RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6053
(614 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 = 344 bits (884), Expect = e-114
Identities = 131/316 (41%), Positives = 195/316 (61%), Gaps = 2/316 (0%)
Query: 103 KTLFMTGASGFLGKVLLEKILRKSPNVKKIYILMRQKKGKNARQRIEELFASPLFNLLKS 162
K++ +TGA+GFLGKVLLEK+LR P++ KIY+L+R K G++A +R+ EL LF+ ++
Sbjct: 1 KSVLITGATGFLGKVLLEKLLRSCPDIGKIYLLIRGKSGQSAEERLRELLKDKLFDRGRN 60
Query: 163 VHGQKIIDKVLPISGDAEADELAIKESDRQLLASEVDIMIHGAATIRFDEALKKAVLLNT 222
++ K++PI GD L + + D Q L EV+I+IH AAT+ FDE L +A+ +N
Sbjct: 61 LN-PLFESKIVPIEGDLSEPNLGLSDEDLQTLIEEVNIIIHCAATVTFDERLDEALSINV 119
Query: 223 RGTKMMLSLAKEMKHLELFVHISTAYCHLQEKVLYEKPYPPPTDPHKLIERVEMMSEDTV 282
GT +L LAK K L+ FVH+STAY + +++ EK YPPP DP KLI+ +E+M + +
Sbjct: 120 LGTLRLLELAKRCKKLKAFVHVSTAYVNGDRQLIEEKVYPPPADPEKLIDILELMDDLEL 179
Query: 283 EKRAKEFLGEFPNSYAYTKCLSEGLVVEAMNNGMPCLMLRPSIIIPVWREPLPGWTDNIN 342
E+ + LG PN+Y +TK L+E LV++ N +P +++RPSI+ +EP PGW DN N
Sbjct: 180 ERATPKLLGGHPNTYTFTKALAERLVLKERGN-LPLVIVRPSIVGATLKEPFPGWIDNFN 238
Query: 343 GPTGLLIGAGKGVIRTMFCDNTGYADFLPVDITINGIFVAIWAYLSQKEHRQSIVHLTSS 402
GP GL + GKG++RTM D AD +PVD+ N + A +K + H SS
Sbjct: 239 GPDGLFLAYGKGILRTMNADPNAVADIIPVDVVANALLAAAAYSGVRKPRELEVYHCGSS 298
Query: 403 QEWQVSWQEIIDIGKS 418
+W E ++
Sbjct: 299 DVNPFTWGEAEELINQ 314
>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 = 242 bits (621), Expect = 2e-76
Identities = 109/274 (39%), Positives = 148/274 (54%), Gaps = 32/274 (11%)
Query: 108 TGASGFLGKVLLEKILRKSPNVKKIYILMRQKKGKNARQRI-EELFASPLFNLLKSVHGQ 166
TGA+GFLGKVLLEK+LR +P VK IY L+R K G++A +R+ +EL LF+ LK
Sbjct: 2 TGATGFLGKVLLEKLLRSTPEVK-IYCLVRAKDGESALERLRQELLKYGLFDRLK----- 55
Query: 167 KIIDKVLPISGDAEADELAIKESDRQLLASEVDIMIHGAATIRFDEALKKAVLLNTRGTK 226
+++++P++GD L + + D Q LA EVD++IH AAT+ F E N GT+
Sbjct: 56 -ALERIIPVAGDLSEPNLGLSDEDFQELAEEVDVIIHNAATVNFVEPYSDLRATNVLGTR 114
Query: 227 MMLSLAKEMKHLELFVHISTAYCHLQEKVLYEKPYPPPTDPHKLIERVEMMSEDTVEKRA 286
+L LAK+MK L F H+STAY + L E+ + ED
Sbjct: 115 EVLRLAKQMKKL-PFHHVSTAYVN-------------GERGGLLEEKPYKLDEDEPAL-- 158
Query: 287 KEFLGEFPNSYAYTKCLSEGLVVEAMNNGMPCLMLRPSIIIPVWREPLPGWTDNIN-GPT 345
LG PN Y +K L+E LV EA G+P ++ RPSII E GW + + GP
Sbjct: 159 ---LGGLPNGYTQSKWLAEQLVREAA-GGLPVVIYRPSIITG---ESRTGWINGDDFGPR 211
Query: 346 GLLIGAGKGVIRTMFCDNTGYADFLPVDITINGI 379
GLL GAG GV+ + D D +PVD N I
Sbjct: 212 GLLGGAGLGVLPDILGDPDARLDLVPVDYVANAI 245
>gnl|CDD|215538 PLN02996, PLN02996, fatty acyl-CoA reductase.
Length = 491
Score = 200 bits (511), Expect = 2e-57
Identities = 108/344 (31%), Positives = 189/344 (54%), Gaps = 32/344 (9%)
Query: 103 KTLFMTGASGFLGKVLLEKILRKSPNVKKIYILMRQKKGKNARQRI-EELFASPLFNLLK 161
KT+ +TGA+GFL K+ +EKILR PNVKK+Y+L+R K+A QR+ +E+ LF +L+
Sbjct: 12 KTILVTGATGFLAKIFVEKILRVQPNVKKLYLLLRASDAKSATQRLHDEVIGKDLFKVLR 71
Query: 162 SVHGQK----IIDKVLPISGDAEADELAIKESD-RQLLASEVDIMIHGAATIRFDEALKK 216
G+ I +KV P+ GD D+L +K+S+ R+ + E+DI+++ AAT FDE
Sbjct: 72 EKLGENLNSLISEKVTPVPGDISYDDLGVKDSNLREEMWKEIDIVVNLAATTNFDERYDV 131
Query: 217 AVLLNTRGTKMMLSLAKEMKHLELFVHISTAY-CHLQEKVLYEKPYP-----------PP 264
A+ +NT G +L+ AK+ +++ +H+STAY C + ++ EKP+
Sbjct: 132 ALGINTLGALNVLNFAKKCVKVKMLLHVSTAYVCGEKSGLILEKPFHMGETLNGNRKLDI 191
Query: 265 TDPHKLIE------RVEMMSEDTVEKRAKEF------LGEFPNSYAYTKCLSEGLVVEAM 312
+ KL++ + SE+ + + K+ L +PN+Y +TK + E L+
Sbjct: 192 NEEKKLVKEKLKELNEQDASEEEITQAMKDLGMERAKLHGWPNTYVFTKAMGEMLLGNFK 251
Query: 313 NNGMPCLMLRPSIIIPVWREPLPGWTDNINGPTGLLIGAGKGVIRTMFCDNTGYADFLPV 372
N +P +++RP++I ++EP PGW + + +++G GKG + D D +P
Sbjct: 252 EN-LPLVIIRPTMITSTYKEPFPGWIEGLRTIDSVIVGYGKGKLTCFLADPNSVLDVIPA 310
Query: 373 DITINGIFVAIWAYLSQKEHRQSIVHLTSSQEWQVSWQEIIDIG 416
D+ +N + VA+ A+ + + + I H+ SS + V + + D
Sbjct: 311 DMVVNAMIVAMAAH-AGGQGSEIIYHVGSSLKNPVKFSNLHDFA 353
>gnl|CDD|215279 PLN02503, PLN02503, fatty acyl-CoA reductase 2.
Length = 605
Score = 179 bits (456), Expect = 8e-49
Identities = 109/391 (27%), Positives = 190/391 (48%), Gaps = 43/391 (10%)
Query: 51 EFIRCEVIVSELVMAANKVNNMNVPYETFYKPPVLSEEYRNLPDRIG--ETFTGKTLFMT 108
+ + LV++ N P S + D IG E GK +T
Sbjct: 68 QHVAACRDAGSLVLSPNG--KGQPEIAVKDLVPYGSSSAVEMADGIGIAEFLRGKNFLIT 125
Query: 109 GASGFLGKVLLEKILRKSPNVKKIYILMRQKKGKNARQRIE-ELFASPLFNLLKSVHGQK 167
GA+GFL KVL+EKILR +P+V KIY+L++ K + A +R++ E+ + LF L+ HG+
Sbjct: 126 GATGFLAKVLIEKILRTNPDVGKIYLLIKAKDKEAAIERLKNEVIDAELFKCLQETHGKS 185
Query: 168 ----IIDKVLPISGDAEADELAIKESDRQLLASEVDIMIHGAATIRFDEALKKAVLLNTR 223
++ K++P+ G+ L ++ +A EVD++I+ AA FDE A+ +NTR
Sbjct: 186 YQSFMLSKLVPVVGNVCESNLGLEPDLADEIAKEVDVIINSAANTTFDERYDVAIDINTR 245
Query: 224 GTKMMLSLAKEMKHLELFVHISTAYCHLQEK-VLYEKPY-----------PPPTDPHKL- 270
G ++S AK+ K L+LF+ +STAY + Q + + EKP+ + PH
Sbjct: 246 GPCHLMSFAKKCKKLKLFLQVSTAYVNGQRQGRIMEKPFRMGDCIARELGISNSLPHNRP 305
Query: 271 ---IERVEM----------MSEDTVEKRAKEFLGE------FPNSYAYTKCLSEGLVVEA 311
IE E+ ++ ++ K+ E + ++Y +TK + E +V+ +
Sbjct: 306 ALDIEA-EIKLALDSKRHGFQSNSFAQKMKDLGLERAKLYGWQDTYVFTKAMGE-MVINS 363
Query: 312 MNNGMPCLMLRPSIIIPVWREPLPGWTDNINGPTGLLIGAGKGVIRTMFCDNTGYADFLP 371
M +P +++RPS+I W++P PGW + +++ GKG + D G D +P
Sbjct: 364 MRGDIPVVIIRPSVIESTWKDPFPGWMEGNRMMDPIVLYYGKGQLTGFLADPNGVLDVVP 423
Query: 372 VDITINGIFVAIWAYLSQKEHRQSIVHLTSS 402
D+ +N A+ + + ++ + SS
Sbjct: 424 ADMVVNATLAAMAKHGGAAKPEINVYQIASS 454
>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 = 114 bits (288), Expect = 2e-28
Identities = 91/333 (27%), Positives = 137/333 (41%), Gaps = 58/333 (17%)
Query: 104 TLFMTGASGFLGKVLLEKILRKSPNVKKIYILMRQKKGKNARQRIEELFASPLFNLLKSV 163
T+ +TGA+GFLG LL ++L K NV KIY L+R K + A +R+ + L ++
Sbjct: 1 TVLLTGATGFLGAYLLRELL-KRKNVSKIYCLVRAKDEEAALERLIDN----LKEYGLNL 55
Query: 164 HGQKIIDKVLPISGDAEADELAIKESDRQLLASEVDIMIHGAATIRF---DEALKKAVLL 220
+ + ++ + GD L + + D Q LA EVD++IH A + + E LK A
Sbjct: 56 WDELELSRIKVVVGDLSKPNLGLSDDDYQELAEEVDVIIHNGANVNWVYPYEELKPA--- 112
Query: 221 NTRGTKMMLSLAKEMKHLELFVHISTAYCHLQEKVLYEKPYPPPTDPHKLIERVEMMSED 280
N GTK +L LA K L+ +ST V + Y D E + M
Sbjct: 113 NVLGTKELLKLAATGK-LKPLHFVSTLS------VFSAEEYNALDD-----EESDDML-- 158
Query: 281 TVEKRAKEFLGEFPNSYAYTKCLSEGLVVEAMNNGMPCLMLRPSIIIPVWREPLPGWTDN 340
E PN Y +K ++E L+ EA N G+P ++RP I D+
Sbjct: 159 -------ESQNGLPNGYIQSKWVAEKLLREAANRGLPVAIIRPGNIFG----------DS 201
Query: 341 INGPT------GLLIGAGKGVIRT-MFCDNTGYADFLPVDITINGIFVAIWAYLSQKEHR 393
G L+ KG ++ ++ + D PVD I V + A E
Sbjct: 202 ETGIGNTDDFFWRLL---KGCLQLGIYPISGAPLDLSPVDWVARAI-VKL-ALNESNEF- 255
Query: 394 QSIVHLTSS--QEWQVSWQEIIDIGKSIVTTEV 424
SI HL + + + G SI
Sbjct: 256 -SIYHLLNPPLISLNDLLDALEEKGYSIKEVSY 287
>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 = 107 bits (269), Expect = 6e-28
Identities = 30/92 (32%), Positives = 54/92 (58%)
Query: 450 FFHMIPAYFLDAIIFLSGNKPCLVKIQDRINKGFEVFEYYANNQWEFRNEYVHVLRKIMN 509
F H++PAY LD ++ L G KP L+K+ +I+K ++ EY+ N+W F N+ L + ++
Sbjct: 1 FLHLLPAYLLDLLLRLLGRKPRLLKLYRKIHKLLDLLEYFTTNEWRFDNDNTRALWERLS 60
Query: 510 KRERIEYKIDGEDLDIKKYFQDCIMATRIFIL 541
+ +R + D +D YF++ I R ++L
Sbjct: 61 EEDRELFNFDIRSIDWDDYFENYIPGLRKYLL 92
>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 = 112 bits (283), Expect = 1e-27
Identities = 85/317 (26%), Positives = 132/317 (41%), Gaps = 58/317 (18%)
Query: 105 LFMTGASGFLGKVLLEKILRKSPNVKKIYILMRQKKGKNARQRIEELFASPLFNLLKSVH 164
+F+TG +GFLG+ L++++L N K+ +L+R + A +RIEE
Sbjct: 1 VFVTGGTGFLGRHLVKRLL---ENGFKVLVLVRSESLGEAHERIEEAGLEA--------- 48
Query: 165 GQKIIDKVLPISGDAEADELAIKESDRQLLASEVDIMIHGAATIRFDEALKKAVLLNTRG 224
D+V + GD L + + + LA +VD +IH AA+ F + A N G
Sbjct: 49 -----DRVRVLEGDLTQPNLGLSAAASRELAGKVDHVIHCAASYDFQAPNEDAWRTNIDG 103
Query: 225 TKMMLSLAKEMKHLELFVHISTAY-CHLQEKVLYEKPYPPPTDPHKLIERVEMMSEDTVE 283
T+ +L LA ++ F ++STAY +E + E P
Sbjct: 104 TEHVLELAAR-LDIQRFHYVSTAYVAGNREGNIRETELNPGQ------------------ 144
Query: 284 KRAKEFLGEFPNSYAYTKCLSEGLVVEAMNNGMPCLMLRPSIIIPVWREPLPGWTDNING 343
F N Y +K +E LV A +P + RPSI++ + G + I+G
Sbjct: 145 --------NFKNPYEQSKAEAEQLVRAAATQ-IPLTVYRPSIVVGDSKT---GRIEKIDG 192
Query: 344 PTGLLIG-AGKGVIRTMFCDNTGYADFLPVDITINGIFVAIWAYLSQKEHR-QSIVHLTS 401
LL A G M + + +PVD + I YLS+K I HLT
Sbjct: 193 LYELLNLLAKLGRWLPMPGNKGARLNLVPVDYVADAIV-----YLSKKPEANGQIFHLTD 247
Query: 402 SQEWQVSWQEIIDIGKS 418
+ +EI D+ KS
Sbjct: 248 PTPQTL--REIADLFKS 262
>gnl|CDD|111859 pfam03015, Sterile, Male sterility protein. This family represents
the C-terminal region of the male sterility protein in a
number of arabidopsis and drosophila. A sequence-related
jojoba acyl CoA reductase is also included.
Length = 94
Score = 91.2 bits (227), Expect = 3e-22
Identities = 38/94 (40%), Positives = 61/94 (64%)
Query: 450 FFHMIPAYFLDAIIFLSGNKPCLVKIQDRINKGFEVFEYYANNQWEFRNEYVHVLRKIMN 509
F+H +PAYFLD ++ L G KP LVK+ +I+KG EV + ++ N+W F N+ LR+ M+
Sbjct: 1 FYHTLPAYFLDLLLRLYGQKPRLVKLYRKIHKGLEVLQPFSLNEWIFDNKNTRELREKMS 60
Query: 510 KRERIEYKIDGEDLDIKKYFQDCIMATRIFILKE 543
+ ++ + D E LD +YF++ I R ++LKE
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 = 87.5 bits (217), Expect = 1e-18
Identities = 59/227 (25%), Positives = 101/227 (44%), Gaps = 35/227 (15%)
Query: 104 TLFMTGASGFLGKVLLEKILRKSPNVKKIYILMRQKKGKNARQRIEELFASPLFNLLKSV 163
T+ +TGA+GFLG LLE++LR+S K+ L+R ++A +R+ E S L
Sbjct: 1 TVLLTGATGFLGAYLLEELLRRSTQA-KVICLVRAASEEHAMERLREALRS---YRLWHE 56
Query: 164 HGQKIIDKVLPISGDAEADELAIKESDRQLLASEVDIMIHGAATIRF---DEALKKAVLL 220
+++ ++GD L + +++ + LA VD ++H A + + L+ A
Sbjct: 57 DL--ARERIEVVAGDLSEPRLGLSDAEWERLAENVDTIVHNGALVNWVYPYSELRGA--- 111
Query: 221 NTRGTKMMLSLAKEMKHLELFVHISTAYCHLQEKVLYEKPYPPPTDPHKLIERVEMMSED 280
N GT+ +L LA + ++ST V D + E +
Sbjct: 112 NVLGTREVLRLA-ASGRAKPLHYVSTI------SVG------AAIDLSTVTE-----DDA 153
Query: 281 TVEKRAKEFLGEFPNSYAYTKCLSEGLVVEAMNNGMPCLMLRPSIII 327
TV YA +K ++E LV EA + G+P ++RP I+
Sbjct: 154 TVTP-----PPGLAGGYAQSKWVAELLVREASDRGLPVTIVRPGRIL 195
>gnl|CDD|225857 COG3320, COG3320, Putative dehydrogenase domain of multifunctional
non-ribosomal peptide synthetases and related enzymes
[Secondary metabolites biosynthesis, transport, and
catabolism].
Length = 382
Score = 80.9 bits (200), Expect = 2e-16
Identities = 57/228 (25%), Positives = 94/228 (41%), Gaps = 33/228 (14%)
Query: 103 KTLFMTGASGFLGKVLLEKILRKSPNVKKIYILMRQKKGKNARQRIEELFASPLFNLLKS 162
+ + +TGA+GFLG LL ++L +S K+ L+R + + A R+E+ F L+
Sbjct: 1 RNVLLTGATGFLGAYLLLELLDRSD--AKVICLVRAQSDEAALARLEKTF--DLYRHWDE 56
Query: 163 VHGQKIIDKVLPISGDAEADELAIKESDRQLLASEVDIMIHGAATIRF---DEALKKAVL 219
+ ++ ++GD +L + E Q LA VD++IH AA + L+ A
Sbjct: 57 LSADRVE----VVAGDLAEPDLGLSERTWQELAENVDLIIHNAALVNHVFPYSELRGA-- 110
Query: 220 LNTRGTKMMLSLAKEMKHLELFVHISTAYCHLQEKVLYEKPYPPPTDPHKLIERVEMMSE 279
N GT +L LA + ++S+ + E Y
Sbjct: 111 -NVLGTAEVLRLA-ATGKPKPLHYVSSI-------SVGETEYYSNFTVD------FDEIS 155
Query: 280 DTVEKRAKEFLGEFPNSYAYTKCLSEGLVVEAMNNGMPCLMLRPSIII 327
T G Y +K ++E LV EA + G+P + RP I
Sbjct: 156 PTRNVGQGLAGG-----YGRSKWVAEKLVREAGDRGLPVTIFRPGYIT 198
>gnl|CDD|223528 COG0451, WcaG, Nucleoside-diphosphate-sugar epimerases [Cell
envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 314
Score = 58.4 bits (141), Expect = 3e-09
Identities = 59/320 (18%), Positives = 109/320 (34%), Gaps = 76/320 (23%)
Query: 103 KTLFMTGASGFLGKVLLEKILRKSPNVKKIYILMRQKKGKNARQRIEELFASPLFNLLKS 162
+ +TG +GF+G L+E++L +V+ + L
Sbjct: 1 MRILVTGGAGFIGSHLVERLLAAGHDVRGLDRLRDGLDPL-------------------- 40
Query: 163 VHGQKIIDKVLPISGDAEADELAIKESDRQLLASEVDIMIHGAATIRFDEAL----KKAV 218
+ V + D +L +L D +IH AA ++ + +
Sbjct: 41 ------LSGVEFVVLDLTDRDLV-----DELAKGVPDAVIHLAAQSSVPDSNASDPAEFL 89
Query: 219 LLNTRGTKMMLSLAKEMKHLELFVHISTAYCHLQEKVLYEKPYPPPTDPHKLIERVEMMS 278
+N GT +L A+ ++ FV S+ V+Y P P P D R
Sbjct: 90 DVNVDGTLNLLEAARAA-GVKRFVFASSVS------VVYGDPPPLPIDEDLGPPR----- 137
Query: 279 EDTVEKRAKEFLGEFPNSYAYTKCLSEGLVVEAMN-NGMPCLMLRPSIII-PVWREPLPG 336
N Y +K +E L+ G+P ++LRP + P + L
Sbjct: 138 --------------PLNPYGVSKLAAEQLLRAYARLYGLPVVILRPFNVYGPGDKPDLSS 183
Query: 337 WTDNINGPTGLLIGAGKGV-IRTMFCDNTGYADFLPVDITINGIFVAIWAYLSQKEHRQS 395
+ + KG I + D + DF+ VD + + +A+ E+
Sbjct: 184 G-----VVSAFIRQLLKGEPIIVIGGDGSQTRDFVYVDDVADALLLAL-------ENPDG 231
Query: 396 IVHLTSSQEWQVSWQEIIDI 415
V S +++ +E+ +
Sbjct: 232 GVFNIGSGTAEITVRELAEA 251
>gnl|CDD|235962 PRK07201, PRK07201, short chain dehydrogenase; Provisional.
Length = 657
Score = 58.0 bits (141), Expect = 9e-09
Identities = 61/244 (25%), Positives = 109/244 (44%), Gaps = 55/244 (22%)
Query: 104 TLFMTGASGFLGKVLLEKILRKSPNVKKIYILMRQKKGKNARQRIEELFASPLFNLLKSV 163
F+TG +GF+G+ L+ ++L + +++L+R++ + R+E L A
Sbjct: 2 RYFVTGGTGFIGRRLVSRLLDRRRE-ATVHVLVRRQ----SLSRLEALAA---------- 46
Query: 164 HGQKIIDKVLPISGDAEADELAIKESDRQLLASEVDIMIHGAAT--IRFDEALKKAVLLN 221
D+V+P+ GD L + E+D L ++D ++H AA + DE ++A N
Sbjct: 47 --YWGADRVVPLVGDLTEPGLGLSEADIAELG-DIDHVVHLAAIYDLTADEEAQRAA--N 101
Query: 222 TRGTKMMLSLAKEMKHLELFVHISTAYCHLQEKVLYEKPYPPPTDPHKLIERVEMMSEDT 281
GT+ ++ LA+ ++ F H+S+ + YE + ED
Sbjct: 102 VDGTRNVVELAERLQA-ATFHHVSS----IAVAGDYEGVF----------------REDD 140
Query: 282 VEKRAKEFLGE-FPNSYAYTKCLSEGLVVEAMNNGMPCLMLRPSIIIPVWREPLPGWTDN 340
+ G+ P Y TK +E LV E G+P + RP++++ R G D
Sbjct: 141 FD------EGQGLPTPYHRTKFEAEKLVREE--CGLPWRVYRPAVVVGDSRT---GEMDK 189
Query: 341 INGP 344
I+GP
Sbjct: 190 IDGP 193
>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 = 52.3 bits (126), Expect = 3e-07
Identities = 52/228 (22%), Positives = 75/228 (32%), Gaps = 67/228 (29%)
Query: 106 FMTGASGFLGKVLLEKILRKSPNVKKIYILMRQKKGKNARQRIEELFASPLFNLLKSVHG 165
+TGA+GFLG L+ +L + V+ L+R L P
Sbjct: 2 LVTGATGFLGSNLVRALLAQGYRVR---ALVRSG------SDAVLLDGLP---------- 42
Query: 166 QKIIDKVLPISGDAEADELAIKESDRQLLA---SEVDIMIHGAATIRFDEALKKAVLL-- 220
++ V GD D LA D + H AA K L
Sbjct: 43 ---VEVVE---GDLT---------DAASLAAAMKGCDRVFHLAAFTSL--WAKDRKELYR 85
Query: 221 -NTRGTKMMLSLAKEMKHLELFVHISTAYCHLQEKVLYEKPYPPPTDPHKLIERVEMMSE 279
N GT+ +L A E + VH S+ L P I+
Sbjct: 86 TNVEGTRNVLDAALE-AGVRRVVHTSSIAA-LGG------------PPDGRIDE------ 125
Query: 280 DTVEKRAKEFLGEFPNSYAYTKCLSEGLVVEAMNNGMPCLMLRPSIII 327
T FPN Y +K L+E V+EA G+ +++ PS +
Sbjct: 126 -TTPWNE----RPFPNDYYRSKLLAELEVLEAAAEGLDVVIVNPSAVF 168
>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 = 53.1 bits (128), Expect = 4e-07
Identities = 25/105 (23%), Positives = 52/105 (49%), Gaps = 7/105 (6%)
Query: 103 KTLFMTGASGFLGKVLLEKILRKSPN-VKKIYILMRQKKGKNARQRIEELFASPLFNLLK 161
T+F+TGA+GFLG +L +L + N K++ +R K + +R+ + + +
Sbjct: 972 ITVFLTGATGFLGSFILRDLLTRRSNSNFKVFAHVRAKSEEAGLERLRK--TGTTYGIWD 1029
Query: 162 SVHGQKIIDKVLPISGDAEADELAIKESDRQLLASEVDIMIHGAA 206
++ ++ + GD ++ + + L +EVD++IH A
Sbjct: 1030 ----EEWASRIEVVLGDLSKEKFGLSDEKWSDLTNEVDVIIHNGA 1070
>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 = 47.7 bits (114), Expect = 4e-06
Identities = 36/191 (18%), Positives = 65/191 (34%), Gaps = 41/191 (21%)
Query: 199 DIMIHGAATIRFDEALKKAVLL---NTRGTKMMLSLAKEMKHLELFVHISTA--YCHLQE 253
D+++H AA + + N GT +L A++ ++ FV+ S+A Y +
Sbjct: 32 DVVVHLAALVGVPASWDNPDEDFETNVVGTLNLLEAARKAG-VKRFVYASSASVYGSPEG 90
Query: 254 KVLYEKPYPPPTDPHKLIERVEMMSEDTVEKRAKEFLGEFPNSYAYTKCLSEGLVVEAMN 313
E+ P P P Y +K +E L+
Sbjct: 91 LPEEEETPPRPLSP-----------------------------YGVSKLAAEHLLRSYGE 121
Query: 314 -NGMPCLMLRPSIIIPVWREPLPGWTDNINGPTGLLIGAGKGVIRTMFCDNTGYADFLPV 372
G+P ++LR + + + P +N + T+F DF+ V
Sbjct: 122 SYGLPVVILRLANVYGPGQR--PRLDGVVNDFIRRALEGKP---LTVFGGGNQTRDFIHV 176
Query: 373 DITINGIFVAI 383
D + I A+
Sbjct: 177 DDVVRAILHAL 187
>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 = 46.5 bits (111), Expect = 2e-05
Identities = 43/153 (28%), Positives = 71/153 (46%), Gaps = 32/153 (20%)
Query: 101 TGKTLFMTGASGFLGKVLLEKILRKSPNVKKIYILMRQKKGKNARQRIEELFASPLFNLL 160
GKT+ +TG +G +G L+ +IL+ P KK+ + R + L L+
Sbjct: 1 KGKTILVTGGAGSIGSELVRQILKFGP--KKLIVFDRDENK--------------LHELV 44
Query: 161 KSVHGQKIIDKVLPISGDAEADELAIKESDRQLLASEVDIMIHGAAT--IR-----FDEA 213
+ + + DK+ I GD D+ ++ + ++ DI+ H AA + +EA
Sbjct: 45 RELRSRFPHDKLRFIIGDV-RDKERLRRAFKER---GPDIVFHAAALKHVPSMEDNPEEA 100
Query: 214 LKKAVLLNTRGTKMMLSLAKEMKHLELFVHIST 246
+K VL GTK ++ A E +E FV IST
Sbjct: 101 IKTNVL----GTKNVIDAAIENG-VEKFVCIST 128
>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 = 41.5 bits (98), Expect = 6e-04
Identities = 43/223 (19%), Positives = 74/223 (33%), Gaps = 62/223 (27%)
Query: 106 FMTGASGFLGKVLLEKILRKSPNVKKIYILMRQKKGKNARQRIEELFASPLFNLLKSVHG 165
+TG +GF+G L+ ++L++ V + R + R R E +L
Sbjct: 2 LVTGGTGFIGSHLVRRLLQEGYEVIVLGRRRRSESLNTGRIRFHEG------DLTDPDAL 55
Query: 166 QKIIDKVLPISGDAEADELAIKESDRQLLASEVDIMIHGAATIRFDEALKKAVLL---NT 222
++++ +V P D +IH AA + + N
Sbjct: 56 ERLLAEVQP------------------------DAVIHLAAQSGVGASFEDPADFIRANV 91
Query: 223 RGTKMMLSLAKEMKHLELFVHISTAYCHLQEKVLYEKPYPPPTDPHKLIERVEMMSEDTV 282
GT +L A+ ++ FV S++ +Y PP EDT
Sbjct: 92 LGTLRLLEAARRAG-VKRFVFASSS-E------VYGDVADPPIT------------EDT- 130
Query: 283 EKRAKEFLGEFPNSYAYTKCLSEGLVVEAMN-NGMPCLMLRPS 324
+ YA K +E LV G+ ++LR
Sbjct: 131 -------PLGPLSPYAAAKLAAERLVEAYARAYGLRAVILRLF 166
>gnl|CDD|224011 COG1086, COG1086, Predicted nucleoside-diphosphate sugar epimerases
[Cell envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 588
Score = 40.7 bits (96), Expect = 0.002
Identities = 41/163 (25%), Positives = 68/163 (41%), Gaps = 40/163 (24%)
Query: 95 RIGETFTGKTLFMTGASGFLGKVLLEKILRKSPNVKKIYILMRQKKGKNARQRIEELFAS 154
IG TGKT+ +TG G +G L +IL+ +P K+I + R +
Sbjct: 243 LIGAMLTGKTVLVTGGGGSIGSELCRQILKFNP--KEIILFSRDEYK------------- 287
Query: 155 PLFNLLKSVHGQKIIDKVLPISGD-AEADELAIKESDRQLLASEVDIMIHGAATIRFDEA 213
L+ + + + K+ GD + D + +R + +VDI+ H A A
Sbjct: 288 -LYLIDMELREKFPELKLRFYIGDVRDRDRV-----ERAMEGHKVDIVFHAA-------A 334
Query: 214 LK----------KAVLLNTRGTKMMLSLAKEMKHLELFVHIST 246
LK +A+ N GT+ + A + ++ FV IST
Sbjct: 335 LKHVPLVEYNPEEAIKTNVLGTENVAEAAIKNG-VKKFVLIST 376
>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 = 38.4 bits (90), Expect = 0.007
Identities = 46/221 (20%), Positives = 71/221 (32%), Gaps = 60/221 (27%)
Query: 199 DIMIHGAATIRFDEA---LKKAVLLNTRGTKMMLSLAKEMKHLELFVHISTAYCHLQEKV 255
D++I+ AA R D+ + A +N + + AKE+ +HIST Y V
Sbjct: 57 DVIINCAAYTRVDKCESDPELAYRVNVLAPENLARAAKEVG--ARLIHISTDY------V 108
Query: 256 L-YEKPYPPPTDPHKLIERVEMMSEDTVEKRAKEFLGEFPNSYAYTKCLSEGLVVEAMNN 314
+K D + N Y +K L E V+ A
Sbjct: 109 FDGKKGPYKEEDAPNPL-----------------------NVYGKSKLLGEVAVLNANPR 145
Query: 315 GMPCLMLRPSIIIPVWREPLPGWTDNINGPTGLLIGAGKGVIRTMFCDNTG---YADFLP 371
L+LR S + + N +L A + + D G YA L
Sbjct: 146 ---YLILRTSWLY-------GELKNGENFVEWMLRLAAERKEVNVVHDQIGSPTYAADL- 194
Query: 372 VDITINGIFVAIWAYLSQKEHRQSIVHLTSSQEWQVSWQEI 412
AI + + I HL++S +S E
Sbjct: 195 --------ADAILELIERNSLT-GIYHLSNSG--PISKYEF 224
>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 = 37.4 bits (87), Expect = 0.008
Identities = 42/199 (21%), Positives = 70/199 (35%), Gaps = 43/199 (21%)
Query: 106 FMTGASGFLGKVLLEKILRKSPNVKKIYILMRQKKGKNARQRIEELFASPLFNLLKSVHG 165
+ GA+GF+G+ L ++L + ++ +L+R K + +
Sbjct: 2 LILGATGFIGRALARELLEQG---HEVTLLVRNTKRLSKEDQ------------------ 40
Query: 166 QKIIDKVLPISGDAEADELAIKESDRQLLASEVDIMIHGAATIRFDEALKKAVLLNTRGT 225
+ V + GD + VD++IH A R ++ GT
Sbjct: 41 ----EPVAVVEGDLRDLDSLSD------AVQGVDVVIHLAGAPRDTRDF---CEVDVEGT 87
Query: 226 KMMLSLAKE--MKHLELFVHIST--AYCHLQEKVLYEKPYPPPTDPHKLIERV-EMMSED 280
+ +L AKE +KH F+ IS+ AY L E+ P P E V S
Sbjct: 88 RNVLEAAKEAGVKH---FIFISSLGAYGDLHEE-TEPSPSSPYLAVKAKTEAVLREASLP 143
Query: 281 TVEKRAKEFLGEFPNSYAY 299
R G+ + A
Sbjct: 144 YTIVRPGVIYGDLARAIAN 162
>gnl|CDD|187612 cd05354, SDR_c7, classical (c) SDR, subgroup 7. These proteins are
members of the classical SDR family, with a canonical
active site triad (and also an active site Asn) and a
typical Gly-rich NAD-binding motif. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold (alpha/beta folding pattern with a central
beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRS are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes have a
3-glycine N-terminal NAD(P)(H)-binding pattern
(typically, TGxxxGxG in classical SDRs and TGxxGxxG in
extended SDRs), while substrate binding is in the
C-terminal region. A critical catalytic Tyr residue
(Tyr-151, human 15-hydroxyprostaglandin dehydrogenase
(15-PGDH) numbering), is often found in a conserved
YXXXK pattern. In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) or additional
Ser, contributing to the active site. Substrates for
these enzymes include sugars, steroids, alcohols, and
aromatic compounds. The standard reaction mechanism is a
proton relay involving the conserved Tyr and Lys, as
well as Asn (or Ser). Some SDR family members, including
17 beta-hydroxysteroid dehydrogenase contain an
additional helix-turn-helix motif that is not generally
found among SDRs.
Length = 235
Score = 35.5 bits (82), Expect = 0.048
Identities = 38/142 (26%), Positives = 57/142 (40%), Gaps = 35/142 (24%)
Query: 100 FTGKTLFMTGASGFLGKVLLEKILRKSPNVKKIYILMRQKKGKNARQRIEELFASPLFNL 159
KT+ +TGA+ +GK +E +L KK+Y +R L A
Sbjct: 1 IKDKTVLVTGANRGIGKAFVESLLAHG--AKKVYAAVRDPGS------AAHLVA------ 46
Query: 160 LKSVHGQKIIDKVLPISGDAEADELAIKESDRQLLASEVDIMI--------HGAATIRFD 211
K DKV+P+ D D +IK + Q A +VD++I
Sbjct: 47 -------KYGDKVVPLRLDV-TDPESIKAAAAQ--AKDVDVVINNAGVLKPATLLEEGAL 96
Query: 212 EALKKAVLLNTRGTKMMLSLAK 233
EALK+ + +N G L LA+
Sbjct: 97 EALKQEMDVNVFGL---LRLAQ 115
>gnl|CDD|215146 PLN02260, PLN02260, probable rhamnose biosynthetic enzyme.
Length = 668
Score = 34.7 bits (80), Expect = 0.14
Identities = 35/153 (22%), Positives = 65/153 (42%), Gaps = 24/153 (15%)
Query: 97 GETFTGKTLFMTGASGFLGKVLLEKILRKSPNVKKIYILMRQKKGKNARQRIEELFASPL 156
T+ K + +TGA+GF+ + +++R P+ KI +L + N + + +SP
Sbjct: 1 MATYEPKNILITGAAGFIASHVANRLIRNYPDY-KIVVLDKLDYCSNLKN-LNPSKSSPN 58
Query: 157 FNLLKSVHGQKIIDKVLPISGDAEADELAIKESDRQLLASEVDIMIHGAATIRFDEALKK 216
F +K GD + +L + L+ +D ++H AA D +
Sbjct: 59 FKFVK---------------GDIASADLV----NYLLITEGIDTIMHFAAQTHVDNSFGN 99
Query: 217 AVLL---NTRGTKMMLSLAKEMKHLELFVHIST 246
+ N GT ++L K + F+H+ST
Sbjct: 100 SFEFTKNNIYGTHVLLEACKVTGQIRRFIHVST 132
>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 = 33.6 bits (77), Expect = 0.28
Identities = 46/216 (21%), Positives = 79/216 (36%), Gaps = 50/216 (23%)
Query: 105 LFMTGASGFLGKVLLEKILRKSPNVKKIYILMRQKKGKNARQRIEELFASPLFNLLKSVH 164
+TG GFLG+ ++ +L + +K+I +L + G + E+ K+
Sbjct: 2 CLVTGGGGFLGQHIIRLLLERKEELKEIRVL-DKAFGPELIEHFEKS-------QGKT-- 51
Query: 165 GQKIIDKVLPISGD-AEADELAIKESDRQLLASEVDIMIHGAATIRFDEALKKAVL--LN 221
V I GD + L V ++IH AA + L +N
Sbjct: 52 ------YVTDIEGDIKDLSFLFRACQG-------VSVVIHTAAIVDVFGPPNYEELEEVN 98
Query: 222 TRGTKMMLSLAKEMKHLELFVHISTAYCHLQEKVLYEKPYPPPTDPHKLIERVEMMSEDT 281
GT+ +L + +++ V+ S+ +V P + V EDT
Sbjct: 99 VNGTQAVLEACVQ-NNVKRLVYTSSI------EVAG-----PNFKGRPIFNGV----EDT 142
Query: 282 VEKRAKEFLGEFPNSYAYTKCLSEGLVVEAMNNGMP 317
+ YA +K L+E +V+ A NG P
Sbjct: 143 ------PYEDTSTPPYASSKLLAENIVLNA--NGAP 170
>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 = 33.5 bits (77), Expect = 0.29
Identities = 33/146 (22%), Positives = 59/146 (40%), Gaps = 24/146 (16%)
Query: 104 TLFMTGASGFLGKVLLEKILRKSPNVKKIYILMRQKKGKNARQRIEELFASPLFNLLKSV 163
+ +TG +GF+G + IL + P+ + + +L + N + + +L +P + +K
Sbjct: 1 RILVTGGAGFIGSNFVRYILNEHPDAE-VIVLDKLTYAGN-LENLADLEDNPRYRFVK-- 56
Query: 164 HGQKIIDKVLPISGDAEADELAIKESDRQLLASEVDIMIHGAATIRFDEALKKA---VLL 220
GD EL R + D ++H AA D ++ +
Sbjct: 57 -------------GDIGDRELV----SRLFTEHQPDAVVHFAAESHVDRSISGPAAFIET 99
Query: 221 NTRGTKMMLSLAKEMKHLELFVHIST 246
N GT +L ++ H F HIST
Sbjct: 100 NVVGTYTLLEAVRKYWHEFRFHHIST 125
>gnl|CDD|224155 COG1234, ElaC, Metal-dependent hydrolases of the beta-lactamase
superfamily III [General function prediction only].
Length = 292
Score = 33.2 bits (76), Expect = 0.35
Identities = 35/138 (25%), Positives = 54/138 (39%), Gaps = 30/138 (21%)
Query: 139 KKGKNARQRIEELFASPLFNLLKSVHGQKI-------------IDKVLPISGDAEADELA 185
+ G+ ++++ L PL LK+ H + K + SGD +
Sbjct: 146 RPGRFDAEKLKGLPPGPLITALKAGHPVEERVITPADRIGEPRKGKSVVYSGDTRPCDEL 205
Query: 186 IKESDRQLLASEVDIMIHGAATIRFDEALKKAVLLNTRG---TKMMLSLAKEM--KHLEL 240
I LA D++IH A F++ L+ L N G + +AKE K L L
Sbjct: 206 ID------LAKGADLLIHEAT---FEDDLED--LANEGGHSTAEEAAEIAKEAGVKKLIL 254
Query: 241 FVHISTAYCHLQEKVLYE 258
H S Y E++L E
Sbjct: 255 T-HFSPRYPKDDEELLKE 271
>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 = 32.7 bits (75), Expect = 0.36
Identities = 16/37 (43%), Positives = 25/37 (67%), Gaps = 1/37 (2%)
Query: 103 KTLFMTGASGFLGKVLLEKILRKSPNVKKIYILMRQK 139
KT + GA+G +GK LL ++L KSP K+ ++R+K
Sbjct: 1 KTALVLGATGLVGKHLLRELL-KSPYYSKVTAIVRRK 36
>gnl|CDD|130625 TIGR01562, FdhE, formate dehydrogenase accessory protein FdhE.
This model describes an accessory protein required for
the assembly of formate dehydrogenase of certain
proteobacteria although not present in the final
complex. The exact nature of the function of FdhE in the
assembly of the complex is unknown, but considering the
presence of selenocysteine, molybdopterin, iron-sulfur
clusters and cytochrome b556, it is likely to have
something to do with the insertion of cofactors. The
only sequence scoring between trusted and noise is that
from Aquifex aeolicus, which shows certain structural
differences from the proteobacterial forms in the
alignment. However it is notable that A. aeolicus also
has a sequence scoring above trusted to the alpha
subunit of formate dehydrogenase (TIGR01553).
Length = 305
Score = 33.0 bits (75), Expect = 0.42
Identities = 18/61 (29%), Positives = 25/61 (40%), Gaps = 6/61 (9%)
Query: 219 LLNTRGTKMMLSLAKEMKHLELFVHISTAYCHLQEKVLYEKPYPPPTDPHKLIERVEMMS 278
L N R ++ L LA E L ++ C LQ+ +L P P DP ER+
Sbjct: 29 LFNRRAERL-LQLA-EGHPLGDYLRFVAGICRLQQALLDNPPALAPLDP----ERLRKAR 82
Query: 279 E 279
Sbjct: 83 A 83
>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 = 32.6 bits (75), Expect = 0.54
Identities = 36/149 (24%), Positives = 54/149 (36%), Gaps = 34/149 (22%)
Query: 103 KTLFMTGASGFLGKVLLEKILRKSPNVKKIYILMRQKKGKNARQRIEELFASPLFNLLKS 162
K + +TG +GFLG L +++L V + G+ ++ IE L P F ++
Sbjct: 1 KRILITGGAGFLGSHLCDRLLEDGHEV---ICVDNFFTGR--KRNIEHLIGHPNFEFIR- 54
Query: 163 VHGQKIIDKVLPISGDAEADELAIKESDRQLLASEVDIMIHGAA---TIRFDEALKKAVL 219
H D P+ EVD + H A + + K +
Sbjct: 55 -H-----DVTEPLYL-------------------EVDQIYHLACPASPVHYQYNPIKTLK 89
Query: 220 LNTRGTKMMLSLAKEMKHLELFVHISTAY 248
N GT ML LAK + L S Y
Sbjct: 90 TNVLGTLNMLGLAKRVGARVLLASTSEVY 118
>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 = 32.4 bits (74), Expect = 0.69
Identities = 14/38 (36%), Positives = 21/38 (55%), Gaps = 1/38 (2%)
Query: 100 FTGKTLFMTGASGFLGKVLLEKILRKSPNVKKIYILMR 137
F K++ +TG +G GK + ++L N KKI I R
Sbjct: 2 FNNKSILITGGTGSFGKAFISRLLENY-NPKKIIIYSR 38
>gnl|CDD|237079 PRK12367, PRK12367, short chain dehydrogenase; Provisional.
Length = 245
Score = 31.9 bits (73), Expect = 0.84
Identities = 13/28 (46%), Positives = 17/28 (60%)
Query: 98 ETFTGKTLFMTGASGFLGKVLLEKILRK 125
T+ GK + +TGASG LGK L + K
Sbjct: 10 STWQGKRIGITGASGALGKALTKAFRAK 37
>gnl|CDD|236055 PRK07575, PRK07575, dihydroorotase; Provisional.
Length = 438
Score = 32.0 bits (73), Expect = 0.92
Identities = 26/97 (26%), Positives = 42/97 (43%), Gaps = 22/97 (22%)
Query: 162 SVHGQKIIDK-----------VLPISGDAEADELAIKESDRQLLASEVDIMIHGAATIRF 210
S HG ++D+ I+ AE D+ I+ R A D H I+
Sbjct: 151 SSHGPLLVDEEAALERIFAEGTRLIAVHAE-DQARIRAR-RAEFAGISDPADHSQ--IQD 206
Query: 211 DEALKKAVLLNTRGTKMMLSLAKEMKHLELFVHISTA 247
+EA A+L T++ L L+K+ + +H+STA
Sbjct: 207 EEA---ALL----ATRLALKLSKKYQRRLHILHLSTA 236
>gnl|CDD|165812 PLN02166, PLN02166, dTDP-glucose 4,6-dehydratase.
Length = 436
Score = 31.9 bits (72), Expect = 1.1
Identities = 38/147 (25%), Positives = 59/147 (40%), Gaps = 34/147 (23%)
Query: 105 LFMTGASGFLGKVLLEKILRKSPNVKKIYILMRQKKGKNARQRIEELFASPLFNLLKSVH 164
+ +TG +GF+G L++K++ + V I +K + + LF +P F L++
Sbjct: 123 IVVTGGAGFVGSHLVDKLIGRGDEVIVIDNFFTGRK-----ENLVHLFGNPRFELIRH-- 175
Query: 165 GQKIIDKVLPISGDAEADELAIKESDRQLLASEVDIMIH---GAATIRFDEALKKAVLLN 221
D V PI LL EVD + H A+ + + K + N
Sbjct: 176 -----DVVEPI-----------------LL--EVDQIYHLACPASPVHYKYNPVKTIKTN 211
Query: 222 TRGTKMMLSLAKEMKHLELFVHISTAY 248
GT ML LAK + L S Y
Sbjct: 212 VMGTLNMLGLAKRVGARFLLTSTSEVY 238
>gnl|CDD|224564 COG1650, COG1650, Uncharacterized protein conserved in archaea
[Function unknown].
Length = 266
Score = 31.6 bits (72), Expect = 1.1
Identities = 12/44 (27%), Positives = 24/44 (54%), Gaps = 1/44 (2%)
Query: 109 GASGFLGKVLLEKILRKSPNVKKIYILMRQKKGKNARQRIEELF 152
L +V+L++ ++KSP +K + + K N R+R++ L
Sbjct: 214 YDHDALTEVVLKQAVKKSPAAEKAIVDRKGSKS-NVRRRVKSLA 256
>gnl|CDD|235631 PRK05866, PRK05866, short chain dehydrogenase; Provisional.
Length = 293
Score = 31.6 bits (72), Expect = 1.1
Identities = 35/141 (24%), Positives = 55/141 (39%), Gaps = 41/141 (29%)
Query: 81 KPPVLSEEYRNLPDRIGETFTGKTLFMTGASGFLGKVLLEKILRKSPNVKKIYILMRQKK 140
+PP+ + N P R TGK + +TGAS +G+ E+ R+ V + +
Sbjct: 19 RPPISPQLLINRPPRQPVDLTGKRILLTGASSGIGEAAAEQFARRGATV----VAV---- 70
Query: 141 GKNARQRIEELFASPLFNLLKSVHGQKIIDKVLPISGDAEA-----------DELAIKES 189
AR+ E+L + + D++ GDA A D L
Sbjct: 71 ---ARR--EDLLDA-------------VADRITRAGGDAMAVPCDLSDLDAVDALVADVE 112
Query: 190 DRQLLASEVDIMIHGAA-TIR 209
R VDI+I+ A +IR
Sbjct: 113 KR---IGGVDILINNAGRSIR 130
>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 = 31.6 bits (72), Expect = 1.1
Identities = 62/274 (22%), Positives = 108/274 (39%), Gaps = 65/274 (23%)
Query: 108 TGASGFLGKVLLEKILRKSPNVKKIYILMRQKKGKNARQRIEELFASPLFNLLKSVHGQK 167
G SGFLG+ L+E++LR+ N + ++ P F L S G+
Sbjct: 5 VGGSGFLGRHLVEQLLRRG----------------NPTVHVFDIR--PTFELDPSSSGR- 45
Query: 168 IIDKVLPISGDAEADELAIKESD--RQLLASEVDIMIHGAATI-RFDEALKKAVLLNTRG 224
V +GD D + +++ H A+ ++ L V N +G
Sbjct: 46 ----VQFHTGDLT------DPQDLEKAFNEKGPNVVFHTASPDHGSNDDLYYKV--NVQG 93
Query: 225 TKMMLSLAKEMKHLELFVHISTAYCHLQEKVLYEKPYPPPTDPHKLIERVEMMSEDTVEK 284
T+ ++ ++ ++ V+ S+A V++ +I E + +K
Sbjct: 94 TRNVIEACRK-CGVKKLVYTSSA------SVVFNG--------QDIINGDESL--PYPDK 136
Query: 285 RAKEFLGEFPNSYAYTKCLSEGLVVEAMNNGMPCLM---LRPSIII-PVWREPLPGWTDN 340
++Y TK L+E LV++A N+ L+ LRP+ I P R+ +PG
Sbjct: 137 --------HQDAYNETKALAEKLVLKA-NDPESGLLTCALRPAGIFGPGDRQLVPGLLKA 187
Query: 341 I-NGPTGLLIGAGKGVIRTMFCDNTGYADFLPVD 373
NG T IG G + + +N +A L D
Sbjct: 188 AKNGKTKFQIGDGNNLFDFTYVENVAHAHILAAD 221
>gnl|CDD|187672 cd09812, 3b-HSD_like_1_SDR_e, 3beta-hydroxysteroid dehydrogenase
(3b-HSD)-like, subgroup1, extended (e) SDRs. An
uncharacterized subgroup of the 3b-HSD-like extended-SDR
family. Proteins in this subgroup 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. 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 = 339
Score = 31.7 bits (72), Expect = 1.2
Identities = 27/116 (23%), Positives = 44/116 (37%), Gaps = 22/116 (18%)
Query: 290 LGEFPNSYAYTKCLSEGLVVEAMNNGMP----------CLMLRPSIIIPVWREPLPGWTD 339
L + Y+ TK ++E LV++A N MP C + I P + LP
Sbjct: 134 LDLHVDHYSRTKSIAEQLVLKA--NNMPLPNNGGVLRTCALRPAGIYGPGEQRHLPRIVS 191
Query: 340 NINGPTGLLIGAGKGVIRTMFCDNTGYADFLPVDITINGIFVAIWAYLSQKEHRQS 395
I KG+ ++ D +F+ VD + +A A + K + S
Sbjct: 192 YIE----------KGLFMFVYGDPKSLVEFVHVDNLVQAHILAAEALTTAKGYIAS 237
>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 = 31.3 bits (72), Expect = 1.2
Identities = 38/152 (25%), Positives = 60/152 (39%), Gaps = 44/152 (28%)
Query: 108 TGASGFLGKVLLEKILRKSPNVKKIYILMRQKKGKNARQRIEELFASPLFNLLKSVHGQK 167
TG G +G L +IL+ +P KKI + R + L+ + + + +
Sbjct: 4 TGGGGSIGSELCRQILKFNP--KKIILFSRDEFK--------------LYEIRQELRQEY 47
Query: 168 IIDKVLPISGDAEADELAIKESDRQLLASE---VDIMIHGAATIRFDEALK--------- 215
K+ GD +++ +R A E VD + H A ALK
Sbjct: 48 NDPKLRFFIGD-------VRDRERLERAMEQHGVDTVFHAA-------ALKHVPLVEYNP 93
Query: 216 -KAVLLNTRGTKMMLSLAKEMKHLELFVHIST 246
+A+ N GT+ + A E +E FV IST
Sbjct: 94 MEAIKTNVLGTENVAEAAIENG-VEKFVLIST 124
>gnl|CDD|178567 PLN02986, PLN02986, cinnamyl-alcohol dehydrogenase family protein.
Length = 322
Score = 31.1 bits (70), Expect = 1.4
Identities = 56/250 (22%), Positives = 106/250 (42%), Gaps = 47/250 (18%)
Query: 102 GKTLFMTGASGFLGKVLLEKILRKSPNVKKIYILMRQKKGKNARQRIEELFASPLFNLLK 161
GK + +TGASG++ +++ +L + VK + R++ E L A
Sbjct: 5 GKLVCVTGASGYIASWIVKLLLLRGYTVKATV------RDLTDRKKTEHLLA-------- 50
Query: 162 SVHGQKIIDKVLPISGDAEADELAIKESDRQLLASEVDIMIHGAATIRFDEALKKAVLLN 221
+ G K K+ +AD L +ES + D + H A+ + F + L++
Sbjct: 51 -LDGAKERLKLF------KADLL--EESSFEQAIEGCDAVFHTASPVFFTVKDPQTELID 101
Query: 222 T--RGTKMMLSLAKEMKHLELFVHISTAYCHLQEKVLYEKPYPPPTDPHKLIERVEMMSE 279
+GT +L+ KE ++ + S+ VL+ + PP + + +++ S+
Sbjct: 102 PALKGTINVLNTCKETPSVKRVILTSST-----AAVLFRQ---PPIEANDVVDET-FFSD 152
Query: 280 DTVEKRAKEFLGEFPNSYAYTKCLSEGLVVE-AMNNGMPCLMLRPSIIIPVWREPLPGWT 338
++ + K N Y +K L+E E A +NG+ ++L P I +P ++
Sbjct: 153 PSLCRETK-------NWYPLSKILAENAAWEFAKDNGIDMVVLNPGFICGPLLQPTLNFS 205
Query: 339 -----DNING 343
D ING
Sbjct: 206 VELIVDFING 215
>gnl|CDD|219655 pfam07946, DUF1682, Protein of unknown function (DUF1682). The
members of this family are all hypothetical eukaryotic
proteins of unknown function. One member is described as
being an adipocyte-specific protein, but no evidence of
this was found.
Length = 322
Score = 31.1 bits (71), Expect = 1.6
Identities = 11/49 (22%), Positives = 18/49 (36%)
Query: 566 KTLFFVFILYTLSSYSETLRNLFQVFFNIVQYISGLFVIPSSKAKITEL 614
K L F L E L L + +V ++ L + P K+ +
Sbjct: 216 KRLIISFNLPKSKEDLEDLLPLLNLVLYLVDKLANLKLSPEVLRKVDKT 264
>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 = 31.1 bits (70), Expect = 1.8
Identities = 16/49 (32%), Positives = 27/49 (55%), Gaps = 3/49 (6%)
Query: 100 FTGKTLFMTGASGFLGKVLLEKILRKSPNVKKIYILMR-QKKGKNARQR 147
F K L +TG +G G +L + L ++K+I I R +KK + R++
Sbjct: 2 FKDKILLITGGTGSFGNAVLRRFL--DTDIKEIRIFSRDEKKQDDMRKK 48
>gnl|CDD|187663 cd09762, HSDL2_SDR_c, human hydroxysteroid dehydrogenase-like
protein 2 (HSDL2), classical (c) SDRs. This subgroup
includes human HSDL2 and related protens. These are
members of the classical SDR family, with a canonical
Gly-rich NAD-binding motif and the typical YXXXK active
site motif. However, the rest of the catalytic tetrad is
not strongly conserved. HSDL2 may play a part in fatty
acid metabolism, as it is found in peroxisomes. SDRs are
a functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold (alpha/beta folding pattern with a central
beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRS are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes have a
3-glycine N-terminal NAD(P)(H)-binding pattern
(typically, TGxxxGxG in classical SDRs and TGxxGxxG in
extended SDRs), while substrate binding is in the
C-terminal region. A critical catalytic Tyr residue
(Tyr-151, human 15-hydroxyprostaglandin dehydrogenase
(15-PGDH) numbering), is often found in a conserved
YXXXK pattern. In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) or additional
Ser, contributing to the active site. Substrates for
these enzymes include sugars, steroids, alcohols, and
aromatic compounds. The standard reaction mechanism is a
proton relay involving the conserved Tyr and Lys, as
well as Asn (or Ser). Some SDR family members, including
17 beta-hydroxysteroid dehydrogenase contain an
additional helix-turn-helix motif that is not generally
found among SDRs.
Length = 243
Score = 30.5 bits (69), Expect = 1.9
Identities = 38/140 (27%), Positives = 59/140 (42%), Gaps = 32/140 (22%)
Query: 100 FTGKTLFMTGASGFLGKVLLEKILRKSPNVKKIYILMRQKKGKNARQRIEELFASPLFNL 159
GKTLF+TGAS +GK + K R NV I A P L
Sbjct: 1 LAGKTLFITGASRGIGKAIALKAARDGANVV-----------------IAAKTAEPHPKL 43
Query: 160 LKSVH-GQKIID----KVLPISGDAEADELAIKESDRQLLAS--EVDIMIHGAATIRF-- 210
+++ + I+ K LP D DE ++ + + + +DI+++ A+ I
Sbjct: 44 PGTIYTAAEEIEAAGGKALPCIVDIR-DEDQVRAAVEKAVEKFGGIDILVNNASAISLTG 102
Query: 211 --DEALKKAVLL---NTRGT 225
D +K+ L+ NTRGT
Sbjct: 103 TLDTPMKRYDLMMGVNTRGT 122
>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 = 30.6 bits (70), Expect = 2.2
Identities = 39/147 (26%), Positives = 62/147 (42%), Gaps = 25/147 (17%)
Query: 103 KTLFMTGASGFLGKVLLEKILRKSPNVKKIYILMRQKKGKNARQRIEELFASPLFNLLKS 162
+ +TG +GF+G + +L K P+ K I L + N +E++ +SP +
Sbjct: 1 MKILVTGGAGFIGSNFVRYLLNKYPDYK-IINLDKLTYAGNLE-NLEDVSSSPRYRF--- 55
Query: 163 VHGQKIIDKVLPISGDAEADELAIKESDRQLLASEVDIMIHGAATIRFDEALKKAVLL-- 220
V G I DAE + +E +D +IH AA D ++
Sbjct: 56 VKGD--------IC-DAELVDRLFEEEK-------IDAVIHFAAESHVDRSISDPEPFIR 99
Query: 221 -NTRGTKMMLSLAKEMKHLELFVHIST 246
N GT +L A++ + FVHIST
Sbjct: 100 TNVLGTYTLLEAARKYGV-KRFVHIST 125
>gnl|CDD|236016 PRK07424, PRK07424, bifunctional sterol desaturase/short chain
dehydrogenase; Validated.
Length = 406
Score = 30.4 bits (69), Expect = 2.6
Identities = 15/41 (36%), Positives = 26/41 (63%), Gaps = 3/41 (7%)
Query: 92 LPDRI---GETFTGKTLFMTGASGFLGKVLLEKILRKSPNV 129
L D++ + GKT+ +TGASG LG+ LL+++ ++ V
Sbjct: 165 LVDKLMGTALSLKGKTVAVTGASGTLGQALLKELHQQGAKV 205
>gnl|CDD|218026 pfam04321, RmlD_sub_bind, RmlD substrate binding domain.
L-rhamnose is a saccharide required for the virulence of
some bacteria. Its precursor, dTDP-L-rhamnose, is
synthesised by four different enzymes the final one of
which is RmlD. The RmlD substrate binding domain is
responsible for binding a sugar nucleotide.
Length = 284
Score = 30.3 bits (69), Expect = 2.7
Identities = 15/54 (27%), Positives = 24/54 (44%), Gaps = 7/54 (12%)
Query: 199 DIMIHGAATIRFDEALK---KAVLLNTRGTKMMLSLAKEMKHLE-LFVHISTAY 248
D++++ AA D+A A +N G +LA+ +HIST Y
Sbjct: 51 DVVVNAAAYTAVDKAESEPELAYAVNALGPG---NLAEACAARGAPLIHISTDY 101
>gnl|CDD|225600 COG3058, FdhE, Uncharacterized protein involved in formate
dehydrogenase formation [Posttranslational modification,
protein turnover, chaperones].
Length = 308
Score = 30.1 bits (68), Expect = 3.1
Identities = 12/53 (22%), Positives = 21/53 (39%), Gaps = 1/53 (1%)
Query: 220 LNTRGTKMMLSLAKEMKHLELFVHISTAYCHLQEKVLYEKPYPPPTDPHKLIE 272
L R + + LA E L +++ + Q+ VL + P +L E
Sbjct: 31 LFNRRAERLRQLA-ENHPLGDYLNFAAGIAEAQQSVLSDHPLLMDLTDARLEE 82
>gnl|CDD|233030 TIGR00575, dnlj, DNA ligase, NAD-dependent. All proteins in this
family with known functions are NAD-dependent DNA
ligases. Functions of these proteins include DNA repair,
DNA replication, and DNA recombination. This family is
based on the phylogenomic analysis of JA Eisen (1999,
Ph.D. Thesis, Stanford University). The member of this
family from Treponema pallidum differs in having three
rather than just one copy of the BRCT (BRCA1 C Terminus)
domain (pfam00533) at the C-terminus. It is included in
the seed [DNA metabolism, DNA replication,
recombination, and repair].
Length = 652
Score = 30.3 bits (69), Expect = 3.5
Identities = 12/40 (30%), Positives = 19/40 (47%), Gaps = 2/40 (5%)
Query: 481 KGFEVFEYYANNQWEFRNEYVHVLRKIMNKRERIEYKIDG 520
GF V + + E + R+I KR+ + Y+IDG
Sbjct: 236 WGFPVSPHIRLC--DSIEEVLEYYREIEEKRDSLPYEIDG 273
>gnl|CDD|224016 COG1091, RfbD, dTDP-4-dehydrorhamnose reductase [Cell envelope
biogenesis, outer membrane].
Length = 281
Score = 30.0 bits (68), Expect = 3.5
Identities = 17/53 (32%), Positives = 25/53 (47%), Gaps = 5/53 (9%)
Query: 199 DIMIHGAATIRFDEA---LKKAVLLNTRGTKMMLSLAKEMKHLELFVHISTAY 248
D++I+ AA D+A + A +N G + + A E VHIST Y
Sbjct: 52 DVVINAAAYTAVDKAESEPELAFAVNATGAENLARAAAE--VGARLVHISTDY 102
>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 = 30.1 bits (68), Expect = 3.6
Identities = 39/177 (22%), Positives = 54/177 (30%), Gaps = 28/177 (15%)
Query: 49 PLEFIRCEVIVSELVMAANKVNNMNVPYETFYKPPVL---------SEEYRNLP--DRIG 97
L+ IRC + VS L + Y K ++R+L I
Sbjct: 151 QLKLIRC-LFVSNLNSQKEPIIRNGKVYYERVKKNSNIKNVYKSGSWGDFRHLLLDLSIL 209
Query: 98 ETF----TGKTLFMTGASGFLGKVLLEKILRKSPNVKKIYILMRQKKGKNARQRIEELFA 153
+T GK+ +TG SG LG +L K L K V+ I IL R I E
Sbjct: 210 KTNYPINLGKSYLITGGSGGLGLEIL-KWLVKRGAVENIIILSRSGMKWELELLIREW-- 266
Query: 154 SPLFNLLKSVHGQKIIDKVLPISGDAEADELAIKESDRQLLASEVDIMIHGAATIRF 210
V D + E AI + + H A +
Sbjct: 267 ---------KSQNIKFHFVSVDVSDVSSLEKAINLILNAPKIGPIGGIFHLAFVLID 314
>gnl|CDD|224013 COG1088, RfbB, dTDP-D-glucose 4,6-dehydratase [Cell envelope
biogenesis, outer membrane].
Length = 340
Score = 29.9 bits (68), Expect = 4.5
Identities = 35/148 (23%), Positives = 58/148 (39%), Gaps = 26/148 (17%)
Query: 103 KTLFMTGASGFLGKVLLEKILRKSPNVKKIYILMRQKKGKNARQRIEEL-FASPLFNLLK 161
+ +TG +GF+G + IL K P+ + +++L +A L NL
Sbjct: 1 MKILVTGGAGFIGSNFVRYILNKHPDDHVV--------------NLDKLTYAGNLENL-A 45
Query: 162 SVHGQKIIDKVLPISGDAEADELAIKESDRQLLASEVDIMIHGAATIRFDEALKKA---V 218
V + + GD D + DR + D ++H AA D ++ +
Sbjct: 46 DVEDS---PRYRFVQGDI-CDR---ELVDRLFKEYQPDAVVHFAAESHVDRSIDGPAPFI 98
Query: 219 LLNTRGTKMMLSLAKEMKHLELFVHIST 246
N GT +L A++ F HIST
Sbjct: 99 QTNVVGTYTLLEAARKYWGKFRFHHIST 126
>gnl|CDD|223959 COG1028, FabG, Dehydrogenases with different specificities (related
to short-chain alcohol dehydrogenases) [Secondary
metabolites biosynthesis, transport, and catabolism /
General function prediction only].
Length = 251
Score = 29.4 bits (66), Expect = 4.8
Identities = 23/157 (14%), Positives = 58/157 (36%), Gaps = 26/157 (16%)
Query: 100 FTGKTLFMTGASGFLGKVLLEKILRKSPNVKKIYILMRQKKGKNARQRIEELFASPLFNL 159
+GK +TGAS +G+ + + R+ ++ + R+ + + A +
Sbjct: 3 LSGKVALVTGASSGIGRAIARALAREG---ARVVVAARRSEEEAAEALAAAI-------- 51
Query: 160 LKSVHGQKIIDKVLPISGDAEADELAIKESDRQLLAS--EVDIMIHGAATIRF------- 210
+ + ++ D DE +++ +DI+++ A
Sbjct: 52 -----KEAGGGRAAAVAADVSDDEESVEALVAAAEEEFGRIDILVNNAGIAGPDAPLEEL 106
Query: 211 -DEALKKAVLLNTRGTKMMLSLAKEMKHLELFVHIST 246
+E + + +N G ++ A + + V+IS+
Sbjct: 107 TEEDWDRVIDVNLLGAFLLTRAALPLMKKQRIVNISS 143
>gnl|CDD|187643 cd08939, KDSR-like_SDR_c, 3-ketodihydrosphingosine reductase (KDSR)
and related proteins, classical (c) SDR. These proteins
include members identified as KDSR, ribitol type
dehydrogenase, and others. The group shows strong
conservation of the active site tetrad and glycine rich
NAD-binding motif of the classical SDRs. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold (alpha/beta folding pattern with a central
beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRs are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes catalyze a
wide range of activities including the metabolism of
steroids, cofactors, carbohydrates, lipids, aromatic
compounds, and amino acids, and act in redox sensing.
Classical SDRs have an TGXXX[AG]XG cofactor binding
motif and a YXXXK active site motif, with the Tyr
residue of the active site motif serving as a critical
catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 239
Score = 29.1 bits (66), Expect = 5.0
Identities = 24/105 (22%), Positives = 48/105 (45%), Gaps = 16/105 (15%)
Query: 102 GKTLFMTGASGFLGKVLLEKILRKSPNVKKIYILMR-QKKGKNARQRIEELFASPLFNLL 160
GK + +TG S +GK L ++++++ + I+ R + K + A + IE +
Sbjct: 1 GKHVLITGGSSGIGKALAKELVKEG---ANVIIVARSESKLEEAVEEIEAEANAS----- 52
Query: 161 KSVHGQKIIDKVLPISGDAEADELAIKESDRQLLASEVDIMIHGA 205
GQK+ +S D E E A ++ + D++++ A
Sbjct: 53 ----GQKVSYISADLS-DYEEVEQAFAQAVEKGGP--PDLVVNCA 90
>gnl|CDD|184628 PRK14331, PRK14331, (dimethylallyl)adenosine tRNA
methylthiotransferase; Provisional.
Length = 437
Score = 29.8 bits (67), Expect = 5.5
Identities = 16/44 (36%), Positives = 25/44 (56%)
Query: 84 VLSEEYRNLPDRIGETFTGKTLFMTGASGFLGKVLLEKILRKSP 127
VL EE + IG T T K + + G+ LGK++ KI++ +P
Sbjct: 383 VLVEEEKEGNKLIGRTRTNKWVSIEGSQEMLGKIVKVKIIKSNP 426
>gnl|CDD|218047 pfam04367, DUF502, Protein of unknown function (DUF502). Predicted
to be an integral membrane protein.
Length = 108
Score = 27.8 bits (63), Expect = 5.8
Identities = 14/39 (35%), Positives = 24/39 (61%), Gaps = 5/39 (12%)
Query: 105 LFMTG--ASGFLGKVLL---EKILRKSPNVKKIYILMRQ 138
+F+ G A F+G+ LL E++L + P V+ IY ++Q
Sbjct: 8 IFLVGLLARNFIGRWLLSLGERLLNRIPLVRSIYSSVKQ 46
>gnl|CDD|181349 PRK08278, PRK08278, short chain dehydrogenase; Provisional.
Length = 273
Score = 29.1 bits (66), Expect = 6.0
Identities = 10/18 (55%), Positives = 14/18 (77%)
Query: 99 TFTGKTLFMTGASGFLGK 116
+ +GKTLF+TGAS +G
Sbjct: 3 SLSGKTLFITGASRGIGL 20
>gnl|CDD|236399 PRK09186, PRK09186, flagellin modification protein A; Provisional.
Length = 256
Score = 29.2 bits (66), Expect = 6.6
Identities = 12/29 (41%), Positives = 17/29 (58%)
Query: 101 TGKTLFMTGASGFLGKVLLEKILRKSPNV 129
GKT+ +TGA G +G L++ IL V
Sbjct: 3 KGKTILITGAGGLIGSALVKAILEAGGIV 31
>gnl|CDD|219347 pfam07247, AATase, Alcohol acetyltransferase. This family contains
a number of alcohol acetyltransferase (EC:2.3.1.84)
enzymes approximately 500 residues long found in both
bacteria and metazoa. These catalyze the esterification
of isoamyl alcohol by acetyl coenzyme A.
Length = 479
Score = 28.9 bits (65), Expect = 8.8
Identities = 15/58 (25%), Positives = 22/58 (37%), Gaps = 2/58 (3%)
Query: 481 KGFEVFEYYANNQWEFRNEYVHVLRK-IMNKRERIEYKIDGEDLDIKKYFQDCIMATR 537
F + E + W+ Y L K I N R +D+D+K Y D + T
Sbjct: 340 SPFSIQESK-EDFWDLVEYYHQRLSKAISNGRSLNGLGGLLKDVDVKDYNLDKLEKTD 396
>gnl|CDD|212492 cd05327, retinol-DH_like_SDR_c_like, retinol dehydrogenase
(retinol-DH), Light dependent Protochlorophyllide
(Pchlide) OxidoReductase (LPOR) and related proteins,
classical (c) SDRs. Classical SDR subgroup containing
retinol-DHs, LPORs, and related proteins. Retinol is
processed by a medium chain alcohol dehydrogenase
followed by retinol-DHs. Pchlide reductases act in
chlorophyll biosynthesis. There are distinct enzymes
that catalyze Pchlide reduction in light or dark
conditions. Light-dependent reduction is via an
NADP-dependent SDR, LPOR. Proteins in this subfamily
share the glycine-rich NAD-binding motif of the
classical SDRs, have a partial match to the canonical
active site tetrad, but lack the typical active site
Ser. This subgroup includes the human proteins: retinol
dehydrogenase -12, -13 ,and -14, dehydrogenase/reductase
SDR family member (DHRS)-12 , -13 and -X (a DHRS on
chromosome X), and WWOX (WW domain-containing
oxidoreductase), as well as a Neurospora crassa SDR
encoded by the blue light inducible bli-4 gene. SDRs are
a functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold (alpha/beta folding pattern with a central
beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRs are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes catalyze a
wide range of activities including the metabolism of
steroids, cofactors, carbohydrates, lipids, aromatic
compounds, and amino acids, and act in redox sensing.
Classical SDRs have an TGXXX[AG]XG cofactor binding
motif and a YXXXK active site motif, with the Tyr
residue of the active site motif serving as a critical
catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 269
Score = 28.7 bits (65), Expect = 9.0
Identities = 18/84 (21%), Positives = 39/84 (46%), Gaps = 13/84 (15%)
Query: 102 GKTLFMTGASGFLGKVLLEKILRKSPNVKKIYILMR-QKKGKNARQRIEE------LFAS 154
GK + +TGA+ +GK ++ ++ +V I R ++KG+ A I++ +
Sbjct: 1 GKVVVITGANSGIGKETARELAKRGAHV---IIACRNEEKGEEAAAEIKKETGNAKVEVI 57
Query: 155 PL-FNLLKSVH--GQKIIDKVLPI 175
L + L SV ++ + + +
Sbjct: 58 QLDLSSLASVRQFAEEFLARFPRL 81
>gnl|CDD|217903 pfam04112, Mak10, Mak10 subunit, NatC N(alpha)-terminal
acetyltransferase. NatC N(alpha)-terminal
acetyltransferases contains Mak10p, Mak31p and Mak3p
subunits. All three subunits are associated with each
other to form the active complex.
Length = 167
Score = 28.1 bits (63), Expect = 9.1
Identities = 16/62 (25%), Positives = 25/62 (40%), Gaps = 7/62 (11%)
Query: 147 RIEELFASPLFNLLKSVHGQKIIDKVLP--ISGDAEADEL----AIKESDRQLLASEV-D 199
+ EL P FNL +++ +I+D + + E + A R L EV
Sbjct: 1 KPGELVKDPKFNLFEAMSALEIMDPKMDSGMIELTEEEPFDLEEAYDTGLRPLDLPEVLA 60
Query: 200 IM 201
IM
Sbjct: 61 IM 62
>gnl|CDD|146145 pfam03357, Snf7, Snf7. This family of proteins are involved in
protein sorting and transport from the endosome to the
vacuole/lysosome in eukaryotic cells. Vacuoles/lysosomes
play an important role in the degradation of both lipids
and cellular proteins. In order to perform this
degradative function, vacuoles/lysosomes contain
numerous hydrolases which have been transported in the
form of inactive precursors via the biosynthetic pathway
and are proteolytically activated upon delivery to the
vacuole/lysosome. The delivery of transmembrane
proteins, such as activated cell surface receptors to
the lumen of the vacuole/lysosome, either for
degradation/downregulation, or in the case of
hydrolases, for proper localisation, requires the
formation of multivesicular bodies (MVBs). These late
endosomal structures are formed by invaginating and
budding of the limiting membrane into the lumen of the
compartment. During this process, a subset of the
endosomal membrane proteins is sorted into the forming
vesicles. Mature MVBs fuse with the vacuole/lysosome,
thereby releasing cargo containing vesicles into its
hydrolytic lumen for degradation. Endosomal proteins
that are not sorted into the intralumenal MVB vesicles
are either recycled back to the plasma membrane or Golgi
complex, or remain in the limiting membrane of the MVB
and are thereby transported to the limiting membrane of
the vacuole/lysosome as a consequence of fusion.
Therefore, the MVB sorting pathway plays a critical role
in the decision between recycling and degradation of
membrane proteins. A few archaeal sequences are also
present within this family.
Length = 169
Score = 28.0 bits (63), Expect = 9.5
Identities = 11/40 (27%), Positives = 21/40 (52%)
Query: 505 RKIMNKRERIEYKIDGEDLDIKKYFQDCIMATRIFILKEM 544
R++ K+E +E KI + +IKK + + +LK+
Sbjct: 11 RELDKKQESLEKKIKKLEAEIKKLAKKGNKDAALILLKQK 50
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.324 0.140 0.422
Gapped
Lambda K H
0.267 0.0766 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 32,543,780
Number of extensions: 3341420
Number of successful extensions: 4523
Number of sequences better than 10.0: 1
Number of HSP's gapped: 4483
Number of HSP's successfully gapped: 73
Length of query: 614
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 511
Effective length of database: 6,369,140
Effective search space: 3254630540
Effective search space used: 3254630540
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 62 (27.6 bits)