RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 011136
(493 letters)
>gnl|CDD|178135 PLN02520, PLN02520, bifunctional 3-dehydroquinate
dehydratase/shikimate dehydrogenase.
Length = 529
Score = 804 bits (2079), Expect = 0.0
Identities = 334/413 (80%), Positives = 364/413 (88%), Gaps = 1/413 (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 DGLRGRLNVSGGVSSALAGKLFVVIGAGGAGKALAYGAKAKGARVVIANRTYG 415
DGLR S S LAGKLFVVIGAGGAGKALAYGAK KGARVVIANRTY
Sbjct: 362 DGLRA-SGSSPASGSPLAGKLFVVIGAGGAGKALAYGAKEKGARVVIANRTYE 413
>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 = 255 bits (653), Expect = 8e-83
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|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 = 227 bits (581), Expect = 5e-72
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 = 208 bits (531), Expect = 1e-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|223782 COG0710, AroD, 3-dehydroquinate dehydratase [Amino acid transport
and metabolism].
Length = 231
Score = 176 bits (449), Expect = 2e-52
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|223247 COG0169, AroE, Shikimate 5-dehydrogenase [Amino acid transport and
metabolism].
Length = 283
Score = 164 bits (418), Expect = 3e-47
Identities = 64/168 (38%), Positives = 101/168 (60%), Gaps = 13/168 (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-DDGKLRGYNTDGIGFLRALKE--- 117
Query: 367 GRLNVSGGVSSALAGKLFVVIGAGGAGKALAYG-AKAKGARVVIANRT 413
G+ + GK +++GAGGA +A+A+ A+A R+ + NRT
Sbjct: 118 ------FGLPVDVTGKRVLILGAGGAARAVAFALAEAGAKRITVVNRT 159
>gnl|CDD|234703 PRK00258, aroE, shikimate 5-dehydrogenase; Reviewed.
Length = 278
Score = 160 bits (407), Expect = 1e-45
Identities = 59/164 (35%), Positives = 94/164 (57%), Gaps = 15/164 (9%)
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-AKAKGARVVIANRT 413
L GK +++GAGGA +A+ A + I NRT
Sbjct: 118 -----GVDLKGKRILILGAGGAARAVILPLLDLGVAEITIVNRT 156
>gnl|CDD|235036 PRK02412, aroD, 3-dehydroquinate dehydratase; Provisional.
Length = 253
Score = 146 bits (371), Expect = 1e-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|137204 PRK09310, aroDE, bifunctional 3-dehydroquinate
dehydratase/shikimate dehydrogenase protein; Reviewed.
Length = 477
Score = 149 bits (379), Expect = 7e-40
Identities = 109/365 (29%), Positives = 172/365 (47%), Gaps = 28/365 (7%)
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 IANRT 413
I NRT
Sbjct: 360 IFNRT 364
>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 = 130 bits (329), Expect = 1e-34
Identities = 64/162 (39%), Positives = 91/162 (56%), Gaps = 15/162 (9%)
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 SGGVSSALAGKLFVVIGAGGAGKALAYGAKAKGARVVIANRT 413
+ ++IGAGGA KA+A V+IANRT
Sbjct: 118 ----------QNVLIIGAGGAAKAVALELLKADCNVIIANRT 149
>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 = 3e-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|184156 PRK13575, PRK13575, 3-dehydroquinate dehydratase; Provisional.
Length = 238
Score = 103 bits (258), Expect = 4e-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|183585 PRK12548, PRK12548, shikimate 5-dehydrogenase; Provisional.
Length = 289
Score = 97.1 bits (242), Expect = 1e-22
Identities = 56/163 (34%), Positives = 83/163 (50%), Gaps = 16/163 (9%)
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--NDDGKLTGHITDGLGFVRNLRE------- 119
Query: 371 VSGGVSSALAGKLFVVIGAGGAGKALAYGAKAKGAR-VVIANR 412
GV + GK VIGAGGA A+ GA+ + I N
Sbjct: 120 --HGVD--VKGKKLTVIGAGGAATAIQVQCALDGAKEITIFNI 158
>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 = 88.8 bits (220), Expect = 9e-20
Identities = 53/163 (32%), Positives = 75/163 (46%), Gaps = 13/163 (7%)
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-ARVVIANRT 413
+ G LAG +VIGAGG +A Y + G + + NR
Sbjct: 116 NIGKFEPLAGFRGLVIGAGGTSRAAVYALASLGVTDITVINRN 158
>gnl|CDD|183721 PRK12749, PRK12749, quinate/shikimate dehydrogenase; Reviewed.
Length = 288
Score = 71.6 bits (175), Expect = 8e-14
Identities = 47/157 (29%), Positives = 78/157 (49%), Gaps = 15/157 (9%)
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 408
SG + GK V++GAGGA A+ +G + +
Sbjct: 118 SG---FDIKGKTMVLLGAGGASTAIGAQGAIEGLKEI 151
>gnl|CDD|183586 PRK12549, PRK12549, shikimate 5-dehydrogenase; Reviewed.
Length = 284
Score = 70.7 bits (174), Expect = 1e-13
Identities = 45/161 (27%), Positives = 71/161 (44%), Gaps = 28/161 (17%)
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 RGRLNVSGGVSSALAGKLFVVIGAGGAGKALAYGAKAKGAR 406
R+ V +GAGGAG A+A+ G
Sbjct: 127 LERV---------------VQLGAGGAGAAVAHALLTLGVE 152
>gnl|CDD|172521 PRK14027, PRK14027, quinate/shikimate dehydrogenase; Provisional.
Length = 283
Score = 58.5 bits (141), Expect = 2e-09
Identities = 44/162 (27%), Positives = 71/162 (43%), Gaps = 19/162 (11%)
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 FNGLNITHPYKQAVLPLLDEVSEQATQLGAVNTVV-IDATGHTTGHNTDVSGFGRGMEEG 121
Query: 365 LRGRLNVSGGVSSALAGKLFVVIGAGGAGKALAYGAKAKGAR 406
L S V +GAGG G A+AY G +
Sbjct: 122 LPNAKLDS-----------VVQVGAGGVGNAVAYALVTHGVQ 152
>gnl|CDD|183587 PRK12550, PRK12550, shikimate 5-dehydrogenase; Reviewed.
Length = 272
Score = 54.6 bits (132), Expect = 3e-08
Identities = 38/115 (33%), Positives = 56/115 (48%), Gaps = 17/115 (14%)
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 GRLNVSGGVSSALAGKLFVVIGAGGAGKALAYGAKAKGAR---VVIANRTYGESL 418
S V L + G+GG KA+A + G +V N G++L
Sbjct: 116 -----SYQVPPDLV---VALRGSGGMAKAVAAALRDAGFTDGTIVARNEKTGKAL 162
>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 = 51.1 bits (123), Expect = 9e-08
Identities = 23/63 (36%), Positives = 34/63 (53%), Gaps = 12/63 (19%)
Query: 352 TDYVGAISAIEDGLRGRLNVSGGVSSALAGKLFVVIGAGGAGKALAYGAKAKGA-RVVIA 410
TD +G + A+E+ L GK +++GAGGA +A+AY GA ++VI
Sbjct: 1 TDGLGFVRALEEAGIE-----------LKGKKVLILGAGGAARAVAYALAELGAAKIVIV 49
Query: 411 NRT 413
NRT
Sbjct: 50 NRT 52
>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 = 48.1 bits (115), Expect = 6e-07
Identities = 16/37 (43%), Positives = 22/37 (59%), Gaps = 1/37 (2%)
Query: 379 LAGKLFVVIGAGGAGKALAYGAKAKGAR-VVIANRTY 414
L GK ++IGAG + A +KGA+ + IANRT
Sbjct: 10 LKGKKVLLIGAGEMARLAAKHLLSKGAKKITIANRTL 46
>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|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 = 0.004
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|198065 smart00997, AdoHcyase_NAD, S-adenosyl-L-homocysteine hydrolase, NAD
binding domain.
Length = 162
Score = 37.4 bits (88), Expect = 0.005
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|180854 PRK07121, PRK07121, hypothetical protein; Validated.
Length = 492
Score = 37.6 bits (88), Expect = 0.013
Identities = 15/31 (48%), Positives = 18/31 (58%)
Query: 385 VVIGAGGAGKALAYGAKAKGARVVIANRTYG 415
VV+G G AG A A A GARV++ R G
Sbjct: 24 VVVGFGAAGACAAIEAAAAGARVLVLERAAG 54
>gnl|CDD|234592 PRK00045, hemA, glutamyl-tRNA reductase; Reviewed.
Length = 423
Score = 37.1 bits (87), Expect = 0.020
Identities = 21/57 (36%), Positives = 29/57 (50%), Gaps = 14/57 (24%)
Query: 372 SGGVSSA-----LAGKLF--------VVIGAGGAGKALAYGAKAKGAR-VVIANRTY 414
+G VS A LA ++F +VIGAG G+ +A KG R + +ANRT
Sbjct: 160 AGAVSVASAAVELAKQIFGDLSGKKVLVIGAGEMGELVAKHLAEKGVRKITVANRTL 216
>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 = 36.7 bits (86), Expect = 0.022
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|240258 PTZ00075, PTZ00075, Adenosylhomocysteinase; Provisional.
Length = 476
Score = 36.6 bits (85), Expect = 0.026
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|181159 PRK07890, PRK07890, short chain dehydrogenase; Provisional.
Length = 258
Score = 36.1 bits (84), Expect = 0.027
Identities = 19/36 (52%), Positives = 22/36 (61%), Gaps = 1/36 (2%)
Query: 379 LAGKLFVVIGAG-GAGKALAYGAKAKGARVVIANRT 413
L GK+ VV G G G G+ LA A GA VV+A RT
Sbjct: 3 LKGKVVVVSGVGPGLGRTLAVRAARAGADVVLAART 38
>gnl|CDD|224169 COG1249, Lpd, Pyruvate/2-oxoglutarate dehydrogenase complex,
dihydrolipoamide dehydrogenase (E3) component, and
related enzymes [Energy production and conversion].
Length = 454
Score = 36.4 bits (85), Expect = 0.030
Identities = 12/28 (42%), Positives = 15/28 (53%)
Query: 385 VVIGAGGAGKALAYGAKAKGARVVIANR 412
VVIGAG AG A A G +V + +
Sbjct: 8 VVIGAGPAGYVAAIRAAQLGLKVALVEK 35
>gnl|CDD|223573 COG0499, SAM1, S-adenosylhomocysteine hydrolase [Coenzyme
metabolism].
Length = 420
Score = 36.5 bits (85), Expect = 0.033
Identities = 18/47 (38%), Positives = 24/47 (51%), Gaps = 6/47 (12%)
Query: 363 DGLRGRLNVSGGVSSALAGKLFVVIGAGGAGKALAYGAKAKGARVVI 409
DG+ NV LAGK VV G G G+ +A + GARV++
Sbjct: 197 DGILRATNVL------LAGKNVVVAGYGWVGRGIAMRLRGMGARVIV 237
>gnl|CDD|223981 COG1053, SdhA, Succinate dehydrogenase/fumarate reductase,
flavoprotein subunit [Energy production and conversion].
Length = 562
Score = 36.2 bits (84), Expect = 0.039
Identities = 12/30 (40%), Positives = 16/30 (53%)
Query: 385 VVIGAGGAGKALAYGAKAKGARVVIANRTY 414
VVIG GGAG A A G +V + ++
Sbjct: 10 VVIGGGGAGLRAAIEAAEAGLKVALLSKAP 39
>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 = 36.1 bits (84), Expect = 0.040
Identities = 12/35 (34%), Positives = 16/35 (45%)
Query: 385 VVIGAGGAGKALAYGAKAKGARVVIANRTYGESLT 419
VVIG+G AG A A A G +V + +
Sbjct: 3 VVIGSGLAGLAAALEAAEAGLKVAVVEKGQPFGGA 37
>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 = 35.4 bits (82), Expect = 0.049
Identities = 16/34 (47%), Positives = 22/34 (64%)
Query: 380 AGKLFVVIGAGGAGKALAYGAKAKGARVVIANRT 413
G +V+GAGG G A AKA GARV++ +R+
Sbjct: 134 PGDTVLVLGAGGVGLLAAQLAKAAGARVIVTDRS 167
>gnl|CDD|235488 PRK05476, PRK05476, S-adenosyl-L-homocysteine hydrolase;
Provisional.
Length = 425
Score = 35.9 bits (84), Expect = 0.051
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|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 = 35.3 bits (82), Expect = 0.053
Identities = 25/77 (32%), Positives = 37/77 (48%), Gaps = 10/77 (12%)
Query: 363 DGLRGRLNVSGGVSSALAGKLFVVIGAGGAGKALAYGAKAKGARVVIANRTYGESLTFLR 422
GL GR LAGK ++G G G +A KA G +V+ +R+ E L
Sbjct: 135 AGLIGRE---------LAGKTVGIVGTGAIGLRVARLFKAFGCKVLAYSRSEKEEAKALG 185
Query: 423 LMSWLLLNTLLFDSVIV 439
+ ++ L+ LL +S IV
Sbjct: 186 I-EYVSLDELLAESDIV 201
>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 = 35.5 bits (82), Expect = 0.054
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|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 = 35.1 bits (81), Expect = 0.074
Identities = 16/46 (34%), Positives = 21/46 (45%), Gaps = 6/46 (13%)
Query: 371 VSGGVSSAL------AGKLFVVIGAGGAGKALAYGAKAKGARVVIA 410
S G +A+ G V G GG G ++ G KA GA +IA
Sbjct: 168 FSTGYGAAVNTAKVTPGSTCAVFGLGGVGLSVIMGCKAAGASRIIA 213
>gnl|CDD|236216 PRK08277, PRK08277, D-mannonate oxidoreductase; Provisional.
Length = 278
Score = 34.9 bits (81), Expect = 0.075
Identities = 15/36 (41%), Positives = 20/36 (55%), Gaps = 1/36 (2%)
Query: 379 LAGKLFVVIGAGGA-GKALAYGAKAKGARVVIANRT 413
L GK+ V+ G GG G A+A GA+V I +R
Sbjct: 8 LKGKVAVITGGGGVLGGAMAKELARAGAKVAILDRN 43
>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 = 35.0 bits (81), Expect = 0.087
Identities = 14/31 (45%), Positives = 17/31 (54%)
Query: 380 AGKLFVVIGAGGAGKALAYGAKAKGARVVIA 410
G+ VIG GG G + AKA GA +IA
Sbjct: 187 PGETVAVIGVGGVGSSAIQLAKAFGASPIIA 217
>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 = 34.4 bits (79), Expect = 0.089
Identities = 17/35 (48%), Positives = 22/35 (62%), Gaps = 1/35 (2%)
Query: 379 LAGKLFVVIGAG-GAGKALAYGAKAKGARVVIANR 412
L GK+ +V GAG G G A A +GARVV+A+
Sbjct: 1 LEGKVAIVTGAGAGIGAACAARLAREGARVVVADI 35
>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 = 34.4 bits (79), Expect = 0.089
Identities = 17/35 (48%), Positives = 24/35 (68%), Gaps = 1/35 (2%)
Query: 379 LAGKLFVVIGAG-GAGKALAYGAKAKGARVVIANR 412
L+GK+ +V GA G G+A+A +GARVV+A R
Sbjct: 3 LSGKVALVTGASSGIGRAIARALAREGARVVVAAR 37
>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 = 0.099
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|223450 COG0373, HemA, Glutamyl-tRNA reductase [Coenzyme metabolism].
Length = 414
Score = 34.5 bits (80), Expect = 0.11
Identities = 14/37 (37%), Positives = 19/37 (51%), Gaps = 1/37 (2%)
Query: 379 LAGKLFVVIGAGGAG-KALAYGAKAKGARVVIANRTY 414
L K +VIGAG G + A+ ++ IANRT
Sbjct: 176 LKDKKVLVIGAGEMGELVAKHLAEKGVKKITIANRTL 212
>gnl|CDD|236241 PRK08324, PRK08324, short chain dehydrogenase; Validated.
Length = 681
Score = 34.8 bits (81), Expect = 0.12
Identities = 18/35 (51%), Positives = 23/35 (65%), Gaps = 1/35 (2%)
Query: 379 LAGKLFVVIGAGGA-GKALAYGAKAKGARVVIANR 412
LAGK+ +V GA G GKA A A+GA VV+A+
Sbjct: 420 LAGKVALVTGAAGGIGKATAKRLAAEGACVVLADL 454
>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 = 34.1 bits (79), Expect = 0.13
Identities = 18/63 (28%), Positives = 30/63 (47%), Gaps = 1/63 (1%)
Query: 379 LAGKLFVVIGAGGAGKALAYGAKAKGARVVIANRTYGESLTFLRLMSWLLLNTLLFDS-V 437
L GK ++G G G+ +A +A G +V+ +RT + L+ LL S V
Sbjct: 138 LEGKTVGIVGLGRIGQRVAKRLQAFGMKVLYYDRTRKPEPEEDLGFRVVSLDELLAQSDV 197
Query: 438 IVI 440
+V+
Sbjct: 198 VVL 200
>gnl|CDD|109716 pfam00670, AdoHcyase_NAD, S-adenosyl-L-homocysteine hydrolase, NAD
binding domain.
Length = 162
Score = 33.5 bits (77), Expect = 0.13
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|180588 PRK06487, PRK06487, glycerate dehydrogenase; Provisional.
Length = 317
Score = 34.3 bits (79), Expect = 0.14
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|237225 PRK12843, PRK12843, putative FAD-binding dehydrogenase; Reviewed.
Length = 578
Score = 34.3 bits (79), Expect = 0.16
Identities = 13/29 (44%), Positives = 18/29 (62%)
Query: 385 VVIGAGGAGKALAYGAKAKGARVVIANRT 413
+VIGAG AG + A A G +V++ RT
Sbjct: 20 IVIGAGAAGMSAALFAAIAGLKVLLVERT 48
>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 = 33.7 bits (78), Expect = 0.19
Identities = 15/34 (44%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 381 GKLFVVIGA-GGAGKALAYGAKAKGARVVIANRT 413
GK+ V+ GA G GK A +GA V+IA R
Sbjct: 1 GKVVVITGANSGIGKETARELAKRGAHVIIACRN 34
>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 = 33.5 bits (77), Expect = 0.19
Identities = 16/36 (44%), Positives = 22/36 (61%), Gaps = 1/36 (2%)
Query: 379 LAGKLFVVIGAG-GAGKALAYGAKAKGARVVIANRT 413
L+GK+ V GA G G+A+A GA VV+A +T
Sbjct: 1 LSGKVAFVTGASRGIGRAIALRLAKAGATVVVAAKT 36
>gnl|CDD|225186 COG2303, BetA, Choline dehydrogenase and related flavoproteins
[Amino acid transport and metabolism].
Length = 542
Score = 34.0 bits (78), Expect = 0.19
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|236101 PRK07803, sdhA, succinate dehydrogenase flavoprotein subunit;
Reviewed.
Length = 626
Score = 33.9 bits (78), Expect = 0.20
Identities = 14/25 (56%), Positives = 17/25 (68%)
Query: 385 VVIGAGGAGKALAYGAKAKGARVVI 409
VVIGAGGAG A A+ +G RV +
Sbjct: 12 VVIGAGGAGLRAAIEARERGLRVAV 36
>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 = 33.3 bits (77), Expect = 0.21
Identities = 19/69 (27%), Positives = 33/69 (47%), Gaps = 1/69 (1%)
Query: 373 GGVSSALAGKLFVVIGAGGAGKALAYGAKAKGARVVIANRTYGESLTFLRL-MSWLLLNT 431
G S L+GK ++G G G+A+A + G V+ +R L + ++ L+
Sbjct: 134 GRPSRELSGKTVGIVGLGNIGRAVARRLRGFGVEVIYYDRFRDPEAEEKDLGVRYVELDE 193
Query: 432 LLFDSVIVI 440
LL +S +V
Sbjct: 194 LLAESDVVS 202
>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 = 33.3 bits (77), Expect = 0.23
Identities = 14/31 (45%), Positives = 20/31 (64%)
Query: 380 AGKLFVVIGAGGAGKALAYGAKAKGARVVIA 410
AG +V+GAG G + AKA+GARV++
Sbjct: 159 AGDTVLVVGAGPIGLGVIQVAKARGARVIVV 189
>gnl|CDD|237626 PRK14154, PRK14154, heat shock protein GrpE; Provisional.
Length = 208
Score = 32.9 bits (74), Expect = 0.23
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|235608 PRK05786, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 238
Score = 33.2 bits (76), Expect = 0.24
Identities = 16/36 (44%), Positives = 21/36 (58%), Gaps = 1/36 (2%)
Query: 379 LAGKLFVVIGAG-GAGKALAYGAKAKGARVVIANRT 413
L GK +IG G G A+AY A +GA+V I +R
Sbjct: 3 LKGKKVAIIGVSEGLGYAVAYFALKEGAQVCINSRN 38
>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 = 33.4 bits (77), Expect = 0.25
Identities = 18/37 (48%), Positives = 21/37 (56%), Gaps = 1/37 (2%)
Query: 379 LAGKLFVVIGAGGAG-KALAYGAKAKGARVVIANRTY 414
L GK +VIGAG G A + A A + IANRTY
Sbjct: 176 LKGKKVLVIGAGEMGELAAKHLAAKGVAEITIANRTY 212
>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 = 0.26
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|218507 pfam05221, AdoHcyase, S-adenosyl-L-homocysteine hydrolase.
Length = 430
Score = 33.2 bits (76), Expect = 0.28
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|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 = 33.1 bits (76), Expect = 0.28
Identities = 13/26 (50%), Positives = 17/26 (65%)
Query: 384 FVVIGAGGAGKALAYGAKAKGARVVI 409
VV+GAG AG + AY KG RV++
Sbjct: 3 VVVVGAGPAGASAAYRLADKGLRVLL 28
>gnl|CDD|234808 PRK00652, lpxK, tetraacyldisaccharide 4'-kinase; Reviewed.
Length = 325
Score = 33.3 bits (77), Expect = 0.29
Identities = 14/39 (35%), Positives = 21/39 (53%), Gaps = 8/39 (20%)
Query: 385 VVIG---AGGAGK-----ALAYGAKAKGARVVIANRTYG 415
+V+G GG GK ALA +A+G + + +R YG
Sbjct: 52 IVVGNITVGGTGKTPVVIALAEQLQARGLKPGVVSRGYG 90
>gnl|CDD|184511 PRK14106, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 450
Score = 33.4 bits (77), Expect = 0.30
Identities = 16/41 (39%), Positives = 24/41 (58%)
Query: 379 LAGKLFVVIGAGGAGKALAYGAKAKGARVVIANRTYGESLT 419
L GK +V+GAG +G ALA K GA+V++ + + L
Sbjct: 3 LKGKKVLVVGAGVSGLALAKFLKKLGAKVILTDEKEEDQLK 43
>gnl|CDD|183772 PRK12823, benD, 1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate
dehydrogenase; Provisional.
Length = 260
Score = 33.0 bits (76), Expect = 0.31
Identities = 18/34 (52%), Positives = 24/34 (70%), Gaps = 1/34 (2%)
Query: 380 AGKLFVVIGAG-GAGKALAYGAKAKGARVVIANR 412
AGK+ VV GA G G+ +A A A+GARVV+ +R
Sbjct: 7 AGKVVVVTGAAQGIGRGVALRAAAEGARVVLVDR 40
>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 = 33.1 bits (76), Expect = 0.31
Identities = 17/32 (53%), Positives = 17/32 (53%)
Query: 379 LAGKLFVVIGAGGAGKALAYGAKAKGARVVIA 410
AGK VIGAG G A A GAR VIA
Sbjct: 128 RAGKTVAVIGAGFIGLLFLQLAAAAGARRVIA 159
>gnl|CDD|225613 COG3071, HemY, Uncharacterized enzyme of heme biosynthesis
[Coenzyme metabolism].
Length = 400
Score = 33.1 bits (76), Expect = 0.31
Identities = 17/61 (27%), Positives = 26/61 (42%), Gaps = 1/61 (1%)
Query: 383 LFVVIGAGGAGKALAYGAKAKGARVVIANRTYGESLTFLRLMSWLLLNTLLFDSVIVIRI 442
LFV++ AG G LA + + N SLT L + + L L ++ R+
Sbjct: 7 LFVLLLAG-IGVGLAIAGQQGYVLIQTDNYNIEMSLTTLVIFLIIALVVLYLLEWLLRRV 65
Query: 443 L 443
L
Sbjct: 66 L 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 = 32.9 bits (76), Expect = 0.32
Identities = 16/46 (34%), Positives = 21/46 (45%), Gaps = 6/46 (13%)
Query: 371 VSGGVSSAL------AGKLFVVIGAGGAGKALAYGAKAKGARVVIA 410
V+ GV + + G VIG GG G GA+ GA +IA
Sbjct: 167 VTTGVGAVVNTARVRPGDTVAVIGCGGVGLNAIQGARIAGASRIIA 212
>gnl|CDD|215463 PLN02858, PLN02858, fructose-bisphosphate aldolase.
Length = 1378
Score = 33.3 bits (76), Expect = 0.34
Identities = 26/89 (29%), Positives = 39/89 (43%), Gaps = 14/89 (15%)
Query: 356 GAISAIEDGLRGRLNVSGGVSSALAGKLFVVIGAGGAGK--------------ALAYGAK 401
G ++ + G L +G V SAL+ KL+V+ G GAG A A A
Sbjct: 456 GTLTIMASGTDEALKSAGSVLSALSEKLYVIKGGCGAGSGVKMVNQLLAGVHIASAAEAM 515
Query: 402 AKGARVVIANRTYGESLTFLRLMSWLLLN 430
A GAR+ + R + ++ SW+ N
Sbjct: 516 AFGARLGLNTRKLFDIISNAGGTSWMFEN 544
>gnl|CDD|235787 PRK06370, PRK06370, mercuric reductase; Validated.
Length = 463
Score = 33.3 bits (77), Expect = 0.34
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|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 = 33.0 bits (76), Expect = 0.34
Identities = 17/55 (30%), Positives = 25/55 (45%), Gaps = 6/55 (10%)
Query: 379 LAGKLFVVIGAGGAGKALAYGAKAKGARVVIANRT------YGESLTFLRLMSWL 427
L G ++GAGG G+AL GA+V+ NR+ E++ RL
Sbjct: 123 LRGSTVAIVGAGGIGRALIPLLAPFGAKVIAVNRSGRPVEGADETVPADRLDEVW 177
>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 = 32.7 bits (75), Expect = 0.38
Identities = 17/59 (28%), Positives = 22/59 (37%)
Query: 385 VVIGAGGAGKALAYGAKAKGARVVIANRTYGESLTFLRLMSWLLLNTLLFDSVIVIRIL 443
V+IG G AG A A G +V + R G L LLL + + L
Sbjct: 3 VIIGGGPAGLAAAIRLARLGLKVALIEREGGTCYNRGCLPKKLLLEVAEGLELAIGLAL 61
>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 = 32.7 bits (75), Expect = 0.38
Identities = 23/70 (32%), Positives = 35/70 (50%), Gaps = 12/70 (17%)
Query: 379 LAGKLFVVIGAGGAGKALAYGAKAKGA-RVVIANRTY-----------GESLTFLRLMSW 426
L GK ++IGAG G+ +A KG +++IANRTY GE++ F L +
Sbjct: 178 LKGKKALLIGAGEMGELVAKHLLRKGVGKILIANRTYERAEDLAKELGGEAVKFEDLEEY 237
Query: 427 LLLNTLLFDS 436
L ++ S
Sbjct: 238 LAEADIVISS 247
>gnl|CDD|224577 COG1663, LpxK, Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope
biogenesis, outer membrane].
Length = 336
Score = 32.7 bits (75), Expect = 0.40
Identities = 14/39 (35%), Positives = 20/39 (51%), Gaps = 8/39 (20%)
Query: 385 VVIG---AGGAGK-----ALAYGAKAKGARVVIANRTYG 415
+ +G GG GK LA +A+G RV + +R YG
Sbjct: 50 ICVGNLTVGGTGKTPVVIWLAEALQARGVRVGVVSRGYG 88
>gnl|CDD|178111 PLN02494, PLN02494, adenosylhomocysteinase.
Length = 477
Score = 32.9 bits (75), Expect = 0.40
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|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 = 32.2 bits (74), Expect = 0.40
Identities = 14/35 (40%), Positives = 19/35 (54%), Gaps = 1/35 (2%)
Query: 381 GKLFVVIGAG-GAGKALAYGAKAKGARVVIANRTY 414
GK ++ G G GKALA +GA V+I R+
Sbjct: 1 GKHVLITGGSSGIGKALAKELVKEGANVIIVARSE 35
>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 = 32.4 bits (74), Expect = 0.42
Identities = 19/36 (52%), Positives = 22/36 (61%), Gaps = 1/36 (2%)
Query: 379 LAGKLFVVIGAG-GAGKALAYGAKAKGARVVIANRT 413
LAGK + GA G GKA+A A GA VVIA +T
Sbjct: 1 LAGKTLFITGASRGIGKAIALKAARDGANVVIAAKT 36
>gnl|CDD|235774 PRK06292, PRK06292, dihydrolipoamide dehydrogenase; Validated.
Length = 460
Score = 32.8 bits (76), Expect = 0.42
Identities = 12/33 (36%), Positives = 16/33 (48%), Gaps = 1/33 (3%)
Query: 384 FVVIGAGGAGKALAYGAKAKGARVVIANR-TYG 415
+VIGAG AG A A G +V + + G
Sbjct: 6 VIVIGAGPAGYVAARRAAKLGKKVALIEKGPLG 38
>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 = 32.6 bits (74), Expect = 0.43
Identities = 17/57 (29%), Positives = 26/57 (45%), Gaps = 3/57 (5%)
Query: 359 SAIEDGLRGRLNVSGGVSSA---LAGKLFVVIGAGGAGKALAYGAKAKGARVVIANR 412
+++ R G +AGK VV+GAG GK A + GA+V+I +
Sbjct: 135 LSVQFIARFLEVQQPGRLGGAPDVAGKTVVVVGAGVVGKEAAQMLRGLGAQVLITDI 191
>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 = 32.7 bits (75), Expect = 0.46
Identities = 16/39 (41%), Positives = 17/39 (43%), Gaps = 3/39 (7%)
Query: 372 SGGVSSALAGKLFVVIGAGGAGKALAYGAKAKGARVVIA 410
V G VV+G GG G GA GAR VIA
Sbjct: 180 IADVR---PGDTVVVMGIGGVGINAVQGAAVAGARKVIA 215
>gnl|CDD|180723 PRK06841, PRK06841, short chain dehydrogenase; Provisional.
Length = 255
Score = 32.3 bits (74), Expect = 0.46
Identities = 18/35 (51%), Positives = 23/35 (65%), Gaps = 1/35 (2%)
Query: 379 LAGKLFVVIG-AGGAGKALAYGAKAKGARVVIANR 412
L+GK+ VV G A G G A+A AKGARV + +R
Sbjct: 13 LSGKVAVVTGGASGIGHAIAELFAAKGARVALLDR 47
>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 = 32.5 bits (75), Expect = 0.47
Identities = 15/35 (42%), Positives = 22/35 (62%)
Query: 379 LAGKLFVVIGAGGAGKALAYGAKAKGARVVIANRT 413
LAGK +++G G G+ +A AKA G RV+ R+
Sbjct: 132 LAGKTVLIVGLGDIGREIARRAKAFGMRVIGVRRS 166
>gnl|CDD|180584 PRK06481, PRK06481, fumarate reductase flavoprotein subunit;
Validated.
Length = 506
Score = 32.5 bits (74), Expect = 0.48
Identities = 13/25 (52%), Positives = 16/25 (64%)
Query: 385 VVIGAGGAGKALAYGAKAKGARVVI 409
V++GAGGAG + A AK G VI
Sbjct: 65 VIVGAGGAGMSAAIEAKDAGMNPVI 89
>gnl|CDD|235628 PRK05855, PRK05855, short chain dehydrogenase; Validated.
Length = 582
Score = 32.6 bits (75), Expect = 0.49
Identities = 16/41 (39%), Positives = 21/41 (51%), Gaps = 1/41 (2%)
Query: 373 GGVSSALAGKLFVVIGAG-GAGKALAYGAKAKGARVVIANR 412
G +GKL VV GAG G G+ A +GA VV ++
Sbjct: 307 GRPRGPFSGKLVVVTGAGSGIGRETALAFAREGAEVVASDI 347
>gnl|CDD|237771 PRK14619, PRK14619, NAD(P)H-dependent glycerol-3-phosphate
dehydrogenase; Provisional.
Length = 308
Score = 32.3 bits (74), Expect = 0.52
Identities = 15/34 (44%), Positives = 19/34 (55%)
Query: 385 VVIGAGGAGKALAYGAKAKGARVVIANRTYGESL 418
++GAG G LA A A G RV + +R G SL
Sbjct: 8 AILGAGAWGSTLAGLASANGHRVRVWSRRSGLSL 41
>gnl|CDD|181131 PRK07814, PRK07814, short chain dehydrogenase; Provisional.
Length = 263
Score = 32.1 bits (73), Expect = 0.53
Identities = 17/36 (47%), Positives = 21/36 (58%), Gaps = 1/36 (2%)
Query: 379 LAGKLFVVIGAG-GAGKALAYGAKAKGARVVIANRT 413
L ++ VV GAG G G A+A GA V+IA RT
Sbjct: 8 LDDQVAVVTGAGRGLGAAIALAFAEAGADVLIAART 43
>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 = 31.9 bits (73), Expect = 0.53
Identities = 10/25 (40%), Positives = 13/25 (52%)
Query: 385 VVIGAGGAGKALAYGAKAKGARVVI 409
VVIG G G + AY +G V +
Sbjct: 3 VVIGGGIVGLSTAYELARRGLSVTL 27
>gnl|CDD|235633 PRK05872, PRK05872, short chain dehydrogenase; Provisional.
Length = 296
Score = 31.9 bits (73), Expect = 0.61
Identities = 16/37 (43%), Positives = 22/37 (59%), Gaps = 1/37 (2%)
Query: 373 GGVSSALAGKLFVVIGAG-GAGKALAYGAKAKGARVV 408
G ++LAGK+ VV GA G G LA A+GA++
Sbjct: 1 GPPMTSLAGKVVVVTGAARGIGAELARRLHARGAKLA 37
>gnl|CDD|202773 pfam03807, F420_oxidored, NADP oxidoreductase coenzyme
F420-dependent.
Length = 93
Score = 30.3 bits (69), Expect = 0.62
Identities = 16/27 (59%), Positives = 18/27 (66%)
Query: 386 VIGAGGAGKALAYGAKAKGARVVIANR 412
+IGAG G+ALA G A G VVIAN
Sbjct: 4 IIGAGNMGEALARGLAAAGHEVVIANS 30
>gnl|CDD|235914 PRK07041, PRK07041, short chain dehydrogenase; Provisional.
Length = 230
Score = 31.5 bits (72), Expect = 0.64
Identities = 16/28 (57%), Positives = 19/28 (67%)
Query: 385 VVIGAGGAGKALAYGAKAKGARVVIANR 412
VV G+ G G ALA A+GARV IA+R
Sbjct: 2 VVGGSSGIGLALARAFAAEGARVTIASR 29
>gnl|CDD|181349 PRK08278, PRK08278, short chain dehydrogenase; Provisional.
Length = 273
Score = 31.8 bits (73), Expect = 0.65
Identities = 16/39 (41%), Positives = 22/39 (56%), Gaps = 1/39 (2%)
Query: 376 SSALAGKLFVVIGAG-GAGKALAYGAKAKGARVVIANRT 413
+L+GK + GA G G A+A A GA +VIA +T
Sbjct: 1 MMSLSGKTLFITGASRGIGLAIALRAARDGANIVIAAKT 39
>gnl|CDD|235975 PRK07231, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 251
Score = 31.7 bits (73), Expect = 0.66
Identities = 16/36 (44%), Positives = 23/36 (63%), Gaps = 1/36 (2%)
Query: 379 LAGKLFVVIGAG-GAGKALAYGAKAKGARVVIANRT 413
L GK+ +V GA G G+ +A A+GARVV+ +R
Sbjct: 3 LEGKVAIVTGASSGIGEGIARRFAAEGARVVVTDRN 38
>gnl|CDD|236025 PRK07476, eutB, threonine dehydratase; Provisional.
Length = 322
Score = 31.9 bits (73), Expect = 0.72
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|223717 COG0644, FixC, Dehydrogenases (flavoproteins) [Energy production
and conversion].
Length = 396
Score = 32.0 bits (73), Expect = 0.75
Identities = 9/25 (36%), Positives = 14/25 (56%)
Query: 385 VVIGAGGAGKALAYGAKAKGARVVI 409
V++GAG AG + A G V++
Sbjct: 7 VIVGAGPAGSSAARRLAKAGLDVLV 31
>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 = 31.8 bits (73), Expect = 0.76
Identities = 15/36 (41%), Positives = 22/36 (61%), Gaps = 1/36 (2%)
Query: 379 LAGKLFVVIGA-GGAGKALAYGAKAKGARVVIANRT 413
L GK+ ++ GA G G+ LAY GAR+V++ R
Sbjct: 1 LQGKVVIITGASSGIGEELAYHLARLGARLVLSARR 36
>gnl|CDD|180440 PRK06172, PRK06172, short chain dehydrogenase; Provisional.
Length = 253
Score = 31.6 bits (72), Expect = 0.78
Identities = 16/39 (41%), Positives = 25/39 (64%), Gaps = 1/39 (2%)
Query: 375 VSSALAGKLFVVIG-AGGAGKALAYGAKAKGARVVIANR 412
+S +GK+ +V G A G G+A A +GA+VV+A+R
Sbjct: 1 MSMTFSGKVALVTGGAAGIGRATALAFAREGAKVVVADR 39
>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 = 30.9 bits (71), Expect = 0.80
Identities = 18/46 (39%), Positives = 19/46 (41%), Gaps = 3/46 (6%)
Query: 364 GLRGRLNVSGGVSSALAGKLFVVIGAGGAGKALAYGAKAKGARVVI 409
G G L G K VVIGAG G A AK GA V +
Sbjct: 6 GGFGML--LTGAGGVPPAK-VVVIGAGVVGLGAAATAKGLGAEVTV 48
>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 = 31.4 bits (71), Expect = 0.85
Identities = 17/35 (48%), Positives = 21/35 (60%), Gaps = 1/35 (2%)
Query: 379 LAGKLFVVIGAG-GAGKALAYGAKAKGARVVIANR 412
L GK+ +V GA G G+A A A+GA V IA R
Sbjct: 1 LQGKVALVTGASSGIGEATARALAAEGAAVAIAAR 35
>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 = 31.7 bits (73), Expect = 0.86
Identities = 15/39 (38%), Positives = 21/39 (53%), Gaps = 8/39 (20%)
Query: 385 VVIG---AGGAGK-----ALAYGAKAKGARVVIANRTYG 415
+V+G GG GK ALA +A+G R + +R YG
Sbjct: 38 IVVGNITVGGTGKTPLVIALAELLRARGLRPGVLSRGYG 76
>gnl|CDD|236372 PRK09072, PRK09072, short chain dehydrogenase; Provisional.
Length = 263
Score = 31.5 bits (72), Expect = 0.94
Identities = 15/36 (41%), Positives = 21/36 (58%), Gaps = 1/36 (2%)
Query: 379 LAGKLFVVIGA-GGAGKALAYGAKAKGARVVIANRT 413
L K ++ GA GG G+ALA A GAR+++ R
Sbjct: 3 LKDKRVLLTGASGGIGQALAEALAAAGARLLLVGRN 38
>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 = 29.3 bits (66), Expect = 0.94
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|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 = 0.98
Identities = 18/45 (40%), Positives = 24/45 (53%), Gaps = 1/45 (2%)
Query: 379 LAGKLFVVIGAG-GAGKALAYGAKAKGARVVIANRTYGESLTFLR 422
AGK +V GAG G G+A GARVV +RT + + +R
Sbjct: 5 FAGKRALVTGAGKGIGRATVKALAKAGARVVAVSRTQADLDSLVR 49
>gnl|CDD|179631 PRK03692, PRK03692, putative UDP-N-acetyl-D-mannosaminuronic acid
transferase; Provisional.
Length = 243
Score = 31.1 bits (71), Expect = 0.99
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|214963 smart00996, AdoHcyase, S-adenosyl-L-homocysteine hydrolase.
Length = 426
Score = 31.7 bits (73), Expect = 0.99
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|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 = 31.2 bits (71), Expect = 1.0
Identities = 15/36 (41%), Positives = 20/36 (55%), Gaps = 1/36 (2%)
Query: 379 LAGKLFVVIGAG-GAGKALAYGAKAKGARVVIANRT 413
L GK+ +V GA G G +A G GA +VI +R
Sbjct: 3 LKGKVALVTGASRGIGFGIASGLAEAGANIVINSRN 38
>gnl|CDD|223990 COG1062, AdhC, Zn-dependent alcohol dehydrogenases, class III
[Energy production and conversion].
Length = 366
Score = 31.4 bits (72), Expect = 1.1
Identities = 14/26 (53%), Positives = 15/26 (57%)
Query: 385 VVIGAGGAGKALAYGAKAKGARVVIA 410
V G GG G A GAKA GA +IA
Sbjct: 190 AVFGLGGVGLAAIQGAKAAGAGRIIA 215
>gnl|CDD|235924 PRK07063, PRK07063, short chain dehydrogenase; Provisional.
Length = 260
Score = 31.2 bits (71), Expect = 1.1
Identities = 15/35 (42%), Positives = 21/35 (60%), Gaps = 1/35 (2%)
Query: 379 LAGKLFVVIGAG-GAGKALAYGAKAKGARVVIANR 412
LAGK+ +V GA G G A+A +GA V +A+
Sbjct: 5 LAGKVALVTGAAQGIGAAIARAFAREGAAVALADL 39
>gnl|CDD|180817 PRK07060, PRK07060, short chain dehydrogenase; Provisional.
Length = 245
Score = 30.8 bits (70), Expect = 1.1
Identities = 18/49 (36%), Positives = 24/49 (48%), Gaps = 5/49 (10%)
Query: 369 LNVSGGVSSALAGKLFVVIGAG-GAGKALAYGAKAKGARVVIANRTYGE 416
+N++ S GK +V GA G G+A A +GARVV A R
Sbjct: 1 MNMAFDFS----GKSVLVTGASSGIGRACAVALAQRGARVVAAARNAAA 45
>gnl|CDD|183489 PRK12384, PRK12384, sorbitol-6-phosphate dehydrogenase;
Provisional.
Length = 259
Score = 31.2 bits (71), Expect = 1.1
Identities = 12/32 (37%), Positives = 18/32 (56%), Gaps = 1/32 (3%)
Query: 381 GKLFVVIGAG-GAGKALAYGAKAKGARVVIAN 411
++ VVIG G G L +G +G RV +A+
Sbjct: 2 NQVAVVIGGGQTLGAFLCHGLAEEGYRVAVAD 33
>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 = 30.6 bits (70), Expect = 1.2
Identities = 14/33 (42%), Positives = 19/33 (57%), Gaps = 1/33 (3%)
Query: 385 VVIGA-GGAGKALAYGAKAKGARVVIANRTYGE 416
+VIGA G G A+A A G V+ A R+ G+
Sbjct: 2 IVIGATGTIGLAVAQLLSAHGHEVITAGRSSGD 34
>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 = 30.4 bits (69), Expect = 1.4
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|216396 pfam01262, AlaDh_PNT_C, Alanine dehydrogenase/PNT, C-terminal
domain. This family now also contains the lysine
2-oxoglutarate reductases.
Length = 150
Score = 30.2 bits (69), Expect = 1.4
Identities = 18/51 (35%), Positives = 19/51 (37%), Gaps = 6/51 (11%)
Query: 373 GGVSSALAGKLFVVIGAGGAGKALAYGAKAKGARVVI-----ANRTYGESL 418
GG K VVIG G G A AK GA V I +SL
Sbjct: 13 GGAGGVPPAK-VVVIGGGVVGLGAAATAKGLGAPVTILDVRPERLEQLDSL 62
>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 = 1.5
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|236399 PRK09186, PRK09186, flagellin modification protein A; Provisional.
Length = 256
Score = 30.7 bits (70), Expect = 1.5
Identities = 13/33 (39%), Positives = 16/33 (48%), Gaps = 1/33 (3%)
Query: 379 LAGKLFVVIGAGG-AGKALAYGAKAKGARVVIA 410
L GK ++ GAGG G AL G V+ A
Sbjct: 2 LKGKTILITGAGGLIGSALVKAILEAGGIVIAA 34
>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 = 1.6
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|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 = 1.6
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|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 = 30.8 bits (71), Expect = 1.7
Identities = 14/37 (37%), Positives = 19/37 (51%), Gaps = 1/37 (2%)
Query: 373 GGVSSALAGKLFVVIGAGGAGKALAYGAKAKGARVVI 409
GGV K+ V++GAG G+ A A GA V +
Sbjct: 161 GGVPGVPPAKV-VILGAGVVGENAARVALGLGAEVTV 196
>gnl|CDD|223249 COG0171, NadE, NAD synthase [Coenzyme metabolism].
Length = 268
Score = 30.7 bits (70), Expect = 1.7
Identities = 13/41 (31%), Positives = 17/41 (41%), Gaps = 10/41 (24%)
Query: 353 DYVGAISAIEDGLRGRLN----------VSGGVSSALAGKL 383
D I+ + D LR L +SGG+ SAL L
Sbjct: 4 DLEEEINRLVDFLRDYLKKAGFKGVVLGLSGGIDSALVLAL 44
>gnl|CDD|236110 PRK07831, PRK07831, short chain dehydrogenase; Provisional.
Length = 262
Score = 30.4 bits (69), Expect = 1.8
Identities = 21/49 (42%), Positives = 27/49 (55%), Gaps = 5/49 (10%)
Query: 379 LAGKLFVVIGAGGA--GKALAYGAKAKGARVVIAN---RTYGESLTFLR 422
LAGK+ +V A G G A A A +GARVVI++ R GE+ L
Sbjct: 15 LAGKVVLVTAAAGTGIGSATARRALEEGARVVISDIHERRLGETADELA 63
>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 = 30.3 bits (69), Expect = 1.8
Identities = 13/30 (43%), Positives = 20/30 (66%), Gaps = 1/30 (3%)
Query: 385 VVIGAG-GAGKALAYGAKAKGARVVIANRT 413
+V GA G G+A+A +GA+VV+A+R
Sbjct: 2 LVTGASSGIGRAIARRLAREGAKVVLADRN 31
>gnl|CDD|225740 COG3199, COG3199, Predicted inorganic polyphosphate/ATP-NAD kinase
[General function prediction only].
Length = 355
Score = 30.5 bits (69), Expect = 1.8
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|235962 PRK07201, PRK07201, short chain dehydrogenase; Provisional.
Length = 657
Score = 30.7 bits (70), Expect = 2.0
Identities = 21/64 (32%), Positives = 27/64 (42%), Gaps = 12/64 (18%)
Query: 360 AIEDGLRGRLNVSGGVSSALAGKLFVVIGA-GGAGKALAYGAKAKGARVVIANRTYGESL 418
A LRG L GK+ ++ GA G G+A A GA V + R GE+L
Sbjct: 360 ARRRDLRGPL----------VGKVVLITGASSGIGRATAIKVAEAGATVFLVARN-GEAL 408
Query: 419 TFLR 422
L
Sbjct: 409 DELV 412
>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 = 30.4 bits (69), Expect = 2.0
Identities = 12/37 (32%), Positives = 15/37 (40%), Gaps = 1/37 (2%)
Query: 378 ALAGKLFVVIG-AGGAGKALAYGAKAKGARVVIANRT 413
L G ++ G G G ALA G V+I R
Sbjct: 2 KLTGNTVLITGGTSGIGLALARKFLEAGNTVIITGRR 38
>gnl|CDD|236094 PRK07774, PRK07774, short chain dehydrogenase; Provisional.
Length = 250
Score = 30.1 bits (68), Expect = 2.1
Identities = 14/35 (40%), Positives = 20/35 (57%), Gaps = 1/35 (2%)
Query: 379 LAGKLFVVIGA-GGAGKALAYGAKAKGARVVIANR 412
K+ +V GA GG G+A A +GA VV+A+
Sbjct: 4 FDDKVAIVTGAAGGIGQAYAEALAREGASVVVADI 38
>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 = 30.3 bits (69), Expect = 2.1
Identities = 15/32 (46%), Positives = 20/32 (62%), Gaps = 1/32 (3%)
Query: 379 LAGKLFVVIGAG-GAGKALAYGAKAKGARVVI 409
LAGK+ +V GA G G+A+A GA VV+
Sbjct: 1 LAGKVALVTGASRGIGRAIAKRLARDGASVVV 32
>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 = 30.9 bits (70), Expect = 2.1
Identities = 16/35 (45%), Positives = 19/35 (54%), Gaps = 2/35 (5%)
Query: 386 VIGAGGAGKALAYGAKAKGARVVIA--NRTYGESL 418
V+GAG AG A A A GARV++ G SL
Sbjct: 168 VVGAGPAGLAAALAAARAGARVILVDEQPEAGGSL 202
>gnl|CDD|235712 PRK06138, PRK06138, short chain dehydrogenase; Provisional.
Length = 252
Score = 30.1 bits (68), Expect = 2.2
Identities = 18/35 (51%), Positives = 25/35 (71%), Gaps = 1/35 (2%)
Query: 379 LAGKLFVVIGAG-GAGKALAYGAKAKGARVVIANR 412
LAG++ +V GAG G G+A A +GARVV+A+R
Sbjct: 3 LAGRVAIVTGAGSGIGRATAKLFAREGARVVVADR 37
>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 = 30.6 bits (69), Expect = 2.2
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|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 = 30.2 bits (68), Expect = 2.3
Identities = 20/47 (42%), Positives = 23/47 (48%), Gaps = 4/47 (8%)
Query: 364 GLRGRLNVSGGVSSALAGKLFVVIGAGGAGKALAYGAKAKGARVVIA 410
GL +N +GGV G VIG GG G A GA GA +IA
Sbjct: 164 GLGAAVN-TGGVKR---GDSVAVIGCGGVGDAAIAGAALAGASKIIA 206
>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 = 30.4 bits (69), Expect = 2.3
Identities = 11/36 (30%), Positives = 19/36 (52%)
Query: 375 VSSALAGKLFVVIGAGGAGKALAYGAKAKGARVVIA 410
+ G++ +VIG G G A+ KA+G ++A
Sbjct: 156 RARLTPGEVALVIGCGPIGLAVIAALKARGVGPIVA 191
>gnl|CDD|223737 COG0665, DadA, Glycine/D-amino acid oxidases (deaminating) [Amino
acid transport and metabolism].
Length = 387
Score = 30.3 bits (68), Expect = 2.4
Identities = 10/25 (40%), Positives = 14/25 (56%)
Query: 385 VVIGAGGAGKALAYGAKAKGARVVI 409
V+IG G G + AY +GA V +
Sbjct: 8 VIIGGGIVGLSAAYYLAERGADVTV 32
>gnl|CDD|178341 PLN02740, PLN02740, Alcohol dehydrogenase-like.
Length = 381
Score = 30.2 bits (68), Expect = 2.5
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|235693 PRK06077, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 252
Score = 30.1 bits (68), Expect = 2.6
Identities = 13/32 (40%), Positives = 20/32 (62%), Gaps = 1/32 (3%)
Query: 379 LAGKLFVVIGAG-GAGKALAYGAKAKGARVVI 409
L K+ VV G+G G G+A+A +G+ VV+
Sbjct: 4 LKDKVVVVTGSGRGIGRAIAVRLAKEGSLVVV 35
>gnl|CDD|184298 PRK13748, PRK13748, putative mercuric reductase; Provisional.
Length = 561
Score = 30.1 bits (68), Expect = 2.7
Identities = 19/50 (38%), Positives = 24/50 (48%)
Query: 363 DGLRGRLNVSGGVSSALAGKLFVVIGAGGAGKALAYGAKAKGARVVIANR 412
D +RG L + S VIG+GGA A A A +GARV + R
Sbjct: 80 DKMRGWLGGADKHSGNERPLHVAVIGSGGAAMAAALKAVEQGARVTLIER 129
>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 = 29.6 bits (67), Expect = 2.9
Identities = 14/33 (42%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 381 GKLFVVIG-AGGAGKALAYGAKAKGARVVIANR 412
G + VV G A G G A A+GA+VVI +
Sbjct: 2 GLVAVVTGGASGLGLATVERLLAQGAKVVILDL 34
>gnl|CDD|235925 PRK07067, PRK07067, sorbitol dehydrogenase; Provisional.
Length = 257
Score = 29.6 bits (67), Expect = 2.9
Identities = 17/34 (50%), Positives = 24/34 (70%), Gaps = 1/34 (2%)
Query: 379 LAGKLFVVIG-AGGAGKALAYGAKAKGARVVIAN 411
L GK+ ++ G A G G+A+A A+GARVVIA+
Sbjct: 4 LQGKVALLTGAASGIGEAVAERYLAEGARVVIAD 37
>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 = 30.0 bits (68), Expect = 3.2
Identities = 13/31 (41%), Positives = 17/31 (54%)
Query: 380 AGKLFVVIGAGGAGKALAYGAKAKGARVVIA 410
G+ V+G GG G + GA A GA V+A
Sbjct: 191 PGQSVAVVGLGGVGLSALLGAVAAGASQVVA 221
>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 = 29.9 bits (68), Expect = 3.2
Identities = 15/36 (41%), Positives = 15/36 (41%)
Query: 375 VSSALAGKLFVVIGAGGAGKALAYGAKAKGARVVIA 410
AG VV GAG G AK GAR VI
Sbjct: 172 AGPVGAGDTVVVQGAGPLGLYAVAAAKLAGARRVIV 207
>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 = 29.8 bits (68), Expect = 3.3
Identities = 15/42 (35%), Positives = 18/42 (42%), Gaps = 3/42 (7%)
Query: 372 SGGVSSAL---AGKLFVVIGAGGAGKALAYGAKAKGARVVIA 410
+G V + L G V GAG G A AK G +IA
Sbjct: 175 AGAVLNVLKPRPGSSIAVFGAGAVGLAAVMAAKIAGCTTIIA 216
>gnl|CDD|237790 PRK14694, PRK14694, putative mercuric reductase; Provisional.
Length = 468
Score = 29.9 bits (67), Expect = 3.5
Identities = 13/27 (48%), Positives = 17/27 (62%)
Query: 386 VIGAGGAGKALAYGAKAKGARVVIANR 412
VIG+GG+ A A A +GARV + R
Sbjct: 11 VIGSGGSAMAAALKATERGARVTLIER 37
>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 = 29.7 bits (67), Expect = 3.6
Identities = 12/36 (33%), Positives = 16/36 (44%), Gaps = 1/36 (2%)
Query: 379 LAGKLFVVIGAGGA-GKALAYGAKAKGARVVIANRT 413
L K+ V+ G G G A+A GA+V R
Sbjct: 3 LKNKVAVITGGTGVLGGAMARALAQAGAKVAALGRN 38
>gnl|CDD|236111 PRK07843, PRK07843, 3-ketosteroid-delta-1-dehydrogenase; Reviewed.
Length = 557
Score = 29.6 bits (67), Expect = 3.9
Identities = 13/35 (37%), Positives = 18/35 (51%), Gaps = 2/35 (5%)
Query: 385 VVIGAGGAGKALAYGAKAKGARVVIANR--TYGES 417
VV+G+G AG A A +G V+ + YG S
Sbjct: 11 VVVGSGAAGMVAALTAAHRGLSTVVVEKAPHYGGS 45
>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 = 29.0 bits (66), Expect = 3.9
Identities = 22/65 (33%), Positives = 34/65 (52%), Gaps = 6/65 (9%)
Query: 379 LAGKLFVVIGAGGAGKALAYGAKAKGARVVIANRTYGESLTFL--RLMSWLLLNTLLFDS 436
L+GK +IG G G+A+A KA G +V+ +R L R +S L+ LL +S
Sbjct: 33 LSGKTVGIIGLGRIGRAVARRLKAFGMKVIAYDRYPKAEAEALGARYVS---LDELLAES 89
Query: 437 -VIVI 440
V+ +
Sbjct: 90 DVVSL 94
>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 = 3.9
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|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 = 29.4 bits (67), Expect = 4.0
Identities = 14/33 (42%), Positives = 21/33 (63%)
Query: 381 GKLFVVIGAGGAGKALAYGAKAKGARVVIANRT 413
GK ++G GG GKA+A A A G +++ NR+
Sbjct: 154 GKTLGILGLGGIGKAIARKAAAFGMKIIYHNRS 186
>gnl|CDD|131680 TIGR02632, RhaD_aldol-ADH, rhamnulose-1-phosphate aldolase/alcohol
dehydrogenase.
Length = 676
Score = 29.8 bits (67), Expect = 4.1
Identities = 16/34 (47%), Positives = 22/34 (64%), Gaps = 1/34 (2%)
Query: 379 LAGKL-FVVIGAGGAGKALAYGAKAKGARVVIAN 411
LA ++ FV GAGG G+ A A+GA VV+A+
Sbjct: 412 LARRVAFVTGGAGGIGRETARRLAAEGAHVVLAD 445
>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 = 4.1
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|236229 PRK08303, PRK08303, short chain dehydrogenase; Provisional.
Length = 305
Score = 29.6 bits (67), Expect = 4.2
Identities = 15/41 (36%), Positives = 22/41 (53%), Gaps = 1/41 (2%)
Query: 374 GVSSALAGKLFVVIGAG-GAGKALAYGAKAKGARVVIANRT 413
+ L GK+ +V GA GAG+ +A A GA V + R+
Sbjct: 1 PMMKPLRGKVALVAGATRGAGRGIAVELGAAGATVYVTGRS 41
>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 = 29.5 bits (67), Expect = 4.2
Identities = 13/31 (41%), Positives = 15/31 (48%)
Query: 380 AGKLFVVIGAGGAGKALAYGAKAKGARVVIA 410
G V G G G A+ GAKA GA +I
Sbjct: 186 PGSTVAVFGLGAVGLAVIQGAKAAGASRIIG 216
>gnl|CDD|181120 PRK07792, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 306
Score = 29.4 bits (66), Expect = 4.2
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|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 = 29.4 bits (66), Expect = 4.3
Identities = 14/36 (38%), Positives = 19/36 (52%)
Query: 375 VSSALAGKLFVVIGAGGAGKALAYGAKAKGARVVIA 410
++ ++GK +V GAG G AKA GA VI
Sbjct: 156 LAGPISGKSVLVTGAGPIGLMAIAVAKASGAYPVIV 191
>gnl|CDD|183787 PRK12844, PRK12844, 3-ketosteroid-delta-1-dehydrogenase; Reviewed.
Length = 557
Score = 29.7 bits (67), Expect = 4.4
Identities = 16/54 (29%), Positives = 22/54 (40%), Gaps = 2/54 (3%)
Query: 384 FVVIGAGGAGKALAYGAKAKGARVVIANRT--YGESLTFLRLMSWLLLNTLLFD 435
VV+G+GG G A A G +I + G S + WL N L+
Sbjct: 9 VVVVGSGGGGMCAALAAADSGLEPLIVEKQDKVGGSTAMSGGVLWLPNNPLMKA 62
>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 = 29.5 bits (66), Expect = 4.5
Identities = 16/28 (57%), Positives = 18/28 (64%)
Query: 381 GKLFVVIGAGGAGKALAYGAKAKGARVV 408
G L +VIGAGG G + AKA GA VV
Sbjct: 167 GDLVIVIGAGGVGGYMVQTAKAMGAAVV 194
>gnl|CDD|235713 PRK06139, PRK06139, short chain dehydrogenase; Provisional.
Length = 330
Score = 29.3 bits (66), Expect = 4.6
Identities = 15/39 (38%), Positives = 22/39 (56%), Gaps = 1/39 (2%)
Query: 375 VSSALAGKLFVVIGAG-GAGKALAYGAKAKGARVVIANR 412
+ L G + V+ GA G G+A A +GAR+V+A R
Sbjct: 1 MMGPLHGAVVVITGASSGIGQATAEAFARRGARLVLAAR 39
>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 = 29.1 bits (66), Expect = 4.6
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|144338 pfam00698, Acyl_transf_1, Acyl transferase domain.
Length = 319
Score = 29.3 bits (66), Expect = 4.7
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|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 = 4.8
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|236099 PRK07791, PRK07791, short chain dehydrogenase; Provisional.
Length = 286
Score = 29.3 bits (66), Expect = 4.9
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|223992 COG1064, AdhP, Zn-dependent alcohol dehydrogenases [General
function prediction only].
Length = 339
Score = 29.1 bits (66), Expect = 5.0
Identities = 16/35 (45%), Positives = 21/35 (60%), Gaps = 2/35 (5%)
Query: 375 VSSALAGKLFVVIGAGGAGK-ALAYGAKAKGARVV 408
++ GK V+GAGG G A+ Y AKA GA V+
Sbjct: 161 KANVKPGKWVAVVGAGGLGHMAVQY-AKAMGAEVI 194
>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 = 28.9 bits (65), Expect = 5.1
Identities = 17/35 (48%), Positives = 23/35 (65%), Gaps = 1/35 (2%)
Query: 379 LAGKLFVVIGAG-GAGKALAYGAKAKGARVVIANR 412
L GK+ +V GAG G G+ +A +GARVVIA+
Sbjct: 3 LEGKVAIVTGAGSGFGEGIARRFAQEGARVVIADI 37
>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 = 29.0 bits (65), Expect = 5.1
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|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 = 5.3
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|235506 PRK05565, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 247
Score = 29.0 bits (66), Expect = 5.4
Identities = 17/33 (51%), Positives = 23/33 (69%), Gaps = 1/33 (3%)
Query: 379 LAGKLFVVIGA-GGAGKALAYGAKAKGARVVIA 410
L GK+ +V GA GG G+A+A +GA+VVIA
Sbjct: 3 LMGKVAIVTGASGGIGRAIAELLAKEGAKVVIA 35
>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 = 5.4
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|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 = 5.5
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|181414 PRK08410, PRK08410, 2-hydroxyacid dehydrogenase; Provisional.
Length = 311
Score = 29.2 bits (66), Expect = 5.5
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|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 = 28.9 bits (65), Expect = 5.6
Identities = 20/66 (30%), Positives = 31/66 (46%), Gaps = 2/66 (3%)
Query: 357 AISAIEDGLRGRLNVSGGVSSALAGKLFVVIGAGGAGKALAYGAKAKGARVVIANRTYGE 416
+I+A E L RL ++ V+ L ++ GAGG G L A+ VIA + E
Sbjct: 128 SITAWEL-LFDRLGINDPVAGD-KRALLIIGGAGGVGSILIQLARQLTGLTVIATASRPE 185
Query: 417 SLTFLR 422
S ++
Sbjct: 186 SQEWVL 191
>gnl|CDD|180300 PRK05875, PRK05875, short chain dehydrogenase; Provisional.
Length = 276
Score = 29.0 bits (65), Expect = 5.7
Identities = 14/39 (35%), Positives = 21/39 (53%), Gaps = 1/39 (2%)
Query: 375 VSSALAGKLFVVIGAG-GAGKALAYGAKAKGARVVIANR 412
+ + + ++V G G G GK +A G A GA V+I R
Sbjct: 1 MQLSFQDRTYLVTGGGSGIGKGVAAGLVAAGAAVMIVGR 39
>gnl|CDD|235591 PRK05755, PRK05755, DNA polymerase I; Provisional.
Length = 880
Score = 29.3 bits (67), Expect = 5.7
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|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 = 28.8 bits (65), Expect = 5.8
Identities = 13/35 (37%), Positives = 15/35 (42%)
Query: 379 LAGKLFVVIGAGGAGKALAYGAKAKGARVVIANRT 413
G VV G G G A AK +GA VV+
Sbjct: 163 RPGDTVVVFGPGPIGLLAAQVAKLQGATVVVVGTE 197
>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 = 29.1 bits (66), Expect = 5.9
Identities = 12/29 (41%), Positives = 15/29 (51%)
Query: 380 AGKLFVVIGAGGAGKALAYGAKAKGARVV 408
G+ V G GG G + A A GARV+
Sbjct: 165 PGEWVAVHGCGGVGLSAVMIASALGARVI 193
>gnl|CDD|223980 COG1052, LdhA, Lactate dehydrogenase and related dehydrogenases
[Energy production and conversion / Coenzyme metabolism
/ General function prediction only].
Length = 324
Score = 29.1 bits (66), Expect = 5.9
Identities = 18/62 (29%), Positives = 30/62 (48%)
Query: 379 LAGKLFVVIGAGGAGKALAYGAKAKGARVVIANRTYGESLTFLRLMSWLLLNTLLFDSVI 438
L GK +IG G G+A+A K G +V+ +R+ ++ L+ LL +S I
Sbjct: 144 LRGKTLGIIGLGRIGQAVARRLKGFGMKVLYYDRSPNPEAEKELGARYVDLDELLAESDI 203
Query: 439 VI 440
+
Sbjct: 204 IS 205
>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 = 29.0 bits (66), Expect = 5.9
Identities = 10/28 (35%), Positives = 14/28 (50%)
Query: 385 VVIGAGGAGKALAYGAKAKGARVVIANR 412
+IG G AG ALA +G +V +
Sbjct: 264 AIIGGGIAGAALALALARRGWQVTLYEA 291
>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 = 29.1 bits (66), Expect = 6.0
Identities = 17/36 (47%), Positives = 19/36 (52%)
Query: 385 VVIGAGGAGKALAYGAKAKGARVVIANRTYGESLTF 420
+VIGAG G A AKA GAR VI + L F
Sbjct: 170 LVIGAGPIGLLHAMLAKASGARKVIVSDLNEFRLEF 205
>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 = 6.1
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|181077 PRK07677, PRK07677, short chain dehydrogenase; Provisional.
Length = 252
Score = 28.9 bits (65), Expect = 6.2
Identities = 18/38 (47%), Positives = 21/38 (55%), Gaps = 4/38 (10%)
Query: 385 VVI---GAGGAGKALAYGAKAKGARVVIANRTYGESLT 419
VVI G+ G GKA+A +GA VVI RT E L
Sbjct: 3 VVIITGGSSGMGKAMAKRFAEEGANVVITGRT-KEKLE 39
>gnl|CDD|181335 PRK08264, PRK08264, short chain dehydrogenase; Validated.
Length = 238
Score = 28.7 bits (65), Expect = 6.2
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|180371 PRK06057, PRK06057, short chain dehydrogenase; Provisional.
Length = 255
Score = 28.5 bits (64), Expect = 6.3
Identities = 15/34 (44%), Positives = 21/34 (61%), Gaps = 1/34 (2%)
Query: 379 LAGKLFVVIGAG-GAGKALAYGAKAKGARVVIAN 411
LAG++ V+ G G G G A A A+GA VV+ +
Sbjct: 5 LAGRVAVITGGGSGIGLATARRLAAEGATVVVGD 38
>gnl|CDD|235800 PRK06436, PRK06436, glycerate dehydrogenase; Provisional.
Length = 303
Score = 28.7 bits (64), Expect = 6.3
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|223189 COG0111, SerA, Phosphoglycerate dehydrogenase and related
dehydrogenases [Amino acid transport and metabolism].
Length = 324
Score = 28.8 bits (65), Expect = 6.4
Identities = 20/76 (26%), Positives = 34/76 (44%), Gaps = 1/76 (1%)
Query: 366 RGRLNVSGGVSSALAGKLFVVIGAGGAGKALAYGAKAKGARVVIANRTYGESL-TFLRLM 424
RG + + LAGK +IG G G+A+A KA G +V+ + ++
Sbjct: 127 RGEWDRKAFRGTELAGKTVGIIGLGRIGRAVAKRLKAFGMKVIGYDPYSPRERAGVDGVV 186
Query: 425 SWLLLNTLLFDSVIVI 440
L+ LL ++ I+
Sbjct: 187 GVDSLDELLAEADILT 202
>gnl|CDD|223137 COG0059, IlvC, Ketol-acid reductoisomerase [Amino acid transport
and metabolism / Coenzyme metabolism].
Length = 338
Score = 28.7 bits (65), Expect = 6.4
Identities = 13/36 (36%), Positives = 16/36 (44%)
Query: 377 SALAGKLFVVIGAGGAGKALAYGAKAKGARVVIANR 412
L GK +IG G G A A + G V+I R
Sbjct: 14 DLLKGKKVAIIGYGSQGHAQALNLRDSGLNVIIGLR 49
>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 = 28.7 bits (65), Expect = 6.5
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|180604 PRK06523, PRK06523, short chain dehydrogenase; Provisional.
Length = 260
Score = 28.7 bits (65), Expect = 6.6
Identities = 16/41 (39%), Positives = 19/41 (46%), Gaps = 1/41 (2%)
Query: 379 LAGKLFVVIGAG-GAGKALAYGAKAKGARVVIANRTYGESL 418
LAGK +V G G G A GARVV R+ + L
Sbjct: 7 LAGKRALVTGGTKGIGAATVARLLEAGARVVTTARSRPDDL 47
>gnl|CDD|225276 COG2413, COG2413, Predicted nucleotidyltransferase [General
function prediction only].
Length = 228
Score = 28.6 bits (64), Expect = 6.6
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|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 = 28.7 bits (65), Expect = 6.7
Identities = 12/30 (40%), Positives = 13/30 (43%)
Query: 380 AGKLFVVIGAGGAGKALAYGAKAKGARVVI 409
G V GAG G AY A +GA V
Sbjct: 176 PGDTVAVFGAGPVGLMAAYSAILRGASRVY 205
>gnl|CDD|223727 COG0654, UbiH, 2-polyprenyl-6-methoxyphenol hydroxylase and related
FAD-dependent oxidoreductases [Coenzyme metabolism /
Energy production and conversion].
Length = 387
Score = 28.9 bits (65), Expect = 6.8
Identities = 14/38 (36%), Positives = 17/38 (44%)
Query: 385 VVIGAGGAGKALAYGAKAKGARVVIANRTYGESLTFLR 422
++GAG AG ALA G V + R E L R
Sbjct: 6 AIVGAGPAGLALALALARAGLDVTLLERAPRELLERGR 43
>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 = 6.8
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|178566 PLN02985, PLN02985, squalene monooxygenase.
Length = 514
Score = 29.1 bits (65), Expect = 6.9
Identities = 13/32 (40%), Positives = 17/32 (53%)
Query: 385 VVIGAGGAGKALAYGAKAKGARVVIANRTYGE 416
+++GAG G ALAY G RV + R E
Sbjct: 47 IIVGAGVGGSALAYALAKDGRRVHVIERDLRE 78
>gnl|CDD|235546 PRK05653, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Validated.
Length = 246
Score = 28.6 bits (65), Expect = 7.2
Identities = 15/36 (41%), Positives = 20/36 (55%), Gaps = 1/36 (2%)
Query: 379 LAGKLFVVIGAGGA-GKALAYGAKAKGARVVIANRT 413
L GK +V GA G+A+A A GA+VVI +
Sbjct: 3 LQGKTALVTGASRGIGRAIALRLAADGAKVVIYDSN 38
>gnl|CDD|223523 COG0446, HcaD, Uncharacterized NAD(FAD)-dependent dehydrogenases
[General function prediction only].
Length = 415
Score = 28.7 bits (64), Expect = 7.2
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|236635 PRK09928, PRK09928, choline transport protein BetT; Provisional.
Length = 679
Score = 28.9 bits (65), Expect = 7.2
Identities = 14/56 (25%), Positives = 26/56 (46%), Gaps = 1/56 (1%)
Query: 429 LNTLLFDSVIVIRILLFTWHLKFFIAANIIHLGNHLEWVTAAFNLFFYLTCNSYVV 484
+N ++F + + ILLF+ F + + L WV+ F ++ L Y+V
Sbjct: 15 INPVVFYTSAGL-ILLFSLTTILFTDFSNRWINRTLNWVSKTFGWYYLLAATLYIV 69
>gnl|CDD|224789 COG1877, OtsB, Trehalose-6-phosphatase [Carbohydrate transport and
metabolism].
Length = 266
Score = 28.5 bits (64), Expect = 7.3
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|235737 PRK06197, PRK06197, short chain dehydrogenase; Provisional.
Length = 306
Score = 28.5 bits (64), Expect = 7.3
Identities = 18/37 (48%), Positives = 21/37 (56%), Gaps = 9/37 (24%)
Query: 381 GKLFVVIGA-GGAG----KALAYGAKAKGARVVIANR 412
G++ VV GA G G ALA AKGA VV+A R
Sbjct: 16 GRVAVVTGANTGLGYETAAALA----AKGAHVVLAVR 48
>gnl|CDD|183833 PRK12939, PRK12939, short chain dehydrogenase; Provisional.
Length = 250
Score = 28.4 bits (64), Expect = 7.4
Identities = 15/35 (42%), Positives = 16/35 (45%), Gaps = 1/35 (2%)
Query: 377 SALAGKLFVVIGAG-GAGKALAYGAKAKGARVVIA 410
S LAGK +V GA G G A A GA V
Sbjct: 3 SNLAGKRALVTGAARGLGAAFAEALAEAGATVAFN 37
>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 = 28.3 bits (64), Expect = 7.8
Identities = 16/35 (45%), Positives = 18/35 (51%), Gaps = 1/35 (2%)
Query: 379 LAGK-LFVVIGAGGAGKALAYGAKAKGARVVIANR 412
L GK F+ G G GKA+A GA V IA R
Sbjct: 1 LKGKVAFITGGGTGIGKAIAKAFAELGASVAIAGR 35
>gnl|CDD|180458 PRK06194, PRK06194, hypothetical protein; Provisional.
Length = 287
Score = 28.4 bits (64), Expect = 8.0
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|176543 cd08601, GDPD_SaGlpQ_like, Glycerophosphodiester phosphodiesterase
domain of Staphylococcus aureus and similar proteins.
This subfamily corresponds to the glycerophosphodiester
phosphodiesterase domain (GDPD) present in
uncharacterized glycerophosphodiester phosphodiesterase
(GP-GDE, EC 3.1.4.46) from Staphylococcus aureus,
Bacillus subtilis and similar proteins. Members in this
family show very high sequence similarity to Escherichia
coli periplasmic phosphodiesterase GlpQ, which catalyzes
the Ca2+-dependent degradation of periplasmic
glycerophosphodiesters to produce
sn-glycerol-3-phosphate (G3P) and the corresponding
alcohols.
Length = 256
Score = 28.4 bits (64), Expect = 8.1
Identities = 10/16 (62%), Positives = 14/16 (87%)
Query: 105 RLAMELGADYIDVELQ 120
LA E+GADYI+++LQ
Sbjct: 22 DLAREMGADYIELDLQ 37
>gnl|CDD|221798 pfam12831, FAD_oxidored, FAD dependent oxidoreductase. This family
of proteins contains FAD dependent oxidoreductases and
related proteins.
Length = 415
Score = 28.7 bits (65), Expect = 8.6
Identities = 13/29 (44%), Positives = 17/29 (58%)
Query: 385 VVIGAGGAGKALAYGAKAKGARVVIANRT 413
VV+G G AG A A A GA+V++ R
Sbjct: 3 VVVGGGPAGVAAAIAAARLGAKVLLVERR 31
>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 = 27.3 bits (61), Expect = 8.8
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|223429 COG0352, ThiE, Thiamine monophosphate synthase [Coenzyme
metabolism].
Length = 211
Score = 28.0 bits (63), Expect = 9.1
Identities = 22/110 (20%), Positives = 42/110 (38%), Gaps = 29/110 (26%)
Query: 102 DVLRLAMELGADYI-----DVELQVAREFNDSIRGKKPEKCKVIVSSHNYQYTPSVEDLS 156
D + LA+ +GAD + D+ L ARE + G + +S+H+ +
Sbjct: 72 DRVDLALAVGADGVHLGQDDMPLAEARE----LLGP---GLIIGLSTHDLE--------- 115
Query: 157 NLVARIQASGADIVK----FATT---ALDITDVARVFQITVHSQVPIIGL 199
+ GAD V F T+ + + +I +P++ +
Sbjct: 116 -EALEAEELGADYVGLGPIFPTSTKPDAPPLGLEGLREIRELVNIPVVAI 164
>gnl|CDD|133445 cd01076, NAD_bind_1_Glu_DH, NAD(P) binding domain of glutamate
dehydrogenase, subgroup 1. 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+. Glutamate DH is a multidomain enzyme that
catalyzes the reaction from glutamate to 2-oxyoglutarate
and ammonia in the presence of NAD or NADP. It is
present in all organisms. Enzymes involved in ammonia
assimilation are typically NADP+-dependent, while those
involved in glutamate catabolism are generally
NAD+-dependent. 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 = 227
Score = 28.3 bits (64), Expect = 9.2
Identities = 11/30 (36%), Positives = 13/30 (43%)
Query: 379 LAGKLFVVIGAGGAGKALAYGAKAKGARVV 408
LAG + G G G A GA+VV
Sbjct: 29 LAGARVAIQGFGNVGSHAARFLHEAGAKVV 58
>gnl|CDD|237529 PRK13841, PRK13841, conjugal transfer protein TrbL; Provisional.
Length = 391
Score = 28.3 bits (63), Expect = 9.2
Identities = 15/36 (41%), Positives = 20/36 (55%)
Query: 372 SGGVSSALAGKLFVVIGAGGAGKALAYGAKAKGARV 407
G +S AG F+ GA GAG A A A+A G+ +
Sbjct: 290 GGQAASFAAGAAFLAAGAAGAGFAAASAARAGGSSL 325
>gnl|CDD|234831 PRK00768, nadE, NAD synthetase; Reviewed.
Length = 268
Score = 28.2 bits (64), Expect = 9.2
Identities = 9/15 (60%), Positives = 11/15 (73%)
Query: 369 LNVSGGVSSALAGKL 383
L +SGG S LAG+L
Sbjct: 43 LGISGGQDSTLAGRL 57
>gnl|CDD|235935 PRK07109, PRK07109, short chain dehydrogenase; Provisional.
Length = 334
Score = 28.3 bits (64), Expect = 9.2
Identities = 12/29 (41%), Positives = 17/29 (58%), Gaps = 1/29 (3%)
Query: 385 VVIGA-GGAGKALAYGAKAKGARVVIANR 412
V+ GA G G+A A +GA+VV+ R
Sbjct: 12 VITGASAGVGRATARAFARRGAKVVLLAR 40
>gnl|CDD|224927 COG2016, COG2016, Predicted RNA-binding protein (contains PUA
domain) [Translation, ribosomal structure and
biogenesis].
Length = 161
Score = 27.6 bits (62), Expect = 9.6
Identities = 11/32 (34%), Positives = 16/32 (50%), Gaps = 2/32 (6%)
Query: 23 PTLICVPIMGESVDKMVVDMG--KANASGADL 52
PTL + + +VVD G K +GAD+
Sbjct: 64 PTLRLLLKLPPGKYVVVVDEGAVKFVLNGADV 95
>gnl|CDD|223377 COG0300, DltE, Short-chain dehydrogenases of various substrate
specificities [General function prediction only].
Length = 265
Score = 28.0 bits (63), Expect = 9.7
Identities = 10/37 (27%), Positives = 17/37 (45%), Gaps = 1/37 (2%)
Query: 378 ALAGKLFVVIGA-GGAGKALAYGAKAKGARVVIANRT 413
+ GK ++ GA G G LA +G +++ R
Sbjct: 3 PMKGKTALITGASSGIGAELAKQLARRGYNLILVARR 39
>gnl|CDD|216319 pfam01134, GIDA, Glucose inhibited division protein A.
Length = 391
Score = 28.3 bits (64), Expect = 9.8
Identities = 11/24 (45%), Positives = 14/24 (58%)
Query: 385 VVIGAGGAGKALAYGAKAKGARVV 408
+VIG G AG A A GA+V+
Sbjct: 3 IVIGGGHAGCEAALAAARMGAKVL 26
>gnl|CDD|235000 PRK02106, PRK02106, choline dehydrogenase; Validated.
Length = 560
Score = 28.6 bits (65), Expect = 9.8
Identities = 8/15 (53%), Positives = 11/15 (73%)
Query: 384 FVVIGAGGAGKALAY 398
+++IGAG AG LA
Sbjct: 8 YIIIGAGSAGCVLAN 22
>gnl|CDD|235412 PRK05329, PRK05329, anaerobic glycerol-3-phosphate dehydrogenase
subunit B; Validated.
Length = 422
Score = 28.3 bits (64), Expect = 9.8
Identities = 11/28 (39%), Positives = 14/28 (50%)
Query: 385 VVIGAGGAGKALAYGAKAKGARVVIANR 412
+VIG G AG A A G RV + +
Sbjct: 6 LVIGGGLAGLTAALAAAEAGKRVALVAK 33
>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 = 28.1 bits (63), Expect = 10.0
Identities = 14/39 (35%), Positives = 18/39 (46%)
Query: 379 LAGKLFVVIGAGGAGKALAYGAKAKGARVVIANRTYGES 417
L GK +IG G G A A + G V++ R G S
Sbjct: 1 LKGKTVAIIGYGSQGHAQALNLRDSGLNVIVGLRKGGAS 39
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.322 0.139 0.410
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: 25,627,354
Number of extensions: 2612767
Number of successful extensions: 3698
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3620
Number of HSP's successfully gapped: 290
Length of query: 493
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 392
Effective length of database: 6,457,848
Effective search space: 2531476416
Effective search space used: 2531476416
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 61 (27.1 bits)