Primersequenzen Teil 1 (Primer Für PAGI-2(C)-Orfs)

Table S2: PCR-primer sequences

productsizeprimer Aprimer B

[bp]

macroarrays

PAGI-2 macroarray:

C1500C1forGGTGAGTTCGGCCTACAACCC1revGTTGCCAATCGGGAACTCGC

C2500C2forGTGCCATCCTCATGCTTCTCCC2revTGAGTCACGACCTCGTAGGG

C4523C4forCGAACAGGCACGCGAAAACGC4revAACCGGAATCTTGCTCGCCG

C5279C5forAAGTGATCCTCCACGCACCGC5revAGATCCATCCCGCTTGCTGC

C6503C6forAGGTTCGAGACCGAGTTGCCC6revCCAAGAATCTTGGAGCGCCC

C7514C7forAGGCAGCGATGATGTTGGCGC7revATCCTGCGTGCCAGAACACG

C8516C8forCGCAGGAATTCAAGGTCGGCC8revGTGCCAGGTTGTCATCGAGG

C10466C10forTTGTTCGCGCTGGGTTTGGG C10revAAGCGGCCTGTGCCAAATGC

C12329C12forCTTTCTGTTCACGGCTCCGGC12revGGCTGCGCAGATTCATGACC

C13415C13forTTTCCTATGGCCGCTGCTCGC13revCACATAGGTTTCCGGCACGC

C14781C14forCTCGCTTTGTTCGCATGGCGC14revGTCCGTTTGCATCGATCGCC

C18458C18forTGACTTTCCGGATCGTGCCGC18revCAGTTCACCAAGCCATCGCG

C20576C20forCGTCAACCATTCACCCTCGGC20revATTTGGCATGCCTGCTCGGC

C21553C21forCCTGCTTGAAGACGGCATCGC21revGCTCAAGTTCACGAGCACGC

C22626C22forACCTGTGGAACGGCTCAAGCC22revCAATCCCTGCGCACGTAACC

C23545C23forACCCTATGGCGATGCCATCCC23revCAGTTGTACGACTCGGGTCC

C25417C25forAACAGCTAAGAGGCCGTGCGC25revTCAACAGGTACGCGACCAGG

C26507C26forTCATCGCGAATATCCCGGGCC26revCGAATGCGTAAGCTCCCAGG

C27519C27forGAAGGCGATGTACCTCTCGGC27revCCATAGCCGTCATAGCTGGC

C29426C29forCCCTGAAATCCATCTCGCCCC29revCGAAGCCCGAAAGCACATGG

C30230C30forGTCGTTTCTACAGGACGGCGC30revTACGGTAGTGCAGGGTCTGC

C31543C31forTCTCGCGCATCATGATCGGCC31revAGCCGAAATTCCAGCCCACG

C32300C32forTTACCGGCAACTGACGCAGGC32revGCGTTCGATGCGTACATCGC

C33319C33forACCACCGACTTCGTTGCGACCC33revCATCGGGTGCGTTGATGACG

C34502C34forCGACGCCTATTTCTCAGCGGC34revCGCGATCTTCTTTGCGAGGG

C35519C35forTGCGCTTGGAACTTGTCCCGC35revTGTCGTTGCGCACAAGGTGG

C36533C36forGCTGGACCCACTCATTCACGC36revGTATGCGGTATCGCTGACGG

C37456C37forTTCATTGCCGATCGCCTGCCC37revCTCCTGAAGCACGGTTTGGG

C38494C38forGATCGATGCCGGTGAACTGCC38revCAACGCCTACCTTTGCTGCC

C39247C39forCGCATCAGCACTGCGGAACGC39revGCTCCCATTCGACGGTATCG

C40541C40forGGACACGAACGGCTACTACGC40revAAACTGCACCACGCTGACCG

C42477C42forGGCTACAACCTGGTCAACGGC42revTTCGTTGGCTGCGACGTTGG

C43462C43forAGCAACACCGGAGAGAACCCC43revCTGGTACACGTGCAACTGCC

C44298C44forAACCCTTGGCCTGGCCATCGC44revACCCAAACTCCATGCGTCGG

C45416C45forATGACTCCTGCCTGGAGTCGC45revTACCCGCACATCGATGAGCG

C46510C46forCCCATCCATTCCGATGCAGGC46revAGACACTGCTCGATCGCTGG

C47a636C47cfGTTCGAGGACACGGTGGTTACGC47crGTCTCGCCCACAGCTTTCTTCG

C47b522C47dfGCAGAGAAGCGCACTGTGCTCACGC47drCTCCACTTCATCGGGGGGCATCG

C49505C49forTGGGGTCAAGAGTGCCAAGCC49revCGAGCCGACATAGGACATGC

C50435C50forCTGATCCTGCTGGACATCGCC50revGAAATCGCCTTGCAGCACGC

C51503C51forTGCAGGCGCACATCAAGACCC51revGATCGGATAACGCACCAGGG

C52306C52forTCAACCGCCATCCCGTTGTCGC52revAGCGCGAGATCAGCACGTGG

C54-55593C55forGGTGGCTTCGATCTGGCTGCC54revCTCAGGACGAGGTACATCGC

C56363C56forTCCAAGATGACCCTTCCCGCC56revCTGCATCAGATCGGCGAACC

C57473C57forATTCACCGCCGTCTACGACGC57revTCGGCGGATGCTTGAGTTGG

C58504C58forGACTGGGAAGACCTCCTTGGC58revTGAGCCGAGGAAAGCTTGCC

C59368C59forGCGATGCGTTGCAGACATGGC59revCTGCGTGGCAATTCCTTGGC

C61535C61forCTGACCGGTTCCTATGCTCGC61revACGACTGGATCTCGCGATCG

C62535C62forACGTCCCATCGAGGTACAGCC62revAGCGCCTTGTCCATGGATGG

C63605C63forTTGTCCTGCCGAATCGCAGGC63revCGCTGAAGACGATCAACGCG

C64500C64forGCACCTGTTCTGGAAGGACCC64revGATAGGTGACCCAAGGCAGC

C65558C65forCGTCATCAACATCGACGCGCC65revTCCGCATGCACGTTGATCGG

C66383C66forGTTCACGGGCCTACTCATGCC66revTCTCGACGTTGACGACCAGG

C67381C67forTCACTGCCGGCCTGTATGCCC67revGCTGCTCCTTCAGGATCTCG

C68641C68forCCGTCGATCCTCCTTTTCGCC68revTGGTTGAGCGTGATGCTGCC

C69497C69forAGAGCCTGATGTGGCTCTGGC69revCAGCAGCACCTGAAGTTGGG

C70449C70forTTCACTATCCCGAACGCCGCC70revGTCATCCGCGTGCAGTTCCC

C71682C71forCTGTTCCACCTGCTGTTCCGC71revCCTTGAAGCCTTCCTGCTCC

C72213C72forGCGCTCATCTTCAGCAGAGGC72revCTGCGAATCGGTGACGATGC

C73263C73forTCCCCAATCCGTTCAAGCGGC73revGCTGGTCTTGACGATCAGCG

C74689C74forGGACCTGATGGACACGATGGC74revGGGTGTCACCTTTGACGACG

C75604C75forCTTCTTCCACGCTGTACCGCC75revTTGGCCGGATACGGATAGGC

C76-77638C77forATCGCGGTCCGAACTGATCGC76revGTGCGGGTTGAAGTGAAGCG

C78299C78forCCACCATCGCTTGCGATACCC78revGCAGTAGCCGAACTCGATCC

C79553C79forCCGAGAAATCTGTTGCGCCCC79revTCCAGTTTCACGGACTCGCC

C80687C80forCTGGTATCCCGCTTTGCTCCC80revGACTAGGTTCTCCTGGACGC

C81805C81forTCGCCTTATCAACCCACCGCC81revTGTGGACCAGCGTCGATTCC

C82-83744C83forACCCGTTCGATGACTGGTGGC82revCAGGTGCTCGGGGGTATCGG

C84514C84forATCATCGACCTGCACGACCGC84revGCGACAGGTACTGCAACAGG

C85673C85forGCCATGCCAAGTACGAAGGCC85revGCCACATAGACGAACTGCGG

C89641C89forCATGATGCCTTCGCTGGTCGC89revTCTGACGGTGCAGTTCCACC

C90231C90forTTCCCCGACCTCATCACACCC90revCACGTGTTTCCACGTGTCGC

C91535C91forCCCAATCCCTTTCTACGCGGC91revGCGTGGAGATCAGCTTGACG

C92606C92forCGAAAGGAGCCTTCATGGCCC92revGATTGATGGTCTCCAGCGCG

C93319C93forGAACCAGCTTTTGCCCCAGGC93revCGACAGTCCTTGGAAGTGGC

C94356C94forCAGCAGCCAGAGTTTCCAGGC94revTTTCGAGGGCACGTTGAGCC

C95289C95forTGCTGATGTCACCCGTTCGCC95revACATGCTGCTTCCACAGGGC

C96439C96forGTGGTACTCACTCGCGATCGC96revCACGCTCATGAACGACTGGG

C97714C97forATACAAGGTGACCGCAGGCGC97revTCGTCCATCAGCAGGATCGC

C98375C98forATGCGGATCGGTGAACTGGGC98revGTTGAGAATGCCGCACTCGC

C99208C99forATGGCTCGGCTTCTTGGTCGC99revCAGCGTGTGCTTTTGCGACC

C100516C100forCGAAAACGACGAGTTGGGCCC100revAGATCCGGGATGTTCGACCC

C101716C101forCTGTACGAGACGCACAAGGCC101revCCCTTCTTCACGAGGTAGCC

C102343C102forCACAATTCATCGGCGAGGGCC102revACAGACTCGATGCGGTACGG

C103408C103forGAACAGCCAGCCTTCATGCGC103revGCATTCCTGTGCTTGCCTGC

C104577C104forAACTCAACCTCGGCTCCCTGC104revTTCTCCAATGCTGCCCGAGC

C105765C105forGATGGCGTCACGGCATTTCCC105revGTTGCGGATGCCATGCTTGC

C106436C106forATCGCATCCGCTCAACCAGGC106revATCGACGTTCCTGCTGCTGG

C107685C107forTCCCACTGTGCTCTATGGCGC107revGTCGATGTACCAGACGTCGG

C108659C108forACTACGAACTGACCCAGCGCC108revCCATTGCGGGAACAACTCGC

C110583C110forTCTATCGTCCCATCGAGGCGC110revGAATAGGGCACGCCTGAAGG

C111382C111forGGTCAGATGGGTAAGCACGGC111revCGAGTTCCGGATCTGAGAGC

pKLC102 macroarray:

CP1 497CP01lCTACGACCTGGTGCTGATCGCP01rCCTTGACCAGTGCTGCTACC

CP2602CP02lCCAACAGGCCAAGTTGACCGCP02rCGTCTGTCCAGAGCTGAAGG

CP3465CP03lCCTCCAGAACCGCAACAACCCP03rAGCACTGCACTTGCCTCTGC

CP4531CP04lCGATACAGCGAGTGGATCCCCP04rGCTGCTGGGTTTAGCTTGGG

CP5423CP05lTCAAGCCCTGTCCACTCTGCCP05rCGTCGTCGTTGCTGGTATCG

CP6 611CP06lAGGTCGAGAAGCTGATGGCCCP06rGTTTTTGCCGTGCTCCCAGC

CP7608CP07lGCATCCGCGAAACCTGGACCCP07rCTCGACCTCCTGAATGGTGC

CP8286CP08lCTTTGCCACCATCGAAGGCCCP08rGGTGATCGCCGACAATGTCC

CP9569CP09lGGAGGAGATCGAGCAGAAGCCP09rGCATCAGCTGCAGGTAGTCG

CP10255CP10lCGGACCACTAGATAGCCAGGCP10rGGACGCCATTGAGTATGCGC

CP11510CP11lACACTGAAGCCCGCTTTCCGCP11rCCTTGCTGAGTGCATCACCG

CP12279CP12lCGTCAAGTTCAATGGCGCCGCP12rGCATCAGCTCGCCTTTCTGG

CP17483CP17lTCCCGGGTAATCCCTCTACCCP17rGCTGGTCGTGTGAGTTCAGG

CP18556CP18lGAAAATCCTGGCCACAGCCGCP18rTGGTGTCGTATCGCCTTCGG

ori2274ori2lCATCATCGAGCAGTGGCAGCori2rCCGAATGAGGTCCTTGAGCC

CP19356CP19lGACGATCCGTACTCCGACTGCP19rCCCGAGAACTGGTAGCTCTG

CP20350CP20lGGCAGCTCGATAAGGACCAGCP20rGTCCTGGCGCAGCATTTCCG

CP21375CP21lGTAAGGCCGTATCCCACTCGCP21rGCAGGTGGTTGTGACTGAGG

CP22304CP22lCAGGGTGGCTACAAGGATCGCP22rCATCCTGCTGAGCAGGTTGC

CP25346CP25lGTCCTCAACTCTCAAGCCGGCP25rCAAAAACCGCCCGCAAGAGG

CP27370CP27lCGCACTACCAGATCCTCTCGCP27rAGGACCACCAGGTACACAGC

CP28271CP28lGGTTTCGGCTTCATCACCCCCP28rGCTGACGGAGATAGTGACG

CP30450CP30lCGAACCGCTACCTGCTTACCCP30rGCTCGCAGAGTTCCTTCAGC

template cosmid pKSCC187

CP32429CP32lGCCAGGTTCGGAACGAAACCCP32rCTTCTTCGCTTGGGTCGTGC

CP33475CP33lACACCCTCCAGGTCCTCTCCCP33rCAGGACTGTGCCAACTGTCG

CP34502CP34lCGAGCTGAAGACCTCGATCCCP34rGGCCAGGTAGCTGTCGTAGC

CP35 310CP35lGACCTCGAGGACATGCTACGCP35rGGTACAGATGGCTGGTGAGC

CP37476CP37lGAAGACCGTCGAGCAGTACCCP37rCATAGACCAGTGGGGTCTGG

template genomic DNA strain C

CP39338CP39lGATCATCATCGCCATCGGGGCP39rTCTTCGCGATCTTGGTGGCC

CP40587CP40lGGGAGTTCCAAGAGATCGGCCP40rGATCTTGTCGCGCATGGACG

CP41568CP41lGCCAACGAGTACCTCTACCGCP41rCGTGCAACGTACACCAGTCC

template cosmid pKSCC050

CP42361CP42lGCTGATGTGGATCGTCCTGGCP42rCGTGACTAACTGGCCGTTGC

CP43375CP43lCCACCAGCTTCGAAATCGGCCP43rAGCAGGTCAGCGGATCAACC

CP44272CP44lGGGTCCGCAAAACTTTCCGCCP44rGCTTGAGGTTGGGCCAATCG

CP46397CP46lGAGCAACAACACCCAAGCCCCP46rCTTCGCATCGTAGACGGTGG

CP47/48535CP47/48lCCATCTTCATCTCGAACTGCCP47/48rCTTTACGCCGAGCCTTCTGG

CP49523CP49lCCCGGCTATGAGAGTTTCCGCP49rGGATCTCCAGGCACTCATCC

CP50316CP50lCTCAACAACCACTCCAGCGCCP50rGGCTTTCTTCCTGCAGCTCG

CP51265CP51lTCCGTCCCTCCTACTACACCCP51rGGAGGGTCCATACCGAAAGG

CP52/53585CP52/53lGGAAGACCTGCTGCGTAAGC CP52/53rCGAACGCTCTTGGTGTGAGG

CP54532CP54lAGAGTGCCCAGACCTGTACGCP54rGATCAGCTCACCGAGAGTGG

CP55504CP55lTGGTCGTGAAGGGTGACACCCP55rAGTCGCTAGGGAGCAACAGG

CP56416CP56lCAACGTACTGCCCGACTACCCP56rGTAGCACTGCCACCTTCAGC

CP57575CP57lGTACCGAGGCTGCTTACTGCCP57rCTCAAAGCTGAGGTCCCTCC

CP58255CP58lGTGCTGTAAACCACTGCCGCCP58rAGAGTTCGGCGCACATTCCC

CP59435CP59lCACAGTCTCACCTTCCCTGGCP59rGCAGACGCGGTAGGTATTCG

CP60337CP60lAGGACGTCTTGTCGGAGAGCCP60rCTGGTAGCTCAGGGCAAACC

CP62481CP62lCCTCAAGCTCCTGGTCATCCCP62rCAGCTCTACGCCTCCAATCC

CP63303CP63lGCTGGGCTACCAGCAATACCCP63rTCCAGCGTCTCCACTGTAGC

CP64319CP64lGTGCTGCTGCTGAGCTATCCCP64rGGTAGGCGAGTTCCTTCTCG

CP65551CP65lGGCAACGTCTGTAATCCGCGCP65rCGAGGACTTGGCTAAGGTGG

CP66312CP66lCAGGTGCGTTTCCAGTTCGCCP66rTGGCGGTGGATGTGATGAGG

CP67555CP67lCCATGGTCAACAAAGCGGGCCP67rCGAGGTGACGGAAATCGTCG

CP68320CP68lCCCAGTTGGCCTATGACTGGCP68rCGCCTTGTGGTAGAGGTAGC

CP69512CP69lCGAGGGACAGGACATCAACCCP69rCCACGTACTGGGTGTAGTCG

CP70587CP70lCAGCGCAGAGTTCAATGGCGCP70rTTGGTAGGCCTTGTGCGTCG

CP73/74321CP73/74lCGGACAGCGCTTCTACTTCGCP73/74rGCTGTCGAGGTTGTTGGTGG

CP75329CP75lGAAACTGTCCACCCTCTGCCCP75rTGGTGGTGGCTTTGGTGACG

CP76267CP76lTTCAGGATGGGACCCTCAGCCP76rGGCGGTAGAACCAGGTATCG

CP77283CP77lGGCGGACTACAAGAGCAACCCP77rGATGACGTGCAACGGGTAGC

CP78581CP78lACTCTACCTGCTCGCCAACGCP78rGATACACGGTGGTGGTGTCG

CP79510CP79lGACGGGACGGTCAATGATCCCP79rGGAGAGGATGCTGTTGAGGG

CP80327CP80lCCAACATGCTCGACGTCTGGCP80rAGTAGTCCTCCGTACGCTCG

CP81525CP81lTGCCCACGGCTTCATCTTCGCP81rCTGGAGGCCTGGTAGAGTGC

CP83451CP83lCGTTGGGGTAGAGCTTCTGGCP83rCGCTGTAATGCCGTTCGACC

template cosmid pKSCC867

CP84518CP84lGCACGGCTACGACTATCTGGCP84rCACACTCCCTGACGACATCC

CP85326CP85lCAAGCTGCAGCCACTGATCGCP85rCACCATGGGTGATCTCCTGC

CP86572CP86lCGAACACCGAGACACACTGGCP86rATCTACCTCTGCGCAGAGCG

CP87326CP87lGGCCGTTGGCTTACTACTGGCP87rAGACCACGTACTGCCTGTCG

CP88570CP88lGCAGTCGTCTCCAGCTATGCCP88rGGTCAGCTCCTGCCATTTCC

CP89354CP89lCAGTCATCCAGAACGCGACCCP89rCGATGCGAATGGGCTTCTGG

CP90297CP90lTGGCAGATACGCTCACCACCCP90rGGATCAGCAACAGCACCAGG

CP91405CP91lGGGTAGCCTGGCTTACTTCCCP91rCTGAGATCGCTGAGGAGAGC

CP92244CP92lAGCTATCTGCCGACTGGAGCCP92rGGTGATCTCGTCGTACTCGC

CP93344CP93lGGCCAAGTACCGCATATCCCCP93rGCTCCAGTCGGCAGATAGCT

CP94a605CP94-1lGCTCGTCCAACCAGTTGAGCCP94-1rCAGGCGTCTTGCTGACAACG

CP94b500CP94-2lTCGAGCCACTCTTCGCATGCCP94-2rGCTCTGGGCGTACCCTTCAT

CP94c540CP94-3lCCTGGTAGACATCCGAGACCCP94-3rGCATTGATGCGCGACAGTCC

CP96510CP96lCCTGGAGCGAGTTACACTGCCP96rCCGAGTTTCTGCAGCTTGCC

CP97337CP97lCGATATCTACGTACCCCGGCCP97rCTTTTTACCCGCAGTGGCGG

CP98478CP98lGCTACAGCCACCAGGTATCGCP98rCTGATGTCCATGTGCACGCC

CP99560CP99lGGTGGAATGCTGCGACTACCCP99rGCCTCTGAATGGAGCAGTCG

CP100535CP100lGCGATAGCCGAAAGCATGGCCP100rCGGCATCTTACAGCCAACGC

CP101301CP101lTCTTGACGGCTGGTGCAAGCCP101rGCTGGTGTAGATCAGGCTGC

CP102536CP102lCGCTCCAGCCTTGATTTGGGCP102rCGACGGTATGCACCAAAGCC

CP103a534CP103alCCGGAAGTTGACCGAGAAGGCP103arGATCCCCTTCCACCAGATCC

CP103b296CP103blGGAGCTGGAACACGTACTCGCP103brGCACAGCAGCGCATTCAACC

control spots on both arrays

P1650cit2CATGTCGACCGCCTCCTGCGcit3GCTTCGTTCGCGCCCCCATG

P2a530fla3aGAGCGCAGAGTCGCTGAACGfla4aGTTGATGGTGTTGTCGAAGCGG

P2b800fla3bTCCGATACCACCACCTTCGGfla4bTCGCAGCCAGGGCGTTATCG

N11289PP5aAGAGATCGCGGACAAGACCGPP5bAAGCAGGGTGGTTATGGGCC

N2300hOb1atttcctgtaattttccchOb2agtggtcctgaggtgacg

additional spots on pKLC102-arrays

ori1324ori1lGTTCGGCATCCGAACTCTGCori1rCGAAGATCCTCGGACACTCG

PA0977275PA0977lAGCCCGCCTTTATAGGTGGGPA0977rCCGAAGCAATCTCGCCTAGC

PA0981320PA0981lGGTCACTGTTTCTGCCAGCGPA0981rGGACCTCACCATACACTGCC

TB-spec503TBspeclTGCTATGCCAGAGCTTCCGG TB-specrGGAAATGGGCTTGAAGGGCG

D8A6506D8A6lGCTTCGAAATGCCCTCCAGGD8A6rCGAAGATTCAGGAGCGCTGG

combinatorial PCR:

spanning PAGI - integration sites

location

genomicg1fTCCAGCGTGAAGCCAAACGCg1rCTTCGACCCAGGCCGAAACC

PAGI-2Cins1fGTGTCCTACAGCCGTCCAGGCins1rGGTATCGGGGATGCTGTAGG

PAGI-3SGins1fCAGGAACCCTCTTTCGCTGCSGins1rGTAGTCTTTGCCAGTCGGGC

spanning pKLC102/PAPI-1 - integration sites

genomicKAD-ACGAATCTCTCTACCCCGACCACCKAD-5rATGGTGGGTCGTGTAGGATTC

KAD-BGGAGTTCGAATCTCTCTACCCKAD-6rTCCTTCCCACAGGCCAGCATTCG

pKLC102KAD-1ATCGTCCTGGAGATGATCCTCKAD-CrATTGCTACGCCTGCAGAATGG

and PAPI-1

All primer sequences are given in 5’  3’ direction.

Table S3. Island-specific “cargo” ORFs of PAGI-2 and PAGI-3

PAGI-2 (52 cargo ORFs)1

ORF no. / gene name / length
[bp / aa] / homologous protein2 / GenBank accession no. 2 / E value2
C5 / 324 / 107 / hypothetical protein XCV2302 (Xanthomonas campestris pathovar vesicatoria 85-10) / CAJ23979 / 5E-29
C6 / 1377 / 458 / putative pyridine nucleotide-disulfide oxidoreductase XCV2303 (X. campestris pv. vesicatoria 85-10) / CAJ23980 / 0
C7 / 807 / 268 / putative membrane protein XCV2304 (X. campestris pv. vesicatoria 85-10) / CAJ23981 / 7E-91
C8 / dsbG / 774 / 257 / thiol-disulfide interchange protein XCV2306 (X. campestris pv. vesicatoria 85-10) / CAJ23983 / 2E-103
C9 / 837 / 278 / putative thiol disulfide interchange protein XCV2307 (X. campestris pv. vesicatoria 85-10) / CAJ23984 / 1E-115
C10 / dsbD / 1854 / 617 / cytochrome C biogenesis protein AjsDRAFT_0272 (Acidovorax species JS42) / ZP_01384748 / 0
C11 / cycH / 882 / 293 / cytochrome C biogenesis factor Neut_0056 (Nitrosomonas eutropha C71) / YP_746309 / 1E-63
C12 / ccmH / 456 / 151 / cytochrome C biogenesis protein Neut_0057 (N. eutropha C71) / YP_746310 / 3E-38
C13 / ccmG / 525 / 174 / periplasmic protein thiol-disulphide oxidoreductase Neut_0058 (N. eutropha C71) / YP_746311 / 2E-65
C14 / ccmF / 1962 / 653 / cytochrome c-type biogenesis protein Neut_0059 (N. eutropha C71) / YP_746312 / 0
C15 / ccmE / 447 / 148 / cytochrome c-type biogenesis protein Neut_0060 (N. eutropha C71) / YP_746313 / 3E-55
C15b / ccmD / 192 / 63 / heme exporter protein D Nmul_A1211 (Nitrosospira multiformis ATCC 25196) / YP_411906 / 1E-5
C16 / ccmC / 738 / 245 / heme exporter protein CcmC Neut_0061 (N. eutropha C71) / YP_746314 / 7E-94
C17 / ccmB / 687 / 228 / heme exporter protein CcmB Neut_0062 (N. eutropha C71) / YP_746315 / 2E-52
C18 / ccmA / 612 / 203 / heme exporter protein CcmA Neut_0063 (N. eutropha C71) / YP_746316 / 4E-50
C19 / armR / 669 / 222 / two-component system regulatory protein XCV2309 (X. campestris pv. vesicatoria 85-10) / CAJ23986 / 7E-106
C20 / armS / 1386 / 461 / two-component system regulatory protein XCV2310 (X. campestris pv. vesicatoria 85-10) / CAJ23987 / 0
C21 / cutE / 1599 / 532 / putative apolipoprotein N-acyltransferase BB1353 (Bordetella bronchiseptica RB50) / NP_887899 / 6E-143
C22 / 2316 / 771 / heavy metal translocating P-type ATPase BamMC406DRAFT_4479 (Burkholderia ambifaria MC40-6) / ZP_01552916 / 3E-96
C23 / 1098 / 365 / putative class I cytochrome C protein NB231_09513 (Nitrococcus mobilis Nb-231) / ZP_01126285 / 1E-67
C24 / 819 / 272 / putative class I cytochrome C protein ShewDRAFT_3076 (Shewanella sp. PV-4) / ZP_00835602 / 3E-29
C25 / ccoO / 642 / 213 / cytochrome C oxidase, mono-heme subunit BamMC406DRAFT_4481 (B. ambifaria MC40-6) / ZP_01552918 / 3E-54
C26 / ccoN / 1557 / 518 / cytochrome oxidase subunit (cbb3-type)
KT71_06177 (Congregibacter litoralis KT71) / EAQ96589 / 9E-148
C27 / 1671 / 556 / hypothetical protein Reut_B3588 (Ralstonia eutropha JMP134) / YP_297790 / 0
C28 / 960 / 319 / beta-lactamase-like protein Reut_B3589 (R. eutropha JMP134) / YP_297791 / 3E-120
C29 / 528 / 175 / putative detoxifying sulphur transferase
BAV2677 (Bordetella avium 197N) / CAJ50288 / 4E-55
C30 / 312 / 103 / ArsR-family transcriptional regulator BAV2678 (Bordetella avium 197N) / CAJ50289 / 2E-33
C31 / 1227 / 408 / major facilitator superfamily MFS_1 protein CtesDRAFT_2021 (Comamonas testosteroni KF-1) / ZP_01518763 / 4E-129
C32 / 378 / 125 / gamma-carboxymuconolactone decarboxylase subunit-like protein Rgel02001269 (Rubrivivax gelatinosus PM1) / ZP_00244444 / 2E-31
C33 / 372 / 123 / DsrE-like protein Pcryo_0027 (Psychrobacter cryohalolentis K5) / YP_579295 / 3E-31
C34 / fenO / 795 / 264 / enoyl-CoA hydratase ebA5318 (Azoarcus sp. EbN1) / YP_160048 / 4E-69
C35 / 996 / 331 / AraC family transcriptional regulator MED193_17344 (Roseobacter sp. MED193) / ZP_01054489 / 1E-77
C56 / 471 / 156 / excisionase-like protein VeisDRAFT_4928 (Verminephrobacter eiseniae EF01-2) / ZP_01398753 / 7E-49
C57 / 576 / 191 / hypothetical protein VeisDRAFT_4927 (V. eiseniae EF01-2) / ZP_01398752 / 2E-85
C58 / 915 / 304 / hypothetical cell division control protein NB311A_13726 (Nitrobacter sp. Nb-311A) / ZP_01047677 / 6E-115
C59 / 471 / 156 / hypothetical protein AjsDRAFT_0034 (A. sp. JS42) / ZP_01384975 / 4E-77
C60 / 501 / 166 / hypothetical protein AjsDRAFT_0027 (A. sp. JS42) / ZP_01384968 / 7E-84
C61 / 903 / 300 / hypothetical protein AjsDRAFT_0028 (A. sp. JS42) / ZP_01384969 / 5E-167
C62 / 960 / 319 / hypothetical protein RPE_2465 (Rhodopseudomonas palustris BisA53) / YP_781384 / 2E-112
C63 / 2625 / 874 / ATPase-like hypothetical protein AjsDRAFT_0030 (A. sp. JS42) / ZP_01384971 / 0
C84 / 642 / 213 / Tn3 transposase Mfla_1495 (Methylobacillus flagellatus KT) / YP_545604 / 1E-91
C84b / 516 / 171 / Tn3 transposase Rmet_4474 (Cupriavidus metallidurans CH34) / YP_586608 / 7E-51
C85 / merA / 1689 / 562 / mercuric reductase DaciDRAFT_3888 (Delftia acidovorans SPH-1) / ZP_01580145 / 0
C86 / merP / 288 / 95 / heavy metal ion chaperone EcolB_01004820 (Escherichia coli B171) / ZP_00708303 / 1E-16
C87 / merT / 351 / 116 / mercuric transport protein AjsDRAFT_2245 (A. sp. JS42) / ZP_01382655 / 2E-27
C88 / merR / 408 / 135 / mercuric resistance operon regulatory protein DaciDRAFT_3891 (Delftia acidovorans SPH-1) / ZP_01580148 / 2E-59
C96 / lspA / 501 / 166 / putative lipoprotein signal peptidase pA81_095 (Achromobacter xylosoxidans A8, plasmid pA81) / YP_195918 / 2E-49
C97 / 2913 / 970 / metal-transporting P-type ATPase pA81_097 (Achromobacter xylosoxidans A8, plasmid pA81) / YP_195920 / 0
C98 / 399 / 132 / merR-like transcriptional regulator pA81_098 (Achromobacter xylosoxidans A8, plasmid pA81) / YP_195921 / 2E-53
C99 / 237 / 78 / hypothetical protein pA81_099 (Achromobacter xylosoxidans A8, plasmid pA81) / YP_195922 / 2E-26
C100 / 636 / 211 / putative integral membrane protein pA81_100 (Achromobacter xylosoxidans A8, plasmid pA81) / YP_195923 / 2E-58
C111 / 501 / 166 / hypothetical protein Meso_3896 (Mesorhizobium sp. BNC1) / YP_676428 / 5E-61

1 The reader may note that in comparison to the initial annotation published in ref. (25) a novel, yet undescribed function could be ascribed to 16 of the 52 cargo ORFs of PAGI-2 and a closer homolog was identified for the other 36 ORFs.

2 closest homolog according to PSI- and PHI-BLAST search; copies of PAGI-2 or PAGI-3 were not considered

PAGI-3 (56 cargo ORFs)3

ORF no. / gene name / length
[bp / aa] / homologous protein4 / GenBank accession no. 4 / E value4
SG2 / hemE / 1062 / 353 / uroporphyrinogen decarboxylase MED92_17923 (Oceanospirillum sp. MED92) / ZP_01166443 / 2E-175
SG3 / 456 / 151 / hypothetical protein CtesDRAFT_0150 (Comamonas testosteroni KF-1) / ZP_01521627 / 2E-11
SG4 / 987 / 328 / chemotaxis sensory transducer PmenDRAFT_2477 (Pseudomonas mendocina ymp) / ZP_01524635 / 6E-68
SG5 / 753 / 250 / phospholipase A2 family protein ebA3785 (Azoarcus sp. EbN1) / YP_159159 / 5E-68
SG6 / istA / 1506 / 501 / putative transposase GuraDRAFT_3383 (Geobacter uraniumreducens Rf4) / ZP_01140466 / 4E-132
SG7 / istB / 744 / 247 / IstB-like ATP-binding protein AjsDRAFT_0383 (A. sp. JS42) / ZP_01384474 / 4E-73
SG8 / 1236 / 411 / diguanylate cyclase GlovDRAFT_1050 (Geobacter lovleyi SZ) / ZP_01594207 / 1E-37
SG9 / 777 / 258 / putative aminohydrolase IpuJ (Pseudomonas sp. KIE171) / CAC81342 / 1E-127
SG10 / gabD / 1455 / 484 / putative aldehyde hydrogenase IpuI (P. sp. KIE171) / CAC81341 / 0
SG11 / 879 / 292 / transposase Cpha266DRAFT_1534 (Chlorobium phaeobacteroides DSM 266) / ZP_00529146 / 1E-82
SG12 / 444 / 147 / transposase PnapDRAFT_3688 (Polaromonas naphthalenivorans CJ2) / ZP_01021338 / 2E-40
SG13 / 318 / 105 / transposase Neut_2190 (N. eutropha C71) / YP_748377 / 1E-21
SG14 / yumC / 981 / 326 / putative reductase IpuA (P. sp. KIE171) / CAC81333 / 1E-165
SG15 / glnA4 / 1383 / 460 / gamma-glutamylisopropylamide synthetase IpuC (P. sp. KIE171) / CAC81335 / 0
SG16 / 1161 / 386 / putative cytochrome P450 protein IpuD (P. sp. KIE171) / CAC81336 / 0
SG17 / 885 / 294 / gamma-glutamyl-L-1-hydroxyisopropylamide hydrolase IpuF (P. sp. KIE171) / CAC81338 / 1E-130
SG18 / 1431 / 476 / putative permease IpuG (P. sp. KIE171) / CAC81339 / 3E-169
SG19 / 1509 / 502 / putative aldehyde dehydrogenase IpuH (P. sp. KIE171) / CAC81340 / 0
SG20 / 1116 / 371 / enoyl-CoA hydratase PputDRAFT_5156 (P. putida F1) / ZP_00898188 / 2E-122
SG21 / 462 / 153 / acyl-CoA dehydrogenase like protein Pfl_2865 (P. fluorescens PfO-1) / YP_348596 / 9E-29
SG22 / pntAA / 1215 / 404 / alanine dehydrogenase / PNT-like protein PmenDRAFT_3459 (P. mendocina ymp) / ZP_01528013 / 4E-170
SG23 / pntAB / 318 / 105 / NAD/NADP transhydrogenase, membrane-spanning dIIa subunit PmenDRAFT_3460 (P. mendocina ymp) / ZP_01528014 / 4E-37
SG24 / pntB / 1464 / 487 / NAD(P) transhydrogenase, beta subunit PSPTO_5464 (P. syringae pv. tomato DC3000) / NP_795188 / 0
SG25 / 99 / 32 / putative transposase Rgel02003307 (Rubrivivax gelatinosus PM1) / ZP_00242458 / 2E-7
SG26 / 546 / 181 / transcriptional regulator (XRE family) Rfer_3227 (Rhodoferax ferrireducens T118) / YP_524467 / 4E-21
SG27 / 753 / 250 / short chain dehydrogenase SAR11_1289 (Candidatus Pelagibacter ubique HTCC1062) / YP_266697 / 3E-51
SG28 / 753 / 250 / putative glutamine amidotransferase AGR_L_2905 (Agrobacterium tumefaciens C58) / NP_357235 / 1E-85
SG29 / adh / 1041 / 346 / putative alcohol dehydrogenase AGR_C_3897 (Agrobacterium tumefaciens C58) / NP_355113 / 5E-124
SG30 / 1308 / 435 / class III aminotransferase BphyDRAFT_0319 (B. phymatum STM815) / ZP_01506118 / 9E-160
SG31 / 486 / 161 / transposase-like protein AvinDRAFT_7638 (Azotobacter vinelandii AvOP) / ZP_00416132 / 5E-31
SG32 / 264 / 87 / transposase ND064 (P. sp. ND6, plasmid pND6-1) / NP_943095 / 6E-8
SG33 / tnp / 981 / 326 / transposase like protein TnpA1 (P. stutzeri AN10) / AAD02143 / 0
SG34 / 183 / 60 / no significant similarities
SG35 / 465 / 154 / transposase-like protein Dhaf_1861 (Desulfitobacterium hafniense DCB-2) / ZP_01372270 / 3E-24
SG36 / tnp / 1050 / 349 / integrase-/transposase-like protein DSY4578 (Desulfitobacterium hafniense Y51) / YP_520811 / 4E-97
SG37 / 180 / 59 / no significant similarity
SG38 / 771 / 256 / beta-lactamase-like protein Pfl_2954 (P. fluorescens PfO-1) / YP_348685 / 2E-86
SG39 / 411 / 136 / ester cyclase-like protein Pfl_2953 (P. fluorescens PfO-1) / YP_348684 / 1E-31
SG40 / 999 / 332 / AraC family transcriptional regulator ECA2247 (Erwinia carotovora subsp. atroseptica SCRI1043) / YP_050342 / 5E-87
SG41 / 489 / 162 / putative recombinase Bxe_A2714 (B. xenovorans LB400) / YP_558302 / 2E-51
SG42 / 393 / 130 / putative monophosphatase Adeh_0432 (Anaeromyxobacter dehalogenans 2CP-C) / YP_463645 / 5E-8
SG43 / 516 / 171 / hypothetical Protein RRSL_04326 (Ralstonia solanacearum UW551) / ZP_00943020 / 1E-50
SG54 / 372 / 123 / hypothetical protein AvinDRAFT_8014 (Azotobacter vinelandii AvOP) / ZP_00415699 / 4E-43
SG55 / 246 / 81 / hypothetical protein MaquDRAFT_2402 (Marinobacter aquaeolei VT8) / ZP_00817334 / 1E-7
SG56 / 387 / 128 / no significant similarity
SG66 / 1506 / 501 / cAMP induced filamentation proteinAvinDRAFT_6584 (Azotobacter vinelandii AvOP) / ZP_00416125 / 0
SG74 / 1431 / 476 / putative transposase TnpA (P. aeruginosa PPV-108) / CAE46715 / 0
SG75 / 453 / 150 / no significant similarity
SG76 / 510 / 169 / FinO conjugation repressor domain protein PputDRAFT_2473 (P. putida F1) / ZP_00900638 / 2E-44
SG77 / 1077 / 358 / putative phage-associated protein NGO1012 (Neisseria gonorrhoeae FA 1090) / YP_208107 / 1E-50
SG78 / 966 / 321 / RelA-/SpoT-like protein RPC_3545 (Rhodopseudomonas palustris BisB18) / YP_533403 / 1E-37
SG79 / 747 / 248 / hypothetical protein V12G01_16672 (Vibrio alginolyticus 12G01) / ZP_01259552 / 1E-24
SG88 / 225 / 74 / no significant similarity
SG94 / 1563 / 520 / putative ATPase AaveDRAFT_2743 (A. avenae subsp. citrulli AAC00-1) / ZP_01405047 / 3E-148
SG95 / 120 / 39 / no significant similarity
SG106 / 219 / 72 / no significant similarity

3 The reader may note that in comparison to the initial annotation published in ref. (25) a novel, yet undescribed function could be ascribed to 17 of the 56 cargo ORFs of PAGI-3 and a closer homolog was identified for 30 ORFs. Annotation remained unchanged for nine ORFs, seven of which are hypotheticals of unknown function.

4 closest homolog according to PSI- and PHI-BLAST search; copies of PAGI-2 or PAGI-3 were not considered