MicroScope Platform Overview
- Overview of the annotation editor
- Annotation Rules
- BLAST results
- Compositional features
- E. coli K12
- B. subtilis
- MaGe/Curated annotations
- Syntonome / Syntonome RefSeq
- Similarities SwissProt / TrEMBL
- Predicted MetaCyc Pathways
MicroScope - Tutorial » MaGe » Gene Annotation Editor » HAMAP
What is HAMAP ?
HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes) is a system, based on manual protein annotation, that identifies and semi-automatically annotates proteins that are part of well-conserved families or subfamilies: the HAMAP families. HAMAP is based on manually created family rules and is applied to bacterial, archaeal and plastid-encoded proteins.
HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot. Lima T et al (2009) Nucleic Acids Res. 2009 Jan;37(Database issue):D471-8.
How to read HAMAP results
This section is filled in when the sequence can be linked to a HAMAP family. The corresponding HAMAP family identifier is given in the first column. If you click on it, it will open a new window on the HAMAP website, giving you a full description of the family.
The evidence column gives an indication about the strength of the hit. The value can be:
The following columns give a description of the HAMAP family with the gene name (if any), the product description, the EC number (if any). The comments column can give you some insight into the corresponding function or the subcellular location of the protein. The last column describes a list of keywords related to the function of the HAMAP family.