RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2326
(181 letters)
>gnl|CDD|143496 cd06822, PLPDE_III_YBL036c_euk, Pyridoxal 5-phosphate (PLP)-binding
TIM barrel domain of Type III PLP-Dependent Enzymes,
Eukaryotic YBL036c-like proteins. This subfamily
contains mostly uncharacterized eukaryotic proteins with
similarity to the yeast hypothetical protein YBL036c,
which is homologous to a Pseudomonas aeruginosa gene
that is co-transcribed with a known proline biosynthetic
gene. YBL036c is a single domain monomeric protein with
a typical TIM barrel fold. It binds the PLP cofactor and
has been shown to exhibit amino acid racemase activity.
The YBL036c structure is similar to the N-terminal
domain of the fold type III PLP-dependent enzymes,
bacterial alanine racemase and eukaryotic ornithine
decarboxylase, which are two-domain dimeric proteins.
The lack of a second domain in YBL036c may explain
limited D- to L-alanine racemase or non-specific
racemase activity. Some members of this subfamily are
also referred to as PROSC (Proline synthetase
co-transcribed bacterial homolog).
Length = 227
Score = 220 bits (562), Expect = 2e-73
Identities = 84/169 (49%), Positives = 106/169 (62%), Gaps = 27/169 (15%)
Query: 6 KDIRWHFIGHLQSNKVPKVIKVPNLEYIETIHDTRLATQVNNAWAKHQPDKKLKVFCQIN 65
DI+WHFIGHLQSNKV K++KVPNL +ET+ +LA ++N AW K + LKV Q+N
Sbjct: 66 IDIKWHFIGHLQSNKVKKLLKVPNLYMVETVDSEKLADKLNKAWEKLGEREPLKVMVQVN 125
Query: 66 TSGEENKHGAHPEHAEALVSHVINSCPNLEFTDKHGAHPEHAEALVSHVINSCPNLEFTG 125
TSGEE+K G E +EA+ LV H+I CPNL+F+G
Sbjct: 126 TSGEESKSGL--EPSEAV-------------------------ELVKHIIEECPNLKFSG 158
Query: 126 LMTIGKYGYDTKHGPNPDFLELAKCRKDVCKKLNLNESNVELSMGMSSD 174
LMTIG +GY GPNPDFL L CRK VC+KL +N ++ELSMGMS+D
Sbjct: 159 LMTIGSFGYSLSSGPNPDFLCLVDCRKKVCEKLGINPDDLELSMGMSAD 207
>gnl|CDD|143483 cd00635, PLPDE_III_YBL036c_like, Type III Pyridoxal 5-phosphate
(PLP)-Dependent Enzymes, YBL036c-like proteins. This
family contains mostly uncharacterized proteins, widely
distributed among eukaryotes, bacteria and archaea, that
bear similarity to the yeast hypothetical protein
YBL036c, which is homologous to a Pseudomonas aeruginosa
gene that is co-transcribed with a known proline
biosynthetic gene. YBL036c is a single domain monomeric
protein with a typical TIM barrel fold. It binds the PLP
cofactor and has been shown to exhibit amino acid
racemase activity. The YBL036c structure is similar to
the N-terminal domain of the fold type III PLP-dependent
enzymes, bacterial alanine racemase and eukaryotic
ornithine decarboxylase, which are two-domain dimeric
proteins. The lack of a second domain in YBL036c may
explain limited D- to L-alanine racemase or non-specific
racemase activity.
Length = 222
Score = 126 bits (318), Expect = 1e-36
Identities = 55/171 (32%), Positives = 75/171 (43%), Gaps = 35/171 (20%)
Query: 7 DIRWHFIGHLQSNKVPKVIKVPNLEYIETIHDTRLATQVNNAWAKHQPDKKLKVFCQINT 66
DI WHFIGHLQ+NKV +++ + I ++ +LA ++N K + L V Q+N
Sbjct: 70 DIEWHFIGHLQTNKVKYAVRLF--DLIHSVDSLKLAEELNKRAEKE--GRVLDVLVQVNI 125
Query: 67 SGEENKHGAHPEHAEALVSHVINSCPNLEFTDKHGAHPEHAEALVSHVINSCPNLEFTGL 126
GEE+K G PE E L+ I + PNL GL
Sbjct: 126 GGEESKSGVAPEELEELLEE----------------------------IAALPNLRIRGL 157
Query: 127 MTIGKYGYDTKHGPNPDFLELAKCRKDVCKKLNLNESNVELSMGMSSDLRE 177
MTI + P F EL + R ++ K +N ELSMGMS D
Sbjct: 158 MTIAPLT-EDPEEVRPYFRELRELRDELGAKGGVNLK--ELSMGMSGDFEI 205
>gnl|CDD|223402 COG0325, COG0325, Predicted enzyme with a TIM-barrel fold [General
function prediction only].
Length = 228
Score = 114 bits (288), Expect = 5e-32
Identities = 57/172 (33%), Positives = 74/172 (43%), Gaps = 36/172 (20%)
Query: 6 KDIRWHFIGHLQSNKVPKVIKVPNLEYIETIHDTRLATQVNNAWAKHQPDKKLKVFCQIN 65
DI WHFIG LQSNKV V + N ++I ++ +LA ++N A P K L V Q+N
Sbjct: 72 PDIEWHFIGPLQSNKVKLVAE--NFDWIHSLDRLKLAKELNKR-ALELP-KPLNVLIQVN 127
Query: 66 TSGEENKHGAHPEHAEALVSHVINSCPNLEFTDKHGAHPEHAEALVSHVINSCPNLEFTG 125
SGEE+K G PE + L + PNLE G
Sbjct: 128 ISGEESKSGVPPEELDELAQE----------------------------VQELPNLELRG 159
Query: 126 LMTIGKYGYDTKHGPNPDFLELAKCRKDVCKKLNLNESNVELSMGMSSDLRE 177
LMTI D + F +L K ++ K ELSMGMS+D
Sbjct: 160 LMTIPPLTDDPE-EIFAVFRKLRKLFDELKAK---YPPIDELSMGMSNDYEI 207
>gnl|CDD|143497 cd06824, PLPDE_III_Yggs_like, Pyridoxal 5-phosphate (PLP)-binding
TIM barrel domain of Type III PLP-Dependent Enzymes,
Yggs-like proteins. This subfamily contains mainly
uncharacterized proteobacterial proteins with similarity
to the hypothetical Escherichia coli protein YggS, a
homolog of yeast YBL036c, which is homologous to a
Pseudomonas aeruginosa gene that is co-transcribed with
a known proline biosynthetic gene. Like yeast YBL036c,
Yggs is a single domain monomeric protein with a typical
TIM-barrel fold. Its structure, which shows a
covalently-bound PLP cofactor, is similar to the
N-terminal domain of the fold type III PLP-dependent
enzymes, bacterial alanine racemase and eukaryotic
ornithine decarboxylase, which are two-domain dimeric
proteins. YggS has not been characterized extensively
and its biological function is still unkonwn.
Length = 224
Score = 91.9 bits (229), Expect = 2e-23
Identities = 47/175 (26%), Positives = 70/175 (40%), Gaps = 44/175 (25%)
Query: 7 DIRWHFIGHLQSNKVPKVIKVPNLEYIETIHDTRLATQVNNAWAKHQPDKKLKVFCQINT 66
DI WHFIG +QSNK + + N +++ ++ ++A ++N+ P L V Q+N
Sbjct: 72 DIEWHFIGPIQSNKTKLIAE--NFDWVHSVDRLKIAKRLNDQRPAGLP--PLNVCIQVNI 127
Query: 67 SGEENKHGAHPEHAEALVSHVINSCPNLEFTDKHGAHPEHAEALVSHVINSCPNLEFTGL 126
SGE++K G PE A L I+ PNL GL
Sbjct: 128 SGEDSKSGVAPEDAAELAEA----------------------------ISQLPNLRLRGL 159
Query: 127 MTIGKYGYDTKHGPNPDFLELAKC---RKDVCKKLNLNESNVE-LSMGMSSDLRE 177
M I P D + + +L +++ LSMGMS DL
Sbjct: 160 MAIPA--------PTDDEAAQRAAFKRLRQLFDQLKKQYPDLDTLSMGMSGDLEA 206
>gnl|CDD|129155 TIGR00044, TIGR00044, pyridoxal phosphate enzyme, YggS family.
Members of this protein family include YggS from
Escherichia coli and YBL036C, an uncharacterized
pyridoxal protein of Saccharomyces cerevisiae [Unknown
function, Enzymes of unknown specificity].
Length = 229
Score = 79.5 bits (196), Expect = 1e-18
Identities = 51/171 (29%), Positives = 68/171 (39%), Gaps = 34/171 (19%)
Query: 7 DIRWHFIGHLQSNKVPKVIKVPNLEYIETIHDTRLATQVNNAWAKHQPDKKLKVFCQINT 66
+ WHFIG LQSNK V V N +++ TI ++A ++N K QP L V QIN
Sbjct: 74 KLEWHFIGPLQSNKDRLV--VENFDWVHTIDSLKIAKKLNEQREKLQPP--LNVLLQINI 129
Query: 67 SGEENKHGAHPEHAEALVSHVINSCPNLEFTDKHGAHPEHAEALVSHVINSCPNLEFTGL 126
S EE+K G PE L I +L+ GL
Sbjct: 130 SDEESKSGIQPEELLELAIQ----------------------------IEELKHLKLRGL 161
Query: 127 MTIGKYGYDTKHGPNPDFLELAKCRKDVCKKLNLNESNVELSMGMSSDLRE 177
MTIG + +F + K+ + + LSMGMS D E
Sbjct: 162 MTIGAPTDSHEDQEE-NFRFMKLL-FWQIKQDSPFGTIDTLSMGMSDDFEE 210
>gnl|CDD|216340 pfam01168, Ala_racemase_N, Alanine racemase, N-terminal domain.
Length = 217
Score = 59.9 bits (146), Expect = 2e-11
Identities = 26/143 (18%), Positives = 42/143 (29%), Gaps = 36/143 (25%)
Query: 33 IETIHDTRLATQVNNAWAKHQPDKKLKVFCQINTSGEENKHGAHPEHAEALVSHVINSCP 92
I T+ A ++ A AK + L+V +++T + G PE AL
Sbjct: 88 IPTVDSLEQAEALSAAAAKA--GRPLRVHLKVDTGM--GRLGFTPEELPALAEA------ 137
Query: 93 NLEFTDKHGAHPEHAEALVSHVINSCPNLEFTGLMTIGKYGYDTKHGPNPDFLELAKCRK 152
+ + P L GLMT D +
Sbjct: 138 ----------------------LAALPGLRLEGLMTHFAC-ADEPDYTERQLARFRELAD 174
Query: 153 DVCKKLNLNESNVELSMGMSSDL 175
+ + LS+G S+ L
Sbjct: 175 RLEAAG---LAPPVLSLGNSAAL 194
>gnl|CDD|143484 cd06808, PLPDE_III, Type III Pyridoxal 5-phosphate (PLP)-Dependent
Enzymes. The fold type III PLP-dependent enzyme family
is predominantly composed of two-domain proteins with
similarity to bacterial alanine racemases (AR) including
eukaryotic ornithine decarboxylases (ODC), prokaryotic
diaminopimelate decarboxylases (DapDC), biosynthetic
arginine decarboxylases (ADC), carboxynorspermidine
decarboxylases (CANSDC), and similar proteins. AR-like
proteins contain an N-terminal PLP-binding TIM-barrel
domain and a C-terminal beta-sandwich domain. They exist
as homodimers with active sites that lie at the
interface between the TIM barrel domain of one subunit
and the beta-sandwich domain of the other subunit. These
proteins play important roles in the biosynthesis of
amino acids and polyamine. The family also includes the
single-domain YBL036c-like proteins, which contain a
single PLP-binding TIM-barrel domain without any N- or
C-terminal extensions. Due to the lack of a second
domain, these proteins may possess only limited D- to
L-alanine racemase activity or non-specific racemase
activity.
Length = 211
Score = 38.8 bits (91), Expect = 6e-04
Identities = 29/171 (16%), Positives = 53/171 (30%), Gaps = 38/171 (22%)
Query: 6 KDIRWHFIGHLQS-NKVPKVIKVPNLEYIETIHDTRLATQVNNAWAKHQPDKKLKVFCQI 64
F+G + +++ + + T+ ++ A K +V +I
Sbjct: 58 PPEPILFLGPCKQVSELEDAAEQGV--IVVTVDSLEELEKLEEAALKA--GPPARVLLRI 113
Query: 65 NTSGEENKHGAHPEHAEALVSHVINSCPNLEFTDKHGAHPEHAEALVSHVINSCPNLEFT 124
+T E K G PE +AL+ E P+L
Sbjct: 114 DTGDENGKFGVRPEELKALL-----------------------ERAKEL-----PHLRLV 145
Query: 125 GLMTIGKYGYDTKHGPNPDFLELAKCRKDVCKKLNLNESNVE-LSMGMSSD 174
GL T + +P L++ +L ++E LS+G S
Sbjct: 146 GLHTHFGSADE---DYSPFVEALSRFV-AALDQLGELGIDLEQLSIGGSFA 192
>gnl|CDD|99876 cd06066, H2MP_NAD-link-bidir, Endopeptidases that belong to the
bidirectional NAD-linked hydrogenase group. This group
of endopeptidases are highly specific carboxyl-terminal
protease (HoxW protease) which releases a 24-amino-acid
peptide from HoxH prior to progression of subunit
assembly. These bidirectional hydrogenases are
heteropentamers encoded by the hox (hydrogen oxidation)
genes, in which complex HoxEFU shows the diaphorase
activity, and HoxYH constitutes the NiFe-hydrogenase.
Length = 139
Score = 30.3 bits (69), Expect = 0.25
Identities = 14/44 (31%), Positives = 16/44 (36%), Gaps = 5/44 (11%)
Query: 74 GAHPEHAEALVSHVINSCPNLEFTDKHGAHPEHAEAL--VSHVI 115
G P AE + P +E H PE AE L VI
Sbjct: 14 GLGPAVAERIEEW---LLPGVEVLAVHQLTPELAEDLAGADRVI 54
>gnl|CDD|223098 COG0019, LysA, Diaminopimelate decarboxylase [Amino acid transport
and metabolism].
Length = 394
Score = 29.6 bits (67), Expect = 0.78
Identities = 13/59 (22%), Positives = 20/59 (33%), Gaps = 13/59 (22%)
Query: 49 WAKHQPDKKLKVFCQIN------------TSGEENKHGAHPEHAEALVSHVINSCPNLE 95
+ P +V +IN T G+ +K G PE A ++ LE
Sbjct: 133 LSAIAPGLVARVSLRINPGVSAGTHEYIATGGKSSKFGISPEEALDVLERAAKL-LGLE 190
>gnl|CDD|233248 TIGR01048, lysA, diaminopimelate decarboxylase. This family
consists of diaminopimelate decarboxylase, an enzyme
which catalyzes the conversion of diaminopimelic acid
into lysine during the last step of lysine biosynthesis
[Amino acid biosynthesis, Aspartate family].
Length = 414
Score = 28.8 bits (65), Expect = 1.5
Identities = 16/63 (25%), Positives = 26/63 (41%), Gaps = 10/63 (15%)
Query: 34 ETIHDTRLATQVN-NAWAKHQPDKKLKVFCQINTSGEENKHGAHPEHAEALVSHVINSCP 92
E R++ +VN AK P I+T +++K G E A + + P
Sbjct: 135 ELGKKARISLRVNPGVDAKTHP--------YISTGLKDSKFGIDVEEALEAYLYALQL-P 185
Query: 93 NLE 95
+LE
Sbjct: 186 HLE 188
>gnl|CDD|143501 cd06828, PLPDE_III_DapDC, Type III Pyridoxal 5-phosphate
(PLP)-Dependent Enzyme Diaminopimelate Decarboxylase.
Diaminopimelate decarboxylase (DapDC, EC 4.1.1.20)
participates in the last step of lysine biosynthesis. It
converts meso-2,6-diaminoheptanedioate to L-lysine. It
is a fold type III PLP-dependent enzyme that contains an
N-terminal PLP-binding TIM-barrel domain and a
C-terminal beta-sandwich domain, similar to bacterial
alanine racemases. DapDC exists as homodimers with
active sites that lie at the interface between the TIM
barrel domain of one subunit and the beta-sandwich
domain of the other subunit. Homodimer formation and the
presence of the PLP cofactor are required for catalytic
activity.
Length = 373
Score = 28.6 bits (65), Expect = 1.6
Identities = 11/40 (27%), Positives = 16/40 (40%), Gaps = 4/40 (10%)
Query: 64 INTSGEENKHGAHPEHAEALVSHVINSCPNLEFTDKHGAH 103
I+T G+++K G E A P L+ G H
Sbjct: 138 ISTGGKDSKFGIPLEQALEAYRRAKEL-PGLKLV---GLH 173
>gnl|CDD|143482 cd00622, PLPDE_III_ODC, Type III Pyridoxal 5-phosphate
(PLP)-Dependent Enzyme Ornithine Decarboxylase. This
subfamily is composed mainly of eukaryotic ornithine
decarboxylases (ODC, EC 4.1.1.17) and ODC-like enzymes
from prokaryotes represented by Vibrio vulnificus
LysineOrnithine decarboxylase. These are fold type III
PLP-dependent enzymes that differ from most bacterial
ODCs which are fold type I PLP-dependent enzymes. ODC
participates in the formation of putrescine by
catalyzing the decarboxylation of ornithine, the first
step in polyamine biosynthesis. Members of this
subfamily contain an N-terminal PLP-binding TIM-barrel
domain and a C-terminal beta-sandwich domain, similar to
bacterial alanine racemases. They exist as homodimers
with active sites that lie at the interface between the
TIM barrel domain of one subunit and the beta-sandwich
domain of the other subunit. Homodimer formation and the
presence of the PLP cofactor are required for catalytic
activity. Also members of this subfamily are proteins
with homology to ODC but do not possess any catalytic
activity, the Antizyme inhibitor (AZI) and ODC-paralogue
(ODC-p). AZI binds to the regulatory protein Antizyme
with a higher affinity than ODC and prevents ODC
degradation. ODC-p is a novel ODC-like protein, present
only in mammals, that is specifically exressed in the
brain and testes. ODC-p may function as a
tissue-specific antizyme inhibitory protein.
Length = 362
Score = 28.6 bits (65), Expect = 1.9
Identities = 14/41 (34%), Positives = 17/41 (41%), Gaps = 8/41 (19%)
Query: 50 AKHQPDKKLKVFCQINTSGEE------NKHGAHPEHAEALV 84
AKH P K+ +I T K GA PE A L+
Sbjct: 107 AKHAPG--AKLLLRIATDDSGALCPLSRKFGADPEEARELL 145
>gnl|CDD|143494 cd06820, PLPDE_III_LS_D-TA_like, Type III Pyridoxal 5-phosphate
(PLP)-Dependent Enzymes, Low Specificity D-Threonine
Aldolase-like. This subfamily is composed of
uncharacterized bacterial proteins with similarity to
low specificity D-threonine aldolase (D-TA), which is a
fold type III PLP-dependent enzyme that catalyzes the
interconversion between D-threonine/D-allo-threonine and
glycine plus acetaldehyde. Both PLP and divalent cations
(eg. Mn2+) are required for catalytic activity. Low
specificity D-TAs show similarity to bacterial alanine
racemase (AR), which contains an N-terminal PLP-binding
TIM-barrel domain and a C-terminal beta-sandwich domain.
AR exists as homodimers with active sites that lie at
the interface between the TIM barrel domain of one
subunit and the beta-sandwich domain of the other
subunit. Based on its similarity to AR, it is possible
that low specificity D-TAs also form dimers in solution.
Experimental data show that the monomeric form of low
specificity D-TAs exhibit full catalytic activity.
Length = 353
Score = 27.3 bits (61), Expect = 4.9
Identities = 13/36 (36%), Positives = 15/36 (41%), Gaps = 1/36 (2%)
Query: 104 PEHAEALVSHVINSCPNLEFTGLMTIGKYGYDTKHG 139
PE A AL I S P L F G+ T + Y
Sbjct: 140 PEDAVALARA-IASAPGLRFRGIFTYPGHSYAPGAL 174
>gnl|CDD|234600 PRK00053, alr, alanine racemase; Reviewed.
Length = 363
Score = 27.1 bits (61), Expect = 5.7
Identities = 10/28 (35%), Positives = 16/28 (57%), Gaps = 1/28 (3%)
Query: 101 GAHPEHAEALVSHVINSCPNLEFTGLMT 128
G PE AEA + + +CPN+ G+ +
Sbjct: 134 GVRPEEAEAALER-LLACPNVRLEGIFS 160
>gnl|CDD|235917 PRK07046, PRK07046, aminotransferase; Validated.
Length = 453
Score = 27.2 bits (61), Expect = 5.8
Identities = 18/59 (30%), Positives = 23/59 (38%), Gaps = 21/59 (35%)
Query: 95 EFTDKHGAHPEHAEALV---SHVINSCPNLEFTGLMTIGKYGYDTKHGPNPDFLELAKC 150
E T ++G LV +H I+S P GY HG PDFL + K
Sbjct: 246 ELTRRYGT------LLVIDETHTISSGPG------------GYTRAHGLEPDFLVVGKP 286
>gnl|CDD|234966 PRK01617, PRK01617, hypothetical protein; Provisional.
Length = 154
Score = 26.5 bits (59), Expect = 5.9
Identities = 14/54 (25%), Positives = 24/54 (44%), Gaps = 8/54 (14%)
Query: 103 HPE-HAEALVSHVINSCPNLEFTGLMTIGKYGYDTKHGPNPD--FLELAKCRKD 153
HP+ HA A + +I N E+ GL T+ ++ G + F+E +
Sbjct: 54 HPDCHAAAWRAEIIAGFANTEWLGL-TV----FEHTWGDADNEGFVEFVARFTE 102
>gnl|CDD|240638 cd12161, GDH_like_1, Putative glycerate dehydrogenase and related
proteins of the D-specific 2-hydroxy dehydrogenase
family. This group contains a variety of proteins
variously identified as glycerate dehydrogenase (GDH,
aka Hydroxypyruvate Reductase) and other enzymes of the
2-hydroxyacid dehydrogenase family. GDH catalyzes the
reversible reaction of (R)-glycerate + NAD+ to
hydroxypyruvate + NADH + H+. 2-hydroxyacid
dehydrogenases catalyze the conversion of a wide variety
of D-2-hydroxy acids to their corresponding keto acids.
The general mechanism is (R)-lactate + acceptor to
pyruvate + reduced acceptor. Formate/glycerate and
related dehydrogenases of the D-specific 2-hydroxyacid
dehydrogenase superfamily include groups such as formate
dehydrogenase, glycerate dehydrogenase, L-alanine
dehydrogenase, and S-adenosylhomocysteine hydrolase.
Despite often low sequence identity, these proteins
typically have a characteristic arrangement of 2 similar
subdomains of the alpha/beta Rossmann-fold NAD+ binding
form. The NAD+ binding domain is inserted within the
linear sequence of the mostly N-terminal catalytic
domain, which has a similar domain structure to the
internal NAD binding domain. Structurally, these domains
are connected by extended alpha helices and create a
cleft in which NAD is bound, primarily to the C-terminal
portion of the 2nd (internal) domain. Some related
proteins have similar structural subdomain but with a
tandem arrangement of the catalytic and NAD-binding
subdomains in the linear sequence. While many members of
this family are dimeric, alanine DH is hexameric and
phosphoglycerate DH is tetrameric.
Length = 315
Score = 26.4 bits (59), Expect = 8.3
Identities = 18/72 (25%), Positives = 30/72 (41%), Gaps = 25/72 (34%)
Query: 113 HVINSCPNLE-----FTGLMTIGKYGYDTKHGPNPDFLELAKCRKDVCKKLNL----NES 163
VI +C NL+ FTG+ D ++L C++ N E+
Sbjct: 62 EVIEACKNLKMISVAFTGV----------------DHVDLEACKERGITVSNAAGYSTEA 105
Query: 164 NVELSMGMSSDL 175
EL++G++ DL
Sbjct: 106 VAELTIGLAIDL 117
>gnl|CDD|107298 cd06303, PBP1_LuxPQ_Quorum_Sensing, Periplasmic binding protein
(LuxP) of autoinducer-2 (AI-2) receptor LuxPQ from
Vibrio harveyi and its close homologs. Periplasmic
binding protein (LuxP) of autoinducer-2 (AI-2) receptor
LuxPQ from Vibrio harveyi and its close homologs from
other bacteria. The members of this group are highly
homologous to a family of periplasmic pentose/hexose
sugar-binding proteins that function as the primary
receptors for chemotaxis and transport of many sugar
based solutes in bacteria and archaea, and that are
members of the type I periplasmic binding protein
superfamily. The Vibrio harveyi AI-2 receptor consists
of two polypeptides, LuxP and LuxQ: LuxP is a
periplasmic binding protein that binds AI-2 by clamping
it between two domains, LuxQ is an integral membrane
protein belonging to the two-component sensor kinase
family. Unlike AI-2 bound to the LsrB receptor in
Salmonella typhimurium, the Vibrio harveyi AI-2
signaling molecule has an unusual furanosyl borate
diester. Hence, many bacteria coordinate their gene
expression according to the local density of their
population by producing species specific AI-2. This
process of quorum sensing allows LuxPQ to control light
production as well as its motility behavior.
Length = 280
Score = 26.6 bits (59), Expect = 8.4
Identities = 11/44 (25%), Positives = 17/44 (38%), Gaps = 13/44 (29%)
Query: 12 FIGHLQSNKVPKVIKVPNLEYIETIHDTRLATQVNNAWAKHQPD 55
I + ++ K+I + N+ T AW KHQP
Sbjct: 76 LIERVLASGKTKII-LQNI------------TTPVKAWLKHQPL 106
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
0.315 0.131 0.402
Gapped
Lambda K H
0.267 0.0768 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,760,069
Number of extensions: 751740
Number of successful extensions: 584
Number of sequences better than 10.0: 1
Number of HSP's gapped: 570
Number of HSP's successfully gapped: 22
Length of query: 181
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 90
Effective length of database: 6,901,388
Effective search space: 621124920
Effective search space used: 621124920
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 56 (25.3 bits)