TABLE 3.
BLAST search results for the Salmonella serovar Typhimurium DT104 fragments generated by genomic subtraction between the Salmonella serovar Typhimurium DT104 and LT2 strains excluding the fragments similar to SGI-I
| Group | Fragment no. | Sequence similarity to: | Accession no. | Similarity regiona | % Similarityb | Present inc: |
|---|---|---|---|---|---|---|
| (B) Phage | ||||||
| (i) ST64B | 4 | Serovar Typhimurium bacteriophage ST64B genome: putative DNA methyltransferase | AY055382.1 | 32607-32895 | 93 | Serovar Typhimurium SL1344 |
| 5 | Serovar Typhimurium bacteriophage ST64B genome: putative transcriptional activator | AY055382.1 | 31896-32507 | 98 | Serovar Typhimurium SL1344 | |
| 59 | Serovar Typhimurium bacteriophage ST64B genome: hypothetical protein Sb40 | AY055382.1 | 29290-29704 | 100 | Serovar Dublin, serovar Enteritidis PT4, serovar Typhimurium SL1344 | |
| 95 | Serovar Typhimurium bacteriophage ST64B genome: putative tail proteins Sb22 and Sb23 | AY055382.1 | 16126-16645 | 97 | Serovar Dublin, serovar Enteritidis PT4, serovar Typhimurium SL1344 | |
| 149 | Serovar Typhimurium bacteriophage ST64B genome: putative DNA methyltransferase Sb44 | AY055382.1 | 32897-33312 | 100 | Serovar Typhimurium SL1344 | |
| 155 | Serovar Typhimurium bacteriophage ST64B genome: hypothetical protein Sb46 | AY055382.1 | 33908-34104 | 98 | Serovar Enteritidis PT4, serovar Typhimurium SL1344 | |
| 170 | Serovar Typhimurium bacteriophage ST64B genome: integrase protein Sb28 | AY055382.1 | 21702-22241 | 99 | Serovar Dublin, serovar Enteritidis PT4, serovar Typhimurium SL1344 | |
| 178 | Serovar Typhimurium bacteriophage ST64B genome: putative tail protein Sb22 | AY055382.1 | 15708-16007 | 97 | Serovar Dublin, serovar Enteritidis PT4, serovar Typhimurium SL 1344 | |
| (ii) ST104 | 2 | Serovar Typhimurium bacteriophage ST104 genome: tailspike protein | AB102868.1 | 40450-40738 | 100 | Serovar Dublin, serovar Paratyphi A, serovar Paratyphi B |
| 17 | Serovar Typhimurium bacteriophage ST104 genome: NinZ | AB102868.1 | 19809-20268 | 99 | S. enterica subsp. diarizonae, serovar Dublin | |
| 36 | Serovar Typhimurium bacteriophage ST104 genome: ORF15 (endopeptidase) and ORF19 (lysozyme) | AB102868.1 | 21707-22377 | 99 | S. enterica subsp. diarizonae, serovar Paratyphi A, serovar Paratyphi B | |
| 50 | Serovar Typhimurium bacteriophage ST104: tail spike protein | AB102868.1 | 41078-41391 | 100 | Serovar Dublin, serovar Paratyphi A, serovar Paratyphi B | |
| 54 | Serovar Typhimurium bacteriophage ST104 genome: | AB102868.1 | 38879-39670 | 100 | Serovar Dublin, serovar Paratyphi A, serovar Paratyphi B | |
| Mnt and tail spike protein | ||||||
| 78 | Serovar Typhimurium bacteriophage ST104 genome: ORF46, ORF47, and ORF48 | AB102868.1 | 23183-24148 | 100 | S. enterica subsp. diarizonae, serovar Dublin, serovar Paratyphi A, serovar Paratyphi B | |
| 98 | Serovar Typhimurium bacteriophage ST104 genome: ORF19 | AB102868.1 | 9548-9791 | 100 | ||
| 101 | Serovar Typhimurium bacteriophage ST104 genome: ORF23 (antitermination protein Q homologue) | AB102868.1 | 20269-21264 | 99 | S. enterica subsp. diarizonae, serovar Paratyphi A, serovar Paratyphi B | |
| 110 | Serovar Typhimurium bacteriophage ST104 genome: NinG | AB102868.1 | 18853-19808 | 99 | S. enterica subsp. diarizonae | |
| 122 | Serovar Typhimurium bacteriophage ST104 genome: SieB | AB102868.1 | 10671-10897 | 99 | S. enterica subsp. diarizonae, serovar Paratyphi A, serovar Paratyphi B | |
| (iii) P27 | 8 | Serovar Typhi CT18 genome segment 6: putative holin of bacteriophage P27 | AL627270.1 | 15663-15915 | 94 | Serovar Paratyphi A, serovar Paratyphi B, serovar Typhi Ty2, serovar Typhi CT18, serovar Typhimurium SL1344 |
| 62 | Serovar Typhi CT18 genome segment 4: putative holin of bacteriophage P27 | AL627268.1 | 266762-267028 | 97 | S. bongori, serovar Enteritidis PT4, serovar Typhi Ty2, serovar Typhi CT18 | |
| 66 | Serovar Typhi CT18 genome segment 6: putative toxin subunit 1 of Bordetella pertussis | AL627270.1 | 14526-15084 | 91 | S. bongori, serovar Paratyphi A, serovar Paratyphi B, serovar Typhi Ty2, serovar Typhi CT18 | |
| (iv) Others | 16 | Putative prophage terminase large subunit of a prophage in serovar Typhi | CAD05440.1 | aa 291-453 | 82 (I), 89 (P) | |
| 22 | Unnamed protein product in Photorhabdus luminescens subsp. laumondii TTO1 | CAE15767.1 | aa 1-132 | 63 (I), 81 (P) | ||
| 56 | Unknown protein of prophage CP-933U in E. coli O157:H7 | AAG57029.1 | aa 23-99 | 61 (I), 79 (P) | ||
| 75 | Unnamed protein product in Photorhabdus luminescens subsp. laumondii TTO1 | CAE15775.1 | aa 142-233 | 65 (I), 75 (P) | ||
| 84d | Unnamed protein product in Photorhabdus luminescens subsp. laumondii TTO1 | CAE15762.1 | aa 1-113 | 59 (I), 78 (P) | ||
| 100 | Exodeoxyribonuclease of Gifsy prophages in serovar Typhimurium LT2 | AAL19943.1 | aa 58-355 | 46 (I), 58 (P) | Serovar Gallinarum, serovar Paratyphi A, serovar Paratyphi B, serovar Typhimurium SL1344 | |
| 158e | DNA fragment of serovar Typhimurium DT104: hypothetical | AF275268.1 | 229-516 | 100 | Serovar Dublin, serovar Gallinarum | |
| protein YdaU of Rac prophage in E. coli K-12 | ||||||
| 168d | S. flexneri 2a genome: putative bacteriophage protein | AE005674.1 | 2693454-2693818 | 93 | ||
| 180d | Hypothetical protein YmfD of prophage e14 in E. coli K-12 | F64858 | aa102-216 | 69 (I), 82 (P) | ||
| (C) Nonphage | 117d | irsA gene in serovar Typhimurium ATCC 14028 | AY328029.1 | 1627-1948 | 99 | Serovar Dublin, serovar Enteritidis PT4, serovar Enteritidis PT8, serovar Gallinarum |
| 144d | LPS biosynthesis enzyme HldD (WaaD) of E. coli O157:H7 | AAC69662.1 | aa 29-111 | 75 (I), 87 (P) | S. bongori | |
| (D) Not significant | 47 | Hypothetical protein in Caenorhabditis elegans | CAA88607.1 | aa 64-216 | 23 (I), 41 (P) | |
| 64 | Hypothetical protein in Anaeromyxobacter dehalogenans 2CP-C | EAL78506.1 | aa 38-155 | 34 (I), 55 (P) |
a
Region of similarity in base pairs or amino acids (aa) based on accession number.
b
Similarities are based on nucleotide or amino acid sequences. When identities (I) and positives (P) are given, values for positives (similarity based on similar amino acid properties) of ≤55% are not significant.
c
Present or partly present, based on >80% similarity by BLASTN analysis, in the genomes listed. All fragments are present in Salmonella serovar Typhimurium DT104.
d
DNA fragment used for PCR detection of genomic fragments.
e
DNA fragment described in the literature as Salmonella serovar Typhimurium DT104 specific (20).