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)