RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11859
(851 letters)
>gnl|CDD|187547 cd05236, FAR-N_SDR_e, fatty acyl CoA reductases (FARs), extended
(e) SDRs. SDRs are Rossmann-fold NAD(P)H-binding
proteins, many of which may function as fatty acyl CoA
reductases (FAR), acting on medium and long chain fatty
acids, and have been reported to be involved in diverse
processes such as biosynthesis of insect pheromones,
plant cuticular wax production, and mammalian wax
biosynthesis. In Arabidopsis thaliana, proteins with
this particular architecture have also been identified
as the MALE STERILITY 2 (MS2) gene product, which is
implicated in male gametogenesis. Mutations in MS2
inhibit the synthesis of exine (sporopollenin),
rendering plants unable to reduce pollen wall fatty
acids to corresponding alcohols. This N-terminal domain
shares the catalytic triad (but not the upstream Asn)
and characteristic NADP-binding motif of the extended
SDR family. 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 = 320
Score = 335 bits (861), Expect = e-108
Identities = 138/320 (43%), Positives = 199/320 (62%), Gaps = 26/320 (8%)
Query: 219 RSVLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFERLRK 278
+SVL+TG TGF+GKVLLEKLLRSCPDIGK+Y+L R K G + + RL E K +F+R R
Sbjct: 1 KSVLITGATGFLGKVLLEKLLRSCPDIGKIYLLIRGKSGQSAEERLRELLKDKLFDRGRN 60
Query: 279 ECPAQLSRLHIIEGDILQANLGIKDSDLLMLQEEVSVVFNGAASLKLEAELKENVAANTR 338
P S++ IEGD+ + NLG+ D DL L EEV+++ + AA++ + L E ++ N
Sbjct: 61 LNPLFESKIVPIEGDLSEPNLGLSDEDLQTLIEEVNIIIHCAATVTFDERLDEALSINVL 120
Query: 339 GTQRLLDIALKMKKLVAFIHFSTAFCHPDQKVLEEKLYPSPVSPHDIMRAMEWMDDETIK 398
GT RLL++A + KKL AF+H STA+ + D++++EEK+YP P P ++ +E MDD ++
Sbjct: 121 GTLRLLELAKRCKKLKAFVHVSTAYVNGDRQLIEEKVYPPPADPEKLIDILELMDDLELE 180
Query: 399 QLTPKILGPHPNSYTFTKRLTETLVDEYKTKLPVVIVRPSIVLPSFQEPVPGWVDSLNGP 458
+ TPK+LG HPN+YTFTK L E LV + + LP+VIVRPSIV + +EP PGW+D+ NGP
Sbjct: 181 RATPKLLGGHPNTYTFTKALAERLVLKERGNLPLVIVRPSIVGATLKEPFPGWIDNFNGP 240
Query: 459 VGVLVASGKGVVRSM--------------------------ILNDLSTETQVFNISSNEV 492
G+ +A GKG++R+M E +V++ S++V
Sbjct: 241 DGLFLAYGKGILRTMNADPNAVADIIPVDVVANALLAAAAYSGVRKPRELEVYHCGSSDV 300
Query: 493 EAITWGEIISRGKQLIYQYP 512
TWGE Q + + P
Sbjct: 301 NPFTWGEAEELINQYLKKNP 320
>gnl|CDD|219687 pfam07993, NAD_binding_4, Male sterility protein. This family
represents the C-terminal region of the male sterility
protein in a number of arabidopsis and drosophila. A
sequence-related jojoba acyl CoA reductase is also
included.
Length = 245
Score = 228 bits (584), Expect = 3e-69
Identities = 98/254 (38%), Positives = 137/254 (53%), Gaps = 32/254 (12%)
Query: 223 VTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARL-AEFSKLPVFERLRKECP 281
+TG TGF+GKVLLEKLLRS P++ K+Y L RAK G + RL E K +F+RL+
Sbjct: 1 LTGATGFLGKVLLEKLLRSTPEV-KIYCLVRAKDGESALERLRQELLKYGLFDRLK---- 55
Query: 282 AQLSRLHIIEGDILQANLGIKDSDLLMLQEEVSVVFNGAASLKLEAELKENVAANTRGTQ 341
L R+ + GD+ + NLG+ D D L EEV V+ + AA++ + A N GT+
Sbjct: 56 -ALERIIPVAGDLSEPNLGLSDEDFQELAEEVDVIIHNAATVNFVEPYSDLRATNVLGTR 114
Query: 342 RLLDIALKMKKLVAFIHFSTAFCHPD-QKVLEEKLYPSPVSPHDIMRAMEWMDDETIKQL 400
+L +A +MKKL F H STA+ + + +LEEK + +
Sbjct: 115 EVLRLAKQMKKL-PFHHVSTAYVNGERGGLLEEK-------------------PYKLDED 154
Query: 401 TPKILGPHPNSYTFTKRLTETLVDEYKTKLPVVIVRPSIVLPSFQEPVPGWVDSLN-GPV 459
P +LG PN YT +K L E LV E LPVVI RPSI+ E GW++ + GP
Sbjct: 155 EPALLGGLPNGYTQSKWLAEQLVREAAGGLPVVIYRPSIITG---ESRTGWINGDDFGPR 211
Query: 460 GVLVASGKGVVRSM 473
G+L +G GV+ +
Sbjct: 212 GLLGGAGLGVLPDI 225
>gnl|CDD|215538 PLN02996, PLN02996, fatty acyl-CoA reductase.
Length = 491
Score = 140 bits (356), Expect = 2e-35
Identities = 88/295 (29%), Positives = 149/295 (50%), Gaps = 33/295 (11%)
Query: 208 DMGDVARWYAGRSVLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARL-AE 266
+ G ++ +++LVTG TGF+ K+ +EK+LR P++ K+Y+L RA + RL E
Sbjct: 1 EEGSCVQFLENKTILVTGATGFLAKIFVEKILRVQPNVKKLYLLLRASDAKSATQRLHDE 60
Query: 267 FSKLPVFERLRKECPAQLS-----RLHIIEGDILQANLGIKDSDLL-MLQEEVSVVFNGA 320
+F+ LR++ L+ ++ + GDI +LG+KDS+L + +E+ +V N A
Sbjct: 61 VIGKDLFKVLREKLGENLNSLISEKVTPVPGDISYDDLGVKDSNLREEMWKEIDIVVNLA 120
Query: 321 ASLKLEAELKENVAANTRGTQRLLDIALKMKKLVAFIHFSTAF-CHPDQKVLEEKLYP-- 377
A+ + + NT G +L+ A K K+ +H STA+ C ++ EK +
Sbjct: 121 ATTNFDERYDVALGINTLGALNVLNFAKKCVKVKMLLHVSTAYVCGEKSGLILEKPFHMG 180
Query: 378 ---SPVSPHDIMRAMEWMD------------DETIKQLTPKILGPH-------PNSYTFT 415
+ DI + + +E I Q K LG PN+Y FT
Sbjct: 181 ETLNGNRKLDINEEKKLVKEKLKELNEQDASEEEITQ-AMKDLGMERAKLHGWPNTYVFT 239
Query: 416 KRLTETLVDEYKTKLPVVIVRPSIVLPSFQEPVPGWVDSLNGPVGVLVASGKGVV 470
K + E L+ +K LP+VI+RP+++ +++EP PGW++ L V+V GKG +
Sbjct: 240 KAMGEMLLGNFKENLPLVIIRPTMITSTYKEPFPGWIEGLRTIDSVIVGYGKGKL 294
>gnl|CDD|215279 PLN02503, PLN02503, fatty acyl-CoA reductase 2.
Length = 605
Score = 133 bits (335), Expect = 3e-32
Identities = 83/279 (29%), Positives = 142/279 (50%), Gaps = 37/279 (13%)
Query: 212 VARWYAGRSVLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLA-EFSKL 270
+A + G++ L+TG TGF+ KVL+EK+LR+ PD+GK+Y+L +AK RL E
Sbjct: 113 IAEFLRGKNFLITGATGFLAKVLIEKILRTNPDVGKIYLLIKAKDKEAAIERLKNEVIDA 172
Query: 271 PVFERLRKECPAQ-----LSRLHIIEGDILQANLGIKDSDLLMLQEEVSVVFNGAASLKL 325
+F+ L++ LS+L + G++ ++NLG++ + +EV V+ N AA+
Sbjct: 173 ELFKCLQETHGKSYQSFMLSKLVPVVGNVCESNLGLEPDLADEIAKEVDVIINSAANTTF 232
Query: 326 EAELKENVAANTRGTQRLLDIALKMKKLVAFIHFSTAFCHPD-QKVLEEK---------- 374
+ + NTRG L+ A K KKL F+ STA+ + Q + EK
Sbjct: 233 DERYDVAIDINTRGPCHLMSFAKKCKKLKLFLQVSTAYVNGQRQGRIMEKPFRMGDCIAR 292
Query: 375 -LYPSPVSPH-----DIMRAMEWMDD------------ETIKQLTPKILGPH--PNSYTF 414
L S PH DI ++ D + +K L + + ++Y F
Sbjct: 293 ELGISNSLPHNRPALDIEAEIKLALDSKRHGFQSNSFAQKMKDLGLERAKLYGWQDTYVF 352
Query: 415 TKRLTETLVDEYKTKLPVVIVRPSIVLPSFQEPVPGWVD 453
TK + E +++ + +PVVI+RPS++ ++++P PGW++
Sbjct: 353 TKAMGEMVINSMRGDIPVVIIRPSVIESTWKDPFPGWME 391
>gnl|CDD|176924 cd09071, FAR_C, C-terminal domain of fatty acyl CoA reductases.
C-terminal domain of fatty acyl CoA reductases, a family
of SDR-like proteins. SDRs or short-chain
dehydrogenases/reductases are Rossmann-fold
NAD(P)H-binding proteins. Many proteins in this FAR_C
family may function as fatty acyl-CoA reductases (FARs),
acting on medium and long chain fatty acids, and have
been reported to be involved in diverse processes such
as the biosynthesis of insect pheromones, plant
cuticular wax production, and mammalian wax
biosynthesis. In Arabidopsis thaliana, proteins with
this particular architecture have also been identified
as the MALE STERILITY 2 (MS2) gene product, which is
implicated in male gametogenesis. Mutations in MS2
inhibit the synthesis of exine (sporopollenin),
rendering plants unable to reduce pollen wall fatty
acids to corresponding alcohols. The function of this
C-terminal domain is unclear.
Length = 92
Score = 109 bits (275), Expect = 1e-28
Identities = 35/92 (38%), Positives = 55/92 (59%)
Query: 537 FTQILPAYLVDFIMVLIRQKTFLVRVQNRIWLGMHLLEYFTTRNWDFKNKRLLALHDNIS 596
F +LPAYL+D ++ L+ +K L+++ +I + LLEYFTT W F N AL + +S
Sbjct: 1 FLHLLPAYLLDLLLRLLGRKPRLLKLYRKIHKLLDLLEYFTTNEWRFDNDNTRALWERLS 60
Query: 597 EKDKQTFYIANIDVNIDDYLKTIILGARQYCL 628
E+D++ F ++ DDY + I G R+Y L
Sbjct: 61 EEDRELFNFDIRSIDWDDYFENYIPGLRKYLL 92
Score = 72.6 bits (179), Expect = 1e-15
Identities = 24/59 (40%), Positives = 34/59 (57%)
Query: 1 MHLLEYFTTRNWDFKNKRLLALHDNISEKDKQTFYIANIDVNIDDYLKTIILGARQYCL 59
+ LLEYFTT W F N AL + +SE+D++ F ++ DDY + I G R+Y L
Sbjct: 34 LDLLEYFTTNEWRFDNDNTRALWERLSEEDRELFNFDIRSIDWDDYFENYIPGLRKYLL 92
Score = 30.6 bits (70), Expect = 0.81
Identities = 9/22 (40%), Positives = 15/22 (68%)
Query: 692 FTQILPAYLVDFIMVLIRQKTF 713
F +LPAYL+D ++ L+ +K
Sbjct: 1 FLHLLPAYLLDLLLRLLGRKPR 22
>gnl|CDD|187573 cd05263, MupV_like_SDR_e, Pseudomonas fluorescens MupV-like,
extended (e) SDRs. This subgroup of extended SDR family
domains have the characteristic active site tetrad and a
well-conserved NAD(P)-binding motif. This subgroup is
not well characterized, its members are annotated as
having a variety of putative functions. One
characterized member is Pseudomonas fluorescens MupV a
protein involved in the biosynthesis of Mupirocin, a
polyketide-derived antibiotic. 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 = 293
Score = 103 bits (260), Expect = 2e-24
Identities = 58/223 (26%), Positives = 97/223 (43%), Gaps = 46/223 (20%)
Query: 221 VLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFERLRKEC 280
V VTGGTGF+G+ L+++LL + KV +L R++ R+ E
Sbjct: 1 VFVTGGTGFLGRHLVKRLL---ENGFKVLVLVRSESLGEAHERIEEAGLEA--------- 48
Query: 281 PAQLSRLHIIEGDILQANLGIKDSDLLMLQEEVSVVFNGAASLKLEAELKENVAANTRGT 340
R+ ++EGD+ Q NLG+ + L +V V + AAS +A ++ N GT
Sbjct: 49 ----DRVRVLEGDLTQPNLGLSAAASRELAGKVDHVIHCAASYDFQAPNEDAWRTNIDGT 104
Query: 341 QRLLDIA--LKMKKLVAFIHFSTAFCHPDQKVLEEKLYPSPVSPHDIMRAMEWMDDETIK 398
+ +L++A L +++ F + STA+ + +R E +
Sbjct: 105 EHVLELAARLDIQR---FHYVSTAYV--------------AGNREGNIR--ETELNPGQN 145
Query: 399 QLTPKILGPHPNSYTFTKRLTETLVDEYKTKLPVVIVRPSIVL 441
N Y +K E LV T++P+ + RPSIV+
Sbjct: 146 F---------KNPYEQSKAEAEQLVRAAATQIPLTVYRPSIVV 179
>gnl|CDD|111859 pfam03015, Sterile, Male sterility protein. This family represents
the C-terminal region of the male sterility protein in a
number of arabidopsis and drosophila. A sequence-related
jojoba acyl CoA reductase is also included.
Length = 94
Score = 91.6 bits (228), Expect = 3e-22
Identities = 33/90 (36%), Positives = 52/90 (57%)
Query: 541 LPAYLVDFIMVLIRQKTFLVRVQNRIWLGMHLLEYFTTRNWDFKNKRLLALHDNISEKDK 600
LPAY +D ++ L QK LV++ +I G+ +L+ F+ W F NK L + +SE+DK
Sbjct: 5 LPAYFLDLLLRLYGQKPRLVKLYRKIHKGLEVLQPFSLNEWIFDNKNTRELREKMSEEDK 64
Query: 601 QTFYIANIDVNIDDYLKTIILGARQYCLKE 630
+ F ++ D+Y + I G R+Y LKE
Sbjct: 65 KLFNFDMESLDWDEYFRNAIRGIRKYLLKE 94
Score = 56.9 bits (138), Expect = 4e-10
Identities = 21/61 (34%), Positives = 34/61 (55%)
Query: 1 MHLLEYFTTRNWDFKNKRLLALHDNISEKDKQTFYIANIDVNIDDYLKTIILGARQYCLK 60
+ +L+ F+ W F NK L + +SE+DK+ F ++ D+Y + I G R+Y LK
Sbjct: 34 LEVLQPFSLNEWIFDNKNTRELREKMSEEDKKLFNFDMESLDWDEYFRNAIRGIRKYLLK 93
Query: 61 E 61
E
Sbjct: 94 E 94
>gnl|CDD|187546 cd05235, SDR_e1, extended (e) SDRs, subgroup 1. This family
consists of an SDR module of multidomain proteins
identified as putative polyketide sythases fatty acid
synthases (FAS), and nonribosomal peptide synthases,
among others. However, unlike the usual ketoreductase
modules of FAS and polyketide synthase, these domains
are related to the extended SDRs, and have canonical
NAD(P)-binding motifs and an active site tetrad.
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 = 290
Score = 93.5 bits (233), Expect = 8e-21
Identities = 72/227 (31%), Positives = 103/227 (45%), Gaps = 32/227 (14%)
Query: 220 SVLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFERLRKE 279
+VL+TG TGF+G LL +LL+ ++ K+Y L RAK RL + K L E
Sbjct: 1 TVLLTGATGFLGAYLLRELLK-RKNVSKIYCLVRAKDEEAALERLIDNLKE-YGLNLWDE 58
Query: 280 CPAQLSRLHIIEGDILQANLGIKDSDLLMLQEEVSVVFNGAASLKL---EAELKENVAAN 336
+LSR+ ++ GD+ + NLG+ D D L EEV V+ + A++ ELK AN
Sbjct: 59 --LELSRIKVVVGDLSKPNLGLSDDDYQELAEEVDVIIHNGANVNWVYPYEELK---PAN 113
Query: 337 TRGTQRLLDIALKMKKLVAFIHFSTAFCHPDQKVLEEKLYPSPVSPHDIMRAMEWMDDET 396
GT+ LL +A KL ST V + Y + DDE
Sbjct: 114 VLGTKELLKLAA-TGKLKPLHFVSTLS------VFSAEEYNAL-------------DDEE 153
Query: 397 IKQLTPKILGPHPNSYTFTKRLTETLVDEYKTK-LPVVIVRPSIVLP 442
+ G PN Y +K + E L+ E + LPV I+RP +
Sbjct: 154 SDDMLESQNG-LPNGYIQSKWVAEKLLREAANRGLPVAIIRPGNIFG 199
>gnl|CDD|233557 TIGR01746, Thioester-redct, thioester reductase domain. This model
includes the terminal domain from the fungal alpha
aminoadipate reductase enzyme (also known as
aminoadipate semialdehyde dehydrogenase) which is
involved in the biosynthesis of lysine , as well as the
reductase-containing component of the myxochelin
biosynthetic gene cluster, MxcG. The mechanism of
reduction involves activation of the substrate by
adenylation and transfer to a covalently-linked
pantetheine cofactor as a thioester. This thioester is
then reduced to give an aldehyde (thus releasing the
product) and a regenerated pantetheine thiol. (In
myxochelin biosynthesis this aldehyde is further reduced
to an alcohol or converted to an amine by an
aminotransferase.) This is a fundamentally different
reaction than beta-ketoreductase domains of polyketide
synthases which act at a carbonyl two carbons removed
from the thioester and forms an alcohol as a product.
This domain is invariably found at the C-terminus of the
proteins which contain it (presumably because it results
in the release of the product). The majority of hits to
this model are non-ribosomal peptide synthetases in
which this domain is similarly located proximal to a
thiolation domain (pfam00550). In some cases this domain
is found at the end of a polyketide synthetase enzyme,
but is unlike ketoreductase domains which are found
before the thiolase domains. Exceptions to this observed
relationship with the thiolase domain include three
proteins which consist of stand-alone reductase domains
(GP|466833 from M. leprae, GP|435954 from Anabaena and
OMNI|NTL02SC1199 from Strep. coelicolor) and one protein
(OMNI|NTL01NS2636 from Nostoc) which contains N-terminal
homology with a small group of hypothetical proteins but
no evidence of a thiolation domain next to the putative
reductase domain. Below the noise cutoff to this model
are proteins containing more distantly related
ketoreductase and dehydratase/epimerase domains. It has
been suggested that a NADP-binding motif can be found in
the N-terminal portion of this domain that may form a
Rossman-type fold.
Length = 367
Score = 83.6 bits (207), Expect = 5e-17
Identities = 64/231 (27%), Positives = 95/231 (41%), Gaps = 45/231 (19%)
Query: 220 SVLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFERLRKE 279
+VL+TG TGF+G LLE+LLR KV L RA + + + ERLR+
Sbjct: 1 TVLLTGATGFLGAYLLEELLRRSTQA-KVICLVRAA---SEEHAM---------ERLREA 47
Query: 280 CPAQL--------SRLHIIEGDILQANLGIKDSDLLMLQEEVSVVFNGAASLKLEAELKE 331
+ R+ ++ GD+ + LG+ D++ L E V + + A + E
Sbjct: 48 LRSYRLWHEDLARERIEVVAGDLSEPRLGLSDAEWERLAENVDTIVHNGALVNWVYPYSE 107
Query: 332 NVAANTRGTQRLLDIALKMKKLVAFIHFSTAFCHPDQKVLEEKLYPSPVSPHDIMRAMEW 391
AN GT+ +L +A + + ST S + D+ E
Sbjct: 108 LRGANVLGTREVLRLAA-SGRAKPLHYVSTI---------------SVGAAIDLSTVTE- 150
Query: 392 MDDETIKQLTPKILGPHPNSYTFTKRLTETLVDEY-KTKLPVVIVRPSIVL 441
DD T +TP Y +K + E LV E LPV IVRP +L
Sbjct: 151 -DDAT---VTPPP--GLAGGYAQSKWVAELLVREASDRGLPVTIVRPGRIL 195
>gnl|CDD|225857 COG3320, COG3320, Putative dehydrogenase domain of multifunctional
non-ribosomal peptide synthetases and related enzymes
[Secondary metabolites biosynthesis, transport, and
catabolism].
Length = 382
Score = 73.6 bits (181), Expect = 9e-14
Identities = 58/234 (24%), Positives = 89/234 (38%), Gaps = 47/234 (20%)
Query: 219 RSVLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFERLRK 278
R+VL+TG TGF+G LL +LL KV L RA+ S RL K
Sbjct: 1 RNVLLTGATGFLGAYLLLELLDRSD--AKVICLVRAQ------------SDEAALARLEK 46
Query: 279 ECPAQL-------SRLHIIEGDILQANLGIKDSDLLMLQEEVSVVFNGAA---SLKLEAE 328
R+ ++ GD+ + +LG+ + L E V ++ + AA + +E
Sbjct: 47 TFDLYRHWDELSADRVEVVAGDLAEPDLGLSERTWQELAENVDLIIHNAALVNHVFPYSE 106
Query: 329 LKENVAANTRGTQRLLDIALKMKKLVAFIHFSTAFCHPDQKVLEEKLYPSPVSPHDIMRA 388
L+ AN GT +L +A K + S+ V E + Y +
Sbjct: 107 LRG---ANVLGTAEVLRLAA-TGKPKPLHYVSSI------SVGETEYY------SNFTVD 150
Query: 389 MEWMDDETIKQLTPKILGPHPNSYTFTKRLTETLVDE-YKTKLPVVIVRPSIVL 441
+ + T + Y +K + E LV E LPV I RP +
Sbjct: 151 FDEISP------TRNVGQGLAGGYGRSKWVAEKLVREAGDRGLPVTIFRPGYIT 198
>gnl|CDD|235962 PRK07201, PRK07201, short chain dehydrogenase; Provisional.
Length = 657
Score = 73.4 bits (181), Expect = 2e-13
Identities = 60/222 (27%), Positives = 95/222 (42%), Gaps = 48/222 (21%)
Query: 222 LVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFERLRKECP 281
VTGGTGF+G+ L+ +LL + V++L R L E L
Sbjct: 4 FVTGGTGFIGRRLVSRLLDRRRE-ATVHVLVRR-------------QSLSRLEALAAYWG 49
Query: 282 AQLSRLHIIEGDILQANLGIKDSDLLMLQEEVSVVFNGAASLKLEAELKENVAANTRGTQ 341
A R+ + GD+ + LG+ ++D+ L ++ V + AA L A+ + AAN GT+
Sbjct: 50 AD--RVVPLVGDLTEPGLGLSEADIAELG-DIDHVVHLAAIYDLTADEEAQRAANVDGTR 106
Query: 342 RLLDIALKMKKLVA--FIHFSTAFCHPDQKVLEEKLYPSPVSPHDIMRAMEWMDDETIKQ 399
++++A ++L A F H S+ + Y E DE +
Sbjct: 107 NVVELA---ERLQAATFHHVSS--------IAVAGDYEGVFR--------EDDFDEG-QG 146
Query: 400 LTPKILGPHPNSYTFTKRLTETLVDEYKTKLPVVIVRPSIVL 441
L P P Y TK E LV E + LP + RP++V+
Sbjct: 147 L------PTP--YHRTKFEAEKLVRE-ECGLPWRVYRPAVVV 179
>gnl|CDD|187539 cd05228, AR_FR_like_1_SDR_e, uncharacterized subgroup of aldehyde
reductase and flavonoid reductase related proteins,
extended (e) SDRs. This subgroup contains proteins of
unknown function related to aldehyde reductase and
flavonoid reductase of the extended SDR-type. Aldehyde
reductase I (aka carbonyl reductase) is an NADP-binding
SDR; it has an NADP-binding motif consensus that is
slightly different from the canonical SDR form and lacks
the Asn of the extended SDR active site tetrad. Aldehyde
reductase I catalyzes the NADP-dependent reduction of
ethyl 4-chloro-3-oxobutanoate to ethyl
(R)-4-chloro-3-hydroxybutanoate. The related flavonoid
reductases act in the NADP-dependent reduction of
flavonoids, ketone-containing plant secondary
metabolites. 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 = 318
Score = 66.9 bits (164), Expect = 8e-12
Identities = 73/267 (27%), Positives = 99/267 (37%), Gaps = 83/267 (31%)
Query: 221 VLVTGGTGFMGKVLLEKLLRSCPDIG-KVYILCRAKRGLTPKARLAEFSKLPVFERLRKE 279
+LVTG TGF+G L+ LL G +V L R + LPV
Sbjct: 1 ILVTGATGFLGSNLVRALLAQ----GYRVRALVR------SGSDAVLLDGLPV------- 43
Query: 280 CPAQLSRLHIIEGDILQANLGIKDSDLLMLQ-EEVSVVFNGAA----SLKLEAELKE-NV 333
++EGD+ D+ L + VF+ AA K EL NV
Sbjct: 44 --------EVVEGDLT-------DAASLAAAMKGCDRVFHLAAFTSLWAKDRKELYRTNV 88
Query: 334 AANTRGTQRLLDIALK--MKKLVAFIHFSTAFC---HPDQKVLEEKLYPSPVSPHDIMRA 388
GT+ +LD AL+ ++++V H S+ PD ++
Sbjct: 89 E----GTRNVLDAALEAGVRRVV---HTSSIAALGGPPDGRI------------------ 123
Query: 389 MEWMDDETIKQLTPKILGPHPNSYTFTKRLTETLVDEYKTK-LPVVIVRPSIVL-PSFQE 446
DET TP P PN Y +K L E V E + L VVIV PS V P +
Sbjct: 124 -----DET----TPWNERPFPNDYYRSKLLAELEVLEAAAEGLDVVIVNPSAVFGPGDEG 174
Query: 447 PVPGW---VDSLNGPVGVLVASGKGVV 470
P +D LNG + G V
Sbjct: 175 PTSTGLDVLDYLNGKLPAYPPGGTSFV 201
>gnl|CDD|223528 COG0451, WcaG, Nucleoside-diphosphate-sugar epimerases [Cell
envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 314
Score = 65.7 bits (160), Expect = 2e-11
Identities = 69/308 (22%), Positives = 104/308 (33%), Gaps = 88/308 (28%)
Query: 221 VLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFERLRKEC 280
+LVTGG GF+G L+E+LL + D V L R + GL
Sbjct: 3 ILVTGGAGFIGSHLVERLLAAGHD---VRGLDRLRDGL---------------------- 37
Query: 281 PAQLSRLHIIEGDILQANLGIKDSDLLMLQEEVSVVFNGAA----SLKLEAELKENVAAN 336
LS + + D+ D + + V + AA ++ E + N
Sbjct: 38 DPLLSGVEFVVLDLTDR-----DLVDELAKGVPDAVIHLAAQSSVPDSNASDPAEFLDVN 92
Query: 337 TRGTQRLLDIALKMKKLVAFIHFSTAFC----HPDQKVLEEKLYPSPVSPHDIMRAMEWM 392
GT LL+ A F+ S+ P + E+ P P++P
Sbjct: 93 VDGTLNLLEAARAAGV-KRFVFASSVSVVYGDPPPLPIDEDLGPPRPLNP---------- 141
Query: 393 DDETIKQLTPKILGPHPNSYTFTKRLTETLVDEY--KTKLPVVIVRPSIVL-PSFQEPVP 449
Y +K E L+ Y LPVVI+RP V P + +
Sbjct: 142 -------------------YGVSKLAAEQLLRAYARLYGLPVVILRPFNVYGPGDKPDLS 182
Query: 450 GWV-----DSLNGPVGVLVASGKG-----------VVRSMILNDLSTETQVFNISSNEVE 493
V L ++V G G V +++L + + VFNI S E
Sbjct: 183 SGVVSAFIRQLLKGEPIIVIGGDGSQTRDFVYVDDVADALLLALENPDGGVFNIGSGTAE 242
Query: 494 AITWGEII 501
IT E+
Sbjct: 243 -ITVRELA 249
>gnl|CDD|234212 TIGR03443, alpha_am_amid, L-aminoadipate-semialdehyde dehydrogenase.
Members of this protein family are
L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31),
product of the LYS2 gene. It is also called
alpha-aminoadipate reductase. In fungi, lysine is
synthesized via aminoadipate. Currently, all members of
this family are fungal.
Length = 1389
Score = 59.7 bits (145), Expect = 7e-09
Identities = 35/111 (31%), Positives = 48/111 (43%), Gaps = 21/111 (18%)
Query: 219 RSVLVTGGTGFMGKVLLEKLL-RSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFERLR 277
+V +TG TGF+G +L LL R KV+ RAK S+ ERLR
Sbjct: 972 ITVFLTGATGFLGSFILRDLLTRRSNSNFKVFAHVRAK------------SEEAGLERLR 1019
Query: 278 KECPAQ-------LSRLHIIEGDILQANLGIKDSDLLMLQEEVSVVF-NGA 320
K SR+ ++ GD+ + G+ D L EV V+ NGA
Sbjct: 1020 KTGTTYGIWDEEWASRIEVVLGDLSKEKFGLSDEKWSDLTNEVDVIIHNGA 1070
>gnl|CDD|187552 cd05241, 3b-HSD-like_SDR_e, 3beta-hydroxysteroid dehydrogenases
(3b-HSD)-like, extended (e) SDRs. Extended SDR family
domains belonging to this subgroup have the
characteristic active site tetrad and a fairly
well-conserved NAD(P)-binding motif. 3b-HSD catalyzes
the NAD-dependent conversion of various steroids, such
as pregnenolone to progesterone, or androstenediol to
testosterone. This subgroup includes an unusual
bifunctional 3b-HSD/C-4 decarboxylase from Arabidopsis
thaliana, and Saccharomyces cerevisiae ERG26, a
3b-HSD/C-4 decarboxylase, involved in the synthesis of
ergosterol, the major sterol of yeast. It also includes
human 3 beta-HSD/HSD3B1 and C(27) 3beta-HSD/
[3beta-hydroxy-delta(5)-C(27)-steroid oxidoreductase;
HSD3B7]. C(27) 3beta-HSD/HSD3B7 is a membrane-bound
enzyme of the endoplasmic reticulum, that catalyzes the
isomerization and oxidation of 7alpha-hydroxylated
sterol intermediates, an early step in bile acid
biosynthesis. Mutations in the human NSDHL (NAD(P)H
steroid dehydrogenase-like protein) cause CHILD syndrome
(congenital hemidysplasia with ichthyosiform nevus and
limb defects), an X-linked dominant, male-lethal trait.
Mutations in the human gene encoding C(27) 3beta-HSD
underlie a rare autosomal recessive form of neonatal
cholestasis. 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 sythase 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 = 331
Score = 54.4 bits (131), Expect = 1e-07
Identities = 63/257 (24%), Positives = 90/257 (35%), Gaps = 60/257 (23%)
Query: 220 SVLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFERLRKE 279
SVLVTGG+GF G+ L+++LL + G Y+ R F P E L
Sbjct: 1 SVLVTGGSGFFGERLVKQLL----ERGGTYV------------RS--FDIAPPGEALSAW 42
Query: 280 CPAQLSRLHIIEGDILQANLGIKDSDLLMLQEEVSVVFNGAASLKLEAELKENVAANTRG 339
+ ++GDI N D+ VF+ AA + L N G
Sbjct: 43 QHPNIE---FLKGDITDRN------DVEQALSGADCVFHTAAIVPLAGPRDLYWEVNVGG 93
Query: 340 TQRLLDI--ALKMKKLVAFIHFSTAFCHPDQKVLEEKLYPSPVSPHDIMRAMEWMDDETI 397
TQ +LD ++K V S F Q +I DET
Sbjct: 94 TQNVLDACQRCGVQKFVYTSSSSVIF--GGQ---------------NIHNG-----DET- 130
Query: 398 KQLTPKILGPHPNSYTFTKRLTETLVDEYKTK--LPVVIVRPSIVL-PSFQEPVPGWVDS 454
P + Y TK + E +V E + L +RP+ + P Q VP +
Sbjct: 131 ---LPY-PPLDSDMYAETKAIAEIIVLEANGRDDLLTCALRPAGIFGPGDQGLVPILFEW 186
Query: 455 -LNGPVGVLVASGKGVV 470
G V + G +V
Sbjct: 187 AEKGLVKFVFGRGNNLV 203
>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 = 52.3 bits (126), Expect = 3e-07
Identities = 40/183 (21%), Positives = 70/183 (38%), Gaps = 46/183 (25%)
Query: 221 VLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFERLRKEC 280
+LVTGGTGF+G L+ +LL+ ++ + R R+
Sbjct: 1 ILVTGGTGFIGSHLVRRLLQEGYEVIVLG-------------------------RRRRSE 35
Query: 281 PAQLSRLHIIEGDILQANLGIKDSDLLMLQEEVSVVFNGAA------SLKLEAELKENVA 334
R+ EGD+ + + L+ + + V + AA S + A+ +
Sbjct: 36 SLNTGRIRFHEGDLTDPDALER----LLAEVQPDAVIHLAAQSGVGASFEDPADF---IR 88
Query: 335 ANTRGTQRLLDIALKMKKLVAFIHFSTA----FCHPDQKVLEEKLYPSPVSPHDIM-RAM 389
AN GT RLL+ A + + F+ S++ + E P+SP+ A
Sbjct: 89 ANVLGTLRLLE-AARRAGVKRFVFASSSEVYGDVADPP--ITEDTPLGPLSPYAAAKLAA 145
Query: 390 EWM 392
E +
Sbjct: 146 ERL 148
>gnl|CDD|212494 cd08946, SDR_e, extended (e) 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 = 200
Score = 48.8 bits (117), Expect = 2e-06
Identities = 38/174 (21%), Positives = 55/174 (31%), Gaps = 51/174 (29%)
Query: 336 NTRGTQRLLDIALKMKKLVAFIHFSTA--FCHPDQKVLEEKLYPSPVSPHDIMRAMEWMD 393
N GT LL+ A K F++ S+A + P+ EE+ P P+SP
Sbjct: 57 NVVGTLNLLEAARKAGV-KRFVYASSASVYGSPEGLPEEEETPPRPLSP----------- 104
Query: 394 DETIKQLTPKILGPHPNSYTFTKRLTETLVDEY--KTKLPVVIVRPSIVL-----PSFQE 446
Y +K E L+ Y LPVVI+R + V P
Sbjct: 105 ------------------YGVSKLAAEHLLRSYGESYGLPVVILRLANVYGPGQRPRLDG 146
Query: 447 PVPGWVDSLNGPVGVLVASGKGVVRS------------MILNDLSTETQVFNIS 488
V ++ + V G R L + V+NI
Sbjct: 147 VVNDFIRRALEGKPLTVFGGGNQTRDFIHVDDVVRAILHALENPLEGGGVYNIG 200
Score = 36.5 bits (85), Expect = 0.031
Identities = 11/25 (44%), Positives = 17/25 (68%)
Query: 221 VLVTGGTGFMGKVLLEKLLRSCPDI 245
+LVTGG GF+G L+ +LL ++
Sbjct: 1 ILVTGGAGFIGSHLVRRLLERGHEV 25
>gnl|CDD|187548 cd05237, UDP_invert_4-6DH_SDR_e, UDP-Glcnac (UDP-linked
N-acetylglucosamine) inverting 4,6-dehydratase, extended
(e) SDRs. UDP-Glcnac inverting 4,6-dehydratase was
identified in Helicobacter pylori as the hexameric flaA1
gene product (FlaA1). FlaA1 is hexameric, possesses
UDP-GlcNAc-inverting 4,6-dehydratase activity, and
catalyzes the first step in the creation of a
pseudaminic acid derivative in protein glycosylation.
Although this subgroup has the NADP-binding motif
characteristic of extended SDRs, its members tend to
have a Met substituted for the active site Tyr found in
most SDR families. 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 = 287
Score = 49.9 bits (120), Expect = 2e-06
Identities = 60/260 (23%), Positives = 103/260 (39%), Gaps = 83/260 (31%)
Query: 217 AGRSVLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFERL 276
G+++LVTGG G +G L+ ++L+ K+ + R + L L
Sbjct: 1 KGKTILVTGGAGSIGSELVRQILKF--GPKKLIVFDRDENKL---------------HEL 43
Query: 277 RKECPAQ--LSRLHIIEGDILQANLGIKDSDLL---MLQEEVSVVFNGAASLK----LEA 327
+E ++ +L I GD ++D + L + +VF+ AA+LK +E
Sbjct: 44 VRELRSRFPHDKLRFIIGD-------VRDKERLRRAFKERGPDIVFH-AAALKHVPSMED 95
Query: 328 ELKENVAANTRGTQRLLDIALKMKKLVA-FIHFSTAFCHPDQKVLEEKLYPSPVSPHDIM 386
+E + N GT+ ++D A++ V F+ ST D+ V +PV+ +M
Sbjct: 96 NPEEAIKTNVLGTKNVIDAAIENG--VEKFVCIST-----DKAV-------NPVN---VM 138
Query: 387 RAMEWMDDETIKQLTPKILGPHPNSYTFTKRLTETLV---DEYKTKLPVVIVRPSIVLPS 443
A TKR+ E L+ +EY + VR VL S
Sbjct: 139 GA--------------------------TKRVAEKLLLAKNEYSSSTKFSTVRFGNVLGS 172
Query: 444 FQEPVPGWVDSL--NGPVGV 461
+P + + GP+ V
Sbjct: 173 RGSVLPLFKKQIKKGGPLTV 192
>gnl|CDD|224013 COG1088, RfbB, dTDP-D-glucose 4,6-dehydratase [Cell envelope
biogenesis, outer membrane].
Length = 340
Score = 49.9 bits (120), Expect = 3e-06
Identities = 56/229 (24%), Positives = 86/229 (37%), Gaps = 58/229 (25%)
Query: 219 RSVLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFERLRK 278
+LVTGG GF+G + +L PD +++ K LT L + +
Sbjct: 1 MKILVTGGAGFIGSNFVRYILNKHPD---DHVVNLDK--LTYAGNLENLADV-------- 47
Query: 279 ECPAQLSRLHIIEGDILQANLGIKDSDLLMLQEEVSVVFNGAA------SLKLEAELKEN 332
R ++GDI L D L + + V + AA S+ A +
Sbjct: 48 ---EDSPRYRFVQGDICDREL----VDRLFKEYQPDAVVHFAAESHVDRSIDGPAPFIQT 100
Query: 333 VAANTRGTQRLLDIALKMKKLVAFIHFSTAFCHPDQKVLEEKLYPSPVSPHDIMRAMEWM 392
N GT LL+ A K F H ST +++Y +
Sbjct: 101 ---NVVGTYTLLEAARKYWGKFRFHHIST-----------DEVYGD-----------LGL 135
Query: 393 DDETIKQLTPKILGPHPNS-YTFTKRLTETLVDEY-KT-KLPVVIVRPS 438
DD+ + TP +P+S Y+ +K ++ LV Y +T LP I R S
Sbjct: 136 DDDAFTETTPY----NPSSPYSASKAASDLLVRAYVRTYGLPATITRCS 180
>gnl|CDD|130249 TIGR01181, dTDP_gluc_dehyt, dTDP-glucose 4,6-dehydratase. This
protein is related to UDP-glucose 4-epimerase (GalE) and
likewise has an NAD cofactor [Cell envelope,
Biosynthesis and degradation of surface polysaccharides
and lipopolysaccharides].
Length = 317
Score = 47.0 bits (112), Expect = 2e-05
Identities = 53/225 (23%), Positives = 80/225 (35%), Gaps = 53/225 (23%)
Query: 220 SVLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFERLRKE 279
+LVTGG GF+G + +L PD +V +L LT L + L
Sbjct: 1 RILVTGGAGFIGSNFVRYILNEHPDA-EVIVL----DKLTYAGNLENLADL--------- 46
Query: 280 CPAQLSRLHIIEGDILQANLGIKDSDLLMLQEEVSVVFNGAASLKLEAELKENVA---AN 336
R ++GDI L L + + V + AA ++ + A N
Sbjct: 47 --EDNPRYRFVKGDIGDREL----VSRLFTEHQPDAVVHFAAESHVDRSISGPAAFIETN 100
Query: 337 TRGTQRLLDIALKMKKLVAFIHFSTAFCHPDQKVLEEKLYPSPVSPHDIMRAMEWMDDET 396
GT LL+ K F H ST + D + +
Sbjct: 101 VVGTYTLLEAVRKYWHEFRFHHISTDEVYGDLE-----------------------KGDA 137
Query: 397 IKQLTPKILGPHPNS-YTFTKRLTETLVDEY-KT-KLPVVIVRPS 438
+ TP P+S Y+ +K ++ LV Y +T LP +I R S
Sbjct: 138 FTETTPL----APSSPYSASKAASDHLVRAYHRTYGLPALITRCS 178
>gnl|CDD|187671 cd09811, 3b-HSD_HSDB1_like_SDR_e, human 3beta-HSD (hydroxysteroid
dehydrogenase) and HSD3B1(delta 5-delta
4-isomerase)-like, extended (e) SDRs. This extended-SDR
subgroup includes human 3 beta-HSD/HSD3B1 and C(27)
3beta-HSD/ [3beta-hydroxy-delta(5)-C(27)-steroid
oxidoreductase; HSD3B7], and related proteins. These
proteins have the characteristic active site tetrad and
NAD(P)-binding motif of extended SDRs. 3 beta-HSD
catalyzes the oxidative conversion of delta 5-3
beta-hydroxysteroids to the delta 4-3-keto
configuration; this activity is essential for the
biosynthesis of all classes of hormonal steroids. C(27)
3beta-HSD is a membrane-bound enzyme of the endoplasmic
reticulum, it catalyzes the isomerization and oxidation
of 7alpha-hydroxylated sterol intermediates, an early
step in bile acid biosynthesis. Mutations in the human
gene encoding C(27) 3beta-HSD underlie a rare autosomal
recessive form of neonatal cholestasis. 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 sythase 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 = 354
Score = 46.7 bits (111), Expect = 3e-05
Identities = 34/129 (26%), Positives = 54/129 (41%), Gaps = 25/129 (19%)
Query: 220 SVLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKAR-LAEFSKLPVFERLRK 278
LVTGG GF+G+ ++ LL ++ ++ +L +A P+ E S+
Sbjct: 1 VCLVTGGGGFLGQHIIRLLLERKEELKEIRVLDKA---FGPELIEHFEKSQGKT------ 51
Query: 279 ECPAQLSRLHIIEGDILQANLGIKDSDLLMLQEEVSVVFNGAASLKLE--AELKENVAAN 336
+ IEGDI S L + VSVV + AA + + +E N
Sbjct: 52 -------YVTDIEGDIKDL------SFLFRACQGVSVVIHTAAIVDVFGPPNYEELEEVN 98
Query: 337 TRGTQRLLD 345
GTQ +L+
Sbjct: 99 VNGTQAVLE 107
>gnl|CDD|187566 cd05256, UDP_AE_SDR_e, UDP-N-acetylglucosamine 4-epimerase,
extended (e) SDRs. This subgroup contains
UDP-N-acetylglucosamine 4-epimerase of Pseudomonas
aeruginosa, WbpP, an extended SDR, that catalyzes the
NAD+ dependent conversion of UDP-GlcNAc and UDPGalNA to
UDP-Glc and UDP-Gal. 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 = 304
Score = 46.4 bits (111), Expect = 4e-05
Identities = 44/168 (26%), Positives = 74/168 (44%), Gaps = 35/168 (20%)
Query: 221 VLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFERLRKEC 280
VLVTGG GF+G L+E+LL ++ + L K+ P+ +
Sbjct: 2 VLVTGGAGFIGSHLVERLLERGHEVIVLDNLSTGKKENLPEVK----------------- 44
Query: 281 PAQLSRLHIIEGDILQANLGIKDSDLL-MLQEEVSVVFNGAASLKLEAELKENVA---AN 336
+ IEGD I+D +L+ E V VF+ AA + +++ + N
Sbjct: 45 ----PNVKFIEGD-------IRDDELVEFAFEGVDYVFHQAAQASVPRSIEDPIKDHEVN 93
Query: 337 TRGTQRLLDIALKMKKLVAFIHFSTAFCHPDQKVL--EEKLYPSPVSP 382
GT LL+ A + + F++ S++ + D L +E P+P+SP
Sbjct: 94 VLGTLNLLE-AARKAGVKRFVYASSSSVYGDPPYLPKDEDHPPNPLSP 140
>gnl|CDD|187575 cd05265, SDR_a1, atypical (a) SDRs, subgroup 1. Atypical SDRs in
this subgroup are poorly defined and have been
identified putatively as isoflavones reductase, sugar
dehydratase, mRNA binding protein etc. Atypical SDRs are
distinct from classical SDRs. Members of this subgroup
retain the canonical active site triad (though not the
upstream Asn found in most SDRs) but have an unusual
putative glycine-rich NAD(P)-binding motif, GGXXXXG, in
the usual location. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and their
glycine-rich NAD(P)-binding motif is often different
from the forms normally seen in classical or extended
SDRs. Atypical SDRs include biliverdin IX beta reductase
(BVR-B,aka flavin reductase), NMRa (a negative
transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 250
Score = 45.7 bits (109), Expect = 4e-05
Identities = 65/307 (21%), Positives = 105/307 (34%), Gaps = 98/307 (31%)
Query: 219 RSVLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFERLRK 278
+L+ GGT F+GK L+E+LL + D V + R + K + E +
Sbjct: 1 MKILIIGGTRFIGKALVEELLAAGHD---VTVFNRGRT------------KPDLPEGVE- 44
Query: 279 ECPAQLSRLHIIEGDI-----LQANLGIKDSDLLMLQEEVSVVFNGAASLKLEAELKENV 333
HI+ GD L+ LG +D D VV + +
Sbjct: 45 ---------HIV-GDRNDRDALEELLGGEDFD---------VVV-------------DTI 72
Query: 334 AANTRGTQRLLDIALKMKKLVAFIHFSTA--FCHPDQKVLEEKLYPSPVSPHDIMRAMEW 391
A R +R LD K + + +I S+A + P + + E +P
Sbjct: 73 AYTPRQVERALDA-FKGR-VKQYIFISSASVYLKPGRVITES-------TPLR------- 116
Query: 392 MDDETIKQLTPKILGPHPNSYTFTKRLTETLVDEYKTKLPVVIVRPSIVLPSFQEP--VP 449
+ + + P G KR E ++ E P IVRP + +
Sbjct: 117 -EPDAVGLSDPWDYGRG-------KRAAEDVLIEA-AAFPYTIVRPPYIYGPGDYTGRLA 167
Query: 450 GWVDSL--NGPVGVLVASG--------KGVVR---SMILNDLSTETQVFNISSNEVEAIT 496
+ D L P+ V K + R N +FNI+ + EA+T
Sbjct: 168 YFFDRLARGRPILVPGDGHSLVQFIHVKDLARALLGAAGNPK-AIGGIFNITGD--EAVT 224
Query: 497 WGEIISR 503
W E++
Sbjct: 225 WDELLEA 231
>gnl|CDD|187557 cd05246, dTDP_GD_SDR_e, dTDP-D-glucose 4,6-dehydratase, extended
(e) SDRs. This subgroup contains dTDP-D-glucose
4,6-dehydratase and related proteins, members of the
extended-SDR family, with the characteristic Rossmann
fold core region, active site tetrad and NAD(P)-binding
motif. dTDP-D-glucose 4,6-dehydratase is closely related
to other sugar epimerases of the SDR family.
dTDP-D-dlucose 4,6,-dehydratase catalyzes the second of
four steps in the dTDP-L-rhamnose pathway (the
dehydration of dTDP-D-glucose to
dTDP-4-keto-6-deoxy-D-glucose) in the synthesis of
L-rhamnose, a cell wall component of some pathogenic
bacteria. In many gram negative bacteria, L-rhamnose is
an important constituent of lipopoylsaccharide
O-antigen. The larger N-terminal portion of
dTDP-D-Glucose 4,6-dehydratase forms a Rossmann fold
NAD-binding domain, while the C-terminus binds the sugar
substrate. 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 = 315
Score = 46.0 bits (110), Expect = 5e-05
Identities = 64/237 (27%), Positives = 91/237 (38%), Gaps = 58/237 (24%)
Query: 219 RSVLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFERLRK 278
+LVTGG GF+G + LL PD I+ K LT L +
Sbjct: 1 MKILVTGGAGFIGSNFVRYLLNKYPD---YKIINLDK--LTYAGNLENLEDV-------- 47
Query: 279 ECPAQLSRLHIIEGDILQANLGIKDSDLLMLQEEVSVVFNGAA------SLKLEAELKEN 332
+ R ++GDI A L D L +E++ V + AA S+
Sbjct: 48 ---SSSPRYRFVKGDICDAEL----VDRLFEEEKIDAVIHFAAESHVDRSISDPEPFIRT 100
Query: 333 VAANTRGTQRLLDIALKMKKLVAFIHFSTAFCHPDQKVLEEKLYPSPVSPHDIMRAMEWM 392
N GT LL+ A K + F+H ST D+ +Y + E+
Sbjct: 101 ---NVLGTYTLLEAARK-YGVKRFVHIST-----DE------VYGDLLDDG------EF- 138
Query: 393 DDETIKQLTPKILGPHPNSYTFTKRLTETLVDEY-KT-KLPVVIVRPSIVLPSFQEP 447
ET +P L P + Y+ +K + LV Y +T LPVVI R S +Q P
Sbjct: 139 -TET----SP--LAPT-SPYSASKAAADLLVRAYHRTYGLPVVITRCSNNYGPYQFP 187
>gnl|CDD|217199 pfam02719, Polysacc_synt_2, Polysaccharide biosynthesis protein.
This is a family of diverse bacterial polysaccharide
biosynthesis proteins including the CapD protein, WalL
protein mannosyl-transferase and several putative
epimerases (e.g. WbiI).
Length = 280
Score = 45.6 bits (109), Expect = 5e-05
Identities = 40/144 (27%), Positives = 63/144 (43%), Gaps = 32/144 (22%)
Query: 221 VLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFERLRKEC 280
VLVTGG G +G L ++L+ + K+ + R EF + + LR+E
Sbjct: 1 VLVTGGGGSIGSELCRQILKF--NPKKIILFSR-----------DEFKLYEIRQELRQEY 47
Query: 281 PAQLSRLHIIEGDILQANLGIKDSDLL---MLQEEVSVVFNGAASLK----LEAELKENV 333
R I GD ++D + L M Q V VF+ AA+LK +E E +
Sbjct: 48 NDPKLRFFI--GD-------VRDRERLERAMEQHGVDTVFH-AAALKHVPLVEYNPMEAI 97
Query: 334 AANTRGTQRLLDIALKM--KKLVA 355
N GT+ + + A++ +K V
Sbjct: 98 KTNVLGTENVAEAAIENGVEKFVL 121
>gnl|CDD|187537 cd05226, SDR_e_a, Extended (e) and atypical (a) SDRs. Extended or
atypical short-chain dehydrogenases/reductases (SDRs,
aka tyrosine-dependent oxidoreductases) are distinct
from classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. Atypical SDRs generally
lack the catalytic residues characteristic of the SDRs,
and their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Atypical SDRs include biliverdin IX beta
reductase (BVR-B,aka flavin reductase), NMRa (a negative
transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Complex
(multidomain) SDRs such as ketoreductase domains of
fatty acid synthase have a GGXGXXG NAD(P)-binding motif
and an altered active site motif (YXXXN). Fungal type
ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding
motif.
Length = 176
Score = 44.3 bits (105), Expect = 6e-05
Identities = 44/222 (19%), Positives = 76/222 (34%), Gaps = 70/222 (31%)
Query: 221 VLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFERLRKEC 280
+L+ G TGF+G+ L +LL +V +L R + RL++ + PV
Sbjct: 1 ILILGATGFIGRALARELLE---QGHEVTLLVRNTK------RLSKEDQEPV-------- 43
Query: 281 PAQLSRLHIIEGDILQANLGIKDSDLLMLQEEVSVVFNGAASLKLEAELKENVAANTRGT 340
++EGD+ + +Q V+ A + ++ + GT
Sbjct: 44 -------AVVEGDLRDLDSLSDA-----VQGVDVVIHLAGAPR----DTRDFCEVDVEGT 87
Query: 341 QRLLDIALKMKKLVAFIHFSTAFCHPDQKVLEEKLYPSPVSPHDIMRAMEWMDDETIKQL 400
+ +L+ A K + FI S+ Y +
Sbjct: 88 RNVLE-AAKEAGVKHFIFISSLG-----------AYGDLHEETE---------------- 119
Query: 401 TPKILGPHPNSYTF-TKRLTETLVDEYKTKLPVVIVRPSIVL 441
P P+S K TE ++ E LP IVRP ++
Sbjct: 120 ------PSPSSPYLAVKAKTEAVLREA--SLPYTIVRPGVIY 153
>gnl|CDD|187551 cd05240, UDP_G4E_3_SDR_e, UDP-glucose 4 epimerase (G4E), subgroup
3, extended (e) SDRs. Members of this bacterial
subgroup are identified as possible sugar epimerases,
such as UDP-glucose 4 epimerase. However, while the
NAD(P)-binding motif is fairly well conserved, not all
members retain the canonical active site tetrad of the
extended 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. 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 = 306
Score = 44.7 bits (106), Expect = 1e-04
Identities = 49/232 (21%), Positives = 79/232 (34%), Gaps = 73/232 (31%)
Query: 221 VLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFERLRKEC 280
+LVTG G +G++L +L S P + V L R + +P E+ +L + R
Sbjct: 1 ILVTGAAGGLGRLLARRLAAS-PRVIGVDGLDRRRPPGSPPK--VEYVRLDI----RDPA 53
Query: 281 PAQLSRLHIIEGDILQANLGIKDSDLLMLQEEVSVVFNGAASL---KLEAELKENVAANT 337
A + R E V + A L + AE N
Sbjct: 54 AADVFRER-----------------------EADAVVHLAFILDPPRDGAERHR---INV 87
Query: 338 RGTQRLLDIALK--MKKLVAFIHFSTAFC---HPDQKVLEEKLYPSPVSPHDIMRAMEWM 392
GTQ +LD + ++V S+ HPD + P SP
Sbjct: 88 DGTQNVLDACAAAGVPRVV---VTSSVAVYGAHPDNPAPLTEDAPLRGSPE--------- 135
Query: 393 DDETIKQLTPKILGPHPNSYTFTKRLTETLVDEYKTKLP---VVIVRPSIVL 441
+Y+ K E L+ E++ + P V ++RP+ +L
Sbjct: 136 -----------------FAYSRDKAEVEQLLAEFRRRHPELNVTVLRPATIL 170
>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 = 42.3 bits (100), Expect = 4e-04
Identities = 36/159 (22%), Positives = 56/159 (35%), Gaps = 35/159 (22%)
Query: 217 AGRSVLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFERL 276
G +VL+TGGT +G L K L + G I+ G RLAE K +
Sbjct: 4 TGNTVLITGGTSGIGLALARKFL----EAGNTVIIT----GRRE-ERLAEAKKE-LPNIH 53
Query: 277 RKECPAQLSRLHIIEG------------DILQANLGIKDSDLLMLQEEVSVVFNGAASL- 323
+ +E DIL N GI ++ + A+ L
Sbjct: 54 TIVL--DVGDAESVEALAEALLSEYPNLDILINNAGI------QRPIDLR---DPASDLD 102
Query: 324 KLEAELKENVAANTRGTQRLLDIALKMKKLVAFIHFSTA 362
K + E+ N+ R + L LK + ++ S+
Sbjct: 103 KADTEIDTNLIGPIRLIKAFLPH-LKKQPEATIVNVSSG 140
>gnl|CDD|224011 COG1086, COG1086, Predicted nucleoside-diphosphate sugar epimerases
[Cell envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 588
Score = 43.4 bits (103), Expect = 5e-04
Identities = 37/149 (24%), Positives = 67/149 (44%), Gaps = 30/149 (20%)
Query: 208 DMGDVARWYAGRSVLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEF 267
D + G++VLVTGG G +G L ++L+ + ++ + R E+
Sbjct: 240 DTELIGAMLTGKTVLVTGGGGSIGSELCRQILKF--NPKEIILFSR-----------DEY 286
Query: 268 SKLPVFERLRKECPAQLSRLHIIEGDILQANLGIKDSDLL---MLQEEVSVVFNGAASLK 324
+ LR++ P +L GD ++D D + M +V +VF+ AA+LK
Sbjct: 287 KLYLIDMELREKFPE--LKLRFYIGD-------VRDRDRVERAMEGHKVDIVFH-AAALK 336
Query: 325 ----LEAELKENVAANTRGTQRLLDIALK 349
+E +E + N GT+ + + A+K
Sbjct: 337 HVPLVEYNPEEAIKTNVLGTENVAEAAIK 365
>gnl|CDD|215146 PLN02260, PLN02260, probable rhamnose biosynthetic enzyme.
Length = 668
Score = 42.8 bits (101), Expect = 8e-04
Identities = 57/234 (24%), Positives = 87/234 (37%), Gaps = 65/234 (27%)
Query: 216 YAGRSVLVTGGTGFMGKVLLEKLLRSCPDIGKVYIL-----CRAKRGLTPKARLAEFSKL 270
Y +++L+TG GF+ + +L+R+ PD K+ +L C + L P F
Sbjct: 4 YEPKNILITGAAGFIASHVANRLIRNYPDY-KIVVLDKLDYCSNLKNLNPSKSSPNFK-- 60
Query: 271 PVFERLRKECPAQLSRLHIIEGDILQANLGIKDSDLLMLQEEVSVVFNGAA------SLK 324
++GDI A+L + L++ E + + + AA S
Sbjct: 61 ------------------FVKGDIASADL----VNYLLITEGIDTIMHFAAQTHVDNSFG 98
Query: 325 LEAELKENVAANTRGTQRLLDIALKMKKLVAFIHFSTAFCHPDQKVLEEKLYPSPVSPHD 384
E +N N GT LL+ ++ FIH ST +V E + V H+
Sbjct: 99 NSFEFTKN---NIYGTHVLLEACKVTGQIRRFIHVST------DEVYGETDEDADVGNHE 149
Query: 385 IMRAMEWMDDETIKQLTPKILGPHPNSYTFTKRLTETLVDEYKTK--LPVVIVR 436
QL P N Y+ TK E LV Y LPV+ R
Sbjct: 150 ------------ASQLLPT------NPYSATKAGAEMLVMAYGRSYGLPVITTR 185
>gnl|CDD|215720 pfam00106, adh_short, short chain dehydrogenase. This family
contains a wide variety of dehydrogenases.
Length = 167
Score = 39.8 bits (94), Expect = 0.001
Identities = 34/161 (21%), Positives = 52/161 (32%), Gaps = 46/161 (28%)
Query: 219 RSVLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFERLRK 278
+VL+TGGTG +G L L + + +L ++RG P A L
Sbjct: 1 GTVLITGGTGGLGLALARWLAA---EGARHLVLV-SRRGPAPGA-----------AELVA 45
Query: 279 ECPAQLSRLHIIEGDI------------LQANLGIKDSDLLMLQEEVSVVFNGAASLKL- 325
E A + + + D+ L A LG + V + A L
Sbjct: 46 ELEALGAEVTVAACDVADRDALAALLAALPAALGP-----------LDGVVHNAGVLDDG 94
Query: 326 ------EAELKENVAANTRGTQRLLDIALKMKKLVAFIHFS 360
+ +A G L + L AF+ FS
Sbjct: 95 PLEELTPERFERVLAPKVTGA-WNLHELTRDLDLGAFVLFS 134
>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 = 40.4 bits (95), Expect = 0.003
Identities = 36/166 (21%), Positives = 55/166 (33%), Gaps = 39/166 (23%)
Query: 212 VARWYAGRSVLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLP 271
A G LVTGG G +G+ L L R ++ +L R L P+ K
Sbjct: 199 SAPLKPGGVYLVTGGAGGIGRALARALARRYG--ARLVLLGR--SPLPPEEE----WKAQ 250
Query: 272 VFERLRKECPAQLSRLHIIEGDILQANLGIKDSDLLMLQEEVS----------VVFNGAA 321
L A +R+ I D+ +D ++ + V + A
Sbjct: 251 TLAALE----ALGARVLYISADV---------TDAAAVRRLLEKVRERYGAIDGVIHAAG 297
Query: 322 SL-------KLEAELKENVAANTRGTQRLLDIALKMKKLVAFIHFS 360
L K + + +A G L AL + L F+ FS
Sbjct: 298 VLRDALLAQKTAEDFEAVLAPKVDGLLNLAQ-ALADEPLDFFVLFS 342
>gnl|CDD|187536 cd05193, AR_like_SDR_e, aldehyde reductase, flavonoid reductase,
and related proteins, extended (e) SDRs. This subgroup
contains aldehyde reductase and flavonoid reductase of
the extended SDR-type and related proteins. Proteins in
this subgroup have a complete SDR-type active site
tetrad and a close match to the canonical extended SDR
NADP-binding motif. Aldehyde reductase I (aka carbonyl
reductase) is an NADP-binding SDR; it catalyzes the
NADP-dependent reduction of ethyl
4-chloro-3-oxobutanoate to ethyl
(R)-4-chloro-3-hydroxybutanoate. The related flavonoid
reductases act in the NADP-dependent reduction of
flavonoids, ketone-containing plant secondary
metabolites. 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 = 295
Score = 39.9 bits (93), Expect = 0.004
Identities = 54/253 (21%), Positives = 89/253 (35%), Gaps = 46/253 (18%)
Query: 221 VLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFERLRKEC 280
VLVTG +GF+ ++E+LL +RG +A + + SK+ +
Sbjct: 1 VLVTGASGFVASHVVEQLL---------------ERGYKVRATVRDPSKVKK-VNHLLDL 44
Query: 281 PAQLSRLHIIEGDI---LQANLGIKDSDLLMLQEEVSVVFNGAASLKLEAE-LKENVAAN 336
A+ RL + D+ + IK VF+ A + ++ E +
Sbjct: 45 DAKPGRLELAVADLTDEQSFDEVIKGCAG---------VFHVATPVSFSSKDPNEVIKPA 95
Query: 337 TRGTQRLLDIALKMKKLVAFIHFSTAFCHPDQKVLEEKLYPSPVSPHDIMRAMEWMDDET 396
GT L A K + F+ S+A K E + + W + E
Sbjct: 96 IGGTLNALKAAAAAKSVKRFVLTSSAGSVLIPKPNVEGIV---------LDEKSW-NLEE 145
Query: 397 IKQLTPKILGPHPNSYTFTKRLTETLVDEYKTKLPVVIVRPSIVL-PSFQEPVP---GWV 452
K + S T ++ DE + ++ V P++ + F P GW
Sbjct: 146 FDSDPKKSAWVYAASKTLAEKAAWKFADE--NNIDLITVIPTLTIGTIFDSETPSSSGWA 203
Query: 453 DSL-NGPVGVLVA 464
SL G GV A
Sbjct: 204 MSLITGNEGVSPA 216
>gnl|CDD|187567 cd05257, Arna_like_SDR_e, Arna decarboxylase_like, extended (e)
SDRs. Decarboxylase domain of ArnA. ArnA, is an enzyme
involved in the modification of outer membrane protein
lipid A of gram-negative bacteria. It is a bifunctional
enzyme that catalyzes the NAD-dependent decarboxylation
of UDP-glucuronic acid and
N-10-formyltetrahydrofolate-dependent formylation of
UDP-4-amino-4-deoxy-l-arabinose; its NAD-dependent
decaboxylating activity is in the C-terminal 360
residues. This subgroup belongs to the extended SDR
family, however the NAD binding motif is not a perfect
match and the upstream Asn of the canonical active site
tetrad is not conserved. 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 = 39.2 bits (92), Expect = 0.006
Identities = 45/156 (28%), Positives = 58/156 (37%), Gaps = 51/156 (32%)
Query: 220 SVLVTGGTGFMGKVLLEKLLRSCPDIG-KVYILC----RAKRGLTPKARLAEFSKLPVFE 274
+VLVTG GF+G L E+LLR G +V L GL A F
Sbjct: 1 NVLVTGADGFIGSHLTERLLRE----GHEVRALDIYNSFNSWGLLDNAVHDRF------- 49
Query: 275 RLRKECPAQLSRLHIIEGDILQANLG---IKDSDLLMLQEEVSVVFNGAA----SLKLEA 327
H I GD+ A+ +K D VVF+ AA A
Sbjct: 50 -------------HFISGDVRDASEVEYLVKKCD---------VVFHLAALIAIPYSYTA 87
Query: 328 ELKENVAANTRGTQRLLDIALKM--KKLVAFIHFST 361
L V N GT +L+ A + K++V H ST
Sbjct: 88 PL-SYVETNVFGTLNVLEAACVLYRKRVV---HTST 119
>gnl|CDD|224012 COG1087, GalE, UDP-glucose 4-epimerase [Cell envelope biogenesis,
outer membrane].
Length = 329
Score = 39.1 bits (92), Expect = 0.006
Identities = 45/195 (23%), Positives = 71/195 (36%), Gaps = 66/195 (33%)
Query: 220 SVLVTGGTGFMG----KVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFER 275
VLVTGG G++G + LL+ G V +
Sbjct: 2 KVLVTGGAGYIGSHTVRQLLKT-------------------GHEVV----------VLDN 32
Query: 276 LRKECPAQLSRLHI--IEGDILQANLGIKDSDLL---MLQEEVSVVFNGAASLKLEAELK 330
L L +L EGD+L D LL + ++ V + AAS +
Sbjct: 33 LSNGHKIALLKLQFKFYEGDLL-------DRALLTAVFEENKIDAVVHFAAS----ISVG 81
Query: 331 ENVA-------ANTRGTQRLLDIALK--MKKLVAFIHF-STA--FCHPDQKVLEEKLYPS 378
E+V N GT L++ L+ +KK + F STA + P + E +
Sbjct: 82 ESVQNPLKYYDNNVVGTLNLIEAMLQTGVKKFI----FSSTAAVYGEPTTSPISETSPLA 137
Query: 379 PVSPHDIMRAM-EWM 392
P++P+ + M E +
Sbjct: 138 PINPYGRSKLMSEEI 152
>gnl|CDD|187673 cd09813, 3b-HSD-NSDHL-like_SDR_e, human NSDHL (NAD(P)H steroid
dehydrogenase-like protein)-like, extended (e) SDRs.
This subgroup includes human NSDHL and related proteins.
These proteins have the characteristic active site
tetrad of extended SDRs, and also have a close match to
their NAD(P)-binding motif. Human NSDHL is a
3beta-hydroxysteroid dehydrogenase (3 beta-HSD) which
functions in the cholesterol biosynthetic pathway. 3
beta-HSD catalyzes the oxidative conversion of delta 5-3
beta-hydroxysteroids to the delta 4-3-keto
configuration; this activity is essential for the
biosynthesis of all classes of hormonal steroids.
Mutations in the gene encoding NSDHL cause CHILD
syndrome (congenital hemidysplasia with ichthyosiform
nevus and limb defects), an X-linked dominant,
male-lethal trait. This subgroup also includes an
unusual bifunctional [3beta-hydroxysteroid dehydrogenase
(3b-HSD)/C-4 decarboxylase from Arabidopsis thaliana,
and Saccharomyces cerevisiae ERG26, a 3b-HSD/C-4
decarboxylase, involved in the synthesis of ergosterol,
the major sterol of yeast. 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 sythase 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 = 335
Score = 39.3 bits (92), Expect = 0.008
Identities = 57/241 (23%), Positives = 95/241 (39%), Gaps = 62/241 (25%)
Query: 220 SVLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFERLRKE 279
S LV GG+GF+G+ L+E+LLR RG + F P FE
Sbjct: 1 SCLVVGGSGFLGRHLVEQLLR---------------RG---NPTVHVFDIRPTFELDPSS 42
Query: 280 CPAQLSRLHIIEGDILQANLGIKDSDLL--MLQEEVSVVFNGAA-SLKLEAELKENVAAN 336
R+ GD+ DL ++ +VVF+ A+ +L V N
Sbjct: 43 SG----RVQFHTGDL------TDPQDLEKAFNEKGPNVVFHTASPDHGSNDDLYYKV--N 90
Query: 337 TRGTQRLLDIALKMKKLVAFIHFSTAFCHPDQKVLEEKLYPSPVSPHDIMRAMEWMDDET 396
+GT+ +++ A + + ++ S+A V+ DI+ DE+
Sbjct: 91 VQGTRNVIE-ACRKCGVKKLVYTSSA------SVVFNG--------QDIING-----DES 130
Query: 397 IKQLTPKILGPHPNSYTFTKRLTETLVDEYK---TKLPVVIVRPSIVL-PSFQEPVPGWV 452
+ P H ++Y TK L E LV + + L +RP+ + P ++ VPG +
Sbjct: 131 L----PYPDK-HQDAYNETKALAEKLVLKANDPESGLLTCALRPAGIFGPGDRQLVPGLL 185
Query: 453 D 453
Sbjct: 186 K 186
>gnl|CDD|182639 PRK10675, PRK10675, UDP-galactose-4-epimerase; Provisional.
Length = 338
Score = 38.6 bits (90), Expect = 0.011
Identities = 51/177 (28%), Positives = 81/177 (45%), Gaps = 42/177 (23%)
Query: 220 SVLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFERLRKE 279
VLVTGG+G++G +LL++ D+ + LC +KR S LPV ERL +
Sbjct: 2 RVLVTGGSGYIGSHTCVQLLQNGHDVVILDNLCNSKR-----------SVLPVIERLGGK 50
Query: 280 CPAQLSRLHIIEGDILQANLGIKDSDLL---MLQEEVSVVFNGAASLKLEAELKENVAA- 335
P +EGD I++ LL + + V + A L+A + E+V
Sbjct: 51 HPT------FVEGD-------IRNEALLTEILHDHAIDTVIHFAG---LKA-VGESVQKP 93
Query: 336 ------NTRGTQRLLDIALKMKKLVAFIHFSTAFCHPDQ-KVLEEKLYP--SPVSPH 383
N GT RL+ A++ + I S+A + DQ K+ + +P +P SP+
Sbjct: 94 LEYYDNNVNGTLRLIS-AMRAANVKNLIFSSSATVYGDQPKIPYVESFPTGTPQSPY 149
>gnl|CDD|227381 COG5048, COG5048, FOG: Zn-finger [General function prediction
only].
Length = 467
Score = 38.5 bits (89), Expect = 0.012
Identities = 26/100 (26%), Positives = 35/100 (35%), Gaps = 9/100 (9%)
Query: 709 RQKTFENLVRTFQCTYPECLKFYAK---MSHLKAHLR--RHSGE--RSFKCDWQDCKWQF 761
++ + + S L HLR HSGE + F C + C F
Sbjct: 274 SPNESDSSSEKGFSLPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLF 333
Query: 762 SRSDELSRHRRSHFGIKPYPCTLCV--KKSLLAILNCPHE 799
SR+D L RH H I P L K + N P +
Sbjct: 334 SRNDALKRHILLHTSISPAKEKLLNSSSKFSPLLNNEPPQ 373
Score = 35.1 bits (80), Expect = 0.18
Identities = 24/62 (38%), Positives = 34/62 (54%), Gaps = 2/62 (3%)
Query: 713 FENLVRTFQCTYPECLKFYAKMSHLKAHLRRHSGERSFKCDWQDCKWQFSRSDELSRHRR 772
N R C P C ++++ HL H+R H+GE+ +C + C FSR ELSRH R
Sbjct: 27 LSNAPRPDSC--PNCTDSFSRLEHLTRHIRSHTGEKPSQCSYSGCDKSFSRPLELSRHLR 84
Query: 773 SH 774
+H
Sbjct: 85 TH 86
Score = 32.4 bits (73), Expect = 1.2
Identities = 13/60 (21%), Positives = 25/60 (41%)
Query: 715 NLVRTFQCTYPECLKFYAKMSHLKAHLRRHSGERSFKCDWQDCKWQFSRSDELSRHRRSH 774
+ + C++ + + S+L H+ H R + C C F+R L H++ H
Sbjct: 382 KNDKKSETLSNSCIRNFKRDSNLSLHIITHLSFRPYNCKNPPCSKSFNRHYNLIPHKKIH 441
>gnl|CDD|183778 PRK12829, PRK12829, short chain dehydrogenase; Provisional.
Length = 264
Score = 37.7 bits (88), Expect = 0.015
Identities = 31/157 (19%), Positives = 52/157 (33%), Gaps = 27/157 (17%)
Query: 216 YAGRSVLVTGGTGFMGKVLLEKLLRSCPDIG-KVYILCRAKRGL-TPKARLAEFSKLPVF 273
G VLVTGG +G+ + E G +V++ ++ L ARL
Sbjct: 9 LDGLRVLVTGGASGIGRAIAEAFAE----AGARVHVCDVSEAALAATAARLPGAKVTATV 64
Query: 274 ERLRKECPAQLSRL--HIIEG----DILQANLGI--KDSDLLMLQEEVSVVFNGAASLKL 325
+ PAQ+ R+ +E D+L N GI + + E +
Sbjct: 65 ADVAD--PAQVERVFDTAVERFGGLDVLVNNAGIAGPTGGIDEITPE-----------QW 111
Query: 326 EAELKENVAANTRGTQRLLDIALKMKKLVAFIHFSTA 362
E L N+ + + + I S+
Sbjct: 112 EQTLAVNLNGQFYFARAAVPLLKASGHGGVIIALSSV 148
>gnl|CDD|222150 pfam13465, zf-H2C2_2, Zinc-finger double domain.
Length = 26
Score = 33.5 bits (77), Expect = 0.015
Identities = 11/20 (55%), Positives = 13/20 (65%)
Query: 766 ELSRHRRSHFGIKPYPCTLC 785
L RH R+H G KPY C +C
Sbjct: 1 NLRRHMRTHTGEKPYKCPVC 20
Score = 31.2 bits (71), Expect = 0.11
Identities = 8/18 (44%), Positives = 14/18 (77%)
Query: 736 HLKAHLRRHSGERSFKCD 753
+L+ H+R H+GE+ +KC
Sbjct: 1 NLRRHMRTHTGEKPYKCP 18
>gnl|CDD|163279 TIGR03466, HpnA, hopanoid-associated sugar epimerase. The
sequences in this family are members of the pfam01370
superfamily of NAD-dependent epimerases and dehydratases
typically acting on nucleotide-sugar substrates. The
genes of the family modeled here are generally in the
same locus with genes involved in the biosynthesis and
elaboration of hopene, the cyclization product of the
polyisoprenoid squalene. This gene and its association
with hopene biosynthesis in Zymomonas mobilis has been
noted in the literature where the gene symbol hpnA was
assigned. Hopanoids are known to be components of the
plasma membrane and to have polar sugar head groups in
Z. mobilis and other species.
Length = 328
Score = 37.3 bits (87), Expect = 0.031
Identities = 61/229 (26%), Positives = 86/229 (37%), Gaps = 73/229 (31%)
Query: 221 VLVTGGTGFMGKVLLEKLL-RSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFERLRKE 279
VLVTG TGF+G ++ LL + +V +L R P + L V
Sbjct: 3 VLVTGATGFVGSAVVRLLLEQGE----EVRVLVR------PTSDRRNLEGLDV------- 45
Query: 280 CPAQLSRLHIIEGDILQANLGIKDSDLLMLQ-EEVSVVFNGAASLKLEAELKENV-AANT 337
I+EGD ++D L +F+ AA +L A E + AAN
Sbjct: 46 --------EIVEGD-------LRDPASLRKAVAGCRALFHVAADYRLWAPDPEEMYAANV 90
Query: 338 RGTQRLLDIALK--MKKLVAFIHFSTAFCHPDQKVLEEKLYPSPVS----PHDIMRAMEW 391
GT+ LL AL+ ++++V Y S V+ D A
Sbjct: 91 EGTRNLLRAALEAGVERVV---------------------YTSSVATLGVRGDGTPA--- 126
Query: 392 MDDETIKQLTPKILGPHPNSYTFTKRLTETLVDEY--KTKLPVVIVRPS 438
DET ++G Y +K L E E + LPVVIV PS
Sbjct: 127 --DETTPSSLDDMIGH----YKRSKFLAEQAALEMAAEKGLPVVIVNPS 169
>gnl|CDD|187574 cd05264, UDP_G4E_5_SDR_e, UDP-glucose 4-epimerase (G4E), subgroup
5, extended (e) SDRs. This subgroup partially conserves
the characteristic active site tetrad and NAD-binding
motif of the extended SDRs, and has been identified as
possible UDP-glucose 4-epimerase (aka UDP-galactose
4-epimerase), a homodimeric member of the extended SDR
family. UDP-glucose 4-epimerase catalyzes the
NAD-dependent conversion of UDP-galactose to
UDP-glucose, the final step in Leloir galactose
synthesis. 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 = 300
Score = 36.9 bits (86), Expect = 0.035
Identities = 57/299 (19%), Positives = 95/299 (31%), Gaps = 94/299 (31%)
Query: 220 SVLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFERLRKE 279
VL+ GG GF+G L++ L L E ++ VF+R
Sbjct: 1 RVLIVGGNGFIGSHLVDAL-------------------------LEEGPQVRVFDRSIPP 35
Query: 280 CPAQLSRLHIIEGDILQANLGIKDSDLLMLQEEVSVVFNGAA-SLKLEAELK--ENVAAN 336
L + I+GD N DL + V + A+ + + ++ N
Sbjct: 36 YELPLGGVDYIKGDY--ENRA----DLESALVGIDTVIHLASTTNPATSNKNPILDIQTN 89
Query: 337 TRGTQRLLD--IALKMKKLVAFIHFSTAFCHPDQKVLEEKLYPSPVSPHDIMRAMEWMDD 394
T +LL+ A + K++ T + P+Q + E P+S + I
Sbjct: 90 VAPTVQLLEACAAAGIGKIIFASSGGTVYGVPEQLPISESDPTLPISSYGI--------- 140
Query: 395 ETIKQLTPKILGPHPNSYTFTKRLTETLVDEYKTK--LPVVIVRPSIVLPSFQEPVPGWV 452
+K E + Y+ L ++R S Q P
Sbjct: 141 --------------------SKLAIEKYLRLYQYLYGLDYTVLRISNPYGPGQRP----- 175
Query: 453 DSLNGPVGVLVAS----------GKG-VVRSMI-LNDL----------STETQVFNISS 489
D G + + + G G +R I ++DL +VFNI S
Sbjct: 176 DGKQGVIPIALNKILRGEPIEIWGDGESIRDYIYIDDLVEALMALLRSKGLEEVFNIGS 234
>gnl|CDD|216283 pfam01073, 3Beta_HSD, 3-beta hydroxysteroid dehydrogenase/isomerase
family. The enzyme 3 beta-hydroxysteroid
dehydrogenase/5-ene-4-ene isomerase (3 beta-HSD)
catalyzes the oxidation and isomerisation of 5-ene-3
beta-hydroxypregnene and 5-ene-hydroxyandrostene steroid
precursors into the corresponding 4-ene-ketosteroids
necessary for the formation of all classes of steroid
hormones.
Length = 280
Score = 36.5 bits (85), Expect = 0.038
Identities = 50/204 (24%), Positives = 82/204 (40%), Gaps = 49/204 (24%)
Query: 222 LVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFERLRKECP 281
LVTGG GF+G+ ++ LLR G++ + +P+ L +FSKL V
Sbjct: 1 LVTGGGGFLGRHIVRLLLR----EGELQEVRVFDLRFSPEL-LEDFSKLQV--------- 46
Query: 282 AQLSRLHIIEGDILQANLGIKDSDLLMLQEEVSVVFNGAASLKLEAELKENV--AANTRG 339
+ IEGD+ DL + VV + AA + + + + N +G
Sbjct: 47 -----ITYIEGDVTDK------QDLRRALQGSDVVIHTAAIIDVFGKAYRDTIMKVNVKG 95
Query: 340 TQRLLDIALKMKKLVAFIHFSTAFCHPDQKVLEEKLYPSPVSPHDIMRAMEWMDDETIKQ 399
TQ +LD +K + ++ S+ E + P+ I+ D+ T +
Sbjct: 96 TQNVLDACVKA-GVRVLVYTSSM----------EVVGPNSYG-QPIVNG----DETTPYE 139
Query: 400 LTPKILGPHPNSYTFTKRLTETLV 423
T + P Y +K L E LV
Sbjct: 140 STHQ----DP--YPESKALAEKLV 157
>gnl|CDD|187660 cd08957, WbmH_like_SDR_e, Bordetella bronchiseptica enzymes WbmH
and WbmG-like, extended (e) SDRs. Bordetella
bronchiseptica enzymes WbmH and WbmG, and related
proteins. This subgroup exhibits the active site tetrad
and NAD-binding motif of the extended SDR family. It has
been proposed that the active site in Bordetella WbmG
and WbmH cannot function as an epimerase, and that it
plays a role in O-antigen synthesis pathway from
UDP-2,3-diacetamido-2,3-dideoxy-l-galacturonic acid.
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 = 307
Score = 36.3 bits (84), Expect = 0.049
Identities = 37/162 (22%), Positives = 63/162 (38%), Gaps = 27/162 (16%)
Query: 221 VLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFERLRKEC 280
VL+TGG G +G L+E LL +V ++ G R+E
Sbjct: 3 VLITGGAGQIGSHLIEHLL---ERGHQVVVIDNFATG-------------------RREH 40
Query: 281 PAQLSRLHIIEGDILQANLGIKDSDLLMLQEEVSVVFNGAASLKLEAELKENVAANTRGT 340
L ++EG I A+ + D + + V + AA+ K + E+ N G
Sbjct: 41 LPDHPNLTVVEGSI--ADKALVDKLFGDFKPD--AVVHTAAAYKDPDDWYEDTLTNVVGG 96
Query: 341 QRLLDIALKMKKLVAFIHFSTAFCHPDQKVLEEKLYPSPVSP 382
++ A K + I+F TA C+ + + + P +P
Sbjct: 97 ANVVQAA-KKAGVKRLIYFQTALCYGLKPMQQPIRLDHPRAP 137
>gnl|CDD|187560 cd05250, CC3_like_SDR_a, CC3(TIP30)-like, atypical (a) SDRs.
Atypical SDRs in this subgroup include CC3 (also known
as TIP30) which is implicated in tumor suppression.
Atypical SDRs are distinct from classical SDRs. Members
of this subgroup have a glycine rich NAD(P)-binding
motif that resembles the extended SDRs, and have an
active site triad of the SDRs (YXXXK and upstream Ser),
although the upstream Asn of the usual SDR active site
is substituted with Asp. For CC3, the Tyr of the triad
is displaced compared to the usual SDRs and the protein
is monomeric, both these observations suggest that the
usual SDR catalytic activity is not present. NADP
appears to serve an important role as a ligand, and may
be important in the interaction with other
macromolecules. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and their
glycine-rich NAD(P)-binding motif is often different
from the forms normally seen in classical or extended
SDRs. Atypical SDRs include biliverdin IX beta reductase
(BVR-B,aka flavin reductase), NMRa (a negative
transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 214
Score = 35.7 bits (83), Expect = 0.059
Identities = 16/35 (45%), Positives = 22/35 (62%), Gaps = 1/35 (2%)
Query: 219 RSVLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCR 253
++ LV G TG +GK LL +LL+S P KV + R
Sbjct: 1 KTALVLGATGLVGKHLLRELLKS-PYYSKVTAIVR 34
>gnl|CDD|223774 COG0702, COG0702, Predicted nucleoside-diphosphate-sugar epimerases
[Cell envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 275
Score = 35.3 bits (81), Expect = 0.095
Identities = 17/58 (29%), Positives = 23/58 (39%), Gaps = 7/58 (12%)
Query: 221 VLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFERLRK 278
+LVTG TGF+G ++ +LL +V R A E V LR
Sbjct: 3 ILVTGATGFVGGAVVRELLA---RGHEVRAAVRNPEAAAALAGGVE----VVLGDLRD 53
>gnl|CDD|223016 PHA03233, PHA03233, DNA packaging protein UL32; Provisional.
Length = 518
Score = 35.1 bits (81), Expect = 0.15
Identities = 17/56 (30%), Positives = 28/56 (50%)
Query: 535 VIFTQILPAYLVDFIMVLIRQKTFLVRVQNRIWLGMHLLEYFTTRNWDFKNKRLLA 590
V+F + YL + + + + V+ R+WL +HL + F +FKNK LA
Sbjct: 435 VLFGTVPAEYLQELKLAICYDNEYPSSVERRVWLYIHLFKAFQIIKRNFKNKTQLA 490
>gnl|CDD|187579 cd05271, NDUFA9_like_SDR_a, NADH dehydrogenase (ubiquinone) 1 alpha
subcomplex, subunit 9, 39 kDa, (NDUFA9) -like, atypical
(a) SDRs. This subgroup of extended SDR-like proteins
are atypical SDRs. They have a glycine-rich
NAD(P)-binding motif similar to the typical SDRs,
GXXGXXG, and have the YXXXK active site motif (though
not the other residues of the SDR tetrad). Members
identified include NDUFA9 (mitochondrial) and putative
nucleoside-diphosphate-sugar epimerase. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Atypical SDRs include
biliverdin IX beta reductase (BVR-B,aka flavin
reductase), NMRa (a negative transcriptional regulator
of various fungi), progesterone 5-beta-reductase like
proteins, phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 273
Score = 34.5 bits (80), Expect = 0.16
Identities = 37/148 (25%), Positives = 54/148 (36%), Gaps = 40/148 (27%)
Query: 221 VLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFERLRKEC 280
V V G TGF+G+ ++ +L AKRG S++ V R C
Sbjct: 3 VTVFGATGFIGRYVVNRL---------------AKRG----------SQVIVPYR----C 33
Query: 281 PAQLSRLHIIEGD-----ILQANLGIKDSDLLMLQEEVSVVFNGAASLKLEAELK-ENVA 334
A RL ++ GD ++ +L D + E VV N L E+V
Sbjct: 34 EAYARRLLVM-GDLGQVLFVEFDL-RDDESIRKALEGSDVVINLVGRLYETKNFSFEDV- 90
Query: 335 ANTRGTQRLLDIALKMKKLVAFIHFSTA 362
+ G +RL A + IH S
Sbjct: 91 -HVEGPERLAKAAKEAGVE-RLIHISAL 116
>gnl|CDD|200998 pfam00096, zf-C2H2, Zinc finger, C2H2 type. The C2H2 zinc finger
is the classical zinc finger domain. The two conserved
cysteines and histidines co-ordinate a zinc ion. The
following pattern describes the zinc finger.
#-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can
be any amino acid, and numbers in brackets indicate the
number of residues. The positions marked # are those
that are important for the stable fold of the zinc
finger. The final position can be either his or cys. The
C2H2 zinc finger is composed of two short beta strands
followed by an alpha helix. The amino terminal part of
the helix binds the major groove in DNA binding zinc
fingers. The accepted consensus binding sequence for Sp1
is usually defined by the asymmetric hexanucleotide core
GGGCGG but this sequence does not include, among others,
the GAG (=CTC) repeat that constitutes a high-affinity
site for Sp1 binding to the wt1 promoter.
Length = 22
Score = 30.4 bits (69), Expect = 0.20
Identities = 12/24 (50%), Positives = 13/24 (54%), Gaps = 2/24 (8%)
Query: 751 KCDWQDCKWQFSRSDELSRHRRSH 774
KC DC FSR L RH R+H
Sbjct: 1 KC--PDCGKSFSRKSNLKRHLRTH 22
Score = 28.9 bits (65), Expect = 0.63
Identities = 11/24 (45%), Positives = 17/24 (70%), Gaps = 2/24 (8%)
Query: 721 QCTYPECLKFYAKMSHLKAHLRRH 744
+C P+C K +++ S+LK HLR H
Sbjct: 1 KC--PDCGKSFSRKSNLKRHLRTH 22
>gnl|CDD|222146 pfam13460, NAD_binding_10, NADH(P)-binding.
Length = 182
Score = 33.8 bits (78), Expect = 0.20
Identities = 28/177 (15%), Positives = 53/177 (29%), Gaps = 50/177 (28%)
Query: 221 VLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFERLRKEC 280
+ V G TG G+ L+++LL RG A S R
Sbjct: 1 IAVIGATGKTGRRLVKELLA---------------RGHQVTA----LS--------RNPS 33
Query: 281 PAQLSRLHIIEGDILQANLGIKDSDLLMLQEEVSVVFNGAASLKLEAELKENV--AANTR 338
A + ++ D+ +L L V V + + +++ +++ AA
Sbjct: 34 KAPAPGVTPVQKDLF--DLADLAEAL----AGVDAVVDAFGARPDDSDGVKHLLDAAARA 87
Query: 339 GTQRLLDIALKMKKLVAFIHFSTAFCHPDQKVLEEKLYPSPVSPHDIMRAMEWMDDE 395
G +R++ + S A + D RA ++
Sbjct: 88 GVRRIVVV-------------SAAGLYRD--EPGTFRLDDAPLFPPYARAKAAAEEL 129
>gnl|CDD|223959 COG1028, FabG, Dehydrogenases with different specificities (related
to short-chain alcohol dehydrogenases) [Secondary
metabolites biosynthesis, transport, and catabolism /
General function prediction only].
Length = 251
Score = 34.0 bits (78), Expect = 0.21
Identities = 25/155 (16%), Positives = 50/155 (32%), Gaps = 25/155 (16%)
Query: 217 AGRSVLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFERL 276
+G+ LVTG + +G+ + L R + +V + R +A A +
Sbjct: 4 SGKVALVTGASSGIGRAIARALAR---EGARVVVAARRSEEEAAEALAAAIKE------- 53
Query: 277 RKECPAQLSRLHIIEGDILQANLGIKD--SDLLMLQEEVSVVFNGAASLKL--------E 326
A R + D+ ++ + + ++ N A E
Sbjct: 54 -----AGGGRAAAVAADVSDDEESVEALVAAAEEEFGRIDILVNNAGIAGPDAPLEELTE 108
Query: 327 AELKENVAANTRGTQRLLDIALKMKKLVAFIHFST 361
+ + N G L AL + K ++ S+
Sbjct: 109 EDWDRVIDVNLLGAFLLTRAALPLMKKQRIVNISS 143
>gnl|CDD|233909 TIGR02520, pilus_B_mal_scr, type IVB pilus formation outer membrane
protein, R64 PilN family. Several related protein
families encode outer membrane pore proteins for type II
secretion, type III secretion, and type IV pilus
formation. This protein family appears to encode a
secretin for pilus formation, although it is quite
different from PilQ. Members include the PilN
lipoprotein of the plasmid R64 thin pilus, a type IV
pilus. Scoring between the trusted and noise cutoffs are
examples of bundle-forming pilus B (bfpB) [Cell
envelope, Surface structures, Protein fate, Protein and
peptide secretion and trafficking].
Length = 497
Score = 34.5 bits (79), Expect = 0.22
Identities = 25/102 (24%), Positives = 39/102 (38%), Gaps = 7/102 (6%)
Query: 428 TKLPVVIVRPSIVLPSFQEPVPGWVDSLNGPVGVLVASGKGVVRSM--ILNDLSTETQVF 485
+PVVI P + G V + VL +G + L ST+++
Sbjct: 50 CGVPVVIA-PDAMSALSGSSSQGGVGAARAIPAVLPRPDEGGRPPLPSGLGATSTQSEGP 108
Query: 486 NISSNEVEAITWGEIISRGKQLIYQYPLEAGL-W-YPNGQIR 525
++ + I+W G L+ Q GL W Y NG +R
Sbjct: 109 GGTAGLITDISWEGEPLGG--LLDQVTSRLGLSWKYENGAVR 148
>gnl|CDD|213592 TIGR01179, galE, UDP-glucose-4-epimerase GalE. Alternate name:
UDPgalactose 4-epimerase This enzyme interconverts
UDP-glucose and UDP-galactose. A set of related
proteins, some of which are tentatively identified as
UDP-glucose-4-epimerase in Thermotoga maritima, Bacillus
halodurans, and several archaea, but deeply branched
from this set and lacking experimental evidence, are
excluded from This model and described by a separate
model [Energy metabolism, Sugars].
Length = 328
Score = 33.5 bits (77), Expect = 0.40
Identities = 41/181 (22%), Positives = 70/181 (38%), Gaps = 36/181 (19%)
Query: 221 VLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFERLRKEC 280
+LVTGG G++G + +LL S ++ + L R LP ER+
Sbjct: 2 ILVTGGAGYIGSHTVRQLLESGHEVVILDNLSNGSR-----------EALPRGERITP-- 48
Query: 281 PAQLSRLHIIEGDILQANLGIKDSDLLMLQEEVSVVFNGAA------SLKLEAELKENVA 334
+ +EGD+ L D L + ++ V + A S++ + N
Sbjct: 49 ------VTFVEGDLRDREL----LDRLFEEHKIDAVIHFAGLIAVGESVQKPLKYYRN-- 96
Query: 335 ANTRGTQRLLDIALKMKKLVAFIHFSTA--FCHPDQKVLEEKLYPSPVSPHDIMRAM-EW 391
N GT LL+ + FI S+A + P + E P++P+ + M E
Sbjct: 97 -NVVGTLNLLEAMQQAGV-KKFIFSSSAAVYGEPSSIPISEDSPLGPINPYGRSKLMSEQ 154
Query: 392 M 392
+
Sbjct: 155 I 155
>gnl|CDD|187549 cd05238, Gne_like_SDR_e, Escherichia coli Gne (a
nucleoside-diphosphate-sugar 4-epimerase)-like, extended
(e) SDRs. Nucleoside-diphosphate-sugar 4-epimerase has
the characteristic active site tetrad and NAD-binding
motif of the extended SDR, and is related to more
specifically defined epimerases such as UDP-glucose 4
epimerase (aka UDP-galactose-4-epimerase), which
catalyzes the NAD-dependent conversion of UDP-galactose
to UDP-glucose, the final step in Leloir galactose
synthesis. This subgroup includes Escherichia coli
055:H7 Gne, a UDP-GlcNAc 4-epimerase, essential for O55
antigen synthesis. 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 = 305
Score = 33.5 bits (77), Expect = 0.46
Identities = 56/231 (24%), Positives = 87/231 (37%), Gaps = 70/231 (30%)
Query: 220 SVLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFERLRKE 279
VL+TG +GF+G+ L E+LL S ++ ++ PKA
Sbjct: 2 KVLITGASGFVGQRLAERLL-SDVPNERLILIDVVS----PKA----------------- 39
Query: 280 CPAQLSRLHIIEGDILQANLGIKDSDLLMLQEEVSVVFNGAASLKLEAELKENV--AANT 337
P+ R+ I GD A + ++ + VVF+ AA + AE ++ N
Sbjct: 40 -PSGAPRVTQIAGD--LAVPALIEA---LANGRPDVVFHLAAIVSGGAEADFDLGYRVNV 93
Query: 338 RGTQRLLDIALKMKKLVAFIHFST--AFCHPDQKVLEEKLYPSPVSPHDIMRAMEWMDDE 395
GT+ LL+ K F+ S+ + P P+PV D
Sbjct: 94 DGTRNLLEALRKNGPKPRFVFTSSLAVYGLP---------LPNPV------------TDH 132
Query: 396 TIKQLTPKILGPHPNSYTFTKRLTETLVDEYKTK---------LPVVIVRP 437
T L P +SY K + E L+++Y + LP V VRP
Sbjct: 133 TA--LDPA------SSYGAQKAMCELLLNDYSRRGFVDGRTLRLPTVCVRP 175
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 29.4 bits (66), Expect = 0.49
Identities = 7/25 (28%), Positives = 10/25 (40%), Gaps = 2/25 (8%)
Query: 750 FKCDWQDCKWQFSRSDELSRHRRSH 774
++C C F L H R+H
Sbjct: 1 YRCPE--CGKVFKSKSALREHMRTH 23
>gnl|CDD|236116 PRK07856, PRK07856, short chain dehydrogenase; Provisional.
Length = 252
Score = 33.0 bits (76), Expect = 0.53
Identities = 18/52 (34%), Positives = 24/52 (46%), Gaps = 4/52 (7%)
Query: 216 YAGRSVLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEF 267
GR VLVTGGT +G + L + G ++C + T R AEF
Sbjct: 4 LTGRVVLVTGGTRGIGAGIARAFLAA----GATVVVCGRRAPETVDGRPAEF 51
>gnl|CDD|233570 TIGR01777, yfcH, TIGR01777 family protein. This model represents a
clade of proteins of unknown function including the E.
coli yfcH protein [Hypothetical proteins, Conserved].
Length = 291
Score = 33.0 bits (76), Expect = 0.60
Identities = 15/38 (39%), Positives = 24/38 (63%), Gaps = 5/38 (13%)
Query: 221 VLVTGGTGFMGKVLLEKLLRSCPDIG-KVYILCRAKRG 257
+L+TGGTGF+G+ L ++L + G +V IL R+
Sbjct: 1 ILITGGTGFIGRALTQRLTKR----GHEVTILTRSPPP 34
>gnl|CDD|200431 TIGR04180, EDH_00030, NAD dependent epimerase/dehydratase,
LLPSF_EDH_00030 family. This clade within the NAD
dependent epimerase/dehydratase superfamily (pfam01370)
is characterized by inclusion of its members within a
cassette of seven distinctive enzymes. These include
four genes homologous to the elements of the neuraminic
(sialic) acid biosynthesis cluster (NeuABCD), an
aminotransferase and a nucleotidyltransferase in
addition to the epimerase/dehydratase. Together it is
very likely that these enzymes direct the biosynthesis
of a nine-carbon sugar analagous to CMP-neuraminic acid.
These seven genes form the core of the cassette,
although they are often accompanied by additional genes
that may further modify the product sugar. Although this
cassette is widely distributed in bacteria, the family
nomenclature arises from the instance in Leptospira
interrogans serovar Lai, str. 56601, where it appears as
the 30th gene in the 91-gene lipopolysaccharide
biosynthesis cluster.
Length = 297
Score = 32.7 bits (75), Expect = 0.65
Identities = 33/148 (22%), Positives = 60/148 (40%), Gaps = 34/148 (22%)
Query: 221 VLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFERLRKEC 280
VLVTG GF+G L+E L+R +G +A ++ + L
Sbjct: 1 VLVTGADGFIGSHLVEALVR---------------QGYEVRA-FVLYNSFNSWGWLDTSP 44
Query: 281 PAQLSRLHIIEGDILQANLGIKDSDLLMLQEEVSVVFNGAASLKL-------EAELKENV 333
P ++ ++ GDI + ++ + + VVF+ AA + + ++ + NV
Sbjct: 45 PEVKDKIEVVTGDIRDPD-SVRKA-----MKGCDVVFHLAALIAIPYSYIAPDSYVDTNV 98
Query: 334 AANTRGTQRLLDIALKMKKLVAFIHFST 361
GT +L A + + +H ST
Sbjct: 99 ----TGTLNVLQAARDL-GVEKVVHTST 121
>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 = 32.6 bits (75), Expect = 0.67
Identities = 36/145 (24%), Positives = 51/145 (35%), Gaps = 36/145 (24%)
Query: 221 VLVTGGTGFMGKVLLEKLLRSCPDIG-KVYILCRAKRGLTPKARLAEFSKLPVF------ 273
LVTG + +G+ + +L R G KV + R + L A + V
Sbjct: 1 ALVTGASSGIGRAIARRLARE----GAKVVLADRNEEALAELAAIEALGGNAVAVQADVS 56
Query: 274 -----ERLRKECPAQLSRLHIIEGDILQANLGIKDSDLLMLQEEVSVVFNGAASLKLEAE 328
E L +E + RL DIL N GI L EE++ + +
Sbjct: 57 DEEDVEALVEEALEEFGRL-----DILVNNAGIARPGPL---EELT-----------DED 97
Query: 329 LKENVAANTRGTQRLLDIALK-MKK 352
+ N G L AL MKK
Sbjct: 98 WDRVLDVNLTGVFLLTRAALPHMKK 122
>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 = 0.86
Identities = 20/87 (22%), Positives = 35/87 (40%), Gaps = 17/87 (19%)
Query: 218 GRSVLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCR-AKRGLTPKARLAEFSK------- 269
G+ V++TG +GK +L + V I CR ++G A + + +
Sbjct: 1 GKVVVITGANSGIGKETARELAKRG---AHVIIACRNEEKGEEAAAEIKKETGNAKVEVI 57
Query: 270 ---LPVFERLRK---ECPAQLSRLHII 290
L +R+ E A+ RL I+
Sbjct: 58 QLDLSSLASVRQFAEEFLARFPRLDIL 84
>gnl|CDD|187538 cd05227, AR_SDR_e, aldehyde reductase, extended (e) SDRs. This
subgroup contains aldehyde reductase of the extended
SDR-type and related proteins. Aldehyde reductase I (aka
carbonyl reductase) is an NADP-binding SDR; it has an
NADP-binding motif consensus that is slightly different
from the canonical SDR form and lacks the Asn of the
extended SDR active site tetrad. Aldehyde reductase I
catalyzes the NADP-dependent reduction of ethyl
4-chloro-3-oxobutanoate to ethyl
(R)-4-chloro-3-hydroxybutanoate. 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 = 301
Score = 32.2 bits (74), Expect = 0.93
Identities = 11/20 (55%), Positives = 16/20 (80%)
Query: 221 VLVTGGTGFMGKVLLEKLLR 240
VLVTG TGF+ ++E+LL+
Sbjct: 2 VLVTGATGFIASHIVEQLLK 21
>gnl|CDD|206065 pfam13894, zf-C2H2_4, C2H2-type zinc finger. This family contains
a number of divergent C2H2 type zinc fingers.
Length = 24
Score = 28.4 bits (63), Expect = 1.00
Identities = 12/25 (48%), Positives = 12/25 (48%), Gaps = 2/25 (8%)
Query: 750 FKCDWQDCKWQFSRSDELSRHRRSH 774
FKC C FS D L RH R H
Sbjct: 1 FKCPL--CGKSFSSKDALKRHLRKH 23
>gnl|CDD|187562 cd05252, CDP_GD_SDR_e, CDP-D-glucose 4,6-dehydratase, extended (e)
SDRs. This subgroup contains CDP-D-glucose
4,6-dehydratase, an extended SDR, which catalyzes the
conversion of CDP-D-glucose to
CDP-4-keto-6-deoxy-D-glucose. 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 = 336
Score = 32.3 bits (74), Expect = 1.0
Identities = 42/179 (23%), Positives = 64/179 (35%), Gaps = 38/179 (21%)
Query: 216 YAGRSVLVTGGTGFMGKVLLEKLLRSCPDIG-KVYILCRAKRGLTPKARLAEFSKLPVFE 274
+ G+ VLVTG TGF G L L ++G KV L P + +FE
Sbjct: 2 WQGKRVLVTGHTGFKGSWLSLWLQ----ELGAKVIGY-----SLDP------PTNPNLFE 46
Query: 275 RLRKECPAQLSRLHIIEGDILQANLGIKDSDLLMLQE-----EVSVVFNGAAS---LKLE 326
GDI DL L+E E +VF+ AA
Sbjct: 47 LAN---LDNKISSTR--GDI---------RDLNALREAIREYEPEIVFHLAAQPLVRLSY 92
Query: 327 AELKENVAANTRGTQRLLDIALKMKKLVAFIHFSTAFCHPDQKVLEEKLYPSPVSPHDI 385
+ E N GT LL+ + + A ++ ++ C+ +++ P+ HD
Sbjct: 93 KDPVETFETNVMGTVNLLEAIRETGSVKAVVNVTSDKCYENKEWGWGYRENDPLGGHDP 151
>gnl|CDD|181335 PRK08264, PRK08264, short chain dehydrogenase; Validated.
Length = 238
Score = 31.8 bits (73), Expect = 1.3
Identities = 15/44 (34%), Positives = 21/44 (47%), Gaps = 2/44 (4%)
Query: 217 AGRSVLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTP 260
G+ VLVTG +G+ +E+LL KVY R +T
Sbjct: 5 KGKVVLVTGANRGIGRAFVEQLLAR--GAAKVYAAARDPESVTD 46
>gnl|CDD|187652 cd08948, 5beta-POR_like_SDR_a, progesterone 5-beta-reductase-like
proteins (5beta-POR), atypical (a) SDRs. 5beta-POR
catalyzes the reduction of progesterone to
5beta-pregnane-3,20-dione in Digitalis plants. This
subgroup of atypical-extended SDRs, shares the structure
of an extended SDR, but has a different glycine-rich
nucleotide binding motif (GXXGXXG) and lacks the YXXXK
active site motif of classical and extended SDRs.
Tyr-179 and Lys 147 are present in the active site, but
not in the usual SDR configuration. Given these
differences, it has been proposed that this subfamily
represents a new SDR class. Other atypical SDRs include
biliverdin IX beta reductase (BVR-B,aka flavin
reductase), NMRa (a negative transcriptional regulator
of various fungi), phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 308
Score = 31.8 bits (73), Expect = 1.3
Identities = 18/49 (36%), Positives = 19/49 (38%)
Query: 220 SVLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFS 268
LV G TG G L+E LL KVY L R RL E
Sbjct: 1 VALVVGATGISGWALVEHLLSDPGTWWKVYGLSRRPLPTEDDPRLVEHI 49
>gnl|CDD|183775 PRK12826, PRK12826, 3-ketoacyl-(acyl-carrier-protein) reductase;
Reviewed.
Length = 251
Score = 31.8 bits (73), Expect = 1.3
Identities = 22/97 (22%), Positives = 32/97 (32%), Gaps = 22/97 (22%)
Query: 218 GRSVLVTGGTGFMGKVLLEKLLRSCPDIG-KVYILCR------------AKRGLTPKARL 264
GR LVTG +G+ + +L G +V ++ G +AR
Sbjct: 6 GRVALVTGAARGIGRAIAVRLAAD----GAEVIVVDICGDDAAATAELVEAAGGKARARQ 61
Query: 265 AEFSKLPVFERLRKECPAQLSRLHIIEGDILQANLGI 301
+ + RL DIL AN GI
Sbjct: 62 VDVRDRAALKAAVAAGVEDFGRL-----DILVANAGI 93
>gnl|CDD|237218 PRK12825, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 249
Score = 31.4 bits (72), Expect = 1.8
Identities = 17/77 (22%), Positives = 28/77 (36%), Gaps = 17/77 (22%)
Query: 218 GRSVLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFERLR 277
GR LVTG +G+ + +L R+ D V + R+ E L
Sbjct: 6 GRVALVTGAARGLGRAIALRLARAGAD---VVVHYRSDE-----EAAEE---------LV 48
Query: 278 KECPAQLSRLHIIEGDI 294
+ A R ++ D+
Sbjct: 49 EAVEALGRRAQAVQADV 65
>gnl|CDD|187572 cd05262, SDR_a7, atypical (a) SDRs, subgroup 7. This subgroup
contains atypical SDRs of unknown function. Members of
this subgroup have a glycine-rich NAD(P)-binding motif
consensus that matches the extended SDRs, TGXXGXXG, but
lacks the characteristic active site residues of the
SDRs. This subgroup has basic residues (HXXXR) in place
of the active site motif YXXXK, these may have a
catalytic role. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and their
glycine-rich NAD(P)-binding motif is often different
from the forms normally seen in classical or extended
SDRs. Atypical SDRs include biliverdin IX beta reductase
(BVR-B,aka flavin reductase), NMRa (a negative
transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 291
Score = 31.6 bits (72), Expect = 1.8
Identities = 9/19 (47%), Positives = 14/19 (73%)
Query: 221 VLVTGGTGFMGKVLLEKLL 239
V VTG TGF+G ++ +L+
Sbjct: 3 VFVTGATGFIGSAVVRELV 21
>gnl|CDD|236035 PRK07508, PRK07508, aminodeoxychorismate synthase; Provisional.
Length = 378
Score = 31.5 bits (72), Expect = 1.8
Identities = 23/88 (26%), Positives = 29/88 (32%), Gaps = 28/88 (31%)
Query: 231 GKVLLEKLLRSCPDIGKVYILC------------RAKRGLTPKARLAEFSK-------LP 271
G +L KL P+ + +LC R ARL +
Sbjct: 57 GYLLEPKLAPLMPEGRETPLLCFGVFDAPSPEAPAPARPSENAARLRDPVARWDFADYAQ 116
Query: 272 VFERLRKECPAQLSRLHIIEGDILQANL 299
FERL + HI GD QANL
Sbjct: 117 RFERLHR---------HIRAGDCYQANL 135
>gnl|CDD|187541 cd05230, UGD_SDR_e, UDP-glucuronate decarboxylase (UGD) and related
proteins, extended (e) SDRs. UGD catalyzes the
formation of UDP-xylose from UDP-glucuronate; it is an
extended-SDR, and has the characteristic glycine-rich
NAD-binding pattern, TGXXGXXG, and active site tetrad.
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 = 305
Score = 31.5 bits (72), Expect = 2.0
Identities = 10/20 (50%), Positives = 15/20 (75%)
Query: 221 VLVTGGTGFMGKVLLEKLLR 240
+L+TGG GF+G L ++LL
Sbjct: 3 ILITGGAGFLGSHLCDRLLE 22
>gnl|CDD|215748 pfam00147, Fibrinogen_C, Fibrinogen beta and gamma chains,
C-terminal globular domain.
Length = 221
Score = 30.9 bits (70), Expect = 2.6
Identities = 13/41 (31%), Positives = 19/41 (46%), Gaps = 2/41 (4%)
Query: 76 YRKTCEELALLGVTESNVYLIDIDGNGRFPPARVKCEFQED 116
K C ++ G S +Y I DG + P RV C+ + D
Sbjct: 1 SPKDCSDILQNGGETSGLYTIQPDGANK--PLRVYCDMETD 39
>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 = 30.8 bits (70), Expect = 3.0
Identities = 44/172 (25%), Positives = 71/172 (41%), Gaps = 42/172 (24%)
Query: 218 GRSVLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFERLR 277
+S+L+TGGTG GK + +LL + + K+ I R + + E + LR
Sbjct: 4 NKSILITGGTGSFGKAFISRLLENY-NPKKIIIYSRD------ELKQWEMQQKFPAPCLR 56
Query: 278 KECPAQLSRLHIIEGDILQANLGIKDSD-LLMLQEEVSVVFNGAASLK----LEAELKEN 332
I GD ++D + L V V + AA+LK E E
Sbjct: 57 ----------FFI-GD-------VRDKERLTRALRGVDYVVH-AAALKQVPAAEYNPFEC 97
Query: 333 VAANTRGTQRLLDIALK--MKKLVAFIHFST-AFCHP-----DQKVLEEKLY 376
+ N G Q ++D A+ +K++VA ST +P K+ +KL+
Sbjct: 98 IRTNINGAQNVIDAAIDNGVKRVVA---LSTDKAANPINLYGATKLASDKLF 146
>gnl|CDD|131715 TIGR02667, moaB_proteo, molybdenum cofactor biosynthesis protein B,
proteobacterial. This model represents the MoaB protein
molybdopterin biosynthesis regions in Proteobacteria.
This crystallized but incompletely characterized protein
is thought to be involved in, though not required for,
early steps in molybdopterin biosynthesis. It may bind a
molybdopterin precursor. A distinctive conserved motif
PCN near the C-terminus helps distinguish this clade
from other homologs, including sets of proteins
designated MogA [Biosynthesis of cofactors, prosthetic
groups, and carriers, Molybdopterin].
Length = 163
Score = 30.1 bits (68), Expect = 3.1
Identities = 24/67 (35%), Positives = 29/67 (43%), Gaps = 20/67 (29%)
Query: 212 VARWYAGRSV---LVTGGTGFMGK--------VLLEK-------LLR--SCPDIGKVYIL 251
V+ W A V L+TGGTGF G+ L +K L R S +IG I
Sbjct: 55 VSAWIADPDVQVILITGGTGFTGRDVTPEALEPLFDKTVEGFGELFRQLSYEEIGTSTIQ 114
Query: 252 CRAKRGL 258
RA GL
Sbjct: 115 SRALAGL 121
>gnl|CDD|187545 cd05234, UDP_G4E_2_SDR_e, UDP-glucose 4 epimerase, subgroup 2,
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 is comprised of
archaeal and bacterial proteins, and 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 = 305
Score = 30.3 bits (69), Expect = 3.7
Identities = 11/20 (55%), Positives = 16/20 (80%)
Query: 221 VLVTGGTGFMGKVLLEKLLR 240
+LVTGG GF+G L+++LL
Sbjct: 2 ILVTGGAGFIGSHLVDRLLE 21
>gnl|CDD|220311 pfam09609, Cas_GSU0054, CRISPR-associated protein, GSU0054 family
(Cas_GSU0054). This entry represents a rare
CRISPR-associated protein. So far, members are found in
Geobacter sulfurreducens and in two unpublished genomes:
Gemmata obscuriglobus and Actinomyces naeslundii.
CRISPR-associated proteins typically are found near
CRISPR repeats and other CRISPR-associated proteins,
have low levels of sequence identify, have sequence
relationships that suggest lateral transfer, and show
some sequence similarity to DNA-active proteins such as
helicases and repair proteins.
Length = 519
Score = 30.7 bits (69), Expect = 3.7
Identities = 19/68 (27%), Positives = 27/68 (39%), Gaps = 12/68 (17%)
Query: 396 TIKQLTPKILGPHPNSYTFTKRLTETLVDEYKTKL-------PVVIVRPSIV-----LPS 443
T +TP IL +PN + ++L L L PV + SI PS
Sbjct: 396 TWASVTPVILDRYPNCAPYARKLHLMLEYGVLPDLSGMQIDGPVSQLAFSIDRAGLPQPS 455
Query: 444 FQEPVPGW 451
EP+P +
Sbjct: 456 SIEPLPAY 463
>gnl|CDD|187556 cd05245, SDR_a2, atypical (a) SDRs, subgroup 2. This subgroup
contains atypical SDRs, one member is identified as
Escherichia coli protein ybjT, function unknown.
Atypical SDRs are distinct from classical SDRs. Members
of this subgroup have a glycine-rich NAD(P)-binding
motif consensus that generally matches the extended
SDRs, TGXXGXXG, but lacks the characteristic active site
residues of the SDRs. This subgroup has basic residues
(HXXXR) in place of the active site motif YXXXK, these
may have a catalytic role. Atypical SDRs generally lack
the catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Atypical SDRs include biliverdin IX beta
reductase (BVR-B,aka flavin reductase), NMRa (a negative
transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 293
Score = 30.4 bits (69), Expect = 3.8
Identities = 15/45 (33%), Positives = 22/45 (48%), Gaps = 3/45 (6%)
Query: 221 VLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLA 265
VLVTG TG++G L+ +LL+ V L R+ L +
Sbjct: 1 VLVTGATGYVGGRLVPRLLQEGHQ---VRALVRSPEKLADRPWSE 42
>gnl|CDD|224015 COG1090, COG1090, Predicted nucleoside-diphosphate sugar epimerase
[General function prediction only].
Length = 297
Score = 30.3 bits (69), Expect = 3.9
Identities = 13/33 (39%), Positives = 19/33 (57%), Gaps = 3/33 (9%)
Query: 221 VLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCR 253
+L+TGGTG +G+ L +L + V IL R
Sbjct: 1 ILITGGTGLIGRALTARLRKGGHQ---VTILTR 30
>gnl|CDD|131396 TIGR02343, chap_CCT_epsi, T-complex protein 1, epsilon subunit.
Members of this family, all eukaryotic, are part of the
group II chaperonin complex called CCT (chaperonin
containing TCP-1) or TRiC. The archaeal equivalent group
II chaperonin is often called the thermosome. Both are
somewhat related to the group I chaperonin of bacterial,
GroEL/GroES. This family consists exclusively of the CCT
epsilon chain (part of a paralogous family) from
animals, plants, fungi, and other eukaryotes.
Length = 532
Score = 30.5 bits (69), Expect = 4.1
Identities = 20/62 (32%), Positives = 32/62 (51%), Gaps = 9/62 (14%)
Query: 785 CVKKSLLAILNCPHEAECTPTFKHRAEKTSTPGPSMCKRHLAKHLKVHERQKYKMMMKSM 844
VK + +AIL CP E P KH+ + +S K L+ +E+QK+K M+ +
Sbjct: 237 EVKDAKIAILTCPFEPP-KPKTKHKLDISSVEE--------YKKLQKYEQQKFKEMIDDI 287
Query: 845 RK 846
+K
Sbjct: 288 KK 289
>gnl|CDD|215370 PLN02686, PLN02686, cinnamoyl-CoA reductase.
Length = 367
Score = 30.1 bits (68), Expect = 4.6
Identities = 16/40 (40%), Positives = 23/40 (57%)
Query: 201 RGSCECADMGDVARWYAGRSVLVTGGTGFMGKVLLEKLLR 240
RG + A+ GD R V VTGG F+G ++++LLR
Sbjct: 36 RGGGKEANAGDAGADAEARLVCVTGGVSFLGLAIVDRLLR 75
>gnl|CDD|235738 PRK06199, PRK06199, ornithine cyclodeaminase; Validated.
Length = 379
Score = 30.1 bits (68), Expect = 5.7
Identities = 25/86 (29%), Positives = 35/86 (40%), Gaps = 17/86 (19%)
Query: 175 APLDLHSATWFTSAANQSVDYVGDVKRGSCECADMGDVARWYAGRSVLVTG--GTGFMGK 232
APL + SA ++ +V VG AR A + V G G G MGK
Sbjct: 124 APLAIMSANLLSAYRTGAVPGVG---------------ARHLARKDSKVVGLLGPGVMGK 168
Query: 233 VLLEKLLRSCPDIGKVYILCRAKRGL 258
+L + CP I + I R ++ L
Sbjct: 169 TILAAFMAVCPGIDTIKIKGRGQKSL 194
>gnl|CDD|177883 PLN02240, PLN02240, UDP-glucose 4-epimerase.
Length = 352
Score = 29.9 bits (68), Expect = 5.8
Identities = 9/15 (60%), Positives = 13/15 (86%)
Query: 217 AGRSVLVTGGTGFMG 231
GR++LVTGG G++G
Sbjct: 4 MGRTILVTGGAGYIG 18
>gnl|CDD|187553 cd05242, SDR_a8, atypical (a) SDRs, subgroup 8. This subgroup
contains atypical SDRs of unknown function. Proteins in
this subgroup have a glycine-rich NAD(P)-binding motif
consensus that resembles that of the extended SDRs,
(GXXGXXG or GGXGXXG), but lacks the characteristic
active site residues of the SDRs. A Cys often replaces
the usual Lys of the YXXXK active site motif, while the
upstream Ser is generally present and Arg replaces the
usual Asn. Atypical SDRs generally lack the catalytic
residues characteristic of the SDRs, and their
glycine-rich NAD(P)-binding motif is often different
from the forms normally seen in classical or extended
SDRs. Atypical SDRs include biliverdin IX beta reductase
(BVR-B,aka flavin reductase), NMRa (a negative
transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 296
Score = 29.9 bits (68), Expect = 6.0
Identities = 13/34 (38%), Positives = 22/34 (64%), Gaps = 5/34 (14%)
Query: 221 VLVTGGTGFMGKVLLEKLLRSCPDIG-KVYILCR 253
+++TGGTGF+G+ L +L + G +V +L R
Sbjct: 2 IVITGGTGFIGRALTRRLTAA----GHEVVVLSR 31
>gnl|CDD|238562 cd01142, TroA_e, Periplasmic binding protein TroA_e. These
proteins are predicted to function as initial receptors
in the ABC metal ion uptake in eubacteria and archaea.
They belong to the TroA superfamily of helical backbone
metal receptor proteins that share a distinct fold and
ligand binding mechanism. A typical TroA protein is
comprised of two globular subdomains connected by a
single helix and can bind their ligands in the cleft
between these domains.
Length = 289
Score = 29.6 bits (67), Expect = 6.0
Identities = 15/51 (29%), Positives = 21/51 (41%), Gaps = 5/51 (9%)
Query: 218 GRSVLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRA--KRGLTPKARLAE 266
G +V G+V LE+LL+ PD V I+ A K + R
Sbjct: 195 GINVASEATKKGSGEVSLEQLLKWNPD---VIIVGNADTKAAILADPRWQN 242
>gnl|CDD|181206 PRK08042, PRK08042, formate hydrogenlyase subunit 3; Reviewed.
Length = 593
Score = 30.2 bits (68), Expect = 6.3
Identities = 11/30 (36%), Positives = 16/30 (53%)
Query: 441 LPSFQEPVPGWVDSLNGPVGVLVASGKGVV 470
L SFQ+ + GW+ + G VG L + G
Sbjct: 8 LFSFQKALSGWIAGIGGAVGSLYTAAAGFT 37
>gnl|CDD|239131 cd02666, Peptidase_C19J, A subfamily of Peptidase C19. Peptidase
C19 contains ubiquitinyl hydrolases. They are
intracellular peptidases that remove ubiquitin molecules
from polyubiquinated peptides by cleavage of isopeptide
bonds. They hydrolyze bonds involving the carboxyl group
of the C-terminal Gly residue of ubiquitin. The purpose
of the de-ubiquitination is thought to be editing of the
ubiquitin conjugates, which could rescue them from
degradation, as well as recycling of the ubiquitin. The
ubiquitin/proteasome system is responsible for most
protein turnover in the mammalian cell, and with over 50
members, family C19 is one of the largest families of
peptidases in the human genome.
Length = 343
Score = 29.8 bits (67), Expect = 6.5
Identities = 11/55 (20%), Positives = 23/55 (41%)
Query: 109 VKCEFQEDSTKTIVEHNLPDQTDVRGIHETDFKFTIKYREFTQEMLSELISHSLY 163
+K F + + +V ++ +Q VR E + + +E++ L LY
Sbjct: 138 IKRLFSGKTKQQLVPESMGNQPSVRTKTERFLSLLVDVGKKGREIVVLLEPKDLY 192
>gnl|CDD|203548 pfam06929, Rotavirus_VP3, Rotavirus VP3 protein. This family
consists of several Rotavirus specific VP3 proteins. VP3
is known to be a viral guanylyltransferase and is
thought to posses methyltransferase activity and
therefore VP3 is a predicted multifunctional capping
enzyme.
Length = 684
Score = 29.9 bits (67), Expect = 6.7
Identities = 18/78 (23%), Positives = 34/78 (43%), Gaps = 4/78 (5%)
Query: 518 WYPNGQIRSNRFWHYFFVIFTQILPAYLVDFIMVLIRQ----KTFLVRVQNRIWLGMHLL 573
+Y N +IR+++FW I +LP + + ++ R+ + + QN +
Sbjct: 96 YYKNNEIRTDQFWLTKTNIEEYLLPGWKLTYVGRGGRETRGHYEYSFKCQNTATDDDIIY 155
Query: 574 EYFTTRNWDFKNKRLLAL 591
+Y + DFKN L
Sbjct: 156 KYIYSNGTDFKNFVLFMR 173
>gnl|CDD|217556 pfam03435, Saccharop_dh, Saccharopine dehydrogenase. This family
comprised of three structural domains that can not be
separated in the linear sequence. In some organisms this
enzyme is found as a bifunctional polypeptide with
lysine ketoglutarate reductase. The saccharopine
dehydrogenase can also function as a saccharopine
reductase.
Length = 380
Score = 29.6 bits (67), Expect = 6.9
Identities = 16/77 (20%), Positives = 29/77 (37%), Gaps = 9/77 (11%)
Query: 221 VLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFE--RLRK 278
VL+ G G +G+ + L R ++ + R+ LA F +
Sbjct: 1 VLIIGA-GGVGQGVAPLLARHGD--LEITVADRSLEKA---QALAAPKLGLRFIAIAVDA 54
Query: 279 ECPAQLSRLHIIEGDIL 295
+ L L + EGD++
Sbjct: 55 DNYEALVAL-LKEGDLV 70
>gnl|CDD|187661 cd08958, FR_SDR_e, flavonoid reductase (FR), extended (e) SDRs.
This subgroup contains FRs of the extended SDR-type and
related proteins. These FRs act in the NADP-dependent
reduction of flavonoids, ketone-containing plant
secondary metabolites; they have the characteristic
active site triad of the SDRs (though not the upstream
active site Asn) and a NADP-binding motif that is very
similar to the typical extended SDR motif. 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 = 293
Score = 29.5 bits (67), Expect = 7.7
Identities = 10/20 (50%), Positives = 16/20 (80%)
Query: 221 VLVTGGTGFMGKVLLEKLLR 240
V VTG +GF+G L+++LL+
Sbjct: 1 VCVTGASGFIGSWLVKRLLQ 20
>gnl|CDD|233954 TIGR02622, CDP_4_6_dhtase, CDP-glucose 4,6-dehydratase. Members of
this protein family are CDP-glucose 4,6-dehydratase from
a variety of Gram-negative and Gram-positive bacteria.
Members typically are encoded next to a gene that
encodes a glucose-1-phosphate cytidylyltransferase,
which produces the substrate, CDP-D-glucose, used by
this enzyme to produce CDP-4-keto-6-deoxyglucose [Cell
envelope, Biosynthesis and degradation of surface
polysaccharides and lipopolysaccharides].
Length = 349
Score = 29.6 bits (67), Expect = 7.9
Identities = 10/16 (62%), Positives = 12/16 (75%)
Query: 216 YAGRSVLVTGGTGFMG 231
+ G+ VLVTG TGF G
Sbjct: 2 WQGKKVLVTGHTGFKG 17
>gnl|CDD|215365 PLN02680, PLN02680, carbon-monoxide oxygenase.
Length = 232
Score = 29.0 bits (65), Expect = 8.9
Identities = 20/62 (32%), Positives = 25/62 (40%), Gaps = 8/62 (12%)
Query: 640 RQIKFLYVLDR-IGHA-LILFLLGSVPKLISTTGLWYPNGQIRSNRF---WHYFFVIFTQ 694
+ I Y L +G A L LF L ++ WYP G S WH FF I+
Sbjct: 108 KGIDNFYSLHSWLGLACLFLFSLQWAAGFVT---FWYPGGSRNSRASLLPWHVFFGIYIY 164
Query: 695 IL 696
L
Sbjct: 165 AL 166
>gnl|CDD|224328 COG1410, MetH, Methionine synthase I, cobalamin-binding domain
[Amino acid transport and metabolism].
Length = 842
Score = 29.6 bits (67), Expect = 9.6
Identities = 16/52 (30%), Positives = 23/52 (44%), Gaps = 15/52 (28%)
Query: 261 KARLAEFSKLPVFERLR---------------KECPAQLSRLHIIEGDILQA 297
+AR AE+ LPV ERL+ +E Q L +IEG ++
Sbjct: 312 EARDAEWRSLPVEERLKHAIVDGIREGLEEDLEEARQQKPPLEVIEGPLMDG 363
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
0.324 0.138 0.427
Gapped
Lambda K H
0.267 0.0655 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 43,923,795
Number of extensions: 4429037
Number of successful extensions: 5497
Number of sequences better than 10.0: 1
Number of HSP's gapped: 5457
Number of HSP's successfully gapped: 118
Length of query: 851
Length of database: 10,937,602
Length adjustment: 105
Effective length of query: 746
Effective length of database: 6,280,432
Effective search space: 4685202272
Effective search space used: 4685202272
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 63 (28.2 bits)