RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16545
(600 letters)
>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 = 269 bits (690), Expect = 1e-85
Identities = 90/159 (56%), Positives = 114/159 (71%), Gaps = 3/159 (1%)
Query: 64 THDIDCVIHFAAVKAVGESMQEPLMYYKNNLIATINLLEVMKSHGVYQLVFSSSCTVYGE 123
H ID VIHFAA+KAVGES+Q+PL YY NN++ T+NLLE M++HGV VFSSS VYGE
Sbjct: 67 EHKIDAVIHFAALKAVGESVQKPLKYYDNNVVGTLNLLEAMRAHGVKNFVFSSSAAVYGE 126
Query: 124 PQFLPITEDHPTGNIKNVYGKTKHFIEEMLKDLSKAHKEWNIISLRYFNPVGAHPSGRIG 183
P+ +PITE+ P N YG+TK +E++L+DL+KA N + LRYFNP GAHPSG IG
Sbjct: 127 PETVPITEEAPLNPT-NPYGRTKLMVEQILRDLAKAP-GLNYVILRYFNPAGAHPSGLIG 184
Query: 184 EDPTKSFTNIMPYLAQVAIGSKPHFTVFGADYETEDGTG 222
EDP N++PY+ QVA+G + +FG DY T DGT
Sbjct: 185 EDPQIP-NNLIPYVLQVALGRREKLAIFGDDYPTPDGTC 222
Score = 200 bits (510), Expect = 4e-59
Identities = 107/301 (35%), Positives = 147/301 (48%), Gaps = 60/301 (19%)
Query: 202 IGSKPHFTVF--GADYETEDGTGKVVAIDNFVNSVHIGDTPCSIRAIEQFTGKKVDFYSC 259
IGS H V A Y+ VV +DN N A+ + +++FY
Sbjct: 11 IGS--HTVVELLEAGYD-------VVVLDNLSNG--------HREALPRIEKIRIEFYEG 53
Query: 260 DLVDKNRLGEIFAKHDIDCVIHFAAVKAVGESMQEPLMYYKNNLIATINLLEVMKSHGVY 319
D+ D+ L ++FA+H ID VIHFAA+KAVGES+Q+PL YY NN++ T+NLLE M++HGV
Sbjct: 54 DIRDRAALDKVFAEHKIDAVIHFAALKAVGESVQKPLKYYDNNVVGTLNLLEAMRAHGVK 113
Query: 320 QLVFSSSCTVYGEPQFLPITEDHPTGNIKNFYNLGTGQGTSVL---QLLRTFERVTGNKP 376
VFSSS VYGEP+ +PITE+ P N Y G + L Q+LR + G
Sbjct: 114 NFVFSSSAAVYGEPETVPITEEAPLNPT-NPY------GRTKLMVEQILRDLAKAPGLNY 166
Query: 377 VPYIFYNL-------GTGQGTSVLQLL--RTFERVTGNKPVPYIF---YNLGTGQGTSV- 423
V ++N G+ + L + G + IF Y T GT V
Sbjct: 167 VILRYFNPAGAHPSGLIGEDPQIPNNLIPYVLQVALGRREKLAIFGDDYP--TPDGTCVR 224
Query: 424 ------------LQLLRTFERVTGKPVPYIFYNLGTGQGTSVLQLLRTFERVTGKPVPYI 471
+ L E G YNLGTG+G SVL+++ FE+V+GKP+PY
Sbjct: 225 DYIHVVDLADAHVLALEKLENGGG----SEIYNLGTGRGYSVLEVVEAFEKVSGKPIPYE 280
Query: 472 F 472
Sbjct: 281 I 281
Score = 94.1 bits (235), Expect = 4e-21
Identities = 30/66 (45%), Positives = 46/66 (69%), Gaps = 2/66 (3%)
Query: 3 NKFYNLGTGQGTSVLQLLRTFERVTGKPVPYIVEARREGDIVSMYANTDLAQKELGWSAR 62
++ YNLGTG+G SVL+++ FE+V+GKP+PY + RR GD S+ A+ A++ELGW
Sbjct: 249 SEIYNLGTGRGYSVLEVVEAFEKVSGKPIPYEIAPRRAGDPASLVADPSKAREELGWKP- 307
Query: 63 CTHDID 68
D++
Sbjct: 308 -KRDLE 312
Score = 93.0 bits (232), Expect = 1e-20
Identities = 29/57 (50%), Positives = 41/57 (71%)
Query: 533 YNLGTGQGTSVLQLLRTFERVTGKPVPYIVEARREGDIVSMYANTDLAQRELGWSAR 589
YNLGTG+G SVL+++ FE+V+GKP+PY + RR GD S+ A+ A+ ELGW +
Sbjct: 252 YNLGTGRGYSVLEVVEAFEKVSGKPIPYEIAPRRAGDPASLVADPSKAREELGWKPK 308
Score = 56.8 bits (138), Expect = 1e-08
Identities = 18/30 (60%), Positives = 25/30 (83%)
Query: 473 YNLGTGQGTSVLQLLRTFERVTGKPVPYIF 502
YNLGTG+G SVL+++ FE+V+GKP+PY
Sbjct: 252 YNLGTGRGYSVLEVVEAFEKVSGKPIPYEI 281
>gnl|CDD|177883 PLN02240, PLN02240, UDP-glucose 4-epimerase.
Length = 352
Score = 264 bits (678), Expect = 2e-83
Identities = 97/158 (61%), Positives = 117/158 (74%), Gaps = 1/158 (0%)
Query: 65 HDIDCVIHFAAVKAVGESMQEPLMYYKNNLIATINLLEVMKSHGVYQLVFSSSCTVYGEP 124
D VIHFA +KAVGES+ +PL+YY NNL+ TINLLEVM HG +LVFSSS TVYG+P
Sbjct: 80 TRFDAVIHFAGLKAVGESVAKPLLYYDNNLVGTINLLEVMAKHGCKKLVFSSSATVYGQP 139
Query: 125 QFLPITEDHPTGNIKNVYGKTKHFIEEMLKDLSKAHKEWNIISLRYFNPVGAHPSGRIGE 184
+ +P TE+ P N YG+TK FIEE+ +D+ + EW II LRYFNPVGAHPSGRIGE
Sbjct: 140 EEVPCTEEFPLSAT-NPYGRTKLFIEEICRDIHASDPEWKIILLRYFNPVGAHPSGRIGE 198
Query: 185 DPTKSFTNIMPYLAQVAIGSKPHFTVFGADYETEDGTG 222
DP N+MPY+ QVA+G +P TVFG DY T+DGTG
Sbjct: 199 DPKGIPNNLMPYVQQVAVGRRPELTVFGNDYPTKDGTG 236
Score = 165 bits (419), Expect = 7e-46
Identities = 62/125 (49%), Positives = 81/125 (64%), Gaps = 8/125 (6%)
Query: 223 KVVAIDNFVNSVHIGDTPCSIRAIEQFTG---KKVDFYSCDLVDKNRLGEIFAKHDIDCV 279
KVV IDN NS ++R +++ G + F+ DL DK L ++FA D V
Sbjct: 31 KVVVIDNLDNSSEE-----ALRRVKELAGDLGDNLVFHKVDLRDKEALEKVFASTRFDAV 85
Query: 280 IHFAAVKAVGESMQEPLMYYKNNLIATINLLEVMKSHGVYQLVFSSSCTVYGEPQFLPIT 339
IHFA +KAVGES+ +PL+YY NNL+ TINLLEVM HG +LVFSSS TVYG+P+ +P T
Sbjct: 86 IHFAGLKAVGESVAKPLLYYDNNLVGTINLLEVMAKHGCKKLVFSSSATVYGQPEEVPCT 145
Query: 340 EDHPT 344
E+ P
Sbjct: 146 EEFPL 150
Score = 88.9 bits (221), Expect = 4e-19
Identities = 29/61 (47%), Positives = 44/61 (72%)
Query: 533 YNLGTGQGTSVLQLLRTFERVTGKPVPYIVEARREGDIVSMYANTDLAQRELGWSARCTV 592
YNLGTG+GTSVL+++ FE+ +GK +P + RR GD +YA+T+ A++ELGW A+ +
Sbjct: 268 YNLGTGKGTSVLEMVAAFEKASGKKIPLKLAPRRPGDAEEVYASTEKAEKELGWKAKYGI 327
Query: 593 K 593
Sbjct: 328 D 328
Score = 88.9 bits (221), Expect = 4e-19
Identities = 30/57 (52%), Positives = 43/57 (75%)
Query: 6 YNLGTGQGTSVLQLLRTFERVTGKPVPYIVEARREGDIVSMYANTDLAQKELGWSAR 62
YNLGTG+GTSVL+++ FE+ +GK +P + RR GD +YA+T+ A+KELGW A+
Sbjct: 268 YNLGTGKGTSVLEMVAAFEKASGKKIPLKLAPRRPGDAEEVYASTEKAEKELGWKAK 324
Score = 53.0 bits (128), Expect = 2e-07
Identities = 16/30 (53%), Positives = 23/30 (76%)
Query: 413 YNLGTGQGTSVLQLLRTFERVTGKPVPYIF 442
YNLGTG+GTSVL+++ FE+ +GK +P
Sbjct: 268 YNLGTGKGTSVLEMVAAFEKASGKKIPLKL 297
Score = 53.0 bits (128), Expect = 2e-07
Identities = 16/30 (53%), Positives = 23/30 (76%)
Query: 443 YNLGTGQGTSVLQLLRTFERVTGKPVPYIF 472
YNLGTG+GTSVL+++ FE+ +GK +P
Sbjct: 268 YNLGTGKGTSVLEMVAAFEKASGKKIPLKL 297
Score = 53.0 bits (128), Expect = 2e-07
Identities = 16/30 (53%), Positives = 23/30 (76%)
Query: 473 YNLGTGQGTSVLQLLRTFERVTGKPVPYIF 502
YNLGTG+GTSVL+++ FE+ +GK +P
Sbjct: 268 YNLGTGKGTSVLEMVAAFEKASGKKIPLKL 297
Score = 48.4 bits (116), Expect = 6e-06
Identities = 16/31 (51%), Positives = 23/31 (74%), Gaps = 1/31 (3%)
Query: 351 YNLGTGQGTSVLQLLRTFERVTGNKPVPYIF 381
YNLGTG+GTSVL+++ FE+ +G K +P
Sbjct: 268 YNLGTGKGTSVLEMVAAFEKASG-KKIPLKL 297
Score = 48.4 bits (116), Expect = 6e-06
Identities = 16/31 (51%), Positives = 23/31 (74%), Gaps = 1/31 (3%)
Query: 382 YNLGTGQGTSVLQLLRTFERVTGNKPVPYIF 412
YNLGTG+GTSVL+++ FE+ +G K +P
Sbjct: 268 YNLGTGKGTSVLEMVAAFEKASG-KKIPLKL 297
>gnl|CDD|224012 COG1087, GalE, UDP-glucose 4-epimerase [Cell envelope biogenesis,
outer membrane].
Length = 329
Score = 249 bits (639), Expect = 6e-78
Identities = 71/159 (44%), Positives = 102/159 (64%), Gaps = 3/159 (1%)
Query: 64 THDIDCVIHFAAVKAVGESMQEPLMYYKNNLIATINLLEVMKSHGVYQLVFSSSCTVYGE 123
+ ID V+HFAA +VGES+Q PL YY NN++ T+NL+E M GV + +FSS+ VYGE
Sbjct: 65 ENKIDAVVHFAASISVGESVQNPLKYYDNNVVGTLNLIEAMLQTGVKKFIFSSTAAVYGE 124
Query: 124 PQFLPITEDHPTGNIKNVYGKTKHFIEEMLKDLSKAHKEWNIISLRYFNPVGAHPSGRIG 183
P PI+E P I N YG++K EE+L+D +KA+ + ++ LRYFN GA P G +G
Sbjct: 125 PTTSPISETSPLAPI-NPYGRSKLMSEEILRDAAKANP-FKVVILRYFNVAGACPDGTLG 182
Query: 184 EDPTKSFTNIMPYLAQVAIGSKPHFTVFGADYETEDGTG 222
+ T ++P A+ A+G + +FG DY+T+DGT
Sbjct: 183 QRY-PGATLLIPVAAEAALGKRDKLFIFGDDYDTKDGTC 220
Score = 155 bits (394), Expect = 2e-42
Identities = 55/148 (37%), Positives = 77/148 (52%), Gaps = 22/148 (14%)
Query: 202 IGSKPHFTVF--GADYETEDGTGKVVAIDNFVNSVHIGDTPCSIRAIEQFTGKKVDFYSC 259
IGS H +E VV +DN N ++ ++ FY
Sbjct: 12 IGS--HTVRQLLKTGHE-------VVVLDNLSNG-----HKIALLKLQ------FKFYEG 51
Query: 260 DLVDKNRLGEIFAKHDIDCVIHFAAVKAVGESMQEPLMYYKNNLIATINLLEVMKSHGVY 319
DL+D+ L +F ++ ID V+HFAA +VGES+Q PL YY NN++ T+NL+E M GV
Sbjct: 52 DLLDRALLTAVFEENKIDAVVHFAASISVGESVQNPLKYYDNNVVGTLNLIEAMLQTGVK 111
Query: 320 QLVFSSSCTVYGEPQFLPITEDHPTGNI 347
+ +FSS+ VYGEP PI+E P I
Sbjct: 112 KFIFSSTAAVYGEPTTSPISETSPLAPI 139
Score = 90.3 bits (225), Expect = 8e-20
Identities = 23/67 (34%), Positives = 41/67 (61%), Gaps = 1/67 (1%)
Query: 6 YNLGTGQGTSVLQLLRTFERVTGKPVPYIVEARREGDIVSMYANTDLAQKELGWSARCTH 65
+NLG+G G SVL+++ ++VTG+ +P + RR GD + A++ A++ LGW
Sbjct: 250 FNLGSGNGFSVLEVIEAAKKVTGRDIPVEIAPRRAGDPAILVADSSKARQILGWQPTYD- 308
Query: 66 DIDCVIH 72
D++ +I
Sbjct: 309 DLEDIIK 315
Score = 90.3 bits (225), Expect = 9e-20
Identities = 21/57 (36%), Positives = 36/57 (63%)
Query: 533 YNLGTGQGTSVLQLLRTFERVTGKPVPYIVEARREGDIVSMYANTDLAQRELGWSAR 589
+NLG+G G SVL+++ ++VTG+ +P + RR GD + A++ A++ LGW
Sbjct: 250 FNLGSGNGFSVLEVIEAAKKVTGRDIPVEIAPRRAGDPAILVADSSKARQILGWQPT 306
Score = 55.3 bits (134), Expect = 3e-08
Identities = 12/30 (40%), Positives = 21/30 (70%)
Query: 413 YNLGTGQGTSVLQLLRTFERVTGKPVPYIF 442
+NLG+G G SVL+++ ++VTG+ +P
Sbjct: 250 FNLGSGNGFSVLEVIEAAKKVTGRDIPVEI 279
Score = 55.3 bits (134), Expect = 3e-08
Identities = 12/30 (40%), Positives = 21/30 (70%)
Query: 443 YNLGTGQGTSVLQLLRTFERVTGKPVPYIF 472
+NLG+G G SVL+++ ++VTG+ +P
Sbjct: 250 FNLGSGNGFSVLEVIEAAKKVTGRDIPVEI 279
Score = 55.3 bits (134), Expect = 3e-08
Identities = 12/30 (40%), Positives = 21/30 (70%)
Query: 473 YNLGTGQGTSVLQLLRTFERVTGKPVPYIF 502
+NLG+G G SVL+++ ++VTG+ +P
Sbjct: 250 FNLGSGNGFSVLEVIEAAKKVTGRDIPVEI 279
Score = 51.8 bits (125), Expect = 4e-07
Identities = 14/37 (37%), Positives = 23/37 (62%), Gaps = 1/37 (2%)
Query: 345 GNIKNFYNLGTGQGTSVLQLLRTFERVTGNKPVPYIF 381
G N +NLG+G G SVL+++ ++VTG + +P
Sbjct: 244 GGSNNIFNLGSGNGFSVLEVIEAAKKVTG-RDIPVEI 279
Score = 50.6 bits (122), Expect = 1e-06
Identities = 12/31 (38%), Positives = 21/31 (67%), Gaps = 1/31 (3%)
Query: 382 YNLGTGQGTSVLQLLRTFERVTGNKPVPYIF 412
+NLG+G G SVL+++ ++VTG + +P
Sbjct: 250 FNLGSGNGFSVLEVIEAAKKVTG-RDIPVEI 279
>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 = 238 bits (608), Expect = 2e-73
Identities = 91/172 (52%), Positives = 118/172 (68%), Gaps = 2/172 (1%)
Query: 51 DLAQKELGWSARCTHDIDCVIHFAAVKAVGESMQEPLMYYKNNLIATINLLEVMKSHGVY 110
DL +EL H ID VIHFA + AVGES+Q+PL YY+NN++ T+NLLE M+ GV
Sbjct: 55 DLRDRELLDRLFEEHKIDAVIHFAGLIAVGESVQKPLKYYRNNVVGTLNLLEAMQQAGVK 114
Query: 111 QLVFSSSCTVYGEPQFLPITEDHPTGNIKNVYGKTKHFIEEMLKDLSKAHKEWNIISLRY 170
+ +FSSS VYGEP +PI+ED P G I N YG++K E++L+DL KA +W+ + LRY
Sbjct: 115 KFIFSSSAAVYGEPSSIPISEDSPLGPI-NPYGRSKLMSEQILRDLQKADPDWSYVILRY 173
Query: 171 FNPVGAHPSGRIGEDPTKSFTNIMPYLAQVAIGSKPHFTVFGADYETEDGTG 222
FN GAHPSG IGEDP T+++PY QVA+G + T+FG DY T DGT
Sbjct: 174 FNVAGAHPSGDIGEDPPGI-THLIPYACQVAVGKRDKLTIFGTDYPTPDGTC 224
Score = 161 bits (409), Expect = 9e-45
Identities = 96/278 (34%), Positives = 133/278 (47%), Gaps = 47/278 (16%)
Query: 223 KVVAIDNFVNSVHIGDTPCSIRAIEQFTGKKVDFYSCDLVDKNRLGEIFAKHDIDCVIHF 282
+VV +DN N + ++ E+ T V F DL D+ L +F +H ID VIHF
Sbjct: 25 EVVILDNLSNG-----SREALPRGERIT--PVTFVEGDLRDRELLDRLFEEHKIDAVIHF 77
Query: 283 AAVKAVGESMQEPLMYYKNNLIATINLLEVMKSHGVYQLVFSSSCTVYGEPQFLPITEDH 342
A + AVGES+Q+PL YY+NN++ T+NLLE M+ GV + +FSSS VYGEP +PI+ED
Sbjct: 78 AGLIAVGESVQKPLKYYRNNVVGTLNLLEAMQQAGVKKFIFSSSAAVYGEPSSIPISEDS 137
Query: 343 PTGNIKNFYNLGTGQGTS--VLQ------------LLRTFERVTGNKPVPYIFYNLGTGQ 388
P G I N Y G + S +L+ +LR F V G P ++G
Sbjct: 138 PLGPI-NPY--GRSKLMSEQILRDLQKADPDWSYVILRYFN-VAGAHPS----GDIGEDP 189
Query: 389 GTSVLQLLRTFERVTGNKPVPYIF-YNLGTGQGTSV-------------LQLLRTFERVT 434
+ + G + IF + T GT V L L
Sbjct: 190 PGITHLIPYACQVAVGKRDKLTIFGTDYPTPDGTCVRDYIHVMDLADAHLAALEYLLNGG 249
Query: 435 GKPVPYIFYNLGTGQGTSVLQLLRTFERVTGKPVPYIF 472
G V YNLG GQG SVL+++ F++V+GK P
Sbjct: 250 GSHV----YNLGYGQGFSVLEVIEAFKKVSGKDFPVEL 283
Score = 73.9 bits (182), Expect = 2e-14
Identities = 29/72 (40%), Positives = 39/72 (54%), Gaps = 4/72 (5%)
Query: 517 LRTFERVTGKPVPYIFYNLGTGQGTSVLQLLRTFERVTGKPVPYIVEARREGDIVSMYAN 576
L G V YNLG GQG SVL+++ F++V+GK P + RR GD S+ A+
Sbjct: 242 LEYLLNGGGSHV----YNLGYGQGFSVLEVIEAFKKVSGKDFPVELAPRRPGDPASLVAD 297
Query: 577 TDLAQRELGWSA 588
+RELGW
Sbjct: 298 ASKIRRELGWQP 309
Score = 73.5 bits (181), Expect = 4e-14
Identities = 28/66 (42%), Positives = 43/66 (65%), Gaps = 1/66 (1%)
Query: 6 YNLGTGQGTSVLQLLRTFERVTGKPVPYIVEARREGDIVSMYANTDLAQKELGWSARCTH 65
YNLG GQG SVL+++ F++V+GK P + RR GD S+ A+ ++ELGW + T
Sbjct: 254 YNLGYGQGFSVLEVIEAFKKVSGKDFPVELAPRRPGDPASLVADASKIRRELGWQPKYT- 312
Query: 66 DIDCVI 71
D++ +I
Sbjct: 313 DLEEII 318
Score = 47.3 bits (113), Expect = 1e-05
Identities = 18/46 (39%), Positives = 24/46 (52%), Gaps = 4/46 (8%)
Query: 457 LRTFERVTGKPVPYIFYNLGTGQGTSVLQLLRTFERVTGKPVPYIF 502
L G V YNLG GQG SVL+++ F++V+GK P
Sbjct: 242 LEYLLNGGGSHV----YNLGYGQGFSVLEVIEAFKKVSGKDFPVEL 283
>gnl|CDD|182639 PRK10675, PRK10675, UDP-galactose-4-epimerase; Provisional.
Length = 338
Score = 215 bits (548), Expect = 1e-64
Identities = 104/235 (44%), Positives = 142/235 (60%), Gaps = 22/235 (9%)
Query: 19 LLRTFERVTGK-PVPYIVEARREGDIVSMYANTDLAQKELGWSARCTHDIDCVIHFAAVK 77
+L ER+ GK P EGDI N L + L H ID VIHFA +K
Sbjct: 40 VLPVIERLGGKHPTFV------EGDI----RNEALLTEILH-----DHAIDTVIHFAGLK 84
Query: 78 AVGESMQEPLMYYKNNLIATINLLEVMKSHGVYQLVFSSSCTVYGEPQFLPITEDHPTGN 137
AVGES+Q+PL YY NN+ T+ L+ M++ V L+FSSS TVYG+ +P E PTG
Sbjct: 85 AVGESVQKPLEYYDNNVNGTLRLISAMRAANVKNLIFSSSATVYGDQPKIPYVESFPTGT 144
Query: 138 IKNVYGKTKHFIEEMLKDLSKAHKEWNIISLRYFNPVGAHPSGRIGEDPTKSFTNIMPYL 197
++ YGK+K +E++L DL KA +W+I LRYFNPVGAHPSG +GEDP N+MPY+
Sbjct: 145 PQSPYGKSKLMVEQILTDLQKAQPDWSIALLRYFNPVGAHPSGDMGEDPQGIPNNLMPYI 204
Query: 198 AQVAIGSKPHFTVFGADYETEDGTGKVVAIDNFVNSVHIGDTPCSIRAIEQFTGK 252
AQVA+G + +FG DY TEDGTG + ++++ + + D + A+E+ K
Sbjct: 205 AQVAVGRRDSLAIFGNDYPTEDGTG----VRDYIHVMDLADG--HVAAMEKLANK 253
Score = 151 bits (382), Expect = 7e-41
Identities = 115/377 (30%), Positives = 155/377 (41%), Gaps = 105/377 (27%)
Query: 224 VVAIDNFVNSVHIGDTPCSIRAIEQFTGKKVDFYSCDLVDKNRLGEIFAKHDIDCVIHFA 283
VV +DN NS + IE+ GK F D+ ++ L EI H ID VIHFA
Sbjct: 27 VVILDNLCNS-----KRSVLPVIERLGGKHPTFVEGDIRNEALLTEILHDHAIDTVIHFA 81
Query: 284 AVKAVGESMQEPLMYYKNNLIATINLLEVMKSHGVYQLVFSSSCTVYGEPQFLPITEDHP 343
+KAVGES+Q+PL YY NN+ T+ L+ M++ V L+FSSS TVYG+ +P E P
Sbjct: 82 GLKAVGESVQKPLEYYDNNVNGTLRLISAMRAANVKNLIFSSSATVYGDQPKIPYVESFP 141
Query: 344 TGNIKNFYNLGTGQGTSVLQLLRTFERVTGNKPVPYIFYNLGTGQGTSVLQLLRTFERV- 402
TG ++ Y G S L V I +L Q + LLR F V
Sbjct: 142 TGTPQSPY------GKSKLM-------------VEQILTDLQKAQPDWSIALLRYFNPVG 182
Query: 403 ------TGNKP-------VPYIFYNLGTGQGTSVLQLLRTFERVTGKPVPYIFYNLGTGQ 449
G P +PYI + G+ S+ + G P T
Sbjct: 183 AHPSGDMGEDPQGIPNNLMPYI-AQVAVGRRDSL--------AIFGNDYP-------TED 226
Query: 450 GTSVLQLLRTFERVTGKPVPYIFYNLGTGQGTSVLQLLRTFERVTGKPVPYIFYNLGTGQ 509
GT V R + V +L G ++ +L KP +I YNLG G
Sbjct: 227 GTGV----RDYIHVM---------DLADGHVAAMEKL-------ANKPGVHI-YNLGAGV 265
Query: 510 GTSVLQLLRTFERVTGKPVPYIFYNLGTGQGTSVLQLLRTFERVTGKPVPYIVEARREGD 569
G+SVL ++ F + GKPV Y F RREGD
Sbjct: 266 GSSVLDVVNAFSKACGKPVNYHF------------------------------APRREGD 295
Query: 570 IVSMYANTDLAQRELGW 586
+ + +A+ A REL W
Sbjct: 296 LPAYWADASKADRELNW 312
Score = 65.6 bits (160), Expect = 2e-11
Identities = 28/63 (44%), Positives = 38/63 (60%), Gaps = 2/63 (3%)
Query: 6 YNLGTGQGTSVLQLLRTFERVTGKPVPYIVEARREGDIVSMYANTDLAQKELGWSARCTH 65
YNLG G G+SVL ++ F + GKPV Y RREGD+ + +A+ A +EL W R T
Sbjct: 259 YNLGAGVGSSVLDVVNAFSKACGKPVNYHFAPRREGDLPAYWADASKADRELNW--RVTR 316
Query: 66 DID 68
+D
Sbjct: 317 TLD 319
>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 = 119 bits (301), Expect = 1e-30
Identities = 50/159 (31%), Positives = 78/159 (49%), Gaps = 16/159 (10%)
Query: 65 HDIDCVIHFAAVKAVGESMQEPLMYYKNNLIATINLLEVMKSHGVYQLVFSSSCTVYGEP 124
D VIH AA VG S ++P + + N++ T+ LLE + GV + VF+SS VYG+
Sbjct: 62 VQPDAVIHLAAQSGVGASFEDPADFIRANVLGTLRLLEAARRAGVKRFVFASSSEVYGDV 121
Query: 125 QFLPITEDHPTGNIKNVYGKTKHFIEEMLKDLSKAHKEWNIISLRYFNPVGAHPSGRIGE 184
PITED P G + + Y K E +++ ++A+ + LR FN G
Sbjct: 122 ADPPITEDTPLGPL-SPYAAAKLAAERLVEAYARAYG-LRAVILRLFNVYGPG------- 172
Query: 185 DPTKSFTNIMPYLAQVAIGSKPHFTVFGADYETEDGTGK 223
+P T+++P L + + KP + G DGT +
Sbjct: 173 NPDPFVTHVIPALIRRILEGKP-ILLLG------DGTQR 204
Score = 99.7 bits (249), Expect = 1e-23
Identities = 39/102 (38%), Positives = 56/102 (54%)
Query: 244 RAIEQFTGKKVDFYSCDLVDKNRLGEIFAKHDIDCVIHFAAVKAVGESMQEPLMYYKNNL 303
R E ++ F+ DL D + L + A+ D VIH AA VG S ++P + + N+
Sbjct: 32 RRSESLNTGRIRFHEGDLTDPDALERLLAEVQPDAVIHLAAQSGVGASFEDPADFIRANV 91
Query: 304 IATINLLEVMKSHGVYQLVFSSSCTVYGEPQFLPITEDHPTG 345
+ T+ LLE + GV + VF+SS VYG+ PITED P G
Sbjct: 92 LGTLRLLEAARRAGVKRFVFASSSEVYGDVADPPITEDTPLG 133
>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 = 113 bits (286), Expect = 5e-29
Identities = 44/145 (30%), Positives = 71/145 (48%), Gaps = 11/145 (7%)
Query: 68 DCVIHFAAVKAVGESMQEPLMYYKNNLIATINLLEVMKSHGVYQLVFSSSCTVYGEPQFL 127
D V+H AA+ V S P ++ N++ T+NLLE + GV + V++SS +VYG P+ L
Sbjct: 32 DVVVHLAALVGVPASWDNPDEDFETNVVGTLNLLEAARKAGVKRFVYASSASVYGSPEGL 91
Query: 128 PITEDHPTGNIKNVYGKTKHFIEEMLKDLSKAHKEWNIISLRYFNPVGAHPSGRIGEDPT 187
P E+ P + YG +K E +L+ +++ ++ LR N G R
Sbjct: 92 PEEEETPP-RPLSPYGVSKLAAEHLLRSYGESYG-LPVVILRLANVYGPGQRPR------ 143
Query: 188 KSFTNIMPYLAQVAIGSKPHFTVFG 212
++ + A+ KP TVFG
Sbjct: 144 --LDGVVNDFIRRALEGKP-LTVFG 165
Score = 79.7 bits (197), Expect = 5e-17
Identities = 28/75 (37%), Positives = 43/75 (57%), Gaps = 1/75 (1%)
Query: 277 DCVIHFAAVKAVGESMQEPLMYYKNNLIATINLLEVMKSHGVYQLVFSSSCTVYGEPQFL 336
D V+H AA+ V S P ++ N++ T+NLLE + GV + V++SS +VYG P+ L
Sbjct: 32 DVVVHLAALVGVPASWDNPDEDFETNVVGTLNLLEAARKAGVKRFVYASSASVYGSPEGL 91
Query: 337 PITEDHPTGNIKNFY 351
P E+ P + Y
Sbjct: 92 PEEEETPP-RPLSPY 105
>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 = 97.7 bits (244), Expect = 2e-22
Identities = 71/261 (27%), Positives = 115/261 (44%), Gaps = 47/261 (18%)
Query: 224 VVAIDNFVNSVHIGDTPCSIRAIEQFTGKKVDFYSCDLVDKNRLGEIFAKHDIDCVIHFA 283
V+ +DN + + V F D+ D + F +D V H A
Sbjct: 26 VIVLDNLSTG--------KKENLPEVKPN-VKFIEGDIRDDELVEFAF--EGVDYVFHQA 74
Query: 284 AVKAVGESMQEPLMYYKNNLIATINLLEVMKSHGVYQLVFSSSCTVYGEPQFLPITEDHP 343
A +V S+++P+ ++ N++ T+NLLE + GV + V++SS +VYG+P +LP EDHP
Sbjct: 75 AQASVPRSIEDPIKDHEVNVLGTLNLLEAARKAGVKRFVYASSSSVYGDPPYLPKDEDHP 134
Query: 344 TGNIKNFYNLGTGQGTSVL--QLLRTFERVTGNKPVPYIFYNL-GTGQGTS-----VLQL 395
N + Y + + + F R+ G V ++N+ G Q + V+
Sbjct: 135 -PNPLSPYAV-----SKYAGELYCQVFARLYGLPTVSLRYFNVYGPRQDPNGGYAAVIP- 187
Query: 396 LRTF-ERVTGNKPVPYIFYNLGTGQGT-------SVLQ--LLRTFERVTGKPVPYIFYNL 445
F ER +P P I+ G G+ T V++ LL G+ YN+
Sbjct: 188 --IFIERALKGEP-PTIY---GDGEQTRDFTYVEDVVEANLLAATAGAGGE-----VYNI 236
Query: 446 GTGQGTSVLQLLRTFERVTGK 466
GTG+ TSV +L + GK
Sbjct: 237 GTGKRTSVNELAELIREILGK 257
Score = 96.9 bits (242), Expect = 4e-22
Identities = 53/172 (30%), Positives = 90/172 (52%), Gaps = 13/172 (7%)
Query: 49 NTDLAQKELGWSARCTHDIDCVIHFAAVKAVGESMQEPLMYYKNNLIATINLLEVMKSHG 108
D+ EL +D V H AA +V S+++P+ ++ N++ T+NLLE + G
Sbjct: 51 EGDIRDDELV--EFAFEGVDYVFHQAAQASVPRSIEDPIKDHEVNVLGTLNLLEAARKAG 108
Query: 109 VYQLVFSSSCTVYGEPQFLPITEDHPTGNIKNVYGKTKHFIEEMLKDLSKAHK-EWNIIS 167
V + V++SS +VYG+P +LP EDHP N + Y +K+ E + ++ + +S
Sbjct: 109 VKRFVYASSSSVYGDPPYLPKDEDHP-PNPLSPYAVSKYAGELYCQVFARLYGLPT--VS 165
Query: 168 LRYFNPVGAHPSGRIGEDPTKSFTNIMPYLAQVAIGSKPHFTVFGADYETED 219
LRYFN G P +DP + ++P + A+ +P T++G +T D
Sbjct: 166 LRYFNVYG--P----RQDPNGGYAAVIPIFIERALKGEP-PTIYGDGEQTRD 210
Score = 51.8 bits (125), Expect = 4e-07
Identities = 21/65 (32%), Positives = 32/65 (49%), Gaps = 2/65 (3%)
Query: 533 YNLGTGQGTSVLQLLRTFERVTGKPVPYIVEARREGDIVSMYANTDLAQRELGWSARCTV 592
YN+GTG+ TSV +L + GK + + R GD+ A+ A++ LGW + V
Sbjct: 234 YNIGTGKRTSVNELAELIREILGKELEPVYAPPRPGDVRHSLADISKAKKLLGWEPK--V 291
Query: 593 KISGG 597
G
Sbjct: 292 SFEEG 296
Score = 51.5 bits (124), Expect = 6e-07
Identities = 20/60 (33%), Positives = 31/60 (51%)
Query: 3 NKFYNLGTGQGTSVLQLLRTFERVTGKPVPYIVEARREGDIVSMYANTDLAQKELGWSAR 62
+ YN+GTG+ TSV +L + GK + + R GD+ A+ A+K LGW +
Sbjct: 231 GEVYNIGTGKRTSVNELAELIREILGKELEPVYAPPRPGDVRHSLADISKAKKLLGWEPK 290
Score = 30.3 bits (69), Expect = 2.5
Identities = 11/28 (39%), Positives = 16/28 (57%)
Query: 351 YNLGTGQGTSVLQLLRTFERVTGNKPVP 378
YN+GTG+ TSV +L + G + P
Sbjct: 234 YNIGTGKRTSVNELAELIREILGKELEP 261
Score = 30.3 bits (69), Expect = 2.5
Identities = 11/28 (39%), Positives = 16/28 (57%)
Query: 382 YNLGTGQGTSVLQLLRTFERVTGNKPVP 409
YN+GTG+ TSV +L + G + P
Sbjct: 234 YNIGTGKRTSVNELAELIREILGKELEP 261
>gnl|CDD|223528 COG0451, WcaG, Nucleoside-diphosphate-sugar epimerases [Cell
envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 314
Score = 94.6 bits (235), Expect = 2e-21
Identities = 46/163 (28%), Positives = 74/163 (45%), Gaps = 10/163 (6%)
Query: 59 WSARCTHDIDCVIHFAAVKAVGESM-QEPLMYYKNNLIATINLLEVMKSHGVYQLVFSSS 117
D VIH AA +V +S +P + N+ T+NLLE ++ GV + VF+SS
Sbjct: 57 VDELAKGVPDAVIHLAAQSSVPDSNASDPAEFLDVNVDGTLNLLEAARAAGVKRFVFASS 116
Query: 118 C-TVYGEPQFLPITEDHPTGNIKNVYGKTKHFIEEMLKDLSKAHKEWNIISLRYFNPVGA 176
VYG+P LPI ED N YG +K E++L+ ++ + ++ LR FN G
Sbjct: 117 VSVVYGDPPPLPIDEDLGPPRPLNPYGVSKLAAEQLLRAYARLYG-LPVVILRPFNVYGP 175
Query: 177 HPSGRIGEDPTKSFTNIMPYLAQVAIGSKPHFTVFGADYETED 219
D + ++ + + +P + G +T D
Sbjct: 176 G-------DKPDLSSGVVSAFIRQLLKGEPIIVIGGDGSQTRD 211
Score = 91.9 bits (228), Expect = 3e-20
Identities = 67/260 (25%), Positives = 104/260 (40%), Gaps = 31/260 (11%)
Query: 224 VVAIDNFVNSVHIGDTPCSIRAIEQFTGKKVDFYSCDLVDKNRLGEIFAKHDIDCVIHFA 283
V +D + + + V+F DL D++ + E+ D VIH A
Sbjct: 27 VRGLDRLRDGLDPLLSG-------------VEFVVLDLTDRDLVDELAKGVP-DAVIHLA 72
Query: 284 AVKAVGESM-QEPLMYYKNNLIATINLLEVMKSHGVYQLVFSSSC-TVYGEPQFLPITED 341
A +V +S +P + N+ T+NLLE ++ GV + VF+SS VYG+P LPI ED
Sbjct: 73 AQSSVPDSNASDPAEFLDVNVDGTLNLLEAARAAGVKRFVFASSVSVVYGDPPPLPIDED 132
Query: 342 HPTGNIKNFYNLGTGQGTSVL---QLLRTFERVTGNKPV---PYIFYNLGTGQGTSVLQL 395
N Y G S L QLLR + R+ G V P+ Y G S +
Sbjct: 133 LGPPRPLNPY------GVSKLAAEQLLRAYARLYGLPVVILRPFNVYGPGDKPDLSSGVV 186
Query: 396 LRTFERVTGNKPVPYIFYNLGTGQG-TSVLQLLRTFERVTGKPVPYIFYNLGTGQG-TSV 453
++ +P+ I + + V + P + +N+G+G +V
Sbjct: 187 SAFIRQLLKGEPIIVIGGDGSQTRDFVYVDDVADALLLALENPDGGV-FNIGSGTAEITV 245
Query: 454 LQLLRTFERVTGKPVPYIFY 473
+L G P I Y
Sbjct: 246 RELAEAVAEAVGSKAPLIVY 265
Score = 41.1 bits (96), Expect = 0.001
Identities = 21/106 (19%), Positives = 40/106 (37%), Gaps = 6/106 (5%)
Query: 493 VTGKPVPYIFYNLGTGQG-TSVLQLLRTFERVTGKPVPYIFYNLGTGQG-TSVLQLLRTF 550
+ G+P+ I + + V + P + +N+G+G +V +L
Sbjct: 194 LKGEPIIVIGGDGSQTRDFVYVDDVADALLLALENPDGGV-FNIGSGTAEITVRELAEAV 252
Query: 551 ERVTGKPVPYIV--EARREGDIV-SMYANTDLAQRELGWSARCTVK 593
G P IV R GD+ + A+ LGW + +++
Sbjct: 253 AEAVGSKAPLIVYIPLGRRGDLREGKLLDISKARAALGWEPKVSLE 298
Score = 39.2 bits (91), Expect = 0.005
Identities = 16/66 (24%), Positives = 26/66 (39%), Gaps = 4/66 (6%)
Query: 3 NKFYNLGTGQG-TSVLQLLRTFERVTGKPVPYIV--EARREGDIV-SMYANTDLAQKELG 58
+N+G+G +V +L G P IV R GD+ + A+ LG
Sbjct: 231 GGVFNIGSGTAEITVRELAEAVAEAVGSKAPLIVYIPLGRRGDLREGKLLDISKARAALG 290
Query: 59 WSARCT 64
W + +
Sbjct: 291 WEPKVS 296
>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 = 85.8 bits (213), Expect = 2e-18
Identities = 44/124 (35%), Positives = 64/124 (51%), Gaps = 12/124 (9%)
Query: 222 GKVVAIDNFVNSVHIGDTPCSIRAIEQFTGKK-VDFYSCDLVDKNRLGEIFAKHDIDCVI 280
+VV +DN + G IE K F DL+D + AK D D V
Sbjct: 24 NEVVVVDNLSS----GRR----ENIEPEFENKAFRFVKRDLLDTA---DKVAKKDGDTVF 72
Query: 281 HFAAVKAVGESMQEPLMYYKNNLIATINLLEVMKSHGVYQLVFSSSCTVYGEPQFLPITE 340
H AA V +P + + N++AT N+LE M+++GV ++VF+SS TVYGE + +P E
Sbjct: 73 HLAANPDVRLGATDPDIDLEENVLATYNVLEAMRANGVKRIVFASSSTVYGEAKVIPTPE 132
Query: 341 DHPT 344
D+P
Sbjct: 133 DYPP 136
Score = 77.7 bits (192), Expect = 1e-15
Identities = 41/112 (36%), Positives = 63/112 (56%), Gaps = 6/112 (5%)
Query: 66 DIDCVIHFAAVKAVGESMQEPLMYYKNNLIATINLLEVMKSHGVYQLVFSSSCTVYGEPQ 125
D D V H AA V +P + + N++AT N+LE M+++GV ++VF+SS TVYGE +
Sbjct: 67 DGDTVFHLAANPDVRLGATDPDIDLEENVLATYNVLEAMRANGVKRIVFASSSTVYGEAK 126
Query: 126 FLPITEDHPTGNIKNVYGKTKHFIEEMLKDLSKAH--KEWNIISLRYFNPVG 175
+P ED+P I +VYG +K E ++ + + W R+ N VG
Sbjct: 127 VIPTPEDYPPLPI-SVYGASKLAAEALISAYAHLFGFQAWIF---RFANIVG 174
>gnl|CDD|206121 pfam13950, Epimerase_Csub, UDP-glucose 4-epimerase C-term
subunit. This domain is the very C-terminal subunit of
UDP-glucose 4-epimerase.
Length = 62
Score = 76.3 bits (189), Expect = 2e-17
Identities = 19/47 (40%), Positives = 28/47 (59%), Gaps = 2/47 (4%)
Query: 22 TFERVTGKPVPYIVEARREGDIVSMYANTDLAQKELGWSARCTHDID 68
FE+ +GK +PY + RR GD+ YA+ A+KELGW A ++
Sbjct: 1 AFEKASGKKIPYEIVPRRPGDVAECYADPSKAEKELGWKA--ERGLE 45
Score = 75.2 bits (186), Expect = 5e-17
Identities = 18/45 (40%), Positives = 28/45 (62%)
Query: 549 TFERVTGKPVPYIVEARREGDIVSMYANTDLAQRELGWSARCTVK 593
FE+ +GK +PY + RR GD+ YA+ A++ELGW A ++
Sbjct: 1 AFEKASGKKIPYEIVPRRPGDVAECYADPSKAEKELGWKAERGLE 45
Score = 30.1 bits (69), Expect = 0.41
Identities = 6/14 (42%), Positives = 9/14 (64%)
Query: 429 TFERVTGKPVPYIF 442
FE+ +GK +PY
Sbjct: 1 AFEKASGKKIPYEI 14
Score = 30.1 bits (69), Expect = 0.41
Identities = 6/14 (42%), Positives = 9/14 (64%)
Query: 459 TFERVTGKPVPYIF 472
FE+ +GK +PY
Sbjct: 1 AFEKASGKKIPYEI 14
Score = 30.1 bits (69), Expect = 0.41
Identities = 6/14 (42%), Positives = 9/14 (64%)
Query: 489 TFERVTGKPVPYIF 502
FE+ +GK +PY
Sbjct: 1 AFEKASGKKIPYEI 14
>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 = 78.1 bits (193), Expect = 7e-16
Identities = 63/238 (26%), Positives = 105/238 (44%), Gaps = 38/238 (15%)
Query: 254 VDFYSCDLVDKNRLGEIFAKHDIDCVIHFAAVKAVGESMQEPLMYYKNNLIATINLLEVM 313
VD+ D ++ L ID VIH A+ S + P++ + N+ T+ LLE
Sbjct: 43 VDYIKGDYENRADLESAL--VGIDTVIHLASTTNPATSNKNPILDIQTNVAPTVQLLEAC 100
Query: 314 KSHGVYQLVF-SSSCTVYGEPQFLPITEDHPTGNIKNFYNLGTGQGTSVL---QLLRTFE 369
+ G+ +++F SS TVYG P+ LPI+E PT I ++ G S L + LR ++
Sbjct: 101 AAAGIGKIIFASSGGTVYGVPEQLPISESDPTLPISSY-------GISKLAIEKYLRLYQ 153
Query: 370 RVTGNKPV------PYIFYNLGTGQGTSVLQ-LLRTF-ERVTGNKPVPYIFYNLGTGQGT 421
+ G PY G GQ Q ++ ++ +P+ I+ G G
Sbjct: 154 YLYGLDYTVLRISNPY-----GPGQRPDGKQGVIPIALNKILRGEPIE-IW-----GDGE 202
Query: 422 SVL------QLLRTFERVTGKPVPYIFYNLGTGQGTSVLQLLRTFERVTGKPVPYIFY 473
S+ L+ + +N+G+G G S+ +L+ E+VTG+ V I+
Sbjct: 203 SIRDYIYIDDLVEALMALLRSKGLEEVFNIGSGIGYSLAELIAEIEKVTGRSVQVIYT 260
Score = 75.8 bits (187), Expect = 5e-15
Identities = 45/126 (35%), Positives = 66/126 (52%), Gaps = 5/126 (3%)
Query: 65 HDIDCVIHFAAVKAVGESMQEPLMYYKNNLIATINLLEVMKSHGVYQLVF-SSSCTVYGE 123
ID VIH A+ S + P++ + N+ T+ LLE + G+ +++F SS TVYG
Sbjct: 61 VGIDTVIHLASTTNPATSNKNPILDIQTNVAPTVQLLEACAAAGIGKIIFASSGGTVYGV 120
Query: 124 PQFLPITEDHPTGNIKNVYGKTKHFIEEMLKDLSKAHKEWNIISLRYFNPVGA--HPSGR 181
P+ LPI+E PT I + YG +K IE+ L+ L + + LR NP G P G+
Sbjct: 121 PEQLPISESDPTLPI-SSYGISKLAIEKYLR-LYQYLYGLDYTVLRISNPYGPGQRPDGK 178
Query: 182 IGEDPT 187
G P
Sbjct: 179 QGVIPI 184
Score = 43.8 bits (104), Expect = 1e-04
Identities = 20/58 (34%), Positives = 33/58 (56%)
Query: 532 FYNLGTGQGTSVLQLLRTFERVTGKPVPYIVEARREGDIVSMYANTDLAQRELGWSAR 589
+N+G+G G S+ +L+ E+VTG+ V I R D+ + + A+ ELGWS +
Sbjct: 229 VFNIGSGIGYSLAELIAEIEKVTGRSVQVIYTPARTTDVPKIVLDISRARAELGWSPK 286
Score = 42.7 bits (101), Expect = 3e-04
Identities = 20/58 (34%), Positives = 33/58 (56%)
Query: 5 FYNLGTGQGTSVLQLLRTFERVTGKPVPYIVEARREGDIVSMYANTDLAQKELGWSAR 62
+N+G+G G S+ +L+ E+VTG+ V I R D+ + + A+ ELGWS +
Sbjct: 229 VFNIGSGIGYSLAELIAEIEKVTGRSVQVIYTPARTTDVPKIVLDISRARAELGWSPK 286
>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 = 77.0 bits (190), Expect = 3e-15
Identities = 36/92 (39%), Positives = 52/92 (56%), Gaps = 4/92 (4%)
Query: 256 FYSCDLVDKNRLGEIFAKHDIDCVIHFAAVKAVGESMQEPLMYYKNNLIATINLLEVMKS 315
F DL D+ L +F H+ D VIH AA V S++ P Y +N++ +NLLE+ +
Sbjct: 57 FVKGDLEDREALRRLFKDHEFDAVIHLAAQAGVRYSLENPHAYVDSNIVGFLNLLELCRH 116
Query: 316 HGVYQLVFSSSCTVYGEPQFLPITE----DHP 343
GV LV++SS +VYG +P +E DHP
Sbjct: 117 FGVKHLVYASSSSVYGLNTKMPFSEDDRVDHP 148
Score = 73.1 bits (180), Expect = 5e-14
Identities = 43/122 (35%), Positives = 62/122 (50%), Gaps = 13/122 (10%)
Query: 65 HDIDCVIHFAAVKAVGESMQEPLMYYKNNLIATINLLEVMKSHGVYQLVFSSSCTVYGEP 124
H+ D VIH AA V S++ P Y +N++ +NLLE+ + GV LV++SS +VYG
Sbjct: 75 HEFDAVIHLAAQAGVRYSLENPHAYVDSNIVGFLNLLELCRHFGVKHLVYASSSSVYGLN 134
Query: 125 QFLPITEDHPTGNIKNVYGKTKHFIEEMLKDLSKAHKE---WNI--ISLRYFNPVGAHPS 179
+P +ED + ++Y TK E M AH + I LR+F G P
Sbjct: 135 TKMPFSEDDRVDHPISLYAATKKANELM------AHTYSHLYGIPTTGLRFFTVYG--PW 186
Query: 180 GR 181
GR
Sbjct: 187 GR 188
Score = 50.0 bits (120), Expect = 2e-06
Identities = 16/67 (23%), Positives = 30/67 (44%)
Query: 527 PVPYIFYNLGTGQGTSVLQLLRTFERVTGKPVPYIVEARREGDIVSMYANTDLAQRELGW 586
PY YN+G ++ + E+ GK ++GD+ YA+ QR LG+
Sbjct: 253 SAPYRVYNIGNNSPVKLMDFIEALEKALGKKAKKNYLPMQKGDVPETYADISKLQRLLGY 312
Query: 587 SARCTVK 593
+ +++
Sbjct: 313 KPKTSLE 319
Score = 44.2 bits (105), Expect = 1e-04
Identities = 13/61 (21%), Positives = 27/61 (44%)
Query: 4 KFYNLGTGQGTSVLQLLRTFERVTGKPVPYIVEARREGDIVSMYANTDLAQKELGWSARC 63
+ YN+G ++ + E+ GK ++GD+ YA+ Q+ LG+ +
Sbjct: 257 RVYNIGNNSPVKLMDFIEALEKALGKKAKKNYLPMQKGDVPETYADISKLQRLLGYKPKT 316
Query: 64 T 64
+
Sbjct: 317 S 317
>gnl|CDD|187551 cd05240, UDP_G4E_3_SDR_e, UDP-glucose 4 epimerase (G4E), subgroup
3, extended (e) SDRs. Members of this bacterial
subgroup are identified as possible sugar epimerases,
such as UDP-glucose 4 epimerase. However, while the
NAD(P)-binding motif is fairly well conserved, not all
members retain the canonical active site tetrad of the
extended SDRs. UDP-glucose 4 epimerase (aka
UDP-galactose-4-epimerase), is a homodimeric extended
SDR. It catalyzes the NAD-dependent conversion of
UDP-galactose to UDP-glucose, the final step in Leloir
galactose synthesis. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 306
Score = 73.6 bits (181), Expect = 3e-14
Identities = 33/116 (28%), Positives = 56/116 (48%), Gaps = 6/116 (5%)
Query: 65 HDIDCVIHFAAVKAVGESMQEPLMYYKNNLIATINLLEVMKSHGVYQLVFSSSCTVYG-- 122
+ D V+H A + E ++ N+ T N+L+ + GV ++V +SS VYG
Sbjct: 61 READAVVHLAFILDPPRDGAE---RHRINVDGTQNVLDACAAAGVPRVVVTSSVAVYGAH 117
Query: 123 EPQFLPITEDHPT-GNIKNVYGKTKHFIEEMLKDLSKAHKEWNIISLRYFNPVGAH 177
P+TED P G+ + Y + K +E++L + + H E N+ LR +G
Sbjct: 118 PDNPAPLTEDAPLRGSPEFAYSRDKAEVEQLLAEFRRRHPELNVTVLRPATILGPG 173
Score = 65.1 bits (159), Expect = 2e-11
Identities = 34/120 (28%), Positives = 54/120 (45%), Gaps = 8/120 (6%)
Query: 253 KVDFYSCDLVDKNRLGEIFAKHDIDCVIHFAAVKAVGESMQEPLMYYKNNLIATINLLEV 312
KV++ D+ D ++F + + D V+H A + E ++ N+ T N+L+
Sbjct: 41 KVEYVRLDIRDPA-AADVFREREADAVVHLAFILDPPRDGAE---RHRINVDGTQNVLDA 96
Query: 313 MKSHGVYQLVFSSSCTVYG--EPQFLPITEDHPTGNIKNFYNLGTGQGTSVLQLLRTFER 370
+ GV ++V +SS VYG P+TED P F + V QLL F R
Sbjct: 97 CAAAGVPRVVVTSSVAVYGAHPDNPAPLTEDAPLRGSPEFA--YSRDKAEVEQLLAEFRR 154
>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 = 69.3 bits (170), Expect = 7e-13
Identities = 44/183 (24%), Positives = 71/183 (38%), Gaps = 27/183 (14%)
Query: 68 DCVIHFAAVKAVGESMQEPLMYYKNNLIATINLLEVMKSHG-VYQLVFSSSCTVYGEPQF 126
D V H AA+ + G + + + Y+ N+ T NLLE ++ +G + VF+SS VYG P
Sbjct: 68 DVVFHLAAIVS-GGAEADFDLGYRVNVDGTRNLLEALRKNGPKPRFVFTSSLAVYGLPLP 126
Query: 127 LPITEDHPTGNIKNVYGKTKHFIEEMLKDLSKAHKEWNI------ISLRYFNPVGAHPS- 179
P+T DH + + YG K E +L D S+ + +R P A +
Sbjct: 127 NPVT-DHTALDPASSYGAQKAMCELLLNDYSRRGFVDGRTLRLPTVCVRPGRPNKAASAF 185
Query: 180 -GRIGEDPTKSFTNIMPYLAQVAIGSKPHFTVFGADYETEDGTGKVVAIDNFVNSVHIGD 238
I +P +P + T A+ NFV++ +
Sbjct: 186 ASTIIREPLVGEEAGLPV--------AEQLRYWLKSVAT--------AVANFVHAAELPA 229
Query: 239 TPC 241
Sbjct: 230 EKF 232
Score = 50.8 bits (122), Expect = 7e-07
Identities = 28/76 (36%), Positives = 41/76 (53%), Gaps = 3/76 (3%)
Query: 269 EIFAKHDIDCVIHFAAVKAVGESMQEPLMYYKNNLIATINLLEVMKSHG-VYQLVFSSSC 327
E A D V H AA+ + G + + + Y+ N+ T NLLE ++ +G + VF+SS
Sbjct: 60 EALANGRPDVVFHLAAIVS-GGAEADFDLGYRVNVDGTRNLLEALRKNGPKPRFVFTSSL 118
Query: 328 TVYGEPQFLPITEDHP 343
VYG P P+T DH
Sbjct: 119 AVYGLPLPNPVT-DHT 133
>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 = 64.2 bits (157), Expect = 3e-11
Identities = 34/113 (30%), Positives = 52/113 (46%), Gaps = 4/113 (3%)
Query: 66 DIDCVIHFAAVKAVGESMQEPLMYYKNNLIATINLLEVMKSHGVYQLVFSSSCTVYGEPQ 125
D V H AA+ A+ S PL Y + N+ T+N+LE ++V +S+ VYG Q
Sbjct: 68 KCDVVFHLAALIAIPYSYTAPLSYVETNVFGTLNVLEAACVLYRKRVVHTSTSEVYGTAQ 127
Query: 126 FLPITEDHPTGNIKN---VYGKTKHFIEEMLKDLSKAHKEWNIISLRYFNPVG 175
+PI EDHP I Y +K + + ++ + +R FN G
Sbjct: 128 DVPIDEDHPLLYINKPRSPYSASKQGADRLAYSYGRSF-GLPVTIIRPFNTYG 179
Score = 62.3 bits (152), Expect = 1e-10
Identities = 33/103 (32%), Positives = 51/103 (49%), Gaps = 2/103 (1%)
Query: 247 EQFTGKKVDFYSCDLVDKNRLGEIFAKHDIDCVIHFAAVKAVGESMQEPLMYYKNNLIAT 306
+ + F S D+ D + + + K D+ V H AA+ A+ S PL Y + N+ T
Sbjct: 42 DNAVHDRFHFISGDVRDASEVEYLVKKCDV--VFHLAALIAIPYSYTAPLSYVETNVFGT 99
Query: 307 INLLEVMKSHGVYQLVFSSSCTVYGEPQFLPITEDHPTGNIKN 349
+N+LE ++V +S+ VYG Q +PI EDHP I
Sbjct: 100 LNVLEAACVLYRKRVVHTSTSEVYGTAQDVPIDEDHPLLYINK 142
>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 = 62.7 bits (153), Expect = 1e-10
Identities = 62/224 (27%), Positives = 98/224 (43%), Gaps = 46/224 (20%)
Query: 66 DIDCVIHFAAVKAVGESMQEPLMYYKNNLIATINLLEVMKSHGVYQLVFSSSCTVYGEPQ 125
D V H AA+ A+ S P Y N+ T+N+L+ + GV ++V +S+ VYG Q
Sbjct: 70 GCDVVFHLAALIAIPYSYIAPDSYVDTNVTGTLNVLQAARDLGVEKVVHTSTSEVYGTAQ 129
Query: 126 FLPITEDHPTGNIKNVYGKTKHFIEEMLKDLSKAHKEWN--IISLRYFNPVGAHPSGR-- 181
++PI E HP ++ Y +K +++ LS ++ +N + +R FN G S R
Sbjct: 130 YVPIDEKHPL-QGQSPYSASKIGADQLA--LS-FYRSFNTPVTIIRPFNTYGPRQSARAV 185
Query: 182 ----IGE-------------DPTKSFTNIMPYLAQVAIGSKPHFTVFGADYETEDGTGKV 224
I + PT+ F Y+ G F A E++ G+V
Sbjct: 186 IPTIITQIASGKRRIKLGSLSPTRDFN----YVTDTVRG-------FIAIAESDKTVGEV 234
Query: 225 VAI-DNFVNSVHIGDTPCSIRAIEQFTGKKVDFYSCDLVDKNRL 267
+ I NF + IGDT I I G +V+ + D+ RL
Sbjct: 235 INIGSNF--EISIGDTVKLIAEI---MGSEVEIET----DEERL 269
Score = 61.9 bits (151), Expect = 2e-10
Identities = 30/92 (32%), Positives = 50/92 (54%), Gaps = 2/92 (2%)
Query: 252 KKVDFYSCDLVDKNRLGEIFAKHDIDCVIHFAAVKAVGESMQEPLMYYKNNLIATINLLE 311
K++ + D+ D + + + A D V H AA+ A+ S P Y N+ T+N+L+
Sbjct: 49 DKIEVVTGDIRDPDSVRK--AMKGCDVVFHLAALIAIPYSYIAPDSYVDTNVTGTLNVLQ 106
Query: 312 VMKSHGVYQLVFSSSCTVYGEPQFLPITEDHP 343
+ GV ++V +S+ VYG Q++PI E HP
Sbjct: 107 AARDLGVEKVVHTSTSEVYGTAQYVPIDEKHP 138
>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 = 61.5 bits (150), Expect = 3e-10
Identities = 30/97 (30%), Positives = 44/97 (45%), Gaps = 7/97 (7%)
Query: 251 GKKVDFYSCDLVDKNRLGEIFAKHDIDCVIHFAAVKAVGESMQEPLMYYKNNLIATINLL 310
++ + DL D + L K D + H AA V S +P + N + T+NLL
Sbjct: 48 KDRITLHYGDLTDSSSLRRAIEKVRPDEIYHLAAQSHVKVSFDDPEYTAEVNAVGTLNLL 107
Query: 311 EVMKSHG----VYQLVFSSSCTVYGEPQFLPITEDHP 343
E ++ G YQ +SS YG+ Q LP +E P
Sbjct: 108 EAIRILGLDARFYQ---ASSSEEYGKVQELPQSETTP 141
Score = 50.7 bits (122), Expect = 9e-07
Identities = 25/71 (35%), Positives = 35/71 (49%), Gaps = 7/71 (9%)
Query: 68 DCVIHFAAVKAVGESMQEPLMYYKNNLIATINLLEVMKSHG----VYQLVFSSSCTVYGE 123
D + H AA V S +P + N + T+NLLE ++ G YQ +SS YG+
Sbjct: 74 DEIYHLAAQSHVKVSFDDPEYTAEVNAVGTLNLLEAIRILGLDARFYQ---ASSSEEYGK 130
Query: 124 PQFLPITEDHP 134
Q LP +E P
Sbjct: 131 VQELPQSETTP 141
Score = 31.4 bits (72), Expect = 1.3
Identities = 13/67 (19%), Positives = 25/67 (37%), Gaps = 4/67 (5%)
Query: 533 YNLGTGQGTSVLQLLRT-FERVTGKPVPYIV---EARREGDIVSMYANTDLAQRELGWSA 588
Y + TG+ SV + + FE + R ++ + + A+ ELGW
Sbjct: 240 YVIATGETHSVREFVELAFEESGLTGDIEVEIDPRYFRPTEVDLLLGDPSKAREELGWKP 299
Query: 589 RCTVKIS 595
+ +
Sbjct: 300 EVSFEEL 306
Score = 31.0 bits (71), Expect = 1.7
Identities = 13/65 (20%), Positives = 26/65 (40%), Gaps = 4/65 (6%)
Query: 6 YNLGTGQGTSVLQLLRT-FERVTGKPVPYIV---EARREGDIVSMYANTDLAQKELGWSA 61
Y + TG+ SV + + FE + R ++ + + A++ELGW
Sbjct: 240 YVIATGETHSVREFVELAFEESGLTGDIEVEIDPRYFRPTEVDLLLGDPSKAREELGWKP 299
Query: 62 RCTHD 66
+ +
Sbjct: 300 EVSFE 304
>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 = 60.1 bits (146), Expect = 1e-09
Identities = 35/102 (34%), Positives = 50/102 (49%), Gaps = 5/102 (4%)
Query: 243 IRAIEQFTGKKVDFYSCDLVDKNRLGEIFAKHDIDCVIHFAAVKAVGESM---QEPLMYY 299
+RA ++ TGK ++FY D D L E+ A H+ D V+HFA ++ SM +
Sbjct: 57 LRAWKELTGKTIEFYVGDACDYEFLAELLASHEPDAVVHFAEQRSAPYSMIDREHANYTQ 116
Query: 300 KNNLIATINLLEVMKSHGV-YQLVFSSSCTVYGEPQFLPITE 340
NN+I T+NLL +K LV + YG P I E
Sbjct: 117 HNNVIGTLNLLFAIKEFDPDCHLVKLGTMGEYGTPNI-DIPE 157
Score = 37.0 bits (86), Expect = 0.023
Identities = 32/116 (27%), Positives = 50/116 (43%), Gaps = 19/116 (16%)
Query: 20 LRTFERVTGKPVPYIVEARREGDIVSMYANTDLAQKELGWSARCTHDIDCVIHFAAVKAV 79
LR ++ +TGK + + V GD + + + L +H+ D V+HFA ++
Sbjct: 57 LRAWKELTGKTIEFYV-----GDA----CDYEFLAELLA-----SHEPDAVVHFAEQRSA 102
Query: 80 GESM---QEPLMYYKNNLIATINLLEVMKSHGV-YQLVFSSSCTVYGEPQFLPITE 131
SM + NN+I T+NLL +K LV + YG P I E
Sbjct: 103 PYSMIDREHANYTQHNNVIGTLNLLFAIKEFDPDCHLVKLGTMGEYGTPNI-DIPE 157
>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 = 59.6 bits (145), Expect = 1e-09
Identities = 36/121 (29%), Positives = 61/121 (50%), Gaps = 7/121 (5%)
Query: 223 KVVAIDNFVNSVHIGDTPCSIRAIEQFTGKKVDFYSCDLVDKNRLGEIFAKHDIDCVIHF 282
+V+ DN + G+ ++A V F D+ ++N L ++F DID +IH
Sbjct: 26 EVIGFDNLMRRGSFGNLA-WLKANR--EDGGVRFVHGDIRNRNDLEDLFE--DIDLIIHT 80
Query: 283 AAVKAVGESMQEPLMYYKNNLIATINLLEVMKSHGVYQ-LVFSSSCTVYG-EPQFLPITE 340
AA +V S P + ++ N + T+N+LE + H +F+S+ VYG P +LP+ E
Sbjct: 81 AAQPSVTTSASSPRLDFETNALGTLNVLEAARQHAPNAPFIFTSTNKVYGDLPNYLPLEE 140
Query: 341 D 341
Sbjct: 141 L 141
Score = 53.4 bits (129), Expect = 2e-07
Identities = 60/263 (22%), Positives = 96/263 (36%), Gaps = 75/263 (28%)
Query: 66 DIDCVIHFAAVKAVGESMQEPLMYYKNNLIATINLLEVMKSHGVYQ-LVFSSSCTVYG-E 123
DID +IH AA +V S P + ++ N + T+N+LE + H +F+S+ VYG
Sbjct: 73 DIDLIIHTAAQPSVTTSASSPRLDFETNALGTLNVLEAARQHAPNAPFIFTSTNKVYGDL 132
Query: 124 PQFLP-------------------ITEDHPTGNIKNVYGKTKHFIEEMLKDLSKAHKEWN 164
P +LP I+E P ++YG +K ++ +++ +
Sbjct: 133 PNYLPLEELETRYELAPEGWSPAGISESFPLDFSHSLYGASKGAADQYVQEYGRIFG-LK 191
Query: 165 IISLRYFNPVGAHPSGRIGEDPTKSFTNIMPYLAQVAIGSKPHFTVFGADYETEDGTGK- 223
+ R G G ED + Y + A+ KP T+F G G
Sbjct: 192 TVVFRCGCLTGPRQFGT--ED-----QGWVAYFLKCAVTGKP-LTIF--------GYGGK 235
Query: 224 ----VVAIDNFVNSVH---------------IGDTP---CSIRA----IEQFTGKKVDFY 257
V+ + VN IG S+ E+ TG+K++ Y
Sbjct: 236 QVRDVLHSADLVNLYLRQFQNPDRRKGEVFNIGGGRENSVSLLELIALCEEITGRKMESY 295
Query: 258 SCDLVDKNRLGEIFAKHDIDCVI 280
D+NR G D I
Sbjct: 296 K----DENRPG------DQIWYI 308
Score = 39.6 bits (93), Expect = 0.004
Identities = 28/104 (26%), Positives = 45/104 (43%), Gaps = 9/104 (8%)
Query: 493 VTGKPVPYIFYNLGTGQGTSVLQ---LLRTFERVTGKPVPYI--FYNLGTGQGTSV--LQ 545
VTGKP+ Y G Q VL L+ + R P +N+G G+ SV L+
Sbjct: 222 VTGKPLTIFGY--GGKQVRDVLHSADLVNLYLRQFQNPDRRKGEVFNIGGGRENSVSLLE 279
Query: 546 LLRTFERVTGKPVPYIVEARREGDIVSMYANTDLAQRELGWSAR 589
L+ E +TG+ + + R GD + ++ + + GW
Sbjct: 280 LIALCEEITGRKMESYKDENRPGDQIWYISDIRKIKEKPGWKPE 323
Score = 38.4 bits (90), Expect = 0.008
Identities = 15/59 (25%), Positives = 30/59 (50%), Gaps = 2/59 (3%)
Query: 6 YNLGTGQGTSV--LQLLRTFERVTGKPVPYIVEARREGDIVSMYANTDLAQKELGWSAR 62
+N+G G+ SV L+L+ E +TG+ + + R GD + ++ +++ GW
Sbjct: 265 FNIGGGRENSVSLLELIALCEEITGRKMESYKDENRPGDQIWYISDIRKIKEKPGWKPE 323
>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 = 58.7 bits (143), Expect = 3e-09
Identities = 31/92 (33%), Positives = 47/92 (51%), Gaps = 7/92 (7%)
Query: 256 FYSCDLVDKNRLGEIFAKHDIDCVIHFAAVKAVGESMQEPLMYYKNNLIATINLLEVMKS 315
F D+ D + +F + ID VIHFAA V S+ +P + + N++ T LLE +
Sbjct: 55 FVKGDICDAELVDRLFEEEKIDAVIHFAAESHVDRSISDPEPFIRTNVLGTYTLLEAARK 114
Query: 316 HGVYQLVFSSSCTVYGE----PQFLPITEDHP 343
+GV + V S+ VYG+ +F TE P
Sbjct: 115 YGVKRFVHISTDEVYGDLLDDGEF---TETSP 143
Score = 51.4 bits (124), Expect = 6e-07
Identities = 27/75 (36%), Positives = 39/75 (52%), Gaps = 7/75 (9%)
Query: 64 THDIDCVIHFAAVKAVGESMQEPLMYYKNNLIATINLLEVMKSHGVYQLVFSSSCTVYGE 123
ID VIHFAA V S+ +P + + N++ T LLE + +GV + V S+ VYG+
Sbjct: 72 EEKIDAVIHFAAESHVDRSISDPEPFIRTNVLGTYTLLEAARKYGVKRFVHISTDEVYGD 131
Query: 124 ----PQFLPITEDHP 134
+F TE P
Sbjct: 132 LLDDGEF---TETSP 143
Score = 29.8 bits (68), Expect = 3.6
Identities = 31/101 (30%), Positives = 42/101 (41%), Gaps = 15/101 (14%)
Query: 495 GKPVP-YIFYNLGTGQGTS----VLQLLRTFERVTGKPVPYIFYNLGTGQGTSVLQLLRT 549
GKP+P Y G G V R E V K YN+G G + L+L++
Sbjct: 201 GKPLPIY-----GDGLNVRDWLYVEDHARAIELVLEKGRVGEIYNIGGGNELTNLELVKL 255
Query: 550 FERVTGKPVPYI--VEARREGDIVSMYA-NTDLAQRELGWS 587
+ GK I V+ R D YA ++ +RELGW
Sbjct: 256 ILELLGKDESLITYVKDRPGHDR--RYAIDSSKIRRELGWR 294
>gnl|CDD|185103 PRK15181, PRK15181, Vi polysaccharide biosynthesis protein TviC;
Provisional.
Length = 348
Score = 58.6 bits (141), Expect = 3e-09
Identities = 35/134 (26%), Positives = 68/134 (50%), Gaps = 8/134 (5%)
Query: 62 RCTHDIDCVIHFAAVKAVGESMQEPLMYYKNNLIATINLLEVMKSHGVYQLVFSSSCTVY 121
+ ++D V+H AA+ +V S+++P+ N+ +N+L + V +++S + Y
Sbjct: 86 KACKNVDYVLHQAALGSVPRSLKDPIATNSANIDGFLNMLTAARDAHVSSFTYAASSSTY 145
Query: 122 GEPQFLPITEDHPTGNIKNVYGKTKHFIEEMLKDLSKAHKEWNIISLRYFNPVGAHPSGR 181
G+ LP E+ G + Y TK ++ E+ D+ E+N I LRYFN G
Sbjct: 146 GDHPDLPKIEER-IGRPLSPYAVTK-YVNELYADVFARSYEFNAIGLRYFNVFGRR---- 199
Query: 182 IGEDPTKSFTNIMP 195
++P +++ ++P
Sbjct: 200 --QNPNGAYSAVIP 211
Score = 38.5 bits (89), Expect = 0.008
Identities = 19/70 (27%), Positives = 38/70 (54%)
Query: 272 AKHDIDCVIHFAAVKAVGESMQEPLMYYKNNLIATINLLEVMKSHGVYQLVFSSSCTVYG 331
A ++D V+H AA+ +V S+++P+ N+ +N+L + V +++S + YG
Sbjct: 87 ACKNVDYVLHQAALGSVPRSLKDPIATNSANIDGFLNMLTAARDAHVSSFTYAASSSTYG 146
Query: 332 EPQFLPITED 341
+ LP E+
Sbjct: 147 DHPDLPKIEE 156
>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 = 57.4 bits (139), Expect = 6e-09
Identities = 31/105 (29%), Positives = 43/105 (40%), Gaps = 4/105 (3%)
Query: 59 WSARCTHDIDCVIHFAA-VKAVGESMQEPL-MYYKNNLIATINLLEVMKSHGVYQLVFSS 116
+D V+H AA V + + +PL Y K N T L GV + VF S
Sbjct: 50 SFTDLFLGVDAVVHLAARVHVMNDQGADPLSDYRKVNTELTRRLARAAARQGVKRFVFLS 109
Query: 117 SCTVYGEP-QFLPITEDHPTGNIKNVYGKTKHFIEEMLKDLSKAH 160
S V GE P E P ++ YG++K E L +L +
Sbjct: 110 SVKVNGEGTVGAPFDETDPP-APQDAYGRSKLEAERALLELGASD 153
Score = 49.3 bits (118), Expect = 3e-06
Identities = 28/87 (32%), Positives = 38/87 (43%), Gaps = 5/87 (5%)
Query: 260 DLVDKNRLGEIFAKHDIDCVIHFAA-VKAVGESMQEPL-MYYKNNLIATINLLEVMKSHG 317
+L D + ++F +D V+H AA V + + +PL Y K N T L G
Sbjct: 44 ELPDIDSFTDLFL--GVDAVVHLAARVHVMNDQGADPLSDYRKVNTELTRRLARAAARQG 101
Query: 318 VYQLVFSSSCTVYGEP-QFLPITEDHP 343
V + VF SS V GE P E P
Sbjct: 102 VKRFVFLSSVKVNGEGTVGAPFDETDP 128
>gnl|CDD|187559 cd05248, ADP_GME_SDR_e, ADP-L-glycero-D-mannoheptose 6-epimerase
(GME), extended (e) SDRs. This subgroup contains
ADP-L-glycero-D-mannoheptose 6-epimerase, an extended
SDR, which catalyzes the NAD-dependent interconversion
of ADP-D-glycero-D-mannoheptose and
ADP-L-glycero-D-mannoheptose. This subgroup has the
canonical active site tetrad and NAD(P)-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 = 317
Score = 56.9 bits (138), Expect = 9e-09
Identities = 32/114 (28%), Positives = 50/114 (43%), Gaps = 7/114 (6%)
Query: 66 DIDCVIHFAAVKAVGESMQEPLMYYKNNLIATINLLEVMKSHGVYQLVFSSSCTVYGEPQ 125
I+ + H A E+ + +M NN T LL + + +++SS VYG
Sbjct: 68 KIEAIFHQGACSDTTETDGKYMM--DNNYQYTKELLHYCLEKKI-RFIYASSAAVYGNGS 124
Query: 126 FLPITEDHPTGNIK--NVYGKTKHFIEEMLKDLSKAHKEWNIISLRYFNPVGAH 177
L ED T N++ NVYG +K ++ + K ++ LRYFN G
Sbjct: 125 -LGFAEDIETPNLRPLNVYGYSKLLFDQWARRHGKE-VLSQVVGLRYFNVYGPR 176
>gnl|CDD|224013 COG1088, RfbB, dTDP-D-glucose 4,6-dehydratase [Cell envelope
biogenesis, outer membrane].
Length = 340
Score = 56.1 bits (136), Expect = 2e-08
Identities = 22/80 (27%), Positives = 40/80 (50%), Gaps = 1/80 (1%)
Query: 254 VDFYSCDLVDKNRLGEIFAKHDIDCVIHFAAVKAVGESMQEPLMYYKNNLIATINLLEVM 313
F D+ D+ + +F ++ D V+HFAA V S+ P + + N++ T LLE
Sbjct: 53 YRFVQGDICDRELVDRLFKEYQPDAVVHFAAESHVDRSIDGPAPFIQTNVVGTYTLLEAA 112
Query: 314 KSHGV-YQLVFSSSCTVYGE 332
+ + ++ S+ VYG+
Sbjct: 113 RKYWGKFRFHHISTDEVYGD 132
Score = 44.1 bits (105), Expect = 1e-04
Identities = 21/75 (28%), Positives = 36/75 (48%), Gaps = 1/75 (1%)
Query: 50 TDLAQKELGWSARCTHDIDCVIHFAAVKAVGESMQEPLMYYKNNLIATINLLEVMKSHGV 109
D+ +EL + D V+HFAA V S+ P + + N++ T LLE + +
Sbjct: 58 GDICDRELVDRLFKEYQPDAVVHFAAESHVDRSIDGPAPFIQTNVVGTYTLLEAARKYWG 117
Query: 110 -YQLVFSSSCTVYGE 123
++ S+ VYG+
Sbjct: 118 KFRFHHISTDEVYGD 132
Score = 29.5 bits (67), Expect = 4.5
Identities = 21/61 (34%), Positives = 30/61 (49%), Gaps = 9/61 (14%)
Query: 533 YNLGTGQGTSVLQLLRTFERVTGKPVP----YI--VEARREGDIVSMYA-NTDLAQRELG 585
YN+G G + L++++T + GK P I VE R D YA + +RELG
Sbjct: 241 YNIGGGNERTNLEVVKTICELLGKDKPDYRDLITFVEDRPGHD--RRYAIDASKIKRELG 298
Query: 586 W 586
W
Sbjct: 299 W 299
Score = 28.7 bits (65), Expect = 8.7
Identities = 20/61 (32%), Positives = 30/61 (49%), Gaps = 9/61 (14%)
Query: 6 YNLGTGQGTSVLQLLRTFERVTGKPVP----YI--VEARREGDIVSMYA-NTDLAQKELG 58
YN+G G + L++++T + GK P I VE R D YA + ++ELG
Sbjct: 241 YNIGGGNERTNLEVVKTICELLGKDKPDYRDLITFVEDRPGHD--RRYAIDASKIKRELG 298
Query: 59 W 59
W
Sbjct: 299 W 299
>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 = 54.4 bits (132), Expect = 5e-08
Identities = 26/87 (29%), Positives = 43/87 (49%), Gaps = 12/87 (13%)
Query: 246 IEQFTGKKVDFYSCDLVDKNRLGEIFAKHDIDCVIHFAAVKAVGESMQEPLMYY------ 299
+++ K+ F+ D+ D+ RL +H +D V H AA+K V PL+ Y
Sbjct: 44 RQEYNDPKLRFFIGDVRDRERLERAMEQHGVDTVFHAAALKHV------PLVEYNPMEAI 97
Query: 300 KNNLIATINLLEVMKSHGVYQLVFSSS 326
K N++ T N+ E +GV + V S+
Sbjct: 98 KTNVLGTENVAEAAIENGVEKFVLIST 124
Score = 40.5 bits (96), Expect = 0.001
Identities = 32/121 (26%), Positives = 48/121 (39%), Gaps = 31/121 (25%)
Query: 64 THDIDCVIHFAAVKAVGESMQEPLMYY------KNNLIATINLLEVMKSHGVYQLVF-SS 116
H +D V H AA+K V PL+ Y K N++ T N+ E +GV + V S+
Sbjct: 71 QHGVDTVFHAAALKHV------PLVEYNPMEAIKTNVLGTENVAEAAIENGVEKFVLIST 124
Query: 117 SCTVYGEPQFLPITEDHPTGNIKNVYGKTKHFIEEML--KDLSKAHKEWNIISLRYFNPV 174
V PT NV G TK E++ + + +R+ N +
Sbjct: 125 DKAVN------------PT----NVMGATKRLAEKLFQAANRESGSGKTRFSVVRFGNVL 168
Query: 175 G 175
G
Sbjct: 169 G 169
>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 = 53.9 bits (130), Expect = 1e-07
Identities = 22/73 (30%), Positives = 39/73 (53%), Gaps = 1/73 (1%)
Query: 260 DLVDKNRLGEIFAKHDIDCVIHFAAVKAVGESMQEPLMYYKNNLIATINLLEVMKSHGV- 318
D+ D+ + +F +H D V+HFAA V S+ P + + N++ T LLE ++ +
Sbjct: 58 DIGDRELVSRLFTEHQPDAVVHFAAESHVDRSISGPAAFIETNVVGTYTLLEAVRKYWHE 117
Query: 319 YQLVFSSSCTVYG 331
++ S+ VYG
Sbjct: 118 FRFHHISTDEVYG 130
Score = 44.7 bits (106), Expect = 8e-05
Identities = 19/60 (31%), Positives = 31/60 (51%), Gaps = 1/60 (1%)
Query: 64 THDIDCVIHFAAVKAVGESMQEPLMYYKNNLIATINLLEVMKSHGV-YQLVFSSSCTVYG 122
H D V+HFAA V S+ P + + N++ T LLE ++ + ++ S+ VYG
Sbjct: 71 EHQPDAVVHFAAESHVDRSISGPAAFIETNVVGTYTLLEAVRKYWHEFRFHHISTDEVYG 130
Score = 31.2 bits (71), Expect = 1.4
Identities = 33/108 (30%), Positives = 46/108 (42%), Gaps = 13/108 (12%)
Query: 493 VTGKPVPYIFYNLGTGQGTS----VLQLLRTFERVTGKPVPYIFYNLGTGQGTSVLQLLR 548
+ GKP+P Y G GQ V R V K YN+G G + L+++
Sbjct: 199 LAGKPLP--VY--GDGQQVRDWLYVEDHCRAIYLVLEKGRVGETYNIGGGNERTNLEVVE 254
Query: 549 TFERVTGKPVPYI--VEARREGDIVSMYA-NTDLAQRELGWSARCTVK 593
T + GK I VE R D YA + +RELGW+ + T +
Sbjct: 255 TILELLGKDEDLITHVEDRPGHDR--RYAIDASKIKRELGWAPKYTFE 300
>gnl|CDD|233775 TIGR02197, heptose_epim, ADP-L-glycero-D-manno-heptose-6-epimerase.
This family consists of examples of
ADP-L-glycero-D-mannoheptose-6-epimerase, an enzyme
involved in biosynthesis of the inner core of
lipopolysaccharide (LPS) for Gram-negative bacteria.
This enzyme is homologous to UDP-glucose 4-epimerase
(TIGR01179) and belongs to the NAD dependent
epimerase/dehydratase family (pfam01370) [Cell envelope,
Biosynthesis and degradation of surface polysaccharides
and lipopolysaccharides].
Length = 314
Score = 53.4 bits (129), Expect = 1e-07
Identities = 28/109 (25%), Positives = 49/109 (44%), Gaps = 7/109 (6%)
Query: 66 DIDCVIHFAAVKAVGESMQEPLMYYKNNLIATINLLEVMKSHGVYQLVFSSSCTVYGEPQ 125
I+ + H A E+ E +M +NN + LL+ G+ +++SS YG+ +
Sbjct: 66 KIEAIFHQGACSDTTETDGEYMM--ENNYQYSKRLLDWCAEKGI-PFIYASSAATYGDGE 122
Query: 126 FLPITEDHPTGNIKNVYGKTKHFIEEMLKD--LSKAHKEWNIISLRYFN 172
E NVYG +K ++ ++ L +A ++ LRYFN
Sbjct: 123 -AGFREGRELERPLNVYGYSKFLFDQYVRRRVLPEALSA-QVVGLRYFN 169
Score = 41.5 bits (98), Expect = 0.001
Identities = 24/118 (20%), Positives = 43/118 (36%), Gaps = 22/118 (18%)
Query: 218 EDGTGKVVAIDNFVNSVHIGDTPCSIRAIEQFTG-KKVDFYSCDLVDKNRLGEIFAKH-- 274
E G ++ +DN + +F + D +DK + K
Sbjct: 20 ERGITDILVVDNLRDG-------------HKFLNLADLVIA--DYIDKEDFLDRLEKGAF 64
Query: 275 -DIDCVIHFAAVKAVGESMQEPLMYYKNNLIATINLLEVMKSHGVYQLVFSSSCTVYG 331
I+ + H A E+ E +M +NN + LL+ G+ +++SS YG
Sbjct: 65 GKIEAIFHQGACSDTTETDGEYMM--ENNYQYSKRLLDWCAEKGI-PFIYASSAATYG 119
>gnl|CDD|224011 COG1086, COG1086, Predicted nucleoside-diphosphate sugar epimerases
[Cell envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 588
Score = 53.8 bits (130), Expect = 2e-07
Identities = 28/86 (32%), Positives = 43/86 (50%), Gaps = 12/86 (13%)
Query: 247 EQFTGKKVDFYSCDLVDKNRLGEIFAKHDIDCVIHFAAVKAVGESMQEPLMYY------K 300
E+F K+ FY D+ D++R+ H +D V H AA+K V PL+ Y K
Sbjct: 297 EKFPELKLRFYIGDVRDRDRVERAMEGHKVDIVFHAAALKHV------PLVEYNPEEAIK 350
Query: 301 NNLIATINLLEVMKSHGVYQLVFSSS 326
N++ T N+ E +GV + V S+
Sbjct: 351 TNVLGTENVAEAAIKNGVKKFVLIST 376
Score = 42.3 bits (100), Expect = 6e-04
Identities = 32/121 (26%), Positives = 49/121 (40%), Gaps = 31/121 (25%)
Query: 64 THDIDCVIHFAAVKAVGESMQEPLMYY------KNNLIATINLLEVMKSHGVYQLVF-SS 116
H +D V H AA+K V PL+ Y K N++ T N+ E +GV + V S+
Sbjct: 323 GHKVDIVFHAAALKHV------PLVEYNPEEAIKTNVLGTENVAEAAIKNGVKKFVLIST 376
Query: 117 SCTVYGEPQFLPITEDHPTGNIKNVYGKTKHFIEEMLKDLSKAHKEW--NIISLRYFNPV 174
V PT NV G TK E++ + ++ +R+ N +
Sbjct: 377 DKAVN------------PT----NVMGATKRLAEKLFQAANRNVSGTGTRFCVVRFGNVL 420
Query: 175 G 175
G
Sbjct: 421 G 421
>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 = 53.1 bits (128), Expect = 2e-07
Identities = 29/120 (24%), Positives = 51/120 (42%), Gaps = 16/120 (13%)
Query: 228 DNFVNSVHIGDTPCSIRAIEQFTGKKVDFYSCDLVDKNRLGEIFAKHDIDCVIHFAAVKA 287
N ++ + S R D+ D N L E +++ + V H AA
Sbjct: 42 PNLFELANLDNKISSTRG--------------DIRDLNALREAIREYEPEIVFHLAAQPL 87
Query: 288 VGESMQEPLMYYKNNLIATINLLEVMKSHG-VYQLVFSSSCTVYG-EPQFLPITEDHPTG 345
V S ++P+ ++ N++ T+NLLE ++ G V +V +S Y + E+ P G
Sbjct: 88 VRLSYKDPVETFETNVMGTVNLLEAIRETGSVKAVVNVTSDKCYENKEWGWGYRENDPLG 147
Score = 42.3 bits (100), Expect = 5e-04
Identities = 21/71 (29%), Positives = 36/71 (50%), Gaps = 2/71 (2%)
Query: 68 DCVIHFAAVKAVGESMQEPLMYYKNNLIATINLLEVMKSHG-VYQLVFSSSCTVYG-EPQ 125
+ V H AA V S ++P+ ++ N++ T+NLLE ++ G V +V +S Y +
Sbjct: 77 EIVFHLAAQPLVRLSYKDPVETFETNVMGTVNLLEAIRETGSVKAVVNVTSDKCYENKEW 136
Query: 126 FLPITEDHPTG 136
E+ P G
Sbjct: 137 GWGYRENDPLG 147
>gnl|CDD|187550 cd05239, GDP_FS_SDR_e, GDP-fucose synthetase, extended (e) SDRs.
GDP-fucose synthetase (aka 3, 5-epimerase-4-reductase)
acts in the NADP-dependent synthesis of GDP-fucose from
GDP-mannose. Two activities have been proposed for the
same active site: epimerization and reduction. Proteins
in this subgroup are extended SDRs, which have a
characteristic active site tetrad and an NADP-binding
motif, [AT]GXXGXXG, that is a close match to the
archetypical form. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 300
Score = 52.6 bits (127), Expect = 2e-07
Identities = 57/230 (24%), Positives = 88/230 (38%), Gaps = 35/230 (15%)
Query: 259 CDLVDKNRLGEIFAKHDIDCVIHFAA-VKAVGESMQEPLMYYKNNLIATINLLEVMKSHG 317
DL D+ + F K D VIH AA V + +M P + ++NL+ N++ G
Sbjct: 35 LDLTDQEAVRAFFEKEKPDYVIHLAAKVGGIVANMTYPADFLRDNLLINDNVIHAAHRFG 94
Query: 318 VYQLVF-SSSCTVYGEPQFLPITED-------HPTGNIKNF-YNLGTGQGTSVLQLLRTF 368
V +LVF SSC Y + PI E PT N Y + + L+L +
Sbjct: 95 VKKLVFLGSSCI-YPDLAPQPIDESDLLTGPPEPT----NEGYAIAK---RAGLKLCEAY 146
Query: 369 ERVTGNKPVPYIFYNL------GTGQGTSVL-QLLRTFER--VTGNKPVPYIFYNLGTG- 418
+ G + + NL + + V+ L+R F + G K V G+G
Sbjct: 147 RKQYGCDYISVMPTNLYGPHDNFDPENSHVIPALIRKFHEAKLRGGKEVT----VWGSGT 202
Query: 419 ---QGTSVLQLLRTFERVTGKPVPYIFYNLGTGQGTSVLQLLRTFERVTG 465
+ L R + I N+G+G S+ +L V G
Sbjct: 203 PRREFLYSDDLARAIVFLLENYDEPIIVNVGSGVEISIRELAEAIAEVVG 252
Score = 41.8 bits (99), Expect = 6e-04
Identities = 30/103 (29%), Positives = 44/103 (42%), Gaps = 15/103 (14%)
Query: 68 DCVIHFAA-VKAVGESMQEPLMYYKNNLIATINLLEVMKSHGVYQLVF-SSSCTVYGEPQ 125
D VIH AA V + +M P + ++NL+ N++ GV +LVF SSC Y +
Sbjct: 53 DYVIHLAAKVGGIVANMTYPADFLRDNLLINDNVIHAAHRFGVKKLVFLGSSCI-YPDLA 111
Query: 126 FLPITED-------HPTGNIKN-VYGKTKHFIEEMLKDLSKAH 160
PI E PT N Y K ++ + K +
Sbjct: 112 PQPIDESDLLTGPPEPT----NEGYAIAKRAGLKLCEAYRKQY 150
>gnl|CDD|187548 cd05237, UDP_invert_4-6DH_SDR_e, UDP-Glcnac (UDP-linked
N-acetylglucosamine) inverting 4,6-dehydratase, extended
(e) SDRs. UDP-Glcnac inverting 4,6-dehydratase was
identified in Helicobacter pylori as the hexameric flaA1
gene product (FlaA1). FlaA1 is hexameric, possesses
UDP-GlcNAc-inverting 4,6-dehydratase activity, and
catalyzes the first step in the creation of a
pseudaminic acid derivative in protein glycosylation.
Although this subgroup has the NADP-binding motif
characteristic of extended SDRs, its members tend to
have a Met substituted for the active site Tyr found in
most SDR families. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 287
Score = 50.7 bits (122), Expect = 7e-07
Identities = 31/125 (24%), Positives = 49/125 (39%), Gaps = 21/125 (16%)
Query: 51 DLAQKELGWSARCTHDIDCVIHFAAVKAVGESMQEPLMYYKNNLIATINLLEVMKSHGVY 110
D+ KE A D V H AA+K V P K N++ T N+++ +GV
Sbjct: 62 DVRDKERLRRAFKERGPDIVFHAAALKHVPSMEDNPEEAIKTNVLGTKNVIDAAIENGVE 121
Query: 111 QLVFSSSCTVYGEPQFLPITED---HPTGNIKNVYGKTKHFIEEMLKDLSKAHKEWNIIS 167
+ V S+ D +P NV G TK E++L ++ +
Sbjct: 122 KFVCIST--------------DKAVNPV----NVMGATKRVAEKLLLAKNEYSSSTKFST 163
Query: 168 LRYFN 172
+R+ N
Sbjct: 164 VRFGN 168
Score = 47.2 bits (113), Expect = 9e-06
Identities = 25/80 (31%), Positives = 38/80 (47%)
Query: 247 EQFTGKKVDFYSCDLVDKNRLGEIFAKHDIDCVIHFAAVKAVGESMQEPLMYYKNNLIAT 306
+F K+ F D+ DK RL F + D V H AA+K V P K N++ T
Sbjct: 49 SRFPHDKLRFIIGDVRDKERLRRAFKERGPDIVFHAAALKHVPSMEDNPEEAIKTNVLGT 108
Query: 307 INLLEVMKSHGVYQLVFSSS 326
N+++ +GV + V S+
Sbjct: 109 KNVIDAAIENGVEKFVCIST 128
>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 = 50.2 bits (120), Expect = 1e-06
Identities = 54/229 (23%), Positives = 92/229 (40%), Gaps = 43/229 (18%)
Query: 223 KVVAIDNFVNSV--HIGDTPCSIRAIEQFTGKKVDFYSCDLVDKNRLGEIFAKHDIDCVI 280
+VV IDNF H+ D P + + DK + ++F D V+
Sbjct: 26 QVVVIDNFATGRREHLPDHP------------NLTVVEGSIADKALVDKLFGDFKPDAVV 73
Query: 281 HFAAVKAVGESMQEPLMYYKN---NLIATINLLEVMKSHGVYQLVFSSSCTVYG-EPQFL 336
H AA + ++P +Y++ N++ N+++ K GV +L++ + YG +P
Sbjct: 74 HTAA------AYKDPDDWYEDTLTNVVGGANVVQAAKKAGVKRLIYFQTALCYGLKPMQQ 127
Query: 337 PITEDHPTGNIKNFYNLGTGQGTSVLQL----LRTFE--RVTGNK----PVPYIFYNLGT 386
PI DHP + Y + G L+L TF VTG + P+P + L
Sbjct: 128 PIRLDHPRAPPGSSYAISKTAGEYYLELSGVDFVTFRLANVTGPRNVIGPLPTFYQRLKA 187
Query: 387 GQGTSVLQLLRTFERVTG---------NKPVPYIFYNLGTGQGTSVLQL 426
G+ V R F V + + Y+ +G+ S+ +L
Sbjct: 188 GKKCFVTDTRRDFVFVKDLARVVDKALDGIRGHGAYHFSSGEDVSIKEL 236
Score = 46.0 bits (109), Expect = 3e-05
Identities = 33/128 (25%), Positives = 59/128 (46%), Gaps = 25/128 (19%)
Query: 68 DCVIHFAAVKAVGESMQEPLMYYKN---NLIATINLLEVMKSHGVYQLVFSSSCTVYG-E 123
D V+H AA + ++P +Y++ N++ N+++ K GV +L++ + YG +
Sbjct: 70 DAVVHTAA------AYKDPDDWYEDTLTNVVGGANVVQAAKKAGVKRLIYFQTALCYGLK 123
Query: 124 PQFLPITEDHPTGNIKNVYGKTK----HFIEEMLKDLSKAHKEWNIISLRYFNPVGAHPS 179
P PI DHP + Y +K +++E L + + ++ R N G P
Sbjct: 124 PMQQPIRLDHPRAPPGSSYAISKTAGEYYLE--LSGV-------DFVTFRLANVTG--PR 172
Query: 180 GRIGEDPT 187
IG PT
Sbjct: 173 NVIGPLPT 180
>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 = 48.8 bits (117), Expect = 3e-06
Identities = 45/226 (19%), Positives = 76/226 (33%), Gaps = 32/226 (14%)
Query: 256 FYSCDLVDKNRLGEIFAKHDIDCVIHFAAVKAVGESMQEPLMYYKNNLIATINLLEVMKS 315
+ DL D + + E + D +I+ AA V + +P + Y+ N++A NL K
Sbjct: 36 LFKLDLTDPDAVEEAIRDYKPDVIINCAAYTRVDKCESDPELAYRVNVLAPENLARAAKE 95
Query: 316 HGVYQLVFSSSCTVY-GEPQFLPITEDHPTGNIKNFYNLGTGQG-TSVLQL------LRT 367
G + S+ V+ G+ P E+ N N Y G +VL LRT
Sbjct: 96 VGARLIHISTDY-VFDGKK--GPYKEEDAP-NPLNVYGKSKLLGEVAVLNANPRYLILRT 151
Query: 368 FERVTGNKPVPYIFYNLGTGQG--TSVLQLLRTFERVTGNKPVPYIFYNLGTGQGTSVLQ 425
+++ L G+ +L+L + V + G T
Sbjct: 152 ----------SWLYGELKNGENFVEWMLRLAAERKEVNV--------VHDQIGSPTYAAD 193
Query: 426 LLRTFERVTGKPVPYIFYNLGTGQGTSVLQLLRTFERVTGKPVPYI 471
L + + Y+L S + + G P I
Sbjct: 194 LADAILELIERNSLTGIYHLSNSGPISKYEFAKLIADALGLPDVEI 239
Score = 48.8 bits (117), Expect = 3e-06
Identities = 26/95 (27%), Positives = 44/95 (46%), Gaps = 5/95 (5%)
Query: 67 IDCVIHFAAVKAVGESMQEPLMYYKNNLIATINLLEVMKSHGVYQLVFSSSCTVY-GEPQ 125
D +I+ AA V + +P + Y+ N++A NL K G + S+ V+ G+
Sbjct: 56 PDVIINCAAYTRVDKCESDPELAYRVNVLAPENLARAAKEVGARLIHISTDY-VFDGKK- 113
Query: 126 FLPITEDHPTGNIKNVYGKTKHFIEEMLKDLSKAH 160
P E+ N NVYGK+K E + + + +
Sbjct: 114 -GPYKEEDAP-NPLNVYGKSKLLGEVAVLNANPRY 146
>gnl|CDD|187580 cd05272, TDH_SDR_e, L-threonine dehydrogenase, extended (e) SDRs.
This subgroup contains members identified as L-threonine
dehydrogenase (TDH). TDH catalyzes the zinc-dependent
formation of 2-amino-3-ketobutyrate from L-threonine via
NAD(H)-dependent oxidation. This group is distinct from
TDHs that are members of the medium chain
dehydrogenase/reductase family. This group has the
NAD-binding motif and active site tetrad of the extended
SDRs. Extended SDRs are distinct from classical SDRs. In
addition to the Rossmann fold (alpha/beta folding
pattern with a central beta-sheet) core region typical
of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 308
Score = 47.7 bits (114), Expect = 8e-06
Identities = 23/74 (31%), Positives = 38/74 (51%), Gaps = 4/74 (5%)
Query: 260 DLVDKNRLGEIFAKHDIDCVIHFAAV-KAVGESMQEPLMYYKNNLIATINLLEVMKSHGV 318
D++D L EI H I +IH AA+ AVGE + P + + N+ N+LE+ + H
Sbjct: 50 DVLDFKSLEEIVVNHKITWIIHLAALLSAVGE--KNPPLAWDVNMNGLHNVLELAREHN- 106
Query: 319 YQLVFSSSCTVYGE 332
++ S+ +G
Sbjct: 107 LRIFVPSTIGAFGP 120
Score = 40.8 bits (96), Expect = 0.002
Identities = 24/88 (27%), Positives = 42/88 (47%), Gaps = 14/88 (15%)
Query: 65 HDIDCVIHFAAV-KAVGESMQEPLMYYKNNLIATINLLEVMKSHGVYQLVFSSSCTVYGE 123
H I +IH AA+ AVGE + P + + N+ N+LE+ + H ++ S+ +G
Sbjct: 64 HKITWIIHLAALLSAVGE--KNPPLAWDVNMNGLHNVLELAREHN-LRIFVPSTIGAFG- 119
Query: 124 PQFLPITEDHPTGNI-----KNVYGKTK 146
P T + T + + +YG +K
Sbjct: 120 ----PTTPRNNTPDDTIQRPRTIYGVSK 143
>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 = 47.7 bits (114), Expect = 9e-06
Identities = 24/101 (23%), Positives = 38/101 (37%), Gaps = 4/101 (3%)
Query: 61 ARCTHDIDCVIHFAAVKAVGESMQEPLMYYKNNLIATINLLEVMKSHGVYQLVFSSSCTV 120
A D V H AA ++ Y+ N+ T N+L+ GV ++V +SS
Sbjct: 57 AAAMKGCDRVFHLAAF--TSLWAKDRKELYRTNVEGTRNVLDAALEAGVRRVVHTSSIAA 114
Query: 121 YGEPQFLPITED--HPTGNIKNVYGKTKHFIEEMLKDLSKA 159
G P I E N Y ++K E + + +
Sbjct: 115 LGGPPDGRIDETTPWNERPFPNDYYRSKLLAELEVLEAAAE 155
Score = 39.6 bits (93), Expect = 0.003
Identities = 27/89 (30%), Positives = 39/89 (43%), Gaps = 8/89 (8%)
Query: 503 YNLGTGQGTSVLQLLRTFERVTGKPVPYIFYNLGTGQGTSVLQLLRTFERVTGKPVPYIV 562
Y LG G+ S QL T +TG P + + L L R+TGKP +
Sbjct: 223 YILG-GENLSFKQLFETLAEITGVKPPRRTIPPWLLKAVAALSEL--KARLTGKPP---L 276
Query: 563 EARREGDIVS--MYANTDLAQRELGWSAR 589
R ++ ++D A+RELG+S R
Sbjct: 277 LTPRTARVLRRNYLYSSDKARRELGYSPR 305
Score = 37.6 bits (88), Expect = 0.015
Identities = 20/69 (28%), Positives = 29/69 (42%), Gaps = 2/69 (2%)
Query: 275 DIDCVIHFAAVKAVGESMQEPLMYYKNNLIATINLLEVMKSHGVYQLVFSSSCTVYGEPQ 334
D V H AA ++ Y+ N+ T N+L+ GV ++V +SS G P
Sbjct: 62 GCDRVFHLAAF--TSLWAKDRKELYRTNVEGTRNVLDAALEAGVRRVVHTSSIAALGGPP 119
Query: 335 FLPITEDHP 343
I E P
Sbjct: 120 DGRIDETTP 128
>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 = 47.7 bits (114), Expect = 1e-05
Identities = 19/58 (32%), Positives = 34/58 (58%)
Query: 260 DLVDKNRLGEIFAKHDIDCVIHFAAVKAVGESMQEPLMYYKNNLIATINLLEVMKSHG 317
D+ D +L + A+ + V H AA V +S +PL ++ N++ T+NLLE +++ G
Sbjct: 60 DIRDAAKLRKAIAEFKPEIVFHLAAQPLVRKSYADPLETFETNVMGTVNLLEAIRAIG 117
Score = 37.7 bits (88), Expect = 0.013
Identities = 15/41 (36%), Positives = 26/41 (63%)
Query: 68 DCVIHFAAVKAVGESMQEPLMYYKNNLIATINLLEVMKSHG 108
+ V H AA V +S +PL ++ N++ T+NLLE +++ G
Sbjct: 77 EIVFHLAAQPLVRKSYADPLETFETNVMGTVNLLEAIRAIG 117
>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 = 47.4 bits (113), Expect = 1e-05
Identities = 28/97 (28%), Positives = 49/97 (50%), Gaps = 5/97 (5%)
Query: 233 SVHIGDTPCSIRAIEQFTGKKVDFYSCDLVDKNRLGEIFAKHDIDCVIHFAAVKAVGESM 292
+VH+ D + +G+ V F++ DL D L + F + + V H A+ +
Sbjct: 26 TVHVFDIRPTFELDPSSSGR-VQFHTGDLTDPQDLEKAFNEKGPNVVFHTASP----DHG 80
Query: 293 QEPLMYYKNNLIATINLLEVMKSHGVYQLVFSSSCTV 329
+YYK N+ T N++E + GV +LV++SS +V
Sbjct: 81 SNDDLYYKVNVQGTRNVIEACRKCGVKKLVYTSSASV 117
Score = 37.3 bits (87), Expect = 0.017
Identities = 29/123 (23%), Positives = 53/123 (43%), Gaps = 18/123 (14%)
Query: 39 REGDIVSMYANTDLAQKELGWSARCTHDIDCVIHFAAVKAVGESMQEPLMYYKNNLIATI 98
G + + DL + A + V H A+ + +YYK N+ T
Sbjct: 42 SSGRVQ--FHTGDLTDPQDLEKAFNEKGPNVVFHTASP----DHGSNDDLYYKVNVQGTR 95
Query: 99 NLLEVMKSHGVYQLVFSSSCTVY--GEP-----QFLPITEDHPTGNIKNVYGKTKHFIEE 151
N++E + GV +LV++SS +V G+ + LP + H ++ Y +TK E+
Sbjct: 96 NVIEACRKCGVKKLVYTSSASVVFNGQDIINGDESLPYPDKH-----QDAYNETKALAEK 150
Query: 152 MLK 154
++
Sbjct: 151 LVL 153
>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 = 45.5 bits (108), Expect = 1e-05
Identities = 33/152 (21%), Positives = 48/152 (31%), Gaps = 23/152 (15%)
Query: 9 GTGQ--GTSVLQLLRTFERVTG-----KPVPYIVEARREGDIVSMYANTDLAQKELGWSA 61
TG +LL VT K + + + + D +
Sbjct: 6 ATGFIGRALARELLEQGHEVTLLVRNTKRLSKEDQEPVA-VVEGDLRDLDSLSDAV---- 60
Query: 62 RCTHDIDCVIHFAAVKAVGESMQEPLMYYKNNLIATINLLEVMKSHGVYQLVFSSSCTVY 121
+D VIH A E ++ T N+LE K GV +F SS Y
Sbjct: 61 ---QGVDVVIHLAGAPRDTRDFCE------VDVEGTRNVLEAAKEAGVKHFIFISSLGAY 111
Query: 122 GEPQFLPITEDHPTGNIKNVYGKTKHFIEEML 153
G+ TE P+ V KT+ + E
Sbjct: 112 GDLH--EETEPSPSSPYLAVKAKTEAVLREAS 141
Score = 35.8 bits (83), Expect = 0.029
Identities = 26/92 (28%), Positives = 34/92 (36%), Gaps = 10/92 (10%)
Query: 260 DLVDKNRLGEIFAKHDIDCVIHFAAVKAVGESMQEPLMYYKNNLIATINLLEVMKSHGVY 319
DL D + L A +D VIH A E ++ T N+LE K GV
Sbjct: 49 DLRDLDSL--SDAVQGVDVVIHLAGAPRDTRDFCE------VDVEGTRNVLEAAKEAGVK 100
Query: 320 QLVFSSSCTVYGEPQFLPITEDHPTGNIKNFY 351
+F SS YG+ TE P+
Sbjct: 101 HFIFISSLGAYGDLH--EETEPSPSSPYLAVK 130
>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 = 46.9 bits (112), Expect = 2e-05
Identities = 46/192 (23%), Positives = 85/192 (44%), Gaps = 34/192 (17%)
Query: 64 THDIDCVIHFAAVKAVGESMQEPLMYYKNNLIATINLLEVMKSHGVYQLVFSSSCTVYGE 123
++D + H A + P+ K N++ T+N+L + K G +++ +S+ VYG+
Sbjct: 62 YLEVDQIYHLACPASPVHYQYNPIKTLKTNVLGTLNMLGLAKRVGA-RVLLASTSEVYGD 120
Query: 124 PQFLPITEDH-----PTGNIKNVYGKTKHFIEEMLKDLSKAHK-EWNIISLRYFNPVGA- 176
P+ P E + P G ++ Y + K E + + H + I R FN G
Sbjct: 121 PEVHPQPESYWGNVNPIG-PRSCYDEGKRVAETLCMAYHRQHGVDVRIA--RIFNTYGPR 177
Query: 177 -HPS-GRIGEDPTKSFTNIMPYLAQVAIGSKPHFTVFGADYETE---------DGTGKVV 225
HP+ GR+ +N ++ Q A+ +P TV+G +T +G +++
Sbjct: 178 MHPNDGRV-------VSN---FIVQ-ALRGEP-ITVYGDGTQTRSFQYVSDLVEGLIRLM 225
Query: 226 AIDNFVNSVHIG 237
D F V++G
Sbjct: 226 NSDYFGGPVNLG 237
Score = 44.9 bits (107), Expect = 7e-05
Identities = 33/131 (25%), Positives = 57/131 (43%), Gaps = 18/131 (13%)
Query: 213 ADYETEDGTGKVVAIDNFVNSVHIGDTPCSIRAIEQFTGK-KVDFYSCDLVDKNRLGEIF 271
D EDG +V+ +DNF G R IE G +F D+ +
Sbjct: 17 CDRLLEDGH-EVICVDNF----FTG----RKRNIEHLIGHPNFEFIRHDVTE-------P 60
Query: 272 AKHDIDCVIHFAAVKAVGESMQEPLMYYKNNLIATINLLEVMKSHGVYQLVFSSSCTVYG 331
++D + H A + P+ K N++ T+N+L + K G +++ +S+ VYG
Sbjct: 61 LYLEVDQIYHLACPASPVHYQYNPIKTLKTNVLGTLNMLGLAKRVGA-RVLLASTSEVYG 119
Query: 332 EPQFLPITEDH 342
+P+ P E +
Sbjct: 120 DPEVHPQPESY 130
>gnl|CDD|187573 cd05263, MupV_like_SDR_e, Pseudomonas fluorescens MupV-like,
extended (e) SDRs. This subgroup of extended SDR family
domains have the characteristic active site tetrad and a
well-conserved NAD(P)-binding motif. This subgroup is
not well characterized, its members are annotated as
having a variety of putative functions. One
characterized member is Pseudomonas fluorescens MupV a
protein involved in the biosynthesis of Mupirocin, a
polyketide-derived antibiotic. Extended SDRs are
distinct from classical SDRs. In addition to the
Rossmann fold (alpha/beta folding pattern with a central
beta-sheet) core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids. Extended SDRs are a
diverse collection of proteins, and include isomerases,
epimerases, oxidoreductases, and lyases; they typically
have a TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 293
Score = 46.2 bits (110), Expect = 2e-05
Identities = 39/197 (19%), Positives = 76/197 (38%), Gaps = 24/197 (12%)
Query: 51 DLAQKELGWSARCTH----DIDCVIHFAAVKAVGESMQEPLMYYKNNLIATINLLEVMKS 106
DL Q LG SA + +D VIH AA ++ ++ N+ T ++LE+
Sbjct: 57 DLTQPNLGLSAAASRELAGKVDHVIHCAASYDFQAPNED---AWRTNIDGTEHVLELAAR 113
Query: 107 HGVYQLVFSSSCTVYGEPQ-FLPITEDHPTGNIKNVYGKTKHFIEEMLKDLSKAHKEWNI 165
+ + + S+ V G + + TE +P N KN Y ++K E++++ + +
Sbjct: 114 LDIQRFHYVSTAYVAGNREGNIRETELNPGQNFKNPYEQSKAEAEQLVRAAATQIP-LTV 172
Query: 166 ISLRYFNPVGAHPSGRIGEDPTKSFTNIM-PYLAQVAIGSKPHFTVFGADYETEDGTGKV 224
PS +G+ T I Y + + + + +
Sbjct: 173 Y----------RPSIVVGDSKTGRIEKIDGLYELLNLLAKLGRWLPMPGN---KGARLNL 219
Query: 225 VAIDNFVNS-VHIGDTP 240
V +D ++ V++ P
Sbjct: 220 VPVDYVADAIVYLSKKP 236
Score = 32.0 bits (73), Expect = 0.92
Identities = 20/79 (25%), Positives = 36/79 (45%), Gaps = 4/79 (5%)
Query: 275 DIDCVIHFAAVKAVGESMQEPLMYYKNNLIATINLLEVMKSHGVYQLVFSSSCTVYGEPQ 334
+D VIH AA ++ ++ N+ T ++LE+ + + + S+ V G +
Sbjct: 76 KVDHVIHCAASYDFQAPNED---AWRTNIDGTEHVLELAARLDIQRFHYVSTAYVAGNRE 132
Query: 335 -FLPITEDHPTGNIKNFYN 352
+ TE +P N KN Y
Sbjct: 133 GNIRETELNPGQNFKNPYE 151
>gnl|CDD|216283 pfam01073, 3Beta_HSD, 3-beta hydroxysteroid dehydrogenase/isomerase
family. The enzyme 3 beta-hydroxysteroid
dehydrogenase/5-ene-4-ene isomerase (3 beta-HSD)
catalyzes the oxidation and isomerisation of 5-ene-3
beta-hydroxypregnene and 5-ene-hydroxyandrostene steroid
precursors into the corresponding 4-ene-ketosteroids
necessary for the formation of all classes of steroid
hormones.
Length = 280
Score = 45.8 bits (109), Expect = 3e-05
Identities = 25/85 (29%), Positives = 36/85 (42%), Gaps = 3/85 (3%)
Query: 247 EQFTGKKVDFYSCDLVDKNRLGEIFAKHDIDCVIHFAAVKAVGESMQEPLMYYKNNLIAT 306
+ + + + D+ DK L A D VIH AA+ V K N+ T
Sbjct: 40 DFSKLQVITYIEGDVTDKQDLRR--ALQGSDVVIHTAAIIDVF-GKAYRDTIMKVNVKGT 96
Query: 307 INLLEVMKSHGVYQLVFSSSCTVYG 331
N+L+ GV LV++SS V G
Sbjct: 97 QNVLDACVKAGVRVLVYTSSMEVVG 121
Score = 42.7 bits (101), Expect = 3e-04
Identities = 28/104 (26%), Positives = 42/104 (40%), Gaps = 16/104 (15%)
Query: 61 ARCTHDIDCVIHFAAVKAVGESMQEPLMYYKNNLIATINLLEVMKSHGVYQLVFSSSCTV 120
R D VIH AA+ V K N+ T N+L+ GV LV++SS V
Sbjct: 61 RRALQGSDVVIHTAAIIDVF-GKAYRDTIMKVNVKGTQNVLDACVKAGVRVLVYTSSMEV 119
Query: 121 -----YGEPQF-----LPITEDHPTGNIKNVYGKTKHFIEEMLK 154
YG+P P H ++ Y ++K E+++
Sbjct: 120 VGPNSYGQPIVNGDETTPYESTH-----QDPYPESKALAEKLVL 158
>gnl|CDD|182313 PRK10217, PRK10217, dTDP-glucose 4,6-dehydratase; Provisional.
Length = 355
Score = 45.8 bits (108), Expect = 4e-05
Identities = 20/61 (32%), Positives = 33/61 (54%)
Query: 256 FYSCDLVDKNRLGEIFAKHDIDCVIHFAAVKAVGESMQEPLMYYKNNLIATINLLEVMKS 315
F D+ D+ L +F +H DCV+H AA V S+ P + + N++ T LLE ++
Sbjct: 55 FEKVDICDRAELARVFTEHQPDCVMHLAAESHVDRSIDGPAAFIETNIVGTYTLLEAARA 114
Query: 316 H 316
+
Sbjct: 115 Y 115
Score = 35.0 bits (80), Expect = 0.11
Identities = 15/43 (34%), Positives = 24/43 (55%)
Query: 65 HDIDCVIHFAAVKAVGESMQEPLMYYKNNLIATINLLEVMKSH 107
H DCV+H AA V S+ P + + N++ T LLE +++
Sbjct: 73 HQPDCVMHLAAESHVDRSIDGPAAFIETNIVGTYTLLEAARAY 115
>gnl|CDD|178326 PLN02725, PLN02725,
GDP-4-keto-6-deoxymannose-3,5-epimerase-4-reductase.
Length = 306
Score = 45.1 bits (107), Expect = 5e-05
Identities = 25/82 (30%), Positives = 38/82 (46%), Gaps = 1/82 (1%)
Query: 260 DLVDKNRLGEIFAKHDIDCVIHFAA-VKAVGESMQEPLMYYKNNLIATINLLEVMKSHGV 318
DL + + FAK VI AA V + +M P + + NL N+++ HGV
Sbjct: 34 DLTRQADVEAFFAKEKPTYVILAAAKVGGIHANMTYPADFIRENLQIQTNVIDAAYRHGV 93
Query: 319 YQLVFSSSCTVYGEPQFLPITE 340
+L+F S +Y + PI E
Sbjct: 94 KKLLFLGSSCIYPKFAPQPIPE 115
Score = 40.1 bits (94), Expect = 0.002
Identities = 20/63 (31%), Positives = 31/63 (49%), Gaps = 1/63 (1%)
Query: 70 VIHFAA-VKAVGESMQEPLMYYKNNLIATINLLEVMKSHGVYQLVFSSSCTVYGEPQFLP 128
VI AA V + +M P + + NL N+++ HGV +L+F S +Y + P
Sbjct: 53 VILAAAKVGGIHANMTYPADFIRENLQIQTNVIDAAYRHGVKKLLFLGSSCIYPKFAPQP 112
Query: 129 ITE 131
I E
Sbjct: 113 IPE 115
>gnl|CDD|224014 COG1089, Gmd, GDP-D-mannose dehydratase [Cell envelope biogenesis,
outer membrane].
Length = 345
Score = 45.0 bits (107), Expect = 7e-05
Identities = 26/95 (27%), Positives = 44/95 (46%), Gaps = 2/95 (2%)
Query: 251 GKKVDFYSCDLVDKNRLGEIFAKHDIDCVIHFAAVKAVGESMQEPLMYYKNNLIATINLL 310
++ + DL D + L I + D + + AA VG S ++P + I T+ LL
Sbjct: 54 DPRLHLHYGDLTDSSNLLRILEEVQPDEIYNLAAQSHVGVSFEQPEYTADVDAIGTLRLL 113
Query: 311 EVMKSHGVYQLVF--SSSCTVYGEPQFLPITEDHP 343
E ++ G + F +S+ +YG Q +P E P
Sbjct: 114 EAIRILGEKKTRFYQASTSELYGLVQEIPQKETTP 148
Score = 35.8 bits (83), Expect = 0.049
Identities = 21/69 (30%), Positives = 34/69 (49%), Gaps = 2/69 (2%)
Query: 68 DCVIHFAAVKAVGESMQEPLMYYKNNLIATINLLEVMKSHGVYQLVF--SSSCTVYGEPQ 125
D + + AA VG S ++P + I T+ LLE ++ G + F +S+ +YG Q
Sbjct: 80 DEIYNLAAQSHVGVSFEQPEYTADVDAIGTLRLLEAIRILGEKKTRFYQASTSELYGLVQ 139
Query: 126 FLPITEDHP 134
+P E P
Sbjct: 140 EIPQKETTP 148
>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 = 44.1 bits (105), Expect = 1e-04
Identities = 44/141 (31%), Positives = 61/141 (43%), Gaps = 22/141 (15%)
Query: 9 GTGQ-GTSVLQLLRTFERVTGKPVPYIVEARREGDIVSMYANTDLAQ-KELGWSARCTHD 66
GQ G + +LL + V + R E D+ TD L AR
Sbjct: 6 ANGQLGRELTRLLA------ERGVEVVALDRPELDL------TDPEAVAALVREARP--- 50
Query: 67 IDCVIHFAAVKAVGESMQEPLMYYKNNLIATINLLEVMKSHGVYQLVFSSSCTVY-GEPQ 125
D V++ AA AV ++ EP + Y N + NL E + G L+ S+ V+ G
Sbjct: 51 -DVVVNAAAYTAVDKAESEPELAYAVNALGPGNLAEACAARGAP-LIHISTDYVFDGAKG 108
Query: 126 FLPITEDHPTGNIKNVYGKTK 146
P ED PTG + NVYG+TK
Sbjct: 109 -GPYREDDPTGPL-NVYGRTK 127
Score = 38.4 bits (90), Expect = 0.007
Identities = 30/112 (26%), Positives = 47/112 (41%), Gaps = 9/112 (8%)
Query: 246 IEQFTGKKVDFYSC-----DLVDKNRLGEIFAKHDIDCVIHFAAVKAVGESMQEPLMYYK 300
+ V+ + DL D + + + D V++ AA AV ++ EP + Y
Sbjct: 15 TRLLAERGVEVVALDRPELDLTDPEAVAALVREARPDVVVNAAAYTAVDKAESEPELAYA 74
Query: 301 NNLIATINLLEVMKSHGVYQLVFSSSCTVY-GEPQFLPITEDHPTGNIKNFY 351
N + NL E + G L+ S+ V+ G P ED PTG + N Y
Sbjct: 75 VNALGPGNLAEACAARGAP-LIHISTDYVFDGAKG-GPYREDDPTGPL-NVY 123
>gnl|CDD|187552 cd05241, 3b-HSD-like_SDR_e, 3beta-hydroxysteroid dehydrogenases
(3b-HSD)-like, extended (e) SDRs. Extended SDR family
domains belonging to this subgroup have the
characteristic active site tetrad and a fairly
well-conserved NAD(P)-binding motif. 3b-HSD catalyzes
the NAD-dependent conversion of various steroids, such
as pregnenolone to progesterone, or androstenediol to
testosterone. This subgroup includes an unusual
bifunctional 3b-HSD/C-4 decarboxylase from Arabidopsis
thaliana, and Saccharomyces cerevisiae ERG26, a
3b-HSD/C-4 decarboxylase, involved in the synthesis of
ergosterol, the major sterol of yeast. It also includes
human 3 beta-HSD/HSD3B1 and C(27) 3beta-HSD/
[3beta-hydroxy-delta(5)-C(27)-steroid oxidoreductase;
HSD3B7]. C(27) 3beta-HSD/HSD3B7 is a membrane-bound
enzyme of the endoplasmic reticulum, that catalyzes the
isomerization and oxidation of 7alpha-hydroxylated
sterol intermediates, an early step in bile acid
biosynthesis. Mutations in the human NSDHL (NAD(P)H
steroid dehydrogenase-like protein) cause CHILD syndrome
(congenital hemidysplasia with ichthyosiform nevus and
limb defects), an X-linked dominant, male-lethal trait.
Mutations in the human gene encoding C(27) 3beta-HSD
underlie a rare autosomal recessive form of neonatal
cholestasis. Extended SDRs are distinct from classical
SDRs. In addition to the Rossmann fold (alpha/beta
folding pattern with a central beta-sheet) core region
typical of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid sythase have
a GGXGXXG NAD(P)-binding motif and an altered active
site motif (YXXXN). Fungal type ketoacyl reductases have
a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 331
Score = 44.0 bits (104), Expect = 1e-04
Identities = 23/92 (25%), Positives = 40/92 (43%), Gaps = 7/92 (7%)
Query: 66 DIDCVIHFAAVKAVGESMQEPLMYYKNNLIATINLLEVMKSHGVYQLVFSSSCTVYGEPQ 125
DCV H AA+ +Y++ N+ T N+L+ + GV + V++SS +V Q
Sbjct: 66 GADCVFHTAAI---VPLAGPRDLYWEVNVGGTQNVLDACQRCGVQKFVYTSSSSVIFGGQ 122
Query: 126 FLPITEDHPTGNI---KNVYGKTKHFIEEMLK 154
D ++Y +TK E ++
Sbjct: 123 -NIHNGDETLPYPPLDSDMYAETKAIAEIIVL 153
Score = 41.6 bits (98), Expect = 7e-04
Identities = 27/108 (25%), Positives = 47/108 (43%), Gaps = 6/108 (5%)
Query: 234 VHIGDTPCSIRAIEQFTGKKVDFYSCDLVDKNRLGEIFAKHDIDCVIHFAAVKAVGESMQ 293
V D A+ + ++F D+ D+N + + A DCV H AA+
Sbjct: 27 VRSFDIAPPGEALSAWQHPNIEFLKGDITDRNDVEQ--ALSGADCVFHTAAI---VPLAG 81
Query: 294 EPLMYYKNNLIATINLLEVMKSHGVYQLVFSSSCTVYGEPQFLPITED 341
+Y++ N+ T N+L+ + GV + V++SS +V Q D
Sbjct: 82 PRDLYWEVNVGGTQNVLDACQRCGVQKFVYTSSSSVIFGGQ-NIHNGD 128
>gnl|CDD|236649 PRK10084, PRK10084, dTDP-glucose 4,6 dehydratase; Provisional.
Length = 352
Score = 42.1 bits (99), Expect = 5e-04
Identities = 22/75 (29%), Positives = 38/75 (50%), Gaps = 5/75 (6%)
Query: 242 SIRAIEQFTGKKVDFYSCDLVDKNRLGEIFAKHDIDCVIHFAAVKAVGESMQEPLMYYKN 301
+ E++ + D CD + +R IFA+H D V+H AA V S+ P + +
Sbjct: 45 DVSDSERYVFEHADI--CDRAELDR---IFAQHQPDAVMHLAAESHVDRSITGPAAFIET 99
Query: 302 NLIATINLLEVMKSH 316
N++ T LLE +++
Sbjct: 100 NIVGTYVLLEAARNY 114
Score = 29.8 bits (67), Expect = 4.4
Identities = 14/43 (32%), Positives = 23/43 (53%)
Query: 65 HDIDCVIHFAAVKAVGESMQEPLMYYKNNLIATINLLEVMKSH 107
H D V+H AA V S+ P + + N++ T LLE +++
Sbjct: 72 HQPDAVMHLAAESHVDRSITGPAAFIETNIVGTYVLLEAARNY 114
>gnl|CDD|224016 COG1091, RfbD, dTDP-4-dehydrorhamnose reductase [Cell envelope
biogenesis, outer membrane].
Length = 281
Score = 41.9 bits (99), Expect = 6e-04
Identities = 27/93 (29%), Positives = 40/93 (43%), Gaps = 2/93 (2%)
Query: 68 DCVIHFAAVKAVGESMQEPLMYYKNNLIATINLLEVMKSHGVYQLVFSSSCTVYGEPQFL 127
D VI+ AA AV ++ EP + + N NL G LV S+ V+ +
Sbjct: 52 DVVINAAAYTAVDKAESEPELAFAVNATGAENLARAAAEVGAR-LVHISTDYVFDGEKGG 110
Query: 128 PITEDHPTGNIKNVYGKTKHFIEEMLKDLSKAH 160
P E + NVYG++K EE ++ H
Sbjct: 111 PYKETDTPNPL-NVYGRSKLAGEEAVRAAGPRH 142
Score = 39.2 bits (92), Expect = 0.004
Identities = 40/218 (18%), Positives = 69/218 (31%), Gaps = 27/218 (12%)
Query: 258 SCDLVDKNRLGEIFAKHDIDCVIHFAAVKAVGESMQEPLMYYKNNLIATINLLEVMKSHG 317
D+ D + + E+ + D VI+ AA AV ++ EP + + N NL G
Sbjct: 33 ELDITDPDAVLEVIRETRPDVVINAAAYTAVDKAESEPELAFAVNATGAENLARAAAEVG 92
Query: 318 VYQLVFSSSCTVYGEPQFLPITEDHPTGNIKNFYNLGTGQG-TSVLQ------LLRTFER 370
LV S+ V+ + P E + N Y G +V +LRT
Sbjct: 93 AR-LVHISTDYVFDGEKGGPYKETDTPNPL-NVYGRSKLAGEEAVRAAGPRHLILRT--- 147
Query: 371 VTGNKPVPYIFYNLGTGQGTSVLQLLRTFERVTGNKPVPYIFYNLGTGQGTSVLQLLRTF 430
+++ G ++L+L + + + G T L
Sbjct: 148 -------SWVYGEYGNNFVKTMLRLAKEGKELKVVDDQ--------YGSPTYTEDLADAI 192
Query: 431 ERVTGKPVPYIFYNLGTGQGTSVLQLLRTFERVTGKPV 468
+ K Y+L S + + G
Sbjct: 193 LELLEKEKEGGVYHLVNSGECSWYEFAKAIFEEAGVDG 230
>gnl|CDD|215310 PLN02572, PLN02572, UDP-sulfoquinovose synthase.
Length = 442
Score = 42.1 bits (99), Expect = 6e-04
Identities = 22/75 (29%), Positives = 39/75 (52%), Gaps = 3/75 (4%)
Query: 243 IRAIEQFTGKKVDFYSCDLVDKNRLGEIFAKHDIDCVIHFAAVKAVGESM---QEPLMYY 299
+R ++ +GK+++ Y D+ D L E F + D V+HF ++ SM +
Sbjct: 104 VRRWKEVSGKEIELYVGDICDFEFLSEAFKSFEPDAVVHFGEQRSAPYSMIDRSRAVFTQ 163
Query: 300 KNNLIATINLLEVMK 314
NN+I T+N+L +K
Sbjct: 164 HNNVIGTLNVLFAIK 178
>gnl|CDD|219687 pfam07993, NAD_binding_4, Male sterility protein. This family
represents the C-terminal region of the male sterility
protein in a number of arabidopsis and drosophila. A
sequence-related jojoba acyl CoA reductase is also
included.
Length = 245
Score = 40.7 bits (96), Expect = 0.001
Identities = 34/169 (20%), Positives = 60/169 (35%), Gaps = 32/169 (18%)
Query: 51 DLAQKELGWSA----RCTHDIDCVIHFAAVKAVGESMQEPLMYYKN-NLIATINLLEVMK 105
DL++ LG S ++D +IH AA V + EP + N++ T +L + K
Sbjct: 66 DLSEPNLGLSDEDFQELAEEVDVIIHNAAT--V--NFVEPYSDLRATNVLGTREVLRLAK 121
Query: 106 SHGVYQLVFSSS----CTVYGEPQFLPITEDHPT----GNIKNVYGKTKHFIEEMLKDLS 157
S+ G + P D G + N Y ++K E++++
Sbjct: 122 QMKKLPFHHVSTAYVNGERGGLLEEKPYKLDEDEPALLGGLPNGYTQSKWLAEQLVR--- 178
Query: 158 KAHKEWNIISLRYFNP--VGAHP-SGRIGEDPTKSFTNIMPYLAQVAIG 203
+A ++ R P + +G I D + P G
Sbjct: 179 EAAGGLPVVIYR---PSIITGESRTGWINGD------DFGPRGLLGGAG 218
Score = 29.1 bits (66), Expect = 5.9
Identities = 23/91 (25%), Positives = 39/91 (42%), Gaps = 11/91 (12%)
Query: 252 KKVDFYSCDLVDKNRLG---EIFAK--HDIDCVIHFAAVKAVGESMQEPLMYYKN-NLIA 305
+++ + DL + LG E F + ++D +IH AA V + EP + N++
Sbjct: 58 ERIIPVAGDLS-EPNLGLSDEDFQELAEEVDVIIHNAAT--V--NFVEPYSDLRATNVLG 112
Query: 306 TINLLEVMKSHGVYQLVFSSSCTVYGEPQFL 336
T +L + K S+ V GE L
Sbjct: 113 TREVLRLAKQMKKLPFHHVSTAYVNGERGGL 143
>gnl|CDD|215146 PLN02260, PLN02260, probable rhamnose biosynthetic enzyme.
Length = 668
Score = 41.3 bits (97), Expect = 0.001
Identities = 30/92 (32%), Positives = 42/92 (45%), Gaps = 6/92 (6%)
Query: 242 SIRAIEQFTGKKVDFYSCDLVDKNRLGEIFAKHDIDCVIHFAAVKAVGESMQEPLMYYKN 301
++ F K D S DLV+ + E ID ++HFAA V S + KN
Sbjct: 52 PSKSSPNFKFVKGDIASADLVNYLLITE-----GIDTIMHFAAQTHVDNSFGNSFEFTKN 106
Query: 302 NLIATINLLEVMKSHG-VYQLVFSSSCTVYGE 332
N+ T LLE K G + + + S+ VYGE
Sbjct: 107 NIYGTHVLLEACKVTGQIRRFIHVSTDEVYGE 138
Score = 40.9 bits (96), Expect = 0.002
Identities = 30/90 (33%), Positives = 39/90 (43%), Gaps = 11/90 (12%)
Query: 64 THDIDCVIHFAAVKAVGESMQEPLMYYKNNLIATINLLEVMKSHG-VYQLVFSSSCTVYG 122
T ID ++HFAA V S + KNN+ T LLE K G + + + S+ VYG
Sbjct: 78 TEGIDTIMHFAAQTHVDNSFGNSFEFTKNNIYGTHVLLEACKVTGQIRRFIHVSTDEVYG 137
Query: 123 EPQFLPITEDH------PTGNIKNVYGKTK 146
E +H PT N Y TK
Sbjct: 138 ETDEDADVGNHEASQLLPT----NPYSATK 163
Score = 33.6 bits (77), Expect = 0.31
Identities = 20/87 (22%), Positives = 41/87 (47%), Gaps = 11/87 (12%)
Query: 93 NLIATINLLEVMKSHGVYQLVFSSSCTV-----YGEPQFLPITEDHPTGNIKNVYGKTKH 147
N++ T+ L +V + +G+ + F++ C + E + E+ + Y KTK
Sbjct: 458 NVVGTLTLADVCRENGLLMMNFATGCIFEYDAKHPEGSGIGFKEEDKPNFTGSFYSKTKA 517
Query: 148 FIEEMLKDLSKAHKEWNIISLRYFNPV 174
+EE+L++ N+ +LR P+
Sbjct: 518 MVEELLREYD------NVCTLRVRMPI 538
>gnl|CDD|200085 TIGR01214, rmlD, dTDP-4-dehydrorhamnose reductase. This enzyme
catalyzes the last of 4 steps in making dTDP-rhamnose, a
precursor of LPS core antigen, O-antigen, etc [Cell
envelope, Biosynthesis and degradation of surface
polysaccharides and lipopolysaccharides].
Length = 287
Score = 40.1 bits (94), Expect = 0.002
Identities = 25/79 (31%), Positives = 36/79 (45%), Gaps = 2/79 (2%)
Query: 68 DCVIHFAAVKAVGESMQEPLMYYKNNLIATINLLEVMKSHGVYQLVFSSSCTVYGEPQFL 127
D V++ AA V + +P + N +A NL HG LV S+ V+
Sbjct: 52 DAVVNTAAYTDVDGAESDPEKAFAVNALAPQNLARAAARHGAR-LVHISTDYVFDGEGKR 110
Query: 128 PITEDHPTGNIKNVYGKTK 146
P ED T + NVYG++K
Sbjct: 111 PYREDDATNPL-NVYGQSK 128
Score = 36.6 bits (85), Expect = 0.027
Identities = 28/113 (24%), Positives = 41/113 (36%), Gaps = 7/113 (6%)
Query: 239 TPCSIRAIEQFTGKKVDFYSCDLVDKNRLGEIFAKHDIDCVIHFAAVKAVGESMQEPLMY 298
R + T ++D L D L + D V++ AA V + +P
Sbjct: 19 LSPEGRVVVALTRSQLD-----LTDPEALERLLRAIRPDAVVNTAAYTDVDGAESDPEKA 73
Query: 299 YKNNLIATINLLEVMKSHGVYQLVFSSSCTVYGEPQFLPITEDHPTGNIKNFY 351
+ N +A NL HG LV S+ V+ P ED T + N Y
Sbjct: 74 FAVNALAPQNLARAAARHGAR-LVHISTDYVFDGEGKRPYREDDATNPL-NVY 124
>gnl|CDD|200381 TIGR04130, FnlA, UDP-N-acetylglucosamine
4,6-dehydratase/5-epimerase. The FnlA enzyme is the
first step in the biosynthesis of UDP-FucNAc from
UDP-GlcNAc in E. coli (along with FnlB and FnlC). The
proteins identified by this model include FnlA homologs
in the O-antigen clusters of O4, O25, O26, O29 (Shigella
D11), O118, O145 and O172 serotype strains, all of which
produce O-antigens containing FucNAc (or the further
modified FucNAm). A homolog from Pseudomonas aerugiosa
serotype O11, WbjB, also involved in the biosynthesis of
UDP-FucNAc has been characterized and is now believed to
carry out both the initial 4,6-dehydratase reaction and
the subsequent epimerization of the resulting methyl
group at C-5. A phylogenetic tree of related sequences
shows a distinct clade of enzymes involved in the
biosynthesis of UDP-QuiNAc (Qui=qinovosamine). This
clade appears to be descendant from the common ancestor
of the Pseudomonas and E. coli fucose-biosynthesis
enzymes. It has been hypothesized that the first step in
the biosynthesis of these two compounds may be the same,
and thus that these enzymes all have the same function.
At present, lacking sufficient confirmation of this, the
current model trusted cutoff only covers the tree
segment surrounding the E. coli genes. The clades
containing the Pseudomonas and QuiNAc biosynthesis
enzymes score above the noise cutoff. Immediately below
the noise cutoff are enzymes involved in the
biosynthesis of UDP-RhaNAc (Rha=rhamnose), which again
may or may not produce the same product.
Length = 337
Score = 38.4 bits (89), Expect = 0.008
Identities = 25/85 (29%), Positives = 44/85 (51%), Gaps = 3/85 (3%)
Query: 247 EQFTGKKVDFYSCDLVDKNRLGEIFAKHDIDCVIHFAAVKAVGESMQEPLMYYKNNLIAT 306
+++ K+ FY D+ D + + A +D + H AA+K V P+ K N++ T
Sbjct: 47 KKYNNSKLKFYIGDVRDYRSI--LNATRGVDFIYHAAALKQVPSCEFHPMEAVKTNVLGT 104
Query: 307 INLLEVMKSHGVYQLV-FSSSCTVY 330
N+LE ++GV ++V S+ VY
Sbjct: 105 ENVLEAAIANGVKRVVCLSTDKAVY 129
Score = 32.6 bits (74), Expect = 0.54
Identities = 20/59 (33%), Positives = 32/59 (54%), Gaps = 1/59 (1%)
Query: 64 THDIDCVIHFAAVKAVGESMQEPLMYYKNNLIATINLLEVMKSHGVYQLV-FSSSCTVY 121
T +D + H AA+K V P+ K N++ T N+LE ++GV ++V S+ VY
Sbjct: 71 TRGVDFIYHAAALKQVPSCEFHPMEAVKTNVLGTENVLEAAIANGVKRVVCLSTDKAVY 129
>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 = 37.8 bits (88), Expect = 0.011
Identities = 55/229 (24%), Positives = 92/229 (40%), Gaps = 38/229 (16%)
Query: 55 KELGWSARCTHDIDCVIHFAA-VKAVGESMQEPLMYYKNNLIATINLLEVMKSHGVYQLV 113
+E+ + T +D V H AA + +G + NN + N+LE + +GV + +
Sbjct: 53 REMENCLKATEGVDHVFHLAADMGGMGYIQSNHAVIMYNNTLINFNMLEAARINGVERFL 112
Query: 114 FSSSCTVYGEPQFLPIT--------EDHPTGNIKNVYGKTKHFIEEMLKDLSKAHK-EWN 164
F+SS VY P+F + ED ++ YG K E + + ++ + E
Sbjct: 113 FASSACVY--PEFKQLETTVVRLREEDAWPAEPQDAYGWEKLATERLCQHYNEDYGIETR 170
Query: 165 IISLRYFNPVGAHPSGRIGEDPTKSFTNIMPYLA-QVAIGSKPH-FTVFGADYETEDG-- 220
I+ R+ N G P G D + + +VA F ++G DG
Sbjct: 171 IV--RFHNIYG--PRGTW--DGGREK--APAAMCRKVATAKDGDRFEIWG------DGLQ 216
Query: 221 TGKVVAIDNFVNSVHIGDTPCSIRAIEQFTGKKVDFYSCDLVDKNRLGE 269
T ID+ V + R +E G+ V+ S ++V N L E
Sbjct: 217 TRSFTYIDDCVEGLR--------RLMESDFGEPVNLGSDEMVSMNELAE 257
Score = 37.5 bits (87), Expect = 0.015
Identities = 28/114 (24%), Positives = 43/114 (37%), Gaps = 17/114 (14%)
Query: 224 VVAIDNFVNSVHIGDTPCSIRAIEQFTGKKVDFYSCDLVDKNRLGEIFAKHDIDCVIHFA 283
V D T E F+ DL + + A +D V H A
Sbjct: 27 VRGADWKSPEHMTQPT----DDDE--------FHLVDL--REMENCLKATEGVDHVFHLA 72
Query: 284 A-VKAVGESMQEPLMYYKNNLIATINLLEVMKSHGVYQLVFSSSCTVYGEPQFL 336
A + +G + NN + N+LE + +GV + +F+SS VY P+F
Sbjct: 73 ADMGGMGYIQSNHAVIMYNNTLINFNMLEAARINGVERFLFASSACVY--PEFK 124
Score = 34.0 bits (78), Expect = 0.22
Identities = 20/71 (28%), Positives = 31/71 (43%), Gaps = 5/71 (7%)
Query: 516 LLRTFERVTGKPVPYIFYNLGTGQGTSVLQLLRTFERVTGKPVPYIVEARREGDIVSMYA 575
L R E G+PV NLG+ + S+ +L +GKP+ I + +
Sbjct: 230 LRRLMESDFGEPV-----NLGSDEMVSMNELAEMVLSFSGKPLEIIHHTPGPQGVRGRNS 284
Query: 576 NTDLAQRELGW 586
+ L + ELGW
Sbjct: 285 DNTLLKEELGW 295
Score = 31.3 bits (71), Expect = 1.5
Identities = 14/53 (26%), Positives = 25/53 (47%)
Query: 7 NLGTGQGTSVLQLLRTFERVTGKPVPYIVEARREGDIVSMYANTDLAQKELGW 59
NLG+ + S+ +L +GKP+ I + ++ L ++ELGW
Sbjct: 243 NLGSDEMVSMNELAEMVLSFSGKPLEIIHHTPGPQGVRGRNSDNTLLKEELGW 295
Score = 29.4 bits (66), Expect = 5.8
Identities = 17/56 (30%), Positives = 26/56 (46%), Gaps = 6/56 (10%)
Query: 426 LLRTFERVTGKPVPYIFYNLGTGQGTSVLQLLRTFERVTGKPVPYIFYNLGTGQGT 481
L R E G+PV NLG+ + S+ +L +GKP+ I ++ QG
Sbjct: 230 LRRLMESDFGEPV-----NLGSDEMVSMNELAEMVLSFSGKPLEII-HHTPGPQGV 279
Score = 29.4 bits (66), Expect = 5.8
Identities = 17/56 (30%), Positives = 26/56 (46%), Gaps = 6/56 (10%)
Query: 456 LLRTFERVTGKPVPYIFYNLGTGQGTSVLQLLRTFERVTGKPVPYIFYNLGTGQGT 511
L R E G+PV NLG+ + S+ +L +GKP+ I ++ QG
Sbjct: 230 LRRLMESDFGEPV-----NLGSDEMVSMNELAEMVLSFSGKPLEII-HHTPGPQGV 279
Score = 29.4 bits (66), Expect = 5.8
Identities = 17/56 (30%), Positives = 26/56 (46%), Gaps = 6/56 (10%)
Query: 486 LLRTFERVTGKPVPYIFYNLGTGQGTSVLQLLRTFERVTGKPVPYIFYNLGTGQGT 541
L R E G+PV NLG+ + S+ +L +GKP+ I ++ QG
Sbjct: 230 LRRLMESDFGEPV-----NLGSDEMVSMNELAEMVLSFSGKPLEII-HHTPGPQGV 279
>gnl|CDD|178377 PLN02778, PLN02778, 3,5-epimerase/4-reductase.
Length = 298
Score = 37.8 bits (88), Expect = 0.013
Identities = 22/94 (23%), Positives = 37/94 (39%), Gaps = 25/94 (26%)
Query: 93 NLIATINLLEVMKSHGVYQLVFSSSCTVYGEPQFLPITEDHPTGN------------IKN 140
N++ T+ L +V + G+ T Y + HP G+ +
Sbjct: 87 NVVGTLTLADVCRERGLV-------LTNYATGCIFEYDDAHPLGSGIGFKEEDTPNFTGS 139
Query: 141 VYGKTKHFIEEMLKDLSKAHKEWNIISLRYFNPV 174
Y KTK +EE+LK+ N+ +LR P+
Sbjct: 140 FYSKTKAMVEELLKNYE------NVCTLRVRMPI 167
>gnl|CDD|132628 TIGR03589, PseB, UDP-N-acetylglucosamine 4,6-dehydratase. This
enzyme catalyzes the first step in the biosynthesis of
pseudaminic acid, the conversion of
UDP-N-acetylglucosamine to
UDP-4-keto-6-deoxy-N-acetylglucosamine. These sequences
are members of the broader pfam01073 (3-beta
hydroxysteroid dehydrogenase/isomerase family) family.
Length = 324
Score = 37.4 bits (87), Expect = 0.015
Identities = 21/76 (27%), Positives = 38/76 (50%), Gaps = 2/76 (2%)
Query: 247 EQFTGKKVDFYSCDLVDKNRLGEIFAKHDIDCVIHFAAVKAVGESMQEPLMYYKNNLIAT 306
++F + F+ D+ DK RL A +D V+H AA+K V + P + N+
Sbjct: 48 QKFPAPCLRFFIGDVRDKERL--TRALRGVDYVVHAAALKQVPAAEYNPFECIRTNINGA 105
Query: 307 INLLEVMKSHGVYQLV 322
N+++ +GV ++V
Sbjct: 106 QNVIDAAIDNGVKRVV 121
Score = 29.3 bits (66), Expect = 6.2
Identities = 14/52 (26%), Positives = 26/52 (50%)
Query: 62 RCTHDIDCVIHFAAVKAVGESMQEPLMYYKNNLIATINLLEVMKSHGVYQLV 113
R +D V+H AA+K V + P + N+ N+++ +GV ++V
Sbjct: 70 RALRGVDYVVHAAALKQVPAAEYNPFECIRTNINGAQNVIDAAIDNGVKRVV 121
>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 = 35.3 bits (82), Expect = 0.057
Identities = 42/180 (23%), Positives = 61/180 (33%), Gaps = 27/180 (15%)
Query: 308 NLLEVMKSHGVYQLVFSSSCTVYGEPQFLPITEDHPTGNIKNFYNLGTGQGTSVLQLLRT 367
L+ K V Q +F SS +VY +P ITE P +G + R
Sbjct: 81 RALDAFKGR-VKQYIFISSASVYLKPG-RVITESTPLREP---DAVGLSDPWDYGRGKRA 135
Query: 368 FERVTGNKPV-PYI----FYNLGTGQGTSVLQLLRTFERVTGNKPVPYIFYNLGTGQGTS 422
E V PY Y G G T L F+R+ +P+ G G S
Sbjct: 136 AEDVLIEAAAFPYTIVRPPYIYGPGDYTGRLAYF--FDRLARGRPILV------PGDGHS 187
Query: 423 VLQ------LLRTFERVTGKPVPY--IFYNLGTGQGTSVLQLLRTFERVTGKPVPYIFYN 474
++Q L R G P I +N+ + + +LL + GK +
Sbjct: 188 LVQFIHVKDLARALLGAAGNPKAIGGI-FNITGDEAVTWDELLEACAKALGKEAEIVHVE 246
Score = 30.7 bits (70), Expect = 1.9
Identities = 20/64 (31%), Positives = 28/64 (43%), Gaps = 9/64 (14%)
Query: 99 NLLEVMKSHGVYQLVFSSSCTVYGEPQFLPITEDHPTGNIKNV-------YGKTKHFIEE 151
L+ K V Q +F SS +VY +P ITE P V YG+ K E+
Sbjct: 81 RALDAFKGR-VKQYIFISSASVYLKPG-RVITESTPLREPDAVGLSDPWDYGRGKRAAED 138
Query: 152 MLKD 155
+L +
Sbjct: 139 VLIE 142
>gnl|CDD|187555 cd05244, BVR-B_like_SDR_a, biliverdin IX beta reductase (BVR-B, aka
flavin reductase)-like proteins; atypical (a) SDRs.
Human BVR-B catalyzes pyridine nucleotide-dependent
production of bilirubin-IX beta during fetal
development; in the adult BVR-B has flavin and ferric
reductase activities. Human BVR-B catalyzes the
reduction of FMN, FAD, and riboflavin. Recognition of
flavin occurs mostly by hydrophobic interactions,
accounting for the broad substrate specificity. Atypical
SDRs are distinct from classical SDRs. BVR-B does not
share the key catalytic triad, or conserved tyrosine
typical of SDRs. The glycine-rich NADP-binding motif of
BVR-B is GXXGXXG, which is similar but not identical to
the pattern seen in extended SDRs. 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 = 207
Score = 34.1 bits (79), Expect = 0.11
Identities = 17/86 (19%), Positives = 28/86 (32%), Gaps = 30/86 (34%)
Query: 96 ATINLLEVMKSHGVYQLVFSSS--------------CTVYGEPQFLPITEDHPTGNIKNV 141
T N++ MK+ GV +L+ T+ P + EDH
Sbjct: 85 GTRNIVSAMKAAGVKRLIVVGGAGSLDDRPKVTLVLDTLLFPPALRRVAEDH-------- 136
Query: 142 YGKTKHFIEEMLKDLSKAHKEWNIIS 167
MLK L ++ +W +
Sbjct: 137 --------ARMLKVLRESGLDWTAVR 154
Score = 28.7 bits (65), Expect = 6.6
Identities = 19/97 (19%), Positives = 32/97 (32%), Gaps = 23/97 (23%)
Query: 260 DLVDKNRLGEIFAKHDIDCVIHFAAVKAVGESMQEPLMYYKNNLIATINLLEVMKSHGVY 319
D++D + E D A + A+G + T N++ MK+ GV
Sbjct: 49 DVLDLEDVKEALEGQD-------AVISALGTRNDLSP--TTLHSEGTRNIVSAMKAAGVK 99
Query: 320 QLVFSSS--------------CTVYGEPQFLPITEDH 342
+L+ T+ P + EDH
Sbjct: 100 RLIVVGGAGSLDDRPKVTLVLDTLLFPPALRRVAEDH 136
>gnl|CDD|165812 PLN02166, PLN02166, dTDP-glucose 4,6-dehydratase.
Length = 436
Score = 33.1 bits (75), Expect = 0.48
Identities = 39/157 (24%), Positives = 69/157 (43%), Gaps = 17/157 (10%)
Query: 66 DIDCVIHFAAVKAVGESMQEPLMYYKNNLIATINLLEVMKSHGVYQLVFSSSCTVYGEPQ 125
++D + H A + P+ K N++ T+N+L + K G + + +S+ VYG+P
Sbjct: 184 EVDQIYHLACPASPVHYKYNPVKTIKTNVMGTLNMLGLAKRVGA-RFLLTSTSEVYGDPL 242
Query: 126 FLPITEDH-----PTGNIKNVYGKTKHFIEEMLKDLSKAHKEWNIISLRYFNPVGAHPSG 180
P E + P G ++ Y + K E + D + + R FN G
Sbjct: 243 EHPQKETYWGNVNPIG-ERSCYDEGKRTAETLAMDYHRG-AGVEVRIARIFNTYGP---- 296
Query: 181 RIGEDPTKSFTNIMPYLAQVAIGSKPHFTVFGADYET 217
R+ D + +N ++AQ I +P TV+G +T
Sbjct: 297 RMCLDDGRVVSN---FVAQ-TIRKQP-MTVYGDGKQT 328
Score = 30.7 bits (69), Expect = 2.2
Identities = 32/130 (24%), Positives = 56/130 (43%), Gaps = 26/130 (20%)
Query: 223 KVVAIDNFV-----NSVHIGDTPCSIRAIEQFTGKKVDFYSCDLVDKNRLGEIFAKHDID 277
+V+ IDNF N VH+ F + + D+V+ L ++D
Sbjct: 146 EVIVIDNFFTGRKENLVHL------------FGNPRFELIRHDVVEPILL-------EVD 186
Query: 278 CVIHFAAVKAVGESMQEPLMYYKNNLIATINLLEVMKSHGVYQLVFSSSCTVYGEPQFLP 337
+ H A + P+ K N++ T+N+L + K G + + +S+ VYG+P P
Sbjct: 187 QIYHLACPASPVHYKYNPVKTIKTNVMGTLNMLGLAKRVGA-RFLLTSTSEVYGDPLEHP 245
Query: 338 ITEDHPTGNI 347
E + GN+
Sbjct: 246 QKETY-WGNV 254
>gnl|CDD|177856 PLN02206, PLN02206, UDP-glucuronate decarboxylase.
Length = 442
Score = 33.0 bits (75), Expect = 0.49
Identities = 42/158 (26%), Positives = 74/158 (46%), Gaps = 19/158 (12%)
Query: 66 DIDCVIHFAAVKAVGESMQEPLMYYKNNLIATINLLEVMKSHGVYQLVFSSSCTVYGEPQ 125
++D + H A + P+ K N++ T+N+L + K G + + +S+ VYG+P
Sbjct: 183 EVDQIYHLACPASPVHYKFNPVKTIKTNVVGTLNMLGLAKRVGA-RFLLTSTSEVYGDPL 241
Query: 126 FLPITEDH-----PTGNIKNVYGKTKHFIEEMLKDLSK-AHKEWNIISLRYFNPVGAHPS 179
P E + P G +++ Y + K E + D + A+ E I R FN G
Sbjct: 242 QHPQVETYWGNVNPIG-VRSCYDEGKRTAETLTMDYHRGANVEVRIA--RIFNTYGP--- 295
Query: 180 GRIGEDPTKSFTNIMPYLAQVAIGSKPHFTVFGADYET 217
R+ D + +N ++AQ A+ +P TV+G +T
Sbjct: 296 -RMCIDDGRVVSN---FVAQ-ALRKEP-LTVYGDGKQT 327
Score = 30.3 bits (68), Expect = 3.0
Identities = 20/73 (27%), Positives = 37/73 (50%), Gaps = 2/73 (2%)
Query: 275 DIDCVIHFAAVKAVGESMQEPLMYYKNNLIATINLLEVMKSHGVYQLVFSSSCTVYGEPQ 334
++D + H A + P+ K N++ T+N+L + K G + + +S+ VYG+P
Sbjct: 183 EVDQIYHLACPASPVHYKFNPVKTIKTNVVGTLNMLGLAKRVGA-RFLLTSTSEVYGDPL 241
Query: 335 FLPITEDHPTGNI 347
P E + GN+
Sbjct: 242 QHPQVETY-WGNV 253
>gnl|CDD|163279 TIGR03466, HpnA, hopanoid-associated sugar epimerase. The
sequences in this family are members of the pfam01370
superfamily of NAD-dependent epimerases and dehydratases
typically acting on nucleotide-sugar substrates. The
genes of the family modeled here are generally in the
same locus with genes involved in the biosynthesis and
elaboration of hopene, the cyclization product of the
polyisoprenoid squalene. This gene and its association
with hopene biosynthesis in Zymomonas mobilis has been
noted in the literature where the gene symbol hpnA was
assigned. Hopanoids are known to be components of the
plasma membrane and to have polar sugar head groups in
Z. mobilis and other species.
Length = 328
Score = 32.7 bits (75), Expect = 0.49
Identities = 25/103 (24%), Positives = 45/103 (43%), Gaps = 13/103 (12%)
Query: 90 YKNNLIATINLLEVMKSHGVYQLVFSSSC---TVYGEPQFLPITEDHPT--GNIKNVYGK 144
Y N+ T NLL GV ++V++SS V G+ P E P+ ++ Y +
Sbjct: 86 YAANVEGTRNLLRAALEAGVERVVYTSSVATLGVRGDGT--PADETTPSSLDDMIGHYKR 143
Query: 145 TKHFIEEMLKDLSKAHKEWNIISLRYFNPVGAH-----PSGRI 182
+K E+ +++ ++ + P+G P+GRI
Sbjct: 144 SKFLAEQAALEMAAEKGL-PVVIVNPSTPIGPRDIKPTPTGRI 185
Score = 31.5 bits (72), Expect = 1.3
Identities = 25/94 (26%), Positives = 41/94 (43%), Gaps = 18/94 (19%)
Query: 503 YNLGTGQGTSVLQLLRTFERVTGKPVP------YIFYNLGTGQGTSVLQLLRTFERVTGK 556
Y LG G+ ++ Q+L +TG+P P ++ + G R+TGK
Sbjct: 227 YILG-GENLTLKQILDKLAEITGRPAPRVKLPRWLLLPVAWGA--------EALARLTGK 277
Query: 557 PVPYI-VEARREGDIVSMYANTDLAQRELGWSAR 589
P + V+ R M+ ++ A RELG+ R
Sbjct: 278 E-PRVTVDGVRMAK-KKMFFSSAKAVRELGYRQR 309
>gnl|CDD|187546 cd05235, SDR_e1, extended (e) SDRs, subgroup 1. This family
consists of an SDR module of multidomain proteins
identified as putative polyketide sythases fatty acid
synthases (FAS), and nonribosomal peptide synthases,
among others. However, unlike the usual ketoreductase
modules of FAS and polyketide synthase, these domains
are related to the extended SDRs, and have canonical
NAD(P)-binding motifs and an active site tetrad.
Extended SDRs are distinct from classical SDRs. In
addition to the Rossmann fold (alpha/beta folding
pattern with a central beta-sheet) core region typical
of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 290
Score = 31.9 bits (73), Expect = 0.85
Identities = 25/109 (22%), Positives = 45/109 (41%), Gaps = 19/109 (17%)
Query: 51 DLAQKELGWS----ARCTHDIDCVIHFAA-VKAVG--ESMQEPLMYYKNNLIATINLLEV 103
DL++ LG S ++D +IH A V V E ++ N++ T LL++
Sbjct: 70 DLSKPNLGLSDDDYQELAEEVDVIIHNGANVNWVYPYEELKPA------NVLGTKELLKL 123
Query: 104 MKSHGVYQLVFSSSCTVYGEPQ--FLPITEDHPT----GNIKNVYGKTK 146
+ + L F S+ +V+ + L E + N Y ++K
Sbjct: 124 AATGKLKPLHFVSTLSVFSAEEYNALDDEESDDMLESQNGLPNGYIQSK 172
>gnl|CDD|187625 cd05367, SPR-like_SDR_c, sepiapterin reductase (SPR)-like,
classical (c) SDRs. Human SPR, a member of the SDR
family, catalyzes the NADP-dependent reduction of
sepiaptern to 7,8-dihydrobiopterin (BH2). In addition to
SPRs, this subgroup also contains Bacillus cereus yueD,
a benzil reductase, which catalyzes the stereospecific
reduction of benzil to (S)-benzoin. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold (alpha/beta folding pattern with a central
beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRs are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes catalyze a
wide range of activities including the metabolism of
steroids, cofactors, carbohydrates, lipids, aromatic
compounds, and amino acids, and act in redox sensing.
Classical SDRs have an TGXXX[AG]XG cofactor binding
motif and a YXXXK active site motif, with the Tyr
residue of the active site motif serving as a critical
catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 241
Score = 31.5 bits (72), Expect = 0.89
Identities = 21/95 (22%), Positives = 35/95 (36%), Gaps = 15/95 (15%)
Query: 247 EQFTGKKVDFYSCDLVDKNRLGEIFA-----KHDIDCVIHFAA----VKAVGE-SMQEPL 296
E G +V DL D + ++ + D +I+ A V + + E
Sbjct: 44 ELRPGLRVTTVKADLSDAAGVEQLLEAIRKLDGERDLLINNAGSLGPVSKIEFIDLDELQ 103
Query: 297 MYYKNNLIATINL----LEVMKSHGVYQL-VFSSS 326
Y+ NL + + L L K G+ + V SS
Sbjct: 104 KYFDLNLTSPVCLTSTLLRAFKKRGLKKTVVNVSS 138
>gnl|CDD|181044 PRK07577, PRK07577, short chain dehydrogenase; Provisional.
Length = 234
Score = 31.6 bits (72), Expect = 0.99
Identities = 12/46 (26%), Positives = 23/46 (50%), Gaps = 7/46 (15%)
Query: 244 RAIEQFTGKKVDFYSCDLVDKNR----LGEIFAKHDIDCVIHFAAV 285
AI+ F G+ ++CDL D + L +I H +D +++ +
Sbjct: 36 SAIDDFPGE---LFACDLADIEQTAATLAQINEIHPVDAIVNNVGI 78
>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 = 31.3 bits (71), Expect = 1.4
Identities = 29/100 (29%), Positives = 42/100 (42%), Gaps = 10/100 (10%)
Query: 61 ARCTHDIDCVIHFAA-VKAVGESMQEPLMYYKNNLIATINLLEVMKSHGVYQLVFSSSCT 119
R + VIH AA V G E L + N+ T +LE + V +LV++SS
Sbjct: 67 FRACQGVSVVIHTAAIVDVFGPPNYEELE--EVNVNGTQAVLEACVQNNVKRLVYTSSIE 124
Query: 120 V-----YGEPQFLPITEDHPTGNI-KNVYGKTKHFIEEML 153
V G P F + ED P + Y +K E ++
Sbjct: 125 VAGPNFKGRPIFNGV-EDTPYEDTSTPPYASSKLLAENIV 163
Score = 30.2 bits (68), Expect = 3.4
Identities = 34/112 (30%), Positives = 47/112 (41%), Gaps = 14/112 (12%)
Query: 247 EQFTGK-KVDFYSCDLVDKNRLGEIF-AKHDIDCVIHFAA-VKAVGESMQEPLMYYKNNL 303
E+ GK V D+ D L +F A + VIH AA V G E L + N+
Sbjct: 45 EKSQGKTYVTDIEGDIKD---LSFLFRACQGVSVVIHTAAIVDVFGPPNYEELE--EVNV 99
Query: 304 IATINLLEVMKSHGVYQLVFSSSCTV-----YGEPQFLPITEDHPTGNIKNF 350
T +LE + V +LV++SS V G P F + ED P +
Sbjct: 100 NGTQAVLEACVQNNVKRLVYTSSIEVAGPNFKGRPIFNGV-EDTPYEDTSTP 150
>gnl|CDD|99799 cd06202, Nitric_oxide_synthase, The ferredoxin-reductase (FNR) like
C-terminal domain of the nitric oxide synthase (NOS)
fuses with a heme-containing N-terminal oxidase domain.
The reductase portion is similar in structure to NADPH
dependent cytochrome-450 reductase (CYPOR), having an
inserted connecting sub-domain within the FAD binding
portion of FNR. NOS differs from CYPOR in a requirement
for the cofactor tetrahydrobiopterin and unlike most
CYPOR is dimeric. Nitric oxide synthase produces nitric
oxide in the conversion of L-arginine to L-citruline.
NOS has been implicated in a variety of processes
including cytotoxicity, anti-inflamation,
neurotransmission, and vascular smooth muscle
relaxation.
Length = 406
Score = 31.1 bits (71), Expect = 1.7
Identities = 17/46 (36%), Positives = 22/46 (47%), Gaps = 3/46 (6%)
Query: 207 HFTVFGADYETEDGTGKVV--AIDNFVNSVHIGDT-PCSIRAIEQF 249
H TV Y T DG G V ++N + GDT PC +R+ F
Sbjct: 194 HLTVAVVSYRTRDGQGPVHHGVCSTWLNGLTPGDTVPCFVRSAPSF 239
>gnl|CDD|178298 PLN02695, PLN02695, GDP-D-mannose-3',5'-epimerase.
Length = 370
Score = 30.9 bits (70), Expect = 1.8
Identities = 22/79 (27%), Positives = 38/79 (48%), Gaps = 11/79 (13%)
Query: 87 LMYYKNNLIATINLLEVMKSHGVYQLVFSSSCTVYGEPQFLPITE-------DHPTGNIK 139
+MY NN + + N+LE + +GV + ++SS +Y P+F + D +
Sbjct: 109 IMY--NNTMISFNMLEAARINGVKRFFYASSACIY--PEFKQLETNVSLKESDAWPAEPQ 164
Query: 140 NVYGKTKHFIEEMLKDLSK 158
+ YG K EE+ K +K
Sbjct: 165 DAYGLEKLATEELCKHYTK 183
Score = 29.8 bits (67), Expect = 3.8
Identities = 13/37 (35%), Positives = 23/37 (62%), Gaps = 2/37 (5%)
Query: 296 LMYYKNNLIATINLLEVMKSHGVYQLVFSSSCTVYGE 332
+MY NN + + N+LE + +GV + ++SS +Y E
Sbjct: 109 IMY--NNTMISFNMLEAARINGVKRFFYASSACIYPE 143
>gnl|CDD|225917 COG3382, COG3382, Solo B3/4 domain (OB-fold DNA/RNA-binding) of
Phe-aaRS-beta [General function prediction only].
Length = 229
Score = 30.8 bits (70), Expect = 1.8
Identities = 24/109 (22%), Positives = 38/109 (34%), Gaps = 28/109 (25%)
Query: 143 GKTKHFIEEMLKDLSK---------AHKEWNIISLRYFNPVGAHPSGRIGEDPTKSFTNI 193
KT+ E +L+ + K +N SL+Y P+G + + +I D +
Sbjct: 78 TKTRPSAEALLRRVLKGNSLPRINPVVDIYNAASLKYAVPIGGYDADKIVGDLRLTL--- 134
Query: 194 MPYLAQVAIGSKPHFTVFGADYETE--------DGTGKVVAIDNFVNSV 234
A G + F GA E D G N+ +SV
Sbjct: 135 -------ADGGE-TFDTLGAKNEPPLEGEIVLVDDEGAFCRRWNWRDSV 175
>gnl|CDD|107294 cd06299, PBP1_LacI_like_13, Ligand-binding domain of DNA-binding
regulatory protein from Corynebacterium glutamicum which
has a unique ability to produce significant amounts of
L-glutamate directly from cheap sugar and ammonia. This
group includes the ligand-binding domain of DNA-binding
regulatory protein from Corynebacterium glutamicum which
has a unique ability to produce significant amounts of
L-glutamate directly from cheap sugar and ammonia. This
regulatory protein is a member of the LacI-GalR family
of bacterial transcription repressors. The LacI-GalR
family repressors are composed of two functional
domains: an N-terminal HTH (helix-turn-helix) domain,
which is responsible for the DNA-binding specificity,
and a C-terminal ligand-binding domain, which is
homologous to the sugar-binding domain of ABC-type
transport systems that contain the type I periplasmic
binding protein-like fold. As also observed in the
periplasmic binding proteins, the C-terminal domain of
the bacterial transcription repressor undergoes a
conformational change upon ligand binding which in turn
changes the DNA binding affinity of the repressor.
Length = 265
Score = 30.8 bits (70), Expect = 1.9
Identities = 13/58 (22%), Positives = 20/58 (34%), Gaps = 7/58 (12%)
Query: 210 VFGADYETEDG-TGKVVAIDNFVNSVHIGDTPCSIRAIEQF------TGKKVDFYSCD 260
V Y E G G +D ++ GD+ +I AI G+ + D
Sbjct: 154 VVLGGYSQESGYAGATKLLDQGATAIIAGDSMMTIGAIRAIHDAGLVIGEDISLIGFD 211
>gnl|CDD|187540 cd05229, SDR_a3, atypical (a) SDRs, subgroup 3. These atypical SDR
family members of unknown function have a glycine-rich
NAD(P)-binding motif consensus that is very similar to
the extended SDRs, GXXGXXG. Generally, this group has
poor conservation of the active site tetrad, However,
individual sequences do contain matches to the YXXXK
active site motif, and generally Tyr or Asn in place of
the upstream Ser found in most SDRs. 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 = 302
Score = 30.4 bits (69), Expect = 2.3
Identities = 10/24 (41%), Positives = 13/24 (54%)
Query: 111 QLVFSSSCTVYGEPQFLPITEDHP 134
+LV + +YG PITED P
Sbjct: 97 KLVLPGNVYMYGPQAGSPITEDTP 120
Score = 30.4 bits (69), Expect = 2.3
Identities = 10/24 (41%), Positives = 13/24 (54%)
Query: 320 QLVFSSSCTVYGEPQFLPITEDHP 343
+LV + +YG PITED P
Sbjct: 97 KLVLPGNVYMYGPQAGSPITEDTP 120
>gnl|CDD|149922 pfam09015, NgoMIV_restric, NgoMIV restriction enzyme. Members of
this family are prokaryotic DNA restriction enzymes,
exhibiting an alpha/beta structure, with a central
region comprising a mixed six-stranded beta-sheet with
alpha-helices on each side. A long 'arm' protrudes out
of the core of the domain between strands beta2 and
beta3 and is mainly involved in the tetramerisation
interface of the protein. These restriction enzymes
recognise the double-stranded sequence GCCGGC and cleave
after G-1.
Length = 277
Score = 30.1 bits (68), Expect = 2.8
Identities = 15/32 (46%), Positives = 17/32 (53%), Gaps = 6/32 (18%)
Query: 64 THDIDCVIHFA------AVKAVGESMQEPLMY 89
T DIDCV HFA AVKA+G L+
Sbjct: 226 TGDIDCVYHFALPELEAAVKALGNEDALDLLQ 257
Score = 29.0 bits (65), Expect = 7.4
Identities = 14/30 (46%), Positives = 16/30 (53%), Gaps = 6/30 (20%)
Query: 275 DIDCVIHFA------AVKAVGESMQEPLMY 298
DIDCV HFA AVKA+G L+
Sbjct: 228 DIDCVYHFALPELEAAVKALGNEDALDLLQ 257
>gnl|CDD|222146 pfam13460, NAD_binding_10, NADH(P)-binding.
Length = 182
Score = 29.6 bits (67), Expect = 3.5
Identities = 21/101 (20%), Positives = 33/101 (32%), Gaps = 15/101 (14%)
Query: 243 IRAIEQFTGKKVDFYSCDLVDKNRLGEIFAKHDIDCVIHFAAVKAVGESMQEPLMYYKNN 302
R + V DL D L E A D V F A + ++
Sbjct: 29 SRNPSKAPAPGVTPVQKDLFDLADLAEALAGVDA-VVDAFGARPDDSDGVK--------- 78
Query: 303 LIATINLLEVMKSHGVYQLVFSSSCTVYGEPQFLPITEDHP 343
+LL+ GV ++V S+ +Y + +D P
Sbjct: 79 -----HLLDAAARAGVRRIVVVSAAGLYRDEPGTFRLDDAP 114
Score = 28.4 bits (64), Expect = 7.4
Identities = 9/39 (23%), Positives = 17/39 (43%)
Query: 96 ATINLLEVMKSHGVYQLVFSSSCTVYGEPQFLPITEDHP 134
+LL+ GV ++V S+ +Y + +D P
Sbjct: 76 GVKHLLDAAARAGVRRIVVVSAAGLYRDEPGTFRLDDAP 114
>gnl|CDD|187554 cd05243, SDR_a5, atypical (a) SDRs, subgroup 5. This subgroup
contains atypical SDRs, some of which are identified as
putative NAD(P)-dependent epimerases, one as a putative
NAD-dependent epimerase/dehydratase. Atypical SDRs are
distinct from classical SDRs. Members of this subgroup
have a glycine-rich NAD(P)-binding motif that is very
similar to the extended SDRs, GXXGXXG, and binds NADP.
Generally, this subgroup has poor conservation of the
active site tetrad; however, individual sequences do
contain matches to the YXXXK active site motif, the
upstream Ser, and there is a highly conserved Asp in
place of the usual active site Asn throughout the
subgroup. Atypical SDRs generally lack the catalytic
residues characteristic of the SDRs, and their
glycine-rich NAD(P)-binding motif is often different
from the forms normally seen in classical or extended
SDRs. Atypical SDRs include biliverdin IX beta reductase
(BVR-B,aka flavin reductase), NMRa (a negative
transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 203
Score = 29.5 bits (67), Expect = 3.6
Identities = 22/83 (26%), Positives = 29/83 (34%), Gaps = 7/83 (8%)
Query: 244 RAIEQFTGKKVDFYSCDLVDKNRLGEIFAKHDIDCVIHFAAVKAVGESMQEPLMYYKNNL 303
E+ + DL D L A ID VI AA G + +
Sbjct: 34 SQAEKLEAAGAEVVVGDLTDAESL--AAALEGIDAVI-SAA----GSGGKGGPRTEAVDY 86
Query: 304 IATINLLEVMKSHGVYQLVFSSS 326
INL++ K GV + V SS
Sbjct: 87 DGNINLIDAAKKAGVKRFVLVSS 109
>gnl|CDD|222413 pfam13843, DDE_Tnp_1_7, Transposase IS4.
Length = 352
Score = 29.9 bits (68), Expect = 3.6
Identities = 21/96 (21%), Positives = 31/96 (32%), Gaps = 27/96 (28%)
Query: 220 GTGKVVAIDNFVNSVHIGDTPCSIRAIEQFTGKKVDFYSCDLVDKNRLG--EIFAKHDID 277
GTG+ V +DNF S+ ++ K Y+ + NR G + K
Sbjct: 208 GTGRHVYMDNFY---------TSLPLAQEL--LKKGTYAVGTLRSNRAGLPKALKKK--- 253
Query: 278 CVIHFAAVKAVGESM---QEPLMYYKNNLIATINLL 310
G + PLM K + LL
Sbjct: 254 --------LPRGSILYRYDGPLMLVKWRDKKVVLLL 281
>gnl|CDD|227291 COG4955, COG4955, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 343
Score = 29.8 bits (67), Expect = 4.4
Identities = 11/46 (23%), Positives = 19/46 (41%), Gaps = 3/46 (6%)
Query: 112 LVFSSSCTVYGEPQFLPITEDHPTGN-IKNVYGKTKHFIEEMLKDL 156
LV S G F+P+T+++ +K V K ++ L
Sbjct: 116 LVQVLSNKKQGVFHFVPVTQNNKVQQWVKIVLNYQKE--IQLAIRL 159
>gnl|CDD|238999 cd02044, ov-serpin, ovalbumin family of serpins (ov-serpins).
Family of closely related proteins, whose members can be
secreted (ovalbumin), cytosolic (leukocyte elastase
inhibitor, LEI), or targeted to both compartments
(plasminogen activator inhibitor 2, PAI-2). This
subgroup corresponds to clade B of the serpin
superfamily. In general, serpins exhibit conformational
polymorphism shifting from native to cleaved, latent,
delta, or polymorphic forms. Many serpins, such as
antitrypsin and antichymotrypsin, function as serine
protease inhibitors which regulate blood coagulation
cascades. Non-inhibitory serpins perform many diverse
functions such as chaperoning proteins or transporting
hormones. Serpins are of medical interest because
mutants can cause blood clotting disorders, emphysema,
cirrhosis, and dementia.
Length = 370
Score = 29.8 bits (67), Expect = 4.6
Identities = 29/117 (24%), Positives = 44/117 (37%), Gaps = 36/117 (30%)
Query: 148 FIEEMLKDLSKAHKEWNIISLRYFNPVGAHPSGRIGEDPTKSFTNIMPYLAQVAIGSKPH 207
F ++ K+LSK N+ +F+P+ IM LA V +G+K
Sbjct: 8 FAVDVFKELSKKSALQNV----FFSPIA-----------------IMSSLAMVYLGAKG- 45
Query: 208 FTVFGADYETEDGTGKVVAIDNFVNSVHIGDTPCSIRAIEQFTGKKVDFYSCDLVDK 264
T + GKV+ DN D S + + K FYS LV++
Sbjct: 46 --------STANQIGKVLHFDNVK------DVHSSFQTLLSDINKLNSFYSLKLVNR 88
>gnl|CDD|179300 PRK01528, truB, tRNA pseudouridine synthase B; Provisional.
Length = 292
Score = 29.5 bits (66), Expect = 4.9
Identities = 23/68 (33%), Positives = 33/68 (48%), Gaps = 9/68 (13%)
Query: 197 LAQVAIGSKPH--FTV-FGADYETEDGTGKVVAIDNFVNSVHIGDTPCS--IRAIEQ--- 248
L Q+ I +K FTV FG ++ D GKV+A +++ S CS I I Q
Sbjct: 56 LVQLLIDAKKTYIFTVKFGKQTDSGDYAGKVIATKDYIPSKEEAYAVCSKFIGNITQIPP 115
Query: 249 -FTGKKVD 255
F+ KV+
Sbjct: 116 AFSALKVN 123
>gnl|CDD|235681 PRK06039, ileS, isoleucyl-tRNA synthetase; Reviewed.
Length = 975
Score = 29.7 bits (68), Expect = 5.1
Identities = 15/32 (46%), Positives = 16/32 (50%), Gaps = 5/32 (15%)
Query: 194 MPYLAQVAIGSKPHFTVFGADY-ETEDGTGKV 224
PY A K F V AD+ TEDGTG V
Sbjct: 291 FPYFADE----KNAFRVVLADFVTTEDGTGIV 318
>gnl|CDD|220303 pfam09592, DUF2031, Protein of unknown function (DUF2031). This
protein is expressed in Plasmodium; its function is
unknown. It may be the product of gene family pyst-b.
Length = 228
Score = 29.2 bits (66), Expect = 5.6
Identities = 11/26 (42%), Positives = 16/26 (61%)
Query: 137 NIKNVYGKTKHFIEEMLKDLSKAHKE 162
++ NV KTK I E+ K+L + KE
Sbjct: 102 DLNNVDKKTKKLINELRKELEEVKKE 127
>gnl|CDD|215949 pfam00496, SBP_bac_5, Bacterial extracellular solute-binding
proteins, family 5 Middle. The borders of this family
are based on the PDBSum definitions of the domain edges
for Salmonella typhimurium oppA.
Length = 362
Score = 29.4 bits (66), Expect = 5.7
Identities = 19/94 (20%), Positives = 30/94 (31%), Gaps = 4/94 (4%)
Query: 489 TFERVTGKPVPYIFYNLGTGQGTSVLQLL-RTFERVTGKPVPYIFYNLGTGQGTSVLQLL 547
+FER+ P +L V + T KP P L V +
Sbjct: 43 SFERLLDPDTPSPAASLLLADIVGVEAVDDYTVRITLKKPNPLFLPLLAALAAAIVKKED 102
Query: 548 RTFERVTGKPV---PYIVEARREGDIVSMYANTD 578
KP+ PY +++ G + + N D
Sbjct: 103 DDSGDFAEKPIGTGPYKLKSWVPGQRIVLERNPD 136
>gnl|CDD|107263 cd06268, PBP1_ABC_transporter_LIVBP_like, Periplasmic binding
domain of ATP-binding cassette transporter-like systems
that belong to the type I periplasmic binding fold
protein superfamily. Periplasmic binding domain of
ATP-binding cassette transporter-like systems that
belong to the type I periplasmic binding fold protein
superfamily. They are mostly present in archaea and
eubacteria, and are primarily involved in scavenging
solutes from the environment. ABC-type transporters
couple ATP hydrolysis with the uptake and efflux of a
wide range of substrates across bacterial membranes,
including amino acids, peptides, lipids and sterols, and
various drugs. These systems are comprised of
transmembrane domains, nucleotide binding domains, and
in most bacterial uptake systems, periplasmic binding
proteins (PBPs) which transfer the ligand to the
extracellular gate of the transmembrane domains. These
PBPs bind their substrates selectively and with high
affinity. Members of this group include ABC-type
Leucine-Isoleucine-Valine-Binding Proteins (LIVBP),
which are homologous to the aliphatic amidase
transcriptional repressor, AmiC, of Pseudomonas
aeruginosa. The uncharacterized periplasmic components
of various ABC-type transport systems are included in
this group.
Length = 298
Score = 29.3 bits (66), Expect = 5.8
Identities = 25/120 (20%), Positives = 43/120 (35%), Gaps = 13/120 (10%)
Query: 432 RVTGKPVPYIFYNLGTG--QGTSVLQLLRTFERVTGKPVPYIFYNLGTGQGTSVLQLLR- 488
+TGK PY+F + Q ++ L E+ K V I Y+ G + R
Sbjct: 102 ALTGKGNPYVFRTAPSDAQQAAALADYLA--EKGKVKKV-AIIYD-DYAYGRGLAAAFRE 157
Query: 489 TFERVTGKPVPYIFYNLGTGQGTSVLQLLRTFERVTGKPVPYIFYNLGTGQGTSVLQLLR 548
+++ G+ V Y G + ++ L+ P +F G L+ R
Sbjct: 158 ALKKLGGEVVAEETYPPGATDFSPLIAKLKAA-----GPDA-VFLAGYGGDAALFLKQAR 211
>gnl|CDD|235756 PRK06259, PRK06259, succinate dehydrogenase/fumarate reductase
iron-sulfur subunit; Provisional.
Length = 486
Score = 29.2 bits (66), Expect = 6.6
Identities = 10/21 (47%), Positives = 13/21 (61%), Gaps = 2/21 (9%)
Query: 260 DLVDKNRLGEIFAKHDIDCVI 280
+L KN EIF K D+D V+
Sbjct: 317 ELKKKNL--EIFNKLDVDTVV 335
>gnl|CDD|130109 TIGR01037, pyrD_sub1_fam, dihydroorotate dehydrogenase (subfamily
1) family protein. This family includes subfamily 1
dihydroorotate dehydrogenases while excluding the
closely related subfamily 2 (TIGR01036). This family
also includes a number of uncharacterized proteins and a
domain of dihydropyrimidine dehydrogenase. The
uncharacterized proteins might all be dihydroorotate
dehydrogenase.
Length = 300
Score = 28.9 bits (65), Expect = 7.2
Identities = 19/66 (28%), Positives = 28/66 (42%)
Query: 125 QFLPITEDHPTGNIKNVYGKTKHFIEEMLKDLSKAHKEWNIISLRYFNPVGAHPSGRIGE 184
+ P+ E+ PT I +VYG + E+ + L KA + L P IG+
Sbjct: 81 ELKPVREEFPTPLIASVYGSSVEEFAEVAEKLEKAPPYVDAYELNLSCPHVKGGGIAIGQ 140
Query: 185 DPTKSF 190
DP S
Sbjct: 141 DPELSA 146
>gnl|CDD|224662 COG1748, LYS9, Saccharopine dehydrogenase and related proteins
[Amino acid transport and metabolism].
Length = 389
Score = 28.8 bits (65), Expect = 9.5
Identities = 20/77 (25%), Positives = 28/77 (36%), Gaps = 9/77 (11%)
Query: 220 GTGKVVAID---NFVNSVHIGD-TPCSIRAIEQFTGKKVDFYSCDLVDKNRLGEIFAKHD 275
G G VVA N V I D + I + G KV+ D D + L + D
Sbjct: 11 GVGSVVAHKLAQNGDGEVTIADRSKEKCARIAELIGGKVEALQVDAADVDALVALIKDFD 70
Query: 276 --IDCV---IHFAAVKA 287
I+ + +KA
Sbjct: 71 LVINAAPPFVDLTILKA 87
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 0.139 0.414
Gapped
Lambda K H
0.267 0.0869 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 31,230,343
Number of extensions: 3129226
Number of successful extensions: 3464
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3372
Number of HSP's successfully gapped: 237
Length of query: 600
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 498
Effective length of database: 6,413,494
Effective search space: 3193920012
Effective search space used: 3193920012
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: 62 (27.4 bits)