Pseudomonas sp. 273 annotation
Robert W. Murdoch
December 3, 2018
Annotation overview
Pseudomonas sp. 273 was sequenced via PacBio and a completed 1 contig genome was provided by an external company.
You will receive:
- A zipped file containing the annotated genome in a wide variety of formats (genes, proteins, gbk, gff, etc). The genes/proteins are annotated by the prokka system here.
- A table with rich annotations from KO, GO, COG/eggNOG systems (generation and contents described below)
The general strategy is to:
- Annotate by a standard Prokka application (v. 1.13.3). Prokka calls genes using Prodigal and annotates using a database based on UniProt.
- present summary statistics of the detected genes
- Take the list of proteins (*.faa) file and annotate via EggNOG-mapper (http://eggnogdb.embl.de/app/emapper#/app/home), which provides KO and COG annotations
Annotation summary (gene count and stats)
library(Biostrings)
library(reshape2)
P273.prokka.biostring <- readAAStringSet("PROKKA_12032018/PROKKA_12032018.faa")
name <- as.character(names(P273.prokka.biostring))
sequence <- paste(P273.prokka.biostring)
length <- width(P273.prokka.biostring)
P273.prokka <- data.frame(name, length, sequence, stringsAsFactors = F)
name.split <- colsplit(P273.prokka$name, " ", c("locus","prokka_function"))
P273.prokka <- cbind(name.split,P273.prokka[-1])
cat("### Subset of the anotations")Subset of the anotations
kable(head(P273.prokka))| locus | prokka_function | length | sequence |
|---|---|---|---|
| P273_00001 | DNase CdiA | 1899 | MNNNGTLGALGALDLTSQGIANGADSLLFSGGDMTLRAASLSNRYGDLYSQGNLSFAGQDGGRAQSLSNRSGTIEAQGDIHLDVANLENTRDVFAFEQTTTFGEFDVQCGQHCGGHDSFKRGKIDVSETIEERITQNSPAAWLTAGGNLSIDADAVENRNSTIAANGDLTINANSLLNQGNTSRTGNKVVVINVVPGDYGKIPTGQWDAMENLARAFNNKMAAGTFDQDLYDQLWAIYNGDRWAIGTPVVSWSEDGAQSAPATLQAGNRVTLNVAHNLQNGTVSEYSQAQLTGQLAGSLLGGQLGTVNLTLNKQSSDAQARGPQTVQSVTHTAADGSQQVSFIPVDYTGVPFAAVDPTAADTFRLPQGQYGMFIRSPDPQSHYLIETNPALTDLGRFLNSDYLLGKLGFDPDQAWKRLGDGAYETRLIREAIQAQTGQRFLDGLTSDYDQFQYLMDNALAAKDALQLSVGVGLSAEQVAALTHDIVWMETRVVDGQQVLVPVVYLAQTDARNLRGGSLIQGRDLNLMAGGDLTNVGTLRASEDLTATAGGSILQGGLVDAGQRVSLLAGDSIRNALAGQIRGDQVDLTALKGDIVNDRTAVTAGIGGDEYRSFLDAGASISARSELSLDAGRDITNRGSLASGGDSYLGAGRDINLQAVTDASRLRDIQQGGHHVTTTTVAQNHGSSLTAGGDLVLDAGRDLNVVGSQASAKGDLTAAAGRDINLRAVEDAASVEVRSKTSSTRTVEQTGQTRQLGAQLTAGGDLVASAGQDLNLTASTISASNEAYLYATRDVNLQAAAETDSHALSKTKRSHGLLSSSEKKTEDTSLYTTQQGSLVSADKVAIRAGQDIGVSGSDVASTNGTSLLAGRNVLIDGATETSETSHAESKKKSGVMSSGGLGFTLGSASTQATQTNHNEQTRGSTIGSVLGNVDIQAGKDLTIRGSDVVAGKDINLIGQNVDILAAQNENRSEQTYKSKTSGLTLALSGSVGSAMDSGYQTAKQAKHEDDSRLSALQGIKAGLTGVQAWQAAQQGTEGGGVSQFFGISASLGSQKSSSKQTQEQSVSQGSSLTAGNNLNILATGAGKVGQDGDIRIQGSQLKAGNDVLLAANRDITLEAAANTQKLDGKNKSSGGAVGVSVGYSADNGVGLSIFANANQGSGKEVGTGTTWTETTLDAGNQVKLVSGRDTTLKGAQVNGEQIIANVGRDLTLQSLQDSDYYDSKQKNVSAGASVAIIGTGGSASVSASQSKIDSNYKSVQEQTGLYAGKGGFQIDVGNHTQLDGSVIASTAEAEKNRLSTGTLGWSSIDNKADYKSQQQSVSLSSGSDGSGKFISNMPSGMLVAYNHGDSASGTTGSAISSGTLEIRDPASQQQDVASLSRDVEHANGSISPIFDKEKEQNRLKQVQLIAEIGTQAMDIVRTQGEIEAAEEGRKELKTQGKDNPTQKELEATVAYQNVMREYGTGSDYQRAAQAVTAALQYLAGGDIGGAIAGASAPYIAHLIKQQTGDNDTARIMAQALLGAVVAGVQGNSSVAGGIGAATGELIAANLYPGKKPEDLTENERQIVSALSSLAAGMAGGLASGDTAGAVAAAGAGKTAVDNNFLSGDQAKAFDHEMQQCTKEGDCTKVIKKYVALNDENRELLKATCSEKPWVCYGNSRDFVLTGLNSADPSRPVSSGGIENDNVRLFVQYENSLDLQYINKNTDTLYKALVFASEPENFMLMFGGLANLTNASGTSIATGAGLSMAANGGVQLATGSTGDKFDWIGFMTSGVTGGMSAGQTLTPTLQTNIGGAYISSQLNGQSSLDAMMGAMIGASLGYGAGATITSQMEKNYVNKIFGLSRNSVNALKYSEAANFPGSYLLKETPMSPIPGILGGATGSVVSESSNNAVLNGANNGK |
| P273_00002 | RNA 2’-phosphotransferase | 182 | MDTKLLNETSKFLSYVLRHEPQAIGLQLDSEGWANINALIAGAAKKGKNLDSEIIQKVVASSDKKRFSISSDGQRIRAVQGHSTPTVTLQHTEKEPPELLYHGTASRFLDSIKTQGLIPGARHYVHLSQDEQTAVEVGKRYGKPVILKIEALRMHRQGFKFFQAENGVWLADKIPANFILTE |
| P273_00003 | hypothetical protein | 70 | MMRPDAKVKAVYLYPKPVDFRKSIDGLAALVELDIKVAVFDPVLFVFLERGLLYFSYSKADHSGRIRVLK |
| P273_00004 | hypothetical protein | 93 | MATHNVVLPQPMEKSIDDLVSEGRYQNFSEVVRAGLRLLLEREAEESAKLVALRNATSSGIMQLETGRFVEIASEAQLEKYLGELGQLASSRQ |
| P273_00005 | hypothetical protein | 121 | MSDPQFRLSLDAQTDLIDILRFTQVKFGEDVRRRYQGLLRAAFVSLSAESERAGSIAREQLETGLRSLHLLYCRSEAPNGRVDRPRHVVFYRLGHDQVIEIVRILHDAMEVERHLQKVPAG |
| P273_00006 | Putative lipoprotein/NMB1164 | 225 | MKMSQGLLLGVASAALLMVGGCATESSRALPVQQVESVGKPYSGVRSPIAVGKFDNRSSYMRGIFSDGVDRLGGQAKTILITHLQQTNRFNVLDRDNMSEIQQEAAIKGQAQRLKGADYVVTGDVTEFGRKEVGDRQLFGILGRGKTQVAYAKVALNIVNISTSEVVYSTQGAGEYELSNREIIGFGGTASYDSTLNGKVLDLAMREAVNKLVNAVDSGSWNPAR |
There are 6754 protein-encoding genes detected
Median gene length is 275 amino acids.
Adding annotations from EggNOG
The protein sequences were annotated via the EggNOG database. EggNOG provides links to several databases. Importing and adding the annotations to the annotation table and attaching to the annotation table:
eggnog.full <- read.csv("PROKKA_12032018.faa.emapper.annotations", sep = "\t", header = F, stringsAsFactors = FALSE)
colnames(eggnog.full) <- c("locus","Seed.Ortholo","evalue","score","Predicted.name","GO.terms","KEGG.KO","BiGG.reactions","tax.scope","eggNOG.OGs","best.OG","COG.Cat.","eggNOG.HMM.Desc.")
eggnog <- eggnog.full[c(1,6,7,10,13)]
library(dplyr)
P273.prokka.eggnog <- dplyr::left_join(P273.prokka, eggnog, by="locus")We now have, for each gene, annotations from:
- prokka (uniprot)
- KO
- GO
- COG/NOG
The last addition is to translate the KO terms into protein function descriptions
library(dplyr)
KO.to.name <- read.csv("../KO.to.name.map.csv", header = T, stringsAsFactors = F)
colnames(KO.to.name)[1] = "KEGG.KO"
P273.prokka.eggnog.KO <- dplyr::left_join(P273.prokka.eggnog, KO.to.name, by = "KEGG.KO")
P273.prokka.eggnog.KO <- P273.prokka.eggnog.KO[c(1,3,2,6,9,8,7,5,4)]
write.csv(P273.prokka.eggnog.KO, "P273.full.annotations.csv")
cat("# Full annotation is provided in csv and xlsx formats under the name P273.full.annotations")Full annotation is provided in csv and xlsx formats under the name P273.full.annotations
This table now contains clean sorted information from many different databases along with the actual protein sequence.
Annotation table summary
Column names and descriptions:
- locus; gene locus tag, found at beginning of gene and protein names
- length; protein length (not nucleotide)
- prokka_function; name assigned by prokka program, broadly from the uniprot database. These are usually less informative than other systems.
- KEGG.KO; KEGG orthology family name. Can be uploaded (one or many) at https://www.genome.jp/kegg/tool/map_pathway1.html to map to pathways
- KEGG.name; name/function associated with the KO.
- eggNOG.HMM.Desc; this is a name assigned by the eggNOG system
- eggNOG.OGs; these are Orthology Groups in the eggNOG system, groups of related proteins assigned a function
- GO.terms; orthology groups from the Gene Ontology system (another database)
- sequence; the protein sequence