RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 028437
(209 letters)
>gnl|CDD|215058 PLN00106, PLN00106, malate dehydrogenase.
Length = 323
Score = 356 bits (915), Expect = e-125
Identities = 131/177 (74%), Positives = 149/177 (84%)
Query: 18 ARGYSSESVPDRKVAVLGAAGGIGQPLALLMKLNPLVSRLALYDIANTPGVAADVGHINT 77
+ P KVAVLGAAGGIGQPL+LLMK+NPLVS L LYDIANTPGVAADV HINT
Sbjct: 8 RACRAKGGAPGFKVAVLGAAGGIGQPLSLLMKMNPLVSELHLYDIANTPGVAADVSHINT 67
Query: 78 RSEVAGYMGNDQLGQALEDSDVVIIPAGVPRKPGMTRDDLFNINAGIVKDLCSAIAKYCP 137
++V G++G+DQLG AL+ +D+VIIPAGVPRKPGMTRDDLFNINAGIVK LC A+AK+CP
Sbjct: 68 PAQVRGFLGDDQLGDALKGADLVIIPAGVPRKPGMTRDDLFNINAGIVKTLCEAVAKHCP 127
Query: 138 NAIVNMISNPVNSTVPIAAEVFKKAGTYNEKKLFGVTTLDVVRAKTFYAGKANVNVA 194
NA+VN+ISNPVNSTVPIAAEV KKAG Y+ KKLFGVTTLDVVRA TF A K ++ A
Sbjct: 128 NALVNIISNPVNSTVPIAAEVLKKAGVYDPKKLFGVTTLDVVRANTFVAEKKGLDPA 184
>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 = 320 bits (824), Expect = e-111
Identities = 121/165 (73%), Positives = 143/165 (86%)
Query: 30 KVAVLGAAGGIGQPLALLMKLNPLVSRLALYDIANTPGVAADVGHINTRSEVAGYMGNDQ 89
KVAVLGAAGGIGQPL+LL+KLNPLVS LALYDI NTPGVAAD+ HINT ++V GY+G ++
Sbjct: 2 KVAVLGAAGGIGQPLSLLLKLNPLVSELALYDIVNTPGVAADLSHINTPAKVTGYLGPEE 61
Query: 90 LGQALEDSDVVIIPAGVPRKPGMTRDDLFNINAGIVKDLCSAIAKYCPNAIVNMISNPVN 149
L +AL+ +DVV+IPAGVPRKPGMTRDDLFNINAGIV+DL +A+AK CP A++ +ISNPVN
Sbjct: 62 LKKALKGADVVVIPAGVPRKPGMTRDDLFNINAGIVRDLATAVAKACPKALILIISNPVN 121
Query: 150 STVPIAAEVFKKAGTYNEKKLFGVTTLDVVRAKTFYAGKANVNVA 194
STVPIAAEV KKAG Y+ K+LFGVTTLDVVRA TF A ++ A
Sbjct: 122 STVPIAAEVLKKAGVYDPKRLFGVTTLDVVRANTFVAELLGLDPA 166
>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 = 255 bits (654), Expect = 8e-86
Identities = 114/191 (59%), Positives = 139/191 (72%), Gaps = 13/191 (6%)
Query: 30 KVAVLGAAGGIGQPLALLMKLNPLVSRLALYDIANTPGVAADVGHINTRSEVAGYMGNDQ 89
KVAVLGAAGGIGQPL+LL+KL P VS L+LYDIA GVAAD+ HI T + V G+ G +
Sbjct: 1 KVAVLGAAGGIGQPLSLLLKLQPYVSELSLYDIAGAAGVAADLSHIPTAASVKGFSGEEG 60
Query: 90 LGQALEDSDVVIIPAGVPRKPGMTRDDLFNINAGIVKDLCSAIAKYCPNAIVNMISNPVN 149
L AL+ +DVV+IPAGVPRKPGMTRDDLFN+NAGIVKDL +A+A+ CP A++ +I+NPVN
Sbjct: 61 LENALKGADVVVIPAGVPRKPGMTRDDLFNVNAGIVKDLVAAVAESCPKAMILVITNPVN 120
Query: 150 STVPIAAEVFKKAGTYNEKKLFGVTTLDVVRAKTFYA-------GKANVNVAG------L 196
STVPIAAEV KK G Y+ KLFGVTTLD+VRA TF A + NV V G +
Sbjct: 121 STVPIAAEVLKKKGVYDPNKLFGVTTLDIVRANTFVAELKGKDPMEVNVPVIGGHSGETI 180
Query: 197 LKLLTHKNLVF 207
+ L++
Sbjct: 181 IPLISQCPGKV 191
>gnl|CDD|235340 PRK05086, PRK05086, malate dehydrogenase; Provisional.
Length = 312
Score = 241 bits (616), Expect = 5e-80
Identities = 101/167 (60%), Positives = 121/167 (72%), Gaps = 3/167 (1%)
Query: 30 KVAVLGAAGGIGQPLALLMKLN-PLVSRLALYDIAN-TPGVAADVGHINTRSEVAGYMGN 87
KVAVLGAAGGIGQ LALL+K P S L+LYDIA TPGVA D+ HI T ++ G+ G
Sbjct: 2 KVAVLGAAGGIGQALALLLKTQLPAGSELSLYDIAPVTPGVAVDLSHIPTAVKIKGFSGE 61
Query: 88 DQLGQALEDSDVVIIPAGVPRKPGMTRDDLFNINAGIVKDLCSAIAKYCPNAIVNMISNP 147
D ALE +DVV+I AGV RKPGM R DLFN+NAGIVK+L +AK CP A + +I+NP
Sbjct: 62 D-PTPALEGADVVLISAGVARKPGMDRSDLFNVNAGIVKNLVEKVAKTCPKACIGIITNP 120
Query: 148 VNSTVPIAAEVFKKAGTYNEKKLFGVTTLDVVRAKTFYAGKANVNVA 194
VN+TV IAAEV KKAG Y++ KLFGVTTLDV+R++TF A
Sbjct: 121 VNTTVAIAAEVLKKAGVYDKNKLFGVTTLDVIRSETFVAELKGKQPG 167
>gnl|CDD|240360 PTZ00325, PTZ00325, malate dehydrogenase; Provisional.
Length = 321
Score = 228 bits (582), Expect = 9e-75
Identities = 106/163 (65%), Positives = 127/163 (77%)
Query: 30 KVAVLGAAGGIGQPLALLMKLNPLVSRLALYDIANTPGVAADVGHINTRSEVAGYMGNDQ 89
KVAVLGAAGGIGQPL+LL+K NP VS L+LYDI PGVAAD+ HI+T ++V GY +
Sbjct: 10 KVAVLGAAGGIGQPLSLLLKQNPHVSELSLYDIVGAPGVAADLSHIDTPAKVTGYADGEL 69
Query: 90 LGQALEDSDVVIIPAGVPRKPGMTRDDLFNINAGIVKDLCSAIAKYCPNAIVNMISNPVN 149
+AL +D+V+I AGVPRKPGMTRDDLFN NA IV+DL +A+A P AIV ++SNPVN
Sbjct: 70 WEKALRGADLVLICAGVPRKPGMTRDDLFNTNAPIVRDLVAAVASSAPKAIVGIVSNPVN 129
Query: 150 STVPIAAEVFKKAGTYNEKKLFGVTTLDVVRAKTFYAGKANVN 192
STVPIAAE KKAG Y+ +KLFGVTTLDVVRA+ F A +N
Sbjct: 130 STVPIAAETLKKAGVYDPRKLFGVTTLDVVRARKFVAEALGMN 172
>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 = 179 bits (457), Expect = 3e-58
Identities = 71/146 (48%), Positives = 90/146 (61%), Gaps = 6/146 (4%)
Query: 29 RKVAVLGAAGGIGQPLALLMKLNPLVSRLALYDIA--NTPGVAADVGHINTRSEVAGYMG 86
KVAV+GA GG+G LA + L L L L DI GVA D+ H +T V G +G
Sbjct: 1 VKVAVVGAGGGVGSSLAFALALQGLADELVLVDINKDKAEGVAMDLSHGSTFLSVPGIVG 60
Query: 87 NDQLGQALEDSDVVIIPAGVPRKPGMTRDDLFNINAGIVKDLCSAIAKYCPNAIVNMISN 146
D +AL+D+DVV+I AGVPRKPGMTR DL N NAGI KD+ AIAK P+AIV ++SN
Sbjct: 61 GDD-YEALKDADVVVITAGVPRKPGMTRLDLLNRNAGIFKDIVPAIAKSAPDAIVLVVSN 119
Query: 147 PVNSTVPIAAEVFKKAGTYNEKKLFG 172
PV+ IA +V +G E+ +
Sbjct: 120 PVDILTYIAWKV---SGLPPERVIGS 142
>gnl|CDD|223117 COG0039, Mdh, Malate/lactate dehydrogenases [Energy production and
conversion].
Length = 313
Score = 167 bits (425), Expect = 3e-51
Identities = 71/168 (42%), Positives = 93/168 (55%), Gaps = 6/168 (3%)
Query: 29 RKVAVLGAAGGIGQPLALLMKLNPLVSRLALYDIAN--TPGVAADVGHINTRSEVAGYMG 86
KVAV+GA G +G LA L+ L L S L L DI GVA D+ H +
Sbjct: 1 MKVAVIGA-GNVGSSLAFLLLLQGLGSELVLIDINEEKAEGVALDLSHAAAPLGSDVKIT 59
Query: 87 NDQLGQALEDSDVVIIPAGVPRKPGMTRDDLFNINAGIVKDLCSAIAKYCPNAIVNMISN 146
D + L+ +D+V+I AGVPRKPGMTR DL NA IVKD+ AIAKY P+AIV +++N
Sbjct: 60 GDGDYEDLKGADIVVITAGVPRKPGMTRLDLLEKNAKIVKDIAKAIAKYAPDAIVLVVTN 119
Query: 147 PVNSTVPIAAEVFKKAGTYNEKKLFGVTTLDVVRAKTFYAGKANVNVA 194
PV+ IA + +G + + T LD R +TF A K V+
Sbjct: 120 PVDILTYIAMKF---SGFPKNRVIGSGTVLDSARFRTFLAEKLGVSPK 164
>gnl|CDD|180477 PRK06223, PRK06223, malate dehydrogenase; Reviewed.
Length = 307
Score = 120 bits (303), Expect = 4e-33
Identities = 66/171 (38%), Positives = 99/171 (57%), Gaps = 17/171 (9%)
Query: 30 KVAVLGAAGGIGQPLALLMKLNPLVSRLALYDIA-NTP-GVAADVGH----INTRSEVAG 83
K++++GA G +G LA L+ L L + L+DI P G A D+ +++ G
Sbjct: 4 KISIIGA-GNVGATLAHLLALKELGD-VVLFDIVEGVPQGKALDIAEAAPVEGFDTKITG 61
Query: 84 YMGNDQLGQALEDSDVVIIPAGVPRKPGMTRDDLFNINAGIVKDLCSAIAKYCPNAIVNM 143
ND + + SDVV+I AGVPRKPGM+RDDL INA I+KD+ I KY P+AIV +
Sbjct: 62 --TNDY--EDIAGSDVVVITAGVPRKPGMSRDDLLGINAKIMKDVAEGIKKYAPDAIVIV 117
Query: 144 ISNPVNSTVPIAAEVFKKAGTYNEKKLFGVTT-LDVVRAKTFYAGKANVNV 193
++NPV++ +A K + + ++ G+ LD R +TF A + NV+V
Sbjct: 118 VTNPVDAMTYVA----LKESGFPKNRVIGMAGVLDSARFRTFIAEELNVSV 164
>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 = 114 bits (289), Expect = 4e-31
Identities = 63/171 (36%), Positives = 94/171 (54%), Gaps = 17/171 (9%)
Query: 31 VAVLGAAGGIGQPLALLMKLNPLVSRLALYDIA-NTP-GVAADVGH----INTRSEVAGY 84
++++GA G +G LA L+ L L + L DI P G A D+ + + ++V G
Sbjct: 1 ISIIGA-GNVGATLAQLLALKELGD-VVLLDIVEGLPQGKALDISQAAPILGSDTKVTG- 57
Query: 85 MGNDQLGQALEDSDVVIIPAGVPRKPGMTRDDLFNINAGIVKDLCSAIAKYCPNAIVNMI 144
ND + + SDVV+I AG+PRKPGM+RDDL NA IVK++ I KY PNAIV ++
Sbjct: 58 -TNDY--EDIAGSDVVVITAGIPRKPGMSRDDLLGTNAKIVKEVAENIKKYAPNAIVIVV 114
Query: 145 SNPVNSTVPIAAEVFKKAGTYNEKKLFGV-TTLDVVRAKTFYAGKANVNVA 194
+NP++ V KA + ++ G+ LD R + F A + V+V
Sbjct: 115 TNPLDVMT----YVAYKASGFPRNRVIGMAGVLDSARFRYFIAEELGVSVK 161
>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 = 113 bits (285), Expect = 6e-31
Identities = 60/165 (36%), Positives = 83/165 (50%), Gaps = 8/165 (4%)
Query: 31 VAVLGAAGGIGQPLALLM--KLNPLVSRLALYDI--ANTPGVAADVGHINTRSEVAGYMG 86
+AV+GA G +G LA + L L LYDI GVA D+
Sbjct: 1 IAVIGAGGNVGPALAFGLADGSVLLAIELVLYDIDEEKLKGVAMDLQDAVEPLADIKVSI 60
Query: 87 NDQLGQALEDSDVVIIPAGVPRKPGMTRDDLFNINAGIVKDLCSAIAKYCPNAIVNMISN 146
D +A +D+DVVII AGV RKPGM R DL N IVK++ I KY P+A + ++SN
Sbjct: 61 TDDPYEAFKDADVVIITAGVGRKPGMGRLDLLKRNVPIVKEIGDNIEKYSPDAWIIVVSN 120
Query: 147 PVNSTVPIAAEVFKKAGTYNEKKLFGVTTLDVVRAKTFYAGKANV 191
PV+ I + + ++K+ G+ TLD +R + A K V
Sbjct: 121 PVD----IITYLVWRYSGLPKEKVIGLGTLDPIRFRRILAEKLGV 161
>gnl|CDD|173409 PTZ00117, PTZ00117, malate dehydrogenase; Provisional.
Length = 319
Score = 95.2 bits (237), Expect = 2e-23
Identities = 57/166 (34%), Positives = 88/166 (53%), Gaps = 9/166 (5%)
Query: 30 KVAVLGAAGGIGQPLALLMKLNPLVSRLALYDIAN--TPGVAADVGHINTRSEVAGYMGN 87
K++++GA G IG +ALL+ L + LYD+ G A D+ H +T +
Sbjct: 7 KISMIGA-GQIGSTVALLILQKNL-GDVVLYDVIKGVPQGKALDLKHFSTLVGSNINILG 64
Query: 88 DQLGQALEDSDVVIIPAGVPRKPGMTRDDLFNINAGIVKDLCSAIAKYCPNAIVNMISNP 147
+ ++DSDVV+I AGV RK MTR+DL IN I+K + ++ KYCPNA V ++NP
Sbjct: 65 TNNYEDIKDSDVVVITAGVQRKEEMTREDLLTINGKIMKSVAESVKKYCPNAFVICVTNP 124
Query: 148 VNSTVPIAAEVFKKAGTYNEKKLFGVT-TLDVVRAKTFYAGKANVN 192
++ +VF++ K+ G+ LD R + A K V+
Sbjct: 125 LD----CMVKVFQEKSGIPSNKICGMAGVLDSSRFRCNLAEKLGVS 166
>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 = 90.9 bits (226), Expect = 4e-22
Identities = 61/182 (33%), Positives = 95/182 (52%), Gaps = 35/182 (19%)
Query: 30 KVAVLGAAGGIGQPLALLMKLNP------LVSR-----------LALYDIANTPGVAADV 72
KV+++GA+G +G ALL+ L+SR L +YD G+ A++
Sbjct: 2 KVSIIGASGRVGSATALLLAKEDVVKEINLISRPKSLEKLKGLRLDIYDALAAAGIDAEI 61
Query: 73 GHINTRSEVAGYMGNDQLGQALEDSDVVIIPAGVPRKPGMTRDDLFNINAGIVKDLCSAI 132
+ S+VAG SD+VII AGVPRK GM+R DL NA IVK I
Sbjct: 62 KISSDLSDVAG-------------SDIVIITAGVPRKEGMSRLDLAKKNAKIVKKYAKQI 108
Query: 133 AKYCPNAIVNMISNPVNSTVPIAAEVFKKAGTYNEKKLFGVTT-LDVVRAKTFYAGKANV 191
A++ P+ + +++NPV+ A K++G +++ ++FG+ T LD +R K A NV
Sbjct: 109 AEFAPDTKILVVTNPVDVMTYKA---LKESG-FDKNRVFGLGTHLDSLRFKVAIAKHFNV 164
Query: 192 NV 193
++
Sbjct: 165 HI 166
>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 = 86.2 bits (214), Expect = 3e-20
Identities = 57/169 (33%), Positives = 88/169 (52%), Gaps = 17/169 (10%)
Query: 31 VAVLGAAGGIGQPLALLMKLNPLVSRLALYDI--ANTPGVAADVGH----INTRSEVAGY 84
+ ++GA G +G +A + L S L L D+ G A D+ H + T + V G
Sbjct: 1 ITIIGA-GNVGAAVAFALIAKGLASELVLVDVNEEKAKGDALDLSHASAFLATGTIVRGG 59
Query: 85 MGNDQLGQALEDSDVVIIPAGVPRKPGMTRDDLFNINAGIVKDLCSAIAKYCPNAIVNMI 144
D D+D+V+I AG PRKPG TR DL N NA I++ + + + KY P+AI+ ++
Sbjct: 60 DYAD-----AADADIVVITAGAPRKPGETRLDLINRNAPILRSVITNLKKYGPDAIILVV 114
Query: 145 SNPVNSTVPIAAEVFKKAGTYNEKKLFGV-TTLDVVRAKTFYAGKANVN 192
SNPV+ I V +K + ++ G T LD R ++ A K +V+
Sbjct: 115 SNPVD----ILTYVAQKLSGLPKNRVIGSGTLLDSARFRSLLAEKLDVD 159
>gnl|CDD|173376 PTZ00082, PTZ00082, L-lactate dehydrogenase; Provisional.
Length = 321
Score = 85.1 bits (211), Expect = 9e-20
Identities = 62/181 (34%), Positives = 100/181 (55%), Gaps = 22/181 (12%)
Query: 25 SVPDRKVAVLGAAGGIGQPLALLMKLNPLVSRLALYDIA-NTP-GVAADVGHIN----TR 78
+ RK++++G+ G IG +A L+ L L + L+DI N P G A D+ H N +
Sbjct: 3 MIKRRKISLIGS-GNIGGVMAYLIVLKNL-GDVVLFDIVKNIPQGKALDISHSNVIAGSN 60
Query: 79 SEVAGYMGNDQLGQALEDSDVVIIPAGVPRKPGMT-----RDDLFNINAGIVKDLCSAIA 133
S+V G N+ + + SDVVI+ AG+ ++PG + RDDL +NA I+ ++ I
Sbjct: 61 SKVIG--TNNY--EDIAGSDVVIVTAGLTKRPGKSDKEWNRDDLLPLNAKIMDEVAEGIK 116
Query: 134 KYCPNAIVNMISNPVNSTVPIAAEVFKKAGTYNEKKLFGVT-TLDVVRAKTFYAGKANVN 192
KYCPNA V +I+NP++ V ++ ++ + K+ G+ LD R +T+ A K VN
Sbjct: 117 KYCPNAFVIVITNPLDVMV----KLLQEHSGLPKNKVCGMAGVLDSSRLRTYIAEKLGVN 172
Query: 193 V 193
Sbjct: 173 P 173
>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 = 84.5 bits (209), Expect = 9e-20
Identities = 60/173 (34%), Positives = 98/173 (56%), Gaps = 19/173 (10%)
Query: 29 RKVAVLGAAGGIGQPLALLMKLNPLVSRLALYDIANTP--GVAAD------VGHINTRSE 80
+K++V+GA G +G A + L + L L D+ G A D VG +T+
Sbjct: 2 KKISVIGA-GFVGATTAFRLAEKEL-ADLVLLDVVEGIPQGKALDMYEASPVGGFDTK-- 57
Query: 81 VAGYMGNDQLGQALEDSDVVIIPAGVPRKPGMTRDDLFNINAGIVKDLCSAIAKYCPNAI 140
V G N+ A +SD+V+I AG+PRKPGM+R+DL ++NAGIV+++ I ++ PN I
Sbjct: 58 VTG--TNNYADTA--NSDIVVITAGLPRKPGMSREDLLSMNAGIVREVTGRIMEHSPNPI 113
Query: 141 VNMISNPVNSTVPIAAEVFKKAGTYNEKKLFGVTTLDVVRAKTFYAGKANVNV 193
+ ++SNP+++ +A + K+G E+ + LD R +TF A + V+V
Sbjct: 114 IVVVSNPLDAMTYVAWQ---KSGFPKERVIGQAGVLDSARFRTFIAMELGVSV 163
>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 = 81.4 bits (202), Expect = 1e-18
Identities = 47/127 (37%), Positives = 65/127 (51%), Gaps = 15/127 (11%)
Query: 29 RKVAVLGAAGGIGQPLALLMKLNPLVSRLALYDI--ANTPGVAADVGH----INTRSEVA 82
KVA++GA G +G A + L L S + L DI A G A D+ H + A
Sbjct: 1 MKVAIVGA-GFVGSTTAYALLLRGLASEIVLVDINKAKAEGEAMDLAHGTPFVKPVRIYA 59
Query: 83 G-YMGNDQLGQALEDSDVVIIPAGVPRKPGMTRDDLFNINAGIVKDLCSAIAKYCPNAIV 141
G Y + +DVV+I AG +KPG TR DL N I K++ I KY P+AI+
Sbjct: 60 GDY-------ADCKGADVVVITAGANQKPGETRLDLLKRNVAIFKEIIPQILKYAPDAIL 112
Query: 142 NMISNPV 148
+++NPV
Sbjct: 113 LVVTNPV 119
>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 = 70.6 bits (174), Expect = 1e-14
Identities = 49/167 (29%), Positives = 75/167 (44%), Gaps = 9/167 (5%)
Query: 29 RKVAVLGAAGGIGQPLALLMKLNPLVSRLALYDIANTPGVAADVGHINTRSEVAGYMGND 88
RKV ++GA G +G A + + L L DI N + +
Sbjct: 1 RKVVIIGA-GHVGSSFAYSLVNQGIADELVLIDI-NEEKAEGEALDLEDALAFLPSPVKI 58
Query: 89 QLG--QALEDSDVVIIPAGVPRKPGMTRDDLFNINAGIVKDLCSAIAKYCPNAIVNMISN 146
+ G +D+D+V+I AG P+KPG TR DL NA I+K + I + I + SN
Sbjct: 59 KAGDYSDCKDADIVVITAGAPQKPGETRLDLLEKNAKIMKSIVPKIKASGFDGIFLVASN 118
Query: 147 PVNSTVPIAAEVFKKAGTYNEKKLFGV-TTLDVVRAKTFYAGKANVN 192
PV+ + V +K + ++ G T+LD R + A K NV+
Sbjct: 119 PVD----VITYVVQKLSGLPKNRVIGTGTSLDTARLRRALAEKLNVD 161
>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 = 70.8 bits (174), Expect = 1e-14
Identities = 59/180 (32%), Positives = 74/180 (41%), Gaps = 26/180 (14%)
Query: 30 KVAVLGAAGGIGQPLA-------LLMKLNPLVSRLALYDIANTPGVAADVGHINTRSE-- 80
V + GAAG IG L L P++ L L DI P + A G E
Sbjct: 2 HVLITGAAGQIGYNLLFLIASGELFGDDQPVI--LHLLDI--PPAMKALEG---VVMELQ 54
Query: 81 ------VAGYMGNDQLGQALEDSDVVIIPAGVPRKPGMTRDDLFNINAGIVKDLCSAIAK 134
+ G + +A +D DV I+ PRKPGM R DL NA I K+ A+ K
Sbjct: 55 DCAFPLLKGVVITTDPEEAFKDVDVAILVGAFPRKPGMERADLLRKNAKIFKEQGEALNK 114
Query: 135 YC-PNAIVNMISNPVNSTVPIAAEVFKKAGTYNEKKLFGVTTLDVVRAKTFYAGKANVNV 193
P V ++ NP N+ IA K A K +T LD RAK A K V V
Sbjct: 115 VAKPTVKVLVVGNPANTNALIAL---KNAPNLPPKNFTALTRLDHNRAKAQVARKLGVRV 171
>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 = 69.9 bits (172), Expect = 2e-14
Identities = 45/165 (27%), Positives = 72/165 (43%), Gaps = 20/165 (12%)
Query: 37 AGGIGQPLALLMKLNPLVSRLALYDIAN--TPGVAADVGH----INTRSEV--AGYMGND 88
AG +G A + + + L DI G A D+ H + T ++ Y
Sbjct: 4 AGNVGSSTAFALLNQGIADEIVLIDINKDKAEGEAMDLQHAASFLPTPKKIRSGDY---- 59
Query: 89 QLGQALEDSDVVIIPAGVPRKPGMTRDDLFNINAGIVKDLCSAIAKYCPNAIVNMISNPV 148
+D+D+V+I AG P+KPG TR +L N I+K + + K + I + +NPV
Sbjct: 60 ---SDCKDADLVVITAGAPQKPGETRLELVGRNVRIMKSIVPEVVKSGFDGIFLVATNPV 116
Query: 149 NSTVPIAAEVFKKAGTYNEKKLFGV-TTLDVVRAKTFYAGKANVN 192
+ I V K + + ++ G T LD R + A K V+
Sbjct: 117 D----ILTYVAWKLSGFPKNRVIGSGTVLDTARLRYLLAEKLGVD 157
>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 = 68.5 bits (168), Expect = 6e-14
Identities = 58/184 (31%), Positives = 81/184 (44%), Gaps = 33/184 (17%)
Query: 30 KVAVLGAAGGIG-QPLALLMKLNPLVSRLALYDIANTPGVAA----DVGH-------INT 77
K+ V+GA G +G L + L L S + L D+ GVA D H NT
Sbjct: 1 KLVVIGA-GHVGSAVLNYALALG-LFSEIVLIDV--NEGVAEGEALDFHHATALTYSTNT 56
Query: 78 RSEVAGYMGNDQLGQALEDSDVVIIPAGVPRKPGMT--RDDLFNINAGIVKDLCSAIAKY 135
+ Y D+D+++I AG PG T R DL NA I++++ I K
Sbjct: 57 KIRAGDY-------DDCADADIIVITAGPSIDPGNTDDRLDLAQTNAKIIREIMGNITKV 109
Query: 136 CPNAIVNMISNPVNSTVPIAAEVFKKAGTYNEKKLFGV-TTLDVVRAKTFYAGKANV--- 191
A++ +I+NP++ V IAA F Y K+ G T LD R + A K V
Sbjct: 110 TKEAVIILITNPLDIAVYIAATEFD----YPANKVIGTGTMLDTARLRRIVADKYGVDPK 165
Query: 192 NVAG 195
NV G
Sbjct: 166 NVTG 169
>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 = 66.6 bits (163), Expect = 3e-13
Identities = 59/181 (32%), Positives = 77/181 (42%), Gaps = 26/181 (14%)
Query: 30 KVAVLGAAGGIGQPLA-------LLMKLNPLVSRLALYDIANTPGVAADVGHINTRSE-- 80
+VAV GAAG IG L L K P+V L L DI V E
Sbjct: 5 RVAVTGAAGQIGYSLLFRIASGELFGKDQPVV--LHLLDIPPAMKALEGV-----AMELE 57
Query: 81 ------VAGYMGNDQLGQALEDSDVVIIPAGVPRKPGMTRDDLFNINAGIVKDLCSAIAK 134
+AG + +A +D D ++ PRKPGM R DL + N I K+ A+ K
Sbjct: 58 DCAFPLLAGVVATTDPEEAFKDVDAALLVGAFPRKPGMERADLLSKNGKIFKEQGKALNK 117
Query: 135 YC-PNAIVNMISNPVNSTVPIAAEVFKKAGTYNEKKLFGVTTLDVVRAKTFYAGKANVNV 193
+ V ++ NP N+ IA+ K A K +T LD RAK A KA V V
Sbjct: 118 VAKKDVKVLVVGNPANTNALIAS---KNAPDIPPKNFSAMTRLDHNRAKYQLAAKAGVPV 174
Query: 194 A 194
+
Sbjct: 175 S 175
>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 = 65.7 bits (161), Expect = 8e-13
Identities = 52/184 (28%), Positives = 73/184 (39%), Gaps = 34/184 (18%)
Query: 30 KVAVLGAAGGIGQPLALLMKLNPLVSR-----------LALYDIANTPGVAADVGHINTR 78
+V V GAAG I L P++++ L L DI V
Sbjct: 4 RVLVTGAAGQIAYSLL------PMIAKGDVFGPDQPVILHLLDIPPALKALEGV-----V 52
Query: 79 SE--------VAGYMGNDQLGQALEDSDVVIIPAGVPRKPGMTRDDLFNINAGIVKDLCS 130
E + + +A +D DV I+ +PRK GM R DL N I K+
Sbjct: 53 MELQDCAFPLLKSVVATTDPEEAFKDVDVAILVGAMPRKEGMERKDLLKANVKIFKEQGE 112
Query: 131 AIAKYC-PNAIVNMISNPVNSTVPIAAEVFKKAGTYNEKKLFGVTTLDVVRAKTFYAGKA 189
A+ KY N V ++ NP N+ I K A + ++ +T LD RAK+ A K
Sbjct: 113 ALDKYAKKNVKVLVVGNPANTNALILL---KYAPSIPKENFTALTRLDHNRAKSQIALKL 169
Query: 190 NVNV 193
V V
Sbjct: 170 GVPV 173
>gnl|CDD|178836 PRK00066, ldh, L-lactate dehydrogenase; Reviewed.
Length = 315
Score = 64.5 bits (158), Expect = 2e-12
Identities = 37/127 (29%), Positives = 54/127 (42%), Gaps = 15/127 (11%)
Query: 29 RKVAVLGAAGGIGQPLALLMKLNPLVSRLALYDIA--NTPGVAADVGHI-----NTRSEV 81
KV ++G G +G A + + L + DI G A D+ H T+
Sbjct: 7 NKVVLVGD-GAVGSSYAYALVNQGIADELVIIDINKEKAEGDAMDLSHAVPFTSPTKIYA 65
Query: 82 AGYMGNDQLGQALEDSDVVIIPAGVPRKPGMTRDDLFNINAGIVKDLCSAIAKYCPNAIV 141
Y +D+D+V+I AG P+KPG TR DL N I K + + + I
Sbjct: 66 GDY-------SDCKDADLVVITAGAPQKPGETRLDLVEKNLKIFKSIVGEVMASGFDGIF 118
Query: 142 NMISNPV 148
+ SNPV
Sbjct: 119 LVASNPV 125
>gnl|CDD|235468 PRK05442, PRK05442, malate dehydrogenase; Provisional.
Length = 326
Score = 58.7 bits (143), Expect = 2e-10
Identities = 58/186 (31%), Positives = 80/186 (43%), Gaps = 26/186 (13%)
Query: 30 KVAVLGAAGGIGQPL-------ALLMKLNPLVSRLALYDIANTPGVAADVGHINTRSE-- 80
+VAV GAAG IG L +L K P+ L L +I P + A G E
Sbjct: 6 RVAVTGAAGQIGYSLLFRIASGDMLGKDQPV--ILQLLEI--PPALKALEG---VVMELD 58
Query: 81 ------VAGYMGNDQLGQALEDSDVVIIPAGVPRKPGMTRDDLFNINAGIVKDLCSAIAK 134
+AG + D A +D+DV ++ PR PGM R DL N I A+ +
Sbjct: 59 DCAFPLLAGVVITDDPNVAFKDADVALLVGARPRGPGMERKDLLEANGAIFTAQGKALNE 118
Query: 135 YC-PNAIVNMISNPVNSTVPIAAEVFKKAGTYNEKKLFGVTTLDVVRAKTFYAGKANVNV 193
+ V ++ NP N+ IA K A + +T LD RA + A KA V V
Sbjct: 119 VAARDVKVLVVGNPANTNALIAM---KNAPDLPAENFTAMTRLDHNRALSQLAAKAGVPV 175
Query: 194 AGLLKL 199
A + K+
Sbjct: 176 ADIKKM 181
>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 = 58.0 bits (140), Expect = 4e-10
Identities = 37/114 (32%), Positives = 53/114 (46%), Gaps = 4/114 (3%)
Query: 81 VAGYMGNDQLGQALEDSDVVIIPAGVPRKPGMTRDDLFNINAGIVKDLCSAIAKYC-PNA 139
+AG + +L +A +D D + A VP KPG R DL N I K A+++Y P
Sbjct: 45 LAGTIVTTKLEEAFKDIDCAFLVASVPLKPGEVRADLLTKNTPIFKATGEALSEYAKPTV 104
Query: 140 IVNMISNPVNSTVPIAAEVFKKAGTYNEKKLFGVTTLDVVRAKTFYAGKANVNV 193
V +I NPVN+ +A A + + + LD RA + A K V V
Sbjct: 105 KVLVIGNPVNTNCLVA---MLHAPKLSAENFSSLCMLDHNRAVSRIASKLKVPV 155
>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 = 56.8 bits (137), Expect = 8e-10
Identities = 53/180 (29%), Positives = 72/180 (40%), Gaps = 26/180 (14%)
Query: 30 KVAVLGAAGGIGQPLA-------LLMKLNPLVSRLALYDIANTPGVAADVGHINTRSEV- 81
+V V GAAG IG L +L K P++ L L DI V V E+
Sbjct: 1 RVVVTGAAGQIGYALLPMIARGRMLGKDQPII--LHLLDIPPAMKVLEGV-----VMELM 53
Query: 82 -------AGYMGNDQLGQALEDSDVVIIPAGVPRKPGMTRDDLFNINAGIVKDLCSAIAK 134
G + A D DV I+ PRK GM R DL + N I K+ A+ K
Sbjct: 54 DCAFPLLDGVVPTHDPAVAFTDVDVAILVGAFPRKEGMERRDLLSKNVKIFKEQGRALDK 113
Query: 135 YC-PNAIVNMISNPVNSTVPIAAEVFKKAGTYNEKKLFGVTTLDVVRAKTFYAGKANVNV 193
+ V ++ NP N+ + + A + K +T LD RA A +A V V
Sbjct: 114 LAKKDCKVLVVGNPANTNALVLSNY---APSIPPKNFSALTRLDHNRALAQVAERAGVPV 170
>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 = 56.1 bits (136), Expect = 1e-09
Identities = 53/187 (28%), Positives = 74/187 (39%), Gaps = 28/187 (14%)
Query: 30 KVAVLGAAGGIGQPLALLMKL---------NPLVSRLALYDIANT----PGVA---ADVG 73
+VAV GAAG IG +LL ++ P++ L L ++ GVA D
Sbjct: 4 RVAVTGAAGQIGY--SLLFRIASGEMFGPDQPVI--LQLLELPQALKALEGVAMELEDCA 59
Query: 74 HINTRSEVAGYMGNDQLGQALEDSDVVIIPAGVPRKPGMTRDDLFNINAGIVKDLCSAIA 133
V D A +D+D ++ PR PGM R DL N I A+
Sbjct: 60 FPLLAEIVIT----DDPNVAFKDADWALLVGAKPRGPGMERADLLKANGKIFTAQGKALN 115
Query: 134 KYC-PNAIVNMISNPVNSTVPIAAEVFKKAGTYNEKKLFGVTTLDVVRAKTFYAGKANVN 192
+ V ++ NP N+ IA K A +T LD RAK+ A KA V
Sbjct: 116 DVASRDVKVLVVGNPCNTNALIAM---KNAPDIPPDNFTAMTRLDHNRAKSQLAKKAGVP 172
Query: 193 VAGLLKL 199
V + +
Sbjct: 173 VTDVKNM 179
>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 = 56.1 bits (136), Expect = 2e-09
Identities = 49/172 (28%), Positives = 75/172 (43%), Gaps = 21/172 (12%)
Query: 30 KVAVLGA-AGGIGQPLALLMKLNPLVSRLALYDIAN--TPGVAADVGHINTRSEVAGYMG 86
KV V+G G+ +++L K L L L D+ G A D+ H + ++
Sbjct: 5 KVTVVGVGQVGMACAISILAK--GLADELVLVDVVEDKLKGEAMDLQH------GSAFLK 56
Query: 87 N-----DQLGQALEDSDVVIIPAGVPRKPGMTRDDLFNINAGIVKDLCSAIAKYCPNAIV 141
N D+ +S VVI+ AG + G +R DL N I K + + KY PNAI+
Sbjct: 57 NPKIEADKDYSVTANSKVVIVTAGARQNEGESRLDLVQRNVDIFKGIIPKLVKYSPNAIL 116
Query: 142 NMISNPVNSTVPIAAEVFKKAGTYNEKKLFGV-TTLDVVRAKTFYAGKANVN 192
++SNPV+ I V K + ++ G LD R + A + V
Sbjct: 117 LVVSNPVD----IMTYVAWKLSGLPKHRVIGSGCNLDSARFRYLIAERLGVA 164
>gnl|CDD|177744 PLN00135, PLN00135, malate dehydrogenase.
Length = 309
Score = 50.9 bits (122), Expect = 9e-08
Identities = 32/104 (30%), Positives = 53/104 (50%), Gaps = 4/104 (3%)
Query: 92 QALEDSDVVIIPAGVPRKPGMTRDDLFNINAGIVKDLCSAIAKYC-PNAIVNMISNPVNS 150
+A + ++ ++ G PRK GM R D+ + N I K SA+ K+ P+ V +++NP N+
Sbjct: 54 EACKGVNIAVMVGGFPRKEGMERKDVMSKNVSIYKSQASALEKHAAPDCKVLVVANPANT 113
Query: 151 TVPIAAEVFKKAGTYNEKKLFGVTTLDVVRAKTFYAGKANVNVA 194
I E A + EK + +T LD RA + + V V+
Sbjct: 114 NALILKEF---APSIPEKNITCLTRLDHNRALGQISERLGVPVS 154
>gnl|CDD|178212 PLN02602, PLN02602, lactate dehydrogenase.
Length = 350
Score = 49.8 bits (119), Expect = 3e-07
Identities = 49/179 (27%), Positives = 80/179 (44%), Gaps = 16/179 (8%)
Query: 22 SSESVPDR---KVAVLGAAGGIGQPLALLMKLNPLVSRLALYDIA--NTPGVAADVGH-- 74
SS P R KV+V+G G +G +A + L LAL D+ G D+ H
Sbjct: 28 SSPPSPTRRHTKVSVVGV-GNVGMAIAQTILTQDLADELALVDVNPDKLRGEMLDLQHAA 86
Query: 75 -INTRSEVAGYMGNDQLGQALEDSDVVIIPAGVPRKPGMTRDDLFNINAGIVKDLCSAIA 133
R+++ SD+ I+ AG + PG +R +L N + + + +A
Sbjct: 87 AFLPRTKILA----STDYAVTAGSDLCIVTAGARQIPGESRLNLLQRNVALFRKIIPELA 142
Query: 134 KYCPNAIVNMISNPVNSTVPIAAEVFKKAGTYNEKKLFGVTTLDVVRAKTFYAGKANVN 192
KY P+ I+ ++SNPV+ +A +K +G + + T LD R + A +VN
Sbjct: 143 KYSPDTILLIVSNPVDVLTYVA---WKLSGFPANRVIGSGTNLDSSRFRFLIADHLDVN 198
>gnl|CDD|215060 PLN00112, PLN00112, malate dehydrogenase (NADP); Provisional.
Length = 444
Score = 44.8 bits (106), Expect = 1e-05
Identities = 32/98 (32%), Positives = 44/98 (44%), Gaps = 4/98 (4%)
Query: 95 EDSDVVIIPAGVPRKPGMTRDDLFNINAGIVKDLCSAI-AKYCPNAIVNMISNPVNSTVP 153
+D++ ++ PR PGM R DL +IN I + A+ N V ++ NP N+
Sbjct: 175 QDAEWALLIGAKPRGPGMERADLLDINGQIFAEQGKALNEVASRNVKVIVVGNPCNTNAL 234
Query: 154 IAAEVFKKAGTYNEKKLFGVTTLDVVRAKTFYAGKANV 191
I K A K +T LD RAK A KA V
Sbjct: 235 IC---LKNAPNIPAKNFHALTRLDENRAKCQLALKAGV 269
>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 = 44.2 bits (104), Expect = 2e-05
Identities = 37/113 (32%), Positives = 49/113 (43%), Gaps = 12/113 (10%)
Query: 92 QALEDSDVVIIPAGVPRKPGMTRDDLFNINAGIVKDLCSAIAKYCP-NAIVNMISNPVNS 150
+ ED+D ++ PR PGM R DL +IN I D A+ N V ++ NP N+
Sbjct: 116 EVFEDADWALLIGAKPRGPGMERADLLDINGQIFADQGKALNAVASKNCKVLVVGNPCNT 175
Query: 151 TVPIAAEVFKKAGTYNEKKLFGVTTLDVVRAK--------TFYAGKANVNVAG 195
IA K A K +T LD RAK FY +NV + G
Sbjct: 176 NALIA---MKNAPNIPRKNFHALTRLDENRAKCQLALKSGKFYTSVSNVTIWG 225
>gnl|CDD|224403 COG1486, CelF, Alpha-galactosidases/6-phospho-beta-glucosidases,
family 4 of glycosyl hydrolases [Carbohydrate transport
and metabolism].
Length = 442
Score = 36.1 bits (84), Expect = 0.009
Identities = 33/149 (22%), Positives = 51/149 (34%), Gaps = 34/149 (22%)
Query: 30 KVAVLGAAGGIGQPLALLMKLNPL----VSRLALYDIANTPGVAADVGHINTR------S 79
K+ ++G G P LL L V LALYDI + + + +
Sbjct: 5 KIVIIGG-GSTYTPKLLLGDLARTEELPVRELALYDI--DEERLKIIAILAKKLVEEAGA 61
Query: 80 EVAGYMGNDQLGQALEDSDVVIIPA------------GVPRKPGMTRDDLFNI------- 120
V D +ALE +D VI +P K G+ +
Sbjct: 62 PVKVEATTD-RREALEGADFVITQIRVGGLEAREKDERIPLKHGLYGQETNGPGGIFYGL 120
Query: 121 -NAGIVKDLCSAIAKYCPNAIVNMISNPV 148
++ D+ + K CPNA + +NP
Sbjct: 121 RTIPVILDIAKDMEKVCPNAWMLNYTNPA 149
>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 = 35.6 bits (83), Expect = 0.013
Identities = 29/128 (22%), Positives = 47/128 (36%), Gaps = 43/128 (33%)
Query: 55 SRLALYDIANTPGVAADVGHINTRSEVAGYMGNDQLG------------QALEDSDVVII 102
S +AL DI D + T +A + ++LG +AL+ +D VI
Sbjct: 30 STIALMDI--------DEERLETVEILAKKI-VEELGAPLKIEATTDRREALDGADFVIN 80
Query: 103 ---PAG---------VPRKPG------MTRD--DLFNINAGI--VKDLCSAIAKYCPNAI 140
G +P K G T +F I + D+ I + CP+A
Sbjct: 81 TIQVGGHEYTETDFEIPEKYGYYQTVGDTSGPGGIFRALRTIPVLLDIARDIEELCPDAW 140
Query: 141 VNMISNPV 148
+ +NP+
Sbjct: 141 LLNYANPM 148
>gnl|CDD|216304 pfam01113, DapB_N, Dihydrodipicolinate reductase, N-terminus.
Dihydrodipicolinate reductase (DapB) reduces the
alpha,beta-unsaturated cyclic imine,
dihydro-dipicolinate. This reaction is the second
committed step in the biosynthesis of L-lysine and its
precursor meso-diaminopimelate, which are critical for
both protein and cell wall biosynthesis. The N-terminal
domain of DapB binds the dinucleotide NADPH.
Length = 122
Score = 34.1 bits (79), Expect = 0.015
Identities = 22/72 (30%), Positives = 35/72 (48%), Gaps = 3/72 (4%)
Query: 30 KVAVLGAAGGIGQPLALLMKLNPLVSRLALYDIANTPGVAADVGHINTRSEVAGYMGNDQ 89
KVAV+GA+G +G+ L + P +A D + + +D G + V D
Sbjct: 2 KVAVVGASGRMGRELIKAILEAPDFELVAAVDRPGSSLLGSDAGELAGPLGVP---VTDD 58
Query: 90 LGQALEDSDVVI 101
L + L D+DV+I
Sbjct: 59 LEEVLADADVLI 70
>gnl|CDD|223936 COG1004, Ugd, Predicted UDP-glucose 6-dehydrogenase [Cell envelope
biogenesis, outer membrane].
Length = 414
Score = 35.3 bits (82), Expect = 0.017
Identities = 22/83 (26%), Positives = 34/83 (40%), Gaps = 12/83 (14%)
Query: 93 ALEDSDVVIIPAGVPRKPGMTRDDLFNINAGIVKDLCSAIAKYCPNAIVNMISNPVNSTV 152
A++D+DVV I G P + + V+ + I + V ++ + STV
Sbjct: 73 AVKDADVVFIAVGTPPDE------DGSADLSYVEAVAKDIGEILDGKAV-VV---IKSTV 122
Query: 153 PI--AAEVFKKAGTYNEKKLFGV 173
P+ EV K N K F V
Sbjct: 123 PVGTTEEVRAKIREENSGKDFEV 145
>gnl|CDD|216283 pfam01073, 3Beta_HSD, 3-beta hydroxysteroid dehydrogenase/isomerase
family. The enzyme 3 beta-hydroxysteroid
dehydrogenase/5-ene-4-ene isomerase (3 beta-HSD)
catalyzes the oxidation and isomerisation of 5-ene-3
beta-hydroxypregnene and 5-ene-hydroxyandrostene steroid
precursors into the corresponding 4-ene-ketosteroids
necessary for the formation of all classes of steroid
hormones.
Length = 280
Score = 34.6 bits (80), Expect = 0.025
Identities = 24/93 (25%), Positives = 45/93 (48%), Gaps = 4/93 (4%)
Query: 32 AVLGAAGGIGQPLA-LLMKLNPLVSRLALYDIANTPGVAADVGHINTRSEVAGYMGN-DQ 89
V G G +G+ + LL++ L + ++D+ +P + D + + + G + +
Sbjct: 1 LVTGGGGFLGRHIVRLLLREGEL-QEVRVFDLRFSPELLEDFSKLQVITYIEGDVTDKQD 59
Query: 90 LGQALEDSDVVIIPAGVPRKPGM-TRDDLFNIN 121
L +AL+ SDVVI A + G RD + +N
Sbjct: 60 LRRALQGSDVVIHTAAIIDVFGKAYRDTIMKVN 92
>gnl|CDD|202102 pfam02056, Glyco_hydro_4, Family 4 glycosyl hydrolase.
Length = 183
Score = 33.9 bits (78), Expect = 0.029
Identities = 34/147 (23%), Positives = 48/147 (32%), Gaps = 30/147 (20%)
Query: 30 KVAVLGAAGGIGQPLALLMKLNPL----VSRLALYDIANTPGVAADVGHINTRSEVAG-- 83
K+ ++G G P LL L+ LALYDI A E
Sbjct: 1 KIVIIGG-GSTITPKNLLGDLDHTEELPGRELALYDIDEERLDAIQTACKKLVDEAGPDI 59
Query: 84 -YMGNDQLGQALEDSDVVIIPAGVPRKPGMTRDDLFNINAGIVK---------------- 126
+ +AL D+D VI V P D+ + G+V
Sbjct: 60 KFEKTTDRKEALTDADFVINAIRVGLLPARELDEKIPLRHGVVGTIQETVGPGGIFRGLR 119
Query: 127 ------DLCSAIAKYCPNAIVNMISNP 147
D+ I + CP+A V +NP
Sbjct: 120 TIPVFFDIAKDIEELCPDAWVLNYTNP 146
>gnl|CDD|223366 COG0289, DapB, Dihydrodipicolinate reductase [Amino acid transport
and metabolism].
Length = 266
Score = 32.6 bits (75), Expect = 0.11
Identities = 22/80 (27%), Positives = 36/80 (45%), Gaps = 4/80 (5%)
Query: 30 KVAVLGAAGGIGQPLALLMKLNPLVSRLALYDIANTPGVAADVGHINTRSEVAGYMGNDQ 89
KVAV GA+G +G+ L + P + +A +D + + +D G + + G D
Sbjct: 4 KVAVAGASGRMGRTLIRAVLEAPDLELVAAFDRPGSLSLGSDAGELAGLGLL-GVPVTDD 62
Query: 90 LGQALEDSDVVI---IPAGV 106
L D+DV+I P
Sbjct: 63 LLLVKADADVLIDFTTPEAT 82
>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 = 31.9 bits (73), Expect = 0.15
Identities = 11/19 (57%), Positives = 13/19 (68%)
Query: 174 TTLDVVRAKTFYAGKANVN 192
TTLD RA+TF A K V+
Sbjct: 1 TTLDTARARTFLAEKFGVD 19
>gnl|CDD|180408 PRK06114, PRK06114, short chain dehydrogenase; Provisional.
Length = 254
Score = 32.1 bits (73), Expect = 0.17
Identities = 16/50 (32%), Positives = 24/50 (48%), Gaps = 2/50 (4%)
Query: 28 DRKVAVLGAAGGIGQPLALLMKLNPLVSRLALYDIANTPGVAADVGHINT 77
+ V GA GIGQ +A + L + +AL+D+ G+A HI
Sbjct: 8 GQVAFVTGAGSGIGQRIA--IGLAQAGADVALFDLRTDDGLAETAEHIEA 55
>gnl|CDD|187540 cd05229, SDR_a3, atypical (a) SDRs, subgroup 3. These atypical SDR
family members of unknown function have a glycine-rich
NAD(P)-binding motif consensus that is very similar to
the extended SDRs, GXXGXXG. Generally, this group has
poor conservation of the active site tetrad, However,
individual sequences do contain matches to the YXXXK
active site motif, and generally Tyr or Asn in place of
the upstream Ser found in most SDRs. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Atypical SDRs include
biliverdin IX beta reductase (BVR-B,aka flavin
reductase), NMRa (a negative transcriptional regulator
of various fungi), progesterone 5-beta-reductase like
proteins, phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 302
Score = 31.1 bits (71), Expect = 0.31
Identities = 20/86 (23%), Positives = 31/86 (36%), Gaps = 22/86 (25%)
Query: 30 KVAVLGAAGGIGQPLALLMK--------LNPLVSRLALYDIANTPGVAADVGHINTRSEV 81
VLGA+G IG+ +A ++ ++ S+LA VAAD
Sbjct: 1 TAHVLGASGPIGREVARELRRRGWDVRLVSRSGSKLAWLPGVEI--VAADA--------- 49
Query: 82 AGYMGNDQLGQALEDSDVVIIPAGVP 107
M + A +DV+ A
Sbjct: 50 ---MDASSVIAAARGADVIYHCANPA 72
>gnl|CDD|201603 pfam01118, Semialdhyde_dh, Semialdehyde dehydrogenase, NAD binding
domain. This Pfam entry contains the following members:
N-acetyl-glutamine semialdehyde dehydrogenase (AgrC)
Aspartate-semialdehyde dehydrogenase.
Length = 121
Score = 29.0 bits (66), Expect = 0.68
Identities = 22/79 (27%), Positives = 38/79 (48%), Gaps = 3/79 (3%)
Query: 30 KVAVLGAAGGIGQPLALLMKLNPLVSRLALYDIANTPGVAADVGHINTRSEVAGYMGNDQ 89
KVA++GA G +GQ L L+ +P + +AL + + G + + +
Sbjct: 1 KVAIVGATGYVGQELLRLLAEHPPLELVALVASSRSAGKKVAFAYPILEGGKDLLLEDVD 60
Query: 90 LGQALEDSDVVII--PAGV 106
+ L+D D+V + PAGV
Sbjct: 61 P-EDLKDVDIVFLALPAGV 78
>gnl|CDD|107197 PHA02515, PHA02515, hypothetical protein; Provisional.
Length = 508
Score = 30.1 bits (67), Expect = 0.75
Identities = 25/80 (31%), Positives = 34/80 (42%), Gaps = 2/80 (2%)
Query: 32 AVLGAAGGIGQPLALLMKLNPLVSRLALYDIANTPGVAADVGHINTRSEVAGYMGNDQLG 91
AV+G A I A +N +V LA D+ G+AADV + +GND G
Sbjct: 362 AVVGNANNINAVAANEGNVNTVVDNLA--DVQTVAGIAADVSTVAENEAAVAALGNDLTG 419
Query: 92 QALEDSDVVIIPAGVPRKPG 111
Q + + PA P P
Sbjct: 420 QPMVIDYGDLSPASNPAAPA 439
>gnl|CDD|163691 cd08060, MPN_UPF0172, Mov34/MPN/PAD-1 family: UPF0172 family of
unknown function includes neighbor of COX4 (Noc4p).
This family includes Noc4p (neighbor of COX4; neighbor
of Cytochrome c Oxidase 4; nucleolar complex associated
4 homolog) which belongs to the family of unknown
function, UPF0172, with MPN/JAMM-like domains. Proteins
in this family are homologs of the NOC4 gene which is
conserved in eukaryotic members including human, dog,
mouse, rat, chicken, zebrafish, fruit fly, mosquito,
S.pombe, K.lactis, E.gossypii, M.grisea, N.crassa,
A.thaliana, and rice. NOC4 highly expressed in the
pancreas and moderately in liver, heart, lung, kidney,
brain, skeletal muscle, and placenta. This nucleolar
protein forms a complex with Nop14p that mediates
maturation and nuclear export of 40S ribosomal subunits.
This family of eukaryotic MPN-like domains lacks the key
residues that coordinate a metal ion and therefore does
not show catalytic isopeptidase activity.
Length = 182
Score = 29.6 bits (67), Expect = 0.88
Identities = 21/80 (26%), Positives = 32/80 (40%), Gaps = 11/80 (13%)
Query: 130 SAIAKYCPNAIVNMISNPVNSTVP-IAAEVF--KKAGTYNEKKLFGVTTLDVVRAKTFYA 186
IA+ NA + M+ N + A V K G + K+L G+ L
Sbjct: 96 DKIAENFSNACLLMVDNEKLTLDCKGNALVVYKDKGGRWKVKELRGINLLL--------W 147
Query: 187 GKANVNVAGLLKLLTHKNLV 206
AN ++ LL ++NLV
Sbjct: 148 ESANEILSALLSSKAYRNLV 167
>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 = 29.7 bits (67), Expect = 1.2
Identities = 28/111 (25%), Positives = 40/111 (36%), Gaps = 7/111 (6%)
Query: 89 QLGQALEDSDVVIIPAGVPRKPGMTRDDLFNINAGIVKDLCSAIAKYCPNAIVNMIS--- 145
L A +D+ V+++ K G + I + I K V +I
Sbjct: 192 DLDVAFKDAHVIVLLDDFLIKEGEDLEGCIRSRVAICQLYGPLIEKNA-KEDVKVIVAGR 250
Query: 146 NPVNSTVPIAAEVFKKAGTYNEKKLFGVTTLDVVRAKTFYAGKANVNVAGL 196
+N I K A + K + V L RAK A K NVN AG+
Sbjct: 251 TFLNLKTSILI---KYAPSIPRKNIIAVARLQENRAKALLARKLNVNSAGI 298
>gnl|CDD|187569 cd05259, PCBER_SDR_a, phenylcoumaran benzylic ether reductase
(PCBER) like, atypical (a) SDRs. PCBER and
pinoresinol-lariciresinol reductases are NADPH-dependent
aromatic alcohol reductases, and are atypical members of
the SDR family. Other proteins in this subgroup are
identified as eugenol synthase. These proteins contain
an N-terminus characteristic of NAD(P)-binding proteins
and a small C-terminal domain presumed to be involved in
substrate binding, but they do not have the conserved
active site Tyr residue typically found in SDRs.
Numerous other members have unknown functions. The
glycine rich NADP-binding motif in this subgroup is of 2
forms: GXGXXG and G[GA]XGXXG; it tends to be atypical
compared with the forms generally seen in classical or
extended SDRs. The usual SDR active site tetrad is not
present, but a critical active site Lys at the usual SDR
position has been identified in various members, though
other charged and polar residues are found at this
position in this subgroup. Atypical SDR-related proteins
retain the Rossmann fold of the SDRs, but have limited
sequence identity and generally lack the catalytic
properties of the archetypical members. Atypical SDRs
include biliverdin IX beta reductase (BVR-B,aka flavin
reductase), NMRa (a negative transcriptional regulator
of various fungi), progesterone 5-beta-reductase like
proteins, phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 282
Score = 29.2 bits (66), Expect = 1.2
Identities = 19/75 (25%), Positives = 30/75 (40%), Gaps = 6/75 (8%)
Query: 30 KVAVLGAAGGIGQPL--ALLMKLNPLVSRLALYDIANTPGVAADVGHINTRSEVAGYMGN 87
K+A+ GA G +G P+ ALL V+ L ++ + Y +
Sbjct: 1 KIAIAGATGTLGGPIVSALLASPGFTVTVLTRPSSTSSNEFQP----SGVKVVPVDYASH 56
Query: 88 DQLGQALEDSDVVII 102
+ L AL+ D VI
Sbjct: 57 ESLVAALKGVDAVIS 71
>gnl|CDD|217666 pfam03665, UPF0172, Uncharacterized protein family (UPF0172). In
Chlamydomonas reinhardtii the protein TLA1 (truncated
light-harvesting chlorophyll antenna size) apparently
regulates genes that define the chlorophyll-a antenna
size in the photosynthetic apparatus. This family was
formerly known as UPF0172.
Length = 195
Score = 29.2 bits (66), Expect = 1.3
Identities = 16/89 (17%), Positives = 34/89 (38%), Gaps = 14/89 (15%)
Query: 124 IVKDLCSAIAKYCPNAIVNMISN------PVNSTVPIAAEVFKKAGTYNEKKLFGVTTLD 177
+ K + IA+ NA++ ++ N P + + + KK + + D
Sbjct: 95 VAKKIADKIAENFNNAVLLLVDNEKLESDPRVPALQVYEKDGKKGWRWKKADKSLEAVED 154
Query: 178 VVRAKTFYAGKANVNVAGLLKLLTHKNLV 206
+AN ++ LL+ ++ LV
Sbjct: 155 --------WEEANEILSALLQSGAYRQLV 175
>gnl|CDD|181139 PRK07832, PRK07832, short chain dehydrogenase; Provisional.
Length = 272
Score = 28.9 bits (65), Expect = 1.9
Identities = 15/50 (30%), Positives = 22/50 (44%), Gaps = 3/50 (6%)
Query: 29 RKVAVLGAAGGIGQPLALLMKLNPLVSRLALYDIANTPGVAADVGHINTR 78
++ V GAA GIG+ AL + + L L D + G+A V
Sbjct: 1 KRCFVTGAASGIGRATALRLAAQG--AELFLTDR-DADGLAQTVADARAL 47
>gnl|CDD|187549 cd05238, Gne_like_SDR_e, Escherichia coli Gne (a
nucleoside-diphosphate-sugar 4-epimerase)-like, extended
(e) SDRs. Nucleoside-diphosphate-sugar 4-epimerase has
the characteristic active site tetrad and NAD-binding
motif of the extended SDR, and is related to more
specifically defined epimerases such as UDP-glucose 4
epimerase (aka UDP-galactose-4-epimerase), which
catalyzes the NAD-dependent conversion of UDP-galactose
to UDP-glucose, the final step in Leloir galactose
synthesis. This subgroup includes Escherichia coli
055:H7 Gne, a UDP-GlcNAc 4-epimerase, essential for O55
antigen synthesis. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 305
Score = 28.9 bits (65), Expect = 1.9
Identities = 23/79 (29%), Positives = 37/79 (46%), Gaps = 6/79 (7%)
Query: 30 KVAVLGAAGGIGQPLALLMKLNPLVSRLALYDIANTPGVAADVGHINTRSEVAGYMGNDQ 89
KV + GA+G +GQ LA + + RL L D+ +P + + +AG +
Sbjct: 2 KVLITGASGFVGQRLAERLLSDVPNERLILIDVV-SPKAPSGAPRVTQ---IAGDLAVPA 57
Query: 90 LGQALED--SDVVIIPAGV 106
L +AL + DVV A +
Sbjct: 58 LIEALANGRPDVVFHLAAI 76
>gnl|CDD|181185 PRK07979, PRK07979, acetolactate synthase 3 catalytic subunit;
Validated.
Length = 574
Score = 29.0 bits (65), Expect = 2.1
Identities = 13/33 (39%), Positives = 17/33 (51%), Gaps = 7/33 (21%)
Query: 132 IAKYCPNAIV-------NMISNPVNSTVPIAAE 157
+AKYCPNA V IS V + +PI +
Sbjct: 291 LAKYCPNATVLHIDIDPTSISKTVTADIPIVGD 323
>gnl|CDD|236372 PRK09072, PRK09072, short chain dehydrogenase; Provisional.
Length = 263
Score = 28.8 bits (65), Expect = 2.2
Identities = 26/95 (27%), Positives = 37/95 (38%), Gaps = 23/95 (24%)
Query: 27 PDRKVAVLGAAGGIGQPLALLM---------------KLNPLVSRLALYDIANTPGVAAD 71
D++V + GA+GGIGQ LA + KL L +RL V AD
Sbjct: 4 KDKRVLLTGASGGIGQALAEALAAAGARLLLVGRNAEKLEALAARLPYPGRHRW--VVAD 61
Query: 72 VGHINTRSEVAGYMGNDQLGQALEDSDVVIIPAGV 106
+ R V + + +V+I AGV
Sbjct: 62 LTSEAGREAV------LARAREMGGINVLINNAGV 90
>gnl|CDD|223980 COG1052, LdhA, Lactate dehydrogenase and related dehydrogenases
[Energy production and conversion / Coenzyme metabolism
/ General function prediction only].
Length = 324
Score = 28.4 bits (64), Expect = 2.5
Identities = 18/87 (20%), Positives = 36/87 (41%), Gaps = 14/87 (16%)
Query: 16 AGARGYSSESVPDRKVAVLGAAGGIGQPLALLMKLNPLVSRLALYDIANTPGVAADVGHI 75
G + + + ++G G IGQ A+ +L ++ YD + P ++G
Sbjct: 134 GGPDPLLGFDLRGKTLGIIGL-GRIGQ--AVARRLKGFGMKVLYYDRSPNPEAEKELG-- 188
Query: 76 NTRSEVAGYMGNDQLGQALEDSDVVII 102
A Y+ L + L +SD++ +
Sbjct: 189 ------ARYV---DLDELLAESDIISL 206
>gnl|CDD|171820 PRK12936, PRK12936, 3-ketoacyl-(acyl-carrier-protein) reductase
NodG; Reviewed.
Length = 245
Score = 28.0 bits (62), Expect = 3.3
Identities = 27/98 (27%), Positives = 45/98 (45%), Gaps = 16/98 (16%)
Query: 29 RKVAVLGAAGGIGQPLALLMKLNPLVSRLALYDIANTPGVAADVG--------HINTRSE 80
RK V GA+GGIG+ +A L+ + L + +AA++G +++ R E
Sbjct: 7 RKALVTGASGGIGEEIARLLHAQGAIVGLHGTRVEKLEALAAELGERVKIFPANLSDRDE 66
Query: 81 VAGYMGNDQLGQALEDSDVVIIPAGVPRKPGMTRDDLF 118
V + LE D+++ AG+ T+D LF
Sbjct: 67 VKAL--GQKAEADLEGVDILVNNAGI------TKDGLF 96
>gnl|CDD|214856 smart00852, MoCF_biosynth, Probable molybdopterin binding domain.
This domain is found a variety of proteins involved in
biosynthesis of molybdopterin cofactor. The domain is
presumed to bind molybdopterin. The structure of this
domain is known, and it forms an alpha/beta structure.
In the known structure of Gephyrin this domain mediates
trimerisation.
Length = 138
Score = 27.2 bits (61), Expect = 3.5
Identities = 21/87 (24%), Positives = 34/87 (39%), Gaps = 16/87 (18%)
Query: 88 DQLGQALEDSDVVIIPAGVPRKPGMTRDDLFNINAGIVKDLCSAIAKYCPNAIVN--MIS 145
+ L +AL ++DVVI G G DDL + A+A+ ++ +
Sbjct: 51 EALREALAEADVVITTGGT----GPGPDDL-------TPE---ALAELGGRELLGHGVAM 96
Query: 146 NPVNSTVPIAAEVFKKAGTYNEKKLFG 172
P P+A G +K +FG
Sbjct: 97 RPGGPPGPLANLSGTAPGVRGKKPVFG 123
>gnl|CDD|234595 PRK00048, PRK00048, dihydrodipicolinate reductase; Provisional.
Length = 257
Score = 27.8 bits (63), Expect = 4.3
Identities = 21/85 (24%), Positives = 28/85 (32%), Gaps = 22/85 (25%)
Query: 30 KVAVLGAAGGIGQPLALLMKLNPLVSRLALYDIANTPG---VAADV--GHINTRSEVAGY 84
KVAV GA+G +G+ + + VAA G G
Sbjct: 3 KVAVAGASGRMGR----------ELIEA----VEAAEDLELVAAVDRPGSPLVGQGALGV 48
Query: 85 MGNDQLGQALEDSDVVI---IPAGV 106
D L L D+DV+I P
Sbjct: 49 AITDDLEAVLADADVLIDFTTPEAT 73
>gnl|CDD|227770 COG5483, COG5483, Uncharacterized conserved protein [Function
unknown].
Length = 289
Score = 27.6 bits (61), Expect = 4.4
Identities = 15/59 (25%), Positives = 22/59 (37%), Gaps = 6/59 (10%)
Query: 62 IANTPGVAADVGHINTRSEVAGYMGNDQLGQALEDSDVVI--IPAGVPRKPGMTRDDLF 118
I N+ V DV + + L LE+S++ IP + G R DL
Sbjct: 167 IQNSIDVLVDVRKNPFSMKF--DFTKNSLKNYLENSEIRYLHIPELGIK--GEKRKDLR 221
>gnl|CDD|133443 cd01065, NAD_bind_Shikimate_DH, NAD(P) binding domain of Shikimate
dehydrogenase. Shikimate dehydrogenase (DH) is an amino
acid DH family member. Shikimate pathway links
metabolism of carbohydrates to de novo biosynthesis of
aromatic amino acids, quinones and folate. It is
essential in plants, bacteria, and fungi but absent in
mammals, thus making enzymes involved in this pathway
ideal targets for broad spectrum antibiotics and
herbicides. Shikimate DH catalyzes the reduction of
3-hydroshikimate to shikimate using the cofactor NADH.
Amino acid DH-like NAD(P)-binding domains are members of
the Rossmann fold superfamily and include glutamate,
leucine, and phenylalanine DHs, methylene
tetrahydrofolate DH, methylene-tetrahydromethanopterin
DH, methylene-tetrahydropholate DH/cyclohydrolase,
Shikimate DH-like proteins, malate oxidoreductases, and
glutamyl tRNA reductase. Amino acid DHs catalyze the
deamination of amino acids to keto acids with NAD(P)+ as
a cofactor. The NAD(P)-binding Rossmann fold superfamily
includes a wide variety of protein families including
NAD(P)- binding domains of alcohol DHs,
tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate DH, lactate/malate DHs,
formate/glycerate DHs, siroheme synthases,
6-phosphogluconate DHs, amino acid DHs, repressor rex,
NAD-binding potassium channel domain, CoA-binding, and
ornithine cyclodeaminase-like domains. These domains
have an alpha-beta-alpha configuration. NAD binding
involves numerous hydrogen and van der Waals contacts.
Length = 155
Score = 27.2 bits (61), Expect = 4.5
Identities = 21/110 (19%), Positives = 43/110 (39%), Gaps = 14/110 (12%)
Query: 25 SVPDRKVAVLGAAGGIGQPLAL-LMKLNPLVSRLALY--DIANTPGVAADVGHINTRSEV 81
+ +KV +LG AGG + +A L +L +++ + + +A
Sbjct: 16 ELKGKKVLILG-AGGAARAVAYALAELG--AAKIVIVNRTLEKAKALAE---RFGELGIA 69
Query: 82 AGYMGNDQLGQALEDSDVVI--IPAGVPRKPGMTRDDLFNINAGIVKDLC 129
Y+ L + L ++D++I P G+ + G+V D+
Sbjct: 70 IAYL---DLEELLAEADLIINTTPVGMKPGDELPLPPSLLKPGGVVYDVV 116
>gnl|CDD|187548 cd05237, UDP_invert_4-6DH_SDR_e, UDP-Glcnac (UDP-linked
N-acetylglucosamine) inverting 4,6-dehydratase,
extended (e) SDRs. UDP-Glcnac inverting
4,6-dehydratase was identified in Helicobacter pylori
as the hexameric flaA1 gene product (FlaA1). FlaA1 is
hexameric, possesses UDP-GlcNAc-inverting
4,6-dehydratase activity, and catalyzes the first step
in the creation of a pseudaminic acid derivative in
protein glycosylation. Although this subgroup has the
NADP-binding motif characteristic of extended SDRs, its
members tend to have a Met substituted for the active
site Tyr found in most SDR families. Extended SDRs are
distinct from classical SDRs. In addition to the
Rossmann fold (alpha/beta folding pattern with a
central beta-sheet) core region typical of all SDRs,
extended SDRs have a less conserved C-terminal
extension of approximately 100 amino acids. Extended
SDRs are a diverse collection of proteins, and include
isomerases, epimerases, oxidoreductases, and lyases;
they typically have a TGXXGXXG cofactor binding motif.
SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving
as a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton
relay involving the conserved Tyr and Lys, a water
molecule stabilized by Asn, and nicotinamide. Atypical
SDRs generally lack the catalytic residues
characteristic of the SDRs, and their glycine-rich
NAD(P)-binding motif is often different from the forms
normally seen in classical or extended SDRs. Complex
(multidomain) SDRs such as ketoreductase domains of
fatty acid synthase have a GGXGXXG NAD(P)-binding motif
and an altered active site motif (YXXXN). Fungal type
ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding
motif.
Length = 287
Score = 27.6 bits (62), Expect = 4.7
Identities = 11/39 (28%), Positives = 18/39 (46%), Gaps = 3/39 (7%)
Query: 28 DRKVAVLGAAGGIGQPLAL-LMKLNPLVSRLALYDIANT 65
+ + V G AG IG L ++K P +L ++D
Sbjct: 2 GKTILVTGGAGSIGSELVRQILKFGP--KKLIVFDRDEN 38
>gnl|CDD|240642 cd12165, 2-Hacid_dh_6, Putative D-isomer specific 2-hydroxyacid
dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 314
Score = 27.6 bits (62), Expect = 5.3
Identities = 19/85 (22%), Positives = 30/85 (35%), Gaps = 14/85 (16%)
Query: 18 ARGYSSESVPDRKVAVLGAAGGIGQPLALLMKLNPLVSRLALYDIANTPGVAADVGHINT 77
S+ + + V +LG G IG+ +A L+K A V
Sbjct: 127 GEEPESKELRGKTVGILGY-GHIGREIARLLK-------------AFGMRVIGVSRSPKE 172
Query: 78 RSEVAGYMGNDQLGQALEDSDVVII 102
L +ALE +DVV++
Sbjct: 173 DEGADFVGTLSDLDEALEQADVVVV 197
>gnl|CDD|223959 COG1028, FabG, Dehydrogenases with different specificities (related
to short-chain alcohol dehydrogenases) [Secondary
metabolites biosynthesis, transport, and catabolism /
General function prediction only].
Length = 251
Score = 27.1 bits (60), Expect = 6.4
Identities = 25/143 (17%), Positives = 43/143 (30%), Gaps = 29/143 (20%)
Query: 28 DRKVAVLGAAGGIGQPLALLM-----------------KLNPLVSRLALYDIANTPGVAA 70
+ V GA+ GIG+ +A + L + + VAA
Sbjct: 5 GKVALVTGASSGIGRAIARALAREGARVVVAARRSEEEAAEALAAAIKEAGGGRAAAVAA 64
Query: 71 DVGHINTRSEVAGYMGNDQLGQALEDSDVVIIPAGVPRKPGMTR-------DDLFNINAG 123
DV + V + + D+++ AG+ D + ++N
Sbjct: 65 DVS--DDEESVEALV--AAAEEEFGRIDILVNNAGIAGPDAPLEELTEEDWDRVIDVNLL 120
Query: 124 IVKDLCSAIAKYC-PNAIVNMIS 145
L A IVN+ S
Sbjct: 121 GAFLLTRAALPLMKKQRIVNISS 143
>gnl|CDD|107330 cd06335, PBP1_ABC_ligand_binding_like_2, Type I periplasmic
ligand-binding domain of uncharacterized ABC (ATPase
Binding Cassette)-type active transport systems that
are predicted to be involved in transport of amino
acids, peptides, or inorganic ions. This subgroup
includes the type I periplasmic ligand-binding domain
of uncharacterized ABC (ATPase Binding Cassette)-type
active transport systems that are predicted to be
involved in transport of amino acids, peptides, or
inorganic ions. Members of this group are
sequence-similar to members of the family of ABC-type
hydrophobic amino acid transporters, such as
leucine-isoleucine-valine-binding protein (LIVBP);
however their ligand specificity has not been
determined experimentally.
Length = 347
Score = 27.2 bits (61), Expect = 6.7
Identities = 14/46 (30%), Positives = 23/46 (50%), Gaps = 4/46 (8%)
Query: 36 AAGGI-GQPLALLMK---LNPLVSRLALYDIANTPGVAADVGHINT 77
AAGG+ G+ L L+ + NP ++A V A +G ++T
Sbjct: 32 AAGGVLGRKLELVERDDRGNPARGLQNAQELAADEKVVAVLGGLHT 77
>gnl|CDD|234372 TIGR03843, TIGR03843, conserved hypothetical protein. This model
represents a protein family largely restricted to the
Actinobacteria (high-GC Gram-positives), although it is
also found in the Chloroflexi. Distant similarity to the
phosphatidylinositol 3- and 4-kinase is suggested by the
matching of some members to pfam00454.
Length = 253
Score = 26.9 bits (60), Expect = 6.8
Identities = 12/39 (30%), Positives = 22/39 (56%)
Query: 24 ESVPDRKVAVLGAAGGIGQPLALLMKLNPLVSRLALYDI 62
VP+ + VL A G+P+ L+ +P + R+A++D
Sbjct: 105 GEVPEGWLPVLRAEDEEGEPVVLVHADHPQLRRMAVFDA 143
>gnl|CDD|222146 pfam13460, NAD_binding_10, NADH(P)-binding.
Length = 182
Score = 26.9 bits (60), Expect = 7.0
Identities = 18/80 (22%), Positives = 31/80 (38%), Gaps = 9/80 (11%)
Query: 31 VAVLGAAGGIGQPLALLMKLNPLVSR-LALYDIANTPGVAADVGHINTRSEVAGYMGNDQ 89
+AV+GA G G+ L L++R + ++ P A G + ++
Sbjct: 1 IAVIGATGKTGRRLVKE-----LLARGHQVTALSRNPSKAPAPGVTPVQKDLFDLAD--- 52
Query: 90 LGQALEDSDVVIIPAGVPRK 109
L +AL D V+ G
Sbjct: 53 LAEALAGVDAVVDAFGARPD 72
>gnl|CDD|187584 cd05323, ADH_SDR_c_like, insect type alcohol dehydrogenase
(ADH)-like, classical (c) SDRs. This subgroup contains
insect type ADH, and 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) type I; these proteins are
classical SDRs. ADH catalyzes the NAD+-dependent
oxidation of alcohols to aldehydes/ketones. This
subgroup is distinct from the zinc-dependent alcohol
dehydrogenases of the medium chain
dehydrogenase/reductase family, and evolved in fruit
flies to allow the digestion of fermenting fruit.
15-PGDH catalyzes the NAD-dependent interconversion of
(5Z,13E)-(15S)-11alpha,
15-dihydroxy-9-oxoprost-13-enoate and
(5Z,13E)-11alpha-hydroxy-9,15-dioxoprost-13-enoate, and
has a typical SDR glycine-rich NAD-binding motif, which
is not fully present in ADH. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold
(alpha/beta folding pattern with a central beta-sheet),
an NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRs are
approximately 350 residues. Sequence identity between
different SDR enzymes are typically in the 15-30%
range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes catalyze a
wide range of activities including the metabolism of
steroids, cofactors, carbohydrates, lipids, aromatic
compounds, and amino acids, and act in redox sensing.
Classical SDRs have an TGXXX[AG]XG cofactor binding
motif and a YXXXK active site motif, with the Tyr
residue of the active site motif serving as a critical
catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 244
Score = 26.9 bits (60), Expect = 7.1
Identities = 20/54 (37%), Positives = 31/54 (57%), Gaps = 5/54 (9%)
Query: 30 KVAVL-GAAGGIGQPLA-LLMKLNPLVSRLALYDIANTPGVAADVGHINTRSEV 81
KVA++ G A GIG A LL+K +++A+ D PG AA++ IN + +
Sbjct: 1 KVAIITGGASGIGLATAKLLLKKG---AKVAILDRNENPGAAAELQAINPKVKA 51
>gnl|CDD|176157 cd08468, PBP2_Pa0477, The C-terminal substrate biniding domain of
an uncharacterized LysR-like transcriptional regulator
Pa0477 related to DntR, contains the type 2 periplasmic
binding fold. LysR-type transcriptional regulator
Pa0477 is related to DntR, which controls genes encoding
enzymes for oxidative degradation of the nitro-aromatic
compound 2,4-dinitrotoluene. The transcription of the
genes encoding enzymes involved in such degradation is
regulated and expression of these enzymes is enhanced by
inducers, which are either an intermediate in the
metabolic pathway or compounds to be degraded. The
topology of this substrate-binding domain is most
similar to that of the type 2 periplasmic binding
proteins (PBP2), which are responsible for the uptake of
a variety of substrates such as phosphate, sulfate,
polysaccharides, lysine/arginine/ornithine, and
histidine. The PBP2 bind their ligand in the cleft
between these domains in a manner resembling a Venus
flytrap. After binding their specific ligand with high
affinity, they can interact with a cognate membrane
transport complex comprised of two integral membrane
domains and two cytoplasmically located ATPase domains.
This interaction triggers the ligand translocation
across the cytoplasmic membrane energized by ATP
hydrolysis.
Length = 202
Score = 27.0 bits (60), Expect = 7.2
Identities = 22/80 (27%), Positives = 30/80 (37%), Gaps = 10/80 (12%)
Query: 44 LALLMKLNPLVSRLALYDIANTPGVAADVGHINTRSEVAGYMGNDQLGQAL-------ED 96
+A L +L P V ++ P A G I+ GY +D L ED
Sbjct: 19 MARLEELAPSVRLNLVHAEQKLPLDALLAGEIDF---ALGYSHDDGAEPRLIEERDWWED 75
Query: 97 SDVVIIPAGVPRKPGMTRDD 116
+ VVI PR +T D
Sbjct: 76 TYVVIASRDHPRLSRLTLDA 95
>gnl|CDD|99993 cd03823, GT1_ExpE7_like, This family is most closely related to the
GT1 family of glycosyltransferases. ExpE7 in
Sinorhizobium meliloti has been shown to be involved in
the biosynthesis of galactoglucans (exopolysaccharide
II).
Length = 359
Score = 26.8 bits (60), Expect = 7.9
Identities = 6/29 (20%), Positives = 14/29 (48%)
Query: 75 INTRSEVAGYMGNDQLGQALEDSDVVIIP 103
+ R E G +++ + DV+++P
Sbjct: 241 GDPRVEFLGAYPQEEIDDFYAEIDVLVVP 269
>gnl|CDD|217480 pfam03298, Stanniocalcin, Stanniocalcin family.
Length = 209
Score = 26.6 bits (59), Expect = 8.0
Identities = 11/21 (52%), Positives = 12/21 (57%), Gaps = 1/21 (4%)
Query: 127 DLCSAIAKYCPNAIVNMISNP 147
DLCS AK P AI +I P
Sbjct: 133 DLCSV-AKENPEAIGEVIQLP 152
>gnl|CDD|187555 cd05244, BVR-B_like_SDR_a, biliverdin IX beta reductase (BVR-B, aka
flavin reductase)-like proteins; atypical (a) SDRs.
Human BVR-B catalyzes pyridine nucleotide-dependent
production of bilirubin-IX beta during fetal
development; in the adult BVR-B has flavin and ferric
reductase activities. Human BVR-B catalyzes the
reduction of FMN, FAD, and riboflavin. Recognition of
flavin occurs mostly by hydrophobic interactions,
accounting for the broad substrate specificity. Atypical
SDRs are distinct from classical SDRs. BVR-B does not
share the key catalytic triad, or conserved tyrosine
typical of SDRs. The glycine-rich NADP-binding motif of
BVR-B is GXXGXXG, which is similar but not identical to
the pattern seen in extended SDRs. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Atypical SDRs include
biliverdin IX beta reductase (BVR-B,aka flavin
reductase), NMRa (a negative transcriptional regulator
of various fungi), progesterone 5-beta-reductase like
proteins, phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 207
Score = 26.8 bits (60), Expect = 8.3
Identities = 18/92 (19%), Positives = 33/92 (35%), Gaps = 19/92 (20%)
Query: 30 KVAVLGAAGGIGQPLALLMKLNPLVSRLAL---YDIA----NTPGVAADVGHINTRSEVA 82
K+A++GA G G + R AL +++ + + A+ +
Sbjct: 1 KIAIIGATGRTGSAIV----------REALARGHEVTALVRDPAKLPAEHEKLKVV--QG 48
Query: 83 GYMGNDQLGQALEDSDVVIIPAGVPRKPGMTR 114
+ + + +ALE D VI G T
Sbjct: 49 DVLDLEDVKEALEGQDAVISALGTRNDLSPTT 80
>gnl|CDD|187537 cd05226, SDR_e_a, Extended (e) and atypical (a) SDRs. Extended or
atypical short-chain dehydrogenases/reductases (SDRs,
aka tyrosine-dependent oxidoreductases) are distinct
from classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. Atypical SDRs generally
lack the catalytic residues characteristic of the SDRs,
and their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Atypical SDRs include biliverdin IX beta
reductase (BVR-B,aka flavin reductase), NMRa (a negative
transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Complex
(multidomain) SDRs such as ketoreductase domains of
fatty acid synthase have a GGXGXXG NAD(P)-binding motif
and an altered active site motif (YXXXN). Fungal type
ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding
motif.
Length = 176
Score = 26.6 bits (59), Expect = 8.7
Identities = 25/100 (25%), Positives = 38/100 (38%), Gaps = 12/100 (12%)
Query: 31 VAVLGAAGGIGQPLA--LLMKLNP--LVSRLALYDIANTPGVAADVGHINTRSEVAGYMG 86
+ +LGA G IG+ LA LL + + L+ R V + R
Sbjct: 1 ILILGATGFIGRALARELLEQGHEVTLLVRNTKRLS-KEDQEPVAVVEGDLRDL------ 53
Query: 87 NDQLGQALEDSDVVIIPAGVPRKPGMTRDDLFNINAGIVK 126
D L A++ DVVI AG PR + +++
Sbjct: 54 -DSLSDAVQGVDVVIHLAGAPRDTRDFCEVDVEGTRNVLE 92
>gnl|CDD|234531 TIGR04282, glyco_like_cofC, transferase 1,
rSAM/selenodomain-associated. Members of this protein
family show strongly correlated phylogenetic
distribution, and in most cases co-clustering, with an
unusual radical SAM enzyme (TIGR04167) whose C-terminal
pfam12345 domain often contains a selenocysteine
residue. Other members of the conserved gene
neighborhood include another putative
glycosyltransferase, an alkylhydroperoxidase family
protein (TIGR04169), and a phosphoesterase family
protein (TIGR04168). The cassette is likely to be
biosynthetic but its exact function is unknown [Unknown
function, Enzymes of unknown specificity].
Length = 189
Score = 26.3 bits (59), Expect = 9.2
Identities = 9/13 (69%), Positives = 11/13 (84%)
Query: 92 QALEDSDVVIIPA 104
+ALED DVV+ PA
Sbjct: 119 EALEDHDVVLGPA 131
>gnl|CDD|187592 cd05331, DH-DHB-DH_SDR_c, 2,3 dihydro-2,3 dihydrozybenzoate
dehydrogenases, classical (c) SDRs. 2,3 dihydro-2,3
dihydrozybenzoate dehydrogenase shares the
characteristics of the classical SDRs. This subgroup
includes Escherichai coli EntA which catalyzes the
NAD+-dependent oxidation of
2,3-dihydro-2,3-dihydroxybenzoate to
2,3-dihydroxybenzoate during biosynthesis of the
siderophore Enterobactin. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold
(alpha/beta folding pattern with a central beta-sheet),
an NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRs are approximately
350 residues. Sequence identity between different SDR
enzymes are typically in the 15-30% range, but the
enzymes share the Rossmann fold NAD-binding motif and
characteristic NAD-binding and catalytic sequence
patterns. These enzymes catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) numbering). In addition to the
Tyr and Lys, there is often an upstream Ser (Ser-138,
15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH
numbering) contributing to the active site; while
substrate binding is in the C-terminal region, which
determines specificity. The standard reaction mechanism
is a 4-pro-S hydride transfer and proton relay involving
the conserved Tyr and Lys, a water molecule stabilized
by Asn, and nicotinamide. Extended SDRs have additional
elements in the C-terminal region, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Some atypical SDRs have lost catalytic activity and/or
have an unusual NAD(P)-binding motif and missing or
unusual active site residues. Reactions catalyzed within
the SDR family include isomerization, decarboxylation,
epimerization, C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 244
Score = 26.7 bits (59), Expect = 9.5
Identities = 34/147 (23%), Positives = 49/147 (33%), Gaps = 44/147 (29%)
Query: 31 VAVLGAAGGIGQPLALLMKLN-----------------PLVSRLALYDIANTPGVAADVG 73
V V GAA GIG+ +A + RL D+A+ V
Sbjct: 1 VIVTGAAQGIGRAVARHLLQAGATVIALDLPFVLLLEYGDPLRLTPLDVADAAAVREVC- 59
Query: 74 HINTRSEVAGYMGNDQLGQALEDSDVVIIPAGVPRKPGMTRDD-------LFNINAGIVK 126
+L D ++ AGV R PG T F +N V
Sbjct: 60 --------------SRLLAEHGPIDALVNCAGVLR-PGATDPLSTEDWEQTFAVNVTGVF 104
Query: 127 DLCSAIAKYCPN----AIVNMISNPVN 149
+L A+A + + AIV + SN +
Sbjct: 105 NLLQAVAPHMKDRRTGAIVTVASNAAH 131
>gnl|CDD|218565 pfam05346, DUF747, Eukaryotic membrane protein family. This family
is a family of eukaryotic membrane proteins. It was
previously annotated as including a putative receptor
for human cytomegalovirus gH but this has has since been
disputed. Analysis of the mouse Tapt1 protein
(transmembrane anterior posterior transformation 1) has
shown it to be involved in patterning of the vertebrate
axial skeleton.
Length = 320
Score = 26.5 bits (59), Expect = 9.7
Identities = 13/37 (35%), Positives = 21/37 (56%), Gaps = 6/37 (16%)
Query: 143 MISNPVNSTVPIAAEVFKKAGTYNEKKLFGVTTLDVV 179
++SN I + VFKK ++++ LF +T DVV
Sbjct: 128 LLSN---QFAEIKSSVFKK---FDKESLFQITCADVV 158
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
0.318 0.135 0.379
Gapped
Lambda K H
0.267 0.0829 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,526,061
Number of extensions: 1017552
Number of successful extensions: 1311
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1274
Number of HSP's successfully gapped: 140
Length of query: 209
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 116
Effective length of database: 6,812,680
Effective search space: 790270880
Effective search space used: 790270880
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 (21.7 bits)
S2: 57 (25.5 bits)