RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7538
(543 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 = 333 bits (856), Expect = e-111
Identities = 127/316 (40%), Positives = 189/316 (59%), Gaps = 3/316 (0%)
Query: 31 KSIFLSGGSGFLGKVLIEKILRLEPNVKKIYLLMRTKKGKTPNQRVEELFESPVFDALKT 90
KS+ ++G +GFLGKVL+EK+LR P++ KIYLL+R K G++ +R+ EL + +FD +
Sbjct: 1 KSVLITGATGFLGKVLLEKLLRSCPDIGKIYLLIRGKSGQSAEERLRELLKDKLFDRGRN 60
Query: 91 LRGKSILQKIQVISGDITQLKLGISEIDKKELIDNVDIVYHVAATIRFDEPIKTAVILNT 150
L KI I GD+++ LG+S+ D + LI+ V+I+ H AAT+ FDE + A+ +N
Sbjct: 61 LNPLF-ESKIVPIEGDLSEPNLGLSDEDLQTLIEEVNIIIHCAATVTFDERLDEALSINV 119
Query: 151 RGTRDMLELSKQMKNLKCFTYISTAYCHPSEKVLEERTYLPPDDPHQVILRAESMKEEDL 210
GT +LEL+K+ K LK F ++STAY + +++EE+ Y PP DP ++I E M + +L
Sbjct: 120 LGTLRLLELAKRCKKLKAFVHVSTAYVNGDRQLIEEKVYPPPADPEKLIDILELMDDLEL 179
Query: 211 EVFRQDILGEFPNSYAYTKCLAEGLVAECMELGMPCMILRPSIVVPIYKEPLPGWTDNIN 270
E +LG PN+Y +TK LAE LV + +P +I+RPSIV KEP PGW DN N
Sbjct: 180 ERATPKLLGGHPNTYTFTKALAERLVLKERG-NLPLVIVRPSIVGATLKEPFPGWIDNFN 238
Query: 271 GPTGLLIGAGKGVIRSMYCKNTGMADFLPADVAINGVFLFTWDFLNSKESERKSVCNLTS 330
GP GL + GKG++R+M +AD +P DV N + K E + V + S
Sbjct: 239 GPDGLFLAYGKGILRTMNADPNAVADIIPVDVVANALLAAAAYSGVRKPRELE-VYHCGS 297
Query: 331 NKDYKITWQEICDIGK 346
+ TW E ++
Sbjct: 298 SDVNPFTWGEAEELIN 313
>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 = 250 bits (642), Expect = 4e-80
Identities = 102/275 (37%), Positives = 149/275 (54%), Gaps = 32/275 (11%)
Query: 35 LSGGSGFLGKVLIEKILRLEPNVKKIYLLMRTKKGKTPNQRV-EELFESPVFDALKTLRG 93
L+G +GFLGKVL+EK+LR P VK IY L+R K G++ +R+ +EL + +FD LK
Sbjct: 1 LTGATGFLGKVLLEKLLRSTPEVK-IYCLVRAKDGESALERLRQELLKYGLFDRLK---- 55
Query: 94 KSILQKIQVISGDITQLKLGISEIDKKELIDNVDIVYHVAATIRFDEPIKTAVILNTRGT 153
L++I ++GD+++ LG+S+ D +EL + VD++ H AAT+ F EP N GT
Sbjct: 56 --ALERIIPVAGDLSEPNLGLSDEDFQELAEEVDVIIHNAATVNFVEPYSDLRATNVLGT 113
Query: 154 RDMLELSKQMKNLKCFTYISTAYCHPSEKVLEERTYLPPDDPHQVILRAESMKEEDLEVF 213
R++L L+KQMK F ++STAY + +L + K ++ E
Sbjct: 114 REVLRLAKQMKK-LPFHHVSTAYV---------------NGERGGLLEEKPYKLDEDE-- 155
Query: 214 RQDILGEFPNSYAYTKCLAEGLVAECMELGMPCMILRPSIVVPIYKEPLPGWTDNIN-GP 272
+LG PN Y +K LAE LV E G+P +I RPSI+ E GW + + GP
Sbjct: 156 -PALLGGLPNGYTQSKWLAEQLVREAAG-GLPVVIYRPSIITG---ESRTGWINGDDFGP 210
Query: 273 TGLLIGAGKGVIRSMYCKNTGMADFLPADVAINGV 307
GLL GAG GV+ + D +P D N +
Sbjct: 211 RGLLGGAGLGVLPDILGDPDARLDLVPVDYVANAI 245
>gnl|CDD|215538 PLN02996, PLN02996, fatty acyl-CoA reductase.
Length = 491
Score = 172 bits (437), Expect = 2e-47
Identities = 96/310 (30%), Positives = 170/310 (54%), Gaps = 33/310 (10%)
Query: 29 ENKSIFLSGGSGFLGKVLIEKILRLEPNVKKIYLLMRTKKGKTPNQRV-EELFESPVFDA 87
ENK+I ++G +GFL K+ +EKILR++PNVKK+YLL+R K+ QR+ +E+ +F
Sbjct: 10 ENKTILVTGATGFLAKIFVEKILRVQPNVKKLYLLLRASDAKSATQRLHDEVIGKDLFKV 69
Query: 88 LKTLRGKS----ILQKIQVISGDITQLKLGISEID-KKELIDNVDIVYHVAATIRFDEPI 142
L+ G++ I +K+ + GDI+ LG+ + + ++E+ +DIV ++AAT FDE
Sbjct: 70 LREKLGENLNSLISEKVTPVPGDISYDDLGVKDSNLREEMWKEIDIVVNLAATTNFDERY 129
Query: 143 KTAVILNTRGTRDMLELSKQMKNLKCFTYISTAY-CHPSEKVLEERTY-----------L 190
A+ +NT G ++L +K+ +K ++STAY C ++ E+ + L
Sbjct: 130 DVALGINTLGALNVLNFAKKCVKVKMLLHVSTAYVCGEKSGLILEKPFHMGETLNGNRKL 189
Query: 191 PPDDPHQVI------LRAESMKEE-------DLEVFRQDILGEFPNSYAYTKCLAEGLVA 237
++ +++ L + EE DL + R + G +PN+Y +TK + E L+
Sbjct: 190 DINEEKKLVKEKLKELNEQDASEEEITQAMKDLGMERAKLHG-WPNTYVFTKAMGEMLLG 248
Query: 238 ECMELGMPCMILRPSIVVPIYKEPLPGWTDNINGPTGLLIGAGKGVIRSMYCKNTGMADF 297
E +P +I+RP+++ YKEP PGW + + +++G GKG + + D
Sbjct: 249 NFKE-NLPLVIIRPTMITSTYKEPFPGWIEGLRTIDSVIVGYGKGKLTCFLADPNSVLDV 307
Query: 298 LPADVAINGV 307
+PAD+ +N +
Sbjct: 308 IPADMVVNAM 317
>gnl|CDD|215279 PLN02503, PLN02503, fatty acyl-CoA reductase 2.
Length = 605
Score = 155 bits (392), Expect = 1e-40
Identities = 93/321 (28%), Positives = 161/321 (50%), Gaps = 43/321 (13%)
Query: 24 IAKTYENKSIFLSGGSGFLGKVLIEKILRLEPNVKKIYLLMRTKKGKTPNQRVE-ELFES 82
IA+ K+ ++G +GFL KVLIEKILR P+V KIYLL++ K + +R++ E+ ++
Sbjct: 113 IAEFLRGKNFLITGATGFLAKVLIEKILRTNPDVGKIYLLIKAKDKEAAIERLKNEVIDA 172
Query: 83 PVFDALKTLRGKS----ILQKIQVISGDITQLKLGISEIDKKELIDNVDIVYHVAATIRF 138
+F L+ GKS +L K+ + G++ + LG+ E+ VD++ + AA F
Sbjct: 173 ELFKCLQETHGKSYQSFMLSKLVPVVGNVCESNLGLEPDLADEIAKEVDVIINSAANTTF 232
Query: 139 DEPIKTAVILNTRGTRDMLELSKQMKNLKCFTYISTAYCHPSEK--VLEE---------R 187
DE A+ +NTRG ++ +K+ K LK F +STAY + + ++E+ R
Sbjct: 233 DERYDVAIDINTRGPCHLMSFAKKCKKLKLFLQVSTAYVNGQRQGRIMEKPFRMGDCIAR 292
Query: 188 TYLPPDDP----------HQVILR-------------AESMKEEDLEVFRQDILGEFPNS 224
+ ++ L A+ MK+ LE R + G + ++
Sbjct: 293 ELGISNSLPHNRPALDIEAEIKLALDSKRHGFQSNSFAQKMKDLGLE--RAKLYG-WQDT 349
Query: 225 YAYTKCLAEGLVAECMELGMPCMILRPSIVVPIYKEPLPGWTDNINGPTGLLIGAGKGVI 284
Y +TK + E +V M +P +I+RPS++ +K+P PGW + +++ GKG +
Sbjct: 350 YVFTKAMGE-MVINSMRGDIPVVIIRPSVIESTWKDPFPGWMEGNRMMDPIVLYYGKGQL 408
Query: 285 RSMYCKNTGMADFLPADVAIN 305
G+ D +PAD+ +N
Sbjct: 409 TGFLADPNGVLDVVPADMVVN 429
>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 = 123 bits (311), Expect = 1e-31
Identities = 81/318 (25%), Positives = 144/318 (45%), Gaps = 49/318 (15%)
Query: 32 SIFLSGGSGFLGKVLIEKILRLEPNVKKIYLLMRTKKGKTPNQRVEELFESPVFDALKTL 91
++ L+G +GFLG L+ ++L+ NV KIY L+R K + +R+ + + L
Sbjct: 1 TVLLTGATGFLGAYLLRELLK-RKNVSKIYCLVRAKDEEAALERLIDNLKE----YGLNL 55
Query: 92 RGKSILQKIQVISGDITQLKLGISEIDKKELIDNVDIVYHVAATIRF---DEPIKTAVIL 148
+ L +I+V+ GD+++ LG+S+ D +EL + VD++ H A + + E +K A
Sbjct: 56 WDELELSRIKVVVGDLSKPNLGLSDDDYQELAEEVDVIIHNGANVNWVYPYEELKPA--- 112
Query: 149 NTRGTRDMLELSKQMKNLKCFTYISTAYCHPSEKVLEERTYLPPDDPHQVILRAESMKEE 208
N GT+++L+L+ K LK ++ST +E+ + +
Sbjct: 113 NVLGTKELLKLAATGK-LKPLHFVSTLSVFSAEEYNALDDE----------------ESD 155
Query: 209 DLEVFRQDILGEFPNSYAYTKCLAEGLVAECMELGMPCMILRPSIVVPIYKEPLPGWTDN 268
D+ + + PN Y +K +AE L+ E G+P I+RP + + G TD+
Sbjct: 156 DMLESQNGL----PNGYIQSKWVAEKLLREAANRGLPVAIIRPGNIFGDSETG-IGNTDD 210
Query: 269 INGPTGLLIGAGKGVIR-SMYCKNTGMADFLPAD-VAINGVFLFTWDFLNSKESERKSVC 326
L+ KG ++ +Y + D P D VA V L ES S+
Sbjct: 211 F---FWRLL---KGCLQLGIYPISGAPLDLSPVDWVARAIV------KLALNESNEFSIY 258
Query: 327 NLTSNKDYKITWQEICDI 344
+L + I+ ++ D
Sbjct: 259 HLLNPP--LISLNDLLDA 274
>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 = 115 bits (291), Expect = 5e-29
Identities = 72/244 (29%), Positives = 113/244 (46%), Gaps = 47/244 (19%)
Query: 33 IFLSGGSGFLGKVLIEKILRLEPNVKKIYLLMRTKKGKTPNQRVEELFESPVFDALKTLR 92
+F++GG+GFLG+ L++ RL N K+ +L+R++ ++R+EE
Sbjct: 1 VFVTGGTGFLGRHLVK---RLLENGFKVLVLVRSESLGEAHERIEE-------------- 43
Query: 93 GKSILQKIQVISGDITQLKLGISEIDKKELIDNVDIVYHVAATIRFDEPIKTAVILNTRG 152
+++V+ GD+TQ LG+S +EL VD V H AA+ F P + A N G
Sbjct: 44 AGLEADRVRVLEGDLTQPNLGLSAAASRELAGKVDHVIHCAASYDFQAPNEDAWRTNIDG 103
Query: 153 TRDMLELSKQMKNLKCFTYISTAYCHPSEKVLEERTYLPPDDPHQVILRAESMKEEDLEV 212
T +LEL+ + +++ F Y+STAY R +++E +L
Sbjct: 104 TEHVLELAAR-LDIQRFHYVSTAYV--------------------AGNREGNIRETELNP 142
Query: 213 FRQDILGEFPNSYAYTKCLAEGLVAECMELGMPCMILRPSIVVPIYKEPLPGWTDNINGP 272
+ F N Y +K AE LV +P + RPSIVV K G + I+G
Sbjct: 143 GQ-----NFKNPYEQSKAEAEQLVRAAATQ-IPLTVYRPSIVVGDSKT---GRIEKIDGL 193
Query: 273 TGLL 276
LL
Sbjct: 194 YELL 197
>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 = 91.5 bits (228), Expect = 1e-22
Identities = 28/92 (30%), Positives = 49/92 (53%)
Query: 379 LFHWIPAYFLDAVILISGNKPCLVRIQERIHRGFDVFEYYANNEWEFKNGNLHQTRPKRN 438
H +PAY LD ++ + G KP L+++ +IH+ D+ EY+ NEW F N N + +
Sbjct: 1 FLHLLPAYLLDLLLRLLGRKPRLLKLYRKIHKLLDLLEYFTTNEWRFDNDNTRALWERLS 60
Query: 439 AREIVQYCVENDNVDIVKYFEKAVYGARYFLM 470
+ + + ++D YFE + G R +L+
Sbjct: 61 EEDRELFNFDIRSIDWDDYFENYIPGLRKYLL 92
>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 = 86.5 bits (215), Expect = 1e-20
Identities = 33/94 (35%), Positives = 58/94 (61%)
Query: 379 LFHWIPAYFLDAVILISGNKPCLVRIQERIHRGFDVFEYYANNEWEFKNGNLHQTRPKRN 438
+H +PAYFLD ++ + G KP LV++ +IH+G +V + ++ NEW F N N + R K +
Sbjct: 1 FYHTLPAYFLDLLLRLYGQKPRLVKLYRKIHKGLEVLQPFSLNEWIFDNKNTRELREKMS 60
Query: 439 AREIVQYCVENDNVDIVKYFEKAVYGARYFLMKE 472
+ + + +++D +YF A+ G R +L+KE
Sbjct: 61 EEDKKLFNFDMESLDWDEYFRNAIRGIRKYLLKE 94
>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 = 87.9 bits (218), Expect = 8e-19
Identities = 57/221 (25%), Positives = 96/221 (43%), Gaps = 31/221 (14%)
Query: 32 SIFLSGGSGFLGKVLIEKILRLEPNVKKIYLLMRTKKGKTPNQRVEELFESPVFDALKTL 91
++ L+G +GFLG L+E++LR K + L+R + +R+ E S L
Sbjct: 1 TVLLTGATGFLGAYLLEELLRRSTQAK-VICLVRAASEEHAMERLREALRS------YRL 53
Query: 92 RGKS-ILQKIQVISGDITQLKLGISEIDKKELIDNVDIVYHVAATIRFDEPIKTAVILNT 150
+ ++I+V++GD+++ +LG+S+ + + L +NVD + H A + + P N
Sbjct: 54 WHEDLARERIEVVAGDLSEPRLGLSDAEWERLAENVDTIVHNGALVNWVYPYSELRGANV 113
Query: 151 RGTRDMLELSKQMKNLKCFTYISTAYCHPSEKVLEERTYLPPDDPHQVILRAESMKEEDL 210
GTR++L L+ K Y+ST V ED
Sbjct: 114 LGTREVLRLA-ASGRAKPLHYVSTI------SVGAAIDLSTV--------------TEDD 152
Query: 211 EVFRQDILGEFPNSYAYTKCLAEGLVAECMELGMPCMILRP 251
YA +K +AE LV E + G+P I+RP
Sbjct: 153 ATVTPPP--GLAGGYAQSKWVAELLVREASDRGLPVTIVRP 191
>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 = 85.9 bits (213), Expect = 4e-18
Identities = 56/230 (24%), Positives = 100/230 (43%), Gaps = 37/230 (16%)
Query: 31 KSIFLSGGSGFLGKVLIEKILRLEPNVKKIYLLMRTKKGKTPNQRVEELFE-SPVFDALK 89
+++ L+G +GFLG L+ ++L K+ L+R + + R+E+ F+ +D L
Sbjct: 1 RNVLLTGATGFLGAYLLLELLDRSD--AKVICLVRAQSDEAALARLEKTFDLYRHWDELS 58
Query: 90 TLRGKSILQKIQVISGDITQLKLGISEIDKKELIDNVDIVYHVAATIRFDEPIKTAVILN 149
+++V++GD+ + LG+SE +EL +NVD++ H AA + P N
Sbjct: 59 A-------DRVEVVAGDLAEPDLGLSERTWQELAENVDLIIHNAALVNHVFPYSELRGAN 111
Query: 150 TRGTRDMLELSKQMKNLKCFTYIST----AYCHPSEKVLEERTYLPPDDPHQVILRAESM 205
GT ++L L+ K K Y+S+ + S ++ P + Q +
Sbjct: 112 VLGTAEVLRLAATGK-PKPLHYVSSISVGETEYYSNFTVDFDEISPTRNVGQGL------ 164
Query: 206 KEEDLEVFRQDILGEFPNSYAYTKCLAEGLVAECMELGMPCMILRPSIVV 255
Y +K +AE LV E + G+P I RP +
Sbjct: 165 ----------------AGGYGRSKWVAEKLVREAGDRGLPVTIFRPGYIT 198
>gnl|CDD|235962 PRK07201, PRK07201, short chain dehydrogenase; Provisional.
Length = 657
Score = 80.8 bits (200), Expect = 6e-16
Identities = 66/247 (26%), Positives = 110/247 (44%), Gaps = 65/247 (26%)
Query: 34 FLSGGSGFLGKVLIEKILRLEPNVKKIYLLMRTKKGKTPNQRVEELFESPVFDALKTLRG 93
F++GG+GF+G+ L+ ++L +++L+R + R+E L
Sbjct: 4 FVTGGTGFIGRRLVSRLLDRRRE-ATVHVLVR----RQSLSRLEA------------LAA 46
Query: 94 KSILQKIQVISGDITQLKLGISEIDKKELIDNVDIVYHVAAT--IRFDEPIKTAVILNTR 151
++ + GD+T+ LG+SE D EL ++D V H+AA + DE + A N
Sbjct: 47 YWGADRVVPLVGDLTEPGLGLSEADIAEL-GDIDHVVHLAAIYDLTADEEAQRAA--NVD 103
Query: 152 GTRDMLELSKQMKNLKCFTYIST---AYCHPSEKVLEERTYLPPDDPHQVILRAESMKEE 208
GTR+++EL+++++ F ++S+ A +
Sbjct: 104 GTRNVVELAERLQA-ATFHHVSSIAVAGDYEG---------------------------- 134
Query: 209 DLEVFRQDILGE---FPNSYAYTKCLAEGLVAECMELGMPCMILRPSIVVPIYKEPLPGW 265
VFR+D E P Y TK AE LV E E G+P + RP++VV + G
Sbjct: 135 ---VFREDDFDEGQGLPTPYHRTKFEAEKLVRE--ECGLPWRVYRPAVVV---GDSRTGE 186
Query: 266 TDNINGP 272
D I+GP
Sbjct: 187 MDKIDGP 193
>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 = 67.8 bits (166), Expect = 8e-12
Identities = 63/262 (24%), Positives = 118/262 (45%), Gaps = 43/262 (16%)
Query: 7 APDLV-TIPKELQALPDRIAKTYENKSIFLSGGSGFLGKVLIEKILRLEPN-VKKIYLLM 64
A LV ++PK + + A T ++FL+G +GFLG ++ +L N K++ +
Sbjct: 949 AKTLVDSLPKSYPSRKELDAST--PITVFLTGATGFLGSFILRDLLTRRSNSNFKVFAHV 1006
Query: 65 RTKKGKTPNQRVEELFESPVFDALKTLRG---KSILQKIQVISGDITQLKLGISEIDKKE 121
R K+ +E L ++ T G + +I+V+ GD+++ K G+S+ +
Sbjct: 1007 R---AKSEEAGLERLRKT------GTTYGIWDEEWASRIEVVLGDLSKEKFGLSDEKWSD 1057
Query: 122 LIDNVDIVYHVAATIRFDEPIKTAVILNTRGTRDMLELSKQMKNLKCFTYIST------- 174
L + VD++ H A + + P N GT ++L L + K K F+++S+
Sbjct: 1058 LTNEVDVIIHNGALVHWVYPYSKLRDANVIGTINVLNLCAEGKA-KQFSFVSSTSALDTE 1116
Query: 175 AYCHPSEKVLEE-RTYLPPDDPHQVILRAESMKEEDLEVFRQDILGEFPNSYAYTKCLAE 233
Y + S+++++ +P D DL + LG Y +K +AE
Sbjct: 1117 YYVNLSDELVQAGGAGIPESD--------------DLMGSSKG-LG---TGYGQSKWVAE 1158
Query: 234 GLVAECMELGMPCMILRPSIVV 255
++ E + G+ I+RP V
Sbjct: 1159 YIIREAGKRGLRGCIVRPGYVT 1180
>gnl|CDD|223528 COG0451, WcaG, Nucleoside-diphosphate-sugar epimerases [Cell
envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 314
Score = 60.7 bits (147), Expect = 4e-10
Identities = 74/375 (19%), Positives = 126/375 (33%), Gaps = 87/375 (23%)
Query: 31 KSIFLSGGSGFLGKVLIEKILRLEPNVKKIYLLMRTKKGKTPNQRVEELFESPVFDALKT 90
I ++GG+GF+G L+E++L +V+ D L+
Sbjct: 1 MRILVTGGAGFIGSHLVERLLAAGHDVR-------------------------GLDRLRD 35
Query: 91 LRGKSILQKIQVISGDITQLKLGISEIDKKELIDNVDIVYHVAA----TIRFDEPIKTAV 146
+ V+ D+T ++ + D V H+AA +
Sbjct: 36 GLDPLLSGVEFVV-LDLTDR-----DLVDELAKGVPDAVIHLAAQSSVPDSNASDPAEFL 89
Query: 147 ILNTRGTRDMLELSKQMKNLKCFTYISTAYCHPSEKVLEERTYLPPDDPHQVILRAESMK 206
+N GT ++LE ++ +K F + S+ + D P I
Sbjct: 90 DVNVDGTLNLLEAARAA-GVKRFVFASSVSV------------VYGDPPPLPI------D 130
Query: 207 EEDLEVFRQDILGEFPNSYAYTKCLAEGLVAECMEL-GMPCMILRPSIVVPIYKEPLPGW 265
E+ N Y +K AE L+ L G+P +ILRP V PG
Sbjct: 131 EDLGPP-------RPLNPYGVSKLAAEQLLRAYARLYGLPVVILRPFNVYG------PGD 177
Query: 266 TDNING--PTGLLIGAGKGV-IRSMYCKNTGMADFL-PADVAINGVFLFTWDFLNSKESE 321
+++ + + KG I + + DF+ DVA L E+
Sbjct: 178 KPDLSSGVVSAFIRQLLKGEPIIVIGGDGSQTRDFVYVDDVA--DALLLAL------ENP 229
Query: 322 RKSVCNLTSNKDYKITWQEICDIGKDIVTSKIPFNSTLWYPGGTMTQSRLTHFICCLLFH 381
V N+ S +IT +E+ + + V SK P ++ P G R +
Sbjct: 230 DGGVFNIGSG-TAEITVRELAEAVAEAVGSKAPL--IVYIPLGRRGDLREGKLLDISKAR 286
Query: 382 ----WIPAYFLDAVI 392
W P L+ +
Sbjct: 287 AALGWEPKVSLEEGL 301
>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 = 55.4 bits (134), Expect = 8e-09
Identities = 42/198 (21%), Positives = 64/198 (32%), Gaps = 51/198 (25%)
Query: 123 IDNVDIVYHVAATIRFDEPIKTAVIL---NTRGTRDMLELSKQMKNLKCFTYISTA--YC 177
ID +D+V H+AA + N GT ++LE +++ +K F Y S+A Y
Sbjct: 28 IDRLDVVVHLAALVGVPASWDNPDEDFETNVVGTLNLLEAARKA-GVKRFVYASSASVYG 86
Query: 178 HPSEKVLEERTYLPPDDPHQVILRAESMKEEDLEVFRQDILGEFPNSYAYTKCLAEGLVA 237
P EE T P P Y +K AE L+
Sbjct: 87 SPEGLPEEEETPPRPLSP-----------------------------YGVSKLAAEHLLR 117
Query: 238 E-CMELGMPCMILRPSIVV-----PIYKEPLPGWTDNINGPTGLLIGAGKGVIRSMYCKN 291
G+P +ILR + V P + + L + G R
Sbjct: 118 SYGESYGLPVVILRLANVYGPGQRPRLDGVVNDFIRRALEGKPLTVFGGGNQTR------ 171
Query: 292 TGMADFLPADVAINGVFL 309
DF+ D + +
Sbjct: 172 ----DFIHVDDVVRAILH 185
Score = 28.0 bits (63), Expect = 9.3
Identities = 9/25 (36%), Positives = 16/25 (64%)
Query: 33 IFLSGGSGFLGKVLIEKILRLEPNV 57
I ++GG+GF+G L+ ++L V
Sbjct: 1 ILVTGGAGFIGSHLVRRLLERGHEV 25
>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 = 54.0 bits (130), Expect = 8e-08
Identities = 39/145 (26%), Positives = 61/145 (42%), Gaps = 25/145 (17%)
Query: 32 SIFLSGGSGFLGKVLIEKILRLEPNVKKIYLLMRTKKGKTPNQRVEELFESPVFDALKTL 91
++GG GFLG+ +I +L + +K+I +L K + E FE
Sbjct: 1 VCLVTGGGGFLGQHIIRLLLERKEELKEIRVL-----DKAFGPELIEHFE--------KS 47
Query: 92 RGKSILQKIQVISGDITQLKLGISEIDKKELIDNVDIVYHVAATIRFDEPIKTAVI--LN 149
+GK+ + I GDI L S + V +V H AA + P + +N
Sbjct: 48 QGKT---YVTDIEGDIKDL----SFL--FRACQGVSVVIHTAAIVDVFGPPNYEELEEVN 98
Query: 150 TRGTRDMLELSKQMKNLKCFTYIST 174
GT+ +LE Q N+K Y S+
Sbjct: 99 VNGTQAVLEACVQ-NNVKRLVYTSS 122
>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 = 53.4 bits (129), Expect = 1e-07
Identities = 50/229 (21%), Positives = 80/229 (34%), Gaps = 67/229 (29%)
Query: 33 IFLSGGSGFLGKVLIEKILRLEPNVKKIYLLMRTKKGKTPNQRVEELFESPVFDALKTLR 92
I ++G +GFLG L+ +L V+ L+R L PV
Sbjct: 1 ILVTGATGFLGSNLVRALLAQGYRVR---ALVR------SGSDAVLLDGLPV-------- 43
Query: 93 GKSILQKIQVISGDITQLKLGISEIDKKELID---NVDIVYHVAATIRFDEPIKTAVI-L 148
+V+ GD+T D L D V+H+AA + +
Sbjct: 44 --------EVVEGDLT---------DAASLAAAMKGCDRVFHLAAFTSLWAKDRKELYRT 86
Query: 149 NTRGTRDMLELSKQMKNLKCFTYIST--AYCHPSEKVLEERTYLPPDDPHQVILRAESMK 206
N GTR++L+ + + ++ + S+ A P + ++E T
Sbjct: 87 NVEGTRNVLDAALE-AGVRRVVHTSSIAALGGPPDGRIDETTPWNER------------- 132
Query: 207 EEDLEVFRQDILGEFPNSYAYTKCLAEGLVAECMELGMPCMILRPSIVV 255
FPN Y +K LAE V E G+ +I+ PS V
Sbjct: 133 -------------PFPNDYYRSKLLAELEVLEAAAEGLDVVIVNPSAVF 168
>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 = 50.7 bits (122), Expect = 7e-07
Identities = 38/153 (24%), Positives = 74/153 (48%), Gaps = 32/153 (20%)
Query: 29 ENKSIFLSGGSGFLGKVLIEKILRLEPNVKKIYLLMRTKKGKTPNQRVEELFESPVFDAL 88
+ K+I ++GG+G +G L+ +IL+ P KK+ + R E+ + + +
Sbjct: 1 KGKTILVTGGAGSIGSELVRQILKFGP--KKLIVFDRD--------------ENKLHELV 44
Query: 89 KTLRGKSILQKIQVISGDITQLKLGISEIDKKELIDNVDIVYHVAAT--IR-----FDEP 141
+ LR + K++ I GD+ + + K+ DIV+H AA + +E
Sbjct: 45 RELRSRFPHDKLRFIIGDVRDKER-LRRAFKER---GPDIVFHAAALKHVPSMEDNPEEA 100
Query: 142 IKTAVILNTRGTRDMLELSKQMKNLKCFTYIST 174
IKT V+ GT+++++ + + ++ F IST
Sbjct: 101 IKTNVL----GTKNVIDAAIE-NGVEKFVCIST 128
>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 = 44.9 bits (107), Expect = 6e-05
Identities = 41/171 (23%), Positives = 70/171 (40%), Gaps = 42/171 (24%)
Query: 37 GGSGFLGKVLIEKILRLEPNVKKIYLLMRTKKGKTPNQRVEELFESPVFDALKTLRGKSI 96
GG+GF+G L+E++L V V D L T + +++
Sbjct: 6 GGAGFIGSHLVERLLER-------------------GHEVI------VLDNLSTGKKENL 40
Query: 97 ---LQKIQVISGDITQLKLGISEIDKKELIDNVDIVYHVAA----TIRFDEPIKTAVILN 149
++ I GDI +L + + VD V+H AA ++PIK + N
Sbjct: 41 PEVKPNVKFIEGDIRDDEL------VEFAFEGVDYVFHQAAQASVPRSIEDPIKDHEV-N 93
Query: 150 TRGTRDMLELSKQMKNLKCFTYISTAYCHPSEKVL--EERTYLPPDDPHQV 198
GT ++LE +++ +K F Y S++ + L +E P P+ V
Sbjct: 94 VLGTLNLLEAARK-AGVKRFVYASSSSVYGDPPYLPKDEDHPPNPLSPYAV 143
>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 = 45.0 bits (107), Expect = 6e-05
Identities = 47/224 (20%), Positives = 79/224 (35%), Gaps = 54/224 (24%)
Query: 32 SIFLSGGSGFLGKVLIEKILRLEPNVKKIYLLMRTKKGKTPNQRVEELFESPVFDALKTL 91
++ ++G GF+G L E++LR V+ + + N L
Sbjct: 1 NVLVTGADGFIGSHLTERLLREGHEVRALDIY---------NSFNSWG-----------L 40
Query: 92 RGKSILQKIQVISGDITQLKLGISEIDKKELIDNVDIVYHVAATIRFDEPIK---TAVIL 148
++ + ISGD+ L+ D+V+H+AA I + V
Sbjct: 41 LDNAVHDRFHFISGDVRDASEVE------YLVKKCDVVFHLAALIAIPYSYTAPLSYVET 94
Query: 149 NTRGTRDMLELSKQMKNLKCFTYISTAYCHPSEKVLEERTYLPPDDPHQVILRAESMKEE 208
N GT ++LE + K + ST SE V +P D+ H +
Sbjct: 95 NVFGTLNVLEAACV-LYRKRVVHTST-----SE-VYGTAQDVPIDEDHPL---------- 137
Query: 209 DLEVFRQDILGEFPNSYAYTKCLAEGLV-AECMELGMPCMILRP 251
P Y+ +K A+ L + G+P I+RP
Sbjct: 138 -----LYINKPRSP--YSASKQGADRLAYSYGRSFGLPVTIIRP 174
>gnl|CDD|224011 COG1086, COG1086, Predicted nucleoside-diphosphate sugar epimerases
[Cell envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 588
Score = 45.0 bits (107), Expect = 8e-05
Identities = 42/164 (25%), Positives = 67/164 (40%), Gaps = 42/164 (25%)
Query: 23 RIAKTYENKSIFLSGGSGFLGKVLIEKILRLEPNVKKIYLLMRTKKGKTPNQRVEELFES 82
I K++ ++GG G +G L +IL+ P K+I L R E
Sbjct: 243 LIGAMLTGKTVLVTGGGGSIGSELCRQILKFNP--KEIILFSRD--------------EY 286
Query: 83 PVFDALKTLRGKSILQKIQVISGDITQLKLGISEIDKKELID-----NVDIVYHVAA--- 134
++ LR K K++ GD+ D+ + VDIV+H AA
Sbjct: 287 KLYLIDMELREKFPELKLRFYIGDVR---------DRDRVERAMEGHKVDIVFHAAALKH 337
Query: 135 --TIRF--DEPIKTAVILNTRGTRDMLELSKQMKNLKCFTYIST 174
+ + +E IKT V+ GT ++ E + + +K F IST
Sbjct: 338 VPLVEYNPEEAIKTNVL----GTENVAEAAIKNG-VKKFVLIST 376
>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 = 43.4 bits (103), Expect = 1e-04
Identities = 44/227 (19%), Positives = 73/227 (32%), Gaps = 68/227 (29%)
Query: 33 IFLSGGSGFLGKVLIEKILRLEPNVKKIYLLMRTKKGKTPNQRVEELFESPVFDALKTLR 92
I ++GG+GF+G L+ ++L+ V + + F
Sbjct: 1 ILVTGGTGFIGSHLVRRLLQEGYEVIVLG---------RRRRSESLNTGRIRF------- 44
Query: 93 GKSILQKIQVISGDITQLKLGISEIDKKELIDNVDIVYHVAATIR----FDEPIKTAVIL 148
GD+T +++ D V H+AA F++P
Sbjct: 45 ----------HEGDLT----DPDALERLLAEVQPDAVIHLAAQSGVGASFEDPADFIRA- 89
Query: 149 NTRGTRDMLELSKQMKNLKCFTYISTA--YCHPSEKVLEERTYLPPDDPHQVILRAESMK 206
N GT +LE +++ +K F + S++ Y D I
Sbjct: 90 NVLGTLRLLEAARRA-GVKRFVFASSSEVY---------------GDVADPPI------T 127
Query: 207 EEDLEVFRQDILGEFPNSYAYTKCLAEGLV-AECMELGMPCMILRPS 252
E+ + YA K AE LV A G+ +ILR
Sbjct: 128 EDTPLGPL--------SPYAAAKLAAERLVEAYARAYGLRAVILRLF 166
>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 = 42.4 bits (100), Expect = 1e-04
Identities = 38/171 (22%), Positives = 68/171 (39%), Gaps = 37/171 (21%)
Query: 33 IFLSGGSGFLGKVLIEKILRLEPNVKKIYLLMRTKKGKTPNQRVEELFESPVFDALKTLR 92
I + G +GF+G+ L ++L ++ LL+R +R+ + + PV
Sbjct: 1 ILILGATGFIGRALARELLEQ---GHEVTLLVRNT------KRLSKEDQEPV-------- 43
Query: 93 GKSILQKIQVISGDITQLKLGISEIDKKELIDNVDIVYHVAATIRFDEPIKTAVILNTRG 152
V+ GD+ L + + VD+V H+A R ++ G
Sbjct: 44 --------AVVEGDLRDLD------SLSDAVQGVDVVIHLAGAPRDTRDFCE---VDVEG 86
Query: 153 TRDMLELSKQMKNLKCFTYISTAYCHPSEKVLEERTYLPPDDPHQVILRAE 203
TR++LE +K+ +K F +IS+ + EE P V + E
Sbjct: 87 TRNVLEAAKEA-GVKHFIFISSLGAYGDLH--EETEPSPSSPYLAVKAKTE 134
>gnl|CDD|187568 cd05258, CDP_TE_SDR_e, CDP-tyvelose 2-epimerase, extended (e) SDRs.
CDP-tyvelose 2-epimerase is a tetrameric SDR that
catalyzes the conversion of CDP-D-paratose to
CDP-D-tyvelose, the last step in tyvelose biosynthesis.
This subgroup is a member of the extended SDR subfamily,
with a characteristic active site tetrad and NAD-binding
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 = 337
Score = 43.8 bits (104), Expect = 1e-04
Identities = 49/235 (20%), Positives = 84/235 (35%), Gaps = 46/235 (19%)
Query: 31 KSIFLSGGSGFLGKVLIEKILRLEPNVKKIYLLMRTKKGKTPNQRVEELFESPVFDALKT 90
+ ++GG+GF+G L L+ V LMR +G F L
Sbjct: 1 MRVLITGGAGFIGSNLARFFLKQGWEVIGFDNLMR--RG--------------SFGNLAW 44
Query: 91 LRGKSILQKIQVISGDITQLKLGISEIDKKELIDNVDIVYHVAA----TIRFDEPIKTAV 146
L+ ++ + GDI D ++L +++D++ H AA T P +
Sbjct: 45 LKANREDGGVRFVHGDIRNRN------DLEDLFEDIDLIIHTAAQPSVTTSASSP-RLDF 97
Query: 147 ILNTRGTRDMLELSKQMKNLKCFTYISTAYCHP----SEKVLEERTYLPPDDPHQVILRA 202
N GT ++LE ++Q F + ST + + E T
Sbjct: 98 ETNALGTLNVLEAARQHAPNAPFIFTSTNKVYGDLPNYLPLEELETRYELAPEG------ 151
Query: 203 ESMKEEDL-EVFRQDILGEFPNS-YAYTKCLAEGLVAECMEL-GMPCMILRPSIV 254
+ E F D F +S Y +K A+ V E + G+ ++ R +
Sbjct: 152 --WSPAGISESFPLD----FSHSLYGASKGAADQYVQEYGRIFGLKTVVFRCGCL 200
>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 = 43.1 bits (102), Expect = 2e-04
Identities = 53/210 (25%), Positives = 84/210 (40%), Gaps = 66/210 (31%)
Query: 37 GGSGFLGKVLIEKILRLEPNVKKIYLLMRTKKGKTPNQRVEELFESPVFDALKTLRGKSI 96
GG GFLG+ ++ +LR ++++ RV +L SP + L S
Sbjct: 4 GGGGFLGRHIVRLLLREGE-LQEV--------------RVFDLRFSP-----ELLEDFSK 43
Query: 97 LQKIQVISGDITQLKLGISEIDKKEL---IDNVDIVYHVAATI------RFDEPIKTAVI 147
LQ I I GD+T DK++L + D+V H AA I D +K
Sbjct: 44 LQVITYIEGDVT---------DKQDLRRALQGSDVVIHTAAIIDVFGKAYRDTIMK---- 90
Query: 148 LNTRGTRDMLELSKQMKNLKCFTYISTAYCHPSEKVLEERTYLPPDDPHQVILRA-ESMK 206
+N +GT+++L+ + ++ Y S+ E V P+ Q I+ E+
Sbjct: 91 VNVKGTQNVLDACVKA-GVRVLVYTSSM-----EVVG-------PNSYGQPIVNGDETTP 137
Query: 207 EEDLEVFRQDILGEFPNSYAYTKCLAEGLV 236
E + Y +K LAE LV
Sbjct: 138 YEST----------HQDPYPESKALAEKLV 157
>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 = 40.8 bits (96), Expect = 0.001
Identities = 38/158 (24%), Positives = 67/158 (42%), Gaps = 35/158 (22%)
Query: 28 YENKSIFLSGGSGFLGKVLIEKILRLEPNVKKIYLLMRTKKGKTPNQRVEELFESPVFDA 87
++ K + ++G +GF G L + L V L T PN LFE
Sbjct: 2 WQGKRVLVTGHTGFKGSWLSLWLQELGAKVIGYSLDPPTN----PN-----LFEL----- 47
Query: 88 LKTLRGKSILQKIQVISGDI---TQLKLGISEIDKKELIDNVDIVYHVAAT--IR--FDE 140
++ KI GDI L+ I E + +IV+H+AA +R + +
Sbjct: 48 ------ANLDNKISSTRGDIRDLNALREAIREYEP-------EIVFHLAAQPLVRLSYKD 94
Query: 141 PIKTAVILNTRGTRDMLELSKQMKNLKCFTYISTAYCH 178
P++T N GT ++LE ++ ++K +++ C+
Sbjct: 95 PVETFET-NVMGTVNLLEAIRETGSVKAVVNVTSDKCY 131
>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 = 39.8 bits (94), Expect = 0.002
Identities = 37/149 (24%), Positives = 65/149 (43%), Gaps = 32/149 (21%)
Query: 33 IFLSGGSGFLGKVLIEKILRLEPNVKKIYLLMRTKKGKTPNQRVEELFESPVFDALKTLR 92
+ ++GG G +G L +IL+ P KKI L R E +++ + LR
Sbjct: 1 VLVTGGGGSIGSELCRQILKFNP--KKIILFSRD--------------EFKLYEIRQELR 44
Query: 93 GKSILQKIQVISGDITQLKLGISEIDKKELIDNVDIVYHVAA-----TIRFD--EPIKTA 145
+ K++ GD+ + +++ VD V+H AA + ++ E IKT
Sbjct: 45 QEYNDPKLRFFIGDVRDRERLERAMEQHG----VDTVFHAAALKHVPLVEYNPMEAIKT- 99
Query: 146 VILNTRGTRDMLELSKQMKNLKCFTYIST 174
N GT ++ E + + ++ F IST
Sbjct: 100 ---NVLGTENVAEAAIEN-GVEKFVLIST 124
>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 = 39.6 bits (93), Expect = 0.003
Identities = 37/158 (23%), Positives = 68/158 (43%), Gaps = 35/158 (22%)
Query: 28 YENKSIFLSGGSGFLGKVLIEKILRLEPNVKKIYLLMRTKKGKTPNQRVEELFESPVFDA 87
++ K + ++G +GF G L +L L V L T PN +F+
Sbjct: 2 WQGKKVLVTGHTGFKGSWLSLWLLELGAEVYGYSLDPPTS----PN----------LFEL 47
Query: 88 LKTLRGKSILQKIQVISGDIT-QLKLGISEIDKKELIDNV--DIVYHVAA----TIRFDE 140
L + +KI+ GDI KL ++ I +IV+H+AA + +
Sbjct: 48 LN------LAKKIEDHFGDIRDAAKL-------RKAIAEFKPEIVFHLAAQPLVRKSYAD 94
Query: 141 PIKTAVILNTRGTRDMLELSKQMKNLKCFTYISTAYCH 178
P++T N GT ++LE + + ++K +++ C+
Sbjct: 95 PLETFET-NVMGTVNLLEAIRAIGSVKAVVNVTSDKCY 131
>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 = 39.6 bits (93), Expect = 0.003
Identities = 73/305 (23%), Positives = 119/305 (39%), Gaps = 75/305 (24%)
Query: 32 SIFLSGGSGFLGKVLIEKILRLEPNVKKIYLLMRTKKGKTPNQRVEELFESPVFDALKTL 91
S + GGSGFLG+ L+E++LR P V ++ P F+ +
Sbjct: 1 SCLVVGGSGFLGRHLVEQLLRRG----------------NPTVHVFDIR--PTFELDPSS 42
Query: 92 RGKSILQKIQVISGDITQLKLGISEIDKKELIDNVDIVYHVAATI-RFDEPIKTAVILNT 150
G ++Q +GD+T +++K ++V+H A+ ++ + V N
Sbjct: 43 SG-----RVQFHTGDLTDP----QDLEKAFNEKGPNVVFHTASPDHGSNDDLYYKV--NV 91
Query: 151 RGTRDMLELSKQMKNLKCFTYISTAYCHPSEKVLEERTYLPPDDPHQVILRAESMKEEDL 210
+GTR+++E ++ +K Y S+A V+ + + D
Sbjct: 92 QGTRNVIEACRK-CGVKKLVYTSSA---------------------SVVFNGQDIINGD- 128
Query: 211 EVFRQDILGEFPNSYAYTKCLAEGLV--AECMELGMPCMILRPSIVV-PIYKEPLPGWTD 267
E + ++Y TK LAE LV A E G+ LRP+ + P ++ +PG
Sbjct: 129 E--SLPYPDKHQDAYNETKALAEKLVLKANDPESGLLTCALRPAGIFGPGDRQLVPGLLK 186
Query: 268 NI-NGPTGLLIGAGKGVIRSMYCKNTGMADFLPAD--------VAING-VFLFT------ 311
NG T IG G + Y +N A L AD + G F T
Sbjct: 187 AAKNGKTKFQIGDGNNLFDFTYVENVAHAHILAADALLSSSHAETVAGEAFFITNDEPIY 246
Query: 312 -WDFL 315
WDF
Sbjct: 247 FWDFA 251
>gnl|CDD|187657 cd08954, KR_1_FAS_SDR_x, beta-ketoacyl reductase (KR) domain of
fatty acid synthase (FAS), subgroup 1, complex (x) SDRs.
NADP-dependent KR domain of the multidomain type I FAS,
a complex SDR family. This subfamily also includes
proteins identified as polyketide synthase (PKS), a
protein with related modular protein architecture and
similar function. It includes the KR domains of
mammalian and chicken FAS, and Dictyostelium discoideum
putative polyketide synthases (PKSs). These KR domains
contain two subdomains, each of which is related to SDR
Rossmann fold domains. However, while the C-terminal
subdomain has an active site similar to the other SDRs
and a NADP-binding capability, the N-terminal SDR-like
subdomain is truncated and lacks these functions,
serving a supportive structural role. In some instances,
such as porcine FAS, an enoyl reductase (a Rossman fold
NAD-binding domain of the medium-chain
dehydrogenase/reductase, MDR family) module is inserted
between the sub-domains. Fatty acid synthesis occurs via
the stepwise elongation of a chain (which is attached to
acyl carrier protein, ACP) with 2-carbon units.
Eukaryotic systems consists of large, multifunctional
synthases (type I) while bacterial, type II systems, use
single function proteins. Fungal fatty acid synthesis
uses a dodecamer of 6 alpha and 6 beta subunits. In
mammalian type FAS cycles, ketoacyl synthase forms
acetoacetyl-ACP which is reduced by the NADP-dependent
beta-ketoacyl reductase (KR), forming
beta-hydroxyacyl-ACP, which is in turn dehydrated by
dehydratase to a beta-enoyl intermediate, which is
reduced by NADP-dependent beta-enoyl reductase (ER);
this KR and ER are members of the SDR family. This KR
subfamily has an active site tetrad with a similar 3D
orientation compared to archetypical SDRs, but the
active site Lys and Asn residue positions are swapped.
The characteristic NADP-binding is typical of the
multidomain complex SDRs, with a GGXGXXG NADP binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold (alpha/beta folding
pattern with a central beta-sheet), an NAD(P)(H)-binding
region, and a structurally diverse C-terminal region.
Classical SDRs are typically about 250 residues long,
while extended SDRs are approximately 350 residues.
Sequence identity between different SDR enzymes are
typically in the 15-30% range, but the enzymes share the
Rossmann fold NAD-binding motif and characteristic
NAD-binding and catalytic sequence patterns. These
enzymes catalyze a wide range of activities including
the metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
prostaglandin dehydrogenase (PGDH) numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser (Ser-138, PGDH numbering) and/or an Asn (Asn-107,
PGDH numbering) contributing to the active site; while
substrate binding is in the C-terminal region, which
determines specificity. The standard reaction mechanism
is a 4-pro-S hydride transfer and proton relay involving
the conserved Tyr and Lys, a water molecule stabilized
by Asn, and nicotinamide. Extended SDRs have additional
elements in the C-terminal region, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type KRs have
a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 452
Score = 38.6 bits (90), Expect = 0.007
Identities = 22/127 (17%), Positives = 43/127 (33%), Gaps = 20/127 (15%)
Query: 16 ELQALPDRIAKTYENKSIFLSGGSGFLGKVLIEKILRLEPNVKKIYLL----MRTKKGKT 71
++ KS ++GGSG LG ++ K L V+ I +L M+ +
Sbjct: 204 LDLSILKTNYPINLGKSYLITGGSGGLGLEIL-KWLVKRGAVENIIILSRSGMKWELELL 262
Query: 72 PNQRVEELFESPVFDALKTLRGKSILQKIQVISGDITQLKLGISEIDKKELIDNVDIVYH 131
+ + V D++ L+ I+ I I + ++H
Sbjct: 263 IR---------------EWKSQNIKFHFVSVDVSDVSSLEKAINLILNAPKIGPIGGIFH 307
Query: 132 VAATIRF 138
+A +
Sbjct: 308 LAFVLID 314
>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 = 37.7 bits (88), Expect = 0.012
Identities = 35/152 (23%), Positives = 54/152 (35%), Gaps = 36/152 (23%)
Query: 32 SIFLSGGSGFLGKVLIEKILRLEPNVKKIYLLMRTKKGKTPNQRVEELFESPVFDALK-- 89
I ++GG+GF+G + IL + P+ V V D L
Sbjct: 1 RILVTGGAGFIGSNFVRYILN-----------------EHPDAEV------IVLDKLTYA 37
Query: 90 ----TLRGKSILQKIQVISGDITQLKLGISEIDKKELIDNVDIVYHVAATIRFDEPIKTA 145
L + + + GDI +L +S + + D V H AA D I
Sbjct: 38 GNLENLADLEDNPRYRFVKGDIGDREL-VSRLFTEH---QPDAVVHFAAESHVDRSISGP 93
Query: 146 VIL---NTRGTRDMLELSKQMKNLKCFTYIST 174
N GT +LE ++ + F +IST
Sbjct: 94 AAFIETNVVGTYTLLEAVRKYWHEFRFHHIST 125
>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 = 37.6 bits (87), Expect = 0.012
Identities = 43/237 (18%), Positives = 80/237 (33%), Gaps = 67/237 (28%)
Query: 35 LSGGSGFLG----KVLIEK------ILRLEPNVKKIYLLMRTKKGKTPNQRVEELFESPV 84
++G SGF+ + L+E+ +R VKK+ L+
Sbjct: 3 VTGASGFVASHVVEQLLERGYKVRATVRDPSKVKKVNHLLDLDAKPGR------------ 50
Query: 85 FDALKTLRGKSILQKIQVISGDITQLKLGISEIDKKELIDNVDIVYHVAATIRF-----D 139
L+ E E+I V+HVA + F +
Sbjct: 51 ---LELAVADLTD------------------EQSFDEVIKGCAGVFHVATPVSFSSKDPN 89
Query: 140 EPIKTAVILNTRGTRDMLELSKQMKNLKCFTYISTAYCHPSEKVLEERTYLPPDDPHQVI 199
E IK A+ GT + L+ + K++K F S+A +P + ++
Sbjct: 90 EVIKPAI----GGTLNALKAAAAAKSVKRFVLTSSAGS----------VLIPKPNVEGIV 135
Query: 200 LRAESMKEEDLEVFRQDILGEFPNSYAYTKCLAEGLVAE-CMELGMPCMILRPSIVV 255
L +S E+ + + + S K LAE + E + + + P++ +
Sbjct: 136 LDEKSWNLEEFDSDPKKSAWVYAAS----KTLAEKAAWKFADENNIDLITVIPTLTI 188
>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 = 36.1 bits (84), Expect = 0.033
Identities = 62/347 (17%), Positives = 110/347 (31%), Gaps = 116/347 (33%)
Query: 31 KSIFLSGGSGFLGKVLIEKILRLEPNVKKIYLLMRTKKGKTPNQRVEELFESPVFDALKT 90
I + GG+ F+GK L+E++L +V + R + + VE
Sbjct: 1 MKILIIGGTRFIGKALVEELLAAGHDV---TVFNRGRTKPDLPEGVEH------------ 45
Query: 91 LRGKSILQKIQVISGDITQLKLGISEIDKKELI--DNVDIVYHVAATIRFDEPIKTAVIL 148
I GD +EL+ ++ D+V A
Sbjct: 46 ------------IVGDRN------DRDALEELLGGEDFDVVVDTIAY------------- 74
Query: 149 NTRGTRDMLELSKQMKNLKCFTYISTA--YCHPSEKVLEERTYLPPDDPHQVILRAESMK 206
R L+ K +K + +IS+A Y P + E P +P V L
Sbjct: 75 TPRQVERALDAFKG--RVKQYIFISSASVYLKPGRVITES---TPLREPDAVGLSD---- 125
Query: 207 EEDLEVFRQDILGEFPNSYAYTKCLAEGLVAECMELGMPCMILRPSIVV----PIYKEPL 262
P Y K AE ++ E P I+RP + +
Sbjct: 126 ---------------PWDYGRGKRAAEDVLIE--AAAFPYTIVRPPYIYGPGDYTGRLAY 168
Query: 263 PGWTDNI--NGPTGLLI-GAGKGVIRSMYCKNTGMADFLPA----DVAINGVFLFTWDFL 315
+ D + P +L+ G G +++ ++ K+ +A L AI G+F
Sbjct: 169 --FFDRLARGRP--ILVPGDGHSLVQFIHVKD--LARALLGAAGNPKAIGGIF------- 215
Query: 316 NSKESERKSVCNLTSNKDYKITWQEICDIGKDIVTSKIPFNSTLWYP 362
N+T ++ +TW E+ + + + +
Sbjct: 216 -----------NITGDE--AVTWDELLEACAKALGKEAEI---VHVE 246
>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 = 36.1 bits (84), Expect = 0.038
Identities = 37/155 (23%), Positives = 58/155 (37%), Gaps = 36/155 (23%)
Query: 31 KSIFLSGGSGFLGKVLIEKILRLEPNVKKIYLLMRTKKGKTPNQRVEELFESPVFDALKT 90
K I ++GG+GFLG L +++L V + G+ N ++
Sbjct: 1 KRILITGGAGFLGSHLCDRLLEDGHEV---ICVDNFFTGRKRN--------------IEH 43
Query: 91 LRGKSILQKIQVISGDITQLKLGISEIDKKELIDNVDIVYHVAA---TIRFDE-PIKTAV 146
L G + I D+T+ VD +YH+A + + PIKT
Sbjct: 44 LIGHP---NFEFIRHDVTEPLYL-----------EVDQIYHLACPASPVHYQYNPIKTLK 89
Query: 147 ILNTRGTRDMLELSKQMKNLKCFTYISTAYCHPSE 181
N GT +ML L+K++ S Y P
Sbjct: 90 T-NVLGTLNMLGLAKRVGARVLLASTSEVYGDPEV 123
>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 = 35.4 bits (82), Expect = 0.061
Identities = 31/162 (19%), Positives = 52/162 (32%), Gaps = 39/162 (24%)
Query: 33 IFLSGGSGFLGKVLIEKILRLEPNVKKIYLLMRTKKGKTPNQRVEELFESPVFDALKTLR 92
I ++GG+GF+G L++++L V + L ++ + + F D L
Sbjct: 2 ILVTGGAGFIGSHLVDRLLEEGNEVVVVDNLSSGRRENIEPEFENKAFRFVKRD-LLDTA 60
Query: 93 GKSILQKIQVISGDITQLKLGISEIDKKELIDNVDIVYHVAAT--IRFDEPIKTAVIL-- 148
K + D V+H+AA +R + L
Sbjct: 61 DKVAK--------------------------KDGDTVFHLAANPDVRL-GATDPDIDLEE 93
Query: 149 NTRGTRDMLELSKQMKNLKC----FTYISTAYCHPSEKVLEE 186
N T ++LE M+ F ST Y E
Sbjct: 94 NVLATYNVLEA---MRANGVKRIVFASSSTVYGEAKVIPTPE 132
>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 = 33.7 bits (78), Expect = 0.20
Identities = 35/153 (22%), Positives = 58/153 (37%), Gaps = 37/153 (24%)
Query: 31 KSIFLSGGSGFLGKVLIEKILRLEPNVKKIYLLMRTKKGKTPNQRVEELFESPVFDAL-- 88
I ++GG+GF+G + +L P+ K I D L
Sbjct: 1 MKILVTGGAGFIGSNFVRYLLNKYPDYKII-----------------------NLDKLTY 37
Query: 89 ----KTLRGKSILQKIQVISGDITQLKLGISEIDKKELIDNVDIVYHVAATIRFDEPIKT 144
+ L S + + + GDI +L + + ++E +D V H AA D I
Sbjct: 38 AGNLENLEDVSSSPRYRFVKGDICDAEL-VDRLFEEE---KIDAVIHFAAESHVDRSISD 93
Query: 145 AVIL---NTRGTRDMLELSKQMKNLKCFTYIST 174
N GT +LE +++ + F +IST
Sbjct: 94 PEPFIRTNVLGTYTLLEAARKYGVKR-FVHIST 125
>gnl|CDD|204152 pfam09152, DUF1937, Domain of unknown function (DUF1937). This
domain is found in a set of hypothetical bacterial
proteins. Their exact function has not, as yet, been
described.
Length = 111
Score = 31.7 bits (72), Expect = 0.25
Identities = 23/104 (22%), Positives = 37/104 (35%), Gaps = 20/104 (19%)
Query: 170 TYISTAYCHPSEKVLEERTYLPPDDPHQVILRAESMKEEDLEVFRQDILGEFPNSYAYTK 229
+++ Y H V+E R ++V R + E VF Q + S+
Sbjct: 3 IFLACPYSHADADVVEARFL----ACNRVAAR---LIEAGHAVFSQVSM-----SHPINL 50
Query: 230 CLAEGLVAEC----MELGMPCMILRPSIVVPIYKEPLPGWTDNI 269
LA G + P + ++VV LPGW D+
Sbjct: 51 PLAGGDDPAIGVLWAPVDAPFLDACEALVVL----DLPGWEDSG 90
>gnl|CDD|165812 PLN02166, PLN02166, dTDP-glucose 4,6-dehydratase.
Length = 436
Score = 33.8 bits (77), Expect = 0.25
Identities = 40/161 (24%), Positives = 70/161 (43%), Gaps = 37/161 (22%)
Query: 33 IFLSGGSGFLGKVLIEKILRLEPNVKKIYLLMRTKKGKTPNQRVEELFESPVFDALKTLR 92
I ++GG+GF+G L++K++ V I +K + + LF +P F
Sbjct: 123 IVVTGGAGFVGSHLVDKLIGRGDEVIVIDNFFTGRK-----ENLVHLFGNPRF------- 170
Query: 93 GKSILQKIQVISGDITQLKLGISEIDKKELIDNVDIVYHV---AATIRFD-EPIKTAVIL 148
++I D+ + ++ VD +YH+ A+ + + P+KT +
Sbjct: 171 --------ELIRHDVVE-----------PILLEVDQIYHLACPASPVHYKYNPVKT-IKT 210
Query: 149 NTRGTRDMLELSKQMKNLKCFTYISTAYCHPSEKVLEERTY 189
N GT +ML L+K++ T S Y P E +E TY
Sbjct: 211 NVMGTLNMLGLAKRVGARFLLTSTSEVYGDPLEHPQKE-TY 250
>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 = 33.5 bits (77), Expect = 0.27
Identities = 32/110 (29%), Positives = 44/110 (40%), Gaps = 33/110 (30%)
Query: 30 NKSIFLSGGSGFLGKVLIEKILRLEPNVKKIYLLMRTKKGKTPNQRVEELFESPVFDALK 89
NKSI ++GG+G GK I ++L N KKI + R D LK
Sbjct: 4 NKSILITGGTGSFGKAFISRLLE-NYNPKKIIIYSR--------------------DELK 42
Query: 90 TLRGKSILQKIQVISGDITQLKLGISEI-DKKELI---DNVDIVYHVAAT 135
+ +Q Q L+ I ++ DK+ L VD V H AA
Sbjct: 43 ----QWEMQ--QKFPAP--CLRFFIGDVRDKERLTRALRGVDYVVHAAAL 84
>gnl|CDD|239171 cd02770, MopB_DmsA-EC, This CD (MopB_DmsA-EC) includes the DmsA
enzyme of the dmsABC operon encoding the anaerobic
dimethylsulfoxide reductase (DMSOR) of Escherichia coli
and other related DMSOR-like enzymes. Unlike other
DMSOR-like enzymes, this group has a predicted
N-terminal iron-sulfur [4Fe-4S] cluster binding site.
These members belong to the molybdopterin_binding (MopB)
superfamily of proteins.
Length = 617
Score = 33.1 bits (76), Expect = 0.38
Identities = 17/56 (30%), Positives = 27/56 (48%), Gaps = 15/56 (26%)
Query: 1 MKNIGGAPD-----------LVTIPKELQALPDRIAKTYENKSIFLSGGSGFLGKV 45
MK +G + L TI EL+ RI + Y N++I+++ G+G G V
Sbjct: 64 MKRVGKRGEGKFVRISWDEALDTIASELK----RIIEKYGNEAIYVNYGTGTYGGV 115
>gnl|CDD|187581 cd05273, GME-like_SDR_e, Arabidopsis thaliana
GDP-mannose-3',5'-epimerase (GME)-like, extended (e)
SDRs. This subgroup of NDP-sugar epimerase/dehydratases
are extended SDRs; they have the characteristic active
site tetrad, and an NAD-binding motif: TGXXGXX[AG],
which is a close match to the canonical NAD-binding
motif. Members include Arabidopsis thaliana
GDP-mannose-3',5'-epimerase (GME) which catalyzes the
epimerization of two positions of GDP-alpha-D-mannose to
form GDP-beta-L-galactose. 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 = 328
Score = 32.1 bits (73), Expect = 0.74
Identities = 36/198 (18%), Positives = 72/198 (36%), Gaps = 46/198 (23%)
Query: 31 KSIFLSGGSGFLGKVLIEKILRLEPNVKKIYLLMRTKKGKTPNQRVEELFESPVFDALKT 90
+ ++G GF+G L E++ V R + SP
Sbjct: 1 QRALVTGAGGFIGSHLAERLKAEGHYV-----------------RGADWK-SPEH----- 37
Query: 91 LRGKSILQKIQVISGDITQLKLGISEIDKKELIDNVDIVYHVAATIRFDEPIKT--AVIL 148
+ D+ +++ + + + VD V+H+AA + I++ AVI+
Sbjct: 38 --MTQPTDDDEFHLVDLREMENCL------KATEGVDHVFHLAADMGGMGYIQSNHAVIM 89
Query: 149 NTRGTRD--MLELSKQMKNLKCFTYISTAYCHPSEKVL--------EERTYLPPDDPHQV 198
+ MLE + ++ ++ F + S+A +P K L EE + P +P
Sbjct: 90 YNNTLINFNMLE-AARINGVERFLFASSACVYPEFKQLETTVVRLREEDAW--PAEPQDA 146
Query: 199 ILRAESMKEEDLEVFRQD 216
+ E + + +D
Sbjct: 147 YGWEKLATERLCQHYNED 164
>gnl|CDD|224015 COG1090, COG1090, Predicted nucleoside-diphosphate sugar
epimerase [General function prediction only].
Length = 297
Score = 31.9 bits (73), Expect = 0.88
Identities = 16/80 (20%), Positives = 30/80 (37%), Gaps = 22/80 (27%)
Query: 33 IFLSGGSGFLGKVLIEKILRLEPNVKKIYLLMRTKKGKTPNQRVEELFESPV-------- 84
I ++GG+G +G+ L RL ++ +L R + + V
Sbjct: 1 ILITGGTGLIGRALTA---RLRKGGHQVTILTRRP------PKASQNLHPNVTLWEGLAD 51
Query: 85 -----FDALKTLRGKSILQK 99
DA+ L G+ I ++
Sbjct: 52 ALTLGIDAVINLAGEPIAER 71
>gnl|CDD|152003 pfam11567, PfUIS3, Plasmodium falciparum UIS3 membrane protein.
UIS3 is a membrane protein essential for sporozoite
development in infected hepatocytes. This family is
130-229 of the Plasmodium falciparum UIS3 protein which
is compact and has an all alpha-helical
structure.PfUIS3(130-229) interacts with lipids,
phospholipid lysosomes, the human liver fatty
acid-binding protein and with the lipid
phosphatidylethanolamine. The interaction with liver
fatty acid-binding protein provides the parasite with a
method to import essential fatty acids/lipids during
rapid growth phases of sporozoites.
Length = 101
Score = 30.0 bits (67), Expect = 1.0
Identities = 14/34 (41%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 440 REIVQYCVENDNVDIVKYFE-KAVYGARYFLMKE 472
++ VQ EN N+ + KY E KAV +Y L K
Sbjct: 58 QKFVQGLQENRNISLSKYQENKAVLDLKYHLQKV 91
>gnl|CDD|200381 TIGR04130, FnlA, UDP-N-acetylglucosamine
4,6-dehydratase/5-epimerase. The FnlA enzyme is the
first step in the biosynthesis of UDP-FucNAc from
UDP-GlcNAc in E. coli (along with FnlB and FnlC). The
proteins identified by this model include FnlA homologs
in the O-antigen clusters of O4, O25, O26, O29 (Shigella
D11), O118, O145 and O172 serotype strains, all of which
produce O-antigens containing FucNAc (or the further
modified FucNAm). A homolog from Pseudomonas aerugiosa
serotype O11, WbjB, also involved in the biosynthesis of
UDP-FucNAc has been characterized and is now believed to
carry out both the initial 4,6-dehydratase reaction and
the subsequent epimerization of the resulting methyl
group at C-5. A phylogenetic tree of related sequences
shows a distinct clade of enzymes involved in the
biosynthesis of UDP-QuiNAc (Qui=qinovosamine). This
clade appears to be descendant from the common ancestor
of the Pseudomonas and E. coli fucose-biosynthesis
enzymes. It has been hypothesized that the first step in
the biosynthesis of these two compounds may be the same,
and thus that these enzymes all have the same function.
At present, lacking sufficient confirmation of this, the
current model trusted cutoff only covers the tree
segment surrounding the E. coli genes. The clades
containing the Pseudomonas and QuiNAc biosynthesis
enzymes score above the noise cutoff. Immediately below
the noise cutoff are enzymes involved in the
biosynthesis of UDP-RhaNAc (Rha=rhamnose), which again
may or may not produce the same product.
Length = 337
Score = 31.5 bits (71), Expect = 1.1
Identities = 34/159 (21%), Positives = 70/159 (44%), Gaps = 41/159 (25%)
Query: 28 YENKSIFLSGGSGFLGKVLIEKILRLEPNVKKIYLLMRTKKGKTPNQRVEELFESPVFDA 87
+++K + ++GG+G G ++ + L+ ++K+I + R +K +
Sbjct: 2 FKDKILLITGGTGSFGNAVLRRF--LDTDIKEIRIFSRDEKKQ----------------- 42
Query: 88 LKTLRGKSILQKIQVISGDITQLKLGISEIDKKELID---NVDIVYHVAA-----TIRFD 139
+R K K++ GD+ D + +++ VD +YH AA + F
Sbjct: 43 -DDMRKKYNNSKLKFYIGDVR---------DYRSILNATRGVDFIYHAAALKQVPSCEF- 91
Query: 140 EPIKTAVILNTRGTRDMLE--LSKQMKNLKCFTYISTAY 176
P++ AV N GT ++LE ++ +K + C + Y
Sbjct: 92 HPME-AVKTNVLGTENVLEAAIANGVKRVVCLSTDKAVY 129
>gnl|CDD|185103 PRK15181, PRK15181, Vi polysaccharide biosynthesis protein TviC;
Provisional.
Length = 348
Score = 31.2 bits (70), Expect = 1.3
Identities = 41/167 (24%), Positives = 67/167 (40%), Gaps = 27/167 (16%)
Query: 31 KSIFLSGGSGFLGKVLIEKILRLEPNVKKIYLLMRTKKGKTPNQRVEELFESPVFDALKT 90
K ++G +GF+G L+E++L L V L G N D ++T
Sbjct: 16 KRWLITGVAGFIGSGLLEELLFLNQTVIG---LDNFSTGYQHN-----------LDDVRT 61
Query: 91 LRGKSILQKIQVISGDITQLKLGISEIDKKELIDNVDIVYHVAATIRFDEPIKTAVILNT 150
+ + I GDI + D ++ NVD V H AA +K + N+
Sbjct: 62 SVSEEQWSRFIFIQGDIRKFT------DCQKACKNVDYVLHQAALGSVPRSLKDPIATNS 115
Query: 151 R---GTRDMLELSKQMKNLKCFTYISTAYC---HPSEKVLEERTYLP 191
G +ML ++ ++ FTY +++ HP +EER P
Sbjct: 116 ANIDGFLNMLTAARD-AHVSSFTYAASSSTYGDHPDLPKIEERIGRP 161
>gnl|CDD|215257 PLN02464, PLN02464, glycerol-3-phosphate dehydrogenase.
Length = 627
Score = 31.7 bits (72), Expect = 1.3
Identities = 24/76 (31%), Positives = 34/76 (44%), Gaps = 3/76 (3%)
Query: 455 VKYFEKAVYGARYFLMKESPESLESARKKMKVMYALHIT-ARCIFLALFLWFLSNNFHVF 513
V+Y EKAV+ Y +K +LE RK++ + A H+ A I + WF +
Sbjct: 121 VRYLEKAVFQLDYGQLKLVFHALEE-RKQL-IENAPHLCHALPIMTPCYDWFEVPYYWAG 178
Query: 514 LKLGLFVRGLASLVFS 529
LK V G L S
Sbjct: 179 LKAYDLVAGPRLLHLS 194
>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 = 31.1 bits (71), Expect = 1.5
Identities = 20/74 (27%), Positives = 34/74 (45%), Gaps = 10/74 (13%)
Query: 33 IFLSGGSGFLGKVLIEKILRLEPNVKKIYLLMRTK------KGKTPNQRVEELFES-PVF 85
I ++GG+GF+G+ L + RL ++ +L R+ K + E +S
Sbjct: 1 ILITGGTGFIGRALTQ---RLTKRGHEVTILTRSPPPGANTKWEGYKPWAGEDADSLEGA 57
Query: 86 DALKTLRGKSILQK 99
DA+ L G+ I K
Sbjct: 58 DAVINLAGEPIADK 71
>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 = 30.7 bits (70), Expect = 2.0
Identities = 45/247 (18%), Positives = 84/247 (34%), Gaps = 77/247 (31%)
Query: 33 IFLSGGSGFLGKVLIEKILRLEPNVKKIYLLMRTKKGKTPNQRVEELFESPVFDALKTLR 92
+ ++G +GF+ ++E++L K Y + T + + + +++ L +
Sbjct: 2 VLVTGATGFIASHIVEQLL------KAGYKVRGTVRSLSKSAKLKALL-----------K 44
Query: 93 GKSILQKIQVISGDITQLKLGISEIDK----KELIDNVDIVYHVAATIRF------DEPI 142
+++ + D ++ E + VD V HVA+ F D+ I
Sbjct: 45 AAGYNDRLEFVIVD---------DLTAPNAWDEALKGVDYVIHVASPFPFTGPDAEDDVI 95
Query: 143 KTAVILNTRGTRDMLELSKQMKNLKCFTYISTA------YCHPSEKVLEERTYLPPDDPH 196
AV GT ++LE +K ++K S+ KV E +
Sbjct: 96 DPAVE----GTLNVLEAAKAAGSVKRVVLTSSVAAVGDPTAEDPGKVFTEEDWNDLTISK 151
Query: 197 QVILRAESMKEEDLEVFRQDILGEFPNSYAYTKCLAE----GLVAEC---MELG--MPCM 247
++Y +K LAE V E EL P
Sbjct: 152 S----------------------NGLDAYIASKTLAEKAAWEFVKENKPKFELITINPGY 189
Query: 248 ILRPSIV 254
+L PS++
Sbjct: 190 VLGPSLL 196
>gnl|CDD|187543 cd05232, UDP_G4E_4_SDR_e, UDP-glucose 4 epimerase, subgroup 4,
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
bacterial proteins, and includes the Staphylococcus
aureus capsular polysaccharide Cap5N, which may have a
role in the synthesis of UDP-N-acetyl-d-fucosamine. 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 = 303
Score = 30.4 bits (69), Expect = 2.3
Identities = 34/160 (21%), Positives = 60/160 (37%), Gaps = 34/160 (21%)
Query: 102 VISGDITQLKLGISEIDKKE-LIDNVDIVYHVAATI-----RFDEPIKTAVILNTRGTRD 155
+ + + + + +ID L VD V H+AA + + +P+ +NT TR
Sbjct: 33 AENAEPSVVLAELPDIDSFTDLFLGVDAVVHLAARVHVMNDQGADPLSDYRKVNTELTRR 92
Query: 156 MLELSKQMKNLKCFTYISTAYCHPSEKVLEERTYLPPDDPHQVILRAESMKEEDLEVFRQ 215
+ + + + +K F ++S S KV E + +D
Sbjct: 93 LARAAAR-QGVKRFVFLS------SVKVNGE------GTVGAPFDETDPPAPQD------ 133
Query: 216 DILGEFPNSYAYTKCLAE-GLVAECMELGMPCMILRPSIV 254
+Y +K AE L+ GM +ILRP +V
Sbjct: 134 --------AYGRSKLEAERALLELGASDGMEVVILRPPMV 165
>gnl|CDD|224013 COG1088, RfbB, dTDP-D-glucose 4,6-dehydratase [Cell envelope
biogenesis, outer membrane].
Length = 340
Score = 30.3 bits (69), Expect = 2.5
Identities = 33/153 (21%), Positives = 53/153 (34%), Gaps = 36/153 (23%)
Query: 31 KSIFLSGGSGFLGKVLIEKILRLEPNVKKIYLLMRTKKGKTPNQRVEELFESPVFDAL-- 88
I ++GG+GF+G + IL P+ + D L
Sbjct: 1 MKILVTGGAGFIGSNFVRYILNKHPDDHVV-----------------------NLDKLTY 37
Query: 89 ----KTLRGKSILQKIQVISGDITQLKLGISEIDKKELIDNVDIVYHVAATIRFDEPIKT 144
+ L + + + GDI +L + + K+ D V H AA D I
Sbjct: 38 AGNLENLADVEDSPRYRFVQGDICDREL-VDRLFKE---YQPDAVVHFAAESHVDRSIDG 93
Query: 145 AVIL---NTRGTRDMLELSKQMKNLKCFTYIST 174
N GT +LE +++ F +IST
Sbjct: 94 PAPFIQTNVVGTYTLLEAARKYWGKFRFHHIST 126
>gnl|CDD|238932 cd01972, Nitrogenase_VnfE_like, Nitrogenase_VnfE_like: VnfE subunit
of the VnfEN complex_like. This group in addition to
VnfE contains a subset of the alpha subunit of the
nitrogenase MoFe protein and NifE-like proteins. The
nitrogenase enzyme system catalyzes the ATP-dependent
reduction of dinitrogen to ammonia. NifEN participates
in the synthesis of the iron-molybdenum cofactor
(FeMoco) of MoFe protein of the
molybdenum(Mo)-nitrogenase. NifB-co (an iron and sulfur
containing precursor of the FeMoco) from NifB is
transferred to NifEN where it is further processed to
FeMoco. VnfEN may similarly be a scaffolding protein
for the iron-vanadium cofactor (FeVco) of the
vanadium-dependent (V)-nitrogenase. NifE and NifN are
essential for the Mo-nitrogenase, VnfE and VnfN are not
essential for the V-nitrogenase. NifE and NifN can
substitute when the vnfEN genes are inactivated.
Length = 426
Score = 30.5 bits (69), Expect = 2.6
Identities = 16/69 (23%), Positives = 22/69 (31%), Gaps = 4/69 (5%)
Query: 157 LELSKQMKNLKCFTYISTAYCHPSEKVLEERTYLPPDDPHQVILRAESMKEEDLEVFRQD 216
EL K +K K AY H VL E + V+L D +D
Sbjct: 285 EELRKALKGKKAIVETGAAYGHLLIAVLRELGFGEVP----VVLVFHHDPTYDRGDSEKD 340
Query: 217 ILGEFPNSY 225
+L +
Sbjct: 341 LLEHGVDPE 349
>gnl|CDD|224213 COG1294, AppB, Cytochrome bd-type quinol oxidase, subunit 2 [Energy
production and conversion].
Length = 346
Score = 30.3 bits (69), Expect = 2.7
Identities = 11/53 (20%), Positives = 18/53 (33%), Gaps = 2/53 (3%)
Query: 461 AVYGARYFLMKESPESLESARKKMKVMYALHITARCIFLALFLWFLSNNFHVF 513
++GA + L+K E ARK + A +T L +
Sbjct: 180 VLHGAAWLLLKTEGALQERARKLAR--IAALLTLVGFLLFGVWVTPGLDGFAA 230
>gnl|CDD|183700 PRK12721, PRK12721, secretion system apparatus protein SsaU;
Reviewed.
Length = 349
Score = 30.0 bits (68), Expect = 3.2
Identities = 14/51 (27%), Positives = 25/51 (49%)
Query: 471 KESPESLESARKKMKVMYALHITARCIFLALFLWFLSNNFHVFLKLGLFVR 521
K + + L ARKK +V+ ++ IT+ AL L+FL + + +
Sbjct: 7 KPTEKKLRDARKKGQVVKSVEITSGVQLAALLLYFLLEGPSLVEAIIGLIN 57
>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 = 29.6 bits (67), Expect = 3.5
Identities = 16/72 (22%), Positives = 29/72 (40%), Gaps = 4/72 (5%)
Query: 31 KSIFLSGGSGFLGKVLIEKILRLEPNVKKIYLLMRTKKGKTPNQRVEELFESPVFDALKT 90
K+ + G +G +GK L+ ++L+ P K+ ++R K +E V D +
Sbjct: 1 KTALVLGATGLVGKHLLRELLK-SPYYSKVTAIVRR---KLTFPEAKEKLVQIVVDFERL 56
Query: 91 LRGKSILQKIQV 102
Q V
Sbjct: 57 DEYLEAFQNPDV 68
>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 = 29.6 bits (67), Expect = 3.7
Identities = 32/134 (23%), Positives = 53/134 (39%), Gaps = 36/134 (26%)
Query: 33 IFLSGGSGFLGKVLIEKILRLEPNVKKIYLL-MRTKKGKTPNQRVEELFESPVFDALKTL 91
+ ++G GF+G L+E ++R V+ L G L SP
Sbjct: 1 VLVTGADGFIGSHLVEALVRQGYEVRAFVLYNSFNSWG--------WLDTSP-------- 44
Query: 92 RGKSILQKIQVISGDITQLKLGISEIDKKELIDNVDIVYHVAATIRF-------DEPIKT 144
+ KI+V++GDI + + K D+V+H+AA I D + T
Sbjct: 45 --PEVKDKIEVVTGDIRD-PDSVRKAMK-----GCDVVFHLAALIAIPYSYIAPDSYVDT 96
Query: 145 AVILNTRGTRDMLE 158
N GT ++L+
Sbjct: 97 ----NVTGTLNVLQ 106
>gnl|CDD|216416 pfam01292, Ni_hydr_CYTB, Prokaryotic cytochrome b561. This family
includes cytochrome b561 and related proteins, in
addition to the nickel-dependent hydrogenases b-type
cytochrome subunit. Cytochrome b561 is a secretory
vesicle-specific electron transport protein. It is an
integral membrane protein, that binds two heme groups
non-covalently. This is a prokaryotic family. Members of
the 'eukaryotic cytochrome b561' family can be found in
Pfam: PF03188.
Length = 140
Score = 28.5 bits (64), Expect = 5.0
Identities = 12/36 (33%), Positives = 16/36 (44%)
Query: 485 KVMYALHITARCIFLALFLWFLSNNFHVFLKLGLFV 520
LH + +FLAL L L H+ L L L +
Sbjct: 38 VAARNLHKSLGLVFLALLLLRLLWAVHLLLYLLLLL 73
>gnl|CDD|239152 cd02751, MopB_DMSOR-like, The MopB_DMSOR-like CD contains
dimethylsulfoxide reductase (DMSOR), biotin sulfoxide
reductase (BSOR), trimethylamine N-oxide reductase
(TMAOR) and other related proteins. DMSOR catalyzes the
reduction of DMSO to dimethylsulfide, but its cellular
location and oligomerization state are
organism-dependent. For example, in Rhodobacter
sphaeriodes and Rhodobacter capsulatus, it is an 82-kDa
monomeric soluble protein found in the periplasmic
space; in E. coli, it is membrane-bound and exists as a
heterotrimer. BSOR catalyzes the reduction of biotin
sulfixode to biotin, and is unique among Mo enzymes
because no additional auxiliary proteins or cofactors
are required. TMAOR is similar to DMSOR, but its only
natural substrate is TMAO. Also included in this group
is the pyrogallol-phloroglucinol transhydroxylase from
Pelobacter acidigallici. Members of the MopB_DMSOR-like
CD belong to the molybdopterin_binding (MopB)
superfamily of proteins.
Length = 609
Score = 29.5 bits (67), Expect = 5.9
Identities = 9/35 (25%), Positives = 14/35 (40%), Gaps = 4/35 (11%)
Query: 12 TIPKELQALPDRIAKTYENKSIFLSGGSGFLGKVL 46
+ EL+ RI + Y N++IF L
Sbjct: 84 LVASELK----RIREKYGNEAIFGGSYGWASAGRL 114
>gnl|CDD|233901 TIGR02505, RTPR, ribonucleoside-triphosphate reductase,
adenosylcobalamin-dependent. This model represents a
group of adenosylcobalamin(B12)-dependent ribonucleotide
reductases (RNR) related to the characterized species
from Lactococcus leichmannii. RNR's are responsible for
the conversion of the ribose sugar of RNA into the
deoxyribose sugar of DNA. This is the rate-limiting step
of DNA biosynthesis. Thus model identifies NrdJ enzymes
only in cyanobacteria, lactococcus and certain
bacteriophage. A separate model (TIGR02504) identifies a
larger group of divergent B12-dependent RNR's [Purines,
pyrimidines, nucleosides, and nucleotides,
2'-Deoxyribonucleotide metabolism].
Length = 713
Score = 29.5 bits (66), Expect = 6.2
Identities = 14/74 (18%), Positives = 24/74 (32%), Gaps = 19/74 (25%)
Query: 370 RLTHFICCLLFHWIPAYFLDAVILISGNKPCLVRIQERIHRGFDVFEYYANNEWE-FKNG 428
RLT + + I +++GN VR + + E+E FK
Sbjct: 255 RLTAVDAADICNLI------GKAVVAGN----VRRSAEMALF-----SNDDPEFESFKQA 299
Query: 429 N---LHQTRPKRNA 439
+H N+
Sbjct: 300 KEKLMHHRWASNNS 313
>gnl|CDD|187580 cd05272, TDH_SDR_e, L-threonine dehydrogenase, extended (e) SDRs.
This subgroup contains members identified as L-threonine
dehydrogenase (TDH). TDH catalyzes the zinc-dependent
formation of 2-amino-3-ketobutyrate from L-threonine via
NAD(H)-dependent oxidation. This group is distinct from
TDHs that are members of the medium chain
dehydrogenase/reductase family. This group has the
NAD-binding motif and active site tetrad of the extended
SDRs. Extended SDRs are distinct from classical SDRs. In
addition to the Rossmann fold (alpha/beta folding
pattern with a central beta-sheet) core region typical
of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 308
Score = 28.8 bits (65), Expect = 6.5
Identities = 16/67 (23%), Positives = 31/67 (46%), Gaps = 7/67 (10%)
Query: 106 DITQLKLGISEIDKKELIDNVDIVYHVAA--TIRFDEPIKTAVILNTRGTRDMLELSKQM 163
D+ K + EI + + H+AA + ++ A +N G ++LEL+++
Sbjct: 50 DVLDFK-SLEEIVVNH---KITWIIHLAALLSAVGEKNPPLAWDVNMNGLHNVLELAREH 105
Query: 164 KNLKCFT 170
NL+ F
Sbjct: 106 -NLRIFV 111
>gnl|CDD|234904 PRK01117, PRK01117, adenylosuccinate synthetase; Provisional.
Length = 430
Score = 29.2 bits (67), Expect = 6.7
Identities = 9/18 (50%), Positives = 13/18 (72%), Gaps = 1/18 (5%)
Query: 254 VVPIYKEPLPGWTDNING 271
PIY+E LPGW+++ G
Sbjct: 367 CEPIYEE-LPGWSESTTG 383
>gnl|CDD|219137 pfam06687, SUR7, SUR7/PalI family. This family consists of several
fungal-specific SUR7 proteins. Its activity regulates
expression of RVS161, a homologue of human endophilin,
suggesting a function for both in endocytosis. The
protein carries four transmembrane domains and is thus
likely to act as an anchoring protein for the eisosome
to the plasma membrane. Eisosomes are the immobile
protein complexes, that include the proteins Pil1 and
Lsp1, which co-localise with sites of protein and lipid
endocytosis at the plasma membrane. SUR7 protein may
play a role in sporulation. This family also includes
PalI which is part of a pH signal transduction cascade.
Based on the similarity of PalI to the yeast Rim9
meiotic signal transduction component it has been
suggested that PalI might be a membrane sensor for
ambient pH.
Length = 205
Score = 28.5 bits (64), Expect = 7.0
Identities = 12/62 (19%), Positives = 20/62 (32%), Gaps = 8/62 (12%)
Query: 474 PESLESARKK----MKVMYALHITARC-IFLALFLWFLSNNFH---VFLKLGLFVRGLAS 525
P S + M+ +H A +AL L + +F + + LA
Sbjct: 95 PSSFRDNLNTYYYLSRFMFIVHPIALFFTVIALILAGILAHFSSPRRGSLVNFLLSLLAF 154
Query: 526 LV 527
L
Sbjct: 155 LF 156
>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 = 28.9 bits (65), Expect = 7.6
Identities = 11/29 (37%), Positives = 19/29 (65%)
Query: 32 SIFLSGGSGFLGKVLIEKILRLEPNVKKI 60
+ ++G SGF+G+ L E++L PN + I
Sbjct: 2 KVLITGASGFVGQRLAERLLSDVPNERLI 30
>gnl|CDD|130471 TIGR01404, FlhB_rel_III, type III secretion protein, YscU/HrpY
family. This model represents one of several families
of proteins related to bacterial flagellar biosynthesis
proteins and involved in bacterial type III protein
secretion systems. This family is homologous to, but
distinguished from, flagellar biosynthetic protein FlhB
(TIGRFAMs model TIGR00328). This model may not identify
all type III secretion system FlhB homologs [Protein
fate, Protein and peptide secretion and trafficking,
Cellular processes, Pathogenesis].
Length = 342
Score = 28.8 bits (65), Expect = 8.1
Identities = 15/51 (29%), Positives = 24/51 (47%)
Query: 471 KESPESLESARKKMKVMYALHITARCIFLALFLWFLSNNFHVFLKLGLFVR 521
K +P+ L ARKK +V + +T+ + LA F + LS L +
Sbjct: 6 KPTPKKLRDARKKGQVAKSKDLTSAVLLLAGFFYLLSLASVFEEMLIALLI 56
>gnl|CDD|237818 PRK14792, PRK14792, lipoprotein signal peptidase; Provisional.
Length = 159
Score = 28.0 bits (63), Expect = 8.7
Identities = 9/29 (31%), Positives = 14/29 (48%), Gaps = 1/29 (3%)
Query: 297 FLPADVAIN-GVFLFTWDFLNSKESERKS 324
F AD+AIN V F D + ++ +
Sbjct: 131 FNIADIAINIAVICFIIDLIKNRRGSKHG 159
>gnl|CDD|176234 cd08273, MDR8, Medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
This group is a member of the medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, but lacks the zinc-binding
sites of the zinc-dependent alcohol dehydrogenases. The
medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P)-binding Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 331
Score = 28.4 bits (64), Expect = 9.4
Identities = 14/56 (25%), Positives = 23/56 (41%), Gaps = 17/56 (30%)
Query: 9 DLVTIPKEL----------------QALPDRIAKTYENKSIFLSGGSGFLGKVLIE 48
LV +P+ + Q L R AK + + + G SG +G+ L+E
Sbjct: 104 YLVPVPEGVDAAEAVCLVLNYVTAYQML-HRAAKVLTGQRVLIHGASGGVGQALLE 158
>gnl|CDD|187564 cd05254, dTDP_HR_like_SDR_e, dTDP-6-deoxy-L-lyxo-4-hexulose
reductase and related proteins, extended (e) SDRs.
dTDP-6-deoxy-L-lyxo-4-hexulose reductase, an extended
SDR, synthesizes dTDP-L-rhamnose from
alpha-D-glucose-1-phosphate, providing the precursor of
L-rhamnose, an essential cell wall component of many
pathogenic bacteria. This subgroup has the
characteristic active site tetrad and NADP-binding
motif. This subgroup also contains human MAT2B, the
regulatory subunit of methionine adenosyltransferase
(MAT); MAT catalyzes S-adenosylmethionine synthesis. The
human gene encoding MAT2B encodes two major splicing
variants which are induced in human cell liver cancer
and regulate HuR, an mRNA-binding protein which
stabilizes the mRNA of several cyclins, to affect cell
proliferation. Both MAT2B variants include this extended
SDR domain. 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 = 280
Score = 28.4 bits (64), Expect = 9.4
Identities = 38/183 (20%), Positives = 64/183 (34%), Gaps = 51/183 (27%)
Query: 78 ELFESPVFDALKTLRGKSILQKIQVISGDITQLKLGISEIDKKELIDNV--DIVYHVAAT 135
L + ++ + T R ++ L K+ D+T + +E I + D++ + AA
Sbjct: 17 RLLKERGYEVIGTGRSRASLFKL-----DLTDP----DAV--EEAIRDYKPDVIINCAAY 65
Query: 136 IRFD----EPIKTAVILNTRGTRDMLELSKQMKNLKCFTYISTAYCHPSEKVLEERTYLP 191
R D +P A +N ++ +K++ +IST Y +K
Sbjct: 66 TRVDKCESDPEL-AYRVNVLAPENLARAAKEVGAR--LIHISTDYVFDGKK--------G 114
Query: 192 PDDPHQVILRAESMKEEDLEVFRQDILGEFPNSYAYTKCLAEGLVAECMELGMPCMILRP 251
P KEED N Y +K L E V +ILR
Sbjct: 115 P------------YKEEDAPNPL--------NVYGKSKLLGEVAVLNANPR---YLILRT 151
Query: 252 SIV 254
S +
Sbjct: 152 SWL 154
>gnl|CDD|181983 PRK09603, PRK09603, bifunctional DNA-directed RNA polymerase subunit
beta/beta'; Reviewed.
Length = 2890
Score = 28.7 bits (64), Expect = 9.8
Identities = 12/55 (21%), Positives = 22/55 (40%), Gaps = 1/55 (1%)
Query: 69 GKTPNQRVEELFESPVFDALKTLRGKSILQKIQVISGDITQLKLGISEIDKKELI 123
GK +++ + E D K LR K +L+ I+ + +EL+
Sbjct: 1149 GKEFGKQIASMLEDKTKDFAKELRAK-MLEIANAINEKDPLTIHALENCSDEELL 1202
>gnl|CDD|217751 pfam03830, PTSIIB_sorb, PTS system sorbose subfamily IIB component.
Length = 151
Score = 27.8 bits (63), Expect = 9.9
Identities = 13/36 (36%), Positives = 22/36 (61%), Gaps = 1/36 (2%)
Query: 67 KKGKTPNQRVEELFESPVFDALKTLRGKSILQKIQV 102
KKGK Q+V L ++P DAL+ + G ++++ V
Sbjct: 69 KKGKYDKQKVFLLVKNPQ-DALRLVEGGVPIKELNV 103
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
0.322 0.139 0.418
Gapped
Lambda K H
0.267 0.0809 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 27,979,011
Number of extensions: 2793817
Number of successful extensions: 2847
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2791
Number of HSP's successfully gapped: 87
Length of query: 543
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 441
Effective length of database: 6,413,494
Effective search space: 2828350854
Effective search space used: 2828350854
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 61 (27.1 bits)