RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 020875
(320 letters)
>gnl|CDD|177744 PLN00135, PLN00135, malate dehydrogenase.
Length = 309
Score = 614 bits (1585), Expect = 0.0
Identities = 258/279 (92%), Positives = 266/279 (95%)
Query: 24 MIARGVMLGTDQPVILHMLDIPPAAEALNGVKMELVDAAFPLLKGVVATTDAVEACTGVN 83
MIARGVMLG DQPVILHMLDIPPAAEALNGVKMEL+DAAFPLLKGVVATTD VEAC GVN
Sbjct: 1 MIARGVMLGPDQPVILHMLDIPPAAEALNGVKMELIDAAFPLLKGVVATTDVVEACKGVN 60
Query: 84 IAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEQHAAPNCKVLVVANPANTNALILKE 143
IAVMVGGFPRKEGMERKDVMSKNVSIYK+QASALE+HAAP+CKVLVVANPANTNALILKE
Sbjct: 61 IAVMVGGFPRKEGMERKDVMSKNVSIYKSQASALEKHAAPDCKVLVVANPANTNALILKE 120
Query: 144 FAPSIPAKNITCLTRLDHNRALGQISEKLNVQVSDVKNVIIWGNHSSSQYPDVNHATVNT 203
FAPSIP KNITCLTRLDHNRALGQISE+L V VSDVKNVIIWGNHSS+QYPDVNHATV T
Sbjct: 121 FAPSIPEKNITCLTRLDHNRALGQISERLGVPVSDVKNVIIWGNHSSTQYPDVNHATVKT 180
Query: 204 AAGEKPVRELVKDDAWLNGEFITTVQQRGAAIIKARKLSSALSAASSACDHIRDWVLGTP 263
+GEKPVRELV DDAWLNGEFITTVQQRGAAIIKARKLSSALSAASSACDHIRDWVLGTP
Sbjct: 181 PSGEKPVRELVADDAWLNGEFITTVQQRGAAIIKARKLSSALSAASSACDHIRDWVLGTP 240
Query: 264 EGTWVSMGVYSDGSYNVPAGLIYSFPVTCRNGEWTIVQG 302
EGTWVSMGVYSDGSY VP GLIYSFPVTC GEW+IVQG
Sbjct: 241 EGTWVSMGVYSDGSYGVPPGLIYSFPVTCEKGEWSIVQG 279
>gnl|CDD|133421 cd01336, MDH_cytoplasmic_cytosolic, Cytoplasmic and cytosolic
Malate dehydrogenases. MDH is one of the key enzymes in
the citric acid cycle, facilitating both the conversion
of malate to oxaloacetate and replenishing levels of
oxalacetate by reductive carboxylation of pyruvate.
Members of this subfamily are eukaryotic MDHs localized
to the cytoplasm and cytosol. MDHs are part of the
NAD(P)-binding Rossmann fold superfamily, which includes
a wide variety of protein families including the
NAD(P)-binding domains of alcohol dehydrogenases,
tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate dehydrogenases,
formate/glycerate dehydrogenases, siroheme synthases,
6-phosphogluconate dehydrogenases, aminoacid
dehydrogenases, repressor rex, and NAD-binding potassium
channel domains, among others.
Length = 325
Score = 602 bits (1554), Expect = 0.0
Identities = 214/299 (71%), Positives = 246/299 (82%)
Query: 4 EPVRVLVTGAAGQIGYALVPMIARGVMLGTDQPVILHMLDIPPAAEALNGVKMELVDAAF 63
EP+RVLVTGAAGQI Y+L+PMIA+G + G DQPVILH+LDIPPA +AL GV MEL D AF
Sbjct: 1 EPIRVLVTGAAGQIAYSLLPMIAKGDVFGPDQPVILHLLDIPPALKALEGVVMELQDCAF 60
Query: 64 PLLKGVVATTDAVEACTGVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEQHAAP 123
PLLK VVATTD EA V++A++VG PRKEGMERKD++ NV I+K Q AL+++A
Sbjct: 61 PLLKSVVATTDPEEAFKDVDVAILVGAMPRKEGMERKDLLKANVKIFKEQGEALDKYAKK 120
Query: 124 NCKVLVVANPANTNALILKEFAPSIPAKNITCLTRLDHNRALGQISEKLNVQVSDVKNVI 183
N KVLVV NPANTNALIL ++APSIP +N T LTRLDHNRA QI+ KL V VSDVKNVI
Sbjct: 121 NVKVLVVGNPANTNALILLKYAPSIPKENFTALTRLDHNRAKSQIALKLGVPVSDVKNVI 180
Query: 184 IWGNHSSSQYPDVNHATVNTAAGEKPVRELVKDDAWLNGEFITTVQQRGAAIIKARKLSS 243
IWGNHSS+QYPDVNHATV KP RE VKDDAWLNGEFI+TVQ+RGAA+IKARKLSS
Sbjct: 181 IWGNHSSTQYPDVNHATVELNGKGKPAREAVKDDAWLNGEFISTVQKRGAAVIKARKLSS 240
Query: 244 ALSAASSACDHIRDWVLGTPEGTWVSMGVYSDGSYNVPAGLIYSFPVTCRNGEWTIVQG 302
A+SAA + CDH+ DW GTPEG +VSMGVYSDGSY VP GLI+SFPVTC+NG+W IVQG
Sbjct: 241 AMSAAKAICDHVHDWWFGTPEGEFVSMGVYSDGSYGVPEGLIFSFPVTCKNGKWKIVQG 299
>gnl|CDD|130819 TIGR01758, MDH_euk_cyt, malate dehydrogenase, NAD-dependent. This
model represents the NAD-dependent cytosolic malate
dehydrogenase from eukaryotes. The enzyme from pig has
been studied by X-ray crystallography.
Length = 324
Score = 537 bits (1384), Expect = 0.0
Identities = 215/297 (72%), Positives = 250/297 (84%), Gaps = 1/297 (0%)
Query: 7 RVLVTGAAGQIGYALVPMIARGVMLGTDQPVILHMLDIPPAAEALNGVKMELVDAAFPLL 66
RV+VTGAAGQIGYAL+PMIARG MLG DQP+ILH+LDIPPA + L GV MEL+D AFPLL
Sbjct: 1 RVVVTGAAGQIGYALLPMIARGRMLGKDQPIILHLLDIPPAMKVLEGVVMELMDCAFPLL 60
Query: 67 KGVVATTDAVEACTGVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEQHAAPNCK 126
GVV T D A T V++A++VG FPRKEGMER+D++SKNV I+K Q AL++ A +CK
Sbjct: 61 DGVVPTHDPAVAFTDVDVAILVGAFPRKEGMERRDLLSKNVKIFKEQGRALDKLAKKDCK 120
Query: 127 VLVVANPANTNALILKEFAPSIPAKNITCLTRLDHNRALGQISEKLNVQVSDVKNVIIWG 186
VLVV NPANTNAL+L +APSIP KN + LTRLDHNRAL Q++E+ V VSDVKNVIIWG
Sbjct: 121 VLVVGNPANTNALVLSNYAPSIPPKNFSALTRLDHNRALAQVAERAGVPVSDVKNVIIWG 180
Query: 187 NHSSSQYPDVNHATVNTAAGEKPVRELVKDDAWLNGEFITTVQQRGAAIIKARKLSSALS 246
NHSS+QYPDVNHATV +KPVRE +KDDA+L+GEFITTVQQRGAAII+ARKLSSALS
Sbjct: 181 NHSSTQYPDVNHATVTKGGKQKPVREAIKDDAYLDGEFITTVQQRGAAIIRARKLSSALS 240
Query: 247 AASSACDHIRDWVLGTPEGTWVSMGVYSDGS-YNVPAGLIYSFPVTCRNGEWTIVQG 302
AA +A D + DWVLGTPEGT+VSMGVYSDGS Y VP GLI+SFPVTC+NGEW IV+G
Sbjct: 241 AAKAAVDQMHDWVLGTPEGTFVSMGVYSDGSPYGVPKGLIFSFPVTCKNGEWKIVEG 297
>gnl|CDD|130820 TIGR01759, MalateDH-SF1, malate dehydrogenase. This model
represents a family of malate dehydrogenases in bacteria
and eukaryotes which utilize either NAD or NADP
depending on the species and context. MDH interconverts
malate and oxaloacetate and is a part of the citric acid
cycle as well as the C4 cycle in certain photosynthetic
organisms.
Length = 323
Score = 511 bits (1317), Expect = 0.0
Identities = 195/302 (64%), Positives = 231/302 (76%), Gaps = 6/302 (1%)
Query: 3 KEPVRVLVTGAAGQIGYALVPMIARGVMLGTDQPVILHMLDIPPAAEALNGVKMELVDAA 62
K+PVRV VTGAAGQIGY+L+ IA G + G DQPV+LH+LDIPPA +AL GV MEL D A
Sbjct: 1 KKPVRVAVTGAAGQIGYSLLFRIASGELFGKDQPVVLHLLDIPPAMKALEGVAMELEDCA 60
Query: 63 FPLLKGVVATTDAVEACTGVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEQHAA 122
FPLL GVVATTD EA V+ A++VG FPRK GMER D++SKN I+K Q AL + A
Sbjct: 61 FPLLAGVVATTDPEEAFKDVDAALLVGAFPRKPGMERADLLSKNGKIFKEQGKALNKVAK 120
Query: 123 PNCKVLVVANPANTNALILKEFAPSIPAKNITCLTRLDHNRALGQISEKLNVQVSDVKNV 182
+ KVLVV NPANTNALI + AP IP KN + +TRLDHNRA Q++ K V VSDVKNV
Sbjct: 121 KDVKVLVVGNPANTNALIASKNAPDIPPKNFSAMTRLDHNRAKYQLAAKAGVPVSDVKNV 180
Query: 183 IIWGNHSSSQYPDVNHATVNTAAGEKPVRELVKDDAWLNGEFITTVQQRGAAIIKARKLS 242
IIWGNHS++Q PD HATV +PV+E++KDD WL GEFI TVQQRGAA+I+AR S
Sbjct: 181 IIWGNHSNTQVPDFTHATV----DGRPVKEVIKDDKWLEGEFIPTVQQRGAAVIEARGAS 236
Query: 243 SALSAASSACDHIRDWVLGTPEGTWVSMGVYSDG-SYNVPAGLIYSFPVTC-RNGEWTIV 300
SA SAA++A DH+RDWV GTPEG WVSMGVYSDG Y +P G+I+SFPVTC +GEW IV
Sbjct: 237 SAASAANAAIDHVRDWVTGTPEGDWVSMGVYSDGNPYGIPEGIIFSFPVTCKGDGEWEIV 296
Query: 301 QG 302
+G
Sbjct: 297 EG 298
>gnl|CDD|235468 PRK05442, PRK05442, malate dehydrogenase; Provisional.
Length = 326
Score = 489 bits (1262), Expect = e-176
Identities = 184/301 (61%), Positives = 223/301 (74%), Gaps = 4/301 (1%)
Query: 2 AKEPVRVLVTGAAGQIGYALVPMIARGVMLGTDQPVILHMLDIPPAAEALNGVKMELVDA 61
K PVRV VTGAAGQIGY+L+ IA G MLG DQPVIL +L+IPPA +AL GV MEL D
Sbjct: 1 MKAPVRVAVTGAAGQIGYSLLFRIASGDMLGKDQPVILQLLEIPPALKALEGVVMELDDC 60
Query: 62 AFPLLKGVVATTDAVEACTGVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEQHA 121
AFPLL GVV T D A ++A++VG PR GMERKD++ N +I+ AQ AL + A
Sbjct: 61 AFPLLAGVVITDDPNVAFKDADVALLVGARPRGPGMERKDLLEANGAIFTAQGKALNEVA 120
Query: 122 APNCKVLVVANPANTNALILKEFAPSIPAKNITCLTRLDHNRALGQISEKLNVQVSDVKN 181
A + KVLVV NPANTNALI + AP +PA+N T +TRLDHNRAL Q++ K V V+D+K
Sbjct: 121 ARDVKVLVVGNPANTNALIAMKNAPDLPAENFTAMTRLDHNRALSQLAAKAGVPVADIKK 180
Query: 182 VIIWGNHSSSQYPDVNHATVNTAAGEKPVRELVKDDAWLNGEFITTVQQRGAAIIKARKL 241
+ +WGNHS++QYPD HAT++ KP E++ D AWL FI TVQ+RGAAII+AR
Sbjct: 181 MTVWGNHSATQYPDFRHATIDG----KPAAEVINDQAWLEDTFIPTVQKRGAAIIEARGA 236
Query: 242 SSALSAASSACDHIRDWVLGTPEGTWVSMGVYSDGSYNVPAGLIYSFPVTCRNGEWTIVQ 301
SSA SAA++A DH+RDWVLGTPEG WVSMGV SDGSY +P GLI+ FPVTC NGE+ IVQ
Sbjct: 237 SSAASAANAAIDHVRDWVLGTPEGDWVSMGVPSDGSYGIPEGLIFGFPVTCENGEYEIVQ 296
Query: 302 G 302
G
Sbjct: 297 G 297
>gnl|CDD|133423 cd01338, MDH_choloroplast_like, Chloroplast-like malate
dehydrogenases. MDH is one of the key enzymes in the
citric acid cycle, facilitating both the conversion of
malate to oxaloacetate and replenishing levels of
oxalacetate by reductive carboxylation of pyruvate.
Members of this subfamily are bacterial MDHs, and plant
MDHs localized to the choloroplasts. MDHs are part of
the NAD(P)-binding Rossmann fold superfamily, which
includes a wide variety of protein families including
the NAD(P)-binding domains of alcohol dehydrogenases,
tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate dehydrogenases,
formate/glycerate dehydrogenases, siroheme synthases,
6-phosphogluconate dehydrogenases, aminoacid
dehydrogenases, repressor rex, and NAD-binding potassium
channel domains, among others.
Length = 322
Score = 462 bits (1191), Expect = e-165
Identities = 173/299 (57%), Positives = 211/299 (70%), Gaps = 4/299 (1%)
Query: 4 EPVRVLVTGAAGQIGYALVPMIARGVMLGTDQPVILHMLDIPPAAEALNGVKMELVDAAF 63
+PVRV VTGAAGQIGY+L+ IA G M G DQPVIL +L++P A +AL GV MEL D AF
Sbjct: 1 KPVRVAVTGAAGQIGYSLLFRIASGEMFGPDQPVILQLLELPQALKALEGVAMELEDCAF 60
Query: 64 PLLKGVVATTDAVEACTGVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEQHAAP 123
PLL +V T D A + A++VG PR GMER D++ N I+ AQ AL A+
Sbjct: 61 PLLAEIVITDDPNVAFKDADWALLVGAKPRGPGMERADLLKANGKIFTAQGKALNDVASR 120
Query: 124 NCKVLVVANPANTNALILKEFAPSIPAKNITCLTRLDHNRALGQISEKLNVQVSDVKNVI 183
+ KVLVV NP NTNALI + AP IP N T +TRLDHNRA Q+++K V V+DVKN++
Sbjct: 121 DVKVLVVGNPCNTNALIAMKNAPDIPPDNFTAMTRLDHNRAKSQLAKKAGVPVTDVKNMV 180
Query: 184 IWGNHSSSQYPDVNHATVNTAAGEKPVRELVKDDAWLNGEFITTVQQRGAAIIKARKLSS 243
IWGNHS +QYPD +AT+ G KP E++ D AWL EFI TVQ+RGAAIIKAR SS
Sbjct: 181 IWGNHSPTQYPDFTNATI----GGKPAAEVINDRAWLEDEFIPTVQKRGAAIIKARGASS 236
Query: 244 ALSAASSACDHIRDWVLGTPEGTWVSMGVYSDGSYNVPAGLIYSFPVTCRNGEWTIVQG 302
A SAA++A DH+RDWVLGTPEG W SM V SDGSY +P GLI+SFPV + G + IV+G
Sbjct: 237 AASAANAAIDHMRDWVLGTPEGDWFSMAVPSDGSYGIPEGLIFSFPVRSKGGGYEIVEG 295
>gnl|CDD|133420 cd00704, MDH, Malate dehydrogenase. Malate dehydrogenase (MDH) is
one of the key enzymes in the citric acid cycle,
facilitating both the conversion of malate to
oxaloacetate and replenishing levels of oxalacetate by
reductive carboxylation of pyruvate. MDHs belong to the
NAD-dependent, lactate dehydrogenase (LDH)-like,
2-hydroxycarboxylate dehydrogenase family, which also
includes the GH4 family of glycoside hydrolases. They
are part of the NAD(P)-binding Rossmann fold
superfamily, which includes a wide variety of protein
families including the NAD(P)-binding domains of alcohol
dehydrogenases, tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate dehydrogenases,
formate/glycerate dehydrogenases, siroheme synthases,
6-phosphogluconate dehydrogenases, aminoacid
dehydrogenases, repressor rex, and NAD-binding potassium
channel domains, among others.
Length = 323
Score = 460 bits (1185), Expect = e-164
Identities = 177/298 (59%), Positives = 219/298 (73%), Gaps = 2/298 (0%)
Query: 6 VRVLVTGAAGQIGYALVPMIARGVMLGTDQPVILHMLDIPPAAEALNGVKMELVDAAFPL 65
+ VL+TGAAGQIGY L+ +IA G + G DQPVILH+LDIPPA +AL GV MEL D AFPL
Sbjct: 1 LHVLITGAAGQIGYNLLFLIASGELFGDDQPVILHLLDIPPAMKALEGVVMELQDCAFPL 60
Query: 66 LKGVVATTDAVEACTGVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEQHAAPNC 125
LKGVV TTD EA V++A++VG FPRK GMER D++ KN I+K Q AL + A P
Sbjct: 61 LKGVVITTDPEEAFKDVDVAILVGAFPRKPGMERADLLRKNAKIFKEQGEALNKVAKPTV 120
Query: 126 KVLVVANPANTNALILKEFAPSIPAKNITCLTRLDHNRALGQISEKLNVQVSDVKNVIIW 185
KVLVV NPANTNALI + AP++P KN T LTRLDHNRA Q++ KL V+VSDVKNVIIW
Sbjct: 121 KVLVVGNPANTNALIALKNAPNLPPKNFTALTRLDHNRAKAQVARKLGVRVSDVKNVIIW 180
Query: 186 GNHSSSQYPDVNHATVNTAAGEKPVRELVKDDAWLNGEFITTVQQRGAAIIKARKLSSAL 245
GNHS++Q PD+++A V G + V + D+ WLN EF+ TVQ+RGAAIIK R SSA
Sbjct: 181 GNHSNTQVPDLSNAVVYGPGGTEWV-LDLLDEEWLNDEFVKTVQKRGAAIIKKRGASSAA 239
Query: 246 SAASSACDHIRDWVLGTPEGTWVSMGVYSDG-SYNVPAGLIYSFPVTCRNGEWTIVQG 302
SAA + DH++DW+ GTP G VSMGVYS G Y +P G+++SFP TC+ G W +V+
Sbjct: 240 SAAKAIADHVKDWLFGTPPGEIVSMGVYSPGNPYGIPPGIVFSFPCTCKGGGWHVVED 297
>gnl|CDD|215060 PLN00112, PLN00112, malate dehydrogenase (NADP); Provisional.
Length = 444
Score = 285 bits (730), Expect = 9e-94
Identities = 134/304 (44%), Positives = 178/304 (58%), Gaps = 10/304 (3%)
Query: 3 KEPVRVLVTGAAGQIGYALVPMIARGVMLGTDQPVILHMLDIPPAAEALNGVKMELVDAA 62
K+ + V V+GAAG I L+ +A G + G DQP+ L +L + +AL GV MEL D+
Sbjct: 98 KKLINVAVSGAAGMISNHLLFKLASGEVFGPDQPIALKLLGSERSKQALEGVAMELEDSL 157
Query: 63 FPLLKGVVATTDAVEACTGVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEQHAA 122
+PLL+ V D E A+++G PR GMER D++ N I+ Q AL + A+
Sbjct: 158 YPLLREVSIGIDPYEVFQDAEWALLIGAKPRGPGMERADLLDINGQIFAEQGKALNEVAS 217
Query: 123 PNCKVLVVANPANTNALILKEFAPSIPAKNITCLTRLDHNRALGQISEKLNVQVSDVKNV 182
N KV+VV NP NTNALI + AP+IPAKN LTRLD NRA Q++ K V V NV
Sbjct: 218 RNVKVIVVGNPCNTNALICLKNAPNIPAKNFHALTRLDENRAKCQLALKAGVFYDKVSNV 277
Query: 183 IIWGNHSSSQYPDVNHATVNTAAGEKPVRELVKDDAWLNGEFITTVQQRGAAIIKARKLS 242
IWGNHS++Q PD +N PV+E++ D WL EF VQ+RG +IK S
Sbjct: 278 TIWGNHSTTQVPDF----LNAKINGLPVKEVITDHKWLEEEFTPKVQKRGGVLIKKWGRS 333
Query: 243 SALSAASSACDHIRDWVLGTPEGTWVSMGVYSDGS-YNVPAGLIYSFPVTCR---NGEWT 298
SA S A S D I+ V TPEG W S GVY+DG+ Y + GL++S P CR +G++
Sbjct: 334 SAASTAVSIADAIKSLVTPTPEGDWFSTGVYTDGNPYGIAEGLVFSMP--CRSKGDGDYE 391
Query: 299 IVQG 302
IV+
Sbjct: 392 IVKD 395
>gnl|CDD|130818 TIGR01757, Malate-DH_plant, malate dehydrogenase, NADP-dependent.
This model represents the NADP-dependent malate
dehydrogenase found in plants, mosses and green algae
and localized to the chloroplast. Malate dehydrogenase
converts oxaloacetate into malate, a critical step in
the C4 cycle which allows circumvention of the effects
of photorespiration. Malate is subsequenctly transported
from the chloroplast to the cytoplasm (and then to the
bundle sheath cells in C4 plants). The plant and moss
enzymes are light regulated via cysteine disulfide
bonds. The enzyme from Sorghum has been crystallized.
Length = 387
Score = 265 bits (679), Expect = 5e-87
Identities = 139/304 (45%), Positives = 182/304 (59%), Gaps = 10/304 (3%)
Query: 3 KEPVRVLVTGAAGQIGYALVPMIARGVMLGTDQPVILHMLDIPPAAEALNGVKMELVDAA 62
K+ V V V+GAAG I L+ M+A G + G DQP+ L +L + EAL GV MEL D+
Sbjct: 42 KKTVNVAVSGAAGMISNHLLFMLASGEVFGQDQPIALKLLGSERSKEALEGVAMELEDSL 101
Query: 63 FPLLKGVVATTDAVEACTGVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEQHAA 122
+PLL+ V D E + A+++G PR GMER D++ N I+ Q AL A+
Sbjct: 102 YPLLREVSIGIDPYEVFEDADWALLIGAKPRGPGMERADLLDINGQIFADQGKALNAVAS 161
Query: 123 PNCKVLVVANPANTNALILKEFAPSIPAKNITCLTRLDHNRALGQISEKLNVQVSDVKNV 182
NCKVLVV NP NTNALI + AP+IP KN LTRLD NRA Q++ K + V NV
Sbjct: 162 KNCKVLVVGNPCNTNALIAMKNAPNIPRKNFHALTRLDENRAKCQLALKSGKFYTSVSNV 221
Query: 183 IIWGNHSSSQYPDVNHATVNTAAGEKPVRELVKDDAWLNGEFITTVQQRGAAIIKARKLS 242
IWGNHS++Q PD VN G +P +E++KD WL EF TVQ+RG A+IK S
Sbjct: 222 TIWGNHSTTQVPDF----VNAKIGGRPAKEVIKDTKWLEEEFTPTVQKRGGALIKKWGRS 277
Query: 243 SALSAASSACDHIRDWVLGTPEGTWVSMGVYSDGS-YNVPAGLIYSFPVTCR---NGEWT 298
SA S A S D I+ V+ TPEG W S GVY+DG+ Y + GL++S P CR +G++
Sbjct: 278 SAASTAVSIADAIKSLVVPTPEGDWFSTGVYTDGNPYGIAEGLVFSMP--CRSKGDGDYE 335
Query: 299 IVQG 302
+
Sbjct: 336 LATD 339
>gnl|CDD|130817 TIGR01756, LDH_protist, lactate dehydrogenase. This model
represents a family of protist lactate dehydrogenases
which have aparrently evolved from a recent protist
malate dehydrogenase ancestor. Lactate dehydrogenase
converts the hydroxyl at C-2 of lactate to a carbonyl in
the product, pyruvate. The preference of this enzyme for
NAD or NADP has not been determined. A critical residue
in malate dehydrogenase, arginine-91 (T. vaginalis
numbering) has been mutated to a leucine, eliminating
the positive charge which complemeted the carboxylate in
malate which is absent in lactate. Several other more
subtle changes are proposed to make the active site
smaller to accomadate the less bulky lactate molecule.
Length = 313
Score = 252 bits (644), Expect = 2e-82
Identities = 106/281 (37%), Positives = 158/281 (56%), Gaps = 5/281 (1%)
Query: 25 IARGVMLGTDQPVILHMLDIPPAAEALNGVKMELVDAAFPLLKGVVATTDAVEACTGVNI 84
IA G + G ++PV LH+L+IPPA L + MEL D AFP L G + TT EA ++
Sbjct: 5 IANGDLYG-NRPVCLHLLEIPPALNRLEALAMELEDCAFPNLAGTIVTTKLEEAFKDIDC 63
Query: 85 AVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEQHAAPNCKVLVVANPANTNALILKEF 144
A +V P K G R D+++KN I+KA AL ++A P KVLV+ NP NTN L+
Sbjct: 64 AFLVASVPLKPGEVRADLLTKNTPIFKATGEALSEYAKPTVKVLVIGNPVNTNCLVAMLH 123
Query: 145 APSIPAKNITCLTRLDHNRALGQISEKLNVQVSDVKNVIIWGNHSSSQYPDVNHATVNTA 204
AP + A+N + L LDHNRA+ +I+ KL V V + +V++WGNH+ S D+ HA
Sbjct: 124 APKLSAENFSSLCMLDHNRAVSRIASKLKVPVDHIYHVVVWGNHAESMVADLTHAEFTKN 183
Query: 205 AGEKPVRELVKDDAWLNGEFITTVQQRGAAIIKARKLSSALSAASSACDHIRDWVLGTPE 264
+ V + + D + +F + QR I++ R +SA S ++ H++ W+ GT
Sbjct: 184 GKHQKVFDELCRD-YPEPDFFEVIAQRAWKILEMRGFTSAASPVKASLQHMKAWLFGTRP 242
Query: 265 GTWVSMG--VYSDGSYNVPAGLIYSFPVTC-RNGEWTIVQG 302
G +SMG V Y + G+I+SFP T +G+ +V+
Sbjct: 243 GEVLSMGIPVPEGNPYGIKPGVIFSFPCTVDEDGKVHVVEN 283
>gnl|CDD|133431 cd05295, MDH_like, Malate dehydrogenase-like. These MDH-like
proteins are related to other groups in the MDH family
but do not have conserved substrate and cofactor binding
residues. MDH is one of the key enzymes in the citric
acid cycle, facilitating both the conversion of malate
to oxaloacetate and replenishing levels of oxalacetate
by reductive carboxylation of pyruvate. Members of this
subgroup are uncharacterized MDH-like proteins from
animals. They are part of the NAD(P)-binding Rossmann
fold superfamily, which includes a wide variety of
protein families including the NAD(P)-binding domains of
alcohol dehydrogenases, tyrosine-dependent
oxidoreductases, glyceraldehyde-3-phosphate
dehydrogenases, formate/glycerate dehydrogenases,
siroheme synthases, 6-phosphogluconate dehydrogenases,
aminoacid dehydrogenases, repressor rex, and NAD-binding
potassium channel domains, among others.
Length = 452
Score = 254 bits (652), Expect = 6e-82
Identities = 106/307 (34%), Positives = 169/307 (55%), Gaps = 13/307 (4%)
Query: 5 PVRVLVTGAAGQIGYALVPMIARGVMLGTDQPVILHMLDIPPAAEALNGVKMELVDAAFP 64
P++V +T A+ + Y L+P +A G + G ++ + +H+LD P E L G+ ME+ D AFP
Sbjct: 123 PLQVCITNASAPLCYHLIPSLASGEVFGMEEEISIHLLDSPENLEKLKGLVMEVEDLAFP 182
Query: 65 LLKGVVATTDAVEACTGVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEQHAAPN 124
LL+G+ TTD A ++ V++ F KEG + + + V+I + +E++A +
Sbjct: 183 LLRGISVTTDLDVAFKDAHVIVLLDDFLIKEGEDLEGCIRSRVAICQLYGPLIEKNAKED 242
Query: 125 CKVLVVA-NPANTNALILKEFAPSIPAKNITCLTRLDHNRALGQISEKLNVQVSDVKNVI 183
KV+V N IL ++APSIP KNI + RL NRA ++ KLNV + +K+VI
Sbjct: 243 VKVIVAGRTFLNLKTSILIKYAPSIPRKNIIAVARLQENRAKALLARKLNVNSAGIKDVI 302
Query: 184 IWGNHSSSQYPDVNHATVNTAAG--------EKPVRELVKDDAWLNGEFITTVQQRGAAI 235
+WGN + Y D++ A V +PV ELV D W+NGEF+ T++ +
Sbjct: 303 VWGNIGGNTYIDLSKARVYRYDSAIWGPPNYSRPVLELVHDSKWINGEFVATLKSLSS-- 360
Query: 236 IKARKLSSALSAASSACDHIRDWVLGTPEGTWVSMGVYSDGSYNVPAGLIYSFPVTCRNG 295
+ +A+S A + + W G+P G S+GV S+G Y +P G+++S PV +NG
Sbjct: 361 --SLNHEAAISPAHAIATTLSYWYHGSPPGEIFSLGVISEGWYGIPEGIVFSMPVKFQNG 418
Query: 296 EWTIVQG 302
W +V
Sbjct: 419 SWEVVTD 425
>gnl|CDD|223117 COG0039, Mdh, Malate/lactate dehydrogenases [Energy production and
conversion].
Length = 313
Score = 218 bits (558), Expect = 2e-69
Identities = 95/298 (31%), Positives = 140/298 (46%), Gaps = 20/298 (6%)
Query: 6 VRVLVTGAAGQIGYALVPMIARGVMLGTDQPVILHMLDIPPAAEALNGVKMELVDAAFPL 65
++V V GA G +G +L ++ LG++ L ++DI E GV ++L AA PL
Sbjct: 1 MKVAVIGA-GNVGSSLAFLLLLQ-GLGSE----LVLIDINE--EKAEGVALDLSHAAAPL 52
Query: 66 LKGVVATTDA-VEACTGVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEQHAAPN 124
V T D E G +I V+ G PRK GM R D++ KN I K A A+ ++A P+
Sbjct: 53 GSDVKITGDGDYEDLKGADIVVITAGVPRKPGMTRLDLLEKNAKIVKDIAKAIAKYA-PD 111
Query: 125 CKVLVVANPANTNALILKEFAPSIPAKNITCLTRLDHNRALGQISEKLNVQVSDVKNVII 184
VLVV NP + I +F+ + I T LD R ++EKL V DV +I
Sbjct: 112 AIVLVVTNPVDILTYIAMKFSGFPKNRVIGSGTVLDSARFRTFLAEKLGVSPKDVHAYVI 171
Query: 185 WGNHSSSQYPDVNHATVNTAAGEKPVRELVK-DDAWLNGEFITTVQQRGAAIIKARKLSS 243
G H + P + ATV G KP+ EL+K D E I V+ GA II+A+ +
Sbjct: 172 -GEHGDTMVPLWSQATV----GGKPLEELLKEDTEEDLEELIERVRNAGAEIIEAKGAGT 226
Query: 244 ALSAASSACDHIRDWVLGTPEGTWVSMGVYSDGSYNVPAGLIYSFPVT-CRNGEWTIV 300
A++ + + E + + VY DG Y + + P +NG I+
Sbjct: 227 YYGPAAALARMVEAILRD--EKRVLPVSVYLDGEYG-VEDVYFGVPAVLGKNGVEEIL 281
>gnl|CDD|133419 cd00650, LDH_MDH_like, NAD-dependent, lactate dehydrogenase-like,
2-hydroxycarboxylate dehydrogenase family. Members of
this family include ubiquitous enzymes like L-lactate
dehydrogenases (LDH), L-2-hydroxyisocaproate
dehydrogenases, and some malate dehydrogenases (MDH).
LDH catalyzes the last step of glycolysis in which
pyruvate is converted to L-lactate. MDH is one of the
key enzymes in the citric acid cycle, facilitating both
the conversion of malate to oxaloacetate and
replenishing levels of oxalacetate by reductive
carboxylation of pyruvate. The LDH/MDH-like proteins are
part of the NAD(P)-binding Rossmann fold superfamily,
which includes a wide variety of protein families
including the NAD(P)-binding domains of alcohol
dehydrogenases, tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate dehydrogenases,
formate/glycerate dehydrogenases, siroheme synthases,
6-phosphogluconate dehydrogenases, aminoacid
dehydrogenases, repressor rex, and NAD-binding potassium
channel domains, among others.
Length = 263
Score = 174 bits (444), Expect = 4e-53
Identities = 77/292 (26%), Positives = 118/292 (40%), Gaps = 57/292 (19%)
Query: 8 VLVTGAAGQIGYALVPMIARGVMLGTDQPVILHMLDIPPAAEALNGVKMELVDAAFPL-L 66
+ V GA G +G AL +A G + L + DI E L GV M+L DA PL
Sbjct: 1 IAVIGAGGNVGPALAFGLADG---SVLLAIELVLYDIDE--EKLKGVAMDLQDAVEPLAD 55
Query: 67 KGVVATTDAVEACTGVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEQHAAPNCK 126
V T D EA ++ ++ G RK GM R D++ +NV I K +E++ +P+
Sbjct: 56 IKVSITDDPYEAFKDADVVIITAGVGRKPGMGRLDLLKRNVPIVKEIGDNIEKY-SPDAW 114
Query: 127 VLVVANPANTNALILKEFAPSIPAKNITCLTRLDHNRALGQISEKLNVQVSDVKNVIIWG 186
++VV+NP + ++ ++ +P + + L LD R ++EKL V DVK V I G
Sbjct: 115 IIVVSNPVDIITYLVWRYSG-LPKEKVIGLGTLDPIRFRRILAEKLGVDPDDVK-VYILG 172
Query: 187 NHSSSQYPDVNHATVNTAAGEKPVRELVKDDAWLNGEFITTVQQRGAAIIKARKLSSALS 246
H SQ PD +
Sbjct: 173 EHGGSQVPDWSTVR---------------------------------------------- 186
Query: 247 AASSACDHIRDWVLGTPEGTWVSMGVYSDGSYNVPAGLIYSFPVTCRNGEWT 298
A+S D IR + EG + +GV ++G +P ++ S P
Sbjct: 187 IATSIADLIRSLL--NDEGEILPVGVRNNGQIGIPDDVVVSVPCIVGKNGVE 236
>gnl|CDD|202437 pfam02866, Ldh_1_C, lactate/malate dehydrogenase, alpha/beta
C-terminal domain. L-lactate dehydrogenases are
metabolic enzymes which catalyze the conversion of
L-lactate to pyruvate, the last step in anaerobic
glycolysis. L-2-hydroxyisocaproate dehydrogenases are
also members of the family. Malate dehydrogenases
catalyze the interconversion of malate to oxaloacetate.
The enzyme participates in the citric acid cycle.
L-lactate dehydrogenase is also found as a lens
crystallin in bird and crocodile eyes.
Length = 173
Score = 143 bits (363), Expect = 3e-42
Identities = 52/147 (35%), Positives = 75/147 (51%), Gaps = 4/147 (2%)
Query: 157 TRLDHNRALGQISEKLNVQVSDVKNVIIWGNHSSSQYPDVNHATVNTAAGEKPVRELVKD 216
T LD RA ++EK V V NV + G HS +Q+PD +HA V V+E +KD
Sbjct: 1 TTLDTARARTFLAEKFGVDPRSV-NVYVIGEHSGTQFPDWSHAKVTIIPLISQVKENLKD 59
Query: 217 DAWLNGEFITTVQQRGAAIIKARKLSSALSAASSACDHIRDWVLGTPEGTWVSMGVYSDG 276
W E I VQ G +I+A+ S+ S A +A + + GT G +S+GVY DG
Sbjct: 60 TDWELEELIERVQNAGYEVIEAKAGSTTYSMAYAAARIAKAILRGT--GGVLSVGVYLDG 117
Query: 277 SYNVPAGLIYSFPVTC-RNGEWTIVQG 302
Y P + +S PV ++G +V+
Sbjct: 118 YYGSPDDIYFSVPVVLGKDGVEKVVEI 144
>gnl|CDD|200963 pfam00056, Ldh_1_N, lactate/malate dehydrogenase, NAD binding
domain. L-lactate dehydrogenases are metabolic enzymes
which catalyze the conversion of L-lactate to pyruvate,
the last step in anaerobic glycolysis.
L-2-hydroxyisocaproate dehydrogenases are also members
of the family. Malate dehydrogenases catalyze the
interconversion of malate to oxaloacetate. The enzyme
participates in the citric acid cycle. L-lactate
dehydrogenase is also found as a lens crystallin in bird
and crocodile eyes. N-terminus (this family) is a
Rossmann NAD-binding fold. C-terminus is an unusual
alpha+beta fold.
Length = 142
Score = 128 bits (325), Expect = 7e-37
Identities = 45/150 (30%), Positives = 72/150 (48%), Gaps = 8/150 (5%)
Query: 6 VRVLVTGAAGQIGYALVPMIARGVMLGTDQPVILHMLDIPPAAEALNGVKMELVDAAFPL 65
V+V V GA G +G +L +A L + L ++DI + GV M+L + L
Sbjct: 1 VKVAVVGAGGGVGSSLAFALA-LQGLADE----LVLVDINK--DKAEGVAMDLSHGSTFL 53
Query: 66 LKGVVATTDAVEACTGVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEQHAAPNC 125
+ D EA ++ V+ G PRK GM R D++++N I+K A+ + AP+
Sbjct: 54 SVPGIVGGDDYEALKDADVVVITAGVPRKPGMTRLDLLNRNAGIFKDIVPAIAKS-APDA 112
Query: 126 KVLVVANPANTNALILKEFAPSIPAKNITC 155
VLVV+NP + I + + P + I
Sbjct: 113 IVLVVSNPVDILTYIAWKVSGLPPERVIGS 142
>gnl|CDD|133424 cd01339, LDH-like_MDH, L-lactate dehydrogenase-like malate
dehydrogenase proteins. Members of this subfamily have
an LDH-like structure and an MDH enzymatic activity.
Some members, like MJ0490 from Methanococcus jannaschii,
exhibit both MDH and LDH activities. Tetrameric MDHs,
including those from phototrophic bacteria, are more
similar to LDHs than to other MDHs. LDH catalyzes the
last step of glycolysis in which pyruvate is converted
to L-lactate. MDH is one of the key enzymes in the
citric acid cycle, facilitating both the conversion of
malate to oxaloacetate and replenishing levels of
oxalacetate by reductive carboxylation of pyruvate. The
LDH-like MDHs are part of the NAD(P)-binding Rossmann
fold superfamily, which includes a wide variety of
protein families including the NAD(P)-binding domains of
alcohol dehydrogenases, tyrosine-dependent
oxidoreductases, glyceraldehyde-3-phosphate
dehydrogenases, formate/glycerate dehydrogenases,
siroheme synthases, 6-phosphogluconate dehydrogenases,
aminoacid dehydrogenases, repressor rex, and NAD-binding
potassium channel domains, among others.
Length = 300
Score = 80.2 bits (199), Expect = 3e-17
Identities = 54/196 (27%), Positives = 86/196 (43%), Gaps = 33/196 (16%)
Query: 69 VVATTDAVEACTGVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEQHAAPNCKVL 128
V T D E G ++ V+ G PRK GM R D++ N I K A ++++ APN V+
Sbjct: 55 VTGTNDY-EDIAGSDVVVITAGIPRKPGMSRDDLLGTNAKIVKEVAENIKKY-APNAIVI 112
Query: 129 VVANPANTNALILKEFAPSIPAKNITCLTRLDHNRALGQ------------ISEKLNVQV 176
VV NP + + + + NR +G I+E+L V V
Sbjct: 113 VVTNPLDVMTYVAYKA------------SGFPRNRVIGMAGVLDSARFRYFIAEELGVSV 160
Query: 177 SDVKNVIIWGNHSSSQYPDVNHATVNTAAGEKPVRELVKDDAWLNGEFITTVQQRGAAII 236
DV+ +++ G H + P ++TV G P+ EL+ + E + + GA I+
Sbjct: 161 KDVQAMVL-GGHGDTMVPLPRYSTVG---G-IPLTELITKEEI--DEIVERTRNGGAEIV 213
Query: 237 KARKLSSALSAASSAC 252
K SA A ++A
Sbjct: 214 NLLKTGSAYYAPAAAI 229
>gnl|CDD|173409 PTZ00117, PTZ00117, malate dehydrogenase; Provisional.
Length = 319
Score = 75.9 bits (187), Expect = 1e-15
Identities = 61/213 (28%), Positives = 99/213 (46%), Gaps = 14/213 (6%)
Query: 73 TDAVEACTGVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEQHAAPNCKVLVVAN 132
T+ E ++ V+ G RKE M R+D+++ N I K+ A +++++ PN V+ V N
Sbjct: 65 TNNYEDIKDSDVVVITAGVQRKEEMTREDLLTINGKIMKSVAESVKKY-CPNAFVICVTN 123
Query: 133 PANTNALILKEFAPSIPAKNITCLT-RLDHNRALGQISEKLNVQVSDVKNVIIWGNHSSS 191
P + + +E + IP+ I + LD +R ++EKL V DV V+I G H
Sbjct: 124 PLDCMVKVFQEKS-GIPSNKICGMAGVLDSSRFRCNLAEKLGVSPGDVSAVVI-GGHGDL 181
Query: 192 QYPDVNHATVNTAAGEKPVRELVKDDAWLNGEFITTVQQR---GAAIIKARKLSSALSA- 247
P + TVN P+ + VK A E +++ G I+K K SA A
Sbjct: 182 MVPLPRYCTVNGI----PLSDFVKKGAITEKEINEIIKKTRNMGGEIVKLLKKGSAFFAP 237
Query: 248 ASSACDHIRDWVLGTPEGTWVSMGVYSDGSYNV 280
A++ I ++ E + VY +G YN
Sbjct: 238 AAAIVAMIEAYL--KDEKRVLVCSVYLNGQYNC 268
>gnl|CDD|133430 cd05294, LDH-like_MDH_nadp, A lactate dehydrogenases-like structure
with malate dehydrogenase enzymatic activity. The
LDH-like MDH proteins have a lactate
dehyhydrogenase-like (LDH-like) structure and malate
dehydrogenase (MDH) enzymatic activity. This subgroup is
composed of some archaeal LDH-like MDHs that prefer
NADP(H) rather than NAD(H) as a cofactor. One member,
MJ0490 from Methanococcus jannaschii, has been observed
to form dimers and tetramers during crystalization,
although it is believed to exist primarilly as a
tetramer in solution. In addition to its MDH activity,
MJ0490 also possesses
fructose-1,6-bisphosphate-activated LDH activity.
Members of this subgroup have a higher sequence
similarity to LDHs than to other MDHs. LDH catalyzes the
last step of glycolysis in which pyruvate is converted
to L-lactate. MDH is one of the key enzymes in the
citric acid cycle, facilitating both the conversion of
malate to oxaloacetate and replenishing levels of
oxalacetate by reductive carboxylation of pyruvate. The
LDH-like MDHs are part of the NAD(P)-binding Rossmann
fold superfamily, which includes a wide variety of
protein families including the NAD(P)- binding domains
of alcohol dehydrogenases, tyrosine-dependent
oxidoreductases, glyceraldehyde-3-phosphate
dehydrogenases, formate/glycerate dehydrogenases,
siroheme synthases, 6-phosphogluconate dehydrogenase,
aminoacid dehydrogenases, repressor rex, and NAD-binding
potassium channel domains, among others.
Length = 309
Score = 73.6 bits (181), Expect = 6e-15
Identities = 64/237 (27%), Positives = 113/237 (47%), Gaps = 22/237 (9%)
Query: 6 VRVLVTGAAGQIGYALVPMIARGVMLGTDQPVI--LHMLDIPPAAEALNGVKMELVDAAF 63
++V + GA+G++G A ++A+ + V+ ++++ P + E L G+++++ DA
Sbjct: 1 MKVSIIGASGRVGSATALLLAK-------EDVVKEINLISRPKSLEKLKGLRLDIYDALA 53
Query: 64 PLLKGVVATTDAVEACT-GVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEQHAA 122
+ + G +I ++ G PRKEGM R D+ KN I K A + + A
Sbjct: 54 AAGIDAEIKISSDLSDVAGSDIVIITAGVPRKEGMSRLDLAKKNAKIVKKYAKQIAEF-A 112
Query: 123 PNCKVLVVANPANT---NALILKEFAPSIPAKNITCLTRLDHNRALGQISEKLNVQVSDV 179
P+ K+LVV NP + AL F + + T LD R I++ NV +S+V
Sbjct: 113 PDTKILVVTNPVDVMTYKALKESGFDKN---RVFGLGTHLDSLRFKVAIAKHFNVHISEV 169
Query: 180 KNVIIWGNHSSSQYPDVNHATVNTAAGEKPVRELVKDDAWLNGEFITTVQQRGAAII 236
II G H S P ++ +T+ G P++ + + + + TV+ G II
Sbjct: 170 HTRII-GEHGDSMVPLIS----STSIGGIPIKRFPEYKDFDVEKIVETVKNAGQNII 221
>gnl|CDD|180477 PRK06223, PRK06223, malate dehydrogenase; Reviewed.
Length = 307
Score = 73.2 bits (181), Expect = 7e-15
Identities = 67/253 (26%), Positives = 113/253 (44%), Gaps = 45/253 (17%)
Query: 14 AGQIGYALVPMIARGVMLGTDQPVILHMLDIPPAAEALNGVKMELVDAAFPLLK--GVVA 71
AG +G L ++A + + + DI G +++ +AA P+ +
Sbjct: 10 AGNVGATLAHLLAL------KELGDVVLFDI--VEGVPQGKALDIAEAA-PVEGFDTKIT 60
Query: 72 TTDAVEACTGVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEQHAAPNCKVLVVA 131
T+ E G ++ V+ G PRK GM R D++ N I K A ++++ AP+ V+VV
Sbjct: 61 GTNDYEDIAGSDVVVITAGVPRKPGMSRDDLLGINAKIMKDVAEGIKKY-APDAIVIVVT 119
Query: 132 NPANT-NALILKEFAPSIPAKNITCLTRLDHNRALGQ------------ISEKLNVQVSD 178
NP + + LKE + NR +G I+E+LNV V D
Sbjct: 120 NPVDAMTYVALKE-------------SGFPKNRVIGMAGVLDSARFRTFIAEELNVSVKD 166
Query: 179 VKNVIIWGNHSSSQYPDVNHATVNTAAGEKPVRELVKDDAWLNGEFITTVQQRGAAIIKA 238
V ++ G H S P V ++TV G P+ +L+ + L+ E + ++ GA I+
Sbjct: 167 VTAFVL-GGHGDSMVPLVRYSTV----GGIPLEDLLSKEK-LD-EIVERTRKGGAEIVGL 219
Query: 239 RKLSSALSAASSA 251
K SA A +++
Sbjct: 220 LKTGSAYYAPAAS 232
>gnl|CDD|133418 cd00300, LDH_like, L-lactate dehydrogenase-like enzymes. Members
of this subfamily are tetrameric NAD-dependent
2-hydroxycarboxylate dehydrogenases including LDHs,
L-2-hydroxyisocaproate dehydrogenases (L-HicDH), and
LDH-like malate dehydrogenases (MDH). Dehydrogenases
catalyze the conversion of carbonyl compounds to
alcohols or amino acids. LDHs catalyze the last step of
glycolysis in which pyruvate is converted to L-lactate.
Vertebrate LDHs are non-allosteric, but some bacterial
LDHs are activated by an allosteric effector such as
fructose-1,6-bisphosphate. L-HicDH catalyzes the
conversion of a variety of 2-oxo carboxylic acids with
medium-sized aliphatic or aromatic side chains. MDH is
one of the key enzymes in the citric acid cycle,
facilitating both the conversion of malate to
oxaloacetate and replenishing levels of oxalacetate by
reductive carboxylation of pyruvate. The LDH-like
subfamily is part of the NAD(P)-binding Rossmann fold
superfamily, which includes a wide variety of protein
families including the NAD(P)-binding domains of alcohol
dehydrogenases, tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate dehydrogenases,
formate/glycerate dehydrogenases, siroheme synthases,
6-phosphogluconate dehydrogenases, aminoacid
dehydrogenases, repressor rex, and NAD-binding potassium
channel domains, among others.
Length = 300
Score = 70.4 bits (173), Expect = 8e-14
Identities = 61/256 (23%), Positives = 110/256 (42%), Gaps = 13/256 (5%)
Query: 41 MLDIPPAAEALNGVKMELVDAAFPLLKGVVATTDAVEACTGVNIAVMVGGFPRKEGMERK 100
++D+ E G ++L A+ L G + +I V+ G PRK G R
Sbjct: 28 LVDVNE--EKAKGDALDLSHASAFLATGTIVRGGDYADAADADIVVITAGAPRKPGETRL 85
Query: 101 DVMSKNVSIYKAQASALEQHAAPNCKVLVVANPANTNALILKEFAPSIPAKNITCLTRLD 160
D++++N I ++ + L+++ P+ +LVV+NP + + ++ + + I T LD
Sbjct: 86 DLINRNAPILRSVITNLKKY-GPDAIILVVSNPVDILTYVAQKLSGLPKNRVIGSGTLLD 144
Query: 161 HNRALGQISEKLNVQVSDVKNVIIWGNHSSSQYPDVNHATVNTAAGEKPVRELVKDDAWL 220
R ++EKL+V V ++ G H SQ + ATV P+ EL
Sbjct: 145 SARFRSLLAEKLDVDPQSVHAYVL-GEHGDSQVVAWSTATVGG----LPLEELAPFTKLD 199
Query: 221 NGEFITTVQQRGAAIIKARKLSSALSAASSACDHIRDWVLGTPEGTWVSMGVYSDGSYNV 280
V+ G II+ K ++ A++ D ++ +L E + + +G Y +
Sbjct: 200 LEAIEEEVRTSGYEIIR-LKGATNYGIATAIADIVKS-ILLD-ERRVLPVSAVQEGQYGI 256
Query: 281 PAGLIYSFP-VTCRNG 295
+ S P V R G
Sbjct: 257 E-DVALSVPAVVGREG 271
>gnl|CDD|130833 TIGR01772, MDH_euk_gproteo, malate dehydrogenase, NAD-dependent.
This model represents the NAD-dependent malate
dehydrogenase found in eukaryotes and certain gamma
proteobacteria. The enzyme is involved in the citric
acid cycle as well as the glyoxalate cycle. Several
isoforms exidt in eukaryotes. In S. cereviseae, for
example, there are cytoplasmic, mitochondrial and
peroxisomal forms. Although malate dehydrogenases have
in some cases been mistaken for lactate dehydrogenases
due to the similarity of these two substrates and the
apparent ease with which evolution can toggle these
activities, critical residues have been identified which
can discriminate between the two activities. At the time
of the creation of this model no hits above the trusted
cutoff contained critical residues typical of lactate
dehydrogenases [Energy metabolism, TCA cycle].
Length = 312
Score = 64.7 bits (158), Expect = 6e-12
Identities = 58/191 (30%), Positives = 84/191 (43%), Gaps = 23/191 (12%)
Query: 7 RVLVTGAAGQIGYALVPMIARGVMLGTDQPVI--LHMLDIPPAAEALNGVKMEL--VDAA 62
+V V GAAG IG L ++ QP + L + DI AA GV +L + A
Sbjct: 1 KVAVLGAAGGIGQPLSLLLKL-------QPYVSELSLYDIAGAA----GVAADLSHIPTA 49
Query: 63 FPLLKGVVATTDAVEACTGVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEQHAA 122
+KG A G ++ V+ G PRK GM R D+ + N I K +A+ +
Sbjct: 50 -ASVKGFSGEEGLENALKGADVVVIPAGVPRKPGMTRDDLFNVNAGIVKDLVAAVAES-C 107
Query: 123 PNCKVLVVANPANTN----ALILKEFAPSIPAKNITCLTRLDHNRALGQISEKLNVQVSD 178
P +LV+ NP N+ A +LK+ P + +T LD RA ++E
Sbjct: 108 PKAMILVITNPVNSTVPIAAEVLKKKGVYDP-NKLFGVTTLDIVRANTFVAELKGKD-PM 165
Query: 179 VKNVIIWGNHS 189
NV + G HS
Sbjct: 166 EVNVPVIGGHS 176
>gnl|CDD|133422 cd01337, MDH_glyoxysomal_mitochondrial, Glyoxysomal and
mitochondrial malate dehydrogenases. MDH is one of the
key enzymes in the citric acid cycle, facilitating both
the conversion of malate to oxaloacetate and
replenishing levels of oxalacetate by reductive
carboxylation of pyruvate. Members of this subfamily are
localized to the glycosome and mitochondria. MDHs are
part of the NAD(P)-binding Rossmann fold superfamily,
which includes a wide variety of protein families
including the NAD(P)-binding domains of alcohol
dehydrogenases, tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate dehydrogenases,
formate/glycerate dehydrogenases, siroheme synthases,
6-phosphogluconate dehydrogenases, aminoacid
dehydrogenases, repressor rex, and NAD-binding potassium
channel domains, among others.
Length = 310
Score = 63.3 bits (155), Expect = 2e-11
Identities = 57/193 (29%), Positives = 91/193 (47%), Gaps = 25/193 (12%)
Query: 6 VRVLVTGAAGQIGYALVPMIARGVMLGTDQPVI--LHMLDIPPAAEALNGVKMEL--VDA 61
V+V V GAAG IG L +L P++ L + DI GV +L ++
Sbjct: 1 VKVAVLGAAGGIGQPLS-------LLLKLNPLVSELALYDI----VNTPGVAADLSHINT 49
Query: 62 AFPLLKGVVATTDAVEACTGVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEQHA 121
+ G + + +A G ++ V+ G PRK GM R D+ + N I + A+A+ +
Sbjct: 50 P-AKVTGYLGPEELKKALKGADVVVIPAGVPRKPGMTRDDLFNINAGIVRDLATAVAKA- 107
Query: 122 APNCKVLVVANPANTN----ALILKEFAPSIPAKNITCLTRLDHNRALGQISEKLNVQVS 177
P +L+++NP N+ A +LK+ P K + +T LD RA ++E L + +
Sbjct: 108 CPKALILIISNPVNSTVPIAAEVLKKAGVYDP-KRLFGVTTLDVVRANTFVAELLGLDPA 166
Query: 178 DVK-NVIIWGNHS 189
V VI G HS
Sbjct: 167 KVNVPVI--GGHS 177
>gnl|CDD|233562 TIGR01763, MalateDH_bact, malate dehydrogenase, NAD-dependent.
This enzyme converts malate into oxaloacetate in the
citric acid cycle. The critical residues which
discriminate malate dehydrogenase from lactate
dehydrogenase have been characterized , and have been
used to set the cutoffs for this model. Sequences
showing [aflimv][ap]R[rk]pgM[st] and [ltv][ilm]gGhgd
were kept above trusted, while those in which the
capitalized residues in the patterns were found to be Q,
E and E were kept below the noise cutoff. Some sequences
in the grey zone have been annotated as malate
dehydrogenases, but none have been characterized.
Phylogenetically, a clade of sequences from eukaryotes
such as Toxoplasma and Plasmodium which include a
characterized lactate dehydrogenase and show abiguous
critical residue patterns appears to be more closely
related to these bacterial sequences than other
eukaryotic sequences. These are relatively long branch
and have been excluded from the model. All other
sequences falling below trusted appear to be
phylogenetically outside of the clade including the
trusted hits. The annotation of Botryococcus braunii as
lactate dehydrogenase appears top be in error. This was
initially annotated as MDH by Swiss-Prot and then
changed. The rationale for either of these annotations
is not traceable [Energy metabolism, TCA cycle].
Length = 305
Score = 58.0 bits (140), Expect = 1e-09
Identities = 54/218 (24%), Positives = 97/218 (44%), Gaps = 18/218 (8%)
Query: 37 VILHMLDIPPAAEALNGVK---MELVDAAFPLLKGVVATTDAVEACTGVNIAVMVGGFPR 93
V+L +++ P +AL+ + + D V T+ +I V+ G PR
Sbjct: 29 VLLDVVEGIPQGKALDMYEASPVGGFDTK-------VTGTNNYADTANSDIVVITAGLPR 81
Query: 94 KEGMERKDVMSKNVSIYKAQASALEQHAAPNCKVLVVANPANTNALILKEFAPSIPAKNI 153
K GM R+D++S N I + + +H +PN ++VV+NP + + + + + I
Sbjct: 82 KPGMSREDLLSMNAGIVREVTGRIMEH-SPNPIIVVVSNPLDAMTYVAWQKSGFPKERVI 140
Query: 154 TCLTRLDHNRALGQISEKLNVQVSDVKNVIIWGNHSSSQYPDVNHATVNTAAGEKPVREL 213
LD R I+ +L V V DV ++ G H + P V ++TV PV +L
Sbjct: 141 GQAGVLDSARFRTFIAMELGVSVQDVTACVL-GGHGDAMVPLVRYSTV----AGIPVADL 195
Query: 214 VKDDAWLNGEFITTVQQRGAAIIKARKLSSALSAASSA 251
+ + E + ++ G I+ K SA A +++
Sbjct: 196 ISAERI--AEIVERTRKGGGEIVNLLKQGSAYYAPAAS 231
>gnl|CDD|133429 cd05293, LDH_1, A subgroup of L-lactate dehydrogenases. L-lactate
dehydrogenases (LDH) are tetrameric enzymes catalyzing
the last step of glycolysis in which pyruvate is
converted to L-lactate. This subgroup is composed of
eukaryotic LDHs. Vertebrate LDHs are non-allosteric.
This is in contrast to some bacterial LDHs that are
activated by an allosteric effector such as
fructose-1,6-bisphosphate. LDHs are part of the
NAD(P)-binding Rossmann fold superfamily, which includes
a wide variety of protein families including the
NAD(P)-binding domains of alcohol dehydrogenases,
tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate dehydrogenases,
formate/glycerate dehydrogenases, siroheme synthases,
6-phosphogluconate dehydrogenases, aminoacid
dehydrogenases, repressor rex, and NAD-binding potassium
channel domains, among others.
Length = 312
Score = 57.6 bits (140), Expect = 2e-09
Identities = 71/262 (27%), Positives = 106/262 (40%), Gaps = 36/262 (13%)
Query: 3 KEPVRVLVTGAAGQIGYALVPMI-ARGVMLGTDQPVILHMLDIPPAAEALNGVKMELVD- 60
K +V V G GQ+G A I A+G+ D+ L ++D+ + +K E +D
Sbjct: 1 KPRNKVTVVGV-GQVGMACAISILAKGL---ADE---LVLVDVVE-----DKLKGEAMDL 48
Query: 61 ---AAFPLLKGVVATTDAVEACTGVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASAL 117
+AF + A D + ++ G + EG R D++ +NV I+K L
Sbjct: 49 QHGSAFLKNPKIEADKD-YSVTANSKVVIVTAGARQNEGESRLDLVQRNVDIFKGIIPKL 107
Query: 118 EQHAAPNCKVLVVANPANTNALILKEFAPSI----PAKNITCLTRLDHNRALGQISEKLN 173
+++ PN +LVV+NP + I+ A + + I LD R I+E+L
Sbjct: 108 VKYS-PNAILLVVSNPVD----IMTYVAWKLSGLPKHRVIGSGCNLDSARFRYLIAERLG 162
Query: 174 VQVSDVKNVIIWGNHSSSQYP---DVNHATVNTAAGEKPVRELVKDDAWLNGEFITTVQQ 230
V S V II G H S P VN A V P KD E V
Sbjct: 163 VAPSSVHGWII-GEHGDSSVPVWSGVNVAGVRLQDL-NPDIGTDKDPEKWK-EVHKQVVD 219
Query: 231 RGAAIIKARKLSS---ALSAAS 249
+IK + +S LS A
Sbjct: 220 SAYEVIKLKGYTSWAIGLSVAD 241
>gnl|CDD|235340 PRK05086, PRK05086, malate dehydrogenase; Provisional.
Length = 312
Score = 56.2 bits (136), Expect = 5e-09
Identities = 59/205 (28%), Positives = 92/205 (44%), Gaps = 27/205 (13%)
Query: 7 RVLVTGAAGQIGYALVPMIARGVMLGTDQPVILHMLDIPPAAEALNGVKMELVDAAFPL- 65
+V V GAAG IG AL ++ + G++ L + DI P GV ++L +
Sbjct: 2 KVAVLGAAGGIGQALALLLKTQLPAGSE----LSLYDIAPVTP---GVAVDLSHIPTAVK 54
Query: 66 LKGVVATTDAVEACTGVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEQHAA--P 123
+KG + D A G ++ ++ G RK GM+R D+ + N I K + +E+ A P
Sbjct: 55 IKGF-SGEDPTPALEGADVVLISAGVARKPGMDRSDLFNVNAGIVK---NLVEKVAKTCP 110
Query: 124 NCKVLVVANPANTNALILKEF---APSIPAKNITCLTRLDHNRALGQISEKLNVQVSDVK 180
+ ++ NP NT I E A + +T LD R+ ++E Q +V+
Sbjct: 111 KACIGIITNPVNTTVAIAAEVLKKAGVYDKNKLFGVTTLDVIRSETFVAELKGKQPGEVE 170
Query: 181 -NVIIWGNHSS-------SQYPDVN 197
VI G HS SQ P V+
Sbjct: 171 VPVI--GGHSGVTILPLLSQVPGVS 193
>gnl|CDD|173376 PTZ00082, PTZ00082, L-lactate dehydrogenase; Provisional.
Length = 321
Score = 55.9 bits (135), Expect = 7e-09
Identities = 42/153 (27%), Positives = 67/153 (43%), Gaps = 15/153 (9%)
Query: 70 VATTDAVEACTGVNIAVMVGGFPRKEGME-----RKDVMSKNVSIYKAQASALEQHAAPN 124
V T+ E G ++ ++ G ++ G R D++ N I A ++++ PN
Sbjct: 63 VIGTNNYEDIAGSDVVIVTAGLTKRPGKSDKEWNRDDLLPLNAKIMDEVAEGIKKYC-PN 121
Query: 125 CKVLVVANPANTNALILKEFAPSIPAKNITC--LTRLDHNRALGQISEKLNVQVSDVKNV 182
V+V+ NP + +L+E +P KN C LD +R I+EKL V DV
Sbjct: 122 AFVIVITNPLDVMVKLLQE-HSGLP-KNKVCGMAGVLDSSRLRTYIAEKLGVNPRDVHAS 179
Query: 183 IIWGNHSSSQYPDVNHATVNTAAGEKPVRELVK 215
+I G H P + TV P+ E +K
Sbjct: 180 VI-GAHGDKMVPLPRYVTVGGI----PLSEFIK 207
>gnl|CDD|215058 PLN00106, PLN00106, malate dehydrogenase.
Length = 323
Score = 54.2 bits (131), Expect = 2e-08
Identities = 54/188 (28%), Positives = 90/188 (47%), Gaps = 19/188 (10%)
Query: 7 RVLVTGAAGQIGYALVPMIARGVMLGTDQPVILHMLDIPPAAEALNGVKMEL--VDAAFP 64
+V V GAAG IG L ++ ++ LH+ DI GV ++ ++
Sbjct: 20 KVAVLGAAGGIGQPLSLLMKMNPLVSE-----LHLYDIANTP----GVAADVSHINTP-A 69
Query: 65 LLKGVVATTDAVEACTGVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEQHAAPN 124
++G + +A G ++ ++ G PRK GM R D+ + N I K A+ +H PN
Sbjct: 70 QVRGFLGDDQLGDALKGADLVIIPAGVPRKPGMTRDDLFNINAGIVKTLCEAVAKH-CPN 128
Query: 125 CKVLVVANPANTN----ALILKEFAPSIPAKNITCLTRLDHNRALGQISEKLNVQVSDVK 180
V +++NP N+ A +LK+ A K + +T LD RA ++EK + +DV
Sbjct: 129 ALVNIISNPVNSTVPIAAEVLKK-AGVYDPKKLFGVTTLDVVRANTFVAEKKGLDPADV- 186
Query: 181 NVIIWGNH 188
+V + G H
Sbjct: 187 DVPVVGGH 194
>gnl|CDD|178836 PRK00066, ldh, L-lactate dehydrogenase; Reviewed.
Length = 315
Score = 51.0 bits (123), Expect = 2e-07
Identities = 47/178 (26%), Positives = 78/178 (43%), Gaps = 32/178 (17%)
Query: 77 EACTGVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEQHAAPNCKVLVVANPANT 136
C ++ V+ G P+K G R D++ KN+ I+K+ + + LV +NP +
Sbjct: 69 SDCKDADLVVITAGAPQKPGETRLDLVEKNLKIFKSIVGEVMAS-GFDGIFLVASNPVD- 126
Query: 137 NALIL-----------KEFAPSIPAKNITCLTRLDHNRALGQISEKLNVQVSDVKNVIIW 185
IL KE + I T LD R +SEKL+V V II
Sbjct: 127 ---ILTYATWKLSGFPKE-------RVIGSGTSLDSARFRYMLSEKLDVDPRSVHAYII- 175
Query: 186 GNHSSSQYPDVNHATVNTAAGEKPVRELVKDDAWLNGEFITTVQQ--RGAA--IIKAR 239
G H +++P +HA V P+ E ++++ + E + + + R AA II+ +
Sbjct: 176 GEHGDTEFPVWSHANV----AGVPLEEYLEENEQYDEEDLDEIFENVRDAAYEIIEKK 229
>gnl|CDD|233566 TIGR01771, L-LDH-NAD, L-lactate dehydrogenase. This model
represents the NAD-dependent L-lactate dehydrogenases
from bacteria and eukaryotes. This enzyme function as as
the final step in anaerobic glycolysis. Although lactate
dehydrogenases have in some cases been mistaken for
malate dehydrogenases due to the similarity of these two
substrates and the apparent ease with which evolution
can toggle these activities, critical residues have been
identified which can discriminate between the two
activities. At the time of the creation of this model no
hits above the trusted cutoff contained critical
residues typical of malate dehydrogenases [Energy
metabolism, Anaerobic, Energy metabolism,
Glycolysis/gluconeogenesis].
Length = 299
Score = 50.7 bits (122), Expect = 3e-07
Identities = 43/172 (25%), Positives = 68/172 (39%), Gaps = 30/172 (17%)
Query: 56 MELVDAAFPLLKGVVATTDAVEACTGVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQAS 115
M+L AA L + C ++ V+ G P+K G R +++ +NV I K+
Sbjct: 39 MDLQHAASFLPTPKKIRSGDYSDCKDADLVVITAGAPQKPGETRLELVGRNVRIMKSIVP 98
Query: 116 ALEQHAAPNCKVLVVANPANTNALILKEFAPSIPAKNITCLTRLDHNRALGQ-------- 167
+ + + LV NP + IL A L+ NR +G
Sbjct: 99 EV-VKSGFDGIFLVATNPVD----ILTYVAWK--------LSGFPKNRVIGSGTVLDTAR 145
Query: 168 ----ISEKLNVQVSDVKNVIIWGNHSSSQYPDVNHATVNTAAGEKPVRELVK 215
++EKL V V II G H S+ P + AT+ G P+ + +K
Sbjct: 146 LRYLLAEKLGVDPQSVHAYII-GEHGDSEVPVWSSATI----GGVPLLDYLK 192
>gnl|CDD|178212 PLN02602, PLN02602, lactate dehydrogenase.
Length = 350
Score = 47.8 bits (114), Expect = 3e-06
Identities = 48/194 (24%), Positives = 92/194 (47%), Gaps = 14/194 (7%)
Query: 3 KEPVRVLVTGAAGQIGYALVPMIARGVMLGTDQPVILHMLDIPPAAEALNGVKMELVDAA 62
+ +V V G G +G A+ I L D L ++D+ P + L G ++L AA
Sbjct: 35 RRHTKVSVVGV-GNVGMAIAQTI-----LTQDLADELALVDVNP--DKLRGEMLDLQHAA 86
Query: 63 --FPLLKGVVATTDAVEACTGVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEQH 120
P K ++A+TD G ++ ++ G + G R +++ +NV++++ L ++
Sbjct: 87 AFLPRTK-ILASTD-YAVTAGSDLCIVTAGARQIPGESRLNLLQRNVALFRKIIPELAKY 144
Query: 121 AAPNCKVLVVANPANTNALILKEFAPSIPAKNITCLTRLDHNRALGQISEKLNVQVSDVK 180
+P+ +L+V+NP + + + + + I T LD +R I++ L+V DV+
Sbjct: 145 -SPDTILLIVSNPVDVLTYVAWKLSGFPANRVIGSGTNLDSSRFRFLIADHLDVNAQDVQ 203
Query: 181 NVIIWGNHSSSQYP 194
I+ G H S
Sbjct: 204 AYIV-GEHGDSSVA 216
>gnl|CDD|240360 PTZ00325, PTZ00325, malate dehydrogenase; Provisional.
Length = 321
Score = 47.3 bits (113), Expect = 4e-06
Identities = 56/190 (29%), Positives = 84/190 (44%), Gaps = 19/190 (10%)
Query: 6 VRVLVTGAAGQIGYALVPMIARGVMLGTDQPVILHMLDIPPAAEALNGVKMEL--VDAAF 63
+V V GAAG IG L ++ + ++ L + DI A GV +L +D
Sbjct: 9 FKVAVLGAAGGIGQPL-SLLLKQNPHVSE----LSLYDIVGAP----GVAADLSHIDTP- 58
Query: 64 PLLKGVVATTDAVEACTGVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEQHAAP 123
+ G +A G ++ ++ G PRK GM R D+ + N I + A +AP
Sbjct: 59 AKVTGYADGELWEKALRGADLVLICAGVPRKPGMTRDDLFNTNAPIVR-DLVAAVASSAP 117
Query: 124 NCKVLVVANPANTNALILKEFAPSI----PAKNITCLTRLDHNRALGQISEKLNVQVSDV 179
V +V+NP N+ I E P K + +T LD RA ++E L + DV
Sbjct: 118 KAIVGIVSNPVNSTVPIAAETLKKAGVYDPRK-LFGVTTLDVVRARKFVAEALGMNPYDV 176
Query: 180 KNVIIWGNHS 189
NV + G HS
Sbjct: 177 -NVPVVGGHS 185
>gnl|CDD|133428 cd05292, LDH_2, A subgroup of L-lactate dehydrogenases. L-lactate
dehydrogenases (LDH) are tetrameric enzymes catalyzing
the last step of glycolysis in which pyruvate is
converted to L-lactate. This subgroup is composed
predominantly of bacterial LDHs and a few fungal LDHs.
Bacterial LDHs may be non-allosteric or may be activated
by an allosteric effector such as
fructose-1,6-bisphosphate. LDHs are part of the
NAD(P)-binding Rossmann fold superfamily, which includes
a wide variety of protein families including the
NAD(P)-binding domains of alcohol dehydrogenases,
tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate dehydrogenases,
formate/glycerate dehydrogenases, siroheme synthases,
6-phosphogluconate dehydrogenases, aminoacid
dehydrogenases, repressor rex, and NAD-binding potassium
channel domains, among others.
Length = 308
Score = 41.7 bits (99), Expect = 2e-04
Identities = 42/150 (28%), Positives = 66/150 (44%), Gaps = 11/150 (7%)
Query: 56 MELVDAAFPLLKGVVATTDAVEACTGVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQAS 115
M+L P +K V C G ++ V+ G +K G R D++ +NV+I+K
Sbjct: 43 MDLAHGT-PFVKPVRIYAGDYADCKGADVVVITAGANQKPGETRLDLLKRNVAIFKEIIP 101
Query: 116 ALEQHAAPNCKVLVVANPANTNALILKEFAPSI----PAKNITCLTRLDHNRALGQISEK 171
+ ++ AP+ +LVV NP + +L A + P + I T LD R + E
Sbjct: 102 QILKY-APDAILLVVTNPVD----VLTYVAYKLSGLPPNRVIGSGTVLDTARFRYLLGEH 156
Query: 172 LNVQVSDVKNVIIWGNHSSSQYPDVNHATV 201
L V V II G H S+ + A +
Sbjct: 157 LGVDPRSVHAYII-GEHGDSEVAVWSSANI 185
>gnl|CDD|133427 cd05291, HicDH_like, L-2-hydroxyisocapronate dehydrogenases and
some bacterial L-lactate dehydrogenases.
L-2-hydroxyisocapronate dehydrogenase (HicDH) catalyzes
the conversion of a variety of 2-oxo carboxylic acids
with medium-sized aliphatic or aromatic side chains.
This subfamily is composed of HicDHs and some bacterial
L-lactate dehydrogenases (LDH). LDHs catalyze the last
step of glycolysis in which pyruvate is converted to
L-lactate. Bacterial LDHs can be non-allosteric or may
be activated by an allosteric effector such as
fructose-1,6-bisphosphate. Members of this subfamily
with known structures such as the HicDH of Lactobacillus
confusus, the non-allosteric LDH of Lactobacillus
pentosus, and the allosteric LDH of Bacillus
stearothermophilus, show that they exist as
homotetramers. The HicDH-like subfamily is part of the
NAD(P)-binding Rossmann fold superfamily, which includes
a wide variety of protein families including the
NAD(P)-binding domains of alcohol dehydrogenases,
tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate dehydrogenases,
formate/glycerate dehydrogenases, siroheme synthases,
6-phosphogluconate dehydrogenases, aminoacid
dehydrogenases, repressor rex, and NAD-binding potassium
channel domains, among others.
Length = 306
Score = 40.9 bits (97), Expect = 4e-04
Identities = 41/162 (25%), Positives = 65/162 (40%), Gaps = 48/162 (29%)
Query: 77 EACTGVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEQHAAPNCK-------VLV 129
C +I V+ G P+K G R D++ KN I K P K LV
Sbjct: 64 SDCKDADIVVITAGAPQKPGETRLDLLEKNAKIMK--------SIVPKIKASGFDGIFLV 115
Query: 130 VANPANTNALILKEFAPSIPAKNITCLTRLDHNRALGQ------------ISEKLNVQVS 177
+NP + ++++ L+ L NR +G ++EKLNV
Sbjct: 116 ASNPVDVITYVVQK------------LSGLPKNRVIGTGTSLDTARLRRALAEKLNV--- 160
Query: 178 DVKNVI--IWGNHSSSQYPDVNHATVNTAAGEKPVRELVKDD 217
D ++V + G H SQ+ + TV KP+ +L+K+
Sbjct: 161 DPRSVHAYVLGEHGDSQFVAWSTVTVGG----KPLLDLLKEG 198
>gnl|CDD|236399 PRK09186, PRK09186, flagellin modification protein A;
Provisional.
Length = 256
Score = 34.2 bits (79), Expect = 0.058
Identities = 20/73 (27%), Positives = 30/73 (41%), Gaps = 5/73 (6%)
Query: 7 RVLVTGAAGQIGYALVPMIARGVMLGTDQPVILHMLDIPPAAEALNGVKMELVDAAFPLL 66
+L+TGA G IG ALV I L VI +D E L + E L+
Sbjct: 6 TILITGAGGLIGSALVKAI-----LEAGGIVIAADIDKEALNELLESLGKEFKSKKLSLV 60
Query: 67 KGVVATTDAVEAC 79
+ + +++E
Sbjct: 61 ELDITDQESLEEF 73
>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 = 34.1 bits (79), Expect = 0.079
Identities = 14/38 (36%), Positives = 17/38 (44%), Gaps = 6/38 (15%)
Query: 7 RVLVTGAAGQIGYALVPMIARGVMLGTDQPVILHMLDI 44
+LVTG AG IG LV I + P L + D
Sbjct: 4 TILVTGGAGSIGSELVRQILKF------GPKKLIVFDR 35
>gnl|CDD|178256 PLN02650, PLN02650, dihydroflavonol-4-reductase.
Length = 351
Score = 33.6 bits (77), Expect = 0.11
Identities = 29/90 (32%), Positives = 42/90 (46%), Gaps = 17/90 (18%)
Query: 1 MAKEPVRVLVTGAAGQIGYALV-PMIARGVML------GTDQPVILHMLDIPPAAEALNG 53
M + V VTGA+G IG LV ++ RG + + + H+LD+P A L
Sbjct: 1 MGSQKETVCVTGASGFIGSWLVMRLLERGYTVRATVRDPANVKKVKHLLDLPGATTRLTL 60
Query: 54 VKMEL-VDAAFPLLKGVVATTDAVEACTGV 82
K +L V+ +F DA+ CTGV
Sbjct: 61 WKADLAVEGSF---------DDAIRGCTGV 81
>gnl|CDD|236207 PRK08261, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 450
Score = 33.7 bits (78), Expect = 0.13
Identities = 23/59 (38%), Positives = 27/59 (45%), Gaps = 7/59 (11%)
Query: 7 RVLVTGAAGQIGYALVPMIARGVMLGTDQPVILHMLDIPPAAEALNGVKMELVDAAFPL 65
LVTGAA IG A IA V+ V+ LD+P A EAL V + A L
Sbjct: 212 VALVTGAARGIGAA----IAE-VLARDGAHVVC--LDVPAAGEALAAVANRVGGTALAL 263
>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 = 32.7 bits (75), Expect = 0.20
Identities = 18/47 (38%), Positives = 25/47 (53%), Gaps = 3/47 (6%)
Query: 7 RVLVTGAAGQIGYALVPMIARGVMLGTDQPVILHMLDIPPAAEALNG 53
R+L+TG GQIG L ++ + G D VI + PPA L+G
Sbjct: 1 RILITGGLGQIGSELAKLLRK--RYGKDN-VIASDIRKPPAHVVLSG 44
>gnl|CDD|223528 COG0451, WcaG, Nucleoside-diphosphate-sugar epimerases [Cell
envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 314
Score = 32.6 bits (74), Expect = 0.21
Identities = 11/21 (52%), Positives = 13/21 (61%)
Query: 7 RVLVTGAAGQIGYALVPMIAR 27
R+LVTG AG IG LV +
Sbjct: 2 RILVTGGAGFIGSHLVERLLA 22
>gnl|CDD|187661 cd08958, FR_SDR_e, flavonoid reductase (FR), extended (e) SDRs.
This subgroup contains FRs of the extended SDR-type and
related proteins. These FRs act in the NADP-dependent
reduction of flavonoids, ketone-containing plant
secondary metabolites; they have the characteristic
active site triad of the SDRs (though not the upstream
active site Asn) and a NADP-binding motif that is very
similar to the typical extended SDR motif. Extended
SDRs are distinct from classical SDRs. In addition to
the Rossmann fold (alpha/beta folding pattern with a
central beta-sheet) core region typical of all SDRs,
extended SDRs have a less conserved C-terminal
extension of approximately 100 amino acids. Extended
SDRs are a diverse collection of proteins, and include
isomerases, epimerases, oxidoreductases, and lyases;
they typically have a TGXXGXXG cofactor binding motif.
SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving
as a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton
relay involving the conserved Tyr and Lys, a water
molecule stabilized by Asn, and nicotinamide. Atypical
SDRs generally lack the catalytic residues
characteristic of the SDRs, and their glycine-rich
NAD(P)-binding motif is often different from the forms
normally seen in classical or extended SDRs. Complex
(multidomain) SDRs such as ketoreductase domains of
fatty acid synthase have a GGXGXXG NAD(P)-binding motif
and an altered active site motif (YXXXN). Fungal type
ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding
motif.
Length = 293
Score = 32.2 bits (74), Expect = 0.30
Identities = 26/82 (31%), Positives = 38/82 (46%), Gaps = 15/82 (18%)
Query: 8 VLVTGAAGQIGYALVPM-IARG------VMLGTDQPVILHMLDIPPAAEALNGVKMELVD 60
V VTGA+G IG LV + RG V D+ + H+L++ A E L K +L+D
Sbjct: 1 VCVTGASGFIGSWLVKRLLQRGYTVRATVRDPGDEKKVAHLLELEGAKERLKLFKADLLD 60
Query: 61 AAFPLLKGVVATTDAVEACTGV 82
+ A++ C GV
Sbjct: 61 YG--------SFDAAIDGCDGV 74
>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 = 31.1 bits (71), Expect = 0.45
Identities = 24/75 (32%), Positives = 34/75 (45%), Gaps = 10/75 (13%)
Query: 8 VLVTGAAGQIGYALVPM-IARG--VMLGTDQPVILHMLDIPPAAEALNGVKMELVDAAFP 64
+LVTG AG IG LV + RG V++ V++H+ AA + D F
Sbjct: 1 ILVTGGAGFIGSHLVRRLLERGHEVVVIDRLDVVVHL-----AALVGVPASWDNPDEDF- 54
Query: 65 LLKGVVATTDAVEAC 79
VV T + +EA
Sbjct: 55 -ETNVVGTLNLLEAA 68
>gnl|CDD|187564 cd05254, dTDP_HR_like_SDR_e, dTDP-6-deoxy-L-lyxo-4-hexulose
reductase and related proteins, extended (e) SDRs.
dTDP-6-deoxy-L-lyxo-4-hexulose reductase, an extended
SDR, synthesizes dTDP-L-rhamnose from
alpha-D-glucose-1-phosphate, providing the precursor
of L-rhamnose, an essential cell wall component of many
pathogenic bacteria. This subgroup has the
characteristic active site tetrad and NADP-binding
motif. This subgroup also contains human MAT2B, the
regulatory subunit of methionine adenosyltransferase
(MAT); MAT catalyzes S-adenosylmethionine synthesis.
The human gene encoding MAT2B encodes two major
splicing variants which are induced in human cell liver
cancer and regulate HuR, an mRNA-binding protein which
stabilizes the mRNA of several cyclins, to affect cell
proliferation. Both MAT2B variants include this
extended SDR domain. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids. Extended SDRs are a diverse collection
of proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 280
Score = 31.1 bits (71), Expect = 0.65
Identities = 9/18 (50%), Positives = 14/18 (77%)
Query: 7 RVLVTGAAGQIGYALVPM 24
++L+TGA G +G ALV +
Sbjct: 1 KILITGATGMLGRALVRL 18
>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 = 30.9 bits (70), Expect = 0.76
Identities = 26/94 (27%), Positives = 40/94 (42%), Gaps = 15/94 (15%)
Query: 7 RVLVTGAAGQIGYALVPMIARGVMLGTDQPVILHMLDIPPAAEALNGVKMELVDAAFPLL 66
VLVTG +G G LV + GT + DI P EAL+ + ++ L
Sbjct: 1 SVLVTGGSGFFGERLVKQLLE--RGGTY----VRSFDIAPPGEALSAWQHPNIE----FL 50
Query: 67 KGVVATTDAVE-ACTGVN----IAVMVGGFPRKE 95
KG + + VE A +G + A +V ++
Sbjct: 51 KGDITDRNDVEQALSGADCVFHTAAIVPLAGPRD 84
>gnl|CDD|216461 pfam01370, Epimerase, NAD dependent epimerase/dehydratase family.
This family of proteins utilise NAD as a cofactor. The
proteins in this family use nucleotide-sugar substrates
for a variety of chemical reactions.
Length = 233
Score = 30.7 bits (70), Expect = 0.87
Identities = 9/20 (45%), Positives = 12/20 (60%)
Query: 8 VLVTGAAGQIGYALVPMIAR 27
+LVTG G IG LV + +
Sbjct: 1 ILVTGGTGFIGSHLVRRLLQ 20
>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 = 30.1 bits (68), Expect = 1.5
Identities = 10/22 (45%), Positives = 15/22 (68%)
Query: 7 RVLVTGAAGQIGYALVPMIARG 28
R+L+TGA GQ+G LV ++
Sbjct: 1 RILITGANGQLGRELVQQLSPE 22
>gnl|CDD|180823 PRK07074, PRK07074, short chain dehydrogenase; Provisional.
Length = 257
Score = 29.7 bits (67), Expect = 1.7
Identities = 28/83 (33%), Positives = 32/83 (38%), Gaps = 11/83 (13%)
Query: 8 VLVTGAAGQIGYALVPMIARGVMLGTDQPVILHMLDIPPAAEALNGVKMELVDAAFPLLK 67
LVTGAAG IG A +AR +L LDI A AL L DA F +
Sbjct: 5 ALVTGAAGGIGQA----LARR--FLAAGDRVL-ALDID--AAALAAFADALGDARF--VP 53
Query: 68 GVVATTDAVEACTGVNIAVMVGG 90
TDA + A G
Sbjct: 54 VACDLTDAASLAAALANAAAERG 76
>gnl|CDD|224207 COG1288, COG1288, Predicted membrane protein [Function unknown].
Length = 481
Score = 30.0 bits (68), Expect = 1.9
Identities = 15/52 (28%), Positives = 26/52 (50%), Gaps = 1/52 (1%)
Query: 2 AKEPVRVLVTGAAGQIGYALVPMIARGVMLGTDQPVILHMLDIPPAAEALNG 53
+ + GA+ +G AL+ +ARG+ L D +IL + + A L+G
Sbjct: 322 ENDIASSFIEGASDLLGVALIIGLARGINLIMDDGMILDTI-LNYLASLLSG 372
>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II
[Transcription / DNA replication, recombination, and
repair].
Length = 442
Score = 29.7 bits (67), Expect = 2.1
Identities = 14/62 (22%), Positives = 24/62 (38%), Gaps = 2/62 (3%)
Query: 161 HNRALG-QISEKLNVQVSDVKNV-IIWGNHSSSQYPDVNHATVNTAAGEKPVRELVKDDA 218
+ L Q +E L + + I G + V ATV T A + + E + ++
Sbjct: 88 PTKELLDQWAEALKKFLLLNDEIGIYGGGEKELEPAKVTVATVQTLARRQLLDEFLGNEF 147
Query: 219 WL 220
L
Sbjct: 148 GL 149
>gnl|CDD|168574 PRK06484, PRK06484, short chain dehydrogenase; Validated.
Length = 520
Score = 29.8 bits (67), Expect = 2.1
Identities = 15/33 (45%), Positives = 18/33 (54%), Gaps = 2/33 (6%)
Query: 8 VLVTGAAGQIGYALVPMIARG--VMLGTDQPVI 38
VLVTGAAG IG A AR ++ D+ V
Sbjct: 8 VLVTGAAGGIGRAACQRFARAGDQVVVADRNVE 40
>gnl|CDD|222146 pfam13460, NAD_binding_10, NADH(P)-binding.
Length = 182
Score = 29.2 bits (66), Expect = 2.2
Identities = 27/98 (27%), Positives = 36/98 (36%), Gaps = 16/98 (16%)
Query: 8 VLVTGAAGQIGYALVPM-IARGV------------MLGTDQPVILHMLDIPPAAEALNGV 54
+ V GA G+ G LV +ARG PV + D+ AEAL GV
Sbjct: 1 IAVIGATGKTGRRLVKELLARGHQVTALSRNPSKAPAPGVTPVQKDLFDLADLAEALAGV 60
Query: 55 KMELVDAAFPLLKGVVATTDAVEAC--TGVNIAVMVGG 90
+VDA ++A GV V+V
Sbjct: 61 DA-VVDAFGARPDDSDGVKHLLDAAARAGVRRIVVVSA 97
>gnl|CDD|217636 pfam03606, DcuC, C4-dicarboxylate anaerobic carrier.
Length = 456
Score = 29.6 bits (67), Expect = 2.4
Identities = 12/30 (40%), Positives = 17/30 (56%)
Query: 2 AKEPVRVLVTGAAGQIGYALVPMIARGVML 31
+ V GAA +G+ALV +ARGV +
Sbjct: 298 ENDIVEAFYEGAADLLGFALVVGLARGVGV 327
>gnl|CDD|187584 cd05323, ADH_SDR_c_like, insect type alcohol dehydrogenase
(ADH)-like, classical (c) SDRs. This subgroup contains
insect type ADH, and 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) type I; these proteins are
classical SDRs. ADH catalyzes the NAD+-dependent
oxidation of alcohols to aldehydes/ketones. This
subgroup is distinct from the zinc-dependent alcohol
dehydrogenases of the medium chain
dehydrogenase/reductase family, and evolved in fruit
flies to allow the digestion of fermenting fruit.
15-PGDH catalyzes the NAD-dependent interconversion of
(5Z,13E)-(15S)-11alpha,
15-dihydroxy-9-oxoprost-13-enoate and
(5Z,13E)-11alpha-hydroxy-9,15-dioxoprost-13-enoate, and
has a typical SDR glycine-rich NAD-binding motif, which
is not fully present in ADH. 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 = 244
Score = 29.2 bits (66), Expect = 2.6
Identities = 13/46 (28%), Positives = 20/46 (43%), Gaps = 6/46 (13%)
Query: 8 VLVTGAAGQIGYALVP-MIARGVMLGTDQPVILHMLDIPPAAEALN 52
++TG A IG A ++ +G + IL + P AA L
Sbjct: 3 AIITGGASGIGLATAKLLLKKGAKV-----AILDRNENPGAAAELQ 43
>gnl|CDD|236040 PRK07523, PRK07523, gluconate 5-dehydrogenase; Provisional.
Length = 255
Score = 29.4 bits (66), Expect = 2.6
Identities = 34/91 (37%), Positives = 42/91 (46%), Gaps = 15/91 (16%)
Query: 7 RVLVTGAAGQIGYALVPMIARGVMLGTDQPVILHMLD---IPPAAEALNGVKMELVDAAF 63
R LVTG++ IGYAL A G + VIL+ D + AAE+L G + AF
Sbjct: 12 RALVTGSSQGIGYAL----AEG-LAQAGAEVILNGRDPAKLAAAAESLKGQGLSAHALAF 66
Query: 64 PLL--KGVVATTDAVEACTG-----VNIAVM 87
+ V A DA EA G VN A M
Sbjct: 67 DVTDHDAVRAAIDAFEAEIGPIDILVNNAGM 97
>gnl|CDD|224011 COG1086, COG1086, Predicted nucleoside-diphosphate sugar epimerases
[Cell envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 588
Score = 29.5 bits (67), Expect = 2.9
Identities = 10/21 (47%), Positives = 11/21 (52%)
Query: 7 RVLVTGAAGQIGYALVPMIAR 27
VLVTG G IG L I +
Sbjct: 252 TVLVTGGGGSIGSELCRQILK 272
>gnl|CDD|217089 pfam02535, Zip, ZIP Zinc transporter. The ZIP family consists of
zinc transport proteins and many putative metal
transporters. The main contribution to this family is
from the Arabidopsis thaliana ZIP protein family these
proteins are responsible for zinc uptake in the plant.
Also found within this family are C. elegans proteins
of unknown function which are annotated as being
similar to human growth arrest inducible gene product,
although this protein in not found within this family.
Length = 314
Score = 29.2 bits (66), Expect = 3.0
Identities = 15/47 (31%), Positives = 20/47 (42%), Gaps = 5/47 (10%)
Query: 25 IARGVMLGTDQPVILHMLDIPPAAEALNGVKMELVDAAFPLLKGVVA 71
A GV+LGT LH+L P A EAL + G++
Sbjct: 43 FAAGVLLGT---AFLHLL--PEALEALESSPCLGDHGPWHPFAGLIV 84
>gnl|CDD|223513 COG0436, COG0436, Aspartate/tyrosine/aromatic aminotransferase
[Amino acid transport and metabolism].
Length = 393
Score = 29.2 bits (66), Expect = 3.2
Identities = 11/36 (30%), Positives = 17/36 (47%), Gaps = 1/36 (2%)
Query: 110 YKAQASALEQHAAPNCKVLVVANPAN-TNALILKEF 144
+K LE P K +++ +P N T A+ KE
Sbjct: 149 FKPDLEDLEAAITPKTKAIILNSPNNPTGAVYSKEE 184
>gnl|CDD|217199 pfam02719, Polysacc_synt_2, Polysaccharide biosynthesis protein.
This is a family of diverse bacterial polysaccharide
biosynthesis proteins including the CapD protein, WalL
protein mannosyl-transferase and several putative
epimerases (e.g. WbiI).
Length = 280
Score = 29.0 bits (66), Expect = 3.4
Identities = 10/20 (50%), Positives = 11/20 (55%)
Query: 8 VLVTGAAGQIGYALVPMIAR 27
VLVTG G IG L I +
Sbjct: 1 VLVTGGGGSIGSELCRQILK 20
>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 = 28.7 bits (65), Expect = 4.0
Identities = 9/15 (60%), Positives = 11/15 (73%)
Query: 8 VLVTGAAGQIGYALV 22
+LVTGA GQ+G L
Sbjct: 1 ILVTGANGQLGRELT 15
>gnl|CDD|201378 pfam00658, PABP, Poly-adenylate binding protein, unique domain.
The region featured in this family is found towards the
C-terminus of poly(A)-binding proteins (PABPs). These
are eukaryotic proteins that, through their binding of
the 3' poly(A) tail on mRNA, have very important roles
in the pathways of gene expression. They seem to
provide a scaffold on which other proteins can bind and
mediate processes such as export, translation and
turnover of the transcripts. Moreover, they may act as
antagonists to the binding of factors that allow mRNA
degradation, regulating mRNA longevity. PABPs are also
involved in nuclear transport. PABPs interact with
poly(A) tails via RNA-recognition motifs (pfam00076).
Note that the PABP C-terminal region is also found in
members of the hyperplastic discs protein (HYD) family
of ubiquitin ligases that contain HECT domains - these
are also included in this family.
Length = 72
Score = 26.8 bits (60), Expect = 4.0
Identities = 12/44 (27%), Positives = 20/44 (45%), Gaps = 10/44 (22%)
Query: 17 IGYALVPMIAR----------GVMLGTDQPVILHMLDIPPAAEA 50
+G L P+I G++L D +LH+L+ A +A
Sbjct: 20 LGERLYPLIQAMHPELAGKITGMLLEMDNSELLHLLESDEALKA 63
>gnl|CDD|187545 cd05234, UDP_G4E_2_SDR_e, UDP-glucose 4 epimerase, subgroup 2,
extended (e) SDRs. UDP-glucose 4 epimerase (aka
UDP-galactose-4-epimerase), is a homodimeric extended
SDR. It catalyzes the NAD-dependent conversion of
UDP-galactose to UDP-glucose, the final step in Leloir
galactose synthesis. This subgroup is comprised of
archaeal and bacterial proteins, and has the
characteristic active site tetrad and NAD-binding motif
of the extended SDRs. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 305
Score = 28.4 bits (64), Expect = 4.3
Identities = 33/149 (22%), Positives = 57/149 (38%), Gaps = 17/149 (11%)
Query: 7 RVLVTGAAGQIGYALVPMIARGVMLGTDQPVILHMLDIPPAAEALNGVKMELVDAAFPLL 66
R+LVTG AG IG LV + G + V+ ++ ++ ++ E + AF +
Sbjct: 1 RILVTGGAGFIGSHLVDRLLE---EGNEVVVVDNL-----SSGRRENIEPEFENKAFRFV 52
Query: 67 KGVVATTDAVEACTGVNIAVMVGGFP--RKEGMERKDVMSKNVSIYKAQASALEQHAAPN 124
K + T A + + P R + + +NV A + LE A
Sbjct: 53 KRDLLDTADKVAKKDGDTVFHLAANPDVRLGATDPDIDLEENVL---ATYNVLEAMRANG 109
Query: 125 CKVLVVANPA----NTNALILKEFAPSIP 149
K +V A+ + + E P +P
Sbjct: 110 VKRIVFASSSTVYGEAKVIPTPEDYPPLP 138
>gnl|CDD|237220 PRK12828, PRK12828, short chain dehydrogenase; Provisional.
Length = 239
Score = 28.2 bits (63), Expect = 5.2
Identities = 20/91 (21%), Positives = 34/91 (37%), Gaps = 12/91 (13%)
Query: 8 VLVTGAAGQIGYA----LVPMIARGVMLGTDQ-PVILHMLDIPPAAEALNGVKMELVDAA 62
V +TG G +G A L AR ++G P+ + +P A + G+ + AA
Sbjct: 10 VAITGGFGGLGRATAAWLAARGARVALIGRGAAPLSQTLPGVPADALRIGGIDLVDPQAA 69
Query: 63 FPLLKGVVATTDAVEACTGVNIAVMV-GGFP 92
A + ++ V + G F
Sbjct: 70 ------RRAVDEVNRQFGRLDALVNIAGAFV 94
>gnl|CDD|187635 cd08930, SDR_c8, classical (c) SDR, subgroup 8. This subgroup
has a fairly well conserved active site tetrad and
domain size of the classical SDRs, but has an atypical
NAD-binding motif ([ST]G[GA]XGXXG). 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 = 250
Score = 28.1 bits (63), Expect = 5.7
Identities = 9/19 (47%), Positives = 12/19 (63%)
Query: 8 VLVTGAAGQIGYALVPMIA 26
+L+TGAAG IG A +
Sbjct: 5 ILITGAAGLIGKAFCKALL 23
>gnl|CDD|224670 COG1756, Mra1, Uncharacterized conserved protein [Function
unknown].
Length = 223
Score = 28.1 bits (63), Expect = 5.9
Identities = 13/34 (38%), Positives = 20/34 (58%)
Query: 83 NIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASA 116
IAV++GGFP + E + +++ SIY SA
Sbjct: 172 GIAVIIGGFPHGDFREETEFVAEKYSIYDEPLSA 205
>gnl|CDD|223774 COG0702, COG0702, Predicted nucleoside-diphosphate-sugar
epimerases [Cell envelope biogenesis, outer membrane /
Carbohydrate transport and metabolism].
Length = 275
Score = 27.9 bits (62), Expect = 6.3
Identities = 12/24 (50%), Positives = 17/24 (70%), Gaps = 1/24 (4%)
Query: 7 RVLVTGAAGQIGYALVPM-IARGV 29
++LVTGA G +G A+V +ARG
Sbjct: 2 KILVTGATGFVGGAVVRELLARGH 25
>gnl|CDD|240338 PTZ00262, PTZ00262, subtilisin-like protease; Provisional.
Length = 639
Score = 28.0 bits (62), Expect = 7.1
Identities = 14/46 (30%), Positives = 22/46 (47%), Gaps = 5/46 (10%)
Query: 174 VQVSDVKNVIIWGNHSSSQYPDVNHATVNTAAGEKPVRELVKDDAW 219
VQ+ +KN + WG Y D++HA A + E+ K +W
Sbjct: 591 VQLPSLKNKVKWGG-----YLDIHHAVNLAIASKHGRTEIAKSQSW 631
>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 = 28.0 bits (63), Expect = 7.2
Identities = 12/16 (75%), Positives = 12/16 (75%)
Query: 7 RVLVTGAAGQIGYALV 22
RVLVTG AG IG LV
Sbjct: 1 RVLVTGGAGFIGSHLV 16
>gnl|CDD|187632 cd05374, 17beta-HSD-like_SDR_c, 17beta hydroxysteroid
dehydrogenase-like, classical (c) SDRs.
17beta-hydroxysteroid dehydrogenases are a group of
isozymes that catalyze activation and inactivation of
estrogen and androgens. 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 = 248
Score = 27.6 bits (62), Expect = 7.4
Identities = 9/20 (45%), Positives = 12/20 (60%)
Query: 8 VLVTGAAGQIGYALVPMIAR 27
VL+TG + IG AL +A
Sbjct: 3 VLITGCSSGIGLALALALAA 22
>gnl|CDD|236389 PRK09134, PRK09134, short chain dehydrogenase; Provisional.
Length = 258
Score = 27.6 bits (62), Expect = 7.5
Identities = 11/27 (40%), Positives = 14/27 (51%)
Query: 1 MAKEPVRVLVTGAAGQIGYALVPMIAR 27
P LVTGAA +IG A+ +A
Sbjct: 5 SMAAPRAALVTGAARRIGRAIALDLAA 31
>gnl|CDD|163582 TIGR03870, ABC_MoxJ, methanol oxidation system protein MoxJ. This
predicted periplasmic protein, called MoxJ or MxaJ, is
required for methanol oxidation in Methylobacterium
extorquens. Two differing lines of evidence suggest two
different roles. Forming one view, homology suggests it
is the substrate-binding protein of an ABC transporter
associated with methanol oxidation. The gene,
furthermore, is found regular in genomes with, and only
two or three genes away from, a corresponding permease
and ATP-binding cassette gene pair. The other view is
that this protein is an accessory factor or additional
subunit of methanol dehydrogenase itself. Mutational
studies show a dependence on this protein for expression
of the PQQ-dependent, two-subunit methanol dehydrogenase
(MxaF and MxaI) in Methylobacterium extorquens, as if it
is a chaperone for enzyme assembly or a third subunit. A
homologous N-terminal sequence was found in Paracoccus
denitrificans as a 32Kd third subunit. This protein may,
in fact, be both, a component of a periplasmic enzyme
that converts methanol to formaldehyde and a component
of an ABC transporter that delivers the resulting
formaldehyde to the cell's interior [Transport and
binding proteins, Carbohydrates, organic alcohols, and
acids, Energy metabolism, Other].
Length = 246
Score = 27.8 bits (62), Expect = 7.5
Identities = 21/74 (28%), Positives = 31/74 (41%), Gaps = 5/74 (6%)
Query: 6 VRVLVTGAAGQIGYALVPMIARGVMLGTDQPVILHMLDIPPAAEALNGVKMEL-VDAAFP 64
V + TG A + A P +AR V P L M IP A +G K+ + D +
Sbjct: 156 VSEVATGKAD-LAVAFAPEVARYV---KASPEPLRMTVIPDDATRSDGAKIPMQYDQSMG 211
Query: 65 LLKGVVATTDAVEA 78
+ K A ++A
Sbjct: 212 VRKDDTALLAEIDA 225
>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 = 27.6 bits (62), Expect = 7.9
Identities = 10/21 (47%), Positives = 12/21 (57%)
Query: 7 RVLVTGAAGQIGYALVPMIAR 27
RVL+TG AG IG L +
Sbjct: 2 RVLITGGAGFIGSNLARFFLK 22
>gnl|CDD|187535 cd02266, SDR, Short-chain dehydrogenases/reductases (SDR). SDRs
are a functionally diverse family of oxidoreductases
that have a single domain with a structurally conserved
Rossmann fold (alpha/beta folding pattern with a
central beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRs are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes catalyze a
wide range of activities including the metabolism of
steroids, cofactors, carbohydrates, lipids, aromatic
compounds, and amino acids, and act in redox sensing.
Classical SDRs have an TGXXX[AG]XG cofactor binding
motif and a YXXXK active site motif, with the Tyr
residue of the active site motif serving as a critical
catalytic residue (Tyr-151, human prostaglandin
dehydrogenase (PGDH) numbering). In addition to the Tyr
and Lys, there is often an upstream Ser (Ser-138, PGDH
numbering) and/or an Asn (Asn-107, PGDH numbering)
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. Extended SDRs have additional
elements in the C-terminal region, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase (KR) domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type KRs have
a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical
SDRs have lost catalytic activity and/or have an
unusual NAD(P)-binding motif and missing or unusual
active site residues. Reactions catalyzed within the
SDR family include isomerization, decarboxylation,
epimerization, C=N bond reduction, dehydratase
activity, dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 186
Score = 27.5 bits (61), Expect = 8.7
Identities = 16/57 (28%), Positives = 29/57 (50%), Gaps = 5/57 (8%)
Query: 8 VLVTGAAGQIGYALVPMIARGVMLGTDQPVILHMLD--IPPAAEALNGVKMELVDAA 62
VLVTG +G IG A+ +A G+ + +++ D + AA +G ++L +
Sbjct: 1 VLVTGGSGGIGGAIARWLASR---GSPKVLVVSRRDVVVHNAAILDDGRLIDLTGSR 54
>gnl|CDD|213929 TIGR04316, dhbA_paeA, 2,3-dihydro-2,3-dihydroxybenzoate
dehydrogenase. Members of this family are
2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase (EC
1.3.1.28), the third enzyme in the biosynthesis of
2,3-dihydroxybenzoic acid (DHB) from chorismate. The
first two enzymes are isochorismate synthase (EC
5.4.4.2) and isochorismatase (EC 3.3.2.1). Synthesis is
often followed by adenylation by the enzyme DHBA-AMP
ligase (EC 2.7.7.58) to activate (DHB) for a
non-ribosomal peptide synthetase.
Length = 250
Score = 27.6 bits (62), Expect = 8.8
Identities = 22/76 (28%), Positives = 29/76 (38%), Gaps = 11/76 (14%)
Query: 8 VLVTGAAGQIGYALVPMIAR--GVMLGTDQPVILHMLDIPPAAEALNGVKMELVDAAFPL 65
VLVTGAA IGYA+ +A + D+ L A G A + L
Sbjct: 1 VLVTGAAQGIGYAVARALAEAGARVAAVDRNF--EQLLELVADLRRYGYPF----ATYKL 54
Query: 66 LKGVVATTDAVEACTG 81
VA + AV+
Sbjct: 55 ---DVADSAAVDEVVQ 67
>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 = 27.6 bits (62), Expect = 8.9
Identities = 11/23 (47%), Positives = 16/23 (69%), Gaps = 1/23 (4%)
Query: 8 VLVTGAAGQIGYALVP-MIARGV 29
+LVTGA G +G LV ++A+G
Sbjct: 1 ILVTGATGFLGSNLVRALLAQGY 23
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.318 0.133 0.394
Gapped
Lambda K H
0.267 0.0728 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,157,614
Number of extensions: 1536047
Number of successful extensions: 1673
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1612
Number of HSP's successfully gapped: 122
Length of query: 320
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 223
Effective length of database: 6,635,264
Effective search space: 1479663872
Effective search space used: 1479663872
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 59 (26.5 bits)