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. 2012 Oct;50(10):3249–3257. doi: 10.1128/JCM.00885-12

Table 2.

BLAST GenBank search with sequences of DNA fragments found in 28 clones after subtractive hybridization of clinical outbreak strain EN-373 and plant isolates 501R3 and E6

Subtractive hybridization Clone
 Database information about homologous genes
Namea % C+G Segment (bp) with homologyb Accession no. Homologous gene(s) Species, serovar, and plasmidc Homologous regione % IDd Scoref Protein function
EN-373 and 501R3 A-114 56 1–288 BX664015 Hypothetical SEMA pR478 71129–70840 97 511 Putative ATP/GTP-binding protein integrated in tellurium resistance operon
A-073 56 1–275 BX664015 Hypothetical SEMA pR478 71123–70848 96 468 Putative ATP/GTP-binding protein integrated in tellurium resistance operon
B-036 56 21–214 BX664015 Hypothetical SEMA pR478 71169–70976 99 377 Putative ATP/GTP-binding protein integrated in tellurium resistance operon
B-007 48 87–321 AY492000 nirA and -B and nreA and -B homologues KLOX 1318–1553 92 325 Nickel/cobalt resistance determinant; CCUG15788 integral membrane protein
AY030282 LEPN
A-104 55 19–447 AF067954 silS SATM pMG101 2624–2196 82 242 sil operon (plasmidal silver resistance genes)
BX664015 SEMA pR478 127176–126824 83 226
A-007 49 87–267 AY492000 nirAB, nreAB, and ncrABC homologues KLOX 1318–1499 91 226 Nickel/cobalt resistance determinant CCUG15788 integral membrane protein
AY030282 LEPN 1690–1875 226
AF322866 HAAL pNRS148 143
A-051 52 245–415 AE008877 ibpB and ibpA SATM LT2 12266–12437 88 174 Small heat shock protein
D-007 63 32–170 AE016840 hcr SATY Ty2 255337–255475 89 165 NADH oxidoreductase
C-005 58 54–212 AE016762 dacD ESCO CFT073 261785–261943 84 117 Putative enzyme d-alanyl-d-alanine carboxypeptidase
B-031 57 26–188 AE005674 ycfW SHFL 2a 1166030–1166192 82 101 Putative kinase
A-000 55 23–165 AE008886 trkH SATM LT2 6464–6322 83 101 Trk family potassium transport protein
A-053 59 174–244 AE008803 yfbE SATM LT2 4172–4242 88 78 Putative DegT/DnrJ/EryC1/StrS family regulatory system
C-007 48 13–48 AE008706 yafB SATM LT2 15741–15706 94 56 2,5-Diketo-d-gluconate reductase B
A-088 61 139–225 BA000007 Hypothetical ESCO O157:H7 3370219–3370306 82 48 Ecs3386, unknown function
C-006 60 1–24 KPN293850 EVGA KLPN 56–79 95 40 Putative positive transcription regulator EVGA
EN-373 and E6 E-013 48 1–624 AF550679 orf18 ESCO p1658/97 54236–54860 99 1199 Unknown
E-001 and E-007 47 1–571 SMU60283 trag1 SEMA pR478 386–958 99 1098 Putative restriction methylase
19–125, 491–510 AF250878 SATY pR27 47386–47468 86 101
E-022 42 1–451 SMU62007 PR478 intergenic region between RepHI1A and tra2 SEMA pR478 2288–2738 99 886 None; RepHI1A, putative Rep protein Tra2; putative pilin precursor; similar to TrhA from SATY plasmid HCM1
E-010 42 1–386 SMU62007 Like traE of F plasmid SEMA pR478 4201–4586 95 632 Plasmid transfer protein
22–204 AF250878.1 SATY pR27 36704–36522 80 100
E-009 42 153–457 STYFIMCLUS Putative tnpB SHFL 2a 1356–1052 97 541 Putative transposase B
E-011 44 1–275 AE000134 insA-2 ESCO 4764–5038 96 472 IS element 30
E-034 44 8–188 EAU67194 IS4321R ENAE pR751 14134–13954 100 359 Putative transposase binding site
E-037 31 1–169 SMU62007 htdV SEMA IncHI2 plasmid R478 7640–7472 84 183 Putative transfer-associated protein
E-002 42 531–612 AF550679 tnpA ESCO p1658/97 68019–68100 92 115 Transposase
AF342826 7419–7338 92 115
E-023 43 83–330 AF250878 R0009, putative gene SATY pR27 12627–12380 80 103 Hypothetical cell surface glycoprotein (S-layer protein)
83–330 STYPPHCM1 SATY CT18 pHCM1 69452–69699 80 103
E-029 48 1–247 AF250878 R0135, putative gene SATY pR27 121746–121500 79 86 Cell envelope; putative outer membrane constituents
1–247 STYPPHCM1 SATY CT18 pHCM1 187835–188081 79 86
E-033 50 51–139, 216–268, 330–450 AF250878 R0156 SATY pR27 142955–143354 83 68 Unknown
STYPPHCM1 Putative gene SATY pHCM1 137009–137129 83 68
a

Clones A-117, A-008, A-018, A-056, A-087, B-008, B-018, C-001, C-004, C-011, E-004, E-005, E-008, E-014, E-015, E-017, E-019, E-020, E-021, E-024, E-025, E-030, E-031, E-032, and E-035 are novel sequences.

b

Sequence section of insert of respective clone with homology to the genes with the indicated accession numbers.

c

ENAE, Enterobacter aerogenes; ENCL, Enterobacter cloacae; ESCO, Escherichia coli; HAAL, Hafnia alvei; LEPN, Legionella pneumophila; KLOX, Klebsiella oxytoca; KLPN, Klebsiella pneumoniae; SAEN, Salmonella enterica serotype Enteritidis; SATY, Salmonella enterica serotype Typhi; SATM, Salmonella enterica serotype Typhimurium; SHFL, Shigella flexneri.

d

Percent nucleotide identity.

e

Sequence section of accession number with homology to insert of respective clone.

f

BLASTN 2.2.5 score (bits).