7D1

JEP131 95 bp then into vector
 

JEP132 551 bp

 
Composite sequence:

TGAAAGACAA TCTAAAGTAT GGTAAGTCCC TTGAACTGAG CCTTGGCTAT
TTTTATTTGC GTACTGTTCA GCCAGTTTTT CACCTGGCCA ANAAA

TGNNNAGTTC AAATGCATCC ATCGGCAGTT TACTCAATTC TAAATAGGCG
GAAGCGGAAC GGAAGGCGTC TTGCTTGGTT CTTTCTGAGT CAGTGGACTT
CCCAATGCAG CGGCTGGTTA ACCAATTTTT ATAAAGTGCC TCTTGCGATA
AAGCATTGAG CGAGTTTTCA GCAAGGACTA CATGGCTTCC GAGCAGCAGA
GACATTAAAA AGTACGTGTA TCTTCTCATC CGAGATAACC TTTGATATGA
GCCGTCGTTT GAGCAACTCT GATATCAGTT GTCGTCTTTT CCTTGGTATT
TCTTGATGAT GGCTTGCAGC TCTTGGCTGT GTACAAGATC GATGCACTTG
GCCATCGTCA TCGGCTCCCC TGACATACTG TCATAGGGCT TTGCCAGAAA
TTCTTTTGCC AGCGCCCTGA CGGCGGTATG CGCTTCAGAG AATAATCGCC
GAATTCCGGG AACCCCGAGC GGCGGCGGCG GCATCGTTTT GACTTCTTTG
CTGAGNCCCC TCGGCATGCA ACGCTAACGC GTAGTTTGAG GACTTTCGGG
G

Note: This sequence is identical in part to the sequence obtained with the mutant 22D9, (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 = 48.9 bits (115), Expect = 1e-05
 Identities = 27/103 (26%), Positives = 48/103 (46%)
 Frame = -2

Query: 312 TYFLMSLLLGSHVVLAENSLNALSQEALYKNWLTSRCIGKSTDSERTKQDAFRSASAYLE 133
           T+ +  +L+       E      SQ  L KNW  S C+      +  K DA  +ASAYLE
Sbjct: 12  TFSISGMLVWQPSFAQEALTTQYSQSELLKNWALSHCLALVYKDDVVKNDARATASAYLE 71

Query: 132 LSKLPMDAFELXIXWPGEKLAEQYANKNSQGSVQGTYHTLDCL 4
             K  ++ +        +++A++Y+     GS+   ++T+ C+
Sbjct: 72  YGKQSVEIYHEI-----DEIAKKYSGLKYNGSISSDFNTMKCI 109


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

 Score = 45.4 bits (106), Expect = 1e-04
 Identities = 26/48 (54%), Positives = 31/48 (64%), Gaps = 1/48 (2%)
 Frame = -2

Query: 531 EAHTAVRALAKEFLAKPYDSMSGEP-MTMAKCIDLVHSQELQAIIKKY 391
           EA+  V  LAK+FL K Y S +GE  +T+ KCIDL  S EL AI  KY
Sbjct: 93  EAYEEVSELAKKFLEKKYISKNGESKLTVMKCIDLSQSSELSAIKDKY 140


 Score = 40.0 bits (92), Expect = 0.005
 Identities = 21/86 (24%), Positives = 42/86 (48%)
 Frame = -2

Query: 291 LLGSHVVLAENSLNALSQEALYKNWLTSRCIGKSTDSERTKQDAFRSASAYLELSKLPMD 112
           L+    + AE + N + Q+   +N+  S C+ +         +AF +  AY+EL   P++
Sbjct: 34  LISFSTLAAEVNQNKVQQKNNLENFALSICLAEGFPDGEINSEAFSAVGAYVELGAYPVE 93

Query: 111 AFELXIXWPGEKLAEQYANKNSQGSV 34
           A+E       + L ++Y +KN +  +
Sbjct: 94  AYEEVSELAKKFLEKKYISKNGESKL 119

The transposon is thus inserted in a 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 YPO1552, the upstream gene in Serratia would appear to be a paralogue.

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).