzyme
GRMguf	GRM BMC with glycyl radical enzyme of unknown function	A function of the glycyl radical enzyme has recently proposed as isethionate C-S bond cleavage (link)
HO	BMCs related to Haliangium ochraceum model BMC locus
MIC	Metabolosome loci where the majority of loci do not encode an AlcDH and/or PTAC (incomplete core)
MUF	Metabolosome microcompartment of unknown function
PDU	Propanediol utilization microcompartment
PVM	Planctomycete and Verrucomicrobia microcompartment
PVMlike	Microcompartment with similar enzyme complement as PVM
RMM	Rhodococcus and Mycobacteria microcompartment	RMM are also known as AAUM for aminoacetone utilizing microcompartment (link)
SPU	Sugar phosphate utilization microcompartment