RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12825
(488 letters)
>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 = 502 bits (1296), Expect = e-178
Identities = 191/308 (62%), Positives = 250/308 (81%)
Query: 179 KITVVGAGQVGMACTYSILTQGIYSNFCLIDSNEDRCKGEMLDLQHGAPFLRSPKIESGS 238
K+TVVG GQVGMAC SIL +G+ L+D ED+ KGE +DLQHG+ FL++PKIE+
Sbjct: 5 KVTVVGVGQVGMACAISILAKGLADELVLVDVVEDKLKGEAMDLQHGSAFLKNPKIEADK 64
Query: 239 DIAMSEGSRIVIITAGVRSLVGETRLQLVDRNVKIFKDLIPKIAKGSPDCILLIISNPVD 298
D +++ S++VI+TAG R GE+RL LV RNV IFK +IPK+ K SP+ ILL++SNPVD
Sbjct: 65 DYSVTANSKVVIVTAGARQNEGESRLDLVQRNVDIFKGIIPKLVKYSPNAILLVVSNPVD 124
Query: 299 VLTYISWKLSGFPKNRVIGSGTNLDSMRFRVLLAQKLGLSPESVHGFIIGEHGDSSVPVW 358
++TY++WKLSG PK+RVIGSG NLDS RFR L+A++LG++P SVHG+IIGEHGDSSVPVW
Sbjct: 125 IMTYVAWKLSGLPKHRVIGSGCNLDSARFRYLIAERLGVAPSSVHGWIIGEHGDSSVPVW 184
Query: 359 SGVNVAGVTLKELNPTIGTEQDTENFVRLHADVVNSAYEVIKLKGYTSWALGLSVASISH 418
SGVNVAGV L++LNP IGT++D E + +H VV+SAYEVIKLKGYTSWA+GLSVA +
Sbjct: 185 SGVNVAGVRLQDLNPDIGTDKDPEKWKEVHKQVVDSAYEVIKLKGYTSWAIGLSVADLVD 244
Query: 419 TLLNNTNKIHAVSTLIQGHHGIEEEVFLSLPCVMADNGVTHIINQNLTPDEAEKLRKSAA 478
+L NT ++H+VSTL++G HGIE+EVFLSLPC++ +NG+TH+I Q LT +E EKL+KSA
Sbjct: 245 AILRNTGRVHSVSTLVKGLHGIEDEVFLSLPCILGENGITHVIKQPLTEEEQEKLQKSAD 304
Query: 479 TISQIQKG 486
T+ ++QK
Sbjct: 305 TLWEVQKQ 312
>gnl|CDD|178212 PLN02602, PLN02602, lactate dehydrogenase.
Length = 350
Score = 409 bits (1054), Expect = e-141
Identities = 170/336 (50%), Positives = 226/336 (67%), Gaps = 2/336 (0%)
Query: 154 MARDAVSTVDRLLSQVAPSIESPDQ-KITVVGAGQVGMACTYSILTQGIYSNFCLIDSNE 212
D + + +P + K++VVG G VGMA +ILTQ + L+D N
Sbjct: 13 GGLDLSQAFFKPIHNSSPPSPTRRHTKVSVVGVGNVGMAIAQTILTQDLADELALVDVNP 72
Query: 213 DRCKGEMLDLQHGAPFLRSPKIESGSDIAMSEGSRIVIITAGVRSLVGETRLQLVDRNVK 272
D+ +GEMLDLQH A FL KI + +D A++ GS + I+TAG R + GE+RL L+ RNV
Sbjct: 73 DKLRGEMLDLQHAAAFLPRTKILASTDYAVTAGSDLCIVTAGARQIPGESRLNLLQRNVA 132
Query: 273 IFKDLIPKIAKGSPDCILLIISNPVDVLTYISWKLSGFPKNRVIGSGTNLDSMRFRVLLA 332
+F+ +IP++AK SPD ILLI+SNPVDVLTY++WKLSGFP NRVIGSGTNLDS RFR L+A
Sbjct: 133 LFRKIIPELAKYSPDTILLIVSNPVDVLTYVAWKLSGFPANRVIGSGTNLDSSRFRFLIA 192
Query: 333 QKLGLSPESVHGFIIGEHGDSSVPVWSGVNVAGVTLKELNPTIGTEQDTENFVRLHADVV 392
L ++ + V +I+GEHGDSSV +WS V+V GV + + E +H VV
Sbjct: 193 DHLDVNAQDVQAYIVGEHGDSSVALWSSVSVGGVPVLSFLEKQQIAYEKETLEEIHRAVV 252
Query: 393 NSAYEVIKLKGYTSWALGLSVASISHTLLNNTNKIHAVSTLIQGHHGI-EEEVFLSLPCV 451
+SAYEVIKLKGYTSWA+G SVAS+ +LL + +IH VS L +G HGI E +VFLSLP
Sbjct: 253 DSAYEVIKLKGYTSWAIGYSVASLVRSLLRDQRRIHPVSVLAKGFHGIDEGDVFLSLPAQ 312
Query: 452 MADNGVTHIINQNLTPDEAEKLRKSAATISQIQKGL 487
+ NGV ++N +LT +EAE+LRKSA T+ ++Q L
Sbjct: 313 LGRNGVLGVVNVHLTDEEAERLRKSAKTLWEVQSQL 348
>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 = 396 bits (1021), Expect = e-137
Identities = 139/299 (46%), Positives = 200/299 (66%), Gaps = 2/299 (0%)
Query: 182 VVGAGQVGMACTYSILTQGIYSNFCLIDSNEDRCKGEMLDLQHGAPFLRSPKIESGSDIA 241
++GAG VG + +++L QGI LID N+D+ +GE +DLQH A FL +PK D +
Sbjct: 1 IIGAGNVGSSTAFALLNQGIADEIVLIDINKDKAEGEAMDLQHAASFLPTPKKIRSGDYS 60
Query: 242 MSEGSRIVIITAGVRSLVGETRLQLVDRNVKIFKDLIPKIAKGSPDCILLIISNPVDVLT 301
+ + +V+ITAG GETRL+LV RNV+I K ++P++ K D I L+ +NPVD+LT
Sbjct: 61 DCKDADLVVITAGAPQKPGETRLELVGRNVRIMKSIVPEVVKSGFDGIFLVATNPVDILT 120
Query: 302 YISWKLSGFPKNRVIGSGTNLDSMRFRVLLAQKLGLSPESVHGFIIGEHGDSSVPVWSGV 361
Y++WKLSGFPKNRVIGSGT LD+ R R LLA+KLG+ P+SVH +IIGEHGDS VPVWS
Sbjct: 121 YVAWKLSGFPKNRVIGSGTVLDTARLRYLLAEKLGVDPQSVHAYIIGEHGDSEVPVWSSA 180
Query: 362 NVAGVTLKELNPTIGTEQDTENFVRLHADVVNSAYEVIKLKGYTSWALGLSVASISHTLL 421
+ GV L + GTE D + + +V ++AYE+I KG T + +G++VA I +L
Sbjct: 181 TIGGVPLLDYLKAKGTETDLDLE-EIEKEVRDAAYEIINRKGATYYGIGMAVARIVEAIL 239
Query: 422 NNTNKIHAVSTLIQGHHGIEEEVFLSLPCVMADNGVTHIINQNLTPDEAEKLRKSAATI 480
++ N++ VS + G +GI ++V++ +P V+ NGV II L+ +E E +KSA T+
Sbjct: 240 HDENRVLPVSAYLDGEYGI-KDVYIGVPAVLGRNGVEEIIELPLSDEEKEAFQKSAETL 297
>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 = 383 bits (986), Expect = e-132
Identities = 145/309 (46%), Positives = 207/309 (66%), Gaps = 2/309 (0%)
Query: 179 KITVVGAGQVGMACTYSILTQGIYSNFCLIDSNEDRCKGEMLDLQHGAPFLRSPKIESGS 238
K+ +VGAG VG Y++L +G+ S L+D N+ + +GE +DL HG PF++ +I +G
Sbjct: 2 KVAIVGAGFVGSTTAYALLLRGLASEIVLVDINKAKAEGEAMDLAHGTPFVKPVRIYAG- 60
Query: 239 DIAMSEGSRIVIITAGVRSLVGETRLQLVDRNVKIFKDLIPKIAKGSPDCILLIISNPVD 298
D A +G+ +V+ITAG GETRL L+ RNV IFK++IP+I K +PD ILL+++NPVD
Sbjct: 61 DYADCKGADVVVITAGANQKPGETRLDLLKRNVAIFKEIIPQILKYAPDAILLVVTNPVD 120
Query: 299 VLTYISWKLSGFPKNRVIGSGTNLDSMRFRVLLAQKLGLSPESVHGFIIGEHGDSSVPVW 358
VLTY+++KLSG P NRVIGSGT LD+ RFR LL + LG+ P SVH +IIGEHGDS V VW
Sbjct: 121 VLTYVAYKLSGLPPNRVIGSGTVLDTARFRYLLGEHLGVDPRSVHAYIIGEHGDSEVAVW 180
Query: 359 SGVNVAGVTLKELNPTIGTEQDTENFVRLHADVVNSAYEVIKLKGYTSWALGLSVASISH 418
S N+ GV L E G D E + +V N+AYE+I+ KG T +A+GL++A I
Sbjct: 181 SSANIGGVPLDEFCKLCGRPFDEEVREEIFEEVRNAAYEIIERKGATYYAIGLALARIVE 240
Query: 419 TLLNNTNKIHAVSTLIQGHHGIEEEVFLSLPCVMADNGVTHIINQNLTPDEAEKLRKSAA 478
+L + N + VS+L+ G +GI ++V LSLPC++ +GV ++ L+ +E E LR SA
Sbjct: 241 AILRDENSVLTVSSLLDGQYGI-KDVALSLPCIVGRSGVERVLPPPLSEEEEEALRASAE 299
Query: 479 TISQIQKGL 487
+ + + L
Sbjct: 300 VLKEAIESL 308
>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 = 350 bits (899), Expect = e-118
Identities = 134/306 (43%), Positives = 196/306 (64%), Gaps = 6/306 (1%)
Query: 180 ITVVGAGQVGMACTYSILTQGIYSNFCLIDSNEDRCKGEMLDLQHGAPFLRSPKIESGSD 239
IT++GAG VG A ++++ +G+ S L+D NE++ KG+ LDL H + FL + I G D
Sbjct: 1 ITIIGAGNVGAAVAFALIAKGLASELVLVDVNEEKAKGDALDLSHASAFLATGTIVRGGD 60
Query: 240 IAMSEGSRIVIITAGVRSLVGETRLQLVDRNVKIFKDLIPKIAKGSPDCILLIISNPVDV 299
A + + IV+ITAG GETRL L++RN I + +I + K PD I+L++SNPVD+
Sbjct: 61 YADAADADIVVITAGAPRKPGETRLDLINRNAPILRSVITNLKKYGPDAIILVVSNPVDI 120
Query: 300 LTYISWKLSGFPKNRVIGSGTNLDSMRFRVLLAQKLGLSPESVHGFIIGEHGDSSVPVWS 359
LTY++ KLSG PKNRVIGSGT LDS RFR LLA+KL + P+SVH +++GEHGDS V WS
Sbjct: 121 LTYVAQKLSGLPKNRVIGSGTLLDSARFRSLLAEKLDVDPQSVHAYVLGEHGDSQVVAWS 180
Query: 360 GVNVAGVTLKELNPTIGTEQDTENFVRLHADVVNSAYEVIKLKGYTSWALGLSVASISHT 419
V G+ L+EL P + + +V S YE+I+LKG T++ + ++A I +
Sbjct: 181 TATVGGLPLEELAPF-----TKLDLEAIEEEVRTSGYEIIRLKGATNYGIATAIADIVKS 235
Query: 420 LLNNTNKIHAVSTLIQGHHGIEEEVFLSLPCVMADNGVTHIINQNLTPDEAEKLRKSAAT 479
+L + ++ VS + +G +GI E+V LS+P V+ GV I+ LT DE KL+KSA
Sbjct: 236 ILLDERRVLPVSAVQEGQYGI-EDVALSVPAVVGREGVVRILEIPLTEDEEAKLQKSAEA 294
Query: 480 ISQIQK 485
+ ++
Sbjct: 295 LKEVLN 300
>gnl|CDD|178836 PRK00066, ldh, L-lactate dehydrogenase; Reviewed.
Length = 315
Score = 343 bits (883), Expect = e-116
Identities = 132/310 (42%), Positives = 198/310 (63%), Gaps = 3/310 (0%)
Query: 178 QKITVVGAGQVGMACTYSILTQGIYSNFCLIDSNEDRCKGEMLDLQHGAPFLRSPKIESG 237
K+ +VG G VG + Y+++ QGI +ID N+++ +G+ +DL H PF KI +G
Sbjct: 7 NKVVLVGDGAVGSSYAYALVNQGIADELVIIDINKEKAEGDAMDLSHAVPFTSPTKIYAG 66
Query: 238 SDIAMSEGSRIVIITAGVRSLVGETRLQLVDRNVKIFKDLIPKIAKGSPDCILLIISNPV 297
D + + + +V+ITAG GETRL LV++N+KIFK ++ ++ D I L+ SNPV
Sbjct: 67 -DYSDCKDADLVVITAGAPQKPGETRLDLVEKNLKIFKSIVGEVMASGFDGIFLVASNPV 125
Query: 298 DVLTYISWKLSGFPKNRVIGSGTNLDSMRFRVLLAQKLGLSPESVHGFIIGEHGDSSVPV 357
D+LTY +WKLSGFPK RVIGSGT+LDS RFR +L++KL + P SVH +IIGEHGD+ PV
Sbjct: 126 DILTYATWKLSGFPKERVIGSGTSLDSARFRYMLSEKLDVDPRSVHAYIIGEHGDTEFPV 185
Query: 358 WSGVNVAGVTLKELNPTIGTEQDTENFVRLHADVVNSAYEVIKLKGYTSWALGLSVASIS 417
WS NVAGV L+E + D E+ + +V ++AYE+I+ KG T + + +++A I+
Sbjct: 186 WSHANVAGVPLEEYLEENE-QYDEEDLDEIFENVRDAAYEIIEKKGATYYGIAMALARIT 244
Query: 418 HTLLNNTNKIHAVSTLIQGHHGIEEEVFLSLPCVMADNGVTHIINQNLTPDEAEKLRKSA 477
+LNN N + VS ++G +G EE+V++ +P V+ NG+ I+ L DE +K SA
Sbjct: 245 KAILNNENAVLPVSAYLEGQYG-EEDVYIGVPAVVNRNGIREIVELPLNDDEKQKFAHSA 303
Query: 478 ATISQIQKGL 487
+ +I
Sbjct: 304 DVLKEIMDEA 313
>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 = 339 bits (871), Expect = e-114
Identities = 134/312 (42%), Positives = 193/312 (61%), Gaps = 11/312 (3%)
Query: 178 QKITVVGAGQVGMACTYSILTQGIYSNFCLIDSNEDRCKGEMLDLQHGAPFLRSP-KIES 236
+K+ ++GAG VG + YS++ QGI LID NE++ +GE LDL+ FL SP KI++
Sbjct: 1 RKVVIIGAGHVGSSFAYSLVNQGIADELVLIDINEEKAEGEALDLEDALAFLPSPVKIKA 60
Query: 237 G--SDIAMSEGSRIVIITAGVRSLVGETRLQLVDRNVKIFKDLIPKIAKGSPDCILLIIS 294
G SD ++ IV+ITAG GETRL L+++N KI K ++PKI D I L+ S
Sbjct: 61 GDYSDCKDAD---IVVITAGAPQKPGETRLDLLEKNAKIMKSIVPKIKASGFDGIFLVAS 117
Query: 295 NPVDVLTYISWKLSGFPKNRVIGSGTNLDSMRFRVLLAQKLGLSPESVHGFIIGEHGDSS 354
NPVDV+TY+ KLSG PKNRVIG+GT+LD+ R R LA+KL + P SVH +++GEHGDS
Sbjct: 118 NPVDVITYVVQKLSGLPKNRVIGTGTSLDTARLRRALAEKLNVDPRSVHAYVLGEHGDSQ 177
Query: 355 VPVWSGVNVAGVTLKELNPTIGTEQDTE-NFVRLHADVVNSAYEVIKLKGYTSWALGLSV 413
WS V V G L +L + + +E + + DV + YE+I KG T + + ++
Sbjct: 178 FVAWSTVTVGGKPLLDL---LKEGKLSELDLDEIEEDVRKAGYEIINGKGATYYGIATAL 234
Query: 414 ASISHTLLNNTNKIHAVSTLIQGHHGIEEEVFLSLPCVMADNGVTHIINQNLTPDEAEKL 473
A I +LN+ N I VS + G +G E++V++ +P ++ NGV +I +LT +E EK
Sbjct: 235 ARIVKAILNDENAILPVSAYLDGEYG-EKDVYIGVPAIIGRNGVEEVIELDLTEEEQEKF 293
Query: 474 RKSAATISQIQK 485
KSA I + K
Sbjct: 294 EKSADIIKENIK 305
>gnl|CDD|223117 COG0039, Mdh, Malate/lactate dehydrogenases [Energy production and
conversion].
Length = 313
Score = 318 bits (818), Expect = e-106
Identities = 138/304 (45%), Positives = 192/304 (63%), Gaps = 7/304 (2%)
Query: 179 KITVVGAGQVGMACTYSILTQGIYSNFCLIDSNEDRCKGEMLDLQHGAPFLRSP-KIESG 237
K+ V+GAG VG + + +L QG+ S LID NE++ +G LDL H A L S KI
Sbjct: 2 KVAVIGAGNVGSSLAFLLLLQGLGSELVLIDINEEKAEGVALDLSHAAAPLGSDVKITGD 61
Query: 238 SDIAMSEGSRIVIITAGVRSLVGETRLQLVDRNVKIFKDLIPKIAKGSPDCILLIISNPV 297
D +G+ IV+ITAGV G TRL L+++N KI KD+ IAK +PD I+L+++NPV
Sbjct: 62 GDYEDLKGADIVVITAGVPRKPGMTRLDLLEKNAKIVKDIAKAIAKYAPDAIVLVVTNPV 121
Query: 298 DVLTYISWKLSGFPKNRVIGSGTNLDSMRFRVLLAQKLGLSPESVHGFIIGEHGDSSVPV 357
D+LTYI+ K SGFPKNRVIGSGT LDS RFR LA+KLG+SP+ VH ++IGEHGD+ VP+
Sbjct: 122 DILTYIAMKFSGFPKNRVIGSGTVLDSARFRTFLAEKLGVSPKDVHAYVIGEHGDTMVPL 181
Query: 358 WSGVNVAGVTLKELNPTIGTEQDTENFVRLHADVVNSAYEVIKLKGY-TSWALGLSVASI 416
WS V G L+EL TE+D E + V N+ E+I+ KG T + ++A +
Sbjct: 182 WSQATVGGKPLEELLKED-TEEDLEELIE---RVRNAGAEIIEAKGAGTYYGPAAALARM 237
Query: 417 SHTLLNNTNKIHAVSTLIQGHHGIEEEVFLSLPCVMADNGVTHIINQNLTPDEAEKLRKS 476
+L + ++ VS + G +G+ E+V+ +P V+ NGV I+ L+ DE EKL KS
Sbjct: 238 VEAILRDEKRVLPVSVYLDGEYGV-EDVYFGVPAVLGKNGVEEILELLLSDDEQEKLDKS 296
Query: 477 AATI 480
A +
Sbjct: 297 AEEL 300
>gnl|CDD|180477 PRK06223, PRK06223, malate dehydrogenase; Reviewed.
Length = 307
Score = 269 bits (690), Expect = 3e-87
Identities = 100/306 (32%), Positives = 160/306 (52%), Gaps = 12/306 (3%)
Query: 179 KITVVGAGQVGMACTYSILTQGIYSNFCLIDSNEDRCKGEMLDLQHGAPFLRSP-KIESG 237
KI+++GAG VG + + + + L D E +G+ LD+ AP KI
Sbjct: 4 KISIIGAGNVGATLAHLLALKE-LGDVVLFDIVEGVPQGKALDIAEAAPVEGFDTKITGT 62
Query: 238 SDIAMSEGSRIVIITAGVRSLVGETRLQLVDRNVKIFKDLIPKIAKGSPDCILLIISNPV 297
+D GS +V+ITAGV G +R L+ N KI KD+ I K +PD I+++++NPV
Sbjct: 63 NDYEDIAGSDVVVITAGVPRKPGMSRDDLLGINAKIMKDVAEGIKKYAPDAIVIVVTNPV 122
Query: 298 DVLTYISWKLSGFPKNRVIGSGTNLDSMRFRVLLAQKLGLSPESVHGFIIGEHGDSSVPV 357
D +TY++ K SGFPKNRVIG LDS RFR +A++L +S + V F++G HGDS VP+
Sbjct: 123 DAMTYVALKESGFPKNRVIGMAGVLDSARFRTFIAEELNVSVKDVTAFVLGGHGDSMVPL 182
Query: 358 WSGVNVAGVTLKELNPTIGTEQDTENFVRLHADVVNSAYEVIKL--KGYTSWALGLSVAS 415
V G+ L++L ++ + V E++ L G +A S+A
Sbjct: 183 VRYSTVGGIPLEDLLS----KEKLDEIV---ERTRKGGAEIVGLLKTGSAYYAPAASIAE 235
Query: 416 ISHTLLNNTNKIHAVSTLIQGHHGIEEEVFLSLPCVMADNGVTHIINQNLTPDEAEKLRK 475
+ +L + ++ S ++G +G+ ++V++ +P + NGV II L +E K
Sbjct: 236 MVEAILKDKKRVLPCSAYLEGEYGV-KDVYVGVPVKLGKNGVEKIIELELDDEEKAAFDK 294
Query: 476 SAATIS 481
S +
Sbjct: 295 SVEAVK 300
Score = 30.5 bits (70), Expect = 2.0
Identities = 7/18 (38%), Positives = 12/18 (66%)
Query: 132 KITVVGAGQVGMACTYSI 149
KI+++GAG VG + +
Sbjct: 4 KISIIGAGNVGATLAHLL 21
>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 = 260 bits (666), Expect = 1e-83
Identities = 101/305 (33%), Positives = 171/305 (56%), Gaps = 12/305 (3%)
Query: 180 ITVVGAGQVGMACTYSILTQGIYSNFCLIDSNEDRCKGEMLDLQHGAPFLRSP-KIESGS 238
I+++GAG VG + + + + L+D E +G+ LD+ AP L S K+ +
Sbjct: 1 ISIIGAGNVGATLAQLLALKEL-GDVVLLDIVEGLPQGKALDISQAAPILGSDTKVTGTN 59
Query: 239 DIAMSEGSRIVIITAGVRSLVGETRLQLVDRNVKIFKDLIPKIAKGSPDCILLIISNPVD 298
D GS +V+ITAG+ G +R L+ N KI K++ I K +P+ I+++++NP+D
Sbjct: 60 DYEDIAGSDVVVITAGIPRKPGMSRDDLLGTNAKIVKEVAENIKKYAPNAIVIVVTNPLD 119
Query: 299 VLTYISWKLSGFPKNRVIGSGTNLDSMRFRVLLAQKLGLSPESVHGFIIGEHGDSSVPVW 358
V+TY+++K SGFP+NRVIG LDS RFR +A++LG+S + V ++G HGD+ VP+
Sbjct: 120 VMTYVAYKASGFPRNRVIGMAGVLDSARFRYFIAEELGVSVKDVQAMVLGGHGDTMVPLP 179
Query: 359 SGVNVAGVTLKELNPTIGTEQDTENFVRLHADVVNSAYEVIKLKGYTS--WALGLSVASI 416
V G+ L EL T+++ + V N E++ L S +A ++A +
Sbjct: 180 RYSTVGGIPLTELI----TKEEIDEIVE---RTRNGGAEIVNLLKTGSAYYAPAAAIAEM 232
Query: 417 SHTLLNNTNKIHAVSTLIQGHHGIEEEVFLSLPCVMADNGVTHIINQNLTPDEAEKLRKS 476
+L + ++ S ++G +GI +++F+ +P V+ NGV II +LT +E E KS
Sbjct: 233 VEAILKDKKRVLPCSAYLEGEYGI-KDIFVGVPVVLGKNGVEKIIELDLTDEEKEAFDKS 291
Query: 477 AATIS 481
++
Sbjct: 292 VESVK 296
>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 = 248 bits (635), Expect = 4e-79
Identities = 113/309 (36%), Positives = 173/309 (55%), Gaps = 8/309 (2%)
Query: 179 KITVVGAGQVGMACTYSILTQGIYSNFCLIDSNEDRCKGEMLDLQHGAPFLRSP--KIES 236
K+ V+GAG VG A L G++S LID NE +GE LD H S KI +
Sbjct: 1 KLVVIGAGHVGSAVLNYALALGLFSEIVLIDVNEGVAEGEALDFHHATALTYSTNTKIRA 60
Query: 237 GSDIAMSEGSRIVIITAGVRSLVGET--RLQLVDRNVKIFKDLIPKIAKGSPDCILLIIS 294
G D + I++ITAG G T RL L N KI ++++ I K + + ++++I+
Sbjct: 61 G-DYDDCADADIIVITAGPSIDPGNTDDRLDLAQTNAKIIREIMGNITKVTKEAVIILIT 119
Query: 295 NPVDVLTYISWKLSGFPKNRVIGSGTNLDSMRFRVLLAQKLGLSPESVHGFIIGEHGDSS 354
NP+D+ YI+ +P N+VIG+GT LD+ R R ++A K G+ P++V G+++GEHG +
Sbjct: 120 NPLDIAVYIAATEFDYPANKVIGTGTMLDTARLRRIVADKYGVDPKNVTGYVLGEHGSHA 179
Query: 355 VPVWSGVNVAGVTLKELNPTIGTEQDTENFVRLHADVVNSAYEVIKLKGYTSWALGLSVA 414
PVWS VN+AG+ L EL G E ++ + +VV +AY+V KG+T+ + S +
Sbjct: 180 FPVWSLVNIAGLPLDELEALFGKEPIDKDELL--EEVVQAAYDVFNRKGWTNAGIAKSAS 237
Query: 415 SISHTLLNNTNKIHAVSTLIQGHHGIEEEVFLSLPCVMADNGVTHIINQNLTPDEAEKLR 474
+ +L + I V TL+ G +G+ +V LSLP V+ G+ ++ L E EKL
Sbjct: 238 RLIKAILLDERSILPVCTLLSGEYGL-SDVALSLPTVIGAKGIERVLEIPLDEWELEKLH 296
Query: 475 KSAATISQI 483
KSA I +
Sbjct: 297 KSAKAIRET 305
>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 = 231 bits (592), Expect = 3e-73
Identities = 109/310 (35%), Positives = 156/310 (50%), Gaps = 51/310 (16%)
Query: 180 ITVVGA-GQVGMACTYSILTQGIYS--NFCLIDSNEDRCKGEMLDLQHGAPFLRSPKIES 236
I V+GA G VG A + + + L D +E++ KG +DLQ L K+
Sbjct: 1 IAVIGAGGNVGPALAFGLADGSVLLAIELVLYDIDEEKLKGVAMDLQDAVEPLADIKVSI 60
Query: 237 GSDI-AMSEGSRIVIITAGVRSLVGETRLQLVDRNVKIFKDLIPKIAKGSPDCILLIISN 295
D + + +VIITAGV G RL L+ RNV I K++ I K SPD ++++SN
Sbjct: 61 TDDPYEAFKDADVVIITAGVGRKPGMGRLDLLKRNVPIVKEIGDNIEKYSPDAWIIVVSN 120
Query: 296 PVDVLTYISWKLSGFPKNRVIGSGTNLDSMRFRVLLAQKLGLSPESVHGFIIGEHGDSSV 355
PVD++TY+ W+ SG PK +VIG GT LD +RFR +LA+KLG+ P+ V +I+GEHG S V
Sbjct: 121 PVDIITYLVWRYSGLPKEKVIGLGT-LDPIRFRRILAEKLGVDPDDVKVYILGEHGGSQV 179
Query: 356 PVWSGVNVAGVTLKELNPTIGTEQDTENFVRLHADVVNSAYEVIKLKGYTSWALGLSVAS 415
P WS V +A S+A
Sbjct: 180 PDWSTVRIA----------------------------------------------TSIAD 193
Query: 416 ISHTLLNNTNKIHAVSTLIQGHHGIEEEVFLSLPCVMADNGVTHIINQNLTPDEAEKLRK 475
+ +LLN+ +I V G GI ++V +S+PC++ NGV I LT E EKL+K
Sbjct: 194 LIRSLLNDEGEILPVGVRNNGQIGIPDDVVVSVPCIVGKNGVEEPIEVGLTDFELEKLQK 253
Query: 476 SAATISQIQK 485
SA T+ + +
Sbjct: 254 SADTLKKELE 263
>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 = 193 bits (492), Expect = 7e-58
Identities = 110/307 (35%), Positives = 171/307 (55%), Gaps = 11/307 (3%)
Query: 179 KITVVGA-GQVGMACTYSILTQGIYSNFCLI--DSNEDRCKGEMLDLQHG-APFLRSPKI 234
K++++GA G+VG A + + + LI + ++ KG LD+ A +I
Sbjct: 2 KVSIIGASGRVGSATALLLAKEDVVKEINLISRPKSLEKLKGLRLDIYDALAAAGIDAEI 61
Query: 235 ESGSDIAMSEGSRIVIITAGVRSLVGETRLQLVDRNVKIFKDLIPKIAKGSPDCILLIIS 294
+ SD++ GS IVIITAGV G +RL L +N KI K +IA+ +PD +L+++
Sbjct: 62 KISSDLSDVAGSDIVIITAGVPRKEGMSRLDLAKKNAKIVKKYAKQIAEFAPDTKILVVT 121
Query: 295 NPVDVLTYISWKLSGFPKNRVIGSGTNLDSMRFRVLLAQKLGLSPESVHGFIIGEHGDSS 354
NPVDV+TY + K SGF KNRV G GT+LDS+RF+V +A+ + VH IIGEHGDS
Sbjct: 122 NPVDVMTYKALKESGFDKNRVFGLGTHLDSLRFKVAIAKHFNVHISEVHTRIIGEHGDSM 181
Query: 355 VPVWSGVNVAGVTLKELNPTIGTEQDTENFVRLHADVVNSAYEVIKLKGYTSWALGLSVA 414
VP+ S ++ G+ +K + D E V V N+ +I LKG + + +++
Sbjct: 182 VPLISSTSIGGIPIKRFPEY--KDFDVEKIVE---TVKNAGQNIISLKGGSEYGPASAIS 236
Query: 415 SISHTLLNNTNKIHAVSTLIQGH-HGIEEEVFLSLPCVMADNGVTHIINQNLTPDEAEKL 473
++ T+ N+ +I VST ++G GI +V + +P + NG+ I+ + DE E
Sbjct: 237 NLVRTIANDERRILTVSTYLEGEIDGI-RDVCIGVPVKLGKNGIEEIVPIEMDDDEREAF 295
Query: 474 RKSAATI 480
RKSA +
Sbjct: 296 RKSAEIV 302
>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 = 181 bits (462), Expect = 2e-55
Identities = 69/142 (48%), Positives = 96/142 (67%), Gaps = 1/142 (0%)
Query: 178 QKITVVGA-GQVGMACTYSILTQGIYSNFCLIDSNEDRCKGEMLDLQHGAPFLRSPKIES 236
K+ VVGA G VG + +++ QG+ L+D N+D+ +G +DL HG+ FL P I
Sbjct: 1 VKVAVVGAGGGVGSSLAFALALQGLADELVLVDINKDKAEGVAMDLSHGSTFLSVPGIVG 60
Query: 237 GSDIAMSEGSRIVIITAGVRSLVGETRLQLVDRNVKIFKDLIPKIAKGSPDCILLIISNP 296
G D + + +V+ITAGV G TRL L++RN IFKD++P IAK +PD I+L++SNP
Sbjct: 61 GDDYEALKDADVVVITAGVPRKPGMTRLDLLNRNAGIFKDIVPAIAKSAPDAIVLVVSNP 120
Query: 297 VDVLTYISWKLSGFPKNRVIGS 318
VD+LTYI+WK+SG P RVIGS
Sbjct: 121 VDILTYIAWKVSGLPPERVIGS 142
>gnl|CDD|173376 PTZ00082, PTZ00082, L-lactate dehydrogenase; Provisional.
Length = 321
Score = 182 bits (463), Expect = 2e-53
Identities = 94/321 (29%), Positives = 165/321 (51%), Gaps = 16/321 (4%)
Query: 175 SPDQKITVVGAGQVGMACTYSILTQGIYSNFCLIDSNEDRCKGEMLDLQHGAPFLRSP-K 233
+KI+++G+G +G Y I+ + + + L D ++ +G+ LD+ H S K
Sbjct: 4 IKRRKISLIGSGNIGGVMAYLIVLKNL-GDVVLFDIVKNIPQGKALDISHSNVIAGSNSK 62
Query: 234 IESGSDIAMSEGSRIVIITAGVRSLVGET-----RLQLVDRNVKIFKDLIPKIAKGSPDC 288
+ ++ GS +VI+TAG+ G++ R L+ N KI ++ I K P+
Sbjct: 63 VIGTNNYEDIAGSDVVIVTAGLTKRPGKSDKEWNRDDLLPLNAKIMDEVAEGIKKYCPNA 122
Query: 289 ILLIISNPVDVLTYISWKLSGFPKNRVIGSGTNLDSMRFRVLLAQKLGLSPESVHGFIIG 348
+++I+NP+DV+ + + SG PKN+V G LDS R R +A+KLG++P VH +IG
Sbjct: 123 FVIVITNPLDVMVKLLQEHSGLPKNKVCGMAGVLDSSRLRTYIAEKLGVNPRDVHASVIG 182
Query: 349 EHGDSSVPVWSGVNVAGVTLKEL--NPTIGTEQDTENFVRLHADVVNSAYEVIKLKGYTS 406
HGD VP+ V V G+ L E I E+ E R N+ E++ L G S
Sbjct: 183 AHGDKMVPLPRYVTVGGIPLSEFIKKGLITQEEIDEIVER----TRNTGKEIVDLLGTGS 238
Query: 407 --WALGLSVASISHTLLNNTNKIHAVSTLIQGHHGIEEEVFLSLPCVMADNGVTHIINQN 464
+A + ++ L + ++ S ++G +G +++++ P V+ NGV II +
Sbjct: 239 AYFAPAAAAIEMAEAYLKDKKRVLPCSAYLEGQYGH-KDIYMGTPAVIGANGVEKIIELD 297
Query: 465 LTPDEAEKLRKSAATISQIQK 485
LTP+E +K +S + +++
Sbjct: 298 LTPEEQKKFDESIKEVKRLEA 318
>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 = 172 bits (438), Expect = 5e-50
Identities = 100/316 (31%), Positives = 167/316 (52%), Gaps = 18/316 (5%)
Query: 178 QKITVVGAGQVGMACTYSILTQGIYSNFCLIDSNEDRCKGEMLDLQHGAPF-LRSPKIES 236
+KI+V+GAG VG A T L + ++ L+D E +G+ LD+ +P K+
Sbjct: 2 KKISVIGAGFVG-ATTAFRLAEKELADLVLLDVVEGIPQGKALDMYEASPVGGFDTKVTG 60
Query: 237 GSDIAMSEGSRIVIITAGVRSLVGETRLQLVDRNVKIFKDLIPKIAKGSPDCILLIISNP 296
++ A + S IV+ITAG+ G +R L+ N I +++ +I + SP+ I++++SNP
Sbjct: 61 TNNYADTANSDIVVITAGLPRKPGMSREDLLSMNAGIVREVTGRIMEHSPNPIIVVVSNP 120
Query: 297 VDVLTYISWKLSGFPKNRVIGSGTNLDSMRFRVLLAQKLGLSPESVHGFIIGEHGDSSVP 356
+D +TY++W+ SGFPK RVIG LDS RFR +A +LG+S + V ++G HGD+ VP
Sbjct: 121 LDAMTYVAWQKSGFPKERVIGQAGVLDSARFRTFIAMELGVSVQDVTACVLGGHGDAMVP 180
Query: 357 VWSGVNVAGVTLKELNPTIGTEQDTENFVRLHADVVN-----SAYEVIKLKGYTSWALGL 411
+ VAG+ + +L + E + ++VN SAY +A
Sbjct: 181 LVRYSTVAGIPVADLISAERIAEIVERTRKGGGEIVNLLKQGSAY----------YAPAA 230
Query: 412 SVASISHTLLNNTNKIHAVSTLIQGHHGIEEEVFLSLPCVMADNGVTHIINQNLTPDEAE 471
SV + +L + ++ + + G +GI + +++ +P ++ NGV HI L E
Sbjct: 231 SVVEMVEAILKDRKRVLPCAAYLDGQYGI-DGIYVGVPVILGKNGVEHIYELKLDQSELA 289
Query: 472 KLRKSAATISQIQKGL 487
L KSA + + K L
Sbjct: 290 LLNKSAKIVDENCKML 305
>gnl|CDD|173409 PTZ00117, PTZ00117, malate dehydrogenase; Provisional.
Length = 319
Score = 156 bits (397), Expect = 6e-44
Identities = 89/307 (28%), Positives = 154/307 (50%), Gaps = 9/307 (2%)
Query: 179 KITVVGAGQVGMACTYSILTQGIYSNFCLIDSNEDRCKGEMLDLQHGAPFLRSP-KIESG 237
KI+++GAGQ+G IL + + + L D + +G+ LDL+H + + S I
Sbjct: 7 KISMIGAGQIGSTVALLILQKNL-GDVVLYDVIKGVPQGKALDLKHFSTLVGSNINILGT 65
Query: 238 SDIAMSEGSRIVIITAGVRSLVGETRLQLVDRNVKIFKDLIPKIAKGSPDCILLIISNPV 297
++ + S +V+ITAGV+ TR L+ N KI K + + K P+ ++ ++NP+
Sbjct: 66 NNYEDIKDSDVVVITAGVQRKEEMTREDLLTINGKIMKSVAESVKKYCPNAFVICVTNPL 125
Query: 298 DVLTYISWKLSGFPKNRVIGSGTNLDSMRFRVLLAQKLGLSPESVHGFIIGEHGDSSVPV 357
D + + + SG P N++ G LDS RFR LA+KLG+SP V +IG HGD VP+
Sbjct: 126 DCMVKVFQEKSGIPSNKICGMAGVLDSSRFRCNLAEKLGVSPGDVSAVVIGGHGDLMVPL 185
Query: 358 WSGVNVAGVTLKE-LNPTIGTEQDTENFVRLHADVVNSAYEVIKL--KGYTSWALGLSVA 414
V G+ L + + TE++ ++ N E++KL KG +A ++
Sbjct: 186 PRYCTVNGIPLSDFVKKGAITEKEINEIIKKTR---NMGGEIVKLLKKGSAFFAPAAAIV 242
Query: 415 SISHTLLNNTNKIHAVSTLIQGHHGIEEEVFLSLPCVMADNGVTHIINQNLTPDEAEKLR 474
++ L + ++ S + G + + +F+ +P V+ G+ +I L +E E
Sbjct: 243 AMIEAYLKDEKRVLVCSVYLNGQYNC-KNLFVGVPVVIGGKGIEKVIELELNAEEKELFD 301
Query: 475 KSAATIS 481
KS +I
Sbjct: 302 KSIESIQ 308
>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 = 120 bits (302), Expect = 5e-32
Identities = 56/173 (32%), Positives = 94/173 (54%), Gaps = 8/173 (4%)
Query: 320 TNLDSMRFRVLLAQKLGLSPESVHGFIIGEHGDSSVPVWSGVNVAGVTLKEL-NPTIG-T 377
T LD+ R R LA+K G+ P SV+ ++IGEH + P WS V + L + T
Sbjct: 1 TTLDTARARTFLAEKFGVDPRSVNVYVIGEHSGTQFPDWSHAKVTIIPLISQVKENLKDT 60
Query: 378 EQDTENFVRLHADVVNSAYEVIKLK-GYTSWALGLSVASISHTLLNNTNKIHAVSTLIQG 436
+ + E + V N+ YEVI+ K G T++++ + A I+ +L T + +V + G
Sbjct: 61 DWELEELIE---RVQNAGYEVIEAKAGSTTYSMAYAAARIAKAILRGTGGVLSVGVYLDG 117
Query: 437 HHGIEEEVFLSLPCVMADNGVTHIINQ-NLTPDEAEKLRKSAATISQ-IQKGL 487
++G ++++ S+P V+ +GV ++ L E EKL KSAA + + I+KG
Sbjct: 118 YYGSPDDIYFSVPVVLGKDGVEKVVEILPLNDFEREKLEKSAAELKKEIEKGF 170
>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 = 78.3 bits (194), Expect = 5e-16
Identities = 73/270 (27%), Positives = 117/270 (43%), Gaps = 55/270 (20%)
Query: 244 EGSRIVIITAGVRSLVGETRLQLVDRNVKIFKDLIPKIAKGSPDCILLIISNPVDVLTYI 303
+G+ +V+I AGV G TR L + N I +DL +AK P ++LIISNPV+ I
Sbjct: 67 KGADVVVIPAGVPRKPGMTRDDLFNINAGIVRDLATAVAKACPKALILIISNPVNSTVPI 126
Query: 304 S---WKLSG-FPKNRVIGSGTNLDSMRFRVLLAQKLGLSPESVHGFIIGEH-GDSSVPVW 358
+ K +G + R+ G T LD +R +A+ LGL P V+ +IG H G + +P+
Sbjct: 127 AAEVLKKAGVYDPKRLFGV-TTLDVVRANTFVAELLGLDPAKVNVPVIGGHSGVTILPLL 185
Query: 359 SGVNVAGVTLKELNPTIGTEQDTENFV-RLHADVVNSAYEVIKLKGYTSWALGLSVASIS 417
S P +++ E R + EV+K K A LS+A
Sbjct: 186 SQCQP---------PFTFDQEEIEALTHR----IQFGGDEVVKAKAGAGSAT-LSMA--- 228
Query: 418 HTLLNNTNKIHA----VSTLIQGHHGIEEEV--------------FLSLPCVMADNGVT- 458
+A ++L++G G E+ V F + P + NGV
Sbjct: 229 ----------YAGARFANSLLRGLKG-EKGVIECAYVESDVTEAPFFATPVELGKNGVEK 277
Query: 459 HIINQNLTPDEAEKLRKSAATISQ-IQKGL 487
++ L E + L + + + I+KG+
Sbjct: 278 NLGLGKLNDYEKKLLEAALPELKKNIEKGV 307
>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 = 78.2 bits (193), Expect = 6e-16
Identities = 86/327 (26%), Positives = 139/327 (42%), Gaps = 38/327 (11%)
Query: 179 KITVVGA-GQVGMACTYSILTQGIYSNFCLIDSNEDRCKGEMLDLQHGAPFLRSPKIESG 237
K+ V+GA G +G + + Q S L D G DL H P S K SG
Sbjct: 1 KVAVLGAAGGIGQPLSLLLKLQPYVSELSLYDIAG--AAGVAADLSH-IPTAASVKGFSG 57
Query: 238 SDIAMS--EGSRIVIITAGVRSLVGETRLQLVDRNVKIFKDLIPKIAKGSPDCILLIISN 295
+ + +G+ +V+I AGV G TR L + N I KDL+ +A+ P ++L+I+N
Sbjct: 58 EEGLENALKGADVVVIPAGVPRKPGMTRDDLFNVNAGIVKDLVAAVAESCPKAMILVITN 117
Query: 296 PVDVLTYISW----KLSGFPKNRVIGSGTNLDSMRFRVLLAQKLGLSPESVHGFIIGEH- 350
PV+ I+ K + N++ G T LD +R +A+ G P V+ +IG H
Sbjct: 118 PVNSTVPIAAEVLKKKGVYDPNKLFGV-TTLDIVRANTFVAELKGKDPMEVNVPVIGGHS 176
Query: 351 GDSSVPVWSGVNVAGVTLKELNPTIGTEQDTENFVRLHADVVNSAYEVIKLK-GYTSWAL 409
G++ +P+ S + TE E + + N+ EV+K K G S L
Sbjct: 177 GETIIPLISQCP---------GKVLFTEDQLEALIH---RIQNAGTEVVKAKAGAGSATL 224
Query: 410 GLSVASISHTL-----LNNTNKIHAVSTL-IQGHHGIEEEVFLSLPCVMADNGV--THII 461
++ A L L + + + G F + P ++ NGV I
Sbjct: 225 SMAFAGARFVLSLVRGLKGEEGVVECAYVESDGVTEAT---FFATPLLLGKNGVEKRLGI 281
Query: 462 NQNLTPDEAEKLRKSAATISQ-IQKGL 487
+ L+ E + L + + + I+KG
Sbjct: 282 GK-LSSFEEKMLNGALPELKKNIKKGE 307
>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 = 73.1 bits (180), Expect = 3e-14
Identities = 63/242 (26%), Positives = 99/242 (40%), Gaps = 18/242 (7%)
Query: 248 IVIITAGVRSLVGETRLQLVDRNVKIFKD---LIPKIAKGSPDCILLIISNPVDVLTYIS 304
+ I+ G R L+ +N KIFK+ + K+AK P +L++ NP + I+
Sbjct: 79 VAILVGAFPRKPGMERADLLRKNAKIFKEQGEALNKVAK--PTVKVLVVGNPANTNALIA 136
Query: 305 WKLSGFPKNRVIGSGTNLDSMRFRVLLAQKLGLSPESVHGFII-GEHGDSSVPVWSGVNV 363
K + + + T LD R + +A+KLG+ V II G H ++ VP S V
Sbjct: 137 LKNAPNLPPKNFTALTRLDHNRAKAQVARKLGVRVSDVKNVIIWGNHSNTQVPDLSNAVV 196
Query: 364 AGVTLKELNPTI-GTEQDTENFVRLHADVVNSAYEVIKLKGYTSWALGLSVASISH--TL 420
G E + E + FV+ V +IK +G +S A + A H
Sbjct: 197 YGPGGTEWVLDLLDEEWLNDEFVK---TVQKRGAAIIKKRGASS-AASAAKAIADHVKDW 252
Query: 421 LNNTNKIHAVSTLI---QGHHGIEEEVFLSLPCVMADNGVTHII-NQNLTPDEAEKLRKS 476
L T VS + +GI + S PC G H++ + L EKL+ +
Sbjct: 253 LFGTPPGEIVSMGVYSPGNPYGIPPGIVFSFPCT-CKGGGWHVVEDLKLNDWLREKLKAT 311
Query: 477 AA 478
Sbjct: 312 EE 313
>gnl|CDD|240360 PTZ00325, PTZ00325, malate dehydrogenase; Provisional.
Length = 321
Score = 69.3 bits (170), Expect = 7e-13
Identities = 69/257 (26%), Positives = 112/257 (43%), Gaps = 30/257 (11%)
Query: 244 EGSRIVIITAGVRSLVGETRLQLVDRNVKIFKDLIPKIAKGSPDCILLIISNPVDVLTYI 303
G+ +V+I AGV G TR L + N I +DL+ +A +P I+ I+SNPV+ I
Sbjct: 75 RGADLVLICAGVPRKPGMTRDDLFNTNAPIVRDLVAAVASSAPKAIVGIVSNPVNSTVPI 134
Query: 304 SW----KLSGFPKNRVIGSGTNLDSMRFRVLLAQKLGLSPESVHGFIIGEHGDSS-VPVW 358
+ K + ++ G T LD +R R +A+ LG++P V+ ++G H + VP+
Sbjct: 135 AAETLKKAGVYDPRKLFGV-TTLDVVRARKFVAEALGMNPYDVNVPVVGGHSGVTIVPLL 193
Query: 359 SGVNVAGVTLKELNPTIGTEQDTENFVRLHADVVNSAYEVIKLK-GYTSWALGLSVASIS 417
S G++L E E ++ V EV+K K G S L ++ A+
Sbjct: 194 SQ---TGLSLPE-----------EQVEQITHRVQVGGDEVVKAKEGAGSATLSMAYAAAE 239
Query: 418 HTL-----LNNTNKIHAVSTLIQGHHGIEEEVFLSLPCVMADNGVTHIINQN-LTPDEAE 471
+ L I ++ E F S P + GV ++ L E E
Sbjct: 240 WSTSVLKALRGDKGI-VECAFVES-DMRPECPFFSSPVELGKEGVERVLPIGPLNAYEEE 297
Query: 472 KLRKSAATISQ-IQKGL 487
L + + + I+KGL
Sbjct: 298 LLEAAVPDLKKNIEKGL 314
>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 = 68.1 bits (167), Expect = 2e-12
Identities = 75/321 (23%), Positives = 128/321 (39%), Gaps = 32/321 (9%)
Query: 179 KITVVGA-GQVGMACTYSILT-------QGIYSNFCLIDSNEDRCKGEMLDLQHGA-PFL 229
++ V GA GQ+G + + I + Q + + I +G ++L+ A P L
Sbjct: 5 RVAVTGAAGQIGYSLLFRIASGELFGKDQPVVLHLLDIPPAMKALEGVAMELEDCAFPLL 64
Query: 230 RSPKIESGSDIAMS-EGSRIVIITAGVRSLVGETRLQLVDRNVKIFKD---LIPKIAKGS 285
+ + +D + + ++ G R L+ +N KIFK+ + K+AK
Sbjct: 65 A--GVVATTDPEEAFKDVDAALLVGAFPRKPGMERADLLSKNGKIFKEQGKALNKVAK-- 120
Query: 286 PDCILLIISNPVDVLTYISWKLSGFPKNRVIGSGTNLDSMRFRVLLAQKLGLSPESVHGF 345
D +L++ NP + I+ K + + + T LD R + LA K G+ V
Sbjct: 121 KDVKVLVVGNPANTNALIASKNAPDIPPKNFSAMTRLDHNRAKYQLAAKAGVPVSDVKNV 180
Query: 346 II-GEHGDSSVPVWSGVNVAGVTLKELNPTIGTEQDTEN-FVRLHADVVNSAYEVIKLKG 403
II G H ++ VP A V + + I ++ E F+ V VI+ +G
Sbjct: 181 IIWGNHSNTQVP---DFTHATVDGRPVKEVIKDDKWLEGEFIPT---VQQRGAAVIEARG 234
Query: 404 YTSWALGLSVASISH--TLLNNTNKIHAVST--LIQG-HHGIEEEVFLSLPCVMADNGVT 458
+S A + A+I H + T + VS G +GI E + S P +G
Sbjct: 235 ASS-AASAANAAIDHVRDWVTGTPEGDWVSMGVYSDGNPYGIPEGIIFSFPVTCKGDGEW 293
Query: 459 HII-NQNLTPDEAEKLRKSAA 478
I+ L KL +
Sbjct: 294 EIVEGLPLDDFVRGKLDATED 314
>gnl|CDD|215058 PLN00106, PLN00106, malate dehydrogenase.
Length = 323
Score = 64.6 bits (158), Expect = 2e-11
Identities = 40/111 (36%), Positives = 59/111 (53%), Gaps = 5/111 (4%)
Query: 244 EGSRIVIITAGVRSLVGETRLQLVDRNVKIFKDLIPKIAKGSPDCILLIISNPVDVLTYI 303
+G+ +VII AGV G TR L + N I K L +AK P+ ++ IISNPV+ I
Sbjct: 85 KGADLVIIPAGVPRKPGMTRDDLFNINAGIVKTLCEAVAKHCPNALVNIISNPVNSTVPI 144
Query: 304 S---WKLSG-FPKNRVIGSGTNLDSMRFRVLLAQKLGLSPESVHGFIIGEH 350
+ K +G + ++ G T LD +R +A+K GL P V ++G H
Sbjct: 145 AAEVLKKAGVYDPKKLFGV-TTLDVVRANTFVAEKKGLDPADVDVPVVGGH 194
>gnl|CDD|235340 PRK05086, PRK05086, malate dehydrogenase; Provisional.
Length = 312
Score = 63.9 bits (156), Expect = 3e-11
Identities = 52/148 (35%), Positives = 76/148 (51%), Gaps = 16/148 (10%)
Query: 244 EGSRIVIITAGVRSLVGETRLQLVDRNVKIFKDLIPKIAKGSPDCILLIISNPVDVLTYI 303
EG+ +V+I+AGV G R L + N I K+L+ K+AK P + II+NPV+ I
Sbjct: 68 EGADVVLISAGVARKPGMDRSDLFNVNAGIVKNLVEKVAKTCPKACIGIITNPVNTTVAI 127
Query: 304 S---WKLSG-FPKNRVIGSGTNLDSMRFRVLLAQKLGLSPESVHGFIIGEH-GDSSVPVW 358
+ K +G + KN++ G T LD +R +A+ G P V +IG H G + +P+
Sbjct: 128 AAEVLKKAGVYDKNKLFGV-TTLDVIRSETFVAELKGKQPGEVEVPVIGGHSGVTILPLL 186
Query: 359 SGVNVAGVTLKE-----LNPTI---GTE 378
S V GV+ E L I GTE
Sbjct: 187 S--QVPGVSFTEQEVADLTKRIQNAGTE 212
>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 = 51.1 bits (123), Expect = 5e-07
Identities = 81/330 (24%), Positives = 130/330 (39%), Gaps = 50/330 (15%)
Query: 179 KITVVGA-GQVGMACTYSILT-------QGIYSNFCLIDSNEDRCKGEMLDLQHGA-PFL 229
++ V GA GQ+ + I Q + + I +G +++LQ A P L
Sbjct: 4 RVLVTGAAGQIAYSLLPMIAKGDVFGPDQPVILHLLDIPPALKALEGVVMELQDCAFPLL 63
Query: 230 RSPKIESGSDIAMS-EGSRIVIITAGVRSLVGETRLQLVDRNVKIFK---DLIPKIAKGS 285
+S + + +D + + + I+ + G R L+ NVKIFK + + K AK
Sbjct: 64 KS--VVATTDPEEAFKDVDVAILVGAMPRKEGMERKDLLKANVKIFKEQGEALDKYAK-- 119
Query: 286 PDCILLIISNPVDVLTYISWKL-SGFPKNRVIGSGTNLDSMRFRVLLAQKLGLSPESVHG 344
+ +L++ NP + I K PK + T LD R + +A KLG+ V
Sbjct: 120 KNVKVLVVGNPANTNALILLKYAPSIPK-ENFTALTRLDHNRAKSQIALKLGVPVSDVKN 178
Query: 345 FII-GEHGDSSVPVWSGVNVAGVTLKELNPTIGTEQDTENFVR----LHAD----VVNSA 395
II G H + P VN A V L G + V+ L+ + V
Sbjct: 179 VIIWGNHSSTQYP---DVNHATVELN------GKGKPAREAVKDDAWLNGEFISTVQKRG 229
Query: 396 YEVIKLKGYTSWALGLSVASIS----HTLLNNTNKIHAVSTLI--QGHHGIEEEVFLSLP 449
VIK + +S +S A H T + VS + G +G+ E + S P
Sbjct: 230 AAVIKARKLSS---AMSAAKAICDHVHDWWFGTPEGEFVSMGVYSDGSYGVPEGLIFSFP 286
Query: 450 CVMADNGVTHIINQNLTPDEA--EKLRKSA 477
+ I Q L+ D+ EK+ +A
Sbjct: 287 VTCKNGKWK--IVQGLSIDDFSREKIDATA 314
>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 = 49.1 bits (118), Expect = 2e-06
Identities = 75/326 (23%), Positives = 129/326 (39%), Gaps = 44/326 (13%)
Query: 179 KITVVGA-GQVGMACTYSIL-----------TQGIYSNFCLIDSNEDRCKGEMLDLQHGA 226
++ V GA GQ+G YS+L Q + + +G ++L+ A
Sbjct: 4 RVAVTGAAGQIG----YSLLFRIASGEMFGPDQPVILQLLELPQALKALEGVAMELEDCA 59
Query: 227 -PFLRSPKIESGSDIAMSEGSRIVIITAGVRSLVGETRLQLVDRNVKIFKD---LIPKIA 282
P L I ++A + +++ A R G R L+ N KIF + +A
Sbjct: 60 FPLLAEIVITDDPNVAFKDADWALLVGAKPRG-PGMERADLLKANGKIFTAQGKALNDVA 118
Query: 283 KGSPDCILLIISNPVDVLTYISWKLS-GFPKNRVIGSGTNLDSMRFRVLLAQKLGLSPES 341
S D +L++ NP + I+ K + P + + T LD R + LA+K G+
Sbjct: 119 --SRDVKVLVVGNPCNTNALIAMKNAPDIPPDN-FTAMTRLDHNRAKSQLAKKAGVPVTD 175
Query: 342 VHGFII-GEHGDSSVPVWSGVNVAGVTLKELNPTIGTEQD--TENFVRLHADVVNSAYEV 398
V +I G H + P ++ + G E + ++ + F+ V +
Sbjct: 176 VKNMVIWGNHSPTQYPDFTNATIGGKPAAE----VINDRAWLEDEFIP---TVQKRGAAI 228
Query: 399 IKLKGYTSWALGLSVASISH--TLLNNTNKIHAVSTLI--QGHHGIEEEVFLSLPCVMAD 454
IK +G +S A + A+I H + T + S + G +GI E + S P
Sbjct: 229 IKARGASS-AASAANAAIDHMRDWVLGTPEGDWFSMAVPSDGSYGIPEGLIFSFPVRSKG 287
Query: 455 NGVTHIINQNLTPDEA--EKLRKSAA 478
G I + L D+ EK+ + A
Sbjct: 288 GGYE--IVEGLEIDDFAREKIDATLA 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 = 48.7 bits (116), Expect = 3e-06
Identities = 66/288 (22%), Positives = 123/288 (42%), Gaps = 42/288 (14%)
Query: 213 DRCKGEMLDLQ-----HGAPFLRSPKIE---SGSDIAMSEGSRIVIITAGVRSLVGETRL 264
+R + ++L+ + A + + K+E D A + A V GE R
Sbjct: 28 NRLEALAMELEDCAFPNLAGTIVTTKLEEAFKDIDCAF--------LVASVPLKPGEVRA 79
Query: 265 QLVDRNVKIFK---DLIPKIAKGSPDCILLIISNPVDVLTYISW----KLSGFPKNRVIG 317
L+ +N IFK + + + AK P +L+I NPV+ ++ KLS +N
Sbjct: 80 DLLTKNTPIFKATGEALSEYAK--PTVKVLVIGNPVNTNCLVAMLHAPKLS--AEN--FS 133
Query: 318 SGTNLDSMRFRVLLAQKLGLSPESVHGFII-GEHGDSSVPVWSGVNVA-GVTLKELNPTI 375
S LD R +A KL + + ++ ++ G H +S V + +++ +
Sbjct: 134 SLCMLDHNRAVSRIASKLKVPVDHIYHVVVWGNHAESMVADLTHAEFTKNGKHQKVFDEL 193
Query: 376 GTEQDTENFVRLHADVVNSAYEVIKLKGYTSWALGLSVASISH--TLLNNTNKIHAVSTL 433
+ +F + + A+++++++G+TS A AS+ H L T +S
Sbjct: 194 CRDYPEPDFFEV---IAQRAWKILEMRGFTS-AASPVKASLQHMKAWLFGTRPGEVLSMG 249
Query: 434 I----QGHHGIEEEVFLSLPCVMADNGVTHII-NQNLTPDEAEKLRKS 476
I +GI+ V S PC + ++G H++ N L P KL ++
Sbjct: 250 IPVPEGNPYGIKPGVIFSFPCTVDEDGKVHVVENFELNPWLKTKLAQT 297
>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 = 46.4 bits (110), Expect = 2e-05
Identities = 56/238 (23%), Positives = 98/238 (41%), Gaps = 24/238 (10%)
Query: 260 GETRLQLVDRNVKIFKD---LIPKIAKGSPDCILLIISNPVDVLTYISWKLSGFPKNRVI 316
G R L+ +NVKIFK+ + K+AK DC +L++ NP + + + +
Sbjct: 90 GMERRDLLSKNVKIFKEQGRALDKLAK--KDCKVLVVGNPANTNALVLSNYAPSIPPKNF 147
Query: 317 GSGTNLDSMRFRVLLAQKLGLSPESVHGFII-GEHGDSSVP-VWSGVNVAGVTLKELNPT 374
+ T LD R +A++ G+ V II G H + P V G K +
Sbjct: 148 SALTRLDHNRALAQVAERAGVPVSDVKNVIIWGNHSSTQYPDVNHATVTKGGKQKPVREA 207
Query: 375 IGTEQ-DTENFVRLHADVVNSAYEVIKLKGYTSWALGLSVASIS----HTLLNNTNKIHA 429
I + F+ V +I+ + +S LS A + H + T +
Sbjct: 208 IKDDAYLDGEFI---TTVQQRGAAIIRARKLSS---ALSAAKAAVDQMHDWVLGTPEGTF 261
Query: 430 VSTLIQG---HHGIEEEVFLSLPCVMADNGVTHIINQNLTPDEAEKLRKSAATISQIQ 484
VS + +G+ + + S P V NG I+ + L D++ + +K A T +++
Sbjct: 262 VSMGVYSDGSPYGVPKGLIFSFP-VTCKNGEWKIV-EGLCVDDSSR-KKLALTAKELE 316
>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 = 39.6 bits (92), Expect = 0.003
Identities = 62/229 (27%), Positives = 101/229 (44%), Gaps = 14/229 (6%)
Query: 260 GETRLQLVDRNVKIFKDLIPKI-AKGSPDCILLIISNPVDVLTYISWKLSGFPKNRVIGS 318
G R L+D N +IF D + A S +C +L++ NP + I+ K + + +
Sbjct: 135 GMERADLLDINGQIFADQGKALNAVASKNCKVLVVGNPCNTNALIAMKNAPNIPRKNFHA 194
Query: 319 GTNLDSMRFRVLLAQKLGLSPESVHGFII-GEHGDSSVPVWSGVNVAGVTLKELNPTIGT 377
T LD R + LA K G SV I G H + VP + + G KE+ T
Sbjct: 195 LTRLDENRAKCQLALKSGKFYTSVSNVTIWGNHSTTQVPDFVNAKIGGRPAKEV--IKDT 252
Query: 378 EQDTENFVRLHADVVNSAYEVIKLKGYTSWA-LGLSVASISHTLLNNTNKIHAVSTLI-- 434
+ E F V +IK G +S A +S+A +L+ T + ST +
Sbjct: 253 KWLEEEFTPT---VQKRGGALIKKWGRSSAASTAVSIADAIKSLVVPTPEGDWFSTGVYT 309
Query: 435 QGH-HGIEEEVFLSLPCVMADNGVTHIINQNLTPDE--AEKLRKSAATI 480
G+ +GI E + S+PC +G + +++ D+ E++RKS +
Sbjct: 310 DGNPYGIAEGLVFSMPCRSKGDGDYELAT-DVSMDDFLRERIRKSEDEL 357
>gnl|CDD|177744 PLN00135, PLN00135, malate dehydrogenase.
Length = 309
Score = 36.3 bits (84), Expect = 0.031
Identities = 73/299 (24%), Positives = 122/299 (40%), Gaps = 52/299 (17%)
Query: 219 MLDLQHGAPFLRSPKIE-------------SGSDIAMS-EGSRIVIITAGVRSLVGETRL 264
MLD+ A L K+E + +D+ + +G I ++ G G R
Sbjct: 18 MLDIPPAAEALNGVKMELIDAAFPLLKGVVATTDVVEACKGVNIAVMVGGFPRKEGMERK 77
Query: 265 QLVDRNVKIFKDLIPKIAK-GSPDCILLIISNPVDVLTYISWKLSGFP-----KNRVIGS 318
++ +NV I+K + K +PDC +L+++NP + I L F KN I
Sbjct: 78 DVMSKNVSIYKSQASALEKHAAPDCKVLVVANPANTNALI---LKEFAPSIPEKN--ITC 132
Query: 319 GTNLDSMRFRVLLAQKLGLSPESVHGFII-GEHGDSSVPVWSGVNVAGVTL----KELNP 373
T LD R ++++LG+ V II G H + P VN A V K +
Sbjct: 133 LTRLDHNRALGQISERLGVPVSDVKNVIIWGNHSSTQYP---DVNHATVKTPSGEKPVRE 189
Query: 374 TIGTEQ--DTENFVRLHADVVNSAYEVIKLKGYTSWALGLSVASIS----HTLLNNTNKI 427
+ + + E F+ V +IK + +S LS AS + + T +
Sbjct: 190 LVADDAWLNGE-FI---TTVQQRGAAIIKARKLSS---ALSAASSACDHIRDWVLGTPEG 242
Query: 428 HAVSTLI--QGHHGIEEEVFLSLPCVMADNGVTHIINQNLTPDEA--EKLRKSAATISQ 482
VS + G +G+ + S P V + G I+ Q L+ DE +K+ +A + +
Sbjct: 243 TWVSMGVYSDGSYGVPPGLIYSFP-VTCEKGEWSIV-QGLSIDEFSRKKMDATAKELKE 299
>gnl|CDD|235468 PRK05442, PRK05442, malate dehydrogenase; Provisional.
Length = 326
Score = 35.9 bits (84), Expect = 0.039
Identities = 78/334 (23%), Positives = 128/334 (38%), Gaps = 60/334 (17%)
Query: 179 KITVVG-AGQVGMACTYSIL-----------TQGIYSNFCLIDSNEDRCKGEMLDLQHGA 226
++ V G AGQ+G YS+L Q + I +G +++L A
Sbjct: 6 RVAVTGAAGQIG----YSLLFRIASGDMLGKDQPVILQLLEIPPALKALEGVVMELDDCA 61
Query: 227 -PFLRSPKIES-------GSDIAMSEGSRIVIITAGVRSLVGETRLQLVDRNVKIFK--- 275
P L I +D+A+ G+R R G R L++ N IF
Sbjct: 62 FPLLAGVVITDDPNVAFKDADVALLVGAR-------PRG-PGMERKDLLEANGAIFTAQG 113
Query: 276 DLIPKIAKGSPDCILLIISNPVDVLTYISWK-LSGFPKNRVIGSGTNLDSMRFRVLLAQK 334
+ ++A + D +L++ NP + I+ K P + T LD R LA K
Sbjct: 114 KALNEVA--ARDVKVLVVGNPANTNALIAMKNAPDLPAEN-FTAMTRLDHNRALSQLAAK 170
Query: 335 LGLSPESVHGFII-GEHGDSSVPVWSGVNVAGVTLKELNPTIGTEQDTEN-FVRLHADVV 392
G+ + + G H + P + + G E+ I + E+ F+ V
Sbjct: 171 AGVPVADIKKMTVWGNHSATQYPDFRHATIDGKPAAEV---INDQAWLEDTFIP---TVQ 224
Query: 393 NSAYEVIKLKGYTSWALGLSVAS--ISH--TLLNNTNKIHAVSTLI--QGHHGIEEEVFL 446
+I+ +G +S A S A+ I H + T + VS + G +GI E +
Sbjct: 225 KRGAAIIEARGASSAA---SAANAAIDHVRDWVLGTPEGDWVSMGVPSDGSYGIPEGLIF 281
Query: 447 SLPCVMADNGVTHIINQNLTPDE--AEKLRKSAA 478
P +NG I+ Q L D+ EK+ + A
Sbjct: 282 GFPVTC-ENGEYEIV-QGLEIDDFSREKIDATLA 313
>gnl|CDD|133433 cd05297, GH4_alpha_glucosidase_galactosidase, Glycoside Hydrolases
Family 4; Alpha-glucosidases and alpha-galactosidases.
Glucosidases cleave glycosidic bonds to release glucose
from oligosaccharides. Alpha-glucosidases and
alpha-galactosidases release alpha-D-glucose and
alpha-D-galactose, respectively, via the hydrolysis of
alpha-glycopyranoside bonds. Some bacteria
simultaneously translocate and phosphorylate
disaccharides via the phosphoenolpyruvate-dependent
phosphotransferase system (PEP-PTS). After
translocation, these phospho-disaccharides may be
hydrolyzed by the GH4 glycoside hydrolases such as the
alpha-glucosidases. Other organsisms (such as archaea
and Thermotoga maritima) lack the PEP-PTS system, but
have several enzymes normally associated with the
PEP-PTS operon. Alpha-glucosidases and
alpha-galactosidases 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 = 423
Score = 35.2 bits (82), Expect = 0.075
Identities = 39/162 (24%), Positives = 61/162 (37%), Gaps = 50/162 (30%)
Query: 179 KITVVGAGQVG--------MACTYSILTQGIYSNFCLIDSNEDRCK-----GEMLDLQHG 225
KI +GAG V + T + S L+D +E+R + + + + G
Sbjct: 2 KIAFIGAGSVVFTKNLVGDLLKTPELSG----STIALMDIDEERLETVEILAKKIVEELG 57
Query: 226 APFLRSPKIESGSDIAMS-EGSRIVIITA------------------GVRSLVGET---- 262
AP KIE+ +D + +G+ VI T G VG+T
Sbjct: 58 AP----LKIEATTDRREALDGADFVINTIQVGGHEYTETDFEIPEKYGYYQTVGDTSGPG 113
Query: 263 ---RLQLVDRNVKIFKDLIPKIAKGSPDCILLIISNPVDVLT 301
R R + + D+ I + PD LL +NP+ LT
Sbjct: 114 GIFRAL---RTIPVLLDIARDIEELCPDAWLLNYANPMAELT 152
>gnl|CDD|214912 smart00919, Malic_M, Malic enzyme, NAD binding domain. Malic
enzymes (malate oxidoreductases) catalyse the oxidative
decarboxylation of malate to form pyruvate.
Length = 231
Score = 34.3 bits (80), Expect = 0.087
Identities = 13/36 (36%), Positives = 19/36 (52%), Gaps = 1/36 (2%)
Query: 177 DQKITVVGAGQVGMACTYSILTQGI-YSNFCLIDSN 211
DQ+I V GAG G+ ++ G+ N L+DS
Sbjct: 25 DQRIVVNGAGAAGIGIAKLLVAAGVKRKNIWLVDSK 60
Score = 30.5 bits (70), Expect = 1.4
Identities = 11/35 (31%), Positives = 17/35 (48%)
Query: 130 DQKITVVGAGQVGMACTYSILTQTMARDAVSTVDR 164
DQ+I V GAG G+ ++ + R + VD
Sbjct: 25 DQRIVVNGAGAAGIGIAKLLVAAGVKRKNIWLVDS 59
>gnl|CDD|223358 COG0281, SfcA, Malic enzyme [Energy production and conversion].
Length = 432
Score = 34.1 bits (79), Expect = 0.15
Identities = 25/126 (19%), Positives = 49/126 (38%), Gaps = 26/126 (20%)
Query: 177 DQKITVVGAGQVGMACTYSILTQGI-YSNFCLIDS----NEDRCKGEMLDLQHGAPFLRS 231
DQKI + GAG G+A ++ G+ N ++D + R ++ Q
Sbjct: 199 DQKIVINGAGAAGIAIADLLVAAGVKEENIFVVDRKGLLYDGR--EDLTMNQKKYAKAIE 256
Query: 232 PKIESGSDIAMSEGSRIVIITAGVRSLVGETRLQLVDRNVKIFKDLIPKIAKGSPDCILL 291
E D+A+ G+ ++I +G V F + + + + + I+
Sbjct: 257 DTGERTLDLAL-AGADVLIGVSG----------------VGAFTEEM--VKEMAKHPIIF 297
Query: 292 IISNPV 297
++NP
Sbjct: 298 ALANPT 303
Score = 32.2 bits (74), Expect = 0.64
Identities = 12/35 (34%), Positives = 19/35 (54%)
Query: 130 DQKITVVGAGQVGMACTYSILTQTMARDAVSTVDR 164
DQKI + GAG G+A ++ + + + VDR
Sbjct: 199 DQKIVINGAGAAGIAIADLLVAAGVKEENIFVVDR 233
>gnl|CDD|224403 COG1486, CelF, Alpha-galactosidases/6-phospho-beta-glucosidases,
family 4 of glycosyl hydrolases [Carbohydrate transport
and metabolism].
Length = 442
Score = 33.8 bits (78), Expect = 0.20
Identities = 43/199 (21%), Positives = 79/199 (39%), Gaps = 48/199 (24%)
Query: 176 PDQKITVVGAG------QVGMACTYSILTQGIY-SNFCLIDSNEDRCK------GEMLDL 222
KI ++G G + T+ + L D +E+R K ++++
Sbjct: 2 KKFKIVIIGGGSTYTPKLLLGDLA---RTEELPVRELALYDIDEERLKIIAILAKKLVE- 57
Query: 223 QHGAPFLRSPKIESGSDI--AMSEGSRIVIITAGVRSL---VGETRLQL---VD------ 268
+ GAP K+E+ +D A+ EG+ VI V L + R+ L +
Sbjct: 58 EAGAPV----KVEATTDRREAL-EGADFVITQIRVGGLEAREKDERIPLKHGLYGQETNG 112
Query: 269 --------RNVKIFKDLIPKIAKGSPDCILLIISNPVDVLTYISWKLSGFPKNRVIGSGT 320
R + + D+ + K P+ +L +NP ++T +L +PK +++G
Sbjct: 113 PGGIFYGLRTIPVILDIAKDMEKVCPNAWMLNYTNPAAIVTEAVRRL--YPKIKIVGLCH 170
Query: 321 NLDSMRFRVLLAQKLGLSP 339
+ LA+ LGL P
Sbjct: 171 GPIGIAME--LAEVLGLEP 187
>gnl|CDD|214992 smart01045, BURP, The BURP domain is found at the C-terminus of
several different plant proteins. It was named after
the proteins in which it was first identified: the BNM2
clone-derived protein from Brassica napus; USPs and
USP-like proteins; RD22 from Arabidopsis thaliana; and
PG1beta from Lycopersicon esculentum. This domain is
around 230 amino acid residues long. It possesses the
following conserved features: two phenylalanine residues
at its N-terminus; two cysteine residues; and four
repeated cysteine-histidine motifs, arranged as:
CH-X(10)-CH-X(25-27)-CH-X(25-26)-CH, where X can be any
amino acid. The function of this domain is unknown.
Length = 222
Score = 31.4 bits (71), Expect = 0.77
Identities = 31/150 (20%), Positives = 49/150 (32%), Gaps = 35/150 (23%)
Query: 7 PRVSNKGLPRAKGLTEG-TETAKALSSKAENIIR--GLTEGTETAKALSSRNRGGRQDRR 63
P + + +P+ L + SSK + I+R T+ + A + G +
Sbjct: 18 PFIKDDLMPKRPFLPRQIADLLPFSSSKIDEILRVFSATKNSPMAGIIKETV--GECEAP 75
Query: 64 KPAVPRTLSGQDKICPG-LESNPQPSAYKTDAPPTKLARLATSTMAR---DAVSTVDRLL 119
+ G+ K C LES + ATS + R +T
Sbjct: 76 A------IEGETKRCVTSLES---------------MIDFATSVLGRYVVKVRTT----- 109
Query: 120 SQVAPSIESPDQKITVVGAGQVGMACTYSI 149
V S TVV A G+ T S+
Sbjct: 110 EVVVGSKNKALHNYTVVIAKVKGLNGTKSV 139
>gnl|CDD|176242 cd08282, PFDH_like, Pseudomonas putida aldehyde-dismutating
formaldehyde dehydrogenase (PFDH). Formaldehyde
dehydrogenase (FDH) is a member of the
zinc-dependent/medium chain alcohol dehydrogenase
family. Unlike typical FDH, Pseudomonas putida
aldehyde-dismutating FDH (PFDH) is
glutathione-independent. PFDH converts 2 molecules of
aldehydes to corresponding carboxylic acid and alcohol.
MDH family uses NAD(H) as a cofactor in the
interconversion of alcohols and aldehydes, or ketones.
Like the zinc-dependent alcohol dehydrogenases (ADH) of
the medium chain alcohol dehydrogenase/reductase family
(MDR), these tetrameric FDHs have a catalytic zinc that
resides between the catalytic and NAD(H)binding domains
and a structural zinc in a lobe of the catalytic domain.
Unlike ADH, where NAD(P)(H) acts as a cofactor, NADH in
FDH is a tightly bound redox cofactor (similar to
nicotinamide proteins). The medium chain alcohol
dehydrogenase family (MDR) has a NAD(P)(H)-binding
domain in a Rossmann fold of an beta-alpha form. The
N-terminal region typically has an all-beta catalytic
domain. These proteins typically form dimers (typically
higher plants, mammals) or tetramers (yeast, bacteria),
and have 2 tightly bound zinc atoms per subunit.
Length = 375
Score = 31.8 bits (73), Expect = 0.81
Identities = 17/50 (34%), Positives = 23/50 (46%), Gaps = 14/50 (28%)
Query: 182 VVGAGQVGMACTYSILTQG---IYSNFCLIDSNEDRCKGEMLDL--QHGA 226
V GAG VG+ YS + +G +Y +D +R LDL GA
Sbjct: 182 VFGAGPVGLMAAYSAILRGASRVYV----VDHVPER-----LDLAESIGA 222
>gnl|CDD|217809 pfam03949, Malic_M, Malic enzyme, NAD binding domain.
Length = 255
Score = 31.4 bits (72), Expect = 0.82
Identities = 27/136 (19%), Positives = 51/136 (37%), Gaps = 29/136 (21%)
Query: 176 PDQKITVVGAGQVGMACTYSIL----TQGI-----YSNFCLIDSN----EDRCKGEMLDL 222
DQKI GAG G+ ++ +G+ N ++D E R ++
Sbjct: 24 SDQKIVFFGAGAAGIGIAELLVAAMVREGLSEEEARKNIWMVDRKGLLTEGR--EDLNPF 81
Query: 223 QHGAPFLRSPKIESGSDIAMSEGSRIVIITAGVRSLVGETRLQLVDRNVKIF-KDLIPKI 281
+ PF R E ++E + L+G V +F ++++ +
Sbjct: 82 K--KPFAR-KTNEVKGWGTLAEAVKGAKPDV----LIG------VSGVPGVFTEEIVRAM 128
Query: 282 AKGSPDCILLIISNPV 297
A+ + I+ +SNP
Sbjct: 129 AEHTERPIIFALSNPT 144
Score = 28.3 bits (64), Expect = 7.7
Identities = 8/28 (28%), Positives = 12/28 (42%)
Query: 129 PDQKITVVGAGQVGMACTYSILTQTMAR 156
DQKI GAG G+ ++ +
Sbjct: 24 SDQKIVFFGAGAAGIGIAELLVAAMVRE 51
>gnl|CDD|133425 cd05197, GH4_glycoside_hydrolases, Glycoside Hydrases Family 4.
Glycoside hydrolases cleave glycosidic bonds to release
smaller sugars from oligo- or polysaccharides. Some
bacteria simultaneously translocate and phosphorylate
disaccharides via the phosphoenolpyruvate-dependent
phosphotransferase system (PEP-PTS). After
translocation, these phospho-disaccharides may be
hydrolyzed by GH4 glycoside hydrolases. Other organisms
(such as archaea and Thermotoga maritima) lack the
PEP-PTS system, but have several enzymes normally
associated with the PEP-PTS operon. GH4 family members
include 6-phospho-beta-glucosidases,
6-phospho-alpha-glucosidases,
alpha-glucosidases/alpha-glucuronidases (only from
Thermotoga), and alpha-galactosidases. They require two
cofactors, NAD+ and a divalent metal (Mn2+, Ni2+, Mg2+),
for activity. Some also require reducing conditions. GH4
glycoside hydrolases 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 = 425
Score = 31.7 bits (72), Expect = 0.90
Identities = 22/96 (22%), Positives = 36/96 (37%), Gaps = 19/96 (19%)
Query: 394 SAYEVIKLKGYTSWALGLSVASISHTLLNNTNKIHAVSTLIQGH-HGIEEEVFLSLPCVM 452
S E+IK G + + LLN+ V+T G I+++V + +PC++
Sbjct: 300 SVVELIKRGGRKY---SEAAIPLIRALLNDNGARFVVNTRNNGAIANIDDDVVVEVPCLV 356
Query: 453 ADNGVTHIINQNLTPDEAEKLRKSAATISQIQKGLL 488
NG I + + KGLL
Sbjct: 357 DKNGPHPI---------------KVGPLDRFVKGLL 377
>gnl|CDD|183733 PRK12769, PRK12769, putative oxidoreductase Fe-S binding subunit;
Reviewed.
Length = 654
Score = 31.3 bits (71), Expect = 1.3
Identities = 17/48 (35%), Positives = 26/48 (54%), Gaps = 11/48 (22%)
Query: 119 LSQVAPSIESPDQKITVVGAGQVGMACTYSILTQTMARDAVSTV--DR 164
LSQV S D+++ ++GAG G+AC +AR+ V+ DR
Sbjct: 320 LSQVTKS----DKRVAIIGAGPAGLAC-----ADVLARNGVAVTVYDR 358
Score = 29.3 bits (66), Expect = 5.5
Identities = 12/27 (44%), Positives = 18/27 (66%), Gaps = 4/27 (14%)
Query: 166 LSQVAPSIESPDQKITVVGAGQVGMAC 192
LSQV S D+++ ++GAG G+AC
Sbjct: 320 LSQVTKS----DKRVAIIGAGPAGLAC 342
>gnl|CDD|99731 cd06410, PB1_UP2, Uncharacterized protein 2. The PB1 domain is a
modular domain mediating specific protein-protein
interaction which play a role in many critical cell
processes such as osteoclastogenesis, angiogenesis,
early cardiovascular development, and cell polarity. A
canonical PB1-PB1 interaction, which involves
heterodimerization of two PB1 domains, is required for
the formation of macromolecular signaling complexes
ensuring specificity and fidelity during cellular
signaling. The interaction between two PB1 domain
depends on the type of PB1. There are three types of PB1
domains: type I which contains an OPCA motif, acidic
aminoacid cluster, type II which contains a basic
cluster, and type I/II which contains both an OPCA motif
and a basic cluster. Interactions of PB1 domains with
other protein domains have been described as
noncanonical PB1-interactions.
Length = 97
Score = 28.3 bits (64), Expect = 2.9
Identities = 11/24 (45%), Positives = 19/24 (79%), Gaps = 1/24 (4%)
Query: 260 GETRLQLVDRNVKIFKDLIPKIAK 283
GETR+ VDR++ FK+L+ K+++
Sbjct: 22 GETRIVSVDRSIS-FKELVSKLSE 44
>gnl|CDD|222355 pfam13738, Pyr_redox_3, Pyridine nucleotide-disulphide
oxidoreductase.
Length = 202
Score = 29.6 bits (67), Expect = 3.1
Identities = 11/33 (33%), Positives = 15/33 (45%), Gaps = 1/33 (3%)
Query: 181 TVVGAGQVGMACTYSILTQGIYSNFCLIDSNED 213
VVGAG GMA +L G + ++D
Sbjct: 1 LVVGAGAAGMAFADHLLDLGD-APVIIVDRGAQ 32
>gnl|CDD|238363 cd00707, Pancreat_lipase_like, Pancreatic lipase-like enzymes.
Lipases are esterases that can hydrolyze long-chain
acyl-triglycerides into di- and monoglycerides,
glycerol, and free fatty acids at a water/lipid
interface. A typical feature of lipases is "interfacial
activation," the process of becoming active at the
lipid/water interface, although several examples of
lipases have been identified that do not undergo
interfacial activation . The active site of a lipase
contains a catalytic triad consisting of Ser - His -
Asp/Glu, but unlike most serine proteases, the active
site is buried inside the structure. A "lid" or "flap"
covers the active site, making it inaccessible to
solvent and substrates. The lid opens during the process
of interfacial activation, allowing the lipid substrate
access to the active site.
Length = 275
Score = 29.5 bits (67), Expect = 3.7
Identities = 21/70 (30%), Positives = 27/70 (38%), Gaps = 20/70 (28%)
Query: 331 LAQKLGLSPESVHGFIIGEHGDSSVPVWSGVNVAGVTLKELNPTIGT----------EQD 380
L GLS E+VH +IG H S+ G +VAG K LN +G
Sbjct: 103 LVDNTGLSLENVH--LIG-H---SL----GAHVAGFAGKRLNGKLGRITGLDPAGPLFSG 152
Query: 381 TENFVRLHAD 390
+ RL
Sbjct: 153 ADPEDRLDPS 162
>gnl|CDD|202102 pfam02056, Glyco_hydro_4, Family 4 glycosyl hydrolase.
Length = 183
Score = 28.9 bits (65), Expect = 4.0
Identities = 12/49 (24%), Positives = 25/49 (51%), Gaps = 2/49 (4%)
Query: 269 RNVKIFKDLIPKIAKGSPDCILLIISNPVDVLTYISWKLSGFPKNRVIG 317
R + +F D+ I + PD +L +NP ++T ++ +P + +G
Sbjct: 119 RTIPVFFDIAKDIEELCPDAWVLNYTNPAAMVTEAVYRR--YPNIKAVG 165
>gnl|CDD|224983 COG2072, TrkA, Predicted flavoprotein involved in K+ transport
[Inorganic ion transport and metabolism].
Length = 443
Score = 29.7 bits (67), Expect = 4.3
Identities = 15/73 (20%), Positives = 27/73 (36%), Gaps = 15/73 (20%)
Query: 182 VVGAGQVGMACTYSILTQGIYSNFCLIDSNED-------------RCKGEMLDLQH-GAP 227
++GAGQ G+A Y++ G+ +F + + +D R L P
Sbjct: 13 IIGAGQSGLAAAYALKQAGV-PDFVIFEKRDDVGGTWRYNRYPGLRLDSPKWLLGFPFLP 71
Query: 228 FLRSPKIESGSDI 240
F ++I
Sbjct: 72 FRWDEAFAPFAEI 84
>gnl|CDD|181018 PRK07530, PRK07530, 3-hydroxybutyryl-CoA dehydrogenase; Validated.
Length = 292
Score = 29.2 bits (66), Expect = 4.5
Identities = 31/127 (24%), Positives = 49/127 (38%), Gaps = 30/127 (23%)
Query: 178 QKITVVGAGQVG------MACT------YSILTQGIYSNFCLIDSNEDR--CKGEMLDLQ 223
+K+ V+GAGQ+G A + + + I+ N R KG++ +
Sbjct: 5 KKVGVIGAGQMGNGIAHVCALAGYDVLLNDVSADRLEAGLATINGNLARQVAKGKISEEA 64
Query: 224 HGAPFLRSPKIESGSDIAMSEGSRIVIITAGVRSLVGETRLQLVDRNVKIFKDLIPKIAK 283
A R I + +D+ +VI A T + V R KIF L P +
Sbjct: 65 RAAALAR---ISTATDLEDLADCDLVIEAA--------TEDETVKR--KIFAQLCPVL-- 109
Query: 284 GSPDCIL 290
P+ IL
Sbjct: 110 -KPEAIL 115
>gnl|CDD|227226 COG4889, COG4889, Predicted helicase [General function prediction
only].
Length = 1518
Score = 29.8 bits (67), Expect = 4.8
Identities = 31/118 (26%), Positives = 46/118 (38%), Gaps = 26/118 (22%)
Query: 364 AGVTLKELNPTIGT--------EQDTENFVRLHADVVNSAYEVI--KLKGYTSWA-LGLS 412
A V KE G+ E T L D+ + Y + K+ W
Sbjct: 619 AMVDFKEKIKIFGSDDASNPDDEGKTLFDAILLQDLAEAIYNKMVTKVGDRNYWENWAKD 678
Query: 413 VASISHTLLNNTNKIHAVSTLIQGHHGIEEEVFLSLPCVMADNGVTHIINQNLTPDEA 470
VA+I+ TL N+I L+ G + IE E FL+ + IN+++ DEA
Sbjct: 679 VANIARTL---INRIK----LLFGKNPIEFENFLT--------SLRGNINESIKEDEA 721
>gnl|CDD|238279 cd00501, Peptidase_C15, Pyroglutamyl peptidase (PGP) type I, also
known as pyrrolidone carboxyl peptidase (pcp) type I:
Enzymes responsible for cleaving pyroglutamate (pGlu)
from the N-terminal end of specialized proteins. The
N-terminal pGlu protects these proteins from proteolysis
by other proteases until the pGlu is removed by a PGP.
PGPs are cysteine proteases with a Cys-His-Glu/Asp
catalytic triad. Type I PGPs are found in a wide variety
of prokaryotes and eukaryotes. It is not clear whether
the functional form is a monomer, a homodimer, or a
homotetramer.
Length = 194
Score = 28.8 bits (65), Expect = 5.3
Identities = 13/60 (21%), Positives = 21/60 (35%), Gaps = 8/60 (13%)
Query: 156 RDAVSTVDRLLSQVAPSIESPDQKITVVGAGQVGMACTYSILTQGIYSNFCLIDSNEDRC 215
+ AV + L+ + P + V+ G G T +I I + I NE
Sbjct: 46 QKAVEVLPELIEEHKPDL--------VIHVGLAGGRSTITIERVAINIDDARIPDNEGNQ 97
>gnl|CDD|234452 TIGR04063, stp3, PEP-CTERM/exosortase A-associated
glycosyltransferase, Daro_2409 family.
PEP-CTERM/exosortase is a protein-sorting system
associated with exopolysaccharide production. Members of
this protein family are group 1 glycosyltransferases
(see pfam00534) in which the overwhelming majority occur
in species with the EpsH1 form of exosortase (see
TIGR03109), and usually co-clustered with the
exosortase. A typical member is Daro_2409 from
Dechloromonas aromatica RCB.
Length = 397
Score = 29.2 bits (66), Expect = 6.1
Identities = 15/44 (34%), Positives = 19/44 (43%), Gaps = 6/44 (13%)
Query: 309 GFPKNR--VIGSGTNLDSMRFRV----LLAQKLGLSPESVHGFI 346
G P + VI + +LD LA +LGL V GFI
Sbjct: 176 GIPAEKITVIPNAVDLDLFGLPAPRDPALAAELGLEGAPVIGFI 219
>gnl|CDD|236541 PRK09496, trkA, potassium transporter peripheral membrane
component; Reviewed.
Length = 453
Score = 28.5 bits (65), Expect = 8.3
Identities = 20/64 (31%), Positives = 34/64 (53%), Gaps = 16/64 (25%)
Query: 179 KITVVGAGQVG--MACTYSILTQGIYSNFCLIDSNEDRCK--GEMLDLQ----HGAPFLR 230
KI +VGAGQVG +A S + +ID++E+R + + LD++ +G+
Sbjct: 2 KIIIVGAGQVGYTLAENLSGENNDVT----VIDTDEERLRRLQDRLDVRTVVGNGS---- 53
Query: 231 SPKI 234
SP +
Sbjct: 54 SPDV 57
>gnl|CDD|176246 cd08286, FDH_like_ADH2, formaldehyde dehydrogenase (FDH)-like.
This group is related to formaldehyde dehydrogenase
(FDH), which is a member of the zinc-dependent/medium
chain alcohol dehydrogenase family. This family uses
NAD(H) as a cofactor in the interconversion of alcohols
and aldehydes, or ketones. Another member is identified
as a dihydroxyacetone reductase. Like the zinc-dependent
alcohol dehydrogenases (ADH) of the medium chain alcohol
dehydrogenase/reductase family (MDR), tetrameric FDHs
have a catalytic zinc that resides between the catalytic
and NAD(H)binding domains and a structural zinc in a
lobe of the catalytic domain. Unlike ADH, where
NAD(P)(H) acts as a cofactor, NADH in FDH is a tightly
bound redox cofactor (similar to nicotinamide proteins).
The medium chain alcohol dehydrogenase family (MDR) has
a NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The N-terminal region typically has an
all-beta catalytic domain. These proteins typically form
dimers (typically higher plants, mammals) or tetramers
(yeast, bacteria), and have 2 tightly bound zinc atoms
per subunit.
Length = 345
Score = 28.4 bits (64), Expect = 9.1
Identities = 15/48 (31%), Positives = 26/48 (54%), Gaps = 5/48 (10%)
Query: 169 VAPSIESPDQKITVVGAGQVGMACTYSILTQGIYS--NFCLIDSNEDR 214
V P + +VGAG VG+A ++LT +YS ++D +++R
Sbjct: 159 VLNGKVKPGDTVAIVGAGPVGLA---ALLTAQLYSPSKIIMVDLDDNR 203
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
0.315 0.131 0.370
Gapped
Lambda K H
0.267 0.0593 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 24,034,713
Number of extensions: 2328414
Number of successful extensions: 2008
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1945
Number of HSP's successfully gapped: 90
Length of query: 488
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 387
Effective length of database: 6,457,848
Effective search space: 2499187176
Effective search space used: 2499187176
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: 42 (22.0 bits)
S2: 61 (27.6 bits)