RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 010101
(518 letters)
>gnl|CDD|178135 PLN02520, PLN02520, bifunctional 3-dehydroquinate
dehydratase/shikimate dehydrogenase.
Length = 529
Score = 603 bits (1556), Expect = 0.0
Identities = 264/516 (51%), Positives = 355/516 (68%), Gaps = 14/516 (2%)
Query: 4 AAKNSLLVCTQLECETTEEMQASIEQAKVEGADLVELCIDSME-FSHISEVDKLIQHPTL 62
+N L+C + ++ ++M + +AK GADLVE+ +D ++ F+ ++ LI+ L
Sbjct: 18 VRRNPTLICVPIMADSVDKMLIEMAKAKELGADLVEIRLDFLKNFNPREDLKTLIKQSPL 77
Query: 63 PAIVSYRLK--SSRKSSDEACKNTCLQVLRRALDLDVEFVEMDYEVASDPLMSEIIYSRS 120
P +V+YR K + DE N LR A++L ++V+++ +VA ++ I +
Sbjct: 78 PTLVTYRPKWEGGQYEGDE---NKRQDALRLAMELGADYVDVELKVA-HEFINSISGKKP 133
Query: 121 -NTKIIVSSYLNGGGKPTTEKLGDVIACMQATGADVMKLEIAVDSITDLAPVFEMLTHCQ 179
K+IVSS+ N P+ E+LG+++A +QATGAD++K+ ITD+A +F++ H Q
Sbjct: 134 EKCKVIVSSH-NYENTPSVEELGNLVARIQATGADIVKIATTALDITDVARMFQITVHSQ 192
Query: 180 VPLIALAVGSRGLISQLLGPKFGGFLVYGSL--GGKSVPGLPTLVSLKQVYQLEHINPDT 237
VP I L +G RGLIS++L PKFGG+L +G+L G S PG PT+ L +Y I PDT
Sbjct: 193 VPTIGLVMGERGLISRILCPKFGGYLTFGTLEAGKVSAPGQPTIKDLLDLYNFRQIGPDT 252
Query: 238 KIFGLVSNPVGHSKGPILHNPAFRHTRFNGIYVPMLVDDVKEFFRTYSGTDFAGFSVGIP 297
K++G++ PVGHSK PILHN AF+ FNG+YV +LVDD+ +F +TYS DFAGFS IP
Sbjct: 253 KVYGIIGKPVGHSKSPILHNEAFKSVGFNGVYVHLLVDDLAKFLQTYSSPDFAGFSCTIP 312
Query: 298 HKEPAVACCDEVHPLAKSIGAVNTIIRRPIDGKLVGYNTDCESAISAIEDALRERQGING 357
HKE A+ CCDEV P+AKSIGA+NTIIRRP DGKLVGYNTD AISAIED LR
Sbjct: 313 HKEDALKCCDEVDPIAKSIGAINTIIRRPSDGKLVGYNTDYIGAISAIEDGLR---ASGS 369
Query: 358 VASHTSPIAGKIFVLVGAGGAGRALAFGAKSRGARVIIFNRNYERAKALADAVSGEALHF 417
+ SP+AGK+FV++GAGGAG+ALA+GAK +GARV+I NR YERAK LADAV G+AL
Sbjct: 370 SPASGSPLAGKLFVVIGAGGAGKALAYGAKEKGARVVIANRTYERAKELADAVGGQALTL 429
Query: 418 EYLHEFFPEKGMILANASAIGMEPNSDQSPVPKEALKAYELVFDAVYTPRNTRLLREAAE 477
L F PE+GMILAN +++GM+PN D++P+ K ALK Y LVFDAVYTP+ TRLLREA E
Sbjct: 430 ADLENFHPEEGMILANTTSVGMQPNVDETPISKHALKHYSLVFDAVYTPKITRLLREAEE 489
Query: 478 VGATVVSGVEMFIRQALGQFRLFTGGLAPEDFMRKL 513
GA +VSG EMFIRQA QF FTG AP++ R++
Sbjct: 490 SGAIIVSGTEMFIRQAYEQFERFTGLPAPKELFREI 525
>gnl|CDD|223247 COG0169, AroE, Shikimate 5-dehydrogenase [Amino acid transport and
metabolism].
Length = 283
Score = 257 bits (660), Expect = 1e-82
Identities = 110/294 (37%), Positives = 154/294 (52%), Gaps = 22/294 (7%)
Query: 233 INPDTKIFGLVSNPVGHSKGPILHNPAFRHTRFNGIYVPMLV--DDVKEFFRTYSGTDFA 290
+N TK+FG++ NP+ HS P +HN AFR + +Y+ V +D+ E F
Sbjct: 2 MNGKTKLFGVIGNPISHSLSPRMHNAAFRALGLDYVYLAFEVPPEDLPEAVSGIRALGFR 61
Query: 291 GFSVGIPHKEPAVACCDEVHPLAKSIGAVNTIIRRPIDGKLVGYNTDCESAISAIEDALR 350
G +V IP KE A+ DE+ P A+ IGAVNT++R DGKL GYNTD + A+++
Sbjct: 62 GLNVTIPFKEAALPLLDELSPRARLIGAVNTLVRED-DGKLRGYNTDGIGFLRALKEFGL 120
Query: 351 ERQGINGVASHTSPIAGKIFVLVGAGGAGRALAFGAKSRGA-RVIIFNRNYERAKALAD- 408
+ GK +++GAGGA RA+AF GA R+ + NR ERA+ LAD
Sbjct: 121 PV-----------DVTGKRVLILGAGGAARAVAFALAEAGAKRITVVNRTRERAEELADL 169
Query: 409 ----AVSGEALHFEYLHEFFPEKGMILANASAIGMEPNSDQSPVPKEALKAYELVFDAVY 464
+ EA L E+ +L NA+ +GM SPVP E L +V+D VY
Sbjct: 170 FGELGAAVEAAALADLEGL--EEADLLINATPVGMAGPEGDSPVPAELLPKGAIVYDVVY 227
Query: 465 TPRNTRLLREAAEVGATVVSGVEMFIRQALGQFRLFTGGLAPEDFMRKLVLEQF 518
P T LLREA GA + G+ M + QA F L+TG P D M++ ++E
Sbjct: 228 NPLETPLLREARAQGAKTIDGLGMLVHQAAEAFELWTGVEPPVDVMKEALIEAL 281
>gnl|CDD|234703 PRK00258, aroE, shikimate 5-dehydrogenase; Reviewed.
Length = 278
Score = 242 bits (620), Expect = 1e-76
Identities = 91/290 (31%), Positives = 142/290 (48%), Gaps = 18/290 (6%)
Query: 233 INPDTKIFGLVSNPVGHSKGPILHNPAFRHTRFNGIYVPMLV--DDVKEFFRTYSGTDFA 290
I T+++ ++ NP+ HSK P++HN AF+ +G+Y+ +LV +D+++ + +
Sbjct: 1 ITGKTRLYAVIGNPIAHSKSPLIHNAAFKQLGLDGVYLAILVPPEDLEDAVKGFFALGGR 60
Query: 291 GFSVGIPHKEPAVACCDEVHPLAKSIGAVNTIIRRPIDGKLVGYNTDCESAISAIEDALR 350
G +V +P KE A A DE+ A+ IGAVNT++ DG+L+G NTD + A L
Sbjct: 61 GANVTVPFKEAAFALADELSERARLIGAVNTLVLE--DGRLIGDNTDGIGFVRA----LE 114
Query: 351 ERQGINGVASHTSPIAGKIFVLVGAGGAGRALAFGAKSRG-ARVIIFNRNYERAKALADA 409
ER G+ + GK +++GAGGA RA+ G A + I NR ERA+ LA
Sbjct: 115 ERLGV--------DLKGKRILILGAGGAARAVILPLLDLGVAEITIVNRTVERAEELAKL 166
Query: 410 VSGEALHFEYLHEFFPEKGM-ILANASAIGMEPNSDQSPVPKEALKAYELVFDAVYTPRN 468
L ++ NA++ GM P+P L+ +V+D +Y P
Sbjct: 167 FGALGKAELDLELQEELADFDLIINATSAGMSGELPLPPLPLSLLRPGTIVYDMIYGPLP 226
Query: 469 TRLLREAAEVGATVVSGVEMFIRQALGQFRLFTGGLAPEDFMRKLVLEQF 518
T L A GA + G+ M + QA F L+TG P + M +
Sbjct: 227 TPFLAWAKAQGARTIDGLGMLVHQAAEAFELWTGVRPPVEPMLAALRAAL 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 = 210 bits (536), Expect = 2e-64
Identities = 96/285 (33%), Positives = 143/285 (50%), Gaps = 20/285 (7%)
Query: 238 KIFGLVSNPVGHSKGPILHNPAFRHTRFNGIYVPMLV--DDVKEFFRTYSGTDFAGFSVG 295
K++G++ NP+ HSK P++HN F+ G Y+ LV DD+++ + F G +V
Sbjct: 1 KLYGVIGNPIAHSKSPLIHNAFFKQLGLEGPYIAFLVPPDDLEDALSGFFALGFKGANVT 60
Query: 296 IPHKEPAVACCDEVHPLAKSIGAVNTIIRRPIDGKLVGYNTDCESAISAIEDALRERQGI 355
P KE A DE+ AK GAVNT++ DGKLVGYNTD +S +E +
Sbjct: 61 SPFKERAFQFLDEIDGRAKLAGAVNTLVLE--DGKLVGYNTDGIGLVSDLEQLIP----- 113
Query: 356 NGVASHTSPIAGKIFVLVGAGGAGRALAFGAKSRGARVIIFNRNYERAKALADAVS--GE 413
+ +++GAGGA +A+A VII NR +A+ LA+ GE
Sbjct: 114 --------LRPNQNVLIIGAGGAAKAVALELLKADCNVIIANRTVSKAEELAERFQRYGE 165
Query: 414 ALHFEYLHEFFPEKGMILANASAIGMEPNSDQSPVPKEALKAYELVFDAVYTPRNTRLLR 473
F + E + ++ NA++ GM N D+ PVP E LK +LV+D VY P T L
Sbjct: 166 IQAFS-MDELPLHRVDLIINATSAGMSGNIDEPPVPAEYLKEGKLVYDLVYNPLETPFLA 224
Query: 474 EAAEVGATVVSGVEMFIRQALGQFRLFTGGLAPEDFMRKLVLEQF 518
EA +G + G+ M + QA F L+TG + M + ++
Sbjct: 225 EAKSLGTKTIDGLGMLVYQAALSFELWTGVEPDIEKMFEQLISVL 269
>gnl|CDD|183585 PRK12548, PRK12548, shikimate 5-dehydrogenase; Provisional.
Length = 289
Score = 151 bits (382), Expect = 7e-42
Identities = 90/298 (30%), Positives = 144/298 (48%), Gaps = 33/298 (11%)
Query: 233 INPDTKIFGLVSNPVGHSKGPILHNPAFRHTRFNGIYVP--MLVDDVKEFFRTYSGTDFA 290
I+ T + GL+ +PVGHS P ++N +F+ + Y+ + VD V + + +
Sbjct: 5 ISGTTGLLGLIGSPVGHSGSPAMYNYSFQKAGLDYAYLAFDIPVDKVPDAIKAIKTFNMR 64
Query: 291 GFSVGIPHKEPAVACCDEVHPLAKSIGAVNTIIRRPIDGKLVGYNTDCESAISAIEDALR 350
G +V +P K A DE+ P A+ IGAVNTI+ DGKL G+ TD + + +
Sbjct: 65 GANVTMPCKSEAAKYMDELSPAARIIGAVNTIVND--DGKLTGHITDGLGFVRNLRE--- 119
Query: 351 ERQGINGVASHTSPIAGKIFVLVGAGGAGRALAFGAKSRGARVI-IFNRN---YERAK-- 404
+GV + GK ++GAGGA A+ GA+ I IFN YERA+
Sbjct: 120 -----HGVD-----VKGKKLTVIGAGGAATAIQVQCALDGAKEITIFNIKDDFYERAEQT 169
Query: 405 --ALADAVSGEALHF------EYLHEFFPEKGMILANASAIGMEPNSDQSPVPKEALKAY 456
+ V ++ E L IL NA+ +GM+PN ++ + ++
Sbjct: 170 AEKIKQEVPECIVNVYDLNDTEKLKAEI-ASSDILVNATLVGMKPNDGETNIKDTSVFRK 228
Query: 457 ELVF-DAVYTPRNTRLLREAAEVGATVVSGVEMFIRQALGQFRLFTGGLAPEDFMRKL 513
+LV D VY P+ T+LL +A G V G+ M + Q ++L+TG P + +++L
Sbjct: 229 DLVVADTVYNPKKTKLLEDAEAAGCKTVGGLGMLLWQGAEAYKLYTGKDMPVEEVKEL 286
>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 = 133 bits (338), Expect = 4e-37
Identities = 59/169 (34%), Positives = 90/169 (53%), Gaps = 16/169 (9%)
Query: 336 TDCESAISAIEDALRERQGINGVASHTSPIAGKIFVLVGAGGAGRALAFGAKSRGA-RVI 394
TD + A+E+A E + GK +++GAGGA RA+A+ GA +++
Sbjct: 1 TDGLGFVRALEEAGIE-------------LKGKKVLILGAGGAARAVAYALAELGAAKIV 47
Query: 395 IFNRNYERAKALADAVSGEALHFEYLHEF-FPEKGMILANASAIGMEPNSDQSPVPKEAL 453
I NR E+AKALA+ + YL + ++ N + +GM+P D+ P+P L
Sbjct: 48 IVNRTLEKAKALAERFGELGIAIAYLDLEELLAEADLIINTTPVGMKP-GDELPLPPSLL 106
Query: 454 KAYELVFDAVYTPRNTRLLREAAEVGATVVSGVEMFIRQALGQFRLFTG 502
K +V+D VY P T LL+EA +GA + G+EM + QA F L+TG
Sbjct: 107 KPGGVVYDVVYNPLETPLLKEARALGAKTIDGLEMLVYQAAEAFELWTG 155
>gnl|CDD|137204 PRK09310, aroDE, bifunctional 3-dehydroquinate
dehydratase/shikimate dehydrogenase protein; Reviewed.
Length = 477
Score = 142 bits (359), Expect = 6e-37
Identities = 115/421 (27%), Positives = 181/421 (42%), Gaps = 46/421 (10%)
Query: 93 LDLDVEFVEMDYEVASDPLMSEIIYSRSNTKIIVSSYLNGGGKPTTEKLGDVIACMQATG 152
LD+D +F + + I KII+S + + E + + M A+
Sbjct: 83 LDIDKDFPKEA--------LIRIRKLHPKIKIILSYHTS-----EHEDIIQLYNEMLASA 129
Query: 153 ADVMKLEIAVDSITDLAPVFEMLTHCQVPLIALAVGSRGLISQLLGPKFGGFLVYGSLGG 212
AD K+ ++ S TDL + L +G G S++L P Y + G
Sbjct: 130 ADYYKIAVSSSSSTDLLNIIHQKRSLPENTTVLCMGGMGRPSRILSPLLQNAFNYAAGIG 189
Query: 213 --KSVPGLPTLVSLKQVYQLEHINPDTKIFGLVSNPVGHSKGPILHNPAFRHTRFNGIYV 270
PG +L L Y +++ + I+GL+ +PV S + HNP F N Y+
Sbjct: 190 APPVAPGQLSLEHL-LFYNYANLSAQSPIYGLIGDPVDRSISHLSHNPLFSQLSLNCPYI 248
Query: 271 PMLVD--DVKEFFRTYSGTDFAGFSVGIPHKEPAVACCDEVHPLAKSIGAVNTIIRRPID 328
+ + ++ +FF T F G SV +P K + D++ P K G+ NT++ R +
Sbjct: 249 KLPLTPQELPKFFSTIRDLPFLGLSVTMPLKTAVLDFLDKLDPSVKLCGSCNTLVFR--N 306
Query: 329 GKLVGYNTDCESAISAIEDALRERQGINGVASHTSPIAGKIFVLVGAGGAGRALAFGAKS 388
GK+ GYNTD E S ++ P+ + +VGAGGA +A+A
Sbjct: 307 GKIEGYNTDGEGLFSLLK-------------QKNIPLNNQHVAIVGAGGAAKAIATTLAR 353
Query: 389 RGARVIIFNRNYERAKALADAVSGEALHFEYLHEFFPEKGMILANASAIGMEPNSDQSPV 448
GA ++IFNR A+ALA G+A E L E +I + P+ +
Sbjct: 354 AGAELLIFNRTKAHAEALASRCQGKAFPLESLPELHRIDIIINC------LPPSVT---I 404
Query: 449 PKEALKAYELVFDAVYTPRNTRLLREAAEVGATVVSGVEMFIRQALGQFRL-FTGGLAPE 507
P +A V D P+++ + A G++++ G EMF QAL QFRL F L
Sbjct: 405 P-KAFPP--CVVDINTLPKHSPYTQYARSQGSSIIYGYEMFAEQALLQFRLWFPTLLFKH 461
Query: 508 D 508
Sbjct: 462 L 462
>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 = 128 bits (324), Expect = 3e-34
Identities = 80/231 (34%), Positives = 122/231 (52%), Gaps = 22/231 (9%)
Query: 12 CTQLECETTEEMQASIEQAKVEGADLVELCIDSMEFSHISEVD----KLIQHPTLPAIVS 67
C + + EE A +E+ + EGAD VEL +D +E +V L + LP I +
Sbjct: 1 CVPVTGPSLEEALAELEELE-EGADAVELRLDLLEDVDAEDVSEQLSALREKTGLPIIFT 59
Query: 68 YRLKSS----RKSSDEACKNTCLQVLRRALDLDVEFVEMDYEVASDPLMSEIIYSRSNTK 123
R KS S +E L++L+ AL L ++++++ A D L++ II + TK
Sbjct: 60 VRTKSEGGRFDGSEEEY-----LELLKEALRLGPDYIDIELSSAPDELLAVIIAKKGGTK 114
Query: 124 IIVSSYLNGGGKPTTEKLGDVIACMQATGADVMKLEIAV--DSITDLAPVFEMLTHCQ-- 179
II+S Y + G P+ E L + MQ GAD++K IAV +SI D+ + + +
Sbjct: 115 IILS-YHDFEGTPSWEDLLSLYEEMQKLGADIVK--IAVMANSIEDVLRLLRFTSEAKEL 171
Query: 180 -VPLIALAVGSRGLISQLLGPKFGGFLVYGSLGGKSVPGLPTLVSLKQVYQ 229
PLIA+++G G IS++LGP FG L Y SLG S PG TL L++ +
Sbjct: 172 DKPLIAISMGELGRISRILGPVFGSVLTYASLGKASAPGQITLEELREALE 222
>gnl|CDD|183587 PRK12550, PRK12550, shikimate 5-dehydrogenase; Reviewed.
Length = 272
Score = 126 bits (320), Expect = 4e-33
Identities = 71/215 (33%), Positives = 101/215 (46%), Gaps = 24/215 (11%)
Query: 291 GFSVGIPHKEPAVACCDEVHPLAKSIGAVNTIIRRPIDGKLVGYNTDCESAISAIEDALR 350
G +V +P KE + DE+ P A++I +VNTI+ DG L YNTD AI L
Sbjct: 62 GCAVSMPFKEAVIPLVDELDPSAQAIESVNTIVNT--DGHLKAYNTDYI----AIAKLLA 115
Query: 351 ERQGINGVASHTSPIAGKIFVLVGAGGAGRALAFGAKSRG-ARVIIFNRNYERAKALADA 409
V L G+GG +A+A + G I RN + KALA+
Sbjct: 116 S----YQVPPDLV------VALRGSGGMAKAVAAALRDAGFTDGTIVARNEKTGKALAEL 165
Query: 410 VSGEALHFEYLHEFFPEKGMILANASAIGME--PNSDQSPVPKEALKAYELVFDAVYTPR 467
+E+ + + IL N + IGM P +D+ P+ + A +VFD V P
Sbjct: 166 -----YGYEWRPDLGGIEADILVNVTPIGMAGGPEADKLAFPEAEIDAASVVFDVVALPA 220
Query: 468 NTRLLREAAEVGATVVSGVEMFIRQALGQFRLFTG 502
T L+R A G TV++G E+ QA+ QF L+TG
Sbjct: 221 ETPLIRYARARGKTVITGAEVIALQAVEQFVLYTG 255
>gnl|CDD|183721 PRK12749, PRK12749, quinate/shikimate dehydrogenase; Reviewed.
Length = 288
Score = 123 bits (310), Expect = 9e-32
Identities = 88/293 (30%), Positives = 139/293 (47%), Gaps = 32/293 (10%)
Query: 238 KIFGLVSNPVGHSKGPILHNPAFRHTRFNGIYVPMLVDDVKEFFRTYSGTD---FAGFSV 294
++ GL++ P+ HS P + N A Y+ VD+ F G G V
Sbjct: 8 ELIGLMAYPIRHSLSPEMQNKALEKAGLPFTYMAFEVDN-DSFPGAIEGLKALKMRGTGV 66
Query: 295 GIPHKEPAVACCDEVHPLAKSIGAVNTIIRRPIDGKLVGYNTDCESAISAIEDALRERQG 354
+P+K+ A DE+ P AK +GA+NTI+ DG L GYNTD I AI+++ G
Sbjct: 67 SMPNKQLACEYVDELTPAAKLVGAINTIVND--DGYLRGYNTDGTGHIRAIKES-----G 119
Query: 355 INGVASHTSPIAGKIFVLVGAGGAGRALAFGAKSRGARVI-IFNRN---YERAKALADAV 410
+ I GK VL+GAGGA A+ G + I +FNR +++A A A V
Sbjct: 120 FD--------IKGKTMVLLGAGGASTAIGAQGAIEGLKEIKLFNRRDEFFDKALAFAQRV 171
Query: 411 SGEALHFEYLHEFFPEKGM--------ILANASAIGMEPNSDQSPV-PKEALKAYELVFD 461
+ + + ++ IL N + +GM+P ++S V L LV +
Sbjct: 172 NENTDCVVTVTDLADQQAFAEALASADILTNGTKVGMKPLENESLVNDISLLHPGLLVTE 231
Query: 462 AVYTPRNTRLLREAAEVGATVVSGVEMFIRQALGQFRLFTGGLAPEDFMRKLV 514
VY P T+LL++A + G + G M + Q QF L+TG P +++++++
Sbjct: 232 CVYNPHMTKLLQQAQQAGCKTIDGYGMLLWQGAEQFTLWTGKDFPLEYVKQVM 284
>gnl|CDD|183586 PRK12549, PRK12549, shikimate 5-dehydrogenase; Reviewed.
Length = 284
Score = 121 bits (307), Expect = 3e-31
Identities = 84/290 (28%), Positives = 120/290 (41%), Gaps = 60/290 (20%)
Query: 241 GLVSNPVGHSKGPILHNPAFRHTRFNGIYVP-------MLVDDVKEFFRTYSGTDFAGFS 293
GL+ + S P +H +Y + D + E FAG +
Sbjct: 9 GLIGAGIQASLSPAMHEAEGDAQGLRYVYRLIDLDALGLTADALPELLDAAERMGFAGLN 68
Query: 294 VGIPHKEPAVACCDEVHPLAKSIGAVNTIIRRPIDGKLVGYNTDC----ESAISAIEDAL 349
+ P K+ + DE+ A+++GAVNT++ R DG+ +G+NTD ES + DA
Sbjct: 69 ITHPCKQAVIPHLDELSDDARALGAVNTVVFR--DGRRIGHNTDWSGFAESFRRGLPDAS 126
Query: 350 RERQGINGVASHTSPIAGKIFVLVGAGGAGRALAFGAKSRGA-RVIIFNRNYERAKALAD 408
ER V +GAGGAG A+A + G R+ IF+ + RA ALAD
Sbjct: 127 LER-----------------VVQLGAGGAGAAVAHALLTLGVERLTIFDVDPARAAALAD 169
Query: 409 AVSGEALHFEYLHEFFPEKGMI--------------LANASAIGM--EPNSDQSPVPKEA 452
++ FP L +A+ GM P P+P E
Sbjct: 170 ELNA----------RFPAARATAGSDLAAALAAADGLVHATPTGMAKHPGL---PLPAEL 216
Query: 453 LKAYELVFDAVYTPRNTRLLREAAEVGATVVSGVEMFIRQALGQFRLFTG 502
L+ V D VY P T LLR A +G + G M + QA+ F LFTG
Sbjct: 217 LRPGLWVADIVYFPLETELLRAARALGCRTLDGGGMAVFQAVDAFELFTG 266
>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 = 109 bits (275), Expect = 2e-27
Identities = 76/235 (32%), Positives = 114/235 (48%), Gaps = 24/235 (10%)
Query: 10 LVCTQLE-CETTEEMQASIEQAKVEGADLVELCIDSMEFSHIS----EVDKLIQHPTLPA 64
+C L + EE + +E + GAD VEL +D +E I ++ L + LP
Sbjct: 1 KICVPLTGPDLLEEALSLLE--LLLGADAVELRVDLLEDPSIDDVAEQLSLLRELTPLPI 58
Query: 65 IVSYRLKSS----RKSSDEACKNTCLQVLRRALDLDVEFVEMDYEVASDPLMSEI-IYSR 119
I + R KS S +E L++L AL L ++V D E+ S L I +
Sbjct: 59 IFTVRTKSEGGNFEGSEEEY-----LELLEEALKLGPDYV--DIELDSALLEELINSRKK 111
Query: 120 SNTKIIVSSYLNGGGKPTTEKLGDVIACMQATGADVMKLEIAVDSITDLAPVFEMLTHCQ 179
NTKII S Y + G P+ E+L + M A GAD++K+ + +SI D + + +
Sbjct: 112 GNTKIIGS-YHDFSGTPSDEELVSRLEKMAALGADIVKIAVMANSIEDNLRLLKFTRQVK 170
Query: 180 ----VPLIALAVGSRGLISQLLGPKFGGFLVYGSLGGKSVPGLPTLVSLKQVYQL 230
+PLIA+ +G G +S++L P FG L Y SL S PG ++ LKQ L
Sbjct: 171 NLYDIPLIAINMGELGKLSRILSPVFGSPLTYASLPEPSAPGQLSVEELKQALSL 225
>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 = 109 bits (274), Expect = 7e-27
Identities = 74/285 (25%), Positives = 112/285 (39%), Gaps = 24/285 (8%)
Query: 238 KIFGLVSNPVGHSKGPILHNPAFRHTRFNGIYVPMLVDDVKEFFRTYSGT--DFAGFSVG 295
K ++ P+ HS+ P LHN + +E SG F G SV
Sbjct: 6 KKAFIIGKPIAHSRSPHLHNAGYEILGLPDKTYEFETCSAEELKEVLSGFGPQFGGASVT 65
Query: 296 IPHKEPAVACCDEVHPLAKSIGAVNTIIRRPIDGKLVGYNTDCESAISAIEDALRERQGI 355
IP K + DE A IG+VNT++R +G G NTD + A+ +
Sbjct: 66 IPLKFAILRFADEHTDRASLIGSVNTLLRTQ-NGIWKGDNTDWDGIAGALAN-------- 116
Query: 356 NGVASHTSPIAGKIFVLVGAGGAGRALAFGAKSRGARVI-IFNRNYERAKALADAV--SG 412
G P+AG +++GAGG RA + S G I + NRN ++ L D G
Sbjct: 117 IGKFE---PLAGFRGLVIGAGGTSRAAVYALASLGVTDITVINRNPDKLSRLVDLGVQVG 173
Query: 413 EALHFEYLHEFFPEKGMILANASAIGMEPNSDQSPVP-------KEALKAYELVFDAVYT 465
E + S + + +D + + + + DA Y
Sbjct: 174 VITRLEGDSGGLAIEKAAEVLVSTVPADVPADYVDLFATVPFLLLKRKSSEGIFLDAAYD 233
Query: 466 PRNTRLLREAAEVGATVVSGVEMFIRQALGQFRLFTGGLAPEDFM 510
P T L+ + G V+SG++M + Q QF +TG AP + M
Sbjct: 234 PWPTPLVAIVSAAGWRVISGLQMLLHQGFAQFEQWTGMPAPREAM 278
>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 = 99 bits (250), Expect = 1e-25
Identities = 39/83 (46%), Positives = 50/83 (60%), Gaps = 2/83 (2%)
Query: 242 LVSNPVGHSKGPILHNPAFRHTRFNGIYVPMLV--DDVKEFFRTYSGTDFAGFSVGIPHK 299
L+ NP+ HS P++HN AF+ NG+YV V D++ EF F G +V IPHK
Sbjct: 1 LIGNPISHSLSPLIHNAAFKALGLNGVYVAFEVPPDNLPEFVEGLRALGFRGLNVTIPHK 60
Query: 300 EPAVACCDEVHPLAKSIGAVNTI 322
E A+ DE+ P AK IGAVNTI
Sbjct: 61 EAAIPLLDELSPEAKRIGAVNTI 83
>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 = 102 bits (256), Expect = 7e-25
Identities = 69/236 (29%), Positives = 117/236 (49%), Gaps = 25/236 (10%)
Query: 10 LVCTQLECETTEEMQASIEQAKVEGADLVELCIDSMEF-SHISEVDKLIQ-----HPTLP 63
+ L EE A+ E+ GAD+VEL +D ++ S ++VD LI+ P P
Sbjct: 1 KIFVPLTAPDLEEALATAEKICK-GADIVELRVDLLKDPSSNNDVDALIEQLSQLRPDKP 59
Query: 64 AIVSYRLKS---SRKSSDEACKNTCLQVLRRALD-LDVEFVEMDYEVASDPLMSEIIYS- 118
I + R S ++E L+ L+RA D +FV D E+ + + +
Sbjct: 60 LIFTIRTISEGGKFPGNEEEY----LEELKRAADSPGPDFV--DIELFLPDDAVKELINI 113
Query: 119 --RSNTKIIVSSYLNGGGKPTTEKLGDVIACMQATGADVMKLEIAVDSITDLAPVFEMLT 176
+ TKII+S Y + P+ E++ + + + GAD++K+ + +S D+ + E+
Sbjct: 114 AKKGGTKIIMS-YHDFQKTPSWEEIVERLEKALSYGADIVKIAVMANSKEDVLTLLEITN 172
Query: 177 HCQ----VPLIALAVGSRGLISQLLGPKFGGFLVYGSLGGKSVPGLPTLVSLKQVY 228
VPLI +++G RG IS++LG FG L +GSLG S PG ++ L+++
Sbjct: 173 KVDEHADVPLITMSMGDRGKISRVLGAVFGSVLTFGSLGKASAPGQISVDDLRELL 228
>gnl|CDD|172521 PRK14027, PRK14027, quinate/shikimate dehydrogenase; Provisional.
Length = 283
Score = 90.9 bits (225), Expect = 2e-20
Identities = 80/289 (27%), Positives = 123/289 (42%), Gaps = 32/289 (11%)
Query: 234 NPDTKIFGLVSNPVGHSKGPILHNP-------AFRHTRFNGIYVPMLVDDVKEFFRTYSG 286
D+ + GL+ + S+ P +H A + R + + D+K
Sbjct: 1 MNDSILLGLIGQGLDLSRTPAMHEAEGLAQGRATVYRRIDTLGSRASGQDLKTLLDAALY 60
Query: 287 TDFAGFSVGIPHKEPAVACCDEVHPLAKSIGAVNTIIRRPIDGKLVGYNTDCESAISAIE 346
F G ++ P+K+ + DEV A +GAVNT++ G G+NTD +E
Sbjct: 61 LGFNGLNITHPYKQAVLPLLDEVSEQATQLGAVNTVVIDA-TGHTTGHNTDVSGFGRGME 119
Query: 347 DALRERQGINGVASHTSPIAGKIFVLVGAGGAGRALAFGAKSRGARVI-IFNRNYERAKA 405
+ L A S V VGAGG G A+A+ + G + + + + + RA+A
Sbjct: 120 EGLPN-------AKLDS------VVQVGAGGVGNAVAYALVTHGVQKLQVADLDTSRAQA 166
Query: 406 LADAVSGEALHFEYLH-------EFFPEKGMILANASAIGMEPNSDQSPVPKEALKAYEL 458
LAD ++ A+ E + E + NA+ +GM P + L
Sbjct: 167 LADVIN-NAVGREAVVGVDARGIEDVIAAADGVVNATPMGM-PAHPGTAFDVSCLTKDHW 224
Query: 459 VFDAVYTPRNTRLLREAAEVGATVVSGVEMFIRQALGQFRLFTGGLAPE 507
V D VY P T LL+ A +G + G M I QA+ FRLFT GL P+
Sbjct: 225 VGDVVYMPIETELLKAARALGCETLDGTRMAIHQAVDAFRLFT-GLEPD 272
>gnl|CDD|223782 COG0710, AroD, 3-dehydroquinate dehydratase [Amino acid transport
and metabolism].
Length = 231
Score = 82.4 bits (204), Expect = 8e-18
Identities = 56/237 (23%), Positives = 109/237 (45%), Gaps = 22/237 (9%)
Query: 11 VCTQLECETTEEMQASIEQAKVEGADLVELCIDSMEFSHISEVDKLIQH-----PTLPAI 65
+ + E++ E++K AD+VEL +D EV ++ + P P I
Sbjct: 4 IIVPVVGLDIAELKEQAEKSKELDADIVELRVDL--LESNVEVLEVAKALREKDPDKPLI 61
Query: 66 VSYRLKS--SRKSSDEACKNTCLQVLRRALDL-DVEFVEMDYEVASDPLMSEIIYSRSNT 122
++R E +++L++ +L ++++++ + + + EII
Sbjct: 62 FTFRTVKEGGEFPGSEEEY---IELLKKLAELNGPDYIDIELS-SPEDDVKEIIKFAKKH 117
Query: 123 KIIVSSYLNGGGKPTTEKLGDVIACMQATGADVMKLEIAV--DSITDLAPVFEMLTHCQV 180
+IVS Y + P E++ + + M++ GAD++K IAV S D+ + E +
Sbjct: 118 GVIVS-YHDFEKTPPLEEIIERLDKMESLGADIVK--IAVMPQSKEDVLDLLEATREFKE 174
Query: 181 ---PLIALAVGSRGLISQLLGPKFGGFLVYGSLGGKSVPGLPTLVSLKQVYQLEHIN 234
P+I +++G G IS++ GP FG + Y SL S PG ++ L+++ L
Sbjct: 175 AEKPVITISMGKTGKISRVAGPVFGSPITYASLDKPSAPGQISVDELRKILTLLGYI 231
>gnl|CDD|235036 PRK02412, aroD, 3-dehydroquinate dehydratase; Provisional.
Length = 253
Score = 60.3 bits (147), Expect = 3e-10
Identities = 56/230 (24%), Positives = 102/230 (44%), Gaps = 31/230 (13%)
Query: 19 TTEEMQASIEQAKVEGADLVELCIDSMEFSHISEVDKLIQH--------PTLPAIVSYRL 70
T EE+ A AD++E D IS+V+ ++ P + ++R
Sbjct: 26 TLEEVLAEALAISKYDADIIEWRADF--LEKISDVESVLAAAPAIREKFAGKPLLFTFRT 83
Query: 71 KS---SRKSSDEACKNTCLQVLRRALDL-DVEFVEMDYEVASDP-LMSEII-YSRSNTKI 124
SDE L +++ + +++ D E+ S ++ E++ ++ +
Sbjct: 84 AKEGGEIALSDEEY----LALIKAVIKSGLPDYI--DVELFSGKDVVKEMVAFAHEHGVK 137
Query: 125 IVSSYLNGGGKPTTEKLGDVIACMQATGADVMKLEIAV------DSITDLAPVFEMLTHC 178
+V SY + P E++ + + M++ GAD++K IAV D +T L EM
Sbjct: 138 VVLSYHDFEKTPPKEEIVERLRKMESLGADIVK--IAVMPQSEQDVLTLLNATREMKELY 195
Query: 179 -QVPLIALAVGSRGLISQLLGPKFGGFLVYGSLGGKSVPGLPTLVSLKQV 227
PLI +++G G IS+L G FG + SL S PG ++ L+++
Sbjct: 196 ADQPLITMSMGKLGRISRLAGEVFGSSWTFASLDKASAPGQISVEDLRRI 245
>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 = 56.2 bits (136), Expect = 1e-09
Identities = 35/115 (30%), Positives = 52/115 (45%), Gaps = 18/115 (15%)
Query: 363 SPIAGKIFVLVGAGGAGRALAFGAKSRGAR-VIIFNRNYERAKALADAVSG--EALHFEY 419
+ GK +L+GAG R A S+GA+ + I NR E+AK LA+ EAL +
Sbjct: 8 GDLKGKKVLLIGAGEMARLAAKHLLSKGAKKITIANRTLEKAKELAEEFPVGGEALPLDE 67
Query: 420 LHEFFPEKGMILANASAIGMEPNSDQSPVPKEALKAYE-----LVFD-AVYTPRN 468
L E +LA A + ++ + KE ++ L D AV PR+
Sbjct: 68 LEE-------LLAEADIVISATSAPTPIITKEMVEEALKARPLLFVDIAV--PRD 113
>gnl|CDD|184156 PRK13575, PRK13575, 3-dehydroquinate dehydratase; Provisional.
Length = 238
Score = 51.7 bits (124), Expect = 2e-07
Identities = 43/208 (20%), Positives = 87/208 (41%), Gaps = 23/208 (11%)
Query: 36 DLVELCIDSMEFSHISEVDKLIQ-----HPTLPAIVSYRLKSSRKSSDEACKNTCLQVLR 90
D++EL ID E + ++ ++I + +V+YR + + + L +L
Sbjct: 32 DIIELRIDQWENVTVDQLAEMITKLKVLQDSFKLLVTYR-TKLQGGYGQFTNDLYLNLLS 90
Query: 91 RALD------LDVEFVEMDYEVASDPLMSEIIYSRSNTKIIVSSYLNGGGKPTTEKLGDV 144
+ +D+E+ ++ + I + + K +V S+ N P ++L +
Sbjct: 91 DLANINGIDMIDIEW---QADIDIEKHQRLITHLQQYNKEVVISHHNFESTPPLDELKFI 147
Query: 145 IACMQATGADVMKLEIAVDSITDLAPVFEML------THCQVPLIALAVGSRGLISQLLG 198
MQ + +KL + + D+ + + + C+V + +++ GLIS+
Sbjct: 148 FFKMQKFNPEYVKLAVMPHNKNDVLNLLQAMSTFSDTMDCKV--VGISMSKLGLISRTAQ 205
Query: 199 PKFGGFLVYGSLGGKSVPGLPTLVSLKQ 226
FGG L YG +G PG + LK
Sbjct: 206 GVFGGALSYGCIGEPQAPGQIHVTDLKA 233
>gnl|CDD|223450 COG0373, HemA, Glutamyl-tRNA reductase [Coenzyme metabolism].
Length = 414
Score = 52.6 bits (127), Expect = 3e-07
Identities = 34/109 (31%), Positives = 54/109 (49%), Gaps = 9/109 (8%)
Query: 365 IAGKIFVLVGAGGAGRALAFGAKSRG-ARVIIFNRNYERAKALADAVSGEALHFEYLHEF 423
+ K +++GAG G +A +G ++ I NR ERA+ LA + EA+ E L E
Sbjct: 176 LKDKKVLVIGAGEMGELVAKHLAEKGVKKITIANRTLERAEELAKKLGAEAVALEELLEA 235
Query: 424 FPEKGMILANASAIGMEPNSDQSPVPKEALKA--YELVFD-AVYTPRNT 469
E +++++ SA P + V + ALK L+ D AV PR+
Sbjct: 236 LAEADVVISSTSA--PHPIITREMV-ERALKIRKRLLIVDIAV--PRDV 279
>gnl|CDD|234592 PRK00045, hemA, glutamyl-tRNA reductase; Reviewed.
Length = 423
Score = 52.5 bits (127), Expect = 3e-07
Identities = 21/66 (31%), Positives = 34/66 (51%), Gaps = 5/66 (7%)
Query: 363 SPIAGKIFVLVGAGGAGRALAFGAKSRGAR-VIIFNRNYERAKALADAVSGEALHFE--- 418
++GK +++GAG G +A +G R + + NR ERA+ LA+ GEA+ +
Sbjct: 178 GDLSGKKVLVIGAGEMGELVAKHLAEKGVRKITVANRTLERAEELAEEFGGEAIPLDELP 237
Query: 419 -YLHEF 423
L E
Sbjct: 238 EALAEA 243
>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 = 50.0 bits (120), Expect = 1e-06
Identities = 33/108 (30%), Positives = 48/108 (44%), Gaps = 8/108 (7%)
Query: 365 IAGKIFVLVGAGGAGR-ALAFGAKSRGARVIIFNRNYERAKALADAVSGEALHFEYLHEF 423
+ GK +++GAG G A A A + I NR YERA+ LA + G A+ + L E
Sbjct: 176 LKGKKVLVIGAGEMGELAAKHLAAKGVAEITIANRTYERAEELAKELGGNAVPLDELLEL 235
Query: 424 FPEKGMILANASAIG-MEPNSDQSPVPKEALKAYELVFD-AVYTPRNT 469
E +++ SA G K+ L+ D AV PR+
Sbjct: 236 LNEADVVI---SATGAPHYAKIVERAMKKRSGKPRLIVDLAV--PRDI 278
>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 = 47.4 bits (113), Expect = 1e-05
Identities = 27/73 (36%), Positives = 44/73 (60%), Gaps = 1/73 (1%)
Query: 365 IAGKIFVLVGAGGAGRALAFGAKSRGA-RVIIFNRNYERAKALADAVSGEALHFEYLHEF 423
+ GK +L+GAG G +A +G +++I NR YERA+ LA + GEA+ FE L E+
Sbjct: 178 LKGKKALLIGAGEMGELVAKHLLRKGVGKILIANRTYERAEDLAKELGGEAVKFEDLEEY 237
Query: 424 FPEKGMILANASA 436
E +++++ A
Sbjct: 238 LAEADIVISSTGA 250
>gnl|CDD|236216 PRK08277, PRK08277, D-mannonate oxidoreductase; Provisional.
Length = 278
Score = 41.8 bits (99), Expect = 5e-04
Identities = 22/58 (37%), Positives = 33/58 (56%), Gaps = 4/58 (6%)
Query: 365 IAGKIFVLVGAGGA-GRALAFGAKSRGARVIIFNRNYERAKALADAVS---GEALHFE 418
+ GK+ V+ G GG G A+A GA+V I +RN E+A+A+ + GEAL +
Sbjct: 8 LKGKVAVITGGGGVLGGAMAKELARAGAKVAILDRNQEKAEAVVAEIKAAGGEALAVK 65
>gnl|CDD|183775 PRK12826, PRK12826, 3-ketoacyl-(acyl-carrier-protein) reductase;
Reviewed.
Length = 251
Score = 39.5 bits (93), Expect = 0.002
Identities = 17/53 (32%), Positives = 26/53 (49%), Gaps = 1/53 (1%)
Query: 362 TSPIAGKI-FVLVGAGGAGRALAFGAKSRGARVIIFNRNYERAKALADAVSGE 413
T + G++ V A G GRA+A + GA VI+ + + A A A+ V
Sbjct: 1 TRDLEGRVALVTGAARGIGRAIAVRLAADGAEVIVVDICGDDAAATAELVEAA 53
>gnl|CDD|235633 PRK05872, PRK05872, short chain dehydrogenase; Provisional.
Length = 296
Score = 39.6 bits (93), Expect = 0.003
Identities = 17/57 (29%), Positives = 28/57 (49%), Gaps = 1/57 (1%)
Query: 363 SPIAGKIFVLVGAG-GAGRALAFGAKSRGARVIIFNRNYERAKALADAVSGEALHFE 418
+ +AGK+ V+ GA G G LA +RGA++ + + ALA + G+
Sbjct: 5 TSLAGKVVVVTGAARGIGAELARRLHARGAKLALVDLEEAELAALAAELGGDDRVLT 61
>gnl|CDD|240638 cd12161, GDH_like_1, Putative glycerate dehydrogenase and related
proteins of the D-specific 2-hydroxy dehydrogenase
family. This group contains a variety of proteins
variously identified as glycerate dehydrogenase (GDH,
aka Hydroxypyruvate Reductase) and other enzymes of the
2-hydroxyacid dehydrogenase family. GDH catalyzes the
reversible reaction of (R)-glycerate + NAD+ to
hydroxypyruvate + NADH + H+. 2-hydroxyacid
dehydrogenases catalyze the conversion of a wide variety
of D-2-hydroxy acids to their corresponding keto acids.
The general mechanism is (R)-lactate + acceptor to
pyruvate + reduced acceptor. Formate/glycerate and
related dehydrogenases of the D-specific 2-hydroxyacid
dehydrogenase superfamily include groups such as formate
dehydrogenase, glycerate dehydrogenase, L-alanine
dehydrogenase, and S-adenosylhomocysteine hydrolase.
Despite often low sequence identity, these proteins
typically have a characteristic arrangement of 2 similar
subdomains of the alpha/beta Rossmann-fold NAD+ binding
form. The NAD+ binding domain is inserted within the
linear sequence of the mostly N-terminal catalytic
domain, which has a similar domain structure to the
internal NAD binding domain. Structurally, these domains
are connected by extended alpha helices and create a
cleft in which NAD is bound, primarily to the C-terminal
portion of the 2nd (internal) domain. Some related
proteins have similar structural subdomain but with a
tandem arrangement of the catalytic and NAD-binding
subdomains in the linear sequence. While many members of
this family are dimeric, alanine DH is hexameric and
phosphoglycerate DH is tetrameric.
Length = 315
Score = 39.1 bits (92), Expect = 0.004
Identities = 19/70 (27%), Positives = 33/70 (47%), Gaps = 3/70 (4%)
Query: 342 ISAIEDALRERQGINGVASHTSPIAGKIFVLVGAGGAGRALAFGAKSRGARVIIFNRNYE 401
I + A+R G+ +AGK +VG G G +A K+ G +V+ ++R E
Sbjct: 121 IVPCDAAVRAGGTKAGLIGRE--LAGKTVGIVGTGAIGLRVARLFKAFGCKVLAYSR-SE 177
Query: 402 RAKALADAVS 411
+ +A A +
Sbjct: 178 KEEAKALGIE 187
>gnl|CDD|235546 PRK05653, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Validated.
Length = 246
Score = 38.6 bits (91), Expect = 0.004
Identities = 17/45 (37%), Positives = 26/45 (57%), Gaps = 2/45 (4%)
Query: 371 VLV--GAGGAGRALAFGAKSRGARVIIFNRNYERAKALADAVSGE 413
LV + G GRA+A + GA+V+I++ N E A+ALA +
Sbjct: 8 ALVTGASRGIGRAIALRLAADGAKVVIYDSNEEAAEALAAELRAA 52
>gnl|CDD|236241 PRK08324, PRK08324, short chain dehydrogenase; Validated.
Length = 681
Score = 39.4 bits (93), Expect = 0.004
Identities = 20/51 (39%), Positives = 30/51 (58%), Gaps = 3/51 (5%)
Query: 364 PIAGKIFVLV--GAGGAGRALAFGAKSRGARVIIFNRNYERAKALADAVSG 412
P+AGK+ LV AGG G+A A + GA V++ + + E A+A A + G
Sbjct: 419 PLAGKV-ALVTGAAGGIGKATAKRLAAEGACVVLADLDEEAAEAAAAELGG 468
>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 = 38.7 bits (90), Expect = 0.005
Identities = 20/57 (35%), Positives = 28/57 (49%), Gaps = 1/57 (1%)
Query: 365 IAGKIFVLVGAG-GAGRALAFGAKSRGARVIIFNRNYERAKALADAVSGEALHFEYL 420
+ GK+ ++ GA G G A A + GA V I R +R +ALAD + E L
Sbjct: 1 LQGKVALVTGASSGIGEATARALAAEGAAVAIAARRVDRLEALADELEAEGGKALVL 57
>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 = 38.1 bits (89), Expect = 0.007
Identities = 27/66 (40%), Positives = 35/66 (53%), Gaps = 11/66 (16%)
Query: 371 VLV-GAGGAGRALAFGAKSRGARVIIFNRNYER---AKAL-ADAVSGEALHFEYLHEFFP 425
VLV GAGG G A AK+ GARVI+ +R+ E+ AK L AD V +Y E
Sbjct: 138 VLVLGAGGVGLLAAQLAKAAGARVIVTDRSDEKLELAKELGADHV------IDYKEEDLE 191
Query: 426 EKGMIL 431
E+ +
Sbjct: 192 EELRLT 197
>gnl|CDD|212492 cd05327, retinol-DH_like_SDR_c_like, retinol dehydrogenase
(retinol-DH), Light dependent Protochlorophyllide
(Pchlide) OxidoReductase (LPOR) and related proteins,
classical (c) SDRs. Classical SDR subgroup containing
retinol-DHs, LPORs, and related proteins. Retinol is
processed by a medium chain alcohol dehydrogenase
followed by retinol-DHs. Pchlide reductases act in
chlorophyll biosynthesis. There are distinct enzymes
that catalyze Pchlide reduction in light or dark
conditions. Light-dependent reduction is via an
NADP-dependent SDR, LPOR. Proteins in this subfamily
share the glycine-rich NAD-binding motif of the
classical SDRs, have a partial match to the canonical
active site tetrad, but lack the typical active site
Ser. This subgroup includes the human proteins: retinol
dehydrogenase -12, -13 ,and -14, dehydrogenase/reductase
SDR family member (DHRS)-12 , -13 and -X (a DHRS on
chromosome X), and WWOX (WW domain-containing
oxidoreductase), as well as a Neurospora crassa SDR
encoded by the blue light inducible bli-4 gene. SDRs are
a functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold (alpha/beta folding pattern with a central
beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRs are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes catalyze a
wide range of activities including the metabolism of
steroids, cofactors, carbohydrates, lipids, aromatic
compounds, and amino acids, and act in redox sensing.
Classical SDRs have an TGXXX[AG]XG cofactor binding
motif and a YXXXK active site motif, with the Tyr
residue of the active site motif serving as a critical
catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 269
Score = 38.0 bits (89), Expect = 0.008
Identities = 18/43 (41%), Positives = 23/43 (53%), Gaps = 1/43 (2%)
Query: 367 GKIFVLVGA-GGAGRALAFGAKSRGARVIIFNRNYERAKALAD 408
GK+ V+ GA G G+ A RGA VII RN E+ + A
Sbjct: 1 GKVVVITGANSGIGKETARELAKRGAHVIIACRNEEKGEEAAA 43
>gnl|CDD|180669 PRK06720, PRK06720, hypothetical protein; Provisional.
Length = 169
Score = 36.9 bits (85), Expect = 0.008
Identities = 20/59 (33%), Positives = 33/59 (55%), Gaps = 4/59 (6%)
Query: 365 IAGKIFVLVGAG-GAGRALAFGAKSRGARVIIFNRNYERAKALADAVS---GEALHFEY 419
+AGK+ ++ G G G GR A +GA+VI+ + + E +A + ++ GEAL Y
Sbjct: 14 LAGKVAIVTGGGIGIGRNTALLLAKQGAKVIVTDIDQESGQATVEEITNLGGEALFVSY 72
>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 = 37.8 bits (89), Expect = 0.010
Identities = 15/31 (48%), Positives = 20/31 (64%)
Query: 365 IAGKIFVLVGAGGAGRALAFGAKSRGARVII 395
IAGK+ V+ G G G+ A A+ GARVI+
Sbjct: 193 IAGKVVVVAGYGWVGKGCAMRARGLGARVIV 223
>gnl|CDD|216255 pfam01031, Dynamin_M, Dynamin central region. This region lies
between the GTPase domain, see pfam00350, and the
pleckstrin homology (PH) domain, see pfam00169.
Length = 296
Score = 37.5 bits (88), Expect = 0.013
Identities = 21/96 (21%), Positives = 36/96 (37%), Gaps = 23/96 (23%)
Query: 271 PMLVDDVKEFFRTYSGTDFAGFSVGIPHK--------------EPAVACCDEVHPLAKSI 316
+ ++++ R Y G F +P K EPA+ C D V+ + I
Sbjct: 167 KLSDEEIRTAIRNYRGRRLPLF---VPEKAFELLVKKQIKRLEEPALKCVDLVYEELRRI 223
Query: 317 GAVNTIIRRPIDGKLVGYNTDCESAISAIEDALRER 352
I + +L + E+ +ED LRE+
Sbjct: 224 --FLKIASK----ELSRFPNLKEAIKEVVEDILREQ 253
>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 = 37.6 bits (88), Expect = 0.014
Identities = 20/57 (35%), Positives = 28/57 (49%), Gaps = 4/57 (7%)
Query: 358 VASHTSPIAGKIFVLVGAGGAGRALAFGAKSRGARVIIFNRNYER---AKA-LADAV 410
AG ++VGAG G + AK+RGARVI+ + + ER A+ AD
Sbjct: 151 AVRRAGVTAGDTVLVVGAGPIGLGVIQVAKARGARVIVVDIDDERLEFARELGADDT 207
>gnl|CDD|236372 PRK09072, PRK09072, short chain dehydrogenase; Provisional.
Length = 263
Score = 36.5 bits (85), Expect = 0.023
Identities = 20/53 (37%), Positives = 30/53 (56%), Gaps = 1/53 (1%)
Query: 365 IAGKIFVLVGA-GGAGRALAFGAKSRGARVIIFNRNYERAKALADAVSGEALH 416
+ K +L GA GG G+ALA + GAR+++ RN E+ +ALA + H
Sbjct: 3 LKDKRVLLTGASGGIGQALAEALAAAGARLLLVGRNAEKLEALAARLPYPGRH 55
>gnl|CDD|235996 PRK07340, PRK07340, ornithine cyclodeaminase; Validated.
Length = 304
Score = 36.5 bits (85), Expect = 0.026
Identities = 28/127 (22%), Positives = 45/127 (35%), Gaps = 22/127 (17%)
Query: 370 FVLVGAG--GAGRALAFGAKSRGARVIIFNRNYERAKALADAVSGEALHFEYL--HEFFP 425
+L+G G AF A RV + R A A E L
Sbjct: 128 LLLIGTGVQARAHLEAFAAGLPVRRVWVRGRTAASAAAFCAHARALGPTAEPLDGEAIPE 187
Query: 426 EKGMILANASAIGMEPNSDQSPVPKEALKAYELVFDAV--YTPRNTRLLREAAEVGATVV 483
+++ ++ ++PV EA +A LV AV +TP + AE+ V
Sbjct: 188 AVDLVVTATTS--------RTPVYPEAARAGRLVV-AVGAFTP-------DMAELAPRTV 231
Query: 484 SGVEMFI 490
G +++
Sbjct: 232 RGSRLYV 238
>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 = 36.6 bits (85), Expect = 0.027
Identities = 15/31 (48%), Positives = 20/31 (64%)
Query: 365 IAGKIFVLVGAGGAGRALAFGAKSRGARVII 395
IAGK V+ G G G+ +A A+ GARVI+
Sbjct: 194 IAGKTVVVAGYGWCGKGIAMRARGMGARVIV 224
>gnl|CDD|235628 PRK05855, PRK05855, short chain dehydrogenase; Validated.
Length = 582
Score = 36.9 bits (86), Expect = 0.028
Identities = 17/54 (31%), Positives = 26/54 (48%), Gaps = 1/54 (1%)
Query: 358 VASHTSPIAGKIFVLVGAG-GAGRALAFGAKSRGARVIIFNRNYERAKALADAV 410
V P +GK+ V+ GAG G GR A GA V+ + + A+ A+ +
Sbjct: 306 VGRPRGPFSGKLVVVTGAGSGIGRETALAFAREGAEVVASDIDEAAAERTAELI 359
>gnl|CDD|240625 cd05300, 2-Hacid_dh_1, Putative D-isomer specific 2-hydroxyacid
dehydrogenase. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomains but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric. Formate dehydrogenase (FDH) catalyzes the
NAD+-dependent oxidation of formate ion to carbon
dioxide with the concomitant reduction of NAD+ to NADH.
FDHs of this family contain no metal ions or prosthetic
groups. Catalysis occurs though direct transfer of the
hydride ion to NAD+ without the stages of acid-base
catalysis typically found in related dehydrogenases.
FDHs are found in all methylotrophic microorganisms in
energy production and in the stress responses of plants.
Length = 313
Score = 36.3 bits (85), Expect = 0.028
Identities = 23/65 (35%), Positives = 31/65 (47%), Gaps = 4/65 (6%)
Query: 362 TSPIAGKIFVLVGAGGAGRALAFGAKSRGARVIIFNRNYERAKALADAVSGEALHFEYLH 421
+AGK ++VG G GR +A AK+ G RVI R+ A + D V + L
Sbjct: 129 VRELAGKTVLIVGLGDIGREIARRAKAFGMRVIGVRRSGRPAPPVVDEV----YTPDELD 184
Query: 422 EFFPE 426
E PE
Sbjct: 185 ELLPE 189
>gnl|CDD|237219 PRK12827, PRK12827, short chain dehydrogenase; Provisional.
Length = 249
Score = 35.9 bits (83), Expect = 0.031
Identities = 17/54 (31%), Positives = 30/54 (55%), Gaps = 1/54 (1%)
Query: 362 TSPIAGK-IFVLVGAGGAGRALAFGAKSRGARVIIFNRNYERAKALADAVSGEA 414
+ + + + + G+GG GRA+A + GA VI+ + + R +A ADAV+
Sbjct: 1 MASLDSRRVLITGGSGGLGRAIAVRLAADGADVIVLDIHPMRGRAEADAVAAGI 54
>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 = 36.1 bits (83), Expect = 0.037
Identities = 27/96 (28%), Positives = 41/96 (42%), Gaps = 5/96 (5%)
Query: 339 ESAISAIEDALRERQGINGVASHTSPIAGKIFVLVGAGGAGRALAFGAKSRGARVIIFNR 398
E ++ I L +Q G +AGK V+VGAG G+ A + GA+V+I +
Sbjct: 134 ELSVQFIARFLEVQQP--GRLGGAPDVAGKTVVVVGAGVVGKEAAQMLRGLGAQVLITDI 191
Query: 399 NYERAKALADAVSGEALHFEYLHEFFPEKGMILANA 434
N E + L + E L E E +I+
Sbjct: 192 NVEALEQLE---ELGGKNVEELEEALAEADVIVTTT 224
>gnl|CDD|235935 PRK07109, PRK07109, short chain dehydrogenase; Provisional.
Length = 334
Score = 35.7 bits (83), Expect = 0.045
Identities = 23/56 (41%), Positives = 31/56 (55%), Gaps = 4/56 (7%)
Query: 364 PIAGKIFVLVGA-GGAGRALAFGAKSRGARVIIFNRNYERAKALADAVS---GEAL 415
PI ++ V+ GA G GRA A RGA+V++ R E +ALA + GEAL
Sbjct: 5 PIGRQVVVITGASAGVGRATARAFARRGAKVVLLARGEEGLEALAAEIRAAGGEAL 60
>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 = 35.8 bits (84), Expect = 0.047
Identities = 20/59 (33%), Positives = 27/59 (45%), Gaps = 7/59 (11%)
Query: 354 GINGVASHTSPIAGKIFVLVGAGGAGRALAFGAKSRGARVIIFNRNYERAKALADAVSG 412
G+ GV K+ V++GAG G A A GA V + + N ER + L D G
Sbjct: 162 GVPGVPP------AKV-VILGAGVVGENAARVALGLGAEVTVLDINLERLRYLDDIFGG 213
>gnl|CDD|223189 COG0111, SerA, Phosphoglycerate dehydrogenase and related
dehydrogenases [Amino acid transport and metabolism].
Length = 324
Score = 35.4 bits (82), Expect = 0.057
Identities = 21/62 (33%), Positives = 30/62 (48%), Gaps = 4/62 (6%)
Query: 365 IAGKIFVLVGAGGAGRALAFGAKSRGARVIIFNRNYERAKALADAVSGEALHFEYLHEFF 424
+AGK ++G G GRA+A K+ G +VI ++ R +A D V G L E
Sbjct: 140 LAGKTVGIIGLGRIGRAVAKRLKAFGMKVIGYDPYSPRERAGVDGVVGVDS----LDELL 195
Query: 425 PE 426
E
Sbjct: 196 AE 197
>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 = 0.057
Identities = 18/52 (34%), Positives = 30/52 (57%), Gaps = 1/52 (1%)
Query: 365 IAGKIFVLVGAG-GAGRALAFGAKSRGARVIIFNRNYERAKALADAVSGEAL 415
+ GK+ ++ GAG G G A A GARV++ + + A+A+ ++G AL
Sbjct: 1 LEGKVAIVTGAGAGIGAACAARLAREGARVVVADIDGGAAQAVVAQIAGGAL 52
>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 = 34.9 bits (81), Expect = 0.062
Identities = 20/50 (40%), Positives = 29/50 (58%), Gaps = 4/50 (8%)
Query: 365 IAGKIFVLVGAG-GAGRALAFGAKSRGARVIIFNRNYERAKALADAVSGE 413
+AGK+ ++ GA G GRA+A GA V++ NY +KA A+ V E
Sbjct: 1 LAGKVALVTGASRGIGRAIAKRLARDGASVVV---NYASSKAAAEEVVAE 47
>gnl|CDD|235975 PRK07231, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 251
Score = 35.2 bits (82), Expect = 0.063
Identities = 18/52 (34%), Positives = 27/52 (51%), Gaps = 5/52 (9%)
Query: 366 AGKIFVLVGAG---GAGRALAFGAKSRGARVIIFNRNYERAKALADAVSGEA 414
GK+ ++ GA G G A F A GARV++ +RN E A+ +A +
Sbjct: 4 EGKVAIVTGASSGIGEGIARRFAA--EGARVVVTDRNEEAAERVAAEILAGG 53
>gnl|CDD|216777 pfam01905, DevR, CRISPR-associated negative auto-regulator
DevR/Csa2. This group of families is one of several
protein families that are always found associated with
prokaryotic CRISPRs, themselves a family of clustered
regularly interspaced short palindromic repeats, DNA
repeats found in nearly half of all bacterial and
archaeal genomes. These DNA repeat regions have a
remarkably regular structure: unique sequences of
constant size, called spacers, sit between each pair of
repeats. It has been shown that the CRISPRs are
virus-derived sequences acquired by the host to enable
them to resist viral infection. The Cas proteins from
the host use the CRISPRs to mediate an antiviral
response. After transcription of the CRISPR, a complex
of Cas proteins termed Cascade cleaves a CRISPR RNA
precursor in each repeat and retains the cleavage
products containing the virus-derived sequence. Assisted
by the helicase Cas3, these mature CRISPR RNAs then
serve as small guide RNAs that enable Cascade to
interfere with virus proliferation. Cas5 contains an
endonuclease motif, whose inactivation leads to loss of
resistance, even in the presence of phage-derived
spacers. This family used to be known as DUF73. DevR
appears to be negative auto-regulator within the system.
Length = 258
Score = 35.0 bits (81), Expect = 0.073
Identities = 27/126 (21%), Positives = 44/126 (34%), Gaps = 21/126 (16%)
Query: 389 RGARVIIFNRNYERAKALADAVSGEAL---HFEYLHEFFPEKGMILANASAIGM------ 439
R A V++ R A+SGE+L + E L + E G+ L G+
Sbjct: 24 RKAPVVLKTGYKVR---YVPAISGESLKHAYQETLVKLALENGLPLCELCKRGIGDRGFI 80
Query: 440 ------EPNSDQSPVPKEALKAYEL--VFDAVYTPRNTRLLREAAEVGATVVSGVEMFIR 491
+ D E + + VF +YT + +R + V + V R
Sbjct: 81 KFATDKDLKKDDRDDEDEIILKCVVEDVFGFLYTETG-KSVRRTSPVKFSYAVPVLDSDR 139
Query: 492 QALGQF 497
+ QF
Sbjct: 140 ETDAQF 145
>gnl|CDD|236399 PRK09186, PRK09186, flagellin modification protein A; Provisional.
Length = 256
Score = 35.0 bits (81), Expect = 0.073
Identities = 14/46 (30%), Positives = 21/46 (45%), Gaps = 1/46 (2%)
Query: 367 GKIFVLVGAGG-AGRALAFGAKSRGARVIIFNRNYERAKALADAVS 411
GK ++ GAGG G AL G VI + + E L +++
Sbjct: 4 GKTILITGAGGLIGSALVKAILEAGGIVIAADIDKEALNELLESLG 49
>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 = 35.0 bits (81), Expect = 0.074
Identities = 33/118 (27%), Positives = 49/118 (41%), Gaps = 17/118 (14%)
Query: 370 FVLVGAGGAGRALAFGAKSRGARVIIFNR-NYERAKALADAVSGEALH-FEYLHEFFPEK 427
V+VGAG AG + A+ +G RV++ + ++ R K A+S AL + E
Sbjct: 3 VVVVGAGPAGASAAYRLADKGLRVLLLEKKSFPRYKPCGGALSPRALEELDLPGELI--- 59
Query: 428 GMILANASAIGMEPNSDQSPVPKEALKAYEL---VFDAVYTPRNTRLLREAAEVGATV 482
+ L + PN D +P E AY + FD L A E GA +
Sbjct: 60 -VNLVRGARF-FSPNGDSVEIPIETELAYVIDRDAFDEQ-------LAERAQEAGAEL 108
>gnl|CDD|180854 PRK07121, PRK07121, hypothetical protein; Validated.
Length = 492
Score = 35.2 bits (82), Expect = 0.075
Identities = 19/44 (43%), Positives = 24/44 (54%), Gaps = 6/44 (13%)
Query: 371 VLVGAGGAGRALAFGAKSRGARVIIFNRNYERAKAL--ADAVSG 412
V+VG G AG A A + GARV++ ERA A A+SG
Sbjct: 24 VVVGFGAAGACAAIEAAAAGARVLVL----ERAAGAGGATALSG 63
>gnl|CDD|240642 cd12165, 2-Hacid_dh_6, Putative D-isomer specific 2-hydroxyacid
dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 314
Score = 34.9 bits (81), Expect = 0.075
Identities = 16/60 (26%), Positives = 25/60 (41%), Gaps = 5/60 (8%)
Query: 367 GKIFVLVGAGGAGRALAFGAKSRGARVIIFNRNYERAKALADAVSGEALHFEYLHEFFPE 426
GK ++G G GR +A K+ G RVI +R+ + D + L E +
Sbjct: 137 GKTVGILGYGHIGREIARLLKAFGMRVIGVSRSPKE-----DEGADFVGTLSDLDEALEQ 191
>gnl|CDD|223573 COG0499, SAM1, S-adenosylhomocysteine hydrolase [Coenzyme
metabolism].
Length = 420
Score = 34.9 bits (81), Expect = 0.085
Identities = 14/31 (45%), Positives = 19/31 (61%)
Query: 365 IAGKIFVLVGAGGAGRALAFGAKSRGARVII 395
+AGK V+ G G GR +A + GARVI+
Sbjct: 207 LAGKNVVVAGYGWVGRGIAMRLRGMGARVIV 237
>gnl|CDD|187607 cd05349, BKR_2_SDR_c, putative beta-ketoacyl acyl carrier protein
[ACP]reductase (BKR), subgroup 2, classical (c) SDR.
This subgroup includes Rhizobium sp. NGR234 FabG1. The
Escherichai coli K12 BKR, FabG, belongs to a different
subgroup. BKR catalyzes the NADPH-dependent reduction of
ACP in the first reductive step of de novo fatty acid
synthesis (FAS). FAS consists of four elongation steps,
which are repeated to extend the fatty acid chain
through the addition of two-carbo units from malonyl
acyl-carrier protein (ACP): condensation, reduction,
dehydration, and a final reduction. Type II FAS, typical
of plants and many bacteria, maintains these activities
on discrete polypeptides, while type I FAS utilizes one
or two multifunctional polypeptides. BKR resembles enoyl
reductase, which catalyzes the second reduction step in
FAS. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold (alpha/beta folding
pattern with a central beta-sheet), an NAD(P)(H)-binding
region, and a structurally diverse C-terminal region.
Classical SDRs are typically about 250 residues long,
while extended SDRS are approximately 350 residues.
Sequence identity between different SDR enzymes are
typically in the 15-30% range, but the enzymes share the
Rossmann fold NAD-binding motif and characteristic
NAD-binding and catalytic sequence patterns. These
enzymes have a 3-glycine N-terminal NAD(P)(H)-binding
pattern (typically, TGxxxGxG in classical SDRs and
TGxxGxxG in extended SDRs), while substrate binding is
in the C-terminal region. A critical catalytic Tyr
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) numbering), is often found in a
conserved YXXXK pattern. In addition to the Tyr and Lys,
there is often an upstream Ser (Ser-138, 15-PGDH
numbering) and/or an Asn (Asn-107, 15-PGDH numbering) or
additional Ser, contributing to the active site.
Substrates for these enzymes include sugars, steroids,
alcohols, and aromatic compounds. The standard reaction
mechanism is a proton relay involving the conserved Tyr
and Lys, as well as Asn (or Ser). Some SDR family
members, including 17 beta-hydroxysteroid dehydrogenase
contain an additional helix-turn-helix motif that is not
generally found among SDRs.
Length = 246
Score = 34.4 bits (79), Expect = 0.100
Identities = 16/50 (32%), Positives = 28/50 (56%), Gaps = 2/50 (4%)
Query: 368 KIFVLVGAG-GAGRALAFGAKSRGARVII-FNRNYERAKALADAVSGEAL 415
++ ++ GA G G A+A GARV++ + R+ E A+A+A A+
Sbjct: 1 QVVLVTGASRGLGAAIARSFAREGARVVVNYYRSTESAEAVAAEAGERAI 50
>gnl|CDD|168574 PRK06484, PRK06484, short chain dehydrogenase; Validated.
Length = 520
Score = 34.8 bits (80), Expect = 0.12
Identities = 25/89 (28%), Positives = 41/89 (46%), Gaps = 15/89 (16%)
Query: 374 GAGGAGRALAFGAKSRGARVIIFNRNYERAKALADAVSGEALH--------------FEY 419
GA G GRA+A + G R++I +R+ E AK LA+A+ E L F
Sbjct: 277 GARGIGRAVADRFAAAGDRLLIIDRDAEGAKKLAEALGDEHLSVQADITDEAAVESAFAQ 336
Query: 420 LHEFFPEKGMILANASAIG-MEPNSDQSP 447
+ + +++ NA +P+ +QS
Sbjct: 337 IQARWGRLDVLVNNAGIAEVFKPSLEQSA 365
Score = 29.0 bits (65), Expect = 7.8
Identities = 29/95 (30%), Positives = 40/95 (42%), Gaps = 16/95 (16%)
Query: 369 IFVLVGAGGAGRALAFGAKSRGARVIIFNRNYERAKALADA-----------VSGEAL-- 415
+ V AGG GRA G +V++ +RN ERA+ AD+ VS EA
Sbjct: 8 VLVTGAAGGIGRAACQRFARAGDQVVVADRNVERARERADSLGPDHHALAMDVSDEAQIR 67
Query: 416 -HFEYLHEFFPEKGMILANASAIG--MEPNSDQSP 447
FE LH F +++ NA M D +
Sbjct: 68 EGFEQLHREFGRIDVLVNNAGVTDPTMTATLDTTL 102
>gnl|CDD|235488 PRK05476, PRK05476, S-adenosyl-L-homocysteine hydrolase;
Provisional.
Length = 425
Score = 34.7 bits (81), Expect = 0.12
Identities = 14/31 (45%), Positives = 19/31 (61%)
Query: 365 IAGKIFVLVGAGGAGRALAFGAKSRGARVII 395
IAGK+ V+ G G G+ A + GARVI+
Sbjct: 210 IAGKVVVVAGYGDVGKGCAQRLRGLGARVIV 240
>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 = 34.2 bits (79), Expect = 0.12
Identities = 14/46 (30%), Positives = 24/46 (52%), Gaps = 1/46 (2%)
Query: 367 GKIFVLVGAGGA-GRALAFGAKSRGARVIIFNRNYERAKALADAVS 411
KI ++ GA G G+A S GAR+I+ + N + L + ++
Sbjct: 2 DKIILITGAAGLIGKAFCKALLSAGARLILADINAPALEQLKEELT 47
>gnl|CDD|187643 cd08939, KDSR-like_SDR_c, 3-ketodihydrosphingosine reductase (KDSR)
and related proteins, classical (c) SDR. These proteins
include members identified as KDSR, ribitol type
dehydrogenase, and others. The group shows strong
conservation of the active site tetrad and glycine rich
NAD-binding motif of the classical SDRs. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold (alpha/beta folding pattern with a central
beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRs are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes catalyze a
wide range of activities including the metabolism of
steroids, cofactors, carbohydrates, lipids, aromatic
compounds, and amino acids, and act in redox sensing.
Classical SDRs have an TGXXX[AG]XG cofactor binding
motif and a YXXXK active site motif, with the Tyr
residue of the active site motif serving as a critical
catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 239
Score = 34.2 bits (79), Expect = 0.12
Identities = 16/51 (31%), Positives = 24/51 (47%), Gaps = 1/51 (1%)
Query: 367 GKIFVLVGAG-GAGRALAFGAKSRGARVIIFNRNYERAKALADAVSGEALH 416
GK ++ G G G+ALA GA VII R+ + + + + EA
Sbjct: 1 GKHVLITGGSSGIGKALAKELVKEGANVIIVARSESKLEEAVEEIEAEANA 51
>gnl|CDD|180723 PRK06841, PRK06841, short chain dehydrogenase; Provisional.
Length = 255
Score = 34.2 bits (79), Expect = 0.13
Identities = 18/55 (32%), Positives = 31/55 (56%), Gaps = 1/55 (1%)
Query: 364 PIAGKIFVLVG-AGGAGRALAFGAKSRGARVIIFNRNYERAKALADAVSGEALHF 417
++GK+ V+ G A G G A+A ++GARV + +R+ + A+ A + G A
Sbjct: 12 DLSGKVAVVTGGASGIGHAIAELFAAKGARVALLDRSEDVAEVAAQLLGGNAKGL 66
>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 = 33.9 bits (78), Expect = 0.13
Identities = 18/57 (31%), Positives = 31/57 (54%), Gaps = 5/57 (8%)
Query: 365 IAGKIFVLVGAG---GAGRALAFGAKSRGARVIIFNRNYERAKALADAVSGEALHFE 418
+ GK+ ++ GAG G G A F + GARV+I + N + A+ +A + A+ +
Sbjct: 3 LEGKVAIVTGAGSGFGEGIARRFAQE--GARVVIADINADGAERVAADIGEAAIAIQ 57
>gnl|CDD|130194 TIGR01124, ilvA_2Cterm, threonine ammonia-lyase, biosynthetic, long
form. This model describes a form of threonine
ammonia-lyase, a pyridoxal-phosphate dependent enzyme,
with two copies of the threonine dehydratase C-terminal
domain (pfam00585). Members with known function
participate in isoleucine biosynthesis and are inhibited
by isoleucine. Alternate name: threonine deaminase,
threonine dehydratase. Forms scoring between the trusted
and noise cutoff tend to branch with this subgroup of
threonine ammonia-lyase phylogenetically but have only a
single copy of the C-terminal domain [Amino acid
biosynthesis, Pyruvate family].
Length = 499
Score = 34.3 bits (79), Expect = 0.14
Identities = 26/122 (21%), Positives = 50/122 (40%), Gaps = 26/122 (21%)
Query: 387 KSRGARVIIFNRNYERAKALADAVSGEALHFEYLHEFFPEKGMILANASAIGMEPNSDQS 446
+ G V++ N++ AKA A +S E ++H F + +++A + +
Sbjct: 108 RGFGGEVVLHGANFDDAKAKAIELSQEK-GLTFIHPF--DDPLVIAGQGTLAL------- 157
Query: 447 PVPKEALKAYELVFDAVYTPRNTRLLREAAEVGATVVSGVEMFIRQALGQFRLFTGGLAP 506
E L+ DAV+ P G + +GV I+Q + + ++ G+ P
Sbjct: 158 ----EILRQVANPLDAVFVPVG----------GGGLAAGVAALIKQLMPEIKVI--GVEP 201
Query: 507 ED 508
D
Sbjct: 202 TD 203
>gnl|CDD|235924 PRK07063, PRK07063, short chain dehydrogenase; Provisional.
Length = 260
Score = 33.9 bits (78), Expect = 0.14
Identities = 15/47 (31%), Positives = 25/47 (53%), Gaps = 1/47 (2%)
Query: 365 IAGKIFVLVGAG-GAGRALAFGAKSRGARVIIFNRNYERAKALADAV 410
+AGK+ ++ GA G G A+A GA V + + + A+ A A+
Sbjct: 5 LAGKVALVTGAAQGIGAAIARAFAREGAAVALADLDAALAERAAAAI 51
>gnl|CDD|131680 TIGR02632, RhaD_aldol-ADH, rhamnulose-1-phosphate aldolase/alcohol
dehydrogenase.
Length = 676
Score = 34.4 bits (79), Expect = 0.15
Identities = 19/51 (37%), Positives = 30/51 (58%), Gaps = 1/51 (1%)
Query: 364 PIAGK-IFVLVGAGGAGRALAFGAKSRGARVIIFNRNYERAKALADAVSGE 413
+A + FV GAGG GR A + GA V++ + N E A+A+A ++G+
Sbjct: 411 TLARRVAFVTGGAGGIGRETARRLAAEGAHVVLADLNLEAAEAVAAEINGQ 461
>gnl|CDD|198065 smart00997, AdoHcyase_NAD, S-adenosyl-L-homocysteine hydrolase, NAD
binding domain.
Length = 162
Score = 32.8 bits (76), Expect = 0.17
Identities = 13/31 (41%), Positives = 19/31 (61%)
Query: 365 IAGKIFVLVGAGGAGRALAFGAKSRGARVII 395
+AGK V+ G G G+ +A + GARVI+
Sbjct: 21 LAGKNVVVAGYGDVGKGVAARLRGLGARVIV 51
>gnl|CDD|223981 COG1053, SdhA, Succinate dehydrogenase/fumarate reductase,
flavoprotein subunit [Energy production and conversion].
Length = 562
Score = 34.3 bits (79), Expect = 0.17
Identities = 12/42 (28%), Positives = 19/42 (45%)
Query: 371 VLVGAGGAGRALAFGAKSRGARVIIFNRNYERAKALADAVSG 412
V++G GGAG A A G +V + ++ + A G
Sbjct: 10 VVIGGGGAGLRAAIEAAEAGLKVALLSKAPPKRGHTVAAQGG 51
>gnl|CDD|240645 cd12168, Mand_dh_like, D-Mandelate Dehydrogenase-like
dehydrogenases. D-Mandelate dehydrogenase (D-ManDH),
identified as an enzyme that interconverts
benzoylformate and D-mandelate, is a D-2-hydroxyacid
dehydrogenase family member that catalyzes the
conversion of c3-branched 2-ketoacids. D-ManDH exhibits
broad substrate specificities for 2-ketoacids with large
hydrophobic side chains, particularly those with
C3-branched side chains. 2-hydroxyacid dehydrogenases
catalyze the conversion of a wide variety of D-2-hydroxy
acids to their corresponding keto acids. The general
mechanism is (R)-lactate + acceptor to pyruvate +
reduced acceptor. Glycerate dehydrogenase catalyzes the
reaction (R)-glycerate + NAD+ to hydroxypyruvate + NADH
+ H+. Formate/glycerate and related dehydrogenases of
the D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain.
Length = 321
Score = 33.7 bits (78), Expect = 0.18
Identities = 24/72 (33%), Positives = 36/72 (50%), Gaps = 8/72 (11%)
Query: 342 ISAIEDALRE---RQGINGVASHTSPIAGKIFVLVGAGGAGRALAFGAKSRGARVIIFNR 398
S E + R R ++ +H P GK ++G GG G+A+A A + G ++I NR
Sbjct: 128 FSRAERSARAGKWRGFLDLTLAH-DP-RGKTLGILGLGGIGKAIARKAAAFGMKIIYHNR 185
Query: 399 N---YERAKALA 407
+ E KALA
Sbjct: 186 SRLPEELEKALA 197
>gnl|CDD|223377 COG0300, DltE, Short-chain dehydrogenases of various substrate
specificities [General function prediction only].
Length = 265
Score = 33.8 bits (78), Expect = 0.18
Identities = 16/51 (31%), Positives = 26/51 (50%), Gaps = 1/51 (1%)
Query: 364 PIAGKIFVLVGA-GGAGRALAFGAKSRGARVIIFNRNYERAKALADAVSGE 413
P+ GK ++ GA G G LA RG +I+ R ++ +ALA + +
Sbjct: 3 PMKGKTALITGASSGIGAELAKQLARRGYNLILVARREDKLEALAKELEDK 53
>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 = 33.6 bits (77), Expect = 0.19
Identities = 16/58 (27%), Positives = 26/58 (44%), Gaps = 4/58 (6%)
Query: 365 IAGKIFVLVGAGGA-GRALAFGAKSRGARVIIFNRNYERAKALADAVS---GEALHFE 418
+ K+ V+ G G G A+A GA+V RN E+ +A ++ G A+
Sbjct: 3 LKNKVAVITGGTGVLGGAMARALAQAGAKVAALGRNQEKGDKVAKEITALGGRAIALA 60
>gnl|CDD|235608 PRK05786, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 238
Score = 33.2 bits (76), Expect = 0.23
Identities = 15/41 (36%), Positives = 23/41 (56%), Gaps = 1/41 (2%)
Query: 367 GKIFVLVGAG-GAGRALAFGAKSRGARVIIFNRNYERAKAL 406
GK ++G G G A+A+ A GA+V I +RN + K +
Sbjct: 5 GKKVAIIGVSEGLGYAVAYFALKEGAQVCINSRNENKLKRM 45
>gnl|CDD|236094 PRK07774, PRK07774, short chain dehydrogenase; Provisional.
Length = 250
Score = 33.2 bits (76), Expect = 0.23
Identities = 15/49 (30%), Positives = 26/49 (53%), Gaps = 1/49 (2%)
Query: 366 AGKIFVLVGA-GGAGRALAFGAKSRGARVIIFNRNYERAKALADAVSGE 413
K+ ++ GA GG G+A A GA V++ + N E A+ +A + +
Sbjct: 5 DDKVAIVTGAAGGIGQAYAEALAREGASVVVADINAEGAERVAKQIVAD 53
>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 = 32.9 bits (75), Expect = 0.25
Identities = 17/50 (34%), Positives = 27/50 (54%), Gaps = 1/50 (2%)
Query: 365 IAGKIFVLVGAG-GAGRALAFGAKSRGARVIIFNRNYERAKALADAVSGE 413
+ +I ++ GA G GR A GA VI+ RN E+ + +AD ++ E
Sbjct: 2 LNDRIILVTGASDGIGREAALTYARYGATVILLGRNEEKLRQVADHINEE 51
>gnl|CDD|133449 cd05191, NAD_bind_amino_acid_DH, NAD(P) binding domain of amino
acid dehydrogenase-like proteins. Amino acid
dehydrogenase(DH)-like NAD(P)-binding domains are
members of the Rossmann fold superfamily and are found
in glutamate, leucine, and phenylalanine DHs (DHs),
methylene tetrahydrofolate DH,
methylene-tetrahydromethanopterin DH,
methylene-tetrahydropholate DH/cyclohydrolase, Shikimate
DH-like proteins, malate oxidoreductases, and glutamyl
tRNA reductase. Amino acid DHs catalyze the deamination
of amino acids to keto acids with NAD(P)+ as a cofactor.
The NAD(P)-binding Rossmann fold superfamily includes a
wide variety of protein families including NAD(P)-
binding domains of alcohol DHs, tyrosine-dependent
oxidoreductases, glyceraldehyde-3-phosphate DH,
lactate/malate DHs, formate/glycerate DHs, siroheme
synthases, 6-phosphogluconate DH, amino acid DHs,
repressor rex, NAD-binding potassium channel domain,
CoA-binding, and ornithine cyclodeaminase-like domains.
These domains have an alpha-beta-alpha configuration.
NAD binding involves numerous hydrogen and van der Waals
contacts.
Length = 86
Score = 30.8 bits (70), Expect = 0.28
Identities = 12/36 (33%), Positives = 21/36 (58%), Gaps = 1/36 (2%)
Query: 364 PIAGKIFVLVGAGGAGRALA-FGAKSRGARVIIFNR 398
+ GK V++GAG G+ +A A G +V++ +R
Sbjct: 20 SLKGKTVVVLGAGEVGKGIAKLLADEGGKKVVLCDR 55
>gnl|CDD|235962 PRK07201, PRK07201, short chain dehydrogenase; Provisional.
Length = 657
Score = 33.4 bits (77), Expect = 0.29
Identities = 17/48 (35%), Positives = 23/48 (47%), Gaps = 1/48 (2%)
Query: 364 PIAGKIFVLVGA-GGAGRALAFGAKSRGARVIIFNRNYERAKALADAV 410
P+ GK+ ++ GA G GRA A GA V + RN E L +
Sbjct: 368 PLVGKVVLITGASSGIGRATAIKVAEAGATVFLVARNGEALDELVAEI 415
>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 = 32.1 bits (74), Expect = 0.30
Identities = 16/61 (26%), Positives = 22/61 (36%), Gaps = 1/61 (1%)
Query: 366 AGKIFVLVGAGGAGRALAFGAKSRGARVIIFNRNYERAKALADAVSGEALHFEYLHEFFP 425
K+ V+ GAG G A AK GA V + + R + L + E
Sbjct: 20 PAKVVVI-GAGVVGLGAAATAKGLGAEVTVLDVRPARLRQLESLLGARFTTLYSQAELLE 78
Query: 426 E 426
E
Sbjct: 79 E 79
>gnl|CDD|176220 cd08259, Zn_ADH5, Alcohol dehydrogenases of the MDR family.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. This group contains proteins that
share the characteristic catalytic and structural
zinc-binding sites of the zinc-dependent alcohol
dehydrogenase family. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which have a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES. These
proteins typically form dimers (typically higher plants,
mammals) or tetramers (yeast, bacteria), and have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. NAD(H)-binding occurs in the cleft
between the catalytic and coenzyme-binding domains at
the active site, and coenzyme binding induces a
conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
In human ADH catalysis, the zinc ion helps coordinate
the alcohol, followed by deprotonation of a histidine
(His-51), the ribose of NAD, a serine (Ser-48), then the
alcohol, which allows the transfer of a hydride to NAD+,
creating NADH and a zinc-bound aldehyde or ketone. In
yeast and some bacteria, the active site zinc binds an
aldehyde, polarizing it, and leading to the reverse
reaction.
Length = 332
Score = 33.1 bits (76), Expect = 0.30
Identities = 20/49 (40%), Positives = 25/49 (51%), Gaps = 5/49 (10%)
Query: 367 GKIFVLVGAGGA-GRALAFGAKSRGARVIIFNRNYERAKAL----ADAV 410
G ++ GAGG G AK+ GARVI R+ E+ K L AD V
Sbjct: 163 GDTVLVTGAGGGVGIHAIQLAKALGARVIAVTRSPEKLKILKELGADYV 211
>gnl|CDD|223774 COG0702, COG0702, Predicted nucleoside-diphosphate-sugar epimerases
[Cell envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 275
Score = 33.0 bits (75), Expect = 0.32
Identities = 17/45 (37%), Positives = 19/45 (42%)
Query: 367 GKIFVLVGAGGAGRALAFGAKSRGARVIIFNRNYERAKALADAVS 411
KI V G G A+ +RG V RN E A ALA V
Sbjct: 1 MKILVTGATGFVGGAVVRELLARGHEVRAAVRNPEAAAALAGGVE 45
>gnl|CDD|183489 PRK12384, PRK12384, sorbitol-6-phosphate dehydrogenase;
Provisional.
Length = 259
Score = 32.7 bits (75), Expect = 0.32
Identities = 14/48 (29%), Positives = 24/48 (50%), Gaps = 1/48 (2%)
Query: 367 GKIFVLVGAG-GAGRALAFGAKSRGARVIIFNRNYERAKALADAVSGE 413
++ V++G G G L G G RV + + N E+A +A ++ E
Sbjct: 2 NQVAVVIGGGQTLGAFLCHGLAEEGYRVAVADINSEKAANVAQEINAE 49
>gnl|CDD|237220 PRK12828, PRK12828, short chain dehydrogenase; Provisional.
Length = 239
Score = 32.8 bits (75), Expect = 0.34
Identities = 18/51 (35%), Positives = 23/51 (45%), Gaps = 1/51 (1%)
Query: 367 GKIFVLVGA-GGAGRALAFGAKSRGARVIIFNRNYERAKALADAVSGEALH 416
GK+ + G GG GRA A +RGARV + R V +AL
Sbjct: 7 GKVVAITGGFGGLGRATAAWLAARGARVALIGRGAAPLSQTLPGVPADALR 57
>gnl|CDD|181517 PRK08642, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 253
Score = 32.8 bits (75), Expect = 0.35
Identities = 18/48 (37%), Positives = 30/48 (62%), Gaps = 3/48 (6%)
Query: 371 VLV--GAGGAGRALAFGAKSRGARVII-FNRNYERAKALADAVSGEAL 415
VLV G+ G G A+A GARV++ ++++ + A+ALAD + A+
Sbjct: 8 VLVTGGSRGLGAAIARAFAREGARVVVNYHQSEDAAEALADELGDRAI 55
>gnl|CDD|109716 pfam00670, AdoHcyase_NAD, S-adenosyl-L-homocysteine hydrolase, NAD
binding domain.
Length = 162
Score = 31.9 bits (73), Expect = 0.36
Identities = 15/31 (48%), Positives = 20/31 (64%)
Query: 365 IAGKIFVLVGAGGAGRALAFGAKSRGARVII 395
IAGK+ V+ G G G+ A K +GARVI+
Sbjct: 21 IAGKVAVVCGYGDVGKGCAASLKGQGARVIV 51
>gnl|CDD|180371 PRK06057, PRK06057, short chain dehydrogenase; Provisional.
Length = 255
Score = 32.8 bits (75), Expect = 0.39
Identities = 19/49 (38%), Positives = 28/49 (57%), Gaps = 1/49 (2%)
Query: 365 IAGKIFVLVGAG-GAGRALAFGAKSRGARVIIFNRNYERAKALADAVSG 412
+AG++ V+ G G G G A A + GA V++ + + E KA AD V G
Sbjct: 5 LAGRVAVITGGGSGIGLATARRLAAEGATVVVGDIDPEAGKAAADEVGG 53
>gnl|CDD|187609 cd05351, XR_like_SDR_c, xylulose reductase-like, classical (c)
SDRs. Members of this subgroup include proteins
identified as L-xylulose reductase (XR) and carbonyl
reductase; they are members of the SDR family. XR,
catalyzes the NADP-dependent reduction of L-xyulose and
other sugars. Tetrameric mouse carbonyl reductase is
involved in the metabolism of biogenic and xenobiotic
carbonyl compounds. This subgroup also includes
tetrameric chicken liver D-erythrulose reductase, which
catalyzes the reduction of D-erythrulose to D-threitol.
SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold (alpha/beta folding
pattern with a central beta-sheet), an NAD(P)(H)-binding
region, and a structurally diverse C-terminal region.
Classical SDRs are typically about 250 residues long,
while extended SDRS are approximately 350 residues.
Sequence identity between different SDR enzymes are
typically in the 15-30% range, but the enzymes share the
Rossmann fold NAD-binding motif and characteristic
NAD-binding and catalytic sequence patterns. These
enzymes have a 3-glycine N-terminal NAD(P)(H)-binding
pattern (typically, TGxxxGxG in classical SDRs and
TGxxGxxG in extended SDRs), while substrate binding is
in the C-terminal region. A critical catalytic Tyr
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) numbering), is often found in a
conserved YXXXK pattern. In addition to the Tyr and Lys,
there is often an upstream Ser (Ser-138, 15-PGDH
numbering) and/or an Asn (Asn-107, 15-PGDH numbering) or
additional Ser, contributing to the active site.
Substrates for these enzymes include sugars, steroids,
alcohols, and aromatic compounds. The standard reaction
mechanism is a proton relay involving the conserved Tyr
and Lys, as well as Asn (or Ser).
Length = 244
Score = 32.4 bits (74), Expect = 0.42
Identities = 16/43 (37%), Positives = 21/43 (48%), Gaps = 1/43 (2%)
Query: 366 AGKIFVLVGAG-GAGRALAFGAKSRGARVIIFNRNYERAKALA 407
AGK ++ GAG G GRA GARV+ +R +L
Sbjct: 6 AGKRALVTGAGKGIGRATVKALAKAGARVVAVSRTQADLDSLV 48
>gnl|CDD|240258 PTZ00075, PTZ00075, Adenosylhomocysteinase; Provisional.
Length = 476
Score = 32.7 bits (75), Expect = 0.44
Identities = 13/31 (41%), Positives = 18/31 (58%)
Query: 365 IAGKIFVLVGAGGAGRALAFGAKSRGARVII 395
IAGK V+ G G G+ A + GARV++
Sbjct: 252 IAGKTVVVCGYGDVGKGCAQALRGFGARVVV 282
>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 = 32.4 bits (74), Expect = 0.47
Identities = 16/50 (32%), Positives = 25/50 (50%), Gaps = 1/50 (2%)
Query: 367 GKIFVLVGAG-GAGRALAFGAKSRGARVIIFNRNYERAKALADAVSGEAL 415
GK ++ GA G G+ A RGARVI+ R+ + + A + + L
Sbjct: 1 GKTVIITGANTGIGKETARELARRGARVIMACRDMAKCEEAAAEIRRDTL 50
>gnl|CDD|223959 COG1028, FabG, Dehydrogenases with different specificities (related
to short-chain alcohol dehydrogenases) [Secondary
metabolites biosynthesis, transport, and catabolism /
General function prediction only].
Length = 251
Score = 32.5 bits (74), Expect = 0.48
Identities = 17/44 (38%), Positives = 25/44 (56%), Gaps = 1/44 (2%)
Query: 365 IAGKIFVLVGAG-GAGRALAFGAKSRGARVIIFNRNYERAKALA 407
++GK+ ++ GA G GRA+A GARV++ R E A A
Sbjct: 3 LSGKVALVTGASSGIGRAIARALAREGARVVVAARRSEEEAAEA 46
>gnl|CDD|235800 PRK06436, PRK06436, glycerate dehydrogenase; Provisional.
Length = 303
Score = 32.5 bits (74), Expect = 0.50
Identities = 14/41 (34%), Positives = 22/41 (53%)
Query: 360 SHTSPIAGKIFVLVGAGGAGRALAFGAKSRGARVIIFNRNY 400
S T + K ++G GG GR +A AK+ G + + R+Y
Sbjct: 115 SPTKLLYNKSLGILGYGGIGRRVALLAKAFGMNIYAYTRSY 155
>gnl|CDD|180446 PRK06180, PRK06180, short chain dehydrogenase; Provisional.
Length = 277
Score = 32.2 bits (74), Expect = 0.51
Identities = 15/50 (30%), Positives = 21/50 (42%), Gaps = 1/50 (2%)
Query: 367 GKIFVLVGAG-GAGRALAFGAKSRGARVIIFNRNYERAKALADAVSGEAL 415
K +++ G G GRALA A + G RV+ R+ AL
Sbjct: 4 MKTWLITGVSSGFGRALAQAALAAGHRVVGTVRSEAARADFEALHPDRAL 53
>gnl|CDD|237008 PRK11880, PRK11880, pyrroline-5-carboxylate reductase; Reviewed.
Length = 267
Score = 32.0 bits (74), Expect = 0.52
Identities = 11/45 (24%), Positives = 20/45 (44%), Gaps = 3/45 (6%)
Query: 368 KIFVLVGAGGAGRALAFGAKSRG---ARVIIFNRNYERAKALADA 409
K +G G A+ G + G +I+ + + E+ ALA+
Sbjct: 3 KKIGFIGGGNMASAIIGGLLASGVPAKDIIVSDPSPEKRAALAEE 47
>gnl|CDD|236209 PRK08265, PRK08265, short chain dehydrogenase; Provisional.
Length = 261
Score = 32.3 bits (74), Expect = 0.53
Identities = 18/57 (31%), Positives = 30/57 (52%), Gaps = 2/57 (3%)
Query: 362 TSPIAGKIFVLVG-AGGAGRALAFGAKSRGARVIIFNRNYERAKALADAVSGEALHF 417
+AGK+ ++ G A G A+A + GARV I + + + A+A ++ GE F
Sbjct: 1 MIGLAGKVAIVTGGATLIGAAVARALVAAGARVAIVDIDADNGAAVAASL-GERARF 56
>gnl|CDD|217563 pfam03446, NAD_binding_2, NAD binding domain of 6-phosphogluconate
dehydrogenase. The NAD binding domain of
6-phosphogluconate dehydrogenase adopts a Rossmann fold.
Length = 163
Score = 31.7 bits (73), Expect = 0.54
Identities = 10/38 (26%), Positives = 16/38 (42%)
Query: 372 LVGAGGAGRALAFGAKSRGARVIIFNRNYERAKALADA 409
+G G G +A G V ++NR E+ + L
Sbjct: 5 FIGLGVMGSPMALNLLKAGYTVTVYNRTPEKVEELVAE 42
>gnl|CDD|187540 cd05229, SDR_a3, atypical (a) SDRs, subgroup 3. These atypical SDR
family members of unknown function have a glycine-rich
NAD(P)-binding motif consensus that is very similar to
the extended SDRs, GXXGXXG. Generally, this group has
poor conservation of the active site tetrad, However,
individual sequences do contain matches to the YXXXK
active site motif, and generally Tyr or Asn in place of
the upstream Ser found in most SDRs. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Atypical SDRs include
biliverdin IX beta reductase (BVR-B,aka flavin
reductase), NMRa (a negative transcriptional regulator
of various fungi), progesterone 5-beta-reductase like
proteins, phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they 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 numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, 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. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, 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.
Length = 302
Score = 32.3 bits (74), Expect = 0.55
Identities = 13/47 (27%), Positives = 24/47 (51%), Gaps = 2/47 (4%)
Query: 371 VLVGAGGAGRALAFGAKSRGARVIIFNRNYERAKAL--ADAVSGEAL 415
VL +G GR +A + RG V + +R+ + L + V+ +A+
Sbjct: 4 VLGASGPIGREVARELRRRGWDVRLVSRSGSKLAWLPGVEIVAADAM 50
>gnl|CDD|132745 cd06947, NR_LBD_GR_Like, Ligand binding domain of nuclear hormone
receptors:glucocorticoid receptor, mineralocorticoid
receptor , progesterone receptor, and androgen receptor.
The ligand binding domain of GR_like nuclear receptors:
This family of NRs includes four distinct, but closely
related nuclear hormone receptors: glucocorticoid
receptor (GR), mineralocorticoid receptor (MR),
progesterone receptor (PR), and androgen receptor (AR).
These four receptors play key roles in some of the most
fundamental physiological functions such as the stress
response, metabolism, electrolyte homeostasis, immune
function, growth, development, and reproduction. The NRs
in this family use multiple signaling pathways and share
similar functional mechanisms. The dominant signaling
pathway is via direct DNA binding and transcriptional
regulation of target genes. Another mechanism is via
protein-protein interactions, mainly with other
transcription factors such as nuclear factor-kappaB and
activator protein-1, to regulate gene expression
patterns. Both pathways can up-regulate or down-regulate
gene expression and require ligand activation of the
receptor and recruitment of other cofactors such as
chaperone proteins and coregulator proteins. Like other
members of the nuclear receptor (NR) superfamily of
ligand-activated transcription factors, GR, MR, PR, and
AR share the same modular structure with a central well
conserved DNA binding domain (DBD), a variable
N-terminal domain, a flexible hinge and a C-terminal
ligand binding domain (LBD).
Length = 246
Score = 31.9 bits (73), Expect = 0.55
Identities = 23/103 (22%), Positives = 34/103 (33%), Gaps = 22/103 (21%)
Query: 41 CIDSMEFSHISEVDKLIQ-HPTLPAIVSYR------LKSSRKSSDEACKNTCLQVLRRAL 93
D M ++I E+ K I + R L S + C ++
Sbjct: 155 AFDEMRMNYIKELRKAIVKREKNSSQSWQRFYQLTKLLDSMHDLVKNLLQFCFYTFIQSH 214
Query: 94 DLDVEFVEMDYEVASDPLMSEIIYSRSNTKIIVSSYLNGGGKP 136
L VEF EM + EII + + L+G KP
Sbjct: 215 ALSVEFPEM---------LVEIISDQ------LPKVLSGNVKP 242
>gnl|CDD|235925 PRK07067, PRK07067, sorbitol dehydrogenase; Provisional.
Length = 257
Score = 32.3 bits (74), Expect = 0.55
Identities = 18/50 (36%), Positives = 27/50 (54%), Gaps = 1/50 (2%)
Query: 367 GKIFVLVG-AGGAGRALAFGAKSRGARVIIFNRNYERAKALADAVSGEAL 415
GK+ +L G A G G A+A + GARV+I + RA+ A + A+
Sbjct: 6 GKVALLTGAASGIGEAVAERYLAEGARVVIADIKPARARLAALEIGPAAI 55
>gnl|CDD|187605 cd05347, Ga5DH-like_SDR_c, gluconate 5-dehydrogenase (Ga5DH)-like,
classical (c) SDRs. Ga5DH catalyzes the NADP-dependent
conversion of carbon source D-gluconate and
5-keto-D-gluconate. This SDR subgroup has a classical
Gly-rich NAD(P)-binding motif and a conserved active
site tetrad pattern. However, it has been proposed that
Arg104 (Streptococcus suis Ga5DH numbering), as well as
an active site Ca2+, play a critical role in catalysis.
In addition to Ga5DHs this subgroup contains Erwinia
chrysanthemi KduD which is involved in pectin
degradation, and is a putative
2,5-diketo-3-deoxygluconate dehydrogenase. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold (alpha/beta folding pattern with a central
beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRs are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes catalyze a
wide range of activities including the metabolism of
steroids, cofactors, carbohydrates, lipids, aromatic
compounds, and amino acids, and act in redox sensing.
Classical SDRs have an TGXXX[AG]XG cofactor binding
motif and a YXXXK active site motif, with the Tyr
residue of the active site motif serving as a critical
catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107,15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 248
Score = 31.9 bits (73), Expect = 0.56
Identities = 16/57 (28%), Positives = 28/57 (49%), Gaps = 1/57 (1%)
Query: 365 IAGKIFVLVGAG-GAGRALAFGAKSRGARVIIFNRNYERAKALADAVSGEALHFEYL 420
+ GK+ ++ GA G G +A G GA ++I +RN E+A+ + E +
Sbjct: 3 LKGKVALVTGASRGIGFGIASGLAEAGANIVINSRNEEKAEEAQQLIEKEGVEATAF 59
>gnl|CDD|183778 PRK12829, PRK12829, short chain dehydrogenase; Provisional.
Length = 264
Score = 32.0 bits (73), Expect = 0.61
Identities = 17/57 (29%), Positives = 25/57 (43%), Gaps = 1/57 (1%)
Query: 361 HTSPIAGK-IFVLVGAGGAGRALAFGAKSRGARVIIFNRNYERAKALADAVSGEALH 416
P+ G + V GA G GRA+A GARV + + + A A + G +
Sbjct: 5 LLKPLDGLRVLVTGGASGIGRAIAEAFAEAGARVHVCDVSEAALAATAARLPGAKVT 61
>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 = 0.66
Identities = 17/57 (29%), Positives = 30/57 (52%), Gaps = 4/57 (7%)
Query: 370 FVLVGAGGAGRALAFGAKSRGARVIIFNRNYERAKALAD----AVSGEALHFEYLHE 422
+++G G GR+LA + G V++ +++ ER + L + V G+A E L E
Sbjct: 1 IIIIGYGRVGRSLAEELREGGPDVVVIDKDPERVEELREEGVPVVVGDATDEEVLEE 57
>gnl|CDD|181136 PRK07825, PRK07825, short chain dehydrogenase; Provisional.
Length = 273
Score = 31.8 bits (73), Expect = 0.68
Identities = 15/48 (31%), Positives = 21/48 (43%), Gaps = 1/48 (2%)
Query: 363 SPIAGKIFVLVGAG-GAGRALAFGAKSRGARVIIFNRNYERAKALADA 409
+ GK+ + G G G A A + GARV I + + AK A
Sbjct: 1 DDLRGKVVAITGGARGIGLATARALAALGARVAIGDLDEALAKETAAE 48
>gnl|CDD|223992 COG1064, AdhP, Zn-dependent alcohol dehydrogenases [General
function prediction only].
Length = 339
Score = 32.2 bits (74), Expect = 0.71
Identities = 18/47 (38%), Positives = 22/47 (46%), Gaps = 1/47 (2%)
Query: 361 HTSPIAGKIFVLVGAGGAGRALAFGAKSRGARVIIFNRNYERAKALA 407
+ GK +VGAGG G AK+ GA VI R+ E LA
Sbjct: 161 KANVKPGKWVAVVGAGGLGHMAVQYAKAMGAEVIAITRS-EEKLELA 206
>gnl|CDD|176229 cd08268, MDR2, Medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
This group is a member of the medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, but lacks the zinc-binding
sites of the zinc-dependent alcohol dehydrogenases. The
medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P)-binding Rossmann fold domain of 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 = 328
Score = 31.8 bits (73), Expect = 0.76
Identities = 29/119 (24%), Positives = 39/119 (32%), Gaps = 23/119 (19%)
Query: 370 FVLVGA--GGAGRALAFGAKSRGARVIIFNRNYERAKALADAVSGEALHFEYLHEFFPEK 427
VL+ A G A A + GA VI R E+ AL G A E +
Sbjct: 147 SVLITAASSSVGLAAIQIANAAGATVIATTRTSEKRDALLAL--GAAHVIVTDEEDLVAE 204
Query: 428 GMILANASAIGMEPNSDQSPVPKEALKAYELVFDAVYTPRNTRLLREAAEVGATVVSGV 486
+ + K ++VFD V P+ +L A G VV G
Sbjct: 205 VLRITGG-------------------KGVDVVFDPVGGPQFAKLADALAPGGTLVVYGA 244
>gnl|CDD|235914 PRK07041, PRK07041, short chain dehydrogenase; Provisional.
Length = 230
Score = 31.5 bits (72), Expect = 0.77
Identities = 19/44 (43%), Positives = 26/44 (59%)
Query: 371 VLVGAGGAGRALAFGAKSRGARVIIFNRNYERAKALADAVSGEA 414
V+ G+ G G ALA + GARV I +R+ +R A A A+ G A
Sbjct: 2 VVGGSSGIGLALARAFAAEGARVTIASRSRDRLAAAARALGGGA 45
>gnl|CDD|180462 PRK06198, PRK06198, short chain dehydrogenase; Provisional.
Length = 260
Score = 31.5 bits (72), Expect = 0.77
Identities = 16/48 (33%), Positives = 25/48 (52%), Gaps = 2/48 (4%)
Query: 363 SPIAGKIFVLVGAG-GAGRALAFGAKSRGAR-VIIFNRNYERAKALAD 408
+ GK+ ++ G G G A+A RGA ++I RN E+ +A A
Sbjct: 2 GRLDGKVALVTGGTQGLGAAIARAFAERGAAGLVICGRNAEKGEAQAA 49
>gnl|CDD|235726 PRK06181, PRK06181, short chain dehydrogenase; Provisional.
Length = 263
Score = 31.5 bits (72), Expect = 0.81
Identities = 21/53 (39%), Positives = 31/53 (58%), Gaps = 4/53 (7%)
Query: 367 GKIFVLVGA-GGAGRALAFGAKSRGARVIIFNRNYERAKALADAVS---GEAL 415
GK+ ++ GA G GRALA GA++++ RN R +LA ++ GEAL
Sbjct: 1 GKVVIITGASEGIGRALAVRLARAGAQLVLAARNETRLASLAQELADHGGEAL 53
>gnl|CDD|187593 cd05332, 11beta-HSD1_like_SDR_c, 11beta-hydroxysteroid
dehydrogenase type 1 (11beta-HSD1)-like, classical (c)
SDRs. Human 11beta_HSD1 catalyzes the NADP(H)-dependent
interconversion of cortisone and cortisol. This subgroup
also includes human dehydrogenase/reductase SDR family
member 7C (DHRS7C) and DHRS7B. These proteins have the
GxxxGxG nucleotide binding motif and S-Y-K catalytic
triad characteristic of the SDRs, but have an atypical
C-terminal domain that contributes to homodimerization
contacts. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold (alpha/beta folding
pattern with a central beta-sheet), an NAD(P)(H)-binding
region, and a structurally diverse C-terminal region.
Classical SDRs are typically about 250 residues long,
while extended SDRs are approximately 350 residues.
Sequence identity between different SDR enzymes are
typically in the 15-30% range, but the enzymes share the
Rossmann fold NAD-binding motif and characteristic
NAD-binding and catalytic sequence patterns. These
enzymes catalyze a wide range of activities including
the metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 257
Score = 31.4 bits (72), Expect = 0.83
Identities = 14/46 (30%), Positives = 24/46 (52%), Gaps = 1/46 (2%)
Query: 365 IAGKIFVLVGA-GGAGRALAFGAKSRGARVIIFNRNYERAKALADA 409
+ GK+ ++ GA G G LA+ GAR+++ R ER + +
Sbjct: 1 LQGKVVIITGASSGIGEELAYHLARLGARLVLSARREERLEEVKSE 46
>gnl|CDD|240622 cd05198, formate_dh_like, Formate/glycerate and related
dehydrogenases of the D-specific 2-hydroxy acid
dehydrogenase family. Formate dehydrogenase, D-specific
2-hydroxy acid dehydrogenase, Phosphoglycerate
Dehydrogenase, Lactate dehydrogenase, Thermostable
Phosphite Dehydrogenase, and Hydroxy(phenyl)pyruvate
reductase, among others, share a characteristic
arrangement of 2 similar subdomains of the alpha/beta
Rossmann fold NAD+ binding form. 2-hydroxyacid
dehydrogenases are enzymes that catalyze the conversion
of a wide variety of D-2-hydroxy acids to their
corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
The NAD+ binding domain is inserted within the linear
sequence of the mostly N-terminal catalytic domain,
which has a similar domain structure to the internal NAD
binding domain. Structurally, these domains are
connected by extended alpha helices and create a cleft
in which NAD is bound, primarily to the C-terminal
portion of the 2nd (internal) domain. Some related
proteins have similar structural subdomain but with a
tandem arrangement of the catalytic and NAD-binding
subdomains in the linear sequence. Formate dehydrogenase
(FDH) catalyzes the NAD+-dependent oxidation of formate
ion to carbon dioxide with the concomitant reduction of
NAD+ to NADH. FDHs of this family contain no metal ions
or prosthetic groups. Catalysis occurs though direct
transfer of hydride ion to NAD+ without the stages of
acid-base catalysis typically found in related
dehydrogenases. FDHs are found in all methylotrophic
microorganisms in energy production and in the stress
responses of plants. Formate/glycerate and related
dehydrogenases of the D-specific 2-hydroxyacid
dehydrogenase superfamily include groups such as formate
dehydrogenase, glycerate dehydrogenase, L-alanine
dehydrogenase, and S-Adenosylhomocysteine Hydrolase,
among others. While many members of this family are
dimeric, alanine DH is hexameric and phosphoglycerate DH
is tetrameric.
Length = 302
Score = 31.8 bits (73), Expect = 0.85
Identities = 19/106 (17%), Positives = 36/106 (33%), Gaps = 17/106 (16%)
Query: 333 GYNTD--CESAISAI----------EDALRERQGINGVASHTSPIAGKIFVLVGAGGAGR 380
G N + E A+ + + A+R G + GK +VG G G+
Sbjct: 94 GANAEAVAEHALGLLLALLRRLPRADAAVRRGWGWLWAGFPGYELEGKTVGIVGLGRIGQ 153
Query: 381 ALAFGAKSRGARVIIFNRNYERAKALADAVSGEALHFEYLHEFFPE 426
+A ++ G +V+ ++R + L E +
Sbjct: 154 RVAKRLQAFGMKVLYYDR-----TRKPEPEEDLGFRVVSLDELLAQ 194
>gnl|CDD|236313 PRK08618, PRK08618, ornithine cyclodeaminase; Validated.
Length = 325
Score = 31.6 bits (72), Expect = 0.89
Identities = 15/45 (33%), Positives = 23/45 (51%), Gaps = 2/45 (4%)
Query: 368 KIFVLVGAGG--AGRALAFGAKSRGARVIIFNRNYERAKALADAV 410
K L+G GG G+ A A RV +++R +E+A A A +
Sbjct: 128 KTLCLIGTGGQAKGQLEAVLAVRDIERVRVYSRTFEKAYAFAQEI 172
>gnl|CDD|237770 PRK14618, PRK14618, NAD(P)H-dependent glycerol-3-phosphate
dehydrogenase; Provisional.
Length = 328
Score = 31.8 bits (72), Expect = 0.92
Identities = 19/47 (40%), Positives = 25/47 (53%), Gaps = 5/47 (10%)
Query: 361 HTSPIAGKIFVLVGAGGAGRALAFGAKSRGARVIIFNRNYERAKALA 407
H +A ++GAG G ALA A S+G V ++ R E A ALA
Sbjct: 3 HGMRVA-----VLGAGAWGTALAVLAASKGVPVRLWARRPEFAAALA 44
>gnl|CDD|223422 COG0345, ProC, Pyrroline-5-carboxylate reductase [Amino acid
transport and metabolism].
Length = 266
Score = 31.4 bits (72), Expect = 0.94
Identities = 15/45 (33%), Positives = 21/45 (46%), Gaps = 4/45 (8%)
Query: 368 KIFVLVGAGGAGRALAFGAKSRGA----RVIIFNRNYERAKALAD 408
+GAG G A+ G GA +I+ NR+ E+ ALA
Sbjct: 2 MKIGFIGAGNMGEAILSGLLKSGALPPEEIIVTNRSEEKRAALAA 46
>gnl|CDD|235712 PRK06138, PRK06138, short chain dehydrogenase; Provisional.
Length = 252
Score = 31.3 bits (71), Expect = 0.96
Identities = 19/49 (38%), Positives = 32/49 (65%), Gaps = 1/49 (2%)
Query: 365 IAGKIFVLVGAG-GAGRALAFGAKSRGARVIIFNRNYERAKALADAVSG 412
+AG++ ++ GAG G GRA A GARV++ +R+ E A+ +A A++
Sbjct: 3 LAGRVAIVTGAGSGIGRATAKLFAREGARVVVADRDAEAAERVAAAIAA 51
>gnl|CDD|224527 COG1611, COG1611, Predicted Rossmann fold nucleotide-binding
protein [General function prediction only].
Length = 205
Score = 31.1 bits (71), Expect = 0.96
Identities = 15/75 (20%), Positives = 28/75 (37%), Gaps = 5/75 (6%)
Query: 365 IAGKIFVLVGAGGAG--RALAFGAKSRGARVIIFNRNYERAKALADAVSGEALHFEYLHE 422
+A + +++ GG G A+A GA G V+ + + E + E
Sbjct: 43 LAKRGLLVITGGGPGVMEAVARGALEAGGLVVGILPGLLHEQEPPNYEVIELITGMDFAE 102
Query: 423 FFPEKGMILANASAI 437
K ++ +A A
Sbjct: 103 ---RKRAMVRSADAF 114
>gnl|CDD|176181 cd05278, FDH_like, Formaldehyde dehydrogenases. Formaldehyde
dehydrogenase (FDH) is a member of the
zinc-dependent/medium chain alcohol dehydrogenase
family. Formaldehyde dehydrogenase (aka ADH3) may be
the ancestral form of alcohol dehydrogenase, which
evolved to detoxify formaldehyde. This CD contains
glutathione dependant FDH, glutathione independent FDH,
and related alcohol dehydrogenases. 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. Unlike typical FDH, Pseudomonas
putida aldehyde-dismutating FDH (PFDH) is
glutathione-independent. 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.
Length = 347
Score = 31.5 bits (72), Expect = 1.0
Identities = 15/52 (28%), Positives = 25/52 (48%), Gaps = 1/52 (1%)
Query: 367 GKIFVLVGAGGAGRALAFGAKSRGA-RVIIFNRNYERAKALADAVSGEALHF 417
G ++GAG G GA+ GA R+I + N ER +A + + ++
Sbjct: 168 GSTVAVIGAGPVGLCAVAGARLLGAARIIAVDSNPERLDLAKEAGATDIINP 219
>gnl|CDD|169556 PRK08703, PRK08703, short chain dehydrogenase; Provisional.
Length = 239
Score = 31.1 bits (70), Expect = 1.0
Identities = 13/48 (27%), Positives = 26/48 (54%), Gaps = 1/48 (2%)
Query: 364 PIAGKIFVLVGAG-GAGRALAFGAKSRGARVIIFNRNYERAKALADAV 410
++ K ++ GA G G +A + GA VI+ R+ ++ + + DA+
Sbjct: 3 TLSDKTILVTGASQGLGEQVAKAYAAAGATVILVARHQKKLEKVYDAI 50
>gnl|CDD|217556 pfam03435, Saccharop_dh, Saccharopine dehydrogenase. This family
comprised of three structural domains that can not be
separated in the linear sequence. In some organisms this
enzyme is found as a bifunctional polypeptide with
lysine ketoglutarate reductase. The saccharopine
dehydrogenase can also function as a saccharopine
reductase.
Length = 380
Score = 31.5 bits (72), Expect = 1.1
Identities = 32/145 (22%), Positives = 54/145 (37%), Gaps = 23/145 (15%)
Query: 370 FVLVGAGGAGRALA-FGAKSRGARVIIFNRNYERAKALADAVSGEALHFEY--------L 420
+++GAGG G+ +A A+ + + +R+ E+A+ALA G L
Sbjct: 1 VLIIGAGGVGQGVAPLLARHGDLEITVADRSLEKAQALAAPKLGLRFIAIAVDADNYEAL 60
Query: 421 HEFFPEKGMILANASAIGMEPNSDQSPVPKEALKAYELVFDAVYTPRNTR-LLREAAEVG 479
E +++ N + P V K ++ D Y L +A + G
Sbjct: 61 VALLKEGDLVI-NLA-----PPFLSLTVLKACIETGVHYVDTSYLREAQLALHEKAKDAG 114
Query: 480 ATVVSG-------VEMFIRQALGQF 497
T V G V +F + AL
Sbjct: 115 VTAVLGCGFDPGLVSLFAKYALDDL 139
>gnl|CDD|187628 cd05370, SDR_c2, classical (c) SDR, subgroup 2. Short-chain
dehydrogenases/reductases (SDRs, aka Tyrosine-dependent
oxidoreductases) are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold (alpha/beta folding
pattern with a central beta-sheet), an NAD(P)(H)-binding
region, and a structurally diverse C-terminal region.
Classical SDRs are typically about 250 residues long,
while extended SDRs are approximately 350 residues.
Sequence identity between different SDR enzymes are
typically in the 15-30% range, but the enzymes share the
Rossmann fold NAD-binding motif and characteristic
NAD-binding and catalytic sequence patterns. These
enzymes catalyze a wide range of activities including
the metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 228
Score = 31.1 bits (71), Expect = 1.1
Identities = 26/81 (32%), Positives = 33/81 (40%), Gaps = 15/81 (18%)
Query: 368 KIFVLVGAGGAGRALAFGAKSRGARVIIFNRNYER---AKA-----------LADAVSGE 413
+ + G G G ALA G VII R ER AK + DA S E
Sbjct: 7 TVLITGGTSGIGLALARKFLEAGNTVIITGRREERLAEAKKELPNIHTIVLDVGDAESVE 66
Query: 414 ALHFEYLHEFFPEKGMILANA 434
AL L E +P +++ NA
Sbjct: 67 ALAEALLSE-YPNLDILINNA 86
>gnl|CDD|133446 cd01078, NAD_bind_H4MPT_DH, NADP binding domain of methylene
tetrahydromethanopterin dehydrogenase. Methylene
Tetrahydromethanopterin Dehydrogenase (H4MPT DH) NADP
binding domain. NADP-dependent H4MPT DH catalyzes the
dehydrogenation of methylene- H4MPT and
methylene-tetrahydrofolate (H4F) with NADP+ as cofactor.
H4F and H4MPT are both cofactors that carry the
one-carbon units between the formyl and methyl oxidation
level. H4F and H4MPT are structurally analogous to each
other with respect to the pterin moiety, but each has
distinct side chain. H4MPT is present only in anaerobic
methanogenic archaea and aerobic methylotrophic
proteobacteria. H4MPT seems to have evolved
independently from H4F and functions as a distinct
carrier in C1 metabolism. Amino acid DH-like
NAD(P)-binding domains are members of the Rossmann fold
superfamily and include glutamate, leucine, and
phenylalanine DHs, methylene tetrahydrofolate DH,
methylene-tetrahydromethanopterin DH,
methylene-tetrahydropholate DH/cyclohydrolase, Shikimate
DH-like proteins, malate oxidoreductases, and glutamyl
tRNA reductase. Amino acid DHs catalyze the deamination
of amino acids to keto acids with NAD(P)+ as a cofactor.
The NAD(P)-binding Rossmann fold superfamily includes a
wide variety of protein families including NAD(P)-
binding domains of alcohol DHs, tyrosine-dependent
oxidoreductases, glyceraldehyde-3-phosphate DH,
lactate/malate DHs, formate/glycerate DHs, siroheme
synthases, 6-phosphogluconate DH, amino acid DHs,
repressor rex, NAD-binding potassium channel domain,
CoA-binding, and ornithine cyclodeaminase-like domains.
These domains have an alpha-beta-alpha configuration.
NAD binding involves numerous hydrogen and van der Waals
contacts.
Length = 194
Score = 30.8 bits (70), Expect = 1.1
Identities = 25/79 (31%), Positives = 36/79 (45%), Gaps = 10/79 (12%)
Query: 333 GYNTDCESAISAIEDALRERQGINGVASHTSPIAGK-IFVLVGAGGAGRALAFGAKSRGA 391
G NT +A++A AL + GK VL G G G+ A GA
Sbjct: 3 GSNTTAAAAVAAAGKALELMGK---------DLKGKTAVVLGGTGPVGQRAAVLLAREGA 53
Query: 392 RVIIFNRNYERAKALADAV 410
RV++ R+ ERA+ AD++
Sbjct: 54 RVVLVGRDLERAQKAADSL 72
>gnl|CDD|178111 PLN02494, PLN02494, adenosylhomocysteinase.
Length = 477
Score = 31.8 bits (72), Expect = 1.1
Identities = 15/31 (48%), Positives = 20/31 (64%)
Query: 365 IAGKIFVLVGAGGAGRALAFGAKSRGARVII 395
IAGK+ V+ G G G+ A K+ GARVI+
Sbjct: 252 IAGKVAVICGYGDVGKGCAAAMKAAGARVIV 282
>gnl|CDD|143594 cd07570, GAT_Gln-NAD-synth, Glutamine aminotransferase (GAT,
glutaminase) domain of glutamine-dependent NAD
synthetases (class 7 and 8 nitrilases).
Glutamine-dependent NAD synthetases are bifunctional
enzymes, which have an N-terminal GAT domain and a
C-terminal NAD+ synthetase domain. The GAT domain is a
glutaminase (EC 3.5.1.2) which hydrolyses L-glutamine
to L-glutamate and ammonia. The ammonia is used by the
NAD+ synthetase domain in the ATP-dependent amidation
of nicotinic acid adenine dinucleotide. Glutamine
aminotransferases are categorized depending on their
active site residues into different unrelated classes.
This class of GAT domain belongs to a larger nitrilase
superfamily comprised of nitrile- or amide-hydrolyzing
enzymes and amide-condensing enzymes, which depend on a
Glu-Lys-Cys catalytic triad. This superfamily has been
classified in the literature based on global and
structure based sequence analysis into thirteen
different enzyme classes (referred to as 1-13), this
subgroup corresponds to classes 7 and 8. Members of
this superfamily generally form homomeric complexes,
the basic building block of which is a homodimer.
Mycobacterium tuberculosis glutamine-dependent NAD+
synthetase forms a homooctamer.
Length = 261
Score = 31.3 bits (72), Expect = 1.2
Identities = 11/26 (42%), Positives = 17/26 (65%), Gaps = 3/26 (11%)
Query: 20 TEEMQASIEQAKVEGADLV---ELCI 42
E++ +I +AK +GADLV EL +
Sbjct: 18 AEKILEAIREAKAQGADLVVFPELSL 43
>gnl|CDD|223717 COG0644, FixC, Dehydrogenases (flavoproteins) [Energy production
and conversion].
Length = 396
Score = 31.3 bits (71), Expect = 1.2
Identities = 28/121 (23%), Positives = 42/121 (34%), Gaps = 16/121 (13%)
Query: 371 VLVGAGGAGRALAFGAKSRGARVIIFNRNYE-RAKALADAVSGEALHFEYLHEFFPE-KG 428
V+VGAG AG + A G V++ + E AK G L L E P+
Sbjct: 7 VIVGAGPAGSSAARRLAKAGLDVLVLEKGSEPGAK----PCCGGGLSPRALEELIPDFDE 62
Query: 429 MILANASAIGMEPNSDQSPVPKEALKAYEL---VFDAVYTPRNTRLLREAAEVGATVVSG 485
I + + ++ + + Y + FD L A E GA + G
Sbjct: 63 EIERKVTGARIYFPGEKVAIEVPVGEGYIVDRAKFDK-------WLAERAEEAGAELYPG 115
Query: 486 V 486
Sbjct: 116 T 116
>gnl|CDD|223528 COG0451, WcaG, Nucleoside-diphosphate-sugar epimerases [Cell
envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 314
Score = 31.1 bits (70), Expect = 1.2
Identities = 12/43 (27%), Positives = 16/43 (37%)
Query: 368 KIFVLVGAGGAGRALAFGAKSRGARVIIFNRNYERAKALADAV 410
+I V GAG G L + G V +R + L V
Sbjct: 2 RILVTGGAGFIGSHLVERLLAAGHDVRGLDRLRDGLDPLLSGV 44
>gnl|CDD|184511 PRK14106, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 450
Score = 31.5 bits (72), Expect = 1.2
Identities = 16/35 (45%), Positives = 22/35 (62%)
Query: 367 GKIFVLVGAGGAGRALAFGAKSRGARVIIFNRNYE 401
GK ++VGAG +G ALA K GA+VI+ + E
Sbjct: 5 GKKVLVVGAGVSGLALAKFLKKLGAKVILTDEKEE 39
>gnl|CDD|236101 PRK07803, sdhA, succinate dehydrogenase flavoprotein subunit;
Reviewed.
Length = 626
Score = 31.5 bits (72), Expect = 1.3
Identities = 13/25 (52%), Positives = 17/25 (68%)
Query: 371 VLVGAGGAGRALAFGAKSRGARVII 395
V++GAGGAG A A+ RG RV +
Sbjct: 12 VVIGAGGAGLRAAIEARERGLRVAV 36
>gnl|CDD|218507 pfam05221, AdoHcyase, S-adenosyl-L-homocysteine hydrolase.
Length = 430
Score = 31.2 bits (71), Expect = 1.3
Identities = 14/31 (45%), Positives = 20/31 (64%)
Query: 365 IAGKIFVLVGAGGAGRALAFGAKSRGARVII 395
IAGK+ V+ G G G+ A + +GARVI+
Sbjct: 208 IAGKVAVVCGYGDVGKGCAASLRGQGARVIV 238
>gnl|CDD|153421 cd07936, SCAN, SCAN oligomerization domain. The SCAN domain (named
after SRE-ZBP, CTfin51, AW-1 and Number 18 cDNA) is
found in several vertebrate proteins that contain C2H2
zinc finger motifs, many of which may be transcription
factors playing roles in cell survival and
differentiation. This protein-interaction domain is able
to mediate homo- and hetero-oligomerization of
SCAN-containing proteins. Some SCAN-containing proteins,
including those of lower vertebrates, do not contain
zinc finger motifs. It has been noted that the SCAN
domain resembles a domain-swapped version of the
C-terminal domain of the HIV capsid protein. This domain
model features elements common to the three general
groups of SCAN domains (SCAN-A1, SCAN-A2, and SCAN-B).
The SCAND1 protein is truncated at the C-terminus with
respect to this model, the SCAND2 protein appears to
have a truncated central helix.
Length = 85
Score = 29.2 bits (66), Expect = 1.3
Identities = 14/34 (41%), Positives = 17/34 (50%), Gaps = 6/34 (17%)
Query: 491 RQALGQFR-LFTGGLAP-----EDFMRKLVLEQF 518
R+AL + R L L P E + LVLEQF
Sbjct: 20 REALQRLRELCRQWLRPEIHTKEQILELLVLEQF 53
>gnl|CDD|240639 cd12162, 2-Hacid_dh_4, Putative D-isomer specific 2-hydroxyacid
dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine yydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 307
Score = 31.3 bits (72), Expect = 1.3
Identities = 24/93 (25%), Positives = 41/93 (44%), Gaps = 24/93 (25%)
Query: 365 IAGKIFVLVGAGGAGRALAFGAKSRGARVIIFNRN-----------YERAKALADAVSGE 413
+AGK ++G G G+A+A A++ G +V+ R + A +D +S
Sbjct: 145 LAGKTLGIIGYGNIGQAVARIARAFGMKVLFAERKGAPPLREGYVSLDELLAQSDVIS-- 202
Query: 414 ALHFEYLH-EFFPE-KGMILANASAIG-MEPNS 443
LH PE + +I NA + M+P +
Sbjct: 203 ------LHCPLTPETRNLI--NAEELAKMKPGA 227
>gnl|CDD|185411 PTZ00044, PTZ00044, ubiquitin; Provisional.
Length = 76
Score = 29.0 bits (65), Expect = 1.3
Identities = 9/35 (25%), Positives = 23/35 (65%)
Query: 322 IIRRPIDGKLVGYNTDCESAISAIEDALRERQGIN 356
I+ + + GK +N + ++ + ++ AL+E++GI+
Sbjct: 3 ILIKTLTGKKQSFNFEPDNTVQQVKMALQEKEGID 37
>gnl|CDD|187627 cd05369, TER_DECR_SDR_a, Trans-2-enoyl-CoA reductase (TER) and
2,4-dienoyl-CoA reductase (DECR), atypical (a) SDR.
TTER is a peroxisomal protein with a proposed role in
fatty acid elongation. Fatty acid synthesis is known to
occur in the both endoplasmic reticulum and
mitochondria; peroxisomal TER has been proposed as an
additional fatty acid elongation system, it reduces the
double bond at C-2 as the last step of elongation. This
system resembles the mitochondrial system in that
acetyl-CoA is used as a carbon donor. TER may also
function in phytol metabolism, reducting phytenoyl-CoA
to phytanoyl-CoA in peroxisomes. DECR processes double
bonds in fatty acids to increase their utility in fatty
acid metabolism; it reduces 2,4-dienoyl-CoA to an
enoyl-CoA. DECR is active in mitochondria and
peroxisomes. This subgroup has the Gly-rich NAD-binding
motif of the classical SDR family, but does not display
strong identity to the canonical active site tetrad, and
lacks the characteristic Tyr at the usual position. SDRs
are a functionally diverse family of oxidoreductases
that have a single domain with a structurally conserved
Rossmann fold (alpha/beta folding pattern with a central
beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRS are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes have a
3-glycine N-terminal NAD(P)(H)-binding pattern
(typically, TGxxxGxG in classical SDRs and TGxxGxxG in
extended SDRs), while substrate binding is in the
C-terminal region. A critical catalytic Tyr residue
(Tyr-151, human 15-hydroxyprostaglandin dehydrogenase
(15-PGDH) numbering), is often found in a conserved
YXXXK pattern. In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) or additional
Ser, contributing to the active site. Substrates for
these enzymes include sugars, steroids, alcohols, and
aromatic compounds. The standard reaction mechanism is a
proton relay involving the conserved Tyr and Lys, as
well as Asn (or Ser). Some SDR family members, including
17 beta-hydroxysteroid dehydrogenase contain an
additional helix-turn-helix motif that is not generally
found among SDRs.
Length = 249
Score = 31.0 bits (71), Expect = 1.4
Identities = 18/55 (32%), Positives = 25/55 (45%), Gaps = 5/55 (9%)
Query: 366 AGKI-FVLVGAGGAGRALAFGAKSRGARVIIFNRNYER----AKALADAVSGEAL 415
GK+ F+ G G G+A+A GA V I R E A+ ++ A G A
Sbjct: 2 KGKVAFITGGGTGIGKAIAKAFAELGASVAIAGRKPEVLEAAAEEISSATGGRAH 56
>gnl|CDD|235739 PRK06200, PRK06200, 2,3-dihydroxy-2,3-dihydrophenylpropionate
dehydrogenase; Provisional.
Length = 263
Score = 31.1 bits (71), Expect = 1.4
Identities = 15/49 (30%), Positives = 25/49 (51%), Gaps = 1/49 (2%)
Query: 362 TSPIAGKIFVLVGAG-GAGRALAFGAKSRGARVIIFNRNYERAKALADA 409
+ G++ ++ G G G GRAL + GARV + R+ E+ +L
Sbjct: 1 MGWLHGQVALITGGGSGIGRALVERFLAEGARVAVLERSAEKLASLRQR 49
>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 = 30.7 bits (69), Expect = 1.4
Identities = 19/42 (45%), Positives = 23/42 (54%), Gaps = 1/42 (2%)
Query: 367 GKIFVLVG-AGGAGRALAFGAKSRGARVIIFNRNYERAKALA 407
GK ++ G A G GRA A GARV I + N E A+A A
Sbjct: 3 GKTALITGSARGIGRAFAQAYVREGARVAIADINLEAARATA 44
>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 = 31.1 bits (71), Expect = 1.5
Identities = 10/25 (40%), Positives = 15/25 (60%)
Query: 371 VLVGAGGAGRALAFGAKSRGARVII 395
V++G+G AG A A A G +V +
Sbjct: 3 VVIGSGLAGLAAALEAAEAGLKVAV 27
>gnl|CDD|212491 cd05233, SDR_c, classical (c) SDRs. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold
(alpha/beta folding pattern with a central beta-sheet),
an NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRs are approximately
350 residues. Sequence identity between different SDR
enzymes are typically in the 15-30% range, but the
enzymes share the Rossmann fold NAD-binding motif and
characteristic NAD-binding and catalytic sequence
patterns. These enzymes catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human prostaglandin dehydrogenase
(PGDH) numbering). In addition to the Tyr and Lys, there
is often an upstream Ser (Ser-138, PGDH numbering)
and/or an Asn (Asn-107, PGDH numbering) contributing to
the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 234
Score = 30.7 bits (70), Expect = 1.5
Identities = 15/41 (36%), Positives = 21/41 (51%), Gaps = 2/41 (4%)
Query: 371 VLV--GAGGAGRALAFGAKSRGARVIIFNRNYERAKALADA 409
LV + G GRA+A GA+V++ +RN E LA
Sbjct: 1 ALVTGASSGIGRAIARRLAREGAKVVLADRNEEALAELAAI 41
>gnl|CDD|236040 PRK07523, PRK07523, gluconate 5-dehydrogenase; Provisional.
Length = 255
Score = 30.5 bits (69), Expect = 1.8
Identities = 15/40 (37%), Positives = 22/40 (55%)
Query: 377 GAGRALAFGAKSRGARVIIFNRNYERAKALADAVSGEALH 416
G G ALA G GA VI+ R+ + A A+++ G+ L
Sbjct: 21 GIGYALAEGLAQAGAEVILNGRDPAKLAAAAESLKGQGLS 60
>gnl|CDD|219686 pfam07992, Pyr_redox_2, Pyridine nucleotide-disulphide
oxidoreductase. This family includes both class I and
class II oxidoreductases and also NADH oxidases and
peroxidases. This domain is actually a small NADH
binding domain within a larger FAD binding domain.
Length = 283
Score = 30.4 bits (69), Expect = 1.8
Identities = 10/29 (34%), Positives = 14/29 (48%)
Query: 371 VLVGAGGAGRALAFGAKSRGARVIIFNRN 399
V++G G AG A A G +V + R
Sbjct: 3 VIIGGGPAGLAAAIRLARLGLKVALIERE 31
>gnl|CDD|217244 pfam02826, 2-Hacid_dh_C, D-isomer specific 2-hydroxyacid
dehydrogenase, NAD binding domain. This domain is
inserted into the catalytic domain, the large
dehydrogenase and D-lactate dehydrogenase families in
SCOP. N-terminal portion of which is represented by
family pfam00389.
Length = 175
Score = 30.1 bits (69), Expect = 1.9
Identities = 23/64 (35%), Positives = 34/64 (53%), Gaps = 10/64 (15%)
Query: 365 IAGKIFVLVGAGGAGRALAFGAKSRGARVIIFNRNYERAKALADAVSGEALHFEY--LHE 422
++GK ++G G GRA+A K+ G +VI ++R Y +A+A EAL Y L E
Sbjct: 33 LSGKTVGIIGLGRIGRAVARRLKAFGMKVIAYDR-YPKAEA-------EALGARYVSLDE 84
Query: 423 FFPE 426
E
Sbjct: 85 LLAE 88
>gnl|CDD|179490 PRK02877, PRK02877, hypothetical protein; Provisional.
Length = 106
Score = 29.0 bits (65), Expect = 2.1
Identities = 20/58 (34%), Positives = 32/58 (55%), Gaps = 4/58 (6%)
Query: 379 GRALAFGAKSRGARVIIFNRNYERAKAL-ADAVSGEALHFEYLHEFFPEKGMILANAS 435
GR+ A+ + R AR I F E+A+AL ADAV G + +E + + M++ + S
Sbjct: 45 GRSGAYEKELRKAREIAFEELGEQARALGADAVVGIDIDYETVGQ---NGSMLMVSVS 99
>gnl|CDD|132407 TIGR03364, HpnW_proposed, FAD dependent oxidoreductase TIGR03364.
This clade of FAD dependent oxidoreductases (members of
the pfam01266 family) is syntenically associated with a
family of proposed phosphonatase-like enzymes
(TIGR03351) and is also found (less frequently) in
association with phosphonate transporter components. A
likely role for this enzyme involves the oxidative
deamination of an aminophosphonate differring slightly
from 2-aminoethylphosphonate, possibly
1-hydroxy-2-aminoethylphosphonate (see the comments for
TIGR03351). Many members of the larger FAD dependent
oxidoreductase family act as amino acid oxidative
deaminases.
Length = 365
Score = 30.3 bits (69), Expect = 2.1
Identities = 12/29 (41%), Positives = 17/29 (58%)
Query: 371 VLVGAGGAGRALAFGAKSRGARVIIFNRN 399
++VGAG G A A+ A RG V + R+
Sbjct: 4 IIVGAGILGLAHAYAAARRGLSVTVIERS 32
>gnl|CDD|235693 PRK06077, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 252
Score = 30.1 bits (68), Expect = 2.2
Identities = 11/30 (36%), Positives = 18/30 (60%), Gaps = 1/30 (3%)
Query: 367 GKIFVLVGAG-GAGRALAFGAKSRGARVII 395
K+ V+ G+G G GRA+A G+ V++
Sbjct: 6 DKVVVVTGSGRGIGRAIAVRLAKEGSLVVV 35
>gnl|CDD|223439 COG0362, Gnd, 6-phosphogluconate dehydrogenase [Carbohydrate
transport and metabolism].
Length = 473
Score = 30.7 bits (70), Expect = 2.2
Identities = 17/70 (24%), Positives = 29/70 (41%), Gaps = 7/70 (10%)
Query: 372 LVGAGGAGRALAFGAKSRGARVIIFNRNYERAKA-LADAVSGEALH-FEYLHEFF----- 424
++G G LA G V ++NR E+ LA+ G+ + + EF
Sbjct: 8 VIGLAVMGSNLALNIADHGYTVAVYNRTTEKTDEFLAERAKGKNIVPAYSIEEFVASLEK 67
Query: 425 PEKGMILANA 434
P K +++ A
Sbjct: 68 PRKILLMVKA 77
>gnl|CDD|234978 PRK01747, mnmC, bifunctional tRNA
(mnm(5)s(2)U34)-methyltransferase/FAD-dependent
cmnm(5)s(2)U34 oxidoreductase; Reviewed.
Length = 662
Score = 30.6 bits (70), Expect = 2.2
Identities = 20/54 (37%), Positives = 25/54 (46%), Gaps = 5/54 (9%)
Query: 359 ASHTSPIAGKIFVLVGAGGAGRALAFGAKSRGARVIIFNRNYERAKALADAVSG 412
A SP A + +G G AG ALA RG +V + YE +A A SG
Sbjct: 253 ARPGSPKARDAAI-IGGGIAGAALALALARRGWQVTL----YEADEAPAQGASG 301
>gnl|CDD|224662 COG1748, LYS9, Saccharopine dehydrogenase and related proteins
[Amino acid transport and metabolism].
Length = 389
Score = 30.4 bits (69), Expect = 2.3
Identities = 21/117 (17%), Positives = 46/117 (39%), Gaps = 23/117 (19%)
Query: 368 KIFVLVGAGGAGRALAFG-AKSRGARVIIFNRNYERAKALADAVSGEALHFEYLHEFFPE 426
+++GAGG G +A A++ V I +R+ E+ +A+ + G+ E
Sbjct: 2 MKILVIGAGGVGSVVAHKLAQNGDGEVTIADRSKEKCARIAELIGGKV-------EA--- 51
Query: 427 KGMILANASAIGMEPNSDQSPVPKEALKAYELVFDAVYTPRNTRLLREAAEVGATVV 483
++ ++ +K ++LV +A + +L+ + G V
Sbjct: 52 ------------LQVDAADVDALVALIKDFDLVINAAPPFVDLTILKACIKTGVDYV 96
>gnl|CDD|181159 PRK07890, PRK07890, short chain dehydrogenase; Provisional.
Length = 258
Score = 30.3 bits (69), Expect = 2.3
Identities = 21/55 (38%), Positives = 27/55 (49%), Gaps = 4/55 (7%)
Query: 366 AGKIFVLVGAG-GAGRALAFGAKSRGARVIIFNRNYERAKALA---DAVSGEALH 416
GK+ V+ G G G GR LA A GA V++ R ER +A D + AL
Sbjct: 4 KGKVVVVSGVGPGLGRTLAVRAARAGADVVLAARTAERLDEVAAEIDDLGRRALA 58
>gnl|CDD|216396 pfam01262, AlaDh_PNT_C, Alanine dehydrogenase/PNT, C-terminal
domain. This family now also contains the lysine
2-oxoglutarate reductases.
Length = 150
Score = 29.4 bits (67), Expect = 2.3
Identities = 14/39 (35%), Positives = 18/39 (46%)
Query: 368 KIFVLVGAGGAGRALAFGAKSRGARVIIFNRNYERAKAL 406
V++G G G A AK GA V I + ER + L
Sbjct: 21 AKVVVIGGGVVGLGAAATAKGLGAPVTILDVRPERLEQL 59
>gnl|CDD|180584 PRK06481, PRK06481, fumarate reductase flavoprotein subunit;
Validated.
Length = 506
Score = 30.6 bits (69), Expect = 2.3
Identities = 13/28 (46%), Positives = 17/28 (60%)
Query: 371 VLVGAGGAGRALAFGAKSRGARVIIFNR 398
V+VGAGGAG + A AK G +I +
Sbjct: 65 VIVGAGGAGMSAAIEAKDAGMNPVILEK 92
>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 = 30.4 bits (69), Expect = 2.3
Identities = 18/51 (35%), Positives = 22/51 (43%), Gaps = 4/51 (7%)
Query: 352 RQGINGVASHTSPIAG---KIFVLVGAGGAGRALAFGAKSRGARVIIFNRN 399
R G + T P ++ V VG G AG A A RG RV +F R
Sbjct: 362 RAGREEWGTVTLPPPRRRKRVLV-VGGGPAGLEAAATAARRGHRVTLFERE 411
>gnl|CDD|183787 PRK12844, PRK12844, 3-ketosteroid-delta-1-dehydrogenase; Reviewed.
Length = 557
Score = 30.5 bits (69), Expect = 2.5
Identities = 10/26 (38%), Positives = 13/26 (50%)
Query: 370 FVLVGAGGAGRALAFGAKSRGARVII 395
V+VG+GG G A A G +I
Sbjct: 9 VVVVGSGGGGMCAALAAADSGLEPLI 34
>gnl|CDD|187634 cd08929, SDR_c4, classical (c) SDR, subgroup 4. This subgroup has
a canonical active site tetrad and a typical Gly-rich
NAD-binding motif. SDRs are a functionally diverse
family of oxidoreductases that have a single domain with
a structurally conserved Rossmann fold (alpha/beta
folding pattern with a central beta-sheet), an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRs are approximately
350 residues. Sequence identity between different SDR
enzymes are typically in the 15-30% range, but the
enzymes share the Rossmann fold NAD-binding motif and
characteristic NAD-binding and catalytic sequence
patterns. These enzymes catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) numbering). In addition to the
Tyr and Lys, there is often an upstream Ser (Ser-138,
15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH
numbering) contributing to the active site; while
substrate binding is in the C-terminal region, which
determines specificity. The standard reaction mechanism
is a 4-pro-S hydride transfer and proton relay involving
the conserved Tyr and Lys, a water molecule stabilized
by Asn, and nicotinamide. Extended SDRs have additional
elements in the C-terminal region, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Some atypical SDRs have lost catalytic activity and/or
have an unusual NAD(P)-binding motif and missing or
unusual active site residues. Reactions catalyzed within
the SDR family include isomerization, decarboxylation,
epimerization, C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 226
Score = 29.8 bits (67), Expect = 2.8
Identities = 14/49 (28%), Positives = 17/49 (34%)
Query: 367 GKIFVLVGAGGAGRALAFGAKSRGARVIIFNRNYERAKALADAVSGEAL 415
V + G G A A + G RV I R+ R A A L
Sbjct: 1 KAALVTGASRGIGEATARLLHAEGYRVGICARDEARLAAAAAQELEGVL 49
>gnl|CDD|232969 TIGR00422, valS, valyl-tRNA synthetase. The valyl-tRNA synthetase
(ValS) is a class I amino acyl-tRNA ligase and is
particularly closely related to the isoleucyl tRNA
synthetase [Protein synthesis, tRNA aminoacylation].
Length = 861
Score = 30.4 bits (69), Expect = 2.8
Identities = 15/53 (28%), Positives = 25/53 (47%), Gaps = 4/53 (7%)
Query: 418 EYLHEFFPEKGMILANASAIGMEPNSDQSPVPKEALKAYELVFDAVYTPRNTR 470
E + + F E + S P D V +EA KA+EL+ + + + RN +
Sbjct: 692 EEIWQHFKEGADSIMLQSY----PVVDAEFVDEEAEKAFELLKEIIVSIRNLK 740
>gnl|CDD|238385 cd00756, MoaE, MoaE family. Members of this family are involved in
biosynthesis of the molybdenum cofactor (Moco), an
essential cofactor for a diverse group of redox enzymes.
Moco biosynthesis is an evolutionarily conserved pathway
present in eubacteria, archaea and eukaryotes. Moco
contains a tricyclic pyranopterin, termed molybdopterin
(MPT), which carries the cis-dithiolene group
responsible for molybdenum ligation. This dithiolene
group is generated by MPT synthase in the second major
step in Moco biosynthesis. MPT synthase is a
heterotetramer consisting of two large (MoaE) and two
small (MoaD) subunits.
Length = 124
Score = 29.0 bits (66), Expect = 2.8
Identities = 26/87 (29%), Positives = 32/87 (36%), Gaps = 14/87 (16%)
Query: 313 AKSIGAVNT---IIRRPIDGKLV------GYNTDCESAISAIEDALRERQGINGVASHTS 363
GAV T +R +GK V Y E + I + RER G+ VA
Sbjct: 12 DPEAGAVVTFVGTVRDHDEGKGVEALEYEAYPPMAEKELEEIAEEARERWGLLRVAIIHR 71
Query: 364 ----PIAGKIFVLVGAGGAGRALAFGA 386
P G+ VLV R AF A
Sbjct: 72 VGRLPP-GEAIVLVAVSSPHRKEAFEA 97
>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 = 30.0 bits (68), Expect = 2.8
Identities = 12/39 (30%), Positives = 19/39 (48%)
Query: 369 IFVLVGAGGAGRALAFGAKSRGARVIIFNRNYERAKALA 407
+ G G GRAL + GA+V + +R+ E+ L
Sbjct: 7 ALITGGGSGLGRALVERFVAEGAKVAVLDRSAEKVAELR 45
>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 = 29.8 bits (68), Expect = 2.9
Identities = 13/44 (29%), Positives = 22/44 (50%), Gaps = 2/44 (4%)
Query: 371 VLV--GAGGAGRALAFGAKSRGARVIIFNRNYERAKALADAVSG 412
LV + G GRA+A + GA+V + +R+ E A + +
Sbjct: 3 ALVTGASRGIGRAIALRLAAEGAKVAVTDRSEEAAAETVEEIKA 46
>gnl|CDD|179297 PRK01438, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 480
Score = 30.0 bits (68), Expect = 2.9
Identities = 22/60 (36%), Positives = 29/60 (48%), Gaps = 3/60 (5%)
Query: 357 GVASHTSPIAGKIFVLVGAGGAGRALAFGAKSRGARVIIFN-RNYERAKALADAVSGEAL 415
G+ S S G V+ G G +G A A GARV + + + ER +ALA EAL
Sbjct: 6 GLTSWHSDWQGLRVVVAGLGVSGFAAADALLELGARVTVVDDGDDERHRALAAI--LEAL 63
>gnl|CDD|202773 pfam03807, F420_oxidored, NADP oxidoreductase coenzyme
F420-dependent.
Length = 93
Score = 28.3 bits (64), Expect = 2.9
Identities = 19/49 (38%), Positives = 27/49 (55%), Gaps = 1/49 (2%)
Query: 373 VGAGGAGRALAFGAKSRGARVII-FNRNYERAKALADAVSGEALHFEYL 420
+GAG G ALA G + G V+I +RN E+A ALA+ + +A
Sbjct: 5 IGAGNMGEALARGLAAAGHEVVIANSRNPEKAAALAEELGVKATAVSNE 53
>gnl|CDD|235703 PRK06125, PRK06125, short chain dehydrogenase; Provisional.
Length = 259
Score = 30.0 bits (68), Expect = 3.0
Identities = 16/51 (31%), Positives = 26/51 (50%), Gaps = 5/51 (9%)
Query: 365 IAGKIFVLVGAG---GAGRALAFGAKSRGARVIIFNRNYERAKALADAVSG 412
+AGK ++ GA GA A AF A+ G + + R+ + +ALA +
Sbjct: 5 LAGKRVLITGASKGIGAAAAEAFAAE--GCHLHLVARDADALEALAADLRA 53
>gnl|CDD|183772 PRK12823, benD, 1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate
dehydrogenase; Provisional.
Length = 260
Score = 29.9 bits (68), Expect = 3.0
Identities = 24/57 (42%), Positives = 33/57 (57%), Gaps = 5/57 (8%)
Query: 366 AGKIFVLVGAG-GAGRALAFGAKSRGARVIIFNRN---YERAKALADAVSGEALHFE 418
AGK+ V+ GA G GR +A A + GARV++ +R+ +E A L A GEAL
Sbjct: 7 AGKVVVVTGAAQGIGRGVALRAAAEGARVVLVDRSELVHEVAAELR-AAGGEALALT 62
>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 = 30.1 bits (68), Expect = 3.2
Identities = 16/45 (35%), Positives = 23/45 (51%), Gaps = 4/45 (8%)
Query: 366 AGKIFVLVGAGGAGRALAFGAKSRGA-RVI---IFNRNYERAKAL 406
G + G GG G ++ G K+ GA R+I I +E+AK L
Sbjct: 183 PGSTCAVFGLGGVGLSVIMGCKAAGASRIIAVDINKDKFEKAKQL 227
>gnl|CDD|214832 smart00817, Amelin, Ameloblastin precursor (Amelin). This family
consists of several mammalian Ameloblastin precursor
(Amelin) proteins. Matrix proteins of tooth enamel
consist mainly of amelogenin but also of non-amelogenin
proteins, which, although their volumetric percentage is
low, have an important role in enamel mineralisation.
One of the non-amelogenin proteins is ameloblastin, also
known as amelin and sheathlin. Ameloblastin (AMBN) is
one of the enamel sheath proteins which is though to
have a role in determining the prismatic structure of
growing enamel crystals.
Length = 411
Score = 29.9 bits (67), Expect = 3.2
Identities = 19/61 (31%), Positives = 24/61 (39%), Gaps = 8/61 (13%)
Query: 234 NPDTKIFGLVSNPVGHSKGPILHNPAFRHTRFNGIYVPMLVDDVKEFFRTYSGTDFAGFS 293
P+ I L NP G SKGP PA P+L ++ E + TY D
Sbjct: 320 FPNDNIPNLARNPQGQSKGPPGVTPAAAD--------PLLTPELAEVYETYGADDTTPLG 371
Query: 294 V 294
V
Sbjct: 372 V 372
>gnl|CDD|202093 pfam02023, SCAN, SCAN domain. The SCAN domain (named after
SRE-ZBP, CTfin51, AW-1 and Number 18 cDNA) is found in
several pfam00096 proteins. The domain has been shown to
be able to mediate homo- and hetero-oligomerisation.
Length = 93
Score = 27.9 bits (63), Expect = 3.3
Identities = 14/34 (41%), Positives = 17/34 (50%), Gaps = 6/34 (17%)
Query: 491 RQALGQFR-LFTGGLAPE-----DFMRKLVLEQF 518
R+AL + R L L PE + LVLEQF
Sbjct: 22 REALSRLRELCRQWLRPEIHTKEQILELLVLEQF 55
>gnl|CDD|135765 PRK06113, PRK06113, 7-alpha-hydroxysteroid dehydrogenase;
Validated.
Length = 255
Score = 29.8 bits (67), Expect = 3.4
Identities = 14/46 (30%), Positives = 25/46 (54%), Gaps = 1/46 (2%)
Query: 367 GKIFVLVGAG-GAGRALAFGAKSRGARVIIFNRNYERAKALADAVS 411
GK ++ GAG G G+ +A + GA V++ + N + A + D +
Sbjct: 11 GKCAIITGAGAGIGKEIAITFATAGASVVVSDINADAANHVVDEIQ 56
>gnl|CDD|187664 cd09763, DHRS1-like_SDR_c, human dehydrogenase/reductase (SDR
family) member 1 (DHRS1) -like, classical (c) SDRs.
This subgroup includes human DHRS1 and related proteins.
These are members of the classical SDR family, with a
canonical Gly-rich NAD-binding motif and the typical
YXXXK active site motif. However, the rest of the
catalytic tetrad is not strongly conserved. DHRS1 mRNA
has been detected in many tissues, liver, heart,
skeletal muscle, kidney and pancreas; a longer
transcript is predominantly expressed in the liver , a
shorter one in the heart. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold
(alpha/beta folding pattern with a central beta-sheet),
an NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRS are approximately
350 residues. Sequence identity between different SDR
enzymes are typically in the 15-30% range, but the
enzymes share the Rossmann fold NAD-binding motif and
characteristic NAD-binding and catalytic sequence
patterns. These enzymes have a 3-glycine N-terminal
NAD(P)(H)-binding pattern (typically, TGxxxGxG in
classical SDRs and TGxxGxxG in extended SDRs), while
substrate binding is in the C-terminal region. A
critical catalytic Tyr residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering), is often found in a conserved YXXXK pattern.
In addition to the Tyr and Lys, there is often an
upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn
(Asn-107, 15-PGDH numbering) or additional Ser,
contributing to the active site. Substrates for these
enzymes include sugars, steroids, alcohols, and aromatic
compounds. The standard reaction mechanism is a proton
relay involving the conserved Tyr and Lys, as well as
Asn (or Ser). Some SDR family members, including 17
beta-hydroxysteroid dehydrogenase contain an additional
helix-turn-helix motif that is not generally found among
SDRs.
Length = 265
Score = 29.7 bits (67), Expect = 3.5
Identities = 14/35 (40%), Positives = 19/35 (54%), Gaps = 1/35 (2%)
Query: 365 IAGKIFVLVGAG-GAGRALAFGAKSRGARVIIFNR 398
++GKI ++ GA G GR +A GA V I R
Sbjct: 1 LSGKIALVTGASRGIGRGIALQLGEAGATVYITGR 35
>gnl|CDD|235631 PRK05866, PRK05866, short chain dehydrogenase; Provisional.
Length = 293
Score = 29.7 bits (67), Expect = 3.5
Identities = 19/60 (31%), Positives = 26/60 (43%), Gaps = 1/60 (1%)
Query: 355 INGVASHTSPIAGKIFVLVGAG-GAGRALAFGAKSRGARVIIFNRNYERAKALADAVSGE 413
IN + GK +L GA G G A A RGA V+ R + A+AD ++
Sbjct: 28 INRPPRQPVDLTGKRILLTGASSGIGEAAAEQFARRGATVVAVARREDLLDAVADRITRA 87
>gnl|CDD|224169 COG1249, Lpd, Pyruvate/2-oxoglutarate dehydrogenase complex,
dihydrolipoamide dehydrogenase (E3) component, and
related enzymes [Energy production and conversion].
Length = 454
Score = 29.9 bits (68), Expect = 3.5
Identities = 10/25 (40%), Positives = 14/25 (56%)
Query: 371 VLVGAGGAGRALAFGAKSRGARVII 395
V++GAG AG A A G +V +
Sbjct: 8 VVIGAGPAGYVAAIRAAQLGLKVAL 32
>gnl|CDD|232882 TIGR00222, panB, 3-methyl-2-oxobutanoate hydroxymethyltransferase.
Members of this family are 3-methyl-2-oxobutanoate
hydroxymethyltransferase, the first enzyme of the
pantothenate biosynthesis pathway. An alternate name is
ketopantoate hydroxymethyltransferase [Biosynthesis of
cofactors, prosthetic groups, and carriers, Pantothenate
and coenzyme A].
Length = 263
Score = 29.4 bits (66), Expect = 3.8
Identities = 24/68 (35%), Positives = 31/68 (45%), Gaps = 9/68 (13%)
Query: 141 LGDVIACMQATGADVMKLEIAVDSITDLAPVFEMLTHCQVPLIALAVGSRGLISQLLGPK 200
L + MQ TGA+ +KLE L +MLT VP+ VG GL Q +
Sbjct: 95 LKNAARVMQETGANAVKLEGG----EWLVETVQMLTERGVPV----VGHLGLTPQSVN-I 145
Query: 201 FGGFLVYG 208
GG+ V G
Sbjct: 146 LGGYKVQG 153
>gnl|CDD|235506 PRK05565, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 247
Score = 29.4 bits (67), Expect = 3.9
Identities = 15/44 (34%), Positives = 24/44 (54%), Gaps = 1/44 (2%)
Query: 374 GAGGAGRALAFGAKSRGARVII-FNRNYERAKALADAVSGEALH 416
+GG GRA+A GA+V+I ++ N E A+ L + + E
Sbjct: 13 ASGGIGRAIAELLAKEGAKVVIAYDINEEAAQELLEEIKEEGGD 56
>gnl|CDD|236074 PRK07666, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 239
Score = 29.3 bits (66), Expect = 4.1
Identities = 18/49 (36%), Positives = 25/49 (51%), Gaps = 1/49 (2%)
Query: 365 IAGKIFVLVGAG-GAGRALAFGAKSRGARVIIFNRNYERAKALADAVSG 412
+ GK ++ GAG G GRA+A G V + R E KA+A+ V
Sbjct: 5 LQGKNALITGAGRGIGRAVAIALAKEGVNVGLLARTEENLKAVAEEVEA 53
>gnl|CDD|187618 cd05360, SDR_c3, classical (c) SDR, subgroup 3. These proteins are
members of the classical SDR family, with a canonical
active site triad (and also active site Asn) and a
typical Gly-rich NAD-binding motif. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold (alpha/beta folding pattern with a central
beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRS are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes have a
3-glycine N-terminal NAD(P)(H)-binding pattern
(typically, TGxxxGxG in classical SDRs and TGxxGxxG in
extended SDRs), while substrate binding is in the
C-terminal region. A critical catalytic Tyr residue
(Tyr-151, human 15-hydroxyprostaglandin dehydrogenase
(15-PGDH) numbering), is often found in a conserved
YXXXK pattern. In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) or additional
Ser, contributing to the active site. Substrates for
these enzymes include sugars, steroids, alcohols, and
aromatic compounds. The standard reaction mechanism is a
proton relay involving the conserved Tyr and Lys, as
well as Asn (or Ser). Some SDR family members, including
17 beta-hydroxysteroid dehydrogenase contain an
additional helix-turn-helix motif that is not generally
found among SDRs.
Length = 233
Score = 29.3 bits (66), Expect = 4.1
Identities = 20/49 (40%), Positives = 26/49 (53%), Gaps = 4/49 (8%)
Query: 371 VLVGA-GGAGRALAFGAKSRGARVIIFNRNYERAKALADAVS---GEAL 415
V+ GA G GRA A RGA+V++ R+ E LA V GEA+
Sbjct: 4 VITGASSGIGRATALAFAERGAKVVLAARSAEALHELAREVRELGGEAI 52
>gnl|CDD|181077 PRK07677, PRK07677, short chain dehydrogenase; Provisional.
Length = 252
Score = 29.3 bits (66), Expect = 4.2
Identities = 15/53 (28%), Positives = 25/53 (47%), Gaps = 3/53 (5%)
Query: 369 IFVLVGAGGAGRALAFGAKSRGARVIIFNRNYER---AKALADAVSGEALHFE 418
+ + G+ G G+A+A GA V+I R E+ AK + G+ L +
Sbjct: 4 VIITGGSSGMGKAMAKRFAEEGANVVITGRTKEKLEEAKLEIEQFPGQVLTVQ 56
>gnl|CDD|240636 cd12159, 2-Hacid_dh_2, Putative D-isomer specific 2-hydroxyacid
dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 303
Score = 29.5 bits (67), Expect = 4.3
Identities = 16/33 (48%), Positives = 19/33 (57%)
Query: 367 GKIFVLVGAGGAGRALAFGAKSRGARVIIFNRN 399
G +VGAGG GRAL GA+VI NR+
Sbjct: 125 GSTVAIVGAGGIGRALIPLLAPFGAKVIAVNRS 157
>gnl|CDD|223523 COG0446, HcaD, Uncharacterized NAD(FAD)-dependent dehydrogenases
[General function prediction only].
Length = 415
Score = 29.5 bits (66), Expect = 4.4
Identities = 19/71 (26%), Positives = 24/71 (33%), Gaps = 2/71 (2%)
Query: 346 EDALRERQGINGVASHTSPIAGKIFVLVGAGGAGRALAFGAKSRGARVIIFNRNYERAKA 405
LR R+ + K V+VGAG G A A RG +V +
Sbjct: 117 VVTLRLREDAEALKGGA--EPPKDVVVVGAGPIGLEAAEAAAKRGKKVTLIEAADRLGGQ 174
Query: 406 LADAVSGEALH 416
L D E L
Sbjct: 175 LLDPEVAEELA 185
>gnl|CDD|226347 COG3826, COG3826, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 236
Score = 29.1 bits (65), Expect = 4.7
Identities = 19/70 (27%), Positives = 27/70 (38%)
Query: 286 GTDFAGFSVGIPHKEPAVACCDEVHPLAKSIGAVNTIIRRPIDGKLVGYNTDCESAISAI 345
GTDF G + + P + V PL + G V + RP+ G Y +S +
Sbjct: 161 GTDFTGGEFVLVEQRPRMQSRPTVVPLRQGDGVVFAVRDRPVQGTRGWYRVPLRHGVSRL 220
Query: 346 EDALRERQGI 355
R GI
Sbjct: 221 RSGERHTVGI 230
>gnl|CDD|180802 PRK07035, PRK07035, short chain dehydrogenase; Provisional.
Length = 252
Score = 29.2 bits (66), Expect = 4.7
Identities = 18/45 (40%), Positives = 28/45 (62%), Gaps = 1/45 (2%)
Query: 367 GKIFVLVGAG-GAGRALAFGAKSRGARVIIFNRNYERAKALADAV 410
GKI ++ GA G G A+A +GA VI+ +R + +A+ADA+
Sbjct: 8 GKIALVTGASRGIGEAIAKLLAQQGAHVIVSSRKLDGCQAVADAI 52
>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 = 29.7 bits (67), Expect = 5.0
Identities = 16/37 (43%), Positives = 19/37 (51%)
Query: 373 VGAGGAGRALAFGAKSRGARVIIFNRNYERAKALADA 409
VGAG AG A A A GARVI+ + E +L
Sbjct: 169 VGAGPAGLAAALAAARAGARVILVDEQPEAGGSLLSE 205
>gnl|CDD|223643 COG0569, TrkA, K+ transport systems, NAD-binding component
[Inorganic ion transport and metabolism].
Length = 225
Score = 28.8 bits (65), Expect = 5.2
Identities = 16/61 (26%), Positives = 28/61 (45%), Gaps = 6/61 (9%)
Query: 368 KIFVLVGAGGAGRALAFGAKSRGARVIIFNRNYERAKALAD------AVSGEALHFEYLH 421
+++GAG GR++A G V++ +R+ ER + V G+A + L
Sbjct: 1 MKIIIIGAGRVGRSVARELSEEGHNVVLIDRDEERVEEFLADELDTHVVIGDATDEDVLE 60
Query: 422 E 422
E
Sbjct: 61 E 61
>gnl|CDD|223391 COG0314, MoaE, Molybdopterin converting factor, large subunit
[Coenzyme metabolism].
Length = 149
Score = 28.4 bits (64), Expect = 5.2
Identities = 25/86 (29%), Positives = 34/86 (39%), Gaps = 12/86 (13%)
Query: 313 AKSIGAVNT---IIRRPIDGKLVG------YNTDCESAISAIEDALRERQGINGVASH-- 361
GA+ T I+R DG+ V Y E + I +E+ G+ VA
Sbjct: 25 PSEAGAIVTFVGIVREENDGRRVEALEYEAYPEMAEKELEEIAAEAKEKWGLLRVAIIHR 84
Query: 362 TSPIA-GKIFVLVGAGGAGRALAFGA 386
+ G+ VLVG A R AF A
Sbjct: 85 IGELKIGEAIVLVGVASAHRKEAFEA 110
>gnl|CDD|223758 COG0686, Ald, Alanine dehydrogenase [Amino acid transport and
metabolism].
Length = 371
Score = 29.2 bits (66), Expect = 5.2
Identities = 27/96 (28%), Positives = 38/96 (39%), Gaps = 25/96 (26%)
Query: 371 VLVGAGGAGRALAFGAKSRGARVIIFNRNYERAKALADAVSGEALHFEYLHEFFPEKGMI 430
V++G G G A A GA V I + N +R + L D + G +H Y
Sbjct: 172 VVLGGGVVGTNAAKIAIGLGADVTILDLNIDRLRQL-DDLFGGRVHTLY----------- 219
Query: 431 LANASAIGMEPNSDQSPVPKEALKAYELVFDAVYTP 466
+ S I +EA+K +LV AV P
Sbjct: 220 -STPSNI------------EEAVKKADLVIGAVLIP 242
>gnl|CDD|176237 cd08276, MDR7, Medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
This group is a member of the medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, but lacks the zinc-binding
sites of the zinc-dependent alcohol dehydrogenases. The
medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P)-binding Rossmann fold domain of 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 = 336
Score = 29.0 bits (66), Expect = 5.3
Identities = 24/60 (40%), Positives = 31/60 (51%), Gaps = 6/60 (10%)
Query: 356 NGVASHTSPIAGKIFVLVGAGG-AGRALAFGAKSRGARVIIFNRNY---ERAKAL-ADAV 410
N + G ++ G GG + AL F AK+ GARVI + + ERAKAL AD V
Sbjct: 150 NALFGLGPLKPGDTVLVQGTGGVSLFALQF-AKAAGARVIATSSSDEKLERAKALGADHV 208
>gnl|CDD|181297 PRK08217, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 253
Score = 29.2 bits (66), Expect = 5.3
Identities = 16/57 (28%), Positives = 27/57 (47%), Gaps = 4/57 (7%)
Query: 365 IAGKIFVLVGAG-GAGRALAFGAKSRGARVIIFNRN---YERAKALADAVSGEALHF 417
+ K+ V+ G G GRA+A +GA++ + + N E A A A+ E +
Sbjct: 3 LKDKVIVITGGAQGLGRAMAEYLAQKGAKLALIDLNQEKLEEAVAECGALGTEVRGY 59
>gnl|CDD|187646 cd08942, RhlG_SDR_c, RhlG and related beta-ketoacyl reductases,
classical (c) SDRs. Pseudomonas aeruginosa RhlG is an
SDR-family beta-ketoacyl reductase involved in
Rhamnolipid biosynthesis. RhlG is similar to but
distinct from the FabG family of beta-ketoacyl-acyl
carrier protein (ACP) of type II fatty acid synthesis.
RhlG and related proteins are classical SDRs, with a
canonical active site tetrad and glycine-rich
NAD(P)-binding motif. SDRs are a functionally diverse
family of oxidoreductases that have a single domain with
a structurally conserved Rossmann fold (alpha/beta
folding pattern with a central beta-sheet), an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRs are approximately
350 residues. Sequence identity between different SDR
enzymes are typically in the 15-30% range, but the
enzymes share the Rossmann fold NAD-binding motif and
characteristic NAD-binding and catalytic sequence
patterns. These enzymes catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) numbering). In addition to the
Tyr and Lys, there is often an upstream Ser (Ser-138,
15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH
numbering) contributing to the active site; while
substrate binding is in the C-terminal region, which
determines specificity. The standard reaction mechanism
is a 4-pro-S hydride transfer and proton relay involving
the conserved Tyr and Lys, a water molecule stabilized
by Asn, and nicotinamide. Extended SDRs have additional
elements in the C-terminal region, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Some atypical SDRs have lost catalytic activity and/or
have an unusual NAD(P)-binding motif and missing or
unusual active site residues. Reactions catalyzed within
the SDR family include isomerization, decarboxylation,
epimerization, C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 250
Score = 29.0 bits (65), Expect = 5.5
Identities = 22/46 (47%), Positives = 28/46 (60%), Gaps = 4/46 (8%)
Query: 365 IAGKIFVLVGAG-GAGRALAFGAKSRGARVIIFNRNYERAKALADA 409
+AGKI ++ G G GR +A G GARVII R +A+A ADA
Sbjct: 4 VAGKIVLVTGGSRGIGRMIAQGFLEAGARVIISAR---KAEACADA 46
>gnl|CDD|224995 COG2084, MmsB, 3-hydroxyisobutyrate dehydrogenase and related
beta-hydroxyacid dehydrogenases [Lipid metabolism].
Length = 286
Score = 29.1 bits (66), Expect = 5.5
Identities = 12/43 (27%), Positives = 17/43 (39%)
Query: 372 LVGAGGAGRALAFGAKSRGARVIIFNRNYERAKALADAVSGEA 414
+G G G +A G V ++NR E+A L A
Sbjct: 5 FIGLGIMGSPMAANLLKAGHEVTVYNRTPEKAAELLAAAGATV 47
>gnl|CDD|235737 PRK06197, PRK06197, short chain dehydrogenase; Provisional.
Length = 306
Score = 29.2 bits (66), Expect = 5.6
Identities = 17/53 (32%), Positives = 28/53 (52%), Gaps = 9/53 (16%)
Query: 367 GKIFVLVGA-GGAG----RALAFGAKSRGARVIIFNRNYERAKALADAVSGEA 414
G++ V+ GA G G ALA ++GA V++ RN ++ KA A ++
Sbjct: 16 GRVAVVTGANTGLGYETAAALA----AKGAHVVLAVRNLDKGKAAAARITAAT 64
>gnl|CDD|235713 PRK06139, PRK06139, short chain dehydrogenase; Provisional.
Length = 330
Score = 29.3 bits (66), Expect = 5.6
Identities = 20/56 (35%), Positives = 32/56 (57%), Gaps = 4/56 (7%)
Query: 364 PIAGKIFVLVGAG-GAGRALAFGAKSRGARVIIFNRNYERAKALAD---AVSGEAL 415
P+ G + V+ GA G G+A A RGAR+++ R+ E +A+A+ A+ E L
Sbjct: 4 PLHGAVVVITGASSGIGQATAEAFARRGARLVLAARDEEALQAVAEECRALGAEVL 59
>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 = 28.8 bits (65), Expect = 5.6
Identities = 18/50 (36%), Positives = 23/50 (46%), Gaps = 2/50 (4%)
Query: 371 VLV-GAG-GAGRALAFGAKSRGARVIIFNRNYERAKALADAVSGEALHFE 418
VLV GA G G A+A GARV +RN+E+ L + F
Sbjct: 1 VLVTGAAQGIGYAVARALAEAGARVAAVDRNFEQLLELVADLRRYGYPFA 50
>gnl|CDD|224786 COG1874, LacA, Beta-galactosidase [Carbohydrate transport and
metabolism].
Length = 673
Score = 29.3 bits (66), Expect = 5.7
Identities = 20/54 (37%), Positives = 29/54 (53%), Gaps = 5/54 (9%)
Query: 445 QSPVPKEALKAYELVFDAVYTPRNTRLLREAAEVGATVVSGVEMFIRQALGQFR 498
QSP P+E K+++ V V + NTRL RE A VG + S + + +A Q
Sbjct: 354 QSPSPRE--KSHDGVISPVLSE-NTRLFREVAAVGEELKSLPD--VMEARVQAY 402
>gnl|CDD|181225 PRK08085, PRK08085, gluconate 5-dehydrogenase; Provisional.
Length = 254
Score = 29.0 bits (65), Expect = 5.7
Identities = 15/46 (32%), Positives = 20/46 (43%)
Query: 368 KIFVLVGAGGAGRALAFGAKSRGARVIIFNRNYERAKALADAVSGE 413
I + A G G LA G GA +II + ERA+ + E
Sbjct: 11 NILITGSAQGIGFLLATGLAEYGAEIIINDITAERAELAVAKLRQE 56
>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 = 5.8
Identities = 18/48 (37%), Positives = 27/48 (56%), Gaps = 3/48 (6%)
Query: 374 GAGGAGRALAFGAKSRGARVIIFNRNYERAKALADAVS---GEALHFE 418
GA G G+A+A GA V+I + E A+A+A A+ G+A+ E
Sbjct: 7 GAAGIGKAIAGTLAKAGASVVIADLKSEGAEAVAAAIQQAGGQAIGLE 54
>gnl|CDD|223318 COG0240, GpsA, Glycerol-3-phosphate dehydrogenase [Energy
production and conversion].
Length = 329
Score = 29.1 bits (66), Expect = 6.2
Identities = 32/126 (25%), Positives = 49/126 (38%), Gaps = 25/126 (19%)
Query: 368 KIFVLVGAGGAGRALAFGAKSRGARVIIFNRNYERAKALADAVSGEALHFEYLHEFFPEK 427
KI V+ GAG G ALA G V ++ R+ E + + + +YL
Sbjct: 3 KIAVI-GAGSWGTALAKVLARNGHEVRLWGRDEEIVAEINE----TRENPKYL------P 51
Query: 428 GMILANASAIGMEPNSDQSPVPKEALKAYELVFDAV---YTPRNTRLLREAAEVGATVVS 484
G++L PN + EAL +++ AV R L+ A +VS
Sbjct: 52 GILLP--------PNLKATTDLAEALDGADIIVIAVPSQALREVLRQLKPLLLKDAIIVS 103
Query: 485 ---GVE 487
G+E
Sbjct: 104 ATKGLE 109
>gnl|CDD|237225 PRK12843, PRK12843, putative FAD-binding dehydrogenase; Reviewed.
Length = 578
Score = 29.3 bits (66), Expect = 6.2
Identities = 10/28 (35%), Positives = 17/28 (60%)
Query: 371 VLVGAGGAGRALAFGAKSRGARVIIFNR 398
+++GAG AG + A A G +V++ R
Sbjct: 20 IVIGAGAAGMSAALFAAIAGLKVLLVER 47
>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 = 6.2
Identities = 15/57 (26%), Positives = 21/57 (36%), Gaps = 13/57 (22%)
Query: 341 AISAIEDALRERQGINGVASHTSPIAGKIFVLVGAGG-AGRALAFGAKSRGARVIIF 396
A++ I A E + GV ++ GG G ALA A G + I
Sbjct: 35 ALNLILLAEEEGKLPKGV------------IIESTGGNTGIALAAAAARLGLKCTIV 79
>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 = 28.7 bits (64), Expect = 6.3
Identities = 17/57 (29%), Positives = 26/57 (45%), Gaps = 4/57 (7%)
Query: 365 IAGKIFVLVG-AGGAGRALAFGAKSRGARVIIFNRNYERAKALADAVS---GEALHF 417
+ K ++ G GG G A GA+V +F+ N E A+ +A + G A F
Sbjct: 1 LKDKTAIVTGGGGGIGGATCRRFAEEGAKVAVFDLNREAAEKVAADIRAKGGNAQAF 57
>gnl|CDD|180817 PRK07060, PRK07060, short chain dehydrogenase; Provisional.
Length = 245
Score = 28.5 bits (64), Expect = 6.6
Identities = 20/51 (39%), Positives = 24/51 (47%), Gaps = 1/51 (1%)
Query: 366 AGKIFVLVGAG-GAGRALAFGAKSRGARVIIFNRNYERAKALADAVSGEAL 415
+GK ++ GA G GRA A RGARV+ RN LA E L
Sbjct: 8 SGKSVLVTGASSGIGRACAVALAQRGARVVAAARNAAALDRLAGETGCEPL 58
>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 = 28.7 bits (65), Expect = 6.6
Identities = 25/119 (21%), Positives = 35/119 (29%), Gaps = 31/119 (26%)
Query: 368 KIFVLVGAGGAGRALAFGAKSRGARVI--IFNRNYERAKALADAVSGEALHFEYLHEFFP 425
+ + AGG G AK+RGARVI N + ++L G +Y
Sbjct: 147 TVLIHGAAGGVGSFAVQLAKARGARVIATASAANADFLRSL-----GADEVIDY------ 195
Query: 426 EKGMILANASAIGMEPNSDQSPVPKEALKAYELVFDAVYTPRNTRLLREAAEVGATVVS 484
+ A + V D V R L G +VS
Sbjct: 196 -----------------TKGDFERAAAPGGVDAVLDTVGGETLARSLALVKP-GGRLVS 236
>gnl|CDD|240646 cd12169, PGDH_like_1, Putative D-3-Phosphoglycerate Dehydrogenases.
Phosphoglycerate dehydrogenases (PGDHs) catalyze the
initial step in the biosynthesis of L-serine from
D-3-phosphoglycerate. PGDHs come in 3 distinct
structural forms, with this first group being related to
2-hydroxy acid dehydrogenases, sharing structural
similarity to formate and glycerate dehydrogenases of
the D-specific 2-hydroxyacid dehydrogenase superfamily,
which also include groups such as L-alanine
dehydrogenase and S-adenosylhomocysteine hydrolase.
Despite often low sequence identity, these proteins
typically have a characteristic arrangement of 2 similar
subdomains of the alpha/beta Rossmann fold NAD+ binding
form. The NAD+ binding domain is inserted within the
linear sequence of the mostly N-terminal catalytic
domain, which has a similar domain structure to the
internal NAD binding domain. Structurally, these domains
are connected by extended alpha helices and create a
cleft in which NAD is bound, primarily to the C-terminal
portion of the 2nd (internal) domain. Some related
proteins have similar structural subdomain but with a
tandem arrangement of the catalytic and NAD-binding
subdomains in the linear sequence. Many, not all,
members of this family are dimeric.
Length = 308
Score = 28.6 bits (65), Expect = 6.8
Identities = 22/54 (40%), Positives = 28/54 (51%), Gaps = 4/54 (7%)
Query: 366 AGKIFVLVGAGGAGRALAFGAKSRGARVIIFNRNY--ERAKAL--ADAVSGEAL 415
AGK +VG G G +A ++ G RVI ++ N ERA A AVS E L
Sbjct: 141 AGKTLGIVGLGRIGARVARIGQAFGMRVIAWSSNLTAERAAAAGVEAAVSKEEL 194
>gnl|CDD|181120 PRK07792, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 306
Score = 29.0 bits (65), Expect = 6.8
Identities = 15/41 (36%), Positives = 25/41 (60%), Gaps = 1/41 (2%)
Query: 356 NGVASHTSPIAGKIFVLVGAG-GAGRALAFGAKSRGARVII 395
+ ++T+ ++GK+ V+ GA G GRA A G GA V++
Sbjct: 1 SPRTTNTTDLSGKVAVVTGAAAGLGRAEALGLARLGATVVV 41
>gnl|CDD|176260 cd08300, alcohol_DH_class_III, class III alcohol dehydrogenases.
Members identified as glutathione-dependent formaldehyde
dehydrogenase(FDH), a member of the zinc
dependent/medium chain alcohol dehydrogenase family.
FDH converts formaldehyde and NAD(P) to formate and
NAD(P)H. The initial step in this process the
spontaneous formation of a S-(hydroxymethyl)glutathione
adduct from formaldehyde and glutathione, followed by
FDH-mediated oxidation (and detoxification) of the
adduct to S-formylglutathione. MDH family uses NAD(H)
as a cofactor in the interconversion of alcohols and
aldehydes or ketones. Like many zinc-dependent alcohol
dehydrogenases (ADH) of the medium chain alcohol
dehydrogenase/reductase family (MDR), these FDHs form
dimers, with 4 zinc ions per dimer. The medium chain
alcohol dehydrogenase family (MDR) have a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The N-terminal region typically has an
all-beta catalytic domain. These proteins typically form
dimers (typically higher plants, mammals) or tetramers
(yeast, bacteria), and have 2 tightly bound zinc atoms
per subunit. Alcohol dehydrogenase in the liver
converts ethanol and NAD+ to acetaldehyde and NADH,
while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which have a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES.
These proteins typically form dimers (typically higher
plants, mammals) or tetramers (yeast, bacteria), and
have 2 tightly bound zinc atoms per subunit, a catalytic
zinc at the active site and a structural zinc in a lobe
of the catalytic domain. NAD(H) binding occurs in the
cleft between the catalytic and coenzyme-binding
domains at the active site, and coenzyme binding induces
a conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
Length = 368
Score = 28.7 bits (65), Expect = 6.9
Identities = 14/40 (35%), Positives = 20/40 (50%), Gaps = 1/40 (2%)
Query: 357 GVASHTSPI-AGKIFVLVGAGGAGRALAFGAKSRGARVII 395
G +T+ + G + G G G A+ GAK+ GA II
Sbjct: 176 GAVLNTAKVEPGSTVAVFGLGAVGLAVIQGAKAAGASRII 215
>gnl|CDD|178341 PLN02740, PLN02740, Alcohol dehydrogenase-like.
Length = 381
Score = 29.0 bits (65), Expect = 6.9
Identities = 17/40 (42%), Positives = 24/40 (60%), Gaps = 1/40 (2%)
Query: 357 GVASHTSPI-AGKIFVLVGAGGAGRALAFGAKSRGARVII 395
G A +T+ + AG + G G G A+A GA++RGA II
Sbjct: 188 GAAWNTANVQAGSSVAIFGLGAVGLAVAEGARARGASKII 227
>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 = 28.7 bits (65), Expect = 7.0
Identities = 18/52 (34%), Positives = 25/52 (48%), Gaps = 2/52 (3%)
Query: 371 VLV--GAGGAGRALAFGAKSRGARVIIFNRNYERAKALADAVSGEALHFEYL 420
VL+ G G GR LA RGA+V+I + N + A+ A+ V Y
Sbjct: 2 VLITGGGSGIGRLLALEFAKRGAKVVILDINEKGAEETANNVRKAGGKVHYY 53
>gnl|CDD|237790 PRK14694, PRK14694, putative mercuric reductase; Provisional.
Length = 468
Score = 28.8 bits (64), Expect = 7.3
Identities = 12/27 (44%), Positives = 17/27 (62%)
Query: 372 LVGAGGAGRALAFGAKSRGARVIIFNR 398
++G+GG+ A A A RGARV + R
Sbjct: 11 VIGSGGSAMAAALKATERGARVTLIER 37
>gnl|CDD|234353 TIGR03788, marine_srt_targ, marine proteobacterial sortase target
protein. Members of this protein family are restricted
to the Proteobacteria. Each contains a C-terminal
sortase-recognition motif, transmembrane domain, and
basic residues cluster at the the C-terminus, and is
encoded adjacent to a sortase gene. This protein is
frequently the only sortase target in its genome, which
is as unusual its occurrence in Gram-negative rather
than Gram-positive genomes. Many bacteria with this
system are marine. In addition to the LPXTG signal,
members carry a vault protein inter-alpha-trypsin
inhibitor domain (pfam08487) and a von Willebrand factor
type A domain (pfam00092).
Length = 596
Score = 28.9 bits (65), Expect = 7.3
Identities = 15/26 (57%), Positives = 16/26 (61%), Gaps = 3/26 (11%)
Query: 490 IRQALGQFRLFTGGL--APED-FMRK 512
IR LG RLFT G+ AP FMRK
Sbjct: 391 IRTKLGDSRLFTVGIGSAPNSYFMRK 416
>gnl|CDD|176242 cd08282, PFDH_like, Pseudomonas putida aldehyde-dismutating
formaldehyde dehydrogenase (PFDH). Formaldehyde
dehydrogenase (FDH) is a member of the
zinc-dependent/medium chain alcohol dehydrogenase
family. Unlike typical FDH, Pseudomonas putida
aldehyde-dismutating FDH (PFDH) is
glutathione-independent. PFDH converts 2 molecules of
aldehydes to corresponding carboxylic acid and alcohol.
MDH family uses NAD(H) as a cofactor in the
interconversion of alcohols and aldehydes, or ketones.
Like the zinc-dependent alcohol dehydrogenases (ADH) of
the medium chain alcohol dehydrogenase/reductase family
(MDR), these tetrameric FDHs have a catalytic zinc that
resides between the catalytic and NAD(H)binding domains
and a structural zinc in a lobe of the catalytic domain.
Unlike ADH, where NAD(P)(H) acts as a cofactor, NADH in
FDH is a tightly bound redox cofactor (similar to
nicotinamide proteins). The medium chain alcohol
dehydrogenase family (MDR) has a NAD(P)(H)-binding
domain in a Rossmann fold of an beta-alpha form. The
N-terminal region typically has an all-beta catalytic
domain. These proteins typically form dimers (typically
higher plants, mammals) or tetramers (yeast, bacteria),
and have 2 tightly bound zinc atoms per subunit.
Length = 375
Score = 28.7 bits (65), Expect = 7.3
Identities = 21/85 (24%), Positives = 26/85 (30%), Gaps = 29/85 (34%)
Query: 374 GAGGAGRALAFGAKSRGA-RVIIFNRNYERAKALADAVSGEALHFEYLHEFFPEKGMILA 432
GAG G A+ A RGA RV + + ER L
Sbjct: 184 GAGPVGLMAAYSAILRGASRVYVVDHVPER----------------------------LD 215
Query: 433 NASAIGMEPNSDQSPVPKEALKAYE 457
A +IG P P E + E
Sbjct: 216 LAESIGAIPIDFSDGDPVEQILGLE 240
>gnl|CDD|236453 PRK09287, PRK09287, 6-phosphogluconate dehydrogenase; Validated.
Length = 459
Score = 28.9 bits (66), Expect = 7.5
Identities = 15/47 (31%), Positives = 22/47 (46%), Gaps = 2/47 (4%)
Query: 379 GRALAFGAKSRGARVIIFNRNYERAKA-LADAVSGEALH-FEYLHEF 423
G+ LA S G V ++NR E+ LA+ G+ + L EF
Sbjct: 2 GKNLALNIASHGYTVAVYNRTPEKTDEFLAEEGKGKKIVPAYTLEEF 48
>gnl|CDD|217856 pfam04041, DUF377, Domain of unknown function (DUF377). This
family contains many hypothetical proteins, some of
which are predicted to be glycosyl hydrolases. This
family was noted to belong to the Beta fructosidase
superfamily in.
Length = 311
Score = 28.6 bits (64), Expect = 7.5
Identities = 20/108 (18%), Positives = 34/108 (31%), Gaps = 15/108 (13%)
Query: 265 FNGIYVPMLVDDVKEFFRTYSGTDFAGFSVGI------------PHKEPAVACCDEVHPL 312
F G+ P +V ++ TY+G D + + K +
Sbjct: 89 FWGVEDPRVVKIGSRYYMTYTGYDGKYARLCVATTKNFLTWARLGVKFAEFEGNYDRPSG 148
Query: 313 AKSIGAVNTIIRRPIDGKLVGYNTDCESAISAIEDALRERQGINGVAS 360
GA I I+GK V Y D ++ +D + + S
Sbjct: 149 WTKSGA---IFPVKINGKYVMYFRDSNIWLAVSDDGVHWENEREPLGS 193
>gnl|CDD|184298 PRK13748, PRK13748, putative mercuric reductase; Provisional.
Length = 561
Score = 29.0 bits (65), Expect = 7.7
Identities = 15/47 (31%), Positives = 22/47 (46%)
Query: 352 RQGINGVASHTSPIAGKIFVLVGAGGAGRALAFGAKSRGARVIIFNR 398
R + G H+ ++G+GGA A A A +GARV + R
Sbjct: 83 RGWLGGADKHSGNERPLHVAVIGSGGAAMAAALKAVEQGARVTLIER 129
>gnl|CDD|187636 cd08931, SDR_c9, classical (c) SDR, subgroup 9. This subgroup has
the canonical active site tetrad and NAD-binding motif
of the classical SDRs. SDRs are a functionally diverse
family of oxidoreductases that have a single domain with
a structurally conserved Rossmann fold (alpha/beta
folding pattern with a central beta-sheet), an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRs are approximately
350 residues. Sequence identity between different SDR
enzymes are typically in the 15-30% range, but the
enzymes share the Rossmann fold NAD-binding motif and
characteristic NAD-binding and catalytic sequence
patterns. These enzymes catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) numbering). In addition to the
Tyr and Lys, there is often an upstream Ser (Ser-138,
15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH
numbering) contributing to the active site; while
substrate binding is in the C-terminal region, which
determines specificity. The standard reaction mechanism
is a 4-pro-S hydride transfer and proton relay involving
the conserved Tyr and Lys, a water molecule stabilized
by Asn, and nicotinamide. Extended SDRs have additional
elements in the C-terminal region, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Some atypical SDRs have lost catalytic activity and/or
have an unusual NAD(P)-binding motif and missing or
unusual active site residues. Reactions catalyzed within
the SDR family include isomerization, decarboxylation,
epimerization, C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 227
Score = 28.6 bits (64), Expect = 7.7
Identities = 13/48 (27%), Positives = 21/48 (43%)
Query: 369 IFVLVGAGGAGRALAFGAKSRGARVIIFNRNYERAKALADAVSGEALH 416
IF+ A G GR A G V +++ + + ALA + E +
Sbjct: 3 IFITGAASGIGRETALLFARNGWFVGLYDIDEDGLAALAAELGAENVV 50
>gnl|CDD|181131 PRK07814, PRK07814, short chain dehydrogenase; Provisional.
Length = 263
Score = 28.6 bits (64), Expect = 7.9
Identities = 14/49 (28%), Positives = 24/49 (48%), Gaps = 1/49 (2%)
Query: 365 IAGKIFVLVGAG-GAGRALAFGAKSRGARVIIFNRNYERAKALADAVSG 412
+ ++ V+ GAG G G A+A GA V+I R + +A+ +
Sbjct: 8 LDDQVAVVTGAGRGLGAAIALAFAEAGADVLIAARTESQLDEVAEQIRA 56
>gnl|CDD|225885 COG3349, COG3349, Uncharacterized conserved protein [Function
unknown].
Length = 485
Score = 28.9 bits (65), Expect = 8.0
Identities = 16/55 (29%), Positives = 23/55 (41%), Gaps = 1/55 (1%)
Query: 371 VLVGAGGAGRALAFGAKSRGARVIIFNRNYERAKALADAVSGEALHFEY-LHEFF 424
+ GAG AG A A+ G V ++ +A + H E+ LH FF
Sbjct: 4 AIAGAGLAGLAAAYELADAGYDVTLYEARDRLGGKVASWRDSDGNHVEHGLHVFF 58
>gnl|CDD|176232 cd08271, MDR5, Medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
This group is a member of the medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, but lacks the zinc-binding
sites of the zinc-dependent alcohol dehydrogenases. The
medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P)-binding Rossmann fold domain of 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 = 325
Score = 28.8 bits (65), Expect = 8.0
Identities = 30/122 (24%), Positives = 40/122 (32%), Gaps = 27/122 (22%)
Query: 316 IGAVNTIIRRPIDGKLVGYNTD-------CESAISAIEDALRERQGINGVASHTSPIAG- 367
+ AV + G V Y+ E + L ++ + P AG
Sbjct: 68 VVAVGAKVTGWKVGDRVAYHASLARGGSFAEYTVVDARAVLPLPDSLSFEEAAALPCAGL 127
Query: 368 ----------------KIFVLVGAGGAGRALAFGAKSRGARVIIF--NRNYERAKAL-AD 408
I + GAGG G AK G RVI RN+E K+L AD
Sbjct: 128 TAYQALFKKLRIEAGRTILITGGAGGVGSFAVQLAKRAGLRVITTCSKRNFEYVKSLGAD 187
Query: 409 AV 410
V
Sbjct: 188 HV 189
>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 = 28.4 bits (64), Expect = 8.1
Identities = 15/32 (46%), Positives = 22/32 (68%), Gaps = 5/32 (15%)
Query: 367 GKIFVLVGAGGA-GR--ALAFGAKSRGARVII 395
G++ ++ GAGG GR ALAF RGA+V++
Sbjct: 5 GRVVLVTGAGGGLGRAYALAFAE--RGAKVVV 34
>gnl|CDD|235702 PRK06124, PRK06124, gluconate 5-dehydrogenase; Provisional.
Length = 256
Score = 28.5 bits (64), Expect = 8.4
Identities = 15/57 (26%), Positives = 26/57 (45%), Gaps = 1/57 (1%)
Query: 365 IAGKIFVLVGAG-GAGRALAFGAKSRGARVIIFNRNYERAKALADAVSGEALHFEYL 420
+AG++ ++ G+ G G +A GA V++ RN +A A+ E L
Sbjct: 9 LAGQVALVTGSARGLGFEIARALAGAGAHVLVNGRNAATLEAAVAALRAAGGAAEAL 65
>gnl|CDD|172692 PRK14204, PRK14204, camphor resistance protein CrcB; Provisional.
Length = 127
Score = 27.6 bits (61), Expect = 8.5
Identities = 21/61 (34%), Positives = 30/61 (49%), Gaps = 5/61 (8%)
Query: 193 ISQLLGPKFGGFLVYGSLGG---KSVPGLPTLVSLKQVYQLEHIN--PDTKIFGLVSNPV 247
++ G FG F V G LGG S GL TL L++ +E I+ T + GL+ +
Sbjct: 59 AKKVFGDDFGIFFVTGVLGGFTTFSSYGLDTLKLLQKSQYIEAISYVLGTNLLGLIGVAI 118
Query: 248 G 248
G
Sbjct: 119 G 119
>gnl|CDD|240649 cd12172, PGDH_like_2, Putative D-3-Phosphoglycerate Dehydrogenases,
NAD-binding and catalytic domains. Phosphoglycerate
dehydrogenases (PGDHs) catalyze the initial step in the
biosynthesis of L-serine from D-3-phosphoglycerate.
PGDHs come in 3 distinct structural forms, with this
first group being related to 2-hydroxy acid
dehydrogenases, sharing structural similarity to formate
and glycerate dehydrogenases of the D-specific
2-hydroxyacid dehydrogenase superfamily, which also
include groups such as L-alanine dehydrogenase and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. Many, not all, members of this family are
dimeric.
Length = 306
Score = 28.6 bits (65), Expect = 8.5
Identities = 10/43 (23%), Positives = 20/43 (46%)
Query: 365 IAGKIFVLVGAGGAGRALAFGAKSRGARVIIFNRNYERAKALA 407
+ GK ++G G G+A+A G +V+ ++ + A
Sbjct: 140 LYGKTLGIIGLGRIGKAVARRLSGFGMKVLAYDPYPDEEFAKE 182
>gnl|CDD|176189 cd05286, QOR2, Quinone oxidoreductase (QOR). Quinone
oxidoreductase (QOR) and 2-haloacrylate reductase. 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. 2-haloacrylate reductase,
a member of this subgroup, catalyzes the NADPH-dependent
reduction of a carbon-carbon double bond in
organohalogen compounds. Although similar to QOR,
Burkholderia 2-haloacrylate reductase does not act on
the quinones 1,4-benzoquinone and 1,4-naphthoquinone.
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 = 320
Score = 28.6 bits (65), Expect = 8.5
Identities = 14/27 (51%), Positives = 15/27 (55%), Gaps = 2/27 (7%)
Query: 370 FVLV--GAGGAGRALAFGAKSRGARVI 394
VLV AGG G L AK+ GA VI
Sbjct: 139 TVLVHAAAGGVGLLLTQWAKALGATVI 165
>gnl|CDD|233635 TIGR01915, npdG, NADPH-dependent F420 reductase. This model
represents a subset of a parent family described by
pfam03807. Unlike the parent family, members of this
family are found only in species with evidence of
coenzyme F420. All members of this family are believed
to act as NADPH-dependent F420 reductase [Energy
metabolism, Electron transport].
Length = 219
Score = 28.2 bits (63), Expect = 8.8
Identities = 18/49 (36%), Positives = 25/49 (51%)
Query: 368 KIFVLVGAGGAGRALAFGAKSRGARVIIFNRNYERAKALADAVSGEALH 416
KI VL G G G+ LA G ++II +R+ E+A+ A E H
Sbjct: 2 KIAVLGGTGDQGKGLALRLAKAGNKIIIGSRDLEKAEEAAAKALEELGH 50
>gnl|CDD|223137 COG0059, IlvC, Ketol-acid reductoisomerase [Amino acid transport
and metabolism / Coenzyme metabolism].
Length = 338
Score = 28.3 bits (64), Expect = 8.8
Identities = 14/47 (29%), Positives = 22/47 (46%), Gaps = 4/47 (8%)
Query: 363 SPIAGKIFVLVGAGGAGRALAFGAKSRGARVIIFNR----NYERAKA 405
+ GK ++G G G A A + G VII R ++++AK
Sbjct: 14 DLLKGKKVAIIGYGSQGHAQALNLRDSGLNVIIGLRKGSSSWKKAKE 60
>gnl|CDD|217590 pfam03486, HI0933_like, HI0933-like protein.
Length = 405
Score = 28.7 bits (65), Expect = 9.1
Identities = 10/29 (34%), Positives = 17/29 (58%)
Query: 371 VLVGAGGAGRALAFGAKSRGARVIIFNRN 399
+++G G AG A A RG RV++ ++
Sbjct: 4 IVIGGGAAGLMAAISAAKRGRRVLLIDKG 32
>gnl|CDD|240287 PTZ00142, PTZ00142, 6-phosphogluconate dehydrogenase; Provisional.
Length = 470
Score = 28.6 bits (64), Expect = 9.2
Identities = 12/33 (36%), Positives = 19/33 (57%)
Query: 370 FVLVGAGGAGRALAFGAKSRGARVIIFNRNYER 402
L+G G+ LA SRG ++ ++NR YE+
Sbjct: 4 IGLIGLAVMGQNLALNIASRGFKISVYNRTYEK 36
>gnl|CDD|131083 TIGR02028, ChlP, geranylgeranyl reductase. This model represents
the reductase which acts reduces the geranylgeranyl
group to the phytyl group in the side chain of
chlorophyll. It is unclear whether the enzyme has a
preference for acting before or after the attachment of
the side chain to chlorophyllide a by chlorophyll
synthase. This clade is restricted to plants and
cyanobacteria to separate it from the homologues which
act in the biosynthesis of bacteriochlorophyll
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Chlorophyll and bacteriochlorphyll].
Length = 398
Score = 28.3 bits (63), Expect = 9.3
Identities = 29/115 (25%), Positives = 51/115 (44%), Gaps = 5/115 (4%)
Query: 372 LVGAGGAGRALAFGAKSRGARVIIFNRNYERAKALADAVSGEALHFEYLHEFFPEKGMIL 431
+VG G AG + A S G + + R + AK G A+ + EF + +I
Sbjct: 5 VVGGGPAGASAAETLASAGIQTFLLERKPDNAKP-----CGGAIPLCMVDEFALPRDIID 59
Query: 432 ANASAIGMEPNSDQSPVPKEALKAYELVFDAVYTPRNTRLLREAAEVGATVVSGV 486
+ + M S+ + LK +E + ++ L R AA+ GAT+++G+
Sbjct: 60 RRVTKMKMISPSNIAVDIGRTLKEHEYIGMLRREVLDSFLRRRAADAGATLINGL 114
>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 = 28.3 bits (63), Expect = 9.4
Identities = 24/104 (23%), Positives = 37/104 (35%), Gaps = 14/104 (13%)
Query: 370 FVLVGAGGAGRALAFGAKSRGARVIIFNRN--------YERAKALADAVSGEALHFEYLH 421
+L GG GRALA RG R+++ R+ E A L L
Sbjct: 2 LILGATGGIGRALARALAGRGWRLLLSGRDAGALAGLAAEVGALARPADVAAELEVWALA 61
Query: 422 EFFPEKGMILANASAIGMEPNSDQSPVPKEALKAYELVFDAVYT 465
+ +++ A AI P+ + A+ + DA T
Sbjct: 62 QELGPLDLLVYAAGAI------LGKPLARTKPAAWRRILDANLT 99
>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 = 9.5
Identities = 15/47 (31%), Positives = 20/47 (42%), Gaps = 7/47 (14%)
Query: 371 VLVGAGG--AGRALAFGAKSRGARVIIFN-RNYERAKALADAVSGEA 414
V+V AG AGR A +R A + + E A+A V A
Sbjct: 206 VIVQAGSSEAGREFA----ARHAEAVFTAQQTLEEAQAFYADVKARA 248
>gnl|CDD|187537 cd05226, SDR_e_a, Extended (e) and atypical (a) SDRs. Extended or
atypical short-chain dehydrogenases/reductases (SDRs,
aka tyrosine-dependent oxidoreductases) are distinct
from classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. Atypical SDRs generally
lack the catalytic residues characteristic of the SDRs,
and their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Atypical SDRs include biliverdin IX beta
reductase (BVR-B,aka flavin reductase), NMRa (a negative
transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they 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 numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, 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. 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.
Length = 176
Score = 27.8 bits (62), Expect = 9.5
Identities = 13/42 (30%), Positives = 17/42 (40%)
Query: 369 IFVLVGAGGAGRALAFGAKSRGARVIIFNRNYERAKALADAV 410
I +L G GRALA +G V + RN +R
Sbjct: 1 ILILGATGFIGRALARELLEQGHEVTLLVRNTKRLSKEDQEP 42
>gnl|CDD|129951 TIGR00873, gnd, 6-phosphogluconate dehydrogenase (decarboxylating).
This model does not specify whether the cofactor is
NADP only (EC 1.1.1.44), NAD only, or both. The model
does not assign an EC number for that reason [Energy
metabolism, Pentose phosphate pathway].
Length = 467
Score = 28.5 bits (64), Expect = 9.7
Identities = 19/72 (26%), Positives = 30/72 (41%), Gaps = 7/72 (9%)
Query: 372 LVGAGGAGRALAFGAKSRGARVIIFNRNYERAKA-LADAVSGEALH-FEYLHEFF----- 424
++G G LA G V ++NR E+ LA+ G+ + + EF
Sbjct: 4 VIGLAVMGSNLALNMADHGFTVSVYNRTPEKTDEFLAEHAKGKKIVGAYSIEEFVQSLER 63
Query: 425 PEKGMILANASA 436
P K M++ A A
Sbjct: 64 PRKIMLMVKAGA 75
>gnl|CDD|180822 PRK07069, PRK07069, short chain dehydrogenase; Validated.
Length = 251
Score = 28.1 bits (63), Expect = 9.8
Identities = 14/48 (29%), Positives = 23/48 (47%), Gaps = 1/48 (2%)
Query: 368 KIFVLVGAGGAGRALAFGAKSRGARVIIFNRNYER-AKALADAVSGEA 414
+ F+ AGG GRA+A +GA+V + + N A A ++
Sbjct: 1 RAFITGAAGGLGRAIARRMAEQGAKVFLTDINDAAGLDAFAAEINAAH 48
>gnl|CDD|187555 cd05244, BVR-B_like_SDR_a, biliverdin IX beta reductase (BVR-B, aka
flavin reductase)-like proteins; atypical (a) SDRs.
Human BVR-B catalyzes pyridine nucleotide-dependent
production of bilirubin-IX beta during fetal
development; in the adult BVR-B has flavin and ferric
reductase activities. Human BVR-B catalyzes the
reduction of FMN, FAD, and riboflavin. Recognition of
flavin occurs mostly by hydrophobic interactions,
accounting for the broad substrate specificity. Atypical
SDRs are distinct from classical SDRs. BVR-B does not
share the key catalytic triad, or conserved tyrosine
typical of SDRs. The glycine-rich NADP-binding motif of
BVR-B is GXXGXXG, which is similar but not identical to
the pattern seen in extended SDRs. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Atypical SDRs include
biliverdin IX beta reductase (BVR-B,aka flavin
reductase), NMRa (a negative transcriptional regulator
of various fungi), progesterone 5-beta-reductase like
proteins, phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they 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 numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, 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. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, 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.
Length = 207
Score = 28.0 bits (63), Expect = 9.9
Identities = 11/43 (25%), Positives = 19/43 (44%)
Query: 368 KIFVLVGAGGAGRALAFGAKSRGARVIIFNRNYERAKALADAV 410
KI ++ G G A+ A +RG V R+ + A + +
Sbjct: 1 KIAIIGATGRTGSAIVREALARGHEVTALVRDPAKLPAEHEKL 43
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 0.136 0.391
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: 26,819,167
Number of extensions: 2715213
Number of successful extensions: 3528
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3441
Number of HSP's successfully gapped: 305
Length of query: 518
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 417
Effective length of database: 6,457,848
Effective search space: 2692922616
Effective search space used: 2692922616
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)