RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 007151
(616 letters)
>gnl|CDD|178135 PLN02520, PLN02520, bifunctional 3-dehydroquinate
dehydratase/shikimate dehydrogenase.
Length = 529
Score = 1015 bits (2625), Expect = 0.0
Identities = 421/516 (81%), Positives = 460/516 (89%), Gaps = 1/516 (0%)
Query: 3 SPNLLVASGSKLVSGGMRKNPTLICVPIMGESVDKMVVDMGKANASGADLVEIRLDGLKN 62
+AS SGG+R+NPTLICVPIM +SVDKM+++M KA GADLVEIRLD LKN
Sbjct: 2 VSTASLASDDLQGSGGVRRNPTLICVPIMADSVDKMLIEMAKAKELGADLVEIRLDFLKN 61
Query: 63 FNPRENIKTLIKESPVPTLFTYRPIWEGGQYDGDENERVDVLRLAMELGADYIDVELQVA 122
FNPRE++KTLIK+SP+PTL TYRP WEGGQY+GDEN+R D LRLAMELGADY+DVEL+VA
Sbjct: 62 FNPREDLKTLIKQSPLPTLVTYRPKWEGGQYEGDENKRQDALRLAMELGADYVDVELKVA 121
Query: 123 REFNDSIRGKKPEKCKVIVSSHNYQYTPSVEDLSNLVARIQASGADIVKFATTALDITDV 182
EF +SI GKKPEKCKVIVSSHNY+ TPSVE+L NLVARIQA+GADIVK ATTALDITDV
Sbjct: 122 HEFINSISGKKPEKCKVIVSSHNYENTPSVEELGNLVARIQATGADIVKIATTALDITDV 181
Query: 183 ARVFQITVHSQVPIIGLVMGERGLISRILCAKFGGFLTFGTLENGIVSAPGQPTIKDLLD 242
AR+FQITVHSQVP IGLVMGERGLISRILC KFGG+LTFGTLE G VSAPGQPTIKDLLD
Sbjct: 182 ARMFQITVHSQVPTIGLVMGERGLISRILCPKFGGYLTFGTLEAGKVSAPGQPTIKDLLD 241
Query: 243 LYNFRQMGPDTKVFGIIGKPVGHSKSPILYNEAFKSVGFNGVFVHLLVDDIAKFFQTYSS 302
LYNFRQ+GPDTKV+GIIGKPVGHSKSPIL+NEAFKSVGFNGV+VHLLVDD+AKF QTYSS
Sbjct: 242 LYNFRQIGPDTKVYGIIGKPVGHSKSPILHNEAFKSVGFNGVYVHLLVDDLAKFLQTYSS 301
Query: 303 NDFAGFSCTIPHKEAAVKCCDEVDTVAKSIGAVNCIIRRQSDGKLFGYNTDYVGAISAIE 362
DFAGFSCTIPHKE A+KCCDEVD +AKSIGA+N IIRR SDGKL GYNTDY+GAISAIE
Sbjct: 302 PDFAGFSCTIPHKEDALKCCDEVDPIAKSIGAINTIIRRPSDGKLVGYNTDYIGAISAIE 361
Query: 363 DGLRGRLNVSGGVSSALAGKLFVVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAE 422
DGLR S S LAGKLFVVIGAGGAGKALAYGAK KGARVVIANRTY+RA+ELA+
Sbjct: 362 DGLRA-SGSSPASGSPLAGKLFVVIGAGGAGKALAYGAKEKGARVVIANRTYERAKELAD 420
Query: 423 TVGGHALSLADLENFNPEDGMILANTTSIGMQPKVDETPIPKHALGHYALVFDAVYTPKI 482
VGG AL+LADLENF+PE+GMILANTTS+GMQP VDETPI KHAL HY+LVFDAVYTPKI
Sbjct: 421 AVGGQALTLADLENFHPEEGMILANTTSVGMQPNVDETPISKHALKHYSLVFDAVYTPKI 480
Query: 483 TRLLREAEESGATIVSGLEMFIGQAYEQYERFTGLP 518
TRLLREAEESGA IVSG EMFI QAYEQ+ERFTGLP
Sbjct: 481 TRLLREAEESGAIIVSGTEMFIRQAYEQFERFTGLP 516
>gnl|CDD|223247 COG0169, AroE, Shikimate 5-dehydrogenase [Amino acid transport and
metabolism].
Length = 283
Score = 262 bits (672), Expect = 3e-83
Identities = 108/277 (38%), Positives = 160/277 (57%), Gaps = 20/277 (7%)
Query: 249 MGPDTKVFGIIGKPVGHSKSPILYNEAFKSVGFNGVFVHLLV--DDIAKFFQTYSSNDFA 306
M TK+FG+IG P+ HS SP ++N AF+++G + V++ V +D+ + + F
Sbjct: 2 MNGKTKLFGVIGNPISHSLSPRMHNAAFRALGLDYVYLAFEVPPEDLPEAVSGIRALGFR 61
Query: 307 GFSCTIPHKEAAVKCCDEVDTVAKSIGAVNCIIRRQSDGKLFGYNTDYVGAISAIEDGLR 366
G + TIP KEAA+ DE+ A+ IGAVN ++R DGKL GYNTD +G + A+++
Sbjct: 62 GLNVTIPFKEAALPLLDELSPRARLIGAVNTLVRE-DDGKLRGYNTDGIGFLRALKEF-- 118
Query: 367 GRLNVSGGVSSALAGKLFVVIGAGGAGKALAYG-AKAKGARVVIANRTYDRARELAETVG 425
G+ + GK +++GAGGA +A+A+ A+A R+ + NRT +RA ELA+ G
Sbjct: 119 -------GLPVDVTGKRVLILGAGGAARAVAFALAEAGAKRITVVNRTRERAEELADLFG 171
Query: 426 -----GHALSLADLENFNPEDGMILANTTSIGMQPKVDETPIPKHALGHYALVFDAVYTP 480
A +LADLE D +L N T +GM ++P+P L A+V+D VY P
Sbjct: 172 ELGAAVEAAALADLEGLEEAD--LLINATPVGMAGPEGDSPVPAELLPKGAIVYDVVYNP 229
Query: 481 KITRLLREAEESGATIVSGLEMFIGQAYEQYERFTGL 517
T LLREA GA + GL M + QA E +E +TG+
Sbjct: 230 LETPLLREARAQGAKTIDGLGMLVHQAAEAFELWTGV 266
>gnl|CDD|216526 pfam01487, DHquinase_I, Type I 3-dehydroquinase. Type I
3-dehydroquinase, (3-dehydroquinate dehydratase or
DHQase.) catalyzes the cis-dehydration of
3-dehydroquinate via a covalent imine intermediate
giving dehydroshikimate. Dehydroquinase functions in the
shikimate pathway which is involved in the biosynthesis
of aromatic amino acids. Type II 3-dehydroquinase
catalyzes the trans-dehydration of 3-dehydroshikimate
see pfam01220.
Length = 222
Score = 256 bits (656), Expect = 9e-82
Identities = 87/225 (38%), Positives = 135/225 (60%), Gaps = 9/225 (4%)
Query: 27 CVPIMGESVDKMVVDMGKANASGADLVEIRLDGLKNFNPR---ENIKTLIKESPVPTLFT 83
CVP+ G S+++ + ++ + GAD VE+RLD L++ + E + L +++ +P +FT
Sbjct: 1 CVPVTGPSLEEALAELEEL-EEGADAVELRLDLLEDVDAEDVSEQLSALREKTGLPIIFT 59
Query: 84 YRPIWEGGQYDGDENERVDVLRLAMELGADYIDVELQVAREFNDSIRGKKPEKCKVIVSS 143
R EGG++DG E E +++L+ A+ LG DYID+EL A + ++ K K+I+S
Sbjct: 60 VRTKSEGGRFDGSEEEYLELLKEALRLGPDYIDIELSSAPDELLAVIIAKKGGTKIILSY 119
Query: 144 HNYQYTPSVEDLSNLVARIQASGADIVKFATTALDITDVARVFQITVHSQ---VPIIGLV 200
H+++ TPS EDL +L +Q GADIVK A A I DV R+ + T ++ P+I +
Sbjct: 120 HDFEGTPSWEDLLSLYEEMQKLGADIVKIAVMANSIEDVLRLLRFTSEAKELDKPLIAIS 179
Query: 201 MGERGLISRILCAKFGGFLTFGTLENGIVSAPGQPTIKDLLDLYN 245
MGE G ISRIL FG LT+ +L SAPGQ T+++L +
Sbjct: 180 MGELGRISRILGPVFGSVLTYASLGK--ASAPGQITLEELREALE 222
>gnl|CDD|234703 PRK00258, aroE, shikimate 5-dehydrogenase; Reviewed.
Length = 278
Score = 257 bits (659), Expect = 2e-81
Identities = 94/270 (34%), Positives = 146/270 (54%), Gaps = 16/270 (5%)
Query: 253 TKVFGIIGKPVGHSKSPILYNEAFKSVGFNGVFVHLLV--DDIAKFFQTYSSNDFAGFSC 310
T+++ +IG P+ HSKSP+++N AFK +G +GV++ +LV +D+ + + + G +
Sbjct: 5 TRLYAVIGNPIAHSKSPLIHNAAFKQLGLDGVYLAILVPPEDLEDAVKGFFALGGRGANV 64
Query: 311 TIPHKEAAVKCCDEVDTVAKSIGAVNCIIRRQSDGKLFGYNTDYVGAISAIEDGLRGRLN 370
T+P KEAA DE+ A+ IGAVN ++ DG+L G NTD +G + A+E+ L
Sbjct: 65 TVPFKEAAFALADELSERARLIGAVNTLVLE--DGRLIGDNTDGIGFVRALEERL----- 117
Query: 371 VSGGVSSALAGKLFVVIGAGGAGKALAYG-AKAKGARVVIANRTYDRARELAETVGGHAL 429
L GK +++GAGGA +A+ A + I NRT +RA ELA+ G
Sbjct: 118 -----GVDLKGKRILILGAGGAARAVILPLLDLGVAEITIVNRTVERAEELAKLFGALGK 172
Query: 430 SLADLENFNPEDGM-ILANTTSIGMQPKVDETPIPKHALGHYALVFDAVYTPKITRLLRE 488
+ DLE ++ N TS GM ++ P+P L +V+D +Y P T L
Sbjct: 173 AELDLELQEELADFDLIINATSAGMSGELPLPPLPLSLLRPGTIVYDMIYGPLPTPFLAW 232
Query: 489 AEESGATIVSGLEMFIGQAYEQYERFTGLP 518
A+ GA + GL M + QA E +E +TG+
Sbjct: 233 AKAQGARTIDGLGMLVHQAAEAFELWTGVR 262
>gnl|CDD|233268 TIGR01093, aroD, 3-dehydroquinate dehydratase, type I. This model
detects 3-dehydroquinate dehydratase, type I, either as
a monofunctional protein or as a domain of a larger,
multifunctional protein. It is often found fused to
shikimate 5-dehydrogenase (EC 1.1.1.25), and sometimes
additional domains. Type II 3-dehydroquinate
dehydratase, designated AroQ, is described by the model
TIGR01088 [Amino acid biosynthesis, Aromatic amino acid
family].
Length = 228
Score = 228 bits (584), Expect = 4e-71
Identities = 84/231 (36%), Positives = 129/231 (55%), Gaps = 14/231 (6%)
Query: 25 LICVPIMGESVDKMVVDMGKANASGADLVEIRLDGLKNFNPRENIKTLIKE-----SPVP 79
I VP+ +++ + K GAD+VE+R+D LK+ + ++ LI++ P
Sbjct: 1 KIFVPLTAPDLEEALATAEKIC-KGADIVELRVDLLKDPSSNNDVDALIEQLSQLRPDKP 59
Query: 80 TLFTYRPIWEGGQYDGDENERVDVL-RLAMELGADYIDVELQVAREF-NDSIRGKKPEKC 137
+FT R I EGG++ G+E E ++ L R A G D++D+EL + + + I K
Sbjct: 60 LIFTIRTISEGGKFPGNEEEYLEELKRAADSPGPDFVDIELFLPDDAVKELINIAKKGGT 119
Query: 138 KVIVSSHNYQYTPSVEDLSNLVARIQASGADIVKFATTALDITDVARVFQITVHSQ---- 193
K+I+S H++Q TPS E++ + + + GADIVK A A DV + +IT
Sbjct: 120 KIIMSYHDFQKTPSWEEIVERLEKALSYGADIVKIAVMANSKEDVLTLLEITNKVDEHAD 179
Query: 194 VPIIGLVMGERGLISRILCAKFGGFLTFGTLENGIVSAPGQPTIKDLLDLY 244
VP+I + MG+RG ISR+L A FG LTFG+L SAPGQ ++ DL +L
Sbjct: 180 VPLITMSMGDRGKISRVLGAVFGSVLTFGSLGK--ASAPGQISVDDLRELL 228
>gnl|CDD|188633 cd00502, DHQase_I, Type I 3-dehydroquinase, (3-dehydroquinate
dehydratase or DHQase). Type I 3-dehydroquinase,
(3-dehydroquinate dehydratase or DHQase). Catalyzes the
cis-dehydration of 3-dehydroquinate via a covalent imine
intermediate to produce dehydroshikimate. Dehydroquinase
is the third enzyme in the shikimate pathway, which is
involved in the biosynthesis of aromatic amino acids.
Type I DHQase exists as a homodimer. Type II
3-dehydroquinase also catalyzes the same overall
reaction, but is unrelated in terms of sequence and
structure, and utilizes a completely different reaction
mechanism.
Length = 225
Score = 209 bits (534), Expect = 8e-64
Identities = 81/231 (35%), Positives = 127/231 (54%), Gaps = 15/231 (6%)
Query: 25 LICVPIMGESVDKMVVDMGKA--NASGADLVEIRLDGLKNFNPR---ENIKTLIKESPVP 79
ICVP+ G ++ + GAD VE+R+D L++ + E + L + +P+P
Sbjct: 1 KICVPLTG---PDLLEEALSLLELLLGADAVELRVDLLEDPSIDDVAEQLSLLRELTPLP 57
Query: 80 TLFTYRPIWEGGQYDGDENERVDVLRLAMELGADYIDVELQVAREFNDSIRGKKPEKCKV 139
+FT R EGG ++G E E +++L A++LG DY+D+EL A + I +K K+
Sbjct: 58 IIFTVRTKSEGGNFEGSEEEYLELLEEALKLGPDYVDIELDSAL-LEELINSRKKGNTKI 116
Query: 140 IVSSHNYQYTPSVEDLSNLVARIQASGADIVKFATTALDITDVARVFQITV----HSQVP 195
I S H++ TPS E+L + + ++ A GADIVK A A I D R+ + T +P
Sbjct: 117 IGSYHDFSGTPSDEELVSRLEKMAALGADIVKIAVMANSIEDNLRLLKFTRQVKNLYDIP 176
Query: 196 IIGLVMGERGLISRILCAKFGGFLTFGTLENGIVSAPGQPTIKDLLDLYNF 246
+I + MGE G +SRIL FG LT+ +L SAPGQ ++++L +
Sbjct: 177 LIAINMGELGKLSRILSPVFGSPLTYASLPE--PSAPGQLSVEELKQALSL 225
>gnl|CDD|161904 TIGR00507, aroE, shikimate 5-dehydrogenase. This model finds
proteins from prokaryotes and functionally equivalent
domains from larger, multifunctional proteins of fungi
and plants. Below the trusted cutoff of 180, but above
the noise cutoff of 20, are the putative shikimate
dehydrogenases of Thermotoga maritima and Mycobacterium
tuberculosis, and uncharacterized paralogs of shikimate
dehydrogenase from E. coli and H. influenzae. The
related enzyme quinate 5-dehydrogenase scores below the
noise cutoff. A neighbor-joining tree, constructed with
quinate 5-dehydrogenases as the outgroup, shows the
Clamydial homolog as clustering among the shikimate
dehydrogenases, although the sequence is unusual in the
degree of sequence divergence and the presence of an
additional N-terminal domain [Amino acid biosynthesis,
Aromatic amino acid family].
Length = 270
Score = 195 bits (498), Expect = 4e-58
Identities = 101/269 (37%), Positives = 141/269 (52%), Gaps = 22/269 (8%)
Query: 254 KVFGIIGKPVGHSKSPILYNEAFKSVGFNGVFVHLLV--DDIAKFFQTYSSNDFAGFSCT 311
K++G+IG P+ HSKSP+++N FK +G G ++ LV DD+ + + F G + T
Sbjct: 1 KLYGVIGNPIAHSKSPLIHNAFFKQLGLEGPYIAFLVPPDDLEDALSGFFALGFKGANVT 60
Query: 312 IPHKEAAVKCCDEVDTVAKSIGAVNCIIRRQSDGKLFGYNTDYVGAISAIEDGLRGRLNV 371
P KE A + DE+D AK GAVN ++ DGKL GYNTD +G +S +E + R N
Sbjct: 61 SPFKERAFQFLDEIDGRAKLAGAVNTLVLE--DGKLVGYNTDGIGLVSDLEQLIPLRPN- 117
Query: 372 SGGVSSALAGKLFVVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAE----TVGGH 427
+ ++IGAGGA KA+A V+IANRT +A ELAE
Sbjct: 118 ----------QNVLIIGAGGAAKAVALELLKADCNVIIANRTVSKAEELAERFQRYGEIQ 167
Query: 428 ALSLADLENFNPEDGMILANTTSIGMQPKVDETPIPKHALGHYALVFDAVYTPKITRLLR 487
A S+ +L ++ N TS GM +DE P+P L LV+D VY P T L
Sbjct: 168 AFSMDELP---LHRVDLIINATSAGMSGNIDEPPVPAEYLKEGKLVYDLVYNPLETPFLA 224
Query: 488 EAEESGATIVSGLEMFIGQAYEQYERFTG 516
EA+ G + GL M + QA +E +TG
Sbjct: 225 EAKSLGTKTIDGLGMLVYQAALSFELWTG 253
>gnl|CDD|223782 COG0710, AroD, 3-dehydroquinate dehydratase [Amino acid transport
and metabolism].
Length = 231
Score = 177 bits (450), Expect = 1e-51
Identities = 75/223 (33%), Positives = 125/223 (56%), Gaps = 9/223 (4%)
Query: 24 TLICVPIMGESVDKMVVDMGKANASGADLVEIRLDGLKN-FNPRENIKTLIKESPV-PTL 81
I VP++G + ++ K+ AD+VE+R+D L++ E K L ++ P P +
Sbjct: 2 PKIIVPVVGLDIAELKEQAEKSKELDADIVELRVDLLESNVEVLEVAKALREKDPDKPLI 61
Query: 82 FTYRPIWEGGQYDGDENERVDVLR-LAMELGADYIDVELQVAREFNDSIRGKKPEKCKVI 140
FT+R + EGG++ G E E +++L+ LA G DYID+EL + I K +K VI
Sbjct: 62 FTFRTVKEGGEFPGSEEEYIELLKKLAELNGPDYIDIELSSPEDDVKEII-KFAKKHGVI 120
Query: 141 VSSHNYQYTPSVEDLSNLVARIQASGADIVKFATTALDITDVARVFQITVHSQV---PII 197
VS H+++ TP +E++ + ++++ GADIVK A DV + + T + P+I
Sbjct: 121 VSYHDFEKTPPLEEIIERLDKMESLGADIVKIAVMPQSKEDVLDLLEATREFKEAEKPVI 180
Query: 198 GLVMGERGLISRILCAKFGGFLTFGTLENGIVSAPGQPTIKDL 240
+ MG+ G ISR+ FG +T+ +L+ SAPGQ ++ +L
Sbjct: 181 TISMGKTGKISRVAGPVFGSPITYASLDK--PSAPGQISVDEL 221
>gnl|CDD|137204 PRK09310, aroDE, bifunctional 3-dehydroquinate
dehydratase/shikimate dehydrogenase protein; Reviewed.
Length = 477
Score = 181 bits (462), Expect = 1e-50
Identities = 137/463 (29%), Positives = 209/463 (45%), Gaps = 40/463 (8%)
Query: 51 DLVEIRLDGLKNFNPRENIKTLIKESPVPTLFTYRPIWEGGQYDGDENERVDVLRLAMEL 110
D +E+R+D L + + E +K LI+ +P+P L T++ Q + + LA +L
Sbjct: 26 DCIELRVDLLLSLSDLE-LKKLIELAPIPIL-TWKKHESCSQAAWIDK----MQSLA-KL 78
Query: 111 GADYIDVELQVAREFNDSIRGKKPEKCKVIVSSHNYQYTPSVEDLSNLVARIQASGADIV 170
+Y+D++ +E IR P K K+I+S H T ED+ L + AS AD
Sbjct: 79 NPNYLDIDKDFPKEALIRIRKLHP-KIKIILSYH----TSEHEDIIQLYNEMLASAADYY 133
Query: 171 KFATTALDITDVARVFQITVHSQVPIIGLVMGERGLISRILCAKFGGFLTFGTLENGIVS 230
K A ++ TD+ + L MG G SRIL +
Sbjct: 134 KIAVSSSSSTDLLNIIHQKRSLPENTTVLCMGGMGRPSRILSPLLQNAFNYAAGIGAPPV 193
Query: 231 APGQPTIKDLLDLYNFRQMGPDTKVFGIIGKPVGHSKSPILYNEAFKSVGFNGVFVHLLV 290
APGQ +++ LL YN+ + + ++G+IG PV S S + +N F + N ++ L +
Sbjct: 194 APGQLSLEHLL-FYNYANLSAQSPIYGLIGDPVDRSISHLSHNPLFSQLSLNCPYIKLPL 252
Query: 291 D--DIAKFFQTYSSNDFAGFSCTIPHKEAAVKCCDEVDTVAKSIGAVNCIIRRQSDGKLF 348
++ KFF T F G S T+P K A + D++D K G+ N ++ R GK+
Sbjct: 253 TPQELPKFFSTIRDLPFLGLSVTMPLKTAVLDFLDKLDPSVKLCGSCNTLVFRN--GKIE 310
Query: 349 GYNTDYVGAISAIEDGLRGRLNVSGGVSSALAGKLFVVIGAGGAGKALAYGAKAKGARVV 408
GYNTD G S ++ + N+ L + ++GAGGA KA+A GA ++
Sbjct: 311 GYNTDGEGLFSLLK-----QKNIP------LNNQHVAIVGAGGAAKAIATTLARAGAELL 359
Query: 409 IANRTYDRARELAETVGGHALSLADLENFNPEDGMILANTTSIGMQPKVDETPIPKHALG 468
I NRT A LA G A L L + D +I + P V IPK
Sbjct: 360 IFNRTKAHAEALASRCQGKAFPLESLPELHRIDIIINC------LPPSVT---IPK---A 407
Query: 469 HYALVFDAVYTPKITRLLREAEESGATIVSGLEMFIGQAYEQY 511
V D PK + + A G++I+ G EMF QA Q+
Sbjct: 408 FPPCVVDINTLPKHSPYTQYARSQGSSIIYGYEMFAEQALLQF 450
>gnl|CDD|183585 PRK12548, PRK12548, shikimate 5-dehydrogenase; Provisional.
Length = 289
Score = 161 bits (409), Expect = 4e-45
Identities = 97/281 (34%), Positives = 138/281 (49%), Gaps = 29/281 (10%)
Query: 253 TKVFGIIGKPVGHSKSPILYNEAFKSVGFNGVFV--HLLVDDIAKFFQTYSSNDFAGFSC 310
T + G+IG PVGHS SP +YN +F+ G + ++ + VD + + + + G +
Sbjct: 9 TGLLGLIGSPVGHSGSPAMYNYSFQKAGLDYAYLAFDIPVDKVPDAIKAIKTFNMRGANV 68
Query: 311 TIPHKEAAVKCCDEVDTVAKSIGAVNCIIRRQSDGKLFGYNTDYVGAISAIEDGLRGRLN 370
T+P K A K DE+ A+ IGAVN I+ DGKL G+ TD +G + + +
Sbjct: 69 TMPCKSEAAKYMDELSPAARIIGAVNTIV--NDDGKLTGHITDGLGFVRNLREH------ 120
Query: 371 VSGGVSSALAGKLFVVIGAGGAGKALAYGAKAKGAR-VVIANRT---YDRARELAETVGG 426
GV + GK VIGAGGA A+ GA+ + I N Y+RA + AE +
Sbjct: 121 ---GVD--VKGKKLTVIGAGGAATAIQVQCALDGAKEITIFNIKDDFYERAEQTAEKIKQ 175
Query: 427 -------HALSLADLENFNPE--DGMILANTTSIGMQPKVDETPIPKHALGHYALVF-DA 476
+ L D E E IL N T +GM+P ET I ++ LV D
Sbjct: 176 EVPECIVNVYDLNDTEKLKAEIASSDILVNATLVGMKPNDGETNIKDTSVFRKDLVVADT 235
Query: 477 VYTPKITRLLREAEESGATIVSGLEMFIGQAYEQYERFTGL 517
VY PK T+LL +AE +G V GL M + Q E Y+ +TG
Sbjct: 236 VYNPKKTKLLEDAEAAGCKTVGGLGMLLWQGAEAYKLYTGK 276
>gnl|CDD|133443 cd01065, NAD_bind_Shikimate_DH, NAD(P) binding domain of Shikimate
dehydrogenase. Shikimate dehydrogenase (DH) is an amino
acid DH family member. Shikimate pathway links
metabolism of carbohydrates to de novo biosynthesis of
aromatic amino acids, quinones and folate. It is
essential in plants, bacteria, and fungi but absent in
mammals, thus making enzymes involved in this pathway
ideal targets for broad spectrum antibiotics and
herbicides. Shikimate DH catalyzes the reduction of
3-hydroshikimate to shikimate using the cofactor NADH.
Amino acid DH-like NAD(P)-binding domains are members of
the Rossmann fold superfamily and include glutamate,
leucine, and phenylalanine DHs, methylene
tetrahydrofolate DH, methylene-tetrahydromethanopterin
DH, methylene-tetrahydropholate DH/cyclohydrolase,
Shikimate DH-like proteins, malate oxidoreductases, and
glutamyl tRNA reductase. Amino acid DHs catalyze the
deamination of amino acids to keto acids with NAD(P)+ as
a cofactor. The NAD(P)-binding Rossmann fold superfamily
includes a wide variety of protein families including
NAD(P)- binding domains of alcohol DHs,
tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate DH, lactate/malate DHs,
formate/glycerate DHs, siroheme synthases,
6-phosphogluconate DHs, amino acid DHs, repressor rex,
NAD-binding potassium channel domain, CoA-binding, and
ornithine cyclodeaminase-like domains. These domains
have an alpha-beta-alpha configuration. NAD binding
involves numerous hydrogen and van der Waals contacts.
Length = 155
Score = 152 bits (387), Expect = 1e-43
Identities = 66/168 (39%), Positives = 95/168 (56%), Gaps = 16/168 (9%)
Query: 352 TDYVGAISAIEDGLRGRLNVSGGVSSALAGKLFVVIGAGGAGKALAYGAKAKGA-RVVIA 410
TD +G + A+E+ L GK +++GAGGA +A+AY GA ++VI
Sbjct: 1 TDGLGFVRALEEAGIE-----------LKGKKVLILGAGGAARAVAYALAELGAAKIVIV 49
Query: 411 NRTYDRARELAETVG--GHALSLADLENFNPEDGMILANTTSIGMQPKVDETPIPKHALG 468
NRT ++A+ LAE G G A++ DLE + ++ NTT +GM+P DE P+P L
Sbjct: 50 NRTLEKAKALAERFGELGIAIAYLDLEEL-LAEADLIINTTPVGMKP-GDELPLPPSLLK 107
Query: 469 HYALVFDAVYTPKITRLLREAEESGATIVSGLEMFIGQAYEQYERFTG 516
+V+D VY P T LL+EA GA + GLEM + QA E +E +TG
Sbjct: 108 PGGVVYDVVYNPLETPLLKEARALGAKTIDGLEMLVYQAAEAFELWTG 155
>gnl|CDD|235036 PRK02412, aroD, 3-dehydroquinate dehydratase; Provisional.
Length = 253
Score = 146 bits (371), Expect = 4e-40
Identities = 67/229 (29%), Positives = 119/229 (51%), Gaps = 14/229 (6%)
Query: 24 TLICVPIMGESVDKMVVDMGKANASGADLVEIRLDGLKNFNPRENIKTLIKE-----SPV 78
I VPIMG+++++++ + + AD++E R D L+ + E++ +
Sbjct: 16 PKIIVPIMGKTLEEVLAEALAISKYDADIIEWRADFLEKISDVESVLAAAPAIREKFAGK 75
Query: 79 PTLFTYRPIWEGGQYDGDENERVDVLRLAMELGA-DYIDVELQVARE-FNDSIRGKKPEK 136
P LFT+R EGG+ + E + +++ ++ G DYIDVEL ++ + +
Sbjct: 76 PLLFTFRTAKEGGEIALSDEEYLALIKAVIKSGLPDYIDVELFSGKDVVKEMVAFAHEHG 135
Query: 137 CKVIVSSHNYQYTPSVEDLSNLVARIQASGADIVKFATTALDITDVARVFQITVH----- 191
KV++S H+++ TP E++ + ++++ GADIVK A DV + T
Sbjct: 136 VKVVLSYHDFEKTPPKEEIVERLRKMESLGADIVKIAVMPQSEQDVLTLLNATREMKELY 195
Query: 192 SQVPIIGLVMGERGLISRILCAKFGGFLTFGTLENGIVSAPGQPTIKDL 240
+ P+I + MG+ G ISR+ FG TF +L+ SAPGQ +++DL
Sbjct: 196 ADQPLITMSMGKLGRISRLAGEVFGSSWTFASLDK--ASAPGQISVEDL 242
>gnl|CDD|233580 TIGR01809, Shik-DH-AROM, shikimate-5-dehydrogenase, fungal
AROM-type. This model represents a clade of
shikimate-5-dehydrogenases found in Corynebacterium,
Mycobacteria and fungi. The fungal sequences are
pentafunctional proteins known as AroM which contain the
central five seven steps in the chorismate biosynthesis
pathway. The Corynebacterium and Mycobacterial sequences
represent the sole shikimate-5-dehydrogenases in species
which otherwise have every enzyme of the chorismate
biosynthesis pathway [Amino acid biosynthesis, Aromatic
amino acid family].
Length = 282
Score = 126 bits (317), Expect = 2e-32
Identities = 78/283 (27%), Positives = 121/283 (42%), Gaps = 24/283 (8%)
Query: 254 KVFGIIGKPVGHSKSPILYNEAFKSVGFNGVFVHLLVDDIAKFFQTYSSN--DFAGFSCT 311
K IIGKP+ HS+SP L+N ++ +G + + S F G S T
Sbjct: 6 KKAFIIGKPIAHSRSPHLHNAGYEILGLPDKTYEFETCSAEELKEVLSGFGPQFGGASVT 65
Query: 312 IPHKEAAVKCCDEVDTVAKSIGAVNCIIRRQSDGKLFGYNTDYVGAISAIEDGLRGRLNV 371
IP K A ++ DE A IG+VN ++R Q +G G NTD+ G A+
Sbjct: 66 IPLKFAILRFADEHTDRASLIGSVNTLLRTQ-NGIWKGDNTDWDGIAGAL---------A 115
Query: 372 SGGVSSALAGKLFVVIGAGGAGKALAYGAKAKG-ARVVIANRTYDRARELAET-VGGHAL 429
+ G LAG +VIGAGG +A Y + G + + NR D+ L + V +
Sbjct: 116 NIGKFEPLAGFRGLVIGAGGTSRAAVYALASLGVTDITVINRNPDKLSRLVDLGVQVGVI 175
Query: 430 ----SLADLENFNPEDGMILANT--TSIGMQPKVDETPIPKHALGHYALV---FDAVYTP 480
+ + +L +T + +P L + DA Y P
Sbjct: 176 TRLEGDSGGLAIE-KAAEVLVSTVPADVPADYVDLFATVPFLLLKRKSSEGIFLDAAYDP 234
Query: 481 KITRLLREAEESGATIVSGLEMFIGQAYEQYERFTGLPGKMNA 523
T L+ +G ++SGL+M + Q + Q+E++TG+P A
Sbjct: 235 WPTPLVAIVSAAGWRVISGLQMLLHQGFAQFEQWTGMPAPREA 277
>gnl|CDD|183586 PRK12549, PRK12549, shikimate 5-dehydrogenase; Reviewed.
Length = 284
Score = 121 bits (307), Expect = 6e-31
Identities = 85/290 (29%), Positives = 127/290 (43%), Gaps = 45/290 (15%)
Query: 257 GIIGKPVGHSKSPILYNEAFKSVGFNGVF-------VHLLVDDIAKFFQTYSSNDFAGFS 309
G+IG + S SP ++ + G V+ + L D + + FAG +
Sbjct: 9 GLIGAGIQASLSPAMHEAEGDAQGLRYVYRLIDLDALGLTADALPELLDAAERMGFAGLN 68
Query: 310 CTIPHKEAAVKCCDEVDTVAKSIGAVNCIIRRQSDGKLFGYNTDYVGAISAIEDGL---- 365
T P K+A + DE+ A+++GAVN ++ R DG+ G+NTD+ G + GL
Sbjct: 69 ITHPCKQAVIPHLDELSDDARALGAVNTVVFR--DGRRIGHNTDWSGFAESFRRGLPDAS 126
Query: 366 RGRLNVSGGVSSALAGKLFVVIGAGGAGKALAYGAKAKGA-RVVIANRTYDRARELAETV 424
R+ V +GAGGAG A+A+ G R+ I + RA LA+ +
Sbjct: 127 LERV---------------VQLGAGGAGAAVAHALLTLGVERLTIFDVDPARAAALADEL 171
Query: 425 GGH-----ALSLADLENFNPE-DGMILANTTSIGMQPKVDETPIPKHAL--GHYALVFDA 476
A + +DL DG++ + T GM K P+P L G + V D
Sbjct: 172 NARFPAARATAGSDLAAALAAADGLV--HATPTGM-AKHPGLPLPAELLRPGLW--VADI 226
Query: 477 VYTPKITRLLREAEESGATIVSGLEMFIGQAYEQYERFTGL---PGKMNA 523
VY P T LLR A G + G M + QA + +E FTG +M A
Sbjct: 227 VYFPLETELLRAARALGCRTLDGGGMAVFQAVDAFELFTGREPDAERMLA 276
>gnl|CDD|183721 PRK12749, PRK12749, quinate/shikimate dehydrogenase; Reviewed.
Length = 288
Score = 117 bits (293), Expect = 4e-29
Identities = 84/278 (30%), Positives = 139/278 (50%), Gaps = 28/278 (10%)
Query: 254 KVFGIIGKPVGHSKSPILYNEAFKSVGFNGVFVHLLVDD--IAKFFQTYSSNDFAGFSCT 311
++ G++ P+ HS SP + N+A + G ++ VD+ + + G +
Sbjct: 8 ELIGLMAYPIRHSLSPEMQNKALEKAGLPFTYMAFEVDNDSFPGAIEGLKALKMRGTGVS 67
Query: 312 IPHKEAAVKCCDEVDTVAKSIGAVNCIIRRQSDGKLFGYNTDYVGAISAIEDGLRGRLNV 371
+P+K+ A + DE+ AK +GA+N I+ DG L GYNTD G I AI++
Sbjct: 68 MPNKQLACEYVDELTPAAKLVGAINTIV--NDDGYLRGYNTDGTGHIRAIKE-------- 117
Query: 372 SGGVSSALAGKLFVVIGAGGAGKALAYGAKAKGARVV-IANRT---YDRARELAETVGGH 427
SG + GK V++GAGGA A+ +G + + + NR +D+A A+ V +
Sbjct: 118 SG---FDIKGKTMVLLGAGGASTAIGAQGAIEGLKEIKLFNRRDEFFDKALAFAQRVNEN 174
Query: 428 A------LSLADLENFNPE--DGMILANTTSIGMQPKVDETPIPKHALGHYAL-VFDAVY 478
LAD + F IL N T +GM+P +E+ + +L H L V + VY
Sbjct: 175 TDCVVTVTDLADQQAFAEALASADILTNGTKVGMKPLENESLVNDISLLHPGLLVTECVY 234
Query: 479 TPKITRLLREAEESGATIVSGLEMFIGQAYEQYERFTG 516
P +T+LL++A+++G + G M + Q EQ+ +TG
Sbjct: 235 NPHMTKLLQQAQQAGCKTIDGYGMLLWQGAEQFTLWTG 272
>gnl|CDD|149523 pfam08501, Shikimate_dh_N, Shikimate dehydrogenase substrate
binding domain. This domain is the substrate binding
domain of shikimate dehydrogenase.
Length = 83
Score = 106 bits (268), Expect = 6e-28
Identities = 39/83 (46%), Positives = 55/83 (66%), Gaps = 2/83 (2%)
Query: 258 IIGKPVGHSKSPILYNEAFKSVGFNGVFVHLLV--DDIAKFFQTYSSNDFAGFSCTIPHK 315
+IG P+ HS SP+++N AFK++G NGV+V V D++ +F + + F G + TIPHK
Sbjct: 1 LIGNPISHSLSPLIHNAAFKALGLNGVYVAFEVPPDNLPEFVEGLRALGFRGLNVTIPHK 60
Query: 316 EAAVKCCDEVDTVAKSIGAVNCI 338
EAA+ DE+ AK IGAVN I
Sbjct: 61 EAAIPLLDELSPEAKRIGAVNTI 83
>gnl|CDD|183587 PRK12550, PRK12550, shikimate 5-dehydrogenase; Reviewed.
Length = 272
Score = 109 bits (274), Expect = 1e-26
Identities = 71/214 (33%), Positives = 101/214 (47%), Gaps = 24/214 (11%)
Query: 307 GFSCTIPHKEAAVKCCDEVDTVAKSIGAVNCIIRRQSDGKLFGYNTDYVGAISAIEDGLR 366
G + ++P KEA + DE+D A++I +VN I+ +DG L YNTDY+ AI L
Sbjct: 62 GCAVSMPFKEAVIPLVDELDPSAQAIESVNTIV--NTDGHLKAYNTDYI----AIAKLLA 115
Query: 367 GRLNVSGGVSSALAGKLFVVIGAGGAGKALAYGAKAKG-ARVVIANRTYDRARELAETVG 425
S V L + G+GG KA+A + G I R + LAE G
Sbjct: 116 -----SYQVPPDLV---VALRGSGGMAKAVAAALRDAGFTDGTIVARNEKTGKALAELYG 167
Query: 426 -GHALSLADLENFNPEDGMILANTTSIGMQ--PKVDETPIPKHALGHYALVFDAVYTPKI 482
DL + IL N T IGM P+ D+ P+ + ++VFD V P
Sbjct: 168 YEWR---PDLGGIEAD---ILVNVTPIGMAGGPEADKLAFPEAEIDAASVVFDVVALPAE 221
Query: 483 TRLLREAEESGATIVSGLEMFIGQAYEQYERFTG 516
T L+R A G T+++G E+ QA EQ+ +TG
Sbjct: 222 TPLIRYARARGKTVITGAEVIALQAVEQFVLYTG 255
>gnl|CDD|184156 PRK13575, PRK13575, 3-dehydroquinate dehydratase; Provisional.
Length = 238
Score = 103 bits (258), Expect = 6e-25
Identities = 60/228 (26%), Positives = 103/228 (45%), Gaps = 18/228 (7%)
Query: 33 ESVDKMVVDMGKANASGADLVEIRLDGLKNFNPR---ENIKTL-IKESPVPTLFTYRPIW 88
S+++ ++ D++E+R+D +N E I L + + L TYR
Sbjct: 14 LSIEETLIQKINHRIDAIDIIELRIDQWENVTVDQLAEMITKLKVLQDSFKLLVTYRTKL 73
Query: 89 EGGQYDGDENERVDVLR-LAMELGADYIDVELQVAREFN---DSIRGKKPEKCKVIVSSH 144
+GG + +++L LA G D ID+E Q + I + +V++S H
Sbjct: 74 QGGYGQFTNDLYLNLLSDLANINGIDMIDIEWQADIDIEKHQRLITHLQQYNKEVVISHH 133
Query: 145 NYQYTPSVEDLSNLVARIQASGADIVKFATTALDITDVARVFQI------TVHSQVPIIG 198
N++ TP +++L + ++Q + VK A + DV + Q T+ +V +G
Sbjct: 134 NFESTPPLDELKFIFFKMQKFNPEYVKLAVMPHNKNDVLNLLQAMSTFSDTMDCKV--VG 191
Query: 199 LVMGERGLISRILCAKFGGFLTFGTLENGIVSAPGQPTIKDLLDLYNF 246
+ M + GLISR FGG L++G + G APGQ + DL
Sbjct: 192 ISMSKLGLISRTAQGVFGGALSYGCI--GEPQAPGQIHVTDLKAQVTL 237
>gnl|CDD|172521 PRK14027, PRK14027, quinate/shikimate dehydrogenase; Provisional.
Length = 283
Score = 88.9 bits (220), Expect = 1e-19
Identities = 81/282 (28%), Positives = 122/282 (43%), Gaps = 31/282 (10%)
Query: 252 DTKVFGIIGKPVGHSKSPILYNEAFKSVGFNGVF--VHLLVD-----DIAKFFQTYSSND 304
D+ + G+IG+ + S++P ++ + G V+ + L D+
Sbjct: 3 DSILLGLIGQGLDLSRTPAMHEAEGLAQGRATVYRRIDTLGSRASGQDLKTLLDAALYLG 62
Query: 305 FAGFSCTIPHKEAAVKCCDEVDTVAKSIGAVNCIIRRQSDGKLFGYNTDYVGAISAIEDG 364
F G + T P+K+A + DEV A +GAVN ++ + G G+NTD G +E+G
Sbjct: 63 FNGLNITHPYKQAVLPLLDEVSEQATQLGAVNTVVI-DATGHTTGHNTDVSGFGRGMEEG 121
Query: 365 LRGRLNVSGGVSSALAGKLFVVIGAGGAGKALAYGAKAKGA-RVVIANRTYDRARELAET 423
L S V +GAGG G A+AY G ++ +A+ RA+ LA+
Sbjct: 122 LPNAKLDS-----------VVQVGAGGVGNAVAYALVTHGVQKLQVADLDTSRAQALADV 170
Query: 424 ----VGGHALSLADL----ENFNPEDGMILANTTSIGMQPKVDETPIPKHALGHYALVFD 475
VG A+ D + DG++ N T +GM P T L V D
Sbjct: 171 INNAVGREAVVGVDARGIEDVIAAADGVV--NATPMGM-PAHPGTAFDVSCLTKDHWVGD 227
Query: 476 AVYTPKITRLLREAEESGATIVSGLEMFIGQAYEQYERFTGL 517
VY P T LL+ A G + G M I QA + + FTGL
Sbjct: 228 VVYMPIETELLKAARALGCETLDGTRMAIHQAVDAFRLFTGL 269
>gnl|CDD|216527 pfam01488, Shikimate_DH, Shikimate / quinate 5-dehydrogenase. This
family contains both shikimate and quinate
dehydrogenases. Shikimate 5-dehydrogenase catalyzes the
conversion of shikimate to 5-dehydroshikimate. This
reaction is part of the shikimate pathway which is
involved in the biosynthesis of aromatic amino acids.
Quinate 5-dehydrogenase catalyzes the conversion of
quinate to 5-dehydroquinate. This reaction is part of
the quinate pathway where quinic acid is exploited as a
source of carbon in prokaryotes and microbial
eukaryotes. Both the shikimate and quinate pathways
share two common pathway metabolites 3-dehydroquinate
and dehydroshikimate.
Length = 133
Score = 72.7 bits (179), Expect = 2e-15
Identities = 31/81 (38%), Positives = 43/81 (53%), Gaps = 6/81 (7%)
Query: 379 LAGKLFVVIGAGGAGKALAYGAKAKGAR-VVIANRTYDRARELAETVGG--HALSLADLE 435
L GK ++IGAG + A +KGA+ + IANRT ++A+ELAE AL L +LE
Sbjct: 10 LKGKKVLLIGAGEMARLAAKHLLSKGAKKITIANRTLEKAKELAEEFPVGGEALPLDELE 69
Query: 436 NFNPE-DGMILANTTSIGMQP 455
E D I+ + TS
Sbjct: 70 ELLAEAD--IVISATSAPTPI 88
>gnl|CDD|234592 PRK00045, hemA, glutamyl-tRNA reductase; Reviewed.
Length = 423
Score = 64.4 bits (158), Expect = 5e-11
Identities = 32/78 (41%), Positives = 43/78 (55%), Gaps = 14/78 (17%)
Query: 372 SGGVSSA-----LAGKLF--------VVIGAGGAGKALAYGAKAKGAR-VVIANRTYDRA 417
+G VS A LA ++F +VIGAG G+ +A KG R + +ANRT +RA
Sbjct: 160 AGAVSVASAAVELAKQIFGDLSGKKVLVIGAGEMGELVAKHLAEKGVRKITVANRTLERA 219
Query: 418 RELAETVGGHALSLADLE 435
ELAE GG A+ L +L
Sbjct: 220 EELAEEFGGEAIPLDELP 237
>gnl|CDD|133452 cd05213, NAD_bind_Glutamyl_tRNA_reduct, NADP-binding domain of
glutamyl-tRNA reductase. Glutamyl-tRNA reductase
catalyzes the conversion of glutamyl-tRNA to
glutamate-1-semialdehyde, initiating the synthesis of
tetrapyrrole. Whereas tRNAs are generally associated
with peptide bond formation in protein translation, here
the tRNA activates glutamate in the initiation of
tetrapyrrole biosynthesis in archaea, plants and many
bacteria. In the first step, activated glutamate is
reduced to glutamate-1-semi-aldehyde via the NADPH
dependent glutamyl-tRNA reductase. Glutamyl-tRNA
reductase forms a V-shaped dimer. Each monomer has 3
domains: an N-terminal catalytic domain, a classic
nucleotide binding domain, and a C-terminal dimerization
domain. Although the representative structure 1GPJ lacks
a bound NADPH, a theoretical binding pocket has been
described. (PMID 11172694). Amino acid dehydrogenase
(DH)-like NAD(P)-binding domains are members of the
Rossmann fold superfamily and include glutamate,
leucine, and phenylalanine DHs, methylene
tetrahydrofolate DH, methylene-tetrahydromethanopterin
DH, methylene-tetrahydropholate DH/cyclohydrolase,
Shikimate DH-like proteins, malate oxidoreductases, and
glutamyl tRNA reductase. Amino acid DHs catalyze the
deamination of amino acids to keto acids with NAD(P)+ as
a cofactor. The NAD(P)-binding Rossmann fold superfamily
includes a wide variety of protein families including
NAD(P)- binding domains of alcohol DHs,
tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate DH, lactate/malate DHs,
formate/glycerate DHs, siroheme synthases,
6-phosphogluconate DH, amino acid DHs, repressor rex,
NAD-binding potassium channel domain, CoA-binding, and
ornithine cyclodeaminase-like domains. These domains
have an alpha-beta-alpha configuration. NAD binding
involves numerous hydrogen and van der Waals contacts.
Length = 311
Score = 60.0 bits (146), Expect = 1e-09
Identities = 28/58 (48%), Positives = 37/58 (63%), Gaps = 1/58 (1%)
Query: 379 LAGKLFVVIGAGGAG-KALAYGAKAKGARVVIANRTYDRARELAETVGGHALSLADLE 435
L GK +VIGAG G A + A A + IANRTY+RA ELA+ +GG+A+ L +L
Sbjct: 176 LKGKKVLVIGAGEMGELAAKHLAAKGVAEITIANRTYERAEELAKELGGNAVPLDELL 233
>gnl|CDD|223450 COG0373, HemA, Glutamyl-tRNA reductase [Coenzyme metabolism].
Length = 414
Score = 57.6 bits (140), Expect = 7e-09
Identities = 25/70 (35%), Positives = 38/70 (54%), Gaps = 2/70 (2%)
Query: 379 LAGKLFVVIGAGGAG-KALAYGAKAKGARVVIANRTYDRARELAETVGGHALSLADLENF 437
L K +VIGAG G + A+ ++ IANRT +RA ELA+ +G A++L +L
Sbjct: 176 LKDKKVLVIGAGEMGELVAKHLAEKGVKKITIANRTLERAEELAKKLGAEAVALEELLEA 235
Query: 438 -NPEDGMILA 446
D +I +
Sbjct: 236 LAEADVVISS 245
>gnl|CDD|233242 TIGR01035, hemA, glutamyl-tRNA reductase. This enzyme, together
with glutamate-1-semialdehyde-2,1-aminomutase
(TIGR00713), leads to the production of
delta-amino-levulinic acid from Glu-tRNA [Biosynthesis
of cofactors, prosthetic groups, and carriers, Heme,
porphyrin, and cobalamin].
Length = 417
Score = 52.8 bits (127), Expect = 3e-07
Identities = 29/73 (39%), Positives = 48/73 (65%), Gaps = 1/73 (1%)
Query: 379 LAGKLFVVIGAGGAGKALAYGAKAKGA-RVVIANRTYDRARELAETVGGHALSLADLENF 437
L GK ++IGAG G+ +A KG +++IANRTY+RA +LA+ +GG A+ DLE +
Sbjct: 178 LKGKKALLIGAGEMGELVAKHLLRKGVGKILIANRTYERAEDLAKELGGEAVKFEDLEEY 237
Query: 438 NPEDGMILANTTS 450
E +++++T +
Sbjct: 238 LAEADIVISSTGA 250
>gnl|CDD|237433 PRK13576, PRK13576, 3-dehydroquinate dehydratase; Provisional.
Length = 216
Score = 48.6 bits (116), Expect = 2e-06
Identities = 39/133 (29%), Positives = 61/133 (45%), Gaps = 11/133 (8%)
Query: 46 NASGADLVEIRLDGLKNFNPRENIKTLIKESPVPTLFTYRPIWEGGQYDGDENERVDVLR 105
N ADL+E+RLD LK+ I+ L K + T R EGG + D+ ++ +L+
Sbjct: 22 NFLDADLIELRLDYLKDR-EVSVIEFLDKYKD-KLIVTLRDKAEGGINELDDELKISLLK 79
Query: 106 LAMELGADYIDVELQVAREFNDSIRGKKPEKCKVIVSSHNYQYTPSVEDLSNLVARIQAS 165
+ Y DVE +++N K IVS H + Y P+ E++ +V++
Sbjct: 80 ELYDKQFLY-DVEASFLQKYNVPYDNK-------IVSIHYFDYLPTSEEVKEIVSKFYEK 131
Query: 166 GADIVKFATTALD 178
A VK A L
Sbjct: 132 -AFSVKIAVLGLK 143
>gnl|CDD|187648 cd08944, SDR_c12, classical (c) SDR, subgroup 12. These are
classical SDRs, with the canonical active site tetrad
and glycine-rich NAD-binding motif. 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 = 246
Score = 45.6 bits (108), Expect = 3e-05
Identities = 22/55 (40%), Positives = 31/55 (56%), Gaps = 1/55 (1%)
Query: 379 LAGKLFVVIGAG-GAGKALAYGAKAKGARVVIANRTYDRARELAETVGGHALSLA 432
L GK+ +V GAG G G A A +GARVV+A+ A+ + + G AL+L
Sbjct: 1 LEGKVAIVTGAGAGIGAACAARLAREGARVVVADIDGGAAQAVVAQIAGGALALR 55
>gnl|CDD|181159 PRK07890, PRK07890, short chain dehydrogenase; Provisional.
Length = 258
Score = 44.6 bits (106), Expect = 7e-05
Identities = 25/58 (43%), Positives = 33/58 (56%), Gaps = 4/58 (6%)
Query: 379 LAGKLFVVIGAG-GAGKALAYGAKAKGARVVIANRTYDRARELAETV---GGHALSLA 432
L GK+ VV G G G G+ LA A GA VV+A RT +R E+A + G AL++
Sbjct: 3 LKGKVVVVSGVGPGLGRTLAVRAARAGADVVLAARTAERLDEVAAEIDDLGRRALAVP 60
>gnl|CDD|187639 cd08934, CAD_SDR_c, clavulanic acid dehydrogenase (CAD), classical
(c) SDR. CAD catalyzes the NADP-dependent reduction of
clavulanate-9-aldehyde to clavulanic acid, a
beta-lactamase inhibitor. 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 = 243
Score = 44.1 bits (104), Expect = 9e-05
Identities = 27/57 (47%), Positives = 31/57 (54%), Gaps = 4/57 (7%)
Query: 379 LAGKLFVVIGAG-GAGKALAYGAKAKGARVVIANRTYDRARELA---ETVGGHALSL 431
L GK+ +V GA G G+A A A+GA V IA R DR LA E GG AL L
Sbjct: 1 LQGKVALVTGASSGIGEATARALAAEGAAVAIAARRVDRLEALADELEAEGGKALVL 57
>gnl|CDD|236216 PRK08277, PRK08277, D-mannonate oxidoreductase; Provisional.
Length = 278
Score = 43.7 bits (104), Expect = 2e-04
Identities = 20/58 (34%), Positives = 31/58 (53%), Gaps = 4/58 (6%)
Query: 379 LAGKLFVVIGAGGA-GKALAYGAKAKGARVVIANRTYDRARELAETV---GGHALSLA 432
L GK+ V+ G GG G A+A GA+V I +R ++A + + GG AL++
Sbjct: 8 LKGKVAVITGGGGVLGGAMAKELARAGAKVAILDRNQEKAEAVVAEIKAAGGEALAVK 65
>gnl|CDD|183772 PRK12823, benD, 1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate
dehydrogenase; Provisional.
Length = 260
Score = 43.0 bits (102), Expect = 2e-04
Identities = 30/63 (47%), Positives = 41/63 (65%), Gaps = 6/63 (9%)
Query: 380 AGKLFVVIGAG-GAGKALAYGAKAKGARVVIANRT---YDRARELAETVGGHALSL-ADL 434
AGK+ VV GA G G+ +A A A+GARVV+ +R+ ++ A EL GG AL+L ADL
Sbjct: 7 AGKVVVVTGAAQGIGRGVALRAAAEGARVVLVDRSELVHEVAAELRAA-GGEALALTADL 65
Query: 435 ENF 437
E +
Sbjct: 66 ETY 68
>gnl|CDD|181517 PRK08642, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 253
Score = 43.2 bits (102), Expect = 2e-04
Identities = 23/74 (31%), Positives = 37/74 (50%), Gaps = 3/74 (4%)
Query: 382 KLFVVIGAG-GAGKALAYGAKAKGARVVIA-NRTYDRARELAETVGGHALSL-ADLENFN 438
+ +V G G G A+A +GARVV+ +++ D A LA+ +G A++L AD+ +
Sbjct: 6 QTVLVTGGSRGLGAAIARAFAREGARVVVNYHQSEDAAEALADELGDRAIALQADVTDRE 65
Query: 439 PEDGMILANTTSIG 452
M T G
Sbjct: 66 QVQAMFATATEHFG 79
>gnl|CDD|217556 pfam03435, Saccharop_dh, Saccharopine dehydrogenase. This family
comprised of three structural domains that can not be
separated in the linear sequence. In some organisms this
enzyme is found as a bifunctional polypeptide with
lysine ketoglutarate reductase. The saccharopine
dehydrogenase can also function as a saccharopine
reductase.
Length = 380
Score = 43.4 bits (103), Expect = 3e-04
Identities = 27/120 (22%), Positives = 50/120 (41%), Gaps = 4/120 (3%)
Query: 384 FVVIGAGGAGKALA-YGAKAKGARVVIANRTYDRARELAETVGGHALSLADLENFNPED- 441
++IGAGG G+ +A A+ + +A+R+ ++A+ LA G ++ N E
Sbjct: 1 VLIIGAGGVGQGVAPLLARHGDLEITVADRSLEKAQALAAPKLGLRFIAIAVDADNYEAL 60
Query: 442 -GMILANTTSIGMQPKVDETPIPKHALGHYALVFDAVY-TPKITRLLREAEESGATIVSG 499
++ I + P + K + D Y L +A+++G T V G
Sbjct: 61 VALLKEGDLVINLAPPFLSLTVLKACIETGVHYVDTSYLREAQLALHEKAKDAGVTAVLG 120
>gnl|CDD|176178 cd05188, MDR, Medium chain reductase/dehydrogenase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
The medium chain reductase/dehydrogenases
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH) , quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. ADH-like proteins
typically form dimers (typically higher plants, mammals)
or tetramers (yeast, bacteria), and generally have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. The active site zinc is
coordinated by a histidine, two cysteines, and a water
molecule. The second zinc seems to play a structural
role, affects subunit interactions, and is typically
coordinated by 4 cysteines. Other MDR members have only
a catalytic zinc, and some contain no coordinated zinc.
Length = 271
Score = 42.3 bits (100), Expect = 4e-04
Identities = 20/49 (40%), Positives = 30/49 (61%), Gaps = 1/49 (2%)
Query: 380 AGKLFVVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAETVGGHA 428
G +V+GAGG G A AKA GARV++ +R+ ++ ELA+ +G
Sbjct: 134 PGDTVLVLGAGGVGLLAAQLAKAAGARVIVTDRSDEK-LELAKELGADH 181
>gnl|CDD|235633 PRK05872, PRK05872, short chain dehydrogenase; Provisional.
Length = 296
Score = 42.3 bits (100), Expect = 5e-04
Identities = 20/57 (35%), Positives = 29/57 (50%), Gaps = 1/57 (1%)
Query: 373 GGVSSALAGKLFVVIGAG-GAGKALAYGAKAKGARVVIANRTYDRARELAETVGGHA 428
G ++LAGK+ VV GA G G LA A+GA++ + + LA +GG
Sbjct: 1 GPPMTSLAGKVVVVTGAARGIGAELARRLHARGAKLALVDLEEAELAALAAELGGDD 57
>gnl|CDD|236241 PRK08324, PRK08324, short chain dehydrogenase; Validated.
Length = 681
Score = 42.9 bits (102), Expect = 5e-04
Identities = 25/57 (43%), Positives = 33/57 (57%), Gaps = 3/57 (5%)
Query: 379 LAGKLFVVIGAGGA-GKALAYGAKAKGARVVIANRTYDRARELAETVGG--HALSLA 432
LAGK+ +V GA G GKA A A+GA VV+A+ + A A +GG AL +A
Sbjct: 420 LAGKVALVTGAAGGIGKATAKRLAAEGACVVLADLDEEAAEAAAAELGGPDRALGVA 476
>gnl|CDD|202773 pfam03807, F420_oxidored, NADP oxidoreductase coenzyme
F420-dependent.
Length = 93
Score = 39.1 bits (92), Expect = 6e-04
Identities = 22/41 (53%), Positives = 27/41 (65%), Gaps = 1/41 (2%)
Query: 386 VIGAGGAGKALAYGAKAKGARVVIAN-RTYDRARELAETVG 425
+IGAG G+ALA G A G VVIAN R ++A LAE +G
Sbjct: 4 IIGAGNMGEALARGLAAAGHEVVIANSRNPEKAAALAEELG 44
>gnl|CDD|235925 PRK07067, PRK07067, sorbitol dehydrogenase; Provisional.
Length = 257
Score = 41.6 bits (98), Expect = 7e-04
Identities = 33/99 (33%), Positives = 49/99 (49%), Gaps = 19/99 (19%)
Query: 379 LAGKLFVVIG-AGGAGKALAYGAKAKGARVVIANRTYDRARELAETVGGHALSL------ 431
L GK+ ++ G A G G+A+A A+GARVVIA+ RAR A +G A+++
Sbjct: 4 LQGKVALLTGAASGIGEAVAERYLAEGARVVIADIKPARARLAALEIGPAAIAVSLDVTR 63
Query: 432 ---------ADLENFNPEDGMILANTTSI-GMQPKVDET 460
A +E F D IL N ++ M P +D +
Sbjct: 64 QDSIDRIVAAAVERFGGID--ILFNNAALFDMAPILDIS 100
>gnl|CDD|235975 PRK07231, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 251
Score = 41.0 bits (97), Expect = 0.001
Identities = 21/57 (36%), Positives = 34/57 (59%), Gaps = 3/57 (5%)
Query: 379 LAGKLFVVIGAG-GAGKALAYGAKAKGARVVIANRTYDRARELAETVG--GHALSLA 432
L GK+ +V GA G G+ +A A+GARVV+ +R + A +A + G A+++A
Sbjct: 3 LEGKVAIVTGASSGIGEGIARRFAAEGARVVVTDRNEEAAERVAAEILAGGRAIAVA 59
>gnl|CDD|214966 smart01002, AlaDh_PNT_C, Alanine dehydrogenase/PNT, C-terminal
domain. Alanine dehydrogenase catalyzes the
NAD-dependent reversible reductive amination of pyruvate
into alanine.
Length = 149
Score = 39.4 bits (93), Expect = 0.001
Identities = 23/69 (33%), Positives = 28/69 (40%), Gaps = 3/69 (4%)
Query: 364 GLRGRLNVSGGVSSALAGKLFVVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAET 423
G G L G K VVIGAG G A AK GA V + + R R+L
Sbjct: 6 GGFGML--LTGAGGVPPAK-VVVIGAGVVGLGAAATAKGLGAEVTVLDVRPARLRQLESL 62
Query: 424 VGGHALSLA 432
+G +L
Sbjct: 63 LGARFTTLY 71
>gnl|CDD|240630 cd05305, L-AlaDH, Alanine dehydrogenase NAD-binding and catalytic
domains. Alanine dehydrogenase (L-AlaDH) catalyzes the
NAD-dependent conversion of pyruvate to L-alanine via
reductive amination. Like formate dehydrogenase and
related enzymes, L-AlaDH is comprised of 2 domains
connected by a long alpha helical stretch, each
resembling a Rossmann fold NAD-binding domain. The
NAD-binding domain is inserted within the linear
sequence of the more divergent catalytic domain. Ligand
binding and active site residues are found in the cleft
between the subdomains. L-AlaDH is typically hexameric
and is critical in carbon and nitrogen metabolism in
micro-organisms.
Length = 359
Score = 40.1 bits (95), Expect = 0.002
Identities = 19/55 (34%), Positives = 27/55 (49%), Gaps = 1/55 (1%)
Query: 373 GGVSSALAGKLFVVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAETVGGH 427
GGV K+ V++GAG G+ A A GA V + + +R R L + GG
Sbjct: 161 GGVPGVPPAKV-VILGAGVVGENAARVALGLGAEVTVLDINLERLRYLDDIFGGR 214
>gnl|CDD|235914 PRK07041, PRK07041, short chain dehydrogenase; Provisional.
Length = 230
Score = 39.3 bits (92), Expect = 0.003
Identities = 22/44 (50%), Positives = 27/44 (61%)
Query: 385 VVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAETVGGHA 428
VV G+ G G ALA A+GARV IA+R+ DR A +GG A
Sbjct: 2 VVGGSSGIGLALARAFAAEGARVTIASRSRDRLAAAARALGGGA 45
>gnl|CDD|183833 PRK12939, PRK12939, short chain dehydrogenase; Provisional.
Length = 250
Score = 39.2 bits (92), Expect = 0.003
Identities = 26/63 (41%), Positives = 31/63 (49%), Gaps = 5/63 (7%)
Query: 377 SALAGKLFVVIGAG-GAGKALAYGAKAKGARVVIANRTYDRARELAETV---GGHALSL- 431
S LAGK +V GA G G A A GA V + ARELA + GG A ++
Sbjct: 3 SNLAGKRALVTGAARGLGAAFAEALAEAGATVAFNDGLAAEARELAAALEAAGGRAHAIA 62
Query: 432 ADL 434
ADL
Sbjct: 63 ADL 65
>gnl|CDD|183489 PRK12384, PRK12384, sorbitol-6-phosphate dehydrogenase;
Provisional.
Length = 259
Score = 39.2 bits (92), Expect = 0.003
Identities = 14/45 (31%), Positives = 25/45 (55%), Gaps = 1/45 (2%)
Query: 381 GKLFVVIGAG-GAGKALAYGAKAKGARVVIANRTYDRARELAETV 424
++ VVIG G G L +G +G RV +A+ ++A +A+ +
Sbjct: 2 NQVAVVIGGGQTLGAFLCHGLAEEGYRVAVADINSEKAANVAQEI 46
>gnl|CDD|198065 smart00997, AdoHcyase_NAD, S-adenosyl-L-homocysteine hydrolase, NAD
binding domain.
Length = 162
Score = 38.2 bits (90), Expect = 0.004
Identities = 19/47 (40%), Positives = 24/47 (51%), Gaps = 6/47 (12%)
Query: 363 DGLRGRLNVSGGVSSALAGKLFVVIGAGGAGKALAYGAKAKGARVVI 409
DG+ NV LAGK VV G G GK +A + GARV++
Sbjct: 11 DGILRATNVL------LAGKNVVVAGYGDVGKGVAARLRGLGARVIV 51
>gnl|CDD|240619 cd00401, SAHH, S-Adenosylhomocysteine Hydrolase, NAD-binding and
catalytic domains. S-adenosyl-L-homocysteine hydrolase
(SAHH, AdoHycase) catalyzes the hydrolysis of
S-adenosyl-L-homocysteine (AdoHyc) to form adenosine
(Ado) and homocysteine (Hcy). The equilibrium lies far
on the side of AdoHyc synthesis, but in nature the
removal of Ado and Hyc is sufficiently fast, so that the
net reaction is in the direction of hydrolysis. Since
AdoHyc is a potent inhibitor of S-adenosyl-L-methionine
dependent methyltransferases, AdoHycase plays a critical
role in the modulation of the activity of various
methyltransferases. The enzyme forms homotetramers, with
each monomer binding one molecule of NAD+.
Length = 402
Score = 39.4 bits (93), Expect = 0.005
Identities = 15/31 (48%), Positives = 20/31 (64%)
Query: 379 LAGKLFVVIGAGGAGKALAYGAKAKGARVVI 409
+AGK+ VV G G GK A A+ GARV++
Sbjct: 193 IAGKVVVVAGYGWVGKGCAMRARGLGARVIV 223
>gnl|CDD|181131 PRK07814, PRK07814, short chain dehydrogenase; Provisional.
Length = 263
Score = 38.6 bits (90), Expect = 0.005
Identities = 29/76 (38%), Positives = 38/76 (50%), Gaps = 7/76 (9%)
Query: 379 LAGKLFVVIGAG-GAGKALAYGAKAKGARVVIANRTYDRARELAETV---GGHALSL-AD 433
L ++ VV GAG G G A+A GA V+IA RT + E+AE + G A + AD
Sbjct: 8 LDDQVAVVTGAGRGLGAAIALAFAEAGADVLIAARTESQLDEVAEQIRAAGRRAHVVAAD 67
Query: 434 LENFNPEDGMILANTT 449
L +PE LA
Sbjct: 68 LA--HPEATAGLAGQA 81
>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 = 38.7 bits (91), Expect = 0.006
Identities = 20/65 (30%), Positives = 30/65 (46%), Gaps = 7/65 (10%)
Query: 381 GKLFVVIGA-GGAGKALAYGAKAKGARVVIANRTYDRARELAETV----GGHALSL--AD 433
GK+ V+ GA G GK A +GA V+IA R ++ E A + G + + D
Sbjct: 1 GKVVVITGANSGIGKETARELAKRGAHVIIACRNEEKGEEAAAEIKKETGNAKVEVIQLD 60
Query: 434 LENFN 438
L +
Sbjct: 61 LSSLA 65
>gnl|CDD|187643 cd08939, KDSR-like_SDR_c, 3-ketodihydrosphingosine reductase (KDSR)
and related proteins, classical (c) SDR. These proteins
include members identified as KDSR, ribitol type
dehydrogenase, and others. The group shows strong
conservation of the active site tetrad and glycine rich
NAD-binding motif of the classical SDRs. 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 = 239
Score = 38.4 bits (90), Expect = 0.006
Identities = 17/50 (34%), Positives = 24/50 (48%), Gaps = 1/50 (2%)
Query: 381 GKLFVVIGAG-GAGKALAYGAKAKGARVVIANRTYDRARELAETVGGHAL 429
GK ++ G G GKALA +GA V+I R+ + E E + A
Sbjct: 1 GKHVLITGGSSGIGKALAKELVKEGANVIIVARSESKLEEAVEEIEAEAN 50
>gnl|CDD|235935 PRK07109, PRK07109, short chain dehydrogenase; Provisional.
Length = 334
Score = 38.7 bits (91), Expect = 0.006
Identities = 20/58 (34%), Positives = 31/58 (53%), Gaps = 5/58 (8%)
Query: 385 VVIGA-GGAGKALAYGAKAKGARVVIANRTYDRARELAETV---GGHALSL-ADLENF 437
V+ GA G G+A A +GA+VV+ R + LA + GG AL++ AD+ +
Sbjct: 12 VITGASAGVGRATARAFARRGAKVVLLARGEEGLEALAAEIRAAGGEALAVVADVADA 69
>gnl|CDD|180723 PRK06841, PRK06841, short chain dehydrogenase; Provisional.
Length = 255
Score = 38.5 bits (90), Expect = 0.007
Identities = 25/55 (45%), Positives = 34/55 (61%), Gaps = 1/55 (1%)
Query: 379 LAGKLFVVIG-AGGAGKALAYGAKAKGARVVIANRTYDRARELAETVGGHALSLA 432
L+GK+ VV G A G G A+A AKGARV + +R+ D A A+ +GG+A L
Sbjct: 13 LSGKVAVVTGGASGIGHAIAELFAAKGARVALLDRSEDVAEVAAQLLGGNAKGLV 67
>gnl|CDD|180817 PRK07060, PRK07060, short chain dehydrogenase; Provisional.
Length = 245
Score = 38.2 bits (89), Expect = 0.007
Identities = 23/64 (35%), Positives = 29/64 (45%), Gaps = 5/64 (7%)
Query: 369 LNVSGGVSSALAGKLFVVIGAG-GAGKALAYGAKAKGARVVIANRTYDRARELAETVGGH 427
+N++ S GK +V GA G G+A A +GARVV A R LA G
Sbjct: 1 MNMAFDFS----GKSVLVTGASSGIGRACAVALAQRGARVVAAARNAAALDRLAGETGCE 56
Query: 428 ALSL 431
L L
Sbjct: 57 PLRL 60
>gnl|CDD|176222 cd08261, Zn_ADH7, Alcohol dehydrogenases of the MDR family. This
group contains members identified as related to
zinc-dependent alcohol dehydrogenase and other members
of the MDR family. The medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, which contains the
zinc-dependent alcohol dehydrogenase (ADH-Zn) and
related proteins, is a diverse group of proteins related
to the first identified member, class I mammalian ADH.
MDRs display a broad range of activities and are
distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P)-binding Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group includes
various activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has a
catalytic role, while structural zinc aids in stability.
ADH-like proteins typically form dimers (typically
higher plants, mammals) or tetramers (yeast, bacteria),
and generally have 2 tightly bound zinc atoms per
subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 337
Score = 38.3 bits (90), Expect = 0.008
Identities = 27/119 (22%), Positives = 41/119 (34%), Gaps = 23/119 (19%)
Query: 380 AGKLFVVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAETVGGHALSLADLENFNP 439
AG +V+GAG G + AKA+GARV++ + D E A +G + +
Sbjct: 159 AGDTVLVVGAGPIGLGVIQVAKARGARVIVVD-IDDERLEFARELGADDT----INVGDE 213
Query: 440 EDG-MILANTTSIGMQPKVDETPIPKHALGHYALVFDAVYTPKITRLLREAEESGATIV 497
+ + T G +V DA P E G +V
Sbjct: 214 DVAARLRELTDGEGAD-----------------VVIDATGNPASMEEAVELVAHGGRVV 255
>gnl|CDD|235628 PRK05855, PRK05855, short chain dehydrogenase; Validated.
Length = 582
Score = 38.8 bits (91), Expect = 0.008
Identities = 21/60 (35%), Positives = 27/60 (45%), Gaps = 4/60 (6%)
Query: 373 GGVSSALAGKLFVVIGAG-GAGKALAYGAKAKGARVVIANRTYDRARELAETV---GGHA 428
G +GKL VV GAG G G+ A +GA VV ++ A AE + G A
Sbjct: 307 GRPRGPFSGKLVVVTGAGSGIGRETALAFAREGAEVVASDIDEAAAERTAELIRAAGAVA 366
>gnl|CDD|237219 PRK12827, PRK12827, short chain dehydrogenase; Provisional.
Length = 249
Score = 38.2 bits (89), Expect = 0.008
Identities = 22/71 (30%), Positives = 36/71 (50%), Gaps = 9/71 (12%)
Query: 376 SSALAGK-LFVVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAETV-------GGH 427
++L + + + G+GG G+A+A A GA V++ + R R A+ V GG
Sbjct: 1 MASLDSRRVLITGGSGGLGRAIAVRLAADGADVIVLDIHPMRGRAEADAVAAGIEAAGGK 60
Query: 428 ALSL-ADLENF 437
AL L D+ +F
Sbjct: 61 ALGLAFDVRDF 71
>gnl|CDD|235608 PRK05786, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 238
Score = 37.8 bits (88), Expect = 0.009
Identities = 17/50 (34%), Positives = 29/50 (58%), Gaps = 1/50 (2%)
Query: 379 LAGKLFVVIGAG-GAGKALAYGAKAKGARVVIANRTYDRARELAETVGGH 427
L GK +IG G G A+AY A +GA+V I +R ++ + + +T+ +
Sbjct: 3 LKGKKVAIIGVSEGLGYAVAYFALKEGAQVCINSRNENKLKRMKKTLSKY 52
>gnl|CDD|181349 PRK08278, PRK08278, short chain dehydrogenase; Provisional.
Length = 273
Score = 38.0 bits (89), Expect = 0.009
Identities = 24/68 (35%), Positives = 32/68 (47%), Gaps = 13/68 (19%)
Query: 376 SSALAGKLFVVIGAG-GAGKALAYGAKAKGARVVIANRT-----------YDRARELAET 423
+L+GK + GA G G A+A A GA +VIA +T + A E+ E
Sbjct: 1 MMSLSGKTLFITGASRGIGLAIALRAARDGANIVIAAKTAEPHPKLPGTIHTAAEEI-EA 59
Query: 424 VGGHALSL 431
GG AL L
Sbjct: 60 AGGQALPL 67
>gnl|CDD|187603 cd05345, BKR_3_SDR_c, putative beta-ketoacyl acyl carrier protein
[ACP] reductase (BKR), subgroup 3, classical (c) SDR.
This subgroup includes the putative Brucella melitensis
biovar Abortus 2308 BKR, FabG, Mesorhizobium loti
MAFF303099 FabG, and other classical SDRs. BKR, a member
of the SDR family, catalyzes the NADPH-dependent
reduction of acyl carrier protein in the first reductive
step of de novo fatty acid synthesis (FAS). FAS
consists of 4 elongation steps, which are repeated to
extend the fatty acid chain thru the addition of
two-carbo units from malonyl acyl-carrier protein (ACP):
condensation, reduction, dehydration, and final
reduction. Type II FAS, typical of plants and many
bacteria, maintains these activities on discrete
polypeptides, while type I Fas utilizes one or 2
multifunctional polypeptides. BKR resembles enoyl
reductase, which catalyzes the second reduction step in
FAS. 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 have a 3-glycine N-terminal NAD(P)(H)-binding
pattern (typically, TGxxxGxG in classical SDRs and
TGxxGxxG in extended SDRs), while substrate binding is
in the C-terminal region. A critical catalytic Tyr
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) numbering), is often found in a
conserved YXXXK pattern. 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) or
additional Ser, contributing to the active site.
Substrates for these enzymes include sugars, steroids,
alcohols, and aromatic compounds. The standard reaction
mechanism is a proton relay involving the conserved Tyr
and Lys, as well as Asn (or Ser). Some SDR family
members, including 17 beta-hydroxysteroid dehydrogenase
contain an additional helix-turn-helix motif that is not
generally found among SDRs.
Length = 248
Score = 37.8 bits (88), Expect = 0.009
Identities = 22/55 (40%), Positives = 33/55 (60%), Gaps = 1/55 (1%)
Query: 379 LAGKLFVVIGAG-GAGKALAYGAKAKGARVVIANRTYDRARELAETVGGHALSLA 432
L GK+ +V GAG G G+ +A +GARVVIA+ D A +A +G A+++
Sbjct: 3 LEGKVAIVTGAGSGFGEGIARRFAQEGARVVIADINADGAERVAADIGEAAIAIQ 57
>gnl|CDD|222258 pfam13604, AAA_30, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily. Many of the proteins in this family are
conjugative transfer proteins. There is a Walker A and
Walker B.
Length = 195
Score = 37.5 bits (88), Expect = 0.010
Identities = 35/121 (28%), Positives = 49/121 (40%), Gaps = 26/121 (21%)
Query: 385 VVIGAGGAGK-----ALAYGAKAKGARVVIANRTYDRARELAETVGGHALSLADLENFNP 439
VV G G GK A +A G RV+ T A+ L E +G A +LA L +
Sbjct: 22 VVQGPAGTGKTTSLKAAREAWEAAGYRVIGLAPTGKAAKVLGEELGIEARTLASLLHRWD 81
Query: 440 EDGMILANTTSIGMQPKVDETPIPKHALGHYALVFD---AVYTPKITRLLREAEESGATI 496
+ + + L LV D V T ++ RLLR AE++GA +
Sbjct: 82 --------------KGEDPGRVLDAGTL----LVVDEAGMVGTRQMARLLRLAEKAGAKV 123
Query: 497 V 497
V
Sbjct: 124 V 124
>gnl|CDD|187663 cd09762, HSDL2_SDR_c, human hydroxysteroid dehydrogenase-like
protein 2 (HSDL2), classical (c) SDRs. This subgroup
includes human HSDL2 and related protens. These are
members of the classical SDR family, with a canonical
Gly-rich NAD-binding motif and the typical YXXXK active
site motif. However, the rest of the catalytic tetrad is
not strongly conserved. HSDL2 may play a part in fatty
acid metabolism, as it is found in peroxisomes. 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 have a
3-glycine N-terminal NAD(P)(H)-binding pattern
(typically, TGxxxGxG in classical SDRs and TGxxGxxG in
extended SDRs), while substrate binding is in the
C-terminal region. A critical catalytic Tyr residue
(Tyr-151, human 15-hydroxyprostaglandin dehydrogenase
(15-PGDH) numbering), is often found in a conserved
YXXXK pattern. 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) or additional
Ser, contributing to the active site. Substrates for
these enzymes include sugars, steroids, alcohols, and
aromatic compounds. The standard reaction mechanism is a
proton relay involving the conserved Tyr and Lys, as
well as Asn (or Ser). Some SDR family members, including
17 beta-hydroxysteroid dehydrogenase contain an
additional helix-turn-helix motif that is not generally
found among SDRs.
Length = 243
Score = 37.8 bits (88), Expect = 0.010
Identities = 27/66 (40%), Positives = 31/66 (46%), Gaps = 13/66 (19%)
Query: 379 LAGKLFVVIGAG-GAGKALAYGAKAKGARVVIANRT-----------YDRARELAETVGG 426
LAGK + GA G GKA+A A GA VVIA +T Y A E+ E GG
Sbjct: 1 LAGKTLFITGASRGIGKAIALKAARDGANVVIAAKTAEPHPKLPGTIYTAAEEI-EAAGG 59
Query: 427 HALSLA 432
AL
Sbjct: 60 KALPCI 65
>gnl|CDD|176241 cd08281, liver_ADH_like1, Zinc-dependent alcohol dehydrogenases
(ADH) and class III ADG (AKA formaldehyde
dehydrogenase). NAD(P)(H)-dependent oxidoreductases are
the major enzymes in the interconversion of alcohols and
aldehydes or ketones. This group contains members
identified as zinc dependent alcohol dehydrogenases
(ADH), and class III ADG (aka formaldehyde
dehydrogenase, FDH). Alcohol dehydrogenase in the liver
converts ethanol and NAD+ to acetaldehyde and NADH,
while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. NAD(P)(H)-dependent
oxidoreductases are the major enzymes in the
interconversion of alcohols and aldehydes or ketones.
Alcohol dehydrogenase in the liver converts ethanol and
NAD+ to acetaldehyde and NADH, while in yeast and some
other microorganisms ADH catalyzes the conversion
acetaldehyde to ethanol in alcoholic fermentation.
Class III ADH are also know as glutathione-dependent
formaldehyde dehydrogenase (FDH), which convert
aldehydes to the corresponding carboxylic acid and
alcohol. ADH is a member of the medium chain alcohol
dehydrogenase family (MDR), which have a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES. These
proteins typically form dimers (typically higher plants,
mammals) or tetramers (yeast, bacteria), and have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. NAD(H) binding occurs in the
cleft between the catalytic and coenzyme-binding domains
at the active site, and coenzyme binding induces a
conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
In human ADH catalysis, the zinc ion helps coordinate
the alcohol, followed by deprotonation of a histidine,
the ribose of NAD, a serine, then the alcohol, which
allows the transfer of a hydride to NAD+, creating NADH
and a zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 371
Score = 38.1 bits (89), Expect = 0.011
Identities = 19/57 (33%), Positives = 25/57 (43%)
Query: 380 AGKLFVVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAETVGGHALSLADLEN 436
G+ V+G GG G + GA A GA V+A + LA +G A A N
Sbjct: 191 PGQSVAVVGLGGVGLSALLGAVAAGASQVVAVDLNEDKLALARELGATATVNAGDPN 247
>gnl|CDD|187597 cd05338, DHRS1_HSDL2-like_SDR_c, human dehydrogenase/reductase (SDR
family) member 1 (DHRS1) and human hydroxysteroid
dehydrogenase-like protein 2 (HSDL2), classical (c)
SDRs. This subgroup includes human DHRS1 and human
HSDL2 and related proteins. These are members of the
classical SDR family, with a canonical Gly-rich
NAD-binding motif and the typical YXXXK active site
motif. However, the rest of the catalytic tetrad is not
strongly conserved. DHRS1 mRNA has been detected in many
tissues, liver, heart, skeletal muscle, kidney and
pancreas; a longer transcript is predominantly expressed
in the liver , a shorter one in the heart. HSDL2 may
play a part in fatty acid metabolism, as it is found in
peroxisomes. 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 have a 3-glycine N-terminal NAD(P)(H)-binding
pattern (typically, TGxxxGxG in classical SDRs and
TGxxGxxG in extended SDRs), while substrate binding is
in the C-terminal region. A critical catalytic Tyr
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) numbering), is often found in a
conserved YXXXK pattern. 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) or
additional Ser, contributing to the active site.
Substrates for these enzymes include sugars, steroids,
alcohols, and aromatic compounds. The standard reaction
mechanism is a proton relay involving the conserved Tyr
and Lys, as well as Asn (or Ser). Some SDR family
members, including 17 beta-hydroxysteroid dehydrogenase
contain an additional helix-turn-helix motif that is not
generally found among SDRs.
Length = 246
Score = 37.8 bits (88), Expect = 0.011
Identities = 29/112 (25%), Positives = 42/112 (37%), Gaps = 29/112 (25%)
Query: 379 LAGKLFVVIGAG-GAGKALAYGAKAKGARVVIANRTYD---------------RARELAE 422
L+GK+ V GA G G+A+A GA VV+A +T E E
Sbjct: 1 LSGKVAFVTGASRGIGRAIALRLAKAGATVVVAAKTASEGDNGSAKSLPGTIEETAEEIE 60
Query: 423 TVGGHALSL-ADLENFNPEDGM------------ILANTTSIGMQPKVDETP 461
GG AL + D+ + + + IL N V++TP
Sbjct: 61 AAGGQALPIVVDVRDEDQVRALVEATVDQFGRLDILVNNAGAIWLSLVEDTP 112
>gnl|CDD|223573 COG0499, SAM1, S-adenosylhomocysteine hydrolase [Coenzyme
metabolism].
Length = 420
Score = 38.0 bits (89), Expect = 0.012
Identities = 29/106 (27%), Positives = 40/106 (37%), Gaps = 29/106 (27%)
Query: 363 DGLRGRLNVSGGVSSALAGKLFVVIGAGGAGKALAYGAKAKGARVVIAN----------- 411
DG+ NV LAGK VV G G G+ +A + GARV++
Sbjct: 197 DGILRATNVL------LAGKNVVVAGYGWVGRGIAMRLRGMGARVIVTEVDPIRALEAAM 250
Query: 412 -----RTYDRARELAE---TVGG--HALSLADLENFNPEDGMILAN 447
T + A + + T G + E +DG ILAN
Sbjct: 251 DGFRVMTMEEAAKTGDIFVTATGNKDVIRKEHFEKM--KDGAILAN 294
>gnl|CDD|233693 TIGR02032, GG-red-SF, geranylgeranyl reductase family. This model
represents a subfamily which includes geranylgeranyl
reductases involved in chlorophyll and
bacteriochlorophyll biosynthesis as well as other
related enzymes which may also act on geranylgeranyl
groups or related substrates [Biosynthesis of cofactors,
prosthetic groups, and carriers, Chlorophyll and
bacteriochlorphyll].
Length = 295
Score = 37.7 bits (88), Expect = 0.012
Identities = 32/118 (27%), Positives = 46/118 (38%), Gaps = 17/118 (14%)
Query: 384 FVVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAETVGGHALSLADLENFNPEDGM 443
VV+GAG AG + AY KG RV++ ++ G ALS LE + +
Sbjct: 3 VVVVGAGPAGASAAYRLADKGLRVLL----LEKKSFPRYKPCGGALSPRALEELDLPGEL 58
Query: 444 ILANT----TSIGMQPKVDETPIPKHALGHYALVFD-AVYTPKITRLLREAEESGATI 496
I+ V E PI A V D + + L A+E+GA +
Sbjct: 59 IVNLVRGARFFSPNGDSV-EIPIE----TELAYVIDRDAFDEQ---LAERAQEAGAEL 108
>gnl|CDD|240631 cd12154, FDH_GDH_like, Formate/glycerate dehydrogenases, D-specific
2-hydroxy acid dehydrogenases and related
dehydrogenases. The formate/glycerate dehydrogenase
like family contains a diverse group of enzymes such as
formate dehydrogenase (FDH), glycerate dehydrogenase
(GDH), D-lactate dehydrogenase, L-alanine dehydrogenase,
and S-Adenosylhomocysteine hydrolase, that share a
common 2-domain structure. Despite often low sequence
identity, these proteins typically have a characteristic
arrangement of 2 similar domains of the alpha/beta
Rossmann fold NAD+ binding form. The NAD(P) binding
domain is inserted within the linear sequence of the
mostly N-terminal catalytic domain. Structurally, these
domains are connected by extended alpha helices and
create a cleft in which NAD(P) is bound, primarily to
the C-terminal portion of the 2nd (internal) domain.
While many members of this family are dimeric, alanine
DH is hexameric and phosphoglycerate DH is tetrameric.
2-hydroxyacid dehydrogenases are enzymes that catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate dehydrogenase (FDH) catalyzes the NAD+-dependent
oxidation of formate ion to carbon dioxide with the
concomitant reduction of NAD+ to NADH. FDHs of this
family contain no metal ions or prosthetic groups.
Catalysis occurs though direct transfer of a hydride ion
to NAD+ without the stages of acid-base catalysis
typically found in related dehydrogenases.
Length = 310
Score = 38.0 bits (88), Expect = 0.012
Identities = 27/93 (29%), Positives = 42/93 (45%), Gaps = 6/93 (6%)
Query: 359 SAIEDGLRGRLNVSGGVSSA---LAGKLFVVIGAGGAGKALAYGAKAKGARVVIANRTYD 415
+++ R G +AGK VV+GAG GK A + GA+V+I +
Sbjct: 135 LSVQFIARFLEVQQPGRLGGAPDVAGKTVVVVGAGVVGKEAAQMLRGLGAQVLITDIN-V 193
Query: 416 RARELAETVGGHALSLADLENFNPEDGMILANT 448
A E E +GG ++ +LE E +I+ T
Sbjct: 194 EALEQLEELGGK--NVEELEEALAEADVIVTTT 224
>gnl|CDD|236101 PRK07803, sdhA, succinate dehydrogenase flavoprotein subunit;
Reviewed.
Length = 626
Score = 38.1 bits (89), Expect = 0.013
Identities = 26/60 (43%), Positives = 34/60 (56%), Gaps = 7/60 (11%)
Query: 385 VVIGAGGAGKALAYGAKAKGARV-VIANRTYDRARE-LAETVGGHALSLADLENFNPEDG 442
VVIGAGGAG A A+ +G RV V+ + +A +AE GG A A + N NP+D
Sbjct: 12 VVIGAGGAGLRAAIEARERGLRVAVVCKSLFGKAHTVMAE--GGCA---AAMGNVNPKDN 66
>gnl|CDD|176240 cd08279, Zn_ADH_class_III, Class III alcohol dehydrogenase.
Glutathione-dependent formaldehyde dehydrogenases (FDHs,
Class III ADH) are members of the zinc-dependent/medium
chain alcohol dehydrogenase family. FDH converts
formaldehyde and NAD(P) to formate and NAD(P)H. The
initial step in this process the spontaneous formation
of a S-(hydroxymethyl)glutathione adduct from
formaldehyde and glutathione, followed by FDH-mediated
oxidation (and detoxification) of the adduct to
S-formylglutathione. NAD(P)(H)-dependent oxidoreductases
are the major enzymes in the interconversion of alcohols
and aldehydes or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. Class III ADH are also known as
glutathione-dependent formaldehyde dehydrogenase (FDH),
which convert aldehydes to corresponding carboxylic acid
and alcohol. ADH is a member of the medium chain
alcohol dehydrogenase family (MDR), which has a
NAD(P)(H)-binding domain in a Rossmann fold of an
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES. These
proteins typically form dimers (typically higher plants,
mammals) or tetramers (yeast, bacteria), and have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. NAD(H) binding occurs in the
cleft between the catalytic and coenzyme-binding
domains at the active site, and coenzyme binding induces
a conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
Length = 363
Score = 37.9 bits (89), Expect = 0.013
Identities = 20/61 (32%), Positives = 25/61 (40%), Gaps = 6/61 (9%)
Query: 371 VSGGVSSAL------AGKLFVVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAETV 424
V+ GV + + G VIG GG G GA+ GA +IA ELA
Sbjct: 167 VTTGVGAVVNTARVRPGDTVAVIGCGGVGLNAIQGARIAGASRIIAVDPVPEKLELARRF 226
Query: 425 G 425
G
Sbjct: 227 G 227
>gnl|CDD|236372 PRK09072, PRK09072, short chain dehydrogenase; Provisional.
Length = 263
Score = 37.2 bits (87), Expect = 0.015
Identities = 22/60 (36%), Positives = 32/60 (53%), Gaps = 4/60 (6%)
Query: 379 LAGKLFVVIGA-GGAGKALAYGAKAKGARVVIANRTYDRARELAETV---GGHALSLADL 434
L K ++ GA GG G+ALA A GAR+++ R ++ LA + G H +ADL
Sbjct: 3 LKDKRVLLTGASGGIGQALAEALAAAGARLLLVGRNAEKLEALAARLPYPGRHRWVVADL 62
>gnl|CDD|224169 COG1249, Lpd, Pyruvate/2-oxoglutarate dehydrogenase complex,
dihydrolipoamide dehydrogenase (E3) component, and
related enzymes [Energy production and conversion].
Length = 454
Score = 37.6 bits (88), Expect = 0.019
Identities = 16/42 (38%), Positives = 19/42 (45%), Gaps = 8/42 (19%)
Query: 385 VVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAETVGG 426
VVIGAG AG A A G +V + E E +GG
Sbjct: 8 VVIGAGPAGYVAAIRAAQLGLKVALV--------EKGERLGG 41
>gnl|CDD|129775 TIGR00692, tdh, L-threonine 3-dehydrogenase. This protein is a
tetrameric, zinc-binding, NAD-dependent enzyme of
threonine catabolism. Closely related proteins include
sorbitol dehydrogenase, xylitol dehydrogenase, and
benzyl alcohol dehydrogenase. Eukaryotic examples of
this enzyme have been demonstrated experimentally but do
not appear in database search results.E. coli His-90
modulates substrate specificity and is believed part of
the active site [Energy metabolism, Amino acids and
amines].
Length = 340
Score = 37.1 bits (86), Expect = 0.021
Identities = 18/51 (35%), Positives = 27/51 (52%)
Query: 375 VSSALAGKLFVVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAETVG 425
++ ++GK +V GAG G AKA GA VI + + ELA+ +G
Sbjct: 156 LAGPISGKSVLVTGAGPIGLMAIAVAKASGAYPVIVSDPNEYRLELAKKMG 206
>gnl|CDD|240639 cd12162, 2-Hacid_dh_4, Putative D-isomer specific 2-hydroxyacid
dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine yydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 307
Score = 37.0 bits (87), Expect = 0.024
Identities = 16/35 (45%), Positives = 22/35 (62%)
Query: 379 LAGKLFVVIGAGGAGKALAYGAKAKGARVVIANRT 413
LAGK +IG G G+A+A A+A G +V+ A R
Sbjct: 145 LAGKTLGIIGYGNIGQAVARIARAFGMKVLFAERK 179
>gnl|CDD|180371 PRK06057, PRK06057, short chain dehydrogenase; Provisional.
Length = 255
Score = 36.6 bits (85), Expect = 0.024
Identities = 19/49 (38%), Positives = 28/49 (57%), Gaps = 1/49 (2%)
Query: 379 LAGKLFVVIGAG-GAGKALAYGAKAKGARVVIANRTYDRARELAETVGG 426
LAG++ V+ G G G G A A A+GA VV+ + + + A+ VGG
Sbjct: 5 LAGRVAVITGGGSGIGLATARRLAAEGATVVVGDIDPEAGKAAADEVGG 53
>gnl|CDD|223959 COG1028, FabG, Dehydrogenases with different specificities (related
to short-chain alcohol dehydrogenases) [Secondary
metabolites biosynthesis, transport, and catabolism /
General function prediction only].
Length = 251
Score = 36.7 bits (85), Expect = 0.024
Identities = 24/64 (37%), Positives = 36/64 (56%), Gaps = 8/64 (12%)
Query: 379 LAGKLFVVIGAG-GAGKALAYGAKAKGARVVIANRTYDR------ARELAETVGGHALSL 431
L+GK+ +V GA G G+A+A +GARVV+A R + A + E GG A ++
Sbjct: 3 LSGKVALVTGASSGIGRAIARALAREGARVVVAARRSEEEAAEALAAAIKEAGGGRAAAV 62
Query: 432 -ADL 434
AD+
Sbjct: 63 AADV 66
>gnl|CDD|187605 cd05347, Ga5DH-like_SDR_c, gluconate 5-dehydrogenase (Ga5DH)-like,
classical (c) SDRs. Ga5DH catalyzes the NADP-dependent
conversion of carbon source D-gluconate and
5-keto-D-gluconate. This SDR subgroup has a classical
Gly-rich NAD(P)-binding motif and a conserved active
site tetrad pattern. However, it has been proposed that
Arg104 (Streptococcus suis Ga5DH numbering), as well as
an active site Ca2+, play a critical role in catalysis.
In addition to Ga5DHs this subgroup contains Erwinia
chrysanthemi KduD which is involved in pectin
degradation, and is a putative
2,5-diketo-3-deoxygluconate dehydrogenase. 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 = 248
Score = 36.6 bits (85), Expect = 0.025
Identities = 30/102 (29%), Positives = 43/102 (42%), Gaps = 21/102 (20%)
Query: 379 LAGKLFVVIGAG-GAGKALAYGAKAKGARVVIANRT---YDRARELAETVGGHALSLA-D 433
L GK+ +V GA G G +A G GA +VI +R + A++L E G A + D
Sbjct: 3 LKGKVALVTGASRGIGFGIASGLAEAGANIVINSRNEEKAEEAQQLIEKEGVEATAFTCD 62
Query: 434 L--------------ENFNPEDGMILANTTSIGMQPKVDETP 461
+ E+F D IL N I + +E P
Sbjct: 63 VSDEEAIKAAVEAIEEDFGKID--ILVNNAGIIRRHPAEEFP 102
>gnl|CDD|176182 cd05279, Zn_ADH1, Liver alcohol dehydrogenase and related
zinc-dependent alcohol dehydrogenases.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. There are 7 vertebrate ADH 7
classes, 6 of which have been identified in humans.
Class III, glutathione-dependent formaldehyde
dehydrogenase, has been identified as the primordial
form and exists in diverse species, including plants,
micro-organisms, vertebrates, and invertebrates. Class
I, typified by liver dehydrogenase, is an evolving
form. Gene duplication and functional specialization of
ADH into ADH classes and subclasses created numerous
forms in vertebrates. For example, the A, B and C
(formerly alpha, beta, gamma) human class I subunits
have high overall structural similarity, but differ in
the substrate binding pocket and therefore in substrate
specificity. In human ADH catalysis, the zinc ion helps
coordinate the alcohol, followed by deprotonation of a
histidine (His-51), the ribose of NAD, a serine
(Ser-48), then the alcohol, which allows the transfer of
a hydride to NAD+, creating NADH and a zinc-bound
aldehyde or ketone. In yeast and some bacteria, the
active site zinc binds an aldehyde, polarizing it, and
leading to the reverse reaction. ADH is a member of the
medium chain alcohol dehydrogenase family (MDR), which
has a NAD(P)(H)-binding domain in a Rossmann fold of an
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES.
These proteins typically form dimers (typically higher
plants, mammals) or tetramers (yeast, bacteria), and
have 2 tightly bound zinc atoms per subunit, a catalytic
zinc at the active site and a structural zinc in a lobe
of the catalytic domain. NAD(H) binding occurs in the
cleft between the catalytic and coenzyme-binding domains
at the active site, and coenzyme binding induces a
conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
Length = 365
Score = 36.6 bits (85), Expect = 0.028
Identities = 19/61 (31%), Positives = 26/61 (42%), Gaps = 6/61 (9%)
Query: 371 VSGGVSSAL------AGKLFVVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAETV 424
S G +A+ G V G GG G ++ G KA GA +IA E A+ +
Sbjct: 168 FSTGYGAAVNTAKVTPGSTCAVFGLGGVGLSVIMGCKAAGASRIIAVDINKDKFEKAKQL 227
Query: 425 G 425
G
Sbjct: 228 G 228
>gnl|CDD|235996 PRK07340, PRK07340, ornithine cyclodeaminase; Validated.
Length = 304
Score = 36.5 bits (85), Expect = 0.028
Identities = 29/142 (20%), Positives = 42/142 (29%), Gaps = 30/142 (21%)
Query: 377 SALAGKLFV--------VIGAG--GAGKALAYGAKAKGARVVIANRTYDRARELAETVGG 426
S LA + +IG G A+ A RV + RT A
Sbjct: 113 SLLAARTLAPAPPGDLLLIGTGVQARAHLEAFAAGLPVRRVWVRGRTAASAAAFCAHARA 172
Query: 427 HALSLA--DLENFNPEDGMILANTTSIGMQPKVDETPIPKHALGHYALVFDAV--YTPKI 482
+ D E +++ TTS P E LV AV +TP
Sbjct: 173 LGPTAEPLDGEAIPEAVDLVVTATTS--RTPVYPEAARAGR------LVV-AVGAFTP-- 221
Query: 483 TRLLREAEESGATIVSGLEMFI 504
+ E V G +++
Sbjct: 222 -----DMAELAPRTVRGSRLYV 238
>gnl|CDD|235546 PRK05653, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Validated.
Length = 246
Score = 36.3 bits (85), Expect = 0.029
Identities = 23/63 (36%), Positives = 32/63 (50%), Gaps = 5/63 (7%)
Query: 379 LAGKLFVVIGAGGA-GKALAYGAKAKGARVVIANRTYDRARELAETV---GGHALSL-AD 433
L GK +V GA G+A+A A GA+VVI + + A LA + GG A L D
Sbjct: 3 LQGKTALVTGASRGIGRAIALRLAADGAKVVIYDSNEEAAEALAAELRAAGGEARVLVFD 62
Query: 434 LEN 436
+ +
Sbjct: 63 VSD 65
>gnl|CDD|181136 PRK07825, PRK07825, short chain dehydrogenase; Provisional.
Length = 273
Score = 36.5 bits (85), Expect = 0.029
Identities = 22/63 (34%), Positives = 29/63 (46%), Gaps = 4/63 (6%)
Query: 379 LAGKLFVVIGAG-GAGKALAYGAKAKGARVVIANRTYDRARELAETVG---GHALSLADL 434
L GK+ + G G G A A A GARV I + A+E A +G G L + D
Sbjct: 3 LRGKVVAITGGARGIGLATARALAALGARVAIGDLDEALAKETAAELGLVVGGPLDVTDP 62
Query: 435 ENF 437
+F
Sbjct: 63 ASF 65
>gnl|CDD|240258 PTZ00075, PTZ00075, Adenosylhomocysteinase; Provisional.
Length = 476
Score = 36.9 bits (86), Expect = 0.032
Identities = 15/31 (48%), Positives = 18/31 (58%)
Query: 379 LAGKLFVVIGAGGAGKALAYGAKAKGARVVI 409
+AGK VV G G GK A + GARVV+
Sbjct: 252 IAGKTVVVCGYGDVGKGCAQALRGFGARVVV 282
>gnl|CDD|236094 PRK07774, PRK07774, short chain dehydrogenase; Provisional.
Length = 250
Score = 36.3 bits (84), Expect = 0.032
Identities = 25/79 (31%), Positives = 38/79 (48%), Gaps = 13/79 (16%)
Query: 379 LAGKLFVVIGA-GGAGKALAYGAKAKGARVVIANRTYDRARELAETV-------GGHALS 430
K+ +V GA GG G+A A +GA VV+A D E AE V GG A++
Sbjct: 4 FDDKVAIVTGAAGGIGQAYAEALAREGASVVVA----DINAEGAERVAKQIVADGGTAIA 59
Query: 431 LADLENFNPEDGMILANTT 449
++ +P+ +A+ T
Sbjct: 60 -VQVDVSDPDSAKAMADAT 77
>gnl|CDD|187621 cd05363, SDH_SDR_c, Sorbitol dehydrogenase (SDH), classical (c)
SDR. This bacterial subgroup includes Rhodobacter
sphaeroides SDH, and other SDHs. SDH preferentially
interconverts D-sorbitol (D-glucitol) and D-fructose,
but also interconverts L-iditol/L-sorbose and
galactitol/D-tagatose. SDH is NAD-dependent and is a
dimeric member of the SDR family. 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 have a
3-glycine N-terminal NAD(P)(H)-binding pattern
(typically, TGxxxGxG in classical SDRs and TGxxGxxG in
extended SDRs), while substrate binding is in the
C-terminal region. A critical catalytic Tyr residue
(Tyr-151, human 15-hydroxyprostaglandin dehydrogenase
(15-PGDH) numbering), is often found in a conserved
YXXXK pattern. 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) or additional
Ser, contributing to the active site. Substrates for
these enzymes include sugars, steroids, alcohols, and
aromatic compounds. The standard reaction mechanism is a
proton relay involving the conserved Tyr and Lys, as
well as Asn (or Ser). Some SDR family members, including
17 beta-hydroxysteroid dehydrogenase contain an
additional helix-turn-helix motif that is not generally
found among SDRs.
Length = 254
Score = 36.1 bits (83), Expect = 0.033
Identities = 27/98 (27%), Positives = 43/98 (43%), Gaps = 17/98 (17%)
Query: 379 LAGKLFVVIG-AGGAGKALAYGAKAKGARVVIANRTYDRARELAETVGGHALSL------ 431
L GK ++ G A G G+A A +GARV IA+ + AR A +G A ++
Sbjct: 1 LDGKTALITGSARGIGRAFAQAYVREGARVAIADINLEAARATAAEIGPAACAISLDVTD 60
Query: 432 ---------ADLENFNPEDGMILANTTSIGMQPKVDET 460
A ++ + D +++ N + P VD T
Sbjct: 61 QASIDRCVAALVDRWGSID-ILVNNAALFDLAPIVDIT 97
>gnl|CDD|176195 cd08233, butanediol_DH_like, (2R,3R)-2,3-butanediol dehydrogenase.
(2R,3R)-2,3-butanediol dehydrogenase, a zinc-dependent
medium chain alcohol dehydrogenase, catalyzes the
NAD(+)-dependent oxidation of (2R,3R)-2,3-butanediol and
meso-butanediol to acetoin. BDH functions as a
homodimer. NAD(P)(H)-dependent oxidoreductases are the
major enzymes in the interconversion of alcohols and
aldehydes, or ketones. The medium chain alcohol
dehydrogenase family (MDR) have a NAD(P)(H)-binding
domain in a Rossmann fold of a beta-alpha form. The
N-terminal region typically has an all-beta catalytic
domain. These proteins typically form dimers (typically
higher plants, mammals) or tetramers (yeast, bacteria),
and have 2 tightly bound zinc atoms per subunit.
Sorbitol and aldose reductase are NAD(+) binding
proteins of the polyol pathway, which interconverts
glucose and fructose. Sorbitol dehydrogenase is
tetrameric and has a single catalytic zinc per subunit.
Length = 351
Score = 36.4 bits (85), Expect = 0.033
Identities = 18/53 (33%), Positives = 24/53 (45%)
Query: 375 VSSALAGKLFVVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAETVGGH 427
S G +V+GAG G KA GA +I + + RELAE +G
Sbjct: 167 RSGFKPGDTALVLGAGPIGLLTILALKAAGASKIIVSEPSEARRELAEELGAT 219
>gnl|CDD|212491 cd05233, SDR_c, classical (c) SDRs. 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 prostaglandin dehydrogenase
(PGDH) numbering). In addition to the Tyr and Lys, there
is often an upstream Ser (Ser-138, PGDH numbering)
and/or an Asn (Asn-107, 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 = 234
Score = 36.1 bits (84), Expect = 0.035
Identities = 22/56 (39%), Positives = 37/56 (66%), Gaps = 4/56 (7%)
Query: 385 VVIGAG-GAGKALAYGAKAKGARVVIANRTYDRARELA--ETVGGHALSL-ADLEN 436
+V GA G G+A+A +GA+VV+A+R + ELA E +GG+A+++ AD+ +
Sbjct: 2 LVTGASSGIGRAIARRLAREGAKVVLADRNEEALAELAAIEALGGNAVAVQADVSD 57
>gnl|CDD|176224 cd08263, Zn_ADH10, Alcohol dehydrogenases of the MDR family.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which have a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES. These
proteins typically form dimers (typically higher plants,
mammals) or tetramers (yeast, bacteria), and have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. NAD(H)-binding occurs in the
cleft between the catalytic and coenzyme-binding
domains at the active site, and coenzyme binding induces
a conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
In human ADH catalysis, the zinc ion helps coordinate
the alcohol, followed by deprotonation of a histidine,
the ribose of NAD, a serine, then the alcohol, which
allows the transfer of a hydride to NAD+, creating NADH
and a zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 367
Score = 36.6 bits (85), Expect = 0.037
Identities = 17/46 (36%), Positives = 22/46 (47%)
Query: 380 AGKLFVVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAETVG 425
G+ VIG GG G + AKA GA +IA D A+ +G
Sbjct: 187 PGETVAVIGVGGVGSSAIQLAKAFGASPIIAVDVRDEKLAKAKELG 232
>gnl|CDD|238309 cd00553, NAD_synthase, NAD+ synthase is a homodimer, which
catalyzes the final step in de novo nicotinamide adenine
dinucleotide (NAD+) biosynthesis, an amide transfer from
either ammonia or glutamine to nicotinic acid adenine
dinucleotide (NaAD). The conversion of NaAD to NAD+
occurs via an NAD-adenylate intermediate and requires
ATP and Mg2+. The intemediate is subsequently cleaved
into NAD+ and AMP. In many prokaryotes, such as E. coli
, NAD synthetase consists of a single domain and is
strictly ammonia dependent. In contrast, eukaryotes and
other prokaryotes have an additional N-terminal
amidohydrolase domain that prefer glutamine,
Interestingly, NAD+ synthases in these prokaryotes, can
also utilize ammonia as an amide source .
Length = 248
Score = 36.0 bits (84), Expect = 0.038
Identities = 25/92 (27%), Positives = 34/92 (36%), Gaps = 34/92 (36%)
Query: 353 DYVGAISAIEDGLRGRLN----------VSGGVSSALAGKLFVVIGAGGAGKALAYGAKA 402
D I+A+ LR L +SGG+ SAL L V +A
Sbjct: 2 DLEEIINALVLFLRDYLRKSGFKGVVLGLSGGIDSALVAALAV---------------RA 46
Query: 403 KGARVVIA---------NRTYDRARELAETVG 425
G V+A T + A+ELAE +G
Sbjct: 47 LGRENVLALFMPSRYSSEETREDAKELAEALG 78
>gnl|CDD|181077 PRK07677, PRK07677, short chain dehydrogenase; Provisional.
Length = 252
Score = 36.2 bits (84), Expect = 0.038
Identities = 24/63 (38%), Positives = 34/63 (53%), Gaps = 7/63 (11%)
Query: 385 VVI---GAGGAGKALAYGAKAKGARVVIANRTYDR---ARELAETVGGHALSLADLENFN 438
VVI G+ G GKA+A +GA VVI RT ++ A+ E G L++ ++ N
Sbjct: 3 VVIITGGSSGMGKAMAKRFAEEGANVVITGRTKEKLEEAKLEIEQFPGQVLTV-QMDVRN 61
Query: 439 PED 441
PED
Sbjct: 62 PED 64
>gnl|CDD|236399 PRK09186, PRK09186, flagellin modification protein A; Provisional.
Length = 256
Score = 36.1 bits (84), Expect = 0.039
Identities = 17/48 (35%), Positives = 24/48 (50%), Gaps = 1/48 (2%)
Query: 379 LAGKLFVVIGAGG-AGKALAYGAKAKGARVVIANRTYDRARELAETVG 425
L GK ++ GAGG G AL G V+ A+ + EL E++G
Sbjct: 2 LKGKTILITGAGGLIGSALVKAILEAGGIVIAADIDKEALNELLESLG 49
>gnl|CDD|188504 TIGR03989, Rxyl_3153, oxidoreductase, Rxyl_3153 family. This model
describes a clade within the family pfam00107 of
zinc-binding dehydrogenases. The family pfam00107
contains class III alcohol dehydrogenases, including
enzymes designated S-(hydroxymethyl)glutathione
dehydrogenase and NAD/mycothiol-dependent formaldehyde
dehydrogenase. Members of the current family occur only
in species that contain the very small protein
mycofactocin (TIGR03969), a possible cofactor precursor,
and radical SAM protein TIGR03962. We name this family
for Rxyl_3153, where the lone member of the family
co-clusters with these markers in Rubrobacter
xylanophilus [Unknown function, Enzymes of unknown
specificity].
Length = 369
Score = 36.1 bits (84), Expect = 0.042
Identities = 22/58 (37%), Positives = 24/58 (41%), Gaps = 4/58 (6%)
Query: 372 SGGVSSALAGKLFVVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAETVGG-HA 428
V G VV+G GG G GA GAR VIA + RE A G HA
Sbjct: 180 IADVR---PGDTVVVMGIGGVGINAVQGAAVAGARKVIAVDPVEFKREQALKFGATHA 234
>gnl|CDD|235506 PRK05565, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 247
Score = 36.0 bits (84), Expect = 0.042
Identities = 26/62 (41%), Positives = 40/62 (64%), Gaps = 6/62 (9%)
Query: 379 LAGKLFVVIGA-GGAGKALAYGAKAKGARVVIA-NRTYDRARELAETV---GGHALSL-A 432
L GK+ +V GA GG G+A+A +GA+VVIA + + A+EL E + GG A+++ A
Sbjct: 3 LMGKVAIVTGASGGIGRAIAELLAKEGAKVVIAYDINEEAAQELLEEIKEEGGDAIAVKA 62
Query: 433 DL 434
D+
Sbjct: 63 DV 64
>gnl|CDD|223990 COG1062, AdhC, Zn-dependent alcohol dehydrogenases, class III
[Energy production and conversion].
Length = 366
Score = 36.0 bits (84), Expect = 0.042
Identities = 18/41 (43%), Positives = 20/41 (48%)
Query: 385 VVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAETVG 425
V G GG G A GAKA GA +IA ELA+ G
Sbjct: 190 AVFGLGGVGLAAIQGAKAAGAGRIIAVDINPEKLELAKKFG 230
>gnl|CDD|132409 TIGR03366, HpnZ_proposed, putative phosphonate catabolism
associated alcohol dehydrogenase. This clade of
zinc-binding alcohol dehydrogenases (members of
pfam00107) are repeatedly associated with genes proposed
to be involved with the catabolism of phosphonate
compounds.
Length = 280
Score = 35.9 bits (83), Expect = 0.045
Identities = 21/58 (36%), Positives = 29/58 (50%)
Query: 378 ALAGKLFVVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAETVGGHALSLADLE 435
L G+ +V+GAG G A A A GA V+A RELA + G AL+ ++
Sbjct: 118 DLKGRRVLVVGAGMLGLTAAAAAAAAGAARVVAADPSPDRRELALSFGATALAEPEVL 175
>gnl|CDD|180773 PRK06949, PRK06949, short chain dehydrogenase; Provisional.
Length = 258
Score = 35.9 bits (83), Expect = 0.045
Identities = 40/120 (33%), Positives = 53/120 (44%), Gaps = 24/120 (20%)
Query: 374 GVSSALAGKLFVVIGA-GGAGKALAYGAKAKGARVVIANRTYDRAREL---AETVGG--H 427
G S L GK+ +V GA G G A GA+VV+A+R +R +EL E GG H
Sbjct: 2 GRSINLEGKVALVTGASSGLGARFAQVLAQAGAKVVLASRRVERLKELRAEIEAEGGAAH 61
Query: 428 ALSL---------ADLENFNPEDGM--ILANTTSIG-MQPKVDETPIPKHALGHYALVFD 475
+SL A + + E G IL N + + Q VD TP + VFD
Sbjct: 62 VVSLDVTDYQSIKAAVAHAETEAGTIDILVNNSGVSTTQKLVDVTP------ADFDFVFD 115
>gnl|CDD|131680 TIGR02632, RhaD_aldol-ADH, rhamnulose-1-phosphate aldolase/alcohol
dehydrogenase.
Length = 676
Score = 36.4 bits (84), Expect = 0.050
Identities = 36/144 (25%), Positives = 56/144 (38%), Gaps = 31/144 (21%)
Query: 379 LAGKL-FVVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAETVG---GHALSLADL 434
LA ++ FV GAGG G+ A A+GA VV+A+ + A +A + G ++A
Sbjct: 412 LARRVAFVTGGAGGIGRETARRLAAEGAHVVLADLNLEAAEAVAAEINGQFGAGRAVALK 471
Query: 435 ENFNPEDGM---------------ILANTTSIGMQPKVDETPIPKHALGH------YALV 473
+ E + I+ N I +ET + + L Y LV
Sbjct: 472 MDVTDEQAVKAAFADVALAYGGVDIVVNNAGIATSSPFEETTLQEWQLNLDILATGYFLV 531
Query: 474 FDAVYTPKITRLLREAEESGATIV 497
+ R +RE + G IV
Sbjct: 532 AREAF-----RQMRE-QGLGGNIV 549
>gnl|CDD|180440 PRK06172, PRK06172, short chain dehydrogenase; Provisional.
Length = 253
Score = 35.5 bits (82), Expect = 0.051
Identities = 25/65 (38%), Positives = 35/65 (53%), Gaps = 10/65 (15%)
Query: 375 VSSALAGKLFVVIG-AGGAGKALAYGAKAKGARVVIANRTYDRARELAETV------GGH 427
+S +GK+ +V G A G G+A A +GA+VV+A+R A ETV GG
Sbjct: 1 MSMTFSGKVALVTGGAAGIGRATALAFAREGAKVVVADR---DAAGGEETVALIREAGGE 57
Query: 428 ALSLA 432
AL +A
Sbjct: 58 ALFVA 62
>gnl|CDD|187620 cd05362, THN_reductase-like_SDR_c,
tetrahydroxynaphthalene/trihydroxynaphthalene
reductase-like, classical (c) SDRs.
1,3,6,8-tetrahydroxynaphthalene reductase (4HNR) of
Magnaporthe grisea and the related
1,3,8-trihydroxynaphthalene reductase (3HNR) are typical
members of the SDR family containing the canonical
glycine rich NAD(P)-binding site and active site tetrad,
and function in fungal melanin biosynthesis. This
subgroup also includes an SDR from Norway spruce that
may function to protect against both biotic and abitoic
stress. 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 = 243
Score = 35.7 bits (83), Expect = 0.052
Identities = 24/67 (35%), Positives = 36/67 (53%), Gaps = 12/67 (17%)
Query: 379 LAGKLFVVIGAG-GAGKALAYGAKAKGARVVIANRTYDRARELAETV-------GGHALS 430
LAGK+ +V GA G G+A+A GA VV+ Y ++ AE V GG A++
Sbjct: 1 LAGKVALVTGASRGIGRAIAKRLARDGASVVV---NYASSKAAAEEVVAEIEAAGGKAIA 57
Query: 431 L-ADLEN 436
+ AD+ +
Sbjct: 58 VQADVSD 64
>gnl|CDD|216396 pfam01262, AlaDh_PNT_C, Alanine dehydrogenase/PNT, C-terminal
domain. This family now also contains the lysine
2-oxoglutarate reductases.
Length = 150
Score = 34.4 bits (80), Expect = 0.053
Identities = 18/48 (37%), Positives = 21/48 (43%), Gaps = 1/48 (2%)
Query: 373 GGVSSALAGKLFVVIGAGGAGKALAYGAKAKGARVVIANRTYDRAREL 420
GG K VVIG G G A AK GA V I + +R +L
Sbjct: 13 GGAGGVPPAK-VVVIGGGVVGLGAAATAKGLGAPVTILDVRPERLEQL 59
>gnl|CDD|223981 COG1053, SdhA, Succinate dehydrogenase/fumarate reductase,
flavoprotein subunit [Energy production and conversion].
Length = 562
Score = 36.2 bits (84), Expect = 0.053
Identities = 12/30 (40%), Positives = 16/30 (53%)
Query: 385 VVIGAGGAGKALAYGAKAKGARVVIANRTY 414
VVIG GGAG A A G +V + ++
Sbjct: 10 VVIGGGGAGLRAAIEAAEAGLKVALLSKAP 39
>gnl|CDD|132492 TIGR03451, mycoS_dep_FDH, S-(hydroxymethyl)mycothiol dehydrogenase.
Members of this protein family are mycothiol-dependent
formaldehyde dehydrogenase (EC 1.2.1.66). This protein
is found, so far, only in the Actinobacteria
(Mycobacterium sp., Streptomyces sp., Corynebacterium
sp., and related species), where mycothione replaces
glutathione [Cellular processes, Detoxification].
Length = 358
Score = 35.9 bits (83), Expect = 0.054
Identities = 25/64 (39%), Positives = 30/64 (46%), Gaps = 8/64 (12%)
Query: 364 GLRGRLNVSGGVSSALAGKLFVVIGAGGAGKALAYGAKAKGARVVIA----NRTYDRARE 419
GL +N +GGV G VIG GG G A GA GA +IA +R + ARE
Sbjct: 164 GLGAAVN-TGGVKR---GDSVAVIGCGGVGDAAIAGAALAGASKIIAVDIDDRKLEWARE 219
Query: 420 LAET 423
T
Sbjct: 220 FGAT 223
>gnl|CDD|235488 PRK05476, PRK05476, S-adenosyl-L-homocysteine hydrolase;
Provisional.
Length = 425
Score = 35.9 bits (84), Expect = 0.058
Identities = 18/47 (38%), Positives = 25/47 (53%), Gaps = 6/47 (12%)
Query: 363 DGLRGRLNVSGGVSSALAGKLFVVIGAGGAGKALAYGAKAKGARVVI 409
DG++ NV +AGK+ VV G G GK A + GARV++
Sbjct: 200 DGIKRATNVL------IAGKVVVVAGYGDVGKGCAQRLRGLGARVIV 240
>gnl|CDD|216176 pfam00890, FAD_binding_2, FAD binding domain. This family includes
members that bind FAD. This family includes the
flavoprotein subunits from succinate and fumarate
dehydrogenase, aspartate oxidase and the alpha subunit
of adenylylsulphate reductase.
Length = 401
Score = 35.7 bits (83), Expect = 0.058
Identities = 12/30 (40%), Positives = 16/30 (53%)
Query: 385 VVIGAGGAGKALAYGAKAKGARVVIANRTY 414
VVIG+G AG A A A G +V + +
Sbjct: 3 VVIGSGLAGLAAALEAAEAGLKVAVVEKGQ 32
>gnl|CDD|176223 cd08262, Zn_ADH8, Alcohol dehydrogenases of the MDR family. The
medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P)-binding Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 341
Score = 35.7 bits (83), Expect = 0.060
Identities = 15/55 (27%), Positives = 26/55 (47%)
Query: 375 VSSALAGKLFVVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAETVGGHAL 429
+ G++ +VIG G G A+ KA+G ++A+ R LA +G +
Sbjct: 156 RARLTPGEVALVIGCGPIGLAVIAALKARGVGPIVASDFSPERRALALAMGADIV 210
>gnl|CDD|213572 TIGR00936, ahcY, adenosylhomocysteinase. This enzyme hydrolyzes
adenosylhomocysteine as part of a cycle for the
regeneration of the methyl donor S-adenosylmethionine.
Species that lack this enzyme are likely to have
adenosylhomocysteine nucleosidase (EC 3.2.2.9), an
enzyme which also acts as 5'-methyladenosine
nucleosidase (see TIGR01704) [Energy metabolism, Amino
acids and amines].
Length = 407
Score = 35.8 bits (83), Expect = 0.066
Identities = 15/31 (48%), Positives = 20/31 (64%)
Query: 379 LAGKLFVVIGAGGAGKALAYGAKAKGARVVI 409
+AGK VV G G GK +A A+ GARV++
Sbjct: 194 IAGKTVVVAGYGWCGKGIAMRARGMGARVIV 224
>gnl|CDD|236209 PRK08265, PRK08265, short chain dehydrogenase; Provisional.
Length = 261
Score = 35.4 bits (82), Expect = 0.069
Identities = 21/57 (36%), Positives = 29/57 (50%), Gaps = 1/57 (1%)
Query: 377 SALAGKLFVVIG-AGGAGKALAYGAKAKGARVVIANRTYDRARELAETVGGHALSLA 432
LAGK+ +V G A G A+A A GARV I + D +A ++G A +A
Sbjct: 2 IGLAGKVAIVTGGATLIGAAVARALVAAGARVAIVDIDADNGAAVAASLGERARFIA 58
>gnl|CDD|176219 cd08258, Zn_ADH4, Alcohol dehydrogenases of the MDR family. This
group shares the zinc coordination sites of the
zinc-dependent alcohol dehydrogenases. The medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, which contains the
zinc-dependent alcohol dehydrogenase (ADH-Zn) and
related proteins, is a diverse group of proteins related
to the first identified member, class I mammalian ADH.
MDRs display a broad range of activities and are
distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P)-binding Rossmann fold domain of an
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 306
Score = 35.4 bits (82), Expect = 0.069
Identities = 17/49 (34%), Positives = 23/49 (46%), Gaps = 1/49 (2%)
Query: 379 LAGKLFVVIGAGGAGKALAYGAKAKGARVVIANRTYDRAR-ELAETVGG 426
G VV G G G A AK +GA VV+ D R ++A+ +G
Sbjct: 163 RPGDTVVVFGPGPIGLLAAQVAKLQGATVVVVGTEKDEVRLDVAKELGA 211
>gnl|CDD|223377 COG0300, DltE, Short-chain dehydrogenases of various substrate
specificities [General function prediction only].
Length = 265
Score = 35.3 bits (82), Expect = 0.070
Identities = 13/46 (28%), Positives = 22/46 (47%), Gaps = 1/46 (2%)
Query: 378 ALAGKLFVVIGA-GGAGKALAYGAKAKGARVVIANRTYDRARELAE 422
+ GK ++ GA G G LA +G +++ R D+ LA+
Sbjct: 3 PMKGKTALITGASSGIGAELAKQLARRGYNLILVARREDKLEALAK 48
>gnl|CDD|223991 COG1063, Tdh, Threonine dehydrogenase and related Zn-dependent
dehydrogenases [Amino acid transport and metabolism /
General function prediction only].
Length = 350
Score = 35.4 bits (82), Expect = 0.079
Identities = 32/114 (28%), Positives = 40/114 (35%), Gaps = 19/114 (16%)
Query: 384 FVVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAETVGGHALSLADLENFNPEDGM 443
VV+GAG G AK GA VVI ELA+ GG AD+ ED
Sbjct: 172 VVVVGAGPIGLLAIALAKLLGASVVIVVDRSPERLELAKEAGG-----ADVVVNPSEDDA 226
Query: 444 ILANTTSIGMQPKVDETPIPKHALGHYALVFDAVYTPKITRLLREAEESGATIV 497
+ D +V +AV +P EA G T+V
Sbjct: 227 GAE-ILELTGGRGAD-------------VVIEAVGSPPALDQALEALRPGGTVV 266
>gnl|CDD|235736 PRK06196, PRK06196, oxidoreductase; Provisional.
Length = 315
Score = 35.4 bits (82), Expect = 0.080
Identities = 38/119 (31%), Positives = 49/119 (41%), Gaps = 30/119 (25%)
Query: 379 LAGKLFVVIG-AGGAG----KALAYGAKAKGARVVIANRTYDRARELAETVGG---HALS 430
L+GK +V G G G +ALA GA V++ R D ARE + G L
Sbjct: 24 LSGKTAIVTGGYSGLGLETTRALA----QAGAHVIVPARRPDVAREALAGIDGVEVVMLD 79
Query: 431 LADLENF-----------NPEDGMILANTTSIGMQPK---VD--ETPIPKHALGHYALV 473
LADLE+ D IL N + P+ D E + LGH+ALV
Sbjct: 80 LADLESVRAFAERFLDSGRRID--ILINNAGVMACPETRVGDGWEAQFATNHLGHFALV 136
>gnl|CDD|215101 PLN00203, PLN00203, glutamyl-tRNA reductase.
Length = 519
Score = 35.5 bits (82), Expect = 0.080
Identities = 28/82 (34%), Positives = 37/82 (45%), Gaps = 19/82 (23%)
Query: 360 AIEDGLRGR--LNVSGG---VSSA-------------LAGKLFVVIGAGGAGKALAYGAK 401
AI G R R N++ G VSSA A +VIGAG GK L
Sbjct: 227 AITAGKRVRTETNIASGAVSVSSAAVELALMKLPESSHASARVLVIGAGKMGKLLVKHLV 286
Query: 402 AKG-ARVVIANRTYDRARELAE 422
+KG ++V+ NR+ +R L E
Sbjct: 287 SKGCTKMVVVNRSEERVAALRE 308
>gnl|CDD|187627 cd05369, TER_DECR_SDR_a, Trans-2-enoyl-CoA reductase (TER) and
2,4-dienoyl-CoA reductase (DECR), atypical (a) SDR.
TTER is a peroxisomal protein with a proposed role in
fatty acid elongation. Fatty acid synthesis is known to
occur in the both endoplasmic reticulum and
mitochondria; peroxisomal TER has been proposed as an
additional fatty acid elongation system, it reduces the
double bond at C-2 as the last step of elongation. This
system resembles the mitochondrial system in that
acetyl-CoA is used as a carbon donor. TER may also
function in phytol metabolism, reducting phytenoyl-CoA
to phytanoyl-CoA in peroxisomes. DECR processes double
bonds in fatty acids to increase their utility in fatty
acid metabolism; it reduces 2,4-dienoyl-CoA to an
enoyl-CoA. DECR is active in mitochondria and
peroxisomes. This subgroup has the Gly-rich NAD-binding
motif of the classical SDR family, but does not display
strong identity to the canonical active site tetrad, and
lacks the characteristic Tyr at the usual position. 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 have a
3-glycine N-terminal NAD(P)(H)-binding pattern
(typically, TGxxxGxG in classical SDRs and TGxxGxxG in
extended SDRs), while substrate binding is in the
C-terminal region. A critical catalytic Tyr residue
(Tyr-151, human 15-hydroxyprostaglandin dehydrogenase
(15-PGDH) numbering), is often found in a conserved
YXXXK pattern. 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) or additional
Ser, contributing to the active site. Substrates for
these enzymes include sugars, steroids, alcohols, and
aromatic compounds. The standard reaction mechanism is a
proton relay involving the conserved Tyr and Lys, as
well as Asn (or Ser). Some SDR family members, including
17 beta-hydroxysteroid dehydrogenase contain an
additional helix-turn-helix motif that is not generally
found among SDRs.
Length = 249
Score = 34.9 bits (81), Expect = 0.080
Identities = 21/59 (35%), Positives = 27/59 (45%), Gaps = 5/59 (8%)
Query: 379 LAGK-LFVVIGAGGAGKALAYGAKAKGARVVIANRTYDR----ARELAETVGGHALSLA 432
L GK F+ G G GKA+A GA V IA R + A E++ GG A +
Sbjct: 1 LKGKVAFITGGGTGIGKAIAKAFAELGASVAIAGRKPEVLEAAAEEISSATGGRAHPIQ 59
>gnl|CDD|180854 PRK07121, PRK07121, hypothetical protein; Validated.
Length = 492
Score = 35.2 bits (82), Expect = 0.088
Identities = 14/30 (46%), Positives = 17/30 (56%)
Query: 385 VVIGAGGAGKALAYGAKAKGARVVIANRTY 414
VV+G G AG A A A GARV++ R
Sbjct: 24 VVVGFGAAGACAAIEAAAAGARVLVLERAA 53
>gnl|CDD|176239 cd08278, benzyl_alcohol_DH, Benzyl alcohol dehydrogenase. Benzyl
alcohol dehydrogenase is similar to liver alcohol
dehydrogenase, but has some amino acid substitutions
near the active site, which may determine the enzyme's
specificity of oxidizing aromatic substrates. Also
known as aryl-alcohol dehydrogenases, they catalyze the
conversion of an aromatic alcohol + NAD+ to an aromatic
aldehyde + NADH + H+. NAD(P)(H)-dependent
oxidoreductases are the major enzymes in the
interconversion of alcohols and aldehydes, or ketones.
Alcohol dehydrogenase in the liver converts ethanol and
NAD+ to acetaldehyde and NADH, while in yeast and some
other microorganisms ADH catalyzes the conversion
acetaldehyde to ethanol in alcoholic fermentation. ADH
is a member of the medium chain alcohol dehydrogenase
family (MDR), which has a NAD(P)(H)-binding domain in a
Rossmann fold of a beta-alpha form. The NAD(H)-binding
region is comprised of 2 structurally similar halves,
each of which contacts a mononucleotide. A GxGxxG motif
after the first mononucleotide contact half allows the
close contact of the coenzyme with the ADH backbone.
The N-terminal catalytic domain has a distant homology
to GroES. These proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and have 2 tightly bound zinc atoms per
subunit, a catalytic zinc at the active site and a
structural zinc in a lobe of the catalytic domain.
NAD(H) binding occurs in the cleft between the catalytic
and coenzyme-binding domains at the active site, and
coenzyme binding induces a conformational closing of
this cleft. Coenzyme binding typically precedes and
contributes to substrate binding. In human ADH
catalysis, the zinc ion helps coordinate the alcohol,
followed by deprotonation of a histidine, the ribose of
NAD, a serine, then the alcohol, which allows the
transfer of a hydride to NAD+, creating NADH and a
zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 365
Score = 35.2 bits (82), Expect = 0.091
Identities = 35/118 (29%), Positives = 48/118 (40%), Gaps = 24/118 (20%)
Query: 372 SGGVSSAL---AGKLFVVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAETVGG-H 427
+G V + L G V GAG G A AK G +IA D ELA+ +G H
Sbjct: 175 AGAVLNVLKPRPGSSIAVFGAGAVGLAAVMAAKIAGCTTIIAVDIVDSRLELAKELGATH 234
Query: 428 ALSLADLENFNPEDGMILA---NTTSIGMQPKVDETPIPK------HAL---GHYALV 473
+ NP++ ++A T G+ +D T +P AL G ALV
Sbjct: 235 VI--------NPKEEDLVAAIREITGGGVDYALDTTGVPAVIEQAVDALAPRGTLALV 284
>gnl|CDD|237225 PRK12843, PRK12843, putative FAD-binding dehydrogenase; Reviewed.
Length = 578
Score = 35.5 bits (82), Expect = 0.093
Identities = 17/42 (40%), Positives = 22/42 (52%), Gaps = 8/42 (19%)
Query: 385 VVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAETVGG 426
+VIGAG AG + A A G +V++ RT E VGG
Sbjct: 20 IVIGAGAAGMSAALFAAIAGLKVLLVERT--------EYVGG 53
>gnl|CDD|223980 COG1052, LdhA, Lactate dehydrogenase and related dehydrogenases
[Energy production and conversion / Coenzyme metabolism
/ General function prediction only].
Length = 324
Score = 34.9 bits (81), Expect = 0.096
Identities = 17/56 (30%), Positives = 28/56 (50%), Gaps = 2/56 (3%)
Query: 379 LAGKLFVVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAETVGGHALSLADL 434
L GK +IG G G+A+A K G +V+ +R+ E + +G + L +L
Sbjct: 144 LRGKTLGIIGLGRIGQAVARRLKGFGMKVLYYDRS--PNPEAEKELGARYVDLDEL 197
>gnl|CDD|223422 COG0345, ProC, Pyrroline-5-carboxylate reductase [Amino acid
transport and metabolism].
Length = 266
Score = 34.9 bits (81), Expect = 0.10
Identities = 14/47 (29%), Positives = 22/47 (46%), Gaps = 4/47 (8%)
Query: 384 FVVIGAGGAGKALAYGAKAKGA----RVVIANRTYDRARELAETVGG 426
IGAG G+A+ G GA +++ NR+ ++ LA G
Sbjct: 4 IGFIGAGNMGEAILSGLLKSGALPPEEIIVTNRSEEKRAALAAEYGV 50
>gnl|CDD|176230 cd08269, Zn_ADH9, Alcohol dehydrogenases of the MDR family. The
medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P)-binding Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability.
Length = 312
Score = 35.0 bits (81), Expect = 0.10
Identities = 20/47 (42%), Positives = 21/47 (44%)
Query: 379 LAGKLFVVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAETVG 425
AGK VIGAG G A A GAR VIA LA +G
Sbjct: 128 RAGKTVAVIGAGFIGLLFLQLAAAAGARRVIAIDRRPARLALARELG 174
>gnl|CDD|240652 cd12175, 2-Hacid_dh_11, Putative D-isomer specific 2-hydroxyacid
dehydrogenases, NAD-binding and catalytic domains.
2-Hydroxyacid dehydrogenases catalyze the conversion of
a wide variety of D-2-hydroxy acids to their
corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 311
Score = 34.9 bits (81), Expect = 0.11
Identities = 15/56 (26%), Positives = 25/56 (44%)
Query: 373 GGVSSALAGKLFVVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAETVGGHA 428
G S L+GK ++G G G+A+A + G V+ +R D E + +
Sbjct: 134 GRPSRELSGKTVGIVGLGNIGRAVARRLRGFGVEVIYYDRFRDPEAEEKDLGVRYV 189
>gnl|CDD|187593 cd05332, 11beta-HSD1_like_SDR_c, 11beta-hydroxysteroid
dehydrogenase type 1 (11beta-HSD1)-like, classical (c)
SDRs. Human 11beta_HSD1 catalyzes the NADP(H)-dependent
interconversion of cortisone and cortisol. This subgroup
also includes human dehydrogenase/reductase SDR family
member 7C (DHRS7C) and DHRS7B. These proteins have the
GxxxGxG nucleotide binding motif and S-Y-K catalytic
triad characteristic of the SDRs, but have an atypical
C-terminal domain that contributes to homodimerization
contacts. 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 = 257
Score = 34.5 bits (80), Expect = 0.12
Identities = 17/45 (37%), Positives = 26/45 (57%), Gaps = 1/45 (2%)
Query: 379 LAGKLFVVIGA-GGAGKALAYGAKAKGARVVIANRTYDRARELAE 422
L GK+ ++ GA G G+ LAY GAR+V++ R +R E+
Sbjct: 1 LQGKVVIITGASSGIGEELAYHLARLGARLVLSARREERLEEVKS 45
>gnl|CDD|109716 pfam00670, AdoHcyase_NAD, S-adenosyl-L-homocysteine hydrolase, NAD
binding domain.
Length = 162
Score = 33.9 bits (78), Expect = 0.12
Identities = 15/31 (48%), Positives = 20/31 (64%)
Query: 379 LAGKLFVVIGAGGAGKALAYGAKAKGARVVI 409
+AGK+ VV G G GK A K +GARV++
Sbjct: 21 IAGKVAVVCGYGDVGKGCAASLKGQGARVIV 51
>gnl|CDD|236110 PRK07831, PRK07831, short chain dehydrogenase; Provisional.
Length = 262
Score = 34.6 bits (80), Expect = 0.12
Identities = 21/48 (43%), Positives = 26/48 (54%), Gaps = 5/48 (10%)
Query: 379 LAGKLFVVIGAGGAG--KALAYGAKAKGARVVIANRTYDRARELAETV 424
LAGK+ +V A G G A A A +GARVVI++ R L ET
Sbjct: 15 LAGKVVLVTAAAGTGIGSATARRALEEGARVVISDI---HERRLGETA 59
>gnl|CDD|235924 PRK07063, PRK07063, short chain dehydrogenase; Provisional.
Length = 260
Score = 34.3 bits (79), Expect = 0.12
Identities = 17/45 (37%), Positives = 23/45 (51%), Gaps = 1/45 (2%)
Query: 379 LAGKLFVVIGAG-GAGKALAYGAKAKGARVVIANRTYDRARELAE 422
LAGK+ +V GA G G A+A +GA V +A+ A A
Sbjct: 5 LAGKVALVTGAAQGIGAAIARAFAREGAAVALADLDAALAERAAA 49
>gnl|CDD|176221 cd08260, Zn_ADH6, Alcohol dehydrogenases of the MDR family.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. This group has the characteristic
catalytic and structural zinc sites of the
zinc-dependent alcohol dehydrogenases. Alcohol
dehydrogenase in the liver converts ethanol and NAD+ to
acetaldehyde and NADH, while in yeast and some other
microorganisms ADH catalyzes the conversion acetaldehyde
to ethanol in alcoholic fermentation. ADH is a member of
the medium chain alcohol dehydrogenase family (MDR),
which has a NAD(P)(H)-binding domain in a Rossmann fold
of a beta-alpha form. The NAD(H)-binding region is
comprised of 2 structurally similar halves, each of
which contacts a mononucleotide. A GxGxxG motif after
the first mononucleotide contact half allows the close
contact of the coenzyme with the ADH backbone. The
N-terminal catalytic domain has a distant homology to
GroES. These proteins typically form dimers (typically
higher plants, mammals) or tetramers (yeast, bacteria),
and have 2 tightly bound zinc atoms per subunit, a
catalytic zinc at the active site and a structural zinc
in a lobe of the catalytic domain. NAD(H)-binding occurs
in the cleft between the catalytic and coenzyme-binding
domains at the active site, and coenzyme binding induces
a conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
In human ADH catalysis, the zinc ion helps coordinate
the alcohol, followed by deprotonation of a histidine,
the ribose of NAD, a serine, then the alcohol, which
allows the transfer of a hydride to NAD+, creating NADH
and a zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 345
Score = 34.5 bits (80), Expect = 0.13
Identities = 19/50 (38%), Positives = 24/50 (48%), Gaps = 5/50 (10%)
Query: 380 AGKLFVVIGAGGAGKALAYGAKAKGARVV---IANRTYDRAREL--AETV 424
G+ V G GG G + A A GARV+ I + + AREL TV
Sbjct: 165 PGEWVAVHGCGGVGLSAVMIASALGARVIAVDIDDDKLELARELGAVATV 214
>gnl|CDD|187607 cd05349, BKR_2_SDR_c, putative beta-ketoacyl acyl carrier protein
[ACP]reductase (BKR), subgroup 2, classical (c) SDR.
This subgroup includes Rhizobium sp. NGR234 FabG1. The
Escherichai coli K12 BKR, FabG, belongs to a different
subgroup. BKR catalyzes the NADPH-dependent reduction of
ACP in the first reductive step of de novo fatty acid
synthesis (FAS). FAS consists of four elongation steps,
which are repeated to extend the fatty acid chain
through the addition of two-carbo units from malonyl
acyl-carrier protein (ACP): condensation, reduction,
dehydration, and a final reduction. Type II FAS, typical
of plants and many bacteria, maintains these activities
on discrete polypeptides, while type I FAS utilizes one
or two multifunctional polypeptides. BKR resembles enoyl
reductase, which catalyzes the second reduction step in
FAS. 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 have a 3-glycine N-terminal NAD(P)(H)-binding
pattern (typically, TGxxxGxG in classical SDRs and
TGxxGxxG in extended SDRs), while substrate binding is
in the C-terminal region. A critical catalytic Tyr
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) numbering), is often found in a
conserved YXXXK pattern. 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) or
additional Ser, contributing to the active site.
Substrates for these enzymes include sugars, steroids,
alcohols, and aromatic compounds. The standard reaction
mechanism is a proton relay involving the conserved Tyr
and Lys, as well as Asn (or Ser). Some SDR family
members, including 17 beta-hydroxysteroid dehydrogenase
contain an additional helix-turn-helix motif that is not
generally found among SDRs.
Length = 246
Score = 34.4 bits (79), Expect = 0.14
Identities = 29/104 (27%), Positives = 46/104 (44%), Gaps = 10/104 (9%)
Query: 382 KLFVVIGAG-GAGKALAYGAKAKGARVVIA-NRTYDRARELAETVGGHALSL-ADLENFN 438
++ +V GA G G A+A +GARVV+ R+ + A +A G A+++ AD+ + +
Sbjct: 1 QVVLVTGASRGLGAAIARSFAREGARVVVNYYRSTESAEAVAAEAGERAIAIQADVRDRD 60
Query: 439 PEDGMILANTTSIGMQPKVDETPIPKHALGHYALVFDAVYTPKI 482
MI G VD I +AL + FD
Sbjct: 61 QVQAMIEEAKNHFG---PVDT--IVNNALIDF--PFDPDQRKTF 97
>gnl|CDD|129609 TIGR00518, alaDH, alanine dehydrogenase. The family of known
L-alanine dehydrogenases includes representatives from
the Proteobacteria, Firmicutes, and Cyanobacteria, all
with about 50 % identity or better. An outlier to this
group in both sequence and gap pattern is the homolog
from Helicobacter pylori, an epsilon division
Proteobacteria, which must be considered a putative
alanine dehydrogenase. Related proteins include
saccharopine dehydrogenase and the N-terminal half of
the NAD(P) transhydrogenase alpha subunit. All of these
related proteins bind NAD and/or NADP [Energy
metabolism, Amino acids and amines].
Length = 370
Score = 34.5 bits (79), Expect = 0.14
Identities = 22/60 (36%), Positives = 27/60 (45%), Gaps = 1/60 (1%)
Query: 367 GRLNVSGGVSSALAGKLFVVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAETVGG 426
GR + GGV G + +IG G G A A GA V I + DR R+L GG
Sbjct: 154 GRGVLLGGVPGVEPGDV-TIIGGGVVGTNAAKMANGLGATVTILDINIDRLRQLDAEFGG 212
>gnl|CDD|180993 PRK07478, PRK07478, short chain dehydrogenase; Provisional.
Length = 254
Score = 34.1 bits (79), Expect = 0.14
Identities = 23/61 (37%), Positives = 33/61 (54%), Gaps = 10/61 (16%)
Query: 379 LAGKLFVVIGAG-GAGKALAYGAKAKGARVVIANRTYDRARELAETV------GGHALSL 431
L GK+ ++ GA G G+A A +GA+VV+ R R EL + V GG A++L
Sbjct: 4 LNGKVAIITGASSGIGRAAAKLFAREGAKVVVGAR---RQAELDQLVAEIRAEGGEAVAL 60
Query: 432 A 432
A
Sbjct: 61 A 61
>gnl|CDD|240638 cd12161, GDH_like_1, Putative glycerate dehydrogenase and related
proteins of the D-specific 2-hydroxy dehydrogenase
family. This group contains a variety of proteins
variously identified as glycerate dehydrogenase (GDH,
aka Hydroxypyruvate Reductase) and other enzymes of the
2-hydroxyacid dehydrogenase family. GDH catalyzes the
reversible reaction of (R)-glycerate + NAD+ to
hydroxypyruvate + NADH + H+. 2-hydroxyacid
dehydrogenases catalyze the conversion of a wide variety
of D-2-hydroxy acids to their corresponding keto acids.
The general mechanism is (R)-lactate + acceptor to
pyruvate + reduced acceptor. Formate/glycerate and
related dehydrogenases of the D-specific 2-hydroxyacid
dehydrogenase superfamily include groups such as formate
dehydrogenase, glycerate dehydrogenase, L-alanine
dehydrogenase, and S-adenosylhomocysteine hydrolase.
Despite often low sequence identity, these proteins
typically have a characteristic arrangement of 2 similar
subdomains of the alpha/beta Rossmann-fold NAD+ binding
form. The NAD+ binding domain is inserted within the
linear sequence of the mostly N-terminal catalytic
domain, which has a similar domain structure to the
internal NAD binding domain. Structurally, these domains
are connected by extended alpha helices and create a
cleft in which NAD is bound, primarily to the C-terminal
portion of the 2nd (internal) domain. Some related
proteins have similar structural subdomain but with a
tandem arrangement of the catalytic and NAD-binding
subdomains in the linear sequence. While many members of
this family are dimeric, alanine DH is hexameric and
phosphoglycerate DH is tetrameric.
Length = 315
Score = 34.5 bits (80), Expect = 0.14
Identities = 23/72 (31%), Positives = 35/72 (48%), Gaps = 12/72 (16%)
Query: 363 DGLRGRLNVSGGVSSALAGKLFVVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAE 422
GL GR LAGK ++G G G +A KA G +V+ +R+ +E A+
Sbjct: 135 AGLIGRE---------LAGKTVGIVGTGAIGLRVARLFKAFGCKVLAYSRS---EKEEAK 182
Query: 423 TVGGHALSLADL 434
+G +SL +L
Sbjct: 183 ALGIEYVSLDEL 194
>gnl|CDD|107335 cd06340, PBP1_ABC_ligand_binding_like_6, Type I periplasmic
ligand-binding domain of uncharacterized ABC (ATPase
Binding Cassette)-type active transport systems that are
predicted to be involved in transport of amino acids,
peptides, or inorganic ions. This subgroup includes the
type I periplasmic ligand-binding domain of
uncharacterized ABC (ATPase Binding Cassette)-type
active transport systems that are predicted to be
involved in transport of amino acids, peptides, or
inorganic ions. This subgroup has high sequence
similarity to members of the family of hydrophobic amino
acid transporters (HAAT), such as
leucine-isoleucine-valine-binding protein (LIVBP);
however their ligand specificity has not been determined
experimentally.
Length = 347
Score = 34.6 bits (80), Expect = 0.15
Identities = 21/108 (19%), Positives = 39/108 (36%), Gaps = 26/108 (24%)
Query: 148 YTPSVEDLSNLVARIQASGADIVKFATTALDITDVARVFQITVHSQVPIIGLVMGERGLI 207
Y + DL++ V +++A+ D + A+ D + R M E+ +
Sbjct: 181 YPANARDLTSEVLKLKAANPDAILPASYTNDAILLVR---------------TMKEQRVE 225
Query: 208 SRILCAKFGGFL------TFGTLENGIVSA-----PGQPTIKDLLDLY 244
+ + + GG G GI++ P P KDL +
Sbjct: 226 PKAVYSVGGGAEDPSFVKALGKDAEGILTRNEWSDPKDPMAKDLNKRF 273
>gnl|CDD|180588 PRK06487, PRK06487, glycerate dehydrogenase; Provisional.
Length = 317
Score = 34.3 bits (79), Expect = 0.15
Identities = 14/34 (41%), Positives = 19/34 (55%)
Query: 379 LAGKLFVVIGAGGAGKALAYGAKAKGARVVIANR 412
L GK ++G G G A+A A+A G RV+I
Sbjct: 146 LEGKTLGLLGHGELGGAVARLAEAFGMRVLIGQL 179
>gnl|CDD|187640 cd08935, mannonate_red_SDR_c, putative D-mannonate oxidoreductase,
classical (c) SDR. D-mannonate oxidoreductase catalyzes
the NAD-dependent interconversion of D-mannonate and
D-fructuronate. This subgroup includes Bacillus
subtitils UxuB/YjmF, a putative D-mannonate
oxidoreductase; the B. subtilis UxuB gene is part of a
putative ten-gene operon (the Yjm operon) involved in
hexuronate catabolism. Escherichia coli UxuB does not
belong to this subgroup. This subgroup has a canonical
active site tetrad and a typical Gly-rich NAD-binding
motif. 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 = 271
Score = 34.4 bits (79), Expect = 0.16
Identities = 18/58 (31%), Positives = 29/58 (50%), Gaps = 4/58 (6%)
Query: 379 LAGKLFVVIGAGGA-GKALAYGAKAKGARVVIANRTYDRARELA---ETVGGHALSLA 432
L K+ V+ G G G A+A GA+V R ++ ++A +GG A++LA
Sbjct: 3 LKNKVAVITGGTGVLGGAMARALAQAGAKVAALGRNQEKGDKVAKEITALGGRAIALA 60
>gnl|CDD|176193 cd08231, MDR_TM0436_like, Hypothetical enzyme TM0436 resembles the
zinc-dependent alcohol dehydrogenases (ADH). This group
contains the hypothetical TM0436 alcohol dehydrogenase
from Thermotoga maritima, proteins annotated as
5-exo-alcohol dehydrogenase, and other members of the
medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
MDR, which contains the zinc-dependent alcohol
dehydrogenase (ADH-Zn) and related proteins, is a
diverse group of proteins related to the first
identified member, class I mammalian ADH. MDRs display
a broad range of activities and are distinguished from
the smaller short chain dehydrogenases (~ 250 amino
acids vs. the ~ 350 amino acids of the MDR). The MDR
proteins have 2 domains: a C-terminal NAD(P)
binding-Rossmann fold domain of a beta-alpha form and an
N-terminal catalytic domain with distant homology to
GroES. The MDR group contains a host of activities,
including the founding alcohol dehydrogenase (ADH),
quinone reductase, sorbitol dehydrogenase, formaldehyde
dehydrogenase, butanediol DH, ketose reductase, cinnamyl
reductase, and numerous others. The zinc-dependent
alcohol dehydrogenases (ADHs) catalyze the
NAD(P)(H)-dependent interconversion of alcohols to
aldehydes or ketones. Active site zinc has a catalytic
role, while structural zinc aids in stability.
Length = 361
Score = 34.2 bits (79), Expect = 0.16
Identities = 20/55 (36%), Positives = 20/55 (36%)
Query: 375 VSSALAGKLFVVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAETVGGHAL 429
AG VV GAG G AK GAR VI ELA G A
Sbjct: 172 AGPVGAGDTVVVQGAGPLGLYAVAAAKLAGARRVIVIDGSPERLELAREFGADAT 226
>gnl|CDD|235962 PRK07201, PRK07201, short chain dehydrogenase; Provisional.
Length = 657
Score = 34.5 bits (80), Expect = 0.17
Identities = 20/66 (30%), Positives = 25/66 (37%), Gaps = 14/66 (21%)
Query: 360 AIEDGLRGRLNVSGGVSSALAGKLFVVIGA-GGAGKALAYGAKAKGARVVIANRTYDRAR 418
A LRG L GK+ ++ GA G G+A A GA V + R
Sbjct: 360 ARRRDLRGPL----------VGKVVLITGASSGIGRATAIKVAEAGATVFLVAR---NGE 406
Query: 419 ELAETV 424
L E V
Sbjct: 407 ALDELV 412
>gnl|CDD|217244 pfam02826, 2-Hacid_dh_C, D-isomer specific 2-hydroxyacid
dehydrogenase, NAD binding domain. This domain is
inserted into the catalytic domain, the large
dehydrogenase and D-lactate dehydrogenase families in
SCOP. N-terminal portion of which is represented by
family pfam00389.
Length = 175
Score = 33.2 bits (77), Expect = 0.17
Identities = 20/56 (35%), Positives = 31/56 (55%), Gaps = 3/56 (5%)
Query: 379 LAGKLFVVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAETVGGHALSLADL 434
L+GK +IG G G+A+A KA G +V+ +R + AE +G +SL +L
Sbjct: 33 LSGKTVGIIGLGRIGRAVARRLKAFGMKVIAYDRY---PKAEAEALGARYVSLDEL 85
>gnl|CDD|187642 cd08937, DHB_DH-like_SDR_c,
1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate
dehydrogenase (DHB DH)-like, classical (c) SDR. DHB DH
(aka 1,2-dihydroxycyclohexa-3,5-diene-1-carboxylate
dehydrogenase) catalyzes the NAD-dependent conversion of
1,2-dihydroxycyclohexa-3,4-diene carboxylate to a
catechol. This subgroup also contains Pseudomonas putida
F1 CmtB, 2,3-dihydroxy-2,3-dihydro-p-cumate
dehydrogenase, the second enzyme in the pathway for
catabolism of p-cumate catabolism. This subgroup shares
the glycine-rich NAD-binding motif of the classical SDRs
and shares the same catalytic triad; however, the
upstream Asn implicated in cofactor binding or catalysis
in other SDRs is generally substituted by a Ser. 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 = 256
Score = 34.0 bits (78), Expect = 0.19
Identities = 23/73 (31%), Positives = 37/73 (50%), Gaps = 6/73 (8%)
Query: 379 LAGKLFVVIGAG-GAGKALAYGAKAKGARVVIANRT---YDRARELAETVGGHALSL-AD 433
GK+ VV GA G G+ +A +GARV++ +R+ ++ E+ G A AD
Sbjct: 2 FEGKVVVVTGAAQGIGRGVAERLAGEGARVLLVDRSELVHEVLAEILAA-GDAAHVHTAD 60
Query: 434 LENFNPEDGMILA 446
LE + G++ A
Sbjct: 61 LETYAGAQGVVRA 73
>gnl|CDD|240636 cd12159, 2-Hacid_dh_2, Putative D-isomer specific 2-hydroxyacid
dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 303
Score = 34.2 bits (79), Expect = 0.19
Identities = 19/59 (32%), Positives = 25/59 (42%), Gaps = 4/59 (6%)
Query: 379 LAGKLFVVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAETVG----GHALSLAD 433
L G ++GAGG G+AL GA+V+ NR+ ETV AD
Sbjct: 123 LRGSTVAIVGAGGIGRALIPLLAPFGAKVIAVNRSGRPVEGADETVPADRLDEVWPDAD 181
>gnl|CDD|234662 PRK00141, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 473
Score = 34.4 bits (79), Expect = 0.20
Identities = 17/56 (30%), Positives = 28/56 (50%), Gaps = 1/56 (1%)
Query: 378 ALAGKLFVVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAETVGGHALSLAD 433
L+G++ V GAG +G+ +A G VV+A+ +L E G +S A+
Sbjct: 13 ELSGRVLVA-GAGVSGRGIAAMLSELGCDVVVADDNETARHKLIEVTGVADISTAE 67
>gnl|CDD|180446 PRK06180, PRK06180, short chain dehydrogenase; Provisional.
Length = 277
Score = 33.7 bits (78), Expect = 0.20
Identities = 16/53 (30%), Positives = 23/53 (43%), Gaps = 1/53 (1%)
Query: 381 GKLFVVIGAG-GAGKALAYGAKAKGARVVIANRTYDRARELAETVGGHALSLA 432
K +++ G G G+ALA A A G RVV R+ + AL+
Sbjct: 4 MKTWLITGVSSGFGRALAQAALAAGHRVVGTVRSEAARADFEALHPDRALARL 56
>gnl|CDD|188170 TIGR01832, kduD, 2-deoxy-D-gluconate 3-dehydrogenase. This model
describes 2-deoxy-D-gluconate 3-dehydrogenase (also
called 2-keto-3-deoxygluconate oxidoreductase), a member
of the family of short-chain-alcohol dehydrogenases
(pfam00106). This protein has been characterized in
Erwinia chrysanthemi as an enzyme of pectin degradation
[Energy metabolism, Biosynthesis and degradation of
polysaccharides].
Length = 248
Score = 33.6 bits (77), Expect = 0.22
Identities = 23/69 (33%), Positives = 35/69 (50%), Gaps = 3/69 (4%)
Query: 379 LAGKLFVVIGAG-GAGKALAYGAKAKGARVVIANRT-YDRARELAETVGGHALSL-ADLE 435
L GK+ +V GA G G+ +A G GA +V A R+ ++ E +G LSL ADL
Sbjct: 3 LEGKVALVTGANTGLGQGIAVGLAEAGADIVGAGRSEPSETQQQVEALGRRFLSLTADLS 62
Query: 436 NFNPEDGMI 444
+ ++
Sbjct: 63 DIEAIKALV 71
>gnl|CDD|236040 PRK07523, PRK07523, gluconate 5-dehydrogenase; Provisional.
Length = 255
Score = 33.6 bits (77), Expect = 0.23
Identities = 26/91 (28%), Positives = 37/91 (40%), Gaps = 15/91 (16%)
Query: 379 LAGKLFVVIGAG-GAGKALAYGAKAKGARVVIANRTYDRARELAETVGG----------- 426
L G+ +V G+ G G ALA G GA V++ R + AE++ G
Sbjct: 8 LTGRRALVTGSSQGIGYALAEGLAQAGAEVILNGRDPAKLAAAAESLKGQGLSAHALAFD 67
Query: 427 ---HALSLADLENFNPEDGMILANTTSIGMQ 454
H A ++ F E G I + GMQ
Sbjct: 68 VTDHDAVRAAIDAFEAEIGPIDILVNNAGMQ 98
>gnl|CDD|176217 cd08255, 2-desacetyl-2-hydroxyethyl_bacteriochlorophyllide_like,
2-desacetyl-2-hydroxyethyl bacteriochlorophyllide and
other MDR family members. This subgroup of the medium
chain dehydrogenases/reductase (MDR)/zinc-dependent
alcohol dehydrogenase-like family has members identified
as 2-desacetyl-2-hydroxyethyl bacteriochlorophyllide A
dehydrogenase and alcohol dehydrogenases. The medium
chain dehydrogenases/reductase (MDR)/zinc-dependent
alcohol dehydrogenase-like family, which contains the
zinc-dependent alcohol dehydrogenase (ADH-Zn) and
related proteins, is a diverse group of proteins related
to the first identified member, class I mammalian ADH.
MDRs display a broad range of activities and are
distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability.
Length = 277
Score = 33.8 bits (78), Expect = 0.23
Identities = 21/59 (35%), Positives = 25/59 (42%)
Query: 384 FVVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAETVGGHALSLADLENFNPEDG 442
V+G G G A AKA GAR V+ RELAE +G AD + G
Sbjct: 101 VAVVGLGLVGLLAAQLAKAAGAREVVGVDPDAARRELAEALGPADPVAADTADEIGGRG 159
>gnl|CDD|223717 COG0644, FixC, Dehydrogenases (flavoproteins) [Energy production
and conversion].
Length = 396
Score = 34.0 bits (78), Expect = 0.23
Identities = 17/57 (29%), Positives = 26/57 (45%), Gaps = 5/57 (8%)
Query: 385 VVIGAGGAGKALAYGAKAKGARVVIANRTYDRAREL-AETVGGHALSLADLENFNPE 440
V++GAG AG + A G V++ ++ E A+ G LS LE P+
Sbjct: 7 VIVGAGPAGSSAARRLAKAGLDVLV----LEKGSEPGAKPCCGGGLSPRALEELIPD 59
>gnl|CDD|217563 pfam03446, NAD_binding_2, NAD binding domain of 6-phosphogluconate
dehydrogenase. The NAD binding domain of
6-phosphogluconate dehydrogenase adopts a Rossmann fold.
Length = 163
Score = 32.8 bits (76), Expect = 0.24
Identities = 15/49 (30%), Positives = 20/49 (40%)
Query: 386 VIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAETVGGHALSLADL 434
IG G G +A G V + NRT ++ EL A S A+
Sbjct: 5 FIGLGVMGSPMALNLLKAGYTVTVYNRTPEKVEELVAEGAVGAASPAEF 53
>gnl|CDD|176184 cd05281, TDH, Threonine dehydrogenase. L-threonine dehydrogenase
(TDH) catalyzes the zinc-dependent formation of
2-amino-3-ketobutyrate from L-threonine via NAD(H)-
dependent oxidation. THD is a member of the
zinc-requiring, medium chain NAD(H)-dependent alcohol
dehydrogenase family (MDR). MDRs have a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. NAD(P)(H)-dependent oxidoreductases are
the major enzymes in the interconversion of alcohols and
aldehydes, or ketones. The N-terminal region typically
has an all-beta catalytic domain. These proteins
typically form dimers (typically higher plants, mammals)
or tetramers (yeast, bacteria) and have 2 tightly bound
zinc atoms per subunit. Sorbitol and aldose reductase
are NAD(+) binding proteins of the polyol pathway, which
interconverts glucose and fructose.
Length = 341
Score = 33.7 bits (78), Expect = 0.24
Identities = 18/50 (36%), Positives = 27/50 (54%), Gaps = 2/50 (4%)
Query: 379 LAGKLFVVIGAGGAGKALAYG-AKAKGARVVIANRTYDRARELAETVGGH 427
++GK ++ G G G +A AKA GA +VIA+ ELA+ +G
Sbjct: 162 VSGKSVLITGCGPIG-LMAIAVAKAAGASLVIASDPNPYRLELAKKMGAD 210
>gnl|CDD|225186 COG2303, BetA, Choline dehydrogenase and related flavoproteins
[Amino acid transport and metabolism].
Length = 542
Score = 34.0 bits (78), Expect = 0.24
Identities = 9/26 (34%), Positives = 15/26 (57%)
Query: 384 FVVIGAGGAGKALAYGAKAKGARVVI 409
+V++G+G AG LA G V++
Sbjct: 10 YVIVGSGSAGSVLAARLSDAGLSVLV 35
>gnl|CDD|176197 cd08235, iditol_2_DH_like, L-iditol 2-dehydrogenase. Putative
L-iditol 2-dehydrogenase based on annotation of some
members in this subgroup. L-iditol 2-dehydrogenase
catalyzes the NAD+-dependent conversion of L-iditol to
L-sorbose in fructose and mannose metabolism. This
enzyme is related to sorbitol dehydrogenase, alcohol
dehydrogenase, and other medium chain
dehydrogenase/reductases. The zinc-dependent alcohol
dehydrogenase (ADH-Zn)-like family of proteins is a
diverse group of proteins related to the first
identified member, class I mammalian ADH. This group is
also called the medium chain dehydrogenases/reductase
family (MDR) to highlight its broad range of activities
and to distinguish from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal GroES-like catalytic
domain. The MDR group contains a host of activities,
including the founding alcohol dehydrogenase (ADH),
quinone reductase, sorbitol dehydrogenase, formaldehyde
dehydrogenase, butanediol DH, ketose reductase, cinnamyl
reductase, and numerous others. The zinc-dependent
alcohol dehydrogenases (ADHs) catalyze the
NAD(P)(H)-dependent interconversion of alcohols to
aldehydes or ketones. Active site zinc has a catalytic
role, while structural zinc aids in stability. ADH-like
proteins typically form dimers (typically higher
plants, mammals) or tetramers (yeast, bacteria), and
generally have 2 tightly bound zinc atoms per subunit.
The active site zinc is coordinated by a histidine, two
cysteines, and a water molecule. The second zinc seems
to play a structural role, affects subunit interactions,
and is typically coordinated by 4 cysteines.
Length = 343
Score = 33.7 bits (78), Expect = 0.24
Identities = 18/45 (40%), Positives = 23/45 (51%)
Query: 385 VVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAETVGGHAL 429
+VIGAG G A AKA GAR VI + + E A+ +G
Sbjct: 170 LVIGAGPIGLLHAMLAKASGARKVIVSDLNEFRLEFAKKLGADYT 214
>gnl|CDD|235712 PRK06138, PRK06138, short chain dehydrogenase; Provisional.
Length = 252
Score = 33.6 bits (77), Expect = 0.25
Identities = 22/50 (44%), Positives = 30/50 (60%), Gaps = 2/50 (4%)
Query: 379 LAGKLFVVIGAG-GAGKALAYGAKAKGARVVIANRTYDRA-RELAETVGG 426
LAG++ +V GAG G G+A A +GARVV+A+R + A R A G
Sbjct: 3 LAGRVAIVTGAGSGIGRATAKLFAREGARVVVADRDAEAAERVAAAIAAG 52
>gnl|CDD|223774 COG0702, COG0702, Predicted nucleoside-diphosphate-sugar epimerases
[Cell envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 275
Score = 33.7 bits (77), Expect = 0.26
Identities = 17/53 (32%), Positives = 21/53 (39%), Gaps = 1/53 (1%)
Query: 382 KLFVVIGA-GGAGKALAYGAKAKGARVVIANRTYDRARELAETVGGHALSLAD 433
+V GA G G A+ A+G V A R + A LA V L D
Sbjct: 1 MKILVTGATGFVGGAVVRELLARGHEVRAAVRNPEAAAALAGGVEVVLGDLRD 53
>gnl|CDD|240642 cd12165, 2-Hacid_dh_6, Putative D-isomer specific 2-hydroxyacid
dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 314
Score = 33.4 bits (77), Expect = 0.28
Identities = 15/54 (27%), Positives = 24/54 (44%)
Query: 360 AIEDGLRGRLNVSGGVSSALAGKLFVVIGAGGAGKALAYGAKAKGARVVIANRT 413
+ G+ S L GK ++G G G+ +A KA G RV+ +R+
Sbjct: 116 DLRRGIWHGRAGEEPESKELRGKTVGILGYGHIGREIARLLKAFGMRVIGVSRS 169
>gnl|CDD|168574 PRK06484, PRK06484, short chain dehydrogenase; Validated.
Length = 520
Score = 33.7 bits (77), Expect = 0.28
Identities = 24/84 (28%), Positives = 40/84 (47%), Gaps = 9/84 (10%)
Query: 355 VGAISAIEDGLRGRLNVSGGVSSAL-------AGKLFVVIGAG-GAGKALAYGAKAKGAR 406
G+ + DG SG S+A + ++ + G G G+A+A A G R
Sbjct: 237 TGSTLVV-DGGWTVYGGSGPASTAQAPSPLAESPRVVAITGGARGIGRAVADRFAAAGDR 295
Query: 407 VVIANRTYDRARELAETVGGHALS 430
++I +R + A++LAE +G LS
Sbjct: 296 LLIIDRDAEGAKKLAEALGDEHLS 319
Score = 33.7 bits (77), Expect = 0.30
Identities = 20/53 (37%), Positives = 32/53 (60%), Gaps = 1/53 (1%)
Query: 381 GKLFVVIGA-GGAGKALAYGAKAKGARVVIANRTYDRARELAETVGGHALSLA 432
++ +V GA GG G+A G +VV+A+R +RARE A+++G +LA
Sbjct: 5 SRVVLVTGAAGGIGRAACQRFARAGDQVVVADRNVERARERADSLGPDHHALA 57
>gnl|CDD|235726 PRK06181, PRK06181, short chain dehydrogenase; Provisional.
Length = 263
Score = 33.4 bits (77), Expect = 0.30
Identities = 31/99 (31%), Positives = 43/99 (43%), Gaps = 21/99 (21%)
Query: 381 GKLFVVIGA-GGAGKALAYGAKAKGARVVIANRTYDRARELAETV---GGHALSL-ADL- 434
GK+ ++ GA G G+ALA GA++V+A R R LA+ + GG AL + D+
Sbjct: 1 GKVVIITGASEGIGRALAVRLARAGAQLVLAARNETRLASLAQELADHGGEALVVPTDVS 60
Query: 435 -------------ENFNPEDGMILANTTSIGMQPKVDET 460
F D IL N I M + DE
Sbjct: 61 DAEACERLIEAAVARFGGID--ILVNNAGITMWSRFDEL 97
>gnl|CDD|216949 pfam02254, TrkA_N, TrkA-N domain. This domain is found in a wide
variety of proteins. These protein include potassium
channels, phosphoesterases, and various other
transporters. This domain binds to NAD.
Length = 116
Score = 31.8 bits (73), Expect = 0.32
Identities = 21/69 (30%), Positives = 32/69 (46%), Gaps = 6/69 (8%)
Query: 384 FVVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAE----TVGGHALSLADLENFNP 439
++IG G G++LA + G VV+ ++ +R EL E V G A LE
Sbjct: 1 IIIIGYGRVGRSLAEELREGGPDVVVIDKDPERVEELREEGVPVVVGDATDEEVLEEAGI 60
Query: 440 E--DGMILA 446
E D ++ A
Sbjct: 61 EEADAVVAA 69
>gnl|CDD|224995 COG2084, MmsB, 3-hydroxyisobutyrate dehydrogenase and related
beta-hydroxyacid dehydrogenases [Lipid metabolism].
Length = 286
Score = 33.3 bits (77), Expect = 0.32
Identities = 14/41 (34%), Positives = 18/41 (43%)
Query: 386 VIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAETVGG 426
IG G G +A G V + NRT ++A EL G
Sbjct: 5 FIGLGIMGSPMAANLLKAGHEVTVYNRTPEKAAELLAAAGA 45
>gnl|CDD|237008 PRK11880, PRK11880, pyrroline-5-carboxylate reductase; Reviewed.
Length = 267
Score = 33.2 bits (77), Expect = 0.32
Identities = 12/47 (25%), Positives = 21/47 (44%), Gaps = 3/47 (6%)
Query: 382 KLFVVIGAGGAGKALAYGAKAKG---ARVVIANRTYDRARELAETVG 425
K IG G A+ G A G +++++ + ++ LAE G
Sbjct: 3 KKIGFIGGGNMASAIIGGLLASGVPAKDIIVSDPSPEKRAALAEEYG 49
>gnl|CDD|212495 cd09807, retinol-DH_like_SDR_c, retinol dehydrogenases
(retinol-DHs), classical (c) SDRs. Classical SDR-like
subgroup containing retinol-DHs and related proteins.
Retinol is processed by a medium chain alcohol
dehydrogenase followed by retinol-DHs. 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. 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 = 274
Score = 33.2 bits (76), Expect = 0.33
Identities = 32/116 (27%), Positives = 45/116 (38%), Gaps = 24/116 (20%)
Query: 381 GKLFVVIGAG-GAGKALAYGAKAKGARVVIANRTYDRARELA-----ETVGGHA----LS 430
GK ++ GA G GK A +GARV++A R + E A +T+ L
Sbjct: 1 GKTVIITGANTGIGKETARELARRGARVIMACRDMAKCEEAAAEIRRDTLNHEVIVRHLD 60
Query: 431 LADL--------ENFNPEDGM-ILANTTSIGMQPKVD-----ETPIPKHALGHYAL 472
LA L E ED + +L N + P E + LGH+ L
Sbjct: 61 LASLKSIRAFAAEFLAEEDRLDVLINNAGVMRCPYSKTEDGFEMQFGVNHLGHFLL 116
>gnl|CDD|180408 PRK06114, PRK06114, short chain dehydrogenase; Provisional.
Length = 254
Score = 33.2 bits (76), Expect = 0.33
Identities = 21/61 (34%), Positives = 29/61 (47%), Gaps = 9/61 (14%)
Query: 379 LAGKLFVVIGAG-GAGKALAYGAKAKGARVVIANRTYDRARELAETV------GGHALSL 431
L G++ V GAG G G+ +A G GA V + + D LAET G A+ +
Sbjct: 6 LDGQVAFVTGAGSGIGQRIAIGLAQAGADVALFDLRTDDG--LAETAEHIEAAGRRAIQI 63
Query: 432 A 432
A
Sbjct: 64 A 64
>gnl|CDD|240622 cd05198, formate_dh_like, Formate/glycerate and related
dehydrogenases of the D-specific 2-hydroxy acid
dehydrogenase family. Formate dehydrogenase, D-specific
2-hydroxy acid dehydrogenase, Phosphoglycerate
Dehydrogenase, Lactate dehydrogenase, Thermostable
Phosphite Dehydrogenase, and Hydroxy(phenyl)pyruvate
reductase, among others, share a characteristic
arrangement of 2 similar subdomains of the alpha/beta
Rossmann fold NAD+ binding form. 2-hydroxyacid
dehydrogenases are enzymes that catalyze the conversion
of a wide variety of D-2-hydroxy acids to their
corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
The NAD+ binding domain is inserted within the linear
sequence of the mostly N-terminal catalytic domain,
which has a similar domain structure to the internal NAD
binding domain. Structurally, these domains are
connected by extended alpha helices and create a cleft
in which NAD is bound, primarily to the C-terminal
portion of the 2nd (internal) domain. Some related
proteins have similar structural subdomain but with a
tandem arrangement of the catalytic and NAD-binding
subdomains in the linear sequence. Formate dehydrogenase
(FDH) catalyzes the NAD+-dependent oxidation of formate
ion to carbon dioxide with the concomitant reduction of
NAD+ to NADH. FDHs of this family contain no metal ions
or prosthetic groups. Catalysis occurs though direct
transfer of hydride ion to NAD+ without the stages of
acid-base catalysis typically found in related
dehydrogenases. FDHs are found in all methylotrophic
microorganisms in energy production and in the stress
responses of plants. Formate/glycerate and related
dehydrogenases of the D-specific 2-hydroxyacid
dehydrogenase superfamily include groups such as formate
dehydrogenase, glycerate dehydrogenase, L-alanine
dehydrogenase, and S-Adenosylhomocysteine Hydrolase,
among others. While many members of this family are
dimeric, alanine DH is hexameric and phosphoglycerate DH
is tetrameric.
Length = 302
Score = 33.4 bits (77), Expect = 0.33
Identities = 19/56 (33%), Positives = 30/56 (53%), Gaps = 2/56 (3%)
Query: 379 LAGKLFVVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAETVGGHALSLADL 434
L GK ++G G G+ +A +A G +V+ +RT R E E +G +SL +L
Sbjct: 138 LEGKTVGIVGLGRIGQRVAKRLQAFGMKVLYYDRT--RKPEPEEDLGFRVVSLDEL 191
>gnl|CDD|218507 pfam05221, AdoHcyase, S-adenosyl-L-homocysteine hydrolase.
Length = 430
Score = 33.6 bits (77), Expect = 0.33
Identities = 14/31 (45%), Positives = 20/31 (64%)
Query: 379 LAGKLFVVIGAGGAGKALAYGAKAKGARVVI 409
+AGK+ VV G G GK A + +GARV++
Sbjct: 208 IAGKVAVVCGYGDVGKGCAASLRGQGARVIV 238
>gnl|CDD|240625 cd05300, 2-Hacid_dh_1, Putative D-isomer specific 2-hydroxyacid
dehydrogenase. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomains but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric. Formate dehydrogenase (FDH) catalyzes the
NAD+-dependent oxidation of formate ion to carbon
dioxide with the concomitant reduction of NAD+ to NADH.
FDHs of this family contain no metal ions or prosthetic
groups. Catalysis occurs though direct transfer of the
hydride ion to NAD+ without the stages of acid-base
catalysis typically found in related dehydrogenases.
FDHs are found in all methylotrophic microorganisms in
energy production and in the stress responses of plants.
Length = 313
Score = 33.3 bits (77), Expect = 0.36
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 5/60 (8%)
Query: 379 LAGKLFVVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAETVGGH-----ALSLAD 433
LAGK +++G G G+ +A AKA G RV+ R+ A + + V L AD
Sbjct: 132 LAGKTVLIVGLGDIGREIARRAKAFGMRVIGVRRSGRPAPPVVDEVYTPDELDELLPEAD 191
>gnl|CDD|236229 PRK08303, PRK08303, short chain dehydrogenase; Provisional.
Length = 305
Score = 33.0 bits (76), Expect = 0.36
Identities = 24/69 (34%), Positives = 31/69 (44%), Gaps = 14/69 (20%)
Query: 374 GVSSALAGKLFVVIGAG-GAGKALAYGAKAKGARVVIANRT-------YDRA---RELAE 422
+ L GK+ +V GA GAG+ +A A GA V + R+ YDR E AE
Sbjct: 1 PMMKPLRGKVALVAGATRGAGRGIAVELGAAGATVYVTGRSTRARRSEYDRPETIEETAE 60
Query: 423 TV---GGHA 428
V GG
Sbjct: 61 LVTAAGGRG 69
>gnl|CDD|179297 PRK01438, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 480
Score = 33.5 bits (77), Expect = 0.37
Identities = 17/50 (34%), Positives = 22/50 (44%), Gaps = 1/50 (2%)
Query: 377 SALAGKLFVVIGAGGAGKALAYGAKAKGARVVIANRT-YDRARELAETVG 425
S G VV G G +G A A GARV + + +R R LA +
Sbjct: 12 SDWQGLRVVVAGLGVSGFAAADALLELGARVTVVDDGDDERHRALAAILE 61
>gnl|CDD|235787 PRK06370, PRK06370, mercuric reductase; Validated.
Length = 463
Score = 33.3 bits (77), Expect = 0.40
Identities = 13/28 (46%), Positives = 16/28 (57%)
Query: 385 VVIGAGGAGKALAYGAKAKGARVVIANR 412
+VIGAG AG LA A G +V + R
Sbjct: 9 IVIGAGQAGPPLAARAAGLGMKVALIER 36
>gnl|CDD|180300 PRK05875, PRK05875, short chain dehydrogenase; Provisional.
Length = 276
Score = 32.9 bits (75), Expect = 0.40
Identities = 17/52 (32%), Positives = 26/52 (50%), Gaps = 1/52 (1%)
Query: 375 VSSALAGKLFVVIGAG-GAGKALAYGAKAKGARVVIANRTYDRARELAETVG 425
+ + + ++V G G G GK +A G A GA V+I R D+ AE +
Sbjct: 1 MQLSFQDRTYLVTGGGSGIGKGVAAGLVAAGAAVMIVGRNPDKLAAAAEEIE 52
>gnl|CDD|237626 PRK14154, PRK14154, heat shock protein GrpE; Provisional.
Length = 208
Score = 32.5 bits (73), Expect = 0.41
Identities = 18/51 (35%), Positives = 27/51 (52%), Gaps = 1/51 (1%)
Query: 141 VSSHNYQYTPSVEDLSNLVARIQASGADIVKFATTALDITDVARVFQITVH 191
V + QY + ++ NL RI+ ADI+KF + L ITD+ V +H
Sbjct: 68 VDEYKTQYLRAQAEMDNLRKRIEREKADIIKFGSKQL-ITDLLPVADSLIH 117
>gnl|CDD|223758 COG0686, Ald, Alanine dehydrogenase [Amino acid transport and
metabolism].
Length = 371
Score = 33.1 bits (76), Expect = 0.41
Identities = 22/54 (40%), Positives = 27/54 (50%), Gaps = 1/54 (1%)
Query: 373 GGVSSALAGKLFVVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAETVGG 426
GGV L K+ VV+G G G A A GA V I + DR R+L + GG
Sbjct: 161 GGVPGVLPAKV-VVLGGGVVGTNAAKIAIGLGADVTILDLNIDRLRQLDDLFGG 213
>gnl|CDD|223992 COG1064, AdhP, Zn-dependent alcohol dehydrogenases [General
function prediction only].
Length = 339
Score = 32.9 bits (76), Expect = 0.43
Identities = 21/54 (38%), Positives = 30/54 (55%), Gaps = 3/54 (5%)
Query: 375 VSSALAGKLFVVIGAGGAGK-ALAYGAKAKGARVVIANRTYDRARELAETVGGH 427
++ GK V+GAGG G A+ Y AKA GA V+ R+ + ELA+ +G
Sbjct: 161 KANVKPGKWVAVVGAGGLGHMAVQY-AKAMGAEVIAITRS-EEKLELAKKLGAD 212
>gnl|CDD|187618 cd05360, SDR_c3, classical (c) SDR, subgroup 3. These proteins are
members of the classical SDR family, with a canonical
active site triad (and also active site Asn) and a
typical Gly-rich NAD-binding motif. 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 have a
3-glycine N-terminal NAD(P)(H)-binding pattern
(typically, TGxxxGxG in classical SDRs and TGxxGxxG in
extended SDRs), while substrate binding is in the
C-terminal region. A critical catalytic Tyr residue
(Tyr-151, human 15-hydroxyprostaglandin dehydrogenase
(15-PGDH) numbering), is often found in a conserved
YXXXK pattern. 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) or additional
Ser, contributing to the active site. Substrates for
these enzymes include sugars, steroids, alcohols, and
aromatic compounds. The standard reaction mechanism is a
proton relay involving the conserved Tyr and Lys, as
well as Asn (or Ser). Some SDR family members, including
17 beta-hydroxysteroid dehydrogenase contain an
additional helix-turn-helix motif that is not generally
found among SDRs.
Length = 233
Score = 32.7 bits (75), Expect = 0.43
Identities = 22/58 (37%), Positives = 34/58 (58%), Gaps = 5/58 (8%)
Query: 385 VVIGA-GGAGKALAYGAKAKGARVVIANRTYDRARELAETV---GGHALSL-ADLENF 437
V+ GA G G+A A +GA+VV+A R+ + ELA V GG A+++ AD+ +
Sbjct: 4 VITGASSGIGRATALAFAERGAKVVLAARSAEALHELAREVRELGGEAIAVVADVADA 61
>gnl|CDD|235693 PRK06077, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 252
Score = 32.8 bits (75), Expect = 0.45
Identities = 23/64 (35%), Positives = 35/64 (54%), Gaps = 10/64 (15%)
Query: 379 LAGKLFVVIGAG-GAGKALAYGAKAKGARVVIANRTYDRARELAETV------GGHALS- 430
L K+ VV G+G G G+A+A +G+ VV+ + RA E+ ET+ GG +
Sbjct: 4 LKDKVVVVTGSGRGIGRAIAVRLAKEGSLVVVNAKK--RAEEMNETLKMVKENGGEGIGV 61
Query: 431 LADL 434
LAD+
Sbjct: 62 LADV 65
>gnl|CDD|237771 PRK14619, PRK14619, NAD(P)H-dependent glycerol-3-phosphate
dehydrogenase; Provisional.
Length = 308
Score = 33.0 bits (76), Expect = 0.45
Identities = 26/103 (25%), Positives = 43/103 (41%), Gaps = 17/103 (16%)
Query: 385 VVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAETVGG-----HALSLA------- 432
++GAG G LA A A G RV + +R + LA + A+S+
Sbjct: 8 AILGAGAWGSTLAGLASANGHRVRVWSRRSGLS--LAAVLADADVIVSAVSMKGVRPVAE 65
Query: 433 DLENFNPEDGMILANTTSIGMQPKVDETP--IPKHALGHYALV 473
++ N I+ T G+ P+ TP I + A ++ +V
Sbjct: 66 QVQALNLPPETIIVTATK-GLDPETTRTPSQIWQAAFPNHPVV 107
>gnl|CDD|184298 PRK13748, PRK13748, putative mercuric reductase; Provisional.
Length = 561
Score = 33.2 bits (76), Expect = 0.48
Identities = 45/148 (30%), Positives = 57/148 (38%), Gaps = 37/148 (25%)
Query: 363 DGLRGRLNVSGGVSSALAGKLFVVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAE 422
D +RG L + S VIG+GGA A A A +GARV + R
Sbjct: 80 DKMRGWLGGADKHSGNERPLHVAVIGSGGAAMAAALKAVEQGARVTLIERG--------- 130
Query: 423 TVGG--------------HALSLADLENFNPEDGMILANTTSI-------GMQPKVDETP 461
T+GG A +A L +P DG I A +I Q +VDE
Sbjct: 131 TIGGTCVNVGCVPSKIMIRAAHIAHLRRESPFDGGIAATVPTIDRSRLLAQQQARVDEL- 189
Query: 462 IPKHALGHYALVFDAVYTPKITRLLREA 489
+HA Y + D P IT L EA
Sbjct: 190 --RHA--KYEGILDG--NPAITVLHGEA 211
>gnl|CDD|178111 PLN02494, PLN02494, adenosylhomocysteinase.
Length = 477
Score = 32.9 bits (75), Expect = 0.52
Identities = 15/31 (48%), Positives = 20/31 (64%)
Query: 379 LAGKLFVVIGAGGAGKALAYGAKAKGARVVI 409
+AGK+ V+ G G GK A KA GARV++
Sbjct: 252 IAGKVAVICGYGDVGKGCAAAMKAAGARVIV 282
>gnl|CDD|226160 COG3634, AhpF, Alkyl hydroperoxide reductase, large subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 520
Score = 32.8 bits (75), Expect = 0.54
Identities = 19/52 (36%), Positives = 22/52 (42%), Gaps = 10/52 (19%)
Query: 386 VIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAETVGGHALSLADLENF 437
V+G G AG A A A KG R + AE GG L +ENF
Sbjct: 216 VVGGGPAGAAAAIYAARKGIRTGLV----------AERFGGQVLDTMGIENF 257
>gnl|CDD|216400 pfam01266, DAO, FAD dependent oxidoreductase. This family includes
various FAD dependent oxidoreductases:
Glycerol-3-phosphate dehydrogenase EC:1.1.99.5,
Sarcosine oxidase beta subunit EC:1.5.3.1, D-alanine
oxidase EC:1.4.99.1, D-aspartate oxidase EC:1.4.3.1.
Length = 234
Score = 32.3 bits (74), Expect = 0.55
Identities = 10/25 (40%), Positives = 13/25 (52%)
Query: 385 VVIGAGGAGKALAYGAKAKGARVVI 409
VVIG G G + AY +G V +
Sbjct: 3 VVIGGGIVGLSTAYELARRGLSVTL 27
>gnl|CDD|181585 PRK08936, PRK08936, glucose-1-dehydrogenase; Provisional.
Length = 261
Score = 32.4 bits (74), Expect = 0.56
Identities = 20/58 (34%), Positives = 34/58 (58%), Gaps = 5/58 (8%)
Query: 379 LAGKLFVVIGAG-GAGKALAYGAKAKGARVVIANRT-YDRARELAETV---GGHALSL 431
L GK+ V+ G G G+A+A + A+VVI R+ + A ++AE + GG A+++
Sbjct: 5 LEGKVVVITGGSTGLGRAMAVRFGKEKAKVVINYRSDEEEANDVAEEIKKAGGEAIAV 62
>gnl|CDD|240626 cd05301, GDH, D-glycerate dehydrogenase/hydroxypyruvate reductase
(GDH). D-glycerate dehydrogenase (GDH, also known as
hydroxypyruvate reductase, HPR) catalyzes the reversible
reaction of (R)-glycerate + NAD+ to hydroxypyruvate +
NADH + H+. In humans, HPR deficiency causes primary
hyperoxaluria type 2, characterized by over-excretion of
L-glycerate and oxalate in the urine, possibly due to an
imbalance in competition with L-lactate dehydrogenase,
another formate dehydrogenase (FDH)-like enzyme. GDH,
like FDH and other members of the D-specific hydroxyacid
dehydrogenase family that also includes L-alanine
dehydrogenase and S-adenosylhomocysteine hydrolase,
typically have a characteristic arrangement of 2 similar
subdomains of the alpha/beta Rossmann-fold NAD+ binding
form, despite often low sequence identity. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 309
Score = 32.4 bits (75), Expect = 0.56
Identities = 20/56 (35%), Positives = 31/56 (55%), Gaps = 2/56 (3%)
Query: 379 LAGKLFVVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAETVGGHALSLADL 434
L GK ++G G G+A+A AK G +++ NR+ R E E +G +SL +L
Sbjct: 142 LHGKTLGIVGMGRIGQAVARRAKGFGMKILYHNRS--RKPEAEEELGARYVSLDEL 195
>gnl|CDD|237806 PRK14727, PRK14727, putative mercuric reductase; Provisional.
Length = 479
Score = 33.0 bits (75), Expect = 0.56
Identities = 24/89 (26%), Positives = 32/89 (35%), Gaps = 29/89 (32%)
Query: 386 VIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAETVGG--------------HALSL 431
+IG+G A A A A GARV I A+ +GG A L
Sbjct: 21 IIGSGSAAFAAAIKAAEHGARVTIIEG--------ADVIGGCCVNVGCVPSKILIRAAQL 72
Query: 432 ADLENFNPEDGMILANTTSIGMQPKVDET 460
A + NP DG + + P +D
Sbjct: 73 AHQQRSNPFDG--VEA-----VAPSIDRG 94
>gnl|CDD|233689 TIGR02023, BchP-ChlP, geranylgeranyl reductase. This model
represents a group of geranylgeranyl reductases specific
for the biosyntheses of bacteriochlorophyll and
chlorophyll. It is unclear whether the processes of
isoprenoid ligation to the chlorin ring and reduction of
the geranylgeranyl chain to a phytyl chain are
necessarily ordered the same way in all species (see
introduction to ) [Biosynthesis of cofactors, prosthetic
groups, and carriers, Chlorophyll and
bacteriochlorphyll].
Length = 388
Score = 32.8 bits (75), Expect = 0.57
Identities = 30/120 (25%), Positives = 47/120 (39%), Gaps = 14/120 (11%)
Query: 385 VVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAETVGGHALSLADLENFNPEDGMI 444
VIG G +G A G ++ R + G A+ +E F+ D +I
Sbjct: 4 AVIGGGPSGATAAETLARAGIETILLERALSNIKPC-----GGAIPPCLIEEFDIPDSLI 58
Query: 445 LANTTSIGM-QPKVDET--PIPKHALGHYALVFDAVYTPKITRLLRE-AEESGATIVSGL 500
T + M P IP G+ +V V+ LRE A+++GA ++ GL
Sbjct: 59 DRRVTQMRMISPSRVPIKVTIPSED-GYVGMVRREVFDS----YLRERAQKAGAELIHGL 113
>gnl|CDD|224662 COG1748, LYS9, Saccharopine dehydrogenase and related proteins
[Amino acid transport and metabolism].
Length = 389
Score = 32.7 bits (75), Expect = 0.58
Identities = 33/121 (27%), Positives = 55/121 (45%), Gaps = 7/121 (5%)
Query: 384 FVVIGAGGAGKALAYGAKAKGA-RVVIANRTYDRARELAETVGGHALSLADLENFNPEDG 442
+VIGAGG G +A+ G V IA+R+ ++ +AE +GG + ++ + +
Sbjct: 4 ILVIGAGGVGSVVAHKLAQNGDGEVTIADRSKEKCARIAELIGG-KVEALQVDAADVDAL 62
Query: 443 MILANTTSIGMQ---PKVDETPIPKHALGHYALVFDAVYTPKITRLLR-EAEESGATIVS 498
+ L + + P VD T I K + D Y + L EA+++G T V
Sbjct: 63 VALIKDFDLVINAAPPFVDLT-ILKACIKTGVDYVDTSYYEEPPWKLDEEAKKAGITAVL 121
Query: 499 G 499
G
Sbjct: 122 G 122
>gnl|CDD|184025 PRK13394, PRK13394, 3-hydroxybutyrate dehydrogenase; Provisional.
Length = 262
Score = 32.2 bits (73), Expect = 0.61
Identities = 27/73 (36%), Positives = 37/73 (50%), Gaps = 5/73 (6%)
Query: 377 SALAGKLFVVIGA-GGAGKALAYGAKAKGARVVIANRTYDRARELAETV---GGHALSLA 432
S L GK VV GA G GK +A GA V IA+ D A +A+ + GG A+ +A
Sbjct: 3 SNLNGKTAVVTGAASGIGKEIALELARAGAAVAIADLNQDGANAVADEINKAGGKAIGVA 62
Query: 433 -DLENFNPEDGMI 444
D+ N + + I
Sbjct: 63 MDVTNEDAVNAGI 75
>gnl|CDD|227782 COG5495, COG5495, Uncharacterized conserved protein [Function
unknown].
Length = 289
Score = 32.6 bits (74), Expect = 0.61
Identities = 16/47 (34%), Positives = 23/47 (48%), Gaps = 1/47 (2%)
Query: 387 IGAGGAGKALAYGAKAKGARV-VIANRTYDRARELAETVGGHALSLA 432
+G G G+A A I++R+ DRA+ LAET L +A
Sbjct: 16 VGTGRLGRAALLRADHVVVACSAISSRSRDRAQNLAETYVAPPLDVA 62
>gnl|CDD|182130 PRK09880, PRK09880, L-idonate 5-dehydrogenase; Provisional.
Length = 343
Score = 32.4 bits (74), Expect = 0.63
Identities = 15/51 (29%), Positives = 20/51 (39%)
Query: 379 LAGKLFVVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAETVGGHAL 429
L GK V G G G + K GA ++ R+ LA +G L
Sbjct: 168 LQGKRVFVSGVGPIGCLIVAAVKTLGAAEIVCADVSPRSLSLAREMGADKL 218
>gnl|CDD|133449 cd05191, NAD_bind_amino_acid_DH, NAD(P) binding domain of amino
acid dehydrogenase-like proteins. Amino acid
dehydrogenase(DH)-like NAD(P)-binding domains are
members of the Rossmann fold superfamily and are found
in glutamate, leucine, and phenylalanine DHs (DHs),
methylene tetrahydrofolate DH,
methylene-tetrahydromethanopterin DH,
methylene-tetrahydropholate DH/cyclohydrolase, Shikimate
DH-like proteins, malate oxidoreductases, and glutamyl
tRNA reductase. Amino acid DHs catalyze the deamination
of amino acids to keto acids with NAD(P)+ as a cofactor.
The NAD(P)-binding Rossmann fold superfamily includes a
wide variety of protein families including NAD(P)-
binding domains of alcohol DHs, tyrosine-dependent
oxidoreductases, glyceraldehyde-3-phosphate DH,
lactate/malate DHs, formate/glycerate DHs, siroheme
synthases, 6-phosphogluconate DH, amino acid DHs,
repressor rex, NAD-binding potassium channel domain,
CoA-binding, and ornithine cyclodeaminase-like domains.
These domains have an alpha-beta-alpha configuration.
NAD binding involves numerous hydrogen and van der Waals
contacts.
Length = 86
Score = 30.0 bits (68), Expect = 0.65
Identities = 16/50 (32%), Positives = 24/50 (48%), Gaps = 1/50 (2%)
Query: 364 GLRGRLNVSGGVSSALAGKLFVVIGAGGAGKALA-YGAKAKGARVVIANR 412
+ + +L GK VV+GAG GK +A A G +VV+ +R
Sbjct: 6 AVALLKAAGKVTNKSLKGKTVVVLGAGEVGKGIAKLLADEGGKKVVLCDR 55
>gnl|CDD|180584 PRK06481, PRK06481, fumarate reductase flavoprotein subunit;
Validated.
Length = 506
Score = 32.5 bits (74), Expect = 0.65
Identities = 13/25 (52%), Positives = 16/25 (64%)
Query: 385 VVIGAGGAGKALAYGAKAKGARVVI 409
V++GAGGAG + A AK G VI
Sbjct: 65 VIVGAGGAGMSAAIEAKDAGMNPVI 89
>gnl|CDD|187606 cd05348, BphB-like_SDR_c,
cis-biphenyl-2,3-dihydrodiol-2,3-dehydrogenase
(BphB)-like, classical (c) SDRs.
cis-biphenyl-2,3-dihydrodiol-2,3-dehydrogenase (BphB) is
a classical SDR, it is of particular importance for its
role in the degradation of biphenyl/polychlorinated
biphenyls(PCBs); PCBs are a significant source of
environmental contamination. This subgroup also includes
Pseudomonas putida F1
cis-biphenyl-1,2-dihydrodiol-1,2-dehydrogenase (aka
cis-benzene glycol dehydrogenase, encoded by the bnzE
gene), which participates in benzene metabolism. In
addition it includes Pseudomonas sp. C18 putative
1,2-dihydroxy-1,2-dihydronaphthalene dehydrogenase (aka
dibenzothiophene dihydrodiol dehydrogenase, encoded by
the doxE gene) which participates in an upper
naphthalene catabolic pathway. 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 = 257
Score = 32.3 bits (74), Expect = 0.66
Identities = 16/52 (30%), Positives = 29/52 (55%), Gaps = 1/52 (1%)
Query: 379 LAGKLFVVIGAG-GAGKALAYGAKAKGARVVIANRTYDRARELAETVGGHAL 429
L G++ ++ G G G G+AL A+GA+V + +R+ ++ EL G +
Sbjct: 2 LKGEVALITGGGSGLGRALVERFVAEGAKVAVLDRSAEKVAELRADFGDAVV 53
>gnl|CDD|187602 cd05344, BKR_like_SDR_like, putative beta-ketoacyl acyl carrier
protein [ACP] reductase (BKR)-like, SDR. This subgroup
resembles the SDR family, but does not have a perfect
match to the NAD-binding motif or the catalytic tetrad
characteristic of the SDRs. It includes the SDRs, Q9HYA2
from Pseudomonas aeruginosa PAO1 and APE0912 from
Aeropyrum pernix K1. BKR catalyzes the NADPH-dependent
reduction of ACP in the first reductive step of de novo
fatty acid synthesis (FAS). FAS consists of four
elongation steps, which are repeated to extend the fatty
acid chain through the addition of two-carbo units from
malonyl acyl-carrier protein (ACP): condensation,
reduction, dehydration, and a final reduction. Type II
FAS, typical of plants and many bacteria, maintains
these activities on discrete polypeptides, while type I
FAS utilizes one or two multifunctional polypeptides.
BKR resembles enoyl reductase, which catalyzes the
second reduction step in FAS. 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 have a 3-glycine N-terminal
NAD(P)(H)-binding pattern (typically, TGxxxGxG in
classical SDRs and TGxxGxxG in extended SDRs), while
substrate binding is in the C-terminal region. A
critical catalytic Tyr residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering), is often found in a conserved YXXXK pattern.
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) or additional Ser,
contributing to the active site. Substrates for these
enzymes include sugars, steroids, alcohols, and aromatic
compounds. The standard reaction mechanism is a proton
relay involving the conserved Tyr and Lys, as well as
Asn (or Ser). Some SDR family members, including 17
beta-hydroxysteroid dehydrogenase contain an additional
helix-turn-helix motif that is not generally found among
SDRs.
Length = 253
Score = 32.2 bits (74), Expect = 0.66
Identities = 21/59 (35%), Positives = 27/59 (45%), Gaps = 5/59 (8%)
Query: 381 GKLFVVIGAG-GAGKALAYGAKAKGARVVIANRTYDR----ARELAETVGGHALSLADL 434
GK+ +V A G G A+A +GARV I R + A EL G +ADL
Sbjct: 1 GKVALVTAASSGIGLAIARALAREGARVAICARNRENLERAASELRAGGAGVLAVVADL 59
>gnl|CDD|222005 pfam13245, AAA_19, Part of AAA domain.
Length = 73
Score = 29.6 bits (67), Expect = 0.68
Identities = 22/64 (34%), Positives = 29/64 (45%), Gaps = 6/64 (9%)
Query: 375 VSSALAG-KLFVVIGAGGAGK-----ALAYGAKAKGARVVIANRTYDRARELAETVGGHA 428
V +A +G LFVV G G GK A+ A G V++ T AR L E +
Sbjct: 3 VEAAASGRSLFVVDGGPGTGKTATAAAIIARLLAAGRSVLVVAPTGRAARRLRERLAALD 62
Query: 429 LSLA 432
L+ A
Sbjct: 63 LADA 66
>gnl|CDD|184511 PRK14106, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 450
Score = 32.3 bits (74), Expect = 0.71
Identities = 15/34 (44%), Positives = 22/34 (64%)
Query: 379 LAGKLFVVIGAGGAGKALAYGAKAKGARVVIANR 412
L GK +V+GAG +G ALA K GA+V++ +
Sbjct: 3 LKGKKVLVVGAGVSGLALAKFLKKLGAKVILTDE 36
>gnl|CDD|235631 PRK05866, PRK05866, short chain dehydrogenase; Provisional.
Length = 293
Score = 32.0 bits (73), Expect = 0.72
Identities = 22/65 (33%), Positives = 33/65 (50%), Gaps = 8/65 (12%)
Query: 379 LAGKLFVVIGAG-GAGKALAYGAKAKGARVVIANRTYDRARELAETV---GGHALS---- 430
L GK ++ GA G G+A A +GA VV R D +A+ + GG A++
Sbjct: 38 LTGKRILLTGASSGIGEAAAEQFARRGATVVAVARREDLLDAVADRITRAGGDAMAVPCD 97
Query: 431 LADLE 435
L+DL+
Sbjct: 98 LSDLD 102
>gnl|CDD|180983 PRK07453, PRK07453, protochlorophyllide oxidoreductase; Validated.
Length = 322
Score = 32.3 bits (74), Expect = 0.75
Identities = 30/110 (27%), Positives = 47/110 (42%), Gaps = 16/110 (14%)
Query: 385 VVIGAGGAGKALAYGAKA---KGARVVIANRTYDRARELAETVGGHALSLADLENFNPED 441
V+I +G L Y AKA +G V++A R +A A+ +G S +
Sbjct: 9 VIITGASSGVGL-YAAKALAKRGWHVIMACRNLKKAEAAAQELGIPPDSYTIIH------ 61
Query: 442 GMILANTTSIGMQPKVDETPIPKHALGHYALVFD-AVYTPKITRLLREAE 490
+ L + S+ + VD+ L ALV + AVY P + LR +
Sbjct: 62 -IDLGDLDSV--RRFVDDFRALGKPLD--ALVCNAAVYMPLLKEPLRSPQ 106
>gnl|CDD|235737 PRK06197, PRK06197, short chain dehydrogenase; Provisional.
Length = 306
Score = 31.9 bits (73), Expect = 0.77
Identities = 27/69 (39%), Positives = 31/69 (44%), Gaps = 18/69 (26%)
Query: 381 GKLFVVIGA-GGAG----KALAYGAKAKGARVVIANRTYDR-----ARELAETVGGH--- 427
G++ VV GA G G ALA AKGA VV+A R D+ AR A T G
Sbjct: 16 GRVAVVTGANTGLGYETAAALA----AKGAHVVLAVRNLDKGKAAAARITAATPGADVTL 71
Query: 428 -ALSLADLE 435
L L L
Sbjct: 72 QELDLTSLA 80
>gnl|CDD|183775 PRK12826, PRK12826, 3-ketoacyl-(acyl-carrier-protein) reductase;
Reviewed.
Length = 251
Score = 31.8 bits (73), Expect = 0.77
Identities = 15/43 (34%), Positives = 20/43 (46%)
Query: 384 FVVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAETVGG 426
V A G G+A+A A GA V++ + D A AE V
Sbjct: 10 LVTGAARGIGRAIAVRLAADGAEVIVVDICGDDAAATAELVEA 52
>gnl|CDD|223677 COG0604, Qor, NADPH:quinone reductase and related Zn-dependent
oxidoreductases [Energy production and conversion /
General function prediction only].
Length = 326
Score = 31.9 bits (73), Expect = 0.78
Identities = 33/111 (29%), Positives = 39/111 (35%), Gaps = 29/111 (26%)
Query: 372 SGGVSSA---LAGKL--FVVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAE---- 422
+GGV SA LA L VV + K K GA VI R D ++ E
Sbjct: 152 AGGVGSAAIQLAKALGATVVAVVSSSEKLEL--LKELGADHVINYREEDFVEQVRELTGG 209
Query: 423 --------TVGG--HALSLADLENFNPEDGMILANTTSIGMQPKVDETPIP 463
TVGG A SLA L G + SIG P+
Sbjct: 210 KGVDVVLDTVGGDTFAASLAAL----APGGRL----VSIGALSGGPPVPLN 252
Score = 28.9 bits (65), Expect = 7.6
Identities = 17/55 (30%), Positives = 25/55 (45%), Gaps = 1/55 (1%)
Query: 380 AGKLFVVIGAGGA-GKALAYGAKAKGARVVIANRTYDRARELAETVGGHALSLAD 433
G+ +V GA G G A AKA GA VV + ++ L E H ++ +
Sbjct: 142 PGETVLVHGAAGGVGSAAIQLAKALGATVVAVVSSSEKLELLKELGADHVINYRE 196
>gnl|CDD|187616 cd05358, GlcDH_SDR_c, glucose 1 dehydrogenase (GlcDH), classical
(c) SDRs. GlcDH, is a tetrameric member of the SDR
family, it catalyzes the NAD(P)-dependent oxidation of
beta-D-glucose to D-glucono-delta-lactone. GlcDH has a
typical NAD-binding site glycine-rich pattern as well as
the canonical active site tetrad (YXXXK motif plus
upstream Ser and Asn). SDRs are a functionally diverse
family of oxidoreductases that have a single domain with
a structurally conserved Rossmann fold (alpha/beta
folding pattern with a central beta-sheet), an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRS are approximately
350 residues. Sequence identity between different SDR
enzymes are typically in the 15-30% range, but the
enzymes share the Rossmann fold NAD-binding motif and
characteristic NAD-binding and catalytic sequence
patterns. These enzymes have a 3-glycine N-terminal
NAD(P)(H)-binding pattern (typically, TGxxxGxG in
classical SDRs and TGxxGxxG in extended SDRs), while
substrate binding is in the C-terminal region. A
critical catalytic Tyr residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering), is often found in a conserved YXXXK pattern.
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) or additional Ser,
contributing to the active site. Substrates for these
enzymes include sugars, steroids, alcohols, and aromatic
compounds. The standard reaction mechanism is a proton
relay involving the conserved Tyr and Lys, as well as
Asn (or Ser). Some SDR family members, including 17
beta-hydroxysteroid dehydrogenase contain an additional
helix-turn-helix motif that is not generally found among
SDRs.
Length = 253
Score = 32.0 bits (73), Expect = 0.79
Identities = 24/57 (42%), Positives = 32/57 (56%), Gaps = 5/57 (8%)
Query: 379 LAGKLFVVIGAG-GAGKALAYGAKAKGARVVIANRTY-DRARELAE---TVGGHALS 430
L GK+ +V GA G GKA+A GA VV+ R+ D A E+ E VGG A++
Sbjct: 1 LKGKVALVTGASSGIGKAIAIRLATAGANVVVNYRSKEDAAEEVVEEIKAVGGKAIA 57
>gnl|CDD|176256 cd08296, CAD_like, Cinnamyl alcohol dehydrogenases (CAD). Cinnamyl
alcohol dehydrogenases (CAD), members of the medium
chain dehydrogenase/reductase family, reduce
cinnamaldehydes to cinnamyl alcohols in the last step of
monolignal metabolism in plant cells walls. CAD binds 2
zinc ions and is NADPH- dependent. CAD family members
are also found in non-plant species, e.g. in yeast where
they have an aldehyde reductase activity. The medium
chain dehydrogenases/reductase (MDR)/zinc-dependent
alcohol dehydrogenase-like family, which contains the
zinc-dependent alcohol dehydrogenase (ADH-Zn) and
related proteins, is a diverse group of proteins related
to the first identified member, class I mammalian ADH.
MDRs display a broad range of activities and are
distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADHs), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 333
Score = 32.2 bits (74), Expect = 0.81
Identities = 22/53 (41%), Positives = 27/53 (50%), Gaps = 3/53 (5%)
Query: 376 SSALAGKLFVVIGAGGAGK-ALAYGAKAKGARVVIANRTYDRARELAETVGGH 427
S A G L V G GG G A+ Y A G R V +R D+A +LA +G H
Sbjct: 159 SGAKPGDLVAVQGIGGLGHLAVQY-AAKMGFRTVAISRGSDKA-DLARKLGAH 209
>gnl|CDD|224577 COG1663, LpxK, Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope
biogenesis, outer membrane].
Length = 336
Score = 31.9 bits (73), Expect = 0.82
Identities = 20/66 (30%), Positives = 26/66 (39%), Gaps = 18/66 (27%)
Query: 385 VVIG---AGGAGK-----ALAYGAKAKGARVVIANRTY----------DRARELAETVGG 426
+ +G GG GK LA +A+G RV + +R Y D A VG
Sbjct: 50 ICVGNLTVGGTGKTPVVIWLAEALQARGVRVGVVSRGYGGKLKVVPLVDNIHTTAAEVGD 109
Query: 427 HALSLA 432
L LA
Sbjct: 110 EPLLLA 115
>gnl|CDD|236025 PRK07476, eutB, threonine dehydratase; Provisional.
Length = 322
Score = 31.9 bits (73), Expect = 0.84
Identities = 17/45 (37%), Positives = 22/45 (48%)
Query: 365 LRGRLNVSGGVSSALAGKLFVVIGAGGAGKALAYGAKAKGARVVI 409
LRG N +S+ + V G G+ALAY A+A G R I
Sbjct: 51 LRGATNALLSLSAQERARGVVTASTGNHGRALAYAARALGIRATI 95
>gnl|CDD|237790 PRK14694, PRK14694, putative mercuric reductase; Provisional.
Length = 468
Score = 32.2 bits (73), Expect = 0.84
Identities = 32/133 (24%), Positives = 51/133 (38%), Gaps = 35/133 (26%)
Query: 386 VIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAETVGG--------------HALSL 431
VIG+GG+ A A A +GARV + R T+GG A +
Sbjct: 11 VIGSGGSAMAAALKATERGARVTLIERG---------TIGGTCVNIGCVPSKIMIRAAHI 61
Query: 432 ADLENFNPEDGMILANTTSIGMQPKVDETPIPKHALGHYALVFDAVYTPKITRLLREAEE 491
A L +P D + A P VD + + + ++ Y +LR E
Sbjct: 62 AHLRRESPFDDGLSAQA------PVVDRSALLAQQQARVEELRESKY----QSILR--EN 109
Query: 492 SGATIVSGLEMFI 504
+ T+++G F+
Sbjct: 110 AAITVLNGEARFV 122
>gnl|CDD|235703 PRK06125, PRK06125, short chain dehydrogenase; Provisional.
Length = 259
Score = 31.9 bits (73), Expect = 0.86
Identities = 21/66 (31%), Positives = 28/66 (42%), Gaps = 9/66 (13%)
Query: 379 LAGKLFVVIGAG-GAGKALAYGAKAKGARVVIANRTYDRARELAETVGG--------HAL 429
LAGK ++ GA G G A A A+G + + R D LA + HAL
Sbjct: 5 LAGKRVLITGASKGIGAAAAEAFAAEGCHLHLVARDADALEALAADLRAAHGVDVAVHAL 64
Query: 430 SLADLE 435
L+ E
Sbjct: 65 DLSSPE 70
>gnl|CDD|235774 PRK06292, PRK06292, dihydrolipoamide dehydrogenase; Validated.
Length = 460
Score = 32.1 bits (74), Expect = 0.93
Identities = 11/29 (37%), Positives = 15/29 (51%)
Query: 384 FVVIGAGGAGKALAYGAKAKGARVVIANR 412
+VIGAG AG A A G +V + +
Sbjct: 6 VIVIGAGPAGYVAARRAAKLGKKVALIEK 34
>gnl|CDD|223189 COG0111, SerA, Phosphoglycerate dehydrogenase and related
dehydrogenases [Amino acid transport and metabolism].
Length = 324
Score = 31.9 bits (73), Expect = 0.95
Identities = 23/69 (33%), Positives = 33/69 (47%), Gaps = 1/69 (1%)
Query: 366 RGRLNVSGGVSSALAGKLFVVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAETVG 425
RG + + LAGK +IG G G+A+A KA G +V+ + R R + V
Sbjct: 127 RGEWDRKAFRGTELAGKTVGIIGLGRIGRAVAKRLKAFGMKVIGYDPYSPRERAGVDGVV 186
Query: 426 GHALSLADL 434
G SL +L
Sbjct: 187 GVD-SLDEL 194
>gnl|CDD|223727 COG0654, UbiH, 2-polyprenyl-6-methoxyphenol hydroxylase and related
FAD-dependent oxidoreductases [Coenzyme metabolism /
Energy production and conversion].
Length = 387
Score = 32.0 bits (73), Expect = 0.95
Identities = 20/47 (42%), Positives = 24/47 (51%), Gaps = 5/47 (10%)
Query: 385 VVIGAGGAGKALAYGAKAKGARVVIANRTYDRA-RELAETVGGHALS 430
++GAG AG ALA G V + +RA REL E G ALS
Sbjct: 6 AIVGAGPAGLALALALARAGLDVTL----LERAPRELLERGRGIALS 48
>gnl|CDD|234119 TIGR03140, AhpF, alkyl hydroperoxide reductase subunit F. This
enzyme is the partner of the peroxiredoxin (alkyl
hydroperoxide reductase) AhpC which contains the
peroxide-reactive cysteine. AhpF contains the reductant
(NAD(P)H) binding domain (pfam00070) and presumably acts
to resolve the disulfide which forms after oxidation of
the active site cysteine in AphC. This proteins contains
two paired conserved cysteine motifs, CxxCP and CxHCDGP
[Cellular processes, Detoxification, Cellular processes,
Adaptations to atypical conditions].
Length = 515
Score = 31.9 bits (73), Expect = 0.97
Identities = 17/52 (32%), Positives = 22/52 (42%), Gaps = 10/52 (19%)
Query: 386 VIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAETVGGHALSLADLENF 437
V+G G AG A A A KG R + +AE +GG +EN
Sbjct: 217 VVGGGPAGAAAAIYAARKGLRTAM----------VAERIGGQVKDTVGIENL 258
>gnl|CDD|187628 cd05370, SDR_c2, classical (c) SDR, subgroup 2. Short-chain
dehydrogenases/reductases (SDRs, aka Tyrosine-dependent
oxidoreductases) 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 = 228
Score = 31.5 bits (72), Expect = 0.99
Identities = 16/51 (31%), Positives = 20/51 (39%), Gaps = 4/51 (7%)
Query: 378 ALAGKLFVVIG-AGGAGKALAYGAKAKGARVVIANRTYDRARELAETVGGH 427
L G ++ G G G ALA G V+I R +R LAE
Sbjct: 2 KLTGNTVLITGGTSGIGLALARKFLEAGNTVIITGRREER---LAEAKKEL 49
>gnl|CDD|237770 PRK14618, PRK14618, NAD(P)H-dependent glycerol-3-phosphate
dehydrogenase; Provisional.
Length = 328
Score = 31.8 bits (72), Expect = 1.0
Identities = 16/38 (42%), Positives = 20/38 (52%)
Query: 386 VIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAET 423
V+GAG G ALA A +KG V + R + A LA
Sbjct: 9 VLGAGAWGTALAVLAASKGVPVRLWARRPEFAAALAAE 46
>gnl|CDD|135631 PRK05867, PRK05867, short chain dehydrogenase; Provisional.
Length = 253
Score = 31.5 bits (71), Expect = 1.1
Identities = 25/79 (31%), Positives = 36/79 (45%), Gaps = 5/79 (6%)
Query: 379 LAGKLFVVIGAG-GAGKALAYGAKAKGARVVIANRTYDRARELAE---TVGGHALSL-AD 433
L GK ++ GA G GK +A GA+V IA R D +LA+ T GG + + D
Sbjct: 7 LHGKRALITGASTGIGKRVALAYVEAGAQVAIAARHLDALEKLADEIGTSGGKVVPVCCD 66
Query: 434 LENFNPEDGMILANTTSIG 452
+ M+ T +G
Sbjct: 67 VSQHQQVTSMLDQVTAELG 85
>gnl|CDD|187609 cd05351, XR_like_SDR_c, xylulose reductase-like, classical (c)
SDRs. Members of this subgroup include proteins
identified as L-xylulose reductase (XR) and carbonyl
reductase; they are members of the SDR family. XR,
catalyzes the NADP-dependent reduction of L-xyulose and
other sugars. Tetrameric mouse carbonyl reductase is
involved in the metabolism of biogenic and xenobiotic
carbonyl compounds. This subgroup also includes
tetrameric chicken liver D-erythrulose reductase, which
catalyzes the reduction of D-erythrulose to D-threitol.
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 have a 3-glycine N-terminal NAD(P)(H)-binding
pattern (typically, TGxxxGxG in classical SDRs and
TGxxGxxG in extended SDRs), while substrate binding is
in the C-terminal region. A critical catalytic Tyr
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) numbering), is often found in a
conserved YXXXK pattern. 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) or
additional Ser, contributing to the active site.
Substrates for these enzymes include sugars, steroids,
alcohols, and aromatic compounds. The standard reaction
mechanism is a proton relay involving the conserved Tyr
and Lys, as well as Asn (or Ser).
Length = 244
Score = 31.3 bits (71), Expect = 1.1
Identities = 18/44 (40%), Positives = 21/44 (47%), Gaps = 1/44 (2%)
Query: 379 LAGKLFVVIGAG-GAGKALAYGAKAKGARVVIANRTYDRARELA 421
AGK +V GAG G G+A GARVV +RT L
Sbjct: 5 FAGKRALVTGAGKGIGRATVKALAKAGARVVAVSRTQADLDSLV 48
>gnl|CDD|176187 cd05284, arabinose_DH_like, D-arabinose dehydrogenase. This group
contains arabinose dehydrogenase (AraDH) and related
alcohol dehydrogenases. AraDH is a member of the medium
chain dehydrogenase/reductase family and catalyzes the
NAD(P)-dependent oxidation of D-arabinose and other
pentoses, the initial step in the metabolism of
d-arabinose into 2-oxoglutarate. Like the alcohol
dehydrogenases, AraDH binds a zinc in the catalytic
cleft as well as a distal structural zinc. AraDH forms
homotetramers as a dimer of dimers. AraDH replaces a
conserved catalytic His with replace with Arg, compared
to the canonical ADH site. NAD(P)(H)-dependent
oxidoreductases are the major enzymes in the
interconversion of alcohols and aldehydes, or ketones.
Alcohol dehydrogenase in the liver converts ethanol and
NAD+ to acetaldehyde and NADH, while in yeast and some
other microorganisms ADH catalyzes the conversion
acetaldehyde to ethanol in alcoholic fermentation. ADH
is a member of the medium chain alcohol dehydrogenase
family (MDR), which has a NAD(P)(H)-binding domain in a
Rossmann fold of a beta-alpha form. The NAD(H)-binding
region is comprised of 2 structurally similar halves,
each of which contacts a mononucleotide. A GxGxxG motif
after the first mononucleotide contact half allows the
close contact of the coenzyme with the ADH backbone.
The N-terminal catalytic domain has a distant homology
to GroES. These proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and have 2 tightly bound zinc atoms per
subunit, a catalytic zinc at the active site and a
structural zinc in a lobe of the catalytic domain.
NAD(H) binding occurs in the cleft between the catalytic
and coenzyme-binding domains at the active site, and
coenzyme binding induces a conformational closing of
this cleft. Coenzyme binding typically precedes and
contributes to substrate binding. In human ADH
catalysis, the zinc ion helps coordinate the alcohol,
followed by deprotonation of a histidine, the ribose of
NAD, a serine, then the alcohol, which allows the
transfer of a hydride to NAD+, creating NADH and a
zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 340
Score = 31.8 bits (73), Expect = 1.1
Identities = 19/55 (34%), Positives = 25/55 (45%), Gaps = 2/55 (3%)
Query: 380 AGKLFVVIGAGGAGK-ALAYGAKAKGARVVIANRTYDRARELAETVGGHALSLAD 433
G VVIG GG G A+ +A VIA + A +LAE +G + A
Sbjct: 167 PGSTVVVIGVGGLGHIAVQI-LRALTPATVIAVDRSEEALKLAERLGADHVLNAS 220
>gnl|CDD|234978 PRK01747, mnmC, bifunctional tRNA
(mnm(5)s(2)U34)-methyltransferase/FAD-dependent
cmnm(5)s(2)U34 oxidoreductase; Reviewed.
Length = 662
Score = 31.7 bits (73), Expect = 1.1
Identities = 12/38 (31%), Positives = 18/38 (47%), Gaps = 4/38 (10%)
Query: 385 VVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAE 422
+IG G AG ALA +G +V + Y+ A+
Sbjct: 264 AIIGGGIAGAALALALARRGWQVTL----YEADEAPAQ 297
>gnl|CDD|187635 cd08930, SDR_c8, classical (c) SDR, subgroup 8. This subgroup has
a fairly well conserved active site tetrad and domain
size of the classical SDRs, but has an atypical
NAD-binding motif ([ST]G[GA]XGXXG). 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 = 250
Score = 31.5 bits (72), Expect = 1.1
Identities = 13/48 (27%), Positives = 23/48 (47%), Gaps = 1/48 (2%)
Query: 381 GKLFVVIGAGGA-GKALAYGAKAKGARVVIANRTYDRARELAETVGGH 427
K+ ++ GA G GKA + GAR+++A+ +L E +
Sbjct: 2 DKIILITGAAGLIGKAFCKALLSAGARLILADINAPALEQLKEELTNL 49
>gnl|CDD|176201 cd08239, THR_DH_like, L-threonine dehydrogenase (TDH)-like.
MDR/AHD-like proteins, including a protein annotated as
a threonine dehydrogenase. L-threonine dehydrogenase
(TDH) catalyzes the zinc-dependent formation of
2-amino-3-ketobutyrate from L-threonine via
NAD(H)-dependent oxidation. The zinc-dependent alcohol
dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent
interconversion of alcohols to aldehydes or ketones.
Zinc-dependent ADHs are medium chain
dehydrogenase/reductase type proteins (MDRs) and have a
NAD(P)(H)-binding domain in a Rossmann fold of an
beta-alpha form. The N-terminal region typically has an
all-beta catalytic domain. In addition to alcohol
dehydrogenases, this group includes quinone reductase,
sorbitol dehydrogenase, formaldehyde dehydrogenase,
butanediol DH, ketose reductase, cinnamyl reductase, and
numerous others. These proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 339
Score = 31.5 bits (72), Expect = 1.2
Identities = 19/58 (32%), Positives = 25/58 (43%), Gaps = 7/58 (12%)
Query: 368 RLNVSGGVSSALAGKLFVVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAETVG 425
R+ VSG + V+GAG G A+A GA VI ELA+ +G
Sbjct: 158 RVGVSGRDTVL-------VVGAGPVGLGALMLARALGAEDVIGVDPSPERLELAKALG 208
>gnl|CDD|180669 PRK06720, PRK06720, hypothetical protein; Provisional.
Length = 169
Score = 30.7 bits (69), Expect = 1.2
Identities = 19/63 (30%), Positives = 32/63 (50%), Gaps = 4/63 (6%)
Query: 371 VSGGVSSALAGKLFVVIGAG-GAGKALAYGAKAKGARVVIANRTYDRARELAETV---GG 426
+ G + LAGK+ +V G G G G+ A +GA+V++ + + + E + GG
Sbjct: 6 IEGVMKMKLAGKVAIVTGGGIGIGRNTALLLAKQGAKVIVTDIDQESGQATVEEITNLGG 65
Query: 427 HAL 429
AL
Sbjct: 66 EAL 68
>gnl|CDD|214963 smart00996, AdoHcyase, S-adenosyl-L-homocysteine hydrolase.
Length = 426
Score = 31.7 bits (73), Expect = 1.2
Identities = 14/31 (45%), Positives = 20/31 (64%)
Query: 379 LAGKLFVVIGAGGAGKALAYGAKAKGARVVI 409
+AGK+ VV G G GK A + +GARV++
Sbjct: 205 IAGKVAVVCGYGDVGKGCAQSLRGQGARVIV 235
>gnl|CDD|237942 PRK15317, PRK15317, alkyl hydroperoxide reductase subunit F;
Provisional.
Length = 517
Score = 31.7 bits (73), Expect = 1.2
Identities = 21/54 (38%), Positives = 25/54 (46%), Gaps = 12/54 (22%)
Query: 385 VVIGAGGAGKALA-YGAKAKGARVVIANRTYDRARELAETVGGHALSLADLENF 437
+V+G G AG A A Y A+ KG R I AE GG L +ENF
Sbjct: 215 LVVGGGPAGAAAAIYAAR-KGIRTGIV----------AERFGGQVLDTMGIENF 257
>gnl|CDD|133446 cd01078, NAD_bind_H4MPT_DH, NADP binding domain of methylene
tetrahydromethanopterin dehydrogenase. Methylene
Tetrahydromethanopterin Dehydrogenase (H4MPT DH) NADP
binding domain. NADP-dependent H4MPT DH catalyzes the
dehydrogenation of methylene- H4MPT and
methylene-tetrahydrofolate (H4F) with NADP+ as cofactor.
H4F and H4MPT are both cofactors that carry the
one-carbon units between the formyl and methyl oxidation
level. H4F and H4MPT are structurally analogous to each
other with respect to the pterin moiety, but each has
distinct side chain. H4MPT is present only in anaerobic
methanogenic archaea and aerobic methylotrophic
proteobacteria. H4MPT seems to have evolved
independently from H4F and functions as a distinct
carrier in C1 metabolism. Amino acid DH-like
NAD(P)-binding domains are members of the Rossmann fold
superfamily and include glutamate, leucine, and
phenylalanine DHs, methylene tetrahydrofolate DH,
methylene-tetrahydromethanopterin DH,
methylene-tetrahydropholate DH/cyclohydrolase, Shikimate
DH-like proteins, malate oxidoreductases, and glutamyl
tRNA reductase. Amino acid DHs catalyze the deamination
of amino acids to keto acids with NAD(P)+ as a cofactor.
The NAD(P)-binding Rossmann fold superfamily includes a
wide variety of protein families including NAD(P)-
binding domains of alcohol DHs, tyrosine-dependent
oxidoreductases, glyceraldehyde-3-phosphate DH,
lactate/malate DHs, formate/glycerate DHs, siroheme
synthases, 6-phosphogluconate DH, amino acid DHs,
repressor rex, NAD-binding potassium channel domain,
CoA-binding, and ornithine cyclodeaminase-like domains.
These domains have an alpha-beta-alpha configuration.
NAD binding involves numerous hydrogen and van der Waals
contacts.
Length = 194
Score = 31.2 bits (71), Expect = 1.2
Identities = 24/78 (30%), Positives = 36/78 (46%), Gaps = 8/78 (10%)
Query: 349 GYNTDYVGAISAIEDGLRGRLNVSGGVSSALAGKLFVVIGAGGA-GKALAYGAKAKGARV 407
G NT A++A L L GK VV+G G G+ A +GARV
Sbjct: 3 GSNTTAAAAVAAAGKALELM-------GKDLKGKTAVVLGGTGPVGQRAAVLLAREGARV 55
Query: 408 VIANRTYDRARELAETVG 425
V+ R +RA++ A+++
Sbjct: 56 VLVGRDLERAQKAADSLR 73
>gnl|CDD|179631 PRK03692, PRK03692, putative UDP-N-acetyl-D-mannosaminuronic acid
transferase; Provisional.
Length = 243
Score = 31.1 bits (71), Expect = 1.2
Identities = 16/34 (47%), Positives = 18/34 (52%), Gaps = 2/34 (5%)
Query: 140 IVSSHNYQYTPSVEDLSNLVARIQASGADIVKFA 173
IV S + +TP E L RI ASGA IV A
Sbjct: 133 IVGSQDGYFTP--EQRQALFERIHASGAKIVTVA 164
>gnl|CDD|235713 PRK06139, PRK06139, short chain dehydrogenase; Provisional.
Length = 330
Score = 31.2 bits (71), Expect = 1.3
Identities = 19/60 (31%), Positives = 30/60 (50%), Gaps = 4/60 (6%)
Query: 375 VSSALAGKLFVVIGAG-GAGKALAYGAKAKGARVVIANRTYDRARELAET---VGGHALS 430
+ L G + V+ GA G G+A A +GAR+V+A R + + +AE +G L
Sbjct: 1 MMGPLHGAVVVITGASSGIGQATAEAFARRGARLVLAARDEEALQAVAEECRALGAEVLV 60
>gnl|CDD|183914 PRK13243, PRK13243, glyoxylate reductase; Reviewed.
Length = 333
Score = 31.3 bits (71), Expect = 1.3
Identities = 19/56 (33%), Positives = 29/56 (51%), Gaps = 2/56 (3%)
Query: 379 LAGKLFVVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAETVGGHALSLADL 434
+ GK +IG G G+A+A AK G R++ +RT R E + +G L +L
Sbjct: 148 VYGKTIGIIGFGRIGQAVARRAKGFGMRILYYSRT--RKPEAEKELGAEYRPLEEL 201
>gnl|CDD|233382 TIGR01372, soxA, sarcosine oxidase, alpha subunit family,
heterotetrameric form. This model describes the alpha
subunit of a family of known and putative
heterotetrameric sarcosine oxidases. Five operons of
such oxidases are found in Mesorhizobium loti and three
in Agrobacterium tumefaciens, a high enough copy number
to suggest that not all members are share the same
function. The model is designated as subfamily rather
than equivalog for this reason.Sarcosine oxidase
catalyzes the oxidative demethylation of sarcosine to
glycine. The reaction converts tetrahydrofolate to
5,10-methylene-tetrahydrofolate. The enzyme is known in
monomeric and heterotetrameric (alpha,beta,gamma,delta)
forms [Energy metabolism, Amino acids and amines].
Length = 985
Score = 31.6 bits (72), Expect = 1.4
Identities = 24/76 (31%), Positives = 36/76 (47%), Gaps = 11/76 (14%)
Query: 386 VIGAGGAGKALAYGAKAKGARVVIANRTYD---RARELAETVGGH------ALSLADLEN 436
V+GAG AG A A A GARV++ + + AET+ G A ++A+L
Sbjct: 168 VVGAGPAGLAAALAAARAGARVILVDEQPEAGGSLLSEAETIDGKPAADWAAATVAELTA 227
Query: 437 FNPEDGMILANTTSIG 452
+ +L TT+ G
Sbjct: 228 M--PEVTLLPRTTAFG 241
>gnl|CDD|240645 cd12168, Mand_dh_like, D-Mandelate Dehydrogenase-like
dehydrogenases. D-Mandelate dehydrogenase (D-ManDH),
identified as an enzyme that interconverts
benzoylformate and D-mandelate, is a D-2-hydroxyacid
dehydrogenase family member that catalyzes the
conversion of c3-branched 2-ketoacids. D-ManDH exhibits
broad substrate specificities for 2-ketoacids with large
hydrophobic side chains, particularly those with
C3-branched side chains. 2-hydroxyacid dehydrogenases
catalyze the conversion of a wide variety of D-2-hydroxy
acids to their corresponding keto acids. The general
mechanism is (R)-lactate + acceptor to pyruvate +
reduced acceptor. Glycerate dehydrogenase catalyzes the
reaction (R)-glycerate + NAD+ to hydroxypyruvate + NADH
+ H+. Formate/glycerate and related dehydrogenases of
the D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain.
Length = 321
Score = 31.4 bits (72), Expect = 1.4
Identities = 19/54 (35%), Positives = 31/54 (57%), Gaps = 1/54 (1%)
Query: 381 GKLFVVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAETVGGHALSLADL 434
GK ++G GG GKA+A A A G +++ NR+ EL + + + +SL +L
Sbjct: 154 GKTLGILGLGGIGKAIARKAAAFGMKIIYHNRSRL-PEELEKALATYYVSLDEL 206
>gnl|CDD|234024 TIGR02817, adh_fam_1, zinc-binding alcohol dehydrogenase family
protein. Members of this model form a distinct subset
of the larger family of oxidoreductases that includes
zinc-binding alcohol dehydrogenases and NADPH:quinone
reductases (pfam00107). While some current members of
this family carry designations as putative alginate
lyase, it seems no sequence with a direct
characterization as such is detected by this model
[Energy metabolism, Fermentation].
Length = 336
Score = 31.2 bits (71), Expect = 1.4
Identities = 21/72 (29%), Positives = 33/72 (45%), Gaps = 2/72 (2%)
Query: 357 AISAIEDGLRGRLNVSGGVSSALAGKLFVVIGAGGAGKALAYGAKAKGARVVIANRTYDR 416
+I+A E L RL ++ V+ L ++ GAGG G L A+ VIA +
Sbjct: 128 SITAWEL-LFDRLGINDPVAGD-KRALLIIGGAGGVGSILIQLARQLTGLTVIATASRPE 185
Query: 417 ARELAETVGGHA 428
++E +G H
Sbjct: 186 SQEWVLELGAHH 197
>gnl|CDD|187587 cd05326, secoisolariciresinol-DH_like_SDR_c, secoisolariciresinol
dehydrogenase (secoisolariciresinol-DH)-like, classical
(c) SDRs. Podophyllum secoisolariciresinol-DH is a homo
tetrameric, classical SDR that catalyzes the
NAD-dependent conversion of (-)-secoisolariciresinol to
(-)-matairesinol via a (-)-lactol intermediate.
(-)-Matairesinol is an intermediate to various
8'-lignans, including the cancer-preventive mammalian
lignan, and those involved in vascular plant defense.
This subgroup also includes rice momilactone A synthase
which catalyzes the conversion of
3beta-hydroxy-9betaH-pimara-7,15-dien-19,6beta-olide
into momilactone A, Arabidopsis ABA2 which during
abscisic acid (ABA) biosynthesis, catalyzes the
conversion of xanthoxin to abscisic aldehyde and, maize
Tasselseed2 which participate in the maize sex
determination pathway. 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, 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 = 249
Score = 30.9 bits (70), Expect = 1.5
Identities = 20/55 (36%), Positives = 29/55 (52%), Gaps = 1/55 (1%)
Query: 379 LAGKLFVVIG-AGGAGKALAYGAKAKGARVVIANRTYDRARELAETVGGHALSLA 432
L GK+ ++ G A G G+A A GARVVIA+ D + +A +G +S
Sbjct: 2 LDGKVAIITGGASGIGEATARLFAKHGARVVIADIDDDAGQAVAAELGDPDISFV 56
>gnl|CDD|223137 COG0059, IlvC, Ketol-acid reductoisomerase [Amino acid transport
and metabolism / Coenzyme metabolism].
Length = 338
Score = 31.4 bits (72), Expect = 1.5
Identities = 14/46 (30%), Positives = 20/46 (43%)
Query: 377 SALAGKLFVVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAE 422
L GK +IG G G A A + G V+I R + + A+
Sbjct: 14 DLLKGKKVAIIGYGSQGHAQALNLRDSGLNVIIGLRKGSSSWKKAK 59
>gnl|CDD|187599 cd05340, Ycik_SDR_c, Escherichia coli K-12 YCIK-like, classical (c)
SDRs. Escherichia coli K-12 YCIK and related proteins
have a canonical classical SDR nucleotide-binding motif
and active site tetrad. They are predicted oxoacyl-(acyl
carrier protein/ACP) reductases. 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 have a 3-glycine N-terminal
NAD(P)(H)-binding pattern (typically, TGxxxGxG in
classical SDRs and TGxxGxxG in extended SDRs), while
substrate binding is in the C-terminal region. A
critical catalytic Tyr residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering), is often found in a conserved YXXXK pattern.
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) or additional Ser,
contributing to the active site. Substrates for these
enzymes include sugars, steroids, alcohols, and aromatic
compounds. The standard reaction mechanism is a proton
relay involving the conserved Tyr and Lys, as well as
Asn (or Ser). Some SDR family members, including 17
beta-hydroxysteroid dehydrogenase contain an additional
helix-turn-helix motif that is not generally found among
SDRs.
Length = 236
Score = 31.0 bits (70), Expect = 1.5
Identities = 13/47 (27%), Positives = 25/47 (53%), Gaps = 1/47 (2%)
Query: 379 LAGKLFVVIGAG-GAGKALAYGAKAKGARVVIANRTYDRARELAETV 424
L ++ +V GA G G+ A GA V++ R ++ R++A+ +
Sbjct: 2 LNDRIILVTGASDGIGREAALTYARYGATVILLGRNEEKLRQVADHI 48
>gnl|CDD|223737 COG0665, DadA, Glycine/D-amino acid oxidases (deaminating) [Amino
acid transport and metabolism].
Length = 387
Score = 31.4 bits (71), Expect = 1.6
Identities = 12/44 (27%), Positives = 18/44 (40%), Gaps = 4/44 (9%)
Query: 385 VVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAETVGGHA 428
V+IG G G + AY +GA V + + G +A
Sbjct: 8 VIIGGGIVGLSAAYYLAERGADVTV----LEAGEAGGGAAGRNA 47
>gnl|CDD|216395 pfam01261, AP_endonuc_2, Xylose isomerase-like TIM barrel. This
TIM alpha/beta barrel structure is found in xylose
isomerase and in endonuclease IV (EC:3.1.21.2). This
domain is also found in the N termini of bacterial
myo-inositol catabolism proteins. These are involved in
the myo-inositol catabolism pathway, and is required for
growth on myo-inositol in Rhizobium leguminosarum bv.
viciae.
Length = 202
Score = 30.8 bits (70), Expect = 1.6
Identities = 16/79 (20%), Positives = 29/79 (36%), Gaps = 7/79 (8%)
Query: 44 KANASGADLVEIRLDGLKNFNPRENIKTLIKES-----PVPTLFTYRPIWEGGQYDGDEN 98
A G D VE+ D + + +E I+ L + +L + E +++
Sbjct: 3 AAAELGFDGVELFFDYPRPASDKEEIEELKALLKEYGLEISSLNPSLGLLEPDEHERAAA 62
Query: 99 ERV--DVLRLAMELGADYI 115
+ LA LGA +
Sbjct: 63 LEALKRAIELAAALGAKVV 81
>gnl|CDD|225740 COG3199, COG3199, Predicted inorganic polyphosphate/ATP-NAD kinase
[General function prediction only].
Length = 355
Score = 31.2 bits (71), Expect = 1.7
Identities = 16/55 (29%), Positives = 25/55 (45%), Gaps = 10/55 (18%)
Query: 151 SVEDLSNLVARIQASGADIVKFA---TTALDITDVARVFQITVHSQVPIIGLVMG 202
+ ED N V R+ G D++ FA TA D+ + VP++G+ G
Sbjct: 85 TAEDTINAVRRMVERGVDLIVFAGGDGTARDVAEAVGA-------DVPVLGIPAG 132
>gnl|CDD|226674 COG4221, COG4221, Short-chain alcohol dehydrogenase of unknown
specificity [General function prediction only].
Length = 246
Score = 30.7 bits (70), Expect = 1.7
Identities = 24/56 (42%), Positives = 34/56 (60%), Gaps = 2/56 (3%)
Query: 379 LAGKLFVVIGAG-GAGKALAYGAKAKGARVVIANRTYDRARELAETVG-GHALSLA 432
L GK+ ++ GA G G+A A GA+VV+A R +R LA+ +G G AL+LA
Sbjct: 4 LKGKVALITGASSGIGEATARALAEAGAKVVLAARREERLEALADEIGAGAALALA 59
>gnl|CDD|176198 cd08236, sugar_DH, NAD(P)-dependent sugar dehydrogenases. This
group contains proteins identified as sorbitol
dehydrogenases and other sugar dehydrogenases of the
medium-chain dehydrogenase/reductase family (MDR), which
includes zinc-dependent alcohol dehydrogenase and
related proteins. Sorbitol and aldose reductase are
NAD(+) binding proteins of the polyol pathway, which
interconverts glucose and fructose. Sorbitol
dehydrogenase is tetrameric and has a single catalytic
zinc per subunit. NAD(P)(H)-dependent oxidoreductases
are the major enzymes in the interconversion of alcohols
and aldehydes, or ketones. Related proteins include
threonine dehydrogenase, formaldehyde dehydrogenase, and
butanediol dehydrogenase. The medium chain alcohol
dehydrogenase family (MDR) has a NAD(P)(H)-binding
domain in a Rossmann fold of a beta-alpha form. The
N-terminal region typically has an all-beta catalytic
domain. These proteins typically form dimers (typically
higher plants, mammals) or tetramers (yeast, bacteria),
and have 2 tightly bound zinc atoms per subunit. Horse
liver alcohol dehydrogenase is a dimeric enzyme and each
subunit has two domains. The NAD binding domain is in a
Rossmann fold and the catalytic domain contains a zinc
ion to which substrates bind. There is a cleft between
the domains that closes upon formation of the ternary
complex.
Length = 343
Score = 31.0 bits (71), Expect = 1.7
Identities = 30/134 (22%), Positives = 42/134 (31%), Gaps = 28/134 (20%)
Query: 376 SSALAGKLFVVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAETVGGHALSLADLE 435
+ G VVIGAG G K GA+ VIA D +A +G
Sbjct: 155 AGITLGDTVVVIGAGTIGLLAIQWLKILGAKRVIAVDIDDEKLAVARELGADDT------ 208
Query: 436 NFNPEDGMILANTTSIGMQPKVDETPIPKHALGHYA-LVFDAVYTPKITRLLREAEESGA 494
NP++ D + + G A LV +A +P G
Sbjct: 209 -INPKEE---------------DVEKVRELTEGRGADLVIEAAGSPATIEQALALARPGG 252
Query: 495 TIVSGLEMFIGQAY 508
+V +G Y
Sbjct: 253 KVV-----LVGIPY 261
>gnl|CDD|181139 PRK07832, PRK07832, short chain dehydrogenase; Provisional.
Length = 272
Score = 30.8 bits (70), Expect = 1.8
Identities = 18/62 (29%), Positives = 28/62 (45%), Gaps = 8/62 (12%)
Query: 382 KLFVVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAE-------TVGGH-ALSLAD 433
+ FV A G G+A A A+GA + + +R D + TV H AL ++D
Sbjct: 2 RCFVTGAASGIGRATALRLAAQGAELFLTDRDADGLAQTVADARALGGTVPEHRALDISD 61
Query: 434 LE 435
+
Sbjct: 62 YD 63
>gnl|CDD|180802 PRK07035, PRK07035, short chain dehydrogenase; Provisional.
Length = 252
Score = 30.8 bits (70), Expect = 1.8
Identities = 21/58 (36%), Positives = 35/58 (60%), Gaps = 4/58 (6%)
Query: 379 LAGKLFVVIGAG-GAGKALAYGAKAKGARVVIANRTYDRARELAETV---GGHALSLA 432
L GK+ +V GA G G+A+A +GA V++++R D + +A+ + GG A +LA
Sbjct: 6 LTGKIALVTGASRGIGEAIAKLLAQQGAHVIVSSRKLDGCQAVADAIVAAGGKAEALA 63
>gnl|CDD|218263 pfam04784, DUF547, Protein of unknown function, DUF547. Family of
uncharacterized proteins from C. elegans and A.
thaliana.
Length = 112
Score = 29.4 bits (67), Expect = 1.8
Identities = 21/77 (27%), Positives = 30/77 (38%), Gaps = 30/77 (38%)
Query: 423 TVGGHALSLADLENFNPEDGMILANTTSIGMQPKVDETPIPKHALGHYAL---------V 473
TVGG ALSL D+E+ G++ N P++ H+AL +
Sbjct: 51 TVGGQALSLDDIEH-----GILRGNW----PDPRI-----------HFALNCGSISCPPL 90
Query: 474 FDAVYTP-KITRLLREA 489
YT + L EA
Sbjct: 91 RPEAYTAENLDEQLEEA 107
>gnl|CDD|187634 cd08929, SDR_c4, classical (c) SDR, subgroup 4. This subgroup has
a canonical active site tetrad and a typical Gly-rich
NAD-binding motif. 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 = 226
Score = 30.6 bits (69), Expect = 1.8
Identities = 16/49 (32%), Positives = 19/49 (38%)
Query: 384 FVVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAETVGGHALSLA 432
V + G G+A A A+G RV I R R A L LA
Sbjct: 4 LVTGASRGIGEATARLLHAEGYRVGICARDEARLAAAAAQELEGVLGLA 52
>gnl|CDD|187610 cd05352, MDH-like_SDR_c, mannitol dehydrogenase (MDH)-like,
classical (c) SDRs. NADP-mannitol dehydrogenase
catalyzes the conversion of fructose to mannitol, an
acyclic 6-carbon sugar. MDH is a tetrameric member of
the SDR family. This subgroup also includes various
other tetrameric SDRs, including Pichia stipitis
D-arabinitol dehydrogenase (aka polyol dehydrogenase),
Candida albicans Sou1p, a sorbose reductase, and Candida
parapsilosis (S)-specific carbonyl reductase (SCR, aka
S-specific alcohol dehydrogenase) which catalyzes the
enantioselective reduction of 2-hydroxyacetophenone into
(S)-1-phenyl-1,2-ethanediol. 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 have a 3-glycine N-terminal
NAD(P)(H)-binding pattern (typically, TGxxxGxG in
classical SDRs and TGxxGxxG in extended SDRs), while
substrate binding is in the C-terminal region. A
critical catalytic Tyr residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering), is often found in a conserved YXXXK pattern.
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) or additional Ser,
contributing to the active site. Substrates for these
enzymes include sugars, steroids, alcohols, and aromatic
compounds. The standard reaction mechanism is a proton
relay involving the conserved Tyr and Lys, as well as
Asn (or Ser).
Length = 252
Score = 30.8 bits (70), Expect = 1.8
Identities = 18/49 (36%), Positives = 23/49 (46%), Gaps = 1/49 (2%)
Query: 379 LAGKLFVVIGA-GGAGKALAYGAKAKGARVVIANRTYDRARELAETVGG 426
L GK+ +V G G G A+A GA V I + RA E AE +
Sbjct: 6 LKGKVAIVTGGSRGIGLAIARALAEAGADVAIIYNSAPRAEEKAEELAK 54
>gnl|CDD|132036 TIGR02991, ectoine_eutB, ectoine utilization protein EutB. Members
of this protein family are EutB, a predicted
arylmalonate decarboxylase found in a conserved ectoine
utilization operon of species that include Sinorhizobium
meliloti 1021 (where it is known to be induced by
ectoine), Mesorhizobium loti, Silicibacter pomeroyi,
Agrobacterium tumefaciens, and Pseudomonas putida.
Members of this family resemble threonine dehydratases.
Length = 317
Score = 31.0 bits (70), Expect = 1.8
Identities = 16/45 (35%), Positives = 19/45 (42%)
Query: 365 LRGRLNVSGGVSSALAGKLFVVIGAGGAGKALAYGAKAKGARVVI 409
LRG N +S V G G+ALAY A +G R I
Sbjct: 51 LRGATNAVLSLSDTQRAAGVVAASTGNHGRALAYAAAEEGVRATI 95
>gnl|CDD|176226 cd08265, Zn_ADH3, Alcohol dehydrogenases of the MDR family. This
group resembles the zinc-dependent alcohol dehydrogenase
and has the catalytic and structural zinc-binding sites
characteristic of this group. The medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, which contains the
zinc-dependent alcohol dehydrogenase (ADH-Zn) and
related proteins, is a diverse group of proteins related
to the first identified member, class I mammalian ADH.
MDRs display a broad range of activities and are
distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines. Other MDR members have only a catalytic zinc,
and some contain no coordinated zinc.
Length = 384
Score = 30.9 bits (70), Expect = 1.8
Identities = 24/86 (27%), Positives = 35/86 (40%), Gaps = 2/86 (2%)
Query: 381 GKLFVVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAETVGG-HALSLADLENFNP 439
G VV GAG G A AKA GA VIA + R LA+ +G + + + +
Sbjct: 204 GAYVVVYGAGPIGLAAIALAKAAGASKVIAFEISEERRNLAKEMGADYVFNPTKMRDCLS 263
Query: 440 EDGMILANTTSIGMQPKVDETPIPKH 465
++ T G +V+ P
Sbjct: 264 G-EKVMEVTKGWGADIQVEAAGAPPA 288
>gnl|CDD|233583 TIGR01813, flavo_cyto_c, flavocytochrome c. This model describes a
family of redox proteins related to the succinate
dehydrogenases and fumarate reductases of E. coli,
mitochondria, and other well-characterized systems. A
member of this family from Shewanella frigidimarina
NCIMB400 is characterized as a water-soluble periplasmic
protein with four heme groups, a non-covalently bound
FAD, and essentially unidirectional fumarate reductase
activity. At least seven distinct members of this family
are found in Shewanella oneidensis, a species able to
use a wide variety of pathways for respiraton [Energy
metabolism, Electron transport].
Length = 439
Score = 31.2 bits (71), Expect = 1.9
Identities = 12/25 (48%), Positives = 16/25 (64%)
Query: 385 VVIGAGGAGKALAYGAKAKGARVVI 409
VV+G+G AG + A AK GA V+
Sbjct: 3 VVVGSGFAGLSAALSAKKAGAANVV 27
>gnl|CDD|187631 cd05373, SDR_c10, classical (c) SDR, subgroup 10. This subgroup
resembles the classical SDRs, but has an incomplete
match to the canonical glycine rich NAD-binding motif
and lacks the typical active site tetrad (instead of the
critical active site Tyr, it has Phe, but contains the
nearby Lys). 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 = 238
Score = 30.8 bits (70), Expect = 1.9
Identities = 17/53 (32%), Positives = 24/53 (45%), Gaps = 5/53 (9%)
Query: 385 VVIGAG-GAGKALAYGAKAKGARVVIANRTYDRARELA----ETVGGHALSLA 432
V+GAG G G A+A A+G V +A R + L GG A ++
Sbjct: 3 AVVGAGDGLGAAIARRFAAEGFSVALAARREAKLEALLVDIIRDAGGSAKAVP 55
>gnl|CDD|223364 COG0287, TyrA, Prephenate dehydrogenase [Amino acid transport and
metabolism].
Length = 279
Score = 30.8 bits (70), Expect = 1.9
Identities = 13/42 (30%), Positives = 16/42 (38%)
Query: 385 VVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAETVGG 426
++G G G +LA K G V I R A A G
Sbjct: 7 GIVGLGLMGGSLARALKEAGLVVRIIGRDRSAATLKAALELG 48
>gnl|CDD|233635 TIGR01915, npdG, NADPH-dependent F420 reductase. This model
represents a subset of a parent family described by
pfam03807. Unlike the parent family, members of this
family are found only in species with evidence of
coenzyme F420. All members of this family are believed
to act as NADPH-dependent F420 reductase [Energy
metabolism, Electron transport].
Length = 219
Score = 30.5 bits (69), Expect = 2.0
Identities = 17/63 (26%), Positives = 28/63 (44%), Gaps = 3/63 (4%)
Query: 382 KLFVVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELA---ETVGGHALSLADLENFN 438
K+ V+ G G GK LA G +++I +R ++A E A GH S + +
Sbjct: 2 KIAVLGGTGDQGKGLALRLAKAGNKIIIGSRDLEKAEEAAAKALEELGHGGSDIKVTGAD 61
Query: 439 PED 441
+
Sbjct: 62 NAE 64
>gnl|CDD|222144 pfam13458, Peripla_BP_6, Periplasmic binding protein. This family
includes a diverse range of periplasmic binding
proteins.
Length = 343
Score = 30.7 bits (70), Expect = 2.0
Identities = 10/26 (38%), Positives = 15/26 (57%)
Query: 145 NYQYTPSVEDLSNLVARIQASGADIV 170
Y D S++V +I+ASG D+V
Sbjct: 169 EVYYPLGTTDFSSVVLQIKASGPDVV 194
>gnl|CDD|176242 cd08282, PFDH_like, Pseudomonas putida aldehyde-dismutating
formaldehyde dehydrogenase (PFDH). Formaldehyde
dehydrogenase (FDH) is a member of the
zinc-dependent/medium chain alcohol dehydrogenase
family. Unlike typical FDH, Pseudomonas putida
aldehyde-dismutating FDH (PFDH) is
glutathione-independent. PFDH converts 2 molecules of
aldehydes to corresponding carboxylic acid and alcohol.
MDH family uses NAD(H) as a cofactor in the
interconversion of alcohols and aldehydes, or ketones.
Like the zinc-dependent alcohol dehydrogenases (ADH) of
the medium chain alcohol dehydrogenase/reductase family
(MDR), these tetrameric FDHs have a catalytic zinc that
resides between the catalytic and NAD(H)binding domains
and a structural zinc in a lobe of the catalytic domain.
Unlike ADH, where NAD(P)(H) acts as a cofactor, NADH in
FDH is a tightly bound redox cofactor (similar to
nicotinamide proteins). The medium chain alcohol
dehydrogenase family (MDR) has a NAD(P)(H)-binding
domain in a Rossmann fold of an beta-alpha form. The
N-terminal region typically has an all-beta catalytic
domain. These proteins typically form dimers (typically
higher plants, mammals) or tetramers (yeast, bacteria),
and have 2 tightly bound zinc atoms per subunit.
Length = 375
Score = 31.0 bits (71), Expect = 2.1
Identities = 18/47 (38%), Positives = 25/47 (53%), Gaps = 2/47 (4%)
Query: 380 AGKLFVVIGAGGAGKALAYGAKAKGA-RVVIANRTYDRARELAETVG 425
G V GAG G AY A +GA RV + + +R +LAE++G
Sbjct: 176 PGDTVAVFGAGPVGLMAAYSAILRGASRVYVVDHVPERL-DLAESIG 221
>gnl|CDD|187594 cd05333, BKR_SDR_c, beta-Keto acyl carrier protein reductase (BKR),
involved in Type II FAS, classical (c) SDRs. This
subgroup includes the Escherichai coli K12 BKR, FabG.
BKR catalyzes the NADPH-dependent reduction of ACP in
the first reductive step of de novo fatty acid synthesis
(FAS). FAS consists of four elongation steps, which are
repeated to extend the fatty acid chain through the
addition of two-carbo units from malonyl acyl-carrier
protein (ACP): condensation, reduction, dehydration, and
a final reduction. Type II FAS, typical of plants and
many bacteria, maintains these activities on discrete
polypeptides, while type I FAS utilizes one or two
multifunctional polypeptides. BKR resembles enoyl
reductase, which catalyzes the second reduction step in
FAS. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with
structurally conserved Rossmann fold (alpha/beta folding
pattern with a central beta-sheet) 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 have a 3-glycine N-terminal NAD(P)(H) binding
pattern: TGxxxGxG in classical SDRs. 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 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. A critical catalytic Tyr residue
(Tyr-151, human 15-hydroxyprostaglandin dehydrogenase
(15-PGDH) numbering), is often found in a conserved
YXXXK pattern. 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) or additional
Ser, contributing to the active site. Substrates for
these enzymes include sugars, steroids, alcohols, and
aromatic compounds. The standard reaction mechanism is a
proton relay involving the conserved Tyr-151 and
Lys-155, and well as Asn-111 (or Ser). Some SDR family
members, including 17 beta-hydroxysteroid dehydrogenase
contain an additional helix-turn-helix motif that is not
generally found among SDRs.
Length = 240
Score = 30.6 bits (70), Expect = 2.1
Identities = 20/62 (32%), Positives = 33/62 (53%), Gaps = 5/62 (8%)
Query: 382 KLFVVIGAG-GAGKALAYGAKAKGARVVIANRTYDRARELAETV----GGHALSLADLEN 436
K+ +V GA G G+A+A A+GA+V + +R+ + A E E + G A AD+ +
Sbjct: 1 KVALVTGASRGIGRAIALRLAAEGAKVAVTDRSEEAAAETVEEIKALGGNAAALEADVSD 60
Query: 437 FN 438
Sbjct: 61 RE 62
>gnl|CDD|187600 cd05341, 3beta-17beta-HSD_like_SDR_c, 3beta17beta hydroxysteroid
dehydrogenase-like, classical (c) SDRs. This subgroup
includes members identified as 3beta17beta
hydroxysteroid dehydrogenase, 20beta hydroxysteroid
dehydrogenase, and R-alcohol dehydrogenase. These
proteins exhibit the canonical active site tetrad and
glycine rich NAD(P)-binding motif of the classical SDRs.
17beta-dehydrogenases are a group of isozymes that
catalyze activation and inactivation of estrogen and
androgens, and include members of the SDR family. 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 have a
3-glycine N-terminal NAD(P)(H)-binding pattern
(typically, TGxxxGxG in classical SDRs and TGxxGxxG in
extended SDRs), while substrate binding is in the
C-terminal region. A critical catalytic Tyr residue
(Tyr-151, human 15-hydroxyprostaglandin dehydrogenase
(15-PGDH) numbering), is often found in a conserved
YXXXK pattern. 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) or additional
Ser, contributing to the active site. Substrates for
these enzymes include sugars, steroids, alcohols, and
aromatic compounds. The standard reaction mechanism is a
proton relay involving the conserved Tyr and Lys, as
well as Asn (or Ser). Some SDR family members, including
17 beta-hydroxysteroid dehydrogenase contain an
additional helix-turn-helix motif that is not generally
found among SDRs.
Length = 247
Score = 30.4 bits (69), Expect = 2.1
Identities = 18/51 (35%), Positives = 28/51 (54%), Gaps = 1/51 (1%)
Query: 379 LAGKLFVVIG-AGGAGKALAYGAKAKGARVVIANRTYDRARELAETVGGHA 428
L GK+ +V G A G G A A A+GA+VV+++ + + A +G A
Sbjct: 3 LKGKVAIVTGGARGLGLAHARLLVAEGAKVVLSDILDEEGQAAAAELGDAA 53
>gnl|CDD|223249 COG0171, NadE, NAD synthase [Coenzyme metabolism].
Length = 268
Score = 30.7 bits (70), Expect = 2.1
Identities = 23/89 (25%), Positives = 33/89 (37%), Gaps = 24/89 (26%)
Query: 353 DYVGAISAIEDGLRGRLN----------VSGGVSSALAGKLFVVIGAGGAGKALAYGAKA 402
D I+ + D LR L +SGG+ SAL L A +AL G
Sbjct: 4 DLEEEINRLVDFLRDYLKKAGFKGVVLGLSGGIDSALVLAL--------AVRALGKGDSK 55
Query: 403 KGARVVI------ANRTYDRARELAETVG 425
+ V + A++LAE +G
Sbjct: 56 ENVLAVRLPYGYTVQADEEDAQDLAEALG 84
>gnl|CDD|205628 pfam13450, NAD_binding_8, NAD(P)-binding Rossmann-like domain.
Length = 66
Score = 28.2 bits (64), Expect = 2.2
Identities = 13/48 (27%), Positives = 23/48 (47%), Gaps = 8/48 (16%)
Query: 386 VIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAETVGGHALSLAD 433
++GAG +G AY +G V++ ++ + GG+A S D
Sbjct: 1 IVGAGLSGLVAAYLLAKRGKDVLV----LEKRDRI----GGNAYSERD 40
>gnl|CDD|222146 pfam13460, NAD_binding_10, NADH(P)-binding.
Length = 182
Score = 30.0 bits (68), Expect = 2.3
Identities = 20/65 (30%), Positives = 27/65 (41%), Gaps = 3/65 (4%)
Query: 385 VVIGA-GGAGKALAYGAKAKGARVVIANRTYDRARE-LAETVGGHALSLADL-ENFNPED 441
VIGA G G+ L A+G +V +R +A V LADL E D
Sbjct: 2 AVIGATGKTGRRLVKELLARGHQVTALSRNPSKAPAPGVTPVQKDLFDLADLAEALAGVD 61
Query: 442 GMILA 446
++ A
Sbjct: 62 AVVDA 66
>gnl|CDD|176260 cd08300, alcohol_DH_class_III, class III alcohol dehydrogenases.
Members identified as glutathione-dependent formaldehyde
dehydrogenase(FDH), a member of the zinc
dependent/medium chain alcohol dehydrogenase family.
FDH converts formaldehyde and NAD(P) to formate and
NAD(P)H. The initial step in this process the
spontaneous formation of a S-(hydroxymethyl)glutathione
adduct from formaldehyde and glutathione, followed by
FDH-mediated oxidation (and detoxification) of the
adduct to S-formylglutathione. MDH family uses NAD(H)
as a cofactor in the interconversion of alcohols and
aldehydes or ketones. Like many zinc-dependent alcohol
dehydrogenases (ADH) of the medium chain alcohol
dehydrogenase/reductase family (MDR), these FDHs form
dimers, with 4 zinc ions per dimer. The medium chain
alcohol dehydrogenase family (MDR) have a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The N-terminal region typically has an
all-beta catalytic domain. These proteins typically form
dimers (typically higher plants, mammals) or tetramers
(yeast, bacteria), and have 2 tightly bound zinc atoms
per subunit. Alcohol dehydrogenase in the liver
converts ethanol and NAD+ to acetaldehyde and NADH,
while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which have a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES.
These proteins typically form dimers (typically higher
plants, mammals) or tetramers (yeast, bacteria), and
have 2 tightly bound zinc atoms per subunit, a catalytic
zinc at the active site and a structural zinc in a lobe
of the catalytic domain. NAD(H) binding occurs in the
cleft between the catalytic and coenzyme-binding
domains at the active site, and coenzyme binding induces
a conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
Length = 368
Score = 30.7 bits (70), Expect = 2.3
Identities = 17/46 (36%), Positives = 20/46 (43%)
Query: 380 AGKLFVVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAETVG 425
G V G G G A+ GAKA GA +I ELA+ G
Sbjct: 186 PGSTVAVFGLGAVGLAVIQGAKAAGASRIIGIDINPDKFELAKKFG 231
>gnl|CDD|187662 cd09761, A3DFK9-like_SDR_c, Clostridium thermocellum A3DFK9-like, a
putative carbohydrate or polyalcohol metabolizing SDR,
classical (c) SDRs. This subgroup includes a putative
carbohydrate or polyalcohol metabolizing SDR (A3DFK9)
from Clostridium thermocellum. Its members have a
TGXXXGXG classical-SDR glycine-rich NAD-binding motif,
and some have a canonical SDR active site tetrad (A3DFK9
lacks the upstream Asn). SDRs are a functionally diverse
family of oxidoreductases that have a single domain with
a structurally conserved Rossmann fold (alpha/beta
folding pattern with a central beta-sheet), an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRs are approximately
350 residues. Sequence identity between different SDR
enzymes are typically in the 15-30% range, but the
enzymes share the Rossmann fold NAD-binding motif and
characteristic NAD-binding and catalytic sequence
patterns. These enzymes catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) numbering). In addition to the
Tyr and Lys, there is often an upstream Ser (Ser-138,
15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH
numbering) contributing to the active site; while
substrate binding is in the C-terminal region, which
determines specificity. The standard reaction mechanism
is a 4-pro-S hydride transfer and proton relay involving
the conserved Tyr and Lys, a water molecule stabilized
by Asn, and nicotinamide. Extended SDRs have additional
elements in the C-terminal region, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Some atypical SDRs have lost catalytic activity and/or
have an unusual NAD(P)-binding motif and missing or
unusual active site residues. Reactions catalyzed within
the SDR family include isomerization, decarboxylation,
epimerization, C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 242
Score = 30.2 bits (68), Expect = 2.4
Identities = 16/49 (32%), Positives = 24/49 (48%), Gaps = 1/49 (2%)
Query: 381 GKLFVVIGAG-GAGKALAYGAKAKGARVVIANRTYDRARELAETVGGHA 428
GK+ +V G G G GK + G +VV A+ +R + AE G +
Sbjct: 1 GKVAIVTGGGHGIGKQICLDFLEAGDKVVFADIDEERGADFAEAEGPNL 49
>gnl|CDD|132250 TIGR03206, benzo_BadH, 2-hydroxycyclohexanecarboxyl-CoA
dehydrogenase. Members of this protein family are the
enzyme 2-hydroxycyclohexanecarboxyl-CoA dehydrogenase.
The enzymatic properties were confirmed experimentally
in Rhodopseudomonas palustris; the enzyme is
homotetrameric, and not sensitive to oxygen. This enzyme
is part of proposed pathway for degradation of
benzoyl-CoA to 3-hydroxypimeloyl-CoA that differs from
the analogous in Thauera aromatica. It also may occur in
degradation of the non-aromatic compound
cyclohexane-1-carboxylate.
Length = 250
Score = 30.3 bits (68), Expect = 2.4
Identities = 21/79 (26%), Positives = 38/79 (48%), Gaps = 5/79 (6%)
Query: 379 LAGKLFVVIG-AGGAGKALAYGAKAKGARVVIANRTYDRARELAETV---GGHALSLA-D 433
L K +V G GG G A +GA+V + + + A ++A + GG+A + A D
Sbjct: 1 LKDKTAIVTGGGGGIGGATCRRFAEEGAKVAVFDLNREAAEKVAADIRAKGGNAQAFACD 60
Query: 434 LENFNPEDGMILANTTSIG 452
+ + + D + A ++G
Sbjct: 61 ITDRDSVDTAVAAAEQALG 79
>gnl|CDD|176220 cd08259, Zn_ADH5, Alcohol dehydrogenases of the MDR family.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. This group contains proteins that
share the characteristic catalytic and structural
zinc-binding sites of the zinc-dependent alcohol
dehydrogenase family. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which have a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES. These
proteins typically form dimers (typically higher plants,
mammals) or tetramers (yeast, bacteria), and have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. NAD(H)-binding occurs in the cleft
between the catalytic and coenzyme-binding domains at
the active site, and coenzyme binding induces a
conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
In human ADH catalysis, the zinc ion helps coordinate
the alcohol, followed by deprotonation of a histidine
(His-51), the ribose of NAD, a serine (Ser-48), then the
alcohol, which allows the transfer of a hydride to NAD+,
creating NADH and a zinc-bound aldehyde or ketone. In
yeast and some bacteria, the active site zinc binds an
aldehyde, polarizing it, and leading to the reverse
reaction.
Length = 332
Score = 30.4 bits (69), Expect = 2.7
Identities = 17/43 (39%), Positives = 23/43 (53%), Gaps = 1/43 (2%)
Query: 381 GKLFVVIGAGGA-GKALAYGAKAKGARVVIANRTYDRARELAE 422
G +V GAGG G AKA GARV+ R+ ++ + L E
Sbjct: 163 GDTVLVTGAGGGVGIHAIQLAKALGARVIAVTRSPEKLKILKE 205
>gnl|CDD|236185 PRK08205, sdhA, succinate dehydrogenase flavoprotein subunit;
Reviewed.
Length = 583
Score = 30.7 bits (70), Expect = 2.7
Identities = 19/56 (33%), Positives = 26/56 (46%), Gaps = 1/56 (1%)
Query: 385 VVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAETVGGHALSLADLENFNPE 440
V++GAGGAG A A AR + + Y GG +LA++E N E
Sbjct: 9 VIVGAGGAGMRAAIEA-GPRARTAVLTKLYPTRSHTGAAQGGMCAALANVEEDNWE 63
>gnl|CDD|187629 cd05371, HSD10-like_SDR_c, 17hydroxysteroid dehydrogenase type 10
(HSD10)-like, classical (c) SDRs. HSD10, also known as
amyloid-peptide-binding alcohol dehydrogenase (ABAD),
was previously identified as a L-3-hydroxyacyl-CoA
dehydrogenase, HADH2. In fatty acid metabolism, HADH2
catalyzes the third step of beta-oxidation, the
conversion of a hydroxyl to a keto group in the
NAD-dependent oxidation of L-3-hydroxyacyl CoA. In
addition to alcohol dehydrogenase and HADH2 activites,
HSD10 has steroid dehydrogenase activity. Although the
mechanism is unclear, HSD10 is implicated in the
formation of amyloid beta-petide in the brain (which is
linked to the development of Alzheimer's disease).
Although HSD10 is normally concentrated in the
mitochondria, in the presence of amyloid beta-peptide it
translocates into the plasma membrane, where it's action
may generate cytotoxic aldehydes and may lower estrogen
levels through its use of 17-beta-estradiol as a
substrate. HSD10 is a member of the SRD family, but
differs from other SDRs by the presence of two
insertions of unknown function. 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 = 252
Score = 30.3 bits (69), Expect = 2.8
Identities = 15/43 (34%), Positives = 21/43 (48%), Gaps = 1/43 (2%)
Query: 381 GKLFVVIG-AGGAGKALAYGAKAKGARVVIANRTYDRARELAE 422
G + VV G A G G A A+GA+VVI + +A+
Sbjct: 2 GLVAVVTGGASGLGLATVERLLAQGAKVVILDLPNSPGETVAK 44
>gnl|CDD|167786 PRK04308, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 445
Score = 30.6 bits (69), Expect = 2.9
Identities = 13/56 (23%), Positives = 18/56 (32%), Gaps = 5/56 (8%)
Query: 380 AGKLFVVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAETVGGHALSLADLE 435
K +V G GG G ++ + GA V + A E V L
Sbjct: 4 QNKKILVAGLGGTGISMIAYLRKNGAEVAAYD-----AELKPERVAQIGKMFDGLV 54
>gnl|CDD|135765 PRK06113, PRK06113, 7-alpha-hydroxysteroid dehydrogenase;
Validated.
Length = 255
Score = 30.2 bits (68), Expect = 2.9
Identities = 19/58 (32%), Positives = 29/58 (50%), Gaps = 4/58 (6%)
Query: 379 LAGKLFVVIGAG-GAGKALAYGAKAKGARVVIANRTYDRARELAETV---GGHALSLA 432
L GK ++ GAG G GK +A GA VV+++ D A + + + GG A +
Sbjct: 9 LDGKCAIITGAGAGIGKEIAITFATAGASVVVSDINADAANHVVDEIQQLGGQAFACR 66
>gnl|CDD|181723 PRK09245, PRK09245, enoyl-CoA hydratase; Provisional.
Length = 266
Score = 29.9 bits (68), Expect = 3.0
Identities = 17/44 (38%), Positives = 22/44 (50%), Gaps = 6/44 (13%)
Query: 392 AGKALAYGAKAKGARVVIANRTYDRARELAETVG---GHALSLA 432
A AL +G + RVV A++ AR LAE + HAL L
Sbjct: 176 AATALEWGLVS---RVVPADQLLPAARALAERIAANPPHALRLT 216
>gnl|CDD|212497 cd11731, Lin1944_like_SDR_c, Lin1944 and related proteins,
classical (c) SDRs. Lin1944 protein from Listeria
Innocua is a classical SDR, it contains a glycine-rich
motif similar to the canonical motif of the SDR
NAD(P)-binding site. However, the typical SDR active
site residues are absent in this subgroup of proteins of
undetermined function. 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 prostaglandin dehydrogenase
(PGDH) numbering). In addition to the Tyr and Lys, there
is often an upstream Ser (Ser-138, PGDH numbering)
and/or an Asn (Asn-107, 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 = 198
Score = 29.9 bits (68), Expect = 3.0
Identities = 13/30 (43%), Positives = 17/30 (56%), Gaps = 1/30 (3%)
Query: 385 VVIGA-GGAGKALAYGAKAKGARVVIANRT 413
+VIGA G G A+A A G V+ A R+
Sbjct: 2 IVIGATGTIGLAVAQLLSAHGHEVITAGRS 31
>gnl|CDD|237218 PRK12825, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 249
Score = 29.8 bits (68), Expect = 3.1
Identities = 15/45 (33%), Positives = 19/45 (42%), Gaps = 1/45 (2%)
Query: 384 FVVIGAGGAGKALAYGAKAKGARVVI-ANRTYDRARELAETVGGH 427
V A G G+A+A GA VV+ + A EL E V
Sbjct: 10 LVTGAARGLGRAIALRLARAGADVVVHYRSDEEAAEELVEAVEAL 54
>gnl|CDD|187601 cd05343, Mgc4172-like_SDR_c, human Mgc4172-like, classical (c)
SDRs. Human Mgc4172-like proteins, putative SDRs. These
proteins are members of the SDR family, with a canonical
active site tetrad and a typical Gly-rich NAD-binding
motif. 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 = 250
Score = 29.8 bits (67), Expect = 3.3
Identities = 15/49 (30%), Positives = 21/49 (42%), Gaps = 1/49 (2%)
Query: 379 LAGKLFVVIGA-GGAGKALAYGAKAKGARVVIANRTYDRARELAETVGG 426
G++ +V GA G G A+A G +VV R D+ LA
Sbjct: 4 WRGRVALVTGASVGIGAAVARALVQHGMKVVGCARRVDKIEALAAECQS 52
>gnl|CDD|132245 TIGR03201, dearomat_had, 6-hydroxycyclohex-1-ene-1-carbonyl-CoA
dehydrogenase. Members of this protein family are
6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase, an
enzyme in the anaerobic metabolism of aromatic enzymes
by way of benzoyl-CoA, as seen in Thauera aromatica,
Geobacter metallireducens, and Azoarcus sp. The
experimentally characterized form from T. aromatica uses
only NAD+, not NADP+. Note that Rhodopseudomonas
palustris uses a different pathway to perform a similar
degradation of benzoyl-CoA to 3-hydroxpimelyl-CoA.
Length = 349
Score = 30.3 bits (68), Expect = 3.3
Identities = 21/67 (31%), Positives = 26/67 (38%), Gaps = 19/67 (28%)
Query: 381 GKLFVVIGAGGAGKALAYGAKAKGARVV-------------------IANRTYDRARELA 421
G L +VIGAGG G + AKA GA VV N ARE+
Sbjct: 167 GDLVIVIGAGGVGGYMVQTAKAMGAAVVAIDIDPEKLEMMKGFGADLTLNPKDKSAREVK 226
Query: 422 ETVGGHA 428
+ + A
Sbjct: 227 KLIKAFA 233
>gnl|CDD|235702 PRK06124, PRK06124, gluconate 5-dehydrogenase; Provisional.
Length = 256
Score = 30.1 bits (68), Expect = 3.4
Identities = 17/59 (28%), Positives = 27/59 (45%), Gaps = 4/59 (6%)
Query: 378 ALAGKLFVVIGAG-GAGKALAYGAKAKGARVVIANRTYDRARELAETV---GGHALSLA 432
+LAG++ +V G+ G G +A GA V++ R + GG A +LA
Sbjct: 8 SLAGQVALVTGSARGLGFEIARALAGAGAHVLVNGRNAATLEAAVAALRAAGGAAEALA 66
>gnl|CDD|178341 PLN02740, PLN02740, Alcohol dehydrogenase-like.
Length = 381
Score = 30.2 bits (68), Expect = 3.4
Identities = 18/45 (40%), Positives = 24/45 (53%), Gaps = 6/45 (13%)
Query: 371 VSGGVSSAL------AGKLFVVIGAGGAGKALAYGAKAKGARVVI 409
VS GV +A AG + G G G A+A GA+A+GA +I
Sbjct: 183 VSTGVGAAWNTANVQAGSSVAIFGLGAVGLAVAEGARARGASKII 227
>gnl|CDD|176194 cd08232, idonate-5-DH, L-idonate 5-dehydrogenase. L-idonate
5-dehydrogenase (L-ido 5-DH ) catalyzes the conversion
of L-lodonate to 5-ketogluconate in the metabolism of
L-Idonate to 6-P-gluconate. In E. coli, this GntII
pathway is a subsidiary pathway to the canonical GntI
system, which also phosphorylates and transports
gluconate. L-ido 5-DH is found in an operon with a
regulator indR, transporter idnT, 5-keto-D-gluconate
5-reductase, and Gnt kinase. L-ido 5-DH is a
zinc-dependent alcohol dehydrogenase-like protein. The
alcohol dehydrogenase ADH-like family of proteins is a
diverse group of proteins related to the first
identified member, class I mammalian ADH. This group is
also called the medium chain dehydrogenases/reductase
family (MDR) which displays a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases(~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal GroES-like catalytic
domain. The MDR group contains a host of activities,
including the founding alcohol dehydrogenase (ADH),
quinone reductase, sorbitol dehydrogenase, formaldehyde
dehydrogenase, butanediol DH, ketose reductase, cinnamyl
reductase, and numerous others. The zinc-dependent
alcohol dehydrogenases (ADHs) catalyze the
NAD(P)(H)-dependent interconversion of alcohols to
aldehydes or ketones. ADH-like proteins typically form
dimers (typically higher plants, mammals) or tetramers
(yeast, bacteria), and generally have 2 tightly bound
zinc atoms per subunit. The active site zinc is
coordinated by a histidine, two cysteines, and a water
molecule. The second zinc seems to play a structural
role, affects subunit interactions, and is typically
coordinated by 4 cysteines.
Length = 339
Score = 30.3 bits (69), Expect = 3.4
Identities = 18/56 (32%), Positives = 27/56 (48%), Gaps = 1/56 (1%)
Query: 379 LAGKLFVVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAETVGG-HALSLAD 433
LAGK +V GAG G + A+ GA ++A D +A +G ++LA
Sbjct: 164 LAGKRVLVTGAGPIGALVVAAARRAGAAEIVATDLADAPLAVARAMGADETVNLAR 219
>gnl|CDD|221803 pfam12846, AAA_10, AAA-like domain. This family of domains contain
a P-loop motif that is characteristic of the AAA
superfamily. Many of the proteins in this family are
conjugative transfer proteins.
Length = 316
Score = 30.1 bits (68), Expect = 3.6
Identities = 17/63 (26%), Positives = 29/63 (46%), Gaps = 8/63 (12%)
Query: 384 FVVIGAGGAGK-----ALAYGAKAKGARVVIANRTYDRARELAETVGGHALSLADLEN-- 436
+++G G+GK LA A+G RV++ + + + LA +GG + L
Sbjct: 4 MLIVGPSGSGKSTLLKLLALRLLARGGRVIVIDPKGEYSG-LARALGGEVIDLGPGSGIS 62
Query: 437 FNP 439
NP
Sbjct: 63 LNP 65
>gnl|CDD|203546 pfam06917, Pectate_lyase_2, Periplasmic pectate lyase. This family
consists of several Enterobacterial periplasmic pectate
lyase proteins (EC:4.2.2.2). A major virulence
determinant of the plant-pathogenic enterobacterium
Erwinia chrysanthemi is the production of pectate lyase
enzymes that degrade plant cell walls.
Length = 533
Score = 30.2 bits (68), Expect = 3.8
Identities = 16/61 (26%), Positives = 24/61 (39%), Gaps = 20/61 (32%)
Query: 38 MVVDMGK-ANASGADLVEIRLDGLKNF-----NPRENIKTLIKESPVPTLFTYRPIWEGG 91
M + + K GA+L+ +DGLK F N +N T+RP+ G
Sbjct: 300 MQLQLAKQLGQPGAELLTWTVDGLKAFAKYAYNVPDN--------------TFRPMLANG 345
Query: 92 Q 92
Sbjct: 346 T 346
>gnl|CDD|176244 cd08284, FDH_like_2, Glutathione-dependent formaldehyde
dehydrogenase related proteins, child 2.
Glutathione-dependent formaldehyde dehydrogenases (FDHs)
are members of the zinc-dependent/medium chain alcohol
dehydrogenase family. Formaldehyde dehydrogenase (FDH)
is a member of the zinc-dependent/medium chain alcohol
dehydrogenase family. FDH converts formaldehyde and NAD
to formate and NADH. The initial step in this process
the spontaneous formation of a
S-(hydroxymethyl)glutathione adduct from formaldehyde
and glutathione, followed by FDH-mediated oxidation (and
detoxification) of the adduct to S-formylglutathione.
These tetrameric FDHs have a catalytic zinc that resides
between the catalytic and NAD(H)binding domains and a
structural zinc in a lobe of the catalytic domain. The
medium chain alcohol dehydrogenase family (MDR) has a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The N-terminal region typically has an
all-beta catalytic domain. These proteins typically form
dimers (typically higher plants, mammals) or tetramers
(yeast, bacteria), and have 2 tightly bound zinc atoms
per subunit.
Length = 344
Score = 29.9 bits (68), Expect = 3.8
Identities = 19/66 (28%), Positives = 25/66 (37%), Gaps = 4/66 (6%)
Query: 373 GGVSSAL--AGKLFVVIGAGGAGKALAYGAKAKGARVVIA-NRTYDRARELAETVGGHAL 429
G A G VIG G G A+ GA V A + +R E A +G +
Sbjct: 158 FGAKRAQVRPGDTVAVIGCGPVGLCAVLSAQVLGAARVFAVDPVPER-LERAAALGAEPI 216
Query: 430 SLADLE 435
+ D E
Sbjct: 217 NFEDAE 222
>gnl|CDD|187623 cd05365, 7_alpha_HSDH_SDR_c, 7 alpha-hydroxysteroid dehydrogenase
(7 alpha-HSDH), classical (c) SDRs. This bacterial
subgroup contains 7 alpha-HSDHs, including Escherichia
coli 7 alpha-HSDH. 7 alpha-HSDH, a member of the SDR
family, catalyzes the NAD+ -dependent dehydrogenation of
a hydroxyl group at position 7 of the steroid skeleton
of bile acids. In humans the two primary bile acids are
cholic and chenodeoxycholic acids, these are formed from
cholesterol in the liver. Escherichia coli 7 alpha-HSDH
dehydroxylates these bile acids in the human intestine.
Mammalian 7 alpha-HSDH activity has been found in
livers. 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 have a 3-glycine N-terminal NAD(P)(H)-binding
pattern (typically, TGxxxGxG in classical SDRs and
TGxxGxxG in extended SDRs), while substrate binding is
in the C-terminal region. A critical catalytic Tyr
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) numbering), is often found in a
conserved YXXXK pattern. 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) or
additional Ser, contributing to the active site.
Substrates for these enzymes include sugars, steroids,
alcohols, and aromatic compounds. The standard reaction
mechanism is a proton relay involving the conserved Tyr
and Lys, as well as Asn (or Ser). Some SDR family
members, including 17 beta-hydroxysteroid dehydrogenase
contain an additional helix-turn-helix motif that is not
generally found among SDRs.
Length = 242
Score = 29.8 bits (67), Expect = 3.9
Identities = 19/47 (40%), Positives = 25/47 (53%), Gaps = 3/47 (6%)
Query: 388 GAGGAGKALAYGAKAKGARVVIANRTYDRARELAETV---GGHALSL 431
GA G GKA+A GA VVIA+ + A +A + GG A+ L
Sbjct: 7 GAAGIGKAIAGTLAKAGASVVIADLKSEGAEAVAAAIQQAGGQAIGL 53
>gnl|CDD|187598 cd05339, 17beta-HSDXI-like_SDR_c, human 17-beta-hydroxysteroid
dehydrogenase XI-like, classical (c) SDRs.
17-beta-hydroxysteroid dehydrogenases (17betaHSD) are a
group of isozymes that catalyze activation and
inactivation of estrogen and androgens. 17betaHSD type
XI, a classical SDR, preferentially converts
3alpha-adiol to androsterone but not numerous other
tested steroids. This subgroup of classical SDRs also
includes members identified as retinol dehydrogenases,
which convert retinol to retinal, a property that
overlaps with 17betaHSD activity. 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 have a
3-glycine N-terminal NAD(P)(H)-binding pattern
(typically, TGxxxGxG in classical SDRs and TGxxGxxG in
extended SDRs), while substrate binding is in the
C-terminal region. A critical catalytic Tyr residue
(Tyr-151, human 15-hydroxyprostaglandin dehydrogenase
(15-PGDH) numbering), is often found in a conserved
YXXXK pattern. 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) or additional
Ser, contributing to the active site. Substrates for
these enzymes include sugars, steroids, alcohols, and
aromatic compounds. The standard reaction mechanism is a
proton relay involving the conserved Tyr and Lys, as
well as Asn (or Ser). Some SDR family members, including
17 beta-hydroxysteroid dehydrogenase contain an
additional helix-turn-helix motif that is not generally
found among SDRs.
Length = 243
Score = 29.5 bits (67), Expect = 4.1
Identities = 16/44 (36%), Positives = 21/44 (47%), Gaps = 2/44 (4%)
Query: 385 VVI--GAGGAGKALAYGAKAKGARVVIANRTYDRARELAETVGG 426
V+I G G G+ LA +GA+VVI + A E A V
Sbjct: 2 VLITGGGSGIGRLLALEFAKRGAKVVILDINEKGAEETANNVRK 45
>gnl|CDD|223895 COG0825, AccA, Acetyl-CoA carboxylase alpha subunit [Lipid
metabolism].
Length = 317
Score = 29.9 bits (68), Expect = 4.2
Identities = 30/100 (30%), Positives = 40/100 (40%), Gaps = 34/100 (34%)
Query: 373 GGVSSALAGKLF-----------VVIGAGGAGKALAYGAKAKGARVVIA-NRTY------ 414
G S A+A L +VIG GG+G ALA G RV++ N TY
Sbjct: 171 RGQSEAIARNLREMARLKVPIISIVIGEGGSGGALAIGV---ADRVLMLENSTYSVISPE 227
Query: 415 ----------DRARELAETVGGHALSLADLENFNPEDGMI 444
+A+E AE + A DL+ DG+I
Sbjct: 228 GCASILWKDASKAKEAAEAMKITA---HDLKELGIIDGII 264
>gnl|CDD|237220 PRK12828, PRK12828, short chain dehydrogenase; Provisional.
Length = 239
Score = 29.4 bits (66), Expect = 4.3
Identities = 19/72 (26%), Positives = 31/72 (43%), Gaps = 1/72 (1%)
Query: 379 LAGKLFVVIGA-GGAGKALAYGAKAKGARVVIANRTYDRARELAETVGGHALSLADLENF 437
L GK+ + G GG G+A A A+GARV + R + V AL + ++
Sbjct: 5 LQGKVVAITGGFGGLGRATAAWLAARGARVALIGRGAAPLSQTLPGVPADALRIGGIDLV 64
Query: 438 NPEDGMILANTT 449
+P+ +
Sbjct: 65 DPQAARRAVDEV 76
>gnl|CDD|240058 cd04703, Asparaginase_2_like, A subfamily of the L-Asparaginase
type 2-like enzymes. The wider family, a member of the
Ntn-hydrolase superfamily, includes
Glycosylasparaginase, Taspase 1 and L-Asparaginase type
2 enzymes. The proenzymes undergo autoproteolytic
cleavage before a threonine to generate alpha and beta
subunits. The threonine becomes the N-terminal residue
of the beta subunit and is the catalytic residue.
Length = 246
Score = 29.7 bits (67), Expect = 4.4
Identities = 23/71 (32%), Positives = 31/71 (43%), Gaps = 7/71 (9%)
Query: 352 TDYVGAISAIEDGLRGRLNVSGGVSSALAGKL--FVVIGAG----GAGKALAYGAKAKGA 405
D VGA++ L + +GG ALAG++ GAG G A GA A
Sbjct: 127 HDTVGAVARDGGRLAAATS-TGGRWPALAGRVGDVPQPGAGFYAGPRGAVSATGAGEAIA 185
Query: 406 RVVIANRTYDR 416
R +A Y+R
Sbjct: 186 RNTLARSAYNR 196
>gnl|CDD|240628 cd05303, PGDH_2, Phosphoglycerate dehydrogenase (PGDH) NAD-binding
and catalytic domains. Phosphoglycerate dehydrogenase
(PGDH) catalyzes the initial step in the biosynthesis of
L-serine from D-3-phosphoglycerate. PGDH comes in 3
distinct structural forms, with this first group being
related to 2-hydroxy acid dehydrogenases, sharing
structural similarity to formate and glycerate
dehydrogenases. PGDH in E. coli and Mycobacterium
tuberculosis form tetramers, with subunits containing a
Rossmann-fold NAD binding domain. Formate/glycerate and
related dehydrogenases of the D-specific 2-hydroxyacid
dehydrogenase superfamily include groups such as formate
dehydrogenase, glycerate dehydrogenase, L-alanine
dehydrogenase, and S-Adenosylhomocysteine Hydrolase.
Despite often low sequence identity, these proteins
typically have a characteristic arrangement of 2 similar
subdomains of the alpha/beta Rossmann fold NAD+ binding
form. The NAD+ binding domain is inserted within the
linear sequence of the mostly N-terminal catalytic
domain, which has a similar domain structure to the
internal NAD binding domain. Structurally, these domains
are connected by extended alpha helices and create a
cleft in which NAD is bound, primarily to the C-terminal
portion of the 2nd (internal) domain. Some related
proteins have similar structural subdomain but with a
tandem arrangement of the catalytic and NAD-binding
subdomains in the linear sequence.
Length = 301
Score = 29.4 bits (67), Expect = 4.6
Identities = 20/58 (34%), Positives = 28/58 (48%), Gaps = 6/58 (10%)
Query: 379 LAGKLFVVIGAGGAGKALAYGAKAKGARVVIANRTYDR--ARELAETVGGHALSLADL 434
L GK +IG G G+ +A A+A G V+ YD E A +G +SL +L
Sbjct: 137 LRGKTLGIIGFGRIGREVAKIARALGMNVI----AYDPYPKDEQAVELGVKTVSLEEL 190
>gnl|CDD|235739 PRK06200, PRK06200, 2,3-dihydroxy-2,3-dihydrophenylpropionate
dehydrogenase; Provisional.
Length = 263
Score = 29.5 bits (67), Expect = 4.7
Identities = 20/63 (31%), Positives = 30/63 (47%), Gaps = 8/63 (12%)
Query: 379 LAGKLFVVIGAG-GAGKALAYGAKAKGARVVIANRTYDRARELA-------ETVGGHALS 430
L G++ ++ G G G G+AL A+GARV + R+ ++ L V G S
Sbjct: 4 LHGQVALITGGGSGIGRALVERFLAEGARVAVLERSAEKLASLRQRFGDHVLVVEGDVTS 63
Query: 431 LAD 433
AD
Sbjct: 64 YAD 66
>gnl|CDD|215893 pfam00389, 2-Hacid_dh, D-isomer specific 2-hydroxyacid
dehydrogenase, catalytic domain. This family represents
the largest portion of the catalytic domain of
2-hydroxyacid dehydrogenases as the NAD binding domain
is inserted within the structural domain.
Length = 312
Score = 29.6 bits (67), Expect = 4.7
Identities = 24/84 (28%), Positives = 28/84 (33%), Gaps = 1/84 (1%)
Query: 366 RGRLNVSGGVSSALAGKLFVVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAETVG 425
G G + L GK VIG GG G A AKA G VV + Y E
Sbjct: 121 AGDWKKGGPIGLELYGKTLGVIGGGGIGGIGAAIAKALGMGVVAYDP-YPNPERAEEGGV 179
Query: 426 GHALSLADLENFNPEDGMILANTT 449
L L + D +I
Sbjct: 180 EVLLLDLLLLDLKESDDLINLAPP 203
>gnl|CDD|215463 PLN02858, PLN02858, fructose-bisphosphate aldolase.
Length = 1378
Score = 30.2 bits (68), Expect = 4.7
Identities = 15/41 (36%), Positives = 23/41 (56%)
Query: 356 GAISAIEDGLRGRLNVSGGVSSALAGKLFVVIGAGGAGKAL 396
G ++ + G L +G V SAL+ KL+V+ G GAG +
Sbjct: 456 GTLTIMASGTDEALKSAGSVLSALSEKLYVIKGGCGAGSGV 496
>gnl|CDD|234436 TIGR03997, mycofact_OYE_2, mycofactocin system FadH/OYE family
oxidoreductase 2. The yeast protein called old yellow
enzyme and FadH from Escherichia coli (2,4-dienoyl CoA
reductase) are enzymes with 4Fe-4S, FMN, and FAD
prosthetic groups, and interact with NADPH as well as
substrate. Members of this related protein family occur
in the vicinity of the putative mycofactocin
biosynthesis operon in a number of Actinobacteria such
as Frankia sp. and Rhodococcus sp., in Pelotomaculum
thermopropionicum SI (Firmicutes), and in Geobacter
uraniireducens Rf4 (Deltaproteobacteria). The function
of this oxidoreductase is unknown.
Length = 645
Score = 29.7 bits (67), Expect = 5.1
Identities = 13/49 (26%), Positives = 21/49 (42%), Gaps = 4/49 (8%)
Query: 372 SGGVSSALAGKLFVVIGAGGAGKALAYGAKAKGARVVIANRTYDRAREL 420
+ + K +V+G G AG A A +G RV + ++R L
Sbjct: 370 TVTLPPPRRRKRVLVVGGGPAGLEAAATAARRGHRVTL----FEREDRL 414
>gnl|CDD|187615 cd05357, PR_SDR_c, pteridine reductase (PR), classical (c) SDRs.
Pteridine reductases (PRs), members of the SDR family,
catalyzes the NAD-dependent reduction of folic acid,
dihydrofolate and related compounds. In Leishmania,
pteridine reductase (PTR1) acts to circumvent the
anti-protozoan drugs that attack dihydrofolate reductase
activity. Proteins in this subgroup have an N-terminal
NAD-binding motif and a YxxxK active site motif, but
have an Asp instead of the usual upstream catalytic Ser.
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 have a 3-glycine N-terminal NAD(P)(H)-binding
pattern (typically, TGxxxGxG in classical SDRs and
TGxxGxxG in extended SDRs), while substrate binding is
in the C-terminal region. A critical catalytic Tyr
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) numbering), is often found in a
conserved YXXXK pattern. 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) or
additional Ser, contributing to the active site.
Substrates for these enzymes include sugars, steroids,
alcohols, and aromatic compounds. The standard reaction
mechanism is a proton relay involving the conserved Tyr
and Lys, as well as Asn (or Ser). Some SDR family
members, including 17 beta-hydroxysteroid dehydrogenase
contain an additional helix-turn-helix motif that is not
generally found among SDRs.
Length = 234
Score = 29.2 bits (66), Expect = 5.1
Identities = 19/57 (33%), Positives = 30/57 (52%), Gaps = 8/57 (14%)
Query: 390 GGA---GKALAYGAKAKGARVVI-ANRTYDRARELAETV---GGHALSL-ADLENFN 438
G A G+A+A A+G RVV+ NR+ A+ L + + A+ + ADL +F
Sbjct: 7 GAAKRIGRAIAEALAAEGYRVVVHYNRSEAEAQRLKDELNALRNSAVLVQADLSDFA 63
>gnl|CDD|219686 pfam07992, Pyr_redox_2, Pyridine nucleotide-disulphide
oxidoreductase. This family includes both class I and
class II oxidoreductases and also NADH oxidases and
peroxidases. This domain is actually a small NADH
binding domain within a larger FAD binding domain.
Length = 283
Score = 29.3 bits (66), Expect = 5.1
Identities = 10/25 (40%), Positives = 13/25 (52%)
Query: 385 VVIGAGGAGKALAYGAKAKGARVVI 409
V+IG G AG A A G +V +
Sbjct: 3 VIIGGGPAGLAAAIRLARLGLKVAL 27
>gnl|CDD|181120 PRK07792, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 306
Score = 29.4 bits (66), Expect = 5.1
Identities = 16/32 (50%), Positives = 20/32 (62%), Gaps = 1/32 (3%)
Query: 379 LAGKLFVVIGAG-GAGKALAYGAKAKGARVVI 409
L+GK+ VV GA G G+A A G GA VV+
Sbjct: 10 LSGKVAVVTGAAAGLGRAEALGLARLGATVVV 41
>gnl|CDD|215442 PLN02827, PLN02827, Alcohol dehydrogenase-like.
Length = 378
Score = 29.5 bits (66), Expect = 5.2
Identities = 19/62 (30%), Positives = 28/62 (45%)
Query: 364 GLRGRLNVSGGVSSALAGKLFVVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAET 423
G+ L + V+ G V+ G G G ++A GAK +GA +I E A+T
Sbjct: 177 GVAAGLGAAWNVADVSKGSSVVIFGLGTVGLSVAQGAKLRGASQIIGVDINPEKAEKAKT 236
Query: 424 VG 425
G
Sbjct: 237 FG 238
>gnl|CDD|132407 TIGR03364, HpnW_proposed, FAD dependent oxidoreductase TIGR03364.
This clade of FAD dependent oxidoreductases (members of
the pfam01266 family) is syntenically associated with a
family of proposed phosphonatase-like enzymes
(TIGR03351) and is also found (less frequently) in
association with phosphonate transporter components. A
likely role for this enzyme involves the oxidative
deamination of an aminophosphonate differring slightly
from 2-aminoethylphosphonate, possibly
1-hydroxy-2-aminoethylphosphonate (see the comments for
TIGR03351). Many members of the larger FAD dependent
oxidoreductase family act as amino acid oxidative
deaminases.
Length = 365
Score = 29.6 bits (67), Expect = 5.2
Identities = 11/29 (37%), Positives = 17/29 (58%)
Query: 385 VVIGAGGAGKALAYGAKAKGARVVIANRT 413
+++GAG G A AY A +G V + R+
Sbjct: 4 IIVGAGILGLAHAYAAARRGLSVTVIERS 32
>gnl|CDD|236099 PRK07791, PRK07791, short chain dehydrogenase; Provisional.
Length = 286
Score = 29.3 bits (66), Expect = 5.4
Identities = 16/35 (45%), Positives = 22/35 (62%), Gaps = 1/35 (2%)
Query: 376 SSALAGKLFVVIGAG-GAGKALAYGAKAKGARVVI 409
L G++ +V GAG G G+A A A+GARVV+
Sbjct: 1 MGLLDGRVVIVTGAGGGIGRAHALAFAAEGARVVV 35
>gnl|CDD|232901 TIGR00275, TIGR00275, flavoprotein, HI0933 family. The model when
searched with a partial length search brings in proteins
with a dinucleotide-binding motif (Rossman fold) over
the initial 40 residues of the model, including
oxidoreductases and dehydrogenases. Partially
characterized members include an FAD-binding protein
from Bacillus cereus and flavoprotein HI0933 from
Haemophilus influenzae [Unknown function, Enzymes of
unknown specificity].
Length = 400
Score = 29.5 bits (67), Expect = 5.4
Identities = 14/63 (22%), Positives = 28/63 (44%), Gaps = 5/63 (7%)
Query: 385 VVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAETVGG-----HALSLADLENFNP 439
++IG G AG A A +G V++ + ++L + GG ++ + + P
Sbjct: 1 IIIGGGAAGLMAAITAAREGLSVLLLEKNKKIGKKLLISGGGRCNLTNSCPTPEFVAYYP 60
Query: 440 EDG 442
+G
Sbjct: 61 RNG 63
>gnl|CDD|223643 COG0569, TrkA, K+ transport systems, NAD-binding component
[Inorganic ion transport and metabolism].
Length = 225
Score = 29.2 bits (66), Expect = 5.4
Identities = 15/47 (31%), Positives = 27/47 (57%), Gaps = 1/47 (2%)
Query: 384 FVVIGAGGAGKALAYGAKAKGARVVIANRTYDRARE-LAETVGGHAL 429
++IGAG G+++A +G VV+ +R +R E LA+ + H +
Sbjct: 3 IIIIGAGRVGRSVARELSEEGHNVVLIDRDEERVEEFLADELDTHVV 49
>gnl|CDD|187611 cd05353, hydroxyacyl-CoA-like_DH_SDR_c-like, (3R)-hydroxyacyl-CoA
dehydrogenase-like, classical(c)-like SDRs. Beta
oxidation of fatty acids in eukaryotes occurs by a
four-reaction cycle, that may take place in mitochondria
or in peroxisomes. (3R)-hydroxyacyl-CoA dehydrogenase is
part of rat peroxisomal multifunctional MFE-2, it is a
member of the NAD-dependent SDRs, but contains an
additional small C-terminal domain that completes the
active site pocket and participates in dimerization. The
atypical, additional C-terminal extension allows for
more extensive dimerization contact than other SDRs.
MFE-2 catalyzes the second and third reactions of the
peroxisomal beta oxidation cycle. Proteins in this
subgroup have a typical catalytic triad, but have a His
in place of the usual upstream Asn. This subgroup also
contains members identified as 17-beta-hydroxysteroid
dehydrogenases, including human peroxisomal
17-beta-hydroxysteroid dehydrogenase type 4 (17beta-HSD
type 4, aka MFE-2, encoded by HSD17B4 gene) which is
involved in fatty acid beta-oxidation and steroid
metabolism. This subgroup also includes two SDR domains
of the Neurospora crassa and Saccharomyces cerevisiae
multifunctional beta-oxidation protein (MFP, aka Fox2).
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 have a 3-glycine N-terminal NAD(P)(H)-binding
pattern (typically, TGxxxGxG in classical SDRs and
TGxxGxxG in extended SDRs), while substrate binding is
in the C-terminal region. A critical catalytic Tyr
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) numbering), is often found in a
conserved YXXXK pattern. 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) or
additional Ser, contributing to the active site.
Substrates for these enzymes include sugars, steroids,
alcohols, and aromatic compounds. The standard reaction
mechanism is a proton relay involving the conserved Tyr
and Lys, as well as Asn (or Ser). Some SDR family
members, including 17 beta-hydroxysteroid dehydrogenase
contain an additional helix-turn-helix motif that is not
generally found among SDRs.
Length = 250
Score = 29.2 bits (66), Expect = 5.4
Identities = 26/85 (30%), Positives = 40/85 (47%), Gaps = 9/85 (10%)
Query: 381 GKLFVVIGAGGA-GKALAYGAKAKGARVVIANRTYDRARELAETVGGHALSLADL--ENF 437
G++ +V GAGG G+A A +GA+VV+ + DR G + S AD +
Sbjct: 5 GRVVLVTGAGGGLGRAYALAFAERGAKVVVNDLGGDRKGS------GKSSSAADKVVDEI 58
Query: 438 NPEDGMILANTTSIGMQPKVDETPI 462
G +AN S+ K+ +T I
Sbjct: 59 KAAGGKAVANYDSVEDGEKIVKTAI 83
>gnl|CDD|176257 cd08297, CAD3, Cinnamyl alcohol dehydrogenases (CAD). These
alcohol dehydrogenases are related to the cinnamyl
alcohol dehydrogenases (CAD), members of the medium
chain dehydrogenase/reductase family.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. Cinnamyl alcohol dehydrogenases
(CAD) reduce cinnamaldehydes to cinnamyl alcohols in the
last step of monolignal metabolism in plant cells walls.
CAD binds 2 zinc ions and is NADPH- dependent. CAD
family members are also found in non-plant species, e.g.
in yeast where they have an aldehyde reductase activity.
The medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 341
Score = 29.4 bits (67), Expect = 5.5
Identities = 21/46 (45%), Positives = 25/46 (54%), Gaps = 4/46 (8%)
Query: 385 VVIGAGGA-GK-ALAYGAKAKGARVVIANRTYDRARELAETVGGHA 428
V+ GAGG G + Y AKA G R VIA D ELA+ +G A
Sbjct: 170 VISGAGGGLGHLGVQY-AKAMGLR-VIAIDVGDEKLELAKELGADA 213
>gnl|CDD|183773 PRK12824, PRK12824, acetoacetyl-CoA reductase; Provisional.
Length = 245
Score = 29.3 bits (66), Expect = 5.5
Identities = 15/46 (32%), Positives = 22/46 (47%), Gaps = 2/46 (4%)
Query: 382 KLFVVIGA-GGAGKALAYGAKAKGARVVIANRT-YDRARELAETVG 425
K+ +V GA G G A+A G RV+ + D A++ E G
Sbjct: 3 KIALVTGAKRGIGSAIARELLNDGYRVIATYFSGNDCAKDWFEEYG 48
>gnl|CDD|107338 cd06343, PBP1_ABC_ligand_binding_like_8, Type I periplasmic
ligand-binding domain of uncharacterized ABC (ATPase
Binding Cassette)-type active transport systems that are
predicted to be involved in uptake of amino acids,
peptides, or inorganic ions. This subgroup includes the
type I periplasmic ligand-binding domain of
uncharacterized ABC (ATPase Binding Cassette)-type
active transport systems that are predicted to be
involved in uptake of amino acids, peptides, or
inorganic ions. This subgroup has high sequence
similarity to members of the family of hydrophobic amino
acid transporters (HAAT), such as
leucine/isoleucine/valine binding protein (LIVBP);
however its ligand specificity has not been determined
experimentally.
Length = 362
Score = 29.5 bits (67), Expect = 5.6
Identities = 12/28 (42%), Positives = 19/28 (67%)
Query: 148 YTPSVEDLSNLVARIQASGADIVKFATT 175
Y + D + VA+++A+GAD+V ATT
Sbjct: 181 YEVTEPDFDSQVAKLKAAGADVVVLATT 208
>gnl|CDD|240655 cd12178, 2-Hacid_dh_13, Putative D-isomer specific 2-hydroxyacid
dehydrogenases, NAD-binding and catalytic domains.
2-Hydroxyacid dehydrogenases catalyze the conversion of
a wide variety of D-2-hydroxy acids to their
corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 317
Score = 29.5 bits (67), Expect = 5.6
Identities = 16/35 (45%), Positives = 22/35 (62%)
Query: 379 LAGKLFVVIGAGGAGKALAYGAKAKGARVVIANRT 413
LAGK +IG G G+A+A AKA G +++ NR
Sbjct: 142 LAGKTLGIIGMGRIGQAVARRAKAFGMKILYYNRH 176
>gnl|CDD|235990 PRK07326, PRK07326, short chain dehydrogenase; Provisional.
Length = 237
Score = 29.2 bits (66), Expect = 5.7
Identities = 20/68 (29%), Positives = 31/68 (45%), Gaps = 4/68 (5%)
Query: 377 SALAGKLFVVIGAG-GAGKALAYGAKAKGARVVIANRTYDRARELAETVG--GHALSLA- 432
+L GK+ ++ G G G A+A A+G +V I R E A + G+ L LA
Sbjct: 2 MSLKGKVALITGGSKGIGFAIAEALLAEGYKVAITARDQKELEEAAAELNNKGNVLGLAA 61
Query: 433 DLENFNPE 440
D+ +
Sbjct: 62 DVRDEADV 69
>gnl|CDD|187646 cd08942, RhlG_SDR_c, RhlG and related beta-ketoacyl reductases,
classical (c) SDRs. Pseudomonas aeruginosa RhlG is an
SDR-family beta-ketoacyl reductase involved in
Rhamnolipid biosynthesis. RhlG is similar to but
distinct from the FabG family of beta-ketoacyl-acyl
carrier protein (ACP) of type II fatty acid synthesis.
RhlG and related proteins are classical SDRs, with a
canonical active site tetrad and glycine-rich
NAD(P)-binding motif. 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 = 250
Score = 29.4 bits (66), Expect = 5.7
Identities = 19/49 (38%), Positives = 27/49 (55%), Gaps = 5/49 (10%)
Query: 379 LAGKLFVVIGAG-GAGKALAYGAKAKGARVVIANRT----YDRARELAE 422
+AGK+ +V G G G+ +A G GARV+I+ R D A EL+
Sbjct: 4 VAGKIVLVTGGSRGIGRMIAQGFLEAGARVIISARKAEACADAAEELSA 52
>gnl|CDD|131083 TIGR02028, ChlP, geranylgeranyl reductase. This model represents
the reductase which acts reduces the geranylgeranyl
group to the phytyl group in the side chain of
chlorophyll. It is unclear whether the enzyme has a
preference for acting before or after the attachment of
the side chain to chlorophyllide a by chlorophyll
synthase. This clade is restricted to plants and
cyanobacteria to separate it from the homologues which
act in the biosynthesis of bacteriochlorophyll
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Chlorophyll and bacteriochlorphyll].
Length = 398
Score = 29.5 bits (66), Expect = 5.7
Identities = 30/122 (24%), Positives = 48/122 (39%), Gaps = 19/122 (15%)
Query: 386 VIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAETVGGHALSLADLENFNPEDGMIL 445
V+G G AG + A + G + + R D A+ G A+ L ++ F +I
Sbjct: 5 VVGGGPAGASAAETLASAGIQTFLLERKPDNAKPC-----GGAIPLCMVDEFALPRDIID 59
Query: 446 ANTTSIGM-QPKVDETPIPKHALGHYALVFDAVYTPKITR------LLREAEESGATIVS 498
T + M P I L + Y + R L R A ++GAT+++
Sbjct: 60 RRVTKMKMISPSNIAVDI-GRTLKEHE------YIGMLRREVLDSFLRRRAADAGATLIN 112
Query: 499 GL 500
GL
Sbjct: 113 GL 114
>gnl|CDD|133418 cd00300, LDH_like, L-lactate dehydrogenase-like enzymes. Members
of this subfamily are tetrameric NAD-dependent
2-hydroxycarboxylate dehydrogenases including LDHs,
L-2-hydroxyisocaproate dehydrogenases (L-HicDH), and
LDH-like malate dehydrogenases (MDH). Dehydrogenases
catalyze the conversion of carbonyl compounds to
alcohols or amino acids. LDHs catalyze the last step of
glycolysis in which pyruvate is converted to L-lactate.
Vertebrate LDHs are non-allosteric, but some bacterial
LDHs are activated by an allosteric effector such as
fructose-1,6-bisphosphate. L-HicDH catalyzes the
conversion of a variety of 2-oxo carboxylic acids with
medium-sized aliphatic or aromatic side chains. MDH is
one of the key enzymes in the citric acid cycle,
facilitating both the conversion of malate to
oxaloacetate and replenishing levels of oxalacetate by
reductive carboxylation of pyruvate. The LDH-like
subfamily is part of the NAD(P)-binding Rossmann fold
superfamily, which includes a wide variety of protein
families including the NAD(P)-binding domains of alcohol
dehydrogenases, tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate dehydrogenases,
formate/glycerate dehydrogenases, siroheme synthases,
6-phosphogluconate dehydrogenases, aminoacid
dehydrogenases, repressor rex, and NAD-binding potassium
channel domains, among others.
Length = 300
Score = 29.2 bits (66), Expect = 5.8
Identities = 18/51 (35%), Positives = 25/51 (49%), Gaps = 9/51 (17%)
Query: 385 VVIGAGGAGKALAYGAKAKGARVVIANRT--YDRARELAETVGGHALSLAD 433
+IGAG G A+A+ AKG +A+ D E A+ G AL L+
Sbjct: 2 TIIGAGNVGAAVAFALIAKG----LASELVLVDVNEEKAK---GDALDLSH 45
>gnl|CDD|107263 cd06268, PBP1_ABC_transporter_LIVBP_like, Periplasmic binding
domain of ATP-binding cassette transporter-like systems
that belong to the type I periplasmic binding fold
protein superfamily. Periplasmic binding domain of
ATP-binding cassette transporter-like systems that
belong to the type I periplasmic binding fold protein
superfamily. They are mostly present in archaea and
eubacteria, and are primarily involved in scavenging
solutes from the environment. ABC-type transporters
couple ATP hydrolysis with the uptake and efflux of a
wide range of substrates across bacterial membranes,
including amino acids, peptides, lipids and sterols, and
various drugs. These systems are comprised of
transmembrane domains, nucleotide binding domains, and
in most bacterial uptake systems, periplasmic binding
proteins (PBPs) which transfer the ligand to the
extracellular gate of the transmembrane domains. These
PBPs bind their substrates selectively and with high
affinity. Members of this group include ABC-type
Leucine-Isoleucine-Valine-Binding Proteins (LIVBP),
which are homologous to the aliphatic amidase
transcriptional repressor, AmiC, of Pseudomonas
aeruginosa. The uncharacterized periplasmic components
of various ABC-type transport systems are included in
this group.
Length = 298
Score = 29.3 bits (66), Expect = 5.8
Identities = 12/40 (30%), Positives = 19/40 (47%)
Query: 148 YTPSVEDLSNLVARIQASGADIVKFATTALDITDVARVFQ 187
Y P D S L+A+++A+G D V A D + +
Sbjct: 172 YPPGATDFSPLIAKLKAAGPDAVFLAGYGGDAALFLKQAR 211
>gnl|CDD|133444 cd01075, NAD_bind_Leu_Phe_Val_DH, NAD(P) binding domain of leucine
dehydrogenase, phenylalanine dehydrogenase, and valine
dehydrogenase. Amino acid dehydrogenase (DH) is a
widely distributed family of enzymes that catalyzes the
oxidative deamination of an amino acid to its keto acid
and ammonia with concomitant reduction of NADP+. For
example, leucine DH catalyzes the reversible oxidative
deamination of L-leucine and several other straight or
branched chain amino acids to the corresponding
2-oxoacid derivative. Amino acid DH -like NAD(P)-binding
domains are members of the Rossmann fold superfamily and
include glutamate, leucine, and phenylalanine DHs,
methylene tetrahydrofolate DH,
methylene-tetrahydromethanopterin DH,
methylene-tetrahydropholate DH/cyclohydrolase, Shikimate
DH-like proteins, malate oxidoreductases, and glutamyl
tRNA reductase. Amino acid DHs catalyze the deamination
of amino acids to keto acids with NAD(P)+ as a cofactor.
The NAD(P)-binding Rossmann fold superfamily includes a
wide variety of protein families including NAD(P)-
binding domains of alcohol DHs, tyrosine-dependent
oxidoreductases, glyceraldehyde-3-phosphate DH,
lactate/malate DHs, formate/glycerate DHs, siroheme
synthases, 6-phosphogluconate DH, amino acid DHs,
repressor rex, NAD-binding potassium channel domain,
CoA-binding, and ornithine cyclodeaminase-like domains.
These domains have an alpha-beta-alpha configuration.
NAD binding involves numerous hydrogen and van der Waals
contacts.
Length = 200
Score = 29.1 bits (66), Expect = 5.9
Identities = 15/47 (31%), Positives = 22/47 (46%)
Query: 379 LAGKLFVVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAETVG 425
L GK V G G G LA +GA++++A+ + AE G
Sbjct: 26 LEGKTVAVQGLGKVGYKLAEHLLEEGAKLIVADINEEAVARAAELFG 72
>gnl|CDD|237100 PRK12429, PRK12429, 3-hydroxybutyrate dehydrogenase; Provisional.
Length = 258
Score = 29.1 bits (66), Expect = 5.9
Identities = 22/58 (37%), Positives = 31/58 (53%), Gaps = 4/58 (6%)
Query: 379 LAGKLFVVIGAG-GAGKALAYGAKAKGARVVIANRTYDRARELAET---VGGHALSLA 432
L GK+ +V GA G G +A +GA+VVIA+ + A AE GG A+ +A
Sbjct: 2 LKGKVALVTGAASGIGLEIALALAKEGAKVVIADLNDEAAAAAAEALQKAGGKAIGVA 59
>gnl|CDD|240657 cd12180, 2-Hacid_dh_15, Putative D-isomer specific 2-hydroxyacid
dehydrogenases, NAD-binding and catalytic domains.
2-Hydroxyacid dehydrogenases catalyze the conversion of
a wide variety of D-2-hydroxy acids to their
corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 308
Score = 29.2 bits (66), Expect = 6.0
Identities = 15/35 (42%), Positives = 20/35 (57%)
Query: 379 LAGKLFVVIGAGGAGKALAYGAKAKGARVVIANRT 413
LAG ++G G G+ALA A A G RV+ R+
Sbjct: 133 LAGSTLGIVGFGAIGQALARRALALGMRVLALRRS 167
>gnl|CDD|187664 cd09763, DHRS1-like_SDR_c, human dehydrogenase/reductase (SDR
family) member 1 (DHRS1) -like, classical (c) SDRs.
This subgroup includes human DHRS1 and related proteins.
These are members of the classical SDR family, with a
canonical Gly-rich NAD-binding motif and the typical
YXXXK active site motif. However, the rest of the
catalytic tetrad is not strongly conserved. DHRS1 mRNA
has been detected in many tissues, liver, heart,
skeletal muscle, kidney and pancreas; a longer
transcript is predominantly expressed in the liver , a
shorter one in the heart. 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 have a 3-glycine N-terminal
NAD(P)(H)-binding pattern (typically, TGxxxGxG in
classical SDRs and TGxxGxxG in extended SDRs), while
substrate binding is in the C-terminal region. A
critical catalytic Tyr residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering), is often found in a conserved YXXXK pattern.
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) or additional Ser,
contributing to the active site. Substrates for these
enzymes include sugars, steroids, alcohols, and aromatic
compounds. The standard reaction mechanism is a proton
relay involving the conserved Tyr and Lys, as well as
Asn (or Ser). Some SDR family members, including 17
beta-hydroxysteroid dehydrogenase contain an additional
helix-turn-helix motif that is not generally found among
SDRs.
Length = 265
Score = 29.3 bits (66), Expect = 6.0
Identities = 15/36 (41%), Positives = 20/36 (55%), Gaps = 1/36 (2%)
Query: 379 LAGKLFVVIGAG-GAGKALAYGAKAKGARVVIANRT 413
L+GK+ +V GA G G+ +A GA V I RT
Sbjct: 1 LSGKIALVTGASRGIGRGIALQLGEAGATVYITGRT 36
>gnl|CDD|236046 PRK07538, PRK07538, hypothetical protein; Provisional.
Length = 413
Score = 29.5 bits (67), Expect = 6.1
Identities = 22/92 (23%), Positives = 34/92 (36%), Gaps = 27/92 (29%)
Query: 385 VVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAET-VG----GHAL-SLADLENFN 438
++ G G G LA +G VV+ ++ A EL VG HA+ LA+L
Sbjct: 4 LIAGGGIGGLTLALTLHQRGIEVVV----FEAAPELRPLGVGINLLPHAVRELAEL---- 55
Query: 439 PEDGMILANTTSIGMQPKVDETPIPKHALGHY 470
G+ +D I L ++
Sbjct: 56 -------------GLLDALDAIGIRTRELAYF 74
>gnl|CDD|144338 pfam00698, Acyl_transf_1, Acyl transferase domain.
Length = 319
Score = 29.3 bits (66), Expect = 6.1
Identities = 13/52 (25%), Positives = 24/52 (46%)
Query: 130 RGKKPEKCKVIVSSHNYQYTPSVEDLSNLVARIQASGADIVKFATTALDITD 181
RG + V +SH+ Q + L+ +A I + ++TT+ D +D
Sbjct: 179 RGVRARVIAVDYASHSPQVEAIGDALALALADIAPRTPRVPFYSTTSGDPSD 230
>gnl|CDD|236034 PRK07502, PRK07502, cyclohexadienyl dehydrogenase; Validated.
Length = 307
Score = 29.2 bits (66), Expect = 6.1
Identities = 21/59 (35%), Positives = 27/59 (45%), Gaps = 10/59 (16%)
Query: 386 VIGAGGAGKALAYGAKAKG--ARVVIANR---TYDRAREL-----AETVGGHALSLADL 434
+IG G G +LA + G +V A+R T RAREL T A+ ADL
Sbjct: 11 LIGIGLIGSSLARAIRRLGLAGEIVGADRSAETRARARELGLGDRVTTSAAEAVKGADL 69
>gnl|CDD|181334 PRK08263, PRK08263, short chain dehydrogenase; Provisional.
Length = 275
Score = 29.2 bits (66), Expect = 6.2
Identities = 19/53 (35%), Positives = 25/53 (47%), Gaps = 1/53 (1%)
Query: 381 GKLFVVIGAG-GAGKALAYGAKAKGARVVIANRTYDRARELAETVGGHALSLA 432
K++ + GA G G+A A +G RVV R +LAE G L LA
Sbjct: 3 EKVWFITGASRGFGRAWTEAALERGDRVVATARDTATLADLAEKYGDRLLPLA 55
>gnl|CDD|181371 PRK08306, PRK08306, dipicolinate synthase subunit A; Reviewed.
Length = 296
Score = 29.0 bits (66), Expect = 6.2
Identities = 18/51 (35%), Positives = 24/51 (47%), Gaps = 3/51 (5%)
Query: 386 VIGAGGAGKALAYGAKAKGARV-VIANRTYDRARELAETVGGHALSLADLE 435
V+G G G LA KA GA V V A ++ AR +G L++L
Sbjct: 157 VLGFGRTGMTLARTLKALGANVTVGARKSAHLAR--ITEMGLSPFHLSELA 205
>gnl|CDD|181414 PRK08410, PRK08410, 2-hydroxyacid dehydrogenase; Provisional.
Length = 311
Score = 29.2 bits (66), Expect = 6.4
Identities = 14/30 (46%), Positives = 20/30 (66%)
Query: 379 LAGKLFVVIGAGGAGKALAYGAKAKGARVV 408
+ GK + +IG G GK +A A+A GA+VV
Sbjct: 143 IKGKKWGIIGLGTIGKRVAKIAQAFGAKVV 172
>gnl|CDD|240649 cd12172, PGDH_like_2, Putative D-3-Phosphoglycerate Dehydrogenases,
NAD-binding and catalytic domains. Phosphoglycerate
dehydrogenases (PGDHs) catalyze the initial step in the
biosynthesis of L-serine from D-3-phosphoglycerate.
PGDHs come in 3 distinct structural forms, with this
first group being related to 2-hydroxy acid
dehydrogenases, sharing structural similarity to formate
and glycerate dehydrogenases of the D-specific
2-hydroxyacid dehydrogenase superfamily, which also
include groups such as L-alanine dehydrogenase and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. Many, not all, members of this family are
dimeric.
Length = 306
Score = 29.0 bits (66), Expect = 6.4
Identities = 19/56 (33%), Positives = 27/56 (48%), Gaps = 2/56 (3%)
Query: 379 LAGKLFVVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAETVGGHALSLADL 434
L GK +IG G GKA+A G +V+ + D E A+ G +SL +L
Sbjct: 140 LYGKTLGIIGLGRIGKAVARRLSGFGMKVLAYDPYPD--EEFAKEHGVEFVSLEEL 193
>gnl|CDD|236313 PRK08618, PRK08618, ornithine cyclodeaminase; Validated.
Length = 325
Score = 29.3 bits (66), Expect = 6.5
Identities = 26/83 (31%), Positives = 37/83 (44%), Gaps = 13/83 (15%)
Query: 356 GAISAIEDG-----LR-GRLNVSGGVSSALA---GKLFVVIGAGGAGKAL--AYGAKAKG 404
G + AI DG +R G L SG + LA K +IG GG K A A
Sbjct: 95 GEVLAILDGTYLTQIRTGAL--SGVATKYLAREDAKTLCLIGTGGQAKGQLEAVLAVRDI 152
Query: 405 ARVVIANRTYDRARELAETVGGH 427
RV + +RT+++A A+ +
Sbjct: 153 ERVRVYSRTFEKAYAFAQEIQSK 175
>gnl|CDD|181335 PRK08264, PRK08264, short chain dehydrogenase; Validated.
Length = 238
Score = 29.1 bits (66), Expect = 6.6
Identities = 13/33 (39%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 379 LAGKLFVVIGA-GGAGKALAYGAKAKGARVVIA 410
+ GK+ +V GA G G+A A+GA V A
Sbjct: 4 IKGKVVLVTGANRGIGRAFVEQLLARGAAKVYA 36
>gnl|CDD|107261 cd04509, PBP1_ABC_transporter_GCPR_C_like, Family C of G-protein
coupled receptors and their close homologs, the type I
periplasmic-binding proteins of ATP-binding cassette
transporter-like systems. This CD includes members of
the family C of G-protein coupled receptors and their
close homologs, the type I periplasmic-binding proteins
of ATP-binding cassette transporter-like systems. The
family C GPCR includes glutamate/glycine-gated ion
channels such as the NMDA receptor, G-protein-coupled
receptors, metabotropic glutamate, GABA-B, calcium
sensing, phermone receptors, and atrial natriuretic
peptide-guanylate cyclase receptors. The glutamate
receptors that form cation-selective ion channels,
iGluR, can be classified into three different subgroups
according to their binding-affinity for the agonists
NMDA (N-methyl-D-asparate), AMPA
(alpha-amino-3-dihydro-5-methyl-3-oxo-4-
isoxazolepropionic acid), and kainate. L-glutamate is a
major neurotransmitter in the brain of vertebrates and
acts through either mGluRs or iGluRs. mGluRs subunits
possess seven transmembrane segments and a large
N-terminal extracellular domain. ABC-type
leucine-isoleucine-valine-binding protein (LIVBP) is a
bacterial periplasmic binding protein that has homology
with the amino-terminal domain of the glutamate-receptor
ion channels (iGluRs). The extracellular regions of
iGluRs are made of two PBP-like domains in tandem, a
LIVBP-like domain that constitutes the N terminus -
which is included in this CD - followed by a domain
related to lysine-arginine-ornithine-binding protein
(LAOBP) that belongs to the type II periplasmic binding
fold protein superfamily. The uncharacterized
periplasmic components of various ABC-type transport
systems are included in this group.
Length = 299
Score = 29.0 bits (65), Expect = 6.6
Identities = 14/88 (15%), Positives = 32/88 (36%), Gaps = 1/88 (1%)
Query: 148 YTPSVEDLSNLVARIQASGADIVKFATTALDITDVARVFQIT-VHSQVPIIGLVMGERGL 206
Y D ++L+ +++A+ D++ + D + + + PI+G+ +G +
Sbjct: 173 YPLGTTDFTSLLQKLKAAKPDVIVLCGSGEDAATILKQAAEAGLTGGYPILGITLGLSDV 232
Query: 207 ISRILCAKFGGFLTFGTLENGIVSAPGQ 234
+ G LT G
Sbjct: 233 LLEAGGEAAEGVLTGTPYFPGDPPPESF 260
>gnl|CDD|233700 TIGR02053, MerA, mercuric reductase. This model represents the
mercuric reductase found in the mer operon for the
detoxification of mercury compounds. MerA is a
FAD-containing flavoprotein which reduces Hg(II) to
Hg(0) utilizing NADPH [Cellular processes,
Detoxification].
Length = 463
Score = 29.3 bits (66), Expect = 6.7
Identities = 12/28 (42%), Positives = 15/28 (53%)
Query: 385 VVIGAGGAGKALAYGAKAKGARVVIANR 412
V+IG+G A A A A GA V + R
Sbjct: 4 VIIGSGAAAFAAAIKAAELGASVAMVER 31
>gnl|CDD|233018 TIGR00551, nadB, L-aspartate oxidase. L-aspartate oxidase is the B
protein, NadB, of the quinolinate synthetase complex.
Quinolinate synthetase makes a precursor of the pyridine
nucleotide portion of NAD. This model identifies
proteins that cluster as L-aspartate oxidase (a
flavoprotein difficult to separate from the set of
closely related flavoprotein subunits of succinate
dehydrogenase and fumarate reductase) by both UPGMA and
neighbor-joining trees. The most distant protein
accepted as an L-aspartate oxidase (NadB), that from
Pyrococcus horikoshii, not only clusters with other NadB
but is just one gene away from NadA [Biosynthesis of
cofactors, prosthetic groups, and carriers, Pyridine
nucleotides].
Length = 488
Score = 29.4 bits (66), Expect = 6.7
Identities = 28/134 (20%), Positives = 52/134 (38%), Gaps = 21/134 (15%)
Query: 385 VVIGAGGAGKALAYGAKAKGARVVIANR-TYDRARELAETVGGHALSLADLENFNPE--- 440
VVIG+G AG + A +G +V++ + A+ GG A LA+ ++ +
Sbjct: 6 VVIGSGAAGLSAALALADQGRVIVLSKAPVTEGNSFYAQ--GGIAAVLAETDSIDSHVED 63
Query: 441 ---------DGMILANTTSIGMQPKVDET----PIPKHALGHYALVFDAVYTPKITRLLR 487
D + S +H G YAL + ++ + R+L
Sbjct: 64 TLAAGAGICDREAVEFVVSDARSAVQWLVDQGVLFDRHEQGSYALTREGGHSYR--RILH 121
Query: 488 EAEESGATIVSGLE 501
A+ +G +++ L
Sbjct: 122 AADATGREVITTLV 135
>gnl|CDD|236111 PRK07843, PRK07843, 3-ketosteroid-delta-1-dehydrogenase; Reviewed.
Length = 557
Score = 29.2 bits (66), Expect = 6.9
Identities = 14/42 (33%), Positives = 18/42 (42%), Gaps = 8/42 (19%)
Query: 385 VVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAETVGG 426
VV+G+G AG A A +G V+ E A GG
Sbjct: 11 VVVGSGAAGMVAALTAAHRGLSTVVV--------EKAPHYGG 44
>gnl|CDD|240643 cd12166, 2-Hacid_dh_7, Putative D-isomer specific 2-hydroxyacid
dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 300
Score = 29.1 bits (66), Expect = 6.9
Identities = 18/73 (24%), Positives = 30/73 (41%), Gaps = 9/73 (12%)
Query: 375 VSSALAGKLFVVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAETVGGHALSLADL 434
+ +LA + +++G G G+A+ RV RT AR G + +L
Sbjct: 126 RTPSLADRRVLIVGYGSIGRAIERRLAPFEVRVTRVART---ARP-----GEQVHGIDEL 177
Query: 435 ENFNPE-DGMILA 446
PE D ++L
Sbjct: 178 PALLPEADVVVLI 190
>gnl|CDD|223523 COG0446, HcaD, Uncharacterized NAD(FAD)-dependent dehydrogenases
[General function prediction only].
Length = 415
Score = 29.1 bits (65), Expect = 7.1
Identities = 10/25 (40%), Positives = 14/25 (56%)
Query: 385 VVIGAGGAGKALAYGAKAKGARVVI 409
VV+GAG G A A +G +V +
Sbjct: 140 VVVGAGPIGLEAAEAAAKRGKKVTL 164
>gnl|CDD|176215 cd08253, zeta_crystallin, Zeta-crystallin with NADP-dependent
quinone reductase activity (QOR). Zeta-crystallin is a
eye lens protein with NADP-dependent quinone reductase
activity (QOR). It has been cited as a structural
component in mammalian eyes, but also has homology to
quinone reductases in unrelated species. QOR catalyzes
the conversion of a quinone and NAD(P)H to a
hydroquinone and NAD(P+. Quinones are cyclic diones
derived from aromatic compounds. Membrane bound QOR acts
in the respiratory chains of bacteria and mitochondria,
while soluble QOR acts to protect from toxic quinones
(e.g. DT-diaphorase) or as a soluble eye-lens protein in
some vertebrates (e.g. zeta-crystalin). QOR reduces
quinones through a semi-quinone intermediate via a
NAD(P)H-dependent single electron transfer. QOR is a
member of the medium chain dehydrogenase/reductase
family, but lacks the zinc-binding sites of the
prototypical alcohol dehydrogenases of this group.
Alcohol dehydrogenase in the liver converts ethanol and
NAD+ to acetaldehyde and NADH, while in yeast and some
other microorganisms ADH catalyzes the conversion
acetaldehyde to ethanol in alcoholic fermentation. ADH
is a member of the medium chain alcohol dehydrogenase
family (MDR), which has a NAD(P)(H)-binding domain in a
Rossmann fold of a beta-alpha form. The NAD(H)-binding
region is comprised of 2 structurally similar halves,
each of which contacts a mononucleotide. The N-terminal
catalytic domain has a distant homology to GroES. These
proteins typically form dimers (typically higher plants,
mammals) or tetramers (yeast, bacteria), and have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site, and a structural zinc in a lobe of
the catalytic domain. NAD(H)-binding occurs in the
cleft between the catalytic and coenzyme-binding domains
at the active site, and coenzyme binding induces a
conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
In human ADH catalysis, the zinc ion helps coordinate
the alcohol, followed by deprotonation of a histidine,
the ribose of NAD, a serine, then the alcohol, which
allows the transfer of a hydride to NAD+, creating NADH
and a zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 325
Score = 29.1 bits (66), Expect = 7.2
Identities = 18/52 (34%), Positives = 23/52 (44%), Gaps = 2/52 (3%)
Query: 378 ALAGKLFVVIGAGGA-GKALAYGAKAKGARVVIANRTYDRARELAETVGGHA 428
A AG+ +V G GA G A A+ GARV+ + EL G A
Sbjct: 142 AKAGETVLVHGGSGAVGHAAVQLARWAGARVIATASS-AEGAELVRQAGADA 192
>gnl|CDD|236056 PRK07576, PRK07576, short chain dehydrogenase; Provisional.
Length = 264
Score = 28.8 bits (65), Expect = 7.2
Identities = 16/53 (30%), Positives = 25/53 (47%), Gaps = 5/53 (9%)
Query: 379 LAGKLFVVIGAGGA---GKALAYGAKAKGARVVIANRTYDRARELAETVGGHA 428
AGK VV+G G A A+ A+A GA V +A+R+ ++ +
Sbjct: 7 FAGKNVVVVGGTSGINLGIAQAF-ARA-GANVAVASRSQEKVDAAVAQLQQAG 57
>gnl|CDD|213181 cd03214, ABC_Iron-Siderophores_B12_Hemin, ATP-binding component of
iron-siderophores, vitamin B12 and hemin transporters
and related proteins. ABC transporters, involved in the
uptake of siderophores, heme, and vitamin B12, are
widely conserved in bacteria and archaea. Only very few
species lack representatives of the siderophore family
transporters. The E. coli BtuCD protein is an ABC
transporter mediating vitamin B12 uptake. The two
ATP-binding cassettes (BtuD) are in close contact with
each other, as are the two membrane-spanning subunits
(BtuC); this arrangement is distinct from that observed
for the E. coli lipid flippase MsbA. The BtuC subunits
provide 20 transmembrane helices grouped around a
translocation pathway that is closed to the cytoplasm by
a gate region, whereas the dimer arrangement of the BtuD
subunits resembles the ATP-bound form of the Rad50 DNA
repair enzyme. A prominent cytoplasmic loop of BtuC
forms the contact region with the ATP-binding cassette
and represent a conserved motif among the ABC
transporters.
Length = 180
Score = 28.6 bits (65), Expect = 7.4
Identities = 19/74 (25%), Positives = 31/74 (41%), Gaps = 10/74 (13%)
Query: 374 GVS-SALAGKLFVVIGAGGAGK-----ALAYGAKAKGARVVIANRTYDR--ARELAETVG 425
+S S AG++ ++G GAGK LA K +++ + +ELA +
Sbjct: 17 DLSLSIEAGEIVGILGPNGAGKSTLLKTLAGLLKPSSGEILLDGKDLASLSPKELARKIA 76
Query: 426 --GHALSLADLENF 437
AL L L +
Sbjct: 77 YVPQALELLGLAHL 90
>gnl|CDD|225276 COG2413, COG2413, Predicted nucleotidyltransferase [General
function prediction only].
Length = 228
Score = 28.6 bits (64), Expect = 7.5
Identities = 19/71 (26%), Positives = 26/71 (36%), Gaps = 13/71 (18%)
Query: 217 GFLTFGTLENGIVSAPGQPTIKDLLDLYNF-------------RQMGPDTKVFGIIGKPV 263
G+L LE VS P L+ Y F R G + ++ II
Sbjct: 95 GYLALDDLEERTVSFPLTRPTDRELEFYAFGGTVDPEGLEEKERVPGVNKRLILIIPTER 154
Query: 264 GHSKSPILYNE 274
GH + P+L E
Sbjct: 155 GHVEIPVLGRE 165
>gnl|CDD|235591 PRK05755, PRK05755, DNA polymerase I; Provisional.
Length = 880
Score = 29.3 bits (67), Expect = 7.5
Identities = 13/55 (23%), Positives = 25/55 (45%), Gaps = 1/55 (1%)
Query: 124 EFNDSIRGKKPEKCKVIVSSHNYQYTPSVEDLSNLVARIQASGADIVKFATTALD 178
EF S+ + + +Y+ E+L +A+++A+G TT+LD
Sbjct: 275 EFK-SLLRRAAAAEAAPLDEEDYETILDEEELEAWLAKLKAAGLFAFDTETTSLD 328
>gnl|CDD|235800 PRK06436, PRK06436, glycerate dehydrogenase; Provisional.
Length = 303
Score = 29.1 bits (65), Expect = 7.6
Identities = 13/36 (36%), Positives = 19/36 (52%)
Query: 379 LAGKLFVVIGAGGAGKALAYGAKAKGARVVIANRTY 414
L K ++G GG G+ +A AKA G + R+Y
Sbjct: 120 LYNKSLGILGYGGIGRRVALLAKAFGMNIYAYTRSY 155
>gnl|CDD|239432 cd03316, MR_like, Mandelate racemase (MR)-like subfamily of the
enolase superfamily. Enzymes of this subgroup share
three conserved carboxylate ligands for the essential
divalent metal ion (usually Mg2+), two aspartates and a
glutamate, and conserved catalytic residues, a
Lys-X-Lys motif and a conserved histidine-aspartate
dyad. Members of the MR subgroup are mandelate racemase,
D-glucarate/L-idarate dehydratase (GlucD),
D-altronate/D-mannonate dehydratase , D-galactonate
dehydratase (GalD) , D-gluconate dehydratase (GlcD), and
L-rhamnonate dehydratase (RhamD).
Length = 357
Score = 29.1 bits (66), Expect = 7.6
Identities = 18/61 (29%), Positives = 25/61 (40%), Gaps = 8/61 (13%)
Query: 131 GKKPEKCKVIVSSHNYQYTPSVEDLSNLVARIQASGADIVKFATTALDIT------DVAR 184
GK ++ +V S Y +P E+L+ R A G VK D D+AR
Sbjct: 121 GKVRDRVRVYASGGGYDDSP--EELAEEAKRAVAEGFTAVKLKVGGPDSGGEDLREDLAR 178
Query: 185 V 185
V
Sbjct: 179 V 179
>gnl|CDD|224996 COG2085, COG2085, Predicted dinucleotide-binding enzymes [General
function prediction only].
Length = 211
Score = 28.5 bits (64), Expect = 7.7
Identities = 12/37 (32%), Positives = 16/37 (43%)
Query: 385 VVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELA 421
+IG G G ALA G V+I + +A A
Sbjct: 5 AIIGTGNIGSALALRLAKAGHEVIIGSSRGPKALAAA 41
>gnl|CDD|183787 PRK12844, PRK12844, 3-ketosteroid-delta-1-dehydrogenase; Reviewed.
Length = 557
Score = 29.3 bits (66), Expect = 7.8
Identities = 10/26 (38%), Positives = 13/26 (50%)
Query: 384 FVVIGAGGAGKALAYGAKAKGARVVI 409
VV+G+GG G A A G +I
Sbjct: 9 VVVVGSGGGGMCAALAAADSGLEPLI 34
>gnl|CDD|187647 cd08943, R1PA_ADH_SDR_c, rhamnulose-1-phosphate aldolase/alcohol
dehydrogenase, classical (c) SDRs. This family has
bifunctional proteins with an N-terminal aldolase and a
C-terminal classical SDR domain. One member is
identified as a rhamnulose-1-phosphate aldolase/alcohol
dehydrogenase. The SDR domain has a canonical SDR
glycine-rich NAD(P) binding motif and a match to the
characteristic active site triad. However, it lacks an
upstream active site Asn typical of SDRs. 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 = 250
Score = 28.9 bits (65), Expect = 7.8
Identities = 20/53 (37%), Positives = 30/53 (56%), Gaps = 1/53 (1%)
Query: 381 GKLFVVIG-AGGAGKALAYGAKAKGARVVIANRTYDRARELAETVGGHALSLA 432
GK+ +V G A G G A+A A+GA VV+A+ + A ++AE G +L
Sbjct: 1 GKVALVTGGASGIGLAIAKRLAAEGAAVVVADIDPEIAEKVAEAAQGGPRALG 53
>gnl|CDD|240663 cd12187, LDH_like_1, D-Lactate and related Dehydrogenase like
proteins, NAD-binding and catalytic domains. D-Lactate
dehydrogenase (LDH) catalyzes the interconversion of
pyruvate and lactate, and is a member of the
2-hydroxyacid dehydrogenase family. LDH is homologous to
D-2-Hydroxyisocaproic acid dehydrogenase(D-HicDH) and
shares the 2 domain structure of formate dehydrogenase.
D-2-hydroxyisocaproate dehydrogenase-like (HicDH)
proteins are NAD-dependent members of the
hydroxycarboxylate dehydrogenase family, and share the
Rossmann fold typical of many NAD binding proteins.
HicDH from Lactobacillus casei forms a monomer and
catalyzes the reaction R-CO-COO(-) + NADH + H+ to
R-COH-COO(-) + NAD+. D-HicDH, like the structurally
distinct L-HicDH, exhibits low side-chain R specificity,
accepting a wide range of 2-oxocarboxylic acid side
chains. Formate/glycerate and related dehydrogenases of
the D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-Adenosylhomocysteine Hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain.
Length = 329
Score = 28.8 bits (65), Expect = 7.8
Identities = 26/74 (35%), Positives = 35/74 (47%), Gaps = 15/74 (20%)
Query: 363 DGLRGRLNVSGGVSSALAGKLFVVIGAGGAGKALAYGAKAKGARVVIANRTYDRA--REL 420
GLRG LAGK V+G G G+ +A A+ G +V+ YD EL
Sbjct: 130 AGLRGF---------ELAGKTLGVVGTGRIGRRVARIARGFGMKVL----AYDVVPDEEL 176
Query: 421 AETVGGHALSLADL 434
AE +G +SL +L
Sbjct: 177 AERLGFRYVSLEEL 190
>gnl|CDD|224789 COG1877, OtsB, Trehalose-6-phosphatase [Carbohydrate transport and
metabolism].
Length = 266
Score = 28.9 bits (65), Expect = 8.0
Identities = 38/201 (18%), Positives = 55/201 (27%), Gaps = 53/201 (26%)
Query: 144 HNYQYTPSVEDLSNLVARIQASGADIVKFATTALDITDVARVFQITVHSQVPIIGLVMGE 203
H P LS L AS V + + ++ R+F VP IGL+ E
Sbjct: 35 HPEAAVPDDRLLSLLQD--LASDPRNVVAIISGRSLAELERLFG------VPGIGLI-AE 85
Query: 204 RGLISRILCAKFGGFLTFGT-----------LENGIVSAPGQPT-IKDLLDLYNFRQMGP 251
G R K+ L LE + PG K ++R
Sbjct: 86 HGAEVRDPNGKWWINLAEEADLRWLKEVAAILEYYVERTPGSYIERKGFAVALHYRNAED 145
Query: 252 DTKVFGIIG----------------------KPVGHSKSPILYNEAFKSVGFNGVFVHLL 289
D + +P G SK + + F+G F
Sbjct: 146 DEGAALALAEAATLINELKLRVTPGKMVVELRPPGVSKGAAI-KYIMDELPFDGRFPIFA 204
Query: 290 VDDIAKFFQTYSSNDFAGFSC 310
DD+ D F+
Sbjct: 205 GDDLT---------DEDAFAA 216
>gnl|CDD|223429 COG0352, ThiE, Thiamine monophosphate synthase [Coenzyme
metabolism].
Length = 211
Score = 28.8 bits (65), Expect = 8.1
Identities = 25/114 (21%), Positives = 45/114 (39%), Gaps = 32/114 (28%)
Query: 98 NERVDVLRLAMELGADYI-----DVELQVAREFNDSIRGKKPEKCKVIVSSHNYQYTPSV 152
N+RVD LA+ +GAD + D+ L ARE + G + +S+H+ +
Sbjct: 71 NDRVD---LALAVGADGVHLGQDDMPLAEARE----LLGP---GLIIGLSTHDLE----- 115
Query: 153 EDLSNLVARIQASGADIVK----FATT---ALDITDVARVFQITVHSQVPIIGL 199
+ GAD V F T+ + + +I +P++ +
Sbjct: 116 -----EALEAEELGADYVGLGPIFPTSTKPDAPPLGLEGLREIRELVNIPVVAI 164
>gnl|CDD|225826 COG3288, PntA, NAD/NADP transhydrogenase alpha subunit [Energy
production and conversion].
Length = 356
Score = 28.9 bits (65), Expect = 8.1
Identities = 26/84 (30%), Positives = 33/84 (39%), Gaps = 11/84 (13%)
Query: 355 VGAISAIEDGLRGRLNVSGGVSSALAGKLFVVIGAGGAGKALAYGAKAKGARVVIANRTY 414
+GA A ++ +G VS A +VIGAG AG A A GA V
Sbjct: 142 IGAALAYGRFFPMQITAAGTVSPAKV----LVIGAGVAGLAAIATAVRLGAIV----TAR 193
Query: 415 DRARELAETV---GGHALSLADLE 435
D E V G L++ D E
Sbjct: 194 DLRMFKKEQVESLGAKFLAVEDEE 217
>gnl|CDD|177834 PLN02178, PLN02178, cinnamyl-alcohol dehydrogenase.
Length = 375
Score = 28.8 bits (64), Expect = 8.2
Identities = 16/50 (32%), Positives = 25/50 (50%)
Query: 380 AGKLFVVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAETVGGHAL 429
+GK V G GG G KA G RV + +R+ ++ RE + +G +
Sbjct: 178 SGKRLGVNGLGGLGHIAVKIGKAFGLRVTVISRSSEKEREAIDRLGADSF 227
>gnl|CDD|107326 cd06331, PBP1_AmiC_like, Type I periplasmic components of
amide-binding protein (AmiC) and the active transport
system for short-chain and urea (FmdDEF). This group
includes the type I periplasmic components of
amide-binding protein (AmiC) and the active transport
system for short-chain and urea (FmdDEF), found in
bacteria and Archaea. AmiC controls expression of the
amidase operon by a ligand-triggered conformational
switch. In the absence of ligand or presence of
butyramide (repressor), AmiC (the ligand sensor and
negative regulator) adopts an open conformation and
inhibits the transcription antitermination function of
AmiR by direct protein-protein interaction. In the
presence of inducing ligands such as acetamide, AmiC
adopts a closed conformation which disrupts a silencing
AmiC-AmiR complex and the expression of amidase and
other genes of the operon is induced. FmdDEF is
predicted to be an ATP-dependent transporter and closely
resembles the periplasmic binding protein and the two
transmembrane proteins present in various hydrophobic
amino acid-binding transport systems.
Length = 333
Score = 29.0 bits (66), Expect = 8.2
Identities = 8/25 (32%), Positives = 16/25 (64%), Gaps = 1/25 (4%)
Query: 147 QYTP-SVEDLSNLVARIQASGADIV 170
+Y P D +++ +I+A+G D+V
Sbjct: 167 EYLPLGTSDFGSVIEKIKAAGPDVV 191
>gnl|CDD|129557 TIGR00465, ilvC, ketol-acid reductoisomerase. This is the second
enzyme in the parallel isoleucine-valine biosynthetic
pathway [Amino acid biosynthesis, Pyruvate family].
Length = 314
Score = 28.9 bits (65), Expect = 8.3
Identities = 19/84 (22%), Positives = 32/84 (38%), Gaps = 4/84 (4%)
Query: 379 LAGKLFVVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAETVGGHALSLADLENFN 438
L GK +IG G G A A + G V++ R + + A G ++ +
Sbjct: 1 LKGKTVAIIGYGSQGHAQALNLRDSGLNVIVGLRKGGASWKKATEDGFKVGTVEEA---- 56
Query: 439 PEDGMILANTTSIGMQPKVDETPI 462
++ N +Q +V E I
Sbjct: 57 IPQADLIMNLLPDEVQHEVYEAEI 80
>gnl|CDD|234629 PRK00094, gpsA, NAD(P)H-dependent glycerol-3-phosphate
dehydrogenase; Validated.
Length = 325
Score = 28.9 bits (66), Expect = 8.3
Identities = 13/38 (34%), Positives = 18/38 (47%)
Query: 386 VIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAET 423
V+GAG G ALA G V + R ++A E+
Sbjct: 6 VLGAGSWGTALAIVLARNGHDVTLWARDPEQAAEINAD 43
>gnl|CDD|176203 cd08241, QOR1, Quinone oxidoreductase (QOR). QOR catalyzes the
conversion of a quinone + NAD(P)H to a hydroquinone +
NAD(P)+. Quinones are cyclic diones derived from
aromatic compounds. Membrane bound QOR acts in the
respiratory chains of bacteria and mitochondria, while
soluble QOR acts to protect from toxic quinones (e.g.
DT-diaphorase) or as a soluble eye-lens protein in some
vertebrates (e.g. zeta-crystalin). QOR reduces quinones
through a semi-quinone intermediate via a
NAD(P)H-dependent single electron transfer. QOR is a
member of the medium chain dehydrogenase/reductase
family, but lacks the zinc-binding sites of the
prototypical alcohol dehydrogenases of this group.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which has a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES. These
proteins typically form dimers (typically higher plants,
mammals) or tetramers (yeast, bacteria), and have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site, and a structural zinc in a lobe of
the catalytic domain. NAD(H)-binding occurs in the
cleft between the catalytic and coenzyme-binding domains
at the active site, and coenzyme binding induces a
conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
In human ADH catalysis, the zinc ion helps coordinate
the alcohol, followed by deprotonation of a histidine,
the ribose of NAD, a serine, then the alcohol, which
allows the transfer of a hydride to NAD+, creating NADH
and a zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 323
Score = 29.0 bits (66), Expect = 8.4
Identities = 19/62 (30%), Positives = 23/62 (37%), Gaps = 9/62 (14%)
Query: 372 SGGVSSALA---GKLF---VVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAETVG 425
+GGV A A K V+ A K A+A GA VI R D + G
Sbjct: 149 AGGVGLA-AVQLAKALGARVIAAASSEEKLAL--ARALGADHVIDYRDPDLRERVKALTG 205
Query: 426 GH 427
G
Sbjct: 206 GR 207
>gnl|CDD|223755 COG0683, LivK, ABC-type branched-chain amino acid transport
systems, periplasmic component [Amino acid transport and
metabolism].
Length = 366
Score = 28.9 bits (65), Expect = 8.5
Identities = 14/37 (37%), Positives = 17/37 (45%)
Query: 148 YTPSVEDLSNLVARIQASGADIVKFATTALDITDVAR 184
Y P D S LVA+I+A+G D V D R
Sbjct: 185 YAPGDTDFSALVAKIKAAGPDAVLVGGYGPDAALFLR 221
>gnl|CDD|176252 cd08292, ETR_like_2, 2-enoyl thioester reductase (ETR) like
proteins, child 2. 2-enoyl thioester reductase (ETR)
like proteins. ETR catalyzes the NADPH-dependent
conversion of trans-2-enoyl acyl carrier
protein/coenzyme A (ACP/CoA) to acyl-(ACP/CoA) in fatty
acid synthesis. 2-enoyl thioester reductase activity has
been linked in Candida tropicalis as essential in
maintaining mitiochondrial respiratory function. This
ETR family is a part of the medium chain
dehydrogenase/reductase family, but lack the zinc
coordination sites characteristic of the 2-enoyl
thioester reductase (ETR) like proteins. ETR catalyzes
the NADPH-dependent dependent conversion of
trans-2-enoyl acyl carrier protein/coenzyme A (ACP/CoA)
to acyl-(ACP/CoA) in fatty acid synthesis. 2-enoyl
thioester reductase activity has been linked in Candida
tropicalis as essential in maintaining mitiochondrial
respiratory function. This ETR family is a part of the
medium chain dehydrogenase/reductase family, but lack
the zinc coordination sites characteristic of the
alcohol dehydrogenases in this family.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which has a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. The N-terminal catalytic domain has a
distant homology to GroES. These proteins typically
form dimers (typically higher plants, mammals) or
tetramers (yeast, bacteria), and have 2 tightly bound
zinc atoms per subunit, a catalytic zinc at the active
site, and a structural zinc in a lobe of the catalytic
domain. NAD(H) binding occurs in the cleft between the
catalytic and coenzyme-binding domains, at the active
site, and coenzyme binding induces a conformational
closing of this cleft. Coenzyme binding typically
precedes and contributes to substrate binding. Candida
tropicalis enoyl thioester reductase (Etr1p) catalyzes
the NADPH-dependent reduction of trans-2-enoyl
thioesters in mitochondrial fatty acid synthesis. Etr1p
forms homodimers, with each subunit containing a
nucleotide-binding Rossmann fold domain and a catalytic
domain.
Length = 324
Score = 28.8 bits (65), Expect = 8.5
Identities = 17/55 (30%), Positives = 23/55 (41%), Gaps = 1/55 (1%)
Query: 380 AGKLFVVIGAGGA-GKALAYGAKAKGARVVIANRTYDRARELAETVGGHALSLAD 433
G+ + AGGA GK +A A A+G V+ R EL G +S
Sbjct: 139 PGQWLIQNAAGGAVGKLVAMLAAARGINVINLVRRDAGVAELRALGIGPVVSTEQ 193
>gnl|CDD|187583 cd05322, SDH_SDR_c_like, Sorbitol 6-phosphate dehydrogenase (SDH),
classical (c) SDRs. Sorbitol 6-phosphate dehydrogenase
(SDH, aka glucitol 6-phosphate dehydrogenase) catalyzes
the NAD-dependent interconversion of D-fructose
6-phosphate to D-sorbitol 6-phosphate. SDH is a member
of the classical SDRs, with the characteristic catalytic
tetrad, but without a complete match to the typical
NAD-binding motif. 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 = 257
Score = 28.6 bits (64), Expect = 8.5
Identities = 13/47 (27%), Positives = 24/47 (51%), Gaps = 1/47 (2%)
Query: 381 GKLFVVIGAGGA-GKALAYGAKAKGARVVIANRTYDRARELAETVGG 426
++ VVIG G G+ L +G G V +A+ + A ++A+ +
Sbjct: 2 NQVAVVIGGGQTLGEFLCHGLAEAGYDVAVADINSENAEKVADEINA 48
>gnl|CDD|201778 pfam01408, GFO_IDH_MocA, Oxidoreductase family, NAD-binding
Rossmann fold. This family of enzymes utilise NADP or
NAD. This family is called the GFO/IDH/MOCA family in
swiss-prot.
Length = 120
Score = 27.6 bits (62), Expect = 8.7
Identities = 15/48 (31%), Positives = 22/48 (45%), Gaps = 3/48 (6%)
Query: 384 FVVIGAGGAGK--ALAYGAKAKGARVV-IANRTYDRARELAETVGGHA 428
++GAG G+ A GA +V I + RA +AE+ G A
Sbjct: 3 VGIVGAGKIGRRHLRALNESQDGAELVGILDPDPARAEAVAESFGVPA 50
>gnl|CDD|181225 PRK08085, PRK08085, gluconate 5-dehydrogenase; Provisional.
Length = 254
Score = 28.6 bits (64), Expect = 8.7
Identities = 16/47 (34%), Positives = 24/47 (51%), Gaps = 1/47 (2%)
Query: 378 ALAGKLFVVIGAG-GAGKALAYGAKAKGARVVIANRTYDRARELAET 423
+LAGK ++ G+ G G LA G GA ++I + T +RA
Sbjct: 6 SLAGKNILITGSAQGIGFLLATGLAEYGAEIIINDITAERAELAVAK 52
>gnl|CDD|239537 cd03453, SAV4209_like, SAV4209_like. Similar in sequence to the
Streptomyces avermitilis SAV4209 protein, with a hot dog
fold that is similar to those of (R)-specific enoyl-CoA
hydratase, the peroxisomal
Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the
fatty acid synthase beta subunit.
Length = 127
Score = 27.7 bits (62), Expect = 9.1
Identities = 11/20 (55%), Positives = 12/20 (60%), Gaps = 1/20 (5%)
Query: 269 PILYNEAF-KSVGFNGVFVH 287
PI Y+E F K VG GV H
Sbjct: 29 PIHYDEDFAKKVGLPGVIAH 48
>gnl|CDD|211705 TIGR01963, PHB_DH, 3-hydroxybutyrate dehydrogenase. This model
represents a subfamily of the short chain
dehydrogenases. Characterized members so far as
3-hydroxybutyrate dehydrogenases and are found in
species that accumulate ester polmers called
polyhydroxyalkanoic acids (PHAs) under certain
conditions. Several members of the family are from
species not known to accumulate PHAs, including
Oceanobacillus iheyensis and Bacillus subtilis. However,
polymer formation is not required for there be a role
for 3-hydroxybutyrate dehydrogenase; it may be members
of this family have the same function in those species.
Length = 255
Score = 28.5 bits (64), Expect = 9.4
Identities = 17/49 (34%), Positives = 23/49 (46%), Gaps = 1/49 (2%)
Query: 381 GKLFVVIGA-GGAGKALAYGAKAKGARVVIANRTYDRARELAETVGGHA 428
GK +V GA G G A+A A GA VV+ + + A A+ G
Sbjct: 1 GKTALVTGAASGIGLAIARALAAAGANVVVNDFGEEGAEAAAKVAGDAG 49
>gnl|CDD|181113 PRK07775, PRK07775, short chain dehydrogenase; Provisional.
Length = 274
Score = 28.6 bits (64), Expect = 9.5
Identities = 16/52 (30%), Positives = 24/52 (46%), Gaps = 4/52 (7%)
Query: 385 VVIGAG-GAGKALAYGAKAKGARVVIANRTYDRARELAETV---GGHALSLA 432
+V GA G G A A A G V + R ++ EL + + GG A++
Sbjct: 14 LVAGASSGIGAATAIELAAAGFPVALGARRVEKCEELVDKIRADGGEAVAFP 65
>gnl|CDD|237529 PRK13841, PRK13841, conjugal transfer protein TrbL; Provisional.
Length = 391
Score = 28.6 bits (64), Expect = 9.5
Identities = 18/61 (29%), Positives = 26/61 (42%), Gaps = 5/61 (8%)
Query: 372 SGGVSSALAGKLFVVIGAGGAGKALAYGAKAKGARVVIANRTYDRARELAETVGGHALSL 431
G +S AG F+ GA GAG A A A+A G+ + A R + +G +
Sbjct: 290 GGQAASFAAGAAFLAAGAAGAGFAAASAARAGGSSLAGA-----ALRGMGAGIGSAGSAA 344
Query: 432 A 432
Sbjct: 345 G 345
>gnl|CDD|217138 pfam02606, LpxK, Tetraacyldisaccharide-1-P 4'-kinase. This family
consists of tetraacyldisaccharide-1-P 4'-kinase also
known as Lipid-A 4'-kinase or Lipid A biosynthesis
protein LpxK, EC:2.7.1.130. This enzyme catalyzes the
reaction: ATP + 2,3-bis(3-hydroxytetradecanoyl)-D
-glucosaminyl-(beta-D-1,6)-2,
3-bis(3-hydroxytetradecanoyl)-D-glu cosam inyl
beta-phosphate <=> ADP +
2,3,2',3'-tetrakis(3-hydroxytetradecanoyl)-D-
glucosaminyl-1,6-beta-D-glucosamine 1,4'-bisphosphate.
This enzyme is involved in the synthesis of lipid A
portion of the bacterial lipopolysaccharide layer (LPS).
The family contains a P-loop motif at the N terminus.
Length = 318
Score = 28.7 bits (65), Expect = 9.6
Identities = 18/65 (27%), Positives = 23/65 (35%), Gaps = 31/65 (47%)
Query: 385 VVIG---AGGAGK-----ALA----------------YGAKAKGARVVIANRTYDRAREL 420
+V+G GG GK ALA YG K+KG +V +
Sbjct: 38 IVVGNITVGGTGKTPLVIALAELLRARGLRPGVLSRGYGGKSKGPVLVDPGSS------- 90
Query: 421 AETVG 425
A VG
Sbjct: 91 AAEVG 95
>gnl|CDD|176196 cd08234, threonine_DH_like, L-threonine dehydrogenase. L-threonine
dehydrogenase (TDH) catalyzes the zinc-dependent
formation of 2-amino-3-ketobutyrate from L-threonine,
via NAD(H)-dependent oxidation. THD is a member of the
zinc-requiring, medium chain NAD(H)-dependent alcohol
dehydrogenase family (MDR). MDRs have a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. NAD(P)(H)-dependent oxidoreductases are
the major enzymes in the interconversion of alcohols and
aldehydes, or ketones. The N-terminal region typically
has an all-beta catalytic domain. These proteins
typically form dimers (typically higher plants, mammals)
or tetramers (yeast, bacteria), and have 2 tightly
bound zinc atoms per subunit. Sorbitol and aldose
reductase are NAD(+) binding proteins of the polyol
pathway, which interconverts glucose and fructose.
Length = 334
Score = 28.6 bits (65), Expect = 9.6
Identities = 17/43 (39%), Positives = 23/43 (53%), Gaps = 2/43 (4%)
Query: 385 VVIGAGGAGKALAYGAKAKGA-RVVIANRTYDRARELAETVGG 426
+V GAG G LA K GA RV +A ++ ELA+ +G
Sbjct: 164 LVFGAGPIGLLLAQLLKLNGASRVTVAEPNEEK-LELAKKLGA 205
>gnl|CDD|180458 PRK06194, PRK06194, hypothetical protein; Provisional.
Length = 287
Score = 28.4 bits (64), Expect = 9.6
Identities = 14/33 (42%), Positives = 19/33 (57%), Gaps = 1/33 (3%)
Query: 379 LAGKLFVVIGAG-GAGKALAYGAKAKGARVVIA 410
AGK+ V+ GA G G A A A G ++V+A
Sbjct: 4 FAGKVAVITGAASGFGLAFARIGAALGMKLVLA 36
>gnl|CDD|178566 PLN02985, PLN02985, squalene monooxygenase.
Length = 514
Score = 28.7 bits (64), Expect = 9.8
Identities = 12/28 (42%), Positives = 16/28 (57%)
Query: 385 VVIGAGGAGKALAYGAKAKGARVVIANR 412
+++GAG G ALAY G RV + R
Sbjct: 47 IIVGAGVGGSALAYALAKDGRRVHVIER 74
>gnl|CDD|233821 TIGR02322, phosphon_PhnN, phosphonate metabolism
protein/1,5-bisphosphokinase (PRPP-forming) PhnN.
Members of this family resemble PhnN of phosphonate
utilization operons, where different such operons confer
the ability to use somewhat different profiles of C-P
bond-containing compounds (see PMID:15231805), including
phosphites as well as phosphonates. PhnN in E. coli
shows considerable homology to guanylate kinases (EC
2.7.4.8), and has actually been shown to act as a ribose
1,5-bisphosphokinase (PRPP forming). This suggests an
analogous kinase reaction for phosphonate metabolism,
converting 5-phosphoalpha-1-(methylphosphono)ribose to
methylphosphono-PRPP [Central intermediary metabolism,
Phosphorus compounds].
Length = 179
Score = 28.1 bits (63), Expect = 9.8
Identities = 22/70 (31%), Positives = 29/70 (41%), Gaps = 7/70 (10%)
Query: 381 GKLFVVIGAGGAGK----ALAYGAKAKGARVVIANRTYDRARELAETVGGHALSLADLEN 436
G+L V+G GAGK A A RV R R A G + ++L+ E
Sbjct: 1 GRLIYVVGPSGAGKDTLLDYARARLAGDPRVHFVRRVITRP---ASAGGENHIALSTEEF 57
Query: 437 FNPEDGMILA 446
+ EDG A
Sbjct: 58 DHREDGGAFA 67
>gnl|CDD|240646 cd12169, PGDH_like_1, Putative D-3-Phosphoglycerate Dehydrogenases.
Phosphoglycerate dehydrogenases (PGDHs) catalyze the
initial step in the biosynthesis of L-serine from
D-3-phosphoglycerate. PGDHs come in 3 distinct
structural forms, with this first group being related to
2-hydroxy acid dehydrogenases, sharing structural
similarity to formate and glycerate dehydrogenases of
the D-specific 2-hydroxyacid dehydrogenase superfamily,
which also include groups such as L-alanine
dehydrogenase and S-adenosylhomocysteine hydrolase.
Despite often low sequence identity, these proteins
typically have a characteristic arrangement of 2 similar
subdomains of the alpha/beta Rossmann fold NAD+ binding
form. The NAD+ binding domain is inserted within the
linear sequence of the mostly N-terminal catalytic
domain, which has a similar domain structure to the
internal NAD binding domain. Structurally, these domains
are connected by extended alpha helices and create a
cleft in which NAD is bound, primarily to the C-terminal
portion of the 2nd (internal) domain. Some related
proteins have similar structural subdomain but with a
tandem arrangement of the catalytic and NAD-binding
subdomains in the linear sequence. Many, not all,
members of this family are dimeric.
Length = 308
Score = 28.6 bits (65), Expect = 10.0
Identities = 16/50 (32%), Positives = 25/50 (50%), Gaps = 2/50 (4%)
Query: 373 GGVSSALAGKLFVVIGAGGAGKALAYGAKAKGARVVI--ANRTYDRAREL 420
+ + LAGK ++G G G +A +A G RV+ +N T +RA
Sbjct: 134 TTLGTGLAGKTLGIVGLGRIGARVARIGQAFGMRVIAWSSNLTAERAAAA 183
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
0.321 0.138 0.406
Gapped
Lambda K H
0.267 0.0831 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 32,128,240
Number of extensions: 3298066
Number of successful extensions: 4593
Number of sequences better than 10.0: 1
Number of HSP's gapped: 4473
Number of HSP's successfully gapped: 421
Length of query: 616
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 513
Effective length of database: 6,369,140
Effective search space: 3267368820
Effective search space used: 3267368820
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 62 (27.5 bits)