RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 024237
(270 letters)
>gnl|CDD|215368 PLN02683, PLN02683, pyruvate dehydrogenase E1 component subunit
beta.
Length = 356
Score = 498 bits (1284), Expect = e-180
Identities = 224/258 (86%), Positives = 240/258 (93%), Gaps = 1/258 (0%)
Query: 13 GGSPVARIRPVVSNL-RNYSSAVKQMMVREALNSALDEEMSADPKVFLMGEEVGEYQGAY 71
G + R RP + R Y+SA K+M VR+ALNSALDEEMSADPKVF+MGEEVGEYQGAY
Sbjct: 2 LGQLLRRTRPAAAAAARGYASAAKEMTVRDALNSALDEEMSADPKVFIMGEEVGEYQGAY 61
Query: 72 KISKGLLEKYGPERVLDTPITEAGFTGIGVGAAYYGLKPVVEFMTFNFSMQAIDHIINSA 131
KI+KGLL+KYGP+RVLDTPITEAGFTGIGVGAAY GLKPVVEFMTFNFSMQAIDHIINSA
Sbjct: 62 KITKGLLQKYGPDRVLDTPITEAGFTGIGVGAAYAGLKPVVEFMTFNFSMQAIDHIINSA 121
Query: 132 AKSNYMSSGQISVPIVFRGPNGAAAGVGAQHSHCYAAWYASVPGLKVLSPYSSEDARGLL 191
AK+NYMS+GQISVPIVFRGPNGAAAGVGAQHS C+AAWY+SVPGLKVL+PYSSEDARGLL
Sbjct: 122 AKTNYMSAGQISVPIVFRGPNGAAAGVGAQHSQCFAAWYSSVPGLKVLAPYSSEDARGLL 181
Query: 192 KAAIRDPDPVVFLENELLYGESFPVSAEVLDSSFCLPIGKAKIEREGKDVTITAFSKIVG 251
KAAIRDPDPVVFLENELLYGESFPVSAEVLDSSF LPIGKAKIEREGKDVTI AFSK+VG
Sbjct: 182 KAAIRDPDPVVFLENELLYGESFPVSAEVLDSSFVLPIGKAKIEREGKDVTIVAFSKMVG 241
Query: 252 LSLKAAEILAKEGISAEV 269
+LKAAEILAKEGISAEV
Sbjct: 242 YALKAAEILAKEGISAEV 259
>gnl|CDD|237011 PRK11892, PRK11892, pyruvate dehydrogenase subunit beta;
Provisional.
Length = 464
Score = 440 bits (1135), Expect = e-155
Identities = 164/235 (69%), Positives = 192/235 (81%), Gaps = 3/235 (1%)
Query: 35 KQMMVREALNSALDEEMSADPKVFLMGEEVGEYQGAYKISKGLLEKYGPERVLDTPITEA 94
M VREAL A+ EEM D VF+MGEEV EYQGAYK+++GLL+++G RV+DTPITE
Sbjct: 140 VTMTVREALRDAMAEEMRRDEDVFVMGEEVAEYQGAYKVTQGLLQEFGARRVIDTPITEH 199
Query: 95 GFTGIGVGAAYYGLKPVVEFMTFNFSMQAIDHIINSAAKSNYMSSGQISVPIVFRGPNGA 154
GF GIGVGAA+ GLKP+VEFMTFNF+MQAID IINSAAK+ YMS GQ+ PIVFRGPNGA
Sbjct: 200 GFAGIGVGAAFAGLKPIVEFMTFNFAMQAIDQIINSAAKTLYMSGGQMGCPIVFRGPNGA 259
Query: 155 AAGVGAQHSHCYAAWYASVPGLKVLSPYSSEDARGLLKAAIRDPDPVVFLENELLYGESF 214
AA V AQHS YAAWY+ +PGLKV++PYS+ DA+GLLKAAIRDP+PV+FLENE+LYG+SF
Sbjct: 260 AARVAAQHSQDYAAWYSHIPGLKVVAPYSAADAKGLLKAAIRDPNPVIFLENEILYGQSF 319
Query: 215 PVSAEVLDSSFCLPIGKAKIEREGKDVTITAFSKIVGLSLKAAEILAKEGISAEV 269
V LD F LPIGKA+I REGKDVTI +FS + +LKAAE LAKEGI AEV
Sbjct: 320 DVP--KLD-DFVLPIGKARIHREGKDVTIVSFSIGMTYALKAAEELAKEGIDAEV 371
>gnl|CDD|185502 PTZ00182, PTZ00182, 3-methyl-2-oxobutanate dehydrogenase;
Provisional.
Length = 355
Score = 397 bits (1023), Expect = e-140
Identities = 145/253 (57%), Positives = 176/253 (69%), Gaps = 7/253 (2%)
Query: 21 RPVVSNLRNYS----SAVKQMMVREALNSALDEEMSADPKVFLMGEEVGEYQGAYKISKG 76
S R+ S A +M VREA+NSALDEE++ DPKVF++GE+V +Y G YK +KG
Sbjct: 15 NSFSSASRSSSTESKGATVKMNVREAINSALDEELARDPKVFVLGEDVAQYGGVYKCTKG 74
Query: 77 LLEKYGPERVLDTPITEAGFTGIGVGAAYYGLKPVVEFMTFNFSMQAIDHIINSAAKSNY 136
LL+KYGP+RV DTPITE GF G +GAA GL+P+ EFM +F A D I+N AAK Y
Sbjct: 75 LLDKYGPDRVFDTPITEQGFAGFAIGAAMNGLRPIAEFMFADFIFPAFDQIVNEAAKYRY 134
Query: 137 MSSGQISVPIVFRGPNGAAAGVGAQHSHCYAAWYASVPGLKVLSPYSSEDARGLLKAAIR 196
MS GQ PIV RGPNGA GA HS + A++A VPGLKV++P EDA+GLLKAAIR
Sbjct: 135 MSGGQFDCPIVIRGPNGAVGHGGAYHSQSFEAYFAHVPGLKVVAPSDPEDAKGLLKAAIR 194
Query: 197 DPDPVVFLENELLYGESFPVSAEVLDSSFCLPIGKAKIEREGKDVTITAFSKIVGLSLKA 256
DP+PVVF E +LLY ES V E + LP+GKAK+ REGKDVTI + V ++LKA
Sbjct: 195 DPNPVVFFEPKLLYRESVEVVPEA---DYTLPLGKAKVVREGKDVTIVGYGSQVHVALKA 251
Query: 257 AEILAKEGISAEV 269
AE LAKEGIS EV
Sbjct: 252 AEELAKEGISCEV 264
>gnl|CDD|169719 PRK09212, PRK09212, pyruvate dehydrogenase subunit beta; Validated.
Length = 327
Score = 396 bits (1020), Expect = e-140
Identities = 161/235 (68%), Positives = 191/235 (81%), Gaps = 4/235 (1%)
Query: 35 KQMMVREALNSALDEEMSADPKVFLMGEEVGEYQGAYKISKGLLEKYGPERVLDTPITEA 94
Q+ VREAL A+ EEM DPKVFLMGEEVGEYQGAYK+++GLLE++GP+RV+DTPITE
Sbjct: 2 AQLTVREALRDAMQEEMERDPKVFLMGEEVGEYQGAYKVTQGLLEQFGPKRVIDTPITEH 61
Query: 95 GFTGIGVGAAYYGLKPVVEFMTFNFSMQAIDHIINSAAKSNYMSSGQISVPIVFRGPNGA 154
GF G+ VGAA+ GL+P+VEFMTFNFSMQAID I+NSAAK+NYMS GQ+ PIVFRGPNGA
Sbjct: 62 GFAGLAVGAAFAGLRPIVEFMTFNFSMQAIDQIVNSAAKTNYMSGGQLKCPIVFRGPNGA 121
Query: 155 AAGVGAQHSHCYAAWYASVPGLKVLSPYSSEDARGLLKAAIRDPDPVVFLENELLYGESF 214
AA V AQHS CYAAWY+ +PGLKV++PY + D +GLLK AIRDP+PV+FLENE+LYG S
Sbjct: 122 AARVAAQHSQCYAAWYSHIPGLKVVAPYFAADCKGLLKTAIRDPNPVIFLENEILYGHSH 181
Query: 215 PVSAEVLDSSFCLPIGKAKIEREGKDVTITAFSKIVGLSLKAAEILAKEGISAEV 269
EV + +PIGKA I REG DVTI FS V L+L+AAE+L KEGIS EV
Sbjct: 182 ----EVPEEEESIPIGKAAILREGSDVTIVTFSIQVKLALEAAELLEKEGISVEV 232
>gnl|CDD|223101 COG0022, AcoB, Pyruvate/2-oxoglutarate dehydrogenase complex,
dehydrogenase (E1) component, eukaryotic type, beta
subunit [Energy production and conversion].
Length = 324
Score = 372 bits (958), Expect = e-130
Identities = 127/234 (54%), Positives = 162/234 (69%), Gaps = 3/234 (1%)
Query: 36 QMMVREALNSALDEEMSADPKVFLMGEEVGEYQGAYKISKGLLEKYGPERVLDTPITEAG 95
QM + EA+N A+DEEM D +V ++GE+VG Y G ++++KGL EK+G ERV+DTPI E+G
Sbjct: 1 QMTMIEAINEAMDEEMERDERVVVLGEDVGVYGGVFRVTKGLQEKFGEERVIDTPIAESG 60
Query: 96 FTGIGVGAAYYGLKPVVEFMTFNFSMQAIDHIINSAAKSNYMSSGQISVPIVFRGPNGAA 155
GI VGAA GL+P+VE +F A D I+N AAK Y S GQ +VPIV R PNG
Sbjct: 61 IAGIAVGAALTGLRPIVEIQFADFIYPAFDQIVNQAAKIRYRSGGQFTVPIVIRTPNGGG 120
Query: 156 AGVGAQHSHCYAAWYASVPGLKVLSPYSSEDARGLLKAAIRDPDPVVFLENELLYGESFP 215
G GAQHS A +A +PGLKV+ P + DA+GLLKAAIRDPDPV+FLE++ LY
Sbjct: 121 IGGGAQHSQSLEALFAHIPGLKVVMPSTPYDAKGLLKAAIRDPDPVIFLEHKRLYRSF-- 178
Query: 216 VSAEVLDSSFCLPIGKAKIEREGKDVTITAFSKIVGLSLKAAEILAKEGISAEV 269
EV + + +P+GKAKI REG DVTI + +V +L+AAE L KEGISAEV
Sbjct: 179 -KGEVPEEDYTIPLGKAKIVREGSDVTIVTYGAMVHTALEAAEELEKEGISAEV 231
>gnl|CDD|132919 cd07036, TPP_PYR_E1-PDHc-beta_like, Pyrimidine (PYR) binding domain
of the beta subunits of the E1 components of human
pyruvate dehydrogenase complex (E1- PDHc) and related
proteins. Thiamine pyrophosphate (TPP) family,
pyrimidine (PYR) binding domain of the beta subunits of
the E1 components of: human pyruvate dehydrogenase
complex (E1- PDHc), the acetoin dehydrogenase complex
(ADC), and the branched chain alpha-keto acid
dehydrogenase/2-oxoisovalerate dehydrogenase complex
(BCADC), subfamily. The PYR domain is found in many key
metabolic enzymes which use TPP (also known as thiamine
diphosphate) as a cofactor. TPP binds in the cleft
formed by a PYR domain and a PP domain. The PYR domain,
binds the aminopyrimidine ring of TPP, the PP domain
binds the diphosphate residue. A polar interaction
between the conserved glutamate of the PYR domain and
the N1' of the TPP aminopyrimidine ring is shared by
most TPP-dependent enzymes, and participates in the
activation of TPP. The PYR and PP domains have a common
fold, but do not share strong sequence conservation. The
PP domain is not included in this sub-family. E1-PDHc is
an alpha2beta2 dimer-of-heterodimers having two active
sites lying between PYR and PP domains of separate
subunits, the PYR domains are arranged on the beta
subunit, the PP domains on the alpha subunits. PDHc
catalyzes the irreversible oxidative decarboxylation of
pyruvate to produce acetyl-CoA in the bridging step
between glycolysis and the citric acid cycle. ADC
participates in the breakdown of acetoin. BCADC
catalyzes the oxidative decarboxylation of
4-methyl-2-oxopentanoate, 3-methyl-2-oxopentanoate and
3-methyl-2-oxobutanoate during the breakdown of branched
chain amino acids.
Length = 167
Score = 305 bits (785), Expect = e-107
Identities = 99/167 (59%), Positives = 129/167 (77%)
Query: 41 EALNSALDEEMSADPKVFLMGEEVGEYQGAYKISKGLLEKYGPERVLDTPITEAGFTGIG 100
+A+N ALDEEM DP+V ++GE+VG+Y G +K++KGLL+K+GP+RV+DTPI EAG G+
Sbjct: 1 QAINEALDEEMERDPRVVVLGEDVGDYGGVFKVTKGLLDKFGPDRVIDTPIAEAGIVGLA 60
Query: 101 VGAAYYGLKPVVEFMTFNFSMQAIDHIINSAAKSNYMSSGQISVPIVFRGPNGAAAGVGA 160
VGAA GL+P+VE M +F++ A D I+N AAK YMS GQ VPIV RGPNG G GA
Sbjct: 61 VGAAMNGLRPIVEIMFADFALPAFDQIVNEAAKLRYMSGGQFKVPIVIRGPNGGGIGGGA 120
Query: 161 QHSHCYAAWYASVPGLKVLSPYSSEDARGLLKAAIRDPDPVVFLENE 207
QHS AW+A +PGLKV++P + DA+GLLKAAIRD DPV+FLE++
Sbjct: 121 QHSQSLEAWFAHIPGLKVVAPSTPYDAKGLLKAAIRDDDPVIFLEHK 167
>gnl|CDD|177066 CHL00144, odpB, pyruvate dehydrogenase E1 component beta subunit;
Validated.
Length = 327
Score = 228 bits (582), Expect = 9e-74
Identities = 103/234 (44%), Positives = 158/234 (67%), Gaps = 4/234 (1%)
Query: 36 QMMVREALNSALDEEMSADPKVFLMGEEVGEYQGAYKISKGLLEKYGPERVLDTPITEAG 95
++ + EAL A+DEEM+ DP+VF++GE+VG Y G+YK++KGL EKYG RVLDTPI E
Sbjct: 3 EVFLFEALREAIDEEMARDPRVFVIGEDVGHYGGSYKVTKGLHEKYGDLRVLDTPIAENS 62
Query: 96 FTGIGVGAAYYGLKPVVEFMTFNFSMQAIDHIINSAAKSNYMSSGQISVPIVFRGPNGAA 155
FTG+ +GAA GL+P+VE M F + A + I N+A +Y S G ++PIV RGP G
Sbjct: 63 FTGMAIGAAMTGLRPIVEGMNMGFLLLAFNQISNNAGMLHYTSGGNFTIPIVIRGPGGVG 122
Query: 156 AGVGAQHSHCYAAWYASVPGLKVLSPYSSEDARGLLKAAIRDPDPVVFLENELLYGESFP 215
+GA+HS +++ SVPGL++++ + +A+GLLK+AIR +PV+F E+ LLY
Sbjct: 123 RQLGAEHSQRLESYFQSVPGLQIVACSTPYNAKGLLKSAIRSNNPVIFFEHVLLYN---- 178
Query: 216 VSAEVLDSSFCLPIGKAKIEREGKDVTITAFSKIVGLSLKAAEILAKEGISAEV 269
+ E+ D+ + LP+ KA++ R G D+TI +S++ L+A ++L ++G E+
Sbjct: 179 LKEEIPDNEYLLPLEKAEVVRPGNDITILTYSRMRHHVLQAVKVLVEKGYDPEI 232
>gnl|CDD|217226 pfam02779, Transket_pyr, Transketolase, pyrimidine binding domain.
This family includes transketolase enzymes, pyruvate
dehydrogenases, and branched chain alpha-keto acid
decarboxylases.
Length = 172
Score = 165 bits (421), Expect = 2e-51
Identities = 60/179 (33%), Positives = 85/179 (47%), Gaps = 9/179 (5%)
Query: 35 KQMMVREALNSALDEEMSADPKVFLMGEEVGEYQGAYKISKGLLEKYGPERVLDTPITEA 94
K++ R+A AL E DP+V G +V G + ++KGLL G RV+DT I E
Sbjct: 1 KKIATRKASGEALAELAKRDPRVVGGGADVA--GGTFTVTKGLLHPQGDGRVIDTGIAEQ 58
Query: 95 GFTGIGVGAAYYGLKPVVEFMTFNFSMQAIDHIINSAAKSNYMSSGQISVP-IVFRGPNG 153
GI G A +GL P VE +F+ A +Y + G++ VP +V R P G
Sbjct: 59 AMVGIANGMALHGLLPPVEATFGDFAN------RADDAIRHYAALGKLPVPFVVTRDPIG 112
Query: 154 AAAGVGAQHSHCYAAWYASVPGLKVLSPYSSEDARGLLKAAIRDPDPVVFLENELLYGE 212
S A+ ++P LKV+ P + + +GLL+AAI D PVV L
Sbjct: 113 VGEDGPTHQSQEDLAFLRAIPNLKVVRPSDAAETKGLLRAAIEDDGPVVLRLPRQLLRH 171
>gnl|CDD|214865 smart00861, Transket_pyr, Transketolase, pyrimidine binding domain.
Transketolase (TK) catalyzes the reversible transfer of
a two-carbon ketol unit from xylulose 5-phosphate to an
aldose receptor, such as ribose 5-phosphate, to form
sedoheptulose 7-phosphate and glyceraldehyde 3-
phosphate. This enzyme, together with transaldolase,
provides a link between the glycolytic and
pentose-phosphate pathways. TK requires thiamine
pyrophosphate as a cofactor. In most sources where TK
has been purified, it is a homodimer of approximately 70
Kd subunits. TK sequences from a variety of eukaryotic
and prokaryotic sources show that the enzyme has been
evolutionarily conserved. In the peroxisomes of
methylotrophic yeast Hansenula polymorpha, there is a
highly related enzyme, dihydroxy-acetone synthase (DHAS)
(also known as formaldehyde transketolase), which
exhibits a very unusual specificity by including
formaldehyde amongst its substrates.
Length = 136
Score = 106 bits (267), Expect = 8e-29
Identities = 51/128 (39%), Positives = 67/128 (52%), Gaps = 12/128 (9%)
Query: 87 LDTPITEAGFTGIGVGAAYYGLKPVVEFMTFNFSMQAIDHIINSAAKSNYMSSGQISVPI 146
+DT I E G G A +GL+PVVE F F +A D I ++ A N VP+
Sbjct: 18 IDTGIAEQAMVGFAAGLALHGLRPVVEIF-FTFFDRAKDQIRSAGASGN--------VPV 68
Query: 147 VFR-GPNGAAAGVGA-QHSHCYAAWYASVPGLKVLSPYSSEDARGLLKAAIRDPDP-VVF 203
VFR G G HS A ++PGLKV++P +A+GLL+AAIRD P V+
Sbjct: 69 VFRHDGGGGVGEDGPTHHSIEDEALLRAIPGLKVVAPSDPAEAKGLLRAAIRDDGPVVIR 128
Query: 204 LENELLYG 211
LE + LY
Sbjct: 129 LERKSLYR 136
>gnl|CDD|132916 cd07033, TPP_PYR_DXS_TK_like, Pyrimidine (PYR) binding domain of
1-deoxy-D-xylulose-5-phosphate synthase (DXS),
transketolase (TK), and related proteins. Thiamine
pyrophosphate (TPP) family, pyrimidine (PYR) binding
domain of 1-deoxy-D-xylulose-5-phosphate synthase (DXS),
transketolase (TK), and the beta subunits of the E1
component of the human pyruvate dehydrogenase complex
(E1- PDHc), subfamily. The PYR domain is found in many
key metabolic enzymes which use TPP (also known as
thiamine diphosphate) as a cofactor. TPP binds in the
cleft formed by a PYR domain and a PP domain. The PYR
domain, binds the aminopyrimidine ring of TPP, the PP
domain binds the diphosphate residue. A polar
interaction between the conserved glutamate of the PYR
domain and the N1' of the TPP aminopyrimidine ring is
shared by most TPP-dependent enzymes, and participates
in the activation of TPP. The PYR and PP domains have a
common fold, but do not share strong sequence
conservation. The PP domain is not included in this
sub-family. Like many TPP-dependent enzymes DXS and TK
are homodimers having a PYR and a PP domain on the same
subunit. TK has two active sites per dimer which lie
between PYR and PP domains of different subunits. For
DXS each active site is located at the interface of a
PYR and a PP domain from the same subunit. E1-PDHc is an
alpha2beta2 dimer-of-heterodimers having two active
sites but having the PYR and PP domains arranged on
separate subunits, the PYR domains on the beta subunits,
the PP domains on the alpha subunits. DXS is a
regulatory enzyme of the mevalonate-independent pathway
involved in terpenoid biosynthesis, it catalyzes a
transketolase-type condensation of pyruvate with
D-glyceraldehyde-3-phosphate to form
1-deoxy-D-xylulose-5-phosphate (DXP) and carbon dioxide.
TK catalyzes the transfer of a two-carbon unit from
ketose phosphates to aldose phosphates. In heterotrophic
organisms, TK provides a link between glycolysis and the
pentose phosphate pathway and provides precursors for
nucleotide, aromatic amino acid and vitamin
biosynthesis. TK also plays a central role in the Calvin
cycle in plants. PDHc catalyzes the irreversible
oxidative decarboxylation of pyruvate to produce
acetyl-CoA in the bridging step between glycolysis and
the citric acid cycle. This subfamily includes the beta
subunits of the E1 component of the acetoin
dehydrogenase complex (ADC) and the branched chain
alpha-keto acid dehydrogenase/2-oxoisovalerate
dehydrogenase complex (BCADC). ADC participates in the
breakdown of acetoin. BCADC catalyzes the oxidative
decarboxylation of 4-methyl-2-oxopentanoate,
3-methyl-2-oxopentanoate and 3-methyl-2-oxobutanoate
during the breakdown of branched chain amino acids.
Length = 156
Score = 83.6 bits (208), Expect = 5e-20
Identities = 47/167 (28%), Positives = 69/167 (41%), Gaps = 19/167 (11%)
Query: 41 EALNSALDEEMSADPKVFLMGEEVGEYQGAYKISKGLLEKYGPERVLDTPITEAGFTGIG 100
+A AL E DP++ + ++G G K +K P+R +D I E GI
Sbjct: 1 KAFGEALLELAKKDPRIVALSADLGGSTGLDKFAKKF-----PDRFIDVGIAEQNMVGIA 55
Query: 101 VGAAYYGLKPVVEFMTFNFSMQAIDHIINSAAKSNYMSSGQISVPIVFRGPNGAAAGVGA 160
G A +GLKP V +F F +A D I + A N +P+ F G A VG
Sbjct: 56 AGLALHGLKPFVSTFSF-FLQRAYDQIRHDVALQN--------LPVKFVG-THAGISVGE 105
Query: 161 ----QHSHCYAAWYASVPGLKVLSPYSSEDARGLLKAAIRDPDPVVF 203
A ++P + VL P + + L+AA+ PV
Sbjct: 106 DGPTHQGIEDIALLRAIPNMTVLRPADANETAAALEAALEYDGPVYI 152
>gnl|CDD|132915 cd06586, TPP_enzyme_PYR, Pyrimidine (PYR) binding domain of
thiamine pyrophosphate (TPP)-dependent enzymes.
Thiamine pyrophosphate (TPP) family, pyrimidine (PYR)
binding domain; found in many key metabolic enzymes
which use TPP (also known as thiamine diphosphate) as a
cofactor. TPP binds in the cleft formed by a PYR domain
and a PP domain. The PYR domain, binds the
aminopyrimidine ring of TPP, the PP domain binds the
diphosphate residue. A polar interaction between the
conserved glutamate of the PYR domain and the N1' of the
TPP aminopyrimidine ring is shared by most TPP-dependent
enzymes, and participates in the activation of TPP. The
PYR and PP domains have a common fold, but do not share
strong sequence conservation. The PP domain is not
included in this group. Most TPP-dependent enzymes have
the PYR and PP domains on the same subunit although
these domains can be alternatively arranged in the
primary structure. In the case of 2-oxoisovalerate
dehydrogenase (2OXO), sulfopyruvate decarboxylase
(ComDE), and the E1 component of human pyruvate
dehydrogenase complex (E1- PDHc) the PYR and PP domains
appear on different subunits. TPP-dependent enzymes are
multisubunit proteins, the smallest catalytic unit being
a dimer-of-active sites. For many of these enzymes the
active sites lie between PP and PYR domains on different
subunits. However, for the homodimeric enzymes
1-deoxy-D-xylulose 5-phosphate synthase (DXS) and
Desulfovibrio africanus pyruvate:ferredoxin
oxidoreductase (PFOR), each active site lies at the
interface of the PYR and PP domains from the same
subunit.
Length = 154
Score = 80.9 bits (200), Expect = 6e-19
Identities = 41/169 (24%), Positives = 63/169 (37%), Gaps = 23/169 (13%)
Query: 46 ALDEEMSADPKVFLMGEEVGEYQGAYKISKGLLE--KYGPERVLDTPITEAGFTGIGVGA 103
A E ++A + G E LL+ + G +R++DT I E G G G
Sbjct: 2 AFAEVLTAWGVRHVFGYPGDEI-------SSLLDALREGDKRIIDTVIHELGAAGAAAGY 54
Query: 104 AYYGLKPVVEFMTFNFSMQAIDHIINSAAKSNYMSSGQISVPIVFRG--PNGAAAGVGAQ 161
A G PVV + + AI+ + ++AA+ +P+VF +A
Sbjct: 55 ARAGGPPVVIVTSGTGLLNAINGLADAAAE---------HLPVVFLIGARGISAQAKQTF 105
Query: 162 HSHCYAAWYASVPGLKVLSPYSSEDARGLLKAAIRD---PDPVVFLENE 207
S Y S+P + SP +E G+ A PVV
Sbjct: 106 QSMFDLGMYRSIPEANISSPSPAELPAGIDHAIRTAYASQGPVVVRLPR 154
>gnl|CDD|226467 COG3958, COG3958, Transketolase, C-terminal subunit [Carbohydrate
transport and metabolism].
Length = 312
Score = 78.9 bits (195), Expect = 5e-17
Identities = 64/237 (27%), Positives = 98/237 (41%), Gaps = 28/237 (11%)
Query: 39 VREALNSALDEEMSADPKVFLMGEEVGEYQGAYKISKGLLEKYGPERVLDTPITEAGFTG 98
+R+ L E + + ++ ++ G K P+R + I E G
Sbjct: 9 LRKVYGETLAELGRKNSDIVVLDADLSSSTKT-----GYFAKEFPDRFFNVGIAEQDMVG 63
Query: 99 IGVGAAYYGLKPVVEFMTFNFSM----QAIDHIINSAAKSNYMSSGQISVPIVFRGPNGA 154
G A G KP V F+ +A + I NS A +N ++V IV
Sbjct: 64 TAAGLALAGKKPFV----STFAAFLSRRAWEQIRNSIAYNN------LNVKIVATHAGVT 113
Query: 155 AAGVGAQHSHCYA--AWYASVPGLKVLSPYSSEDARGLLKAAIRDPDPVVFLENELLYGE 212
G+ H A +P + V++P + + R +L PV ++ L
Sbjct: 114 YGEDGSSH-QALEDIAIMRGLPNMTVIAPADAVETRAILDQIADYKGPV-YMR---LGRG 168
Query: 213 SFPVSAEVLDSSFCLPIGKAKIEREGKDVTITAFSKIVGLSLKAAEILAKEGISAEV 269
PV + +F IGKA + R+G D+TI A +V +L+AAEIL KEGISA V
Sbjct: 169 KVPVVVDEGGYTF--EIGKANVLRDGSDLTIIATGVMVAEALEAAEILKKEGISAAV 223
>gnl|CDD|224076 COG1154, Dxs, Deoxyxylulose-5-phosphate synthase [Coenzyme
metabolism / Lipid metabolism].
Length = 627
Score = 65.3 bits (160), Expect = 5e-12
Identities = 56/195 (28%), Positives = 82/195 (42%), Gaps = 27/195 (13%)
Query: 83 PERVLDTPITEAGFTGIGVGAAYYGLKPVVE-FMTFNFSMQ-AIDHIINSAAKSNYMSSG 140
P+R D I E G A G+KPVV + TF +Q A D +I+ A N
Sbjct: 357 PDRFFDVGIAEQHAVTFAAGLAAEGMKPVVAIYSTF---LQRAYDQLIHDVAIQN----- 408
Query: 141 QISVPIVF---RGPNGAAAGVGAQHSHCYA-AWYASVPGLKVLSPYSSEDARGLLKAAIR 196
+P+ F R G G H + ++ +P + +++P E+ R +L A+
Sbjct: 409 ---LPVTFAIDRA--GIVGADGPTHQGLFDLSFLRCIPNMVIMAPRDEEELRQMLYTALA 463
Query: 197 -DPDPVVF-LENELLYGESFPVSAEVLDSSFCLPIGKAKIEREGKDVTITAFSKIVGLSL 254
D PV G E L IGK ++ +EG+ V I AF ++ +L
Sbjct: 464 QDDGPVAIRYPRGNGVGVILTPELEPL------EIGKGELLKEGEKVAILAFGTMLPEAL 517
Query: 255 KAAEILAKEGISAEV 269
K AE L GIS V
Sbjct: 518 KVAEKLNAYGISVTV 532
>gnl|CDD|217227 pfam02780, Transketolase_C, Transketolase, C-terminal domain. The
C-terminal domain of transketolase has been proposed as
a regulatory molecule binding site.
Length = 124
Score = 59.1 bits (144), Expect = 3e-11
Identities = 27/40 (67%), Positives = 32/40 (80%)
Query: 230 GKAKIEREGKDVTITAFSKIVGLSLKAAEILAKEGISAEV 269
GKA+I REG DVTI A+ +V +L+AAE LAKEGISAEV
Sbjct: 1 GKAEILREGDDVTIVAYGSMVHEALEAAEELAKEGISAEV 40
>gnl|CDD|183601 PRK12571, PRK12571, 1-deoxy-D-xylulose-5-phosphate synthase;
Provisional.
Length = 641
Score = 59.4 bits (144), Expect = 4e-10
Identities = 56/203 (27%), Positives = 85/203 (41%), Gaps = 29/203 (14%)
Query: 76 GLLEKYGPERVLDTPITEAGFTGIGVGAAYYGLKPVVEFMTFNFSMQAIDHIINSAAKSN 135
L+K P RV D I E G A GLKP + F + D +++ A N
Sbjct: 353 DKLQKRFPNRVFDVGIAEQHAVTFAAGLAAAGLKPFCAVYS-TFLQRGYDQLLHDVALQN 411
Query: 136 YMSSGQISVPIVF---RGPNGAAAGV----GAQHSHCY-AAWYASVPGLKVLSPYSSEDA 187
+P+ F R AG+ GA H+ + A+ ++P + V++P +
Sbjct: 412 --------LPVRFVLDR------AGLVGADGATHAGAFDLAFLTNLPNMTVMAPRDEAEL 457
Query: 188 RGLLKAAI-RDPDPVVFLENELLYGESFPVSAEVLDSSFCLPIGKAKIEREGKDVTITAF 246
R +L+ A D P+ + V E+ L IGK ++ REG DV I +
Sbjct: 458 RHMLRTAAAHDDGPIAVR-----FPRGEGVGVEIPAEGTILGIGKGRVPREGPDVAILSV 512
Query: 247 SKIVGLSLKAAEILAKEGISAEV 269
+ L AA++L EGIS V
Sbjct: 513 GAHLHECLDAADLLEAEGISVTV 535
>gnl|CDD|235470 PRK05444, PRK05444, 1-deoxy-D-xylulose-5-phosphate synthase;
Provisional.
Length = 580
Score = 58.2 bits (142), Expect = 1e-09
Identities = 60/203 (29%), Positives = 90/203 (44%), Gaps = 51/203 (25%)
Query: 79 EKYGPERVLDTPITE------AGFTGIGVGAAYYGLKPVVE-FMTFNFSMQ-AIDHIINS 130
+++ P+R D I E A G A GLKPVV + TF +Q A D +I+
Sbjct: 317 KRF-PDRYFDVGIAEQHAVTFAA------GLATEGLKPVVAIYSTF---LQRAYDQVIHD 366
Query: 131 AAKSNYMSSGQISVPIVF---RGPNGAAAGV----GAQHSHCY-AAWYASVPGLKVLSPY 182
A N +P+ F R AG+ G H + ++ +P + +++P
Sbjct: 367 VALQN--------LPVTFAIDR------AGLVGADGPTHQGAFDLSYLRCIPNMVIMAPS 412
Query: 183 SSEDARGLLKAAIRDPD-PVVFLENELLY--GESFPVSAEVLDSSFCLPIGKAKIEREGK 239
+ R +L A+ D P+ Y G V L+ LPIGK ++ REG+
Sbjct: 413 DENELRQMLYTALAYDDGPIAIR-----YPRGNGVGVELPELEP---LPIGKGEVLREGE 464
Query: 240 DVTITAFSKIVGLSLKAAEILAK 262
DV I AF ++ +LKAAE LA
Sbjct: 465 DVAILAFGTMLAEALKAAERLAS 487
>gnl|CDD|129308 TIGR00204, dxs, 1-deoxy-D-xylulose-5-phosphate synthase. DXP
synthase is a thiamine diphosphate-dependent enzyme
related to transketolase and the pyruvate dehydrogenase
E1-beta subunit. By an acyloin condensation of pyruvate
with glyceraldehyde 3-phosphate, it produces
1-deoxy-D-xylulose 5-phosphate, a precursor of thiamine
diphosphate (TPP), pyridoxal phosphate, and the
isoprenoid building block isopentenyl diphosphate (IPP)
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Other, Biosynthesis of cofactors, prosthetic
groups, and carriers, Pyridoxine, Biosynthesis of
cofactors, prosthetic groups, and carriers, Thiamine].
Length = 617
Score = 51.7 bits (124), Expect = 1e-07
Identities = 47/197 (23%), Positives = 80/197 (40%), Gaps = 18/197 (9%)
Query: 76 GLLEKYGPERVLDTPITEAGFTGIGVGAAYYGLKPVVEFMTFNFSMQAIDHIINSAAKSN 135
K+ P+R D I E G A G KP V + F +A D +++
Sbjct: 345 KFSRKF-PDRYFDVAIAEQHAVTFAAGMAIEGYKPFVAIYS-TFLQRAYDQVVHDVCIQK 402
Query: 136 YMSSGQISVPIVFRGPNGAAAGV-GAQHSHCY-AAWYASVPGLKVLSPYSSEDARGLLKA 193
+P++F G G H + ++ +P + +++P + R +L
Sbjct: 403 --------LPVLFAIDRAGIVGADGETHQGAFDISYLRCIPNMVIMAPSDENELRQMLYT 454
Query: 194 AIR-DPDPVVFLENELLYGESFPVSAEVLDSSFCLPIGKAKIEREGKDVTITAFSKIVGL 252
D P+ Y V E+ LPIGK+++ R+G+ + I F +V
Sbjct: 455 GYHYDDGPIAVR-----YPRGNAVGVELTPEPEKLPIGKSEVLRKGEKILILGFGTLVPE 509
Query: 253 SLKAAEILAKEGISAEV 269
+L+ AE L ++GI A V
Sbjct: 510 ALEVAESLNEKGIEATV 526
>gnl|CDD|177878 PLN02234, PLN02234, 1-deoxy-D-xylulose-5-phosphate synthase.
Length = 641
Score = 46.6 bits (110), Expect = 7e-06
Identities = 55/228 (24%), Positives = 90/228 (39%), Gaps = 22/228 (9%)
Query: 46 ALDEEMSADPKVFLMGEEVGEYQGAYKISKGLLEKYGPERVLDTPITEAGFTGIGVGAAY 105
AL E AD + + +G G ++ L E P R D I E G A
Sbjct: 366 ALIAEAEADKDIVAIHAAMG---GGTMLN--LFESRFPTRCFDVGIAEQHAVTFAAGLAC 420
Query: 106 YGLKPVVEFMTFNFSMQAIDHIINSAAKSNYMSSGQISVPIVFRGPNGAAAGVGAQHSHC 165
GLKP + +F +A D +++ +P+ F G +HC
Sbjct: 421 EGLKPFCTIYS-SFMQRAYDQVVHDVDLQK--------LPVRFAIDRAGLMGADGP-THC 470
Query: 166 YA---AWYASVPGLKVLSPYSSEDARGLL-KAAIRDPDPVVFLENELLYGESFPVSAEVL 221
A + A +P + V++P + ++ AA D P F + G VS
Sbjct: 471 GAFDVTFMACLPNMIVMAPSDEAELFNMVATAAAIDDRPSCFRYHR---GNGIGVSLPPG 527
Query: 222 DSSFCLPIGKAKIEREGKDVTITAFSKIVGLSLKAAEILAKEGISAEV 269
+ L IG+ +I R+G+ V + + V L+AA +L++ G+ V
Sbjct: 528 NKGVPLQIGRGRILRDGERVALLGYGSAVQRCLEAASMLSERGLKITV 575
>gnl|CDD|237053 PRK12315, PRK12315, 1-deoxy-D-xylulose-5-phosphate synthase;
Provisional.
Length = 581
Score = 41.5 bits (98), Expect = 3e-04
Identities = 56/255 (21%), Positives = 99/255 (38%), Gaps = 53/255 (20%)
Query: 28 RNYSSAVKQMMVRE--------ALNSALDEEMSADPKVFLMGEEVGEYQGAYKISKGLLE 79
+YSS ++++ A+N+A+ P VF + E +Y
Sbjct: 278 ESYSSVTLDYLLKKIKEGKPVVAINAAI-------PGVFGLKEFRKKY------------ 318
Query: 80 KYGPERVLDTPITEAGFTGIGVGAAYYGLKPVVEFMTFNFSMQAIDHIINSAAKSNYMSS 139
P++ +D I E G A G +PV+ F+ F +A D + + A +N
Sbjct: 319 ---PDQYVDVGIAEQESVAFASGIAANGARPVI-FVNSTFLQRAYDQLSHDLAINNN--- 371
Query: 140 GQISVPIVFRGPNGAAAGVGAQHSHCYA-AWYASVPGLKVLSPYSSEDARGLLKAAIRDP 198
P V G+ +G H + +++P L L+P + E+ +L+ A+
Sbjct: 372 -----PAVMIVFGGSISGNDVTHLGIFDIPMISNIPNLVYLAPTTKEELIAMLEWALTQH 426
Query: 199 DPVVFL---ENELLYGESFPVSAEVLDSSFCLPIGKAKIEREGKDVTITAFSKIVGLSLK 255
+ V + E+ + G D S K ++ + G+ V I A L K
Sbjct: 427 EHPVAIRVPEHGVESGP-----TVDTDYSTL----KYEVTKAGEKVAILALGDFYELGEK 477
Query: 256 AAEILAKE-GISAEV 269
A+ L +E GI A +
Sbjct: 478 VAKKLKEELGIDATL 492
>gnl|CDD|178194 PLN02582, PLN02582, 1-deoxy-D-xylulose-5-phosphate synthase.
Length = 677
Score = 38.3 bits (89), Expect = 0.003
Identities = 48/192 (25%), Positives = 74/192 (38%), Gaps = 19/192 (9%)
Query: 83 PERVLDTPITEAGFTGIGVGAAYYGLKPVVEFMTFNFSMQAIDHIINSAAKSNYMSSGQI 142
P R D I E G A GLKP + F + D +++
Sbjct: 397 PTRCFDVGIAEQHAVTFAAGLACEGLKPFCAIYSS-FLQRGYDQVVHDVDLQK------- 448
Query: 143 SVPIVFRGPNGAAAGVGAQH-SHCYA---AWYASVPGLKVLSPYSSEDARGLL-KAAIRD 197
+P+ F A VGA +HC A + A +P + V++P + ++ AA D
Sbjct: 449 -LPVRF--AMDRAGLVGADGPTHCGAFDVTYMACLPNMVVMAPSDEAELFHMVATAAAID 505
Query: 198 PDPVVFLENELLYGESFPVSAEVLDSSFCLPIGKAKIEREGKDVTITAFSKIVGLSLKAA 257
P F G V + + +GK +I EG+ V + + V L AA
Sbjct: 506 DRPSCF---RYPRGNGIGVQLPPNNKGIPIEVGKGRILLEGERVALLGYGTAVQSCLAAA 562
Query: 258 EILAKEGISAEV 269
+L + G+SA V
Sbjct: 563 SLLERHGLSATV 574
>gnl|CDD|177870 PLN02225, PLN02225, 1-deoxy-D-xylulose-5-phosphate synthase.
Length = 701
Score = 35.5 bits (81), Expect = 0.025
Identities = 55/257 (21%), Positives = 103/257 (40%), Gaps = 44/257 (17%)
Query: 23 VVSNLRNYSSAVKQMMVREALNSALDEEMSADPKVFLMGEEVGEYQGAYKISKGLLEKYG 82
+V + R YS + +V EA E D V G E+ ++ E++
Sbjct: 376 MVKDRRTYSDCFVEALVMEA-------EKDRDIVVVHAGMEMDASLITFQ------ERF- 421
Query: 83 PERVLDTPITEAGFTGIGVGAAYYGLKPVVEFMTFNFSMQAIDHIINSAAKSNYMSSGQI 142
P+R + + E G + GLKP + F +A D +++ + +
Sbjct: 422 PDRFFNVGMAEQHAVTFSAGLSSGGLKPFC-IIPSAFLQRAYDQVVHDVDRQR----KAV 476
Query: 143 SVPIVFRGPNGAAAGVGAQHSHCYA---AWYASVPGLKVLSPYSSEDARGLLKAAIRDPD 199
I G G+ V C A A+ +S+P + ++P ++ ++ A D
Sbjct: 477 RFVITSAGLVGSDGPV-----QCGAFDIAFMSSLPNMIAMAPADEDELVNMVATAAYVTD 531
Query: 200 -PVVFLENELLYGESFPVSAEVLDSSFCLP------IGKAKIEREGKDVTITAFSKIVGL 252
PV F FP +++ ++ +P IG+ ++ EG+DV + + +V
Sbjct: 532 RPVCF---------RFP-RGSIVNMNYLVPTGLPIEIGRGRVLVEGQDVALLGYGAMVQN 581
Query: 253 SLKAAEILAKEGISAEV 269
L A +L+K G++ V
Sbjct: 582 CLHAHSLLSKLGLNVTV 598
>gnl|CDD|193549 cd05674, M20_yscS, M20 Peptidase, carboxypeptidase yscS. Peptidase
M20 family, yscS (GlyX-carboxypeptidase, CPS1,
carboxypeptidase S, carboxypeptidase a, carboxypeptidase
yscS, glycine carboxypeptidase)-like subfamily. This
group mostly contains proteins that have been
uncharacterized to date, but also includes vacuolar
proteins involved in nitrogen metabolism which are
essential for use of certain peptides that are sole
nitrogen sources. YscS releases a C-terminal amino acid
from a peptide that has glycine as the penultimate
residue. It is synthesized as one polypeptide chain
precursor which yields two active precursor molecules
after carbohydrate modification in the secretory
pathway. The proteolytically unprocessed forms are
associated with the membrane, whereas the mature forms
of the enzyme are soluble. Enzymes in this subfamily
may also cleave intracellularly generated peptides in
order to recycle amino acids for protein synthesis.
Length = 441
Score = 34.1 bits (79), Expect = 0.073
Identities = 24/68 (35%), Positives = 34/68 (50%), Gaps = 10/68 (14%)
Query: 62 EEVGEYQGAYKISKGLLEKYG--PERVLD--TPITEAGFTGIGVGAAYYGLKPVVE--FM 115
EEVG +GA I++ LLE+YG VLD I E F G+G A G V E ++
Sbjct: 144 EEVGGTRGAAAIAE-LLERYGVDLAFVLDEGGAILEGLFPGVGTPVALIG---VAEKGYL 199
Query: 116 TFNFSMQA 123
+++
Sbjct: 200 DVRLTVRG 207
>gnl|CDD|235639 PRK05899, PRK05899, transketolase; Reviewed.
Length = 586
Score = 34.0 bits (79), Expect = 0.084
Identities = 14/43 (32%), Positives = 20/43 (46%)
Query: 227 LPIGKAKIEREGKDVTITAFSKIVGLSLKAAEILAKEGISAEV 269
+ R+ DV + A V L+L+AA+ L EGI V
Sbjct: 461 GVAKGGYVLRDDPDVILIATGSEVHLALEAADELEAEGIKVRV 503
>gnl|CDD|173866 cd08501, PBP2_Lpqw, The substrate-binding domain of mycobacterial
lipoprotein Lpqw contains type 2 periplasmic binding
fold. LpqW is one of key players in synthesis and
transport of the unique components of the mycobacterial
cell wall which is a complex structure rich in two
related lipoglycans, the phosphatidylinositol mannosides
(PIMs) and lipoarabinomannans (LAMs). Lpqw is a highly
conserved lipoprotein that transport intermediates from
a pathway for mature PIMs production into a pathway for
LAMs biosynthesis, thus controlling the relative
abundance of these two essential components of cell
wall. LpqW is thought to have been adapted by the
cell-wall biosynthesis machinery of mycobacteria and
other closely related pathogens, evolving to play an
important role in PIMs/LAMs biosynthesis. Most of
periplasmic binding proteins are comprised of only two
globular subdomains corresponding to domains I and III
of the LpqW protein. The structural topology of these
domains 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
ligand-binding domains from ionotropic glutamate
receptors, LysR-type transcriptional regulators, and
unorthodox sensor proteins involved in signal
transduction.
Length = 486
Score = 31.9 bits (73), Expect = 0.34
Identities = 37/222 (16%), Positives = 64/222 (28%), Gaps = 50/222 (22%)
Query: 39 VREALNSALDEE---------MSADPKVFLMGEEVGEYQGAYKISKGLLEKYGPERVLDT 89
VR+A A+D + + + + + Q Y+ + KY PE
Sbjct: 268 VRKAFLKAIDRDTIARIAFGGLPPEAEP-PGSHLLLPGQAGYEDNSSAYGKYDPEAAKKL 326
Query: 90 PITEAGFTGIGVGAAYYGLKPVVEFMTFNFSMQA---------------IDHIINSAAKS 134
+AG+T G G G + A I + S +
Sbjct: 327 L-DDAGYTLGGDGIEKDGKPLTLRIAYDGDDPTAVAAAELIQDMLAKAGIKVTVVSVPSN 385
Query: 135 NY--MSSGQISVPIV---FRGPNGAAAGVGAQHSHCYAAWYASVPGLKVLSPYSSEDARG 189
++ V ++G G A Y S S + +
Sbjct: 386 DFSKTLLSGGDYDAVLFGWQGTPGVANA---------GQIYGSCSESSNFSGFCDPEIDE 436
Query: 190 LLKAAIR--DPDPVVFLENELLYGESFPVSAEVLDSSFCLPI 229
L+ A+ DPD L NE + + ++ LP+
Sbjct: 437 LIAEALTTTDPDEQAELLNE--------ADKLLWEQAYTLPL 470
>gnl|CDD|232887 TIGR00232, tktlase_bact, transketolase, bacterial and yeast. This
model is designed to capture orthologs of bacterial
transketolases. The group includes two from the yeast
Saccharomyces cerevisiae but excludes dihydroxyactetone
synthases (formaldehyde transketolases) from various
yeasts and the even more distant mammalian
transketolases. Among the family of thiamine
diphosphate-dependent enzymes that includes
transketolases, dihydroxyacetone synthases, pyruvate
dehydrogenase E1-beta subunits, and
deoxyxylulose-5-phosphate synthases, mammalian and
bacterial transketolases seem not to be orthologous
[Energy metabolism, Pentose phosphate pathway].
Length = 653
Score = 32.0 bits (73), Expect = 0.34
Identities = 12/35 (34%), Positives = 20/35 (57%)
Query: 235 EREGKDVTITAFSKIVGLSLKAAEILAKEGISAEV 269
+ +G D+ + A V L+++AA+ LA E I V
Sbjct: 537 DSKGPDIILIATGSEVSLAVEAAKKLAAENIKVRV 571
>gnl|CDD|223460 COG0383, AMS1, Alpha-mannosidase [Carbohydrate transport and
metabolism].
Length = 943
Score = 31.3 bits (71), Expect = 0.55
Identities = 14/43 (32%), Positives = 20/43 (46%)
Query: 226 CLPIGKAKIEREGKDVTITAFSKIVGLSLKAAEILAKEGISAE 268
L IG+ ER GK + + F G +A ++ GISA
Sbjct: 103 NLLIGEFDAERFGKAMKLGYFPDTFGNLGQAPQLYENAGISAV 145
>gnl|CDD|223100 COG0021, TktA, Transketolase [Carbohydrate transport and
metabolism].
Length = 663
Score = 31.4 bits (72), Expect = 0.60
Identities = 24/103 (23%), Positives = 43/103 (41%), Gaps = 12/103 (11%)
Query: 172 SVPGLKVLSPYSSEDARGLLKAAI-RDPDPVVFLENELLYGESFPVSAEVLDSSFCLPIG 230
++P L V+ P + + K A+ R P + L ++ PV + +
Sbjct: 484 AIPNLSVIRPADANETAAAWKYALERKDGPTALI----LTRQNLPV---LERTDLEGVAK 536
Query: 231 KAKIEREGK----DVTITAFSKIVGLSLKAAEILAKEGISAEV 269
A + ++ DV + A V L+++AA+ L EGI V
Sbjct: 537 GAYVLKDSGGEDPDVILIATGSEVELAVEAAKELEAEGIKVRV 579
>gnl|CDD|150043 pfam09230, DFF40, DNA fragmentation factor 40 kDa. Members of
this family of eukaryotic apoptotic proteins induce DNA
fragmentation and chromatin condensation during
apoptosis.
Length = 227
Score = 28.2 bits (63), Expect = 3.8
Identities = 8/30 (26%), Positives = 12/30 (40%)
Query: 19 RIRPVVSNLRNYSSAVKQMMVREALNSALD 48
RIR ++ Y + V RE L+
Sbjct: 66 RIRGYFYEVKEYLTKVANAKAREEYLRVLE 95
>gnl|CDD|222998 PHA03140, PHA03140, helicase-primase primase subunit; Provisional.
Length = 772
Score = 28.8 bits (64), Expect = 4.1
Identities = 13/68 (19%), Positives = 23/68 (33%), Gaps = 2/68 (2%)
Query: 161 QHSHCYAAWYASVPGLKVLSPYSSEDARGLLKAAIRDPDPVVFLENELLYGESFPVSAEV 220
+ Y W A+ P + S + G + P V + + FP+ +
Sbjct: 659 RGDVRY--WSATAPIGDWGAVPRSALSGGDMLDKDHKPRQYVLVRGHIPEAAPFPLPWTL 716
Query: 221 LDSSFCLP 228
+ CLP
Sbjct: 717 YRAPVCLP 724
>gnl|CDD|221653 pfam12588, PSDC, Phophatidylserine decarboxylase. This domain
family is found in bacteria and eukaryotes, and is
approximately 140 amino acids in length. The family is
found in association with pfam02666. Phosphatidylserine
decarboxylase (PSD) is an important enzyme in the
synthesis of phosphatidylethanolamine in both
prokaryotes and eukaryotes.
Length = 141
Score = 27.6 bits (62), Expect = 4.5
Identities = 12/39 (30%), Positives = 21/39 (53%), Gaps = 2/39 (5%)
Query: 121 MQAIDHIINSAAKSNYMSSGQISVPI--VFRGPNGAAAG 157
+Q ++HI+ +A + N SG + PI + P G +G
Sbjct: 51 LQLLNHILTTAPEFNDHPSGLVGFPINALLDWPMGTPSG 89
>gnl|CDD|213038 cd11740, YajQ_like, Proteins similar to Escherichia coli YajQ. In
Pseudomonas syringae, YajQ functions as a host protein
involved in the temporal control of bacteriophage Phi6
gene transcription. It has been shown to bind to the
phage's major structural core protein P1, most likely
activating transcription by acting indirectly on the RNA
polymerase. YajQ may remain bound to the phage particles
throughout the infection period. Earlier, YajQ was
characterized as a putative nucleic acid-binding protein
based on the similarity of its (ferredoxin-like)
three-dimensional topology with that of RNP-like
RNA-binding domains.
Length = 159
Score = 27.3 bits (62), Expect = 5.6
Identities = 15/51 (29%), Positives = 22/51 (43%), Gaps = 15/51 (29%)
Query: 231 KAKIEREGKDVTITA-------------FSKIV--GLSLKAAEILAKEGIS 266
KA IE + +T+TA SK++ G+ LKA + E S
Sbjct: 35 KASIELNEETITLTADSDFKLKQVLDILRSKLIKRGIDLKALDYGKPEPAS 85
>gnl|CDD|240377 PTZ00352, PTZ00352, 60S ribosomal protein L13; Provisional.
Length = 212
Score = 27.4 bits (61), Expect = 6.5
Identities = 10/19 (52%), Positives = 13/19 (68%)
Query: 6 RQKVAAGGGSPVARIRPVV 24
++K AA G PV +RPVV
Sbjct: 38 QKKAAAAGPRPVELLRPVV 56
>gnl|CDD|153183 cd04911, ACT_AKiii-YclM-BS_1, ACT domains located C-terminal to the
catalytic domain of the lysine plus threonine-sensitive
aspartokinase isoenzyme AKIII. This CD includes the
first of two ACT domains located C-terminal to the
catalytic domain of the lysine plus threonine-sensitive
aspartokinase isoenzyme AKIII, a monofunctional class
enzyme found in Bacilli (Bacillus subtilis (BS) YclM)
and Clostridia species. Aspartokinase is the first
enzyme in the aspartate metabolic pathway and catalyzes
the conversion of aspartate and ATP to aspartylphosphate
and ADP. Bacillus subtilis YclM is reported to be a
single polypeptide of 50 kD. AKIII from Bacillus
subtilis strain 168 is induced by lysine and repressed
by threonine and it is synergistically inhibited by
lysine and threonine. Members of this CD belong to the
superfamily of ACT regulatory domains.
Length = 76
Score = 26.0 bits (58), Expect = 6.6
Identities = 9/19 (47%), Positives = 9/19 (47%)
Query: 250 VGLSLKAAEILAKEGISAE 268
VG K IL GIS E
Sbjct: 15 VGFGRKLLSILEDNGISYE 33
>gnl|CDD|223294 COG0216, PrfA, Protein chain release factor A [Translation,
ribosomal structure and biogenesis].
Length = 363
Score = 27.6 bits (62), Expect = 6.7
Identities = 14/52 (26%), Positives = 22/52 (42%), Gaps = 6/52 (11%)
Query: 18 ARIRPVVSNLRNYSSAVKQMM-VREALNSALDEEMSADPKVFLMGEEVGEYQ 68
A + P+V R Y A + + +E L D EM + EE+ E +
Sbjct: 43 AELEPIVEKYREYKKAQEDLEDAKEMLAEEKDPEMRE-----MAEEEIKELE 89
>gnl|CDD|235781 PRK06333, PRK06333, 3-oxoacyl-(acyl carrier protein) synthase II;
Reviewed.
Length = 424
Score = 27.7 bits (62), Expect = 8.0
Identities = 13/29 (44%), Positives = 18/29 (62%), Gaps = 5/29 (17%)
Query: 137 MSSGQISVPIVFRGPNGA-----AAGVGA 160
M++G +S+ F+GP GA AAGV A
Sbjct: 151 MAAGHVSIRYGFKGPLGAPVTACAAGVQA 179
>gnl|CDD|239273 cd02975, PfPDO_like_N, Pyrococcus furiosus protein disulfide
oxidoreductase (PfPDO)-like family, N-terminal TRX-fold
subdomain; composed of proteins with similarity to
PfPDO, a redox active thermostable protein believed to
be the archaeal counterpart of bacterial DsbA and
eukaryotic protein disulfide isomerase (PDI), which are
both involved in oxidative protein folding. PfPDO
contains two redox active CXXC motifs in two contiguous
TRX-fold subdomains. The active site in the N-terminal
TRX-fold subdomain is required for isomerase but not for
reductase activity of PfPDO. The exclusive presence of
PfPDO-like proteins in extremophiles may suggest that
they have a special role in adaptation to extreme
conditions.
Length = 113
Score = 26.2 bits (58), Expect = 8.9
Identities = 17/44 (38%), Positives = 20/44 (45%), Gaps = 2/44 (4%)
Query: 74 SKGLLEKYGPERVLDTPITEAGFTGIGVGAAYYGLKPVVEFMTF 117
K EKYG ERV T + G G+ YYGL EF +
Sbjct: 64 DKEKAEKYGVERVPTTIFLQDGGKDGGI--RYYGLPAGYEFASL 105
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
0.316 0.134 0.381
Gapped
Lambda K H
0.267 0.0843 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,081,475
Number of extensions: 1380495
Number of successful extensions: 1521
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1492
Number of HSP's successfully gapped: 54
Length of query: 270
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 175
Effective length of database: 6,723,972
Effective search space: 1176695100
Effective search space used: 1176695100
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: 58 (25.9 bits)