Computational protocol: A novel bifunctional GH51 exo-α-l-arabinofuranosidase/endo-xylanase from Alicyclobacillus sp. A4 with significant biomass-degrading capacity

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Protocol publication

[…] The gene fragment of Ac-abf51A (no signal peptide coding sequence based on SignalP 4.0 prediction) was amplified from the genome of strain A4 by PCR using the expression primers (abf51F: 5′-CGCCATATGTCCAAGTCGATTGCACGTATG-3′ and abf51R: 5′-GACGCGGCCGCCACGCGCAATCGAATGACG-3′, NdeI and NotI sites underlined, respectively). The PCR products were gel-purified with Agarose Gel DNA Purification kit (TaKaRa), ligated into a pGEMT easy vector (Promega), and transformed into E. coli Trans I-T1 for sequencing. The nucleotide sequence was assembled and analyzed using Vector NTI Advance 11.5 software (Invitrogen). BlastN and BlastP programs (http://www.ncbi.nlm.nih.gov/BLAST/) were used to analyze the nucleotide and deduced amino acid sequences, respectively. […]

Pipeline specifications

Software tools SignalP, Vector NTI Advance, BLASTN, BLASTP
Application Protein sequence analysis
Organisms Thermoanaerobacter mathranii, Escherichia coli, Beta vulgaris subsp. vulgaris, Triticum aestivum
Chemicals Ethanol, Arabinose, Xylose