Table 1.
Binding sites of transcriptional regulators putatively involved in CPS biosynthesis of S. pneumoniae
| Organism | Transcriptional regulator (Accession no.) | Binding site | S. pneumoniae ortholog (Accession no.) | Identity/similarity (log10E value) | Sequence (5′ position)a |
|
|---|---|---|---|---|---|---|
| Wzy-dependentb | Synthase-dependent | |||||
| S. pneumoniae | ||||||
| ComX1 (Q8CM18) | TACGAATA | — | — | TACtAAgA (−75f) | TgaGAATA (+19f) | |
| TAacAATA (−152r) | TAttAATA (+25f) | |||||
| TAaGAAcA (−111r) | TAatAATR (+28f) | |||||
| TACGAtTA (−4r) | TAttAATA (+25r) | |||||
| CopY (Q8DQJ7) | KACAN2TGTA | — | — | TAgARTaGTA (−186f) | GAggACTGTA (+44f) | |
| TACACATcTg (−178f) | GACtGTaGTA (+47f) | |||||
| TAaAGATGcA (−63f) | ||||||
| aAaAGGTGTA (−44f) | ||||||
| TAtAATcGTA (−13f) | ||||||
| TAtAGGTGTt (+10f) | ||||||
| TACtAYTcTA (−177r) | ||||||
| cAgATGTGTA (−169r) | ||||||
| GACAAATtgA (−120r) | ||||||
| TgCATCTtTA (−54r) | ||||||
| TACACCTtTt (−35r) | ||||||
| TACgATTaTA (−4r) | ||||||
| aACACCTaTA (+19r) | ||||||
| MalR (P0A4T2) | AAACGTTTc | — | — | AAWCGaTT (−149f) | AAAaGTTT (−52f) | |
| AAAgGTgT (−43f) | AAACtaTT (−5f) | |||||
| AAtCGWTT (−142r) | AAACtTTT (−45r) | |||||
| AcACcTTT (−36r) | AAtaGTTT (+3r) | |||||
| GlnR (Q8DQX7) | TGTNAN7TNACA | — | — | TcTAAAAHATTKTTAgA (−166f) | TGaTATTCCCCTTGACA (−45f) | |
| TcTTATTTCATTTTACt (−115f) | TtTTAAATAAAGTGAgA (+7f) | |||||
| TcTAAMAATATTTTAgA (−150r) | TGaGAATATTAATAAtR (+19f) | |||||
| aGTAAAATGAAATAAgA (−99r) | TGTCAAGGGGAATAtCA (−29r) | |||||
| TcTCACTTTATTTAAaA (+23r) | ||||||
| YaTTATTAATATTCtCA (+35r) | ||||||
| RitR (Q04M91) | WNATTANW3RWYRR | — | — | ATATTATATTGAaAc (−201f) | TAATcAGTTTAACGG (−101f) | |
| TGATcAATTTGTCAt (−132f) | AGATaAAATTATTAt (−26f) | |||||
| TTAcTATATTtTTGG (−103f) | AAATTATTATATaAt (−21f) | |||||
| AAtaTAGTAAAATGA (−94r) | TTATTATATAATTAA (−18f) | |||||
| TAATTAAAcTATTGc (−10f) | ||||||
| AAgTgAGAATATTAA (+16f) | ||||||
| TGAgaATATTAATAA (+19f) | ||||||
| ATATTAATAAtgCAG (+24f) | ||||||
| TGATTACTTTccTAA (−96r) | ||||||
| TAATaATTTTATCtA (−13r) | ||||||
| TAATTATATAATaAt (−5r) | ||||||
| TTAaTtATATAATAA (−4r) | ||||||
| AGtTTAATTAtATAA (+1r) | ||||||
| TTATTtAAAAAgCAA (+16r) | ||||||
| ACtTTATTTAAAaAG (+19r) | ||||||
| AdcR (Q04I02) | TAACYRGTTAA | — | — | — | TAAtCAGTTtA (−91f) | |
| TAtCCcGTTAA (−83r) | ||||||
| S. pyogenes | ||||||
| CovR/CsrR (Q8P2J8) | DDHHATTARAR | CsrR (Q8DR53) | 45/68 (−49) | TTATATTgAAA (−198f) | GGTTAggAAAG (−112f) | |
| TGAAAcTAGAR (−192f) | AGTAATYAGtt (−103f) | |||||
| TGCTtcTAAAA (−170f) | ATCTtTTcAAA (−83f) | |||||
| HATTkTTAGAA (−159f) | TGATAcTaAGG (−70f) | |||||
| GTCTAcTAAgA (−78f) | TGACAaTAGAt (−33f) | |||||
| AGATAcTtAAA (−70f) | AATAgaTAAAA (−29f) | |||||
| GATAcTTAAAG (−69f) | TAAAATTAttA (−23f) | |||||
| AGATAgTgAAA (−54f) | AATTATTAtAt (−20f) | |||||
| GATAgTgAAAA (−53f) | ATATAaTtAAA (−13f) | |||||
| AGACATTAccG (−35f) | TATAATTAAAc (−12f) | |||||
| TTACcgTAAAA (−30f) | TGCTtTTtAAA (+3f) | |||||
| TACCgTaAAAA (−29f) | TTTAAaTAAAG (+8f) | |||||
| TTTCAaTAtAA (−188r) | TAAAgTgAGAA (+14f) | |||||
| TACTATTctAG (−177r) | GAATATTAAtA (+22f) | |||||
| ATDTtTTAGAA (−157r) | TATTAaTAAtR (+25f) | |||||
| GGACAgTyAAA (−133r) | TAATAaTRcAG (+28f) | |||||
| GAACATgAcAA (−114r) | ||||||
| TGAAAYaAGAA (−106r) | ||||||
| TAAAATgAAAt (−101r) | ||||||
| GTAAAaTgAAA (−100r) | ||||||
| ATATAgTAAAA (−95r) | ||||||
| GTATcTTAGtA (−65r) | ||||||
| ATACATTgAAc (+12r) | ||||||
| S. agalactiae | ||||||
| RovS (Q8E447) | AWAAWVHTDAWN6/7 WTKWWAMDWAK | SPD_0939 | 52/73 (−76) | — | ATAtAATTAAACTATTGCTTTTTAAATAa (−13f) | |
| B. subtilis | ||||||
| CitT (O34534) | WWCAAA | RpsI (A5MLP7)d | 27/50 (−17) | TTgAAA (−193f) | AACAgA (−118f) | |
| TACAcA (−178f) | TTCAAA (−78f) | |||||
| TTCtAA (−167f) | TACtAA (−67f) | |||||
| TAgAAA (−153f) | cACAAA (−59f) | |||||
| ATCAAt (−130f) | AAaAAA (−55f) | |||||
| TACtAA (−75f) | AAaAAA (−54f) | |||||
| AAaAAA (−46f) | ATaAAA (−24f) | |||||
| TAaAAA (−24f) | ATtAAA (−8f) | |||||
| AAaAAA (−23f) | TTtAAA (+8f) | |||||
| TTCAAt (+3f) | AAtAAA (+12f) | |||||
| TTCAAt (−189r) | TRCAgA (+34f) | |||||
| AACAAt (−153r) | AACtRA (−93r) | |||||
| TTCtAA (−149r) | TTgAAA (−74r) | |||||
| gTCAAA (−138r) | ATCAAA (−42r) | |||||
| gACAAA (−120r) | TAaAAA (+11r) | |||||
| ATgAAA (−105r) | TTaAAA (+12r) | |||||
| AcCAAA (−88r) | TTtAAA (+13r) | |||||
| AACcAA (−87r) | ||||||
| DeoR (P39140) | TTCAAT | Spr0228 (Q8DRC3)d | 28/50 (−30) | aTCAAT (−130f) | TTCAAa (−78f) | |
| TTCAWT (−109f) | TTaAAT (+9f) | |||||
| TTCAAT (+3f) | TTtAAT (−3r) | |||||
| TTCAAT (−189r) | ||||||
| TTCAcT (−45r) | ||||||
| GerE (P11470) | RWWTRGGYN2YY | RR03 (Q8DR45) | 49/67 (−6)e | GATTtGaCTGTC (−145f) | AATTAaaCTATT (−9f) | |
| ATTTGacTGTCC (−144f) | GAAaAGaTATCC (−76r) | |||||
| GTATAGGTRTTa (+10f) | ||||||
| AAATcGWTTTCT (−141r) | ||||||
| cTTTAaGTATCT (−59r) | ||||||
| GATTAtaTCACT (−7r) | ||||||
| CcpA (P25144) | WTGNAANCGNWN2CW | CcpA (Q97NM1) | 54/74 (−96) | TaGAAAWCGATTTrA (−152f) | TTcAAAGCtGATACT (−78f) | |
| ATaTAATCGTAAGaT (−14f) | ||||||
| gTyAAATCGWTTTCT (−138r) | ||||||
| Spo0A (P06 534) | TGTCGAA | RR09 (Q8DQN8) | 38/62 (−10) | TaTtGAA (−195f) | TtTCaAA (−79f) | |
| TGTaGAc (−38f) | TGTaGtA (+50f) | |||||
| TGTtcAA (+1f) | TaTCaAA (−41r) | |||||
| TtTaGAA (−161r) | TGTCaAg (−29r) | |||||
| TtTCtAA (−148r) | ||||||
| aGTCaAA (−137r) | ||||||
| TGaCaAA (−119r) | ||||||
| TGTCtAc (−31r) | ||||||
af and r indicate whether the sequence corresponds to the forward or reverse sequence of that included in the EMBL database (AF026471 or Z47210), respectively. Unless otherwise stated, a maximum of two mismatches were allowed.
bSequences corresponding to those common to all strains are indicated with a gray background. Mismatches are indicated by lowercase lettering.
cThis sequence is a subset of the CcpA binding site.
dOnly one mismatch was allowed.
eSimilarity restricted to part of the protein (from residue 145 to 197 of the pneumococcal protein and 12 to 64 of that of B. subtilis).