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Sequence Analysis of Putative potB, potC, and potD Genes from Serratia Rubidae

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Fig 1 (Left) PCR reaction products. Putative were sized approximately 1800 bp; (Right) Line1: Recombinant plasmid uncut. Line 2: Recombinant plasmid cut by RI. M: marker (1 kb DNA ladder).

potBCD

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Fig 2 Nucleotide sequence of , and genes from . SD denotes putative Shine- Delgarno sequence. Codon start indicated by “M” and codon stop indicated by “*”. Grey boxes indicate a pair of primers.

potB potC potD S. rubidae

M PotD

RERC

FERC

PotB

PotC M

SD *

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Fig 3 Sequence alignment of putative PotB protein from and PotB from Acc Number M 64519.1 which were aligned using the Clustal W algorithm. Grey boxes indicate the six predicted transmembrane segments (TM1 to TM6). Consensus symbols; identical residues: '' '', conserved substitutions: '' '', semi-conserved substitutions: '' ''.

S. rubidae E. coli

*

: .

Fig 4 Sequence alignment of putative PotC protein from and PotC from Acc number M64519.1 using the Clustal W algorithm. Grey boxes indicate the six predicted transmembrane segments (TM 1 to TM 6). Consensus symbols; identical residues: '' '', conserved substitutions: '' '', semi-conserved substitutions: '' ''.

S. rubidae E. coli

* :

.

PotB_S.rubidae : ---

---PotB_E.coli :MIVTIVGWLV LFVFLPNLMIIGTSFLTRDDASFVKMVFTLDNYTRLLDPLYFEVLLHSLN 60

PotB_S.rubidae : --- ---PQKVRPLLLFLLIVPFWTNSLIRIYGLKIFLSTKGYL 37

PotB_E.coli :MALIATLACLVLGYPFAWFLAKLPHKVRPLLLFLLIVPFWTNSLIRIYGLKIFLSTKGYL 120

* :* ******** *******************************

PotB_S.rubidae :NEFLLWLGVIETPIRIMFTPGAVIIGLVYILLPF MVMPLYSSIEKLDK PLLEAAKDLGAS 97

PotB_E.coli :NEFLLWLGVIDTPIRIMFTPSAVIIGLVYILLPF MVMPLYSSIEKLD KPLLEAARDLGAS 180

****************************************************************** *********

PotB_S.rubidae :KLQTFVRIIIPLT MPGIIAGCLLVMLPAMGLFYVSDLMGGAKNLLIGNVIKSQFLNIRDW 157

PotB_E.coli :KLQTFI RIIIPLTMPGIIAGCLLVMLPAMGLFYVSDLMGGAKNLLIGNVIKVQFLNIRDW 240

****** : *******************************************************************

PotB_S.rubidae :PFGSATSITLTVVMGLMLLVYWRASRLLNKKVELE 192

PotB_E.coli :PFGAATSITLTI VMGLMLLVYWRASRLLNKKVELE 275

*** : ****************************************

PotC_S.rubidae : MIGRLLRGGFMTAIHAYLYIPIIILIVNSFNSSRFGINWQ GFTTKWYGLLMNNDSLLQAA 60

PotC_E.coli : MIGRLLRGGFMTAIYAYLYIPIIILI VNSFNSSRFGINWQ GFTTKWYSLLMNNDSLLQAA 60

***************** : ************************************** .****************

PotC_S.rubidae :QHSLTMAVFFATFAT LIGSLTAVALYRYRFRGKPFVSGMLFVVMMSPDIVMAISLLVLFM120

PotC_E.coli :QHSLTMAVFSATFAT LIGSLTAVALYRYRFRGKPFVSGMLFVVMMSPDIVMAISLLVLFM120

*********** ************************************************ ***************

PotC_S.rubidae :LLGVQLGFWSLLFSHITFCLPFVVVTVYARLKGFDVRMLEAAKDLGASEMTILRKIILPL180

PotC_E.coli :LLG I QLGFWSLLFSHITFCLPFVVVTVYSRLKGFDVRMLEAAKDLGASEFTILRKIILPL180

*** : ****************************** * :************************** :*** *********

PotC_S.rubidae :AMPAVAAGWLL SFTLSMDDVVVSSFVTGPSYEILPLKIYSMVKVGVSPEVNALATILLVL240

PotC_E.coli :AMPAVAAGWVISFTLSMDDVVVSSFVTGPSYEILPLKIYSMVKVGVSPEVNALATILLVL 240

************* : ************************************************************* *

PotC_S.rubidae :SLVLVIASQVIARDKTK - SQGTQK 263

PotC_E.coli :SLVMVIASQLIARDKTKGNTGDVK 264

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Fig 5 Sequence alignment between putative PotD protein from and PotD from Acc. number M 64519.1 Based on Sugiyama (1996) the active residue which binds to spermidine are indicated by grey boxes. Consensus symbols; identical residues: '' '', conserved substitutions: '' '', semi-conserved substitutions: '' ''.

S. rubidae E. coli et al.

* :

.

PotD_S.rubidae :MKKM - - - LAAAATGARNWAAAHAGDCKTLYFYNWTEYVPPGLLEQFTKETGIKVIYSTYE 57 PotD_E.coli :MKKWSRHLLAAGALA LGMSAAHADDNNTLYFY NWTEYVPPGLLEQFTKETGIKVIYSTYE 60

*** * ** . : * . : **** . * .* : ******************************************

Signal sequence βA α1 βB

PotD_S.rubidae :SNETMYAKLKTYKDGAYDLVVP STYF VDKMRKEGMIQKIDKSKLTNFSNLDPEMLNKPED 117 PotD_E.coli :SNETMYAKLKTYKDGAYDLVVP STYYVDKMRKEGMIQKIDKSKLTNFSNLDPDMLNKPED 120

*********** ********************** : ********************************** : *********

α2 βB α3

PotD_S.rubidae :PNNDYSIPYIWGATAIGVNSDA I DPKRVSSWADLWKPEYKNSL --- 160 PotD_E.coli :PNNDYSIPYIWGATAIGVNGDAVDPKRVTSWADLWKPEYKGSLLLTD DAREVFQMALRKL 180

*********** ************ . ** : *** * : **************** . **

βD βE βF α4

PotD_S.rubidae : --- ---PotD_E.coli :GYSGNTTDPKEIEAAYNELKKLMPNVAAFNSDNPANPYMEGEVNLGMIWNGSAFVARQAG 240

α5 βG α6 βH α7

PotD_S.rubidae : ---PotD_E.coli : TPIDVVWPKEGGIFWMDSLAIPANAKNKEGALKLINFLLRPDVAKQVAETIGYPTPNLAA 300

βI βJ α8 α9 α10

PotD_S.rubidae : ---PotD_E.coli : RKLLSPEVANDKTLYPDAETIKNGEWQNDVGAASSIYEEYYQKLKAGR 348

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Gambar

Fig 1potBCDwere sizedapproximately 1800 bp; (Right) Line1: Recombinant plasmid uncut. Line 2:Recombinantplasmidcutby(Left) PCR reaction products
Fig 2 Nucleotide sequence ofandpotDgenes fromandcodonstopindicatedby“*”.Greyboxes indicateapairofprimers.potB potC,S
Fig 3 Sequence alignment of putative PotB protein from*:and PotB fromAcc Number M 64519.1 which were aligned using the Clustal Walgorithm
Fig 5 Sequence alignment between putative PotD protein fromAcc. number M 64519.1 Based on Sugiyamaet al.*:(1996)the active residue which binds to spermidine are indicated by grey boxes

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