RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 017410
(372 letters)
>gnl|CDD|185502 PTZ00182, PTZ00182, 3-methyl-2-oxobutanate dehydrogenase;
Provisional.
Length = 355
Score = 540 bits (1394), Expect = 0.0
Identities = 196/318 (61%), Positives = 237/318 (74%), Gaps = 4/318 (1%)
Query: 35 GSGKSLNLYSAINQALHIALETDPRAYVFGEDVG-FGGVFRCTTGLADRFGKSRVFNTPL 93
G+ +N+ AIN AL L DP+ +V GEDV +GGV++CT GL D++G RVF+TP+
Sbjct: 30 GATVKMNVREAINSALDEELARDPKVFVLGEDVAQYGGVYKCTKGLLDKYGPDRVFDTPI 89
Query: 94 CEQGIVGFAIGLAAMGNRAIAEIQFADYIFPAFDQIVNEAAKFRYRSGNQFNCGGLTVRA 153
EQG GFAIG A G R IAE FAD+IFPAFDQIVNEAAK+RY SG QF+C + +R
Sbjct: 90 TEQGFAGFAIGAAMNGLRPIAEFMFADFIFPAFDQIVNEAAKYRYMSGGQFDCP-IVIRG 148
Query: 154 PYGAVGHGGHYHSQSPEAFFCHVPGLKVVIPRSPRQAKGLLLSCIRDPNPVVFFEPKWLY 213
P GAVGHGG YHSQS EA+F HVPGLKVV P P AKGLL + IRDPNPVVFFEPK LY
Sbjct: 149 PNGAVGHGGAYHSQSFEAYFAHVPGLKVVAPSDPEDAKGLLKAAIRDPNPVVFFEPKLLY 208
Query: 214 RLSVEEVPEDDYMLPLSEAEVIREGSDITLVGWGAQLSIMEQACLDAEKEGISCELIDLK 273
R SVE VPE DY LPL +A+V+REG D+T+VG+G+Q+ + +A + KEGISCE+IDL+
Sbjct: 209 RESVEVVPEADYTLPLGKAKVVREGKDVTIVGYGSQVHVALKAAEELAKEGISCEVIDLR 268
Query: 274 TLIPWDKETVEASVRKTGRLLISHEAPVTGGFGAEISASILERCFLRLEAPVARVCGLDT 333
+L PWD+ET+ SV+KTGR +I HEAP T G GAEI+A I+E CFL LEAP+ RVCG DT
Sbjct: 269 SLRPWDRETIVKSVKKTGRCVIVHEAPPTCGIGAEIAAQIMEDCFLYLEAPIKRVCGADT 328
Query: 334 PFPLV--FEPFYMPTKNK 349
PFP EP Y+P K K
Sbjct: 329 PFPYAKNLEPAYLPDKEK 346
>gnl|CDD|223101 COG0022, AcoB, Pyruvate/2-oxoglutarate dehydrogenase complex,
dehydrogenase (E1) component, eukaryotic type, beta
subunit [Energy production and conversion].
Length = 324
Score = 464 bits (1197), Expect = e-165
Identities = 173/314 (55%), Positives = 217/314 (69%), Gaps = 4/314 (1%)
Query: 39 SLNLYSAINQALHIALETDPRAYVFGEDVGF-GGVFRCTTGLADRFGKSRVFNTPLCEQG 97
+ + AIN+A+ +E D R V GEDVG GGVFR T GL ++FG+ RV +TP+ E G
Sbjct: 1 QMTMIEAINEAMDEEMERDERVVVLGEDVGVYGGVFRVTKGLQEKFGEERVIDTPIAESG 60
Query: 98 IVGFAIGLAAMGNRAIAEIQFADYIFPAFDQIVNEAAKFRYRSGNQFNCGGLTVRAPYGA 157
I G A+G A G R I EIQFAD+I+PAFDQIVN+AAK RYRSG QF + +R P G
Sbjct: 61 IAGIAVGAALTGLRPIVEIQFADFIYPAFDQIVNQAAKIRYRSGGQFTVP-IVIRTPNGG 119
Query: 158 VGHGGHYHSQSPEAFFCHVPGLKVVIPRSPRQAKGLLLSCIRDPNPVVFFEPKWLYRLSV 217
GG HSQS EA F H+PGLKVV+P +P AKGLL + IRDP+PV+F E K LYR
Sbjct: 120 GIGGGAQHSQSLEALFAHIPGLKVVMPSTPYDAKGLLKAAIRDPDPVIFLEHKRLYRSFK 179
Query: 218 EEVPEDDYMLPLSEAEVIREGSDITLVGWGAQLSIMEQACLDAEKEGISCELIDLKTLIP 277
EVPE+DY +PL +A+++REGSD+T+V +GA + +A + EKEGIS E+IDL+TL P
Sbjct: 180 GEVPEEDYTIPLGKAKIVREGSDVTIVTYGAMVHTALEAAEELEKEGISAEVIDLRTLSP 239
Query: 278 WDKETVEASVRKTGRLLISHEAPVTGGFGAEISASILERCFLRLEAPVARVCGLDTPFP- 336
DKET+ ASV+KTGRL+I HEAP TGG GAEI+A I E F L+AP+ RV G DTP P
Sbjct: 240 LDKETIIASVKKTGRLVIVHEAPKTGGIGAEIAALIAEEAFDYLDAPILRVAGPDTPVPY 299
Query: 337 -LVFEPFYMPTKNK 349
E Y+P +
Sbjct: 300 SAALEKAYLPNPER 313
>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 = 287 bits (736), Expect = 1e-97
Identities = 97/167 (58%), Positives = 114/167 (68%), Gaps = 2/167 (1%)
Query: 45 AINQALHIALETDPRAYVFGEDVG-FGGVFRCTTGLADRFGKSRVFNTPLCEQGIVGFAI 103
AIN+AL +E DPR V GEDVG +GGVF+ T GL D+FG RV +TP+ E GIVG A+
Sbjct: 2 AINEALDEEMERDPRVVVLGEDVGDYGGVFKVTKGLLDKFGPDRVIDTPIAEAGIVGLAV 61
Query: 104 GLAAMGNRAIAEIQFADYIFPAFDQIVNEAAKFRYRSGNQFNCGGLTVRAPYGAVGHGGH 163
G A G R I EI FAD+ PAFDQIVNEAAK RY SG QF + +R P G GG
Sbjct: 62 GAAMNGLRPIVEIMFADFALPAFDQIVNEAAKLRYMSGGQFKV-PIVIRGPNGGGIGGGA 120
Query: 164 YHSQSPEAFFCHVPGLKVVIPRSPRQAKGLLLSCIRDPNPVVFFEPK 210
HSQS EA+F H+PGLKVV P +P AKGLL + IRD +PV+F E K
Sbjct: 121 QHSQSLEAWFAHIPGLKVVAPSTPYDAKGLLKAAIRDDDPVIFLEHK 167
>gnl|CDD|169719 PRK09212, PRK09212, pyruvate dehydrogenase subunit beta; Validated.
Length = 327
Score = 284 bits (728), Expect = 3e-94
Identities = 131/293 (44%), Positives = 178/293 (60%), Gaps = 3/293 (1%)
Query: 45 AINQALHIALETDPRAYVFGEDVG-FGGVFRCTTGLADRFGKSRVFNTPLCEQGIVGFAI 103
A+ A+ +E DP+ ++ GE+VG + G ++ T GL ++FG RV +TP+ E G G A+
Sbjct: 9 ALRDAMQEEMERDPKVFLMGEEVGEYQGAYKVTQGLLEQFGPKRVIDTPITEHGFAGLAV 68
Query: 104 GLAAMGNRAIAEIQFADYIFPAFDQIVNEAAKFRYRSGNQFNCGGLTVRAPYGAVGHGGH 163
G A G R I E ++ A DQIVN AAK Y SG Q C + R P GA
Sbjct: 69 GAAFAGLRPIVEFMTFNFSMQAIDQIVNSAAKTNYMSGGQLKCP-IVFRGPNGAAARVAA 127
Query: 164 YHSQSPEAFFCHVPGLKVVIPRSPRQAKGLLLSCIRDPNPVVFFEPKWLYRLSVEEVPED 223
HSQ A++ H+PGLKVV P KGLL + IRDPNPV+F E + LY S EVPE+
Sbjct: 128 QHSQCYAAWYSHIPGLKVVAPYFAADCKGLLKTAIRDPNPVIFLENEILYGHS-HEVPEE 186
Query: 224 DYMLPLSEAEVIREGSDITLVGWGAQLSIMEQACLDAEKEGISCELIDLKTLIPWDKETV 283
+ +P+ +A ++REGSD+T+V + Q+ + +A EKEGIS E+IDL+TL P D ET+
Sbjct: 187 EESIPIGKAAILREGSDVTIVTFSIQVKLALEAAELLEKEGISVEVIDLRTLRPLDTETI 246
Query: 284 EASVRKTGRLLISHEAPVTGGFGAEISASILERCFLRLEAPVARVCGLDTPFP 336
SV+KT RL++ E G GAEI+A I++ F L+APV RV G D P P
Sbjct: 247 IESVKKTNRLVVVEEGWPFAGVGAEIAALIMKEAFDYLDAPVERVTGKDVPLP 299
>gnl|CDD|237011 PRK11892, PRK11892, pyruvate dehydrogenase subunit beta;
Provisional.
Length = 464
Score = 261 bits (669), Expect = 1e-83
Identities = 127/298 (42%), Positives = 170/298 (57%), Gaps = 12/298 (4%)
Query: 45 AINQALHIALETDPRAYVFGEDVG-FGGVFRCTTGLADRFGKSRVFNTPLCEQGIVGFAI 103
A+ A+ + D +V GE+V + G ++ T GL FG RV +TP+ E G G +
Sbjct: 147 ALRDAMAEEMRRDEDVFVMGEEVAEYQGAYKVTQGLLQEFGARRVIDTPITEHGFAGIGV 206
Query: 104 GLAAMGNRAIAEIQFADYIFPAFDQIVNEAAKFRYRSGNQFNCGGLTVRAPYGAVGHGGH 163
G A G + I E ++ A DQI+N AAK Y SG Q C + R P GA
Sbjct: 207 GAAFAGLKPIVEFMTFNFAMQAIDQIINSAAKTLYMSGGQMGCP-IVFRGPNGAAARVAA 265
Query: 164 YHSQSPEAFFCHVPGLKVVIPRSPRQAKGLLLSCIRDPNPVVFFEPKWLYRLSVEEVPE- 222
HSQ A++ H+PGLKVV P S AKGLL + IRDPNPV+F E + LY S + VP+
Sbjct: 266 QHSQDYAAWYSHIPGLKVVAPYSAADAKGLLKAAIRDPNPVIFLENEILYGQSFD-VPKL 324
Query: 223 DDYMLPLSEAEVIREGSDITLVGWGAQLSIMEQACLDA----EKEGISCELIDLKTLIPW 278
DD++LP+ +A + REG D+T+V + SI L A KEGI E+IDL+T+ P
Sbjct: 325 DDFVLPIGKARIHREGKDVTIVSF----SIGMTYALKAAEELAKEGIDAEVIDLRTIRPM 380
Query: 279 DKETVEASVRKTGRLLISHEAPVTGGFGAEISASILERCFLRLEAPVARVCGLDTPFP 336
D ET+ SV+KT RL+ E G GAEI+A ++E+ F L+APV RV G D P P
Sbjct: 381 DTETIVESVKKTNRLVTVEEGWPQSGVGAEIAARVMEQAFDYLDAPVLRVTGKDVPMP 438
>gnl|CDD|215368 PLN02683, PLN02683, pyruvate dehydrogenase E1 component subunit
beta.
Length = 356
Score = 250 bits (641), Expect = 7e-81
Identities = 120/305 (39%), Positives = 176/305 (57%), Gaps = 5/305 (1%)
Query: 36 SGKSLNLYSAINQALHIALETDPRAYVFGEDVG-FGGVFRCTTGLADRFGKSRVFNTPLC 94
+ K + + A+N AL + DP+ ++ GE+VG + G ++ T GL ++G RV +TP+
Sbjct: 23 AAKEMTVRDALNSALDEEMSADPKVFIMGEEVGEYQGAYKITKGLLQKYGPDRVLDTPIT 82
Query: 95 EQGIVGFAIGLAAMGNRAIAEIQFADYIFPAFDQIVNEAAKFRYRSGNQFNCGGLTVRAP 154
E G G +G A G + + E ++ A D I+N AAK Y S Q + + R P
Sbjct: 83 EAGFTGIGVGAAYAGLKPVVEFMTFNFSMQAIDHIINSAAKTNYMSAGQISVP-IVFRGP 141
Query: 155 YGAVGHGGHYHSQSPEAFFCHVPGLKVVIPRSPRQAKGLLLSCIRDPNPVVFFEPKWLYR 214
GA G HSQ A++ VPGLKV+ P S A+GLL + IRDP+PVVF E + LY
Sbjct: 142 NGAAAGVGAQHSQCFAAWYSSVPGLKVLAPYSSEDARGLLKAAIRDPDPVVFLENELLYG 201
Query: 215 LSV---EEVPEDDYMLPLSEAEVIREGSDITLVGWGAQLSIMEQACLDAEKEGISCELID 271
S EV + ++LP+ +A++ REG D+T+V + + +A KEGIS E+I+
Sbjct: 202 ESFPVSAEVLDSSFVLPIGKAKIEREGKDVTIVAFSKMVGYALKAAEILAKEGISAEVIN 261
Query: 272 LKTLIPWDKETVEASVRKTGRLLISHEAPVTGGFGAEISASILERCFLRLEAPVARVCGL 331
L+++ P D++T+ ASVRKT RL+ E G GAEI AS++E F L+APV R+ G
Sbjct: 262 LRSIRPLDRDTINASVRKTNRLVTVEEGWPQHGVGAEICASVVEESFDYLDAPVERIAGA 321
Query: 332 DTPFP 336
D P P
Sbjct: 322 DVPMP 326
>gnl|CDD|177066 CHL00144, odpB, pyruvate dehydrogenase E1 component beta subunit;
Validated.
Length = 327
Score = 248 bits (634), Expect = 4e-80
Identities = 126/297 (42%), Positives = 175/297 (58%), Gaps = 5/297 (1%)
Query: 42 LYSAINQALHIALETDPRAYVFGEDVG-FGGVFRCTTGLADRFGKSRVFNTPLCEQGIVG 100
L+ A+ +A+ + DPR +V GEDVG +GG ++ T GL +++G RV +TP+ E G
Sbjct: 6 LFEALREAIDEEMARDPRVFVIGEDVGHYGGSYKVTKGLHEKYGDLRVLDTPIAENSFTG 65
Query: 101 FAIGLAAMGNRAIAEIQFADYIFPAFDQIVNEAAKFRYRSGNQFNCGGLTVRAPYGAVGH 160
AIG A G R I E ++ AF+QI N A Y SG F + +R P G VG
Sbjct: 66 MAIGAAMTGLRPIVEGMNMGFLLLAFNQISNNAGMLHYTSGGNFTIP-IVIRGP-GGVGR 123
Query: 161 G-GHYHSQSPEAFFCHVPGLKVVIPRSPRQAKGLLLSCIRDPNPVVFFEPKWLYRLSVEE 219
G HSQ E++F VPGL++V +P AKGLL S IR NPV+FFE LY L EE
Sbjct: 124 QLGAEHSQRLESYFQSVPGLQIVACSTPYNAKGLLKSAIRSNNPVIFFEHVLLYNLK-EE 182
Query: 220 VPEDDYMLPLSEAEVIREGSDITLVGWGAQLSIMEQACLDAEKEGISCELIDLKTLIPWD 279
+P+++Y+LPL +AEV+R G+DIT++ + + QA ++G E+IDL +L P D
Sbjct: 183 IPDNEYLLPLEKAEVVRPGNDITILTYSRMRHHVLQAVKVLVEKGYDPEIIDLISLKPLD 242
Query: 280 KETVEASVRKTGRLLISHEAPVTGGFGAEISASILERCFLRLEAPVARVCGLDTPFP 336
T+ SV+KT ++LI E TGG GAE+ A I E F L+AP+ R+ D P P
Sbjct: 243 LGTISKSVKKTHKVLIVEECMKTGGIGAELIAQINEHLFDELDAPIVRLSSQDVPTP 299
>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 = 150 bits (382), Expect = 2e-44
Identities = 60/171 (35%), Positives = 75/171 (43%), Gaps = 7/171 (4%)
Query: 45 AINQALHIALETDPRAYVFGEDVGFGGVFRCTTGLADRFGKSRVFNTPLCEQGIVGFAIG 104
A +AL + DPR G DV GG F T GL G RV +T + EQ +VG A G
Sbjct: 8 ASGEALAELAKRDPRVVGGGADVA-GGTFTVTKGLLHPQGDGRVIDTGIAEQAMVGIANG 66
Query: 105 LAAMGNRAIAEIQFADYIFPAFDQIVNEAAKFRYRSGNQFNCGGLTVRAPYGAVGHGGHY 164
+A G E F D+ A D I Y + + + R P G G +
Sbjct: 67 MALHGLLPPVEATFGDFANRADDAI------RHYAALGKLPVPFVVTRDPIGVGEDGPTH 120
Query: 165 HSQSPEAFFCHVPGLKVVIPRSPRQAKGLLLSCIRDPNPVVFFEPKWLYRL 215
SQ AF +P LKVV P + KGLL + I D PVV P+ L R
Sbjct: 121 QSQEDLAFLRAIPNLKVVRPSDAAETKGLLRAAIEDDGPVVLRLPRQLLRH 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 = 135 bits (342), Expect = 3e-39
Identities = 51/106 (48%), Positives = 76/106 (71%)
Query: 231 EAEVIREGSDITLVGWGAQLSIMEQACLDAEKEGISCELIDLKTLIPWDKETVEASVRKT 290
+AE++REG D+T+V +G+ + +A + KEGIS E+IDL+T+ P D++T+ SV+KT
Sbjct: 2 KAEILREGDDVTIVAYGSMVHEALEAAEELAKEGISAEVIDLRTVKPLDEDTILESVKKT 61
Query: 291 GRLLISHEAPVTGGFGAEISASILERCFLRLEAPVARVCGLDTPFP 336
GRL++ EA GGFG+E++A++ E F L+APV RV G DTP P
Sbjct: 62 GRLVVVEEAVKRGGFGSEVAAALAEEGFDYLDAPVLRVGGPDTPIP 107
>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 = 134 bits (341), Expect = 8e-39
Identities = 49/129 (37%), Positives = 61/129 (47%), Gaps = 13/129 (10%)
Query: 89 FNTPLCEQGIVGFAIGLAAMGNRAIAEIQFADYIFPAFDQIVNEAAKFRYRSGNQFNCGG 148
+T + EQ +VGFA GLA G R + EI F + AK + RS
Sbjct: 18 IDTGIAEQAMVGFAAGLALHGLRPVVEIFFTFFDR----------AKDQIRSAGASGNVP 67
Query: 149 LTVRAPYGAVGH--GGHYHSQSPEAFFCHVPGLKVVIPRSPRQAKGLLLSCIRDPNP-VV 205
+ R G G +HS EA +PGLKVV P P +AKGLL + IRD P V+
Sbjct: 68 VVFRHDGGGGVGEDGPTHHSIEDEALLRAIPGLKVVAPSDPAEAKGLLRAAIRDDGPVVI 127
Query: 206 FFEPKWLYR 214
E K LYR
Sbjct: 128 RLERKSLYR 136
>gnl|CDD|226467 COG3958, COG3958, Transketolase, C-terminal subunit [Carbohydrate
transport and metabolism].
Length = 312
Score = 93.1 bits (232), Expect = 2e-21
Identities = 76/277 (27%), Positives = 120/277 (43%), Gaps = 47/277 (16%)
Query: 76 TTGLADRFGKSRVFNTPLCEQGIVGFAIGLAAMGNRAIAEIQFADYIFPAFDQIVNEAAK 135
T A F R FN + EQ +VG A GLA G + A A++QI N A
Sbjct: 40 TGYFAKEFPD-RFFNVGIAEQDMVGTAAGLALAGKKPFVSTFAAFLSRRAWEQIRNSIAY 98
Query: 136 FRYRSGNQFNC------GGLTVRAPYGAVGHGGHYHSQSPE--AFFCHVPGLKVVIPRSP 187
N N G+T G G H Q+ E A +P + V+ P
Sbjct: 99 ------NNLNVKIVATHAGVTY-------GEDGSSH-QALEDIAIMRGLPNMTVIAPADA 144
Query: 188 RQAKGLLLSCIRDPNPVVFFEPKWLYRLSVEEVP----EDDYMLPLSEAEVIREGSDITL 243
+ + +L PV RL +VP E Y + +A V+R+GSD+T+
Sbjct: 145 VETRAILDQIADYKGPV-------YMRLGRGKVPVVVDEGGYTFEIGKANVLRDGSDLTI 197
Query: 244 VGWGAQLSIMEQACLDA----EKEGISCELIDLKTLIPWDKETVEASVRKTGRLLISHEA 299
+ G +M L+A +KEGIS +I++ T+ P D++ + + R+TGR++ + E
Sbjct: 198 IATG----VMVAEALEAAEILKKEGISAAVINMFTIKPIDEQAILKAARETGRIVTAEEH 253
Query: 300 PVTGGFGAEISASILERCFLRLEAPVARVCGLDTPFP 336
+ GG G+ ++ + E P+ R+ G+ F
Sbjct: 254 SIIGGLGSAVAEVLSENG----PTPMRRI-GVPDTFG 285
>gnl|CDD|224076 COG1154, Dxs, Deoxyxylulose-5-phosphate synthase [Coenzyme
metabolism / Lipid metabolism].
Length = 627
Score = 82.2 bits (204), Expect = 5e-17
Identities = 60/246 (24%), Positives = 108/246 (43%), Gaps = 31/246 (12%)
Query: 77 TGLADRFGK---SRVFNTPLCEQGIVGFAIGLAAMGNRAIAEIQFADYIFPAFDQIVNEA 133
TGL +F K R F+ + EQ V FA GLAA G + + I ++ ++ A+DQ++++
Sbjct: 347 TGL-VKFSKKFPDRFFDVGIAEQHAVTFAAGLAAEGMKPVVAI-YSTFLQRAYDQLIHDV 404
Query: 134 AKFRYRSGNQFNCGGLTV-----RAPYGAVGHGGHYHSQSPE-AFFCHVPGLKVVIPRSP 187
A L V RA G VG G H + +F +P + ++ PR
Sbjct: 405 A-----------IQNLPVTFAIDRA--GIVGADGPTHQGLFDLSFLRCIPNMVIMAPRDE 451
Query: 188 RQAKGLLLSCIR-DPNPVVFFEPKWLYRLSVEEVPEDDYM--LPLSEAEVIREGSDITLV 244
+ + +L + + D PV P R + V + L + + E+++EG + ++
Sbjct: 452 EELRQMLYTALAQDDGPVAIRYP----RGNGVGVILTPELEPLEIGKGELLKEGEKVAIL 507
Query: 245 GWGAQLSIMEQACLDAEKEGISCELIDLKTLIPWDKETVEASVRKTGRLLISHEAPVTGG 304
+G L + GIS ++D + + P D+ + + ++ E V GG
Sbjct: 508 AFGTMLPEALKVAEKLNAYGISVTVVDPRFVKPLDEALLLELAKSHDLVVTLEENVVDGG 567
Query: 305 FGAEIS 310
FG+ +
Sbjct: 568 FGSAVL 573
>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 = 77.5 bits (191), Expect = 2e-15
Identities = 53/234 (22%), Positives = 107/234 (45%), Gaps = 14/234 (5%)
Query: 78 GLADRFGKSRVFNTPLCEQGIVGFAIGLAAMGNRAIAEIQFADYIFPAFDQIVNEAAKFR 137
+ +F R F+ + EQ V FA G+A G + I ++ ++ A+DQ+V++
Sbjct: 345 KFSRKFPD-RYFDVAIAEQHAVTFAAGMAIEGYKPFVAI-YSTFLQRAYDQVVHDVCI-- 400
Query: 138 YRSGNQFNCGGLTVRAPYGAVGHGGHYHSQSPE-AFFCHVPGLKVVIPRSPRQAKGLLLS 196
+ RA G VG G H + + ++ +P + ++ P + + +L +
Sbjct: 401 -QKLPVLFA---IDRA--GIVGADGETHQGAFDISYLRCIPNMVIMAPSDENELRQMLYT 454
Query: 197 CIR-DPNPVVFFEPKWLYRLSVEEVPEDDYMLPLSEAEVIREGSDITLVGWGAQLSIMEQ 255
D P+ P+ + VE PE + LP+ ++EV+R+G I ++G+G + +
Sbjct: 455 GYHYDDGPIAVRYPRGNA-VGVELTPEPE-KLPIGKSEVLRKGEKILILGFGTLVPEALE 512
Query: 256 ACLDAEKEGISCELIDLKTLIPWDKETVEASVRKTGRLLISHEAPVTGGFGAEI 309
++GI ++D + + P D+E + +L+ E + GG G+ +
Sbjct: 513 VAESLNEKGIEATVVDARFVKPLDEELILEIAASHEKLVTVEENAIMGGAGSAV 566
>gnl|CDD|183601 PRK12571, PRK12571, 1-deoxy-D-xylulose-5-phosphate synthase;
Provisional.
Length = 641
Score = 75.1 bits (185), Expect = 9e-15
Identities = 72/268 (26%), Positives = 117/268 (43%), Gaps = 29/268 (10%)
Query: 62 VFGED-----------VGFGGVFRCTTGLADRFGKS---RVFNTPLCEQGIVGFAIGLAA 107
VFGE+ V TGL D+ K RVF+ + EQ V FA GLAA
Sbjct: 324 VFGEELTKEAAEDSDIVAITAAMPLGTGL-DKLQKRFPNRVFDVGIAEQHAVTFAAGLAA 382
Query: 108 MGNRAIAEIQFADYIFPAFDQIVNEAAKFRYRSGNQFNCGGLTVRAPYGAVGHGGHYHSQ 167
G + + ++ ++ +DQ++++ A N V G VG G H+
Sbjct: 383 AGLKPFCAV-YSTFLQRGYDQLLHDVA--------LQNLPVRFVLDRAGLVGADGATHAG 433
Query: 168 SPE-AFFCHVPGLKVVIPRSPRQAKGLLLSCI-RDPNPVVFFEPKWLYRLSVEEVPEDDY 225
+ + AF ++P + V+ PR + + +L + D P+ P+ E+P +
Sbjct: 434 AFDLAFLTNLPNMTVMAPRDEAELRHMLRTAAAHDDGPIAVRFPRGEGV--GVEIPAEGT 491
Query: 226 MLPLSEAEVIREGSDITLVGWGAQLSIMEQACLDAEKEGISCELIDLKTLIPWDKETVEA 285
+L + + V REG D+ ++ GA L A E EGIS + D + + P D+ +
Sbjct: 492 ILGIGKGRVPREGPDVAILSVGAHLHECLDAADLLEAEGISVTVADPRFVKPLDEALTDL 551
Query: 286 SVRKTGRLLISHEAPVTGGFGAEISASI 313
VR ++I E GGFGA + +
Sbjct: 552 LVRHH-IVVIVEEQGAMGGFGAHVLHHL 578
>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 = 62.5 bits (153), Expect = 7e-12
Identities = 41/172 (23%), Positives = 60/172 (34%), Gaps = 31/172 (18%)
Query: 45 AINQALHIALETDPRAYVFGEDVGFGGVFRCTTGLADRFGKSRVFNTPLCEQGIVGFAIG 104
A +AL + DPR D+G G A +F R + + EQ +VG A G
Sbjct: 2 AFGEALLELAKKDPRIVALSADLG-GSTG--LDKFAKKFPD-RFIDVGIAEQNMVGIAAG 57
Query: 105 LAAMGNRAIAEIQ--FADYIFPAFDQIVNEAAKFRYRSGNQFNC------GGLTVRAPYG 156
LA G + F A+DQI ++ A G++
Sbjct: 58 LALHGLKPFVSTFSFFLQR---AYDQIRHDVAL------QNLPVKFVGTHAGIS------ 102
Query: 157 AVGHGGHYHSQSPE--AFFCHVPGLKVVIPRSPRQAKGLLLSCIRDPNPVVF 206
VG G H Q E A +P + V+ P + L + + PV
Sbjct: 103 -VGEDGPTH-QGIEDIALLRAIPNMTVLRPADANETAAALEAALEYDGPVYI 152
>gnl|CDD|235470 PRK05444, PRK05444, 1-deoxy-D-xylulose-5-phosphate synthase;
Provisional.
Length = 580
Score = 63.9 bits (157), Expect = 4e-11
Identities = 63/255 (24%), Positives = 110/255 (43%), Gaps = 44/255 (17%)
Query: 77 TGLADRFGK---SRVFNTPLCEQGIVGFAIGLAAMGNRAIAEI-----QFADYIFPAFDQ 128
TGL +F K R F+ + EQ V FA GLA G + + I Q A+DQ
Sbjct: 310 TGL-VKFSKRFPDRYFDVGIAEQHAVTFAAGLATEGLKPVVAIYSTFLQ------RAYDQ 362
Query: 129 IVNEAAKFRYRSGNQFNCGGLTV-----RAPYGAVGHGGHYHSQSPE-AFFCHVPGLKVV 182
++++ A Q L V RA G VG G H + + ++ +P + ++
Sbjct: 363 VIHDVAL-------Q----NLPVTFAIDRA--GLVGADGPTHQGAFDLSYLRCIPNMVIM 409
Query: 183 IPRSPRQAKGLLLSCIR-DPNPVVFFEPKWLYRLSVEEVPEDD-YMLPLSEAEVIREGSD 240
P + + +L + + D P+ P R + V + LP+ + EV+REG D
Sbjct: 410 APSDENELRQMLYTALAYDDGPIAIRYP----RGNGVGVELPELEPLPIGKGEVLREGED 465
Query: 241 ITLVGWGAQLSIMEQACLDAEKEGISCELIDLKTLIPWDKETVEASVRKTGRLLISHEAP 300
+ ++ +G L L A + S ++D + + P D+E + K ++ E
Sbjct: 466 VAILAFGTML----AEALKAAERLASATVVDARFVKPLDEELLLELAAKHDLVVTVEEGA 521
Query: 301 VTGGFGAEISASILE 315
+ GGFG+ + + +
Sbjct: 522 IMGGFGSAVLEFLAD 536
>gnl|CDD|177870 PLN02225, PLN02225, 1-deoxy-D-xylulose-5-phosphate synthase.
Length = 701
Score = 56.6 bits (136), Expect = 1e-08
Identities = 64/246 (26%), Positives = 109/246 (44%), Gaps = 36/246 (14%)
Query: 81 DRFGKSRVFNTPLCEQGIVGFAIGLAAMGNRAIAEIQFADYIFPAFDQIVNEAAKFRYRS 140
+RF R FN + EQ V F+ GL++ G + I A ++ A+DQ+V++ R R
Sbjct: 419 ERF-PDRFFNVGMAEQHAVTFSAGLSSGGLKPFCIIPSA-FLQRAYDQVVHDVD--RQRK 474
Query: 141 GNQFNCGGLTVRAPYGAVGHGGHYHSQSPE-AFFCHVPGLKVVIPRSPRQAKGLLLSC-- 197
+F V G VG G + + AF +P + + P + ++ +
Sbjct: 475 AVRF------VITSAGLVGSDGPVQCGAFDIAFMSSLPNMIAMAPADEDELVNMVATAAY 528
Query: 198 IRDPNPVVFFEPKWLYRLSVEEVPEDDYMLP------LSEAEVIREGSDITLVGWGAQLS 251
+ D PV F P+ + +Y++P + V+ EG D+ L+G+GA
Sbjct: 529 VTD-RPVCFRFPR-------GSIVNMNYLVPTGLPIEIGRGRVLVEGQDVALLGYGA--- 577
Query: 252 IMEQACLDAE----KEGISCELIDLKTLIPWDKETVEASVRKTGRLLISHEAPVTGGFGA 307
M Q CL A K G++ + D + P D + V + + + LI+ E GGFG+
Sbjct: 578 -MVQNCLHAHSLLSKLGLNVTVADARFCKPLDIKLVR-DLCQNHKFLITVEEGCVGGFGS 635
Query: 308 EISASI 313
++ I
Sbjct: 636 HVAQFI 641
>gnl|CDD|178194 PLN02582, PLN02582, 1-deoxy-D-xylulose-5-phosphate synthase.
Length = 677
Score = 51.4 bits (123), Expect = 5e-07
Identities = 66/257 (25%), Positives = 110/257 (42%), Gaps = 52/257 (20%)
Query: 77 TGL---ADRFGKSRVFNTPLCEQGIVGFAIGLAAMGNRAIAEIQFADYIFPAFDQIVNEA 133
TGL A RF +R F+ + EQ V FA GLA G + I ++ ++ +DQ+V++
Sbjct: 387 TGLNLFARRF-PTRCFDVGIAEQHAVTFAAGLACEGLKPFCAI-YSSFLQRGYDQVVHDV 444
Query: 134 ------AKFRY-RSG-----NQFNCGGLTVRAPYGAVGHGGHYHSQSPEAFFCHVPGLKV 181
+F R+G +CG V Y A + S EA H+
Sbjct: 445 DLQKLPVRFAMDRAGLVGADGPTHCGAFDV--TYMACLPNMVVMAPSDEAELFHMVATAA 502
Query: 182 VIPRSPRQAKGLLLSCIRDP--NPVVFFEPKWLYRLSVEEVPEDDYMLPLS--EAEVIRE 237
I P SC R P N + ++P ++ +P+ + ++ E
Sbjct: 503 AIDDRP--------SCFRYPRGNGIGV------------QLPPNNKGIPIEVGKGRILLE 542
Query: 238 GSDITLVGWGAQLSIMEQACLDA----EKEGISCELIDLKTLIPWDKETVEASVRKTGRL 293
G + L+G+G Q+CL A E+ G+S + D + P D+ + S+ K+ +
Sbjct: 543 GERVALLGYGT----AVQSCLAAASLLERHGLSATVADARFCKPLDRALIR-SLAKSHEV 597
Query: 294 LISHEAPVTGGFGAEIS 310
LI+ E GGFG+ ++
Sbjct: 598 LITVEEGSIGGFGSHVA 614
>gnl|CDD|177878 PLN02234, PLN02234, 1-deoxy-D-xylulose-5-phosphate synthase.
Length = 641
Score = 46.2 bits (109), Expect = 2e-05
Identities = 56/235 (23%), Positives = 104/235 (44%), Gaps = 30/235 (12%)
Query: 86 SRVFNTPLCEQGIVGFAIGLAAMGNRAIAEIQFADYIFPAFDQIVNEAAKFRYRSGNQFN 145
+R F+ + EQ V FA GLA G + I ++ ++ A+DQ+V++ +
Sbjct: 399 TRCFDVGIAEQHAVTFAAGLACEGLKPFCTI-YSSFMQRAYDQVVHDV-----------D 446
Query: 146 CGGLTVRAPY---GAVGHGGHYHSQSPE-AFFCHVPGLKVVIPRSPRQAKGLLLSCIR-D 200
L VR G +G G H + + F +P + V+ P + ++ + D
Sbjct: 447 LQKLPVRFAIDRAGLMGADGPTHCGAFDVTFMACLPNMIVMAPSDEAELFNMVATAAAID 506
Query: 201 PNPVVFFEPKWLYRLSVEEVPEDDYMLPLS--EAEVIREGSDITLVGWGAQLSIMEQACL 258
P F + + V +P + +PL ++R+G + L+G+G+ + Q CL
Sbjct: 507 DRPSCFRYHRG-NGIGVS-LPPGNKGVPLQIGRGRILRDGERVALLGYGSAV----QRCL 560
Query: 259 DA----EKEGISCELIDLKTLIPWDKETVEASVRKTGRLLISHEAPVTGGFGAEI 309
+A + G+ + D + P D + S+ K+ +LI+ E GGFG+ +
Sbjct: 561 EAASMLSERGLKITVADARFCKPLDVALIR-SLAKSHEVLITVEEGSIGGFGSHV 614
>gnl|CDD|161785 TIGR00239, 2oxo_dh_E1, 2-oxoglutarate dehydrogenase, E1 component.
The 2-oxoglutarate dehydrogenase complex consists of
this thiamine pyrophosphate-binding subunit (E1),
dihydrolipoamide succinyltransferase (E2), and lipoamide
dehydrogenase (E3). The E1 ortholog from Corynebacterium
glutamicum is unusual in having an N-terminal extension
that resembles the dihydrolipoamide succinyltransferase
(E2) component of 2-oxoglutarate dehydrogenase [Energy
metabolism, TCA cycle].
Length = 929
Score = 46.0 bits (109), Expect = 2e-05
Identities = 48/167 (28%), Positives = 71/167 (42%), Gaps = 23/167 (13%)
Query: 70 GGVFRCTTGLADRFGKSRVFNTPLCEQGIVGFAIGLAAMGNR--AIAEIQFADYIFPA-- 125
G + L + G RV+N+ L E+ ++GF G A R I E QF D+ A
Sbjct: 631 GSTYTPLQHLHNGQGAFRVWNSVLSEESVLGFEYGYATTSPRTLVIWEAQFGDFANGAQV 690
Query: 126 -FDQIVNEA-AKFRYRSGNQFNCGGLTVRAPYGAVGHGGHYHSQSPEAF--FCHVPGLKV 181
DQ ++ K+ S GL + P+G G G + S E F ++V
Sbjct: 691 VIDQFISSGEQKWGQMS-------GLVMLLPHGYEGQGPEHSSGRLERFLQLAAEQNMQV 743
Query: 182 VIPRSPRQAKGLL----LSCIRDPNPVVFFEPKWLYR--LSVEEVPE 222
+P +P Q +L L +R P+V PK L R L+V + E
Sbjct: 744 CVPTTPAQVFHILRRQALRGMR--RPLVVMSPKSLLRHPLAVSSLEE 788
>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 = 41.6 bits (98), Expect = 1e-04
Identities = 30/154 (19%), Positives = 50/154 (32%), Gaps = 19/154 (12%)
Query: 62 VFGEDVGFGGVFRCTTGLADRFGKSRVFNTPLCEQGIVGFAIGLAAMGNRAIAEIQFADY 121
VFG A R G R+ +T + E G G A G A G + +
Sbjct: 15 VFGYPGDEISSLL----DALREGDKRIIDTVIHELGAAGAAAGYARAGGPPVVIVTSGTG 70
Query: 122 IFPAFDQIVNEAAKFRYRSGNQFNCGGLTVRAPYGAVGHG-GHYHSQSPEAFFCHVPGLK 180
+ A + + + AA+ + + + G + S + +P
Sbjct: 71 LLNAINGLADAAAE---------HLPVVFLIGARGISAQAKQTFQSMFDLGMYRSIPEAN 121
Query: 181 VVIPRSPRQAKGLLLSCIR----DPNPVVFFEPK 210
+ P SP + + IR PVV P+
Sbjct: 122 ISSP-SPAELPAGIDHAIRTAYASQGPVVVRLPR 154
>gnl|CDD|223641 COG0567, SucA, 2-oxoglutarate dehydrogenase complex, dehydrogenase
(E1) component, and related enzymes [Energy production
and conversion].
Length = 906
Score = 39.2 bits (92), Expect = 0.003
Identities = 48/162 (29%), Positives = 68/162 (41%), Gaps = 31/162 (19%)
Query: 79 LADRFGKSRVFNTPLCEQGIVGFAIG--LAAMGNRAIAEIQFADYIFPA---FDQ-IVNE 132
L+ GK V N+PL E+ ++GF G LA + E QF D+ A DQ I +
Sbjct: 620 LSKGQGKFEVINSPLSEEAVLGFEYGYSLANPKTLVLWEAQFGDFANGAQVVIDQFISSG 679
Query: 133 AAKFRYRSGNQFNCGGLTVRAPYGAVGHGGHYHSQSPEAFF--CHVPGLKVVIPRSP--- 187
K+ S GL + P+G G G + S E F C ++VV+P +P
Sbjct: 680 EQKWGRMS-------GLVMLLPHGYEGQGPEHSSARLERFLQLCAENNMQVVVPSTPAQY 732
Query: 188 -----RQAKGLLLSCIRDPNPVVFFEPKWLYR--LSVEEVPE 222
RQA P++ PK L R L+V + E
Sbjct: 733 FHLLRRQALRDF------RKPLIVMTPKSLLRHKLAVSSLEE 768
>gnl|CDD|223746 COG0674, PorA, Pyruvate:ferredoxin oxidoreductase and related
2-oxoacid:ferredoxin oxidoreductases, alpha subunit
[Energy production and conversion].
Length = 365
Score = 33.1 bits (76), Expect = 0.20
Identities = 14/60 (23%), Positives = 30/60 (50%), Gaps = 1/60 (1%)
Query: 237 EGSDITLVGWGAQLSIMEQACLDA-EKEGISCELIDLKTLIPWDKETVEASVRKTGRLLI 295
E ++I +V G+ +A +D +G L+ ++TL P+ E + + KT +++
Sbjct: 255 EDAEIVIVAMGSSKGSTAEAVVDLLRDKGEKVGLLKVRTLRPFPAEEIREVLPKTNAVVV 314
>gnl|CDD|237030 PRK12270, kgd, alpha-ketoglutarate decarboxylase; Reviewed.
Length = 1228
Score = 33.3 bits (77), Expect = 0.24
Identities = 48/162 (29%), Positives = 69/162 (42%), Gaps = 34/162 (20%)
Query: 79 LADRFGKSRVFNTPLCEQGIVGFAIGLAAMGNRAIA--EIQFADYIFPA---FDQIVNEA 133
L+D GK V+++ L E +GF G + A+ E QF D+ A D+ ++
Sbjct: 941 LSDDQGKFLVYDSLLSEYAAMGFEYGYSVERPDALVLWEAQFGDFANGAQTIIDEFISSG 1000
Query: 134 -AKFRYRSGNQFNCGGLTVRAPYGAVGHGGHYHSQSPEAFF--CHVPGLKVVIPRSP--- 187
AK+ RS G+ + P+G G G + S E F C + V P +P
Sbjct: 1001 EAKWGQRS-------GVVLLLPHGYEGQGPDHSSARIERFLQLCAEGNMTVAQPSTPANY 1053
Query: 188 -----RQAKGLLLSCIRDPNPVVFFEPKWLYRL-----SVEE 219
RQA LS R P+V F PK + RL VE+
Sbjct: 1054 FHLLRRQA----LSGPR--RPLVVFTPKSMLRLKAAVSDVED 1089
>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 = 32.1 bits (74), Expect = 0.48
Identities = 14/59 (23%), Positives = 30/59 (50%)
Query: 237 EGSDITLVGWGAQLSIMEQACLDAEKEGISCELIDLKTLIPWDKETVEASVRKTGRLLI 295
E +D+ ++GWG+ + +A EGI L+ L+ L P+ K + + ++++
Sbjct: 462 EDADVLIIGWGSTYGAIREAVERLRAEGIKVALLHLRLLYPFPKNELAELLEGAKKVIV 520
>gnl|CDD|225364 COG2805, PilT, Tfp pilus assembly protein, pilus retraction ATPase
PilT [Cell motility and secretion / Intracellular
trafficking and secretion].
Length = 353
Score = 30.3 bits (69), Expect = 1.8
Identities = 16/51 (31%), Positives = 23/51 (45%), Gaps = 11/51 (21%)
Query: 24 KQLIQQHDGGV------GSGKSLNLYSAIN-----QALHIALETDPRAYVF 63
++L + G + GSGKS L + I+ +A HI DP YV
Sbjct: 118 RELAESPRGLILVTGPTGSGKSTTLAAMIDYINKHKAKHILTIEDPIEYVH 168
>gnl|CDD|182281 PRK10170, PRK10170, hydrogenase 1 large subunit; Provisional.
Length = 597
Score = 29.6 bits (66), Expect = 2.7
Identities = 17/71 (23%), Positives = 28/71 (39%), Gaps = 1/71 (1%)
Query: 145 NCGGLT-VRAPYGAVGHGGHYHSQSPEAFFCHVPGLKVVIPRSPRQAKGLLLSCIRDPNP 203
C G+ AP GA+GH + + C VP PR P+ G + + +
Sbjct: 498 ECRGVGFTEAPRGALGHWAAIRDGKIDLYQCVVPTTWNASPRDPKGQIGAYEAALMNTKM 557
Query: 204 VVFFEPKWLYR 214
+ +P + R
Sbjct: 558 AIPEQPLEILR 568
>gnl|CDD|233406 TIGR01420, pilT_fam, pilus retraction protein PilT. This model
represents the PilT subfamily of proteins related to
GspE, a protein involved in type II secretion (also
called the General Secretion Pathway). PilT is an
apparent cytosolic ATPase associated with type IV pilus
systems. It is not required for pilin biogenesis, but is
required for twitching motility and social gliding
behaviors, shown in some species, powered by pilus
retraction. Members of this family may be found in some
species that type IV pili but have related structures
for DNA uptake and natural transformation [Cell
envelope, Surface structures, Cellular processes,
Chemotaxis and motility].
Length = 343
Score = 29.6 bits (67), Expect = 2.8
Identities = 17/37 (45%), Positives = 18/37 (48%), Gaps = 5/37 (13%)
Query: 32 GGVGSGKSLNLYSAI-----NQALHIALETDPRAYVF 63
G GSGKS L S I N+A HI DP YV
Sbjct: 129 GPTGSGKSTTLASMIDYINKNKAYHIITIEDPIEYVH 165
>gnl|CDD|133146 cd05479, RP_DDI, RP_DDI; retropepsin-like domain of DNA damage
inducible protein. The family represents the
retropepsin-like domain of DNA damage inducible protein.
DNA damage inducible protein has a retropepsin-like
domain and an amino-terminal ubiquitin-like domain
and/or a UBA (ubiquitin-associated) domain. This CD
represents the retropepsin-like domain of DDI.
Length = 124
Score = 28.3 bits (64), Expect = 3.2
Identities = 15/29 (51%), Positives = 19/29 (65%), Gaps = 3/29 (10%)
Query: 243 LVGWGAQLSIMEQACLDAEKEGISCELID 271
V GAQ++IM +AC AEK G+ LID
Sbjct: 31 FVDSGAQMTIMSKAC--AEKCGLM-RLID 56
>gnl|CDD|225090 COG2179, COG2179, Predicted hydrolase of the HAD superfamily
[General function prediction only].
Length = 175
Score = 28.0 bits (63), Expect = 6.3
Identities = 10/29 (34%), Positives = 15/29 (51%), Gaps = 1/29 (3%)
Query: 261 EKEGISCELIDL-KTLIPWDKETVEASVR 288
+ GI ++DL TL+PWD +R
Sbjct: 24 KAHGIKGVILDLDNTLVPWDNPDATPELR 52
>gnl|CDD|181526 PRK08659, PRK08659, 2-oxoglutarate ferredoxin oxidoreductase
subunit alpha; Validated.
Length = 376
Score = 28.3 bits (64), Expect = 6.8
Identities = 14/59 (23%), Positives = 31/59 (52%)
Query: 237 EGSDITLVGWGAQLSIMEQACLDAEKEGISCELIDLKTLIPWDKETVEASVRKTGRLLI 295
E +++ +V +G+ +A +A +EGI L L T+ P+ +E + +K +++
Sbjct: 272 EDAEVVVVAYGSVARSARRAVKEAREEGIKVGLFRLITVWPFPEEAIRELAKKVKAIVV 330
>gnl|CDD|238551 cd01131, PilT, Pilus retraction ATPase PilT. PilT is a nucleotide
binding protein responsible for the retraction of type
IV pili, likely by pili disassembly. This retraction
provides the force required for travel of bacteria in
low water environments by a mechanism known as
twitching motility.
Length = 198
Score = 28.1 bits (63), Expect = 6.9
Identities = 14/37 (37%), Positives = 17/37 (45%), Gaps = 5/37 (13%)
Query: 32 GGVGSGKSLNLYSAI-----NQALHIALETDPRAYVF 63
G GSGKS L + I N+ HI DP +V
Sbjct: 8 GPTGSGKSTTLAAMIDYINKNKTHHILTIEDPIEFVH 44
>gnl|CDD|118200 pfam09668, Asp_protease, Aspartyl protease. This family of
eukaryotic aspartyl proteases have a fold similar to
retroviral proteases which implies they function
proteolytically during regulated protein turnover.
Length = 124
Score = 26.9 bits (60), Expect = 8.5
Identities = 13/25 (52%), Positives = 15/25 (60%), Gaps = 3/25 (12%)
Query: 247 GAQLSIMEQACLDAEKEGISCELID 271
GAQ SIM C AE+ GI L+D
Sbjct: 43 GAQTSIMSPRC--AERCGIM-RLLD 64
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.322 0.139 0.429
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: 19,228,580
Number of extensions: 1893361
Number of successful extensions: 1435
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1393
Number of HSP's successfully gapped: 43
Length of query: 372
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 274
Effective length of database: 6,590,910
Effective search space: 1805909340
Effective search space used: 1805909340
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 60 (26.7 bits)