K-PAM: Klebsiella species serotype predictor and surface antigens modeler

... An In silico Diagnostic Tool



Serotype predictor

Capsular polysaccharides and lipopolysaccharides are major virulence factors in Klebsiella species. Multidrug-resistant infections by Klebsiella have been increasingly reported and hence, strain typing is important to identify clonal groups which would aid in epidemiological investigations. Pulsed-field gel electrophoresis (PFGE), capsular polysaccharide characterization, and multilocus sequence typing (MLST) have been employed to characterize Klebsiella isolates. Traditionally, tube agglutination has been used for O-typing. To overcome the limitations of traditional typing methods, PCR genotyping has been adopted to identify serotypes.
A FASTA database has been constructed for serotype prediction using makeblastdb command line tool. The gene/protein sequences with known serotypes (K- and O-antigens) were retrieved from NCBI database along with different variants of each gene, with each variant being compared with sequences from reference strains.The local database is prepared with wzi, wza, wzb, wzc, wzx, wzy, wbap, wcaj, wzm and wzt protein coding gene sequences along with their respective protein sequences.



Schematic representation of proteins involved in the biosynthesis and export of O and K antigens respectively.



Note: Before submitting the input sequences, visit "Input for K-antigen typing" part of Serotype Prediction division in Documentation subpage as K-PAM follows certain format for input sequences for serotype prediction.







Examples for using the serotype prediction forms

[Click the submit button to see the output. To try/submit new job, use the required form given above.]

Example 1. for K-type prediction with multiple coding regions in the query.
Note that in the form NCBI genbank ID is given for the query sequence, the option "all" is chosen from the gene list and "Protein-Protein(PP)" option is chosen from input type. Here the NCBI genbank ID is used to retrieve all the coding sequences stored against the genbank ID in FASTA protein format and process further in the local machine for the prediction. If "DNA-DNA(NN)" or "DNA-Protein(NP)" option would be chosen, then the coding sequence in FASTA nucleotide format would be retrieved from the NCBI webserver.



LT174536.1

Select gene: Select input type:


Example 2. K-type prediction with single gene (wzi) query sequence and the input query sequence is manually given at the place assigned (in FASTA format).
Note that in the form the wzi nucleotide sequence is given as input, the option "Wzi" is chosen from the gene list and "DNA-DNA(NN)" option is chosen from input type. The input sequence is obtained from NCBI web server. Similarly, protein sequence can also be submitted by choosing "Protein-Protein(PP)" option from input type list. Genpept genbank ID can also be submitted through the "NCBI Genbank ID" option along with gene type "Wzi" and input type "Protein-Protein(PP)".



Type or paste your FASTA sequence:

>AB371296.1:2798-4312 Klebsiella pneumoniae capsule polysaccharide synthesis gene cluster, complete cds, strain: VGH525 GTGCCGCGAGCGCTTTCTATCTTGGTATTCCCCTCATTCTCATTGAGATACGACAGCGGGGCTGAAAATG GATCTTGTACAATGATAAAAATTGCGCGCATTGCCGTGACGTTGGGTTTGCTTTCCTCCCTGGGAGCCCA GGCTTACGCGGCCGGGTTAGTGGTAAATGACAACGACTTGCGTAACGACCTGGCCTGGCTTTCCGATCGC GGGGTCATCCATCTGAGCCTGTCGACCTGGCCGCTGAGCCAGGAAGAGATCTCCCGGGCGCTAAAAAAGG CCAAACCGTCCTATTCTTCTGAACAAGTGGTGCTGGCGCGTATTAACCAGCGCCTGTCTGCCTTAAAAGC GGATTTCCGGGTTACCGGCTACACTTCAACCGATAAGCCGGGCACTCCGCAGGGGTTTGGTCAGACACAG CCGGCAGATAACTCGTTAGGCCTGGCGTTCAACAACAGCGGCGAGTGGTGGGATGTCCACCTCCAGGGCA ACGTCGAAGGAGGGGAGCGGATCAGCAACGGCTCGCGCTTCAACGCCAACGGCGCATACGGCGCGGTGAA GTTCTGGAACCAGTGGCTCTCTTTTGGTCAGGTTCCGCAGTGGTGGGGACCGGGCTATGAAGGAAGCCTG ATCCGCGGGGATGCGATGCGGCCGATGACCGGCTTTTTAATGCAGCGTGCCGAGCAGGCGGCGCCGGAAA CCTGGTGGCTGCGCTGGGTGGGTCCATGGCAGTACCAAATCTCCGCTAGTCAGATGAATCAATATACCGC GGTGCCCCATGCCAAAATTATTGGCGGACGCTTCACCTTTACGCCGTTTCAGTCATTAGAATTAGGTGCA TCGCGCATTATGCAGTGGGGCGGGGAAGGTCGACCGCAATCATTCAGCAGTTTCTGGGATGGCTTCACTG GCCATGATAATACCGGGACAGATAACGAACCGGGTAACCAGCTGGCAGGGTTTGACTTTAAGTTCAAACT TGAACCAACTCTTGGCTGGCCAGTGAGTTTCTATGGGCAGATGGTTGGTGAGGATGAGTCTGGTTACCTA CCATCGGCGAATATGTTCCTTGGCGGGATTGAAGGGCACCACGGCTGGGGTAAGGATGCGGTTAACTGGT ATGTGGAAGCGCATGATACACGTACCAATATGAGCCGGACCAATTACAGCTATACCCACCACATCTACAA AGATGGTTATTACCAACAAGGGTATCCACTGGGCGATGCGATGGGAGGGGATGGTCAGTTGTTCGCAGGC AAGGTAGAACTGATTACTGAGAATAATCAGCGTTGGAGCACGCGCCTTGCATATGCCAAGGTGAATCCAA AAGATCAATCAATTAACAAGGCATTCCCTCATTCGGACACGTTGAAAGGTGTACAACTGGGCTGGAGCGG TGACGTTTATCAGTCGGTTCGTCTGAATACCTCTTTGTGGTACACCAACGCTAACAACAGCGACAGCGAT GACGTTGGGGCAAGCGCAGGGATAGAAATACCATTTAGTTTATAA

Select gene: Select input type:



Example 3. O-type prediction with single gene (wzm) query sequence and the input query sequence is manually given at the place assigned (in FASTA format).
Note that in the form the wzm protein sequence is given as input, the option "Wzm" is chosen from the gene list and "Protein-Protein(PP)" option is chosen from input type. The input sequence is obtained from NCBI web server.


O-antigen Prediction
Type or paste your FASTA sequence:

>BAA28339.1 integral membrane component of ABC-transporter [Klebsiella pneumoniae] MFSAIYRYRGFIIDSVKRDFQSRYQTSFLGAAWLILQPIAMISVYTLIFSELMRARLAGMDGPFAYSIYL CSGVLTWGLFTETLGNLVNVFLTNANILKKLSFPRICLPIIVTASAFINFLIIFGLFVLFLIVTGNFPGM IFFEIIPVLIVQMLFTLGLGIILGVLNVFVRDVGQFVNILLQFWFWFTPIVYVSKTLPEWVSGLLAYNPM ATIIGSYQNVMLYHQSPNWMALLPVTVVSIILFLFAWRLFKKHAADIVDEI

Select gene: Select input type: