RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 006969
(623 letters)
>gnl|CDD|215182 PLN02321, PLN02321, 2-isopropylmalate synthase.
Length = 632
Score = 1072 bits (2773), Expect = 0.0
Identities = 472/625 (75%), Positives = 521/625 (83%), Gaps = 6/625 (0%)
Query: 2 AATTAAAAFFTNRQPTFI---SSSPKTKANASQLFFHCNNSKPFFKTTISCSLQKPPPSL 58
++ TAA+ + T SS+ + A ++ + + S PS
Sbjct: 8 SSATAASPAKSLSAFTPAPTRSSASSARFPAFLARP--AAARSPSLASRASSALAASPSR 65
Query: 59 YPRITATRPEYIPNRIPDPNYVRVFDTTLRDGEQSPGATLTSKEKLDIARQLAKLGVDII 118
RPEYIPNRI DPNYVR+FDTTLRDGEQSPGATLTSKEKLDIARQLAKLGVDII
Sbjct: 66 PQVARRPRPEYIPNRIDDPNYVRIFDTTLRDGEQSPGATLTSKEKLDIARQLAKLGVDII 125
Query: 119 EAGFPAASKEDFEAVRTIAKEVGNAVDAESGYVPVICGLSRCNERDIKTAWEAVKYAKRP 178
EAGFP AS +D EAV+TIAKEVGN VD E GYVPVICGLSRCN++DI AWEAVK+AKRP
Sbjct: 126 EAGFPIASPDDLEAVKTIAKEVGNEVD-EDGYVPVICGLSRCNKKDIDAAWEAVKHAKRP 184
Query: 179 RIHTFIATSGIHMEHKLRKTKQQVVEIARSMVKFARSLGCDDVEFSPEDAGRSDRKFLYE 238
RIHTFIATS IHMEHKLRKT +VVEIAR MVK+ARSLGC+DVEFSPEDAGRSD +FLY
Sbjct: 185 RIHTFIATSEIHMEHKLRKTPDEVVEIARDMVKYARSLGCEDVEFSPEDAGRSDPEFLYR 244
Query: 239 ILGEVIKVGATTLNIPDTVGITMPTEFGKLIADIKANTPGIENVVISTHCQNDLGLSTAN 298
ILGEVIK GATTLNIPDTVG T+P+EFG+LIADIKANTPGIENV+ISTHCQNDLGLSTAN
Sbjct: 245 ILGEVIKAGATTLNIPDTVGYTLPSEFGQLIADIKANTPGIENVIISTHCQNDLGLSTAN 304
Query: 299 TIAGACAGARQVEVTINGIGERAGNASLEEVVMAFKCRGEHILGGLYTGINTRHIVMASK 358
T+AGA AGARQVEVTINGIGERAGNASLEEVVMA KCRG+ LGGLYTGIN HI SK
Sbjct: 305 TLAGAHAGARQVEVTINGIGERAGNASLEEVVMAIKCRGDEQLGGLYTGINPVHITPTSK 364
Query: 359 MVEEYTGLHVQPHKAIVGANAFAHESGIHQDGMLKHKGTYEIISPEDIGLERSSEAGIVL 418
MV EYTG+ VQPHKAIVGANAFAHESGIHQDGMLKHKGTYEIISPEDIGL R ++AGIVL
Sbjct: 365 MVSEYTGMQVQPHKAIVGANAFAHESGIHQDGMLKHKGTYEIISPEDIGLFRGNDAGIVL 424
Query: 419 GKLSGRHALKDRLKELGYELNDEQLGTIFWHFKAVAEQKKRVTDADLIALVSDEIFQPEV 478
GKLSGRHALK RLKELGYEL+D++L +F FKAVAE+KK VTD DLIALVSDE+FQPEV
Sbjct: 425 GKLSGRHALKSRLKELGYELDDDELDDVFKRFKAVAEKKKGVTDEDLIALVSDEVFQPEV 484
Query: 479 VWKLLDMQVTCGTLGLSTATVKLMDANGEEHVACSTGTGPVDSAYKAVDLIVKEPATLLE 538
VWKLLD+QVTCGTLGLSTATVKL+ +G EH+ACS GTGPVD+AYKAVDLIVKEP TLLE
Sbjct: 485 VWKLLDLQVTCGTLGLSTATVKLIGPDGVEHIACSVGTGPVDAAYKAVDLIVKEPVTLLE 544
Query: 539 YSMNAVTAGIDAIATTRVLIRGEKSQLSTHASTGETVQRTFSGTGAGMDIVVSSVKAYIG 598
YSMNAVT GIDAIATTRV+IRGE S STHA TGE+VQRTFSG+GA MDIVVSSV+AY+
Sbjct: 545 YSMNAVTEGIDAIATTRVVIRGENSYSSTHAQTGESVQRTFSGSGADMDIVVSSVRAYVS 604
Query: 599 ALNKMLGFKDQLPAKDSVERTSVSA 623
ALNKMLGFK+ AK + ER++
Sbjct: 605 ALNKMLGFKEASKAKSASERSTSVV 629
>gnl|CDD|234864 PRK00915, PRK00915, 2-isopropylmalate synthase; Validated.
Length = 513
Score = 798 bits (2064), Expect = 0.0
Identities = 288/539 (53%), Positives = 367/539 (68%), Gaps = 30/539 (5%)
Query: 76 DPNYVRVFDTTLRDGEQSPGATLTSKEKLDIARQLAKLGVDIIEAGFPAASKEDFEAVRT 135
+ V +FDTTLRDGEQSPGA+LT +EKL IA+QL +LGVD+IEAGFPA+S DFEAV+
Sbjct: 1 MMDRVIIFDTTLRDGEQSPGASLTVEEKLQIAKQLERLGVDVIEAGFPASSPGDFEAVKR 60
Query: 136 IAKEVGNAVDAESGYVPVICGLSRCNERDIKTAWEAVKYAKRPRIHTFIATSGIHMEHKL 195
IA+ V N +CGL+R ++DI A EA+K A+ PRIHTFIATS IHME+KL
Sbjct: 61 IARTVKN---------STVCGLARAVKKDIDAAAEALKPAEAPRIHTFIATSPIHMEYKL 111
Query: 196 RKTKQQVVEIARSMVKFARSLGCDDVEFSPEDAGRSDRKFLYEILGEVIKVGATTLNIPD 255
+ ++++V+E+A VK+ARS DDVEFS EDA R+D FL ++ I GATT+NIPD
Sbjct: 112 KMSREEVLEMAVEAVKYARSY-TDDVEFSAEDATRTDLDFLCRVVEAAIDAGATTINIPD 170
Query: 256 TVGITMPTEFGKLIADIKANTPGIENVVISTHCQNDLGLSTANTIAGACAGARQVEVTIN 315
TVG T P EFG+LI ++ P I+ +IS HC NDLGL+ AN++A AGARQVE TIN
Sbjct: 171 TVGYTTPEEFGELIKTLRERVPNIDKAIISVHCHNDLGLAVANSLAAVEAGARQVECTIN 230
Query: 316 GIGERAGNASLEEVVMAFKCRGEHILGGLYTGINTRHIVMASKMVEEYTGLHVQPHKAIV 375
GIGERAGNA+LEEVVMA K R + G+ TGINT I S++V + TG+ VQP+KAIV
Sbjct: 231 GIGERAGNAALEEVVMALKTRKDIY--GVETGINTEEIYRTSRLVSQLTGMPVQPNKAIV 288
Query: 376 GANAFAHESGIHQDGMLKHKGTYEIISPEDIGLERSSEAGIVLGKLSGRHALKDRLKELG 435
GANAFAHESGIHQDG+LK++ TYEI++PE +GL+ + +VLGK SGRHA K RL+ELG
Sbjct: 289 GANAFAHESGIHQDGVLKNRETYEIMTPESVGLKANR---LVLGKHSGRHAFKHRLEELG 345
Query: 436 YELNDEQLGTIFWHFKAVAEQKKRVTDADLIALVSDEI-FQPEVVWKLLDMQVTCGTLGL 494
Y+L+DE+L F FK +A++KK V D DL ALV DE + +KL +QV G+ G
Sbjct: 346 YKLSDEELDKAFERFKELADKKKEVFDEDLEALVEDETQQEEPEHYKLESLQVQSGSSGT 405
Query: 495 STATVKLMDANGEEHVACSTGTGPVDSAYKAVDLIVKEPATLLEYSMNAVTAGIDAIATT 554
TATVKL D +GEE +TG GPVD+ Y A++ IV LLEYS+NA+T G DA+
Sbjct: 406 PTATVKLRDIDGEEKEEAATGNGPVDAVYNAINRIVGSDIELLEYSVNAITGGTDALGEV 465
Query: 555 RVLIRGEKSQLSTHASTGETVQRTFSGTGAGMDIVVSSVKAYIGALNKMLGFKDQLPAK 613
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 = 658 bits (1698), Expect = 0.0
Identities = 282/414 (68%), Positives = 350/414 (84%), Gaps = 2/414 (0%)
Query: 62 ITATRPEYIPNRIPDPNYVRVFDTTLRDGEQSPGATLTSKEKLDIARQLAKLGVDIIEAG 121
I PEYIPN++PD NYVRV DTTLRDGEQSPG +LT +KL+IARQLAKL VDI+E G
Sbjct: 67 IVERWPEYIPNKLPDKNYVRVLDTTLRDGEQSPGGSLTPPQKLEIARQLAKLRVDIMEVG 126
Query: 122 FPAASKEDFEAVRTIAKEVGNAVDAESGYVPVICGLSRCNERDIKTAWEAVKYAKRPRIH 181
FP +S+E+FEAV+TIAK VGN VD E+GYVPVICG++RC +RDI+ AWEA+KYAKRPRI
Sbjct: 127 FPGSSEEEFEAVKTIAKTVGNEVDEETGYVPVICGIARCKKRDIEAAWEALKYAKRPRIL 186
Query: 182 TFIATSGIHMEHKLRKTKQQVVEIARSMVKFARSLGCDDVEFSPEDAGRSDRKFLYEILG 241
F +TS IHM++KL+KTK++V+E+A S +++A+SLG D++F ED GRSD++FL +ILG
Sbjct: 187 AFTSTSDIHMKYKLKKTKEEVIEMAVSSIRYAKSLGFHDIQFGCEDGGRSDKEFLCKILG 246
Query: 242 EVIKVGATTLNIPDTVGITMPTEFGKLIADIKANTPGIENVVISTHCQNDLGLSTANTIA 301
E IK GAT++ I DTVGI MP EFG+L+ +KANTPGI+++V S HC NDLGL+TANTIA
Sbjct: 247 EAIKAGATSVGIADTVGINMPHEFGELVTYVKANTPGIDDIVFSVHCHNDLGLATANTIA 306
Query: 302 GACAGARQVEVTINGIGERAGNASLEEVVMAFKCRGEHILGGLYTGINTRHIVMASKMVE 361
G CAGARQVEVTINGIGER+GNASLEEVVMA KCRG +++ G+YTGI+TR I+ SKMV+
Sbjct: 307 GICAGARQVEVTINGIGERSGNASLEEVVMALKCRGAYLMNGVYTGIDTRQIMATSKMVQ 366
Query: 362 EYTGLHVQPHKAIVGANAFAHESGIHQDGMLKHKGTYEIISPEDIGLERSSEAGIVLGKL 421
EYTG++VQPHK IVGAN F HESGIHQDG+LK++ TYEI+SPEDIG+ +S +GIVLGKL
Sbjct: 367 EYTGMYVQPHKPIVGANCFVHESGIHQDGILKNRSTYEILSPEDIGIVKSQNSGIVLGKL 426
Query: 422 SGRHALKDRLKELGYELNDEQLGTIFWHFKAVAEQKKRVTDADLIALV--SDEI 473
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 = 637 bits (1645), Expect = 0.0
Identities = 288/525 (54%), Positives = 363/525 (69%), Gaps = 35/525 (6%)
Query: 80 VRVFDTTLRDGEQSPGATLTSKEKLDIARQLAKLGVDIIEAGFPAASKEDFEAVRTIAKE 139
+ +FDTTLRDGEQSPGA+LT +EKL IA L +LGVDIIEAGFP +S DFEAV+ IA+
Sbjct: 2 IIIFDTTLRDGEQSPGASLTVEEKLQIALALERLGVDIIEAGFPVSSPGDFEAVQRIART 61
Query: 140 VGNAVDAESGYVPVICGLSRCNERDIKTAWEAVKYAKRPRIHTFIATSGIHMEHKLRKTK 199
V N P +CGL+RC E+DI A EA+K A++ RIHTFIATS IH+EHKL+ T+
Sbjct: 62 VKN---------PRVCGLARCVEKDIDAAAEALKPAEKFRIHTFIATSPIHLEHKLKMTR 112
Query: 200 QQVVEIARSMVKFARSLGCDDVEFSPEDAGRSDRKFLYEILGEVIKVGATTLNIPDTVGI 259
+V+E A MVK+A++ DDVEFS EDAGR++ FL I+ I GATT+NIPDTVG
Sbjct: 113 DEVLERAVGMVKYAKNF-TDDVEFSCEDAGRTEIPFLARIVEAAINAGATTINIPDTVGY 171
Query: 260 TMPTEFGKLIADIKANTPGIENVVISTHCQNDLGLSTANTIAGACAGARQVEVTINGIGE 319
+P E+G LI ++ N P I+ ++S HC NDLGL+ AN++A GARQVE TINGIGE
Sbjct: 172 ALPAEYGNLIKGLRENVPNIDKAILSVHCHNDLGLAVANSLAAVQNGARQVECTINGIGE 231
Query: 320 RAGNASLEEVVMAFKCRGEHILGGLYTGINTRHIVMASKMVEEYTGLHVQPHKAIVGANA 379
RAGNA+LEEVVMA K R + + G+ TGINT+ I S++V + TG+ VQP+KAIVG NA
Sbjct: 232 RAGNAALEEVVMALKVRKDFL--GVETGINTKEIYRTSRLVSQLTGMPVQPNKAIVGDNA 289
Query: 380 FAHESGIHQDGMLKHKGTYEIISPEDIGLERSSEAGIVLGKLSGRHALKDRLKELGYELN 439
FAHESGIHQDG+LK+K TYEI+SPEDIGL +VLGK SGRHA KDRL+ELG++L+
Sbjct: 290 FAHESGIHQDGVLKNKETYEIMSPEDIGLTAEQ---LVLGKHSGRHAFKDRLEELGFKLD 346
Query: 440 DEQLGTIFWHFKAVAEQKKRVTDADLIALVSDEIFQ-PEVVWKLLDMQVTCGTLGLSTAT 498
DE+L +F FK +A++KK VTD DL ALV +E Q PE +KLL QV GT + TAT
Sbjct: 347 DEELDKLFEKFKELADKKKEVTDEDLEALVFEEKRQEPEEGYKLLHFQVHSGTNQVPTAT 406
Query: 499 VKLMDANGEEHVACSTGTGPVDSAYKAVDLIVKEPATLLEYSMNAVTAGIDAIATTRVLI 558
VKL GE+ A +TG GPVD+ YKA++ + LLEYS+ AV G DA+ V++
Sbjct: 407 VKL-KNGGEKREAAATGNGPVDAVYKAINRALGIEVELLEYSITAVGEGKDALGQVDVVL 465
Query: 559 R--GEKSQLSTHASTGETVQRTFSGTGAGMDIVVSSVKAYIGALN 601
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 = 475 bits (1226), Expect = e-167
Identities = 163/281 (58%), Positives = 205/281 (72%), Gaps = 13/281 (4%)
Query: 82 VFDTTLRDGEQSPGATLTSKEKLDIARQLAKLGVDIIEAGFPAASKEDFEAVRTIAKEVG 141
+FDTTLRDGEQ+PG +LT +EKL+IARQL +LGVD+IEAGFPAAS DFEAV+ IA+EV
Sbjct: 1 IFDTTLRDGEQTPGVSLTPEEKLEIARQLDELGVDVIEAGFPAASPGDFEAVKRIAREVL 60
Query: 142 NAVDAESGYVPVICGLSRCNERDIKTAWEAVKYAKRPRIHTFIATSGIHMEHKLRKTKQQ 201
N ICGL+R ++DI A EA+K AK RIHTFIATS IH+++KL+KT+++
Sbjct: 61 N---------AEICGLARAVKKDIDAAAEALKPAKVDRIHTFIATSDIHLKYKLKKTREE 111
Query: 202 VVEIARSMVKFARSLGCDDVEFSPEDAGRSDRKFLYEILGEVIKVGATTLNIPDTVGITM 261
V+E A V++A+S G DVEFS EDA R+D FL E++ I+ GATT+NIPDTVG
Sbjct: 112 VLERAVEAVEYAKSHG-LDVEFSAEDATRTDLDFLIEVVEAAIEAGATTINIPDTVGYLT 170
Query: 262 PTEFGKLIADIKANTPGIENVVISTHCQNDLGLSTANTIAGACAGARQVEVTINGIGERA 321
P EFG+LI +K N P I V IS HC NDLGL+ AN++A AGARQVE TINGIGERA
Sbjct: 171 PEEFGELIKKLKENVPNI-KVPISVHCHNDLGLAVANSLAAVEAGARQVECTINGIGERA 229
Query: 322 GNASLEEVVMAFKCRGEHILGGLYTGINTRHIVMASKMVEE 362
GNA+LEEVVMA K R ++ G+ TGI+T + S++V
Sbjct: 230 GNAALEEVVMALKTRYDY--YGVETGIDTEELYETSRLVSR 268
>gnl|CDD|223197 COG0119, LeuA, Isopropylmalate/homocitrate/citramalate synthases
[Amino acid transport and metabolism].
Length = 409
Score = 455 bits (1172), Expect = e-156
Identities = 207/428 (48%), Positives = 277/428 (64%), Gaps = 25/428 (5%)
Query: 80 VRVFDTTLRDGEQSPGATLTSKEKLDIARQLAKLGVDIIEAGFPAASKEDFEAVRTIAKE 139
V +FDTTLRDGEQ+PG + + +EK+ IA+ L LGVD IEAGFP AS DFE VR IA++
Sbjct: 3 VIIFDTTLRDGEQAPGVSFSVEEKIRIAKALDDLGVDYIEAGFPVASPGDFEFVRAIAEK 62
Query: 140 VGNAVDAESGYVPVICGLSRCNERDIKTAWEAVKYAKRPRIHTFIATSGIHMEHKLRKTK 199
G IC L R IK EA+ A RIH FIATS +H+ +KL+KT+
Sbjct: 63 AGL----------FICALIAALARAIKRDIEALLEAGVDRIHIFIATSDLHLRYKLKKTR 112
Query: 200 QQVVEIARSMVKFARSLGCDDVEFSPEDAGRSDRKFLYEILGEVIKVGATTLNIPDTVGI 259
++V+E A V++AR G +V FS EDA R+D +FL E++ I+ GA +N+PDTVG+
Sbjct: 113 EEVLERAVDAVEYARDHG-LEVRFSAEDATRTDPEFLAEVVKAAIEAGADRINLPDTVGV 171
Query: 260 TMPTEFGKLIADIKANTPGIENVVISTHCQNDLGLSTANTIAGACAGARQVEVTINGIGE 319
P E +I +KAN P V++S HC NDLG++ AN++A AGA QVE T+NGIGE
Sbjct: 172 ATPNEVADIIEALKANVP--NKVILSVHCHNDLGMAVANSLAAVEAGADQVEGTVNGIGE 229
Query: 320 RAGNASLEEVVMAFKCRGEHILGGLYTGINTRHIVMASKMVEEYTGLHVQPHKAIVGANA 379
RAGNA+LEEVV+A R ++ G+ TGI+ + AS++VE TG+ V P+K IVG NA
Sbjct: 230 RAGNAALEEVVLALALRKDY---GVDTGIDLEKLTEASRLVERLTGIPVPPNKPIVGENA 286
Query: 380 FAHESGIHQDGMLKHKGTYEIISPEDIGLERSSEAGIVLGKLSGRHALKDRLKELGYELN 439
FAHESGIHQDG+LK+ TYE I PED+G R ++ GK SGR A+K +L+ELG EL+
Sbjct: 287 FAHESGIHQDGVLKNPETYEPIDPEDVGRRRRI---VIGGKHSGRKAVKAKLEELGIELD 343
Query: 440 DEQLGTIFWHFKAVAEQKKR--VTDADLIALVSDE--IFQPEVVWKLLDMQVTCGTLGLS 495
+E+L +F K +A++ K+ VTDADL ALV +E +P L + V G +
Sbjct: 344 EEELDKLFSRVKELADKGKKKEVTDADLEALVEEELGSREPFEKISLDVLTVQSG--NVP 401
Query: 496 TATVKLMD 503
TA+VKL
Sbjct: 402 TASVKLEV 409
>gnl|CDD|236493 PRK09389, PRK09389, (R)-citramalate synthase; Provisional.
Length = 488
Score = 457 bits (1179), Expect = e-156
Identities = 233/531 (43%), Positives = 314/531 (59%), Gaps = 51/531 (9%)
Query: 80 VRVFDTTLRDGEQSPGATLTSKEKLDIARQLAKLGVDIIEAGFPAASKEDFEAVRTIAKE 139
VR+ DTTLRDGEQ+PG +LT +EKL+IAR+L +LGVD+IEAG S+ + EA++ + E
Sbjct: 3 VRILDTTLRDGEQTPGVSLTPEEKLEIARKLDELGVDVIEAGSAITSEGEREAIKAVTDE 62
Query: 140 VGNAVDAESGYVPVICGLSRCNERDIKTAWEA-VKYAKRPRIHTFIATSGIHMEHKLRKT 198
++AE IC +R + DI A E V +H + TS +H+E+KL+KT
Sbjct: 63 ---GLNAE------ICSFARAVKVDIDAALECDVD-----SVHLVVPTSDLHIEYKLKKT 108
Query: 199 KQQVVEIARSMVKFARSLGCDDVEFSPEDAGRSDRKFLYEILGEVIKVGATTLNIPDTVG 258
+++V+E A V++A+ G VE S EDA R+D FL E+ I+ GA + DTVG
Sbjct: 109 REEVLETAVEAVEYAKDHGLI-VELSGEDASRADLDFLKELYKAGIEAGADRICFCDTVG 167
Query: 259 ITMPTEFGKLIADIKANTPGIENVVISTHCQNDLGLSTANTIAGACAGARQVEVTINGIG 318
I P + +L + +S HC ND GL+ ANT+A AGA QV VTINGIG
Sbjct: 168 ILTPEKTYELFKRLSELV----KGPVSIHCHNDFGLAVANTLAALAAGADQVHVTINGIG 223
Query: 319 ERAGNASLEEVVMAFKCRGEHILGGLYTGINTRHIVMASKMVEEYTGLHVQPHKAIVGAN 378
ERAGNASLEEVVMA K L + TGI + S++V TG+ V P+KAIVG N
Sbjct: 224 ERAGNASLEEVVMALK-----HLYDVETGIKLEELYELSRLVSRLTGIPVPPNKAIVGEN 278
Query: 379 AFAHESGIHQDGMLKHKGTYEIISPEDIGLERSSEAGIVLGKLSGRHALKDRLKELGYEL 438
AFAHESGIH DG+LK TYE I+PE +G ER IVLGK +GR ALK LKE+G E+
Sbjct: 279 AFAHESGIHVDGLLKDTETYEPITPETVGRERR----IVLGKHAGRAALKAALKEMGIEV 334
Query: 439 NDEQLGTIFWHFKAVAEQKKRVTDADLIALVSD--EIFQPEVVWKLLDMQVTCGTLGLST 496
+D+QL I K + ++ KRVTDADL+A+ D I + V KL ++ V G T
Sbjct: 335 SDDQLNEIVSRVKELGDRGKRVTDADLLAIAEDVLGIERERKV-KLDELTVVSGNKVTPT 393
Query: 497 ATVKLMDANGEEHVACSTGTGPVDSAYKAVDLIVKEPA--TLLEYSMNAVTAGIDAIATT 554
A+VKL + +GEE V TG GPVD+A AV + A L EY ++A+T G DA+
Sbjct: 394 ASVKL-NVDGEEIVEAGTGVGPVDAAINAVRKALSGVADIELEEYHVDAITGGTDALVEV 452
Query: 555 RV-LIRGEKSQLSTHASTGETVQRTFSGTGAGMDIVVSSVKAYIGALNKML 604
V L RG+ R + GA DI+++SV+A + +N++L
Sbjct: 453 EVKLSRGD---------------RVVTVRGADADIIMASVEAMMDGINRLL 488
>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: 76 DPNYVRVFDTTLRDGEQSPGATLTSKEKLDIARQLAKLGVDIIEAGFPAASKEDFEAVRT 135
P + + DTTLRDGEQ+PG T++EKL IAR L ++GVD IEAGFPA S+++ EA++
Sbjct: 1 KPKDIEIVDTTLRDGEQTPGVVFTNEEKLAIARMLDEIGVDQIEAGFPAVSEDEKEAIKA 60
Query: 136 IAKEVGNAVDAESGYVPVICGLSRCNERDIKTAWEA-VKYAKRPRIHTFIATSGIHMEHK 194
IAK NA I L+R + DI + + V +H FIATS IH++HK
Sbjct: 61 IAKLGLNAS---------ILALNRAVKSDIDASIDCGVD-----AVHIFIATSDIHIKHK 106
Query: 195 LRKTKQQVVEIARSMVKFARSLGCDDVEFSPEDAGRSDRKFLYEILGEVIKVGATTLNIP 254
L+KT+++V+E V++A+ G V FS EDA R+D FL E + GA +
Sbjct: 107 LKKTREEVLERMVEAVEYAKDHGLY-VSFSAEDASRTDLDFLIEFAKAAEEAGADRVRFC 165
Query: 255 DTVGITMPTEFGKLIADIKANTPGIENVVISTHCQNDLGLSTANTIAGACAGARQVEVTI 314
DTVGI P +L+ ++ ++ I HC ND G++TAN +AG AGA+QV T+
Sbjct: 166 DTVGILDPFTMYELVKELVEAV----DIPIEVHCHNDFGMATANALAGIEAGAKQVHTTV 221
Query: 315 NGIGERAGNASLEEVVMAFKCRGEHILGGLYTGINTRHIVMASKMVEEYTGLHVQPHKAI 374
NG+GERAGNA+LEEVVMA K L G+ GI+T + S++V + +G+ V P+KAI
Sbjct: 222 NGLGERAGNAALEEVVMALKY-----LYGIDLGIDTERLYELSRLVSKASGIPVPPNKAI 276
Query: 375 VGANAFAHESGIHQDGMLKHKGTYEIISPEDIGLERSSEAGIVLGKLSGRHALKDRLKEL 434
VG NAFAHESGIH DG+LK+ TYE PE++GLER IVLGK SGRHALK++LKE
Sbjct: 277 VGENAFAHESGIHVDGVLKNPLTYEPFLPEEVGLERR----IVLGKHSGRHALKNKLKEY 332
Query: 435 GYELNDEQLGTIFWHFKAVAEQKKR-VTDADLIALVSD 471
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: 80 VRVFDTTLRDGEQSPGATLTSKEKLDIARQLAKLGVDIIEAGFPAASKEDFEAVRTIAKE 139
V +FDTTLRDGEQ+PG +LT ++K++IAR+L +LGVD+IEAGFP AS+ +FEA++ I++E
Sbjct: 1 VYIFDTTLRDGEQTPGVSLTVEQKVEIARKLDELGVDVIEAGFPIASEGEFEAIKKISQE 60
Query: 140 VGNAVDAESGYVPVICGLSRCNERDIKTAWEAVKYAKRPRIHTFIATSGIHMEHKLRKTK 199
++AE IC L+R ++DI A + IHTFIATS IH+++KL+K++
Sbjct: 61 ---GLNAE------ICSLARALKKDIDKAID----CGVDSIHTFIATSPIHLKYKLKKSR 107
Query: 200 QQVVEIARSMVKFARSLGCDDVEFSPEDAGRSDRKFLYEILGEVIKVGATTLNIPDTVGI 259
+V+E A V++A+ G VEFS EDA R+D FL ++ + GA +NI DTVG+
Sbjct: 108 DEVLEKAVEAVEYAKEHGL-IVEFSAEDATRTDIDFLIKVFKRAEEAGADRINIADTVGV 166
Query: 260 TMPTEFGKLIADIKANTPGIENVVISTHCQNDLGLSTANTIAGACAGARQVEVTINGIGE 319
P + +LI +K N + IS HC ND GL+TAN+IAG AGA QV VT+NGIGE
Sbjct: 167 LTPQKMEELIKKLKENV----KLPISVHCHNDFGLATANSIAGVKAGAEQVHVTVNGIGE 222
Query: 320 RAGNASLEEVVMAFKCRGEHILGGLYTGINTRHIVMASKMVEEYTGLHVQPHKAIVGANA 379
RAGNA+LEEVVMA K L G+ T I T + S++V E +G+ V P+KAIVG NA
Sbjct: 223 RAGNAALEEVVMALK-----YLYGVKTKIKTEKLYETSRLVSELSGVKVPPNKAIVGENA 277
Query: 380 FAHESGIHQDGMLKHKGTYEIISPEDIGLERSSEAGIVLGKLSGRHALKDRLKELGYELN 439
FAHESGIH DG++++ TYE ISPE +G +R I+LGK SGRHA++ +LKELG ++
Sbjct: 278 FAHESGIHVDGVIENPLTYEPISPEVVGNKRR----IILGKHSGRHAVEAKLKELGIKVT 333
Query: 440 DEQLGTIFWHFKAVAEQKKRVTDADLIALV 469
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 = 305 bits (783), Expect = 1e-98
Identities = 155/392 (39%), Positives = 208/392 (53%), Gaps = 30/392 (7%)
Query: 80 VRVFDTTLRDGEQSPGATLTSKEKLDIARQLAKLGVDIIEAGFPAASKEDFEAVRTIAKE 139
V + DTTLRDGEQ+PG T+ EKL IAR L + GVD +E G PA +E+ +R I
Sbjct: 2 VIINDTTLRDGEQAPGVAFTAAEKLAIARALDEAGVDELEVGIPAMGEEERAVIRAIVAL 61
Query: 140 VGNAVDAESGYVPVICGLSRCNERDIKTAWEA-VKYAKRPRIHTFIATSGIHMEHKLRKT 198
A + R + DI+ A V +H I S + +E KLRK
Sbjct: 62 GLPAR---------LMAWCRARDADIEAAARCGVD-----AVHISIPVSDLQIEAKLRKD 107
Query: 199 KQQVVEIARSMVKFARSLGCDDVEFSPEDAGRSDRKFLYEILGEVIKVGATTLNIPDTVG 258
+ V+E +V FAR G V EDA R+D FL E+ + GA DTVG
Sbjct: 108 RAWVLERLARLVSFARDRG-LFVSVGGEDASRADPDFLVELAEVAAEAGADRFRFADTVG 166
Query: 259 ITMPTEFGKLIADIKANTPGIENVVISTHCQNDLGLSTANTIAGACAGARQVEVTINGIG 318
I P +L+ ++ + H NDLG++TANT+A AGA V T+NG+G
Sbjct: 167 ILDPFSTYELVRALRQAVDL----PLEMHAHNDLGMATANTLAAVRAGATHVNTTVNGLG 222
Query: 319 ERAGNASLEEVVMAFKCRGEHILGGLYTGINTRHIVMASKMVEEYTGLHVQPHKAIVGAN 378
ERAGNA+LEEV MA K L G TGI+T + S++V +G + P K +VG +
Sbjct: 223 ERAGNAALEEVAMALK-----RLLGRDTGIDTSRLPALSQLVARASGRPIPPQKPVVGES 277
Query: 379 AFAHESGIHQDGMLKHKGTYEIISPEDIGLERSSEAGIVLGKLSGRHALKDRLKELGYEL 438
F HESGIH DG+LK TYE PE +G R IV+GK SGR AL + L +LG L
Sbjct: 278 VFTHESGIHVDGLLKDPRTYEPFDPELVGRSRR----IVIGKHSGRAALINALAQLGIPL 333
Query: 439 NDEQLGTIFWHFKAVAEQKKR-VTDADLIALV 469
++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 = 272 bits (698), Expect = 9e-88
Identities = 117/249 (46%), Positives = 154/249 (61%), Gaps = 13/249 (5%)
Query: 89 DGEQSPGATLTSKEKLDIARQLAKLGVDIIEAGFPAASKEDFEAVRTIAKEVGNAVDAES 148
DGEQ+ GA + +EKL IAR L + GVD IE GFP S DFE+VR IA+ + A
Sbjct: 1 DGEQALGAAFSVEEKLAIARALDEAGVDEIEVGFPFMSPTDFESVRAIAEVLKKAK---- 56
Query: 149 GYVPVICGLSRCNERDIKTAWEAVKYAKRPRIHTFIATSGIHMEHKLRKTKQQVVEIARS 208
I L R E DI A EA K A R+H FIATS +H ++KL K +++V + A +
Sbjct: 57 -----IQALLRPVEHDIDAAVEAAKGAGADRVHVFIATSDLHRKYKLNKDREEVADRAVA 111
Query: 209 MVKFARSLGCDDVEFSPEDAGRSDRKFLYEILGEVIKVGATTLNIPDTVGITMPTEFGKL 268
V+ ARS G D VE EDAGR+D FL E++ + GAT +NI DTVG+ P E L
Sbjct: 112 AVEAARSAGID-VELGCEDAGRTDLAFLIEVVEVAQEAGATRINIADTVGVLTPNEAADL 170
Query: 269 IADIKANTPGIENVVISTHCQNDLGLSTANTIAGACAGARQVEVTINGIGERAGNASLEE 328
I+ +K P V+I HC NDLG++ AN++A AGA +V+ T+NG+GERAGNA+LEE
Sbjct: 171 ISALKDRVP---PVIIEVHCHNDLGMAVANSLAAVEAGADRVDGTVNGLGERAGNAALEE 227
Query: 329 VVMAFKCRG 337
+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 = 271 bits (696), Expect = 5e-87
Identities = 98/288 (34%), Positives = 155/288 (53%), Gaps = 31/288 (10%)
Query: 83 FDTTLRDGEQSPGATLTSKEKLDIARQLAKLGVDIIEAGFPAASKE------DFEAVRTI 136
DTTLRDG QS GAT ++++KL+IA L + GVD IE G A+ K D+E +R I
Sbjct: 1 TDTTLRDGLQSEGATFSTEDKLEIAEALDEAGVDSIEVGSGASPKAVPQMEDDWEVLRAI 60
Query: 137 AKEVGNAVDAESGYVPVICGLSRCNERDIKTAWEAVKYAKRPRIHTFIATSGIHMEHKLR 196
K V N + L R E+ I+ A EA + F + S H L
Sbjct: 61 RKLVPNVK---------LQALVRNREKGIERALEAG----VDEVRIFDSASETHSRKNLN 107
Query: 197 KTKQQVVEIARSMVKFARSLGCDDVEFSPEDAGR--SDRKFLYEILGEVIKVGATTLNIP 254
K++++ +E A ++ A+ G +VE S EDA +D +++ E+ + + GA +++
Sbjct: 108 KSREEDLENAEEAIEAAKEAG-LEVEGSLEDAFGCKTDPEYVLEVAKALEEAGADEISLK 166
Query: 255 DTVGITMPTEFGKLIADIKANTPGIENVVISTHCQNDLGLSTANTIAGACAGARQVEVTI 314
DTVG+ P E +L+ ++ P + + H N LGL+ AN++A AGA +V+ ++
Sbjct: 167 DTVGLATPEEVAELVKALREALPDVP---LGLHTHNTLGLAVANSLAALEAGADRVDGSV 223
Query: 315 NGIGERAGNASLEEVVMAFKCRGEHILGGLYTGINTRHIVMASKMVEE 362
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 = 229 bits (586), Expect = 6e-71
Identities = 115/279 (41%), Positives = 148/279 (53%), Gaps = 23/279 (8%)
Query: 84 DTTLRDGEQSPGATLTSKEKLDIARQLAKLGVDIIEAGFPAASKEDFEAVRTIAKEVGNA 143
DTTLRDGEQ+PG + +EKL IAR L + GVD IE G PA +E+ EA+R I
Sbjct: 3 DTTLRDGEQAPGVAFSREEKLAIARALDEAGVDEIEVGIPAMGEEEREAIRAIVALG--- 59
Query: 144 VDAESGYVPVICGLSRCNERDIKTAWEAVKYAKRPRIHTFIATSGIHMEHKLRKTKQQVV 203
+ A + R + DI EA +H I S IH+ HKL K + V+
Sbjct: 60 LPAR------LIVWCRAVKEDI----EAALRCGVTAVHISIPVSDIHLAHKLGKDRAWVL 109
Query: 204 EIARSMVKFARSLGCDDVEFSPEDAGRSDRKFLYEILGEVIKVGATTLNIPDTVGITMPT 263
+ R +V A+ G V EDA R+D FL E + GA L DTVGI P
Sbjct: 110 DQLRRLVGRAKDRGLF-VSVGAEDASRADPDFLIEFAEVAQEAGADRLRFADTVGILDPF 168
Query: 264 EFGKLIADIKANTPGIENVVISTHCQNDLGLSTANTIAGACAGARQVEVTINGIGERAGN 323
+LI ++A T + + H NDLGL+TANT+A AGA V VT+NG+GERAGN
Sbjct: 169 TTYELIRRLRAATD-LP---LEFHAHNDLGLATANTLAAVRAGATHVSVTVNGLGERAGN 224
Query: 324 ASLEEVVMAFKCRGEHILGGLYTGINTRHIVMASKMVEE 362
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 (519), Expect = 5e-58
Identities = 155/537 (28%), Positives = 248/537 (46%), Gaps = 108/537 (20%)
Query: 75 PDPNYVRVFDTTLRDGEQSPGATLTSKEKLDIARQLAKLGVDIIEAGFPAASKED---FE 131
+ ++DTTLRDG Q G + + ++KL IAR+L +LGVD IE G+P ++ +D F+
Sbjct: 1 MMMERIELYDTTLRDGAQGEGISFSVEDKLRIARKLDELGVDYIEGGWPGSNPKDTEFFK 60
Query: 132 AVRTI----AKEV--------GNAVDA--------ESGYVPVICGLSRCNERDIKTAWEA 171
+ + AK G + + ++G PV+ I
Sbjct: 61 RAKELKLKHAKLAAFGSTRRAGVSAEEDPNLQALLDAG-TPVVT---------I------ 104
Query: 172 VKYAKRPRIHTFIATSGIHMEHKLRKTKQQVVEIARSMVKFARSLGCDDVEFSPE---DA 228
+ K + +H+ LR T ++ + + R V + ++ G +V F E D
Sbjct: 105 --FGK---------SWDLHVTEALRTTLEENLAMIRDSVAYLKAHG-REVIFDAEHFFDG 152
Query: 229 GRSDRKFLYEILGEVIKVGATTLNIPDTVGITMPTEFGKLIADIKANTP---GIENVVIS 285
+++ ++ L + GA + + DT G T+P E +++A+++A GI
Sbjct: 153 YKANPEYALATLKAAAEAGADWVVLCDTNGGTLPHEVAEIVAEVRAAPGVPLGI------ 206
Query: 286 THCQNDLGLSTANTIAGACAGARQVEVTINGIGERAGNASLEEVV------MAFKCRGEH 339
H ND G + AN++A AGARQV+ TING GER GNA+L ++ M ++C E
Sbjct: 207 -HAHNDSGCAVANSLAAVEAGARQVQGTINGYGERCGNANLCSIIPNLQLKMGYECLPEE 265
Query: 340 ILGGLYTGINTRHIVMASKMVEEYTGLHVQPHKAIVGANAFAHESGIHQDGMLKHKGTYE 399
L L T S+ V E L PH+ VGA+AFAH+ GIH +LK TYE
Sbjct: 266 KLKEL-----TE----VSRFVSEIANLAPDPHQPYVGASAFAHKGGIHVSAVLKDPRTYE 316
Query: 400 IISPEDIGLERSSEAGIVLGKLSGRHALKDRLKELGYEL--NDEQLGTIFWHFKAVAEQK 457
I PE +G R +++ +L+GR + + KELG +L +D +L + + K
Sbjct: 317 HIDPELVGNRRR----VLVSELAGRSNILAKAKELGIDLDKDDPRLKRL------LERIK 366
Query: 458 KR--------VTDADLIALVSDEIFQPEVVWKLLDMQVTC--GTLGLSTATVKLMDANGE 507
+ +A L+ E+ + ++L +V G+S ATVK+ GE
Sbjct: 367 ELEAEGYQFEAAEASFELLLRRELGEYPPFFELESFRVIVEKRGDGVSEATVKVR-VGGE 425
Query: 508 EHVACSTGTGPV---DSA-YKAVDLIVKEPAT--LLEYSMNAVTAGIDAIATTRVLI 558
+ 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 (481), Expect = 1e-54
Identities = 115/361 (31%), Positives = 175/361 (48%), Gaps = 29/361 (8%)
Query: 84 DTTLRDGEQSPGATLTSKEKLDIARQLAKLGVDIIEAGFPAASKEDFEAVRTIAKEVGNA 143
D+TLR+GEQ PGA ++++K++IA+ L + G+D IE PAASK+ + IA
Sbjct: 3 DSTLREGEQFPGANFSTEQKIEIAKALDEFGIDYIEVTHPAASKQSRIDIEIIAS----- 57
Query: 144 VDAESGYVPVICGLSRCNERDIKTAWEA-VKYAKRPRIHTFIATSGIHMEHKLRKTKQQV 202
G I RC D K A E V I F TS + + R + +
Sbjct: 58 ----LGLKANIVTHIRCRLDDAKVAVELGVDG-----IDIFFGTSKLLRIAEHRSDAKSI 108
Query: 203 VEIARSMVKFARSLGCDDVEFSPEDAGRSDRKFLYEILGEVIKVGATTLNIPDTVGITMP 262
+E AR +++A+S G +V FS ED RS+ L I V G + I DTVG P
Sbjct: 109 LESARETIEYAKSAGL-EVRFSAEDTFRSELADLLSIYETVGVFGVDRVGIADTVGKAAP 167
Query: 263 TEFGKLIADIKANTPGIENVVISTHCQNDLGLSTANTIAGACAGARQVEVTINGIGERAG 322
+ +LI + PG++ H ND G + AN GA V+ T+ GIGER G
Sbjct: 168 RQVYELIRTVVRVVPGVDI---ELHAHNDTGCAVANAYNAIEGGATIVDTTVLGIGERNG 224
Query: 323 NASLEEVVMAFKCRGEHILGGLYTGINTRHIVMASKMVEEYTGLHVQPHKAIVGANAFAH 382
L ++ +Y ++ ++MV G+ + + I G AF H
Sbjct: 225 ITPLGGILARLY-----YHTPMYV-YKLGKLIELTRMVAGEVGVTIPFNNPITGELAFTH 278
Query: 383 ESGIHQDGMLKHKGTYEIISPEDIGLERSSEAGIVLGKLSGRHALKDRLKELGYELNDEQ 442
++GIH +L + TYE + PE G +R I++ +L+G+HA+K R ++LG +L +E+
Sbjct: 279 KAGIHVKAILGNPRTYEFLPPEVFGRKRH----ILIARLTGKHAIKARKEKLGVKLIEEE 334
Query: 443 L 443
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 = 181 bits (461), Expect = 4e-50
Identities = 127/508 (25%), Positives = 233/508 (45%), Gaps = 55/508 (10%)
Query: 80 VRVFDTTLRDGEQSPGATLTSKEKLDIARQLAKLGVDIIEAGFPAASKED---FEAVRTI 136
+ ++DTTLRDG Q G + + ++K+ IA +L LG+ IE G+P A+ +D F ++
Sbjct: 2 LWLYDTTLRDGAQREGVSFSLEDKIRIAERLDDLGIHYIEGGWPGANPKDVQFFWQLK-- 59
Query: 137 AKEVGNAVDAESGYVPVICGLSRCNER-DIKTAWEAVKYAKRPRIHTFIATSGIHMEHKL 195
++ ++ + C R +++ + +A+ A+ P + F + +H+ L
Sbjct: 60 ------EMNFKNAKIVAFCSTRRPHKKVEEDKMLQALIKAETPVVTIFGKSWDLHVLEAL 113
Query: 196 RKTKQQVVEIARSMVKFARSLGCDDVEFSPE---DAGRSDRKFLYEILGEVIKVGATTLN 252
+ T ++ + + V + + G D+V + E D +++ ++ L + GA L
Sbjct: 114 QTTLEENLAMIYDTVAYLKRQG-DEVIYDAEHFFDGYKANPEYALATLATAQQAGADWLV 172
Query: 253 IPDTVGITMPTEFGKLIADIKANTPGIENVVISTHCQNDLGLSTANTIAGACAGARQVEV 312
+ DT G T+P E ++ +K + ++ + H ND G + AN++ AGA V+
Sbjct: 173 LCDTNGGTLPHEISEITTKVKRS---LKQPQLGIHAHNDSGTAVANSLLAVEAGATMVQG 229
Query: 313 TINGIGERAGNASLEEVV------MAFKCRGEHILGGLYTGINTRHIVMASKMVEEYTGL 366
TING GER GNA+L ++ + + N + + +++V E L
Sbjct: 230 TINGYGERCGNANLCSLIPNLQLKLGYDVIPPE---------NLKKLTSTARLVAEIVNL 280
Query: 367 HVQPHKAIVGANAFAHESGIHQDGMLKHKGTYEIISPEDIGLERSSEAGIVLGKLSGRHA 426
+ VG +AFAH+ G+H + ++ TYE I+PE +G ER IV+ +L+G
Sbjct: 281 PPDDNMPYVGRSAFAHKGGVHVSAVQRNPFTYEHIAPELVGNERR----IVVSELAGLSN 336
Query: 427 LKDRLKELGYELNDE--QLGTIFWHFKAVAEQ--KKRVTDADLIALVSDEIFQPEVVWKL 482
+ + KE G E++ + TI K + +Q +A L+ + + +
Sbjct: 337 VLSKAKEFGIEIDRQSPACRTILAKIKELEQQGYHFEAAEASFELLMRQAMGDRKPYFLF 396
Query: 483 LDMQVTC------GTLGLSTATVKLMDANGEEHVACSTGTGPVDSAYKAVDLIVKE---- 532
QV C + + ATV++ EH A + G GPV + +A+ ++
Sbjct: 397 QGFQVHCDKLRDAESYRNALATVRVTVEGQNEHTA-AEGNGPVSALDRALRKALERFYPQ 455
Query: 533 --PATLLEYSMNAVTAGIDAIATTRVLI 558
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 = 146 bits (372), Expect = 9e-42
Identities = 61/146 (41%), Positives = 83/146 (56%), Gaps = 15/146 (10%)
Query: 459 RVTDADLIALVSDEIFQPEVVWKLLDMQVTCGTLGLSTATVKLMDANGEEHVACSTGTGP 518
VTD DL AL SDE + E +KL +QV G+ G+ TATVKL + +GEE +TG GP
Sbjct: 1 EVTDEDLEALFSDEYGEAEERFKLESLQVQSGSNGIPTATVKL-EVDGEEKEEAATGNGP 59
Query: 519 VDSAYKAVDLIVKEPATLLEYSMNAVTAGIDAIATTRVLIRGEKSQLSTHASTGETVQRT 578
VD+ Y A+ I+ LL+YS++A+T G DA+A V + + R
Sbjct: 60 VDALYNALRKILGVDIKLLDYSVHAITGGTDALAEVYVELEYDG--------------RI 105
Query: 579 FSGTGAGMDIVVSSVKAYIGALNKML 604
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: 84 DTTLRDGEQSPGATLTSKEKLDIARQL-AKLGVDIIEAGFPAASKEDFEAVRTI---AKE 139
DTTLRDGEQ+ G + + EKL+IA+ L +L VD IE S+ +FEAV+ I A E
Sbjct: 2 DTTLRDGEQTSGVSFSPSEKLNIAKILLQELKVDRIEVASARVSEGEFEAVQKIIDWAAE 61
Query: 140 VGNAVDAES-GYVPVICGLSRCNERDIKTAWEAVKYAKRPRIHTFIATSGIHMEHKLRKT 198
G E G+V + D W +K A ++ S H +LRKT
Sbjct: 62 EGLLDRIEVLGFV----------DGDKSVDW--IKSAGAKVLNLLTKGSLKHCTEQLRKT 109
Query: 199 KQQVVEIARSMVKFARSLGCDDVEFSPEDAG---RSDRKFLYEILGEVIKVGATTLNIPD 255
++ R ++++A G + V ED R ++++++ + + + +PD
Sbjct: 110 PEEHFADIREVIEYAIKNGIE-VNIYLEDWSNGMRDSPDYVFQLVDFLSDLPIKRIMLPD 168
Query: 256 TVGITMPTEFGKLIADIKANTPGIENVVISTHCQNDLGLSTANTIAGACAGARQVEVTIN 315
T+GI P E I+D+ P N+ H ND L+ AN +A AG + + T+N
Sbjct: 169 TLGILSPFETYTYISDMVKRYP---NLHFDFHAHNDYDLAVANVLAAVKAGIKGLHTTVN 225
Query: 316 GIGERAGNASLEEVVMAFKCRGEHILGGLYTGINTRHIVMASKMVEEYTGLHVQPHKAIV 375
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 = 148/606 (24%), Positives = 235/606 (38%), Gaps = 112/606 (18%)
Query: 55 PPSLYPRITATRPEYIPNRIPDPNYVRVFDTTLRDGEQSPGATLTSKEKLDIARQLAKLG 114
P L R T P+ + R P R T LRDG Q+ ++ K L ++G
Sbjct: 10 PIRLRNR---TWPDRVITRAP-----RWLSTDLRDGNQALPDPMSPARKRRYFDLLVRIG 61
Query: 115 VDIIEAGFPAASKEDFEAVRTIAKEVGNAVDAESGYVP---VICGLSRCNERDIKTAWEA 171
IE GFP+AS+ DF+ VR I E G +P I L++ E I+ +EA
Sbjct: 62 FKEIEVGFPSASQTDFDFVREII---------EQGAIPDDVTIQVLTQSREELIERTFEA 112
Query: 172 VKYAKRPRIHTFIATSGIHMEHKLRKTKQQVVEIARSMVKFARSLGCDDV---------E 222
+ AKR +H + ATS + E R ++ +V IA K R E
Sbjct: 113 LSGAKRATVHFYNATSILFREVVFRASRAEVQAIATDGTKLVRKCTKQAAKYPGTQWRFE 172
Query: 223 FSPEDAGRSDRKFLYEILGEVIKVGATT------LNIPDTVGITMPTEFGKLIADIKANT 276
+SPE ++ +F E+ V +V A T N+P TV +T P + I N
Sbjct: 173 YSPESFSDTELEFAKEVCEAVKEVWAPTPERPIIFNLPATVEMTTPNVYADSIEYFSTNI 232
Query: 277 PGIENVVISTHCQNDLGLSTANTIAGACAGARQVEVTINGIGERAGNASLEEVVMAFKCR 336
E V +S H ND G + A G AGA ++E + G GER GN L + + +
Sbjct: 233 AEREKVCLSLHPHNDRGTAVAAAELGFLAGADRIEGCLFGNGERTGNVDLVTLALNLYTQ 292
Query: 337 GEHILGGLYTGINTRHIVMASKMVEEYTGLHVQPHKAIVGANAFAHESGIHQDGMLKH-- 394
G+ ++ ++ + VE + V G + SG HQD + K
Sbjct: 293 ------GVSPNLDFSNLDEIRRTVEYCNKIPVHERHPYGGDLVYTAFSGSHQDAINKGLD 346
Query: 395 -------------KGTYEIISPEDIGLERSSEAGIVLGKLSGR----------------- 424
+ Y + P D+G R+ EA I + SG+
Sbjct: 347 AMKLDAAAADMLWQVPYLPLDPRDVG--RTYEAVIRVNSQSGKGGVAYIMKTDHGLDLPR 404
Query: 425 -------HALKDRLKELGYELNDEQLGTIFWH-FKAVAEQKKRVTDADLIALVSDEIFQP 476
++D G EL+ +++ +F + A E +R++ D+
Sbjct: 405 RLQIEFSSVVQDIADGEGGELSPKEISDLFAEEYLAPVEPLERISQHVYA--ADDDGTGT 462
Query: 477 EVVWKLLDMQVTCGTLGLSTATVKLMDANGEEHVACSTGTGPVDSAYKAVDLIVKEPATL 536
+ TATVK+ NG E +G GP+ + A+ + +
Sbjct: 463 TSI----------------TATVKI---NGVETDIEGSGNGPLSALVDALADVGNFDFAV 503
Query: 537 LEYSMNAVTAGIDAIATTRVLIRGEKSQLSTHASTGETVQRTFSGTGAGMDIVVSSVKAY 596
L+Y +A+ +G DA A + V + T G G D+ +S++A
Sbjct: 504 LDYYEHAMGSGDDAQAASYVEA--------SVTIASPAQPGTVWGVGIAPDVTTASLRAV 555
Query: 597 IGALNK 602
+ A+N+
Sbjct: 556 VSAVNR 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 (351), Expect = 3e-37
Identities = 80/248 (32%), Positives = 118/248 (47%), Gaps = 18/248 (7%)
Query: 80 VRVFDTTLRDGEQSPGATLTSKEKLDIARQLAKLGVDIIEAGFPAASKEDFEAVRTIAKE 139
++ D+TLR+GEQ A +++K++IA+ L GVD IE PAAS + IAK
Sbjct: 1 FKIIDSTLREGEQFANAFFDTEDKIEIAKALDAFGVDYIELTSPAASPQSRADCEAIAK- 59
Query: 140 VGNAVDAESGYVPVICGLSRCNERDIKTAWEAVKYAKRPRIHTFIATSGIHMEHKLRKTK 199
G I RC+ D + A E + TS E K+
Sbjct: 60 --------LGLKAKILTHIRCHMDDARIAVETGVDG----VDLVFGTSPFLREASHGKSI 107
Query: 200 QQVVEIARSMVKFARSLGCDDVEFSPEDAGRSDRKFLYEILGEVIKVGATTLNIPDTVGI 259
+++E A +++F +S G +V FS ED+ RSD L + V K+G + I DTVGI
Sbjct: 108 TEIIESAVEVIEFVKSKGI-EVRFSSEDSFRSDLVDLLRVYRAVDKLGVNRVGIADTVGI 166
Query: 260 TMPTEFGKLIADIKANTPGIENVVISTHCQNDLGLSTANTIAGACAGARQVEVTINGIGE 319
P + +L+ ++ G+ + I H ND G + AN A AGA ++ T+ GIGE
Sbjct: 167 ATPRQVYELVRTLR----GVVSCDIEFHGHNDTGCAIANAYAALEAGATHIDTTVLGIGE 222
Query: 320 RAGNASLE 327
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: 85 TTLRDGEQSPGATLTSKEKLDIARQLAKLGVDIIEAGFPAASKEDFEAVRTIAKEVGNAV 144
LRDG Q+ ++ ++KL + L K+G IE GFP+AS+ DF+ VR +
Sbjct: 7 VDLRDGNQALAEPMSVEQKLRFFKLLVKIGFKEIEVGFPSASQTDFDFVREL-------- 58
Query: 145 DAESGYVP---VICGLSRCNERDIKTAWEAVKYAKRPRIHTFIATSGIHMEHKLRKTKQQ 201
E +P I L++ E I+ +EA++ AK+ +H + ATS + K+K++
Sbjct: 59 -IEEDLIPDDVTIQVLTQAREDLIERTFEALRGAKKAIVHLYNATSPLQRRVVFGKSKEE 117
Query: 202 VVEIARSMVKFARSLGCDDV------EFSPEDAGRSDRKFLYEILGEVIKVGATT----- 250
++EIA K + L E+SPE ++ F E+ VI V T
Sbjct: 118 IIEIAVDGAKLVKELAAKYPETDWRFEYSPESFSDTELDFALEVCEAVIDVWQPTPENKI 177
Query: 251 -LNIPDTVGITMPTEFGKLIADIKANTPGIENVVISTHCQNDLGLSTANTIAGACAGARQ 309
LN+P TV + P + I N E+V+IS H ND G A AGA +
Sbjct: 178 ILNLPATVEVATPNVYADQIEWFCRNLSRRESVIISLHPHNDRGTGVAAAELALLAGADR 237
Query: 310 VEVTINGIGERAGNASLEEVVMAFKCRG 337
VE T+ G GER GN L + + +G
Sbjct: 238 VEGTLFGNGERTGNVDLVTLALNLYSQG 265
>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 (332), Expect = 2e-34
Identities = 82/271 (30%), Positives = 130/271 (47%), Gaps = 57/271 (21%)
Query: 82 VFDTTLRDGEQSPGATLTSKEKLDIARQLAKLGVDIIEAGFPAASKED---FEAVRTI-- 136
++DTTLRDG Q G + + ++KL IAR+L +LGVD IE G+P ++ +D F + +
Sbjct: 1 IYDTTLRDGTQGEGISFSVEDKLRIARKLDELGVDYIEGGWPGSNPKDTEFFARAKKLKL 60
Query: 137 --AKEV--------GNAVD--------AESGYVPVICGLSRCNERDIKTAWEAVKYAKRP 178
AK G + E+G PV+ I + K
Sbjct: 61 KHAKLAAFGSTRRAGVKAEEDPNLQALLEAG-TPVVT---------I--------FGK-- 100
Query: 179 RIHTFIATSGIHMEHKLRKTKQQVVEIARSMVKFARSLGCDDVEFSPE---DAGRSDRKF 235
+ +H+ L T ++ + + R V + +S G +V F E D +++ ++
Sbjct: 101 -------SWDLHVTEALGTTLEENLAMIRDSVAYLKSHG-REVIFDAEHFFDGYKANPEY 152
Query: 236 LYEILGEVIKVGATTLNIPDTVGITMPTEFGKLIADIKANTPGIENVVISTHCQNDLGLS 295
L + GA L + DT G T+P E +++ +++ PG V + H ND GL+
Sbjct: 153 ALATLKAAAEAGADWLVLCDTNGGTLPHEIAEIVKEVRERLPG---VPLGIHAHNDSGLA 209
Query: 296 TANTIAGACAGARQVEVTINGIGERAGNASL 326
AN++A AGA QV+ TING GER GNA+L
Sbjct: 210 VANSLAAVEAGATQVQGTINGYGERCGNANL 240
>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 = 126 bits (319), Expect = 2e-34
Identities = 55/145 (37%), Positives = 79/145 (54%), Gaps = 16/145 (11%)
Query: 460 VTDADLIALVSDEIFQPEV-VWKLLDMQVTCGTLGLSTATVKLMDANGEEHVACSTGTGP 518
VTD DL AL DE + E ++L ++V+ G+ G+ TATVKL +GEE +TG GP
Sbjct: 2 VTDEDLEALFEDEYGEAEPERFELESLRVSSGSGGVPTATVKL-KVDGEEVTEAATGNGP 60
Query: 519 VDSAYKAVDLIVKEPATLLEYSMNAVTAGIDAIATTRVLIRGEKSQLSTHASTGETVQRT 578
VD+ + A+ I+ LL+YS++A+T G DA+A V + G R
Sbjct: 61 VDALFNALRKILGSDVELLDYSVHALTGGTDALAEVYVELE----------YGG----RI 106
Query: 579 FSGTGAGMDIVVSSVKAYIGALNKM 603
G G DIV +S KA + ALN++
Sbjct: 107 VWGVGIDTDIVEASAKALVSALNRL 131
>gnl|CDD|235154 PRK03739, PRK03739, 2-isopropylmalate synthase; Validated.
Length = 552
Score = 131 bits (333), Expect = 1e-32
Identities = 159/567 (28%), Positives = 239/567 (42%), Gaps = 98/567 (17%)
Query: 85 TTLRDGEQS---PGATLTSKEKLDIARQLAKLGVDIIEAGFPAASKEDFEAVRTIAKEVG 141
LRDG Q+ P ++ + KL + L K+G IE GFP+AS+ DF+ VR +
Sbjct: 36 VDLRDGNQALIEP---MSPERKLRMFDLLVKIGFKEIEVGFPSASQTDFDFVREL----- 87
Query: 142 NAVDAESGYVP---VICGLSRCNERDIKTAWEAVKYAKRPRIHTFIATSGIHMEHKLRKT 198
E G +P I L++ E I+ +EA++ AKR +H + +TS + K
Sbjct: 88 ----IEEGLIPDDVTIQVLTQAREHLIERTFEALEGAKRAIVHLYNSTSPLQRRVVFGKD 143
Query: 199 KQQVVEIA----RSMVKFARSLGCDDV--EFSPEDAGRSDRKFLYEILGEVIKV-GATT- 250
+ + IA R + + A + E+SPE ++ F E+ VI V T
Sbjct: 144 RDGIKAIAVDGARLVKELAAKYPETEWRFEYSPESFTGTELDFALEVCDAVIDVWQPTPE 203
Query: 251 ----LNIPDTVGITMPTEFGKLIAD----IKANTPGIENVVISTHCQNDLGLSTANTIAG 302
LN+P TV ++ P + AD + N ++V++S H ND G A
Sbjct: 204 RKVILNLPATVEMSTPNVY----ADQIEWMCRNLARRDSVILSLHPHNDRGTGVAAAELA 259
Query: 303 ACAGARQVEVTINGIGERAGNASLEEVVMAFKCRGEHILGGLYT-GI-------NTRHIV 354
AGA +VE + G GER GN L V +A LYT G+ + I
Sbjct: 260 LMAGADRVEGCLFGNGERTGNVDL--VTLALN---------LYTQGVDPGLDFSDIDEIR 308
Query: 355 MASKMVEEYTGLHVQPHKAIVGANAFAHESGIHQD----GMLKHKGTYEI-------ISP 403
+ VE L V P G F SG HQD G K + I P
Sbjct: 309 ---RTVEYCNQLPVHPRHPYAGDLVFTAFSGSHQDAIKKGFAAQKADAIVWEVPYLPIDP 365
Query: 404 EDIGLERSSEAGIVLGKLSGR----HALKDRLKELGYELNDEQLGTIF-WHFKAVAEQKK 458
D+G RS EA I + SG+ + L+ ++ G +L +L F +AV + +
Sbjct: 366 ADVG--RSYEAVIRVNSQSGKGGVAYLLE---QDYGLDL-PRRLQIEFSRVVQAVTDAEG 419
Query: 459 R-VTDADLIALVSDEIFQPEVVWKLLDMQVTCGTLGLSTATVKLMDANGEEHVACSTGTG 517
++ ++ L E P LL + G T T ++ D NGEE G G
Sbjct: 420 GELSAEEIWDLFEREYLAPRGRPVLLRVHRLSEEDGTRTITAEV-DVNGEERTIEGEGNG 478
Query: 518 PVDSAYKAVDLIVKEPATLLEYSMNAVTAGIDAIATTRVLIRGEKSQLSTHASTGETVQR 577
P+D+ A+ + +L+Y +A+ AG DA A V +R R
Sbjct: 479 PIDAFVNALSQALGVDVRVLDYEEHALGAGSDAQAAAYVELRVG--------------GR 524
Query: 578 TFSGTGAGMDIVVSSVKAYIGALNKML 604
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 = 3e-18
Identities = 71/271 (26%), Positives = 119/271 (43%), Gaps = 41/271 (15%)
Query: 84 DTTLRDGEQSPGATLTSKEKLDIARQLAKLG--VDIIEAG-FPAASKEDFEAVRTIAKEV 140
DTT RDG+Q+ T ++ + I L +LG +I F +++D EAV
Sbjct: 5 DTTFRDGQQARPP-YTVEQIVKIYDYLHELGGGSGVIRQTEFFLYTEKDREAVEACL--- 60
Query: 141 GNAVDAESGY-VPVICGLSRCNERDIKTAWEAVKYAKRPRIHTFIATSGIHMEHKLRKTK 199
+ GY P + G R N+ D+K VK ++ S H+ KL+ T+
Sbjct: 61 ------DRGYKFPEVTGWIRANKEDLKL----VKEMGLKETGILMSVSDYHIFKKLKMTR 110
Query: 200 QQVVEIARSMVKFARSLG----CDDVEFSPEDAGRSD-RKFLYEILGEVIKV-----GAT 249
++ +E +V+ A G C ED R+D F+ + +++K+
Sbjct: 111 EEAMEKYLEIVEEALDHGIKPRC-----HLEDITRADIYGFVLPFVNKLMKLSKESGIPV 165
Query: 250 TLNIPDTVG-------ITMPTEFGKLIADIKANTPGIENVVISTHCQNDLGLSTANTIAG 302
+ + DT+G ++P K+I ++ G+ + + H ND + AN +A
Sbjct: 166 KIRLCDTLGYGVPYPGASLPRSVPKIIYGLR-KDCGVPSENLEWHGHNDFYKAVANAVAA 224
Query: 303 ACAGARQVEVTINGIGERAGNASLEEVVMAF 333
GA V T+ GIGER GN LE +V+ +
Sbjct: 225 WLYGASWVNCTLLGIGERTGNCPLEAMVIEY 255
>gnl|CDD|184849 PRK14847, PRK14847, hypothetical protein; Provisional.
Length = 333
Score = 85.4 bits (211), Expect = 4e-18
Identities = 76/314 (24%), Positives = 133/314 (42%), Gaps = 29/314 (9%)
Query: 71 PNRIPDPNYVRVFDTTLRDGEQSPGATLTSKEKLDIARQLAKLGVDIIEAGFPAASKEDF 130
P R P + + T LRDG Q+ + KL + QL +G+ IE FP+AS+ DF
Sbjct: 25 PARRPAAAPIWM-STDLRDGNQALIEPMDGARKLRLFEQLVAVGLKEIEVAFPSASQTDF 83
Query: 131 EAVRTIAKE--VGNAVDAESGYVPVICGLSRCNERDIKTAWEAVKYAKRPRIHTFIATSG 188
+ VR + E + + V E+ SR + I +EA+ + R +H + +
Sbjct: 84 DFVRKLIDERRIPDDVTIEA-LTQ-----SRPDL--IARTFEALAGSPRAIVHLYNPIAP 135
Query: 189 IHMEHKLRKTKQQVVEIARSMVKFARSLGCDD------VEFSPEDAGRSDRKFLYEILGE 242
++ ++ EIA + + R+L + E+SPE ++ F E+
Sbjct: 136 QWRRIVFGMSRAEIKEIALAGTRQIRALADANPGTQWIYEYSPETFSLAELDFAREVCDA 195
Query: 243 VIKVGATT------LNIPDTVGITMPTEFGKLIADIKANTPGIENVVISTHCQNDLGLST 296
V + T +N+P TV + + I + + + +V+S H ND G +
Sbjct: 196 VSAIWGPTPQRKMIINLPATVESSTANVYADQIEWMHRSLARRDCIVLSVHPHNDRGTAV 255
Query: 297 ANTIAGACAGARQVEVTINGIGERAGNASLEEVVMAFKCRGEHILGGLYTGINTRHIVMA 356
A AGA ++E + G GER GN L + + + + G+ +G++ R +
Sbjct: 256 AAAELAVLAGAERIEGCLFGNGERTGNVDLVALALNLERQ------GIASGLDFRDMAAL 309
Query: 357 SKMVEEYTGLHVQP 370
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 = 77.2 bits (191), Expect = 1e-15
Identities = 68/282 (24%), Positives = 107/282 (37%), Gaps = 71/282 (25%)
Query: 80 VRVFDTTLRDGEQSPGATLTSKEKLDIARQLAKLGVDIIE-------------AGFPAAS 126
V + D TLRDG + T ++ IAR L GV +IE GF A +
Sbjct: 1 VYIHDVTLRDGMHAVRHQFTLEQVRAIARALDAAGVPLIEVGHGDGLGGSSLNYGFAAHT 60
Query: 127 KEDFEAVRTIAKEVGNAVDAESGYVPVICGLSRCNERDIKTAWEA-VKYAKRPRIHTFIA 185
D E + A+ + A + V+ D+K A + V + +A
Sbjct: 61 --DEEYLEAAAEALKQAK------LGVLLLPGIGTVDDLKMAADLGVDVVR-------VA 105
Query: 186 TSGIHMEHKLRKTKQQVVE--IARSMVKFARSLGCDDVEF-------SPEDAGRSDRKFL 236
T E ++ + AR LG D V F SPE+ +
Sbjct: 106 T--------------HCTEADVSEQHIGAARKLGMDVVGFLMMSHMASPEELAEQAKLM- 150
Query: 237 YEILGEVIKVGATTLNIPDTVGITMPTEFGKLIADIKANTPGIENVVIST----HCQNDL 292
GA + + D+ G M L D++ + + T H N+L
Sbjct: 151 -------ESYGADCVYVTDSAG-AM------LPDDVRERVRALREALDPTPVGFHGHNNL 196
Query: 293 GLSTANTIAGACAGARQVEVTINGIGERAGNASLEEVVMAFK 334
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 = 73.1 bits (180), Expect = 5e-14
Identities = 75/283 (26%), Positives = 111/283 (39%), Gaps = 72/283 (25%)
Query: 80 VRVFDTTLRDGEQSPGATLTSKEKLDIARQLAKLGVDIIEA-------------GFPAAS 126
+ + D TLRDG + T ++ IA L + GVD IE GF A +
Sbjct: 3 LYITDVTLRDGMHAIRHQFTIEQVRAIAAALDEAGVDAIEVTHGDGLGGSSFNYGFSAHT 62
Query: 127 KEDFEAVRTIAKEVGNAVDAESGYVPVICGLSRCNERDIKTAWEAVKYAKRPRIHTFIAT 186
D E + A V A A +P I + D+K A++A A+ R+ T
Sbjct: 63 --DLEYIEAAADVVKRAKVA-VLLLPGIGTV-----HDLKAAYDA--GARTVRVATHCTE 112
Query: 187 SGIHMEHKLRKTKQQVVEIARSMVKFARSLGCDDVEF-------SPEDAGRSDRKFLYEI 239
+ + +H + AR LG D V F PE
Sbjct: 113 ADVSEQH----------------IGMARELGMDTVGFLMMSHMTPPE------------K 144
Query: 240 LGEVIKV----GATTLNIPDTVGITMPTE----FGKLIADIKANTPGIENVVISTHCQND 291
L E K+ GA + I D+ G +P + L A +K T + H ++
Sbjct: 145 LAEQAKLMESYGADCVYIVDSAGAMLPDDVRDRVRALKAVLKPETQ------VGFHAHHN 198
Query: 292 LGLSTANTIAGACAGARQVEVTINGIGERAGNASLEEVVMAFK 334
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 = 65.6 bits (161), Expect = 1e-11
Identities = 70/282 (24%), Positives = 110/282 (39%), Gaps = 64/282 (22%)
Query: 80 VRVFDTTLRDGEQSPGATLTSKEKLDIARQLAKLGVDIIEA-------------GFPAAS 126
+ + D TLRDG + T ++ IAR L GV +IE GF A +
Sbjct: 4 IYISDVTLRDGMHAVRHQYTLEQVRAIARALDAAGVPVIEVTHGDGLGGSSFNYGFGAHT 63
Query: 127 KEDFEAVRTIAKEVGNAVDAESGYVPVICGLSRCNERDIKTAWEAVKYAKRPRIHTFIAT 186
D E + A+ V A A ++ G+ D+K A++A + R+ T
Sbjct: 64 --DEEYIEAAAEVVKQAKIA----ALLLPGIGTV--DDLKMAYDA--GVRVVRVATHCTE 113
Query: 187 SGIHMEHKLRKTKQQVVEIARSMVKFARSLGCDDVEF-------SPEDAGRSDRKFLYEI 239
+ + +H + AR LG D V F PE +
Sbjct: 114 ADVSEQH----------------IGLARELGMDTVGFLMMSHMAPPEKLAEQAKLM---- 153
Query: 240 LGEVIKVGATTLNIPDTVGITMPTE----FGKLIADIKANTPGIENVVISTHCQNDLGLS 295
GA + + D+ G +P + L A +K +T + H N+LGL
Sbjct: 154 ----ESYGAQCVYVVDSAGALLPEDVRDRVRALRAALKPDTQ------VGFHGHNNLGLG 203
Query: 296 TANTIAGACAGARQVEVTINGIGERAGNASLEEVVMAFKCRG 337
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: 82 VFDTTLRDGE-----QSPGATLTSKEKLDIARQLAKLGVDIIEAGFPAASKEDFEAVRTI 136
+ D TLRDG + I R LA G+D +E G+ +S E ++
Sbjct: 1 ILDCTLRDGGYVNNWDFGDEFVK-----AIYRALAAAGIDYVEIGY-RSSPEKEFKGKSA 54
Query: 137 ------AKEVGNAVDAESGYVPVICGLSRCNERDIKTAWEAVKYAKRPRIHTFIATSGIH 190
+ + + ++ + ++ A + S +
Sbjct: 55 FCDDEFLRRLLGDSKGNTKIAVMVDY-GNDDIDLLEPA----------------SGSVVD 97
Query: 191 MEHKLRKT--KQQVVEIARSMVKFARSLGCDDVEFSP-EDAGRSDRKFLYEILGEVIKVG 247
M +R K + E A ++K + G + V F+ +G SD + L E+L V ++
Sbjct: 98 M---IRVAFHKHEFDE-ALPLIKAIKEKGYE-VFFNLMAISGYSDEELL-ELLELVNEIK 151
Query: 248 ATTLNIPDTVGITMPTEFGKLIADIKANTPGIENVVISTHCQNDLGLSTANTIAGACAGA 307
I D+ G P + ++I+ +++N ++ + H N+L L+ ANT+ G
Sbjct: 152 PDVFYIVDSFGSMYPEDIKRIISLLRSNLDK--DIKLGFHAHNNLQLALANTLEAIELGV 209
Query: 308 RQVEVTINGIGERAGNASLEEVVM 331
++ 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 = 57/306 (18%), Positives = 119/306 (38%), Gaps = 69/306 (22%)
Query: 88 RDGEQSPGATLTSKEKLDIARQLAKLGVDIIEAG-F--PAASKEDFEAVRTI-----AKE 139
RDG Q+ + +++K+++ L+ G+ IE F P + A+E
Sbjct: 7 RDGLQNEKTFIPTEDKIELIDALSAAGLRRIEVTSFVSPKW----------VPQMADAEE 56
Query: 140 VGNAVDAESGYV-PVICGLSRCNERDIKTAWEA-VKYAKRPRIHTFIATSGIHMEHKLRK 197
V + G + N R + A A V + F++ S + +
Sbjct: 57 VLAGLPRRPGVRYSALVP----NLRGAERALAAGVDE-----VAVFVSASETFSQKNINC 107
Query: 198 TKQQVVEIARSMVKFAR------------SLGC---DDVEFSPEDAGRSDRKFLYEILGE 242
+ + +E + + A+ + GC +V PE E+
Sbjct: 108 SIAESLERFEPVAELAKAAGLRVRGYVSTAFGCPYEGEV--PPERV--------AEVAER 157
Query: 243 VIKVGATTLNIPDTVGITMPTEFGKLIADIKANTPGIENVVISTHCQNDLGLSTANTIAG 302
++ +G +++ DT+G+ P + +L+ + P + ++ H + G + AN +A
Sbjct: 158 LLDLGCDEISLGDTIGVATPAQVRRLLEAVLERFPDEK---LALHFHDTRGQALANILAA 214
Query: 303 ACAGARQVEVTINGIG------ERAGNASLEEVVMAFKCRGEHILGGLYTGINTRHIVMA 356
AG R+ + ++ G+G GN + E++V + G TGI+ ++ A
Sbjct: 215 LEAGVRRFDSSVGGLGGCPFAPGATGNVATEDLVYMLEGMGIE------TGIDLDKLLAA 268
Query: 357 SKMVEE 362
++ + E
Sbjct: 269 ARWISE 274
>gnl|CDD|227349 COG5016, COG5016, Pyruvate/oxaloacetate carboxyltransferase [Energy
production and conversion].
Length = 472
Score = 46.2 bits (110), Expect = 4e-05
Identities = 67/293 (22%), Positives = 111/293 (37%), Gaps = 84/293 (28%)
Query: 80 VRVFDTTLRDGEQSPGAT-LTSKEKLDIARQLAKLGVDIIE----AGFPAAS---KED-F 130
+++ DT LRDG QS AT + +++ L IA L K+G +E A F A ED +
Sbjct: 6 IKITDTVLRDGHQSLLATRMRTEDMLPIAEALDKVGYWSLEVWGGATFDACIRFLNEDPW 65
Query: 131 EAVRTIAKEVGNA---------------------VD------AESGYVPVICGLSRCNE- 162
E +R + K V N V+ AE+G + V N+
Sbjct: 66 ERLRELKKAVPNTKLQMLLRGQNLVGYRHYADDVVEKFVEKAAENG-IDVFRIFDALNDV 124
Query: 163 RDIKTAWEAVK-YAKRPRIHTFIATSGIHMEHKLRKTKQQVVEIARSMVKFARSLGCDDV 221
R++KTA +A K + + TS +H T + VE+A+ +++ +G D +
Sbjct: 125 RNLKTAIKAAKKHGAHVQGTISYTTSPVH-------TLEYYVELAKELLE----MGVDSI 173
Query: 222 EFSPEDAGRSDRKFLYEILGEVIKVGATTLNIPDTVGITMPTEFGKLIADIKANTPGIEN 281
IK D G+ P E +L+ IK P
Sbjct: 174 ---------------------CIK---------DMAGLLTPYEAYELVKAIKKELP---- 199
Query: 282 VVISTHCQNDLGLSTANTIAGACAGARQVEVTINGIGERAGNASLEEVVMAFK 334
V + H G++ + AG ++ I+ + + E +V A +
Sbjct: 200 VPVELHTHATSGMAEMTYLKAVEAGVDGIDTAISPLSGGTSQPATETMVAALR 252
>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: 235 FLYEILGEVIKVGATTLNIPDTVGITMPTEFGKLIADIKANTPGIENVVISTHCQNDLGL 294
+ ++ E++++GA ++ I D GI P +L++ IKA T N+ + H G+
Sbjct: 164 YYLSLVKELVEMGADSICIKDMAGILTPKAAKELVSGIKAMT----NLPLIVHTHATSGI 219
Query: 295 STANTIAGACAGARQVEVTINGIGERAGNASLEEVVMAFKCRGEHI 340
S +A AGA +++ ++ E + E + +A K G I
Sbjct: 220 SQMTYLAAVEAGADRIDTALSPFSEGTSQPATESMYLALKEAGYDI 265
>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 = 42.0 bits (100), Expect = 4e-04
Identities = 66/296 (22%), Positives = 107/296 (36%), Gaps = 98/296 (33%)
Query: 84 DTTLRDGEQSPGAT-LTSKEKLDIARQLAKLGVDIIEAG----FPAA---SKED-FEAVR 134
DTTLRD QS AT + +++ L IA L + G +E F ED +E +R
Sbjct: 3 DTTLRDAHQSLLATRMRTEDMLPIAEALDEAGFFSLEVWGGATFDVCMRFLNEDPWERLR 62
Query: 135 TIAKE---------------VG------NAVD------AESGYVPVICGLSRC----NE- 162
+ K VG + V+ A++G + + R N+
Sbjct: 63 ELRKAMPNTPLQMLLRGQNLVGYRHYPDDVVELFVEKAAKNG-IDIF----RIFDALNDV 117
Query: 163 RDIKTAWEAVKYAKRPRIHTFIA----TSGIHMEHKLRKTKQQVVEIARSMVKFARSLGC 218
R+++ A +AVK A H A S +H T + V++A+ + +G
Sbjct: 118 RNLEVAIKAVKKAG---KHVEGAICYTGSPVH-------TLEYYVKLAKELED----MGA 163
Query: 219 DDVEFSPEDAGRSDRKFLYEILGEVIKVGATTLNIPDTVGITMPTEFGKLIADIKANTPG 278
D + IK D G+ P +L+ +K
Sbjct: 164 D-------------------SIC--IK---------DMAGLLTPYAAYELVKALKKEVG- 192
Query: 279 IENVVISTHCQNDLGLSTANTIAGACAGARQVEVTINGIGERAGNASLEEVVMAFK 334
+ I H + GL+ A +A A AG V+ I+ + S E +V A +
Sbjct: 193 ---LPIHLHTHDTSGLAVATYLAAAEAGVDIVDTAISPLSGGTSQPSTESMVAALR 245
>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: 476 PEVVWKLLDMQVTCGTLGLSTATVKLMDANGEEHVACSTGTGPVDSAYKAVDLIVKEPAT 535
P ++ K+L V T+G T ++ G EHV C VD K +V PA
Sbjct: 138 PAMLPKILGAGVKL-TIGNDEDTAAAIEKMGGEHVDCPVDDIVVDEENK----VVTTPAY 192
Query: 536 LLEYSMNAVTAGID 549
+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 = 0.008
Identities = 33/133 (24%), Positives = 52/133 (39%), Gaps = 14/133 (10%)
Query: 232 DRKFLYEILGEVIKVGATTLNIPDTVGITMPTEFGKLIADIKANTPGIENVVISTHCQND 291
D K+ + E+ K GA L I D G+ P LI ++ T ++ I H +
Sbjct: 687 DLKYYTNLAVELEKAGAHILGIKDMAGLLKPAAAKLLIKALREKT----DLPIHFHTHDT 742
Query: 292 LGLSTANTIAGACAGARQVEVTINGIGERAGNASLEEVVMAFKCRGEHILGG--LYTGIN 349
G++ A+ +A AG V+V ++ + SL +V L G G+N
Sbjct: 743 SGIAVASMLAAVEAGVDVVDVAVDSMSGLTSQPSLGAIV--------AALEGSERDPGLN 794
Query: 350 TRHIVMASKMVEE 362
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: 80 VRVFDTTLRDGEQSPGAT-LTSKEKLDIARQLAKLGVDIIE----AGFPAASK---ED-F 130
+++ +T LRDG+QS AT +T++E L I +L G +E A F A + ED +
Sbjct: 4 IKITETVLRDGQQSLIATRMTTEEMLPILEKLDNAGYHSLEMWGGATFDACLRFLNEDPW 63
Query: 131 EAVRTIAKEVGN 142
E +R I K V
Sbjct: 64 ERLRKIRKAVKK 75
>gnl|CDD|237592 PRK14040, PRK14040, oxaloacetate decarboxylase; Provisional.
Length = 593
Score = 36.4 bits (85), Expect = 0.039
Identities = 24/84 (28%), Positives = 39/84 (46%), Gaps = 4/84 (4%)
Query: 247 GATTLNIPDTVGITMPTEFGKLIADIKANTPGIENVVISTHCQNDLGLSTANTIAGACAG 306
G +L I D G+ P +L++ IK +V + HC GLSTA + AG
Sbjct: 168 GVDSLCIKDMAGLLKPYAAYELVSRIKKRV----DVPLHLHCHATTGLSTATLLKAIEAG 223
Query: 307 ARQVEVTINGIGERAGNASLEEVV 330
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 = 35.7 bits (83), Expect = 0.047
Identities = 31/98 (31%), Positives = 41/98 (41%), Gaps = 13/98 (13%)
Query: 106 IARQLAKLGVDIIEAGFPAASKEDFEAVRTIAKEVGNA-VDAESGYVPVICGLSRCNERD 164
AR+LAK G +I A E EA I KE GNA V+ + LS +
Sbjct: 17 TARELAKRGAHVIIACRNEEKGE--EAAAEIKKETGNAKVEV------IQLDLS--SLAS 66
Query: 165 IKTAWEAVKYAKRPRIHTFIATSGIHMEHKLRKTKQQV 202
++ 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: 80 VRVFDTTLRDGEQSPGAT-LTSKEKLDIARQLAKLG 114
V++ DTTLRD QS AT + +++ L IA +L K+G
Sbjct: 4 VKITDTTLRDAHQSLLATRMRTEDMLPIAEKLDKVG 39
Score = 29.4 bits (67), Expect = 6.8
Identities = 13/66 (19%), Positives = 27/66 (40%), Gaps = 4/66 (6%)
Query: 242 EVIKVGATTLNIPDTVGITMPTEFGKLIADIKANTPGIENVVISTHCQNDLGLSTANTIA 301
E+ ++G ++ I D G+ P +L+ +K ++ + H GL+ +
Sbjct: 162 ELEEMGCDSICIKDMAGLLTPYAAYELVKALKEEV----DLPVQLHSHCTSGLAPMTYLK 217
Query: 302 GACAGA 307
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 = 0.29
Identities = 24/86 (27%), Positives = 40/86 (46%), Gaps = 6/86 (6%)
Query: 476 PEVVWKLLDMQVTCGTLGLSTATVKLMDANGEEHVACSTGTGPVDSAYKAVDLIVKEPAT 535
P ++ K+ + T+G T + ++ G EHV C VD K +V PA
Sbjct: 138 PAMLPKIFGFPLRL-TIGNDIDTAEALEEMGAEHVPCPVDDIVVDEDNK----VVTTPAY 192
Query: 536 LLEYSMNAVTAGIDAIATTRVLIRGE 561
+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 = 0.39
Identities = 16/41 (39%), Positives = 25/41 (60%), Gaps = 1/41 (2%)
Query: 104 LDIARQLAKLGVDIIEAGFPAASKEDFEAVRTIAKEVGNAV 144
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 = 0.50
Identities = 22/75 (29%), Positives = 33/75 (44%), Gaps = 5/75 (6%)
Query: 476 PEVVWKLLDMQVTCGTLGLSTATVKLMDANGEEHVACSTGTGPVDSAYKAVDLIVKEPAT 535
P + K+L V T+G T ++ G EHV C VD K +V PA
Sbjct: 135 PALAAKILGEGVEV-TIGNDAGTAAAIEKMGAEHVNCPVEEIVVDEKNK----VVTTPAY 189
Query: 536 LLEYSMNAVTAGIDA 550
+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 = 0.57
Identities = 33/140 (23%), Positives = 54/140 (38%), Gaps = 26/140 (18%)
Query: 101 KEKLDIARQLAKLGVDIIEAGFPAASKEDFEAVRTIAK-------------EVGNAVDAE 147
KE+L+ R KLG D + AA++E FE VR + +V A
Sbjct: 131 KEELEEYR---KLGADYLGVAEDAANEELFEKVRKTSGSPHSWERYWEFLEKVAEAFGKG 187
Query: 148 SGYVPVICGLSRCNERDI-KTAWEAVKYAKRPRIHTFIAT--SGIHMEHKLRKTKQQVVE 204
+ +I GL +++DI +T + + F T G ME++ VE
Sbjct: 188 RVGIHLIVGLG-ESDKDIVETIKRV--RKRGGIVSLFAFTPLKGTQMENRKPPP----VE 240
Query: 205 IARSMVKFARSLGCDDVEFS 224
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 = 0.77
Identities = 21/57 (36%), Positives = 27/57 (47%), Gaps = 3/57 (5%)
Query: 86 TLRDGEQSPGATLTSKEKLDIARQLAKLGVDIIEAGFPAASKEDFEAVRTIAKEVGN 142
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: 238 EILGEVIKVGATTLNIPDTVGITMPTEFGKLIADIKANTPGIENVVISTHCQND 291
+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 = 0.84
Identities = 17/51 (33%), Positives = 25/51 (49%), Gaps = 5/51 (9%)
Query: 104 LDIARQLAKLGVDII----EAGFPAASKEDFEAVRTIAKEVGNAVDAESGY 150
L+ AR+L +GVD I AG K +E V+ + K+ G V+ S
Sbjct: 156 LEFARELVDMGVDSICIKDMAGL-LTPKRAYELVKALKKKFGVPVEVHSHC 205
Score = 30.5 bits (69), Expect = 2.9
Identities = 22/73 (30%), Positives = 35/73 (47%), Gaps = 9/73 (12%)
Query: 80 VRVFDTTLRDGEQSPGAT-LTSKEKLDIARQLAKLGVDIIE----AGFPAASK---ED-F 130
V DTTLRDG QS AT + +++ L ++G +E A F + E+ +
Sbjct: 3 VMFVDTTLRDGHQSLIATRMRTEDMLPALEAFDRMGFYSMEVWGGATFDVCVRFLNENPW 62
Query: 131 EAVRTIAKEVGNA 143
E ++ I K + N
Sbjct: 63 ERLKEIRKRLKNT 75
Score = 29.4 bits (66), Expect = 6.2
Identities = 23/99 (23%), Positives = 41/99 (41%), Gaps = 8/99 (8%)
Query: 238 EILGEVIKVGATTLNIPDTVGITMPTEFGKLIADIKA--NTPGIENVVISTHCQNDLGLS 295
E E++ +G ++ I D G+ P +L+ +K P V + +HC GL+
Sbjct: 157 EFARELVDMGVDSICIKDMAGLLTPKRAYELVKALKKKFGVP----VEVHSHCTT--GLA 210
Query: 296 TANTIAGACAGARQVEVTINGIGERAGNASLEEVVMAFK 334
+ +A AGA + I+ E + AF+
Sbjct: 211 SLAYLAAVEAGADMFDTAISPFSMGTSQPPFESMYYAFR 249
>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 = 1.0
Identities = 10/39 (25%), Positives = 16/39 (41%)
Query: 189 IHMEHKLRKTKQQVVEIARSMVKFARSLGCDDVEFSPED 227
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: 98 LTSKEKLDIARQLAKLGVDIIEAGFPAASKEDFEAVRTIAKEVGN 142
LT K+K DI + A+ GVD I F S ED E R + +E G
Sbjct: 171 LTEKDKADI-KFAAEQGVDYIAVSFVR-SAEDVEEARRLLREAGC 213
>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: 77 PNYVRVFDTTLRDGEQSPGATLTSKEKLDIARQLAKLGVDIIEAG-------FP--AASK 127
P +V++ + RDG Q+ + + K+++ ++L G+ ++EA P A +K
Sbjct: 44 PKFVKIVEVGPRDGLQNEKNIVPTSVKVELIQRLVSSGLPVVEATSFVSPKWVPQLADAK 103
Query: 128 EDFEAVRTIAKEVGNAVDAESGYVPVICGLSRCNERDIKTAWEAVKYAKRPRIHTFIATS 187
+ AVR + E PV+ N + + A A + F + S
Sbjct: 104 DVMAAVR----------NLEGARFPVLTP----NLKGFEAAIA----AGAKEVAVFASAS 145
Query: 188 GIHMEHKLRKTKQQVVEIARSMVKFARSLG--------CDDVEFSPEDAGRSDRKFLYEI 239
+ + + ++ + R + A+ C V P + K Y +
Sbjct: 146 ESFSKSNINCSIEESLVRYREVALAAKKHSIPVRGYVSC--VVGCPIEGPVPPSKVAY-V 202
Query: 240 LGEVIKVGATTLNIPDTVGITMPTEFGKLIADIKANTPGIENVVISTHCQNDLGLSTANT 299
E+ +G +++ DT+G+ P ++ + A P ++ ++ H + G + AN
Sbjct: 203 AKELYDMGCYEISLGDTIGVGTPGTVVPMLEAVMAVVP-VDK--LAVHFHDTYGQALANI 259
Query: 300 IAGACAGARQVEVTINGIG------ERAGNASLEEVVMAFKCRGEHILGGL--YTGINTR 351
+ G V+ ++ G+G +GN + E+VV ++L GL T ++
Sbjct: 260 LVSLQMGISTVDSSVAGLGGCPYAKGASGNVATEDVV--------YMLNGLGVSTNVDLG 311
Query: 352 HIVMASKMVEEYTG 365
++ A + ++ G
Sbjct: 312 KLMAAGDFISKHLG 325
>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: 238 EILGEVIKVGATTLNIPDTVGITMPTEFGKLIADIKANTPGIENVVISTHCQNDLGLSTA 297
++ E++++G ++ I D GI P +L++ +K + + H G++
Sbjct: 153 DLAEELLEMGVDSICIKDMAGILTPKAAYELVSALKKRFG----LPVHLHSHATTGMAEM 208
Query: 298 NTIAGACAGARQVEVTINGIGERAGNASLEEVVMAFK 334
+ 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: 99 TSKEKLDIARQL------AKLGVDIIEAGFPAASKEDFEAVRTIAKEV 140
T + L++ ++ + DII GFP ++EDFE + KEV
Sbjct: 280 TREYYLELVEKIKSNIPDVAITTDII-VGFPGETEEDFEETLDLVKEV 326
>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 = 1.4
Identities = 20/72 (27%), Positives = 31/72 (43%), Gaps = 18/72 (25%)
Query: 98 LTSKEK-LDIARQLAKLGVDIIEAGFPAASKEDFEAVRTIAKEVGNAVDAESGYVPVICG 156
L E+ ++IA ++A VDIIE G P E AVR + + + ++
Sbjct: 12 LLDLEEAIEIAEEVAD-YVDIIEVGTPLIKAEGMRAVRALRELFPDK--------IIVA- 61
Query: 157 LSRCNERDIKTA 168
D+KTA
Sbjct: 62 -------DLKTA 66
>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: 104 LDIARQLAKLGVDIIEAGFPAASKEDFEAVRTIAKE 139
++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: 200 QQVVEIARSMVKFARSLGCDDVEFSP-EDAGRSDR---KFLYEIL 240
++++++ 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: 113 LGVDIIEAGFPAASKEDFEAVRTIAKEVG 141
L DII GFP ++EDF+ ++ EVG
Sbjct: 290 LSTDII-VGFPGETEEDFQETLSLYDEVG 317
>gnl|CDD|237263 PRK12999, PRK12999, pyruvate carboxylase; Reviewed.
Length = 1146
Score = 30.5 bits (70), Expect = 3.0
Identities = 21/67 (31%), Positives = 29/67 (43%), Gaps = 6/67 (8%)
Query: 54 PPPSLYPRITATR-----PEYIPNRIPDPNYVRVFDTTLRDGEQSPGAT-LTSKEKLDIA 107
+ P T PE + + D V + DTT RD QS AT + +K+ L IA
Sbjct: 502 DLSAPPPAGTKQILDELGPEGFADWLRDQKRVLLTDTTFRDAHQSLLATRVRTKDLLRIA 561
Query: 108 RQLAKLG 114
A+L
Sbjct: 562 PATARLL 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: 107 ARQLAKLGVDIIEAGFPAASKEDFEAVRTIAKEVGNAVDAESGYVP-------VICGLSR 159
+R LA+ G+ +++AG P + F + K G V +VP ++
Sbjct: 394 SRHLAETGLMVVQAGSPYFTPRVFWRIDATIKSAGYRVWPYHVHVPTFGEWGFILAAPGD 453
Query: 160 CNERDIKTAWEAVKYAKRPRIHTF 183
+ ++ +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 = 4.3
Identities = 16/57 (28%), Positives = 24/57 (42%), Gaps = 3/57 (5%)
Query: 97 TLTSKEKLDIARQLAKLGVDIIEAGFPAASKEDFEAVRTIAKEVGNAVDAESGYVPV 153
T KE + + R L K G+ IE P A +D E + + G + A+ V
Sbjct: 104 AWTPKEAIRLIRALEKYGLAWIEE--PCAP-DDLEGYAALRRRTGIPIAADESVTTV 157
>gnl|CDD|237285 PRK13111, trpA, tryptophan synthase subunit alpha; Provisional.
Length = 258
Score = 29.7 bits (68), Expect = 4.5
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 104 LDIARQLAKLGVDIIEAGFP 123
L+I + L + G DIIE G P
Sbjct: 29 LEIIKALVEAGADIIELGIP 48
>gnl|CDD|172808 PRK14332, PRK14332, (dimethylallyl)adenosine tRNA
methylthiotransferase; Provisional.
Length = 449
Score = 30.0 bits (67), Expect = 4.7
Identities = 25/98 (25%), Positives = 45/98 (45%), Gaps = 19/98 (19%)
Query: 54 PPPSLYP----RITATRPEYIPN-RIP-DPNYVRVFDTTLRDGEQSPGATLTSKEKLDIA 107
P P +P + A P + PN +P RV L + ++S + +E LD+
Sbjct: 241 PHPKDFPDHLLSLMAKNPRFCPNIHLPLQAGNTRV----LEEMKRS----YSKEEFLDVV 292
Query: 108 RQLAKLGVDI-----IEAGFPAASKEDFEAVRTIAKEV 140
+++ + D+ I GFP ++E+FE + +EV
Sbjct: 293 KEIRNIVPDVGITTDIIVGFPNETEEEFEDTLAVVREV 330
>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 = 4.7
Identities = 22/80 (27%), Positives = 32/80 (40%), Gaps = 14/80 (17%)
Query: 104 LDIARQLAKLGVDIIEAGFPAASKEDFEA--------VRTIAK-EVGNAVDAESGYVP-- 152
+ +AR L + G+ ++E G P K A VR + K + +D P
Sbjct: 289 IPLARFLTRCGMIVVEVGTPYLDKRFQAAELELLPPMVRIVEKPDNYRQLDRIRELRPDL 348
Query: 153 VICGLSRCN---ERDIKTAW 169
V+ GL N R I T W
Sbjct: 349 VVTGLGLANPLEARGITTKW 368
>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 = 5.1
Identities = 16/42 (38%), Positives = 24/42 (57%), Gaps = 1/42 (2%)
Query: 97 TLTSKEKLDIARQLAKLGVDIIEAGFPAASKEDFEAVRTIAK 138
L +E L++A ++A VDIIE G P E EAV+ + +
Sbjct: 8 LLDIEEALELAEKVAD-YVDIIEIGTPLIKNEGIEAVKEMKE 48
>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 = 5.7
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 104 LDIARQLAKLGVDIIEAGFP 123
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 = 29.0 bits (65), Expect = 6.4
Identities = 15/46 (32%), Positives = 21/46 (45%)
Query: 99 TSKEKLDIARQLAKLGVDIIEAGFPAASKEDFEAVRTIAKEVGNAV 144
TS L IAR LA G +I+ GF A++ + AK +
Sbjct: 11 TSGIGLGIARALAAAGANIVLNGFGDAAEIEAVRAGLAAKHGVKVL 56
>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: 297 ANTIAGACAGARQVEVTINGIGE 319
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 = 29.5 bits (67), Expect = 6.7
Identities = 17/49 (34%), Positives = 25/49 (51%), Gaps = 7/49 (14%)
Query: 99 TSKEKLDIARQLAK------LGVDIIEAGFPAASKEDFEAVRTIAKEVG 141
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 = 6.8
Identities = 19/84 (22%), Positives = 33/84 (39%), Gaps = 17/84 (20%)
Query: 368 VQPHKAIVGANAFAHESGIHQDGMLKHKGTY-------EIISPEDIGLER---------- 410
VQP + + A+ + ++ K + + E+IG+E
Sbjct: 124 VQPKELGIPTKAYYAVEEVKENATQKSQKVFVHVPSEIGAHEAEEIGVEHLLRDVKDTTV 183
Query: 411 SSEAGIVLGKLSGRHALKDRLKEL 434
S+ A V GKL+ L RL+E+
Sbjct: 184 STLATEVTGKLTALKGLDARLREI 207
>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 = 6.9
Identities = 13/45 (28%), Positives = 21/45 (46%), Gaps = 2/45 (4%)
Query: 98 LTSKEK-LDIARQLAKLGVDIIEAGFPAASKEDFEAVRTIAKEVG 141
+ E+ L++A L VDII+ G E E V+ + + G
Sbjct: 8 VPDLEEALELADALGDS-VDIIKVGTELFLAEGPEGVKELKELFG 51
>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 = 29.2 bits (65), Expect = 7.0
Identities = 14/45 (31%), Positives = 19/45 (42%), Gaps = 6/45 (13%)
Query: 31 QLFFHCNNSKPFFKTT------ISCSLQKPPPSLYPRITATRPEY 69
F + P F TT S ++ PPP PR T +RP +
Sbjct: 314 HFLFKPGGTSPLFCTTSPGYPLTSSTVYSPPPRPLPRNTFSRPAF 358
>gnl|CDD|223237 COG0159, TrpA, Tryptophan synthase alpha chain [Amino acid
transport and metabolism].
Length = 265
Score = 28.7 bits (65), Expect = 7.8
Identities = 9/20 (45%), Positives = 13/20 (65%)
Query: 104 LDIARQLAKLGVDIIEAGFP 123
L+I + L + G DI+E G P
Sbjct: 34 LEIIKTLVEAGADILELGVP 53
>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 = 8.2
Identities = 16/52 (30%), Positives = 25/52 (48%), Gaps = 7/52 (13%)
Query: 95 GATLTSKEKLDIARQL------AKLGVDIIEAGFPAASKEDFEAVRTIAKEV 140
T + L++ R+L + DII GFP ++EDFE + +EV
Sbjct: 276 KRGYTREWYLNLVRKLRAACPNVSISTDII-VGFPGETEEDFEETLDLLREV 326
>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: 300 IAGACAGARQVEVTINGIGERAGNA 324
+ GA AGAR + + ERAG++
Sbjct: 510 LLGALAGARTATPALGAVLERAGSS 534
>gnl|CDD|183494 PRK12390, PRK12390, 1-aminocyclopropane-1-carboxylate deaminase;
Provisional.
Length = 337
Score = 28.8 bits (65), Expect = 9.9
Identities = 16/45 (35%), Positives = 22/45 (48%), Gaps = 3/45 (6%)
Query: 188 GIHMEHKLRKTKQQVVEIAR---SMVKFARSLGCDDVEFSPEDAG 229
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
0.316 0.132 0.377
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: 31,365,700
Number of extensions: 3138684
Number of successful extensions: 3746
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3614
Number of HSP's successfully gapped: 113
Length of query: 623
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 520
Effective length of database: 6,369,140
Effective search space: 3311952800
Effective search space used: 3311952800
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 62 (27.5 bits)