RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 015415
(407 letters)
>gnl|CDD|177066 CHL00144, odpB, pyruvate dehydrogenase E1 component beta subunit;
Validated.
Length = 327
Score = 642 bits (1659), Expect = 0.0
Identities = 258/323 (79%), Positives = 283/323 (87%)
Query: 85 HELLLFEALREGLEEEMDRDPHVCVMGEDVGHYGGSYKVTKGLADKYGDLRVLDTPIAEN 144
E+ LFEALRE ++EEM RDP V V+GEDVGHYGGSYKVTKGL +KYGDLRVLDTPIAEN
Sbjct: 2 SEVFLFEALREAIDEEMARDPRVFVIGEDVGHYGGSYKVTKGLHEKYGDLRVLDTPIAEN 61
Query: 145 SFTGMGIGAAMTGLRPIVEGMNMGFLLLAFNQISNNCGMLHYTSGGQFTIPIVIRGPGGV 204
SFTGM IGAAMTGLRPIVEGMNMGFLLLAFNQISNN GMLHYTSGG FTIPIVIRGPGGV
Sbjct: 62 SFTGMAIGAAMTGLRPIVEGMNMGFLLLAFNQISNNAGMLHYTSGGNFTIPIVIRGPGGV 121
Query: 205 GRQLGAEHSQRLESYFQSIPGIQMVACSTPYNAKGLMKAAIRSENPVILFEHVLLYNLKE 264
GRQLGAEHSQRLESYFQS+PG+Q+VACSTPYNAKGL+K+AIRS NPVI FEHVLLYNLKE
Sbjct: 122 GRQLGAEHSQRLESYFQSVPGLQIVACSTPYNAKGLLKSAIRSNNPVIFFEHVLLYNLKE 181
Query: 265 RIPDEEYICNLEEAEMVRPGEHVTILTYSRMRYHVMQAAKTLVNKGYDPEVIDIRSLKPF 324
IPD EY+ LE+AE+VRPG +TILTYSRMR+HV+QA K LV KGYDPE+ID+ SLKP
Sbjct: 182 EIPDNEYLLPLEKAEVVRPGNDITILTYSRMRHHVLQAVKVLVEKGYDPEIIDLISLKPL 241
Query: 325 DLYTIGNSIKKTHRVLIVEECMRTGGIGASLTAAITENFHDYLDAPIVCLSSQDVPTPYA 384
DL TI S+KKTH+VLIVEECM+TGGIGA L A I E+ D LDAPIV LSSQDVPTPY
Sbjct: 242 DLGTISKSVKKTHKVLIVEECMKTGGIGAELIAQINEHLFDELDAPIVRLSSQDVPTPYN 301
Query: 385 GTLEEWTVVQPAQIVTAVEQLCQ 407
G LEE TV+QPAQI+ AVEQ+
Sbjct: 302 GPLEEATVIQPAQIIEAVEQIIT 324
>gnl|CDD|223101 COG0022, AcoB, Pyruvate/2-oxoglutarate dehydrogenase complex,
dehydrogenase (E1) component, eukaryotic type, beta
subunit [Energy production and conversion].
Length = 324
Score = 466 bits (1201), Expect = e-165
Identities = 162/323 (50%), Positives = 222/323 (68%), Gaps = 1/323 (0%)
Query: 86 ELLLFEALREGLEEEMDRDPHVCVMGEDVGHYGGSYKVTKGLADKYGDLRVLDTPIAENS 145
++ + EA+ E ++EEM+RD V V+GEDVG YGG ++VTKGL +K+G+ RV+DTPIAE+
Sbjct: 1 QMTMIEAINEAMDEEMERDERVVVLGEDVGVYGGVFRVTKGLQEKFGEERVIDTPIAESG 60
Query: 146 FTGMGIGAAMTGLRPIVEGMNMGFLLLAFNQISNNCGMLHYTSGGQFTIPIVIRGPGGVG 205
G+ +GAA+TGLRPIVE F+ AF+QI N + Y SGGQFT+PIVIR P G G
Sbjct: 61 IAGIAVGAALTGLRPIVEIQFADFIYPAFDQIVNQAAKIRYRSGGQFTVPIVIRTPNGGG 120
Query: 206 RQLGAEHSQRLESYFQSIPGIQMVACSTPYNAKGLMKAAIRSENPVILFEHVLLYN-LKE 264
GA+HSQ LE+ F IPG+++V STPY+AKGL+KAAIR +PVI EH LY K
Sbjct: 121 IGGGAQHSQSLEALFAHIPGLKVVMPSTPYDAKGLLKAAIRDPDPVIFLEHKRLYRSFKG 180
Query: 265 RIPDEEYICNLEEAEMVRPGEHVTILTYSRMRYHVMQAAKTLVNKGYDPEVIDIRSLKPF 324
+P+E+Y L +A++VR G VTI+TY M + ++AA+ L +G EVID+R+L P
Sbjct: 181 EVPEEDYTIPLGKAKIVREGSDVTIVTYGAMVHTALEAAEELEKEGISAEVIDLRTLSPL 240
Query: 325 DLYTIGNSIKKTHRVLIVEECMRTGGIGASLTAAITENFHDYLDAPIVCLSSQDVPTPYA 384
D TI S+KKT R++IV E +TGGIGA + A I E DYLDAPI+ ++ D P PY+
Sbjct: 241 DKETIIASVKKTGRLVIVHEAPKTGGIGAEIAALIAEEAFDYLDAPILRVAGPDTPVPYS 300
Query: 385 GTLEEWTVVQPAQIVTAVEQLCQ 407
LE+ + P +IV AV+++ +
Sbjct: 301 AALEKAYLPNPERIVAAVKKVLE 323
>gnl|CDD|185502 PTZ00182, PTZ00182, 3-methyl-2-oxobutanate dehydrogenase;
Provisional.
Length = 355
Score = 449 bits (1156), Expect = e-158
Identities = 158/342 (46%), Positives = 205/342 (59%), Gaps = 1/342 (0%)
Query: 66 NAVATKADSAASTSASKQGHELLLFEALREGLEEEMDRDPHVCVMGEDVGHYGGSYKVTK 125
+ A ++ST + ++ + EA+ L+EE+ RDP V V+GEDV YGG YK TK
Sbjct: 14 PNSFSSASRSSSTESKGATVKMNVREAINSALDEELARDPKVFVLGEDVAQYGGVYKCTK 73
Query: 126 GLADKYGDLRVLDTPIAENSFTGMGIGAAMTGLRPIVEGMNMGFLLLAFNQISNNCGMLH 185
GL DKYG RV DTPI E F G IGAAM GLRPI E M F+ AF+QI N
Sbjct: 74 GLLDKYGPDRVFDTPITEQGFAGFAIGAAMNGLRPIAEFMFADFIFPAFDQIVNEAAKYR 133
Query: 186 YTSGGQFTIPIVIRGPGGVGRQLGAEHSQRLESYFQSIPGIQMVACSTPYNAKGLMKAAI 245
Y SGGQF PIVIRGP G GA HSQ E+YF +PG+++VA S P +AKGL+KAAI
Sbjct: 134 YMSGGQFDCPIVIRGPNGAVGHGGAYHSQSFEAYFAHVPGLKVVAPSDPEDAKGLLKAAI 193
Query: 246 RSENPVILFEHVLLYNLKERIPDEE-YICNLEEAEMVRPGEHVTILTYSRMRYHVMQAAK 304
R NPV+ FE LLY + E Y L +A++VR G+ VTI+ Y + ++AA+
Sbjct: 194 RDPNPVVFFEPKLLYRESVEVVPEADYTLPLGKAKVVREGKDVTIVGYGSQVHVALKAAE 253
Query: 305 TLVNKGYDPEVIDIRSLKPFDLYTIGNSIKKTHRVLIVEECMRTGGIGASLTAAITENFH 364
L +G EVID+RSL+P+D TI S+KKT R +IV E T GIGA + A I E+
Sbjct: 254 ELAKEGISCEVIDLRSLRPWDRETIVKSVKKTGRCVIVHEAPPTCGIGAEIAAQIMEDCF 313
Query: 365 DYLDAPIVCLSSQDVPTPYAGTLEEWTVVQPAQIVTAVEQLC 406
YL+API + D P PYA LE + ++V A +++
Sbjct: 314 LYLEAPIKRVCGADTPFPYAKNLEPAYLPDKEKVVEAAKRVL 355
>gnl|CDD|169719 PRK09212, PRK09212, pyruvate dehydrogenase subunit beta; Validated.
Length = 327
Score = 371 bits (954), Expect = e-128
Identities = 141/316 (44%), Positives = 206/316 (65%)
Query: 91 EALREGLEEEMDRDPHVCVMGEDVGHYGGSYKVTKGLADKYGDLRVLDTPIAENSFTGMG 150
EALR+ ++EEM+RDP V +MGE+VG Y G+YKVT+GL +++G RV+DTPI E+ F G+
Sbjct: 8 EALRDAMQEEMERDPKVFLMGEEVGEYQGAYKVTQGLLEQFGPKRVIDTPITEHGFAGLA 67
Query: 151 IGAAMTGLRPIVEGMNMGFLLLAFNQISNNCGMLHYTSGGQFTIPIVIRGPGGVGRQLGA 210
+GAA GLRPIVE M F + A +QI N+ +Y SGGQ PIV RGP G ++ A
Sbjct: 68 VGAAFAGLRPIVEFMTFNFSMQAIDQIVNSAAKTNYMSGGQLKCPIVFRGPNGAAARVAA 127
Query: 211 EHSQRLESYFQSIPGIQMVACSTPYNAKGLMKAAIRSENPVILFEHVLLYNLKERIPDEE 270
+HSQ +++ IPG+++VA + KGL+K AIR NPVI E+ +LY +P+EE
Sbjct: 128 QHSQCYAAWYSHIPGLKVVAPYFAADCKGLLKTAIRDPNPVIFLENEILYGHSHEVPEEE 187
Query: 271 YICNLEEAEMVRPGEHVTILTYSRMRYHVMQAAKTLVNKGYDPEVIDIRSLKPFDLYTIG 330
+ +A ++R G VTI+T+S ++AA+ L +G EVID+R+L+P D TI
Sbjct: 188 ESIPIGKAAILREGSDVTIVTFSIQVKLALEAAELLEKEGISVEVIDLRTLRPLDTETII 247
Query: 331 NSIKKTHRVLIVEECMRTGGIGASLTAAITENFHDYLDAPIVCLSSQDVPTPYAGTLEEW 390
S+KKT+R+++VEE G+GA + A I + DYLDAP+ ++ +DVP PYA LE+
Sbjct: 248 ESVKKTNRLVVVEEGWPFAGVGAEIAALIMKEAFDYLDAPVERVTGKDVPLPYAANLEKL 307
Query: 391 TVVQPAQIVTAVEQLC 406
+ I+ AV+++C
Sbjct: 308 ALPSEEDIIEAVKKVC 323
>gnl|CDD|237011 PRK11892, PRK11892, pyruvate dehydrogenase subunit beta;
Provisional.
Length = 464
Score = 345 bits (887), Expect = e-115
Identities = 140/317 (44%), Positives = 208/317 (65%), Gaps = 1/317 (0%)
Query: 91 EALREGLEEEMDRDPHVCVMGEDVGHYGGSYKVTKGLADKYGDLRVLDTPIAENSFTGMG 150
EALR+ + EEM RD V VMGE+V Y G+YKVT+GL ++G RV+DTPI E+ F G+G
Sbjct: 146 EALRDAMAEEMRRDEDVFVMGEEVAEYQGAYKVTQGLLQEFGARRVIDTPITEHGFAGIG 205
Query: 151 IGAAMTGLRPIVEGMNMGFLLLAFNQISNNCGMLHYTSGGQFTIPIVIRGPGGVGRQLGA 210
+GAA GL+PIVE M F + A +QI N+ Y SGGQ PIV RGP G ++ A
Sbjct: 206 VGAAFAGLKPIVEFMTFNFAMQAIDQIINSAAKTLYMSGGQMGCPIVFRGPNGAAARVAA 265
Query: 211 EHSQRLESYFQSIPGIQMVACSTPYNAKGLMKAAIRSENPVILFEHVLLYNLKERIPD-E 269
+HSQ +++ IPG+++VA + +AKGL+KAAIR NPVI E+ +LY +P +
Sbjct: 266 QHSQDYAAWYSHIPGLKVVAPYSAADAKGLLKAAIRDPNPVIFLENEILYGQSFDVPKLD 325
Query: 270 EYICNLEEAEMVRPGEHVTILTYSRMRYHVMQAAKTLVNKGYDPEVIDIRSLKPFDLYTI 329
+++ + +A + R G+ VTI+++S + ++AA+ L +G D EVID+R+++P D TI
Sbjct: 326 DFVLPIGKARIHREGKDVTIVSFSIGMTYALKAAEELAKEGIDAEVIDLRTIRPMDTETI 385
Query: 330 GNSIKKTHRVLIVEECMRTGGIGASLTAAITENFHDYLDAPIVCLSSQDVPTPYAGTLEE 389
S+KKT+R++ VEE G+GA + A + E DYLDAP++ ++ +DVP PYA LE+
Sbjct: 386 VESVKKTNRLVTVEEGWPQSGVGAEIAARVMEQAFDYLDAPVLRVTGKDVPMPYAANLEK 445
Query: 390 WTVVQPAQIVTAVEQLC 406
+ A++V AV+ +C
Sbjct: 446 LALPSVAEVVEAVKAVC 462
>gnl|CDD|215368 PLN02683, PLN02683, pyruvate dehydrogenase E1 component subunit
beta.
Length = 356
Score = 323 bits (829), Expect = e-108
Identities = 143/345 (41%), Positives = 216/345 (62%), Gaps = 10/345 (2%)
Query: 69 ATKADSAASTSASKQGHELLLFEALREGLEEEMDRDPHVCVMGEDVGHYGGSYKVTKGLA 128
A +AA+ + E+ + +AL L+EEM DP V +MGE+VG Y G+YK+TKGL
Sbjct: 9 TRPAAAAAARGYASAAKEMTVRDALNSALDEEMSADPKVFIMGEEVGEYQGAYKITKGLL 68
Query: 129 DKYGDLRVLDTPIAENSFTGMGIGAAMTGLRPIVEGMNMGFLLLAFNQISNNCGMLHYTS 188
KYG RVLDTPI E FTG+G+GAA GL+P+VE M F + A + I N+ +Y S
Sbjct: 69 QKYGPDRVLDTPITEAGFTGIGVGAAYAGLKPVVEFMTFNFSMQAIDHIINSAAKTNYMS 128
Query: 189 GGQFTIPIVIRGPGGVGRQLGAEHSQRLESYFQSIPGIQMVACSTPYN---AKGLMKAAI 245
GQ ++PIV RGP G +GA+HSQ +++ S+PG++++A PY+ A+GL+KAAI
Sbjct: 129 AGQISVPIVFRGPNGAAAGVGAQHSQCFAAWYSSVPGLKVLA---PYSSEDARGLLKAAI 185
Query: 246 RSENPVILFEHVLLYN----LKERIPDEEYICNLEEAEMVRPGEHVTILTYSRMRYHVMQ 301
R +PV+ E+ LLY + + D ++ + +A++ R G+ VTI+ +S+M + ++
Sbjct: 186 RDPDPVVFLENELLYGESFPVSAEVLDSSFVLPIGKAKIEREGKDVTIVAFSKMVGYALK 245
Query: 302 AAKTLVNKGYDPEVIDIRSLKPFDLYTIGNSIKKTHRVLIVEECMRTGGIGASLTAAITE 361
AA+ L +G EVI++RS++P D TI S++KT+R++ VEE G+GA + A++ E
Sbjct: 246 AAEILAKEGISAEVINLRSIRPLDRDTINASVRKTNRLVTVEEGWPQHGVGAEICASVVE 305
Query: 362 NFHDYLDAPIVCLSSQDVPTPYAGTLEEWTVVQPAQIVTAVEQLC 406
DYLDAP+ ++ DVP PYA LE + Q IV A ++ C
Sbjct: 306 ESFDYLDAPVERIAGADVPMPYAANLERLALPQVEDIVRAAKRAC 350
>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 = 301 bits (773), Expect = e-103
Identities = 103/167 (61%), Positives = 125/167 (74%)
Query: 91 EALREGLEEEMDRDPHVCVMGEDVGHYGGSYKVTKGLADKYGDLRVLDTPIAENSFTGMG 150
+A+ E L+EEM+RDP V V+GEDVG YGG +KVTKGL DK+G RV+DTPIAE G+
Sbjct: 1 QAINEALDEEMERDPRVVVLGEDVGDYGGVFKVTKGLLDKFGPDRVIDTPIAEAGIVGLA 60
Query: 151 IGAAMTGLRPIVEGMNMGFLLLAFNQISNNCGMLHYTSGGQFTIPIVIRGPGGVGRQLGA 210
+GAAM GLRPIVE M F L AF+QI N L Y SGGQF +PIVIRGP G G GA
Sbjct: 61 VGAAMNGLRPIVEIMFADFALPAFDQIVNEAAKLRYMSGGQFKVPIVIRGPNGGGIGGGA 120
Query: 211 EHSQRLESYFQSIPGIQMVACSTPYNAKGLMKAAIRSENPVILFEHV 257
+HSQ LE++F IPG+++VA STPY+AKGL+KAAIR ++PVI EH
Sbjct: 121 QHSQSLEAWFAHIPGLKVVAPSTPYDAKGLLKAAIRDDDPVIFLEHK 167
>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 = 190 bits (484), Expect = 3e-59
Identities = 65/174 (37%), Positives = 88/174 (50%), Gaps = 9/174 (5%)
Query: 91 EALREGLEEEMDRDPHVCVMGEDVGHYGGSYKVTKGLADKYGDLRVLDTPIAENSFTGMG 150
+A E L E RDP V G DV GG++ VTKGL GD RV+DT IAE + G+
Sbjct: 7 KASGEALAELAKRDPRVVGGGADVA--GGTFTVTKGLLHPQGDGRVIDTGIAEQAMVGIA 64
Query: 151 IGAAMTGLRPIVEGMNMGFLLLAFNQISNNCGMLHYTSGGQFTIP-IVIRGPGGVGRQLG 209
G A+ GL P VE F A + I HY + G+ +P +V R P GVG
Sbjct: 65 NGMALHGLLPPVEATFGDFANRADDAIR------HYAALGKLPVPFVVTRDPIGVGEDGP 118
Query: 210 AEHSQRLESYFQSIPGIQMVACSTPYNAKGLMKAAIRSENPVILFEHVLLYNLK 263
SQ ++ ++IP +++V S KGL++AAI + PV+L L K
Sbjct: 119 THQSQEDLAFLRAIPNLKVVRPSDAAETKGLLRAAIEDDGPVVLRLPRQLLRHK 172
>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 = 143 bits (364), Expect = 5e-42
Identities = 49/121 (40%), Positives = 77/121 (63%)
Query: 277 EAEMVRPGEHVTILTYSRMRYHVMQAAKTLVNKGYDPEVIDIRSLKPFDLYTIGNSIKKT 336
+AE++R G+ VTI+ Y M + ++AA+ L +G EVID+R++KP D TI S+KKT
Sbjct: 2 KAEILREGDDVTIVAYGSMVHEALEAAEELAKEGISAEVIDLRTVKPLDEDTILESVKKT 61
Query: 337 HRVLIVEECMRTGGIGASLTAAITENFHDYLDAPIVCLSSQDVPTPYAGTLEEWTVVQPA 396
R+++VEE ++ GG G+ + AA+ E DYLDAP++ + D P P+ LE + A
Sbjct: 62 GRLVVVEEAVKRGGFGSEVAAALAEEGFDYLDAPVLRVGGPDTPIPHGPALELAYLGLTA 121
Query: 397 Q 397
+
Sbjct: 122 E 122
>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 = 110 bits (277), Expect = 3e-29
Identities = 50/129 (38%), Positives = 67/129 (51%), Gaps = 14/129 (10%)
Query: 137 LDTPIAENSFTGMGIGAAMTGLRPIVEGMNMGFLLLAFNQISNNCGMLHYTSGGQFT-IP 195
+DT IAE + G G A+ GLRP+VE F A +QI S G +P
Sbjct: 18 IDTGIAEQAMVGFAAGLALHGLRPVVEIFFT-FFDRAKDQI---------RSAGASGNVP 67
Query: 196 IVIR-GPGGVGRQLGAEH-SQRLESYFQSIPGIQMVACSTPYNAKGLMKAAIRSENP-VI 252
+V R GG + G H S E+ ++IPG+++VA S P AKGL++AAIR + P VI
Sbjct: 68 VVFRHDGGGGVGEDGPTHHSIEDEALLRAIPGLKVVAPSDPAEAKGLLRAAIRDDGPVVI 127
Query: 253 LFEHVLLYN 261
E LY
Sbjct: 128 RLERKSLYR 136
>gnl|CDD|226467 COG3958, COG3958, Transketolase, C-terminal subunit [Carbohydrate
transport and metabolism].
Length = 312
Score = 83.1 bits (206), Expect = 8e-18
Identities = 61/274 (22%), Positives = 118/274 (43%), Gaps = 16/274 (5%)
Query: 91 EALREGLEEEMDRDPHVCVMGEDVGHYGGSYKVTKGLADKYGDLRVLDTPIAENSFTGMG 150
+ E L E ++ + V+ D+ S T A ++ D R + IAE G
Sbjct: 11 KVYGETLAELGRKNSDIVVLDADLS----SSTKTGYFAKEFPD-RFFNVGIAEQDMVGTA 65
Query: 151 IGAAMTGLRPIVEGMNMGFLLLAFNQISNNCGMLHYTSGGQFTIPIVIRGPGGVGRQLGA 210
G A+ G +P V A+ QI N+ + IV G + G+
Sbjct: 66 AGLALAGKKPFVSTFAAFLSRRAWEQIRNSIAYN------NLNVKIVATHAGVTYGEDGS 119
Query: 211 EHSQRLE--SYFQSIPGIQMVACSTPYNAKGLMKAAIRSENPVILFEHVLLYNLKERIPD 268
H Q LE + + +P + ++A + + ++ + PV + + + + +
Sbjct: 120 SH-QALEDIAIMRGLPNMTVIAPADAVETRAILDQIADYKGPVYM--RLGRGKVPVVVDE 176
Query: 269 EEYICNLEEAEMVRPGEHVTILTYSRMRYHVMQAAKTLVNKGYDPEVIDIRSLKPFDLYT 328
Y + +A ++R G +TI+ M ++AA+ L +G VI++ ++KP D
Sbjct: 177 GGYTFEIGKANVLRDGSDLTIIATGVMVAEALEAAEILKKEGISAAVINMFTIKPIDEQA 236
Query: 329 IGNSIKKTHRVLIVEECMRTGGIGASLTAAITEN 362
I + ++T R++ EE GG+G+++ ++EN
Sbjct: 237 ILKAARETGRIVTAEEHSIIGGLGSAVAEVLSEN 270
>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 = 70.5 bits (174), Expect = 1e-14
Identities = 41/167 (24%), Positives = 75/167 (44%), Gaps = 19/167 (11%)
Query: 91 EALREGLEEEMDRDPHVCVMGEDVGHYGGSYKVTKGLADKYGDLRVLDTPIAENSFTGMG 150
+A E L E +DP + + D+G G A K+ D R +D IAE + G+
Sbjct: 1 KAFGEALLELAKKDPRIVALSADLGGSTG----LDKFAKKFPD-RFIDVGIAEQNMVGIA 55
Query: 151 IGAAMTGLRPIVEGMNMGFLLLAFNQISNNCGMLHYTSGGQFTIPIVIRGPGG--VGRQL 208
G A+ GL+P V + FL A++QI ++ + + +P+ G +
Sbjct: 56 AGLALHGLKPFVSTFSF-FLQRAYDQIRHDVALQN--------LPVKFVGTHAGISVGED 106
Query: 209 GAEHSQRLE--SYFQSIPGIQMVACSTPYNAKGLMKAAIRSENPVIL 253
G H Q +E + ++IP + ++ + ++AA+ + PV +
Sbjct: 107 GPTH-QGIEDIALLRAIPNMTVLRPADANETAAALEAALEYDGPVYI 152
>gnl|CDD|224076 COG1154, Dxs, Deoxyxylulose-5-phosphate synthase [Coenzyme
metabolism / Lipid metabolism].
Length = 627
Score = 69.2 bits (170), Expect = 1e-12
Identities = 57/239 (23%), Positives = 105/239 (43%), Gaps = 29/239 (12%)
Query: 135 RVLDTPIAENSFTGMGIGAAMTGLRPIVEGMNMGFLLLAFNQISNNCGMLHYTSGGQFTI 194
R D IAE G A G++P+V + FL A++Q+ ++ + + +
Sbjct: 359 RFFDVGIAEQHAVTFAAGLAAEGMKPVV-AIYSTFLQRAYDQLIHDVAIQN--------L 409
Query: 195 PIVI---RGPGGVGRQLGAEHSQRLE-SYFQSIPGIQMVACSTPYNAKGLMKAAIR-SEN 249
P+ R G VG G H + S+ + IP + ++A + ++ A+ +
Sbjct: 410 PVTFAIDRA-GIVGAD-GPTHQGLFDLSFLRCIPNMVIMAPRDEEELRQMLYTALAQDDG 467
Query: 250 PVILFEHVLLY---NLKERIPDEEYICNLE--EAEMVRPGEHVTILTYSRMRYHVMQAAK 304
PV + Y N I E LE + E+++ GE V IL + M ++ A+
Sbjct: 468 PV-----AIRYPRGNGVGVILTPEL-EPLEIGKGELLKEGEKVAILAFGTMLPEALKVAE 521
Query: 305 TLVNKGYDPEVIDIRSLKPFDLYTIGNSIKKTHRVLI-VEECMRTGGIGASLTAAITEN 362
L G V+D R +KP D + + K+H +++ +EE + GG G+++ + +
Sbjct: 522 KLNAYGISVTVVDPRFVKPLDEALL-LELAKSHDLVVTLEENVVDGGFGSAVLEFLAAH 579
>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 = 66.3 bits (162), Expect = 1e-11
Identities = 62/251 (24%), Positives = 105/251 (41%), Gaps = 36/251 (14%)
Query: 126 GLADKYGDLRVLDTPIAENSFTGMGIGAAMTGLRPIVEGMNMGFLLLAFNQISNNCGMLH 185
+ K+ D R D IAE G A+ G +P V + FL A++Q+ +H
Sbjct: 345 KFSRKFPD-RYFDVAIAEQHAVTFAAGMAIEGYKPFV-AIYSTFLQRAYDQV------VH 396
Query: 186 YTSGGQFTIPIVIRGPGGVGRQLGAEHSQRLE-SYFQSIPGI------------QMVACS 232
+ + I G VG G H + SY + IP + QM+
Sbjct: 397 DVCIQKLPVLFAIDRAGIVGAD-GETHQGAFDISYLRCIPNMVIMAPSDENELRQMLYTG 455
Query: 233 TPYNAKGLMKAAIRSENPVILFEHVLLYNLKERIPDEEYICNLEEAEMVRPGEHVTILTY 292
Y+ A+R P V L E++P + ++E++R GE + IL +
Sbjct: 456 YHYDDG---PIAVRY--PRGNAVGVELTPEPEKLP-------IGKSEVLRKGEKILILGF 503
Query: 293 SRMRYHVMQAAKTLVNKGYDPEVIDIRSLKPFDLYTIGNSIKKTH-RVLIVEECMRTGGI 351
+ ++ A++L KG + V+D R +KP D I I +H +++ VEE GG
Sbjct: 504 GTLVPEALEVAESLNEKGIEATVVDARFVKPLDEELI-LEIAASHEKLVTVEENAIMGGA 562
Query: 352 GASLTAAITEN 362
G+++ + +
Sbjct: 563 GSAVLEFLMDQ 573
>gnl|CDD|183601 PRK12571, PRK12571, 1-deoxy-D-xylulose-5-phosphate synthase;
Provisional.
Length = 641
Score = 62.0 bits (151), Expect = 2e-10
Identities = 55/227 (24%), Positives = 93/227 (40%), Gaps = 10/227 (4%)
Query: 135 RVLDTPIAENSFTGMGIGAAMTGLRPIVEGMNMGFLLLAFNQISNNCGMLHYTSGGQFTI 194
RV D IAE G A GL+P + FL ++Q+ ++ L +
Sbjct: 362 RVFDVGIAEQHAVTFAAGLAAAGLKPFC-AVYSTFLQRGYDQLLHDVA-LQ-----NLPV 414
Query: 195 PIVIRGPGGVGRQLGAEHSQRLE-SYFQSIPGIQMVACSTPYNAKGLMKAAIRSENPVIL 253
V+ G VG GA H+ + ++ ++P + ++A + +++ A ++ I
Sbjct: 415 RFVLDRAGLVGAD-GATHAGAFDLAFLTNLPNMTVMAPRDEAELRHMLRTAAAHDDGPIA 473
Query: 254 FEHVLLYNLKERIPDEEYICNLEEAEMVRPGEHVTILTYSRMRYHVMQAAKTLVNKGYDP 313
+ IP E I + + + R G V IL+ + + AA L +G
Sbjct: 474 VRFPRGEGVGVEIPAEGTILGIGKGRVPREGPDVAILSVGAHLHECLDAADLLEAEGISV 533
Query: 314 EVIDIRSLKPFDLYTIGNSIKKTHRVLIVEECMRTGGIGASLTAAIT 360
V D R +KP D ++ H V+IVEE GG GA + +
Sbjct: 534 TVADPRFVKPLDEALTDLLVRH-HIVVIVEEQGAMGGFGAHVLHHLA 579
>gnl|CDD|235470 PRK05444, PRK05444, 1-deoxy-D-xylulose-5-phosphate synthase;
Provisional.
Length = 580
Score = 57.0 bits (139), Expect = 8e-09
Identities = 24/86 (27%), Positives = 43/86 (50%), Gaps = 6/86 (6%)
Query: 278 AEMVRPGEHVTILTYSRMRYHVMQAAKTLVNKGYDPEVIDIRSLKPFDLYTIGNSIKKTH 337
E++R GE V IL + M ++AA+ L V+D R +KP D + + H
Sbjct: 457 GEVLREGEDVAILAFGTMLAEALKAAERL----ASATVVDARFVKPLDEELL-LELAAKH 511
Query: 338 RVLI-VEECMRTGGIGASLTAAITEN 362
+++ VEE GG G+++ + ++
Sbjct: 512 DLVVTVEEGAIMGGFGSAVLEFLADH 537
>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 = 47.0 bits (112), Expect = 2e-06
Identities = 30/143 (20%), Positives = 49/143 (34%), Gaps = 15/143 (10%)
Query: 118 GGSYKVTKGLADKYGDLRVLDTPIAENSFTGMGIGAAMTGLRPIVEGMNMGFLLLAFNQI 177
G + GD R++DT I E G G A G P+V + LL A N +
Sbjct: 20 GDEISSLLDALRE-GDKRIIDTVIHELGAAGAAAGYARAGGPPVVIVTSGTGLLNAINGL 78
Query: 178 SNNCGMLHYTSGGQFTIPIVIRG--PGGVGRQLGAEHSQRLESYFQSIPGIQMVACSTPY 235
+ + +P+V G + S ++SIP + + S
Sbjct: 79 --------ADAAAEH-LPVVFLIGARGISAQAKQTFQSMFDLGMYRSIPEANISSPSPAE 129
Query: 236 NAKGLMKAAIRSEN---PVILFE 255
G+ A + PV++
Sbjct: 130 LPAGIDHAIRTAYASQGPVVVRL 152
>gnl|CDD|237053 PRK12315, PRK12315, 1-deoxy-D-xylulose-5-phosphate synthase;
Provisional.
Length = 581
Score = 46.9 bits (112), Expect = 1e-05
Identities = 57/267 (21%), Positives = 110/267 (41%), Gaps = 24/267 (8%)
Query: 91 EALREGLEEEMDRDPHVCVMGEDV-GHYGGSYKVTKGLADKYGDLRVLDTPIAENSFTGM 149
+ L +++ V + + G +G K KY D + +D IAE
Sbjct: 282 SVTLDYLLKKIKEGKPVVAINAAIPGVFG-----LKEFRKKYPD-QYVDVGIAEQESVAF 335
Query: 150 GIGAAMTGLRPIVEGMNMGFLLLAFNQISNNCGMLHYTSGGQFTIPIVIRGPGGVGRQLG 209
G A G RP++ +N FL A++Q+S++ + + P V+ GG
Sbjct: 336 ASGIAANGARPVI-FVNSTFLQRAYDQLSHDLAINNN--------PAVMIVFGGSISGND 386
Query: 210 AEHSQRLE-SYFQSIPGIQMVACSTPYNAKGLMKAAIR-SENPVILFEHVLLYNLKERIP 267
H + +IP + +A +T +++ A+ E+PV + V + ++
Sbjct: 387 VTHLGIFDIPMISNIPNLVYLAPTTKEELIAMLEWALTQHEHPVAI--RVPEHGVESGPT 444
Query: 268 DEEYICNLEEAEMVRPGEHVTILTYSRMRYHVMQAAKTLVNK-GYDPEVIDIRSLKPFDL 326
+ L + E+ + GE V IL + AK L + G D +I+ + + D
Sbjct: 445 VDTDYSTL-KYEVTKAGEKVAILALGDFYELGEKVAKKLKEELGIDATLINPKFITGLDE 503
Query: 327 YTIGNSIKKTHRVLI-VEECMRTGGIG 352
+ +K+ H +++ +E+ + GG G
Sbjct: 504 ELL-EKLKEDHELVVTLEDGILDGGFG 529
>gnl|CDD|177878 PLN02234, PLN02234, 1-deoxy-D-xylulose-5-phosphate synthase.
Length = 641
Score = 46.6 bits (110), Expect = 2e-05
Identities = 53/222 (23%), Positives = 89/222 (40%), Gaps = 12/222 (5%)
Query: 135 RVLDTPIAENSFTGMGIGAAMTGLRPIVEGMNMGFLLLAFNQISNNCGMLHYTSGGQFTI 194
R D IAE G A GL+P + F+ A++Q+ +H + +
Sbjct: 400 RCFDVGIAEQHAVTFAAGLACEGLKPFCT-IYSSFMQRAYDQV------VHDVDLQKLPV 452
Query: 195 PIVIRGPGGVGRQLGAEHSQRLESYFQS-IPGIQMVACSTPYNAKGLMKAAIRSENPVIL 253
I G +G G H + F + +P + ++A S ++ A ++
Sbjct: 453 RFAIDRAGLMGAD-GPTHCGAFDVTFMACLPNMIVMAPSDEAELFNMVATAAAIDDRPSC 511
Query: 254 FEHVLLYNLKERIP--DEEYICNLEEAEMVRPGEHVTILTYSRMRYHVMQAAKTLVNKGY 311
F + + +P ++ + ++R GE V +L Y ++AA L +G
Sbjct: 512 FRYHRGNGIGVSLPPGNKGVPLQIGRGRILRDGERVALLGYGSAVQRCLEAASMLSERGL 571
Query: 312 DPEVIDIRSLKPFDLYTIGNSIKKTHRVLIVEECMRTGGIGA 353
V D R KP D+ I S+ K+H VLI E GG G+
Sbjct: 572 KITVADARFCKPLDVALI-RSLAKSHEVLITVEEGSIGGFGS 612
>gnl|CDD|177870 PLN02225, PLN02225, 1-deoxy-D-xylulose-5-phosphate synthase.
Length = 701
Score = 38.9 bits (90), Expect = 0.004
Identities = 59/265 (22%), Positives = 104/265 (39%), Gaps = 18/265 (6%)
Query: 97 LEEEMDRDPHVCVMGEDVGHYGGSYKVTKGLADKYGDLRVLDTPIAENSFTGMGIGAAMT 156
+E E DRD V G ++ +++ +++ D R + +AE G +
Sbjct: 393 MEAEKDRDIVVVHAGMEMDASLITFQ------ERFPD-RFFNVGMAEQHAVTFSAGLSSG 445
Query: 157 GLRPIVEGMNMGFLLLAFNQISNNCGMLHYTSGGQFTIPIVIRGPGGVGRQLGAEHSQRL 216
GL+P + FL A++Q+ +H + + VI G VG +
Sbjct: 446 GLKPFCI-IPSAFLQRAYDQV------VHDVDRQRKAVRFVITSAGLVGSDGPVQCGAFD 498
Query: 217 ESYFQSIPG-IQMVACSTPYNAKGLMKAAIRSENPVIL-FEHVLLYNLKERIPDEEYICN 274
++ S+P I M + AA ++ PV F + N+ +P I
Sbjct: 499 IAFMSSLPNMIAMAPADEDELVNMVATAAYVTDRPVCFRFPRGSIVNMNYLVPTGLPI-E 557
Query: 275 LEEAEMVRPGEHVTILTYSRMRYHVMQAAKTLVNKGYDPEVIDIRSLKPFDLYTIGNSIK 334
+ ++ G+ V +L Y M + + A L G + V D R KP D+ + +
Sbjct: 558 IGRGRVLVEGQDVALLGYGAMVQNCLHAHSLLSKLGLNVTVADARFCKPLDIKLV-RDLC 616
Query: 335 KTHRVLIVEECMRTGGIGASLTAAI 359
+ H+ LI E GG G+ + I
Sbjct: 617 QNHKFLITVEEGCVGGFGSHVAQFI 641
>gnl|CDD|178194 PLN02582, PLN02582, 1-deoxy-D-xylulose-5-phosphate synthase.
Length = 677
Score = 37.6 bits (87), Expect = 0.011
Identities = 26/70 (37%), Positives = 31/70 (44%), Gaps = 1/70 (1%)
Query: 284 GEHVTILTYSRMRYHVMQAAKTLVNKGYDPEVIDIRSLKPFDLYTIGNSIKKTHRVLIVE 343
GE V +L Y + AA L G V D R KP D I S+ K+H VLI
Sbjct: 543 GERVALLGYGTAVQSCLAAASLLERHGLSATVADARFCKPLDRALI-RSLAKSHEVLITV 601
Query: 344 ECMRTGGIGA 353
E GG G+
Sbjct: 602 EEGSIGGFGS 611
>gnl|CDD|223968 COG1038, PycA, Pyruvate carboxylase [Energy production and
conversion].
Length = 1149
Score = 35.4 bits (82), Expect = 0.055
Identities = 23/66 (34%), Positives = 32/66 (48%), Gaps = 10/66 (15%)
Query: 90 FEALREGLEEEMDRDPHVCVMGEDVGHYGGSYKVTK---GLADKYGDLRVLDTPIAENSF 146
FEA+R+ LEE++ R+ DV Y KV + + YGD+ VL TP F
Sbjct: 957 FEAIRKELEEKLGREVSDQ----DVASYLLYPKVFEDYQKHRETYGDVSVLPTP---TFF 1009
Query: 147 TGMGIG 152
G+ G
Sbjct: 1010 YGLRPG 1015
>gnl|CDD|130302 TIGR01235, pyruv_carbox, pyruvate carboxylase. This enzyme plays a
role in gluconeogensis but not glycolysis [Energy
metabolism, Glycolysis/gluconeogenesis].
Length = 1143
Score = 34.8 bits (80), Expect = 0.094
Identities = 26/87 (29%), Positives = 38/87 (43%), Gaps = 12/87 (13%)
Query: 90 FEALREGLEEEMDRDPHVCVMGEDVGHYGGSYKVTKGLA---DKYGDLRVLDTPIAENSF 146
+A+R+ L+E+ +R+ V DV Y KV A D YG + VL TP F
Sbjct: 952 LDAIRKDLQEKHERE----VSDFDVASYAMYPKVFTDFAKARDTYGPVSVLPTPAF---F 1004
Query: 147 TGMGIGAAMTGLRPIVEGMNMGFLLLA 173
G+ G + I +G + L A
Sbjct: 1005 YGLADGEEIEVD--IEKGKTLIIKLQA 1029
>gnl|CDD|237263 PRK12999, PRK12999, pyruvate carboxylase; Reviewed.
Length = 1146
Score = 32.8 bits (76), Expect = 0.39
Identities = 24/70 (34%), Positives = 32/70 (45%), Gaps = 18/70 (25%)
Query: 90 FEALREGLEEEMDRDPHVCVMGEDVGHYGGSY----KVTKGLA---DKYGDLRVLDTPIA 142
FEA R LEE++ R+ DV SY KV + ++YGD+ VL TP
Sbjct: 954 FEAERAELEEKLGREVTD----RDVL----SYLLYPKVFEDYIKHREEYGDVSVLPTPTF 1005
Query: 143 ENSFTGMGIG 152
F G+ G
Sbjct: 1006 ---FYGLRPG 1012
>gnl|CDD|182720 PRK10775, PRK10775, cell division protein FtsQ; Provisional.
Length = 276
Score = 30.5 bits (69), Expect = 1.4
Identities = 11/41 (26%), Positives = 20/41 (48%), Gaps = 1/41 (2%)
Query: 24 KFQLSTRRSLSGRKPWFLVVRSDGSVNLGSNQRSRRTQQLI 64
KF L +++ R+ W L + +D + LG +R + I
Sbjct: 185 KFTLKEA-AMTARRSWQLTLNNDIRLELGRGDTMKRLARFI 224
>gnl|CDD|237851 PRK14894, PRK14894, glycyl-tRNA synthetase; Provisional.
Length = 539
Score = 30.7 bits (69), Expect = 1.6
Identities = 28/104 (26%), Positives = 48/104 (46%), Gaps = 10/104 (9%)
Query: 190 GQFTIPIVIRGPGGVGRQLGAEHSQRL-ESYFQSIPGIQMVACSTPYNAKGLMKAAIRSE 248
G+ +P VI GVGR + A + E ++IPG ++ A A +K+ RSE
Sbjct: 307 GRHVVPYVIEPSAGVGRCMLAVMCEGYAEELTKAIPGEKLAAVGDALEA--FLKSVGRSE 364
Query: 249 -------NPVILFEHVLLYNLKERIPDEEYICNLEEAEMVRPGE 285
+ ++ LL L ER+P+ E + + A+ + G+
Sbjct: 365 KLAGEARDAILARGEALLQALPERLPEVEQLLAMPGADQIELGK 408
>gnl|CDD|176760 cd08782, Death_DAPK1, Death domain found in death-associated
protein kinase 1. Death domain (DD) found in
death-associated protein kinase 1 (DAPK1). DAPK1 is
composed of several functional domains, including a
kinase domain, a CaM regulatory domain, ankyrin repeats,
a cytoskeletal binding domain and a C-terminal DD. It
plays important roles in a diverse range of signal
transduction pathways including apoptosis, growth factor
signalling, and autophagy. Loss of DAPK1 expression,
usually because of DNA methylation, is implicated in
many tumor types. DAPK1 is highly abundant in the brain
and has also been associated with neurodegeneration. In
general, DDs are protein-protein interaction domains
found in a variety of domain architectures. Their common
feature is that they form homodimers by self-association
or heterodimers by associating with other members of the
DD superfamily including CARD (Caspase activation and
recruitment domain), DED (Death Effector Domain), and
PYRIN. They serve as adaptors in signaling pathways and
can recruit other proteins into signaling complexes.
Length = 82
Score = 27.7 bits (62), Expect = 2.9
Identities = 11/36 (30%), Positives = 20/36 (55%)
Query: 370 PIVCLSSQDVPTPYAGTLEEWTVVQPAQIVTAVEQL 405
P + +S +P+P L+EW P+ I T +++L
Sbjct: 34 PQLDTNSSSLPSPTDALLQEWATAPPSTIGTLIDKL 69
>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 = 29.8 bits (68), Expect = 3.0
Identities = 21/105 (20%), Positives = 43/105 (40%), Gaps = 19/105 (18%)
Query: 247 SENPVILFEHVLLY--------NLKERIPDEEYICNLEEAEMVRPGEHVTILTYSRMRYH 298
SE+P V + + + IP+ E E+A+ V I+ +
Sbjct: 429 SEDPEN---RVKMMEKRARKLETIAKEIPEPEVY-GDEDAD-------VLIIGWGSTYGA 477
Query: 299 VMQAAKTLVNKGYDPEVIDIRSLKPFDLYTIGNSIKKTHRVLIVE 343
+ +A + L +G ++ +R L PF + ++ +V++VE
Sbjct: 478 IREAVERLRAEGIKVALLHLRLLYPFPKNELAELLEGAKKVIVVE 522
>gnl|CDD|188628 cd09908, H3TH_EXO1, H3TH domain of Exonuclease-1, a
structure-specific, divalent-metal-ion dependent, 5'
nuclease. Exonuclease-1 (EXO1) is involved in multiple,
eukaryotic DNA metabolic pathways, including DNA
replication processes (5' flap DNA endonuclease activity
and double stranded DNA 5'-exonuclease activity), DNA
repair processes (DNA mismatch repair (MMR) and
post-replication repair (PRR), recombination, and
telomere integrity. EXO1 functions in the MMS2
error-free branch of the PRR pathway in the maintenance
and repair of stalled replication forks. Studies also
suggest that EXO1 plays both structural and catalytic
roles during MMR-mediated mutation avoidance. Members of
this subgroup include the H3TH (helix-3-turn-helix)
domains of EXO1 and other similar eukaryotic 5'
nucleases. These nucleases contain a PIN (PilT N
terminus) domain with a helical arch/clamp region/I
domain (not included here) and inserted within the PIN
domain is an atypical helix-hairpin-helix-2 (HhH2)-like
region. This atypical HhH2 region, the H3TH domain, has
an extended loop with at least three turns between the
first two helices, and only three of the four helices
appear to be conserved. Both the H3TH domain and the
helical arch/clamp region are involved in DNA binding.
Studies suggest that a glycine-rich loop in the H3TH
domain contacts the phosphate backbone of the template
strand in the downstream DNA duplex. These nucleases
have a carboxylate rich active site that is involved in
binding essential divalent metal ion cofactors (Mg2+ or
Mn2+) required for nuclease activity. The first metal
binding site is composed entirely of Asp/Glu residues
from the PIN domain, whereas, the second metal binding
site is composed generally of two Asp residues from the
PIN domain and one Asp residue from the H3TH domain.
Together with the helical arch and network of amino
acids interacting with metal binding ions, the H3TH
region defines a positively charged active-site
DNA-binding groove in structure-specific 5' nucleases.
EXO1 nucleases also have C-terminal Mlh1- and
Msh2-binding domains which allow interaction with MMR
and PRR proteins, respectively.
Length = 73
Score = 27.5 bits (62), Expect = 3.0
Identities = 13/61 (21%), Positives = 25/61 (40%), Gaps = 11/61 (18%)
Query: 219 YFQSIPGIQMVACSTPYNAKGLMKAAIRSENPVILFEHVLLYNLKERIPDEEYICNLEEA 278
Y S+PGI A L++ R + + L ++ K+ +P +Y ++A
Sbjct: 14 YLPSLPGI------GLKKAYKLVR---RHRTIEKVIKA-LRFDGKKEVPP-DYEEGFQKA 62
Query: 279 E 279
Sbjct: 63 L 63
>gnl|CDD|224091 COG1169, MenF, Isochorismate synthase [Coenzyme metabolism /
Secondary metabolites biosynthesis, transport, and
catabolism].
Length = 423
Score = 29.6 bits (67), Expect = 3.4
Identities = 19/53 (35%), Positives = 28/53 (52%), Gaps = 4/53 (7%)
Query: 40 FLVVRSDGSVNLGSN-QR--SRRTQQLITNAVA-TKADSAASTSASKQGHELL 88
FLV DG LG++ +R RR QL+T A+A + A ++ G+ LL
Sbjct: 211 FLVALGDGGAFLGASPERLVRRRGGQLVTEALAGSAPRGADPVEDAQLGNWLL 263
>gnl|CDD|223871 COG0800, Eda, 2-keto-3-deoxy-6-phosphogluconate aldolase
[Carbohydrate transport and metabolism].
Length = 211
Score = 29.1 bits (66), Expect = 3.5
Identities = 9/30 (30%), Positives = 11/30 (36%), Gaps = 7/30 (23%)
Query: 344 ECMRTGGIGASLTAAITENFHDYLDAPIVC 373
TGG+ N DYL A +V
Sbjct: 155 RFCPTGGVSLD-------NAADYLAAGVVA 177
>gnl|CDD|183595 PRK12560, PRK12560, adenine phosphoribosyltransferase; Provisional.
Length = 187
Score = 28.6 bits (64), Expect = 4.2
Identities = 16/51 (31%), Positives = 26/51 (50%), Gaps = 1/51 (1%)
Query: 311 YDPEVIDIRSLKPFDLYTIGNSIKKTHRVLIVEECMRTGGIGASLTAAITE 361
+ V++I S F+ N I+K RV I+++ + TGG +L AI
Sbjct: 90 LNYNVVEIGSEY-FEGVVYLNGIEKGDRVAIIDDTLSTGGTVIALIKAIEN 139
>gnl|CDD|181817 PRK09392, ftrB, transcriptional activator FtrB; Provisional.
Length = 236
Score = 28.8 bits (65), Expect = 4.7
Identities = 26/97 (26%), Positives = 37/97 (38%), Gaps = 11/97 (11%)
Query: 40 FLVVRSDGSVNLGSNQRSRRTQQLITNAVAT-------KADSAASTSASKQGHELLLFEA 92
FL V DG V L ++ + R T I V+T ++ + +L+ A
Sbjct: 50 FLFVVLDGLVELSASSQDRETTLAILRPVSTFILAAVVLDAPYLMSARTLTRSRVLMIPA 109
Query: 93 LREGLEEEMDRDPHV--CVMGEDVGHYGGSYKVTKGL 127
E + E M DP V+ E G Y G K K
Sbjct: 110 --ELVREAMSEDPGFMRAVVFELAGCYRGLVKSLKNQ 144
>gnl|CDD|183114 PRK11388, PRK11388, DNA-binding transcriptional regulator DhaR;
Provisional.
Length = 638
Score = 29.3 bits (66), Expect = 4.8
Identities = 24/111 (21%), Positives = 40/111 (36%), Gaps = 34/111 (30%)
Query: 153 AAMTGLRPIVEGMNMGFLLL----------AFNQISN-----------NCGMLHYTSGGQ 191
A+ L+PI+EG F+LL +Q+ + M G+
Sbjct: 283 DAVITLKPIIEGQGTSFILLLHPVEQMRQLMTSQLGKVSHTFDHMPQDSPQMRRLIHFGR 342
Query: 192 FTI----PIVIRGPGGVGRQLGAE--H--SQRLESYF-----QSIPGIQMV 229
P+++ G GVG+ L A+ H S+R + Q P +
Sbjct: 343 QAAKSSFPVLLCGEEGVGKALLAQAIHNESERAAGPYIAVNCQLYPDEALA 393
>gnl|CDD|217032 pfam02436, PYC_OADA, Conserved carboxylase domain. This domain
represents a conserved region in pyruvate carboxylase
(PYC), oxaloacetate decarboxylase alpha chain (OADA),
and transcarboxylase 5s subunit. The domain is found
adjacent to the HMGL-like domain (pfam00682) and often
close to the biotin_lipoyl domain (pfam00364) of biotin
requiring enzymes.
Length = 198
Score = 28.3 bits (64), Expect = 5.7
Identities = 25/70 (35%), Positives = 31/70 (44%), Gaps = 18/70 (25%)
Query: 90 FEALREGLEEEMDRDPHVCVMGEDVGHYGGSY----KVTKGLA---DKYGDLRVLDTPIA 142
E LR LEE+ R EDV SY KV + ++YGD+ VL TP
Sbjct: 124 LEKLRAELEEKAGRKLSD----EDVL----SYALFPKVAEKFLEHREEYGDVSVLPTP-- 173
Query: 143 ENSFTGMGIG 152
F GM +G
Sbjct: 174 -VFFYGMEVG 182
>gnl|CDD|235639 PRK05899, PRK05899, transketolase; Reviewed.
Length = 586
Score = 28.2 bits (64), Expect = 8.8
Identities = 10/45 (22%), Positives = 20/45 (44%)
Query: 281 VRPGEHVTILTYSRMRYHVMQAAKTLVNKGYDPEVIDIRSLKPFD 325
+R V ++ + ++AA L +G V+ + S + FD
Sbjct: 469 LRDDPDVILIATGSEVHLALEAADELEAEGIKVRVVSMPSTELFD 513
>gnl|CDD|130205 TIGR01135, glmS, glucosamine--fructose-6-phosphate aminotransferase
(isomerizing). The member from Methanococcus jannaschii
contains an intein [Cell envelope, Biosynthesis and
degradation of murein sacculus and peptidoglycan,
Central intermediary metabolism, Amino sugars].
Length = 607
Score = 28.4 bits (64), Expect = 8.9
Identities = 16/45 (35%), Positives = 23/45 (51%), Gaps = 6/45 (13%)
Query: 193 TIPIVIRGPGGVGRQLGAEHSQRLESYFQSIPGIQMVACSTPYNA 237
T+ I G V +LGAE +++ IQ+VAC T Y+A
Sbjct: 267 TLEGRISEAGVVLEELGAE------ELLKNVDRIQIVACGTSYHA 305
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
0.319 0.135 0.394
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: 20,768,696
Number of extensions: 2037546
Number of successful extensions: 1882
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1859
Number of HSP's successfully gapped: 49
Length of query: 407
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 308
Effective length of database: 6,546,556
Effective search space: 2016339248
Effective search space used: 2016339248
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 (21.7 bits)
S2: 60 (26.7 bits)