Added O1 sub-typing logic

klebgenomics · Dec 1, 2023 · b533b2e · b533b2e
1 parent 4aca18d
commit b533b2e
Show file tree

Hide file tree

Showing 2 changed files with 74 additions and 7 deletions.
diff --git a/reference_database/Klebsiella_o_locus_primary_reference.gbk b/reference_database/Klebsiella_o_locus_primary_reference.gbk
@@ -4973,4 +4973,65 @@ ORIGIN
      2101 caatacatca acatcatacc ccttttttgc caaagtagtg gcaagagcag tgaaagcagt
      2161 accgataccg ccgttacgga caggcccctc aatgtccggc gtcattataa gaattttctt
      2221 cat
+//
+LOCUS       UGMM01000004             810 bp    DNA              UNK 01-JAN-1980
+DEFINITION  Klebsiella pneumoniae strain NCTC11682 genome assembly, contig:
+            ERS670329SCcontig000004, whole genome shotgun sequence.
+ACCESSION   UGMM01000004
+VERSION     UGMM01000004.1  GI:1440143122
+DBLINK      BioProject: PRJEB6403
+            BioSample: SAMEA3282963
+KEYWORDS    WGS.
+SOURCE      Klebsiella pneumoniae
+  ORGANISM  Klebsiella pneumoniae
+            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
+            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
+REFERENCE   1
+  AUTHORS   Doyle,S.
+  CONSRTM   Pathogen Informatics
+  TITLE     Direct Submission
+  JOURNAL   Submitted (06-JUN-2018) WTSI, Pathogen Informatics, Wellcome Trust
+            Sanger Institute, CB10 1SA, United Kingdom
+FEATURES             Location/Qualifiers
+     source          1..3130
+                     /organism="Klebsiella pneumoniae"
+                     /mol_type="genomic DNA"
+                     /strain="NCTC11682"
+                     /serovar="not available: to be reported later"
+                     /db_xref="taxon:573"
+                     /note="contig: ERS670329SCcontig000004"
+                     /note="Extra genes: wbbZ"
+                     /note="Sequence edited to trim wbbZ only, Tom Stanton
+                     December 2023"
+     gene            complement(1..810)
+                     /locus_tag="NCTC11682_05451"
+     CDS             complement(1..810)
+                     /inference="ab initio prediction:Prodigal:2.60"
+                     /codon_start=1
+                     /transl_table=11
+                     /product="Exopolysaccharide biosynthesis protein"
+                     /protein_id="STV47229.1"
+                     /db_xref="GI:1440147897"
+                     /translation="MTNMKLKFDLLLKSYHLSHRFVYKANPGNAGDGVIASATYDFFER
+                     NALTYIPYRDGERYSSETDILIFGGGGNLIEGLYSEGHDFIQNNIGKFHKVIIMPSTIR
+                     GYSDLFINNIDKFVVFCRENITFDYIKSLNYEPNKNVFITDDMAFYLDLNKYLSLKPIY
+                     KKQANCFRTDSESLTGDYKENNHDISLTWNGDYWDNEFLARNSTRCMINFLEEYKVVNT
+                     DRLHVAILASLLGKEVNFYPNSYYKNEAVYNYSLFNRYPKTCFITAS"
+                     /gene="wbbZ"
+                     /locus_tag="Extra_genes_wbbZ_01_wbbZ"
+ORIGIN
+        1 tcaacttgcc gtaataaagc atgtttttgg ataacgatta aaaagtgaat aattgtaaac
+       61 agcttcattt ttgtaatatg agttaggata gaagttgact tctttgccaa gcagagatgc
+      121 taaaattgcc acatgcagcc tgtcggtatt gacaacttta tactcttcaa gaaagtttat
+      181 catgcaacgg gtagaattac gcgccagaaa ttcattatcc caataatcgc cattccaggt
+      241 gagcgaaata tcatgattgt tttctttata gtctccagtt agagattcgg agtccgttct
+      301 gaagcagttg gcctgttttt tatagatggg tttaagtgac aggtatttat taagatcgag
+      361 ataaaatgcc atatcatcag taatgaatac gttcttgttt ggttcgtagt tgagagattt
+      421 aatataatcg aaggtgatat tttcgcgaca aaaaacaaca aacttatcaa tattgttgat
+      481 gaataaatcg ctataccctc tgattgtcga cggcattatt attactttat gaaacttccc
+      541 aatattattc tggataaagt catgaccttc agaatacaat ccttctatca ggtttcctcc
+      601 gcctccaaaa attaaaatat cagtttcaga actgtagcgc tcgccatctc tgtaagggat
+      661 ataggtaaga gcatttcgtt caaaaaagtc atatgtcgca gatgcaatta caccatcacc
+      721 agcattacca gggtttgcct tatagacaaa tcgatgagat agatgataag attttagaag
+      781 caaatcaaat tttaacttca tattggtcat
 //
diff --git a/reference_database/Klebsiella_o_locus_primary_reference.logic b/reference_database/Klebsiella_o_locus_primary_reference.logic
@@ -3,9 +3,9 @@ O1/O2v1	None	O2a
 O1/O2v2	None	O2afg
 O1/O2v3	None	O2a
 O8	None	O2a
-O1/O2v1	wbbY	O1
-O1/O2v2	wbbY	O1
-O1/O2v3	wbbY	O1
+O1/O2v1	wbbY	O1a
+O1/O2v2	wbbY	O1a
+O1/O2v3	wbbY	O1a
 O8	wbbY	O8
 O1/O2v1	wbmVW	O2ac
 O1/O2v2	wbmVW	O2ac
@@ -15,7 +15,13 @@ O1/O2v1	gmlABD	O2aeh
 O1/O2v2	gmlABD	O2aeh
 O1/O2v3	gmlABD	O2aeh
 O8	gmlABD	O2aeh
-O1/O2v1	wbbY,wbmVW	O1 (O2ac)
-O1/O2v2	wbbY,wbmVW	O1 (O2ac)
-O1/O2v3	wbbY,wbmVW	O1 (O2ac)
-O8	wbbY,wbmVW	O1 (O2ac)
+O1/O2v1	wbbY,wbmVW	O1a (O2ac)
+O1/O2v2	wbbY,wbmVW	O1a (O2ac)
+O1/O2v3	wbbY,wbmVW	O1a (O2ac)
+O8	wbbY,wbmVW	O1a (O2ac)
+O1/O2v1	wbbY,wbbZ	O1ab
+O1/O2v2	wbbY,wbbZ	O1ab
+O1/O2v3	wbbY,wbbZ	O1ab
+O1/O2v1	wbbY,wbbZ,wbmVW	O1ab (O2ac)
+O1/O2v2	wbbY,wbbZ,wbmVW	O1ab (O2ac)
+O1/O2v3	wbbY,wbbZ,wbmVW	O1ab (O2ac)