RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 017740
(366 letters)
>gnl|CDD|177744 PLN00135, PLN00135, malate dehydrogenase.
Length = 309
Score = 677 bits (1749), Expect = 0.0
Identities = 283/309 (91%), Positives = 293/309 (94%)
Query: 58 MIARGIMLGPDQPVILHMLDIEPAAEALNGVKMELIDAAFPLLKGVVATTDVVEACKDVN 117
MIARG+MLGPDQPVILHMLDI PAAEALNGVKMELIDAAFPLLKGVVATTDVVEACK VN
Sbjct: 1 MIARGVMLGPDQPVILHMLDIPPAAEALNGVKMELIDAAFPLLKGVVATTDVVEACKGVN 60
Query: 118 IAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEKHAAPNCKVLVVANPANTNALILKE 177
IAVMVGGFPRKEGMERKDVMSKNVSIYK+QASALEKHAAP+CKVLVVANPANTNALILKE
Sbjct: 61 IAVMVGGFPRKEGMERKDVMSKNVSIYKSQASALEKHAAPDCKVLVVANPANTNALILKE 120
Query: 178 FAPSIPAKNITCLTRLDHNRAMGQISERLKVHVSDVKNVIIWGNHSSTQYPDVNHATVTT 237
FAPSIP KNITCLTRLDHNRA+GQISERL V VSDVKNVIIWGNHSSTQYPDVNHATV T
Sbjct: 121 FAPSIPEKNITCLTRLDHNRALGQISERLGVPVSDVKNVIIWGNHSSTQYPDVNHATVKT 180
Query: 238 SKGEKPVREAVADDNWLNTEFITTVQQRGAAIIKARKLSSALSAASSACDHIRDWVLGTP 297
GEKPVRE VADD WLN EFITTVQQRGAAIIKARKLSSALSAASSACDHIRDWVLGTP
Sbjct: 181 PSGEKPVRELVADDAWLNGEFITTVQQRGAAIIKARKLSSALSAASSACDHIRDWVLGTP 240
Query: 298 KGTWVSMGVYSDGSYGIPEGLIYSFPVTCEKGEWSIVKGLKVDEFSRAKMDATAEELAEE 357
+GTWVSMGVYSDGSYG+P GLIYSFPVTCEKGEWSIV+GL +DEFSR KMDATA+EL EE
Sbjct: 241 EGTWVSMGVYSDGSYGVPPGLIYSFPVTCEKGEWSIVQGLSIDEFSRKKMDATAKELKEE 300
Query: 358 KTLAYSCLN 366
K LAYSCL+
Sbjct: 301 KELAYSCLS 309
>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 = 642 bits (1659), Expect = 0.0
Identities = 228/325 (70%), Positives = 266/325 (81%)
Query: 38 EPCRVLVTGATGQIGYALVPMIARGIMLGPDQPVILHMLDIEPAAEALNGVKMELIDAAF 97
EP RVLVTGA GQI Y+L+PMIA+G + GPDQPVILH+LDI PA +AL GV MEL D AF
Sbjct: 1 EPIRVLVTGAAGQIAYSLLPMIAKGDVFGPDQPVILHLLDIPPALKALEGVVMELQDCAF 60
Query: 98 PLLKGVVATTDVVEACKDVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEKHAAP 157
PLLK VVATTD EA KDV++A++VG PRKEGMERKD++ NV I+K Q AL+K+A
Sbjct: 61 PLLKSVVATTDPEEAFKDVDVAILVGAMPRKEGMERKDLLKANVKIFKEQGEALDKYAKK 120
Query: 158 NCKVLVVANPANTNALILKEFAPSIPAKNITCLTRLDHNRAMGQISERLKVHVSDVKNVI 217
N KVLVV NPANTNALIL ++APSIP +N T LTRLDHNRA QI+ +L V VSDVKNVI
Sbjct: 121 NVKVLVVGNPANTNALILLKYAPSIPKENFTALTRLDHNRAKSQIALKLGVPVSDVKNVI 180
Query: 218 IWGNHSSTQYPDVNHATVTTSKGEKPVREAVADDNWLNTEFITTVQQRGAAIIKARKLSS 277
IWGNHSSTQYPDVNHATV + KP REAV DD WLN EFI+TVQ+RGAA+IKARKLSS
Sbjct: 181 IWGNHSSTQYPDVNHATVELNGKGKPAREAVKDDAWLNGEFISTVQKRGAAVIKARKLSS 240
Query: 278 ALSAASSACDHIRDWVLGTPKGTWVSMGVYSDGSYGIPEGLIYSFPVTCEKGEWSIVKGL 337
A+SAA + CDH+ DW GTP+G +VSMGVYSDGSYG+PEGLI+SFPVTC+ G+W IV+GL
Sbjct: 241 AMSAAKAICDHVHDWWFGTPEGEFVSMGVYSDGSYGVPEGLIFSFPVTCKNGKWKIVQGL 300
Query: 338 KVDEFSRAKMDATAEELAEEKTLAY 362
+D+FSR K+DATA+EL EEK A
Sbjct: 301 SIDDFSREKIDATAKELVEEKETAL 325
>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 = 566 bits (1461), Expect = 0.0
Identities = 226/324 (69%), Positives = 266/324 (82%), Gaps = 1/324 (0%)
Query: 41 RVLVTGATGQIGYALVPMIARGIMLGPDQPVILHMLDIEPAAEALNGVKMELIDAAFPLL 100
RV+VTGA GQIGYAL+PMIARG MLG DQP+ILH+LDI PA + L GV MEL+D AFPLL
Sbjct: 1 RVVVTGAAGQIGYALLPMIARGRMLGKDQPIILHLLDIPPAMKVLEGVVMELMDCAFPLL 60
Query: 101 KGVVATTDVVEACKDVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEKHAAPNCK 160
GVV T D A DV++A++VG FPRKEGMER+D++SKNV I+K Q AL+K A +CK
Sbjct: 61 DGVVPTHDPAVAFTDVDVAILVGAFPRKEGMERRDLLSKNVKIFKEQGRALDKLAKKDCK 120
Query: 161 VLVVANPANTNALILKEFAPSIPAKNITCLTRLDHNRAMGQISERLKVHVSDVKNVIIWG 220
VLVV NPANTNAL+L +APSIP KN + LTRLDHNRA+ Q++ER V VSDVKNVIIWG
Sbjct: 121 VLVVGNPANTNALVLSNYAPSIPPKNFSALTRLDHNRALAQVAERAGVPVSDVKNVIIWG 180
Query: 221 NHSSTQYPDVNHATVTTSKGEKPVREAVADDNWLNTEFITTVQQRGAAIIKARKLSSALS 280
NHSSTQYPDVNHATVT +KPVREA+ DD +L+ EFITTVQQRGAAII+ARKLSSALS
Sbjct: 181 NHSSTQYPDVNHATVTKGGKQKPVREAIKDDAYLDGEFITTVQQRGAAIIRARKLSSALS 240
Query: 281 AASSACDHIRDWVLGTPKGTWVSMGVYSDGS-YGIPEGLIYSFPVTCEKGEWSIVKGLKV 339
AA +A D + DWVLGTP+GT+VSMGVYSDGS YG+P+GLI+SFPVTC+ GEW IV+GL V
Sbjct: 241 AAKAAVDQMHDWVLGTPEGTFVSMGVYSDGSPYGVPKGLIFSFPVTCKNGEWKIVEGLCV 300
Query: 340 DEFSRAKMDATAEELAEEKTLAYS 363
D+ SR K+ TA+EL EE+ A S
Sbjct: 301 DDSSRKKLALTAKELEEERDEALS 324
>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 = 543 bits (1400), Expect = 0.0
Identities = 209/327 (63%), Positives = 247/327 (75%), Gaps = 6/327 (1%)
Query: 37 KEPCRVLVTGATGQIGYALVPMIARGIMLGPDQPVILHMLDIEPAAEALNGVKMELIDAA 96
K+P RV VTGA GQIGY+L+ IA G + G DQPV+LH+LDI PA +AL GV MEL D A
Sbjct: 1 KKPVRVAVTGAAGQIGYSLLFRIASGELFGKDQPVVLHLLDIPPAMKALEGVAMELEDCA 60
Query: 97 FPLLKGVVATTDVVEACKDVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEKHAA 156
FPLL GVVATTD EA KDV+ A++VG FPRK GMER D++SKN I+K Q AL K A
Sbjct: 61 FPLLAGVVATTDPEEAFKDVDAALLVGAFPRKPGMERADLLSKNGKIFKEQGKALNKVAK 120
Query: 157 PNCKVLVVANPANTNALILKEFAPSIPAKNITCLTRLDHNRAMGQISERLKVHVSDVKNV 216
+ KVLVV NPANTNALI + AP IP KN + +TRLDHNRA Q++ + V VSDVKNV
Sbjct: 121 KDVKVLVVGNPANTNALIASKNAPDIPPKNFSAMTRLDHNRAKYQLAAKAGVPVSDVKNV 180
Query: 217 IIWGNHSSTQYPDVNHATVTTSKGEKPVREAVADDNWLNTEFITTVQQRGAAIIKARKLS 276
IIWGNHS+TQ PD HATV +PV+E + DD WL EFI TVQQRGAA+I+AR S
Sbjct: 181 IIWGNHSNTQVPDFTHATVDG----RPVKEVIKDDKWLEGEFIPTVQQRGAAVIEARGAS 236
Query: 277 SALSAASSACDHIRDWVLGTPKGTWVSMGVYSDG-SYGIPEGLIYSFPVTCEK-GEWSIV 334
SA SAA++A DH+RDWV GTP+G WVSMGVYSDG YGIPEG+I+SFPVTC+ GEW IV
Sbjct: 237 SAASAANAAIDHVRDWVTGTPEGDWVSMGVYSDGNPYGIPEGIIFSFPVTCKGDGEWEIV 296
Query: 335 KGLKVDEFSRAKMDATAEELAEEKTLA 361
+GL +D+F R K+DAT +EL EEK A
Sbjct: 297 EGLPLDDFVRGKLDATEDELLEEKEEA 323
>gnl|CDD|235468 PRK05442, PRK05442, malate dehydrogenase; Provisional.
Length = 326
Score = 526 bits (1358), Expect = 0.0
Identities = 195/322 (60%), Positives = 239/322 (74%), Gaps = 4/322 (1%)
Query: 37 KEPCRVLVTGATGQIGYALVPMIARGIMLGPDQPVILHMLDIEPAAEALNGVKMELIDAA 96
K P RV VTGA GQIGY+L+ IA G MLG DQPVIL +L+I PA +AL GV MEL D A
Sbjct: 2 KAPVRVAVTGAAGQIGYSLLFRIASGDMLGKDQPVILQLLEIPPALKALEGVVMELDDCA 61
Query: 97 FPLLKGVVATTDVVEACKDVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEKHAA 156
FPLL GVV T D A KD ++A++VG PR GMERKD++ N +I+ AQ AL + AA
Sbjct: 62 FPLLAGVVITDDPNVAFKDADVALLVGARPRGPGMERKDLLEANGAIFTAQGKALNEVAA 121
Query: 157 PNCKVLVVANPANTNALILKEFAPSIPAKNITCLTRLDHNRAMGQISERLKVHVSDVKNV 216
+ KVLVV NPANTNALI + AP +PA+N T +TRLDHNRA+ Q++ + V V+D+K +
Sbjct: 122 RDVKVLVVGNPANTNALIAMKNAPDLPAENFTAMTRLDHNRALSQLAAKAGVPVADIKKM 181
Query: 217 IIWGNHSSTQYPDVNHATVTTSKGEKPVREAVADDNWLNTEFITTVQQRGAAIIKARKLS 276
+WGNHS+TQYPD HAT+ KP E + D WL FI TVQ+RGAAII+AR S
Sbjct: 182 TVWGNHSATQYPDFRHATI----DGKPAAEVINDQAWLEDTFIPTVQKRGAAIIEARGAS 237
Query: 277 SALSAASSACDHIRDWVLGTPKGTWVSMGVYSDGSYGIPEGLIYSFPVTCEKGEWSIVKG 336
SA SAA++A DH+RDWVLGTP+G WVSMGV SDGSYGIPEGLI+ FPVTCE GE+ IV+G
Sbjct: 238 SAASAANAAIDHVRDWVLGTPEGDWVSMGVPSDGSYGIPEGLIFGFPVTCENGEYEIVQG 297
Query: 337 LKVDEFSRAKMDATAEELAEEK 358
L++D+FSR K+DAT EL EE+
Sbjct: 298 LEIDDFSREKIDATLAELEEER 319
>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 = 504 bits (1301), Expect = 0.0
Identities = 193/322 (59%), Positives = 237/322 (73%), Gaps = 2/322 (0%)
Query: 41 RVLVTGATGQIGYALVPMIARGIMLGPDQPVILHMLDIEPAAEALNGVKMELIDAAFPLL 100
VL+TGA GQIGY L+ +IA G + G DQPVILH+LDI PA +AL GV MEL D AFPLL
Sbjct: 2 HVLITGAAGQIGYNLLFLIASGELFGDDQPVILHLLDIPPAMKALEGVVMELQDCAFPLL 61
Query: 101 KGVVATTDVVEACKDVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEKHAAPNCK 160
KGVV TTD EA KDV++A++VG FPRK GMER D++ KN I+K Q AL K A P K
Sbjct: 62 KGVVITTDPEEAFKDVDVAILVGAFPRKPGMERADLLRKNAKIFKEQGEALNKVAKPTVK 121
Query: 161 VLVVANPANTNALILKEFAPSIPAKNITCLTRLDHNRAMGQISERLKVHVSDVKNVIIWG 220
VLVV NPANTNALI + AP++P KN T LTRLDHNRA Q++ +L V VSDVKNVIIWG
Sbjct: 122 VLVVGNPANTNALIALKNAPNLPPKNFTALTRLDHNRAKAQVARKLGVRVSDVKNVIIWG 181
Query: 221 NHSSTQYPDVNHATVTTSKGEKPVREAVADDNWLNTEFITTVQQRGAAIIKARKLSSALS 280
NHS+TQ PD+++A V G + V + D+ WLN EF+ TVQ+RGAAIIK R SSA S
Sbjct: 182 NHSNTQVPDLSNAVVYGPGGTEWV-LDLLDEEWLNDEFVKTVQKRGAAIIKKRGASSAAS 240
Query: 281 AASSACDHIRDWVLGTPKGTWVSMGVYSDG-SYGIPEGLIYSFPVTCEKGEWSIVKGLKV 339
AA + DH++DW+ GTP G VSMGVYS G YGIP G+++SFP TC+ G W +V+ LK+
Sbjct: 241 AAKAIADHVKDWLFGTPPGEIVSMGVYSPGNPYGIPPGIVFSFPCTCKGGGWHVVEDLKL 300
Query: 340 DEFSRAKMDATAEELAEEKTLA 361
+++ R K+ AT EEL EEK +A
Sbjct: 301 NDWLREKLKATEEELIEEKEIA 322
>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 = 504 bits (1300), Expect = 0.0
Identities = 186/321 (57%), Positives = 229/321 (71%), Gaps = 4/321 (1%)
Query: 38 EPCRVLVTGATGQIGYALVPMIARGIMLGPDQPVILHMLDIEPAAEALNGVKMELIDAAF 97
+P RV VTGA GQIGY+L+ IA G M GPDQPVIL +L++ A +AL GV MEL D AF
Sbjct: 1 KPVRVAVTGAAGQIGYSLLFRIASGEMFGPDQPVILQLLELPQALKALEGVAMELEDCAF 60
Query: 98 PLLKGVVATTDVVEACKDVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEKHAAP 157
PLL +V T D A KD + A++VG PR GMER D++ N I+ AQ AL A+
Sbjct: 61 PLLAEIVITDDPNVAFKDADWALLVGAKPRGPGMERADLLKANGKIFTAQGKALNDVASR 120
Query: 158 NCKVLVVANPANTNALILKEFAPSIPAKNITCLTRLDHNRAMGQISERLKVHVSDVKNVI 217
+ KVLVV NP NTNALI + AP IP N T +TRLDHNRA Q++++ V V+DVKN++
Sbjct: 121 DVKVLVVGNPCNTNALIAMKNAPDIPPDNFTAMTRLDHNRAKSQLAKKAGVPVTDVKNMV 180
Query: 218 IWGNHSSTQYPDVNHATVTTSKGEKPVREAVADDNWLNTEFITTVQQRGAAIIKARKLSS 277
IWGNHS TQYPD +AT+ G KP E + D WL EFI TVQ+RGAAIIKAR SS
Sbjct: 181 IWGNHSPTQYPDFTNATI----GGKPAAEVINDRAWLEDEFIPTVQKRGAAIIKARGASS 236
Query: 278 ALSAASSACDHIRDWVLGTPKGTWVSMGVYSDGSYGIPEGLIYSFPVTCEKGEWSIVKGL 337
A SAA++A DH+RDWVLGTP+G W SM V SDGSYGIPEGLI+SFPV + G + IV+GL
Sbjct: 237 AASAANAAIDHMRDWVLGTPEGDWFSMAVPSDGSYGIPEGLIFSFPVRSKGGGYEIVEGL 296
Query: 338 KVDEFSRAKMDATAEELAEEK 358
++D+F+R K+DAT EL EE+
Sbjct: 297 EIDDFAREKIDATLAELLEER 317
>gnl|CDD|215060 PLN00112, PLN00112, malate dehydrogenase (NADP); Provisional.
Length = 444
Score = 312 bits (800), Expect = e-103
Identities = 144/326 (44%), Positives = 194/326 (59%), Gaps = 10/326 (3%)
Query: 37 KEPCRVLVTGATGQIGYALVPMIARGIMLGPDQPVILHMLDIEPAAEALNGVKMELIDAA 96
K+ V V+GA G I L+ +A G + GPDQP+ L +L E + +AL GV MEL D+
Sbjct: 98 KKLINVAVSGAAGMISNHLLFKLASGEVFGPDQPIALKLLGSERSKQALEGVAMELEDSL 157
Query: 97 FPLLKGVVATTDVVEACKDVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEKHAA 156
+PLL+ V D E +D A+++G PR GMER D++ N I+ Q AL + A+
Sbjct: 158 YPLLREVSIGIDPYEVFQDAEWALLIGAKPRGPGMERADLLDINGQIFAEQGKALNEVAS 217
Query: 157 PNCKVLVVANPANTNALILKEFAPSIPAKNITCLTRLDHNRAMGQISERLKVHVSDVKNV 216
N KV+VV NP NTNALI + AP+IPAKN LTRLD NRA Q++ + V V NV
Sbjct: 218 RNVKVIVVGNPCNTNALICLKNAPNIPAKNFHALTRLDENRAKCQLALKAGVFYDKVSNV 277
Query: 217 IIWGNHSSTQYPDVNHATVTTSKGEKPVREAVADDNWLNTEFITTVQQRGAAIIKARKLS 276
IWGNHS+TQ PD +A + PV+E + D WL EF VQ+RG +IK S
Sbjct: 278 TIWGNHSTTQVPDFLNAKI----NGLPVKEVITDHKWLEEEFTPKVQKRGGVLIKKWGRS 333
Query: 277 SALSAASSACDHIRDWVLGTPKGTWVSMGVYSDGS-YGIPEGLIYSFPVTCEK---GEWS 332
SA S A S D I+ V TP+G W S GVY+DG+ YGI EGL++S P C G++
Sbjct: 334 SAASTAVSIADAIKSLVTPTPEGDWFSTGVYTDGNPYGIAEGLVFSMP--CRSKGDGDYE 391
Query: 333 IVKGLKVDEFSRAKMDATAEELAEEK 358
IVK +++D++ R ++ + EL EK
Sbjct: 392 IVKDVEIDDYLRERIKKSEAELLAEK 417
>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 = 288 bits (738), Expect = 4e-95
Identities = 144/324 (44%), Positives = 197/324 (60%), Gaps = 6/324 (1%)
Query: 37 KEPCRVLVTGATGQIGYALVPMIARGIMLGPDQPVILHMLDIEPAAEALNGVKMELIDAA 96
K+ V V+GA G I L+ M+A G + G DQP+ L +L E + EAL GV MEL D+
Sbjct: 42 KKTVNVAVSGAAGMISNHLLFMLASGEVFGQDQPIALKLLGSERSKEALEGVAMELEDSL 101
Query: 97 FPLLKGVVATTDVVEACKDVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEKHAA 156
+PLL+ V D E +D + A+++G PR GMER D++ N I+ Q AL A+
Sbjct: 102 YPLLREVSIGIDPYEVFEDADWALLIGAKPRGPGMERADLLDINGQIFADQGKALNAVAS 161
Query: 157 PNCKVLVVANPANTNALILKEFAPSIPAKNITCLTRLDHNRAMGQISERLKVHVSDVKNV 216
NCKVLVV NP NTNALI + AP+IP KN LTRLD NRA Q++ + + V NV
Sbjct: 162 KNCKVLVVGNPCNTNALIAMKNAPNIPRKNFHALTRLDENRAKCQLALKSGKFYTSVSNV 221
Query: 217 IIWGNHSSTQYPDVNHATVTTSKGEKPVREAVADDNWLNTEFITTVQQRGAAIIKARKLS 276
IWGNHS+TQ PD +A + G +P +E + D WL EF TVQ+RG A+IK S
Sbjct: 222 TIWGNHSTTQVPDFVNAKI----GGRPAKEVIKDTKWLEEEFTPTVQKRGGALIKKWGRS 277
Query: 277 SALSAASSACDHIRDWVLGTPKGTWVSMGVYSDGS-YGIPEGLIYSFPVTCE-KGEWSIV 334
SA S A S D I+ V+ TP+G W S GVY+DG+ YGI EGL++S P + G++ +
Sbjct: 278 SAASTAVSIADAIKSLVVPTPEGDWFSTGVYTDGNPYGIAEGLVFSMPCRSKGDGDYELA 337
Query: 335 KGLKVDEFSRAKMDATAEELAEEK 358
+ +D+F R ++ + +EL +EK
Sbjct: 338 TDVSMDDFLRERIRKSEDELLKEK 361
>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 = 270 bits (691), Expect = 6e-89
Identities = 117/310 (37%), Positives = 180/310 (58%), Gaps = 5/310 (1%)
Query: 59 IARGIMLGPDQPVILHMLDIEPAAEALNGVKMELIDAAFPLLKGVVATTDVVEACKDVNI 118
IA G + G ++PV LH+L+I PA L + MEL D AFP L G + TT + EA KD++
Sbjct: 5 IANGDLYG-NRPVCLHLLEIPPALNRLEALAMELEDCAFPNLAGTIVTTKLEEAFKDIDC 63
Query: 119 AVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEKHAAPNCKVLVVANPANTNALILKEF 178
A +V P K G R D+++KN I+KA AL ++A P KVLV+ NP NTN L+
Sbjct: 64 AFLVASVPLKPGEVRADLLTKNTPIFKATGEALSEYAKPTVKVLVIGNPVNTNCLVAMLH 123
Query: 179 APSIPAKNITCLTRLDHNRAMGQISERLKVHVSDVKNVIIWGNHSSTQYPDVNHATVTTS 238
AP + A+N + L LDHNRA+ +I+ +LKV V + +V++WGNH+ + D+ HA T +
Sbjct: 124 APKLSAENFSSLCMLDHNRAVSRIASKLKVPVDHIYHVVVWGNHAESMVADLTHAEFTKN 183
Query: 239 KGEKPVREAVADDNWLNTEFITTVQQRGAAIIKARKLSSALSAASSACDHIRDWVLGTPK 298
+ V + + D + +F + QR I++ R +SA S ++ H++ W+ GT
Sbjct: 184 GKHQKVFDELCRD-YPEPDFFEVIAQRAWKILEMRGFTSAASPVKASLQHMKAWLFGTRP 242
Query: 299 GTWVSMG--VYSDGSYGIPEGLIYSFPVTC-EKGEWSIVKGLKVDEFSRAKMDATAEELA 355
G +SMG V YGI G+I+SFP T E G+ +V+ +++ + + K+ T ++L
Sbjct: 243 GEVLSMGIPVPEGNPYGIKPGVIFSFPCTVDEDGKVHVVENFELNPWLKTKLAQTEKDLF 302
Query: 356 EEKTLAYSCL 365
EE+ A L
Sbjct: 303 EERETALKAL 312
>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 = 268 bits (687), Expect = 2e-86
Identities = 113/332 (34%), Positives = 181/332 (54%), Gaps = 13/332 (3%)
Query: 39 PCRVLVTGATGQIGYALVPMIARGIMLGPDQPVILHMLDIEPAAEALNGVKMELIDAAFP 98
P +V +T A+ + Y L+P +A G + G ++ + +H+LD E L G+ ME+ D AFP
Sbjct: 123 PLQVCITNASAPLCYHLIPSLASGEVFGMEEEISIHLLDSPENLEKLKGLVMEVEDLAFP 182
Query: 99 LLKGVVATTDVVEACKDVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEKHAAPN 158
LL+G+ TTD+ A KD ++ V++ F KEG + + + V+I + +EK+A +
Sbjct: 183 LLRGISVTTDLDVAFKDAHVIVLLDDFLIKEGEDLEGCIRSRVAICQLYGPLIEKNAKED 242
Query: 159 CKVLVVA-NPANTNALILKEFAPSIPAKNITCLTRLDHNRAMGQISERLKVHVSDVKNVI 217
KV+V N IL ++APSIP KNI + RL NRA ++ +L V+ + +K+VI
Sbjct: 243 VKVIVAGRTFLNLKTSILIKYAPSIPRKNIIAVARLQENRAKALLARKLNVNSAGIKDVI 302
Query: 218 IWGNHSSTQYPDVNHATVTTSKG--------EKPVREAVADDNWLNTEFITTVQQRGAAI 269
+WGN Y D++ A V +PV E V D W+N EF+ T++ +
Sbjct: 303 VWGNIGGNTYIDLSKARVYRYDSAIWGPPNYSRPVLELVHDSKWINGEFVATLKSLSS-- 360
Query: 270 IKARKLSSALSAASSACDHIRDWVLGTPKGTWVSMGVYSDGSYGIPEGLIYSFPVTCEKG 329
+ +A+S A + + W G+P G S+GV S+G YGIPEG+++S PV + G
Sbjct: 361 --SLNHEAAISPAHAIATTLSYWYHGSPPGEIFSLGVISEGWYGIPEGIVFSMPVKFQNG 418
Query: 330 EWSIVKGLKVDEFSRAKMDATAEELAEEKTLA 361
W +V L++ E R + +L +EK +A
Sbjct: 419 SWEVVTDLELSEILREVLKRITSDLIQEKLVA 450
>gnl|CDD|223117 COG0039, Mdh, Malate/lactate dehydrogenases [Energy production and
conversion].
Length = 313
Score = 229 bits (587), Expect = 3e-73
Identities = 103/324 (31%), Positives = 153/324 (47%), Gaps = 21/324 (6%)
Query: 41 RVLVTGATGQIGYALVPMIARGIMLGPDQPVILHMLDIEPAAEALNGVKMELIDAAFPLL 100
+V V GA G +G +L ++ LG + L ++DI E GV ++L AA PL
Sbjct: 2 KVAVIGA-GNVGSSLAFLLLLQ-GLGSE----LVLIDINE--EKAEGVALDLSHAAAPLG 53
Query: 101 KGVVATTDV-VEACKDVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEKHAAPNC 159
V T D E K +I V+ G PRK GM R D++ KN I K A A+ K+A P+
Sbjct: 54 SDVKITGDGDYEDLKGADIVVITAGVPRKPGMTRLDLLEKNAKIVKDIAKAIAKYA-PDA 112
Query: 160 KVLVVANPANTNALILKEFAPSIPAKNITCLTRLDHNRAMGQISERLKVHVSDVKNVIIW 219
VLVV NP + I +F+ + I T LD R ++E+L V DV +I
Sbjct: 113 IVLVVTNPVDILTYIAMKFSGFPKNRVIGSGTVLDSARFRTFLAEKLGVSPKDVHAYVI- 171
Query: 220 GNHSSTQYPDVNHATVTTSKGEKPVREAV-ADDNWLNTEFITTVQQRGAAIIKARKLSSA 278
G H T P + ATV G KP+ E + D E I V+ GA II+A+ +
Sbjct: 172 GEHGDTMVPLWSQATV----GGKPLEELLKEDTEEDLEELIERVRNAGAEIIEAKGAGTY 227
Query: 279 LSAASSACDHIRDWVLGTPKGTWVSMGVYSDGSYGIPEGLIYSFPVT-CEKGEWSIVKGL 337
A++ + + + + + VY DG YG+ E + + P + G I++ L
Sbjct: 228 YGPAAALARMVEAILRD--EKRVLPVSVYLDGEYGV-EDVYFGVPAVLGKNGVEEILELL 284
Query: 338 KVDEFSRAKMDATAEELAEEKTLA 361
D+ + K+D +AEEL + L
Sbjct: 285 LSDD-EQEKLDKSAEELKKNIELV 307
>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 = 199 bits (507), Expect = 7e-62
Identities = 85/318 (26%), Positives = 136/318 (42%), Gaps = 57/318 (17%)
Query: 42 VLVTGATGQIGYALVPMIARGIMLGPDQPVILHMLDIEPAAEALNGVKMELIDAAFPL-L 100
+ V GA G +G AL +A G + L + DI+ E L GV M+L DA PL
Sbjct: 1 IAVIGAGGNVGPALAFGLADG---SVLLAIELVLYDIDE--EKLKGVAMDLQDAVEPLAD 55
Query: 101 KGVVATTDVVEACKDVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEKHAAPNCK 160
V T D EA KD ++ ++ G RK GM R D++ +NV I K +EK+ +P+
Sbjct: 56 IKVSITDDPYEAFKDADVVIITAGVGRKPGMGRLDLLKRNVPIVKEIGDNIEKY-SPDAW 114
Query: 161 VLVVANPANTNALILKEFAPSIPAKNITCLTRLDHNRAMGQISERLKVHVSDVKNVIIWG 220
++VV+NP + ++ ++ +P + + L LD R ++E+L V DVK V I G
Sbjct: 115 IIVVSNPVDIITYLVWRYSG-LPKEKVIGLGTLDPIRFRRILAEKLGVDPDDVK-VYILG 172
Query: 221 NHSSTQYPDVNHATVTTSKGEKPVREAVADDNWLNTEFITTVQQRGAAIIKARKLSSALS 280
H +Q PD +
Sbjct: 173 EHGGSQVPDWSTVR---------------------------------------------- 186
Query: 281 AASSACDHIRDWVLGTPKGTWVSMGVYSDGSYGIPEGLIYSFPVTCEKGEWSIVKGLKVD 340
A+S D IR + +G + +GV ++G GIP+ ++ S P K + +
Sbjct: 187 IATSIADLIRSLL--NDEGEILPVGVRNNGQIGIPDDVVVSVPCIVGKNGVEEPIEVGLT 244
Query: 341 EFSRAKMDATAEELAEEK 358
+F K+ +A+ L +E
Sbjct: 245 DFELEKLQKSADTLKKEL 262
>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 = 164 bits (416), Expect = 1e-49
Identities = 61/172 (35%), Positives = 91/172 (52%), Gaps = 4/172 (2%)
Query: 191 TRLDHNRAMGQISERLKVHVSDVKNVIIWGNHSSTQYPDVNHATVTTSKGEKPVREAVAD 250
T LD RA ++E+ V NV + G HS TQ+PD +HA VT V+E + D
Sbjct: 1 TTLDTARARTFLAEKFGV-DPRSVNVYVIGEHSGTQFPDWSHAKVTIIPLISQVKENLKD 59
Query: 251 DNWLNTEFITTVQQRGAAIIKARKLSSALSAASSACDHIRDWVLGTPKGTWVSMGVYSDG 310
+W E I VQ G +I+A+ S+ S A +A + + GT G +S+GVY DG
Sbjct: 60 TDWELEELIERVQNAGYEVIEAKAGSTTYSMAYAAARIAKAILRGT--GGVLSVGVYLDG 117
Query: 311 SYGIPEGLIYSFPVTCEK-GEWSIVKGLKVDEFSRAKMDATAEELAEEKTLA 361
YG P+ + +S PV K G +V+ L +++F R K++ +A EL +E
Sbjct: 118 YYGSPDDIYFSVPVVLGKDGVEKVVEILPLNDFEREKLEKSAAELKKEIEKG 169
>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 = 131 bits (332), Expect = 2e-37
Identities = 47/150 (31%), Positives = 73/150 (48%), Gaps = 8/150 (5%)
Query: 40 CRVLVTGATGQIGYALVPMIARGIMLGPDQPVILHMLDIEPAAEALNGVKMELIDAAFPL 99
+V V GA G +G +L +A L + L ++DI + GV M+L + L
Sbjct: 1 VKVAVVGAGGGVGSSLAFALA-LQGLADE----LVLVDINK--DKAEGVAMDLSHGSTFL 53
Query: 100 LKGVVATTDVVEACKDVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEKHAAPNC 159
+ D EA KD ++ V+ G PRK GM R D++++N I+K A+ K AP+
Sbjct: 54 SVPGIVGGDDYEALKDADVVVITAGVPRKPGMTRLDLLNRNAGIFKDIVPAIAKS-APDA 112
Query: 160 KVLVVANPANTNALILKEFAPSIPAKNITC 189
VLVV+NP + I + + P + I
Sbjct: 113 IVLVVSNPVDILTYIAWKVSGLPPERVIGS 142
>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 = 83.9 bits (208), Expect = 3e-18
Identities = 78/317 (24%), Positives = 140/317 (44%), Gaps = 22/317 (6%)
Query: 42 VLVTGATGQIGYALVPMIARGIMLGPDQPVILHMLDIEPAAEALNGVKMELIDAAFPLLK 101
+ + GA G +G A +A ++ ++ ++D+ E G ++L A+ L
Sbjct: 1 ITIIGA-GNVGAA----VAFALIAKGLASELV-LVDVNE--EKAKGDALDLSHASAFLAT 52
Query: 102 GVVATTDVVEACKDVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEKHAAPNCKV 161
G + D +I V+ G PRK G R D++++N I ++ + L+K+ P+ +
Sbjct: 53 GTIVRGGDYADAADADIVVITAGAPRKPGETRLDLINRNAPILRSVITNLKKY-GPDAII 111
Query: 162 LVVANPANTNALILKEFAPSIPAKNITCLTRLDHNRAMGQISERLKVHVSDVKNVIIWGN 221
LVV+NP + + ++ + + I T LD R ++E+L V V ++ G
Sbjct: 112 LVVSNPVDILTYVAQKLSGLPKNRVIGSGTLLDSARFRSLLAEKLDVDPQSVHAYVL-GE 170
Query: 222 HSSTQYPDVNHATVTTSKGEKPVREAVADDNWLNTEFITTVQQRGAAIIKARKLSSALSA 281
H +Q + ATV G P+ E V+ G II+ K ++
Sbjct: 171 HGDSQVVAWSTATV----GGLPLEELAPFTKLDLEAIEEEVRTSGYEIIR-LKGATNYGI 225
Query: 282 ASSACDHIRDWVLGTPKGTWVSMGVYSDGSYGIPEGLIYSFP-VTCEKGEWSIVKG-LKV 339
A++ D ++ +L + + + +G YGI E + S P V +G I++ L
Sbjct: 226 ATAIADIVKS-ILLDERRV-LPVSAVQEGQYGI-EDVALSVPAVVGREGVVRILEIPLTE 282
Query: 340 DEFSRAKMDATAEELAE 356
DE AK+ +AE L E
Sbjct: 283 DE--EAKLQKSAEALKE 297
>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 = 79.4 bits (197), Expect = 8e-17
Identities = 68/266 (25%), Positives = 109/266 (40%), Gaps = 35/266 (13%)
Query: 103 VVATTDVVEACKDVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEKHAAPNCKVL 162
V T D E ++ V+ G PRK GM R D++ N I K A ++K+ APN V+
Sbjct: 55 VTGTNDY-EDIAGSDVVVITAGIPRKPGMSRDDLLGTNAKIVKEVAENIKKY-APNAIVI 112
Query: 163 VVANPANTNALILKEFAPSIPAKNITCLTRLDHNRAMGQ------------ISERLKVHV 210
VV NP + + + + NR +G I+E L V V
Sbjct: 113 VVTNPLDVMTYVAYKA------------SGFPRNRVIGMAGVLDSARFRYFIAEELGVSV 160
Query: 211 SDVKNVIIWGNHSSTQYPDVNHATVTTSKGEKPVREAVADDNWLNTEFITTVQQRGAAII 270
DV+ +++ G H T P ++TV G P+ E + + E + + GA I+
Sbjct: 161 KDVQAMVL-GGHGDTMVPLPRYSTV----GGIPLTELITKEEI--DEIVERTRNGGAEIV 213
Query: 271 KARKLSSALSAASSACDHIRDWVLGTPKGTWVSMGVYSDGSYGIPEGLIYSFPVTCEKGE 330
K SA A ++A + + +L K Y +G YGI + + PV K
Sbjct: 214 NLLKTGSAYYAPAAAIAEMVEAILKDKKRVLPC-SAYLEGEYGI-KDIFVGVPVVLGKNG 271
Query: 331 WSIVKGLKVDEFSRAKMDATAEELAE 356
+ L + + + D + E + E
Sbjct: 272 VEKIIELDLTDEEKEAFDKSVESVKE 297
>gnl|CDD|180477 PRK06223, PRK06223, malate dehydrogenase; Reviewed.
Length = 307
Score = 77.5 bits (192), Expect = 5e-16
Identities = 79/336 (23%), Positives = 141/336 (41%), Gaps = 58/336 (17%)
Query: 41 RVLVTGATGQIGYALVPMIARGIMLGPDQPVILHMLDIEPAAEALNGVKMELIDAAFPLL 100
++ + GA G +G L ++A + + + DI G +++ +AA
Sbjct: 4 KISIIGA-GNVGATLAHLLAL------KELGDVVLFDI--VEGVPQGKALDIAEAA---- 50
Query: 101 KGVVATTDVV-------EACKDVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEK 153
V D E ++ V+ G PRK GM R D++ N I K A ++K
Sbjct: 51 --PVEGFDTKITGTNDYEDIAGSDVVVITAGVPRKPGMSRDDLLGINAKIMKDVAEGIKK 108
Query: 154 HAAPNCKVLVVANPANT-NALILKEFAPSIPAKNITCLTRLDHNRAMGQ----------- 201
+ AP+ V+VV NP + + LKE + NR +G
Sbjct: 109 Y-APDAIVIVVTNPVDAMTYVALKE-------------SGFPKNRVIGMAGVLDSARFRT 154
Query: 202 -ISERLKVHVSDVKNVIIWGNHSSTQYPDVNHATVTTSKGEKPVREAVADDNWLNTEFIT 260
I+E L V V DV ++ G H + P V ++TV G P+ + ++ + L+ E +
Sbjct: 155 FIAEELNVSVKDVTAFVL-GGHGDSMVPLVRYSTV----GGIPLEDLLSKEK-LD-EIVE 207
Query: 261 TVQQRGAAIIKARKLSSALSAASSACDHIRDWVLGTPKGTWVSMGVYSDGSYGIPEGLIY 320
++ GA I+ K SA A +++ + + +L K + Y +G YG+ + +
Sbjct: 208 RTRKGGAEIVGLLKTGSAYYAPAASIAEMVEAILKD-KKRVLPCSAYLEGEYGV-KDVYV 265
Query: 321 SFPVTCEKGEWSIVKGLKVDEFSRAKMDATAEELAE 356
PV K + L++D+ +A D + E + +
Sbjct: 266 GVPVKLGKNGVEKIIELELDDEEKAAFDKSVEAVKK 301
>gnl|CDD|173409 PTZ00117, PTZ00117, malate dehydrogenase; Provisional.
Length = 319
Score = 74.0 bits (182), Expect = 9e-15
Identities = 61/208 (29%), Positives = 98/208 (47%), Gaps = 6/208 (2%)
Query: 107 TDVVEACKDVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEKHAAPNCKVLVVAN 166
T+ E KD ++ V+ G RKE M R+D+++ N I K+ A +++K+ PN V+ V N
Sbjct: 65 TNNYEDIKDSDVVVITAGVQRKEEMTREDLLTINGKIMKSVAESVKKY-CPNAFVICVTN 123
Query: 167 PANTNALILKEFAPSIPAKNITCLT-RLDHNRAMGQISERLKVHVSDVKNVIIWGNHSST 225
P + + +E + IP+ I + LD +R ++E+L V DV V+I G H
Sbjct: 124 PLDCMVKVFQEKS-GIPSNKICGMAGVLDSSRFRCNLAEKLGVSPGDVSAVVI-GGHGDL 181
Query: 226 QYPDVNHATVTTSKGEKPVREAVADDNWLNTEFITTVQQRGAAIIKARKLSSALSAASSA 285
P + TV V++ + +N E I + G I+K K SA A ++A
Sbjct: 182 MVPLPRYCTVNGIPLSDFVKKGAITEKEIN-EIIKKTRNMGGEIVKLLKKGSAFFAPAAA 240
Query: 286 CDHIRDWVLGTPKGTWVSMGVYSDGSYG 313
+ + L K V VY +G Y
Sbjct: 241 IVAMIEAYLKDEKRVLVC-SVYLNGQYN 267
>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 = 72.1 bits (177), Expect = 3e-14
Identities = 64/244 (26%), Positives = 115/244 (47%), Gaps = 38/244 (15%)
Query: 41 RVLVTGATGQIGYALVPMIARGIMLGPDQPVI--LHMLDIEPAAEALNGVKMELIDAAFP 98
+V + GA+G++G A ++A+ + V+ ++++ + E L G+++++ DA
Sbjct: 2 KVSIIGASGRVGSATALLLAK-------EDVVKEINLISRPKSLEKLKGLRLDIYDA--- 51
Query: 99 LLKGVVATTDV---VEACKDV------NIAVMVGGFPRKEGMERKDVMSKNVSIYKAQAS 149
+A + ++ D+ +I ++ G PRKEGM R D+ KN I K A
Sbjct: 52 -----LAAAGIDAEIKISSDLSDVAGSDIVIITAGVPRKEGMSRLDLAKKNAKIVKKYAK 106
Query: 150 ALEKHAAPNCKVLVVANPANT---NALILKEFAPSIPAKNITCLTRLDHNRAMGQISERL 206
+ + AP+ K+LVV NP + AL F + + T LD R I++
Sbjct: 107 QIAEF-APDTKILVVTNPVDVMTYKALKESGFDKN---RVFGLGTHLDSLRFKVAIAKHF 162
Query: 207 KVHVSDVKNVIIWGNHSSTQYPDVNHATVTTSKGEKPVREAVADDNWLNTEFITTVQQRG 266
VH+S+V II G H + P ++ +TS G P++ ++ + + TV+ G
Sbjct: 163 NVHISEVHTRII-GEHGDSMVPLIS----STSIGGIPIKRFPEYKDFDVEKIVETVKNAG 217
Query: 267 AAII 270
II
Sbjct: 218 QNII 221
>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 = 69.9 bits (172), Expect = 2e-13
Identities = 90/334 (26%), Positives = 137/334 (41%), Gaps = 40/334 (11%)
Query: 37 KEPCRVLVTGATGQIGYALVPMI-ARGIMLGPDQPVILHMLDIEPAAEALNGVKMEL-ID 94
K +V V G GQ+G A I A+G+ D+ L ++D+ + L G M+L
Sbjct: 1 KPRNKVTVVGV-GQVGMACAISILAKGLA---DE---LVLVDVVE--DKLKGEAMDLQHG 51
Query: 95 AAFPLLKGVVATTDVVEACKDVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEKH 154
+AF + A D + + ++ G + EG R D++ +NV I+K L K+
Sbjct: 52 SAFLKNPKIEADKDY-SVTANSKVVIVTAGARQNEGESRLDLVQRNVDIFKGIIPKLVKY 110
Query: 155 AAPNCKVLVVANPANTNALILKEFAPSI----PAKNITCLTRLDHNRAMGQISERLKVHV 210
+ PN +LVV+NP + I+ A + + I LD R I+ERL V
Sbjct: 111 S-PNAILLVVSNPVD----IMTYVAWKLSGLPKHRVIGSGCNLDSARFRYLIAERLGVAP 165
Query: 211 SDVKNVIIWGNHSSTQYP---DVNHATVTTSKGEKPVREAVADDNWLNTEFITTVQQRGA 267
S V II G H + P VN A V + + W E V
Sbjct: 166 SSVHGWII-GEHGDSSVPVWSGVNVAGVRLQDLNPDIGTDKDPEKW--KEVHKQVVDSAY 222
Query: 268 AIIKARKLSS---ALSAASSACDHIRDWVLGTPKGTWVSMGVYSDGSYGIPEGLIYSFPV 324
+IK + +S LS A + D +L G S+ G +GI + + S P
Sbjct: 223 EVIKLKGYTSWAIGLSVAD-----LVDAIL-RNTGRVHSVSTLVKGLHGIEDEVFLSLP- 275
Query: 325 TCEKGEWSIVKGLKV--DEFSRAKMDATAEELAE 356
C GE I +K E + K+ +A+ L E
Sbjct: 276 -CILGENGITHVIKQPLTEEEQEKLQKSADTLWE 308
>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 = 69.5 bits (170), Expect = 3e-13
Identities = 63/240 (26%), Positives = 110/240 (45%), Gaps = 10/240 (4%)
Query: 117 NIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEKHAAPNCKVLVVANPANTNALILK 176
+I V+ G PRK GM R+D++S N I + + +H +PN ++VV+NP + +
Sbjct: 71 DIVVITAGLPRKPGMSREDLLSMNAGIVREVTGRIMEH-SPNPIIVVVSNPLDAMTYVAW 129
Query: 177 EFAPSIPAKNITCLTRLDHNRAMGQISERLKVHVSDVKNVIIWGNHSSTQYPDVNHATVT 236
+ + + I LD R I+ L V V DV ++ G H P V ++TV
Sbjct: 130 QKSGFPKERVIGQAGVLDSARFRTFIAMELGVSVQDVTACVL-GGHGDAMVPLVRYSTV- 187
Query: 237 TSKGEKPVREAVADDNWLNTEFITTVQQRGAAIIKARKLSSALSAASSACDHIRDWVLGT 296
PV + ++ + E + ++ G I+ K SA A +++ + + +L
Sbjct: 188 ---AGIPVADLISAERI--AEIVERTRKGGGEIVNLLKQGSAYYAPAASVVEMVEAILKD 242
Query: 297 PKGTWVSMGVYSDGSYGIPEGLIYSFPVTCEKGEWSIVKGLKVDEFSRAKMDATAEELAE 356
K + Y DG YGI +G+ PV K + LK+D+ A ++ +A+ + E
Sbjct: 243 RKRV-LPCAAYLDGQYGI-DGIYVGVPVILGKNGVEHIYELKLDQSELALLNKSAKIVDE 300
>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 = 67.0 bits (164), Expect = 2e-12
Identities = 71/255 (27%), Positives = 105/255 (41%), Gaps = 35/255 (13%)
Query: 41 RVLVTGATGQIGYALVPMIARGIMLGPDQPVI--LHMLDIEPAAEALNGVKMEL--IDAA 96
+V V GA G IG L ++ QP + L + DI AA GV +L I A
Sbjct: 1 KVAVLGAAGGIGQPLSLLLKL-------QPYVSELSLYDIAGAA----GVAADLSHIPTA 49
Query: 97 FPLLKGVVATTDVVEACKDVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEKHAA 156
+KG + A K ++ V+ G PRK GM R D+ + N I K +A+ +
Sbjct: 50 -ASVKGFSGEEGLENALKGADVVVIPAGVPRKPGMTRDDLFNVNAGIVKDLVAAVAES-C 107
Query: 157 PNCKVLVVANPANTN----ALILKEFAPSIPAKNITCLTRLDHNRAMGQISERLKVHVSD 212
P +LV+ NP N+ A +LK+ P + +T LD RA ++E LK
Sbjct: 108 PKAMILVITNPVNSTVPIAAEVLKKKGVYDP-NKLFGVTTLDIVRANTFVAE-LKGKDPM 165
Query: 213 VKNVIIWGNHSSTQYPDVNHATVTTSKGEKPVREAVADDNWLNTEFITTVQQRGAAIIKA 272
NV + G HS + + EA I +Q G ++KA
Sbjct: 166 EVNVPVIGGHSGETIIPLISQCPGKVLFTEDQLEA----------LIHRIQNAGTEVVKA 215
Query: 273 R--KLSSALSAASSA 285
+ S+ LS A +
Sbjct: 216 KAGAGSATLSMAFAG 230
>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 = 61.4 bits (150), Expect = 1e-10
Identities = 57/192 (29%), Positives = 90/192 (46%), Gaps = 25/192 (13%)
Query: 41 RVLVTGATGQIGYALVPMIARGIMLGPDQPVI--LHMLDIEPAAEALNGVKMEL--IDAA 96
+V V GA G IG L +L P++ L + DI GV +L I+
Sbjct: 2 KVAVLGAAGGIGQPLS-------LLLKLNPLVSELALYDIV----NTPGVAADLSHINTP 50
Query: 97 FPLLKGVVATTDVVEACKDVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEKHAA 156
+ G + ++ +A K ++ V+ G PRK GM R D+ + N I + A+A+ K
Sbjct: 51 -AKVTGYLGPEELKKALKGADVVVIPAGVPRKPGMTRDDLFNINAGIVRDLATAVAKA-C 108
Query: 157 PNCKVLVVANPANTN----ALILKEFAPSIPAKNITCLTRLDHNRAMGQISERLKVHVSD 212
P +L+++NP N+ A +LK+ P K + +T LD RA ++E L + +
Sbjct: 109 PKALILIISNPVNSTVPIAAEVLKKAGVYDP-KRLFGVTTLDVVRANTFVAELLGLDPAK 167
Query: 213 VK-NVIIWGNHS 223
V VI G HS
Sbjct: 168 VNVPVI--GGHS 177
>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 = 56.1 bits (136), Expect = 7e-09
Identities = 68/302 (22%), Positives = 113/302 (37%), Gaps = 52/302 (17%)
Query: 75 MLDIEPAAEALNGVKMELIDAAFPLLKGVVATTDVVEACKDVNIAVMVGGFPRKEGMERK 134
++DI + G M+L AA L + CKD ++ V+ G P+K G R
Sbjct: 26 LIDINK--DKAEGEAMDLQHAASFLPTPKKIRSGDYSDCKDADLVVITAGAPQKPGETRL 83
Query: 135 DVMSKNVSIYKAQASALEKHAAPNCKVLVVANPANTNALILKEFAPSIPAKNITCLTRLD 194
+++ +NV I K+ + K + LV NP + IL A L+
Sbjct: 84 ELVGRNVRIMKSIVPEVVKS-GFDGIFLVATNPVD----ILTYVAWK--------LSGFP 130
Query: 195 HNRAMGQ------------ISERLKVHVSDVKNVIIWGNHSSTQYPDVNHATVTTSKGEK 242
NR +G ++E+L V V II G H ++ P + AT+ G
Sbjct: 131 KNRVIGSGTVLDTARLRYLLAEKLGVDPQSVHAYII-GEHGDSEVPVWSSATI----GGV 185
Query: 243 PVREAVADDNWLNTEFITT--------VQQRGAA--IIKARKLSSALSAASSACDHIRDW 292
P+ + +L + T + R AA II RK ++ + +
Sbjct: 186 PLLD------YLKAKGTETDLDLEEIEKEVRDAAYEIIN-RKGATYYGIGMAVARIVEAI 238
Query: 293 VLGTPKGTWVSMGVYSDGSYGIPEGLIYSFPVTCEKGEWSIVKGLKVDEFSRAKMDATAE 352
+ + VS Y DG YGI + + P + + L + + + +AE
Sbjct: 239 LHDENRVLPVS--AYLDGEYGI-KDVYIGVPAVLGRNGVEEIIELPLSDEEKEAFQKSAE 295
Query: 353 EL 354
L
Sbjct: 296 TL 297
>gnl|CDD|178836 PRK00066, ldh, L-lactate dehydrogenase; Reviewed.
Length = 315
Score = 53.7 bits (130), Expect = 5e-08
Identities = 70/266 (26%), Positives = 113/266 (42%), Gaps = 46/266 (17%)
Query: 111 EACKDVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEKHAAPNCKVLVVANPANT 170
CKD ++ V+ G P+K G R D++ KN+ I+K+ + + LV +NP +
Sbjct: 69 SDCKDADLVVITAGAPQKPGETRLDLVEKNLKIFKSIVGEVMAS-GFDGIFLVASNPVD- 126
Query: 171 NALIL-----------KEFAPSIPAKNITCLTRLDHNRAMGQISERLKVHVSDVKNVIIW 219
IL KE + I T LD R +SE+L V V II
Sbjct: 127 ---ILTYATWKLSGFPKE-------RVIGSGTSLDSARFRYMLSEKLDVDPRSVHAYII- 175
Query: 220 GNHSSTQYPDVNHATVTTSKGEKPVREAVADDNWLNTEFITTVQQ--RGAA--IIKARKL 275
G H T++P +HA V P+ E + ++ + E + + + R AA II+ +
Sbjct: 176 GEHGDTEFPVWSHANV----AGVPLEEYLEENEQYDEEDLDEIFENVRDAAYEIIEKKGA 231
Query: 276 SS-----ALSAASSACDHIRDWVLGTPKGTWVSMGVYSDGSYGIPEGLIYSFPVTCEKGE 330
+ AL+ + A + + VL VS Y +G YG + I V G
Sbjct: 232 TYYGIAMALARITKAILNNENAVLP------VS--AYLEGQYGEEDVYIGVPAVVNRNGI 283
Query: 331 WSIVKGLKVDEFSRAKMDATAEELAE 356
IV+ L +++ + K +A+ L E
Sbjct: 284 REIVE-LPLNDDEKQKFAHSADVLKE 308
>gnl|CDD|215058 PLN00106, PLN00106, malate dehydrogenase.
Length = 323
Score = 53.0 bits (128), Expect = 7e-08
Identities = 56/190 (29%), Positives = 91/190 (47%), Gaps = 23/190 (12%)
Query: 41 RVLVTGATGQIGYALVPMIARGIMLGPDQPVI--LHMLDIEPAAEALNGVKMEL--IDAA 96
+V V GA G IG L +L P++ LH+ DI GV ++ I+
Sbjct: 20 KVAVLGAAGGIGQPLS-------LLMKMNPLVSELHLYDIANTP----GVAADVSHINTP 68
Query: 97 FPLLKGVVATTDVVEACKDVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEKHAA 156
++G + + +A K ++ ++ G PRK GM R D+ + N I K A+ KH
Sbjct: 69 -AQVRGFLGDDQLGDALKGADLVIIPAGVPRKPGMTRDDLFNINAGIVKTLCEAVAKH-C 126
Query: 157 PNCKVLVVANPANTN----ALILKEFAPSIPAKNITCLTRLDHNRAMGQISERLKVHVSD 212
PN V +++NP N+ A +LK+ A K + +T LD RA ++E+ + +D
Sbjct: 127 PNALVNIISNPVNSTVPIAAEVLKK-AGVYDPKKLFGVTTLDVVRANTFVAEKKGLDPAD 185
Query: 213 VKNVIIWGNH 222
V +V + G H
Sbjct: 186 V-DVPVVGGH 194
>gnl|CDD|173376 PTZ00082, PTZ00082, L-lactate dehydrogenase; Provisional.
Length = 321
Score = 51.6 bits (124), Expect = 2e-07
Identities = 35/129 (27%), Positives = 58/129 (44%), Gaps = 11/129 (8%)
Query: 114 KDVNIAVMVGGFPRKEGME-----RKDVMSKNVSIYKAQASALEKHAAPNCKVLVVANPA 168
++ ++ G ++ G R D++ N I A ++K+ PN V+V+ NP
Sbjct: 73 AGSDVVIVTAGLTKRPGKSDKEWNRDDLLPLNAKIMDEVAEGIKKYC-PNAFVIVITNPL 131
Query: 169 NTNALILKEFAPSIPAKNITC--LTRLDHNRAMGQISERLKVHVSDVKNVIIWGNHSSTQ 226
+ +L+E +P KN C LD +R I+E+L V+ DV +I G H
Sbjct: 132 DVMVKLLQE-HSGLP-KNKVCGMAGVLDSSRLRTYIAEKLGVNPRDVHASVI-GAHGDKM 188
Query: 227 YPDVNHATV 235
P + TV
Sbjct: 189 VPLPRYVTV 197
>gnl|CDD|240360 PTZ00325, PTZ00325, malate dehydrogenase; Provisional.
Length = 321
Score = 51.2 bits (123), Expect = 3e-07
Identities = 55/189 (29%), Positives = 84/189 (44%), Gaps = 19/189 (10%)
Query: 41 RVLVTGATGQIGYALVPMIARGIMLGPDQPVILHMLDIEPAAEALNGVKMEL--IDAAFP 98
+V V GA G IG L ++ + + L + DI A GV +L ID
Sbjct: 10 KVAVLGAAGGIGQPL-SLLLKQNPHVSE----LSLYDIVGAP----GVAADLSHIDTP-A 59
Query: 99 LLKGVVATTDVVEACKDVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEKHAAPN 158
+ G +A + ++ ++ G PRK GM R D+ + N I + +A+ AP
Sbjct: 60 KVTGYADGELWEKALRGADLVLICAGVPRKPGMTRDDLFNTNAPIVRDLVAAVASS-APK 118
Query: 159 CKVLVVANPANTNALILKEFAPSI----PAKNITCLTRLDHNRAMGQISERLKVHVSDVK 214
V +V+NP N+ I E P K + +T LD RA ++E L ++ DV
Sbjct: 119 AIVGIVSNPVNSTVPIAAETLKKAGVYDPRK-LFGVTTLDVVRARKFVAEALGMNPYDV- 176
Query: 215 NVIIWGNHS 223
NV + G HS
Sbjct: 177 NVPVVGGHS 185
>gnl|CDD|235340 PRK05086, PRK05086, malate dehydrogenase; Provisional.
Length = 312
Score = 50.4 bits (121), Expect = 6e-07
Identities = 55/193 (28%), Positives = 85/193 (44%), Gaps = 22/193 (11%)
Query: 41 RVLVTGATGQIGYALVPMIARGIMLGPDQPVILHMLDIEPAAEALNGVKMEL--IDAAFP 98
+V V GA G IG AL ++ + G + L + DI P GV ++L I A
Sbjct: 2 KVAVLGAAGGIGQALALLLKTQLPAGSE----LSLYDIAPVTP---GVAVDLSHIPTAVK 54
Query: 99 LLKGVVATTDVVEACKDVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEKHAA-- 156
+ KG + D A + ++ ++ G RK GM+R D+ + N I K + +EK A
Sbjct: 55 I-KGF-SGEDPTPALEGADVVLISAGVARKPGMDRSDLFNVNAGIVK---NLVEKVAKTC 109
Query: 157 PNCKVLVVANPANTNALILKEF---APSIPAKNITCLTRLDHNRAMGQISERLKVHVSDV 213
P + ++ NP NT I E A + +T LD R+ ++E +V
Sbjct: 110 PKACIGIITNPVNTTVAIAAEVLKKAGVYDKNKLFGVTTLDVIRSETFVAELKGKQPGEV 169
Query: 214 K-NVIIWGNHSST 225
+ VI G HS
Sbjct: 170 EVPVI--GGHSGV 180
>gnl|CDD|178212 PLN02602, PLN02602, lactate dehydrogenase.
Length = 350
Score = 49.4 bits (118), Expect = 1e-06
Identities = 49/195 (25%), Positives = 93/195 (47%), Gaps = 14/195 (7%)
Query: 36 PKEPCRVLVTGATGQIGYALVPMIARGIMLGPDQPVILHMLDIEPAAEALNGVKMELIDA 95
+ +V V G G +G A IA+ I L D L ++D+ P + L G ++L A
Sbjct: 34 TRRHTKVSVVGV-GNVGMA----IAQTI-LTQDLADELALVDVNP--DKLRGEMLDLQHA 85
Query: 96 A--FPLLKGVVATTDVVEACKDVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEK 153
A P K ++A+TD ++ ++ G + G R +++ +NV++++ L K
Sbjct: 86 AAFLPRTK-ILASTDY-AVTAGSDLCIVTAGARQIPGESRLNLLQRNVALFRKIIPELAK 143
Query: 154 HAAPNCKVLVVANPANTNALILKEFAPSIPAKNITCLTRLDHNRAMGQISERLKVHVSDV 213
+ +P+ +L+V+NP + + + + + I T LD +R I++ L V+ DV
Sbjct: 144 Y-SPDTILLIVSNPVDVLTYVAWKLSGFPANRVIGSGTNLDSSRFRFLIADHLDVNAQDV 202
Query: 214 KNVIIWGNHSSTQYP 228
+ I+ G H +
Sbjct: 203 QAYIV-GEHGDSSVA 216
>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 = 45.6 bits (109), Expect = 2e-05
Identities = 47/168 (27%), Positives = 73/168 (43%), Gaps = 19/168 (11%)
Query: 75 MLDIEPA---AEALNGVKMELIDAAFPLLKGVVATTDVVEACKDVNIAVMVGGFPRKEGM 131
++DI A EA M+L P +K V CK ++ V+ G +K G
Sbjct: 30 LVDINKAKAEGEA-----MDLAHGT-PFVKPVRIYAGDYADCKGADVVVITAGANQKPGE 83
Query: 132 ERKDVMSKNVSIYKAQASALEKHAAPNCKVLVVANPANTNALILKEFAPSI----PAKNI 187
R D++ +NV+I+K + K+ AP+ +LVV NP + +L A + P + I
Sbjct: 84 TRLDLLKRNVAIFKEIIPQILKY-APDAILLVVTNPVD----VLTYVAYKLSGLPPNRVI 138
Query: 188 TCLTRLDHNRAMGQISERLKVHVSDVKNVIIWGNHSSTQYPDVNHATV 235
T LD R + E L V V II G H ++ + A +
Sbjct: 139 GSGTVLDTARFRYLLGEHLGVDPRSVHAYII-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 = 41.3 bits (98), Expect = 4e-04
Identities = 37/153 (24%), Positives = 66/153 (43%), Gaps = 30/153 (19%)
Query: 111 EACKDVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEKHAAPNCKVLVVANPANT 170
CKD +I V+ G P+K G R D++ KN I K+ + K + + LV +NP +
Sbjct: 64 SDCKDADIVVITAGAPQKPGETRLDLLEKNAKIMKSIVPKI-KASGFDGIFLVASNPVDV 122
Query: 171 NALILKEFAPSIPAKNITCLTRLDHNRAMGQ------------ISERLKVHVSDVKNVII 218
++++ L+ L NR +G ++E+L V V ++
Sbjct: 123 ITYVVQK------------LSGLPKNRVIGTGTSLDTARLRRALAEKLNVDPRSVHAYVL 170
Query: 219 WGNHSSTQYPDVNHATVTTSKGEKPVREAVADD 251
G H +Q+ + TV G KP+ + + +
Sbjct: 171 -GEHGDSQFVAWSTVTV----GGKPLLDLLKEG 198
>gnl|CDD|222146 pfam13460, NAD_binding_10, NADH(P)-binding.
Length = 182
Score = 37.3 bits (87), Expect = 0.005
Identities = 25/98 (25%), Positives = 37/98 (37%), Gaps = 16/98 (16%)
Query: 42 VLVTGATGQIGYALVPM-IARG------------IMLGPDQPVILHMLDIEPAAEALNGV 88
+ V GATG+ G LV +ARG PV + D+ AEAL GV
Sbjct: 1 IAVIGATGKTGRRLVKELLARGHQVTALSRNPSKAPAPGVTPVQKDLFDLADLAEALAGV 60
Query: 89 KMELIDAAFPLLKGVVATTDVVEACKDVNIA--VMVGG 124
++DA +++A + V+V
Sbjct: 61 DA-VVDAFGARPDDSDGVKHLLDAAARAGVRRIVVVSA 97
>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 = 34.6 bits (80), Expect = 0.039
Identities = 21/87 (24%), Positives = 34/87 (39%), Gaps = 22/87 (25%)
Query: 42 VLVTGATGQIGYALVPM-IARGIMLGPDQPVILHMLDI--------EPAAEALNGVKMEL 92
+LVTG G IG LV + RG + V++ LD+ A N +
Sbjct: 1 ILVTGGAGFIGSHLVRRLLERG-----HEVVVIDRLDVVVHLAALVGVPASWDNPDEDFE 55
Query: 93 IDAAFPLLKGVVATTDVVEACKDVNIA 119
+ VV T +++EA + +
Sbjct: 56 TN--------VVGTLNLLEAARKAGVK 74
>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 = 34.1 bits (79), Expect = 0.091
Identities = 10/18 (55%), Positives = 15/18 (83%)
Query: 41 RVLVTGATGQIGYALVPM 58
++L+TGATG +G ALV +
Sbjct: 1 KILITGATGMLGRALVRL 18
>gnl|CDD|187548 cd05237, UDP_invert_4-6DH_SDR_e, UDP-Glcnac (UDP-linked
N-acetylglucosamine) inverting 4,6-dehydratase,
extended (e) SDRs. UDP-Glcnac inverting
4,6-dehydratase was identified in Helicobacter pylori
as the hexameric flaA1 gene product (FlaA1). FlaA1 is
hexameric, possesses UDP-GlcNAc-inverting
4,6-dehydratase activity, and catalyzes the first step
in the creation of a pseudaminic acid derivative in
protein glycosylation. Although this subgroup has the
NADP-binding motif characteristic of extended SDRs, its
members tend to have a Met substituted for the active
site Tyr found in most SDR families. Extended SDRs are
distinct from classical SDRs. In addition to the
Rossmann fold (alpha/beta folding pattern with a
central beta-sheet) core region typical of all SDRs,
extended SDRs have a less conserved C-terminal
extension of approximately 100 amino acids. Extended
SDRs are a diverse collection of proteins, and include
isomerases, epimerases, oxidoreductases, and lyases;
they typically have a TGXXGXXG cofactor binding motif.
SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving
as a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton
relay involving the conserved Tyr and Lys, a water
molecule stabilized by Asn, and nicotinamide. Atypical
SDRs generally lack the catalytic residues
characteristic of the SDRs, and their glycine-rich
NAD(P)-binding motif is often different from the forms
normally seen in classical or extended SDRs. Complex
(multidomain) SDRs such as ketoreductase domains of
fatty acid synthase have a GGXGXXG NAD(P)-binding motif
and an altered active site motif (YXXXN). Fungal type
ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding
motif.
Length = 287
Score = 33.4 bits (77), Expect = 0.14
Identities = 13/38 (34%), Positives = 16/38 (42%), Gaps = 6/38 (15%)
Query: 41 RVLVTGATGQIGYALVPMIARGIMLGPDQPVILHMLDI 78
+LVTG G IG LV I + P L + D
Sbjct: 4 TILVTGGAGSIGSELVRQILKF------GPKKLIVFDR 35
>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 = 0.30
Identities = 10/21 (47%), Positives = 12/21 (57%)
Query: 41 RVLVTGATGQIGYALVPMIAR 61
R+LVTG G IG LV +
Sbjct: 2 RILVTGGAGFIGSHLVERLLA 22
>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 = 31.9 bits (73), Expect = 0.45
Identities = 17/63 (26%), Positives = 25/63 (39%), Gaps = 13/63 (20%)
Query: 41 RVLVTGATGQIGYALVP----------MIARGIMLGPDQPVILHMLDIEPAAEALNGVKM 90
R+L+TG GQIG L +IA I P V+ + + L+ +
Sbjct: 1 RILITGGLGQIGSELAKLLRKRYGKDNVIASDIRKPPAHVVLSGPFEY---LDVLDFKSL 57
Query: 91 ELI 93
E I
Sbjct: 58 EEI 60
>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 = 31.5 bits (72), Expect = 0.47
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 42 VLVTGATGQIGYALVPMIAR 61
+LVTG TG IG LV + +
Sbjct: 1 ILVTGGTGFIGSHLVRRLLQ 20
>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 = 31.9 bits (73), Expect = 0.47
Identities = 28/107 (26%), Positives = 43/107 (40%), Gaps = 26/107 (24%)
Query: 42 VLVTGATGQIGYALVP-MIARGI------------MLGPDQPVILH---MLDIEPAAEAL 85
+LVTGATG +G LV ++A+G +L PV + + D A A+
Sbjct: 1 ILVTGATGFLGSNLVRALLAQGYRVRALVRSGSDAVLLDGLPVEVVEGDLTDAASLAAAM 60
Query: 86 NGVKMELIDAAFPLLKG----------VVATTDVVEACKDVNIAVMV 122
G AAF L V T +V++A + + +V
Sbjct: 61 KGCDRVFHLAAFTSLWAKDRKELYRTNVEGTRNVLDAALEAGVRRVV 107
>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 = 31.6 bits (72), Expect = 0.52
Identities = 25/94 (26%), Positives = 37/94 (39%), Gaps = 15/94 (15%)
Query: 41 RVLVTGATGQIGYALVPMIARGIMLGPDQPVILHMLDIEPAAEALNGVKMELIDAAFPLL 100
VLVTG +G G LV + G + DI P EAL+ + I+ L
Sbjct: 1 SVLVTGGSGFFGERLVKQLLE--RGGTY----VRSFDIAPPGEALSAWQHPNIE----FL 50
Query: 101 KGVVATTDVVE-ACKDVN----IAVMVGGFPRKE 129
KG + + VE A + A +V ++
Sbjct: 51 KGDITDRNDVEQALSGADCVFHTAAIVPLAGPRD 84
>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 = 31.6 bits (72), Expect = 0.56
Identities = 24/84 (28%), Positives = 33/84 (39%), Gaps = 10/84 (11%)
Query: 41 RVLVTGATGQIGYALVPMIARGIMLGPDQPVILHM-LDIEPAAEALNGVKMELIDAAFP- 98
R+L+TGA GQ+G LV ++ G + LD+ L+ A P
Sbjct: 1 RILITGANGQLGRELVQQLSPE---GRVVVALTRSQLDLTDPEAL-----ERLLRAIRPD 52
Query: 99 LLKGVVATTDVVEACKDVNIAVMV 122
+ A TDV A D A V
Sbjct: 53 AVVNTAAYTDVDGAESDPEKAFAV 76
>gnl|CDD|236399 PRK09186, PRK09186, flagellin modification protein A; Provisional.
Length = 256
Score = 31.1 bits (71), Expect = 0.73
Identities = 23/77 (29%), Positives = 32/77 (41%), Gaps = 9/77 (11%)
Query: 41 RVLVTGATGQIGYALVPMI--ARGIMLGPDQPVILHMLDIEPAAEALNGVKMELIDAAFP 98
+L+TGA G IG ALV I A GI VI +D E E L + E
Sbjct: 6 TILITGAGGLIGSALVKAILEAGGI-------VIAADIDKEALNELLESLGKEFKSKKLS 58
Query: 99 LLKGVVATTDVVEACKD 115
L++ + + +E
Sbjct: 59 LVELDITDQESLEEFLS 75
>gnl|CDD|223774 COG0702, COG0702, Predicted nucleoside-diphosphate-sugar
epimerases [Cell envelope biogenesis, outer membrane /
Carbohydrate transport and metabolism].
Length = 275
Score = 31.0 bits (70), Expect = 0.77
Identities = 13/23 (56%), Positives = 18/23 (78%), Gaps = 1/23 (4%)
Query: 41 RVLVTGATGQIGYALVPM-IARG 62
++LVTGATG +G A+V +ARG
Sbjct: 2 KILVTGATGFVGGAVVRELLARG 24
>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 = 30.9 bits (71), Expect = 0.87
Identities = 10/20 (50%), Positives = 11/20 (55%)
Query: 42 VLVTGATGQIGYALVPMIAR 61
VLVTG G IG L I +
Sbjct: 1 VLVTGGGGSIGSELCRQILK 20
>gnl|CDD|236372 PRK09072, PRK09072, short chain dehydrogenase; Provisional.
Length = 263
Score = 30.7 bits (70), Expect = 0.90
Identities = 13/24 (54%), Positives = 16/24 (66%), Gaps = 1/24 (4%)
Query: 40 CRVLVTGATGQIGYALV-PMIARG 62
RVL+TGA+G IG AL + A G
Sbjct: 6 KRVLLTGASGGIGQALAEALAAAG 29
>gnl|CDD|225990 COG3459, COG3459, Cellobiose phosphorylase [Carbohydrate transport
and metabolism].
Length = 1056
Score = 31.2 bits (71), Expect = 0.93
Identities = 25/108 (23%), Positives = 39/108 (36%), Gaps = 16/108 (14%)
Query: 257 EFITTVQQRGAAIIKARKLSSALSAASSACDHIRDWVLGTPKGTWVSMGVYSDGSY-GIP 315
F + RG +A + + A A + W G W G DG+ G P
Sbjct: 769 TFKELAKARGD-EARADTWAKHVEALREALE-TNGWD-----GEWYRRGYGDDGTPLGSP 821
Query: 316 ---EGLIYSFPVTCEKGEWSIVKGLKVDEFSRAKMDATAEELAEEKTL 360
E I S P + WS++ G E + MD+ + L + +
Sbjct: 822 EDEECQIDSIPQS-----WSVLSGEGDKERAEKAMDSVMKYLVDPDGV 864
>gnl|CDD|216827 pfam01983, CofC, Guanylyl transferase CofC like. Coenzyme F420 is
a hydride carrier cofactor that functions during
methanogenesis. This family of proteins represents CofC,
a nucleotidyl transferase that is involved in coenzyme
F420 biosynthesis. CofC has been shown to catalyze the
formation of lactyl-2-diphospho-5'-guanosine from
2-phospho-L-lactate and GTP.
Length = 217
Score = 30.6 bits (69), Expect = 0.97
Identities = 26/144 (18%), Positives = 47/144 (32%), Gaps = 18/144 (12%)
Query: 75 MLDIEPAAEALNGVKMELIDAAFPLLKGVVATTDVVEACKDVNIAVMVGGFPRKEGMERK 134
+LD+ A + ++ + + P V+ VVE D+N AV +
Sbjct: 34 LLDVIDALKPVDVLVFSEDEVVLPSALDVLGVEVVVETESDLNTAV-------NQAFMAP 86
Query: 135 D------VMSKNVSIYKAQASALEKHAAPNCKVLVVANPANTNALILKEFAPSIPAKNIT 188
+ + S I K + V+ TN L+L++ + +
Sbjct: 87 EEAPVIIIPSDIPLISKEVLKRFLETEGRADVVIAPGRGGGTNMLLLRKRGFRVSYHFGS 146
Query: 189 CLTRLDHNRAMGQISERLKVHVSD 212
L+ R G LK + D
Sbjct: 147 FFKHLEEARKRG-----LKAKIYD 165
>gnl|CDD|224011 COG1086, COG1086, Predicted nucleoside-diphosphate sugar epimerases
[Cell envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 588
Score = 31.1 bits (71), Expect = 1.1
Identities = 10/21 (47%), Positives = 11/21 (52%)
Query: 41 RVLVTGATGQIGYALVPMIAR 61
VLVTG G IG L I +
Sbjct: 252 TVLVTGGGGSIGSELCRQILK 272
>gnl|CDD|218026 pfam04321, RmlD_sub_bind, RmlD substrate binding domain.
L-rhamnose is a saccharide required for the virulence
of some bacteria. Its precursor, dTDP-L-rhamnose, is
synthesised by four different enzymes the final one of
which is RmlD. The RmlD substrate binding domain is
responsible for binding a sugar nucleotide.
Length = 284
Score = 30.7 bits (70), Expect = 1.2
Identities = 9/15 (60%), Positives = 11/15 (73%)
Query: 42 VLVTGATGQIGYALV 56
+LVTGA GQ+G L
Sbjct: 1 ILVTGANGQLGRELT 15
>gnl|CDD|178263 PLN02657, PLN02657, 3,8-divinyl protochlorophyllide a 8-vinyl
reductase.
Length = 390
Score = 30.1 bits (68), Expect = 1.9
Identities = 14/33 (42%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 31 SFLDIPKEPCRVLVTGATGQIGYALV-PMIARG 62
SF + VLV GATG IG +V ++ RG
Sbjct: 52 SFRSKEPKDVTVLVVGATGYIGKFVVRELVRRG 84
>gnl|CDD|187572 cd05262, SDR_a7, atypical (a) SDRs, subgroup 7. This subgroup
contains atypical SDRs of unknown function. Members of
this subgroup have a glycine-rich NAD(P)-binding motif
consensus that matches the extended SDRs, TGXXGXXG, but
lacks the characteristic active site residues of the
SDRs. This subgroup has basic residues (HXXXR) in place
of the active site motif YXXXK, these may have a
catalytic role. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Atypical SDRs include biliverdin IX beta
reductase (BVR-B,aka flavin reductase), NMRa (a
negative transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane
reductase, isoflavone reductases, and others. SDRs are
a functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. In addition to the Rossmann fold
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids, and typically have a TGXXGXXG cofactor
binding motif. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 291
Score = 30.0 bits (68), Expect = 2.1
Identities = 13/23 (56%), Positives = 17/23 (73%), Gaps = 1/23 (4%)
Query: 41 RVLVTGATGQIGYALVP-MIARG 62
+V VTGATG IG A+V ++A G
Sbjct: 2 KVFVTGATGFIGSAVVRELVAAG 24
>gnl|CDD|187554 cd05243, SDR_a5, atypical (a) SDRs, subgroup 5. This subgroup
contains atypical SDRs, some of which are identified as
putative NAD(P)-dependent epimerases, one as a putative
NAD-dependent epimerase/dehydratase. Atypical SDRs are
distinct from classical SDRs. Members of this subgroup
have a glycine-rich NAD(P)-binding motif that is very
similar to the extended SDRs, GXXGXXG, and binds NADP.
Generally, this subgroup has poor conservation of the
active site tetrad; however, individual sequences do
contain matches to the YXXXK active site motif, the
upstream Ser, and there is a highly conserved Asp in
place of the usual active site Asn throughout the
subgroup. Atypical SDRs generally lack the catalytic
residues characteristic of the SDRs, and their
glycine-rich NAD(P)-binding motif is often different
from the forms normally seen in classical or extended
SDRs. Atypical SDRs include biliverdin IX beta
reductase (BVR-B,aka flavin reductase), NMRa (a
negative transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane
reductase, isoflavone reductases, and others. SDRs are
a functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. In addition to the Rossmann fold
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids, and typically have a TGXXGXXG cofactor
binding motif. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 203
Score = 29.5 bits (67), Expect = 2.1
Identities = 11/23 (47%), Positives = 17/23 (73%), Gaps = 1/23 (4%)
Query: 41 RVLVTGATGQIGYALVP-MIARG 62
+VLV GATG++G +V ++ RG
Sbjct: 1 KVLVVGATGKVGRHVVRELLDRG 23
>gnl|CDD|180823 PRK07074, PRK07074, short chain dehydrogenase; Provisional.
Length = 257
Score = 29.7 bits (67), Expect = 2.1
Identities = 22/56 (39%), Positives = 25/56 (44%), Gaps = 9/56 (16%)
Query: 42 VLVTGATGQIGYALVPMIARGIMLGPDQPVILHMLDIEPAAEALNGVKMELIDAAF 97
LVTGA G IG A +AR +L LDI+ A AL L DA F
Sbjct: 5 ALVTGAAGGIGQA----LARR--FLAAGDRVL-ALDID--AAALAAFADALGDARF 51
>gnl|CDD|223513 COG0436, COG0436, Aspartate/tyrosine/aromatic aminotransferase
[Amino acid transport and metabolism].
Length = 393
Score = 29.9 bits (68), Expect = 2.2
Identities = 11/36 (30%), Positives = 17/36 (47%), Gaps = 1/36 (2%)
Query: 144 YKAQASALEKHAAPNCKVLVVANPAN-TNALILKEF 178
+K LE P K +++ +P N T A+ KE
Sbjct: 149 FKPDLEDLEAAITPKTKAIILNSPNNPTGAVYSKEE 184
>gnl|CDD|214793 smart00730, PSN, Presenilin, signal peptide peptidase, family.
Presenilin 1 and presenilin 2 are polytopic membrane
proteins, whose genes are mutated in some individuals
with Alzheimer's disease. Distant homologues, present in
eukaryotes and archaea, also contain conserved aspartic
acid residues which are predicted to contribute to
catalysis. At least one member of this family has been
shown to possess signal peptide peptidase activity.
Length = 249
Score = 29.5 bits (67), Expect = 2.5
Identities = 21/98 (21%), Positives = 31/98 (31%), Gaps = 17/98 (17%)
Query: 14 VVLFCVALFWKIIRHMWSFLDIPKEPCRVLVTGATGQIGYALV-PMIARGIMLGPDQPVI 72
+L + I F P RV+V ATG+ V P + +
Sbjct: 112 WILLGALFIYDIF---AVF--GTPGPLRVMVEVATGRDEPIKVFPALLY----------V 156
Query: 73 LHMLDIEPAAEALNGVKMELIDAAFP-LLKGVVATTDV 109
++ E + L D FP +L A DV
Sbjct: 157 PRLVVSFEDDEEERFSMLGLGDIVFPGILVASAARFDV 194
>gnl|CDD|224207 COG1288, COG1288, Predicted membrane protein [Function unknown].
Length = 481
Score = 30.0 bits (68), Expect = 2.5
Identities = 25/99 (25%), Positives = 42/99 (42%), Gaps = 22/99 (22%)
Query: 10 QKILVVLFC---VALFWKIIRHMWSFLDIP------------------KEPCRVLVTGAT 48
K++++LF V + W +I W F +I + + GA+
Sbjct: 275 DKLVLLLFTLTFVIMIWGVIVLGWWFPEIAAQFLAMGIIIGLIGGLSENDIASSFIEGAS 334
Query: 49 GQIGYALVPMIARGIMLGPDQPVILHMLDIEPAAEALNG 87
+G AL+ +ARGI L D +IL + + A L+G
Sbjct: 335 DLLGVALIIGLARGINLIMDDGMILDTI-LNYLASLLSG 372
>gnl|CDD|224016 COG1091, RfbD, dTDP-4-dehydrorhamnose reductase [Cell envelope
biogenesis, outer membrane].
Length = 281
Score = 29.6 bits (67), Expect = 2.5
Identities = 8/16 (50%), Positives = 12/16 (75%)
Query: 41 RVLVTGATGQIGYALV 56
++L+TGA GQ+G L
Sbjct: 2 KILITGANGQLGTELR 17
>gnl|CDD|187543 cd05232, UDP_G4E_4_SDR_e, UDP-glucose 4 epimerase, subgroup 4,
extended (e) SDRs. UDP-glucose 4 epimerase (aka
UDP-galactose-4-epimerase), is a homodimeric extended
SDR. It catalyzes the NAD-dependent conversion of
UDP-galactose to UDP-glucose, the final step in Leloir
galactose synthesis. This subgroup is comprised of
bacterial proteins, and includes the Staphylococcus
aureus capsular polysaccharide Cap5N, which may have a
role in the synthesis of UDP-N-acetyl-d-fucosamine.
This subgroup has the characteristic active site tetrad
and NAD-binding motif of the extended SDRs. Extended
SDRs are distinct from classical SDRs. In addition to
the Rossmann fold (alpha/beta folding pattern with a
central beta-sheet) core region typical of all SDRs,
extended SDRs have a less conserved C-terminal
extension of approximately 100 amino acids. Extended
SDRs are a diverse collection of proteins, and include
isomerases, epimerases, oxidoreductases, and lyases;
they typically have a TGXXGXXG cofactor binding motif.
SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving
as a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton
relay involving the conserved Tyr and Lys, a water
molecule stabilized by Asn, and nicotinamide. Atypical
SDRs generally lack the catalytic residues
characteristic of the SDRs, and their glycine-rich
NAD(P)-binding motif is often different from the forms
normally seen in classical or extended SDRs. Complex
(multidomain) SDRs such as ketoreductase domains of
fatty acid synthase have a GGXGXXG NAD(P)-binding motif
and an altered active site motif (YXXXN). Fungal type
ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding
motif.
Length = 303
Score = 29.6 bits (67), Expect = 2.6
Identities = 19/58 (32%), Positives = 28/58 (48%), Gaps = 10/58 (17%)
Query: 41 RVLVTGATGQIGYALVP-MIARGIML---------GPDQPVILHMLDIEPAAEALNGV 88
+VLVTGA G IG ALV +++RG + V+ + DI+ + GV
Sbjct: 1 KVLVTGANGFIGRALVDKLLSRGEEVRIAVRNAENAEPSVVLAELPDIDSFTDLFLGV 58
>gnl|CDD|224403 COG1486, CelF, Alpha-galactosidases/6-phospho-beta-glucosidases,
family 4 of glycosyl hydrolases [Carbohydrate transport
and metabolism].
Length = 442
Score = 29.5 bits (67), Expect = 2.7
Identities = 31/134 (23%), Positives = 50/134 (37%), Gaps = 29/134 (21%)
Query: 73 LHMLDIEPAAEALNGVKME-LIDAAFPLLKGVVATTDVVEACKDVNI---AVMVGGFPRK 128
L + DI+ + + + L++ A +K V ATTD EA + + + VGG +
Sbjct: 35 LALYDIDEERLKIIAILAKKLVEEAGAPVK-VEATTDRREALEGADFVITQIRVGGLEAR 93
Query: 129 EGMERKDVMSKNVSIYKAQ--------------------ASALEKHAAPNCKVLVVANPA 168
E ER + +Y + A +EK PN +L NPA
Sbjct: 94 EKDER---IPLKHGLYGQETNGPGGIFYGLRTIPVILDIAKDMEKVC-PNAWMLNYTNPA 149
Query: 169 NTNALILKEFAPSI 182
++ P I
Sbjct: 150 AIVTEAVRRLYPKI 163
>gnl|CDD|187551 cd05240, UDP_G4E_3_SDR_e, UDP-glucose 4 epimerase (G4E), subgroup
3, extended (e) SDRs. Members of this bacterial
subgroup are identified as possible sugar epimerases,
such as UDP-glucose 4 epimerase. However, while the
NAD(P)-binding motif is fairly well conserved, not all
members retain the canonical active site tetrad of the
extended SDRs. UDP-glucose 4 epimerase (aka
UDP-galactose-4-epimerase), is a homodimeric extended
SDR. It catalyzes the NAD-dependent conversion of
UDP-galactose to UDP-glucose, the final step in Leloir
galactose synthesis. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 306
Score = 29.3 bits (66), Expect = 3.0
Identities = 24/100 (24%), Positives = 36/100 (36%), Gaps = 27/100 (27%)
Query: 42 VLVTGATGQIGYALVP-------------MIARGIMLGPDQPVILHMLDIEPAAEALNGV 88
+LVTGA G +G L + R P + + + DI A A
Sbjct: 1 ILVTGAAGGLGRLLARRLAASPRVIGVDGLDRRRPPGSPPKVEYVRL-DIRDPAAADVFR 59
Query: 89 KME---LIDAAF---PLLKG-------VVATTDVVEACKD 115
+ E ++ AF P G V T +V++AC
Sbjct: 60 EREADAVVHLAFILDPPRDGAERHRINVDGTQNVLDACAA 99
>gnl|CDD|223377 COG0300, DltE, Short-chain dehydrogenases of various substrate
specificities [General function prediction only].
Length = 265
Score = 29.1 bits (66), Expect = 3.1
Identities = 9/21 (42%), Positives = 12/21 (57%)
Query: 41 RVLVTGATGQIGYALVPMIAR 61
L+TGA+ IG L +AR
Sbjct: 8 TALITGASSGIGAELAKQLAR 28
>gnl|CDD|217628 pfam03587, EMG1, EMG1/NEP1 methyltransferase. Members of this
family are essential for 40S ribosomal biogenesis. The
structure of EMG1 has revealed that it is a novel member
of the superfamily of alpha/beta knot fold
methyltransferases.
Length = 200
Score = 29.1 bits (66), Expect = 3.2
Identities = 11/51 (21%), Positives = 23/51 (45%), Gaps = 4/51 (7%)
Query: 103 VVATTDVVEACKDVNIAVMVGGFPR---KEGMERKDVMSKNVSIYKAQASA 150
V+ ++V + +A ++G FP + ++ K ++ SI SA
Sbjct: 139 KVSPKELVSELLNKPVAFVIGAFPHGDFSDEVDYKKA-DESYSISNYPLSA 188
>gnl|CDD|181335 PRK08264, PRK08264, short chain dehydrogenase; Validated.
Length = 238
Score = 28.7 bits (65), Expect = 3.7
Identities = 25/84 (29%), Positives = 33/84 (39%), Gaps = 17/84 (20%)
Query: 41 RVLVTGATGQIGYALV-PMIARGIMLGPDQPVILHMLDIEPAAEALNGV---KMELIDAA 96
VLVTGA IG A V ++ARG V D E + V ++++ D A
Sbjct: 8 VVLVTGANRGIGRAFVEQLLARGAA-----KVYAAARDPESVTDLGPRVVPLQLDVTDPA 62
Query: 97 FPLLKGVVATTDVVEACKDVNIAV 120
+ EA DV I V
Sbjct: 63 --------SVAAAAEAASDVTILV 78
>gnl|CDD|187556 cd05245, SDR_a2, atypical (a) SDRs, subgroup 2. This subgroup
contains atypical SDRs, one member is identified as
Escherichia coli protein ybjT, function unknown.
Atypical SDRs are distinct from classical SDRs. Members
of this subgroup have a glycine-rich NAD(P)-binding
motif consensus that generally matches the extended
SDRs, TGXXGXXG, but lacks the characteristic active
site residues of the SDRs. This subgroup has basic
residues (HXXXR) in place of the active site motif
YXXXK, these may have a catalytic role. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif
is often different from the forms normally seen in
classical or extended SDRs. Atypical SDRs include
biliverdin IX beta reductase (BVR-B,aka flavin
reductase), NMRa (a negative transcriptional regulator
of various fungi), progesterone 5-beta-reductase like
proteins, phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane
reductase, isoflavone reductases, and others. SDRs are
a functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. In addition to the Rossmann fold
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids, and typically have a TGXXGXXG cofactor
binding motif. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 293
Score = 28.9 bits (65), Expect = 3.7
Identities = 12/16 (75%), Positives = 13/16 (81%)
Query: 42 VLVTGATGQIGYALVP 57
VLVTGATG +G LVP
Sbjct: 1 VLVTGATGYVGGRLVP 16
>gnl|CDD|234190 TIGR03376, glycerol3P_DH, glycerol-3-phosphate dehydrogenase
(NAD(+)). Members of this protein family are the
eukaryotic enzyme, glycerol-3-phosphate dehydrogenase
(NAD(+)) (EC 1.1.1.8). Enzymatic activity for 1.1.1.8 is
defined as sn-glycerol 3-phosphate + NAD(+) = glycerone
phosphate + NADH. Note the very similar reactions of
enzymes defined as EC 1.1.1.94 and 1.1.99.5, assigned to
families of proteins in the bacteria.
Length = 342
Score = 29.2 bits (66), Expect = 3.9
Identities = 11/25 (44%), Positives = 14/25 (56%)
Query: 98 PLLKGVVATTDVVEACKDVNIAVMV 122
L +VA D+VEA K +I V V
Sbjct: 65 KLPANLVAVPDLVEAAKGADILVFV 89
>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 = 28.8 bits (65), Expect = 4.0
Identities = 12/33 (36%), Positives = 17/33 (51%), Gaps = 4/33 (12%)
Query: 42 VLVTGATGQIGYALVPMI----ARGIMLGPDQP 70
+L+TGA G IG A + AR I+ + P
Sbjct: 5 ILITGAAGLIGKAFCKALLSAGARLILADINAP 37
>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 = 28.7 bits (65), Expect = 4.0
Identities = 9/20 (45%), Positives = 12/20 (60%)
Query: 42 VLVTGATGQIGYALVPMIAR 61
VL+TG + IG AL +A
Sbjct: 3 VLITGCSSGIGLALALALAA 22
>gnl|CDD|176231 cd08270, MDR4, Medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
This group is a member of the medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, but lacks the zinc-binding
sites of the zinc-dependent alcohol dehydrogenases. The
medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P)-binding Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 305
Score = 28.9 bits (65), Expect = 4.4
Identities = 11/22 (50%), Positives = 14/22 (63%)
Query: 41 RVLVTGATGQIGYALVPMIARG 62
RVLVTGA+G +G V + A
Sbjct: 135 RVLVTGASGGVGRFAVQLAALA 156
>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 = 4.5
Identities = 12/44 (27%), Positives = 21/44 (47%), Gaps = 10/44 (22%)
Query: 51 IGYALVPMIAR----------GIMLGPDQPVILHMLDIEPAAEA 84
+G L P+I G++L D +LH+L+ + A +A
Sbjct: 20 LGERLYPLIQAMHPELAGKITGMLLEMDNSELLHLLESDEALKA 63
>gnl|CDD|187537 cd05226, SDR_e_a, Extended (e) and atypical (a) SDRs. Extended
or atypical short-chain dehydrogenases/reductases
(SDRs, aka tyrosine-dependent oxidoreductases) are
distinct from classical SDRs. In addition to the
Rossmann fold (alpha/beta folding pattern with a
central beta-sheet) core region typical of all SDRs,
extended SDRs have a less conserved C-terminal
extension of approximately 100 amino acids. Extended
SDRs are a diverse collection of proteins, and include
isomerases, epimerases, oxidoreductases, and lyases;
they typically have a TGXXGXXG cofactor binding motif.
Atypical SDRs generally lack the catalytic residues
characteristic of the SDRs, and their glycine-rich
NAD(P)-binding motif is often different from the forms
normally seen in classical or extended SDRs. Atypical
SDRs include biliverdin IX beta reductase (BVR-B,aka
flavin reductase), NMRa (a negative transcriptional
regulator of various fungi), progesterone
5-beta-reductase like proteins, phenylcoumaran benzylic
ether and pinoresinol-lariciresinol reductases,
phenylpropene synthases, eugenol synthase,
triphenylmethane reductase, isoflavone reductases, and
others. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving
as a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton
relay involving the conserved Tyr and Lys, a water
molecule stabilized by Asn, and nicotinamide. Complex
(multidomain) SDRs such as ketoreductase domains of
fatty acid synthase have a GGXGXXG NAD(P)-binding motif
and an altered active site motif (YXXXN). Fungal type
ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding
motif.
Length = 176
Score = 28.1 bits (63), Expect = 4.5
Identities = 9/15 (60%), Positives = 11/15 (73%)
Query: 42 VLVTGATGQIGYALV 56
+L+ GATG IG AL
Sbjct: 1 ILILGATGFIGRALA 15
>gnl|CDD|224015 COG1090, COG1090, Predicted nucleoside-diphosphate sugar
epimerase [General function prediction only].
Length = 297
Score = 28.4 bits (64), Expect = 5.3
Identities = 10/21 (47%), Positives = 14/21 (66%)
Query: 42 VLVTGATGQIGYALVPMIARG 62
+L+TG TG IG AL + +G
Sbjct: 1 ILITGGTGLIGRALTARLRKG 21
>gnl|CDD|187661 cd08958, FR_SDR_e, flavonoid reductase (FR), extended (e) SDRs.
This subgroup contains FRs of the extended SDR-type and
related proteins. These FRs act in the NADP-dependent
reduction of flavonoids, ketone-containing plant
secondary metabolites; they have the characteristic
active site triad of the SDRs (though not the upstream
active site Asn) and a NADP-binding motif that is very
similar to the typical extended SDR motif. Extended
SDRs are distinct from classical SDRs. In addition to
the Rossmann fold (alpha/beta folding pattern with a
central beta-sheet) core region typical of all SDRs,
extended SDRs have a less conserved C-terminal
extension of approximately 100 amino acids. Extended
SDRs are a diverse collection of proteins, and include
isomerases, epimerases, oxidoreductases, and lyases;
they typically have a TGXXGXXG cofactor binding motif.
SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving
as a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton
relay involving the conserved Tyr and Lys, a water
molecule stabilized by Asn, and nicotinamide. Atypical
SDRs generally lack the catalytic residues
characteristic of the SDRs, and their glycine-rich
NAD(P)-binding motif is often different from the forms
normally seen in classical or extended SDRs. Complex
(multidomain) SDRs such as ketoreductase domains of
fatty acid synthase have a GGXGXXG NAD(P)-binding motif
and an altered active site motif (YXXXN). Fungal type
ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding
motif.
Length = 293
Score = 28.3 bits (64), Expect = 5.7
Identities = 24/68 (35%), Positives = 33/68 (48%), Gaps = 12/68 (17%)
Query: 42 VLVTGATGQIGYALVPM-IARGIML------GPDQPVILHMLDIEPAAEALNGVKMEL-- 92
V VTGA+G IG LV + RG + D+ + H+L++E A E L K +L
Sbjct: 1 VCVTGASGFIGSWLVKRLLQRGYTVRATVRDPGDEKKVAHLLELEGAKERLKLFKADLLD 60
Query: 93 ---IDAAF 97
DAA
Sbjct: 61 YGSFDAAI 68
>gnl|CDD|187647 cd08943, R1PA_ADH_SDR_c, rhamnulose-1-phosphate aldolase/alcohol
dehydrogenase, classical (c) SDRs. This family has
bifunctional proteins with an N-terminal aldolase and a
C-terminal classical SDR domain. One member is
identified as a rhamnulose-1-phosphate aldolase/alcohol
dehydrogenase. The SDR domain has a canonical SDR
glycine-rich NAD(P) binding motif and a match to the
characteristic active site triad. However, it lacks an
upstream active site Asn typical of SDRs. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold (alpha/beta folding pattern with a central
beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRs are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes catalyze a
wide range of activities including the metabolism of
steroids, cofactors, carbohydrates, lipids, aromatic
compounds, and amino acids, and act in redox sensing.
Classical SDRs have an TGXXX[AG]XG cofactor binding
motif and a YXXXK active site motif, with the Tyr
residue of the active site motif serving as a critical
catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 250
Score = 28.1 bits (63), Expect = 5.9
Identities = 17/83 (20%), Positives = 28/83 (33%), Gaps = 9/83 (10%)
Query: 42 VLVTGATGQIGYALVPMIARGIMLGPDQPVILHMLDIEPAAEALNGVKMELIDAAFPLLK 101
LVTG IG A+ +A + + + DI+P + A +
Sbjct: 4 ALVTGGASGIGLAIAKRLAA-------EGAAVVVADIDPEIAEKVAEAAQGGPRALGVQC 56
Query: 102 GVVATTDVVEACKDVNIAVMVGG 124
V + V A + + GG
Sbjct: 57 DVTSEAQVQSAFE--QAVLEFGG 77
>gnl|CDD|176191 cd05289, MDR_like_2, alcohol dehydrogenase and quinone
reductase-like medium chain degydrogenases/reductases.
Members identified as zinc-dependent alcohol
dehydrogenases and quinone oxidoreductase. QOR catalyzes
the conversion of a quinone + NAD(P)H to a hydroquinone
+ NAD(P)+. Quinones are cyclic diones derived from
aromatic compounds. Membrane bound QOR actin the
respiratory chains of bacteria and mitochondria, while
soluble QOR acts to protect from toxic quinones (e.g.
DT-diaphorase) or as a soluble eye-lens protein in some
vertebrates (e.g. zeta-crystalin). QOR reduces quinones
through a semi-quinone intermediate via a
NAD(P)H-dependent single electron transfer. QOR is a
member of the medium chain dehydrogenase/reductase
family, but lacks the zinc-binding sites of the
prototypical alcohol dehydrogenases of this group.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which has a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES. These
proteins typically form dimers (typically higher plants,
mammals) or tetramers (yeast, bacteria), and have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. NAD(H) binding occurs in the
cleft between the catalytic and coenzyme-binding domains
at the active site, and coenzyme binding induces a
conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
In human ADH catalysis, the zinc ion helps coordinate
the alcohol, followed by deprotonation of a histidine,
the ribose of NAD, a serine, then the alcohol, which
allows the transfer of a hydride to NAD+, creating NADH
and a zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 309
Score = 28.3 bits (64), Expect = 6.0
Identities = 25/101 (24%), Positives = 36/101 (35%), Gaps = 28/101 (27%)
Query: 33 LDIPKEPCRVLVTGATGQIGYALVPM--------IA----------RGIMLGPDQPVILH 74
L K VL+ GA G +G V + IA R LG D+ +
Sbjct: 139 LGGLKAGQTVLIHGAAGGVGSFAVQLAKARGARVIATASAANADFLRS--LGADEVIDYT 196
Query: 75 MLDIEPAAE------ALNGVKMELIDAAFPLLK--GVVATT 107
D E AA L+ V E + + L+K G + +
Sbjct: 197 KGDFERAAAPGGVDAVLDTVGGETLARSLALVKPGGRLVSI 237
>gnl|CDD|181298 PRK08219, PRK08219, short chain dehydrogenase; Provisional.
Length = 227
Score = 28.0 bits (63), Expect = 6.2
Identities = 21/59 (35%), Positives = 28/59 (47%), Gaps = 11/59 (18%)
Query: 42 VLVTGATGQIGYALVPMIARGIMLGPDQPVILHMLDIEPAAEALNGVKMELIDA-AFPL 99
L+TGA+ IG A IAR L P ++L AE L+ + EL A FP+
Sbjct: 6 ALITGASRGIGAA----IAR--ELAPTHTLLLGGRP----AERLDELAAELPGATPFPV 54
>gnl|CDD|236612 PRK09685, PRK09685, DNA-binding transcriptional activator FeaR;
Provisional.
Length = 302
Score = 28.5 bits (64), Expect = 6.5
Identities = 9/24 (37%), Positives = 12/24 (50%)
Query: 183 PAKNITCLTRLDHNRAMGQISERL 206
P + C RL + M Q+S RL
Sbjct: 132 PGQKPACAGRLSASLPMVQLSHRL 155
>gnl|CDD|235737 PRK06197, PRK06197, short chain dehydrogenase; Provisional.
Length = 306
Score = 28.1 bits (63), Expect = 6.9
Identities = 18/69 (26%), Positives = 30/69 (43%), Gaps = 8/69 (11%)
Query: 30 WSFLDIPKEPCRV-LVTGATGQIGYALVPMIA-RGIMLGPDQPVILHMLDIEPAAEALNG 87
W+ DIP + RV +VTGA +GY +A +G V+L + +++ A
Sbjct: 6 WTAADIPDQSGRVAVVTGANTGLGYETAAALAAKG------AHVVLAVRNLDKGKAAAAR 59
Query: 88 VKMELIDAA 96
+ A
Sbjct: 60 ITAATPGAD 68
>gnl|CDD|237972 PRK15483, PRK15483, type III restriction-modification system StyLTI
enzyme res; Provisional.
Length = 986
Score = 28.5 bits (64), Expect = 6.9
Identities = 4/38 (10%), Positives = 13/38 (34%)
Query: 225 TQYPDVNHATVTTSKGEKPVREAVADDNWLNTEFITTV 262
Q P + ++ V + + +E++ +
Sbjct: 718 RQIPTQVQQRLVSNDDNGRVEVSQREGELAASEYLNGM 755
>gnl|CDD|212492 cd05327, retinol-DH_like_SDR_c_like, retinol dehydrogenase
(retinol-DH), Light dependent Protochlorophyllide
(Pchlide) OxidoReductase (LPOR) and related proteins,
classical (c) SDRs. Classical SDR subgroup containing
retinol-DHs, LPORs, and related proteins. Retinol is
processed by a medium chain alcohol dehydrogenase
followed by retinol-DHs. Pchlide reductases act in
chlorophyll biosynthesis. There are distinct enzymes
that catalyze Pchlide reduction in light or dark
conditions. Light-dependent reduction is via an
NADP-dependent SDR, LPOR. Proteins in this subfamily
share the glycine-rich NAD-binding motif of the
classical SDRs, have a partial match to the canonical
active site tetrad, but lack the typical active site
Ser. This subgroup includes the human proteins: retinol
dehydrogenase -12, -13 ,and -14,
dehydrogenase/reductase SDR family member (DHRS)-12 ,
-13 and -X (a DHRS on chromosome X), and WWOX (WW
domain-containing oxidoreductase), as well as a
Neurospora crassa SDR encoded by the blue light
inducible bli-4 gene. SDRs are a functionally diverse
family of oxidoreductases that have a single domain
with a structurally conserved Rossmann fold (alpha/beta
folding pattern with a central beta-sheet), an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRs are
approximately 350 residues. Sequence identity between
different SDR enzymes are typically in the 15-30%
range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes catalyze a
wide range of activities including the metabolism of
steroids, cofactors, carbohydrates, lipids, aromatic
compounds, and amino acids, and act in redox sensing.
Classical SDRs have an TGXXX[AG]XG cofactor binding
motif and a YXXXK active site motif, with the Tyr
residue of the active site motif serving as a critical
catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 269
Score = 28.0 bits (63), Expect = 7.1
Identities = 15/51 (29%), Positives = 22/51 (43%), Gaps = 5/51 (9%)
Query: 41 RVLVTGATGQIGYALVPMIARGIMLGPDQPVILHMLDIEPAAEALNGVKME 91
V++TGA IG +A+ G VI+ + E EA +K E
Sbjct: 3 VVVITGANSGIGKETARELAK---RGAH--VIIACRNEEKGEEAAAEIKKE 48
>gnl|CDD|168574 PRK06484, PRK06484, short chain dehydrogenase; Validated.
Length = 520
Score = 28.3 bits (63), Expect = 7.5
Identities = 23/93 (24%), Positives = 33/93 (35%), Gaps = 12/93 (12%)
Query: 42 VLVTGATGQIGYALVPMIARG--IMLGPDQPVILHMLDIEPAAEALNGVKMEL-----ID 94
VLVTGA G IG A AR ++ D+ V + + + M++ I
Sbjct: 8 VLVTGAAGGIGRAACQRFARAGDQVVVADRNVERARERADSLGPDHHALAMDVSDEAQIR 67
Query: 95 AAFPLLKGVVATTDVVEACKDVNIAVMVGGFPR 127
F L DV+ VN A +
Sbjct: 68 EGFEQLHREFGRIDVL-----VNNAGVTDPTMT 95
>gnl|CDD|224670 COG1756, Mra1, Uncharacterized conserved protein [Function
unknown].
Length = 223
Score = 27.7 bits (62), Expect = 7.9
Identities = 13/36 (36%), Positives = 20/36 (55%)
Query: 115 DVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASA 150
IAV++GGFP + E + +++ SIY SA
Sbjct: 170 LKGIAVIIGGFPHGDFREETEFVAEKYSIYDEPLSA 205
>gnl|CDD|235596 PRK05764, PRK05764, aspartate aminotransferase; Provisional.
Length = 393
Score = 28.2 bits (64), Expect = 7.9
Identities = 11/35 (31%), Positives = 17/35 (48%), Gaps = 1/35 (2%)
Query: 144 YKAQASALEKHAAPNCKVLVVANPAN-TNALILKE 177
+K LE P K L++ +P+N T A+ E
Sbjct: 150 FKLTVEQLEAAITPKTKALILNSPSNPTGAVYSPE 184
>gnl|CDD|233570 TIGR01777, yfcH, TIGR01777 family protein. This model represents
a clade of proteins of unknown function including the
E. coli yfcH protein [Hypothetical proteins,
Conserved].
Length = 291
Score = 28.0 bits (63), Expect = 8.1
Identities = 9/16 (56%), Positives = 11/16 (68%)
Query: 42 VLVTGATGQIGYALVP 57
+L+TG TG IG AL
Sbjct: 1 ILITGGTGFIGRALTQ 16
>gnl|CDD|234091 TIGR03022, WbaP_sugtrans, Undecaprenyl-phosphate galactose
phosphotransferase, WbaP. The WbaP (formerly RfbP)
protein has been characterized as the first enzyme in
O-antigen biosynthesis in Salmonella typhimurium. The
enzyme transfers galactose from UDP-galactose to a
polyprenyl carrier (utilizing the highly conserved
C-terminal sugar transferase domain, pfam02397) a
reaction which takes place at the cytoplasmic face of
the inner membrane. The N-terminal hydrophobic domain is
then believed to facilitate the "flippase" function of
transferring the liposaccharide unit from the
cytoplasmic face to the periplasmic face of the inner
membrane. This model includes the enterobacterial
enzymes, where the function is presumed to be identical
to the S. typhimurium enzyme as well as a somewhat
broader group which are likely to catalyze the same or
highly similar reactions based on a phylogenetic
tree-building analysis of the broader sugar transferase
family. Most of these genes are found within large
operons dedicated to the production of complex
exopolysaccharides such as the enterobacterial
O-antigen. The most likely heterogeneity would be in the
precise nature of the sugar molecule transferred.
Length = 456
Score = 28.1 bits (63), Expect = 8.2
Identities = 18/97 (18%), Positives = 29/97 (29%), Gaps = 14/97 (14%)
Query: 1 MEYFYIVLFQKILVVLFCVALFWKIIRHMWSFLDIPKEPCRVLVTGATGQIGYALVPMIA 60
Y +V + L V L ++R + S P ++ G I Y +
Sbjct: 89 EPYSRLVFLLAWGLALVLVPLARILVRKLLSRRGWWGRPAVIIGAGQNAAILYR---ALQ 145
Query: 61 RGIMLG-----------PDQPVILHMLDIEPAAEALN 86
LG +L L + A +AL
Sbjct: 146 SNPQLGLRPLAVVDTDPAASGRLLTGLPVVGADDALR 182
>gnl|CDD|187590 cd05329, TR_SDR_c, tropinone reductase-I and II (TR-1, and
TR-II)-like, classical (c) SDRs. This subgroup
includes TR-I and TR-II; these proteins are members of
the SDR family. TRs catalyze the NADPH-dependent
reductions of the 3-carbonyl group of tropinone, to a
beta-hydroxyl group. TR-I and TR-II produce different
stereoisomers from tropinone, TR-I produces tropine
(3alpha-hydroxytropane), and TR-II, produces
pseudotropine (sigma-tropine, 3beta-hydroxytropane).
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 = 251
Score = 27.8 bits (62), Expect = 8.3
Identities = 12/28 (42%), Positives = 14/28 (50%), Gaps = 5/28 (17%)
Query: 29 MWSFLDIPKEPCRVLVTGATGQIGYALV 56
W+ E LVTG T IGYA+V
Sbjct: 1 RWNL-----EGKTALVTGGTKGIGYAIV 23
>gnl|CDD|187570 cd05260, GDP_MD_SDR_e, GDP-mannose 4,6 dehydratase, extended (e)
SDRs. GDP-mannose 4,6 dehydratase, a homodimeric SDR,
catalyzes the NADP(H)-dependent conversion of
GDP-(D)-mannose to GDP-4-keto, 6-deoxy-(D)-mannose in
the fucose biosynthesis pathway. These proteins have
the canonical active site triad and NAD-binding
pattern, however the active site Asn is often missing
and may be substituted with Asp. A Glu residue has been
identified as an important active site base. Extended
SDRs are distinct from classical SDRs. In addition to
the Rossmann fold (alpha/beta folding pattern with a
central beta-sheet) core region typical of all SDRs,
extended SDRs have a less conserved C-terminal
extension of approximately 100 amino acids. Extended
SDRs are a diverse collection of proteins, and include
isomerases, epimerases, oxidoreductases, and lyases;
they typically have a TGXXGXXG cofactor binding motif.
SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving
as a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton
relay involving the conserved Tyr and Lys, a water
molecule stabilized by Asn, and nicotinamide. Atypical
SDRs generally lack the catalytic residues
characteristic of the SDRs, and their glycine-rich
NAD(P)-binding motif is often different from the forms
normally seen in classical or extended SDRs. Complex
(multidomain) SDRs such as ketoreductase domains of
fatty acid synthase have a GGXGXXG NAD(P)-binding motif
and an altered active site motif (YXXXN). Fungal type
ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding
motif.
Length = 316
Score = 27.9 bits (63), Expect = 8.3
Identities = 9/16 (56%), Positives = 10/16 (62%)
Query: 41 RVLVTGATGQIGYALV 56
R L+TG TGQ G L
Sbjct: 1 RALITGITGQDGSYLA 16
>gnl|CDD|240639 cd12162, 2-Hacid_dh_4, Putative D-isomer specific 2-hydroxyacid
dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine yydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 307
Score = 27.8 bits (63), Expect = 8.5
Identities = 13/35 (37%), Positives = 18/35 (51%), Gaps = 6/35 (17%)
Query: 91 ELIDAAFPLLK--GVVAT-TDVV--EACKDVNIAV 120
E++ P LK GV+AT + V A K+ I V
Sbjct: 58 EVLAQL-PNLKLIGVLATGYNNVDLAAAKERGITV 91
>gnl|CDD|187578 cd05269, TMR_SDR_a, triphenylmethane reductase (TMR)-like
proteins, NMRa-like, atypical (a) SDRs. TMR is an
atypical NADP-binding protein of the SDR family. It
lacks the active site residues of the SDRs but has a
glycine rich NAD(P)-binding motif that matches the
extended SDRs. Proteins in this subgroup however, are
more similar in length to the classical SDRs. TMR was
identified as a reducer of triphenylmethane dyes,
important environmental pollutants. This subgroup also
includes Escherichia coli NADPH-dependent quinine
oxidoreductase (QOR2), which catalyzes two-electron
reduction of quinone; but is unlikely to play a major
role in protecting against quinone cytotoxicity.
Atypical SDRs are distinct from classical SDRs.
Atypical SDRs include biliverdin IX beta reductase
(BVR-B,aka flavin reductase), NMRa (a negative
transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane
reductase, isoflavone reductases, and others. SDRs are
a functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. In addition to the Rossmann fold
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids, and typically have a TGXXGXXG cofactor
binding motif. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 272
Score = 27.6 bits (62), Expect = 8.8
Identities = 10/14 (71%), Positives = 13/14 (92%)
Query: 43 LVTGATGQIGYALV 56
LVTGATG++G A+V
Sbjct: 2 LVTGATGKLGTAVV 15
>gnl|CDD|187553 cd05242, SDR_a8, atypical (a) SDRs, subgroup 8. This subgroup
contains atypical SDRs of unknown function. Proteins in
this subgroup have a glycine-rich NAD(P)-binding motif
consensus that resembles that of the extended SDRs,
(GXXGXXG or GGXGXXG), but lacks the characteristic
active site residues of the SDRs. A Cys often replaces
the usual Lys of the YXXXK active site motif, while the
upstream Ser is generally present and Arg replaces the
usual Asn. Atypical SDRs generally lack the catalytic
residues characteristic of the SDRs, and their
glycine-rich NAD(P)-binding motif is often different
from the forms normally seen in classical or extended
SDRs. Atypical SDRs include biliverdin IX beta
reductase (BVR-B,aka flavin reductase), NMRa (a
negative transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane
reductase, isoflavone reductases, and others. SDRs are
a functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. In addition to the Rossmann fold
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids, and typically have a TGXXGXXG cofactor
binding motif. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 296
Score = 28.0 bits (63), Expect = 9.0
Identities = 8/17 (47%), Positives = 12/17 (70%)
Query: 41 RVLVTGATGQIGYALVP 57
++++TG TG IG AL
Sbjct: 1 KIVITGGTGFIGRALTR 17
>gnl|CDD|163279 TIGR03466, HpnA, hopanoid-associated sugar epimerase. The
sequences in this family are members of the pfam01370
superfamily of NAD-dependent epimerases and
dehydratases typically acting on nucleotide-sugar
substrates. The genes of the family modeled here are
generally in the same locus with genes involved in the
biosynthesis and elaboration of hopene, the cyclization
product of the polyisoprenoid squalene. This gene and
its association with hopene biosynthesis in Zymomonas
mobilis has been noted in the literature where the gene
symbol hpnA was assigned. Hopanoids are known to be
components of the plasma membrane and to have polar
sugar head groups in Z. mobilis and other species.
Length = 328
Score = 27.7 bits (62), Expect = 9.8
Identities = 11/16 (68%), Positives = 14/16 (87%)
Query: 41 RVLVTGATGQIGYALV 56
+VLVTGATG +G A+V
Sbjct: 2 KVLVTGATGFVGSAVV 17
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.320 0.134 0.402
Gapped
Lambda K H
0.267 0.0760 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 18,502,657
Number of extensions: 1775161
Number of successful extensions: 2027
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1959
Number of HSP's successfully gapped: 121
Length of query: 366
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 268
Effective length of database: 6,590,910
Effective search space: 1766363880
Effective search space used: 1766363880
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 60 (26.8 bits)