RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 019990
(332 letters)
>gnl|CDD|177744 PLN00135, PLN00135, malate dehydrogenase.
Length = 309
Score = 669 bits (1728), Expect = 0.0
Identities = 283/309 (91%), Positives = 293/309 (94%)
Query: 24 MIARGIMLGPDQPVILHMLDIEPAAEALNGVKMELIDAAFPLLKGVVATTDVVEACKDVN 83
MIARG+MLGPDQPVILHMLDI PAAEALNGVKMELIDAAFPLLKGVVATTDVVEACK VN
Sbjct: 1 MIARGVMLGPDQPVILHMLDIPPAAEALNGVKMELIDAAFPLLKGVVATTDVVEACKGVN 60
Query: 84 IAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEKHAAPNCKVLVVANPANTNALILKE 143
IAVMVGGFPRKEGMERKDVMSKNVSIYK+QASALEKHAAP+CKVLVVANPANTNALILKE
Sbjct: 61 IAVMVGGFPRKEGMERKDVMSKNVSIYKSQASALEKHAAPDCKVLVVANPANTNALILKE 120
Query: 144 FAPSIPAKNITCLTRLDHNRAMGQISERLKVHVSDVKNVIIWGNHSSTQYPDVNHATVTT 203
FAPSIP KNITCLTRLDHNRA+GQISERL V VSDVKNVIIWGNHSSTQYPDVNHATV T
Sbjct: 121 FAPSIPEKNITCLTRLDHNRALGQISERLGVPVSDVKNVIIWGNHSSTQYPDVNHATVKT 180
Query: 204 SKGEKPVREAVADDNWLNTEFITTVQQRGAAIIKARKLSSALSAASSACDHIRDWVLGTP 263
GEKPVRE VADD WLN EFITTVQQRGAAIIKARKLSSALSAASSACDHIRDWVLGTP
Sbjct: 181 PSGEKPVRELVADDAWLNGEFITTVQQRGAAIIKARKLSSALSAASSACDHIRDWVLGTP 240
Query: 264 KGTWVSMGVYSDGSYGIPEGLIYSFPVTCEKGEWSIVKGLKVDEFSRAKMDATAEELAEE 323
+GTWVSMGVYSDGSYG+P GLIYSFPVTCEKGEWSIV+GL +DEFSR KMDATA+EL EE
Sbjct: 241 EGTWVSMGVYSDGSYGVPPGLIYSFPVTCEKGEWSIVQGLSIDEFSRKKMDATAKELKEE 300
Query: 324 KTLAYSCLN 332
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 = 640 bits (1654), Expect = 0.0
Identities = 228/324 (70%), Positives = 267/324 (82%)
Query: 5 PLRVLVTGAAGQIGYALVPMIARGIMLGPDQPVILHMLDIEPAAEALNGVKMELIDAAFP 64
P+RVLVTGAAGQI Y+L+PMIA+G + GPDQPVILH+LDI PA +AL GV MEL D AFP
Sbjct: 2 PIRVLVTGAAGQIAYSLLPMIAKGDVFGPDQPVILHLLDIPPALKALEGVVMELQDCAFP 61
Query: 65 LLKGVVATTDVVEACKDVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEKHAAPN 124
LLK VVATTD EA KDV++A++VG PRKEGMERKD++ NV I+K Q AL+K+A N
Sbjct: 62 LLKSVVATTDPEEAFKDVDVAILVGAMPRKEGMERKDLLKANVKIFKEQGEALDKYAKKN 121
Query: 125 CKVLVVANPANTNALILKEFAPSIPAKNITCLTRLDHNRAMGQISERLKVHVSDVKNVII 184
KVLVV NPANTNALIL ++APSIP +N T LTRLDHNRA QI+ +L V VSDVKNVII
Sbjct: 122 VKVLVVGNPANTNALILLKYAPSIPKENFTALTRLDHNRAKSQIALKLGVPVSDVKNVII 181
Query: 185 WGNHSSTQYPDVNHATVTTSKGEKPVREAVADDNWLNTEFITTVQQRGAAIIKARKLSSA 244
WGNHSSTQYPDVNHATV + KP REAV DD WLN EFI+TVQ+RGAA+IKARKLSSA
Sbjct: 182 WGNHSSTQYPDVNHATVELNGKGKPAREAVKDDAWLNGEFISTVQKRGAAVIKARKLSSA 241
Query: 245 LSAASSACDHIRDWVLGTPKGTWVSMGVYSDGSYGIPEGLIYSFPVTCEKGEWSIVKGLK 304
+SAA + CDH+ DW GTP+G +VSMGVYSDGSYG+PEGLI+SFPVTC+ G+W IV+GL
Sbjct: 242 MSAAKAICDHVHDWWFGTPEGEFVSMGVYSDGSYGVPEGLIFSFPVTCKNGKWKIVQGLS 301
Query: 305 VDEFSRAKMDATAEELAEEKTLAY 328
+D+FSR K+DATA+EL EEK A
Sbjct: 302 IDDFSREKIDATAKELVEEKETAL 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 = 561 bits (1447), Expect = 0.0
Identities = 227/324 (70%), Positives = 267/324 (82%), Gaps = 1/324 (0%)
Query: 7 RVLVTGAAGQIGYALVPMIARGIMLGPDQPVILHMLDIEPAAEALNGVKMELIDAAFPLL 66
RV+VTGAAGQIGYAL+PMIARG MLG DQP+ILH+LDI PA + L GV MEL+D AFPLL
Sbjct: 1 RVVVTGAAGQIGYALLPMIARGRMLGKDQPIILHLLDIPPAMKVLEGVVMELMDCAFPLL 60
Query: 67 KGVVATTDVVEACKDVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEKHAAPNCK 126
GVV T D A DV++A++VG FPRKEGMER+D++SKNV I+K Q AL+K A +CK
Sbjct: 61 DGVVPTHDPAVAFTDVDVAILVGAFPRKEGMERRDLLSKNVKIFKEQGRALDKLAKKDCK 120
Query: 127 VLVVANPANTNALILKEFAPSIPAKNITCLTRLDHNRAMGQISERLKVHVSDVKNVIIWG 186
VLVV NPANTNAL+L +APSIP KN + LTRLDHNRA+ Q++ER V VSDVKNVIIWG
Sbjct: 121 VLVVGNPANTNALVLSNYAPSIPPKNFSALTRLDHNRALAQVAERAGVPVSDVKNVIIWG 180
Query: 187 NHSSTQYPDVNHATVTTSKGEKPVREAVADDNWLNTEFITTVQQRGAAIIKARKLSSALS 246
NHSSTQYPDVNHATVT +KPVREA+ DD +L+ EFITTVQQRGAAII+ARKLSSALS
Sbjct: 181 NHSSTQYPDVNHATVTKGGKQKPVREAIKDDAYLDGEFITTVQQRGAAIIRARKLSSALS 240
Query: 247 AASSACDHIRDWVLGTPKGTWVSMGVYSDGS-YGIPEGLIYSFPVTCEKGEWSIVKGLKV 305
AA +A D + DWVLGTP+GT+VSMGVYSDGS YG+P+GLI+SFPVTC+ GEW IV+GL V
Sbjct: 241 AAKAAVDQMHDWVLGTPEGTFVSMGVYSDGSPYGVPKGLIFSFPVTCKNGEWKIVEGLCV 300
Query: 306 DEFSRAKMDATAEELAEEKTLAYS 329
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 = 539 bits (1390), Expect = 0.0
Identities = 210/327 (64%), Positives = 248/327 (75%), Gaps = 6/327 (1%)
Query: 3 KNPLRVLVTGAAGQIGYALVPMIARGIMLGPDQPVILHMLDIEPAAEALNGVKMELIDAA 62
K P+RV VTGAAGQIGY+L+ IA G + G DQPV+LH+LDI PA +AL GV MEL D A
Sbjct: 1 KKPVRVAVTGAAGQIGYSLLFRIASGELFGKDQPVVLHLLDIPPAMKALEGVAMELEDCA 60
Query: 63 FPLLKGVVATTDVVEACKDVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEKHAA 122
FPLL GVVATTD EA KDV+ A++VG FPRK GMER D++SKN I+K Q AL K A
Sbjct: 61 FPLLAGVVATTDPEEAFKDVDAALLVGAFPRKPGMERADLLSKNGKIFKEQGKALNKVAK 120
Query: 123 PNCKVLVVANPANTNALILKEFAPSIPAKNITCLTRLDHNRAMGQISERLKVHVSDVKNV 182
+ KVLVV NPANTNALI + AP IP KN + +TRLDHNRA Q++ + V VSDVKNV
Sbjct: 121 KDVKVLVVGNPANTNALIASKNAPDIPPKNFSAMTRLDHNRAKYQLAAKAGVPVSDVKNV 180
Query: 183 IIWGNHSSTQYPDVNHATVTTSKGEKPVREAVADDNWLNTEFITTVQQRGAAIIKARKLS 242
IIWGNHS+TQ PD HATV +PV+E + DD WL EFI TVQQRGAA+I+AR S
Sbjct: 181 IIWGNHSNTQVPDFTHATVDG----RPVKEVIKDDKWLEGEFIPTVQQRGAAVIEARGAS 236
Query: 243 SALSAASSACDHIRDWVLGTPKGTWVSMGVYSDG-SYGIPEGLIYSFPVTCEK-GEWSIV 300
SA SAA++A DH+RDWV GTP+G WVSMGVYSDG YGIPEG+I+SFPVTC+ GEW IV
Sbjct: 237 SAASAANAAIDHVRDWVTGTPEGDWVSMGVYSDGNPYGIPEGIIFSFPVTCKGDGEWEIV 296
Query: 301 KGLKVDEFSRAKMDATAEELAEEKTLA 327
+GL +D+F R K+DAT +EL EEK A
Sbjct: 297 EGLPLDDFVRGKLDATEDELLEEKEEA 323
>gnl|CDD|235468 PRK05442, PRK05442, malate dehydrogenase; Provisional.
Length = 326
Score = 523 bits (1351), Expect = 0.0
Identities = 196/323 (60%), Positives = 241/323 (74%), Gaps = 4/323 (1%)
Query: 2 AKNPLRVLVTGAAGQIGYALVPMIARGIMLGPDQPVILHMLDIEPAAEALNGVKMELIDA 61
K P+RV VTGAAGQIGY+L+ IA G MLG DQPVIL +L+I PA +AL GV MEL D
Sbjct: 1 MKAPVRVAVTGAAGQIGYSLLFRIASGDMLGKDQPVILQLLEIPPALKALEGVVMELDDC 60
Query: 62 AFPLLKGVVATTDVVEACKDVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEKHA 121
AFPLL GVV T D A KD ++A++VG PR GMERKD++ N +I+ AQ AL + A
Sbjct: 61 AFPLLAGVVITDDPNVAFKDADVALLVGARPRGPGMERKDLLEANGAIFTAQGKALNEVA 120
Query: 122 APNCKVLVVANPANTNALILKEFAPSIPAKNITCLTRLDHNRAMGQISERLKVHVSDVKN 181
A + KVLVV NPANTNALI + AP +PA+N T +TRLDHNRA+ Q++ + V V+D+K
Sbjct: 121 ARDVKVLVVGNPANTNALIAMKNAPDLPAENFTAMTRLDHNRALSQLAAKAGVPVADIKK 180
Query: 182 VIIWGNHSSTQYPDVNHATVTTSKGEKPVREAVADDNWLNTEFITTVQQRGAAIIKARKL 241
+ +WGNHS+TQYPD HAT+ KP E + D WL FI TVQ+RGAAII+AR
Sbjct: 181 MTVWGNHSATQYPDFRHATI----DGKPAAEVINDQAWLEDTFIPTVQKRGAAIIEARGA 236
Query: 242 SSALSAASSACDHIRDWVLGTPKGTWVSMGVYSDGSYGIPEGLIYSFPVTCEKGEWSIVK 301
SSA SAA++A DH+RDWVLGTP+G WVSMGV SDGSYGIPEGLI+ FPVTCE GE+ IV+
Sbjct: 237 SSAASAANAAIDHVRDWVLGTPEGDWVSMGVPSDGSYGIPEGLIFGFPVTCENGEYEIVQ 296
Query: 302 GLKVDEFSRAKMDATAEELAEEK 324
GL++D+FSR K+DAT EL EE+
Sbjct: 297 GLEIDDFSREKIDATLAELEEER 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 = 506 bits (1305), Expect = 0.0
Identities = 195/323 (60%), Positives = 239/323 (73%), Gaps = 2/323 (0%)
Query: 6 LRVLVTGAAGQIGYALVPMIARGIMLGPDQPVILHMLDIEPAAEALNGVKMELIDAAFPL 65
L VL+TGAAGQIGY L+ +IA G + G DQPVILH+LDI PA +AL GV MEL D AFPL
Sbjct: 1 LHVLITGAAGQIGYNLLFLIASGELFGDDQPVILHLLDIPPAMKALEGVVMELQDCAFPL 60
Query: 66 LKGVVATTDVVEACKDVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEKHAAPNC 125
LKGVV TTD EA KDV++A++VG FPRK GMER D++ KN I+K Q AL K A P
Sbjct: 61 LKGVVITTDPEEAFKDVDVAILVGAFPRKPGMERADLLRKNAKIFKEQGEALNKVAKPTV 120
Query: 126 KVLVVANPANTNALILKEFAPSIPAKNITCLTRLDHNRAMGQISERLKVHVSDVKNVIIW 185
KVLVV NPANTNALI + AP++P KN T LTRLDHNRA Q++ +L V VSDVKNVIIW
Sbjct: 121 KVLVVGNPANTNALIALKNAPNLPPKNFTALTRLDHNRAKAQVARKLGVRVSDVKNVIIW 180
Query: 186 GNHSSTQYPDVNHATVTTSKGEKPVREAVADDNWLNTEFITTVQQRGAAIIKARKLSSAL 245
GNHS+TQ PD+++A V G + V + D+ WLN EF+ TVQ+RGAAIIK R SSA
Sbjct: 181 GNHSNTQVPDLSNAVVYGPGGTEWV-LDLLDEEWLNDEFVKTVQKRGAAIIKKRGASSAA 239
Query: 246 SAASSACDHIRDWVLGTPKGTWVSMGVYSDG-SYGIPEGLIYSFPVTCEKGEWSIVKGLK 304
SAA + DH++DW+ GTP G VSMGVYS G YGIP G+++SFP TC+ G W +V+ LK
Sbjct: 240 SAAKAIADHVKDWLFGTPPGEIVSMGVYSPGNPYGIPPGIVFSFPCTCKGGGWHVVEDLK 299
Query: 305 VDEFSRAKMDATAEELAEEKTLA 327
++++ R K+ AT EEL EEK +A
Sbjct: 300 LNDWLREKLKATEEELIEEKEIA 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 = 502 bits (1295), Expect = 0.0
Identities = 187/321 (58%), Positives = 230/321 (71%), Gaps = 4/321 (1%)
Query: 4 NPLRVLVTGAAGQIGYALVPMIARGIMLGPDQPVILHMLDIEPAAEALNGVKMELIDAAF 63
P+RV VTGAAGQIGY+L+ IA G M GPDQPVIL +L++ A +AL GV MEL D AF
Sbjct: 1 KPVRVAVTGAAGQIGYSLLFRIASGEMFGPDQPVILQLLELPQALKALEGVAMELEDCAF 60
Query: 64 PLLKGVVATTDVVEACKDVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEKHAAP 123
PLL +V T D A KD + A++VG PR GMER D++ N I+ AQ AL A+
Sbjct: 61 PLLAEIVITDDPNVAFKDADWALLVGAKPRGPGMERADLLKANGKIFTAQGKALNDVASR 120
Query: 124 NCKVLVVANPANTNALILKEFAPSIPAKNITCLTRLDHNRAMGQISERLKVHVSDVKNVI 183
+ KVLVV NP NTNALI + AP IP N T +TRLDHNRA Q++++ V V+DVKN++
Sbjct: 121 DVKVLVVGNPCNTNALIAMKNAPDIPPDNFTAMTRLDHNRAKSQLAKKAGVPVTDVKNMV 180
Query: 184 IWGNHSSTQYPDVNHATVTTSKGEKPVREAVADDNWLNTEFITTVQQRGAAIIKARKLSS 243
IWGNHS TQYPD +AT+ G KP E + D WL EFI TVQ+RGAAIIKAR SS
Sbjct: 181 IWGNHSPTQYPDFTNATI----GGKPAAEVINDRAWLEDEFIPTVQKRGAAIIKARGASS 236
Query: 244 ALSAASSACDHIRDWVLGTPKGTWVSMGVYSDGSYGIPEGLIYSFPVTCEKGEWSIVKGL 303
A SAA++A DH+RDWVLGTP+G W SM V SDGSYGIPEGLI+SFPV + G + IV+GL
Sbjct: 237 AASAANAAIDHMRDWVLGTPEGDWFSMAVPSDGSYGIPEGLIFSFPVRSKGGGYEIVEGL 296
Query: 304 KVDEFSRAKMDATAEELAEEK 324
++D+F+R K+DAT EL EE+
Sbjct: 297 EIDDFAREKIDATLAELLEER 317
>gnl|CDD|215060 PLN00112, PLN00112, malate dehydrogenase (NADP); Provisional.
Length = 444
Score = 310 bits (797), Expect = e-103
Identities = 145/326 (44%), Positives = 195/326 (59%), Gaps = 10/326 (3%)
Query: 3 KNPLRVLVTGAAGQIGYALVPMIARGIMLGPDQPVILHMLDIEPAAEALNGVKMELIDAA 62
K + V V+GAAG I L+ +A G + GPDQP+ L +L E + +AL GV MEL D+
Sbjct: 98 KKLINVAVSGAAGMISNHLLFKLASGEVFGPDQPIALKLLGSERSKQALEGVAMELEDSL 157
Query: 63 FPLLKGVVATTDVVEACKDVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEKHAA 122
+PLL+ V D E +D A+++G PR GMER D++ N I+ Q AL + A+
Sbjct: 158 YPLLREVSIGIDPYEVFQDAEWALLIGAKPRGPGMERADLLDINGQIFAEQGKALNEVAS 217
Query: 123 PNCKVLVVANPANTNALILKEFAPSIPAKNITCLTRLDHNRAMGQISERLKVHVSDVKNV 182
N KV+VV NP NTNALI + AP+IPAKN LTRLD NRA Q++ + V V NV
Sbjct: 218 RNVKVIVVGNPCNTNALICLKNAPNIPAKNFHALTRLDENRAKCQLALKAGVFYDKVSNV 277
Query: 183 IIWGNHSSTQYPDVNHATVTTSKGEKPVREAVADDNWLNTEFITTVQQRGAAIIKARKLS 242
IWGNHS+TQ PD +A + PV+E + D WL EF VQ+RG +IK S
Sbjct: 278 TIWGNHSTTQVPDFLNAKI----NGLPVKEVITDHKWLEEEFTPKVQKRGGVLIKKWGRS 333
Query: 243 SALSAASSACDHIRDWVLGTPKGTWVSMGVYSDGS-YGIPEGLIYSFPVTCEK---GEWS 298
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: 299 IVKGLKVDEFSRAKMDATAEELAEEK 324
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 = 286 bits (732), Expect = 1e-94
Identities = 145/324 (44%), Positives = 198/324 (61%), Gaps = 6/324 (1%)
Query: 3 KNPLRVLVTGAAGQIGYALVPMIARGIMLGPDQPVILHMLDIEPAAEALNGVKMELIDAA 62
K + V V+GAAG I L+ M+A G + G DQP+ L +L E + EAL GV MEL D+
Sbjct: 42 KKTVNVAVSGAAGMISNHLLFMLASGEVFGQDQPIALKLLGSERSKEALEGVAMELEDSL 101
Query: 63 FPLLKGVVATTDVVEACKDVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEKHAA 122
+PLL+ V D E +D + A+++G PR GMER D++ N I+ Q AL A+
Sbjct: 102 YPLLREVSIGIDPYEVFEDADWALLIGAKPRGPGMERADLLDINGQIFADQGKALNAVAS 161
Query: 123 PNCKVLVVANPANTNALILKEFAPSIPAKNITCLTRLDHNRAMGQISERLKVHVSDVKNV 182
NCKVLVV NP NTNALI + AP+IP KN LTRLD NRA Q++ + + V NV
Sbjct: 162 KNCKVLVVGNPCNTNALIAMKNAPNIPRKNFHALTRLDENRAKCQLALKSGKFYTSVSNV 221
Query: 183 IIWGNHSSTQYPDVNHATVTTSKGEKPVREAVADDNWLNTEFITTVQQRGAAIIKARKLS 242
IWGNHS+TQ PD +A + G +P +E + D WL EF TVQ+RG A+IK S
Sbjct: 222 TIWGNHSTTQVPDFVNAKI----GGRPAKEVIKDTKWLEEEFTPTVQKRGGALIKKWGRS 277
Query: 243 SALSAASSACDHIRDWVLGTPKGTWVSMGVYSDGS-YGIPEGLIYSFPVTCE-KGEWSIV 300
SA S A S D I+ V+ TP+G W S GVY+DG+ YGI EGL++S P + G++ +
Sbjct: 278 SAASTAVSIADAIKSLVVPTPEGDWFSTGVYTDGNPYGIAEGLVFSMPCRSKGDGDYELA 337
Query: 301 KGLKVDEFSRAKMDATAEELAEEK 324
+ +D+F R ++ + +EL +EK
Sbjct: 338 TDVSMDDFLRERIRKSEDELLKEK 361
>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 = 275 bits (705), Expect = 9e-90
Identities = 115/333 (34%), Positives = 183/333 (54%), Gaps = 13/333 (3%)
Query: 4 NPLRVLVTGAAGQIGYALVPMIARGIMLGPDQPVILHMLDIEPAAEALNGVKMELIDAAF 63
NPL+V +T A+ + Y L+P +A G + G ++ + +H+LD E L G+ ME+ D AF
Sbjct: 122 NPLQVCITNASAPLCYHLIPSLASGEVFGMEEEISIHLLDSPENLEKLKGLVMEVEDLAF 181
Query: 64 PLLKGVVATTDVVEACKDVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEKHAAP 123
PLL+G+ TTD+ A KD ++ V++ F KEG + + + V+I + +EK+A
Sbjct: 182 PLLRGISVTTDLDVAFKDAHVIVLLDDFLIKEGEDLEGCIRSRVAICQLYGPLIEKNAKE 241
Query: 124 NCKVLVVA-NPANTNALILKEFAPSIPAKNITCLTRLDHNRAMGQISERLKVHVSDVKNV 182
+ KV+V N IL ++APSIP KNI + RL NRA ++ +L V+ + +K+V
Sbjct: 242 DVKVIVAGRTFLNLKTSILIKYAPSIPRKNIIAVARLQENRAKALLARKLNVNSAGIKDV 301
Query: 183 IIWGNHSSTQYPDVNHATVTTSKG--------EKPVREAVADDNWLNTEFITTVQQRGAA 234
I+WGN Y D++ A V +PV E V D W+N EF+ T++ +
Sbjct: 302 IVWGNIGGNTYIDLSKARVYRYDSAIWGPPNYSRPVLELVHDSKWINGEFVATLKSLSS- 360
Query: 235 IIKARKLSSALSAASSACDHIRDWVLGTPKGTWVSMGVYSDGSYGIPEGLIYSFPVTCEK 294
+ +A+S A + + W G+P G S+GV S+G YGIPEG+++S PV +
Sbjct: 361 ---SLNHEAAISPAHAIATTLSYWYHGSPPGEIFSLGVISEGWYGIPEGIVFSMPVKFQN 417
Query: 295 GEWSIVKGLKVDEFSRAKMDATAEELAEEKTLA 327
G W +V L++ E R + +L +EK +A
Sbjct: 418 GSWEVVTDLELSEILREVLKRITSDLIQEKLVA 450
>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 = 269 bits (688), Expect = 5e-89
Identities = 117/310 (37%), Positives = 180/310 (58%), Gaps = 5/310 (1%)
Query: 25 IARGIMLGPDQPVILHMLDIEPAAEALNGVKMELIDAAFPLLKGVVATTDVVEACKDVNI 84
IA G + G ++PV LH+L+I PA L + MEL D AFP L G + TT + EA KD++
Sbjct: 5 IANGDLYG-NRPVCLHLLEIPPALNRLEALAMELEDCAFPNLAGTIVTTKLEEAFKDIDC 63
Query: 85 AVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEKHAAPNCKVLVVANPANTNALILKEF 144
A +V P K G R D+++KN I+KA AL ++A P KVLV+ NP NTN L+
Sbjct: 64 AFLVASVPLKPGEVRADLLTKNTPIFKATGEALSEYAKPTVKVLVIGNPVNTNCLVAMLH 123
Query: 145 APSIPAKNITCLTRLDHNRAMGQISERLKVHVSDVKNVIIWGNHSSTQYPDVNHATVTTS 204
AP + A+N + L LDHNRA+ +I+ +LKV V + +V++WGNH+ + D+ HA T +
Sbjct: 124 APKLSAENFSSLCMLDHNRAVSRIASKLKVPVDHIYHVVVWGNHAESMVADLTHAEFTKN 183
Query: 205 KGEKPVREAVADDNWLNTEFITTVQQRGAAIIKARKLSSALSAASSACDHIRDWVLGTPK 264
+ V + + D + +F + QR I++ R +SA S ++ H++ W+ GT
Sbjct: 184 GKHQKVFDELCRD-YPEPDFFEVIAQRAWKILEMRGFTSAASPVKASLQHMKAWLFGTRP 242
Query: 265 GTWVSMG--VYSDGSYGIPEGLIYSFPVTC-EKGEWSIVKGLKVDEFSRAKMDATAEELA 321
G +SMG V YGI G+I+SFP T E G+ +V+ +++ + + K+ T ++L
Sbjct: 243 GEVLSMGIPVPEGNPYGIKPGVIFSFPCTVDEDGKVHVVENFELNPWLKTKLAQTEKDLF 302
Query: 322 EEKTLAYSCL 331
EE+ A L
Sbjct: 303 EERETALKAL 312
>gnl|CDD|223117 COG0039, Mdh, Malate/lactate dehydrogenases [Energy production and
conversion].
Length = 313
Score = 227 bits (581), Expect = 9e-73
Identities = 103/324 (31%), Positives = 153/324 (47%), Gaps = 21/324 (6%)
Query: 7 RVLVTGAAGQIGYALVPMIARGIMLGPDQPVILHMLDIEPAAEALNGVKMELIDAAFPLL 66
+V V GA G +G +L ++ LG + L ++DI E GV ++L AA PL
Sbjct: 2 KVAVIGA-GNVGSSLAFLLLLQ-GLGSE----LVLIDINE--EKAEGVALDLSHAAAPLG 53
Query: 67 KGVVATTDV-VEACKDVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEKHAAPNC 125
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: 126 KVLVVANPANTNALILKEFAPSIPAKNITCLTRLDHNRAMGQISERLKVHVSDVKNVIIW 185
VLVV NP + I +F+ + I T LD R ++E+L V DV +I
Sbjct: 113 IVLVVTNPVDILTYIAMKFSGFPKNRVIGSGTVLDSARFRTFLAEKLGVSPKDVHAYVI- 171
Query: 186 GNHSSTQYPDVNHATVTTSKGEKPVREAV-ADDNWLNTEFITTVQQRGAAIIKARKLSSA 244
G H T P + ATV G KP+ E + D E I V+ GA II+A+ +
Sbjct: 172 GEHGDTMVPLWSQATV----GGKPLEELLKEDTEEDLEELIERVRNAGAEIIEAKGAGTY 227
Query: 245 LSAASSACDHIRDWVLGTPKGTWVSMGVYSDGSYGIPEGLIYSFPVT-CEKGEWSIVKGL 303
A++ + + + + + VY DG YG+ E + + P + G I++ L
Sbjct: 228 YGPAAALARMVEAILRD--EKRVLPVSVYLDGEYGV-EDVYFGVPAVLGKNGVEEILELL 284
Query: 304 KVDEFSRAKMDATAEELAEEKTLA 327
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 (508), Expect = 1e-62
Identities = 85/318 (26%), Positives = 136/318 (42%), Gaps = 57/318 (17%)
Query: 8 VLVTGAAGQIGYALVPMIARGIMLGPDQPVILHMLDIEPAAEALNGVKMELIDAAFPL-L 66
+ V GA G +G AL +A G + L + DI+ E L GV M+L DA PL
Sbjct: 1 IAVIGAGGNVGPALAFGLADG---SVLLAIELVLYDIDE--EKLKGVAMDLQDAVEPLAD 55
Query: 67 KGVVATTDVVEACKDVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEKHAAPNCK 126
V T D EA KD ++ ++ G RK GM R D++ +NV I K +EK+ +P+
Sbjct: 56 IKVSITDDPYEAFKDADVVIITAGVGRKPGMGRLDLLKRNVPIVKEIGDNIEKY-SPDAW 114
Query: 127 VLVVANPANTNALILKEFAPSIPAKNITCLTRLDHNRAMGQISERLKVHVSDVKNVIIWG 186
++VV+NP + ++ ++ +P + + L LD R ++E+L V DVK V I G
Sbjct: 115 IIVVSNPVDIITYLVWRYSG-LPKEKVIGLGTLDPIRFRRILAEKLGVDPDDVK-VYILG 172
Query: 187 NHSSTQYPDVNHATVTTSKGEKPVREAVADDNWLNTEFITTVQQRGAAIIKARKLSSALS 246
H +Q PD +
Sbjct: 173 EHGGSQVPDWSTVR---------------------------------------------- 186
Query: 247 AASSACDHIRDWVLGTPKGTWVSMGVYSDGSYGIPEGLIYSFPVTCEKGEWSIVKGLKVD 306
A+S D IR + +G + +GV ++G GIP+ ++ S P K + +
Sbjct: 187 IATSIADLIRSLL--NDEGEILPVGVRNNGQIGIPDDVVVSVPCIVGKNGVEEPIEVGLT 244
Query: 307 EFSRAKMDATAEELAEEK 324
+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 = 162 bits (413), Expect = 2e-49
Identities = 61/172 (35%), Positives = 91/172 (52%), Gaps = 4/172 (2%)
Query: 157 TRLDHNRAMGQISERLKVHVSDVKNVIIWGNHSSTQYPDVNHATVTTSKGEKPVREAVAD 216
T LD RA ++E+ V NV + G HS TQ+PD +HA VT V+E + D
Sbjct: 1 TTLDTARARTFLAEKFGV-DPRSVNVYVIGEHSGTQFPDWSHAKVTIIPLISQVKENLKD 59
Query: 217 DNWLNTEFITTVQQRGAAIIKARKLSSALSAASSACDHIRDWVLGTPKGTWVSMGVYSDG 276
+W E I VQ G +I+A+ S+ S A +A + + GT G +S+GVY DG
Sbjct: 60 TDWELEELIERVQNAGYEVIEAKAGSTTYSMAYAAARIAKAILRGT--GGVLSVGVYLDG 117
Query: 277 SYGIPEGLIYSFPVTCEK-GEWSIVKGLKVDEFSRAKMDATAEELAEEKTLA 327
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 = 7e-38
Identities = 47/150 (31%), Positives = 74/150 (49%), Gaps = 8/150 (5%)
Query: 6 LRVLVTGAAGQIGYALVPMIARGIMLGPDQPVILHMLDIEPAAEALNGVKMELIDAAFPL 65
++V V GA G +G +L +A L + L ++DI + GV M+L + L
Sbjct: 1 VKVAVVGAGGGVGSSLAFALA-LQGLADE----LVLVDINK--DKAEGVAMDLSHGSTFL 53
Query: 66 LKGVVATTDVVEACKDVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEKHAAPNC 125
+ D EA KD ++ V+ G PRK GM R D++++N I+K A+ K AP+
Sbjct: 54 SVPGIVGGDDYEALKDADVVVITAGVPRKPGMTRLDLLNRNAGIFKDIVPAIAKS-APDA 112
Query: 126 KVLVVANPANTNALILKEFAPSIPAKNITC 155
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 = 82.7 bits (205), Expect = 4e-18
Identities = 77/311 (24%), Positives = 137/311 (44%), Gaps = 21/311 (6%)
Query: 14 AGQIGYALVPMIARGIMLGPDQPVILHMLDIEPAAEALNGVKMELIDAAFPLLKGVVATT 73
AG +G A +A ++ ++ ++D+ E G ++L A+ L G +
Sbjct: 6 AGNVGAA----VAFALIAKGLASELV-LVDVNE--EKAKGDALDLSHASAFLATGTIVRG 58
Query: 74 DVVEACKDVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEKHAAPNCKVLVVANP 133
D +I V+ G PRK G R D++++N I ++ + L+K+ P+ +LVV+NP
Sbjct: 59 GDYADAADADIVVITAGAPRKPGETRLDLINRNAPILRSVITNLKKY-GPDAIILVVSNP 117
Query: 134 ANTNALILKEFAPSIPAKNITCLTRLDHNRAMGQISERLKVHVSDVKNVIIWGNHSSTQY 193
+ + ++ + + I T LD R ++E+L V V ++ G H +Q
Sbjct: 118 VDILTYVAQKLSGLPKNRVIGSGTLLDSARFRSLLAEKLDVDPQSVHAYVL-GEHGDSQV 176
Query: 194 PDVNHATVTTSKGEKPVREAVADDNWLNTEFITTVQQRGAAIIKARKLSSALSAASSACD 253
+ ATV G P+ E V+ G II+ K ++ A++ D
Sbjct: 177 VAWSTATV----GGLPLEELAPFTKLDLEAIEEEVRTSGYEIIR-LKGATNYGIATAIAD 231
Query: 254 HIRDWVLGTPKGTWVSMGVYSDGSYGIPEGLIYSFP-VTCEKGEWSIVKG-LKVDEFSRA 311
++ +L + + + +G YGI E + S P V +G I++ L DE A
Sbjct: 232 IVKS-ILLDERRV-LPVSAVQEGQYGI-EDVALSVPAVVGREGVVRILEIPLTEDE--EA 286
Query: 312 KMDATAEELAE 322
K+ +AE L E
Sbjct: 287 KLQKSAEALKE 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 = 78.7 bits (195), Expect = 1e-16
Identities = 68/266 (25%), Positives = 109/266 (40%), Gaps = 35/266 (13%)
Query: 69 VVATTDVVEACKDVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEKHAAPNCKVL 128
V T D E ++ V+ G PRK GM R D++ N I K A ++K+ APN V+
Sbjct: 55 VTGTNDY-EDIAGSDVVVITAGIPRKPGMSRDDLLGTNAKIVKEVAENIKKY-APNAIVI 112
Query: 129 VVANPANTNALILKEFAPSIPAKNITCLTRLDHNRAMGQ------------ISERLKVHV 176
VV NP + + + + NR +G I+E L V V
Sbjct: 113 VVTNPLDVMTYVAYKA------------SGFPRNRVIGMAGVLDSARFRYFIAEELGVSV 160
Query: 177 SDVKNVIIWGNHSSTQYPDVNHATVTTSKGEKPVREAVADDNWLNTEFITTVQQRGAAII 236
DV+ +++ G H T P ++TV G P+ E + + E + + GA I+
Sbjct: 161 KDVQAMVL-GGHGDTMVPLPRYSTV----GGIPLTELITKEEI--DEIVERTRNGGAEIV 213
Query: 237 KARKLSSALSAASSACDHIRDWVLGTPKGTWVSMGVYSDGSYGIPEGLIYSFPVTCEKGE 296
K SA A ++A + + +L K Y +G YGI + + PV K
Sbjct: 214 NLLKTGSAYYAPAAAIAEMVEAILKDKKRVLPC-SAYLEGEYGI-KDIFVGVPVVLGKNG 271
Query: 297 WSIVKGLKVDEFSRAKMDATAEELAE 322
+ L + + + D + E + E
Sbjct: 272 VEKIIELDLTDEEKEAFDKSVESVKE 297
>gnl|CDD|180477 PRK06223, PRK06223, malate dehydrogenase; Reviewed.
Length = 307
Score = 77.1 bits (191), Expect = 4e-16
Identities = 78/329 (23%), Positives = 137/329 (41%), Gaps = 57/329 (17%)
Query: 14 AGQIGYALVPMIARGIMLGPDQPVILHMLDIEPAAEALNGVKMELIDAAFPLLKGVVATT 73
AG +G L ++A + + + DI G +++ +AA V
Sbjct: 10 AGNVGATLAHLLAL------KELGDVVLFDI--VEGVPQGKALDIAEAA------PVEGF 55
Query: 74 DVV-------EACKDVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEKHAAPNCK 126
D E ++ V+ G PRK GM R D++ N I K A ++K+ AP+
Sbjct: 56 DTKITGTNDYEDIAGSDVVVITAGVPRKPGMSRDDLLGINAKIMKDVAEGIKKY-APDAI 114
Query: 127 VLVVANPANT-NALILKEFAPSIPAKNITCLTRLDHNRAMGQ------------ISERLK 173
V+VV NP + + LKE + NR +G I+E L
Sbjct: 115 VIVVTNPVDAMTYVALKE-------------SGFPKNRVIGMAGVLDSARFRTFIAEELN 161
Query: 174 VHVSDVKNVIIWGNHSSTQYPDVNHATVTTSKGEKPVREAVADDNWLNTEFITTVQQRGA 233
V V DV ++ G H + P V ++TV G P+ + ++ + L+ E + ++ GA
Sbjct: 162 VSVKDVTAFVL-GGHGDSMVPLVRYSTV----GGIPLEDLLSKEK-LD-EIVERTRKGGA 214
Query: 234 AIIKARKLSSALSAASSACDHIRDWVLGTPKGTWVSMGVYSDGSYGIPEGLIYSFPVTCE 293
I+ K SA A +++ + + +L K + Y +G YG+ + + PV
Sbjct: 215 EIVGLLKTGSAYYAPAASIAEMVEAILKD-KKRVLPCSAYLEGEYGV-KDVYVGVPVKLG 272
Query: 294 KGEWSIVKGLKVDEFSRAKMDATAEELAE 322
K + L++D+ +A D + E + +
Sbjct: 273 KNGVEKIIELELDDEEKAAFDKSVEAVKK 301
>gnl|CDD|173409 PTZ00117, PTZ00117, malate dehydrogenase; Provisional.
Length = 319
Score = 73.2 bits (180), Expect = 1e-14
Identities = 61/208 (29%), Positives = 98/208 (47%), Gaps = 6/208 (2%)
Query: 73 TDVVEACKDVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEKHAAPNCKVLVVAN 132
T+ E KD ++ V+ G RKE M R+D+++ N I K+ A +++K+ PN V+ V N
Sbjct: 65 TNNYEDIKDSDVVVITAGVQRKEEMTREDLLTINGKIMKSVAESVKKY-CPNAFVICVTN 123
Query: 133 PANTNALILKEFAPSIPAKNITCLT-RLDHNRAMGQISERLKVHVSDVKNVIIWGNHSST 191
P + + +E + IP+ I + LD +R ++E+L V DV V+I G H
Sbjct: 124 PLDCMVKVFQEKS-GIPSNKICGMAGVLDSSRFRCNLAEKLGVSPGDVSAVVI-GGHGDL 181
Query: 192 QYPDVNHATVTTSKGEKPVREAVADDNWLNTEFITTVQQRGAAIIKARKLSSALSAASSA 251
P + TV V++ + +N E I + G I+K K SA A ++A
Sbjct: 182 MVPLPRYCTVNGIPLSDFVKKGAITEKEIN-EIIKKTRNMGGEIVKLLKKGSAFFAPAAA 240
Query: 252 CDHIRDWVLGTPKGTWVSMGVYSDGSYG 279
+ + 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 = 70.1 bits (172), Expect = 1e-13
Identities = 64/245 (26%), Positives = 116/245 (47%), Gaps = 38/245 (15%)
Query: 6 LRVLVTGAAGQIGYALVPMIARGIMLGPDQPVI--LHMLDIEPAAEALNGVKMELIDAAF 63
++V + GA+G++G A ++A+ + V+ ++++ + E L G+++++ DA
Sbjct: 1 MKVSIIGASGRVGSATALLLAK-------EDVVKEINLISRPKSLEKLKGLRLDIYDA-- 51
Query: 64 PLLKGVVATTDV---VEACKDV------NIAVMVGGFPRKEGMERKDVMSKNVSIYKAQA 114
+A + ++ D+ +I ++ G PRKEGM R D+ KN I K A
Sbjct: 52 ------LAAAGIDAEIKISSDLSDVAGSDIVIITAGVPRKEGMSRLDLAKKNAKIVKKYA 105
Query: 115 SALEKHAAPNCKVLVVANPANT---NALILKEFAPSIPAKNITCLTRLDHNRAMGQISER 171
+ + AP+ K+LVV NP + AL F + + T LD R I++
Sbjct: 106 KQIAEF-APDTKILVVTNPVDVMTYKALKESGFDKN---RVFGLGTHLDSLRFKVAIAKH 161
Query: 172 LKVHVSDVKNVIIWGNHSSTQYPDVNHATVTTSKGEKPVREAVADDNWLNTEFITTVQQR 231
VH+S+V II G H + P ++ +TS G P++ ++ + + TV+
Sbjct: 162 FNVHISEVHTRII-GEHGDSMVPLIS----STSIGGIPIKRFPEYKDFDVEKIVETVKNA 216
Query: 232 GAAII 236
G II
Sbjct: 217 GQNII 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 = 69.2 bits (170), Expect = 3e-13
Identities = 89/330 (26%), Positives = 136/330 (41%), Gaps = 40/330 (12%)
Query: 7 RVLVTGAAGQIGYALVPMI-ARGIMLGPDQPVILHMLDIEPAAEALNGVKMEL-IDAAFP 64
+V V G GQ+G A I A+G+ D+ L ++D+ + L G M+L +AF
Sbjct: 5 KVTVVGV-GQVGMACAISILAKGLA---DE---LVLVDVVE--DKLKGEAMDLQHGSAFL 55
Query: 65 LLKGVVATTDVVEACKDVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEKHAAPN 124
+ A D + + ++ G + EG R D++ +NV I+K L K++ PN
Sbjct: 56 KNPKIEADKDY-SVTANSKVVIVTAGARQNEGESRLDLVQRNVDIFKGIIPKLVKYS-PN 113
Query: 125 CKVLVVANPANTNALILKEFAPSI----PAKNITCLTRLDHNRAMGQISERLKVHVSDVK 180
+LVV+NP + I+ A + + I LD R I+ERL V S V
Sbjct: 114 AILLVVSNPVD----IMTYVAWKLSGLPKHRVIGSGCNLDSARFRYLIAERLGVAPSSVH 169
Query: 181 NVIIWGNHSSTQYP---DVNHATVTTSKGEKPVREAVADDNWLNTEFITTVQQRGAAIIK 237
II G H + P VN A V + + W E V +IK
Sbjct: 170 GWII-GEHGDSSVPVWSGVNVAGVRLQDLNPDIGTDKDPEKW--KEVHKQVVDSAYEVIK 226
Query: 238 ARKLSS---ALSAASSACDHIRDWVLGTPKGTWVSMGVYSDGSYGIPEGLIYSFPVTCEK 294
+ +S LS A + D +L G S+ G +GI + + S P C
Sbjct: 227 LKGYTSWAIGLSVAD-----LVDAIL-RNTGRVHSVSTLVKGLHGIEDEVFLSLP--CIL 278
Query: 295 GEWSIVKGLKV--DEFSRAKMDATAEELAE 322
GE I +K E + K+ +A+ L E
Sbjct: 279 GENGITHVIKQPLTEEEQEKLQKSADTLWE 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 = 68.0 bits (166), Expect = 7e-13
Identities = 63/240 (26%), Positives = 110/240 (45%), Gaps = 10/240 (4%)
Query: 83 NIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEKHAAPNCKVLVVANPANTNALILK 142
+I V+ G PRK GM R+D++S N I + + +H +PN ++VV+NP + +
Sbjct: 71 DIVVITAGLPRKPGMSREDLLSMNAGIVREVTGRIMEH-SPNPIIVVVSNPLDAMTYVAW 129
Query: 143 EFAPSIPAKNITCLTRLDHNRAMGQISERLKVHVSDVKNVIIWGNHSSTQYPDVNHATVT 202
+ + + I LD R I+ L V V DV ++ G H P V ++TV
Sbjct: 130 QKSGFPKERVIGQAGVLDSARFRTFIAMELGVSVQDVTACVL-GGHGDAMVPLVRYSTV- 187
Query: 203 TSKGEKPVREAVADDNWLNTEFITTVQQRGAAIIKARKLSSALSAASSACDHIRDWVLGT 262
PV + ++ + E + ++ G I+ K SA A +++ + + +L
Sbjct: 188 ---AGIPVADLISAERI--AEIVERTRKGGGEIVNLLKQGSAYYAPAASVVEMVEAILKD 242
Query: 263 PKGTWVSMGVYSDGSYGIPEGLIYSFPVTCEKGEWSIVKGLKVDEFSRAKMDATAEELAE 322
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 = 1e-12
Identities = 72/255 (28%), Positives = 106/255 (41%), Gaps = 35/255 (13%)
Query: 7 RVLVTGAAGQIGYALVPMIARGIMLGPDQPVI--LHMLDIEPAAEALNGVKMEL--IDAA 62
+V V GAAG IG L ++ QP + L + DI AA GV +L I A
Sbjct: 1 KVAVLGAAGGIGQPLSLLLKL-------QPYVSELSLYDIAGAA----GVAADLSHIPTA 49
Query: 63 FPLLKGVVATTDVVEACKDVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEKHAA 122
+KG + A K ++ V+ G PRK GM R D+ + N I K +A+ +
Sbjct: 50 -ASVKGFSGEEGLENALKGADVVVIPAGVPRKPGMTRDDLFNVNAGIVKDLVAAVAES-C 107
Query: 123 PNCKVLVVANPANTN----ALILKEFAPSIPAKNITCLTRLDHNRAMGQISERLKVHVSD 178
P +LV+ NP N+ A +LK+ P + +T LD RA ++E LK
Sbjct: 108 PKAMILVITNPVNSTVPIAAEVLKKKGVYDP-NKLFGVTTLDIVRANTFVAE-LKGKDPM 165
Query: 179 VKNVIIWGNHSSTQYPDVNHATVTTSKGEKPVREAVADDNWLNTEFITTVQQRGAAIIKA 238
NV + G HS + + EA I +Q G ++KA
Sbjct: 166 EVNVPVIGGHSGETIIPLISQCPGKVLFTEDQLEA----------LIHRIQNAGTEVVKA 215
Query: 239 R--KLSSALSAASSA 251
+ 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 = 63.3 bits (155), Expect = 2e-11
Identities = 58/193 (30%), Positives = 92/193 (47%), Gaps = 25/193 (12%)
Query: 6 LRVLVTGAAGQIGYALVPMIARGIMLGPDQPVI--LHMLDIEPAAEALNGVKMEL--IDA 61
++V V GAAG IG L +L P++ L + DI GV +L I+
Sbjct: 1 VKVAVLGAAGGIGQPLS-------LLLKLNPLVSELALYDIV----NTPGVAADLSHINT 49
Query: 62 AFPLLKGVVATTDVVEACKDVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEKHA 121
+ G + ++ +A K ++ V+ G PRK GM R D+ + N I + A+A+ K
Sbjct: 50 P-AKVTGYLGPEELKKALKGADVVVIPAGVPRKPGMTRDDLFNINAGIVRDLATAVAKA- 107
Query: 122 APNCKVLVVANPANTN----ALILKEFAPSIPAKNITCLTRLDHNRAMGQISERLKVHVS 177
P +L+++NP N+ A +LK+ P K + +T LD RA ++E L + +
Sbjct: 108 CPKALILIISNPVNSTVPIAAEVLKKAGVYDP-KRLFGVTTLDVVRANTFVAELLGLDPA 166
Query: 178 DVK-NVIIWGNHS 189
V VI G HS
Sbjct: 167 KVNVPVI--GGHS 177
>gnl|CDD|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 = 55.3 bits (134), Expect = 1e-08
Identities = 68/302 (22%), Positives = 113/302 (37%), Gaps = 52/302 (17%)
Query: 41 MLDIEPAAEALNGVKMELIDAAFPLLKGVVATTDVVEACKDVNIAVMVGGFPRKEGMERK 100
++DI + G M+L AA L + CKD ++ V+ G P+K G R
Sbjct: 26 LIDINK--DKAEGEAMDLQHAASFLPTPKKIRSGDYSDCKDADLVVITAGAPQKPGETRL 83
Query: 101 DVMSKNVSIYKAQASALEKHAAPNCKVLVVANPANTNALILKEFAPSIPAKNITCLTRLD 160
+++ +NV I K+ + K + LV NP + IL A L+
Sbjct: 84 ELVGRNVRIMKSIVPEVVKS-GFDGIFLVATNPVD----ILTYVAWK--------LSGFP 130
Query: 161 HNRAMGQ------------ISERLKVHVSDVKNVIIWGNHSSTQYPDVNHATVTTSKGEK 208
NR +G ++E+L V V II G H ++ P + AT+ G
Sbjct: 131 KNRVIGSGTVLDTARLRYLLAEKLGVDPQSVHAYII-GEHGDSEVPVWSSATI----GGV 185
Query: 209 PVREAVADDNWLNTEFITT--------VQQRGAA--IIKARKLSSALSAASSACDHIRDW 258
P+ + +L + T + R AA II RK ++ + +
Sbjct: 186 PLLD------YLKAKGTETDLDLEEIEKEVRDAAYEIIN-RKGATYYGIGMAVARIVEAI 238
Query: 259 VLGTPKGTWVSMGVYSDGSYGIPEGLIYSFPVTCEKGEWSIVKGLKVDEFSRAKMDATAE 318
+ + VS Y DG YGI + + P + + L + + + +AE
Sbjct: 239 LHDENRVLPVS--AYLDGEYGI-KDVYIGVPAVLGRNGVEEIIELPLSDEEKEAFQKSAE 295
Query: 319 EL 320
L
Sbjct: 296 TL 297
>gnl|CDD|215058 PLN00106, PLN00106, malate dehydrogenase.
Length = 323
Score = 54.6 bits (132), Expect = 2e-08
Identities = 57/190 (30%), Positives = 92/190 (48%), Gaps = 23/190 (12%)
Query: 7 RVLVTGAAGQIGYALVPMIARGIMLGPDQPVI--LHMLDIEPAAEALNGVKMEL--IDAA 62
+V V GAAG IG L +L P++ LH+ DI GV ++ I+
Sbjct: 20 KVAVLGAAGGIGQPLS-------LLMKMNPLVSELHLYDIANTP----GVAADVSHINTP 68
Query: 63 FPLLKGVVATTDVVEACKDVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEKHAA 122
++G + + +A K ++ ++ G PRK GM R D+ + N I K A+ KH
Sbjct: 69 -AQVRGFLGDDQLGDALKGADLVIIPAGVPRKPGMTRDDLFNINAGIVKTLCEAVAKH-C 126
Query: 123 PNCKVLVVANPANTN----ALILKEFAPSIPAKNITCLTRLDHNRAMGQISERLKVHVSD 178
PN V +++NP N+ A +LK+ A K + +T LD RA ++E+ + +D
Sbjct: 127 PNALVNIISNPVNSTVPIAAEVLKK-AGVYDPKKLFGVTTLDVVRANTFVAEKKGLDPAD 185
Query: 179 VKNVIIWGNH 188
V +V + G H
Sbjct: 186 V-DVPVVGGH 194
>gnl|CDD|178836 PRK00066, ldh, L-lactate dehydrogenase; Reviewed.
Length = 315
Score = 53.0 bits (128), Expect = 7e-08
Identities = 66/255 (25%), Positives = 111/255 (43%), Gaps = 24/255 (9%)
Query: 77 EACKDVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEKHAAPNCKVLVVANPANT 136
CKD ++ V+ G P+K G R D++ KN+ I+K+ + + LV +NP +
Sbjct: 69 SDCKDADLVVITAGAPQKPGETRLDLVEKNLKIFKSIVGEVMAS-GFDGIFLVASNPVDI 127
Query: 137 NALILKEFAPSIPAKNITCLTRLDHNRAMGQISERLKVHVSDVKNVIIWGNHSSTQYPDV 196
+ + + I T LD R +SE+L V V II G H T++P
Sbjct: 128 LTYATWKLSGFPKERVIGSGTSLDSARFRYMLSEKLDVDPRSVHAYII-GEHGDTEFPVW 186
Query: 197 NHATVTTSKGEKPVREAVADDNWLNTEFITTVQQ--RGAA--IIKARKLSS-----ALSA 247
+HA V P+ E + ++ + E + + + R AA II+ + + AL+
Sbjct: 187 SHANV----AGVPLEEYLEENEQYDEEDLDEIFENVRDAAYEIIEKKGATYYGIAMALAR 242
Query: 248 ASSACDHIRDWVLGTPKGTWVSMGVYSDGSYGIPEGLIYSFPVTCEKGEWSIVKGLKVDE 307
+ A + + VL VS Y +G YG + I V G IV+ L +++
Sbjct: 243 ITKAILNNENAVLP------VS--AYLEGQYGEEDVYIGVPAVVNRNGIREIVE-LPLND 293
Query: 308 FSRAKMDATAEELAE 322
+ K +A+ L E
Sbjct: 294 DEKQKFAHSADVLKE 308
>gnl|CDD|235340 PRK05086, PRK05086, malate dehydrogenase; Provisional.
Length = 312
Score = 51.9 bits (125), Expect = 1e-07
Identities = 56/194 (28%), Positives = 87/194 (44%), Gaps = 22/194 (11%)
Query: 6 LRVLVTGAAGQIGYALVPMIARGIMLGPDQPVILHMLDIEPAAEALNGVKMEL--IDAAF 63
++V V GAAG IG AL ++ + G + L + DI P GV ++L I A
Sbjct: 1 MKVAVLGAAGGIGQALALLLKTQLPAGSE----LSLYDIAPVTP---GVAVDLSHIPTAV 53
Query: 64 PLLKGVVATTDVVEACKDVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEKHAA- 122
+ KG + D A + ++ ++ G RK GM+R D+ + N I K + +EK A
Sbjct: 54 KI-KGF-SGEDPTPALEGADVVLISAGVARKPGMDRSDLFNVNAGIVK---NLVEKVAKT 108
Query: 123 -PNCKVLVVANPANTNALILKEF---APSIPAKNITCLTRLDHNRAMGQISERLKVHVSD 178
P + ++ NP NT I E A + +T LD R+ ++E +
Sbjct: 109 CPKACIGIITNPVNTTVAIAAEVLKKAGVYDKNKLFGVTTLDVIRSETFVAELKGKQPGE 168
Query: 179 VK-NVIIWGNHSST 191
V+ VI G HS
Sbjct: 169 VEVPVI--GGHSGV 180
>gnl|CDD|173376 PTZ00082, PTZ00082, L-lactate dehydrogenase; Provisional.
Length = 321
Score = 51.2 bits (123), Expect = 2e-07
Identities = 32/127 (25%), Positives = 55/127 (43%), Gaps = 7/127 (5%)
Query: 80 KDVNIAVMVGGFPRKEGME-----RKDVMSKNVSIYKAQASALEKHAAPNCKVLVVANPA 134
++ ++ G ++ G R D++ N I A ++K+ PN V+V+ NP
Sbjct: 73 AGSDVVIVTAGLTKRPGKSDKEWNRDDLLPLNAKIMDEVAEGIKKYC-PNAFVIVITNPL 131
Query: 135 NTNALILKEFAPSIPAKNITCLTRLDHNRAMGQISERLKVHVSDVKNVIIWGNHSSTQYP 194
+ +L+E + K LD +R I+E+L V+ DV +I G H P
Sbjct: 132 DVMVKLLQEHSGLPKNKVCGMAGVLDSSRLRTYIAEKLGVNPRDVHASVI-GAHGDKMVP 190
Query: 195 DVNHATV 201
+ TV
Sbjct: 191 LPRYVTV 197
>gnl|CDD|240360 PTZ00325, PTZ00325, malate dehydrogenase; Provisional.
Length = 321
Score = 50.8 bits (122), Expect = 4e-07
Identities = 56/189 (29%), Positives = 85/189 (44%), Gaps = 19/189 (10%)
Query: 7 RVLVTGAAGQIGYALVPMIARGIMLGPDQPVILHMLDIEPAAEALNGVKMEL--IDAAFP 64
+V V GAAG IG L ++ + + L + DI A GV +L ID
Sbjct: 10 KVAVLGAAGGIGQPL-SLLLKQNPHVSE----LSLYDIVGAP----GVAADLSHIDTP-A 59
Query: 65 LLKGVVATTDVVEACKDVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEKHAAPN 124
+ G +A + ++ ++ G PRK GM R D+ + N I + +A+ AP
Sbjct: 60 KVTGYADGELWEKALRGADLVLICAGVPRKPGMTRDDLFNTNAPIVRDLVAAVASS-APK 118
Query: 125 CKVLVVANPANTNALILKEFAPSI----PAKNITCLTRLDHNRAMGQISERLKVHVSDVK 180
V +V+NP N+ I E P K + +T LD RA ++E L ++ DV
Sbjct: 119 AIVGIVSNPVNSTVPIAAETLKKAGVYDPRK-LFGVTTLDVVRARKFVAEALGMNPYDV- 176
Query: 181 NVIIWGNHS 189
NV + G HS
Sbjct: 177 NVPVVGGHS 185
>gnl|CDD|178212 PLN02602, PLN02602, lactate dehydrogenase.
Length = 350
Score = 48.6 bits (116), Expect = 2e-06
Identities = 35/154 (22%), Positives = 71/154 (46%), Gaps = 16/154 (10%)
Query: 41 MLDIEPAAEALNGVKMELIDAAFPLLKGVVATTDVVEACKDVNIAVMVGGFPRKEGMERK 100
MLD++ AA L K ++A+TD ++ ++ G + G R
Sbjct: 79 MLDLQHAAAFLPRTK-------------ILASTDY-AVTAGSDLCIVTAGARQIPGESRL 124
Query: 101 DVMSKNVSIYKAQASALEKHAAPNCKVLVVANPANTNALILKEFAPSIPAKNITCLTRLD 160
+++ +NV++++ L K+ +P+ +L+V+NP + + + + + I T LD
Sbjct: 125 NLLQRNVALFRKIIPELAKY-SPDTILLIVSNPVDVLTYVAWKLSGFPANRVIGSGTNLD 183
Query: 161 HNRAMGQISERLKVHVSDVKNVIIWGNHSSTQYP 194
+R I++ L V+ DV+ I+ G H +
Sbjct: 184 SSRFRFLIADHLDVNAQDVQAYIV-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 = 44.8 bits (107), Expect = 3e-05
Identities = 47/168 (27%), Positives = 73/168 (43%), Gaps = 19/168 (11%)
Query: 41 MLDIEPA---AEALNGVKMELIDAAFPLLKGVVATTDVVEACKDVNIAVMVGGFPRKEGM 97
++DI A EA M+L P +K V CK ++ V+ G +K G
Sbjct: 30 LVDINKAKAEGEA-----MDLAHGT-PFVKPVRIYAGDYADCKGADVVVITAGANQKPGE 83
Query: 98 ERKDVMSKNVSIYKAQASALEKHAAPNCKVLVVANPANTNALILKEFAPSI----PAKNI 153
R D++ +NV+I+K + K+ AP+ +LVV NP + +L A + P + I
Sbjct: 84 TRLDLLKRNVAIFKEIIPQILKY-APDAILLVVTNPVD----VLTYVAYKLSGLPPNRVI 138
Query: 154 TCLTRLDHNRAMGQISERLKVHVSDVKNVIIWGNHSSTQYPDVNHATV 201
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 = 40.9 bits (97), Expect = 5e-04
Identities = 37/153 (24%), Positives = 66/153 (43%), Gaps = 30/153 (19%)
Query: 77 EACKDVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEKHAAPNCKVLVVANPANT 136
CKD +I V+ G P+K G R D++ KN I K+ + K + + LV +NP +
Sbjct: 64 SDCKDADIVVITAGAPQKPGETRLDLLEKNAKIMKSIVPKI-KASGFDGIFLVASNPVDV 122
Query: 137 NALILKEFAPSIPAKNITCLTRLDHNRAMGQ------------ISERLKVHVSDVKNVII 184
++++ L+ L NR +G ++E+L V V ++
Sbjct: 123 ITYVVQK------------LSGLPKNRVIGTGTSLDTARLRRALAEKLNVDPRSVHAYVL 170
Query: 185 WGNHSSTQYPDVNHATVTTSKGEKPVREAVADD 217
G H +Q+ + TV G KP+ + + +
Sbjct: 171 -GEHGDSQFVAWSTVTV----GGKPLLDLLKEG 198
>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 = 35.4 bits (82), Expect = 0.023
Identities = 22/87 (25%), Positives = 35/87 (40%), Gaps = 22/87 (25%)
Query: 8 VLVTGAAGQIGYALVPM-IARGIMLGPDQPVILHMLDI--------EPAAEALNGVKMEL 58
+LVTG AG IG LV + RG + V++ LD+ A N +
Sbjct: 1 ILVTGGAGFIGSHLVRRLLERG-----HEVVVIDRLDVVVHLAALVGVPASWDNPDEDFE 55
Query: 59 IDAAFPLLKGVVATTDVVEACKDVNIA 85
+ VV T +++EA + +
Sbjct: 56 TN--------VVGTLNLLEAARKAGVK 74
>gnl|CDD|222146 pfam13460, NAD_binding_10, NADH(P)-binding.
Length = 182
Score = 34.2 bits (79), Expect = 0.046
Identities = 24/98 (24%), Positives = 36/98 (36%), Gaps = 16/98 (16%)
Query: 8 VLVTGAAGQIGYALVPM-IARG------------IMLGPDQPVILHMLDIEPAAEALNGV 54
+ V GA G+ G LV +ARG PV + D+ AEAL GV
Sbjct: 1 IAVIGATGKTGRRLVKELLARGHQVTALSRNPSKAPAPGVTPVQKDLFDLADLAEALAGV 60
Query: 55 KMELIDAAFPLLKGVVATTDVVEACKDVNIA--VMVGG 90
++DA +++A + V+V
Sbjct: 61 DA-VVDAFGARPDDSDGVKHLLDAAARAGVRRIVVVSA 97
>gnl|CDD|187548 cd05237, UDP_invert_4-6DH_SDR_e, UDP-Glcnac (UDP-linked
N-acetylglucosamine) inverting 4,6-dehydratase,
extended (e) SDRs. UDP-Glcnac inverting
4,6-dehydratase was identified in Helicobacter pylori
as the hexameric flaA1 gene product (FlaA1). FlaA1 is
hexameric, possesses UDP-GlcNAc-inverting
4,6-dehydratase activity, and catalyzes the first step
in the creation of a pseudaminic acid derivative in
protein glycosylation. Although this subgroup has the
NADP-binding motif characteristic of extended SDRs, its
members tend to have a Met substituted for the active
site Tyr found in most SDR families. Extended SDRs are
distinct from classical SDRs. In addition to the
Rossmann fold (alpha/beta folding pattern with a
central beta-sheet) core region typical of all SDRs,
extended SDRs have a less conserved C-terminal
extension of approximately 100 amino acids. Extended
SDRs are a diverse collection of proteins, and include
isomerases, epimerases, oxidoreductases, and lyases;
they typically have a TGXXGXXG cofactor binding motif.
SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving
as a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton
relay involving the conserved Tyr and Lys, a water
molecule stabilized by Asn, and nicotinamide. Atypical
SDRs generally lack the catalytic residues
characteristic of the SDRs, and their glycine-rich
NAD(P)-binding motif is often different from the forms
normally seen in classical or extended SDRs. Complex
(multidomain) SDRs such as ketoreductase domains of
fatty acid synthase have a GGXGXXG NAD(P)-binding motif
and an altered active site motif (YXXXN). Fungal type
ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding
motif.
Length = 287
Score = 33.7 bits (78), Expect = 0.11
Identities = 14/38 (36%), Positives = 17/38 (44%), Gaps = 6/38 (15%)
Query: 7 RVLVTGAAGQIGYALVPMIARGIMLGPDQPVILHMLDI 44
+LVTG AG IG LV I + P L + D
Sbjct: 4 TILVTGGAGSIGSELVRQILKF------GPKKLIVFDR 35
>gnl|CDD|236399 PRK09186, PRK09186, flagellin modification protein A;
Provisional.
Length = 256
Score = 33.0 bits (76), Expect = 0.16
Identities = 23/77 (29%), Positives = 32/77 (41%), Gaps = 9/77 (11%)
Query: 7 RVLVTGAAGQIGYALVPMI--ARGIMLGPDQPVILHMLDIEPAAEALNGVKMELIDAAFP 64
+L+TGA G IG ALV I A GI VI +D E E L + E
Sbjct: 6 TILITGAGGLIGSALVKAILEAGGI-------VIAADIDKEALNELLESLGKEFKSKKLS 58
Query: 65 LLKGVVATTDVVEACKD 81
L++ + + +E
Sbjct: 59 LVELDITDQESLEEFLS 75
>gnl|CDD|223528 COG0451, WcaG, Nucleoside-diphosphate-sugar epimerases [Cell
envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 314
Score = 33.0 bits (75), Expect = 0.20
Identities = 11/21 (52%), Positives = 13/21 (61%)
Query: 7 RVLVTGAAGQIGYALVPMIAR 27
R+LVTG AG 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 = 0.43
Identities = 17/63 (26%), Positives = 25/63 (39%), Gaps = 13/63 (20%)
Query: 7 RVLVTGAAGQIGYALVP----------MIARGIMLGPDQPVILHMLDIEPAAEALNGVKM 56
R+L+TG GQIG L +IA I P V+ + + L+ +
Sbjct: 1 RILITGGLGQIGSELAKLLRKRYGKDNVIASDIRKPPAHVVLSGPFEY---LDVLDFKSL 57
Query: 57 ELI 59
E I
Sbjct: 58 EEI 60
>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 = 0.45
Identities = 25/94 (26%), Positives = 37/94 (39%), Gaps = 15/94 (15%)
Query: 7 RVLVTGAAGQIGYALVPMIARGIMLGPDQPVILHMLDIEPAAEALNGVKMELIDAAFPLL 66
VLVTG +G G LV + G + DI P EAL+ + I+ L
Sbjct: 1 SVLVTGGSGFFGERLVKQLLE--RGGTY----VRSFDIAPPGEALSAWQHPNIE----FL 50
Query: 67 KGVVATTDVVE-ACKDVN----IAVMVGGFPRKE 95
KG + + VE A + A +V ++
Sbjct: 51 KGDITDRNDVEQALSGADCVFHTAAIVPLAGPRD 84
>gnl|CDD|187564 cd05254, dTDP_HR_like_SDR_e, dTDP-6-deoxy-L-lyxo-4-hexulose
reductase and related proteins, extended (e) SDRs.
dTDP-6-deoxy-L-lyxo-4-hexulose reductase, an extended
SDR, synthesizes dTDP-L-rhamnose from
alpha-D-glucose-1-phosphate, providing the precursor
of L-rhamnose, an essential cell wall component of many
pathogenic bacteria. This subgroup has the
characteristic active site tetrad and NADP-binding
motif. This subgroup also contains human MAT2B, the
regulatory subunit of methionine adenosyltransferase
(MAT); MAT catalyzes S-adenosylmethionine synthesis.
The human gene encoding MAT2B encodes two major
splicing variants which are induced in human cell liver
cancer and regulate HuR, an mRNA-binding protein which
stabilizes the mRNA of several cyclins, to affect cell
proliferation. Both MAT2B variants include this
extended SDR domain. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids. Extended SDRs are a diverse collection
of proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 280
Score = 31.1 bits (71), Expect = 0.71
Identities = 9/18 (50%), Positives = 14/18 (77%)
Query: 7 RVLVTGAAGQIGYALVPM 24
++L+TGA G +G ALV +
Sbjct: 1 KILITGATGMLGRALVRL 18
>gnl|CDD|216461 pfam01370, Epimerase, NAD dependent epimerase/dehydratase family.
This family of proteins utilise NAD as a cofactor. The
proteins in this family use nucleotide-sugar substrates
for a variety of chemical reactions.
Length = 233
Score = 30.7 bits (70), Expect = 0.76
Identities = 9/20 (45%), Positives = 12/20 (60%)
Query: 8 VLVTGAAGQIGYALVPMIAR 27
+LVTG G IG LV + +
Sbjct: 1 ILVTGGTGFIGSHLVRRLLQ 20
>gnl|CDD|180823 PRK07074, PRK07074, short chain dehydrogenase; Provisional.
Length = 257
Score = 30.9 bits (70), Expect = 0.80
Identities = 23/56 (41%), Positives = 26/56 (46%), Gaps = 9/56 (16%)
Query: 8 VLVTGAAGQIGYALVPMIARGIMLGPDQPVILHMLDIEPAAEALNGVKMELIDAAF 63
LVTGAAG IG A +AR +L LDI+ A AL L DA F
Sbjct: 5 ALVTGAAGGIGQA----LARR--FLAAGDRVL-ALDID--AAALAAFADALGDARF 51
>gnl|CDD|225990 COG3459, COG3459, Cellobiose phosphorylase [Carbohydrate transport
and metabolism].
Length = 1056
Score = 31.2 bits (71), Expect = 0.80
Identities = 25/108 (23%), Positives = 39/108 (36%), Gaps = 16/108 (14%)
Query: 223 EFITTVQQRGAAIIKARKLSSALSAASSACDHIRDWVLGTPKGTWVSMGVYSDGSY-GIP 281
F + RG +A + + A A + W G W G DG+ G P
Sbjct: 769 TFKELAKARGD-EARADTWAKHVEALREALE-TNGWD-----GEWYRRGYGDDGTPLGSP 821
Query: 282 ---EGLIYSFPVTCEKGEWSIVKGLKVDEFSRAKMDATAEELAEEKTL 326
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 = 0.89
Identities = 26/144 (18%), Positives = 47/144 (32%), Gaps = 18/144 (12%)
Query: 41 MLDIEPAAEALNGVKMELIDAAFPLLKGVVATTDVVEACKDVNIAVMVGGFPRKEGMERK 100
+LD+ A + ++ + + P V+ VVE D+N AV +
Sbjct: 34 LLDVIDALKPVDVLVFSEDEVVLPSALDVLGVEVVVETESDLNTAV-------NQAFMAP 86
Query: 101 D------VMSKNVSIYKAQASALEKHAAPNCKVLVVANPANTNALILKEFAPSIPAKNIT 154
+ + S I K + V+ TN L+L++ + +
Sbjct: 87 EEAPVIIIPSDIPLISKEVLKRFLETEGRADVVIAPGRGGGTNMLLLRKRGFRVSYHFGS 146
Query: 155 CLTRLDHNRAMGQISERLKVHVSD 178
L+ R G LK + D
Sbjct: 147 FFKHLEEARKRG-----LKAKIYD 165
>gnl|CDD|200085 TIGR01214, rmlD, dTDP-4-dehydrorhamnose reductase. This enzyme
catalyzes the last of 4 steps in making dTDP-rhamnose,
a precursor of LPS core antigen, O-antigen, etc [Cell
envelope, Biosynthesis and degradation of surface
polysaccharides and lipopolysaccharides].
Length = 287
Score = 30.8 bits (70), Expect = 0.91
Identities = 24/84 (28%), Positives = 33/84 (39%), Gaps = 10/84 (11%)
Query: 7 RVLVTGAAGQIGYALVPMIARGIMLGPDQPVILHM-LDIEPAAEALNGVKMELIDAAFP- 64
R+L+TGA GQ+G LV ++ G + LD+ L+ A P
Sbjct: 1 RILITGANGQLGRELVQQLSPE---GRVVVALTRSQLDLTDPEAL-----ERLLRAIRPD 52
Query: 65 LLKGVVATTDVVEACKDVNIAVMV 88
+ A TDV A D A V
Sbjct: 53 AVVNTAAYTDVDGAESDPEKAFAV 76
>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 = 30.1 bits (68), Expect = 1.4
Identities = 18/83 (21%), Positives = 29/83 (34%), Gaps = 9/83 (10%)
Query: 8 VLVTGAAGQIGYALVPMIARGIMLGPDQPVILHMLDIEPAAEALNGVKMELIDAAFPLLK 67
LVTG A IG A+ +A + + + DI+P + A +
Sbjct: 4 ALVTGGASGIGLAIAKRLAA-------EGAAVVVADIDPEIAEKVAEAAQGGPRALGVQC 56
Query: 68 GVVATTDVVEACKDVNIAVMVGG 90
V + V A + + GG
Sbjct: 57 DVTSEAQVQSAFE--QAVLEFGG 77
>gnl|CDD|223513 COG0436, COG0436, Aspartate/tyrosine/aromatic aminotransferase
[Amino acid transport and metabolism].
Length = 393
Score = 29.9 bits (68), Expect = 2.0
Identities = 11/36 (30%), Positives = 17/36 (47%), Gaps = 1/36 (2%)
Query: 110 YKAQASALEKHAAPNCKVLVVANPAN-TNALILKEF 144
+K LE P K +++ +P N T A+ KE
Sbjct: 149 FKPDLEDLEAAITPKTKAIILNSPNNPTGAVYSKEE 184
>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 = 2.3
Identities = 31/134 (23%), Positives = 50/134 (37%), Gaps = 29/134 (21%)
Query: 39 LHMLDIEPAAEALNGVKME-LIDAAFPLLKGVVATTDVVEACKDVNI---AVMVGGFPRK 94
L + DI+ + + + L++ A +K V ATTD EA + + + VGG +
Sbjct: 35 LALYDIDEERLKIIAILAKKLVEEAGAPVK-VEATTDRREALEGADFVITQIRVGGLEAR 93
Query: 95 EGMERKDVMSKNVSIYKAQ--------------------ASALEKHAAPNCKVLVVANPA 134
E ER + +Y + A +EK PN +L NPA
Sbjct: 94 EKDER---IPLKHGLYGQETNGPGGIFYGLRTIPVILDIAKDMEKVC-PNAWMLNYTNPA 149
Query: 135 NTNALILKEFAPSI 148
++ P I
Sbjct: 150 AIVTEAVRRLYPKI 163
>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 = 2.4
Identities = 11/51 (21%), Positives = 23/51 (45%), Gaps = 4/51 (7%)
Query: 69 VVATTDVVEACKDVNIAVMVGGFPR---KEGMERKDVMSKNVSIYKAQASA 116
V+ ++V + +A ++G FP + ++ K ++ SI SA
Sbjct: 139 KVSPKELVSELLNKPVAFVIGAFPHGDFSDEVDYKKA-DESYSISNYPLSA 188
>gnl|CDD|224207 COG1288, COG1288, Predicted membrane protein [Function unknown].
Length = 481
Score = 29.6 bits (67), Expect = 2.6
Identities = 16/44 (36%), Positives = 25/44 (56%), Gaps = 1/44 (2%)
Query: 10 VTGAAGQIGYALVPMIARGIMLGPDQPVILHMLDIEPAAEALNG 53
+ GA+ +G AL+ +ARGI L D +IL + + A L+G
Sbjct: 330 IEGASDLLGVALIIGLARGINLIMDDGMILDTI-LNYLASLLSG 372
>gnl|CDD|236207 PRK08261, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 450
Score = 29.4 bits (67), Expect = 2.6
Identities = 22/59 (37%), Positives = 28/59 (47%), Gaps = 7/59 (11%)
Query: 7 RVLVTGAAGQIGYALVPMIARGIMLGPDQPVILHMLDIEPAAEALNGVKMELIDAAFPL 65
LVTGAA IG A+ ++AR G V+ LD+ A EAL V + A L
Sbjct: 212 VALVTGAARGIGAAIAEVLARD---GAH--VVC--LDVPAAGEALAAVANRVGGTALAL 263
>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 = 29.2 bits (66), Expect = 2.9
Identities = 13/33 (39%), Positives = 18/33 (54%), Gaps = 4/33 (12%)
Query: 8 VLVTGAAGQIGYALVPMI----ARGIMLGPDQP 36
+L+TGAAG IG A + AR I+ + P
Sbjct: 5 ILITGAAGLIGKAFCKALLSAGARLILADINAP 37
>gnl|CDD|224011 COG1086, COG1086, Predicted nucleoside-diphosphate sugar epimerases
[Cell envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 588
Score = 29.5 bits (67), Expect = 2.9
Identities = 27/121 (22%), Positives = 42/121 (34%), Gaps = 39/121 (32%)
Query: 7 RVLVTGAAGQIGYALVPMIARG-----IMLGPDQ--------------------PVILHM 41
VLVTG G IG L I + I+ D+ I +
Sbjct: 252 TVLVTGGGGSIGSELCRQILKFNPKEIILFSRDEYKLYLIDMELREKFPELKLRFYIGDV 311
Query: 42 LDIEPAAEALNGVKMELI--DAAF---PLLK---------GVVATTDVVEACKDVNIAVM 87
D + A+ G K++++ AA PL++ V+ T +V EA +
Sbjct: 312 RDRDRVERAMEGHKVDIVFHAAALKHVPLVEYNPEEAIKTNVLGTENVAEAAIKNGVKKF 371
Query: 88 V 88
V
Sbjct: 372 V 372
>gnl|CDD|217636 pfam03606, DcuC, C4-dicarboxylate anaerobic carrier.
Length = 456
Score = 29.2 bits (66), Expect = 3.1
Identities = 10/26 (38%), Positives = 16/26 (61%)
Query: 6 LRVLVTGAAGQIGYALVPMIARGIML 31
+ GAA +G+ALV +ARG+ +
Sbjct: 302 VEAFYEGAADLLGFALVVGLARGVGV 327
>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 = 28.9 bits (65), Expect = 3.5
Identities = 25/100 (25%), Positives = 37/100 (37%), Gaps = 27/100 (27%)
Query: 8 VLVTGAAGQIGYALVP-------------MIARGIMLGPDQPVILHMLDIEPAAEALNGV 54
+LVTGAAG +G L + R P + + + DI A A
Sbjct: 1 ILVTGAAGGLGRLLARRLAASPRVIGVDGLDRRRPPGSPPKVEYVRL-DIRDPAAADVFR 59
Query: 55 KME---LIDAAF---PLLKG-------VVATTDVVEACKD 81
+ E ++ AF P G V T +V++AC
Sbjct: 60 EREADAVVHLAFILDPPRDGAERHRINVDGTQNVLDACAA 99
>gnl|CDD|168574 PRK06484, PRK06484, short chain dehydrogenase; Validated.
Length = 520
Score = 29.0 bits (65), Expect = 3.5
Identities = 24/93 (25%), Positives = 34/93 (36%), Gaps = 12/93 (12%)
Query: 8 VLVTGAAGQIGYALVPMIARG--IMLGPDQPVILHMLDIEPAAEALNGVKMEL-----ID 60
VLVTGAAG IG A AR ++ D+ V + + + M++ I
Sbjct: 8 VLVTGAAGGIGRAACQRFARAGDQVVVADRNVERARERADSLGPDHHALAMDVSDEAQIR 67
Query: 61 AAFPLLKGVVATTDVVEACKDVNIAVMVGGFPR 93
F L DV+ VN A +
Sbjct: 68 EGFEQLHREFGRIDVL-----VNNAGVTDPTMT 95
>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 = 28.8 bits (65), Expect = 3.6
Identities = 11/25 (44%), Positives = 14/25 (56%)
Query: 64 PLLKGVVATTDVVEACKDVNIAVMV 88
L +VA D+VEA K +I V V
Sbjct: 65 KLPANLVAVPDLVEAAKGADILVFV 89
>gnl|CDD|218026 pfam04321, RmlD_sub_bind, RmlD substrate binding domain.
L-rhamnose is a saccharide required for the virulence
of some bacteria. Its precursor, dTDP-L-rhamnose, is
synthesised by four different enzymes the final one of
which is RmlD. The RmlD substrate binding domain is
responsible for binding a sugar nucleotide.
Length = 284
Score = 28.7 bits (65), Expect = 3.7
Identities = 9/15 (60%), Positives = 11/15 (73%)
Query: 8 VLVTGAAGQIGYALV 22
+LVTGA GQ+G L
Sbjct: 1 ILVTGANGQLGRELT 15
>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 = 28.6 bits (65), Expect = 3.9
Identities = 10/20 (50%), Positives = 11/20 (55%)
Query: 8 VLVTGAAGQIGYALVPMIAR 27
VLVTG G IG L I +
Sbjct: 1 VLVTGGGGSIGSELCRQILK 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 = 28.8 bits (65), Expect = 4.0
Identities = 27/107 (25%), Positives = 42/107 (39%), Gaps = 26/107 (24%)
Query: 8 VLVTGAAGQIGYALVP-MIARGI------------MLGPDQPVILH---MLDIEPAAEAL 51
+LVTGA G +G LV ++A+G +L PV + + D A A+
Sbjct: 1 ILVTGATGFLGSNLVRALLAQGYRVRALVRSGSDAVLLDGLPVEVVEGDLTDAASLAAAM 60
Query: 52 NGVKMELIDAAFPLLKG----------VVATTDVVEACKDVNIAVMV 88
G AAF L V T +V++A + + +V
Sbjct: 61 KGCDRVFHLAAFTSLWAKDRKELYRTNVEGTRNVLDAALEAGVRRVV 107
>gnl|CDD|223774 COG0702, COG0702, Predicted nucleoside-diphosphate-sugar
epimerases [Cell envelope biogenesis, outer membrane /
Carbohydrate transport and metabolism].
Length = 275
Score = 28.3 bits (63), Expect = 5.0
Identities = 12/23 (52%), Positives = 17/23 (73%), Gaps = 1/23 (4%)
Query: 7 RVLVTGAAGQIGYALVPM-IARG 28
++LVTGA G +G A+V +ARG
Sbjct: 2 KILVTGATGFVGGAVVRELLARG 24
>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 = 5.1
Identities = 24/91 (26%), Positives = 35/91 (38%), Gaps = 24/91 (26%)
Query: 7 RVLVTGAAGQIGYALVPM-IARGIM---------------LGPDQPVILHMLDIEPAAE- 49
VL+ GAAG +G V + ARG LG D+ + D E AA
Sbjct: 147 TVLIHGAAGGVGSFAVQLAKARGARVIATASAANADFLRSLGADEVIDYTKGDFERAAAP 206
Query: 50 -----ALNGVKMELIDAAFPLLK--GVVATT 73
L+ V E + + L+K G + +
Sbjct: 207 GGVDAVLDTVGGETLARSLALVKPGGRLVSI 237
>gnl|CDD|236389 PRK09134, PRK09134, short chain dehydrogenase; Provisional.
Length = 258
Score = 28.4 bits (64), Expect = 5.4
Identities = 11/27 (40%), Positives = 14/27 (51%)
Query: 1 MAKNPLRVLVTGAAGQIGYALVPMIAR 27
P LVTGAA +IG A+ +A
Sbjct: 5 SMAAPRAALVTGAARRIGRAIALDLAA 31
>gnl|CDD|236612 PRK09685, PRK09685, DNA-binding transcriptional activator FeaR;
Provisional.
Length = 302
Score = 28.1 bits (63), Expect = 5.8
Identities = 9/24 (37%), Positives = 12/24 (50%)
Query: 149 PAKNITCLTRLDHNRAMGQISERL 172
P + C RL + M Q+S RL
Sbjct: 132 PGQKPACAGRLSASLPMVQLSHRL 155
>gnl|CDD|237972 PRK15483, PRK15483, type III restriction-modification system StyLTI
enzyme res; Provisional.
Length = 986
Score = 28.5 bits (64), Expect = 5.8
Identities = 4/38 (10%), Positives = 13/38 (34%)
Query: 191 TQYPDVNHATVTTSKGEKPVREAVADDNWLNTEFITTV 228
Q P + ++ V + + +E++ +
Sbjct: 718 RQIPTQVQQRLVSNDDNGRVEVSQREGELAASEYLNGM 755
>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 = 26.4 bits (59), Expect = 5.9
Identities = 12/44 (27%), Positives = 21/44 (47%), Gaps = 10/44 (22%)
Query: 17 IGYALVPMIAR----------GIMLGPDQPVILHMLDIEPAAEA 50
+G L P+I G++L D +LH+L+ + A +A
Sbjct: 20 LGERLYPLIQAMHPELAGKITGMLLEMDNSELLHLLESDEALKA 63
>gnl|CDD|187574 cd05264, UDP_G4E_5_SDR_e, UDP-glucose 4-epimerase (G4E), subgroup
5, extended (e) SDRs. This subgroup partially conserves
the characteristic active site tetrad and NAD-binding
motif of the extended SDRs, and has been identified as
possible UDP-glucose 4-epimerase (aka UDP-galactose
4-epimerase), a homodimeric member of the extended SDR
family. UDP-glucose 4-epimerase catalyzes the
NAD-dependent conversion of UDP-galactose to
UDP-glucose, the final step in Leloir galactose
synthesis. Extended SDRs are distinct from classical
SDRs. In addition to the Rossmann fold (alpha/beta
folding pattern with a central beta-sheet) core region
typical of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 300
Score = 28.1 bits (63), Expect = 6.2
Identities = 45/228 (19%), Positives = 73/228 (32%), Gaps = 60/228 (26%)
Query: 7 RVLVTGAAGQIGYALVP-MIARGIML--------GPDQP---VILHMLDIEPAA---EAL 51
RVL+ G G IG LV ++ G + + P V D E A AL
Sbjct: 1 RVLIVGGNGFIGSHLVDALLEEGPQVRVFDRSIPPYELPLGGVDYIKGDYENRADLESAL 60
Query: 52 NGVK--MELIDAAFP----------LLKGVVATTDVVEACKDVNIAVMV----GG----- 90
G+ + L P + V T ++EAC I ++ GG
Sbjct: 61 VGIDTVIHLASTTNPATSNKNPILDIQTNVAPTVQLLEACAAAGIGKIIFASSGGTVYGV 120
Query: 91 ---FPRKEGMERKDVMSKNVSIYKAQASALEK-------HAAPNCKVLVVANPANTNALI 140
P E + +S Y A+EK + VL ++NP
Sbjct: 121 PEQLPISE-----SDPTLPISSYGISKLAIEKYLRLYQYLYGLDYTVLRISNPYGPGQRP 175
Query: 141 LKEFAPSIPAKNITCLTRLDHNRAMGQI----SERLKVHVSDVKNVII 184
+ IP L ++ + S R +++ D+ ++
Sbjct: 176 DGKQG-VIP----IALNKILRGEPIEIWGDGESIRDYIYIDDLVEALM 218
>gnl|CDD|224670 COG1756, Mra1, Uncharacterized conserved protein [Function
unknown].
Length = 223
Score = 28.1 bits (63), Expect = 6.3
Identities = 13/36 (36%), Positives = 20/36 (55%)
Query: 81 DVNIAVMVGGFPRKEGMERKDVMSKNVSIYKAQASA 116
IAV++GGFP + E + +++ SIY SA
Sbjct: 170 LKGIAVIIGGFPHGDFREETEFVAEKYSIYDEPLSA 205
>gnl|CDD|177856 PLN02206, PLN02206, UDP-glucuronate decarboxylase.
Length = 442
Score = 28.4 bits (63), Expect = 6.5
Identities = 14/24 (58%), Positives = 18/24 (75%), Gaps = 1/24 (4%)
Query: 6 LRVLVTGAAGQIGYALVP-MIARG 28
LRV+VTG AG +G LV ++ARG
Sbjct: 120 LRVVVTGGAGFVGSHLVDRLMARG 143
>gnl|CDD|216283 pfam01073, 3Beta_HSD, 3-beta hydroxysteroid
dehydrogenase/isomerase family. The enzyme 3
beta-hydroxysteroid dehydrogenase/5-ene-4-ene isomerase
(3 beta-HSD) catalyzes the oxidation and isomerisation
of 5-ene-3 beta-hydroxypregnene and
5-ene-hydroxyandrostene steroid precursors into the
corresponding 4-ene-ketosteroids necessary for the
formation of all classes of steroid hormones.
Length = 280
Score = 28.1 bits (63), Expect = 6.6
Identities = 24/99 (24%), Positives = 42/99 (42%), Gaps = 18/99 (18%)
Query: 9 LVTGAAGQIGYALVPMIARGIMLGPDQPVILHMLDIEPAAEALNGV-KMELIDAAFPLLK 67
LVTG G +G +V ++ R G Q V + D+ + E L K+++I ++
Sbjct: 1 LVTGGGGFLGRHIVRLLLR---EGELQEV--RVFDLRFSPELLEDFSKLQVITY----IE 51
Query: 68 G-VVATTDVVEACKDVNI------AVMVGG-FPRKEGME 98
G V D+ A + ++ + V G R M+
Sbjct: 52 GDVTDKQDLRRALQGSDVVIHTAAIIDVFGKAYRDTIMK 90
>gnl|CDD|187566 cd05256, UDP_AE_SDR_e, UDP-N-acetylglucosamine 4-epimerase,
extended (e) SDRs. This subgroup contains
UDP-N-acetylglucosamine 4-epimerase of Pseudomonas
aeruginosa, WbpP, an extended SDR, that catalyzes the
NAD+ dependent conversion of UDP-GlcNAc and UDPGalNA to
UDP-Glc and UDP-Gal. This subgroup has the
characteristic active site tetrad and NAD-binding motif
of the extended SDRs. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids. Extended SDRs are a diverse collection
of proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 304
Score = 28.0 bits (63), Expect = 7.1
Identities = 12/16 (75%), Positives = 12/16 (75%)
Query: 7 RVLVTGAAGQIGYALV 22
RVLVTG AG IG LV
Sbjct: 1 RVLVTGGAGFIGSHLV 16
>gnl|CDD|187632 cd05374, 17beta-HSD-like_SDR_c, 17beta hydroxysteroid
dehydrogenase-like, classical (c) SDRs.
17beta-hydroxysteroid dehydrogenases are a group of
isozymes that catalyze activation and inactivation of
estrogen and androgens. SDRs are a functionally diverse
family of oxidoreductases that have a single domain
with a structurally conserved Rossmann fold (alpha/beta
folding pattern with a central beta-sheet), an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRs are
approximately 350 residues. Sequence identity between
different SDR enzymes are typically in the 15-30%
range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes catalyze a
wide range of activities including the metabolism of
steroids, cofactors, carbohydrates, lipids, aromatic
compounds, and amino acids, and act in redox sensing.
Classical SDRs have an TGXXX[AG]XG cofactor binding
motif and a YXXXK active site motif, with the Tyr
residue of the active site motif serving as a critical
catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 248
Score = 28.0 bits (63), Expect = 7.1
Identities = 9/20 (45%), Positives = 12/20 (60%)
Query: 8 VLVTGAAGQIGYALVPMIAR 27
VL+TG + IG AL +A
Sbjct: 3 VLITGCSSGIGLALALALAA 22
>gnl|CDD|235596 PRK05764, PRK05764, aspartate aminotransferase; Provisional.
Length = 393
Score = 27.8 bits (63), Expect = 7.7
Identities = 11/35 (31%), Positives = 17/35 (48%), Gaps = 1/35 (2%)
Query: 110 YKAQASALEKHAAPNCKVLVVANPAN-TNALILKE 143
+K LE P K L++ +P+N T A+ E
Sbjct: 150 FKLTVEQLEAAITPKTKALILNSPSNPTGAVYSPE 184
>gnl|CDD|187568 cd05258, CDP_TE_SDR_e, CDP-tyvelose 2-epimerase, extended (e)
SDRs. CDP-tyvelose 2-epimerase is a tetrameric SDR
that catalyzes the conversion of CDP-D-paratose to
CDP-D-tyvelose, the last step in tyvelose biosynthesis.
This subgroup is a member of the extended SDR
subfamily, with a characteristic active site tetrad and
NAD-binding motif. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids. Extended SDRs are a diverse collection
of proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 337
Score = 28.0 bits (63), Expect = 7.8
Identities = 10/21 (47%), Positives = 12/21 (57%)
Query: 7 RVLVTGAAGQIGYALVPMIAR 27
RVL+TG AG IG L +
Sbjct: 2 RVLITGGAGFIGSNLARFFLK 22
>gnl|CDD|223377 COG0300, DltE, Short-chain dehydrogenases of various substrate
specificities [General function prediction only].
Length = 265
Score = 27.6 bits (62), Expect = 8.0
Identities = 9/27 (33%), Positives = 12/27 (44%)
Query: 1 MAKNPLRVLVTGAAGQIGYALVPMIAR 27
L+TGA+ IG L +AR
Sbjct: 2 GPMKGKTALITGASSGIGAELAKQLAR 28
>gnl|CDD|218112 pfam04497, Pox_E2-like, Poxviridae protein. This family of
proteins is restricted to Poxviridae. It contains a
number of differently named uncharacterized proteins.
Length = 727
Score = 28.1 bits (63), Expect = 8.1
Identities = 11/53 (20%), Positives = 17/53 (32%), Gaps = 1/53 (1%)
Query: 204 SKGEKPVREAVADDNWLNTEFITTVQQRGAAI-IKARKLSSALSAASSACDHI 255
KG P+ + + W N E I K +KL S + +
Sbjct: 381 KKGADPLTDYLFSTFWFNPELIRLFLLSYGFCKTKMKKLLFEYPLTSESTTRL 433
>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 = 9.0
Identities = 13/35 (37%), Positives = 18/35 (51%), Gaps = 6/35 (17%)
Query: 57 ELIDAAFPLLK--GVVAT-TDVV--EACKDVNIAV 86
E++ P LK GV+AT + V A K+ I V
Sbjct: 58 EVLAQL-PNLKLIGVLATGYNNVDLAAAKERGITV 91
>gnl|CDD|240373 PTZ00345, PTZ00345, glycerol-3-phosphate dehydrogenase;
Provisional.
Length = 365
Score = 27.7 bits (62), Expect = 9.1
Identities = 22/98 (22%), Positives = 42/98 (42%), Gaps = 18/98 (18%)
Query: 3 KNPLRVLVTGAAGQIGYALVPMIARGIMLGP--DQPVILHMLDIEPAAEALNGVKM-ELI 59
PL+V V G+ G G A+ ++ V + +L+ E + G K+ ++I
Sbjct: 9 CGPLKVSVIGS-GNWGSAISKVVGENTQRNYIFHNEVRMWVLE-----EIVEGEKLSDII 62
Query: 60 DA---------AFPLLKGVVATTDVVEACKDVNIAVMV 88
+ L +VA +D+ EA +D ++ + V
Sbjct: 63 NTKHENVKYLPGIKLPDNIVAVSDLKEAVEDADLLIFV 100
>gnl|CDD|224016 COG1091, RfbD, dTDP-4-dehydrorhamnose reductase [Cell envelope
biogenesis, outer membrane].
Length = 281
Score = 27.6 bits (62), Expect = 9.3
Identities = 8/17 (47%), Positives = 13/17 (76%)
Query: 6 LRVLVTGAAGQIGYALV 22
+++L+TGA GQ+G L
Sbjct: 1 MKILITGANGQLGTELR 17
>gnl|CDD|201664 pfam01210, NAD_Gly3P_dh_N, NAD-dependent glycerol-3-phosphate
dehydrogenase N-terminus. NAD-dependent
glycerol-3-phosphate dehydrogenase (GPDH) catalyzes the
interconversion of dihydroxyacetone phosphate and
L-glycerol-3-phosphate. This family represents the
N-terminal NAD-binding domain.
Length = 157
Score = 26.8 bits (60), Expect = 9.7
Identities = 24/78 (30%), Positives = 31/78 (39%), Gaps = 11/78 (14%)
Query: 14 AGQIGYALVPMIARGIMLGPDQPVILHMLDIEPAAEALNGV---KMELIDAAFPLLKGVV 70
AG G AL ++AR V L D E E +N L P +
Sbjct: 7 AGSWGTALAKVLARN-----GHEVRLWGRD-EELIEEINTTRENVKYLPGIKLP--DNLR 58
Query: 71 ATTDVVEACKDVNIAVMV 88
ATTD+ EA K +I V+
Sbjct: 59 ATTDLEEAIKGADIIVLA 76
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
0.316 0.131 0.383
Gapped
Lambda K H
0.267 0.0728 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,601,958
Number of extensions: 1573852
Number of successful extensions: 1826
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1757
Number of HSP's successfully gapped: 125
Length of query: 332
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 235
Effective length of database: 6,635,264
Effective search space: 1559287040
Effective search space used: 1559287040
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 59 (26.5 bits)