This is the official repository of the Biosynthetic Gene Cluster Library, a Python library with classes and methods for manipulation and analysis of BGCs.
For more information on BGClib, see here.
This is a tool that facilitates domain annotation of protein data from GenBank and fasta files. For this, it harnesses the capabilities of BGClib.
- Annotate domains
- Generate high quality SVG files
Additionally, if you are working with biosynthetic gene clusters, you can:
- Use antiSMASH results as input to label proteins as core biosynthetic proteins (CBPs)
- Extract protein (sub)sequences of CBPs
- Print metadata of the files per BGC and CBP (e.g. protein id, CBP content, internal CBP identifiers)
And finally, if you're working with fungal biosynthetic gene clusters in particular, you also can:
- Classify some CBPs into more specific types using included hmm models (e.g. T1PKS -> reducing/non-reducing PKS)
Other features:
- GenBank, fasta and binary 1 input
- Input filters (default values tailored for antiSMASH output; based on file/BGC name)
- Domain annotation using multiple hmm libraries.
- Save as binary files 1
Installation of the required libraries to make BGClib work through (mini)conda is recommended. Here's a list of what you'll need. Version in parenthesis is the one that is known to work, but newer versions should work as well.
- biopython (1.78)
- hmmer (3.3.2)
- lxml (4.5.0)
Please see the BGCtoolkit wiki for the documentation
A quick overview of results using the example output from fungiSMASH (on Aspergillus fumigatus Af293).
BGGtoolkit can produce metadata from all the input files, such as:
Metadata at BGC level (BGC Metadata):
| BGC | antiSMASH products | Core Biosynthetic Protein content | Core Biosynthetic Protein IDs | Core Biosynthetic Protein Identifiers | Metabolites |
|---|---|---|---|---|---|
| CM000169.1.region001 | T1PKS | rPKS | EAL87813.1 | CM000169.1.region001~L0+CDS7 | |
| CM000169.1.region002 | NRPS | NRPS | EAL90366.1 | CM000169.1.region002~L0+CDS8 | |
| CM000169.1.region003 | terpene | ||||
| CM000169.1.region004 | betalactone | NRPS-like | EAL90832.1 | CM000169.1.region004~L0+CDS5 |
Metadata at CBP level (CBP Metadata):
| BGC | Core Biosynthetic Protein type | Protein identifier | Protein Id | Gene Id | Domain architecture |
|---|---|---|---|---|---|
| CM000169.1.region001 | rPKS | CM000169.1.region001~L0+CDS7 | EAL87813.1 | KS | KS_C | KS_Ce | AT | DH | CMeT | KR | T/ACP > |
|
| CM000169.1.region002 | NRPS | CM000169.1.region002~L0+CDS8 | EAL90366.1 | A | T/ACP | C | C | A | C | A | T/ACP | C | A | T/ACP | C | C | T/ACP | C | T/ACP > |
|
| CM000169.1.region004 | NRPS-like | CM000169.1.region004~L0+CDS5 | EAL90832.1 | DMAP_binding | A | A > |
|
| CM000169.1.region005 | NRPS-like | CM000169.1.region005~L0+CDS9 | EAL91049.1 | A | A_C > |
Also, a summary of all the regions found, and their CBP compositions:
AfumigatusAf293 summary file
This collection contains
* 37 BGCs
* 0 Proteins
Core Biosynthetic Composition count (BGCs):
7 NRPS
6 NRPS-like
5 rPKS
...
fungiSMASH results report a 80% similarity between region CM000175.1.region001 and neosartoricin B (cluster BGC00001144 in MIBiG). Here's a comparison of both regions (top: MIBiG entry; bottom, CM000175.1.region001):
Here, colored boxes represent genomic regions that will code for predicted domains. Introns are drawn by default.
Finally, the sequences of all detected KS domains (and their metadata) can be extracted:
>CM000170.1.region002~L0+CDS9_KS1 ProteinId:EAL94057.1 GeneId:
SKIAIIGMSGRFPEADGIEAFWDLLYKGLDVHKKVPPERWDVDAHVDLTGTKRNTSKVPYGCWINEPGLFDARFFNMSPR
EALQADPAQRLALLSAYEALEMAGFVPNSSPSTQRDRVGIFMGMTSDDYREINSGQDIDTYFIPGGNRAFTPGRINYYFK
FSGPSVSVDTACSSSLAAIHLACNAIWRNDCDTAISGGVNLLTNPDNHAGLDRGHFLSRTGNCNTFDDGADGYCRADGVG
TIVLKRLEDA
>CM000169.1.region006~L0+CDS6_KS1 ProteinId:EAL91103.2 GeneId:
PFNLDRFYHPTGSHHGTTNIRQAYLLSEDVRAFDAKFFSVPPGDAEAIDPQQRLLLEVTYEALESSGHTLADLSNSNTGA
FVGLMSQDYFALNGQDVDSVPTYAASGTAASNASSRLSYFFNWHGPSMAIDTACSSNLVAVNEAVQALRNGTSRVAVACG
TNLCLSAFTFITLSKLSMLSPTSRCHMWDADADGYARGEGVACVVLKTLSDA
>CM000171.1.region002~L0+CDS2_KS1 ProteinId:EAL86536.1 GeneId:
PIAVVGMGMRLPGGVRTVDDFWDALISQKDCSSEVPQTRYNIDAFYHPDKPQSVRTRRGYFLEDDCLQKADTNFLQWIPG
FSTSELDPQQRLLLEVIWECMENAGQTGWRGKDIGCYVGVFGEDWHELTAKESQMIPRTHAFANGGFALSNRVSFEFDLK
GPSLTIATACSSSLSALHEACQALQTGSCSSAIVAGTNMLLTPSMSVTMSENMVLSPDGLCKTFDADANGYARGEAVNAV
YIKTLDKA
...
This can be useful for making phylogenetic studies of the CBPs (sub)sequences, which can include characterized data (e.g. from MIBiG) in order to to study evolution and de-replicate BGCs for prioritization.