RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 013466
(442 letters)
>gnl|CDD|215060 PLN00112, PLN00112, malate dehydrogenase (NADP); Provisional.
Length = 444
Score = 849 bits (2196), Expect = 0.0
Identities = 363/448 (81%), Positives = 393/448 (87%), Gaps = 11/448 (2%)
Query: 2 AVVAQLSPSSYTET-----TRLSSSQLSLSSTHLSSLRRRAFRPIIGPRNPTISCSVNQV 56
VA+LS T +RL SSQL LS THLS+ RRA P N ISCSVNQ
Sbjct: 1 MAVAELSTPKVTSPFLNTSSRLRSSQLGLSRTHLSNHFRRALLPRRRATNARISCSVNQA 60
Query: 57 -QAPVAVEQDDPKSKTNDCYGVFCLTYDLKAEEETKSWKKMVNIAVSGAAGMIANHLLFK 115
QAP AV++ K+K +CYGVFCLTYDLKAEEETKSWKK++N+AVSGAAGMI+NHLLFK
Sbjct: 61 SQAPAAVQEKGVKTK-KECYGVFCLTYDLKAEEETKSWKKLINVAVSGAAGMISNHLLFK 119
Query: 116 LAAGEVLGPDQPIALKLLGSERSLQALEGVAMELEDSLFPLLREVKIGINPYELFEDAEW 175
LA+GEV GPDQPIALKLLGSERS QALEGVAMELEDSL+PLLREV IGI+PYE+F+DAEW
Sbjct: 120 LASGEVFGPDQPIALKLLGSERSKQALEGVAMELEDSLYPLLREVSIGIDPYEVFQDAEW 179
Query: 176 ALLIGAKPRGPGMERAGLLDINGQIFAEQGKALNAVASRNVKVIVVGNPCNTNALICLKN 235
ALLIGAKPRGPGMERA LLDINGQIFAEQGKALN VASRNVKVIVVGNPCNTNALICLKN
Sbjct: 180 ALLIGAKPRGPGMERADLLDINGQIFAEQGKALNEVASRNVKVIVVGNPCNTNALICLKN 239
Query: 236 APSIPAKNFHALTRLDENRAKCQLALKAGVFYDKVSNMTIWGNHSTTQVPDFLNARINGL 295
AP+IPAKNFHALTRLDENRAKCQLALKAGVFYDKVSN+TIWGNHSTTQVPDFLNA+INGL
Sbjct: 240 APNIPAKNFHALTRLDENRAKCQLALKAGVFYDKVSNVTIWGNHSTTQVPDFLNAKINGL 299
Query: 296 PVKEIIKDHKWLEEGFTETIQKVRLRGGLLIKKWGRSSAASTAVSIVDAMKSLVTPTPEG 355
PVKE+I DHKWLEE FT +QK RGG+LIKKWGRSSAASTAVSI DA+KSLVTPTPEG
Sbjct: 300 PVKEVITDHKWLEEEFTPKVQK---RGGVLIKKWGRSSAASTAVSIADAIKSLVTPTPEG 356
Query: 356 DWFSSGVYTNGNPYGIAEDIVFSMPCRSKGDGDYELVKDVIFDDYLRKRIAKTEQELLAE 415
DWFS+GVYT+GNPYGIAE +VFSMPCRSKGDGDYE+VKDV DDYLR+RI K+E ELLAE
Sbjct: 357 DWFSTGVYTDGNPYGIAEGLVFSMPCRSKGDGDYEIVKDVEIDDYLRERIKKSEAELLAE 416
Query: 416 KKCVAHLTGEGIAFCDL-PEDTMLPGEM 442
K+CVAHLTGEG AFCDL PEDTMLPGEM
Sbjct: 417 KRCVAHLTGEGGAFCDLRPEDTMLPGEM 444
>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 = 680 bits (1756), Expect = 0.0
Identities = 306/392 (78%), Positives = 341/392 (86%), Gaps = 8/392 (2%)
Query: 52 SVNQVQAPVAVEQDDPKSKTNDCYGVFCLTYDLKAEEE--TKSWKKMVNIAVSGAAGMIA 109
+ QVQA VA + + T CYGVFCL+YDLK E++ TKSWKK VN+AVSGAAGMI+
Sbjct: 1 AAKQVQAGVATAE---AAATKKCYGVFCLSYDLKNEDKSLTKSWKKTVNVAVSGAAGMIS 57
Query: 110 NHLLFKLAAGEVLGPDQPIALKLLGSERSLQALEGVAMELEDSLFPLLREVKIGINPYEL 169
NHLLF LA+GEV G DQPIALKLLGSERS +ALEGVAMELEDSL+PLLREV IGI+PYE+
Sbjct: 58 NHLLFMLASGEVFGQDQPIALKLLGSERSKEALEGVAMELEDSLYPLLREVSIGIDPYEV 117
Query: 170 FEDAEWALLIGAKPRGPGMERAGLLDINGQIFAEQGKALNAVASRNVKVIVVGNPCNTNA 229
FEDA+WALLIGAKPRGPGMERA LLDINGQIFA+QGKALNAVAS+N KV+VVGNPCNTNA
Sbjct: 118 FEDADWALLIGAKPRGPGMERADLLDINGQIFADQGKALNAVASKNCKVLVVGNPCNTNA 177
Query: 230 LICLKNAPSIPAKNFHALTRLDENRAKCQLALKAGVFYDKVSNMTIWGNHSTTQVPDFLN 289
LI +KNAP+IP KNFHALTRLDENRAKCQLALK+G FY VSN+TIWGNHSTTQVPDF+N
Sbjct: 178 LIAMKNAPNIPRKNFHALTRLDENRAKCQLALKSGKFYTSVSNVTIWGNHSTTQVPDFVN 237
Query: 290 ARINGLPVKEIIKDHKWLEEGFTETIQKVRLRGGLLIKKWGRSSAASTAVSIVDAMKSLV 349
A+I G P KE+IKD KWLEE FT T+QK RGG LIKKWGRSSAASTAVSI DA+KSLV
Sbjct: 238 AKIGGRPAKEVIKDTKWLEEEFTPTVQK---RGGALIKKWGRSSAASTAVSIADAIKSLV 294
Query: 350 TPTPEGDWFSSGVYTNGNPYGIAEDIVFSMPCRSKGDGDYELVKDVIFDDYLRKRIAKTE 409
PTPEGDWFS+GVYT+GNPYGIAE +VFSMPCRSKGDGDYEL DV DD+LR+RI K+E
Sbjct: 295 VPTPEGDWFSTGVYTDGNPYGIAEGLVFSMPCRSKGDGDYELATDVSMDDFLRERIRKSE 354
Query: 410 QELLAEKKCVAHLTGEGIAFCDLPEDTMLPGE 441
ELL EK+CVAHL GEG A+C +PEDTMLPGE
Sbjct: 355 DELLKEKECVAHLIGEGNAYCAVPEDTMLPGE 386
>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 = 573 bits (1480), Expect = 0.0
Identities = 195/327 (59%), Positives = 235/327 (71%), Gaps = 5/327 (1%)
Query: 95 KMVNIAVSGAAGMIANHLLFKLAAGEVLGPDQPIALKLLGSERSLQALEGVAMELEDSLF 154
K V +AV+GAAG I LLF++A+GE+ GPDQP+ L+LL ++L+ALEGVAMELED F
Sbjct: 1 KPVRVAVTGAAGQIGYSLLFRIASGEMFGPDQPVILQLLELPQALKALEGVAMELEDCAF 60
Query: 155 PLLREVKIGINPYELFEDAEWALLIGAKPRGPGMERAGLLDINGQIFAEQGKALNAVASR 214
PLL E+ I +P F+DA+WALL+GAKPRGPGMERA LL NG+IF QGKALN VASR
Sbjct: 61 PLLAEIVITDDPNVAFKDADWALLVGAKPRGPGMERADLLKANGKIFTAQGKALNDVASR 120
Query: 215 NVKVIVVGNPCNTNALICLKNAPSIPAKNFHALTRLDENRAKCQLALKAGVFYDKVSNMT 274
+VKV+VVGNPCNTNALI +KNAP IP NF A+TRLD NRAK QLA KAGV V NM
Sbjct: 121 DVKVLVVGNPCNTNALIAMKNAPDIPPDNFTAMTRLDHNRAKSQLAKKAGVPVTDVKNMV 180
Query: 275 IWGNHSTTQVPDFLNARINGLPVKEIIKDHKWLEEGFTETIQKVRLRGGLLIKKWGRSSA 334
IWGNHS TQ PDF NA I G P E+I D WLE+ F T+QK RG +IK G SSA
Sbjct: 181 IWGNHSPTQYPDFTNATIGGKPAAEVINDRAWLEDEFIPTVQK---RGAAIIKARGASSA 237
Query: 335 ASTAVSIVDAMKSLVTPTPEGDWFSSGVYTNGNPYGIAEDIVFSMPCRSKGDGDYELVKD 394
AS A + +D M+ V TPEGDWFS V ++G YGI E ++FS P RSKG G YE+V+
Sbjct: 238 ASAANAAIDHMRDWVLGTPEGDWFSMAVPSDG-SYGIPEGLIFSFPVRSKGGG-YEIVEG 295
Query: 395 VIFDDYLRKRIAKTEQELLAEKKCVAH 421
+ DD+ R++I T ELL E++ V H
Sbjct: 296 LEIDDFAREKIDATLAELLEEREAVKH 322
>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 = 518 bits (1336), Expect = 0.0
Identities = 190/326 (58%), Positives = 235/326 (72%), Gaps = 3/326 (0%)
Query: 94 KKMVNIAVSGAAGMIANHLLFKLAAGEVLGPDQPIALKLLGSERSLQALEGVAMELEDSL 153
KK V +AV+GAAG I LLF++A+GE+ G DQP+ L LL +++ALEGVAMELED
Sbjct: 1 KKPVRVAVTGAAGQIGYSLLFRIASGELFGKDQPVVLHLLDIPPAMKALEGVAMELEDCA 60
Query: 154 FPLLREVKIGINPYELFEDAEWALLIGAKPRGPGMERAGLLDINGQIFAEQGKALNAVAS 213
FPLL V +P E F+D + ALL+GA PR PGMERA LL NG+IF EQGKALN VA
Sbjct: 61 FPLLAGVVATTDPEEAFKDVDAALLVGAFPRKPGMERADLLSKNGKIFKEQGKALNKVAK 120
Query: 214 RNVKVIVVGNPCNTNALICLKNAPSIPAKNFHALTRLDENRAKCQLALKAGVFYDKVSNM 273
++VKV+VVGNP NTNALI KNAP IP KNF A+TRLD NRAK QLA KAGV V N+
Sbjct: 121 KDVKVLVVGNPANTNALIASKNAPDIPPKNFSAMTRLDHNRAKYQLAAKAGVPVSDVKNV 180
Query: 274 TIWGNHSTTQVPDFLNARINGLPVKEIIKDHKWLEEGFTETIQKVRLRGGLLIKKWGRSS 333
IWGNHS TQVPDF +A ++G PVKE+IKD KWLE F T+Q+ RG +I+ G SS
Sbjct: 181 IIWGNHSNTQVPDFTHATVDGRPVKEVIKDDKWLEGEFIPTVQQ---RGAAVIEARGASS 237
Query: 334 AASTAVSIVDAMKSLVTPTPEGDWFSSGVYTNGNPYGIAEDIVFSMPCRSKGDGDYELVK 393
AAS A + +D ++ VT TPEGDW S GVY++GNPYGI E I+FS P KGDG++E+V+
Sbjct: 238 AASAANAAIDHVRDWVTGTPEGDWVSMGVYSDGNPYGIPEGIIFSFPVTCKGDGEWEIVE 297
Query: 394 DVIFDDYLRKRIAKTEQELLAEKKCV 419
+ DD++R ++ TE ELL EK+
Sbjct: 298 GLPLDDFVRGKLDATEDELLEEKEEA 323
>gnl|CDD|235468 PRK05442, PRK05442, malate dehydrogenase; Provisional.
Length = 326
Score = 489 bits (1261), Expect = e-174
Identities = 176/329 (53%), Positives = 229/329 (69%), Gaps = 5/329 (1%)
Query: 94 KKMVNIAVSGAAGMIANHLLFKLAAGEVLGPDQPIALKLLGSERSLQALEGVAMELEDSL 153
K V +AV+GAAG I LLF++A+G++LG DQP+ L+LL +L+ALEGV MEL+D
Sbjct: 2 KAPVRVAVTGAAGQIGYSLLFRIASGDMLGKDQPVILQLLEIPPALKALEGVVMELDDCA 61
Query: 154 FPLLREVKIGINPYELFEDAEWALLIGAKPRGPGMERAGLLDINGQIFAEQGKALNAVAS 213
FPLL V I +P F+DA+ ALL+GA+PRGPGMER LL+ NG IF QGKALN VA+
Sbjct: 62 FPLLAGVVITDDPNVAFKDADVALLVGARPRGPGMERKDLLEANGAIFTAQGKALNEVAA 121
Query: 214 RNVKVIVVGNPCNTNALICLKNAPSIPAKNFHALTRLDENRAKCQLALKAGVFYDKVSNM 273
R+VKV+VVGNP NTNALI +KNAP +PA+NF A+TRLD NRA QLA KAGV + M
Sbjct: 122 RDVKVLVVGNPANTNALIAMKNAPDLPAENFTAMTRLDHNRALSQLAAKAGVPVADIKKM 181
Query: 274 TIWGNHSTTQVPDFLNARINGLPVKEIIKDHKWLEEGFTETIQKVRLRGGLLIKKWGRSS 333
T+WGNHS TQ PDF +A I+G P E+I D WLE+ F T+QK RG +I+ G SS
Sbjct: 182 TVWGNHSATQYPDFRHATIDGKPAAEVINDQAWLEDTFIPTVQK---RGAAIIEARGASS 238
Query: 334 AASTAVSIVDAMKSLVTPTPEGDWFSSGVYTNGNPYGIAEDIVFSMPCRSKGDGDYELVK 393
AAS A + +D ++ V TPEGDW S GV ++G+ YGI E ++F P + +G+YE+V+
Sbjct: 239 AASAANAAIDHVRDWVLGTPEGDWVSMGVPSDGS-YGIPEGLIFGFPVTCE-NGEYEIVQ 296
Query: 394 DVIFDDYLRKRIAKTEQELLAEKKCVAHL 422
+ DD+ R++I T EL E+ V HL
Sbjct: 297 GLEIDDFSREKIDATLAELEEERDAVKHL 325
>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 = 486 bits (1252), Expect = e-172
Identities = 172/327 (52%), Positives = 223/327 (68%), Gaps = 7/327 (2%)
Query: 97 VNIAVSGAAGMIANHLLFKLAAGEVLGPDQPIALKLLGSERSLQALEGVAMELEDSLFPL 156
+++ ++GAAG I +LLF +A+GE+ G DQP+ L LL +++ALEGV MEL+D FPL
Sbjct: 1 LHVLITGAAGQIGYNLLFLIASGELFGDDQPVILHLLDIPPAMKALEGVVMELQDCAFPL 60
Query: 157 LREVKIGINPYELFEDAEWALLIGAKPRGPGMERAGLLDINGQIFAEQGKALNAVASRNV 216
L+ V I +P E F+D + A+L+GA PR PGMERA LL N +IF EQG+ALN VA V
Sbjct: 61 LKGVVITTDPEEAFKDVDVAILVGAFPRKPGMERADLLRKNAKIFKEQGEALNKVAKPTV 120
Query: 217 KVIVVGNPCNTNALICLKNAPSIPAKNFHALTRLDENRAKCQLALKAGVFYDKVSNMTIW 276
KV+VVGNP NTNALI LKNAP++P KNF ALTRLD NRAK Q+A K GV V N+ IW
Sbjct: 121 KVLVVGNPANTNALIALKNAPNLPPKNFTALTRLDHNRAKAQVARKLGVRVSDVKNVIIW 180
Query: 277 GNHSTTQVPDFLNARINGLPVKEIIKDH---KWLEEGFTETIQKVRLRGGLLIKKWGRSS 333
GNHS TQVPD NA + G E + D +WL + F +T+QK RG +IKK G SS
Sbjct: 181 GNHSNTQVPDLSNAVVYGPGGTEWVLDLLDEEWLNDEFVKTVQK---RGAAIIKKRGASS 237
Query: 334 AASTAVSIVDAMKSLVTPTPEGDWFSSGVYTNGNPYGIAEDIVFSMPCRSKGDGDYELVK 393
AAS A +I D +K + TP G+ S GVY+ GNPYGI IVFS PC KG G + +V+
Sbjct: 238 AASAAKAIADHVKDWLFGTPPGEIVSMGVYSPGNPYGIPPGIVFSFPCTCKGGG-WHVVE 296
Query: 394 DVIFDDYLRKRIAKTEQELLAEKKCVA 420
D+ +D+LR+++ TE+EL+ EK+
Sbjct: 297 DLKLNDWLREKLKATEEELIEEKEIAL 323
>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 = 402 bits (1036), Expect = e-140
Identities = 162/324 (50%), Positives = 213/324 (65%), Gaps = 9/324 (2%)
Query: 97 VNIAVSGAAGMIANHLLFKLAAGEVLGPDQPIALKLLGSERSLQALEGVAMELEDSLFPL 156
+ + V+GAAG IA LL +A G+V GPDQP+ L LL +L+ALEGV MEL+D FPL
Sbjct: 3 IRVLVTGAAGQIAYSLLPMIAKGDVFGPDQPVILHLLDIPPALKALEGVVMELQDCAFPL 62
Query: 157 LREVKIGINPYELFEDAEWALLIGAKPRGPGMERAGLLDINGQIFAEQGKALNAVASRNV 216
L+ V +P E F+D + A+L+GA PR GMER LL N +IF EQG+AL+ A +NV
Sbjct: 63 LKSVVATTDPEEAFKDVDVAILVGAMPRKEGMERKDLLKANVKIFKEQGEALDKYAKKNV 122
Query: 217 KVIVVGNPCNTNALICLKNAPSIPAKNFHALTRLDENRAKCQLALKAGVFYDKVSNMTIW 276
KV+VVGNP NTNALI LK APSIP +NF ALTRLD NRAK Q+ALK GV V N+ IW
Sbjct: 123 KVLVVGNPANTNALILLKYAPSIPKENFTALTRLDHNRAKSQIALKLGVPVSDVKNVIIW 182
Query: 277 GNHSTTQVPDFLNARIN----GLPVKEIIKDHKWLEEGFTETIQKVRLRGGLLIKKWGRS 332
GNHS+TQ PD +A + G P +E +KD WL F T+QK RG +IK S
Sbjct: 183 GNHSSTQYPDVNHATVELNGKGKPAREAVKDDAWLNGEFISTVQK---RGAAVIKARKLS 239
Query: 333 SAASTAVSIVDAMKSLVTPTPEGDWFSSGVYTNGNPYGIAEDIVFSMPCRSKGDGDYELV 392
SA S A +I D + TPEG++ S GVY++G+ YG+ E ++FS P K +G +++V
Sbjct: 240 SAMSAAKAICDHVHDWWFGTPEGEFVSMGVYSDGS-YGVPEGLIFSFPVTCK-NGKWKIV 297
Query: 393 KDVIFDDYLRKRIAKTEQELLAEK 416
+ + DD+ R++I T +EL+ EK
Sbjct: 298 QGLSIDDFSREKIDATAKELVEEK 321
>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 = 319 bits (820), Expect = e-107
Identities = 152/322 (47%), Positives = 204/322 (63%), Gaps = 8/322 (2%)
Query: 99 IAVSGAAGMIANHLLFKLAAGEVLGPDQPIALKLLGSERSLQALEGVAMELEDSLFPLLR 158
+ V+GAAG I LL +A G +LG DQPI L LL +++ LEGV MEL D FPLL
Sbjct: 2 VVVTGAAGQIGYALLPMIARGRMLGKDQPIILHLLDIPPAMKVLEGVVMELMDCAFPLLD 61
Query: 159 EVKIGINPYELFEDAEWALLIGAKPRGPGMERAGLLDINGQIFAEQGKALNAVASRNVKV 218
V +P F D + A+L+GA PR GMER LL N +IF EQG+AL+ +A ++ KV
Sbjct: 62 GVVPTHDPAVAFTDVDVAILVGAFPRKEGMERRDLLSKNVKIFKEQGRALDKLAKKDCKV 121
Query: 219 IVVGNPCNTNALICLKNAPSIPAKNFHALTRLDENRAKCQLALKAGVFYDKVSNMTIWGN 278
+VVGNP NTNAL+ APSIP KNF ALTRLD NRA Q+A +AGV V N+ IWGN
Sbjct: 122 LVVGNPANTNALVLSNYAPSIPPKNFSALTRLDHNRALAQVAERAGVPVSDVKNVIIWGN 181
Query: 279 HSTTQVPDFLNARING----LPVKEIIKDHKWLEEGFTETIQKVRLRGGLLIKKWGRSSA 334
HS+TQ PD +A + PV+E IKD +L+ F T+Q+ RG +I+ SSA
Sbjct: 182 HSSTQYPDVNHATVTKGGKQKPVREAIKDDAYLDGEFITTVQQ---RGAAIIRARKLSSA 238
Query: 335 ASTAVSIVDAMKSLVTPTPEGDWFSSGVYTNGNPYGIAEDIVFSMPCRSKGDGDYELVKD 394
S A + VD M V TPEG + S GVY++G+PYG+ + ++FS P K +G++++V+
Sbjct: 239 LSAAKAAVDQMHDWVLGTPEGTFVSMGVYSDGSPYGVPKGLIFSFPVTCK-NGEWKIVEG 297
Query: 395 VIFDDYLRKRIAKTEQELLAEK 416
+ DD RK++A T +EL E+
Sbjct: 298 LCVDDSSRKKLALTAKELEEER 319
>gnl|CDD|177744 PLN00135, PLN00135, malate dehydrogenase.
Length = 309
Score = 266 bits (681), Expect = 2e-86
Identities = 126/305 (41%), Positives = 179/305 (58%), Gaps = 9/305 (2%)
Query: 116 LAAGEVLGPDQPIALKLLGSERSLQALEGVAMELEDSLFPLLREVKIGINPYELFEDAEW 175
+A G +LGPDQP+ L +L + +AL GV MEL D+ FPLL+ V + E +
Sbjct: 2 IARGVMLGPDQPVILHMLDIPPAAEALNGVKMELIDAAFPLLKGVVATTDVVEACKGVNI 61
Query: 176 ALLIGAKPRGPGMERAGLLDINGQIFAEQGKALNAVASRNVKVIVVGNPCNTNALICLKN 235
A+++G PR GMER ++ N I+ Q AL A+ + KV+VV NP NTNALI +
Sbjct: 62 AVMVGGFPRKEGMERKDVMSKNVSIYKSQASALEKHAAPDCKVLVVANPANTNALILKEF 121
Query: 236 APSIPAKNFHALTRLDENRAKCQLALKAGVFYDKVSNMTIWGNHSTTQVPDFLNARIN-- 293
APSIP KN LTRLD NRA Q++ + GV V N+ IWGNHS+TQ PD +A +
Sbjct: 122 APSIPEKNITCLTRLDHNRALGQISERLGVPVSDVKNVIIWGNHSSTQYPDVNHATVKTP 181
Query: 294 --GLPVKEIIKDHKWLEEGFTETIQKVRLRGGLLIKKWGRSSAASTAVSIVDAMKSLVTP 351
PV+E++ D WL F T+Q+ RG +IK SSA S A S D ++ V
Sbjct: 182 SGEKPVRELVADDAWLNGEFITTVQQ---RGAAIIKARKLSSALSAASSACDHIRDWVLG 238
Query: 352 TPEGDWFSSGVYTNGNPYGIAEDIVFSMPCRSKGDGDYELVKDVIFDDYLRKRIAKTEQE 411
TPEG W S GVY++G+ YG+ +++S P + G++ +V+ + D++ RK++ T +E
Sbjct: 239 TPEGTWVSMGVYSDGS-YGVPPGLIYSFPVTCEK-GEWSIVQGLSIDEFSRKKMDATAKE 296
Query: 412 LLAEK 416
L EK
Sbjct: 297 LKEEK 301
>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 = 226 bits (577), Expect = 2e-71
Identities = 95/320 (29%), Positives = 139/320 (43%), Gaps = 58/320 (18%)
Query: 99 IAVSGAAGMIANHLLFKLAAGEVLGPDQPIALKLLGSERSLQALEGVAMELEDSLFPL-L 157
IAV GA G + L F LA G V I L L + + L+GVAM+L+D++ PL
Sbjct: 1 IAVIGAGGNVGPALAFGLADGSV---LLAIELVLYDIDE--EKLKGVAMDLQDAVEPLAD 55
Query: 158 REVKIGINPYELFEDAEWALLIGAKPRGPGMERAGLLDINGQIFAEQGKALNAVASRNVK 217
+V I +PYE F+DA+ ++ R PGM R LL N I E G + + +
Sbjct: 56 IKVSITDDPYEAFKDADVVIITAGVGRKPGMGRLDLLKRNVPIVKEIGDNIEKYSP-DAW 114
Query: 218 VIVVGNPCNTNALICLKNAPSIPAKNFHALTRLDENRAKCQLALKAGVFYDKVSNMTIWG 277
+IVV NP + + + + +P + L LD R + LA K GV D V + I G
Sbjct: 115 IIVVSNPVDIITYLVWRYSG-LPKEKVIGLGTLDPIRFRRILAEKLGVDPDDV-KVYILG 172
Query: 278 NHSTTQVPDFLNARINGLPVKEIIKDHKWLEEGFTETIQKVRLRGGLLIKKWGRSSAAST 337
H +QVPD+ RI
Sbjct: 173 EHGGSQVPDWSTVRI--------------------------------------------- 187
Query: 338 AVSIVDAMKSLVTPTPEGDWFSSGVYTNGNPYGIAEDIVFSMPCRSKGDGDYELVKDVIF 397
A SI D ++SL+ EG+ GV NG GI +D+V S+PC +G E ++ V
Sbjct: 188 ATSIADLIRSLL--NDEGEILPVGVRNNGQ-IGIPDDVVVSVPCIVGKNGVEEPIE-VGL 243
Query: 398 DDYLRKRIAKTEQELLAEKK 417
D+ +++ K+ L E +
Sbjct: 244 TDFELEKLQKSADTLKKELE 263
>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 = 220 bits (563), Expect = 7e-69
Identities = 104/307 (33%), Positives = 167/307 (54%), Gaps = 2/307 (0%)
Query: 112 LLFKLAAGEVLGPDQPIALKLLGSERSLQALEGVAMELEDSLFPLLREVKIGINPYELFE 171
L +A G++ G ++P+ L LL +L LE +AMELED FP L + E F+
Sbjct: 1 LSHWIANGDLYG-NRPVCLHLLEIPPALNRLEALAMELEDCAFPNLAGTIVTTKLEEAFK 59
Query: 172 DAEWALLIGAKPRGPGMERAGLLDINGQIFAEQGKALNAVASRNVKVIVVGNPCNTNALI 231
D + A L+ + P PG RA LL N IF G+AL+ A VKV+V+GNP NTN L+
Sbjct: 60 DIDCAFLVASVPLKPGEVRADLLTKNTPIFKATGEALSEYAKPTVKVLVIGNPVNTNCLV 119
Query: 232 CLKNAPSIPAKNFHALTRLDENRAKCQLALKAGVFYDKVSNMTIWGNHSTTQVPDFLNAR 291
+ +AP + A+NF +L LD NRA ++A K V D + ++ +WGNH+ + V D +A
Sbjct: 120 AMLHAPKLSAENFSSLCMLDHNRAVSRIASKLKVPVDHIYHVVVWGNHAESMVADLTHAE 179
Query: 292 INGLPVKEIIKDHKWLEEGFTETIQKVRLRGGLLIKKWGRSSAASTAVSIVDAMKSLVTP 351
+ + D + + + + R +++ G +SAAS + + MK+ +
Sbjct: 180 FTKNGKHQKVFDELCRDYPEPDFFEVIAQRAWKILEMRGFTSAASPVKASLQHMKAWLFG 239
Query: 352 TPEGDWFSSGV-YTNGNPYGIAEDIVFSMPCRSKGDGDYELVKDVIFDDYLRKRIAKTEQ 410
T G+ S G+ GNPYGI ++FS PC DG +V++ + +L+ ++A+TE+
Sbjct: 240 TRPGEVLSMGIPVPEGNPYGIKPGVIFSFPCTVDEDGKVHVVENFELNPWLKTKLAQTEK 299
Query: 411 ELLAEKK 417
+L E++
Sbjct: 300 DLFEERE 306
>gnl|CDD|223117 COG0039, Mdh, Malate/lactate dehydrogenases [Energy production and
conversion].
Length = 313
Score = 208 bits (533), Expect = 3e-64
Identities = 92/326 (28%), Positives = 157/326 (48%), Gaps = 20/326 (6%)
Query: 99 IAVSGAAGMIANHLLFKLAAGEVLGPDQPIALKLLGSERSLQALEGVAMELEDSLFPLLR 158
+AV GA G + + L F L + LG + L L+ + + + EGVA++L + PL
Sbjct: 3 VAVIGA-GNVGSSLAF-LLLLQGLGSE----LVLI--DINEEKAEGVALDLSHAAAPLGS 54
Query: 159 EVKI-GINPYELFEDAEWALLIGAKPRGPGMERAGLLDINGQIFAEQGKALNAVASRNVK 217
+VKI G YE + A+ ++ PR PGM R LL+ N +I + KA+ A +
Sbjct: 55 DVKITGDGDYEDLKGADIVVITAGVPRKPGMTRLDLLEKNAKIVKDIAKAIAKYAP-DAI 113
Query: 218 VIVVGNPCNTNALICLKNAPSIPAKNFHALTRLDENRAKCQLALKAGVFYDKVSNMTIWG 277
V+VV NP + I +K + + + T LD R + LA K GV V I G
Sbjct: 114 VLVVTNPVDILTYIAMKFSGFPKNRVIGSGTVLDSARFRTFLAEKLGVSPKDVHAYVI-G 172
Query: 278 NHSTTQVPDFLNARINGLPVKEIIK-DHKWLEEGFTETIQKVRLRGGLLIKKWGRSSAAS 336
H T VP + A + G P++E++K D + E E ++ G +I+ G +
Sbjct: 173 EHGDTMVPLWSQATVGGKPLEELLKEDTEEDLEELIERVRN---AGAEIIEAKGAGTYYG 229
Query: 337 TAVSIVDAMKSLVTPTPEGDWFSSGVYTNGNPYGIAEDIVFSMPCRSKGDGDYELVKDVI 396
A ++ +++++ E VY +G YG+ ED+ F +P +G E++ +++
Sbjct: 230 PAAALARMVEAIL--RDEKRVLPVSVYLDGE-YGV-EDVYFGVPAVLGKNGVEEIL-ELL 284
Query: 397 FDDYLRKRIAKTEQELLAEKKCVAHL 422
D ++++ K+ +EL + V L
Sbjct: 285 LSDDEQEKLDKSAEELKKNIELVKEL 310
>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 = 201 bits (514), Expect = 7e-60
Identities = 110/350 (31%), Positives = 171/350 (48%), Gaps = 27/350 (7%)
Query: 83 DLKAEEETKSWKKMVN---IAVSGAAGMIANHLLFKLAAGEVLGPDQPIALKLLGSERSL 139
+++ EEE + +N + ++ A+ + HL+ LA+GEV G ++ I++ LL S +L
Sbjct: 109 EVEKEEEEL--RSKINPLQVCITNASAPLCYHLIPSLASGEVFGMEEEISIHLLDSPENL 166
Query: 140 QALEGVAMELEDSLFPLLREVKIGINPYELFEDAEWALLIGAKPRGPGMERAGLLDINGQ 199
+ L+G+ ME+ED FPLLR + + + F+DA +L+ G + G +
Sbjct: 167 EKLKGLVMEVEDLAFPLLRGISVTTDLDVAFKDAHVIVLLDDFLIKEGEDLEGCIRSRVA 226
Query: 200 IFAEQGKALNAVASRNVKVIVVG-NPCNTNALICLKNAPSIPAKNFHALTRLDENRAKCQ 258
I G + A +VKVIV G N I +K APSIP KN A+ RL ENRAK
Sbjct: 227 ICQLYGPLIEKNAKEDVKVIVAGRTFLNLKTSILIKYAPSIPRKNIIAVARLQENRAKAL 286
Query: 259 LALKAGVFYDKVSNMTIWGNHSTTQVPDFLNARINGL------------PVKEIIKDHKW 306
LA K V + ++ +WGN D AR+ PV E++ D KW
Sbjct: 287 LARKLNVNSAGIKDVIVWGNIGGNTYIDLSKARVYRYDSAIWGPPNYSRPVLELVHDSKW 346
Query: 307 LEEGFTETIQKVRLRGGLLIKKWGRSSAASTAVSIVDAMKSLVTPTPEGDWFSSGVYTNG 366
+ F T++ + +A S A +I + +P G+ FS GV + G
Sbjct: 347 INGEFVATLKSLSSSL-------NHEAAISPAHAIATTLSYWYHGSPPGEIFSLGVISEG 399
Query: 367 NPYGIAEDIVFSMPCRSKGDGDYELVKDVIFDDYLRKRIAKTEQELLAEK 416
YGI E IVFSMP + + G +E+V D+ + LR+ + + +L+ EK
Sbjct: 400 W-YGIPEGIVFSMPVKFQN-GSWEVVTDLELSEILREVLKRITSDLIQEK 447
>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 = 169 bits (431), Expect = 5e-51
Identities = 58/180 (32%), Positives = 90/180 (50%), Gaps = 11/180 (6%)
Query: 248 TRLDENRAKCQLALKAGVFYDKVSNMTIWGNHSTTQVPDFLNARINGLP----VKEIIKD 303
T LD RA+ LA K GV + N+ + G HS TQ PD+ +A++ +P VKE +KD
Sbjct: 1 TTLDTARARTFLAEKFGV-DPRSVNVYVIGEHSGTQFPDWSHAKVTIIPLISQVKENLKD 59
Query: 304 HKWLEEGFTETIQKVRLRGGLLIKKWGRSSAASTAVSIVDAMKSLVTPTPEGDWFSSGVY 363
W E E +Q G +I+ S+ S A + K+++ T G S GVY
Sbjct: 60 TDWELEELIERVQN---AGYEVIEAKAGSTTYSMAYAAARIAKAILRGT--GGVLSVGVY 114
Query: 364 TNGNPYGIAEDIVFSMPCRSKGDGDYELVKDVIFDDYLRKRIAKTEQELLAEKKCVAHLT 423
+G YG +DI FS+P DG ++V+ + +D+ R+++ K+ EL E +
Sbjct: 115 LDGY-YGSPDDIYFSVPVVLGKDGVEKVVEILPLNDFEREKLEKSAAELKKEIEKGFAFV 173
>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 = 148 bits (375), Expect = 4e-43
Identities = 46/150 (30%), Positives = 69/150 (46%), Gaps = 8/150 (5%)
Query: 97 VNIAVSGAAGMIANHLLFKLAAGEVLGPDQPIALKLLGSERSLQALEGVAMELEDSLFPL 156
V +AV GA G + + L F LA + L + L L+ + EGVAM+L L
Sbjct: 1 VKVAVVGAGGGVGSSLAFALA-LQGLADE----LVLVDINK--DKAEGVAMDLSHGSTFL 53
Query: 157 LREVKIGINPYELFEDAEWALLIGAKPRGPGMERAGLLDINGQIFAEQGKALNAVASRNV 216
+G + YE +DA+ ++ PR PGM R LL+ N IF + A+ A +
Sbjct: 54 SVPGIVGGDDYEALKDADVVVITAGVPRKPGMTRLDLLNRNAGIFKDIVPAIAKSAP-DA 112
Query: 217 KVIVVGNPCNTNALICLKNAPSIPAKNFHA 246
V+VV NP + I K + P + +
Sbjct: 113 IVLVVSNPVDILTYIAWKVSGLPPERVIGS 142
>gnl|CDD|173409 PTZ00117, PTZ00117, malate dehydrogenase; Provisional.
Length = 319
Score = 74.8 bits (184), Expect = 7e-15
Identities = 60/206 (29%), Positives = 93/206 (45%), Gaps = 7/206 (3%)
Query: 163 GINPYELFEDAEWALLIGAKPRGPGMERAGLLDINGQIFAEQGKALNAVASRNVKVIVVG 222
G N YE +D++ ++ R M R LL ING+I +++ N VI V
Sbjct: 64 GTNNYEDIKDSDVVVITAGVQRKEEMTREDLLTINGKIMKSVAESVK-KYCPNAFVICVT 122
Query: 223 NPCNTNALICLKNAPSIPAKNFHALT-RLDENRAKCQLALKAGVFYDKVSNMTIWGNHST 281
NP + + + IP+ + LD +R +C LA K GV VS + I G H
Sbjct: 123 NPLDCMVKV-FQEKSGIPSNKICGMAGVLDSSRFRCNLAEKLGVSPGDVSAVVI-GGHGD 180
Query: 282 TQVPDFLNARINGLPVKEIIKDHKWLEEGFTETIQKVRLRGGLLIKKWGRSSAA-STAVS 340
VP +NG+P+ + +K E+ E I+K R GG ++K + SA + A +
Sbjct: 181 LMVPLPRYCTVNGIPLSDFVKKGAITEKEINEIIKKTRNMGGEIVKLLKKGSAFFAPAAA 240
Query: 341 IVDAMKSLVTPTPEGDWFSSGVYTNG 366
IV +++ + E VY NG
Sbjct: 241 IVAMIEAYL--KDEKRVLVCSVYLNG 264
>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 = 67.8 bits (166), Expect = 1e-12
Identities = 55/237 (23%), Positives = 105/237 (44%), Gaps = 11/237 (4%)
Query: 97 VNIAVSGAAGMIANHLLFKLAAGEVLGPDQPIALKLLGSERSLQALEGVAMELEDSLFPL 156
+ +++ GA+G + + LA +V+ + L+ +SL+ L+G+ +++ D+L
Sbjct: 1 MKVSIIGASGRVGSATALLLAKEDVVK-----EINLISRPKSLEKLKGLRLDIYDALAAA 55
Query: 157 LREVKIGIN-PYELFEDAEWALLIGAKPRGPGMERAGLLDINGQIFAEQGKALNAVASRN 215
+ +I I+ ++ ++ PR GM R L N +I + K + A + +
Sbjct: 56 GIDAEIKISSDLSDVAGSDIVIITAGVPRKEGMSRLDLAKKNAKIVKKYAKQI-AEFAPD 114
Query: 216 VKVIVVGNPCNTNALICLKNAPSIPAKNFHALTRLDENRAKCQLALKAGVFYDKVSNMTI 275
K++VV NP + LK + + F T LD R K +A V +V I
Sbjct: 115 TKILVVTNPVDVMTYKALKESGFDKNRVFGLGTHLDSLRFKVAIAKHFNVHISEVHTRII 174
Query: 276 WGNHSTTQVPDFLNARINGLPVKEIIKDHKWLEEGFTETIQKVRLRGGLLIKKWGRS 332
G H + VP + I G+P+K ++ + + ++ V+ G +I G S
Sbjct: 175 -GEHGDSMVPLISSTSIGGIPIKRFP---EYKDFDVEKIVETVKNAGQNIISLKGGS 227
>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 = 65.6 bits (161), Expect = 7e-12
Identities = 70/264 (26%), Positives = 113/264 (42%), Gaps = 33/264 (12%)
Query: 143 EGVAMELEDSLFPLLR-EVKI-GINPYELFEDAEWALLIGA-KPRGPGMERAGLLDINGQ 199
+G A+++ + P+L + K+ G N YE ++ ++I A PR PGM R LL N +
Sbjct: 36 QGKALDISQAA-PILGSDTKVTGTNDYEDIAGSD-VVVITAGIPRKPGMSRDDLLGTNAK 93
Query: 200 IFAEQGKALNAVASRNVKVIVVGNPCNTNALICLKNAPSIPAKNFHALTRLDENRAKCQL 259
I E + + A N VIVV NP + + K + + LD R + +
Sbjct: 94 IVKEVAENIKKYAP-NAIVIVVTNPLDVMTYVAYKASGFPRNRVIGMAGVLDSARFRYFI 152
Query: 260 ALKAGVFYDKVSNMTIWGNHSTTQVPDFLNARINGLPVKEIIKDHKWLEEGFTETIQKVR 319
A + GV V M + G H T VP + + G+P+ E+I + E +++ R
Sbjct: 153 AEELGVSVKDVQAMVL-GGHGDTMVPLPRYSTVGGIPLTELITKEEI-----DEIVERTR 206
Query: 320 LRGGLLIKKWGRSSA----ASTAVSIVDAM---KSLVTPTPEGDWFSSGVYTNGNPYGIA 372
G ++ SA A+ +V+A+ K V P Y G YGI
Sbjct: 207 NGGAEIVNLLKTGSAYYAPAAAIAEMVEAILKDKKRVLPC--------SAYLEGE-YGI- 256
Query: 373 EDIVFSMPCRSKGDGDYELVKDVI 396
+DI +P +G V+ +I
Sbjct: 257 KDIFVGVPVVLGKNG----VEKII 276
>gnl|CDD|180477 PRK06223, PRK06223, malate dehydrogenase; Reviewed.
Length = 307
Score = 62.1 bits (152), Expect = 9e-11
Identities = 72/301 (23%), Positives = 126/301 (41%), Gaps = 44/301 (14%)
Query: 95 KMVNIAVSGAAGMIANHLLFKLAA---GEVLGPDQPIALKLLGSERSLQALEGVAMELED 151
I++ GA G + L LA G+V+ L +G A+++ +
Sbjct: 1 ARKKISIIGA-GNVGATLAHLLALKELGDVV---------LFD--IVEGVPQGKALDIAE 48
Query: 152 SLFPLLREVKI-GINPYELFEDAEWALLIGAK-PRGPGMERAGLLDINGQIFAEQGKALN 209
+ + KI G N YE ++ ++I A PR PGM R LL IN +I + + +
Sbjct: 49 AAPVEGFDTKITGTNDYEDIAGSD-VVVITAGVPRKPGMSRDDLLGINAKIMKDVAEGIK 107
Query: 210 AVASRNVKVIVVGNPCNTNALICLKNAPSIPAKNFHAL-TRLDENRAKCQLALKAGVFYD 268
A + VIVV NP + + LK P + LD R + +A + V
Sbjct: 108 KYAP-DAIVIVVTNPVDAMTYVALK-ESGFPKNRVIGMAGVLDSARFRTFIAEELNVSVK 165
Query: 269 KVSNMTIWGNHSTTQVPDFLNARINGLPVKEIIKDHKWLEEGFTETIQKVRLRGGLLIKK 328
V+ + G H + VP + + G+P+++++ K L+ E +++ R G ++
Sbjct: 166 DVTAFVL-GGHGDSMVPLVRYSTVGGIPLEDLLSKEK-LD----EIVERTRKGGAEIVGL 219
Query: 329 WGRSSA----ASTAVSIVDAM---KSLVTPTPEGDWFSSGVYTNGNPYGIAEDIVFSMPC 381
SA A++ +V+A+ K V P Y G YG+ +D+ +P
Sbjct: 220 LKTGSAYYAPAASIAEMVEAILKDKKRVLPC--------SAYLEGE-YGV-KDVYVGVPV 269
Query: 382 R 382
+
Sbjct: 270 K 270
>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 = 55.3 bits (133), Expect = 2e-08
Identities = 67/293 (22%), Positives = 123/293 (41%), Gaps = 30/293 (10%)
Query: 128 IALKLLGSERSLQALEGV----AMELEDSLFPLLREVKI-GINPYELFEDAEWALLIGAK 182
+A K L L +EG+ A+++ ++ + K+ G N Y +++ ++
Sbjct: 20 LAEKELADLVLLDVVEGIPQGKALDMYEASPVGGFDTKVTGTNNYADTANSDIVVITAGL 79
Query: 183 PRGPGMERAGLLDINGQIFAEQGKALNAVASRNVKVIVVGNPCNTNALICLKNAPSIPAK 242
PR PGM R LL +N I E + S N ++VV NP + + + + +
Sbjct: 80 PRKPGMSREDLLSMNAGIVREVTGRI-MEHSPNPIIVVVSNPLDAMTYVAWQKSGFPKER 138
Query: 243 NFHALTRLDENRAKCQLALKAGVFYDKVSNMTIWGNHSTTQVPDFLNARINGLPVKEIIK 302
LD R + +A++ GV V+ + G H VP + + G+PV ++I
Sbjct: 139 VIGQAGVLDSARFRTFIAMELGVSVQDVTACVL-GGHGDAMVPLVRYSTVAGIPVADLIS 197
Query: 303 DHKWLEEGFTETIQKVRLRGGLLIKKWGRSSA----ASTAVSIVDAM---KSLVTPTPEG 355
E E +++ R GG ++ + SA A++ V +V+A+ + V P
Sbjct: 198 -----AERIAEIVERTRKGGGEIVNLLKQGSAYYAPAASVVEMVEAILKDRKRVLPC--- 249
Query: 356 DWFSSGVYTNGNPYGIAEDIVFSMPCRSKGDGDYELVKDVIFDDYLRKRIAKT 408
Y +G YGI + I +P +G E + ++ D + K+
Sbjct: 250 -----AAYLDGQ-YGI-DGIYVGVPVILGKNG-VEHIYELKLDQSELALLNKS 294
>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 = 48.5 bits (116), Expect = 3e-06
Identities = 62/271 (22%), Positives = 94/271 (34%), Gaps = 44/271 (16%)
Query: 160 VKIGINPYELFEDAEWALLIGAKPR---GPGMERAGLLDINGQIFAEQGKALNAVASRNV 216
KI Y+ DA+ ++I A P G +R L N +I E + V V
Sbjct: 56 TKIRAGDYDDCADAD-IIVITAGPSIDPGNTDDRLDLAQTNAKIIREIMGNITKVTKEAV 114
Query: 217 KVIVVGNPCNTNALICLKNAPSIPAKNFHALTRLDENRAKCQLALKAGVFYDKVSNMTIW 276
+I++ NP + I K T LD R + +A K GV V+ +
Sbjct: 115 -IILITNPLDIAVYIAATEFDYPANKVIGTGTMLDTARLRRIVADKYGVDPKNVTGYVL- 172
Query: 277 GNHSTTQVPDFLNARINGLPVKEIIK-------DHKWLEEGFTETIQKVRLRGGLLIKKW 329
G H + P + I GLP+ E+ D L E + V K W
Sbjct: 173 GEHGSHAFPVWSLVNIAGLPLDELEALFGKEPIDKDELLEEVVQAAYDV-----FNRKGW 227
Query: 330 GRSSAASTAVSIVDAMK---SLVTP--TPEGDWFSSGVYTNGNPYGIAEDIVFSMPCRSK 384
+ A +A ++ A+ + P T SG Y D+ S+P
Sbjct: 228 TNAGIAKSASRLIKAILLDERSILPVCTL-----LSGEYGL-------SDVALSLPTVIG 275
Query: 385 GDGDYELVKDVIFDDYLRKRIAKTEQELLAE 415
G E V ++ D+ E E L +
Sbjct: 276 AKG-IERVLEIPLDE--------WELEKLHK 297
>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 = 48.0 bits (115), Expect = 5e-06
Identities = 64/264 (24%), Positives = 109/264 (41%), Gaps = 12/264 (4%)
Query: 125 DQPIALKLLGSERSLQALEGVAMELEDSLFPLLREVKIGINPYELFEDAEWALLIGAKPR 184
+ +A +L+ + + + +G A++L + L + Y DA+ ++ PR
Sbjct: 19 AKGLASELVLVDVNEEKAKGDALDLSHASAFLATGTIVRGGDYADAADADIVVITAGAPR 78
Query: 185 GPGMERAGLLDINGQIFAEQGKALNAVASRNVKVIVVGNPCNTNALICLKNAPSIPAKNF 244
PG R L++ N I L + ++VV NP + + K + +
Sbjct: 79 KPGETRLDLINRNAPILRSVITNLKK-YGPDAIILVVSNPVDILTYVAQKLSGLPKNRVI 137
Query: 245 HALTRLDENRAKCQLALKAGVFYDKVSNMTIWGNHSTTQVPDFLNARINGLPVKEIIKDH 304
+ T LD R + LA K V V + + G H +QV + A + GLP++E+
Sbjct: 138 GSGTLLDSARFRSLLAEKLDVDPQSV-HAYVLGEHGDSQVVAWSTATVGGLPLEELAPFT 196
Query: 305 KW-LEEGFTETIQKVRLRGGLLIKKWGRSSAASTAVSIVDAMKSLVTPTPEGDWFSSGVY 363
K LE E R G +I+ G ++ A +I D +KS++ E
Sbjct: 197 KLDLEAIEEEV----RTSGYEIIRLKGATNYG-IATAIADIVKSIL--LDERRVLPVSAV 249
Query: 364 TNGNPYGIAEDIVFSMPCRSKGDG 387
G YGI ED+ S+P +G
Sbjct: 250 QEGQ-YGI-EDVALSVPAVVGREG 271
>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 = 47.5 bits (114), Expect = 6e-06
Identities = 63/246 (25%), Positives = 101/246 (41%), Gaps = 21/246 (8%)
Query: 143 EGVAMELEDSLFPLLREVKIGINPYELFEDAEWALLIGAKPRGPGMERAGLLDINGQIFA 202
EG A++LED+L L VKI Y +DA+ ++ P+ PG R LL+ N +I
Sbjct: 39 EGEALDLEDALAFLPSPVKIKAGDYSDCKDADIVVITAGAPQKPGETRLDLLEKNAKIMK 98
Query: 203 EQGKALNAVASRNVKVIVVGNPCN--TNALICLKNAPSIPAKNFHALTRLDENRAKCQLA 260
+ A + +V NP + T + L P + T LD R + LA
Sbjct: 99 SIVPKIKASGFDGI-FLVASNPVDVITYVVQKLSGLP--KNRVIGTGTSLDTARLRRALA 155
Query: 261 LKAGVFYDKVSNMTIWGNHSTTQVPDFLNARINGLPVKEIIKDHKWLEEGFTETIQKVRL 320
K V V + G H +Q + + G P+ +++K+ K E E + VR
Sbjct: 156 EKLNVDPRSVHAYVL-GEHGDSQFVAWSTVTVGGKPLLDLLKEGKLSELDLDEIEEDVRK 214
Query: 321 RGGLLIKKWGRSS--AASTAVSIVDAM---KSLVTPTPEGDWFSSGVYTNGNPYGIAEDI 375
G +I G + A+ IV A+ ++ + P Y +G YG +D+
Sbjct: 215 AGYEIINGKGATYYGIATALARIVKAILNDENAILPV--------SAYLDGE-YGE-KDV 264
Query: 376 VFSMPC 381
+P
Sbjct: 265 YIGVPA 270
>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 = 46.6 bits (111), Expect = 1e-05
Identities = 66/276 (23%), Positives = 104/276 (37%), Gaps = 61/276 (22%)
Query: 98 NIAVSGAAGMIANHLLFKLAAGEVLGPDQPIALKL----LGSERSLQALE---GVAMELE 150
+AV GAAG I QP++L L SE SL + GVA +L
Sbjct: 1 KVAVLGAAGGIG----------------QPLSLLLKLQPYVSELSLYDIAGAAGVAADLS 44
Query: 151 DSLFPLLREVKIGINPY-------ELFEDAEWALLIGAKPRGPGMERAGLLDINGQIFAE 203
+ + + A+ ++ PR PGM R L ++N I +
Sbjct: 45 HI------PTAASVKGFSGEEGLENALKGADVVVIPAGVPRKPGMTRDDLFNVNAGIVKD 98
Query: 204 QGKALNAVASRNVKVIVVGNPCNTNALIC---LKNAPSIPAKNFHALTRLDENRAKCQLA 260
A+ A + ++V+ NP N+ I LK +T LD RA +A
Sbjct: 99 LVAAV-AESCPKAMILVITNPVNSTVPIAAEVLKKKGVYDPNKLFGVTTLDIVRANTFVA 157
Query: 261 LKAGVFYDKVSNMTIWGNHS-TTQVPDFLNARINGLPVKEIIKDHKWLEEGFTETIQKVR 319
G +V N+ + G HS T +P L ++ G + E+ I +++
Sbjct: 158 ELKGKDPMEV-NVPVIGGHSGETIIP--LISQCPGKVLFT--------EDQLEALIHRIQ 206
Query: 320 LRGGLLIK-KWGRSSA--------ASTAVSIVDAMK 346
G ++K K G SA A +S+V +K
Sbjct: 207 NAGTEVVKAKAGAGSATLSMAFAGARFVLSLVRGLK 242
>gnl|CDD|240360 PTZ00325, PTZ00325, malate dehydrogenase; Provisional.
Length = 321
Score = 45.4 bits (108), Expect = 3e-05
Identities = 86/305 (28%), Positives = 121/305 (39%), Gaps = 67/305 (21%)
Query: 92 SWKKMVNIAVSGAAGMIANHLLFKLAAGEVLGPDQPIALKL--LGSERSLQAL---EGVA 146
S KM +AV GAAG I L + LK SE SL + GVA
Sbjct: 4 SALKMFKVAVLGAAGGIGQPLS--------------LLLKQNPHVSELSLYDIVGAPGVA 49
Query: 147 MELE--DSLFPLLREVKIGINPYELFEDAEWALLIGAKPRGPGMERAGLLDINGQIFAEQ 204
+L D+ + G + A+ L+ PR PGM R L + N I +
Sbjct: 50 ADLSHIDTP-AKVTGYADGELWEKALRGADLVLICAGVPRKPGMTRDDLFNTNAPIVRD- 107
Query: 205 GKALNAVASRNVKVI--VVGNPCNTNALIC---LKNAPSI-PAKNFHALTRLDENRAKCQ 258
+ AVAS K I +V NP N+ I LK A P K F +T LD RA+
Sbjct: 108 --LVAAVASSAPKAIVGIVSNPVNSTVPIAAETLKKAGVYDPRKLF-GVTTLDVVRARKF 164
Query: 259 LALKAGVF-YDKVSNMTIWGNHS-TTQVPDFLNARING-LPVKEIIKDHKWLEEGFTETI 315
+A G+ YD N+ + G HS T VP L ++ LP +++ + ++ G E +
Sbjct: 165 VAEALGMNPYD--VNVPVVGGHSGVTIVP--LLSQTGLSLPEEQVEQITHRVQVGGDEVV 220
Query: 316 QKVRLRGGLLIKKWGRSSAA-STA-------VSIVDAMKSLVTPT----------PEGDW 357
+ K G SA S A S++ A++ PE +
Sbjct: 221 K----------AKEGAGSATLSMAYAAAEWSTSVLKALRGDKGIVECAFVESDMRPECPF 270
Query: 358 FSSGV 362
FSS V
Sbjct: 271 FSSPV 275
>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 = 44.5 bits (106), Expect = 6e-05
Identities = 64/265 (24%), Positives = 107/265 (40%), Gaps = 30/265 (11%)
Query: 142 LEGVAMELEDSLFPLLREVKIGINPYELFEDAEWALLIGAKPRGPGMERAGLLDINGQIF 201
EG AM+L+ + L KI Y +DA+ ++ P+ PG R L+ N +I
Sbjct: 34 AEGEAMDLQHAASFLPTPKKIRSGDYSDCKDADLVVITAGAPQKPGETRLELVGRNVRIM 93
Query: 202 AEQGKALNAVASR-NVKVIVVGNPCN--TNALICLKNAPSIPAKNFHALTRLDENRAKCQ 258
V S + +V NP + T L P + + T LD R +
Sbjct: 94 KS--IVPEVVKSGFDGIFLVATNPVDILTYVAWKLSGFP--KNRVIGSGTVLDTARLRYL 149
Query: 259 LALKAGVFYDKVSNMTIWGNHSTTQVPDFLNARINGLPVKEIIKDHKWLEEGFTETI-QK 317
LA K GV + + I G H ++VP + +A I G+P+ + +K + E I ++
Sbjct: 150 LAEKLGV-DPQSVHAYIIGEHGDSEVPVWSSATIGGVPLLDYLKAKGTETDLDLEEIEKE 208
Query: 318 VRLRGGLLIKKWGRSS--AASTAVSIVDA----MKSLVTPTPEGDWFSSGVYTNGNPYGI 371
VR +I + G + IV+A ++ Y +G YGI
Sbjct: 209 VRDAAYEIINRKGATYYGIGMAVARIVEAILHDENRVLP---------VSAYLDGE-YGI 258
Query: 372 AEDIVFSMPCRSKGDGDYELVKDVI 396
+D+ +P +G V+++I
Sbjct: 259 -KDVYIGVPAVLGRNG----VEEII 278
>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 = 42.1 bits (100), Expect = 4e-04
Identities = 67/255 (26%), Positives = 111/255 (43%), Gaps = 38/255 (14%)
Query: 143 EGVAMELEDSLFPLLREVKIGINPYELFEDAEWALLI---GAKPRGPGMERAGLLDINGQ 199
EG AM+L P ++ V+I Y + A +++ GA + PG R LL N
Sbjct: 39 EGEAMDLAHGT-PFVKPVRIYAGDYADCKGA--DVVVITAGANQK-PGETRLDLLKRNVA 94
Query: 200 IFAEQGKALNAVASRNVKVIVVGNPCNTNALICLK--NAPSIPAKNFHALTRLDENRAKC 257
IF E + + + ++VV NP + + K P P + + T LD R +
Sbjct: 95 IFKEIIPQI-LKYAPDAILLVVTNPVDVLTYVAYKLSGLP--PNRVIGSGTVLDTARFRY 151
Query: 258 QLALKAGVFYDKVSNM--TIWGNHSTTQVPDFLNARINGLPVKEIIKDHK--WLEEGFTE 313
L GV ++ I G H ++V + +A I G+P+ E K + EE E
Sbjct: 152 LLGEHLGV---DPRSVHAYIIGEHGDSEVAVWSSANIGGVPLDEFCKLCGRPFDEEVREE 208
Query: 314 TIQKVRLRGGLLIKKWGRSS---AASTAVSIVDAM----KSLVTPTPEGDWFSSGVYTNG 366
++VR +I++ G + + A IV+A+ S++T S + +G
Sbjct: 209 IFEEVRNAAYEIIERKGATYYAIGLALA-RIVEAILRDENSVLTV--------SSL-LDG 258
Query: 367 NPYGIAEDIVFSMPC 381
YGI +D+ S+PC
Sbjct: 259 -QYGI-KDVALSLPC 271
>gnl|CDD|235340 PRK05086, PRK05086, malate dehydrogenase; Provisional.
Length = 312
Score = 41.9 bits (99), Expect = 4e-04
Identities = 50/175 (28%), Positives = 71/175 (40%), Gaps = 39/175 (22%)
Query: 99 IAVSGAAGMIANHLLFKLAAGEVLGPDQPIALKL-----LGSERSLQALE----GVAMEL 149
+AV GAAG I Q +AL L GSE SL + GVA++L
Sbjct: 3 VAVLGAAGGIG----------------QALALLLKTQLPAGSELSLYDIAPVTPGVAVDL 46
Query: 150 EDSLFPLLREVK--IGINPYELFEDAEWALLIGAKPRGPGMERAGLLDINGQI---FAEQ 204
S P ++K G +P E A+ L+ R PGM+R+ L ++N I E+
Sbjct: 47 --SHIPTAVKIKGFSGEDPTPALEGADVVLISAGVARKPGMDRSDLFNVNAGIVKNLVEK 104
Query: 205 GKALNAVASRNVKVIVVGNPCNTNALIC---LKNAPSIPAKNFHALTRLDENRAK 256
A + ++ NP NT I LK A +T LD R++
Sbjct: 105 V----AKTCPKACIGIITNPVNTTVAIAAEVLKKAGVYDKNKLFGVTTLDVIRSE 155
>gnl|CDD|178836 PRK00066, ldh, L-lactate dehydrogenase; Reviewed.
Length = 315
Score = 41.0 bits (97), Expect = 8e-04
Identities = 54/196 (27%), Positives = 88/196 (44%), Gaps = 16/196 (8%)
Query: 142 LEGVAMELEDSLFPLLREVKIGINPYELFEDAEWALLIGAKPRGPGMERAGLLDINGQIF 201
EG AM+L ++ P KI Y +DA+ ++ P+ PG R L++ N +IF
Sbjct: 44 AEGDAMDLSHAV-PFTSPTKIYAGDYSDCKDADLVVITAGAPQKPGETRLDLVEKNLKIF 102
Query: 202 AEQGKALNAVASRNVKVI--VVGNPCN--TNALICLKNAPSIPAKN--FHALTRLDENRA 255
+ +AS I V NP + T A L P K + T LD R
Sbjct: 103 --KSIVGEVMAS-GFDGIFLVASNPVDILTYATWKLSGFP----KERVIGSGTSLDSARF 155
Query: 256 KCQLALKAGVFYDKVSNMTIWGNHSTTQVPDFLNARINGLPVKEIIKDHKWLEEGFTETI 315
+ L+ K V V I G H T+ P + +A + G+P++E +++++ +E + I
Sbjct: 156 RYMLSEKLDVDPRSVHAYII-GEHGDTEFPVWSHANVAGVPLEEYLEENEQYDEEDLDEI 214
Query: 316 -QKVRLRGGLLIKKWG 330
+ VR +I+K G
Sbjct: 215 FENVRDAAYEIIEKKG 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 = 39.4 bits (93), Expect = 0.003
Identities = 63/209 (30%), Positives = 85/209 (40%), Gaps = 46/209 (22%)
Query: 97 VNIAVSGAAGMIANHLLFKLAAGEVLGPDQPIALKL----LGSERSLQ---ALEGVAMEL 149
V +AV GAAG I QP++L L L SE +L GVA +L
Sbjct: 1 VKVAVLGAAGGIG----------------QPLSLLLKLNPLVSELALYDIVNTPGVAADL 44
Query: 150 EDSLFPLLREVKIGINPYELFEDAEWALLIGAK--------PRGPGMERAGLLDINGQIF 201
S +V G E + A L GA PR PGM R L +IN I
Sbjct: 45 --SHINTPAKVT-GYLGPEELKKA----LKGADVVVIPAGVPRKPGMTRDDLFNINAGIV 97
Query: 202 AEQGKALNAVASRNVKVIVVGNPCNTNALIC----LKNAPSIPAKNFHALTRLDENRAKC 257
+ A+ A A ++++ NP N+ I K P + F +T LD RA
Sbjct: 98 RDLATAV-AKACPKALILIISNPVNSTVPIAAEVLKKAGVYDPKRLF-GVTTLDVVRANT 155
Query: 258 QLALKAGVFYDKVSNMTIWGNHS-TTQVP 285
+A G+ KV N+ + G HS T +P
Sbjct: 156 FVAELLGLDPAKV-NVPVIGGHSGVTILP 183
>gnl|CDD|215058 PLN00106, PLN00106, malate dehydrogenase.
Length = 323
Score = 32.6 bits (75), Expect = 0.37
Identities = 33/89 (37%), Positives = 40/89 (44%), Gaps = 10/89 (11%)
Query: 183 PRGPGMERAGLLDINGQIFAEQGKAL-NAVASR--NVKVIVVGNPCNTNALIC---LKNA 236
PR PGM R L +IN I K L AVA N V ++ NP N+ I LK A
Sbjct: 97 PRKPGMTRDDLFNINAGIV----KTLCEAVAKHCPNALVNIISNPVNSTVPIAAEVLKKA 152
Query: 237 PSIPAKNFHALTRLDENRAKCQLALKAGV 265
K +T LD RA +A K G+
Sbjct: 153 GVYDPKKLFGVTTLDVVRANTFVAEKKGL 181
>gnl|CDD|227633 COG5323, COG5323, Uncharacterized conserved protein [Function
unknown].
Length = 410
Score = 30.7 bits (69), Expect = 1.6
Identities = 14/75 (18%), Positives = 27/75 (36%), Gaps = 4/75 (5%)
Query: 152 SLFPLLREVKIGINPYELFEDAEWA--LLIGAKPRGPGMERAGLLDINGQIFAEQGKALN 209
L P ++ + + W L++G RG G RAG + + AL
Sbjct: 13 QLEPEDQQWLLSAALAQASPFGPWRTWLMLGG--RGSGKTRAGAEWVTWNALGKPSIALV 70
Query: 210 AVASRNVKVIVVGNP 224
+ + +++ P
Sbjct: 71 GETLHDAREVMIDGP 85
>gnl|CDD|221989 pfam13224, DUF4032, Domain of unknown function (DUF4032). This
presumed domain is functionally uncharacterized. This
domain family is found in bacteria, and is approximately
170 amino acids in length. The family is found in
association with pfam06293.
Length = 165
Score = 29.8 bits (68), Expect = 1.6
Identities = 23/71 (32%), Positives = 33/71 (46%), Gaps = 11/71 (15%)
Query: 290 ARINGLPVKEIIKDHKWLEEGFTETIQKV--RLRGGL---------LIKKWGRSSAASTA 338
A +G V E + H+WL E F T++ V LRG L L +W S A
Sbjct: 90 ATTDGQDVDEEVAAHRWLTEVFEPTVRAVPRELRGKLEPAELFHEVLEHRWYLSERAGRD 149
Query: 339 VSIVDAMKSLV 349
V + +A++S V
Sbjct: 150 VGLDEAVQSYV 160
>gnl|CDD|216162 pfam00866, Ring_hydroxyl_B, Ring hydroxylating beta subunit. This
subunit has a similar structure to NTF-2 and scytalone
dehydratase.
Length = 145
Score = 29.1 bits (66), Expect = 2.2
Identities = 15/43 (34%), Positives = 21/43 (48%), Gaps = 6/43 (13%)
Query: 371 IAEDIVFSMPCRS---KGDGDYELVKDVIFDD---YLRKRIAK 407
+AEDI + MP R + D D + IFDD L R+ +
Sbjct: 18 LAEDIHYWMPARDTRTRRDRDPQSEASAIFDDDRRGLEDRVFR 60
>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 = 29.9 bits (68), Expect = 3.0
Identities = 28/121 (23%), Positives = 55/121 (45%), Gaps = 6/121 (4%)
Query: 275 IWGNHSTTQVPDFLNARINGLPVKEIIKD--HKWLEEGFTETIQKVRLRGGLLIKKWGRS 332
I G H + VP + + G+ ++++ D E + E ++V +IK G +
Sbjct: 172 IIGEHGDSSVPVWSGVNVAGVRLQDLNPDIGTDKDPEKWKEVHKQVVDSAYEVIKLKGYT 231
Query: 333 SAASTAVSIVDAMKSLVTPTPEGDWFSSGVYTNGNPYGIAEDIVFSMPCRSKGDGDYELV 392
S A +S+ D + +++ T G S G +GI +++ S+PC +G ++
Sbjct: 232 SWA-IGLSVADLVDAILRNT--GRVHSVSTLVKGL-HGIEDEVFLSLPCILGENGITHVI 287
Query: 393 K 393
K
Sbjct: 288 K 288
>gnl|CDD|206498 pfam14330, DUF4387, Domain of unknown function (DUF4387). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria, archaea and
eukaryotes. Proteins in this family are approximately
110 amino acids in length. There is a conserved RSKN
sequence motif.
Length = 99
Score = 27.9 bits (63), Expect = 3.8
Identities = 11/19 (57%), Positives = 13/19 (68%)
Query: 381 CRSKGDGDYELVKDVIFDD 399
RSK G +EL D+IFDD
Sbjct: 8 IRSKNAGPFELTFDIIFDD 26
>gnl|CDD|223386 COG0309, HypE, Hydrogenase maturation factor [Posttranslational
modification, protein turnover, chaperones].
Length = 339
Score = 28.8 bits (65), Expect = 5.5
Identities = 14/45 (31%), Positives = 22/45 (48%), Gaps = 7/45 (15%)
Query: 144 GVAMELEDSLFPLLREVKI-----GINPYELFEDAEWALLIGAKP 183
GV + +E+ P+ EV+ G++P EL E L+I P
Sbjct: 242 GVGISIEEEKIPVREEVRGVCELLGLDPLELA--NEGKLVIAVPP 284
>gnl|CDD|187567 cd05257, Arna_like_SDR_e, Arna decarboxylase_like, extended (e)
SDRs. Decarboxylase domain of ArnA. ArnA, is an enzyme
involved in the modification of outer membrane protein
lipid A of gram-negative bacteria. It is a bifunctional
enzyme that catalyzes the NAD-dependent decarboxylation
of UDP-glucuronic acid and
N-10-formyltetrahydrofolate-dependent formylation of
UDP-4-amino-4-deoxy-l-arabinose; its NAD-dependent
decaboxylating activity is in the C-terminal 360
residues. This subgroup belongs to the extended SDR
family, however the NAD binding motif is not a perfect
match and the upstream Asn of the canonical active site
tetrad is not conserved. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 316
Score = 28.8 bits (65), Expect = 6.5
Identities = 13/31 (41%), Positives = 17/31 (54%), Gaps = 2/31 (6%)
Query: 98 NIAVSGAAGMIANHLLFKL-AAG-EVLGPDQ 126
N+ V+GA G I +HL +L G EV D
Sbjct: 1 NVLVTGADGFIGSHLTERLLREGHEVRALDI 31
>gnl|CDD|234172 TIGR03345, VI_ClpV1, type VI secretion ATPase, ClpV1 family.
Members of this protein family are homologs of ClpB, an
ATPase associated with chaperone-related functions.
These ClpB homologs, designated ClpV1, are a key
component of the bacterial pathogenicity-associated type
VI secretion system [Protein fate, Protein and peptide
secretion and trafficking, Cellular processes,
Pathogenesis].
Length = 852
Score = 28.8 bits (65), Expect = 6.8
Identities = 25/67 (37%), Positives = 33/67 (49%), Gaps = 2/67 (2%)
Query: 115 KLAAGEVLGPDQPIALKLLGSERSLQALEGVAMELEDSLFPLLREVKIGINPYELFEDAE 174
++AAG+V + + L L LQA V E E+ L ++ EVK P LF D E
Sbjct: 231 RIAAGDVPPALRNVRLLSLDLGL-LQAGASVKGEFENRLKSVIDEVKASPQPIILFID-E 288
Query: 175 WALLIGA 181
LIGA
Sbjct: 289 AHTLIGA 295
>gnl|CDD|227040 COG4696, COG4696, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 180
Score = 28.0 bits (62), Expect = 7.2
Identities = 20/77 (25%), Positives = 26/77 (33%), Gaps = 12/77 (15%)
Query: 111 HLLFKLAAGEVLGPDQPIALKLLGSERSLQALEGVAMELEDSL-FPLLREVKIGINPYEL 169
H AA +VL + Q L G L D L F V +GI+P +
Sbjct: 72 HQAVDQAANKVLS-----------KGHAEQDLIGQVDALADLLYFTYGSLVLMGIDPDAI 120
Query: 170 FEDAEWALLIGAKPRGP 186
F A + P G
Sbjct: 121 FAAVHRANMGKIFPDGK 137
>gnl|CDD|187563 cd05253, UDP_GE_SDE_e, UDP glucuronic acid epimerase, extended (e)
SDRs. This subgroup contains UDP-D-glucuronic acid
4-epimerase, an extended SDR, which catalyzes the
conversion of UDP-alpha-D-glucuronic acid to
UDP-alpha-D-galacturonic acid. This group has the SDR's
canonical catalytic tetrad and the TGxxGxxG NAD-binding
motif of the extended SDRs. Extended SDRs are distinct
from classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 332
Score = 28.1 bits (63), Expect = 9.1
Identities = 13/30 (43%), Positives = 17/30 (56%), Gaps = 2/30 (6%)
Query: 98 NIAVSGAAGMIANHLLFKLAAG--EVLGPD 125
I V+GAAG I H+ +L EV+G D
Sbjct: 2 KILVTGAAGFIGFHVAKRLLERGDEVVGID 31
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
0.317 0.134 0.393
Gapped
Lambda K H
0.267 0.0813 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 22,652,652
Number of extensions: 2230058
Number of successful extensions: 1913
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1854
Number of HSP's successfully gapped: 54
Length of query: 442
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 342
Effective length of database: 6,502,202
Effective search space: 2223753084
Effective search space used: 2223753084
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: 61 (27.1 bits)