RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy616
(1152 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 = 587 bits (1517), Expect = 0.0
Identities = 202/422 (47%), Positives = 271/422 (64%), Gaps = 10/422 (2%)
Query: 633 IAIIGMSGRFPAARNINEFWKILINNKDVISEIPEKIFDWKLYYENPIKSSNKINSKWYG 692
IAI+GM+ RFP A + +EFW+ L+ +D ISEIPE +D YY +P K K ++ G
Sbjct: 3 IAIVGMACRFPGAADPDEFWENLLEGRDAISEIPEDRWDADGYYPDPGKP-GKTYTRRGG 61
Query: 693 SIPGIDEFDPLFFEISPLEAERMDPRQRHLLQESWLALEDAGYGPNQIANQKIGMFVGVE 752
+ +D FD FF ISP EAE MDP+QR LL+ +W ALEDAGY P +A + G+FVG
Sbjct: 62 FLDDVDAFDAAFFGISPREAEAMDPQQRLLLEVAWEALEDAGYSPESLAGSRTGVFVGAS 121
Query: 753 EGSNYQDRLDQVN-------LTSTHNAILSARLAYFMDLKGPVMAINTACSSSLVATHIA 805
S+Y + L + T T A L+ R++YF DL+GP + ++TACSSSLVA H+A
Sbjct: 122 -SSDYLELLARDPDEIDAYAATGTSRAFLANRISYFFDLRGPSLTVDTACSSSLVALHLA 180
Query: 806 CQSLRQHECDTAISAGVNLMISPEAYIAMTSAGMLSPDGKCYVFDERANGLVPSEAVVAV 865
CQSLR ECD A+ GVNL++SP+ ++ + AGMLSPDG+C FD A+G V E V V
Sbjct: 181 CQSLRSGECDLALVGGVNLILSPDMFVGFSKAGMLSPDGRCRPFDADADGYVRGEGVGVV 240
Query: 866 VLKRLSRALSDGDPIHAIIRGSGINYDGKTNGITAPNGISQTELIKSVYKKSNLNPEDIN 925
VLKRLS AL DGD I+A+IRGS +N DG+T GITAP+G +Q LI+ Y ++ ++P DI+
Sbjct: 241 VLKRLSDALRDGDRIYAVIRGSAVNQDGRTKGITAPSGEAQAALIRRAYARAGVDPSDID 300
Query: 926 YIITHGTGTKLGDPVEINALHDVFKNKTYNQKFCAITSNKSNIGHTFAASGLVSLINLVQ 985
Y+ HGTGT LGDP+E+ AL VF + I S KSNIGH AA+GL LI +V
Sbjct: 301 YVEAHGTGTPLGDPIEVEALAKVFGGSRSADQPLLIGSVKSNIGHLEAAAGLAGLIKVVL 360
Query: 986 SIKYKIIPASLHCEKENNYIILKNSPFYINKSNKKWNTVNEKLRIGAVSAFGMSGTNAHI 1045
++++ +IP +LH E N I + SP + + W R G VS+FG GTNAH+
Sbjct: 361 ALEHGVIPPNLHFETPNPKIDFEESPLRVPTEARPWPAPAGPRRAG-VSSFGFGGTNAHV 419
Query: 1046 VL 1047
+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 = 581 bits (1500), Expect = 0.0
Identities = 211/526 (40%), Positives = 296/526 (56%), Gaps = 18/526 (3%)
Query: 628 NSEELIAIIGMSGRFPAARNINEFWKILINNKDVISEIPEKIFDWKLYYENPIKSSNKIN 687
E IAIIGM+ RFP A + EFW +L +D I+E+P +D YY+ K
Sbjct: 1 QLIEPIAIIGMACRFPGADSPEEFWDLLKEGRDEITEVPADRWDVDAYYDPDPTVPGKSY 60
Query: 688 SKWYGSIPGIDEFDPLFFEISPLEAERMDPRQRHLLQESWLALEDAGYGPNQIANQKIGM 747
S+W G + +D+FD LFF ISP EAE MDP+QR LL+ +W ALEDAG P+ + G+
Sbjct: 61 SRWGGFLDDVDDFDALFFGISPREAEAMDPQQRLLLEVAWEALEDAGIYPDSLRGSATGV 120
Query: 748 FVGVEEGSNYQDRL-------DQVNLTSTHNAILSARLAYFMDLKGPVMAINTACSSSLV 800
F G Y L + +T +++ + R++Y + L GP + ++TACSSSLV
Sbjct: 121 FAGASVAD-YLLLLLADDEAEPEYAITGNSSSVAAGRISYVLGLSGPSVTVDTACSSSLV 179
Query: 801 ATHIACQSLRQHECDTAISAGVNLMISPEAYIAMTSAGMLSPDGKCYVFDERANGLVPSE 860
A H+ACQSLR ECD A++ GVNL++SPE+ ++ GMLSPDG+C FD A+G V E
Sbjct: 180 AVHLACQSLRLGECDLALAGGVNLVLSPESSYLFSAGGMLSPDGRCKAFDADADGYVRGE 239
Query: 861 AVVAVVLKRLSRALSDGDPIHAIIRGSGINYDGKTNGITAPNGISQTELIKSVYKKSNLN 920
VVLKRLS A DGD I+A+IRGS +N DG++NG+TAPN +Q ++I+ + ++
Sbjct: 240 GAGVVVLKRLSDAERDGDRIYAVIRGSAVNQDGRSNGLTAPNLEAQADVIREALADAGID 299
Query: 921 PEDINYIITHGTGTKLGDPVEINALHDVFKNKTYNQKFCAITSNKSNIGHTFAASGLVSL 980
P + Y+ HGTGT LGDP+E NAL V+ Q CAI S KSNIGH AA+G+ L
Sbjct: 300 PATVQYVEAHGTGTPLGDPIEANALGAVYGEGAPAQ-PCAIGSVKSNIGHLEAAAGIAGL 358
Query: 981 INLVQSIKYKIIPASLHCEKENNYIILKNSPFYINKSNKKWNTVNEKLRIGAVSAFGMSG 1040
I ++K+ IP +LH + N I +SPF + W T R VS+FG G
Sbjct: 359 IKTALALKHGYIPPTLHFDTPNPEIDFDSSPFVVPTEATPWPTGGGPRR-AGVSSFGFGG 417
Query: 1041 TNAHIVLQEYISTNFKNIKNNTFISSNPYHMVVLSAKTKISLKEKMKQILLFLRKN-NTV 1099
TNAH++L+E + ++VLSAKT L ++ L +
Sbjct: 418 TNAHVILEEA-------PPRAESTIPSSPRLLVLSAKTAERLAATAPRLADRLELQGGLL 470
Query: 1100 CIENFVYTLMQGRHHFQYRCAIIISSIEEVVKIINDTLNSKEKILH 1145
+ + 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 = 444 bits (1144), Expect = e-147
Identities = 157/417 (37%), Positives = 207/417 (49%), Gaps = 119/417 (28%)
Query: 633 IAIIGMSGRFPAARNINEFWKILINNKDVISEIPEKIFDWKLYYENPIKSSNKINSKWYG 692
IAI+GMS RFP A + EFW +L+
Sbjct: 1 IAIVGMSCRFPGADDPEEFWDLLLA----------------------------------- 25
Query: 693 SIPGIDEFDPLFFEISPLEAERMDPRQRHLLQESWLALEDAGYGPNQIANQKIGMFVGVE 752
+ +D FD FF ISP EAE MDP+QR LL+ +W ALEDAG P + + G+FVGV
Sbjct: 26 GLDDVDLFDAAFFGISPREAEAMDPQQRLLLEVAWEALEDAGIDPESLRGSRTGVFVGV- 84
Query: 753 EGSNYQDRLDQVNLTSTHNAILSARLAYFMDLKGPVMAINTACSSSLVATHIACQSLRQH 812
+ D Y + ++TACSSSLVA H+ACQSLR
Sbjct: 85 ---SSSD--------------------Y-------SVTVDTACSSSLVALHLACQSLRSG 114
Query: 813 ECDTAISAGVNLMISPEAYIAMTSAGMLSPDGKCYVFDERANGLVPSEAVVAVVLKRLSR 872
ECD A++ GVNL++SP+ ++ ++ AGMLSPDG+C FD A+G V E V VVLKRLS
Sbjct: 115 ECDMALAGGVNLILSPDTFVGLSRAGMLSPDGRCKTFDASADGYVRGEGVGVVVLKRLSD 174
Query: 873 ALSDGDPIHAIIRGSGINYDGKTNGITAPNGISQTELIKSVYKKSNLNPEDINYIITHGT 932
AL DGDPI A+IRGS +N DG++NGITAP+G +Q
Sbjct: 175 ALRDGDPILAVIRGSAVNQDGRSNGITAPSGPAQ-------------------------- 208
Query: 933 GTKLGDPVEINALHDVFKNKTYNQKFCAITSNKSNIGHTFAASGLVSLINLVQSIKYKII 992
I S KSNIGH AA+G+ LI +V ++K+ +I
Sbjct: 209 --------------------------LLIGSVKSNIGHLEAAAGVAGLIKVVLALKHGVI 242
Query: 993 PASLHCEKENNYIILKNSPFYINKSNKKWNTVNEKLRIGAVSAFGMSGTNAHIVLQE 1049
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 = 271 bits (694), Expect = 2e-83
Identities = 99/257 (38%), Positives = 137/257 (53%), Gaps = 33/257 (12%)
Query: 633 IAIIGMSGRFPAARNINEFWKILINNKDVISEIPEKIFDWKLYYENPIKSSNKINSKWYG 692
+AI GM RFP EFW++L+ +D I E P D Y + G
Sbjct: 4 VAITGMGCRFPGGVGPEEFWELLLAGRDAIREFPA---DLSGLYPPSRVA---------G 51
Query: 693 SIPGIDEFDPLFFEISPLEAERMDPRQRHLLQESWLALEDAGYGPNQI-ANQKIGMFVGV 751
I G +FD FF ISP EAE MDP+QR L+ +W ALEDAG P + + + G+FVG
Sbjct: 52 EIYG-FDFDAAFFGISPREAEAMDPQQRLALEAAWEALEDAGLDPASLRGSDRTGVFVG- 109
Query: 752 EEGSNYQDRLDQVNLTSTHN--------------AILSARLAYFMDLKGPVMAINTACSS 797
S D + L S ++ + R++Y + L+GP + ++TACSS
Sbjct: 110 ---SGSGDYAELQALDSAGGPRRVSPYLTGAWMPSVAAGRISYRLGLRGPSVTVDTACSS 166
Query: 798 SLVATHIACQSLRQHECDTAISAGVNLMISPEAYIAMTSAG-MLSPDGKCYVFDERANGL 856
SLVA H A +S+R+ ECD A++ GV ++P + ++AG +LSPDG C FD A+G
Sbjct: 167 SLVALHAAVRSIRRGECDLALAGGVEAPLTPGGFAGFSAAGALLSPDGPCKAFDPFADGF 226
Query: 857 VPSEAVVAVVLKRLSRA 873
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 = 216 bits (551), Expect = 1e-62
Identities = 83/337 (24%), Positives = 149/337 (44%), Gaps = 24/337 (7%)
Query: 719 QRHLLQESWLALEDAGYGPNQIANQKIGMFVG-----VEEGSNYQDRLDQVN---LTSTH 770
+ + A+ DAG N +G+ VG D + V +T
Sbjct: 12 SILGFEAAERAIADAGLSREYQKNPIVGVVVGTGGGSPRFQVFGADAMRAVGPYVVTKAM 71
Query: 771 NAILSARLAYFMDLKGPVMAINTACSSSLVATHIACQSLRQHECDTAISAGVNLMISPEA 830
S ++A + + GP ++ AC+ SL A +A +++ + D ++ G + +P
Sbjct: 72 FPGASGQIATPLGIHGPAYDVSAACAGSLHALSLAADAVQNGKQDIVLAGGSEELAAPMD 131
Query: 831 YIAMTSAGMLSPDGKCYVFDERANGLVPSEAVVAVVLKRLSRALSDGDPIHAIIRGSGIN 890
+ +P+ FD A+G V + A+V++ L AL+ G I+A I G+
Sbjct: 132 CEFDAMGALSTPEKASRTFDAAADGFVFGDGAGALVVEELEHALARGAHIYAEIVGTAAT 191
Query: 891 YDGKTNGITAPNGISQTELIKSVYKKSNLNPEDINYIITHGTGTKLGDPVEINALHDVFK 950
DG G AP+ K + L DI+Y++ HGTGT +GD E+ L F
Sbjct: 192 IDGAGMGAFAPSAEGLARAAKEALAVAGLTVWDIDYLVAHGTGTPIGDVKELKLLRSEFG 251
Query: 951 NKTYNQKFCAITSNKSNIGHTFAASGLVSLINLVQSIKYKIIPASLHCEKENNYIILKNS 1010
+K+ A+++ K+ G+ +A+ ++++ V +++ IP S+H E+ + +
Sbjct: 252 DKSP-----AVSATKAMTGNLSSAAVVLAVDEAVLMLEHGFIPPSIHIEELDEAGL---- 302
Query: 1011 PFYINKSNKKWNTVNEKLRIGAVSAFGMSGTNAHIVL 1047
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 = 207 bits (530), Expect = 9e-59
Identities = 107/425 (25%), Positives = 177/425 (41%), Gaps = 51/425 (12%)
Query: 643 PAARNINEFWKILINNKDVISEIPEKIFDWKLYYENPIKSSNKINSKWYGSIPGIDEFDP 702
P + EFW+ L+ + I I FD + S+ G +P D D
Sbjct: 13 PLGNGVEEFWEALLAGRSGIRPITR--FDASGFP-----------SRIAGEVPDFDPEDY 59
Query: 703 LFFEISPLEAERMDPRQRHLLQESWLALEDAGYGPNQIANQKIGMFVGVEEGS------- 755
+ E RMD + L + AL DAG P ++ ++IG+ +G G
Sbjct: 60 ----LDRKELRRMDRFAQFALAAAEEALADAGLDPEELDPERIGVVIGSGIGGLATIEEA 115
Query: 756 --NYQDRLDQVNLTSTHNAIL----SARLAYFMDLKGPVMAINTACSSSLVATHIACQSL 809
++ + L + ++A + L+GP ++TAC+S A A + +
Sbjct: 116 YRALLEKGPRRVSPFFVPMALPNMAAGQVAIRLGLRGPNYTVSTACASGAHAIGDAARLI 175
Query: 810 RQHECDTAISAGVNLMISPEAYIAMTSAGMLS-----PDGKCYVFDERANGLVPSEAVVA 864
R D I+ G +I+P + LS P+ FD+ +G V E
Sbjct: 176 RLGRADVVIAGGAEALITPLTLAGFAALRALSTRNDDPEKASRPFDKDRDGFVLGEGAGV 235
Query: 865 VVLKRLSRALSDGDPIHAIIRGSGINYDGKTNGITAP--NGISQTELIKSVYKKSNLNPE 922
+VL+ L A + G I+A I G G + D ITAP +G +++ + L+PE
Sbjct: 236 LVLESLEHAKARGAKIYAEILGYGASSDA--YHITAPDPDGEGAARAMRAALADAGLSPE 293
Query: 923 DINYIITHGTGTKLGDPVEINALHDVFKNKTYNQKFCAITSNKSNIGHTFAASGLVSLIN 982
DI+YI HGT T L D E A+ VF ++S KS GH A+G V I
Sbjct: 294 DIDYINAHGTSTPLNDAAESKAIKRVFGEHAKK---VPVSSTKSMTGHLLGAAGAVEAIA 350
Query: 983 LVQSIKYKIIPASLHCEKENNYIILKNSPFYINKSNKKWNTVNEKLRIGAVSAFGMSGTN 1042
+ +++ ++P +++ E+ + L Y+ ++ +R ++FG G N
Sbjct: 351 TLLALRDGVLPPTINLEEPDPECDLD----YVPNEAREA-----PIRYALSNSFGFGGHN 401
Query: 1043 AHIVL 1047
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 (555), Expect = 3e-57
Identities = 135/456 (29%), Positives = 213/456 (46%), Gaps = 40/456 (8%)
Query: 633 IAIIGMSGRFPAARNINEFWKILINNKDVISEIPEKIFDWKLYYENPIKSSNKINSKWYG 692
IAI+GM+ F +R +N+FW ++ D I+++P + YY++ ++K K G
Sbjct: 9 IAIVGMASIFANSRYLNKFWDLIFEKIDAITDVPSDHWAKDDYYDSDKSEADKSYCKRGG 68
Query: 693 SIPGIDEFDPLFFEISPLEAERMDPRQRHLLQESWLALEDAGYGPNQIANQKIGMFVGVE 752
+P +D F+P+ F + P E D Q L + L DAG P+ KIG+ +GV
Sbjct: 69 FLPEVD-FNPMEFGLPPNILELTDISQLLSLVVAKEVLNDAGL-PDGYDRDKIGITLGVG 126
Query: 753 EG----SNYQDRLDQVNLTSTHNA---------------------------------ILS 775
G S+ RL L A ++S
Sbjct: 127 GGQKQSSSLNARLQYPVLKKVFKASGVEDEDSEMLIKKFQDQYIHWEENSFPGSLGNVIS 186
Query: 776 ARLAYFMDLKGPVMAINTACSSSLVATHIACQSLRQHECDTAISAGVNLMISPEAYIAMT 835
R+A DL G ++ AC+ SL A +A L + + I+ GV SP Y++ +
Sbjct: 187 GRIANRFDLGGMNCVVDAACAGSLAAIRMALSELLEGRSEMMITGGVCTDNSPFMYMSFS 246
Query: 836 SAGMLSPDGKCYVFDERANGLVPSEAVVAVVLKRLSRALSDGDPIHAIIRGSGINYDGKT 895
+ + FD + G++ E + + LKRL A DGD I+A+I+G G + DGK
Sbjct: 247 KTPAFTTNEDIQPFDIDSKGMMIGEGIGMMALKRLEDAERDGDRIYAVIKGVGASSDGKF 306
Query: 896 NGITAPNGISQTELIKSVYKKSNLNPEDINYIITHGTGTKLGDPVEINALHDVFKNKTYN 955
I AP Q + +K Y + P I HGTGT GD E L VF
Sbjct: 307 KSIYAPRPEGQAKALKRAYDDAGFAPHTCGLIEAHGTGTAAGDVAEFGGLVSVFSQDNDQ 366
Query: 956 QKFCAITSNKSNIGHTFAASGLVSLINLVQSIKYKIIPASLHCEKENNYIILKNSPFYIN 1015
++ A+ S KS IGHT + +G +I V ++ +K++P +++ ++ N + ++NSPFY+N
Sbjct: 367 KQHIALGSVKSQIGHTKSTAGTAGMIKAVLALHHKVLPPTINVDQPNPKLDIENSPFYLN 426
Query: 1016 KSNKKW-NTVNEKLRIGAVSAFGMSGTNAHIVLQEY 1050
+ W + R +S+FG GTN H+VL+EY
Sbjct: 427 TETRPWMQREDGTPRRAGISSFGFGGTNFHMVLEEY 462
Score = 55.8 bits (134), Expect = 2e-07
Identities = 46/186 (24%), Positives = 77/186 (41%), Gaps = 18/186 (9%)
Query: 287 AIYIQVDVSDKLKMISEINSIINNIGPIDGVLHIAGISGLTSNILEANYKNFYSVLSSKI 346
A Y DV++ + + + + +N I G++H AG+ +I + + F +V +K+
Sbjct: 2096 AEYASADVTNSVSVAATV-QPLNKTLQITGIIHGAGVLA-DKHIQDKTLEEFNAVYGTKV 2153
Query: 347 SGTIALNYALENTILKLQKNKLDFVCYFSSSSAILGDFGSCDYAMGNRFQTVYAKYLNNK 406
G L + + L + + FSS++ G+ G DYAM N A L
Sbjct: 2154 DG-------LLSLLAALNAENIKLLALFSSAAGFYGNTGQSDYAMSNDILNKAALQLKAL 2206
Query: 407 NIYKKYTNKLITINWPLWNNSKFKIGNNEQTDFYFKSSKQKVLHENDGLKLF-EQLLIQD 465
N + K+++ NW W+ N F V+ + G +LF QLL
Sbjct: 2207 NP----SAKVMSFNWGPWDGGMV----NPALKKMFNDRGVYVIPLDAGAELFVSQLLSDT 2258
Query: 466 KIQYLV 471
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 = 192 bits (491), Expect = 2e-53
Identities = 112/439 (25%), Positives = 173/439 (39%), Gaps = 53/439 (12%)
Query: 633 IAIIGMSGRFPAARNINEFWKILINNKDVISEIPEKIFDWKLYYENPIKSSNKINSKWYG 692
+ I G+ + E W L+ K I I FD + K G
Sbjct: 5 VVITGLGIVSSLGNGVEEVWAALLAGKSGIRPITR--FDAS-----------GLGVKIAG 51
Query: 693 SIPGIDEFDPLFFEISPLEAERMDPRQRHLLQESWLALEDAGYGPNQIANQKIGMFVGVE 752
I +D+ I+ E MD + + + ALEDAG + ++G+ +G
Sbjct: 52 EIKDLDDQ------IAKKERRFMDRFSQLAVVAAVEALEDAGLDNELNVDMRVGVAIGSG 105
Query: 753 EGS--NYQDRLDQVNLTSTHNAI------------LSARLAYFMDLKGPVMAINTACSSS 798
G + + LD + L I + +A LKGP TAC++
Sbjct: 106 IGGLEDIEFDLDALLLEGLRKRISPFLVPKMLPNLAAGNVAIVFGLKGPNYTPVTACATG 165
Query: 799 LVATHIACQSLRQHECDTAISAGVNLMISPEAYIAMTSAGMLS-----PDGKCYVFDERA 853
A A + +R + D I+ G I+P + LS P+ FD+
Sbjct: 166 AHAIGDAVRLIRLGKADVVIAGGAEAAITPLGIAGFEAMRALSTRNDDPEKASRPFDKNR 225
Query: 854 NGLVPSEAVVAVVLKRLSRALSDGDPIHAIIRGSGINYDGKTNGITAP--NGISQTELIK 911
+G V E A+VL+ L AL+ G I+A I G G D ITAP +G ++
Sbjct: 226 DGFVIGEGAGALVLEELEHALARGAKIYAEIVGYGTTSDA--YHITAPAPDGEGAIRAMR 283
Query: 912 SVYKKSNLNPEDINYIITHGTGTKLGDPVEINALHDVFKNKTYNQKFCAITSNKSNIGHT 971
+ + L PEDI+YI HGT T D E A+ VF + ++S KS GHT
Sbjct: 284 AALADAGLTPEDIDYINAHGTSTPANDKAESLAIKRVFGEHAKSL---PVSSTKSLTGHT 340
Query: 972 FAASGLVSLINLVQSIKYKIIPASLHCEKENNYIILKNSPFYINKSNKKWNTVNEKLRIG 1031
A+G V I + +++ IIP ++ N ++ + +R
Sbjct: 341 LGAAGAVEAIISLLALRDGIIPPTI------NLDNPDPEAADLDVVPNE--ARTGAVRAA 392
Query: 1032 AVSAFGMSGTNAHIVLQEY 1050
++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 = 177 bits (451), Expect = 6e-48
Identities = 73/248 (29%), Positives = 105/248 (42%), Gaps = 20/248 (8%)
Query: 233 IKQGGTYLITGGTGRLGMLFSDYLINKYSTNLILSGRSKLNSII------YKKLKKFNNK 286
+K GG YL+TGG G +G + L +Y L+L GRS L L+ +
Sbjct: 202 LKPGGVYLVTGGAGGIGRALARALARRYGARLVLLGRSPLPPEEEWKAQTLAALEALGAR 261
Query: 287 AIYIQVDVSDKLKMISEINSIINNIGPIDGVLHIAGISGLTSNILEANYKNFYSVLSSKI 346
+YI DV+D + + + G IDGV+H AG+ + +F +VL+ K+
Sbjct: 262 VLYISADVTDAAAVRRLLEKVRERYGAIDGVIHAAGVLRDALLAQKTAE-DFEAVLAPKV 320
Query: 347 SGTIALNYALENTILKLQKNKLDFVCYFSSSSAILGDFGSCDYAMGNRFQTVYAKYLNNK 406
G + L AL + LDF FSS SA G G DYA N F +A YL
Sbjct: 321 DGLLNLAQALAD-------EPLDFFVLFSSVSAFFGGAGQADYAAANAFLDAFAAYLRQ- 372
Query: 407 NIYKKYTNKLITINWPLWNNSKFKIGNNEQTDFYFKSSKQKVLHENDGLKLFEQLLIQDK 466
+ ++++INWP W + + +GL+ EQ L D
Sbjct: 373 ---RGPQGRVLSINWPAWREGGMAADL--GARELLARAGLLPIEPEEGLQALEQALSSDL 427
Query: 467 IQYLVLSG 474
Q LV G
Sbjct: 428 PQVLVSPG 435
Score = 33.5 bits (77), Expect = 0.69
Identities = 8/11 (72%), Positives = 10/11 (90%)
Query: 1036 FGMSGTNAHIV 1046
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 = 161 bits (409), Expect = 3e-46
Identities = 53/120 (44%), Positives = 78/120 (65%), Gaps = 2/120 (1%)
Query: 881 HAIIRGSGINYDG-KTNGITAPNGISQTELIKSVYKKSNLNPEDINYIITHGTGTKLGDP 939
+A+IRGS +N DG NG+TAPNG +Q I++ + L+PED++Y+ HGTGT LGDP
Sbjct: 1 YAVIRGSAVNQDGAAHNGLTAPNGPAQARAIRAALADAGLDPEDVDYVEAHGTGTPLGDP 60
Query: 940 VEINALHDVFKNKTYNQKFCAITSNKSNIGHTFAASGLVSLINLVQSIKYKIIPASLHCE 999
+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 = 162 bits (412), Expect = 4e-43
Identities = 84/337 (24%), Positives = 143/337 (42%), Gaps = 30/337 (8%)
Query: 729 ALEDAGYGPNQ-IANQKIGMFVG------VEEGSNYQDRLDQVNLTSTHNAILSARLA-- 779
AL DAG + ++G+ VG + VN + +LS
Sbjct: 83 ALADAGITDPYEVHPSEVGVVVGSGMGGLRFLRRGGKLDARAVNPYVSPKWMLSPNTVAG 142
Query: 780 ----YFMDLKGPVMAINTACSSSLVATHIACQSLRQHECDTAISAGVNLMISPE---AYI 832
+ GP+ AC+++L A +A +++R + D + GV E +
Sbjct: 143 WVNILLLSSHGPIKTPVGACATALEALDLAVEAIRSGKADIVVVGGVED-PLEEGLSGFA 201
Query: 833 AM--TSAGMLSPDGKCYVFDERANGLVPSEAVVAVVLKRLSRALSDGDPIHAIIRGSGIN 890
M S P+ FDE +G V +E +VL+R AL+ G PI+ + G+
Sbjct: 202 NMGALSTAEEEPEEMSRPFDETRDGFVEAEGAGVLVLERAELALARGAPIYGRVAGTAST 261
Query: 891 YDGKTNGITAPNGISQTELIKSVYKKSNLNPEDINYIITHGTGTKLGDPVEINALHDVFK 950
DG + A G I++ K+ L+ +D++ I HGT T D E A+ +V
Sbjct: 262 TDGAGRSVPAG-GKGIARAIRTALAKAGLSLDDLDVISAHGTSTPANDVAESRAIAEVAG 320
Query: 951 NKTYNQKFCAITSNKSNIGHTFAASGLVSLINLVQSIKYKIIPASLHCEKENNYIILKNS 1010
+T+ K+ GH+ A+G + LI +QS+++ +IP + + + +
Sbjct: 321 ALGAPL---PVTAQKALFGHSKGAAGALQLIGALQSLEHGLIPPTANLDDVD---PDVEH 374
Query: 1011 PFYINKSNKKWNTVNEKLRIGAVSAFGMSGTNAHIVL 1047
+ 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 = 144 bits (364), Expect = 2e-38
Identities = 71/332 (21%), Positives = 117/332 (35%), Gaps = 85/332 (25%)
Query: 718 RQRHLLQESWL-ALEDAGYGPNQIANQKIGMFVGVEEGSNYQDRLDQVNLTSTHNAILSA 776
L E+ A+ DAG I +G G E S +
Sbjct: 6 TASELGFEAAEQAIADAGLSKGPIVGVIVGTTGGSGEFSG-----------------AAG 48
Query: 777 RLAYFMDLK-GPVMAINTACSSSLVATHIACQSLRQHECDTAISAGVNLMISPEAYIAMT 835
+LAY + + GP ++N AC++ L A +A Q ++ + D ++ G
Sbjct: 49 QLAYHLGISGGPAYSVNQACATGLTALALAVQQVQNGKADIVLAGGSEE----------- 97
Query: 836 SAGMLSPDGKCYVFDERANGLVPSEAVVAVVLKRLSRALSDGDPIHAIIRGSGINYDGKT 895
V + A V++ AL G A I + +DG +
Sbjct: 98 --------------------FVFGDGAAAAVVESEEHALRRGAHPQAEIVSTAATFDGAS 137
Query: 896 NGITAPNGISQTELIKSVYKKSNLNPEDINYIITHGTGTKLGDPVEINALHDVFKNKTYN 955
+ A +G + + + L P DI+Y+ HGTGT +GD VE+ D
Sbjct: 138 -MVPAVSGEGLARAARKALEGAGLTPSDIDYVEAHGTGTPIGDAVELALGLDPD-----G 191
Query: 956 QKFCAITSNKSNIGHTFAASGLVSLINLVQSIKYKIIPASLHCEKENNYIILKNSPFYIN 1015
+ A+++ GH A+GL L L+ ++++ IP
Sbjct: 192 VRSPAVSATLIMTGHPLGAAGLAILDELLLMLEHEFIP---------------------- 229
Query: 1016 KSNKKWNTVNEKLRIGAVSAFGMSGTNAHIVL 1047
+ 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 = 134 bits (339), Expect = 5e-36
Identities = 53/194 (27%), Positives = 88/194 (45%), Gaps = 22/194 (11%)
Query: 237 GTYLITGGTGRLGMLFSDYLINKYSTNLILSGRSKLNS----IIYKKLKKFNNKAIYIQV 292
GTYLITGG G LG + +L + + L+L RS ++ + +L+ + +
Sbjct: 1 GTYLITGGLGGLGRALARWLAERGARRLVLLSRSGPDAPGAAALLAELEAAGARVTVVAC 60
Query: 293 DVSDKLKMISEINSIINNIGPIDGVLHIAGISGLTSNILEANYKNFYSVLSSKISGTIAL 352
DV+D+ + + + +I GP+ GV+H AG+ + + F +VL+ K +G L
Sbjct: 61 DVADRDALAAVLAAIPAVEGPLTGVIHAAGVLDDGV-LASLTPERFAAVLAPKAAGAWNL 119
Query: 353 NYALENTILKLQKNKLDFVCYFSSSSAILGDFGSCDYAMGNRFQTVYAKYLNNKNIYKKY 412
+ + LDF FSS + +LG G +YA N F A+Y +
Sbjct: 120 HELTADL-------PLDFFVLFSSIAGVLGSPGQANYAAANAFLDALAEYRRARG----- 167
Query: 413 TNKL--ITINWPLW 424
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 = 130 bits (329), Expect = 1e-34
Identities = 53/193 (27%), Positives = 89/193 (46%), Gaps = 20/193 (10%)
Query: 237 GTYLITGGTGRLGMLFSDYLINKYSTNLILSGRSKLNS-----IIYKKLKKFNNKAIYIQ 291
GTYL+TGG G LG+ + +L + + +L+L RS ++ +L+ + +
Sbjct: 1 GTYLVTGGLGGLGLELARWLAERGARHLVLLSRSGAPDPEAEALL-AELEARGAEVTVVA 59
Query: 292 VDVSDKLKMISEINSIINNIGPIDGVLHIAGISGLTSNILEANYKNFYSVLSSKISGTIA 351
DVSD+ + + + I + P+ GV+H AG+ + ++F VL+ K++G
Sbjct: 60 CDVSDRDAVRALLAEIRADGPPLRGVIHAAGVLRDAL-LANMTAEDFARVLAPKVTGAWN 118
Query: 352 LNYALENTILKLQKNKLDFVCYFSSSSAILGDFGSCDYAMGNRFQTVYAKYLNNKNIYKK 411
L+ A + LDF FSS + +LG G +YA N F A Y + +
Sbjct: 119 LHEATRDR-------PLDFFVLFSSIAGVLGSPGQANYAAANAFLDALAHYRRAQGL--- 168
Query: 412 YTNKLITINWPLW 424
+INW W
Sbjct: 169 ---PATSINWGPW 178
>gnl|CDD|235653 PRK05952, PRK05952, 3-oxoacyl-(acyl carrier protein) synthase II;
Reviewed.
Length = 381
Score = 134 bits (340), Expect = 5e-34
Identities = 92/340 (27%), Positives = 141/340 (41%), Gaps = 46/340 (13%)
Query: 729 ALEDAGYGP-------------------NQIANQKIGMFVGVEEGSNYQDRLDQVNLTST 769
AL+DAG P ++A Q +E + ++ LD T
Sbjct: 67 ALKDAGLTPPLTDCGVVIGSSRGCQGQWEKLARQMYQGDDSPDEELDLENWLD----TLP 122
Query: 770 H-NAILSARLAYFMDLKGPVMAINTACSSSLVATHIACQSLRQHECDTAISAGVNLMISP 828
H AI +AR +GPV+A AC++ L A + ++ +C I+ V I+P
Sbjct: 123 HQAAIAAARQI---GTQGPVLAPMAACATGLWAIAQGVELIQTGQCQRVIAGAVEAPITP 179
Query: 829 EAYIAMTSAGMLSPDGKCYVFDERANGLVPSEAVVAVVLKRLSRALSDGDPIHAIIRGSG 888
G L+ G Y FD + GLV E +VL+ A G I+ I G G
Sbjct: 180 LTLAGFQQMGALAKTG-AYPFDRQREGLVLGEGGAILVLESAELAQKRGAKIYGQILGFG 238
Query: 889 INYDGKTNGITAPNGISQTELIKSVYKKSNLNPEDINYIITHGTGTKLGDPVEINALHDV 948
+ D P+G S I+ +S L PEDI+YI HGT T+L D E N + +
Sbjct: 239 LTCDAYHMSAPEPDGKSAIAAIQQCLARSGLTPEDIDYIHAHGTATRLNDQREANLIQAL 298
Query: 949 FKNKTYNQKFCAITSNKSNIGHTFAASGLVSLINLVQSIKYKIIPASLHCEKENNYIILK 1008
F ++ A++S K GHT ASG + + + +++++ +P C + L+
Sbjct: 299 FPHRV------AVSSTKGATGHTLGASGALGVAFSLLALRHQQLPP---C------VGLQ 343
Query: 1009 NSPFYINKSNKKWNTVNEKLRIGAVSAFGMSGTNAHIVLQ 1048
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 = 132 bits (336), Expect = 4e-33
Identities = 113/434 (26%), Positives = 187/434 (43%), Gaps = 69/434 (15%)
Query: 643 PAARNINEFWKILINNKDVISEIPEKIFDWKLYYENPIKSSNKINSKWYGSIPGIDEFDP 702
P + EFW+ L+ K I I FD ++ + K G + FDP
Sbjct: 13 PLGNGVEEFWENLLAGKSGIGPI--TRFD-----------ASDLPVKIAGEVKD---FDP 56
Query: 703 LFFEISPLEAERMDPRQRHLLQESWLALEDAGYGPNQIANQKIGMFV-----GVEEGSNY 757
+ I EA RMD ++ L + A+ED+G + +++G+ + G+E
Sbjct: 57 EDY-IDKKEARRMDRFIQYALAAAKEAVEDSGLDIEEEDAERVGVIIGSGIGGLETIEEQ 115
Query: 758 QDRLDQ---------------VNLTSTHNAILSARLAYFMDLKGPVMAINTACSSSLVAT 802
L + +N+ + +I KGP A+ TAC++ A
Sbjct: 116 HIVLLEKGPRRVSPFFIPMSIINMAAGQISI-------RYGAKGPNHAVVTACATGTHAI 168
Query: 803 HIACQSLRQHECDTAISAGVNLMISPEAYIAMTSAGMLS-----PDGKCYVFDERANGLV 857
A + +++ + D I+ G I+P + LS P+ FD+ +G V
Sbjct: 169 GDAFRLIQRGDADVMIAGGAEAAITPLGIAGFAAMKALSTRNDDPEKASRPFDKDRDGFV 228
Query: 858 PSEAVVAVVLKRLSRALSDGDPIHAIIRGSGINYDGKTNGITAP--NGISQTELIKSVYK 915
E +VL+ L A + G I+A I G G++ D ITAP G +++ K
Sbjct: 229 MGEGAGVLVLEELEHAKARGAKIYAEIVGYGMSGDA--YHITAPAPEGEGAARAMRAALK 286
Query: 916 KSNLNPEDINYIITHGTGTKLGDPVEINALHDVFKNKTYNQKFCAITSNKSNIGHTFAAS 975
+ +NPED++YI HGT T LGD E A+ VF + Y A++S KS GH A+
Sbjct: 287 DAGINPEDVDYINAHGTSTPLGDKAETKAIKRVFGDHAYK---LAVSSTKSMTGHLLGAA 343
Query: 976 GLVSLINLVQSIKYKIIPASLHCEKENNYIILKNSPFYINKSNKKWNTVNEKLRIG-AVS 1034
G + I V +++ I+P +++ + + L P N++ + +I A+S
Sbjct: 344 GAIEAIFTVLALRDGIVPPTINLDNPDPECDLDYVP---NEA--------REAKIDYALS 392
Query: 1035 -AFGMSGTNAHIVL 1047
+FG G NA +V
Sbjct: 393 NSFGFGGHNASLVF 406
>gnl|CDD|240245 PTZ00050, PTZ00050, 3-oxoacyl-acyl carrier protein synthase;
Provisional.
Length = 421
Score = 132 bits (333), Expect = 1e-32
Identities = 103/442 (23%), Positives = 175/442 (39%), Gaps = 58/442 (13%)
Query: 643 PAARNINEFWKILINNKDVISEIPE-------KIFDWKLYYENPIKSSNKINSKWYGSIP 695
P W+ LI K I ++ E I + K +I ++ S
Sbjct: 4 PLGVGAESTWEALIAGKSGIRKLTEFPKFLPDCIPEQKALENLVAAMPCQIAAEVDQS-- 61
Query: 696 GIDEFDPLFFEISPLEAERMDPRQRHLLQESWLALEDAGYGPNQIANQ-KIGMFVGVEEG 754
EFDP F + E + + AL DA +Q +IG+ +G G
Sbjct: 62 ---EFDPSDFAPTKRE----SRATHFAMAAAREALADAKLDILSEKDQERIGVNIGSGIG 114
Query: 755 S----------NYQDRLDQVN-------LTSTHNAILSARLAYFMDLKGPVMAINTACSS 797
S Y+ +V+ L + +++ + LKGP + TAC++
Sbjct: 115 SLADLTDEMKTLYEKGHSRVSPYFIPKILGNMAAGLVAIKH----KLKGPSGSAVTACAT 170
Query: 798 SLVATHIACQSLRQHECDTAISAGVNLMISPEAYIAMTSAGMLS------PDGKCYVFDE 851
A + ++ E D I G I+P ++ + L P FD+
Sbjct: 171 GAHCIGEAFRWIKYGEADIMICGGTEASITPVSFAGFSRMRALCTKYNDDPQRASRPFDK 230
Query: 852 RANGLVPSEAVVAVVLKRLSRALSDGDPIHAIIRGSGINYDGKTNGITAP--NGISQTEL 909
G V E +VL+ L AL G I+A IRG G + D + ITAP +G
Sbjct: 231 DRAGFVMGEGAGILVLEELEHALRRGAKIYAEIRGYGSSSDA--HHITAPHPDGRGARRC 288
Query: 910 IKSVYKKS-NLNPEDINYIITHGTGTKLGDPVEINALHDVFKNKTYNQKFCAITSNKSNI 968
+++ K N+N D++Y+ H T T +GD +E+ A+ VF + + ++S K +
Sbjct: 289 MENALKDGANININDVDYVNAHATSTPIGDKIELKAIKKVFGDSGAPK--LYVSSTKGGL 346
Query: 969 GHTFAASGLVSLINLVQSIKYKIIPASLHCEKENNYIILKNSPFYINKSNKKWNTVNEKL 1028
GH A+G V I + S+ +IIP +++ E ++ +N K + +
Sbjct: 347 GHLLGAAGAVESIVTILSLYEQIIPPTINLEN-------PDAECDLNLVQGKTAHPLQSI 399
Query: 1029 RIGAVSAFGMSGTNAHIVLQEY 1050
++FG G N ++ +Y
Sbjct: 400 DAVLSTSFGFGGVNTALLFTKY 421
>gnl|CDD|235781 PRK06333, PRK06333, 3-oxoacyl-(acyl carrier protein) synthase II;
Reviewed.
Length = 424
Score = 126 bits (318), Expect = 8e-31
Identities = 104/463 (22%), Positives = 184/463 (39%), Gaps = 89/463 (19%)
Query: 633 IAIIGMSGRFPAARNINEFWKILINNKDVISEIPEKIFDWKLYYENPIKSSNKINSKWYG 692
I + GM P + FW+ L+ + I + + + +K G
Sbjct: 6 IVVTGMGAVSPLGCGVETFWQRLLAGQSGIRTLTDFPVG-------------DLATKIGG 52
Query: 693 SIPGIDE-----FDPLFFEISPLEAERMDPRQRHLLQESWLALEDAGYGPNQIANQK--- 744
+P + E FDP + + P + +MD + + AL AG+ P+ + +++
Sbjct: 53 QVPDLAEDAEAGFDPDRY-LDPKDQRKMDRFILFAMAAAKEALAQAGWDPDTLEDRERTA 111
Query: 745 ------IGMFVGVEEGSNYQDRLDQ---------------VNLTSTHNAILSARLAYFMD 783
+G F + E LD N+ + H +I R +
Sbjct: 112 TIIGSGVGGFPAIAEA---VRTLDSRGPRRLSPFTIPSFLTNMAAGHVSI---RYGF--- 162
Query: 784 LKGPVMAINTACSSSLVATHIACQSLRQHECDTAISAGVNLMISPEAYIAMTSAGMLS-- 841
KGP+ A TAC++ + A A + +R E D A+ G I + +A LS
Sbjct: 163 -KGPLGAPVTACAAGVQAIGDAARLIRSGEADVAVCGGTEAAIDRVSLAGFAAARALSTR 221
Query: 842 ----PDGKCYVFDERANGLVPSEAVVAVVLKRLSRALSDGDPIHAIIRGSGINYDGKTNG 897
P+ FD +G V E +V++ L AL+ G P A + G G + D
Sbjct: 222 FNDAPEQASRPFDRDRDGFVMGEGAGILVIETLEHALARGAPPLAELVGYGTSADAYH-- 279
Query: 898 ITAP--NGISQTELIKSVYKKSNLNPEDINYIITHGTGTKLGDPVEINALHDVFKNKTYN 955
+TA +G + +++ + PE++ ++ H T T +GD E+ A+ VF +
Sbjct: 280 MTAGPEDGEGARRAMLIALRQAGIPPEEVQHLNAHATSTPVGDLGEVAAIKKVFG----H 335
Query: 956 QKFCAITSNKSNIGHTFAASGLVSLINLVQSIKYKIIPASLHCE------KENNYIILKN 1009
A++S KS GH A+G V I + +++ +I P +L+ E + + + K
Sbjct: 336 VSGLAVSSTKSATGHLLGAAGGVEAIFTILALRDQIAPPTLNLENPDPAAEGLDVVANKA 395
Query: 1010 SPFYINKSNKKWNTVNEKLRIGAVS-AFGMSGTNAHIVLQEYI 1051
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 = 123 bits (311), Expect = 8e-30
Identities = 114/438 (26%), Positives = 183/438 (41%), Gaps = 71/438 (16%)
Query: 643 PAARNINEFWKILINNKDVISEIPEKIFDWKLYYENPIKSSNKINSKWYGSIPGIDEFDP 702
P ++ WK L+ K I I L K G + F+P
Sbjct: 14 PLGNDVESTWKNLLAGKSGIGPI-THFDTSDL------------AVKIAGEVKD---FNP 57
Query: 703 LFFEISPLEAERMDPRQRHLLQESWLALEDAGYGPNQIANQKIGMFVG--------VEEG 754
+ +S EA RMD ++ + + A+EDAG + +IG+ +G +EE
Sbjct: 58 DDY-MSRKEARRMDRFIQYGIAAAKQAVEDAGLEITEENADRIGVIIGSGIGGLETIEEQ 116
Query: 755 SNYQDRLDQ---------------VNLTSTHNAILSARLAYFMDLKGPVMAINTACSSSL 799
L + +N+ + H +I KGP +I TAC++
Sbjct: 117 ---HITLLEKGPRRVSPFFVPMAIINMAAGHVSIR-------YGAKGPNHSIVTACATGA 166
Query: 800 VATHIACQSLRQHECDTAISAGVNLMISPEAYIAMTSAGMLS-----PDGKCYVFDERAN 854
A A + + + D ++ G I+P +A LS P+ FD+ +
Sbjct: 167 HAIGDAARLIAYGDADVMVAGGAEAAITPLGIAGFAAARALSTRNDDPERASRPFDKDRD 226
Query: 855 GLVPSEAVVAVVLKRLSRALSDGDPIHAIIRGSGINYDGKTNGITAP--NGISQTELIKS 912
G V E +VL+ L A + G I+A + G G+ D +TAP +G +K
Sbjct: 227 GFVMGEGAGILVLEELEHAKARGAKIYAEVVGYGMTGDAYH--MTAPAPDGEGAARAMKL 284
Query: 913 VYKKSNLNPEDINYIITHGTGTKLGDPVEINALHDVFKNKTYNQKFCAITSNKSNIGHTF 972
K + +NPEDI+YI HGT T GD E A+ VF Y A++S KS GH
Sbjct: 285 ALKDAGINPEDIDYINAHGTSTPAGDKAETQAIKRVFGEHAYK---VAVSSTKSMTGHLL 341
Query: 973 AASGLVSLINLVQSIKYKIIPASLHCEKENNYIILKNSPFYINKSNKKWNTVNEKLRIGA 1032
A+G V I V +I+ ++IP +++ + + L P N++ ++ K+
Sbjct: 342 GAAGAVEAIFSVLAIRDQVIPPTINLDNPDEECDLDYVP---NEARER------KIDYAL 392
Query: 1033 VSAFGMSGTNAHIVLQEY 1050
++FG GTNA +V + Y
Sbjct: 393 SNSFGFGGTNASLVFKRY 410
>gnl|CDD|180839 PRK07103, PRK07103, polyketide beta-ketoacyl:acyl carrier protein
synthase; Validated.
Length = 410
Score = 122 bits (308), Expect = 1e-29
Identities = 84/288 (29%), Positives = 127/288 (44%), Gaps = 43/288 (14%)
Query: 723 LQESWLALEDAGYGPNQIANQKIGMFVGVEEGSNYQDRLDQVNLTST---HNAILSARLA 779
+E+W DA GP +IG+ VG GSN Q R +Q + T A L
Sbjct: 88 AREAW---RDAALGPVDPD--RIGLVVG---GSNLQQR-EQALVHETYRDRPAFLRPSYG 138
Query: 780 -YFMD------------LKGPVMAINTACSSSLVATHIACQSLRQHECDTAISAGVNLM- 825
FMD ++G + A +S +A A + ++ D I+ G LM
Sbjct: 139 LSFMDTDLVGLCSEQFGIRGEGFTVGGASASGQLAVIQAARLVQSGSVDACIAVG-ALMD 197
Query: 826 ISPEAYIAMTSAG-MLS------PDGKCYVFDERANGLVPSEAVVAVVLKRLSRALSDGD 878
+S A+ S G M S P+ C FD+ +G + EA AVVL+ A G
Sbjct: 198 LSYWECQALRSLGAMGSDRFADEPEAACRPFDQDRDGFIYGEACGAVVLESAESARRRGA 257
Query: 879 PIHAIIRGSGINYDGKTNGITAPNGISQTELIKSVYKKSNLNPEDINYIITHGTGTKLGD 938
+A + G + D P+ + +I++ +++ L PEDI+Y+ HGTG+ LGD
Sbjct: 258 RPYAKLLGWSMRLDANRG--PDPSLEGEMRVIRAALRRAGLGPEDIDYVNPHGTGSPLGD 315
Query: 939 PVEINALHDVFKNKTYNQKFCAITSNKSNIGHTFAASGLVSLI-NLVQ 985
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 = 112 bits (281), Expect = 6e-26
Identities = 101/373 (27%), Positives = 162/373 (43%), Gaps = 64/373 (17%)
Query: 692 GSIPGIDEFDPLFFEISPLEAERMDPRQRHLLQESWLALEDAGYGPNQIANQKIGMFVGV 751
G PG PLF P+E E W A +A VG
Sbjct: 95 GDFPG-----PLFLAAPPVELE-------------WPARF-------ALAAA-----VGD 124
Query: 752 EEGSNYQDRLDQVNLTSTHNAI--------LSARLAYFMDLKGPVMAINTACSSSLVATH 803
+ +Y DRL + +A+ ++ RLA +G ++++TAC+S A
Sbjct: 125 NDAPSY-DRLLRAARGGRFDALHERFQFGSIADRLADRFGTRGLPISLSTACASGATAIQ 183
Query: 804 IACQSLRQHECDTAISAGVNLMISPEAYI--AMTSAGMLS-----PDGKCYVFDERANGL 856
+ +++R+ E D A+ + +S EA I ++ SA LS P+ F + +G
Sbjct: 184 LGVEAIRRGETDRALCIATDGSVSAEALIRFSLLSA--LSTQNDPPEKASKPFSKDRDGF 241
Query: 857 VPSEAVVAVVLKRLSRALSDGDPIHAIIRGSGINYDGKTNGITAPNGISQTELIKSVYKK 916
V +E A+VL+ L A++ G I I+ G G D ++P+G I++
Sbjct: 242 VMAEGAGALVLESLESAVARGAKILGIVAGCGEKADSFHRTRSSPDGSPAIGAIRAALAD 301
Query: 917 SNLNPEDINYIITHGTGTKLGDPVEINALHDVFKNKTYNQKFCAITSNKSNIGHTFAASG 976
+ L PE I+YI HGT T D +E L VF + + ++SNKS IGHT A+G
Sbjct: 302 AGLTPEQIDYINAHGTSTPENDKMEYLGLSAVFGERLAS---IPVSSNKSMIGHTLTAAG 358
Query: 977 LVSLINLVQSIKYKIIPASLHCEKENNYIILKNSPFYINKSNKKWNTVNEKLRIGAV--S 1034
V + + +I+ +P +++ + + I L P N R+ AV +
Sbjct: 359 AVEAVFSLLTIQTGRLPPTINYDNPDPAIPLDVVP------NVA-----RDARVTAVLSN 407
Query: 1035 AFGMSGTNAHIVL 1047
+FG G NA +VL
Sbjct: 408 SFGFGGQNASLVL 420
>gnl|CDD|215449 PLN02836, PLN02836, 3-oxoacyl-[acyl-carrier-protein] synthase.
Length = 437
Score = 109 bits (274), Expect = 4e-25
Identities = 106/458 (23%), Positives = 180/458 (39%), Gaps = 75/458 (16%)
Query: 633 IAIIGMSGRFPAARNINEFWKILINNKDVISEI-----PEKIFDWKLYYENPIKSSNKIN 687
+ + G+ P + W+ LI + + + K D E + + +++
Sbjct: 8 VVVTGLGLVTPLGCGVETTWRRLIAGECGVRALTQDDLKMKSED----EETQLYTLDQLP 63
Query: 688 SKWYGSIP---GIDEFDPLFFEISPLEAERMDPRQRHLLQESWLALEDAGYGP-NQIANQ 743
S+ +P G +FD E L + + L + AL DA + P A +
Sbjct: 64 SRVAALVPRGTGPGDFD----EELWLNSRSSSRFIGYALCAADEALSDARWLPSEDEAKE 119
Query: 744 KIGMFVGVEEGS-------------NYQDRLDQ-------VNLTSTHNAILSARLAYFMD 783
+ G+ +G GS RL +N+ + H +S R
Sbjct: 120 RTGVSIGGGIGSITDILEAAQLICEKRLRRLSPFFVPRILINMAAGH---VSIRYG---- 172
Query: 784 LKGPVMAINTACSSSLVATHIACQSLRQHECDTAISAGVNLMISPEAYIAMTSAGMLS-- 841
+GP A TAC++ + A + ++ + D ++ G I + + + LS
Sbjct: 173 FQGPNHAAVTACATGAHSIGDAFRMIQFGDADVMVAGGTESSIDALSIAGFSRSRALSTK 232
Query: 842 ----PDGKCYVFDERANGLVPSEAVVAVVLKRLSRALSDGDPIHAIIRGSGINYDGKTNG 897
P FD +G V E +VL+ L A G I+A +RG G++ D +
Sbjct: 233 FNSCPTEASRPFDCDRDGFVIGEGAGVLVLEELEHAKRRGAKIYAEVRGYGMSGDA--HH 290
Query: 898 ITAP--NGISQTELIKSVYKKSNLNPEDINYIITHGTGTKLGDPVEINALHDVFKNKTYN 955
IT P +G + ++S L+P ++Y+ H T T LGD VE A+ VF +
Sbjct: 291 ITQPHEDGRGAVLAMTRALQQSGLHPNQVDYVNAHATSTPLGDAVEARAIKTVFSEHATS 350
Query: 956 QKFCAITSNKSNIGHTFAASGLVSLINLVQSIKYKIIPASLHCEK-----ENNYIILKNS 1010
A +S K GH A+G V I V +I + I P +L+ E+ ++ ++ L S
Sbjct: 351 GGL-AFSSTKGATGHLLGAAGAVEAIFSVLAIHHGIAPPTLNLERPDPIFDDGFVPLTAS 409
Query: 1011 PFYINKSNKKWNTVNEKLRIGAVS-AFGMSGTNAHIVL 1047
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 = 105 bits (263), Expect = 2e-24
Identities = 79/294 (26%), Positives = 130/294 (44%), Gaps = 25/294 (8%)
Query: 764 VNLTSTHNAILSARLAYFMDLKGPVMAINTACSSSLVATHIACQSLRQHECDTAISAGVN 823
VNL + H +I KGP+ A TAC++ + A A + +R +E D A+ G
Sbjct: 67 VNLAAGHVSIKH-------HFKGPIGAPVTACAAGVQAIGDAVRMIRNNEADVALCGGAE 119
Query: 824 LMISPEAYIAMTSAGMLS------PDGKCYVFDERANGLVPSEAVVAVVLKRLSRALSDG 877
+I + +A LS P+ FD +G V E ++++ L AL+ G
Sbjct: 120 AVIDTVSLAGFAAARALSTHFNSTPEKASRPFDTARDGFVMGEGAGLLIIEELEHALARG 179
Query: 878 DPIHAIIRGSGINYDGKTNGITAPNGISQTELIKSVYKKSNLNPEDINYIITHGTGTKLG 937
A I G G + D A +G +K +++ + PE + ++ H T T +G
Sbjct: 180 AKPLAEIVGYGTSADAYHMTSGAEDGDGAYRAMKIALRQAGITPEQVQHLNAHATSTPVG 239
Query: 938 DPVEINALHDVFKNKTYNQKFCAITSNKSNIGHTFAASGLVSLINLVQSIKYKIIPASLH 997
D EINA+ +F AITS KS GH A+G + I V +++ +I+PA+L+
Sbjct: 240 DLGEINAIKHLFGESNA----LAITSTKSATGHLLGAAGGLETIFTVLALRDQIVPATLN 295
Query: 998 CEKENNYIILKNSPFYINKSNKKWNTVNEKLRIGAVSAFGMSGTNAHIVLQEYI 1051
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 = 96.6 bits (241), Expect = 4e-21
Identities = 48/164 (29%), Positives = 83/164 (50%), Gaps = 15/164 (9%)
Query: 237 GTYLITGGTGRLGMLFSDYLINKYSTNLILSGRSKLNSIIYKKLKKFNNKAIYI---QVD 293
TYLITGG G LG+L +++L+ + + +L+L+GR ++ + + + D
Sbjct: 150 ATYLITGGLGGLGLLVAEWLVERGARHLVLTGRRAPSAAARQAIAALEEAGAEVVVLAAD 209
Query: 294 VSDKLKMISEINSIINNIGPIDGVLHIAGI--SGLTSNILEANYKNFYSVLSSKISGTIA 351
VSD+ + + + I ++ P+ GV+H AG+ G+ +N F VL+ K+ G
Sbjct: 210 VSDRDALAAALAQIRASLPPLRGVIHAAGVLDDGVLANQDWE---RFRKVLAPKVQGAWN 266
Query: 352 LNYALENTILKLQKNKLDFVCYFSSSSAILGDFGSCDYAMGNRF 395
L+ ++ LDF FSS +++LG G +YA N F
Sbjct: 267 LHQLTQD-------LPLDFFVLFSSVASLLGSPGQANYAAANAF 303
>gnl|CDD|215720 pfam00106, adh_short, short chain dehydrogenase. This family
contains a wide variety of dehydrogenases.
Length = 167
Score = 89.9 bits (224), Expect = 1e-20
Identities = 44/163 (26%), Positives = 77/163 (47%), Gaps = 13/163 (7%)
Query: 237 GTYLITGGTGRLGMLFSDYLINKYSTNLILSGRS----KLNSIIYKKLKKFNNKAIYIQV 292
GT LITGGTG LG+ + +L + + +L+L R ++ +L+ +
Sbjct: 1 GTVLITGGTGGLGLALARWLAAEGARHLVLVSRRGPAPGAAELV-AELEALGAEVTVAAC 59
Query: 293 DVSDKLKMISEINSIINNIGPIDGVLHIAGISGLTSNILEANYKNFYSVLSSKISGTIAL 352
DV+D+ + + + ++ +GP+DGV+H AG+ + E + F VL+ K++G L
Sbjct: 60 DVADRDALAALLAALPAALGPLDGVVHNAGVLDDG-PLEELTPERFERVLAPKVTGAWNL 118
Query: 353 NYALENTILKLQKNKLDFVCYFSSSSAILGDFGSCDYAMGNRF 395
+ + L FSS + +LG G +YA N
Sbjct: 119 HEL-------TRDLDLGAFVLFSSVAGVLGSPGQANYAAANAA 154
>gnl|CDD|181657 PRK09116, PRK09116, 3-oxoacyl-(acyl carrier protein) synthase II;
Reviewed.
Length = 405
Score = 95.4 bits (238), Expect = 1e-20
Identities = 78/273 (28%), Positives = 114/273 (41%), Gaps = 38/273 (13%)
Query: 728 LALEDAG-YGPNQIANQKIGMFVGVEEGSN-----YQDRL---DQVNLTST-------HN 771
LALEDAG G + + ++G+ G GS + L +T+T H
Sbjct: 83 LALEDAGLLGDPILTDGRMGIAYGSSTGSTDPIGAFGTMLLEGSMSGITATTYVRMMPHT 142
Query: 772 AILSARLAYFMDLKGPVMAINTACSSSLVATHIACQSLRQHECDTAISAGVNLMISPEAY 831
+ + F LKG V+ ++AC+S A ++++ ++ G + EA
Sbjct: 143 T--AVNVGLFFGLKGRVIPTSSACTSGSQGIGYAYEAIKYGYQTVMLAGGAEELCPTEAA 200
Query: 832 I--------AMTSAGMLSPDGKCYVFDERANGLVPSEAVVAVVLKRLSRALSDGDPIHAI 883
+ A L+P FD +GLV E +VL+ L A + G I+A
Sbjct: 201 VFDTLFATSTRNDAPELTPRP----FDANRDGLVIGEGAGTLVLEELEHAKARGATIYAE 256
Query: 884 IRGSGINYDGKTNGITAPNGISQTELIKSVYKKSNLNPEDINYIITHGTGTKLGDPVEIN 943
I G G N DG +T P + ++ K + L PEDI Y+ HGT T GD E
Sbjct: 257 IVGFGTNSDGAH--VTQPQAETMQIAMELALKDAGLAPEDIGYVNAHGTATDRGDIAESQ 314
Query: 944 ALHDVFKNKTYNQKFCAITSNKSNIGHTFAASG 976
A VF + I+S KS GHT A G
Sbjct: 315 ATAAVFGARM------PISSLKSYFGHTLGACG 341
>gnl|CDD|236129 PRK07910, PRK07910, 3-oxoacyl-(acyl carrier protein) synthase II;
Reviewed.
Length = 418
Score = 94.8 bits (236), Expect = 2e-20
Identities = 76/281 (27%), Positives = 112/281 (39%), Gaps = 38/281 (13%)
Query: 785 KGPVMAINTACSSSLVATHIACQSLRQHECDTAISAGVNLMIS--PEAYIAMTSAGMLS- 841
K V+ +AC+S A A + + E D AI GV I P A A M +
Sbjct: 161 KAGVITPVSACASGSEAIAQAWRQIVLGEADIAICGGVETRIEAVPIAGFAQMRIVMSTN 220
Query: 842 ---PDGKCYVFDERANGLVPSEAVVAVVLKRLSRALSDGDPIHAIIRGSGINYDGKTNGI 898
P G C FD+ +G V E +V++ A + G I A I G+ I DG
Sbjct: 221 NDDPAGACRPFDKDRDGFVFGEGGALMVIETEEHAKARGANILARIMGASITSDGFHMVA 280
Query: 899 TAPNGISQTELIKSVYKKSNLNPEDINYIITHGTGTKLGDPVEINALHDVFKNKTYNQKF 958
PNG + + + L P DI+++ H TGT +GD E A+ N
Sbjct: 281 PDPNGERAGHAMTRAIELAGLTPGDIDHVNAHATGTSVGDVAEGKAI-----NNALGGHR 335
Query: 959 CAITSNKSNIGHTFAASGLVSLINLVQSIKYKIIPASLHCEKENNYI---ILKNSP---- 1011
A+ + KS +GH+ A G V I V +++ +IP +L+ E + I ++ P
Sbjct: 336 PAVYAPKSALGHSVGAVGAVESILTVLALRDGVIPPTLNLENLDPEIDLDVVAGEPRPGN 395
Query: 1012 --FYINKSNKKWNTVNEKLRIGAVSAFGMSGTNAHIVLQEY 1050
+ 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 = 92.1 bits (229), Expect = 1e-19
Identities = 53/174 (30%), Positives = 81/174 (46%), Gaps = 22/174 (12%)
Query: 235 QGGTYLITGGTGRLGMLFSDYLINKYSTNLILSGRSKLNSIIYKKLKKFNNKAIYI---Q 291
GTYLITGG G LG+L + +L + + +L+L R + + +
Sbjct: 149 LDGTYLITGGLGGLGLLVARWLAARGARHLVLLSRRGPAPRAAARAALLRAGGARVSVVR 208
Query: 292 VDVSDK--LK-MISEINSIINNIGPIDGVLHIAGI--SGLTSNILEANYKNFYSVLSSKI 346
DV+D L +++E+ GP+ GV+H AG+ L + + A F +VL++K+
Sbjct: 209 CDVTDPAALAALLAELA----AGGPLAGVIHAAGVLRDALLAELTPAA---FAAVLAAKV 261
Query: 347 SGTIALNYALENTILKLQKNKLDFVCYFSSSSAILGDFGSCDYAMGNRFQTVYA 400
+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 = 91.2 bits (226), Expect = 3e-19
Identities = 93/442 (21%), Positives = 179/442 (40%), Gaps = 51/442 (11%)
Query: 629 SEELIAIIGMSGRFPAARNINEFWKILINNKDVISEIPEKIFDWKLYYENPIKSSNKINS 688
S+ + + GM P + WK L+ + I I FD + ++
Sbjct: 2 SKRRVVVTGMGMLSPVGNTVESSWKALLAGQSGIVNIEH--FD-----------TTNFST 48
Query: 689 KWYGSIPGIDEFDPLFFEISPLEAERMDPRQRHLLQESWLALEDAGYGPNQIANQKIGMF 748
++ G + F+ + +S +A +MD ++ + AL+D+G + +IG+
Sbjct: 49 RFAGLVKD---FNCEEY-MSKKDARKMDLFIQYGIAAGIQALDDSGLEVTEENAHRIGVA 104
Query: 749 VG----------------VEEGSNYQDRLDQVNLTSTHNAILSARLAYFMDLKGPVMAIN 792
+G VE+G ++ + ST +++ L+ L+GP +AI+
Sbjct: 105 IGSGIGGLGLIEAGHQALVEKGPR---KVSPFFVPSTIVNMIAGNLSIMRGLRGPNIAIS 161
Query: 793 TACSSSLVATHIACQSLRQHECDTAISAGVNLMISPEAYIAMTSAGMLS-----PDGKCY 847
TAC++ L A + + + D ++ G +P +A LS P
Sbjct: 162 TACTTGLHNIGHAARMIAYGDADAMVAGGAEKASTPLGMAGFGAAKALSTRNDEPQKASR 221
Query: 848 VFDERANGLVPSEAVVAVVLKRLSRALSDGDPIHAIIRGSGINYDGKTNGITAPNGISQT 907
+D+ +G V + +VL+ A + G I+A + G G++ D + +G
Sbjct: 222 PWDKDRDGFVLGDGAGMMVLEEYEHAKARGAKIYAELVGFGMSGDAYHMTSPSEDGSGGA 281
Query: 908 ELIKSVYKKSNLNPEDINYIITHGTGTKLGDPVEINALHDVFKNKTYNQKFCAITSNKSN 967
+++ + + + E I Y+ HGT T GD EI + Q ++S KS
Sbjct: 282 LAMEAAMRDAGVTGEQIGYVNAHGTSTPAGDVAEIKGIKRALGEAGSKQVL--VSSTKSM 339
Query: 968 IGHTFAASGLVSLINLVQSIKYKIIPASLHCEKENNYIILKNSPFYINKSNKKWNTVNEK 1027
GH A+G V I V S+ +I+P +++ + + + P K E
Sbjct: 340 TGHLLGAAGSVEAIITVMSLVDQIVPPTINLDDPEEGLDIDLVPHTARKV--------ES 391
Query: 1028 LRIGAVSAFGMSGTNAHIVLQE 1049
+ ++FG GTN ++ ++
Sbjct: 392 MEYAICNSFGFGGTNGSLIFKK 413
>gnl|CDD|215421 PLN02787, PLN02787, 3-oxoacyl-[acyl-carrier-protein] synthase II.
Length = 540
Score = 92.0 bits (228), Expect = 5e-19
Identities = 113/459 (24%), Positives = 178/459 (38%), Gaps = 68/459 (14%)
Query: 622 NKNTDINSEELIAIIGMSGRFPAARNINEFWKILINNKDVISEIPEKIFDWKLYYENPIK 681
K ++ + GM P + + F+ L+ ISEI FD + P +
Sbjct: 121 KKKPLTKQRRVV-VTGMGVVSPLGHDPDVFYNNLLEGVSGISEIER--FDCSQF---PTR 174
Query: 682 SSNKINS----KWYGSIPGIDEFDPLFFEISPLEAERMDPRQRHLLQESWLALEDAGYGP 737
+ +I S W ++P ++RMD +LL AL D G
Sbjct: 175 IAGEIKSFSTDGW----------------VAPKLSKRMDKFMLYLLTAGKKALADGGITE 218
Query: 738 ---NQIANQKIGMFVGVEEGSN--YQDRLDQVNLT-----------STHNAILSARLAYF 781
++ K G+ +G G + D ++ + ++ +T N + SA LA
Sbjct: 219 DVMKELDKTKCGVLIGSAMGGMKVFNDAIEALRISYRKMNPFCVPFATTN-MGSAMLA-- 275
Query: 782 MDL--KGPVMAINTACSSSLVATHIACQSLRQHECDTAISAGVNLMISPEAYIAMTSAGM 839
MDL GP +I+TAC++S A + + E D + G + I P +
Sbjct: 276 MDLGWMGPNYSISTACATSNFCILNAANHIIRGEADVMLCGGSDAAIIPIGLGGFVACRA 335
Query: 840 LS-----PDGKCYVFDERANGLVPSEAVVAVVLKRLSRALSDGDPIHAIIRGSGINYDGK 894
LS P +D +G V E ++L+ L A G I+A G D
Sbjct: 336 LSQRNDDPTKASRPWDMNRDGFVMGEGAGVLLLEELEHAKKRGANIYAEFLGGSFTCDAY 395
Query: 895 TNGITAPNGISQTELIKSVYKKSNLNPEDINYIITHGTGTKLGDPVEINALHDVFKNKTY 954
P G I+ +S ++ ED+NYI H T TK GD E AL F
Sbjct: 396 HMTEPHPEGAGVILCIEKALAQSGVSKEDVNYINAHATSTKAGDLKEYQALMRCFGQ--- 452
Query: 955 NQKFCAITSNKSNIGHTFAASGLVSLINLVQSIKYKIIPASLHCEKENNYIILKNSPFYI 1014
N + + S KS IGH A+G V I VQ+I+ + +++ E + + K +
Sbjct: 453 NPEL-RVNSTKSMIGHLLGAAGAVEAIATVQAIRTGWVHPNINLENPESGVDTK----VL 507
Query: 1015 NKSNKKWNTVNEKLRIGAV--SAFGMSGTNAHIVLQEYI 1051
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 = 85.9 bits (213), Expect = 2e-17
Identities = 86/346 (24%), Positives = 150/346 (43%), Gaps = 47/346 (13%)
Query: 729 ALEDAGYGPNQIANQKIGMFVGVEEGSNYQ--------------DRLDQVNLTSTHNAIL 774
A+ DAG Q++N + G+ G GS R+ +T + +
Sbjct: 82 AIADAGLSEEQVSNPRTGLIAGSGGGSTRNQVEAADAMRGPRGPKRVGPYAVTKAMASTV 141
Query: 775 SARLAYFMDLKGPVMAINTACSSSLVATHIACQSLRQHECDTAISAGV-----NLMISPE 829
SA LA +KG +I++AC++S A + ++ + D + G + +
Sbjct: 142 SACLATPFKIKGVNYSISSACATSAHCIGNAVEQIQLGKQDIVFAGGGEELDWEMSCLFD 201
Query: 830 AYIAMTSAGMLSPDGKCYVFDERANGLVPSEAVVAVVLKRLSRALSDGDPIHAIIRGSGI 889
A A+++ +P+ +D +G V + VV++ L AL+ G I+A I G G
Sbjct: 202 AMGALSTKYNDTPEKASRAYDANRDGFVIAGGGGVVVVEELEHALARGAKIYAEIVGYGA 261
Query: 890 NYDGKTNGITAPNGISQTELIKSVYKKSNLNPEDINYIITHGTGTKLGDPVEINALHDVF 949
DG + AP+G ++ + I+YI THGT T +GD E+ A+ +VF
Sbjct: 262 TSDGYD--MVAPSGEGAVRCMQMALATVD---TPIDYINTHGTSTPVGDVKELGAIREVF 316
Query: 950 KNKTYNQKFCAITSNKSNIGHTFAASGLVSLINLVQSIKYKIIPASLHCEK-----ENNY 1004
+K+ AI++ KS GH+ A+G+ I + +++ I S + E+
Sbjct: 317 GDKS-----PAISATKSLTGHSLGAAGVQEAIYSLLMMEHGFIAPSANIEELDPQAAGMP 371
Query: 1005 IILKNSPFYINKSNKKWNTVNEKLRIGAVSAFGMSGTNAHIVLQEY 1050
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 = 79.4 bits (196), Expect = 2e-15
Identities = 94/373 (25%), Positives = 163/373 (43%), Gaps = 37/373 (9%)
Query: 697 IDEFDPLFFEISPLEAERMDPRQRHL-LQESWLALEDAGYGPNQIANQK--------IGM 747
I +FDP + P E ++ D R L L+ + A++DAG+ P ++ ++ IG
Sbjct: 52 ITDFDPTEV-MDPKEVKKAD-RFIQLGLKAAREAMKDAGFLPEELDAERFGVSSASGIGG 109
Query: 748 FVGVEEGSNY-----QDRLDQVNLTSTHNAILSARLAYFMDLKGPVMAINTACSSSLVAT 802
+E+ S ++ + S +L ++ LKGP ++ TAC++ A
Sbjct: 110 LPNIEKNSIICFEKGPRKISPFFIPSALVNMLGGFISIEHGLKGPNLSSVTACAAGTHAI 169
Query: 803 HIACQSLRQHECDTAISAGVNLMISPEAYIAMTSAGMLS-----PDGKCYVFDERANGLV 857
A +++ D + G I P + LS P FD+ +G V
Sbjct: 170 IEAVKTIMLGGADKMLVVGAESAICPVGIGGFAAMKALSTRNDDPKKASRPFDKDRDGFV 229
Query: 858 PSEAVVAVVLKRLSRALSDGDPIHAIIRGSGINYDGKTNGITAPNGISQTELIKSVYKKS 917
E A+VL+ A G I+A I G G G N IT+P +K+ + +
Sbjct: 230 MGEGAGALVLEEYESAKKRGAKIYAEIIGFG--ESGDANHITSPAPEGPLRAMKAALEMA 287
Query: 918 NLNPEDINYIITHGTGTKLGDPVEINALHDVFKNKTYNQKFCAITSNKSNIGHTFAASGL 977
NP+ I+YI HGT T D E AL ++F +K +K ++S K IGH A+G
Sbjct: 288 G-NPK-IDYINAHGTSTPYNDKNETAALKELFGSK---EKVPPVSSTKGQIGHCLGAAGA 342
Query: 978 VSLINLVQSIKYKIIPASLHCEKENNYIILKNSPFYINKSNKKWNTVNEKLRIGAVSAFG 1037
+ + + +++ I+P +++ E + L P N + K +L + ++FG
Sbjct: 343 IEAVISIMAMRDGILPPTINQETPDPECDLDYIP---NVARKA------ELNVVMSNSFG 393
Query: 1038 MSGTNAHIVLQEY 1050
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 = 75.9 bits (187), Expect = 3e-14
Identities = 85/370 (22%), Positives = 147/370 (39%), Gaps = 53/370 (14%)
Query: 650 EFWKILINNKDVISEIPEKIFDWKLYYENPIKSSNKINSKWYGSIPGIDEFDPLFFEISP 709
E+WK +++ + + I FD Y P + + G +P D + L + P
Sbjct: 20 EYWKAVLDGRSGLGPITR--FDPSGY---PARLA--------GEVPDFDAAEHLPGRLLP 66
Query: 710 LEAERMDPRQRHLLQESWLALEDAGYGPNQIANQKIGMFV-----GVEEGSNYQDRLDQV 764
+ D R L + AL DAG P + +G+ G E G Q L
Sbjct: 67 ----QTDRMTRLALAAADWALADAGVDPAALPPYDMGVVTASAAGGFEFG---QRELQ-- 117
Query: 765 NLTSTHNAILSA--RLAYFM-----------DLKGPVMAINTACSSSLVATHIACQSLRQ 811
L S +SA A+F ++GP + + L A A + +R+
Sbjct: 118 KLWSKGPRHVSAYQSFAWFYAVNTGQISIRHGMRGPSGVVVAEQAGGLDALAQARRLVRR 177
Query: 812 HECDTAISAGVNLMISPEAYIAMTSAGMLSPDG---KCYV-FDERANGLVPSEAVVAVVL 867
+S GV+ + P ++A S+G LS + Y+ FD A G VP E +VL
Sbjct: 178 GTP-LVVSGGVDSALCPWGWVAQLSSGRLSTSDDPARAYLPFDAAAAGYVPGEGGAILVL 236
Query: 868 KRLSRALSDGDPIHAIIRGSGINYDGKTNGITAPNGISQTELIKSVYKKSNLNPEDINYI 927
+ + A G ++ I G +D G P G+++ I+ + L PED++ +
Sbjct: 237 EDAAAARERGARVYGEIAGYAATFDPPP-GSGRPPGLAR--AIRLALADAGLTPEDVDVV 293
Query: 928 ITHGTGTKLGDPVEINALHDVFKNKTYNQKFCAITSNKSNIGHTFAASGLVSLINLVQSI 987
G D E AL VF + +T+ K+ G +A + + + ++
Sbjct: 294 FADAAGVPELDRAEAAALAAVFGPRG-----VPVTAPKTMTGRLYAGGAPLDVATALLAL 348
Query: 988 KYKIIPASLH 997
+ +IP +++
Sbjct: 349 RDGVIPPTVN 358
>gnl|CDD|236398 PRK09185, PRK09185, 3-oxoacyl-(acyl carrier protein) synthase I;
Reviewed.
Length = 392
Score = 74.9 bits (185), Expect = 5e-14
Identities = 66/226 (29%), Positives = 95/226 (42%), Gaps = 30/226 (13%)
Query: 779 AYFMDLKGPVMAINTACSSSLVATHIACQSLRQHECDTAISAGVNLMISPEAYIAMT--- 835
AY L GP I+TACSSS A + L CD AI GV+ + +T
Sbjct: 145 AYL-GLSGPAYTISTACSSSAKVFASARRLLEAGLCDAAIVGGVDSLC------RLTLNG 197
Query: 836 --SAGMLSPDGKCYVFDERANGLVPSEAVVAVVLKRLSRALSDGDPIHAIIRGSGINYDG 893
S LSP C F +G+ EA A L L R D + + G G + D
Sbjct: 198 FNSLESLSP-QPCRPFSANRDGINIGEAA-AFFL--LERE--DDAAV--ALLGVGESSDA 249
Query: 894 KTNGITAPN--GISQTELIKSVYKKSNLNPEDINYIITHGTGTKLGDPVEINALHDVFKN 951
+ ++AP+ G+ ++ + L P DI YI HGT T L D +E A+ VF +
Sbjct: 250 --HHMSAPHPEGLGAILAMQQALADAGLAPADIGYINLHGTATPLNDAMESRAVAAVFGD 307
Query: 952 KTYNQKFCAITSNKSNIGHTFAASGLVSLINLVQSIKYKIIPASLH 997
+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 = 70.9 bits (174), Expect = 2e-12
Identities = 61/181 (33%), Positives = 96/181 (53%), Gaps = 14/181 (7%)
Query: 230 NSYIKQGGTYLITGGTGRLGMLFSDYLINKYST-NLILSGRSKLN---SIIYKKLKKFNN 285
N I G +YLITGG+G LG+ +L+ + + N+I+ RS + ++ ++ K N
Sbjct: 212 NYPINLGKSYLITGGSGGLGLEILKWLVKRGAVENIIILSRSGMKWELELLIREWKSQNI 271
Query: 286 KAIYIQVDVSDKLKMISEINSIIN--NIGPIDGVLHIAGISGLTSNILEANYKN-FYSVL 342
K ++ VDVSD + IN I+N IGPI G+ H+A + L +LE + ++ F SV
Sbjct: 272 KFHFVSVDVSDVSSLEKAINLILNAPKIGPIGGIFHLAFV--LIDKVLEIDTESLFISVN 329
Query: 343 SSKISGTIALNYALENTILKLQKNKLDFVCYFSSSSAILGDFGSCDYAMGNRFQTVYAKY 402
+K+ G I L+ +I + K LD+ FSS S+I G G C+Y N ++Y
Sbjct: 330 KAKVMGAINLH---NQSIKRCWK--LDYFVLFSSVSSIRGSAGQCNYVCANSVLDSLSRY 384
Query: 403 L 403
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 = 52.9 bits (128), Expect = 6e-09
Identities = 18/65 (27%), Positives = 30/65 (46%), Gaps = 1/65 (1%)
Query: 509 IKNHICNILNTKKSEIYKNKNLADYGFDSISLAEFSRILSKFYSLDIMPSIFFSYSTLER 568
++ + +L EI + +L D G DS+ E L + + ++I PS F + TL
Sbjct: 3 LREIVAEVLGIP-DEIDPDDDLFDLGLDSLLAVELLARLEEEFGVEIPPSDLFEHPTLGE 61
Query: 569 LITYF 573
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 = 57.3 bits (139), Expect = 3e-08
Identities = 50/190 (26%), Positives = 78/190 (41%), Gaps = 66/190 (34%)
Query: 237 GTYLITGGTGRLGMLFSDYLINKYS-TNLILSGRS---------------KLNSIIYKKL 280
GT LITGGTG LG L + +L+ ++ +L+L R L
Sbjct: 194 GTVLITGGTGTLGALLARHLVTEHGVRHLLLVSRRGPDAPGAAELVAELAALG------- 246
Query: 281 KKFNNKAIYIQV-----DVSDKLKMISEINSIINNI---GPIDGVLHIAG------ISGL 326
A +V DV+D+ + + +++ + P+ V+H AG ++ L
Sbjct: 247 ------A---EVTVAACDVADR----AALAALLAAVPADHPLTAVVHAAGVLDDGVLTSL 293
Query: 327 TSNILEANYKNFYSVLSSKISGTIALNYALENTILKLQKNKLD-FVCYFSSSSAILGDFG 385
T L+A VL K+ L+ E T + L FV FSS++ +LG G
Sbjct: 294 TPERLDA-------VLRPKVDAAWHLH---ELT----RDLDLAAFV-LFSSAAGVLGSPG 338
Query: 386 SCDYAMGNRF 395
+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 = 51.0 bits (122), Expect = 1e-06
Identities = 33/161 (20%), Positives = 65/161 (40%), Gaps = 10/161 (6%)
Query: 235 QGGTYLITGGTGRLGMLFSDYLINKYSTNLILSGRS---KLNSIIYKKLKKFNNKAIYIQ 291
G L+TG + +G + L + + ++ + RS ++ + +A +
Sbjct: 4 SGKVALVTGASSGIGRAIARALAREGARVVVAARRSEEEAAEALAAAIKEAGGGRAAAVA 63
Query: 292 VDVSDKLKMISE-INSIINNIGPIDGVLHIAGISGLTSNILEANYKNFYSVLSSKISGTI 350
DVSD + + + + G ID +++ AGI+G + + E +++ V+ + G
Sbjct: 64 ADVSDDEESVEALVAAAEEEFGRIDILVNNAGIAGPDAPLEELTEEDWDRVIDVNLLGAF 123
Query: 351 ALNYALENTILKLQKNKLDFVCYFSSSSAILGDFGSCDYAM 391
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 = 46.1 bits (110), Expect = 3e-06
Identities = 10/43 (23%), Positives = 16/43 (37%)
Query: 530 LADYGFDSISLAEFSRILSKFYSLDIMPSIFFSYSTLERLITY 572
D G DS+ E L L + ++ F + T L +
Sbjct: 39 FRDLGLDSLMAVELRNRLEAATGLRLPATLVFDHPTPAALAEH 81
>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 = 47.3 bits (113), Expect = 2e-05
Identities = 23/121 (19%), Positives = 53/121 (43%), Gaps = 10/121 (8%)
Query: 240 LITGGTGRLGM----LFSDYLINKYSTNLILSGRSKLNSIIYKKLKKFNNKAIYIQVDVS 295
L+TG + +G + + ++L+ R++ ++ A+ +Q DVS
Sbjct: 2 LVTGASSGIGRAIARRLA-----REGAKVVLADRNEEALAELAAIEALGGNAVAVQADVS 56
Query: 296 DKLKMISEINSIINNIGPIDGVLHIAGISGLTSNILEANYKNFYSVLSSKISGTIALNYA 355
D+ + + + + G +D +++ AGI+ + E +++ VL ++G L A
Sbjct: 57 DEEDVEALVEEALEEFGRLDILVNNAGIARP-GPLEELTDEDWDRVLDVNLTGVFLLTRA 115
Query: 356 L 356
Sbjct: 116 A 116
>gnl|CDD|223377 COG0300, DltE, Short-chain dehydrogenases of various substrate
specificities [General function prediction only].
Length = 265
Score = 47.6 bits (114), Expect = 2e-05
Identities = 32/123 (26%), Positives = 52/123 (42%), Gaps = 14/123 (11%)
Query: 234 KQGGTYLITGGTGRLGMLFSDYLINKYSTNLILSGRS--KLNSIIYKKLKKFNNKAIYIQ 291
+G T LITG + +G + L + NLIL R KL ++ + K + I
Sbjct: 4 MKGKTALITGASSGIGAELAKQLARR-GYNLILVARREDKLEALAKELEDKTGVEVEVIP 62
Query: 292 VDVSDKLKMISEI-NSIINNIGPIDGVLHIAGISGLTSNILEANYKNFYSVLSSKISGTI 350
D+SD + + + + + GPID +++ AG G LE + + I
Sbjct: 63 ADLSD-PEALERLEDELKERGGPIDVLVNNAGF-GTFGPFLELSLD--------EEEEMI 112
Query: 351 ALN 353
LN
Sbjct: 113 QLN 115
>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 = 5e-05
Identities = 40/184 (21%), Positives = 77/184 (41%), Gaps = 12/184 (6%)
Query: 240 LITGGTGRLGMLFSDYLINKYSTNLILSGRSK--LNSIIYKKLKKFNNKAIYIQVDVSDK 297
LITG + +G + N+ L+ R L+ + +L N +DV+D+
Sbjct: 2 LITGASSGIGRALAREFAKA-GYNVALAARRTDRLDELK-AELLNPNPSVEVEILDVTDE 59
Query: 298 LKMISEINSIINNIGPIDGVLHIAGISGLTSNILEANYKNFYSVLSSKISGTIA-LNYAL 356
+ I + +G +D V+ AG+ G +++ + ++K F + + + G A L AL
Sbjct: 60 ERNQLVIAELEAELGGLDLVIINAGV-GKGTSLGDLSFKAFRETIDTNLLGAAAILEAAL 118
Query: 357 ENTILKLQKNKLDFVCYFSSSSAILGDFGSCDYAMGNRFQTVYAKYLNNKNIYKKYTNKL 416
+ + + SS +A+ G G+ Y+ + A+ L KK ++
Sbjct: 119 P----QFRAKGRGHLVLISSVAALRGLPGAAAYSASKAALSSLAESLRYD--VKKRGIRV 172
Query: 417 ITIN 420
IN
Sbjct: 173 TVIN 176
>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 = 45.3 bits (108), Expect = 1e-04
Identities = 23/98 (23%), Positives = 34/98 (34%), Gaps = 18/98 (18%)
Query: 729 ALEDAGYGPNQIANQKIGMFVGVEEGSNYQDRLDQVNLTSTHNAILSARLAYFMDLKG-P 787
AL+DAG P I + VG G +Q A +A ++ L G P
Sbjct: 27 ALDDAGLEPADI----DAVVVGNAAGGRFQS-------------FPGALIAEYLGLLGKP 69
Query: 788 VMAINTACSSSLVATHIACQSLRQHECDTAISAGVNLM 825
+ A +S A A ++ D + G M
Sbjct: 70 ATRVEAAGASGSAAVRAAAAAIASGLADVVLVVGAEKM 107
>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 = 44.6 bits (106), Expect = 1e-04
Identities = 40/166 (24%), Positives = 70/166 (42%), Gaps = 22/166 (13%)
Query: 236 GGTYLITGGTGRLGMLFSDYLINKYSTNLILSGRS--KLNSIIYKKLKKFNN---KAIYI 290
G LITGG+ +G + L+ + N+I+ RS KL + + + N K YI
Sbjct: 1 GKHVLITGGSSGIGKALAKELVKE-GANVIIVARSESKLEEAVEEIEAEANASGQKVSYI 59
Query: 291 QVDVSDKLKMISEINSIINNIGPIDGVLHIAGIS------GLTSNILEANYKNFYSVLSS 344
D+SD ++ + GP D V++ AGIS LT+ E Y
Sbjct: 60 SADLSDYEEVEQAFAQAVEKGGPPDLVVNCAGISIPGLFEDLTAEEFERGMDVNY----- 114
Query: 345 KISGTIALNYALENTILKLQKNKLDFVCYFSSSSAILGDFGSCDYA 390
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 = 2e-04
Identities = 25/121 (20%), Positives = 52/121 (42%), Gaps = 1/121 (0%)
Query: 235 QGGTYLITGGTGRLGMLFSDYLINKYSTNLILSGRSKLNSIIYKKLKKFNNKAIYIQVDV 294
+G L+TG + +G + L + +I S + + ++K +A DV
Sbjct: 4 KGKVALVTGASRGIGFGIASGLAEAGANIVINSRNEEKAEEAQQLIEKEGVEATAFTCDV 63
Query: 295 SDKLKMISEINSIINNIGPIDGVLHIAGISGLTSNILEANYKNFYSVLSSKISGTIALNY 354
SD+ + + + +I + G ID +++ AGI E + V+ ++G ++
Sbjct: 64 SDEEAIKAAVEAIEEDFGKIDILVNNAGI-IRRHPAEEFPEAEWRDVIDVNLNGVFFVSQ 122
Query: 355 A 355
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 = 2e-04
Identities = 29/120 (24%), Positives = 53/120 (44%), Gaps = 5/120 (4%)
Query: 235 QGGTYLITGGTGRLGMLFSDYLINKYSTNLILSGRS--KLNSIIYKKLKKFNNKAIYIQV 292
+ LITG G +G F L++ LIL+ + L + + + N+ I +++
Sbjct: 1 EDKIILITGAAGLIGKAFCKALLS-AGARLILADINAPALEQLKEELTNLYKNRVIALEL 59
Query: 293 DVSDKLKMISEINSIINNIGPIDGVLHIAGIS--GLTSNILEANYKNFYSVLSSKISGTI 350
D++ K + I S + G ID +++ A S S E Y+ + VL+ + G
Sbjct: 60 DITSKESIKELIESYLEKFGRIDILINNAYPSPKVWGSRFEEFPYEQWNEVLNVNLGGAF 119
>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 = 43.4 bits (103), Expect = 4e-04
Identities = 17/67 (25%), Positives = 30/67 (44%), Gaps = 2/67 (2%)
Query: 787 PVMAINTACSSSLVATHIACQSLRQHECDTAISAGVNLMISPEAYIAMTSAGMLSPDGKC 846
P + IN C S L A +A Q++R + D ++ GV M A + ++ + + G
Sbjct: 78 PAVTINKVCGSGLKAVALAAQAIRAGDADIVVAGGVESM--SNAPYVLPASRVGARMGDA 135
Query: 847 YVFDERA 853
+ D
Sbjct: 136 KLVDTML 142
>gnl|CDD|223261 COG0183, PaaJ, Acetyl-CoA acetyltransferase [Lipid metabolism].
Length = 392
Score = 42.3 bits (100), Expect = 0.001
Identities = 20/71 (28%), Positives = 33/71 (46%), Gaps = 8/71 (11%)
Query: 772 AILSARLAYFMDLKGPVMAINTACSSSLVATHIACQSLRQHECDTAISAGV----NLMIS 827
A L+A L + P + +N AC+S L A +A Q++ E D ++ GV + +
Sbjct: 73 AALAAGLPGSV----PAVTVNRACASGLAAVRLAAQAIASGEADVVLAGGVEKMSDAPMG 128
Query: 828 PEAYIAMTSAG 838
E + SA
Sbjct: 129 REGVRVLDSAV 139
>gnl|CDD|187628 cd05370, SDR_c2, classical (c) SDR, subgroup 2. Short-chain
dehydrogenases/reductases (SDRs, aka Tyrosine-dependent
oxidoreductases) are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold (alpha/beta folding
pattern with a central beta-sheet), an NAD(P)(H)-binding
region, and a structurally diverse C-terminal region.
Classical SDRs are typically about 250 residues long,
while extended SDRs are approximately 350 residues.
Sequence identity between different SDR enzymes are
typically in the 15-30% range, but the enzymes share the
Rossmann fold NAD-binding motif and characteristic
NAD-binding and catalytic sequence patterns. These
enzymes catalyze a wide range of activities including
the metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 228
Score = 41.1 bits (97), Expect = 0.001
Identities = 24/88 (27%), Positives = 38/88 (43%), Gaps = 14/88 (15%)
Query: 235 QGGTYLITGGTGRLGMLFSDYLINKYSTNLILSGRSKLNSIIYKKLKKFNNKAIYIQVDV 294
G T LITGGT +G+ + + +T +I++GR + + KK I +DV
Sbjct: 4 TGNTVLITGGTSGIGLALARKFLEAGNT-VIITGRREER---LAEAKKELPNIHTIVLDV 59
Query: 295 SDK----------LKMISEINSIINNIG 312
D L ++ +INN G
Sbjct: 60 GDAESVEALAEALLSEYPNLDILINNAG 87
>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: 236 GGTYLITGGTGRLGMLFSDYLINKYSTNLILSGRSKLNSIIYKKL-KKFNNKAIYIQVDV 294
G ++TGG+ +G+ + L + I+ + ++L KK+ K + DV
Sbjct: 8 GKVAIVTGGSRGIGLAIARALAEAGADVAIIYNSAPRAEEKAEELAKKYGVKTKAYKCDV 67
Query: 295 SDKLKMISEINSIINNIGPIDGVLHIAGISGLTSNILEANYKNFYSVLSSKISGT 349
S + + I + G ID ++ AGI+ L+ Y+ + V+ ++G
Sbjct: 68 SSQESVEKTFKQIQKDFGKIDILIANAGITVHKP-ALDYTYEQWNKVIDVNLNGV 121
>gnl|CDD|235546 PRK05653, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Validated.
Length = 246
Score = 40.5 bits (96), Expect = 0.003
Identities = 20/93 (21%), Positives = 44/93 (47%), Gaps = 4/93 (4%)
Query: 235 QGGTYLITGGTGRLGMLFSDYLINKYSTNLILSGRS--KLNSIIYKKLKKFNNKAIYIQV 292
QG T L+TG + +G + L +++ + ++ +L+ +A +
Sbjct: 4 QGKTALVTGASRGIGRAIALRLA-ADGAKVVIYDSNEEAAEALA-AELRAAGGEARVLVF 61
Query: 293 DVSDKLKMISEINSIINNIGPIDGVLHIAGISG 325
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 = 40.3 bits (95), Expect = 0.003
Identities = 30/148 (20%), Positives = 62/148 (41%), Gaps = 27/148 (18%)
Query: 240 LITGGTGRLGMLFSDYLINKYSTNLILSGRSKLNSIIYKKLKKFNNKAIYIQVDVSDKLK 299
L+TGGTG +G L+ + ++L R + S+ +++ + D++D
Sbjct: 2 LVTGGTGFIGSHLVRRLLQEGYEVIVLGRRRRSESLNTGRIRF-------HEGDLTDP-- 52
Query: 300 MISEINSIINNIGPIDGVLHIAGISGLTSNILEANYKNFYSVLSSKISGTI-ALNYALEN 358
+ ++ + P D V+H+A SG+ ++ + + + + GT+ L A
Sbjct: 53 --DALERLLAEVQP-DAVIHLAAQSGVGASFEDPAD-----FIRANVLGTLRLLEAARRA 104
Query: 359 TILKLQKNKLDFVCYFSSSSAILGDFGS 386
+ + F+SSS + GD
Sbjct: 105 GVKRF---------VFASSSEVYGDVAD 123
>gnl|CDD|223314 COG0236, AcpP, Acyl carrier protein [Lipid metabolism / Secondary
metabolites biosynthesis, transport, and catabolism].
Length = 80
Score = 36.9 bits (86), Expect = 0.004
Identities = 18/75 (24%), Positives = 31/75 (41%), Gaps = 1/75 (1%)
Query: 505 IENDIKNHICNILNTKKSEIYKNKNLA-DYGFDSISLAEFSRILSKFYSLDIMPSIFFSY 563
IE +K+ I L + EI + D G DS+ L E L + + ++I +
Sbjct: 6 IEERVKDIIAEQLGVDEEEITTEASFVEDLGLDSLDLVELVMALEEEFGIEIPDEELENI 65
Query: 564 STLERLITYFIKNHN 578
T+ L+ Y +
Sbjct: 66 KTVGDLVDYIEELLA 80
>gnl|CDD|181146 PRK07851, PRK07851, acetyl-CoA acetyltransferase; Provisional.
Length = 406
Score = 40.4 bits (95), Expect = 0.004
Identities = 27/91 (29%), Positives = 38/91 (41%), Gaps = 24/91 (26%)
Query: 787 PVMAINTACSSSLVATHIACQSLRQHECDTAISAGVNLMISPEAYIAMTSAGMLSPDGKC 846
P +N CSSSL T +A +++ E D ISAGV +S + S + PD K
Sbjct: 82 PGTTVNRYCSSSLQTTRMAFHAIKAGEGDVFISAGVE-TVS--RFAKGNSDSL--PDTKN 136
Query: 847 YVFDE-------------------RANGLVP 858
+F E R +GL+P
Sbjct: 137 PLFAEAQARTAARAEGGAEAWHDPREDGLLP 167
>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: 776 ARLAYF---MDLKGPVMAINTACSSSLVATHIACQSLRQHECDTAISAGVNLM 825
AR A + P +N C+S L A +A Q +R E D ++ GV M
Sbjct: 61 ARQAALLAGLPESVPAYTVNRQCASGLQAVILAAQLIRAGEADVVVAGGVESM 113
>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 = 39.4 bits (93), Expect = 0.007
Identities = 48/243 (19%), Positives = 74/243 (30%), Gaps = 65/243 (26%)
Query: 729 ALEDAGYGPNQIANQKIGMFVGVEEGSNYQDRLDQVNLTSTHNAIL---SARLAYFMDLK 785
ALEDAG + I D + + TST + + + + + K
Sbjct: 61 ALEDAGIDADDI------------------DLI--IVATSTPDYLFPATACLVQARLGAK 100
Query: 786 G-PVMAINTACSSSLVATHIACQSLRQHECDTAISAGVNLMISPEAYIAMT-----SAGM 839
IN ACS L A +R L++ E + S +
Sbjct: 101 NAAAFDINAACSGFLYGLSTAAGLIRSGGAKNV------LVVGAETLSRILDWTDRSTAV 154
Query: 840 LSPDGKCYVFDERANGLVPSEAVVAVVLKRLSRALSDGDPIHAI-IRGSGINYDGKTNGI 898
L DG V E ++ VL SDG + I G +
Sbjct: 155 LFGDGAGAVVLEATEE---DPGILDSVLG------SDGSGADLLTIPAGGSRSPFEDAEG 205
Query: 899 TAPNGISQ------------TELIKSVYKKSNLNPEDINYIITH--------GTGTKLGD 938
P + E I+ +K+ L P+DI++ + H +LG
Sbjct: 206 GDPYLVMDGREVFKFAVRLMPESIEEALEKAGLTPDDIDWFVPHQANLRIIEAVAKRLGL 265
Query: 939 PVE 941
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: 239 YLITGGTGRLGMLFSDYLINKYSTNLILSGRSKLNSIIYKKLKKFNNKAIYIQVDVSDKL 298
LITG + +G+ L+ + + +I + R + L +++ +++DV+D++
Sbjct: 1 VLITGASRGIGLELVRQLLARGNNTVIATCRDPSAATELAALGASHSRLHILELDVTDEI 60
Query: 299 KMISEINSIINNIGPIDGVLHIAGISGLTSNILEANYKNFYSVLSSKISGTIAL 352
+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 = 0.014
Identities = 28/121 (23%), Positives = 61/121 (50%), Gaps = 3/121 (2%)
Query: 238 TYLITGGTGRLGMLFSDYLINKYSTNLILSGR--SKLNSIIYKKLKKFNNKAIYIQVDVS 295
T LITG + +G + K LIL+GR +L + + KF K + +Q+DVS
Sbjct: 2 TVLITGASSGIG-EATARRFAKAGAKLILTGRRAERLQELADELGAKFPVKVLPLQLDVS 60
Query: 296 DKLKMISEINSIINNIGPIDGVLHIAGISGLTSNILEANYKNFYSVLSSKISGTIALNYA 355
D+ + + + ++ ID +++ AG++ EA+ +++ +++ + + G + +
Sbjct: 61 DRESIEAALENLPEEFRDIDILVNNAGLALGLDPAQEADLEDWETMIDTNVKGLLNVTRL 120
Query: 356 L 356
+
Sbjct: 121 I 121
>gnl|CDD|235688 PRK06064, PRK06064, acetyl-CoA acetyltransferase; Provisional.
Length = 389
Score = 38.3 bits (90), Expect = 0.018
Identities = 40/136 (29%), Positives = 53/136 (38%), Gaps = 30/136 (22%)
Query: 713 ERMDPRQRHLLQESWL-ALEDAGYGPNQI-----ANQKIGMFVGVEEGSNYQDRLDQVNL 766
E D R L E+ L ALEDAG I N G+FV E
Sbjct: 16 ELWDVSLRDLAVEAGLEALEDAGIDGKDIDAMYVGNMSAGLFVSQE-------------- 61
Query: 767 TSTHNAILSARLAYFMDLKG-PVMAINTACSSSLVATHIACQSLRQHECDTAISAGVNLM 825
H A L +A + L P + AC+S A A ++ E D ++AGV M
Sbjct: 62 ---HIAAL---IADYAGLAPIPATRVEAACASGGAALRQAYLAVASGEADVVLAAGVEKM 115
Query: 826 I---SPEAYIAMTSAG 838
+P+A A+ AG
Sbjct: 116 TDVPTPDATEAIARAG 131
>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 = 38.6 bits (91), Expect = 0.018
Identities = 14/39 (35%), Positives = 19/39 (48%)
Query: 787 PVMAINTACSSSLVATHIACQSLRQHECDTAISAGVNLM 825
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 = 0.022
Identities = 21/83 (25%), Positives = 34/83 (40%), Gaps = 10/83 (12%)
Query: 240 LITGGTGRLGMLFSDYLINKYSTNLILSGRSKLNSIIYKKLKKFNNKAIYIQVDVSDK-- 297
LITGG +G L + + + +IL K ++K K Y + DVS +
Sbjct: 3 LITGGGSGIGRLLALEFAKRGAKVVILDINEKGAEETANNVRKAGGKVHYYKCDVSKREE 62
Query: 298 --------LKMISEINSIINNIG 312
K + ++ +INN G
Sbjct: 63 VYEAAKKIKKEVGDVTILINNAG 85
>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 = 0.027
Identities = 10/13 (76%), Positives = 11/13 (84%)
Query: 237 GTYLITGGTGRLG 249
GT L+TGGTG LG
Sbjct: 231 GTVLVTGGTGALG 243
>gnl|CDD|168156 PRK05656, PRK05656, acetyl-CoA acetyltransferase; Provisional.
Length = 393
Score = 37.9 bits (88), Expect = 0.030
Identities = 26/100 (26%), Positives = 42/100 (42%), Gaps = 16/100 (16%)
Query: 730 LEDAGYGPNQIANQKIGMFVGVEEGSNYQDRLDQVNLTSTHNAILSARLAYFMDLKGPVM 789
LE G P Q+ +G + G N A + A L + + P M
Sbjct: 38 LEQTGLDPAQVDEVILGQVLTAGAGQN-----------PARQAAIKAGLPHSV----PAM 82
Query: 790 AINTACSSSLVATHIACQSLRQHECDTAISAGV-NLMISP 828
+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 = 37.0 bits (86), Expect = 0.033
Identities = 19/88 (21%), Positives = 35/88 (39%), Gaps = 4/88 (4%)
Query: 240 LITGGTGRLGMLFSDYLINKYSTNLILSGRSKLNSIIYKKLKKFNNKAIYIQVDVSDKLK 299
L+TG + +G+ + L + + L R N L + D D
Sbjct: 4 LVTGASRGIGIEIARALA-RDGYRVSLGLR---NPEDLAALSASGGDVEAVPYDARDPED 59
Query: 300 MISEINSIINNIGPIDGVLHIAGISGLT 327
+ ++++ + G ID ++H AGI T
Sbjct: 60 ARALVDALRDRFGRIDVLVHNAGIGRPT 87
>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 = 0.039
Identities = 20/89 (22%), Positives = 43/89 (48%), Gaps = 4/89 (4%)
Query: 236 GGTYLITGGTGRLGMLFSDYLINKYSTNLILSGRSKLNSIIYKKLKKFNNKAIYIQVDVS 295
G ++TGG LG+ + L+ + + +IL L + + + K + ++ VDV+
Sbjct: 2 GLVAVVTGGASGLGLATVERLLAQGAKVVILD----LPNSPGETVAKLGDNCRFVPVDVT 57
Query: 296 DKLKMISEINSIINNIGPIDGVLHIAGIS 324
+ + + + G +D V++ AGI+
Sbjct: 58 SEKDVKAALALAKAKFGRLDIVVNCAGIA 86
>gnl|CDD|180563 PRK06445, PRK06445, acetyl-CoA acetyltransferase; Provisional.
Length = 394
Score = 37.4 bits (87), Expect = 0.041
Identities = 29/112 (25%), Positives = 42/112 (37%), Gaps = 17/112 (15%)
Query: 714 RMDPRQRHLLQESWLALEDAGYGPNQIANQKIGMFVGVEEGSNYQDRLDQVNLTSTHNAI 773
R + L+ +E G P +I + G + V E Y R + I
Sbjct: 31 RPEELAAMLINRL---IEKTGIKPEEIDDIITGCALQVGENWLYGGR----------HPI 77
Query: 774 LSARLAYFMDLKGPVMAINTACSSSLVATHIACQSLRQHECDTAISAGVNLM 825
ARL Y + P MA++ C+SSL I + D I+ GV M
Sbjct: 78 FLARLPYNI----PAMAVDRQCASSLTTVSIGAMEIATGMADIVIAGGVEHM 125
>gnl|CDD|223409 COG0332, FabH, 3-oxoacyl-[acyl-carrier-protein].
Length = 323
Score = 37.2 bits (87), Expect = 0.042
Identities = 47/236 (19%), Positives = 75/236 (31%), Gaps = 83/236 (35%)
Query: 729 ALEDAGYGPNQIANQKIGMFVGVEEGSNYQDRLDQVNLTSTHN-------AILSARLAYF 781
ALEDAG I+ I + + TST + ++ ARL
Sbjct: 63 ALEDAG-----ISPDDIDLII---------------VATSTPDHLFPSTACLVQARLG-- 100
Query: 782 MDLKG-PVMAINTACSSSLVATHIACQSLRQHECDTAISAGVNLMISPEAYIAMTSAGML 840
L G P + ACS L A +A +R L++ E T + +L
Sbjct: 101 --LGGAPAFDLQAACSGFLYALSVADGLIRSGGYKNV------LVVGAE-----TLSRIL 147
Query: 841 SPDGKCYVFDERANGLVPSEAVVAVVLKR--------LSRALSDGDPIHAIIRGSGINYD 892
+ +R ++ + AVVL+ + SDG + Y
Sbjct: 148 D-------WTDRDTCVLFGDGAGAVVLEATEDDNGILDTDLGSDGS-------QGDLLYL 193
Query: 893 GKTNGITAPNGIS------------------QTELIKSVYKKSNLNPEDINYIITH 930
T + I+ V +K+ L PEDI++ + H
Sbjct: 194 PGGGSATPKEESGGGLLVMDGREVFKFAVRAMPKAIEEVLEKAGLTPEDIDWFVPH 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 = 0.059
Identities = 35/154 (22%), Positives = 59/154 (38%), Gaps = 36/154 (23%)
Query: 238 TYLITGGTGRLGMLFSDYLIN-KYST----NLILSGRSKLNSIIYKKLKKFNNKAIYIQV 292
L+TGG G +G L+ Y NL R L I +++ + +
Sbjct: 1 KVLVTGGAGYIGSHTVVELLEAGYDVVVLDNLSNGHREALPRIEKIRIE-------FYEG 53
Query: 293 DVSDKLKMISEINSIINNIGPIDGVLHIAGISGL---TSNILEANYKNFYSVLSSKISGT 349
D+ D+ + + + ID V+H A + + L+ +Y + GT
Sbjct: 54 DIRDRAAL----DKVFAEH-KIDAVIHFAALKAVGESVQKPLK-----YYDN---NVVGT 100
Query: 350 IALNYALENTILKLQKNKLDFVCYFSSSSAILGD 383
+ 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 = 0.063
Identities = 29/117 (24%), Positives = 50/117 (42%), Gaps = 11/117 (9%)
Query: 240 LITGGTGRLGMLFSDYLINKYSTNLILSGRSKLNSIIYKKLKKFN--NKAIYIQVDVSDK 297
+ITGG +G+ + L+ K + IL + +L+ N KA ++Q DV+
Sbjct: 4 IITGGASGIGLATAKLLLKKGAKVAILDRNENPGAA--AELQAINPKVKATFVQCDVTSW 61
Query: 298 LKMISEINSIINNIGPIDGVLHIAGISGLTSNILEANYKNFYSVLSSKISGTIALNY 354
++ + 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 = 0.091
Identities = 24/90 (26%), Positives = 41/90 (45%), Gaps = 11/90 (12%)
Query: 236 GGTYLITGGTGRLGMLFSDYLINKYSTN-LILSGRSKLNSIIYKKLKKFNNKAI-YIQVD 293
+ LITGGTG G F L+ Y+ +I+ R +L ++ +KF + + D
Sbjct: 4 NKSILITGGTGSFGKAFISRLLENYNPKKIIIYSRDELKQ--WEMQQKFPAPCLRFFIGD 61
Query: 294 VSDKLKMISEINSIINNIGPIDGVLHIAGI 323
V DK ++ + +D V+H A +
Sbjct: 62 VRDKERLTRALRG-------VDYVVHAAAL 84
>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: 235 QGGTYLITGGTGRLGMLFSDYLINKYSTNLILS--GRSKLNSIIYKKLKKFNNKAIYIQV 292
+ +ITGG LG ++YL K L L + KL + + +
Sbjct: 4 KDKVIVITGGAQGLGRAMAEYLAQK-GAKLALIDLNQEKLEEAV-AECGALGTEVRGYAA 61
Query: 293 DVSDKLKMISEINSIINNIGPIDGVLHIAGI 323
+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 = 35.6 bits (82), Expect = 0.12
Identities = 35/153 (22%), Positives = 64/153 (41%), Gaps = 5/153 (3%)
Query: 240 LITGGTGRLGMLFSDYLINKYSTNLILSGRSKLNSIIYKKLKKFNNKA--IYIQVDVSDK 297
LITGG LG+ + L + + ++ + L + A + I+ DVSD+
Sbjct: 7 LITGGGSGLGLATAVRLAKEGAKLSLVDLNEEGLEAAKAALLEIAPDAEVLLIKADVSDE 66
Query: 298 LKMISEINSIINNIGPIDGVLHIAGISGLTSNILEANYKNFYSVLSSKISGTIALNYALE 357
++ + +++ + G IDG + AGI G + + F V+S + G Y LE
Sbjct: 67 AQVEAYVDATVEQFGRIDGFFNNAGIEGKQNLTEDFGADEFDKVVSINLRGVF---YGLE 123
Query: 358 NTILKLQKNKLDFVCYFSSSSAILGDFGSCDYA 390
+ +++ + +S I G YA
Sbjct: 124 KVLKVMREQGSGMIVNTASVGGIRGVGNQSGYA 156
>gnl|CDD|235506 PRK05565, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 247
Score = 35.2 bits (82), Expect = 0.13
Identities = 20/87 (22%), Positives = 45/87 (51%), Gaps = 3/87 (3%)
Query: 240 LITGGTGRLGMLFSDYLINKYSTNLILSGRSKLNSIIY--KKLKKFNNKAIYIQVDVSDK 297
++TG +G +G + L+ K ++++ + +++K+ AI ++ DVS +
Sbjct: 9 IVTGASGGIGRAIA-ELLAKEGAKVVIAYDINEEAAQELLEEIKEEGGDAIAVKADVSSE 67
Query: 298 LKMISEINSIINNIGPIDGVLHIAGIS 324
+ + + I+ G ID +++ AGIS
Sbjct: 68 EDVENLVEQIVEKFGKIDILVNNAGIS 94
>gnl|CDD|181298 PRK08219, PRK08219, short chain dehydrogenase; Provisional.
Length = 227
Score = 34.9 bits (81), Expect = 0.15
Identities = 22/94 (23%), Positives = 42/94 (44%), Gaps = 15/94 (15%)
Query: 238 TYLITGGTGRLGMLFSDYLINKYSTNLILSGRSKLNSIIYKKLKKFNNK---AIYIQVDV 294
T LITG + +G + L + L+L GR ++L + + A VD+
Sbjct: 5 TALITGASRGIGAAIARELAPTH--TLLLGGRPA------ERLDELAAELPGATPFPVDL 56
Query: 295 SDKLKMISEINSIINNIGPIDGVLHIAGISGLTS 328
+D + + + + G +D ++H AG++ L
Sbjct: 57 TDPEAIAAAVEQL----GRLDVLVHNAGVADLGP 86
>gnl|CDD|181625 PRK09051, PRK09051, beta-ketothiolase; Provisional.
Length = 394
Score = 35.3 bits (82), Expect = 0.16
Identities = 27/105 (25%), Positives = 41/105 (39%), Gaps = 15/105 (14%)
Query: 729 ALEDAGYGPNQIANQKIGMFVGVEEGSNYQDRLDQVNLTSTHNAILSARLAYFMDLKGPV 788
AL AG P+Q+ + G + E Y R+ A ++A + + P
Sbjct: 38 ALARAGVDPDQVGHVVFGHVIPTEPRDMYLSRV----------AAINAGVP----QETPA 83
Query: 789 MAINTACSSSLVATHIACQSLRQHECDTAISAGVNLMISPEAYIA 833
+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 = 0.25
Identities = 23/84 (27%), Positives = 40/84 (47%), Gaps = 4/84 (4%)
Query: 241 ITGGTGRLGMLFSDYLINKYSTNLILSGRS--KLNSIIYKKLKKFNNKAIYIQVDVSDKL 298
ITGGTG LG + L + + GR+ K + + K++ +AI + DV D+
Sbjct: 10 ITGGTGVLGGAMARALA-QAGAKVAALGRNQEKGDKVA-KEITALGGRAIALAADVLDRA 67
Query: 299 KMISEINSIINNIGPIDGVLHIAG 322
+ 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 = 0.28
Identities = 14/39 (35%), Positives = 20/39 (51%)
Query: 787 PVMAINTACSSSLVATHIACQSLRQHECDTAISAGVNLM 825
+ +N C+S L A +A +R E D I+AGV M
Sbjct: 87 GGVTVNRFCASGLQAVAMAADRIRVGEADVMIAAGVESM 125
>gnl|CDD|187648 cd08944, SDR_c12, classical (c) SDR, subgroup 12. These are
classical SDRs, with the canonical active site tetrad
and glycine-rich NAD-binding motif. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold (alpha/beta folding pattern with a central
beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRs are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes catalyze a
wide range of activities including the metabolism of
steroids, cofactors, carbohydrates, lipids, aromatic
compounds, and amino acids, and act in redox sensing.
Classical SDRs have an TGXXX[AG]XG cofactor binding
motif and a YXXXK active site motif, with the Tyr
residue of the active site motif serving as a critical
catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 246
Score = 34.0 bits (78), Expect = 0.33
Identities = 14/63 (22%), Positives = 34/63 (53%)
Query: 287 AIYIQVDVSDKLKMISEINSIINNIGPIDGVLHIAGISGLTSNILEANYKNFYSVLSSKI 346
A+ ++VDV+D+ ++ + + G +D +++ AG LT I++ + + ++ +
Sbjct: 51 ALALRVDVTDEQQVAALFERAVEEFGGLDLLVNNAGAMHLTPAIIDTDLAVWDQTMAINL 110
Query: 347 SGT 349
GT
Sbjct: 111 RGT 113
>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 = 0.35
Identities = 23/93 (24%), Positives = 45/93 (48%), Gaps = 5/93 (5%)
Query: 235 QGGTYLITGGTGRLGMLFSDYLINKYSTNLILSGRS--KLNSIIYKKLKKFNNKAIYIQV 292
QG +ITG + +G + Y + + L+LS R +L + + L+ + +
Sbjct: 2 QGKVVIITGASSGIGEELA-YHLARLGARLVLSARREERLEEVKSECLELGAPSPHVVPL 60
Query: 293 DVSDKLKMISE-INSIINNIGPIDGVLHIAGIS 324
D+SD L+ + + + G +D +++ AGIS
Sbjct: 61 DMSD-LEDAEQVVEEALKLFGGLDILINNAGIS 92
>gnl|CDD|180595 PRK06504, PRK06504, acetyl-CoA acetyltransferase; Provisional.
Length = 390
Score = 34.3 bits (79), Expect = 0.36
Identities = 23/72 (31%), Positives = 34/72 (47%), Gaps = 13/72 (18%)
Query: 771 NAILSARLAYFMDLKGPVMAINTACSSSLVATHIACQSLRQHECDTAISAGVNLMISPEA 830
NA+L+++L + P +I+ C SS A H A Q++ D I+AGV
Sbjct: 69 NAVLASKLPESV----PGTSIDRQCGSSQQALHFAAQAVMSGTMDIVIAAGVE------- 117
Query: 831 YIAMTSAGMLSP 842
+MT M SP
Sbjct: 118 --SMTRVPMGSP 127
>gnl|CDD|236074 PRK07666, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 239
Score = 33.9 bits (78), Expect = 0.37
Identities = 27/91 (29%), Positives = 47/91 (51%), Gaps = 2/91 (2%)
Query: 235 QGGTYLITGGTGRLGMLFSDYLINKYSTNLILSGRSKLN-SIIYKKLKKFNNKAIYIQVD 293
QG LITG +G + L K N+ L R++ N + ++++ + K + D
Sbjct: 6 QGKNALITGAGRGIGRAVAIALA-KEGVNVGLLARTEENLKAVAEEVEAYGVKVVIATAD 64
Query: 294 VSDKLKMISEINSIINNIGPIDGVLHIAGIS 324
VSD ++ + I + N +G ID +++ AGIS
Sbjct: 65 VSDYEEVTAAIEQLKNELGSIDILINNAGIS 95
>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 = 33.4 bits (77), Expect = 0.57
Identities = 28/147 (19%), Positives = 57/147 (38%), Gaps = 9/147 (6%)
Query: 238 TYLITGGTGRLGMLFSDYLINK-YSTNLILSGRSK--LNSIIYKKLKKFNNKAI-YIQVD 293
++TG + +G ++ L+ + + ++L RS+ L K + + ++ D
Sbjct: 1 VIILTGASRGIGRALAEELLKRGSPSVVVLLARSEEPLQE---LKEELRPGLRVTTVKAD 57
Query: 294 VSDKLKMISEINSIINNIGPIDGVLHIAGISGLTSNILEANYKNFYSVLSSKISGTIALN 353
+SD + + +I G D +++ AG G S I + ++ + L
Sbjct: 58 LSDAAGVEQLLEAIRKLDGERDLLINNAGSLGPVSKIEFIDLDELQKYFDLNLTSPVCLT 117
Query: 354 YALENTILKLQKNKLDFVCYFSSSSAI 380
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 = 0.58
Identities = 31/133 (23%), Positives = 64/133 (48%), Gaps = 9/133 (6%)
Query: 236 GGTYLITGGTGRLGMLFSDYLINKYSTNLILSGRSKLNSI--IYKKLKKFNNKAIYIQVD 293
G L+TG + +G + L N++++ RSK ++ + +++K KAI +Q D
Sbjct: 3 GKVALVTGASSGIGKAIAIRLA-TAGANVVVNYRSKEDAAEEVVEEIKAVGGKAIAVQAD 61
Query: 294 VSDKLKMISEINSIINNIGPIDGVLHIAGISGLTSNILEANYKNFYSVLSSKISGTI--- 350
VS + +++ S I G +D +++ AG+ G S E +++ V+ ++G
Sbjct: 62 VSKEEDVVALFQSAIKEFGTLDILVNNAGLQGDAS-SHEMTLEDWNKVIDVNLTGQFLCA 120
Query: 351 --ALNYALENTIL 361
A+ ++ I
Sbjct: 121 REAIKRFRKSKIK 133
>gnl|CDD|236216 PRK08277, PRK08277, D-mannonate oxidoreductase; Provisional.
Length = 278
Score = 33.3 bits (77), Expect = 0.60
Identities = 22/85 (25%), Positives = 43/85 (50%), Gaps = 4/85 (4%)
Query: 240 LITGGTGRLGMLFSDYLINKYSTNLILSGRS--KLNSIIYKKLKKFNNKAIYIQVDVSDK 297
+ITGG G LG + L + + + R+ K +++ ++K +A+ ++ DV DK
Sbjct: 14 VITGGGGVLGGAMAKELA-RAGAKVAILDRNQEKAEAVV-AEIKAAGGEALAVKADVLDK 71
Query: 298 LKMISEINSIINNIGPIDGVLHIAG 322
+ 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 = 0.65
Identities = 39/152 (25%), Positives = 66/152 (43%), Gaps = 17/152 (11%)
Query: 235 QGGTYLITG---GTGRLGMLFSDYLINKYSTNLILSGR--SKLNSIIYKKLKKFNNK--A 287
+ L+TG G GR L Y ++ +IL GR KL ++ Y +++ A
Sbjct: 11 KDRIILVTGAGDGIGREAAL--TYA--RHGATVILLGRTEEKLEAV-YDEIEAAGGPQPA 65
Query: 288 IY-IQVDVSDKLKMISEINSIINNIGPIDGVLHIAGISGLTSNILEANYKNFYSVLSSKI 346
I + + + ++I G +DGVLH AG+ G + + + + + V+ +
Sbjct: 66 IIPLDLLTATPQNYQQLADTIEEQFGRLDGVLHNAGLLGELGPMEQQDPEVWQDVMQVNV 125
Query: 347 SGTIALNYALENTILKLQKNKLDFVCYFSSSS 378
+ T L AL +LK L F+SSS
Sbjct: 126 NATFMLTQALLPLLLKSPAASL----VFTSSS 153
>gnl|CDD|180439 PRK06171, PRK06171, sorbitol-6-phosphate 2-dehydrogenase;
Provisional.
Length = 266
Score = 33.1 bits (76), Expect = 0.75
Identities = 21/91 (23%), Positives = 38/91 (41%), Gaps = 13/91 (14%)
Query: 235 QGGTYLITGGTGRLGMLFSDYLINK--YSTNLILSGRSKLNSIIYKKLKKFNNKAIYIQV 292
QG ++TGG+ +G+ L+ N + G ++ ++
Sbjct: 8 QGKIIIVTGGSSGIGLAIVKELLANGANVVNADIHG----GDGQHENY-------QFVPT 56
Query: 293 DVSDKLKMISEINSIINNIGPIDGVLHIAGI 323
DVS ++ + II G IDG+++ AGI
Sbjct: 57 DVSSAEEVNHTVAEIIEKFGRIDGLVNNAGI 87
>gnl|CDD|180193 PRK05675, sdhA, succinate dehydrogenase flavoprotein subunit;
Reviewed.
Length = 570
Score = 33.6 bits (77), Expect = 0.77
Identities = 19/59 (32%), Positives = 31/59 (52%), Gaps = 4/59 (6%)
Query: 204 FSIMYYGNDLIRYQ----LNIKSIILKDFKNSYIKQGGTYLITGGTGRLGMLFSDYLIN 258
F +Y DL++ Q + + +I ++ + YIK T L TGG GR+ ++ LIN
Sbjct: 143 FLNEWYAVDLVKNQDGAVVGVIAICIETGETVYIKSKATVLATGGAGRIYASTTNALIN 201
>gnl|CDD|215439 PLN02819, PLN02819, lysine-ketoglutarate reductase/saccharopine
dehydrogenase.
Length = 1042
Score = 33.6 bits (77), Expect = 0.80
Identities = 17/71 (23%), Positives = 35/71 (49%), Gaps = 3/71 (4%)
Query: 612 NVSKKSNFILN--KNTDINSEELIAIIGMSGRFPAARNINEFWKILINNKD-VISEIPEK 668
NVS+ + I +T + +L + G+S + + + + + ++ ++D V + P K
Sbjct: 213 NVSQGAQEIFKLLPHTFVEPSKLPELKGISQNKISTKRVYQVYGCVVTSQDMVEHKDPSK 272
Query: 669 IFDWKLYYENP 679
FD YY +P
Sbjct: 273 QFDKADYYAHP 283
>gnl|CDD|181305 PRK08226, PRK08226, short chain dehydrogenase; Provisional.
Length = 263
Score = 32.9 bits (75), Expect = 0.80
Identities = 22/88 (25%), Positives = 38/88 (43%), Gaps = 1/88 (1%)
Query: 236 GGTYLITGGTGRLGMLFSDYLINKYSTNLILSGRSKLNSIIYKKLKKFNNKAIYIQVDVS 295
G T LITG +G + + ++ NLIL S + +L ++ + DV
Sbjct: 6 GKTALITGALQGIGEGIA-RVFARHGANLILLDISPEIEKLADELCGRGHRCTAVVADVR 64
Query: 296 DKLKMISEINSIINNIGPIDGVLHIAGI 323
D + + I G ID +++ AG+
Sbjct: 65 DPASVAAAIKRAKEKEGRIDILVNNAGV 92
>gnl|CDD|181518 PRK08643, PRK08643, acetoin reductase; Validated.
Length = 256
Score = 32.8 bits (75), Expect = 0.94
Identities = 18/66 (27%), Positives = 37/66 (56%), Gaps = 2/66 (3%)
Query: 278 KKLKKFNNKAIYIQVDVSDKLKMISEINSIINNIGPIDGVLHIAGISGLT--SNILEANY 335
KL K KAI ++ DVSD+ ++ + + +++ G ++ V++ AG++ T I E +
Sbjct: 44 DKLSKDGGKAIAVKADVSDRDQVFAAVRQVVDTFGDLNVVVNNAGVAPTTPIETITEEQF 103
Query: 336 KNFYSV 341
Y++
Sbjct: 104 DKVYNI 109
>gnl|CDD|237218 PRK12825, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 249
Score = 32.5 bits (75), Expect = 1.0
Identities = 18/85 (21%), Positives = 37/85 (43%), Gaps = 1/85 (1%)
Query: 240 LITGGTGRLGMLFSDYLINK-YSTNLILSGRSKLNSIIYKKLKKFNNKAIYIQVDVSDKL 298
L+TG LG + L + + + + ++ +A +Q DV+DK
Sbjct: 10 LVTGAARGLGRAIALRLARAGADVVVHYRSDEEAAEELVEAVEALGRRAQAVQADVTDKA 69
Query: 299 KMISEINSIINNIGPIDGVLHIAGI 323
+ + + + + G ID +++ AGI
Sbjct: 70 ALEAAVAAAVERFGRIDILVNNAGI 94
>gnl|CDD|227546 COG5221, DOP1, Dopey and related predicted leucine zipper
transcription factors [Transcription].
Length = 1618
Score = 33.4 bits (76), Expect = 1.1
Identities = 32/172 (18%), Positives = 55/172 (31%), Gaps = 23/172 (13%)
Query: 459 EQLLIQDKIQYLVLSGELEKLNQIINNIAPKVSENKKINNFNIEKFIENDIKNHICNILN 518
E+ I++ E N + IA + + I D+ H
Sbjct: 363 ERDYIEEYAPPDAFESERSSENIDVEKIARAFLTTDLDSVWKILYLQLKDVLLHS----- 417
Query: 519 TKKSEIYKNKNLADYGFDSISLAEFSRILSKFYSLDIMPSIFFSYSTLERLITYFIKNHN 578
K + N +L + + S+ YSL M IF ++ E
Sbjct: 418 --KEFMLLNMDLTNDEEFNDSMVREEM-----YSLHSMSLIFNEITSSECFALG------ 464
Query: 579 NTMIKFYRNKYPLKTESKNISILYD-----NKINENYENVSKKSNFILNKNT 625
++++ Y+ YP+ S + ++ EN ENVS N N
Sbjct: 465 ASLLEVYKGAYPMSESSLLEEMELKCKGLLGRVVENRENVSNWIKDANNPNQ 516
>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: 263 NLILSGRS--KLNSIIYKKLKKFNNKAIYIQVDVSDKLKMISEINSIINNIGPIDGVLHI 320
++L+ R +L ++ ++ A+ + +DV+D+ + + I ++ G ID +++
Sbjct: 32 KVVLAARREERLEALA-DEIGA--GAALALALDVTDRAAVEAAIEALPEEFGRIDILVNN 88
Query: 321 AGISGLTSNILEAN 334
AG++ L + EA+
Sbjct: 89 AGLA-LGDPLDEAD 101
>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 = 1.1
Identities = 12/26 (46%), Positives = 16/26 (61%)
Query: 233 IKQGGTYLITGGTGRLGMLFSDYLIN 258
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 = 1.2
Identities = 28/112 (25%), Positives = 45/112 (40%), Gaps = 23/112 (20%)
Query: 240 LITGGTGRLGMLFSDYLINK-YSTNLILSGRSKLNSIIYKKLKKFNNKAIYIQVDVSDKL 298
LITG TG+ G +++L+ K Y + I+ S N+ L ++ D++D
Sbjct: 3 LITGITGQDGSYLAEFLLEKGYEVHGIVRRSSSFNTDRIDHLYINKDRITLHYGDLTD-- 60
Query: 299 KMISEINSIINNIGPIDGVLHIAGIS-----------------GLTSNILEA 333
S + I + P D + H+A S T N+LEA
Sbjct: 61 --SSSLRRAIEKVRP-DEIYHLAAQSHVKVSFDDPEYTAEVNAVGTLNLLEA 109
>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 = 1.3
Identities = 26/113 (23%), Positives = 51/113 (45%), Gaps = 1/113 (0%)
Query: 238 TYLITGGTGRLGMLFSDYLINKYSTNLILSGRSKLNSIIYKKLKKFNNKAIYIQVDVSDK 297
L+TGG +G ++ L + + K++ + KA+ ++DVSDK
Sbjct: 2 VALVTGGAQGIGKGIAERLAKDGFAVAVADLNEETAKETAKEINQAGGKAVAYKLDVSDK 61
Query: 298 LKMISEINSIINNIGPIDGVLHIAGISGLTSNILEANYKNFYSVLSSKISGTI 350
++ S I+ G D +++ AG++ +T ILE + V + + G +
Sbjct: 62 DQVFSAIDQAAEKFGGFDVMVNNAGVAPITP-ILEITEEELKKVYNVNVKGVL 113
>gnl|CDD|223696 COG0623, FabI, Enoyl-[acyl-carrier-protein].
Length = 259
Score = 32.2 bits (74), Expect = 1.4
Identities = 11/64 (17%), Positives = 29/64 (45%), Gaps = 3/64 (4%)
Query: 278 KKLKKFNNKAIYIQVDVSDKLKMISEINSIINNIGPIDGVLHIAGIS---GLTSNILEAN 334
++L + + + DV++ + + +I G +DG++H + L + L+ +
Sbjct: 49 EELAEELGSDLVLPCDVTNDESIDALFATIKKKWGKLDGLVHSIAFAPKEELKGDYLDTS 108
Query: 335 YKNF 338
+ 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 = 1.4
Identities = 21/93 (22%), Positives = 41/93 (44%), Gaps = 8/93 (8%)
Query: 236 GGTYLITGGTGRLGMLFS-DYLINKYSTNLILSGRSKLNSI-IYKKLKKF--NNKAIYIQ 291
G +ITG G+ + K ++I++ R++ ++KK N K IQ
Sbjct: 1 GKVVVITGANS--GIGKETARELAKRGAHVIIACRNEEKGEEAAAEIKKETGNAKVEVIQ 58
Query: 292 VDVSDKLKMISEI-NSIINNIGPIDGVLHIAGI 323
+D+S L + + + +D +++ AGI
Sbjct: 59 LDLSS-LASVRQFAEEFLARFPRLDILINNAGI 90
>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 = 1.6
Identities = 23/85 (27%), Positives = 40/85 (47%), Gaps = 13/85 (15%)
Query: 240 LITGGTGRLGMLFSDYLINKYST-NLILSGRSKLNSIIYKKLKKFNNKAIYIQVDVSDKL 298
LITGG G++G + L +Y N+I S K + + + +DV D
Sbjct: 3 LITGGLGQIGSELAKLLRKRYGKDNVIASDIRKPPA------HVVLSG-PFEYLDVLD-F 54
Query: 299 KMISEINSIINNIGPIDGVLHIAGI 323
K + EI ++N+ I ++H+A +
Sbjct: 55 KSLEEI--VVNH--KITWIIHLAAL 75
>gnl|CDD|181508 PRK08628, PRK08628, short chain dehydrogenase; Provisional.
Length = 258
Score = 31.9 bits (73), Expect = 1.9
Identities = 26/100 (26%), Positives = 51/100 (51%), Gaps = 5/100 (5%)
Query: 240 LITGGTGRLGMLFSDYLINKYSTNLILSGRSKLNSIIYKKLKKFNNKAIYIQVDVSDKLK 299
++TGG +G S L + + +I GRS + ++L+ +A ++QVD++D +
Sbjct: 11 IVTGGASGIGAAISLRLAEEGAIPVIF-GRSAPDDEFAEELRALQPRAEFVQVDLTDDAQ 69
Query: 300 MISEINSIINNIGPIDGVLHIAGISGLTSNI-LEANYKNF 338
+ + G IDG+++ AG++ + LEA + F
Sbjct: 70 CRDAVEQTVAKFGRIDGLVNNAGVN---DGVGLEAGREAF 106
>gnl|CDD|236094 PRK07774, PRK07774, short chain dehydrogenase; Provisional.
Length = 250
Score = 31.6 bits (72), Expect = 2.0
Identities = 26/111 (23%), Positives = 52/111 (46%), Gaps = 5/111 (4%)
Query: 236 GGTYLITGGTGRLGMLFSDYLINKYSTNLILSGRSKLNSIIYKKLKKFNNKAIYIQVDVS 295
++TG G +G +++ L + ++ ++ ++ + K++ AI +QVDVS
Sbjct: 6 DKVAIVTGAAGGIGQAYAEALAREGASVVVADINAEGAERVAKQIVADGGTAIAVQVDVS 65
Query: 296 DKLKMISEINSIINNIGPIDGVLHIAGISG-----LTSNILEANYKNFYSV 341
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 = 2.2
Identities = 34/152 (22%), Positives = 60/152 (39%), Gaps = 39/152 (25%)
Query: 240 LITGGTGRLGMLFSDYLINK-YST----NLILSGRSKLNSIIYKKLKKFNNKAIYIQVDV 294
L+TGG G +G L+ + NL + L + +K + + D+
Sbjct: 4 LVTGGAGYIGSHTVRQLLKTGHEVVVLDNLSNGHKIALLKLQFK----------FYEGDL 53
Query: 295 SDKLKMISEINSIINNIGPIDGVLHIAGISGL---TSNILEANYKNFYSVLSSKISGTIA 351
D+ + + ID V+H A + N L+ Y N + GT+
Sbjct: 54 LDRALLTAVFEEN-----KIDAVVHFAASISVGESVQNPLKY-YDN-------NVVGTLN 100
Query: 352 LNYALENTILKLQKNKLDFVCYFSSSSAILGD 383
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 = 2.4
Identities = 20/89 (22%), Positives = 37/89 (41%), Gaps = 4/89 (4%)
Query: 235 QGGTYLITGGTGRLGMLFSDYLINKYSTNLILSGRSKLNSIIYKKLKKFNNKAIYIQVDV 294
G T LITGG +G+ + + +I+ GR N + K N + DV
Sbjct: 4 TGNTILITGGASGIGLALAKRF-LELGNTVIICGR---NEERLAEAKAENPEIHTEVCDV 59
Query: 295 SDKLKMISEINSIINNIGPIDGVLHIAGI 323
+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 = 2.5
Identities = 15/56 (26%), Positives = 31/56 (55%)
Query: 287 AIYIQVDVSDKLKMISEINSIINNIGPIDGVLHIAGISGLTSNILEANYKNFYSVL 342
AI IQ DV+ + + + + + ++ G +D +++ AGI+ +LE + + F V
Sbjct: 53 AIAIQADVTKRADVEAMVEAALSKFGRLDILVNNAGITHRNKPMLEVDEEEFDRVF 108
>gnl|CDD|235771 PRK06289, PRK06289, acetyl-CoA acetyltransferase; Provisional.
Length = 403
Score = 31.6 bits (72), Expect = 2.7
Identities = 15/32 (46%), Positives = 17/32 (53%)
Query: 794 ACSSSLVATHIACQSLRQHECDTAISAGVNLM 825
AC+S VAT A LR D A+ GV LM
Sbjct: 89 ACASGSVATLAAMADLRAGRYDVALVVGVELM 120
>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 = 31.3 bits (71), Expect = 2.8
Identities = 13/36 (36%), Positives = 23/36 (63%)
Query: 286 KAIYIQVDVSDKLKMISEINSIINNIGPIDGVLHIA 321
+AI IQ DV D+ ++ + I N+ GP+D +++ A
Sbjct: 48 RAIAIQADVRDRDQVQAMIEEAKNHFGPVDTIVNNA 83
>gnl|CDD|177878 PLN02234, PLN02234, 1-deoxy-D-xylulose-5-phosphate synthase.
Length = 641
Score = 31.6 bits (71), Expect = 2.9
Identities = 47/197 (23%), Positives = 76/197 (38%), Gaps = 39/197 (19%)
Query: 821 GVNLMISPEAYIAMTSAGMLSPDGKCYVFDER------ANGLVPSEAVVAVVLKRLSRAL 874
G M + +AY AM +AG L + + D + AN P++ V A LS AL
Sbjct: 207 GDGAMTAGQAYEAMNNAGYLHSNMIVILNDNKQVSLPTANLDGPTQPVGA-----LSCAL 261
Query: 875 SDGDPIHAIIRGS--------GINYDGKTNGITAPNGISQTELIKSVYKKSNLNPEDINY 926
S +IR + G +Y G +G + +S E +KS + P I+
Sbjct: 262 SRLQSNCGMIRETSSTLFEELGFHYVGPVDGHNIDDLVSILETLKST---KTIGPVLIHV 318
Query: 927 IITHGTGTKLG-------------DPVEINALHDVFKNKTYNQKFC-AITSNKS---NIG 969
+ G G DP ++ K ++Y F A+ + +I
Sbjct: 319 VTEKGRGYPYAERADDKYHGVLKFDPETGKQFKNISKTQSYTSCFVEALIAEAEADKDIV 378
Query: 970 HTFAASGLVSLINLVQS 986
AA G +++NL +S
Sbjct: 379 AIHAAMGGGTMLNLFES 395
>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 = 3.1
Identities = 18/86 (20%), Positives = 41/86 (47%), Gaps = 4/86 (4%)
Query: 240 LITGGTGRLGMLFSDYLINKYSTNLILSGRS--KLNSIIYKKLKKFNNKAIYIQVDVSDK 297
L+TG + +G + + + ++ RS + +++K A ++ DVSD+
Sbjct: 4 LVTGASRGIGRAIA-LRLAAEGAKVAVTDRSEEAAAETV-EEIKALGGNAAALEADVSDR 61
Query: 298 LKMISEINSIINNIGPIDGVLHIAGI 323
+ + + + GP+D +++ AGI
Sbjct: 62 EAVEALVEKVEAEFGPVDILVNNAGI 87
>gnl|CDD|181077 PRK07677, PRK07677, short chain dehydrogenase; Provisional.
Length = 252
Score = 30.8 bits (70), Expect = 3.2
Identities = 19/90 (21%), Positives = 44/90 (48%), Gaps = 8/90 (8%)
Query: 236 GGTYLITGGTGRLGMLFSDYLINKYS---TNLILSGRSKLNSIIYKK-LKKFNNKAIYIQ 291
+ITGG+ +G + +++ N++++GR+K K +++F + + +Q
Sbjct: 1 EKVVIITGGSSGMG----KAMAKRFAEEGANVVITGRTKEKLEEAKLEIEQFPGQVLTVQ 56
Query: 292 VDVSDKLKMISEINSIINNIGPIDGVLHIA 321
+DV + + + I G ID +++ A
Sbjct: 57 MDVRNPEDVQKMVEQIDEKFGRIDALINNA 86
>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 = 29.5 bits (67), Expect = 3.3
Identities = 23/85 (27%), Positives = 35/85 (41%), Gaps = 14/85 (16%)
Query: 858 PSEAVVAVVLKRLSRALSDGDPIHAIIRGSGINYDGKTNGITAPNGISQTELIKSVYKKS 917
P+ A + +L +L G ++R Y K G+ P +S ELI ++
Sbjct: 36 PTAAELRELLAKL------GISPRDLLRTKEAPY--KELGLADPE-LSDEELIDAMAA-- 84
Query: 918 NLNPEDINY-IITHGTGTKLGDPVE 941
+P I I+ G G LG P E
Sbjct: 85 --HPILIERPIVVTGDGAVLGRPPE 107
>gnl|CDD|240419 PTZ00440, PTZ00440, reticulocyte binding protein 2-like protein;
Provisional.
Length = 2722
Score = 31.7 bits (72), Expect = 3.5
Identities = 44/203 (21%), Positives = 75/203 (36%), Gaps = 36/203 (17%)
Query: 445 KQKVLHENDGLKLFEQLLIQDKIQYLVLSGELEKLNQII------NNIAPKVSENKKINN 498
+ L +++ LK + I++KI+Y+ ++ + II +NI ++ E
Sbjct: 551 SIETLIKDEKLKRSMKNDIKNKIKYI--EENVDHIKDIISLNDEIDNIIQQIEELINEAL 608
Query: 499 FNIEKFIENDIKNHICNILNTKKSEIYKNKNLADYGFDSISLAEFSRILSKFYS------ 552
FN EKFI N L K I D L+ F Y
Sbjct: 609 FNKEKFINEK------NDLQEKVKYILNKFYKGDLQELLDELSHFLDDHKYLYHEAKSKE 662
Query: 553 --LDIMPSIFFSYSTLERLITYFIKNHNNTMIKFYRNKYPLKTESKNISILYDNKINENY 610
++ + Y LE + + ++ + +IK LK E +N+ L +N I +
Sbjct: 663 DLQTLLNTSKNEYEKLEFMKS----DNIDNIIK------NLKKELQNLLSLKENIIKKQL 712
Query: 611 ENV----SKKSNFILNKNTDINS 629
N+ S N K D+ S
Sbjct: 713 NNIEQDISNSLNQYTIKYNDLKS 735
>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 = 4.2
Identities = 14/58 (24%), Positives = 26/58 (44%), Gaps = 4/58 (6%)
Query: 882 AIIRGSGINYDGKTNGITAPNGISQTELIKSVYKKSNLNPEDINYIITHGTGTKLGDP 939
+ GI+ + +G+ G++ L ++ L PEDI ++ G G +L P
Sbjct: 131 STDASGGISQE---SGLLVSYGVNLRTLTPGTWQAMTL-PEDIKALVGPGVGLRLDAP 184
>gnl|CDD|226840 COG4409, NanH, Neuraminidase (sialidase) [Carbohydrate transport
and metabolism].
Length = 728
Score = 31.0 bits (70), Expect = 4.2
Identities = 21/117 (17%), Positives = 32/117 (27%), Gaps = 11/117 (9%)
Query: 188 KNWINILFKELQEPKLFSIMYYGNDLIRYQLNIKSIILKDFKNSYIKQGGTYLITGGTGR 247
K W + I +G ++ I SY I G
Sbjct: 318 KTWHKPEVTGQFDDATTQIAIWGREVTLRNGQISL------SQSYSDSSIVEDIKDGKLF 371
Query: 248 LGMLFSDYLINKYSTNLILSGRSKLNSIIYKKLKK-----FNNKAIYIQVDVSDKLK 299
L M+ K + +I SG + +Y K + F A SD+
Sbjct: 372 LFMVVMPDGNYKTTAAIIDSGSKNIAGNVYLKSEDDGDTDFEYTATENGKIFSDETN 428
>gnl|CDD|181225 PRK08085, PRK08085, gluconate 5-dehydrogenase; Provisional.
Length = 254
Score = 30.5 bits (69), Expect = 4.4
Identities = 26/96 (27%), Positives = 48/96 (50%), Gaps = 2/96 (2%)
Query: 229 KNSYIKQGGTYLITGGTGRLGMLFSDYLINKYSTNLILSGRSKLNS-IIYKKLKKFNNKA 287
+ + G LITG +G L + L +Y +I++ + + + KL++ KA
Sbjct: 2 NDLFSLAGKNILITGSAQGIGFLLATGL-AEYGAEIIINDITAERAELAVAKLRQEGIKA 60
Query: 288 IYIQVDVSDKLKMISEINSIINNIGPIDGVLHIAGI 323
+V+ K ++ + I I +IGPID +++ AGI
Sbjct: 61 HAAPFNVTHKQEVEAAIEHIEKDIGPIDVLINNAGI 96
>gnl|CDD|237418 PRK13534, PRK13534, 7-cyano-7-deazaguanine tRNA-ribosyltransferase;
Provisional.
Length = 639
Score = 30.7 bits (70), Expect = 5.0
Identities = 27/114 (23%), Positives = 41/114 (35%), Gaps = 25/114 (21%)
Query: 608 ENYENVSKKSNFILNKNTDINSEELIAIIGMSGRFPAARNINEFWKILINNKDVISEIPE 667
E Y+ VSKKS F E L + P + + + ++K + +
Sbjct: 350 EKYDPVSKKSAFFY-----TGYESL--------KRPEVYRHKKRLERIKSDKKYTTVVSS 396
Query: 668 KIFDWKLYYENPIKSSNKINSKWYGSIPGIDEFDPLFFEISPLEAERMDPRQRH 721
KI WK Y EN N + + DP+F I PL + P +
Sbjct: 397 KI--WKPYSEN----LNNVRCDV-----DVLIKDPVFGLI-PLYLDTTYPLAQS 438
>gnl|CDD|222222 pfam13561, adh_short_C2, Enoyl-(Acyl carrier protein) reductase.
Length = 239
Score = 30.3 bits (69), Expect = 5.0
Identities = 14/80 (17%), Positives = 30/80 (37%), Gaps = 7/80 (8%)
Query: 264 LILSGRS-KLNSIIYKKL-KKFNNKAIYIQVDVSDKLKMISEINSIINNIGPIDGVLHIA 321
++L+ L +L K+ I +DV+ + + + G ID ++H
Sbjct: 23 VVLTTWPPALRMGAVDELAKELPADVIP--LDVTSDEDIDELFEKVKEDGGKIDFLVHSI 80
Query: 322 GISG---LTSNILEANYKNF 338
+S L+ + + F
Sbjct: 81 AMSPEIRKGKPYLDTSREGF 100
>gnl|CDD|181585 PRK08936, PRK08936, glucose-1-dehydrogenase; Provisional.
Length = 261
Score = 30.5 bits (69), Expect = 5.1
Identities = 19/88 (21%), Positives = 49/88 (55%), Gaps = 6/88 (6%)
Query: 278 KKLKKFNNKAIYIQVDVSDKLKMISEINSIINNIGPIDGVLHIAGISGLTSNILEANYKN 337
+++KK +AI ++ DV+ + +++ I + + G +D +++ AGI + E + ++
Sbjct: 50 EEIKKAGGEAIAVKGDVTVESDVVNLIQTAVKEFGTLDVMINNAGIENAVPS-HEMSLED 108
Query: 338 FYSVLSSKISGTI-----ALNYALENTI 360
+ V+++ ++G A+ Y +E+ I
Sbjct: 109 WNKVINTNLTGAFLGSREAIKYFVEHDI 136
>gnl|CDD|223982 COG1054, COG1054, Predicted sulfurtransferase [General function
prediction only].
Length = 308
Score = 30.3 bits (69), Expect = 5.7
Identities = 9/25 (36%), Positives = 11/25 (44%), Gaps = 1/25 (4%)
Query: 843 DGKCYVFDERANGLVPSEAVVAVVL 867
DGKC+VFDER +
Sbjct: 222 DGKCFVFDERV-AVPIGLVEGDHTP 245
>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 = 30.5 bits (69), Expect = 5.8
Identities = 26/135 (19%), Positives = 44/135 (32%), Gaps = 6/135 (4%)
Query: 578 NNTMIKFYRNKYPLKTESKNISILYDNKINENYENVSKKSNFILN-KNTDINSEELIAI- 635
NT ++++ KI E +N + F +I +E +
Sbjct: 58 GNTYKLPIIPGTIFPKVAQDLYKEEIKKIYEFRKNDFLQEKFYTEEAGYEIELDEDLEEN 117
Query: 636 -IGMSGRFPA--ARNINEFWKILINNKDVISEIPEKIFDWKLYYEN-PIKSSNKINSKWY 691
IG R+ + KI + KDV EKI + + N + ++ W+
Sbjct: 118 KIGYYLRYDFLFYSKEKQAEKITLYIKDVEPSRVEKILELEKKVLNVSKEDFGELKENWF 177
Query: 692 GSIPGIDEFDPLFFE 706
D FFE
Sbjct: 178 FGQVYAFLLDNDFFE 192
>gnl|CDD|214368 CHL00117, rpoC2, RNA polymerase beta'' subunit; Reviewed.
Length = 1364
Score = 30.7 bits (70), Expect = 5.9
Identities = 67/405 (16%), Positives = 117/405 (28%), Gaps = 102/405 (25%)
Query: 119 IYFLQAVKKSKLYLRKLIISGISINKKNEEDLYYCYFNSWVAFERSLHIIMPETQISIVF 178
I+F K + LI G E +W+ +R I P + V
Sbjct: 722 IHFPGETDKISRHSGILIPPGTGKKNSKESK----KIKNWIYVQR----ITPTKKKYFVL 773
Query: 179 AEKITNFNIKNWINI----LFKELQEP-----KLFSIMYYGN----------DLIRYQLN 219
+ + I + IN+ LQE ++ + + YGN L+R L
Sbjct: 774 VRPVVTYEIADGINLATLFPQDLLQEKDNLQLRVVNYILYGNGKPIRGISSIQLVRTCLV 833
Query: 220 IKSIILKDFKNSYIKQGGTYLITGGTGRLGMLFSDYLINKYSTNLILSGRSKLNSIIYKK 279
+ +D K+S I++ + R L D+L + I R + +
Sbjct: 834 LN--WDQDKKSSSIEEARASFVEV---RTNGLIRDFLRINLVKSPISYIRKRNDPSSSGL 888
Query: 280 LKKFNNKAIYIQVDVSDKLKMISEINSIINNIGPIDGVLHIAGISGLTSNILEANYKNFY 339
L + NN D + S+ ++ G +
Sbjct: 889 LVQSNNF--------LDSTNIYSKAEIQSQSLSQNQGTIRT------------------- 921
Query: 340 SVLSSKISGTIALNYALENTILKLQKNKLDFVCYFSSSSAILGDFGSCDYAMGNRFQTVY 399
L + + + SSS + F+
Sbjct: 922 ---------------------LLNRNKESQSLLILSSS---------------DCFRIGP 945
Query: 400 AKYLNNKNIYKKYTNKLITINWPLWNNSKFKIGNNEQTDFYFKSSKQKVLHENDGLKLFE 459
+K K +N LI I L N + ++ + Q ++ K +
Sbjct: 946 FNGKKSKYHNIKESNPLIPIRNSLGPLGTVLQIANFSSSYHLLTHNQILV-----TKYLQ 1000
Query: 460 QLLIQDKIQYLVLSGELEKLNQIINNIAPKVSENKKINNFNIEKF 504
++ Q VL L N I N P N +N FN+ +
Sbjct: 1001 LDNLKQTFQVKVLKYYLIDENGKIYNPDPCS--NIILNPFNLNWY 1043
>gnl|CDD|234663 PRK00142, PRK00142, putative rhodanese-related sulfurtransferase;
Provisional.
Length = 314
Score = 30.2 bits (69), Expect = 6.1
Identities = 9/10 (90%), Positives = 9/10 (90%)
Query: 843 DGKCYVFDER 852
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 = 6.4
Identities = 20/89 (22%), Positives = 41/89 (46%), Gaps = 13/89 (14%)
Query: 238 TYLITGGTGRLGMLFSDYLINKYSTNLI-----LSGRSKLNSIIYKKLKKFNNKAIYIQV 292
L+TGG G +G F Y++NK+ + + L+ L ++ + + + ++Q
Sbjct: 2 KILVTGGAGFIGSNFVRYILNKHPDDHVVNLDKLTYAGNLENL---ADVEDSPRYRFVQG 58
Query: 293 DVSDKLKMISEINSIINNIGPIDGVLHIA 321
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 = 30.0 bits (68), Expect = 6.5
Identities = 23/77 (29%), Positives = 36/77 (46%), Gaps = 11/77 (14%)
Query: 610 YENVSKK-SNFIL--NKNTDINSEELIAIIGMS--GRFPAARNINEFW-----KILINNK 659
+ENVSK+ N + N I E + +IG S G+ + IN +ILI+ +
Sbjct: 4 FENVSKRYGNKKAVDDVNLTIEEGEFLVLIGPSGSGKTTTLKMINRLIEPTSGEILIDGE 63
Query: 660 DVISEIPEKIFDWKLYY 676
D IS++ K+ Y
Sbjct: 64 D-ISDLDPVELRRKIGY 79
>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 = 30.1 bits (68), Expect = 6.8
Identities = 20/91 (21%), Positives = 40/91 (43%), Gaps = 4/91 (4%)
Query: 236 GGTYLITGGTGRLGMLFSDYLINKYSTNLILSG---RSKLNSIIYKKLKKFNNKAIYIQV 292
G L+TG T +G+ + L N++L+G +++ ++ K K +Y
Sbjct: 2 GKVALVTGSTSGIGLGIARALA-AAGANIVLNGFGDAAEIEAVRAGLAAKHGVKVLYHGA 60
Query: 293 DVSDKLKMISEINSIINNIGPIDGVLHIAGI 323
D+S + + G +D +++ AGI
Sbjct: 61 DLSKPAAIEDMVAYAQRQFGGVDILVNNAGI 91
>gnl|CDD|234811 PRK00685, PRK00685, metal-dependent hydrolase; Provisional.
Length = 228
Score = 29.8 bits (68), Expect = 7.3
Identities = 16/30 (53%), Positives = 20/30 (66%), Gaps = 3/30 (10%)
Query: 916 KSNLNPEDIN--YI-ITHGTGTKLGDPVEI 942
++L PED+ YI +THG G LGD VEI
Sbjct: 31 LADLKPEDVKVDYILLTHGHGDHLGDTVEI 60
>gnl|CDD|179922 PRK05066, PRK05066, arginine repressor; Provisional.
Length = 156
Score = 29.2 bits (66), Expect = 8.1
Identities = 18/66 (27%), Positives = 32/66 (48%), Gaps = 15/66 (22%)
Query: 530 LADYGFDSISLAEFSRILSKF-------------YSLDIMPSIFFSYSTLERLITYFIKN 576
L + GFD+I+ ++ SR+L+KF Y L + + S L+ L+ +
Sbjct: 33 LQEQGFDNINQSKVSRMLTKFGAVRTRNAKMEMVYCLPAELGVPTTSSPLKNLVLDI--D 90
Query: 577 HNNTMI 582
HN+ +I
Sbjct: 91 HNDALI 96
>gnl|CDD|227393 COG5061, ERO1, Oxidoreductin, endoplasmic reticulum
membrane-associated protein involved in disulfide bond
formation [Posttranslational modification, protein
turnover, chaperones / Intracellular trafficking and
secretion].
Length = 425
Score = 29.9 bits (67), Expect = 8.6
Identities = 16/74 (21%), Positives = 23/74 (31%), Gaps = 10/74 (13%)
Query: 44 IVESISSYTDIIFIEQSDNIKISPNDTVHYKIN--KDNINDYTFILNKIYEKDKKIDSVF 101
I + IS + I + I IS D I + +L + D +F
Sbjct: 4 ITKLISIWNAIWNFKLDPEIIISQTDNSSTGIYQMNSKVRSLLPVLT-------ESDYMF 56
Query: 102 YLW-PLEDKNCIYN 114
Y L K C
Sbjct: 57 YYRLNLYAKACTLW 70
>gnl|CDD|235794 PRK06398, PRK06398, aldose dehydrogenase; Validated.
Length = 258
Score = 29.4 bits (66), Expect = 8.9
Identities = 16/39 (41%), Positives = 26/39 (66%)
Query: 285 NKAIYIQVDVSDKLKMISEINSIINNIGPIDGVLHIAGI 323
N Y +VDVS+K ++I I+ +I+ G ID +++ AGI
Sbjct: 44 NDVDYFKVDVSNKEQVIKGIDYVISKYGRIDILVNNAGI 82
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 0.389
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: 58,445,199
Number of extensions: 5977402
Number of successful extensions: 6986
Number of sequences better than 10.0: 1
Number of HSP's gapped: 6707
Number of HSP's successfully gapped: 362
Length of query: 1152
Length of database: 10,937,602
Length adjustment: 107
Effective length of query: 1045
Effective length of database: 6,191,724
Effective search space: 6470351580
Effective search space used: 6470351580
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: 65 (28.4 bits)