RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 017714
(367 letters)
>gnl|CDD|215368 PLN02683, PLN02683, pyruvate dehydrogenase E1 component subunit
beta.
Length = 356
Score = 666 bits (1719), Expect = 0.0
Identities = 298/338 (88%), Positives = 318/338 (94%), Gaps = 1/338 (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 LSLKAAEILAKEGISAEVINLRSIRPLDRSTINASVRKTNRLVTVEEGFPQHGVGAEICA 311
+LKAAEILAKEGISAEVINLRSIRPLDR TINASVRKTNRLVTVEEG+PQHGVGAEICA
Sbjct: 242 YALKAAEILAKEGISAEVINLRSIRPLDRDTINASVRKTNRLVTVEEGWPQHGVGAEICA 301
Query: 312 SVIEESFGYLDAPVERIAGADVPMPYAANLERMAVPQV 349
SV+EESF YLDAPVERIAGADVPMPYAANLER+A+PQV
Sbjct: 302 SVVEESFDYLDAPVERIAGADVPMPYAANLERLALPQV 339
>gnl|CDD|237011 PRK11892, PRK11892, pyruvate dehydrogenase subunit beta;
Provisional.
Length = 464
Score = 586 bits (1512), Expect = 0.0
Identities = 220/315 (69%), Positives = 260/315 (82%), Gaps = 3/315 (0%)
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 PVSAEVLDSSFCLPIGKAKIEREGKDVTITAFSKIVGLSLKAAEILAKEGISAEVINLRS 274
V LD F LPIGKA+I REGKDVTI +FS + +LKAAE LAKEGI AEVI+LR+
Sbjct: 320 DVP--KLD-DFVLPIGKARIHREGKDVTIVSFSIGMTYALKAAEELAKEGIDAEVIDLRT 376
Query: 275 IRPLDRSTINASVRKTNRLVTVEEGFPQHGVGAEICASVIEESFGYLDAPVERIAGADVP 334
IRP+D TI SV+KTNRLVTVEEG+PQ GVGAEI A V+E++F YLDAPV R+ G DVP
Sbjct: 377 IRPMDTETIVESVKKTNRLVTVEEGWPQSGVGAEIAARVMEQAFDYLDAPVLRVTGKDVP 436
Query: 335 MPYAANLERMAVPQV 349
MPYAANLE++A+P V
Sbjct: 437 MPYAANLEKLALPSV 451
>gnl|CDD|169719 PRK09212, PRK09212, pyruvate dehydrogenase subunit beta; Validated.
Length = 327
Score = 524 bits (1352), Expect = 0.0
Identities = 213/315 (67%), Positives = 257/315 (81%), Gaps = 4/315 (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 PVSAEVLDSSFCLPIGKAKIEREGKDVTITAFSKIVGLSLKAAEILAKEGISAEVINLRS 274
EV + +PIGKA I REG DVTI FS V L+L+AAE+L KEGIS EVI+LR+
Sbjct: 182 ----EVPEEEESIPIGKAAILREGSDVTIVTFSIQVKLALEAAELLEKEGISVEVIDLRT 237
Query: 275 IRPLDRSTINASVRKTNRLVTVEEGFPQHGVGAEICASVIEESFGYLDAPVERIAGADVP 334
+RPLD TI SV+KTNRLV VEEG+P GVGAEI A +++E+F YLDAPVER+ G DVP
Sbjct: 238 LRPLDTETIIESVKKTNRLVVVEEGWPFAGVGAEIAALIMKEAFDYLDAPVERVTGKDVP 297
Query: 335 MPYAANLERMAVPQV 349
+PYAANLE++A+P
Sbjct: 298 LPYAANLEKLALPSE 312
>gnl|CDD|185502 PTZ00182, PTZ00182, 3-methyl-2-oxobutanate dehydrogenase;
Provisional.
Length = 355
Score = 521 bits (1344), Expect = 0.0
Identities = 188/333 (56%), Positives = 231/333 (69%), Gaps = 7/333 (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 AEILAKEGISAEVINLRSIRPLDRSTINASVRKTNRLVTVEEGFPQHGVGAEICASVIEE 316
AE LAKEGIS EVI+LRS+RP DR TI SV+KT R V V E P G+GAEI A ++E+
Sbjct: 252 AEELAKEGISCEVIDLRSLRPWDRETIVKSVKKTGRCVIVHEAPPTCGIGAEIAAQIMED 311
Query: 317 SFGYLDAPVERIAGADVPMPYAANLERMAVPQV 349
F YL+AP++R+ GAD P PYA NLE +P
Sbjct: 312 CFLYLEAPIKRVCGADTPFPYAKNLEPAYLPDK 344
>gnl|CDD|223101 COG0022, AcoB, Pyruvate/2-oxoglutarate dehydrogenase complex,
dehydrogenase (E1) component, eukaryotic type, beta
subunit [Energy production and conversion].
Length = 324
Score = 495 bits (1278), Expect = e-178
Identities = 170/314 (54%), Positives = 219/314 (69%), Gaps = 3/314 (0%)
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 VSAEVLDSSFCLPIGKAKIEREGKDVTITAFSKIVGLSLKAAEILAKEGISAEVINLRSI 275
EV + + +P+GKAKI REG DVTI + +V +L+AAE L KEGISAEVI+LR++
Sbjct: 179 -KGEVPEEDYTIPLGKAKIVREGSDVTIVTYGAMVHTALEAAEELEKEGISAEVIDLRTL 237
Query: 276 RPLDRSTINASVRKTNRLVTVEEGFPQHGVGAEICASVIEESFGYLDAPVERIAGADVPM 335
PLD+ TI ASV+KT RLV V E G+GAEI A + EE+F YLDAP+ R+AG D P+
Sbjct: 238 SPLDKETIIASVKKTGRLVIVHEAPKTGGIGAEIAALIAEEAFDYLDAPILRVAGPDTPV 297
Query: 336 PYAANLERMAVPQV 349
PY+A LE+ +P
Sbjct: 298 PYSAALEKAYLPNP 311
>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 = 307 bits (789), Expect = e-106
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 = 303 bits (777), Expect = e-102
Identities = 139/313 (44%), Positives = 209/313 (66%), Gaps = 4/313 (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 VSAEVLDSSFCLPIGKAKIEREGKDVTITAFSKIVGLSLKAAEILAKEGISAEVINLRSI 275
+ E+ D+ + LP+ KA++ R G D+TI +S++ L+A ++L ++G E+I+L S+
Sbjct: 179 LKEEIPDNEYLLPLEKAEVVRPGNDITILTYSRMRHHVLQAVKVLVEKGYDPEIIDLISL 238
Query: 276 RPLDRSTINASVRKTNRLVTVEEGFPQHGVGAEICASVIEESFGYLDAPVERIAGADVPM 335
+PLD TI+ SV+KT++++ VEE G+GAE+ A + E F LDAP+ R++ DVP
Sbjct: 239 KPLDLGTISKSVKKTHKVLIVEECMKTGGIGAELIAQINEHLFDELDAPIVRLSSQDVPT 298
Query: 336 PYAANLERMAVPQ 348
PY LE V Q
Sbjct: 299 PYNGPLEEATVIQ 311
>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 = 166 bits (422), Expect = 2e-50
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|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 = 156 bits (396), Expect = 3e-47
Identities = 65/120 (54%), Positives = 84/120 (70%)
Query: 230 GKAKIEREGKDVTITAFSKIVGLSLKAAEILAKEGISAEVINLRSIRPLDRSTINASVRK 289
GKA+I REG DVTI A+ +V +L+AAE LAKEGISAEVI+LR+++PLD TI SV+K
Sbjct: 1 GKAEILREGDDVTIVAYGSMVHEALEAAEELAKEGISAEVIDLRTVKPLDEDTILESVKK 60
Query: 290 TNRLVTVEEGFPQHGVGAEICASVIEESFGYLDAPVERIAGADVPMPYAANLERMAVPQV 349
T RLV VEE + G G+E+ A++ EE F YLDAPV R+ G D P+P+ LE +
Sbjct: 61 TGRLVVVEEAVKRGGFGSEVAAALAEEGFDYLDAPVLRVGGPDTPIPHGPALELAYLGLT 120
>gnl|CDD|226467 COG3958, COG3958, Transketolase, C-terminal subunit [Carbohydrate
transport and metabolism].
Length = 312
Score = 116 bits (292), Expect = 8e-30
Identities = 84/301 (27%), Positives = 130/301 (43%), Gaps = 32/301 (10%)
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 SFPVSAEVLDSSFCLPIGKAKIEREGKDVTITAFSKIVGLSLKAAEILAKEGISAEVINL 272
PV + +F IGKA + R+G D+TI A +V +L+AAEIL KEGISA VIN+
Sbjct: 169 KVPVVVDEGGYTF--EIGKANVLRDGSDLTIIATGVMVAEALEAAEILKKEGISAAVINM 226
Query: 273 RSIRPLDRSTINASVRKTNRLVTVEEGFPQHGVGAEICASVIEESFGYLDAPVERIAGAD 332
+I+P+D I + R+T R+VT EE G+G+ + + E P+ RI D
Sbjct: 227 FTIKPIDEQAILKAARETGRIVTAEEHSIIGGLGSAVAEVLSENG----PTPMRRIGVPD 282
Query: 333 V 333
Sbjct: 283 T 283
>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 = 4e-28
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|224076 COG1154, Dxs, Deoxyxylulose-5-phosphate synthase [Coenzyme
metabolism / Lipid metabolism].
Length = 627
Score = 97.7 bits (244), Expect = 4e-22
Identities = 66/235 (28%), Positives = 104/235 (44%), Gaps = 27/235 (11%)
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 KAAEILAKEGISAEVINLRSIRPLDRSTINASVRKTNRLVTVEEGFPQHGVGAEI 309
K AE L GIS V++ R ++PLD + + + + +VT+EE G G+ +
Sbjct: 518 KVAEKLNAYGISVTVVDPRFVKPLDEALLLELAKSHDLVVTLEENVVDGGFGSAV 572
>gnl|CDD|235470 PRK05444, PRK05444, 1-deoxy-D-xylulose-5-phosphate synthase;
Provisional.
Length = 580
Score = 94.4 bits (236), Expect = 4e-21
Identities = 80/270 (29%), Positives = 122/270 (45%), Gaps = 58/270 (21%)
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 DVTITAFSKIVGLSLKAAEILAKEGISAEVINLRSIRPLDRSTINASVRKTNRLVTVEEG 299
DV I AF ++ +LKAAE LA SA V++ R ++PLD + K + +VTVEEG
Sbjct: 465 DVAILAFGTMLAEALKAAERLA----SATVVDARFVKPLDEELLLELAAKHDLVVTVEEG 520
Query: 300 FPQHGVGAEICASVIEESFGYLDAPVERIA 329
G G+ + + + LD PV +
Sbjct: 521 AIMGGFGSAVLEFLADHG---LDVPVLNLG 547
>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 = 2e-19
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 = 81.6 bits (202), Expect = 1e-18
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|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 = 84.4 bits (209), Expect = 9e-18
Identities = 66/266 (24%), Positives = 112/266 (42%), Gaps = 21/266 (7%)
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 SLKAAEILAKEGISAEVINLRSIRPLDRSTINASVRKTNRLVTVEEGFPQHGVGAEICAS 312
+L+ AE L ++GI A V++ R ++PLD I +LVTVEE G G+ +
Sbjct: 510 ALEVAESLNEKGIEATVVDARFVKPLDEELILEIAASHEKLVTVEENAIMGGAGSAV-LE 568
Query: 313 VIEESFGYLDAPVERIAGADVPMPYA 338
+ + L PV+R+ D +P+
Sbjct: 569 FLMDQ-NKL-VPVKRLGIPDFFIPHG 592
>gnl|CDD|183601 PRK12571, PRK12571, 1-deoxy-D-xylulose-5-phosphate synthase;
Provisional.
Length = 641
Score = 75.5 bits (186), Expect = 7e-15
Identities = 67/243 (27%), Positives = 105/243 (43%), Gaps = 30/243 (12%)
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 SKIVGLSLKAAEILAKEGISAEVINLRSIRPLDRSTINASVRKTNRLVTVEEGFPQHGVG 306
+ L AA++L EGIS V + R ++PLD + + VR ++ E+G G G
Sbjct: 513 GAHLHECLDAADLLEAEGISVTVADPRFVKPLDEALTDLLVRHHIVVIVEEQG-AMGGFG 571
Query: 307 AEI 309
A +
Sbjct: 572 AHV 574
>gnl|CDD|177878 PLN02234, PLN02234, 1-deoxy-D-xylulose-5-phosphate synthase.
Length = 641
Score = 67.4 bits (164), Expect = 3e-12
Identities = 66/258 (25%), Positives = 107/258 (41%), Gaps = 22/258 (8%)
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 DSSFCLPIGKAKIEREGKDVTITAFSKIVGLSLKAAEILAKEGISAEVINLRSIRPLDRS 281
+ L IG+ +I R+G+ V + + V L+AA +L++ G+ V + R +PLD +
Sbjct: 528 NKGVPLQIGRGRILRDGERVALLGYGSAVQRCLEAASMLSERGLKITVADARFCKPLDVA 587
Query: 282 TINASVRKTNRLVTVEEG 299
I + + L+TVEEG
Sbjct: 588 LIRSLAKSHEVLITVEEG 605
>gnl|CDD|237053 PRK12315, PRK12315, 1-deoxy-D-xylulose-5-phosphate synthase;
Provisional.
Length = 581
Score = 61.6 bits (150), Expect = 2e-10
Identities = 70/296 (23%), Positives = 121/296 (40%), Gaps = 55/296 (18%)
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 D-PVVFL--ENELLYGESFPVSAEVLDSSFCLPIGKAKIEREGKDVTITAFSKIVGLSLK 255
+ PV E+ + G D S K ++ + G+ V I A L K
Sbjct: 427 EHPVAIRVPEHGVESGP-----TVDTDYSTL----KYEVTKAGEKVAILALGDFYELGEK 477
Query: 256 AAEILAKE-GISAEVINLRSIRPLDRSTINASVRKTNRLV-TVEEGFPQHGVGAEI 309
A+ L +E GI A +IN + I LD + +++ + LV T+E+G G G +I
Sbjct: 478 VAKKLKEELGIDATLINPKFITGLDEELLE-KLKEDHELVVTLEDGILDGGFGEKI 532
>gnl|CDD|178194 PLN02582, PLN02582, 1-deoxy-D-xylulose-5-phosphate synthase.
Length = 677
Score = 59.9 bits (145), Expect = 9e-10
Identities = 60/222 (27%), Positives = 92/222 (41%), Gaps = 19/222 (8%)
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 EILAKEGISAEVINLRSIRPLDRSTINASVRKTNRLVTVEEG 299
+L + G+SA V + R +PLDR+ I + + L+TVEEG
Sbjct: 563 SLLERHGLSATVADARFCKPLDRALIRSLAKSHEVLITVEEG 604
>gnl|CDD|177870 PLN02225, PLN02225, 1-deoxy-D-xylulose-5-phosphate synthase.
Length = 701
Score = 51.6 bits (123), Expect = 4e-07
Identities = 65/287 (22%), Positives = 118/287 (41%), Gaps = 44/287 (15%)
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 SLKAAEILAKEGISAEVINLRSIRPLDRSTINASVRKTNRLVTVEEG 299
L A +L+K G++ V + R +PLD + + L+TVEEG
Sbjct: 582 CLHAHSLLSKLGLNVTVADARFCKPLDIKLVRDLCQNHKFLITVEEG 628
>gnl|CDD|235639 PRK05899, PRK05899, transketolase; Reviewed.
Length = 586
Score = 43.6 bits (104), Expect = 1e-04
Identities = 23/80 (28%), Positives = 34/80 (42%), Gaps = 10/80 (12%)
Query: 227 LPIGKAKIEREGKDVTITAFSKIVGLSLKAAEILAKEGISAEVINLRSIRPLDR------ 280
+ R+ DV + A V L+L+AA+ L EGI V+++ S D
Sbjct: 461 GVAKGGYVLRDDPDVILIATGSEVHLALEAADELEAEGIKVRVVSMPSTELFDEQDAAYK 520
Query: 281 -STINASVRKTNRLVTVEEG 299
S + A+V V VE G
Sbjct: 521 ESVLPAAVTAR---VAVEAG 537
>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 = 37.4 bits (87), Expect = 0.012
Identities = 14/46 (30%), Positives = 26/46 (56%)
Query: 235 EREGKDVTITAFSKIVGLSLKAAEILAKEGISAEVINLRSIRPLDR 280
+ +G D+ + A V L+++AA+ LA E I V+++ S D+
Sbjct: 537 DSKGPDIILIATGSEVSLAVEAAKKLAAENIKVRVVSMPSFDLFDK 582
>gnl|CDD|223100 COG0021, TktA, Transketolase [Carbohydrate transport and
metabolism].
Length = 663
Score = 35.3 bits (82), Expect = 0.051
Identities = 30/140 (21%), Positives = 57/140 (40%), Gaps = 22/140 (15%)
Query: 172 SVPGLKVLSPYSSEDARGLLKAAI-RDPDPVVFLENELLYGESFPVSAEVLDSSFCLPIG 230
++P L V+ P + + K A+ R P + L ++ PV + +
Sbjct: 484 AIPNLSVIRPADANETAAAWKYALERKDGPTALI----LTRQNLPV---LERTDLEGVAK 536
Query: 231 KAKIEREGK----DVTITAFSKIVGLSLKAAEILAKEGISAEVINLRSIRPLDR------ 280
A + ++ DV + A V L+++AA+ L EGI V+++ S ++
Sbjct: 537 GAYVLKDSGGEDPDVILIATGSEVELAVEAAKELEAEGIKVRVVSMPSFELFEKQDEEYR 596
Query: 281 -STINASVRKTNRLVTVEEG 299
S + +V V +E G
Sbjct: 597 ESVLPGAVTA---RVAIEAG 613
>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 = 0.11
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|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 = 32.3 bits (74), Expect = 0.42
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|223460 COG0383, AMS1, Alpha-mannosidase [Carbohydrate transport and
metabolism].
Length = 943
Score = 32.0 bits (73), Expect = 0.49
Identities = 14/45 (31%), Positives = 20/45 (44%)
Query: 226 CLPIGKAKIEREGKDVTITAFSKIVGLSLKAAEILAKEGISAEVI 270
L IG+ ER GK + + F G +A ++ GISA
Sbjct: 103 NLLIGEFDAERFGKAMKLGYFPDTFGNLGQAPQLYENAGISAVAF 147
>gnl|CDD|181999 PRK09622, porA, pyruvate flavodoxin oxidoreductase subunit alpha;
Reviewed.
Length = 407
Score = 32.0 bits (73), Expect = 0.53
Identities = 15/41 (36%), Positives = 22/41 (53%)
Query: 237 EGKDVTITAFSKIVGLSLKAAEILAKEGISAEVINLRSIRP 277
E +V I A ++ AA+ + KEGI A V +R +RP
Sbjct: 266 EDAEVAIVALGTTYESAIVAAKEMRKEGIKAGVATIRVLRP 306
>gnl|CDD|132240 TIGR03196, pucD, xanthine dehydrogenase D subunit. This gene has
been characterized in B. subtilis as the molybdopterin
binding-subunit of xanthine dehydrogenase (pucD), acting
in conjunction with pucC, the FAD-binding subunit and
pucE, the FeS-binding subunit. The more common XDH
complex (GenProp0640) includes the xdhB gene which is
related to pucD. It appears that most of the relatives
of pucD outside of this narrow clade are involved in
other processes as they are found in unrelated genomic
contexts, contain the more common XDH complex and/or do
not appear to process purines to allantoin.
Length = 768
Score = 30.0 bits (67), Expect = 2.5
Identities = 20/68 (29%), Positives = 25/68 (36%), Gaps = 6/68 (8%)
Query: 266 SAEVINLRSIRPLDRSTI------NASVRKTNRLVTVEEGFPQHGVGAEICASVIEESFG 319
+AEVI + RPL ++ I + R E G Q G GA I G
Sbjct: 400 AAEVIEAIASRPLPKAPILKKANRAVTALPGGRPAAAECGRLQRGTGAAIAMHGGGFGEG 459
Query: 320 YLDAPVER 327
DA V
Sbjct: 460 MDDAAVAG 467
>gnl|CDD|223746 COG0674, PorA, Pyruvate:ferredoxin oxidoreductase and related
2-oxoacid:ferredoxin oxidoreductases, alpha subunit
[Energy production and conversion].
Length = 365
Score = 29.6 bits (67), Expect = 2.6
Identities = 14/59 (23%), Positives = 28/59 (47%), Gaps = 1/59 (1%)
Query: 240 DVTITAFSKIVGLSLKAAEILA-KEGISAEVINLRSIRPLDRSTINASVRKTNRLVTVE 297
++ I A G + +A L +G ++ +R++RP I + KTN +V ++
Sbjct: 258 EIVIVAMGSSKGSTAEAVVDLLRDKGEKVGLLKVRTLRPFPAEEIREVLPKTNAVVVLD 316
>gnl|CDD|226684 COG4231, COG4231, Indolepyruvate ferredoxin oxidoreductase, alpha
and beta subunits [Energy production and conversion].
Length = 640
Score = 29.6 bits (67), Expect = 2.8
Identities = 24/94 (25%), Positives = 36/94 (38%), Gaps = 17/94 (18%)
Query: 258 EILAKEGISAEVINLRSIRPLDRSTINASVRKTNRLVTVEEGFPQHGVGAEICASVIEES 317
E L G+ E++ L + PL I ++ R++ VEEG P IEE
Sbjct: 264 EALEDLGLDDELLKLGTPYPLPEQLIENFLKGLERVLVVEEGEP-----------FIEEQ 312
Query: 318 F---GYLDAPVERIAGAD---VPMPYAANLERMA 345
Y + G D +PM E++A
Sbjct: 313 VKALLYDAGLPVEVHGKDEGLLPMEGELTPEKIA 346
>gnl|CDD|218580 pfam05409, Peptidase_C30, Coronavirus endopeptidase C30.
Corresponds to Merops family C30. These peptidases are
involved in viral polyprotein processing in replication.
Length = 293
Score = 29.0 bits (65), Expect = 3.5
Identities = 16/47 (34%), Positives = 23/47 (48%), Gaps = 10/47 (21%)
Query: 319 GYLDAPVERIAGADVPMPYAANLERMAVPQVLCFLYDSSIDGCYKFL 365
GY D PV ++ GAD + V+ FLY + I+GC +L
Sbjct: 156 GYEDQPVLQLEGADN----------LVTVNVVAFLYAAIINGCTWWL 192
>gnl|CDD|173754 cd07865, STKc_CDK9, Catalytic domain of the Serine/Threonine
Kinase, Cyclin-Dependent protein Kinase 9.
Serine/Threonine Kinases (STKs), Cyclin-Dependent
protein Kinase 9 (CDK9) subfamily, catalytic (c) domain.
STKs catalyze the transfer of the gamma-phosphoryl group
from ATP to serine/threonine residues on protein
substrates. The CDK9 subfamily is part of a larger
superfamily that includes the catalytic domains of other
protein STKs, protein tyrosine kinases, RIO kinases,
aminoglycoside phosphotransferase, choline kinase, and
phosphoinositide 3-kinase. CDKs belong to a large family
of STKs that are regulated by their cognate cyclins.
Together, they are involved in the control of cell-cycle
progression, transcription, and neuronal function. CDK9
together with a cyclin partner (cyclin T1, T2a, T2b, or
K) is the main component of distinct positive
transcription elongation factors (P-TEFb), which
function as Ser2 C-terminal domain kinases of RNA
polymerase II. P-TEFb participates in multiple steps of
gene expression including transcription elongation, mRNA
synthesis, processing, export, and translation. It also
plays a role in mediating cytokine induced transcription
networks such as IL6-induced STAT3 signaling. In
addition, the CDK9/cyclin T2a complex promotes muscle
differentiation and enhances the function of some
myogenic regulatory factors.
Length = 310
Score = 28.9 bits (65), Expect = 4.7
Identities = 18/51 (35%), Positives = 27/51 (52%), Gaps = 2/51 (3%)
Query: 246 FSKIVGLSLKAAEIL-AKEGISAEVINLRSIRPLDRSTINASVRKTNRLVT 295
+KI+ +KAA IL K+GI ++ + R S + R TNR+VT
Sbjct: 137 RNKILHRDMKAANILITKDGI-LKLADFGLARAFSLSKNSKPNRYTNRVVT 186
>gnl|CDD|234323 TIGR03710, OAFO_sf, 2-oxoacid:acceptor oxidoreductase, alpha
subunit. This family of proteins contains a C-terminal
thiamine diphosphate (TPP) binding domain typical of
flavodoxin/ferredoxin oxidoreductases (pfam01855) as
well as an N-terminal domain similar to the gamma
subunit of the same group of oxidoreductases
(pfam01558). The genes represented by this model are
always found in association with a neighboring gene for
a beta subunit (TIGR02177) which also occurs in a
4-subunit (alpha/beta/gamma/ferredoxin) version of the
system. This alpha/gamma plus beta structure was used to
define the set of sequences to include in this model.
This pair of genes is not consistantly observed in
proximity to any electron acceptor genes, but is found
next to putative ferredoxins or ferredoxin-domain
proteins in Azoarcus sp. EbN1, Bradyrhizobium japonicum
USDA 110, Frankia sp. CcI3, Rhodoferax ferrireducens DSM
15236, Rhodopseudomonas palustris BisB5, Os,
Sphingomonas wittichii RW1 and Streptomyces
clavuligerus. Other potential acceptors are also
sporadically observed in close proximity including
ferritin-like proteins, reberythrin, peroxiredoxin and a
variety of other flavin and iron-sulfur
cluster-containing proteins. The phylogenetic
distribution of this family encompasses archaea, a
number of deeply-branching bacterial clades and only a
small number of firmicutes and proteobacteria. The
enzyme from Sulfolobus has been characterized with
respect to its substrate specificity which is described
as wide, encompassing various 2-oxoacids such as
2-oxoglutarate, 2-oxobutyrate and pyruvate. The enzyme
from Hydrogenobacter thermophilus has been shown to have
a high specificity towards 2-oxoglutarate and is one of
the key enzymes in the reverse TCA cycle in this
organism. Furthermore, considering its binding of
coenzyme A, it can be reasonably inferred that the
product of the reaction is succinyl-CoA. The genes for
this enzyme in Prevotella intermedia 17, Persephonella
marina EX-H1 and Picrophilus torridus DSM 9790 are in
close proximity to a variety of TCA cycle genes.
Persephonella marina and P. torridus are believed to
encode complete TCA cycles, and none of these contains
the lipoate-based 2-oxoglutarate dehydrogenase
(E1/E2/E3) system. That system is presumed to be
replaced by this one. In fact, the lipoate system is
absent in most organisms possessing a member of this
family, providing additional circumstantial evidence
that many of these enzymes are capable of acting as
2-oxoglutarate dehydrogenases and.
Length = 562
Score = 29.0 bits (66), Expect = 5.1
Identities = 11/44 (25%), Positives = 23/44 (52%)
Query: 254 LKAAEILAKEGISAEVINLRSIRPLDRSTINASVRKTNRLVTVE 297
+A E L EGI +++LR + P ++ + + +++ VE
Sbjct: 479 REAVERLRAEGIKVALLHLRLLYPFPKNELAELLEGAKKVIVVE 522
>gnl|CDD|133447 cd01079, NAD_bind_m-THF_DH, NAD binding domain of
methylene-tetrahydrofolate dehydrogenase. The
NAD-binding domain of methylene-tetrahydrofolate
dehydrogenase (m-THF DH). M-THF is a versatile carrier
of activated one-carbon units. The major one-carbon
folate donors are N-5 methyltetrahydrofolate,
N5,N10-m-THF, and N10-formayltetrahydrofolate. The
oxidation of metabolic intermediate m-THF to m-THF
requires the enzyme m-THF DH. M-THF DH is a component of
an unusual monofunctional enzyme; in eukaryotes, m-THF
DH is typically found as part of a multifunctional
protein. NADP-dependent m-THF DHs in mammals, birds and
yeast are components of a trifunctional enzyme with DH,
cyclohydrolase, and synthetase activities. Certain
eukaryotic cells also contain homodimeric bifunctional
DH/cyclodrolase form. In bacteria, monofunctional DH, as
well as bifunctional DH/cyclodrolase are found. In
addition, yeast (S. cerevisiae) also express an
monofunctional DH. This family contains only the
monofunctional DHs from S. cerevisiae and certain
bacteria. M-THF DH, like other amino acid DH-like
NAD(P)-binding domains, is a member of the Rossmann fold
superfamily which includes glutamate, leucine, and
phenylalanine DHs, m-THF DH,
methylene-tetrahydromethanopterin DH, m-THF
DH/cyclohydrolase, Shikimate DH-like proteins, malate
oxidoreductases, and glutamyl tRNA reductase. Amino acid
DHs catalyze the deamination of amino acids to keto
acids with NAD(P)+ as a cofactor. The NAD(P)-binding
Rossmann fold superfamily includes a wide variety of
protein families including NAD(P)- binding domains of
alcohol DHs, tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate DH, lactate/malate DHs,
formate/glycerate DHs, siroheme synthases,
6-phosphogluconate DH, amino acid DHs, repressor rex,
NAD-binding potassium channel domain, CoA-binding, and
ornithine cyclodeaminase-like domains. These domains
have an alpha-beta-alpha configuration. NAD binding
involves numerous hydrogen and van der Waals contacts.
Length = 197
Score = 28.2 bits (63), Expect = 6.1
Identities = 20/62 (32%), Positives = 30/62 (48%), Gaps = 5/62 (8%)
Query: 238 GKDVTITAFSKIVGLSLKAAEILAKEGISAEVINLRSIRPLDRSTINASVRKTNRLVTVE 297
GK +TI S++VG L A +LA +G +++ I+ R S+R VT E
Sbjct: 62 GKTITIINRSEVVGRPL--AALLANDGARVYSVDINGIQVFTR---GESIRHEKHHVTDE 116
Query: 298 EG 299
E
Sbjct: 117 EA 118
>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 = 6.2
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|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 = 6.6
Identities = 8/30 (26%), Positives = 12/30 (40%)
Query: 19 RIRPVVSNLRNYSSAVKQMMVREALNSALD 48
RIR ++ Y + V RE L+
Sbjct: 66 RIRGYFYEVKEYLTKVANAKAREEYLRVLE 95
>gnl|CDD|181526 PRK08659, PRK08659, 2-oxoglutarate ferredoxin oxidoreductase
subunit alpha; Validated.
Length = 376
Score = 28.3 bits (64), Expect = 7.0
Identities = 13/61 (21%), Positives = 26/61 (42%)
Query: 237 EGKDVTITAFSKIVGLSLKAAEILAKEGISAEVINLRSIRPLDRSTINASVRKTNRLVTV 296
E +V + A+ + + +A + +EGI + L ++ P I +K +V
Sbjct: 272 EDAEVVVVAYGSVARSARRAVKEAREEGIKVGLFRLITVWPFPEEAIRELAKKVKAIVVP 331
Query: 297 E 297
E
Sbjct: 332 E 332
>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 = 27.7 bits (63), Expect = 7.0
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|222998 PHA03140, PHA03140, helicase-primase primase subunit; Provisional.
Length = 772
Score = 28.4 bits (63), Expect = 7.2
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|153188 cd04916, ACT_AKiii-YclM-BS_2, ACT domains located C-terminal to the
catalytic domain of the lysine plus threonine-sensitive
aspartokinase isoenzyme AKIII. This CD includes the
second 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. B. subtilis YclM is reported to be a single
polypeptide of 50 kD. AKIII from B. 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 = 66
Score = 26.1 bits (58), Expect = 7.4
Identities = 11/22 (50%), Positives = 15/22 (68%)
Query: 250 VGLSLKAAEILAKEGISAEVIN 271
VG+S +A LAK GI+ +IN
Sbjct: 15 VGVSARATAALAKAGINIRMIN 36
>gnl|CDD|187662 cd09761, A3DFK9-like_SDR_c, Clostridium thermocellum A3DFK9-like, a
putative carbohydrate or polyalcohol metabolizing SDR,
classical (c) SDRs. This subgroup includes a putative
carbohydrate or polyalcohol metabolizing SDR (A3DFK9)
from Clostridium thermocellum. Its members have a
TGXXXGXG classical-SDR glycine-rich NAD-binding motif,
and some have a canonical SDR active site tetrad (A3DFK9
lacks the upstream Asn). SDRs are a functionally diverse
family of oxidoreductases that have a single domain with
a structurally conserved Rossmann fold (alpha/beta
folding pattern with a central beta-sheet), an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRs are approximately
350 residues. Sequence identity between different SDR
enzymes are typically in the 15-30% range, but the
enzymes share the Rossmann fold NAD-binding motif and
characteristic NAD-binding and catalytic sequence
patterns. These enzymes catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) numbering). In addition to the
Tyr and Lys, there is often an upstream Ser (Ser-138,
15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH
numbering) contributing to the active site; while
substrate binding is in the C-terminal region, which
determines specificity. The standard reaction mechanism
is a 4-pro-S hydride transfer and proton relay involving
the conserved Tyr and Lys, a water molecule stabilized
by Asn, and nicotinamide. Extended SDRs have additional
elements in the C-terminal region, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Some atypical SDRs have lost catalytic activity and/or
have an unusual NAD(P)-binding motif and missing or
unusual active site residues. Reactions catalyzed within
the SDR family include isomerization, decarboxylation,
epimerization, C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 242
Score = 27.9 bits (62), Expect = 7.8
Identities = 18/77 (23%), Positives = 30/77 (38%), Gaps = 10/77 (12%)
Query: 291 NRLVTVEEGFPQHGVGAEICASVIEESFGYLDAPVERIAGADVPMPYAANLERMAVPQVL 350
++ V G HG+G +IC +E + A ++ GAD P +
Sbjct: 1 GKVAIVTGG--GHGIGKQICLDFLEAGDKVVFADIDEERGADF--------AEAEGPNLF 50
Query: 351 CFLYDSSIDGCYKFLVY 367
D + + KF+VY
Sbjct: 51 FVHGDVADETLVKFVVY 67
>gnl|CDD|240377 PTZ00352, PTZ00352, 60S ribosomal protein L13; Provisional.
Length = 212
Score = 27.8 bits (62), Expect = 8.5
Identities = 10/19 (52%), Positives = 13/19 (68%)
Query: 6 RQKVAAGGGSPVARIRPVV 24
++K AA G PV +RPVV
Sbjct: 38 QKKAAAAGPRPVELLRPVV 56
>gnl|CDD|234165 TIGR03303, OM_YaeT, outer membrane protein assembly complex, YaeT
protein. Members of this protein family are the YaeT
protein of the YaeT/YfiO complex for assembling proteins
into the outer membrane of Gram-negative bacteria. This
protein is similar in sequence and function to a
non-essential paralog, YtfM, that is also in the Omp85
family. Members of this family typically have five
tandem copies of the surface antigen variable number
repeat (pfam07244), followed by an outer membrane
beta-barrel domain (pfam01103), while the YtfM family
typically has a single pfam07244 repeat [Protein fate,
Protein and peptide secretion and trafficking].
Length = 741
Score = 28.3 bits (64), Expect = 8.5
Identities = 10/59 (16%), Positives = 24/59 (40%), Gaps = 2/59 (3%)
Query: 233 KIEREGKDVTI--TAFSKIVGLSLKAAEILAKEGISAEVINLRSIRPLDRSTINASVRK 289
KIEREG + I I + + + K+ + ++ ++ +R+ + +
Sbjct: 53 KIEREGGVLVIKVKERPIINSIVFSGNKEIKKDQLKKALVGIKKGEIFNRAKLEKDEKA 111
>gnl|CDD|223294 COG0216, PrfA, Protein chain release factor A [Translation,
ribosomal structure and biogenesis].
Length = 363
Score = 27.9 bits (63), Expect = 9.8
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|172654 PRK14166, PRK14166, bifunctional 5,10-methylene-tetrahydrofolate
dehydrogenase/ 5,10-methylene-tetrahydrofolate
cyclohydrolase; Provisional.
Length = 282
Score = 27.7 bits (61), Expect = 9.9
Identities = 24/75 (32%), Positives = 36/75 (48%), Gaps = 11/75 (14%)
Query: 221 LDSSF--CLPIGKAK------IEREGKDVTITAFSKIVGLSLKAAEILAKEGISAEVINL 272
L+S F C P+G K I+ EGKD I S IVG + A +L G + V ++
Sbjct: 132 LESGFLPCTPLGVMKLLKAYEIDLEGKDAVIIGASNIVGRPM--ATMLLNAGATVSVCHI 189
Query: 273 RSIRPLDRSTINASV 287
++ + L T A +
Sbjct: 190 KT-KDLSLYTRQADL 203
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
0.318 0.135 0.389
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: 19,114,210
Number of extensions: 1906781
Number of successful extensions: 1974
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1942
Number of HSP's successfully gapped: 68
Length of query: 367
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 269
Effective length of database: 6,590,910
Effective search space: 1772954790
Effective search space used: 1772954790
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 (21.7 bits)
S2: 60 (26.7 bits)