RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy897
(125 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 = 98.9 bits (247), Expect = 4e-26
Identities = 46/138 (33%), Positives = 68/138 (49%), Gaps = 30/138 (21%)
Query: 16 IFLTGGTGFMGKVLLDTLLRRFPSIHSIYILVRERKGVSPQERIEKMLDNEGPIFKDFAN 75
+ +TG TGF+GKVLL+ LLR P I IY+L+R + G S +ER+ ++L + +F N
Sbjct: 3 VLITGATGFLGKVLLEKLLRSCPDIGKIYLLIRGKSGQSAEERLRELL--KDKLFDRGRN 60
Query: 76 LVRLKTQRIRFI---------FL-------------------ATLRFDEELKIAIRTNIC 107
L L +I I L AT+ FDE L A+ N+
Sbjct: 61 LNPLFESKIVPIEGDLSEPNLGLSDEDLQTLIEEVNIIIHCAATVTFDERLDEALSINVL 120
Query: 108 ATQTVVKLAKQCPHLRLF 125
T +++LAK+C L+ F
Sbjct: 121 GTLRLLELAKRCKKLKAF 138
>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 = 88.0 bits (219), Expect = 1e-22
Identities = 42/130 (32%), Positives = 58/130 (44%), Gaps = 25/130 (19%)
Query: 18 LTGGTGFMGKVLLDTLLRRFPSIHSIYILVRERKGVSPQERIEKMLDNEGPIFKDFANLV 77
LTG TGF+GKVLL+ LLR P + IY LVR + G S ER+ + L + +F L
Sbjct: 1 LTGATGFLGKVLLEKLLRSTPEVK-IYCLVRAKDGESALERLRQELL-KYGLFDRLKALE 58
Query: 78 RLK---------------------TQRIRFIF--LATLRFDEELKIAIRTNICATQTVVK 114
R+ + + I AT+ F E TN+ T+ V++
Sbjct: 59 RIIPVAGDLSEPNLGLSDEDFQELAEEVDVIIHNAATVNFVEPYSDLRATNVLGTREVLR 118
Query: 115 LAKQCPHLRL 124
LAKQ L
Sbjct: 119 LAKQMKKLPF 128
>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 = 60.8 bits (148), Expect = 3e-12
Identities = 34/123 (27%), Positives = 53/123 (43%), Gaps = 16/123 (13%)
Query: 16 IFLTGGTGFMGKVLLDTLLRRFPSIHSIYILVRERKGVSPQERI-------EKMLDNEGP 68
+F+TGGTGF+G+ L+ LL + +LVR ERI +++ EG
Sbjct: 1 VFVTGGTGFLGRHLVKRLLEN---GFKVLVLVRSESLGEAHERIEEAGLEADRVRVLEGD 57
Query: 69 IFK-----DFANLVRLKTQRIRFIFLA-TLRFDEELKIAIRTNICATQTVVKLAKQCPHL 122
+ + A L + I A + F + A RTNI T+ V++LA +
Sbjct: 58 LTQPNLGLSAAASRELAGKVDHVIHCAASYDFQAPNEDAWRTNIDGTEHVLELAARLDIQ 117
Query: 123 RLF 125
R
Sbjct: 118 RFH 120
>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 = 54.2 bits (131), Expect = 1e-09
Identities = 21/54 (38%), Positives = 27/54 (50%), Gaps = 1/54 (1%)
Query: 15 VIFLTGGTGFMGKVLLDTLLRRFPSIHSIYILVRERKGVSPQERIEKMLDNEGP 68
+ LTG TGF+G LL LL+R IY LVR + + ER+ L G
Sbjct: 1 TVLLTGATGFLGAYLLRELLKRKNVSK-IYCLVRAKDEEAALERLIDNLKEYGL 53
>gnl|CDD|215279 PLN02503, PLN02503, fatty acyl-CoA reductase 2.
Length = 605
Score = 49.1 bits (117), Expect = 7e-08
Identities = 35/141 (24%), Positives = 61/141 (43%), Gaps = 32/141 (22%)
Query: 17 FLTGGTGFMGKVLLDTLLRRFPSIHSIYILVRERKGVSPQERIE-KMLDNE--------- 66
+TG TGF+ KVL++ +LR P + IY+L++ + + ER++ +++D E
Sbjct: 123 LITGATGFLAKVLIEKILRTNPDVGKIYLLIKAKDKEAAIERLKNEVIDAELFKCLQETH 182
Query: 67 GPIFKDF--------------------ANLVRLKTQRIRFIF--LATLRFDEELKIAIRT 104
G ++ F +L + + I A FDE +AI
Sbjct: 183 GKSYQSFMLSKLVPVVGNVCESNLGLEPDLADEIAKEVDVIINSAANTTFDERYDVAIDI 242
Query: 105 NICATQTVVKLAKQCPHLRLF 125
N ++ AK+C L+LF
Sbjct: 243 NTRGPCHLMSFAKKCKKLKLF 263
>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 = 45.5 bits (108), Expect = 1e-06
Identities = 19/52 (36%), Positives = 26/52 (50%), Gaps = 1/52 (1%)
Query: 16 IFLTGGTGFMGKVLLDTLLRRFPSIHSIYILVRERKGVSPQERIEKMLDNEG 67
+ LTG TGF+G LL+ LLRR + LVR ER+ + L +
Sbjct: 2 VLLTGATGFLGAYLLEELLRRSTQA-KVICLVRAASEEHAMERLREALRSYR 52
>gnl|CDD|215538 PLN02996, PLN02996, fatty acyl-CoA reductase.
Length = 491
Score = 43.9 bits (104), Expect = 4e-06
Identities = 34/148 (22%), Positives = 60/148 (40%), Gaps = 33/148 (22%)
Query: 10 FYKDGVIFLTGGTGFMGKVLLDTLLRRFPSIHSIYILVRERKGVSPQER-----IEKML- 63
F ++ I +TG TGF+ K+ ++ +LR P++ +Y+L+R S +R I K L
Sbjct: 8 FLENKTILVTGATGFLAKIFVEKILRVQPNVKKLYLLLRASDAKSATQRLHDEVIGKDLF 67
Query: 64 ----DNEGPIFKDFA--------------NL----VRLKTQRIRFI-----FLATLRFDE 96
+ G +L L+ + + I AT FDE
Sbjct: 68 KVLREKLGENLNSLISEKVTPVPGDISYDDLGVKDSNLREEMWKEIDIVVNLAATTNFDE 127
Query: 97 ELKIAIRTNICATQTVVKLAKQCPHLRL 124
+A+ N V+ AK+C +++
Sbjct: 128 RYDVALGINTLGALNVLNFAKKCVKVKM 155
>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 = 43.5 bits (103), Expect = 5e-06
Identities = 19/49 (38%), Positives = 26/49 (53%), Gaps = 2/49 (4%)
Query: 16 IFLTGGTGFMGKVLLDTLLRRFPSIHSIYILVRERKGVSPQERIEKMLD 64
+ LTG TGF+G LL LL R + + LVR + + R+EK D
Sbjct: 3 VLLTGATGFLGAYLLLELLDRSDA--KVICLVRAQSDEAALARLEKTFD 49
>gnl|CDD|233570 TIGR01777, yfcH, TIGR01777 family protein. This model represents a
clade of proteins of unknown function including the E.
coli yfcH protein [Hypothetical proteins, Conserved].
Length = 291
Score = 41.1 bits (97), Expect = 4e-05
Identities = 29/112 (25%), Positives = 43/112 (38%), Gaps = 19/112 (16%)
Query: 16 IFLTGGTGFMGKVLLDTLLRRFPSIHSIYILVRERKGVSPQERIEKMLDNEGPIFKDFAN 75
I +TGGTGF+G+ L L +R H + IL R EG K +A
Sbjct: 1 ILITGGTGFIGRALTQRLTKRG---HEVTILTR-------SPPPGANTKWEGY--KPWAG 48
Query: 76 LVRLKTQRIRFIF------LATLRFDEELKIAIR-TNICATQTVVKLAKQCP 120
+ + +A R+ EE K IR + I T+ +V+
Sbjct: 49 EDADSLEGADAVINLAGEPIADKRWTEERKQEIRDSRIDTTRLLVEAIAAAE 100
>gnl|CDD|235962 PRK07201, PRK07201, short chain dehydrogenase; Provisional.
Length = 657
Score = 38.8 bits (91), Expect = 3e-04
Identities = 34/122 (27%), Positives = 52/122 (42%), Gaps = 31/122 (25%)
Query: 17 FLTGGTGFMGKVLLDTLLRRFPSIHSIYILVRERKGVSPQERIEKMLDNEG-----PIF- 70
F+TGGTGF+G+ L+ LL R ++++LVR R+E + G P+
Sbjct: 4 FVTGGTGFIGRRLVSRLLDRRRE-ATVHVLVRR----QSLSRLEALAAYWGADRVVPLVG 58
Query: 71 -----------KDFANLVRLKTQRIRFIFLAT---LRFDEELKIAIRTNICATQTVVKLA 116
D A L + + LA L DEE N+ T+ VV+LA
Sbjct: 59 DLTEPGLGLSEADIAELGDID----HVVHLAAIYDLTADEE--AQRAANVDGTRNVVELA 112
Query: 117 KQ 118
++
Sbjct: 113 ER 114
>gnl|CDD|187553 cd05242, SDR_a8, atypical (a) SDRs, subgroup 8. This subgroup
contains atypical SDRs of unknown function. Proteins in
this subgroup have a glycine-rich NAD(P)-binding motif
consensus that resembles that of the extended SDRs,
(GXXGXXG or GGXGXXG), but lacks the characteristic
active site residues of the SDRs. A Cys often replaces
the usual Lys of the YXXXK active site motif, while the
upstream Ser is generally present and Arg replaces the
usual Asn. Atypical SDRs generally lack the catalytic
residues characteristic of the SDRs, and their
glycine-rich NAD(P)-binding motif is often different
from the forms normally seen in classical or extended
SDRs. Atypical SDRs include biliverdin IX beta reductase
(BVR-B,aka flavin reductase), NMRa (a negative
transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 296
Score = 37.6 bits (88), Expect = 6e-04
Identities = 28/112 (25%), Positives = 43/112 (38%), Gaps = 15/112 (13%)
Query: 15 VIFLTGGTGFMGKVLLDTLLRRFPSIHSIYILVR-ERKGVSPQERIEKMLDNEGPIFKDF 73
I +TGGTGF+G+ L L H + +L R K E I D +
Sbjct: 1 KIVITGGTGFIGRALTRRLTAAG---HEVVVLSRRPGKAEGLAEVIT--WDGLSLGPWEL 55
Query: 74 AN---LVRLKTQRIRFIFLATLRFDEELKIAIR-TNICATQTVVKLAKQCPH 121
++ L + I A R+ E K I + I +T+ +V+ P
Sbjct: 56 PGADAVINLAGEPI-----ACRRWTEANKKEILSSRIESTRVLVEAIANAPA 102
>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 = 35.8 bits (83), Expect = 0.002
Identities = 24/102 (23%), Positives = 44/102 (43%), Gaps = 7/102 (6%)
Query: 16 IFLTGGTGFMGKVLLDTLLRRFPSIHSIYILVRERKGVSPQERIEKMLDNEGPIFKDFAN 75
I + G TGF+G+ L LL + H + +LVR K +S + ++ + +D +
Sbjct: 1 ILILGATGFIGRALARELLEQG---HEVTLLVRNTKRLS--KEDQEPVAVVEGDLRDLDS 55
Query: 76 LVRLKTQRIRFIFLATLRFDEELKIAIRTNICATQTVVKLAK 117
L I LA + + ++ T+ V++ AK
Sbjct: 56 LSDAVQGVDVVIHLAGA--PRDTRDFCEVDVEGTRNVLEAAK 95
>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 = 36.2 bits (84), Expect = 0.002
Identities = 22/61 (36%), Positives = 32/61 (52%), Gaps = 3/61 (4%)
Query: 4 YPTVEDFYKDGVI--FLTGGTGFMGKVLL-DTLLRRFPSIHSIYILVRERKGVSPQERIE 60
YP+ ++ I FLTG TGF+G +L D L RR S ++ VR + + ER+
Sbjct: 960 YPSRKELDASTPITVFLTGATGFLGSFILRDLLTRRSNSNFKVFAHVRAKSEEAGLERLR 1019
Query: 61 K 61
K
Sbjct: 1020 K 1020
>gnl|CDD|223528 COG0451, WcaG, Nucleoside-diphosphate-sugar epimerases [Cell
envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 314
Score = 35.7 bits (82), Expect = 0.003
Identities = 22/111 (19%), Positives = 40/111 (36%), Gaps = 12/111 (10%)
Query: 16 IFLTGGTGFMGKVLLDTLLRRFPSIHSIYILVRERKGVSPQERIEKMLDNEGPIFKDFAN 75
I +TGG GF+G L++ LL H + L R R G+ + + + D
Sbjct: 3 ILVTGGAGFIGSHLVERLLAA---GHDVRGLDRLRDGL--DPLLSGVEFVVLDLT-DRDL 56
Query: 76 LVRLKTQRIRFIF-LATLRF-----DEELKIAIRTNICATQTVVKLAKQCP 120
+ L + LA + + N+ T +++ A+
Sbjct: 57 VDELAKGVPDAVIHLAAQSSVPDSNASDPAEFLDVNVDGTLNLLEAARAAG 107
>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 = 35.0 bits (81), Expect = 0.005
Identities = 14/47 (29%), Positives = 21/47 (44%), Gaps = 5/47 (10%)
Query: 16 IFLTGGTGFMGKVLLDTLLRRFPSIHSIYILVRERKGVS--PQERIE 60
I +TG TGF+G L+ LL + + + LVR +E
Sbjct: 1 ILVTGATGFLGSNLVRALLAQG---YRVRALVRSGSDAVLLDGLPVE 44
>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 = 33.7 bits (78), Expect = 0.012
Identities = 31/126 (24%), Positives = 51/126 (40%), Gaps = 24/126 (19%)
Query: 12 KDGVIFLTGGTGFMGKVLLDTLLRRFPS-IH-------SIYILVRERKGVSPQERIEKML 63
K I +TGG G +G L+ +L+ P + ++ LVRE R
Sbjct: 1 KGKTILVTGGAGSIGSELVRQILKFGPKKLIVFDRDENKLHELVREL-------RSRFPH 53
Query: 64 DNEGPIFKDFANLVRL----KTQRIRFIF-LATLRF----DEELKIAIRTNICATQTVVK 114
D I D + RL K + +F A L+ ++ + AI+TN+ T+ V+
Sbjct: 54 DKLRFIIGDVRDKERLRRAFKERGPDIVFHAAALKHVPSMEDNPEEAIKTNVLGTKNVID 113
Query: 115 LAKQCP 120
A +
Sbjct: 114 AAIENG 119
>gnl|CDD|224015 COG1090, COG1090, Predicted nucleoside-diphosphate sugar
epimerase [General function prediction only].
Length = 297
Score = 33.0 bits (76), Expect = 0.020
Identities = 14/39 (35%), Positives = 19/39 (48%), Gaps = 3/39 (7%)
Query: 16 IFLTGGTGFMGKVLLDTLLRRFPSIHSIYILVRERKGVS 54
I +TGGTG +G+ L L + H + IL R S
Sbjct: 1 ILITGGTGLIGRALTARLRK---GGHQVTILTRRPPKAS 36
>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 = 33.0 bits (75), Expect = 0.027
Identities = 33/118 (27%), Positives = 59/118 (50%), Gaps = 20/118 (16%)
Query: 11 YKDGVIFLTGGTGFMGKVLLDTLLRRFPS--IHSIYILVRERKGVSPQERIEKMLDNEGP 68
+KD ++ +TGGTG G + +LRRF I I I R+ K Q+ + K +N
Sbjct: 2 FKDKILLITGGTGSFG----NAVLRRFLDTDIKEIRIFSRDEK---KQDDMRKKYNNSKL 54
Query: 69 IF-----KDFANLVRLKTQRIRFIF-LATLRFDEELKI----AIRTNICATQTVVKLA 116
F +D+ +++ T+ + FI+ A L+ + A++TN+ T+ V++ A
Sbjct: 55 KFYIGDVRDYRSILN-ATRGVDFIYHAAALKQVPSCEFHPMEAVKTNVLGTENVLEAA 111
>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 = 32.7 bits (75), Expect = 0.029
Identities = 13/33 (39%), Positives = 19/33 (57%), Gaps = 3/33 (9%)
Query: 16 IFLTGGTGFMGKVLLDTLLRRFPSIHSIYILVR 48
I +TGG GF+G L+ LL R H + ++ R
Sbjct: 1 ILVTGGAGFIGSHLVRRLLERG---HEVVVIDR 30
>gnl|CDD|223774 COG0702, COG0702, Predicted nucleoside-diphosphate-sugar epimerases
[Cell envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 275
Score = 32.2 bits (73), Expect = 0.053
Identities = 22/106 (20%), Positives = 41/106 (38%), Gaps = 10/106 (9%)
Query: 16 IFLTGGTGFMGKVLLDTLLRRFPSIHSIYILVRERKGVSPQER-IEKMLDNEGPIFKDFA 74
I +TG TGF+G ++ LL R H + VR + + +E +L + +D
Sbjct: 3 ILVTGATGFVGGAVVRELLARG---HEVRAAVRNPEAAAALAGGVEVVLGD----LRDPK 55
Query: 75 NLVRLKTQRIRFIFLATLRFDEELKIA--IRTNICATQTVVKLAKQ 118
+LV + ++ L + A + + A + K
Sbjct: 56 SLVAGAKGVDGVLLISGLLDGSDAFRAVQVTAVVRAAEAAGAGVKH 101
>gnl|CDD|187572 cd05262, SDR_a7, atypical (a) SDRs, subgroup 7. This subgroup
contains atypical SDRs of unknown function. Members of
this subgroup have a glycine-rich NAD(P)-binding motif
consensus that matches the extended SDRs, TGXXGXXG, but
lacks the characteristic active site residues of the
SDRs. This subgroup has basic residues (HXXXR) in place
of the active site motif YXXXK, these may have a
catalytic role. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Atypical SDRs include biliverdin IX beta
reductase (BVR-B,aka flavin reductase), NMRa (a
negative transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane
reductase, isoflavone reductases, and others. SDRs are
a functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. In addition to the Rossmann fold
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids, and typically have a TGXXGXXG cofactor
binding motif. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 291
Score = 31.2 bits (71), Expect = 0.11
Identities = 8/19 (42%), Positives = 14/19 (73%)
Query: 16 IFLTGGTGFMGKVLLDTLL 34
+F+TG TGF+G ++ L+
Sbjct: 3 VFVTGATGFIGSAVVRELV 21
>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 = 30.7 bits (70), Expect = 0.14
Identities = 11/21 (52%), Positives = 15/21 (71%)
Query: 16 IFLTGGTGFMGKVLLDTLLRR 36
I +TGGTGF+G L+ LL+
Sbjct: 1 ILVTGGTGFIGSHLVRRLLQE 21
>gnl|CDD|178263 PLN02657, PLN02657, 3,8-divinyl protochlorophyllide a 8-vinyl
reductase.
Length = 390
Score = 30.9 bits (70), Expect = 0.15
Identities = 13/42 (30%), Positives = 26/42 (61%), Gaps = 3/42 (7%)
Query: 12 KDGVIFLTGGTGFMGKVLLDTLLRRFPSIHSIYILVRERKGV 53
KD + + G TG++GK ++ L+RR +++ + RE+ G+
Sbjct: 59 KDVTVLVVGATGYIGKFVVRELVRRG---YNVVAVAREKSGI 97
>gnl|CDD|181205 PRK08040, PRK08040, putative semialdehyde dehydrogenase;
Provisional.
Length = 336
Score = 30.4 bits (69), Expect = 0.21
Identities = 15/36 (41%), Positives = 21/36 (58%), Gaps = 2/36 (5%)
Query: 16 IFLTGGTGFMGKVLLDTLL-RRFPSIHSIYILVRER 50
I L G TG +G+ LL+ L R+FP + +Y L E
Sbjct: 7 IALLGATGAVGEALLELLAERQFP-VGELYALASEE 41
>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 = 30.0 bits (68), Expect = 0.26
Identities = 24/83 (28%), Positives = 32/83 (38%), Gaps = 15/83 (18%)
Query: 17 FLTGGTGFMGKVLLDTLLRRFPSIHSIYILVRERKGVSPQ--ERIEKMLDNEGPIFKDFA 74
+ G TG +GK LL LL+ P + +VR RK P+ E++ I DF
Sbjct: 4 LVLGATGLVGKHLLRELLKS-PYYSKVTAIVR-RKLTFPEAKEKLV-------QIVVDFE 54
Query: 75 NLVRLKTQRIR----FIFLATLR 93
L F L T R
Sbjct: 55 RLDEYLEAFQNPDVGFCCLGTTR 77
>gnl|CDD|187575 cd05265, SDR_a1, atypical (a) SDRs, subgroup 1. Atypical SDRs in
this subgroup are poorly defined and have been
identified putatively as isoflavones reductase, sugar
dehydratase, mRNA binding protein etc. Atypical SDRs
are distinct from classical SDRs. Members of this
subgroup retain the canonical active site triad (though
not the upstream Asn found in most SDRs) but have an
unusual putative glycine-rich NAD(P)-binding motif,
GGXXXXG, in the usual location. Atypical SDRs generally
lack the catalytic residues characteristic of the SDRs,
and their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Atypical SDRs include biliverdin IX beta
reductase (BVR-B,aka flavin reductase), NMRa (a
negative transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane
reductase, isoflavone reductases, and others. SDRs are
a functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. In addition to the Rossmann fold
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids, and typically have a TGXXGXXG cofactor
binding motif. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 250
Score = 29.6 bits (67), Expect = 0.34
Identities = 14/41 (34%), Positives = 20/41 (48%), Gaps = 3/41 (7%)
Query: 20 GGTGFMGKVLLDTLLRRFPSIHSIYILVRERKGVSPQERIE 60
GGT F+GK L++ LL H + + R R E +E
Sbjct: 7 GGTRFIGKALVEELLAAG---HDVTVFNRGRTKPDLPEGVE 44
>gnl|CDD|187554 cd05243, SDR_a5, atypical (a) SDRs, subgroup 5. This subgroup
contains atypical SDRs, some of which are identified as
putative NAD(P)-dependent epimerases, one as a putative
NAD-dependent epimerase/dehydratase. Atypical SDRs are
distinct from classical SDRs. Members of this subgroup
have a glycine-rich NAD(P)-binding motif that is very
similar to the extended SDRs, GXXGXXG, and binds NADP.
Generally, this subgroup has poor conservation of the
active site tetrad; however, individual sequences do
contain matches to the YXXXK active site motif, the
upstream Ser, and there is a highly conserved Asp in
place of the usual active site Asn throughout the
subgroup. 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 = 203
Score = 29.5 bits (67), Expect = 0.35
Identities = 11/42 (26%), Positives = 20/42 (47%), Gaps = 3/42 (7%)
Query: 16 IFLTGGTGFMGKVLLDTLLRRFPSIHSIYILVRERKGVSPQE 57
+ + G TG +G+ ++ LL R + + LVR+ E
Sbjct: 2 VLVVGATGKVGRHVVRELLDRG---YQVRALVRDPSQAEKLE 40
>gnl|CDD|181609 PRK09009, PRK09009, C factor cell-cell signaling protein;
Provisional.
Length = 235
Score = 29.3 bits (66), Expect = 0.45
Identities = 12/31 (38%), Positives = 21/31 (67%), Gaps = 2/31 (6%)
Query: 16 IFLTGGTGFMGKVLLDTLLRRFP--SIHSIY 44
I + GG+G +GK ++ LL R+P ++H+ Y
Sbjct: 3 ILIVGGSGGIGKAMVKQLLERYPDATVHATY 33
>gnl|CDD|187551 cd05240, UDP_G4E_3_SDR_e, UDP-glucose 4 epimerase (G4E), subgroup
3, extended (e) SDRs. Members of this bacterial
subgroup are identified as possible sugar epimerases,
such as UDP-glucose 4 epimerase. However, while the
NAD(P)-binding motif is fairly well conserved, not all
members retain the canonical active site tetrad of the
extended SDRs. UDP-glucose 4 epimerase (aka
UDP-galactose-4-epimerase), is a homodimeric extended
SDR. It catalyzes the NAD-dependent conversion of
UDP-galactose to UDP-glucose, the final step in Leloir
galactose synthesis. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids. Extended SDRs are a diverse collection
of proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 306
Score = 29.3 bits (66), Expect = 0.49
Identities = 13/41 (31%), Positives = 19/41 (46%), Gaps = 1/41 (2%)
Query: 16 IFLTGGTGFMGKVLLDTLLRRFPSIHSIYILVRERKGVSPQ 56
I +TG G +G++L L P + + L R R SP
Sbjct: 1 ILVTGAAGGLGRLLA-RRLAASPRVIGVDGLDRRRPPGSPP 40
>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 = 29.3 bits (66), Expect = 0.51
Identities = 13/34 (38%), Positives = 18/34 (52%), Gaps = 1/34 (2%)
Query: 16 IFLTGGTGFMGKVLLDTLLRRFPSIHSIYILVRE 49
I +TGGTG GK + LL + + I I R+
Sbjct: 7 ILITGGTGSFGKAFISRLLENY-NPKKIIIYSRD 39
>gnl|CDD|187656 cd08953, KR_2_SDR_x, ketoreductase (KR), subgroup 2, complex (x)
SDRs. Ketoreductase, a module of the multidomain
polyketide synthase (PKS), has 2 subdomains, each
corresponding to a SDR family monomer. The C-terminal
subdomain catalyzes the NADPH-dependent reduction of the
beta-carbonyl of a polyketide to a hydroxyl group, a
step in the biosynthesis of polyketides, such as
erythromycin. The N-terminal subdomain, an interdomain
linker, is a truncated Rossmann fold which acts to
stabilizes the catalytic subdomain. Unlike typical SDRs,
the isolated domain does not oligomerize but is composed
of 2 subdomains, each resembling an SDR monomer. The
active site resembles that of typical SDRs, except that
the usual positions of the catalytic Asn and Tyr are
swapped, so that the canonical YXXXK motif changes to
YXXXN. Modular PKSs are multifunctional structures in
which the makeup recapitulates that found in (and may
have evolved from) FAS. Polyketide synthesis also
proceeds via the addition of 2-carbon units as in fatty
acid synthesis. The complex SDR NADP-binding motif,
GGXGXXG, is often present, but is not strictly conserved
in each instance of the module. This subfamily includes
both KR domains of the Bacillus subtilis Pks J,-L, and
PksM, and all three KR domains of PksN, components of
the megacomplex bacillaene synthase, which synthesizes
the antibiotic bacillaene. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold
(alpha/beta folding pattern with a central beta-sheet),
an NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRs are approximately
350 residues. Sequence identity between different SDR
enzymes are typically in the 15-30% range, but the
enzymes share the Rossmann fold NAD-binding motif and
characteristic NAD-binding and catalytic sequence
patterns. These enzymes catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human prostaglandin dehydrogenase
(PGDH) numbering). In addition to the Tyr and Lys, there
is often an upstream Ser (Ser-138, PGDH numbering)
and/or an Asn (Asn-107, PGDH numbering) contributing to
the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type KRs have a TGXXXGX(1-2)G
NAD(P)-binding motif. Some atypical SDRs have lost
catalytic activity and/or have an unusual NAD(P)-binding
motif and missing or unusual active site residues.
Reactions catalyzed within the SDR family include
isomerization, decarboxylation, epimerization, C=N bond
reduction, dehydratase activity, dehalogenation,
Enoyl-CoA reduction, and carbonyl-alcohol
oxidoreduction.
Length = 436
Score = 29.3 bits (66), Expect = 0.58
Identities = 12/28 (42%), Positives = 17/28 (60%), Gaps = 1/28 (3%)
Query: 11 YKDGVIFL-TGGTGFMGKVLLDTLLRRF 37
K G ++L TGG G +G+ L L RR+
Sbjct: 202 LKPGGVYLVTGGAGGIGRALARALARRY 229
>gnl|CDD|203953 pfam08468, MTS_N, Methyltransferase small domain N-terminal. This
domain is found to the N-terminus of the
methyltransferase small domain (pfam05175) in bacterial
proteins.
Length = 155
Score = 28.4 bits (64), Expect = 0.63
Identities = 17/43 (39%), Positives = 21/43 (48%), Gaps = 3/43 (6%)
Query: 29 LLDTLLRRFPSIHSIYILVRERKGVSPQERIEKMLDNEGPIFK 71
LL LL + P I+I+ R GV EKML GP+ K
Sbjct: 87 LLMNLLSKLPIGTEIFIVGENRSGV---RSAEKMLAAYGPLRK 126
>gnl|CDD|224011 COG1086, COG1086, Predicted nucleoside-diphosphate sugar epimerases
[Cell envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 588
Score = 28.8 bits (65), Expect = 0.68
Identities = 26/133 (19%), Positives = 48/133 (36%), Gaps = 36/133 (27%)
Query: 10 FYKDGVIFLTGGTGFMGKVLLDTLLRRFP-----------SIHSIYILVRERKGVSPQER 58
+ +TGG G +G L +L+ P ++ I + +RE+
Sbjct: 247 MLTGKTVLVTGGGGSIGSELCRQILKFNPKEIILFSRDEYKLYLIDMELREKFPE----- 301
Query: 59 IEKMLDNEGPIFKDFANLVRLK----TQRIRFIF-LATL-------RFDEELKIAIRTNI 106
K+ D + R++ ++ +F A L EE AI+TN+
Sbjct: 302 -LKLR----FYIGDVRDRDRVERAMEGHKVDIVFHAAALKHVPLVEYNPEE---AIKTNV 353
Query: 107 CATQTVVKLAKQC 119
T+ V + A +
Sbjct: 354 LGTENVAEAAIKN 366
>gnl|CDD|187661 cd08958, FR_SDR_e, flavonoid reductase (FR), extended (e) SDRs.
This subgroup contains FRs of the extended SDR-type and
related proteins. These FRs act in the NADP-dependent
reduction of flavonoids, ketone-containing plant
secondary metabolites; they have the characteristic
active site triad of the SDRs (though not the upstream
active site Asn) and a NADP-binding motif that is very
similar to the typical extended SDR motif. Extended
SDRs are distinct from classical SDRs. In addition to
the Rossmann fold (alpha/beta folding pattern with a
central beta-sheet) core region typical of all SDRs,
extended SDRs have a less conserved C-terminal
extension of approximately 100 amino acids. Extended
SDRs are a diverse collection of proteins, and include
isomerases, epimerases, oxidoreductases, and lyases;
they typically have a TGXXGXXG cofactor binding motif.
SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving
as a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton
relay involving the conserved Tyr and Lys, a water
molecule stabilized by Asn, and nicotinamide. Atypical
SDRs generally lack the catalytic residues
characteristic of the SDRs, and their glycine-rich
NAD(P)-binding motif is often different from the forms
normally seen in classical or extended SDRs. Complex
(multidomain) SDRs such as ketoreductase domains of
fatty acid synthase have a GGXGXXG NAD(P)-binding motif
and an altered active site motif (YXXXN). Fungal type
ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding
motif.
Length = 293
Score = 28.3 bits (64), Expect = 0.86
Identities = 9/18 (50%), Positives = 13/18 (72%)
Query: 19 TGGTGFMGKVLLDTLLRR 36
TG +GF+G L+ LL+R
Sbjct: 4 TGASGFIGSWLVKRLLQR 21
>gnl|CDD|187545 cd05234, UDP_G4E_2_SDR_e, UDP-glucose 4 epimerase, subgroup 2,
extended (e) SDRs. UDP-glucose 4 epimerase (aka
UDP-galactose-4-epimerase), is a homodimeric extended
SDR. It catalyzes the NAD-dependent conversion of
UDP-galactose to UDP-glucose, the final step in Leloir
galactose synthesis. This subgroup is comprised of
archaeal and bacterial proteins, and has the
characteristic active site tetrad and NAD-binding motif
of the extended SDRs. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids. Extended SDRs are a diverse collection
of proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 305
Score = 28.4 bits (64), Expect = 0.87
Identities = 11/21 (52%), Positives = 14/21 (66%)
Query: 16 IFLTGGTGFMGKVLLDTLLRR 36
I +TGG GF+G L+D LL
Sbjct: 2 ILVTGGAGFIGSHLVDRLLEE 22
>gnl|CDD|187543 cd05232, UDP_G4E_4_SDR_e, UDP-glucose 4 epimerase, subgroup 4,
extended (e) SDRs. UDP-glucose 4 epimerase (aka
UDP-galactose-4-epimerase), is a homodimeric extended
SDR. It catalyzes the NAD-dependent conversion of
UDP-galactose to UDP-glucose, the final step in Leloir
galactose synthesis. This subgroup is comprised of
bacterial proteins, and includes the Staphylococcus
aureus capsular polysaccharide Cap5N, which may have a
role in the synthesis of UDP-N-acetyl-d-fucosamine.
This subgroup has the characteristic active site tetrad
and NAD-binding motif of the extended SDRs. Extended
SDRs are distinct from classical SDRs. In addition to
the Rossmann fold (alpha/beta folding pattern with a
central beta-sheet) core region typical of all SDRs,
extended SDRs have a less conserved C-terminal
extension of approximately 100 amino acids. Extended
SDRs are a diverse collection of proteins, and include
isomerases, epimerases, oxidoreductases, and lyases;
they typically have a TGXXGXXG cofactor binding motif.
SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving
as a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton
relay involving the conserved Tyr and Lys, a water
molecule stabilized by Asn, and nicotinamide. Atypical
SDRs generally lack the catalytic residues
characteristic of the SDRs, and their glycine-rich
NAD(P)-binding motif is often different from the forms
normally seen in classical or extended SDRs. Complex
(multidomain) SDRs such as ketoreductase domains of
fatty acid synthase have a GGXGXXG NAD(P)-binding motif
and an altered active site motif (YXXXN). Fungal type
ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding
motif.
Length = 303
Score = 28.5 bits (64), Expect = 0.88
Identities = 15/53 (28%), Positives = 26/53 (49%), Gaps = 3/53 (5%)
Query: 16 IFLTGGTGFMGKVLLDTLLRRFPSIHSIYILVRERKGVSPQERIEKMLDNEGP 68
+ +TG GF+G+ L+D LL R + I VR + P + ++ D +
Sbjct: 2 VLVTGANGFIGRALVDKLLSRG---EEVRIAVRNAENAEPSVVLAELPDIDSF 51
>gnl|CDD|187574 cd05264, UDP_G4E_5_SDR_e, UDP-glucose 4-epimerase (G4E), subgroup
5, extended (e) SDRs. This subgroup partially
conserves the characteristic active site tetrad and
NAD-binding motif of the extended SDRs, and has been
identified as possible UDP-glucose 4-epimerase (aka
UDP-galactose 4-epimerase), a homodimeric member of the
extended SDR family. UDP-glucose 4-epimerase catalyzes
the NAD-dependent conversion of UDP-galactose to
UDP-glucose, the final step in Leloir galactose
synthesis. Extended SDRs are distinct from classical
SDRs. In addition to the Rossmann fold (alpha/beta
folding pattern with a central beta-sheet) core region
typical of all SDRs, extended SDRs have a less
conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 300
Score = 28.4 bits (64), Expect = 0.93
Identities = 18/75 (24%), Positives = 30/75 (40%), Gaps = 7/75 (9%)
Query: 18 LTGGTGFMGKVLLDTLLRRFPSIHSIYILVRERKGVSPQERIEKMLDNEGPIFKDFANLV 77
+ GG GF+G L+D LL P + +R + P E +D +++ A+L
Sbjct: 4 IVGGNGFIGSHLVDALLEEGPQVRVF-----DRS-IPPYELPLGGVDYIKGDYENRADLE 57
Query: 78 R-LKTQRIRFIFLAT 91
L +T
Sbjct: 58 SALVGIDTVIHLAST 72
>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 = 28.1 bits (63), Expect = 1.1
Identities = 15/64 (23%), Positives = 27/64 (42%), Gaps = 4/64 (6%)
Query: 12 KDGVIFLTGGTGFMGKVLLDTLLRRFPSIHSIYILVRERKGVSPQERIEKMLDNEGPIFK 71
KD + +TG +GK +++LL +Y VR+ + + K D P+
Sbjct: 2 KDKTVLVTGANRGIGKAFVESLLAHGAK--KVYAAVRDPGSAA--HLVAKYGDKVVPLRL 57
Query: 72 DFAN 75
D +
Sbjct: 58 DVTD 61
>gnl|CDD|187562 cd05252, CDP_GD_SDR_e, CDP-D-glucose 4,6-dehydratase, extended
(e) SDRs. This subgroup contains CDP-D-glucose
4,6-dehydratase, an extended SDR, which catalyzes the
conversion of CDP-D-glucose to
CDP-4-keto-6-deoxy-D-glucose. This subgroup has the
characteristic active site tetrad and NAD-binding motif
of the extended SDRs. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids. Extended SDRs are a diverse collection
of proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 336
Score = 28.1 bits (63), Expect = 1.2
Identities = 9/25 (36%), Positives = 13/25 (52%)
Query: 10 FYKDGVIFLTGGTGFMGKVLLDTLL 34
F++ + +TG TGF G L L
Sbjct: 1 FWQGKRVLVTGHTGFKGSWLSLWLQ 25
>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 = 27.8 bits (63), Expect = 1.2
Identities = 26/122 (21%), Positives = 45/122 (36%), Gaps = 26/122 (21%)
Query: 16 IFLTGGTGFMGKVLLDTLLRRFPSIHSIYILVRERKGVSPQERIEKMLDNEGPIFKDFAN 75
+ +TGG G +G L +L+ + I + R+ I + L E K
Sbjct: 1 VLVTGGGGSIGSELCRQILKF--NPKKIILFSRDEFK---LYEIRQELRQEYNDPKLRFF 55
Query: 76 L--VR--------LKTQRIRFIF-LATL-------RFDEELKIAIRTNICATQTVVKLAK 117
+ VR ++ + +F A L E AI+TN+ T+ V + A
Sbjct: 56 IGDVRDRERLERAMEQHGVDTVFHAAALKHVPLVEYNPME---AIKTNVLGTENVAEAAI 112
Query: 118 QC 119
+
Sbjct: 113 EN 114
>gnl|CDD|177856 PLN02206, PLN02206, UDP-glucuronate decarboxylase.
Length = 442
Score = 28.0 bits (62), Expect = 1.3
Identities = 11/25 (44%), Positives = 17/25 (68%)
Query: 16 IFLTGGTGFMGKVLLDTLLRRFPSI 40
+ +TGG GF+G L+D L+ R S+
Sbjct: 122 VVVTGGAGFVGSHLVDRLMARGDSV 146
>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 = 27.9 bits (62), Expect = 1.6
Identities = 12/32 (37%), Positives = 19/32 (59%)
Query: 15 VIFLTGGTGFMGKVLLDTLLRRFPSIHSIYIL 46
V +TGG GF+G+ ++ LL R + I +L
Sbjct: 1 VCLVTGGGGFLGQHIIRLLLERKEELKEIRVL 32
>gnl|CDD|187569 cd05259, PCBER_SDR_a, phenylcoumaran benzylic ether reductase
(PCBER) like, atypical (a) SDRs. PCBER and
pinoresinol-lariciresinol reductases are
NADPH-dependent aromatic alcohol reductases, and are
atypical members of the SDR family. Other proteins in
this subgroup are identified as eugenol synthase. These
proteins contain an N-terminus characteristic of
NAD(P)-binding proteins and a small C-terminal domain
presumed to be involved in substrate binding, but they
do not have the conserved active site Tyr residue
typically found in SDRs. Numerous other members have
unknown functions. The glycine rich NADP-binding motif
in this subgroup is of 2 forms: GXGXXG and G[GA]XGXXG;
it tends to be atypical compared with the forms
generally seen in classical or extended SDRs. The usual
SDR active site tetrad is not present, but a critical
active site Lys at the usual SDR position has been
identified in various members, though other charged and
polar residues are found at this position in this
subgroup. Atypical SDR-related proteins retain the
Rossmann fold of the SDRs, but have limited sequence
identity and generally lack the catalytic properties of
the archetypical members. 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 = 282
Score = 27.7 bits (62), Expect = 1.6
Identities = 9/36 (25%), Positives = 16/36 (44%), Gaps = 2/36 (5%)
Query: 16 IFLTGGTGFMGKVLLDTLLRRFPSIHSIYILVRERK 51
I + G TG +G ++ LL ++ +L R
Sbjct: 2 IAIAGATGTLGGPIVSALLASPG--FTVTVLTRPSS 35
>gnl|CDD|212673 cd10231, YegD_like, Escherichia coli YegD, a putative chaperone
protein, and related proteins. This bacterial subfamily
includes the uncharacterized Escherichia coli YegD. It
belongs to the heat shock protein 70 (HSP70) family of
chaperones that assist in protein folding and assembly
and can direct incompetent "client" proteins towards
degradation. Typically, HSP70s have a nucleotide-binding
domain (NBD) and a substrate-binding domain (SBD). The
nucleotide sits in a deep cleft formed between the two
lobes of the NBD. The two subdomains of each lobe change
conformation between ATP-bound, ADP-bound, and
nucleotide-free states. ATP binding opens up the
substrate-binding site; substrate-binding increases the
rate of ATP hydrolysis. YegD lacks the SBD. HSP70
chaperone activity is regulated by various
co-chaperones: J-domain proteins and nucleotide exchange
factors (NEFs). Some family members are not chaperones
but instead, function as NEFs for their Hsp70 partners,
other family members function as both chaperones and
NEFs.
Length = 415
Score = 27.5 bits (62), Expect = 2.1
Identities = 8/24 (33%), Positives = 12/24 (50%), Gaps = 1/24 (4%)
Query: 15 VIFLTGGTGFMGKVLLDTLLRRFP 38
+FLTGG+ + + RFP
Sbjct: 371 RVFLTGGSSLVP-AVRQAFAARFP 393
>gnl|CDD|204268 pfam09550, DUF2376, Conserved hypothetical phage protein
(DUF2376). This entry describes a family of proteins
found exclusively in phage or in prophage regions of
bacterial genomes, including the phage-like Rhodobacter
capsulatus gene transfer agent, which packages DNA.
Length = 43
Score = 25.3 bits (56), Expect = 2.4
Identities = 8/21 (38%), Positives = 11/21 (52%)
Query: 18 LTGGTGFMGKVLLDTLLRRFP 38
G + + LD L+RRFP
Sbjct: 22 ARAGAAPLDRAGLDALMRRFP 42
>gnl|CDD|163279 TIGR03466, HpnA, hopanoid-associated sugar epimerase. The
sequences in this family are members of the pfam01370
superfamily of NAD-dependent epimerases and
dehydratases typically acting on nucleotide-sugar
substrates. The genes of the family modeled here are
generally in the same locus with genes involved in the
biosynthesis and elaboration of hopene, the cyclization
product of the polyisoprenoid squalene. This gene and
its association with hopene biosynthesis in Zymomonas
mobilis has been noted in the literature where the gene
symbol hpnA was assigned. Hopanoids are known to be
components of the plasma membrane and to have polar
sugar head groups in Z. mobilis and other species.
Length = 328
Score = 26.9 bits (60), Expect = 2.7
Identities = 16/53 (30%), Positives = 26/53 (49%), Gaps = 7/53 (13%)
Query: 14 GVIFLTGGTGFMGKVLLDTLLRRFPSIHSIYILVRERKGVSPQERIEKMLDNE 66
+ +TG TGF+G ++ LL + + +LVR S + +E LD E
Sbjct: 1 MKVLVTGATGFVGSAVVRLLLEQG---EEVRVLVRPT---SDRRNLE-GLDVE 46
>gnl|CDD|187538 cd05227, AR_SDR_e, aldehyde reductase, extended (e) SDRs. This
subgroup contains aldehyde reductase of the extended
SDR-type and related proteins. Aldehyde reductase I
(aka carbonyl reductase) is an NADP-binding SDR; it has
an NADP-binding motif consensus that is slightly
different from the canonical SDR form and lacks the Asn
of the extended SDR active site tetrad. Aldehyde
reductase I catalyzes the NADP-dependent reduction of
ethyl 4-chloro-3-oxobutanoate to ethyl
(R)-4-chloro-3-hydroxybutanoate. Extended SDRs are
distinct from classical SDRs. In addition to the
Rossmann fold (alpha/beta folding pattern with a
central beta-sheet) core region typical of all SDRs,
extended SDRs have a less conserved C-terminal
extension of approximately 100 amino acids. Extended
SDRs are a diverse collection of proteins, and include
isomerases, epimerases, oxidoreductases, and lyases;
they typically have a TGXXGXXG cofactor binding motif.
SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving
as a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton
relay involving the conserved Tyr and Lys, a water
molecule stabilized by Asn, and nicotinamide. Atypical
SDRs generally lack the catalytic residues
characteristic of the SDRs, and their glycine-rich
NAD(P)-binding motif is often different from the forms
normally seen in classical or extended SDRs. Complex
(multidomain) SDRs such as ketoreductase domains of
fatty acid synthase have a GGXGXXG NAD(P)-binding motif
and an altered active site motif (YXXXN). Fungal type
ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding
motif.
Length = 301
Score = 26.8 bits (60), Expect = 3.0
Identities = 7/22 (31%), Positives = 15/22 (68%)
Query: 15 VIFLTGGTGFMGKVLLDTLLRR 36
++ +TG TGF+ +++ LL+
Sbjct: 1 LVLVTGATGFIASHIVEQLLKA 22
>gnl|CDD|201603 pfam01118, Semialdhyde_dh, Semialdehyde dehydrogenase, NAD
binding domain. This Pfam entry contains the following
members: N-acetyl-glutamine semialdehyde dehydrogenase
(AgrC) Aspartate-semialdehyde dehydrogenase.
Length = 121
Score = 26.4 bits (59), Expect = 3.1
Identities = 10/37 (27%), Positives = 19/37 (51%), Gaps = 4/37 (10%)
Query: 14 GVIFLTGGTGFMGKVLLDTLLRRFPSIHSIYILVRER 50
++ G TG++G+ LL LL P + + ++ R
Sbjct: 3 AIV---GATGYVGQELL-RLLAEHPPLELVALVASSR 35
>gnl|CDD|221420 pfam12099, DUF3575, Protein of unknown function (DUF3575). This
family of proteins are functionally uncharacterized.
This family is only found in bacteria. Proteins in this
family are typically between 187 to 236 amino acids in
length.
Length = 186
Score = 26.4 bits (59), Expect = 3.3
Identities = 8/29 (27%), Positives = 15/29 (51%), Gaps = 5/29 (17%)
Query: 83 RIRFIFLATLRFDEEL-----KIAIRTNI 106
+IR++ L L F +A++TN+
Sbjct: 3 KIRYLLLFLLLFCSLSPARAQVVAVKTNL 31
>gnl|CDD|187550 cd05239, GDP_FS_SDR_e, GDP-fucose synthetase, extended (e) SDRs.
GDP-fucose synthetase (aka 3, 5-epimerase-4-reductase)
acts in the NADP-dependent synthesis of GDP-fucose from
GDP-mannose. Two activities have been proposed for the
same active site: epimerization and reduction. Proteins
in this subgroup are extended SDRs, which have a
characteristic active site tetrad and an NADP-binding
motif, [AT]GXXGXXG, that is a close match to the
archetypical form. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids. Extended SDRs are a diverse collection
of proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 300
Score = 26.8 bits (60), Expect = 3.8
Identities = 8/21 (38%), Positives = 12/21 (57%)
Query: 16 IFLTGGTGFMGKVLLDTLLRR 36
I +TG G +G ++ L RR
Sbjct: 2 ILVTGHRGLVGSAIVRVLARR 22
>gnl|CDD|165812 PLN02166, PLN02166, dTDP-glucose 4,6-dehydratase.
Length = 436
Score = 26.5 bits (58), Expect = 4.6
Identities = 11/21 (52%), Positives = 15/21 (71%)
Query: 16 IFLTGGTGFMGKVLLDTLLRR 36
I +TGG GF+G L+D L+ R
Sbjct: 123 IVVTGGAGFVGSHLVDKLIGR 143
>gnl|CDD|218047 pfam04367, DUF502, Protein of unknown function (DUF502).
Predicted to be an integral membrane protein.
Length = 108
Score = 25.5 bits (57), Expect = 4.7
Identities = 16/39 (41%), Positives = 22/39 (56%), Gaps = 5/39 (12%)
Query: 15 VIFLTG--GTGFMGKVLL---DTLLRRFPSIHSIYILVR 48
+IFL G F+G+ LL + LL R P + SIY V+
Sbjct: 7 LIFLVGLLARNFIGRWLLSLGERLLNRIPLVRSIYSSVK 45
>gnl|CDD|233954 TIGR02622, CDP_4_6_dhtase, CDP-glucose 4,6-dehydratase. Members
of this protein family are CDP-glucose 4,6-dehydratase
from a variety of Gram-negative and Gram-positive
bacteria. Members typically are encoded next to a gene
that encodes a glucose-1-phosphate
cytidylyltransferase, which produces the substrate,
CDP-D-glucose, used by this enzyme to produce
CDP-4-keto-6-deoxyglucose [Cell envelope, Biosynthesis
and degradation of surface polysaccharides and
lipopolysaccharides].
Length = 349
Score = 26.5 bits (59), Expect = 4.7
Identities = 7/17 (41%), Positives = 11/17 (64%)
Query: 10 FYKDGVIFLTGGTGFMG 26
F++ + +TG TGF G
Sbjct: 1 FWQGKKVLVTGHTGFKG 17
>gnl|CDD|187566 cd05256, UDP_AE_SDR_e, UDP-N-acetylglucosamine 4-epimerase,
extended (e) SDRs. This subgroup contains
UDP-N-acetylglucosamine 4-epimerase of Pseudomonas
aeruginosa, WbpP, an extended SDR, that catalyzes the
NAD+ dependent conversion of UDP-GlcNAc and UDPGalNA to
UDP-Glc and UDP-Gal. This subgroup has the
characteristic active site tetrad and NAD-binding motif
of the extended SDRs. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids. Extended SDRs are a diverse collection
of proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 304
Score = 26.4 bits (59), Expect = 4.8
Identities = 10/18 (55%), Positives = 13/18 (72%)
Query: 19 TGGTGFMGKVLLDTLLRR 36
TGG GF+G L++ LL R
Sbjct: 5 TGGAGFIGSHLVERLLER 22
>gnl|CDD|236014 PRK07418, PRK07418, acetolactate synthase 3 catalytic subunit;
Reviewed.
Length = 616
Score = 26.6 bits (59), Expect = 4.8
Identities = 7/29 (24%), Positives = 15/29 (51%), Gaps = 2/29 (6%)
Query: 45 ILVRERKGVSPQERIEKMLDNEGPIFKDF 73
+++ ER + I + L ++GP+ D
Sbjct: 530 MVISERDQLKDA--IAEALAHDGPVLIDV 556
>gnl|CDD|178484 PLN02896, PLN02896, cinnamyl-alcohol dehydrogenase.
Length = 353
Score = 26.3 bits (58), Expect = 4.9
Identities = 10/25 (40%), Positives = 18/25 (72%)
Query: 18 LTGGTGFMGKVLLDTLLRRFPSIHS 42
+TG TG++G L+ LL+R ++H+
Sbjct: 15 VTGATGYIGSWLVKLLLQRGYTVHA 39
>gnl|CDD|215370 PLN02686, PLN02686, cinnamoyl-CoA reductase.
Length = 367
Score = 26.3 bits (58), Expect = 5.3
Identities = 16/44 (36%), Positives = 21/44 (47%), Gaps = 9/44 (20%)
Query: 19 TGGTGFMGKVLLDTLLRRFPSIHSIYILVRERKGVSPQERIEKM 62
TGG F+G ++D LLR S+ R V QE EK+
Sbjct: 59 TGGVSFLGLAIVDRLLRHGYSV---------RIAVDTQEDKEKL 93
>gnl|CDD|187660 cd08957, WbmH_like_SDR_e, Bordetella bronchiseptica enzymes WbmH
and WbmG-like, extended (e) SDRs. Bordetella
bronchiseptica enzymes WbmH and WbmG, and related
proteins. This subgroup exhibits the active site tetrad
and NAD-binding motif of the extended SDR family. It
has been proposed that the active site in Bordetella
WbmG and WbmH cannot function as an epimerase, and that
it plays a role in O-antigen synthesis pathway from
UDP-2,3-diacetamido-2,3-dideoxy-l-galacturonic acid.
Extended SDRs are distinct from classical SDRs. In
addition to the Rossmann fold (alpha/beta folding
pattern with a central beta-sheet) core region typical
of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving
as a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton
relay involving the conserved Tyr and Lys, a water
molecule stabilized by Asn, and nicotinamide. Atypical
SDRs generally lack the catalytic residues
characteristic of the SDRs, and their glycine-rich
NAD(P)-binding motif is often different from the forms
normally seen in classical or extended SDRs. Complex
(multidomain) SDRs such as ketoreductase domains of
fatty acid synthase have a GGXGXXG NAD(P)-binding motif
and an altered active site motif (YXXXN). Fungal type
ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding
motif.
Length = 307
Score = 26.3 bits (58), Expect = 5.5
Identities = 9/21 (42%), Positives = 14/21 (66%)
Query: 16 IFLTGGTGFMGKVLLDTLLRR 36
+ +TGG G +G L++ LL R
Sbjct: 3 VLITGGAGQIGSHLIEHLLER 23
>gnl|CDD|187552 cd05241, 3b-HSD-like_SDR_e, 3beta-hydroxysteroid dehydrogenases
(3b-HSD)-like, extended (e) SDRs. Extended SDR family
domains belonging to this subgroup have the
characteristic active site tetrad and a fairly
well-conserved NAD(P)-binding motif. 3b-HSD catalyzes
the NAD-dependent conversion of various steroids, such
as pregnenolone to progesterone, or androstenediol to
testosterone. This subgroup includes an unusual
bifunctional 3b-HSD/C-4 decarboxylase from Arabidopsis
thaliana, and Saccharomyces cerevisiae ERG26, a
3b-HSD/C-4 decarboxylase, involved in the synthesis of
ergosterol, the major sterol of yeast. It also includes
human 3 beta-HSD/HSD3B1 and C(27) 3beta-HSD/
[3beta-hydroxy-delta(5)-C(27)-steroid oxidoreductase;
HSD3B7]. C(27) 3beta-HSD/HSD3B7 is a membrane-bound
enzyme of the endoplasmic reticulum, that catalyzes the
isomerization and oxidation of 7alpha-hydroxylated
sterol intermediates, an early step in bile acid
biosynthesis. Mutations in the human NSDHL (NAD(P)H
steroid dehydrogenase-like protein) cause CHILD
syndrome (congenital hemidysplasia with ichthyosiform
nevus and limb defects), an X-linked dominant,
male-lethal trait. Mutations in the human gene encoding
C(27) 3beta-HSD underlie a rare autosomal recessive
form of neonatal cholestasis. Extended SDRs are
distinct from classical SDRs. In addition to the
Rossmann fold (alpha/beta folding pattern with a
central beta-sheet) core region typical of all SDRs,
extended SDRs have a less conserved C-terminal
extension of approximately 100 amino acids. Extended
SDRs are a diverse collection of proteins, and include
isomerases, epimerases, oxidoreductases, and lyases;
they typically have a TGXXGXXG cofactor binding motif.
SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving
as a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton
relay involving the conserved Tyr and Lys, a water
molecule stabilized by Asn, and nicotinamide. Atypical
SDRs generally lack the catalytic residues
characteristic of the SDRs, and their glycine-rich
NAD(P)-binding motif is often different from the forms
normally seen in classical or extended SDRs. Complex
(multidomain) SDRs such as ketoreductase domains of
fatty acid sythase have a GGXGXXG NAD(P)-binding motif
and an altered active site motif (YXXXN). Fungal type
ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding
motif.
Length = 331
Score = 26.2 bits (58), Expect = 5.7
Identities = 10/18 (55%), Positives = 13/18 (72%)
Query: 19 TGGTGFMGKVLLDTLLRR 36
TGG+GF G+ L+ LL R
Sbjct: 5 TGGSGFFGERLVKQLLER 22
>gnl|CDD|131703 TIGR02655, circ_KaiC, circadian clock protein KaiC. Members of
this family are the circadian clock protein KaiC, part
of the kaiABC operon that controls circadian rhythm. It
may be universal in Cyanobacteria. Each member has two
copies of the KaiC domain (pfam06745), which is also
found in other proteins. KaiC performs
autophosphorylation and acts as its own transcriptional
repressor [Cellular processes, Other].
Length = 484
Score = 26.1 bits (57), Expect = 5.7
Identities = 12/21 (57%), Positives = 14/21 (66%), Gaps = 1/21 (4%)
Query: 10 FYKDGVIFLTGGTGFMGKVLL 30
F+KD +I TG TG GK LL
Sbjct: 260 FFKDSIILATGATG-TGKTLL 279
>gnl|CDD|181335 PRK08264, PRK08264, short chain dehydrogenase; Validated.
Length = 238
Score = 25.6 bits (57), Expect = 6.8
Identities = 8/25 (32%), Positives = 14/25 (56%)
Query: 12 KDGVIFLTGGTGFMGKVLLDTLLRR 36
K V+ +TG +G+ ++ LL R
Sbjct: 5 KGKVVLVTGANRGIGRAFVEQLLAR 29
>gnl|CDD|223640 COG0566, SpoU, rRNA methylases [Translation, ribosomal structure
and biogenesis].
Length = 260
Score = 25.7 bits (57), Expect = 7.3
Identities = 7/46 (15%), Positives = 14/46 (30%), Gaps = 2/46 (4%)
Query: 26 GKVLLDTLLRRFPSIHSIYILVRERKGVSPQERIEKMLDNEGPIFK 71
G+ + L P I I + +E + P++
Sbjct: 26 GEHAVLEALASGPKIVRILVTEGRLPRF--EELLALAAAKGIPVYV 69
>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 = 25.6 bits (57), Expect = 7.6
Identities = 11/28 (39%), Positives = 16/28 (57%)
Query: 16 IFLTGGTGFMGKVLLDTLLRRFPSIHSI 43
I +TGG GF+G + LL ++P I
Sbjct: 3 ILVTGGAGFIGSNFVRYLLNKYPDYKII 30
>gnl|CDD|99786 cd06189, flavin_oxioreductase, NAD(P)H dependent flavin
oxidoreductases use flavin as a substrate in mediating
electron transfer from iron complexes or iron proteins.
Structurally similar to ferredoxin reductases, but with
only 15% sequence identity, flavin reductases reduce
FAD, FMN, or riboflavin via NAD(P)H. Flavin is used as a
substrate, rather than a tightly bound prosthetic group
as in flavoenzymes; weaker binding is due to the absence
of a binding site for the AMP moeity of FAD.
Length = 224
Score = 25.6 bits (57), Expect = 8.5
Identities = 14/39 (35%), Positives = 20/39 (51%), Gaps = 4/39 (10%)
Query: 15 VIFLTGGTGFMG-KVLLDTLLRRFPS--IHSIYILVRER 50
+I + GGTGF K +L+ LL + IH +Y R
Sbjct: 101 LILIAGGTGFAPIKSILEHLLAQGSKRPIH-LYWGARTE 138
>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 = 25.7 bits (57), Expect = 8.6
Identities = 11/21 (52%), Positives = 13/21 (61%)
Query: 16 IFLTGGTGFMGKVLLDTLLRR 36
I +TGG GF+G L D LL
Sbjct: 3 ILITGGAGFLGSHLCDRLLED 23
>gnl|CDD|187579 cd05271, NDUFA9_like_SDR_a, NADH dehydrogenase (ubiquinone) 1
alpha subcomplex, subunit 9, 39 kDa, (NDUFA9) -like,
atypical (a) SDRs. This subgroup of extended SDR-like
proteins are atypical SDRs. They have a glycine-rich
NAD(P)-binding motif similar to the typical SDRs,
GXXGXXG, and have the YXXXK active site motif (though
not the other residues of the SDR tetrad). Members
identified include NDUFA9 (mitochondrial) and putative
nucleoside-diphosphate-sugar epimerase. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif
is often different from the forms normally seen in
classical or extended SDRs. Atypical SDRs include
biliverdin IX beta reductase (BVR-B,aka flavin
reductase), NMRa (a negative transcriptional regulator
of various fungi), progesterone 5-beta-reductase like
proteins, phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane
reductase, isoflavone reductases, and others. SDRs are
a functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. In addition to the Rossmann fold
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids, and typically have a TGXXGXXG cofactor
binding motif. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 273
Score = 25.3 bits (56), Expect = 9.0
Identities = 8/22 (36%), Positives = 16/22 (72%)
Query: 15 VIFLTGGTGFMGKVLLDTLLRR 36
V+ + G TGF+G+ +++ L +R
Sbjct: 2 VVTVFGATGFIGRYVVNRLAKR 23
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
0.330 0.146 0.429
Gapped
Lambda K H
0.267 0.0788 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,729,405
Number of extensions: 625694
Number of successful extensions: 949
Number of sequences better than 10.0: 1
Number of HSP's gapped: 942
Number of HSP's successfully gapped: 97
Length of query: 125
Length of database: 10,937,602
Length adjustment: 85
Effective length of query: 40
Effective length of database: 7,167,512
Effective search space: 286700480
Effective search space used: 286700480
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 53 (24.1 bits)