3
Sprejeto (accepted): 2006-12-20
The RepFIIA replicon of the natural Escherichia coli plasmid pRK100
Replikon RepFIIA naravnega plazmida pRK100 bakterije Escherichia coli
Marjanca STARČIČ ERJAVEC & Darja ŽGUR-BERTOK
Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111,
1000 Ljubljana, Slovenia, Fax: 00386 1 257 3390, E-mail: Marjanca.Starcic.Erjavec@bf.uni-lj.si, 
Darja.Zgur@bf.uni-lj.si.
Abstract. The aim of the presented study was to identify the similarity of the plasmid 
pRK100 RepFIIA replicon (replication region) with similar replicons of other known plasmids 
of Enterobacteriaceae. For this purpose, within the determined nucleotide sequence of pRK100, 
the RepFIIA replicon rep genes/regions were identifi ed. The nucleotide sequences of the pRK100 
determined rep genes/regions were subsequently compared with the nucleotide sequences of other 
RepFIIA replicon rep genes/regions deposited in GenBank. Further, the nucleotide divergence 
between them was calculated. The obtained results clearly demonstrated, that the individual 
pRK100 rep regions are the same/most similar to rep regions from different plasmids. RepA2 of 
pRK100 is most similar to repA2 of pCP301, pINV_F6_M1382, pWR501 and R1, copA is the 
same as copA of plasmids pC15-1a and R100, repA6 of pRK100 is the same as repA6 in plasmids 
pC15-1a, pCP301, pINV_F6_M1382, pWR501, R1 and R100, repA1 is most similar to repA1 
of the plasmid p1658/79, and repA4 of pRK100 is most similar to repA4 of pC15-1a. Hence, the 
composition of the pRK100 RepFIIA replicon is mosaic and unique among the plasmids.
Key words: plasmid, RepFIIA replicon, Enterobacteriaceae, nucleotide divergence
Izvleček. Cilj raziskave je bil označiti podobnost replikona (replikacijske regije) RepFIIA z 
drugimi podobnimi replikoni znanih plazmidov enterobakterij. V ta namen smo v nukleotidnem 
zaporedju replikona RepFIIA plazmida pRK100 poiskali posamezne gene/regije rep in njihovo 
nukleotidno zaporedje primerjali z drugimi, deponiranimi, nukleotidnimi zaporedji RepFIIA ter 
izračunali nukleotidno divergenco. Dobljeni rezultati so jasno pokazali, da so različni geni/regije 
rep v replikonu RepFIIA plazmida pRK100 enaki/zelo podobni rep različnih plazmidov. RepA2 
od pRK100 je najbolj podoben genu repA2 plazmidov pCP301, pINV_F6_M1382, pWR501 in 
R1, copA je enak genu copA na plazmidih pC15-1a in R100, regija repA6 plazmida pRK100 je 
enaka regiji repA6 plazmidov pC15-1a, pCP301, pINV_F6_M1382, pWR501, R1 in R100, gen 
repA1 je najbolj podoben genu repA1 plazmida p1658/79, in regija repA4 plazmida pRK100 
je najbolj podobna regiji repA4 plazmida pC15-1a. Povzamemo lahko, da je replikon RepFIIA 
plazmida pRK100 sestavljen kot mozaik in da ga v takšni sestavi do sedaj še niso našli na no-
benem drugem plazmidu.
Ključne besede: plazmid, replikon RepFIIA, Enterobacteriaceae, nukleotidna divergenca
 ACTA BIOLOGICA SLOVENICA 
 LJUBLJANA 2006 Vol. 49, [t. 2: 3–12
4 Acta Biologica Slovenica, 49 (1), 2006
Introduction
Plasmids, extrachromosomal DNA elements, can be found in all three domains of the living world, 
in Archaea, Bacteria and Eukarya (HOLMES & al. 1995, SOLAR & al. 1998, ZILLIG & al. 1998). These 
elements encode a remarkable array of phenotypic traits of medical, agricultural, environmental and 
commercial importance (HELINSKI & al. 1996). Encoded traits include resistances to heavy metals, 
supplementary metabolic pathways and pathways for degradation of xenobiotics, as well as virulence 
factors and resistances to antibiotics (KADO 1998). Further, plasmids can have the machinery to transfer 
themselves and other parts of the genome into different species, genera, or sometimes even families 
(FIRTH & al. 1996). Plasmids can also incorporate and deliver genes by recombination or transposi-
tion and by this means increase the genetic exchange in- and between bacterial populations (SOLAR 
& al. 1998). 
All plasmids harbour a replicon (replication region), which is needed for the stable propagation 
and maintenance in the host cell. Regardless of plasmid size, the replicon of a plasmid generally 
consists of a contiguous set of information that includes a defi nable origin, where DNA replication 
initiates (ori), a structural gene encoding the plasmid-specifi c protein required for the initiation of 
replication, and one or more adjoining controlling elements. All this information is often contained 
within a segment that is 3 kb or less in size (HELINSKI & al. 1996). The replicons are designated and 
grouped into families (COUTURIER & al. 1988).
Replicons belonging to the RepFIIA family typically consist (Fig. 1) of repA2 encoding a repressor, 
the copA gene that encodes an antisense RNA molecule, a repA1 gene whose protein initiates plasmid 
replication by binding to the downstream ori, the repA6 region encoding a short leader peptide, and 
a repA4 region. The RepA2 repressor is assumed to regulate transcription of repA1 mRNA, while the 
antisense RNA CopA which is complementary to the leader region of repA1 mRNA (CopT), regulates 
translation. When CopA binds to CopT, repA6, which is necessary for RepA1 synthesis, is not expressed 
(BLOMBERG & al. 1992). The repA4 appears to be important for the stability of plasmid maintenance 
(JIANG & al. 1993). Further it is known, that the replicons of this family are mosaic (OSBORN & al. 
2000), i.e. individual genes encoded in this replicon originate from different sources.
pRK100 is an ~145-kb plasmid isolated from a uropathogenic Escherichia coli strain and it has 
been to a large extent characterised. It belongs to the IncF incompatibility group and encodes two 
antibiotic resistances, ampicillin and tetracycline, two colicins, ColV and ColIa, and the aerobactin 
(iuc) and enterochelin (iro) iron uptake system. Further it was demonstrated that pRK100 harbours 
two different replicons, a RepFIB and RepFIIA replicon (ŽGUR-BERTOK & al. 1990, AMBROŽIČ & al. 
1998, STARČIČ ERJAVEC, 2003). In the presented study the genes/regions of the pRK100 RepFIIA rep-
Fig. 1: Map of the RepFIIA replicon.
 Genes/regions of a typical RepFIIA replicon are depicted. To clearly show the individual studied sequences, 
some boxes representing genes/regions are offl ine. The direction of mRNA transcription is also marked. 
ori is the origin of replication, where the RepA1 protein binds and starts the replication. 
Slika 1: Mapa replikona RepFIIA.
 Označeni so geni/regije tipičnega replikona RepFIIA. Zaradi razvidnosti lege preučevanih zaporedij, 
so nekateri okvirčki, ki prikazujejo gene/regije, premaknjeni. Označena je tudi smer prepisa mRNA iz 
posameznega gena. ori je regija, kjer se veže replikatorski protein RepA1 in prične s podvajanjem plaz-
mida.
5M. Starčevič Erjavec & al.: The RepFIIA replicon of the natural Escherichia coli plasmid pRK100
licon were analysed for their similarity with the RepFIIA replicon’s genes/regions of related plasmids 
p1658/79, pB171, pC15-1a, pCP301, pINV_F6_M1382, pO157, pTUC100, pWR501, R1 and R100. 
The nucleotide divergence between pRK100 and the other plasmids was determined. The results of 
our study show that the RepFIIA replicon of pRK100 is mosaic and unique in its composition.
Method
Sequence analysis for open reading frames (ORF)
The determined RepFIIA replicon nucleotide sequence, 2159 bp in length, (GenBank accession 
number AY234375) was analyzed for open reading frames with the help of the program “ORF Finder” 
available on the web site http://www.ncbi.nlm.nih.gov/gorf/orfi g.cgi.
Sequence analysis for DNA similarity
The program Nucleotide-nucleotide BLAST (ALTSCHUL & al. 1997) available on the web site 
http://www.ncbi.nlm.nih.gov/BLAST/ was used to search for nucleotide sequences similar to the 
pRK100 RepFIIA nucleotide sequence. The DNA sequences of rep genes/regions were compiled 
and analysed using the CLUSTAL W (THOMPSON & al. 1994) program for sequence alignment. The 
program DNADIST in the PHYLIP package (FELSENSTEIN 1993, FELSENSTEIN 1989) was used for 
calculating distance matrixes.
Results
Genes/regions of the RepFIIA nucleotide sequence of pRK100 
The pRK100 RepFIIA replicon has been deposited in GenBank under the Accession Number 
AY234377. In this deposited nucleotide sequence, the RepFIIA replicon is harboured from Nt 1401 to 
Nt 3559. To identify the rep genes/regions in the deposited nucleotide sequence of the pRK100 RepFIIA 
replicon, the internet program “ORF Finder” was used. To further defi ne the rep genes/regions, the 
pRK100 RepFIIA sequence was compared to other known rep genes/regions of similar replicons. The 
RepFIIA replicon was found to harbour repA2, copA, repA6, repA1, and repA4 sequences (Tab. 1). 
Table 1: Predicted genes/regions in the pRK100 RepFIIA replicon (AY234377).
Tabela 1: Predvideni geni/regije replikona RepFIIA (AY234377) plazmida pRK100.
Assumed gene/region Frame From (bp) To (bp) Length
repA2 +3 1401 1661 261
copA +1 C 1874 1782  93
repA6 +2 1886 1960  75
repA1 +3 1953 2810 858
repA4 +2 3173 3556 384
A pRK100 RepFIIA-like replicon can be found on many other plasmids
 With the goal to fi nd plasmids with similar replicons, which could be compared with the 
pRK100 RepFIIA replicon, a BLAST search with the nucleotide sequence of pRK100’s RepFIIA 
was performed. The search revealed that many other plasmids carry similar replicons (Tab. 2). The 
most similar RepFIIA replicon was harboured by the Escherichia coli plasmid p1658/9. Most of the 
plasmids with similar replicon sequences were harboured on plasmids hosted by Escherichia coli or 
6 Acta Biologica Slovenica, 49 (1), 2006
Shigella fl exneri however, some plasmids with less similar sequences were harboured also by other 
enteric bacterial species, as Klebsiella pneumoniae, Shigella sonnei and Salmonella Typhimurium. 
All plasmids exhibiting similarity with the pRK100 RepFIIA replicon belong to the broad RepFIIA 
family of replicons, those with higher similarity are members of the same Inc group – the IncFII, and 
plasmids with lower similarity belong to other Inc groups (IncFIA, IncFIC, IncFIV,..)
Table 2:  BLAST hits for the nucleotide sequence of the pRK100 RepFIIA replicon with a score higher than 200.
Tabela 2:  Zadetki z BLAST z rezultatom več kot 200 bitov za replikon RepFIIA plazmida pRK100.
GenBank
Acc. Number
Plasmid Host BLAST score
(bits)
AF550679 p1658/9 Escherichia coli 3733
V00351 R1(RSC13) Escherichia coli 3527
AF177050 pWR100 Shigella fl exneri 3213
AL391753 pWR100 Shigella fl exneri 3166
AF348706 pWR501 Shigella fl exneri 3166
AF386526 pCP301 Shigella fl exneri 2a strain 301 3152
AY458016 pC15-1a Escherichia coli 3019
AP000342 R100 Shigella fl exneri 2b strain 222,
Escherichia coli
2948
AY206448 pINV_F6_M1382 Shigella fl exneri 2843
AB011549 pO157 Escherichia coli 2773
AB024946 pB171 Escherichia coli 2759
AY091607 pTUC100 Escherichia coli 2746
M26937 pSU316 Escherichia coli 2627
V00318 R6-5 Escherichia coli  926
M13472 ColV2-K94 Escherichia coli  924
X55895 pSU212 Escherichia coli  759
M93064 pEI545 Klebsiella pneumoniae  702
AP001918 F Escherichia coli  420
M16167 P307 Escherichia coli  414
M28098 pSU221 Escherichia coli  394
M27528 R124 Escherichia coli  339
AP005147 R64 Salmonella typhimurium  311
AB021078 ColIb-P9 Shigella sonnei (E. coli)  303
K02675 pCG86 Escherichia coli  274
AP002527 R721 Escherichia coli  230
The pRK100 RepFIIA replicon is mosaic and unique in its composition
In order to identify the similarity of the pRK100 RepFIIA rep genes/regions with other known rep 
genes/regions the computer programs CLUSTAL W and DNADIST were used. With these programs 
nucleotide sequences of rep genes/regions of pRK100 with rep sequences of other similar RepFIIA 
replicons, which were found with BLAST search and gave a BLAST score of more then 1000 bits, were 
compiled. For the compilation only those BLAST hits that had a complete RepFIIA replicon nucleotide 
sequence deposited were used, so that entire RepFIIA replicon could be compared. For the comparison 
of RepFIIA genes/regions harboured by different plasmids the original genes/regions, if denoted by 
the submitters of the sequence, were used, otherwise the genes/regions in the deposited sequence were 
searched for using BLAST (Tab. 3). All together the nucleotide sequences of RepFIIA replicons of 10 
plasmids (p1658/79, pB171, pC15-1a, pCP301, pINV_F6_M1382, pO157, pTUC100, pWR501, R1 
and R100) were compared with the nucleotide sequence of pRK100 RepFIIA replicon.
The fi rst region analysed in the RepFIIA replicon is the repA2 gene, encoding a repressor protein, 
which by binding to the promoter represses the synthesis of repA1 mRNA (VANOOTEGHEM & CORNELIS 
1990). The repA2 gene is in plasmids pRK100, p1658/79, pCP301, pINV_F6_M1382, pWR501, and 
R1 261 bp long, in plasmids R100, pO157, pC15-1a and pTUC100 it is 255 bp long and in the plasmid 
7
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7
M. Starčevič Erjavec & al.: The RepFIIA replicon of the natural Escherichia coli plasmid pRK100
8 Acta Biologica Slovenica, 49 (1), 2006
pB171 it is only 249 bp long. The sequence analysis showed, that pRK100 repA2 is most similar to 
repA2 of pCP301, pINV_F6_M1382, pWR501 and R1, since the phylogenetic distance between them 
is the smallest, namely 0,0038 (Fig. 2A).
The second region analysed in the RepFIIA replicon is the copA gene, encoding the antisense 
RNA regulating the translation of repA1 mRNA (VANOOTEGHEM & CORNELIS 1990). The copA gene is 
in most of the compared plasmids approximately 90 bp long. The only exception is the copA gene of 
the plasmid pTUC100, which is 129 bp long. The sequence analysis showed, that there is no nucleotide 
divergence between pRK100 copA and the copA genes of R100 and pC15-1a (Fig. 2B), and hence the 
pRK100 repA gene is identical to the appropriate genes in R100 and pC15-1a.
The third region analysed in the RepFIIA replicon is the repA6. repA6 encodes a short leader 
peptide, whose expression is inhibited by CopA binding, preventing translation of RepA and conse-
quently preventing plasmid replication. (BLOOMBERG & al. 1992). The repA6 is only 75 nucleotides 
long and it has the same size in all compared plasmids. The compared nucleotide sequences of pRK100 
repA6 was completely identical (no nucleotide divergence) to repA6 of plasmids pC15-1a, pCP301, 
pINV_F6_M1382, pWR501, R1 and R100 (Fig. 2C).
The fourth region analysed in the RepFIIA replicon is repA1 gene, encoding the RepA protein 
needed for the plasmid’s replication (HELINSKI & al. 1996). The repA1 genes of plasmids pB171, pC15-
1a, pINV_F6_M1382, pO157, pTUC100, R1 and R100 are 858 bp long, the repA1 of p1658/79 is 869 
bp long, and the repA1 genes of plasmids pCP301 and pWR501 are 870 bp long. The phylogenetic 
distance between the pRK100 repA1 nucleotide sequence and the repA1 of plasmid p1658/79 is the 
smallest, only 0,0154 (Fig. 2D), hence the pRK100 repA1 is most similar to repA1 of plasmid p1658/79.
The fi fth and the last region analysed in the RepFIIA replicon, is repA4. Though it encodes no 
product, it is important for the stability of plasmid maintenance (JIANG & al. 1993). The p1658/79 
repA4 is 207 bp long, while the repA4 sequences of other compared plasmids are around 385 bp long. 
The phylogenetic distance between the pRK100 repA4 nucleotide sequence and repA4 of plasmid 
pCP15-1a is the smallest, 0,0520 (Fig. 2E), therefore the repA4 nucleotide sequence of pRK100 is 
most similar to repA4 of plasmid pCP15-1a.
Since the individual pRK100 rep genes/regions are similar to rep genes/regions of different 
plasmids, it can be concluded, that the pRK100 RepFIIA replicon is mosaic in structure and unique 
among the RepFIIA replicons.
Discussion
Plasmid replicons are essential for plasmid maintenance in the host cell. The replicons can differ 
with regard to their replication control mechanisms, origin of replication sequences and replication 
proteins. Plasmids with very similar origin sequences and replication control mechanisms are as-
signed into families. The pRK100 replicon described in this article belongs to the RepFIIA family 
of replicons.
In order to characterise the RepFIIA replicon of pRK100 its nucleotide sequence was fi rst searched 
for genes/regions. Each RepFIIA replicon consists of fi ve genes/regions, repA2 gene, copA gene, 
repA6 region, repA1 gene and repA4 region. With the help of the computer programs “ORF Finder” 
and BLAST the fi ve genes/regions in the pRK100 RepFIIA replicon were determined, however the 
genes are only putative and more experimental work is needed to confi rm the predicted gene lengths 
and their functions.
To elucidate the similarity of the pRK100 RepFIIA replicon with other known RepFIIA replicons, 
a BLAST search on the complete pRK100 RepFIIA nucleotide sequence was performed. More then 
170 BLAST hits were found, most of them belonging to replicon sequences of plasmids from En-
terobacteriaceae. This is not surprising as the broad RepFIIA replicon family is known to be highly 
prevalent in enteric bacteria (OSBORN & al. 2000). 
9M. Starčevič Erjavec & al.: The RepFIIA replicon of the natural Escherichia coli plasmid pRK100
Fig. 2: Nucleotide divergence of pRK100 RepFIIA rep gene/region sequences and related sequences.
 Nucleotide divergence, as the measurement of the phylogenetic nucleotide distance, was calculated ac-
cording to the Kimura-2 parameter. Nucleotide divergences between pRK100 sequences and sequences 
of other related plasmids are plotted: Panel A – nucleotide divergence of repA2, panel B – nucleotide 
divergence of copA, panel C – nucleotide divergence of repA6, panel D – nucleotide divergence of repA1, 
and panel E – nucleotide divergence of repA4. 
Slika 2: Nukleotidna divergenca dobljenih zaporedij genov/regij rep replikona RepFIIA plazmida pRK100 in 
sorodnih zaporedij.
 Nukleotidna divergenca, kot mera za fi logenetsko razdaljo, je bila izračunana po parametru Kimura-2. 
Nukleotidne divergence med zaporedji plazmida pRK100 in ostalimi sorodnimi zaporedji so prikazana: 
graf A – nukleotidna divergenca repA2, graf B – nukleotidna divergenca copA, graf C – nukleotidna 
divergenca repA6, graf D – nukleotidna divergenca repA1 in graf E – nukleotidna divergenca repA4.
Nucleotide divergence repA2
0,0154
0,7928
0,8175
0,0038
0,0038
0,8175
0,8175
0,0038
0,0038
0,8175
0 0,2 0,4 0,6 0,8 1
p1658/79
pB171
pC15-1a
-pCP301
pINV_F6_M1382
pO157
pTUC100
pWR501
R1
R100
Nucleotide divergence copA
0,0566
0,0572
0,0000
0,0691
0,0691
0,0833
0,0833
0,0742
0,0108
0,0000
0 0,2 0,4 0,6 0,8 1
p1658/79
pB171
-pC15-1a
pCP301
pINV_F6_M1382
pO157
pTUC100
pWR501
R1
R100
Nucleotide divergence repA6
0,0134
0,0134
0,0000
0,0000
0,0000
0,0134
0,0134
0,0000
0,0000
0,0000
0 0,2 0,4 0,6 0,8 1
p1658/79
pB171
pC15-1a
pCP301
pINV_F6_M1382
pO157
pTUC100
pWR501
R1
R100
Nucleotide divergence repA1
0,0154
0,0546
0,0534
0,0597
0,0597
0,0447
0,0571
0,0597
0,0420
0,0534
0 0,2 0,4 0,6 0,8 1
p1658/79
pB171
pC15-1a
pCP301
pINV_F6_M1382
pO157
pTUC100
pWR501
R1
R100
Nucleotide divergence repA4
0,0777
0,0989
0,0520
0,1220
0,1625
0,0841
0,0782
0,1157
0,0664
0,0665
0 0,2 0,4 0,6 0,8 1
p1658/79
pB171
pC15-1a
pCP301
pINV_F6_M1382
pO157
pTUC100
pWR501
R1
R100
A B
C D
E
10 Acta Biologica Slovenica, 49 (1), 2006
The most relevant BLAST hits (BLAST score more then 1000 bits) were used for a detailed similar-
ity analysis. The chosen RepFIIA replicons to be compared with the pRK100 replicon were harboured 
by plasmids p1658/79, pB171, pC15-1a, pCP301, pINV_F6_M1382, pO157, pTUC100, pWR501, R1 
and R100. Since it is known, that the RepFIIA replication family is mosaic in its composition (OSBORN 
& al. 2000), each rep region was analysed separately. Also from our analysis the mosaic structure of 
the pRK100 RepFIIA replicon is evident, since RepA2 of pRK100 is most similar to repA2 of pCP301, 
pINV_F6_M1382, pWR501 and R1, copA is the same as copA of plasmids pC15-1a and R100, the 
repA6 of pRK100 is the same as repA6 in plasmids pC15-1a, pCP301, pINV_F6_M1382, pWR501, R1 
and R100, repA1 is the most similar to repA1 of plasmid p1658/79, and repA4 of pRK100 is the most 
similar to repA4 of pC15-1a. Further, it can also be concluded, that the composition of the pRK100 
RepFIIA replicon is unique.
Even though all nucleotide sequences of genes/regions incorporated into this study, belong to the 
same replicon, the RepFIIA, the nucleotide divergence between different genes/regions is not the same, 
thus the repA6 region is very conserved, while other genes, as copA and repA1, are less conserved. A 
higher level of nucleotide divergence was observed in the repA4 sequence. This fact is not surprising, 
since this sequence has no product and hence no product-connected selection can infl uence the evolu-
tion of this sequence. However, the greatest differences in nucleotide divergence were observed in the 
repA2 gene, encoding the repressor. It might be assumed that the observed differences are important 
for plasmid incompatibility and it would be very interesting to test the ability of the studied plasmids 
to propagate in the same host. 
The observed mosaicism of the pRK100 RepFIIA replicon is not the only example of a mosaic 
sequence of pRK100. In a previous report (STARČIČ ERJAVEC & al. 2002) we also demonstrated, that 
the pRK100 tra region is mosaic. However, overall the studied tra region genes were most similar to 
the tra genes of plasmid F, but in the case of the pRK100 RepFIIA replicon, no overall similarity with 
only one plasmid could be detected. This again illustrates, that plasmid genes are mosaic and formed 
by multiple recombination events between diverse ancestral genes (BOYD & al. 1996). 
Conclusions
To summarise and conclude:
1. the pRK100 RepFIIA replicon harbours 5 genes/regions repA2, copA, repA6, repA1 and 
repA4;
2. the individual rep genes/regions of the pRK100 RepFIIA replicon exhibit different nucleotide 
divergence when compared with different related plasmids;
3. the pRK100 RepFIIA replicon is mosaic and unique;
4. many other plasmids of Enterobacteriaceae carry replicons similar to pRK100 RepFIIA 
replicon.
Povzetek
V predstavljeni raziskavi smo na nivoju nukleotidnih zaporedij preučevali podobnost replikona 
RepFIIA plazmida pRK100 z replikoni RepFIIA ostalih sorodnih plazmidov. S pomočjo računalniških 
programov “ORF Finder” in BLAST smo na zaporedju replikona RepFIIA plazmida pRK100 poiskali 
replikacijske gene/zaporedja repA2, copA, repA6, repA1 in repA4. Z računalniškima programoma 
CLUSTAL W in PHYLIP smo predvidene replikacijske gene/zaporedja primerjali z replikacijskimi 
geni/zaporedji drugih sorodnih plazmidov (p1658/79, pB171, pC15-1a, pCP301, pINV_F6_M1382, 
pO157, pTUC100, pWR501, R1 in R100), ki so deponirani v GenBank in smo jih poiskali z 
računalniškim programom BLAST. Na podlagi dobljenih nukleotidnih divergenc je razvidno, da je gen 
11
RepA2 od pRK100 najbolj podoben genu repA2 plazmidov pCP301, pINV_F6_M1382, pWR501 in 
R1, copA je enak genu copA na plazmidih pC15-1a in R100, regija repA6 plazmida pRK100 je enaka 
regiji repA6 plazmidov pC15-1a, pCP301, pINV_F6_M1382, pWR501, R1 in R100, gen repA1 je 
najbolj podoben genu repA1 plazmida p1658/79, in regija repA4 plazmida pRK100 je najbolj podo-
bna regiji repA4 plazmida pC15-1a. Če povzamemo vse rezultate, lahko zaključimo, da je replikon 
RepFIIA plazmida pRK100 sestavljen kot mozaik in da ga v takšni sestavi do sedaj še niso našli na 
nobenem drugem plazmidu.
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