RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780282|ref|YP_003064695.1| putative transcription regulator protein [Candidatus Liberibacter asiaticus str. psy62] (299 letters) >gnl|CDD|30928 COG0583, LysR, Transcriptional regulator [Transcription]. Length = 297 Score = 151 bits (381), Expect = 3e-37 Identities = 87/295 (29%), Positives = 132/295 (44%), Gaps = 15/295 (5%) Query: 3 FDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQ 62 D +LR F VA GSFT AAE+L LSQS++SRQI LE E+G+ LF R R + LTE Sbjct: 1 MDLRQLRAFVAVAEEGSFTRAAERLGLSQSAVSRQIKRLEEELGVPLFERTTRRVRLTEA 60 Query: 63 GSKLHRVTSEVYHKLETTQIELQE-SSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPD 121 G +L + +LE E + +P G LRIA +LL L F YP+ Sbjct: 61 GERLLERARRILAELEEALAEAARLARGEPGGLLRIAAPSTAASSLLPPLLARFRARYPE 120 Query: 122 IQIQLILDNKDI-DISMDYADCAIRLRKPIQSSSLIQRKLVTIHMH--AYAAPHYLKNCR 178 I+++L ++ + D+ D AIR P L+ R L + + A+ Sbjct: 121 IELELGTSDRLLEDLVEGELDLAIRAGPPPPPDGLVARPLFSEELVLVVPASHPLAARHG 180 Query: 179 EPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLG 238 P +L LI L G L+VNS +++Q G Sbjct: 181 LP----DLPGEPLILLEHG----CILRRLLDQALALAGWRPRIRLEVNSAEALLQAVAAG 232 Query: 239 SGIALLPDYIVKDNPN--LVRIMEDV-ITPSFTVYFCYPEALKNTGKLKAFRNFI 290 GIALLP+ + + + LVR++ +Y + ++ + ++AF +F+ Sbjct: 233 LGIALLPESLARPDLAGRLVRVLPLPPPPLPRPLYLVWRKSRLLSPAVRAFIDFL 287 >gnl|CDD|176114 cd08422, PBP2_CrgA_like, The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain. This CD includes the substrate binding domain of LysR-type transcriptional regulator (LTTR) CrgA and its related homologs. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis further showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Length = 197 Score = 146 bits (370), Expect = 9e-36 Identities = 59/202 (29%), Positives = 100/202 (49%), Gaps = 9/202 (4%) Query: 93 GKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKDIDISMDYADCAIRLRKPIQS 152 G+LRI+ + G+ L L EFL YPD++++L+L ++ +D+ + D AIR+ + Sbjct: 1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIG-ELPD 59 Query: 153 SSLIQRKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVD 212 SSL+ R+L + A+P YL P + ++L +H + + W Sbjct: 60 SSLVARRLGPVRRVLVASPAYLARHGTPQTPEDLARHRCLGYRLPGR----PLRWRFRRG 115 Query: 213 RPIGEPRISC-LQVNSYLSIMQYCVLGSGIALLPDYIVKD---NPNLVRIMEDVITPSFT 268 E R+ L VN ++ + G GIALLPD++V + + LVR++ D P Sbjct: 116 GGEVEVRVRGRLVVNDGEALRAAALAGLGIALLPDFLVAEDLASGRLVRVLPDWRPPPLP 175 Query: 269 VYFCYPEALKNTGKLKAFRNFI 290 +Y YP K++AF +F+ Sbjct: 176 IYAVYPSRRHLPAKVRAFIDFL 197 >gnl|CDD|146222 pfam03466, LysR_substrate, LysR substrate binding domain. The structure of this domain is known and is similar to the periplasmic binding proteins. Length = 209 Score = 100 bits (252), Expect = 4e-22 Identities = 53/206 (25%), Positives = 88/206 (42%), Gaps = 11/206 (5%) Query: 91 PSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKD--ID-ISMDYADCAIRLR 147 P G+LRI LL L F YPD++++L + + +D ++ D AIR Sbjct: 4 PRGRLRIGAPPTFAAYLLPPLLARFRERYPDVELELREGDSEELLDLLAEGELDLAIRRG 63 Query: 148 KPIQSSSLIQRKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNW 207 P L R L + A P + EP+S+++L LI + D Sbjct: 64 -PPDDPGLEARPLFEEPLVLVAPPDHPLAAGEPVSLEDLADEPLILLEP--GSGLRDL-V 119 Query: 208 LATVDRPIGEPRISCLQVNSYLSIMQYCVLGSGIALLPDYIVKD---NPNLVRIMEDVIT 264 ++R PR++ L+VNS +++ G GIALLP V + LV + Sbjct: 120 DRALERAGLRPRVA-LEVNSLEALLAAVAAGLGIALLPRSAVARELADGRLVVLPLPDPP 178 Query: 265 PSFTVYFCYPEALKNTGKLKAFRNFI 290 +Y Y + + + ++AF +F+ Sbjct: 179 LPRPIYLVYRKGRRLSPAVRAFIDFL 204 >gnl|CDD|143900 pfam00126, HTH_1, Bacterial regulatory helix-turn-helix protein, lysR family. Length = 60 Score = 95.5 bits (239), Expect = 2e-20 Identities = 34/59 (57%), Positives = 40/59 (67%) Query: 5 WDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQG 63 +LRVF VA GSFT AAE+L LSQ ++SRQI LE E+G+ LF R RGL LT G Sbjct: 1 LRQLRVFVAVAEEGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGLRLTPAG 59 >gnl|CDD|176169 cd08480, PBP2_CrgA_like_10, The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 10. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Length = 198 Score = 88.5 bits (220), Expect = 2e-18 Identities = 51/177 (28%), Positives = 85/177 (48%), Gaps = 17/177 (9%) Query: 93 GKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKDIDISMDYADCAIRLRKPIQS 152 G+LR+ ++ G + L L FL YP+I + L L ++ +D+ + D AIR+ P+ Sbjct: 1 GRLRVNASVPFGTHFLLPLLPAFLARYPEILVDLSLTDEVVDLLAERTDVAIRV-GPLPD 59 Query: 153 SSLIQRKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWL---- 208 SSL+ RKL A+P YL PL+ Q+L +HN + F + + D W Sbjct: 60 SSLVARKLGESRRVIVASPSYLARHGTPLTPQDLARHNCLGFN--FRRALPD--WPFRDG 115 Query: 209 -ATVDRPIGEPRISCLQVNSYLSIMQYCVLGSGIALLPDYIVKD---NPNLVRIMED 261 V P+ + VN ++ + + G+G+A L + V D LV ++E+ Sbjct: 116 GRIVALPVSGN----ILVNDGEALRRLALAGAGLARLALFHVADDIAAGRLVPVLEE 168 >gnl|CDD|176162 cd08473, PBP2_CrgA_like_4, The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 4. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Length = 202 Score = 81.8 bits (203), Expect = 2e-16 Identities = 53/182 (29%), Positives = 86/182 (47%), Gaps = 20/182 (10%) Query: 91 PSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKDIDISMDYADCAIRLRKPI 150 P G +R++ L Q LL L F+ YP +++QL N+ +D+ + D A+R+R P Sbjct: 1 PRGTVRVSCPPALAQELLAPLLPRFMAAYPQVRLQLEATNRRVDLIEEGIDVALRVRFPP 60 Query: 151 -QSSSLIQRKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLA 209 + SSL+ R L A+P L P S ++L ++ GD+ +W Sbjct: 61 LEDSSLVMRVLGQSRQRLVASPALLARLGRPRSPEDLAGLPTLSLGDV----DGRHSWRL 116 Query: 210 TVDRPIGE-------PRISCLQVNSYLSIMQYCVLGSGIALLPDYIVKD---NPNLVRIM 259 P GE PR+ + L++ Q + G GIALLPD++ ++ LVR++ Sbjct: 117 E--GPDGESITVRHRPRLVT---DDLLTLRQAALAGVGIALLPDHLCREALRAGRLVRVL 171 Query: 260 ED 261 D Sbjct: 172 PD 173 >gnl|CDD|176161 cd08472, PBP2_CrgA_like_3, The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 3. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Length = 202 Score = 81.4 bits (202), Expect = 3e-16 Identities = 50/189 (26%), Positives = 85/189 (44%), Gaps = 13/189 (6%) Query: 93 GKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKDIDISMDYADCAIRLRKPIQS 152 G+LR+ L + LL L +FL YPDI++ L + ++ +D+ + DC IR+ + Sbjct: 1 GRLRVDVPGSLARLLLIPALPDFLARYPDIELDLGVSDRPVDLIREGVDCVIRV-GELAD 59 Query: 153 SSLIQRKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVD 212 SSL+ R+L + M A+P YL P ++L++H + + + W D Sbjct: 60 SSLVARRLGELRMVTCASPAYLARHGTPRHPEDLERHRAVGY--FSARTGRVLPWEFQRD 117 Query: 213 RPI----GEPRISCLQVNSYLSIMQYCVLGSGIALLPDYIVK---DNPNLVRIMEDVITP 265 R+S +YL + G GI +P ++V+ + LV ++ D P Sbjct: 118 GEEREVKLPSRVSVNDSEAYL---AAALAGLGIIQVPRFMVRPHLASGRLVEVLPDWRPP 174 Query: 266 SFTVYFCYP 274 V YP Sbjct: 175 PLPVSLLYP 183 >gnl|CDD|176166 cd08477, PBP2_CrgA_like_8, The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 8. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Length = 197 Score = 80.4 bits (199), Expect = 6e-16 Identities = 59/208 (28%), Positives = 102/208 (49%), Gaps = 21/208 (10%) Query: 93 GKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKDIDISMDYADCAIRLRKPIQS 152 GKLRI+ + G ++L L E+L YPD+++ L+L ++ +D+ + D A R+ + Sbjct: 1 GKLRISAPVTFGSHVLTPALAEYLARYPDVRVDLVLSDRLVDLVEEGFDAAFRI-GELAD 59 Query: 153 SSLIQRKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLA--- 209 SSL+ R L M A+P YL P + ++L +H + F W A Sbjct: 60 SSLVARPLAPYRMVLCASPDYLARHGTPTTPEDLARHECLGFS----------YWRARNR 109 Query: 210 -TVDRPIGE---PRISCLQVNSYLSIMQYCVLGSGIALLPDYIVKDN---PNLVRIMEDV 262 ++ P GE P L VNS ++ + G GI L P+ ++ ++ LV ++ D Sbjct: 110 WRLEGPGGEVKVPVSGRLTVNSGQALRVAALAGLGIVLQPEALLAEDLASGRLVELLPDY 169 Query: 263 ITPSFTVYFCYPEALKNTGKLKAFRNFI 290 + P ++ YP + T KL++F +F+ Sbjct: 170 LPPPRPMHLLYPPDRRPTPKLRSFIDFL 197 >gnl|CDD|176159 cd08470, PBP2_CrgA_like_1, The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding domain. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 1. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Length = 197 Score = 78.1 bits (193), Expect = 3e-15 Identities = 55/193 (28%), Positives = 93/193 (48%), Gaps = 25/193 (12%) Query: 93 GKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKDIDISMDYADCAIRLRKPIQS 152 G LRI + G+ + + +F+ YP +++ + L N+ +D+ + D AIRL + Sbjct: 1 GLLRITCPVAYGERFIAPLVNDFMQRYPKLEVDIELTNRVVDLVSEGFDLAIRLGRL-TD 59 Query: 153 SSLIQRKLVTIHMHAYAAPHYLKNCREPLSIQELDKHN-LITFGDLIPKCMEDFNWLATV 211 SSL+ R+L + + A+P YL+ P S+ +LD+HN L+ D +W Sbjct: 60 SSLMARRLASRRHYVCASPAYLERHGTPHSLADLDRHNCLLGTSD---------HWRFQE 110 Query: 212 D------RPIGEPRISCLQVNSYLSIMQYCVLGSGIALLPDYIVKD---NPNLVRIMEDV 262 + R G R C NS ++++ + G G+A LPDY V + LV ++ED Sbjct: 111 NGRERSVRVQG--RWRC---NSGVALLDAALKGMGLAQLPDYYVDEHLAAGRLVPVLEDY 165 Query: 263 ITPSFTVYFCYPE 275 P ++ YP Sbjct: 166 RPPDEGIWALYPH 178 >gnl|CDD|176163 cd08474, PBP2_CrgA_like_5, The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 5. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Length = 202 Score = 76.7 bits (190), Expect = 8e-15 Identities = 58/218 (26%), Positives = 93/218 (42%), Gaps = 34/218 (15%) Query: 91 PSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKDIDISMDYADCAIRLRKPI 150 P+G LRI + LL L FL YPDI+++L++D+ +DI + D IRL Sbjct: 1 PAGTLRINAPRVAARLLLAPLLARFLARYPDIRLELVVDDGLVDIVAEGFDAGIRL---- 56 Query: 151 QSSSLIQRKLV------TIHMHAYAAPHYLKNCREPLSIQELDKHNLITF-----GDLIP 199 +++ +V + M A+P YL P ++L H I + G L Sbjct: 57 --GESVEKDMVAVPLGPPLRMAVVASPAYLARHGTPEHPRDLLNHRCIRYRFPTSGAL-- 112 Query: 200 KCMEDFNW-LATVDRPI---GEPRISCLQVNSYLSIMQYCVLGSGIALLPDYIVKD---N 252 + W R + E L +N ++ + G GIA L + +V + + Sbjct: 113 -----YRWEFERGGRELEVDVEGP---LILNDSDLMLDAALDGLGIAYLFEDLVAEHLAS 164 Query: 253 PNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFI 290 LVR++ED P Y YP + L+AF +F+ Sbjct: 165 GRLVRVLEDWSPPFPGGYLYYPSRRRVPPALRAFIDFL 202 >gnl|CDD|176168 cd08479, PBP2_CrgA_like_9, The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 9. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Length = 198 Score = 74.6 bits (184), Expect = 3e-14 Identities = 56/210 (26%), Positives = 97/210 (46%), Gaps = 24/210 (11%) Query: 93 GKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKDIDISMDYADCAIRLRKPIQS 152 G LR+ + G+ + L +F YP++++QL L ++ +D+ + D IR+ Sbjct: 1 GLLRVNASFGFGRRHIAPALSDFAKRYPELEVQLELTDRPVDLVEEGFDLDIRVGDLP-D 59 Query: 153 SSLIQRKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITF--GDLIPKCMEDFN-WLA 209 SSLI RKL A+P YL+ P S ++L +H+ + D EDF W Sbjct: 60 SSLIARKLAPNRRILCASPAYLERHGAPASPEDLARHDCLVIREND------EDFGLW-- 111 Query: 210 TVDRPIGEPRISCLQVNSYLS------IMQYCVLGSGIALLPDYIVKDN---PNLVRIME 260 + GE + +V LS ++Q+ + G GI L ++ V LVR++ Sbjct: 112 RLRNGDGEATV---RVRGALSSNDGEVVLQWALDGHGIILRSEWDVAPYLRSGRLVRVLP 168 Query: 261 DVITPSFTVYFCYPEALKNTGKLKAFRNFI 290 D P ++ YP L + +++ F +F+ Sbjct: 169 DWQLPDADIWAVYPSRLSRSARVRVFVDFL 198 >gnl|CDD|176102 cd05466, PBP2_LTTR_substrate, The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily. This model and hierarchy represent the the substrate-binding domain of the LysR-type transcriptional regulators that form the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, oxidative stress responses, nodule formation of nitrogen-fixing bacteria, synthesis of virulence factors, toxin production, attachment and secretion, to name a few. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate-binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction. Length = 197 Score = 73.0 bits (180), Expect = 8e-14 Identities = 41/202 (20%), Positives = 75/202 (37%), Gaps = 10/202 (4%) Query: 94 KLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLI-LDNKDI--DISMDYADCAIRLRKPI 150 LRI + + LL L F YP +++ L+ + ++ + D AI + P+ Sbjct: 1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAI-VALPV 59 Query: 151 QSSSLIQRKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLAT 210 L L + P + R+ +++ +L LI F Sbjct: 60 DDPGLESEPLFEEPLVLVVPPDHPLAKRKSVTLADLADEPLILFE---RGSGLRRLLDRA 116 Query: 211 VDRPIGEPRISCLQVNSYLSIMQYCVLGSGIALLPDYIVK--DNPNLVRIMEDVITPSFT 268 P I+ +V+S +I G GIALLP+ V+ + LV + + S T Sbjct: 117 FAEAGFTPNIAL-EVDSLEAIKALVAAGLGIALLPESAVEELADGGLVVLPLEDPPLSRT 175 Query: 269 VYFCYPEALKNTGKLKAFRNFI 290 + + + + +AF + Sbjct: 176 IGLVWRKGRYLSPAARAFLELL 197 >gnl|CDD|177082 CHL00180, rbcR, LysR transcriptional regulator; Provisional. Length = 305 Score = 71.2 bits (175), Expect = 3e-13 Identities = 47/145 (32%), Positives = 67/145 (46%), Gaps = 10/145 (6%) Query: 1 MSFDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLT 60 + F D+LR+ +A GSF AAE L++SQ ++S QI LE ++ I LF R +LT Sbjct: 3 LPFTLDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLT 62 Query: 61 EQGSKLHRVTSEVYHKLETTQIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYP 120 E G L R + + E T L++ G L I + G L+ + F YP Sbjct: 63 EAGELLLRYGNRILALCEETCRALEDLKNLQRGTLIIGASQTTGTYLMPRLIGLFRQRYP 122 Query: 121 DIQIQLILD----------NKDIDI 135 I +QL + N IDI Sbjct: 123 QINVQLQVHSTRRIAWNVANGQIDI 147 >gnl|CDD|176164 cd08475, PBP2_CrgA_like_6, The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 6. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Length = 199 Score = 69.1 bits (170), Expect = 1e-12 Identities = 47/192 (24%), Positives = 90/192 (46%), Gaps = 15/192 (7%) Query: 93 GKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKDIDISMDYADCAIRLRKPIQS 152 G+LRI + G+ + L E +P+++++L ++ +D+ + D A+R+ + S Sbjct: 1 GRLRIDLPVAFGRLCVAPLLLELARRHPELELELSFSDRFVDLIEEGIDLAVRIGELADS 60 Query: 153 SSLIQRKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITF---GDLIPKCMEDFNW-L 208 + L+ R+L T M A+P YL P ++++L +H I + G +P W L Sbjct: 61 TGLVARRLGTQRMVLCASPAYLARHGTPRTLEDLAEHQCIAYGRGGQPLP-------WRL 113 Query: 209 ATVDRPIGEPRI-SCLQVNSYLSIMQYCVLGSGIALLPDYIVKDNPN---LVRIMEDVIT 264 A + R LQ + +I + G GIA LP ++V D+ LV ++ ++ Sbjct: 114 ADEQGRLVRFRPAPRLQFDDGEAIADAALAGLGIAQLPTWLVADHLQRGELVEVLPELAP 173 Query: 265 PSFTVYFCYPEA 276 ++ +P Sbjct: 174 EGLPIHAVWPRT 185 >gnl|CDD|176160 cd08471, PBP2_CrgA_like_2, The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 2. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Length = 201 Score = 64.9 bits (159), Expect = 2e-11 Identities = 46/201 (22%), Positives = 89/201 (44%), Gaps = 9/201 (4%) Query: 93 GKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKDIDISMDYADCAIRLRKPIQS 152 G L + + G+ + + +FL YP++ ++L+L ++ +++ + D A+R+ + Sbjct: 1 GLLTVTAPVLFGRLHVLPIITDFLDAYPEVSVRLLLLDRVVNLLEEGVDVAVRI-GHLPD 59 Query: 153 SSLIQRKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVD 212 SSL+ ++ ++ A+P YL P +L H+ I F L P W Sbjct: 60 SSLVATRVGSVRRVVCASPAYLARHGTPKHPDDLADHDCIAFTGLSPA----PEWRFREG 115 Query: 213 -RPIGEPRISCLQVNSYLSIMQYCVLGSGIALLPDYIVKD---NPNLVRIMEDVITPSFT 268 + L VN+ + + + G G+ + Y V + L R++ED P Sbjct: 116 GKERSVRVRPRLTVNTVEAAIAAALAGLGLTRVLSYQVAEELAAGRLQRVLEDFEPPPLP 175 Query: 269 VYFCYPEALKNTGKLKAFRNF 289 V+ +PE K++AF +F Sbjct: 176 VHLVHPEGRLAPAKVRAFVDF 196 >gnl|CDD|176123 cd08432, PBP2_GcdR_TrpI_HvrB_AmpR_like, The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate domain of LysR-type transcriptional regulators involved in controlling the expression of glutaryl-CoA dehydrogenase (GcdH), S-adenosyl-L-homocysteine hydrolase, cell division protein FtsW, tryptophan synthase, and beta-lactamase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Length = 194 Score = 62.6 bits (153), Expect = 1e-10 Identities = 48/210 (22%), Positives = 79/210 (37%), Gaps = 25/210 (11%) Query: 95 LRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKDIDISMDYADCAIRLRKP----I 150 L ++ T L L F +PDI ++L ++ +D + + D AIR + Sbjct: 2 LTVSVTPSFAARWLIPRLARFQARHPDIDLRLSTSDRLVDFAREGIDLAIRYGDGDWPGL 61 Query: 151 QSSSLIQRKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLAT 210 ++ L+ +LV +P L LS +L +H L+ P+ + + W A Sbjct: 62 EAERLMDEELV-----PVCSPALLAG-LPLLSPADLARHTLLHDAT-RPEAWQWWLWAAG 114 Query: 211 VDRPIGEPRISCLQVNSYLSIMQYCVLGSGIALLPDYIVKD---NPNLVRIMEDVITPSF 267 V + + +Q V G G+AL P +V D LVR + + Sbjct: 115 VADVDARRGP---RFDDSSLALQAAVAGLGVALAPRALVADDLAAGRLVRPFDLPLPSGG 171 Query: 268 TVYFCYPEALKNTGKLKAFRNFIFLKARDW 297 Y YP + + AF RDW Sbjct: 172 AYYLVYPPGRAESPAVAAF--------RDW 193 >gnl|CDD|176167 cd08478, PBP2_CrgA, The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains the type 2 periplasmic binding domain. This CD represents the substrate binding domain of LysR-type transcriptional regulator (LTTR) CrgA. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis further showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Length = 199 Score = 62.0 bits (151), Expect = 2e-10 Identities = 47/180 (26%), Positives = 82/180 (45%), Gaps = 20/180 (11%) Query: 91 PSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKDIDISMDYADCAIRLRKPI 150 PSG LR+ +LL + +F YPDI+++L+ + ID+ D AIR+ + Sbjct: 1 PSGLLRVDAATPFVLHLLAPLIAKFRERYPDIELELVSNEGIIDLIERKTDVAIRI-GEL 59 Query: 151 QSSSLIQRKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLAT 210 S+L R L + A+P YL P SI++L +H L+ F + P + W Sbjct: 60 TDSTLHARPLGKSRLRILASPDYLARHGTPQSIEDLAQHQLLGFTE--PASLNT--W--- 112 Query: 211 VDRPIGEPRISCLQVNSYLS------IMQYCVLGSGIALLPDYIVKDNPN---LVRIMED 261 PI + + L++ ++ + Q + G GIA L D++ + L+ + + Sbjct: 113 ---PIKDADGNLLKIQPTITASSGETLRQLALSGCGIACLSDFMTDKDIAEGRLIPLFAE 169 >gnl|CDD|176165 cd08476, PBP2_CrgA_like_7, The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 7. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Length = 197 Score = 61.9 bits (151), Expect = 2e-10 Identities = 52/207 (25%), Positives = 97/207 (46%), Gaps = 19/207 (9%) Query: 93 GKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKDIDISMDYADCAIRLRKPIQS 152 G+LR++ + LL L F+ YP+I++ L ++ +D+ + D IR + Sbjct: 1 GRLRVSLPL--VGGLLLPVLAAFMQRYPEIELDLDFSDRLVDVIDEGFDAVIRTGELP-D 57 Query: 153 SSLIQRKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITF-----GDLIPKCMEDFNW 207 S L+ R+L + M A+P YL P + +L +H + + G L P W Sbjct: 58 SRLMSRRLGSFRMVLVASPDYLARHGTPETPADLAEHACLRYRFPTTGKLEP-------W 110 Query: 208 LATVDRPIGEPRISC-LQVNSYLSIMQYCVLGSGIALLPDYIVKD---NPNLVRIMEDVI 263 D E R+ L N+ +++++ + G GIA LPD+ V++ + LV +++D + Sbjct: 111 PLRGDGGDPELRLPTALVCNNIEALIEFALQGLGIACLPDFSVREALADGRLVTVLDDYV 170 Query: 264 TPSFTVYFCYPEALKNTGKLKAFRNFI 290 +P + + KL+ F +F+ Sbjct: 171 EERGQFRLLWPSSRHLSPKLRVFVDFM 197 >gnl|CDD|176170 cd08481, PBP2_GcdR_like, The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, contains the type 2 periplasmic binding fold. GcdR is involved in the glutaconate/glutarate-specific activation of the Pg promoter driving expression of a glutaryl-CoA dehydrogenase-encoding gene (gcdH). The GcdH protein is essential for the anaerobic catabolism of many aromatic compounds and some alicyclic and dicarboxylic acids. The structural topology of this substrate-binding domain is most similar to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Length = 194 Score = 43.8 bits (104), Expect = 5e-05 Identities = 47/206 (22%), Positives = 85/206 (41%), Gaps = 23/206 (11%) Query: 95 LRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKDIDISMDYADCAIRLRKPI---- 150 L +A G L L +FL +PDI + L+ ++ D S D AI P+ Sbjct: 2 LELAVLPTFGTRWLIPRLPDFLARHPDITVNLVTRDEPFDFSQGSFDAAIHFGDPVWPGA 61 Query: 151 QSSSLIQRKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLI---TFGDLIPKCMEDFNW 207 +S L+ ++V + +P L R + +L L+ T P+ D+ Sbjct: 62 ESEYLMDEEVVPV-----CSPALLAG-RALAAPADLAHLPLLQQTT----RPEAWRDWFE 111 Query: 208 LATVDRPIGEPRISCLQVNSYLSIMQYCVLGSGIALLPDYIVKD---NPNLVRIMEDVIT 264 ++ P ++ + + Q V G G+ALLP +++++ LV +T Sbjct: 112 EVGLEVPTAY---RGMRFEQFSMLAQAAVAGLGVALLPRFLIEEELARGRLVVPFNLPLT 168 Query: 265 PSFTVYFCYPEALKNTGKLKAFRNFI 290 Y YPE + ++AFR+++ Sbjct: 169 SDKAYYLVYPEDKAESPPVQAFRDWL 194 >gnl|CDD|176107 cd08415, PBP2_LysR_opines_like, The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the catabolism of opines and that of related regulators, contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulators, OccR and NocR, involved in the catabolism of opines and that of LysR for lysine biosynthesis which clustered together in phylogenetic trees. Opines, such as octopine and nopaline, are low molecular weight compounds found in plant crown gall tumors that are produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. NocR and OccR belong to the family of LysR-type transcriptional regulators that positively regulates the catabolism of nopaline and octopine, respectively. Both nopaline and octopalin are arginine derivatives. In Agrobacterium tumefaciens, NocR regulates expression of the divergently transcribed nocB and nocR genes of the nopaline catabolism (noc) region. OccR protein activates the occQ operon of the Ti plasmid in response to octopine. This operon encodes proteins required for the uptake and catabolism of octopine. The occ operon also encodes the TraR protein, which is a quorum-sensing transcriptional regulator of the Ti plasmid tra regulon. LysR is the transcriptional activator of lysA gene encoding diaminopimelate decarboxylase, an enzyme that catalyses the decarboxylation of diaminopimelate to produce lysine. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Length = 196 Score = 37.9 bits (89), Expect = 0.003 Identities = 31/168 (18%), Positives = 53/168 (31%), Gaps = 38/168 (22%) Query: 95 LRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKDIDIS---MDY-----ADCAIRL 146 LRIA L +LL + F +PD++I L S ++ AD + Sbjct: 2 LRIAALPALALSLLPRAIARFRARHPDVRISL-----HTLSSSTVVEAVLSGQADLGL-A 55 Query: 147 RKPIQSSSLIQRKLVTIHM-------HAYAAPHYLKNCREPLSIQELDKHNLITFGDLIP 199 P+ L L + H A ++ ++ +L LI+ G P Sbjct: 56 SLPLDHPGLESEPLASGRAVCVLPPGHPLAR-------KDVVTPADLAGEPLISLGRGDP 108 Query: 200 KCMEDFNWLATVD---RPIGEPRISCLQVNSYLSIMQYCVLGSGIALL 244 VD G ++ + G G+A++ Sbjct: 109 LRQR-------VDAAFERAGVEPRIVIETQLSHTACALVAAGLGVAIV 149 >gnl|CDD|176172 cd08483, PBP2_HvrB, The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an activator of S-adenosyl-L-homocysteine hydrolase expression, contains the type 2 periplasmic binding fold. The transcriptional regulator HvrB of the LysR family is required for the light-dependent activation of both ahcY, which encoding the enzyme S-adenosyl-L-homocysteine hydrolase (AdoHcyase) that responsible for the reversible hydrolysis of AdoHcy to adenosine and homocysteine, and orf5, a gene of unknown. The topology of this C-terminal domain of HvrB is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Length = 190 Score = 35.0 bits (81), Expect = 0.025 Identities = 21/83 (25%), Positives = 30/83 (36%), Gaps = 1/83 (1%) Query: 95 LRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKDIDISMDYADCAIRLRKPIQSSS 154 L + T N L L F +P+I++ L+ +D+ D D AIR Sbjct: 2 LTVTLTPSFASNWLMPRLGSFWAKHPEIELSLLPSADLVDLRPDGIDVAIRYGNG-DWPG 60 Query: 155 LIQRKLVTIHMHAYAAPHYLKNC 177 L L AAP L + Sbjct: 61 LESEPLTAAPFVVVAAPGLLGDR 83 >gnl|CDD|176176 cd08487, PBP2_BlaA, The C-terminal substrate-binding domain of LysR-type trnascriptional regulator BlaA which involved in control of the beta-lactamase gene expression; contains the type 2 periplasmic binding fold. This CD represents the C-terminal substrate binding domain of LysR-type transcriptional regulator, BlaA, that involved in control of the expression of beta-lactamase genes, blaA and blaB. Beta-lactamases are responsible for bacterial resistance to beta-lactam antibiotics such as penicillins. The blaA gene is located just upstream of blaB in the opposite direction and regulates the expression of the blaB. BlaA also negatively auto-regulates the expression of its own gene, blaA. BlaA (a constitutive class A penicllinase) belongs to the LysR family of transcriptional regulators, whereas BlaB (an inducible class C cephalosporinase or AmpC) can be referred to as a penicillin binding protein but it does not act as a beta-lactamase. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Length = 189 Score = 32.9 bits (75), Expect = 0.12 Identities = 13/34 (38%), Positives = 22/34 (64%) Query: 112 LKEFLLLYPDIQIQLILDNKDIDISMDYADCAIR 145 L EF L+P I+++L +N +D++ + D AIR Sbjct: 19 LAEFRQLHPFIELRLRTNNNVVDLATEGLDFAIR 52 >gnl|CDD|176112 cd08420, PBP2_CysL_like, C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which activates the transcription of the cysJI operon encoding sulfite reductase, contains the type 2 periplasmic binding fold. CysL, also known as YwfK, is a regular of sulfur metabolism in Bacillus subtilis. Sulfur is required for the synthesis of proteins and essential cofactors in all living organism. Sulfur can be assimilated either from inorganic sources (sulfate and thiosulfate), or from organic sources (sulfate esters, sulfamates, and sulfonates). CysL activates the transcription of the cysJI operon encoding sulfite reductase, which reduces sulfite to sulfide. Both cysL mutant and cysJI mutant are unable to grow using sulfate or sulfite as the sulfur source. Like other LysR-type regulators, CysL also negatively regulates its own transcription. In Escherichia coli, three LysR-type activators are involved in the regulation of sulfur metabolism: CysB, Cbl and MetR. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Length = 201 Score = 32.8 bits (76), Expect = 0.13 Identities = 25/105 (23%), Positives = 43/105 (40%), Gaps = 8/105 (7%) Query: 94 KLRIA--TTIDLGQNLLQGNLKEFLLLYPDIQIQLILDN-KDI--DISMDYADCAIRLRK 148 LRI TTI G+ LL L F YP++++ L + N ++I + D + + Sbjct: 1 TLRIGASTTI--GEYLLPRLLARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLGL-VEG 57 Query: 149 PIQSSSLIQRKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLIT 193 P+ LI + P + R+ ++ +EL I Sbjct: 58 PVDHPDLIVEPFAEDELVLVVPPDHPLAGRKEVTAEELAAEPWIL 102 >gnl|CDD|99854 cd06100, CCL_ACL-C, Citryl-CoA lyase (CCL), the C-terminal portion of the single-subunit type ATP-citrate lyase (ACL) and the C-terminal portion of the large subunit of the two-subunit type ACL. CCL cleaves citryl-CoA (CiCoA) to acetyl-CoA (AcCoA) and oxaloacetate (OAA). ACL catalyzes an ATP- and a CoA- dependant cleavage of citrate to form AcCoA and OAA in a multistep reaction, the final step of which is likely to involve the cleavage of CiCoA to generate AcCoA and OAA. In fungi, yeast, plants, and animals ACL is cytosolic and generates AcCoA for lipogenesis. ACL may be required for fruiting body maturation in the filamentous fungus Sordaria macrospore. In several groups of autotrophic prokaryotes and archaea, ACL carries out the citrate-cleavage reaction of the reductive tricarboxylic acid (rTCA) cycle. In the family Aquificaceae this latter reaction in the rTCA cycle is carried out via a two enzyme system the second enzyme of which is CCL; the first enzyme is citryl-CoA synthetase (CCS) which is not included in this group. Chlorobium limicola ACL is an example of a two-subunit type ACL. It is comprised of a large and a small subunit; it has been speculated that the large subunit arose from a fusion of the small subunit of the two subunit CCS with CCL. The small ACL subunit is a homolog of the larger CCS subunit. Mammalian ACL is of the single-subunit type and may have arisen from the two-subunit ACL by another gene fusion. Mammalian ACLs are homotetramers; the ACLs of C. limicola and Arabidopsis are a heterooctomers (alpha4beta4). In cancer cells there is a shift in energy metabolism to aerobic glycolysis, the glycolytic end product pyruvate enters a truncated TCA cycle generating citrate which is cleaved in the cytosol by ACL. Inhibiting ACL limits the in-vitro proliferation and survival of these cancer cells, reduces in vivo tumor growth, and induces differentiation.. Length = 227 Score = 32.5 bits (75), Expect = 0.14 Identities = 12/32 (37%), Positives = 16/32 (50%), Gaps = 1/32 (3%) Query: 1 MSFDWDKLRVFYVVARS-GSFTHAAEQLHLSQ 31 + F LR +V+ RS G HA E+ L Q Sbjct: 184 LGFPPGALRGLFVLGRSPGLIAHALEEKRLGQ 215 >gnl|CDD|176106 cd08414, PBP2_LTTR_aromatics_like, The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold. This CD includes the C-terminal substrate binding domain of LTTRs involved in degradation of aromatic compounds, such as CbnR, BenM, CatM, ClcR and TfdR, as well as that of other transcriptional regulators clustered together in phylogenetic trees, including XapR, HcaR, MprR, IlvR, BudR, AlsR, LysR, and OccR. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate-binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction. Length = 197 Score = 31.3 bits (72), Expect = 0.36 Identities = 39/165 (23%), Positives = 61/165 (36%), Gaps = 24/165 (14%) Query: 95 LRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLI----------LDNKDIDISMDYADCAI 144 LRI LL L+ F YPD++++L L +D+ Sbjct: 2 LRIGFVGSALYGLLPRLLRRFRARYPDVELELREMTTAEQLEALRAGRLDV-------GF 54 Query: 145 RLRKPIQSSSLIQRKLVTIHMHAYAAP--HYLKNCREPLSIQELDKHNLITFGDLIPKCM 202 +R P L R L+ + A P H L RE +S+ +L + F + Sbjct: 55 -VRPPPDPPGLASRPLLREPLVV-ALPADHPL-AARESVSLADLADEPFVLFPREPGPGL 111 Query: 203 EDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLGSGIALLPDY 247 D LA R PRI + + +++ G G+AL+P Sbjct: 112 YDQ-ILALCRRAGFTPRIV-QEASDLQTLLALVAAGLGVALVPAS 154 >gnl|CDD|176117 cd08426, PBP2_LTTR_like_5, The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to a name a few. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Length = 199 Score = 30.4 bits (69), Expect = 0.57 Identities = 30/167 (17%), Positives = 54/167 (32%), Gaps = 32/167 (19%) Query: 94 KLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNK------------DIDISMDYA- 140 ++R+AT L LL + F YP + + + + DI ++ Sbjct: 1 RVRVATGEGLAAELLPSLIARFRQRYPGVFFTVDVASTADVLEAVLSGEADIGLAFSPPP 60 Query: 141 --DCAIRLRKPIQSSSLIQRKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLI 198 + R+P +++ H A + +++ +L + L L Sbjct: 61 EPGIRVHSRQPAPIGAVVPPG------HPLAR-------QPSVTLAQLAGYPLA----LP 103 Query: 199 PKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLGSGIALLP 245 P L G L NS ++ Q G GI+LL Sbjct: 104 PPSFSLRQILDAAFARAGVQLEPVLISNSIETLKQLVAAGGGISLLT 150 >gnl|CDD|176173 cd08484, PBP2_LTTR_beta_lactamase, The C-terminal substrate-domain of LysR-type transcriptional regulators for beta-lactamase genes, contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate binding domain of LysR-type transcriptional regulators, BlaA and AmpR, that are involved in control of the expression of beta-lactamase genes. Beta-lactamases are responsible for bacterial resistance to beta-lactam antibiotics such as penicillins. BlaA (a constitutive class A penicillinase) belongs to the LysR family of transcriptional regulators, while BlaB (an inducible class C cephalosporinase or AmpC) can be referred to as a penicillin-binding protein, but it does not act as a beta-lactamase. AmpR regulates the expression of beta-lactamases in many enterobacterial strains and many other gram-negative bacilli. In contrast to BlaA, AmpR acts an activator only in the presence of the beta-lactam inducer. In the absence of the inducer, AmpR acts as a repressor. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Length = 189 Score = 30.0 bits (68), Expect = 0.75 Identities = 14/34 (41%), Positives = 21/34 (61%) Query: 112 LKEFLLLYPDIQIQLILDNKDIDISMDYADCAIR 145 L EF L+P I ++L +N +DI+ + D AIR Sbjct: 19 LAEFRQLHPFIDLRLSTNNNRVDIAAEGLDFAIR 52 >gnl|CDD|176177 cd08488, PBP2_AmpR, The C-terminal substrate domain of LysR-type transcriptional regulator AmpR that involved in control of the expression of beta-lactamase gene ampC, contains the type 2 periplasmic binding fold. AmpR acts as a transcriptional activator by binding to a DNA region immediately upstream of the ampC promoter. In the absence of a beta-lactam inducer, AmpR represses the synthesis of beta-lactamase, whereas expression is induced in the presence of a beta-lactam inducer. The AmpD, AmpG, and AmpR proteins are involved in the induction of AmpC-type beta-lactamase (class C) which produced by enterobacterial strains and many other gram-negative bacilli. The activation of ampC by AmpR requires ampG for induction or high-level expression of AmpC. It is probable that the AmpD and AmpG work together to modulate the ability of AmpR to activate ampC expression. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Length = 191 Score = 29.8 bits (67), Expect = 0.85 Identities = 38/142 (26%), Positives = 61/142 (42%), Gaps = 24/142 (16%) Query: 112 LKEFLLLYPDIQIQLILDNKDIDISMDYADCAIRLRK----PIQSSSLIQRKLVTIHMHA 167 L +F +P I ++L +N +DI+ + D AIR I ++ L + L + Sbjct: 19 LADFQNRHPFIDLRLSTNNNRVDIAAEGLDYAIRFGSGAWHGIDATRLFEAPLSPL---- 74 Query: 168 YAAPHYLKNCREPLSIQELDKHNLIT--FGDLIPKCMEDFNWL--ATVDRPIGEPRISCL 223 P + REP +L +H L+ D P+ W A V P G P + Sbjct: 75 -CTPELARQLREPA---DLARHTLLRSYRADEWPQ------WFEAAGVGHPCGLPN--SI 122 Query: 224 QVNSYLSIMQYCVLGSGIALLP 245 +S L +M+ + G G+AL P Sbjct: 123 MFDSSLGMMEAALQGLGVALAP 144 >gnl|CDD|176131 cd08440, PBP2_LTTR_like_4, TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to a name a few. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Length = 197 Score = 29.8 bits (68), Expect = 0.99 Identities = 25/112 (22%), Positives = 38/112 (33%), Gaps = 18/112 (16%) Query: 94 KLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKDIDISMDY---------ADCAI 144 ++R+A L LL L F +P I+++L D+S + D I Sbjct: 1 RVRVAALPSLAATLLPPVLAAFRRRHPGIRVRL------RDVSAEQVIEAVRSGEVDFGI 54 Query: 145 RLRKPIQSSSLIQRKLVTIHMHAYAAP-HYLKNCREPLSIQELDKHNLITFG 195 P L L+ H L R ++ EL + LI G Sbjct: 55 GSE-PEADPDLEFEPLLRDPFVLVCPKDHPLAR-RRSVTWAELAGYPLIALG 104 >gnl|CDD|31512 COG1321, TroR, Mn-dependent transcriptional regulator [Transcription]. Length = 154 Score = 29.5 bits (66), Expect = 1.1 Identities = 20/82 (24%), Positives = 34/82 (41%), Gaps = 5/82 (6%) Query: 1 MSFDWDKLRVFYVVARSGSFTHA---AEQLHLSQSSISRQISGLETEVGIKLFYRHARGL 57 + D L Y + F AE+L +S S++ + LE ++ Y G+ Sbjct: 5 SETEEDYLETIYELLEEKGFARTKDIAERLKVSPPSVTEMLKRLERLGLVE--YEPYGGV 62 Query: 58 TLTEQGSKLHRVTSEVYHKLET 79 TLTE+G + + + LE Sbjct: 63 TLTEKGREKAKELLRKHRLLER 84 >gnl|CDD|176135 cd08444, PBP2_Cbl, The C-terminal substrate binding domain of LysR-type transcriptional regulator Cbl, which is required for expression of sulfate starvation-inducible (ssi) genes, contains the type 2 periplasmic binding fold. Cbl is a member of the LysR transcriptional regulators that comprise the largest family of prokaryotic transcription factor. Cbl shows high sequence similarity to CysB, the LysR-type transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the function of Cbl is required for expression of sulfate starvation-inducible (ssi) genes, coupled with the biosynthesis of cysteine from the organic sulfur sources (sulfonates). The ssi genes include the ssuEADCB and tauABCD operons encoding uptake systems for organosulfur compounds, aliphatic sulfonates, and taurine. The genes in these operons encode an ABC-type transport system required for uptake of aliphatic sulfonates and a desulfonation enzyme. Both Cbl and CysB require expression of the tau and ssu genes. Like many other members of the LTTR family, the Cbl is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Length = 198 Score = 29.4 bits (66), Expect = 1.3 Identities = 26/105 (24%), Positives = 43/105 (40%), Gaps = 7/105 (6%) Query: 95 LRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKDIDISM---DYADCAIRLRKPIQ 151 L IATT + L ++ F +P++ + L + + SM AD I Sbjct: 2 LTIATTHTQARYALPWVVQAFKEQFPNVHLVLHQGSPEEIASMLANGQADIGIATEALEN 61 Query: 152 SSSLIQRKLVTIHMHAYAAP--HYLKNCREPLSIQELDKHNLITF 194 L+ H H P H L++ PL+I+ + K +IT+ Sbjct: 62 HPELVSFPYYDWH-HHIIVPVGHPLES-ITPLTIETIAKWPIITY 104 >gnl|CDD|32188 COG2005, ModE, N-terminal domain of molybdenum-binding protein [General function prediction only]. Length = 130 Score = 29.1 bits (65), Expect = 1.6 Identities = 22/85 (25%), Positives = 31/85 (36%), Gaps = 12/85 (14%) Query: 14 VARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRH------------ARGLTLTE 61 +A +GS + AA+ +S S I L +G L R G L E Sbjct: 28 IAETGSISAAAKAAGISYKSAWDYIKALNRLLGEPLVERRRGGKGGGGAVLTDFGERLLE 87 Query: 62 QGSKLHRVTSEVYHKLETTQIELQE 86 + L + E KLE Q+ L Sbjct: 88 EYRLLEKEIEEALRKLEDEQLPLDS 112 >gnl|CDD|110083 pfam01056, Myc_N, Myc amino-terminal region. The myc family belongs to the basic helix-loop-helix leucine zipper class of transcription factors, see pfam00010. Myc forms a heterodimer with Max, and this complex regulates cell growth through direct activation of genes involved in cell replication. Length = 329 Score = 28.8 bits (64), Expect = 1.9 Identities = 10/28 (35%), Positives = 16/28 (57%) Query: 148 KPIQSSSLIQRKLVTIHMHAYAAPHYLK 175 + S +++R V+IH H YAAP + Sbjct: 271 RRHHSPLVLKRCHVSIHQHNYAAPPSTR 298 >gnl|CDD|35595 KOG0374, KOG0374, KOG0374, Serine/threonine specific protein phosphatase PP1, catalytic subunit [Signal transduction mechanisms, General function prediction only]. Length = 331 Score = 28.7 bits (64), Expect = 2.2 Identities = 14/42 (33%), Positives = 22/42 (52%), Gaps = 4/42 (9%) Query: 158 RKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIP 199 RKLVTI ++AP+Y ++ +DK+ +F L P Sbjct: 265 RKLVTI----FSAPNYCGEFDNAGAVMRVDKNLKCSFVILRP 302 >gnl|CDD|176105 cd08413, PBP2_CysB_like, The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold. CysB is a transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the regulation of transcription in response to sulfur source is attributed to two transcriptional regulators, CysB and Cbl. CysB, in association with Cbl, downregulates the expression of ssuEADCB operon which is required for the utilization of sulfur from aliphatic sulfonates, in the presence of cysteine. Also, Cbl and CysB together directly function as transcriptional activators of tauABCD genes, which are required for utilization of taurine as sulfur source for growth. Like many other members of the LTTR family, CysB is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate-binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction. Length = 198 Score = 28.0 bits (63), Expect = 3.3 Identities = 24/111 (21%), Positives = 41/111 (36%), Gaps = 17/111 (15%) Query: 94 KLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKDIDISM---DYADCAIRLRKPI 150 +L IATT + +L + F YP +++ L M AD AI Sbjct: 1 QLTIATTHTQARYVLPPVIAAFRKRYPKVKLSLHQGTPSQIAEMVLKGEADIAIATEALD 60 Query: 151 QSSSLI-------QRKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITF 194 L+ ++ H A PL++++L ++ LIT+ Sbjct: 61 DHPDLVTLPCYRWNHCVIVPPGHPLAD-------LGPLTLEDLAQYPLITY 104 >gnl|CDD|176140 cd08449, PBP2_XapR, The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved in xanthosine catabolism, contains the type 2 periplasmic binding fold. In Escherichia coli, XapR is a positive regulator for the expression of xapA gene, encoding xanthosine phosphorylase, and xapB gene, encoding a polypeptide similar to the nucleotide transport protein NupG. As an operon, the expression of both xapA and xapB is fully dependent on the presence of both XapR and the inducer xanthosine. Expression of the xapR is constitutive but not auto-regulated, unlike many other LysR family proteins. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Length = 197 Score = 27.6 bits (62), Expect = 4.7 Identities = 33/157 (21%), Positives = 58/157 (36%), Gaps = 39/157 (24%) Query: 112 LKEFLLLYPDIQIQLI----------LDNKDIDISMDYADCAIRLRKP-IQSSSLIQRKL 160 L+ F YP++ ++ L +K ID+ + A L P + S L + + Sbjct: 19 LRRFKRQYPNVTVRFHELSPEAQKAALLSKRIDLG--FVRFADTLNDPPLASELLWREPM 76 Query: 161 VTIHMHAYAAPHYLKNCREPLSIQELDKHNLI-------TFGDLIPKCM--EDFNWLATV 211 V A H L R+ L++ +L + F D + C F Sbjct: 77 VV----ALPEEHPLAG-RKSLTLADLRDEPFVFLRLANSRFADFLINCCLQAGFT----- 126 Query: 212 DRPIGEPRISCLQVNSYLSIMQYCVLGSGIALLPDYI 248 P+I+ +V ++M G G+AL+P+ Sbjct: 127 ------PQIT-QEVVEPQTLMALVAAGFGVALVPESY 156 >gnl|CDD|173850 cd01161, VLCAD, Very long chain acyl-CoA dehydrogenase. VLCAD is an acyl-CoA dehydrogenase (ACAD), which is found in the mitochondria of eukaryotes and in some bacteria. It catalyzes the alpha,beta dehydrogenation of the corresponding trans-enoyl-CoA by FAD, which becomes reduced. The reduced form of ACAD is reoxidized in the oxidative half-reaction by electron-transferring flavoprotein (ETF), from which the electrons are transferred to the mitochondrial respiratory chain coupled with ATP synthesis. VLCAD acts as a homodimer. Length = 409 Score = 27.4 bits (61), Expect = 4.8 Identities = 13/38 (34%), Positives = 20/38 (52%) Query: 133 IDISMDYADCAIRLRKPIQSSSLIQRKLVTIHMHAYAA 170 I+ ++DYA+ + K I LIQ KL + + YA Sbjct: 283 IEKAVDYANNRKQFGKKIHEFGLIQEKLANMAILQYAT 320 >gnl|CDD|176125 cd08434, PBP2_GltC_like, The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA expression of glutamate synthase operon, contains type 2 periplasmic binding fold. GltC, a member of the LysR family of bacterial transcriptional factors, activates the expression of gltA gene of glutamate synthase operon and is essential for cell growth in the absence of glutamate. Glutamate synthase is a heterodimeric protein that encoded by gltA and gltB, whose expression is subject to nutritional regulation. GltC also negatively auto-regulates its own expression. This substrate-binding domain has strong homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Length = 195 Score = 27.1 bits (61), Expect = 5.7 Identities = 17/81 (20%), Positives = 33/81 (40%), Gaps = 15/81 (18%) Query: 94 KLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLI----------LDNKDIDISMDYADCA 143 +R+ LG +L+ ++ F YP++ +L L N ++D+ A C+ Sbjct: 1 TVRLGFLHSLGTSLVPDLIRAFRKEYPNVTFELHQGSTDELLDDLKNGELDL----ALCS 56 Query: 144 IRLR-KPIQSSSLIQRKLVTI 163 I+ L +LV + Sbjct: 57 PVPDEPDIEWIPLFTEELVLV 77 >gnl|CDD|176115 cd08423, PBP2_LTTR_like_6, The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to a name a few. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Length = 200 Score = 26.8 bits (60), Expect = 7.5 Identities = 9/30 (30%), Positives = 17/30 (56%), Gaps = 1/30 (3%) Query: 217 EPRISCLQVNSYLSIMQYCVLGSGIALLPD 246 PRI+ + + Y +++ G G+AL+P Sbjct: 128 TPRIAH-EADDYATVLALVAAGLGVALVPR 156 >gnl|CDD|35359 KOG0137, KOG0137, KOG0137, Very-long-chain acyl-CoA dehydrogenase [Lipid transport and metabolism]. Length = 634 Score = 26.8 bits (59), Expect = 8.0 Identities = 11/37 (29%), Positives = 17/37 (45%) Query: 133 IDISMDYADCAIRLRKPIQSSSLIQRKLVTIHMHAYA 169 I+ + DYA + K + LIQ K+ + YA Sbjct: 337 IEEAADYATNRTQFGKKLHDFGLIQEKVAEMASKVYA 373 >gnl|CDD|176134 cd08443, PBP2_CysB, The C-terminal substrate domain of LysR-type transcriptional regulator CysB contains type 2 periplasmic binding fold. CysB is a transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the regulation of transcription in response to sulfur source is attributed to two transcriptional regulators, CysB and Cbl. CysB, in association with Cbl, downregulates the expression of ssuEADCB operon which is required for the utilization of sulfur from aliphatic sulfonates, in the presence of cysteine. Also, Cbl and CysB together directly function as transcriptional activators of tauABCD genes, which are required for utilization of taurine as sulfur source for growth. Like many other members of the LTTR family, CysB is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Length = 198 Score = 26.8 bits (59), Expect = 8.7 Identities = 25/111 (22%), Positives = 43/111 (38%), Gaps = 17/111 (15%) Query: 94 KLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKDIDISM---DYADCAIRLRKPI 150 L +ATT + +L +K F+ YP + +Q+ + M D AI Sbjct: 1 SLYVATTHTQARYVLPPVIKGFIERYPRVSLQMHQGSPTQIAEMVSKGLVDFAIATEALH 60 Query: 151 QSSSLI-------QRKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITF 194 LI R +V H A ++ +SI+EL + ++T+ Sbjct: 61 DYDDLITLPCYHWNRCVVVKRDHPLAD-------KQSISIEELATYPIVTY 104 Database: CddA Posted date: Feb 4, 2011 9:38 PM Number of letters in database: 6,263,737 Number of sequences in database: 21,609 Lambda K H 0.323 0.138 0.410 Gapped Lambda K H 0.267 0.0808 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 3,585,978 Number of extensions: 184095 Number of successful extensions: 473 Number of sequences better than 10.0: 1 Number of HSP's gapped: 435 Number of HSP's successfully gapped: 46 Length of query: 299 Length of database: 6,263,737 Length adjustment: 93 Effective length of query: 206 Effective length of database: 4,254,100 Effective search space: 876344600 Effective search space used: 876344600 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 57 (25.6 bits)