22D9

Site of transposon insertion cloned as PstI fragment into pSP72. 
Sequenced in opposite orientations with JEP131 and JEP132,
from sites at opposing ends of the transposon, to give:

JEP131 470 bp

JEP132 495 bp

 
Composite sequence:

ANAAACCCTA CCCCTAGTGA TTTTTCAAAA GACAAAGGGA TATTGNTTTC
ACTGTCCAGG ATGGAATGAT CCAGCGGACA CGCAACATTA TGGAACGGNC
AACCTGCTCA GATCATTGTT ACTTTCCAAA ATCCAACGAG GCATCTATAT
GGTTACTAAA ATAAAATCCC TGTGTGTTGC AAGCATGATA TTTTTGGGAT
GTATTCAATC GGCTCAAGCC AAAGAAACCT ATACCCCCGA AGAGTACCTC
AAAAACTACG GCGCTTAGCG TTTGCATCGC CGAGGGGTAC TCAGCAAAAG
AAGTCAAAAA CGATGCCGCC GCCGCCGCTC GGGGTTACAC GGAATTCGGC
GATTATTCTC TGGAAGCTGC ATACCGCCGT CAGGGCGCTG GCAAAAGAAT
TTCTGGCAAA GCCCTATGAC AGTATGTCAG GGGAGCCGAT GACGATGGCC
AAGTGCATCG TCTTGACAAA 

GNANAGACTT GTCACAGCCA AGACTGCAAG CCTCATCAAG AAATACCAAG
GAAAAGACGA CAACTGATAT CAGAGTTGCT CAAACGACGG CTCATATCAA
AGGTTATCTC GGATGAGAAG ATACACGTAC TTTTTAATGT CTCTGCTGCT
CGGAAGCCAT GTAGTCCTTG CTGAAAACTC GCTCAATGCT TTATCGCAAG
AGGCACTTTA TAAAAATTGG TTAACCAGCC GCTGCATTGG GAAGTCCACT
GACTCAGAAA GAACCAAGCA AGACGCCTTC CGTTCCGCTT CCGCCTATTT
AGAATTGAGT AAACTGCCGA TGGATGCATT TGAACAAGGT GAAAAACTGG
CTGAACAGTA CGCAAATAAA AATAGCCAAG GCTCAGTTCA AGGGACTTAC
CATACTTTAG ATTGCTTTCA CTGCAGCGAG GCGACGATGG TCATCGCCAG
CAGGCAAAGC AGCCCGTAGT GCAGCAGCTT GCCGCAGGCC AATCC

Note: This sequence is identical in part to the sequence obtained with the mutant 7D1, (see BLAST2 result here).

BLASTX with this sequence (full results here) gives as the only significant hits:



>gi|16763661|ref|NP_459276.1| (NC_003197) putative periplasmic protein [Salmonella typhimurium
           LT2]
           Length = 127

 Score = 55.1 bits (131), Expect = 3e-07
 Identities = 27/97 (27%), Positives = 48/97 (48%)
 Frame = +1

Query: 595 TYFLMSLLLGSHVVLAENSLNALSQEALYKNWLTSRCIGKSTDSERTKQDAFRSASAYLE 774
           T+ +  +L+       E      SQ  L KNW  S C+      +  K DA  +ASAYLE
Sbjct: 12  TFSISGMLVWQPSFAQEALTTQYSQSELLKNWALSHCLALVYKDDVVKNDARATASAYLE 71

Query: 775 LSKLPMDAFEQGEKLAEQYANKNSQGSVQGTYHTLDC 885
             K  ++ + + +++A++Y+     GS+   ++T+ C
Sbjct: 72  YGKQSVEIYHEIDEIAKKYSGLKYNGSISSDFNTMKC 108


 Score = 33.9 bits (76), Expect = 0.70
 Identities = 18/49 (36%), Positives = 23/49 (46%)
 Frame = +3

Query: 261 ALSVCIAEGYSAKEVKNDXXXXXRGYTEFGDYSLEAAYRRQGAGKRISG 407
           ALS C+A  Y    VKND       Y E+G  S+E  +      K+ SG
Sbjct: 44  ALSHCLALVYKDDVVKNDARATASAYLEYGKQSVEIYHEIDEIAKKYSG 92




>gi|16121825|ref|NP_405138.1| (NC_003143) putative exported protein [Yersinia pestis]
 Length = 144

 Score = 42.0 bits (97), Expect = 0.003
 Identities = 20/75 (26%), Positives = 40/75 (52%)
 Frame = +1

Query: 616 LLGSHVVLAENSLNALSQEALYKNWLTSRCIGKSTDSERTKQDAFRSASAYLELSKLPMD 795
           L+    + AE + N + Q+   +N+  S C+ +         +AF +  AY+EL   P++
Sbjct: 34  LISFSTLAAEVNQNKVQQKNNLENFALSICLAEGFPDGEINSEAFSAVGAYVELGAYPVE 93

Query: 796 AFEQGEKLAEQYANK 840
           A+E+  +LA+++  K
Sbjct: 94  AYEEVSELAKKFLEK 108


 Score = 34.7 bits (78), Expect(2) = 3e-04
 Identities = 14/36 (38%), Positives = 21/36 (57%)
 Frame = +3

Query: 261 ALSVCIAEGYSAKEVKNDXXXXXRGYTEFGDYSLEA 368
           ALS+C+AEG+   E+ ++       Y E G Y +EA
Sbjct: 59  ALSICLAEGFPDGEINSEAFSAVGAYVELGAYPVEA 94


 Score = 29.6 bits (65), Expect(2) = 3e-04
 Identities = 17/38 (44%), Positives = 25/38 (65%), Gaps = 1/38 (2%)
 Frame = +1

Query: 379 VRALAKEFLAKPYDSMSGE-PMTMAKCIVLTKXRLVTA 489
           V  LAK+FL K Y S +GE  +T+ KCI L++   ++A
Sbjct: 98  VSELAKKFLEKKYISKNGESKLTVMKCIDLSQSSELSA 135

The transposon is thus inserted upstream of a clear homologue of STM0278 in Salmonella and of YPO1552 in Yersinia. For a direct comparison of these two proteins, see the BLAST2 result.

Given the fact that two different regions of the Serratia sequence are shown to be similar to SMT0278 and YPO1552, there appears to have been a local duplication. Given the results obtained with the mutant 7D1, the upstream gene would appear to encode a protein of at least 140 amino acids. This would mean that the transposon is inserted towards the 3' end of the coding sequence of the upstream gene.

Although these proteins do not contain any identifiable domains, as can be seen from these BLASTP results the Yersinia protein contains a region that is very similar to at least two other predicted proteins. This may explain the comment "Doubtful CDS with no significant database hits. The N-terminal region is similar to a repeat region which is found scattered throughout the genome", found at Genbank for YPO1552.

This does not seem to be the case for SMT0278 (result here).

SMT0278 is a putative periplasmic protein of unknown function, and, according to the Enteric server, is in a region that is not conserved between Salmonella typhimurium and other bacteria (see results here or download the PDF file).