RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3760
(306 letters)
>gnl|CDD|237173 PRK12684, PRK12684, transcriptional regulator CysB-like protein;
Reviewed.
Length = 313
Score = 504 bits (1301), Expect = 0.0
Identities = 190/306 (62%), Positives = 252/306 (82%)
Query: 1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLT 60
MNLHQ RFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELE+EL ++IF RHGKR+RGLT
Sbjct: 1 MNLHQLRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLRGLT 60
Query: 61 KPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFP 120
+PG+ IL S+E I+QE+E LK++GKEF+A D GNLTIATTHTQARYALP IKEF ++P
Sbjct: 61 EPGRIILASVERILQEVENLKRVGKEFAAQDQGNLTIATTHTQARYALPAAIKEFKKRYP 120
Query: 121 KVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLLL 180
KV+LS+LQG+P QI EM+ + QAD+AI TE ++ +L+S+PCYQW + ++VP DHPLL
Sbjct: 121 KVRLSILQGSPTQIAEMVLHGQADLAIATEAIADYKELVSLPCYQWNHCVVVPPDHPLLE 180
Query: 181 LNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGI 240
++L++++ YPLITYD +F+GR K+++ F+L+ L P IVLE I++D+IKTYVEL +G+
Sbjct: 181 RKPLTLEDLAQYPLITYDFAFAGRSKINKAFALRGLKPDIVLEAIDADVIKTYVELGLGV 240
Query: 241 GIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFI 300
GI+A +AFD RD+NLR+I A HLFG++ +R+ +++G YLR YVY+FI+L +P LNRK +
Sbjct: 241 GIVADMAFDPERDRNLRAIDAGHLFGSSTTRLGLRRGAYLRGYVYTFIELFAPTLNRKLV 300
Query: 301 NKILNN 306
+ L
Sbjct: 301 EQALKG 306
>gnl|CDD|183679 PRK12682, PRK12682, transcriptional regulator CysB-like protein;
Reviewed.
Length = 309
Score = 434 bits (1119), Expect = e-155
Identities = 169/304 (55%), Positives = 230/304 (75%)
Query: 1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLT 60
MNL Q RFVREAVR+N NLTEAAKAL+TSQPGVSKAIIELEEEL I+IFIRHGKR++GLT
Sbjct: 1 MNLQQLRFVREAVRRNLNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKGLT 60
Query: 61 KPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFP 120
+PG+A+L IE I++E+ +K+IG +FS D+G LTIATTHTQARY LP+++ F ++P
Sbjct: 61 EPGKAVLDVIERILREVGNIKRIGDDFSNQDSGTLTIATTHTQARYVLPRVVAAFRKRYP 120
Query: 121 KVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLLL 180
KV LSL QG+P +I M+ + +ADI I TE L+ L ++PCY W++ +IVP DHPL
Sbjct: 121 KVNLSLHQGSPDEIARMVISGEADIGIATESLADDPDLATLPCYDWQHAVIVPPDHPLAQ 180
Query: 181 LNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGI 240
I+L++++ YPLITY F+GR ++DR F+ L P IVLE I+SD+IKTYV L +G+
Sbjct: 181 EERITLEDLAEYPLITYHPGFTGRSRIDRAFAAAGLQPDIVLEAIDSDVIKTYVRLGLGV 240
Query: 241 GIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFI 300
GI+A +A+ +RD +L ++ A HLFG + V +K+G YLR+YVY FI+L +P L+R+ I
Sbjct: 241 GIVAEMAYRPDRDGDLVALPAGHLFGPNTAWVALKRGAYLRNYVYKFIELCAPHLSRELI 300
Query: 301 NKIL 304
+ +
Sbjct: 301 KRAV 304
>gnl|CDD|237172 PRK12683, PRK12683, transcriptional regulator CysB-like protein;
Reviewed.
Length = 309
Score = 417 bits (1073), Expect = e-148
Identities = 152/304 (50%), Positives = 218/304 (71%)
Query: 1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLT 60
MN Q R +REAVRQNFNLTE A ALYTSQ GVSK I +LE+EL ++IFIR GKR+ GLT
Sbjct: 1 MNFQQLRIIREAVRQNFNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLTGLT 60
Query: 61 KPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFP 120
+PG+ +L+ +E ++ + E L+++ ++F+ D+G+LT+ATTHTQARYALPK++++F FP
Sbjct: 61 EPGKELLQIVERMLLDAENLRRLAEQFADRDSGHLTVATTHTQARYALPKVVRQFKEVFP 120
Query: 121 KVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLLL 180
KV L+L QG+P++I EM+ N +ADI I TE L L+S P Y W +V++VP HPL
Sbjct: 121 KVHLALRQGSPQEIAEMLLNGEADIGIATEALDREPDLVSFPYYSWHHVVVVPKGHPLTG 180
Query: 181 LNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGI 240
+++L+ I+ YP+ITYD F+GR ++D+ F+ L P IVL +++D+IKTYVEL MG+
Sbjct: 181 RENLTLEAIAEYPIITYDQGFTGRSRIDQAFAEAGLVPDIVLTALDADVIKTYVELGMGV 240
Query: 241 GIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFI 300
GI+A++A+D RD L ++ HLF +RV +++G YLR Y Y FI+L +P L+ I
Sbjct: 241 GIVAAMAYDPQRDTGLVALDTDHLFEANTTRVGLRRGAYLRGYAYRFIELFAPHLSEAEI 300
Query: 301 NKIL 304
L
Sbjct: 301 AAAL 304
>gnl|CDD|183678 PRK12681, cysB, transcriptional regulator CysB; Reviewed.
Length = 324
Score = 338 bits (869), Expect = e-116
Identities = 136/302 (45%), Positives = 194/302 (64%)
Query: 1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLT 60
M L Q R++ E V N N++ A+ LYTSQPG+SK + LE+EL I IF R GK + +T
Sbjct: 1 MKLQQLRYIVEVVNHNLNVSATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLTQVT 60
Query: 61 KPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFP 120
G+ I+R I+ ++E +K + E + D G+L IATTHTQARYALP +IK F ++P
Sbjct: 61 PAGEEIIRIAREILSKVESIKSVAGEHTWPDKGSLYIATTHTQARYALPPVIKGFIERYP 120
Query: 121 KVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLLL 180
+V L + QG+P QI E AD AI TE L D LI +PCY W ++VP DHPL
Sbjct: 121 RVSLHMHQGSPTQIAEAAAKGNADFAIATEALHLYDDLIMLPCYHWNRSVVVPPDHPLAK 180
Query: 181 LNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGI 240
++++E++ YPL+TY F+GR +LD F+ LTP IV ++D+IKTYV L +G+
Sbjct: 181 KKKLTIEELAQYPLVTYVFGFTGRSELDTAFNRAGLTPRIVFTATDADVIKTYVRLGLGV 240
Query: 241 GIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFI 300
G+IAS+A D D +L +I ASHLF + +++ ++GT+LRSY+Y FI+ +P L R +
Sbjct: 241 GVIASMAVDPVADPDLVAIDASHLFSHSTTKIGFRRGTFLRSYMYDFIERFAPHLTRDVV 300
Query: 301 NK 302
K
Sbjct: 301 EK 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 = 299 bits (768), Expect = e-103
Identities = 103/197 (52%), Positives = 140/197 (71%)
Query: 95 LTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSP 154
LTIATTHTQARY LP +I F ++PKVKLSL QG P QI EM+ +ADIAI TE L
Sbjct: 2 LTIATTHTQARYVLPPVIAAFRKRYPKVKLSLHQGTPSQIAEMVLKGEADIAIATEALDD 61
Query: 155 SDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQ 214
L+++PCY+W + +IVP HPL L ++L++++ YPLITYD F+GR +DR F+
Sbjct: 62 HPDLVTLPCYRWNHCVIVPPGHPLADLGPLTLEDLAQYPLITYDFGFTGRSSIDRAFARA 121
Query: 215 KLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSNRDKNLRSISASHLFGTTISRVII 274
L P IVL +++D+IKTYV L +G+GIIA +A+D RD +L ++ A HLFG +R+ +
Sbjct: 122 GLEPNIVLTALDADVIKTYVRLGLGVGIIAEMAYDPQRDADLVALDAGHLFGPNTTRIAL 181
Query: 275 KQGTYLRSYVYSFIKLL 291
++GTYLRSY Y FI+L
Sbjct: 182 RRGTYLRSYAYDFIELF 198
>gnl|CDD|183676 PRK12679, cbl, transcriptional regulator Cbl; Reviewed.
Length = 316
Score = 302 bits (775), Expect = e-102
Identities = 128/295 (43%), Positives = 196/295 (66%)
Query: 1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLT 60
MN Q + +REA RQ++NLTE A L+TSQ GVS+ I ELE+EL I+IFIR GKR+ G+T
Sbjct: 1 MNFQQLKIIREAARQDYNLTEVANMLFTSQSGVSRHIRELEDELGIEIFIRRGKRLLGMT 60
Query: 61 KPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFP 120
+PG+A+L E I+ E ++++ F+ +G LTIATTHTQARY+LP++IK F FP
Sbjct: 61 EPGKALLVIAERILNEASNVRRLADLFTNDTSGVLTIATTHTQARYSLPEVIKAFRELFP 120
Query: 121 KVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLLL 180
+V+L L+QG P++I +++N +ADI I +E LS +L++ P ++W + ++VP DHPL
Sbjct: 121 EVRLELIQGTPQEIATLLQNGEADIGIASERLSNDPQLVAFPWFRWHHSLLVPHDHPLTQ 180
Query: 181 LNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGI 240
+ ++L+ I+ +PLITY +GR ++D F+ + L IVL +SD+IKTYV L +GI
Sbjct: 181 ITPLTLESIAKWPLITYRQGITGRSRIDDAFARKGLLADIVLSAQDSDVIKTYVALGLGI 240
Query: 241 GIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKL 295
G++A + + NL + HLF + +K+G R+YV+ F++L + L
Sbjct: 241 GLVAEQSSGEQEESNLIRLDTRHLFDANTVWLGLKRGQLQRNYVWRFLELCNAGL 295
>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 = 227 bits (581), Expect = 8e-75
Identities = 97/196 (49%), Positives = 136/196 (69%)
Query: 95 LTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSP 154
LTIATTHTQARYALP +++ F QFP V L L QG+P++I M+ N QADI I TE L
Sbjct: 2 LTIATTHTQARYALPWVVQAFKEQFPNVHLVLHQGSPEEIASMLANGQADIGIATEALEN 61
Query: 155 SDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQ 214
+L+S P Y W + IIVP+ HPL + ++++ I+ +P+ITY F+GR ++DR FS
Sbjct: 62 HPELVSFPYYDWHHHIIVPVGHPLESITPLTIETIAKWPIITYHGGFTGRSRIDRAFSRA 121
Query: 215 KLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSNRDKNLRSISASHLFGTTISRVII 274
+LTP IVL +++D+IKTYV L MGIGI+A +AF+ RD NL + SHLFG + + +
Sbjct: 122 ELTPNIVLSALDADVIKTYVGLGMGIGIVAEMAFEGQRDTNLIKLDTSHLFGKNTTWIAL 181
Query: 275 KQGTYLRSYVYSFIKL 290
++G LR++ Y FI+L
Sbjct: 182 RRGGDLRNFAYRFIEL 197
>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 = 217 bits (555), Expect = 6e-71
Identities = 91/196 (46%), Positives = 131/196 (66%)
Query: 95 LTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSP 154
L +ATTHTQARY LP +IK F ++P+V L + QG+P QI EM+ D AI TE L
Sbjct: 2 LYVATTHTQARYVLPPVIKGFIERYPRVSLQMHQGSPTQIAEMVSKGLVDFAIATEALHD 61
Query: 155 SDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQ 214
D LI++PCY W ++V DHPL SIS++E++ YP++TY F+GR +LD F+
Sbjct: 62 YDDLITLPCYHWNRCVVVKRDHPLADKQSISIEELATYPIVTYTFGFTGRSELDTAFNRA 121
Query: 215 KLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSNRDKNLRSISASHLFGTTISRVII 274
LTP IVL ++D+IKTYV L +G+G+IAS+A+D D +L A LF +++++
Sbjct: 122 GLTPNIVLTATDADVIKTYVRLGLGVGVIASMAYDPVDDPDLVIRDARDLFPWSVTKIAF 181
Query: 275 KQGTYLRSYVYSFIKL 290
++GT+LRSY+Y FI+
Sbjct: 182 RRGTFLRSYMYDFIQR 197
>gnl|CDD|183677 PRK12680, PRK12680, transcriptional regulator CysB-like protein;
Reviewed.
Length = 327
Score = 178 bits (452), Expect = 7e-54
Identities = 87/306 (28%), Positives = 163/306 (53%), Gaps = 2/306 (0%)
Query: 1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLT 60
M L Q R++ N+T AA ++ +QPG+SK + +LE+EL +F+R G+ + +T
Sbjct: 1 MTLTQLRYLVAIADAELNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLESVT 60
Query: 61 KPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFP 120
G ++ ++ E ++ G LT+ TTHTQAR+ LP + + +P
Sbjct: 61 PAGVEVIERARAVLSEANNIRTYAANQRRESQGQLTLTTTHTQARFVLPPAVAQIKQAYP 120
Query: 121 KVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPL-L 179
+V + L Q +++ ADIAIV+ I++P Y+W +++VP H L
Sbjct: 121 QVSVHLQQAAESAALDLLGQGDADIAIVSTAGGEPSAGIAVPLYRWRRLVVVPRGHALDT 180
Query: 180 LLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMG 239
+ + ++ +PLI+Y+ S L R F+ L P I L +++D+IKTYV +G
Sbjct: 181 PRRAPDMAALAEHPLISYESSTRPGSSLQRAFAQLGLEPSIALTALDADLIKTYVRAGLG 240
Query: 240 IGIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKF 299
+G++A +A ++N D++LR+ A I+ ++ + LR Y + +L+P+++++
Sbjct: 241 VGLLAEMAVNAN-DEDLRAWPAPAPIAECIAWAVLPRDRVLRDYALELVHVLAPQIDKRD 299
Query: 300 INKILN 305
+ ++L+
Sbjct: 300 LRRVLD 305
>gnl|CDD|223656 COG0583, LysR, Transcriptional regulator [Transcription].
Length = 297
Score = 151 bits (382), Expect = 8e-44
Identities = 81/299 (27%), Positives = 137/299 (45%), Gaps = 8/299 (2%)
Query: 1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLT 60
M+L Q R AV + + T AA+ L SQ VS+ I LEEEL + +F R +R+R LT
Sbjct: 1 MDLRQLR-AFVAVAEEGSFTRAAERLGLSQSAVSRQIKRLEEELGVPLFERTTRRVR-LT 58
Query: 61 KPGQAILRSIEIIMQEIEGLK-KIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQF 119
+ G+ +L I+ E+E + + G L IA T A LP ++ F ++
Sbjct: 59 EAGERLLERARRILAELEEALAEAARLARGEPGGLLRIAAPSTAASSLLPPLLARFRARY 118
Query: 120 PKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLL 179
P+++L L + ++ E + + D+AI P D L++ P + E V++VP HPL
Sbjct: 119 PEIELELGTSD--RLLEDLVEGELDLAIRAGPPPPPDGLVARPLFSEELVLVVPASHPLA 176
Query: 180 LLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMG 239
+ L ++ PLI + R LD+ +L P I LE +++ + V +G
Sbjct: 177 ARH--GLPDLPGEPLILLEHGCILRRLLDQALALAGWRPRIRLEVNSAEALLQAVAAGLG 234
Query: 240 IGIIASIAFDSN-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNR 297
I ++ + + +R + ++ ++ L V +FI L L R
Sbjct: 235 IALLPESLARPDLAGRLVRVLPLPPPPLPRPLYLVWRKSRLLSPAVRAFIDFLREALAR 293
>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 = 139 bits (352), Expect = 2e-40
Identities = 60/200 (30%), Positives = 103/200 (51%), Gaps = 7/200 (3%)
Query: 95 LTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSP 154
L I + + A Y LP ++ F ++P V+LSL++G ++ E + + D+AIV +
Sbjct: 2 LRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDD 61
Query: 155 SDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQ 214
L S P ++ V++VP DHPL S++L ++++ PLI ++ R LDR F+
Sbjct: 62 PG-LESEPLFEEPLVLVVPPDHPLAKRKSVTLADLADEPLILFERGSGLRRLLDRAFAEA 120
Query: 215 KLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSNRDKNLRSISASHLFGTTISR--- 271
TP I LE + + IK V +GI ++ A + D L + L +SR
Sbjct: 121 GFTPNIALEVDSLEAIKALVAAGLGIALLPESAVEELADGGLVVL---PLEDPPLSRTIG 177
Query: 272 VIIKQGTYLRSYVYSFIKLL 291
++ ++G YL +F++LL
Sbjct: 178 LVWRKGRYLSPAARAFLELL 197
>gnl|CDD|217576 pfam03466, LysR_substrate, LysR substrate binding domain. The
structure of this domain is known and is similar to the
periplasmic binding proteins.
Length = 207
Score = 124 bits (314), Expect = 1e-34
Identities = 52/204 (25%), Positives = 94/204 (46%), Gaps = 8/204 (3%)
Query: 92 TGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEI 151
G L I T A Y LP ++ F ++P V+L L++G+ +++ +++ + D+AI
Sbjct: 3 RGRLRIGAPPTFAAYLLPPLLARFRERYPDVELELVEGDSEELLDLLAEGELDLAIRRGP 62
Query: 152 LSPSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREF 211
L + P ++ V++ P DHPL +SL+++++ PLI + R LDR
Sbjct: 63 PDDPG-LEARPLFEEPLVLVAPPDHPLARGEPVSLEDLADEPLILLEPGSGLRDLLDRAL 121
Query: 212 SLQKLTPYIVLETINSDIIKTYVELRMGIGII-ASIAFDSNRDKNLRSISASHLFGTTIS 270
L P + LE + + + V +GI ++ S D L + L +
Sbjct: 122 RAAGLRPRVALEVNSLEALLAAVAAGLGIALLPRSAVARELADGRLVVL---PLPDPPLP 178
Query: 271 R---VIIKQGTYLRSYVYSFIKLL 291
R ++ ++G L V +FI L
Sbjct: 179 RPIYLVYRKGRRLSPAVRAFIDFL 202
>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 = 96.8 bits (242), Expect = 3e-24
Identities = 58/205 (28%), Positives = 104/205 (50%), Gaps = 11/205 (5%)
Query: 94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILS 153
L I + T Y LP+++ F ++P+V++SL GN ++I E + + + D+ +V E
Sbjct: 1 TLRIGASTTIGEYLLPRLLARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLGLV-EGPV 59
Query: 154 PSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSG-RIKLDREFS 212
LI P + E V++VP DHPL ++ +E++ P I + SG R +R +
Sbjct: 60 DHPDLIVEPFAEDELVLVVPPDHPLAGRKEVTAEELAAEPWILRE-PGSGTREVFERALA 118
Query: 213 ---LQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSNRDKNLRSISASHLFGTTI 269
L L IV+E +++ IK VE +GI I++ +A ++ L + A + G +
Sbjct: 119 EAGLDGLDLNIVMELGSTEAIKEAVEAGLGISILSRLAV--RKELELGRLVALPVEGLRL 176
Query: 270 SR---VIIKQGTYLRSYVYSFIKLL 291
+R +I + YL +F++ L
Sbjct: 177 TRPFSLIYHKDKYLSPAAEAFLEFL 201
>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 = 94.9 bits (237), Expect = 2e-23
Identities = 37/147 (25%), Positives = 70/147 (47%), Gaps = 1/147 (0%)
Query: 97 IATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSD 156
+ H+ +P +I+ F ++P V L QG+ ++ + ++N + D+A+ + +
Sbjct: 4 LGFLHSLGTSLVPDLIRAFRKEYPNVTFELHQGSTDELLDDLKNGELDLALCSPV-PDEP 62
Query: 157 KLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKL 216
+ IP + E V++VP DHPL +S+ L E+++ P + F R +D +
Sbjct: 63 DIEWIPLFTEELVLVVPKDHPLAGRDSVDLAELADEPFVLLSPGFGLRPIVDELCAAAGF 122
Query: 217 TPYIVLETINSDIIKTYVELRMGIGII 243
TP I E I V +G+ I+
Sbjct: 123 TPKIAFEGEEDSTIAGLVAAGLGVAIL 149
>gnl|CDD|132382 TIGR03339, phn_lysR, aminoethylphosphonate catabolism associated
LysR family transcriptional regulator. This group of
sequences represents a number of related clades with
numerous examples of members adjacent to operons for the
degradation of 2-aminoethylphosphonate (AEP) in
Pseudomonas, Ralstonia, Bordetella and Burkholderia
species. These are transcriptional regulators of the
LysR family which contain a helix-turn-helix (HTH)
domain (pfam00126) and a periplasmic substrate-binding
protein-like domain (pfam03466).
Length = 279
Score = 94.4 bits (235), Expect = 1e-22
Identities = 60/240 (25%), Positives = 123/240 (51%), Gaps = 7/240 (2%)
Query: 20 TEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEG 79
T AA+ L SQP V+ + +LEE +++F R+G+R+ LT G +L +E + Q+
Sbjct: 15 TRAAERLGLSQPTVTDQVRKLEERYGVELFHRNGRRLE-LTDAGHRLLPIVERLFQQEAE 73
Query: 80 LKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIR 139
+ + +E A G+L IA T A Y + ++ F ++P +++S+ GN +++ + ++
Sbjct: 74 AEFLLRESGALREGSLRIAAT---APYYVLDLVARFRQRYPGIEVSVRIGNSQEVLQALQ 130
Query: 140 NDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDL 199
+ + D+A+ +E++ +L + V +V HPL S++L+E++ PL+ +
Sbjct: 131 SYRVDVAVSSEVVD-DPRLDRVVLGNDPLVAVVHRQHPLAERESVTLEELAGQPLLMREP 189
Query: 200 SFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSNRDKNLRSI 259
R + + + P LE + + I+ V +G+ ++++ RD LR +
Sbjct: 190 GSVTRQTTEEALAAAGVAPRPALEIGSREAIREAVLAGLGVSVVSAAEVG--RDPRLRVL 247
>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 = 88.0 bits (219), Expect = 6e-21
Identities = 40/149 (26%), Positives = 67/149 (44%), Gaps = 1/149 (0%)
Query: 95 LTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSP 154
L IA A LP+ I F + P V++SL + + E + + QAD+ + + L
Sbjct: 2 LRIAALPALALSLLPRAIARFRARHPDVRISLHTLSSSTVVEAVLSGQADLGLASLPLDH 61
Query: 155 SDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQ 214
L S P V ++P HPL + ++ +++ PLI+ R ++D F
Sbjct: 62 PG-LESEPLASGRAVCVLPPGHPLARKDVVTPADLAGEPLISLGRGDPLRQRVDAAFERA 120
Query: 215 KLTPYIVLETINSDIIKTYVELRMGIGII 243
+ P IV+ET S V +G+ I+
Sbjct: 121 GVEPRIVIETQLSHTACALVAAGLGVAIV 149
>gnl|CDD|183051 PRK11242, PRK11242, DNA-binding transcriptional regulator CynR;
Provisional.
Length = 296
Score = 86.5 bits (215), Expect = 1e-19
Identities = 63/218 (28%), Positives = 120/218 (55%), Gaps = 6/218 (2%)
Query: 12 AVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIE 71
AV ++ N T AA+AL+ SQP +S+ I +LEE L + +F R G+ +R LT G+ LR
Sbjct: 11 AVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVR-LTDAGEVYLRYAR 69
Query: 72 IIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNP 131
+Q++E ++ + + G+L +A T T Y + +I F ++P + L++ + +
Sbjct: 70 RALQDLEAGRRAIHDVADLSRGSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIREMSQ 129
Query: 132 KQITEMIRNDQADIAIV-TEILSPSDKLISIPCYQWEYVIIVPLDHPLL-LLNSISLKEI 189
++I ++ +D+ D+ I + SP ++ + P + ++V HPL +++L E+
Sbjct: 130 ERIEALLADDELDVGIAFAPVHSP--EIEAQPLFTETLALVVGRHHPLAARRKALTLDEL 187
Query: 190 SNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINS 227
++ PL+ F+ R ++DR F +TP + +E NS
Sbjct: 188 ADEPLVLLSAEFATREQIDRYFRRHGVTPRVAIEA-NS 224
>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 = 83.0 bits (206), Expect = 4e-19
Identities = 37/172 (21%), Positives = 72/172 (41%), Gaps = 15/172 (8%)
Query: 95 LTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSP 154
+ +A + A LP ++ F + P +++ L + +Q+ E +R+ + D I +E
Sbjct: 2 VRVAALPSLAATLLPPVLAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVDFGIGSE-PEA 60
Query: 155 SDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQ 214
L P + +V++ P DHPL S++ E++ YPLI R +DR +
Sbjct: 61 DPDLEFEPLLRDPFVLVCPKDHPLARRRSVTWAELAGYPLIALGRGSGVRALIDRALAAA 120
Query: 215 KLTPYIVLETINSDIIKTY-------VELRMGIGIIASIAFDSNRDKNLRSI 259
LT E ++ V +G+ ++ ++A L +
Sbjct: 121 GLTLRPAYEV-------SHMSTALGMVAAGLGVAVLPALALPLADHPGLVAR 165
>gnl|CDD|176111 cd08419, PBP2_CbbR_RubisCO_like, The C-terminal substrate binding
of LysR-type transcriptional regulator (CbbR) of RubisCO
operon, which is involved in the carbon dioxide
fixation, contains the type 2 periplasmic binding fold.
CbbR, a LysR-type transcriptional regulator, is required
to activate expression of RubisCO, one of two unique
enzymes in the Calvin-Benson-Bassham (CBB) cycle
pathway. All plants, cyanobacteria, and many autotrophic
bacteria use the CBB cycle to fix carbon dioxide. Thus,
this cycle plays an essential role in assimilating CO2
into organic carbon on earth. The key CBB cycle enzyme
is ribulose 1,5-bisphosphate carboxylase/oxygenase
(RubisCO), which catalyzes the actual CO2 fixation
reaction. The CO2 concentration affects the expression
of RubisCO genes. It has also shown that NADPH enhances
the DNA-binding ability of the CbbR. RubisCO is composed
of eight large (CbbL) and eight small subunits (CbbS).
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 = 197
Score = 80.2 bits (199), Expect = 5e-18
Identities = 43/151 (28%), Positives = 81/151 (53%), Gaps = 6/151 (3%)
Query: 95 LTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSP 154
L +A T A+Y P+++ F + P V++SL GN +Q+ E + +++ D+AI+ P
Sbjct: 2 LRLAVVST-AKYFAPRLLGAFCRRHPGVEVSLRVGNREQVLERLADNEDDLAIMGRP--P 58
Query: 155 SD-KLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSG-RIKLDREFS 212
D L++ P V+I P DHPL I L+ ++ P + + SG R+ ++R F+
Sbjct: 59 EDLDLVAEPFLDNPLVVIAPPDHPLAGQKRIPLERLAREPFLLRE-PGSGTRLAMERFFA 117
Query: 213 LQKLTPYIVLETINSDIIKTYVELRMGIGII 243
+T + +E +++ IK V +G+ ++
Sbjct: 118 EHGVTLRVRMELGSNEAIKQAVMAGLGLSVL 148
>gnl|CDD|177082 CHL00180, rbcR, LysR transcriptional regulator; Provisional.
Length = 305
Score = 81.6 bits (202), Expect = 8e-18
Identities = 66/250 (26%), Positives = 117/250 (46%), Gaps = 7/250 (2%)
Query: 3 LHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKP 62
L Q R ++ A+ + +AA++LY SQP VS I LE++L+I +F R + LT+
Sbjct: 7 LDQLRILK-AIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKAS-LTEA 64
Query: 63 GQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKV 122
G+ +LR I+ E + ++ G L I + T Y +P++I F ++P++
Sbjct: 65 GELLLRYGNRILALCEETCRALEDLKNLQRGTLIIGASQTTGTYLMPRLIGLFRQRYPQI 124
Query: 123 KLSLLQGNPKQITEMIRNDQADIAIVTEILSP--SDKLISIPCYQWEYVIIVPLDHPLLL 180
+ L + ++I + N Q DIAIV + L P + E +I+P HP
Sbjct: 125 NVQLQVHSTRRIAWNVANGQIDIAIVGGEVPTELKKILEITPYVEDELALIIPKSHPFAK 184
Query: 181 LNSISLKEISNYPLITYDLSFSGRIKLD---REFSLQKLTPYIVLETINSDIIKTYVELR 237
L I +++ IT D + + R +D + + I +E + + IK V+
Sbjct: 185 LKKIQKEDLYRLNFITLDSNSTIRKVIDNILIQNGIDSKRFKIEMELNSIEAIKNAVQSG 244
Query: 238 MGIGIIASIA 247
+G ++ A
Sbjct: 245 LGAAFVSVSA 254
>gnl|CDD|182077 PRK09791, PRK09791, putative DNA-binding transcriptional regulator;
Provisional.
Length = 302
Score = 81.0 bits (200), Expect = 1e-17
Identities = 53/194 (27%), Positives = 96/194 (49%), Gaps = 11/194 (5%)
Query: 3 LHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKP 62
+HQ R E RQ ++ A++ L SQP ++K+I ELEE L+ +F R K + LT
Sbjct: 7 IHQIRAFVEVARQG-SIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVT-LTDA 64
Query: 63 GQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKV 122
G++ + +I++E+ ++ ++ G + I + AR +P +I F Q P+V
Sbjct: 65 GESFYQHASLILEELRAAQEDIRQRQGQLAGQINIGMGASIARSLMPAVISRFHQQHPQV 124
Query: 123 KLSLLQGNPKQITEMI---RNDQADIAIVTEILSPSDKLISIP-CYQWEYVIIVPLDHPL 178
K+ +++G Q+ MI R + D I T P D + + ++ + HP
Sbjct: 125 KVRIMEG---QLVSMINELRQGELDFTINTYYQGPYDHEFTFEKLLEKQFAVFCRPGHP- 180
Query: 179 LLLNSISLKEISNY 192
+ + SLK++ +Y
Sbjct: 181 -AIGARSLKQLLDY 193
>gnl|CDD|233862 TIGR02424, TF_pcaQ, pca operon transcription factor PcaQ. Members
of this family are LysR-family transcription factors
associated with operons for catabolism of
protocatechuate. Members occur only in Proteobacteria
[Energy metabolism, Other, Regulatory functions, DNA
interactions].
Length = 300
Score = 78.2 bits (193), Expect = 1e-16
Identities = 66/252 (26%), Positives = 120/252 (47%), Gaps = 19/252 (7%)
Query: 8 FVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAIL 67
FV E RQ ++ AA+AL+ +QP VSK + ELEE L +F R + IR LT+ G+ L
Sbjct: 11 FV-EVARQG-SVKRAAEALHITQPAVSKTLRELEEILGTPLFERDRRGIR-LTRYGELFL 67
Query: 68 R----SIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVK 123
R S+ + Q + L ++G + + I T A +P+++K F + P+++
Sbjct: 68 RHAGASLAALRQGVASLSQLG----EGEGPTVRIGALPTVAARLMPEVVKRFLARAPRLR 123
Query: 124 LSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISI---PCYQWEYVIIVPLDHPLLL 180
+ ++ G + + +R D+ + L + + + Y V +V HPLL
Sbjct: 124 VRIMTGPNAYLLDQLRVGALDLVVGR--LGAPETMQGLSFEHLYNEPVVFVVRAGHPLLA 181
Query: 181 LNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPY-IVLETINSDIIKTYVELRMG 239
S+ + +++YP++ + R +R F + P +ET++ + YV+
Sbjct: 182 APSLPVASLADYPVLLPPEGSAIRPLAERLFIACGIPPPPQRIETVSGSFGRRYVQESDA 241
Query: 240 IGIIAS--IAFD 249
I II+ +A D
Sbjct: 242 IWIISRGVVALD 253
>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 = 73.7 bits (182), Expect = 9e-16
Identities = 37/156 (23%), Positives = 70/156 (44%), Gaps = 4/156 (2%)
Query: 95 LTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSP 154
L I + LP++++ F ++P V+L L + + E +R + D+ V P
Sbjct: 2 LRIGFVGSALYGLLPRLLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGFVRPPPDP 61
Query: 155 SDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRI--KLDREFS 212
L S P + V+ +P DHPL S+SL ++++ P + + + ++
Sbjct: 62 PG-LASRPLLREPLVVALPADHPLAARESVSLADLADEPFVLFPREPGPGLYDQILALCR 120
Query: 213 LQKLTPYIVLETINSDIIKTYVELRMGIGII-ASIA 247
TP IV E + + V +G+ ++ AS+A
Sbjct: 121 RAGFTPRIVQEASDLQTLLALVAAGLGVALVPASVA 156
>gnl|CDD|236819 PRK11013, PRK11013, DNA-binding transcriptional regulator LysR;
Provisional.
Length = 309
Score = 73.9 bits (182), Expect = 5e-15
Identities = 60/236 (25%), Positives = 112/236 (47%), Gaps = 10/236 (4%)
Query: 12 AVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIE 71
AV +LTEAA+ L+TSQP VS+ + E+ + + +F +R+RG P LR E
Sbjct: 14 AVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLF----ERVRGRLHPTVQGLRLFE 69
Query: 72 IIMQEIEGLKKIGKEFSA---YDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLL- 127
+ + GL +I + + G L+IA ++ LP + + F ++P V L+++
Sbjct: 70 EVQRSYYGLDRIVSAAESLREFRQGQLSIACLPVFSQSLLPGLCQPFLARYPDVSLNIVP 129
Query: 128 QGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLK 187
Q +P + E + + D+ + TE L + V ++P HPL ++
Sbjct: 130 QESP-LLEEWLSAQRHDLGL-TETLHTPAGTERTELLTLDEVCVLPAGHPLAAKKVLTPD 187
Query: 188 EISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGII 243
+ + I+ + S R LD+ F+ + +V+ET ++ + V +G+ I+
Sbjct: 188 DFAGENFISLSRTDSYRQLLDQLFAEHGVKRRMVVETHSAASVCAMVRAGVGVSIV 243
>gnl|CDD|182137 PRK09906, PRK09906, DNA-binding transcriptional regulator HcaR;
Provisional.
Length = 296
Score = 73.7 bits (181), Expect = 5e-15
Identities = 65/246 (26%), Positives = 115/246 (46%), Gaps = 8/246 (3%)
Query: 1 MNLHQFR-FVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGL 59
M L R FV AV + N T+AA+ L+T+QP +S+ I +LE + + + +R KR L
Sbjct: 1 MELRHLRYFV--AVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRD-KRKVAL 57
Query: 60 TKPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQF 119
T G+ L+ I+++ E K ++ D LTI + LPK++ F ++
Sbjct: 58 TAAGEVFLQDARAILEQAEKAKLRARKIVQEDR-QLTIGFVPSAEVNLLPKVLPMFRLRH 116
Query: 120 PKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLL 179
P + L+ Q E +R + D+ + + SD++ + V+++P+DHPL
Sbjct: 117 PDTLIELVSLITTQQEEKLRRGELDVGFMRHPVY-SDEIDYLELLDEPLVVVLPVDHPLA 175
Query: 180 LLNSISLKEISNYPLITYDLSFSGRIK--LDREFSLQKLTPYIVLETINSDIIKTYVELR 237
I+ ++ I+ D ++SG + + F+ P IV N + V +
Sbjct: 176 HEKEITAAQLDGVNFISTDPAYSGSLAPIIKAWFAQHNSQPNIVQVATNILVTMNLVGMG 235
Query: 238 MGIGII 243
+G II
Sbjct: 236 LGCTII 241
>gnl|CDD|176104 cd08412, PBP2_PAO1_like, The C-terminal substrate-binding domain of
putative LysR-type transcriptional regulator PAO1-like,
a member of the type 2 periplasmic binding fold protein
superfamily. This family includes the C-terminal
substrate domain of a putative LysR-type transcriptional
regulator from the plant pathogen Pseudomonas aeruginosa
PAO1and its closely related homologs. The LysR-type
transcriptional regulators (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 N2 fixing bacteria, and
synthesis of virulence factors, to a 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 = 198
Score = 68.3 bits (168), Expect = 1e-13
Identities = 41/148 (27%), Positives = 77/148 (52%), Gaps = 2/148 (1%)
Query: 95 LTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSP 154
L I T A Y LP +++ F +P V++ +++GN +++ E +R+ + D+A+ ++ P
Sbjct: 2 LRIGCFSTLAPYYLPGLLRRFREAYPGVEVRVVEGNQEELEEGLRSGELDLALTYDLDLP 61
Query: 155 SDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQ 214
D + P + + +P DHPL + +SL +++ PLI DL S L F+
Sbjct: 62 ED-IAFEPLARLPPYVWLPADHPLAGKDEVSLADLAAEPLILLDLPHSREYFLSL-FAAA 119
Query: 215 KLTPYIVLETINSDIIKTYVELRMGIGI 242
LTP I T + + +++ V +G +
Sbjct: 120 GLTPRIAYRTSSFEAVRSLVANGLGYSL 147
>gnl|CDD|182183 PRK09986, PRK09986, DNA-binding transcriptional activator XapR;
Provisional.
Length = 294
Score = 69.0 bits (169), Expect = 2e-13
Identities = 58/239 (24%), Positives = 102/239 (42%), Gaps = 11/239 (4%)
Query: 12 AVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIE 71
AV + + AA L SQP +S I ELE++L +FIRH + + LT G+ ++
Sbjct: 17 AVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSV-VLTHAGKILMEESR 75
Query: 72 IIMQEIEG----LKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLL 127
++ E +++IG+ + G + I T L ++ F + P V+ L
Sbjct: 76 RLLDNAEQSLARVEQIGR----GEAGRIEIGIVGTALWGRLRPAMRHFLKENPNVEWLLR 131
Query: 128 QGNPKQITEMIRNDQADIAIVTE-ILSPSDKLISIPCYQWEYVIIVPLDHPLLLLNSISL 186
+ +P + + D I L P+ S ++ + + VP +HPL +S+ L
Sbjct: 132 ELSPSMQMAALERRELDAGIWRMADLEPNPGFTSRRLHESAFAVAVPEEHPLASRSSVPL 191
Query: 187 KEISNYPLITYDLSFSGRIK-LDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIA 244
K + N IT S K L R +P I+ + + V + +GI ++
Sbjct: 192 KALRNEYFITLPFVHSDWGKFLQRVCQQAGFSPQIIRQVNEPQTVLAMVSMGIGITLLP 250
>gnl|CDD|182768 PRK10837, PRK10837, putative DNA-binding transcriptional regulator;
Provisional.
Length = 290
Score = 67.0 bits (164), Expect = 9e-13
Identities = 68/230 (29%), Positives = 107/230 (46%), Gaps = 23/230 (10%)
Query: 20 TEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRI------RGLTKPGQAILRSIEII 73
T+A+ L SQ VS A+ +LE +L + +F R GKR+ R L A+L
Sbjct: 21 TQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQ---- 76
Query: 74 MQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQ 133
EIE L + D G L I + T Y LP +I + +P++ L L GN +
Sbjct: 77 AVEIEQLFR-------EDNGALRIYASSTIGNYILPAMIARYRRDYPQLPLELSVGNSQD 129
Query: 134 ITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYP 193
+ + + + DI ++ E S +LIS P + E V+ D P L ++L++++ P
Sbjct: 130 VINAVLDFRVDIGLI-EGPCHSPELISEPWLEDELVVFAAPDSP-LARGPVTLEQLAAAP 187
Query: 194 LITYDLSFSGRIKLDREFSLQKLTPY-IVLETINSDIIKTYVELRMGIGI 242
I + R +D L L + + +E NS+ IK V R G+GI
Sbjct: 188 WILRERGSGTREIVDY-LLLSHLPRFELAMELGNSEAIKHAV--RHGLGI 234
>gnl|CDD|176129 cd08438, PBP2_CidR, The C-terminal substrate binding domain of
LysR-like transcriptional regulator CidR, contains the
type 2 periplasmic binding fold. This CD includes the
substrate binding domain of CidR which positively
up-regulates the expression of cidABC operon in the
presence of acetic acid produced by the metabolism of
excess glucose. The CidR affects the control of murein
hydrolase activity by enhancing cidABC expression in the
presence of acetic acid. Thus, up-regulation of cidABC
expression results in increased murein hydrolase
activity. This substrate binding domain has 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 = 64.1 bits (157), Expect = 3e-12
Identities = 28/137 (20%), Positives = 62/137 (45%), Gaps = 3/137 (2%)
Query: 108 LPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSP-SDKLISIPCYQW 166
++ F ++P ++L L++ K++ + + N + D+ I L ++ S P
Sbjct: 15 FAPLLAAFRQRYPNIELELVEYGGKKVEQAVLNGELDVGITV--LPVDEEEFDSQPLCNE 72
Query: 167 EYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETIN 226
V ++P HPL ++SL ++++ P I ++ F+ ++ TP I +
Sbjct: 73 PLVAVLPRGHPLAGRKTVSLADLADEPFILFNEDFALHDRIIDACQQAGFTPNIAARSSQ 132
Query: 227 SDIIKTYVELRMGIGII 243
D I V +G+ ++
Sbjct: 133 WDFIAELVAAGLGVALL 149
>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 = 63.9 bits (156), Expect = 4e-12
Identities = 36/145 (24%), Positives = 61/145 (42%), Gaps = 1/145 (0%)
Query: 96 TIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPS 155
+AT A LP +I F ++P V ++ + + E + + +ADI +
Sbjct: 3 RVATGEGLAAELLPSLIARFRQRYPGVFFTVDVASTADVLEAVLSGEADIGLAFSPPPEP 62
Query: 156 DKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQK 215
+ +VP HPL S++L +++ YPL SFS R LD F+
Sbjct: 63 G-IRVHSRQPAPIGAVVPPGHPLARQPSVTLAQLAGYPLALPPPSFSLRQILDAAFARAG 121
Query: 216 LTPYIVLETINSDIIKTYVELRMGI 240
+ VL + + + +K V GI
Sbjct: 122 VQLEPVLISNSIETLKQLVAAGGGI 146
>gnl|CDD|215735 pfam00126, HTH_1, Bacterial regulatory helix-turn-helix protein,
lysR family.
Length = 60
Score = 58.9 bits (144), Expect = 9e-12
Identities = 24/62 (38%), Positives = 33/62 (53%), Gaps = 2/62 (3%)
Query: 3 LHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKP 62
L Q R + + T AA+ L SQP VS+ I LEEEL + +F R + +R LT
Sbjct: 1 LRQLRVFVAVAEEG-SFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGLR-LTPA 58
Query: 63 GQ 64
G+
Sbjct: 59 GE 60
>gnl|CDD|176145 cd08456, PBP2_LysR, The C-terminal substrate binding domain of
LysR, transcriptional regulator for lysine biosynthesis,
contains the type 2 periplasmic binding fold. LysR, the
transcriptional activator of lysA encoding
diaminopimelate decarboxylase, catalyses the
decarboxylation of diaminopimelate to produce lysine.
The 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 = 196
Score = 60.5 bits (147), Expect = 6e-11
Identities = 34/166 (20%), Positives = 70/166 (42%), Gaps = 9/166 (5%)
Query: 95 LTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSP 154
L IA ++ LP+ IK F + P V +S+ + + + + Q D+ +V+ + P
Sbjct: 2 LRIAVLPALSQSFLPRAIKAFLQRHPDVTISIHTRDSPTVEQWLSAQQCDLGLVSTLHEP 61
Query: 155 ----SDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDRE 210
++L+ I V ++P H L + ++ ++ P I+ + R ++D
Sbjct: 62 PGIERERLLRIDG-----VCVLPPGHRLAVKKVLTPSDLEGEPFISLARTDGTRQRVDAL 116
Query: 211 FSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSNRDKNL 256
F + IV+ET + I V +G+ ++ + L
Sbjct: 117 FEQAGVKRRIVVETSYAATICALVAAGVGVSVVNPLTALDYAAAGL 162
>gnl|CDD|182999 PRK11151, PRK11151, DNA-binding transcriptional regulator OxyR;
Provisional.
Length = 305
Score = 61.6 bits (150), Expect = 6e-11
Identities = 45/183 (24%), Positives = 88/183 (48%), Gaps = 14/183 (7%)
Query: 22 AAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRI----RGLTKPGQA--ILRSIEIIMQ 75
AA + + SQP +S I +LE+EL + + R +++ GL QA +LR +++ ++
Sbjct: 21 AADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVKV-LK 79
Query: 76 EIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQIT 135
E+ + G+ +G L I T Y LP II FPK+++ L + Q+
Sbjct: 80 EMASQQ--GETM----SGPLHIGLIPTVGPYLLPHIIPMLHQTFPKLEMYLHEAQTHQLL 133
Query: 136 EMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLI 195
+ + + D AI+ + S+ I +P + ++ V DHP + + + +++ L+
Sbjct: 134 AQLDSGKLDCAILALV-KESEAFIEVPLFDEPMLLAVYEDHPWANRDRVPMSDLAGEKLL 192
Query: 196 TYD 198
+
Sbjct: 193 MLE 195
>gnl|CDD|176124 cd08433, PBP2_Nac, The C-teminal substrate binding domain of
LysR-like nitrogen assimilation control (NAC) protein,
contains the type 2 periplasmic binding fold. The NAC
is a LysR-type transcription regulator that activates
expression of operons such as hut (histidine
utilization) and ure (urea utilization), allowing use of
non-preferred (poor) nitrogen sources, and represses
expression of operons, such as glutamate dehydrogenase
(gdh), allowing assimilation of the preferred nitrogen
source. The expression of the nac gene is fully
dependent on the nitrogen regulatory system (NTR) and
the sigma54-containing RNA polymerase (sigma54-RNAP). In
response to nitrogen starvation, NTR system activates
the expression of nac, and NAC activates the expression
of hut, ure, and put (proline utilization). NAC is not
involved in the transcription of Sigma70-RNAP operons
such as glnA, which directly respond by the NTR system,
but activates the transcription of sigma70-RNAP
dependent operons such as hut. Hence, NAC allows the
coupling of sigma70-RNAP dependent operons to the
sigma54-RNAP dependent NTR system. This
substrate-binding domain has 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 = 198
Score = 58.0 bits (141), Expect = 4e-10
Identities = 30/147 (20%), Positives = 65/147 (44%), Gaps = 3/147 (2%)
Query: 95 LTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSP 154
+++ + A +++ ++P ++L +++G + E + N + D+A++ P
Sbjct: 2 VSVGLPPSAASVLAVPLLRAVRRRYPGIRLRIVEGLSGHLLEWLLNGRLDLALLYG-PPP 60
Query: 155 SDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQ 214
L + P + + ++ P D PL + L E++ PLI R +D +
Sbjct: 61 IPGLSTEPLLEEDLFLVGPADAPLPRGAPVPLAELARLPLILPSRGHGLRRLVDEAAARA 120
Query: 215 KLTPYIVLETINSDIIKTYVELRMGIG 241
LT +V+E + +K V G+G
Sbjct: 121 GLTLNVVVEIDSVATLKALV--AAGLG 145
>gnl|CDD|176146 cd08457, PBP2_OccR, The C-terminal substrate-domain of LysR-type
transcriptional regulator, OccR, involved in the
catabolism of octopine, contains the type 2 periplasmic
binding fold. This CD includes the C-terminal
substrate-domain of LysR-type transcriptional regulator
OccR, which is involved in the catabolism of octopine.
Opines are low molecular weight compounds found in plant
crown gall tumors 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. In Agrobacterium tumefaciens,
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, an
arginine derivative. The occ operon also encodes the
TraR protein, which is a quorum-sensing transcriptional
regulator of the Ti plasmid tra regulon. 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 = 57.5 bits (139), Expect = 7e-10
Identities = 37/153 (24%), Positives = 69/153 (45%), Gaps = 9/153 (5%)
Query: 95 LTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSP 154
L IA A LP+ + F P + LSL+ + Q+ E + + +AD+ I L
Sbjct: 2 LRIAAMPALANGFLPRFLAAFLRLRPNLHLSLMGLSSSQVLEAVASGRADLGIADGPLEE 61
Query: 155 SDKLI----SIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDRE 210
+ S+P V+ VP+ HPL L+ +S ++++ +IT + + R++++
Sbjct: 62 RQGFLIETRSLPA-----VVAVPMGHPLAQLDVVSPQDLAGERIITLENGYLFRMRVEVA 116
Query: 211 FSLQKLTPYIVLETINSDIIKTYVELRMGIGII 243
+ ++E S + V +GI II
Sbjct: 117 LGKIGVKRRPIIEVNLSHTALSLVREGLGIAII 149
>gnl|CDD|176126 cd08435, PBP2_GbpR, The C-terminal substrate binding domain of
galactose-binding protein regulator contains the type 2
periplasmic binding fold. Galactose-binding protein
regulator (GbpR), a member of the LysR family of
bacterial transcriptional regulators, regulates the
expression of chromosomal virulence gene chvE. The
chvE gene is involved in the uptake of specific sugars,
in chemotaxis to these sugars, and in the VirA-VirG
two-component signal transduction system. In the
presence of an inducing sugar such as L-arabinose,
D-fucose, or D-galactose, GbpR activates chvE
expression, while in the absence of an inducing sugar,
GbpR represses expression. 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 = 56.5 bits (137), Expect = 1e-09
Identities = 30/134 (22%), Positives = 60/134 (44%), Gaps = 4/134 (2%)
Query: 94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAI--VTEI 151
+ + A LP I + P++ + +++G ++ E +R + D+AI + +
Sbjct: 1 TVRVGAVPAAAPVLLPPAIARLLARHPRLTVRVVEGTSDELLEGLRAGELDLAIGRLADD 60
Query: 152 LSPSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREF 211
P D L S V++ HPL ++L ++++YP + R +L++ F
Sbjct: 61 EQPPD-LASEELADEPLVVVARPGHPLARRARLTLADLADYPWVLPPPGTPLRQRLEQLF 119
Query: 212 SLQKL-TPYIVLET 224
+ L P V+ET
Sbjct: 120 AAAGLPLPRNVVET 133
>gnl|CDD|176103 cd08411, PBP2_OxyR, The C-terminal substrate-binding domain of the
LysR-type transcriptional regulator OxyR, a member of
the type 2 periplasmic binding fold protein superfamily.
OxyR senses hydrogen peroxide and is activated through
the formation of an intramolecular disulfide bond. The
OxyR activation induces the transcription of genes
necessary for the bacterial defense against oxidative
stress. The OxyR of LysR-type transcriptional regulator
family 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 C-terminal domain also
contains the redox-active cysteines that mediate the
redox-dependent conformational switch. Thus, the
interaction between the OxyR-tetramer and DNA is notably
different between the oxidized and reduced forms. 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 = 200
Score = 56.0 bits (136), Expect = 2e-09
Identities = 25/104 (24%), Positives = 53/104 (50%), Gaps = 1/104 (0%)
Query: 93 GNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEIL 152
G L + T A Y LP+++ +PK++L L + +++ E +R+ + D A++ +
Sbjct: 1 GPLRLGVIPTIAPYLLPRLLPALRQAYPKLRLYLREDQTERLLEKLRSGELDAALLA-LP 59
Query: 153 SPSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLIT 196
L P + +++ VP DHPL S++ ++++ L+
Sbjct: 60 VDEPGLEEEPLFDEPFLLAVPKDHPLAKRKSVTPEDLAGERLLL 103
>gnl|CDD|182231 PRK10086, PRK10086, DNA-binding transcriptional regulator DsdC;
Provisional.
Length = 311
Score = 56.2 bits (136), Expect = 4e-09
Identities = 44/133 (33%), Positives = 71/133 (53%), Gaps = 15/133 (11%)
Query: 2 NLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTK 61
LH F A Q+F L AA L + VS I +LEEEL I +F+R +++ LT+
Sbjct: 18 KLHTFEVA--ARHQSFAL--AADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVE-LTE 72
Query: 62 PGQ----AILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTI 117
G+ A+ S++ + QEI +K +E S G LT+ + + A+ L + +FT
Sbjct: 73 EGKRVFWALKSSLDTLNQEILDIK--NQELS----GTLTVYSRPSIAQCWLVPRLADFTR 126
Query: 118 QFPKVKLSLLQGN 130
++P + L++L GN
Sbjct: 127 RYPSISLTILTGN 139
>gnl|CDD|176127 cd08436, PBP2_LTTR_like_3, 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 = 194
Score = 54.9 bits (133), Expect = 4e-09
Identities = 38/166 (22%), Positives = 73/166 (43%), Gaps = 4/166 (2%)
Query: 95 LTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSP 154
L I T + A LP+++ F + P V + L Q + +R + D+A V
Sbjct: 2 LAIGTITSLAAVDLPELLARFHRRHPGVDIRLRQAGSDDLLAAVREGRLDLAFVGLPERR 61
Query: 155 SDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQ 214
L S + V +V DHPL ++L ++++ P + + R ++DR F+
Sbjct: 62 PPGLASRELAREPLVAVVAPDHPLAGRRRVALADLADEPFVDFPPGTGARRQVDRAFAAA 121
Query: 215 KLTPYIVLETINSDIIKTYVELRMGIGII-ASIAFDSNRDKNLRSI 259
+ + E + D++ V +G+ ++ AS+A R L ++
Sbjct: 122 GVRRRVAFEVSDVDLLLDLVARGLGVALLPASVA---ARLPGLAAL 164
>gnl|CDD|236961 PRK11716, PRK11716, DNA-binding transcriptional regulator IlvY;
Provisional.
Length = 269
Score = 55.6 bits (135), Expect = 5e-09
Identities = 55/222 (24%), Positives = 94/222 (42%), Gaps = 25/222 (11%)
Query: 34 SKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTG 93
S+ I LEEEL +F+R + + LT+ G+ + + + + + L+ + +G
Sbjct: 9 SRQIQRLEEELGQPLFVRDNRSVT-LTEAGEELRPFAQQTLLQWQQLRHTLDQQGPSLSG 67
Query: 94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAI--VTEI 151
L++ + T A LP I+ F + P V++ L G+ E +++ +AD+AI E
Sbjct: 68 ELSLFCSVTAAYSHLPPILDRFRAEHPLVEIKLTTGDAADAVEKVQSGEADLAIAAKPET 127
Query: 152 LSPSD----KLISIPCYQWEYVIIVPLDHP----LLLLNSISLKEISNYPLITYDLSFSG 203
L P+ + IP V+I P L I P I L G
Sbjct: 128 L-PASVAFSPIDEIP-----LVLIAPALPCPVRQQLSQEKPDWSRI---PFI---LPEHG 175
Query: 204 --RIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGII 243
R ++D F K+ P I + I + V L G+G++
Sbjct: 176 PARRRIDLWFRRHKIKPNIYATVSGHEAIVSMVALGCGVGLL 217
>gnl|CDD|176142 cd08451, PBP2_BudR, The C-terminal substrate binding domain of
LysR-type transcrptional regulator BudR, which is
responsible for activation of the expression of the
butanediol operon genes; contains the type 2 periplasmic
binding fold. This CD represents the substrate binding
domain of BudR regulator, which is responsible for
induction of the butanediol formation pathway under
fermentative growth conditions. Three enzymes are
involved in the production of 1 mol of 2,3 butanediol
from the condensation of 2 mol of pyruvate with
acetolactate and acetoin as intermediates: acetolactate
synthetase, acetolactate decarboxylase, and acetoin
reductase. In Klebsiella terrigena, BudR regulates the
expression of the budABC operon genes, encoding these
three enzymes of the butanediol pathway. In many
bacterial species, the use of this pathway can prevent
intracellular acidification by diverting metabolism from
acid production to the formation of neutral compounds
(acetoin and butanediol). This substrate-binding domain
has 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 = 54.9 bits (133), Expect = 5e-09
Identities = 25/90 (27%), Positives = 47/90 (52%)
Query: 108 LPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWE 167
+P +I+ F +P V+L+L + N ++ E +R + D A V ++ SD L+ +
Sbjct: 16 VPGLIRRFREAYPDVELTLEEANTAELLEALREGRLDAAFVRPPVARSDGLVLELLLEEP 75
Query: 168 YVIIVPLDHPLLLLNSISLKEISNYPLITY 197
++ +P HPL SI L +++ P I +
Sbjct: 76 MLVALPAGHPLARERSIPLAALADEPFILF 105
>gnl|CDD|185319 PRK15421, PRK15421, DNA-binding transcriptional regulator MetR;
Provisional.
Length = 317
Score = 55.4 bits (133), Expect = 9e-09
Identities = 54/232 (23%), Positives = 110/232 (47%), Gaps = 10/232 (4%)
Query: 11 EAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSI 70
+A+R +L AA L+ +Q +S +LE+ L +F+R + +R T G+ +L+
Sbjct: 11 QALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLR-FTPQGEILLQLA 69
Query: 71 EIIMQEIEGLKKIGKEFSAYDTGNLTIATT-HTQARYALPKIIKEFTIQFPKVKLSLLQG 129
++ +I + E L IA H+ ++ P ++ F +P+V++ G
Sbjct: 70 NQVLPQISQALQACNE---PQQTRLRIAIECHSCIQWLTPA-LENFHKNWPQVEMDFKSG 125
Query: 130 NPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEI 189
++ + D+ + ++IL P L P + +E +++ DHPL I+ +++
Sbjct: 126 VTFDPQPALQQGELDLVMTSDIL-PRSGLHYSPMFDYEVRLVLAPDHPLAAKTRITPEDL 184
Query: 190 SNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETI-NSDIIKTYVELRMGI 240
++ L+ Y + R+ + R F LQ L+++ N+ ++ V RMGI
Sbjct: 185 ASETLLIYPVQ-RSRLDVWRHF-LQPAGVSPSLKSVDNTLLLIQMVAARMGI 234
>gnl|CDD|188320 TIGR03418, chol_sulf_TF, putative choline sulfate-utilization
transcription factor. Members of this protein family
are transcription factors of the LysR family. Their
genes typically are divergently transcribed from
choline-sulfatase genes. That enzyme makes choline, a
precursor to the osmoprotectant glycine-betaine,
available by hydrolysis of choline sulfate.
Length = 291
Score = 54.0 bits (130), Expect = 2e-08
Identities = 42/143 (29%), Positives = 64/143 (44%), Gaps = 9/143 (6%)
Query: 7 RFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAI 66
R A R + T AA+ L ++QP VS+ I LEEEL + +F R R LT+ GQ +
Sbjct: 7 RVFESAARLA-SFTAAARELGSTQPAVSQQIKRLEEELGVPLFER-KHRGVELTEDGQRL 64
Query: 67 LRSIEIIMQEIEGLKKIGKEFSAYDT-GNLTIATTHTQARYALPKIIKEFTIQFPKVKLS 125
E + + ++ + A LT+AT A Y L + F P V +S
Sbjct: 65 F---EAVRRGLDTIDAATAALRARRRRETLTLATDFAFATYWLMPRLHRFKAAMPDVDVS 121
Query: 126 LLQGNPKQITEMIRNDQADIAIV 148
++ + R D D+AI+
Sbjct: 122 IVTSQDSH--DGQR-DDIDVAIL 141
>gnl|CDD|176113 cd08421, PBP2_LTTR_like_1, 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 = 198
Score = 52.1 bits (126), Expect = 4e-08
Identities = 21/88 (23%), Positives = 40/88 (45%), Gaps = 1/88 (1%)
Query: 108 LPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWE 167
LP+ + F P V++ L + I + +AD+ IV + + L + P
Sbjct: 15 LPEDLASFLAAHPDVRIDLEERLSADIVRAVAEGRADLGIVAGNVDAAG-LETRPYRTDR 73
Query: 168 YVIIVPLDHPLLLLNSISLKEISNYPLI 195
V++VP DHPL S++ + ++ +
Sbjct: 74 LVVVVPRDHPLAGRASVAFADTLDHDFV 101
>gnl|CDD|176118 cd08427, PBP2_LTTR_like_2, 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 = 195
Score = 50.7 bits (122), Expect = 1e-07
Identities = 43/185 (23%), Positives = 74/185 (40%), Gaps = 18/185 (9%)
Query: 95 LTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSP 154
L + T LP+ + + P +++ ++ G ++ + + D AIV E P
Sbjct: 2 LRLGAIATVLTGLLPRALARLRRRHPDLEVHIVPGLSAELLARVDAGELDAAIVVEPPFP 61
Query: 155 SDK-LISIPCYQWEYVIIVPLDH----PLLLLNSISLKEISNYPLITYDLS-FSGRIKLD 208
K L+ P + V+I P + P LL + P I YD S + GR+ +D
Sbjct: 62 LPKDLVWTPLVREPLVLIAPAELAGDDPRELL--------ATQPFIRYDRSAWGGRL-VD 112
Query: 209 REFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSNRDKNLRSISASHLFGTT 268
R Q + V+E + + I V +G+ I+ IA +R + L
Sbjct: 113 RFLRRQGIRVREVMELDSLEAIAAMVAQGLGVAIVPDIAVPLPAGPRVRVLP---LGDPA 169
Query: 269 ISRVI 273
SR +
Sbjct: 170 FSRRV 174
>gnl|CDD|131091 TIGR02036, dsdC, D-serine deaminase transcriptional activator.
This family, part of the LysR family of transcriptional
regulators, activates transcription of the gene for
D-serine deaminase, dsdA. Trusted members of this family
so far are found adjacent to dsdA and only in
Gammaproteobacteria, including E. coli, Vibrio cholerae,
and Colwellia psychrerythraea [Regulatory functions, DNA
interactions].
Length = 302
Score = 51.1 bits (122), Expect = 2e-07
Identities = 43/132 (32%), Positives = 72/132 (54%), Gaps = 15/132 (11%)
Query: 3 LHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKP 62
+H F A Q+F+L AA+ L + +S I +LEEEL I +F+R +++ LT
Sbjct: 13 MHTFEVA--ARHQSFSL--AAEELSLTPSAISHRINQLEEELGIQLFVRSHRKVE-LTHE 67
Query: 63 GQ----AILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQ 118
G+ A+ S++ + QEI +K +E S G LT+ + + A+ L I +FT +
Sbjct: 68 GKRIYWALKSSLDTLNQEILDIKN--QELS----GTLTLYSRPSFAQCWLVPRIGDFTRR 121
Query: 119 FPKVKLSLLQGN 130
+P + L++L GN
Sbjct: 122 YPSISLTVLTGN 133
>gnl|CDD|176109 cd08417, PBP2_Nitroaromatics_like, The C-terminal substrate binding
domain of LysR-type transcriptional regulators that
involved in the catabolism of nitroaromatic/naphthalene
compounds and that of related regulators; contains the
type 2 periplasmic binding fold. This CD includes the
C-terminal substrate binding domain of LysR-type
transcriptional regulators involved in the catabolism of
dinitrotoluene and similar compounds, such as DntR,
NahR, and LinR. The transcription of the genes encoding
enzymes involved in such degradation is regulated and
expression of these enzymes is enhanced by inducers,
which are either an intermediate in the metabolic
pathway or compounds to be degraded. Also included are
related LysR-type regulators clustered together in
phylogenetic trees, including NodD, ToxR, LeuO, SyrM,
TdcA, and PnbR. 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 = 49.5 bits (119), Expect = 3e-07
Identities = 28/131 (21%), Positives = 53/131 (40%), Gaps = 6/131 (4%)
Query: 96 TIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPS 155
IA + LP ++ + P V+L + + + E + + + D+AI P
Sbjct: 3 RIAASDYLEALLLPPLLARLRQEAPGVRLRFVPLDRDDLEEALESGEIDLAIGVFPELPP 62
Query: 156 DKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIK--LDREFSL 213
L S P ++ +V + DHP L ++L++ P + S GR +D +
Sbjct: 63 G-LRSQPLFEDRFVCVARKDHP-LAGGPLTLEDYLAAPHVLV--SPRGRGHGLVDDALAE 118
Query: 214 QKLTPYIVLET 224
L+ + L
Sbjct: 119 LGLSRRVALTV 129
>gnl|CDD|182391 PRK10341, PRK10341, DNA-binding transcriptional activator TdcA;
Provisional.
Length = 312
Score = 50.6 bits (121), Expect = 3e-07
Identities = 41/154 (26%), Positives = 74/154 (48%), Gaps = 8/154 (5%)
Query: 22 AAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL- 80
AAK L +QP VSK I ++E+ +++ +R + LT GQ +L E I +E++ +
Sbjct: 27 AAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVT-LTPAGQVLLSRSESITREMKNMV 85
Query: 81 KKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRN 140
+I S +++ + +I +F FPK ++S+ + IR+
Sbjct: 86 NEINGMSSE-AVVDVSFGFPSLIGFTFMSDMINKFKEVFPKAQVSMYEAQLSSFLPAIRD 144
Query: 141 DQADIAIVTEILSPSDKLISI---PCYQWEYVII 171
+ D AI T LS KL + P ++ E+V++
Sbjct: 145 GRLDFAIGT--LSNEMKLQDLHVEPLFESEFVLV 176
>gnl|CDD|183045 PRK11233, PRK11233, nitrogen assimilation transcriptional
regulator; Provisional.
Length = 305
Score = 49.3 bits (118), Expect = 8e-07
Identities = 61/237 (25%), Positives = 111/237 (46%), Gaps = 28/237 (11%)
Query: 19 LTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPG-------QAILRSIE 71
LT+AA+ L+ +QP +S+ + LE EL+ + IR KR T+ G +AILR E
Sbjct: 18 LTQAAEVLHIAQPALSQQVATLEGELNQQLLIR-TKRGVTPTEAGKILYTHARAILRQCE 76
Query: 72 IIMQEIEGLKKIGKEFSAYDTGNLTI--ATTHTQARYALPKIIKEFTIQFPKVKLSLLQG 129
Q + +G+ S G ++I A + +P +++ +FP + L L +
Sbjct: 77 ---QAQLAVHNVGQALS----GQVSIGLAPGTAASSLTMP-LLQAVRAEFPGIVLYLHEN 128
Query: 130 NPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEI 189
+ + E + N Q D+A++ E SP L S P + + ++ D P S+ L +
Sbjct: 129 SGATLNEKLMNGQLDMAVIYE-HSPVAGLSSQPLLKEDLFLVGTQDCP---GQSVDLAAV 184
Query: 190 SNYPLI---TYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGII 243
+ L Y R+++D FSL++LT ++ E + + + MG+ ++
Sbjct: 185 AQMNLFLPRDYSAV---RLRVDEAFSLRRLTAKVIGEIESIATLTAAIASGMGVTVL 238
>gnl|CDD|182990 PRK11139, PRK11139, DNA-binding transcriptional activator GcvA;
Provisional.
Length = 297
Score = 49.1 bits (118), Expect = 9e-07
Identities = 34/142 (23%), Positives = 66/142 (46%), Gaps = 16/142 (11%)
Query: 11 EAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSI 70
EA ++ + T AA+ L+ +Q VS I LE+ L + +F R + + LT+ GQ I
Sbjct: 15 EAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLL-LTEEGQRYFLDI 73
Query: 71 EIIMQEI----EGLKKIGKEFSAYDTGNLTIATTHT-QARYALPKIIKEFTIQFPKVKLS 125
I ++ L+ G LT++ + ++ +P++ F P + +
Sbjct: 74 REIFDQLAEATRKLRARS------AKGALTVSLLPSFAIQWLVPRLSS-FNEAHPDIDVR 126
Query: 126 LLQGNPKQITEMIRNDQADIAI 147
L + ++ + +R+D D+AI
Sbjct: 127 LKAVD--RLEDFLRDD-VDVAI 145
>gnl|CDD|176110 cd08418, PBP2_TdcA, The C-terminal substrate binding domain of
LysR-type transcriptional regulator TdcA, which is
involved in the degradation of L-serine and L-threonine,
contains the type 2 periplasmic binding fold. TdcA, a
member of the LysR family, activates the expression of
the anaerobically-regulated tdcABCDEFG operon which is
involved in the degradation of L-serine and L-threonine
to acetate and propionate, respectively. The tdc operon
is comprised of one regulatory gene tdcA and six
structural genes, tdcB to tdcG. The expression of the
tdc operon is affected by several transcription factors
including the cAMP receptor protein (CRP), integration
host factor (IHF), histone-like protein (HU), and the
operon specific regulators TdcA and TcdR. TcdR is
divergently transcribed from the operon and encodes a
small protein that is required for efficient expression
of the Escherichia coli tdc operon. 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 = 201
Score = 47.7 bits (114), Expect = 1e-06
Identities = 29/98 (29%), Positives = 51/98 (52%), Gaps = 3/98 (3%)
Query: 96 TIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPS 155
+I + A +P +I F QFP V++S+ +G + +R+ + D AI T
Sbjct: 3 SIGVSSLIAHTLMPAVINRFKEQFPDVQISIYEGQLSSLLPELRDGRLDFAIGTLPDEMY 62
Query: 156 DK-LISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNY 192
K LIS P ++ ++V++ DHP L + SL+E+ +
Sbjct: 63 LKELISEPLFESDFVVVARKDHP--LQGARSLEELLDA 98
>gnl|CDD|176128 cd08437, PBP2_MleR, The substrate binding domain of LysR-type
transcriptional regulator MleR which required for
malolactic fermentation, contains type 2 periplasmic
binidning fold. MleR, a transcription activator of
malolactic fermentation system, is found in
gram-positive bacteria and belongs to the lysR family of
bacterial transcriptional regulators. The mleR gene is
required for the expression and induction of malolactic
fermentation. This substrate binding domain has
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 = 198
Score = 47.7 bits (114), Expect = 1e-06
Identities = 41/175 (23%), Positives = 67/175 (38%), Gaps = 7/175 (4%)
Query: 106 YALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSP--SDKLISIPC 163
Y PK+ K+ +++ +G ++ E + DIA + L+P + L S
Sbjct: 13 YYFPKLAKDLIKTGLMIQIDTYEGGSAELLEQLLQGDLDIA-LLGSLTPLENSALHSKII 71
Query: 164 YQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLE 223
++IIV DHPL ++ ++ I + F D P IV
Sbjct: 72 KTQHFMIIVSKDHPLAKAKKVNFADLKKENFILLNEHFVHPKAFDSLCQQANFQPNIVYR 131
Query: 224 TINSDIIKTYVELRMGIGIIASIAFDSNRDKNLRSISAS--HLFGTTISRVIIKQ 276
T + I+K+ V +GIG + IA D +L +I IS K
Sbjct: 132 TNDIHILKSMVRENVGIGFLTDIAV--KPDDHLVAIPLLDNEQPTFYISLAHRKD 184
>gnl|CDD|176133 cd08442, PBP2_YofA_SoxR_like, The C-terminal substrate binding
domain of LysR-type transcriptional regulators, YofA and
SoxR, contains the type 2 periplasmic binding fold.
YofA is a LysR-like transcriptional regulator of cell
growth in Bacillus subtillis. YofA controls cell
viability and the formation of constrictions during cell
division. YofaA positively regulates expression of the
cell division gene ftsW, and thus is essential for cell
viability during stationary-phase growth of Bacillus
substilis. YofA shows significant homology to SoxR from
Arthrobacter sp. TE1826. SoxR is a negative regulator
for the sarcosine oxidase gene soxA. Sarcosine oxidase
catalyzes the oxidative demethylation of sarcosine,
which is involved in the metabolism of creatine and
choline. 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 = 193
Score = 47.2 bits (113), Expect = 2e-06
Identities = 34/149 (22%), Positives = 66/149 (44%), Gaps = 5/149 (3%)
Query: 95 LTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSP 154
L + + T A LP ++ + ++PKV LSL G + + + + D A V +
Sbjct: 2 LRLGSMETTAAVRLPPLLAAYHARYPKVDLSLSTGTTGALIQAVLEGRLDGAFVAGPVEH 61
Query: 155 SDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQ 214
L P +Q E V++ P HP ++++ L+ + S R +L+ + +
Sbjct: 62 PR-LEQEPVFQEELVLVSPKGHP----PVSRAEDLAGSTLLAFRAGCSYRRRLEDWLAEE 116
Query: 215 KLTPYIVLETINSDIIKTYVELRMGIGII 243
++P ++E + I V MGI ++
Sbjct: 117 GVSPGKIMEFGSYHAILGCVAAGMGIALL 145
>gnl|CDD|176116 cd08425, PBP2_CynR, The C-terminal substrate-binding domain of the
LysR-type transcriptional regulator CynR, contains the
type 2 periplasmic binding fold. CynR is a LysR-like
transcriptional regulator of the cyn operon, which
encodes genes that allow cyanate to be used as a sole
source of nitrogen. The operon includes three genes in
the following order: cynT (cyanate permease), cynS
(cyanase), and cynX (a protein of unknown function).
CynR negatively regulates its own expression
independently of cyanate. CynR binds to DNA and induces
bending of DNA in the presence or absence of cyanate,
but the amount of bending is decreased by cyanate. The
CynR of LysR-type transcriptional regulator family 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
(PBP2). The PBP2 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 = 45.0 bits (107), Expect = 1e-05
Identities = 39/146 (26%), Positives = 71/146 (48%), Gaps = 7/146 (4%)
Query: 93 GNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIV-TEI 151
G+L +A T T Y + +I F ++P + LSL + ++I + +D+ D+ I +
Sbjct: 1 GSLRLAMTPTFTAYLIGPLIDRFHARYPGIALSLREMPQERIEAALADDRLDLGIAFAPV 60
Query: 152 LSPSDKLISIPCYQWEYVIIVPLDHPLLLL-NSISLKEISNYPLITYDLSFSGRIKLDRE 210
SP + + P + ++V HPL +++L +++ PL F+ R +DR
Sbjct: 61 RSP--DIDAQPLFDERLALVVGATHPLAQRRTALTLDDLAAEPLALLSPDFATRQHIDRY 118
Query: 211 FSLQKLTPYIVLETINSDIIKTYVEL 236
F Q + P I +E NS I +E+
Sbjct: 119 FQKQGIKPRIAIEA-NS--ISAVLEV 141
>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 = 45.3 bits (108), Expect = 1e-05
Identities = 19/88 (21%), Positives = 37/88 (42%), Gaps = 4/88 (4%)
Query: 95 LTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTE---- 150
L + T A LP + + P +++ L + P + + +R + D+A+V +
Sbjct: 2 LRVGAFPTAAAALLPPALAALRARHPGLEVRLREAEPPESLDALRAGELDLAVVFDYPVT 61
Query: 151 ILSPSDKLISIPCYQWEYVIIVPLDHPL 178
L +P +++P DHPL
Sbjct: 62 PPPDDPGLTRVPLLDDPLDLVLPADHPL 89
>gnl|CDD|176139 cd08448, PBP2_LTTR_aromatics_like_2, The C-terminal substrate
binding domain of an uncharacterized LysR-type
transcriptional regulator similar to regulators involved
in the catabolism of aromatic compounds, contains type 2
periplasmic binding fold. This CD represents the
substrate binding domain of an uncharacterized LysR-type
regulator similar to CbnR which is involved in the
regulation of chlorocatechol breakdown. The
transcription of the genes encoding enzymes involved in
such degradation is regulated and expression of these
enzymes is enhanced by inducers, which are either an
intermediate in the metabolic pathway or compounds to be
degraded. 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 = 45.0 bits (107), Expect = 1e-05
Identities = 30/145 (20%), Positives = 63/145 (43%), Gaps = 17/145 (11%)
Query: 108 LPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWE 167
LP+I++ F ++P ++++L + + + E + + D+ V P+ L + ++
Sbjct: 15 LPRILRAFRAEYPGIEVALHEMSSAEQIEALLRGELDLGFVHSRRLPAG-LSARLLHREP 73
Query: 168 YVIIVPLDHPLLLLNSISLKEISNYPLIT---------YDLSFSGRIKLDREFSLQKLTP 218
+V +P HPL I L+E++ P + YD + + +D F P
Sbjct: 74 FVCCLPAGHPLAARRRIDLRELAGEPFVLFSREVSPDYYDQIIA--LCMDAGFH-----P 126
Query: 219 YIVLETINSDIIKTYVELRMGIGII 243
I E + + V MG+ ++
Sbjct: 127 KIRHEVRHWLTVVALVAAGMGVALV 151
>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 = 45.0 bits (107), Expect = 1e-05
Identities = 34/157 (21%), Positives = 64/157 (40%), Gaps = 5/157 (3%)
Query: 95 LTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNP-KQITEMIRNDQADIAIVTEILS 153
L I + L ++ F Q+P V + + +P Q ++ + D+ V +
Sbjct: 2 LNIGMVGSVLWGGLGPALRRFKRQYPNVTVRFHELSPEAQKAALLSK-RIDLGFVRFADT 60
Query: 154 PSD-KLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFS 212
+D L S ++ V+ +P +HPL S++L ++ + P + L+ S
Sbjct: 61 LNDPPLASELLWREPMVVALPEEHPLAGRKSLTLADLRDEPFVFLRLANSRFADFLINCC 120
Query: 213 LQK-LTPYIVLETINSDIIKTYVELRMGIGII-ASIA 247
LQ TP I E + + V G+ ++ S A
Sbjct: 121 LQAGFTPQITQEVVEPQTLMALVAAGFGVALVPESYA 157
>gnl|CDD|176132 cd08441, PBP2_MetR, The C-terminal substrate binding domain of
LysR-type transcriptional regulator metR, which
regulates the expression of methionine biosynthetic
genes, contains type 2 periplasmic binding fold. MetR,
a member of the LysR family, is a positive regulator for
the metA, metE, metF, and metH genes. The
sulfur-containing amino acid methionine is the universal
initiator of protein synthesis in all known organisms
and its derivative S-adenosylmethionine (SAM) and
autoinducer-2 (AI-2) are involved in various cellular
processes. SAM plays a central role as methyl donor in
methylation reactions, which are essential for the
biosynthesis of phospholipids, proteins, DNA and RNA.
The interspecies signaling molecule AI-2 is involved in
cell-cell communication process (quorum sensing) and
gene regulation in bacteria. Although methionine
biosynthetic enzymes and metabolic pathways are well
conserved in bacteria, the regulation of methionine
biosynthesis involves various regulatory mechanisms. In
Escherichia coli and Salmonella enterica serovar
Typhimurium, MetJ and MetR regulate the expression of
methionine biosynthetic genes. The MetJ repressor
negatively regulates the E. coli met genes, except for
metH. Several of these genes are also under the positive
control of MetR with homocysteine as a co-inducer. In
Bacillus subtilis, the met genes are controlled by S-box
termination-antitermination system. 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 = 198
Score = 43.3 bits (103), Expect = 4e-05
Identities = 25/93 (26%), Positives = 48/93 (51%), Gaps = 7/93 (7%)
Query: 108 LPKIIKEFTIQFPKVKLSLLQG---NPKQITEMIRNDQADIAIVTEILSPSDKLISIPCY 164
L ++ +F ++P V+L L G +P + + D+ I ++ L P + P +
Sbjct: 15 LMPVLDQFRERWPDVELDLSSGFHFDPLP---ALLRGELDLVITSDPL-PLPGIAYEPLF 70
Query: 165 QWEYVIIVPLDHPLLLLNSISLKEISNYPLITY 197
+E V++V DHPL I+ +++++ LITY
Sbjct: 71 DYEVVLVVAPDHPLAAKEFITPEDLADETLITY 103
>gnl|CDD|182601 PRK10632, PRK10632, transcriptional regulator; Provisional.
Length = 309
Score = 44.0 bits (104), Expect = 4e-05
Identities = 28/112 (25%), Positives = 57/112 (50%), Gaps = 1/112 (0%)
Query: 20 TEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEG 79
T AA+ L S +S+ + +LE+EL + + R + I GLT+ G+ + ++ E++
Sbjct: 20 TAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSI-GLTEAGRIYYQGCRRMLHEVQD 78
Query: 80 LKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNP 131
+ + F+ G L I + T A+ L + + ++P + ++L+ G P
Sbjct: 79 VHEQLYAFNNTPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNLVTGIP 130
>gnl|CDD|176143 cd08452, PBP2_AlsR, The C-terminal substrate binding domain of
LysR-type trnascriptional regulator AlsR, which
regulates acetoin formation under stationary phase
growth conditions; contains the type 2 periplasmic
binding fold. AlsR is responsible for activating the
expression of the acetoin operon (alsSD) in response to
inducing signals such as glucose and acetate. Like many
other LysR family proteins, AlsR is transcribed
divergently from the alsSD operon. The alsS gene encodes
acetolactate synthase, an enzyme involved in the
production of acetoin in cells of stationary-phase. AlsS
catalyzes the conversion of two pyruvate molecules to
acetolactate and carbon dioxide. Acetolactate is then
converted to acetoin at low pH by acetolactate
decarboxylase which encoded by the alsD gene. Acetoin is
an important physiological metabolite excreted by many
microorganisms grown on glucose or other fermentable
carbon sources. 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 = 42.9 bits (101), Expect = 5e-05
Identities = 26/95 (27%), Positives = 52/95 (54%), Gaps = 11/95 (11%)
Query: 108 LPKIIKEFTIQFPKVKLSLLQ-GNPKQITEMIRNDQADIAIVTEILSPS----DKLISIP 162
LP I++E+ +FP VK+ L + +P Q+ E+++ + DI + + + + + S P
Sbjct: 15 LPPIVREYRKKFPSVKVELRELSSPDQVEELLKG-RIDIGFLHPPIQHTALHIETVQSSP 73
Query: 163 CYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITY 197
C V+ +P HPL I+++++ + P+IT
Sbjct: 74 C-----VLALPKQHPLASKEEITIEDLRDEPIITV 103
>gnl|CDD|176108 cd08416, PBP2_MdcR, The C-terminal substrate-binding domian of
LysR-type transcriptional regulator MdcR, which involved
in the malonate catabolism contains the type 2
periplasmic binding fold. This family includes the
C-terminal substrate binding domain of LysR-type
transcriptional regulator (LTTR) MdcR that controls the
expression of the malonate decarboxylase (mdc) genes.
Like other members of the LTTRs, MdcR is a positive
regulatory protein for its target promoter and 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
(PBP2). The PBP2 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 = 199
Score = 42.3 bits (100), Expect = 9e-05
Identities = 27/124 (21%), Positives = 59/124 (47%), Gaps = 5/124 (4%)
Query: 108 LPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVT--EILSPSDKLISIPCYQ 165
+P+II ++ P++ + L G+ K + + +++ + D +V E L+ D +P ++
Sbjct: 15 VPRIIMGLKLRRPELDIELTLGSNKDLLKKLKDGELDAILVATPEGLNDPD-FEVVPLFE 73
Query: 166 WEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETI 225
+ + VP PL + I L+++ + +T F+ D F + P +V+
Sbjct: 74 DDIFLAVPATSPLAASSEIDLRDLKDEKFVTLSEGFATYRGFDEAFEIAGFEPNVVMRV- 132
Query: 226 NSDI 229
+DI
Sbjct: 133 -NDI 135
>gnl|CDD|176150 cd08461, PBP2_DntR_like_3, The C-terminal substrate binding domain
of an uncharacterized LysR-type transcriptional
regulator similar to DntR, which is involved in the
catabolism of dinitrotoluene; contains the type 2
periplasmic binding fold. This CD includes an
uncharacterized LysR-type transcriptional regulator
similar to DntR, NahR, and LinR, which are involved in
the degradation of aromatic compounds. The transcription
of the genes encoding enzymes involved in such
degradation is regulated and expression of these enzymes
is enhanced by inducers, which are either an
intermediate in the metabolic pathway or compounds to be
degraded. 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 = 198
Score = 41.9 bits (99), Expect = 1e-04
Identities = 32/148 (21%), Positives = 58/148 (39%), Gaps = 15/148 (10%)
Query: 95 LTIATTHTQARYALPKIIKEFTIQF----PKVKLSLLQGNPKQITEMIRNDQADIAIVTE 150
L IA T YA I+ P V++++ + + + D+A+ T
Sbjct: 2 LVIAATD----YAQKAILPPLLAALRQEAPGVRVAIRDLESDNLEAQLERGEVDLALTTP 57
Query: 151 ILSPSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYP--LITYDL-SFSGRIKL 207
+P D L S P ++ YV + HPLL +SL + +++ F+G
Sbjct: 58 EYAP-DGLRSRPLFEERYVCVTRRGHPLLQGP-LSLDQFCALDHIVVSPSGGGFAGST-- 113
Query: 208 DREFSLQKLTPYIVLETINSDIIKTYVE 235
D + LT +VL + ++ +
Sbjct: 114 DEALAALGLTRNVVLSVPSFLVVPEILA 141
>gnl|CDD|181918 PRK09508, leuO, leucine transcriptional activator; Reviewed.
Length = 314
Score = 41.9 bits (99), Expect = 2e-04
Identities = 20/49 (40%), Positives = 31/49 (63%)
Query: 9 VREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIR 57
V +AV Q N+T AA L SQP VS A+ L+ + ++F+R+G+ I+
Sbjct: 29 VFDAVMQEQNITRAAHNLGMSQPAVSNAVARLKVMFNDELFVRYGRGIQ 77
>gnl|CDD|176121 cd08430, PBP2_IlvY, The C-terminal substrate binding of LysR-type
transcriptional regulator IlvY, which activates the
expression of ilvC gene that encoding acetohydroxy acid
isomeroreductase for the biosynthesis of branched amino
acids; contains the type 2 periplasmic binding fold. In
Escherichia coli, IlvY is required for the regulation of
ilvC gene expression that encodes acetohydroxy acid
isomeroreductase (AHIR), a key enzyme in the
biosynthesis of branched-chain amino acids (isoleucine,
valine, and leucine). The ilvGMEDA operon genes encode
remaining enzyme activities required for the
biosynthesis of these amino acids. Activation of ilvC
transcription by IlvY requires the additional binding of
a co-inducer molecule (either alpha-acetolactate or
alpha-acetohydoxybutyrate, the substrates for AHIR) to a
preformed complex of IlvY protein-DNA. Like many other
LysR-family members, IlvY negatively auto-regulates the
transcription of its own divergently transcribed ilvY
gene in an inducer-independent manner. This
substrate-binding domain has 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 = 40.6 bits (96), Expect = 3e-04
Identities = 39/138 (28%), Positives = 63/138 (45%), Gaps = 4/138 (2%)
Query: 108 LPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWE 167
LP I++ F Q P+V++ L G+P + + N +ADIAI +L +P
Sbjct: 15 LPPILERFRAQHPQVEIKLHTGDPADAIDKVLNGEADIAIAARPDKLPARLAFLPLATSP 74
Query: 168 YVIIVPLDHPLLLLNSISLKEI--SNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETI 225
V I P + +S EI S P I + + R +LD+ F + + P I +
Sbjct: 75 LVFIAPNIAC-AVTQQLSQGEIDWSRLPFILPERGLA-RERLDQWFRRRGIKPNIYAQVA 132
Query: 226 NSDIIKTYVELRMGIGII 243
+ I + V L G+GI+
Sbjct: 133 GHEAIVSMVALGCGVGIV 150
>gnl|CDD|235137 PRK03601, PRK03601, transcriptional regulator HdfR; Provisional.
Length = 275
Score = 40.8 bits (96), Expect = 5e-04
Identities = 22/53 (41%), Positives = 33/53 (62%), Gaps = 1/53 (1%)
Query: 22 AAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIM 74
AA++LY +Q VS I +LE +L +++F RH IR LT G+ +L E +M
Sbjct: 21 AAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIR-LTAAGERLLPYAETLM 72
>gnl|CDD|237907 PRK15092, PRK15092, DNA-binding transcriptional repressor LrhA;
Provisional.
Length = 310
Score = 40.4 bits (95), Expect = 6e-04
Identities = 37/142 (26%), Positives = 70/142 (49%), Gaps = 29/142 (20%)
Query: 22 AAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPG-------QAILR-----S 69
AA A+ +Q VS+ + LE+ + ++F RHG R + LT+ G + ILR
Sbjct: 31 AAAAVCRTQSAVSQQMQRLEQLVGKELFARHG-RNKLLTEHGIQLLGYARKILRFNDEAC 89
Query: 70 IEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSL-LQ 128
++ ++G+ IG ++ DT + TI LP ++ + +PK+ L + ++
Sbjct: 90 SSLMYSNLQGVLTIG---ASDDTAD-TI----------LPFLLNRVSSVYPKLALDVRVK 135
Query: 129 GNPKQITEMIRNDQADIAIVTE 150
N + EM+ + + D+A+ T
Sbjct: 136 RNA-FMMEMLESQEVDLAVTTH 156
>gnl|CDD|182228 PRK10082, PRK10082, cell density-dependent motility repressor;
Provisional.
Length = 303
Score = 40.4 bits (94), Expect = 7e-04
Identities = 30/127 (23%), Positives = 60/127 (47%), Gaps = 4/127 (3%)
Query: 18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEI 77
N ++AA + SQP S+ I LE+ + +++F R ++ L++ G+ I ++Q++
Sbjct: 27 NFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQ-LSEQGKIFHSQIRHLLQQL 85
Query: 78 EGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEM 137
E + S Y + IA H+ + LP II + F ++ + + +
Sbjct: 86 ESNLAELRGGSDYAQRKIKIAAAHSLSLGLLPSIISQMPPLFTWAIEAI---DVDEAVDK 142
Query: 138 IRNDQAD 144
+R Q+D
Sbjct: 143 LREGQSD 149
>gnl|CDD|176138 cd08447, PBP2_LTTR_aromatics_like_1, The C-terminal substrate
binding domain of an uncharacterized LysR-type
transcriptional regulator similar to regulators involved
in the catabolism of aromatic compounds, contains type 2
periplasmic binding fold. This CD represents the
substrate binding domain of an uncharacterized LysR-type
regulator similar to CbnR which is involved in the
regulation of chlorocatechol breakdown. The
transcription of the genes encoding enzymes involved in
such degradation is regulated and expression of these
enzymes is enhanced by inducers, which are either an
intermediate in the metabolic pathway or compounds to be
degraded. 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 = 198
Score = 38.4 bits (90), Expect = 0.002
Identities = 27/112 (24%), Positives = 42/112 (37%), Gaps = 17/112 (15%)
Query: 94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQ--------ADI 145
+L I T A LP+++ P V L L EM+ DQ D+
Sbjct: 1 SLRIGFTAASAYSFLPRLLAAARAALPDVDLVL--------REMVTTDQIEALESGRIDL 52
Query: 146 AIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITY 197
++ L + P + V VP HPL ++L+++ P I Y
Sbjct: 53 GLLRPPF-ARPGLETRPLVREPLVAAVPAGHPLAGAERLTLEDLDGQPFIMY 103
>gnl|CDD|176148 cd08459, PBP2_DntR_NahR_LinR_like, The C-terminal substrate binding
domain of LysR-type transcriptional regulators that are
involved in the catabolism of dinitrotoluene,
naphthalene and gamma-hexachlorohexane; contains the
type 2 periplasmic binding fold. This CD includes
LysR-like bacterial transcriptional regulators, DntR,
NahR, and LinR, which are involved in the degradation of
aromatic compounds. The transcription of the genes
encoding enzymes involved in such degradation is
regulated and expression of these enzymes is enhanced by
inducers, which are either an intermediate in the
metabolic pathway or compounds to be degraded. DntR
from Burkholderia species controls genes encoding
enzymes for oxidative degradation of the nitro-aromatic
compound 2,4-dinitrotoluene. The active form of DntR is
homotetrameric, consisting of a dimer of dimers. NahR is
a salicylate-dependent transcription activator of the
nah and sal operons for naphthalene degradation.
Salicylic acid is an intermediate of the oxidative
degradation of the aromatic ring in soil bacteria. LinR
positively regulates expression of the genes (linD and
linE) encoding enzymes for gamma-hexachlorocyclohexane
(a haloorganic insecticide) degradation. Expression of
linD and linE are induced by their substrates,
2,5-dichlorohydroquinone (2,5-DCHQ) and
chlorohydroquinone (CHQ). 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 = 37.6 bits (88), Expect = 0.003
Identities = 23/132 (17%), Positives = 53/132 (40%), Gaps = 4/132 (3%)
Query: 94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAI-VTEIL 152
IA + Y LP+++ P V++ ++ ++ E + + + D+AI L
Sbjct: 1 TFRIAMSDIGEMYFLPRLLAALREVAPGVRIETVRLPVDELEEALESGEIDLAIGYLPDL 60
Query: 153 SPSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFS 212
++ YV +V DHP + ++++L++ + S +G +++
Sbjct: 61 GAG--FFQQRLFRERYVCLVRKDHP-RIGSTLTLEQFLAARHVVVSASGTGHGLVEQALR 117
Query: 213 LQKLTPYIVLET 224
+ I L
Sbjct: 118 EAGIRRRIALRV 129
>gnl|CDD|221806 pfam12849, PBP_like_2, PBP superfamily domain. This domain belongs
to the periplasmic binding protein superfamily.
Length = 256
Score = 35.1 bits (81), Expect = 0.030
Identities = 28/133 (21%), Positives = 53/133 (39%), Gaps = 20/133 (15%)
Query: 92 TGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEI 151
G + IA + T A L + + F ++P K+ + G + + + N D A+ +
Sbjct: 9 RGTILIAGSSTLAPILL-DLAEAFEEEYPGAKVVVEAGGSGEGIKALLNGDVDFALSSRP 67
Query: 152 LSPSD--------KLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSG 203
L+ + +I +P V++V D+P LL + LK+I F+G
Sbjct: 68 LTEEEFVAEGRVGGIIEVPVAYDGIVLVVNKDNPAGLLTAEQLKKI-----------FAG 116
Query: 204 RIKLDREFSLQKL 216
+I +
Sbjct: 117 KITNWSDLGGPDG 129
>gnl|CDD|176147 cd08458, PBP2_NocR, The C-terminal substrate-domain of LysR-type
transcriptional regulator, NocR, involved in the
catabolism of nopaline, contains the type 2 periplasmic
binding fold. This CD includes the C-terminal
substrate-domain of LysR-type transcriptional regulator
NocR, which is involved in the catabolism of nopaline.
Opines are low molecular weight compounds found in plant
crown gall tumors 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. In Agrobacterium tumefaciens,
NocR regulates expression of the divergently transcribed
nocB and nocR genes of the nopaline catabolism (noc)
region. 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 = 34.7 bits (79), Expect = 0.031
Identities = 27/149 (18%), Positives = 55/149 (36%), Gaps = 1/149 (0%)
Query: 95 LTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSP 154
L +A A + +I+ F P V + L + + E++ D+ I +
Sbjct: 2 LRVACYTAPALSFMSGVIQTFIADRPDVSVYLDTVPSQTVLELVSLQHYDLGIS-ILAGD 60
Query: 155 SDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQ 214
L + P + V ++P H L ++ ++ LI R++ D
Sbjct: 61 YPGLTTEPVPSFRAVCLLPPGHRLEDKETVHATDLEGESLICLSPVSLLRMQTDAALDSC 120
Query: 215 KLTPYIVLETINSDIIKTYVELRMGIGII 243
+ +E+ + + V MG+GI+
Sbjct: 121 GVHCNRRIESSLALNLCDLVSRGMGVGIV 149
>gnl|CDD|234749 PRK00405, rpoB, DNA-directed RNA polymerase subunit beta; Reviewed.
Length = 1112
Score = 35.5 bits (83), Expect = 0.032
Identities = 24/66 (36%), Positives = 32/66 (48%), Gaps = 7/66 (10%)
Query: 197 YDLSFSGRIKLDREFSLQKLTPYIVLETINSDI---IKTYVELRMGIGIIASIAFDSNRD 253
YDLS GR KL+++ L + VL DI IK + LR G G + I NR
Sbjct: 316 YDLSKVGRYKLNKKLGLDEDEDVRVL--TKEDIIATIKYLINLRNGKGEVDDIDHLGNR- 372
Query: 254 KNLRSI 259
+RS+
Sbjct: 373 -RVRSV 377
>gnl|CDD|237357 PRK13348, PRK13348, chromosome replication initiation inhibitor
protein; Provisional.
Length = 294
Score = 34.6 bits (80), Expect = 0.046
Identities = 21/67 (31%), Positives = 34/67 (50%), Gaps = 3/67 (4%)
Query: 21 EAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEII-MQEIEG 79
AA+ L+ + VS+ I LEE L + +R G+ R T GQ +LR + + + E +
Sbjct: 21 RAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRP-TPAGQRLLRHLRQVALLEADL 78
Query: 80 LKKIGKE 86
L + E
Sbjct: 79 LSTLPAE 85
>gnl|CDD|176136 cd08445, PBP2_BenM_CatM_CatR, The C-terminal substrate binding
domain of LysR-type transcriptional regulators involved
in benzoate catabolism; contains the type 2 periplasmic
binding fold. This CD includes the C-terminal of
LysR-type transcription regulators, BenM, CatM, and
CatR, which are involved in the benzoate catabolism. The
BenM and CatM are paralogs with overlapping functions.
BenM responds synergistically to two effectors, benzoate
and cis,cis-muconate, to activate expression of the
benABCDE operon which is involved in benzoate
catabolism, while CatM responses only to muconate. BenM
and CatM share high protein sequence identity and bind
to the operator-promoter regions that have similar DNA
sequences. In Pseudomonas species, phenolic compounds
are converted by different enzymes to central
intermediates, such as protocatechuate and catechols.
Generally, unsubstituted compounds, such as benzoate,
are metabolized by an ortho-cleavage pathway. The catBCA
operon encodes three enzymes of the ortho-pathway
required for benzoate catabolism: muconate lactonizing
enzyme I, muconolactone isomerase, and catechol
1,2-dioxygenase. CatR normally responds to benzoate and
cis,cis-muconate, an inducer molecule, to activate
transcription of the catBCA operon, whose gene products
convert benzoate to catechol. 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 = 203
Score = 33.4 bits (77), Expect = 0.081
Identities = 24/102 (23%), Positives = 45/102 (44%), Gaps = 22/102 (21%)
Query: 107 ALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADI----------AIVTEILSPSD 156
LP++I+ F P V++ L++ Q E ++ + D+ AI +L +
Sbjct: 15 LLPELIRRFRQAAPDVEIELIEMTTVQQIEALKEGRIDVGFGRLRIEDPAIRRIVLR-EE 73
Query: 157 KLISIPCYQWEYVIIVPLDHPLLLL-NSISLKEISNYPLITY 197
L V+ +P HPL ++L ++++ PLI Y
Sbjct: 74 PL----------VVALPAGHPLAQEKAPLTLAQLADEPLILY 105
>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 = 31.6 bits (73), Expect = 0.31
Identities = 17/71 (23%), Positives = 37/71 (52%), Gaps = 6/71 (8%)
Query: 93 GNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAI-VTEI 151
G L I+ + R L ++ EF ++P V+L L+ + ++ +++ + D+AI + E+
Sbjct: 1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSD--RLVDLVE-EGFDLAIRIGEL 57
Query: 152 LSPSDKLISIP 162
S L++
Sbjct: 58 PDSS--LVARR 66
>gnl|CDD|176157 cd08468, PBP2_Pa0477, The C-terminal substrate biniding domain of
an uncharacterized LysR-like transcriptional regulator
Pa0477 related to DntR, contains the type 2 periplasmic
binding fold. LysR-type transcriptional regulator
Pa0477 is related to DntR, which controls genes encoding
enzymes for oxidative degradation of the nitro-aromatic
compound 2,4-dinitrotoluene. The transcription of the
genes encoding enzymes involved in such degradation is
regulated and expression of these enzymes is enhanced by
inducers, which are either an intermediate in the
metabolic pathway or compounds to be degraded. 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 = 202
Score = 30.9 bits (70), Expect = 0.55
Identities = 21/88 (23%), Positives = 35/88 (39%), Gaps = 6/88 (6%)
Query: 96 TIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAI-VTEILSP 154
A T A +P+++ P V+L+L+ K + + + D A+ +
Sbjct: 3 RFAVTDYTALAVMPRLMARLEELAPSVRLNLVHAEQKLPLDALLAGEIDFALGYSHDDGA 62
Query: 155 SDKLISIPCYQW---EYVIIVPLDHPLL 179
+LI W YV+I DHP L
Sbjct: 63 EPRLIEE--RDWWEDTYVVIASRDHPRL 88
>gnl|CDD|182948 PRK11074, PRK11074, putative DNA-binding transcriptional
regulator; Provisional.
Length = 300
Score = 31.1 bits (71), Expect = 0.60
Identities = 22/72 (30%), Positives = 38/72 (52%), Gaps = 4/72 (5%)
Query: 9 VREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAIL- 67
V +AV + + + AA+ L+ VS + +LEE L++ +F R + + LT G+ +
Sbjct: 9 VVDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVE-LTPAGEWFVK 67
Query: 68 --RSIEIIMQEI 77
RS+ MQE
Sbjct: 68 EARSVIKKMQET 79
>gnl|CDD|222203 pfam13531, SBP_bac_11, Bacterial extracellular solute-binding
protein. This family includes bacterial extracellular
solute-binding proteins.
Length = 224
Score = 30.3 bits (69), Expect = 0.88
Identities = 17/65 (26%), Positives = 32/65 (49%), Gaps = 8/65 (12%)
Query: 123 KLSLLQGNPKQITEMIRNDQADIAIV--TEILSPSDKL--ISIPCYQWEYVIIVPLDHPL 178
K+ +L N +Q + + + +AD IV +E L+ L + +P + I P+D+P
Sbjct: 135 KIVVLGENVRQALQFVASGEADAGIVYESEALALGPGLDVVYLP----PELNIPPIDYPA 190
Query: 179 LLLNS 183
+L
Sbjct: 191 AVLKG 195
>gnl|CDD|176153 cd08464, PBP2_DntR_like_2, The C-terminal substrate binding domain
of an uncharacterized LysR-type transcriptional
regulator similar to DntR, which is involved in the
catabolism of dinitrotoluene; contains the type 2
periplasmic binding fold. This CD includes an
uncharacterized LysR-type transcriptional regulator
similar to DntR, NahR, and LinR, which are involved in
the degradation of aromatic compounds. The transcription
of the genes encoding enzymes involved in such
degradation is regulated and expression of these enzymes
is enhanced by inducers, which are either an
intermediate in the metabolic pathway or compounds to be
degraded. 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 = 30.3 bits (69), Expect = 0.96
Identities = 11/48 (22%), Positives = 22/48 (45%)
Query: 108 LPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPS 155
P ++ + P V+L Q +P + +M+ + D+AI P+
Sbjct: 15 APPLLAALRAEAPGVRLVFRQVDPFNVGDMLDRGEIDLAIGVFGELPA 62
>gnl|CDD|184959 PRK14997, PRK14997, LysR family transcriptional regulator;
Provisional.
Length = 301
Score = 30.3 bits (68), Expect = 0.99
Identities = 26/130 (20%), Positives = 53/130 (40%), Gaps = 2/130 (1%)
Query: 1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLT 60
+L+ F + V + A +AL + +S+ I +LEE L + + I+ R +T
Sbjct: 2 TDLNDFAWFVHVVEEG-GFAAAGRALDEPKSKLSRRIAQLEERLGVRL-IQRTTRQFNVT 59
Query: 61 KPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFP 120
+ GQ + ++ E + + G + + T + ++ +F ++P
Sbjct: 60 EVGQTFYEHCKAMLVEAQAAQDAIAALQVEPRGIVKLTCPVTLLHVHIGPMLAKFMARYP 119
Query: 121 KVKLSLLQGN 130
V L L N
Sbjct: 120 DVSLQLEATN 129
>gnl|CDD|237986 cd00019, AP2Ec, AP endonuclease family 2; These endonucleases play
a role in DNA repair. Cleave phosphodiester bonds at
apurinic or apyrimidinic sites; the alignment also
contains hexulose-6-phosphate isomerases, enzymes that
catalyze the epimerization of D-arabino-6-hexulose
3-phosphate to D-fructose 6-phosphate, via cleaving the
phosphoesterbond with the sugar. .
Length = 279
Score = 30.0 bits (68), Expect = 1.5
Identities = 16/92 (17%), Positives = 34/92 (36%), Gaps = 4/92 (4%)
Query: 35 KAIIELEEELSIDIFIRHGKRIRGLTKPGQAIL-RSIEIIMQEIEGLKKIGKEFSAYDTG 93
+ + EE H + L P + +SIE + EIE +++G + G
Sbjct: 48 EKFKAIAEEGPSICLSVHAPYLINLASPDKEKREKSIERLKDEIERCEELGIRLLVFHPG 107
Query: 94 NLTIAT---THTQARYALPKIIKEFTIQFPKV 122
+ + + AL ++I + + +
Sbjct: 108 SYLGQSKEEGLKRVIEALNELIDKAETKGVVI 139
>gnl|CDD|184967 PRK15005, PRK15005, universal stress protein F; Provisional.
Length = 144
Score = 28.6 bits (64), Expect = 2.0
Identities = 15/47 (31%), Positives = 30/47 (63%), Gaps = 1/47 (2%)
Query: 103 QARYALPKIIKEFTIQFPKVKLSLLQGNPK-QITEMIRNDQADIAIV 148
+A+ L +IIK+F + +V + + +G+PK +I E+ + AD+ I+
Sbjct: 67 EAKSQLEEIIKKFKLPTDRVHVHVEEGSPKDRILELAKKIPADMIII 113
>gnl|CDD|213338 cd05136, RasGAP_DAB2IP, Ras-GTPase Activating Domain of DAB2IP and
similar proteins. The DAB2IP family of Ras
GTPase-activating proteins includes DAB2IP, nGAP, and
Syn GAP. Disabled 2 interactive protein, (DAB2IP; also
known as ASK-interacting protein 1 (AIP1)), is a member
of the GTPase-activating proteins, down-regulates
Ras-mediated signal pathways, and mediates TNF-induced
activation of ASK1-JNK signaling pathways. The mechanism
by which TNF signaling is coupled to DAB2IP is not
known.
Length = 324
Score = 29.5 bits (67), Expect = 2.4
Identities = 17/69 (24%), Positives = 26/69 (37%), Gaps = 7/69 (10%)
Query: 186 LKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYI--VLETINSDIIKTYVELRMGIGII 243
L+EIS+ + F G I L RE SL L + ++ +N + L I+
Sbjct: 260 LQEISSPSPSSNSSDFDGYIDLGRELSL--LHSLLVEIISKLNQTTLDKLGPLP---RIL 314
Query: 244 ASIAFDSNR 252
I
Sbjct: 315 NDITEALRN 323
>gnl|CDD|137627 PRK09982, PRK09982, universal stress protein UspD; Provisional.
Length = 142
Score = 28.0 bits (62), Expect = 3.5
Identities = 11/32 (34%), Positives = 22/32 (68%), Gaps = 1/32 (3%)
Query: 117 IQFPKVKLSLLQGN-PKQITEMIRNDQADIAI 147
IQ+PK KL + +G P+ + E+++ +Q D+ +
Sbjct: 77 IQWPKTKLRIERGEMPETLLEIMQKEQCDLLV 108
>gnl|CDD|233685 TIGR02013, rpoB, DNA-directed RNA polymerase, beta subunit. This
model describes orthologs of the beta subunit of
Bacterial RNA polymerase. The core enzyme consists of
two alpha chains, one beta chain, and one beta' subunit
[Transcription, DNA-dependent RNA polymerase].
Length = 1065
Score = 28.9 bits (65), Expect = 3.7
Identities = 20/64 (31%), Positives = 30/64 (46%), Gaps = 3/64 (4%)
Query: 197 YDLSFSGRIKLDREFSLQKLTPYIVLETINS-DIIKTYVELRMGIGIIASIAFDSNRDKN 255
YDL GR K++++ L VL + IK ++LR G G + I NR
Sbjct: 271 YDLGRVGRYKMNKKLGLDVPEDIGVLTKEDIIATIKYLIKLRNGKGEVDDIDHLGNR--R 328
Query: 256 LRSI 259
+RS+
Sbjct: 329 IRSV 332
>gnl|CDD|176137 cd08446, PBP2_Chlorocatechol, The C-terminal substrate binding
domain of LysR-type transcriptional regulators involved
in the chlorocatechol catabolism, contains the type 2
periplasmic binding fold. This CD includes the
substrate binding domain of LysR-type regulators CbnR,
ClcR and TfdR, which are involved in the regulation of
chlorocatechol breakdown. The chlorocatechol-degradative
pathway is often found in bacteria that can use
chlorinated aromatic compounds as carbon and energy
sources. CbnR is found in the 3-chlorobenzoate
degradative bacterium Ralstonia eutropha NH9 and forms a
tetramer. CbnR activates the expression of the cbnABCD
genes, which are responsible for the degradation of
chlorocatechol converted from 3-chlorobenzoate and are
transcribed divergently from cbnR. In soil bacterium
Pseudomonas putida, the 3-chlorocatechol-degradative
pathway is encoded by clcABD operon, which requires the
divergently transcribed clcR for activation. TfdR is
involved in the activation of tfdA and tfdB gene
expression. These genes encode enzymes for the
conversion of 2,4-dichlorophenoxyacetic acid and
2,4-dichlorophenol. 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 = 198
Score = 28.4 bits (64), Expect = 4.0
Identities = 23/105 (21%), Positives = 41/105 (39%), Gaps = 1/105 (0%)
Query: 93 GNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEIL 152
G L + + +P++++ F P V +SL + E +R + I
Sbjct: 1 GELDVGYFGSAILDTVPRLLRAFLTARPDVTVSLHNMTKDEQIEALRAGRIHIG-FGRFY 59
Query: 153 SPSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITY 197
+ Q + VP HPL ++SL ++ N PLI +
Sbjct: 60 PVEPDIAVENVAQERLYLAVPKSHPLAARPAVSLADLRNEPLILF 104
>gnl|CDD|215348 PLN02646, PLN02646, argininosuccinate lyase.
Length = 474
Score = 28.5 bits (64), Expect = 4.7
Identities = 13/56 (23%), Positives = 27/56 (48%), Gaps = 3/56 (5%)
Query: 228 DIIKTYVE-LRMGIGIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRS 282
D + T + L + +I F N ++ +S+ A L TT++ ++++G R
Sbjct: 344 DSVDTVSDMLEVATEFAQNITF--NPERIKKSLPAGMLDATTLADYLVRKGVPFRE 397
>gnl|CDD|200566 cd10941, CE4_PuuE_HpPgdA_like_2, Putative catalytic domain of
uncharacterized prokaryotic polysaccharide deacetylases
similar to bacterial PuuE allantoinases and Helicobacter
pylori peptidoglycan deacetylase (HpPgdA). This family
contains many uncharacterized prokaryotic polysaccharide
deacetylases (DCAs) that show high sequence similarity
to the catalytic domain of bacterial PuuE allantoinases
and Helicobacter pylori peptidoglycan deacetylase
(HpPgdA). PuuE allantoinase appears to be
metal-independent and specifically catalyzes the
hydrolysis of (S)-allantoin into allantoic acid.
Different from PuuE allantoinase, HpPgdA has the ability
to bind a metal ion at the active site and is
responsible for a peptidoglycan modification that
counteracts the host immune response. Both PuuE
allantoinase and HpPgdA function as homotetramers. The
monomer is composed of a 7-stranded barrel with
detectable sequence similarity to the 6-stranded barrel
NodB homology domain of DCA-like proteins in the CE4
superfamily, which removes N-linked or O-linked acetyl
groups from cell wall polysaccharides. In contrast to
typical NodB-like DCAs, PuuE allantoinase and HpPgdA do
not exhibit a solvent-accessible polysaccharide binding
groove and might only bind a small molecule at the
active site.
Length = 258
Score = 28.0 bits (63), Expect = 5.6
Identities = 12/40 (30%), Positives = 18/40 (45%), Gaps = 3/40 (7%)
Query: 259 ISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRK 298
+S + L G R+ + G Y R Y IK L + R+
Sbjct: 173 VSVTKLPGL---RLPLAGGGYFRLLPYRLIKALIKRSLRR 209
>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 = 27.8 bits (63), Expect = 5.8
Identities = 10/35 (28%), Positives = 16/35 (45%)
Query: 92 TGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSL 126
G L I AR L ++ F ++P ++L L
Sbjct: 2 AGTLRINAPRVAARLLLAPLLARFLARYPDIRLEL 36
>gnl|CDD|224258 COG1339, COG1339, Transcriptional regulator of a riboflavin/FAD
biosynthetic operon [Transcription / Coenzyme
metabolism].
Length = 214
Score = 27.7 bits (62), Expect = 7.0
Identities = 20/68 (29%), Positives = 33/68 (48%), Gaps = 12/68 (17%)
Query: 19 LTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAIL---RSIEIIMQ 75
+E AK L S ++ + ELE+E I R ++K GQ I + I+++ +
Sbjct: 22 SSELAKRLGVSSQTAARKLKELEDEGYIT---------RTISKRGQLITITEKGIDLLYK 72
Query: 76 EIEGLKKI 83
E E L +I
Sbjct: 73 EYEDLSRI 80
>gnl|CDD|234094 TIGR03026, NDP-sugDHase, nucleotide sugar dehydrogenase. Enzymes
in this family catalyze the NAD-dependent
alcohol-to-acid oxidation of nucleotide-linked sugars.
Examples include UDP-glucose 6-dehydrogenase (1.1.1.22)
, GDP-mannose 6-dehydrogenase (1.1.1.132) ,
UDP-N-acetylglucosamine 6-dehydrogenase (1.1.1.136),
UDP-N-acetyl-D-galactosaminuronic acid dehydrogenase and
UDP-N-acetyl-D-mannosaminuronic acid dehydrogenase.
These enzymes are most often involved in the
biosynthesis of polysaccharides and are often found in
operons devoted to that purpose. All of these enzymes
contain three Pfam domains, pfam03721, pfam00984, and
pfam03720 for the N-terminal, central, and C-terminal
regions respectively.
Length = 409
Score = 28.0 bits (63), Expect = 7.3
Identities = 28/96 (29%), Positives = 41/96 (42%), Gaps = 18/96 (18%)
Query: 3 LHQFRFVREAVRQNFNLTEAAKALYTSQPG-VSKAIIELEEELSIDIFIRHGKRIR--GL 59
+ + N L EAA+ + SQP V + I +L L GK + GL
Sbjct: 267 PLALIAKAKELGYNPELIEAAREINDSQPDYVVEKIKDLLGAL-------KGKTVLILGL 319
Query: 60 T-KPGQAILR---SIEIIMQEIEGLKKIGKEFSAYD 91
KP +R +++II E LK+ G + AYD
Sbjct: 320 AFKPNTDDVRESPALDII----ELLKEKGAKVKAYD 351
>gnl|CDD|176144 cd08453, PBP2_IlvR, The C-terminal substrate binding domain of
LysR-type transcriptional regulator, IlvR, involved in
the biosynthesis of isoleucine, leucine and valine;
contains type 2 periplasmic binding fold. The IlvR is
an activator of the upstream and divergently transcribed
ilvD gene, which encodes dihydroxy acid dehydratase that
participates in isoleucine, leucine, and valine
biosynthesis. As in the case of other members of the
LysR family, the expression of ilvR gene is repressed in
the presence of its own gene product. 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 = 27.3 bits (61), Expect = 7.3
Identities = 30/150 (20%), Positives = 53/150 (35%), Gaps = 24/150 (16%)
Query: 108 LPKIIKEFTIQFPKVKLSLLQGNPK-QITEMIRNDQADIAIVTEILSPSDKLIS----IP 162
LP++++ F +P V+L L + Q+ ++ + D IV I P P
Sbjct: 15 LPELVRRFREAYPDVELQLREATSDVQLEALLA-GEIDAGIV--IPPPGASAPPALAYRP 71
Query: 163 CYQWEYVIIVPLDHPLLLLNSISLKEISNYPLIT---------YDLSFSGRIKLDREFSL 213
V+ VP ++L ++ PL+ +D +
Sbjct: 72 LLSEPLVLAVPAAWAAEGGAPLALAAVAAEPLVIFPRRIAPAFHDAVT-------GYYRA 124
Query: 214 QKLTPYIVLETINSDIIKTYVELRMGIGII 243
TP I E I I + V MG+ ++
Sbjct: 125 AGQTPRIAQEAIQMQTIISLVSAGMGVALV 154
>gnl|CDD|202582 pfam03248, Rer1, Rer1 family. RER1 family protein are involved in
involved in the retrieval of some endoplasmic reticulum
membrane proteins from the early golgi compartment. The
C terminus of yeast Rer1p interacts with a coatomer
complex.
Length = 175
Score = 27.2 bits (61), Expect = 7.4
Identities = 12/32 (37%), Positives = 17/32 (53%), Gaps = 6/32 (18%)
Query: 269 ISRVIIKQGTYLRSY------VYSFIKLLSPK 294
I RVI+ QG Y+ Y + F+ L+PK
Sbjct: 40 ILRVILAQGWYVVCYALGIYLLNLFLAFLTPK 71
>gnl|CDD|176130 cd08439, PBP2_LrhA_like, The C-terminal substrate domain of
LysR-like regulator LrhA (LysR homologue A) and that of
closely related homologs, contains the type 2
periplasmic binding fold. This CD represents the LrhA
subfamily of LysR-like bacterial transcriptional
regulators, including LrhA, HexA, PecT, and DgdR. LrhA
is involved in control of the transcription of
flagellar, motility, and chemotaxis genes by regulating
the synthesis and concentration of FlhD(2)C(2), the
master regulator for the expression of flagellar and
chemotaxis genes. The LrhA protein has strong homology
to HexA and PecT from plant pathogenic bacteria, in
which HexA and PecT act as repressors of motility and of
virulence factors, such as exoenzymes required for lytic
reactions. DgdR also shares similar characteristics to
those of LrhA, HexA and PecT. 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 = 185
Score = 26.9 bits (60), Expect = 9.9
Identities = 12/56 (21%), Positives = 27/56 (48%)
Query: 95 LTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTE 150
L I A LP ++ F +P++ + ++ ++ EM+ + D+A++T
Sbjct: 2 LRIGCPDDYADTILPFLLNRFASVYPRLAIEVVCKRTPRLMEMLERGEVDLALITH 57
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.322 0.138 0.383
Gapped
Lambda K H
0.267 0.0782 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,931,291
Number of extensions: 1610665
Number of successful extensions: 1703
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1625
Number of HSP's successfully gapped: 111
Length of query: 306
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 209
Effective length of database: 6,635,264
Effective search space: 1386770176
Effective search space used: 1386770176
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 59 (26.4 bits)