RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy612
(1005 letters)
>gnl|CDD|238429 cd00833, PKS, polyketide synthases (PKSs) polymerize simple fatty
acids into a large variety of different products, called
polyketides, by successive decarboxylating Claisen
condensations. PKSs can be divided into 2 groups,
modular type I PKSs consisting of one or more large
multifunctional proteins and iterative type II PKSs,
complexes of several monofunctional subunits.
Length = 421
Score = 585 bits (1511), Expect = 0.0
Identities = 202/422 (47%), Positives = 271/422 (64%), Gaps = 10/422 (2%)
Query: 465 IAIIGMSGRFPAARNINEFWKILINNKDVISEIPEKIFDWKLYYENPIKSSNKINSKWYG 524
IAI+GM+ RFP A + +EFW+ L+ +D ISEIPE +D YY +P K K ++ G
Sbjct: 3 IAIVGMACRFPGAADPDEFWENLLEGRDAISEIPEDRWDADGYYPDPGKP-GKTYTRRGG 61
Query: 525 SIPGIDEFDPLFFEISPLEAERMDPRQRHLLQESWLALEDAGYGPNQIANQKIGMFVGVE 584
+ +D FD FF ISP EAE MDP+QR LL+ +W ALEDAGY P +A + G+FVG
Sbjct: 62 FLDDVDAFDAAFFGISPREAEAMDPQQRLLLEVAWEALEDAGYSPESLAGSRTGVFVGAS 121
Query: 585 EGSNYQDRLDQVN-------LTSTHNAILSARLAYFMDLKGPVMAINTACSSSLVATHIA 637
S+Y + L + T T A L+ R++YF DL+GP + ++TACSSSLVA H+A
Sbjct: 122 -SSDYLELLARDPDEIDAYAATGTSRAFLANRISYFFDLRGPSLTVDTACSSSLVALHLA 180
Query: 638 CQSLRQHECDTAISAGVNLMISPEAYIAMTSAGMLSPDGKCYVFDERANGLVPSEAVVAV 697
CQSLR ECD A+ GVNL++SP+ ++ + AGMLSPDG+C FD A+G V E V V
Sbjct: 181 CQSLRSGECDLALVGGVNLILSPDMFVGFSKAGMLSPDGRCRPFDADADGYVRGEGVGVV 240
Query: 698 VLKRLSRALSDGDPIHAIIRGSGINYDGKTNGITAPNGISQTELIKSVYKKSNLNPEDIN 757
VLKRLS AL DGD I+A+IRGS +N DG+T GITAP+G +Q LI+ Y ++ ++P DI+
Sbjct: 241 VLKRLSDALRDGDRIYAVIRGSAVNQDGRTKGITAPSGEAQAALIRRAYARAGVDPSDID 300
Query: 758 YIITHGTGTKLGDPVEINALHDVFKNKTYNQKFCAITSNKSNIGHTFAASGLVSLINLVQ 817
Y+ HGTGT LGDP+E+ AL VF + I S KSNIGH AA+GL LI +V
Sbjct: 301 YVEAHGTGTPLGDPIEVEALAKVFGGSRSADQPLLIGSVKSNIGHLEAAAGLAGLIKVVL 360
Query: 818 SIKYKIIPASLHCEKENNYIILKNSPFYINKSNKKWNTVNEKLRIGAVSAFGMSGTNAHI 877
++++ +IP +LH E N I + SP + + W R G VS+FG GTNAH+
Sbjct: 361 ALEHGVIPPNLHFETPNPKIDFEESPLRVPTEARPWPAPAGPRRAG-VSSFGFGGTNAHV 419
Query: 878 VL 879
+L
Sbjct: 420 IL 421
>gnl|CDD|225858 COG3321, COG3321, Polyketide synthase modules and related proteins
[Secondary metabolites biosynthesis, transport, and
catabolism].
Length = 1061
Score = 579 bits (1494), Expect = 0.0
Identities = 211/526 (40%), Positives = 296/526 (56%), Gaps = 18/526 (3%)
Query: 460 NSEELIAIIGMSGRFPAARNINEFWKILINNKDVISEIPEKIFDWKLYYENPIKSSNKIN 519
E IAIIGM+ RFP A + EFW +L +D I+E+P +D YY+ K
Sbjct: 1 QLIEPIAIIGMACRFPGADSPEEFWDLLKEGRDEITEVPADRWDVDAYYDPDPTVPGKSY 60
Query: 520 SKWYGSIPGIDEFDPLFFEISPLEAERMDPRQRHLLQESWLALEDAGYGPNQIANQKIGM 579
S+W G + +D+FD LFF ISP EAE MDP+QR LL+ +W ALEDAG P+ + G+
Sbjct: 61 SRWGGFLDDVDDFDALFFGISPREAEAMDPQQRLLLEVAWEALEDAGIYPDSLRGSATGV 120
Query: 580 FVGVEEGSNYQDRL-------DQVNLTSTHNAILSARLAYFMDLKGPVMAINTACSSSLV 632
F G Y L + +T +++ + R++Y + L GP + ++TACSSSLV
Sbjct: 121 FAGASVAD-YLLLLLADDEAEPEYAITGNSSSVAAGRISYVLGLSGPSVTVDTACSSSLV 179
Query: 633 ATHIACQSLRQHECDTAISAGVNLMISPEAYIAMTSAGMLSPDGKCYVFDERANGLVPSE 692
A H+ACQSLR ECD A++ GVNL++SPE+ ++ GMLSPDG+C FD A+G V E
Sbjct: 180 AVHLACQSLRLGECDLALAGGVNLVLSPESSYLFSAGGMLSPDGRCKAFDADADGYVRGE 239
Query: 693 AVVAVVLKRLSRALSDGDPIHAIIRGSGINYDGKTNGITAPNGISQTELIKSVYKKSNLN 752
VVLKRLS A DGD I+A+IRGS +N DG++NG+TAPN +Q ++I+ + ++
Sbjct: 240 GAGVVVLKRLSDAERDGDRIYAVIRGSAVNQDGRSNGLTAPNLEAQADVIREALADAGID 299
Query: 753 PEDINYIITHGTGTKLGDPVEINALHDVFKNKTYNQKFCAITSNKSNIGHTFAASGLVSL 812
P + Y+ HGTGT LGDP+E NAL V+ Q CAI S KSNIGH AA+G+ L
Sbjct: 300 PATVQYVEAHGTGTPLGDPIEANALGAVYGEGAPAQ-PCAIGSVKSNIGHLEAAAGIAGL 358
Query: 813 INLVQSIKYKIIPASLHCEKENNYIILKNSPFYINKSNKKWNTVNEKLRIGAVSAFGMSG 872
I ++K+ IP +LH + N I +SPF + W T R VS+FG G
Sbjct: 359 IKTALALKHGYIPPTLHFDTPNPEIDFDSSPFVVPTEATPWPTGGGPRR-AGVSSFGFGG 417
Query: 873 TNAHIVLQEYISTNFKNIKNNTFISSNPYHMVVLSAKTKISLKEKMKQILLFLRKN-NTV 931
TNAH++L+E + ++VLSAKT L ++ L +
Sbjct: 418 TNAHVILEEA-------PPRAESTIPSSPRLLVLSAKTAERLAATAPRLADRLELQGGLL 470
Query: 932 CIENFVYTLMQGRHHFQYRCAIIISSIEEVVKIINDTLNSKEKILH 977
+ + YTL GR HF++R A++ + EE+ + K K L
Sbjct: 471 SLADVAYTLQAGRPHFEHRLAVVANDREELEAGLRAFAAGKAKALS 516
>gnl|CDD|214836 smart00825, PKS_KS, Beta-ketoacyl synthase. The structure of
beta-ketoacyl synthase is similar to that of the
thiolase family and also chalcone synthase. The active
site of beta-ketoacyl synthase is located between the N
and C-terminal domains.
Length = 298
Score = 442 bits (1139), Expect = e-148
Identities = 157/417 (37%), Positives = 207/417 (49%), Gaps = 119/417 (28%)
Query: 465 IAIIGMSGRFPAARNINEFWKILINNKDVISEIPEKIFDWKLYYENPIKSSNKINSKWYG 524
IAI+GMS RFP A + EFW +L+
Sbjct: 1 IAIVGMSCRFPGADDPEEFWDLLLA----------------------------------- 25
Query: 525 SIPGIDEFDPLFFEISPLEAERMDPRQRHLLQESWLALEDAGYGPNQIANQKIGMFVGVE 584
+ +D FD FF ISP EAE MDP+QR LL+ +W ALEDAG P + + G+FVGV
Sbjct: 26 GLDDVDLFDAAFFGISPREAEAMDPQQRLLLEVAWEALEDAGIDPESLRGSRTGVFVGV- 84
Query: 585 EGSNYQDRLDQVNLTSTHNAILSARLAYFMDLKGPVMAINTACSSSLVATHIACQSLRQH 644
+ D Y + ++TACSSSLVA H+ACQSLR
Sbjct: 85 ---SSSD--------------------Y-------SVTVDTACSSSLVALHLACQSLRSG 114
Query: 645 ECDTAISAGVNLMISPEAYIAMTSAGMLSPDGKCYVFDERANGLVPSEAVVAVVLKRLSR 704
ECD A++ GVNL++SP+ ++ ++ AGMLSPDG+C FD A+G V E V VVLKRLS
Sbjct: 115 ECDMALAGGVNLILSPDTFVGLSRAGMLSPDGRCKTFDASADGYVRGEGVGVVVLKRLSD 174
Query: 705 ALSDGDPIHAIIRGSGINYDGKTNGITAPNGISQTELIKSVYKKSNLNPEDINYIITHGT 764
AL DGDPI A+IRGS +N DG++NGITAP+G +Q
Sbjct: 175 ALRDGDPILAVIRGSAVNQDGRSNGITAPSGPAQ-------------------------- 208
Query: 765 GTKLGDPVEINALHDVFKNKTYNQKFCAITSNKSNIGHTFAASGLVSLINLVQSIKYKII 824
I S KSNIGH AA+G+ LI +V ++K+ +I
Sbjct: 209 --------------------------LLIGSVKSNIGHLEAAAGVAGLIKVVLALKHGVI 242
Query: 825 PASLHCEKENNYIILKNSPFYINKSNKKWNTVNEKLRIGAVSAFGMSGTNAHIVLQE 881
P +LH E N +I L+ SP + W + R VS+FG GTNAH++L+E
Sbjct: 243 PPTLHFETPNPHIDLEESPLRVPTELTPWPP-PGRPRRAGVSSFGFGGTNAHVILEE 298
>gnl|CDD|215723 pfam00109, ketoacyl-synt, Beta-ketoacyl synthase, N-terminal
domain. The structure of beta-ketoacyl synthase is
similar to that of the thiolase family (pfam00108) and
also chalcone synthase. The active site of beta-ketoacyl
synthase is located between the N and C-terminal
domains. The N-terminal domain contains most of the
structures involved in dimer formation and also the
active site cysteine.
Length = 243
Score = 269 bits (689), Expect = 2e-83
Identities = 99/257 (38%), Positives = 137/257 (53%), Gaps = 33/257 (12%)
Query: 465 IAIIGMSGRFPAARNINEFWKILINNKDVISEIPEKIFDWKLYYENPIKSSNKINSKWYG 524
+AI GM RFP EFW++L+ +D I E P D Y + G
Sbjct: 4 VAITGMGCRFPGGVGPEEFWELLLAGRDAIREFPA---DLSGLYPPSRVA---------G 51
Query: 525 SIPGIDEFDPLFFEISPLEAERMDPRQRHLLQESWLALEDAGYGPNQI-ANQKIGMFVGV 583
I G +FD FF ISP EAE MDP+QR L+ +W ALEDAG P + + + G+FVG
Sbjct: 52 EIYG-FDFDAAFFGISPREAEAMDPQQRLALEAAWEALEDAGLDPASLRGSDRTGVFVG- 109
Query: 584 EEGSNYQDRLDQVNLTSTHN--------------AILSARLAYFMDLKGPVMAINTACSS 629
S D + L S ++ + R++Y + L+GP + ++TACSS
Sbjct: 110 ---SGSGDYAELQALDSAGGPRRVSPYLTGAWMPSVAAGRISYRLGLRGPSVTVDTACSS 166
Query: 630 SLVATHIACQSLRQHECDTAISAGVNLMISPEAYIAMTSAG-MLSPDGKCYVFDERANGL 688
SLVA H A +S+R+ ECD A++ GV ++P + ++AG +LSPDG C FD A+G
Sbjct: 167 SLVALHAAVRSIRRGECDLALAGGVEAPLTPGGFAGFSAAGALLSPDGPCKAFDPFADGF 226
Query: 689 VPSEAVVAVVLKRLSRA 705
V E V AV+LK LS A
Sbjct: 227 VRGEGVGAVLLKELSEA 243
>gnl|CDD|238421 cd00825, decarbox_cond_enzymes, decarboxylating condensing enzymes;
Family of enzymes that catalyze the formation of a new
carbon-carbon bond by a decarboxylating Claisen-like
condensation reaction. Members are involved in the
synthesis of fatty acids and polyketides, a diverse
group of natural products. Both pathways are an
iterative series of additions of small carbon units,
usually acetate, to a nascent acyl group. There are 2
classes of decarboxylating condensing enzymes, which can
be distinguished by sequence similarity, type of active
site residues and type of primer units (acetyl CoA or
acyl carrier protein (ACP) linked units).
Length = 332
Score = 213 bits (544), Expect = 6e-62
Identities = 83/337 (24%), Positives = 149/337 (44%), Gaps = 24/337 (7%)
Query: 551 QRHLLQESWLALEDAGYGPNQIANQKIGMFVG-----VEEGSNYQDRLDQVN---LTSTH 602
+ + A+ DAG N +G+ VG D + V +T
Sbjct: 12 SILGFEAAERAIADAGLSREYQKNPIVGVVVGTGGGSPRFQVFGADAMRAVGPYVVTKAM 71
Query: 603 NAILSARLAYFMDLKGPVMAINTACSSSLVATHIACQSLRQHECDTAISAGVNLMISPEA 662
S ++A + + GP ++ AC+ SL A +A +++ + D ++ G + +P
Sbjct: 72 FPGASGQIATPLGIHGPAYDVSAACAGSLHALSLAADAVQNGKQDIVLAGGSEELAAPMD 131
Query: 663 YIAMTSAGMLSPDGKCYVFDERANGLVPSEAVVAVVLKRLSRALSDGDPIHAIIRGSGIN 722
+ +P+ FD A+G V + A+V++ L AL+ G I+A I G+
Sbjct: 132 CEFDAMGALSTPEKASRTFDAAADGFVFGDGAGALVVEELEHALARGAHIYAEIVGTAAT 191
Query: 723 YDGKTNGITAPNGISQTELIKSVYKKSNLNPEDINYIITHGTGTKLGDPVEINALHDVFK 782
DG G AP+ K + L DI+Y++ HGTGT +GD E+ L F
Sbjct: 192 IDGAGMGAFAPSAEGLARAAKEALAVAGLTVWDIDYLVAHGTGTPIGDVKELKLLRSEFG 251
Query: 783 NKTYNQKFCAITSNKSNIGHTFAASGLVSLINLVQSIKYKIIPASLHCEKENNYIILKNS 842
+K+ A+++ K+ G+ +A+ ++++ V +++ IP S+H E+ + +
Sbjct: 252 DKSP-----AVSATKAMTGNLSSAAVVLAVDEAVLMLEHGFIPPSIHIEELDEAGL---- 302
Query: 843 PFYINKSNKKWNTVNEKLRIGAVSAFGMSGTNAHIVL 879
N T +LR ++ FG+ GTNA +VL
Sbjct: 303 -------NIVTETTPRELRTALLNGFGLGGTNATLVL 332
>gnl|CDD|238430 cd00834, KAS_I_II, Beta-ketoacyl-acyl carrier protein (ACP)
synthase (KAS), type I and II. KASs are responsible for
the elongation steps in fatty acid biosynthesis. KASIII
catalyses the initial condensation and KAS I and II
catalyze further elongation steps by Claisen
condensation of malonyl-acyl carrier protein (ACP) with
acyl-ACP.
Length = 406
Score = 205 bits (525), Expect = 3e-58
Identities = 107/425 (25%), Positives = 177/425 (41%), Gaps = 51/425 (12%)
Query: 475 PAARNINEFWKILINNKDVISEIPEKIFDWKLYYENPIKSSNKINSKWYGSIPGIDEFDP 534
P + EFW+ L+ + I I FD + S+ G +P D D
Sbjct: 13 PLGNGVEEFWEALLAGRSGIRPITR--FDASGFP-----------SRIAGEVPDFDPEDY 59
Query: 535 LFFEISPLEAERMDPRQRHLLQESWLALEDAGYGPNQIANQKIGMFVGVEEGS------- 587
+ E RMD + L + AL DAG P ++ ++IG+ +G G
Sbjct: 60 ----LDRKELRRMDRFAQFALAAAEEALADAGLDPEELDPERIGVVIGSGIGGLATIEEA 115
Query: 588 --NYQDRLDQVNLTSTHNAIL----SARLAYFMDLKGPVMAINTACSSSLVATHIACQSL 641
++ + L + ++A + L+GP ++TAC+S A A + +
Sbjct: 116 YRALLEKGPRRVSPFFVPMALPNMAAGQVAIRLGLRGPNYTVSTACASGAHAIGDAARLI 175
Query: 642 RQHECDTAISAGVNLMISPEAYIAMTSAGMLS-----PDGKCYVFDERANGLVPSEAVVA 696
R D I+ G +I+P + LS P+ FD+ +G V E
Sbjct: 176 RLGRADVVIAGGAEALITPLTLAGFAALRALSTRNDDPEKASRPFDKDRDGFVLGEGAGV 235
Query: 697 VVLKRLSRALSDGDPIHAIIRGSGINYDGKTNGITAP--NGISQTELIKSVYKKSNLNPE 754
+VL+ L A + G I+A I G G + D ITAP +G +++ + L+PE
Sbjct: 236 LVLESLEHAKARGAKIYAEILGYGASSDA--YHITAPDPDGEGAARAMRAALADAGLSPE 293
Query: 755 DINYIITHGTGTKLGDPVEINALHDVFKNKTYNQKFCAITSNKSNIGHTFAASGLVSLIN 814
DI+YI HGT T L D E A+ VF ++S KS GH A+G V I
Sbjct: 294 DIDYINAHGTSTPLNDAAESKAIKRVFGEHAKK---VPVSSTKSMTGHLLGAAGAVEAIA 350
Query: 815 LVQSIKYKIIPASLHCEKENNYIILKNSPFYINKSNKKWNTVNEKLRIGAVSAFGMSGTN 874
+ +++ ++P +++ E+ + L Y+ ++ +R ++FG G N
Sbjct: 351 TLLALRDGVLPPTINLEEPDPECDLD----YVPNEAREA-----PIRYALSNSFGFGGHN 401
Query: 875 AHIVL 879
A +V
Sbjct: 402 ASLVF 406
>gnl|CDD|234022 TIGR02813, omega_3_PfaA, polyketide-type polyunsaturated fatty acid
synthase PfaA. Members of the seed for this alignment
are involved in omega-3 polyunsaturated fatty acid
biosynthesis, such as the protein PfaA from the
eicosapentaenoic acid biosynthesis operon in
Photobacterium profundum strain SS9. PfaA is encoded
together with PfaB, PfaC, and PfaD, and the functions of
the individual polypeptides have not yet been described.
More distant homologs of PfaA, also included with the
reach of this model, appear to be involved in
polyketide-like biosynthetic mechanisms of
polyunsaturated fatty acid biosynthesis, an alternative
to the more familiar iterated mechanism of chain
extension and desaturation, and in most cases are
encoded near genes for homologs of PfaB, PfaC, and/or
PfaD.
Length = 2582
Score = 217 bits (553), Expect = 2e-57
Identities = 135/456 (29%), Positives = 213/456 (46%), Gaps = 40/456 (8%)
Query: 465 IAIIGMSGRFPAARNINEFWKILINNKDVISEIPEKIFDWKLYYENPIKSSNKINSKWYG 524
IAI+GM+ F +R +N+FW ++ D I+++P + YY++ ++K K G
Sbjct: 9 IAIVGMASIFANSRYLNKFWDLIFEKIDAITDVPSDHWAKDDYYDSDKSEADKSYCKRGG 68
Query: 525 SIPGIDEFDPLFFEISPLEAERMDPRQRHLLQESWLALEDAGYGPNQIANQKIGMFVGVE 584
+P +D F+P+ F + P E D Q L + L DAG P+ KIG+ +GV
Sbjct: 69 FLPEVD-FNPMEFGLPPNILELTDISQLLSLVVAKEVLNDAGL-PDGYDRDKIGITLGVG 126
Query: 585 EG----SNYQDRLDQVNLTSTHNA---------------------------------ILS 607
G S+ RL L A ++S
Sbjct: 127 GGQKQSSSLNARLQYPVLKKVFKASGVEDEDSEMLIKKFQDQYIHWEENSFPGSLGNVIS 186
Query: 608 ARLAYFMDLKGPVMAINTACSSSLVATHIACQSLRQHECDTAISAGVNLMISPEAYIAMT 667
R+A DL G ++ AC+ SL A +A L + + I+ GV SP Y++ +
Sbjct: 187 GRIANRFDLGGMNCVVDAACAGSLAAIRMALSELLEGRSEMMITGGVCTDNSPFMYMSFS 246
Query: 668 SAGMLSPDGKCYVFDERANGLVPSEAVVAVVLKRLSRALSDGDPIHAIIRGSGINYDGKT 727
+ + FD + G++ E + + LKRL A DGD I+A+I+G G + DGK
Sbjct: 247 KTPAFTTNEDIQPFDIDSKGMMIGEGIGMMALKRLEDAERDGDRIYAVIKGVGASSDGKF 306
Query: 728 NGITAPNGISQTELIKSVYKKSNLNPEDINYIITHGTGTKLGDPVEINALHDVFKNKTYN 787
I AP Q + +K Y + P I HGTGT GD E L VF
Sbjct: 307 KSIYAPRPEGQAKALKRAYDDAGFAPHTCGLIEAHGTGTAAGDVAEFGGLVSVFSQDNDQ 366
Query: 788 QKFCAITSNKSNIGHTFAASGLVSLINLVQSIKYKIIPASLHCEKENNYIILKNSPFYIN 847
++ A+ S KS IGHT + +G +I V ++ +K++P +++ ++ N + ++NSPFY+N
Sbjct: 367 KQHIALGSVKSQIGHTKSTAGTAGMIKAVLALHHKVLPPTINVDQPNPKLDIENSPFYLN 426
Query: 848 KSNKKW-NTVNEKLRIGAVSAFGMSGTNAHIVLQEY 882
+ W + R +S+FG GTN H+VL+EY
Sbjct: 427 TETRPWMQREDGTPRRAGISSFGFGGTNFHMVLEEY 462
Score = 55.4 bits (133), Expect = 1e-07
Identities = 46/186 (24%), Positives = 77/186 (41%), Gaps = 18/186 (9%)
Query: 119 AIYIQVDVSDKLKMISEINSIINNIGPIDGVLHIAGISGLTSNILEANYKNFYSVLSSKI 178
A Y DV++ + + + + +N I G++H AG+ +I + + F +V +K+
Sbjct: 2096 AEYASADVTNSVSVAATV-QPLNKTLQITGIIHGAGVLA-DKHIQDKTLEEFNAVYGTKV 2153
Query: 179 SGTIALNYALENTILKLQKNKLDFVCYFSSSSAILGDFGSCDYAMGNRFQTVYAKYLNNK 238
G L + + L + + FSS++ G+ G DYAM N A L
Sbjct: 2154 DG-------LLSLLAALNAENIKLLALFSSAAGFYGNTGQSDYAMSNDILNKAALQLKAL 2206
Query: 239 NIYKKYTNKLITINWPLWNNSKFKIGNNEQTDFYFKSSKQKVLHENDGLKLF-EQLLIQD 297
N + K+++ NW W+ N F V+ + G +LF QLL
Sbjct: 2207 NP----SAKVMSFNWGPWDGGMV----NPALKKMFNDRGVYVIPLDAGAELFVSQLLSDT 2258
Query: 298 KIQYLV 303
Q LV
Sbjct: 2259 GAQLLV 2264
>gnl|CDD|223381 COG0304, FabB, 3-oxoacyl-(acyl-carrier-protein) synthase [Lipid
metabolism / Secondary metabolites biosynthesis,
transport, and catabolism].
Length = 412
Score = 190 bits (486), Expect = 5e-53
Identities = 112/439 (25%), Positives = 173/439 (39%), Gaps = 53/439 (12%)
Query: 465 IAIIGMSGRFPAARNINEFWKILINNKDVISEIPEKIFDWKLYYENPIKSSNKINSKWYG 524
+ I G+ + E W L+ K I I FD + K G
Sbjct: 5 VVITGLGIVSSLGNGVEEVWAALLAGKSGIRPITR--FDAS-----------GLGVKIAG 51
Query: 525 SIPGIDEFDPLFFEISPLEAERMDPRQRHLLQESWLALEDAGYGPNQIANQKIGMFVGVE 584
I +D+ I+ E MD + + + ALEDAG + ++G+ +G
Sbjct: 52 EIKDLDDQ------IAKKERRFMDRFSQLAVVAAVEALEDAGLDNELNVDMRVGVAIGSG 105
Query: 585 EGS--NYQDRLDQVNLTSTHNAI------------LSARLAYFMDLKGPVMAINTACSSS 630
G + + LD + L I + +A LKGP TAC++
Sbjct: 106 IGGLEDIEFDLDALLLEGLRKRISPFLVPKMLPNLAAGNVAIVFGLKGPNYTPVTACATG 165
Query: 631 LVATHIACQSLRQHECDTAISAGVNLMISPEAYIAMTSAGMLS-----PDGKCYVFDERA 685
A A + +R + D I+ G I+P + LS P+ FD+
Sbjct: 166 AHAIGDAVRLIRLGKADVVIAGGAEAAITPLGIAGFEAMRALSTRNDDPEKASRPFDKNR 225
Query: 686 NGLVPSEAVVAVVLKRLSRALSDGDPIHAIIRGSGINYDGKTNGITAP--NGISQTELIK 743
+G V E A+VL+ L AL+ G I+A I G G D ITAP +G ++
Sbjct: 226 DGFVIGEGAGALVLEELEHALARGAKIYAEIVGYGTTSDA--YHITAPAPDGEGAIRAMR 283
Query: 744 SVYKKSNLNPEDINYIITHGTGTKLGDPVEINALHDVFKNKTYNQKFCAITSNKSNIGHT 803
+ + L PEDI+YI HGT T D E A+ VF + ++S KS GHT
Sbjct: 284 AALADAGLTPEDIDYINAHGTSTPANDKAESLAIKRVFGEHAKSL---PVSSTKSLTGHT 340
Query: 804 FAASGLVSLINLVQSIKYKIIPASLHCEKENNYIILKNSPFYINKSNKKWNTVNEKLRIG 863
A+G V I + +++ IIP ++ N ++ + +R
Sbjct: 341 LGAAGAVEAIISLLALRDGIIPPTI------NLDNPDPEAADLDVVPNE--ARTGAVRAA 392
Query: 864 AVSAFGMSGTNAHIVLQEY 882
++FG GTNA +V + Y
Sbjct: 393 LSNSFGFGGTNASLVFKRY 411
>gnl|CDD|187656 cd08953, KR_2_SDR_x, ketoreductase (KR), subgroup 2, complex (x)
SDRs. Ketoreductase, a module of the multidomain
polyketide synthase (PKS), has 2 subdomains, each
corresponding to a SDR family monomer. The C-terminal
subdomain catalyzes the NADPH-dependent reduction of the
beta-carbonyl of a polyketide to a hydroxyl group, a
step in the biosynthesis of polyketides, such as
erythromycin. The N-terminal subdomain, an interdomain
linker, is a truncated Rossmann fold which acts to
stabilizes the catalytic subdomain. Unlike typical SDRs,
the isolated domain does not oligomerize but is composed
of 2 subdomains, each resembling an SDR monomer. The
active site resembles that of typical SDRs, except that
the usual positions of the catalytic Asn and Tyr are
swapped, so that the canonical YXXXK motif changes to
YXXXN. Modular PKSs are multifunctional structures in
which the makeup recapitulates that found in (and may
have evolved from) FAS. Polyketide synthesis also
proceeds via the addition of 2-carbon units as in fatty
acid synthesis. The complex SDR NADP-binding motif,
GGXGXXG, is often present, but is not strictly conserved
in each instance of the module. This subfamily includes
both KR domains of the Bacillus subtilis Pks J,-L, and
PksM, and all three KR domains of PksN, components of
the megacomplex bacillaene synthase, which synthesizes
the antibiotic bacillaene. 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 KRs 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 = 436
Score = 175 bits (446), Expect = 2e-47
Identities = 73/248 (29%), Positives = 105/248 (42%), Gaps = 20/248 (8%)
Query: 65 IKQGGTYLITGGTGRLGMLFSDYLINKYSTNLILSGRSKLNSII------YKKLKKFNNK 118
+K GG YL+TGG G +G + L +Y L+L GRS L L+ +
Sbjct: 202 LKPGGVYLVTGGAGGIGRALARALARRYGARLVLLGRSPLPPEEEWKAQTLAALEALGAR 261
Query: 119 AIYIQVDVSDKLKMISEINSIINNIGPIDGVLHIAGISGLTSNILEANYKNFYSVLSSKI 178
+YI DV+D + + + G IDGV+H AG+ + +F +VL+ K+
Sbjct: 262 VLYISADVTDAAAVRRLLEKVRERYGAIDGVIHAAGVLRDALLAQKTAE-DFEAVLAPKV 320
Query: 179 SGTIALNYALENTILKLQKNKLDFVCYFSSSSAILGDFGSCDYAMGNRFQTVYAKYLNNK 238
G + L AL + LDF FSS SA G G DYA N F +A YL
Sbjct: 321 DGLLNLAQALAD-------EPLDFFVLFSSVSAFFGGAGQADYAAANAFLDAFAAYLRQ- 372
Query: 239 NIYKKYTNKLITINWPLWNNSKFKIGNNEQTDFYFKSSKQKVLHENDGLKLFEQLLIQDK 298
+ ++++INWP W + + +GL+ EQ L D
Sbjct: 373 ---RGPQGRVLSINWPAWREGGMAADL--GARELLARAGLLPIEPEEGLQALEQALSSDL 427
Query: 299 IQYLVLSG 306
Q LV G
Sbjct: 428 PQVLVSPG 435
Score = 33.1 bits (76), Expect = 0.70
Identities = 8/11 (72%), Positives = 10/11 (90%)
Query: 868 FGMSGTNAHIV 878
FGM GTNAH++
Sbjct: 1 FGMGGTNAHVI 11
>gnl|CDD|217236 pfam02801, Ketoacyl-synt_C, Beta-ketoacyl synthase, C-terminal
domain. The structure of beta-ketoacyl synthase is
similar to that of the thiolase family (pfam00108) and
also chalcone synthase. The active site of beta-ketoacyl
synthase is located between the N and C-terminal
domains.
Length = 119
Score = 159 bits (405), Expect = 9e-46
Identities = 53/120 (44%), Positives = 78/120 (65%), Gaps = 2/120 (1%)
Query: 713 HAIIRGSGINYDG-KTNGITAPNGISQTELIKSVYKKSNLNPEDINYIITHGTGTKLGDP 771
+A+IRGS +N DG NG+TAPNG +Q I++ + L+PED++Y+ HGTGT LGDP
Sbjct: 1 YAVIRGSAVNQDGAAHNGLTAPNGPAQARAIRAALADAGLDPEDVDYVEAHGTGTPLGDP 60
Query: 772 VEINALHDVFKNKTYNQKFCAITSNKSNIGHTFAASGLVSLINLVQSIKYKIIPASLHCE 831
+E AL VF +Q + S KSNIGH AA+G+ LI V ++++ +IP +L+ +
Sbjct: 61 IEAEALKAVFGPGRDSQ-PLPVGSVKSNIGHLEAAAGVAGLIKAVLALRHGVIPPTLNLD 119
>gnl|CDD|238424 cd00828, elong_cond_enzymes, "elongating" condensing enzymes are a
subclass of decarboxylating condensing enzymes,
including beta-ketoacyl [ACP] synthase, type I and II
and polyketide synthases.They are characterized by the
utlization of acyl carrier protein (ACP) thioesters as
primer substrates, as well as the nature of their active
site residues.
Length = 407
Score = 160 bits (407), Expect = 1e-42
Identities = 84/337 (24%), Positives = 143/337 (42%), Gaps = 30/337 (8%)
Query: 561 ALEDAGYGPNQ-IANQKIGMFVG------VEEGSNYQDRLDQVNLTSTHNAILSARLA-- 611
AL DAG + ++G+ VG + VN + +LS
Sbjct: 83 ALADAGITDPYEVHPSEVGVVVGSGMGGLRFLRRGGKLDARAVNPYVSPKWMLSPNTVAG 142
Query: 612 ----YFMDLKGPVMAINTACSSSLVATHIACQSLRQHECDTAISAGVNLMISPE---AYI 664
+ GP+ AC+++L A +A +++R + D + GV E +
Sbjct: 143 WVNILLLSSHGPIKTPVGACATALEALDLAVEAIRSGKADIVVVGGVED-PLEEGLSGFA 201
Query: 665 AM--TSAGMLSPDGKCYVFDERANGLVPSEAVVAVVLKRLSRALSDGDPIHAIIRGSGIN 722
M S P+ FDE +G V +E +VL+R AL+ G PI+ + G+
Sbjct: 202 NMGALSTAEEEPEEMSRPFDETRDGFVEAEGAGVLVLERAELALARGAPIYGRVAGTAST 261
Query: 723 YDGKTNGITAPNGISQTELIKSVYKKSNLNPEDINYIITHGTGTKLGDPVEINALHDVFK 782
DG + A G I++ K+ L+ +D++ I HGT T D E A+ +V
Sbjct: 262 TDGAGRSVPAG-GKGIARAIRTALAKAGLSLDDLDVISAHGTSTPANDVAESRAIAEVAG 320
Query: 783 NKTYNQKFCAITSNKSNIGHTFAASGLVSLINLVQSIKYKIIPASLHCEKENNYIILKNS 842
+T+ K+ GH+ A+G + LI +QS+++ +IP + + + +
Sbjct: 321 ALGAPL---PVTAQKALFGHSKGAAGALQLIGALQSLEHGLIPPTANLDDVD---PDVEH 374
Query: 843 PFYINKSNKKWNTVNEKLRIGAVSAFGMSGTNAHIVL 879
+ S +N K+R V+AFG G+NA +VL
Sbjct: 375 LSVVGLSRD----LNLKVRAALVNAFGFGGSNAALVL 407
>gnl|CDD|238201 cd00327, cond_enzymes, Condensing enzymes; Family of enzymes that
catalyze a (decarboxylating or non-decarboxylating)
Claisen-like condensation reaction. Members are share
strong structural similarity, and are involved in the
synthesis and degradation of fatty acids, and the
production of polyketides, a diverse group of natural
products.
Length = 254
Score = 141 bits (358), Expect = 1e-37
Identities = 71/332 (21%), Positives = 117/332 (35%), Gaps = 85/332 (25%)
Query: 550 RQRHLLQESWL-ALEDAGYGPNQIANQKIGMFVGVEEGSNYQDRLDQVNLTSTHNAILSA 608
L E+ A+ DAG I +G G E S +
Sbjct: 6 TASELGFEAAEQAIADAGLSKGPIVGVIVGTTGGSGEFSG-----------------AAG 48
Query: 609 RLAYFMDLK-GPVMAINTACSSSLVATHIACQSLRQHECDTAISAGVNLMISPEAYIAMT 667
+LAY + + GP ++N AC++ L A +A Q ++ + D ++ G
Sbjct: 49 QLAYHLGISGGPAYSVNQACATGLTALALAVQQVQNGKADIVLAGGSEE----------- 97
Query: 668 SAGMLSPDGKCYVFDERANGLVPSEAVVAVVLKRLSRALSDGDPIHAIIRGSGINYDGKT 727
V + A V++ AL G A I + +DG +
Sbjct: 98 --------------------FVFGDGAAAAVVESEEHALRRGAHPQAEIVSTAATFDGAS 137
Query: 728 NGITAPNGISQTELIKSVYKKSNLNPEDINYIITHGTGTKLGDPVEINALHDVFKNKTYN 787
+ A +G + + + L P DI+Y+ HGTGT +GD VE+ D
Sbjct: 138 -MVPAVSGEGLARAARKALEGAGLTPSDIDYVEAHGTGTPIGDAVELALGLDPD-----G 191
Query: 788 QKFCAITSNKSNIGHTFAASGLVSLINLVQSIKYKIIPASLHCEKENNYIILKNSPFYIN 847
+ A+++ GH A+GL L L+ ++++ IP
Sbjct: 192 VRSPAVSATLIMTGHPLGAAGLAILDELLLMLEHEFIP---------------------- 229
Query: 848 KSNKKWNTVNEKLRIGAVSAFGMSGTNAHIVL 879
+ R + FG+ GTNA +VL
Sbjct: 230 -------PTPREPRTVLLLGFGLGGTNAAVVL 254
>gnl|CDD|214833 smart00822, PKS_KR, This enzymatic domain is part of bacterial
polyketide synthases. It catalyses the first step in
the reductive modification of the beta-carbonyl centres
in the growing polyketide chain. It uses NADPH to reduce
the keto group to a hydroxy group.
Length = 180
Score = 132 bits (336), Expect = 1e-35
Identities = 53/194 (27%), Positives = 88/194 (45%), Gaps = 22/194 (11%)
Query: 69 GTYLITGGTGRLGMLFSDYLINKYSTNLILSGRSKLNS----IIYKKLKKFNNKAIYIQV 124
GTYLITGG G LG + +L + + L+L RS ++ + +L+ + +
Sbjct: 1 GTYLITGGLGGLGRALARWLAERGARRLVLLSRSGPDAPGAAALLAELEAAGARVTVVAC 60
Query: 125 DVSDKLKMISEINSIINNIGPIDGVLHIAGISGLTSNILEANYKNFYSVLSSKISGTIAL 184
DV+D+ + + + +I GP+ GV+H AG+ + + F +VL+ K +G L
Sbjct: 61 DVADRDALAAVLAAIPAVEGPLTGVIHAAGVLDDGV-LASLTPERFAAVLAPKAAGAWNL 119
Query: 185 NYALENTILKLQKNKLDFVCYFSSSSAILGDFGSCDYAMGNRFQTVYAKYLNNKNIYKKY 244
+ + LDF FSS + +LG G +YA N F A+Y +
Sbjct: 120 HELTADL-------PLDFFVLFSSIAGVLGSPGQANYAAANAFLDALAEYRRARG----- 167
Query: 245 TNKL--ITINWPLW 256
L ++I W W
Sbjct: 168 ---LPALSIAWGAW 178
>gnl|CDD|219957 pfam08659, KR, KR domain. This enzymatic domain is part of
bacterial polyketide synthases and catalyzes the first
step in the reductive modification of the beta-carbonyl
centres in the growing polyketide chain. It uses NADPH
to reduce the keto group to a hydroxy group.
Length = 181
Score = 129 bits (326), Expect = 3e-34
Identities = 53/193 (27%), Positives = 89/193 (46%), Gaps = 20/193 (10%)
Query: 69 GTYLITGGTGRLGMLFSDYLINKYSTNLILSGRSKLNS-----IIYKKLKKFNNKAIYIQ 123
GTYL+TGG G LG+ + +L + + +L+L RS ++ +L+ + +
Sbjct: 1 GTYLVTGGLGGLGLELARWLAERGARHLVLLSRSGAPDPEAEALL-AELEARGAEVTVVA 59
Query: 124 VDVSDKLKMISEINSIINNIGPIDGVLHIAGISGLTSNILEANYKNFYSVLSSKISGTIA 183
DVSD+ + + + I + P+ GV+H AG+ + ++F VL+ K++G
Sbjct: 60 CDVSDRDAVRALLAEIRADGPPLRGVIHAAGVLRDAL-LANMTAEDFARVLAPKVTGAWN 118
Query: 184 LNYALENTILKLQKNKLDFVCYFSSSSAILGDFGSCDYAMGNRFQTVYAKYLNNKNIYKK 243
L+ A + LDF FSS + +LG G +YA N F A Y + +
Sbjct: 119 LHEATRDR-------PLDFFVLFSSIAGVLGSPGQANYAAANAFLDALAHYRRAQGL--- 168
Query: 244 YTNKLITINWPLW 256
+INW W
Sbjct: 169 ---PATSINWGPW 178
>gnl|CDD|235653 PRK05952, PRK05952, 3-oxoacyl-(acyl carrier protein) synthase II;
Reviewed.
Length = 381
Score = 134 bits (338), Expect = 9e-34
Identities = 92/340 (27%), Positives = 141/340 (41%), Gaps = 46/340 (13%)
Query: 561 ALEDAGYGP-------------------NQIANQKIGMFVGVEEGSNYQDRLDQVNLTST 601
AL+DAG P ++A Q +E + ++ LD T
Sbjct: 67 ALKDAGLTPPLTDCGVVIGSSRGCQGQWEKLARQMYQGDDSPDEELDLENWLD----TLP 122
Query: 602 H-NAILSARLAYFMDLKGPVMAINTACSSSLVATHIACQSLRQHECDTAISAGVNLMISP 660
H AI +AR +GPV+A AC++ L A + ++ +C I+ V I+P
Sbjct: 123 HQAAIAAARQI---GTQGPVLAPMAACATGLWAIAQGVELIQTGQCQRVIAGAVEAPITP 179
Query: 661 EAYIAMTSAGMLSPDGKCYVFDERANGLVPSEAVVAVVLKRLSRALSDGDPIHAIIRGSG 720
G L+ G Y FD + GLV E +VL+ A G I+ I G G
Sbjct: 180 LTLAGFQQMGALAKTG-AYPFDRQREGLVLGEGGAILVLESAELAQKRGAKIYGQILGFG 238
Query: 721 INYDGKTNGITAPNGISQTELIKSVYKKSNLNPEDINYIITHGTGTKLGDPVEINALHDV 780
+ D P+G S I+ +S L PEDI+YI HGT T+L D E N + +
Sbjct: 239 LTCDAYHMSAPEPDGKSAIAAIQQCLARSGLTPEDIDYIHAHGTATRLNDQREANLIQAL 298
Query: 781 FKNKTYNQKFCAITSNKSNIGHTFAASGLVSLINLVQSIKYKIIPASLHCEKENNYIILK 840
F ++ A++S K GHT ASG + + + +++++ +P C + L+
Sbjct: 299 FPHRV------AVSSTKGATGHTLGASGALGVAFSLLALRHQQLPP---C------VGLQ 343
Query: 841 NSPFYINKSNKKWNTVNEKLRIGAVSAFGMSGTNAHIVLQ 880
F +N L+ +FG G NA I L
Sbjct: 344 EPEFDLNFVR---QAQQSPLQNVLCLSFGFGGQNAAIALG 380
>gnl|CDD|200247 TIGR03150, fabF, beta-ketoacyl-acyl-carrier-protein synthase II.
3-oxoacyl-[acyl-carrier-protein] synthase 2 (KAS-II,
FabF) is involved in the condensation step of fatty acid
biosynthesis in which the malonyl donor group is
decarboxylated and the resulting carbanion used to
attack and extend the acyl group attached to the acyl
carrier protein. Most genomes encoding fatty acid
biosynthesis contain a number of condensing enzymes,
often of all three types: 1, 2 and 3. Synthase 2 is
mechanistically related to synthase 1 (KAS-I, FabB)
containing a number of absolutely conserved catalytic
residues in common. This model is based primarily on
genes which are found in apparent operons with other
essential genes of fatty acid biosynthesis
(GenProp0681). The large gap between the trusted cutoff
and the noise cutoff contains many genes which are not
found adjacent to genes of the fatty acid pathway in
genomes that often also contain a better hit to this
model. These genes may be involved in other processes
such as polyketide biosyntheses. Some genomes contain
more than one above-trusted hit to this model which may
result from recent paralogous expansions. Second hits to
this model which are not next to other fatty acid
biosynthesis genes may be involved in other processes.
FabB sequences should fall well below the noise cutoff
of this model [Fatty acid and phospholipid metabolism,
Biosynthesis].
Length = 407
Score = 131 bits (333), Expect = 7e-33
Identities = 111/434 (25%), Positives = 185/434 (42%), Gaps = 69/434 (15%)
Query: 475 PAARNINEFWKILINNKDVISEIPEKIFDWKLYYENPIKSSNKINSKWYGSIPGIDEFDP 534
P + EFW+ L+ K I I FD ++ + K G + FDP
Sbjct: 13 PLGNGVEEFWENLLAGKSGIGPI--TRFD-----------ASDLPVKIAGEVKD---FDP 56
Query: 535 LFFEISPLEAERMDPRQRHLLQESWLALEDAGYGPNQIANQKIGMFV-----GVEEGSNY 589
+ I EA RMD ++ L + A+ED+G + +++G+ + G+E
Sbjct: 57 EDY-IDKKEARRMDRFIQYALAAAKEAVEDSGLDIEEEDAERVGVIIGSGIGGLETIEEQ 115
Query: 590 QDRLDQ---------------VNLTSTHNAILSARLAYFMDLKGPVMAINTACSSSLVAT 634
L + +N+ + +I KGP A+ TAC++ A
Sbjct: 116 HIVLLEKGPRRVSPFFIPMSIINMAAGQISI-------RYGAKGPNHAVVTACATGTHAI 168
Query: 635 HIACQSLRQHECDTAISAGVNLMISPEAYIAMTSAGMLS-----PDGKCYVFDERANGLV 689
A + +++ + D I+ G I+P + LS P+ FD+ +G V
Sbjct: 169 GDAFRLIQRGDADVMIAGGAEAAITPLGIAGFAAMKALSTRNDDPEKASRPFDKDRDGFV 228
Query: 690 PSEAVVAVVLKRLSRALSDGDPIHAIIRGSGINYDGKTNGITAP--NGISQTELIKSVYK 747
E +VL+ L A + G I+A I G G++ D ITAP G +++ K
Sbjct: 229 MGEGAGVLVLEELEHAKARGAKIYAEIVGYGMSGDA--YHITAPAPEGEGAARAMRAALK 286
Query: 748 KSNLNPEDINYIITHGTGTKLGDPVEINALHDVFKNKTYNQKFCAITSNKSNIGHTFAAS 807
+ +NPED++YI HGT T LGD E A+ VF + Y A++S KS GH A+
Sbjct: 287 DAGINPEDVDYINAHGTSTPLGDKAETKAIKRVFGDHAYK---LAVSSTKSMTGHLLGAA 343
Query: 808 GLVSLINLVQSIKYKIIPASLHCEKENNYIILKNSPFYINKSNKKWNTVNEKLRIGAV-- 865
G + I V +++ I+P +++ + + L P N++ + +I
Sbjct: 344 GAIEAIFTVLALRDGIVPPTINLDNPDPECDLDYVP---NEA--------REAKIDYALS 392
Query: 866 SAFGMSGTNAHIVL 879
++FG G NA +V
Sbjct: 393 NSFGFGGHNASLVF 406
>gnl|CDD|240245 PTZ00050, PTZ00050, 3-oxoacyl-acyl carrier protein synthase;
Provisional.
Length = 421
Score = 130 bits (330), Expect = 2e-32
Identities = 103/442 (23%), Positives = 175/442 (39%), Gaps = 58/442 (13%)
Query: 475 PAARNINEFWKILINNKDVISEIPE-------KIFDWKLYYENPIKSSNKINSKWYGSIP 527
P W+ LI K I ++ E I + K +I ++ S
Sbjct: 4 PLGVGAESTWEALIAGKSGIRKLTEFPKFLPDCIPEQKALENLVAAMPCQIAAEVDQS-- 61
Query: 528 GIDEFDPLFFEISPLEAERMDPRQRHLLQESWLALEDAGYGPNQIANQ-KIGMFVGVEEG 586
EFDP F + E + + AL DA +Q +IG+ +G G
Sbjct: 62 ---EFDPSDFAPTKRE----SRATHFAMAAAREALADAKLDILSEKDQERIGVNIGSGIG 114
Query: 587 S----------NYQDRLDQVN-------LTSTHNAILSARLAYFMDLKGPVMAINTACSS 629
S Y+ +V+ L + +++ + LKGP + TAC++
Sbjct: 115 SLADLTDEMKTLYEKGHSRVSPYFIPKILGNMAAGLVAIKH----KLKGPSGSAVTACAT 170
Query: 630 SLVATHIACQSLRQHECDTAISAGVNLMISPEAYIAMTSAGMLS------PDGKCYVFDE 683
A + ++ E D I G I+P ++ + L P FD+
Sbjct: 171 GAHCIGEAFRWIKYGEADIMICGGTEASITPVSFAGFSRMRALCTKYNDDPQRASRPFDK 230
Query: 684 RANGLVPSEAVVAVVLKRLSRALSDGDPIHAIIRGSGINYDGKTNGITAP--NGISQTEL 741
G V E +VL+ L AL G I+A IRG G + D + ITAP +G
Sbjct: 231 DRAGFVMGEGAGILVLEELEHALRRGAKIYAEIRGYGSSSDA--HHITAPHPDGRGARRC 288
Query: 742 IKSVYKKS-NLNPEDINYIITHGTGTKLGDPVEINALHDVFKNKTYNQKFCAITSNKSNI 800
+++ K N+N D++Y+ H T T +GD +E+ A+ VF + + ++S K +
Sbjct: 289 MENALKDGANININDVDYVNAHATSTPIGDKIELKAIKKVFGDSGAPK--LYVSSTKGGL 346
Query: 801 GHTFAASGLVSLINLVQSIKYKIIPASLHCEKENNYIILKNSPFYINKSNKKWNTVNEKL 860
GH A+G V I + S+ +IIP +++ E ++ +N K + +
Sbjct: 347 GHLLGAAGAVESIVTILSLYEQIIPPTINLEN-------PDAECDLNLVQGKTAHPLQSI 399
Query: 861 RIGAVSAFGMSGTNAHIVLQEY 882
++FG G N ++ +Y
Sbjct: 400 DAVLSTSFGFGGVNTALLFTKY 421
>gnl|CDD|235781 PRK06333, PRK06333, 3-oxoacyl-(acyl carrier protein) synthase II;
Reviewed.
Length = 424
Score = 125 bits (315), Expect = 2e-30
Identities = 104/463 (22%), Positives = 184/463 (39%), Gaps = 89/463 (19%)
Query: 465 IAIIGMSGRFPAARNINEFWKILINNKDVISEIPEKIFDWKLYYENPIKSSNKINSKWYG 524
I + GM P + FW+ L+ + I + + + +K G
Sbjct: 6 IVVTGMGAVSPLGCGVETFWQRLLAGQSGIRTLTDFPVG-------------DLATKIGG 52
Query: 525 SIPGIDE-----FDPLFFEISPLEAERMDPRQRHLLQESWLALEDAGYGPNQIANQK--- 576
+P + E FDP + + P + +MD + + AL AG+ P+ + +++
Sbjct: 53 QVPDLAEDAEAGFDPDRY-LDPKDQRKMDRFILFAMAAAKEALAQAGWDPDTLEDRERTA 111
Query: 577 ------IGMFVGVEEGSNYQDRLDQ---------------VNLTSTHNAILSARLAYFMD 615
+G F + E LD N+ + H +I R +
Sbjct: 112 TIIGSGVGGFPAIAEA---VRTLDSRGPRRLSPFTIPSFLTNMAAGHVSI---RYGF--- 162
Query: 616 LKGPVMAINTACSSSLVATHIACQSLRQHECDTAISAGVNLMISPEAYIAMTSAGMLS-- 673
KGP+ A TAC++ + A A + +R E D A+ G I + +A LS
Sbjct: 163 -KGPLGAPVTACAAGVQAIGDAARLIRSGEADVAVCGGTEAAIDRVSLAGFAAARALSTR 221
Query: 674 ----PDGKCYVFDERANGLVPSEAVVAVVLKRLSRALSDGDPIHAIIRGSGINYDGKTNG 729
P+ FD +G V E +V++ L AL+ G P A + G G + D
Sbjct: 222 FNDAPEQASRPFDRDRDGFVMGEGAGILVIETLEHALARGAPPLAELVGYGTSADAYH-- 279
Query: 730 ITAP--NGISQTELIKSVYKKSNLNPEDINYIITHGTGTKLGDPVEINALHDVFKNKTYN 787
+TA +G + +++ + PE++ ++ H T T +GD E+ A+ VF +
Sbjct: 280 MTAGPEDGEGARRAMLIALRQAGIPPEEVQHLNAHATSTPVGDLGEVAAIKKVFG----H 335
Query: 788 QKFCAITSNKSNIGHTFAASGLVSLINLVQSIKYKIIPASLHCE------KENNYIILKN 841
A++S KS GH A+G V I + +++ +I P +L+ E + + + K
Sbjct: 336 VSGLAVSSTKSATGHLLGAAGGVEAIFTILALRDQIAPPTLNLENPDPAAEGLDVVANKA 395
Query: 842 SPFYINKSNKKWNTVNEKLRIGAVS-AFGMSGTNAHIVLQEYI 883
P ++ A+S FG G NA I+ + +
Sbjct: 396 RPMDMDY---------------ALSNGFGFGGVNASILFRRWE 423
>gnl|CDD|235987 PRK07314, PRK07314, 3-oxoacyl-(acyl carrier protein) synthase II;
Reviewed.
Length = 411
Score = 122 bits (308), Expect = 1e-29
Identities = 114/438 (26%), Positives = 183/438 (41%), Gaps = 71/438 (16%)
Query: 475 PAARNINEFWKILINNKDVISEIPEKIFDWKLYYENPIKSSNKINSKWYGSIPGIDEFDP 534
P ++ WK L+ K I I L K G + F+P
Sbjct: 14 PLGNDVESTWKNLLAGKSGIGPI-THFDTSDL------------AVKIAGEVKD---FNP 57
Query: 535 LFFEISPLEAERMDPRQRHLLQESWLALEDAGYGPNQIANQKIGMFVG--------VEEG 586
+ +S EA RMD ++ + + A+EDAG + +IG+ +G +EE
Sbjct: 58 DDY-MSRKEARRMDRFIQYGIAAAKQAVEDAGLEITEENADRIGVIIGSGIGGLETIEEQ 116
Query: 587 SNYQDRLDQ---------------VNLTSTHNAILSARLAYFMDLKGPVMAINTACSSSL 631
L + +N+ + H +I KGP +I TAC++
Sbjct: 117 ---HITLLEKGPRRVSPFFVPMAIINMAAGHVSIR-------YGAKGPNHSIVTACATGA 166
Query: 632 VATHIACQSLRQHECDTAISAGVNLMISPEAYIAMTSAGMLS-----PDGKCYVFDERAN 686
A A + + + D ++ G I+P +A LS P+ FD+ +
Sbjct: 167 HAIGDAARLIAYGDADVMVAGGAEAAITPLGIAGFAAARALSTRNDDPERASRPFDKDRD 226
Query: 687 GLVPSEAVVAVVLKRLSRALSDGDPIHAIIRGSGINYDGKTNGITAP--NGISQTELIKS 744
G V E +VL+ L A + G I+A + G G+ D +TAP +G +K
Sbjct: 227 GFVMGEGAGILVLEELEHAKARGAKIYAEVVGYGMTGDAYH--MTAPAPDGEGAARAMKL 284
Query: 745 VYKKSNLNPEDINYIITHGTGTKLGDPVEINALHDVFKNKTYNQKFCAITSNKSNIGHTF 804
K + +NPEDI+YI HGT T GD E A+ VF Y A++S KS GH
Sbjct: 285 ALKDAGINPEDIDYINAHGTSTPAGDKAETQAIKRVFGEHAYK---VAVSSTKSMTGHLL 341
Query: 805 AASGLVSLINLVQSIKYKIIPASLHCEKENNYIILKNSPFYINKSNKKWNTVNEKLRIGA 864
A+G V I V +I+ ++IP +++ + + L P N++ ++ K+
Sbjct: 342 GAAGAVEAIFSVLAIRDQVIPPTINLDNPDEECDLDYVP---NEARER------KIDYAL 392
Query: 865 VSAFGMSGTNAHIVLQEY 882
++FG GTNA +V + Y
Sbjct: 393 SNSFGFGGTNASLVFKRY 410
>gnl|CDD|180839 PRK07103, PRK07103, polyketide beta-ketoacyl:acyl carrier protein
synthase; Validated.
Length = 410
Score = 120 bits (304), Expect = 4e-29
Identities = 84/288 (29%), Positives = 127/288 (44%), Gaps = 43/288 (14%)
Query: 555 LQESWLALEDAGYGPNQIANQKIGMFVGVEEGSNYQDRLDQVNLTST---HNAILSARLA 611
+E+W DA GP +IG+ VG GSN Q R +Q + T A L
Sbjct: 88 AREAW---RDAALGPVDPD--RIGLVVG---GSNLQQR-EQALVHETYRDRPAFLRPSYG 138
Query: 612 -YFMD------------LKGPVMAINTACSSSLVATHIACQSLRQHECDTAISAGVNLM- 657
FMD ++G + A +S +A A + ++ D I+ G LM
Sbjct: 139 LSFMDTDLVGLCSEQFGIRGEGFTVGGASASGQLAVIQAARLVQSGSVDACIAVG-ALMD 197
Query: 658 ISPEAYIAMTSAG-MLS------PDGKCYVFDERANGLVPSEAVVAVVLKRLSRALSDGD 710
+S A+ S G M S P+ C FD+ +G + EA AVVL+ A G
Sbjct: 198 LSYWECQALRSLGAMGSDRFADEPEAACRPFDQDRDGFIYGEACGAVVLESAESARRRGA 257
Query: 711 PIHAIIRGSGINYDGKTNGITAPNGISQTELIKSVYKKSNLNPEDINYIITHGTGTKLGD 770
+A + G + D P+ + +I++ +++ L PEDI+Y+ HGTG+ LGD
Sbjct: 258 RPYAKLLGWSMRLDANRG--PDPSLEGEMRVIRAALRRAGLGPEDIDYVNPHGTGSPLGD 315
Query: 771 PVEINALHDVFKNKTYNQKFCAITSNKSNIGHTFAASGLVSLI-NLVQ 817
E+ AL + I + KS GH +A+G+V LI L+Q
Sbjct: 316 ETELAALFASGLAHAW------INATKSLTGHGLSAAGIVELIATLLQ 357
>gnl|CDD|235817 PRK06501, PRK06501, 3-oxoacyl-(acyl carrier protein) synthase II;
Reviewed.
Length = 425
Score = 110 bits (278), Expect = 1e-25
Identities = 101/373 (27%), Positives = 162/373 (43%), Gaps = 64/373 (17%)
Query: 524 GSIPGIDEFDPLFFEISPLEAERMDPRQRHLLQESWLALEDAGYGPNQIANQKIGMFVGV 583
G PG PLF P+E E W A +A VG
Sbjct: 95 GDFPG-----PLFLAAPPVELE-------------WPARF-------ALAAA-----VGD 124
Query: 584 EEGSNYQDRLDQVNLTSTHNAI--------LSARLAYFMDLKGPVMAINTACSSSLVATH 635
+ +Y DRL + +A+ ++ RLA +G ++++TAC+S A
Sbjct: 125 NDAPSY-DRLLRAARGGRFDALHERFQFGSIADRLADRFGTRGLPISLSTACASGATAIQ 183
Query: 636 IACQSLRQHECDTAISAGVNLMISPEAYI--AMTSAGMLS-----PDGKCYVFDERANGL 688
+ +++R+ E D A+ + +S EA I ++ SA LS P+ F + +G
Sbjct: 184 LGVEAIRRGETDRALCIATDGSVSAEALIRFSLLSA--LSTQNDPPEKASKPFSKDRDGF 241
Query: 689 VPSEAVVAVVLKRLSRALSDGDPIHAIIRGSGINYDGKTNGITAPNGISQTELIKSVYKK 748
V +E A+VL+ L A++ G I I+ G G D ++P+G I++
Sbjct: 242 VMAEGAGALVLESLESAVARGAKILGIVAGCGEKADSFHRTRSSPDGSPAIGAIRAALAD 301
Query: 749 SNLNPEDINYIITHGTGTKLGDPVEINALHDVFKNKTYNQKFCAITSNKSNIGHTFAASG 808
+ L PE I+YI HGT T D +E L VF + + ++SNKS IGHT A+G
Sbjct: 302 AGLTPEQIDYINAHGTSTPENDKMEYLGLSAVFGERLAS---IPVSSNKSMIGHTLTAAG 358
Query: 809 LVSLINLVQSIKYKIIPASLHCEKENNYIILKNSPFYINKSNKKWNTVNEKLRIGAV--S 866
V + + +I+ +P +++ + + I L P N R+ AV +
Sbjct: 359 AVEAVFSLLTIQTGRLPPTINYDNPDPAIPLDVVP------NVA-----RDARVTAVLSN 407
Query: 867 AFGMSGTNAHIVL 879
+FG G NA +VL
Sbjct: 408 SFGFGGQNASLVL 420
>gnl|CDD|215449 PLN02836, PLN02836, 3-oxoacyl-[acyl-carrier-protein] synthase.
Length = 437
Score = 107 bits (270), Expect = 1e-24
Identities = 106/458 (23%), Positives = 180/458 (39%), Gaps = 75/458 (16%)
Query: 465 IAIIGMSGRFPAARNINEFWKILINNKDVISEI-----PEKIFDWKLYYENPIKSSNKIN 519
+ + G+ P + W+ LI + + + K D E + + +++
Sbjct: 8 VVVTGLGLVTPLGCGVETTWRRLIAGECGVRALTQDDLKMKSED----EETQLYTLDQLP 63
Query: 520 SKWYGSIP---GIDEFDPLFFEISPLEAERMDPRQRHLLQESWLALEDAGYGP-NQIANQ 575
S+ +P G +FD E L + + L + AL DA + P A +
Sbjct: 64 SRVAALVPRGTGPGDFD----EELWLNSRSSSRFIGYALCAADEALSDARWLPSEDEAKE 119
Query: 576 KIGMFVGVEEGS-------------NYQDRLDQ-------VNLTSTHNAILSARLAYFMD 615
+ G+ +G GS RL +N+ + H +S R
Sbjct: 120 RTGVSIGGGIGSITDILEAAQLICEKRLRRLSPFFVPRILINMAAGH---VSIRYG---- 172
Query: 616 LKGPVMAINTACSSSLVATHIACQSLRQHECDTAISAGVNLMISPEAYIAMTSAGMLS-- 673
+GP A TAC++ + A + ++ + D ++ G I + + + LS
Sbjct: 173 FQGPNHAAVTACATGAHSIGDAFRMIQFGDADVMVAGGTESSIDALSIAGFSRSRALSTK 232
Query: 674 ----PDGKCYVFDERANGLVPSEAVVAVVLKRLSRALSDGDPIHAIIRGSGINYDGKTNG 729
P FD +G V E +VL+ L A G I+A +RG G++ D +
Sbjct: 233 FNSCPTEASRPFDCDRDGFVIGEGAGVLVLEELEHAKRRGAKIYAEVRGYGMSGDA--HH 290
Query: 730 ITAP--NGISQTELIKSVYKKSNLNPEDINYIITHGTGTKLGDPVEINALHDVFKNKTYN 787
IT P +G + ++S L+P ++Y+ H T T LGD VE A+ VF +
Sbjct: 291 ITQPHEDGRGAVLAMTRALQQSGLHPNQVDYVNAHATSTPLGDAVEARAIKTVFSEHATS 350
Query: 788 QKFCAITSNKSNIGHTFAASGLVSLINLVQSIKYKIIPASLHCEK-----ENNYIILKNS 842
A +S K GH A+G V I V +I + I P +L+ E+ ++ ++ L S
Sbjct: 351 GGL-AFSSTKGATGHLLGAAGAVEAIFSVLAIHHGIAPPTLNLERPDPIFDDGFVPLTAS 409
Query: 843 PFYINKSNKKWNTVNEKLRIGAVS-AFGMSGTNAHIVL 879
L A+S +FG GTNA ++
Sbjct: 410 K--------------AMLIRAALSNSFGFGGTNASLLF 433
>gnl|CDD|173154 PRK14691, PRK14691, 3-oxoacyl-(acyl carrier protein) synthase II;
Provisional.
Length = 342
Score = 104 bits (260), Expect = 5e-24
Identities = 79/294 (26%), Positives = 130/294 (44%), Gaps = 25/294 (8%)
Query: 596 VNLTSTHNAILSARLAYFMDLKGPVMAINTACSSSLVATHIACQSLRQHECDTAISAGVN 655
VNL + H +I KGP+ A TAC++ + A A + +R +E D A+ G
Sbjct: 67 VNLAAGHVSIKH-------HFKGPIGAPVTACAAGVQAIGDAVRMIRNNEADVALCGGAE 119
Query: 656 LMISPEAYIAMTSAGMLS------PDGKCYVFDERANGLVPSEAVVAVVLKRLSRALSDG 709
+I + +A LS P+ FD +G V E ++++ L AL+ G
Sbjct: 120 AVIDTVSLAGFAAARALSTHFNSTPEKASRPFDTARDGFVMGEGAGLLIIEELEHALARG 179
Query: 710 DPIHAIIRGSGINYDGKTNGITAPNGISQTELIKSVYKKSNLNPEDINYIITHGTGTKLG 769
A I G G + D A +G +K +++ + PE + ++ H T T +G
Sbjct: 180 AKPLAEIVGYGTSADAYHMTSGAEDGDGAYRAMKIALRQAGITPEQVQHLNAHATSTPVG 239
Query: 770 DPVEINALHDVFKNKTYNQKFCAITSNKSNIGHTFAASGLVSLINLVQSIKYKIIPASLH 829
D EINA+ +F AITS KS GH A+G + I V +++ +I+PA+L+
Sbjct: 240 DLGEINAIKHLFGESNA----LAITSTKSATGHLLGAAGGLETIFTVLALRDQIVPATLN 295
Query: 830 CEKENNYIILKNSPFYINKSNKKWNTVNEKLRIGAVSAFGMSGTNAHIVLQEYI 883
E + P + N + + FG +G NA I+L+ ++
Sbjct: 296 LENPD--------PAAKGLNIIAGNAQPHDMTYALSNGFGFAGVNASILLKRWV 341
>gnl|CDD|187658 cd08955, KR_2_FAS_SDR_x, beta-ketoacyl reductase (KR) domain of
fatty acid synthase (FAS), subgroup 2, complex (x).
Ketoreductase, a module of the multidomain polyketide
synthase, has 2 subdomains, each corresponding to a
short-chain dehydrogenases/reductase (SDR) family
monomer. The C-terminal subdomain catalyzes the
NADPH-dependent reduction of the beta-carbonyl of a
polyketide to a hydroxyl group, a step in the
biosynthesis of polyketides, such as erythromycin. The
N-terminal subdomain, an interdomain linker, is a
truncated Rossmann fold which acts to stabilizes the
catalytic subdomain. Unlike typical SDRs, the isolated
domain does not oligomerizes but is composed of 2
subdomains, each resembling an SDR monomer. In some
instances, as in porcine FAS, an enoyl reductase (a
Rossman fold NAD binding domain of the MDR family)
module is inserted between the sub-domains. The active
site resembles that of typical SDRs, except that the
usual positions of the catalytic asparagine and tyrosine
are swapped, so that the canonical YXXXK motif changes
to YXXXN. Modular polyketide synthases are
multifunctional structures in which the makeup
recapitulates that found in (and may have evolved from)
fatty acid synthase. In some instances, such as
porcine FAS , an enoyl reductase module is inserted
between the sub-domains. Fatty acid synthesis occurs via
the stepwise elongation of a chain (which is attached to
acyl carrier protein, ACP) with 2-carbon units.
Eukaryotic systems consists of large, multifunctional
synthases (type I) while bacterial, type II systems, use
single function proteins. Fungal fatty acid synthesis
uses dodecamer of 6 alpha and 6 beta subunits. In
mammalian type FAS cycles, ketoacyl synthase forms
acetoacetyl-ACP which is reduced by the NADP-dependent
beta-ketoacyl reductase (KR), forming
beta-hydroxyacyl-ACP, which is in turn dehydrated by
dehydratase to a beta-enoyl intermediate, which is
reduced by NADP-dependent beta-enoyl reductase (ER).
Polyketide syntheses also proceeds via the addition of
2-carbon units as in fatty acid synthesis. The complex
SDR NADP binding motif, GGXGXXG, is often present, but
is not strictly conserved in each instance of the
module. This subfamily includes the KR domain of the
Lyngbya majuscule Jam J, -K, and #L which are encoded
on the jam gene cluster and are involved in the
synthesis of the Jamaicamides (neurotoxins); Lyngbya
majuscule Jam P belongs to a different KR_FAS_SDR_x
subfamily. 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 KRs 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 = 376
Score = 96.2 bits (240), Expect = 5e-21
Identities = 48/164 (29%), Positives = 83/164 (50%), Gaps = 15/164 (9%)
Query: 69 GTYLITGGTGRLGMLFSDYLINKYSTNLILSGRSKLNSIIYKKLKKFNNKAIYI---QVD 125
TYLITGG G LG+L +++L+ + + +L+L+GR ++ + + + D
Sbjct: 150 ATYLITGGLGGLGLLVAEWLVERGARHLVLTGRRAPSAAARQAIAALEEAGAEVVVLAAD 209
Query: 126 VSDKLKMISEINSIINNIGPIDGVLHIAGI--SGLTSNILEANYKNFYSVLSSKISGTIA 183
VSD+ + + + I ++ P+ GV+H AG+ G+ +N F VL+ K+ G
Sbjct: 210 VSDRDALAAALAQIRASLPPLRGVIHAAGVLDDGVLANQDWE---RFRKVLAPKVQGAWN 266
Query: 184 LNYALENTILKLQKNKLDFVCYFSSSSAILGDFGSCDYAMGNRF 227
L+ ++ LDF FSS +++LG G +YA N F
Sbjct: 267 LHQLTQD-------LPLDFFVLFSSVASLLGSPGQANYAAANAF 303
>gnl|CDD|181657 PRK09116, PRK09116, 3-oxoacyl-(acyl carrier protein) synthase II;
Reviewed.
Length = 405
Score = 94.7 bits (236), Expect = 2e-20
Identities = 77/273 (28%), Positives = 112/273 (41%), Gaps = 38/273 (13%)
Query: 560 LALEDAG-YGPNQIANQKIGMFVGVEEGS--------NYQDRLDQVNLTST-------HN 603
LALEDAG G + + ++G+ G GS +T+T H
Sbjct: 83 LALEDAGLLGDPILTDGRMGIAYGSSTGSTDPIGAFGTMLLEGSMSGITATTYVRMMPHT 142
Query: 604 AILSARLAYFMDLKGPVMAINTACSSSLVATHIACQSLRQHECDTAISAGVNLMISPEAY 663
+ + F LKG V+ ++AC+S A ++++ ++ G + EA
Sbjct: 143 T--AVNVGLFFGLKGRVIPTSSACTSGSQGIGYAYEAIKYGYQTVMLAGGAEELCPTEAA 200
Query: 664 I--------AMTSAGMLSPDGKCYVFDERANGLVPSEAVVAVVLKRLSRALSDGDPIHAI 715
+ A L+P FD +GLV E +VL+ L A + G I+A
Sbjct: 201 VFDTLFATSTRNDAPELTPRP----FDANRDGLVIGEGAGTLVLEELEHAKARGATIYAE 256
Query: 716 IRGSGINYDGKTNGITAPNGISQTELIKSVYKKSNLNPEDINYIITHGTGTKLGDPVEIN 775
I G G N DG +T P + ++ K + L PEDI Y+ HGT T GD E
Sbjct: 257 IVGFGTNSDGAH--VTQPQAETMQIAMELALKDAGLAPEDIGYVNAHGTATDRGDIAESQ 314
Query: 776 ALHDVFKNKTYNQKFCAITSNKSNIGHTFAASG 808
A VF + I+S KS GHT A G
Sbjct: 315 ATAAVFGARM------PISSLKSYFGHTLGACG 341
>gnl|CDD|215720 pfam00106, adh_short, short chain dehydrogenase. This family
contains a wide variety of dehydrogenases.
Length = 167
Score = 88.8 bits (221), Expect = 2e-20
Identities = 44/163 (26%), Positives = 77/163 (47%), Gaps = 13/163 (7%)
Query: 69 GTYLITGGTGRLGMLFSDYLINKYSTNLILSGRS----KLNSIIYKKLKKFNNKAIYIQV 124
GT LITGGTG LG+ + +L + + +L+L R ++ +L+ +
Sbjct: 1 GTVLITGGTGGLGLALARWLAAEGARHLVLVSRRGPAPGAAELV-AELEALGAEVTVAAC 59
Query: 125 DVSDKLKMISEINSIINNIGPIDGVLHIAGISGLTSNILEANYKNFYSVLSSKISGTIAL 184
DV+D+ + + + ++ +GP+DGV+H AG+ + E + F VL+ K++G L
Sbjct: 60 DVADRDALAALLAALPAALGPLDGVVHNAGVLDDG-PLEELTPERFERVLAPKVTGAWNL 118
Query: 185 NYALENTILKLQKNKLDFVCYFSSSSAILGDFGSCDYAMGNRF 227
+ + L FSS + +LG G +YA N
Sbjct: 119 HEL-------TRDLDLGAFVLFSSVAGVLGSPGQANYAAANAA 154
>gnl|CDD|236129 PRK07910, PRK07910, 3-oxoacyl-(acyl carrier protein) synthase II;
Reviewed.
Length = 418
Score = 94.0 bits (234), Expect = 3e-20
Identities = 76/281 (27%), Positives = 112/281 (39%), Gaps = 38/281 (13%)
Query: 617 KGPVMAINTACSSSLVATHIACQSLRQHECDTAISAGVNLMIS--PEAYIAMTSAGMLS- 673
K V+ +AC+S A A + + E D AI GV I P A A M +
Sbjct: 161 KAGVITPVSACASGSEAIAQAWRQIVLGEADIAICGGVETRIEAVPIAGFAQMRIVMSTN 220
Query: 674 ---PDGKCYVFDERANGLVPSEAVVAVVLKRLSRALSDGDPIHAIIRGSGINYDGKTNGI 730
P G C FD+ +G V E +V++ A + G I A I G+ I DG
Sbjct: 221 NDDPAGACRPFDKDRDGFVFGEGGALMVIETEEHAKARGANILARIMGASITSDGFHMVA 280
Query: 731 TAPNGISQTELIKSVYKKSNLNPEDINYIITHGTGTKLGDPVEINALHDVFKNKTYNQKF 790
PNG + + + L P DI+++ H TGT +GD E A+ N
Sbjct: 281 PDPNGERAGHAMTRAIELAGLTPGDIDHVNAHATGTSVGDVAEGKAI-----NNALGGHR 335
Query: 791 CAITSNKSNIGHTFAASGLVSLINLVQSIKYKIIPASLHCEKENNYI---ILKNSP---- 843
A+ + KS +GH+ A G V I V +++ +IP +L+ E + I ++ P
Sbjct: 336 PAVYAPKSALGHSVGAVGAVESILTVLALRDGVIPPTLNLENLDPEIDLDVVAGEPRPGN 395
Query: 844 --FYINKSNKKWNTVNEKLRIGAVSAFGMSGTNAHIVLQEY 882
+ IN S FG G N + Y
Sbjct: 396 YRYAINNS------------------FGFGGHNVALAFGRY 418
>gnl|CDD|187582 cd05274, KR_FAS_SDR_x, ketoreductase (KR) and fatty acid synthase
(FAS), complex (x) SDRs. Ketoreductase, a module of the
multidomain polyketide synthase (PKS), has 2 subdomains,
each corresponding to a SDR family monomer. The
C-terminal subdomain catalyzes the NADPH-dependent
reduction of the beta-carbonyl of a polyketide to a
hydroxyl group, a step in the biosynthesis of
polyketides, such as erythromycin. The N-terminal
subdomain, an interdomain linker, is a truncated
Rossmann fold which acts to stabilizes the catalytic
subdomain. Unlike typical SDRs, the isolated domain does
not oligomerize but is composed of 2 subdomains, each
resembling an SDR monomer. The active site resembles
that of typical SDRs, except that the usual positions of
the catalytic Asn and Tyr are swapped, so that the
canonical YXXXK motif changes to YXXXN. Modular PKSs are
multifunctional structures in which the makeup
recapitulates that found in (and may have evolved from)
FAS. In some instances, such as porcine FAS, an enoyl
reductase (ER) module is inserted between the
sub-domains. Fatty acid synthesis occurs via the
stepwise elongation of a chain (which is attached to
acyl carrier protein, ACP) with 2-carbon units.
Eukaryotic systems consist of large, multifunctional
synthases (type I) while bacterial, type II systems, use
single function proteins. Fungal fatty acid synthase
uses a dodecamer of 6 alpha and 6 beta subunits. In
mammalian type FAS cycles, ketoacyl synthase forms
acetoacetyl-ACP which is reduced by the NADP-dependent
beta-KR, forming beta-hydroxyacyl-ACP, which is in turn
dehydrated by dehydratase to a beta-enoyl intermediate,
which is reduced by NADP-dependent beta-ER. Polyketide
synthesis also proceeds via the addition of 2-carbon
units as in fatty acid synthesis. The complex SDR
NADP-binding motif, GGXGXXG, is often present, but is
not strictly conserved in each instance of the module.
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 KRs 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 = 375
Score = 90.9 bits (226), Expect = 2e-19
Identities = 53/174 (30%), Positives = 81/174 (46%), Gaps = 22/174 (12%)
Query: 67 QGGTYLITGGTGRLGMLFSDYLINKYSTNLILSGRSKLNSIIYKKLKKFNNKAIYI---Q 123
GTYLITGG G LG+L + +L + + +L+L R + + +
Sbjct: 149 LDGTYLITGGLGGLGLLVARWLAARGARHLVLLSRRGPAPRAAARAALLRAGGARVSVVR 208
Query: 124 VDVSDK--LK-MISEINSIINNIGPIDGVLHIAGI--SGLTSNILEANYKNFYSVLSSKI 178
DV+D L +++E+ GP+ GV+H AG+ L + + A F +VL++K+
Sbjct: 209 CDVTDPAALAALLAELA----AGGPLAGVIHAAGVLRDALLAELTPAA---FAAVLAAKV 261
Query: 179 SGTIALNYALENTILKLQKNKLDFVCYFSSSSAILGDFGSCDYAMGNRFQTVYA 232
+G + L E T LDF FSS +A+LG G YA N F A
Sbjct: 262 AGALNL---HELT----PDLPLDFFVLFSSVAALLGGAGQAAYAAANAFLDALA 308
>gnl|CDD|181539 PRK08722, PRK08722, 3-oxoacyl-(acyl carrier protein) synthase II;
Reviewed.
Length = 414
Score = 90.1 bits (223), Expect = 6e-19
Identities = 93/442 (21%), Positives = 179/442 (40%), Gaps = 51/442 (11%)
Query: 461 SEELIAIIGMSGRFPAARNINEFWKILINNKDVISEIPEKIFDWKLYYENPIKSSNKINS 520
S+ + + GM P + WK L+ + I I FD + ++
Sbjct: 2 SKRRVVVTGMGMLSPVGNTVESSWKALLAGQSGIVNIEH--FD-----------TTNFST 48
Query: 521 KWYGSIPGIDEFDPLFFEISPLEAERMDPRQRHLLQESWLALEDAGYGPNQIANQKIGMF 580
++ G + F+ + +S +A +MD ++ + AL+D+G + +IG+
Sbjct: 49 RFAGLVKD---FNCEEY-MSKKDARKMDLFIQYGIAAGIQALDDSGLEVTEENAHRIGVA 104
Query: 581 VG----------------VEEGSNYQDRLDQVNLTSTHNAILSARLAYFMDLKGPVMAIN 624
+G VE+G ++ + ST +++ L+ L+GP +AI+
Sbjct: 105 IGSGIGGLGLIEAGHQALVEKGPR---KVSPFFVPSTIVNMIAGNLSIMRGLRGPNIAIS 161
Query: 625 TACSSSLVATHIACQSLRQHECDTAISAGVNLMISPEAYIAMTSAGMLS-----PDGKCY 679
TAC++ L A + + + D ++ G +P +A LS P
Sbjct: 162 TACTTGLHNIGHAARMIAYGDADAMVAGGAEKASTPLGMAGFGAAKALSTRNDEPQKASR 221
Query: 680 VFDERANGLVPSEAVVAVVLKRLSRALSDGDPIHAIIRGSGINYDGKTNGITAPNGISQT 739
+D+ +G V + +VL+ A + G I+A + G G++ D + +G
Sbjct: 222 PWDKDRDGFVLGDGAGMMVLEEYEHAKARGAKIYAELVGFGMSGDAYHMTSPSEDGSGGA 281
Query: 740 ELIKSVYKKSNLNPEDINYIITHGTGTKLGDPVEINALHDVFKNKTYNQKFCAITSNKSN 799
+++ + + + E I Y+ HGT T GD EI + Q ++S KS
Sbjct: 282 LAMEAAMRDAGVTGEQIGYVNAHGTSTPAGDVAEIKGIKRALGEAGSKQVL--VSSTKSM 339
Query: 800 IGHTFAASGLVSLINLVQSIKYKIIPASLHCEKENNYIILKNSPFYINKSNKKWNTVNEK 859
GH A+G V I V S+ +I+P +++ + + + P K E
Sbjct: 340 TGHLLGAAGSVEAIITVMSLVDQIVPPTINLDDPEEGLDIDLVPHTARKV--------ES 391
Query: 860 LRIGAVSAFGMSGTNAHIVLQE 881
+ ++FG GTN ++ ++
Sbjct: 392 MEYAICNSFGFGGTNGSLIFKK 413
>gnl|CDD|215421 PLN02787, PLN02787, 3-oxoacyl-[acyl-carrier-protein] synthase II.
Length = 540
Score = 91.2 bits (226), Expect = 8e-19
Identities = 113/459 (24%), Positives = 178/459 (38%), Gaps = 68/459 (14%)
Query: 454 NKNTDINSEELIAIIGMSGRFPAARNINEFWKILINNKDVISEIPEKIFDWKLYYENPIK 513
K ++ + GM P + + F+ L+ ISEI FD + P +
Sbjct: 121 KKKPLTKQRRVV-VTGMGVVSPLGHDPDVFYNNLLEGVSGISEIER--FDCSQF---PTR 174
Query: 514 SSNKINS----KWYGSIPGIDEFDPLFFEISPLEAERMDPRQRHLLQESWLALEDAGYGP 569
+ +I S W ++P ++RMD +LL AL D G
Sbjct: 175 IAGEIKSFSTDGW----------------VAPKLSKRMDKFMLYLLTAGKKALADGGITE 218
Query: 570 ---NQIANQKIGMFVGVEEGSN--YQDRLDQVNLT-----------STHNAILSARLAYF 613
++ K G+ +G G + D ++ + ++ +T N + SA LA
Sbjct: 219 DVMKELDKTKCGVLIGSAMGGMKVFNDAIEALRISYRKMNPFCVPFATTN-MGSAMLA-- 275
Query: 614 MDL--KGPVMAINTACSSSLVATHIACQSLRQHECDTAISAGVNLMISPEAYIAMTSAGM 671
MDL GP +I+TAC++S A + + E D + G + I P +
Sbjct: 276 MDLGWMGPNYSISTACATSNFCILNAANHIIRGEADVMLCGGSDAAIIPIGLGGFVACRA 335
Query: 672 LS-----PDGKCYVFDERANGLVPSEAVVAVVLKRLSRALSDGDPIHAIIRGSGINYDGK 726
LS P +D +G V E ++L+ L A G I+A G D
Sbjct: 336 LSQRNDDPTKASRPWDMNRDGFVMGEGAGVLLLEELEHAKKRGANIYAEFLGGSFTCDAY 395
Query: 727 TNGITAPNGISQTELIKSVYKKSNLNPEDINYIITHGTGTKLGDPVEINALHDVFKNKTY 786
P G I+ +S ++ ED+NYI H T TK GD E AL F
Sbjct: 396 HMTEPHPEGAGVILCIEKALAQSGVSKEDVNYINAHATSTKAGDLKEYQALMRCFGQ--- 452
Query: 787 NQKFCAITSNKSNIGHTFAASGLVSLINLVQSIKYKIIPASLHCEKENNYIILKNSPFYI 846
N + + S KS IGH A+G V I VQ+I+ + +++ E + + K +
Sbjct: 453 NPEL-RVNSTKSMIGHLLGAAGAVEAIATVQAIRTGWVHPNINLENPESGVDTK----VL 507
Query: 847 NKSNKKWNTVNEKLRIGAV--SAFGMSGTNAHIVLQEYI 883
K E+L I ++FG G N+ I+ Y
Sbjct: 508 VGPKK------ERLDIKVALSNSFGFGGHNSSILFAPYK 540
>gnl|CDD|181184 PRK07967, PRK07967, 3-oxoacyl-(acyl carrier protein) synthase I;
Reviewed.
Length = 406
Score = 85.1 bits (211), Expect = 3e-17
Identities = 86/346 (24%), Positives = 150/346 (43%), Gaps = 47/346 (13%)
Query: 561 ALEDAGYGPNQIANQKIGMFVGVEEGSNYQ--------------DRLDQVNLTSTHNAIL 606
A+ DAG Q++N + G+ G GS R+ +T + +
Sbjct: 82 AIADAGLSEEQVSNPRTGLIAGSGGGSTRNQVEAADAMRGPRGPKRVGPYAVTKAMASTV 141
Query: 607 SARLAYFMDLKGPVMAINTACSSSLVATHIACQSLRQHECDTAISAGV-----NLMISPE 661
SA LA +KG +I++AC++S A + ++ + D + G + +
Sbjct: 142 SACLATPFKIKGVNYSISSACATSAHCIGNAVEQIQLGKQDIVFAGGGEELDWEMSCLFD 201
Query: 662 AYIAMTSAGMLSPDGKCYVFDERANGLVPSEAVVAVVLKRLSRALSDGDPIHAIIRGSGI 721
A A+++ +P+ +D +G V + VV++ L AL+ G I+A I G G
Sbjct: 202 AMGALSTKYNDTPEKASRAYDANRDGFVIAGGGGVVVVEELEHALARGAKIYAEIVGYGA 261
Query: 722 NYDGKTNGITAPNGISQTELIKSVYKKSNLNPEDINYIITHGTGTKLGDPVEINALHDVF 781
DG + AP+G ++ + I+YI THGT T +GD E+ A+ +VF
Sbjct: 262 TSDGYD--MVAPSGEGAVRCMQMALATVD---TPIDYINTHGTSTPVGDVKELGAIREVF 316
Query: 782 KNKTYNQKFCAITSNKSNIGHTFAASGLVSLINLVQSIKYKIIPASLHCEK-----ENNY 836
+K+ AI++ KS GH+ A+G+ I + +++ I S + E+
Sbjct: 317 GDKS-----PAISATKSLTGHSLGAAGVQEAIYSLLMMEHGFIAPSANIEELDPQAAGMP 371
Query: 837 IILKNSPFYINKSNKKWNTVNEKLRIGAVSAFGMSGTNAHIVLQEY 882
I+ + N + TV ++FG GTNA +V + Y
Sbjct: 372 IVTE------TTDNAELTTV-------MSNSFGFGGTNATLVFRRY 404
>gnl|CDD|236265 PRK08439, PRK08439, 3-oxoacyl-(acyl carrier protein) synthase II;
Reviewed.
Length = 406
Score = 79.0 bits (195), Expect = 2e-15
Identities = 94/373 (25%), Positives = 163/373 (43%), Gaps = 37/373 (9%)
Query: 529 IDEFDPLFFEISPLEAERMDPRQRHL-LQESWLALEDAGYGPNQIANQK--------IGM 579
I +FDP + P E ++ D R L L+ + A++DAG+ P ++ ++ IG
Sbjct: 52 ITDFDPTEV-MDPKEVKKAD-RFIQLGLKAAREAMKDAGFLPEELDAERFGVSSASGIGG 109
Query: 580 FVGVEEGSNY-----QDRLDQVNLTSTHNAILSARLAYFMDLKGPVMAINTACSSSLVAT 634
+E+ S ++ + S +L ++ LKGP ++ TAC++ A
Sbjct: 110 LPNIEKNSIICFEKGPRKISPFFIPSALVNMLGGFISIEHGLKGPNLSSVTACAAGTHAI 169
Query: 635 HIACQSLRQHECDTAISAGVNLMISPEAYIAMTSAGMLS-----PDGKCYVFDERANGLV 689
A +++ D + G I P + LS P FD+ +G V
Sbjct: 170 IEAVKTIMLGGADKMLVVGAESAICPVGIGGFAAMKALSTRNDDPKKASRPFDKDRDGFV 229
Query: 690 PSEAVVAVVLKRLSRALSDGDPIHAIIRGSGINYDGKTNGITAPNGISQTELIKSVYKKS 749
E A+VL+ A G I+A I G G G N IT+P +K+ + +
Sbjct: 230 MGEGAGALVLEEYESAKKRGAKIYAEIIGFG--ESGDANHITSPAPEGPLRAMKAALEMA 287
Query: 750 NLNPEDINYIITHGTGTKLGDPVEINALHDVFKNKTYNQKFCAITSNKSNIGHTFAASGL 809
NP+ I+YI HGT T D E AL ++F +K +K ++S K IGH A+G
Sbjct: 288 G-NPK-IDYINAHGTSTPYNDKNETAALKELFGSK---EKVPPVSSTKGQIGHCLGAAGA 342
Query: 810 VSLINLVQSIKYKIIPASLHCEKENNYIILKNSPFYINKSNKKWNTVNEKLRIGAVSAFG 869
+ + + +++ I+P +++ E + L P N + K +L + ++FG
Sbjct: 343 IEAVISIMAMRDGILPPTINQETPDPECDLDYIP---NVARKA------ELNVVMSNSFG 393
Query: 870 MSGTNAHIVLQEY 882
GTN ++ ++
Sbjct: 394 FGGTNGVVIFKKV 406
>gnl|CDD|238428 cd00832, CLF, Chain-length factor (CLF) is a factor required for
polyketide chain initiation of aromatic
antibiotic-producing polyketide synthases (PKSs) of
filamentous bacteria. CLFs have been shown to have
decarboxylase activity towards malonyl-acyl carrier
protein (ACP). CLFs are similar to other elongation
ketosynthase domains, but their active site cysteine is
replaced by a conserved glutamine.
Length = 399
Score = 74.3 bits (183), Expect = 8e-14
Identities = 85/370 (22%), Positives = 147/370 (39%), Gaps = 53/370 (14%)
Query: 482 EFWKILINNKDVISEIPEKIFDWKLYYENPIKSSNKINSKWYGSIPGIDEFDPLFFEISP 541
E+WK +++ + + I FD Y P + + G +P D + L + P
Sbjct: 20 EYWKAVLDGRSGLGPITR--FDPSGY---PARLA--------GEVPDFDAAEHLPGRLLP 66
Query: 542 LEAERMDPRQRHLLQESWLALEDAGYGPNQIANQKIGMFV-----GVEEGSNYQDRLDQV 596
+ D R L + AL DAG P + +G+ G E G Q L
Sbjct: 67 ----QTDRMTRLALAAADWALADAGVDPAALPPYDMGVVTASAAGGFEFG---QRELQ-- 117
Query: 597 NLTSTHNAILSA--RLAYFM-----------DLKGPVMAINTACSSSLVATHIACQSLRQ 643
L S +SA A+F ++GP + + L A A + +R+
Sbjct: 118 KLWSKGPRHVSAYQSFAWFYAVNTGQISIRHGMRGPSGVVVAEQAGGLDALAQARRLVRR 177
Query: 644 HECDTAISAGVNLMISPEAYIAMTSAGMLSPDG---KCYV-FDERANGLVPSEAVVAVVL 699
+S GV+ + P ++A S+G LS + Y+ FD A G VP E +VL
Sbjct: 178 GTP-LVVSGGVDSALCPWGWVAQLSSGRLSTSDDPARAYLPFDAAAAGYVPGEGGAILVL 236
Query: 700 KRLSRALSDGDPIHAIIRGSGINYDGKTNGITAPNGISQTELIKSVYKKSNLNPEDINYI 759
+ + A G ++ I G +D G P G+++ I+ + L PED++ +
Sbjct: 237 EDAAAARERGARVYGEIAGYAATFDPPP-GSGRPPGLAR--AIRLALADAGLTPEDVDVV 293
Query: 760 ITHGTGTKLGDPVEINALHDVFKNKTYNQKFCAITSNKSNIGHTFAASGLVSLINLVQSI 819
G D E AL VF + +T+ K+ G +A + + + ++
Sbjct: 294 FADAAGVPELDRAEAAALAAVFGPRG-----VPVTAPKTMTGRLYAGGAPLDVATALLAL 348
Query: 820 KYKIIPASLH 829
+ +IP +++
Sbjct: 349 RDGVIPPTVN 358
>gnl|CDD|236398 PRK09185, PRK09185, 3-oxoacyl-(acyl carrier protein) synthase I;
Reviewed.
Length = 392
Score = 74.1 bits (183), Expect = 9e-14
Identities = 66/226 (29%), Positives = 95/226 (42%), Gaps = 30/226 (13%)
Query: 611 AYFMDLKGPVMAINTACSSSLVATHIACQSLRQHECDTAISAGVNLMISPEAYIAMT--- 667
AY L GP I+TACSSS A + L CD AI GV+ + +T
Sbjct: 145 AYL-GLSGPAYTISTACSSSAKVFASARRLLEAGLCDAAIVGGVDSLC------RLTLNG 197
Query: 668 --SAGMLSPDGKCYVFDERANGLVPSEAVVAVVLKRLSRALSDGDPIHAIIRGSGINYDG 725
S LSP C F +G+ EA A L L R D + + G G + D
Sbjct: 198 FNSLESLSP-QPCRPFSANRDGINIGEAA-AFFL--LERE--DDAAV--ALLGVGESSDA 249
Query: 726 KTNGITAPN--GISQTELIKSVYKKSNLNPEDINYIITHGTGTKLGDPVEINALHDVFKN 783
+ ++AP+ G+ ++ + L P DI YI HGT T L D +E A+ VF +
Sbjct: 250 --HHMSAPHPEGLGAILAMQQALADAGLAPADIGYINLHGTATPLNDAMESRAVAAVFGD 307
Query: 784 KTYNQKFCAITSNKSNIGHTFAASGLVSLINLVQSIKYKIIPASLH 829
+S K GHT A+G V ++++ + P +
Sbjct: 308 GV------PCSSTKGLTGHTLGAAGAVEAAICWLALRHGLPPHGWN 347
>gnl|CDD|187657 cd08954, KR_1_FAS_SDR_x, beta-ketoacyl reductase (KR) domain of
fatty acid synthase (FAS), subgroup 1, complex (x) SDRs.
NADP-dependent KR domain of the multidomain type I FAS,
a complex SDR family. This subfamily also includes
proteins identified as polyketide synthase (PKS), a
protein with related modular protein architecture and
similar function. It includes the KR domains of
mammalian and chicken FAS, and Dictyostelium discoideum
putative polyketide synthases (PKSs). These KR domains
contain two subdomains, each of which is related to SDR
Rossmann fold domains. However, while the C-terminal
subdomain has an active site similar to the other SDRs
and a NADP-binding capability, the N-terminal SDR-like
subdomain is truncated and lacks these functions,
serving a supportive structural role. In some instances,
such as porcine FAS, an enoyl reductase (a Rossman fold
NAD-binding domain of the medium-chain
dehydrogenase/reductase, MDR family) module is inserted
between the sub-domains. Fatty acid synthesis occurs via
the stepwise elongation of a chain (which is attached to
acyl carrier protein, ACP) with 2-carbon units.
Eukaryotic systems consists of large, multifunctional
synthases (type I) while bacterial, type II systems, use
single function proteins. Fungal fatty acid synthesis
uses a dodecamer of 6 alpha and 6 beta subunits. In
mammalian type FAS cycles, ketoacyl synthase forms
acetoacetyl-ACP which is reduced by the NADP-dependent
beta-ketoacyl reductase (KR), forming
beta-hydroxyacyl-ACP, which is in turn dehydrated by
dehydratase to a beta-enoyl intermediate, which is
reduced by NADP-dependent beta-enoyl reductase (ER);
this KR and ER are members of the SDR family. This KR
subfamily has an active site tetrad with a similar 3D
orientation compared to archetypical SDRs, but the
active site Lys and Asn residue positions are swapped.
The characteristic NADP-binding is typical of the
multidomain complex SDRs, with a GGXGXXG NADP 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
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 KRs 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 = 452
Score = 71.3 bits (175), Expect = 1e-12
Identities = 61/181 (33%), Positives = 96/181 (53%), Gaps = 14/181 (7%)
Query: 62 NSYIKQGGTYLITGGTGRLGMLFSDYLINKYST-NLILSGRSKLN---SIIYKKLKKFNN 117
N I G +YLITGG+G LG+ +L+ + + N+I+ RS + ++ ++ K N
Sbjct: 212 NYPINLGKSYLITGGSGGLGLEILKWLVKRGAVENIIILSRSGMKWELELLIREWKSQNI 271
Query: 118 KAIYIQVDVSDKLKMISEINSIIN--NIGPIDGVLHIAGISGLTSNILEANYKN-FYSVL 174
K ++ VDVSD + IN I+N IGPI G+ H+A + L +LE + ++ F SV
Sbjct: 272 KFHFVSVDVSDVSSLEKAINLILNAPKIGPIGGIFHLAFV--LIDKVLEIDTESLFISVN 329
Query: 175 SSKISGTIALNYALENTILKLQKNKLDFVCYFSSSSAILGDFGSCDYAMGNRFQTVYAKY 234
+K+ G I L+ +I + K LD+ FSS S+I G G C+Y N ++Y
Sbjct: 330 KAKVMGAINLH---NQSIKRCWK--LDYFVLFSSVSSIRGSAGQCNYVCANSVLDSLSRY 384
Query: 235 L 235
Sbjct: 385 R 385
>gnl|CDD|215989 pfam00550, PP-binding, Phosphopantetheine attachment site. A
4'-phosphopantetheine prosthetic group is attached
through a serine. This prosthetic group acts as a a
'swinging arm' for the attachment of activated fatty
acid and amino-acid groups. This domain forms a four
helix bundle. This family includes members not included
in Prosite. The inclusion of these members is supported
by sequence analysis and functional evidence. The
related domain of Vibrio anguillarum angR has the
attachment serine replaced by an alanine.
Length = 66
Score = 53.3 bits (129), Expect = 5e-09
Identities = 18/65 (27%), Positives = 30/65 (46%), Gaps = 1/65 (1%)
Query: 341 IKNHICNILNTKKSEIYKNKNLADYGFDSISLAEFSRILSKFYSLDIMPSIFFSYSTLER 400
++ + +L EI + +L D G DS+ E L + + ++I PS F + TL
Sbjct: 3 LREIVAEVLGIP-DEIDPDDDLFDLGLDSLLAVELLARLEEEFGVEIPPSDLFEHPTLGE 61
Query: 401 LITYF 405
L Y
Sbjct: 62 LAAYL 66
>gnl|CDD|187659 cd08956, KR_3_FAS_SDR_x, beta-ketoacyl reductase (KR) domain of
fatty acid synthase (FAS), subgroup 3, complex (x).
Ketoreductase, a module of the multidomain polyketide
synthase (PKS), has 2 subdomains, each corresponding to
a SDR family monomer. The C-terminal subdomain catalyzes
the NADPH-dependent reduction of the beta-carbonyl of a
polyketide to a hydroxyl group, a step in the
biosynthesis of polyketides, such as erythromycin. The
N-terminal subdomain, an interdomain linker, is a
truncated Rossmann fold which acts to stabilizes the
catalytic subdomain. Unlike typical SDRs, the isolated
domain does not oligomerize but is composed of 2
subdomains, each resembling an SDR monomer. The active
site resembles that of typical SDRs, except that the
usual positions of the catalytic Asn and Tyr are
swapped, so that the canonical YXXXK motif changes to
YXXXN. Modular PKSs are multifunctional structures in
which the makeup recapitulates that found in (and may
have evolved from) FAS. In some instances, such as
porcine FAS, an enoyl reductase (ER) module is inserted
between the sub-domains. Fatty acid synthesis occurs via
the stepwise elongation of a chain (which is attached to
acyl carrier protein, ACP) with 2-carbon units.
Eukaryotic systems consists of large, multifunctional
synthases (type I) while bacterial, type II systems, use
single function proteins. Fungal fatty acid synthesis
uses a dodecamer of 6 alpha and 6 beta subunits. In
mammalian type FAS cycles, ketoacyl synthase forms
acetoacetyl-ACP which is reduced by the NADP-dependent
beta-KR, forming beta-hydroxyacyl-ACP, which is in turn
dehydrated by dehydratase to a beta-enoyl intermediate,
which is reduced by NADP-dependent beta- ER. Polyketide
synthesis also proceeds via the addition of 2-carbon
units as in fatty acid synthesis. The complex SDR
NADP-binding motif, GGXGXXG, is often present, but is
not strictly conserved in each instance of the module.
This subfamily includes KR domains found in many
multidomain PKSs, including six of seven Sorangium
cellulosum PKSs (encoded by spiDEFGHIJ) which
participate in the synthesis of the polyketide scaffold
of the cytotoxic spiroketal polyketide spirangien. These
seven PKSs have either a single PKS module (SpiF), two
PKR modules (SpiD,-E,-I,-J), or three PKS modules
(SpiG,-H). This subfamily includes the second KR domains
of SpiE,-G, I, and -J, both KR domains of SpiD, and the
third KR domain of SpiH. The single KR domain of SpiF,
the first and second KR domains of SpiH, the first KR
domains of SpiE,-G,- I, and -J, and the third KR domain
of SpiG, belong to a different KR_FAS_SDR subfamily.
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 KRs 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 = 448
Score = 55.7 bits (135), Expect = 7e-08
Identities = 50/190 (26%), Positives = 78/190 (41%), Gaps = 66/190 (34%)
Query: 69 GTYLITGGTGRLGMLFSDYLINKYS-TNLILSGRS---------------KLNSIIYKKL 112
GT LITGGTG LG L + +L+ ++ +L+L R L
Sbjct: 194 GTVLITGGTGTLGALLARHLVTEHGVRHLLLVSRRGPDAPGAAELVAELAALG------- 246
Query: 113 KKFNNKAIYIQV-----DVSDKLKMISEINSIINNI---GPIDGVLHIAG------ISGL 158
A +V DV+D+ + + +++ + P+ V+H AG ++ L
Sbjct: 247 ------A---EVTVAACDVADR----AALAALLAAVPADHPLTAVVHAAGVLDDGVLTSL 293
Query: 159 TSNILEANYKNFYSVLSSKISGTIALNYALENTILKLQKNKLD-FVCYFSSSSAILGDFG 217
T L+A VL K+ L+ E T + L FV FSS++ +LG G
Sbjct: 294 TPERLDA-------VLRPKVDAAWHLH---ELT----RDLDLAAFV-LFSSAAGVLGSPG 338
Query: 218 SCDYAMGNRF 227
+YA N F
Sbjct: 339 QANYAAANAF 348
>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 = 50.6 bits (121), Expect = 1e-06
Identities = 33/161 (20%), Positives = 65/161 (40%), Gaps = 10/161 (6%)
Query: 67 QGGTYLITGGTGRLGMLFSDYLINKYSTNLILSGRS---KLNSIIYKKLKKFNNKAIYIQ 123
G L+TG + +G + L + + ++ + RS ++ + +A +
Sbjct: 4 SGKVALVTGASSGIGRAIARALAREGARVVVAARRSEEEAAEALAAAIKEAGGGRAAAVA 63
Query: 124 VDVSDKLKMISE-INSIINNIGPIDGVLHIAGISGLTSNILEANYKNFYSVLSSKISGTI 182
DVSD + + + + G ID +++ AGI+G + + E +++ V+ + G
Sbjct: 64 ADVSDDEESVEALVAAAEEEFGRIDILVNNAGIAGPDAPLEELTEEDWDRVIDVNLLGAF 123
Query: 183 ALNYALENTILKLQKNKLDFVCYFSSSSAILGDFGSCDYAM 223
L A L K + SS + + G G YA
Sbjct: 124 LLTRAA------LPLMKKQRIVNISSVAGLGGPPGQAAYAA 158
>gnl|CDD|214834 smart00823, PKS_PP, Phosphopantetheine attachment site.
Phosphopantetheine (or pantetheine 4' phosphate) is the
prosthetic group of acyl carrier proteins (ACP) in some
multienzyme complexes where it serves as a 'swinging
arm' for the attachment of activated fatty acid and
amino-acid groups.
Length = 86
Score = 45.7 bits (109), Expect = 4e-06
Identities = 10/43 (23%), Positives = 16/43 (37%)
Query: 362 LADYGFDSISLAEFSRILSKFYSLDIMPSIFFSYSTLERLITY 404
D G DS+ E L L + ++ F + T L +
Sbjct: 39 FRDLGLDSLMAVELRNRLEAATGLRLPATLVFDHPTPAALAEH 81
>gnl|CDD|223377 COG0300, DltE, Short-chain dehydrogenases of various substrate
specificities [General function prediction only].
Length = 265
Score = 47.2 bits (113), Expect = 2e-05
Identities = 32/123 (26%), Positives = 52/123 (42%), Gaps = 14/123 (11%)
Query: 66 KQGGTYLITGGTGRLGMLFSDYLINKYSTNLILSGRS--KLNSIIYKKLKKFNNKAIYIQ 123
+G T LITG + +G + L + NLIL R KL ++ + K + I
Sbjct: 4 MKGKTALITGASSGIGAELAKQLARR-GYNLILVARREDKLEALAKELEDKTGVEVEVIP 62
Query: 124 VDVSDKLKMISEI-NSIINNIGPIDGVLHIAGISGLTSNILEANYKNFYSVLSSKISGTI 182
D+SD + + + + + GPID +++ AG G LE + + I
Sbjct: 63 ADLSD-PEALERLEDELKERGGPIDVLVNNAGF-GTFGPFLELSLD--------EEEEMI 112
Query: 183 ALN 185
LN
Sbjct: 113 QLN 115
>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 = 46.9 bits (112), Expect = 2e-05
Identities = 23/121 (19%), Positives = 53/121 (43%), Gaps = 10/121 (8%)
Query: 72 LITGGTGRLGM----LFSDYLINKYSTNLILSGRSKLNSIIYKKLKKFNNKAIYIQVDVS 127
L+TG + +G + + ++L+ R++ ++ A+ +Q DVS
Sbjct: 2 LVTGASSGIGRAIARRLA-----REGAKVVLADRNEEALAELAAIEALGGNAVAVQADVS 56
Query: 128 DKLKMISEINSIINNIGPIDGVLHIAGISGLTSNILEANYKNFYSVLSSKISGTIALNYA 187
D+ + + + + G +D +++ AGI+ + E +++ VL ++G L A
Sbjct: 57 DEEDVEALVEEALEEFGRLDILVNNAGIARP-GPLEELTDEDWDRVLDVNLTGVFLLTRA 115
Query: 188 L 188
Sbjct: 116 A 116
>gnl|CDD|187608 cd05350, SDR_c6, classical (c) SDR, subgroup 6. These proteins are
members of the classical SDR family, with a canonical
active site tetrad and a fairly well conserved 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 = 239
Score = 45.8 bits (109), Expect = 4e-05
Identities = 40/184 (21%), Positives = 77/184 (41%), Gaps = 12/184 (6%)
Query: 72 LITGGTGRLGMLFSDYLINKYSTNLILSGRSK--LNSIIYKKLKKFNNKAIYIQVDVSDK 129
LITG + +G + N+ L+ R L+ + +L N +DV+D+
Sbjct: 2 LITGASSGIGRALAREFAKA-GYNVALAARRTDRLDELK-AELLNPNPSVEVEILDVTDE 59
Query: 130 LKMISEINSIINNIGPIDGVLHIAGISGLTSNILEANYKNFYSVLSSKISGTIA-LNYAL 188
+ I + +G +D V+ AG+ G +++ + ++K F + + + G A L AL
Sbjct: 60 ERNQLVIAELEAELGGLDLVIINAGV-GKGTSLGDLSFKAFRETIDTNLLGAAAILEAAL 118
Query: 189 ENTILKLQKNKLDFVCYFSSSSAILGDFGSCDYAMGNRFQTVYAKYLNNKNIYKKYTNKL 248
+ + + SS +A+ G G+ Y+ + A+ L KK ++
Sbjct: 119 P----QFRAKGRGHLVLISSVAALRGLPGAAAYSASKAALSSLAESLRYD--VKKRGIRV 172
Query: 249 ITIN 252
IN
Sbjct: 173 TVIN 176
>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 = 44.2 bits (105), Expect = 1e-04
Identities = 40/166 (24%), Positives = 70/166 (42%), Gaps = 22/166 (13%)
Query: 68 GGTYLITGGTGRLGMLFSDYLINKYSTNLILSGRS--KLNSIIYKKLKKFNN---KAIYI 122
G LITGG+ +G + L+ + N+I+ RS KL + + + N K YI
Sbjct: 1 GKHVLITGGSSGIGKALAKELVKE-GANVIIVARSESKLEEAVEEIEAEANASGQKVSYI 59
Query: 123 QVDVSDKLKMISEINSIINNIGPIDGVLHIAGIS------GLTSNILEANYKNFYSVLSS 176
D+SD ++ + GP D V++ AGIS LT+ E Y
Sbjct: 60 SADLSDYEEVEQAFAQAVEKGGPPDLVVNCAGISIPGLFEDLTAEEFERGMDVNY----- 114
Query: 177 KISGTIALNYALENTILKLQKNKLDFVCYFSSSSAILGDFGSCDYA 222
G++ + +++ + + + SS +A++G +G Y
Sbjct: 115 --FGSL---NVAHAVLPLMKEQRPGHIVFVSSQAALVGIYGYSAYC 155
>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 = 44.3 bits (105), Expect = 1e-04
Identities = 25/121 (20%), Positives = 52/121 (42%), Gaps = 1/121 (0%)
Query: 67 QGGTYLITGGTGRLGMLFSDYLINKYSTNLILSGRSKLNSIIYKKLKKFNNKAIYIQVDV 126
+G L+TG + +G + L + +I S + + ++K +A DV
Sbjct: 4 KGKVALVTGASRGIGFGIASGLAEAGANIVINSRNEEKAEEAQQLIEKEGVEATAFTCDV 63
Query: 127 SDKLKMISEINSIINNIGPIDGVLHIAGISGLTSNILEANYKNFYSVLSSKISGTIALNY 186
SD+ + + + +I + G ID +++ AGI E + V+ ++G ++
Sbjct: 64 SDEEAIKAAVEAIEEDFGKIDILVNNAGI-IRRHPAEEFPEAEWRDVIDVNLNGVFFVSQ 122
Query: 187 A 187
A
Sbjct: 123 A 123
>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 = 44.2 bits (105), Expect = 1e-04
Identities = 29/120 (24%), Positives = 53/120 (44%), Gaps = 5/120 (4%)
Query: 67 QGGTYLITGGTGRLGMLFSDYLINKYSTNLILSGRS--KLNSIIYKKLKKFNNKAIYIQV 124
+ LITG G +G F L++ LIL+ + L + + + N+ I +++
Sbjct: 1 EDKIILITGAAGLIGKAFCKALLS-AGARLILADINAPALEQLKEELTNLYKNRVIALEL 59
Query: 125 DVSDKLKMISEINSIINNIGPIDGVLHIAGIS--GLTSNILEANYKNFYSVLSSKISGTI 182
D++ K + I S + G ID +++ A S S E Y+ + VL+ + G
Sbjct: 60 DITSKESIKELIESYLEKFGRIDILINNAYPSPKVWGSRFEEFPYEQWNEVLNVNLGGAF 119
>gnl|CDD|238425 cd00829, SCP-x_thiolase, Thiolase domain associated with sterol
carrier protein (SCP)-x isoform and related proteins;
SCP-2 has multiple roles in intracellular lipid
circulation and metabolism. The N-terminal presequence
in the SCP-x isoform represents a peroxisomal
3-ketacyl-Coa thiolase specific for branched-chain acyl
CoAs, which is proteolytically cleaved from the sterol
carrier protein.
Length = 375
Score = 44.6 bits (106), Expect = 2e-04
Identities = 23/98 (23%), Positives = 34/98 (34%), Gaps = 18/98 (18%)
Query: 561 ALEDAGYGPNQIANQKIGMFVGVEEGSNYQDRLDQVNLTSTHNAILSARLAYFMDLKG-P 619
AL+DAG P I + VG G +Q A +A ++ L G P
Sbjct: 27 ALDDAGLEPADI----DAVVVGNAAGGRFQS-------------FPGALIAEYLGLLGKP 69
Query: 620 VMAINTACSSSLVATHIACQSLRQHECDTAISAGVNLM 657
+ A +S A A ++ D + G M
Sbjct: 70 ATRVEAAGASGSAAVRAAAAAIASGLADVVLVVGAEKM 107
>gnl|CDD|215722 pfam00108, Thiolase_N, Thiolase, N-terminal domain. Thiolase is
reported to be structurally related to beta-ketoacyl
synthase (pfam00109), and also chalcone synthase.
Length = 262
Score = 43.0 bits (102), Expect = 4e-04
Identities = 17/67 (25%), Positives = 30/67 (44%), Gaps = 2/67 (2%)
Query: 619 PVMAINTACSSSLVATHIACQSLRQHECDTAISAGVNLMISPEAYIAMTSAGMLSPDGKC 678
P + IN C S L A +A Q++R + D ++ GV M A + ++ + + G
Sbjct: 78 PAVTINKVCGSGLKAVALAAQAIRAGDADIVVAGGVESM--SNAPYVLPASRVGARMGDA 135
Query: 679 YVFDERA 685
+ D
Sbjct: 136 KLVDTML 142
>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 = 41.1 bits (97), Expect = 0.001
Identities = 24/88 (27%), Positives = 38/88 (43%), Gaps = 14/88 (15%)
Query: 67 QGGTYLITGGTGRLGMLFSDYLINKYSTNLILSGRSKLNSIIYKKLKKFNNKAIYIQVDV 126
G T LITGGT +G+ + + +T +I++GR + + KK I +DV
Sbjct: 4 TGNTVLITGGTSGIGLALARKFLEAGNT-VIITGRREER---LAEAKKELPNIHTIVLDV 59
Query: 127 SDK----------LKMISEINSIINNIG 144
D L ++ +INN G
Sbjct: 60 GDAESVEALAEALLSEYPNLDILINNAG 87
>gnl|CDD|223261 COG0183, PaaJ, Acetyl-CoA acetyltransferase [Lipid metabolism].
Length = 392
Score = 41.9 bits (99), Expect = 0.001
Identities = 20/71 (28%), Positives = 33/71 (46%), Gaps = 8/71 (11%)
Query: 604 AILSARLAYFMDLKGPVMAINTACSSSLVATHIACQSLRQHECDTAISAGV----NLMIS 659
A L+A L + P + +N AC+S L A +A Q++ E D ++ GV + +
Sbjct: 73 AALAAGLPGSV----PAVTVNRACASGLAAVRLAAQAIASGEADVVLAGGVEKMSDAPMG 128
Query: 660 PEAYIAMTSAG 670
E + SA
Sbjct: 129 REGVRVLDSAV 139
>gnl|CDD|187610 cd05352, MDH-like_SDR_c, mannitol dehydrogenase (MDH)-like,
classical (c) SDRs. NADP-mannitol dehydrogenase
catalyzes the conversion of fructose to mannitol, an
acyclic 6-carbon sugar. MDH is a tetrameric member of
the SDR family. This subgroup also includes various
other tetrameric SDRs, including Pichia stipitis
D-arabinitol dehydrogenase (aka polyol dehydrogenase),
Candida albicans Sou1p, a sorbose reductase, and Candida
parapsilosis (S)-specific carbonyl reductase (SCR, aka
S-specific alcohol dehydrogenase) which catalyzes the
enantioselective reduction of 2-hydroxyacetophenone into
(S)-1-phenyl-1,2-ethanediol. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold
(alpha/beta folding pattern with a central beta-sheet),
an NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRS are approximately
350 residues. Sequence identity between different SDR
enzymes are typically in the 15-30% range, but the
enzymes share the Rossmann fold NAD-binding motif and
characteristic NAD-binding and catalytic sequence
patterns. These enzymes have a 3-glycine N-terminal
NAD(P)(H)-binding pattern (typically, TGxxxGxG in
classical SDRs and TGxxGxxG in extended SDRs), while
substrate binding is in the C-terminal region. A
critical catalytic Tyr residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering), is often found in a conserved YXXXK pattern.
In addition to the Tyr and Lys, there is often an
upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn
(Asn-107, 15-PGDH numbering) or additional Ser,
contributing to the active site. Substrates for these
enzymes include sugars, steroids, alcohols, and aromatic
compounds. The standard reaction mechanism is a proton
relay involving the conserved Tyr and Lys, as well as
Asn (or Ser).
Length = 252
Score = 41.2 bits (97), Expect = 0.002
Identities = 25/115 (21%), Positives = 50/115 (43%), Gaps = 2/115 (1%)
Query: 68 GGTYLITGGTGRLGMLFSDYLINKYSTNLILSGRSKLNSIIYKKL-KKFNNKAIYIQVDV 126
G ++TGG+ +G+ + L + I+ + ++L KK+ K + DV
Sbjct: 8 GKVAIVTGGSRGIGLAIARALAEAGADVAIIYNSAPRAEEKAEELAKKYGVKTKAYKCDV 67
Query: 127 SDKLKMISEINSIINNIGPIDGVLHIAGISGLTSNILEANYKNFYSVLSSKISGT 181
S + + I + G ID ++ AGI+ L+ Y+ + V+ ++G
Sbjct: 68 SSQESVEKTFKQIQKDFGKIDILIANAGITVHKP-ALDYTYEQWNKVIDVNLNGV 121
>gnl|CDD|223314 COG0236, AcpP, Acyl carrier protein [Lipid metabolism / Secondary
metabolites biosynthesis, transport, and catabolism].
Length = 80
Score = 37.7 bits (88), Expect = 0.002
Identities = 18/75 (24%), Positives = 31/75 (41%), Gaps = 1/75 (1%)
Query: 337 IENDIKNHICNILNTKKSEIYKNKNLA-DYGFDSISLAEFSRILSKFYSLDIMPSIFFSY 395
IE +K+ I L + EI + D G DS+ L E L + + ++I +
Sbjct: 6 IEERVKDIIAEQLGVDEEEITTEASFVEDLGLDSLDLVELVMALEEEFGIEIPDEELENI 65
Query: 396 STLERLITYFIKNHN 410
T+ L+ Y +
Sbjct: 66 KTVGDLVDYIEELLA 80
>gnl|CDD|235546 PRK05653, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Validated.
Length = 246
Score = 40.1 bits (95), Expect = 0.003
Identities = 20/93 (21%), Positives = 44/93 (47%), Gaps = 4/93 (4%)
Query: 67 QGGTYLITGGTGRLGMLFSDYLINKYSTNLILSGRS--KLNSIIYKKLKKFNNKAIYIQV 124
QG T L+TG + +G + L +++ + ++ +L+ +A +
Sbjct: 4 QGKTALVTGASRGIGRAIALRLA-ADGAKVVIYDSNEEAAEALA-AELRAAGGEARVLVF 61
Query: 125 DVSDKLKMISEINSIINNIGPIDGVLHIAGISG 157
DVSD+ + + I + + G +D +++ AGI+
Sbjct: 62 DVSDEAAVRALIEAAVEAFGALDILVNNAGITR 94
>gnl|CDD|216461 pfam01370, Epimerase, NAD dependent epimerase/dehydratase family.
This family of proteins utilise NAD as a cofactor. The
proteins in this family use nucleotide-sugar substrates
for a variety of chemical reactions.
Length = 233
Score = 40.0 bits (94), Expect = 0.003
Identities = 30/148 (20%), Positives = 62/148 (41%), Gaps = 27/148 (18%)
Query: 72 LITGGTGRLGMLFSDYLINKYSTNLILSGRSKLNSIIYKKLKKFNNKAIYIQVDVSDKLK 131
L+TGGTG +G L+ + ++L R + S+ +++ + D++D
Sbjct: 2 LVTGGTGFIGSHLVRRLLQEGYEVIVLGRRRRSESLNTGRIRF-------HEGDLTDP-- 52
Query: 132 MISEINSIINNIGPIDGVLHIAGISGLTSNILEANYKNFYSVLSSKISGTI-ALNYALEN 190
+ ++ + P D V+H+A SG+ ++ + + + + GT+ L A
Sbjct: 53 --DALERLLAEVQP-DAVIHLAAQSGVGASFEDPAD-----FIRANVLGTLRLLEAARRA 104
Query: 191 TILKLQKNKLDFVCYFSSSSAILGDFGS 218
+ + F+SSS + GD
Sbjct: 105 GVKRF---------VFASSSEVYGDVAD 123
>gnl|CDD|233642 TIGR01930, AcCoA-C-Actrans, acetyl-CoA acetyltransferases. This
model represents a large family of enzymes which
catalyze the thiolysis of a linear fatty acid CoA (or
acetoacetyl-CoA) using a second CoA molecule to produce
acetyl-CoA and a CoA-ester product two carbons shorter
(or, alternatively, the condensation of two molecules of
acetyl-CoA to produce acetoacetyl-CoA and CoA). This
enzyme is also known as "thiolase", "3-ketoacyl-CoA
thiolase", "beta-ketothiolase" and "Fatty oxidation
complex beta subunit". When catalyzing the degradative
reaction on fatty acids the corresponding EC number is
2.3.1.16. The condensation reaction corresponds to
2.3.1.9. Note that the enzymes which catalyze the
condensation are generally not involved in fatty acid
biosynthesis, which is carried out by a decarboxylating
condensation of acetyl and malonyl esters of acyl
carrier proteins. Rather, this activity may produce
acetoacetyl-CoA for pathways such as IPP biosynthesis in
the absence of sufficient fatty acid oxidation [Fatty
acid and phospholipid metabolism, Other].
Length = 386
Score = 40.3 bits (95), Expect = 0.005
Identities = 17/53 (32%), Positives = 24/53 (45%), Gaps = 3/53 (5%)
Query: 608 ARLAYF---MDLKGPVMAINTACSSSLVATHIACQSLRQHECDTAISAGVNLM 657
AR A + P +N C+S L A +A Q +R E D ++ GV M
Sbjct: 61 ARQAALLAGLPESVPAYTVNRQCASGLQAVILAAQLIRAGEADVVVAGGVESM 113
>gnl|CDD|181146 PRK07851, PRK07851, acetyl-CoA acetyltransferase; Provisional.
Length = 406
Score = 40.0 bits (94), Expect = 0.005
Identities = 27/91 (29%), Positives = 38/91 (41%), Gaps = 24/91 (26%)
Query: 619 PVMAINTACSSSLVATHIACQSLRQHECDTAISAGVNLMISPEAYIAMTSAGMLSPDGKC 678
P +N CSSSL T +A +++ E D ISAGV +S + S + PD K
Sbjct: 82 PGTTVNRYCSSSLQTTRMAFHAIKAGEGDVFISAGVE-TVS--RFAKGNSDSL--PDTKN 136
Query: 679 YVFDE-------------------RANGLVP 690
+F E R +GL+P
Sbjct: 137 PLFAEAQARTAARAEGGAEAWHDPREDGLLP 167
>gnl|CDD|238426 cd00830, KAS_III, Ketoacyl-acyl carrier protein synthase III
(KASIII) initiates the elongation in type II fatty acid
synthase systems. It is found in bacteria and plants.
Elongation of fatty acids in the type II systems occurs
by Claisen condensation of malonyl-acyl carrier protein
(ACP) with acyl-ACP. KASIII initiates this process by
specifically using acetyl-CoA over acyl-CoA.
Length = 320
Score = 39.1 bits (92), Expect = 0.008
Identities = 48/243 (19%), Positives = 74/243 (30%), Gaps = 65/243 (26%)
Query: 561 ALEDAGYGPNQIANQKIGMFVGVEEGSNYQDRLDQVNLTSTHNAIL---SARLAYFMDLK 617
ALEDAG + I D + + TST + + + + + K
Sbjct: 61 ALEDAGIDADDI------------------DLI--IVATSTPDYLFPATACLVQARLGAK 100
Query: 618 G-PVMAINTACSSSLVATHIACQSLRQHECDTAISAGVNLMISPEAYIAMT-----SAGM 671
IN ACS L A +R L++ E + S +
Sbjct: 101 NAAAFDINAACSGFLYGLSTAAGLIRSGGAKNV------LVVGAETLSRILDWTDRSTAV 154
Query: 672 LSPDGKCYVFDERANGLVPSEAVVAVVLKRLSRALSDGDPIHAI-IRGSGINYDGKTNGI 730
L DG V E ++ VL SDG + I G +
Sbjct: 155 LFGDGAGAVVLEATEE---DPGILDSVLG------SDGSGADLLTIPAGGSRSPFEDAEG 205
Query: 731 TAPNGISQ------------TELIKSVYKKSNLNPEDINYIITH--------GTGTKLGD 770
P + E I+ +K+ L P+DI++ + H +LG
Sbjct: 206 GDPYLVMDGREVFKFAVRLMPESIEEALEKAGLTPDDIDWFVPHQANLRIIEAVAKRLGL 265
Query: 771 PVE 773
P E
Sbjct: 266 PEE 268
>gnl|CDD|187586 cd05325, carb_red_sniffer_like_SDR_c, carbonyl reductase
sniffer-like, classical (c) SDRs. Sniffer is an
NADPH-dependent carbonyl reductase of the classical SDR
family. Studies in Drosophila melanogaster implicate
Sniffer in the prevention of neurodegeneration due to
aging and oxidative-stress. This subgroup also includes
Rhodococcus sp. AD45 IsoH, which is an NAD-dependent
1-hydroxy-2-glutathionyl-2-methyl-3-butene dehydrogenase
involved in isoprene metabolism, Aspergillus nidulans
StcE encoded by a gene which is part of a proposed
sterigmatocystin biosynthesis gene cluster, Bacillus
circulans SANK 72073 BtrF encoded by a gene found in the
butirosin biosynthesis gene cluster, and Aspergillus
parasiticus nor-1 involved in the biosynthesis of
aflatoxins. 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 = 233
Score = 38.4 bits (90), Expect = 0.011
Identities = 21/114 (18%), Positives = 50/114 (43%)
Query: 71 YLITGGTGRLGMLFSDYLINKYSTNLILSGRSKLNSIIYKKLKKFNNKAIYIQVDVSDKL 130
LITG + +G+ L+ + + +I + R + L +++ +++DV+D++
Sbjct: 1 VLITGASRGIGLELVRQLLARGNNTVIATCRDPSAATELAALGASHSRLHILELDVTDEI 60
Query: 131 KMISEINSIINNIGPIDGVLHIAGISGLTSNILEANYKNFYSVLSSKISGTIAL 184
+E + +D +++ AGI E + ++ V + G + L
Sbjct: 61 AESAEAVAERLGDAGLDVLINNAGILHSYGPASEVDSEDLLEVFQVNVLGPLLL 114
>gnl|CDD|187604 cd05346, SDR_c5, classical (c) SDR, subgroup 5. These proteins are
members of the classical SDR family, with a canonical
active site tetrad and a typical Gly-rich NAD-binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold (alpha/beta folding
pattern with a central beta-sheet), an NAD(P)(H)-binding
region, and a structurally diverse C-terminal region.
Classical SDRs are typically about 250 residues long,
while extended SDRs are approximately 350 residues.
Sequence identity between different SDR enzymes are
typically in the 15-30% range, but the enzymes share the
Rossmann fold NAD-binding motif and characteristic
NAD-binding and catalytic sequence patterns. These
enzymes catalyze a wide range of activities including
the metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 249
Score = 38.4 bits (90), Expect = 0.012
Identities = 28/121 (23%), Positives = 61/121 (50%), Gaps = 3/121 (2%)
Query: 70 TYLITGGTGRLGMLFSDYLINKYSTNLILSGR--SKLNSIIYKKLKKFNNKAIYIQVDVS 127
T LITG + +G + K LIL+GR +L + + KF K + +Q+DVS
Sbjct: 2 TVLITGASSGIG-EATARRFAKAGAKLILTGRRAERLQELADELGAKFPVKVLPLQLDVS 60
Query: 128 DKLKMISEINSIINNIGPIDGVLHIAGISGLTSNILEANYKNFYSVLSSKISGTIALNYA 187
D+ + + + ++ ID +++ AG++ EA+ +++ +++ + + G + +
Sbjct: 61 DRESIEAALENLPEEFRDIDILVNNAGLALGLDPAQEADLEDWETMIDTNVKGLLNVTRL 120
Query: 188 L 188
+
Sbjct: 121 I 121
>gnl|CDD|238383 cd00751, thiolase, Thiolase are ubiquitous enzymes that catalyze
the reversible thiolytic cleavage of 3-ketoacyl-CoA into
acyl-CoA and acetyl-CoA, a 2-step reaction involving a
covalent intermediate formed with a catalytic cysteine.
They are found in prokaryotes and eukaryotes (cytosol,
microbodies and mitochondria). There are 2 functional
different classes: thiolase-I (3-ketoacyl-CoA thiolase)
and thiolase-II (acetoacetyl-CoA thiolase). Thiolase-I
can cleave longer fatty acid molecules and plays an
important role in the beta-oxidative degradation of
fatty acids. Thiolase-II has a high substrate
specificity. Although it can cleave acetoacyl-CoA, its
main function is the synthesis of acetoacyl-CoA from two
molecules of acetyl-CoA, which gives it importance in
several biosynthetic pathways.
Length = 386
Score = 38.2 bits (90), Expect = 0.018
Identities = 14/39 (35%), Positives = 19/39 (48%)
Query: 619 PVMAINTACSSSLVATHIACQSLRQHECDTAISAGVNLM 657
P +N C S L A +A QS+ E D ++ GV M
Sbjct: 76 PATTVNRVCGSGLQAVALAAQSIAAGEADVVVAGGVESM 114
>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 = 37.6 bits (88), Expect = 0.018
Identities = 21/83 (25%), Positives = 34/83 (40%), Gaps = 10/83 (12%)
Query: 72 LITGGTGRLGMLFSDYLINKYSTNLILSGRSKLNSIIYKKLKKFNNKAIYIQVDVSDK-- 129
LITGG +G L + + + +IL K ++K K Y + DVS +
Sbjct: 3 LITGGGSGIGRLLALEFAKRGAKVVILDINEKGAEETANNVRKAGGKVHYYKCDVSKREE 62
Query: 130 --------LKMISEINSIINNIG 144
K + ++ +INN G
Sbjct: 63 VYEAAKKIKKEVGDVTILINNAG 85
>gnl|CDD|235688 PRK06064, PRK06064, acetyl-CoA acetyltransferase; Provisional.
Length = 389
Score = 38.3 bits (90), Expect = 0.019
Identities = 40/136 (29%), Positives = 53/136 (38%), Gaps = 30/136 (22%)
Query: 545 ERMDPRQRHLLQESWL-ALEDAGYGPNQI-----ANQKIGMFVGVEEGSNYQDRLDQVNL 598
E D R L E+ L ALEDAG I N G+FV E
Sbjct: 16 ELWDVSLRDLAVEAGLEALEDAGIDGKDIDAMYVGNMSAGLFVSQE-------------- 61
Query: 599 TSTHNAILSARLAYFMDLKG-PVMAINTACSSSLVATHIACQSLRQHECDTAISAGVNLM 657
H A L +A + L P + AC+S A A ++ E D ++AGV M
Sbjct: 62 ---HIAAL---IADYAGLAPIPATRVEAACASGGAALRQAYLAVASGEADVVLAAGVEKM 115
Query: 658 I---SPEAYIAMTSAG 670
+P+A A+ AG
Sbjct: 116 TDVPTPDATEAIARAG 131
>gnl|CDD|187655 cd08952, KR_1_SDR_x, ketoreductase (KR), subgroup 1, complex (x)
SDRs. Ketoreductase, a module of the multidomain
polyketide synthase (PKS), has 2 subdomains, each
corresponding to a SDR family monomer. The C-terminal
subdomain catalyzes the NADPH-dependent reduction of the
beta-carbonyl of a polyketide to a hydroxyl group, a
step in the biosynthesis of polyketides, such as
erythromycin. The N-terminal subdomain, an interdomain
linker, is a truncated Rossmann fold which acts to
stabilizes the catalytic subdomain. Unlike typical SDRs,
the isolated domain does not oligomerize but is composed
of 2 subdomains, each resembling an SDR monomer. The
active site resembles that of typical SDRs, except that
the usual positions of the catalytic Asn and Tyr are
swapped, so that the canonical YXXXK motif changes to
YXXXN. Modular PKSs are multifunctional structures in
which the makeup recapitulates that found in (and may
have evolved from) FAS. Polyketide synthesis also
proceeds via the addition of 2-carbon units as in fatty
acid synthesis. The complex SDR NADP-binding motif,
GGXGXXG, is often present, but is not strictly conserved
in each instance of the module. This subfamily includes
KR domains found in many multidomain PKSs, including six
of seven Sorangium cellulosum PKSs (encoded by
spiDEFGHIJ) which participate in the synthesis of the
polyketide scaffold of the cytotoxic spiroketal
polyketide spirangien. These seven PKSs have either a
single PKS module (SpiF), two PKR modules
(SpiD,-E,-I,-J), or three PKS modules (SpiG,-H). This
subfamily includes the single KR domain of SpiF, the
first KR domains of SpiE,-G,H,-I,and #J, the third KR
domain of SpiG, and the second KR domain of SpiH. The
second KR domains of SpiE,-G, I, and #J, and the KR
domains of SpiD, belong to a different KR_FAS_SDR
subfamily. 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 KRs 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 = 480
Score = 37.9 bits (89), Expect = 0.028
Identities = 10/13 (76%), Positives = 11/13 (84%)
Query: 69 GTYLITGGTGRLG 81
GT L+TGGTG LG
Sbjct: 231 GTVLVTGGTGALG 243
>gnl|CDD|168156 PRK05656, PRK05656, acetyl-CoA acetyltransferase; Provisional.
Length = 393
Score = 37.6 bits (87), Expect = 0.032
Identities = 26/100 (26%), Positives = 42/100 (42%), Gaps = 16/100 (16%)
Query: 562 LEDAGYGPNQIANQKIGMFVGVEEGSNYQDRLDQVNLTSTHNAILSARLAYFMDLKGPVM 621
LE G P Q+ +G + G N A + A L + + P M
Sbjct: 38 LEQTGLDPAQVDEVILGQVLTAGAGQN-----------PARQAAIKAGLPHSV----PAM 82
Query: 622 AINTACSSSLVATHIACQSLRQHECDTAISAGV-NLMISP 660
+N C S L A H+A Q++R + + I+ G N+ ++P
Sbjct: 83 TLNKVCGSGLKALHLAAQAIRCGDAEVIIAGGQENMSLAP 122
>gnl|CDD|212493 cd08932, HetN_like_SDR_c, HetN oxidoreductase-like, classical (c)
SDR. This subgroup includes Anabaena sp. strain PCC
7120 HetN, a putative oxidoreductase involved in
heterocyst differentiation, and related proteins. 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 = 223
Score = 36.6 bits (85), Expect = 0.034
Identities = 19/88 (21%), Positives = 35/88 (39%), Gaps = 4/88 (4%)
Query: 72 LITGGTGRLGMLFSDYLINKYSTNLILSGRSKLNSIIYKKLKKFNNKAIYIQVDVSDKLK 131
L+TG + +G+ + L + + L R N L + D D
Sbjct: 4 LVTGASRGIGIEIARALA-RDGYRVSLGLR---NPEDLAALSASGGDVEAVPYDARDPED 59
Query: 132 MISEINSIINNIGPIDGVLHIAGISGLT 159
+ ++++ + G ID ++H AGI T
Sbjct: 60 ARALVDALRDRFGRIDVLVHNAGIGRPT 87
>gnl|CDD|180563 PRK06445, PRK06445, acetyl-CoA acetyltransferase; Provisional.
Length = 394
Score = 37.4 bits (87), Expect = 0.037
Identities = 29/112 (25%), Positives = 42/112 (37%), Gaps = 17/112 (15%)
Query: 546 RMDPRQRHLLQESWLALEDAGYGPNQIANQKIGMFVGVEEGSNYQDRLDQVNLTSTHNAI 605
R + L+ +E G P +I + G + V E Y R + I
Sbjct: 31 RPEELAAMLINRL---IEKTGIKPEEIDDIITGCALQVGENWLYGGR----------HPI 77
Query: 606 LSARLAYFMDLKGPVMAINTACSSSLVATHIACQSLRQHECDTAISAGVNLM 657
ARL Y + P MA++ C+SSL I + D I+ GV M
Sbjct: 78 FLARLPYNI----PAMAVDRQCASSLTTVSIGAMEIATGMADIVIAGGVEHM 125
>gnl|CDD|187629 cd05371, HSD10-like_SDR_c, 17hydroxysteroid dehydrogenase type 10
(HSD10)-like, classical (c) SDRs. HSD10, also known as
amyloid-peptide-binding alcohol dehydrogenase (ABAD),
was previously identified as a L-3-hydroxyacyl-CoA
dehydrogenase, HADH2. In fatty acid metabolism, HADH2
catalyzes the third step of beta-oxidation, the
conversion of a hydroxyl to a keto group in the
NAD-dependent oxidation of L-3-hydroxyacyl CoA. In
addition to alcohol dehydrogenase and HADH2 activites,
HSD10 has steroid dehydrogenase activity. Although the
mechanism is unclear, HSD10 is implicated in the
formation of amyloid beta-petide in the brain (which is
linked to the development of Alzheimer's disease).
Although HSD10 is normally concentrated in the
mitochondria, in the presence of amyloid beta-peptide it
translocates into the plasma membrane, where it's action
may generate cytotoxic aldehydes and may lower estrogen
levels through its use of 17-beta-estradiol as a
substrate. HSD10 is a member of the SRD family, but
differs from other SDRs by the presence of two
insertions of unknown function. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold
(alpha/beta folding pattern with a central beta-sheet),
an NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRs are approximately
350 residues. Sequence identity between different SDR
enzymes are typically in the 15-30% range, but the
enzymes share the Rossmann fold NAD-binding motif and
characteristic NAD-binding and catalytic sequence
patterns. These enzymes catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) numbering). In addition to the
Tyr and Lys, there is often an upstream Ser (Ser-138,
15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH
numbering) contributing to the active site; while
substrate binding is in the C-terminal region, which
determines specificity. The standard reaction mechanism
is a 4-pro-S hydride transfer and proton relay involving
the conserved Tyr and Lys, a water molecule stabilized
by Asn, and nicotinamide. Extended SDRs have additional
elements in the C-terminal region, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Some atypical SDRs have lost catalytic activity and/or
have an unusual NAD(P)-binding motif and missing or
unusual active site residues. Reactions catalyzed within
the SDR family include isomerization, decarboxylation,
epimerization, C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 252
Score = 36.9 bits (86), Expect = 0.038
Identities = 20/89 (22%), Positives = 43/89 (48%), Gaps = 4/89 (4%)
Query: 68 GGTYLITGGTGRLGMLFSDYLINKYSTNLILSGRSKLNSIIYKKLKKFNNKAIYIQVDVS 127
G ++TGG LG+ + L+ + + +IL L + + + K + ++ VDV+
Sbjct: 2 GLVAVVTGGASGLGLATVERLLAQGAKVVILD----LPNSPGETVAKLGDNCRFVPVDVT 57
Query: 128 DKLKMISEINSIINNIGPIDGVLHIAGIS 156
+ + + + G +D V++ AGI+
Sbjct: 58 SEKDVKAALALAKAKFGRLDIVVNCAGIA 86
>gnl|CDD|223409 COG0332, FabH, 3-oxoacyl-[acyl-carrier-protein].
Length = 323
Score = 36.8 bits (86), Expect = 0.043
Identities = 46/229 (20%), Positives = 76/229 (33%), Gaps = 69/229 (30%)
Query: 561 ALEDAGYGPNQIANQKIGMFVGVEEGSNYQDRLDQVNLTSTHNAILSARLAYFMDLKG-P 619
ALEDAG I+ I + + ++ D L + ++ ARL L G P
Sbjct: 63 ALEDAG-----ISPDDIDLIIVA---TSTPDHLFP-----STACLVQARLG----LGGAP 105
Query: 620 VMAINTACSSSLVATHIACQSLRQHECDTAISAGVNLMISPEAYIAMTSAGMLSPDGKCY 679
+ ACS L A +A +R L++ E T + +L
Sbjct: 106 AFDLQAACSGFLYALSVADGLIRSGGYKNV------LVVGAE-----TLSRILD------ 148
Query: 680 VFDERANGLVPSEAVVAVVLKR--------LSRALSDGDPIHAIIRGSGINYDGKTNGIT 731
+ +R ++ + AVVL+ + SDG + Y T
Sbjct: 149 -WTDRDTCVLFGDGAGAVVLEATEDDNGILDTDLGSDGS-------QGDLLYLPGGGSAT 200
Query: 732 APNGIS------------------QTELIKSVYKKSNLNPEDINYIITH 762
+ I+ V +K+ L PEDI++ + H
Sbjct: 201 PKEESGGGLLVMDGREVFKFAVRAMPKAIEEVLEKAGLTPEDIDWFVPH 249
>gnl|CDD|187558 cd05247, UDP_G4E_1_SDR_e, UDP-glucose 4 epimerase, subgroup 1,
extended (e) SDRs. UDP-glucose 4 epimerase (aka
UDP-galactose-4-epimerase), is a homodimeric extended
SDR. It catalyzes the NAD-dependent conversion of
UDP-galactose to UDP-glucose, the final step in Leloir
galactose synthesis. This subgroup has the
characteristic active site tetrad and NAD-binding motif
of the extended SDRs. Extended SDRs 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. 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. 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. 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 = 323
Score = 36.7 bits (86), Expect = 0.050
Identities = 35/154 (22%), Positives = 59/154 (38%), Gaps = 36/154 (23%)
Query: 70 TYLITGGTGRLGMLFSDYLIN-KYST----NLILSGRSKLNSIIYKKLKKFNNKAIYIQV 124
L+TGG G +G L+ Y NL R L I +++ + +
Sbjct: 1 KVLVTGGAGYIGSHTVVELLEAGYDVVVLDNLSNGHREALPRIEKIRIE-------FYEG 53
Query: 125 DVSDKLKMISEINSIINNIGPIDGVLHIAGISGL---TSNILEANYKNFYSVLSSKISGT 181
D+ D+ + + + ID V+H A + + L+ +Y + GT
Sbjct: 54 DIRDRAAL----DKVFAEH-KIDAVIHFAALKAVGESVQKPLK-----YYDN---NVVGT 100
Query: 182 IALNYALENTILKLQKNKLDFVCYFSSSSAILGD 215
+ L LE + FV FSSS+A+ G+
Sbjct: 101 LNL---LE-AMRAHGVKN--FV--FSSSAAVYGE 126
>gnl|CDD|187584 cd05323, ADH_SDR_c_like, insect type alcohol dehydrogenase
(ADH)-like, classical (c) SDRs. This subgroup contains
insect type ADH, and 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) type I; these proteins are
classical SDRs. ADH catalyzes the NAD+-dependent
oxidation of alcohols to aldehydes/ketones. This
subgroup is distinct from the zinc-dependent alcohol
dehydrogenases of the medium chain
dehydrogenase/reductase family, and evolved in fruit
flies to allow the digestion of fermenting fruit.
15-PGDH catalyzes the NAD-dependent interconversion of
(5Z,13E)-(15S)-11alpha,15-dihydroxy-9-oxoprost-13-enoate
and (5Z,13E)-11alpha-hydroxy-9,15-dioxoprost-13-enoate,
and has a typical SDR glycine-rich NAD-binding motif,
which is not fully present in ADH. 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 = 244
Score = 36.1 bits (84), Expect = 0.056
Identities = 29/117 (24%), Positives = 50/117 (42%), Gaps = 11/117 (9%)
Query: 72 LITGGTGRLGMLFSDYLINKYSTNLILSGRSKLNSIIYKKLKKFN--NKAIYIQVDVSDK 129
+ITGG +G+ + L+ K + IL + +L+ N KA ++Q DV+
Sbjct: 4 IITGGASGIGLATAKLLLKKGAKVAILDRNENPGAA--AELQAINPKVKATFVQCDVTSW 61
Query: 130 LKMISEINSIINNIGPIDGVLHIAGISGLTSNILEANYKNFYSVLSSKISGTIALNY 186
++ + I G +D +++ AGI E +Y F L TI +N
Sbjct: 62 EQLAAAFKKAIEKFGRVDILINNAGILD------EKSY-LFAGKLPPPWEKTIDVNL 111
>gnl|CDD|132628 TIGR03589, PseB, UDP-N-acetylglucosamine 4,6-dehydratase. This
enzyme catalyzes the first step in the biosynthesis of
pseudaminic acid, the conversion of
UDP-N-acetylglucosamine to
UDP-4-keto-6-deoxy-N-acetylglucosamine. These sequences
are members of the broader pfam01073 (3-beta
hydroxysteroid dehydrogenase/isomerase family) family.
Length = 324
Score = 36.2 bits (84), Expect = 0.077
Identities = 24/90 (26%), Positives = 41/90 (45%), Gaps = 11/90 (12%)
Query: 68 GGTYLITGGTGRLGMLFSDYLINKYSTN-LILSGRSKLNSIIYKKLKKFNNKAI-YIQVD 125
+ LITGGTG G F L+ Y+ +I+ R +L ++ +KF + + D
Sbjct: 4 NKSILITGGTGSFGKAFISRLLENYNPKKIIIYSRDELKQ--WEMQQKFPAPCLRFFIGD 61
Query: 126 VSDKLKMISEINSIINNIGPIDGVLHIAGI 155
V DK ++ + +D V+H A +
Sbjct: 62 VRDKERLTRALRG-------VDYVVHAAAL 84
>gnl|CDD|235506 PRK05565, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 247
Score = 35.2 bits (82), Expect = 0.11
Identities = 20/87 (22%), Positives = 45/87 (51%), Gaps = 3/87 (3%)
Query: 72 LITGGTGRLGMLFSDYLINKYSTNLILSGRSKLNSIIY--KKLKKFNNKAIYIQVDVSDK 129
++TG +G +G + L+ K ++++ + +++K+ AI ++ DVS +
Sbjct: 9 IVTGASGGIGRAIA-ELLAKEGAKVVIAYDINEEAAQELLEEIKEEGGDAIAVKADVSSE 67
Query: 130 LKMISEINSIINNIGPIDGVLHIAGIS 156
+ + + I+ G ID +++ AGIS
Sbjct: 68 EDVENLVEQIVEKFGKIDILVNNAGIS 94
>gnl|CDD|181297 PRK08217, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 253
Score = 35.3 bits (82), Expect = 0.11
Identities = 21/91 (23%), Positives = 40/91 (43%), Gaps = 4/91 (4%)
Query: 67 QGGTYLITGGTGRLGMLFSDYLINKYSTNLILS--GRSKLNSIIYKKLKKFNNKAIYIQV 124
+ +ITGG LG ++YL K L L + KL + + +
Sbjct: 4 KDKVIVITGGAQGLGRAMAEYLAQK-GAKLALIDLNQEKLEEAV-AECGALGTEVRGYAA 61
Query: 125 DVSDKLKMISEINSIINNIGPIDGVLHIAGI 155
+V+D+ + + I + G ++G+++ AGI
Sbjct: 62 NVTDEEDVEATFAQIAEDFGQLNGLINNAGI 92
>gnl|CDD|187591 cd05330, cyclohexanol_reductase_SDR_c, cyclohexanol reductases,
including levodione reductase, classical (c) SDRs.
Cyloclohexanol reductases,including
(6R)-2,2,6-trimethyl-1,4-cyclohexanedione (levodione)
reductase of Corynebacterium aquaticum, catalyze the
reversible oxidoreduction of hydroxycyclohexanone
derivatives. 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 = 35.2 bits (81), Expect = 0.12
Identities = 35/153 (22%), Positives = 64/153 (41%), Gaps = 5/153 (3%)
Query: 72 LITGGTGRLGMLFSDYLINKYSTNLILSGRSKLNSIIYKKLKKFNNKA--IYIQVDVSDK 129
LITGG LG+ + L + + ++ + L + A + I+ DVSD+
Sbjct: 7 LITGGGSGLGLATAVRLAKEGAKLSLVDLNEEGLEAAKAALLEIAPDAEVLLIKADVSDE 66
Query: 130 LKMISEINSIINNIGPIDGVLHIAGISGLTSNILEANYKNFYSVLSSKISGTIALNYALE 189
++ + +++ + G IDG + AGI G + + F V+S + G Y LE
Sbjct: 67 AQVEAYVDATVEQFGRIDGFFNNAGIEGKQNLTEDFGADEFDKVVSINLRGVF---YGLE 123
Query: 190 NTILKLQKNKLDFVCYFSSSSAILGDFGSCDYA 222
+ +++ + +S I G YA
Sbjct: 124 KVLKVMREQGSGMIVNTASVGGIRGVGNQSGYA 156
>gnl|CDD|181298 PRK08219, PRK08219, short chain dehydrogenase; Provisional.
Length = 227
Score = 34.5 bits (80), Expect = 0.16
Identities = 22/94 (23%), Positives = 42/94 (44%), Gaps = 15/94 (15%)
Query: 70 TYLITGGTGRLGMLFSDYLINKYSTNLILSGRSKLNSIIYKKLKKFNNK---AIYIQVDV 126
T LITG + +G + L + L+L GR ++L + + A VD+
Sbjct: 5 TALITGASRGIGAAIARELAPTH--TLLLGGRPA------ERLDELAAELPGATPFPVDL 56
Query: 127 SDKLKMISEINSIINNIGPIDGVLHIAGISGLTS 160
+D + + + + G +D ++H AG++ L
Sbjct: 57 TDPEAIAAAVEQL----GRLDVLVHNAGVADLGP 86
>gnl|CDD|181625 PRK09051, PRK09051, beta-ketothiolase; Provisional.
Length = 394
Score = 34.9 bits (81), Expect = 0.18
Identities = 27/105 (25%), Positives = 41/105 (39%), Gaps = 15/105 (14%)
Query: 561 ALEDAGYGPNQIANQKIGMFVGVEEGSNYQDRLDQVNLTSTHNAILSARLAYFMDLKGPV 620
AL AG P+Q+ + G + E Y R+ A ++A + + P
Sbjct: 38 ALARAGVDPDQVGHVVFGHVIPTEPRDMYLSRV----------AAINAGVP----QETPA 83
Query: 621 MAINTACSSSLVATHIACQSLRQHECDTAISAGVNLMISPEAYIA 665
+N C S L A A Q++ + D AI G M S Y+
Sbjct: 84 FNVNRLCGSGLQAIVSAAQAILLGDADVAIGGGAESM-SRAPYLL 127
>gnl|CDD|187640 cd08935, mannonate_red_SDR_c, putative D-mannonate oxidoreductase,
classical (c) SDR. D-mannonate oxidoreductase catalyzes
the NAD-dependent interconversion of D-mannonate and
D-fructuronate. This subgroup includes Bacillus
subtitils UxuB/YjmF, a putative D-mannonate
oxidoreductase; the B. subtilis UxuB gene is part of a
putative ten-gene operon (the Yjm operon) involved in
hexuronate catabolism. Escherichia coli UxuB does not
belong to this subgroup. This subgroup has a canonical
active site tetrad and a typical Gly-rich NAD-binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold (alpha/beta folding
pattern with a central beta-sheet), an NAD(P)(H)-binding
region, and a structurally diverse C-terminal region.
Classical SDRs are typically about 250 residues long,
while extended SDRs are approximately 350 residues.
Sequence identity between different SDR enzymes are
typically in the 15-30% range, but the enzymes share the
Rossmann fold NAD-binding motif and characteristic
NAD-binding and catalytic sequence patterns. These
enzymes catalyze a wide range of activities including
the metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 271
Score = 34.4 bits (79), Expect = 0.26
Identities = 23/84 (27%), Positives = 40/84 (47%), Gaps = 4/84 (4%)
Query: 73 ITGGTGRLGMLFSDYLINKYSTNLILSGRS--KLNSIIYKKLKKFNNKAIYIQVDVSDKL 130
ITGGTG LG + L + + GR+ K + + K++ +AI + DV D+
Sbjct: 10 ITGGTGVLGGAMARALA-QAGAKVAALGRNQEKGDKVA-KEITALGGRAIALAADVLDRA 67
Query: 131 KMISEINSIINNIGPIDGVLHIAG 154
+ I+ G +D +++ AG
Sbjct: 68 SLERAREEIVAQFGTVDILINGAG 91
>gnl|CDD|181626 PRK09052, PRK09052, acetyl-CoA acetyltransferase; Provisional.
Length = 399
Score = 34.6 bits (80), Expect = 0.27
Identities = 14/39 (35%), Positives = 20/39 (51%)
Query: 619 PVMAINTACSSSLVATHIACQSLRQHECDTAISAGVNLM 657
+ +N C+S L A +A +R E D I+AGV M
Sbjct: 87 GGVTVNRFCASGLQAVAMAADRIRVGEADVMIAAGVESM 125
>gnl|CDD|187593 cd05332, 11beta-HSD1_like_SDR_c, 11beta-hydroxysteroid
dehydrogenase type 1 (11beta-HSD1)-like, classical (c)
SDRs. Human 11beta_HSD1 catalyzes the NADP(H)-dependent
interconversion of cortisone and cortisol. This subgroup
also includes human dehydrogenase/reductase SDR family
member 7C (DHRS7C) and DHRS7B. These proteins have the
GxxxGxG nucleotide binding motif and S-Y-K catalytic
triad characteristic of the SDRs, but have an atypical
C-terminal domain that contributes to homodimerization
contacts. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold (alpha/beta folding
pattern with a central beta-sheet), an NAD(P)(H)-binding
region, and a structurally diverse C-terminal region.
Classical SDRs are typically about 250 residues long,
while extended SDRs are approximately 350 residues.
Sequence identity between different SDR enzymes are
typically in the 15-30% range, but the enzymes share the
Rossmann fold NAD-binding motif and characteristic
NAD-binding and catalytic sequence patterns. These
enzymes catalyze a wide range of activities including
the metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 257
Score = 34.1 bits (79), Expect = 0.30
Identities = 23/93 (24%), Positives = 45/93 (48%), Gaps = 5/93 (5%)
Query: 67 QGGTYLITGGTGRLGMLFSDYLINKYSTNLILSGRS--KLNSIIYKKLKKFNNKAIYIQV 124
QG +ITG + +G + Y + + L+LS R +L + + L+ + +
Sbjct: 2 QGKVVIITGASSGIGEELA-YHLARLGARLVLSARREERLEEVKSECLELGAPSPHVVPL 60
Query: 125 DVSDKLKMISE-INSIINNIGPIDGVLHIAGIS 156
D+SD L+ + + + G +D +++ AGIS
Sbjct: 61 DMSD-LEDAEQVVEEALKLFGGLDILINNAGIS 92
>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 = 33.6 bits (77), Expect = 0.35
Identities = 14/63 (22%), Positives = 34/63 (53%)
Query: 119 AIYIQVDVSDKLKMISEINSIINNIGPIDGVLHIAGISGLTSNILEANYKNFYSVLSSKI 178
A+ ++VDV+D+ ++ + + G +D +++ AG LT I++ + + ++ +
Sbjct: 51 ALALRVDVTDEQQVAALFERAVEEFGGLDLLVNNAGAMHLTPAIIDTDLAVWDQTMAINL 110
Query: 179 SGT 181
GT
Sbjct: 111 RGT 113
>gnl|CDD|236074 PRK07666, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 239
Score = 33.5 bits (77), Expect = 0.35
Identities = 27/91 (29%), Positives = 47/91 (51%), Gaps = 2/91 (2%)
Query: 67 QGGTYLITGGTGRLGMLFSDYLINKYSTNLILSGRSKLN-SIIYKKLKKFNNKAIYIQVD 125
QG LITG +G + L K N+ L R++ N + ++++ + K + D
Sbjct: 6 QGKNALITGAGRGIGRAVAIALA-KEGVNVGLLARTEENLKAVAEEVEAYGVKVVIATAD 64
Query: 126 VSDKLKMISEINSIINNIGPIDGVLHIAGIS 156
VSD ++ + I + N +G ID +++ AGIS
Sbjct: 65 VSDYEEVTAAIEQLKNELGSIDILINNAGIS 95
>gnl|CDD|180595 PRK06504, PRK06504, acetyl-CoA acetyltransferase; Provisional.
Length = 390
Score = 33.9 bits (78), Expect = 0.38
Identities = 23/72 (31%), Positives = 34/72 (47%), Gaps = 13/72 (18%)
Query: 603 NAILSARLAYFMDLKGPVMAINTACSSSLVATHIACQSLRQHECDTAISAGVNLMISPEA 662
NA+L+++L + P +I+ C SS A H A Q++ D I+AGV
Sbjct: 69 NAVLASKLPESV----PGTSIDRQCGSSQQALHFAAQAVMSGTMDIVIAAGVE------- 117
Query: 663 YIAMTSAGMLSP 674
+MT M SP
Sbjct: 118 --SMTRVPMGSP 127
>gnl|CDD|187625 cd05367, SPR-like_SDR_c, sepiapterin reductase (SPR)-like,
classical (c) SDRs. Human SPR, a member of the SDR
family, catalyzes the NADP-dependent reduction of
sepiaptern to 7,8-dihydrobiopterin (BH2). In addition to
SPRs, this subgroup also contains Bacillus cereus yueD,
a benzil reductase, which catalyzes the stereospecific
reduction of benzil to (S)-benzoin. 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 = 241
Score = 33.0 bits (76), Expect = 0.52
Identities = 28/147 (19%), Positives = 57/147 (38%), Gaps = 9/147 (6%)
Query: 70 TYLITGGTGRLGMLFSDYLINK-YSTNLILSGRSK--LNSIIYKKLKKFNNKAI-YIQVD 125
++TG + +G ++ L+ + + ++L RS+ L K + + ++ D
Sbjct: 1 VIILTGASRGIGRALAEELLKRGSPSVVVLLARSEEPLQE---LKEELRPGLRVTTVKAD 57
Query: 126 VSDKLKMISEINSIINNIGPIDGVLHIAGISGLTSNILEANYKNFYSVLSSKISGTIALN 185
+SD + + +I G D +++ AG G S I + ++ + L
Sbjct: 58 LSDAAGVEQLLEAIRKLDGERDLLINNAGSLGPVSKIEFIDLDELQKYFDLNLTSPVCLT 117
Query: 186 YALENTILKLQKNKLDFVCYFSSSSAI 212
L K K V SS +A+
Sbjct: 118 STLLRAFKKRGLKKT--VVNVSSGAAV 142
>gnl|CDD|187616 cd05358, GlcDH_SDR_c, glucose 1 dehydrogenase (GlcDH), classical
(c) SDRs. GlcDH, is a tetrameric member of the SDR
family, it catalyzes the NAD(P)-dependent oxidation of
beta-D-glucose to D-glucono-delta-lactone. GlcDH has a
typical NAD-binding site glycine-rich pattern as well as
the canonical active site tetrad (YXXXK motif plus
upstream Ser and Asn). SDRs are a functionally diverse
family of oxidoreductases that have a single domain with
a structurally conserved Rossmann fold (alpha/beta
folding pattern with a central beta-sheet), an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRS are approximately
350 residues. Sequence identity between different SDR
enzymes are typically in the 15-30% range, but the
enzymes share the Rossmann fold NAD-binding motif and
characteristic NAD-binding and catalytic sequence
patterns. These enzymes have a 3-glycine N-terminal
NAD(P)(H)-binding pattern (typically, TGxxxGxG in
classical SDRs and TGxxGxxG in extended SDRs), while
substrate binding is in the C-terminal region. A
critical catalytic Tyr residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering), is often found in a conserved YXXXK pattern.
In addition to the Tyr and Lys, there is often an
upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn
(Asn-107, 15-PGDH numbering) or additional Ser,
contributing to the active site. Substrates for these
enzymes include sugars, steroids, alcohols, and aromatic
compounds. The standard reaction mechanism is a proton
relay involving the conserved Tyr and Lys, as well as
Asn (or Ser). Some SDR family members, including 17
beta-hydroxysteroid dehydrogenase contain an additional
helix-turn-helix motif that is not generally found among
SDRs.
Length = 253
Score = 33.1 bits (76), Expect = 0.53
Identities = 31/133 (23%), Positives = 64/133 (48%), Gaps = 9/133 (6%)
Query: 68 GGTYLITGGTGRLGMLFSDYLINKYSTNLILSGRSKLNSI--IYKKLKKFNNKAIYIQVD 125
G L+TG + +G + L N++++ RSK ++ + +++K KAI +Q D
Sbjct: 3 GKVALVTGASSGIGKAIAIRLA-TAGANVVVNYRSKEDAAEEVVEEIKAVGGKAIAVQAD 61
Query: 126 VSDKLKMISEINSIINNIGPIDGVLHIAGISGLTSNILEANYKNFYSVLSSKISGTI--- 182
VS + +++ S I G +D +++ AG+ G S E +++ V+ ++G
Sbjct: 62 VSKEEDVVALFQSAIKEFGTLDILVNNAGLQGDAS-SHEMTLEDWNKVIDVNLTGQFLCA 120
Query: 183 --ALNYALENTIL 193
A+ ++ I
Sbjct: 121 REAIKRFRKSKIK 133
>gnl|CDD|236216 PRK08277, PRK08277, D-mannonate oxidoreductase; Provisional.
Length = 278
Score = 33.3 bits (77), Expect = 0.59
Identities = 22/85 (25%), Positives = 43/85 (50%), Gaps = 4/85 (4%)
Query: 72 LITGGTGRLGMLFSDYLINKYSTNLILSGRS--KLNSIIYKKLKKFNNKAIYIQVDVSDK 129
+ITGG G LG + L + + + R+ K +++ ++K +A+ ++ DV DK
Sbjct: 14 VITGGGGVLGGAMAKELA-RAGAKVAILDRNQEKAEAVV-AEIKAAGGEALAVKADVLDK 71
Query: 130 LKMISEINSIINNIGPIDGVLHIAG 154
+ I+ + GP D +++ AG
Sbjct: 72 ESLEQARQQILEDFGPCDILINGAG 96
>gnl|CDD|236357 PRK08945, PRK08945, putative oxoacyl-(acyl carrier protein)
reductase; Provisional.
Length = 247
Score = 32.9 bits (76), Expect = 0.68
Identities = 39/152 (25%), Positives = 66/152 (43%), Gaps = 17/152 (11%)
Query: 67 QGGTYLITG---GTGRLGMLFSDYLINKYSTNLILSGR--SKLNSIIYKKLKKFNNK--A 119
+ L+TG G GR L Y ++ +IL GR KL ++ Y +++ A
Sbjct: 11 KDRIILVTGAGDGIGREAAL--TYA--RHGATVILLGRTEEKLEAV-YDEIEAAGGPQPA 65
Query: 120 IY-IQVDVSDKLKMISEINSIINNIGPIDGVLHIAGISGLTSNILEANYKNFYSVLSSKI 178
I + + + ++I G +DGVLH AG+ G + + + + + V+ +
Sbjct: 66 IIPLDLLTATPQNYQQLADTIEEQFGRLDGVLHNAGLLGELGPMEQQDPEVWQDVMQVNV 125
Query: 179 SGTIALNYALENTILKLQKNKLDFVCYFSSSS 210
+ T L AL +LK L F+SSS
Sbjct: 126 NATFMLTQALLPLLLKSPAASL----VFTSSS 153
>gnl|CDD|215439 PLN02819, PLN02819, lysine-ketoglutarate reductase/saccharopine
dehydrogenase.
Length = 1042
Score = 33.6 bits (77), Expect = 0.70
Identities = 17/71 (23%), Positives = 35/71 (49%), Gaps = 3/71 (4%)
Query: 444 NVSKKSNFILN--KNTDINSEELIAIIGMSGRFPAARNINEFWKILINNKD-VISEIPEK 500
NVS+ + I +T + +L + G+S + + + + + ++ ++D V + P K
Sbjct: 213 NVSQGAQEIFKLLPHTFVEPSKLPELKGISQNKISTKRVYQVYGCVVTSQDMVEHKDPSK 272
Query: 501 IFDWKLYYENP 511
FD YY +P
Sbjct: 273 QFDKADYYAHP 283
>gnl|CDD|180439 PRK06171, PRK06171, sorbitol-6-phosphate 2-dehydrogenase;
Provisional.
Length = 266
Score = 32.7 bits (75), Expect = 0.71
Identities = 21/91 (23%), Positives = 38/91 (41%), Gaps = 13/91 (14%)
Query: 67 QGGTYLITGGTGRLGMLFSDYLINK--YSTNLILSGRSKLNSIIYKKLKKFNNKAIYIQV 124
QG ++TGG+ +G+ L+ N + G ++ ++
Sbjct: 8 QGKIIIVTGGSSGIGLAIVKELLANGANVVNADIHG----GDGQHENY-------QFVPT 56
Query: 125 DVSDKLKMISEINSIINNIGPIDGVLHIAGI 155
DVS ++ + II G IDG+++ AGI
Sbjct: 57 DVSSAEEVNHTVAEIIEKFGRIDGLVNNAGI 87
>gnl|CDD|227546 COG5221, DOP1, Dopey and related predicted leucine zipper
transcription factors [Transcription].
Length = 1618
Score = 33.4 bits (76), Expect = 0.72
Identities = 32/172 (18%), Positives = 55/172 (31%), Gaps = 23/172 (13%)
Query: 291 EQLLIQDKIQYLVLSGELEKLNQIINNIAPKVSENKKINNFNIEKFIENDIKNHICNILN 350
E+ I++ E N + IA + + I D+ H
Sbjct: 363 ERDYIEEYAPPDAFESERSSENIDVEKIARAFLTTDLDSVWKILYLQLKDVLLHS----- 417
Query: 351 TKKSEIYKNKNLADYGFDSISLAEFSRILSKFYSLDIMPSIFFSYSTLERLITYFIKNHN 410
K + N +L + + S+ YSL M IF ++ E
Sbjct: 418 --KEFMLLNMDLTNDEEFNDSMVREEM-----YSLHSMSLIFNEITSSECFALG------ 464
Query: 411 NTMIKFYRNKYPLKTESKNISILYD-----NKINENYENVSKKSNFILNKNT 457
++++ Y+ YP+ S + ++ EN ENVS N N
Sbjct: 465 ASLLEVYKGAYPMSESSLLEEMELKCKGLLGRVVENRENVSNWIKDANNPNQ 516
>gnl|CDD|181305 PRK08226, PRK08226, short chain dehydrogenase; Provisional.
Length = 263
Score = 32.9 bits (75), Expect = 0.72
Identities = 22/88 (25%), Positives = 38/88 (43%), Gaps = 1/88 (1%)
Query: 68 GGTYLITGGTGRLGMLFSDYLINKYSTNLILSGRSKLNSIIYKKLKKFNNKAIYIQVDVS 127
G T LITG +G + + ++ NLIL S + +L ++ + DV
Sbjct: 6 GKTALITGALQGIGEGIA-RVFARHGANLILLDISPEIEKLADELCGRGHRCTAVVADVR 64
Query: 128 DKLKMISEINSIINNIGPIDGVLHIAGI 155
D + + I G ID +++ AG+
Sbjct: 65 DPASVAAAIKRAKEKEGRIDILVNNAGV 92
>gnl|CDD|180193 PRK05675, sdhA, succinate dehydrogenase flavoprotein subunit;
Reviewed.
Length = 570
Score = 33.2 bits (76), Expect = 0.75
Identities = 19/59 (32%), Positives = 31/59 (52%), Gaps = 4/59 (6%)
Query: 36 FSIMYYGNDLIRYQ----LNIKSIILKDFKNSYIKQGGTYLITGGTGRLGMLFSDYLIN 90
F +Y DL++ Q + + +I ++ + YIK T L TGG GR+ ++ LIN
Sbjct: 143 FLNEWYAVDLVKNQDGAVVGVIAICIETGETVYIKSKATVLATGGAGRIYASTTNALIN 201
>gnl|CDD|181518 PRK08643, PRK08643, acetoin reductase; Validated.
Length = 256
Score = 32.4 bits (74), Expect = 0.86
Identities = 18/66 (27%), Positives = 37/66 (56%), Gaps = 2/66 (3%)
Query: 110 KKLKKFNNKAIYIQVDVSDKLKMISEINSIINNIGPIDGVLHIAGISGLT--SNILEANY 167
KL K KAI ++ DVSD+ ++ + + +++ G ++ V++ AG++ T I E +
Sbjct: 44 DKLSKDGGKAIAVKADVSDRDQVFAAVRQVVDTFGDLNVVVNNAGVAPTTPIETITEEQF 103
Query: 168 KNFYSV 173
Y++
Sbjct: 104 DKVYNI 109
>gnl|CDD|237218 PRK12825, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 249
Score = 32.1 bits (74), Expect = 1.0
Identities = 18/85 (21%), Positives = 37/85 (43%), Gaps = 1/85 (1%)
Query: 72 LITGGTGRLGMLFSDYLINK-YSTNLILSGRSKLNSIIYKKLKKFNNKAIYIQVDVSDKL 130
L+TG LG + L + + + + ++ +A +Q DV+DK
Sbjct: 10 LVTGAARGLGRAIALRLARAGADVVVHYRSDEEAAEELVEAVEALGRRAQAVQADVTDKA 69
Query: 131 KMISEINSIINNIGPIDGVLHIAGI 155
+ + + + + G ID +++ AGI
Sbjct: 70 ALEAAVAAAVERFGRIDILVNNAGI 94
>gnl|CDD|176200 cd08238, sorbose_phosphate_red, L-sorbose-1-phosphate reductase.
L-sorbose-1-phosphate reductase, a member of the MDR
family, catalyzes the NADPH-dependent conversion of
l-sorbose 1-phosphate to d-glucitol 6-phosphate in the
metabolism of L-sorbose to (also converts d-fructose
1-phosphate to d-mannitol 6-phosphate). The medium
chain dehydrogenases/reductase (MDR)/zinc-dependent
alcohol dehydrogenase-like family, which contains the
zinc-dependent alcohol dehydrogenase (ADH-Zn) and
related proteins, is a diverse group of proteins related
to the first identified member, class I mammalian ADH.
MDRs display a broad range of activities and are
distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of an
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases
(ADHs) catalyze the NAD(P)(H)-dependent interconversion
of alcohols to aldehydes or ketones. Active site zinc
has a catalytic role, while structural zinc aids in
stability.
Length = 410
Score = 32.8 bits (75), Expect = 1.0
Identities = 12/26 (46%), Positives = 16/26 (61%)
Query: 65 IKQGGTYLITGGTGRLGMLFSDYLIN 90
IK GG I GG G +G++ DY I+
Sbjct: 173 IKPGGNTAILGGAGPMGLMAIDYAIH 198
>gnl|CDD|187570 cd05260, GDP_MD_SDR_e, GDP-mannose 4,6 dehydratase, extended (e)
SDRs. GDP-mannose 4,6 dehydratase, a homodimeric SDR,
catalyzes the NADP(H)-dependent conversion of
GDP-(D)-mannose to GDP-4-keto, 6-deoxy-(D)-mannose in
the fucose biosynthesis pathway. These proteins have the
canonical active site triad and NAD-binding pattern,
however the active site Asn is often missing and may be
substituted with Asp. A Glu residue has been identified
as an important active site base. Extended SDRs 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. 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. 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. 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 = 316
Score = 32.6 bits (75), Expect = 1.0
Identities = 28/112 (25%), Positives = 45/112 (40%), Gaps = 23/112 (20%)
Query: 72 LITGGTGRLGMLFSDYLINK-YSTNLILSGRSKLNSIIYKKLKKFNNKAIYIQVDVSDKL 130
LITG TG+ G +++L+ K Y + I+ S N+ L ++ D++D
Sbjct: 3 LITGITGQDGSYLAEFLLEKGYEVHGIVRRSSSFNTDRIDHLYINKDRITLHYGDLTD-- 60
Query: 131 KMISEINSIINNIGPIDGVLHIAGIS-----------------GLTSNILEA 165
S + I + P D + H+A S T N+LEA
Sbjct: 61 --SSSLRRAIEKVRP-DEIYHLAAQSHVKVSFDDPEYTAEVNAVGTLNLLEA 109
>gnl|CDD|226674 COG4221, COG4221, Short-chain alcohol dehydrogenase of unknown
specificity [General function prediction only].
Length = 246
Score = 32.2 bits (74), Expect = 1.1
Identities = 16/74 (21%), Positives = 40/74 (54%), Gaps = 6/74 (8%)
Query: 95 NLILSGRS--KLNSIIYKKLKKFNNKAIYIQVDVSDKLKMISEINSIINNIGPIDGVLHI 152
++L+ R +L ++ ++ A+ + +DV+D+ + + I ++ G ID +++
Sbjct: 32 KVVLAARREERLEALA-DEIGA--GAALALALDVTDRAAVEAAIEALPEEFGRIDILVNN 88
Query: 153 AGISGLTSNILEAN 166
AG++ L + EA+
Sbjct: 89 AGLA-LGDPLDEAD 101
>gnl|CDD|131468 TIGR02415, 23BDH, acetoin reductases. One member of this family,
as characterized in Klebsiella terrigena, is described
as able to interconvert acetoin + NADH with
meso-2,3-butanediol + NAD(+). It is also called capable
of irreversible reduction of diacetyl with NADH to
acetoin. Blomqvist, et al. decline to specify either EC
1.1.1.4 which is (R,R)-butanediol dehydrogenase, or EC
1.1.1.5, which is acetoin dehydrogenase without a
specified stereochemistry, for this enzyme. This enzyme
is a homotetramer in the family of short chain
dehydrogenases (pfam00106). Another member of this
family, from Corynebacterium glutamicum, is called
L-2,3-butanediol dehydrogenase (PMID:11577733) [Energy
metabolism, Fermentation].
Length = 254
Score = 32.0 bits (73), Expect = 1.2
Identities = 26/113 (23%), Positives = 51/113 (45%), Gaps = 1/113 (0%)
Query: 70 TYLITGGTGRLGMLFSDYLINKYSTNLILSGRSKLNSIIYKKLKKFNNKAIYIQVDVSDK 129
L+TGG +G ++ L + + K++ + KA+ ++DVSDK
Sbjct: 2 VALVTGGAQGIGKGIAERLAKDGFAVAVADLNEETAKETAKEINQAGGKAVAYKLDVSDK 61
Query: 130 LKMISEINSIINNIGPIDGVLHIAGISGLTSNILEANYKNFYSVLSSKISGTI 182
++ S I+ G D +++ AG++ +T ILE + V + + G +
Sbjct: 62 DQVFSAIDQAAEKFGGFDVMVNNAGVAPITP-ILEITEEELKKVYNVNVKGVL 113
>gnl|CDD|187580 cd05272, TDH_SDR_e, L-threonine dehydrogenase, extended (e) SDRs.
This subgroup contains members identified as L-threonine
dehydrogenase (TDH). TDH catalyzes the zinc-dependent
formation of 2-amino-3-ketobutyrate from L-threonine via
NAD(H)-dependent oxidation. This group is distinct from
TDHs that are members of the medium chain
dehydrogenase/reductase family. This group has the
NAD-binding motif and active site tetrad of the extended
SDRs. Extended SDRs 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. 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. 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. 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 = 308
Score = 32.3 bits (74), Expect = 1.2
Identities = 23/85 (27%), Positives = 40/85 (47%), Gaps = 13/85 (15%)
Query: 72 LITGGTGRLGMLFSDYLINKYST-NLILSGRSKLNSIIYKKLKKFNNKAIYIQVDVSDKL 130
LITGG G++G + L +Y N+I S K + + + +DV D
Sbjct: 3 LITGGLGQIGSELAKLLRKRYGKDNVIASDIRKPPA------HVVLSG-PFEYLDVLD-F 54
Query: 131 KMISEINSIINNIGPIDGVLHIAGI 155
K + EI ++N+ I ++H+A +
Sbjct: 55 KSLEEI--VVNH--KITWIIHLAAL 75
>gnl|CDD|223696 COG0623, FabI, Enoyl-[acyl-carrier-protein].
Length = 259
Score = 32.2 bits (74), Expect = 1.3
Identities = 11/64 (17%), Positives = 29/64 (45%), Gaps = 3/64 (4%)
Query: 110 KKLKKFNNKAIYIQVDVSDKLKMISEINSIINNIGPIDGVLHIAGIS---GLTSNILEAN 166
++L + + + DV++ + + +I G +DG++H + L + L+ +
Sbjct: 49 EELAEELGSDLVLPCDVTNDESIDALFATIKKKWGKLDGLVHSIAFAPKEELKGDYLDTS 108
Query: 167 YKNF 170
+ F
Sbjct: 109 REGF 112
>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 = 32.2 bits (74), Expect = 1.3
Identities = 21/93 (22%), Positives = 41/93 (44%), Gaps = 8/93 (8%)
Query: 68 GGTYLITGGTGRLGMLFS-DYLINKYSTNLILSGRSKLNSI-IYKKLKKF--NNKAIYIQ 123
G +ITG G+ + K ++I++ R++ ++KK N K IQ
Sbjct: 1 GKVVVITGANS--GIGKETARELAKRGAHVIIACRNEEKGEEAAAEIKKETGNAKVEVIQ 58
Query: 124 VDVSDKLKMISEI-NSIINNIGPIDGVLHIAGI 155
+D+S L + + + +D +++ AGI
Sbjct: 59 LDLSS-LASVRQFAEEFLARFPRLDILINNAGI 90
>gnl|CDD|181508 PRK08628, PRK08628, short chain dehydrogenase; Provisional.
Length = 258
Score = 31.5 bits (72), Expect = 1.8
Identities = 26/100 (26%), Positives = 51/100 (51%), Gaps = 5/100 (5%)
Query: 72 LITGGTGRLGMLFSDYLINKYSTNLILSGRSKLNSIIYKKLKKFNNKAIYIQVDVSDKLK 131
++TGG +G S L + + +I GRS + ++L+ +A ++QVD++D +
Sbjct: 11 IVTGGASGIGAAISLRLAEEGAIPVIF-GRSAPDDEFAEELRALQPRAEFVQVDLTDDAQ 69
Query: 132 MISEINSIINNIGPIDGVLHIAGISGLTSNI-LEANYKNF 170
+ + G IDG+++ AG++ + LEA + F
Sbjct: 70 CRDAVEQTVAKFGRIDGLVNNAGVN---DGVGLEAGREAF 106
>gnl|CDD|240419 PTZ00440, PTZ00440, reticulocyte binding protein 2-like protein;
Provisional.
Length = 2722
Score = 32.1 bits (73), Expect = 2.0
Identities = 44/203 (21%), Positives = 75/203 (36%), Gaps = 36/203 (17%)
Query: 277 KQKVLHENDGLKLFEQLLIQDKIQYLVLSGELEKLNQII------NNIAPKVSENKKINN 330
+ L +++ LK + I++KI+Y+ ++ + II +NI ++ E
Sbjct: 551 SIETLIKDEKLKRSMKNDIKNKIKYI--EENVDHIKDIISLNDEIDNIIQQIEELINEAL 608
Query: 331 FNIEKFIENDIKNHICNILNTKKSEIYKNKNLADYGFDSISLAEFSRILSKFYS------ 384
FN EKFI N L K I D L+ F Y
Sbjct: 609 FNKEKFINEK------NDLQEKVKYILNKFYKGDLQELLDELSHFLDDHKYLYHEAKSKE 662
Query: 385 --LDIMPSIFFSYSTLERLITYFIKNHNNTMIKFYRNKYPLKTESKNISILYDNKINENY 442
++ + Y LE + + ++ + +IK LK E +N+ L +N I +
Sbjct: 663 DLQTLLNTSKNEYEKLEFMKS----DNIDNIIK------NLKKELQNLLSLKENIIKKQL 712
Query: 443 ENV----SKKSNFILNKNTDINS 461
N+ S N K D+ S
Sbjct: 713 NNIEQDISNSLNQYTIKYNDLKS 735
>gnl|CDD|236094 PRK07774, PRK07774, short chain dehydrogenase; Provisional.
Length = 250
Score = 31.3 bits (71), Expect = 2.0
Identities = 26/111 (23%), Positives = 52/111 (46%), Gaps = 5/111 (4%)
Query: 68 GGTYLITGGTGRLGMLFSDYLINKYSTNLILSGRSKLNSIIYKKLKKFNNKAIYIQVDVS 127
++TG G +G +++ L + ++ ++ ++ + K++ AI +QVDVS
Sbjct: 6 DKVAIVTGAAGGIGQAYAEALAREGASVVVADINAEGAERVAKQIVADGGTAIAVQVDVS 65
Query: 128 DKLKMISEINSIINNIGPIDGVLHIAGISG-----LTSNILEANYKNFYSV 173
D + ++ ++ G ID +++ A I G L + YK F SV
Sbjct: 66 DPDSAKAMADATVSAFGGIDYLVNNAAIYGGMKLDLLITVPWDYYKKFMSV 116
>gnl|CDD|224012 COG1087, GalE, UDP-glucose 4-epimerase [Cell envelope biogenesis,
outer membrane].
Length = 329
Score = 31.8 bits (73), Expect = 2.0
Identities = 34/152 (22%), Positives = 60/152 (39%), Gaps = 39/152 (25%)
Query: 72 LITGGTGRLGMLFSDYLINK-YST----NLILSGRSKLNSIIYKKLKKFNNKAIYIQVDV 126
L+TGG G +G L+ + NL + L + +K + + D+
Sbjct: 4 LVTGGAGYIGSHTVRQLLKTGHEVVVLDNLSNGHKIALLKLQFK----------FYEGDL 53
Query: 127 SDKLKMISEINSIINNIGPIDGVLHIAGISGL---TSNILEANYKNFYSVLSSKISGTIA 183
D+ + + ID V+H A + N L+ Y N + GT+
Sbjct: 54 LDRALLTAVFEEN-----KIDAVVHFAASISVGESVQNPLKY-YDN-------NVVGTLN 100
Query: 184 LNYALENTILKLQKNKLDFVCYFSSSSAILGD 215
L +E +L+ K F+ FSS++A+ G+
Sbjct: 101 L---IE-AMLQTGVKK--FI--FSSTAAVYGE 124
>gnl|CDD|226476 COG3967, DltE, Short-chain dehydrogenase involved in D-alanine
esterification of lipoteichoic acid and wall teichoic
acid (D-alanine transfer protein) [Cell envelope
biogenesis, outer membrane].
Length = 245
Score = 31.2 bits (71), Expect = 2.3
Identities = 20/89 (22%), Positives = 37/89 (41%), Gaps = 4/89 (4%)
Query: 67 QGGTYLITGGTGRLGMLFSDYLINKYSTNLILSGRSKLNSIIYKKLKKFNNKAIYIQVDV 126
G T LITGG +G+ + + +I+ GR N + K N + DV
Sbjct: 4 TGNTILITGGASGIGLALAKRF-LELGNTVIICGR---NEERLAEAKAENPEIHTEVCDV 59
Query: 127 SDKLKMISEINSIINNIGPIDGVLHIAGI 155
+D+ + + ++ +++ AGI
Sbjct: 60 ADRDSRRELVEWLKKEYPNLNVLINNAGI 88
>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 = 31.2 bits (71), Expect = 2.3
Identities = 15/56 (26%), Positives = 31/56 (55%)
Query: 119 AIYIQVDVSDKLKMISEINSIINNIGPIDGVLHIAGISGLTSNILEANYKNFYSVL 174
AI IQ DV+ + + + + + ++ G +D +++ AGI+ +LE + + F V
Sbjct: 53 AIAIQADVTKRADVEAMVEAALSKFGRLDILVNNAGITHRNKPMLEVDEEEFDRVF 108
>gnl|CDD|239332 cd03034, ArsC_ArsC, Arsenate Reductase (ArsC) family, ArsC
subfamily; arsenic reductases similar to that encoded by
arsC on the R733 plasmid of Escherichia coli. E. coli
ArsC catalyzes the reduction of arsenate [As(V)] to
arsenite [As(III)], the first step in the detoxification
of arsenic, using reducing equivalents derived from
glutathione (GSH) via glutaredoxin (GRX). ArsC contains
a single catalytic cysteine, within a thioredoxin fold,
that forms a covalent thiolate-As(V) intermediate, which
is reduced by GRX through a mixed GSH-arsenate
intermediate. This family of predominantly bacterial
enzymes is unrelated to two other families of arsenate
reductases which show similarity to low-molecular-weight
acid phosphatases and phosphotyrosyl phosphatases.
Length = 112
Score = 29.9 bits (68), Expect = 2.5
Identities = 23/85 (27%), Positives = 35/85 (41%), Gaps = 14/85 (16%)
Query: 690 PSEAVVAVVLKRLSRALSDGDPIHAIIRGSGINYDGKTNGITAPNGISQTELIKSVYKKS 749
P+ A + +L +L G ++R Y K G+ P +S ELI ++
Sbjct: 36 PTAAELRELLAKL------GISPRDLLRTKEAPY--KELGLADPE-LSDEELIDAMAA-- 84
Query: 750 NLNPEDINY-IITHGTGTKLGDPVE 773
+P I I+ G G LG P E
Sbjct: 85 --HPILIERPIVVTGDGAVLGRPPE 107
>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 = 30.9 bits (70), Expect = 2.6
Identities = 13/36 (36%), Positives = 23/36 (63%)
Query: 118 KAIYIQVDVSDKLKMISEINSIINNIGPIDGVLHIA 153
+AI IQ DV D+ ++ + I N+ GP+D +++ A
Sbjct: 48 RAIAIQADVRDRDQVQAMIEEAKNHFGPVDTIVNNA 83
>gnl|CDD|235771 PRK06289, PRK06289, acetyl-CoA acetyltransferase; Provisional.
Length = 403
Score = 31.2 bits (71), Expect = 2.7
Identities = 15/32 (46%), Positives = 17/32 (53%)
Query: 626 ACSSSLVATHIACQSLRQHECDTAISAGVNLM 657
AC+S VAT A LR D A+ GV LM
Sbjct: 89 ACASGSVATLAAMADLRAGRYDVALVVGVELM 120
>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 = 31.0 bits (71), Expect = 3.0
Identities = 18/86 (20%), Positives = 41/86 (47%), Gaps = 4/86 (4%)
Query: 72 LITGGTGRLGMLFSDYLINKYSTNLILSGRS--KLNSIIYKKLKKFNNKAIYIQVDVSDK 129
L+TG + +G + + + ++ RS + +++K A ++ DVSD+
Sbjct: 4 LVTGASRGIGRAIA-LRLAAEGAKVAVTDRSEEAAAETV-EEIKALGGNAAALEADVSDR 61
Query: 130 LKMISEINSIINNIGPIDGVLHIAGI 155
+ + + + GP+D +++ AGI
Sbjct: 62 EAVEALVEKVEAEFGPVDILVNNAGI 87
>gnl|CDD|181077 PRK07677, PRK07677, short chain dehydrogenase; Provisional.
Length = 252
Score = 30.8 bits (70), Expect = 3.0
Identities = 19/90 (21%), Positives = 44/90 (48%), Gaps = 8/90 (8%)
Query: 68 GGTYLITGGTGRLGMLFSDYLINKYS---TNLILSGRSKLNSIIYKK-LKKFNNKAIYIQ 123
+ITGG+ +G + +++ N++++GR+K K +++F + + +Q
Sbjct: 1 EKVVIITGGSSGMG----KAMAKRFAEEGANVVITGRTKEKLEEAKLEIEQFPGQVLTVQ 56
Query: 124 VDVSDKLKMISEINSIINNIGPIDGVLHIA 153
+DV + + + I G ID +++ A
Sbjct: 57 MDVRNPEDVQKMVEQIDEKFGRIDALINNA 86
>gnl|CDD|177878 PLN02234, PLN02234, 1-deoxy-D-xylulose-5-phosphate synthase.
Length = 641
Score = 31.2 bits (70), Expect = 3.2
Identities = 47/197 (23%), Positives = 76/197 (38%), Gaps = 39/197 (19%)
Query: 653 GVNLMISPEAYIAMTSAGMLSPDGKCYVFDER------ANGLVPSEAVVAVVLKRLSRAL 706
G M + +AY AM +AG L + + D + AN P++ V A LS AL
Sbjct: 207 GDGAMTAGQAYEAMNNAGYLHSNMIVILNDNKQVSLPTANLDGPTQPVGA-----LSCAL 261
Query: 707 SDGDPIHAIIRGS--------GINYDGKTNGITAPNGISQTELIKSVYKKSNLNPEDINY 758
S +IR + G +Y G +G + +S E +KS + P I+
Sbjct: 262 SRLQSNCGMIRETSSTLFEELGFHYVGPVDGHNIDDLVSILETLKST---KTIGPVLIHV 318
Query: 759 IITHGTGTKLG-------------DPVEINALHDVFKNKTYNQKFC-AITSNKS---NIG 801
+ G G DP ++ K ++Y F A+ + +I
Sbjct: 319 VTEKGRGYPYAERADDKYHGVLKFDPETGKQFKNISKTQSYTSCFVEALIAEAEADKDIV 378
Query: 802 HTFAASGLVSLINLVQS 818
AA G +++NL +S
Sbjct: 379 AIHAAMGGGTMLNLFES 395
>gnl|CDD|237418 PRK13534, PRK13534, 7-cyano-7-deazaguanine tRNA-ribosyltransferase;
Provisional.
Length = 639
Score = 31.1 bits (71), Expect = 3.6
Identities = 27/114 (23%), Positives = 41/114 (35%), Gaps = 25/114 (21%)
Query: 440 ENYENVSKKSNFILNKNTDINSEELIAIIGMSGRFPAARNINEFWKILINNKDVISEIPE 499
E Y+ VSKKS F E L + P + + + ++K + +
Sbjct: 350 EKYDPVSKKSAFFY-----TGYESL--------KRPEVYRHKKRLERIKSDKKYTTVVSS 396
Query: 500 KIFDWKLYYENPIKSSNKINSKWYGSIPGIDEFDPLFFEISPLEAERMDPRQRH 553
KI WK Y EN N + + DP+F I PL + P +
Sbjct: 397 KI--WKPYSEN----LNNVRCDV-----DVLIKDPVFGLI-PLYLDTTYPLAQS 438
>gnl|CDD|226840 COG4409, NanH, Neuraminidase (sialidase) [Carbohydrate transport
and metabolism].
Length = 728
Score = 31.0 bits (70), Expect = 3.7
Identities = 21/117 (17%), Positives = 32/117 (27%), Gaps = 11/117 (9%)
Query: 20 KNWINILFKELQEPKLFSIMYYGNDLIRYQLNIKSIILKDFKNSYIKQGGTYLITGGTGR 79
K W + I +G ++ I SY I G
Sbjct: 318 KTWHKPEVTGQFDDATTQIAIWGREVTLRNGQISL------SQSYSDSSIVEDIKDGKLF 371
Query: 80 LGMLFSDYLINKYSTNLILSGRSKLNSIIYKKLKK-----FNNKAIYIQVDVSDKLK 131
L M+ K + +I SG + +Y K + F A SD+
Sbjct: 372 LFMVVMPDGNYKTTAAIIDSGSKNIAGNVYLKSEDDGDTDFEYTATENGKIFSDETN 428
>gnl|CDD|180462 PRK06198, PRK06198, short chain dehydrogenase; Provisional.
Length = 260
Score = 30.7 bits (70), Expect = 3.7
Identities = 22/91 (24%), Positives = 44/91 (48%), Gaps = 1/91 (1%)
Query: 67 QGGTYLITGGTGRLGMLFSDYLINKYSTNLILSGRS-KLNSIIYKKLKKFNNKAIYIQVD 125
G L+TGGT LG + + + L++ GR+ + +L+ KA+++Q D
Sbjct: 5 DGKVALVTGGTQGLGAAIARAFAERGAAGLVICGRNAEKGEAQAAELEALGAKAVFVQAD 64
Query: 126 VSDKLKMISEINSIINNIGPIDGVLHIAGIS 156
+SD + + G +D +++ AG++
Sbjct: 65 LSDVEDCRRVVAAADEAFGRLDALVNAAGLT 95
>gnl|CDD|204670 pfam11508, DUF3218, Protein of unknown function (DUF3218). This
family of proteins with unknown function appears to be
restricted to Pseudomonas.
Length = 213
Score = 30.3 bits (68), Expect = 4.0
Identities = 14/58 (24%), Positives = 26/58 (44%), Gaps = 4/58 (6%)
Query: 714 AIIRGSGINYDGKTNGITAPNGISQTELIKSVYKKSNLNPEDINYIITHGTGTKLGDP 771
+ GI+ + +G+ G++ L ++ L PEDI ++ G G +L P
Sbjct: 131 STDASGGISQE---SGLLVSYGVNLRTLTPGTWQAMTL-PEDIKALVGPGVGLRLDAP 184
>gnl|CDD|188234 TIGR02591, cas_Csh1, CRISPR-associated protein Cas8b/Csh1, subtype
I-B/HMARI. This domain is found in the C-terminal 2/3
of a family of CRISPR associated proteins of the Hmari
subtype. Except for the two sequences from halophilic
archaea this domain contains a pair of CXXC motifs
[Mobile and extrachromosomal element functions, Other].
Length = 393
Score = 30.9 bits (70), Expect = 4.0
Identities = 26/135 (19%), Positives = 44/135 (32%), Gaps = 6/135 (4%)
Query: 410 NNTMIKFYRNKYPLKTESKNISILYDNKINENYENVSKKSNFILN-KNTDINSEELIAI- 467
NT ++++ KI E +N + F +I +E +
Sbjct: 58 GNTYKLPIIPGTIFPKVAQDLYKEEIKKIYEFRKNDFLQEKFYTEEAGYEIELDEDLEEN 117
Query: 468 -IGMSGRFPA--ARNINEFWKILINNKDVISEIPEKIFDWKLYYEN-PIKSSNKINSKWY 523
IG R+ + KI + KDV EKI + + N + ++ W+
Sbjct: 118 KIGYYLRYDFLFYSKEKQAEKITLYIKDVEPSRVEKILELEKKVLNVSKEDFGELKENWF 177
Query: 524 GSIPGIDEFDPLFFE 538
D FFE
Sbjct: 178 FGQVYAFLLDNDFFE 192
>gnl|CDD|181225 PRK08085, PRK08085, gluconate 5-dehydrogenase; Provisional.
Length = 254
Score = 30.5 bits (69), Expect = 4.1
Identities = 26/96 (27%), Positives = 48/96 (50%), Gaps = 2/96 (2%)
Query: 61 KNSYIKQGGTYLITGGTGRLGMLFSDYLINKYSTNLILSGRSKLNS-IIYKKLKKFNNKA 119
+ + G LITG +G L + L +Y +I++ + + + KL++ KA
Sbjct: 2 NDLFSLAGKNILITGSAQGIGFLLATGL-AEYGAEIIINDITAERAELAVAKLRQEGIKA 60
Query: 120 IYIQVDVSDKLKMISEINSIINNIGPIDGVLHIAGI 155
+V+ K ++ + I I +IGPID +++ AGI
Sbjct: 61 HAAPFNVTHKQEVEAAIEHIEKDIGPIDVLINNAGI 96
>gnl|CDD|222222 pfam13561, adh_short_C2, Enoyl-(Acyl carrier protein) reductase.
Length = 239
Score = 30.3 bits (69), Expect = 4.6
Identities = 14/80 (17%), Positives = 30/80 (37%), Gaps = 7/80 (8%)
Query: 96 LILSGRS-KLNSIIYKKL-KKFNNKAIYIQVDVSDKLKMISEINSIINNIGPIDGVLHIA 153
++L+ L +L K+ I +DV+ + + + G ID ++H
Sbjct: 23 VVLTTWPPALRMGAVDELAKELPADVIP--LDVTSDEDIDELFEKVKEDGGKIDFLVHSI 80
Query: 154 GISG---LTSNILEANYKNF 170
+S L+ + + F
Sbjct: 81 AMSPEIRKGKPYLDTSREGF 100
>gnl|CDD|223982 COG1054, COG1054, Predicted sulfurtransferase [General function
prediction only].
Length = 308
Score = 30.3 bits (69), Expect = 4.7
Identities = 9/25 (36%), Positives = 11/25 (44%), Gaps = 1/25 (4%)
Query: 675 DGKCYVFDERANGLVPSEAVVAVVL 699
DGKC+VFDER +
Sbjct: 222 DGKCFVFDERV-AVPIGLVEGDHTP 245
>gnl|CDD|181585 PRK08936, PRK08936, glucose-1-dehydrogenase; Provisional.
Length = 261
Score = 30.1 bits (68), Expect = 4.7
Identities = 19/88 (21%), Positives = 49/88 (55%), Gaps = 6/88 (6%)
Query: 110 KKLKKFNNKAIYIQVDVSDKLKMISEINSIINNIGPIDGVLHIAGISGLTSNILEANYKN 169
+++KK +AI ++ DV+ + +++ I + + G +D +++ AGI + E + ++
Sbjct: 50 EEIKKAGGEAIAVKGDVTVESDVVNLIQTAVKEFGTLDVMINNAGIENAVPS-HEMSLED 108
Query: 170 FYSVLSSKISGTI-----ALNYALENTI 192
+ V+++ ++G A+ Y +E+ I
Sbjct: 109 WNKVINTNLTGAFLGSREAIKYFVEHDI 136
>gnl|CDD|234663 PRK00142, PRK00142, putative rhodanese-related sulfurtransferase;
Provisional.
Length = 314
Score = 30.2 bits (69), Expect = 5.0
Identities = 9/10 (90%), Positives = 9/10 (90%)
Query: 675 DGKCYVFDER 684
DGK YVFDER
Sbjct: 221 DGKLYVFDER 230
>gnl|CDD|224013 COG1088, RfbB, dTDP-D-glucose 4,6-dehydratase [Cell envelope
biogenesis, outer membrane].
Length = 340
Score = 30.3 bits (69), Expect = 5.2
Identities = 20/89 (22%), Positives = 41/89 (46%), Gaps = 13/89 (14%)
Query: 70 TYLITGGTGRLGMLFSDYLINKYSTNLI-----LSGRSKLNSIIYKKLKKFNNKAIYIQV 124
L+TGG G +G F Y++NK+ + + L+ L ++ + + + ++Q
Sbjct: 2 KILVTGGAGFIGSNFVRYILNKHPDDHVVNLDKLTYAGNLENL---ADVEDSPRYRFVQG 58
Query: 125 DVSDKLKMISEINSIINNIGPIDGVLHIA 153
D+ D+ ++ + P D V+H A
Sbjct: 59 DICDR----ELVDRLFKEYQP-DAVVHFA 82
>gnl|CDD|224050 COG1125, OpuBA, ABC-type proline/glycine betaine transport systems,
ATPase components [Amino acid transport and metabolism].
Length = 309
Score = 30.3 bits (69), Expect = 5.3
Identities = 23/77 (29%), Positives = 36/77 (46%), Gaps = 11/77 (14%)
Query: 442 YENVSKK-SNFIL--NKNTDINSEELIAIIGMS--GRFPAARNINEFW-----KILINNK 491
+ENVSK+ N + N I E + +IG S G+ + IN +ILI+ +
Sbjct: 4 FENVSKRYGNKKAVDDVNLTIEEGEFLVLIGPSGSGKTTTLKMINRLIEPTSGEILIDGE 63
Query: 492 DVISEIPEKIFDWKLYY 508
D IS++ K+ Y
Sbjct: 64 D-ISDLDPVELRRKIGY 79
>gnl|CDD|234811 PRK00685, PRK00685, metal-dependent hydrolase; Provisional.
Length = 228
Score = 29.8 bits (68), Expect = 6.3
Identities = 16/30 (53%), Positives = 20/30 (66%), Gaps = 3/30 (10%)
Query: 748 KSNLNPEDIN--YI-ITHGTGTKLGDPVEI 774
++L PED+ YI +THG G LGD VEI
Sbjct: 31 LADLKPEDVKVDYILLTHGHGDHLGDTVEI 60
>gnl|CDD|187644 cd08940, HBDH_SDR_c, d-3-hydroxybutyrate dehydrogenase (HBDH),
classical (c) SDRs. DHBDH, an NAD+ -dependent enzyme,
catalyzes the interconversion of D-3-hydroxybutyrate and
acetoacetate. It is a classical SDR, with the canonical
NAD-binding motif and active site tetrad. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold (alpha/beta folding pattern with a central
beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRs are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes catalyze a
wide range of activities including the metabolism of
steroids, cofactors, carbohydrates, lipids, aromatic
compounds, and amino acids, and act in redox sensing.
Classical SDRs have an TGXXX[AG]XG cofactor binding
motif and a YXXXK active site motif, with the Tyr
residue of the active site motif serving as a critical
catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 258
Score = 29.7 bits (67), Expect = 6.4
Identities = 20/91 (21%), Positives = 40/91 (43%), Gaps = 4/91 (4%)
Query: 68 GGTYLITGGTGRLGMLFSDYLINKYSTNLILSG---RSKLNSIIYKKLKKFNNKAIYIQV 124
G L+TG T +G+ + L N++L+G +++ ++ K K +Y
Sbjct: 2 GKVALVTGSTSGIGLGIARALA-AAGANIVLNGFGDAAEIEAVRAGLAAKHGVKVLYHGA 60
Query: 125 DVSDKLKMISEINSIINNIGPIDGVLHIAGI 155
D+S + + G +D +++ AGI
Sbjct: 61 DLSKPAAIEDMVAYAQRQFGGVDILVNNAGI 91
>gnl|CDD|179922 PRK05066, PRK05066, arginine repressor; Provisional.
Length = 156
Score = 29.2 bits (66), Expect = 6.8
Identities = 18/66 (27%), Positives = 32/66 (48%), Gaps = 15/66 (22%)
Query: 362 LADYGFDSISLAEFSRILSKF-------------YSLDIMPSIFFSYSTLERLITYFIKN 408
L + GFD+I+ ++ SR+L+KF Y L + + S L+ L+ +
Sbjct: 33 LQEQGFDNINQSKVSRMLTKFGAVRTRNAKMEMVYCLPAELGVPTTSSPLKNLVLDI--D 90
Query: 409 HNNTMI 414
HN+ +I
Sbjct: 91 HNDALI 96
>gnl|CDD|235794 PRK06398, PRK06398, aldose dehydrogenase; Validated.
Length = 258
Score = 29.8 bits (67), Expect = 7.2
Identities = 16/39 (41%), Positives = 26/39 (66%)
Query: 117 NKAIYIQVDVSDKLKMISEINSIINNIGPIDGVLHIAGI 155
N Y +VDVS+K ++I I+ +I+ G ID +++ AGI
Sbjct: 44 NDVDYFKVDVSNKEQVIKGIDYVISKYGRIDILVNNAGI 82
>gnl|CDD|224865 COG1954, GlpP, Glycerol-3-phosphate responsive antiterminator
(mRNA-binding) [Transcription].
Length = 181
Score = 29.2 bits (66), Expect = 7.8
Identities = 25/96 (26%), Positives = 43/96 (44%), Gaps = 10/96 (10%)
Query: 108 IYKKLKKFNNKAIYIQVDVSDKLKMISEINSIINNIGPIDGVLHIAGISGLTSNILEANY 167
I KKLK K ++I VD+ + L I + DG+ IS ++ I +A
Sbjct: 40 IVKKLKN-RGKTVFIHVDLVEGLSNDEVAIEFIKEVIKPDGI-----ISTKSNVIKKAKK 93
Query: 168 KNFYSVLSSKISGTIALNYALENTILKLQKNKLDFV 203
++ I +IAL I +++K++ DF+
Sbjct: 94 LGILAIQRLFILDSIALE----KGIKQIEKSEPDFI 125
>gnl|CDD|187614 cd05356, 17beta-HSD1_like_SDR_c, 17-beta-hydroxysteroid
dehydrogenases (17beta-HSDs) types -1, -3, and -12,
-like, classical (c) SDRs. This subgroup includes
various 17-beta-hydroxysteroid dehydrogenases and
3-ketoacyl-CoA reductase, these are members of the SDR
family, and contain the canonical active site tetrad and
glycine-rich NAD-binding motif of the classical SDRs.
3-ketoacyl-CoA reductase (KAR, aka 17beta-HSD type 12,
encoded by HSD17B12) acts in fatty acid elongation;
17beta- hydroxysteroid dehydrogenases are isozymes that
catalyze activation and inactivation of estrogen and
androgens, and include members of the SDR family.
17beta-estradiol dehydrogenase (aka 17beta-HSD type 1,
encoded by HSD17B1) converts estrone to estradiol.
Estradiol is the predominant female sex hormone.
17beta-HSD type 3 (aka testosterone
17-beta-dehydrogenase 3, encoded by HSD17B3) catalyses
the reduction of androstenedione to testosterone, it
also accepts estrogens as substrates. This subgroup also
contains a putative steroid dehydrogenase let-767 from
Caenorhabditis elegans, mutation in which results in
hypersensitivity to cholesterol limitation. 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 = 239
Score = 29.1 bits (66), Expect = 9.2
Identities = 19/85 (22%), Positives = 37/85 (43%), Gaps = 16/85 (18%)
Query: 73 ITGGTGRLGMLFSDYL----INKYSTNLILSGRSKLNSIIYKKLKKFNNKAIYIQVDVSD 128
+TG T +G +++ L N LI + KL+++ + +K+ + I D S
Sbjct: 6 VTGATDGIGKAYAEELAKRGFNVI---LISRTQEKLDAVAKEIEEKYGVETKTIAADFSA 62
Query: 129 K-------LKMIS--EINSIINNIG 144
K + +I ++NN+G
Sbjct: 63 GDDIYERIEKELEGLDIGILVNNVG 87
>gnl|CDD|180576 PRK06463, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 255
Score = 29.4 bits (66), Expect = 9.4
Identities = 19/90 (21%), Positives = 43/90 (47%), Gaps = 7/90 (7%)
Query: 67 QGGTYLITGGTGRLGMLFSDYLINKYSTNLILSGRSKLNSIIYKKLKKFNNKAIY-IQVD 125
+G LITGGT +G ++ + + + +L ++ + K+ K ++ I+ D
Sbjct: 6 KGKVALITGGTRGIGRAIAEAFLREGAKVAVLYNSAE------NEAKELREKGVFTIKCD 59
Query: 126 VSDKLKMISEINSIINNIGPIDGVLHIAGI 155
V ++ ++ + G +D +++ AGI
Sbjct: 60 VGNRDQVKKSKEVVEKEFGRVDVLVNNAGI 89
>gnl|CDD|235500 PRK05557, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Validated.
Length = 248
Score = 29.4 bits (67), Expect = 9.7
Identities = 12/38 (31%), Positives = 21/38 (55%)
Query: 118 KAIYIQVDVSDKLKMISEINSIINNIGPIDGVLHIAGI 155
KA+ +Q DVSD + ++ G +D +++ AGI
Sbjct: 56 KALAVQGDVSDAESVERAVDEAKAEFGGVDILVNNAGI 93
>gnl|CDD|180617 PRK06550, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 235
Score = 29.2 bits (66), Expect = 9.9
Identities = 9/35 (25%), Positives = 20/35 (57%), Gaps = 6/35 (17%)
Query: 121 YIQVDVSDKLKMISEINSIINNIGPIDGVLHIAGI 155
++Q+D+SD L+ + + + +D + + AGI
Sbjct: 49 FLQLDLSDDLE------PLFDWVPSVDILCNTAGI 77
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
0.318 0.135 0.386
Gapped
Lambda K H
0.267 0.0940 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 50,919,389
Number of extensions: 5178241
Number of successful extensions: 6243
Number of sequences better than 10.0: 1
Number of HSP's gapped: 5980
Number of HSP's successfully gapped: 335
Length of query: 1005
Length of database: 10,937,602
Length adjustment: 106
Effective length of query: 899
Effective length of database: 6,236,078
Effective search space: 5606234122
Effective search space used: 5606234122
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 64 (28.1 bits)