RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 025639
(250 letters)
>gnl|CDD|165999 PLN02358, PLN02358, glyceraldehyde-3-phosphate dehydrogenase.
Length = 338
Score = 414 bits (1064), Expect = e-147
Identities = 201/226 (88%), Positives = 216/226 (95%), Gaps = 2/226 (0%)
Query: 3 GDKKIKIGINGFGRIGRLVARVALQRDDVELVAVNDPFISTDYMTYMFKYDSVHGQWKHN 62
DKKI+IGINGFGRIGRLVARV LQRDDVELVAVNDPFI+T+YMTYMFKYDSVHGQWKH+
Sbjct: 2 ADKKIRIGINGFGRIGRLVARVVLQRDDVELVAVNDPFITTEYMTYMFKYDSVHGQWKHH 61
Query: 63 ELKVKDEKTLLFGEKPVAVFGFRNPEEIPWAKTGAEYVVESTGVFTDKDKAAAHLKGGAK 122
ELKVKD+KTLLFGEKPV VFG RNPE+IPW + GA++VVESTGVFTDKDKAAAHLKGGAK
Sbjct: 62 ELKVKDDKTLLFGEKPVTVFGIRNPEDIPWGEAGADFVVESTGVFTDKDKAAAHLKGGAK 121
Query: 123 KVVISAPSKDAPMFVVGVNEKEYKPELDIVSNASCTTNCLAPLAKVIHDKFGIVEGLMTT 182
KVVISAPSKDAPMFVVGVNE EYK +LDIVSNASCTTNCLAPLAKVI+D+FGIVEGLMTT
Sbjct: 122 KVVISAPSKDAPMFVVGVNEHEYKSDLDIVSNASCTTNCLAPLAKVINDRFGIVEGLMTT 181
Query: 183 VHSITATQKTVDGPSMKDWRGGRAASFNIIPSSTGAAKVHSVGRVI 228
VHSITATQKTVDGPSMKDWRGGRAASFNIIPSSTGAAK +VG+V+
Sbjct: 182 VHSITATQKTVDGPSMKDWRGGRAASFNIIPSSTGAAK--AVGKVL 225
>gnl|CDD|177912 PLN02272, PLN02272, glyceraldehyde-3-phosphate dehydrogenase.
Length = 421
Score = 388 bits (999), Expect = e-136
Identities = 163/225 (72%), Positives = 184/225 (81%), Gaps = 3/225 (1%)
Query: 4 DKKIKIGINGFGRIGRLVARVALQRDDVELVAVNDPFISTDYMTYMFKYDSVHGQWKHNE 63
K KIGINGFGRIGRLV R+A RDD+E+VAVNDPFI YM YMFKYDS HG +K
Sbjct: 83 SGKTKIGINGFGRIGRLVLRIATSRDDIEVVAVNDPFIDAKYMAYMFKYDSTHGNFK-GT 141
Query: 64 LKVKDEKTLLFGEKPVAVFGFRNPEEIPWAKTGAEYVVESTGVFTDKDKAAAHLKGGAKK 123
+ V D+ TL K + V R+P EIPW GAEYVVES+GVFT +KA+AHLKGGAKK
Sbjct: 142 INVVDDSTLEINGKQIKVTSKRDPAEIPWGDFGAEYVVESSGVFTTVEKASAHLKGGAKK 201
Query: 124 VVISAPSKDAPMFVVGVNEKEYKPELDIVSNASCTTNCLAPLAKVIHDKFGIVEGLMTTV 183
VVISAPS DAPMFVVGVNEK YKP ++IVSNASCTTNCLAPLAKV+H++FGI+EGLMTTV
Sbjct: 202 VVISAPSADAPMFVVGVNEKTYKPNMNIVSNASCTTNCLAPLAKVVHEEFGILEGLMTTV 261
Query: 184 HSITATQKTVDGPSMKDWRGGRAASFNIIPSSTGAAKVHSVGRVI 228
H+ TATQKTVDGPSMKDWRGGR AS NIIPSSTGAAK +VG+V+
Sbjct: 262 HATTATQKTVDGPSMKDWRGGRGASQNIIPSSTGAAK--AVGKVL 304
>gnl|CDD|173322 PTZ00023, PTZ00023, glyceraldehyde-3-phosphate dehydrogenase;
Provisional.
Length = 337
Score = 316 bits (812), Expect = e-108
Identities = 145/225 (64%), Positives = 172/225 (76%), Gaps = 7/225 (3%)
Query: 7 IKIGINGFGRIGRLVARVALQRDDVELVAVNDPFISTDYMTYMFKYDSVHGQWKHNELKV 66
+K+GINGFGRIGRLV R AL+R+DVE+VA+NDPF++ DYM Y+ KYDSVHG E+ V
Sbjct: 3 VKLGINGFGRIGRLVFRAALEREDVEVVAINDPFMTLDYMCYLLKYDSVHGSLPA-EVSV 61
Query: 67 KDEKTLLFGEKPVAVFGFRNPEEIPWAKTGAEYVVESTGVFTDKDKAAAHLKGGAKKVVI 126
D L+ G K V VF ++P IPW K G + V ESTGVF K+KA AHLKGGAKKV++
Sbjct: 62 TDGF-LMIGSKKVHVFFEKDPAAIPWGKNGVDVVCESTGVFLTKEKAQAHLKGGAKKVIM 120
Query: 127 SAPSKD-APMFVVGVNEKEYKPELDIVSNASCTTNCLAPLAKVIHDKFGIVEGLMTTVHS 185
SAP KD P++V+GVN +Y IVSNASCTTNCLAPLAKV++DKFGIVEGLMTTVH+
Sbjct: 121 SAPPKDDTPIYVMGVNHTQYDKSQRIVSNASCTTNCLAPLAKVVNDKFGIVEGLMTTVHA 180
Query: 186 ITATQKTVDGPSM--KDWRGGRAASFNIIPSSTGAAKVHSVGRVI 228
TA Q TVDGPS KDWR GR A NIIP+STGAAK +VG+VI
Sbjct: 181 STANQLTVDGPSKGGKDWRAGRCAGVNIIPASTGAAK--AVGKVI 223
>gnl|CDD|233453 TIGR01534, GAPDH-I, glyceraldehyde-3-phosphate dehydrogenase, type
I. This model represents glyceraldehyde-3-phosphate
dehydrogenase (GAPDH), the enzyme responsible for the
interconversion of 1,3-diphosphoglycerate and
glyceraldehyde-3-phosphate, a central step in glycolysis
and gluconeogenesis. Forms exist which utilize NAD (EC
1.2.1.12), NADP (EC 1.2.1.13) or either (1.2.1.59). In
some species, NAD- and NADP- utilizing forms exist,
generally being responsible for reactions in the
anabolic and catabolic directions respectively. Two PFAM
models cover the two functional domains of this protein;
pfam00044 represents the N-terminal NAD(P)-binding
domain and pfam02800 represents the C-terminal catalytic
domain. An additional form of gap gene is found in gamma
proteobacteria and is responsible for the conversion of
erythrose-4-phosphate (E4P) to 4-phospho-erythronate in
the biosynthesis of pyridoxine. This pathway of
pyridoxine biosynthesis appears to be limited, however,
to a relatively small number of bacterial species
although it is prevalent among the gamma-proteobacteria.
This enzyme is described by TIGR001532. These sequences
generally score between trusted and noise to this GAPDH
model due to the close evolutionary relationship. There
exists the possiblity that some forms of GAPDH may be
bifunctional and act on E4P in species which make
pyridoxine and via hydroxythreonine and lack a separate
E4PDH enzyme (for instance, the GAPDH from Bacillus
stearothermophilus has been shown to posess a limited
E4PD activity as well as a robust GAPDH activity). There
are a great number of sequences in the databases which
score between trusted and noise to this model, nearly
all of them due to fragmentary sequences. It seems that
study of this gene has been carried out in many species
utilizing PCR probes which exclude the extreme ends of
the consenses used to define this model. The noise level
is set relative not to E4PD, but the next closest
outliers, the class II GAPDH's (found in archaea,
TIGR01546) and aspartate semialdehyde dehydrogenase
(ASADH, TIGR01296) both of which have highest-scoring
hits around -225 to the prior model [Energy metabolism,
Glycolysis/gluconeogenesis].
Length = 326
Score = 314 bits (808), Expect = e-108
Identities = 122/224 (54%), Positives = 159/224 (70%), Gaps = 8/224 (3%)
Query: 8 KIGINGFGRIGRLVARVALQRD--DVELVAVNDPFISTDYMTYMFKYDSVHGQWKHNELK 65
K+GINGFGRIGRLV R L++ D+E+VA+ND +Y+ Y+ KYDSVHG+++ E+
Sbjct: 1 KVGINGFGRIGRLVLRAILEKPGNDLEVVAINDL-TDLEYLAYLLKYDSVHGRFEG-EVT 58
Query: 66 VKDEKTLLFGEKPVAVFGFRNPEEIPWAKTGAEYVVESTGVFTDKDKAAAHLKGGAKKVV 125
++ ++ G++ ++VF R+P ++PW G + V+E TG F DK+K HL+ GAKKV+
Sbjct: 59 ADEDGLVVNGKEVISVFSERDPSDLPWKALGVDIVIECTGKFRDKEKLEGHLEAGAKKVL 118
Query: 126 ISAPSK-DAPMFVVGVNEKEYKPELDIVSNASCTTNCLAPLAKVIHDKFGIVEGLMTTVH 184
ISAPSK D V GVN EY P IVSNASCTTNCLAPLAKV+ + FGIV GLMTTVH
Sbjct: 119 ISAPSKGDVKTIVYGVNHDEYDPSERIVSNASCTTNCLAPLAKVLDEAFGIVSGLMTTVH 178
Query: 185 SITATQKTVDGPSMKDWRGGRAASFNIIPSSTGAAKVHSVGRVI 228
S T Q VDGP KD R RAA+ NIIP+STGAAK ++G+V+
Sbjct: 179 SYTNDQNLVDGP-HKDLRRARAAALNIIPTSTGAAK--AIGKVL 219
>gnl|CDD|223135 COG0057, GapA, Glyceraldehyde-3-phosphate
dehydrogenase/erythrose-4-phosphate dehydrogenase
[Carbohydrate transport and metabolism].
Length = 335
Score = 314 bits (807), Expect = e-108
Identities = 127/226 (56%), Positives = 157/226 (69%), Gaps = 9/226 (3%)
Query: 6 KIKIGINGFGRIGRLVARVALQRD-DVELVAVNDPFISTDYMTYMFKYDSVHGQWKHNEL 64
IK+ INGFGRIGRLVAR AL+RD D+E+VA+ND DY+ ++ KYDSVHG++ E+
Sbjct: 1 MIKVAINGFGRIGRLVARAALERDGDIEVVAINDL-TDPDYLAHLLKYDSVHGRFDG-EV 58
Query: 65 KVKDEKTLLFGEKPVAVFGFRNPEEIPWAKTGAEYVVESTGVFTDKDKAAAHL-KGGAKK 123
+V + L+ K + V R+P +PWA G + VVE TG FT ++KA HL GGAKK
Sbjct: 59 EV-KDDALVVNGKGIKVLAERDPANLPWADLGVDIVVECTGKFTGREKAEKHLKAGGAKK 117
Query: 124 VVISAPSKDA-PMFVVGVNEKEYKPELDIVSNASCTTNCLAPLAKVIHDKFGIVEGLMTT 182
V+ISAP KD V GVN Y IVSNASCTTNCLAP+AKV++D FGI +GLMTT
Sbjct: 118 VLISAPGKDDVATVVYGVNHNYYDAGHTIVSNASCTTNCLAPVAKVLNDAFGIEKGLMTT 177
Query: 183 VHSITATQKTVDGPSMKDWRGGRAASFNIIPSSTGAAKVHSVGRVI 228
VH+ T QK VDGP KD R RAA+ NIIP+STGAAK +VG V+
Sbjct: 178 VHAYTNDQKLVDGPH-KDLRRARAAALNIIPTSTGAAK--AVGLVL 220
>gnl|CDD|185323 PRK15425, gapA, glyceraldehyde-3-phosphate dehydrogenase A;
Provisional.
Length = 331
Score = 247 bits (631), Expect = 1e-81
Identities = 133/223 (59%), Positives = 166/223 (74%), Gaps = 7/223 (3%)
Query: 7 IKIGINGFGRIGRLVARVALQRDDVELVAVNDPFISTDYMTYMFKYDSVHGQWKHNELKV 66
IK+GINGFGRIGR+V R A +R D+E+VA+ND + DYM YM KYDS HG++ ++V
Sbjct: 3 IKVGINGFGRIGRIVFRAAQKRSDIEIVAIND-LLDADYMAYMLKYDSTHGRFD-GTVEV 60
Query: 67 KDEKTLLFGEKPVAVFGFRNPEEIPWAKTGAEYVVESTGVFTDKDKAAAHLKGGAKKVVI 126
KD ++ G+K + V R+P + W + G + V E+TG+F + A H+ GAKKVV+
Sbjct: 61 KDGHLIVNGKK-IRVTAERDPANLKWDEVGVDVVAEATGLFLTDETARKHITAGAKKVVM 119
Query: 127 SAPSKD-APMFVVGVNEKEYKPELDIVSNASCTTNCLAPLAKVIHDKFGIVEGLMTTVHS 185
+ PSKD PMFV G N +Y + DIVSNASCTTNCLAPLAKVI+D FGI+EGLMTTVH+
Sbjct: 120 TGPSKDNTPMFVKGANFDKYAGQ-DIVSNASCTTNCLAPLAKVINDNFGIIEGLMTTVHA 178
Query: 186 ITATQKTVDGPSMKDWRGGRAASFNIIPSSTGAAKVHSVGRVI 228
TATQKTVDGPS KDWRGGR AS NIIPSSTGAAK +VG+V+
Sbjct: 179 TTATQKTVDGPSHKDWRGGRGASQNIIPSSTGAAK--AVGKVL 219
>gnl|CDD|185614 PTZ00434, PTZ00434, cytosolic glyceraldehyde 3-phosphate
dehydrogenase; Provisional.
Length = 361
Score = 248 bits (633), Expect = 2e-81
Identities = 129/236 (54%), Positives = 162/236 (68%), Gaps = 16/236 (6%)
Query: 7 IKIGINGFGRIGRLVARVALQRD----DVELVAVNDPFISTDYMTYMFKYDSVHGQWKHN 62
IK+GINGFGRIGR+V + + ++++VAV D + +Y Y KYD+VHG+ K+
Sbjct: 4 IKVGINGFGRIGRMVFQAICDQGLIGTEIDVVAVVDMSTNAEYFAYQMKYDTVHGRPKYT 63
Query: 63 ELKVK-------DEKTLLFGEKPVAVFGFRNPEEIPWAKTGAEYVVESTGVFTDKDKAAA 115
K D+ ++ G + V RNP ++PW K G +YV+ESTG+FTDK A
Sbjct: 64 VETTKSSPSVKTDDVLVVNGHRIKCVKAQRNPADLPWGKLGVDYVIESTGLFTDKLAAEG 123
Query: 116 HLKGGAKKVVISAP-SKDAPMFVVGVNEKEYKP-ELDIVSNASCTTNCLAPLAKVI-HDK 172
HLKGGAKKVVISAP S A V+GVN+ EY P E +VSNASCTTNCLAP+ V+ +
Sbjct: 124 HLKGGAKKVVISAPASGGAKTIVMGVNQHEYSPTEHHVVSNASCTTNCLAPIVHVLTKEG 183
Query: 173 FGIVEGLMTTVHSITATQKTVDGPSMKDWRGGRAASFNIIPSSTGAAKVHSVGRVI 228
FGI GLMTT+HS TATQKTVDG S+KDWRGGRAA+ NIIPS+TGAAK +VG VI
Sbjct: 184 FGIETGLMTTIHSYTATQKTVDGVSVKDWRGGRAAAVNIIPSTTGAAK--AVGMVI 237
>gnl|CDD|236079 PRK07729, PRK07729, glyceraldehyde-3-phosphate dehydrogenase;
Validated.
Length = 343
Score = 233 bits (595), Expect = 7e-76
Identities = 102/218 (46%), Positives = 146/218 (66%), Gaps = 8/218 (3%)
Query: 6 KIKIGINGFGRIGRLVARVALQRDDVELVAVNDPFISTDYMTYMFKYDSVHGQWKHNELK 65
K K+ INGFGRIGR+V R A++ E+VA+N + ++ + ++ KYD+VHG++ +
Sbjct: 2 KTKVAINGFGRIGRMVFRKAIKESAFEIVAINASY-PSETLAHLIKYDTVHGKF---DGT 57
Query: 66 VK-DEKTLLFGEKPVAVFGFRNPEEIPWAKTGAEYVVESTGVFTDKDKAAAHLKGGAKKV 124
V+ E LL K + + R+P+E+PW G + V+E+TG F K+KA H++ GAKKV
Sbjct: 58 VEAFEDHLLVDGKKIRLLNNRDPKELPWTDLGIDIVIEATGKFNSKEKAILHVEAGAKKV 117
Query: 125 VISAPSKDAPM-FVVGVNEKEYKPELD-IVSNASCTTNCLAPLAKVIHDKFGIVEGLMTT 182
+++AP K+ + VVGVNE + E I+SNASCTTNCLAP+ KV+ ++FGI GLMTT
Sbjct: 118 ILTAPGKNEDVTIVVGVNEDQLDIEKHTIISNASCTTNCLAPVVKVLDEQFGIENGLMTT 177
Query: 183 VHSITATQKTVDGPSMKDWRGGRAASFNIIPSSTGAAK 220
VH+ T QK +D P KD R RA +IIP++TGAAK
Sbjct: 178 VHAYTNDQKNIDNPH-KDLRRARACGQSIIPTTTGAAK 214
>gnl|CDD|215675 pfam00044, Gp_dh_N, Glyceraldehyde 3-phosphate dehydrogenase, NAD
binding domain. GAPDH is a tetrameric NAD-binding
enzyme involved in glycolysis and glyconeogenesis.
N-terminal domain is a Rossmann NAD(P) binding fold.
Length = 148
Score = 220 bits (564), Expect = 1e-73
Identities = 86/151 (56%), Positives = 111/151 (73%), Gaps = 4/151 (2%)
Query: 7 IKIGINGFGRIGRLVARVALQRDDVELVAVNDPFISTDYMTYMFKYDSVHGQWKHNELKV 66
IK+GINGFGRIGRLV R AL +DD+E+VA+ND + + Y+ KYDSVHG++ E++V
Sbjct: 1 IKVGINGFGRIGRLVLRAALAQDDLEVVAINDLT-DPETLAYLLKYDSVHGRFDG-EVEV 58
Query: 67 KDEKTLLFGEKPVAVFGFRNPEEIPWAKTGAEYVVESTGVFTDKDKAAAHLKGGAKKVVI 126
++ L+ K + VF R+P E+PW + G + VVESTGVFT +KA AHLK GAKKV+I
Sbjct: 59 DEDG-LIVNGKKIKVFAERDPAELPWGELGVDIVVESTGVFTTAEKAEAHLKAGAKKVII 117
Query: 127 SAPSKD-APMFVVGVNEKEYKPELDIVSNAS 156
SAP+KD P FV GVN ++Y PE DIVSNAS
Sbjct: 118 SAPAKDDDPTFVYGVNHEDYDPEDDIVSNAS 148
>gnl|CDD|214851 smart00846, Gp_dh_N, Glyceraldehyde 3-phosphate dehydrogenase, NAD
binding domain. GAPDH is a tetrameric NAD-binding
enzyme involved in glycolysis and glyconeogenesis.
N-terminal domain is a Rossmann NAD(P) binding fold.
Length = 149
Score = 216 bits (552), Expect = 6e-72
Identities = 85/152 (55%), Positives = 109/152 (71%), Gaps = 4/152 (2%)
Query: 7 IKIGINGFGRIGRLVARVALQRDDVELVAVNDPFISTDYMTYMFKYDSVHGQWKHNELKV 66
IK+GINGFGRIGRLV R AL+R DVE+VA+ND +Y+ Y+ KYDSVHG++ ++V
Sbjct: 1 IKVGINGFGRIGRLVLRAALERPDVEVVAINDL-TDPEYLAYLLKYDSVHGRFPG-TVEV 58
Query: 67 KDEKTLLFGEKPVAVFGFRNPEEIPWAKTGAEYVVESTGVFTDKDKAAAHLKGGAKKVVI 126
+ + L+ K + VF R+P +PW + G + VVE TG FT ++KA+AHLK GAKKV+I
Sbjct: 59 EGD-GLVVNGKAIKVFAERDPANLPWGELGVDIVVECTGGFTTREKASAHLKAGAKKVII 117
Query: 127 SAPSKDA-PMFVVGVNEKEYKPELDIVSNASC 157
SAPSKDA P FV GVN EY E I+SNASC
Sbjct: 118 SAPSKDADPTFVYGVNHDEYDGEDHIISNASC 149
>gnl|CDD|215131 PLN02237, PLN02237, glyceraldehyde-3-phosphate dehydrogenase B.
Length = 442
Score = 217 bits (555), Expect = 1e-68
Identities = 108/220 (49%), Positives = 150/220 (68%), Gaps = 8/220 (3%)
Query: 6 KIKIGINGFGRIGRLVARVALQRDD--VELVAVNDPFISTDYMTYMFKYDSVHGQWKHNE 63
K+K+ INGFGRIGR R R D +++V VND +++ KYDS+ G +K +
Sbjct: 75 KLKVAINGFGRIGRNFLRCWHGRKDSPLDVVVVNDSG-GVKNASHLLKYDSMLGTFK-AD 132
Query: 64 LKVKDEKTLLFGEKPVAVFGFRNPEEIPWAKTGAEYVVESTGVFTDKDKAAAHLKGGAKK 123
+K+ D++T+ KP+ V R+P ++PWA+ G + V+E TGVF D A H++ GAKK
Sbjct: 133 VKIVDDETISVDGKPIKVVSNRDPLKLPWAELGIDIVIEGTGVFVDGPGAGKHIQAGAKK 192
Query: 124 VVISAPSK--DAPMFVVGVNEKEYKPEL-DIVSNASCTTNCLAPLAKVIHDKFGIVEGLM 180
V+I+AP+K D P +VVGVNE +Y E+ +IVSNASCTTNCLAP KV+ ++FGIV+G M
Sbjct: 193 VIITAPAKGADIPTYVVGVNEDDYDHEVANIVSNASCTTNCLAPFVKVLDEEFGIVKGTM 252
Query: 181 TTVHSITATQKTVDGPSMKDWRGGRAASFNIIPSSTGAAK 220
TT HS T Q+ +D S +D R RAA+ NI+P+STGAAK
Sbjct: 253 TTTHSYTGDQRLLDA-SHRDLRRARAAALNIVPTSTGAAK 291
>gnl|CDD|180962 PRK07403, PRK07403, glyceraldehyde-3-phosphate dehydrogenase;
Reviewed.
Length = 337
Score = 213 bits (544), Expect = 3e-68
Identities = 109/221 (49%), Positives = 147/221 (66%), Gaps = 13/221 (5%)
Query: 7 IKIGINGFGRIGRLVARVALQRDD--VELVAVNDPFISTDYMT--YMFKYDSVHGQWKHN 62
I++ INGFGRIGR R L R++ +ELVA+ND ++D T ++ KYDS+ G K N
Sbjct: 2 IRVAINGFGRIGRNFLRCWLGRENSQLELVAIND---TSDPRTNAHLLKYDSMLG--KLN 56
Query: 63 ELKVKDEKTLLFGEKPVAVFGFRNPEEIPWAKTGAEYVVESTGVFTDKDKAAAHLKGGAK 122
DE ++ K + RNP +PW + G + ++ESTGVF K+ A+ H++ GAK
Sbjct: 57 ADISADENSITVNGKTIKCVSDRNPLNLPWKEWGIDLIIESTGVFVTKEGASKHIQAGAK 116
Query: 123 KVVISAPSK--DAPMFVVGVNEKEYKPEL-DIVSNASCTTNCLAPLAKVIHDKFGIVEGL 179
KV+I+AP K D +VVGVN EY E +I+SNASCTTNCLAP+AKV+HD FGI++G
Sbjct: 117 KVLITAPGKGEDIGTYVVGVNHHEYDHEDHNIISNASCTTNCLAPIAKVLHDNFGIIKGT 176
Query: 180 MTTVHSITATQKTVDGPSMKDWRGGRAASFNIIPSSTGAAK 220
MTT HS T Q+ +D S +D R RAA+ NI+P+STGAAK
Sbjct: 177 MTTTHSYTGDQRILDA-SHRDLRRARAAAVNIVPTSTGAAK 216
>gnl|CDD|215572 PLN03096, PLN03096, glyceraldehyde-3-phosphate dehydrogenase A;
Provisional.
Length = 395
Score = 212 bits (542), Expect = 3e-67
Identities = 103/220 (46%), Positives = 140/220 (63%), Gaps = 6/220 (2%)
Query: 4 DKKIKIGINGFGRIGRLVARVALQRDD--VELVAVNDPFISTDYMTYMFKYDSVHGQWKH 61
+ KIK+ INGFGRIGR R R D +++VA+ND +++ KYDS G +
Sbjct: 58 EAKIKVAINGFGRIGRNFLRCWHGRKDSPLDVVAINDTG-GVKQASHLLKYDSTLGTFD- 115
Query: 62 NELKVKDEKTLLFGEKPVAVFGFRNPEEIPWAKTGAEYVVESTGVFTDKDKAAAHLKGGA 121
++K + + K + V RNP +PW + G + V+E TGVF D++ A H++ GA
Sbjct: 116 ADVKPVGDDAISVDGKVIKVVSDRNPLNLPWGELGIDLVIEGTGVFVDREGAGKHIQAGA 175
Query: 122 KKVVISAPSK-DAPMFVVGVNEKEYKPELDIVSNASCTTNCLAPLAKVIHDKFGIVEGLM 180
KKV+I+AP K D P +VVGVN +YK I+SNASCTTNCLAP KV+ KFGI++G M
Sbjct: 176 KKVLITAPGKGDIPTYVVGVNADDYKHSDPIISNASCTTNCLAPFVKVLDQKFGIIKGTM 235
Query: 181 TTVHSITATQKTVDGPSMKDWRGGRAASFNIIPSSTGAAK 220
TT HS T Q+ +D S +D R RAA+ NI+P+STGAAK
Sbjct: 236 TTTHSYTGDQRLLDA-SHRDLRRARAAALNIVPTSTGAAK 274
>gnl|CDD|169599 PRK08955, PRK08955, glyceraldehyde-3-phosphate dehydrogenase;
Validated.
Length = 334
Score = 194 bits (496), Expect = 5e-61
Identities = 88/218 (40%), Positives = 130/218 (59%), Gaps = 8/218 (3%)
Query: 6 KIKIGINGFGRIGRLVARVALQRDDVELVAVNDPFISTDYMTYMFKYDSVHGQWKHNELK 65
IK+GINGFGRIGRL R A ++E V +NDP + ++ ++DSVHG+W H
Sbjct: 2 TIKVGINGFGRIGRLALRAAWDWPELEFVQINDPAGDAATLAHLLEFDSVHGRWHHE--V 59
Query: 66 VKDEKTLLFGEKPVAVFGFRNPEEIPWAKTGAEYVVESTGVFTDKDKAAAHLKGGAKKVV 125
+ ++ K + + + W +G + V+E++GV K A+L G K+VV
Sbjct: 60 TAEGDAIVINGKRIRTTQNKAIADTDW--SGCDVVIEASGVMKTKALLQAYLDQGVKRVV 117
Query: 126 ISAPSKDAPMF--VVGVNEKEYKPELD-IVSNASCTTNCLAPLAKVIHDKFGIVEGLMTT 182
++AP K+ + V+GVN+ + P + IV+ ASCTTNCLAP+ KVIH+K GI G MTT
Sbjct: 118 VTAPVKEEGVLNIVMGVNDHLFDPAIHPIVTAASCTTNCLAPVVKVIHEKLGIKHGSMTT 177
Query: 183 VHSITATQKTVDGPSMKDWRGGRAASFNIIPSSTGAAK 220
+H +T TQ +D P KD R RA ++IP++TG+A
Sbjct: 178 IHDLTNTQTILDAPH-KDLRRARACGMSLIPTTTGSAT 214
>gnl|CDD|184122 PRK13535, PRK13535, erythrose 4-phosphate dehydrogenase;
Provisional.
Length = 336
Score = 174 bits (444), Expect = 3e-53
Identities = 88/222 (39%), Positives = 130/222 (58%), Gaps = 15/222 (6%)
Query: 7 IKIGINGFGRIGRLVARVAL----QRDDVELVAVNDPFISTDYMTYMFKYDSVHGQWKHN 62
I++ INGFGRIGR V R AL +R ++ +VA+N+ + M ++ KYD+ HG++
Sbjct: 2 IRVAINGFGRIGRNVLR-ALYESGRRAEITVVAINE-LADAEGMAHLLKYDTSHGRFAW- 58
Query: 63 ELKVKDEKTLLF-GEKPVAVFGFRNPEEIPWAKTGAEYVVESTGVFTDKDKAAAHLKGGA 121
V+ E+ LF G+ + + R+ +PW + G + V++ TGV+ ++ AH+ GA
Sbjct: 59 --DVRQERDQLFVGDDAIRLLHERDIASLPWRELGVDVVLDCTGVYGSREDGEAHIAAGA 116
Query: 122 KKVVISAPSK---DAPMFVVGVNEKEYKPELDIVSNASCTTNCLAPLAKVIHDKFGIVEG 178
KKV+ S P DA + V GVN + + E IVSNASCTTNC+ P+ K++ D FGI G
Sbjct: 117 KKVLFSHPGSNDLDATV-VYGVNHDQLRAEHRIVSNASCTTNCIIPVIKLLDDAFGIESG 175
Query: 179 LMTTVHSITATQKTVDGPSMKDWRGGRAASFNIIPSSTGAAK 220
+TT+HS Q+ +D D R RAAS +IIP T A
Sbjct: 176 TVTTIHSAMNDQQVIDA-YHPDLRRTRAASQSIIPVDTKLAA 216
>gnl|CDD|130595 TIGR01532, E4PD_g-proteo, erythrose-4-phosphate dehydrogenase.
This model represents the small clade of dehydrogenases
in gamma-proteobacteria which utilize NAD+ to oxidize
erythrose-4-phosphate (E4P) to 4-phospho-erythronate, a
precursor for the de novo synthesis of pyridoxine via
4-hydroxythreonine and D-1-deoxyxylulose. This enzyme
activity appears to have evolved from
glyceraldehyde-3-phosphate dehydrogenase, whose
substrate differs only in the lack of one carbon
relative to E4P. Accordingly, this model is very close
to the corresponding models for GAPDH, and those
sequences which hit above trusted here invariably hit
between trusted and noise to the GAPDH model
(TIGR01534). Similarly, it may be found that there are
species outside of the gamma proteobacteria which
synthesize pyridoxine and have more than one aparrent
GAPDH gene of which one may have E4PD activity - this
may necessitate a readjustment of these models.
Alternatively, some of the GAPDH enzymes may prove to be
bifunctional in certain species [Biosynthesis of
cofactors, prosthetic groups, and carriers, Pyridoxine].
Length = 325
Score = 162 bits (411), Expect = 2e-48
Identities = 83/218 (38%), Positives = 127/218 (58%), Gaps = 9/218 (4%)
Query: 8 KIGINGFGRIGRLVARVALQ---RDDVELVAVNDPFISTDYMTYMFKYDSVHGQWKHNEL 64
++ INGFGRIGR V R + R ++ +VA+N+ M ++ KYD+ HG++ E+
Sbjct: 1 RVAINGFGRIGRNVLRALYESGRRAEITVVAINE-LADAAGMAHLLKYDTSHGRFA-WEV 58
Query: 65 KVKDEKTLLFGEKPVAVFGFRNPEEIPWAKTGAEYVVESTGVFTDKDKAAAHLKGGAKKV 124
+ D L G+ + V R+ + +PW + G + V++ TGV+ ++ AH+ GAKKV
Sbjct: 59 RQ-DRDQLFVGDDAIRVLHERSLQSLPWRELGVDLVLDCTGVYGSREHGEAHIAAGAKKV 117
Query: 125 VISAP-SKDAPMFVV-GVNEKEYKPELDIVSNASCTTNCLAPLAKVIHDKFGIVEGLMTT 182
+ S P + D +V GVN+ + + E IVSNASCTTNC+ P+ K++ D +GI G +TT
Sbjct: 118 LFSHPGASDLDATIVYGVNQDQLRAEHRIVSNASCTTNCIVPVIKLLDDAYGIESGTITT 177
Query: 183 VHSITATQKTVDGPSMKDWRGGRAASFNIIPSSTGAAK 220
+HS Q+ +D D R RAAS +IIP T A
Sbjct: 178 IHSAMNDQQVIDA-YHPDLRRTRAASQSIIPVDTKLAA 214
>gnl|CDD|236219 PRK08289, PRK08289, glyceraldehyde-3-phosphate dehydrogenase;
Reviewed.
Length = 477
Score = 146 bits (371), Expect = 4e-41
Identities = 78/223 (34%), Positives = 119/223 (53%), Gaps = 20/223 (8%)
Query: 13 GFGRIGRLVARVALQR----DDVELVAV-------NDPFISTDYMTYMFKYDSVHGQWKH 61
GFGRIGRL+AR+ +++ + + L A+ D + + + DSVHG +
Sbjct: 134 GFGRIGRLLARLLIEKTGGGNGLRLRAIVVRKGSEGD----LEKRASLLRRDSVHGPFNG 189
Query: 62 NELKVKDEKTLLFGEKPVAVFGFRNPEEIPWAKTGAE--YVVESTGVFTDKDKAAAHLKG 119
++ ++ + V +PEE+ + G VV++TG + D++ + HLK
Sbjct: 190 TITVDEENNAIIANGNYIQVIYANSPEEVDYTAYGINNALVVDNTGKWRDEEGLSQHLKS 249
Query: 120 -GAKKVVISAPSK-DAPMFVVGVNEKEYKPELDIVSNASCTTNCLAPLAKVIHDKFGIVE 177
G KV+++AP K D V GVN + E IVS ASCTTN + P+ K ++DK+GIV
Sbjct: 250 KGVAKVLLTAPGKGDIKNIVHGVNHSDITDEDKIVSAASCTTNAITPVLKAVNDKYGIVN 309
Query: 178 GLMTTVHSITATQKTVDGPSMKDWRGGRAASFNIIPSSTGAAK 220
G + TVHS T Q +D D R GR+A N++ + TGAAK
Sbjct: 310 GHVETVHSYTNDQNLIDNYHKGD-RRGRSAPLNMVITETGAAK 351
>gnl|CDD|173546 PTZ00353, PTZ00353, glycosomal glyceraldehyde-3-phosphate
dehydrogenase; Provisional.
Length = 342
Score = 129 bits (325), Expect = 1e-35
Identities = 70/228 (30%), Positives = 113/228 (49%), Gaps = 7/228 (3%)
Query: 7 IKIGINGFGRIGRLVARVALQRDDVELVAVNDPFISTDYMTYMFKYDSVHGQWKHNELKV 66
I +GINGFG +G+ V +L V +VAVND +S Y+ Y+ + +S ++V
Sbjct: 3 ITVGINGFGPVGKAVLFASLTDPLVTVVAVNDASVSIAYIAYVLEQESPLSAPDGASIRV 62
Query: 67 KDEKTLLFGEKPVAVFGFRNPEEIPWAKTGAEYVVESTGVFTDKDKAAAHLKGGAKKVVI 126
E+ +L G + + V + EI W G +YVVE TG+++ + + H+ GGAK V +
Sbjct: 63 VGEQIVLNGTQKIRVSAKHDLVEIAWRDYGVQYVVECTGLYSTRSRCWGHVTGGAKGVFV 122
Query: 127 SAPSKDAPMFVVGVNEKEYKPELDIVSNASCTTNCLAPLAKVIHDKFGIVEGLMTTVHSI 186
+ S DAP + G N++ L + + LAP+ + +H+ +G+ E T +H +
Sbjct: 123 AGQSADAPTVMAGSNDERLSASLPVCCAGAPIAVALAPVIRALHEVYGVEECSYTAIHGM 182
Query: 187 TATQKT-VDGPSMKDWRGGRAASFNIIPSS-TGAAKV-----HSVGRV 227
+ + +DWR R A I P GA V H VGR+
Sbjct: 183 QPQEPIAARSKNSQDWRQTRVAIDAIAPYRDNGAETVCKLLPHLVGRI 230
>gnl|CDD|217235 pfam02800, Gp_dh_C, Glyceraldehyde 3-phosphate dehydrogenase,
C-terminal domain. GAPDH is a tetrameric NAD-binding
enzyme involved in glycolysis and glyconeogenesis.
C-terminal domain is a mixed alpha/antiparallel beta
fold.
Length = 157
Score = 112 bits (282), Expect = 4e-31
Identities = 46/67 (68%), Positives = 54/67 (80%), Gaps = 3/67 (4%)
Query: 162 LAPLAKVIHDKFGIVEGLMTTVHSITATQKTVDGPSMKDWRGGRAASFNIIPSSTGAAKV 221
LAPLAKV++D FGI +GLMTTVH+ TA QK VD PS KD R GRAA+ NIIP+STGAAK
Sbjct: 1 LAPLAKVLNDNFGIEKGLMTTVHAYTADQKLVD-PSHKDLRRGRAAAPNIIPTSTGAAK- 58
Query: 222 HSVGRVI 228
+VG V+
Sbjct: 59 -AVGLVL 64
>gnl|CDD|223214 COG0136, Asd, Aspartate-semialdehyde dehydrogenase [Amino acid
transport and metabolism].
Length = 334
Score = 44.9 bits (107), Expect = 2e-05
Identities = 38/162 (23%), Positives = 62/162 (38%), Gaps = 31/162 (19%)
Query: 74 FGEKPVAVFGFRNPEEIP--WAKTGAEYVVESTGVFTDKDKAAAHLKGGAK--KVVISAP 129
FG K + V PE+ + + + V + G + A+ VVI
Sbjct: 47 FGGKSIGV-----PEDAADEFVFSDVDIVFFAAG----GSVSKEVEPKAAEAGCVVIDNS 97
Query: 130 S-----KDAPMFVVGVNE---KEYKPELDIVSNASCTTNCLAPLAKVIHDKFGIVEGLMT 181
S D P+ V VN +Y+ I++N +C+T L K +HD FGI +++
Sbjct: 98 SAFRMDPDVPLVVPEVNPEHLIDYQKRGFIIANPNCSTIQLVLALKPLHDAFGIKRVVVS 157
Query: 182 TVHSI----------TATQKTVDGPSMKDWRGGRAASFNIIP 213
T ++ A Q + G +FN+IP
Sbjct: 158 TYQAVSGAGAEGGVELAGQTDALLNGIPILPIGYPLAFNVIP 199
>gnl|CDD|179786 PRK04207, PRK04207, glyceraldehyde-3-phosphate dehydrogenase;
Provisional.
Length = 341
Score = 42.9 bits (102), Expect = 8e-05
Identities = 20/45 (44%), Positives = 26/45 (57%), Gaps = 4/45 (8%)
Query: 6 KIKIGINGFGRIGRLVAR-VALQRDDVELVAVNDPFISTDYMTYM 49
IK+G+NG+G IG+ VA VA Q D+ELV V DY +
Sbjct: 1 MIKVGVNGYGTIGKRVADAVAAQ-PDMELVGVAK--TKPDYEARV 42
>gnl|CDD|234595 PRK00048, PRK00048, dihydrodipicolinate reductase; Provisional.
Length = 257
Score = 41.7 bits (99), Expect = 1e-04
Identities = 40/146 (27%), Positives = 60/146 (41%), Gaps = 34/146 (23%)
Query: 6 KIKIGINGF-GRIGRLVARVALQRDDVELVAVNDPFISTDYMTYMFKYDSVHGQWKHNEL 64
IK+ + G GR+GR + +D+ELVA D S +
Sbjct: 1 MIKVAVAGASGRMGRELIEAVEAAEDLELVAAVDRP------------GSPLVGQGALGV 48
Query: 65 KVKDEKTLLFGEKPVAVFGFRNPE---EIPWAKTGAEY----VVESTGVFTDKDKAAAHL 117
+ D+ + + V + F PE E + E+ V+ +TG FT++ A L
Sbjct: 49 AITDDLEAVLADADVLI-DFTTPEATLEN--LEFALEHGKPLVIGTTG-FTEEQLAE--L 102
Query: 118 KGGAKK--VVISAPSKDAPMFVVGVN 141
+ AKK VVI AP F +GVN
Sbjct: 103 EEAAKKIPVVI------APNFSIGVN 122
>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 = 39.9 bits (94), Expect = 2e-04
Identities = 13/31 (41%), Positives = 19/31 (61%), Gaps = 1/31 (3%)
Query: 7 IKIGINGF-GRIGRLVARVALQRDDVELVAV 36
IK+ + G GR+GR + + L+ D ELVA
Sbjct: 1 IKVAVVGASGRMGRELIKAILEAPDFELVAA 31
>gnl|CDD|223366 COG0289, DapB, Dihydrodipicolinate reductase [Amino acid transport
and metabolism].
Length = 266
Score = 41.5 bits (98), Expect = 2e-04
Identities = 42/145 (28%), Positives = 62/145 (42%), Gaps = 24/145 (16%)
Query: 6 KIKIGINGF-GRIGRLVARVALQRDDVELVAVNDPFISTDYMTYMFKYDSVHGQWKHNEL 64
IK+ + G GR+GR + R L+ D+ELVA D S + +
Sbjct: 2 MIKVAVAGASGRMGRTLIRAVLEAPDLELVAAFDRPGS----LSLGSDAGELAGLGLLGV 57
Query: 65 KVKDEKTLLFGEKPVAVFGFRNPE------EIPWAKTGAEYVVESTGVFTDKDKAAAHLK 118
V D+ L+ + V + F PE E + G V+ +TG FT++ L+
Sbjct: 58 PVTDDLLLVKADADVLI-DFTTPEATLENLEFA-LEHGKPLVIGTTG-FTEEQLEK--LR 112
Query: 119 GGAKK--VVISAPSKDAPMFVVGVN 141
A+K VVI AP F +GVN
Sbjct: 113 EAAEKVPVVI------APNFSLGVN 131
>gnl|CDD|233347 TIGR01296, asd_B, aspartate-semialdehyde dehydrogenase
(peptidoglycan organisms). Two closely related families
of aspartate-semialdehyde dehydrogenase are found. They
differ by a deep split in phylogenetic and percent
identity trees and in gap patterns. This model
represents a branch more closely related to the USG-1
protein than to the other aspartate-semialdehyde
dehydrogenases represented in model TIGR00978 [Amino
acid biosynthesis, Aspartate family].
Length = 338
Score = 40.2 bits (94), Expect = 5e-04
Identities = 24/92 (26%), Positives = 43/92 (46%), Gaps = 9/92 (9%)
Query: 103 STGVFTDKDKAAAHLKGGAKKVVISAPS-----KDAPMFVVGVNEKEYK--PELDIVSNA 155
S G K+ A K G +VI S D P+ V VN ++ K I++N
Sbjct: 68 SAGGSVSKEFAPKAAKAGV--IVIDNTSAFRMDPDVPLVVPEVNFEDLKEFNPKGIIANP 125
Query: 156 SCTTNCLAPLAKVIHDKFGIVEGLMTTVHSIT 187
+C+T + + K +HD+ I +++T +++
Sbjct: 126 NCSTIQMVVVLKPLHDEAKIKRVVVSTYQAVS 157
>gnl|CDD|240648 cd12171, 2-Hacid_dh_10, 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 = 310
Score = 35.6 bits (83), Expect = 0.018
Identities = 16/37 (43%), Positives = 22/37 (59%), Gaps = 2/37 (5%)
Query: 8 KIGINGFGRIGRLVARVALQRDDVELVAVNDPFISTD 44
+GI GFG IGR VA+ L+ E V V DP++ +
Sbjct: 149 TVGIVGFGAIGRRVAKR-LKAFGAE-VLVYDPYVDPE 183
>gnl|CDD|130609 TIGR01546, GAPDH-II_archae, glyceraldehyde-3-phosphate
dehydrogenase, type II. This model describes the type
II glyceraldehyde-3-phosphate dehydrogenases which are
limited to archaea. These enzymes catalyze the
interconversion of 1,3-diphosphoglycerate and
glyceraldehyde-3-phosphate, a central step in
glycolysis and gluconeogenesis. In archaea, either NAD
or NADP may be utilized as the cofactor. The class I
GAPDH's from bacteria and eukaryotes are covered by
TIGR01534. All of the members of the seed are
characterized. See, for instance. This model is very
solid, there are no species falling between trusted and
noise at this time. The closest relatives scoring in
the noise are the class I GAPDH's.
Length = 333
Score = 35.6 bits (82), Expect = 0.019
Identities = 17/43 (39%), Positives = 26/43 (60%), Gaps = 2/43 (4%)
Query: 9 IGINGFGRIGRLVARVALQRDDVELVAVNDPFISTDYMTYMFK 51
+G+NG+G IG+ VA ++DD++LV V S D+ Y K
Sbjct: 1 VGVNGYGTIGKRVADAVTKQDDMKLVGVTK--TSPDFEAYRAK 41
>gnl|CDD|240644 cd12167, 2-Hacid_dh_8, 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 = 330
Score = 35.2 bits (82), Expect = 0.020
Identities = 15/42 (35%), Positives = 22/42 (52%), Gaps = 2/42 (4%)
Query: 8 KIGINGFGRIGRLVARVALQRDDVELVAVNDPFISTDYMTYM 49
+GI GFGRIGR V + L+ + V V DP++ +
Sbjct: 152 TVGIVGFGRIGRAVVEL-LRPFGLR-VLVYDPYLPAAEAAAL 191
>gnl|CDD|201778 pfam01408, GFO_IDH_MocA, Oxidoreductase family, NAD-binding
Rossmann fold. This family of enzymes utilise NADP or
NAD. This family is called the GFO/IDH/MOCA family in
swiss-prot.
Length = 120
Score = 33.3 bits (77), Expect = 0.033
Identities = 14/34 (41%), Positives = 21/34 (61%), Gaps = 1/34 (2%)
Query: 7 IKIGINGFGRIGRLVARVALQ-RDDVELVAVNDP 39
+++GI G G+IGR R + +D ELV + DP
Sbjct: 1 LRVGIVGAGKIGRRHLRALNESQDGAELVGILDP 34
>gnl|CDD|240649 cd12172, PGDH_like_2, Putative D-3-Phosphoglycerate Dehydrogenases,
NAD-binding and catalytic domains. Phosphoglycerate
dehydrogenases (PGDHs) catalyze the initial step in the
biosynthesis of L-serine from D-3-phosphoglycerate.
PGDHs come in 3 distinct structural forms, with this
first group being related to 2-hydroxy acid
dehydrogenases, sharing structural similarity to formate
and glycerate dehydrogenases of the D-specific
2-hydroxyacid dehydrogenase superfamily, which also
include groups such as 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. Many, not all, members of this family are
dimeric.
Length = 306
Score = 34.4 bits (80), Expect = 0.036
Identities = 14/38 (36%), Positives = 21/38 (55%), Gaps = 2/38 (5%)
Query: 8 KIGINGFGRIGRLVARVALQRDDVELVAVNDPFISTDY 45
+GI G GRIG+ VAR L ++ V DP+ ++
Sbjct: 144 TLGIIGLGRIGKAVAR-RLSGFGMK-VLAYDPYPDEEF 179
>gnl|CDD|240650 cd12173, PGDH_4, Phosphoglycerate dehydrogenases, NAD-binding and
catalytic domains. Phosphoglycerate dehydrogenases
(PGDHs) catalyze the initial step in the biosynthesis of
L-serine from D-3-phosphoglycerate. PGDHs come in 3
distinct structural forms, with this first group being
related to 2-hydroxy acid dehydrogenases, sharing
structural similarity to formate and glycerate
dehydrogenases. PGDH in E. coli and Mycobacterium
tuberculosis form tetramers, with subunits containing a
Rossmann-fold NAD binding domain. 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.
Length = 304
Score = 33.9 bits (79), Expect = 0.049
Identities = 17/36 (47%), Positives = 19/36 (52%), Gaps = 6/36 (16%)
Query: 9 IGINGFGRIGRLVARVA--LQRDDVELVAVNDPFIS 42
+GI G GRIGR VAR A V DP+IS
Sbjct: 141 LGIVGLGRIGREVARRARAFGMK----VLAYDPYIS 172
>gnl|CDD|237436 PRK13581, PRK13581, D-3-phosphoglycerate dehydrogenase;
Provisional.
Length = 526
Score = 34.3 bits (80), Expect = 0.058
Identities = 15/34 (44%), Positives = 23/34 (67%), Gaps = 2/34 (5%)
Query: 9 IGINGFGRIGRLVARVALQRDDVELVAVNDPFIS 42
+GI G GRIG VA+ A + ++++A DP+IS
Sbjct: 143 LGIIGLGRIGSEVAKRA-KAFGMKVIA-YDPYIS 174
>gnl|CDD|217244 pfam02826, 2-Hacid_dh_C, D-isomer specific 2-hydroxyacid
dehydrogenase, NAD binding domain. This domain is
inserted into the catalytic domain, the large
dehydrogenase and D-lactate dehydrogenase families in
SCOP. N-terminal portion of which is represented by
family pfam00389.
Length = 175
Score = 33.2 bits (77), Expect = 0.064
Identities = 15/49 (30%), Positives = 25/49 (51%), Gaps = 2/49 (4%)
Query: 8 KIGINGFGRIGRLVARVALQRDDVELVAVNDPFISTDYMTYMFKYDSVH 56
+GI G GRIGR VAR + ++++A D + + +Y S+
Sbjct: 37 TVGIIGLGRIGRAVARRL-KAFGMKVIAY-DRYPKAEAEALGARYVSLD 83
>gnl|CDD|240624 cd05299, CtBP_dh, C-terminal binding protein (CtBP),
D-isomer-specific 2-hydroxyacid dehydrogenases related
repressor. The transcriptional corepressor CtBP is a
dehydrogenase with sequence and structural similarity to
the d2-hydroxyacid dehydrogenase family. CtBP was
initially identified as a protein that bound the PXDLS
sequence at the adenovirus E1A C terminus, causing the
loss of CR-1-mediated transactivation. CtBP binds NAD(H)
within a deep cleft, undergoes a conformational change
upon NAD binding, and has NAD-dependent dehydrogenase
activity.
Length = 312
Score = 33.3 bits (77), Expect = 0.11
Identities = 14/46 (30%), Positives = 20/46 (43%), Gaps = 10/46 (21%)
Query: 9 IGINGFGRIGRLVARVA----LQRDDVELVAVNDPFISTDYMTYMF 50
+G+ GFGRIGR VA+ A + V DP++
Sbjct: 145 LGLVGFGRIGRAVAKRAKAFGFR------VIAYDPYVPDGVAALGG 184
>gnl|CDD|129147 TIGR00036, dapB, dihydrodipicolinate reductase. [Amino acid
biosynthesis, Aspartate family].
Length = 266
Score = 32.4 bits (74), Expect = 0.15
Identities = 12/33 (36%), Positives = 21/33 (63%), Gaps = 1/33 (3%)
Query: 7 IKIGING-FGRIGRLVARVALQRDDVELVAVND 38
IK+ + G GR+GR + + AL + ++LVA +
Sbjct: 2 IKVAVAGAAGRMGRELIKAALAAEGLQLVAAFE 34
>gnl|CDD|233638 TIGR01921, DAP-DH, diaminopimelate dehydrogenase. This model
represents the diaminopimelate dehydrogenase enzyme
which provides an alternate (shortcut) route of lysine
buiosynthesis in Corynebacterium, Bacterioides,
Porphyromonas and scattered other species. The enzyme
from Corynebacterium glutamicum has been crystallized
and characterized.
Length = 324
Score = 32.6 bits (74), Expect = 0.16
Identities = 14/32 (43%), Positives = 20/32 (62%)
Query: 5 KKIKIGINGFGRIGRLVARVALQRDDVELVAV 36
KI+ I G+G +GR V + Q+ D+ELV V
Sbjct: 2 SKIRAAIVGYGNLGRSVEKAIQQQPDMELVGV 33
>gnl|CDD|223189 COG0111, SerA, Phosphoglycerate dehydrogenase and related
dehydrogenases [Amino acid transport and metabolism].
Length = 324
Score = 32.3 bits (74), Expect = 0.17
Identities = 13/35 (37%), Positives = 21/35 (60%), Gaps = 2/35 (5%)
Query: 8 KIGINGFGRIGRLVARVALQRDDVELVAVNDPFIS 42
+GI G GRIGR VA+ L+ ++++ DP+
Sbjct: 144 TVGIIGLGRIGRAVAKR-LKAFGMKVIGY-DPYSP 176
>gnl|CDD|240628 cd05303, PGDH_2, Phosphoglycerate dehydrogenase (PGDH) NAD-binding
and catalytic domains. Phosphoglycerate dehydrogenase
(PGDH) catalyzes the initial step in the biosynthesis of
L-serine from D-3-phosphoglycerate. PGDH comes in 3
distinct structural forms, with this first group being
related to 2-hydroxy acid dehydrogenases, sharing
structural similarity to formate and glycerate
dehydrogenases. PGDH in E. coli and Mycobacterium
tuberculosis form tetramers, with subunits containing a
Rossmann-fold NAD binding domain. 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.
Length = 301
Score = 32.1 bits (74), Expect = 0.19
Identities = 12/18 (66%), Positives = 15/18 (83%)
Query: 9 IGINGFGRIGRLVARVAL 26
+GI GFGRIGR VA++A
Sbjct: 142 LGIIGFGRIGREVAKIAR 159
>gnl|CDD|240652 cd12175, 2-Hacid_dh_11, Putative D-isomer specific 2-hydroxyacid
dehydrogenases, NAD-binding and catalytic domains.
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 = 311
Score = 31.8 bits (73), Expect = 0.30
Identities = 13/30 (43%), Positives = 18/30 (60%), Gaps = 1/30 (3%)
Query: 8 KIGINGFGRIGRLVARVALQRDDVELVAVN 37
+GI G G IGR VAR L+ VE++ +
Sbjct: 144 TVGIVGLGNIGRAVARR-LRGFGVEVIYYD 172
>gnl|CDD|129632 TIGR00541, hisDCase_pyru, histidine decarboxylase, pyruvoyl type.
This enzyme converts histadine to histamine in a single
step by catalyzing the release of CO2. This type is
synthesized as an inactive single chain precursor, then
cleaved into two chains. The Ser at the new N-terminus
at the cleavage site is converted to a pyruvoyl group
essential for activity. This type of histidine
decarboxylase appears is known so far only in some
Gram-positive bacteria, where it may play a role in
amino acid catabolism. There is also a pyridoxal
phosphate type histidine decarboxylase, as found in
human, where histamine is a biologically active amine
[Energy metabolism, Amino acids and amines].
Length = 310
Score = 31.1 bits (70), Expect = 0.41
Identities = 28/101 (27%), Positives = 42/101 (41%), Gaps = 13/101 (12%)
Query: 58 QWKHNELKVKDEKTLLFGEKPVAVFGFRNPEEIPWAKTGAEYVVESTGVFTDKDKAAAHL 117
Q+ +ELK+ D K LL + + +FG A GA + + G ++ K A L
Sbjct: 113 QFDGSELKIYDAKPLL--DAGIELFGTEKDRRFTPAP-GAFIICANKGATAERPKEDADL 169
Query: 118 KGGAKKVVISA--------PSKDAPMFV--VGVNEKEYKPE 148
K G V SA P A +F+ G+ EK +
Sbjct: 170 KEGEAYGVWSAIAISFAKDPDHCADLFIEDAGLWEKNDNED 210
>gnl|CDD|240646 cd12169, PGDH_like_1, Putative D-3-Phosphoglycerate Dehydrogenases.
Phosphoglycerate dehydrogenases (PGDHs) catalyze the
initial step in the biosynthesis of L-serine from
D-3-phosphoglycerate. PGDHs come in 3 distinct
structural forms, with this first group being related to
2-hydroxy acid dehydrogenases, sharing structural
similarity to formate and glycerate dehydrogenases of
the D-specific 2-hydroxyacid dehydrogenase superfamily,
which also include groups such as 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. Many, not all,
members of this family are dimeric.
Length = 308
Score = 31.3 bits (72), Expect = 0.43
Identities = 10/19 (52%), Positives = 12/19 (63%)
Query: 8 KIGINGFGRIGRLVARVAL 26
+GI G GRIG VAR+
Sbjct: 144 TLGIVGLGRIGARVARIGQ 162
>gnl|CDD|240633 cd12156, HPPR, Hydroxy(phenyl)pyruvate Reductase, D-isomer-specific
2-hydroxyacid-related dehydrogenase.
Hydroxy(phenyl)pyruvate reductase (HPPR) catalyzes the
NADP-dependent reduction of hydroxyphenylpyruvates,
hydroxypyruvate, or pyruvate to its respective lactate.
HPPR acts as a dimer and is related to D-isomer-specific
2-hydroxyacid dehydrogenases, a superfamily that
includes 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 = 301
Score = 31.3 bits (72), Expect = 0.44
Identities = 10/16 (62%), Positives = 13/16 (81%)
Query: 8 KIGINGFGRIGRLVAR 23
++GI G GRIGR +AR
Sbjct: 143 RVGIVGLGRIGRAIAR 158
>gnl|CDD|240626 cd05301, GDH, D-glycerate dehydrogenase/hydroxypyruvate reductase
(GDH). D-glycerate dehydrogenase (GDH, also known as
hydroxypyruvate reductase, HPR) catalyzes the reversible
reaction of (R)-glycerate + NAD+ to hydroxypyruvate +
NADH + H+. In humans, HPR deficiency causes primary
hyperoxaluria type 2, characterized by over-excretion of
L-glycerate and oxalate in the urine, possibly due to an
imbalance in competition with L-lactate dehydrogenase,
another formate dehydrogenase (FDH)-like enzyme. GDH,
like FDH and other members of the D-specific hydroxyacid
dehydrogenase family that also includes L-alanine
dehydrogenase and S-adenosylhomocysteine hydrolase,
typically have a characteristic arrangement of 2 similar
subdomains of the alpha/beta Rossmann-fold NAD+ binding
form, despite often low sequence identity. 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 = 309
Score = 30.8 bits (71), Expect = 0.50
Identities = 10/16 (62%), Positives = 12/16 (75%)
Query: 8 KIGINGFGRIGRLVAR 23
+GI G GRIG+ VAR
Sbjct: 146 TLGIVGMGRIGQAVAR 161
>gnl|CDD|240663 cd12187, LDH_like_1, D-Lactate and related Dehydrogenase like
proteins, NAD-binding and catalytic domains. D-Lactate
dehydrogenase (LDH) catalyzes the interconversion of
pyruvate and lactate, and is a member of the
2-hydroxyacid dehydrogenase family. LDH is homologous to
D-2-Hydroxyisocaproic acid dehydrogenase(D-HicDH) and
shares the 2 domain structure of formate dehydrogenase.
D-2-hydroxyisocaproate dehydrogenase-like (HicDH)
proteins are NAD-dependent members of the
hydroxycarboxylate dehydrogenase family, and share the
Rossmann fold typical of many NAD binding proteins.
HicDH from Lactobacillus casei forms a monomer and
catalyzes the reaction R-CO-COO(-) + NADH + H+ to
R-COH-COO(-) + NAD+. D-HicDH, like the structurally
distinct L-HicDH, exhibits low side-chain R specificity,
accepting a wide range of 2-oxocarboxylic acid side
chains. 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.
Length = 329
Score = 30.7 bits (70), Expect = 0.68
Identities = 11/18 (61%), Positives = 14/18 (77%)
Query: 9 IGINGFGRIGRLVARVAL 26
+G+ G GRIGR VAR+A
Sbjct: 142 LGVVGTGRIGRRVARIAR 159
>gnl|CDD|237845 PRK14874, PRK14874, aspartate-semialdehyde dehydrogenase;
Provisional.
Length = 334
Score = 30.5 bits (70), Expect = 0.68
Identities = 26/72 (36%), Positives = 36/72 (50%), Gaps = 14/72 (19%)
Query: 112 KAAAHLKGGAKKVVI---SAPSKDA--PMFVVGVNE---KEYKPELDIVSNASCTTNCLA 163
KAAA GA VVI SA D P+ V VN E++ + I++N +C+T +
Sbjct: 82 KAAAA---GA--VVIDNSSAFRMDPDVPLVVPEVNPEALAEHRKK-GIIANPNCSTIQMV 135
Query: 164 PLAKVIHDKFGI 175
K +HD GI
Sbjct: 136 VALKPLHDAAGI 147
>gnl|CDD|240622 cd05198, formate_dh_like, Formate/glycerate and related
dehydrogenases of the D-specific 2-hydroxy acid
dehydrogenase family. Formate dehydrogenase, D-specific
2-hydroxy acid dehydrogenase, Phosphoglycerate
Dehydrogenase, Lactate dehydrogenase, Thermostable
Phosphite Dehydrogenase, and Hydroxy(phenyl)pyruvate
reductase, among others, share a characteristic
arrangement of 2 similar subdomains of the alpha/beta
Rossmann fold NAD+ binding form. 2-hydroxyacid
dehydrogenases are enzymes that 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.
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. Formate dehydrogenase
(FDH) catalyzes the NAD+-dependent oxidation of formate
ion to carbon dioxide with the concomitant reduction of
NAD+ to NADH. FDHs of this family contain no metal ions
or prosthetic groups. Catalysis occurs though direct
transfer of hydride ion to NAD+ without the stages of
acid-base catalysis typically found in related
dehydrogenases. FDHs are found in all methylotrophic
microorganisms in energy production and in the stress
responses of plants. 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,
among others. While many members of this family are
dimeric, alanine DH is hexameric and phosphoglycerate DH
is tetrameric.
Length = 302
Score = 30.3 bits (69), Expect = 0.83
Identities = 9/18 (50%), Positives = 12/18 (66%)
Query: 8 KIGINGFGRIGRLVARVA 25
+GI G GRIG+ VA+
Sbjct: 142 TVGIVGLGRIGQRVAKRL 159
>gnl|CDD|240639 cd12162, 2-Hacid_dh_4, Putative D-isomer specific 2-hydroxyacid
dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine yydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 307
Score = 30.1 bits (69), Expect = 0.91
Identities = 10/17 (58%), Positives = 14/17 (82%)
Query: 9 IGINGFGRIGRLVARVA 25
+GI G+G IG+ VAR+A
Sbjct: 150 LGIIGYGNIGQAVARIA 166
>gnl|CDD|240635 cd12158, ErythrP_dh, D-Erythronate-4-Phosphate Dehydrogenase
NAD-binding and catalytic domains.
D-Erythronate-4-phosphate Dehydrogenase (E. coli gene
PdxB), a D-specific 2-hydroxyacid dehydrogenase family
member, catalyzes the NAD-dependent oxidation of
erythronate-4-phosphate, which is followed by
transamination to form 4-hydroxy-L-threonine-4-phosphate
within the de novo biosynthesis pathway of vitamin B6.
D-Erythronate-4-phosphate dehydrogenase has the common
architecture shared with D-isomer specific 2-hydroxyacid
dehydrogenases but contains an additional C-terminal
dimerization domain in addition to an NAD-binding domain
and the "lid" domain. The lid domain corresponds to the
catalytic domain of phosphoglycerate dehydrogenase and
other proteins of the D-isomer specific 2-hydroxyacid
dehydrogenase family, which 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.
Length = 343
Score = 30.2 bits (69), Expect = 0.92
Identities = 12/39 (30%), Positives = 19/39 (48%), Gaps = 2/39 (5%)
Query: 5 KKIKIGINGFGRIGRLVARVALQRDDVELVAVNDPFIST 43
K +GI G G +G +AR L+ + V + DP +
Sbjct: 114 KGKTVGIVGVGNVGSRLARR-LEALGMN-VLLCDPPRAE 150
>gnl|CDD|169409 PRK08374, PRK08374, homoserine dehydrogenase; Provisional.
Length = 336
Score = 30.2 bits (68), Expect = 0.93
Identities = 11/27 (40%), Positives = 17/27 (62%)
Query: 5 KKIKIGINGFGRIGRLVARVALQRDDV 31
++K+ I GFG +GR VA V ++ V
Sbjct: 1 MEVKVSIFGFGNVGRAVAEVLAEKSRV 27
>gnl|CDD|240620 cd01619, LDH_like, D-Lactate and related Dehydrogenases,
NAD-binding and catalytic domains. D-Lactate
dehydrogenase (LDH) catalyzes the interconversion of
pyruvate and lactate, and is a member of the
2-hydroxyacid dehydrogenase family. LDH is homologous to
D-2-Hydroxyisocaproic acid dehydrogenase (D-HicDH) and
shares the 2 domain structure of formate dehydrogenase.
D-HicDH is a NAD-dependent member of the
hydroxycarboxylate dehydrogenase family, and shares the
Rossmann fold typical of many NAD binding proteins.
D-HicDH from Lactobacillus casei forms a monomer and
catalyzes the reaction R-CO-COO(-) + NADH + H+ to
R-COH-COO(-) + NAD+. Similar to the structurally
distinct L-HicDH, D-HicDH exhibits low side-chain R
specificity, accepting a wide range of 2-oxocarboxylic
acid side chains. (R)-2-hydroxyglutarate dehydrogenase
(HGDH) catalyzes the NAD-dependent reduction of
2-oxoglutarate to (R)-2-hydroxyglutarate.
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.
Length = 323
Score = 30.0 bits (68), Expect = 0.99
Identities = 16/46 (34%), Positives = 27/46 (58%), Gaps = 2/46 (4%)
Query: 9 IGINGFGRIGRLVARVALQRDDVELVAVNDPFISTDYMTYMFKYDS 54
+G+ G G+IGR VA+ A + ++++A DPF + + KY S
Sbjct: 146 VGVVGTGKIGRAVAQRA-KGFGMKVIAY-DPFRNPELEDKGVKYVS 189
>gnl|CDD|173409 PTZ00117, PTZ00117, malate dehydrogenase; Provisional.
Length = 319
Score = 30.1 bits (68), Expect = 1.1
Identities = 45/173 (26%), Positives = 71/173 (41%), Gaps = 40/173 (23%)
Query: 5 KKIKIGINGFGRIGRLVARVALQRD--DVELVAVNDPFISTDYMTYMFKYDSVHGQWKHN 62
K+ KI + G G+IG VA + LQ++ DV L YD + G +
Sbjct: 4 KRKKISMIGAGQIGSTVALLILQKNLGDVVL------------------YDVIKGVPQGK 45
Query: 63 ELKVKDEKTLLFGEKPVAVFGFRNPEEIPWAKTGAEYVVESTGVFTDKDKAAAHLKGGAK 122
L +K TL+ + + G N E+I ++ VV + GV ++ L
Sbjct: 46 ALDLKHFSTLV--GSNINILGTNNYEDI----KDSDVVVITAGVQRKEEMTREDLLTING 99
Query: 123 KVVISAPSKDAPMFVVGVNEKEYKPELDIVSNASCTTNCLAPLAKVIHDKFGI 175
K++ S V + K+Y P ++ C TN L + KV +K GI
Sbjct: 100 KIMKS----------VAESVKKYCPNAFVI----CVTNPLDCMVKVFQEKSGI 138
>gnl|CDD|181499 PRK08605, PRK08605, D-lactate dehydrogenase; Validated.
Length = 332
Score = 30.1 bits (68), Expect = 1.1
Identities = 17/51 (33%), Positives = 29/51 (56%), Gaps = 1/51 (1%)
Query: 5 KKIKIGINGFGRIGRLVARVALQRDDVELVAVNDPFISTDYMTYMFKYDSV 55
K +K+ + G GRIG VA++ + ++VA DPF + TY+ D++
Sbjct: 145 KDLKVAVIGTGRIGLAVAKIFAKGYGSDVVAY-DPFPNAKAATYVDYKDTI 194
>gnl|CDD|240651 cd12174, PGDH_like_3, Putative D-3-Phosphoglycerate Dehydrogenases,
NAD-binding and catalytic domains. Phosphoglycerate
dehydrogenases (PGDHs) catalyze the initial step in the
biosynthesis of L-serine from D-3-phosphoglycerate.
PGDHs come in 3 distinct structural forms, with this
first group being related to 2-hydroxy acid
dehydrogenases, sharing structural similarity to formate
and glycerate dehydrogenases of the D-specific
2-hydroxyacid dehydrogenase superfamily, which also
include groups such as 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. Many, not all, members of this family are
dimeric.
Length = 305
Score = 29.8 bits (68), Expect = 1.1
Identities = 16/40 (40%), Positives = 21/40 (52%), Gaps = 8/40 (20%)
Query: 8 KIGINGFGRIGRLVARVALQRDDVEL---VAVNDPFISTD 44
+G+ G G IGRLVA AL L V DP++S +
Sbjct: 137 TLGVIGLGNIGRLVANAAL-----ALGMKVIGYDPYLSVE 171
>gnl|CDD|99958 cd05529, Bromo_WDR9_I_like, Bromodomain; WDR9 repeat I_like
subfamily. WDR9 is a human gene located in the Down
Syndrome critical region-2 of chromosome 21. It encodes
for a nuclear protein containing WD40 repeats and two
bromodomains, which may function as a transcriptional
regulator involved in chromatin remodeling and play a
role in embryonic development. Bromodomains are 110
amino acid long domains, that are found in many
chromatin associated proteins. Bromodomains can interact
specifically with acetylated lysine.
Length = 128
Score = 28.8 bits (65), Expect = 1.1
Identities = 13/63 (20%), Positives = 23/63 (36%), Gaps = 5/63 (7%)
Query: 86 NPEEIPWAKTGAEYVVESTGVFTDKDKAAAHLKGGAKKVVISAPSKDAPMFVVGVNEKEY 145
NP W E +D+ L G K+++S + A F V+ + +
Sbjct: 3 NPLSSEW-----ELFDPGWEQPHIRDEERERLISGLDKLLLSLQLEIAEYFEYPVDLRAW 57
Query: 146 KPE 148
P+
Sbjct: 58 YPD 60
>gnl|CDD|183914 PRK13243, PRK13243, glyoxylate reductase; Reviewed.
Length = 333
Score = 29.8 bits (67), Expect = 1.2
Identities = 13/17 (76%), Positives = 14/17 (82%)
Query: 9 IGINGFGRIGRLVARVA 25
IGI GFGRIG+ VAR A
Sbjct: 153 IGIIGFGRIGQAVARRA 169
>gnl|CDD|240640 cd12163, 2-Hacid_dh_5, 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 = 334
Score = 29.9 bits (68), Expect = 1.3
Identities = 10/18 (55%), Positives = 14/18 (77%)
Query: 8 KIGINGFGRIGRLVARVA 25
++GI G+G IGR AR+A
Sbjct: 135 RVGILGYGSIGRQTARLA 152
>gnl|CDD|215528 PLN02977, PLN02977, glutathione synthetase.
Length = 478
Score = 30.0 bits (68), Expect = 1.4
Identities = 22/72 (30%), Positives = 31/72 (43%), Gaps = 14/72 (19%)
Query: 61 HNELKVKDEKTLLFGEKPVAVFGFRN-------PEEIPWAKTGAEYVVE-STGVFTDKDK 112
E + ++ TL +PVAV FR P E W A ++E S+ V K
Sbjct: 247 AAEGSLDEDGTLTVDGQPVAVVYFRAGYAPTDYPSEAEWR---ARLLLERSSAV---KCP 300
Query: 113 AAAHLKGGAKKV 124
+ A+ G KKV
Sbjct: 301 SIAYHLAGTKKV 312
>gnl|CDD|223980 COG1052, LdhA, Lactate dehydrogenase and related dehydrogenases
[Energy production and conversion / Coenzyme metabolism
/ General function prediction only].
Length = 324
Score = 29.5 bits (67), Expect = 1.4
Identities = 10/18 (55%), Positives = 12/18 (66%)
Query: 8 KIGINGFGRIGRLVARVA 25
+GI G GRIG+ VAR
Sbjct: 148 TLGIIGLGRIGQAVARRL 165
>gnl|CDD|240655 cd12178, 2-Hacid_dh_13, Putative D-isomer specific 2-hydroxyacid
dehydrogenases, NAD-binding and catalytic domains.
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 = 317
Score = 29.5 bits (67), Expect = 1.6
Identities = 11/17 (64%), Positives = 13/17 (76%)
Query: 9 IGINGFGRIGRLVARVA 25
+GI G GRIG+ VAR A
Sbjct: 147 LGIIGMGRIGQAVARRA 163
>gnl|CDD|181041 PRK07574, PRK07574, formate dehydrogenase; Provisional.
Length = 385
Score = 29.6 bits (67), Expect = 1.7
Identities = 9/16 (56%), Positives = 10/16 (62%)
Query: 8 KIGINGFGRIGRLVAR 23
+GI G GRIG V R
Sbjct: 194 TVGIVGAGRIGLAVLR 209
>gnl|CDD|240654 cd12177, 2-Hacid_dh_12, Putative D-isomer specific 2-hydroxyacid
dehydrogenases, NAD-binding and catalytic domains.
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 = 321
Score = 28.8 bits (65), Expect = 2.3
Identities = 12/38 (31%), Positives = 24/38 (63%), Gaps = 1/38 (2%)
Query: 9 IGINGFGRIGRLVARVALQRDDVELVAVNDPFISTDYM 46
+GI G+G IG VA + + + +++A DP++S + +
Sbjct: 150 VGIIGYGNIGSRVAEILKEGFNAKVLAY-DPYVSEEVI 186
>gnl|CDD|235287 PRK04342, PRK04342, DNA topoisomerase VI subunit A; Provisional.
Length = 367
Score = 28.7 bits (65), Expect = 3.1
Identities = 14/45 (31%), Positives = 19/45 (42%), Gaps = 11/45 (24%)
Query: 86 NPEEIPWAKTGAEYV--VESTGV--------FTDKDKAA-AHLKG 119
N + I + A++V VE G+ F K A HLKG
Sbjct: 179 NVDNIEFVDVDADFVLAVEKGGMFQRLVEEGFWKKYNAILVHLKG 223
>gnl|CDD|240657 cd12180, 2-Hacid_dh_15, Putative D-isomer specific 2-hydroxyacid
dehydrogenases, NAD-binding and catalytic domains.
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 = 308
Score = 28.5 bits (64), Expect = 3.3
Identities = 11/18 (61%), Positives = 14/18 (77%)
Query: 9 IGINGFGRIGRLVARVAL 26
+GI GFG IG+ +AR AL
Sbjct: 138 LGIVGFGAIGQALARRAL 155
>gnl|CDD|233358 TIGR01327, PGDH, D-3-phosphoglycerate dehydrogenase. This model
represents a long form of D-3-phosphoglycerate
dehydrogenase, the serA gene of one pathway of serine
biosynthesis. Shorter forms, scoring between trusted and
noise cutoff, include SerA from E. coli [Amino acid
biosynthesis, Serine family].
Length = 525
Score = 28.8 bits (65), Expect = 3.3
Identities = 14/35 (40%), Positives = 24/35 (68%), Gaps = 2/35 (5%)
Query: 8 KIGINGFGRIGRLVARVALQRDDVELVAVNDPFIS 42
+G+ G GRIG +VA+ A + ++++A DP+IS
Sbjct: 140 TLGVIGLGRIGSIVAKRA-KAFGMKVLAY-DPYIS 172
>gnl|CDD|240645 cd12168, Mand_dh_like, D-Mandelate Dehydrogenase-like
dehydrogenases. D-Mandelate dehydrogenase (D-ManDH),
identified as an enzyme that interconverts
benzoylformate and D-mandelate, is a D-2-hydroxyacid
dehydrogenase family member that catalyzes the
conversion of c3-branched 2-ketoacids. D-ManDH exhibits
broad substrate specificities for 2-ketoacids with large
hydrophobic side chains, particularly those with
C3-branched side chains. 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. Glycerate dehydrogenase catalyzes the
reaction (R)-glycerate + NAD+ to hydroxypyruvate + NADH
+ H+. 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.
Length = 321
Score = 28.7 bits (65), Expect = 3.3
Identities = 9/18 (50%), Positives = 12/18 (66%)
Query: 8 KIGINGFGRIGRLVARVA 25
+GI G G IG+ +AR A
Sbjct: 156 TLGILGLGGIGKAIARKA 173
>gnl|CDD|235763 PRK06270, PRK06270, homoserine dehydrogenase; Provisional.
Length = 341
Score = 28.7 bits (65), Expect = 3.4
Identities = 12/43 (27%), Positives = 24/43 (55%), Gaps = 9/43 (20%)
Query: 5 KKIKIGINGFGRIGRLVARVALQRD---------DVELVAVND 38
++KI + GFG +G+ VA + ++ D+++VA+ D
Sbjct: 1 MEMKIALIGFGGVGQGVAELLAEKREYLKKRYGLDLKVVAIAD 43
>gnl|CDD|223745 COG0673, MviM, Predicted dehydrogenases and related proteins
[General function prediction only].
Length = 342
Score = 28.3 bits (63), Expect = 3.5
Identities = 15/37 (40%), Positives = 18/37 (48%), Gaps = 2/37 (5%)
Query: 5 KKIKIGINGFGRIGRLVARVALQ--RDDVELVAVNDP 39
K I++GI G G I AL +ELVAV D
Sbjct: 2 KMIRVGIIGAGGIAGKAHLPALAALGGGLELVAVVDR 38
>gnl|CDD|215144 PLN02256, PLN02256, arogenate dehydrogenase.
Length = 304
Score = 28.1 bits (63), Expect = 3.8
Identities = 10/18 (55%), Positives = 14/18 (77%)
Query: 6 KIKIGINGFGRIGRLVAR 23
K+KIGI GFG G+ +A+
Sbjct: 36 KLKIGIVGFGNFGQFLAK 53
>gnl|CDD|233220 TIGR00978, asd_EA, aspartate-semialdehyde dehydrogenase
(non-peptidoglycan organisms). Two closely related
families of aspartate-semialdehyde dehydrogenase are
found. They differ by a deep split in phylogenetic and
percent identity trees and in gap patterns. Separate
models are built for the two types in order to exclude
the USG-1 protein, found in several species, which is
specifically related to the Bacillus subtilis type of
aspartate-semialdehyde dehydrogenase. Members of this
type are found primarily in organisms that lack
peptidoglycan [Amino acid biosynthesis, Aspartate
family].
Length = 341
Score = 28.2 bits (63), Expect = 4.2
Identities = 25/81 (30%), Positives = 38/81 (46%), Gaps = 14/81 (17%)
Query: 121 AKKVVISAPSK-----DAPMFVVGVN---------EKEYKPELDIVSNASCTTNCLAPLA 166
A K V S S D P+ + VN +KE + IV+N +CTT L
Sbjct: 96 AGKPVFSNASNHRMDPDVPLIIPEVNSDHLELLKVQKERGWKGFIVTNPNCTTAGLTLAL 155
Query: 167 KVIHDKFGIVEGLMTTVHSIT 187
K + D FGI + +TT+ +++
Sbjct: 156 KPLIDAFGIKKVHVTTMQAVS 176
>gnl|CDD|223536 COG0460, ThrA, Homoserine dehydrogenase [Amino acid transport and
metabolism].
Length = 333
Score = 27.9 bits (63), Expect = 4.5
Identities = 11/44 (25%), Positives = 21/44 (47%), Gaps = 9/44 (20%)
Query: 4 DKKIKIGINGFGRIGRLVARVALQRD---------DVELVAVND 38
K +K+G+ G G +G V + ++ ++ +VAV D
Sbjct: 1 MKTVKVGLLGLGTVGSGVLEILAEKQEELRKRAGIEIRVVAVAD 44
>gnl|CDD|181414 PRK08410, PRK08410, 2-hydroxyacid dehydrogenase; Provisional.
Length = 311
Score = 28.0 bits (63), Expect = 5.0
Identities = 10/18 (55%), Positives = 13/18 (72%)
Query: 8 KIGINGFGRIGRLVARVA 25
K GI G G IG+ VA++A
Sbjct: 147 KWGIIGLGTIGKRVAKIA 164
>gnl|CDD|176178 cd05188, MDR, Medium chain reductase/dehydrogenase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
The medium chain reductase/dehydrogenases
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH) , quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. ADH-like proteins
typically form dimers (typically higher plants, mammals)
or tetramers (yeast, bacteria), and generally have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. The active site zinc is
coordinated by a histidine, two cysteines, and a water
molecule. The second zinc seems to play a structural
role, affects subunit interactions, and is typically
coordinated by 4 cysteines. Other MDR members have only
a catalytic zinc, and some contain no coordinated zinc.
Length = 271
Score = 27.7 bits (62), Expect = 5.2
Identities = 12/51 (23%), Positives = 22/51 (43%)
Query: 88 EEIPWAKTGAEYVVESTGVFTDKDKAAAHLKGGAKKVVISAPSKDAPMFVV 138
E GA+ V+++ G +A L+ G + VV+ S P+ +
Sbjct: 193 ELRLTGGGGADVVIDAVGGPETLAQALRLLRPGGRIVVVGGTSGGPPLDDL 243
>gnl|CDD|237341 PRK13302, PRK13302, putative L-aspartate dehydrogenase;
Provisional.
Length = 271
Score = 27.5 bits (61), Expect = 6.5
Identities = 16/43 (37%), Positives = 24/43 (55%), Gaps = 5/43 (11%)
Query: 1 MAGDKKIKIGINGFGRIGRLVARVALQRDDVEL----VAVNDP 39
M+ ++++ I G G IG+ +A+ AL R L VAV DP
Sbjct: 1 MSSRPELRVAIAGLGAIGKAIAQ-ALDRGLPGLTLSAVAVRDP 42
>gnl|CDD|235783 PRK06349, PRK06349, homoserine dehydrogenase; Provisional.
Length = 426
Score = 27.7 bits (63), Expect = 7.1
Identities = 11/42 (26%), Positives = 19/42 (45%), Gaps = 11/42 (26%)
Query: 5 KKIKIGINGFGRIGRLVARVALQR----------DDVELVAV 36
K +K+G+ G G +G V R+ L+ +E+ V
Sbjct: 2 KPLKVGLLGLGTVGSGVVRI-LEENAEEIAARAGRPIEIKKV 42
>gnl|CDD|217556 pfam03435, Saccharop_dh, Saccharopine dehydrogenase. This family
comprised of three structural domains that can not be
separated in the linear sequence. In some organisms
this enzyme is found as a bifunctional polypeptide with
lysine ketoglutarate reductase. The saccharopine
dehydrogenase can also function as a saccharopine
reductase.
Length = 380
Score = 27.7 bits (62), Expect = 7.3
Identities = 8/28 (28%), Positives = 15/28 (53%)
Query: 9 IGINGFGRIGRLVARVALQRDDVELVAV 36
+ I G G +G+ VA + + D+E+
Sbjct: 1 VLIIGAGGVGQGVAPLLARHGDLEITVA 28
>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 = 27.2 bits (61), Expect = 8.8
Identities = 9/18 (50%), Positives = 13/18 (72%)
Query: 8 KIGINGFGRIGRLVARVA 25
+GI G+G IGR +AR+
Sbjct: 139 TVGILGYGHIGREIARLL 156
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.319 0.135 0.404
Gapped
Lambda K H
0.267 0.0806 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,821,692
Number of extensions: 1205281
Number of successful extensions: 1259
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1193
Number of HSP's successfully gapped: 92
Length of query: 250
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 155
Effective length of database: 6,723,972
Effective search space: 1042215660
Effective search space used: 1042215660
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 58 (26.0 bits)