LSM2104 Group Project

Weiwei’s Page (U052166X)

CP000523

1.FASTA format for CP000523

    Data retrieved from NCBI Genome

2. Blast Efflux Pump   http://sf01.bic.nus.edu.sg/blast/

 

                 Regular blast

                 Setting: CP000522, blastx, Efflux_pump, No filter. Expect 10, BLOSUM62,

                 Query genetic codes: baterial(11). Database genetic codes: baterial(11),

                 Frame shift penalty: No.  Graphical Overview. Descriptions/alignments:5000

                 Remark: Actually set Descriptions/alignments 50 is more than enough here.

                

Results: Total 10 hits.

Getting the detail for the hits from here: Blast results.xls   Blast results webpage

Acinetobacter baumannii ATCC 17978 plasmid pAB2, complete sequence

3. Identify statistical significant regions

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

4. Find Open reading frame

        http://www.ncbi.nlm.nih.gov/gorf/gorf.html

                 Setting: whole CP000522, FASTA, Bacterial code.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

5. Scan putative functional annotation

5.1. Prosite  http://au.expasy.org/prosite (results save as webpage)

 

ORF 1: With High probability of occurrence: 10 Hits

        Without high probability of occurrence: No hits

 

ORF 2: With High probability of occurrence: 15 Hits

        Without high probability of occurrence: 1 hit

                 hits by patterns: [1 hit (by 1 pattern) on 1 sequence]

                 Hits by PS00061   ADH_SHORT   Short-chain dehydrogenases/reductases family signature

 

ORF 3: With High probability of occurrence: 47 Hits

        Without high probability of occurrence: 1 hit

                 hits by patterns: [1 hit (by 1 pattern) on 1 sequence]

                 Hits by PS00659   GLYCOSYL_HYDROL_F5   Glycosyl hydrolases family 5 signature

 

ORF 4: With High probability of occurrence: 8 Hits

        Without high probability of occurrence: No hits

 

ORF 5: With High probability of occurrence: 6 Hits

        Without high probability of occurrence: No hits

 

 

 

 5.2 pfam  http://www.sanger.ac.uk/Software/Pfam/search.shtml

 

ORF 1:  Potential matches:   Rrf2, HTH_psq, NUMOD1, TrmB, Ribosomal_L44, Flavi_M 168

 

 

ORF 2:  Trusted matches:     adh_short, Epimerase 

                  Matches to Pfam-:  BPfam-B_1

                  Potential matches:  F420_oxidored, KR 13, Saccharop_dh, 3Beta_HSD, DUF1129

 

 

ORF 3: Trusted matches:      Plug, TonB_dep_Rec

                 Matches to Pfam-B: Pfam-B_6284, Pfam-B_5540

                 Potential matches:    Legionella_OMP, Carb_anhydrase, A-2_8-polyST, DUF479

 

 

 

 

ORF 4: Trusted matches:       Abi

                 Potential matches:    TatC, Abi

 

ORF 5: No matches