RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 019933
(334 letters)
>gnl|CDD|177912 PLN02272, PLN02272, glyceraldehyde-3-phosphate dehydrogenase.
Length = 421
Score = 526 bits (1356), Expect = 0.0
Identities = 241/305 (79%), Positives = 261/305 (85%), Gaps = 10/305 (3%)
Query: 1 MAFSSLLRSTASASLV---RADLTSSPSDRVKGSPTAAFSRNLNTSSIFGTSVPSGSSSS 57
MAFSSLLRS A+A +D +SS SD K S ++ SS S S +SS
Sbjct: 1 MAFSSLLRSAATAPAAAARGSDFSSSSSDPSKVS-------SVGFSSSLSFSGSSSGASS 53
Query: 58 SLQTCAAKGIQPIRATATEIPPTIQKSRSDGNTKVGINGFGRIGRLVLRVAAFRDDVDVV 117
SLQ+C+A+ +QPI+ATATE PP + KS S G TK+GINGFGRIGRLVLR+A RDD++VV
Sbjct: 54 SLQSCSARSVQPIKATATEAPPAVLKSSSSGKTKIGINGFGRIGRLVLRIATSRDDIEVV 113
Query: 118 AVNDPFIDAKYMAYMFKYDSTHGVFKGTINVVDDSTLEINGKLIKVFSKRDPAEIPWGDY 177
AVNDPFIDAKYMAYMFKYDSTHG FKGTINVVDDSTLEINGK IKV SKRDPAEIPWGD+
Sbjct: 114 AVNDPFIDAKYMAYMFKYDSTHGNFKGTINVVDDSTLEINGKQIKVTSKRDPAEIPWGDF 173
Query: 178 GVDYVVESSGVFTTIAKASAHMKGGAKKVVISAPSADAPMFVVGVNEKTYKPNMNIVSNA 237
G +YVVESSGVFTT+ KASAH+KGGAKKVVISAPSADAPMFVVGVNEKTYKPNMNIVSNA
Sbjct: 174 GAEYVVESSGVFTTVEKASAHLKGGAKKVVISAPSADAPMFVVGVNEKTYKPNMNIVSNA 233
Query: 238 SCTTNCLAPLAKVVHEEFGILEGLMTTVHATTATQKTVDGPSMKDWRGGRGASQNIIPSS 297
SCTTNCLAPLAKVVHEEFGILEGLMTTVHATTATQKTVDGPSMKDWRGGRGASQNIIPSS
Sbjct: 234 SCTTNCLAPLAKVVHEEFGILEGLMTTVHATTATQKTVDGPSMKDWRGGRGASQNIIPSS 293
Query: 298 TGAAK 302
TGAAK
Sbjct: 294 TGAAK 298
>gnl|CDD|223135 COG0057, GapA, Glyceraldehyde-3-phosphate
dehydrogenase/erythrose-4-phosphate dehydrogenase
[Carbohydrate transport and metabolism].
Length = 335
Score = 321 bits (826), Expect = e-109
Identities = 128/216 (59%), Positives = 149/216 (68%), Gaps = 6/216 (2%)
Query: 90 TKVGINGFGRIGRLVLRVAAFRD-DVDVVAVNDPFIDAKYMAYMFKYDSTHGVFKGTINV 148
KV INGFGRIGRLV R A RD D++VVA+ND D Y+A++ KYDS HG F G + V
Sbjct: 2 IKVAINGFGRIGRLVARAALERDGDIEVVAINDL-TDPDYLAHLLKYDSVHGRFDGEVEV 60
Query: 149 VDDSTLEINGKLIKVFSKRDPAEIPWGDYGVDYVVESSGVFTTIAKASAHM-KGGAKKVV 207
D L +NGK IKV ++RDPA +PW D GVD VVE +G FT KA H+ GGAKKV+
Sbjct: 61 -KDDALVVNGKGIKVLAERDPANLPWADLGVDIVVECTGKFTGREKAEKHLKAGGAKKVL 119
Query: 208 ISAPSADA-PMFVVGVNEKTYKPNMNIVSNASCTTNCLAPLAKVVHEEFGILEGLMTTVH 266
ISAP D V GVN Y IVSNASCTTNCLAP+AKV+++ FGI +GLMTTVH
Sbjct: 120 ISAPGKDDVATVVYGVNHNYYDAGHTIVSNASCTTNCLAPVAKVLNDAFGIEKGLMTTVH 179
Query: 267 ATTATQKTVDGPSMKDWRGGRGASQNIIPSSTGAAK 302
A T QK VDGP KD R R A+ NIIP+STGAAK
Sbjct: 180 AYTNDQKLVDGPH-KDLRRARAAALNIIPTSTGAAK 214
>gnl|CDD|173322 PTZ00023, PTZ00023, glyceraldehyde-3-phosphate dehydrogenase;
Provisional.
Length = 337
Score = 320 bits (821), Expect = e-108
Identities = 136/216 (62%), Positives = 161/216 (74%), Gaps = 4/216 (1%)
Query: 90 TKVGINGFGRIGRLVLRVAAFRDDVDVVAVNDPFIDAKYMAYMFKYDSTHGVFKGTINVV 149
K+GINGFGRIGRLV R A R+DV+VVA+NDPF+ YM Y+ KYDS HG ++V
Sbjct: 3 VKLGINGFGRIGRLVFRAALEREDVEVVAINDPFMTLDYMCYLLKYDSVHGSLPAEVSVT 62
Query: 150 DDSTLEINGKLIKVFSKRDPAEIPWGDYGVDYVVESSGVFTTIAKASAHMKGGAKKVVIS 209
D L I K + VF ++DPA IPWG GVD V ES+GVF T KA AH+KGGAKKV++S
Sbjct: 63 DG-FLMIGSKKVHVFFEKDPAAIPWGKNGVDVVCESTGVFLTKEKAQAHLKGGAKKVIMS 121
Query: 210 AP-SADAPMFVVGVNEKTYKPNMNIVSNASCTTNCLAPLAKVVHEEFGILEGLMTTVHAT 268
AP D P++V+GVN Y + IVSNASCTTNCLAPLAKVV+++FGI+EGLMTTVHA+
Sbjct: 122 APPKDDTPIYVMGVNHTQYDKSQRIVSNASCTTNCLAPLAKVVNDKFGIVEGLMTTVHAS 181
Query: 269 TATQKTVDGPSM--KDWRGGRGASQNIIPSSTGAAK 302
TA Q TVDGPS KDWR GR A NIIP+STGAAK
Sbjct: 182 TANQLTVDGPSKGGKDWRAGRCAGVNIIPASTGAAK 217
>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 = 313 bits (805), Expect = e-106
Identities = 124/216 (57%), Positives = 150/216 (69%), Gaps = 7/216 (3%)
Query: 91 KVGINGFGRIGRLVLRVAAFRD--DVDVVAVNDPFIDAKYMAYMFKYDSTHGVFKGTINV 148
KVGINGFGRIGRLVLR + D++VVA+ND D +Y+AY+ KYDS HG F+G +
Sbjct: 1 KVGINGFGRIGRLVLRAILEKPGNDLEVVAINDL-TDLEYLAYLLKYDSVHGRFEGEVTA 59
Query: 149 VDDSTLEINGKL-IKVFSKRDPAEIPWGDYGVDYVVESSGVFTTIAKASAHMKGGAKKVV 207
+D L +NGK I VFS+RDP+++PW GVD V+E +G F K H++ GAKKV+
Sbjct: 60 DED-GLVVNGKEVISVFSERDPSDLPWKALGVDIVIECTGKFRDKEKLEGHLEAGAKKVL 118
Query: 208 ISAPSA-DAPMFVVGVNEKTYKPNMNIVSNASCTTNCLAPLAKVVHEEFGILEGLMTTVH 266
ISAPS D V GVN Y P+ IVSNASCTTNCLAPLAKV+ E FGI+ GLMTTVH
Sbjct: 119 ISAPSKGDVKTIVYGVNHDEYDPSERIVSNASCTTNCLAPLAKVLDEAFGIVSGLMTTVH 178
Query: 267 ATTATQKTVDGPSMKDWRGGRGASQNIIPSSTGAAK 302
+ T Q VDGP KD R R A+ NIIP+STGAAK
Sbjct: 179 SYTNDQNLVDGP-HKDLRRARAAALNIIPTSTGAAK 213
>gnl|CDD|165999 PLN02358, PLN02358, glyceraldehyde-3-phosphate dehydrogenase.
Length = 338
Score = 304 bits (779), Expect = e-102
Identities = 154/218 (70%), Positives = 178/218 (81%), Gaps = 1/218 (0%)
Query: 86 SDGNTKVGINGFGRIGRLVLRVAAFRDDVDVVAVNDPFIDAKYMAYMFKYDSTHGVFK-G 144
+D ++GINGFGRIGRLV RV RDDV++VAVNDPFI +YM YMFKYDS HG +K
Sbjct: 2 ADKKIRIGINGFGRIGRLVARVVLQRDDVELVAVNDPFITTEYMTYMFKYDSVHGQWKHH 61
Query: 145 TINVVDDSTLEINGKLIKVFSKRDPAEIPWGDYGVDYVVESSGVFTTIAKASAHMKGGAK 204
+ V DD TL K + VF R+P +IPWG+ G D+VVES+GVFT KA+AH+KGGAK
Sbjct: 62 ELKVKDDKTLLFGEKPVTVFGIRNPEDIPWGEAGADFVVESTGVFTDKDKAAAHLKGGAK 121
Query: 205 KVVISAPSADAPMFVVGVNEKTYKPNMNIVSNASCTTNCLAPLAKVVHEEFGILEGLMTT 264
KVVISAPS DAPMFVVGVNE YK +++IVSNASCTTNCLAPLAKV+++ FGI+EGLMTT
Sbjct: 122 KVVISAPSKDAPMFVVGVNEHEYKSDLDIVSNASCTTNCLAPLAKVINDRFGIVEGLMTT 181
Query: 265 VHATTATQKTVDGPSMKDWRGGRGASQNIIPSSTGAAK 302
VH+ TATQKTVDGPSMKDWRGGR AS NIIPSSTGAAK
Sbjct: 182 VHSITATQKTVDGPSMKDWRGGRAASFNIIPSSTGAAK 219
>gnl|CDD|185323 PRK15425, gapA, glyceraldehyde-3-phosphate dehydrogenase A;
Provisional.
Length = 331
Score = 271 bits (694), Expect = 1e-89
Identities = 141/213 (66%), Positives = 165/213 (77%), Gaps = 4/213 (1%)
Query: 91 KVGINGFGRIGRLVLRVAAFRDDVDVVAVNDPFIDAKYMAYMFKYDSTHGVFKGTINVVD 150
KVGINGFGRIGR+V R A R D+++VA+ND +DA YMAYM KYDSTHG F GT+ V
Sbjct: 4 KVGINGFGRIGRIVFRAAQKRSDIEIVAIND-LLDADYMAYMLKYDSTHGRFDGTVEV-K 61
Query: 151 DSTLEINGKLIKVFSKRDPAEIPWGDYGVDYVVESSGVFTTIAKASAHMKGGAKKVVISA 210
D L +NGK I+V ++RDPA + W + GVD V E++G+F T A H+ GAKKVV++
Sbjct: 62 DGHLIVNGKKIRVTAERDPANLKWDEVGVDVVAEATGLFLTDETARKHITAGAKKVVMTG 121
Query: 211 PSAD-APMFVVGVNEKTYKPNMNIVSNASCTTNCLAPLAKVVHEEFGILEGLMTTVHATT 269
PS D PMFV G N Y +IVSNASCTTNCLAPLAKV+++ FGI+EGLMTTVHATT
Sbjct: 122 PSKDNTPMFVKGANFDKYA-GQDIVSNASCTTNCLAPLAKVINDNFGIIEGLMTTVHATT 180
Query: 270 ATQKTVDGPSMKDWRGGRGASQNIIPSSTGAAK 302
ATQKTVDGPS KDWRGGRGASQNIIPSSTGAAK
Sbjct: 181 ATQKTVDGPSHKDWRGGRGASQNIIPSSTGAAK 213
>gnl|CDD|236079 PRK07729, PRK07729, glyceraldehyde-3-phosphate dehydrogenase;
Validated.
Length = 343
Score = 255 bits (653), Expect = 3e-83
Identities = 106/216 (49%), Positives = 146/216 (67%), Gaps = 5/216 (2%)
Query: 89 NTKVGINGFGRIGRLVLRVAAFRDDVDVVAVNDPFIDAKYMAYMFKYDSTHGVFKGTINV 148
TKV INGFGRIGR+V R A ++VA+N + ++ +A++ KYD+ HG F GT+
Sbjct: 2 KTKVAINGFGRIGRMVFRKAIKESAFEIVAINASY-PSETLAHLIKYDTVHGKFDGTVEA 60
Query: 149 VDDSTLEINGKLIKVFSKRDPAEIPWGDYGVDYVVESSGVFTTIAKASAHMKGGAKKVVI 208
+D L ++GK I++ + RDP E+PW D G+D V+E++G F + KA H++ GAKKV++
Sbjct: 61 FEDH-LLVDGKKIRLLNNRDPKELPWTDLGIDIVIEATGKFNSKEKAILHVEAGAKKVIL 119
Query: 209 SAPSADAPM-FVVGVNEKTYKPNMN-IVSNASCTTNCLAPLAKVVHEEFGILEGLMTTVH 266
+AP + + VVGVNE + I+SNASCTTNCLAP+ KV+ E+FGI GLMTTVH
Sbjct: 120 TAPGKNEDVTIVVGVNEDQLDIEKHTIISNASCTTNCLAPVVKVLDEQFGIENGLMTTVH 179
Query: 267 ATTATQKTVDGPSMKDWRGGRGASQNIIPSSTGAAK 302
A T QK +D P KD R R Q+IIP++TGAAK
Sbjct: 180 AYTNDQKNIDNPH-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 = 243 bits (624), Expect = 2e-81
Identities = 94/150 (62%), Positives = 114/150 (76%), Gaps = 3/150 (2%)
Query: 90 TKVGINGFGRIGRLVLRVAAFRDDVDVVAVNDPFIDAKYMAYMFKYDSTHGVFKGTINVV 149
KVGINGFGRIGRLVLR A +DD++VVA+ND D + +AY+ KYDS HG F G + V
Sbjct: 1 IKVGINGFGRIGRLVLRAALAQDDLEVVAINDLT-DPETLAYLLKYDSVHGRFDGEV-EV 58
Query: 150 DDSTLEINGKLIKVFSKRDPAEIPWGDYGVDYVVESSGVFTTIAKASAHMKGGAKKVVIS 209
D+ L +NGK IKVF++RDPAE+PWG+ GVD VVES+GVFTT KA AH+K GAKKV+IS
Sbjct: 59 DEDGLIVNGKKIKVFAERDPAELPWGELGVDIVVESTGVFTTAEKAEAHLKAGAKKVIIS 118
Query: 210 APSAD-APMFVVGVNEKTYKPNMNIVSNAS 238
AP+ D P FV GVN + Y P +IVSNAS
Sbjct: 119 APAKDDDPTFVYGVNHEDYDPEDDIVSNAS 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 = 243 bits (623), Expect = 2e-81
Identities = 95/151 (62%), Positives = 112/151 (74%), Gaps = 3/151 (1%)
Query: 90 TKVGINGFGRIGRLVLRVAAFRDDVDVVAVNDPFIDAKYMAYMFKYDSTHGVFKGTINVV 149
KVGINGFGRIGRLVLR A R DV+VVA+ND D +Y+AY+ KYDS HG F GT+ V
Sbjct: 1 IKVGINGFGRIGRLVLRAALERPDVEVVAINDL-TDPEYLAYLLKYDSVHGRFPGTVEV- 58
Query: 150 DDSTLEINGKLIKVFSKRDPAEIPWGDYGVDYVVESSGVFTTIAKASAHMKGGAKKVVIS 209
+ L +NGK IKVF++RDPA +PWG+ GVD VVE +G FTT KASAH+K GAKKV+IS
Sbjct: 59 EGDGLVVNGKAIKVFAERDPANLPWGELGVDIVVECTGGFTTREKASAHLKAGAKKVIIS 118
Query: 210 APSADA-PMFVVGVNEKTYKPNMNIVSNASC 239
APS DA P FV GVN Y +I+SNASC
Sbjct: 119 APSKDADPTFVYGVNHDEYDGEDHIISNASC 149
>gnl|CDD|185614 PTZ00434, PTZ00434, cytosolic glyceraldehyde 3-phosphate
dehydrogenase; Provisional.
Length = 361
Score = 245 bits (627), Expect = 3e-79
Identities = 128/227 (56%), Positives = 158/227 (69%), Gaps = 15/227 (6%)
Query: 91 KVGINGFGRIGRLVLRVAAFRD----DVDVVAVNDPFIDAKYMAYMFKYDSTHGVFKGTI 146
KVGINGFGRIGR+V + + ++DVVAV D +A+Y AY KYD+ HG K T+
Sbjct: 5 KVGINGFGRIGRMVFQAICDQGLIGTEIDVVAVVDMSTNAEYFAYQMKYDTVHGRPKYTV 64
Query: 147 -------NVVDDSTLEINGKLIK-VFSKRDPAEIPWGDYGVDYVVESSGVFTTIAKASAH 198
+V D L +NG IK V ++R+PA++PWG GVDYV+ES+G+FT A H
Sbjct: 65 ETTKSSPSVKTDDVLVVNGHRIKCVKAQRNPADLPWGKLGVDYVIESTGLFTDKLAAEGH 124
Query: 199 MKGGAKKVVISAP-SADAPMFVVGVNEKTYKP-NMNIVSNASCTTNCLAPLAKV-VHEEF 255
+KGGAKKVVISAP S A V+GVN+ Y P ++VSNASCTTNCLAP+ V E F
Sbjct: 125 LKGGAKKVVISAPASGGAKTIVMGVNQHEYSPTEHHVVSNASCTTNCLAPIVHVLTKEGF 184
Query: 256 GILEGLMTTVHATTATQKTVDGPSMKDWRGGRGASQNIIPSSTGAAK 302
GI GLMTT+H+ TATQKTVDG S+KDWRGGR A+ NIIPS+TGAAK
Sbjct: 185 GIETGLMTTIHSYTATQKTVDGVSVKDWRGGRAAAVNIIPSTTGAAK 231
>gnl|CDD|215131 PLN02237, PLN02237, glyceraldehyde-3-phosphate dehydrogenase B.
Length = 442
Score = 234 bits (597), Expect = 1e-73
Identities = 129/299 (43%), Positives = 173/299 (57%), Gaps = 15/299 (5%)
Query: 9 STASASLVRADLTSSPSDRVKGSPTAAFSRNLNTSSIFGTSVPSGSSSSSLQTCAAKGIQ 68
+ ++S + A K A FS L SS + + +S A +
Sbjct: 3 AALASSRIPATTRLPSKASHKRLEVAEFS-GLRASSCVTFAKNA--REASFFDVVASQLA 59
Query: 69 PIRATATEIPPTIQKSRSDGNTKVGINGFGRIGRLVLRVAAFRDD--VDVVAVNDPFIDA 126
P A +T + + + KV INGFGRIGR LR R D +DVV VND
Sbjct: 60 PKVAGSTPV-----RGETVAKLKVAINGFGRIGRNFLRCWHGRKDSPLDVVVVNDSG-GV 113
Query: 127 KYMAYMFKYDSTHGVFKGTINVVDDSTLEINGKLIKVFSKRDPAEIPWGDYGVDYVVESS 186
K +++ KYDS G FK + +VDD T+ ++GK IKV S RDP ++PW + G+D V+E +
Sbjct: 114 KNASHLLKYDSMLGTFKADVKIVDDETISVDGKPIKVVSNRDPLKLPWAELGIDIVIEGT 173
Query: 187 GVFTTIAKASAHMKGGAKKVVISAPS--ADAPMFVVGVNEKTYKPNM-NIVSNASCTTNC 243
GVF A H++ GAKKV+I+AP+ AD P +VVGVNE Y + NIVSNASCTTNC
Sbjct: 174 GVFVDGPGAGKHIQAGAKKVIITAPAKGADIPTYVVGVNEDDYDHEVANIVSNASCTTNC 233
Query: 244 LAPLAKVVHEEFGILEGLMTTVHATTATQKTVDGPSMKDWRGGRGASQNIIPSSTGAAK 302
LAP KV+ EEFGI++G MTT H+ T Q+ +D S +D R R A+ NI+P+STGAAK
Sbjct: 234 LAPFVKVLDEEFGIVKGTMTTTHSYTGDQRLLDA-SHRDLRRARAAALNIVPTSTGAAK 291
>gnl|CDD|215572 PLN03096, PLN03096, glyceraldehyde-3-phosphate dehydrogenase A;
Provisional.
Length = 395
Score = 231 bits (591), Expect = 2e-73
Identities = 118/285 (41%), Positives = 160/285 (56%), Gaps = 16/285 (5%)
Query: 21 TSSPSDRVKGSPTAAFSRNLNTSSIFGTSVPSGSSSSSLQTCAAKGIQPIRATATEIPPT 80
+ PS + + FS ++S++ T A R TE
Sbjct: 3 AAKPSLQAGSKGFSEFSGLKSSSAVTFGKRSDSLDFVVFATSAVSSSGGARRAVTE---- 58
Query: 81 IQKSRSDGNTKVGINGFGRIGRLVLRVAAFRDD--VDVVAVNDPFIDAKYMAYMFKYDST 138
KV INGFGRIGR LR R D +DVVA+ND K +++ KYDST
Sbjct: 59 -------AKIKVAINGFGRIGRNFLRCWHGRKDSPLDVVAINDTG-GVKQASHLLKYDST 110
Query: 139 HGVFKGTINVVDDSTLEINGKLIKVFSKRDPAEIPWGDYGVDYVVESSGVFTTIAKASAH 198
G F + V D + ++GK+IKV S R+P +PWG+ G+D V+E +GVF A H
Sbjct: 111 LGTFDADVKPVGDDAISVDGKVIKVVSDRNPLNLPWGELGIDLVIEGTGVFVDREGAGKH 170
Query: 199 MKGGAKKVVISAPS-ADAPMFVVGVNEKTYKPNMNIVSNASCTTNCLAPLAKVVHEEFGI 257
++ GAKKV+I+AP D P +VVGVN YK + I+SNASCTTNCLAP KV+ ++FGI
Sbjct: 171 IQAGAKKVLITAPGKGDIPTYVVGVNADDYKHSDPIISNASCTTNCLAPFVKVLDQKFGI 230
Query: 258 LEGLMTTVHATTATQKTVDGPSMKDWRGGRGASQNIIPSSTGAAK 302
++G MTT H+ T Q+ +D S +D R R A+ NI+P+STGAAK
Sbjct: 231 IKGTMTTTHSYTGDQRLLDA-SHRDLRRARAAALNIVPTSTGAAK 274
>gnl|CDD|180962 PRK07403, PRK07403, glyceraldehyde-3-phosphate dehydrogenase;
Reviewed.
Length = 337
Score = 215 bits (549), Expect = 7e-68
Identities = 105/218 (48%), Positives = 147/218 (67%), Gaps = 8/218 (3%)
Query: 90 TKVGINGFGRIGRLVLRVAAFRDD--VDVVAVNDPFIDAKYMAYMFKYDSTHGVFKGTIN 147
+V INGFGRIGR LR R++ +++VA+ND D + A++ KYDS G I+
Sbjct: 2 IRVAINGFGRIGRNFLRCWLGRENSQLELVAINDT-SDPRTNAHLLKYDSMLGKLNADIS 60
Query: 148 VVDDSTLEINGKLIKVFSKRDPAEIPWGDYGVDYVVESSGVFTTIAKASAHMKGGAKKVV 207
D++++ +NGK IK S R+P +PW ++G+D ++ES+GVF T AS H++ GAKKV+
Sbjct: 61 A-DENSITVNGKTIKCVSDRNPLNLPWKEWGIDLIIESTGVFVTKEGASKHIQAGAKKVL 119
Query: 208 ISAP--SADAPMFVVGVNEKTYKPNM-NIVSNASCTTNCLAPLAKVVHEEFGILEGLMTT 264
I+AP D +VVGVN Y NI+SNASCTTNCLAP+AKV+H+ FGI++G MTT
Sbjct: 120 ITAPGKGEDIGTYVVGVNHHEYDHEDHNIISNASCTTNCLAPIAKVLHDNFGIIKGTMTT 179
Query: 265 VHATTATQKTVDGPSMKDWRGGRGASQNIIPSSTGAAK 302
H+ T Q+ +D S +D R R A+ NI+P+STGAAK
Sbjct: 180 THSYTGDQRILDA-SHRDLRRARAAAVNIVPTSTGAAK 216
>gnl|CDD|169599 PRK08955, PRK08955, glyceraldehyde-3-phosphate dehydrogenase;
Validated.
Length = 334
Score = 194 bits (494), Expect = 1e-59
Identities = 92/215 (42%), Positives = 133/215 (61%), Gaps = 7/215 (3%)
Query: 91 KVGINGFGRIGRLVLRVAAFRDDVDVVAVNDPFIDAKYMAYMFKYDSTHGVFKGTINVVD 150
KVGINGFGRIGRL LR A +++ V +NDP DA +A++ ++DS HG + + +
Sbjct: 4 KVGINGFGRIGRLALRAAWDWPELEFVQINDPAGDAATLAHLLEFDSVHGRWHHEV-TAE 62
Query: 151 DSTLEINGKLIKVFSKRDPAEIPWGDYGVDYVVESSGVFTTIAKASAHMKGGAKKVVISA 210
+ INGK I+ + A+ W G D V+E+SGV T A A++ G K+VV++A
Sbjct: 63 GDAIVINGKRIRTTQNKAIADTDWS--GCDVVIEASGVMKTKALLQAYLDQGVKRVVVTA 120
Query: 211 PSADAPMF--VVGVNEKTYKPNMN-IVSNASCTTNCLAPLAKVVHEEFGILEGLMTTVHA 267
P + + V+GVN+ + P ++ IV+ ASCTTNCLAP+ KV+HE+ GI G MTT+H
Sbjct: 121 PVKEEGVLNIVMGVNDHLFDPAIHPIVTAASCTTNCLAPVVKVIHEKLGIKHGSMTTIHD 180
Query: 268 TTATQKTVDGPSMKDWRGGRGASQNIIPSSTGAAK 302
T TQ +D P KD R R ++IP++TG+A
Sbjct: 181 LTNTQTILDAPH-KDLRRARACGMSLIPTTTGSAT 214
>gnl|CDD|184122 PRK13535, PRK13535, erythrose 4-phosphate dehydrogenase;
Provisional.
Length = 336
Score = 190 bits (485), Expect = 3e-58
Identities = 94/229 (41%), Positives = 134/229 (58%), Gaps = 11/229 (4%)
Query: 91 KVGINGFGRIGRLVLRV---AAFRDDVDVVAVNDPFIDAKYMAYMFKYDSTHGVFKGTIN 147
+V INGFGRIGR VLR + R ++ VVA+N+ DA+ MA++ KYD++HG F +
Sbjct: 3 RVAINGFGRIGRNVLRALYESGRRAEITVVAINE-LADAEGMAHLLKYDTSHGRFAWDVR 61
Query: 148 VVDDSTLEINGKLIKVFSKRDPAEIPWGDYGVDYVVESSGVFTTIAKASAHMKGGAKKVV 207
D L + I++ +RD A +PW + GVD V++ +GV+ + AH+ GAKKV+
Sbjct: 62 QERDQ-LFVGDDAIRLLHERDIASLPWRELGVDVVLDCTGVYGSREDGEAHIAAGAKKVL 120
Query: 208 ISAPSA---DAPMFVVGVNEKTYKPNMNIVSNASCTTNCLAPLAKVVHEEFGILEGLMTT 264
S P + DA + V GVN + IVSNASCTTNC+ P+ K++ + FGI G +TT
Sbjct: 121 FSHPGSNDLDATV-VYGVNHDQLRAEHRIVSNASCTTNCIIPVIKLLDDAFGIESGTVTT 179
Query: 265 VHATTATQKTVDGPSMKDWRGGRGASQNIIPSSTGAAKVKYR-YPVFAD 312
+H+ Q+ +D D R R ASQ+IIP T A R +P F D
Sbjct: 180 IHSAMNDQQVIDA-YHPDLRRTRAASQSIIPVDTKLAAGITRIFPQFND 227
>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 = 183 bits (466), Expect = 1e-55
Identities = 93/229 (40%), Positives = 132/229 (57%), Gaps = 11/229 (4%)
Query: 91 KVGINGFGRIGRLVLRV---AAFRDDVDVVAVNDPFIDAKYMAYMFKYDSTHGVFKGTIN 147
+V INGFGRIGR VLR + R ++ VVA+N+ DA MA++ KYD++HG F +
Sbjct: 1 RVAINGFGRIGRNVLRALYESGRRAEITVVAINE-LADAAGMAHLLKYDTSHGRFAWEVR 59
Query: 148 VVDDSTLEINGKLIKVFSKRDPAEIPWGDYGVDYVVESSGVFTTIAKASAHMKGGAKKVV 207
D L + I+V +R +PW + GVD V++ +GV+ + AH+ GAKKV+
Sbjct: 60 Q-DRDQLFVGDDAIRVLHERSLQSLPWRELGVDLVLDCTGVYGSREHGEAHIAAGAKKVL 118
Query: 208 ISAPSA---DAPMFVVGVNEKTYKPNMNIVSNASCTTNCLAPLAKVVHEEFGILEGLMTT 264
S P A DA + V GVN+ + IVSNASCTTNC+ P+ K++ + +GI G +TT
Sbjct: 119 FSHPGASDLDATI-VYGVNQDQLRAEHRIVSNASCTTNCIVPVIKLLDDAYGIESGTITT 177
Query: 265 VHATTATQKTVDGPSMKDWRGGRGASQNIIPSSTGAAKVKYR-YPVFAD 312
+H+ Q+ +D D R R ASQ+IIP T A R +P F D
Sbjct: 178 IHSAMNDQQVIDA-YHPDLRRTRAASQSIIPVDTKLAAGIERFFPQFND 225
>gnl|CDD|236219 PRK08289, PRK08289, glyceraldehyde-3-phosphate dehydrogenase;
Reviewed.
Length = 477
Score = 147 bits (373), Expect = 2e-40
Identities = 80/225 (35%), Positives = 114/225 (50%), Gaps = 25/225 (11%)
Query: 96 GFGRIGRLV-------------LRVAAFRDDVDVVAVNDPFIDAKYMAYMFKYDSTHGVF 142
GFGRIGRL+ LR+ A VV K A + + DS HG F
Sbjct: 134 GFGRIGRLLARLLIEKTGGGNGLRLRAI-----VVRKGSEGDLEK-RASLLRRDSVHGPF 187
Query: 143 KGTINV-VDDSTLEINGKLIKVFSKRDPAEIPWGDYGVD--YVVESSGVFTTIAKASAHM 199
GTI V +++ + NG I+V P E+ + YG++ VV+++G + S H+
Sbjct: 188 NGTITVDEENNAIIANGNYIQVIYANSPEEVDYTAYGINNALVVDNTGKWRDEEGLSQHL 247
Query: 200 KG-GAKKVVISAPS-ADAPMFVVGVNEKTYKPNMNIVSNASCTTNCLAPLAKVVHEEFGI 257
K G KV+++AP D V GVN IVS ASCTTN + P+ K V++++GI
Sbjct: 248 KSKGVAKVLLTAPGKGDIKNIVHGVNHSDITDEDKIVSAASCTTNAITPVLKAVNDKYGI 307
Query: 258 LEGLMTTVHATTATQKTVDGPSMKDWRGGRGASQNIIPSSTGAAK 302
+ G + TVH+ T Q +D D R GR A N++ + TGAAK
Sbjct: 308 VNGHVETVHSYTNDQNLIDNYHKGD-RRGRSAPLNMVITETGAAK 351
>gnl|CDD|173546 PTZ00353, PTZ00353, glycosomal glyceraldehyde-3-phosphate
dehydrogenase; Provisional.
Length = 342
Score = 129 bits (327), Expect = 5e-35
Identities = 72/213 (33%), Positives = 111/213 (52%), Gaps = 2/213 (0%)
Query: 92 VGINGFGRIGRLVLRVAAFRDDVDVVAVNDPFIDAKYMAYMFKYDSTHGVFKGT-INVVD 150
VGINGFG +G+ VL + V VVAVND + Y+AY+ + +S G I VV
Sbjct: 5 VGINGFGPVGKAVLFASLTDPLVTVVAVNDASVSIAYIAYVLEQESPLSAPDGASIRVVG 64
Query: 151 DSTLEINGKLIKVFSKRDPAEIPWGDYGVDYVVESSGVFTTIAKASAHMKGGAKKVVISA 210
+ + + I+V +K D EI W DYGV YVVE +G+++T ++ H+ GGAK V ++
Sbjct: 65 EQIVLNGTQKIRVSAKHDLVEIAWRDYGVQYVVECTGLYSTRSRCWGHVTGGAKGVFVAG 124
Query: 211 PSADAPMFVVGVNEKTYKPNMNIVSNASCTTNCLAPLAKVVHEEFGILEGLMTTVHATTA 270
SADAP + G N++ ++ + + LAP+ + +HE +G+ E T +H
Sbjct: 125 QSADAPTVMAGSNDERLSASLPVCCAGAPIAVALAPVIRALHEVYGVEECSYTAIHGMQP 184
Query: 271 TQKT-VDGPSMKDWRGGRGASQNIIPSSTGAAK 302
+ + +DWR R A I P A+
Sbjct: 185 QEPIAARSKNSQDWRQTRVAIDAIAPYRDNGAE 217
>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 = 107 bits (269), Expect = 3e-28
Identities = 42/59 (71%), Positives = 48/59 (81%), Gaps = 1/59 (1%)
Query: 244 LAPLAKVVHEEFGILEGLMTTVHATTATQKTVDGPSMKDWRGGRGASQNIIPSSTGAAK 302
LAPLAKV+++ FGI +GLMTTVHA TA QK VD PS KD R GR A+ NIIP+STGAAK
Sbjct: 1 LAPLAKVLNDNFGIEKGLMTTVHAYTADQKLVD-PSHKDLRRGRAAAPNIIPTSTGAAK 58
>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 = 44.1 bits (105), Expect = 5e-05
Identities = 25/76 (32%), Positives = 32/76 (42%), Gaps = 8/76 (10%)
Query: 62 CAAKGIQP----IRATATEIPPTIQKSRSDGNTKVGINGFGRIGRLVLR-VAAFRDDVDV 116
A + I RA PT + R VGI GFGRIGR V+ + F
Sbjct: 119 LALRRIPRFAAAYRAGRDWGWPTRRGGRGLYGRTVGIVGFGRIGRAVVELLRPFGLR--- 175
Query: 117 VAVNDPFIDAKYMAYM 132
V V DP++ A A +
Sbjct: 176 VLVYDPYLPAAEAAAL 191
>gnl|CDD|223214 COG0136, Asd, Aspartate-semialdehyde dehydrogenase [Amino acid
transport and metabolism].
Length = 334
Score = 43.8 bits (104), Expect = 6e-05
Identities = 28/100 (28%), Positives = 42/100 (42%), Gaps = 15/100 (15%)
Query: 178 GVDYVVESSGVFTTIAKASAHMKGGAKKVVISAPSA-----DAPMFVVGVNEKT---YKP 229
VD V ++G + + G VVI SA D P+ V VN + Y+
Sbjct: 66 DVDIVFFAAGGSVSKEVEPKAAEAGC--VVIDNSSAFRMDPDVPLVVPEVNPEHLIDYQK 123
Query: 230 NMNIVSNASCTTNCLAPLAKVVHEEFGILEGLMTTVHATT 269
I++N +C+T L K +H+ FGI V +T
Sbjct: 124 RGFIIANPNCSTIQLVLALKPLHDAFGI-----KRVVVST 158
>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 = 43.3 bits (103), Expect = 8e-05
Identities = 20/50 (40%), Positives = 25/50 (50%), Gaps = 5/50 (10%)
Query: 85 RSDGNTKVGINGFGRIGRLV-LRVAAFRDDVDVVAVNDPFIDAKYMAYMF 133
R G T +G+ GFGRIGR V R AF V+A DP++ A
Sbjct: 139 RLRGLT-LGLVGFGRIGRAVAKRAKAF--GFRVIA-YDPYVPDGVAALGG 184
>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 = 38.6 bits (91), Expect = 0.001
Identities = 20/54 (37%), Positives = 26/54 (48%), Gaps = 4/54 (7%)
Query: 91 KVGINGFGRIGRLVLRVA-AFRDDVDVVAVNDPFIDAKYMAYMFKYDSTHGVFK 143
VGI G GRIGR V R AF + V+A D + A+ A +Y S +
Sbjct: 37 TVGIIGLGRIGRAVARRLKAF--GMKVIAY-DRYPKAEAEALGARYVSLDELLA 87
>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 = 39.4 bits (92), Expect = 0.002
Identities = 27/97 (27%), Positives = 45/97 (46%), Gaps = 9/97 (9%)
Query: 178 GVDYVVESSGVFTTIAKASAHMKGGAKKVVISAPSA-----DAPMFVVGVNEKTYK--PN 230
G+D + S+G + A K G +VI SA D P+ V VN + K
Sbjct: 61 GIDIALFSAGGSVSKEFAPKAAKAGV--IVIDNTSAFRMDPDVPLVVPEVNFEDLKEFNP 118
Query: 231 MNIVSNASCTTNCLAPLAKVVHEEFGILEGLMTTVHA 267
I++N +C+T + + K +H+E I +++T A
Sbjct: 119 KGIIANPNCSTIQMVVVLKPLHDEAKIKRVVVSTYQA 155
>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 = 37.1 bits (87), Expect = 0.008
Identities = 15/39 (38%), Positives = 24/39 (61%), Gaps = 4/39 (10%)
Query: 91 KVGINGFGRIGRLV-LRVAAFRDDVDVVAVNDPFIDAKY 128
+GI G GRIG+ V R++ F + V+A DP+ D ++
Sbjct: 144 TLGIIGLGRIGKAVARRLSGF--GMKVLA-YDPYPDEEF 179
>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 = 36.9 bits (86), Expect = 0.010
Identities = 13/51 (25%), Positives = 24/51 (47%)
Query: 170 AEIPWGDYGVDYVVESSGVFTTIAKASAHMKGGAKKVVISAPSADAPMFVV 220
G G D V+++ G T+A+A ++ G + VV+ S P+ +
Sbjct: 193 ELRLTGGGGADVVIDAVGGPETLAQALRLLRPGGRIVVVGGTSGGPPLDDL 243
>gnl|CDD|237845 PRK14874, PRK14874, aspartate-semialdehyde dehydrogenase;
Provisional.
Length = 334
Score = 36.7 bits (86), Expect = 0.014
Identities = 32/115 (27%), Positives = 49/115 (42%), Gaps = 18/115 (15%)
Query: 152 STLEINGKLIKV--FSKRDPAEIPWGDYGVDYVVESSGVFTTIAKASAHMKGGAKKVVIS 209
L GK +KV + D + GVD + S+G +++K A A VVI
Sbjct: 42 KELSFKGKELKVEDLTTFDFS-------GVDIALFSAG--GSVSKKYAPKAAAAGAVVID 92
Query: 210 APSA-----DAPMFVVGVNEKTYK--PNMNIVSNASCTTNCLAPLAKVVHEEFGI 257
SA D P+ V VN + I++N +C+T + K +H+ GI
Sbjct: 93 NSSAFRMDPDVPLVVPEVNPEALAEHRKKGIIANPNCSTIQMVVALKPLHDAAGI 147
>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 = 36.0 bits (84), Expect = 0.019
Identities = 16/37 (43%), Positives = 21/37 (56%), Gaps = 4/37 (10%)
Query: 91 KVGINGFGRIGRLVLRVA-AFRDDVDVVAVNDPFIDA 126
VGI GFG IGR V + AF +V+ DP++D
Sbjct: 149 TVGIVGFGAIGRRVAKRLKAF--GAEVLVY-DPYVDP 182
>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 = 36.0 bits (84), Expect = 0.022
Identities = 18/49 (36%), Positives = 23/49 (46%), Gaps = 4/49 (8%)
Query: 79 PTIQKSRSDGNTKVGINGFGRIGR-LVLRVAAFRDDVDVVAVNDPFIDA 126
P + SR VGI G G IGR + R+ F V+V+ D F D
Sbjct: 132 PEGRPSRELSGKTVGIVGLGNIGRAVARRLRGF--GVEVIYY-DRFRDP 177
>gnl|CDD|181499 PRK08605, PRK08605, D-lactate dehydrogenase; Validated.
Length = 332
Score = 35.9 bits (83), Expect = 0.024
Identities = 24/54 (44%), Positives = 30/54 (55%), Gaps = 2/54 (3%)
Query: 79 PTIQKSRSDGNTKVGINGFGRIGRLVLRVAAFRDDVDVVAVNDPFIDAKYMAYM 132
P I SRS + KV + G GRIG V ++ A DVVA DPF +AK Y+
Sbjct: 137 PPI-LSRSIKDLKVAVIGTGRIGLAVAKIFAKGYGSDVVAY-DPFPNAKAATYV 188
>gnl|CDD|237436 PRK13581, PRK13581, D-3-phosphoglycerate dehydrogenase;
Provisional.
Length = 526
Score = 35.4 bits (83), Expect = 0.035
Identities = 16/36 (44%), Positives = 20/36 (55%), Gaps = 4/36 (11%)
Query: 92 VGINGFGRIGRLV-LRVAAFRDDVDVVAVNDPFIDA 126
+GI G GRIG V R AF + V+A DP+I
Sbjct: 143 LGIIGLGRIGSEVAKRAKAF--GMKVIA-YDPYISP 175
>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 = 35.1 bits (82), Expect = 0.036
Identities = 19/36 (52%), Positives = 23/36 (63%), Gaps = 4/36 (11%)
Query: 92 VGINGFGRIGRLVLRVA-AFRDDVDVVAVNDPFIDA 126
+GI G GRIGR V R A AF + V+A DP+I A
Sbjct: 141 LGIVGLGRIGREVARRARAF--GMKVLA-YDPYISA 173
>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 = 35.0 bits (81), Expect = 0.041
Identities = 20/53 (37%), Positives = 28/53 (52%), Gaps = 4/53 (7%)
Query: 92 VGINGFGRIGRLVLRVA-AFRDDVDVVAVNDPFIDAKYMAYMFKYDSTHGVFK 143
VG+ G G+IGR V + A F + V+A DPF + + KY S +FK
Sbjct: 146 VGVVGTGKIGRAVAQRAKGF--GMKVIAY-DPFRNPELEDKGVKYVSLEELFK 195
>gnl|CDD|176188 cd05285, sorbitol_DH, Sorbitol dehydrogenase. Sorbitol and aldose
reductase are NAD(+) binding proteins of the polyol
pathway, which interconverts glucose and fructose.
Sorbitol dehydrogenase is tetrameric and has a single
catalytic zinc per subunit. Aldose reductase catalyzes
the NADP(H)-dependent conversion of glucose to sorbital,
and SDH uses NAD(H) in the conversion of sorbitol to
fructose. NAD(P)(H)-dependent oxidoreductases are the
major enzymes in the interconversion of alcohols and
aldehydes, or ketones. The medium chain alcohol
dehydrogenase family (MDR) have a NAD(P)(H)-binding
domain in a Rossmann fold of a beta-alpha form. The
N-terminal region typically has an all-beta catalytic
domain. These proteins typically form dimers (typically
higher plants, mammals) or tetramers (yeast, bacteria),
and have 2 tightly bound zinc atoms per subunit.
Length = 343
Score = 33.6 bits (78), Expect = 0.10
Identities = 34/140 (24%), Positives = 55/140 (39%), Gaps = 26/140 (18%)
Query: 90 TKVGINGFGRIGRLVLRVA-AF-RDDVDVVAVNDPFID-AKYMAYMFKYDSTHGVFKGTI 146
V + G G IG L VA AF V V ++ ++ AK + +TH T+
Sbjct: 164 DTVLVFGAGPIGLLTAAVAKAFGATKVVVTDIDPSRLEFAK------ELGATH-----TV 212
Query: 147 NVVDDSTLEINGKLIKVFSKRDPAEIPWGDYGVDYVVESSGVFTTIAKASAHMKGGAKKV 206
NV + T E K+ ++ G G D V+E +G + I A + G V
Sbjct: 213 NVRTEDTPESAEKIAELL----------GGKGPDVVIECTGAESCIQTAIYATRPGGTVV 262
Query: 207 VISAPSADA--PMFVVGVNE 224
++ + P+ + E
Sbjct: 263 LVGMGKPEVTLPLSAASLRE 282
>gnl|CDD|223189 COG0111, SerA, Phosphoglycerate dehydrogenase and related
dehydrogenases [Amino acid transport and metabolism].
Length = 324
Score = 33.8 bits (78), Expect = 0.11
Identities = 15/35 (42%), Positives = 19/35 (54%), Gaps = 4/35 (11%)
Query: 91 KVGINGFGRIGRLVLRVA-AFRDDVDVVAVNDPFI 124
VGI G GRIGR V + AF + V+ DP+
Sbjct: 144 TVGIIGLGRIGRAVAKRLKAF--GMKVIGY-DPYS 175
>gnl|CDD|179786 PRK04207, PRK04207, glyceraldehyde-3-phosphate dehydrogenase;
Provisional.
Length = 341
Score = 33.3 bits (77), Expect = 0.14
Identities = 15/32 (46%), Positives = 22/32 (68%), Gaps = 6/32 (18%)
Query: 91 KVGINGFGRIGRLVLRVA---AFRDDVDVVAV 119
KVG+NG+G IG+ RVA A + D+++V V
Sbjct: 3 KVGVNGYGTIGK---RVADAVAAQPDMELVGV 31
>gnl|CDD|215721 pfam00107, ADH_zinc_N, Zinc-binding dehydrogenase.
Length = 131
Score = 31.9 bits (73), Expect = 0.19
Identities = 15/57 (26%), Positives = 26/57 (45%), Gaps = 3/57 (5%)
Query: 175 GDYGVDYVVESSGVFTTIAKASAHMKGGAKKVVISAPS---ADAPMFVVGVNEKTYK 228
G GVD V++ G T+ +A ++ G + VV+ P P+ + + E T
Sbjct: 56 GGRGVDVVIDCVGAPATLEQALELLRPGGRVVVVGLPGGAPVPFPLRDLLLKELTIL 112
>gnl|CDD|223946 COG1014, PorG, Pyruvate:ferredoxin oxidoreductase and related
2-oxoacid:ferredoxin oxidoreductases, gamma subunit
[Energy production and conversion].
Length = 203
Score = 31.6 bits (72), Expect = 0.34
Identities = 12/84 (14%), Positives = 26/84 (30%), Gaps = 8/84 (9%)
Query: 99 RIGRLVLRVAAFRDDVDVVAVNDPFIDAKYMAYMFKYDSTHGVFKGTINVVDDSTLEING 158
RI +R + DVV DP + + ++D G + +++ +
Sbjct: 54 RISDEPIRPRSLIGQADVVIALDP-------SELERHDVLLKKEGGLV-ILNTDLINPVL 105
Query: 159 KLIKVFSKRDPAEIPWGDYGVDYV 182
+ + E Y +
Sbjct: 106 EKEPEEVYKFLEEKGAKVYVIPAT 129
>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 = 30.6 bits (70), Expect = 0.35
Identities = 14/33 (42%), Positives = 21/33 (63%), Gaps = 1/33 (3%)
Query: 91 KVGINGFGRIGRLVLR-VAAFRDDVDVVAVNDP 122
+VGI G G+IGR LR + +D ++V + DP
Sbjct: 2 RVGIVGAGKIGRRHLRALNESQDGAELVGILDP 34
>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 = 30.3 bits (69), Expect = 0.49
Identities = 10/31 (32%), Positives = 17/31 (54%), Gaps = 1/31 (3%)
Query: 90 TKVGINGF-GRIGRLVLRVAAFRDDVDVVAV 119
KV + G GR+GR +++ D ++VA
Sbjct: 1 IKVAVVGASGRMGRELIKAILEAPDFELVAA 31
>gnl|CDD|223366 COG0289, DapB, Dihydrodipicolinate reductase [Amino acid transport
and metabolism].
Length = 266
Score = 31.1 bits (71), Expect = 0.67
Identities = 11/30 (36%), Positives = 18/30 (60%), Gaps = 1/30 (3%)
Query: 91 KVGINGF-GRIGRLVLRVAAFRDDVDVVAV 119
KV + G GR+GR ++R D+++VA
Sbjct: 4 KVAVAGASGRMGRTLIRAVLEAPDLELVAA 33
>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 = 30.9 bits (71), Expect = 0.81
Identities = 13/28 (46%), Positives = 17/28 (60%), Gaps = 1/28 (3%)
Query: 84 SRSDGNTKVGINGFGRIGRLVL-RVAAF 110
+R +VGI G GRIGR + R+ AF
Sbjct: 136 TRKVSGKRVGIVGLGRIGRAIARRLEAF 163
>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 = 1.1
Identities = 15/37 (40%), Positives = 21/37 (56%), Gaps = 4/37 (10%)
Query: 92 VGINGFGRIGRLVLRVA-AFRDDVDVVAVNDPFIDAK 127
+G+ G GRIGR V R+A F + V+A D D +
Sbjct: 142 LGVVGTGRIGRRVARIARGFG--MKVLAY-DVVPDEE 175
>gnl|CDD|181041 PRK07574, PRK07574, formate dehydrogenase; Provisional.
Length = 385
Score = 30.4 bits (69), Expect = 1.2
Identities = 11/16 (68%), Positives = 11/16 (68%)
Query: 91 KVGINGFGRIGRLVLR 106
VGI G GRIG VLR
Sbjct: 194 TVGIVGAGRIGLAVLR 209
>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 = 1.3
Identities = 12/31 (38%), Positives = 17/31 (54%), Gaps = 3/31 (9%)
Query: 91 KVGINGFGRIGRLVLRVA-AFRDDVDVVAVN 120
VGI G GRIG+ V + AF + V+ +
Sbjct: 142 TVGIVGLGRIGQRVAKRLQAF--GMKVLYYD 170
>gnl|CDD|215540 PLN03010, PLN03010, polygalacturonase.
Length = 409
Score = 30.3 bits (68), Expect = 1.3
Identities = 16/55 (29%), Positives = 28/55 (50%), Gaps = 3/55 (5%)
Query: 259 EGLMTTVHATTAT-QKTVDGPSMKDWRGGRGASQNIIPSSTGAAKVKYRYPVFAD 312
++ VH T T +T +G +K W+GG+G ++NI S + + P+ D
Sbjct: 265 NAKVSDVHVTHCTFNQTTNGARIKTWQGGQGYARNI--SFENITLINTKNPIIID 317
>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 = 30.2 bits (69), Expect = 1.5
Identities = 13/37 (35%), Positives = 20/37 (54%), Gaps = 2/37 (5%)
Query: 91 KVGINGFGRIGRLVLRVAAFRDDVDVVAVNDPFIDAK 127
+G+ G G IGRLV AA + V+ DP++ +
Sbjct: 137 TLGVIGLGNIGRLVAN-AALALGMKVIGY-DPYLSVE 171
>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 = 30.0 bits (68), Expect = 1.7
Identities = 19/60 (31%), Positives = 27/60 (45%), Gaps = 4/60 (6%)
Query: 62 CAAKGIQPIRATATEIPPTIQKSRSDGNTKVGINGFGRIGRLVLRVA-AFRDDVDVVAVN 120
AAK + I E G+T +GI GFG IG+ + R A A + V+A+
Sbjct: 109 AAAKRLPEIWVKGAEQWRREPLGSLAGST-LGIVGFGAIGQALARRALAL--GMRVLALR 165
>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 = 29.8 bits (67), Expect = 1.8
Identities = 22/79 (27%), Positives = 37/79 (46%), Gaps = 4/79 (5%)
Query: 92 VGINGFGRIGRLVLRVAAFRDDVDVVAV--NDPFIDAKYMAYMFKYDSTHGVFKGTINVV 149
VG+NG+G IG+ V +DD+ +V V P +A Y A + + I
Sbjct: 1 VGVNGYGTIGKRVADAVTKQDDMKLVGVTKTSPDFEA-YRAKELGIP-VYAASEEFIPRF 58
Query: 150 DDSTLEINGKLIKVFSKRD 168
+++ +E+ G L + K D
Sbjct: 59 EEAGIEVAGTLEDLLEKVD 77
>gnl|CDD|234595 PRK00048, PRK00048, dihydrodipicolinate reductase; Provisional.
Length = 257
Score = 29.7 bits (68), Expect = 1.8
Identities = 10/31 (32%), Positives = 18/31 (58%), Gaps = 1/31 (3%)
Query: 90 TKVGINGF-GRIGRLVLRVAAFRDDVDVVAV 119
KV + G GR+GR ++ +D+++VA
Sbjct: 2 IKVAVAGASGRMGRELIEAVEAAEDLELVAA 32
>gnl|CDD|223991 COG1063, Tdh, Threonine dehydrogenase and related Zn-dependent
dehydrogenases [Amino acid transport and metabolism /
General function prediction only].
Length = 350
Score = 29.7 bits (67), Expect = 2.1
Identities = 25/131 (19%), Positives = 45/131 (34%), Gaps = 20/131 (15%)
Query: 91 KVGINGFGRIGRLVLRVAAFRDDVDVVAVNDPFIDAKYMAYMFKYDSTHGVFKGTINVVD 150
V + G G IG L + +A V+ V+ + + + VV
Sbjct: 171 TVVVVGAGPIGLLAIALAKLLGASVVIVVD---RSPERLELAKEAGGAD--------VVV 219
Query: 151 DSTLEINGKLIKVFSKRDPAEIPWGDYGVDYVVESSGVFTTIAKASAHMKGGAKKVVISA 210
+ + + G I E+ G G D V+E+ G + +A ++ G VV+
Sbjct: 220 NPSEDDAGAEIL--------ELTGG-RGADVVIEAVGSPPALDQALEALRPGGTVVVVGV 270
Query: 211 PSADAPMFVVG 221
+ G
Sbjct: 271 YGGEDIPLPAG 281
>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 = 29.4 bits (67), Expect = 2.5
Identities = 16/37 (43%), Positives = 23/37 (62%), Gaps = 4/37 (10%)
Query: 93 GINGFGRIGRLVLRVA-AFRDDVDVVAVNDPFIDAKY 128
GI GFGRIGR V ++A A ++V+A DP+ +
Sbjct: 143 GIIGFGRIGREVAKIARAL--GMNVIA-YDPYPKDEQ 176
>gnl|CDD|188459 TIGR03944, dehyd_SbnB_fam, 2,3-diaminopropionate biosynthesis
protein SbnB. Members of this protein family are
probable NAD-dependent dehydrogenases related to the
alanine dehydrogenase of Archaeoglobus fulgidus (see
TIGR02371, PDB structure 1OMO and PMID:15313611) and
more distantly to ornithine cyclodeaminase. Members
include the staphylobactin biosynthesis protein SbnB and
tend to occur in contexts suggesting non-ribosomal
peptide synthesis, always adjacent to (occasionally
fused with) a pyridoxal phosphate-dependent enzyme,
SbnA. The pair appears to provide 2,3-diaminopropionate
for biosynthesis of siderophores or other secondary
metabolites [Cellular processes, Biosynthesis of natural
products].
Length = 327
Score = 29.5 bits (67), Expect = 2.5
Identities = 14/38 (36%), Positives = 20/38 (52%), Gaps = 1/38 (2%)
Query: 85 RSDGNTKVGINGFGRIGRLVLR-VAAFRDDVDVVAVND 121
G T+VGI G G I R +LR + A ++ V + D
Sbjct: 128 AGRGFTRVGIIGCGPIAREILRFLLALGPEIRRVVLYD 165
>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 = 29.5 bits (67), Expect = 2.7
Identities = 13/31 (41%), Positives = 19/31 (61%), Gaps = 3/31 (9%)
Query: 91 KVGINGFGRIGRLVLRVA-AFRDDVDVVAVN 120
VGI G+G IGR + R+ AF + V+ V+
Sbjct: 139 TVGILGYGHIGREIARLLKAF--GMRVIGVS 167
>gnl|CDD|129147 TIGR00036, dapB, dihydrodipicolinate reductase. [Amino acid
biosynthesis, Aspartate family].
Length = 266
Score = 29.3 bits (66), Expect = 3.0
Identities = 10/34 (29%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 89 NTKVGING-FGRIGRLVLRVAAFRDDVDVVAVND 121
KV + G GR+GR +++ A + + +VA +
Sbjct: 1 TIKVAVAGAAGRMGRELIKAALAAEGLQLVAAFE 34
>gnl|CDD|176217 cd08255, 2-desacetyl-2-hydroxyethyl_bacteriochlorophyllide_like,
2-desacetyl-2-hydroxyethyl bacteriochlorophyllide and
other MDR family members. This subgroup of the medium
chain dehydrogenases/reductase (MDR)/zinc-dependent
alcohol dehydrogenase-like family has members identified
as 2-desacetyl-2-hydroxyethyl bacteriochlorophyllide A
dehydrogenase and alcohol dehydrogenases. The medium
chain dehydrogenases/reductase (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. Active site zinc has
a catalytic role, while structural zinc aids in
stability.
Length = 277
Score = 29.2 bits (66), Expect = 3.1
Identities = 23/119 (19%), Positives = 40/119 (33%), Gaps = 28/119 (23%)
Query: 91 KVGINGFGRIGRLVLRVAAFRDDVDVVAVNDPFIDAKYMAYMFKYDSTHGVFKGTINVVD 150
+V + G G +G L ++A +VV V DP D
Sbjct: 100 RVAVVGLGLVGLLAAQLAKAAGAREVVGV-DP---------------------------D 131
Query: 151 DSTLEINGKLIKVFSKRDPAEIPWGDYGVDYVVESSGVFTTIAKASAHMKGGAKKVVIS 209
+ E+ L G G D V+E+SG + + A ++ + V++
Sbjct: 132 AARRELAEALGPADPVAADTADEIGGRGADVVIEASGSPSALETALRLLRDRGRVVLVG 190
>gnl|CDD|223980 COG1052, LdhA, Lactate dehydrogenase and related dehydrogenases
[Energy production and conversion / Coenzyme metabolism
/ General function prediction only].
Length = 324
Score = 29.1 bits (66), Expect = 3.3
Identities = 9/22 (40%), Positives = 11/22 (50%)
Query: 89 NTKVGINGFGRIGRLVLRVAAF 110
+GI G GRIG+ V R
Sbjct: 146 GKTLGIIGLGRIGQAVARRLKG 167
>gnl|CDD|240662 cd12186, LDH, D-Lactate dehydrogenase and D-2-Hydroxyisocaproic
acid dehydrogenase (D-HicDH), NAD-binding and catalytic
domains. D-Lactate dehydrogenase (LDH) catalyzes the
interconversion of pyruvate and lactate, and is a member
of the 2-hydroxyacid dehydrogenases 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. 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 = 29.0 bits (66), Expect = 3.5
Identities = 17/55 (30%), Positives = 26/55 (47%), Gaps = 4/55 (7%)
Query: 84 SRSDGNTKVGINGFGRIGRLVLRV-AAFRDDVDVVAVNDPFIDAKYMAYMFKYDS 137
R + VGI G GRIG ++ F V+A DP+ + + ++ YDS
Sbjct: 140 GREIRDLTVGIIGTGRIGSAAAKIFKGF--GAKVIAY-DPYPNPELEKFLLYYDS 191
>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 = 28.9 bits (66), Expect = 3.8
Identities = 10/21 (47%), Positives = 12/21 (57%), Gaps = 1/21 (4%)
Query: 91 KVGINGFGRIGRLVL-RVAAF 110
+GI G GRIG+ V R F
Sbjct: 146 TLGIVGMGRIGQAVARRAKGF 166
>gnl|CDD|176238 cd08277, liver_alcohol_DH_like, Liver alcohol dehydrogenase.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. There are 7 vertebrate ADH 7
classes, 6 of which have been identified in humans.
Class III, glutathione-dependent formaldehyde
dehydrogenase, has been identified as the primordial
form and exists in diverse species, including plants,
micro-organisms, vertebrates, and invertebrates. Class
I, typified by liver dehydrogenase, is an evolving
form. Gene duplication and functional specialization of
ADH into ADH classes and subclasses created numerous
forms in vertebrates. For example, the A, B and C
(formerly alpha, beta, gamma) human class I subunits
have high overall structural similarity, but differ in
the substrate binding pocket and therefore in substrate
specificity. In human ADH catalysis, the zinc ion helps
coordinate the alcohol, followed by deprotonation of a
histidine (His-51), the ribose of NAD, a serine
(Ser-48) , then the alcohol, which allows the transfer
of a hydride to NAD+, creating NADH and a zinc-bound
aldehyde or ketone. In yeast and some bacteria, the
active site zinc binds an aldehyde, polarizing it, and
leading to the reverse reaction. ADH is a member of the
medium chain alcohol dehydrogenase family (MDR), which
has a NAD(P)(H)-binding domain in a Rossmann fold of an
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES.
These proteins typically form dimers (typically higher
plants, mammals) or tetramers (yeast, bacteria), and
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. NAD(H) binding occurs in the
cleft between the catalytic and coenzyme-binding
domains at the active site, and coenzyme binding induces
a conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
Length = 365
Score = 28.8 bits (65), Expect = 4.6
Identities = 13/42 (30%), Positives = 18/42 (42%), Gaps = 2/42 (4%)
Query: 178 GVDYVVESSGVFTTI--AKASAHMKGGAKKVVISAPSADAPM 217
GVDY E +G + A S + G VV P A+ +
Sbjct: 254 GVDYSFECTGNADLMNEALESTKLGWGVSVVVGVPPGAELSI 295
>gnl|CDD|176643 cd00865, PEBP_bact_arch, PhosphatidylEthanolamine-Binding Protein
(PEBP) domain present in bacteria and archaea.
PhosphatidylEthanolamine-Binding Proteins (PEBPs) are
represented in all three major phylogenetic divisions
(eukaryotes, bacteria, archaea). The members in this
subgroup are present in bacterial and archaea. Members
here include Escherichia coli YBHB and YBCL which are
thought to regulate protein phosphorylation as well as
Sulfolobus solfataricus SsCEI which inhibits serine
proteases alpha-chymotrypsin and elastase. Although
their overall structures are similar, the members of the
PEBP family have very different substrates and
oligomerization states (monomer/dimer/tetramer). In a
few of the bacterial members present here the
dimerization interface is proposed to form the ligand
binding site, unlike in other PEBP members.
Length = 150
Score = 28.0 bits (63), Expect = 4.6
Identities = 10/32 (31%), Positives = 12/32 (37%)
Query: 70 IRATATEIPPTIQKSRSDGNTKVGINGFGRIG 101
I A TE+P + G N FG G
Sbjct: 65 IPADTTELPEGASRGALPAGAVQGRNDFGEAG 96
>gnl|CDD|181327 PRK08256, PRK08256, lipid-transfer protein; Provisional.
Length = 391
Score = 28.7 bits (65), Expect = 4.9
Identities = 21/49 (42%), Positives = 21/49 (42%), Gaps = 5/49 (10%)
Query: 239 CTTNCLAPLAKVVHEEFGILEGLMTTV----HA-TTATQKTVDGPSMKD 282
C C A A V EEF GL V A TT T T DG SM D
Sbjct: 211 CPPTCGAAAAIVCSEEFARKHGLDRAVEIVAQAMTTDTPSTFDGRSMID 259
>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 = 28.3 bits (64), Expect = 6.5
Identities = 11/38 (28%), Positives = 17/38 (44%), Gaps = 4/38 (10%)
Query: 91 KVGINGFGRIGRLVLRVA-AFRDDVDVVAVNDPFIDAK 127
VGI G G +G + R A ++V+ + DP
Sbjct: 117 TVGIVGVGNVGSRLARRLEAL--GMNVL-LCDPPRAEA 151
>gnl|CDD|227709 COG5422, ROM1, RhoGEF, Guanine nucleotide exchange factor for
Rho/Rac/Cdc42-like GTPases [Signal transduction
mechanisms].
Length = 1175
Score = 28.3 bits (63), Expect = 7.1
Identities = 14/66 (21%), Positives = 22/66 (33%), Gaps = 3/66 (4%)
Query: 4 SSLLRSTASASLVRADLTSSPSDRVKGSPTAAFSRNLNTSSIFGTSVPSGSSSSSLQTCA 63
S ST+S + D S SD + +P+ S S G P + L +
Sbjct: 96 PSATSSTSSLNSNDGDQFSPASDSLSFNPS---STQSRKDSGPGDGSPVQKRKNPLLPSS 152
Query: 64 AKGIQP 69
+
Sbjct: 153 STHGTH 158
>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 = 28.1 bits (63), Expect = 8.3
Identities = 15/35 (42%), Positives = 21/35 (60%), Gaps = 4/35 (11%)
Query: 91 KVGINGFGRIGRLV-LRVAAFRDDVDVVAVNDPFI 124
+G+ G GRIG +V R AF + V+A DP+I
Sbjct: 140 TLGVIGLGRIGSIVAKRAKAF--GMKVLAY-DPYI 171
>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 = 27.9 bits (63), Expect = 8.9
Identities = 13/27 (48%), Positives = 16/27 (59%), Gaps = 3/27 (11%)
Query: 93 GINGFGRIGRLVLRVA-AFRDDVDVVA 118
GI G GRIG V R+ AF + V+A
Sbjct: 146 GIVGLGRIGARVARIGQAF--GMRVIA 170
>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 = 27.7 bits (62), Expect = 9.2
Identities = 12/40 (30%), Positives = 20/40 (50%), Gaps = 1/40 (2%)
Query: 92 VGINGFGRIGRLVLRVAAFRDDVDVVAVNDPFIDAKYMAY 131
VGI G+G IG V + + V+A DP++ + +
Sbjct: 150 VGIIGYGNIGSRVAEILKEGFNAKVLAY-DPYVSEEVIKK 188
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
0.316 0.130 0.383
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: 16,253,156
Number of extensions: 1519068
Number of successful extensions: 1520
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1449
Number of HSP's successfully gapped: 83
Length of query: 334
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 237
Effective length of database: 6,635,264
Effective search space: 1572557568
Effective search space used: 1572557568
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 59 (26.4 bits)