RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9582
(329 letters)
>gnl|CDD|235468 PRK05442, PRK05442, malate dehydrogenase; Provisional.
Length = 326
Score = 535 bits (1381), Expect = 0.0
Identities = 188/327 (57%), Positives = 256/327 (78%), Gaps = 5/327 (1%)
Query: 3 KKPVRISITGAAGQIGYNIIFRIANGDLLGKDQPIILQLLEASNKKSQKAIKGVIMEIED 62
K PVR+++TGAAGQIGY+++FRIA+GD+LGKDQP+ILQLLE + KA++GV+ME++D
Sbjct: 2 KAPVRVAVTGAAGQIGYSLLFRIASGDMLGKDQPVILQLLEIP--PALKALEGVVMELDD 59
Query: 63 CIFPLLVDVSVHENPITAFKDANIAILIGSFPRKSNMERSELLAINSSIFIEQGKALNSV 122
C FPLL V + ++P AFKDA++A+L+G+ PR MER +LL N +IF QGKALN V
Sbjct: 60 CAFPLLAGVVITDDPNVAFKDADVALLVGARPRGPGMERKDLLEANGAIFTAQGKALNEV 119
Query: 123 ASRDVKVLVVGNPVNTNTYITMKSAPDLSYKNFTAMLRLDHNRAIAKLASKLNEPVSSIK 182
A+RDVKVLVVGNP NTN I MK+APDL +NFTAM RLDHNRA+++LA+K PV+ IK
Sbjct: 120 AARDVKVLVVGNPANTNALIAMKNAPDLPAENFTAMTRLDHNRALSQLAAKAGVPVADIK 179
Query: 183 KVFVWGNHSLSMYPDYRYATVNGVLIRDMINNNSFWNKNVFLPAISRRGEEIISIRGASS 242
K+ VWGNHS + YPD+R+AT++G ++IN+ + W ++ F+P + +RG II RGASS
Sbjct: 180 KMTVWGNHSATQYPDFRHATIDGKPAAEVINDQA-WLEDTFIPTVQKRGAAIIEARGASS 238
Query: 243 AASAASAAIDHIKDWIFGTEN--WVTMGIPSDGSYNVPKDIIFGFPVKIKNSKYKIIQNL 300
AASAA+AAIDH++DW+ GT WV+MG+PSDGSY +P+ +IFGFPV +N +Y+I+Q L
Sbjct: 239 AASAANAAIDHVRDWVLGTPEGDWVSMGVPSDGSYGIPEGLIFGFPVTCENGEYEIVQGL 298
Query: 301 EIDKFSRKKINLSIEELKNEILSISHL 327
EID FSR+KI+ ++ EL+ E ++ HL
Sbjct: 299 EIDDFSREKIDATLAELEEERDAVKHL 325
>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 = 492 bits (1269), Expect = e-177
Identities = 175/325 (53%), Positives = 241/325 (74%), Gaps = 5/325 (1%)
Query: 4 KPVRISITGAAGQIGYNIIFRIANGDLLGKDQPIILQLLEASNKKSQKAIKGVIMEIEDC 63
KPVR+++TGAAGQIGY+++FRIA+G++ G DQP+ILQLLE + KA++GV ME+EDC
Sbjct: 1 KPVRVAVTGAAGQIGYSLLFRIASGEMFGPDQPVILQLLELPQ--ALKALEGVAMELEDC 58
Query: 64 IFPLLVDVSVHENPITAFKDANIAILIGSFPRKSNMERSELLAINSSIFIEQGKALNSVA 123
FPLL ++ + ++P AFKDA+ A+L+G+ PR MER++LL N IF QGKALN VA
Sbjct: 59 AFPLLAEIVITDDPNVAFKDADWALLVGAKPRGPGMERADLLKANGKIFTAQGKALNDVA 118
Query: 124 SRDVKVLVVGNPVNTNTYITMKSAPDLSYKNFTAMLRLDHNRAIAKLASKLNEPVSSIKK 183
SRDVKVLVVGNP NTN I MK+APD+ NFTAM RLDHNRA ++LA K PV+ +K
Sbjct: 119 SRDVKVLVVGNPCNTNALIAMKNAPDIPPDNFTAMTRLDHNRAKSQLAKKAGVPVTDVKN 178
Query: 184 VFVWGNHSLSMYPDYRYATVNGVLIRDMINNNSFWNKNVFLPAISRRGEEIISIRGASSA 243
+ +WGNHS + YPD+ AT+ G ++IN+ + W ++ F+P + +RG II RGASSA
Sbjct: 179 MVIWGNHSPTQYPDFTNATIGGKPAAEVINDRA-WLEDEFIPTVQKRGAAIIKARGASSA 237
Query: 244 ASAASAAIDHIKDWIFGTE--NWVTMGIPSDGSYNVPKDIIFGFPVKIKNSKYKIIQNLE 301
ASAA+AAIDH++DW+ GT +W +M +PSDGSY +P+ +IF FPV+ K Y+I++ LE
Sbjct: 238 ASAANAAIDHMRDWVLGTPEGDWFSMAVPSDGSYGIPEGLIFSFPVRSKGGGYEIVEGLE 297
Query: 302 IDKFSRKKINLSIEELKNEILSISH 326
ID F+R+KI+ ++ EL E ++ H
Sbjct: 298 IDDFAREKIDATLAELLEEREAVKH 322
>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 = 439 bits (1132), Expect = e-156
Identities = 161/322 (50%), Positives = 217/322 (67%), Gaps = 9/322 (2%)
Query: 5 PVRISITGAAGQIGYNIIFRIANGDLLGKDQPIILQLLEASNKKSQKAIKGVIMEIEDCI 64
P+R+ +TGAAGQI Y+++ IA GD+ G DQP+IL LL+ KA++GV+ME++DC
Sbjct: 2 PIRVLVTGAAGQIAYSLLPMIAKGDVFGPDQPVILHLLDIPPAL--KALEGVVMELQDCA 59
Query: 65 FPLLVDVSVHENPITAFKDANIAILIGSFPRKSNMERSELLAINSSIFIEQGKALNSVAS 124
FPLL V +P AFKD ++AIL+G+ PRK MER +LL N IF EQG+AL+ A
Sbjct: 60 FPLLKSVVATTDPEEAFKDVDVAILVGAMPRKEGMERKDLLKANVKIFKEQGEALDKYAK 119
Query: 125 RDVKVLVVGNPVNTNTYITMKSAPDLSYKNFTAMLRLDHNRAIAKLASKLNEPVSSIKKV 184
++VKVLVVGNP NTN I +K AP + +NFTA+ RLDHNRA +++A KL PVS +K V
Sbjct: 120 KNVKVLVVGNPANTNALILLKYAPSIPKENFTALTRLDHNRAKSQIALKLGVPVSDVKNV 179
Query: 185 FVWGNHSLSMYPDYRYATVN----GVLIRDMINNNSFWNKNVFLPAISRRGEEIISIRGA 240
+WGNHS + YPD +ATV G R+ + +++ W F+ + +RG +I R
Sbjct: 180 IIWGNHSSTQYPDVNHATVELNGKGKPAREAVKDDA-WLNGEFISTVQKRGAAVIKARKL 238
Query: 241 SSAASAASAAIDHIKDWIFGTEN--WVTMGIPSDGSYNVPKDIIFGFPVKIKNSKYKIIQ 298
SSA SAA A DH+ DW FGT +V+MG+ SDGSY VP+ +IF FPV KN K+KI+Q
Sbjct: 239 SSAMSAAKAICDHVHDWWFGTPEGEFVSMGVYSDGSYGVPEGLIFSFPVTCKNGKWKIVQ 298
Query: 299 NLEIDKFSRKKINLSIEELKNE 320
L ID FSR+KI+ + +EL E
Sbjct: 299 GLSIDDFSREKIDATAKELVEE 320
>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 = 435 bits (1121), Expect = e-154
Identities = 171/322 (53%), Positives = 237/322 (73%), Gaps = 7/322 (2%)
Query: 3 KKPVRISITGAAGQIGYNIIFRIANGDLLGKDQPIILQLLEASNKKSQKAIKGVIMEIED 62
KKPVR+++TGAAGQIGY+++FRIA+G+L GKDQP++L LL+ + KA++GV ME+ED
Sbjct: 1 KKPVRVAVTGAAGQIGYSLLFRIASGELFGKDQPVVLHLLDI--PPAMKALEGVAMELED 58
Query: 63 CIFPLLVDVSVHENPITAFKDANIAILIGSFPRKSNMERSELLAINSSIFIEQGKALNSV 122
C FPLL V +P AFKD + A+L+G+FPRK MER++LL+ N IF EQGKALN V
Sbjct: 59 CAFPLLAGVVATTDPEEAFKDVDAALLVGAFPRKPGMERADLLSKNGKIFKEQGKALNKV 118
Query: 123 ASRDVKVLVVGNPVNTNTYITMKSAPDLSYKNFTAMLRLDHNRAIAKLASKLNEPVSSIK 182
A +DVKVLVVGNP NTN I K+APD+ KNF+AM RLDHNRA +LA+K PVS +K
Sbjct: 119 AKKDVKVLVVGNPANTNALIASKNAPDIPPKNFSAMTRLDHNRAKYQLAAKAGVPVSDVK 178
Query: 183 KVFVWGNHSLSMYPDYRYATVNGVLIRDMINNNSFWNKNVFLPAISRRGEEIISIRGASS 242
V +WGNHS + PD+ +ATV+G ++++I ++ W + F+P + +RG +I RGASS
Sbjct: 179 NVIIWGNHSNTQVPDFTHATVDGRPVKEVIKDDK-WLEGEFIPTVQQRGAAVIEARGASS 237
Query: 243 AASAASAAIDHIKDWIFGT--ENWVTMGIPSDG-SYNVPKDIIFGFPVKIK-NSKYKIIQ 298
AASAA+AAIDH++DW+ GT +WV+MG+ SDG Y +P+ IIF FPV K + +++I++
Sbjct: 238 AASAANAAIDHVRDWVTGTPEGDWVSMGVYSDGNPYGIPEGIIFSFPVTCKGDGEWEIVE 297
Query: 299 NLEIDKFSRKKINLSIEELKNE 320
L +D F R K++ + +EL E
Sbjct: 298 GLPLDDFVRGKLDATEDELLEE 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 = 407 bits (1049), Expect = e-143
Identities = 157/321 (48%), Positives = 215/321 (66%), Gaps = 9/321 (2%)
Query: 6 VRISITGAAGQIGYNIIFRIANGDLLGKDQPIILQLLEASNKKSQKAIKGVIMEIEDCIF 65
+ + ITGAAGQIGYN++F IA+G+L G DQP+IL LL+ + KA++GV+ME++DC F
Sbjct: 1 LHVLITGAAGQIGYNLLFLIASGELFGDDQPVILHLLD--IPPAMKALEGVVMELQDCAF 58
Query: 66 PLLVDVSVHENPITAFKDANIAILIGSFPRKSNMERSELLAINSSIFIEQGKALNSVASR 125
PLL V + +P AFKD ++AIL+G+FPRK MER++LL N+ IF EQG+ALN VA
Sbjct: 59 PLLKGVVITTDPEEAFKDVDVAILVGAFPRKPGMERADLLRKNAKIFKEQGEALNKVAKP 118
Query: 126 DVKVLVVGNPVNTNTYITMKSAPDLSYKNFTAMLRLDHNRAIAKLASKLNEPVSSIKKVF 185
VKVLVVGNP NTN I +K+AP+L KNFTA+ RLDHNRA A++A KL VS +K V
Sbjct: 119 TVKVLVVGNPANTNALIALKNAPNLPPKNFTALTRLDHNRAKAQVARKLGVRVSDVKNVI 178
Query: 186 VWGNHSLSMYPDYRYATV---NGVLIRDMINNNSFWNKNVFLPAISRRGEEIISIRGASS 242
+WGNHS + PD A V G + + + N + F+ + +RG II RGASS
Sbjct: 179 IWGNHSNTQVPDLSNAVVYGPGGTEWVLDLLDEEWLN-DEFVKTVQKRGAAIIKKRGASS 237
Query: 243 AASAASAAIDHIKDWIFGTE--NWVTMGIPSDG-SYNVPKDIIFGFPVKIKNSKYKIIQN 299
AASAA A DH+KDW+FGT V+MG+ S G Y +P I+F FP K + ++++
Sbjct: 238 AASAAKAIADHVKDWLFGTPPGEIVSMGVYSPGNPYGIPPGIVFSFPCTCKGGGWHVVED 297
Query: 300 LEIDKFSRKKINLSIEELKNE 320
L+++ + R+K+ + EEL E
Sbjct: 298 LKLNDWLREKLKATEEELIEE 318
>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 = 364 bits (936), Expect = e-126
Identities = 156/321 (48%), Positives = 214/321 (66%), Gaps = 10/321 (3%)
Query: 7 RISITGAAGQIGYNIIFRIANGDLLGKDQPIILQLLEASNKKSQKAIKGVIMEIEDCIFP 66
R+ +TGAAGQIGY ++ IA G +LGKDQPIIL LL+ K ++GV+ME+ DC FP
Sbjct: 1 RVVVTGAAGQIGYALLPMIARGRMLGKDQPIILHLLDIPPAM--KVLEGVVMELMDCAFP 58
Query: 67 LLVDVSVHENPITAFKDANIAILIGSFPRKSNMERSELLAINSSIFIEQGKALNSVASRD 126
LL V +P AF D ++AIL+G+FPRK MER +LL+ N IF EQG+AL+ +A +D
Sbjct: 59 LLDGVVPTHDPAVAFTDVDVAILVGAFPRKEGMERRDLLSKNVKIFKEQGRALDKLAKKD 118
Query: 127 VKVLVVGNPVNTNTYITMKSAPDLSYKNFTAMLRLDHNRAIAKLASKLNEPVSSIKKVFV 186
KVLVVGNP NTN + AP + KNF+A+ RLDHNRA+A++A + PVS +K V +
Sbjct: 119 CKVLVVGNPANTNALVLSNYAPSIPPKNFSALTRLDHNRALAQVAERAGVPVSDVKNVII 178
Query: 187 WGNHSLSMYPDYRYATVNG----VLIRDMINNNSFWNKNVFLPAISRRGEEIISIRGASS 242
WGNHS + YPD +ATV +R+ I +++ + F+ + +RG II R SS
Sbjct: 179 WGNHSSTQYPDVNHATVTKGGKQKPVREAIKDDA-YLDGEFITTVQQRGAAIIRARKLSS 237
Query: 243 AASAASAAIDHIKDWIFGTE--NWVTMGIPSDGS-YNVPKDIIFGFPVKIKNSKYKIIQN 299
A SAA AA+D + DW+ GT +V+MG+ SDGS Y VPK +IF FPV KN ++KI++
Sbjct: 238 ALSAAKAAVDQMHDWVLGTPEGTFVSMGVYSDGSPYGVPKGLIFSFPVTCKNGEWKIVEG 297
Query: 300 LEIDKFSRKKINLSIEELKNE 320
L +D SRKK+ L+ +EL+ E
Sbjct: 298 LCVDDSSRKKLALTAKELEEE 318
>gnl|CDD|177744 PLN00135, PLN00135, malate dehydrogenase.
Length = 309
Score = 315 bits (809), Expect = e-107
Identities = 135/302 (44%), Positives = 192/302 (63%), Gaps = 9/302 (2%)
Query: 25 IANGDLLGKDQPIILQLLEASNKKSQKAIKGVIMEIEDCIFPLLVDVSVHENPITAFKDA 84
IA G +LG DQP+IL +L+ + +A+ GV ME+ D FPLL V + + A K
Sbjct: 2 IARGVMLGPDQPVILHMLDI--PPAAEALNGVKMELIDAAFPLLKGVVATTDVVEACKGV 59
Query: 85 NIAILIGSFPRKSNMERSELLAINSSIFIEQGKALNSVASRDVKVLVVGNPVNTNTYITM 144
NIA+++G FPRK MER ++++ N SI+ Q AL A+ D KVLVV NP NTN I
Sbjct: 60 NIAVMVGGFPRKEGMERKDVMSKNVSIYKSQASALEKHAAPDCKVLVVANPANTNALILK 119
Query: 145 KSAPDLSYKNFTAMLRLDHNRAIAKLASKLNEPVSSIKKVFVWGNHSLSMYPDYRYATVN 204
+ AP + KN T + RLDHNRA+ +++ +L PVS +K V +WGNHS + YPD +ATV
Sbjct: 120 EFAPSIPEKNITCLTRLDHNRALGQISERLGVPVSDVKNVIIWGNHSSTQYPDVNHATVK 179
Query: 205 ----GVLIRDMINNNSFWNKNVFLPAISRRGEEIISIRGASSAASAASAAIDHIKDWIFG 260
+R+++ +++ W F+ + +RG II R SSA SAAS+A DHI+DW+ G
Sbjct: 180 TPSGEKPVRELVADDA-WLNGEFITTVQQRGAAIIKARKLSSALSAASSACDHIRDWVLG 238
Query: 261 TE--NWVTMGIPSDGSYNVPKDIIFGFPVKIKNSKYKIIQNLEIDKFSRKKINLSIEELK 318
T WV+MG+ SDGSY VP +I+ FPV + ++ I+Q L ID+FSRKK++ + +ELK
Sbjct: 239 TPEGTWVSMGVYSDGSYGVPPGLIYSFPVTCEKGEWSIVQGLSIDEFSRKKMDATAKELK 298
Query: 319 NE 320
E
Sbjct: 299 EE 300
>gnl|CDD|215060 PLN00112, PLN00112, malate dehydrogenase (NADP); Provisional.
Length = 444
Score = 312 bits (802), Expect = e-104
Identities = 139/330 (42%), Positives = 218/330 (66%), Gaps = 7/330 (2%)
Query: 3 KKPVRISITGAAGQIGYNIIFRIANGDLLGKDQPIILQLLEASNKKSQKAIKGVIMEIED 62
KK + ++++GAAG I +++F++A+G++ G DQPI L+LL +++S++A++GV ME+ED
Sbjct: 98 KKLINVAVSGAAGMISNHLLFKLASGEVFGPDQPIALKLL--GSERSKQALEGVAMELED 155
Query: 63 CIFPLLVDVSVHENPITAFKDANIAILIGSFPRKSNMERSELLAINSSIFIEQGKALNSV 122
++PLL +VS+ +P F+DA A+LIG+ PR MER++LL IN IF EQGKALN V
Sbjct: 156 SLYPLLREVSIGIDPYEVFQDAEWALLIGAKPRGPGMERADLLDINGQIFAEQGKALNEV 215
Query: 123 ASRDVKVLVVGNPVNTNTYITMKSAPDLSYKNFTAMLRLDHNRAIAKLASKLNEPVSSIK 182
ASR+VKV+VVGNP NTN I +K+AP++ KNF A+ RLD NRA +LA K +
Sbjct: 216 ASRNVKVIVVGNPCNTNALICLKNAPNIPAKNFHALTRLDENRAKCQLALKAGVFYDKVS 275
Query: 183 KVFVWGNHSLSMYPDYRYATVNGVLIRDMINNNSFWNKNVFLPAISRRGEEIISIRGASS 242
V +WGNHS + PD+ A +NG+ ++++I ++ W + F P + +RG +I G SS
Sbjct: 276 NVTIWGNHSTTQVPDFLNAKINGLPVKEVITDHK-WLEEEFTPKVQKRGGVLIKKWGRSS 334
Query: 243 AASAASAAIDHIKDWIFGTE--NWVTMGIPSDGS-YNVPKDIIFGFPVKIK-NSKYKIIQ 298
AAS A + D IK + T +W + G+ +DG+ Y + + ++F P + K + Y+I++
Sbjct: 335 AASTAVSIADAIKSLVTPTPEGDWFSTGVYTDGNPYGIAEGLVFSMPCRSKGDGDYEIVK 394
Query: 299 NLEIDKFSRKKINLSIEELKNEILSISHLI 328
++EID + R++I S EL E ++HL
Sbjct: 395 DVEIDDYLRERIKKSEAELLAEKRCVAHLT 424
>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 = 283 bits (726), Expect = 7e-94
Identities = 138/330 (41%), Positives = 217/330 (65%), Gaps = 7/330 (2%)
Query: 3 KKPVRISITGAAGQIGYNIIFRIANGDLLGKDQPIILQLLEASNKKSQKAIKGVIMEIED 62
KK V ++++GAAG I +++F +A+G++ G+DQPI L+LL +++S++A++GV ME+ED
Sbjct: 42 KKTVNVAVSGAAGMISNHLLFMLASGEVFGQDQPIALKLL--GSERSKEALEGVAMELED 99
Query: 63 CIFPLLVDVSVHENPITAFKDANIAILIGSFPRKSNMERSELLAINSSIFIEQGKALNSV 122
++PLL +VS+ +P F+DA+ A+LIG+ PR MER++LL IN IF +QGKALN+V
Sbjct: 100 SLYPLLREVSIGIDPYEVFEDADWALLIGAKPRGPGMERADLLDINGQIFADQGKALNAV 159
Query: 123 ASRDVKVLVVGNPVNTNTYITMKSAPDLSYKNFTAMLRLDHNRAIAKLASKLNEPVSSIK 182
AS++ KVLVVGNP NTN I MK+AP++ KNF A+ RLD NRA +LA K + +S+
Sbjct: 160 ASKNCKVLVVGNPCNTNALIAMKNAPNIPRKNFHALTRLDENRAKCQLALKSGKFYTSVS 219
Query: 183 KVFVWGNHSLSMYPDYRYATVNGVLIRDMINNNSFWNKNVFLPAISRRGEEIISIRGASS 242
V +WGNHS + PD+ A + G +++I + W + F P + +RG +I G SS
Sbjct: 220 NVTIWGNHSTTQVPDFVNAKIGGRPAKEVIKDTK-WLEEEFTPTVQKRGGALIKKWGRSS 278
Query: 243 AASAASAAIDHIKDWIFGTE--NWVTMGIPSDGS-YNVPKDIIFGFPVKIK-NSKYKIIQ 298
AAS A + D IK + T +W + G+ +DG+ Y + + ++F P + K + Y++
Sbjct: 279 AASTAVSIADAIKSLVVPTPEGDWFSTGVYTDGNPYGIAEGLVFSMPCRSKGDGDYELAT 338
Query: 299 NLEIDKFSRKKINLSIEELKNEILSISHLI 328
++ +D F R++I S +EL E ++HLI
Sbjct: 339 DVSMDDFLRERIRKSEDELLKEKECVAHLI 368
>gnl|CDD|223117 COG0039, Mdh, Malate/lactate dehydrogenases [Energy production and
conversion].
Length = 313
Score = 254 bits (651), Expect = 2e-83
Identities = 86/325 (26%), Positives = 153/325 (47%), Gaps = 16/325 (4%)
Query: 6 VRISITGAAGQIGYNIIFRIANGDLLGKDQPIILQLLEASNKKSQKAIKGVIMEIEDCIF 65
+++++ GA G +G ++ F + LG + L L++ +++ +GV +++
Sbjct: 1 MKVAVIGA-GNVGSSLAFLLLL-QGLGSE----LVLID----INEEKAEGVALDLSHAAA 50
Query: 66 PLLVDVSV-HENPITAFKDANIAILIGSFPRKSNMERSELLAINSSIFIEQGKALNSVAS 124
PL DV + + K A+I ++ PRK M R +LL N+ I + KA+ A
Sbjct: 51 PLGSDVKITGDGDYEDLKGADIVVITAGVPRKPGMTRLDLLEKNAKIVKDIAKAIAKYAP 110
Query: 125 RDVKVLVVGNPVNTNTYITMKSAPDLSYKNFTAMLRLDHNRAIAKLASKLNEPVSSIKKV 184
D VLVV NPV+ TYI MK + + + LD R LA KL +
Sbjct: 111 -DAIVLVVTNPVDILTYIAMKFSGFPKNRVIGSGTVLDSARFRTFLAEKLGVSPKDVH-A 168
Query: 185 FVWGNHSLSMYPDYRYATVNGVLIRDMINNNSFWNKNVFLPAISRRGEEIISIRGASSAA 244
+V G H +M P + ATV G + +++ ++ + + + G EII +GA +
Sbjct: 169 YVIGEHGDTMVPLWSQATVGGKPLEELLKEDTEEDLEELIERVRNAGAEIIEAKGAGTYY 228
Query: 245 SAASAAIDHIKDWIFGTENWVTMGIPSDGSYNVPKDIIFGFPVKI-KNSKYKIIQNLEID 303
A+A ++ + + + + + DG Y +D+ FG P + KN +I+ L +
Sbjct: 229 GPAAALARMVEAILRDEKRVLPVSVYLDGEYG-VEDVYFGVPAVLGKNGVEEIL-ELLLS 286
Query: 304 KFSRKKINLSIEELKNEILSISHLI 328
++K++ S EELK I + L+
Sbjct: 287 DDEQEKLDKSAEELKKNIELVKELV 311
>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 = 246 bits (629), Expect = 4e-80
Identities = 117/307 (38%), Positives = 177/307 (57%), Gaps = 14/307 (4%)
Query: 23 FRIANGDLLGKDQPIILQLLEASNKKSQKAIKGVIMEIEDCIFPLLVDVSVHENPITAFK 82
IANGDL G ++P+ L LLE + ++ + ME+EDC FP L V AFK
Sbjct: 3 HWIANGDLYG-NRPVCLHLLEI--PPALNRLEALAMELEDCAFPNLAGTIVTTKLEEAFK 59
Query: 83 DANIAILIGSFPRKSNMERSELLAINSSIFIEQGKALNSVASRDVKVLVVGNPVNTNTYI 142
D + A L+ S P K R++LL N+ IF G+AL+ A VKVLV+GNPVNTN +
Sbjct: 60 DIDCAFLVASVPLKPGEVRADLLTKNTPIFKATGEALSEYAKPTVKVLVIGNPVNTNCLV 119
Query: 143 TMKSAPDLSYKNFTAMLRLDHNRAIAKLASKLNEPVSSIKKVFVWGNHSLSMYPDYRYAT 202
M AP LS +NF+++ LDHNRA++++ASKL PV I V VWGNH+ SM D +A
Sbjct: 120 AMLHAPKLSAENFSSLCMLDHNRAVSRIASKLKVPVDHIYHVVVWGNHAESMVADLTHAE 179
Query: 203 V--NGV--LIRDMINNNSFWNKNVFLPAISRRGEEIISIRGASSAASAASAAIDHIKDWI 258
NG + D + + + + F I++R +I+ +RG +SAAS A++ H+K W+
Sbjct: 180 FTKNGKHQKVFDELCRD--YPEPDFFEVIAQRAWKILEMRGFTSAASPVKASLQHMKAWL 237
Query: 259 FGTE--NWVTMGI--PSDGSYNVPKDIIFGFPVKI-KNSKYKIIQNLEIDKFSRKKINLS 313
FGT ++MGI P Y + +IF FP + ++ K +++N E++ + + K+ +
Sbjct: 238 FGTRPGEVLSMGIPVPEGNPYGIKPGVIFSFPCTVDEDGKVHVVENFELNPWLKTKLAQT 297
Query: 314 IEELKNE 320
++L E
Sbjct: 298 EKDLFEE 304
>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 = 187 bits (478), Expect = 5e-56
Identities = 100/340 (29%), Positives = 168/340 (49%), Gaps = 26/340 (7%)
Query: 4 KPVRISITGAAGQIGYNIIFRIANGDLLGKDQPIILQLLEASNKKSQKAIKGVIMEIEDC 63
P+++ IT A+ + Y++I +A+G++ G ++ I + LL + ++ + +KG++ME+ED
Sbjct: 122 NPLQVCITNASAPLCYHLIPSLASGEVFGMEEEISIHLL--DSPENLEKLKGLVMEVEDL 179
Query: 64 IFPLLVDVSVHENPITAFKDANIAILIGSFPRKSNMERSELLAINSSIFIEQGKALNSVA 123
FPLL +SV + AFKDA++ +L+ F K + + +I G + A
Sbjct: 180 AFPLLRGISVTTDLDVAFKDAHVIVLLDDFLIKEGEDLEGCIRSRVAICQLYGPLIEKNA 239
Query: 124 SRDVKVLVVG-NPVNTNTYITMKSAPDLSYKNFTAMLRLDHNRAIAKLASKLNEPVSSIK 182
DVKV+V G +N T I +K AP + KN A+ RL NRA A LA KLN + IK
Sbjct: 240 KEDVKVIVAGRTFLNLKTSILIKYAPSIPRKNIIAVARLQENRAKALLARKLNVNSAGIK 299
Query: 183 KVFVWGNHSLSMYPDYRYATVNG--------------VLIRDMINNNSFWNKNVFLPAIS 228
V VWGN + Y D A V VL ++++++ W F+ +
Sbjct: 300 DVIVWGNIGGNTYIDLSKARVYRYDSAIWGPPNYSRPVL--ELVHDSK-WINGEFVATLK 356
Query: 229 RRGEEIISIRGASSAASAASAAIDHIKDWIFGT--ENWVTMGIPSDGSYNVPKDIIFGFP 286
S +A S A A + W G+ ++G+ S+G Y +P+ I+F P
Sbjct: 357 SLS----SSLNHEAAISPAHAIATTLSYWYHGSPPGEIFSLGVISEGWYGIPEGIVFSMP 412
Query: 287 VKIKNSKYKIIQNLEIDKFSRKKINLSIEELKNEILSISH 326
VK +N ++++ +LE+ + R+ + +L E L
Sbjct: 413 VKFQNGSWEVVTDLELSEILREVLKRITSDLIQEKLVALG 452
>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 = 164 bits (418), Expect = 4e-49
Identities = 75/315 (23%), Positives = 131/315 (41%), Gaps = 54/315 (17%)
Query: 8 ISITGAAGQIGYNIIFRIANGDLLGKDQPIILQLLEASNKKSQKAIKGVIMEIEDCIFPL 67
I++ GA G +G + F +A+G I L L + +K +KGV M+++D + PL
Sbjct: 1 IAVIGAGGNVGPALAFGLADG---SVLLAIELVLYDIDEEK----LKGVAMDLQDAVEPL 53
Query: 68 -LVDVSVHENPITAFKDANIAILIGSFPRKSNMERSELLAINSSIFIEQGKALNSVASRD 126
+ VS+ ++P AFKDA++ I+ RK M R +LL N I E G + + D
Sbjct: 54 ADIKVSITDDPYEAFKDADVVIITAGVGRKPGMGRLDLLKRNVPIVKEIGDNIEKYSP-D 112
Query: 127 VKVLVVGNPVNTNTYITMKSAPDLSYKNFTAMLRLDHNRAIAKLASKLNEPVSSIKKVFV 186
++VV NPV+ TY+ + + L + + LD R LA KL + KV++
Sbjct: 113 AWIIVVSNPVDIITYLVWRYSG-LPKEKVIGLGTLDPIRFRRILAEKLGVDPDDV-KVYI 170
Query: 187 WGNHSLSMYPDYRYATVNGVLIRDMINNNSFWNKNVFLPAISRRGEEIISIRGASSAASA 246
G H S PD+
Sbjct: 171 LGEHGGSQVPDWSTVR-------------------------------------------I 187
Query: 247 ASAAIDHIKDWIFGTENWVTMGIPSDGSYNVPKDIIFGFPVKIKNSKYKIIQNLEIDKFS 306
A++ D I+ + + +G+ ++G +P D++ P + + + + + F
Sbjct: 188 ATSIADLIRSLLNDEGEILPVGVRNNGQIGIPDDVVVSVPCIVGKNGVEEPIEVGLTDFE 247
Query: 307 RKKINLSIEELKNEI 321
+K+ S + LK E+
Sbjct: 248 LEKLQKSADTLKKEL 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 = 137 bits (346), Expect = 1e-39
Identities = 52/166 (31%), Positives = 81/166 (48%), Gaps = 5/166 (3%)
Query: 160 RLDHNRAIAKLASKLNEPVSSIKKVFVWGNHSLSMYPDYRYATVNGVLIRDMINNN---S 216
LD RA LA K S+ V+V G HS + +PD+ +A V + + + N +
Sbjct: 2 TLDTARARTFLAEKFGVDPRSVN-VYVIGEHSGTQFPDWSHAKVTIIPLISQVKENLKDT 60
Query: 217 FWNKNVFLPAISRRGEEIISIRGASSAASAASAAIDHIKDWIFGTENWVTMGIPSDGSYN 276
W + + G E+I + S+ S A AA K + GT +++G+ DG Y
Sbjct: 61 DWELEELIERVQNAGYEVIEAKAGSTTYSMAYAAARIAKAILRGTGGVLSVGVYLDGYYG 120
Query: 277 VPKDIIFGFPVKI-KNSKYKIIQNLEIDKFSRKKINLSIEELKNEI 321
P DI F PV + K+ K+++ L ++ F R+K+ S ELK EI
Sbjct: 121 SPDDIYFSVPVVLGKDGVEKVVEILPLNDFEREKLEKSAAELKKEI 166
>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 = 113 bits (286), Expect = 4e-31
Identities = 44/152 (28%), Positives = 73/152 (48%), Gaps = 10/152 (6%)
Query: 6 VRISITGAAGQIGYNIIFRIANGDLLGKDQPIILQLLEASNKKSQKAIKGVIMEIEDCIF 65
V++++ GA G +G ++ F +A L + L L++ + + +GV M++
Sbjct: 1 VKVAVVGAGGGVGSSLAFALALQGL-ADE----LVLVDIN----KDKAEGVAMDLSHGST 51
Query: 66 PLLVDVSVHENPITAFKDANIAILIGSFPRKSNMERSELLAINSSIFIEQGKALNSVASR 125
L V V + A KDA++ ++ PRK M R +LL N+ IF + A+ A
Sbjct: 52 FLSVPGIVGGDDYEALKDADVVVITAGVPRKPGMTRLDLLNRNAGIFKDIVPAIAKSAP- 110
Query: 126 DVKVLVVGNPVNTNTYITMKSAPDLSYKNFTA 157
D VLVV NPV+ TYI K + + +
Sbjct: 111 DAIVLVVSNPVDILTYIAWKVSGLPPERVIGS 142
>gnl|CDD|173409 PTZ00117, PTZ00117, malate dehydrogenase; Provisional.
Length = 319
Score = 86.3 bits (214), Expect = 3e-19
Identities = 64/260 (24%), Positives = 109/260 (41%), Gaps = 12/260 (4%)
Query: 75 ENPITAFKDANIAILIGSFPRKSNMERSELLAINSSIFIEQGKALNSVASRDVKVLVVGN 134
N KD+++ ++ RK M R +LL IN I +++ V+ V N
Sbjct: 65 TNNYEDIKDSDVVVITAGVQRKEEMTREDLLTINGKIMKSVAESVKKYCPNAF-VICVTN 123
Query: 135 PVNTNTYITMKSAPDLSYKNFTAML-RLDHNRAIAKLASKLNEPVSSIKKVFVWGNHSLS 193
P++ + + + M LD +R LA KL + V V G H
Sbjct: 124 PLDCMVKV-FQEKSGIPSNKICGMAGVLDSSRFRCNLAEKLGVSPGDVSAV-VIGGHGDL 181
Query: 194 MYPDYRYATVNGVLIRDMINNNSFWNKNVFLPAISRR----GEEIISIRGASSAASAASA 249
M P RY TVNG+ + D + + K + I ++ G EI+ + SA A +A
Sbjct: 182 MVPLPRYCTVNGIPLSDFVKKGAITEKE--INEIIKKTRNMGGEIVKLLKKGSAFFAPAA 239
Query: 250 AI-DHIKDWIFGTENWVTMGIPSDGSYNVPKDIIFGFPVKIKNSKYKIIQNLEIDKFSRK 308
AI I+ ++ + + + +G YN K++ G PV I + + LE++ ++
Sbjct: 240 AIVAMIEAYLKDEKRVLVCSVYLNGQYNC-KNLFVGVPVVIGGKGIEKVIELELNAEEKE 298
Query: 309 KINLSIEELKNEILSISHLI 328
+ SIE ++ LI
Sbjct: 299 LFDKSIESIQELTQKAKALI 318
>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 = 83.7 bits (208), Expect = 2e-18
Identities = 88/334 (26%), Positives = 142/334 (42%), Gaps = 55/334 (16%)
Query: 8 ISITGAAGQIGYNIIFRIAN---GDLL------GKDQPIILQLLEASNKKSQKAIKGVIM 58
ISI GA G +G + +A GD++ G Q L + +A+ I G
Sbjct: 1 ISIIGA-GNVGATLAQLLALKELGDVVLLDIVEGLPQGKALDISQAA------PILGS-- 51
Query: 59 EIEDCIFPLLVDVSVH-ENPITAFKDANIAILIGSFPRKSNMERSELLAINSSIFIEQGK 117
D V N +++ ++ PRK M R +LL N+ I E +
Sbjct: 52 -----------DTKVTGTNDYEDIAGSDVVVITAGIPRKPGMSRDDLLGTNAKIVKEVAE 100
Query: 118 ALNSVASRDVKVLVVGNPVNTNTYITMKSAPDLSYKNFTAML-RLDHNRAIAKLASKLNE 176
+ A + V+VV NP++ TY+ K++ M LD R +A +L
Sbjct: 101 NIKKYAP-NAIVIVVTNPLDVMTYVAYKAS-GFPRNRVIGMAGVLDSARFRYFIAEELGV 158
Query: 177 PVSSIKKVFVWGNHSLSMYPDYRYATVNGVLIRDMINNNSFWNKNVFLPAISRR----GE 232
V + + V G H +M P RY+TV G+ + ++I + I R G
Sbjct: 159 SVKDV-QAMVLGGHGDTMVPLPRYSTVGGIPLTELITKEE-------IDEIVERTRNGGA 210
Query: 233 EIISIRGASSAASAASAAIDHIKDWIFGTENWVTMGIPS----DGSYNVPKDIIFGFPVK 288
EI+++ SA A +AAI + + I + V +P +G Y + KDI G PV
Sbjct: 211 EIVNLLKTGSAYYAPAAAIAEMVEAILKDKKRV---LPCSAYLEGEYGI-KDIFVGVPVV 266
Query: 289 I-KNSKYKIIQNLEIDKFSRKKINLSIEELKNEI 321
+ KN KII+ L++ ++ + S+E +K I
Sbjct: 267 LGKNGVEKIIE-LDLTDEEKEAFDKSVESVKELI 299
>gnl|CDD|180477 PRK06223, PRK06223, malate dehydrogenase; Reviewed.
Length = 307
Score = 74.4 bits (184), Expect = 4e-15
Identities = 93/333 (27%), Positives = 148/333 (44%), Gaps = 43/333 (12%)
Query: 7 RISITGAAGQIGYNIIFRIAN---GDLLGKDQPIILQLLEASNKKSQKAIKGVIMEIEDC 63
+ISI GA G +G + +A GD++ D I+ + +G ++I +
Sbjct: 4 KISIIGA-GNVGATLAHLLALKELGDVVLFD--IVEGVP-----------QGKALDIAEA 49
Query: 64 IFPLLVDVSVH-ENPITAFKDANIAILIGSFPRKSNMERSELLAINSSIFIEQGKALNSV 122
D + N +++ ++ PRK M R +LL IN+ I + + +
Sbjct: 50 APVEGFDTKITGTNDYEDIAGSDVVVITAGVPRKPGMSRDDLLGINAKIMKDVAEGIKKY 109
Query: 123 ASRDVKVLVVGNPVNTNTYITMKSAPDLSYKNFTAML-RLDHNRAIAKLASKLNEPVSSI 181
A D V+VV NPV+ TY+ +K M LD R +A +LN V +
Sbjct: 110 AP-DAIVIVVTNPVDAMTYVALK-ESGFPKNRVIGMAGVLDSARFRTFIAEELNVSVKDV 167
Query: 182 KKVFVWGNHSLSMYPDYRYATVNGVLIRDMINNNSFWNKNVFLPAISRR----GEEIISI 237
FV G H SM P RY+TV G+ + D+++ L I R G EI+ +
Sbjct: 168 -TAFVLGGHGDSMVPLVRYSTVGGIPLEDLLSKEK-------LDEIVERTRKGGAEIVGL 219
Query: 238 RGASSAASAASAAIDHIKDWIFGTENWVTMGIPS----DGSYNVPKDIIFGFPVKI-KNS 292
SA A +A+I + + I + V +P +G Y V KD+ G PVK+ KN
Sbjct: 220 LKTGSAYYAPAASIAEMVEAILKDKKRV---LPCSAYLEGEYGV-KDVYVGVPVKLGKNG 275
Query: 293 KYKIIQNLEIDKFSRKKINLSIEELKNEILSIS 325
KII+ LE+D + + S+E +K I ++
Sbjct: 276 VEKIIE-LELDDEEKAAFDKSVEAVKKLIEALK 307
>gnl|CDD|133430 cd05294, LDH-like_MDH_nadp, A lactate dehydrogenases-like structure
with malate dehydrogenase enzymatic activity. The
LDH-like MDH proteins have a lactate
dehyhydrogenase-like (LDH-like) structure and malate
dehydrogenase (MDH) enzymatic activity. This subgroup is
composed of some archaeal LDH-like MDHs that prefer
NADP(H) rather than NAD(H) as a cofactor. One member,
MJ0490 from Methanococcus jannaschii, has been observed
to form dimers and tetramers during crystalization,
although it is believed to exist primarilly as a
tetramer in solution. In addition to its MDH activity,
MJ0490 also possesses
fructose-1,6-bisphosphate-activated LDH activity.
Members of this subgroup have a higher sequence
similarity to LDHs than to other MDHs. LDH catalyzes the
last step of glycolysis in which pyruvate is converted
to L-lactate. MDH is one of the key enzymes in the
citric acid cycle, facilitating both the conversion of
malate to oxaloacetate and replenishing levels of
oxalacetate by reductive carboxylation of pyruvate. The
LDH-like MDHs are part of the NAD(P)-binding Rossmann
fold superfamily, which includes a wide variety of
protein families including the NAD(P)- binding domains
of alcohol dehydrogenases, tyrosine-dependent
oxidoreductases, glyceraldehyde-3-phosphate
dehydrogenases, formate/glycerate dehydrogenases,
siroheme synthases, 6-phosphogluconate dehydrogenase,
aminoacid dehydrogenases, repressor rex, and NAD-binding
potassium channel domains, among others.
Length = 309
Score = 73.2 bits (180), Expect = 9e-15
Identities = 78/315 (24%), Positives = 144/315 (45%), Gaps = 14/315 (4%)
Query: 6 VRISITGAAGQIGYNIIFRIANGDLLGKDQPIILQLLEASNKKSQKAIKGVIMEIEDCIF 65
+++SI GA+G++G +A + ++ ++ S KS + +KG+ ++I D +
Sbjct: 1 MKVSIIGASGRVGSATALLLA-------KEDVVKEINLISRPKSLEKLKGLRLDIYDALA 53
Query: 66 PLLVDVSVH-ENPITAFKDANIAILIGSFPRKSNMERSELLAINSSIFIEQGKALNSVAS 124
+D + + ++ ++I I+ PRK M R +L N+ I + K + A
Sbjct: 54 AAGIDAEIKISSDLSDVAGSDIVIITAGVPRKEGMSRLDLAKKNAKIVKKYAKQIAEFAP 113
Query: 125 RDVKVLVVGNPVNTNTYITMKSAPDLSYKNFTAMLRLDHNRAIAKLASKLNEPVSSIKKV 184
D K+LVV NPV+ TY +K + + F LD R +A N +S +
Sbjct: 114 -DTKILVVTNPVDVMTYKALKESGFDKNRVFGLGTHLDSLRFKVAIAKHFNVHISEVHTR 172
Query: 185 FVWGNHSLSMYPDYRYATVNGVLIRDMINNNSFWNKNVFLPAISRRGEEIISIRGASSAA 244
+ G H SM P ++ G+ I+ F + + + + G+ IIS++G S
Sbjct: 173 II-GEHGDSMVPLISSTSIGGIPIKRFPEYKDFDVEKI-VETVKNAGQNIISLKGGSEYG 230
Query: 245 SAASAAIDHIKDWIFGTENWV-TMGIPSDGSYNVPKDIIFGFPVKIKNSKYKIIQNLEID 303
A +AI ++ I E + T+ +G + +D+ G PVK+ + + I +E+D
Sbjct: 231 PA--SAISNLVRTIANDERRILTVSTYLEGEIDGIRDVCIGVPVKLGKNGIEEIVPIEMD 288
Query: 304 KFSRKKINLSIEELK 318
R+ S E +K
Sbjct: 289 DDEREAFRKSAEIVK 303
>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 = 69.6 bits (171), Expect = 2e-13
Identities = 69/295 (23%), Positives = 115/295 (38%), Gaps = 41/295 (13%)
Query: 8 ISITGAAGQIGYNIIFRIANGDLLGKDQPIILQLLEASNKKSQKAIKGVIMEIEDCIFPL 67
I+I GA G +G + F + L + L L++ + +K+ KG +++ L
Sbjct: 1 ITIIGA-GNVGAAVAFALIAKGLASE-----LVLVDVNEEKA----KGDALDLSHASAFL 50
Query: 68 LVDVSVHENPITAFKDANIAILIGSFPRKSNMERSELLAINSSIFIEQGKALNSVASRDV 127
V DA+I ++ PRK R +L+ N+ I L D
Sbjct: 51 ATGTIVRGGDYADAADADIVVITAGAPRKPGETRLDLINRNAPILRSVITNL-KKYGPDA 109
Query: 128 KVLVVGNPVNTNTYITMKSAPDLSYKNFTAMLRLDHNRAI------------AKLASKLN 175
+LVV NPV+ TY+ K + L NR I + LA KL+
Sbjct: 110 IILVVSNPVDILTYVAQK------------LSGLPKNRVIGSGTLLDSARFRSLLAEKLD 157
Query: 176 EPVSSIKKVFVWGNHSLSMYPDYRYATVNGVLIRDMINNNSFWNKNVFLPAISRRGEEII 235
S+ +V G H S + ATV G+ + ++ + + + G EII
Sbjct: 158 VDPQSV-HAYVLGEHGDSQVVAWSTATVGGLPLEELAPFTKLDLEAIE-EEVRTSGYEII 215
Query: 236 SIRGASSAASAASAAIDHIKDWIFGTENWV-TMGIPSDGSYNVPKDIIFGFPVKI 289
++GA++ A + A I I E V + +G Y + +D+ P +
Sbjct: 216 RLKGATNYGIATAIA--DIVKSILLDERRVLPVSAVQEGQYGI-EDVALSVPAVV 267
>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 = 65.7 bits (160), Expect = 3e-12
Identities = 59/248 (23%), Positives = 107/248 (43%), Gaps = 27/248 (10%)
Query: 83 DANIAILIGSFPRKSNMERSELLAINSSIFIEQGKALNSVASRDVK------VLVVGNPV 136
+++I ++ PRK M R +LL++N+ I + V R ++ ++VV NP+
Sbjct: 69 NSDIVVITAGLPRKPGMSREDLLSMNAGI-------VREVTGRIMEHSPNPIIVVVSNPL 121
Query: 137 NTNTYITMKSAPDLSYKNFTAMLRLDHNRAIAKLASKLNEPVSSIKKVFVWGNHSLSMYP 196
+ TY+ + + + LD R +A +L V + V G H +M P
Sbjct: 122 DAMTYVAWQKSGFPKERVIGQAGVLDSARFRTFIAMELGVSVQDVT-ACVLGGHGDAMVP 180
Query: 197 DYRYATVNGVLIRDMINNNSFWNKNVFLPAISRR----GEEIISIRGASSAASAASAAID 252
RY+TV G+ + D+I+ + I R G EI+++ SA A +A++
Sbjct: 181 LVRYSTVAGIPVADLISAER-------IAEIVERTRKGGGEIVNLLKQGSAYYAPAASVV 233
Query: 253 HIKDWIFGTENWVTMGIPS-DGSYNVPKDIIFGFPVKIKNSKYKIIQNLEIDKFSRKKIN 311
+ + I V DG Y + I G PV + + + I L++D+ +N
Sbjct: 234 EMVEAILKDRKRVLPCAAYLDGQYGI-DGIYVGVPVILGKNGVEHIYELKLDQSELALLN 292
Query: 312 LSIEELKN 319
S + +
Sbjct: 293 KSAKIVDE 300
>gnl|CDD|173376 PTZ00082, PTZ00082, L-lactate dehydrogenase; Provisional.
Length = 321
Score = 62.0 bits (151), Expect = 6e-11
Identities = 67/256 (26%), Positives = 111/256 (43%), Gaps = 19/256 (7%)
Query: 76 NPITAFKDANIAILIGSF---PRKSNME--RSELLAINSSIFIEQGKALNSVASRDVKVL 130
N +++ I+ P KS+ E R +LL +N+ I E + + + V+
Sbjct: 67 NNYEDIAGSDVVIVTAGLTKRPGKSDKEWNRDDLLPLNAKIMDEVAEGIKKYCP-NAFVI 125
Query: 131 VVGNPVNTNTYITMKSAPDLSYKNFTAMLR-LDHNRAIAKLASKLNEPVSSIKKVFVWGN 189
V+ NP++ + + + L M LD +R +A KL + V G
Sbjct: 126 VITNPLDVMVKLLQEHS-GLPKNKVCGMAGVLDSSRLRTYIAEKLGVNPRDVHA-SVIGA 183
Query: 190 HSLSMYPDYRYATVNGVLIRDMINNNSFWNKNVFLPAISRR----GEEIISIRGASSAAS 245
H M P RY TV G+ + + I + + I R G+EI+ + G SA
Sbjct: 184 HGDKMVPLPRYVTVGGIPLSEFIKKGLITQEE--IDEIVERTRNTGKEIVDLLGTGSAYF 241
Query: 246 A-ASAAIDHIKDWIFGTENWVTMGIPSDGSYNVPKDIIFGFPVKI-KNSKYKIIQNLEID 303
A A+AAI+ + ++ + + +G Y KDI G P I N KII+ L++
Sbjct: 242 APAAAAIEMAEAYLKDKKRVLPCSAYLEGQYGH-KDIYMGTPAVIGANGVEKIIE-LDLT 299
Query: 304 KFSRKKINLSIEELKN 319
+KK + SI+E+K
Sbjct: 300 PEEQKKFDESIKEVKR 315
>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 = 58.7 bits (143), Expect = 7e-10
Identities = 69/287 (24%), Positives = 106/287 (36%), Gaps = 37/287 (12%)
Query: 51 KAIKGVIMEIEDCIFPLLVDVSVHENPITAFKDANIAILIGSFPRKSNMERSELLAINSS 110
+G M+++ L + + KDA++ ++ P+K R EL+ N
Sbjct: 32 DKAEGEAMDLQHAASFLPTPKKIRSGDYSDCKDADLVVITAGAPQKPGETRLELVGRNVR 91
Query: 111 IFIEQGKALNSVASR-DVKVLVVGNPVNTNTYITMKSAPDLSYKNFTAMLRLDHNRAIAK 169
I + V S D LV NPV+ TY+ K LS NR I
Sbjct: 92 IM--KSIVPEVVKSGFDGIFLVATNPVDILTYVAWK----LS--------GFPKNRVIGS 137
Query: 170 ------------LASKLNEPVSSIKKVFVWGNHSLSMYPDYRYATVNGVLIRDMINNNSF 217
LA KL S+ ++ G H S P + AT+ GV + D
Sbjct: 138 GTVLDTARLRYLLAEKLGVDPQSV-HAYIIGEHGDSEVPVWSSATIGGVPLLDY-LKAKG 195
Query: 218 WNKNVFLPAIS----RRGEEIISIRGASSAASAASAAIDHIKDWIFGTENWV-TMGIPSD 272
++ L I EII+ +GA+ + A I + I EN V + D
Sbjct: 196 TETDLDLEEIEKEVRDAAYEIINRKGATYYGIGMAVA--RIVEAILHDENRVLPVSAYLD 253
Query: 273 GSYNVPKDIIFGFPVKIKNSKYKIIQNLEIDKFSRKKINLSIEELKN 319
G Y + KD+ G P + + + I L + ++ S E LK
Sbjct: 254 GEYGI-KDVYIGVPAVLGRNGVEEIIELPLSDEEKEAFQKSAETLKK 299
>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 = 49.8 bits (120), Expect = 7e-07
Identities = 66/274 (24%), Positives = 106/274 (38%), Gaps = 48/274 (17%)
Query: 71 VSVHENPITAFKDANIAILIGSFPRKSNMERSELLAINSSIFIEQGKALNSVASRDVK-- 128
V + + KDA+I ++ P+K R +LL N+ K + S+ +
Sbjct: 56 VKIKAGDYSDCKDADIVVITAGAPQKPGETRLDLLEKNA-------KIMKSIVPKIKASG 108
Query: 129 ----VLVVGNPVNTNTYITMKSAPDLSYKNFTAMLRLDHNRAIA------------KLAS 172
LV NPV+ TY+ K + L NR I LA
Sbjct: 109 FDGIFLVASNPVDVITYVVQK------------LSGLPKNRVIGTGTSLDTARLRRALAE 156
Query: 173 KLNEPVSSIKKVFVWGNHSLSMYPDYRYATVNGVLIRDMINNNSFWNKNVFLPAIS---- 228
KLN S+ +V G H S + + TV G + D++ + L I
Sbjct: 157 KLNVDPRSV-HAYVLGEHGDSQFVAWSTVTVGGKPLLDLLKEGKL--SELDLDEIEEDVR 213
Query: 229 RRGEEIISIRGASSAASAASAAIDHIKDWIFGTENWV-TMGIPSDGSYNVPKDIIFGFPV 287
+ G EII+ +GA+ A + A I I EN + + DG Y KD+ G P
Sbjct: 214 KAGYEIINGKGATYYGIATALA--RIVKAILNDENAILPVSAYLDGEYGE-KDVYIGVPA 270
Query: 288 KIKNSKYKIIQNLEIDKFSRKKINLSIEELKNEI 321
I + + + L++ + ++K S + +K I
Sbjct: 271 IIGRNGVEEVIELDLTEEEQEKFEKSADIIKENI 304
>gnl|CDD|178836 PRK00066, ldh, L-lactate dehydrogenase; Reviewed.
Length = 315
Score = 49.9 bits (120), Expect = 7e-07
Identities = 63/265 (23%), Positives = 104/265 (39%), Gaps = 48/265 (18%)
Query: 82 KDANIAILIGSFPRKSNMERSELLAINSSIFIEQGKALNSVASRDVK------VLVVGNP 135
KDA++ ++ P+K R +L+ N IF S+ + LV NP
Sbjct: 72 KDADLVVITAGAPQKPGETRLDLVEKNLKIF-------KSIVGEVMASGFDGIFLVASNP 124
Query: 136 VNTNTYITMKSAPDLSYKNFTAMLRLDHNRAIAK------------LASKLNEPVSSIKK 183
V+ TY T K LS R I L+ KL+ S+
Sbjct: 125 VDILTYATWK----LS--------GFPKERVIGSGTSLDSARFRYMLSEKLDVDPRSV-H 171
Query: 184 VFVWGNHSLSMYPDYRYATVNGVLIRDMINNNSFWNKNVFLPAI----SRRGEEIISIRG 239
++ G H + +P + +A V GV + + + N +++ L I EII +G
Sbjct: 172 AYIIGEHGDTEFPVWSHANVAGVPLEEYLEENEQYDEE-DLDEIFENVRDAAYEIIEKKG 230
Query: 240 ASSAASAASAAIDHIKDWIFGTENWV-TMGIPSDGSYNVPKDIIFGFPVKIKNSKYKIIQ 298
A+ A + A I I EN V + +G Y +D+ G P + + + I
Sbjct: 231 ATYYGIAMALA--RITKAILNNENAVLPVSAYLEGQYGE-EDVYIGVPAVVNRNGIREIV 287
Query: 299 NLEIDKFSRKKINLSIEELKNEILS 323
L ++ ++K S + LK EI+
Sbjct: 288 ELPLNDDEKQKFAHSADVLK-EIMD 311
>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 = 48.6 bits (116), Expect = 2e-06
Identities = 62/274 (22%), Positives = 96/274 (35%), Gaps = 55/274 (20%)
Query: 75 ENPIT-AFKDANIAILIGSFPRKSNMERSELLAINSSIFIEQGKALNSVASRDVKVLVVG 133
E + A K A++ ++ PRK M R +L +N+ I + A+ + +LV+
Sbjct: 58 EEGLENALKGADVVVIPAGVPRKPGMTRDDLFNVNAGIVKDLVAAVAESCPK-AMILVIT 116
Query: 134 NPVNTNTYI---TMKSAPDLSYKNFTAMLRLDHNRAIAKLASKLNEPVSSIKKVFVWGNH 190
NPVN+ I +K + LD RA +A + V V G H
Sbjct: 117 NPVNSTVPIAAEVLKKKGVYDPNKLFGVTTLDIVRANTFVAELKGKD-PMEVNVPVIGGH 175
Query: 191 SLSMYPDYRYATVNGVLIRDMINNNSFWNKNVFLP------AISRR----GEEIISIR-G 239
S G I +I+ L A+ R G E++ + G
Sbjct: 176 S-------------GETIIPLISQCPG----KVLFTEDQLEALIHRIQNAGTEVVKAKAG 218
Query: 240 ASSA----ASAASAAIDHIKDWIFGTENWVTMGIPSDGSYNVPKDII-----FGFPVKIK 290
A SA A A + + + + G E V V D + F P+ +
Sbjct: 219 AGSATLSMAFAGARFVLSLVRGLKGEEGVV-------ECAYVESDGVTEATFFATPLLLG 271
Query: 291 N---SKYKIIQNLEIDKFSRKKINLSIEELKNEI 321
K I L F K +N ++ ELK I
Sbjct: 272 KNGVEKRLGIGKL--SSFEEKMLNGALPELKKNI 303
>gnl|CDD|235340 PRK05086, PRK05086, malate dehydrogenase; Provisional.
Length = 312
Score = 40.4 bits (95), Expect = 8e-04
Identities = 33/125 (26%), Positives = 54/125 (43%), Gaps = 15/125 (12%)
Query: 75 ENPITAFKDANIAILIGSFPRKSNMERSELLAINSSI---FIEQGKALNSVASRDVKVLV 131
E+P A + A++ ++ RK M+RS+L +N+ I +E+ VA K +
Sbjct: 61 EDPTPALEGADVVLISAGVARKPGMDRSDLFNVNAGIVKNLVEK------VAKTCPKACI 114
Query: 132 --VGNPVNTNTYI---TMKSAPDLSYKNFTAMLRLDHNRAIAKLASKLNEPVSSIKKVFV 186
+ NPVNT I +K A + LD R+ +A + + +V V
Sbjct: 115 GIITNPVNTTVAIAAEVLKKAGVYDKNKLFGVTTLDVIRSETFVAELKGKQPGEV-EVPV 173
Query: 187 WGNHS 191
G HS
Sbjct: 174 IGGHS 178
>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 = 39.8 bits (94), Expect = 0.001
Identities = 19/59 (32%), Positives = 32/59 (54%), Gaps = 1/59 (1%)
Query: 80 AFKDANIAILIGSFPRKSNMERSELLAINSSIFIEQGKALNSVASRDVKVLVVGNPVNT 138
A K A++ ++ PRK M R +L IN+ I + A+ + A +L++ NPVN+
Sbjct: 65 ALKGADVVVIPAGVPRKPGMTRDDLFNINAGIVRDLATAV-AKACPKALILIISNPVNS 122
>gnl|CDD|240360 PTZ00325, PTZ00325, malate dehydrogenase; Provisional.
Length = 321
Score = 35.4 bits (82), Expect = 0.028
Identities = 24/73 (32%), Positives = 37/73 (50%), Gaps = 8/73 (10%)
Query: 80 AFKDANIAILIGSFPRKSNMERSELLAINSSIFIEQGKALNSVASRDVK--VLVVGNPVN 137
A + A++ ++ PRK M R +L N+ I + + +VAS K V +V NPVN
Sbjct: 73 ALRGADLVLICAGVPRKPGMTRDDLFNTNAPIVRD---LVAAVASSAPKAIVGIVSNPVN 129
Query: 138 TNTYI---TMKSA 147
+ I T+K A
Sbjct: 130 STVPIAAETLKKA 142
>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 = 32.6 bits (75), Expect = 0.22
Identities = 34/132 (25%), Positives = 57/132 (43%), Gaps = 7/132 (5%)
Query: 124 SRDVKVLVVGNPVNTNTYITMKSAPDLSYKNFTAMLRLDHNRAIAKLASKLNEPVSSIKK 183
S + +LVV NPV+ TY+ K + ++ + LD R +A +L SS
Sbjct: 111 SPNAILLVVSNPVDIMTYVAWKLSGLPKHRVIGSGCNLDSARFRYLIAERLGVAPSS-VH 169
Query: 184 VFVWGNHSLSMYPDYRYATVNGVLIRDMINN-----NSFWNKNVFLPAISRRGEEIISIR 238
++ G H S P + V GV ++D+ + + K V + E+I ++
Sbjct: 170 GWIIGEHGDSSVPVWSGVNVAGVRLQDLNPDIGTDKDPEKWKEVHKQ-VVDSAYEVIKLK 228
Query: 239 GASSAASAASAA 250
G +S A S A
Sbjct: 229 GYTSWAIGLSVA 240
>gnl|CDD|133426 cd05290, LDH_3, 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
some bacterial LDHs from firmicutes,
gammaproteobacteria, and actinobacteria. Vertebrate LDHs
are non-allosteric, but some bacterial LDHs 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 dehydrogenase, aminoacid
dehydrogenases, repressor rex, and NAD-binding potassium
channel domains, among others.
Length = 307
Score = 31.9 bits (73), Expect = 0.41
Identities = 48/257 (18%), Positives = 101/257 (39%), Gaps = 12/257 (4%)
Query: 71 VSVHENPITAFKDANIAILIG--SFPRKSNMERSELLAINSSIFIEQGKALNSVASRDVK 128
+ DA+I ++ S + +R +L N+ I E + V V
Sbjct: 56 TKIRAGDYDDCADADIIVITAGPSIDPGNTDDRLDLAQTNAKIIREIMGNITKVTKEAV- 114
Query: 129 VLVVGNPVNTNTYITMKSAPDLSYKNFTAMLRLDHNRAIAKLASKLNEPVSSIKKVFVWG 188
++++ NP++ YI + K LD R +A K ++ +V G
Sbjct: 115 IILITNPLDIAVYIAATEFDYPANKVIGTGTMLDTARLRRIVADKYGVDPKNVTG-YVLG 173
Query: 189 NHSLSMYPDYRYATVNGVLIRDM--INNNSFWNKNVFLPAISRRGEEIISIRGASSAASA 246
H +P + + G+ + ++ + +K+ L + + ++ + +G ++A A
Sbjct: 174 EHGSHAFPVWSLVNIAGLPLDELEALFGKEPIDKDELLEEVVQAAYDVFNRKGWTNAGIA 233
Query: 247 ASAAIDHIKDWIFGTENWVTMGIPSDGSYNVPKDIIFGFPVKIKNSKYKIIQNLEI--DK 304
S A IK + + + + G Y + D+ P I I + LEI D+
Sbjct: 234 KS-ASRLIKAILLDERSILPVCTLLSGEYGL-SDVALSLPTVI--GAKGIERVLEIPLDE 289
Query: 305 FSRKKINLSIEELKNEI 321
+ +K++ S + ++ I
Sbjct: 290 WELEKLHKSAKAIRETI 306
>gnl|CDD|215058 PLN00106, PLN00106, malate dehydrogenase.
Length = 323
Score = 31.1 bits (71), Expect = 0.82
Identities = 36/117 (30%), Positives = 51/117 (43%), Gaps = 11/117 (9%)
Query: 80 AFKDANIAILIGSFPRKSNMERSELLAINSSIFIEQGKAL-NSVASR--DVKVLVVGNPV 136
A K A++ I+ PRK M R +L IN+ I K L +VA + V ++ NPV
Sbjct: 83 ALKGADLVIIPAGVPRKPGMTRDDLFNINAGIV----KTLCEAVAKHCPNALVNIISNPV 138
Query: 137 NTNTYI---TMKSAPDLSYKNFTAMLRLDHNRAIAKLASKLNEPVSSIKKVFVWGNH 190
N+ I +K A K + LD RA +A K + + V V G H
Sbjct: 139 NSTVPIAAEVLKKAGVYDPKKLFGVTTLDVVRANTFVAEKKGLDPADV-DVPVVGGH 194
>gnl|CDD|178212 PLN02602, PLN02602, lactate dehydrogenase.
Length = 350
Score = 30.9 bits (70), Expect = 0.92
Identities = 38/172 (22%), Positives = 71/172 (41%), Gaps = 6/172 (3%)
Query: 83 DANIAILIGSFPRKSNMERSELLAINSSIFIEQGKALNSVASRDVKVLVVGNPVNTNTYI 142
+++ I+ + R LL N ++F + L + S D +L+V NPV+ TY+
Sbjct: 105 GSDLCIVTAGARQIPGESRLNLLQRNVALFRKIIPEL-AKYSPDTILLIVSNPVDVLTYV 163
Query: 143 TMKSAPDLSYKNFTAMLRLDHNRAIAKLASKLNEPVSSIKKVFVWGNHSLSMYPDYRYAT 202
K + + + + LD +R +A L+ + + ++ G H S + +
Sbjct: 164 AWKLSGFPANRVIGSGTNLDSSRFRFLIADHLDVNAQDV-QAYIVGEHGDSSVALWSSVS 222
Query: 203 VNGVLIRDMINNNSFWNKNVFLPAISR----RGEEIISIRGASSAASAASAA 250
V GV + + + L I R E+I ++G +S A S A
Sbjct: 223 VGGVPVLSFLEKQQIAYEKETLEEIHRAVVDSAYEVIKLKGYTSWAIGYSVA 274
>gnl|CDD|223528 COG0451, WcaG, Nucleoside-diphosphate-sugar epimerases [Cell
envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 314
Score = 29.5 bits (66), Expect = 2.6
Identities = 18/95 (18%), Positives = 36/95 (37%), Gaps = 9/95 (9%)
Query: 7 RISITGAAGQIGYNIIFRIANG-------DLLGKDQPIILQLLEASN--KKSQKAIKGVI 57
RI +TG AG IG +++ R+ D L +L +E + + +
Sbjct: 2 RILVTGGAGFIGSHLVERLLAAGHDVRGLDRLRDGLDPLLSGVEFVVLDLTDRDLVDELA 61
Query: 58 MEIEDCIFPLLVDVSVHENPITAFKDANIAILIGS 92
+ D + L SV ++ + + + G+
Sbjct: 62 KGVPDAVIHLAAQSSVPDSNASDPAEFLDVNVDGT 96
>gnl|CDD|234776 PRK00478, scpA, segregation and condensation protein A/unknown
domain fusion protein; Provisional.
Length = 505
Score = 29.5 bits (66), Expect = 2.7
Identities = 17/42 (40%), Positives = 28/42 (66%), Gaps = 3/42 (7%)
Query: 286 PVKIKNSKYKIIQNLEIDKFSRKKI---NLSIEELKNEILSI 324
+K+K++ K+ + L+I + K I LSIE+++NEILSI
Sbjct: 313 VLKLKHAMNKLFEKLKIKTLTNKNIVIEELSIEQVQNEILSI 354
>gnl|CDD|187645 cd08941, 3KS_SDR_c, 3-keto steroid reductase, classical (c) SDRs.
3-keto steroid reductase (in concert with other
enzymes) catalyzes NADP-dependent sterol C-4
demethylation, as part of steroid biosynthesis. 3-keto
reductase is a classical SDR, with a well conserved
canonical active site tetrad and fairly well conserved
characteristic NAD-binding motif. 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 = 290
Score = 28.9 bits (65), Expect = 3.1
Identities = 16/72 (22%), Positives = 34/72 (47%), Gaps = 6/72 (8%)
Query: 4 KPVRISITGAAGQIGYNIIFRIANGDLLGKDQPIILQLLEASNKKSQKAIKGVIMEIEDC 63
+ V + +TGA +G I R+ D ++ + L L + ++++ A + ++ D
Sbjct: 1 RKVVL-VTGANSGLGLAICERLLAEDD--ENPELTLILACRNLQRAEAACRALLASHPDA 57
Query: 64 IF---PLLVDVS 72
+LVD+S
Sbjct: 58 RVVFDYVLVDLS 69
>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 = 28.5 bits (64), Expect = 4.1
Identities = 9/23 (39%), Positives = 15/23 (65%)
Query: 7 RISITGAAGQIGYNIIFRIANGD 29
RI ITGA GQ+G ++ +++
Sbjct: 1 RILITGANGQLGRELVQQLSPEG 23
>gnl|CDD|187581 cd05273, GME-like_SDR_e, Arabidopsis thaliana
GDP-mannose-3',5'-epimerase (GME)-like, extended (e)
SDRs. This subgroup of NDP-sugar
epimerase/dehydratases are extended SDRs; they have the
characteristic active site tetrad, and an NAD-binding
motif: TGXXGXX[AG], which is a close match to the
canonical NAD-binding motif. Members include
Arabidopsis thaliana GDP-mannose-3',5'-epimerase (GME)
which catalyzes the epimerization of two positions of
GDP-alpha-D-mannose to form GDP-beta-L-galactose.
Extended SDRs are distinct from classical SDRs. In
addition to the Rossmann fold (alpha/beta folding
pattern with a central beta-sheet) core region typical
of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving
as a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton
relay involving the conserved Tyr and Lys, a water
molecule stabilized by Asn, and nicotinamide. Atypical
SDRs generally lack the catalytic residues
characteristic of the SDRs, and their glycine-rich
NAD(P)-binding motif is often different from the forms
normally seen in classical or extended SDRs. Complex
(multidomain) SDRs such as ketoreductase domains of
fatty acid synthase have a GGXGXXG NAD(P)-binding motif
and an altered active site motif (YXXXN). Fungal type
ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding
motif.
Length = 328
Score = 28.2 bits (63), Expect = 5.7
Identities = 17/77 (22%), Positives = 27/77 (35%), Gaps = 14/77 (18%)
Query: 7 RISITGAAGQIGYNIIFRIANGDLLGKDQPIILQLLEASNKKSQKAIKGVIMEIEDCIFP 66
R +TGA G IG ++ L + + A K + + D
Sbjct: 2 RALVTGAGGFIGSHLA-----ERLKAEGHYVRG----ADWKS-----PEHMTQPTDDDEF 47
Query: 67 LLVDVSVHENPITAFKD 83
LVD+ EN + A +
Sbjct: 48 HLVDLREMENCLKATEG 64
>gnl|CDD|227375 COG5042, NUP, Purine nucleoside permease [Nucleotide transport and
metabolism].
Length = 349
Score = 28.3 bits (63), Expect = 6.3
Identities = 21/79 (26%), Positives = 30/79 (37%), Gaps = 21/79 (26%)
Query: 160 RLDHNR-AIAKLASKLNEP----------VSSIKKVFVWGNHSLSMYPDYRYATVNGVLI 208
+D NR A+ + AS + P V+S FV +L YR L+
Sbjct: 281 LVDFNRVAVLRTASNFDRPYLGQTAFDSLVNSTSGGFVLATDNL-----YR---AGKPLV 332
Query: 209 RDMINNNSFWNKNVFLPAI 227
D++ S W V AI
Sbjct: 333 DDIVARWSRWEAGV--TAI 349
>gnl|CDD|202435 pfam02863, Arg_repressor_C, Arginine repressor, C-terminal domain.
Length = 67
Score = 25.9 bits (58), Expect = 7.0
Identities = 9/34 (26%), Positives = 15/34 (44%), Gaps = 1/34 (2%)
Query: 229 RRGEEIISIRGASSAASAASAAIDHIK-DWIFGT 261
E ++ I+ A ++ ID +K I GT
Sbjct: 7 DHNENLVVIKTLPGNAQLVASLIDSLKLPEILGT 40
>gnl|CDD|224407 COG1490, Dtd, D-Tyr-tRNAtyr deacylase [Translation, ribosomal
structure and biogenesis].
Length = 145
Score = 27.2 bits (61), Expect = 7.2
Identities = 12/29 (41%), Positives = 19/29 (65%)
Query: 297 IQNLEIDKFSRKKINLSIEELKNEILSIS 325
I NL I + K+NLS++++ EIL +S
Sbjct: 49 ILNLRIFEDEEGKMNLSVQDVGGEILVVS 77
>gnl|CDD|224326 COG1408, COG1408, Predicted phosphohydrolases [General function
prediction only].
Length = 284
Score = 27.8 bits (62), Expect = 7.4
Identities = 18/78 (23%), Positives = 29/78 (37%), Gaps = 10/78 (12%)
Query: 158 MLRLDHNRAIAKLASKLNEPVSSIKKVFVWGNHSLSMYPDYRYATVNGVLIRDMINNNSF 217
+ D +A LA L + + + V GNH DY N V I D++
Sbjct: 83 YVDGDRPPGVAALALFLAKLKAPLGVFAVLGNH------DYGVDRSN-VYIGDLLEELGR 135
Query: 218 ---WNKNVFLPAISRRGE 232
N+ + ++ R E
Sbjct: 136 VVLRNEIAVIDLLALRIE 153
>gnl|CDD|221124 pfam11496, HDA2-3, Class II histone deacetylase complex subunits 2
and 3. This family of class II histone deacetylase
complex subunits HDA2 and HDA3 is found in fungi, The
member from S. pombe is referred to as Ccq1. These
proteins associate with HDA1 to generate the activity of
the HDA1 histone deacetylase complex. HDA1 interacts
with itself and with the HDA2-HDA3 subcomplex to form a
probable tetramer and these interactions are necessary
for catalytic activity. The HDA1 histone deacetylase
complex is responsible for the deacetylation of lysine
residues on the N-terminal part of the core histones
(H2A, H2B, H3 and H4). Histone deacetylation gives a tag
for epigenetic repression and plays an important role in
transcriptional regulation, cell cycle progression and
developmental events. HDA2 and HDA3 have a conserved
coiled-coil domain towards their C-terminus.
Length = 279
Score = 27.7 bits (62), Expect = 9.4
Identities = 19/85 (22%), Positives = 33/85 (38%), Gaps = 4/85 (4%)
Query: 94 PRKSN-MERSELLAINSSIFIEQGKALNSVA--SRDVKVLVVGNPVNTNTYI-TMKSAPD 149
P+ E E LA S F+ +N + RD+ VL++ V T + +
Sbjct: 78 PKSLLLKEPPEHLAETSGKFLVLNDLINLLIRSERDLHVLIISRSVKTLDLVEALLLGKG 137
Query: 150 LSYKNFTAMLRLDHNRAIAKLASKL 174
L+YK + + N ++ L
Sbjct: 138 LNYKRLSGESLYEENHKVSDKKGSL 162
>gnl|CDD|233775 TIGR02197, heptose_epim,
ADP-L-glycero-D-manno-heptose-6-epimerase. This family
consists of examples of
ADP-L-glycero-D-mannoheptose-6-epimerase, an enzyme
involved in biosynthesis of the inner core of
lipopolysaccharide (LPS) for Gram-negative bacteria.
This enzyme is homologous to UDP-glucose 4-epimerase
(TIGR01179) and belongs to the NAD dependent
epimerase/dehydratase family (pfam01370) [Cell
envelope, Biosynthesis and degradation of surface
polysaccharides and lipopolysaccharides].
Length = 314
Score = 27.6 bits (62), Expect = 9.4
Identities = 8/17 (47%), Positives = 11/17 (64%)
Query: 8 ISITGAAGQIGYNIIFR 24
I +TG AG IG N++
Sbjct: 1 IIVTGGAGFIGSNLVKA 17
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.319 0.135 0.381
Gapped
Lambda K H
0.267 0.0709 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,741,213
Number of extensions: 1626942
Number of successful extensions: 1880
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1791
Number of HSP's successfully gapped: 63
Length of query: 329
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 232
Effective length of database: 6,635,264
Effective search space: 1539381248
Effective search space used: 1539381248
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 59 (26.5 bits)