RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15786
(306 letters)
>gnl|CDD|233427 TIGR01472, gmd, GDP-mannose 4,6-dehydratase. Alternate name:
GDP-D-mannose dehydratase. This enzyme converts
GDP-mannose to GDP-4-dehydro-6-deoxy-D-mannose, the
first of three steps for the conversion of GDP-mannose
to GDP-fucose in animals, plants, and bacteria. In
bacteria, GDP-L-fucose acts as a precursor of surface
antigens such as the extracellular polysaccharide
colanic acid of E. coli. Excluded from this model are
members of the clade that score poorly because of highly
dervied (phylogenetically long-branch) sequences, e.g.
Aneurinibacillus thermoaerophilus Gmd, described as a
bifunctional GDP-mannose
4,6-dehydratase/GDP-6-deoxy-D-lyxo-4-hexulose reductase
(PUBMED:11096116) [Cell envelope, Biosynthesis and
degradation of surface polysaccharides and
lipopolysaccharides].
Length = 343
Score = 411 bits (1057), Expect = e-145
Identities = 166/224 (74%), Positives = 191/224 (85%)
Query: 48 EDGSYLAEFLISKGYEVHGIIRRSSSFNTGRIQHLYSNPASHVEGSMKLHYGDMTDSSCL 107
+DGSYLAEFL+ KGYEVHG+IRRSSSFNT RI+H+Y +P + + MKLHYGD+TDSS L
Sbjct: 11 QDGSYLAEFLLEKGYEVHGLIRRSSSFNTQRIEHIYEDPHNVNKARMKLHYGDLTDSSNL 70
Query: 108 VQIISSVQPREVYNLAAQSHVKVSFDMSEYTAEVDAVGTLRLLDAIKTCKFHHQVKFYQA 167
+II ++P E+YNLAAQSHVKVSF++ EYTA+VD +GTLRLL+A++T VKFYQA
Sbjct: 71 RRIIDEIKPTEIYNLAAQSHVKVSFEIPEYTADVDGIGTLRLLEAVRTLGLIKSVKFYQA 130
Query: 168 STSELYGKVVETPQTETTPFYPRSPYACAKLYAYWIVVNYREAYNMFACNGILFNHESPR 227
STSELYGKV E PQ ETTPFYPRSPYA AKLYA+WI VNYREAY +FA NGILFNHESPR
Sbjct: 131 STSELYGKVQEIPQNETTPFYPRSPYAAAKLYAHWITVNYREAYGLFAVNGILFNHESPR 190
Query: 228 RGENFVTRKITRSVAKISLGLMEYVQLGNLDSKRDWGHAKDYVE 271
RGENFVTRKITR+ AKI LGL E + LGNLD+KRDWGHAKDYVE
Sbjct: 191 RGENFVTRKITRAAAKIKLGLQEKLYLGNLDAKRDWGHAKDYVE 234
>gnl|CDD|187570 cd05260, GDP_MD_SDR_e, GDP-mannose 4,6 dehydratase, extended (e)
SDRs. GDP-mannose 4,6 dehydratase, a homodimeric SDR,
catalyzes the NADP(H)-dependent conversion of
GDP-(D)-mannose to GDP-4-keto, 6-deoxy-(D)-mannose in
the fucose biosynthesis pathway. These proteins have the
canonical active site triad and NAD-binding pattern,
however the active site Asn is often missing and may be
substituted with Asp. A Glu residue has been identified
as an important active site base. Extended SDRs are
distinct from classical SDRs. In addition to the
Rossmann fold (alpha/beta folding pattern with a central
beta-sheet) core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids. Extended SDRs are a
diverse collection of proteins, and include isomerases,
epimerases, oxidoreductases, and lyases; they typically
have a TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 316
Score = 397 bits (1023), Expect = e-140
Identities = 152/223 (68%), Positives = 174/223 (78%), Gaps = 7/223 (3%)
Query: 49 DGSYLAEFLISKGYEVHGIIRRSSSFNTGRIQHLYSNPASHVEGSMKLHYGDMTDSSCLV 108
DGSYLAEFL+ KGYEVHGI+RRSSSFNT RI HLY N + + LHYGD+TDSS L
Sbjct: 11 DGSYLAEFLLEKGYEVHGIVRRSSSFNTDRIDHLYIN-----KDRITLHYGDLTDSSSLR 65
Query: 109 QIISSVQPREVYNLAAQSHVKVSFDMSEYTAEVDAVGTLRLLDAIKTCKFHHQVKFYQAS 168
+ I V+P E+Y+LAAQSHVKVSFD EYTAEV+AVGTL LL+AI+ +FYQAS
Sbjct: 66 RAIEKVRPDEIYHLAAQSHVKVSFDDPEYTAEVNAVGTLNLLEAIRILGLD--ARFYQAS 123
Query: 169 TSELYGKVVETPQTETTPFYPRSPYACAKLYAYWIVVNYREAYNMFACNGILFNHESPRR 228
+SE YGKV E PQ+ETTPF PRSPYA +KLYA WI NYREAY +FA NG LFNHE PRR
Sbjct: 124 SSEEYGKVQELPQSETTPFRPRSPYAVSKLYADWITRNYREAYGLFAVNGRLFNHEGPRR 183
Query: 229 GENFVTRKITRSVAKISLGLMEYVQLGNLDSKRDWGHAKDYVE 271
GE FVTRKITR VA+I GL ++LGNLD+KRDWG A+DYVE
Sbjct: 184 GETFVTRKITRQVARIKAGLQPVLKLGNLDAKRDWGDARDYVE 226
>gnl|CDD|224014 COG1089, Gmd, GDP-D-mannose dehydratase [Cell envelope biogenesis,
outer membrane].
Length = 345
Score = 389 bits (1000), Expect = e-136
Identities = 161/225 (71%), Positives = 185/225 (82%), Gaps = 5/225 (2%)
Query: 48 EDGSYLAEFLISKGYEVHGIIRRSSSFNTGRIQHLYSNPASHVEGS-MKLHYGDMTDSSC 106
+DGSYLAE L+ KGYEVHGI RRSSSFNT RI HLY +P H+ + LHYGD+TDSS
Sbjct: 13 QDGSYLAELLLEKGYEVHGIKRRSSSFNTPRI-HLYEDP--HLNDPRLHLHYGDLTDSSN 69
Query: 107 LVQIISSVQPREVYNLAAQSHVKVSFDMSEYTAEVDAVGTLRLLDAIKTCKFHHQVKFYQ 166
L++I+ VQP E+YNLAAQSHV VSF+ EYTA+VDA+GTLRLL+AI+ + +FYQ
Sbjct: 70 LLRILEEVQPDEIYNLAAQSHVGVSFEQPEYTADVDAIGTLRLLEAIRI-LGEKKTRFYQ 128
Query: 167 ASTSELYGKVVETPQTETTPFYPRSPYACAKLYAYWIVVNYREAYNMFACNGILFNHESP 226
ASTSELYG V E PQ ETTPFYPRSPYA AKLYAYWI VNYRE+Y +FACNGILFNHESP
Sbjct: 129 ASTSELYGLVQEIPQKETTPFYPRSPYAVAKLYAYWITVNYRESYGLFACNGILFNHESP 188
Query: 227 RRGENFVTRKITRSVAKISLGLMEYVQLGNLDSKRDWGHAKDYVE 271
RGE FVTRKITR+VA+I LGL + + LGNLD+KRDWGHAKDYVE
Sbjct: 189 LRGETFVTRKITRAVARIKLGLQDKLYLGNLDAKRDWGHAKDYVE 233
>gnl|CDD|178259 PLN02653, PLN02653, GDP-mannose 4,6-dehydratase.
Length = 340
Score = 382 bits (983), Expect = e-133
Identities = 143/226 (63%), Positives = 179/226 (79%), Gaps = 4/226 (1%)
Query: 48 EDGSYLAEFLISKGYEVHGIIRRSSSFNTGRIQHLYSNPASHVEGSMKLHYGDMTDSSCL 107
+DGSYL EFL+SKGYEVHGIIRRSS+FNT R+ H+Y +P + MKLHYGD++D+S L
Sbjct: 17 QDGSYLTEFLLSKGYEVHGIIRRSSNFNTQRLDHIYIDPHPNKA-RMKLHYGDLSDASSL 75
Query: 108 VQIISSVQPREVYNLAAQSHVKVSFDMSEYTAEVDAVGTLRLLDAIKTC--KFHHQVKFY 165
+ + ++P EVYNLAAQSHV VSF+M +YTA+V A G LRLL+A++ + Q+K+Y
Sbjct: 76 RRWLDDIKPDEVYNLAAQSHVAVSFEMPDYTADVVATGALRLLEAVRLHGQETGRQIKYY 135
Query: 166 QASTSELYGKVVETPQTETTPFYPRSPYACAKLYAYWIVVNYREAYNMFACNGILFNHES 225
QA +SE+YG PQ+ETTPF+PRSPYA AK+ A+W VNYREAY +FACNGILFNHES
Sbjct: 136 QAGSSEMYGSTPP-PQSETTPFHPRSPYAVAKVAAHWYTVNYREAYGLFACNGILFNHES 194
Query: 226 PRRGENFVTRKITRSVAKISLGLMEYVQLGNLDSKRDWGHAKDYVE 271
PRRGENFVTRKITR+V +I +GL + + LGNLD+ RDWG A DYVE
Sbjct: 195 PRRGENFVTRKITRAVGRIKVGLQKKLFLGNLDASRDWGFAGDYVE 240
>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 = 227 bits (581), Expect = 2e-74
Identities = 85/225 (37%), Positives = 114/225 (50%), Gaps = 21/225 (9%)
Query: 49 DGSYLAEFLISKGYEV--HGIIRRSSSFNTGRIQHLYSNPASHVEGSMKLHYGDMTDSSC 106
GS+L L+ +GYEV G RRS S NTGRI + H GD+TD
Sbjct: 10 IGSHLVRRLLQEGYEVIVLGRRRRSESLNTGRI---------------RFHEGDLTDPDA 54
Query: 107 LVQIISSVQPREVYNLAAQSHVKVSFDMSEYTAEVDAVGTLRLLDAIKTCKFHHQVKFYQ 166
L ++++ VQP V +LAAQS V SF+ + +GTLRLL+A + +F
Sbjct: 55 LERLLAEVQPDAVIHLAAQSGVGASFEDPADFIRANVLGTLRLLEAARRAGVK---RFVF 111
Query: 167 ASTSELYGKVVETPQTETTPFYPRSPYACAKLYAYWIVVNYREAYNMFACNGILFNHESP 226
AS+SE+YG V + P TE TP P SPYA AKL A +V Y AY + A LFN P
Sbjct: 112 ASSSEVYGDVADPPITEDTPLGPLSPYAAAKLAAERLVEAYARAYGLRAVILRLFNVYGP 171
Query: 227 RRGENFVTRKITRSVAKISLGLMEYVQLGNLDSKRDWGHAKDYVE 271
+ FVT I + +I G + LG+ +RD+ + D
Sbjct: 172 GNPDPFVTHVIPALIRRILEGKPILL-LGDGTQRRDFLYVDDVAR 215
>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 = 105 bits (263), Expect = 3e-27
Identities = 56/227 (24%), Positives = 83/227 (36%), Gaps = 59/227 (25%)
Query: 50 GSYLAEFLISKGYEVHGIIRRSSSFNTGRIQHLYSNPASHVEGSMKLHYGDMTDSSCLVQ 109
GS+L L+ +G+EV I R
Sbjct: 11 GSHLVRRLLERGHEVVVIDRLDV------------------------------------- 33
Query: 110 IISSVQPREVYNLAAQSHVKVSFDMSEYTAEVDAVGTLRLLDAIKTCKFHHQVK-FYQAS 168
V +LAA V S+D + E + VGTL LL+A + VK F AS
Sbjct: 34 ---------VVHLAALVGVPASWDNPDEDFETNVVGTLNLLEAAR----KAGVKRFVYAS 80
Query: 169 TSELYGKVVETPQTETTPFYPRSPYACAKLYAYWIVVNYREAYNMFACNGILFNHESPRR 228
++ +YG P+ E TP P SPY +KL A ++ +Y E+Y + L N P +
Sbjct: 81 SASVYGSPEGLPEEEETPPRPLSPYGVSKLAAEHLLRSYGESYGLPVVILRLANVYGPGQ 140
Query: 229 GENF--VTRKITRSVAKISLGLMEYVQL-GNLDSKRDWGHAKDYVEV 272
V R + + + + G + RD+ H D V
Sbjct: 141 RPRLDGVVNDFIRRALEG-----KPLTVFGGGNQTRDFIHVDDVVRA 182
>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 = 83.4 bits (207), Expect = 2e-18
Identities = 49/163 (30%), Positives = 77/163 (47%), Gaps = 16/163 (9%)
Query: 50 GSYLAEFLISKGYEVHGIIRRSSSFNTGRIQHLYSNPASHVEGSMKLHYGDMTDSSCLVQ 109
GS+L E L+ +G+EV + + +TG+ ++L V+ ++K GD+ D +
Sbjct: 12 GSHLVERLLERGHEVIVL----DNLSTGKKENL-----PEVKPNVKFIEGDIRDDELVEF 62
Query: 110 IISSVQPREVYNLAAQSHVKVSFDMSEYTAEVDAVGTLRLLDAIKTCKFHHQVK-FYQAS 168
V V++ AAQ+ V S + EV+ +GTL LL+A + VK F AS
Sbjct: 63 AFEGVD--YVFHQAAQASVPRSIEDPIKDHEVNVLGTLNLLEAAR----KAGVKRFVYAS 116
Query: 169 TSELYGKVVETPQTETTPFYPRSPYACAKLYAYWIVVNYREAY 211
+S +YG P+ E P P SPYA +K + Y
Sbjct: 117 SSSVYGDPPYLPKDEDHPPNPLSPYAVSKYAGELYCQVFARLY 159
>gnl|CDD|130249 TIGR01181, dTDP_gluc_dehyt, dTDP-glucose 4,6-dehydratase. This
protein is related to UDP-glucose 4-epimerase (GalE) and
likewise has an NAD cofactor [Cell envelope,
Biosynthesis and degradation of surface polysaccharides
and lipopolysaccharides].
Length = 317
Score = 82.4 bits (204), Expect = 4e-18
Identities = 53/178 (29%), Positives = 85/178 (47%), Gaps = 17/178 (9%)
Query: 99 GDMTDSSCLVQIISSVQPREVYNLAAQSHVKVSFDMSEYTAEVDAVGTLRLLDAIKTCKF 158
GD+ D + ++ + QP V + AA+SHV S E + VGT LL+A+ K+
Sbjct: 57 GDIGDRELVSRLFTEHQPDAVVHFAAESHVDRSISGPAAFIETNVVGTYTLLEAV--RKY 114
Query: 159 HHQVKFYQASTSELYGKVVETPQ-TETTPFYPRSPYACAKLYAYWIVVNYREAYNMFA-- 215
H+ +F+ ST E+YG + + TETTP P SPY+ +K + +V Y Y + A
Sbjct: 115 WHEFRFHHISTDEVYGDLEKGDAFTETTPLAPSSPYSASKAASDHLVRAYHRTYGLPALI 174
Query: 216 ---CNGILFNHESPRRGENFVTRKITRSVAKISLGLMEYVQLGNLDSKRDWGHAKDYV 270
N N+ + E + IT ++A L + G+ RDW + +D+
Sbjct: 175 TRCSN----NYGPYQFPEKLIPLMITNALAGKPLPVY-----GDGQQVRDWLYVEDHC 223
>gnl|CDD|223528 COG0451, WcaG, Nucleoside-diphosphate-sugar epimerases [Cell
envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 314
Score = 81.1 bits (200), Expect = 1e-17
Identities = 55/222 (24%), Positives = 92/222 (41%), Gaps = 20/222 (9%)
Query: 50 GSYLAEFLISKGYEVHGIIRRSSSFNTGRIQHLYSNPASHVEGSMKLHYGDMTDSSCLVQ 109
GS+L E L++ G++V G+ R + + ++ D+TD + +
Sbjct: 13 GSHLVERLLAAGHDVRGLDR-------------LRDGLDPLLSGVEFVVLDLTDRDLVDE 59
Query: 110 IISSVQPREVYNLAAQSHVKVS-FDMSEYTAEVDAVGTLRLLDAIKTCKFHHQVKFYQAS 168
+ V P V +LAAQS V S +V+ GTL LL+A + +F AS
Sbjct: 60 LAKGV-PDAVIHLAAQSSVPDSNASDPAEFLDVNVDGTLNLLEAARA---AGVKRFVFAS 115
Query: 169 T-SELYGKVVETPQTET-TPFYPRSPYACAKLYAYWIVVNYREAYNMFACNGILFNHESP 226
+ S +YG P E P P +PY +KL A ++ Y Y + FN P
Sbjct: 116 SVSVVYGDPPPLPIDEDLGPPRPLNPYGVSKLAAEQLLRAYARLYGLPVVILRPFNVYGP 175
Query: 227 RRGENFVTRKITRSVAKISLGLMEYVQLGNLDSKRDWGHAKD 268
+ + ++ + ++ G V G+ RD+ + D
Sbjct: 176 GDKPDLSSGVVSAFIRQLLKGEPIIVIGGDGSQTRDFVYVDD 217
>gnl|CDD|224013 COG1088, RfbB, dTDP-D-glucose 4,6-dehydratase [Cell envelope
biogenesis, outer membrane].
Length = 340
Score = 81.1 bits (201), Expect = 2e-17
Identities = 56/198 (28%), Positives = 92/198 (46%), Gaps = 22/198 (11%)
Query: 84 SNPAS--HVEGSMKLHY--GDMTDSSCLVQIISSVQPREVYNLAAQSHVKVSFDMSEYTA 139
N + VE S + + GD+ D + ++ QP V + AA+SHV S D
Sbjct: 39 GNLENLADVEDSPRYRFVQGDICDRELVDRLFKEYQPDAVVHFAAESHVDRSIDGPAPFI 98
Query: 140 EVDAVGTLRLLDAIKTCKFHHQVKFYQASTSELYGKVVETPQ--TETTPFYPRSPYACAK 197
+ + VGT LL+A + K+ + +F+ ST E+YG + TETTP+ P SPY+ +K
Sbjct: 99 QTNVVGTYTLLEAAR--KYWGKFRFHHISTDEVYGDLGLDDDAFTETTPYNPSSPYSASK 156
Query: 198 LYAYWIVVNYREAYNMFA----CNGILFNHESPRR-GENFVTRKITRSVAKISLGLMEYV 252
+ +V Y Y + A C+ N+ P + E + I ++ L + Y
Sbjct: 157 AASDLLVRAYVRTYGLPATITRCS----NNYGPYQFPEKLIPLMIINALLGKPLPV--Y- 209
Query: 253 QLGNLDSKRDWGHAKDYV 270
G+ RDW + +D+
Sbjct: 210 --GDGLQIRDWLYVEDHC 225
>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 = 78.4 bits (194), Expect = 1e-16
Identities = 35/116 (30%), Positives = 59/116 (50%), Gaps = 4/116 (3%)
Query: 99 GDMTDSSCLVQIISSVQPREVYNLAAQSHVKVSFDMSEYTAEVDAVGTLRLLDAIKTCKF 158
GD+ D+ + ++ + V + AA+SHV S E + +GT LL+A +
Sbjct: 58 GDICDAELVDRLFEEEKIDAVIHFAAESHVDRSISDPEPFIRTNVLGTYTLLEAARK--- 114
Query: 159 HHQVKFYQASTSELYGKVVETPQ-TETTPFYPRSPYACAKLYAYWIVVNYREAYNM 213
+ +F ST E+YG +++ + TET+P P SPY+ +K A +V Y Y +
Sbjct: 115 YGVKRFVHISTDEVYGDLLDDGEFTETSPLAPTSPYSASKAAADLLVRAYHRTYGL 170
>gnl|CDD|200431 TIGR04180, EDH_00030, NAD dependent epimerase/dehydratase,
LLPSF_EDH_00030 family. This clade within the NAD
dependent epimerase/dehydratase superfamily (pfam01370)
is characterized by inclusion of its members within a
cassette of seven distinctive enzymes. These include
four genes homologous to the elements of the neuraminic
(sialic) acid biosynthesis cluster (NeuABCD), an
aminotransferase and a nucleotidyltransferase in
addition to the epimerase/dehydratase. Together it is
very likely that these enzymes direct the biosynthesis
of a nine-carbon sugar analagous to CMP-neuraminic acid.
These seven genes form the core of the cassette,
although they are often accompanied by additional genes
that may further modify the product sugar. Although this
cassette is widely distributed in bacteria, the family
nomenclature arises from the instance in Leptospira
interrogans serovar Lai, str. 56601, where it appears as
the 30th gene in the 91-gene lipopolysaccharide
biosynthesis cluster.
Length = 297
Score = 76.6 bits (189), Expect = 4e-16
Identities = 56/222 (25%), Positives = 100/222 (45%), Gaps = 13/222 (5%)
Query: 50 GSYLAEFLISKGYEVHGIIRRSSSFNTGRIQHLYSNPASHVEGSMKLHYGDMTDSSCLVQ 109
GS+L E L+ +GYEV + +S + G + V+ +++ GD+ D + +
Sbjct: 11 GSHLVEALVRQGYEVRAFVLYNSFNSWGWLDTS----PPEVKDKIEVVTGDIRDPDSVRK 66
Query: 110 IISSVQPREVYNLAAQSHVKVSFDMSEYTAEVDAVGTLRLLDAIKTCKFHHQVKFYQAST 169
+ V++LAA + S+ + + + GTL +L A + K ST
Sbjct: 67 AMKGCD--VVFHLAALIAIPYSYIAPDSYVDTNVTGTLNVLQA---ARDLGVEKVVHTST 121
Query: 170 SELYGKVVETPQTETTPFYPRSPYACAKLYAYWIVVNYREAYNMFACNGILFNHESPRRG 229
SE+YG P E P +SPY+ +K+ A + +++ ++N FN PR+
Sbjct: 122 SEVYGTAQYVPIDEKHPLQGQSPYSASKIGADQLALSFYRSFNTPVTIIRPFNTYGPRQS 181
Query: 230 ENFVTRKITRSVAKISLGLMEYVQLGNLDSKRDWGHAKDYVE 271
V I + +I+ G ++LG+L RD+ + D V
Sbjct: 182 ARAVIPTI---ITQIASG-KRRIKLGSLSPTRDFNYVTDTVR 219
>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 = 66.1 bits (162), Expect = 2e-12
Identities = 47/172 (27%), Positives = 76/172 (44%), Gaps = 31/172 (18%)
Query: 50 GSYLAEFLISKGYEVHGIIRRSSSFNTGR---IQHLYSNPASHVEGSMKLHYGDMTDSSC 106
GS+L + L+ G+EV + +F TGR I+HL +P + E D+T+
Sbjct: 13 GSHLCDRLLEDGHEVICV----DNFFTGRKRNIEHLIGHP--NFE----FIRHDVTEPL- 61
Query: 107 LVQIISSVQPREVYNLAAQ-SHVKVSFDMSEYTAEVDAVGTLRLLDAIKTCKFHHQVKFY 165
++ ++Y+LA S V ++ + T + + +GTL +L K +
Sbjct: 62 ------YLEVDQIYHLACPASPVHYQYNPIK-TLKTNVLGTLNMLGLAKRVG----ARVL 110
Query: 166 QASTSELYGKVVETPQTET-----TPFYPRSPYACAKLYAYWIVVNYREAYN 212
ASTSE+YG PQ E+ P PRS Y K A + + Y +
Sbjct: 111 LASTSEVYGDPEVHPQPESYWGNVNPIGPRSCYDEGKRVAETLCMAYHRQHG 162
>gnl|CDD|182313 PRK10217, PRK10217, dTDP-glucose 4,6-dehydratase; Provisional.
Length = 355
Score = 62.4 bits (151), Expect = 4e-11
Identities = 52/179 (29%), Positives = 81/179 (45%), Gaps = 14/179 (7%)
Query: 100 DMTDSSCLVQIISSVQPREVYNLAAQSHVKVSFDMSEYTAEVDAVGTLRLLDAIKT---- 155
D+ D + L ++ + QP V +LAA+SHV S D E + VGT LL+A +
Sbjct: 59 DICDRAELARVFTEHQPDCVMHLAAESHVDRSIDGPAAFIETNIVGTYTLLEAARAYWNA 118
Query: 156 --CKFHHQVKFYQASTSELYGKVVETPQ--TETTPFYPRSPYACAKLYAYWIVVNYREAY 211
+F+ ST E+YG + T TETTP+ P SPY+ +K + +V + Y
Sbjct: 119 LTEDKKSAFRFHHISTDEVYGDLHSTDDFFTETTPYAPSSPYSASKASSDHLVRAWLRTY 178
Query: 212 NMFACNGILFNHESPRR-GENFVTRKITRSVAKISLGLMEYVQLGNLDSKRDWGHAKDY 269
+ N+ P E + I ++A L + GN RDW + +D+
Sbjct: 179 GLPTLITNCSNNYGPYHFPEKLIPLMILNALAGKPLPVY-----GNGQQIRDWLYVEDH 232
>gnl|CDD|187558 cd05247, UDP_G4E_1_SDR_e, UDP-glucose 4 epimerase, subgroup 1,
extended (e) SDRs. UDP-glucose 4 epimerase (aka
UDP-galactose-4-epimerase), is a homodimeric extended
SDR. It catalyzes the NAD-dependent conversion of
UDP-galactose to UDP-glucose, the final step in Leloir
galactose synthesis. This subgroup has the
characteristic active site tetrad and NAD-binding motif
of the extended SDRs. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 323
Score = 61.8 bits (151), Expect = 7e-11
Identities = 51/192 (26%), Positives = 87/192 (45%), Gaps = 27/192 (14%)
Query: 50 GSYLAEFLISKGYEVHGIIRRSSSFNTGRIQHLYSNPASHVEGSMKLHYGDMTDSSCLVQ 109
GS+ L+ GY+V ++ + + G + L + ++ + GD+ D + L +
Sbjct: 12 GSHTVVELLEAGYDVV-VL---DNLSNGHREAL----PRIEKIRIEFYEGDIRDRAALDK 63
Query: 110 IISSVQPREVYNLAAQSHVKVS--FDMSEYTAEVDAVGTLRLLDAIKTCKFHHQVK-FYQ 166
+ + + V + AA V S + Y V VGTL LL+A++ H VK F
Sbjct: 64 VFAEHKIDAVIHFAALKAVGESVQKPLKYYDNNV--VGTLNLLEAMRA----HGVKNFVF 117
Query: 167 ASTSELYGKVVETPQTETTPFYPRSPYACAKLYAYWIVVNYREAYNMFACNGIL---FN- 222
+S++ +YG+ P TE P P +PY KL I+ + +A + N ++ FN
Sbjct: 118 SSSAAVYGEPETVPITEEAPLNPTNPYGRTKLMVEQILRDLAKAPGL---NYVILRYFNP 174
Query: 223 ---HESPRRGEN 231
H S GE+
Sbjct: 175 AGAHPSGLIGED 186
>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 = 61.9 bits (151), Expect = 7e-11
Identities = 31/114 (27%), Positives = 55/114 (48%), Gaps = 15/114 (13%)
Query: 50 GSYLAEFLISKGYEVHGI----IRRSSSFNTGRIQHLYSNPASHVEGSMKLHYGDMTDSS 105
GS+L+ +L+ G EV+G + F + + H+GD+ D++
Sbjct: 17 GSWLSLWLLELGAEVYGYSLDPPTSPNLFELLNLAKKIED-----------HFGDIRDAA 65
Query: 106 CLVQIISSVQPREVYNLAAQSHVKVSFDMSEYTAEVDAVGTLRLLDAIKTCKFH 159
L + I+ +P V++LAAQ V+ S+ T E + +GT+ LL+AI+
Sbjct: 66 KLRKAIAEFKPEIVFHLAAQPLVRKSYADPLETFETNVMGTVNLLEAIRAIGSV 119
>gnl|CDD|187568 cd05258, CDP_TE_SDR_e, CDP-tyvelose 2-epimerase, extended (e) SDRs.
CDP-tyvelose 2-epimerase is a tetrameric SDR that
catalyzes the conversion of CDP-D-paratose to
CDP-D-tyvelose, the last step in tyvelose biosynthesis.
This subgroup is a member of the extended SDR subfamily,
with a characteristic active site tetrad and NAD-binding
motif. Extended SDRs are distinct from classical SDRs.
In addition to the Rossmann fold (alpha/beta folding
pattern with a central beta-sheet) core region typical
of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 337
Score = 61.2 bits (149), Expect = 1e-10
Identities = 44/187 (23%), Positives = 75/187 (40%), Gaps = 32/187 (17%)
Query: 50 GSYLAEFLISKGYEVHGI--IRRSSSFNTGRIQHLYSNPASHVEGSMKLHYGDMTDSSCL 107
GS LA F + +G+EV G + R SF L A+ +G ++ +GD+ + + L
Sbjct: 13 GSNLARFFLKQGWEVIGFDNLMRRGSFGN-----LAWLKANREDGGVRFVHGDIRNRNDL 67
Query: 108 VQIISSVQPREVYNLAAQSHVKVSFDMSEYTAEVDAVGTLRLLDAIKTCKFHHQVKFYQA 167
+ + + AAQ V S E +A+GTL +L+A + + F
Sbjct: 68 EDLFE--DIDLIIHTAAQPSVTTSASSPRLDFETNALGTLNVLEAAR--QHAPNAPFIFT 123
Query: 168 STSELYG------KVVETPQ--------------TETTPF-YPRSPYACAKLYAYWIVVN 206
ST+++YG + E +E+ P + S Y +K A V
Sbjct: 124 STNKVYGDLPNYLPLEELETRYELAPEGWSPAGISESFPLDFSHSLYGASKGAADQYVQE 183
Query: 207 YREAYNM 213
Y + +
Sbjct: 184 YGRIFGL 190
>gnl|CDD|224012 COG1087, GalE, UDP-glucose 4-epimerase [Cell envelope biogenesis,
outer membrane].
Length = 329
Score = 60.7 bits (148), Expect = 2e-10
Identities = 49/191 (25%), Positives = 81/191 (42%), Gaps = 28/191 (14%)
Query: 50 GSYLAEFLISKGYEVHGIIRRSSSFNTGRIQHLYSNPASHVEGSMKLHYGDMTDSSCLVQ 109
GS+ L+ G+EV + + + G L ++ K + GD+ D + L
Sbjct: 13 GSHTVRQLLKTGHEVVVL----DNLSNGHKIAL-----LKLQF--KFYEGDLLDRALLTA 61
Query: 110 IISSVQPREVYNLAAQSHVKVSFD--MSEYTAEVDAVGTLRLLDAIKTCKFHHQVK-FYQ 166
+ + V + AA V S + Y V VGTL L++A+ VK F
Sbjct: 62 VFEENKIDAVVHFAASISVGESVQNPLKYYDNNV--VGTLNLIEAML----QTGVKKFIF 115
Query: 167 ASTSELYGKVVETPQTETTPFYPRSPYACAKLYAYWIVVNYREAYNMFACNGIL--FN-- 222
+ST+ +YG+ +P +ET+P P +PY +KL + I+ + +A IL FN
Sbjct: 116 SSTAAVYGEPTTSPISETSPLAPINPYGRSKLMSEEILRDAAKANPFKVV--ILRYFNVA 173
Query: 223 --HESPRRGEN 231
G+
Sbjct: 174 GACPDGTLGQR 184
>gnl|CDD|187567 cd05257, Arna_like_SDR_e, Arna decarboxylase_like, extended (e)
SDRs. Decarboxylase domain of ArnA. ArnA, is an enzyme
involved in the modification of outer membrane protein
lipid A of gram-negative bacteria. It is a bifunctional
enzyme that catalyzes the NAD-dependent decarboxylation
of UDP-glucuronic acid and
N-10-formyltetrahydrofolate-dependent formylation of
UDP-4-amino-4-deoxy-l-arabinose; its NAD-dependent
decaboxylating activity is in the C-terminal 360
residues. This subgroup belongs to the extended SDR
family, however the NAD binding motif is not a perfect
match and the upstream Asn of the canonical active site
tetrad is not conserved. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 316
Score = 59.6 bits (145), Expect = 3e-10
Identities = 60/233 (25%), Positives = 97/233 (41%), Gaps = 36/233 (15%)
Query: 50 GSYLAEFLISKGYEVHGIIRRSSSFNTGRIQHLYSNPASHVEGSMKLHYGDMTDSSCLVQ 109
GS+L E L+ +G+EV + +S + A H GD+ D+S +
Sbjct: 12 GSHLTERLLREGHEVRALDIYNS-----FNSWGLLDNAVHD--RFHFISGDVRDASEVEY 64
Query: 110 IISSVQPREVYNLAAQSHVKVSFDMSEYTAEVDAV-----GTLRLLDAIKTCKFHHQVKF 164
++ V++LAA + + + YTA + V GTL +L+A C + + +
Sbjct: 65 LVKKCD--VVFHLAA--LIAIPY---SYTAPLSYVETNVFGTLNVLEA--ACVLYRK-RV 114
Query: 165 YQASTSELYGKVVETPQTETTPFY----PRSPYACAKLYAYWIVVNYREAYNM-FACNGI 219
STSE+YG + P E P PRSPY+ +K A + +Y ++ + I
Sbjct: 115 VHTSTSEVYGTAQDVPIDEDHPLLYINKPRSPYSASKQGADRLAYSYGRSFGLPVT---I 171
Query: 220 L--FNHESPRRGENFVTRKITRSVAKISLGLMEYVQLGNLDSKRDWGHAKDYV 270
+ FN PR+ V I A + LG+ RD+ KD
Sbjct: 172 IRPFNTYGPRQSARAVIPTIISQRAI----GQRLINLGDGSPTRDFNFVKDTA 220
>gnl|CDD|187563 cd05253, UDP_GE_SDE_e, UDP glucuronic acid epimerase, extended (e)
SDRs. This subgroup contains UDP-D-glucuronic acid
4-epimerase, an extended SDR, which catalyzes the
conversion of UDP-alpha-D-glucuronic acid to
UDP-alpha-D-galacturonic acid. This group has the SDR's
canonical catalytic tetrad and the TGxxGxxG 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 = 332
Score = 57.3 bits (139), Expect = 2e-09
Identities = 40/149 (26%), Positives = 67/149 (44%), Gaps = 6/149 (4%)
Query: 50 GSYLAEFLISKGYEVHGIIRRSSSFNTGRIQHLYSNPASHVEGSMKLHYGDMTDSSCLVQ 109
G ++A+ L+ +G EV GI + ++ R++ G K GD+ D L +
Sbjct: 13 GFHVAKRLLERGDEVVGIDNLNDYYDV-RLKE-ARLELLGKSGGFKFVKGDLEDREALRR 70
Query: 110 IISSVQPREVYNLAAQSHVKVSFDMSEYTAEVDAVGTLRLLDAIKTCKFHHQVKFYQAST 169
+ + V +LAAQ+ V+ S + + + VG L LL+ C+ AS+
Sbjct: 71 LFKDHEFDAVIHLAAQAGVRYSLENPHAYVDSNIVGFLNLLEL---CRHFGVKHLVYASS 127
Query: 170 SELYGKVVETPQTETTPF-YPRSPYACAK 197
S +YG + P +E +P S YA K
Sbjct: 128 SSVYGLNTKMPFSEDDRVDHPISLYAATK 156
>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 = 56.2 bits (136), Expect = 5e-09
Identities = 41/168 (24%), Positives = 72/168 (42%), Gaps = 20/168 (11%)
Query: 50 GSYLAEFLISKGYEVHGIIR----RSSSFNTGRIQHLYSNPASHVEGSMKLHYGDMTDSS 105
GS+L+ +L G +V G + F + + + GD+ D +
Sbjct: 17 GSWLSLWLQELGAKVIGYSLDPPTNPNLFELANLDNK-----------ISSTRGDIRDLN 65
Query: 106 CLVQIISSVQPREVYNLAAQSHVKVSFDMSEYTAEVDAVGTLRLLDAIKTCKFHHQVK-F 164
L + I +P V++LAAQ V++S+ T E + +GT+ LL+AI+ VK
Sbjct: 66 ALREAIREYEPEIVFHLAAQPLVRLSYKDPVETFETNVMGTVNLLEAIRETGS---VKAV 122
Query: 165 YQASTSELYGKVVET-PQTETTPFYPRSPYACAKLYAYWIVVNYREAY 211
++ + Y E P PY+ +K A I+ +YR ++
Sbjct: 123 VNVTSDKCYENKEWGWGYRENDPLGGHDPYSSSKGCAELIISSYRNSF 170
>gnl|CDD|236649 PRK10084, PRK10084, dTDP-glucose 4,6 dehydratase; Provisional.
Length = 352
Score = 56.0 bits (135), Expect = 7e-09
Identities = 40/120 (33%), Positives = 55/120 (45%), Gaps = 28/120 (23%)
Query: 100 DMTDSSCLVQIISSVQPREVYNLAAQSHVKVSFDMSEYTAEVDAVGTLRLLDAI------ 153
D+ D + L +I + QP V +LAA+SHV S E + VGT LL+A
Sbjct: 58 DICDRAELDRIFAQHQPDAVMHLAAESHVDRSITGPAAFIETNIVGTYVLLEAARNYWSA 117
Query: 154 ------KTCKFHHQVKFYQASTSELYGKV-----VETPQ-----TETTPFYPRSPYACAK 197
+FHH ST E+YG + VE + TETT + P SPY+ +K
Sbjct: 118 LDEDKKNAFRFHH------ISTDEVYGDLPHPDEVENSEELPLFTETTAYAPSSPYSASK 171
>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 = 52.3 bits (126), Expect = 8e-08
Identities = 41/171 (23%), Positives = 73/171 (42%), Gaps = 21/171 (12%)
Query: 50 GSYLAEFLISKGYEVHGIIRRSSSFNTGRIQHLYSNPASHVEGSMKLHYGDMTDSSCLVQ 109
GS+L + L+ +G EV + SS I+ + N A + D+ D++
Sbjct: 12 GSHLVDRLLEEGNEVVVVDNLSSG-RRENIEPEFENKA------FRFVKRDLLDTA---- 60
Query: 110 IISSVQPR--EVYNLAAQSHVKVSFDMSEYTAEVDAVGTLRLLDAIKT--CKFHHQVKFY 165
+ V++LAA V++ + E + + T +L+A++ K ++ F
Sbjct: 61 -DKVAKKDGDTVFHLAANPDVRLGATDPDIDLEENVLATYNVLEAMRANGVK---RIVF- 115
Query: 166 QASTSELYGKVVETPQTETTPFYPRSPYACAKLYAYWIVVNYREAYNMFAC 216
AS+S +YG+ P E P P S Y +KL A ++ Y + A
Sbjct: 116 -ASSSTVYGEAKVIPTPEDYPPLPISVYGASKLAAEALISAYAHLFGFQAW 165
>gnl|CDD|213592 TIGR01179, galE, UDP-glucose-4-epimerase GalE. Alternate name:
UDPgalactose 4-epimerase This enzyme interconverts
UDP-glucose and UDP-galactose. A set of related
proteins, some of which are tentatively identified as
UDP-glucose-4-epimerase in Thermotoga maritima, Bacillus
halodurans, and several archaea, but deeply branched
from this set and lacking experimental evidence, are
excluded from This model and described by a separate
model [Energy metabolism, Sugars].
Length = 328
Score = 52.0 bits (125), Expect = 1e-07
Identities = 59/236 (25%), Positives = 100/236 (42%), Gaps = 27/236 (11%)
Query: 50 GSYLAEFLISKGYEVHGIIRRSSSFNTGRIQHLYSNPASHVEGSMKLHYGDMTDSSCLVQ 109
GS+ L+ G+EV +I + S G + L P + GD+ D L +
Sbjct: 12 GSHTVRQLLESGHEV--VILDNLS--NGSREAL---PRGERITPVTFVEGDLRDRELLDR 64
Query: 110 IISSVQPREVYNLAAQSHVKVSFD--MSEYTAEVDAVGTLRLLDAIKTCKFHHQVKFYQA 167
+ + V + A V S + Y V VGTL LL+A + KF +
Sbjct: 65 LFEEHKIDAVIHFAGLIAVGESVQKPLKYYRNNV--VGTLNLLEA---MQQAGVKKFIFS 119
Query: 168 STSELYGKVVETPQTETTPFYPRSPYACAKLYAYWIVVNYREAYNMFACNGIL--FN--- 222
S++ +YG+ P +E +P P +PY +KL + I+ + ++A ++ IL FN
Sbjct: 120 SSAAVYGEPSSIPISEDSPLGPINPYGRSKLMSEQILRDLQKADPDWSY-VILRYFNVAG 178
Query: 223 -HESPRRGENFVTRKIT---RSVAKISLGLMEYVQL-GNLDSKRDWGHAKDYVEVS 273
H S GE+ IT ++++G + + + G D +DY+ V
Sbjct: 179 AHPSGDIGED--PPGITHLIPYACQVAVGKRDKLTIFGTDYPTPDGTCVRDYIHVM 232
>gnl|CDD|165812 PLN02166, PLN02166, dTDP-glucose 4,6-dehydratase.
Length = 436
Score = 47.7 bits (113), Expect = 4e-06
Identities = 58/206 (28%), Positives = 88/206 (42%), Gaps = 38/206 (18%)
Query: 50 GSYLAEFLISKGYEVHGIIRRSSSFNTGR---IQHLYSNPASHVEGSMKLHYGDMTDSSC 106
GS+L + LI +G EV I +F TGR + HL+ NP +L D+ +
Sbjct: 133 GSHLVDKLIGRGDEVIVI----DNFFTGRKENLVHLFGNP------RFELIRHDVVEPIL 182
Query: 107 LVQIISSVQPREVYNLAA-QSHVKVSFDMSEYTAEVDAVGTLRLLDAIKTCKFHHQVKFY 165
L + ++Y+LA S V ++ + T + + +GTL +L K +F
Sbjct: 183 L-------EVDQIYHLACPASPVHYKYNPVK-TIKTNVMGTLNMLGLAKRVG----ARFL 230
Query: 166 QASTSELYGKVVETPQTET-----TPFYPRSPYACAKLYAYWIVVNYREAYNMFACNGIL 220
STSE+YG +E PQ ET P RS Y K A + ++Y + +
Sbjct: 231 LTSTSEVYGDPLEHPQKETYWGNVNPIGERSCYDEGKRTAETLAMDYHRGAGVEVRIARI 290
Query: 221 FNHESPRRG-------ENFVTRKITR 239
FN PR NFV + I +
Sbjct: 291 FNTYGPRMCLDDGRVVSNFVAQTIRK 316
>gnl|CDD|215146 PLN02260, PLN02260, probable rhamnose biosynthetic enzyme.
Length = 668
Score = 44.7 bits (106), Expect = 4e-05
Identities = 34/100 (34%), Positives = 52/100 (52%), Gaps = 9/100 (9%)
Query: 119 VYNLAAQSHVKVSFDMS-EYTAEVDAVGTLRLLDAIKTCKFHHQVK-FYQASTSELYGKV 176
+ + AAQ+HV SF S E+T + + GT LL+A CK Q++ F ST E+YG+
Sbjct: 84 IMHFAAQTHVDNSFGNSFEFT-KNNIYGTHVLLEA---CKVTGQIRRFIHVSTDEVYGET 139
Query: 177 VETP---QTETTPFYPRSPYACAKLYAYWIVVNYREAYNM 213
E E + P +PY+ K A +V+ Y +Y +
Sbjct: 140 DEDADVGNHEASQLLPTNPYSATKAGAEMLVMAYGRSYGL 179
>gnl|CDD|187539 cd05228, AR_FR_like_1_SDR_e, uncharacterized subgroup of aldehyde
reductase and flavonoid reductase related proteins,
extended (e) SDRs. This subgroup contains proteins of
unknown function related to aldehyde reductase and
flavonoid reductase of the extended SDR-type. Aldehyde
reductase I (aka carbonyl reductase) is an NADP-binding
SDR; it has an NADP-binding motif consensus that is
slightly different from the canonical SDR form and lacks
the Asn of the extended SDR active site tetrad. Aldehyde
reductase I catalyzes the NADP-dependent reduction of
ethyl 4-chloro-3-oxobutanoate to ethyl
(R)-4-chloro-3-hydroxybutanoate. The related flavonoid
reductases act in the NADP-dependent reduction of
flavonoids, ketone-containing plant secondary
metabolites. Extended SDRs are distinct from classical
SDRs. In addition to the Rossmann fold (alpha/beta
folding pattern with a central beta-sheet) core region
typical of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 318
Score = 43.0 bits (102), Expect = 8e-05
Identities = 37/157 (23%), Positives = 61/157 (38%), Gaps = 28/157 (17%)
Query: 50 GSYLAEFLISKGYEVHGIIRRSSSFNTGRIQHLYSNPASHVEGSMKLHYGDMTDSSCLVQ 109
GS L L+++GY V ++R S + + L +++ GD+TD++ L
Sbjct: 11 GSNLVRALLAQGYRVRALVRSGS--DAVLLDGL----------PVEVVEGDLTDAASLAA 58
Query: 110 IISSVQPREVYNLAAQSHVKVSFDMSEYTA--EVDAVGTLRLLDAIKTCKFHHQVK-FYQ 166
+ V++LAA S + + GT +LDA V+
Sbjct: 59 AMKGCD--RVFHLAAF----TSLWAKDRKELYRTNVEGTRNVLDAAL----EAGVRRVVH 108
Query: 167 ASTSELYGKVVETPQTETTPFYPRS---PYACAKLYA 200
S+ G + ETTP+ R Y +KL A
Sbjct: 109 TSSIAALGGPPDGRIDETTPWNERPFPNDYYRSKLLA 145
>gnl|CDD|177856 PLN02206, PLN02206, UDP-glucuronate decarboxylase.
Length = 442
Score = 43.0 bits (101), Expect = 1e-04
Identities = 53/187 (28%), Positives = 84/187 (44%), Gaps = 31/187 (16%)
Query: 50 GSYLAEFLISKGYEVHGIIRRSSSFNTGR---IQHLYSNPASHVEGSMKLHYGDMTDSSC 106
GS+L + L+++G V + +F TGR + H +SNP + +L D+ +
Sbjct: 132 GSHLVDRLMARGDSVIVV----DNFFTGRKENVMHHFSNP------NFELIRHDVVEPIL 181
Query: 107 LVQIISSVQPREVYNLAA-QSHVKVSFDMSEYTAEVDAVGTLRLLDAIKTCKFHHQVKFY 165
L + ++Y+LA S V F+ + T + + VGTL +L K +F
Sbjct: 182 L-------EVDQIYHLACPASPVHYKFNPVK-TIKTNVVGTLNMLGLAKRVG----ARFL 229
Query: 166 QASTSELYGKVVETPQTET-----TPFYPRSPYACAKLYAYWIVVNYREAYNMFACNGIL 220
STSE+YG ++ PQ ET P RS Y K A + ++Y N+ +
Sbjct: 230 LTSTSEVYGDPLQHPQVETYWGNVNPIGVRSCYDEGKRTAETLTMDYHRGANVEVRIARI 289
Query: 221 FNHESPR 227
FN PR
Sbjct: 290 FNTYGPR 296
>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 = 39.4 bits (92), Expect = 0.001
Identities = 44/151 (29%), Positives = 68/151 (45%), Gaps = 20/151 (13%)
Query: 50 GSYLAEFLISKGYEVHGIIRRSSSFNTGRIQHLYSNPA-SHVEGSMKLHYGDMTDSSCLV 108
GS+L E L+ +G++V I +F TGR +HL +P + VEGS + D + +
Sbjct: 13 GSHLIEHLLERGHQVVVI----DNFATGRREHLPDHPNLTVVEGS-------IADKALVD 61
Query: 109 QIISSVQPREVYNLAAQSHVKVSFDMSEYTAEVDAVGTLRLLDAIKTCKFHHQVKFYQAS 168
++ +P V + AA K D E T + VG ++ A K + F
Sbjct: 62 KLFGDFKPDAVVHTAAA--YKDPDDWYEDTL-TNVVGGANVVQAAKKAGVKRLIYF---Q 115
Query: 169 TSELYG-KVVETPQTETTP-FYPRSPYACAK 197
T+ YG K ++ P P P S YA +K
Sbjct: 116 TALCYGLKPMQQPIRLDHPRAPPGSSYAISK 146
>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 = 39.3 bits (92), Expect = 0.001
Identities = 39/173 (22%), Positives = 66/173 (38%), Gaps = 30/173 (17%)
Query: 50 GSYLAEFLISKGYEVHGIIRRSSSFNTGRIQHLYSNPASHVEGSMKLHYGDMTDSSCLVQ 109
G L + L+S+G EV +R + + + ++ D
Sbjct: 12 GRALVDKLLSRGEEVRIAVRNAENAEPSVVLA------------------ELPDIDSFTD 53
Query: 110 IISSVQPREVYNLAAQSHV---KVSFDMSEYTAEVDAVGTLRLLDAIKTCKFHHQVK-FY 165
+ V V +LAA+ HV + + +S+Y +V+ T RL A VK F
Sbjct: 54 LFLGVD--AVVHLAARVHVMNDQGADPLSDYR-KVNTELTRRLARAAA----RQGVKRFV 106
Query: 166 QASTSELYGK-VVETPQTETTPFYPRSPYACAKLYAYWIVVNYREAYNMFACN 217
S+ ++ G+ V P ET P P+ Y +KL A ++ + M
Sbjct: 107 FLSSVKVNGEGTVGAPFDETDPPAPQDAYGRSKLEAERALLELGASDGMEVVI 159
>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 = 38.5 bits (90), Expect = 0.002
Identities = 43/227 (18%), Positives = 85/227 (37%), Gaps = 26/227 (11%)
Query: 50 GSYLAEFLISKGYEVHGIIRRSSSFNTGRIQHLYSNPASHVEGSMKLHYGDMTDSSCLVQ 109
GS+L + L+ +G +V R Y P V+ GD + + L
Sbjct: 12 GSHLVDALLEEGPQVRVFDRSIP---------PYELPLGGVD----YIKGDYENRADLES 58
Query: 110 IISSVQPREVYNLAAQSHVKVSFDMSEYTAEVDAVGTLRLLDAIKTCKFHHQVKFYQAST 169
+ + V +LA+ ++ S + + T++LL+A + + +S
Sbjct: 59 ALVGI--DTVIHLASTTNPATSNKNPILDIQTNVAPTVQLLEACAAAGIGKII--FASSG 114
Query: 170 SELYGKVVETPQTETTPFYPRSPYACAKLYAYWIVVNYREAYNMFACNGILFN----HES 225
+YG + P +E+ P P S Y +KL + Y+ Y + + N +
Sbjct: 115 GTVYGVPEQLPISESDPTLPISSYGISKLAIEKYLRLYQYLYGLDYTVLRISNPYGPGQR 174
Query: 226 PRRGENFVTRKITRSVAKISLGLMEYVQLGNLDSKRDWGHAKDYVEV 272
P + + + + + + G+ +S RD+ + D VE
Sbjct: 175 PDGKQGVIPIALNKILRGEPIE-----IWGDGESIRDYIYIDDLVEA 216
>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 = 35.1 bits (81), Expect = 0.018
Identities = 36/150 (24%), Positives = 51/150 (34%), Gaps = 30/150 (20%)
Query: 50 GSYLAEFLISKGYEVHGIIRRSSSFNTGRIQHLYSNPASHVEGSMKLHYGDMTDSSCLVQ 109
G LA L+ +G+EV ++R + + V GD+ D
Sbjct: 11 GRALARELLEQGHEVTLLVRNTKRLSKE------DQEPVAV------VEGDLRDLD---S 55
Query: 110 IISSVQ-PREVYNLAAQSHVKVSFDMSEYTAEVDAVGTLRLLDAIKTCKFHHQVKFYQAS 168
+ +VQ V +LA + EVD GT +L+A K F S
Sbjct: 56 LSDAVQGVDVVIHLAGAPRD------TRDFCEVDVEGTRNVLEAAKE---AGVKHFIFIS 106
Query: 169 TSELYGKVVETPQTETTPFYPRSPYACAKL 198
+ YG E T P SPY K
Sbjct: 107 SLGAYG-----DLHEETEPSPSSPYLAVKA 131
>gnl|CDD|187549 cd05238, Gne_like_SDR_e, Escherichia coli Gne (a
nucleoside-diphosphate-sugar 4-epimerase)-like, extended
(e) SDRs. Nucleoside-diphosphate-sugar 4-epimerase has
the characteristic active site tetrad and NAD-binding
motif of the extended SDR, and is related to more
specifically defined epimerases such as UDP-glucose 4
epimerase (aka UDP-galactose-4-epimerase), which
catalyzes the NAD-dependent conversion of UDP-galactose
to UDP-glucose, the final step in Leloir galactose
synthesis. This subgroup includes Escherichia coli
055:H7 Gne, a UDP-GlcNAc 4-epimerase, essential for O55
antigen synthesis. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 305
Score = 35.4 bits (82), Expect = 0.029
Identities = 40/161 (24%), Positives = 67/161 (41%), Gaps = 19/161 (11%)
Query: 50 GSYLAEFLISKGYEVHGIIRRSSSFNTGRIQHLYSNPASHVEGSMKLHYGDMTDSSCLVQ 109
G LAE L+S I + + A V GD+ + L++
Sbjct: 13 GQRLAERLLSDVPNERLI-------LIDVVSPKAPSGAPRV----TQIAGDLAVPA-LIE 60
Query: 110 IISSVQPREVYNLAA--QSHVKVSFDMSEYTAEVDAVGTLRLLDAIKTCKFHHQVKFYQA 167
+++ +P V++LAA + FD+ Y VD GT LL+A++ K + +F
Sbjct: 61 ALANGRPDVVFHLAAIVSGGAEADFDLG-YRVNVD--GTRNLLEALR--KNGPKPRFVFT 115
Query: 168 STSELYGKVVETPQTETTPFYPRSPYACAKLYAYWIVVNYR 208
S+ +YG + P T+ T P S Y K ++ +Y
Sbjct: 116 SSLAVYGLPLPNPVTDHTALDPASSYGAQKAMCELLLNDYS 156
>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 = 34.8 bits (80), Expect = 0.042
Identities = 22/76 (28%), Positives = 33/76 (43%), Gaps = 15/76 (19%)
Query: 140 EVDAVGTLRLLDAIKTCKFHHQVKFYQASTS---------ELYGKVVETPQTETTPFYPR 190
EV+ GT +L+A V Y +S ++ V +TP +T+
Sbjct: 96 EVNVNGTQAVLEACVQNNVKRLV--YTSSIEVAGPNFKGRPIFNGVEDTPYEDTSTP--- 150
Query: 191 SPYACAKLYAYWIVVN 206
PYA +KL A IV+N
Sbjct: 151 -PYASSKLLAENIVLN 165
>gnl|CDD|218026 pfam04321, RmlD_sub_bind, RmlD substrate binding domain.
L-rhamnose is a saccharide required for the virulence of
some bacteria. Its precursor, dTDP-L-rhamnose, is
synthesised by four different enzymes the final one of
which is RmlD. The RmlD substrate binding domain is
responsible for binding a sugar nucleotide.
Length = 284
Score = 33.0 bits (76), Expect = 0.15
Identities = 25/100 (25%), Positives = 38/100 (38%), Gaps = 4/100 (4%)
Query: 99 GDMTDSSCLVQIISSVQPREVYNLAAQSHVKVSFDMSEYTAEVDAVGTLRLLDAIKTCKF 158
D+TD + ++ +P V N AA + V + E V+A+G L +A C
Sbjct: 33 LDLTDPEAVAALVREARPDVVVNAAAYTAVDKAESEPELAYAVNALGPGNLAEA---CA- 88
Query: 159 HHQVKFYQASTSELYGKVVETPQTETTPFYPRSPYACAKL 198
ST ++ P E P P + Y KL
Sbjct: 89 ARGAPLIHISTDYVFDGAKGGPYREDDPTGPLNVYGRTKL 128
>gnl|CDD|187581 cd05273, GME-like_SDR_e, Arabidopsis thaliana
GDP-mannose-3',5'-epimerase (GME)-like, extended (e)
SDRs. This subgroup of NDP-sugar epimerase/dehydratases
are extended SDRs; they have the characteristic active
site tetrad, and an NAD-binding motif: TGXXGXX[AG],
which is a close match to the canonical NAD-binding
motif. Members include Arabidopsis thaliana
GDP-mannose-3',5'-epimerase (GME) which catalyzes the
epimerization of two positions of GDP-alpha-D-mannose to
form GDP-beta-L-galactose. Extended SDRs are distinct
from classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 328
Score = 32.8 bits (75), Expect = 0.17
Identities = 38/185 (20%), Positives = 69/185 (37%), Gaps = 23/185 (12%)
Query: 50 GSYLAEFLISKGYEVHGIIRRSSSFNTGRIQHLYSNPASHVEGSMKLHYGDMTDSSCLVQ 109
GS+LAE L ++G+ V G +S T + H D+ + ++
Sbjct: 13 GSHLAERLKAEGHYVRGADWKSPEHMT------------QPTDDDEFHLVDLREMENCLK 60
Query: 110 IISSVQPREVYNLAAQSHVKVSFDMSEYTAEVDAVGTLRLLDAIKTCKFHHQVKFYQAST 169
V V++LAA + + + A + TL + ++ + + +F AS+
Sbjct: 61 ATEGVD--HVFHLAA-DMGGMGY-IQSNHAVIMYNNTLINFNMLEAARINGVERFLFASS 116
Query: 170 SELY-------GKVVETPQTETTPFYPRSPYACAKLYAYWIVVNYREAYNMFACNGILFN 222
+ +Y VV + + P P+ Y KL + +Y E Y + N
Sbjct: 117 ACVYPEFKQLETTVVRLREEDAWPAEPQDAYGWEKLATERLCQHYNEDYGIETRIVRFHN 176
Query: 223 HESPR 227
PR
Sbjct: 177 IYGPR 181
>gnl|CDD|187564 cd05254, dTDP_HR_like_SDR_e, dTDP-6-deoxy-L-lyxo-4-hexulose
reductase and related proteins, extended (e) SDRs.
dTDP-6-deoxy-L-lyxo-4-hexulose reductase, an extended
SDR, synthesizes dTDP-L-rhamnose from
alpha-D-glucose-1-phosphate, providing the precursor of
L-rhamnose, an essential cell wall component of many
pathogenic bacteria. This subgroup has the
characteristic active site tetrad and NADP-binding
motif. This subgroup also contains human MAT2B, the
regulatory subunit of methionine adenosyltransferase
(MAT); MAT catalyzes S-adenosylmethionine synthesis. The
human gene encoding MAT2B encodes two major splicing
variants which are induced in human cell liver cancer
and regulate HuR, an mRNA-binding protein which
stabilizes the mRNA of several cyclins, to affect cell
proliferation. Both MAT2B variants include this extended
SDR domain. Extended SDRs are distinct from classical
SDRs. In addition to the Rossmann fold (alpha/beta
folding pattern with a central beta-sheet) core region
typical of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 280
Score = 31.8 bits (73), Expect = 0.37
Identities = 24/110 (21%), Positives = 34/110 (30%), Gaps = 22/110 (20%)
Query: 50 GSYLAEFLISKGYEVHGIIRRSSSFNTGRIQHLYSNPASHVEGSMKLHYGDMTDSSCLVQ 109
G L L +GYEV G R +S D+TD + +
Sbjct: 12 GRALVRLLKERGYEVIGTGRSRASL----------------------FKLDLTDPDAVEE 49
Query: 110 IISSVQPREVYNLAAQSHVKVSFDMSEYTAEVDAVGTLRLLDAIKTCKFH 159
I +P + N AA + V E V+ + L A K
Sbjct: 50 AIRDYKPDVIINCAAYTRVDKCESDPELAYRVNVLAPENLARAAKEVGAR 99
>gnl|CDD|178326 PLN02725, PLN02725,
GDP-4-keto-6-deoxymannose-3,5-epimerase-4-reductase.
Length = 306
Score = 31.6 bits (72), Expect = 0.42
Identities = 35/142 (24%), Positives = 54/142 (38%), Gaps = 15/142 (10%)
Query: 99 GDMTDSSCLVQIISSVQPREVYNLAAQSHVKVSFDMSEYTAEVDAVGTLRLLDAIKTCKF 158
D+T + + + +P V AA+ V Y A+ L++ + +
Sbjct: 33 LDLTRQADVEAFFAKEKPTYVILAAAK--VGGIHANMTYPADFIRE-NLQIQTNVIDAAY 89
Query: 159 HHQV-KFYQASTSELYGKVVETPQTETT----PFYPRSP-YACAKLYAYWIVVN--YREA 210
H V K +S +Y K P ET P P + YA AK+ I + YR
Sbjct: 90 RHGVKKLLFLGSSCIYPKFAPQPIPETALLTGPPEPTNEWYAIAKIAG--IKMCQAYRIQ 147
Query: 211 YNMFACNGILFNHESPRRGENF 232
Y A +G+ N P +NF
Sbjct: 148 YGWDAISGMPTNLYGPH--DNF 167
>gnl|CDD|224016 COG1091, RfbD, dTDP-4-dehydrorhamnose reductase [Cell envelope
biogenesis, outer membrane].
Length = 281
Score = 31.5 bits (72), Expect = 0.50
Identities = 26/101 (25%), Positives = 39/101 (38%), Gaps = 8/101 (7%)
Query: 100 DMTDSSCLVQIISSVQPREVYNLAAQSHVKVSFDMSEYTA--EVDAVGTLRLLDAIKTCK 157
D+TD ++++I +P V N AA + V SE V+A G L A
Sbjct: 35 DITDPDAVLEVIRETRPDVVINAAA--YTAVDKAESEPELAFAVNATGAENLARA---AA 89
Query: 158 FHHQVKFYQASTSELYGKVVETPQTETTPFYPRSPYACAKL 198
+ ST ++ P ET P + Y +KL
Sbjct: 90 -EVGARLVHISTDYVFDGEKGGPYKETDTPNPLNVYGRSKL 129
>gnl|CDD|187538 cd05227, AR_SDR_e, aldehyde reductase, extended (e) SDRs. This
subgroup contains aldehyde reductase of the extended
SDR-type and related proteins. Aldehyde reductase I (aka
carbonyl reductase) is an NADP-binding SDR; it has an
NADP-binding motif consensus that is slightly different
from the canonical SDR form and lacks the Asn of the
extended SDR active site tetrad. Aldehyde reductase I
catalyzes the NADP-dependent reduction of ethyl
4-chloro-3-oxobutanoate to ethyl
(R)-4-chloro-3-hydroxybutanoate. Extended SDRs are
distinct from classical SDRs. In addition to the
Rossmann fold (alpha/beta folding pattern with a central
beta-sheet) core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids. Extended SDRs are a
diverse collection of proteins, and include isomerases,
epimerases, oxidoreductases, and lyases; they typically
have a TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 301
Score = 30.7 bits (70), Expect = 0.77
Identities = 29/116 (25%), Positives = 49/116 (42%), Gaps = 22/116 (18%)
Query: 50 GSYLAEFLISKGYEVHGIIRRSSSFNTGRIQHLYSNPASHVEGSMKLHY---GDMTDSSC 106
S++ E L+ GY+V G +R S + +++ L + +L + D+T +
Sbjct: 12 ASHIVEQLLKAGYKVRGTVRSLS--KSAKLKALL----KAAGYNDRLEFVIVDDLTAPNA 65
Query: 107 LVQIISSVQPREVYNLAAQSHVKVSFDMSEYTAEVD----AV-GTLRLLDAIKTCK 157
+ + V Y + HV F + AE D AV GTL +L+A K
Sbjct: 66 WDEALKGVD----YVI----HVASPFPFTGPDAEDDVIDPAVEGTLNVLEAAKAAG 113
>gnl|CDD|187673 cd09813, 3b-HSD-NSDHL-like_SDR_e, human NSDHL (NAD(P)H steroid
dehydrogenase-like protein)-like, extended (e) SDRs.
This subgroup includes human NSDHL and related proteins.
These proteins have the characteristic active site
tetrad of extended SDRs, and also have a close match to
their NAD(P)-binding motif. Human NSDHL is a
3beta-hydroxysteroid dehydrogenase (3 beta-HSD) which
functions in the cholesterol biosynthetic pathway. 3
beta-HSD catalyzes the oxidative conversion of delta 5-3
beta-hydroxysteroids to the delta 4-3-keto
configuration; this activity is essential for the
biosynthesis of all classes of hormonal steroids.
Mutations in the gene encoding NSDHL cause CHILD
syndrome (congenital hemidysplasia with ichthyosiform
nevus and limb defects), an X-linked dominant,
male-lethal trait. This subgroup also includes an
unusual bifunctional [3beta-hydroxysteroid dehydrogenase
(3b-HSD)/C-4 decarboxylase from Arabidopsis thaliana,
and Saccharomyces cerevisiae ERG26, a 3b-HSD/C-4
decarboxylase, involved in the synthesis of ergosterol,
the major sterol of yeast. Extended SDRs are distinct
from classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid sythase have
a GGXGXXG NAD(P)-binding motif and an altered active
site motif (YXXXN). Fungal type ketoacyl reductases have
a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 335
Score = 30.4 bits (69), Expect = 0.97
Identities = 24/102 (23%), Positives = 42/102 (41%), Gaps = 7/102 (6%)
Query: 91 EGSMKLHYGDMTDSSCLVQIISSVQPREVYNLAAQSHVKVSFDMSEYTAEVDAVGTLRLL 150
G ++ H GD+TD L + + P V++ A+ H +V+ GT ++
Sbjct: 43 SGRVQFHTGDLTDPQDLEKAFNEKGPNVVFHTASPDHGSNDDLYY----KVNVQGTRNVI 98
Query: 151 DAIKTCKFHHQVKFYQASTSELYGKVVETPQTETTPFYPRSP 192
+A + C V Y +S S ++ E+ P YP
Sbjct: 99 EACRKCGVKKLV--YTSSASVVFNGQDIINGDESLP-YPDKH 137
>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 = 29.9 bits (68), Expect = 1.1
Identities = 24/115 (20%), Positives = 39/115 (33%), Gaps = 33/115 (28%)
Query: 50 GSYLAEFLISKGYEVHGIIRRSSSFNTGRIQHLYSNPASHVEGSMKLHYGDMTDSSCLVQ 109
G ++ L+ +GY+V ++R S A+ E + GD+TD+ L
Sbjct: 12 GRHVVRELLDRGYQVRALVRDPS--------QAEKLEAAGAE----VVVGDLTDAESLAA 59
Query: 110 -------IISSVQPREVYNLAAQSHVKVSFDMSEYTAEVDAVGTLRLLDAIKTCK 157
+IS+ T VD G + L+DA K
Sbjct: 60 ALEGIDAVISAAGSGG--------------KGGPRTEAVDYDGNINLIDAAKKAG 100
>gnl|CDD|177883 PLN02240, PLN02240, UDP-glucose 4-epimerase.
Length = 352
Score = 30.3 bits (69), Expect = 1.2
Identities = 20/58 (34%), Positives = 30/58 (51%), Gaps = 7/58 (12%)
Query: 144 VGTLRLLDAIKT--CKFHHQVKFYQASTSELYGKVVETPQTETTPFYPRSPYACAKLY 199
VGT+ LL+ + CK K +S++ +YG+ E P TE P +PY KL+
Sbjct: 110 VGTINLLEVMAKHGCK-----KLVFSSSATVYGQPEEVPCTEEFPLSATNPYGRTKLF 162
>gnl|CDD|239611 cd03537, Rieske_RO_Alpha_PrnD, This alignment model represents the
N-terminal rieske domain of the oxygenase alpha subunit
of aminopyrrolnitrin oxygenase (PrnD). PrnD is a novel
Rieske N-oxygenase that catalyzes the final step in the
pyrrolnitrin biosynthetic pathway, the oxidation of the
amino group in aminopyrrolnitrin to a nitro group,
forming the antibiotic pyrrolnitrin. The biosynthesis of
pyrrolnitrin is one of the best examples of
enzyme-catalyzed arylamine oxidation. Although arylamine
oxygenases are widely distributed within the microbial
world and used in a variety of metabolic reactions, PrnD
represents one of only two known examples of arylamine
oxygenases or N-oxygenases involved in arylnitro group
formation, the other being AurF involved in aureothin
biosynthesis.
Length = 123
Score = 28.7 bits (64), Expect = 1.7
Identities = 16/58 (27%), Positives = 21/58 (36%), Gaps = 2/58 (3%)
Query: 148 RLLDAIKTCKFHHQVKFYQASTSELYGKVVETPQTETTPFYPRSP-YACAKLYAY-WI 203
R+ D C FHH Q + G + E P R P A+ Y Y W+
Sbjct: 55 RVKDGCIQCPFHHWRYDEQGQCVHIPGHSTAVRRLEPVPRGARQPTLVTAERYGYVWV 112
>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 = 1.7
Identities = 35/139 (25%), Positives = 46/139 (33%), Gaps = 37/139 (26%)
Query: 50 GSYLAEFLISKGYEVHGIIRRSSSFNTGRIQHLYSNPASHVEGSMKLHYGDMTDSSCLVQ 109
G L E L++ G++V FN GR EG + GD D
Sbjct: 13 GKALVEELLAAGHDVT-------VFNRGR------TKPDLPEGVEHIV-GDRND------ 52
Query: 110 IISSVQPREVYNLAAQSHVKVSFDMSEYTAEVDAVGTLRLLDAIKTCKFHHQVKFYQA-S 168
+ L V D YT R LDA K +VK Y S
Sbjct: 53 ------RDALEELLGGEDFDVVVDTIAYTPR-QV---ERALDAFK-----GRVKQYIFIS 97
Query: 169 TSELYGKVVETPQTETTPF 187
++ +Y K TE+TP
Sbjct: 98 SASVYLK-PGRVITESTPL 115
>gnl|CDD|226415 COG3899, COG3899, Predicted ATPase [General function prediction
only].
Length = 849
Score = 30.1 bits (68), Expect = 2.0
Identities = 12/62 (19%), Positives = 21/62 (33%), Gaps = 10/62 (16%)
Query: 4 LTSKGEFKNPFRIHLYLESRTDLEY----------AVHKIRYRIKTLEDELEEAEDGSYL 53
L K E + + LES ++ + + L + E+A + L
Sbjct: 770 LELKSEAEYELIEKILLESYILPYLLAAKNLNGIGDLYLSKELLLYLFIDAEQAVKLAEL 829
Query: 54 AE 55
AE
Sbjct: 830 AE 831
>gnl|CDD|215310 PLN02572, PLN02572, UDP-sulfoquinovose synthase.
Length = 442
Score = 29.8 bits (67), Expect = 2.2
Identities = 20/65 (30%), Positives = 31/65 (47%), Gaps = 3/65 (4%)
Query: 93 SMKLHYGDMTDSSCLVQIISSVQPREVYNLAAQSHVKVSF-DMSE--YTAEVDAVGTLRL 149
++L+ GD+ D L + S +P V + Q S D S +T + +GTL +
Sbjct: 114 EIELYVGDICDFEFLSEAFKSFEPDAVVHFGEQRSAPYSMIDRSRAVFTQHNNVIGTLNV 173
Query: 150 LDAIK 154
L AIK
Sbjct: 174 LFAIK 178
>gnl|CDD|187535 cd02266, SDR, Short-chain dehydrogenases/reductases (SDR). 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 (KR) 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 = 186
Score = 28.6 bits (64), Expect = 2.7
Identities = 17/86 (19%), Positives = 26/86 (30%), Gaps = 16/86 (18%)
Query: 119 VYNLAAQSHVKVSFDM----SEYTAEVDAVGTLRLLDAIKTCKFHHQVKFYQASTSELYG 174
V + AA D+ E + VGT RLL+A + + G
Sbjct: 35 VVHNAAILDDGRLIDLTGSRIERAIRANVVGTRRLLEAARE---------LMKAKRL--G 83
Query: 175 KVVETPQTETTPFYP-RSPYACAKLY 199
+ + P YA +K
Sbjct: 84 RFILISSVAGLFGAPGLGGYAASKAA 109
>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 = 29.0 bits (66), Expect = 2.9
Identities = 13/67 (19%), Positives = 26/67 (38%), Gaps = 6/67 (8%)
Query: 94 MKLHYGDMTDSSCLVQIISSVQPREVYNLAAQSHVKVSFDMSEYTAEV---DAVGTLRLL 150
++ GD+ D L + + V++ AA HV + + E + +GT +
Sbjct: 52 LRFFIGDVRDRERLERAMEQHGVDTVFHAAALKHVPL---VEYNPMEAIKTNVLGTENVA 108
Query: 151 DAIKTCK 157
+A
Sbjct: 109 EAAIENG 115
>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 = 28.7 bits (65), Expect = 3.3
Identities = 14/54 (25%), Positives = 26/54 (48%), Gaps = 4/54 (7%)
Query: 50 GSYLAEFLISKGYEVHGIIRRSSSFNTGRIQHLYSNPASHVEGSMKLHYGDMTD 103
GS+L + L+ +GY V +R + ++ HL + + +KL D+ D
Sbjct: 11 GSWLVKRLLQRGYTVRATVRDPG--DEKKVAHLLELEGA--KERLKLFKADLLD 60
>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 = 28.9 bits (65), Expect = 3.5
Identities = 26/106 (24%), Positives = 47/106 (44%), Gaps = 20/106 (18%)
Query: 50 GSYLAEFLISKGYEVHGIIRRSSSFNTGRIQHLYSNPASHVEGS-MKLHYGDMTDSSCLV 108
GS + L++ G+EV G+ R + A+ +E + ++H GD+ D L
Sbjct: 13 GSAVVRELVAAGHEVVGLARSDAG-------------AAKLEAAGAQVHRGDLEDLDILR 59
Query: 109 QIISSVQPREVYNLAAQSHVKVSFDMSEYTAEVDAVGTLRLLDAIK 154
+ ++ + V +LA +H FD EVD L +A++
Sbjct: 60 K--AAAEADAVIHLAF-TH---DFDNFAQACEVDRRAIEALGEALR 99
>gnl|CDD|222146 pfam13460, NAD_binding_10, NADH(P)-binding.
Length = 182
Score = 28.4 bits (64), Expect = 3.8
Identities = 7/33 (21%), Positives = 16/33 (48%)
Query: 50 GSYLAEFLISKGYEVHGIIRRSSSFNTGRIQHL 82
G L + L+++G++V + R S + +
Sbjct: 11 GRRLVKELLARGHQVTALSRNPSKAPAPGVTPV 43
>gnl|CDD|187576 cd05266, SDR_a4, atypical (a) SDRs, subgroup 4. Atypical SDRs in
this subgroup are poorly defined, one member is
identified 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 related to,
but is different from, the archetypical SDRs, GXGXXG.
This subgroup also lacks most of the characteristic
active site residues of the SDRs; however, the upstream
Ser is present at the usual place, and some potential
catalytic residues are present in place of the usual
YXXXK active site 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. 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 = 251
Score = 28.4 bits (64), Expect = 3.8
Identities = 31/154 (20%), Positives = 49/154 (31%), Gaps = 34/154 (22%)
Query: 50 GSYLAEFLISKGYEVHGIIRRSSSFNTGR---IQHLYSNPASHVEGSMKLHYGDMTDSSC 106
G LA L+++G++V G R R + L + + D+
Sbjct: 10 GQRLARQLLAQGWQVTGTTRSPEKLAADRPAGVTPL------AADLTQPGLLADVDH--- 60
Query: 107 LVQIISSVQPREVYNLAAQSHVKVSFDMSEYTAEVDAVGTLRLLDAIKTCKFHHQVKFYQ 166
V +L Y D G LLDA+ +V +
Sbjct: 61 -----------LVISLPP--------PAGSYRGGYDP-GLRALLDALAQLPAVQRVIY-- 98
Query: 167 ASTSELYGKVVETPQTETTPFYPRSPYACAKLYA 200
S++ +YG ET+P P + A L A
Sbjct: 99 LSSTGVYGDQQGEWVDETSPPNPSTESGRALLEA 132
>gnl|CDD|216560 pfam01544, CorA, CorA-like Mg2+ transporter protein. The CorA
transport system is the primary Mg2+ influx system of
Salmonella typhimurium and Escherichia coli. CorA is
virtually ubiquitous in the Bacteria and Archaea. There
are also eukaryotic relatives of this protein. The
family includes the MRS2 protein from yeast that is
thought to be an RNA splicing protein. However its
membership of this family suggests that its effect on
splicing is due to altered magnesium levels in the cell.
Length = 291
Score = 28.4 bits (64), Expect = 4.0
Identities = 22/107 (20%), Positives = 41/107 (38%), Gaps = 10/107 (9%)
Query: 2 DLLTSKGEFKNPFRIHLYLESRTDLEYAVHKIRYRIKTLEDELEEAED--GSYLAEFLIS 59
L K+P + L L+ V + ++ LE+EL+E ED L+
Sbjct: 97 RLENLGLGPKSPGDLLYLL-----LDSIVDRYFEILEKLEEELDELEDELEDSTTNELLR 151
Query: 60 KGYEVH---GIIRRSSSFNTGRIQHLYSNPASHVEGSMKLHYGDMTD 103
+ + +RRS + + L S+ ++ K + D+ D
Sbjct: 152 ELLRLRRSLVRLRRSLAPLREVLNRLLSDDGPLIDEEEKEYLRDLLD 198
>gnl|CDD|224212 COG1293, COG1293, Predicted RNA-binding protein homologous to
eukaryotic snRNP [Transcription].
Length = 564
Score = 28.5 bits (64), Expect = 4.5
Identities = 12/48 (25%), Positives = 21/48 (43%), Gaps = 4/48 (8%)
Query: 26 LEYAVHKIRYRIKTLEDELEEAE--DGSY--LAEFLISKGYEVHGIIR 69
LE + K+ +++ EDELEE E E L + + ++
Sbjct: 291 LEKELKKLENKLEKQEDELEELEKAAEELRQKGELLYANLQLIEEGLK 338
>gnl|CDD|187536 cd05193, AR_like_SDR_e, aldehyde reductase, flavonoid reductase,
and related proteins, extended (e) SDRs. This subgroup
contains aldehyde reductase and flavonoid reductase of
the extended SDR-type and related proteins. Proteins in
this subgroup have a complete SDR-type active site
tetrad and a close match to the canonical extended SDR
NADP-binding motif. Aldehyde reductase I (aka carbonyl
reductase) is an NADP-binding SDR; it catalyzes the
NADP-dependent reduction of ethyl
4-chloro-3-oxobutanoate to ethyl
(R)-4-chloro-3-hydroxybutanoate. The related flavonoid
reductases act in the NADP-dependent reduction of
flavonoids, ketone-containing plant secondary
metabolites. Extended SDRs are distinct from classical
SDRs. In addition to the Rossmann fold (alpha/beta
folding pattern with a central beta-sheet) core region
typical of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 295
Score = 28.0 bits (62), Expect = 6.3
Identities = 24/103 (23%), Positives = 41/103 (39%), Gaps = 8/103 (7%)
Query: 50 GSYLAEFLISKGYEVHGIIRRSSSFNTGRIQHLYSNPASHVEGSMKLHYGDMTDSSCLVQ 109
S++ E L+ +GY+V +R S ++ HL A G ++L D+TD +
Sbjct: 11 ASHVVEQLLERGYKVRATVRDPS--KVKKVNHLLDLDAK--PGRLELAVADLTDEQSFDE 66
Query: 110 IISSVQPREVYNLAAQSHVKVSFDMSEYTAEVDAVGTLRLLDA 152
+I V+++A + GTL L A
Sbjct: 67 VIKGCA--GVFHVATPVSFSSKDPNEVIKPAIG--GTLNALKA 105
>gnl|CDD|187565 cd05255, SQD1_like_SDR_e, UDP_sulfoquinovose_synthase (Arabidopsis
thaliana SQD1 and related proteins), extended (e) SDRs.
Arabidopsis thaliana UDP-sulfoquinovose-synthase (
SQD1), an extended SDR, catalyzes the transfer of
SO(3)(-) to UDP-glucose in the biosynthesis of plant
sulfolipids. Members of this subgroup share the
conserved SDR catalytic residues, and a partial match to
the characteristic extended-SDR NAD-binding motif.
Extended SDRs are distinct from classical SDRs. In
addition to the Rossmann fold (alpha/beta folding
pattern with a central beta-sheet) core region typical
of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 382
Score = 28.1 bits (63), Expect = 6.3
Identities = 30/116 (25%), Positives = 46/116 (39%), Gaps = 14/116 (12%)
Query: 53 LAEFLISKGYEVHGI---IRR--------SSSFNTGRIQHLYSNPASHVEGSMKLHYGDM 101
A L +G+EV + +RR S I +++ + GD
Sbjct: 16 TALHLSKRGHEVCIVDNLVRRRIDVELGLESLTPIASIHERLRAWKELTGKTIEFYVGDA 75
Query: 102 TDSSCLVQIISSVQPREVYNLAAQSHVKVSFDMSE---YTAEVDAVGTLRLLDAIK 154
D L ++++S +P V + A Q S E YT + +GTL LL AIK
Sbjct: 76 CDYEFLAELLASHEPDAVVHFAEQRSAPYSMIDREHANYTQHNNVIGTLNLLFAIK 131
>gnl|CDD|223708 COG0635, HemN, Coproporphyrinogen III oxidase and related Fe-S
oxidoreductases [Coenzyme metabolism].
Length = 416
Score = 28.0 bits (63), Expect = 6.5
Identities = 14/51 (27%), Positives = 22/51 (43%), Gaps = 4/51 (7%)
Query: 17 HLYLESRTDLEYAVHKIRYRIKTLEDELEEAEDGSYLAEFLISKGYEVHGI 67
L +E T + + + K L DE E+A+ + E L GY + I
Sbjct: 225 SLAIEPGTKF----AQRKIKGKALPDEDEKADMYELVEELLEKAGYRQYEI 271
>gnl|CDD|219308 pfam07146, DUF1389, Protein of unknown function (DUF1389). This
family consists of several hypothetical bacterial
proteins which seem to be specific to Chlamydia
pneumoniae. Members of this family are typically around
400 residues in length. The function of this family is
unknown.
Length = 311
Score = 28.1 bits (63), Expect = 6.5
Identities = 16/88 (18%), Positives = 30/88 (34%), Gaps = 16/88 (18%)
Query: 216 CNGILFNHESPRRGENFVTRKITRSVAKISLGLMEYVQLGNLDSKRDWGHAKDYVEVSSF 275
+ +F+ + + + I+ EY L N W +D VE +
Sbjct: 162 NSSTIFHPHT-----WVLAQVISEE---------EYQMLLNHARNNTWDQNQDLVE-ALK 206
Query: 276 ERIEWRDFVHTYRLYRDIGHISVTKLQK 303
+R+ + Y+ ISV L +
Sbjct: 207 DRLL-IYLDNYYQYSFSKDKISVLSLTE 233
>gnl|CDD|185103 PRK15181, PRK15181, Vi polysaccharide biosynthesis protein TviC;
Provisional.
Length = 348
Score = 27.8 bits (61), Expect = 7.4
Identities = 23/67 (34%), Positives = 31/67 (46%), Gaps = 9/67 (13%)
Query: 138 TAEVDAVGTLRLLDAIKTCKFHHQVKFYQASTSELYGKVVETPQTETTPFYPRSPYACAK 197
+A +D G L +L A + H F A++S YG + P+ E P SPYA K
Sbjct: 115 SANID--GFLNMLTAARDA---HVSSFTYAASSSTYGDHPDLPKIEERIGRPLSPYAVTK 169
Query: 198 ----LYA 200
LYA
Sbjct: 170 YVNELYA 176
>gnl|CDD|227601 COG5276, COG5276, Uncharacterized conserved protein [Function
unknown].
Length = 370
Score = 27.9 bits (62), Expect = 7.4
Identities = 18/119 (15%), Positives = 32/119 (26%), Gaps = 10/119 (8%)
Query: 79 IQHLYSNPASHVEGSMKLHYGDMTDSSCLVQIISSVQPREVYNLAAQSHVKVSFDMSE-- 136
I A V + +S+V R Y Q + D++
Sbjct: 20 ITGSDDGVAVDVHVGYAY-------VGHFGKGVSAVDVRGAYAYVGQGFILAILDITNVS 72
Query: 137 YTAEVDAVGTLRLLDAIKTCKFHHQVKFYQASTSELYGKVVETPQTET-TPFYPRSPYA 194
+ + D + + + +S L + TP + T F YA
Sbjct: 73 LQTHDVLLSVINARDLFADVRVSEEYVYVADWSSGLRIVDISTPDSPTLIGFLNTDGYA 131
>gnl|CDD|216759 pfam01878, EVE, EVE domain. This domain was formerly known as
DUF55. Crystal structures have shown that this domain is
part of the PUA superfamily. This domain has been named
EVE and is thought to be RNA-binding.
Length = 141
Score = 26.8 bits (60), Expect = 7.9
Identities = 14/47 (29%), Positives = 19/47 (40%), Gaps = 6/47 (12%)
Query: 164 FYQASTSELY----GKVVETPQTETTPFYPRSPYACAKLYAYWIVVN 206
FY + E +VV + T F P SPY K + W V+
Sbjct: 48 FYHSGCKEPGIVGIAEVVSEAYPDPTQFDPESPYYDPK--SRWYRVD 92
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
0.320 0.134 0.397
Gapped
Lambda K H
0.267 0.0728 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,339,002
Number of extensions: 1423729
Number of successful extensions: 1436
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1384
Number of HSP's successfully gapped: 73
Length of query: 306
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 209
Effective length of database: 6,635,264
Effective search space: 1386770176
Effective search space used: 1386770176
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 59 (26.5 bits)