RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 007056
(620 letters)
>gnl|CDD|215182 PLN02321, PLN02321, 2-isopropylmalate synthase.
Length = 632
Score = 1073 bits (2775), Expect = 0.0
Identities = 471/622 (75%), Positives = 518/622 (83%), Gaps = 4/622 (0%)
Query: 2 AATAAFFTNRQPTFILSPPKT---KVNASQLFFHCNNSKPFFKTTISCSLQKPPPSLYPR 58
+ATAA F +P ++ ++ + + S PS
Sbjct: 9 SATAASPAKSLSAFTPAPTRSSASSARFPAFLARPAAARSPSLASRASSALAASPSRPQV 68
Query: 59 ITASRPEYIPNRIPDPNYVRVFDTTLRDGEQSPGATLTSKEKLDIARQLAKLGVDIIEAG 118
RPEYIPNRI DPNYVR+FDTTLRDGEQSPGATLTSKEKLDIARQLAKLGVDIIEAG
Sbjct: 69 ARRPRPEYIPNRIDDPNYVRIFDTTLRDGEQSPGATLTSKEKLDIARQLAKLGVDIIEAG 128
Query: 119 FPAASKEDFEAVRTIAKEVGNAVDAESGYVPVICGLSRCNERDIKTAWEAVKYAKRPRIH 178
FP AS +D EAV+TIAKEVGN VD E GYVPVICGLSRCN++DI AWEAVK+AKRPRIH
Sbjct: 129 FPIASPDDLEAVKTIAKEVGNEVD-EDGYVPVICGLSRCNKKDIDAAWEAVKHAKRPRIH 187
Query: 179 TFIATSGIHMEHKLRKTKQQVVEIARSMVKFARSLGCDDVEFSPEDAGRSDRKFLYEILG 238
TFIATS IHMEHKLRKT +VVEIAR MVK+ARSLGC+DVEFSPEDAGRSD +FLY ILG
Sbjct: 188 TFIATSEIHMEHKLRKTPDEVVEIARDMVKYARSLGCEDVEFSPEDAGRSDPEFLYRILG 247
Query: 239 EVIKVGATTLNIPDTVGITMPTEFGKLIADIKANTPGIENVVISTHCQNDLGLSTANTIA 298
EVIK GATTLNIPDTVG T+P+EFG+LIADIKANTPGIENV+ISTHCQNDLGLSTANT+A
Sbjct: 248 EVIKAGATTLNIPDTVGYTLPSEFGQLIADIKANTPGIENVIISTHCQNDLGLSTANTLA 307
Query: 299 GACAGARQVEVTINGIGERAGNASLEEVVMAFKCRGEHILGGLYTGINTRHIVMASKMVE 358
GA AGARQVEVTINGIGERAGNASLEEVVMA KCRG+ LGGLYTGIN HI SKMV
Sbjct: 308 GAHAGARQVEVTINGIGERAGNASLEEVVMAIKCRGDEQLGGLYTGINPVHITPTSKMVS 367
Query: 359 EYTGLHVQPHKAIVGANAFAHESGIHQDGMLKHKGTYEIISPEDIGLERSSEAGIVLGKL 418
EYTG+ VQPHKAIVGANAFAHESGIHQDGMLKHKGTYEIISPEDIGL R ++AGIVLGKL
Sbjct: 368 EYTGMQVQPHKAIVGANAFAHESGIHQDGMLKHKGTYEIISPEDIGLFRGNDAGIVLGKL 427
Query: 419 SGRHALKDRLKELGYELNDEQLGTIFWHFKAVAEQKKRVTDADLIALVSDEIFQPEVVWK 478
SGRHALK RLKELGYEL+D++L +F FKAVAE+KK VTD DLIALVSDE+FQPEVVWK
Sbjct: 428 SGRHALKSRLKELGYELDDDELDDVFKRFKAVAEKKKGVTDEDLIALVSDEVFQPEVVWK 487
Query: 479 LLDMQVTCGTLGLSTATVKLMDANGEEHVACSTGTGPVDSAYKAVDLIVKEPATLLEYSM 538
LLD+QVTCGTLGLSTATVKL+ +G EH+ACS GTGPVD+AYKAVDLIVKEP TLLEYSM
Sbjct: 488 LLDLQVTCGTLGLSTATVKLIGPDGVEHIACSVGTGPVDAAYKAVDLIVKEPVTLLEYSM 547
Query: 539 NAVTAGIDAIATTRVLIRGEKSQLSTHASTGETVQRTFSGTGAGMDIVVSSVKAYIGALN 598
NAVT GIDAIATTRV+IRGE S STHA TGE+VQRTFSG+GA MDIVVSSV+AY+ ALN
Sbjct: 548 NAVTEGIDAIATTRVVIRGENSYSSTHAQTGESVQRTFSGSGADMDIVVSSVRAYVSALN 607
Query: 599 KMLGFKDQLPAKDSVERTSVSA 620
KMLGFK+ AK + ER++
Sbjct: 608 KMLGFKEASKAKSASERSTSVV 629
>gnl|CDD|234864 PRK00915, PRK00915, 2-isopropylmalate synthase; Validated.
Length = 513
Score = 799 bits (2067), Expect = 0.0
Identities = 288/539 (53%), Positives = 367/539 (68%), Gaps = 30/539 (5%)
Query: 73 DPNYVRVFDTTLRDGEQSPGATLTSKEKLDIARQLAKLGVDIIEAGFPAASKEDFEAVRT 132
+ V +FDTTLRDGEQSPGA+LT +EKL IA+QL +LGVD+IEAGFPA+S DFEAV+
Sbjct: 1 MMDRVIIFDTTLRDGEQSPGASLTVEEKLQIAKQLERLGVDVIEAGFPASSPGDFEAVKR 60
Query: 133 IAKEVGNAVDAESGYVPVICGLSRCNERDIKTAWEAVKYAKRPRIHTFIATSGIHMEHKL 192
IA+ V N +CGL+R ++DI A EA+K A+ PRIHTFIATS IHME+KL
Sbjct: 61 IARTVKN---------STVCGLARAVKKDIDAAAEALKPAEAPRIHTFIATSPIHMEYKL 111
Query: 193 RKTKQQVVEIARSMVKFARSLGCDDVEFSPEDAGRSDRKFLYEILGEVIKVGATTLNIPD 252
+ ++++V+E+A VK+ARS DDVEFS EDA R+D FL ++ I GATT+NIPD
Sbjct: 112 KMSREEVLEMAVEAVKYARSY-TDDVEFSAEDATRTDLDFLCRVVEAAIDAGATTINIPD 170
Query: 253 TVGITMPTEFGKLIADIKANTPGIENVVISTHCQNDLGLSTANTIAGACAGARQVEVTIN 312
TVG T P EFG+LI ++ P I+ +IS HC NDLGL+ AN++A AGARQVE TIN
Sbjct: 171 TVGYTTPEEFGELIKTLRERVPNIDKAIISVHCHNDLGLAVANSLAAVEAGARQVECTIN 230
Query: 313 GIGERAGNASLEEVVMAFKCRGEHILGGLYTGINTRHIVMASKMVEEYTGLHVQPHKAIV 372
GIGERAGNA+LEEVVMA K R + G+ TGINT I S++V + TG+ VQP+KAIV
Sbjct: 231 GIGERAGNAALEEVVMALKTRKDIY--GVETGINTEEIYRTSRLVSQLTGMPVQPNKAIV 288
Query: 373 GANAFAHESGIHQDGMLKHKGTYEIISPEDIGLERSSEAGIVLGKLSGRHALKDRLKELG 432
GANAFAHESGIHQDG+LK++ TYEI++PE +GL+ + +VLGK SGRHA K RL+ELG
Sbjct: 289 GANAFAHESGIHQDGVLKNRETYEIMTPESVGLKANR---LVLGKHSGRHAFKHRLEELG 345
Query: 433 YELNDEQLGTIFWHFKAVAEQKKRVTDADLIALVSDEI-FQPEVVWKLLDMQVTCGTLGL 491
Y+L+DE+L F FK +A++KK V D DL ALV DE + +KL +QV G+ G
Sbjct: 346 YKLSDEELDKAFERFKELADKKKEVFDEDLEALVEDETQQEEPEHYKLESLQVQSGSSGT 405
Query: 492 STATVKLMDANGEEHVACSTGTGPVDSAYKAVDLIVKEPATLLEYSMNAVTAGIDAIATT 551
TATVKL D +GEE +TG GPVD+ Y A++ IV LLEYS+NA+T G DA+
Sbjct: 406 PTATVKLRDIDGEEKEEAATGNGPVDAVYNAINRIVGSDIELLEYSVNAITGGTDALGEV 465
Query: 552 RVLIRGEKSQLSTHASTGETVQRTFSGTGAGMDIVVSSVKAYIGALNKMLGFKDQLPAK 610
V + + R G GA DIV +S KAY+ ALNK+L K+ K
Sbjct: 466 TVRLEYDG--------------RIVHGRGADTDIVEASAKAYLNALNKLLRAKEVAKPK 510
>gnl|CDD|178767 PLN03228, PLN03228, methylthioalkylmalate synthase; Provisional.
Length = 503
Score = 659 bits (1701), Expect = 0.0
Identities = 282/414 (68%), Positives = 350/414 (84%), Gaps = 2/414 (0%)
Query: 59 ITASRPEYIPNRIPDPNYVRVFDTTLRDGEQSPGATLTSKEKLDIARQLAKLGVDIIEAG 118
I PEYIPN++PD NYVRV DTTLRDGEQSPG +LT +KL+IARQLAKL VDI+E G
Sbjct: 67 IVERWPEYIPNKLPDKNYVRVLDTTLRDGEQSPGGSLTPPQKLEIARQLAKLRVDIMEVG 126
Query: 119 FPAASKEDFEAVRTIAKEVGNAVDAESGYVPVICGLSRCNERDIKTAWEAVKYAKRPRIH 178
FP +S+E+FEAV+TIAK VGN VD E+GYVPVICG++RC +RDI+ AWEA+KYAKRPRI
Sbjct: 127 FPGSSEEEFEAVKTIAKTVGNEVDEETGYVPVICGIARCKKRDIEAAWEALKYAKRPRIL 186
Query: 179 TFIATSGIHMEHKLRKTKQQVVEIARSMVKFARSLGCDDVEFSPEDAGRSDRKFLYEILG 238
F +TS IHM++KL+KTK++V+E+A S +++A+SLG D++F ED GRSD++FL +ILG
Sbjct: 187 AFTSTSDIHMKYKLKKTKEEVIEMAVSSIRYAKSLGFHDIQFGCEDGGRSDKEFLCKILG 246
Query: 239 EVIKVGATTLNIPDTVGITMPTEFGKLIADIKANTPGIENVVISTHCQNDLGLSTANTIA 298
E IK GAT++ I DTVGI MP EFG+L+ +KANTPGI+++V S HC NDLGL+TANTIA
Sbjct: 247 EAIKAGATSVGIADTVGINMPHEFGELVTYVKANTPGIDDIVFSVHCHNDLGLATANTIA 306
Query: 299 GACAGARQVEVTINGIGERAGNASLEEVVMAFKCRGEHILGGLYTGINTRHIVMASKMVE 358
G CAGARQVEVTINGIGER+GNASLEEVVMA KCRG +++ G+YTGI+TR I+ SKMV+
Sbjct: 307 GICAGARQVEVTINGIGERSGNASLEEVVMALKCRGAYLMNGVYTGIDTRQIMATSKMVQ 366
Query: 359 EYTGLHVQPHKAIVGANAFAHESGIHQDGMLKHKGTYEIISPEDIGLERSSEAGIVLGKL 418
EYTG++VQPHK IVGAN F HESGIHQDG+LK++ TYEI+SPEDIG+ +S +GIVLGKL
Sbjct: 367 EYTGMYVQPHKPIVGANCFVHESGIHQDGILKNRSTYEILSPEDIGIVKSQNSGIVLGKL 426
Query: 419 SGRHALKDRLKELGYELNDEQLGTIFWHFKAVAEQKKRVTDADLIALV--SDEI 470
SGRHA+KDRLKELGYEL+DE+L +F F+ + ++KKR+TDADL ALV DEI
Sbjct: 427 SGRHAVKDRLKELGYELDDEKLNEVFSRFRDLTKEKKRITDADLKALVVNGDEI 480
>gnl|CDD|130046 TIGR00973, leuA_bact, 2-isopropylmalate synthase, bacterial type.
This is the first enzyme of leucine biosynthesis. A
larger family of homologous proteins includes
homocitrate synthase, distinct lineages of
2-isopropylmalate synthase, several distinct,
uncharacterized, orthologous sets in the Archaea, and
other related enzymes. This model describes a family of
2-isopropylmalate synthases found primarily in Bacteria.
The homologous families in the Archaea may represent
isozymes and/or related enzymes [Amino acid
biosynthesis, Pyruvate family].
Length = 494
Score = 638 bits (1648), Expect = 0.0
Identities = 288/525 (54%), Positives = 363/525 (69%), Gaps = 35/525 (6%)
Query: 77 VRVFDTTLRDGEQSPGATLTSKEKLDIARQLAKLGVDIIEAGFPAASKEDFEAVRTIAKE 136
+ +FDTTLRDGEQSPGA+LT +EKL IA L +LGVDIIEAGFP +S DFEAV+ IA+
Sbjct: 2 IIIFDTTLRDGEQSPGASLTVEEKLQIALALERLGVDIIEAGFPVSSPGDFEAVQRIART 61
Query: 137 VGNAVDAESGYVPVICGLSRCNERDIKTAWEAVKYAKRPRIHTFIATSGIHMEHKLRKTK 196
V N P +CGL+RC E+DI A EA+K A++ RIHTFIATS IH+EHKL+ T+
Sbjct: 62 VKN---------PRVCGLARCVEKDIDAAAEALKPAEKFRIHTFIATSPIHLEHKLKMTR 112
Query: 197 QQVVEIARSMVKFARSLGCDDVEFSPEDAGRSDRKFLYEILGEVIKVGATTLNIPDTVGI 256
+V+E A MVK+A++ DDVEFS EDAGR++ FL I+ I GATT+NIPDTVG
Sbjct: 113 DEVLERAVGMVKYAKNF-TDDVEFSCEDAGRTEIPFLARIVEAAINAGATTINIPDTVGY 171
Query: 257 TMPTEFGKLIADIKANTPGIENVVISTHCQNDLGLSTANTIAGACAGARQVEVTINGIGE 316
+P E+G LI ++ N P I+ ++S HC NDLGL+ AN++A GARQVE TINGIGE
Sbjct: 172 ALPAEYGNLIKGLRENVPNIDKAILSVHCHNDLGLAVANSLAAVQNGARQVECTINGIGE 231
Query: 317 RAGNASLEEVVMAFKCRGEHILGGLYTGINTRHIVMASKMVEEYTGLHVQPHKAIVGANA 376
RAGNA+LEEVVMA K R + + G+ TGINT+ I S++V + TG+ VQP+KAIVG NA
Sbjct: 232 RAGNAALEEVVMALKVRKDFL--GVETGINTKEIYRTSRLVSQLTGMPVQPNKAIVGDNA 289
Query: 377 FAHESGIHQDGMLKHKGTYEIISPEDIGLERSSEAGIVLGKLSGRHALKDRLKELGYELN 436
FAHESGIHQDG+LK+K TYEI+SPEDIGL +VLGK SGRHA KDRL+ELG++L+
Sbjct: 290 FAHESGIHQDGVLKNKETYEIMSPEDIGLTAEQ---LVLGKHSGRHAFKDRLEELGFKLD 346
Query: 437 DEQLGTIFWHFKAVAEQKKRVTDADLIALVSDEIFQ-PEVVWKLLDMQVTCGTLGLSTAT 495
DE+L +F FK +A++KK VTD DL ALV +E Q PE +KLL QV GT + TAT
Sbjct: 347 DEELDKLFEKFKELADKKKEVTDEDLEALVFEEKRQEPEEGYKLLHFQVHSGTNQVPTAT 406
Query: 496 VKLMDANGEEHVACSTGTGPVDSAYKAVDLIVKEPATLLEYSMNAVTAGIDAIATTRVLI 555
VKL GE+ A +TG GPVD+ YKA++ + LLEYS+ AV G DA+ V++
Sbjct: 407 VKL-KNGGEKREAAATGNGPVDAVYKAINRALGIEVELLEYSITAVGEGKDALGQVDVVL 465
Query: 556 R--GEKSQLSTHASTGETVQRTFSGTGAGMDIVVSSVKAYIGALN 598
R G K +SG G DIV +S KAY+ ALN
Sbjct: 466 RHNGVK----------------YSGRGVATDIVEASAKAYLNALN 494
>gnl|CDD|163678 cd07940, DRE_TIM_IPMS, 2-isopropylmalate synthase (IPMS),
N-terminal catalytic TIM barrel domain.
2-isopropylmalate synthase (IPMS) catalyzes an
aldol-type condensation of acetyl-CoA and
2-oxoisovalerate yielding 2-isopropylmalate and CoA, the
first committed step in leucine biosynthesis. This
family includes the Arabidopsis thaliana IPMS1 and IPMS2
proteins, the Glycine max GmN56 protein, and the
Brassica insularis BatIMS protein. This family also
includes a group of archeal IPMS-like proteins
represented by the Methanocaldococcus jannaschii AksA
protein. AksA catalyzes the condensation of
alpha-ketoglutarate and acetyl-CoA to form
trans-homoaconitate, one of 13 steps in the conversion
of alpha-ketoglutarate and acetylCoA to
alpha-ketosuberate, a precursor to coenzyme B and
biotin. AksA also catalyzes the condensation of
alpha-ketoadipate or alpha-ketopimelate with acetylCoA
to form, respectively, the (R)-homocitrate homologs
(R)-2-hydroxy-1,2,5-pentanetricarboxylic acid and
(R)-2-hydroxy-1,2,6- hexanetricarboxylic acid. This
family belongs to the DRE-TIM metallolyase superfamily.
DRE-TIM metallolyases include 2-isopropylmalate synthase
(IPMS), alpha-isopropylmalate synthase (LeuA),
3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate
synthase, citramalate synthase, 4-hydroxy-2-oxovalerate
aldolase, re-citrate synthase, transcarboxylase 5S,
pyruvate carboxylase, AksA, and FrbC. These members all
share a conserved triose-phosphate isomerase (TIM)
barrel domain consisting of a core beta(8)-alpha(8)
motif with the eight parallel beta strands forming an
enclosed barrel surrounded by eight alpha helices. The
domain has a catalytic center containing a divalent
cation-binding site formed by a cluster of invariant
residues that cap the core of the barrel. In addition,
the catalytic site includes three invariant residues -
an aspartate (D), an arginine (R), and a glutamate (E) -
which is the basis for the domain name "DRE-TIM".
Length = 268
Score = 476 bits (1229), Expect = e-167
Identities = 163/281 (58%), Positives = 205/281 (72%), Gaps = 13/281 (4%)
Query: 79 VFDTTLRDGEQSPGATLTSKEKLDIARQLAKLGVDIIEAGFPAASKEDFEAVRTIAKEVG 138
+FDTTLRDGEQ+PG +LT +EKL+IARQL +LGVD+IEAGFPAAS DFEAV+ IA+EV
Sbjct: 1 IFDTTLRDGEQTPGVSLTPEEKLEIARQLDELGVDVIEAGFPAASPGDFEAVKRIAREVL 60
Query: 139 NAVDAESGYVPVICGLSRCNERDIKTAWEAVKYAKRPRIHTFIATSGIHMEHKLRKTKQQ 198
N ICGL+R ++DI A EA+K AK RIHTFIATS IH+++KL+KT+++
Sbjct: 61 N---------AEICGLARAVKKDIDAAAEALKPAKVDRIHTFIATSDIHLKYKLKKTREE 111
Query: 199 VVEIARSMVKFARSLGCDDVEFSPEDAGRSDRKFLYEILGEVIKVGATTLNIPDTVGITM 258
V+E A V++A+S G DVEFS EDA R+D FL E++ I+ GATT+NIPDTVG
Sbjct: 112 VLERAVEAVEYAKSHG-LDVEFSAEDATRTDLDFLIEVVEAAIEAGATTINIPDTVGYLT 170
Query: 259 PTEFGKLIADIKANTPGIENVVISTHCQNDLGLSTANTIAGACAGARQVEVTINGIGERA 318
P EFG+LI +K N P I V IS HC NDLGL+ AN++A AGARQVE TINGIGERA
Sbjct: 171 PEEFGELIKKLKENVPNI-KVPISVHCHNDLGLAVANSLAAVEAGARQVECTINGIGERA 229
Query: 319 GNASLEEVVMAFKCRGEHILGGLYTGINTRHIVMASKMVEE 359
GNA+LEEVVMA K R ++ G+ TGI+T + S++V
Sbjct: 230 GNAALEEVVMALKTRYDY--YGVETGIDTEELYETSRLVSR 268
>gnl|CDD|236493 PRK09389, PRK09389, (R)-citramalate synthase; Provisional.
Length = 488
Score = 458 bits (1181), Expect = e-156
Identities = 233/531 (43%), Positives = 314/531 (59%), Gaps = 51/531 (9%)
Query: 77 VRVFDTTLRDGEQSPGATLTSKEKLDIARQLAKLGVDIIEAGFPAASKEDFEAVRTIAKE 136
VR+ DTTLRDGEQ+PG +LT +EKL+IAR+L +LGVD+IEAG S+ + EA++ + E
Sbjct: 3 VRILDTTLRDGEQTPGVSLTPEEKLEIARKLDELGVDVIEAGSAITSEGEREAIKAVTDE 62
Query: 137 VGNAVDAESGYVPVICGLSRCNERDIKTAWEA-VKYAKRPRIHTFIATSGIHMEHKLRKT 195
++AE IC +R + DI A E V +H + TS +H+E+KL+KT
Sbjct: 63 ---GLNAE------ICSFARAVKVDIDAALECDVD-----SVHLVVPTSDLHIEYKLKKT 108
Query: 196 KQQVVEIARSMVKFARSLGCDDVEFSPEDAGRSDRKFLYEILGEVIKVGATTLNIPDTVG 255
+++V+E A V++A+ G VE S EDA R+D FL E+ I+ GA + DTVG
Sbjct: 109 REEVLETAVEAVEYAKDHGLI-VELSGEDASRADLDFLKELYKAGIEAGADRICFCDTVG 167
Query: 256 ITMPTEFGKLIADIKANTPGIENVVISTHCQNDLGLSTANTIAGACAGARQVEVTINGIG 315
I P + +L + +S HC ND GL+ ANT+A AGA QV VTINGIG
Sbjct: 168 ILTPEKTYELFKRLSELV----KGPVSIHCHNDFGLAVANTLAALAAGADQVHVTINGIG 223
Query: 316 ERAGNASLEEVVMAFKCRGEHILGGLYTGINTRHIVMASKMVEEYTGLHVQPHKAIVGAN 375
ERAGNASLEEVVMA K L + TGI + S++V TG+ V P+KAIVG N
Sbjct: 224 ERAGNASLEEVVMALK-----HLYDVETGIKLEELYELSRLVSRLTGIPVPPNKAIVGEN 278
Query: 376 AFAHESGIHQDGMLKHKGTYEIISPEDIGLERSSEAGIVLGKLSGRHALKDRLKELGYEL 435
AFAHESGIH DG+LK TYE I+PE +G ER IVLGK +GR ALK LKE+G E+
Sbjct: 279 AFAHESGIHVDGLLKDTETYEPITPETVGRERR----IVLGKHAGRAALKAALKEMGIEV 334
Query: 436 NDEQLGTIFWHFKAVAEQKKRVTDADLIALVSD--EIFQPEVVWKLLDMQVTCGTLGLST 493
+D+QL I K + ++ KRVTDADL+A+ D I + V KL ++ V G T
Sbjct: 335 SDDQLNEIVSRVKELGDRGKRVTDADLLAIAEDVLGIERERKV-KLDELTVVSGNKVTPT 393
Query: 494 ATVKLMDANGEEHVACSTGTGPVDSAYKAVDLIVKEPA--TLLEYSMNAVTAGIDAIATT 551
A+VKL + +GEE V TG GPVD+A AV + A L EY ++A+T G DA+
Sbjct: 394 ASVKL-NVDGEEIVEAGTGVGPVDAAINAVRKALSGVADIELEEYHVDAITGGTDALVEV 452
Query: 552 RV-LIRGEKSQLSTHASTGETVQRTFSGTGAGMDIVVSSVKAYIGALNKML 601
V L RG+ R + GA DI+++SV+A + +N++L
Sbjct: 453 EVKLSRGD---------------RVVTVRGADADIIMASVEAMMDGINRLL 488
>gnl|CDD|223197 COG0119, LeuA, Isopropylmalate/homocitrate/citramalate synthases
[Amino acid transport and metabolism].
Length = 409
Score = 455 bits (1173), Expect = e-156
Identities = 207/428 (48%), Positives = 277/428 (64%), Gaps = 25/428 (5%)
Query: 77 VRVFDTTLRDGEQSPGATLTSKEKLDIARQLAKLGVDIIEAGFPAASKEDFEAVRTIAKE 136
V +FDTTLRDGEQ+PG + + +EK+ IA+ L LGVD IEAGFP AS DFE VR IA++
Sbjct: 3 VIIFDTTLRDGEQAPGVSFSVEEKIRIAKALDDLGVDYIEAGFPVASPGDFEFVRAIAEK 62
Query: 137 VGNAVDAESGYVPVICGLSRCNERDIKTAWEAVKYAKRPRIHTFIATSGIHMEHKLRKTK 196
G IC L R IK EA+ A RIH FIATS +H+ +KL+KT+
Sbjct: 63 AGL----------FICALIAALARAIKRDIEALLEAGVDRIHIFIATSDLHLRYKLKKTR 112
Query: 197 QQVVEIARSMVKFARSLGCDDVEFSPEDAGRSDRKFLYEILGEVIKVGATTLNIPDTVGI 256
++V+E A V++AR G +V FS EDA R+D +FL E++ I+ GA +N+PDTVG+
Sbjct: 113 EEVLERAVDAVEYARDHG-LEVRFSAEDATRTDPEFLAEVVKAAIEAGADRINLPDTVGV 171
Query: 257 TMPTEFGKLIADIKANTPGIENVVISTHCQNDLGLSTANTIAGACAGARQVEVTINGIGE 316
P E +I +KAN P V++S HC NDLG++ AN++A AGA QVE T+NGIGE
Sbjct: 172 ATPNEVADIIEALKANVP--NKVILSVHCHNDLGMAVANSLAAVEAGADQVEGTVNGIGE 229
Query: 317 RAGNASLEEVVMAFKCRGEHILGGLYTGINTRHIVMASKMVEEYTGLHVQPHKAIVGANA 376
RAGNA+LEEVV+A R ++ G+ TGI+ + AS++VE TG+ V P+K IVG NA
Sbjct: 230 RAGNAALEEVVLALALRKDY---GVDTGIDLEKLTEASRLVERLTGIPVPPNKPIVGENA 286
Query: 377 FAHESGIHQDGMLKHKGTYEIISPEDIGLERSSEAGIVLGKLSGRHALKDRLKELGYELN 436
FAHESGIHQDG+LK+ TYE I PED+G R ++ GK SGR A+K +L+ELG EL+
Sbjct: 287 FAHESGIHQDGVLKNPETYEPIDPEDVGRRRRI---VIGGKHSGRKAVKAKLEELGIELD 343
Query: 437 DEQLGTIFWHFKAVAEQKKR--VTDADLIALVSDE--IFQPEVVWKLLDMQVTCGTLGLS 492
+E+L +F K +A++ K+ VTDADL ALV +E +P L + V G +
Sbjct: 344 EEELDKLFSRVKELADKGKKKEVTDADLEALVEEELGSREPFEKISLDVLTVQSG--NVP 401
Query: 493 TATVKLMD 500
TA+VKL
Sbjct: 402 TASVKLEV 409
>gnl|CDD|183341 PRK11858, aksA, trans-homoaconitate synthase; Reviewed.
Length = 378
Score = 428 bits (1104), Expect = e-146
Identities = 185/398 (46%), Positives = 251/398 (63%), Gaps = 30/398 (7%)
Query: 73 DPNYVRVFDTTLRDGEQSPGATLTSKEKLDIARQLAKLGVDIIEAGFPAASKEDFEAVRT 132
P + + DTTLRDGEQ+PG T++EKL IAR L ++GVD IEAGFPA S+++ EA++
Sbjct: 1 KPKDIEIVDTTLRDGEQTPGVVFTNEEKLAIARMLDEIGVDQIEAGFPAVSEDEKEAIKA 60
Query: 133 IAKEVGNAVDAESGYVPVICGLSRCNERDIKTAWEA-VKYAKRPRIHTFIATSGIHMEHK 191
IAK NA I L+R + DI + + V +H FIATS IH++HK
Sbjct: 61 IAKLGLNAS---------ILALNRAVKSDIDASIDCGVD-----AVHIFIATSDIHIKHK 106
Query: 192 LRKTKQQVVEIARSMVKFARSLGCDDVEFSPEDAGRSDRKFLYEILGEVIKVGATTLNIP 251
L+KT+++V+E V++A+ G V FS EDA R+D FL E + GA +
Sbjct: 107 LKKTREEVLERMVEAVEYAKDHGLY-VSFSAEDASRTDLDFLIEFAKAAEEAGADRVRFC 165
Query: 252 DTVGITMPTEFGKLIADIKANTPGIENVVISTHCQNDLGLSTANTIAGACAGARQVEVTI 311
DTVGI P +L+ ++ ++ I HC ND G++TAN +AG AGA+QV T+
Sbjct: 166 DTVGILDPFTMYELVKELVEAV----DIPIEVHCHNDFGMATANALAGIEAGAKQVHTTV 221
Query: 312 NGIGERAGNASLEEVVMAFKCRGEHILGGLYTGINTRHIVMASKMVEEYTGLHVQPHKAI 371
NG+GERAGNA+LEEVVMA K L G+ GI+T + S++V + +G+ V P+KAI
Sbjct: 222 NGLGERAGNAALEEVVMALKY-----LYGIDLGIDTERLYELSRLVSKASGIPVPPNKAI 276
Query: 372 VGANAFAHESGIHQDGMLKHKGTYEIISPEDIGLERSSEAGIVLGKLSGRHALKDRLKEL 431
VG NAFAHESGIH DG+LK+ TYE PE++GLER IVLGK SGRHALK++LKE
Sbjct: 277 VGENAFAHESGIHVDGVLKNPLTYEPFLPEEVGLERR----IVLGKHSGRHALKNKLKEY 332
Query: 432 GYELNDEQLGTIFWHFKAVAEQKKR-VTDADLIALVSD 468
G EL+ E+L + K ++E+KKR +TD +L LV D
Sbjct: 333 GIELSREELCELLEKVKELSERKKRSLTDEELKELVED 370
>gnl|CDD|233719 TIGR02090, LEU1_arch, isopropylmalate/citramalate/homocitrate
synthases. Methanogenic archaea contain three closely
related homologs of the 2-isopropylmalate synthases
(LeuA) represented by TIGR00973. Two of these in
Methanococcus janaschii (MJ1392 - CimA ; MJ0503 - AksA )
have been characterized as catalyzing alternative
reactions leaving the third (MJ1195) as the presumptive
LeuA enzyme. CimA is citramalate (2-methylmalate)
synthase which condenses acetyl-CoA with pyruvate. This
enzyme is believed to be involved in the biosynthesis of
isoleucine in methanogens and possibly other species
lacking threonine dehydratase. AksA is a homocitrate
synthase which also produces (homo)2-citrate and
(homo)3-citrate in the biosynthesis of Coenzyme B which
is restricted solely to methanogenic archaea.
Methanogens, then should and aparrently do contain all
three of these enzymes. Unfortunately, phylogenetic
trees do not resolve into three unambiguous clades,
making assignment of function to particular genes
problematic. Other archaea which lack a threonine
dehydratase (mainly Euryarchaeota) should contain both a
CimA and a LeuA gene. This is true of, for example,
archaeoglobus fulgidis, but not for the Pyrococci which
have none in this clade, but one in TIGR00973 and one in
TIGRT00977 which may fulfill these roles. Other species
which have only one hit to this model and lack threonine
dehydratase are very likely LeuA enzymes.
Length = 363
Score = 403 bits (1037), Expect = e-137
Identities = 193/390 (49%), Positives = 264/390 (67%), Gaps = 27/390 (6%)
Query: 77 VRVFDTTLRDGEQSPGATLTSKEKLDIARQLAKLGVDIIEAGFPAASKEDFEAVRTIAKE 136
V +FDTTLRDGEQ+PG +LT ++K++IAR+L +LGVD+IEAGFP AS+ +FEA++ I++E
Sbjct: 1 VYIFDTTLRDGEQTPGVSLTVEQKVEIARKLDELGVDVIEAGFPIASEGEFEAIKKISQE 60
Query: 137 VGNAVDAESGYVPVICGLSRCNERDIKTAWEAVKYAKRPRIHTFIATSGIHMEHKLRKTK 196
++AE IC L+R ++DI A + IHTFIATS IH+++KL+K++
Sbjct: 61 ---GLNAE------ICSLARALKKDIDKAID----CGVDSIHTFIATSPIHLKYKLKKSR 107
Query: 197 QQVVEIARSMVKFARSLGCDDVEFSPEDAGRSDRKFLYEILGEVIKVGATTLNIPDTVGI 256
+V+E A V++A+ G VEFS EDA R+D FL ++ + GA +NI DTVG+
Sbjct: 108 DEVLEKAVEAVEYAKEHGL-IVEFSAEDATRTDIDFLIKVFKRAEEAGADRINIADTVGV 166
Query: 257 TMPTEFGKLIADIKANTPGIENVVISTHCQNDLGLSTANTIAGACAGARQVEVTINGIGE 316
P + +LI +K N + IS HC ND GL+TAN+IAG AGA QV VT+NGIGE
Sbjct: 167 LTPQKMEELIKKLKENV----KLPISVHCHNDFGLATANSIAGVKAGAEQVHVTVNGIGE 222
Query: 317 RAGNASLEEVVMAFKCRGEHILGGLYTGINTRHIVMASKMVEEYTGLHVQPHKAIVGANA 376
RAGNA+LEEVVMA K L G+ T I T + S++V E +G+ V P+KAIVG NA
Sbjct: 223 RAGNAALEEVVMALK-----YLYGVKTKIKTEKLYETSRLVSELSGVKVPPNKAIVGENA 277
Query: 377 FAHESGIHQDGMLKHKGTYEIISPEDIGLERSSEAGIVLGKLSGRHALKDRLKELGYELN 436
FAHESGIH DG++++ TYE ISPE +G +R I+LGK SGRHA++ +LKELG ++
Sbjct: 278 FAHESGIHVDGVIENPLTYEPISPEVVGNKRR----IILGKHSGRHAVEAKLKELGIKVT 333
Query: 437 DEQLGTIFWHFKAVAEQKKRVTDADLIALV 466
DEQL I K + ++ KRVTDAD+ +V
Sbjct: 334 DEQLKEILKRIKEIGDKGKRVTDADVKEIV 363
>gnl|CDD|233965 TIGR02660, nifV_homocitr, homocitrate synthase NifV. This family
consists of the NifV clade of homocitrate synthases,
most of which are found in operons for nitrogen
fixation. Members are closely homologous to enzymes that
include 2-isopropylmalate synthase, (R)-citramalate
synthase, and homocitrate synthases associated with
other processes. The homocitrate made by this enzyme
becomes a part of the iron-molybdenum cofactor of
nitrogenase [Biosynthesis of cofactors, prosthetic
groups, and carriers, Other, Central intermediary
metabolism, Nitrogen fixation].
Length = 365
Score = 306 bits (786), Expect = 4e-99
Identities = 155/392 (39%), Positives = 208/392 (53%), Gaps = 30/392 (7%)
Query: 77 VRVFDTTLRDGEQSPGATLTSKEKLDIARQLAKLGVDIIEAGFPAASKEDFEAVRTIAKE 136
V + DTTLRDGEQ+PG T+ EKL IAR L + GVD +E G PA +E+ +R I
Sbjct: 2 VIINDTTLRDGEQAPGVAFTAAEKLAIARALDEAGVDELEVGIPAMGEEERAVIRAIVAL 61
Query: 137 VGNAVDAESGYVPVICGLSRCNERDIKTAWEA-VKYAKRPRIHTFIATSGIHMEHKLRKT 195
A + R + DI+ A V +H I S + +E KLRK
Sbjct: 62 GLPAR---------LMAWCRARDADIEAAARCGVD-----AVHISIPVSDLQIEAKLRKD 107
Query: 196 KQQVVEIARSMVKFARSLGCDDVEFSPEDAGRSDRKFLYEILGEVIKVGATTLNIPDTVG 255
+ V+E +V FAR G V EDA R+D FL E+ + GA DTVG
Sbjct: 108 RAWVLERLARLVSFARDRG-LFVSVGGEDASRADPDFLVELAEVAAEAGADRFRFADTVG 166
Query: 256 ITMPTEFGKLIADIKANTPGIENVVISTHCQNDLGLSTANTIAGACAGARQVEVTINGIG 315
I P +L+ ++ + H NDLG++TANT+A AGA V T+NG+G
Sbjct: 167 ILDPFSTYELVRALRQAVDL----PLEMHAHNDLGMATANTLAAVRAGATHVNTTVNGLG 222
Query: 316 ERAGNASLEEVVMAFKCRGEHILGGLYTGINTRHIVMASKMVEEYTGLHVQPHKAIVGAN 375
ERAGNA+LEEV MA K L G TGI+T + S++V +G + P K +VG +
Sbjct: 223 ERAGNAALEEVAMALK-----RLLGRDTGIDTSRLPALSQLVARASGRPIPPQKPVVGES 277
Query: 376 AFAHESGIHQDGMLKHKGTYEIISPEDIGLERSSEAGIVLGKLSGRHALKDRLKELGYEL 435
F HESGIH DG+LK TYE PE +G R IV+GK SGR AL + L +LG L
Sbjct: 278 VFTHESGIHVDGLLKDPRTYEPFDPELVGRSRR----IVIGKHSGRAALINALAQLGIPL 333
Query: 436 NDEQLGTIFWHFKAVAEQKKR-VTDADLIALV 466
++E+ + +A A + KR ++DA+LIAL
Sbjct: 334 SEEEAAALLPAVRAFATRLKRPLSDAELIALY 365
>gnl|CDD|201390 pfam00682, HMGL-like, HMGL-like. This family contains a diverse
set of enzymes. These include various aldolases and a
region of pyruvate carboxylase.
Length = 236
Score = 273 bits (700), Expect = 3e-88
Identities = 117/249 (46%), Positives = 154/249 (61%), Gaps = 13/249 (5%)
Query: 86 DGEQSPGATLTSKEKLDIARQLAKLGVDIIEAGFPAASKEDFEAVRTIAKEVGNAVDAES 145
DGEQ+ GA + +EKL IAR L + GVD IE GFP S DFE+VR IA+ + A
Sbjct: 1 DGEQALGAAFSVEEKLAIARALDEAGVDEIEVGFPFMSPTDFESVRAIAEVLKKAK---- 56
Query: 146 GYVPVICGLSRCNERDIKTAWEAVKYAKRPRIHTFIATSGIHMEHKLRKTKQQVVEIARS 205
I L R E DI A EA K A R+H FIATS +H ++KL K +++V + A +
Sbjct: 57 -----IQALLRPVEHDIDAAVEAAKGAGADRVHVFIATSDLHRKYKLNKDREEVADRAVA 111
Query: 206 MVKFARSLGCDDVEFSPEDAGRSDRKFLYEILGEVIKVGATTLNIPDTVGITMPTEFGKL 265
V+ ARS G D VE EDAGR+D FL E++ + GAT +NI DTVG+ P E L
Sbjct: 112 AVEAARSAGID-VELGCEDAGRTDLAFLIEVVEVAQEAGATRINIADTVGVLTPNEAADL 170
Query: 266 IADIKANTPGIENVVISTHCQNDLGLSTANTIAGACAGARQVEVTINGIGERAGNASLEE 325
I+ +K P V+I HC NDLG++ AN++A AGA +V+ T+NG+GERAGNA+LEE
Sbjct: 171 ISALKDRVP---PVIIEVHCHNDLGMAVANSLAAVEAGADRVDGTVNGLGERAGNAALEE 227
Query: 326 VVMAFKCRG 334
+V A + G
Sbjct: 228 LVAALEVLG 236
>gnl|CDD|163674 cd03174, DRE_TIM_metallolyase, DRE-TIM metallolyase superfamily.
The DRE-TIM metallolyase superfamily includes
2-isopropylmalate synthase (IPMS), alpha-isopropylmalate
synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase,
homocitrate synthase, citramalate synthase,
4-hydroxy-2-oxovalerate aldolase, re-citrate synthase,
transcarboxylase 5S, pyruvate carboxylase, AksA, and
FrbC. These members all share a conserved
triose-phosphate isomerase (TIM) barrel domain
consisting of a core beta(8)-alpha(8) motif with the
eight parallel beta strands forming an enclosed barrel
surrounded by eight alpha helices. The domain has a
catalytic center containing a divalent cation-binding
site formed by a cluster of invariant residues that cap
the core of the barrel. In addition, the catalytic site
includes three invariant residues - an aspartate (D), an
arginine (R), and a glutamate (E) - which is the basis
for the domain name "DRE-TIM".
Length = 265
Score = 272 bits (697), Expect = 3e-87
Identities = 98/288 (34%), Positives = 155/288 (53%), Gaps = 31/288 (10%)
Query: 80 FDTTLRDGEQSPGATLTSKEKLDIARQLAKLGVDIIEAGFPAASKE------DFEAVRTI 133
DTTLRDG QS GAT ++++KL+IA L + GVD IE G A+ K D+E +R I
Sbjct: 1 TDTTLRDGLQSEGATFSTEDKLEIAEALDEAGVDSIEVGSGASPKAVPQMEDDWEVLRAI 60
Query: 134 AKEVGNAVDAESGYVPVICGLSRCNERDIKTAWEAVKYAKRPRIHTFIATSGIHMEHKLR 193
K V N + L R E+ I+ A EA + F + S H L
Sbjct: 61 RKLVPNVK---------LQALVRNREKGIERALEAG----VDEVRIFDSASETHSRKNLN 107
Query: 194 KTKQQVVEIARSMVKFARSLGCDDVEFSPEDAGR--SDRKFLYEILGEVIKVGATTLNIP 251
K++++ +E A ++ A+ G +VE S EDA +D +++ E+ + + GA +++
Sbjct: 108 KSREEDLENAEEAIEAAKEAG-LEVEGSLEDAFGCKTDPEYVLEVAKALEEAGADEISLK 166
Query: 252 DTVGITMPTEFGKLIADIKANTPGIENVVISTHCQNDLGLSTANTIAGACAGARQVEVTI 311
DTVG+ P E +L+ ++ P + + H N LGL+ AN++A AGA +V+ ++
Sbjct: 167 DTVGLATPEEVAELVKALREALPDVP---LGLHTHNTLGLAVANSLAALEAGADRVDGSV 223
Query: 312 NGIGERAGNASLEEVVMAFKCRGEHILGGLYTGINTRHIVMASKMVEE 359
NG+GERAGNA+ E++V A + G+ TGI+ ++ S+ VEE
Sbjct: 224 NGLGERAGNAATEDLVAALEGL------GIDTGIDLEKLLEISRYVEE 265
>gnl|CDD|163677 cd07939, DRE_TIM_NifV, Streptomyces rubellomurinus FrbC and related
proteins, catalytic TIM barrel domain. FrbC (NifV) of
Streptomyces rubellomurinus catalyzes the condensation
of acetyl-CoA and alpha-ketoglutarate to form
homocitrate and CoA, a reaction similar to one catalyzed
by homocitrate synthase. The gene encoding FrbC is one
of several genes required for the biosynthesis of
FR900098, a potent antimalarial antibiotic. This
protein is also required for assembly of the nitrogenase
MoFe complex but its exact role is unknown. This
family also includes the NifV proteins of Heliobacterium
chlorum and Gluconacetobacter diazotrophicus, which
appear to be orthologous to FrbC. This family belongs
to the DRE-TIM metallolyase superfamily. DRE-TIM
metallolyases include 2-isopropylmalate synthase (IPMS),
alpha-isopropylmalate synthase (LeuA),
3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate
synthase, citramalate synthase, 4-hydroxy-2-oxovalerate
aldolase, re-citrate synthase, transcarboxylase 5S,
pyruvate carboxylase, AksA, and FrbC. These members all
share a conserved triose-phosphate isomerase (TIM)
barrel domain consisting of a core beta(8)-alpha(8)
motif with the eight parallel beta strands forming an
enclosed barrel surrounded by eight alpha helices. The
domain has a catalytic center containing a divalent
cation-binding site formed by a cluster of invariant
residues that cap the core of the barrel. In addition,
the catalytic site includes three invariant residues -
an aspartate (D), an arginine (R), and a glutamate (E) -
which is the basis for the domain name "DRE-TIM".
Length = 259
Score = 230 bits (589), Expect = 3e-71
Identities = 115/279 (41%), Positives = 148/279 (53%), Gaps = 23/279 (8%)
Query: 81 DTTLRDGEQSPGATLTSKEKLDIARQLAKLGVDIIEAGFPAASKEDFEAVRTIAKEVGNA 140
DTTLRDGEQ+PG + +EKL IAR L + GVD IE G PA +E+ EA+R I
Sbjct: 3 DTTLRDGEQAPGVAFSREEKLAIARALDEAGVDEIEVGIPAMGEEEREAIRAIVALG--- 59
Query: 141 VDAESGYVPVICGLSRCNERDIKTAWEAVKYAKRPRIHTFIATSGIHMEHKLRKTKQQVV 200
+ A + R + DI EA +H I S IH+ HKL K + V+
Sbjct: 60 LPAR------LIVWCRAVKEDI----EAALRCGVTAVHISIPVSDIHLAHKLGKDRAWVL 109
Query: 201 EIARSMVKFARSLGCDDVEFSPEDAGRSDRKFLYEILGEVIKVGATTLNIPDTVGITMPT 260
+ R +V A+ G V EDA R+D FL E + GA L DTVGI P
Sbjct: 110 DQLRRLVGRAKDRGLF-VSVGAEDASRADPDFLIEFAEVAQEAGADRLRFADTVGILDPF 168
Query: 261 EFGKLIADIKANTPGIENVVISTHCQNDLGLSTANTIAGACAGARQVEVTINGIGERAGN 320
+LI ++A T + + H NDLGL+TANT+A AGA V VT+NG+GERAGN
Sbjct: 169 TTYELIRRLRAATD-LP---LEFHAHNDLGLATANTLAAVRAGATHVSVTVNGLGERAGN 224
Query: 321 ASLEEVVMAFKCRGEHILGGLYTGINTRHIVMASKMVEE 359
A+LEEVVMA K L G TGI+T + S++V
Sbjct: 225 AALEEVVMALKH-----LYGRDTGIDTTRLPELSQLVAR 258
>gnl|CDD|237068 PRK12344, PRK12344, putative alpha-isopropylmalate/homocitrate
synthase family transferase; Provisional.
Length = 524
Score = 203 bits (520), Expect = 3e-58
Identities = 155/537 (28%), Positives = 248/537 (46%), Gaps = 108/537 (20%)
Query: 72 PDPNYVRVFDTTLRDGEQSPGATLTSKEKLDIARQLAKLGVDIIEAGFPAASKED---FE 128
+ ++DTTLRDG Q G + + ++KL IAR+L +LGVD IE G+P ++ +D F+
Sbjct: 1 MMMERIELYDTTLRDGAQGEGISFSVEDKLRIARKLDELGVDYIEGGWPGSNPKDTEFFK 60
Query: 129 AVRTI----AKEV--------GNAVDA--------ESGYVPVICGLSRCNERDIKTAWEA 168
+ + AK G + + ++G PV+ I
Sbjct: 61 RAKELKLKHAKLAAFGSTRRAGVSAEEDPNLQALLDAG-TPVVT---------I------ 104
Query: 169 VKYAKRPRIHTFIATSGIHMEHKLRKTKQQVVEIARSMVKFARSLGCDDVEFSPE---DA 225
+ K + +H+ LR T ++ + + R V + ++ G +V F E D
Sbjct: 105 --FGK---------SWDLHVTEALRTTLEENLAMIRDSVAYLKAHG-REVIFDAEHFFDG 152
Query: 226 GRSDRKFLYEILGEVIKVGATTLNIPDTVGITMPTEFGKLIADIKANTP---GIENVVIS 282
+++ ++ L + GA + + DT G T+P E +++A+++A GI
Sbjct: 153 YKANPEYALATLKAAAEAGADWVVLCDTNGGTLPHEVAEIVAEVRAAPGVPLGI------ 206
Query: 283 THCQNDLGLSTANTIAGACAGARQVEVTINGIGERAGNASLEEVV------MAFKCRGEH 336
H ND G + AN++A AGARQV+ TING GER GNA+L ++ M ++C E
Sbjct: 207 -HAHNDSGCAVANSLAAVEAGARQVQGTINGYGERCGNANLCSIIPNLQLKMGYECLPEE 265
Query: 337 ILGGLYTGINTRHIVMASKMVEEYTGLHVQPHKAIVGANAFAHESGIHQDGMLKHKGTYE 396
L L T S+ V E L PH+ VGA+AFAH+ GIH +LK TYE
Sbjct: 266 KLKEL-----TE----VSRFVSEIANLAPDPHQPYVGASAFAHKGGIHVSAVLKDPRTYE 316
Query: 397 IISPEDIGLERSSEAGIVLGKLSGRHALKDRLKELGYEL--NDEQLGTIFWHFKAVAEQK 454
I PE +G R +++ +L+GR + + KELG +L +D +L + + K
Sbjct: 317 HIDPELVGNRRR----VLVSELAGRSNILAKAKELGIDLDKDDPRLKRL------LERIK 366
Query: 455 KR--------VTDADLIALVSDEIFQPEVVWKLLDMQVTC--GTLGLSTATVKLMDANGE 504
+ +A L+ E+ + ++L +V G+S ATVK+ GE
Sbjct: 367 ELEAEGYQFEAAEASFELLLRRELGEYPPFFELESFRVIVEKRGDGVSEATVKVR-VGGE 425
Query: 505 EHVACSTGTGPV---DSA-YKAVDLIVKEPAT--LLEYSMNAVTAGIDAIATTRVLI 555
+ G GPV D+A KA++ E A L++Y + + G A RVLI
Sbjct: 426 REHTAAEGNGPVNALDNALRKALEKFYPELAEVELVDYKVRILDGGKGTAAVVRVLI 482
>gnl|CDD|162728 TIGR02146, LysS_fung_arch, homocitrate synthase. This model
includes the yeast LYS21 gene which carries out the
first step of the alpha-aminoadipate (AAA) lysine
biosynthesis pathway. A related pathway is found in
Thermus thermophilus. This enzyme is closely related to
2-isopropylmalate synthase (LeuA) and citramalate
synthase (CimA), both of which are present in the
euryarchaeota. Some archaea have a separate homocitrate
synthase (AksA) which also synthesizes longer
homocitrate analogs.
Length = 344
Score = 189 bits (482), Expect = 9e-55
Identities = 115/361 (31%), Positives = 175/361 (48%), Gaps = 29/361 (8%)
Query: 81 DTTLRDGEQSPGATLTSKEKLDIARQLAKLGVDIIEAGFPAASKEDFEAVRTIAKEVGNA 140
D+TLR+GEQ PGA ++++K++IA+ L + G+D IE PAASK+ + IA
Sbjct: 3 DSTLREGEQFPGANFSTEQKIEIAKALDEFGIDYIEVTHPAASKQSRIDIEIIAS----- 57
Query: 141 VDAESGYVPVICGLSRCNERDIKTAWEA-VKYAKRPRIHTFIATSGIHMEHKLRKTKQQV 199
G I RC D K A E V I F TS + + R + +
Sbjct: 58 ----LGLKANIVTHIRCRLDDAKVAVELGVDG-----IDIFFGTSKLLRIAEHRSDAKSI 108
Query: 200 VEIARSMVKFARSLGCDDVEFSPEDAGRSDRKFLYEILGEVIKVGATTLNIPDTVGITMP 259
+E AR +++A+S G +V FS ED RS+ L I V G + I DTVG P
Sbjct: 109 LESARETIEYAKSAGL-EVRFSAEDTFRSELADLLSIYETVGVFGVDRVGIADTVGKAAP 167
Query: 260 TEFGKLIADIKANTPGIENVVISTHCQNDLGLSTANTIAGACAGARQVEVTINGIGERAG 319
+ +LI + PG++ H ND G + AN GA V+ T+ GIGER G
Sbjct: 168 RQVYELIRTVVRVVPGVDI---ELHAHNDTGCAVANAYNAIEGGATIVDTTVLGIGERNG 224
Query: 320 NASLEEVVMAFKCRGEHILGGLYTGINTRHIVMASKMVEEYTGLHVQPHKAIVGANAFAH 379
L ++ +Y ++ ++MV G+ + + I G AF H
Sbjct: 225 ITPLGGILARLY-----YHTPMYV-YKLGKLIELTRMVAGEVGVTIPFNNPITGELAFTH 278
Query: 380 ESGIHQDGMLKHKGTYEIISPEDIGLERSSEAGIVLGKLSGRHALKDRLKELGYELNDEQ 439
++GIH +L + TYE + PE G +R I++ +L+G+HA+K R ++LG +L +E+
Sbjct: 279 KAGIHVKAILGNPRTYEFLPPEVFGRKRH----ILIARLTGKHAIKARKEKLGVKLIEEE 334
Query: 440 L 440
L
Sbjct: 335 L 335
>gnl|CDD|130050 TIGR00977, LeuA_rel, 2-isopropylmalate synthase/homocitrate
synthase family protein. This model represents
uncharacterized proteins related to 2-isopropylmalate
synthases and homocitrate synthases but phylogenetically
distint. Each species represented in the seed alignment
also has a member of a known family of 2-isopropylmalate
synthases [Unknown function, General].
Length = 526
Score = 182 bits (462), Expect = 3e-50
Identities = 127/508 (25%), Positives = 233/508 (45%), Gaps = 55/508 (10%)
Query: 77 VRVFDTTLRDGEQSPGATLTSKEKLDIARQLAKLGVDIIEAGFPAASKED---FEAVRTI 133
+ ++DTTLRDG Q G + + ++K+ IA +L LG+ IE G+P A+ +D F ++
Sbjct: 2 LWLYDTTLRDGAQREGVSFSLEDKIRIAERLDDLGIHYIEGGWPGANPKDVQFFWQLK-- 59
Query: 134 AKEVGNAVDAESGYVPVICGLSRCNER-DIKTAWEAVKYAKRPRIHTFIATSGIHMEHKL 192
++ ++ + C R +++ + +A+ A+ P + F + +H+ L
Sbjct: 60 ------EMNFKNAKIVAFCSTRRPHKKVEEDKMLQALIKAETPVVTIFGKSWDLHVLEAL 113
Query: 193 RKTKQQVVEIARSMVKFARSLGCDDVEFSPE---DAGRSDRKFLYEILGEVIKVGATTLN 249
+ T ++ + + V + + G D+V + E D +++ ++ L + GA L
Sbjct: 114 QTTLEENLAMIYDTVAYLKRQG-DEVIYDAEHFFDGYKANPEYALATLATAQQAGADWLV 172
Query: 250 IPDTVGITMPTEFGKLIADIKANTPGIENVVISTHCQNDLGLSTANTIAGACAGARQVEV 309
+ DT G T+P E ++ +K + ++ + H ND G + AN++ AGA V+
Sbjct: 173 LCDTNGGTLPHEISEITTKVKRS---LKQPQLGIHAHNDSGTAVANSLLAVEAGATMVQG 229
Query: 310 TINGIGERAGNASLEEVV------MAFKCRGEHILGGLYTGINTRHIVMASKMVEEYTGL 363
TING GER GNA+L ++ + + N + + +++V E L
Sbjct: 230 TINGYGERCGNANLCSLIPNLQLKLGYDVIPPE---------NLKKLTSTARLVAEIVNL 280
Query: 364 HVQPHKAIVGANAFAHESGIHQDGMLKHKGTYEIISPEDIGLERSSEAGIVLGKLSGRHA 423
+ VG +AFAH+ G+H + ++ TYE I+PE +G ER IV+ +L+G
Sbjct: 281 PPDDNMPYVGRSAFAHKGGVHVSAVQRNPFTYEHIAPELVGNERR----IVVSELAGLSN 336
Query: 424 LKDRLKELGYELNDE--QLGTIFWHFKAVAEQ--KKRVTDADLIALVSDEIFQPEVVWKL 479
+ + KE G E++ + TI K + +Q +A L+ + + +
Sbjct: 337 VLSKAKEFGIEIDRQSPACRTILAKIKELEQQGYHFEAAEASFELLMRQAMGDRKPYFLF 396
Query: 480 LDMQVTC------GTLGLSTATVKLMDANGEEHVACSTGTGPVDSAYKAVDLIVKE---- 529
QV C + + ATV++ EH A + G GPV + +A+ ++
Sbjct: 397 QGFQVHCDKLRDAESYRNALATVRVTVEGQNEHTA-AEGNGPVSALDRALRKALERFYPQ 455
Query: 530 --PATLLEYSMNAVTAGIDAIATTRVLI 555
L +Y + + G A TRVLI
Sbjct: 456 LKDFHLTDYKVRILNEGAGTSAKTRVLI 483
>gnl|CDD|219870 pfam08502, LeuA_dimer, LeuA allosteric (dimerisation) domain. This
is the C-terminal regulatory (R) domain of
alpha-isopropylmalate synthase, which catalyzes the
first committed step in the leucine biosynthetic
pathway. This domain, is an internally duplicated
structure with a novel fold. It comprises two similar
units that are arranged such that the two -helices pack
together in the centre, crossing at an angle of 34
degrees, sandwiched between the two three-stranded,
antiparallel beta-sheets. The overall domain is thus
constructed as a beta-alpha-beta three-layer sandwich.
Length = 131
Score = 147 bits (373), Expect = 6e-42
Identities = 61/146 (41%), Positives = 83/146 (56%), Gaps = 15/146 (10%)
Query: 456 RVTDADLIALVSDEIFQPEVVWKLLDMQVTCGTLGLSTATVKLMDANGEEHVACSTGTGP 515
VTD DL AL SDE + E +KL +QV G+ G+ TATVKL + +GEE +TG GP
Sbjct: 1 EVTDEDLEALFSDEYGEAEERFKLESLQVQSGSNGIPTATVKL-EVDGEEKEEAATGNGP 59
Query: 516 VDSAYKAVDLIVKEPATLLEYSMNAVTAGIDAIATTRVLIRGEKSQLSTHASTGETVQRT 575
VD+ Y A+ I+ LL+YS++A+T G DA+A V + + R
Sbjct: 60 VDALYNALRKILGVDIKLLDYSVHAITGGTDALAEVYVELEYDG--------------RI 105
Query: 576 FSGTGAGMDIVVSSVKAYIGALNKML 601
F G G DIV +S KAY+ ALN++L
Sbjct: 106 FWGVGVDTDIVEASAKAYVSALNRLL 131
>gnl|CDD|163683 cd07945, DRE_TIM_CMS, Leptospira interrogans citramalate synthase
(CMS) and related proteins, N-terminal catalytic TIM
barrel domain. Citramalate synthase (CMS) catalyzes the
conversion of pyruvate and acetyl-CoA to (R)-citramalate
in the first dedicated step of the citramalate pathway.
Citramalate is only found in Leptospira interrogans and
a few other microorganisms. This family belongs to the
DRE-TIM metallolyase superfamily. DRE-TIM metallolyases
include 2-isopropylmalate synthase (IPMS),
alpha-isopropylmalate synthase (LeuA),
3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate
synthase, citramalate synthase, 4-hydroxy-2-oxovalerate
aldolase, re-citrate synthase, transcarboxylase 5S,
pyruvate carboxylase, AksA, and FrbC. These members all
share a conserved triose-phosphate isomerase (TIM)
barrel domain consisting of a core beta(8)-alpha(8)
motif with the eight parallel beta strands forming an
enclosed barrel surrounded by eight alpha helices. The
domain has a catalytic center containing a divalent
cation-binding site formed by a cluster of invariant
residues that cap the core of the barrel. In addition,
the catalytic site includes three invariant residues -
an aspartate (D), an arginine (R), and a glutamate (E) -
which is the basis for the domain name "DRE-TIM".
Length = 280
Score = 145 bits (369), Expect = 1e-39
Identities = 92/300 (30%), Positives = 145/300 (48%), Gaps = 29/300 (9%)
Query: 81 DTTLRDGEQSPGATLTSKEKLDIARQL-AKLGVDIIEAGFPAASKEDFEAVRTI---AKE 136
DTTLRDGEQ+ G + + EKL+IA+ L +L VD IE S+ +FEAV+ I A E
Sbjct: 2 DTTLRDGEQTSGVSFSPSEKLNIAKILLQELKVDRIEVASARVSEGEFEAVQKIIDWAAE 61
Query: 137 VGNAVDAES-GYVPVICGLSRCNERDIKTAWEAVKYAKRPRIHTFIATSGIHMEHKLRKT 195
G E G+V + D W +K A ++ S H +LRKT
Sbjct: 62 EGLLDRIEVLGFV----------DGDKSVDW--IKSAGAKVLNLLTKGSLKHCTEQLRKT 109
Query: 196 KQQVVEIARSMVKFARSLGCDDVEFSPEDAG---RSDRKFLYEILGEVIKVGATTLNIPD 252
++ R ++++A G + V ED R ++++++ + + + +PD
Sbjct: 110 PEEHFADIREVIEYAIKNGIE-VNIYLEDWSNGMRDSPDYVFQLVDFLSDLPIKRIMLPD 168
Query: 253 TVGITMPTEFGKLIADIKANTPGIENVVISTHCQNDLGLSTANTIAGACAGARQVEVTIN 312
T+GI P E I+D+ P N+ H ND L+ AN +A AG + + T+N
Sbjct: 169 TLGILSPFETYTYISDMVKRYP---NLHFDFHAHNDYDLAVANVLAAVKAGIKGLHTTVN 225
Query: 313 GIGERAGNASLEEVVMAFKCRGEHILGGLYTGINTRHIVMASKMVEEYTGLHVQPHKAIV 372
G+GERAGNA L V+ + T I+ + + AS++VE ++G + +K IV
Sbjct: 226 GLGERAGNAPLASVIAVL-----KDKLKVKTNIDEKRLNRASRLVETFSGKRIPANKPIV 280
>gnl|CDD|233216 TIGR00970, leuA_yeast, 2-isopropylmalate synthase, yeast type. A
larger family of homologous proteins includes
homocitrate synthase, distinct lineages of
2-isopropylmalate synthase, several distinct,
uncharacterized, orthologous sets in the Archaea, and
other related enzymes. This model describes a family of
2-isopropylmalate synthases as found in yeasts and in a
minority of studied bacteria [Amino acid biosynthesis,
Pyruvate family].
Length = 564
Score = 146 bits (370), Expect = 2e-37
Identities = 145/595 (24%), Positives = 231/595 (38%), Gaps = 108/595 (18%)
Query: 67 IPNRI-PDPNYVRV---FDTTLRDGEQSPGATLTSKEKLDIARQLAKLGVDIIEAGFPAA 122
+ NR PD R T LRDG Q+ ++ K L ++G IE GFP+A
Sbjct: 13 LRNRTWPDRVITRAPRWLSTDLRDGNQALPDPMSPARKRRYFDLLVRIGFKEIEVGFPSA 72
Query: 123 SKEDFEAVRTIAKEVGNAVDAESGYVP---VICGLSRCNERDIKTAWEAVKYAKRPRIHT 179
S+ DF+ VR I E G +P I L++ E I+ +EA+ AKR +H
Sbjct: 73 SQTDFDFVREII---------EQGAIPDDVTIQVLTQSREELIERTFEALSGAKRATVHF 123
Query: 180 FIATSGIHMEHKLRKTKQQVVEIARSMVKFARSLGCDDV---------EFSPEDAGRSDR 230
+ ATS + E R ++ +V IA K R E+SPE ++
Sbjct: 124 YNATSILFREVVFRASRAEVQAIATDGTKLVRKCTKQAAKYPGTQWRFEYSPESFSDTEL 183
Query: 231 KFLYEILGEVIKVGATT------LNIPDTVGITMPTEFGKLIADIKANTPGIENVVISTH 284
+F E+ V +V A T N+P TV +T P + I N E V +S H
Sbjct: 184 EFAKEVCEAVKEVWAPTPERPIIFNLPATVEMTTPNVYADSIEYFSTNIAEREKVCLSLH 243
Query: 285 CQNDLGLSTANTIAGACAGARQVEVTINGIGERAGNASLEEVVMAFKCRGEHILGGLYTG 344
ND G + A G AGA ++E + G GER GN L + + + G+
Sbjct: 244 PHNDRGTAVAAAELGFLAGADRIEGCLFGNGERTGNVDLVTLALNLYTQ------GVSPN 297
Query: 345 INTRHIVMASKMVEEYTGLHVQPHKAIVGANAFAHESGIHQDGMLKH------------- 391
++ ++ + VE + V G + SG HQD + K
Sbjct: 298 LDFSNLDEIRRTVEYCNKIPVHERHPYGGDLVYTAFSGSHQDAINKGLDAMKLDAAAADM 357
Query: 392 --KGTYEIISPEDIGLERSSEAGIVLGKLSGR------------------------HALK 425
+ Y + P D+G R+ EA I + SG+ ++
Sbjct: 358 LWQVPYLPLDPRDVG--RTYEAVIRVNSQSGKGGVAYIMKTDHGLDLPRRLQIEFSSVVQ 415
Query: 426 DRLKELGYELNDEQLGTIFWH-FKAVAEQKKRVTDADLIALVSDEIFQPEVVWKLLDMQV 484
D G EL+ +++ +F + A E +R++ D+ +
Sbjct: 416 DIADGEGGELSPKEISDLFAEEYLAPVEPLERISQHVYA--ADDDGTGTTSI-------- 465
Query: 485 TCGTLGLSTATVKLMDANGEEHVACSTGTGPVDSAYKAVDLIVKEPATLLEYSMNAVTAG 544
TATVK+ NG E +G GP+ + A+ + +L+Y +A+ +G
Sbjct: 466 --------TATVKI---NGVETDIEGSGNGPLSALVDALADVGNFDFAVLDYYEHAMGSG 514
Query: 545 IDAIATTRVLIRGEKSQLSTHASTGETVQRTFSGTGAGMDIVVSSVKAYIGALNK 599
DA A + V + T G G D+ +S++A + A+N+
Sbjct: 515 DDAQAASYVEA--------SVTIASPAQPGTVWGVGIAPDVTTASLRAVVSAVNR 561
>gnl|CDD|163685 cd07948, DRE_TIM_HCS, Saccharomyces cerevisiae homocitrate synthase
and related proteins, catalytic TIM barrel domain.
Homocitrate synthase (HCS) catalyzes the condensation of
acetyl-CoA and alpha-ketoglutarate to form homocitrate,
the first step in the lysine biosynthesis pathway. This
family includes the Yarrowia lipolytica LYS1 protein as
well as the Saccharomyces cerevisiae LYS20 and LYS21
proteins. This family belongs to the DRE-TIM
metallolyase superfamily. DRE-TIM metallolyases include
2-isopropylmalate synthase (IPMS), alpha-isopropylmalate
synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase,
homocitrate synthase, citramalate synthase,
4-hydroxy-2-oxovalerate aldolase, re-citrate synthase,
transcarboxylase 5S, pyruvate carboxylase, AksA, and
FrbC. These members all share a conserved
triose-phosphate isomerase (TIM) barrel domain
consisting of a core beta(8)-alpha(8) motif with the
eight parallel beta strands forming an enclosed barrel
surrounded by eight alpha helices. The domain has a
catalytic center containing a divalent cation-binding
site formed by a cluster of invariant residues that cap
the core of the barrel. In addition, the catalytic site
includes three invariant residues - an aspartate (D), an
arginine (R), and a glutamate (E) - which is the basis
for the domain name "DRE-TIM".
Length = 262
Score = 139 bits (352), Expect = 2e-37
Identities = 80/248 (32%), Positives = 118/248 (47%), Gaps = 18/248 (7%)
Query: 77 VRVFDTTLRDGEQSPGATLTSKEKLDIARQLAKLGVDIIEAGFPAASKEDFEAVRTIAKE 136
++ D+TLR+GEQ A +++K++IA+ L GVD IE PAAS + IAK
Sbjct: 1 FKIIDSTLREGEQFANAFFDTEDKIEIAKALDAFGVDYIELTSPAASPQSRADCEAIAK- 59
Query: 137 VGNAVDAESGYVPVICGLSRCNERDIKTAWEAVKYAKRPRIHTFIATSGIHMEHKLRKTK 196
G I RC+ D + A E + TS E K+
Sbjct: 60 --------LGLKAKILTHIRCHMDDARIAVETGVDG----VDLVFGTSPFLREASHGKSI 107
Query: 197 QQVVEIARSMVKFARSLGCDDVEFSPEDAGRSDRKFLYEILGEVIKVGATTLNIPDTVGI 256
+++E A +++F +S G +V FS ED+ RSD L + V K+G + I DTVGI
Sbjct: 108 TEIIESAVEVIEFVKSKGI-EVRFSSEDSFRSDLVDLLRVYRAVDKLGVNRVGIADTVGI 166
Query: 257 TMPTEFGKLIADIKANTPGIENVVISTHCQNDLGLSTANTIAGACAGARQVEVTINGIGE 316
P + +L+ ++ G+ + I H ND G + AN A AGA ++ T+ GIGE
Sbjct: 167 ATPRQVYELVRTLR----GVVSCDIEFHGHNDTGCAIANAYAALEAGATHIDTTVLGIGE 222
Query: 317 RAGNASLE 324
R G L
Sbjct: 223 RNGITPLG 230
>gnl|CDD|163680 cd07942, DRE_TIM_LeuA, Mycobacterium tuberculosis LeuA3 and related
proteins, N-terminal catalytic TIM barrel domain.
Alpha-isopropylmalate synthase (LeuA), a key enzyme in
leucine biosynthesis, catalyzes the first committed step
in the pathway, converting acetyl-CoA and
alpha-ketoisovalerate to alpha-isopropyl malate and CoA.
Although the reaction catalyzed by LeuA is similar to
that of the Arabidopsis thaliana IPMS1 protein, the two
fall into phylogenetically distinct families within the
same superfamily. LeuA has and N-terminal TIM barrel
catalytic domain, a helical linker domain, and a
C-terminal regulatory domain. LeuA forms a homodimer in
which the linker domain of one monomer sits over the
catalytic domain of the other, inserting residues into
the active site that may be important for catalysis.
Homologs of LeuA are found in bacteria as well as fungi.
This family includes alpha-isopropylmalate synthases I
(LEU4) and II (LEU9) from Saccharomyces cerevisiae.
This family belongs to the DRE-TIM metallolyase
superfamily. DRE-TIM metallolyases include
2-isopropylmalate synthase (IPMS), alpha-isopropylmalate
synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase,
homocitrate synthase, citramalate synthase,
4-hydroxy-2-oxovalerate aldolase, re-citrate synthase,
transcarboxylase 5S, pyruvate carboxylase, AksA, and
FrbC. These members all share a conserved
triose-phosphate isomerase (TIM) barrel domain
consisting of a core beta(8)-alpha(8) motif with the
eight parallel beta strands forming an enclosed barrel
surrounded by eight alpha helices. The domain has a
catalytic center containing a divalent cation-binding
site formed by a cluster of invariant residues that cap
the core of the barrel. In addition, the catalytic site
includes three invariant residues - an aspartate (D), an
arginine (R), and a glutamate (E) - which is the basis
for the domain name "DRE-TIM".
Length = 284
Score = 133 bits (336), Expect = 8e-35
Identities = 83/268 (30%), Positives = 125/268 (46%), Gaps = 24/268 (8%)
Query: 82 TTLRDGEQSPGATLTSKEKLDIARQLAKLGVDIIEAGFPAASKEDFEAVRTIAKEVGNAV 141
LRDG Q+ ++ ++KL + L K+G IE GFP+AS+ DF+ VR +
Sbjct: 7 VDLRDGNQALAEPMSVEQKLRFFKLLVKIGFKEIEVGFPSASQTDFDFVREL-------- 58
Query: 142 DAESGYVP---VICGLSRCNERDIKTAWEAVKYAKRPRIHTFIATSGIHMEHKLRKTKQQ 198
E +P I L++ E I+ +EA++ AK+ +H + ATS + K+K++
Sbjct: 59 -IEEDLIPDDVTIQVLTQAREDLIERTFEALRGAKKAIVHLYNATSPLQRRVVFGKSKEE 117
Query: 199 VVEIARSMVKFARSLGCDDV------EFSPEDAGRSDRKFLYEILGEVIKVGATT----- 247
++EIA K + L E+SPE ++ F E+ VI V T
Sbjct: 118 IIEIAVDGAKLVKELAAKYPETDWRFEYSPESFSDTELDFALEVCEAVIDVWQPTPENKI 177
Query: 248 -LNIPDTVGITMPTEFGKLIADIKANTPGIENVVISTHCQNDLGLSTANTIAGACAGARQ 306
LN+P TV + P + I N E+V+IS H ND G A AGA +
Sbjct: 178 ILNLPATVEVATPNVYADQIEWFCRNLSRRESVIISLHPHNDRGTGVAAAELALLAGADR 237
Query: 307 VEVTINGIGERAGNASLEEVVMAFKCRG 334
VE T+ G GER GN L + + +G
Sbjct: 238 VEGTLFGNGERTGNVDLVTLALNLYSQG 265
>gnl|CDD|214910 smart00917, LeuA_dimer, LeuA allosteric (dimerisation) domain.
This is the C-terminal regulatory (R) domain of
alpha-isopropylmalate synthase, which catalyses the
first committed step in the leucine biosynthetic
pathway. This domain, is an internally duplicated
structure with a novel fold. It comprises two similar
units that are arranged such that the two -helices pack
together in the centre, crossing at an angle of 34
degrees, sandwiched between the two three-stranded,
antiparallel beta-sheets. The overall domain is thus
constructed as a beta-alpha-beta three-layer sandwich.
Length = 131
Score = 127 bits (321), Expect = 1e-34
Identities = 55/145 (37%), Positives = 79/145 (54%), Gaps = 16/145 (11%)
Query: 457 VTDADLIALVSDEIFQPEV-VWKLLDMQVTCGTLGLSTATVKLMDANGEEHVACSTGTGP 515
VTD DL AL DE + E ++L ++V+ G+ G+ TATVKL +GEE +TG GP
Sbjct: 2 VTDEDLEALFEDEYGEAEPERFELESLRVSSGSGGVPTATVKL-KVDGEEVTEAATGNGP 60
Query: 516 VDSAYKAVDLIVKEPATLLEYSMNAVTAGIDAIATTRVLIRGEKSQLSTHASTGETVQRT 575
VD+ + A+ I+ LL+YS++A+T G DA+A V + G R
Sbjct: 61 VDALFNALRKILGSDVELLDYSVHALTGGTDALAEVYVELE----------YGG----RI 106
Query: 576 FSGTGAGMDIVVSSVKAYIGALNKM 600
G G DIV +S KA + ALN++
Sbjct: 107 VWGVGIDTDIVEASAKALVSALNRL 131
>gnl|CDD|163679 cd07941, DRE_TIM_LeuA3, Desulfobacterium autotrophicum LeuA3 and
related proteins, N-terminal catalytic TIM barrel
domain. Desulfobacterium autotrophicum LeuA3 is
sequence-similar to alpha-isopropylmalate synthase
(LeuA) but its exact function is unknown. Members of
this family have an N-terminal TIM barrel domain that
belongs to the DRE-TIM metallolyase superfamily.
DRE-TIM metallolyases include 2-isopropylmalate synthase
(IPMS), alpha-isopropylmalate synthase (LeuA),
3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate
synthase, citramalate synthase, 4-hydroxy-2-oxovalerate
aldolase, re-citrate synthase, transcarboxylase 5S,
pyruvate carboxylase, AksA, and FrbC. These members all
share a conserved triose-phosphate isomerase (TIM)
barrel domain consisting of a core beta(8)-alpha(8)
motif with the eight parallel beta strands forming an
enclosed barrel surrounded by eight alpha helices. The
domain has a catalytic center containing a divalent
cation-binding site formed by a cluster of invariant
residues that cap the core of the barrel. In addition,
the catalytic site includes three invariant residues -
an aspartate (D), an arginine (R), and a glutamate (E) -
which is the basis for the domain name "DRE-TIM".
Length = 273
Score = 131 bits (333), Expect = 2e-34
Identities = 82/271 (30%), Positives = 130/271 (47%), Gaps = 57/271 (21%)
Query: 79 VFDTTLRDGEQSPGATLTSKEKLDIARQLAKLGVDIIEAGFPAASKED---FEAVRTI-- 133
++DTTLRDG Q G + + ++KL IAR+L +LGVD IE G+P ++ +D F + +
Sbjct: 1 IYDTTLRDGTQGEGISFSVEDKLRIARKLDELGVDYIEGGWPGSNPKDTEFFARAKKLKL 60
Query: 134 --AKEV--------GNAVD--------AESGYVPVICGLSRCNERDIKTAWEAVKYAKRP 175
AK G + E+G PV+ I + K
Sbjct: 61 KHAKLAAFGSTRRAGVKAEEDPNLQALLEAG-TPVVT---------I--------FGK-- 100
Query: 176 RIHTFIATSGIHMEHKLRKTKQQVVEIARSMVKFARSLGCDDVEFSPE---DAGRSDRKF 232
+ +H+ L T ++ + + R V + +S G +V F E D +++ ++
Sbjct: 101 -------SWDLHVTEALGTTLEENLAMIRDSVAYLKSHG-REVIFDAEHFFDGYKANPEY 152
Query: 233 LYEILGEVIKVGATTLNIPDTVGITMPTEFGKLIADIKANTPGIENVVISTHCQNDLGLS 292
L + GA L + DT G T+P E +++ +++ PG V + H ND GL+
Sbjct: 153 ALATLKAAAEAGADWLVLCDTNGGTLPHEIAEIVKEVRERLPG---VPLGIHAHNDSGLA 209
Query: 293 TANTIAGACAGARQVEVTINGIGERAGNASL 323
AN++A AGA QV+ TING GER GNA+L
Sbjct: 210 VANSLAAVEAGATQVQGTINGYGERCGNANL 240
>gnl|CDD|235154 PRK03739, PRK03739, 2-isopropylmalate synthase; Validated.
Length = 552
Score = 132 bits (334), Expect = 1e-32
Identities = 159/567 (28%), Positives = 239/567 (42%), Gaps = 98/567 (17%)
Query: 82 TTLRDGEQS---PGATLTSKEKLDIARQLAKLGVDIIEAGFPAASKEDFEAVRTIAKEVG 138
LRDG Q+ P ++ + KL + L K+G IE GFP+AS+ DF+ VR +
Sbjct: 36 VDLRDGNQALIEP---MSPERKLRMFDLLVKIGFKEIEVGFPSASQTDFDFVREL----- 87
Query: 139 NAVDAESGYVP---VICGLSRCNERDIKTAWEAVKYAKRPRIHTFIATSGIHMEHKLRKT 195
E G +P I L++ E I+ +EA++ AKR +H + +TS + K
Sbjct: 88 ----IEEGLIPDDVTIQVLTQAREHLIERTFEALEGAKRAIVHLYNSTSPLQRRVVFGKD 143
Query: 196 KQQVVEIA----RSMVKFARSLGCDDV--EFSPEDAGRSDRKFLYEILGEVIKV-GATT- 247
+ + IA R + + A + E+SPE ++ F E+ VI V T
Sbjct: 144 RDGIKAIAVDGARLVKELAAKYPETEWRFEYSPESFTGTELDFALEVCDAVIDVWQPTPE 203
Query: 248 ----LNIPDTVGITMPTEFGKLIAD----IKANTPGIENVVISTHCQNDLGLSTANTIAG 299
LN+P TV ++ P + AD + N ++V++S H ND G A
Sbjct: 204 RKVILNLPATVEMSTPNVY----ADQIEWMCRNLARRDSVILSLHPHNDRGTGVAAAELA 259
Query: 300 ACAGARQVEVTINGIGERAGNASLEEVVMAFKCRGEHILGGLYT-GI-------NTRHIV 351
AGA +VE + G GER GN L V +A LYT G+ + I
Sbjct: 260 LMAGADRVEGCLFGNGERTGNVDL--VTLALN---------LYTQGVDPGLDFSDIDEIR 308
Query: 352 MASKMVEEYTGLHVQPHKAIVGANAFAHESGIHQD----GMLKHKGTYEI-------ISP 400
+ VE L V P G F SG HQD G K + I P
Sbjct: 309 ---RTVEYCNQLPVHPRHPYAGDLVFTAFSGSHQDAIKKGFAAQKADAIVWEVPYLPIDP 365
Query: 401 EDIGLERSSEAGIVLGKLSGR----HALKDRLKELGYELNDEQLGTIF-WHFKAVAEQKK 455
D+G RS EA I + SG+ + L+ ++ G +L +L F +AV + +
Sbjct: 366 ADVG--RSYEAVIRVNSQSGKGGVAYLLE---QDYGLDL-PRRLQIEFSRVVQAVTDAEG 419
Query: 456 R-VTDADLIALVSDEIFQPEVVWKLLDMQVTCGTLGLSTATVKLMDANGEEHVACSTGTG 514
++ ++ L E P LL + G T T ++ D NGEE G G
Sbjct: 420 GELSAEEIWDLFEREYLAPRGRPVLLRVHRLSEEDGTRTITAEV-DVNGEERTIEGEGNG 478
Query: 515 PVDSAYKAVDLIVKEPATLLEYSMNAVTAGIDAIATTRVLIRGEKSQLSTHASTGETVQR 574
P+D+ A+ + +L+Y +A+ AG DA A V +R R
Sbjct: 479 PIDAFVNALSQALGVDVRVLDYEEHALGAGSDAQAAAYVELRVG--------------GR 524
Query: 575 TFSGTGAGMDIVVSSVKAYIGALNKML 601
T G G +IV +S+KA + A+N+ L
Sbjct: 525 TVFGVGIDANIVTASLKAVVSAVNRAL 551
>gnl|CDD|163684 cd07947, DRE_TIM_Re_CS, Clostridium kluyveri Re-citrate synthase
and related proteins, catalytic TIM barrel domain.
Re-citrate synthase (Re-CS) is a Clostridium kluyveri
enzyme that converts acetyl-CoA and oxaloacetate to
citrate. In most organisms, this reaction is catalyzed
by Si-citrate synthase which is Si-face stereospecific
with respect to C-2 of oxaloacetate, and
phylogenetically unrelated to Re-citrate synthase.
Re-citrate synthase is also found in a few other
strictly anaerobic organisms. This family belongs to
the DRE-TIM metallolyase superfamily. DRE-TIM
metallolyases include 2-isopropylmalate synthase (IPMS),
alpha-isopropylmalate synthase (LeuA),
3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate
synthase, citramalate synthase, 4-hydroxy-2-oxovalerate
aldolase, re-citrate synthase, transcarboxylase 5S,
pyruvate carboxylase, AksA, and FrbC. These members all
share a conserved triose-phosphate isomerase (TIM)
barrel domain consisting of a core beta(8)-alpha(8)
motif with the eight parallel beta strands forming an
enclosed barrel surrounded by eight alpha helices. The
domain has a catalytic center containing a divalent
cation-binding site formed by a cluster of invariant
residues that cap the core of the barrel. In addition,
the catalytic site includes three invariant residues -
an aspartate (D), an arginine (R), and a glutamate (E) -
which is the basis for the domain name "DRE-TIM".
Length = 279
Score = 84.7 bits (210), Expect = 4e-18
Identities = 71/271 (26%), Positives = 118/271 (43%), Gaps = 41/271 (15%)
Query: 81 DTTLRDGEQSPGATLTSKEKLDIARQLAKLG--VDIIEAG-FPAASKEDFEAVRTIAKEV 137
DTT RDG+Q+ T ++ + I L +LG +I F +++D EAV
Sbjct: 5 DTTFRDGQQARPP-YTVEQIVKIYDYLHELGGGSGVIRQTEFFLYTEKDREAVEACL--- 60
Query: 138 GNAVDAESGY-VPVICGLSRCNERDIKTAWEAVKYAKRPRIHTFIATSGIHMEHKLRKTK 196
+ GY P + G R N+ D+K VK ++ S H+ KL+ T+
Sbjct: 61 ------DRGYKFPEVTGWIRANKEDLKL----VKEMGLKETGILMSVSDYHIFKKLKMTR 110
Query: 197 QQVVEIARSMVKFARSLG----CDDVEFSPEDAGRSD-RKFLYEILGEVIKV-----GAT 246
++ +E +V+ A G C ED R+D F+ + +++K+
Sbjct: 111 EEAMEKYLEIVEEALDHGIKPRC-----HLEDITRADIYGFVLPFVNKLMKLSKESGIPV 165
Query: 247 TLNIPDTVGITMPTEFG-------KLIADIKANTPGIENVVISTHCQNDLGLSTANTIAG 299
+ + DT+G +P K+I ++ G+ + + H ND + AN +A
Sbjct: 166 KIRLCDTLGYGVPYPGASLPRSVPKIIYGLR-KDCGVPSENLEWHGHNDFYKAVANAVAA 224
Query: 300 ACAGARQVEVTINGIGERAGNASLEEVVMAF 330
GA V T+ GIGER GN LE +V+ +
Sbjct: 225 WLYGASWVNCTLLGIGERTGNCPLEAMVIEY 255
>gnl|CDD|184849 PRK14847, PRK14847, hypothetical protein; Provisional.
Length = 333
Score = 85.8 bits (212), Expect = 4e-18
Identities = 76/314 (24%), Positives = 133/314 (42%), Gaps = 29/314 (9%)
Query: 68 PNRIPDPNYVRVFDTTLRDGEQSPGATLTSKEKLDIARQLAKLGVDIIEAGFPAASKEDF 127
P R P + + T LRDG Q+ + KL + QL +G+ IE FP+AS+ DF
Sbjct: 25 PARRPAAAPIWM-STDLRDGNQALIEPMDGARKLRLFEQLVAVGLKEIEVAFPSASQTDF 83
Query: 128 EAVRTIAKE--VGNAVDAESGYVPVICGLSRCNERDIKTAWEAVKYAKRPRIHTFIATSG 185
+ VR + E + + V E+ SR + I +EA+ + R +H + +
Sbjct: 84 DFVRKLIDERRIPDDVTIEA-LTQ-----SRPDL--IARTFEALAGSPRAIVHLYNPIAP 135
Query: 186 IHMEHKLRKTKQQVVEIARSMVKFARSLGCDD------VEFSPEDAGRSDRKFLYEILGE 239
++ ++ EIA + + R+L + E+SPE ++ F E+
Sbjct: 136 QWRRIVFGMSRAEIKEIALAGTRQIRALADANPGTQWIYEYSPETFSLAELDFAREVCDA 195
Query: 240 VIKVGATT------LNIPDTVGITMPTEFGKLIADIKANTPGIENVVISTHCQNDLGLST 293
V + T +N+P TV + + I + + + +V+S H ND G +
Sbjct: 196 VSAIWGPTPQRKMIINLPATVESSTANVYADQIEWMHRSLARRDCIVLSVHPHNDRGTAV 255
Query: 294 ANTIAGACAGARQVEVTINGIGERAGNASLEEVVMAFKCRGEHILGGLYTGINTRHIVMA 353
A AGA ++E + G GER GN L + + + + G+ +G++ R +
Sbjct: 256 AAAELAVLAGAERIEGCLFGNGERTGNVDLVALALNLERQ------GIASGLDFRDMAAL 309
Query: 354 SKMVEEYTGLHVQP 367
V E L +
Sbjct: 310 RACVSECNQLPIDV 323
>gnl|CDD|163681 cd07943, DRE_TIM_HOA, 4-hydroxy-2-oxovalerate aldolase, N-terminal
catalytic TIM barrel domain. 4-hydroxy 2-ketovalerate
aldolase (Also known as 4-hydroxy-2-ketovalerate
aldolase and 4-hydroxy-2-oxopentanoate aldolase (HOA))
converts 4-hydroxy-2-oxopentanoate to acetaldehyde and
pyruvate, the penultimate step in the meta-cleavage
pathway for the degradation of phenols, cresols and
catechol. This family includes the Escherichia coli
MhpE aldolase, the Pseudomonas DmpG aldolase, and the
Burkholderia xenovorans BphI pyruvate aldolase. In
Pseudomonas, the DmpG aldolase tightly associates with a
dehydrogenase (DmpF ) and is inactive without it. HOA
has a canonical TIM-barrel fold with a C-terminal
extension that forms a funnel leading to the active
site. This family belongs to the DRE-TIM metallolyase
superfamily. DRE-TIM metallolyases include
2-isopropylmalate synthase (IPMS), alpha-isopropylmalate
synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase,
homocitrate synthase, citramalate synthase,
4-hydroxy-2-oxovalerate aldolase, re-citrate synthase,
transcarboxylase 5S, pyruvate carboxylase, AksA, and
FrbC. These members all share a conserved
triose-phosphate isomerase (TIM) barrel domain
consisting of a core beta(8)-alpha(8) motif with the
eight parallel beta strands forming an enclosed barrel
surrounded by eight alpha helices. The domain has a
catalytic center containing a divalent cation-binding
site formed by a cluster of invariant residues that cap
the core of the barrel. In addition, the catalytic site
includes three invariant residues - an aspartate (D), an
arginine (R), and a glutamate (E) - which is the basis
for the domain name "DRE-TIM".
Length = 263
Score = 77.5 bits (192), Expect = 9e-16
Identities = 68/282 (24%), Positives = 107/282 (37%), Gaps = 71/282 (25%)
Query: 77 VRVFDTTLRDGEQSPGATLTSKEKLDIARQLAKLGVDIIE-------------AGFPAAS 123
V + D TLRDG + T ++ IAR L GV +IE GF A +
Sbjct: 1 VYIHDVTLRDGMHAVRHQFTLEQVRAIARALDAAGVPLIEVGHGDGLGGSSLNYGFAAHT 60
Query: 124 KEDFEAVRTIAKEVGNAVDAESGYVPVICGLSRCNERDIKTAWEA-VKYAKRPRIHTFIA 182
D E + A+ + A + V+ D+K A + V + +A
Sbjct: 61 --DEEYLEAAAEALKQAK------LGVLLLPGIGTVDDLKMAADLGVDVVR-------VA 105
Query: 183 TSGIHMEHKLRKTKQQVVE--IARSMVKFARSLGCDDVEF-------SPEDAGRSDRKFL 233
T E ++ + AR LG D V F SPE+ +
Sbjct: 106 T--------------HCTEADVSEQHIGAARKLGMDVVGFLMMSHMASPEELAEQAKLM- 150
Query: 234 YEILGEVIKVGATTLNIPDTVGITMPTEFGKLIADIKANTPGIENVVIST----HCQNDL 289
GA + + D+ G M L D++ + + T H N+L
Sbjct: 151 -------ESYGADCVYVTDSAG-AM------LPDDVRERVRALREALDPTPVGFHGHNNL 196
Query: 290 GLSTANTIAGACAGARQVEVTINGIGERAGNASLEEVVMAFK 331
GL+ AN++A AGA +++ ++ G+G AGN LE +V +
Sbjct: 197 GLAVANSLAAVEAGATRIDGSLAGLGAGAGNTPLEVLVAVLE 238
>gnl|CDD|132261 TIGR03217, 4OH_2_O_val_ald, 4-hydroxy-2-oxovalerate aldolase.
Members of this protein family are
4-hydroxy-2-oxovalerate aldolase, also called
4-hydroxy-2-ketovalerate aldolase and
2-oxo-4-hydroxypentanoate aldolase. This enzyme, part of
the pathway for the meta-cleavage of catechol, produces
pyruvate and acetaldehyde. Acetaldehyde is then
converted by acetaldehyde dehydrogenase (acylating)
(DmpF; EC 1.2.1.10) to acetyl-CoA. The two enzymes are
tightly associated [Energy metabolism, Other].
Length = 333
Score = 73.5 bits (181), Expect = 4e-14
Identities = 75/283 (26%), Positives = 111/283 (39%), Gaps = 72/283 (25%)
Query: 77 VRVFDTTLRDGEQSPGATLTSKEKLDIARQLAKLGVDIIEA-------------GFPAAS 123
+ + D TLRDG + T ++ IA L + GVD IE GF A +
Sbjct: 3 LYITDVTLRDGMHAIRHQFTIEQVRAIAAALDEAGVDAIEVTHGDGLGGSSFNYGFSAHT 62
Query: 124 KEDFEAVRTIAKEVGNAVDAESGYVPVICGLSRCNERDIKTAWEAVKYAKRPRIHTFIAT 183
D E + A V A A +P I + D+K A++A A+ R+ T
Sbjct: 63 --DLEYIEAAADVVKRAKVA-VLLLPGIGTV-----HDLKAAYDA--GARTVRVATHCTE 112
Query: 184 SGIHMEHKLRKTKQQVVEIARSMVKFARSLGCDDVEF-------SPEDAGRSDRKFLYEI 236
+ + +H + AR LG D V F PE
Sbjct: 113 ADVSEQH----------------IGMARELGMDTVGFLMMSHMTPPE------------K 144
Query: 237 LGEVIKV----GATTLNIPDTVGITMPTE----FGKLIADIKANTPGIENVVISTHCQND 288
L E K+ GA + I D+ G +P + L A +K T + H ++
Sbjct: 145 LAEQAKLMESYGADCVYIVDSAGAMLPDDVRDRVRALKAVLKPETQ------VGFHAHHN 198
Query: 289 LGLSTANTIAGACAGARQVEVTINGIGERAGNASLEEVVMAFK 331
L L+ AN+IA AGA +++ ++ G+G AGNA LE V
Sbjct: 199 LSLAVANSIAAIEAGATRIDASLRGLGAGAGNAPLEVFVAVLD 241
>gnl|CDD|181282 PRK08195, PRK08195, 4-hyroxy-2-oxovalerate/4-hydroxy-2-oxopentanoic
acid aldolase,; Validated.
Length = 337
Score = 66.0 bits (162), Expect = 1e-11
Identities = 70/282 (24%), Positives = 110/282 (39%), Gaps = 64/282 (22%)
Query: 77 VRVFDTTLRDGEQSPGATLTSKEKLDIARQLAKLGVDIIEA-------------GFPAAS 123
+ + D TLRDG + T ++ IAR L GV +IE GF A +
Sbjct: 4 IYISDVTLRDGMHAVRHQYTLEQVRAIARALDAAGVPVIEVTHGDGLGGSSFNYGFGAHT 63
Query: 124 KEDFEAVRTIAKEVGNAVDAESGYVPVICGLSRCNERDIKTAWEAVKYAKRPRIHTFIAT 183
D E + A+ V A A ++ G+ D+K A++A + R+ T
Sbjct: 64 --DEEYIEAAAEVVKQAKIA----ALLLPGIGTV--DDLKMAYDA--GVRVVRVATHCTE 113
Query: 184 SGIHMEHKLRKTKQQVVEIARSMVKFARSLGCDDVEF-------SPEDAGRSDRKFLYEI 236
+ + +H + AR LG D V F PE +
Sbjct: 114 ADVSEQH----------------IGLARELGMDTVGFLMMSHMAPPEKLAEQAKLM---- 153
Query: 237 LGEVIKVGATTLNIPDTVGITMPTE----FGKLIADIKANTPGIENVVISTHCQNDLGLS 292
GA + + D+ G +P + L A +K +T + H N+LGL
Sbjct: 154 ----ESYGAQCVYVVDSAGALLPEDVRDRVRALRAALKPDTQ------VGFHGHNNLGLG 203
Query: 293 TANTIAGACAGARQVEVTINGIGERAGNASLEEVVMAFKCRG 334
AN++A AGA +++ ++ G+G AGN LE +V G
Sbjct: 204 VANSLAAVEAGATRIDGSLAGLGAGAGNTPLEVLVAVLDRMG 245
>gnl|CDD|163682 cd07944, DRE_TIM_HOA_like, 4-hydroxy-2-oxovalerate aldolase-like,
N-terminal catalytic TIM barrel domain. This family of
bacterial enzymes is sequence-similar to
4-hydroxy-2-oxovalerate aldolase (HOA) but its exact
function is unknown. This family includes the
Bacteroides vulgatus Bvu_2661 protein and belongs to the
DRE-TIM metallolyase superfamily. DRE-TIM metallolyases
include 2-isopropylmalate synthase (IPMS),
alpha-isopropylmalate synthase (LeuA),
3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate
synthase, citramalate synthase, 4-hydroxy-2-oxovalerate
aldolase, re-citrate synthase, transcarboxylase 5S,
pyruvate carboxylase, AksA, and FrbC. These members all
share a conserved triose-phosphate isomerase (TIM)
barrel domain consisting of a core beta(8)-alpha(8)
motif with the eight parallel beta strands forming an
enclosed barrel surrounded by eight alpha helices. The
domain has a catalytic center containing a divalent
cation-binding site formed by a cluster of invariant
residues that cap the core of the barrel. In addition,
the catalytic site includes three invariant residues -
an aspartate (D), an arginine (R), and a glutamate (E) -
which is the basis for the domain name "DRE-TIM".
Length = 266
Score = 61.4 bits (150), Expect = 2e-10
Identities = 55/264 (20%), Positives = 105/264 (39%), Gaps = 45/264 (17%)
Query: 79 VFDTTLRDGE-----QSPGATLTSKEKLDIARQLAKLGVDIIEAGFPAASKEDFEAVRTI 133
+ D TLRDG + I R LA G+D +E G+ +S E ++
Sbjct: 1 ILDCTLRDGGYVNNWDFGDEFVK-----AIYRALAAAGIDYVEIGY-RSSPEKEFKGKSA 54
Query: 134 ------AKEVGNAVDAESGYVPVICGLSRCNERDIKTAWEAVKYAKRPRIHTFIATSGIH 187
+ + + ++ + ++ A + S +
Sbjct: 55 FCDDEFLRRLLGDSKGNTKIAVMVDY-GNDDIDLLEPA----------------SGSVVD 97
Query: 188 MEHKLRKT--KQQVVEIARSMVKFARSLGCDDVEFSP-EDAGRSDRKFLYEILGEVIKVG 244
M +R K + E A ++K + G + V F+ +G SD + L E+L V ++
Sbjct: 98 M---IRVAFHKHEFDE-ALPLIKAIKEKGYE-VFFNLMAISGYSDEELL-ELLELVNEIK 151
Query: 245 ATTLNIPDTVGITMPTEFGKLIADIKANTPGIENVVISTHCQNDLGLSTANTIAGACAGA 304
I D+ G P + ++I+ +++N ++ + H N+L L+ ANT+ G
Sbjct: 152 PDVFYIVDSFGSMYPEDIKRIISLLRSNLDK--DIKLGFHAHNNLQLALANTLEAIELGV 209
Query: 305 RQVEVTINGIGERAGNASLEEVVM 328
++ T+ G+G AGN E ++
Sbjct: 210 EIIDATVYGMGRGAGNLPTELLLD 233
>gnl|CDD|163676 cd07938, DRE_TIM_HMGL, 3-hydroxy-3-methylglutaryl-CoA lyase,
catalytic TIM barrel domain.
3-hydroxy-3-methylglutaryl-CoA lyase (HMGL) catalyzes
the cleavage of HMG-CoA to acetyl-CoA and acetoacetate,
one of the terminal steps in ketone body generation and
leucine degradation, and is a key enzyme in the pathway
that supplies metabolic fuel to extrahepatic tissues.
Mutations in HMGL cause a human autosomal recessive
disorder called primary metabolic aciduria that affects
ketogenesis and leucine catabolism and can be fatal due
to an inability to tolerate hypoglycemia. HMGL has a
TIM barrel domain with a catalytic center containing a
divalent cation-binding site formed by a cluster of
invariant residues that cap the core of the barrel. The
cleavage of HMG-CoA requires the presence of a divalent
cation like Mg2+ or Mn2+, and the reaction is thought to
involve general acid/base catalysis. This family
belongs to the DRE-TIM metallolyase superfamily.
DRE-TIM metallolyases include 2-isopropylmalate synthase
(IPMS), alpha-isopropylmalate synthase (LeuA),
3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate
synthase, citramalate synthase, 4-hydroxy-2-oxovalerate
aldolase, re-citrate synthase, transcarboxylase 5S,
pyruvate carboxylase, AksA, and FrbC. These members all
share a conserved triose-phosphate isomerase (TIM)
barrel domain consisting of a core beta(8)-alpha(8)
motif with the eight parallel beta strands forming an
enclosed barrel surrounded by eight alpha helices. The
domain has a catalytic center containing a divalent
cation-binding site formed by a cluster of invariant
residues that cap the core of the barrel. In addition,
the catalytic site includes three invariant residues -
an aspartate (D), an arginine (R), and a glutamate (E) -
which is the basis for the domain name "DRE-TIM".
Length = 274
Score = 55.5 bits (135), Expect = 2e-08
Identities = 60/310 (19%), Positives = 121/310 (39%), Gaps = 77/310 (24%)
Query: 85 RDGEQSPGATLTSKEKLDIARQLAKLGVDIIEAG-F--PAASKEDFEAVRTI-----AKE 136
RDG Q+ + +++K+++ L+ G+ IE F P + A+E
Sbjct: 7 RDGLQNEKTFIPTEDKIELIDALSAAGLRRIEVTSFVSPKW----------VPQMADAEE 56
Query: 137 VGNAVDAESG--Y---VPVICGLSRCNERDIKTAWEA-VKYAKRPRIHTFIATSGIHMEH 190
V + G Y VP N R + A A V + F++ S +
Sbjct: 57 VLAGLPRRPGVRYSALVP--------NLRGAERALAAGVDE-----VAVFVSASETFSQK 103
Query: 191 KLRKTKQQVVEIARSMVKFAR------------SLGC---DDVEFSPEDAGRSDRKFLYE 235
+ + + +E + + A+ + GC +V PE E
Sbjct: 104 NINCSIAESLERFEPVAELAKAAGLRVRGYVSTAFGCPYEGEV--PPERV--------AE 153
Query: 236 ILGEVIKVGATTLNIPDTVGITMPTEFGKLIADIKANTPGIENVVISTHCQNDLGLSTAN 295
+ ++ +G +++ DT+G+ P + +L+ + P + ++ H + G + AN
Sbjct: 154 VAERLLDLGCDEISLGDTIGVATPAQVRRLLEAVLERFPDEK---LALHFHDTRGQALAN 210
Query: 296 TIAGACAGARQVEVTINGIG------ERAGNASLEEVVMAFKCRGEHILGGLYTGINTRH 349
+A AG R+ + ++ G+G GN + E++V + G TGI+
Sbjct: 211 ILAALEAGVRRFDSSVGGLGGCPFAPGATGNVATEDLVYMLEGMGIE------TGIDLDK 264
Query: 350 IVMASKMVEE 359
++ A++ + E
Sbjct: 265 LLAAARWISE 274
>gnl|CDD|227349 COG5016, COG5016, Pyruvate/oxaloacetate carboxyltransferase [Energy
production and conversion].
Length = 472
Score = 45.8 bits (109), Expect = 4e-05
Identities = 67/293 (22%), Positives = 111/293 (37%), Gaps = 84/293 (28%)
Query: 77 VRVFDTTLRDGEQSPGAT-LTSKEKLDIARQLAKLGVDIIE----AGFPAAS---KED-F 127
+++ DT LRDG QS AT + +++ L IA L K+G +E A F A ED +
Sbjct: 6 IKITDTVLRDGHQSLLATRMRTEDMLPIAEALDKVGYWSLEVWGGATFDACIRFLNEDPW 65
Query: 128 EAVRTIAKEVGNA---------------------VD------AESGYVPVICGLSRCNE- 159
E +R + K V N V+ AE+G + V N+
Sbjct: 66 ERLRELKKAVPNTKLQMLLRGQNLVGYRHYADDVVEKFVEKAAENG-IDVFRIFDALNDV 124
Query: 160 RDIKTAWEAVK-YAKRPRIHTFIATSGIHMEHKLRKTKQQVVEIARSMVKFARSLGCDDV 218
R++KTA +A K + + TS +H T + VE+A+ +++ +G D +
Sbjct: 125 RNLKTAIKAAKKHGAHVQGTISYTTSPVH-------TLEYYVELAKELLE----MGVDSI 173
Query: 219 EFSPEDAGRSDRKFLYEILGEVIKVGATTLNIPDTVGITMPTEFGKLIADIKANTPGIEN 278
IK D G+ P E +L+ IK P
Sbjct: 174 ---------------------CIK---------DMAGLLTPYEAYELVKAIKKELP---- 199
Query: 279 VVISTHCQNDLGLSTANTIAGACAGARQVEVTINGIGERAGNASLEEVVMAFK 331
V + H G++ + AG ++ I+ + + E +V A +
Sbjct: 200 VPVELHTHATSGMAEMTYLKAVEAGVDGIDTAISPLSGGTSQPATETMVAALR 252
>gnl|CDD|163675 cd07937, DRE_TIM_PC_TC_5S, Pyruvate carboxylase and
Transcarboxylase 5S, carboxyltransferase domain. This
family includes the carboxyltransferase domains of
pyruvate carboxylase (PC) and the transcarboxylase (TC)
5S subunit. Transcarboxylase 5S is a cobalt-dependent
metalloenzyme subunit of the biotin-dependent
transcarboxylase multienzyme complex. Transcarboxylase
5S transfers carbon dioxide from the 1.3S biotin to
pyruvate in the second of two carboxylation reactions
catalyzed by TC. The first reaction involves the
transfer of carbon dioxide from methylmalonyl-CoA to the
1.3S biotin, and is catalyzed by the 12S subunit. These
two steps allow a carboxylate group to be transferred
from oxaloacetate to propionyl-CoA to yield pyruvate and
methylmalonyl-CoA. The catalytic domain of
transcarboxylase 5S has a canonical TIM-barrel fold with
a large C-terminal extension that forms a funnel leading
to the active site. Transcarboxylase 5S forms a
homodimer and there are six dimers per complex. In
addition to the catalytic domain, transcarboxylase 5S
has several other domains including a
carbamoyl-phosphate synthase domain, a biotin
carboxylase domain, a carboxyltransferase domain, and an
ATP-grasp domain. Pyruvate carboxylase, like TC, is a
biotin-dependent enzyme that catalyzes the carboxylation
of pyruvate to produce oxaloacetate. In mammals, PC has
critical roles in gluconeogenesis, lipogenesis,
glyceroneogenesis, and insulin secretion. Inherited PC
deficiencies are linked to serious diseases in humans
such as lactic acidemia, hypoglycemia, psychomotor
retardation, and death. PC is a single-chain enzyme and
is active only in its homotetrameric form. PC has three
domains, an N-terminal biotin carboxylase domain, a
carboxyltransferase domain (this alignment model), and a
C-terminal biotin-carboxyl carrier protein domain. This
family belongs to the DRE-TIM metallolyase superfamily.
DRE-TIM metallolyases include 2-isopropylmalate synthase
(IPMS), alpha-isopropylmalate synthase (LeuA),
3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate
synthase, citramalate synthase, 4-hydroxy-2-oxovalerate
aldolase, re-citrate synthase, transcarboxylase 5S,
pyruvate carboxylase, AksA, and FrbC. These members all
share a conserved triose-phosphate isomerase (TIM)
barrel domain consisting of a core beta(8)-alpha(8)
motif with the eight parallel beta strands forming an
enclosed barrel surrounded by eight alpha helices. The
domain has a catalytic center containing a divalent
cation-binding site formed by a cluster of invariant
residues that cap the core of the barrel. In addition,
the catalytic site includes three invariant residues -
an aspartate (D), an arginine (R), and a glutamate (E) -
which is the basis for the domain name "DRE-TIM".
Length = 275
Score = 42.4 bits (101), Expect = 4e-04
Identities = 66/296 (22%), Positives = 107/296 (36%), Gaps = 98/296 (33%)
Query: 81 DTTLRDGEQSPGAT-LTSKEKLDIARQLAKLGVDIIEAG----FPAA---SKED-FEAVR 131
DTTLRD QS AT + +++ L IA L + G +E F ED +E +R
Sbjct: 3 DTTLRDAHQSLLATRMRTEDMLPIAEALDEAGFFSLEVWGGATFDVCMRFLNEDPWERLR 62
Query: 132 TIAKE---------------VG------NAVD------AESGYVPVICGLSRC----NE- 159
+ K VG + V+ A++G + + R N+
Sbjct: 63 ELRKAMPNTPLQMLLRGQNLVGYRHYPDDVVELFVEKAAKNG-IDIF----RIFDALNDV 117
Query: 160 RDIKTAWEAVKYAKRPRIHTFIA----TSGIHMEHKLRKTKQQVVEIARSMVKFARSLGC 215
R+++ A +AVK A H A S +H T + V++A+ + +G
Sbjct: 118 RNLEVAIKAVKKAG---KHVEGAICYTGSPVH-------TLEYYVKLAKELED----MGA 163
Query: 216 DDVEFSPEDAGRSDRKFLYEILGEVIKVGATTLNIPDTVGITMPTEFGKLIADIKANTPG 275
D + IK D G+ P +L+ +K
Sbjct: 164 D-------------------SIC--IK---------DMAGLLTPYAAYELVKALKKEVG- 192
Query: 276 IENVVISTHCQNDLGLSTANTIAGACAGARQVEVTINGIGERAGNASLEEVVMAFK 331
+ I H + GL+ A +A A AG V+ I+ + S E +V A +
Sbjct: 193 ---LPIHLHTHDTSGLAVATYLAAAEAGVDIVDTAISPLSGGTSQPSTESMVAALR 245
>gnl|CDD|79056 PRK12581, PRK12581, oxaloacetate decarboxylase; Provisional.
Length = 468
Score = 42.8 bits (100), Expect = 4e-04
Identities = 27/106 (25%), Positives = 51/106 (48%), Gaps = 4/106 (3%)
Query: 232 FLYEILGEVIKVGATTLNIPDTVGITMPTEFGKLIADIKANTPGIENVVISTHCQNDLGL 291
+ ++ E++++GA ++ I D GI P +L++ IKA T N+ + H G+
Sbjct: 164 YYLSLVKELVEMGADSICIKDMAGILTPKAAKELVSGIKAMT----NLPLIVHTHATSGI 219
Query: 292 STANTIAGACAGARQVEVTINGIGERAGNASLEEVVMAFKCRGEHI 337
S +A AGA +++ ++ E + E + +A K G I
Sbjct: 220 SQMTYLAAVEAGADRIDTALSPFSEGTSQPATESMYLALKEAGYDI 265
>gnl|CDD|236980 PRK11780, PRK11780, isoprenoid biosynthesis protein with
amidotransferase-like domain; Provisional.
Length = 217
Score = 39.0 bits (92), Expect = 0.004
Identities = 22/74 (29%), Positives = 33/74 (44%), Gaps = 5/74 (6%)
Query: 473 PEVVWKLLDMQVTCGTLGLSTATVKLMDANGEEHVACSTGTGPVDSAYKAVDLIVKEPAT 532
P ++ K+L V T+G T ++ G EHV C VD K +V PA
Sbjct: 138 PAMLPKILGAGVKL-TIGNDEDTAAAIEKMGGEHVDCPVDDIVVDEENK----VVTTPAY 192
Query: 533 LLEYSMNAVTAGID 546
+L S+ +GI+
Sbjct: 193 MLAQSIAEAASGIE 206
>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 = 39.0 bits (91), Expect = 0.007
Identities = 33/133 (24%), Positives = 52/133 (39%), Gaps = 14/133 (10%)
Query: 229 DRKFLYEILGEVIKVGATTLNIPDTVGITMPTEFGKLIADIKANTPGIENVVISTHCQND 288
D K+ + E+ K GA L I D G+ P LI ++ T ++ I H +
Sbjct: 687 DLKYYTNLAVELEKAGAHILGIKDMAGLLKPAAAKLLIKALREKT----DLPIHFHTHDT 742
Query: 289 LGLSTANTIAGACAGARQVEVTINGIGERAGNASLEEVVMAFKCRGEHILGG--LYTGIN 346
G++ A+ +A AG V+V ++ + SL +V L G G+N
Sbjct: 743 SGIAVASMLAAVEAGVDVVDVAVDSMSGLTSQPSLGAIV--------AALEGSERDPGLN 794
Query: 347 TRHIVMASKMVEE 359
I S E
Sbjct: 795 VAWIRELSAYWEA 807
>gnl|CDD|183446 PRK12331, PRK12331, oxaloacetate decarboxylase; Provisional.
Length = 448
Score = 38.5 bits (90), Expect = 0.008
Identities = 26/72 (36%), Positives = 39/72 (54%), Gaps = 9/72 (12%)
Query: 77 VRVFDTTLRDGEQSPGAT-LTSKEKLDIARQLAKLGVDIIE----AGFPAASK---ED-F 127
+++ +T LRDG+QS AT +T++E L I +L G +E A F A + ED +
Sbjct: 4 IKITETVLRDGQQSLIATRMTTEEMLPILEKLDNAGYHSLEMWGGATFDACLRFLNEDPW 63
Query: 128 EAVRTIAKEVGN 139
E +R I K V
Sbjct: 64 ERLRKIRKAVKK 75
>gnl|CDD|237592 PRK14040, PRK14040, oxaloacetate decarboxylase; Provisional.
Length = 593
Score = 36.8 bits (86), Expect = 0.038
Identities = 24/84 (28%), Positives = 39/84 (46%), Gaps = 4/84 (4%)
Query: 244 GATTLNIPDTVGITMPTEFGKLIADIKANTPGIENVVISTHCQNDLGLSTANTIAGACAG 303
G +L I D G+ P +L++ IK +V + HC GLSTA + AG
Sbjct: 168 GVDSLCIKDMAGLLKPYAAYELVSRIKKRV----DVPLHLHCHATTGLSTATLLKAIEAG 223
Query: 304 ARQVEVTINGIGERAGNASLEEVV 327
V+ I+ + G+++ E +V
Sbjct: 224 IDGVDTAISSMSMTYGHSATETLV 247
>gnl|CDD|212492 cd05327, retinol-DH_like_SDR_c_like, retinol dehydrogenase
(retinol-DH), Light dependent Protochlorophyllide
(Pchlide) OxidoReductase (LPOR) and related proteins,
classical (c) SDRs. Classical SDR subgroup containing
retinol-DHs, LPORs, and related proteins. Retinol is
processed by a medium chain alcohol dehydrogenase
followed by retinol-DHs. Pchlide reductases act in
chlorophyll biosynthesis. There are distinct enzymes
that catalyze Pchlide reduction in light or dark
conditions. Light-dependent reduction is via an
NADP-dependent SDR, LPOR. Proteins in this subfamily
share the glycine-rich NAD-binding motif of the
classical SDRs, have a partial match to the canonical
active site tetrad, but lack the typical active site
Ser. This subgroup includes the human proteins: retinol
dehydrogenase -12, -13 ,and -14, dehydrogenase/reductase
SDR family member (DHRS)-12 , -13 and -X (a DHRS on
chromosome X), and WWOX (WW domain-containing
oxidoreductase), as well as a Neurospora crassa SDR
encoded by the blue light inducible bli-4 gene. 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 = 269
Score = 36.0 bits (84), Expect = 0.044
Identities = 31/98 (31%), Positives = 41/98 (41%), Gaps = 13/98 (13%)
Query: 103 IARQLAKLGVDIIEAGFPAASKEDFEAVRTIAKEVGNA-VDAESGYVPVICGLSRCNERD 161
AR+LAK G +I A E EA I KE GNA V+ + LS +
Sbjct: 17 TARELAKRGAHVIIACRNEEKGE--EAAAEIKKETGNAKVEV------IQLDLS--SLAS 66
Query: 162 IKTAWEAVKYAKRPRIHTFIATSGIHMEHKLRKTKQQV 199
++ E A+ PR+ I +GI M R TK
Sbjct: 67 VRQFAEEFL-ARFPRLDILINNAGI-MAPPRRLTKDGF 102
>gnl|CDD|236449 PRK09282, PRK09282, pyruvate carboxylase subunit B; Validated.
Length = 592
Score = 34.4 bits (80), Expect = 0.17
Identities = 17/36 (47%), Positives = 25/36 (69%), Gaps = 1/36 (2%)
Query: 77 VRVFDTTLRDGEQSPGAT-LTSKEKLDIARQLAKLG 111
V++ DTTLRD QS AT + +++ L IA +L K+G
Sbjct: 4 VKITDTTLRDAHQSLLATRMRTEDMLPIAEKLDKVG 39
Score = 29.4 bits (67), Expect = 6.9
Identities = 13/66 (19%), Positives = 27/66 (40%), Gaps = 4/66 (6%)
Query: 239 EVIKVGATTLNIPDTVGITMPTEFGKLIADIKANTPGIENVVISTHCQNDLGLSTANTIA 298
E+ ++G ++ I D G+ P +L+ +K ++ + H GL+ +
Sbjct: 162 ELEEMGCDSICIKDMAGLLTPYAAYELVKALKEEV----DLPVQLHSHCTSGLAPMTYLK 217
Query: 299 GACAGA 304
AG
Sbjct: 218 AVEAGV 223
>gnl|CDD|225697 COG3155, ElbB, Uncharacterized protein involved in an early stage
of isoprenoid biosynthesis [Secondary metabolites
biosynthesis, transport, and catabolism].
Length = 217
Score = 33.3 bits (76), Expect = 0.28
Identities = 24/86 (27%), Positives = 40/86 (46%), Gaps = 6/86 (6%)
Query: 473 PEVVWKLLDMQVTCGTLGLSTATVKLMDANGEEHVACSTGTGPVDSAYKAVDLIVKEPAT 532
P ++ K+ + T+G T + ++ G EHV C VD K +V PA
Sbjct: 138 PAMLPKIFGFPLRL-TIGNDIDTAEALEEMGAEHVPCPVDDIVVDEDNK----VVTTPAY 192
Query: 533 LLEYSMNAVTAGIDAIATTRVLIRGE 558
+L ++ +GID + +RVL+ E
Sbjct: 193 MLAQNIAEAASGIDKL-VSRVLVLAE 217
>gnl|CDD|240077 cd04726, KGPDC_HPS, 3-Keto-L-gulonate 6-phosphate decarboxylase
(KGPDC) and D-arabino-3-hexulose-6-phosphate synthase
(HPS). KGPDC catalyzes the formation of L-xylulose
5-phosphate and carbon dioxide from 3-keto-L-gulonate
6-phosphate as part of the anaerobic pathway for
L-ascorbate utilization in some eubacteria. HPS
catalyzes the formation of
D-arabino-3-hexulose-6-phosphate from D-ribulose
5-phosphate and formaldehyde in microorganisms that can
use formaldehyde as a carbon source. Both catalyze
reactions that involve the Mg2+-assisted formation and
stabilization of 1,2-enediolate reaction intermediates.
Length = 202
Score = 32.6 bits (75), Expect = 0.37
Identities = 16/41 (39%), Positives = 25/41 (60%), Gaps = 1/41 (2%)
Query: 101 LDIARQLAKLGVDIIEAGFPAASKEDFEAVRTIAKEVGNAV 141
L++A+++ GVDIIEAG P E EAVR + + + +
Sbjct: 16 LELAKKVPD-GVDIIEAGTPLIKSEGMEAVRALREAFPDKI 55
>gnl|CDD|153227 cd03133, GATase1_ES1, Type 1 glutamine amidotransferase
(GATase1)-like domain found in zebrafish ES1. Type 1
glutamine amidotransferase (GATase1)-like domain found
in zebrafish ES1. This group includes, proteins similar
to ES1, Escherichia coli enhancing lycopene biosynthesis
protein 2, Azospirillum brasilense iaaC and, human HES1.
The catalytic triad typical of GATase1domains is not
conserved in this GATase1-like domain. However, in
common with GATase1domains a reactive cys residue is
found in the sharp turn between a beta strand and an
alpha helix termed the nucleophile elbow. Zebrafish ES1
is expressed specifically in adult photoreceptor cells
and appears to be a cytoplasmic protein. A. brasilense
iaaC is involved in controlling IAA biosynthesis.
Length = 213
Score = 32.2 bits (74), Expect = 0.48
Identities = 22/75 (29%), Positives = 33/75 (44%), Gaps = 5/75 (6%)
Query: 473 PEVVWKLLDMQVTCGTLGLSTATVKLMDANGEEHVACSTGTGPVDSAYKAVDLIVKEPAT 532
P + K+L V T+G T ++ G EHV C VD K +V PA
Sbjct: 135 PALAAKILGEGVEV-TIGNDAGTAAAIEKMGAEHVNCPVEEIVVDEKNK----VVTTPAY 189
Query: 533 LLEYSMNAVTAGIDA 547
+L S++ + GI+
Sbjct: 190 MLADSIHEIADGIEK 204
>gnl|CDD|225314 COG2516, COG2516, Biotin synthase-related enzyme [General function
prediction only].
Length = 339
Score = 32.5 bits (74), Expect = 0.59
Identities = 33/140 (23%), Positives = 54/140 (38%), Gaps = 26/140 (18%)
Query: 98 KEKLDIARQLAKLGVDIIEAGFPAASKEDFEAVRTIAK-------------EVGNAVDAE 144
KE+L+ R KLG D + AA++E FE VR + +V A
Sbjct: 131 KEELEEYR---KLGADYLGVAEDAANEELFEKVRKTSGSPHSWERYWEFLEKVAEAFGKG 187
Query: 145 SGYVPVICGLSRCNERDI-KTAWEAVKYAKRPRIHTFIAT--SGIHMEHKLRKTKQQVVE 201
+ +I GL +++DI +T + + F T G ME++ VE
Sbjct: 188 RVGIHLIVGLG-ESDKDIVETIKRV--RKRGGIVSLFAFTPLKGTQMENRKPPP----VE 240
Query: 202 IARSMVKFARSLGCDDVEFS 221
R + +G +V+
Sbjct: 241 RYRKIQVARYLIGNGEVDLE 260
>gnl|CDD|223545 COG0469, PykF, Pyruvate kinase [Carbohydrate transport and
metabolism].
Length = 477
Score = 32.5 bits (75), Expect = 0.76
Identities = 21/57 (36%), Positives = 27/57 (47%), Gaps = 3/57 (5%)
Query: 83 TLRDGEQSPGATLTSKEKLDIARQLAKLGVDIIEAGFPAASKEDFEAVRTIAKEVGN 139
L + S A LT K+K D+ L + GVD + F + ED E VR I E G
Sbjct: 162 NLPGVDLSLPA-LTEKDKEDLKFGL-EQGVDFVALSFV-RNAEDVEEVREILAETGG 215
>gnl|CDD|215912 pfam00423, HN, Haemagglutinin-neuraminidase.
Length = 545
Score = 32.3 bits (74), Expect = 0.81
Identities = 13/54 (24%), Positives = 23/54 (42%), Gaps = 1/54 (1%)
Query: 235 EILGEVIKVGATTLNIPDTVGITMPTEFGKLIADIKANTPGIENVVISTHCQND 288
+I + ++ I D VG+T+P + L + I N I+ C+N
Sbjct: 52 DISSLISELTPKFKIIGDEVGLTIPQKLSDLGSFISDKIK-FLNPDITQQCRNT 104
>gnl|CDD|237593 PRK14041, PRK14041, oxaloacetate decarboxylase; Provisional.
Length = 467
Score = 32.1 bits (73), Expect = 0.89
Identities = 17/51 (33%), Positives = 25/51 (49%), Gaps = 5/51 (9%)
Query: 101 LDIARQLAKLGVDII----EAGFPAASKEDFEAVRTIAKEVGNAVDAESGY 147
L+ AR+L +GVD I AG K +E V+ + K+ G V+ S
Sbjct: 156 LEFARELVDMGVDSICIKDMAGL-LTPKRAYELVKALKKKFGVPVEVHSHC 205
Score = 30.5 bits (69), Expect = 3.1
Identities = 22/73 (30%), Positives = 35/73 (47%), Gaps = 9/73 (12%)
Query: 77 VRVFDTTLRDGEQSPGAT-LTSKEKLDIARQLAKLGVDIIE----AGFPAASK---ED-F 127
V DTTLRDG QS AT + +++ L ++G +E A F + E+ +
Sbjct: 3 VMFVDTTLRDGHQSLIATRMRTEDMLPALEAFDRMGFYSMEVWGGATFDVCVRFLNENPW 62
Query: 128 EAVRTIAKEVGNA 140
E ++ I K + N
Sbjct: 63 ERLKEIRKRLKNT 75
Score = 29.4 bits (66), Expect = 6.5
Identities = 23/99 (23%), Positives = 41/99 (41%), Gaps = 8/99 (8%)
Query: 235 EILGEVIKVGATTLNIPDTVGITMPTEFGKLIADIKA--NTPGIENVVISTHCQNDLGLS 292
E E++ +G ++ I D G+ P +L+ +K P V + +HC GL+
Sbjct: 157 EFARELVDMGVDSICIKDMAGLLTPKRAYELVKALKKKFGVP----VEVHSHCTT--GLA 210
Query: 293 TANTIAGACAGARQVEVTINGIGERAGNASLEEVVMAFK 331
+ +A AGA + I+ E + AF+
Sbjct: 211 SLAYLAAVEAGADMFDTAISPFSMGTSQPPFESMYYAFR 249
>gnl|CDD|178347 PLN02746, PLN02746, hydroxymethylglutaryl-CoA lyase.
Length = 347
Score = 31.7 bits (72), Expect = 1.1
Identities = 59/314 (18%), Positives = 125/314 (39%), Gaps = 57/314 (18%)
Query: 74 PNYVRVFDTTLRDGEQSPGATLTSKEKLDIARQLAKLGVDIIEAG-------FP--AASK 124
P +V++ + RDG Q+ + + K+++ ++L G+ ++EA P A +K
Sbjct: 44 PKFVKIVEVGPRDGLQNEKNIVPTSVKVELIQRLVSSGLPVVEATSFVSPKWVPQLADAK 103
Query: 125 EDFEAVRTIAKEVGNAVDAESGYVPVICGLSRCNERDIKTAWEAVKYAKRPRIHTFIATS 184
+ AVR + E PV+ N + + A A + F + S
Sbjct: 104 DVMAAVR----------NLEGARFPVLTP----NLKGFEAAIA----AGAKEVAVFASAS 145
Query: 185 GIHMEHKLRKTKQQVVEIARSMVKFARSLG--------CDDVEFSPEDAGRSDRKFLYEI 236
+ + + ++ + R + A+ C V P + K Y +
Sbjct: 146 ESFSKSNINCSIEESLVRYREVALAAKKHSIPVRGYVSC--VVGCPIEGPVPPSKVAY-V 202
Query: 237 LGEVIKVGATTLNIPDTVGITMPTEFGKLIADIKANTPGIENVVISTHCQNDLGLSTANT 296
E+ +G +++ DT+G+ P ++ + A P ++ ++ H + G + AN
Sbjct: 203 AKELYDMGCYEISLGDTIGVGTPGTVVPMLEAVMAVVP-VDK--LAVHFHDTYGQALANI 259
Query: 297 IAGACAGARQVEVTINGIG------ERAGNASLEEVVMAFKCRGEHILGGL--YTGINTR 348
+ G V+ ++ G+G +GN + E+VV ++L GL T ++
Sbjct: 260 LVSLQMGISTVDSSVAGLGGCPYAKGASGNVATEDVV--------YMLNGLGVSTNVDLG 311
Query: 349 HIVMASKMVEEYTG 362
++ A + ++ G
Sbjct: 312 KLMAAGDFISKHLG 325
>gnl|CDD|237981 cd00014, CH, Calponin homology domain; actin-binding domain which
may be present as a single copy or in tandem repeats
(which increases binding affinity). The CH domain is
found in cytoskeletal and signal transduction proteins,
including actin-binding proteins like spectrin,
alpha-actinin, dystrophin, utrophin, and fimbrin,
proteins essential for regulation of cell shape
(cortexillins), and signaling proteins (Vav).
Length = 107
Score = 30.0 bits (68), Expect = 1.1
Identities = 10/39 (25%), Positives = 16/39 (41%)
Query: 186 IHMEHKLRKTKQQVVEIARSMVKFARSLGCDDVEFSPED 224
I + ++ + +E + FA LG V F ED
Sbjct: 47 IDKKKINPLSRFKRLENINLALNFAEKLGVPVVNFDAED 85
>gnl|CDD|235619 PRK05826, PRK05826, pyruvate kinase; Provisional.
Length = 465
Score = 32.0 bits (74), Expect = 1.1
Identities = 19/45 (42%), Positives = 24/45 (53%), Gaps = 2/45 (4%)
Query: 95 LTSKEKLDIARQLAKLGVDIIEAGFPAASKEDFEAVRTIAKEVGN 139
LT K+K DI + A+ GVD I F S ED E R + +E G
Sbjct: 171 LTEKDKADI-KFAAEQGVDYIAVSFVR-SAEDVEEARRLLREAGC 213
>gnl|CDD|223347 COG0269, SgbH, 3-hexulose-6-phosphate synthase and related proteins
[Carbohydrate transport and metabolism].
Length = 217
Score = 31.1 bits (71), Expect = 1.3
Identities = 20/72 (27%), Positives = 31/72 (43%), Gaps = 18/72 (25%)
Query: 95 LTSKEK-LDIARQLAKLGVDIIEAGFPAASKEDFEAVRTIAKEVGNAVDAESGYVPVICG 153
L E+ ++IA ++A VDIIE G P E AVR + + + ++
Sbjct: 12 LLDLEEAIEIAEEVAD-YVDIIEVGTPLIKAEGMRAVRALRELFPDK--------IIVA- 61
Query: 154 LSRCNERDIKTA 165
D+KTA
Sbjct: 62 -------DLKTA 66
>gnl|CDD|233273 TIGR01108, oadA, oxaloacetate decarboxylase alpha subunit. This
model describes the bacterial oxaloacetate decarboxylase
alpha subunit and its equivalents in archaea. The
oxaloacetate decarboxylase Na+ pump is the paradigm of
the family of Na+ transport decarboxylases that present
in bacteria and archaea. It a multi subunit enzyme
consisting of a peripheral alpha-subunit and integral
membrane subunits beta and gamma. The energy released by
the decarboxylation reaction of oxaloacetate is coupled
to Na+ ion pumping across the membrane [Transport and
binding proteins, Cations and iron carrying compounds,
Energy metabolism, Other].
Length = 582
Score = 31.7 bits (72), Expect = 1.3
Identities = 18/97 (18%), Positives = 42/97 (43%), Gaps = 4/97 (4%)
Query: 235 EILGEVIKVGATTLNIPDTVGITMPTEFGKLIADIKANTPGIENVVISTHCQNDLGLSTA 294
++ E++++G ++ I D GI P +L++ +K + + H G++
Sbjct: 153 DLAEELLEMGVDSICIKDMAGILTPKAAYELVSALKKRFG----LPVHLHSHATTGMAEM 208
Query: 295 NTIAGACAGARQVEVTINGIGERAGNASLEEVVMAFK 331
+ AGA ++ I+ + + E +V A +
Sbjct: 209 ALLKAIEAGADGIDTAISSMSGGTSHPPTETMVAALR 245
>gnl|CDD|237675 PRK14328, PRK14328, (dimethylallyl)adenosine tRNA
methylthiotransferase; Provisional.
Length = 439
Score = 31.5 bits (72), Expect = 1.4
Identities = 15/48 (31%), Positives = 24/48 (50%), Gaps = 7/48 (14%)
Query: 96 TSKEKLDIARQL------AKLGVDIIEAGFPAASKEDFEAVRTIAKEV 137
T + L++ ++ + DII GFP ++EDFE + KEV
Sbjct: 280 TREYYLELVEKIKSNIPDVAITTDII-VGFPGETEEDFEETLDLVKEV 326
>gnl|CDD|235912 PRK07028, PRK07028, bifunctional hexulose-6-phosphate
synthase/ribonuclease regulator; Validated.
Length = 430
Score = 31.1 bits (71), Expect = 1.9
Identities = 14/36 (38%), Positives = 20/36 (55%)
Query: 101 LDIARQLAKLGVDIIEAGFPAASKEDFEAVRTIAKE 136
++IA++ G D IEAG P E A+RT+ K
Sbjct: 19 VEIAKEAVAGGADWIEAGTPLIKSEGMNAIRTLRKN 54
>gnl|CDD|212539 cd11593, Agmatinase-like_2, Agmatinase and related proteins. This
family includes known and predicted bacterial and
archaeal agmatinase (agmatine ureohydrolase; AUH; SpeB;
EC=3.5.3.11), a binuclear manganese metalloenzyme that
belongs to the ureohydrolase superfamily. It is a key
enzyme in the synthesis of polyamine putrescine; it
catalyzes hydrolysis of agmatine to yield urea and
putrescine, the precursor for biosynthesis of higher
polyamines, spermidine, and spermine. As compared to E.
coli where two paths to putrescine exist, via
decarboxylation of an amino acid, ornithine or arginine,
a single path is found in Bacillus subtilis, where
polyamine synthesis starts with agmatine; the speE and
speB encode spermidine synthase and agmatinase,
respectively. The level of agmatinase synthesis is very
low, allowing strict control on the synthesis of
putrescine and therefore, of all polyamines, consistent
with polyamine levels in the cell. This subfamily
belongs to the ureohydrolase superfamily, which includes
arginase, agmatinase, proclavaminate amidinohydrolase,
and formiminoglutamase.
Length = 263
Score = 30.5 bits (70), Expect = 2.0
Identities = 12/45 (26%), Positives = 26/45 (57%), Gaps = 4/45 (8%)
Query: 197 QQVVEIARSMVKFARSLGCDDVEFSP-EDAGRSDR---KFLYEIL 237
++++++ R++ + +G D VE SP D G + K +YE++
Sbjct: 219 RELLDLLRALAESKNIVGFDVVELSPDYDGGVTAFLAAKLVYELI 263
>gnl|CDD|184630 PRK14334, PRK14334, (dimethylallyl)adenosine tRNA
methylthiotransferase; Provisional.
Length = 440
Score = 31.0 bits (70), Expect = 2.1
Identities = 13/29 (44%), Positives = 18/29 (62%), Gaps = 1/29 (3%)
Query: 110 LGVDIIEAGFPAASKEDFEAVRTIAKEVG 138
L DII GFP ++EDF+ ++ EVG
Sbjct: 290 LSTDII-VGFPGETEEDFQETLSLYDEVG 317
>gnl|CDD|219055 pfam06484, Ten_N, Teneurin Intracellular Region. This family is
found in the intracellular N-terminal region of the
Teneurin family of proteins. These proteins are
'pair-rule' genes and are involved in tissue patterning,
specifically probably neural patterning. The
intracellular domain is cleaved in response to
homophilic interaction of the extracellular domain, and
translocates to the nucleus. Here it probably carries
out to some transcriptional regulatory activity. The
length of this region and the conservation suggests that
there may be two structural domains here (personal obs:C
Yeats).
Length = 370
Score = 30.8 bits (69), Expect = 2.2
Identities = 15/45 (33%), Positives = 19/45 (42%), Gaps = 6/45 (13%)
Query: 28 QLFFHCNNSKPFFKTT------ISCSLQKPPPSLYPRITASRPEY 66
F + P F TT S ++ PPP PR T SRP +
Sbjct: 314 HFLFKPGGTSPLFCTTSPGYPLTSSTVYSPPPRPLPRNTFSRPAF 358
>gnl|CDD|237263 PRK12999, PRK12999, pyruvate carboxylase; Reviewed.
Length = 1146
Score = 30.5 bits (70), Expect = 3.6
Identities = 19/49 (38%), Positives = 26/49 (53%), Gaps = 1/49 (2%)
Query: 64 PEYIPNRIPDPNYVRVFDTTLRDGEQSPGAT-LTSKEKLDIARQLAKLG 111
PE + + D V + DTT RD QS AT + +K+ L IA A+L
Sbjct: 520 PEGFADWLRDQKRVLLTDTTFRDAHQSLLATRVRTKDLLRIAPATARLL 568
>gnl|CDD|226713 COG4262, COG4262, Predicted spermidine synthase with an N-terminal
membrane domain [General function prediction only].
Length = 508
Score = 30.2 bits (68), Expect = 3.6
Identities = 14/84 (16%), Positives = 29/84 (34%), Gaps = 7/84 (8%)
Query: 104 ARQLAKLGVDIIEAGFPAASKEDFEAVRTIAKEVGNAVDAESGYVP-------VICGLSR 156
+R LA+ G+ +++AG P + F + K G V +VP ++
Sbjct: 394 SRHLAETGLMVVQAGSPYFTPRVFWRIDATIKSAGYRVWPYHVHVPTFGEWGFILAAPGD 453
Query: 157 CNERDIKTAWEAVKYAKRPRIHTF 180
+ ++ +H
Sbjct: 454 ADFEPPTEYRPPTRFLDAEVLHAA 477
>gnl|CDD|238188 cd00308, enolase_like, Enolase-superfamily, characterized by the
presence of an enolate anion intermediate which is
generated by abstraction of the alpha-proton of the
carboxylate substrate by an active site residue and is
stabilized by coordination to the essential Mg2+ ion.
Enolase superfamily contains different enzymes, like
enolases, glutarate-, fucanate- and galactonate
dehydratases, o-succinylbenzoate synthase, N-acylamino
acid racemase, L-alanine-DL-glutamate epimerase,
mandelate racemase, muconate lactonizing enzyme and
3-methylaspartase.
Length = 229
Score = 29.6 bits (67), Expect = 4.0
Identities = 16/57 (28%), Positives = 24/57 (42%), Gaps = 3/57 (5%)
Query: 94 TLTSKEKLDIARQLAKLGVDIIEAGFPAASKEDFEAVRTIAKEVGNAVDAESGYVPV 150
T KE + + R L K G+ IE P A +D E + + G + A+ V
Sbjct: 104 AWTPKEAIRLIRALEKYGLAWIEE--PCAP-DDLEGYAALRRRTGIPIAADESVTTV 157
>gnl|CDD|172808 PRK14332, PRK14332, (dimethylallyl)adenosine tRNA
methylthiotransferase; Provisional.
Length = 449
Score = 30.0 bits (67), Expect = 4.1
Identities = 25/98 (25%), Positives = 45/98 (45%), Gaps = 19/98 (19%)
Query: 51 PPPSLYP----RITASRPEYIPN-RIP-DPNYVRVFDTTLRDGEQSPGATLTSKEKLDIA 104
P P +P + A P + PN +P RV L + ++S + +E LD+
Sbjct: 241 PHPKDFPDHLLSLMAKNPRFCPNIHLPLQAGNTRV----LEEMKRS----YSKEEFLDVV 292
Query: 105 RQLAKLGVDI-----IEAGFPAASKEDFEAVRTIAKEV 137
+++ + D+ I GFP ++E+FE + +EV
Sbjct: 293 KEIRNIVPDVGITTDIIVGFPNETEEEFEDTLAVVREV 330
>gnl|CDD|237285 PRK13111, trpA, tryptophan synthase subunit alpha; Provisional.
Length = 258
Score = 29.7 bits (68), Expect = 4.3
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 101 LDIARQLAKLGVDIIEAGFP 120
L+I + L + G DIIE G P
Sbjct: 29 LEIIKALVEAGADIIELGIP 48
>gnl|CDD|132172 TIGR03128, RuMP_HxlA, 3-hexulose-6-phosphate synthase. Members of
this protein family are 3-hexulose-6-phosphate synthase
(HPS), or the HPS domain of a fusion protein. This
enzyme is part of the ribulose monophosphate (RuMP)
pathway, which in one direction removes the toxic
metabolite formaldehyde by assimilation into
fructose-6-phosphate. In the other direction, in species
lacking a complete pentose phosphate pathway, the RuMP
pathway yields ribulose-5-phosphate, necessary for
nucleotide biosynthesis, at the cost of also yielding
formaldehyde. These latter species tend usually have a
formaldehyde-activating enzyme to attach formaldehyde to
the C1 carrier tetrahydromethanopterin. In these
species, the enzyme is viewed as a lyase rather than a
synthase and is called D-arabino 3-hexulose 6-phosphate
formaldehyde lyase. Note that there is some overlap in
specificity with the Escherichia coli enzyme
3-keto-L-gulonate 6-phosphate decarboxylase.
Length = 206
Score = 29.3 bits (66), Expect = 4.8
Identities = 16/42 (38%), Positives = 24/42 (57%), Gaps = 1/42 (2%)
Query: 94 TLTSKEKLDIARQLAKLGVDIIEAGFPAASKEDFEAVRTIAK 135
L +E L++A ++A VDIIE G P E EAV+ + +
Sbjct: 8 LLDIEEALELAEKVAD-YVDIIEIGTPLIKNEGIEAVKEMKE 48
>gnl|CDD|238937 cd01979, Pchlide_reductase_N, Pchlide_reductase_N: N protein of the
NB protein complex of Protochlorophyllide
(Pchlide)_reductase. Pchlide reductase catalyzes the
reductive formation of chlorophyllide (chlide) from
protochlorophyllide (pchlide) during biosynthesis of
chlorophylls and bacteriochlorophylls. This group
contains both the light-independent Pchlide reductase
(DPOR) and light-dependent Pchlide reductase (LPOR).
Angiosperms contain only LPOR, cyanobacteria, algae and
gymnosperms contain both DPOR and LPOR, primitive
anoxygenic photosynthetic bacteria contain only DPOR. NB
is structurally similar to the FeMo protein of
nitrogenase, forming an N2B2 heterotetramer. N and B are
homologous to the FeMo alpha and beta subunits
respectively. Also in common with nitrogenase in vitro
DPOR activity requires ATP hydrolysis and dithoionite or
ferredoxin as electron donor. The NB protein complex may
serve as a catalytic site for Pchlide reduction similar
to MoFe for nitrogen reduction.
Length = 396
Score = 29.6 bits (67), Expect = 4.9
Identities = 22/80 (27%), Positives = 32/80 (40%), Gaps = 14/80 (17%)
Query: 101 LDIARQLAKLGVDIIEAGFPAASKEDFEA--------VRTIAK-EVGNAVDAESGYVP-- 149
+ +AR L + G+ ++E G P K A VR + K + +D P
Sbjct: 289 IPLARFLTRCGMIVVEVGTPYLDKRFQAAELELLPPMVRIVEKPDNYRQLDRIRELRPDL 348
Query: 150 VICGLSRCN---ERDIKTAW 166
V+ GL N R I T W
Sbjct: 349 VVTGLGLANPLEARGITTKW 368
>gnl|CDD|240075 cd04724, Tryptophan_synthase_alpha, Ttryptophan synthase (TRPS)
alpha subunit (TSA). TPRS is a bifunctional tetrameric
enzyme (2 alpha and 2 beta subunits) that catalyzes the
last two steps of L-tryptophan biosynthesis. Alpha and
beta subunit catalyze two distinct reactions which are
both strongly stimulated by the formation of the
complex. The alpha subunit catalyzes the cleavage of
indole 3-glycerol phosphate (IGP) to indole and
d-glyceraldehyde 3-phosphate (G3P). Indole is then
channeled to the active site of the beta subunit, a
PLP-dependent enzyme that catalyzes a replacement
reaction to convert L-serine into L-tryptophan.
Length = 242
Score = 29.4 bits (67), Expect = 5.6
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 101 LDIARQLAKLGVDIIEAGFP 120
L+I + L + G DIIE G P
Sbjct: 17 LEILKALVEAGADIIELGIP 36
>gnl|CDD|187644 cd08940, HBDH_SDR_c, d-3-hydroxybutyrate dehydrogenase (HBDH),
classical (c) SDRs. DHBDH, an NAD+ -dependent enzyme,
catalyzes the interconversion of D-3-hydroxybutyrate and
acetoacetate. It is a classical SDR, with the canonical
NAD-binding motif and active site tetrad. 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 = 258
Score = 29.3 bits (66), Expect = 6.1
Identities = 15/46 (32%), Positives = 21/46 (45%)
Query: 96 TSKEKLDIARQLAKLGVDIIEAGFPAASKEDFEAVRTIAKEVGNAV 141
TS L IAR LA G +I+ GF A++ + AK +
Sbjct: 11 TSGIGLGIARALAAAGANIVLNGFGDAAEIEAVRAGLAAKHGVKVL 56
>gnl|CDD|214921 smart00934, OMPdecase, Orotidine 5'-phosphate decarboxylase / HUMPS
family. Orotidine 5'-phosphate decarboxylase
(OMPdecase) catalyzes the last step in the de novo
biosynthesis of pyrimidines, the decarboxylation of OMP
into UMP. In higher eukaryotes OMPdecase is part, with
orotate phosphoribosyltransferase, of a bifunctional
enzyme, while the prokaryotic and fungal OMPdecases are
monofunctional protein.
Length = 212
Score = 28.7 bits (65), Expect = 6.6
Identities = 13/45 (28%), Positives = 21/45 (46%), Gaps = 2/45 (4%)
Query: 95 LTSKEK-LDIARQLAKLGVDIIEAGFPAASKEDFEAVRTIAKEVG 138
+ E+ L++A L VDII+ G E E V+ + + G
Sbjct: 8 VPDLEEALELADALGDS-VDIIKVGTELFLAEGPEGVKELKELFG 51
>gnl|CDD|179646 PRK03762, PRK03762, hypothetical protein; Provisional.
Length = 103
Score = 27.7 bits (62), Expect = 6.6
Identities = 10/23 (43%), Positives = 12/23 (52%)
Query: 294 ANTIAGACAGARQVEVTINGIGE 316
AN A +G V V+ NG GE
Sbjct: 29 ANKEFTAKSGGGLVSVSANGKGE 51
>gnl|CDD|223694 COG0621, MiaB, 2-methylthioadenine synthetase [Translation,
ribosomal structure and biogenesis].
Length = 437
Score = 29.1 bits (66), Expect = 6.9
Identities = 17/49 (34%), Positives = 25/49 (51%), Gaps = 7/49 (14%)
Query: 96 TSKEKLDIARQLAK------LGVDIIEAGFPAASKEDFEAVRTIAKEVG 138
T +E L+I +L + DII GFP ++EDFE + +EV
Sbjct: 278 TVEEYLEIIEKLRAARPDIAISTDII-VGFPGETEEDFEETLDLVEEVR 325
>gnl|CDD|215645 PLN03246, PLN03246, 26S proteasome regulatory subunit; Provisional.
Length = 303
Score = 28.9 bits (65), Expect = 7.0
Identities = 19/84 (22%), Positives = 33/84 (39%), Gaps = 17/84 (20%)
Query: 365 VQPHKAIVGANAFAHESGIHQDGMLKHKGTY-------EIISPEDIGLER---------- 407
VQP + + A+ + ++ K + + E+IG+E
Sbjct: 124 VQPKELGIPTKAYYAVEEVKENATQKSQKVFVHVPSEIGAHEAEEIGVEHLLRDVKDTTV 183
Query: 408 SSEAGIVLGKLSGRHALKDRLKEL 431
S+ A V GKL+ L RL+E+
Sbjct: 184 STLATEVTGKLTALKGLDARLREI 207
>gnl|CDD|223237 COG0159, TrpA, Tryptophan synthase alpha chain [Amino acid
transport and metabolism].
Length = 265
Score = 28.7 bits (65), Expect = 7.7
Identities = 9/20 (45%), Positives = 13/20 (65%)
Query: 101 LDIARQLAKLGVDIIEAGFP 120
L+I + L + G DI+E G P
Sbjct: 34 LEIIKTLVEAGADILELGVP 53
>gnl|CDD|234359 TIGR03802, Asp_Ala_antiprt, aspartate-alanine antiporter. All
members of the seed alignment for this model are
asparate-alanine anti-transporters (AspT) encoded next
to the gene for aspartate 4-decarboxylase (AspD), which
converts asparate to alanine, releasing CO2. The
exchange of Asp for Ala is electrogenic, so the
AspD/AspT system confers a proton-motive force. This
transporter contains two copies of the AspT/YidE/YbjL
antiporter duplication domain (TIGR01625).
Length = 562
Score = 29.2 bits (66), Expect = 8.2
Identities = 10/25 (40%), Positives = 15/25 (60%)
Query: 297 IAGACAGARQVEVTINGIGERAGNA 321
+ GA AGAR + + ERAG++
Sbjct: 510 LLGALAGARTATPALGAVLERAGSS 534
>gnl|CDD|233476 TIGR01574, miaB-methiolase, tRNA-N(6)-(isopentenyl)adenosine-37
thiotransferase enzyme MiaB. This model represents
homologs of the MiaB enzyme responsible for the
modification of the isopentenylated adenine-37 base of
most bacterial and eukaryotic tRNAs that read codons
beginning with uracil (all except tRNA(I,V) Ser).
Adenine-37 is next to the anticodon on the 3' side in
these tRNA's, and lack of modification at this site
leads to an increased spontaneous mutation frequency.
Isopentenylated A-37 is modified by methylthiolation at
position 2, either by MiaB alone or in concert with a
separate methylase yet to be discovered (MiaC?). MiaB
contains a 4Fe-4S cluster which is labile under
oxidizing conditions. Additionally, the sequence is
homologous (via PSI-BLAST searches) to the biotin
synthetase, BioB, which utilizes both an iron-sulfur
cluster and S-adenosym methionine (SAM) to generate a
radical which is responsible for initiating the
insertion of sulfur into the substrate. It is reasonable
to surmise that the methyl group of SAM becomes the
methyl group of the product, but this has not been
shown, and the possibility of a separate methylase
exists. This equivalog is a member of a subfamily
(TIGR00089) which contains several other hypothetical
equivalogs which are all probably enzymes with similar
function acting on different substrates. These enzymes
contain a TRAM domain (pfam01938) which is believed to
be responsible for binding to tRNAs. Hits to this model
span all major groups of bacteria and eukaryotes, but
not archaea, which are known to lack this particular
tRNA modification. The enzyme from Thermotoga maritima
has been cloned, expressed, spectroscopically
characterized and shown to complement the E. coli MiaB
enzyme [Protein synthesis, tRNA and rRNA base
modification].
Length = 438
Score = 29.0 bits (65), Expect = 8.4
Identities = 16/52 (30%), Positives = 25/52 (48%), Gaps = 7/52 (13%)
Query: 92 GATLTSKEKLDIARQL------AKLGVDIIEAGFPAASKEDFEAVRTIAKEV 137
T + L++ R+L + DII GFP ++EDFE + +EV
Sbjct: 276 KRGYTREWYLNLVRKLRAACPNVSISTDII-VGFPGETEEDFEETLDLLREV 326
>gnl|CDD|183494 PRK12390, PRK12390, 1-aminocyclopropane-1-carboxylate deaminase;
Provisional.
Length = 337
Score = 28.8 bits (65), Expect = 9.7
Identities = 16/45 (35%), Positives = 22/45 (48%), Gaps = 3/45 (6%)
Query: 185 GIHMEHKLRKTKQQVVEIAR---SMVKFARSLGCDDVEFSPEDAG 226
GI K +T+ QV+ IAR +V+ R + DDV AG
Sbjct: 221 GIDASAKPEQTRAQVLRIARNTAELVELGRDITEDDVVLDERYAG 265
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
0.317 0.133 0.380
Gapped
Lambda K H
0.267 0.0805 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 31,303,897
Number of extensions: 3136538
Number of successful extensions: 3713
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3581
Number of HSP's successfully gapped: 112
Length of query: 620
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 517
Effective length of database: 6,369,140
Effective search space: 3292845380
Effective search space used: 3292845380
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: 62 (27.5 bits)