. 2019 Aug 6;10(4):e01343-19. doi: 10.1128/mBio.01343-19

TABLE 1.

C. trachomatis coding region transposon insertion mutants

ctl gene (ct^c )::Tn bla	Gene name	Predicted function	Genomic position of TN insertion^a	Gene insert site/total gene length (bp)	Modified protein sequence^d	Sequence modification [truncated/normal length] (bp)^d
`ctl0027` `(``ct658` `)`	`sfhB`	`Pseudouridine synthase`	`33827`	`544/1,008`	QVKKLX	`[Y182X; 182/335]`
`ctl0063` `(``ct694` `)`		`Hypothetical`	`76200`	`17/969`	SIRPTNRLDDKSPVX	`[G8R; 16/322]`
`ctl0065` `(``ct696` `)`^e		`Hypothetical`	`79522`	`1,039/1,179`	MRVLLX	`[M347X; 346/392]`
`ctl0101` `(``ct732` `)`^e	`ribH` `(``ribE` `)`	`6,7-Dimethyl-8-ribityllumazine synthase`	`124470`	`44/474`	KDVRVTGWMISPRSDAQWNENSRX	`[A16T; 34/157)`
`ctl0105` `(``ct736` `)`		`Hypothetical phosphatidyl ethanolamine-binding proteins`	`129068`	`191/453`	WIHWITGWMISPRSDAQWNENSRX	`[V65T; 83/150]`
`ctl0125`	`murF`	`UDP-N-acetylmuramoyl-tripeptide-` `d` `-alanyl-` `d` `-alanine ligase`	`169474`	`1,328/1,353`	ELETLTGWMISPRSDAQWNENSRX	`[L404T; 462/450]`
`ctl0175` `(``ct806` `)`^h	`ptr`	`Periplasmic Zn-dependent peptidase`	`223999`	`1,236/2,871`	INSLEYNRLDDKSPVX	`[S422X; 422/957]`
`ctl0184` `(``ct813` `)`^h		`Inclusion membrane protein`	`235508`	`355/795`	QFRIVTGWMISPRSLVAQR-35AA-YFX^f	`[M120T; 171/264]`
`ctl0185` `(``ct814` `)`^e		`Hypothetical membrane-associated protein`	`236256`	`74/300`	FGGFLTGWMISPRSDAQWNENSRX	`[A26T; 44/99]`
`ctl0191` `(``ct819` `)`		`yccA` `-BAX inhibitor`	`242990`	`121/717`	TSLGLX	`[Y41X; 41/238]`
`ctl0201` `(``ctr829` `)`	`trmB`	`tRNA [guanine-N(7)-]-methyltransferase`	`258702`	`68/675`	IANHVTGWMISPRSDAQWNENSRX	`[F24T; 42/224]`
`ctl0202` `(``ct830` `)`		`Putative SAM-dependent methyltransferase`	`259440`	`17/585`	MLTGITGWMISPRSDAQWNENSRX	`[D7T; 16/194]`
`ctl0238b`		`Hypothetical`	`298245`	`184/306`	PYQYDX	`[Y62X; 62/101]`
`ctl0246` `(``ct867` `)`	`cdu2`	`Deubiquitinase and deneddylase`	`302887`	`877/1,020`	QFLAWX	`[Y293X; 293/339]`
`ctl0247` `(``ct868` `)`	`cdu1`	`Deubiquitinase`	`304303`	`889/1,206`	DSLYNX	`[N297X; 297/401]`
`ctl0250` `(``ct871` `)`	`pmpG`	`Polymorphic outer membrane protein`	`312316`	`786/3,039`	HPTCYFNRRSSSKFFQKYCGRVX	`[G738F; 755/1,012]`
`ctl0270` `(``ct015` `)`		`Phosphate-responsive ATPase, PhoH-like protein`	`338386`	`1,277/1,305`	ERSELTGWMISPRSDAQWNENSRX	`[A427T; 445/434]`
`ctl0291` `(``ct036` `)`^h		`Hypothetical, putative Inc`	`363864`	`620/1,158`	LQQHLTGWMISPRSDAQWNENSRX	`[D208T; 226/385]`
`ctl0298` `(``ct042` `)`^h		`Putative glycosyl hydrolase`	`369458`	`681/2,001`	PSRRYNRLDDKSPVX	`[T228N; 237/666]`
`ctl0310` `(``ct054` `)`^h	`sucA`	`2-Oxoglutarate dehydrogenase E1 component`	`385356`	`2,122/2,712`	ARIERX	`[Y708X; 708/903]`
`ctl0310` `(``ct054` `)`^h	`sucA`	`2-Oxoglutarate dehydrogenase E1 component`	`385932`	`2,699/2,712`	TLFSITGWMISPRSDAQWNENSRX	`[G901T; 919/903]`
`ctl0314` `(``ct058` `)`		`Putative membrane-spanning protein`	`390466`	`401/1,092`	GWNCITGWMISPRSDAQWNENSRX	`[E135T; 153/363]`
`ctl0339` `(``ct084` `)`		`Phopholipase D superfamily`	`419045`	`827/1,086`	TPYQLTGWMISPRSDAQWNENSRX	`[H277T; 295/361]`
`ctl0343` `(``ct088` `)`	`ssc1`	`Type III secretion chaperone`	`423934`	`413/441`	ELPDLTGWMISPRSDAQWNENSRX	`[H139T; 157/146]`
`ctl0361` `(``ct106` `)`^h		`tRNA pseudouridine synthase A`	`445244`	`626/825`	HQIRLTGWMISPRSDAQWNENSRX	`[H210T; 228/274]`
`ctl0362` `(``ct107` `)`		`A/G-specific adenine glycosylase`	`447004`	`1,089/1,107`	LEKDGNRLDDKSPVX	`[K364N; 373/368]`
`ctl0367` `(``ct112` `)`	`pepF`	`Oligoendopeptidase F`	`450974`	`1,767/1,825`	TSSAPNRLDDKSPVX	`[M590N; 599/608]`
`ctl0394` `(``ct139` `)`^h	`oppA`	`Oligopeptide transport system binding protein`	`479190`	`336/1,281`	AWEHTNRLDDKSPVX	`[K113N; 122/427]`
`ctl0398` `(``ct143` `)`		`Hypothetical`	`482984`	`708/843`	TSLYSNRLDDKSPVX	`[I237N; 246/280]`
`ctl0401` `(``ct146` `)`	`ligA`	`NAD-dependent DNA ligase`	`487189`	`1,164/1,992`	GINLANRLDDKSPVX	`[K389N; 398/663]`
`ctl0403` `(``ct148` `)`	`mphA`	`FAD-dependent monooxygenase`	`493563`	`487/1,524`	TPKWIX	`[I163X; 163/507]`
`ctl0408` `(``ct153` `)`	`macP`	`Membrane attack complex`	`499954`	`611/2,433`	PPGTKLTGWMISPRSDAQWNENSRX	`[T223X; 223/811]`
`ctl0408` `(``ct153` `)`	`macP`	`Membrane attack complex`	`500482`	`84/2,433`	SIDSDNRLDDKSPVX	`[R29N; 38/811]`
`ctl0413` `(``ct157` `)`		`Phosphatidylcholine-hydrolyzing phospholipase D`	`504003`	`956/1,206`	KESAHNRLDDKSPVX	`[T320N; 329/401]`
`ctl0417a` `(``ct159` `)`		`Hypothetical`	`506473`	`118/282`	MQGAYX	`[Y39X; 39/93]`
`ctl0423` `(``ct170` `)`	`trpB`	`Tryptophan synthase, beta subunit`	`512551`	`512/1,179`	VNQALTGWMISPRSLVAQR-35AA-YFX^f	`[Q172T; 223/392]`
`ctl0423` `(``ct170` `)`	`trpB`	`Tryptophan synthase, beta subunit`	`512763`	`723/1,179`	FFHHFNRLDDKSPVX	`[I242N; 251/392]`
`ctl0496` `(``ct244` `)`^h		`Hypothetical`	`591198`	`596/1,197`	VPVLITGWMISPRSDAQWNENSRX	`[A200T; 218/398]`
`ctl0500` `(``ct248` `)`	`glgP`	`Alpha-1,4 glucan phosphorylase`	`596937`	`845/2,445`	EGQELTGWMISPRSDAQWNENSRX	`[R283T; 301/814]`
`ctl0550` `(``ct298` `)`^h	`radA`	`DNA repair protein`	`650265`	`429/1,365`	ISSNITGWMISPRSDAQWNENSRX	`[I144T; 162/454]`
`ctl0578` `(``ct326` `)`		`Hypothetical`	`685322`	`670/1,545`	FFVTVTGWMISPRSDAQWNENSRX	`[S168T; 186/515]`
`ctl0587` `(``ct333` `)`^h	`uvrA`	`UvrABC system protein A`	`696123`	`1,850/5,361`	VSIPLTGWMISPRSDAQWNENSRX	`[G618T; 636/1,786]`
`ctl0587` `(``ct333` `)`^h	`uvrA`	`UvrABC system protein A`	`697044`	`2,771/5,361`	ELPYLTGWMISPRSDAQWNENSRX	`[P925T; 943/1,786]`
`ctl0587` `(``ct333` `)`^h	`uvrA`	`UvrABC system protein A`	`697874`	`3,601/5,361`	LNHESX	`[Y1201X; 1,201/1,786]`
`ctl0587` `(``ct333` `)`^h	`uvrA`	`UvrABC system protein A`	`698091`	`3,818/5,361`	ESLCLTGWMISPRSDAQWNENSRX	`[G1274T; 1,292/1,786]`
`ctl0587` `(``ct333` `)`^h	`uvrA`	`UvrABC system protein A`	`699439`	`5,165/5,361`	LDEIANRLDDKSPVX	`[T1723N; 1,732/1,786]`
`ctl0593` `(``ct339` `)`^h	`comEC`	`Competence DNA uptake`	`705937`	`1,466/1,530`	ILVYITGWMISPRSDAQWNENSRX	`[G490T; 508/509]`
`ctl0604` `(``ct350` `)`		`Putative lipoprotein`	`718288`	`179/1701`	IQPVTRNSRIVFTTKLSLX	`[R61T; 79/566]`
`ctl0611A` `(``ct357` `)`^h		`Hypothetical`	`728274`	`212/333`	DFSVLTGWMISPRSDAQWNENSRX	`[R61T; 90/110]`
`ctl0625` `(``ct371` `)`		`Putative outer membrane protein`	`742559`	`454/786`	KANLPLTGWMISPRSDAQWNENSRX	`[Y152L; 171/261]`
`ctl0626` `(``ct372` `)`^h	`aaxA`	`Porin`	`743881`	`837/1`,`329`	KWSNLNRLDDKSPVX	`[T280N; 289/442]`
`ctl0639` `(``ct383` `)`		`Putative inner membrane protein`	`755828`	`572/732`	ERYTLTGWMISPRSDAQWNENSRX	`[L192T; 210/243]`
`ctl0641` `(``ct385` `)`		`Histidine triad motif hydrolase`	`757770`	`198/336`	EAGKINRLDDKSP-35AA-SCX^g	`[I67N; 112/111]`
`ctl0648` `(``ct392` `)`^h		`Hypothetical`	`765648`	`762/1,131`	DGPLSINRLDDKSPVX	`[S300X; 300/377]`
`ctl0648` `(``ct392` `)`^h		`Hypothetical`	`766400`	`11/1,131`	MSSITGWMISPRSDAQWNENSRX	`[Q5T; 23/376]`
`ctl0661` `(``ct404` `)`		`N6-adenine-specific DNA methylase`	`781874`	`690/828`	HTPGHNRLDDKSPVX	`[T231N; 240/275]`
`ctl0671` `(``ct414` `)`^h	`pmpC`	`Polymorphic outer membrane protein`	`799909`	`1,559/5,325`	TNSDITGWMISPRSDAQWNENSRX	`[D521T; 539/1,774]`
`ctl0671` `(``ct414` `)`^h	`pmpC`	`Polymorphic outer membrane protein`	`802592`	`4,241/5,326`	APQKGYNRLDDKSPVFGSSENLRKTALQGGFF	`[Q1460X; 1,460/1,775]`
`ctl0671` `(``ct414` `)`^h	`pmpC`	`Polymorphic outer membrane protein`	`802593`	`4,242/5,326`	PQKGYNRLDDKSPVX	`[S1455N; 1,424/1,774]`
`ctl0678` `(``ct421` `)`		`Hypothetical`	`804491`	`686/702`	TSPFITGWMISPRSDAQWNENSRX	`[L444T; 462/450]`
`ctl0707` `(``ct447` `)`	`recJ`	`Single-stranded DNA-specific exonuclease`	`836380`	`1,311/1,755`	DFAAGLNRLDDKSPVX	`[M438L; 447/584]`
`ctl0708a` `(``ct448` `)`		`Bifunctional preprotein translocase subunit` `secDF`	`838006`	`4,005/4,203`	LQKTLTGWMISPRSDAQWNENSRX	`[G1337T; 1,355/1,400]`
`ctl0730` `(``ct470` `)`	`recO`	`DNA repair protein`	`863604`	`492/732`	ESSTIX	`[Y165X; 165/244]`
`ctl0750` `(``ct489` `)`	`glgC`	`Glucose-1-phosphate adenyltransferase`	`884304`	`469/1,326`	RSIVDX	`[Y157X; 157/441]`
`ctl0802` `(``ct540` `)`		`Putative tRNA [cytidine(34)-2`′`-O]-methyltransferase`	`925001`	`418/456`	VGIVMX	`[Y140X; 140/151]`
`ctl0812` `(``ct550` `)`		`Hypothetical`	`938483`	`42/426`	FRRSINRLDDKSPVX	`[T15N; 24/141]`
`ctl0818` `(``ct555` `)`^e		`ATP-dependent helicase`	`946408`	`3,260/3,600`	FIGSLTGWMISPRSDAQWNENSRX	`[L1088T; 1,106/1,199]`
`ctl0837` `(``ct574` `)`^e	`pepP`	`Aminopeptidase P family protein`	`965163`	`87/1,071`	KDEDINRLDDKSPVX	`[S30N; 39/356]`
`ctl0838` `(``ct575` `)`^e ^,^h	`mutL`	`DNA mismatch repair endonuclease`	`966365`	`626/1,731`	KQGFITGWMISPRSDAQWNENSRX	`[E210T; 228/576]`
`ctl0849` `(``ct586` `)`	`uvrB`	`Excinuclease ABC subunit B`	`979090`	`848/2,007`	EGRPVTGWMISPRSDAQWNENSRX	`[E284T; 302/668]`
`ctl0853` `(``ct590` `)`^h		`Hypothetical`	`986413`	`2,164/2,865`	DKSAIX	`[I722X; 722/955]`
`ctl0853` `(``ct590` `)`^h		`Hypothetical`	`988197`	`380/2865`	RVQDLTGWMISPRSDAQWNENSRX	`[I128T; 145/954`
`ctl0855` `(``ct592` `)`	`sdhA`	`Succinate dehydrogenase flavoprotein`	`990457`	`875/1,881`	PWYFLTGWMISPRSDAQWNENSRX	`[E293T; 311/626]`
`ctl0856` `(``ct593` `)`^e	`sdhC`	`Succinate dehydrogenase`	`992076`	`114/862`	HLLTNNRLDDKSPVX	`[I39N; 48/287]`
`ctl0858` `(``ct594` `)`	`tatD`	`Hydrolase`	`992950`	`178/792`	DWMFYNRLDDKSPVX	`[H61N; 69/261]`
`ctl0867` `(``ct604` `)`	`groEL2`	`Molecular chaperone GroEL`	`1002459`	`431/1,602`	LEHTVX	`[Y144V; 144/533`
`ctl_r03` `/``04`		`23S rRNA`	`136240 OR 158284`	`404/2,868`
`ctl0425` `(``ct172` `)`		`Pseudogene`	`514407`
`CDS7` `(``pgp5` `)`	`pgp5`	`Plasmid hypothetical protein`	`229`^b	`165/795`	SGLGANRLDDKSPVX	`[S52N; 61/264]`
`CDS6` `(``pgp4` `)`	`pgp4`	`Plasmid hypothetical protein`	`460`^b	`270/309`	ALIMLNRLDDKSPVX	`[I91N; 100/102]`
`CDS5` `(``pgp3` `)`	`pgp3`	`Plasmid virulence protein`	`1262`^b	`331/795`	ALIMLNRLDDKSPVX	`[I91N; 100/102]`
`CDS3` `(``pgp1` `)`	`pgp1`	`Plasmid helicase`	`2715`^b	`1,354/1,356`	IKKVWX	`[X451X; 451/451]`
`CDS4` `(``pgp2` `)`	`pgp2`	`Plasmid hypothetical protein`	`2715`^b	`5/1,065`	MVTGWMISPRSDAQWNENSRX	`[N6M; 21/354]`

Position generated using C. trachomatis LGV 434/Bu (NC_010287).

Position generated using C. trachomatis LGV 434/Bu plasmid (NC_021051.1).

C. trachomatis serovar D (NC_000117) gene nomenclature.

Himar insertion delineated by underscore; first amino acid shift delineated by bold highlighting and shown in square brackets; stop codon delineated by X. Data were calculated as follows: (protein length after insertion)/(wild-type protein length).

Slow-growing mutants (mutants that required six or more passages to achieve visibly infectious stocks).

Complete C-terminal sequence, QFRIVTGWMISPRSLVAQRTFEKPPCKAVFSFSEQEITRRPKRSQEDHLVNQIKYFX.

Complete C-terminal sequence, EAGKINRLDDKSPVFGSSENLRKTALQGGFFVFRARDYAQTKTISRRSSCX.

Denotes coding regions that were shared as nonsense mutants as reported previously by Kokes et al. (36).