RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 024565
(265 letters)
>gnl|CDD|165999 PLN02358, PLN02358, glyceraldehyde-3-phosphate dehydrogenase.
Length = 338
Score = 486 bits (1253), Expect = e-175
Identities = 241/263 (91%), Positives = 257/263 (97%)
Query: 3 KVKIGINGFGRIGRLVARVILQRDDVELVAVNDPFITTDYMTYMFKYDSVHGQWKHHELK 62
K++IGINGFGRIGRLVARV+LQRDDVELVAVNDPFITT+YMTYMFKYDSVHGQWKHHELK
Sbjct: 5 KIRIGINGFGRIGRLVARVVLQRDDVELVAVNDPFITTEYMTYMFKYDSVHGQWKHHELK 64
Query: 63 VKDDKTLLFGEKPVTVFGVRNPEEIPWAETGAEYVVESTGVFTDKDKAAAHLKGGAKKVI 122
VKDDKTLLFGEKPVTVFG+RNPE+IPW E GA++VVESTGVFTDKDKAAAHLKGGAKKV+
Sbjct: 65 VKDDKTLLFGEKPVTVFGIRNPEDIPWGEAGADFVVESTGVFTDKDKAAAHLKGGAKKVV 124
Query: 123 ISAPSKDAPMFVVGVNEHEYKPELNIVSNASCTTNCLAPLAKVIHDKFGIVEGLMTTVHS 182
ISAPSKDAPMFVVGVNEHEYK +L+IVSNASCTTNCLAPLAKVI+D+FGIVEGLMTTVHS
Sbjct: 125 ISAPSKDAPMFVVGVNEHEYKSDLDIVSNASCTTNCLAPLAKVINDRFGIVEGLMTTVHS 184
Query: 183 ITATQKTVDGPSSKDWRGGRAASFNIIPSSTGAAKAVGKVLPALNGKLTGMAFRVPTVDV 242
ITATQKTVDGPS KDWRGGRAASFNIIPSSTGAAKAVGKVLP+LNGKLTGM+FRVPTVDV
Sbjct: 185 ITATQKTVDGPSMKDWRGGRAASFNIIPSSTGAAKAVGKVLPSLNGKLTGMSFRVPTVDV 244
Query: 243 SVVDLTVRLEKDASYDEIKAAIK 265
SVVDLTVRLEK A+YDEIK AIK
Sbjct: 245 SVVDLTVRLEKAATYDEIKKAIK 267
>gnl|CDD|177912 PLN02272, PLN02272, glyceraldehyde-3-phosphate dehydrogenase.
Length = 421
Score = 473 bits (1220), Expect = e-169
Identities = 199/264 (75%), Positives = 221/264 (83%), Gaps = 1/264 (0%)
Query: 2 GKVKIGINGFGRIGRLVARVILQRDDVELVAVNDPFITTDYMTYMFKYDSVHGQWKHHEL 61
GK KIGINGFGRIGRLV R+ RDD+E+VAVNDPFI YM YMFKYDS HG +K +
Sbjct: 84 GKTKIGINGFGRIGRLVLRIATSRDDIEVVAVNDPFIDAKYMAYMFKYDSTHGNFKGT-I 142
Query: 62 KVKDDKTLLFGEKPVTVFGVRNPEEIPWAETGAEYVVESTGVFTDKDKAAAHLKGGAKKV 121
V DD TL K + V R+P EIPW + GAEYVVES+GVFT +KA+AHLKGGAKKV
Sbjct: 143 NVVDDSTLEINGKQIKVTSKRDPAEIPWGDFGAEYVVESSGVFTTVEKASAHLKGGAKKV 202
Query: 122 IISAPSKDAPMFVVGVNEHEYKPELNIVSNASCTTNCLAPLAKVIHDKFGIVEGLMTTVH 181
+ISAPS DAPMFVVGVNE YKP +NIVSNASCTTNCLAPLAKV+H++FGI+EGLMTTVH
Sbjct: 203 VISAPSADAPMFVVGVNEKTYKPNMNIVSNASCTTNCLAPLAKVVHEEFGILEGLMTTVH 262
Query: 182 SITATQKTVDGPSSKDWRGGRAASFNIIPSSTGAAKAVGKVLPALNGKLTGMAFRVPTVD 241
+ TATQKTVDGPS KDWRGGR AS NIIPSSTGAAKAVGKVLP LNGKLTGMAFRVPT +
Sbjct: 263 ATTATQKTVDGPSMKDWRGGRGASQNIIPSSTGAAKAVGKVLPELNGKLTGMAFRVPTPN 322
Query: 242 VSVVDLTVRLEKDASYDEIKAAIK 265
VSVVDLT RLEK ASY+++KAAIK
Sbjct: 323 VSVVDLTCRLEKSASYEDVKAAIK 346
>gnl|CDD|173322 PTZ00023, PTZ00023, glyceraldehyde-3-phosphate dehydrogenase;
Provisional.
Length = 337
Score = 393 bits (1011), Expect = e-138
Identities = 178/265 (67%), Positives = 205/265 (77%), Gaps = 5/265 (1%)
Query: 4 VKIGINGFGRIGRLVARVILQRDDVELVAVNDPFITTDYMTYMFKYDSVHGQWKHHELKV 63
VK+GINGFGRIGRLV R L+R+DVE+VA+NDPF+T DYM Y+ KYDSVHG E+ V
Sbjct: 3 VKLGINGFGRIGRLVFRAALEREDVEVVAINDPFMTLDYMCYLLKYDSVHGSLPA-EVSV 61
Query: 64 KDDKTLLFGEKPVTVFGVRNPEEIPWAETGAEYVVESTGVFTDKDKAAAHLKGGAKKVII 123
D L+ G K V VF ++P IPW + G + V ESTGVF K+KA AHLKGGAKKVI+
Sbjct: 62 TDG-FLMIGSKKVHVFFEKDPAAIPWGKNGVDVVCESTGVFLTKEKAQAHLKGGAKKVIM 120
Query: 124 SAPSKD-APMFVVGVNEHEYKPELNIVSNASCTTNCLAPLAKVIHDKFGIVEGLMTTVHS 182
SAP KD P++V+GVN +Y IVSNASCTTNCLAPLAKV++DKFGIVEGLMTTVH+
Sbjct: 121 SAPPKDDTPIYVMGVNHTQYDKSQRIVSNASCTTNCLAPLAKVVNDKFGIVEGLMTTVHA 180
Query: 183 ITATQKTVDGPS--SKDWRGGRAASFNIIPSSTGAAKAVGKVLPALNGKLTGMAFRVPTV 240
TA Q TVDGPS KDWR GR A NIIP+STGAAKAVGKV+P LNGKLTGMAFRVP
Sbjct: 181 STANQLTVDGPSKGGKDWRAGRCAGVNIIPASTGAAKAVGKVIPELNGKLTGMAFRVPVP 240
Query: 241 DVSVVDLTVRLEKDASYDEIKAAIK 265
DVSVVDLT +L K A Y+EI AA+K
Sbjct: 241 DVSVVDLTCKLAKPAKYEEIVAAVK 265
>gnl|CDD|223135 COG0057, GapA, Glyceraldehyde-3-phosphate
dehydrogenase/erythrose-4-phosphate dehydrogenase
[Carbohydrate transport and metabolism].
Length = 335
Score = 392 bits (1009), Expect = e-138
Identities = 159/266 (59%), Positives = 194/266 (72%), Gaps = 7/266 (2%)
Query: 3 KVKIGINGFGRIGRLVARVILQRD-DVELVAVNDPFITTDYMTYMFKYDSVHGQWKHHEL 61
+K+ INGFGRIGRLVAR L+RD D+E+VA+ND DY+ ++ KYDSVHG++ E+
Sbjct: 1 MIKVAINGFGRIGRLVARAALERDGDIEVVAINDL-TDPDYLAHLLKYDSVHGRFDG-EV 58
Query: 62 KVKDDKTLLFGEKPVTVFGVRNPEEIPWAETGAEYVVESTGVFTDKDKAAAHL-KGGAKK 120
+VKDD L+ K + V R+P +PWA+ G + VVE TG FT ++KA HL GGAKK
Sbjct: 59 EVKDD-ALVVNGKGIKVLAERDPANLPWADLGVDIVVECTGKFTGREKAEKHLKAGGAKK 117
Query: 121 VIISAPSKDA-PMFVVGVNEHEYKPELNIVSNASCTTNCLAPLAKVIHDKFGIVEGLMTT 179
V+ISAP KD V GVN + Y IVSNASCTTNCLAP+AKV++D FGI +GLMTT
Sbjct: 118 VLISAPGKDDVATVVYGVNHNYYDAGHTIVSNASCTTNCLAPVAKVLNDAFGIEKGLMTT 177
Query: 180 VHSITATQKTVDGPSSKDWRGGRAASFNIIPSSTGAAKAVGKVLPALNGKLTGMAFRVPT 239
VH+ T QK VDGP KD R RAA+ NIIP+STGAAKAVG VLP L GKLTGMA RVPT
Sbjct: 178 VHAYTNDQKLVDGPH-KDLRRARAAALNIIPTSTGAAKAVGLVLPELKGKLTGMAIRVPT 236
Query: 240 VDVSVVDLTVRLEKDASYDEIKAAIK 265
+VSVVDLTV LEK+ + +EI AA+K
Sbjct: 237 PNVSVVDLTVELEKEVTVEEINAALK 262
>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 = 389 bits (1002), Expect = e-137
Identities = 154/264 (58%), Positives = 193/264 (73%), Gaps = 6/264 (2%)
Query: 5 KIGINGFGRIGRLVARVILQRD--DVELVAVNDPFITTDYMTYMFKYDSVHGQWKHHELK 62
K+GINGFGRIGRLV R IL++ D+E+VA+ND +Y+ Y+ KYDSVHG+++ E+
Sbjct: 1 KVGINGFGRIGRLVLRAILEKPGNDLEVVAINDL-TDLEYLAYLLKYDSVHGRFEG-EVT 58
Query: 63 VKDDKTLLFGEKPVTVFGVRNPEEIPWAETGAEYVVESTGVFTDKDKAAAHLKGGAKKVI 122
+D ++ G++ ++VF R+P ++PW G + V+E TG F DK+K HL+ GAKKV+
Sbjct: 59 ADEDGLVVNGKEVISVFSERDPSDLPWKALGVDIVIECTGKFRDKEKLEGHLEAGAKKVL 118
Query: 123 ISAPSK-DAPMFVVGVNEHEYKPELNIVSNASCTTNCLAPLAKVIHDKFGIVEGLMTTVH 181
ISAPSK D V GVN EY P IVSNASCTTNCLAPLAKV+ + FGIV GLMTTVH
Sbjct: 119 ISAPSKGDVKTIVYGVNHDEYDPSERIVSNASCTTNCLAPLAKVLDEAFGIVSGLMTTVH 178
Query: 182 SITATQKTVDGPSSKDWRGGRAASFNIIPSSTGAAKAVGKVLPALNGKLTGMAFRVPTVD 241
S T Q VDGP KD R RAA+ NIIP+STGAAKA+GKVLP L GKLTGMA RVPT +
Sbjct: 179 SYTNDQNLVDGP-HKDLRRARAAALNIIPTSTGAAKAIGKVLPELAGKLTGMAIRVPTPN 237
Query: 242 VSVVDLTVRLEKDASYDEIKAAIK 265
VS+VDL V LEKD + +E+ AA+K
Sbjct: 238 VSLVDLVVNLEKDVTVEEVNAALK 261
>gnl|CDD|185323 PRK15425, gapA, glyceraldehyde-3-phosphate dehydrogenase A;
Provisional.
Length = 331
Score = 313 bits (804), Expect = e-107
Identities = 167/263 (63%), Positives = 204/263 (77%), Gaps = 5/263 (1%)
Query: 4 VKIGINGFGRIGRLVARVILQRDDVELVAVNDPFITTDYMTYMFKYDSVHGQWKHHELKV 63
+K+GINGFGRIGR+V R +R D+E+VA+ND + DYM YM KYDS HG++ ++V
Sbjct: 3 IKVGINGFGRIGRIVFRAAQKRSDIEIVAIND-LLDADYMAYMLKYDSTHGRFDG-TVEV 60
Query: 64 KDDKTLLFGEKPVTVFGVRNPEEIPWAETGAEYVVESTGVFTDKDKAAAHLKGGAKKVII 123
KD ++ G+K + V R+P + W E G + V E+TG+F + A H+ GAKKV++
Sbjct: 61 KDGHLIVNGKK-IRVTAERDPANLKWDEVGVDVVAEATGLFLTDETARKHITAGAKKVVM 119
Query: 124 SAPSKD-APMFVVGVNEHEYKPELNIVSNASCTTNCLAPLAKVIHDKFGIVEGLMTTVHS 182
+ PSKD PMFV G N +Y + +IVSNASCTTNCLAPLAKVI+D FGI+EGLMTTVH+
Sbjct: 120 TGPSKDNTPMFVKGANFDKYAGQ-DIVSNASCTTNCLAPLAKVINDNFGIIEGLMTTVHA 178
Query: 183 ITATQKTVDGPSSKDWRGGRAASFNIIPSSTGAAKAVGKVLPALNGKLTGMAFRVPTVDV 242
TATQKTVDGPS KDWRGGR AS NIIPSSTGAAKAVGKVLP LNGKLTGMAFRVPT +V
Sbjct: 179 TTATQKTVDGPSHKDWRGGRGASQNIIPSSTGAAKAVGKVLPELNGKLTGMAFRVPTPNV 238
Query: 243 SVVDLTVRLEKDASYDEIKAAIK 265
SVVDLTVRLEK A+Y++IKAA+K
Sbjct: 239 SVVDLTVRLEKAATYEQIKAAVK 261
>gnl|CDD|185614 PTZ00434, PTZ00434, cytosolic glyceraldehyde 3-phosphate
dehydrogenase; Provisional.
Length = 361
Score = 308 bits (791), Expect = e-105
Identities = 159/279 (56%), Positives = 196/279 (70%), Gaps = 14/279 (5%)
Query: 1 MGKVKIGINGFGRIGRLVARVILQRD----DVELVAVNDPFITTDYMTYMFKYDSVHGQW 56
M +K+GINGFGRIGR+V + I + ++++VAV D +Y Y KYD+VHG+
Sbjct: 1 MAPIKVGINGFGRIGRMVFQAICDQGLIGTEIDVVAVVDMSTNAEYFAYQMKYDTVHGRP 60
Query: 57 KHHELKVK-------DDKTLLFGEKPVTVFGVRNPEEIPWAETGAEYVVESTGVFTDKDK 109
K+ K DD ++ G + V RNP ++PW + G +YV+ESTG+FTDK
Sbjct: 61 KYTVETTKSSPSVKTDDVLVVNGHRIKCVKAQRNPADLPWGKLGVDYVIESTGLFTDKLA 120
Query: 110 AAAHLKGGAKKVIISAP-SKDAPMFVVGVNEHEYKP-ELNIVSNASCTTNCLAPLAKVI- 166
A HLKGGAKKV+ISAP S A V+GVN+HEY P E ++VSNASCTTNCLAP+ V+
Sbjct: 121 AEGHLKGGAKKVVISAPASGGAKTIVMGVNQHEYSPTEHHVVSNASCTTNCLAPIVHVLT 180
Query: 167 HDKFGIVEGLMTTVHSITATQKTVDGPSSKDWRGGRAASFNIIPSSTGAAKAVGKVLPAL 226
+ FGI GLMTT+HS TATQKTVDG S KDWRGGRAA+ NIIPS+TGAAKAVG V+P+
Sbjct: 181 KEGFGIETGLMTTIHSYTATQKTVDGVSVKDWRGGRAAAVNIIPSTTGAAKAVGMVIPST 240
Query: 227 NGKLTGMAFRVPTVDVSVVDLTVRLEKDASYDEIKAAIK 265
GKLTGM+FRVPT DVSVVDLT R +D S EI AAIK
Sbjct: 241 KGKLTGMSFRVPTPDVSVVDLTFRATRDTSIQEIDAAIK 279
>gnl|CDD|236079 PRK07729, PRK07729, glyceraldehyde-3-phosphate dehydrogenase;
Validated.
Length = 343
Score = 293 bits (751), Expect = 4e-99
Identities = 129/265 (48%), Positives = 185/265 (69%), Gaps = 6/265 (2%)
Query: 3 KVKIGINGFGRIGRLVARVILQRDDVELVAVNDPFITTDYMTYMFKYDSVHGQWKHHELK 62
K K+ INGFGRIGR+V R ++ E+VA+N + ++ + ++ KYD+VHG++ ++
Sbjct: 2 KTKVAINGFGRIGRMVFRKAIKESAFEIVAINASY-PSETLAHLIKYDTVHGKFDG-TVE 59
Query: 63 VKDDKTLLFGEKPVTVFGVRNPEEIPWAETGAEYVVESTGVFTDKDKAAAHLKGGAKKVI 122
+D L+ G+K + + R+P+E+PW + G + V+E+TG F K+KA H++ GAKKVI
Sbjct: 60 AFEDHLLVDGKK-IRLLNNRDPKELPWTDLGIDIVIEATGKFNSKEKAILHVEAGAKKVI 118
Query: 123 ISAPSKDAPM-FVVGVNEHEYKPELN-IVSNASCTTNCLAPLAKVIHDKFGIVEGLMTTV 180
++AP K+ + VVGVNE + E + I+SNASCTTNCLAP+ KV+ ++FGI GLMTTV
Sbjct: 119 LTAPGKNEDVTIVVGVNEDQLDIEKHTIISNASCTTNCLAPVVKVLDEQFGIENGLMTTV 178
Query: 181 HSITATQKTVDGPSSKDWRGGRAASFNIIPSSTGAAKAVGKVLPALNGKLTGMAFRVPTV 240
H+ T QK +D P KD R RA +IIP++TGAAKA+ KVLP LNGKL GMA RVPT
Sbjct: 179 HAYTNDQKNIDNPH-KDLRRARACGQSIIPTTTGAAKALAKVLPHLNGKLHGMALRVPTP 237
Query: 241 DVSVVDLTVRLEKDASYDEIKAAIK 265
+VS+VDL V +++D + +EI A K
Sbjct: 238 NVSLVDLVVDVKRDVTVEEINEAFK 262
>gnl|CDD|180962 PRK07403, PRK07403, glyceraldehyde-3-phosphate dehydrogenase;
Reviewed.
Length = 337
Score = 265 bits (679), Expect = 2e-88
Identities = 134/269 (49%), Positives = 181/269 (67%), Gaps = 13/269 (4%)
Query: 4 VKIGINGFGRIGRLVARVILQRDD--VELVAVNDPFITTDYMT--YMFKYDSVHGQWKHH 59
+++ INGFGRIGR R L R++ +ELVA+ND T+D T ++ KYDS+ G K +
Sbjct: 2 IRVAINGFGRIGRNFLRCWLGRENSQLELVAIND---TSDPRTNAHLLKYDSMLG--KLN 56
Query: 60 ELKVKDDKTLLFGEKPVTVFGVRNPEEIPWAETGAEYVVESTGVFTDKDKAAAHLKGGAK 119
D+ ++ K + RNP +PW E G + ++ESTGVF K+ A+ H++ GAK
Sbjct: 57 ADISADENSITVNGKTIKCVSDRNPLNLPWKEWGIDLIIESTGVFVTKEGASKHIQAGAK 116
Query: 120 KVIISAPSK--DAPMFVVGVNEHEYKPEL-NIVSNASCTTNCLAPLAKVIHDKFGIVEGL 176
KV+I+AP K D +VVGVN HEY E NI+SNASCTTNCLAP+AKV+HD FGI++G
Sbjct: 117 KVLITAPGKGEDIGTYVVGVNHHEYDHEDHNIISNASCTTNCLAPIAKVLHDNFGIIKGT 176
Query: 177 MTTVHSITATQKTVDGPSSKDWRGGRAASFNIIPSSTGAAKAVGKVLPALNGKLTGMAFR 236
MTT HS T Q+ +D S +D R RAA+ NI+P+STGAAKAV V+P L GKL G+A R
Sbjct: 177 MTTTHSYTGDQRILDA-SHRDLRRARAAAVNIVPTSTGAAKAVALVIPELKGKLNGIALR 235
Query: 237 VPTVDVSVVDLTVRLEKDASYDEIKAAIK 265
VPT +VSVVDL V++EK +++ +K
Sbjct: 236 VPTPNVSVVDLVVQVEKRTITEQVNEVLK 264
>gnl|CDD|215131 PLN02237, PLN02237, glyceraldehyde-3-phosphate dehydrogenase B.
Length = 442
Score = 267 bits (683), Expect = 1e-87
Identities = 138/269 (51%), Positives = 185/269 (68%), Gaps = 9/269 (3%)
Query: 3 KVKIGINGFGRIGRLVARVILQRDD--VELVAVNDPFITTDYMTYMFKYDSVHGQWKHHE 60
K+K+ INGFGRIGR R R D +++V VND + +++ KYDS+ G +K +
Sbjct: 75 KLKVAINGFGRIGRNFLRCWHGRKDSPLDVVVVNDSGGVKN-ASHLLKYDSMLGTFKA-D 132
Query: 61 LKVKDDKTLLFGEKPVTVFGVRNPEEIPWAETGAEYVVESTGVFTDKDKAAAHLKGGAKK 120
+K+ DD+T+ KP+ V R+P ++PWAE G + V+E TGVF D A H++ GAKK
Sbjct: 133 VKIVDDETISVDGKPIKVVSNRDPLKLPWAELGIDIVIEGTGVFVDGPGAGKHIQAGAKK 192
Query: 121 VIISAPSK--DAPMFVVGVNEHEYKPEL-NIVSNASCTTNCLAPLAKVIHDKFGIVEGLM 177
VII+AP+K D P +VVGVNE +Y E+ NIVSNASCTTNCLAP KV+ ++FGIV+G M
Sbjct: 193 VIITAPAKGADIPTYVVGVNEDDYDHEVANIVSNASCTTNCLAPFVKVLDEEFGIVKGTM 252
Query: 178 TTVHSITATQKTVDGPSSKDWRGGRAASFNIIPSSTGAAKAVGKVLPALNGKLTGMAFRV 237
TT HS T Q+ +D S +D R RAA+ NI+P+STGAAKAV VLP L GKL G+A RV
Sbjct: 253 TTTHSYTGDQRLLDA-SHRDLRRARAAALNIVPTSTGAAKAVSLVLPQLKGKLNGIALRV 311
Query: 238 PTVDVSVVDLTVRLEKDA-SYDEIKAAIK 265
PT +VSVVDL V +EK + +++ AA +
Sbjct: 312 PTPNVSVVDLVVNVEKKGITAEDVNAAFR 340
>gnl|CDD|215572 PLN03096, PLN03096, glyceraldehyde-3-phosphate dehydrogenase A;
Provisional.
Length = 395
Score = 263 bits (673), Expect = 9e-87
Identities = 131/266 (49%), Positives = 173/266 (65%), Gaps = 6/266 (2%)
Query: 3 KVKIGINGFGRIGRLVARVILQRDD--VELVAVNDPFITTDYMTYMFKYDSVHGQWKHHE 60
K+K+ INGFGRIGR R R D +++VA+ND +++ KYDS G + +
Sbjct: 60 KIKVAINGFGRIGRNFLRCWHGRKDSPLDVVAINDTG-GVKQASHLLKYDSTLGTFDA-D 117
Query: 61 LKVKDDKTLLFGEKPVTVFGVRNPEEIPWAETGAEYVVESTGVFTDKDKAAAHLKGGAKK 120
+K D + K + V RNP +PW E G + V+E TGVF D++ A H++ GAKK
Sbjct: 118 VKPVGDDAISVDGKVIKVVSDRNPLNLPWGELGIDLVIEGTGVFVDREGAGKHIQAGAKK 177
Query: 121 VIISAPSK-DAPMFVVGVNEHEYKPELNIVSNASCTTNCLAPLAKVIHDKFGIVEGLMTT 179
V+I+AP K D P +VVGVN +YK I+SNASCTTNCLAP KV+ KFGI++G MTT
Sbjct: 178 VLITAPGKGDIPTYVVGVNADDYKHSDPIISNASCTTNCLAPFVKVLDQKFGIIKGTMTT 237
Query: 180 VHSITATQKTVDGPSSKDWRGGRAASFNIIPSSTGAAKAVGKVLPALNGKLTGMAFRVPT 239
HS T Q+ +D S +D R RAA+ NI+P+STGAAKAV VLP L GKL G+A RVPT
Sbjct: 238 THSYTGDQRLLDA-SHRDLRRARAAALNIVPTSTGAAKAVALVLPNLKGKLNGIALRVPT 296
Query: 240 VDVSVVDLTVRLEKDASYDEIKAAIK 265
+VSVVDL V++EK +E+ AA +
Sbjct: 297 PNVSVVDLVVQVEKKTFAEEVNAAFR 322
>gnl|CDD|169599 PRK08955, PRK08955, glyceraldehyde-3-phosphate dehydrogenase;
Validated.
Length = 334
Score = 229 bits (585), Expect = 3e-74
Identities = 107/266 (40%), Positives = 164/266 (61%), Gaps = 8/266 (3%)
Query: 3 KVKIGINGFGRIGRLVARVILQRDDVELVAVNDPFITTDYMTYMFKYDSVHGQWKHHELK 62
+K+GINGFGRIGRL R ++E V +NDP + ++ ++DSVHG+W HHE+
Sbjct: 2 TIKVGINGFGRIGRLALRAAWDWPELEFVQINDPAGDAATLAHLLEFDSVHGRW-HHEVT 60
Query: 63 VKDDKTLLFGEKPVTVFGVRNPEEIPWAETGAEYVVESTGVFTDKDKAAAHLKGGAKKVI 122
+ D ++ K + + + W +G + V+E++GV K A+L G K+V+
Sbjct: 61 AEGD-AIVINGKRIRTTQNKAIADTDW--SGCDVVIEASGVMKTKALLQAYLDQGVKRVV 117
Query: 123 ISAPSKDAPMF--VVGVNEHEYKPELN-IVSNASCTTNCLAPLAKVIHDKFGIVEGLMTT 179
++AP K+ + V+GVN+H + P ++ IV+ ASCTTNCLAP+ KVIH+K GI G MTT
Sbjct: 118 VTAPVKEEGVLNIVMGVNDHLFDPAIHPIVTAASCTTNCLAPVVKVIHEKLGIKHGSMTT 177
Query: 180 VHSITATQKTVDGPSSKDWRGGRAASFNIIPSSTGAAKAVGKVLPALNGKLTGMAFRVPT 239
+H +T TQ +D P KD R RA ++IP++TG+A A+ ++ P L GKL G A RVP
Sbjct: 178 IHDLTNTQTILDAP-HKDLRRARACGMSLIPTTTGSATAITEIFPELKGKLNGHAVRVPL 236
Query: 240 VDVSVVDLTVRLEKDASYDEIKAAIK 265
+ S+ D +E+D + +E+ A +K
Sbjct: 237 ANASLTDCVFEVERDTTVEEVNALLK 262
>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 (562), Expect = 3e-73
Identities = 86/151 (56%), Positives = 109/151 (72%), Gaps = 4/151 (2%)
Query: 4 VKIGINGFGRIGRLVARVILQRDDVELVAVNDPFITTDYMTYMFKYDSVHGQWKHHELKV 63
+K+GINGFGRIGRLV R L +DD+E+VA+ND + + Y+ KYDSVHG++ E++V
Sbjct: 1 IKVGINGFGRIGRLVLRAALAQDDLEVVAINDLT-DPETLAYLLKYDSVHGRFDG-EVEV 58
Query: 64 KDDKTLLFGEKPVTVFGVRNPEEIPWAETGAEYVVESTGVFTDKDKAAAHLKGGAKKVII 123
+D L+ K + VF R+P E+PW E G + VVESTGVFT +KA AHLK GAKKVII
Sbjct: 59 DEDG-LIVNGKKIKVFAERDPAELPWGELGVDIVVESTGVFTTAEKAEAHLKAGAKKVII 117
Query: 124 SAPSKD-APMFVVGVNEHEYKPELNIVSNAS 153
SAP+KD P FV GVN +Y PE +IVSNAS
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 = 218 bits (557), Expect = 2e-72
Identities = 86/152 (56%), Positives = 109/152 (71%), Gaps = 4/152 (2%)
Query: 4 VKIGINGFGRIGRLVARVILQRDDVELVAVNDPFITTDYMTYMFKYDSVHGQWKHHELKV 63
+K+GINGFGRIGRLV R L+R DVE+VA+ND +Y+ Y+ KYDSVHG++ ++V
Sbjct: 1 IKVGINGFGRIGRLVLRAALERPDVEVVAINDL-TDPEYLAYLLKYDSVHGRF-PGTVEV 58
Query: 64 KDDKTLLFGEKPVTVFGVRNPEEIPWAETGAEYVVESTGVFTDKDKAAAHLKGGAKKVII 123
+ D L+ K + VF R+P +PW E G + VVE TG FT ++KA+AHLK GAKKVII
Sbjct: 59 EGD-GLVVNGKAIKVFAERDPANLPWGELGVDIVVECTGGFTTREKASAHLKAGAKKVII 117
Query: 124 SAPSKDA-PMFVVGVNEHEYKPELNIVSNASC 154
SAPSKDA P FV GVN EY E +I+SNASC
Sbjct: 118 SAPSKDADPTFVYGVNHDEYDGEDHIISNASC 149
>gnl|CDD|184122 PRK13535, PRK13535, erythrose 4-phosphate dehydrogenase;
Provisional.
Length = 336
Score = 209 bits (533), Expect = 2e-66
Identities = 97/269 (36%), Positives = 158/269 (58%), Gaps = 13/269 (4%)
Query: 4 VKIGINGFGRIGRLVARVILQ---RDDVELVAVNDPFITTDYMTYMFKYDSVHGQWKHHE 60
+++ INGFGRIGR V R + + R ++ +VA+N+ + M ++ KYD+ HG++
Sbjct: 2 IRVAINGFGRIGRNVLRALYESGRRAEITVVAINE-LADAEGMAHLLKYDTSHGRFAW-- 58
Query: 61 LKVKDDKTLLF-GEKPVTVFGVRNPEEIPWAETGAEYVVESTGVFTDKDKAAAHLKGGAK 119
V+ ++ LF G+ + + R+ +PW E G + V++ TGV+ ++ AH+ GAK
Sbjct: 59 -DVRQERDQLFVGDDAIRLLHERDIASLPWRELGVDVVLDCTGVYGSREDGEAHIAAGAK 117
Query: 120 KVIISAPSK---DAPMFVVGVNEHEYKPELNIVSNASCTTNCLAPLAKVIHDKFGIVEGL 176
KV+ S P DA + V GVN + + E IVSNASCTTNC+ P+ K++ D FGI G
Sbjct: 118 KVLFSHPGSNDLDATV-VYGVNHDQLRAEHRIVSNASCTTNCIIPVIKLLDDAFGIESGT 176
Query: 177 MTTVHSITATQKTVDGPSSKDWRGGRAASFNIIPSSTGAAKAVGKVLPALNGKLTGMAFR 236
+TT+HS Q+ +D D R RAAS +IIP T A + ++ P N + ++ R
Sbjct: 177 VTTIHSAMNDQQVIDAYHP-DLRRTRAASQSIIPVDTKLAAGITRIFPQFNDRFEAISVR 235
Query: 237 VPTVDVSVVDLTVRLEKDASYDEIKAAIK 265
VPT++V+ +DL+V ++K +E+ ++
Sbjct: 236 VPTINVTAIDLSVTVKKPVKVNEVNQLLQ 264
>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 = 202 bits (515), Expect = 7e-64
Identities = 99/267 (37%), Positives = 158/267 (59%), Gaps = 11/267 (4%)
Query: 5 KIGINGFGRIGRLVARVILQ---RDDVELVAVNDPFITTDYMTYMFKYDSVHGQWKHHEL 61
++ INGFGRIGR V R + + R ++ +VA+N+ M ++ KYD+ HG++
Sbjct: 1 RVAINGFGRIGRNVLRALYESGRRAEITVVAINE-LADAAGMAHLLKYDTSHGRFAW--- 56
Query: 62 KVKDDKTLLF-GEKPVTVFGVRNPEEIPWAETGAEYVVESTGVFTDKDKAAAHLKGGAKK 120
+V+ D+ LF G+ + V R+ + +PW E G + V++ TGV+ ++ AH+ GAKK
Sbjct: 57 EVRQDRDQLFVGDDAIRVLHERSLQSLPWRELGVDLVLDCTGVYGSREHGEAHIAAGAKK 116
Query: 121 VIISAP-SKDAPMFVV-GVNEHEYKPELNIVSNASCTTNCLAPLAKVIHDKFGIVEGLMT 178
V+ S P + D +V GVN+ + + E IVSNASCTTNC+ P+ K++ D +GI G +T
Sbjct: 117 VLFSHPGASDLDATIVYGVNQDQLRAEHRIVSNASCTTNCIVPVIKLLDDAYGIESGTIT 176
Query: 179 TVHSITATQKTVDGPSSKDWRGGRAASFNIIPSSTGAAKAVGKVLPALNGKLTGMAFRVP 238
T+HS Q+ +D D R RAAS +IIP T A + + P N + +A RVP
Sbjct: 177 TIHSAMNDQQVIDA-YHPDLRRTRAASQSIIPVDTKLAAGIERFFPQFNDRFEAIAVRVP 235
Query: 239 TVDVSVVDLTVRLEKDASYDEIKAAIK 265
TV+V+ +DL+V ++K +E+ ++
Sbjct: 236 TVNVTAIDLSVTVKKPVKANEVNLLLQ 262
>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 = 196 bits (500), Expect = 1e-63
Identities = 77/107 (71%), Positives = 88/107 (82%), Gaps = 1/107 (0%)
Query: 159 LAPLAKVIHDKFGIVEGLMTTVHSITATQKTVDGPSSKDWRGGRAASFNIIPSSTGAAKA 218
LAPLAKV++D FGI +GLMTTVH+ TA QK VD PS KD R GRAA+ NIIP+STGAAKA
Sbjct: 1 LAPLAKVLNDNFGIEKGLMTTVHAYTADQKLVD-PSHKDLRRGRAAAPNIIPTSTGAAKA 59
Query: 219 VGKVLPALNGKLTGMAFRVPTVDVSVVDLTVRLEKDASYDEIKAAIK 265
VG VLP L GKLTGMAFRVPT +VSVVDLTV LEK + +E+ AA+K
Sbjct: 60 VGLVLPELKGKLTGMAFRVPTPNVSVVDLTVELEKPVTVEEVNAALK 106
>gnl|CDD|236219 PRK08289, PRK08289, glyceraldehyde-3-phosphate dehydrogenase;
Reviewed.
Length = 477
Score = 202 bits (515), Expect = 5e-62
Identities = 102/271 (37%), Positives = 153/271 (56%), Gaps = 20/271 (7%)
Query: 10 GFGRIGRLVARVILQR----DDVELVAV-------NDPFITTDYMTYMFKYDSVHGQWKH 58
GFGRIGRL+AR+++++ + + L A+ D + + + DSVHG +
Sbjct: 134 GFGRIGRLLARLLIEKTGGGNGLRLRAIVVRKGSEGD----LEKRASLLRRDSVHGPFNG 189
Query: 59 HELKVKDDKTLLFGEKPVTVFGVRNPEEIPWAETGAE--YVVESTGVFTDKDKAAAHLKG 116
+++ ++ + V +PEE+ + G VV++TG + D++ + HLK
Sbjct: 190 TITVDEENNAIIANGNYIQVIYANSPEEVDYTAYGINNALVVDNTGKWRDEEGLSQHLKS 249
Query: 117 -GAKKVIISAPSK-DAPMFVVGVNEHEYKPELNIVSNASCTTNCLAPLAKVIHDKFGIVE 174
G KV+++AP K D V GVN + E IVS ASCTTN + P+ K ++DK+GIV
Sbjct: 250 KGVAKVLLTAPGKGDIKNIVHGVNHSDITDEDKIVSAASCTTNAITPVLKAVNDKYGIVN 309
Query: 175 GLMTTVHSITATQKTVDGPSSKDWRGGRAASFNIIPSSTGAAKAVGKVLPALNGKLTGMA 234
G + TVHS T Q +D D R GR+A N++ + TGAAKAV K LP L GKLTG A
Sbjct: 310 GHVETVHSYTNDQNLIDNYHKGD-RRGRSAPLNMVITETGAAKAVAKALPELAGKLTGNA 368
Query: 235 FRVPTVDVSVVDLTVRLEKDASYDEIKAAIK 265
RVPT +VS+ L + LEK+ S +E+ ++
Sbjct: 369 IRVPTPNVSMAILNLNLEKETSREELNEYLR 399
>gnl|CDD|173546 PTZ00353, PTZ00353, glycosomal glyceraldehyde-3-phosphate
dehydrogenase; Provisional.
Length = 342
Score = 160 bits (406), Expect = 3e-47
Identities = 78/263 (29%), Positives = 136/263 (51%), Gaps = 1/263 (0%)
Query: 4 VKIGINGFGRIGRLVARVILQRDDVELVAVNDPFITTDYMTYMFKYDSVHGQWKHHELKV 63
+ +GINGFG +G+ V L V +VAVND ++ Y+ Y+ + +S ++V
Sbjct: 3 ITVGINGFGPVGKAVLFASLTDPLVTVVAVNDASVSIAYIAYVLEQESPLSAPDGASIRV 62
Query: 64 KDDKTLLFGEKPVTVFGVRNPEEIPWAETGAEYVVESTGVFTDKDKAAAHLKGGAKKVII 123
++ +L G + + V + EI W + G +YVVE TG+++ + + H+ GGAK V +
Sbjct: 63 VGEQIVLNGTQKIRVSAKHDLVEIAWRDYGVQYVVECTGLYSTRSRCWGHVTGGAKGVFV 122
Query: 124 SAPSKDAPMFVVGVNEHEYKPELNIVSNASCTTNCLAPLAKVIHDKFGIVEGLMTTVHSI 183
+ S DAP + G N+ L + + LAP+ + +H+ +G+ E T +H +
Sbjct: 123 AGQSADAPTVMAGSNDERLSASLPVCCAGAPIAVALAPVIRALHEVYGVEECSYTAIHGM 182
Query: 184 TATQKT-VDGPSSKDWRGGRAASFNIIPSSTGAAKAVGKVLPALNGKLTGMAFRVPTVDV 242
+ +S+DWR R A I P A+ V K+LP L G+++G AF+VP
Sbjct: 183 QPQEPIAARSKNSQDWRQTRVAIDAIAPYRDNGAETVCKLLPHLVGRISGSAFQVPVKKG 242
Query: 243 SVVDLTVRLEKDASYDEIKAAIK 265
+D+ VR ++ S + + +A+
Sbjct: 243 CAIDMLVRTKQPVSKEVVDSALA 265
>gnl|CDD|223214 COG0136, Asd, Aspartate-semialdehyde dehydrogenase [Amino acid
transport and metabolism].
Length = 334
Score = 53.0 bits (128), Expect = 3e-08
Identities = 51/228 (22%), Positives = 84/228 (36%), Gaps = 43/228 (18%)
Query: 71 FGEKPVTVFGVRNPEEIP--WAETGAEYVVESTGVFTDKDKAAAHLKGGAK--KVIISAP 126
FG K + V PE+ + + + V + G + A+ V+I
Sbjct: 47 FGGKSIGV-----PEDAADEFVFSDVDIVFFAAG----GSVSKEVEPKAAEAGCVVIDNS 97
Query: 127 S-----KDAPMFVVGVNEH---EYKPELNIVSNASCTTNCLAPLAKVIHDKFGIVEGLMT 178
S D P+ V VN +Y+ I++N +C+T L K +HD FGI +++
Sbjct: 98 SAFRMDPDVPLVVPEVNPEHLIDYQKRGFIIANPNCSTIQLVLALKPLHDAFGIKRVVVS 157
Query: 179 TVHSI----------TATQKTVDGPSSKDWRGGRAASFNIIP-----SSTGAAKA----- 218
T ++ A Q G +FN+IP G K
Sbjct: 158 TYQAVSGAGAEGGVELAGQTDALLNGIPILPIGYPLAFNVIPHIDGFLDNGYTKEEWKIE 217
Query: 219 --VGKVLPALNGKLTGMAFRVPTVDVSVVDLTVRLEKDASYDEIKAAI 264
K+L + K++ RVP +TV +KD +EI+ +
Sbjct: 218 AETRKILGDPDIKVSATCVRVPVFYGHSEAVTVEFKKDVDPEEIREEL 265
>gnl|CDD|179786 PRK04207, PRK04207, glyceraldehyde-3-phosphate dehydrogenase;
Provisional.
Length = 341
Score = 41.4 bits (98), Expect = 2e-04
Identities = 16/44 (36%), Positives = 25/44 (56%), Gaps = 2/44 (4%)
Query: 3 KVKIGINGFGRIGRLVARVILQRDDVELVAVNDPFITTDYMTYM 46
+K+G+NG+G IG+ VA + + D+ELV V DY +
Sbjct: 1 MIKVGVNGYGTIGKRVADAVAAQPDMELVGVAK--TKPDYEARV 42
Score = 31.0 bits (71), Expect = 0.54
Identities = 19/57 (33%), Positives = 32/57 (56%), Gaps = 4/57 (7%)
Query: 209 IPSSTGAAKAVGKVLPALNGKLTGMAFRVPTVDVSVVDLTVRLEKDASYDEIKAAIK 265
+PS G V VLP L+ +T MA +VPT + + + V L+K + +E+ A++
Sbjct: 190 VPSHHG--PDVKTVLPDLD--ITTMAVKVPTTLMHMHSVNVELKKPVTKEEVLEALE 242
>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 = 39.5 bits (93), Expect = 3e-04
Identities = 13/31 (41%), Positives = 20/31 (64%), Gaps = 1/31 (3%)
Query: 4 VKIGINGF-GRIGRLVARVILQRDDVELVAV 33
+K+ + G GR+GR + + IL+ D ELVA
Sbjct: 1 IKVAVVGASGRMGRELIKAILEAPDFELVAA 31
>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 = 6e-04
Identities = 15/59 (25%), Positives = 31/59 (52%), Gaps = 2/59 (3%)
Query: 128 KDAPMFVVGVNEHEYK--PELNIVSNASCTTNCLAPLAKVIHDKFGIVEGLMTTVHSIT 184
D P+ V VN + K I++N +C+T + + K +HD+ I +++T +++
Sbjct: 99 PDVPLVVPEVNFEDLKEFNPKGIIANPNCSTIQMVVVLKPLHDEAKIKRVVVSTYQAVS 157
>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 = 39.0 bits (91), Expect = 0.002
Identities = 35/130 (26%), Positives = 54/130 (41%), Gaps = 20/130 (15%)
Query: 148 IVSNASCTTNCLAPLAKVIHDKFGIVEGLMTTVHSITATQKTVDGPSSKDWRGGRAASFN 207
IV+N +CTT L K + D FGI + +TT+ +++ G S D N
Sbjct: 140 IVTNPNCTTAGLTLALKPLIDAFGIKKVHVTTMQAVSGAGY--PGVPSMDILD------N 191
Query: 208 IIPSSTGAAKAVGKVLPALNGKLTG------------MAFRVPTVDVSVVDLTVRLEKDA 255
IIP G + + + + GKL RVP +D + V +K
Sbjct: 192 IIPHIGGEEEKIERETRKILGKLENGKIEPAPFSVSATTTRVPVLDGHTESVHVEFDKKF 251
Query: 256 SYDEIKAAIK 265
+EI+ A+K
Sbjct: 252 DIEEIREALK 261
>gnl|CDD|234595 PRK00048, PRK00048, dihydrodipicolinate reductase; Provisional.
Length = 257
Score = 38.6 bits (91), Expect = 0.002
Identities = 11/32 (34%), Positives = 19/32 (59%), Gaps = 1/32 (3%)
Query: 3 KVKIGINGF-GRIGRLVARVILQRDDVELVAV 33
+K+ + G GR+GR + + +D+ELVA
Sbjct: 1 MIKVAVAGASGRMGRELIEAVEAAEDLELVAA 32
>gnl|CDD|223366 COG0289, DapB, Dihydrodipicolinate reductase [Amino acid
transport and metabolism].
Length = 266
Score = 38.0 bits (89), Expect = 0.003
Identities = 13/32 (40%), Positives = 21/32 (65%), Gaps = 1/32 (3%)
Query: 3 KVKIGINGF-GRIGRLVARVILQRDDVELVAV 33
+K+ + G GR+GR + R +L+ D+ELVA
Sbjct: 2 MIKVAVAGASGRMGRTLIRAVLEAPDLELVAA 33
>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 = 35.3 bits (81), Expect = 0.021
Identities = 15/33 (45%), Positives = 22/33 (66%)
Query: 1 MGKVKIGINGFGRIGRLVARVILQRDDVELVAV 33
M K++ I G+G +GR V + I Q+ D+ELV V
Sbjct: 1 MSKIRAAIVGYGNLGRSVEKAIQQQPDMELVGV 33
>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 = 0.021
Identities = 13/28 (46%), Positives = 22/28 (78%)
Query: 6 IGINGFGRIGRLVARVILQRDDVELVAV 33
+G+NG+G IG+ VA + ++DD++LV V
Sbjct: 1 VGVNGYGTIGKRVADAVTKQDDMKLVGV 28
Score = 29.5 bits (66), Expect = 1.8
Identities = 20/53 (37%), Positives = 28/53 (52%), Gaps = 4/53 (7%)
Query: 209 IPSSTGAAKAVGKVLPALNGKLTGMAFRVPTVDVSVVDLTVRLEKDASYDEIK 261
+PS G V V+P LN + MAF VPT + V + V L+K + D+I
Sbjct: 187 VPSHHG--PDVQTVIPNLN--IETMAFVVPTTLMHVHSIMVELKKPVTKDDII 235
>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 = 35.2 bits (82), Expect = 0.025
Identities = 16/41 (39%), Positives = 23/41 (56%), Gaps = 2/41 (4%)
Query: 1 MGKVKIGINGFGRIGRLVARVILQRDDVELVAVNDPFITTD 41
+ +GI GFG IGR VA+ L+ E V V DP++ +
Sbjct: 145 LRGKTVGIVGFGAIGRRVAKR-LKAFGAE-VLVYDPYVDPE 183
>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 = 34.8 bits (81), Expect = 0.033
Identities = 16/41 (39%), Positives = 23/41 (56%), Gaps = 3/41 (7%)
Query: 2 GKVKIGINGFGRIGRLVARVILQRDDVELVAVNDPFITTDY 42
GK +GI G GRIG+ VAR L ++ V DP+ ++
Sbjct: 142 GK-TLGIIGLGRIGKAVAR-RLSGFGMK-VLAYDPYPDEEF 179
>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 = 34.0 bits (79), Expect = 0.042
Identities = 16/49 (32%), Positives = 26/49 (53%), Gaps = 2/49 (4%)
Query: 5 KIGINGFGRIGRLVARVILQRDDVELVAVNDPFITTDYMTYMFKYDSVH 53
+GI G GRIGR VAR L+ ++++A D + + +Y S+
Sbjct: 37 TVGIIGLGRIGRAVAR-RLKAFGMKVIAY-DRYPKAEAEALGARYVSLD 83
>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 = 34.5 bits (80), Expect = 0.050
Identities = 15/42 (35%), Positives = 22/42 (52%), Gaps = 2/42 (4%)
Query: 5 KIGINGFGRIGRLVARVILQRDDVELVAVNDPFITTDYMTYM 46
+GI GFGRIGR V +L+ + V V DP++ +
Sbjct: 152 TVGIVGFGRIGRAVVE-LLRPFGLR-VLVYDPYLPAAEAAAL 191
>gnl|CDD|237845 PRK14874, PRK14874, aspartate-semialdehyde dehydrogenase;
Provisional.
Length = 334
Score = 34.0 bits (79), Expect = 0.068
Identities = 14/46 (30%), Positives = 22/46 (47%), Gaps = 2/46 (4%)
Query: 129 DAPMFVVGVNEHEYK--PELNIVSNASCTTNCLAPLAKVIHDKFGI 172
D P+ V VN + I++N +C+T + K +HD GI
Sbjct: 102 DVPLVVPEVNPEALAEHRKKGIIANPNCSTIQMVVALKPLHDAAGI 147
>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 = 32.6 bits (75), Expect = 0.073
Identities = 14/34 (41%), Positives = 22/34 (64%), Gaps = 1/34 (2%)
Query: 4 VKIGINGFGRIGRLVARVILQ-RDDVELVAVNDP 36
+++GI G G+IGR R + + +D ELV + DP
Sbjct: 1 LRVGIVGAGKIGRRHLRALNESQDGAELVGILDP 34
>gnl|CDD|136022 PRK06728, PRK06728, aspartate-semialdehyde dehydrogenase;
Provisional.
Length = 347
Score = 33.5 bits (76), Expect = 0.087
Identities = 35/170 (20%), Positives = 65/170 (38%), Gaps = 33/170 (19%)
Query: 127 SKDAPMFVVGVNEHEYKPELNIVSNASCTTNCLAPLAKVIHDKFGIVEGLMTT------- 179
+ D P+ V VN H K I++ +C+ + + I FG+ +++T
Sbjct: 105 AHDVPLVVPEVNAHTLKEHKGIIAVPNCSALQMVTALQPIRKVFGLERIIVSTYQAVSGS 164
Query: 180 -VHSITATQKTVDG------------PSSKDWRGGRAASFNIIPS------------STG 214
+H+I ++ P+ KD + +FN++P
Sbjct: 165 GIHAIQELKEQAKSILAGEEVESTILPAKKD-KKHYPIAFNVLPQVDIFTDNDFTFEEVK 223
Query: 215 AAKAVGKVLPALNGKLTGMAFRVPTVDVSVVDLTVRLEKDASYDEIKAAI 264
+ K+L N K+ RVP + + + LEK+A+ EIK +
Sbjct: 224 MIQETKKILEDPNLKMAATCVRVPVISGHSESVYIELEKEATVAEIKEVL 273
>gnl|CDD|237436 PRK13581, PRK13581, D-3-phosphoglycerate dehydrogenase;
Provisional.
Length = 526
Score = 32.7 bits (76), Expect = 0.19
Identities = 15/38 (39%), Positives = 24/38 (63%), Gaps = 3/38 (7%)
Query: 2 GKVKIGINGFGRIGRLVARVILQRDDVELVAVNDPFIT 39
GK +GI G GRIG VA+ + ++++A DP+I+
Sbjct: 140 GKT-LGIIGLGRIGSEVAKR-AKAFGMKVIA-YDPYIS 174
>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 = 32.5 bits (75), Expect = 0.20
Identities = 17/41 (41%), Positives = 22/41 (53%), Gaps = 3/41 (7%)
Query: 1 MGKVKIGINGFGRIGRLVARVILQRDDVELVAVNDPFITTD 41
GK +GI G G IGR VAR L+ VE++ D F +
Sbjct: 141 SGK-TVGIVGLGNIGRAVAR-RLRGFGVEVIYY-DRFRDPE 178
>gnl|CDD|169409 PRK08374, PRK08374, homoserine dehydrogenase; Provisional.
Length = 336
Score = 32.1 bits (73), Expect = 0.27
Identities = 12/26 (46%), Positives = 18/26 (69%)
Query: 3 KVKIGINGFGRIGRLVARVILQRDDV 28
+VK+ I GFG +GR VA V+ ++ V
Sbjct: 2 EVKVSIFGFGNVGRAVAEVLAEKSRV 27
>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 = 32.0 bits (74), Expect = 0.28
Identities = 17/38 (44%), Positives = 25/38 (65%), Gaps = 3/38 (7%)
Query: 2 GKVKIGINGFGRIGRLVARVILQRDDVELVAVNDPFIT 39
GK +GI G GRIGR VAR + ++++A DP+I+
Sbjct: 138 GKT-LGIVGLGRIGREVAR-RARAFGMKVLA-YDPYIS 172
>gnl|CDD|236329 PRK08664, PRK08664, aspartate-semialdehyde dehydrogenase; Reviewed.
Length = 349
Score = 31.7 bits (73), Expect = 0.35
Identities = 45/177 (25%), Positives = 73/177 (41%), Gaps = 40/177 (22%)
Query: 118 AKKVIISAPS-----KDAPMFVVGVN-EH----EYKPELN-----IVSNASCTTNCLAPL 162
A K + S S D P+ + VN EH E + + IV+N +C+T L
Sbjct: 99 AGKPVFSNASAHRMDPDVPLVIPEVNPEHLELIEVQRKRRGWDGFIVTNPNCSTIGLVLA 158
Query: 163 AKVIHDKFGIVEGLMTTVHSITATQKT-VDGPSSKDWRGGRAASFNIIPSSTG-AAKAV- 219
K + D FGI +TT+ +I+ V D N+IP G K
Sbjct: 159 LKPLMD-FGIERVHVTTMQAISGAGYPGVPSMDIVD---------NVIPYIGGEEEKIEK 208
Query: 220 -----------GKVLPALNGKLTGMAFRVPTVDVSVVDLTVRLEKDASYDEIKAAIK 265
GK++PA + ++ RVP +D + V+ ++D +EI+ A++
Sbjct: 209 ETLKILGKFEGGKIVPA-DFPISATCHRVPVIDGHTEAVFVKFKEDVDPEEIREALE 264
>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 = 31.3 bits (72), Expect = 0.42
Identities = 15/50 (30%), Positives = 19/50 (38%), Gaps = 18/50 (36%)
Query: 6 IGINGFGRIGRLVA--------RVILQRDDVELVAVNDPFITTDYMTYMF 47
+G+ GFGRIGR VA RVI DP++
Sbjct: 145 LGLVGFGRIGRAVAKRAKAFGFRVI----------AYDPYVPDGVAALGG 184
>gnl|CDD|223189 COG0111, SerA, Phosphoglycerate dehydrogenase and related
dehydrogenases [Amino acid transport and metabolism].
Length = 324
Score = 31.1 bits (71), Expect = 0.52
Identities = 15/38 (39%), Positives = 23/38 (60%), Gaps = 3/38 (7%)
Query: 1 MGKVKIGINGFGRIGRLVARVILQRDDVELVAVNDPFI 38
GK +GI G GRIGR VA+ L+ ++++ DP+
Sbjct: 141 AGK-TVGIIGLGRIGRAVAKR-LKAFGMKVIGY-DPYS 175
>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 = 0.54
Identities = 12/19 (63%), Positives = 15/19 (78%), Gaps = 1/19 (5%)
Query: 2 GKVKIGINGFGRIGRLVAR 20
GK ++GI G GRIGR +AR
Sbjct: 141 GK-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 = 0.65
Identities = 12/19 (63%), Positives = 14/19 (73%), Gaps = 1/19 (5%)
Query: 2 GKVKIGINGFGRIGRLVAR 20
GK +GI G GRIG+ VAR
Sbjct: 144 GK-TLGIVGMGRIGQAVAR 161
>gnl|CDD|129147 TIGR00036, dapB, dihydrodipicolinate reductase. [Amino acid
biosynthesis, Aspartate family].
Length = 266
Score = 30.8 bits (70), Expect = 0.68
Identities = 39/144 (27%), Positives = 63/144 (43%), Gaps = 22/144 (15%)
Query: 4 VKIGING-FGRIGRLVARVILQRDDVELVAVNDPFITTDYMTYMFKYDSVHGQWKHHELK 62
+K+ + G GR+GR + + L + ++LVA + ++ T + + +
Sbjct: 2 IKVAVAGAAGRMGRELIKAALAAEGLQLVAAFERHGSSLQGTDAGELAGI----GKVGVP 57
Query: 63 VKDDKTLLFGEKPVTV-F----GVRNPEEIPWAETGAEYVVESTGVFTDKDK---AAAHL 114
V DD + + V + F GV N + E G VV +TG F+++DK A
Sbjct: 58 VTDDLEAVETDPDVLIDFTTPEGVLNHLKFA-LEHGVRLVVGTTG-FSEEDKQELADLAE 115
Query: 115 KGGAKKVIISAPSKDAPMFVVGVN 138
K G VI AP F +GVN
Sbjct: 116 KAGIAAVI-------APNFSIGVN 132
>gnl|CDD|223536 COG0460, ThrA, Homoserine dehydrogenase [Amino acid transport and
metabolism].
Length = 333
Score = 30.2 bits (69), Expect = 0.99
Identities = 12/44 (27%), Positives = 22/44 (50%), Gaps = 9/44 (20%)
Query: 1 MGKVKIGINGFGRIGRLVARVILQRD---------DVELVAVND 35
M VK+G+ G G +G V ++ ++ ++ +VAV D
Sbjct: 1 MKTVKVGLLGLGTVGSGVLEILAEKQEELRKRAGIEIRVVAVAD 44
>gnl|CDD|211797 TIGR03212, uraD_N-term-dom, putative urate catabolism protein.
This model represents a protein that is predominantly
found just upstream of the UraD protein (OHCU
decarboxylase) and in a number of instances as a
N-terminal fusion with it. UraD itself catalyzes the
last step in the catabolism of urate to allantoate. The
function of this protein is presently unknown. It shows
homology with the pfam01522 polysaccharide deacetylase
domain family.
Length = 297
Score = 30.1 bits (68), Expect = 1.2
Identities = 18/52 (34%), Positives = 25/52 (48%), Gaps = 16/52 (30%)
Query: 43 MTYMFKYDSVHGQWKHHELKVKDDKTLLFGEK--PVTVFGV-----RNPEEI 87
M +++Y S G W+ L F E+ P+TVFGV RNPE +
Sbjct: 67 MESLYEYGSRAGFWRLLRL---------FTERGLPLTVFGVAMALARNPEAV 109
>gnl|CDD|173409 PTZ00117, PTZ00117, malate dehydrogenase; Provisional.
Length = 319
Score = 29.7 bits (67), Expect = 1.4
Identities = 44/170 (25%), Positives = 69/170 (40%), Gaps = 40/170 (23%)
Query: 5 KIGINGFGRIGRLVARVILQRD--DVELVAVNDPFITTDYMTYMFKYDSVHGQWKHHELK 62
KI + G G+IG VA +ILQ++ DV L YD + G + L
Sbjct: 7 KISMIGAGQIGSTVALLILQKNLGDVVL------------------YDVIKGVPQGKALD 48
Query: 63 VKDDKTLLFGEKPVTVFGVRNPEEIPWAETGAEYVVESTGVFTDKDKAAAHLKGGAKKVI 122
+K TL+ + + G N E+I ++ VV + GV ++ L K++
Sbjct: 49 LKHFSTLV--GSNINILGTNNYEDI----KDSDVVVITAGVQRKEEMTREDLLTINGKIM 102
Query: 123 ISAPSKDAPMFVVGVNEHEYKPELNIVSNASCTTNCLAPLAKVIHDKFGI 172
S V + +Y P ++ C TN L + KV +K GI
Sbjct: 103 KS----------VAESVKKYCPNAFVI----CVTNPLDCMVKVFQEKSGI 138
>gnl|CDD|224459 COG1542, COG1542, Uncharacterized conserved protein [Function
unknown].
Length = 593
Score = 29.8 bits (67), Expect = 1.5
Identities = 29/109 (26%), Positives = 38/109 (34%), Gaps = 37/109 (33%)
Query: 62 KVKDDKTLLFGEKPVTVFGVR-----------NPEEIPWAETGAEYVVESTGVFTDKDKA 110
KV +D EK VT GV+ N E W E E + S G T+K +
Sbjct: 358 KVLED-----LEKSVTADGVKAITYTEEFDAPNAE---WYEQAKEEGLVSRGAITEKGRL 409
Query: 111 AA----------HLKGGAKKVIISAPSK--DAPMFV------VGVNEHE 141
A +L KV+I P K + VG +E E
Sbjct: 410 YAKLSKTIKRKPYLTKYEIKVLIKIPRKYIKRGELIEDIQGHVGGDEEE 458
>gnl|CDD|181499 PRK08605, PRK08605, D-lactate dehydrogenase; Validated.
Length = 332
Score = 29.7 bits (67), Expect = 1.7
Identities = 16/52 (30%), Positives = 28/52 (53%), Gaps = 1/52 (1%)
Query: 1 MGKVKIGINGFGRIGRLVARVILQRDDVELVAVNDPFITTDYMTYMFKYDSV 52
+ +K+ + G GRIG VA++ + ++VA DPF TY+ D++
Sbjct: 144 IKDLKVAVIGTGRIGLAVAKIFAKGYGSDVVAY-DPFPNAKAATYVDYKDTI 194
>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 = 1.8
Identities = 12/19 (63%), Positives = 14/19 (73%), Gaps = 1/19 (5%)
Query: 2 GKVKIGINGFGRIGRLVAR 20
GK +GI G GRIG+ VAR
Sbjct: 146 GK-TLGIIGLGRIGQAVAR 163
>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 = 1.9
Identities = 13/20 (65%), Positives = 16/20 (80%), Gaps = 1/20 (5%)
Query: 2 GKVKIGINGFGRIGRLVARV 21
GK +GI GFGRIGR VA++
Sbjct: 139 GKT-LGIIGFGRIGREVAKI 157
>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 = 29.1 bits (66), Expect = 2.0
Identities = 12/19 (63%), Positives = 14/19 (73%), Gaps = 1/19 (5%)
Query: 2 GKVKIGINGFGRIGRLVAR 20
GK +GI G GRIG+ VAR
Sbjct: 144 GKT-LGIIGMGRIGQAVAR 161
>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 = 29.1 bits (66), Expect = 2.0
Identities = 13/41 (31%), Positives = 23/41 (56%), Gaps = 3/41 (7%)
Query: 1 MGKVKIGINGFGRIGRLVARVILQRDDVELVAVNDPFITTD 41
GK +G+ G G IGRLVA ++++ DP+++ +
Sbjct: 134 RGK-TLGVIGLGNIGRLVAN-AALALGMKVIGY-DPYLSVE 171
>gnl|CDD|181041 PRK07574, PRK07574, formate dehydrogenase; Provisional.
Length = 385
Score = 29.3 bits (66), Expect = 2.2
Identities = 9/16 (56%), Positives = 10/16 (62%)
Query: 5 KIGINGFGRIGRLVAR 20
+GI G GRIG V R
Sbjct: 194 TVGIVGAGRIGLAVLR 209
>gnl|CDD|235763 PRK06270, PRK06270, homoserine dehydrogenase; Provisional.
Length = 341
Score = 29.1 bits (66), Expect = 2.2
Identities = 12/42 (28%), Positives = 25/42 (59%), Gaps = 9/42 (21%)
Query: 3 KVKIGINGFGRIGRLVARVILQRD---------DVELVAVND 35
++KI + GFG +G+ VA ++ ++ D+++VA+ D
Sbjct: 2 EMKIALIGFGGVGQGVAELLAEKREYLKKRYGLDLKVVAIAD 43
>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 = 29.0 bits (66), Expect = 2.3
Identities = 12/20 (60%), Positives = 14/20 (70%), Gaps = 1/20 (5%)
Query: 2 GKVKIGINGFGRIGRLVARV 21
GK +GI G GRIG VAR+
Sbjct: 142 GK-TLGIVGLGRIGARVARI 160
>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 = 29.2 bits (66), Expect = 2.4
Identities = 8/28 (28%), Positives = 16/28 (57%)
Query: 6 IGINGFGRIGRLVARVILQRDDVELVAV 33
+ I G G +G+ VA ++ + D+E+
Sbjct: 1 VLIIGAGGVGQGVAPLLARHGDLEITVA 28
>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 = 28.8 bits (65), Expect = 3.0
Identities = 15/46 (32%), Positives = 25/46 (54%), Gaps = 2/46 (4%)
Query: 6 IGINGFGRIGRLVARVILQRDDVELVAVNDPFITTDYMTYMFKYDS 51
+G+ G G+IGR VA+ + ++++A DPF + KY S
Sbjct: 146 VGVVGTGKIGRAVAQ-RAKGFGMKVIAY-DPFRNPELEDKGVKYVS 189
>gnl|CDD|235287 PRK04342, PRK04342, DNA topoisomerase VI subunit A; Provisional.
Length = 367
Score = 28.7 bits (65), Expect = 3.0
Identities = 14/45 (31%), Positives = 20/45 (44%), Gaps = 11/45 (24%)
Query: 83 NPEEIPWAETGAEYV--VESTGV--------FTDKDKAA-AHLKG 116
N + I + + A++V VE G+ F K A HLKG
Sbjct: 179 NVDNIEFVDVDADFVLAVEKGGMFQRLVEEGFWKKYNAILVHLKG 223
>gnl|CDD|215144 PLN02256, PLN02256, arogenate dehydrogenase.
Length = 304
Score = 28.5 bits (64), Expect = 3.3
Identities = 10/25 (40%), Positives = 17/25 (68%)
Query: 1 MGKVKIGINGFGRIGRLVARVILQR 25
K+KIGI GFG G+ +A+ +++
Sbjct: 34 SRKLKIGIVGFGNFGQFLAKTFVKQ 58
>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 = 28.8 bits (65), Expect = 3.4
Identities = 12/21 (57%), Positives = 15/21 (71%), Gaps = 1/21 (4%)
Query: 1 MGKVKIGINGFGRIGRLVARV 21
GK +G+ G GRIGR VAR+
Sbjct: 138 AGKT-LGVVGTGRIGRRVARI 157
>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 = 28.4 bits (64), Expect = 3.4
Identities = 9/16 (56%), Positives = 12/16 (75%)
Query: 5 KIGINGFGRIGRLVAR 20
+GI G GRIG+ VA+
Sbjct: 142 TVGIVGLGRIGQRVAK 157
>gnl|CDD|185742 cd09001, GH43_XYL_2, Glycosyl hydrolase family 43,
beta-D-xylosidase. This glycosyl hydrolase family 43
(GH43) includes mostly enzymes that have been
characterized to have beta-1,4-xylosidase
(beta-D-xylosidase;xylan 1,4-beta-xylosidase; EC
3.2.1.37) activity. They are part of an array of
hemicellulases that are involved in the final breakdown
of plant cell-wall whereby they degrade xylan. They
hydrolyze beta-1,4 glycosidic bonds between two xylose
units in short xylooligosaccharides. These are inverting
enzymes (i.e. they invert the stereochemistry of the
anomeric carbon atom of the substrate) that have an
aspartate as the catalytic general base, a glutamate as
the catalytic general acid and another aspartate that is
responsible for pKa modulation and orienting the
catalytic acid. A common structural feature of GH43
enzymes is a 5-bladed beta-propeller domain that
contains the catalytic acid and catalytic base. A long
V-shaped groove, partially enclosed at one end, forms a
single extended substrate-binding surface across the
face of the propeller.
Length = 269
Score = 28.3 bits (64), Expect = 3.5
Identities = 12/36 (33%), Positives = 15/36 (41%), Gaps = 1/36 (2%)
Query: 37 FITTDYMTYMFKYDSVHGQWKHHEL-KVKDDKTLLF 71
F T TY++ D G W L D +LLF
Sbjct: 92 FCTNTGGTYIYTADDPEGPWTKTALDGGYHDPSLLF 127
>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 = 3.5
Identities = 10/20 (50%), Positives = 13/20 (65%), Gaps = 1/20 (5%)
Query: 1 MGKVKIGINGFGRIGRLVAR 20
GK +GI G G IG+ +AR
Sbjct: 153 RGKT-LGILGLGGIGKAIAR 171
>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 = 3.9
Identities = 11/33 (33%), Positives = 17/33 (51%), Gaps = 2/33 (6%)
Query: 5 KIGINGFGRIGRLVARVILQRDDVELVAVNDPF 37
+GI G G +G +AR L+ + V + DP
Sbjct: 117 TVGIVGVGNVGSRLARR-LEALGMN-VLLCDPP 147
>gnl|CDD|149729 pfam08759, DUF1792, Domain of unknown function (DUF1792). This
putative domain is probably missannotated as a glycosyl
transferase 8 family member. This domain is found at the
C-terminus of proteins that also contain the glycosyl
transferase domain at the N-terminus.
Length = 225
Score = 28.0 bits (63), Expect = 4.4
Identities = 12/47 (25%), Positives = 21/47 (44%), Gaps = 2/47 (4%)
Query: 37 FITTDYMTYMFKYDSVHGQWKHHELKVKDDKTLLFGEKPVTVFGVRN 83
FI+ Y+ Y K S + H ++ ++ +L E + GV N
Sbjct: 88 FISRPYIDYKDKSKSAR--YFHKLKQIWQNRDILIVEGEKSRSGVGN 132
>gnl|CDD|183914 PRK13243, PRK13243, glyoxylate reductase; Reviewed.
Length = 333
Score = 28.2 bits (63), Expect = 4.4
Identities = 12/15 (80%), Positives = 13/15 (86%)
Query: 6 IGINGFGRIGRLVAR 20
IGI GFGRIG+ VAR
Sbjct: 153 IGIIGFGRIGQAVAR 167
>gnl|CDD|224626 COG1712, COG1712, Predicted dinucleotide-utilizing enzyme
[General function prediction only].
Length = 255
Score = 28.1 bits (63), Expect = 4.5
Identities = 15/32 (46%), Positives = 20/32 (62%), Gaps = 1/32 (3%)
Query: 5 KIGINGFGRIGRLVARVILQ-RDDVELVAVND 35
K+GI G G IG+ + ++ R D ELVAV D
Sbjct: 2 KVGIVGCGAIGKFLLELVRDGRVDFELVAVYD 33
>gnl|CDD|235783 PRK06349, PRK06349, homoserine dehydrogenase; Provisional.
Length = 426
Score = 28.1 bits (64), Expect = 4.6
Identities = 10/42 (23%), Positives = 20/42 (47%), Gaps = 9/42 (21%)
Query: 1 MGKVKIGINGFGRIGRLVARVILQRDD---------VELVAV 33
M +K+G+ G G +G V R++ + + +E+ V
Sbjct: 1 MKPLKVGLLGLGTVGSGVVRILEENAEEIAARAGRPIEIKKV 42
>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 = 28.1 bits (63), Expect = 5.0
Identities = 11/38 (28%), Positives = 25/38 (65%), Gaps = 1/38 (2%)
Query: 6 IGINGFGRIGRLVARVILQRDDVELVAVNDPFITTDYM 43
+GI G+G IG VA ++ + + +++A DP+++ + +
Sbjct: 150 VGIIGYGNIGSRVAEILKEGFNAKVLAY-DPYVSEEVI 186
>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 = 27.8 bits (63), Expect = 5.7
Identities = 11/20 (55%), Positives = 15/20 (75%), Gaps = 1/20 (5%)
Query: 2 GKVKIGINGFGRIGRLVARV 21
GK +GI G+G IG+ VAR+
Sbjct: 147 GK-TLGIIGYGNIGQAVARI 165
>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 = 27.9 bits (63), Expect = 5.8
Identities = 8/20 (40%), Positives = 12/20 (60%)
Query: 1 MGKVKIGINGFGRIGRLVAR 20
+ + +GI G GRIG A+
Sbjct: 143 IRDLTVGIIGTGRIGSAAAK 162
>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 = 27.6 bits (62), Expect = 6.8
Identities = 9/17 (52%), Positives = 13/17 (76%)
Query: 5 KIGINGFGRIGRLVARV 21
++GI G+G IGR AR+
Sbjct: 135 RVGILGYGSIGRQTARL 151
>gnl|CDD|223745 COG0673, MviM, Predicted dehydrogenases and related proteins
[General function prediction only].
Length = 342
Score = 27.5 bits (61), Expect = 7.5
Identities = 12/38 (31%), Positives = 17/38 (44%), Gaps = 2/38 (5%)
Query: 1 MGKVKIGINGFGRIGRL-VARVILQRDD-VELVAVNDP 36
M +++GI G G I + +ELVAV D
Sbjct: 1 MKMIRVGIIGAGGIAGKAHLPALAALGGGLELVAVVDR 38
>gnl|CDD|152128 pfam11692, DUF3289, Protein of unknown function (DUF3289). This
family of proteins with unknown function appears to be
restricted to Proteobacteria.
Length = 277
Score = 27.4 bits (61), Expect = 8.0
Identities = 20/79 (25%), Positives = 33/79 (41%), Gaps = 8/79 (10%)
Query: 119 KKVIISAPSKDAPMFVV-GVNEHEYKPELNIVSNASCTTNCLA-PLAKVIHDKF----GI 172
K+VI+ + ++ + V+ + + + I + L L + KF
Sbjct: 132 KEVILGDKTNNSSLLVIKAILDRGIDWDKKIFPYN--LKDELKTALKSSVLPKFNRLQDR 189
Query: 173 VEGLMTTVHSITATQKTVD 191
GL TVH I ATQ T+D
Sbjct: 190 FNGLGITVHDIYATQITID 208
>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 = 27.3 bits (61), Expect = 9.5
Identities = 10/43 (23%), Positives = 21/43 (48%)
Query: 93 GAEYVVESTGVFTDKDKAAAHLKGGAKKVIISAPSKDAPMFVV 135
GA+ V+++ G +A L+ G + V++ S P+ +
Sbjct: 201 GADVVIDAVGGPETLAQALRLLRPGGRIVVVGGTSGGPPLDDL 243
>gnl|CDD|177941 PLN02306, PLN02306, hydroxypyruvate reductase.
Length = 386
Score = 27.1 bits (60), Expect = 9.8
Identities = 21/82 (25%), Positives = 39/82 (47%), Gaps = 16/82 (19%)
Query: 6 IGINGFGRIGRLVARVILQRDDVELVAVNDPFITTDYMTYMFKYDSVHGQWKHHELKVKD 65
+G+ G GRIG AR++++ + L+ D + +T + K+ + +GQ+
Sbjct: 168 VGVIGAGRIGSAYARMMVEGFKMNLIYY-DLYQSTR----LEKFVTAYGQFLKAN----- 217
Query: 66 DKTLLFGEKPVTVFGVRNPEEI 87
GE+PVT + EE+
Sbjct: 218 ------GEQPVTWKRASSMEEV 233
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.317 0.134 0.391
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: 13,527,257
Number of extensions: 1282829
Number of successful extensions: 1356
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1287
Number of HSP's successfully gapped: 105
Length of query: 265
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 170
Effective length of database: 6,723,972
Effective search space: 1143075240
Effective search space used: 1143075240
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: 58 (26.0 bits)