RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 010050
(519 letters)
>gnl|CDD|178135 PLN02520, PLN02520, bifunctional 3-dehydroquinate
dehydratase/shikimate dehydrogenase.
Length = 529
Score = 672 bits (1735), Expect = 0.0
Identities = 285/516 (55%), Positives = 364/516 (70%), Gaps = 5/516 (0%)
Query: 1 MGVVNITKNTTMICAPLMAQSVEQVLSNMYQAKAEGADVVEIRLDCINNFQPGKDLEIIL 60
G + +N T+IC P+MA SV+++L M +AK GAD+VEIRLD + NF P +DL+ ++
Sbjct: 13 QGSGGVRRNPTLICVPIMADSVDKMLIEMAKAKELGADLVEIRLDFLKNFNPREDLKTLI 72
Query: 61 TKKPLPVLIVYRPKWAGGLYEGDEHKRLEALHLAEDLGADYVDFELKVASNILGKQYSSH 120
+ PLP L+ YRPKW GG YEGDE+KR +AL LA +LGADYVD ELKVA +
Sbjct: 73 KQSPLPTLVTYRPKWEGGQYEGDENKRQDALRLAMELGADYVDVELKVAHEFINSISGKK 132
Query: 121 QSGTRFIVSCNLDCETPSEEDLGYLVSRMQATGADIIKLVFSVNDITEIARIFQLLSHCQ 180
+ IVS + TPS E+LG LV+R+QATGADI+K+ + DIT++AR+FQ+ H Q
Sbjct: 133 PEKCKVIVSSHNYENTPSVEELGNLVARIQATGADIVKIATTALDITDVARMFQITVHSQ 192
Query: 181 VPIIAYSVGERGLVSQLLSPKFNGALVYGSLKGTPVL--GLPTVESLRQTYKVEHINADT 238
VP I +GERGL+S++L PKF G L +G+L+ V G PT++ L Y I DT
Sbjct: 193 VPTIGLVMGERGLISRILCPKFGGYLTFGTLEAGKVSAPGQPTIKDLLDLYNFRQIGPDT 252
Query: 239 KVFGLISKPVGHSKGPILHNPTFRHVNYNGIYVPMFVDDLKKFFSTYSSPDFAGFSVGFP 298
KV+G+I KPVGHSK PILHN F+ V +NG+YV + VDDL KF TYSSPDFAGFS P
Sbjct: 253 KVYGIIGKPVGHSKSPILHNEAFKSVGFNGVYVHLLVDDLAKFLQTYSSPDFAGFSCTIP 312
Query: 299 YKEAVMKFCDEVHPLAQAIAAVNTIIRRPSDGKLIGYNTDCEASITAIEDAIKERGYKNG 358
+KE +K CDEV P+A++I A+NTIIRRPSDGKL+GYNTD +I+AIED ++
Sbjct: 313 HKEDALKCCDEVDPIAKSIGAINTIIRRPSDGKLVGYNTDYIGAISAIEDGLRA---SGS 369
Query: 359 TASFGSPLAGRMFVLAGAGGAGRALAFGAKSRGARVVIFDIDFERAKSLASDVMGAARPF 418
+ + GSPLAG++FV+ GAGGAG+ALA+GAK +GARVVI + +ERAK LA V G A
Sbjct: 370 SPASGSPLAGKLFVVIGAGGAGKALAYGAKEKGARVVIANRTYERAKELADAVGGQALTL 429
Query: 419 EDILNFQPEKGAILANATPLGMHPNTDRVPVSEETLRDYQLVFDAVYTPRKTRLLKDAEA 478
D+ NF PE+G ILAN T +GM PN D P+S+ L+ Y LVFDAVYTP+ TRLL++AE
Sbjct: 430 ADLENFHPEEGMILANTTSVGMQPNVDETPISKHALKHYSLVFDAVYTPKITRLLREAEE 489
Query: 479 AGAIIVSGVEMFLRQAIGQFNLFTGKEAPKEFMREI 514
+GAIIVSG EMF+RQA QF FTG APKE REI
Sbjct: 490 SGAIIVSGTEMFIRQAYEQFERFTGLPAPKELFREI 525
>gnl|CDD|223247 COG0169, AroE, Shikimate 5-dehydrogenase [Amino acid transport and
metabolism].
Length = 283
Score = 265 bits (680), Expect = 1e-85
Identities = 105/293 (35%), Positives = 152/293 (51%), Gaps = 20/293 (6%)
Query: 234 INADTKVFGLISKPVGHSKGPILHNPTFRHVNYNGIYVPMFV--DDLKKFFSTYSSPDFA 291
+N TK+FG+I P+ HS P +HN FR + + +Y+ V +DL + S + F
Sbjct: 2 MNGKTKLFGVIGNPISHSLSPRMHNAAFRALGLDYVYLAFEVPPEDLPEAVSGIRALGFR 61
Query: 292 GFSVGFPYKEAVMKFCDEVHPLAQAIAAVNTIIRRPSDGKLIGYNTDCEASITAIEDAIK 351
G +V P+KEA + DE+ P A+ I AVNT++R DGKL GYNTD A+K
Sbjct: 62 GLNVTIPFKEAALPLLDELSPRARLIGAVNTLVRE-DDGKLRGYNTDGIG----FLRALK 116
Query: 352 ERGYKNGTASFGSPLAGRMFVLAGAGGAGRALAFGAKSRGA-RVVIFDIDFERAKSLASD 410
E G + G+ ++ GAGGA RA+AF GA R+ + + ERA+ LA D
Sbjct: 117 EFGLPV-------DVTGKRVLILGAGGAARAVAFALAEAGAKRITVVNRTRERAEELA-D 168
Query: 411 VMGAARPFEDILNFQPEKGA----ILANATPLGMHPNTDRVPVSEETLRDYQLVFDAVYT 466
+ G + +G +L NATP+GM PV E L +V+D VY
Sbjct: 169 LFGELGAAVEAAALADLEGLEEADLLINATPVGMAGPEGDSPVPAELLPKGAIVYDVVYN 228
Query: 467 PRKTRLLKDAEAAGAIIVSGVEMFLRQAIGQFNLFTGKEAPKEFMREIVLAKF 519
P +T LL++A A GA + G+ M + QA F L+TG E P + M+E ++
Sbjct: 229 PLETPLLREARAQGAKTIDGLGMLVHQAAEAFELWTGVEPPVDVMKEALIEAL 281
>gnl|CDD|234703 PRK00258, aroE, shikimate 5-dehydrogenase; Reviewed.
Length = 278
Score = 235 bits (601), Expect = 7e-74
Identities = 95/291 (32%), Positives = 141/291 (48%), Gaps = 20/291 (6%)
Query: 234 INADTKVFGLISKPVGHSKGPILHNPTFRHVNYNGIYVPMFV--DDLKKFFSTYSSPDFA 291
I T+++ +I P+ HSK P++HN F+ + +G+Y+ + V +DL+ + +
Sbjct: 1 ITGKTRLYAVIGNPIAHSKSPLIHNAAFKQLGLDGVYLAILVPPEDLEDAVKGFFALGGR 60
Query: 292 GFSVGFPYKEAVMKFCDEVHPLAQAIAAVNTIIRRPSDGKLIGYNTDCEASITAIEDAIK 351
G +V P+KEA DE+ A+ I AVNT++ DG+LIG NTD A++
Sbjct: 61 GANVTVPFKEAAFALADELSERARLIGAVNTLVLE--DGRLIGDNTD----GIGFVRALE 114
Query: 352 ERGYKNGTASFGSPLAGRMFVLAGAGGAGRALAFGAKSRG-ARVVIFDIDFERAKSLASD 410
ER G L G+ ++ GAGGA RA+ G A + I + ERA+ LA
Sbjct: 115 ERL--------GVDLKGKRILILGAGGAARAVILPLLDLGVAEITIVNRTVERAEELA-K 165
Query: 411 VMGAARPFEDILNFQPEKGA--ILANATPLGMHPNTDRVPVSEETLRDYQLVFDAVYTPR 468
+ GA E L Q E ++ NAT GM P+ LR +V+D +Y P
Sbjct: 166 LFGALGKAELDLELQEELADFDLIINATSAGMSGELPLPPLPLSLLRPGTIVYDMIYGPL 225
Query: 469 KTRLLKDAEAAGAIIVSGVEMFLRQAIGQFNLFTGKEAPKEFMREIVLAKF 519
T L A+A GA + G+ M + QA F L+TG P E M + A
Sbjct: 226 PTPFLAWAKAQGARTIDGLGMLVHQAAEAFELWTGVRPPVEPMLAALRAAL 276
>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 = 205 bits (524), Expect = 1e-62
Identities = 92/288 (31%), Positives = 145/288 (50%), Gaps = 26/288 (9%)
Query: 239 KVFGLISKPVGHSKGPILHNPTFRHVNYNGIYVPMFV--DDLKKFFSTYSSPDFAGFSVG 296
K++G+I P+ HSK P++HN F+ + G Y+ V DDL+ S + + F G +V
Sbjct: 1 KLYGVIGNPIAHSKSPLIHNAFFKQLGLEGPYIAFLVPPDDLEDALSGFFALGFKGANVT 60
Query: 297 FPYKEAVMKFCDEVHPLAQAIAAVNTIIRRPSDGKLIGYNTDCEASITAIEDAIKERGYK 356
P+KE +F DE+ A+ AVNT++ DGKL+GYNTD ++ +E I R +
Sbjct: 61 SPFKERAFQFLDEIDGRAKLAGAVNTLVLE--DGKLVGYNTDGIGLVSDLEQLIPLRPNQ 118
Query: 357 NGTASFGSPLAGRMFVLAGAGGAGRALAFGAKSRGARVVIFDIDFERAKSLASDVMGAAR 416
N ++ GAGGA +A+A V+I + +A+ LA +
Sbjct: 119 N-------------VLIIGAGGAAKAVALELLKADCNVIIANRTVSKAEELAE----RFQ 161
Query: 417 PFEDILNFQ-----PEKGAILANATPLGMHPNTDRVPVSEETLRDYQLVFDAVYTPRKTR 471
+ +I F + ++ NAT GM N D PV E L++ +LV+D VY P +T
Sbjct: 162 RYGEIQAFSMDELPLHRVDLIINATSAGMSGNIDEPPVPAEYLKEGKLVYDLVYNPLETP 221
Query: 472 LLKDAEAAGAIIVSGVEMFLRQAIGQFNLFTGKEAPKEFMREIVLAKF 519
L +A++ G + G+ M + QA F L+TG E E M E +++
Sbjct: 222 FLAEAKSLGTKTIDGLGMLVYQAALSFELWTGVEPDIEKMFEQLISVL 269
>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 = 192 bits (489), Expect = 3e-58
Identities = 79/223 (35%), Positives = 117/223 (52%), Gaps = 7/223 (3%)
Query: 14 CAPLMAQSVEQVLSNMYQAKAEGADVVEIRLDCINNFQPG---KDLEIILTKKPLPVLIV 70
C P+ S+E+ L+ + + EGAD VE+RLD + + + L + K LP++
Sbjct: 1 CVPVTGPSLEEALAEL-EELEEGADAVELRLDLLEDVDAEDVSEQLSALREKTGLPIIFT 59
Query: 71 YRPKWAGGLYEGDEHKRLEALHLAEDLGADYVDFELKVASNILGKQYSSHQSGTRFIVSC 130
R K GG ++G E + LE L A LG DY+D EL A + L + + GT+ I+S
Sbjct: 60 VRTKSEGGRFDGSEEEYLELLKEALRLGPDYIDIELSSAPDELLAVIIAKKGGTKIILSY 119
Query: 131 NLDCETPSEEDLGYLVSRMQATGADIIKLVFSVNDITEIARIFQLLSHCQ---VPIIAYS 187
+ TPS EDL L MQ GADI+K+ N I ++ R+ + S + P+IA S
Sbjct: 120 HDFEGTPSWEDLLSLYEEMQKLGADIVKIAVMANSIEDVLRLLRFTSEAKELDKPLIAIS 179
Query: 188 VGERGLVSQLLSPKFNGALVYGSLKGTPVLGLPTVESLRQTYK 230
+GE G +S++L P F L Y SL G T+E LR+ +
Sbjct: 180 MGELGRISRILGPVFGSVLTYASLGKASAPGQITLEELREALE 222
>gnl|CDD|183585 PRK12548, PRK12548, shikimate 5-dehydrogenase; Provisional.
Length = 289
Score = 163 bits (414), Expect = 2e-46
Identities = 94/293 (32%), Positives = 138/293 (47%), Gaps = 33/293 (11%)
Query: 234 INADTKVFGLISKPVGHSKGPILHNPTFRHVNYNGIYVP--MFVDDLKKFFSTYSSPDFA 291
I+ T + GLI PVGHS P ++N +F+ + Y+ + VD + + +
Sbjct: 5 ISGTTGLLGLIGSPVGHSGSPAMYNYSFQKAGLDYAYLAFDIPVDKVPDAIKAIKTFNMR 64
Query: 292 GFSVGFPYKEAVMKFCDEVHPLAQAIAAVNTIIRRPSDGKLIGYNTDCEASITAIEDAIK 351
G +V P K K+ DE+ P A+ I AVNTI+ DGKL G+ TD + + +
Sbjct: 65 GANVTMPCKSEAAKYMDELSPAARIIGAVNTIVN--DDGKLTGHITDGLGFVRNLREH-- 120
Query: 352 ERGYKNGTASFGSPLAGRMFVLAGAGGAGRALAFGAKSRGAR-VVIFDID---FERAKSL 407
G + G+ + GAGGA A+ GA+ + IF+I +ERA+
Sbjct: 121 -----------GVDVKGKKLTVIGAGGAATAIQVQCALDGAKEITIFNIKDDFYERAEQT 169
Query: 408 ASDVMGAARP--------FEDI--LNFQPEKGAILANATPLGMHPNTDRVPVSEET-LRD 456
A + P D L + IL NAT +GM PN + + + R
Sbjct: 170 AEKIKQEV-PECIVNVYDLNDTEKLKAEIASSDILVNATLVGMKPNDGETNIKDTSVFRK 228
Query: 457 YQLVFDAVYTPRKTRLLKDAEAAGAIIVSGVEMFLRQAIGQFNLFTGKEAPKE 509
+V D VY P+KT+LL+DAEAAG V G+ M L Q + L+TGK+ P E
Sbjct: 229 DLVVADTVYNPKKTKLLEDAEAAGCKTVGGLGMLLWQGAEAYKLYTGKDMPVE 281
>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 = 153 bits (389), Expect = 1e-43
Identities = 80/230 (34%), Positives = 118/230 (51%), Gaps = 17/230 (7%)
Query: 12 MICAPLMA-QSVEQVLSNMYQAKAEGADVVEIRLDCINN---FQPGKDLEIILTKKPLPV 67
IC PL +E+ LS GAD VE+R+D + + + L ++ PLP+
Sbjct: 1 KICVPLTGPDLLEEALSL--LELLLGADAVELRVDLLEDPSIDDVAEQLSLLRELTPLPI 58
Query: 68 LIVYRPKWAGGLYEGDEHKRLEALHLAEDLGADYVDFELKVASNILGKQYSSHQSG-TRF 126
+ R K GG +EG E + LE L A LG DYVD EL S +L + +S + G T+
Sbjct: 59 IFTVRTKSEGGNFEGSEEEYLELLEEALKLGPDYVDIELD--SALLEELINSRKKGNTKI 116
Query: 127 IVSCNLDCETPSEEDLGYLVSRMQATGADIIKLVFSVNDITEIARIFQLLSHCQ----VP 182
I S + TPS+E+L + +M A GADI+K+ N I + R+ + + +P
Sbjct: 117 IGSYHDFSGTPSDEELVSRLEKMAALGADIVKIAVMANSIEDNLRLLKFTRQVKNLYDIP 176
Query: 183 IIAYSVGERGLVSQLLSPKFNGALVYGSLKG--TPVLGLPTVESLRQTYK 230
+IA ++GE G +S++LSP F L Y SL P G +VE L+Q
Sbjct: 177 LIAINMGELGKLSRILSPVFGSPLTYASLPEPSAP--GQLSVEELKQALS 224
>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 = 148 bits (375), Expect = 2e-41
Identities = 64/230 (27%), Positives = 116/230 (50%), Gaps = 14/230 (6%)
Query: 12 MICAPLMAQSVEQVLSNMYQAKAEGADVVEIRLDCINNFQPGKDL-----EIILTKKPLP 66
I PL A +E+ L+ + +GAD+VE+R+D + + D+ ++ + P
Sbjct: 1 KIFVPLTAPDLEEALATA-EKICKGADIVELRVDLLKDPSSNNDVDALIEQLSQLRPDKP 59
Query: 67 VLIVYRPKWAGGLYEGDEHKRLEALHLAED-LGADYVDFELKVASNILGKQY-SSHQSGT 124
++ R GG + G+E + LE L A D G D+VD EL + + + + + + GT
Sbjct: 60 LIFTIRTISEGGKFPGNEEEYLEELKRAADSPGPDFVDIELFLPDDAVKELINIAKKGGT 119
Query: 125 RFIVSCNLDCE-TPSEEDLGYLVSRMQATGADIIKLVFSVNDITEIARIFQLLSHCQ--- 180
+ I+S D + TPS E++ + + + GADI+K+ N ++ + ++ +
Sbjct: 120 KIIMS-YHDFQKTPSWEEIVERLEKALSYGADIVKIAVMANSKEDVLTLLEITNKVDEHA 178
Query: 181 -VPIIAYSVGERGLVSQLLSPKFNGALVYGSLKGTPVLGLPTVESLRQTY 229
VP+I S+G+RG +S++L F L +GSL G +V+ LR+
Sbjct: 179 DVPLITMSMGDRGKISRVLGAVFGSVLTFGSLGKASAPGQISVDDLRELL 228
>gnl|CDD|137204 PRK09310, aroDE, bifunctional 3-dehydroquinate
dehydratase/shikimate dehydrogenase protein; Reviewed.
Length = 477
Score = 154 bits (391), Expect = 2e-41
Identities = 138/522 (26%), Positives = 228/522 (43%), Gaps = 59/522 (11%)
Query: 12 MICA----PLMAQSVEQVLSNMYQAKAEGADVVEIRLDCINNFQPGKDLEIILTKKPLPV 67
M+CA P ++ +Q+L ++ D +E+R+D + + +L+ ++ P+P+
Sbjct: 1 MLCATISGPSFLEAKQQILRSLKLV-----DCIELRVDLLLSLS-DLELKKLIELAPIPI 54
Query: 68 LIVYRPKWAGGLYEGDEHKRLEALHLAEDLGADYVDFELKVASNILGKQYSSHQSGTRFI 127
L + + + ++ LA+ L +Y+D + L + H + I
Sbjct: 55 LTWKKHE---SCSQAAWIDKM--QSLAK-LNPNYLDIDKDFPKEALIRIRKLHPK-IKII 107
Query: 128 VSCNLDCETPSEEDLGYLVSRMQATGADIIKLVFSVNDITEIARIFQLLSHCQVPIIAYS 187
+S + T ED+ L + M A+ AD K+ S + T++ I
Sbjct: 108 LSYH----TSEHEDIIQLYNEMLASAADYYKIAVSSSSSTDLLNIIHQKRSLPENTTVLC 163
Query: 188 VGERGLVSQLLSPKFNGALVYGSLKGTPVL--GLPTVESLRQTYKVEHINADTKVFGLIS 245
+G G S++LSP A Y + G P + G ++E L Y +++A + ++GLI
Sbjct: 164 MGGMGRPSRILSPLLQNAFNYAAGIGAPPVAPGQLSLEHL-LFYNYANLSAQSPIYGLIG 222
Query: 246 KPVGHSKGPILHNPTFRHVNYNGIYV--PMFVDDLKKFFSTYSSPDFAGFSVGFPYKEAV 303
PV S + HNP F ++ N Y+ P+ +L KFFST F G SV P K AV
Sbjct: 223 DPVDRSISHLSHNPLFSQLSLNCPYIKLPLTPQELPKFFSTIRDLPFLGLSVTMPLKTAV 282
Query: 304 MKFCDEVHPLAQAIAAVNTIIRRPSDGKLIGYNTDCEASITAIEDAIKERGYKNGTASFG 363
+ F D++ P + + NT++ R +GK+ GYNTD E + ++ KN
Sbjct: 283 LDFLDKLDPSVKLCGSCNTLVFR--NGKIEGYNTDGEGLFSLLKQ-------KN------ 327
Query: 364 SPLAGRMFVLAGAGGAGRALAFGAKSRGARVVIFDIDFERAKSLASDVMGAARPFEDILN 423
PL + + GAGGA +A+A GA ++IF+ A++LAS G A P E +
Sbjct: 328 IPLNNQHVAIVGAGGAAKAIATTLARAGAELLIFNRTKAHAEALASRCQGKAFPLESLPE 387
Query: 424 FQPEKGAILANATPLGMHPNTDRVPVSEETLRDYQLVFDAVYTPRKTRLLKDAEAAGAII 483
+ I+ N P P V D P+ + + A + G+ I
Sbjct: 388 LH--RIDIIINCLP----------PSVTIPKAFPPCVVDINTLPKHSPYTQYARSQGSSI 435
Query: 484 VSGVEMFLRQAIGQFNL----FTGKEAPKEFMR--EIVLAKF 519
+ G EMF QA+ QF L K K F R + + F
Sbjct: 436 IYGYEMFAEQALLQFRLWFPTLLFKHLEKTFRRRVANLASLF 477
>gnl|CDD|183586 PRK12549, PRK12549, shikimate 5-dehydrogenase; Reviewed.
Length = 284
Score = 142 bits (361), Expect = 8e-39
Identities = 86/236 (36%), Positives = 114/236 (48%), Gaps = 35/236 (14%)
Query: 290 FAGFSVGFPYKEAVMKFCDEVHPLAQAIAAVNTIIRRPSDGKLIGYNTDC----EASITA 345
FAG ++ P K+AV+ DE+ A+A+ AVNT++ R DG+ IG+NTD E+
Sbjct: 64 FAGLNITHPCKQAVIPHLDELSDDARALGAVNTVVFR--DGRRIGHNTDWSGFAESFRRG 121
Query: 346 IEDAIKERGYKNGTASFGSPLAGRMFVLAGAGGAGRALAFGAKSRGA-RVVIFDIDFERA 404
+ DA ER V GAGGAG A+A + G R+ IFD+D RA
Sbjct: 122 LPDASLERV-----------------VQLGAGGAGAAVAHALLTLGVERLTIFDVDPARA 164
Query: 405 KSLASDVMGAARPFEDILNFQPEKGAI-----LANATPLGM--HPNTDRVPVSEETLRDY 457
+LA D + A P A+ L +ATP GM HP P+ E LR
Sbjct: 165 AALA-DELNARFPAARATAGSDLAAALAAADGLVHATPTGMAKHPGL---PLPAELLRPG 220
Query: 458 QLVFDAVYTPRKTRLLKDAEAAGAIIVSGVEMFLRQAIGQFNLFTGKEAPKEFMRE 513
V D VY P +T LL+ A A G + G M + QA+ F LFTG+E E M
Sbjct: 221 LWVADIVYFPLETELLRAARALGCRTLDGGGMAVFQAVDAFELFTGREPDAERMLA 276
>gnl|CDD|133443 cd01065, NAD_bind_Shikimate_DH, NAD(P) binding domain of Shikimate
dehydrogenase. Shikimate dehydrogenase (DH) is an amino
acid DH family member. Shikimate pathway links
metabolism of carbohydrates to de novo biosynthesis of
aromatic amino acids, quinones and folate. It is
essential in plants, bacteria, and fungi but absent in
mammals, thus making enzymes involved in this pathway
ideal targets for broad spectrum antibiotics and
herbicides. Shikimate DH catalyzes the reduction of
3-hydroshikimate to shikimate using the cofactor NADH.
Amino acid DH-like NAD(P)-binding domains are members of
the Rossmann fold superfamily and include glutamate,
leucine, and phenylalanine DHs, methylene
tetrahydrofolate DH, methylene-tetrahydromethanopterin
DH, methylene-tetrahydropholate DH/cyclohydrolase,
Shikimate DH-like proteins, malate oxidoreductases, and
glutamyl tRNA reductase. Amino acid DHs catalyze the
deamination of amino acids to keto acids with NAD(P)+ as
a cofactor. The NAD(P)-binding Rossmann fold superfamily
includes a wide variety of protein families including
NAD(P)- binding domains of alcohol DHs,
tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate DH, lactate/malate DHs,
formate/glycerate DHs, siroheme synthases,
6-phosphogluconate DHs, amino acid DHs, repressor rex,
NAD-binding potassium channel domain, CoA-binding, and
ornithine cyclodeaminase-like domains. These domains
have an alpha-beta-alpha configuration. NAD binding
involves numerous hydrogen and van der Waals contacts.
Length = 155
Score = 128 bits (324), Expect = 4e-35
Identities = 56/170 (32%), Positives = 86/170 (50%), Gaps = 18/170 (10%)
Query: 337 TDCEASITAIEDAIKERGYKNGTASFGSPLAGRMFVLAGAGGAGRALAFGAKSRGA-RVV 395
TD A++E G L G+ ++ GAGGA RA+A+ GA ++V
Sbjct: 1 TD----GLGFVRALEE---------AGIELKGKKVLILGAGGAARAVAYALAELGAAKIV 47
Query: 396 IFDIDFERAKSLASDVMGAARPFEDILNFQPEKGA--ILANATPLGMHPNTDRVPVSEET 453
I + E+AK+LA + G L+ + ++ N TP+GM P + +P+
Sbjct: 48 IVNRTLEKAKALA-ERFGELGIAIAYLDLEELLAEADLIINTTPVGMKPGDE-LPLPPSL 105
Query: 454 LRDYQLVFDAVYTPRKTRLLKDAEAAGAIIVSGVEMFLRQAIGQFNLFTG 503
L+ +V+D VY P +T LLK+A A GA + G+EM + QA F L+TG
Sbjct: 106 LKPGGVVYDVVYNPLETPLLKEARALGAKTIDGLEMLVYQAAEAFELWTG 155
>gnl|CDD|183587 PRK12550, PRK12550, shikimate 5-dehydrogenase; Reviewed.
Length = 272
Score = 127 bits (322), Expect = 2e-33
Identities = 84/285 (29%), Positives = 127/285 (44%), Gaps = 27/285 (9%)
Query: 233 HINADTKV-FGLISKPVGHSKGPILHNPTFRHVNYNGIYVPMFVDDLKKFFSTYSSPDFA 291
IN DT++ L ++P G HN + + N +Y DL +
Sbjct: 4 MINKDTQLCISLAARPSNF--GTRFHNYLYEALGLNFLYKAFTTTDLTAAIGGVRALGIR 61
Query: 292 GFSVGFPYKEAVMKFCDEVHPLAQAIAAVNTIIRRPSDGKLIGYNTDCEASITAIEDAIK 351
G +V P+KEAV+ DE+ P AQAI +VNTI+ +DG L YNTD AI +
Sbjct: 62 GCAVSMPFKEAVIPLVDELDPSAQAIESVNTIVN--TDGHLKAYNTD----YIAIAKLLA 115
Query: 352 ERGYKNGTASFGSPLAGRMFVLAGAGGAGRALAFGAKSRG-ARVVIFDIDFERAKSLASD 410
L G+GG +A+A + G I + + K+LA +
Sbjct: 116 SYQVPPDLV----------VALRGSGGMAKAVAAALRDAGFTDGTIVARNEKTGKALA-E 164
Query: 411 VMGAARPFEDILNFQPEKGAILANATPLGMH--PNTDRVPVSEETLRDYQLVFDAVYTPR 468
+ G +E + + IL N TP+GM P D++ E + +VFD V P
Sbjct: 165 LYG----YEWRPDLGGIEADILVNVTPIGMAGGPEADKLAFPEAEIDAASVVFDVVALPA 220
Query: 469 KTRLLKDAEAAGAIIVSGVEMFLRQAIGQFNLFTGKEAPKEFMRE 513
+T L++ A A G +++G E+ QA+ QF L+TG E + E
Sbjct: 221 ETPLIRYARARGKTVITGAEVIALQAVEQFVLYTGVRPSDELIAE 265
>gnl|CDD|223782 COG0710, AroD, 3-dehydroquinate dehydratase [Amino acid transport
and metabolism].
Length = 231
Score = 120 bits (304), Expect = 2e-31
Identities = 56/231 (24%), Positives = 109/231 (47%), Gaps = 7/231 (3%)
Query: 11 TMICAPLMAQSVEQVLSNMYQAKAEGADVVEIRLDCI-NNFQPGKDLEIILTKKP-LPVL 68
I P++ + ++ ++K AD+VE+R+D + +N + + + + K P P++
Sbjct: 2 PKIIVPVVGLDIAELKEQAEKSKELDADIVELRVDLLESNVEVLEVAKALREKDPDKPLI 61
Query: 69 IVYRPKWAGGLYEGDEHKRLEALH-LAEDLGADYVDFELKVASNILGKQYSSHQSGTRFI 127
+R GG + G E + +E L LAE G DY+D EL + + + + I
Sbjct: 62 FTFRTVKEGGEFPGSEEEYIELLKKLAELNGPDYIDIELSSPEDDVKEIIKFAKK-HGVI 120
Query: 128 VSCNLDCETPSEEDLGYLVSRMQATGADIIKLVFSVNDITEIARIFQLLSHCQV---PII 184
VS + +TP E++ + +M++ GADI+K+ ++ + + + P+I
Sbjct: 121 VSYHDFEKTPPLEEIIERLDKMESLGADIVKIAVMPQSKEDVLDLLEATREFKEAEKPVI 180
Query: 185 AYSVGERGLVSQLLSPKFNGALVYGSLKGTPVLGLPTVESLRQTYKVEHIN 235
S+G+ G +S++ P F + Y SL G +V+ LR+ +
Sbjct: 181 TISMGKTGKISRVAGPVFGSPITYASLDKPSAPGQISVDELRKILTLLGYI 231
>gnl|CDD|183721 PRK12749, PRK12749, quinate/shikimate dehydrogenase; Reviewed.
Length = 288
Score = 118 bits (297), Expect = 6e-30
Identities = 87/301 (28%), Positives = 136/301 (45%), Gaps = 38/301 (12%)
Query: 234 INADTKVFGLISKPVGHSKGPILHNPTFRHVNYNGIYVPMFVDD--LKKFFSTYSSPDFA 291
+ A ++ GL++ P+ HS P + N Y+ VD+ +
Sbjct: 3 VTAKYELIGLMAYPIRHSLSPEMQNKALEKAGLPFTYMAFEVDNDSFPGAIEGLKALKMR 62
Query: 292 GFSVGFPYKEAVMKFCDEVHPLAQAIAAVNTIIRRPSDGKLIGYNTDCEASITAIEDAIK 351
G V P K+ ++ DE+ P A+ + A+NTI+ DG L GYNTD I AI K
Sbjct: 63 GTGVSMPNKQLACEYVDELTPAAKLVGAINTIVN--DDGYLRGYNTDGTGHIRAI----K 116
Query: 352 ERGYKNGTASFGSPLAGRMFVLAGAGGAGRALAFGAKSRGARVV-IF---DIDFERAKSL 407
E G+ + G+ VL GAGGA A+ G + + +F D F++A +
Sbjct: 117 ESGFD---------IKGKTMVLLGAGGASTAIGAQGAIEGLKEIKLFNRRDEFFDKALAF 167
Query: 408 ASDV------------MGAARPFEDILNFQPEKGAILANATPLGMHPNTDRVPVSEET-L 454
A V + + F + L IL N T +GM P + V++ + L
Sbjct: 168 AQRVNENTDCVVTVTDLADQQAFAEAL----ASADILTNGTKVGMKPLENESLVNDISLL 223
Query: 455 RDYQLVFDAVYTPRKTRLLKDAEAAGAIIVSGVEMFLRQAIGQFNLFTGKEAPKEFMREI 514
LV + VY P T+LL+ A+ AG + G M L Q QF L+TGK+ P E+++++
Sbjct: 224 HPGLLVTECVYNPHMTKLLQQAQQAGCKTIDGYGMLLWQGAEQFTLWTGKDFPLEYVKQV 283
Query: 515 V 515
+
Sbjct: 284 M 284
>gnl|CDD|172521 PRK14027, PRK14027, quinate/shikimate dehydrogenase; Provisional.
Length = 283
Score = 112 bits (281), Expect = 8e-28
Identities = 91/303 (30%), Positives = 129/303 (42%), Gaps = 41/303 (13%)
Query: 235 NADTKVFGLISKPVGHSKGPILHNPTFRHVNYNGIY--VPMFVD-----DLKKFFSTYSS 287
D+ + GLI + + S+ P +H +Y + DLK
Sbjct: 1 MNDSILLGLIGQGLDLSRTPAMHEAEGLAQGRATVYRRIDTLGSRASGQDLKTLLDAALY 60
Query: 288 PDFAGFSVGFPYKEAVMKFCDEVHPLAQAIAAVNTIIRRPSDGKLIGYNTDCEASITAIE 347
F G ++ PYK+AV+ DEV A + AVNT++ + G G+NTD +E
Sbjct: 61 LGFNGLNITHPYKQAVLPLLDEVSEQATQLGAVNTVVI-DATGHTTGHNTDVSGFGRGME 119
Query: 348 DAIKERGYKNGTASFGSPLAGRMFVLAGAGGAGRALAFGAKSRGA-RVVIFDIDFERAKS 406
+ G N V GAGG G A+A+ + G ++ + D+D RA++
Sbjct: 120 E-----GLPNAKLD--------SVVQVGAGGVGNAVAYALVTHGVQKLQVADLDTSRAQA 166
Query: 407 LASDVMGA----------ARPFEDILNFQPEKGAILANATPLGM--HPNTDRVPVSEETL 454
LA + A AR ED++ G + NATP+GM HP T L
Sbjct: 167 LADVINNAVGREAVVGVDARGIEDVI--AAADGVV--NATPMGMPAHPGT---AFDVSCL 219
Query: 455 RDYQLVFDAVYTPRKTRLLKDAEAAGAIIVSGVEMFLRQAIGQFNLFTGKEAPKEFMREI 514
V D VY P +T LLK A A G + G M + QA+ F LFTG E MRE
Sbjct: 220 TKDHWVGDVVYMPIETELLKAARALGCETLDGTRMAIHQAVDAFRLFTGLEPDVSRMRET 279
Query: 515 VLA 517
L+
Sbjct: 280 FLS 282
>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 = 98.4 bits (246), Expect = 4e-25
Identities = 34/83 (40%), Positives = 48/83 (57%), Gaps = 2/83 (2%)
Query: 243 LISKPVGHSKGPILHNPTFRHVNYNGIYVPMFV--DDLKKFFSTYSSPDFAGFSVGFPYK 300
LI P+ HS P++HN F+ + NG+YV V D+L +F + F G +V P+K
Sbjct: 1 LIGNPISHSLSPLIHNAAFKALGLNGVYVAFEVPPDNLPEFVEGLRALGFRGLNVTIPHK 60
Query: 301 EAVMKFCDEVHPLAQAIAAVNTI 323
EA + DE+ P A+ I AVNTI
Sbjct: 61 EAAIPLLDELSPEAKRIGAVNTI 83
>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 = 95.8 bits (238), Expect = 5e-22
Identities = 84/298 (28%), Positives = 114/298 (38%), Gaps = 50/298 (16%)
Query: 239 KVFGLISKPVGHSKGPILHNPTFRHVNYNGIYVPMFVDD---LKKFFSTYSSPDFAGFSV 295
K +I KP+ HS+ P LHN + + LK+ S + P F G SV
Sbjct: 6 KKAFIIGKPIAHSRSPHLHNAGYEILGLPDKTYEFETCSAEELKEVLSGFG-PQFGGASV 64
Query: 296 GFPYKEAVMKFCDEVHPLAQAIAAVNTIIRRPSDGKLIGYNTDCEASITAIEDAIKERGY 355
P K A+++F DE A I +VNT++R +G G NTD I A+ G
Sbjct: 65 TIPLKFAILRFADEHTDRASLIGSVNTLLRT-QNGIWKGDNTD----WDGIAGALANIGK 119
Query: 356 KNGTASFGSPLAGRMFVLAGAGGAGRALAFGAKSRGARVVIFDIDFERAKSLASDVMGAA 415
PLAG ++ GAGG RA + S G I I+ R S
Sbjct: 120 F-------EPLAGFRGLVIGAGGTSRAAVYALASLGVT-DITVIN--RNPDKLS------ 163
Query: 416 RPFEDILNFQPEKGAILANATPLGMHPNTD-RVPVS---EETLRDYQLVF---------- 461
D+ G+ V VS + DY +F
Sbjct: 164 -RLVDLGV--QVGVITRLEGDSGGLAIEKAAEVLVSTVPADVPADYVDLFATVPFLLLKR 220
Query: 462 --------DAVYTPRKTRLLKDAEAAGAIIVSGVEMFLRQAIGQFNLFTGKEAPKEFM 511
DA Y P T L+ AAG ++SG++M L Q QF +TG AP+E M
Sbjct: 221 KSSEGIFLDAAYDPWPTPLVAIVSAAGWRVISGLQMLLHQGFAQFEQWTGMPAPREAM 278
>gnl|CDD|235036 PRK02412, aroD, 3-dehydroquinate dehydratase; Provisional.
Length = 253
Score = 85.3 bits (212), Expect = 9e-19
Identities = 56/244 (22%), Positives = 112/244 (45%), Gaps = 28/244 (11%)
Query: 4 VNITKNTTMICAPLMAQSVEQVLSNMYQAKAEGADVVEIRLDCINNFQPGKDLEIILT-- 61
+ I + I P+M +++E+VL+ AD++E R D + D+E +L
Sbjct: 9 LVIGEGAPKIIVPIMGKTLEEVLAEALAISKYDADIIEWRAD---FLEKISDVESVLAAA 65
Query: 62 ---KKPL---PVLIVYRPKWAGGLYEGDEHKRLEALHLAEDLGA-DYVDFELKVASNILG 114
++ P+L +R GG + + L + G DY+D EL +++
Sbjct: 66 PAIREKFAGKPLLFTFRTAKEGGEIALSDEEYLALIKAVIKSGLPDYIDVELFSGKDVVK 125
Query: 115 KQYS-SHQSGTRFIVSC-NLDCETPSEEDLGYLVSRMQATGADIIKL---------VFSV 163
+ + +H+ G + ++S + + +TP +E++ + +M++ GADI+K+ V ++
Sbjct: 126 EMVAFAHEHGVKVVLSYHDFE-KTPPKEEIVERLRKMESLGADIVKIAVMPQSEQDVLTL 184
Query: 164 NDITEIARIFQLLSHCQVPIIAYSVGERGLVSQLLSPKFNGALVYGSLKGTPVLGLPTVE 223
+ T + P+I S+G+ G +S+L F + + SL G +VE
Sbjct: 185 LNATREMKELYA----DQPLITMSMGKLGRISRLAGEVFGSSWTFASLDKASAPGQISVE 240
Query: 224 SLRQ 227
LR+
Sbjct: 241 DLRR 244
>gnl|CDD|184156 PRK13575, PRK13575, 3-dehydroquinate dehydratase; Provisional.
Length = 238
Score = 59.0 bits (143), Expect = 8e-10
Identities = 47/191 (24%), Positives = 82/191 (42%), Gaps = 15/191 (7%)
Query: 38 DVVEIRLDCINNFQPGKDLEIILTK-----KPLPVLIVYRPKWAGGLYEGDEHKRLEAL- 91
D++E+R+D N L ++TK +L+ YR K GG + L L
Sbjct: 32 DIIELRIDQWENVTV-DQLAEMITKLKVLQDSFKLLVTYRTKLQGGYGQFTNDLYLNLLS 90
Query: 92 HLAEDLGADYVDFELKVASNILGKQY---SSHQSGTRFIVSCNLDCETPSEEDLGYLVSR 148
LA G D +D E + +I Q Q ++S + TP ++L ++ +
Sbjct: 91 DLANINGIDMIDIEWQADIDIEKHQRLITHLQQYNKEVVISHHNFESTPPLDELKFIFFK 150
Query: 149 MQATGADIIKLVFSVNDITEIARIFQLLS----HCQVPIIAYSVGERGLVSQLLSPKFNG 204
MQ + +KL ++ ++ + Q +S ++ S+ + GL+S+ F G
Sbjct: 151 MQKFNPEYVKLAVMPHNKNDVLNLLQAMSTFSDTMDCKVVGISMSKLGLISRTAQGVFGG 210
Query: 205 ALVYGSLKGTP 215
AL YG + G P
Sbjct: 211 ALSYGCI-GEP 220
>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 = 41.9 bits (99), Expect = 9e-05
Identities = 23/77 (29%), Positives = 36/77 (46%), Gaps = 4/77 (5%)
Query: 363 GSPLAGRMFVLAGAGGAGRALAFGAKSRGAR-VVIFDIDFERAKSLASDVMGA--ARPFE 419
L G+ +L GAG R A S+GA+ + I + E+AK LA + A P +
Sbjct: 7 FGDLKGKKVLLIGAGEMARLAAKHLLSKGAKKITIANRTLEKAKELAEEFPVGGEALPLD 66
Query: 420 DILNFQPEKGAILANAT 436
++ E I+ +AT
Sbjct: 67 ELEELLAE-ADIVISAT 82
>gnl|CDD|236241 PRK08324, PRK08324, short chain dehydrogenase; Validated.
Length = 681
Score = 44.8 bits (107), Expect = 9e-05
Identities = 22/53 (41%), Positives = 33/53 (62%), Gaps = 1/53 (1%)
Query: 365 PLAGRM-FVLAGAGGAGRALAFGAKSRGARVVIFDIDFERAKSLASDVMGAAR 416
PLAG++ V AGG G+A A + GA VV+ D+D E A++ A+++ G R
Sbjct: 419 PLAGKVALVTGAAGGIGKATAKRLAAEGACVVLADLDEEAAEAAAAELGGPDR 471
>gnl|CDD|235633 PRK05872, PRK05872, short chain dehydrogenase; Provisional.
Length = 296
Score = 43.8 bits (104), Expect = 1e-04
Identities = 18/61 (29%), Positives = 32/61 (52%), Gaps = 1/61 (1%)
Query: 360 ASFGSPLAGRMFVLAGAG-GAGRALAFGAKSRGARVVIFDIDFERAKSLASDVMGAARPF 418
+ LAG++ V+ GA G G LA +RGA++ + D++ +LA+++ G R
Sbjct: 1 GPPMTSLAGKVVVVTGAARGIGAELARRLHARGAKLALVDLEEAELAALAAELGGDDRVL 60
Query: 419 E 419
Sbjct: 61 T 61
>gnl|CDD|131680 TIGR02632, RhaD_aldol-ADH, rhamnulose-1-phosphate aldolase/alcohol
dehydrogenase.
Length = 676
Score = 43.3 bits (102), Expect = 3e-04
Identities = 38/119 (31%), Positives = 56/119 (47%), Gaps = 20/119 (16%)
Query: 365 PLAGRM-FVLAGAGGAGRALAFGAKSRGARVVIFDIDFERAKSLASDV-----MGAARPF 418
LA R+ FV GAGG GR A + GA VV+ D++ E A+++A+++ G A
Sbjct: 411 TLARRVAFVTGGAGGIGRETARRLAAEGAHVVLADLNLEAAEAVAAEINGQFGAGRAVAL 470
Query: 419 E-DILNFQPEKGAILANATPLGMHPNTDRV----------PVSEETLRDYQLVFDAVYT 466
+ D+ + Q K A A G D V P E TL+++QL D + T
Sbjct: 471 KMDVTDEQAVKAAFADVALAYG---GVDIVVNNAGIATSSPFEETTLQEWQLNLDILAT 526
>gnl|CDD|180371 PRK06057, PRK06057, short chain dehydrogenase; Provisional.
Length = 255
Score = 40.1 bits (94), Expect = 0.001
Identities = 23/49 (46%), Positives = 29/49 (59%), Gaps = 1/49 (2%)
Query: 366 LAGRMFVLAGAG-GAGRALAFGAKSRGARVVIFDIDFERAKSLASDVMG 413
LAGR+ V+ G G G G A A + GA VV+ DID E K+ A +V G
Sbjct: 5 LAGRVAVITGGGSGIGLATARRLAAEGATVVVGDIDPEAGKAAADEVGG 53
>gnl|CDD|235628 PRK05855, PRK05855, short chain dehydrogenase; Validated.
Length = 582
Score = 40.3 bits (95), Expect = 0.002
Identities = 19/48 (39%), Positives = 25/48 (52%), Gaps = 1/48 (2%)
Query: 365 PLAGRMFVLAGAG-GAGRALAFGAKSRGARVVIFDIDFERAKSLASDV 411
P +G++ V+ GAG G GR A GA VV DID A+ A +
Sbjct: 312 PFSGKLVVVTGAGSGIGRETALAFAREGAEVVASDIDEAAAERTAELI 359
>gnl|CDD|183775 PRK12826, PRK12826, 3-ketoacyl-(acyl-carrier-protein) reductase;
Reviewed.
Length = 251
Score = 38.4 bits (90), Expect = 0.005
Identities = 18/48 (37%), Positives = 24/48 (50%), Gaps = 1/48 (2%)
Query: 365 PLAGR-MFVLAGAGGAGRALAFGAKSRGARVVIFDIDFERAKSLASDV 411
L GR V A G GRA+A + GA V++ DI + A + A V
Sbjct: 3 DLEGRVALVTGAARGIGRAIAVRLAADGAEVIVVDICGDDAAATAELV 50
>gnl|CDD|181136 PRK07825, PRK07825, short chain dehydrogenase; Provisional.
Length = 273
Score = 38.4 bits (90), Expect = 0.006
Identities = 17/48 (35%), Positives = 24/48 (50%), Gaps = 1/48 (2%)
Query: 364 SPLAGRMFVLAGAG-GAGRALAFGAKSRGARVVIFDIDFERAKSLASD 410
L G++ + G G G A A + GARV I D+D AK A++
Sbjct: 1 DDLRGKVVAITGGARGIGLATARALAALGARVAIGDLDEALAKETAAE 48
>gnl|CDD|181120 PRK07792, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 306
Score = 38.2 bits (89), Expect = 0.006
Identities = 20/60 (33%), Positives = 30/60 (50%), Gaps = 1/60 (1%)
Query: 357 NGTASFGSPLAGRMFVLAGAG-GAGRALAFGAKSRGARVVIFDIDFERAKSLASDVMGAA 415
+ + + L+G++ V+ GA G GRA A G GA VV+ D+ S D + AA
Sbjct: 1 SPRTTNTTDLSGKVAVVTGAAAGLGRAEALGLARLGATVVVNDVASALDASDVLDEIRAA 60
>gnl|CDD|240631 cd12154, FDH_GDH_like, Formate/glycerate dehydrogenases, D-specific
2-hydroxy acid dehydrogenases and related
dehydrogenases. The formate/glycerate dehydrogenase
like family contains a diverse group of enzymes such as
formate dehydrogenase (FDH), glycerate dehydrogenase
(GDH), D-lactate dehydrogenase, L-alanine dehydrogenase,
and S-Adenosylhomocysteine hydrolase, that share a
common 2-domain structure. Despite often low sequence
identity, these proteins typically have a characteristic
arrangement of 2 similar domains of the alpha/beta
Rossmann fold NAD+ binding form. The NAD(P) binding
domain is inserted within the linear sequence of the
mostly N-terminal catalytic domain. Structurally, these
domains are connected by extended alpha helices and
create a cleft in which NAD(P) is bound, primarily to
the C-terminal portion of the 2nd (internal) domain.
While many members of this family are dimeric, alanine
DH is hexameric and phosphoglycerate DH is tetrameric.
2-hydroxyacid dehydrogenases are enzymes that catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate dehydrogenase (FDH) catalyzes the NAD+-dependent
oxidation of formate ion to carbon dioxide with the
concomitant reduction of NAD+ to NADH. FDHs of this
family contain no metal ions or prosthetic groups.
Catalysis occurs though direct transfer of a hydride ion
to NAD+ without the stages of acid-base catalysis
typically found in related dehydrogenases.
Length = 310
Score = 38.4 bits (89), Expect = 0.008
Identities = 20/73 (27%), Positives = 34/73 (46%), Gaps = 4/73 (5%)
Query: 366 LAGRMFVLAGAGGAGRALAFGAKSRGARVVIFDIDFERAKSLASDVMGAARPFEDILNFQ 425
+AG+ V+ GAG G+ A + GA+V+I DI+ E + L + E++
Sbjct: 158 VAGKTVVVVGAGVVGKEAAQMLRGLGAQVLITDINVEALEQLE---ELGGKNVEELEEAL 214
Query: 426 PEKGAILANATPL 438
E ++ T L
Sbjct: 215 AE-ADVIVTTTLL 226
>gnl|CDD|223450 COG0373, HemA, Glutamyl-tRNA reductase [Coenzyme metabolism].
Length = 414
Score = 38.4 bits (90), Expect = 0.008
Identities = 35/112 (31%), Positives = 50/112 (44%), Gaps = 12/112 (10%)
Query: 362 FGSPLAGRMFVLAGAGGAGRALAFGAKSRG-ARVVIFDIDFERAKSLASDVMGAARPFED 420
FGS L + ++ GAG G +A +G ++ I + ERA+ LA + A E+
Sbjct: 173 FGS-LKDKKVLVIGAGEMGELVAKHLAEKGVKKITIANRTLERAEELAKKLGAEAVALEE 231
Query: 421 ILNFQPEKGA-ILANATPLGMHPNTDRVPVSEETL--RDYQLVFD-AVYTPR 468
+L E I + + P HP R V E L R L+ D AV PR
Sbjct: 232 LLEALAEADVVISSTSAP---HPIITREMV-ERALKIRKRLLIVDIAV--PR 277
>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 = 37.8 bits (88), Expect = 0.012
Identities = 16/39 (41%), Positives = 26/39 (66%)
Query: 366 LAGRMFVLAGAGGAGRALAFGAKSRGARVVIFDIDFERA 404
+AG+ V+AG G G+ +A A+ GARV++ ++D RA
Sbjct: 194 IAGKTVVVAGYGWCGKGIAMRARGMGARVIVTEVDPIRA 232
>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 = 37.3 bits (87), Expect = 0.012
Identities = 22/61 (36%), Positives = 28/61 (45%), Gaps = 5/61 (8%)
Query: 375 GAGGAGRALAFGAKSRGARVVIFDID---FERAKSLASD--VMGAARPFEDILNFQPEKG 429
GAGG G A AK+ GARV++ D E AK L +D + E+ L G
Sbjct: 142 GAGGVGLLAAQLAKAAGARVIVTDRSDEKLELAKELGADHVIDYKEEDLEEELRLTGGGG 201
Query: 430 A 430
A
Sbjct: 202 A 202
>gnl|CDD|236399 PRK09186, PRK09186, flagellin modification protein A; Provisional.
Length = 256
Score = 37.3 bits (87), Expect = 0.013
Identities = 16/47 (34%), Positives = 21/47 (44%), Gaps = 1/47 (2%)
Query: 366 LAGRMFVLAGAGG-AGRALAFGAKSRGARVVIFDIDFERAKSLASDV 411
L G+ ++ GAGG G AL G V+ DID E L +
Sbjct: 2 LKGKTILITGAGGLIGSALVKAILEAGGIVIAADIDKEALNELLESL 48
>gnl|CDD|235924 PRK07063, PRK07063, short chain dehydrogenase; Provisional.
Length = 260
Score = 37.3 bits (87), Expect = 0.013
Identities = 20/54 (37%), Positives = 29/54 (53%), Gaps = 5/54 (9%)
Query: 366 LAGRMFVLAGAG-GAGRALAFGAKSRGARVVIFDIDFER----AKSLASDVMGA 414
LAG++ ++ GA G G A+A GA V + D+D A ++A DV GA
Sbjct: 5 LAGKVALVTGAAQGIGAAIARAFAREGAAVALADLDAALAERAAAAIARDVAGA 58
>gnl|CDD|180669 PRK06720, PRK06720, hypothetical protein; Provisional.
Length = 169
Score = 35.7 bits (82), Expect = 0.020
Identities = 16/47 (34%), Positives = 28/47 (59%), Gaps = 1/47 (2%)
Query: 366 LAGRMFVLAGAG-GAGRALAFGAKSRGARVVIFDIDFERAKSLASDV 411
LAG++ ++ G G G GR A +GA+V++ DID E ++ ++
Sbjct: 14 LAGKVAIVTGGGIGIGRNTALLLAKQGAKVIVTDIDQESGQATVEEI 60
>gnl|CDD|183778 PRK12829, PRK12829, short chain dehydrogenase; Provisional.
Length = 264
Score = 36.6 bits (85), Expect = 0.024
Identities = 20/53 (37%), Positives = 27/53 (50%), Gaps = 1/53 (1%)
Query: 364 SPLAG-RMFVLAGAGGAGRALAFGAKSRGARVVIFDIDFERAKSLASDVMGAA 415
PL G R+ V GA G GRA+A GARV + D+ + A+ + GA
Sbjct: 7 KPLDGLRVLVTGGASGIGRAIAEAFAEAGARVHVCDVSEAALAATAARLPGAK 59
>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 = 33.9 bits (78), Expect = 0.026
Identities = 15/50 (30%), Positives = 21/50 (42%), Gaps = 1/50 (2%)
Query: 353 RGYKNGTASFGSPLAGRMFVLAGAGGAGRALA-FGAKSRGARVVIFDIDF 401
K L G+ V+ GAG G+ +A A G +VV+ D D
Sbjct: 8 ALLKAAGKVTNKSLKGKTVVVLGAGEVGKGIAKLLADEGGKKVVLCDRDI 57
>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 = 36.3 bits (85), Expect = 0.033
Identities = 14/35 (40%), Positives = 24/35 (68%)
Query: 366 LAGRMFVLAGAGGAGRALAFGAKSRGARVVIFDID 400
+AG++ V+AG G G+ A A+ GARV++ ++D
Sbjct: 193 IAGKVVVVAGYGWVGKGCAMRARGLGARVIVTEVD 227
>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 = 36.0 bits (84), Expect = 0.036
Identities = 31/114 (27%), Positives = 43/114 (37%), Gaps = 29/114 (25%)
Query: 375 GAGGAGRALAFGAKSRGARVVIFDIDFER---AKSLASDVMGAARPFEDILNFQPEKGAI 431
GAG G + AK+RGARV++ DID ER A+ L +D D +N E
Sbjct: 167 GAGPIGLGVIQVAKARGARVIVVDIDDERLEFARELGAD---------DTINVGDED--- 214
Query: 432 LANATPLGMHPNTDRVPVSEETLRDY-QLVFDAVYTPRKTRLLKDAEAAGAIIV 484
+ E T + +V DA P + A G +V
Sbjct: 215 -------------VAARLRELTDGEGADVVIDATGNPASMEEAVELVAHGGRVV 255
>gnl|CDD|223573 COG0499, SAM1, S-adenosylhomocysteine hydrolase [Coenzyme
metabolism].
Length = 420
Score = 36.1 bits (84), Expect = 0.041
Identities = 17/39 (43%), Positives = 25/39 (64%)
Query: 366 LAGRMFVLAGAGGAGRALAFGAKSRGARVVIFDIDFERA 404
LAG+ V+AG G GR +A + GARV++ ++D RA
Sbjct: 207 LAGKNVVVAGYGWVGRGIAMRLRGMGARVIVTEVDPIRA 245
>gnl|CDD|234592 PRK00045, hemA, glutamyl-tRNA reductase; Reviewed.
Length = 423
Score = 35.9 bits (84), Expect = 0.041
Identities = 19/61 (31%), Positives = 33/61 (54%), Gaps = 2/61 (3%)
Query: 362 FGSPLAGRMFVLAGAGGAGRALAFGAKSRGAR-VVIFDIDFERAKSLASDVMGAARPFED 420
FG L+G+ ++ GAG G +A +G R + + + ERA+ LA + G A P ++
Sbjct: 177 FGD-LSGKKVLVIGAGEMGELVAKHLAEKGVRKITVANRTLERAEELAEEFGGEAIPLDE 235
Query: 421 I 421
+
Sbjct: 236 L 236
>gnl|CDD|235925 PRK07067, PRK07067, sorbitol dehydrogenase; Provisional.
Length = 257
Score = 35.8 bits (83), Expect = 0.043
Identities = 20/44 (45%), Positives = 26/44 (59%), Gaps = 1/44 (2%)
Query: 366 LAGRMFVLAG-AGGAGRALAFGAKSRGARVVIFDIDFERAKSLA 408
L G++ +L G A G G A+A + GARVVI DI RA+ A
Sbjct: 4 LQGKVALLTGAASGIGEAVAERYLAEGARVVIADIKPARARLAA 47
>gnl|CDD|180723 PRK06841, PRK06841, short chain dehydrogenase; Provisional.
Length = 255
Score = 35.4 bits (82), Expect = 0.045
Identities = 18/55 (32%), Positives = 30/55 (54%), Gaps = 1/55 (1%)
Query: 365 PLAGRMFVLAG-AGGAGRALAFGAKSRGARVVIFDIDFERAKSLASDVMGAARPF 418
L+G++ V+ G A G G A+A ++GARV + D + A+ A + G A+
Sbjct: 12 DLSGKVAVVTGGASGIGHAIAELFAAKGARVALLDRSEDVAEVAAQLLGGNAKGL 66
>gnl|CDD|235975 PRK07231, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 251
Score = 35.6 bits (83), Expect = 0.047
Identities = 19/54 (35%), Positives = 31/54 (57%), Gaps = 5/54 (9%)
Query: 366 LAGRMFVLAGAG---GAGRALAFGAKSRGARVVIFDIDFERAKSLASDVMGAAR 416
L G++ ++ GA G G A F A GARVV+ D + E A+ +A++++ R
Sbjct: 3 LEGKVAIVTGASSGIGEGIARRFAA--EGARVVVTDRNEEAAERVAAEILAGGR 54
>gnl|CDD|233266 TIGR01087, murD, UDP-N-acetylmuramoylalanine--D-glutamate ligase.
[Cell envelope, Biosynthesis and degradation of murein
sacculus and peptidoglycan].
Length = 433
Score = 35.8 bits (83), Expect = 0.050
Identities = 27/122 (22%), Positives = 41/122 (33%), Gaps = 25/122 (20%)
Query: 371 FVLAGAGGAGRALAFGAKSRGARVVIFDIDFERAKSLASDVMGAARPFEDILNFQPEKGA 430
++ G G GRA+A +GA V + D+ MG R E +
Sbjct: 2 ILILGLGKTGRAVARFLHKKGAEVTVTDLKPN---EELEPSMGQLRLNEGSVLHTGLH-- 56
Query: 431 ILANATPLGMHPNTDRVPVSEETLRDYQLVFDAVYTPRKTRLLKDAEAAGAIIVSGVEMF 490
E L + LV + P L++ A G +V +E+F
Sbjct: 57 --------------------LEDLNNADLVVKSPGIPPDHPLVQAAAKRGIPVVGDIELF 96
Query: 491 LR 492
LR
Sbjct: 97 LR 98
>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 = 35.4 bits (82), Expect = 0.053
Identities = 22/53 (41%), Positives = 33/53 (62%), Gaps = 5/53 (9%)
Query: 366 LAGRMFVLAGAG---GAGRALAFGAKSRGARVVIFDIDFERAKSLASDVMGAA 415
L G++ ++ GAG G G A F + GARVVI DI+ + A+ +A+D+ AA
Sbjct: 3 LEGKVAIVTGAGSGFGEGIARRFAQE--GARVVIADINADGAERVAADIGEAA 53
>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 = 35.2 bits (81), Expect = 0.054
Identities = 20/51 (39%), Positives = 30/51 (58%), Gaps = 1/51 (1%)
Query: 366 LAGRMFVLAGAG-GAGRALAFGAKSRGARVVIFDIDFERAKSLASDVMGAA 415
L G++ ++ GAG G G A A GARVV+ DID A+++ + + G A
Sbjct: 1 LEGKVAIVTGAGAGIGAACAARLAREGARVVVADIDGGAAQAVVAQIAGGA 51
>gnl|CDD|216344 pfam01175, Urocanase, Urocanase.
Length = 545
Score = 35.6 bits (83), Expect = 0.056
Identities = 16/44 (36%), Positives = 22/44 (50%)
Query: 362 FGSPLAGRMFVLAGAGGAGRALAFGAKSRGARVVIFDIDFERAK 405
FG LAG++ + AG GG G A A GA + ++D R
Sbjct: 150 FGGDLAGKLILTAGLGGMGGAQPLAATMAGAVCLAVEVDESRID 193
>gnl|CDD|235545 PRK05650, PRK05650, short chain dehydrogenase; Provisional.
Length = 270
Score = 35.4 bits (82), Expect = 0.058
Identities = 11/35 (31%), Positives = 18/35 (51%)
Query: 369 RMFVLAGAGGAGRALAFGAKSRGARVVIFDIDFER 403
R+ + A G GRA+A G R+ + D++ E
Sbjct: 2 RVMITGAASGLGRAIALRWAREGWRLALADVNEEG 36
>gnl|CDD|181139 PRK07832, PRK07832, short chain dehydrogenase; Provisional.
Length = 272
Score = 35.0 bits (81), Expect = 0.060
Identities = 17/59 (28%), Positives = 24/59 (40%), Gaps = 7/59 (11%)
Query: 369 RMFVLAGAGGAGRALAFGAKSRGARVVIFDIDFERAKSLASDV------MGAARPFEDI 421
R FV A G GRA A ++GA + + D D + +D + R DI
Sbjct: 2 RCFVTGAASGIGRATALRLAAQGAELFLTDRDADGLAQTVADARALGGTVPEHRAL-DI 59
>gnl|CDD|182649 PRK10689, PRK10689, transcription-repair coupling factor;
Provisional.
Length = 1147
Score = 35.9 bits (83), Expect = 0.066
Identities = 19/45 (42%), Positives = 26/45 (57%), Gaps = 8/45 (17%)
Query: 83 DEHKRLEALHLAEDLGADYV----DFELKVASNILGKQYSSHQSG 123
D KRLEA+ EDLGA + D E++ A +LG++ QSG
Sbjct: 925 DAQKRLEAIASLEDLGAGFALATHDLEIRGAGELLGEE----QSG 965
>gnl|CDD|236099 PRK07791, PRK07791, short chain dehydrogenase; Provisional.
Length = 286
Score = 35.0 bits (81), Expect = 0.069
Identities = 21/37 (56%), Positives = 26/37 (70%), Gaps = 5/37 (13%)
Query: 366 LAGRMFVLAGAG-GAGR--ALAFGAKSRGARVVIFDI 399
L GR+ ++ GAG G GR ALAF A+ GARVV+ DI
Sbjct: 4 LDGRVVIVTGAGGGIGRAHALAFAAE--GARVVVNDI 38
>gnl|CDD|187647 cd08943, R1PA_ADH_SDR_c, rhamnulose-1-phosphate aldolase/alcohol
dehydrogenase, classical (c) SDRs. This family has
bifunctional proteins with an N-terminal aldolase and a
C-terminal classical SDR domain. One member is
identified as a rhamnulose-1-phosphate aldolase/alcohol
dehydrogenase. The SDR domain has a canonical SDR
glycine-rich NAD(P) binding motif and a match to the
characteristic active site triad. However, it lacks an
upstream active site Asn typical of SDRs. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold (alpha/beta folding pattern with a central
beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRs are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes catalyze a
wide range of activities including the metabolism of
steroids, cofactors, carbohydrates, lipids, aromatic
compounds, and amino acids, and act in redox sensing.
Classical SDRs have an TGXXX[AG]XG cofactor binding
motif and a YXXXK active site motif, with the Tyr
residue of the active site motif serving as a critical
catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 250
Score = 34.7 bits (80), Expect = 0.074
Identities = 19/45 (42%), Positives = 24/45 (53%)
Query: 372 VLAGAGGAGRALAFGAKSRGARVVIFDIDFERAKSLASDVMGAAR 416
V GA G G A+A + GA VV+ DID E A+ +A G R
Sbjct: 6 VTGGASGIGLAIAKRLAAEGAAVVVADIDPEIAEKVAEAAQGGPR 50
>gnl|CDD|187621 cd05363, SDH_SDR_c, Sorbitol dehydrogenase (SDH), classical (c)
SDR. This bacterial subgroup includes Rhodobacter
sphaeroides SDH, and other SDHs. SDH preferentially
interconverts D-sorbitol (D-glucitol) and D-fructose,
but also interconverts L-iditol/L-sorbose and
galactitol/D-tagatose. SDH is NAD-dependent and is a
dimeric member of the SDR family. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold (alpha/beta folding pattern with a central
beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRS are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes have a
3-glycine N-terminal NAD(P)(H)-binding pattern
(typically, TGxxxGxG in classical SDRs and TGxxGxxG in
extended SDRs), while substrate binding is in the
C-terminal region. A critical catalytic Tyr residue
(Tyr-151, human 15-hydroxyprostaglandin dehydrogenase
(15-PGDH) numbering), is often found in a conserved
YXXXK pattern. In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) or additional
Ser, contributing to the active site. Substrates for
these enzymes include sugars, steroids, alcohols, and
aromatic compounds. The standard reaction mechanism is a
proton relay involving the conserved Tyr and Lys, as
well as Asn (or Ser). Some SDR family members, including
17 beta-hydroxysteroid dehydrogenase contain an
additional helix-turn-helix motif that is not generally
found among SDRs.
Length = 254
Score = 34.9 bits (80), Expect = 0.079
Identities = 21/51 (41%), Positives = 30/51 (58%), Gaps = 1/51 (1%)
Query: 366 LAGRMFVLAG-AGGAGRALAFGAKSRGARVVIFDIDFERAKSLASDVMGAA 415
L G+ ++ G A G GRA A GARV I DI+ E A++ A+++ AA
Sbjct: 1 LDGKTALITGSARGIGRAFAQAYVREGARVAIADINLEAARATAAEIGPAA 51
>gnl|CDD|237219 PRK12827, PRK12827, short chain dehydrogenase; Provisional.
Length = 249
Score = 34.7 bits (80), Expect = 0.089
Identities = 17/49 (34%), Positives = 27/49 (55%)
Query: 363 GSPLAGRMFVLAGAGGAGRALAFGAKSRGARVVIFDIDFERAKSLASDV 411
S + R+ + G+GG GRA+A + GA V++ DI R ++ A V
Sbjct: 2 ASLDSRRVLITGGSGGLGRAIAVRLAADGADVIVLDIHPMRGRAEADAV 50
>gnl|CDD|235546 PRK05653, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Validated.
Length = 246
Score = 34.4 bits (80), Expect = 0.089
Identities = 17/44 (38%), Positives = 28/44 (63%)
Query: 371 FVLAGAGGAGRALAFGAKSRGARVVIFDIDFERAKSLASDVMGA 414
V + G GRA+A + GA+VVI+D + E A++LA+++ A
Sbjct: 9 LVTGASRGIGRAIALRLAADGAKVVIYDSNEEAAEALAAELRAA 52
>gnl|CDD|198065 smart00997, AdoHcyase_NAD, S-adenosyl-L-homocysteine hydrolase, NAD
binding domain.
Length = 162
Score = 33.6 bits (78), Expect = 0.099
Identities = 15/35 (42%), Positives = 23/35 (65%)
Query: 366 LAGRMFVLAGAGGAGRALAFGAKSRGARVVIFDID 400
LAG+ V+AG G G+ +A + GARV++ +ID
Sbjct: 21 LAGKNVVVAGYGDVGKGVAARLRGLGARVIVTEID 55
>gnl|CDD|188426 TIGR03911, pyrrolys_PylD, pyrrolysine biosynthesis protein PylD.
This protein is PylD, part of a three-gene cassette that
is sufficient to direct the biosynthesis of pyrrolysine,
the twenty-second amino acid, incorporated in some
species at a UAG canonical stop codon [Amino acid
biosynthesis, Other].
Length = 266
Score = 34.4 bits (79), Expect = 0.12
Identities = 26/103 (25%), Positives = 37/103 (35%), Gaps = 24/103 (23%)
Query: 356 KNGTASFGSPLAGRMFVLA----------------GAGGAGRALAFGAKSRGARVVIFDI 399
K G + S GR + A G G GRA AF +G V ++D
Sbjct: 117 KTGKIADNSEATGRGYAAALDCLTGGLKSKDVLVIGLGPVGRAAAFHLVDKGFHVYVYDK 176
Query: 400 DFERAKSLASDVMGAARPFEDILNFQPE---KGAILANATPLG 439
+ E ++ LA D+ I E K + + ATP
Sbjct: 177 NLEVSEKLAQDL-----CSIGIERELDEAMHKFSAIFEATPEA 214
>gnl|CDD|235488 PRK05476, PRK05476, S-adenosyl-L-homocysteine hydrolase;
Provisional.
Length = 425
Score = 34.7 bits (81), Expect = 0.12
Identities = 13/35 (37%), Positives = 23/35 (65%)
Query: 366 LAGRMFVLAGAGGAGRALAFGAKSRGARVVIFDID 400
+AG++ V+AG G G+ A + GARV++ ++D
Sbjct: 210 IAGKVVVVAGYGDVGKGCAQRLRGLGARVIVTEVD 244
>gnl|CDD|236216 PRK08277, PRK08277, D-mannonate oxidoreductase; Provisional.
Length = 278
Score = 34.1 bits (79), Expect = 0.12
Identities = 16/47 (34%), Positives = 29/47 (61%), Gaps = 1/47 (2%)
Query: 366 LAGRMFVLAGAGGA-GRALAFGAKSRGARVVIFDIDFERAKSLASDV 411
L G++ V+ G GG G A+A GA+V I D + E+A+++ +++
Sbjct: 8 LKGKVAVITGGGGVLGGAMAKELARAGAKVAILDRNQEKAEAVVAEI 54
>gnl|CDD|183489 PRK12384, PRK12384, sorbitol-6-phosphate dehydrogenase;
Provisional.
Length = 259
Score = 34.2 bits (79), Expect = 0.13
Identities = 13/40 (32%), Positives = 21/40 (52%)
Query: 372 VLAGAGGAGRALAFGAKSRGARVVIFDIDFERAKSLASDV 411
V+ G G L G G RV + DI+ E+A ++A ++
Sbjct: 7 VIGGGQTLGAFLCHGLAEEGYRVAVADINSEKAANVAQEI 46
>gnl|CDD|236094 PRK07774, PRK07774, short chain dehydrogenase; Provisional.
Length = 250
Score = 33.9 bits (78), Expect = 0.13
Identities = 16/42 (38%), Positives = 23/42 (54%)
Query: 372 VLAGAGGAGRALAFGAKSRGARVVIFDIDFERAKSLASDVMG 413
V AGG G+A A GA VV+ DI+ E A+ +A ++
Sbjct: 11 VTGAAGGIGQAYAEALAREGASVVVADINAEGAERVAKQIVA 52
>gnl|CDD|172968 PRK14497, PRK14497, putative molybdopterin biosynthesis protein
MoeA/unknown domain fusion protein; Provisional.
Length = 546
Score = 34.4 bits (79), Expect = 0.14
Identities = 28/96 (29%), Positives = 42/96 (43%), Gaps = 14/96 (14%)
Query: 139 EEDLGYLVSRMQATGADIIKLVFSVNDITEIAR-IFQLLSHCQVPII--AYSVGERGLVS 195
E +L YL S++++ G I+ L +D I I + +S V I+ S GE+ V
Sbjct: 205 ESNLHYLYSKLKSEGYKIVGLSLLSDDKESIKNEIKRAISVADVLILTGGTSAGEKDFVH 264
Query: 196 QL-----------LSPKFNGALVYGSLKGTPVLGLP 220
Q L K + G + G PV+GLP
Sbjct: 265 QAIRELGNIIVHGLKIKPGKPTILGIVDGKPVIGLP 300
>gnl|CDD|187587 cd05326, secoisolariciresinol-DH_like_SDR_c, secoisolariciresinol
dehydrogenase (secoisolariciresinol-DH)-like, classical
(c) SDRs. Podophyllum secoisolariciresinol-DH is a homo
tetrameric, classical SDR that catalyzes the
NAD-dependent conversion of (-)-secoisolariciresinol to
(-)-matairesinol via a (-)-lactol intermediate.
(-)-Matairesinol is an intermediate to various
8'-lignans, including the cancer-preventive mammalian
lignan, and those involved in vascular plant defense.
This subgroup also includes rice momilactone A synthase
which catalyzes the conversion of
3beta-hydroxy-9betaH-pimara-7,15-dien-19,6beta-olide
into momilactone A, Arabidopsis ABA2 which during
abscisic acid (ABA) biosynthesis, catalyzes the
conversion of xanthoxin to abscisic aldehyde and, maize
Tasselseed2 which participate in the maize sex
determination pathway. SDRs are a functionally diverse
family of oxidoreductases that have a single domain with
a structurally conserved Rossmann fold (alpha/beta
folding pattern with a central beta-sheet), an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRs are approximately
350 residues. Sequence identity between different SDR
enzymes are typically in the 15-30% range, but the
enzymes share the Rossmann fold NAD-binding motif and
characteristic NAD-binding and catalytic sequence
patterns. These enzymes catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, 15-hydroxyprostaglandin dehydrogenase
(15-PGDH) numbering). In addition to the Tyr and Lys,
there is often an upstream Ser (Ser-138, 15-PGDH
numbering) and/or an Asn (Asn-107, 15-PGDH numbering)
contributing to the active site; while substrate binding
is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. Extended SDRs have additional
elements in the C-terminal region, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Some atypical SDRs have lost catalytic activity and/or
have an unusual NAD(P)-binding motif and missing or
unusual active site residues. Reactions catalyzed within
the SDR family include isomerization, decarboxylation,
epimerization, C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 249
Score = 34.0 bits (78), Expect = 0.15
Identities = 17/47 (36%), Positives = 25/47 (53%)
Query: 372 VLAGAGGAGRALAFGAKSRGARVVIFDIDFERAKSLASDVMGAARPF 418
+ GA G G A A GARVVI DID + +++A+++ F
Sbjct: 9 ITGGASGIGEATARLFAKHGARVVIADIDDDAGQAVAAELGDPDISF 55
>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 = 34.0 bits (78), Expect = 0.17
Identities = 19/60 (31%), Positives = 31/60 (51%), Gaps = 5/60 (8%)
Query: 367 AGRMFVLAGAGGAGRALAFGAKSRGA-RVVIFDID---FERAKSL-ASDVMGAARPFEDI 421
G + G GG G ++ G K+ GA R++ DI+ FE+AK L A++ + + I
Sbjct: 183 PGSTCAVFGLGGVGLSVIMGCKAAGASRIIAVDINKDKFEKAKQLGATECINPRDQDKPI 242
>gnl|CDD|179297 PRK01438, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 480
Score = 33.9 bits (78), Expect = 0.20
Identities = 21/54 (38%), Positives = 28/54 (51%), Gaps = 1/54 (1%)
Query: 358 GTASFGSPLAGRMFVLAGAGGAGRALAFGAKSRGARVVIFD-IDFERAKSLASD 410
G S+ S G V+AG G +G A A GARV + D D ER ++LA+
Sbjct: 6 GLTSWHSDWQGLRVVVAGLGVSGFAAADALLELGARVTVVDDGDDERHRALAAI 59
>gnl|CDD|223842 COG0771, MurD, UDP-N-acetylmuramoylalanine-D-glutamate ligase [Cell
envelope biogenesis, outer membrane].
Length = 448
Score = 33.8 bits (78), Expect = 0.20
Identities = 28/131 (21%), Positives = 43/131 (32%), Gaps = 34/131 (25%)
Query: 366 LAGRMFVLAGAGGAGRALAFGAKSRGARVVIFDIDFERAKSLASDVMGAARPFEDILNFQ 425
G+ ++ G G +G A A GA V + D
Sbjct: 5 FQGKKVLVLGLGKSGLAAARFLLKLGAEVTVSDDR------------------PAPEGLA 46
Query: 426 PEKGAILANATPLGMHPNTDRVPVSEETLRDYQLVFDAVYT----PRKTRLLKDAEAAGA 481
+ + LG H +E L + FD V P L++ A+AAG
Sbjct: 47 AQPLLLEGIEVELGSHD--------DEDLAE----FDLVVKSPGIPPTHPLVEAAKAAGI 94
Query: 482 IIVSGVEMFLR 492
I+ +E+F R
Sbjct: 95 EIIGDIELFYR 105
>gnl|CDD|236209 PRK08265, PRK08265, short chain dehydrogenase; Provisional.
Length = 261
Score = 33.4 bits (77), Expect = 0.22
Identities = 20/54 (37%), Positives = 29/54 (53%), Gaps = 1/54 (1%)
Query: 364 SPLAGRM-FVLAGAGGAGRALAFGAKSRGARVVIFDIDFERAKSLASDVMGAAR 416
LAG++ V GA G A+A + GARV I DID + ++A+ + AR
Sbjct: 2 IGLAGKVAIVTGGATLIGAAVARALVAAGARVAIVDIDADNGAAVAASLGERAR 55
>gnl|CDD|187611 cd05353, hydroxyacyl-CoA-like_DH_SDR_c-like, (3R)-hydroxyacyl-CoA
dehydrogenase-like, classical(c)-like SDRs. Beta
oxidation of fatty acids in eukaryotes occurs by a
four-reaction cycle, that may take place in mitochondria
or in peroxisomes. (3R)-hydroxyacyl-CoA dehydrogenase is
part of rat peroxisomal multifunctional MFE-2, it is a
member of the NAD-dependent SDRs, but contains an
additional small C-terminal domain that completes the
active site pocket and participates in dimerization. The
atypical, additional C-terminal extension allows for
more extensive dimerization contact than other SDRs.
MFE-2 catalyzes the second and third reactions of the
peroxisomal beta oxidation cycle. Proteins in this
subgroup have a typical catalytic triad, but have a His
in place of the usual upstream Asn. This subgroup also
contains members identified as 17-beta-hydroxysteroid
dehydrogenases, including human peroxisomal
17-beta-hydroxysteroid dehydrogenase type 4 (17beta-HSD
type 4, aka MFE-2, encoded by HSD17B4 gene) which is
involved in fatty acid beta-oxidation and steroid
metabolism. This subgroup also includes two SDR domains
of the Neurospora crassa and Saccharomyces cerevisiae
multifunctional beta-oxidation protein (MFP, aka Fox2).
SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold (alpha/beta folding
pattern with a central beta-sheet), an NAD(P)(H)-binding
region, and a structurally diverse C-terminal region.
Classical SDRs are typically about 250 residues long,
while extended SDRS are approximately 350 residues.
Sequence identity between different SDR enzymes are
typically in the 15-30% range, but the enzymes share the
Rossmann fold NAD-binding motif and characteristic
NAD-binding and catalytic sequence patterns. These
enzymes have a 3-glycine N-terminal NAD(P)(H)-binding
pattern (typically, TGxxxGxG in classical SDRs and
TGxxGxxG in extended SDRs), while substrate binding is
in the C-terminal region. A critical catalytic Tyr
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) numbering), is often found in a
conserved YXXXK pattern. In addition to the Tyr and Lys,
there is often an upstream Ser (Ser-138, 15-PGDH
numbering) and/or an Asn (Asn-107, 15-PGDH numbering) or
additional Ser, contributing to the active site.
Substrates for these enzymes include sugars, steroids,
alcohols, and aromatic compounds. The standard reaction
mechanism is a proton relay involving the conserved Tyr
and Lys, as well as Asn (or Ser). Some SDR family
members, including 17 beta-hydroxysteroid dehydrogenase
contain an additional helix-turn-helix motif that is not
generally found among SDRs.
Length = 250
Score = 33.4 bits (77), Expect = 0.22
Identities = 21/48 (43%), Positives = 28/48 (58%), Gaps = 5/48 (10%)
Query: 368 GRMFVLAGAGGA-GR--ALAFGAKSRGARVVIFDIDFERAKSLASDVM 412
GR+ ++ GAGG GR ALAF RGA+VV+ D+ +R S S
Sbjct: 5 GRVVLVTGAGGGLGRAYALAFAE--RGAKVVVNDLGGDRKGSGKSSSA 50
>gnl|CDD|236750 PRK10751, PRK10751, molybdopterin-guanine dinucleotide biosynthesis
protein B; Provisional.
Length = 173
Score = 32.7 bits (75), Expect = 0.23
Identities = 21/48 (43%), Positives = 25/48 (52%), Gaps = 5/48 (10%)
Query: 135 ETPSEE--DLGYLVSRMQATGADIIKLV--FSVNDITEIARIFQLLSH 178
ETP +E DL YL SRM A+ D+I LV F I +IA H
Sbjct: 80 ETPDQEELDLHYLASRMDASKLDLI-LVEGFKHEPIAKIALFRDGAGH 126
>gnl|CDD|240258 PTZ00075, PTZ00075, Adenosylhomocysteinase; Provisional.
Length = 476
Score = 33.5 bits (77), Expect = 0.26
Identities = 14/35 (40%), Positives = 21/35 (60%)
Query: 366 LAGRMFVLAGAGGAGRALAFGAKSRGARVVIFDID 400
+AG+ V+ G G G+ A + GARVV+ +ID
Sbjct: 252 IAGKTVVVCGYGDVGKGCAQALRGFGARVVVTEID 286
>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 = 33.2 bits (76), Expect = 0.29
Identities = 18/65 (27%), Positives = 27/65 (41%), Gaps = 15/65 (23%)
Query: 366 LAGRMFVLAGAGGA-GRALAFGAKSRGARVVIFDIDFE--------------RAKSLASD 410
L ++ V+ G G G A+A GA+V + E RA +LA+D
Sbjct: 3 LKNKVAVITGGTGVLGGAMARALAQAGAKVAALGRNQEKGDKVAKEITALGGRAIALAAD 62
Query: 411 VMGAA 415
V+ A
Sbjct: 63 VLDRA 67
>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 = 33.0 bits (76), Expect = 0.30
Identities = 14/38 (36%), Positives = 19/38 (50%)
Query: 371 FVLAGAGGAGRALAFGAKSRGARVVIFDIDFERAKSLA 408
V + G GRA+A GA+VV+ D + E LA
Sbjct: 2 LVTGASSGIGRAIARRLAREGAKVVLADRNEEALAELA 39
>gnl|CDD|132250 TIGR03206, benzo_BadH, 2-hydroxycyclohexanecarboxyl-CoA
dehydrogenase. Members of this protein family are the
enzyme 2-hydroxycyclohexanecarboxyl-CoA dehydrogenase.
The enzymatic properties were confirmed experimentally
in Rhodopseudomonas palustris; the enzyme is
homotetrameric, and not sensitive to oxygen. This enzyme
is part of proposed pathway for degradation of
benzoyl-CoA to 3-hydroxypimeloyl-CoA that differs from
the analogous in Thauera aromatica. It also may occur in
degradation of the non-aromatic compound
cyclohexane-1-carboxylate.
Length = 250
Score = 33.0 bits (75), Expect = 0.33
Identities = 24/72 (33%), Positives = 35/72 (48%), Gaps = 4/72 (5%)
Query: 372 VLAGAGGAGRALAFGAKSRGARVVIFDIDFERAKSLASDVM---GAARPFE-DILNFQPE 427
V G GG G A GA+V +FD++ E A+ +A+D+ G A+ F DI +
Sbjct: 8 VTGGGGGIGGATCRRFAEEGAKVAVFDLNREAAEKVAADIRAKGGNAQAFACDITDRDSV 67
Query: 428 KGAILANATPLG 439
A+ A LG
Sbjct: 68 DTAVAAAEQALG 79
>gnl|CDD|109716 pfam00670, AdoHcyase_NAD, S-adenosyl-L-homocysteine hydrolase, NAD
binding domain.
Length = 162
Score = 31.9 bits (73), Expect = 0.34
Identities = 14/35 (40%), Positives = 23/35 (65%)
Query: 366 LAGRMFVLAGAGGAGRALAFGAKSRGARVVIFDID 400
+AG++ V+ G G G+ A K +GARV++ +ID
Sbjct: 21 IAGKVAVVCGYGDVGKGCAASLKGQGARVIVTEID 55
>gnl|CDD|235739 PRK06200, PRK06200, 2,3-dihydroxy-2,3-dihydrophenylpropionate
dehydrogenase; Provisional.
Length = 263
Score = 32.6 bits (75), Expect = 0.35
Identities = 16/59 (27%), Positives = 22/59 (37%), Gaps = 7/59 (11%)
Query: 369 RMFVLAGAGGAGRALAFGAKSRGARVVIFDIDFERAKSLASD-------VMGAARPFED 420
+ G G GRAL + GARV + + E+ SL V G + D
Sbjct: 8 VALITGGGSGIGRALVERFLAEGARVAVLERSAEKLASLRQRFGDHVLVVEGDVTSYAD 66
>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 = 31.7 bits (73), Expect = 0.40
Identities = 17/48 (35%), Positives = 25/48 (52%), Gaps = 2/48 (4%)
Query: 367 AGRMFVLAGAGGAGRALAFGAKSRGARVVIFDIDFERAKSLASDVMGA 414
++ V+ GAG G A AK GA V + D+ R + L S ++GA
Sbjct: 20 PAKVVVI-GAGVVGLGAAATAKGLGAEVTVLDVRPARLRQLES-LLGA 65
>gnl|CDD|180592 PRK06498, PRK06498, isocitrate lyase; Provisional.
Length = 531
Score = 33.1 bits (76), Expect = 0.40
Identities = 17/40 (42%), Positives = 22/40 (55%), Gaps = 5/40 (12%)
Query: 27 SNMYQAKA-EGAD-VVEIRLDCINNFQPGKDLEIILTKKP 64
S ++Q + G D V LDCI + Q G DL I T+KP
Sbjct: 320 SGLFQFREGTGEDRCV---LDCITSLQNGADLLWIETEKP 356
>gnl|CDD|234662 PRK00141, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 473
Score = 32.8 bits (75), Expect = 0.49
Identities = 17/50 (34%), Positives = 23/50 (46%), Gaps = 1/50 (2%)
Query: 366 LAGRMFVLAGAGGAGRALAFGAKSRGARVVIFDIDFERAKSLASDVMGAA 415
L+GR+ V AGAG +GR +A G VV+ D + L A
Sbjct: 14 LSGRVLV-AGAGVSGRGIAAMLSELGCDVVVADDNETARHKLIEVTGVAD 62
>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 = 32.4 bits (75), Expect = 0.51
Identities = 16/40 (40%), Positives = 20/40 (50%), Gaps = 1/40 (2%)
Query: 375 GAGGAGRALAFGAKSRGARVVIFDIDFERAKSLASDVMGA 414
GAG G A A GA V + DI+ ER + L D+ G
Sbjct: 175 GAGVVGENAARVALGLGAEVTVLDINLERLRYL-DDIFGG 213
>gnl|CDD|176216 cd08254, hydroxyacyl_CoA_DH, 6-hydroxycyclohex-1-ene-1-carboxyl-CoA
dehydrogenase, N-benzyl-3-pyrrolidinol dehydrogenase,
and other MDR family members. This group contains
enzymes of the zinc-dependent alcohol dehydrogenase
family, including members (aka MDR) identified as
6-hydroxycyclohex-1-ene-1-carboxyl-CoA dehydrogenase and
N-benzyl-3-pyrrolidinol dehydrogenase.
6-hydroxycyclohex-1-ene-1-carboxyl-CoA dehydrogenase
catalyzes the conversion of
6-Hydroxycyclohex-1-enecarbonyl-CoA and NAD+ to
6-Ketoxycyclohex-1-ene-1-carboxyl-CoA,NADH, and H+. This
group displays the characteristic catalytic and
structural zinc sites of the 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. 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 = 338
Score = 32.6 bits (75), Expect = 0.51
Identities = 18/59 (30%), Positives = 24/59 (40%), Gaps = 5/59 (8%)
Query: 375 GAGGAGR-ALAFGAKSRGARVVIFDID---FERAKSLASDVMGAARPFEDILNFQPEKG 429
G GG G A+ AK+ GA V+ DI E AK L +D + + G
Sbjct: 173 GLGGLGLNAVQI-AKAMGAAVIAVDIKEEKLELAKELGADEVLNSLDDSPKDKKAAGLG 230
>gnl|CDD|187635 cd08930, SDR_c8, classical (c) SDR, subgroup 8. This subgroup has
a fairly well conserved active site tetrad and domain
size of the classical SDRs, but has an atypical
NAD-binding motif ([ST]G[GA]XGXXG). SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold (alpha/beta folding pattern with a central
beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRs are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes catalyze a
wide range of activities including the metabolism of
steroids, cofactors, carbohydrates, lipids, aromatic
compounds, and amino acids, and act in redox sensing.
Classical SDRs have an TGXXX[AG]XG cofactor binding
motif and a YXXXK active site motif, with the Tyr
residue of the active site motif serving as a critical
catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 250
Score = 32.3 bits (74), Expect = 0.52
Identities = 12/43 (27%), Positives = 22/43 (51%), Gaps = 1/43 (2%)
Query: 368 GRMFVLAGAGGA-GRALAFGAKSRGARVVIFDIDFERAKSLAS 409
++ ++ GA G G+A S GAR+++ DI+ + L
Sbjct: 2 DKIILITGAAGLIGKAFCKALLSAGARLILADINAPALEQLKE 44
>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 = 32.8 bits (75), Expect = 0.53
Identities = 17/37 (45%), Positives = 20/37 (54%)
Query: 374 AGAGGAGRALAFGAKSRGARVVIFDIDFERAKSLASD 410
GAG AG A A A GARV++ D E SL S+
Sbjct: 169 VGAGPAGLAAALAAARAGARVILVDEQPEAGGSLLSE 205
>gnl|CDD|178111 PLN02494, PLN02494, adenosylhomocysteinase.
Length = 477
Score = 32.5 bits (74), Expect = 0.54
Identities = 14/35 (40%), Positives = 23/35 (65%)
Query: 366 LAGRMFVLAGAGGAGRALAFGAKSRGARVVIFDID 400
+AG++ V+ G G G+ A K+ GARV++ +ID
Sbjct: 252 IAGKVAVICGYGDVGKGCAAAMKAAGARVIVTEID 286
>gnl|CDD|216949 pfam02254, TrkA_N, TrkA-N domain. This domain is found in a wide
variety of proteins. These protein include potassium
channels, phosphoesterases, and various other
transporters. This domain binds to NAD.
Length = 116
Score = 30.6 bits (70), Expect = 0.61
Identities = 14/40 (35%), Positives = 21/40 (52%)
Query: 371 FVLAGAGGAGRALAFGAKSRGARVVIFDIDFERAKSLASD 410
++ G G GR+LA + G VV+ D D ER + L +
Sbjct: 1 IIIIGYGRVGRSLAEELREGGPDVVVIDKDPERVEELREE 40
>gnl|CDD|187599 cd05340, Ycik_SDR_c, Escherichia coli K-12 YCIK-like, classical (c)
SDRs. Escherichia coli K-12 YCIK and related proteins
have a canonical classical SDR nucleotide-binding motif
and active site tetrad. They are predicted oxoacyl-(acyl
carrier protein/ACP) reductases. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold
(alpha/beta folding pattern with a central beta-sheet),
an NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRS are approximately
350 residues. Sequence identity between different SDR
enzymes are typically in the 15-30% range, but the
enzymes share the Rossmann fold NAD-binding motif and
characteristic NAD-binding and catalytic sequence
patterns. These enzymes have a 3-glycine N-terminal
NAD(P)(H)-binding pattern (typically, TGxxxGxG in
classical SDRs and TGxxGxxG in extended SDRs), while
substrate binding is in the C-terminal region. A
critical catalytic Tyr residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering), is often found in a conserved YXXXK pattern.
In addition to the Tyr and Lys, there is often an
upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn
(Asn-107, 15-PGDH numbering) or additional Ser,
contributing to the active site. Substrates for these
enzymes include sugars, steroids, alcohols, and aromatic
compounds. The standard reaction mechanism is a proton
relay involving the conserved Tyr and Lys, as well as
Asn (or Ser). Some SDR family members, including 17
beta-hydroxysteroid dehydrogenase contain an additional
helix-turn-helix motif that is not generally found among
SDRs.
Length = 236
Score = 31.8 bits (72), Expect = 0.63
Identities = 31/147 (21%), Positives = 51/147 (34%), Gaps = 32/147 (21%)
Query: 366 LAGRMFVLAGAG-GAGRALAFGAKSRGARVVIFDIDFERAKSLASDVMGAARPFEDILNF 424
L R+ ++ GA G GR A GA V++ + E+ + +A +
Sbjct: 2 LNDRIILVTGASDGIGREAALTYARYGATVILLGRNEEKLRQVADHINEEGGRQPQWFIL 61
Query: 425 Q--------------------PEKGAILANATPLGMHPNTDRVPVSEETLRDYQLVF--D 462
P +L NA LG D P+SE+ + +Q V +
Sbjct: 62 DLLTCTSENCQQLAQRIAVNYPRLDGVLHNAGLLG-----DVCPLSEQNPQVWQDVXQVN 116
Query: 463 AVYTPRKTR----LLKDAEAAGAIIVS 485
T T+ LL ++A + S
Sbjct: 117 VNATFMLTQALLPLLLKSDAGSLVFTS 143
>gnl|CDD|235448 PRK05414, PRK05414, urocanate hydratase; Provisional.
Length = 556
Score = 32.4 bits (75), Expect = 0.66
Identities = 17/44 (38%), Positives = 22/44 (50%)
Query: 362 FGSPLAGRMFVLAGAGGAGRALAFGAKSRGARVVIFDIDFERAK 405
FG LAGR+ + AG GG G A A GA + ++D R
Sbjct: 161 FGGDLAGRLVLTAGLGGMGGAQPLAATMAGAVCLAVEVDESRID 204
>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 = 32.1 bits (73), Expect = 0.72
Identities = 17/48 (35%), Positives = 19/48 (39%)
Query: 349 AIKERGYKNGTASFGSPLAGRMFVLAGAGGAGRALAFGAKSRGARVVI 396
+ K RG N S V A G GRALA+ A G R I
Sbjct: 48 SFKLRGATNAVLSLSDTQRAAGVVAASTGNHGRALAYAAAEEGVRATI 95
>gnl|CDD|180408 PRK06114, PRK06114, short chain dehydrogenase; Provisional.
Length = 254
Score = 31.7 bits (72), Expect = 0.76
Identities = 14/34 (41%), Positives = 20/34 (58%), Gaps = 1/34 (2%)
Query: 366 LAGRMFVLAGAG-GAGRALAFGAKSRGARVVIFD 398
L G++ + GAG G G+ +A G GA V +FD
Sbjct: 6 LDGQVAFVTGAGSGIGQRIAIGLAQAGADVALFD 39
>gnl|CDD|187606 cd05348, BphB-like_SDR_c,
cis-biphenyl-2,3-dihydrodiol-2,3-dehydrogenase
(BphB)-like, classical (c) SDRs.
cis-biphenyl-2,3-dihydrodiol-2,3-dehydrogenase (BphB) is
a classical SDR, it is of particular importance for its
role in the degradation of biphenyl/polychlorinated
biphenyls(PCBs); PCBs are a significant source of
environmental contamination. This subgroup also includes
Pseudomonas putida F1
cis-biphenyl-1,2-dihydrodiol-1,2-dehydrogenase (aka
cis-benzene glycol dehydrogenase, encoded by the bnzE
gene), which participates in benzene metabolism. In
addition it includes Pseudomonas sp. C18 putative
1,2-dihydroxy-1,2-dihydronaphthalene dehydrogenase (aka
dibenzothiophene dihydrodiol dehydrogenase, encoded by
the doxE gene) which participates in an upper
naphthalene catabolic pathway. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold
(alpha/beta folding pattern with a central beta-sheet),
an NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRs are approximately
350 residues. Sequence identity between different SDR
enzymes are typically in the 15-30% range, but the
enzymes share the Rossmann fold NAD-binding motif and
characteristic NAD-binding and catalytic sequence
patterns. These enzymes catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) numbering). In addition to the
Tyr and Lys, there is often an upstream Ser (Ser-138,
15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH
numbering) contributing to the active site; while
substrate binding is in the C-terminal region, which
determines specificity. The standard reaction mechanism
is a 4-pro-S hydride transfer and proton relay involving
the conserved Tyr and Lys, a water molecule stabilized
by Asn, and nicotinamide. Extended SDRs have additional
elements in the C-terminal region, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Some atypical SDRs have lost catalytic activity and/or
have an unusual NAD(P)-binding motif and missing or
unusual active site residues. Reactions catalyzed within
the SDR family include isomerization, decarboxylation,
epimerization, C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 257
Score = 31.6 bits (72), Expect = 0.82
Identities = 17/57 (29%), Positives = 23/57 (40%), Gaps = 7/57 (12%)
Query: 371 FVLAGAGGAGRALAFGAKSRGARVVIFDIDFERAKSLASD-------VMGAARPFED 420
+ G G GRAL + GA+V + D E+ L +D V G R D
Sbjct: 8 LITGGGSGLGRALVERFVAEGAKVAVLDRSAEKVAELRADFGDAVVGVEGDVRSLAD 64
>gnl|CDD|187602 cd05344, BKR_like_SDR_like, putative beta-ketoacyl acyl carrier
protein [ACP] reductase (BKR)-like, SDR. This subgroup
resembles the SDR family, but does not have a perfect
match to the NAD-binding motif or the catalytic tetrad
characteristic of the SDRs. It includes the SDRs, Q9HYA2
from Pseudomonas aeruginosa PAO1 and APE0912 from
Aeropyrum pernix K1. BKR catalyzes the NADPH-dependent
reduction of ACP in the first reductive step of de novo
fatty acid synthesis (FAS). FAS consists of four
elongation steps, which are repeated to extend the fatty
acid chain through the addition of two-carbo units from
malonyl acyl-carrier protein (ACP): condensation,
reduction, dehydration, and a final reduction. Type II
FAS, typical of plants and many bacteria, maintains
these activities on discrete polypeptides, while type I
FAS utilizes one or two multifunctional polypeptides.
BKR resembles enoyl reductase, which catalyzes the
second reduction step in FAS. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold
(alpha/beta folding pattern with a central beta-sheet),
an NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRS are approximately
350 residues. Sequence identity between different SDR
enzymes are typically in the 15-30% range, but the
enzymes share the Rossmann fold NAD-binding motif and
characteristic NAD-binding and catalytic sequence
patterns. These enzymes have a 3-glycine N-terminal
NAD(P)(H)-binding pattern (typically, TGxxxGxG in
classical SDRs and TGxxGxxG in extended SDRs), while
substrate binding is in the C-terminal region. A
critical catalytic Tyr residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering), is often found in a conserved YXXXK pattern.
In addition to the Tyr and Lys, there is often an
upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn
(Asn-107, 15-PGDH numbering) or additional Ser,
contributing to the active site. Substrates for these
enzymes include sugars, steroids, alcohols, and aromatic
compounds. The standard reaction mechanism is a proton
relay involving the conserved Tyr and Lys, as well as
Asn (or Ser). Some SDR family members, including 17
beta-hydroxysteroid dehydrogenase contain an additional
helix-turn-helix motif that is not generally found among
SDRs.
Length = 253
Score = 31.5 bits (72), Expect = 0.82
Identities = 14/41 (34%), Positives = 20/41 (48%)
Query: 371 FVLAGAGGAGRALAFGAKSRGARVVIFDIDFERAKSLASDV 411
V A + G G A+A GARV I + E + AS++
Sbjct: 5 LVTAASSGIGLAIARALAREGARVAICARNRENLERAASEL 45
>gnl|CDD|227121 COG4782, COG4782, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 377
Score = 31.6 bits (72), Expect = 0.87
Identities = 19/64 (29%), Positives = 28/64 (43%), Gaps = 7/64 (10%)
Query: 292 GFSVGFPYKEAVMKFCDEVHPLAQAIAAVNTIIRRPSDGKLIGYNTD---CEASITAIED 348
GF+ F ++AV + VH V + PS G L+GYN D S A+E
Sbjct: 124 GFNNTF--EDAVYRTAQIVHDSGNDGVPV--VFSWPSRGSLLGYNYDRESTNYSRPALER 179
Query: 349 AIKE 352
++
Sbjct: 180 LLRY 183
>gnl|CDD|225534 COG2987, HutU, Urocanate hydratase [Amino acid transport and
metabolism].
Length = 561
Score = 31.9 bits (73), Expect = 0.88
Identities = 15/44 (34%), Positives = 20/44 (45%)
Query: 362 FGSPLAGRMFVLAGAGGAGRALAFGAKSRGARVVIFDIDFERAK 405
FG L G+ + AG GG G A A GA + ++D R
Sbjct: 161 FGGDLKGKWVLTAGLGGMGGAQPLAATMAGAVCIAVEVDESRID 204
>gnl|CDD|184511 PRK14106, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 450
Score = 31.9 bits (73), Expect = 0.95
Identities = 32/127 (25%), Positives = 48/127 (37%), Gaps = 25/127 (19%)
Query: 366 LAGRMFVLAGAGGAGRALAFGAKSRGARVVIFDIDFERAKSLASDVMGAARPFEDILNFQ 425
L G+ ++ GAG +G ALA K GA+V++ D ++ L
Sbjct: 3 LKGKKVLVVGAGVSGLALAKFLKKLGAKVILTD-------------EKEEDQLKEALEEL 49
Query: 426 PEKGAILANATPLGMHPNTDRVPVSEETLRDYQLVFDAVYTPRKTRLLKDAEAAGAIIVS 485
E G L LG +P EE L LV + P + + A G ++
Sbjct: 50 GELGIELV----LGEYP--------EEFLEGVDLVVVSPGVPLDSPPVVQAHKKGIEVIG 97
Query: 486 GVEMFLR 492
VE+ R
Sbjct: 98 EVELAYR 104
>gnl|CDD|132409 TIGR03366, HpnZ_proposed, putative phosphonate catabolism
associated alcohol dehydrogenase. This clade of
zinc-binding alcohol dehydrogenases (members of
pfam00107) are repeatedly associated with genes proposed
to be involved with the catabolism of phosphonate
compounds.
Length = 280
Score = 31.3 bits (71), Expect = 0.98
Identities = 17/46 (36%), Positives = 22/46 (47%), Gaps = 1/46 (2%)
Query: 365 PLAGRMFVLAGAGGAGRALAFGAKSRGA-RVVIFDIDFERAKSLAS 409
L GR ++ GAG G A A + GA RVV D +R + S
Sbjct: 118 DLKGRRVLVVGAGMLGLTAAAAAAAAGAARVVAADPSPDRRELALS 163
>gnl|CDD|180822 PRK07069, PRK07069, short chain dehydrogenase; Validated.
Length = 251
Score = 31.2 bits (71), Expect = 0.99
Identities = 17/50 (34%), Positives = 26/50 (52%), Gaps = 1/50 (2%)
Query: 369 RMFVLAGAGGAGRALAFGAKSRGARVVIFDI-DFERAKSLASDVMGAARP 417
R F+ AGG GRA+A +GA+V + DI D + A+++ A
Sbjct: 1 RAFITGAAGGLGRAIARRMAEQGAKVFLTDINDAAGLDAFAAEINAAHGE 50
>gnl|CDD|235712 PRK06138, PRK06138, short chain dehydrogenase; Provisional.
Length = 252
Score = 31.3 bits (71), Expect = 1.0
Identities = 24/54 (44%), Positives = 32/54 (59%), Gaps = 1/54 (1%)
Query: 366 LAGRMFVLAGAG-GAGRALAFGAKSRGARVVIFDIDFERAKSLASDVMGAARPF 418
LAGR+ ++ GAG G GRA A GARVV+ D D E A+ +A+ + R F
Sbjct: 3 LAGRVAIVTGAGSGIGRATAKLFAREGARVVVADRDAEAAERVAAAIAAGGRAF 56
>gnl|CDD|218507 pfam05221, AdoHcyase, S-adenosyl-L-homocysteine hydrolase.
Length = 430
Score = 31.6 bits (72), Expect = 1.0
Identities = 13/35 (37%), Positives = 23/35 (65%)
Query: 366 LAGRMFVLAGAGGAGRALAFGAKSRGARVVIFDID 400
+AG++ V+ G G G+ A + +GARV++ +ID
Sbjct: 208 IAGKVAVVCGYGDVGKGCAASLRGQGARVIVTEID 242
>gnl|CDD|212495 cd09807, retinol-DH_like_SDR_c, retinol dehydrogenases
(retinol-DHs), classical (c) SDRs. Classical SDR-like
subgroup containing retinol-DHs and related proteins.
Retinol is processed by a medium chain alcohol
dehydrogenase followed by retinol-DHs. Proteins in this
subfamily share the glycine-rich NAD-binding motif of
the classical SDRs, have a partial match to the
canonical active site tetrad, but lack the typical
active site Ser. This subgroup includes the human
proteins: retinol dehydrogenase -12, -13 ,and -14. SDRs
are a functionally diverse family of oxidoreductases
that have a single domain with a structurally conserved
Rossmann fold (alpha/beta folding pattern with a central
beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRs are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes catalyze a
wide range of activities including the metabolism of
steroids, cofactors, carbohydrates, lipids, aromatic
compounds, and amino acids, and act in redox sensing.
Classical SDRs have an TGXXX[AG]XG cofactor binding
motif and a YXXXK active site motif, with the Tyr
residue of the active site motif serving as a critical
catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 274
Score = 31.3 bits (71), Expect = 1.1
Identities = 13/50 (26%), Positives = 24/50 (48%), Gaps = 1/50 (2%)
Query: 368 GRMFVLAGAG-GAGRALAFGAKSRGARVVIFDIDFERAKSLASDVMGAAR 416
G+ ++ GA G G+ A RGARV++ D + + A+++
Sbjct: 1 GKTVIITGANTGIGKETARELARRGARVIMACRDMAKCEEAAAEIRRDTL 50
>gnl|CDD|181225 PRK08085, PRK08085, gluconate 5-dehydrogenase; Provisional.
Length = 254
Score = 31.3 bits (71), Expect = 1.1
Identities = 17/46 (36%), Positives = 25/46 (54%), Gaps = 1/46 (2%)
Query: 366 LAGRMFVLAGAG-GAGRALAFGAKSRGARVVIFDIDFERAKSLASD 410
LAG+ ++ G+ G G LA G GA ++I DI ERA+ +
Sbjct: 7 LAGKNILITGSAQGIGFLLATGLAEYGAEIIINDITAERAELAVAK 52
>gnl|CDD|236025 PRK07476, eutB, threonine dehydratase; Provisional.
Length = 322
Score = 31.5 bits (72), Expect = 1.1
Identities = 18/49 (36%), Positives = 23/49 (46%)
Query: 349 AIKERGYKNGTASFGSPLAGRMFVLAGAGGAGRALAFGAKSRGARVVIF 397
+ K RG N S + R V A G GRALA+ A++ G R I
Sbjct: 48 SFKLRGATNALLSLSAQERARGVVTASTGNHGRALAYAARALGIRATIC 96
>gnl|CDD|223981 COG1053, SdhA, Succinate dehydrogenase/fumarate reductase,
flavoprotein subunit [Energy production and conversion].
Length = 562
Score = 31.6 bits (72), Expect = 1.1
Identities = 9/24 (37%), Positives = 11/24 (45%)
Query: 375 GAGGAGRALAFGAKSRGARVVIFD 398
G GGAG A A G +V +
Sbjct: 13 GGGGAGLRAAIEAAEAGLKVALLS 36
>gnl|CDD|224118 COG1197, Mfd, Transcription-repair coupling factor (superfamily II
helicase) [DNA replication, recombination, and repair /
Transcription].
Length = 1139
Score = 31.8 bits (73), Expect = 1.1
Identities = 17/42 (40%), Positives = 25/42 (59%), Gaps = 8/42 (19%)
Query: 86 KRLEALHLAEDLGADYV----DFELKVASNILGKQYSSHQSG 123
KRLEA+ +LGA + D E++ A N+LG++ QSG
Sbjct: 922 KRLEAIASFTELGAGFKLAMHDLEIRGAGNLLGEE----QSG 959
>gnl|CDD|212496 cd11730, Tthb094_like_SDR_c, Tthb094 and related proteins,
classical (c) SDRs. Tthb094 from Thermus Thermophilus
is a classical SDR which binds NADP. Members of this
subgroup contain the YXXXK active site characteristic of
SDRs. Also, an upstream Asn residue of the canonical
catalytic tetrad is partially conserved 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 = 206
Score = 31.0 bits (70), Expect = 1.2
Identities = 26/104 (25%), Positives = 42/104 (40%), Gaps = 14/104 (13%)
Query: 371 FVLAGAGGAGRALAFGAKSRGARVVIFDIDFERAKSLASDVMGAARPFEDILNFQPEKGA 430
+L GG GRALA RG R+++ D LA++V ARP + + + E A
Sbjct: 2 LILGATGGIGRALARALAGRGWRLLLSGRDAGALAGLAAEVGALARPAD--VAAELEVWA 59
Query: 431 ILANATPL--------GMHPNTDRVPVSEETLRDYQLVFDAVYT 466
+ PL + P++ ++ + DA T
Sbjct: 60 LAQELGPLDLLVYAAGAILGK----PLARTKPAAWRRILDANLT 99
>gnl|CDD|225172 COG2263, COG2263, Predicted RNA methylase [Translation, ribosomal
structure and biogenesis].
Length = 198
Score = 30.7 bits (70), Expect = 1.2
Identities = 24/75 (32%), Positives = 38/75 (50%), Gaps = 7/75 (9%)
Query: 365 PLAGRMFVLAGAGGAGRALAFGAKSRGA-RVVIFDID---FERAKSLASDVMGAARPFE- 419
L G+ + GAG G LA GA GA RV+ DID E A++ A +++G
Sbjct: 43 DLEGKTVLDLGAG-TGI-LAIGAALLGASRVLAVDIDPEALEIARANAEELLGDVEFVVA 100
Query: 420 DILNFQPEKGAILAN 434
D+ +F+ + ++ N
Sbjct: 101 DVSDFRGKFDTVIMN 115
>gnl|CDD|187598 cd05339, 17beta-HSDXI-like_SDR_c, human 17-beta-hydroxysteroid
dehydrogenase XI-like, classical (c) SDRs.
17-beta-hydroxysteroid dehydrogenases (17betaHSD) are a
group of isozymes that catalyze activation and
inactivation of estrogen and androgens. 17betaHSD type
XI, a classical SDR, preferentially converts
3alpha-adiol to androsterone but not numerous other
tested steroids. This subgroup of classical SDRs also
includes members identified as retinol dehydrogenases,
which convert retinol to retinal, a property that
overlaps with 17betaHSD activity. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold (alpha/beta folding pattern with a central
beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRS are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes have a
3-glycine N-terminal NAD(P)(H)-binding pattern
(typically, TGxxxGxG in classical SDRs and TGxxGxxG in
extended SDRs), while substrate binding is in the
C-terminal region. A critical catalytic Tyr residue
(Tyr-151, human 15-hydroxyprostaglandin dehydrogenase
(15-PGDH) numbering), is often found in a conserved
YXXXK pattern. In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) or additional
Ser, contributing to the active site. Substrates for
these enzymes include sugars, steroids, alcohols, and
aromatic compounds. The standard reaction mechanism is a
proton relay involving the conserved Tyr and Lys, as
well as Asn (or Ser). Some SDR family members, including
17 beta-hydroxysteroid dehydrogenase contain an
additional helix-turn-helix motif that is not generally
found among SDRs.
Length = 243
Score = 31.1 bits (71), Expect = 1.3
Identities = 14/26 (53%), Positives = 16/26 (61%)
Query: 375 GAGGAGRALAFGAKSRGARVVIFDID 400
G G GR LA RGA+VVI DI+
Sbjct: 7 GGSGIGRLLALEFAKRGAKVVILDIN 32
>gnl|CDD|177311 PHA01547, PHA01547, putative internal virion protein A.
Length = 206
Score = 30.8 bits (69), Expect = 1.3
Identities = 17/42 (40%), Positives = 21/42 (50%)
Query: 366 LAGRMFVLAGAGGAGRALAFGAKSRGARVVIFDIDFERAKSL 407
A RM +LAG A +A A G K V DID E ++L
Sbjct: 70 EAKRMAMLAGGSAAAQAAAAGVKGASVDAVALDIDREVGEAL 111
>gnl|CDD|226968 COG4615, PvdE, ABC-type siderophore export system, fused ATPase and
permease components [Secondary metabolites biosynthesis,
transport, and catabolism / Inorganic ion transport and
metabolism].
Length = 546
Score = 31.3 bits (71), Expect = 1.3
Identities = 15/43 (34%), Positives = 22/43 (51%), Gaps = 11/43 (25%)
Query: 424 FQPEKGAILANATPLGMHPNTDRVPVSEETLRDYQLVFDAVYT 466
+QP+ G IL + P VS E L DY+ +F AV++
Sbjct: 373 YQPQSGEILLDGKP-----------VSAEQLEDYRKLFSAVFS 404
>gnl|CDD|233032 TIGR00580, mfd, transcription-repair coupling factor (mfd). All
proteins in this family for which functions are known
are DNA-dependent ATPases that function in the process
of transcription-coupled DNA repair in which the repair
of the transcribed strand of actively transcribed genes
is repaired at a higher rate than the repair of
non-transcribed regions of the genome and than the
non-transcribed strand of the same gene. This family is
based on the phylogenomic analysis of JA Eisen (1999,
Ph.D. Thesis, Stanford University). This family is
closely related to the RecG and UvrB families [DNA
metabolism, DNA replication, recombination, and repair].
Length = 926
Score = 31.6 bits (72), Expect = 1.4
Identities = 16/39 (41%), Positives = 24/39 (61%), Gaps = 4/39 (10%)
Query: 86 KRLEALHLAEDLGADYV----DFELKVASNILGKQYSSH 120
KRLEA+ +LGA + D E++ A N+LG++ S H
Sbjct: 779 KRLEAIQEFSELGAGFKIALHDLEIRGAGNLLGEEQSGH 817
>gnl|CDD|180854 PRK07121, PRK07121, hypothetical protein; Validated.
Length = 492
Score = 31.0 bits (71), Expect = 1.5
Identities = 11/27 (40%), Positives = 16/27 (59%)
Query: 372 VLAGAGGAGRALAFGAKSRGARVVIFD 398
V+ G G AG A A + GARV++ +
Sbjct: 24 VVVGFGAAGACAAIEAAAAGARVLVLE 50
>gnl|CDD|181349 PRK08278, PRK08278, short chain dehydrogenase; Provisional.
Length = 273
Score = 30.6 bits (70), Expect = 1.5
Identities = 12/34 (35%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 364 SPLAGR-MFVLAGAGGAGRALAFGAKSRGARVVI 396
L+G+ +F+ + G G A+A A GA +VI
Sbjct: 2 MSLSGKTLFITGASRGIGLAIALRAARDGANIVI 35
>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 = 30.6 bits (69), Expect = 1.6
Identities = 15/50 (30%), Positives = 25/50 (50%), Gaps = 1/50 (2%)
Query: 366 LAGRMFVLAGAG-GAGRALAFGAKSRGARVVIFDIDFERAKSLASDVMGA 414
L G++ ++ GA G G A A + GA V I +R ++LA ++
Sbjct: 1 LQGKVALVTGASSGIGEATARALAAEGAAVAIAARRVDRLEALADELEAE 50
>gnl|CDD|216703 pfam01791, DeoC, DeoC/LacD family aldolase. This family includes
diverse aldolase enzymes. This family includes the
enzyme deoxyribose-phosphate aldolase EC:4.1.2.4, which
is involved in nucleotide metabolism. The family also
includes a group of related bacterial proteins of
unknown function. The family also includes tagatose
1,6-diphosphate aldolase (EC:4.1.2.40) is part of the
tagatose-6-phosphate pathway of galactose-6-phosphate
degradation.
Length = 231
Score = 30.4 bits (69), Expect = 1.7
Identities = 20/81 (24%), Positives = 32/81 (39%), Gaps = 10/81 (12%)
Query: 31 QAKAEGAD----VVEIRLDCINNFQPGKDLEI-----ILTKKPLPVLIVYRPKWAGGLYE 81
+A A GAD VV I D + + EI + L V++ + +
Sbjct: 82 EAIALGADEVDMVVNIGADGSEDEEQVLA-EIAAVKEACHGEGLKVILEAYLRGEEIKDK 140
Query: 82 GDEHKRLEALHLAEDLGADYV 102
D H +A + + GAD+V
Sbjct: 141 VDPHLVAKATRVGAEAGADFV 161
>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 = 30.8 bits (70), Expect = 1.8
Identities = 26/76 (34%), Positives = 43/76 (56%), Gaps = 3/76 (3%)
Query: 362 FGSPLAGRMFVLAGAGGAGRALAFGAKSRGA-RVVIFDIDFERAKSLASDVMGAARPFED 420
FGS L G+ +L GAG G +A +G +++I + +ERA+ LA ++ G A FED
Sbjct: 175 FGS-LKGKKALLIGAGEMGELVAKHLLRKGVGKILIANRTYERAEDLAKELGGEAVKFED 233
Query: 421 ILNFQPEKGAILANAT 436
+ + E I+ ++T
Sbjct: 234 LEEYLAE-ADIVISST 248
>gnl|CDD|223364 COG0287, TyrA, Prephenate dehydrogenase [Amino acid transport and
metabolism].
Length = 279
Score = 30.8 bits (70), Expect = 1.8
Identities = 13/43 (30%), Positives = 17/43 (39%)
Query: 372 VLAGAGGAGRALAFGAKSRGARVVIFDIDFERAKSLASDVMGA 414
+ G G G +LA K G V I D A A+ +G
Sbjct: 7 GIVGLGLMGGSLARALKEAGLVVRIIGRDRSAATLKAALELGV 49
>gnl|CDD|213929 TIGR04316, dhbA_paeA, 2,3-dihydro-2,3-dihydroxybenzoate
dehydrogenase. Members of this family are
2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase (EC
1.3.1.28), the third enzyme in the biosynthesis of
2,3-dihydroxybenzoic acid (DHB) from chorismate. The
first two enzymes are isochorismate synthase (EC
5.4.4.2) and isochorismatase (EC 3.3.2.1). Synthesis is
often followed by adenylation by the enzyme DHBA-AMP
ligase (EC 2.7.7.58) to activate (DHB) for a
non-ribosomal peptide synthetase.
Length = 250
Score = 30.3 bits (69), Expect = 1.8
Identities = 17/48 (35%), Positives = 23/48 (47%), Gaps = 1/48 (2%)
Query: 373 LAGAG-GAGRALAFGAKSRGARVVIFDIDFERAKSLASDVMGAARPFE 419
+ GA G G A+A GARV D +FE+ L +D+ PF
Sbjct: 3 VTGAAQGIGYAVARALAEAGARVAAVDRNFEQLLELVADLRRYGYPFA 50
>gnl|CDD|218844 pfam05990, DUF900, Alpha/beta hydrolase of unknown function
(DUF900). This family consists of several hypothetical
proteins of unknown function mostly found in Rhizobium
species. Members of this family have an alpha/beta
hydrolase fold.
Length = 230
Score = 30.4 bits (69), Expect = 1.9
Identities = 19/65 (29%), Positives = 28/65 (43%), Gaps = 9/65 (13%)
Query: 292 GFSVGFPYKEAVMKFCDEVHPL-AQAIAAVNTIIRRPSDGKLIGYNTD---CEASITAIE 347
G++ F ++AV +F H L + V T PS L GYN D S A+E
Sbjct: 27 GYNNSF--EDAVYRFAQIAHDLGFPGVPVVFTW---PSGASLFGYNYDRESANYSRDALE 81
Query: 348 DAIKE 352
++
Sbjct: 82 RLLRY 86
>gnl|CDD|133419 cd00650, LDH_MDH_like, NAD-dependent, lactate dehydrogenase-like,
2-hydroxycarboxylate dehydrogenase family. Members of
this family include ubiquitous enzymes like L-lactate
dehydrogenases (LDH), L-2-hydroxyisocaproate
dehydrogenases, and some malate dehydrogenases (MDH).
LDH catalyzes the last step of glycolysis in which
pyruvate is converted to L-lactate. MDH is one of the
key enzymes in the citric acid cycle, facilitating both
the conversion of malate to oxaloacetate and
replenishing levels of oxalacetate by reductive
carboxylation of pyruvate. The LDH/MDH-like proteins are
part of the NAD(P)-binding Rossmann fold superfamily,
which includes a wide variety of protein families
including the NAD(P)-binding domains of alcohol
dehydrogenases, tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate dehydrogenases,
formate/glycerate dehydrogenases, siroheme synthases,
6-phosphogluconate dehydrogenases, aminoacid
dehydrogenases, repressor rex, and NAD-binding potassium
channel domains, among others.
Length = 263
Score = 30.4 bits (69), Expect = 1.9
Identities = 20/54 (37%), Positives = 27/54 (50%), Gaps = 4/54 (7%)
Query: 372 VLAGAGGAGRALAFGAKSRGAR----VVIFDIDFERAKSLASDVMGAARPFEDI 421
V+ G G ALAFG +V++DID E+ K +A D+ A P DI
Sbjct: 3 VIGAGGNVGPALAFGLADGSVLLAIELVLYDIDEEKLKGVAMDLQDAVEPLADI 56
>gnl|CDD|236101 PRK07803, sdhA, succinate dehydrogenase flavoprotein subunit;
Reviewed.
Length = 626
Score = 30.8 bits (70), Expect = 1.9
Identities = 21/50 (42%), Positives = 24/50 (48%), Gaps = 12/50 (24%)
Query: 372 VLAGAGGAGRALAFGAKSRGARVVIFDIDFERAKSL---ASDVM---GAA 415
V+ GAGGAG A A+ RG RV + KSL A VM G A
Sbjct: 12 VVIGAGGAGLRAAIEARERGLRVAVV------CKSLFGKAHTVMAEGGCA 55
>gnl|CDD|234436 TIGR03997, mycofact_OYE_2, mycofactocin system FadH/OYE family
oxidoreductase 2. The yeast protein called old yellow
enzyme and FadH from Escherichia coli (2,4-dienoyl CoA
reductase) are enzymes with 4Fe-4S, FMN, and FAD
prosthetic groups, and interact with NADPH as well as
substrate. Members of this related protein family occur
in the vicinity of the putative mycofactocin
biosynthesis operon in a number of Actinobacteria such
as Frankia sp. and Rhodococcus sp., in Pelotomaculum
thermopropionicum SI (Firmicutes), and in Geobacter
uraniireducens Rf4 (Deltaproteobacteria). The function
of this oxidoreductase is unknown.
Length = 645
Score = 30.8 bits (70), Expect = 2.0
Identities = 21/61 (34%), Positives = 27/61 (44%), Gaps = 4/61 (6%)
Query: 356 KNGTASFGSPLAGRMFVLAGAGGAGRALAFGAKSRGARVVIFDIDFERAKSLASDVMGAA 415
+ GT + P + ++ G G AG A A RG RV + FER L V AA
Sbjct: 367 EWGTVTLPPPRRRKRVLVVGGGPAGLEAAATAARRGHRVTL----FEREDRLGGQVRLAA 422
Query: 416 R 416
R
Sbjct: 423 R 423
>gnl|CDD|180823 PRK07074, PRK07074, short chain dehydrogenase; Provisional.
Length = 257
Score = 30.5 bits (69), Expect = 2.1
Identities = 18/45 (40%), Positives = 23/45 (51%), Gaps = 1/45 (2%)
Query: 372 VLAGAGGAGRALAFGAKSRGARVVIFDIDFERAKSLASDVMGAAR 416
V AGG G+ALA + G RV+ DID + A +G AR
Sbjct: 7 VTGAAGGIGQALARRFLAAGDRVLALDIDAAALAAFADA-LGDAR 50
>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 = 30.7 bits (70), Expect = 2.1
Identities = 17/44 (38%), Positives = 21/44 (47%), Gaps = 1/44 (2%)
Query: 363 GSPLAGRMFVLAGAGGAGRALAFGAKSRGA-RVVIFDIDFERAK 405
G AG V+ GAG G AK GA RV++ D ER +
Sbjct: 173 GPVGAGDTVVVQGAGPLGLYAVAAAKLAGARRVIVIDGSPERLE 216
>gnl|CDD|224169 COG1249, Lpd, Pyruvate/2-oxoglutarate dehydrogenase complex,
dihydrolipoamide dehydrogenase (E3) component, and
related enzymes [Energy production and conversion].
Length = 454
Score = 30.6 bits (70), Expect = 2.2
Identities = 9/24 (37%), Positives = 12/24 (50%)
Query: 375 GAGGAGRALAFGAKSRGARVVIFD 398
GAG AG A A G +V + +
Sbjct: 11 GAGPAGYVAAIRAAQLGLKVALVE 34
>gnl|CDD|176191 cd05289, MDR_like_2, alcohol dehydrogenase and quinone
reductase-like medium chain degydrogenases/reductases.
Members identified as zinc-dependent alcohol
dehydrogenases and quinone oxidoreductase. QOR catalyzes
the conversion of a quinone + NAD(P)H to a hydroquinone
+ NAD(P)+. Quinones are cyclic diones derived from
aromatic compounds. Membrane bound QOR actin the
respiratory chains of bacteria and mitochondria, while
soluble QOR acts to protect from toxic quinones (e.g.
DT-diaphorase) or as a soluble eye-lens protein in some
vertebrates (e.g. zeta-crystalin). QOR reduces quinones
through a semi-quinone intermediate via a
NAD(P)H-dependent single electron transfer. QOR is a
member of the medium chain dehydrogenase/reductase
family, but lacks the zinc-binding sites of the
prototypical alcohol dehydrogenases of this group.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which has a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES. These
proteins typically form dimers (typically higher plants,
mammals) or tetramers (yeast, bacteria), and have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. NAD(H) binding occurs in the
cleft between the catalytic and coenzyme-binding domains
at the active site, and coenzyme binding induces a
conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
In human ADH catalysis, the zinc ion helps coordinate
the alcohol, followed by deprotonation of a histidine,
the ribose of NAD, a serine, then the alcohol, which
allows the transfer of a hydride to NAD+, creating NADH
and a zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 309
Score = 30.2 bits (69), Expect = 2.2
Identities = 14/35 (40%), Positives = 18/35 (51%), Gaps = 1/35 (2%)
Query: 362 FGSPLAG-RMFVLAGAGGAGRALAFGAKSRGARVV 395
G AG + + AGG G AK+RGARV+
Sbjct: 139 LGGLKAGQTVLIHGAAGGVGSFAVQLAKARGARVI 173
>gnl|CDD|235726 PRK06181, PRK06181, short chain dehydrogenase; Provisional.
Length = 263
Score = 30.3 bits (69), Expect = 2.2
Identities = 16/45 (35%), Positives = 26/45 (57%), Gaps = 1/45 (2%)
Query: 368 GRMFVLAGA-GGAGRALAFGAKSRGARVVIFDIDFERAKSLASDV 411
G++ ++ GA G GRALA GA++V+ + R SLA ++
Sbjct: 1 GKVVIITGASEGIGRALAVRLARAGAQLVLAARNETRLASLAQEL 45
>gnl|CDD|179627 PRK03661, PRK03661, hypothetical protein; Validated.
Length = 164
Score = 29.6 bits (67), Expect = 2.6
Identities = 14/39 (35%), Positives = 19/39 (48%)
Query: 449 VSEETLRDYQLVFDAVYTPRKTRLLKDAEAAGAIIVSGV 487
V EETL + V + V LK A A A+ +SG+
Sbjct: 67 VREETLAQHGAVSEPVVVEMAIGALKAARADYAVSISGI 105
>gnl|CDD|236707 PRK10522, PRK10522, multidrug transporter membrane
component/ATP-binding component; Provisional.
Length = 547
Score = 30.3 bits (69), Expect = 2.8
Identities = 15/43 (34%), Positives = 21/43 (48%), Gaps = 11/43 (25%)
Query: 424 FQPEKGAILANATPLGMHPNTDRVPVSEETLRDYQLVFDAVYT 466
+QP+ G IL D PV+ E DY+ +F AV+T
Sbjct: 373 YQPQSGEIL-----------LDGKPVTAEQPEDYRKLFSAVFT 404
>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 = 30.0 bits (68), Expect = 3.1
Identities = 31/144 (21%), Positives = 45/144 (31%), Gaps = 35/144 (24%)
Query: 375 GAGGAGRALAFGAKSRGA-RVVIFDIDFERAKSLASDVMGAAR---PFED--ILNFQPEK 428
G G G A+ K+RG +V D ER LA MGA P D + E
Sbjct: 169 GCGPIGLAVIAALKARGVGPIVASDFSPERRA-LALA-MGADIVVDPAADSPFAAWAAEL 226
Query: 429 GAILANA---------------------------TPLGMHPNTDRVPVSEETLRDYQLVF 461
+G+ +D + + ++ L F
Sbjct: 227 ARAGGPKPAVIFECVGAPGLIQQIIEGAPPGGRIVVVGVCMESDNIEPALAIRKELTLQF 286
Query: 462 DAVYTPRKTRLLKDAEAAGAIIVS 485
YTP + DA A G + V+
Sbjct: 287 SLGYTPEEFADALDALAEGKVDVA 310
>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 = 30.0 bits (68), Expect = 3.2
Identities = 23/87 (26%), Positives = 33/87 (37%), Gaps = 11/87 (12%)
Query: 371 FVLAGAGGAGRALAFGAKSRGARVVIFDI-DFERAKSLASDVMGAAR---PFEDILNFQP 426
V+ GAG AG + A+ +G RV++ + F R K + A L
Sbjct: 3 VVVVGAGPAGASAAYRLADKGLRVLLLEKKSFPRYKPCGGALSPRALEELDLPGELIVNL 62
Query: 427 EKGAILANATPLGMHPNTDRVPVSEET 453
+GA PN D V + ET
Sbjct: 63 VRGARF-------FSPNGDSVEIPIET 82
>gnl|CDD|180817 PRK07060, PRK07060, short chain dehydrogenase; Provisional.
Length = 245
Score = 29.7 bits (67), Expect = 3.2
Identities = 18/56 (32%), Positives = 24/56 (42%), Gaps = 5/56 (8%)
Query: 357 NGTASFGSPLAGRMFVLAGAG-GAGRALAFGAKSRGARVVIFDIDFERAKSLASDV 411
N F +G+ ++ GA G GRA A RGARVV + LA +
Sbjct: 2 NMAFDF----SGKSVLVTGASSGIGRACAVALAQRGARVVAAARNAAALDRLAGET 53
>gnl|CDD|181359 PRK08293, PRK08293, 3-hydroxybutyryl-CoA dehydrogenase; Validated.
Length = 287
Score = 29.9 bits (68), Expect = 3.3
Identities = 15/37 (40%), Positives = 19/37 (51%), Gaps = 3/37 (8%)
Query: 372 VLAGAGGAGRALAFGAKSRGARVVIFDID---FERAK 405
+AGAG G +AF G V I+DI E+AK
Sbjct: 7 TVAGAGVLGSQIAFQTAFHGFDVTIYDISDEALEKAK 43
>gnl|CDD|235693 PRK06077, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 252
Score = 29.7 bits (67), Expect = 3.4
Identities = 12/32 (37%), Positives = 19/32 (59%), Gaps = 1/32 (3%)
Query: 366 LAGRMFVLAGAG-GAGRALAFGAKSRGARVVI 396
L ++ V+ G+G G GRA+A G+ VV+
Sbjct: 4 LKDKVVVVTGSGRGIGRAIAVRLAKEGSLVVV 35
>gnl|CDD|133444 cd01075, NAD_bind_Leu_Phe_Val_DH, NAD(P) binding domain of leucine
dehydrogenase, phenylalanine dehydrogenase, and valine
dehydrogenase. Amino acid dehydrogenase (DH) is a
widely distributed family of enzymes that catalyzes the
oxidative deamination of an amino acid to its keto acid
and ammonia with concomitant reduction of NADP+. For
example, leucine DH catalyzes the reversible oxidative
deamination of L-leucine and several other straight or
branched chain amino acids to the corresponding
2-oxoacid derivative. Amino acid DH -like NAD(P)-binding
domains are members of the Rossmann fold superfamily and
include glutamate, leucine, and phenylalanine DHs,
methylene tetrahydrofolate DH,
methylene-tetrahydromethanopterin DH,
methylene-tetrahydropholate DH/cyclohydrolase, Shikimate
DH-like proteins, malate oxidoreductases, and glutamyl
tRNA reductase. Amino acid DHs catalyze the deamination
of amino acids to keto acids with NAD(P)+ as a cofactor.
The NAD(P)-binding Rossmann fold superfamily includes a
wide variety of protein families including NAD(P)-
binding domains of alcohol DHs, tyrosine-dependent
oxidoreductases, glyceraldehyde-3-phosphate DH,
lactate/malate DHs, formate/glycerate DHs, siroheme
synthases, 6-phosphogluconate DH, amino acid DHs,
repressor rex, NAD-binding potassium channel domain,
CoA-binding, and ornithine cyclodeaminase-like domains.
These domains have an alpha-beta-alpha configuration.
NAD binding involves numerous hydrogen and van der Waals
contacts.
Length = 200
Score = 29.1 bits (66), Expect = 3.7
Identities = 22/78 (28%), Positives = 38/78 (48%), Gaps = 8/78 (10%)
Query: 366 LAGRMFVLAGAGGAGRALAFGAKSRGARVVIFDIDFERAKSLASDVMGAAR-PFEDILN- 423
L G+ + G G G LA GA++++ DI+ E A + A+++ GA E+I +
Sbjct: 26 LEGKTVAVQGLGKVGYKLAEHLLEEGAKLIVADIN-EEAVARAAELFGATVVAPEEIYSV 84
Query: 424 ----FQP-EKGAILANAT 436
F P G ++ + T
Sbjct: 85 DADVFAPCALGGVINDDT 102
>gnl|CDD|135765 PRK06113, PRK06113, 7-alpha-hydroxysteroid dehydrogenase;
Validated.
Length = 255
Score = 29.4 bits (66), Expect = 3.9
Identities = 15/47 (31%), Positives = 27/47 (57%), Gaps = 1/47 (2%)
Query: 366 LAGRMFVLAGAG-GAGRALAFGAKSRGARVVIFDIDFERAKSLASDV 411
L G+ ++ GAG G G+ +A + GA VV+ DI+ + A + ++
Sbjct: 9 LDGKCAIITGAGAGIGKEIAITFATAGASVVVSDINADAANHVVDEI 55
>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 = 3.9
Identities = 16/37 (43%), Positives = 20/37 (54%), Gaps = 4/37 (10%)
Query: 375 GAGGAGRALAFGAKSRGARVVI-FDID---FERAKSL 407
G G G A+ GAK+ GA +I DI+ FE AK
Sbjct: 194 GLGAVGLAVIQGAKAAGASRIIGIDINPDKFELAKKF 230
>gnl|CDD|235935 PRK07109, PRK07109, short chain dehydrogenase; Provisional.
Length = 334
Score = 29.5 bits (67), Expect = 4.2
Identities = 17/48 (35%), Positives = 28/48 (58%), Gaps = 1/48 (2%)
Query: 365 PLAGRMFVLAGA-GGAGRALAFGAKSRGARVVIFDIDFERAKSLASDV 411
P+ ++ V+ GA G GRA A RGA+VV+ E ++LA+++
Sbjct: 5 PIGRQVVVITGASAGVGRATARAFARRGAKVVLLARGEEGLEALAAEI 52
>gnl|CDD|238452 cd00887, MoeA, MoeA family. Members of this family are involved in
biosynthesis of the molybdenum cofactor (MoCF), an
essential cofactor of a diverse group of redox enzymes.
MoCF biosynthesis is an evolutionarily conserved pathway
present in eubacteria, archaea and eukaryotes. MoCF
contains a tricyclic pyranopterin, termed molybdopterin
(MPT). MoeA, together with MoaB, is responsible for the
metal incorporation into MPT, the third step in MoCF
biosynthesis. The plant homolog Cnx1 is a MoeA-MogA
fusion protein. The mammalian homolog gephyrin is a
MogA-MoeA fusion protein, that plays a critical role in
postsynaptic anchoring of inhibitory glycine receptors
and major GABAa receptor subtypes.
Length = 394
Score = 29.8 bits (68), Expect = 4.3
Identities = 22/93 (23%), Positives = 38/93 (40%), Gaps = 17/93 (18%)
Query: 144 YLVSRMQATGADIIKLVFSVNDITEIARIF-QLLSHCQVPII--AYSVGERGLVSQLLSP 200
L + ++ GA+++ L +D + + L V I SVG+ V ++L
Sbjct: 199 MLAALLRELGAEVVDLGIVPDDPEALREALEEALEEADVVITSGGVSVGDYDFVKEVLE- 257
Query: 201 KFNGALV-------------YGSLKGTPVLGLP 220
+ G ++ +G L G PV GLP
Sbjct: 258 ELGGEVLFHGVAMKPGKPLAFGRLGGKPVFGLP 290
>gnl|CDD|235486 PRK05472, PRK05472, redox-sensing transcriptional repressor Rex;
Provisional.
Length = 213
Score = 29.3 bits (67), Expect = 4.3
Identities = 15/32 (46%), Positives = 19/32 (59%), Gaps = 3/32 (9%)
Query: 372 VLAGAGGAGRALA--FGAKSRGARVV-IFDID 400
L GAG GRAL G + RG ++V FD+D
Sbjct: 88 ALVGAGNLGRALLNYNGFEKRGFKIVAAFDVD 119
>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 = 29.5 bits (67), Expect = 4.4
Identities = 19/66 (28%), Positives = 30/66 (45%), Gaps = 2/66 (3%)
Query: 333 IGYNTDCEASITAIEDAIKERGYKNGTASFGSPLAGRMFVLAGAGGAGRALAFGAKSRGA 392
IG D +I + A++ G K G G LAG+ + G G G +A K+ G
Sbjct: 111 IGLAIDLLRNIVPCDAAVRAGGTKAGLI--GRELAGKTVGIVGTGAIGLRVARLFKAFGC 168
Query: 393 RVVIFD 398
+V+ +
Sbjct: 169 KVLAYS 174
>gnl|CDD|183787 PRK12844, PRK12844, 3-ketosteroid-delta-1-dehydrogenase; Reviewed.
Length = 557
Score = 29.7 bits (67), Expect = 4.5
Identities = 9/26 (34%), Positives = 12/26 (46%)
Query: 371 FVLAGAGGAGRALAFGAKSRGARVVI 396
V+ G+GG G A A G +I
Sbjct: 9 VVVVGSGGGGMCAALAAADSGLEPLI 34
>gnl|CDD|236229 PRK08303, PRK08303, short chain dehydrogenase; Provisional.
Length = 305
Score = 29.2 bits (66), Expect = 4.6
Identities = 14/32 (43%), Positives = 20/32 (62%), Gaps = 1/32 (3%)
Query: 364 SPLAGRMFVLAGAG-GAGRALAFGAKSRGARV 394
PL G++ ++AGA GAGR +A + GA V
Sbjct: 4 KPLRGKVALVAGATRGAGRGIAVELGAAGATV 35
>gnl|CDD|240392 PTZ00381, PTZ00381, aldehyde dehydrogenase family protein;
Provisional.
Length = 493
Score = 29.6 bits (67), Expect = 4.6
Identities = 11/18 (61%), Positives = 15/18 (83%)
Query: 312 PLAQAIAAVNTIIRRPSD 329
PLA AIAA NT++ +PS+
Sbjct: 129 PLAGAIAAGNTVVLKPSE 146
>gnl|CDD|238994 cd02037, MRP-like, MRP (Multiple Resistance and pH adaptation) is a
homologue of the Fer4_NifH superfamily. Like the other
members of the superfamily, MRP contains a ATP-binding
domain at the N-termini. It is found in bacteria as a
membrane-spanning protein and functions as a Na+/H+
antiporter.
Length = 169
Score = 28.6 bits (65), Expect = 4.7
Identities = 11/36 (30%), Positives = 17/36 (47%), Gaps = 5/36 (13%)
Query: 371 FVLAGAGGAGRA-----LAFGAKSRGARVVIFDIDF 401
V++G GG G++ LA G +V + D D
Sbjct: 3 AVMSGKGGVGKSTVAVNLALALAKLGYKVGLLDADI 38
>gnl|CDD|180458 PRK06194, PRK06194, hypothetical protein; Provisional.
Length = 287
Score = 29.2 bits (66), Expect = 4.7
Identities = 12/36 (33%), Positives = 20/36 (55%), Gaps = 1/36 (2%)
Query: 366 LAGRMFVLAGAG-GAGRALAFGAKSRGARVVIFDID 400
AG++ V+ GA G G A A + G ++V+ D+
Sbjct: 4 FAGKVAVITGAASGFGLAFARIGAALGMKLVLADVQ 39
>gnl|CDD|132368 TIGR03325, BphB_TodD, cis-2,3-dihydrobiphenyl-2,3-diol
dehydrogenase. Members of this family occur as the BphD
protein of biphenyl catabolism and as the TodD protein
of toluene catabolism. Members catalyze the second step
in each pathway and proved interchangeable when tested;
the first and fourth enzymes in each pathway confer
metabolic specificity. In the context of biphenyl
degradation, the enzyme acts as
cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase (EC
1.3.1.56), while in toluene degradation it acts as
cis-toluene dihydrodiol dehydrogenase.
Length = 262
Score = 29.4 bits (66), Expect = 4.9
Identities = 17/57 (29%), Positives = 23/57 (40%), Gaps = 7/57 (12%)
Query: 371 FVLAGAGGAGRALAFGAKSRGARVVIFDIDFERAKSLASD-------VMGAARPFED 420
V GA G GRA+ + GARV + D + L + V G R +D
Sbjct: 9 LVTGGASGLGRAIVDRFVAEGARVAVLDKSAAGLQELEAAHGDAVVGVEGDVRSLDD 65
>gnl|CDD|135637 PRK05876, PRK05876, short chain dehydrogenase; Provisional.
Length = 275
Score = 29.2 bits (65), Expect = 4.9
Identities = 16/36 (44%), Positives = 19/36 (52%), Gaps = 1/36 (2%)
Query: 366 LAGRMFVL-AGAGGAGRALAFGAKSRGARVVIFDID 400
GR V+ GA G G A RGARVV+ D+D
Sbjct: 4 FPGRGAVITGGASGIGLATGTEFARRGARVVLGDVD 39
>gnl|CDD|236372 PRK09072, PRK09072, short chain dehydrogenase; Provisional.
Length = 263
Score = 29.1 bits (66), Expect = 5.0
Identities = 13/32 (40%), Positives = 20/32 (62%), Gaps = 1/32 (3%)
Query: 366 LAGRMFVLAGA-GGAGRALAFGAKSRGARVVI 396
L + +L GA GG G+ALA + GAR+++
Sbjct: 3 LKDKRVLLTGASGGIGQALAEALAAAGARLLL 34
>gnl|CDD|168574 PRK06484, PRK06484, short chain dehydrogenase; Validated.
Length = 520
Score = 29.4 bits (66), Expect = 5.0
Identities = 23/53 (43%), Positives = 29/53 (54%), Gaps = 3/53 (5%)
Query: 359 TASFGSPLA--GRMFVLAGAG-GAGRALAFGAKSRGARVVIFDIDFERAKSLA 408
TA SPLA R+ + G G GRA+A + G R++I D D E AK LA
Sbjct: 258 TAQAPSPLAESPRVVAITGGARGIGRAVADRFAAAGDRLLIIDRDAEGAKKLA 310
>gnl|CDD|223117 COG0039, Mdh, Malate/lactate dehydrogenases [Energy production and
conversion].
Length = 313
Score = 29.1 bits (66), Expect = 5.2
Identities = 17/46 (36%), Positives = 28/46 (60%), Gaps = 2/46 (4%)
Query: 372 VLAGAGGAGRALAFGA--KSRGARVVIFDIDFERAKSLASDVMGAA 415
+ GAG G +LAF + G+ +V+ DI+ E+A+ +A D+ AA
Sbjct: 4 AVIGAGNVGSSLAFLLLLQGLGSELVLIDINEEKAEGVALDLSHAA 49
>gnl|CDD|220560 pfam10090, DUF2328, Uncharacterized protein conserved in bacteria
(DUF2328). Members of this family of hypothetical
bacterial proteins have no known function.
Length = 181
Score = 28.7 bits (65), Expect = 5.3
Identities = 15/53 (28%), Positives = 22/53 (41%), Gaps = 8/53 (15%)
Query: 383 LAFGAKSRGARVVIFDIDFERAKSLASDVMGAARPFEDILNFQPEKGAILANA 435
LAFGA G + ID AKS+ + R L++Q E+ +
Sbjct: 42 LAFGAAGAGQQ-----IDLAEAKSVLEGYLAGGRI---TLDWQLERDLLPKPE 86
>gnl|CDD|180584 PRK06481, PRK06481, fumarate reductase flavoprotein subunit;
Validated.
Length = 506
Score = 29.4 bits (66), Expect = 5.3
Identities = 13/27 (48%), Positives = 16/27 (59%)
Query: 372 VLAGAGGAGRALAFGAKSRGARVVIFD 398
V+ GAGGAG + A AK G VI +
Sbjct: 65 VIVGAGGAGMSAAIEAKDAGMNPVILE 91
>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 = 29.2 bits (66), Expect = 5.9
Identities = 19/58 (32%), Positives = 31/58 (53%), Gaps = 1/58 (1%)
Query: 366 LAGRMFVLAGAGGAGR-ALAFGAKSRGARVVIFDIDFERAKSLASDVMGAARPFEDIL 422
L G+ ++ GAG G A A A + I + +ERA+ LA ++ G A P +++L
Sbjct: 176 LKGKKVLVIGAGEMGELAAKHLAAKGVAEITIANRTYERAEELAKELGGNAVPLDELL 233
>gnl|CDD|215840 pfam00291, PALP, Pyridoxal-phosphate dependent enzyme. Members of
this family are all pyridoxal-phosphate dependent
enzymes. This family includes: serine dehydratase
EC:4.2.1.13 P20132, threonine dehydratase EC:4.2.1.16,
tryptophan synthase beta chain EC:4.2.1.20, threonine
synthase EC:4.2.99.2, cysteine synthase EC:4.2.99.8
P11096, cystathionine beta-synthase EC:4.2.1.22,
1-aminocyclopropane-1-carboxylate deaminase EC:4.1.99.4.
Length = 295
Score = 28.9 bits (65), Expect = 6.0
Identities = 13/30 (43%), Positives = 15/30 (50%)
Query: 368 GRMFVLAGAGGAGRALAFGAKSRGARVVIF 397
G V A +G GRALA A G +V I
Sbjct: 51 GATVVEASSGNTGRALAAAAARLGLKVTIV 80
>gnl|CDD|205178 pfam12988, DUF3872, Domain of unknown function, B. Theta Gene
description (DUF3872). Based on Bacteroides
thetaiotaomicron gene BT_2593, a conserved protein found
in a conjugate transposon. As seen in gene expression
experiments
(http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22
31). It appears to be upregulated in the presence of
host or other bacterial species vs when in culture.
Length = 137
Score = 28.0 bits (63), Expect = 6.0
Identities = 18/49 (36%), Positives = 25/49 (51%), Gaps = 12/49 (24%)
Query: 424 FQPE-KGAI-LANATPLGMHPNTDRVPVSEETLRDYQLVFDAVYTPRKT 470
FQP+ KG + + + T L PN DR P+ +E R Y YT + T
Sbjct: 72 FQPDGKGTLKMDDGTVL--LPN-DRYPLEKEKFRLY-------YTSQST 110
>gnl|CDD|235608 PRK05786, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 238
Score = 29.0 bits (65), Expect = 6.1
Identities = 12/33 (36%), Positives = 17/33 (51%), Gaps = 1/33 (3%)
Query: 366 LAGRMFVLAGAG-GAGRALAFGAKSRGARVVIF 397
L G+ + G G G A+A+ A GA+V I
Sbjct: 3 LKGKKVAIIGVSEGLGYAVAYFALKEGAQVCIN 35
>gnl|CDD|236210 PRK08267, PRK08267, short chain dehydrogenase; Provisional.
Length = 260
Score = 28.8 bits (65), Expect = 6.4
Identities = 16/43 (37%), Positives = 23/43 (53%), Gaps = 4/43 (9%)
Query: 371 FVLAGAGGAGRALA--FGAKSRGARVVIFDIDFERAKSLASDV 411
F+ A G GRA A F A G RV +DI+ +LA+++
Sbjct: 5 FITGAASGIGRATALLFAA--EGWRVGAYDINEAGLAALAAEL 45
>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 = 29.2 bits (66), Expect = 6.4
Identities = 10/27 (37%), Positives = 15/27 (55%)
Query: 372 VLAGAGGAGRALAFGAKSRGARVVIFD 398
V+ G+G AG A A A G +V + +
Sbjct: 3 VVIGSGLAGLAAALEAAEAGLKVAVVE 29
>gnl|CDD|223745 COG0673, MviM, Predicted dehydrogenases and related proteins
[General function prediction only].
Length = 342
Score = 29.1 bits (65), Expect = 6.4
Identities = 21/76 (27%), Positives = 32/76 (42%), Gaps = 6/76 (7%)
Query: 371 FVLAGAGGAGR---ALAFGAKSRGARVV-IFDIDFERAKSLASDVMGAARPFEDILN-FQ 425
+ GAGG A A G +V + D D ERA++ A + G A+ + D+
Sbjct: 6 VGIIGAGGIAGKAHLPALAALGGGLELVAVVDRDPERAEAFAEE-FGIAKAYTDLEELLA 64
Query: 426 PEKGAILANATPLGMH 441
+ ATP +H
Sbjct: 65 DPDIDAVYIATPNALH 80
>gnl|CDD|223954 COG1023, Gnd, Predicted 6-phosphogluconate dehydrogenase
[Carbohydrate transport and metabolism].
Length = 300
Score = 28.9 bits (65), Expect = 6.8
Identities = 13/57 (22%), Positives = 21/57 (36%), Gaps = 1/57 (1%)
Query: 373 LAGAGGAGRALAFGAKSRGARVVIFDIDFERAKSLASD-VMGAARPFEDILNFQPEK 428
+ G G G L G VV +D++ + L + GAA E + +
Sbjct: 5 MIGLGRMGANLVRRLLDGGHDVVGYDVNQTAVEELKDEGATGAASLDELVAKLSAPR 61
>gnl|CDD|235962 PRK07201, PRK07201, short chain dehydrogenase; Provisional.
Length = 657
Score = 29.1 bits (66), Expect = 7.0
Identities = 13/33 (39%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 365 PLAGRMFVLAGA-GGAGRALAFGAKSRGARVVI 396
PL G++ ++ GA G GRA A GA V +
Sbjct: 368 PLVGKVVLITGASSGIGRATAIKVAEAGATVFL 400
>gnl|CDD|163496 TIGR03784, marine_sortase, sortase, marine proteobacterial type.
Members of this protein family are sortase enzymes,
cysteine transpeptidases involved in protein sorting
activities. Members of this family tend to be found in
proteobacteria, rather than in Gram-positive bacteria
where sortases attach proteins to the Gram-positive cell
wall or participate in pilin cross-linking. Many species
with this sortase appear to contain a signal target
sequence, a protein with a Vault protein
inter-alpha-trypsin domain (pfam08487) and a von
Willebrand factor type A domain (pfam00092), encoded by
an adjacent gene. These sortases are designated
subfamily 6 according to Comfort and Clubb (2004).
Length = 174
Score = 28.1 bits (63), Expect = 7.1
Identities = 12/22 (54%), Positives = 15/22 (68%), Gaps = 2/22 (9%)
Query: 366 LAGRMFVLAGAGGAGRALAFGA 387
L ++VLAGA +GR LAFG
Sbjct: 59 LGASLYVLAGA--SGRNLAFGP 78
>gnl|CDD|187623 cd05365, 7_alpha_HSDH_SDR_c, 7 alpha-hydroxysteroid dehydrogenase
(7 alpha-HSDH), classical (c) SDRs. This bacterial
subgroup contains 7 alpha-HSDHs, including Escherichia
coli 7 alpha-HSDH. 7 alpha-HSDH, a member of the SDR
family, catalyzes the NAD+ -dependent dehydrogenation of
a hydroxyl group at position 7 of the steroid skeleton
of bile acids. In humans the two primary bile acids are
cholic and chenodeoxycholic acids, these are formed from
cholesterol in the liver. Escherichia coli 7 alpha-HSDH
dehydroxylates these bile acids in the human intestine.
Mammalian 7 alpha-HSDH activity has been found in
livers. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold (alpha/beta folding
pattern with a central beta-sheet), an NAD(P)(H)-binding
region, and a structurally diverse C-terminal region.
Classical SDRs are typically about 250 residues long,
while extended SDRS are approximately 350 residues.
Sequence identity between different SDR enzymes are
typically in the 15-30% range, but the enzymes share the
Rossmann fold NAD-binding motif and characteristic
NAD-binding and catalytic sequence patterns. These
enzymes have a 3-glycine N-terminal NAD(P)(H)-binding
pattern (typically, TGxxxGxG in classical SDRs and
TGxxGxxG in extended SDRs), while substrate binding is
in the C-terminal region. A critical catalytic Tyr
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) numbering), is often found in a
conserved YXXXK pattern. In addition to the Tyr and Lys,
there is often an upstream Ser (Ser-138, 15-PGDH
numbering) and/or an Asn (Asn-107, 15-PGDH numbering) or
additional Ser, contributing to the active site.
Substrates for these enzymes include sugars, steroids,
alcohols, and aromatic compounds. The standard reaction
mechanism is a proton relay involving the conserved Tyr
and Lys, as well as Asn (or Ser). Some SDR family
members, including 17 beta-hydroxysteroid dehydrogenase
contain an additional helix-turn-helix motif that is not
generally found among SDRs.
Length = 242
Score = 28.7 bits (64), Expect = 7.2
Identities = 16/40 (40%), Positives = 24/40 (60%)
Query: 372 VLAGAGGAGRALAFGAKSRGARVVIFDIDFERAKSLASDV 411
V GA G G+A+A GA VVI D+ E A+++A+ +
Sbjct: 4 VTGGAAGIGKAIAGTLAKAGASVVIADLKSEGAEAVAAAI 43
>gnl|CDD|143452 cd07134, ALDH_AlkH-like, Pseudomonas putida Aldehyde dehydrogenase
AlkH-like. Aldehyde dehydrogenase AlkH (locus name
P12693, EC=1.2.1.3) of the alkBFGHJKL operon that allows
Pseudomonas putida to metabolize alkanes and the
aldehyde dehydrogenase AldX of Bacillus subtilis (locus
P46329, EC=1.2.1.3), and similar sequences, are present
in this CD.
Length = 433
Score = 28.7 bits (65), Expect = 7.2
Identities = 11/18 (61%), Positives = 13/18 (72%)
Query: 312 PLAQAIAAVNTIIRRPSD 329
PL AIAA NT I +PS+
Sbjct: 120 PLVSAIAAGNTAILKPSE 137
>gnl|CDD|202367 pfam02737, 3HCDH_N, 3-hydroxyacyl-CoA dehydrogenase, NAD binding
domain. This family also includes lambda crystallin.
Length = 180
Score = 28.3 bits (64), Expect = 7.2
Identities = 31/119 (26%), Positives = 45/119 (37%), Gaps = 20/119 (16%)
Query: 375 GAGGAGRALAFGAKSRGARVVIFDID---FERAKSLASDVMGAARPFEDILNFQPEKGAI 431
GAG G +A G VV+ DI E+A++ + AR E + + A+
Sbjct: 6 GAGTMGAGIAQVFARAGLEVVLVDISEEALEKARARIEKSL--ARLVEKGRITEEDADAV 63
Query: 432 LANATPLGMHPNTDRVPVSEETLRDYQLVFDAVY--TPRKTRLLKDAEA---AGAIIVS 485
LA + TD D LV +AV K L + +A AI+ S
Sbjct: 64 LARIS-----FTTDL-----ADAVDADLVIEAVPENLDLKRELFAELDAIAPPDAILAS 112
>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 = 28.4 bits (64), Expect = 7.3
Identities = 17/50 (34%), Positives = 29/50 (58%), Gaps = 4/50 (8%)
Query: 366 LAGRMFVLAGAG-GAGRALAFGAKSRGARVVIFDIDFERAKSLASDVMGA 414
LAG++ ++ GA G GRA+A GA VV +++ +K+ A +V+
Sbjct: 1 LAGKVALVTGASRGIGRAIAKRLARDGASVV---VNYASSKAAAEEVVAE 47
>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 = 28.4 bits (64), Expect = 7.3
Identities = 13/37 (35%), Positives = 20/37 (54%)
Query: 372 VLAGAGGAGRALAFGAKSRGARVVIFDIDFERAKSLA 408
V GA G G A ++GA+VVI D+ +++A
Sbjct: 7 VTGGASGLGLATVERLLAQGAKVVILDLPNSPGETVA 43
>gnl|CDD|107202 cd00640, Trp-synth-beta_II, Tryptophan synthase beta superfamily
(fold type II); this family of pyridoxal phosphate
(PLP)-dependent enzymes catalyzes beta-replacement and
beta-elimination reactions. This CD corresponds to
aminocyclopropane-1-carboxylate deaminase (ACCD),
tryptophan synthase beta chain (Trp-synth_B),
cystathionine beta-synthase (CBS), O-acetylserine
sulfhydrylase (CS), serine dehydratase (Ser-dehyd),
threonine dehydratase (Thr-dehyd), diaminopropionate
ammonia lyase (DAL), and threonine synthase (Thr-synth).
ACCD catalyzes the conversion of
1-aminocyclopropane-1-carboxylate to alpha-ketobutyrate
and ammonia. Tryptophan synthase folds into a tetramer,
where the beta chain is the catalytic PLP-binding
subunit and catalyzes the formation of L-tryptophan from
indole and L-serine. CBS is a tetrameric hemeprotein
that catalyzes condensation of serine and homocysteine
to cystathionine. CS is a homodimer that catalyzes the
formation of L-cysteine from O-acetyl-L-serine.
Ser-dehyd catalyzes the conversion of L- or D-serine to
pyruvate and ammonia. Thr-dehyd is active as a homodimer
and catalyzes the conversion of L-threonine to
2-oxobutanoate and ammonia. DAL is also a homodimer and
catalyzes the alpha, beta-elimination reaction of both
L- and D-alpha, beta-diaminopropionate to form pyruvate
and ammonia. Thr-synth catalyzes the formation of
threonine and inorganic phosphate from
O-phosphohomoserine.
Length = 244
Score = 28.6 bits (65), Expect = 7.3
Identities = 13/54 (24%), Positives = 17/54 (31%), Gaps = 13/54 (24%)
Query: 345 AIEDAIKERGYKNGTASFGSPLAGRMFVLAGAGG-AGRALAFGAKSRGARVVIF 397
I A +E G ++ GG G ALA A G + I
Sbjct: 38 LILLAEEEGKLPKGV------------IIESTGGNTGIALAAAAARLGLKCTIV 79
>gnl|CDD|99992 cd03822, GT1_ecORF704_like, This family is most closely related to
the GT1 family of glycosyltransferases. ORF704 in E.
coli has been shown to be involved in the biosynthesis
of O-specific mannose homopolysaccharides.
Length = 366
Score = 28.8 bits (65), Expect = 7.7
Identities = 23/61 (37%), Positives = 28/61 (45%), Gaps = 13/61 (21%)
Query: 52 PGKDLEI-------ILTKKPLPVLIVYRPKWAGGLYEGDEHKRLEALHLAEDLG-ADYVD 103
P K LE+ ++ K P L+V AG + E R EA LAE LG AD V
Sbjct: 196 PYKGLELLLEALPLLVAKHPDVRLLV-----AGETHPDLERYRGEAYALAERLGLADRVI 250
Query: 104 F 104
F
Sbjct: 251 F 251
>gnl|CDD|181159 PRK07890, PRK07890, short chain dehydrogenase; Provisional.
Length = 258
Score = 28.4 bits (64), Expect = 7.7
Identities = 15/32 (46%), Positives = 20/32 (62%), Gaps = 1/32 (3%)
Query: 366 LAGRMFVLAGAG-GAGRALAFGAKSRGARVVI 396
L G++ V++G G G GR LA A GA VV+
Sbjct: 3 LKGKVVVVSGVGPGLGRTLAVRAARAGADVVL 34
>gnl|CDD|236040 PRK07523, PRK07523, gluconate 5-dehydrogenase; Provisional.
Length = 255
Score = 28.6 bits (64), Expect = 7.8
Identities = 24/81 (29%), Positives = 32/81 (39%), Gaps = 15/81 (18%)
Query: 366 LAGRMFVLAGAG-GAGRALAFGAKSRGARVVIFDIDFER--------------AKSLASD 410
L GR ++ G+ G G ALA G GA V++ D + A +LA D
Sbjct: 8 LTGRRALVTGSSQGIGYALAEGLAQAGAEVILNGRDPAKLAAAAESLKGQGLSAHALAFD 67
Query: 411 VMGAARPFEDILNFQPEKGAI 431
V I F+ E G I
Sbjct: 68 VTDHDAVRAAIDAFEAEIGPI 88
>gnl|CDD|187594 cd05333, BKR_SDR_c, beta-Keto acyl carrier protein reductase (BKR),
involved in Type II FAS, classical (c) SDRs. This
subgroup includes the Escherichai coli K12 BKR, FabG.
BKR catalyzes the NADPH-dependent reduction of ACP in
the first reductive step of de novo fatty acid synthesis
(FAS). FAS consists of four elongation steps, which are
repeated to extend the fatty acid chain through the
addition of two-carbo units from malonyl acyl-carrier
protein (ACP): condensation, reduction, dehydration, and
a final reduction. Type II FAS, typical of plants and
many bacteria, maintains these activities on discrete
polypeptides, while type I FAS utilizes one or two
multifunctional polypeptides. BKR resembles enoyl
reductase, which catalyzes the second reduction step in
FAS. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with
structurally conserved Rossmann fold (alpha/beta folding
pattern with a central beta-sheet) NAD(P)(H) binding
region and a structurally diverse C-terminal region.
Classical SDRs are typically about 250 residues long,
while extended SDRS are approximately 350 residues.
Sequence identity between different SDR enzymes are
typically in the 15-30% range, but the enzymes share the
Rossmann fold NAD binding motif and characteristic
NAD-binding and catalytic sequence patterns. These
enzymes have a 3-glycine N-terminal NAD(P)(H) binding
pattern: TGxxxGxG in classical SDRs. Extended SDRs have
additional elements in the C-terminal region, and
typically have a TGXXGXXG cofactor binding motif.
Complex (multidomain) SDRs such as ketoreductase domains
of fatty acid synthase have a GGXGXXG NAD(P) binding
motif and an altered active site motif (YXXXN). Fungal
type type ketoacyl reductases have a TGXXXGX(1-2)G
NAD(P)-binding motif. Some atypical SDRs have lost
catalytic activity and/or have an unusual NAD(P) binding
motif and missing or unusual active site residues.
Reactions catalyzed within the SDR family include
isomerization, decarboxylation, epimerization, C=N bond
reduction, dehydratase activity, dehalogenation,
Enoyl-CoA reduction, and carbonyl-alcohol
oxidoreduction. A critical catalytic Tyr residue
(Tyr-151, human 15-hydroxyprostaglandin dehydrogenase
(15-PGDH) numbering), is often found in a conserved
YXXXK pattern. In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) or additional
Ser, contributing to the active site. Substrates for
these enzymes include sugars, steroids, alcohols, and
aromatic compounds. The standard reaction mechanism is a
proton relay involving the conserved Tyr-151 and
Lys-155, and well as Asn-111 (or Ser). Some SDR family
members, including 17 beta-hydroxysteroid dehydrogenase
contain an additional helix-turn-helix motif that is not
generally found among SDRs.
Length = 240
Score = 28.3 bits (64), Expect = 7.8
Identities = 12/39 (30%), Positives = 18/39 (46%)
Query: 372 VLAGAGGAGRALAFGAKSRGARVVIFDIDFERAKSLASD 410
V + G GRA+A + GA+V + D E A +
Sbjct: 5 VTGASRGIGRAIALRLAAEGAKVAVTDRSEEAAAETVEE 43
>gnl|CDD|223643 COG0569, TrkA, K+ transport systems, NAD-binding component
[Inorganic ion transport and metabolism].
Length = 225
Score = 28.4 bits (64), Expect = 8.3
Identities = 14/40 (35%), Positives = 21/40 (52%)
Query: 371 FVLAGAGGAGRALAFGAKSRGARVVIFDIDFERAKSLASD 410
++ GAG GR++A G VV+ D D ER + +D
Sbjct: 3 IIIIGAGRVGRSVARELSEEGHNVVLIDRDEERVEEFLAD 42
>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 = 28.4 bits (64), Expect = 8.6
Identities = 19/57 (33%), Positives = 27/57 (47%), Gaps = 5/57 (8%)
Query: 367 AGRMFVLAGAGGAGRALAFGAKSRGAR-VVIFD-IDFERAKSLASDVMGAARPFEDI 421
G V+ G GG G GA GAR V+ D ++F+R ++L GA F +
Sbjct: 185 PGDTVVVMGIGGVGINAVQGAAVAGARKVIAVDPVEFKREQALK---FGATHAFASM 238
>gnl|CDD|133424 cd01339, LDH-like_MDH, L-lactate dehydrogenase-like malate
dehydrogenase proteins. Members of this subfamily have
an LDH-like structure and an MDH enzymatic activity.
Some members, like MJ0490 from Methanococcus jannaschii,
exhibit both MDH and LDH activities. Tetrameric MDHs,
including those from phototrophic bacteria, are more
similar to LDHs than to other MDHs. LDH catalyzes the
last step of glycolysis in which pyruvate is converted
to L-lactate. MDH is one of the key enzymes in the
citric acid cycle, facilitating both the conversion of
malate to oxaloacetate and replenishing levels of
oxalacetate by reductive carboxylation of pyruvate. The
LDH-like MDHs are part of the NAD(P)-binding Rossmann
fold superfamily, which includes a wide variety of
protein families including the NAD(P)-binding domains of
alcohol dehydrogenases, tyrosine-dependent
oxidoreductases, glyceraldehyde-3-phosphate
dehydrogenases, formate/glycerate dehydrogenases,
siroheme synthases, 6-phosphogluconate dehydrogenases,
aminoacid dehydrogenases, repressor rex, and NAD-binding
potassium channel domains, among others.
Length = 300
Score = 28.6 bits (65), Expect = 8.6
Identities = 14/42 (33%), Positives = 18/42 (42%), Gaps = 1/42 (2%)
Query: 375 GAGGAGRALAFGAKSRG-ARVVIFDIDFERAKSLASDVMGAA 415
GAG G LA + VV+ DI + A D+ AA
Sbjct: 5 GAGNVGATLAQLLALKELGDVVLLDIVEGLPQGKALDISQAA 46
>gnl|CDD|238528 cd01095, Nitrilotriacetate_monoxgenase, nitrilotriacetate
monoxygenase oxidizes nitrilotriacetate utilizing
reduced flavin mononucleotide (FMNH2) and oxygen. The
FMNH2 is provided by an NADH:flavin mononucleotide (FMN)
oxidorductase that uses NADH to reduce FMN to FMNH2.
Length = 358
Score = 28.4 bits (64), Expect = 8.8
Identities = 14/47 (29%), Positives = 19/47 (40%), Gaps = 5/47 (10%)
Query: 374 AGAGGAGRALAFGAKSRGARVVIFDI-DFERAKSLASDVMGAARPFE 419
AG+ AGR A +R A V E A++ +DV A
Sbjct: 210 AGSSEAGREFA----ARHAEAVFTAQQTLEEAQAFYADVKARAAAAG 252
>gnl|CDD|170080 PRK09754, PRK09754, phenylpropionate dioxygenase ferredoxin
reductase subunit; Provisional.
Length = 396
Score = 28.7 bits (64), Expect = 8.9
Identities = 20/65 (30%), Positives = 28/65 (43%), Gaps = 11/65 (16%)
Query: 368 GRMFVLAGAGGAGRALAFGAKSRGARVVIFDIDFERAKSLASDVMG--AARPFED-ILNF 424
R V+ GAG G LA A R +V + + LA+ VMG A P + +L
Sbjct: 144 ERSVVIVGAGTIGLELAASATQRRCKVTVIE--------LAATVMGRNAPPPVQRYLLQR 195
Query: 425 QPEKG 429
+ G
Sbjct: 196 HQQAG 200
>gnl|CDD|235706 PRK06129, PRK06129, 3-hydroxyacyl-CoA dehydrogenase; Validated.
Length = 308
Score = 28.5 bits (64), Expect = 9.0
Identities = 18/62 (29%), Positives = 27/62 (43%), Gaps = 5/62 (8%)
Query: 375 GAGGAGRALAFGAKSRGARVVIFDID---FERAKSLASDVMGAARPFEDILNFQPEKGAI 431
GAG GRA A G V ++D D A + + + F D+L+ + A+
Sbjct: 9 GAGLIGRAWAIVFARAGHEVRLWDADPAAAAAAPAYIAGRLEDLAAF-DLLDGEA-PDAV 66
Query: 432 LA 433
LA
Sbjct: 67 LA 68
>gnl|CDD|187595 cd05334, DHPR_SDR_c_like, dihydropteridine reductase (DHPR),
classical (c) SDRs. Dihydropteridine reductase is an
NAD-binding protein related to the SDRs. It converts
dihydrobiopterin into tetrahydrobiopterin, a cofactor
necessary in catecholamines synthesis. Dihydropteridine
reductase has the YXXXK of these tyrosine-dependent
oxidoreductases, but lacks the typical upstream Asn and
Ser catalytic residues. 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 = 221
Score = 28.1 bits (63), Expect = 9.1
Identities = 17/54 (31%), Positives = 24/54 (44%), Gaps = 3/54 (5%)
Query: 367 AGRMFVLAGAGGAGRALAFGAKSRGARVVIFDIDF-ERAKSLASDVMGAARPFE 419
A + V G G G A+ KSRG V ID E ++ AS ++ + F
Sbjct: 1 ARVVLVYGGRGALGSAVVQAFKSRGWWVA--SIDLAENEEADASIIVLDSDSFT 52
>gnl|CDD|235774 PRK06292, PRK06292, dihydrolipoamide dehydrogenase; Validated.
Length = 460
Score = 28.6 bits (65), Expect = 9.4
Identities = 9/24 (37%), Positives = 12/24 (50%)
Query: 375 GAGGAGRALAFGAKSRGARVVIFD 398
GAG AG A A G +V + +
Sbjct: 10 GAGPAGYVAARRAAKLGKKVALIE 33
>gnl|CDD|176206 cd08244, MDR_enoyl_red, Possible enoyl reductase. Member
identified as possible enoyl reductase of the MDR
family. 2-enoyl thioester reductase (ETR) catalyzes the
NADPH-dependent dependent conversion of trans-2-enoyl
acyl carrier protein/coenzyme A (ACP/CoA) to
acyl-(ACP/CoA) in fatty acid synthesis. 2-enoyl
thioester reductase activity has been linked in Candida
tropicalis as essential in maintaining mitiochondrial
respiratory function. This ETR family is a part of the
medium chain dehydrogenase/reductase family, but lack
the zinc coordination sites characteristic of the
alcohol dehydrogenases in this family.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which has a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. The N-terminal catalytic domain has a
distant homology to GroES. These proteins typically
form dimers (typically higher plants, mammals) or
tetramers (yeast, bacteria), and have 2 tightly bound
zinc atoms per subunit, a catalytic zinc at the active
site, and a structural zinc in a lobe of the catalytic
domain. NAD(H) binding occurs in the cleft between the
catalytic and coenzyme-binding domains at the active
site, and coenzyme binding induces a conformational
closing of this cleft. Coenzyme binding typically
precedes and contributes to substrate binding. Candida
tropicalis enoyl thioester reductase (Etr1p) catalyzes
the NADPH-dependent reduction of trans-2-enoyl
thioesters in mitochondrial fatty acid synthesis. Etr1p
forms homodimers, with each subunit containing a
nucleotide-binding Rossmann fold domain and a catalytic
domain.
Length = 324
Score = 28.5 bits (64), Expect = 9.5
Identities = 13/27 (48%), Positives = 15/27 (55%)
Query: 369 RMFVLAGAGGAGRALAFGAKSRGARVV 395
+ V A AGG G L AK+ GA VV
Sbjct: 145 VVLVTAAAGGLGSLLVQLAKAAGATVV 171
>gnl|CDD|223717 COG0644, FixC, Dehydrogenases (flavoproteins) [Energy production
and conversion].
Length = 396
Score = 28.6 bits (64), Expect = 9.6
Identities = 25/114 (21%), Positives = 40/114 (35%), Gaps = 14/114 (12%)
Query: 372 VLAGAGGAGRALAFGAKSRGARVVIFDI-DFERAKSLASDVMGAARPFEDILNFQPEKGA 430
V+ GAG AG + A G V++ + AK + R E++
Sbjct: 7 VIVGAGPAGSSAARRLAKAGLDVLVLEKGSEPGAKPCCGGGLS-PRALEEL--IPDFDEE 63
Query: 431 ILANATPLGMHPNTDRVPVSEETLRDYQL---VFDAVYTPRKTRLLKDAEAAGA 481
I T ++ ++V + Y + FD L + AE AGA
Sbjct: 64 IERKVTGARIYFPGEKVAIEVPVGEGYIVDRAKFDK-------WLAERAEEAGA 110
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
0.320 0.138 0.399
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: 27,250,021
Number of extensions: 2772841
Number of successful extensions: 3722
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3636
Number of HSP's successfully gapped: 260
Length of query: 519
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 418
Effective length of database: 6,457,848
Effective search space: 2699380464
Effective search space used: 2699380464
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 61 (27.1 bits)