RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 025368
(254 letters)
>gnl|CDD|165999 PLN02358, PLN02358, glyceraldehyde-3-phosphate dehydrogenase.
Length = 338
Score = 453 bits (1166), Expect = e-162
Identities = 230/263 (87%), Positives = 246/263 (93%), Gaps = 11/263 (4%)
Query: 3 KVKIGINGFGRIGRLVARVILQRDDVELVA-----------TYMFKYDSVHGQWKHHELK 51
K++IGINGFGRIGRLVARV+LQRDDVELVA TYMFKYDSVHGQWKHHELK
Sbjct: 5 KIRIGINGFGRIGRLVARVVLQRDDVELVAVNDPFITTEYMTYMFKYDSVHGQWKHHELK 64
Query: 52 VKDDKTLLFGEKPVTVFGVRNPEEIPWAETGAEYVVESTGVFTDKDKAAAHLKGGAKKVI 111
VKDDKTLLFGEKPVTVFG+RNPE+IPW E GA++VVESTGVFTDKDKAAAHLKGGAKKV+
Sbjct: 65 VKDDKTLLFGEKPVTVFGIRNPEDIPWGEAGADFVVESTGVFTDKDKAAAHLKGGAKKVV 124
Query: 112 ISAPSKDAPMFVVGVNENEYKPELNIVSNASCTTNCLAPLAKVIHDKFGIVEGLMTTVHS 171
ISAPSKDAPMFVVGVNE+EYK +L+IVSNASCTTNCLAPLAKVI+D+FGIVEGLMTTVHS
Sbjct: 125 ISAPSKDAPMFVVGVNEHEYKSDLDIVSNASCTTNCLAPLAKVINDRFGIVEGLMTTVHS 184
Query: 172 ITATQKTVDGPSSKDWRGGRAASFNIIPSSTGAAKAVGKVLPALNGKLTGMAFRVPTVDV 231
ITATQKTVDGPS KDWRGGRAASFNIIPSSTGAAKAVGKVLP+LNGKLTGM+FRVPTVDV
Sbjct: 185 ITATQKTVDGPSMKDWRGGRAASFNIIPSSTGAAKAVGKVLPSLNGKLTGMSFRVPTVDV 244
Query: 232 SVVDLTVRLEKDASYDEIKAAIK 254
SVVDLTVRLEK A+YDEIK AIK
Sbjct: 245 SVVDLTVRLEKAATYDEIKKAIK 267
>gnl|CDD|177912 PLN02272, PLN02272, glyceraldehyde-3-phosphate dehydrogenase.
Length = 421
Score = 441 bits (1136), Expect = e-157
Identities = 191/264 (72%), Positives = 213/264 (80%), Gaps = 12/264 (4%)
Query: 2 GKVKIGINGFGRIGRLVARVILQRDDVELVA-----------TYMFKYDSVHGQWKHHEL 50
GK KIGINGFGRIGRLV R+ RDD+E+VA YMFKYDS HG +K +
Sbjct: 84 GKTKIGINGFGRIGRLVLRIATSRDDIEVVAVNDPFIDAKYMAYMFKYDSTHGNFKGT-I 142
Query: 51 KVKDDKTLLFGEKPVTVFGVRNPEEIPWAETGAEYVVESTGVFTDKDKAAAHLKGGAKKV 110
V DD TL K + V R+P EIPW + GAEYVVES+GVFT +KA+AHLKGGAKKV
Sbjct: 143 NVVDDSTLEINGKQIKVTSKRDPAEIPWGDFGAEYVVESSGVFTTVEKASAHLKGGAKKV 202
Query: 111 IISAPSKDAPMFVVGVNENEYKPELNIVSNASCTTNCLAPLAKVIHDKFGIVEGLMTTVH 170
+ISAPS DAPMFVVGVNE YKP +NIVSNASCTTNCLAPLAKV+H++FGI+EGLMTTVH
Sbjct: 203 VISAPSADAPMFVVGVNEKTYKPNMNIVSNASCTTNCLAPLAKVVHEEFGILEGLMTTVH 262
Query: 171 SITATQKTVDGPSSKDWRGGRAASFNIIPSSTGAAKAVGKVLPALNGKLTGMAFRVPTVD 230
+ TATQKTVDGPS KDWRGGR AS NIIPSSTGAAKAVGKVLP LNGKLTGMAFRVPT +
Sbjct: 263 ATTATQKTVDGPSMKDWRGGRGASQNIIPSSTGAAKAVGKVLPELNGKLTGMAFRVPTPN 322
Query: 231 VSVVDLTVRLEKDASYDEIKAAIK 254
VSVVDLT RLEK ASY+++KAAIK
Sbjct: 323 VSVVDLTCRLEKSASYEDVKAAIK 346
>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 = 375 bits (966), Expect = e-132
Identities = 151/263 (57%), Positives = 188/263 (71%), Gaps = 15/263 (5%)
Query: 5 KIGINGFGRIGRLVARVILQRD--DVELVA----------TYMFKYDSVHGQWKHHELKV 52
K+GINGFGRIGRLV R IL++ D+E+VA Y+ KYDSVHG+++ E+
Sbjct: 1 KVGINGFGRIGRLVLRAILEKPGNDLEVVAINDLTDLEYLAYLLKYDSVHGRFEG-EVTA 59
Query: 53 KDDKTLLFGEKPVTVFGVRNPEEIPWAETGAEYVVESTGVFTDKDKAAAHLKGGAKKVII 112
+D ++ G++ ++VF R+P ++PW G + V+E TG F DK+K HL+ GAKKV+I
Sbjct: 60 DEDGLVVNGKEVISVFSERDPSDLPWKALGVDIVIECTGKFRDKEKLEGHLEAGAKKVLI 119
Query: 113 SAPSK-DAPMFVVGVNENEYKPELNIVSNASCTTNCLAPLAKVIHDKFGIVEGLMTTVHS 171
SAPSK D V GVN +EY P IVSNASCTTNCLAPLAKV+ + FGIV GLMTTVHS
Sbjct: 120 SAPSKGDVKTIVYGVNHDEYDPSERIVSNASCTTNCLAPLAKVLDEAFGIVSGLMTTVHS 179
Query: 172 ITATQKTVDGPSSKDWRGGRAASFNIIPSSTGAAKAVGKVLPALNGKLTGMAFRVPTVDV 231
T Q VDGP KD R RAA+ NIIP+STGAAKA+GKVLP L GKLTGMA RVPT +V
Sbjct: 180 YTNDQNLVDGPH-KDLRRARAAALNIIPTSTGAAKAIGKVLPELAGKLTGMAIRVPTPNV 238
Query: 232 SVVDLTVRLEKDASYDEIKAAIK 254
S+VDL V LEKD + +E+ AA+K
Sbjct: 239 SLVDLVVNLEKDVTVEEVNAALK 261
>gnl|CDD|223135 COG0057, GapA, Glyceraldehyde-3-phosphate
dehydrogenase/erythrose-4-phosphate dehydrogenase
[Carbohydrate transport and metabolism].
Length = 335
Score = 376 bits (967), Expect = e-132
Identities = 156/265 (58%), Positives = 188/265 (70%), Gaps = 16/265 (6%)
Query: 3 KVKIGINGFGRIGRLVARVILQRD-DVELVA----------TYMFKYDSVHGQWKHHELK 51
+K+ INGFGRIGRLVAR L+RD D+E+VA ++ KYDSVHG++ E++
Sbjct: 1 MIKVAINGFGRIGRLVARAALERDGDIEVVAINDLTDPDYLAHLLKYDSVHGRFDG-EVE 59
Query: 52 VKDDKTLLFGEKPVTVFGVRNPEEIPWAETGAEYVVESTGVFTDKDKAAAHL-KGGAKKV 110
VKDD L+ K + V R+P +PWA+ G + VVE TG FT ++KA HL GGAKKV
Sbjct: 60 VKDD-ALVVNGKGIKVLAERDPANLPWADLGVDIVVECTGKFTGREKAEKHLKAGGAKKV 118
Query: 111 IISAPSKDA-PMFVVGVNENEYKPELNIVSNASCTTNCLAPLAKVIHDKFGIVEGLMTTV 169
+ISAP KD V GVN N Y IVSNASCTTNCLAP+AKV++D FGI +GLMTTV
Sbjct: 119 LISAPGKDDVATVVYGVNHNYYDAGHTIVSNASCTTNCLAPVAKVLNDAFGIEKGLMTTV 178
Query: 170 HSITATQKTVDGPSSKDWRGGRAASFNIIPSSTGAAKAVGKVLPALNGKLTGMAFRVPTV 229
H+ T QK VDGP KD R RAA+ NIIP+STGAAKAVG VLP L GKLTGMA RVPT
Sbjct: 179 HAYTNDQKLVDGPH-KDLRRARAAALNIIPTSTGAAKAVGLVLPELKGKLTGMAIRVPTP 237
Query: 230 DVSVVDLTVRLEKDASYDEIKAAIK 254
+VSVVDLTV LEK+ + +EI AA+K
Sbjct: 238 NVSVVDLTVELEKEVTVEEINAALK 262
>gnl|CDD|173322 PTZ00023, PTZ00023, glyceraldehyde-3-phosphate dehydrogenase;
Provisional.
Length = 337
Score = 363 bits (933), Expect = e-127
Identities = 170/265 (64%), Positives = 195/265 (73%), Gaps = 16/265 (6%)
Query: 4 VKIGINGFGRIGRLVARVILQRDDVELVAT-----------YMFKYDSVHGQWKHHELKV 52
VK+GINGFGRIGRLV R L+R+DVE+VA Y+ KYDSVHG E+ V
Sbjct: 3 VKLGINGFGRIGRLVFRAALEREDVEVVAINDPFMTLDYMCYLLKYDSVHGSLPA-EVSV 61
Query: 53 KDDKTLLFGEKPVTVFGVRNPEEIPWAETGAEYVVESTGVFTDKDKAAAHLKGGAKKVII 112
D L+ G K V VF ++P IPW + G + V ESTGVF K+KA AHLKGGAKKVI+
Sbjct: 62 TDG-FLMIGSKKVHVFFEKDPAAIPWGKNGVDVVCESTGVFLTKEKAQAHLKGGAKKVIM 120
Query: 113 SAPSKD-APMFVVGVNENEYKPELNIVSNASCTTNCLAPLAKVIHDKFGIVEGLMTTVHS 171
SAP KD P++V+GVN +Y IVSNASCTTNCLAPLAKV++DKFGIVEGLMTTVH+
Sbjct: 121 SAPPKDDTPIYVMGVNHTQYDKSQRIVSNASCTTNCLAPLAKVVNDKFGIVEGLMTTVHA 180
Query: 172 ITATQKTVDGPS--SKDWRGGRAASFNIIPSSTGAAKAVGKVLPALNGKLTGMAFRVPTV 229
TA Q TVDGPS KDWR GR A NIIP+STGAAKAVGKV+P LNGKLTGMAFRVP
Sbjct: 181 STANQLTVDGPSKGGKDWRAGRCAGVNIIPASTGAAKAVGKVIPELNGKLTGMAFRVPVP 240
Query: 230 DVSVVDLTVRLEKDASYDEIKAAIK 254
DVSVVDLT +L K A Y+EI AA+K
Sbjct: 241 DVSVVDLTCKLAKPAKYEEIVAAVK 265
>gnl|CDD|185323 PRK15425, gapA, glyceraldehyde-3-phosphate dehydrogenase A;
Provisional.
Length = 331
Score = 298 bits (763), Expect = e-101
Identities = 162/262 (61%), Positives = 198/262 (75%), Gaps = 14/262 (5%)
Query: 4 VKIGINGFGRIGRLVARVILQRDDVELVA----------TYMFKYDSVHGQWKHHELKVK 53
+K+GINGFGRIGR+V R +R D+E+VA YM KYDS HG++ ++VK
Sbjct: 3 IKVGINGFGRIGRIVFRAAQKRSDIEIVAINDLLDADYMAYMLKYDSTHGRFDG-TVEVK 61
Query: 54 DDKTLLFGEKPVTVFGVRNPEEIPWAETGAEYVVESTGVFTDKDKAAAHLKGGAKKVIIS 113
D ++ G+K + V R+P + W E G + V E+TG+F + A H+ GAKKV+++
Sbjct: 62 DGHLIVNGKK-IRVTAERDPANLKWDEVGVDVVAEATGLFLTDETARKHITAGAKKVVMT 120
Query: 114 APSKD-APMFVVGVNENEYKPELNIVSNASCTTNCLAPLAKVIHDKFGIVEGLMTTVHSI 172
PSKD PMFV G N ++Y + +IVSNASCTTNCLAPLAKVI+D FGI+EGLMTTVH+
Sbjct: 121 GPSKDNTPMFVKGANFDKYAGQ-DIVSNASCTTNCLAPLAKVINDNFGIIEGLMTTVHAT 179
Query: 173 TATQKTVDGPSSKDWRGGRAASFNIIPSSTGAAKAVGKVLPALNGKLTGMAFRVPTVDVS 232
TATQKTVDGPS KDWRGGR AS NIIPSSTGAAKAVGKVLP LNGKLTGMAFRVPT +VS
Sbjct: 180 TATQKTVDGPSHKDWRGGRGASQNIIPSSTGAAKAVGKVLPELNGKLTGMAFRVPTPNVS 239
Query: 233 VVDLTVRLEKDASYDEIKAAIK 254
VVDLTVRLEK A+Y++IKAA+K
Sbjct: 240 VVDLTVRLEKAATYEQIKAAVK 261
>gnl|CDD|185614 PTZ00434, PTZ00434, cytosolic glyceraldehyde 3-phosphate
dehydrogenase; Provisional.
Length = 361
Score = 295 bits (755), Expect = e-100
Identities = 155/279 (55%), Positives = 192/279 (68%), Gaps = 25/279 (8%)
Query: 1 MGKVKIGINGFGRIGRLVARVILQRD----DVELVA-----------TYMFKYDSVHGQW 45
M +K+GINGFGRIGR+V + I + ++++VA Y KYD+VHG+
Sbjct: 1 MAPIKVGINGFGRIGRMVFQAICDQGLIGTEIDVVAVVDMSTNAEYFAYQMKYDTVHGRP 60
Query: 46 KHHELKVK-------DDKTLLFGEKPVTVFGVRNPEEIPWAETGAEYVVESTGVFTDKDK 98
K+ K DD ++ G + V RNP ++PW + G +YV+ESTG+FTDK
Sbjct: 61 KYTVETTKSSPSVKTDDVLVVNGHRIKCVKAQRNPADLPWGKLGVDYVIESTGLFTDKLA 120
Query: 99 AAAHLKGGAKKVIISAP-SKDAPMFVVGVNENEYKP-ELNIVSNASCTTNCLAPLAKVI- 155
A HLKGGAKKV+ISAP S A V+GVN++EY P E ++VSNASCTTNCLAP+ V+
Sbjct: 121 AEGHLKGGAKKVVISAPASGGAKTIVMGVNQHEYSPTEHHVVSNASCTTNCLAPIVHVLT 180
Query: 156 HDKFGIVEGLMTTVHSITATQKTVDGPSSKDWRGGRAASFNIIPSSTGAAKAVGKVLPAL 215
+ FGI GLMTT+HS TATQKTVDG S KDWRGGRAA+ NIIPS+TGAAKAVG V+P+
Sbjct: 181 KEGFGIETGLMTTIHSYTATQKTVDGVSVKDWRGGRAAAVNIIPSTTGAAKAVGMVIPST 240
Query: 216 NGKLTGMAFRVPTVDVSVVDLTVRLEKDASYDEIKAAIK 254
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 = 285 bits (732), Expect = 2e-96
Identities = 128/264 (48%), Positives = 180/264 (68%), Gaps = 15/264 (5%)
Query: 3 KVKIGINGFGRIGRLVARVILQRDDVELVA----------TYMFKYDSVHGQWKHHELKV 52
K K+ INGFGRIGR+V R ++ E+VA ++ KYD+VHG++ ++
Sbjct: 2 KTKVAINGFGRIGRMVFRKAIKESAFEIVAINASYPSETLAHLIKYDTVHGKFDG-TVEA 60
Query: 53 KDDKTLLFGEKPVTVFGVRNPEEIPWAETGAEYVVESTGVFTDKDKAAAHLKGGAKKVII 112
+D L+ G+K + + R+P+E+PW + G + V+E+TG F K+KA H++ GAKKVI+
Sbjct: 61 FEDHLLVDGKK-IRLLNNRDPKELPWTDLGIDIVIEATGKFNSKEKAILHVEAGAKKVIL 119
Query: 113 SAPSKDAPM-FVVGVNENEYKPELN-IVSNASCTTNCLAPLAKVIHDKFGIVEGLMTTVH 170
+AP K+ + VVGVNE++ E + I+SNASCTTNCLAP+ KV+ ++FGI GLMTTVH
Sbjct: 120 TAPGKNEDVTIVVGVNEDQLDIEKHTIISNASCTTNCLAPVVKVLDEQFGIENGLMTTVH 179
Query: 171 SITATQKTVDGPSSKDWRGGRAASFNIIPSSTGAAKAVGKVLPALNGKLTGMAFRVPTVD 230
+ T QK +D P KD R RA +IIP++TGAAKA+ KVLP LNGKL GMA RVPT +
Sbjct: 180 AYTNDQKNIDNPH-KDLRRARACGQSIIPTTTGAAKALAKVLPHLNGKLHGMALRVPTPN 238
Query: 231 VSVVDLTVRLEKDASYDEIKAAIK 254
VS+VDL V +++D + +EI A K
Sbjct: 239 VSLVDLVVDVKRDVTVEEINEAFK 262
>gnl|CDD|215131 PLN02237, PLN02237, glyceraldehyde-3-phosphate dehydrogenase B.
Length = 442
Score = 263 bits (673), Expect = 2e-86
Identities = 136/268 (50%), Positives = 180/268 (67%), Gaps = 18/268 (6%)
Query: 3 KVKIGINGFGRIGRLVARVILQRDDVEL------------VATYMFKYDSVHGQWKHHEL 50
K+K+ INGFGRIGR R R D L A+++ KYDS+ G +K ++
Sbjct: 75 KLKVAINGFGRIGRNFLRCWHGRKDSPLDVVVVNDSGGVKNASHLLKYDSMLGTFKA-DV 133
Query: 51 KVKDDKTLLFGEKPVTVFGVRNPEEIPWAETGAEYVVESTGVFTDKDKAAAHLKGGAKKV 110
K+ DD+T+ KP+ V R+P ++PWAE G + V+E TGVF D A H++ GAKKV
Sbjct: 134 KIVDDETISVDGKPIKVVSNRDPLKLPWAELGIDIVIEGTGVFVDGPGAGKHIQAGAKKV 193
Query: 111 IISAPSK--DAPMFVVGVNENEYKPEL-NIVSNASCTTNCLAPLAKVIHDKFGIVEGLMT 167
II+AP+K D P +VVGVNE++Y E+ NIVSNASCTTNCLAP KV+ ++FGIV+G MT
Sbjct: 194 IITAPAKGADIPTYVVGVNEDDYDHEVANIVSNASCTTNCLAPFVKVLDEEFGIVKGTMT 253
Query: 168 TVHSITATQKTVDGPSSKDWRGGRAASFNIIPSSTGAAKAVGKVLPALNGKLTGMAFRVP 227
T HS T Q+ +D S +D R RAA+ NI+P+STGAAKAV VLP L GKL G+A RVP
Sbjct: 254 TTHSYTGDQRLLDA-SHRDLRRARAAALNIVPTSTGAAKAVSLVLPQLKGKLNGIALRVP 312
Query: 228 TVDVSVVDLTVRLEKDA-SYDEIKAAIK 254
T +VSVVDL V +EK + +++ AA +
Sbjct: 313 TPNVSVVDLVVNVEKKGITAEDVNAAFR 340
>gnl|CDD|215572 PLN03096, PLN03096, glyceraldehyde-3-phosphate dehydrogenase A;
Provisional.
Length = 395
Score = 259 bits (663), Expect = 2e-85
Identities = 129/265 (48%), Positives = 168/265 (63%), Gaps = 15/265 (5%)
Query: 3 KVKIGINGFGRIGRLVARVILQRDDVEL------------VATYMFKYDSVHGQWKHHEL 50
K+K+ INGFGRIGR R R D L A+++ KYDS G + ++
Sbjct: 60 KIKVAINGFGRIGRNFLRCWHGRKDSPLDVVAINDTGGVKQASHLLKYDSTLGTFDA-DV 118
Query: 51 KVKDDKTLLFGEKPVTVFGVRNPEEIPWAETGAEYVVESTGVFTDKDKAAAHLKGGAKKV 110
K D + K + V RNP +PW E G + V+E TGVF D++ A H++ GAKKV
Sbjct: 119 KPVGDDAISVDGKVIKVVSDRNPLNLPWGELGIDLVIEGTGVFVDREGAGKHIQAGAKKV 178
Query: 111 IISAPSK-DAPMFVVGVNENEYKPELNIVSNASCTTNCLAPLAKVIHDKFGIVEGLMTTV 169
+I+AP K D P +VVGVN ++YK I+SNASCTTNCLAP KV+ KFGI++G MTT
Sbjct: 179 LITAPGKGDIPTYVVGVNADDYKHSDPIISNASCTTNCLAPFVKVLDQKFGIIKGTMTTT 238
Query: 170 HSITATQKTVDGPSSKDWRGGRAASFNIIPSSTGAAKAVGKVLPALNGKLTGMAFRVPTV 229
HS T Q+ +D S +D R RAA+ NI+P+STGAAKAV VLP L GKL G+A RVPT
Sbjct: 239 HSYTGDQRLLDA-SHRDLRRARAAALNIVPTSTGAAKAVALVLPNLKGKLNGIALRVPTP 297
Query: 230 DVSVVDLTVRLEKDASYDEIKAAIK 254
+VSVVDL V++EK +E+ AA +
Sbjct: 298 NVSVVDLVVQVEKKTFAEEVNAAFR 322
>gnl|CDD|180962 PRK07403, PRK07403, glyceraldehyde-3-phosphate dehydrogenase;
Reviewed.
Length = 337
Score = 253 bits (647), Expect = 9e-84
Identities = 128/266 (48%), Positives = 174/266 (65%), Gaps = 18/266 (6%)
Query: 4 VKIGINGFGRIGRLVARVILQRDD--VELVA----------TYMFKYDSVHGQWKHHELK 51
+++ INGFGRIGR R L R++ +ELVA ++ KYDS+ G K +
Sbjct: 2 IRVAINGFGRIGRNFLRCWLGRENSQLELVAINDTSDPRTNAHLLKYDSMLG--KLNADI 59
Query: 52 VKDDKTLLFGEKPVTVFGVRNPEEIPWAETGAEYVVESTGVFTDKDKAAAHLKGGAKKVI 111
D+ ++ K + RNP +PW E G + ++ESTGVF K+ A+ H++ GAKKV+
Sbjct: 60 SADENSITVNGKTIKCVSDRNPLNLPWKEWGIDLIIESTGVFVTKEGASKHIQAGAKKVL 119
Query: 112 ISAPSK--DAPMFVVGVNENEYKPEL-NIVSNASCTTNCLAPLAKVIHDKFGIVEGLMTT 168
I+AP K D +VVGVN +EY E NI+SNASCTTNCLAP+AKV+HD FGI++G MTT
Sbjct: 120 ITAPGKGEDIGTYVVGVNHHEYDHEDHNIISNASCTTNCLAPIAKVLHDNFGIIKGTMTT 179
Query: 169 VHSITATQKTVDGPSSKDWRGGRAASFNIIPSSTGAAKAVGKVLPALNGKLTGMAFRVPT 228
HS T Q+ +D S +D R RAA+ NI+P+STGAAKAV V+P L GKL G+A RVPT
Sbjct: 180 THSYTGDQRILDA-SHRDLRRARAAAVNIVPTSTGAAKAVALVIPELKGKLNGIALRVPT 238
Query: 229 VDVSVVDLTVRLEKDASYDEIKAAIK 254
+VSVVDL V++EK +++ +K
Sbjct: 239 PNVSVVDLVVQVEKRTITEQVNEVLK 264
>gnl|CDD|169599 PRK08955, PRK08955, glyceraldehyde-3-phosphate dehydrogenase;
Validated.
Length = 334
Score = 213 bits (545), Expect = 3e-68
Identities = 105/266 (39%), Positives = 161/266 (60%), Gaps = 19/266 (7%)
Query: 3 KVKIGINGFGRIGRLVARVILQRDDVELV---------AT--YMFKYDSVHGQWKHHELK 51
+K+GINGFGRIGRL R ++E V AT ++ ++DSVHG+W HHE+
Sbjct: 2 TIKVGINGFGRIGRLALRAAWDWPELEFVQINDPAGDAATLAHLLEFDSVHGRW-HHEVT 60
Query: 52 VKDDKTLLFGEKPVTVFGVRNPEEIPWAETGAEYVVESTGVFTDKDKAAAHLKGGAKKVI 111
+ D ++ K + + + W +G + V+E++GV K A+L G K+V+
Sbjct: 61 AEGD-AIVINGKRIRTTQNKAIADTDW--SGCDVVIEASGVMKTKALLQAYLDQGVKRVV 117
Query: 112 ISAPSKDAPMF--VVGVNENEYKPELN-IVSNASCTTNCLAPLAKVIHDKFGIVEGLMTT 168
++AP K+ + V+GVN++ + P ++ IV+ ASCTTNCLAP+ KVIH+K GI G MTT
Sbjct: 118 VTAPVKEEGVLNIVMGVNDHLFDPAIHPIVTAASCTTNCLAPVVKVIHEKLGIKHGSMTT 177
Query: 169 VHSITATQKTVDGPSSKDWRGGRAASFNIIPSSTGAAKAVGKVLPALNGKLTGMAFRVPT 228
+H +T TQ +D P KD R RA ++IP++TG+A A+ ++ P L GKL G A RVP
Sbjct: 178 IHDLTNTQTILDAP-HKDLRRARACGMSLIPTTTGSATAITEIFPELKGKLNGHAVRVPL 236
Query: 229 VDVSVVDLTVRLEKDASYDEIKAAIK 254
+ 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 = 201 bits (515), Expect = 3e-66
Identities = 84/150 (56%), Positives = 104/150 (69%), Gaps = 13/150 (8%)
Query: 4 VKIGINGFGRIGRLVARVILQRDDVELVA----------TYMFKYDSVHGQWKHHELKVK 53
+K+GINGFGRIGRLV R L +DD+E+VA Y+ KYDSVHG++ E++V
Sbjct: 1 IKVGINGFGRIGRLVLRAALAQDDLEVVAINDLTDPETLAYLLKYDSVHGRFDG-EVEVD 59
Query: 54 DDKTLLFGEKPVTVFGVRNPEEIPWAETGAEYVVESTGVFTDKDKAAAHLKGGAKKVIIS 113
+D L+ K + VF R+P E+PW E G + VVESTGVFT +KA AHLK GAKKVIIS
Sbjct: 60 EDG-LIVNGKKIKVFAERDPAELPWGELGVDIVVESTGVFTTAEKAEAHLKAGAKKVIIS 118
Query: 114 APSKD-APMFVVGVNENEYKPELNIVSNAS 142
AP+KD P FV GVN +Y PE +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 = 199 bits (508), Expect = 3e-65
Identities = 83/151 (54%), Positives = 104/151 (68%), Gaps = 13/151 (8%)
Query: 4 VKIGINGFGRIGRLVARVILQRDDVELVA----------TYMFKYDSVHGQWKHHELKVK 53
+K+GINGFGRIGRLV R L+R DVE+VA Y+ KYDSVHG++ ++V+
Sbjct: 1 IKVGINGFGRIGRLVLRAALERPDVEVVAINDLTDPEYLAYLLKYDSVHGRF-PGTVEVE 59
Query: 54 DDKTLLFGEKPVTVFGVRNPEEIPWAETGAEYVVESTGVFTDKDKAAAHLKGGAKKVIIS 113
D L+ K + VF R+P +PW E G + VVE TG FT ++KA+AHLK GAKKVIIS
Sbjct: 60 GD-GLVVNGKAIKVFAERDPANLPWGELGVDIVVECTGGFTTREKASAHLKAGAKKVIIS 118
Query: 114 APSKDA-PMFVVGVNENEYKPELNIVSNASC 143
APSKDA P FV GVN +EY E +I+SNASC
Sbjct: 119 APSKDADPTFVYGVNHDEYDGEDHIISNASC 149
>gnl|CDD|236219 PRK08289, PRK08289, glyceraldehyde-3-phosphate dehydrogenase;
Reviewed.
Length = 477
Score = 207 bits (530), Expect = 2e-64
Identities = 102/268 (38%), Positives = 152/268 (56%), Gaps = 25/268 (9%)
Query: 10 GFGRIGRLVARVILQR-------------------DDVELVATYMFKYDSVHGQWKHHEL 50
GFGRIGRL+AR+++++ D+E A+ + + DSVHG +
Sbjct: 134 GFGRIGRLLARLLIEKTGGGNGLRLRAIVVRKGSEGDLEKRAS-LLRRDSVHGPFNGTIT 192
Query: 51 KVKDDKTLLFGEKPVTVFGVRNPEEIPWAETGAE--YVVESTGVFTDKDKAAAHLKG-GA 107
+++ ++ + V +PEE+ + G VV++TG + D++ + HLK G
Sbjct: 193 VDEENNAIIANGNYIQVIYANSPEEVDYTAYGINNALVVDNTGKWRDEEGLSQHLKSKGV 252
Query: 108 KKVIISAPSK-DAPMFVVGVNENEYKPELNIVSNASCTTNCLAPLAKVIHDKFGIVEGLM 166
KV+++AP K D V GVN ++ E IVS ASCTTN + P+ K ++DK+GIV G +
Sbjct: 253 AKVLLTAPGKGDIKNIVHGVNHSDITDEDKIVSAASCTTNAITPVLKAVNDKYGIVNGHV 312
Query: 167 TTVHSITATQKTVDGPSSKDWRGGRAASFNIIPSSTGAAKAVGKVLPALNGKLTGMAFRV 226
TVHS T Q +D D R GR+A N++ + TGAAKAV K LP L GKLTG A RV
Sbjct: 313 ETVHSYTNDQNLIDNYHKGD-RRGRSAPLNMVITETGAAKAVAKALPELAGKLTGNAIRV 371
Query: 227 PTVDVSVVDLTVRLEKDASYDEIKAAIK 254
PT +VS+ L + LEK+ S +E+ ++
Sbjct: 372 PTPNVSMAILNLNLEKETSREELNEYLR 399
>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 = 6e-64
Identities = 77/107 (71%), Positives = 88/107 (82%), Gaps = 1/107 (0%)
Query: 148 LAPLAKVIHDKFGIVEGLMTTVHSITATQKTVDGPSSKDWRGGRAASFNIIPSSTGAAKA 207
LAPLAKV++D FGI +GLMTTVH+ TA QK VD PS KD R GRAA+ NIIP+STGAAKA
Sbjct: 1 LAPLAKVLNDNFGIEKGLMTTVHAYTADQKLVD-PSHKDLRRGRAAAPNIIPTSTGAAKA 59
Query: 208 VGKVLPALNGKLTGMAFRVPTVDVSVVDLTVRLEKDASYDEIKAAIK 254
VG VLP L GKLTGMAFRVPT +VSVVDLTV LEK + +E+ AA+K
Sbjct: 60 VGLVLPELKGKLTGMAFRVPTPNVSVVDLTVELEKPVTVEEVNAALK 106
>gnl|CDD|184122 PRK13535, PRK13535, erythrose 4-phosphate dehydrogenase;
Provisional.
Length = 336
Score = 200 bits (510), Expect = 5e-63
Identities = 95/268 (35%), Positives = 154/268 (57%), Gaps = 22/268 (8%)
Query: 4 VKIGINGFGRIGRLVARVILQ---RDDVELVA----------TYMFKYDSVHGQWKHHEL 50
+++ INGFGRIGR V R + + R ++ +VA ++ KYD+ HG++
Sbjct: 2 IRVAINGFGRIGRNVLRALYESGRRAEITVVAINELADAEGMAHLLKYDTSHGRFAW--- 58
Query: 51 KVKDDKTLLF-GEKPVTVFGVRNPEEIPWAETGAEYVVESTGVFTDKDKAAAHLKGGAKK 109
V+ ++ LF G+ + + R+ +PW E G + V++ TGV+ ++ AH+ GAKK
Sbjct: 59 DVRQERDQLFVGDDAIRLLHERDIASLPWRELGVDVVLDCTGVYGSREDGEAHIAAGAKK 118
Query: 110 VIISAPSK---DAPMFVVGVNENEYKPELNIVSNASCTTNCLAPLAKVIHDKFGIVEGLM 166
V+ S P DA + V GVN ++ + E IVSNASCTTNC+ P+ K++ D FGI G +
Sbjct: 119 VLFSHPGSNDLDATV-VYGVNHDQLRAEHRIVSNASCTTNCIIPVIKLLDDAFGIESGTV 177
Query: 167 TTVHSITATQKTVDGPSSKDWRGGRAASFNIIPSSTGAAKAVGKVLPALNGKLTGMAFRV 226
TT+HS Q+ +D D R RAAS +IIP T A + ++ P N + ++ RV
Sbjct: 178 TTIHSAMNDQQVIDAYHP-DLRRTRAASQSIIPVDTKLAAGITRIFPQFNDRFEAISVRV 236
Query: 227 PTVDVSVVDLTVRLEKDASYDEIKAAIK 254
PT++V+ +DL+V ++K +E+ ++
Sbjct: 237 PTINVTAIDLSVTVKKPVKVNEVNQLLQ 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 = 192 bits (490), Expect = 3e-60
Identities = 97/266 (36%), Positives = 155/266 (58%), Gaps = 20/266 (7%)
Query: 5 KIGINGFGRIGRLVARVILQ---RDDVELVA----------TYMFKYDSVHGQWKHHELK 51
++ INGFGRIGR V R + + R ++ +VA ++ KYD+ HG++ +
Sbjct: 1 RVAINGFGRIGRNVLRALYESGRRAEITVVAINELADAAGMAHLLKYDTSHGRFAW---E 57
Query: 52 VKDDKTLLF-GEKPVTVFGVRNPEEIPWAETGAEYVVESTGVFTDKDKAAAHLKGGAKKV 110
V+ D+ LF G+ + V R+ + +PW E G + V++ TGV+ ++ AH+ GAKKV
Sbjct: 58 VRQDRDQLFVGDDAIRVLHERSLQSLPWRELGVDLVLDCTGVYGSREHGEAHIAAGAKKV 117
Query: 111 IISAP-SKDAPMFVV-GVNENEYKPELNIVSNASCTTNCLAPLAKVIHDKFGIVEGLMTT 168
+ S P + D +V GVN+++ + E IVSNASCTTNC+ P+ K++ D +GI G +TT
Sbjct: 118 LFSHPGASDLDATIVYGVNQDQLRAEHRIVSNASCTTNCIVPVIKLLDDAYGIESGTITT 177
Query: 169 VHSITATQKTVDGPSSKDWRGGRAASFNIIPSSTGAAKAVGKVLPALNGKLTGMAFRVPT 228
+HS Q+ +D D R RAAS +IIP T A + + P N + +A RVPT
Sbjct: 178 IHSAMNDQQVIDA-YHPDLRRTRAASQSIIPVDTKLAAGIERFFPQFNDRFEAIAVRVPT 236
Query: 229 VDVSVVDLTVRLEKDASYDEIKAAIK 254
V+V+ +DL+V ++K +E+ ++
Sbjct: 237 VNVTAIDLSVTVKKPVKANEVNLLLQ 262
>gnl|CDD|173546 PTZ00353, PTZ00353, glycosomal glyceraldehyde-3-phosphate
dehydrogenase; Provisional.
Length = 342
Score = 142 bits (359), Expect = 1e-40
Identities = 74/263 (28%), Positives = 129/263 (49%), Gaps = 12/263 (4%)
Query: 4 VKIGINGFGRIGRLVARVILQRDDVELVAT-----------YMFKYDSVHGQWKHHELKV 52
+ +GINGFG +G+ V L V +VA Y+ + +S ++V
Sbjct: 3 ITVGINGFGPVGKAVLFASLTDPLVTVVAVNDASVSIAYIAYVLEQESPLSAPDGASIRV 62
Query: 53 KDDKTLLFGEKPVTVFGVRNPEEIPWAETGAEYVVESTGVFTDKDKAAAHLKGGAKKVII 112
++ +L G + + V + EI W + G +YVVE TG+++ + + H+ GGAK V +
Sbjct: 63 VGEQIVLNGTQKIRVSAKHDLVEIAWRDYGVQYVVECTGLYSTRSRCWGHVTGGAKGVFV 122
Query: 113 SAPSKDAPMFVVGVNENEYKPELNIVSNASCTTNCLAPLAKVIHDKFGIVEGLMTTVHSI 172
+ S DAP + G N+ L + + LAP+ + +H+ +G+ E T +H +
Sbjct: 123 AGQSADAPTVMAGSNDERLSASLPVCCAGAPIAVALAPVIRALHEVYGVEECSYTAIHGM 182
Query: 173 TATQKT-VDGPSSKDWRGGRAASFNIIPSSTGAAKAVGKVLPALNGKLTGMAFRVPTVDV 231
+ +S+DWR R A I P A+ V K+LP L G+++G AF+VP
Sbjct: 183 QPQEPIAARSKNSQDWRQTRVAIDAIAPYRDNGAETVCKLLPHLVGRISGSAFQVPVKKG 242
Query: 232 SVVDLTVRLEKDASYDEIKAAIK 254
+D+ VR ++ S + + +A+
Sbjct: 243 CAIDMLVRTKQPVSKEVVDSALA 265
>gnl|CDD|223214 COG0136, Asd, Aspartate-semialdehyde dehydrogenase [Amino acid
transport and metabolism].
Length = 334
Score = 51.8 bits (125), Expect = 8e-08
Identities = 51/228 (22%), Positives = 84/228 (36%), Gaps = 43/228 (18%)
Query: 60 FGEKPVTVFGVRNPEEIP--WAETGAEYVVESTGVFTDKDKAAAHLKGGAK--KVIISAP 115
FG K + V PE+ + + + V + G + A+ V+I
Sbjct: 47 FGGKSIGV-----PEDAADEFVFSDVDIVFFAAG----GSVSKEVEPKAAEAGCVVIDNS 97
Query: 116 S-----KDAPMFVVGVNEN---EYKPELNIVSNASCTTNCLAPLAKVIHDKFGIVEGLMT 167
S D P+ V VN +Y+ I++N +C+T L K +HD FGI +++
Sbjct: 98 SAFRMDPDVPLVVPEVNPEHLIDYQKRGFIIANPNCSTIQLVLALKPLHDAFGIKRVVVS 157
Query: 168 TVHSI----------TATQKTVDGPSSKDWRGGRAASFNIIP-----SSTGAAKA----- 207
T ++ A Q G +FN+IP G K
Sbjct: 158 TYQAVSGAGAEGGVELAGQTDALLNGIPILPIGYPLAFNVIPHIDGFLDNGYTKEEWKIE 217
Query: 208 --VGKVLPALNGKLTGMAFRVPTVDVSVVDLTVRLEKDASYDEIKAAI 253
K+L + K++ RVP +TV +KD +EI+ +
Sbjct: 218 AETRKILGDPDIKVSATCVRVPVFYGHSEAVTVEFKKDVDPEEIREEL 265
>gnl|CDD|233347 TIGR01296, asd_B, aspartate-semialdehyde dehydrogenase
(peptidoglycan organisms). Two closely related families
of aspartate-semialdehyde dehydrogenase are found. They
differ by a deep split in phylogenetic and percent
identity trees and in gap patterns. This model
represents a branch more closely related to the USG-1
protein than to the other aspartate-semialdehyde
dehydrogenases represented in model TIGR00978 [Amino
acid biosynthesis, Aspartate family].
Length = 338
Score = 40.2 bits (94), Expect = 5e-04
Identities = 15/59 (25%), Positives = 31/59 (52%), Gaps = 2/59 (3%)
Query: 117 KDAPMFVVGVNENEYK--PELNIVSNASCTTNCLAPLAKVIHDKFGIVEGLMTTVHSIT 173
D P+ V VN + K I++N +C+T + + K +HD+ I +++T +++
Sbjct: 99 PDVPLVVPEVNFEDLKEFNPKGIIANPNCSTIQMVVVLKPLHDEAKIKRVVVSTYQAVS 157
>gnl|CDD|223366 COG0289, DapB, Dihydrodipicolinate reductase [Amino acid transport
and metabolism].
Length = 266
Score = 39.9 bits (94), Expect = 7e-04
Identities = 39/140 (27%), Positives = 63/140 (45%), Gaps = 25/140 (17%)
Query: 3 KVKIGINGF-GRIGRLVARVILQRDDVELVATYMFKYDSVHGQWKHH-------ELKVKD 54
+K+ + G GR+GR + R +L+ D+ELVA + G + V D
Sbjct: 2 MIKVAVAGASGRMGRTLIRAVLEAPDLELVAAFDRPGSLSLGSDAGELAGLGLLGVPVTD 61
Query: 55 DKTLLFGEKPVTV-F-----GVRNPEEIPWAETGAEYVVESTGVFTDKDKAAAHLKGGAK 108
D L+ + V + F + N E E G V+ +TG FT++ L+ A+
Sbjct: 62 DLLLVKADADVLIDFTTPEATLENLEFA--LEHGKPLVIGTTG-FTEEQLEK--LREAAE 116
Query: 109 KV-IISAPSKDAPMFVVGVN 127
KV ++ AP+ F +GVN
Sbjct: 117 KVPVVIAPN-----FSLGVN 131
>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 = 38.0 bits (89), Expect = 7e-04
Identities = 13/30 (43%), Positives = 20/30 (66%), Gaps = 1/30 (3%)
Query: 4 VKIGINGF-GRIGRLVARVILQRDDVELVA 32
+K+ + G GR+GR + + IL+ D ELVA
Sbjct: 1 IKVAVVGASGRMGRELIKAILEAPDFELVA 30
>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 = 38.6 bits (90), Expect = 0.002
Identities = 35/130 (26%), Positives = 54/130 (41%), Gaps = 20/130 (15%)
Query: 137 IVSNASCTTNCLAPLAKVIHDKFGIVEGLMTTVHSITATQKTVDGPSSKDWRGGRAASFN 196
IV+N +CTT L K + D FGI + +TT+ +++ G S D N
Sbjct: 140 IVTNPNCTTAGLTLALKPLIDAFGIKKVHVTTMQAVSGAGY--PGVPSMDILD------N 191
Query: 197 IIPSSTGAAKAVGKVLPALNGKLTG------------MAFRVPTVDVSVVDLTVRLEKDA 244
IIP G + + + + GKL RVP +D + V +K
Sbjct: 192 IIPHIGGEEEKIERETRKILGKLENGKIEPAPFSVSATTTRVPVLDGHTESVHVEFDKKF 251
Query: 245 SYDEIKAAIK 254
+EI+ A+K
Sbjct: 252 DIEEIREALK 261
>gnl|CDD|179786 PRK04207, PRK04207, glyceraldehyde-3-phosphate dehydrogenase;
Provisional.
Length = 341
Score = 38.3 bits (90), Expect = 0.002
Identities = 13/29 (44%), Positives = 21/29 (72%)
Query: 3 KVKIGINGFGRIGRLVARVILQRDDVELV 31
+K+G+NG+G IG+ VA + + D+ELV
Sbjct: 1 MIKVGVNGYGTIGKRVADAVAAQPDMELV 29
Score = 31.0 bits (71), Expect = 0.49
Identities = 19/57 (33%), Positives = 32/57 (56%), Gaps = 4/57 (7%)
Query: 198 IPSSTGAAKAVGKVLPALNGKLTGMAFRVPTVDVSVVDLTVRLEKDASYDEIKAAIK 254
+PS G V VLP L+ +T MA +VPT + + + V L+K + +E+ A++
Sbjct: 190 VPSHHG--PDVKTVLPDLD--ITTMAVKVPTTLMHMHSVNVELKKPVTKEEVLEALE 242
>gnl|CDD|234595 PRK00048, PRK00048, dihydrodipicolinate reductase; Provisional.
Length = 257
Score = 37.8 bits (89), Expect = 0.003
Identities = 11/31 (35%), Positives = 19/31 (61%), Gaps = 1/31 (3%)
Query: 3 KVKIGINGF-GRIGRLVARVILQRDDVELVA 32
+K+ + G GR+GR + + +D+ELVA
Sbjct: 1 MIKVAVAGASGRMGRELIEAVEAAEDLELVA 31
>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 = 34.1 bits (78), Expect = 0.051
Identities = 14/34 (41%), Positives = 22/34 (64%)
Query: 1 MGKVKIGINGFGRIGRLVARVILQRDDVELVATY 34
M K++ I G+G +GR V + I Q+ D+ELV +
Sbjct: 1 MSKIRAAIVGYGNLGRSVEKAIQQQPDMELVGVF 34
>gnl|CDD|173409 PTZ00117, PTZ00117, malate dehydrogenase; Provisional.
Length = 319
Score = 34.3 bits (79), Expect = 0.051
Identities = 44/159 (27%), Positives = 69/159 (43%), Gaps = 29/159 (18%)
Query: 5 KIGINGFGRIGRLVARVILQRD--DVELVATYMFKYDSVHGQWKHHELKVKDDKTLLFGE 62
KI + G G+IG VA +ILQ++ DV L YD + G + L +K TL+
Sbjct: 7 KISMIGAGQIGSTVALLILQKNLGDVVL-------YDVIKGVPQGKALDLKHFSTLV--G 57
Query: 63 KPVTVFGVRNPEEIPWAETGAEYVVESTGVFTDKDKAAAHLKGGAKKVIISAPSKDAPMF 122
+ + G N E+I ++ VV + GV ++ L K++ S
Sbjct: 58 SNINILGTNNYEDI----KDSDVVVITAGVQRKEEMTREDLLTINGKIMKS--------- 104
Query: 123 VVGVNENEYKPELNIVSNASCTTNCLAPLAKVIHDKFGI 161
V + +Y P ++ C TN L + KV +K GI
Sbjct: 105 -VAESVKKYCPNAFVI----CVTNPLDCMVKVFQEKSGI 138
>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 = 33.7 bits (77), Expect = 0.069
Identities = 12/26 (46%), Positives = 21/26 (80%)
Query: 6 IGINGFGRIGRLVARVILQRDDVELV 31
+G+NG+G IG+ VA + ++DD++LV
Sbjct: 1 VGVNGYGTIGKRVADAVTKQDDMKLV 26
Score = 29.5 bits (66), Expect = 1.8
Identities = 20/53 (37%), Positives = 28/53 (52%), Gaps = 4/53 (7%)
Query: 198 IPSSTGAAKAVGKVLPALNGKLTGMAFRVPTVDVSVVDLTVRLEKDASYDEIK 250
+PS G V V+P LN + MAF VPT + V + V L+K + D+I
Sbjct: 187 VPSHHG--PDVQTVIPNLN--IETMAFVVPTTLMHVHSIMVELKKPVTKDDII 235
>gnl|CDD|129147 TIGR00036, dapB, dihydrodipicolinate reductase. [Amino acid
biosynthesis, Aspartate family].
Length = 266
Score = 32.0 bits (73), Expect = 0.25
Identities = 40/140 (28%), Positives = 61/140 (43%), Gaps = 25/140 (17%)
Query: 4 VKIGING-FGRIGRLVARVILQRDDVELVATYMFKYDSVHGQ-------WKHHELKVKDD 55
+K+ + G GR+GR + + L + ++LVA + S+ G + V DD
Sbjct: 2 IKVAVAGAAGRMGRELIKAALAAEGLQLVAAFERHGSSLQGTDAGELAGIGKVGVPVTDD 61
Query: 56 KTLLFGEKPVTV-F----GVRNPEEIPWAETGAEYVVESTGVFTDKDK---AAAHLKGGA 107
+ + V + F GV N + E G VV +TG F+++DK A K G
Sbjct: 62 LEAVETDPDVLIDFTTPEGVLNHLKFA-LEHGVRLVVGTTG-FSEEDKQELADLAEKAGI 119
Query: 108 KKVIISAPSKDAPMFVVGVN 127
VI AP F +GVN
Sbjct: 120 AAVI-------APNFSIGVN 132
>gnl|CDD|169409 PRK08374, PRK08374, homoserine dehydrogenase; Provisional.
Length = 336
Score = 32.1 bits (73), Expect = 0.28
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|237845 PRK14874, PRK14874, aspartate-semialdehyde dehydrogenase;
Provisional.
Length = 334
Score = 31.7 bits (73), Expect = 0.29
Identities = 14/46 (30%), Positives = 22/46 (47%), Gaps = 2/46 (4%)
Query: 118 DAPMFVVGVNENEYK--PELNIVSNASCTTNCLAPLAKVIHDKFGI 161
D P+ V VN + I++N +C+T + K +HD GI
Sbjct: 102 DVPLVVPEVNPEALAEHRKKGIIANPNCSTIQMVVALKPLHDAAGI 147
>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 = 31.6 bits (73), Expect = 0.31
Identities = 13/19 (68%), Positives = 14/19 (73%), Gaps = 1/19 (5%)
Query: 2 GKVKIGINGFGRIGRLVAR 20
GK +GI G GRIGR VAR
Sbjct: 138 GKT-LGIVGLGRIGREVAR 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 = 31.7 bits (73), Expect = 0.32
Identities = 12/19 (63%), Positives = 14/19 (73%), Gaps = 1/19 (5%)
Query: 2 GKVKIGINGFGRIGRLVAR 20
GK +GI G GRIG+ VAR
Sbjct: 142 GK-TLGIIGLGRIGKAVAR 159
>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 = 31.7 bits (73), Expect = 0.34
Identities = 10/21 (47%), Positives = 13/21 (61%)
Query: 1 MGKVKIGINGFGRIGRLVARV 21
+ +GI GFG IGR VA+
Sbjct: 145 LRGKTVGIVGFGAIGRRVAKR 165
>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 = 30.5 bits (70), Expect = 0.48
Identities = 11/16 (68%), Positives = 12/16 (75%)
Query: 5 KIGINGFGRIGRLVAR 20
+GI G GRIGR VAR
Sbjct: 37 TVGIIGLGRIGRAVAR 52
>gnl|CDD|240652 cd12175, 2-Hacid_dh_11, Putative D-isomer specific 2-hydroxyacid
dehydrogenases, NAD-binding and catalytic domains.
2-Hydroxyacid dehydrogenases catalyze the conversion of
a wide variety of D-2-hydroxy acids to their
corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 311
Score = 31.0 bits (71), Expect = 0.52
Identities = 15/33 (45%), Positives = 19/33 (57%), Gaps = 2/33 (6%)
Query: 1 MGKVKIGINGFGRIGRLVARVILQRDDVELVAT 33
GK +GI G G IGR VAR L+ VE++
Sbjct: 141 SGK-TVGIVGLGNIGRAVAR-RLRGFGVEVIYY 171
>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 = 0.55
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 = 0.62
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|136022 PRK06728, PRK06728, aspartate-semialdehyde dehydrogenase;
Provisional.
Length = 347
Score = 30.4 bits (68), Expect = 0.78
Identities = 34/170 (20%), Positives = 65/170 (38%), Gaps = 33/170 (19%)
Query: 116 SKDAPMFVVGVNENEYKPELNIVSNASCTTNCLAPLAKVIHDKFGIVEGLMTT------- 168
+ D P+ V VN + K I++ +C+ + + I FG+ +++T
Sbjct: 105 AHDVPLVVPEVNAHTLKEHKGIIAVPNCSALQMVTALQPIRKVFGLERIIVSTYQAVSGS 164
Query: 169 -VHSITATQKTVDG------------PSSKDWRGGRAASFNIIPS------------STG 203
+H+I ++ P+ KD + +FN++P
Sbjct: 165 GIHAIQELKEQAKSILAGEEVESTILPAKKD-KKHYPIAFNVLPQVDIFTDNDFTFEEVK 223
Query: 204 AAKAVGKVLPALNGKLTGMAFRVPTVDVSVVDLTVRLEKDASYDEIKAAI 253
+ K+L N K+ RVP + + + LEK+A+ EIK +
Sbjct: 224 MIQETKKILEDPNLKMAATCVRVPVISGHSESVYIELEKEATVAEIKEVL 273
>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 = 30.3 bits (69), Expect = 0.78
Identities = 17/48 (35%), Positives = 21/48 (43%), Gaps = 11/48 (22%)
Query: 1 MGKVKIGINGFGRIGRLVARVIL----------QRDDVELVATYMFKY 38
GK +G+ G GRIGR VAR+ D EL F+Y
Sbjct: 138 AGKT-LGVVGTGRIGRRVARIARGFGMKVLAYDVVPDEELAERLGFRY 184
>gnl|CDD|236329 PRK08664, PRK08664, aspartate-semialdehyde dehydrogenase; Reviewed.
Length = 349
Score = 30.2 bits (69), Expect = 0.94
Identities = 34/132 (25%), Positives = 57/132 (43%), Gaps = 25/132 (18%)
Query: 137 IVSNASCTTNCLAPLAKVIHDKFGIVEGLMTTVHSITATQKT-VDGPSSKDWRGGRAASF 195
IV+N +C+T L K + D FGI +TT+ +I+ V D
Sbjct: 144 IVTNPNCSTIGLVLALKPLMD-FGIERVHVTTMQAISGAGYPGVPSMDIVD--------- 193
Query: 196 NIIPSSTG-AAKAV------------GKVLPALNGKLTGMAFRVPTVDVSVVDLTVRLEK 242
N+IP G K GK++PA + ++ RVP +D + V+ ++
Sbjct: 194 NVIPYIGGEEEKIEKETLKILGKFEGGKIVPA-DFPISATCHRVPVIDGHTEAVFVKFKE 252
Query: 243 DASYDEIKAAIK 254
D +EI+ A++
Sbjct: 253 DVDPEEIREALE 264
>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 = 29.1 bits (66), Expect = 1.00
Identities = 12/30 (40%), Positives = 19/30 (63%), Gaps = 1/30 (3%)
Query: 4 VKIGINGFGRIGRLVARVILQ-RDDVELVA 32
+++GI G G+IGR R + + +D ELV
Sbjct: 1 LRVGIVGAGKIGRRHLRALNESQDGAELVG 30
>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 = 29.8 bits (68), Expect = 1.1
Identities = 10/16 (62%), Positives = 11/16 (68%)
Query: 5 KIGINGFGRIGRLVAR 20
+GI GFGRIGR V
Sbjct: 152 TVGIVGFGRIGRAVVE 167
>gnl|CDD|99958 cd05529, Bromo_WDR9_I_like, Bromodomain; WDR9 repeat I_like
subfamily. WDR9 is a human gene located in the Down
Syndrome critical region-2 of chromosome 21. It encodes
for a nuclear protein containing WD40 repeats and two
bromodomains, which may function as a transcriptional
regulator involved in chromatin remodeling and play a
role in embryonic development. Bromodomains are 110
amino acid long domains, that are found in many
chromatin associated proteins. Bromodomains can interact
specifically with acetylated lysine.
Length = 128
Score = 28.8 bits (65), Expect = 1.3
Identities = 13/63 (20%), Positives = 22/63 (34%), Gaps = 5/63 (7%)
Query: 72 NPEEIPWAETGAEYVVESTGVFTDKDKAAAHLKGGAKKVIISAPSKDAPMFVVGVNENEY 131
NP W E +D+ L G K+++S + A F V+ +
Sbjct: 3 NPLSSEW-----ELFDPGWEQPHIRDEERERLISGLDKLLLSLQLEIAEYFEYPVDLRAW 57
Query: 132 KPE 134
P+
Sbjct: 58 YPD 60
>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 = 29.4 bits (67), Expect = 1.5
Identities = 10/15 (66%), Positives = 13/15 (86%)
Query: 6 IGINGFGRIGRLVAR 20
+G+ GFGRIGR VA+
Sbjct: 145 LGLVGFGRIGRAVAK 159
>gnl|CDD|223536 COG0460, ThrA, Homoserine dehydrogenase [Amino acid transport and
metabolism].
Length = 333
Score = 29.5 bits (67), Expect = 1.6
Identities = 8/27 (29%), Positives = 16/27 (59%)
Query: 1 MGKVKIGINGFGRIGRLVARVILQRDD 27
M VK+G+ G G +G V ++ ++ +
Sbjct: 1 MKTVKVGLLGLGTVGSGVLEILAEKQE 27
>gnl|CDD|177941 PLN02306, PLN02306, hydroxypyruvate reductase.
Length = 386
Score = 29.4 bits (66), Expect = 1.7
Identities = 20/77 (25%), Positives = 37/77 (48%), Gaps = 17/77 (22%)
Query: 6 IGINGFGRIGRLVARVILQRDDVELV------ATYMFKYDSVHGQWKHHELKVKDDKTLL 59
+G+ G GRIG AR++++ + L+ +T + K+ + +GQ+
Sbjct: 168 VGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQSTRLEKFVTAYGQFLKAN---------- 217
Query: 60 FGEKPVTVFGVRNPEEI 76
GE+PVT + EE+
Sbjct: 218 -GEQPVTWKRASSMEEV 233
>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 = 29.3 bits (66), Expect = 1.7
Identities = 20/79 (25%), Positives = 33/79 (41%), Gaps = 8/79 (10%)
Query: 108 KKVIISAPSKDAPMFVV-GVNENEYKPELNIVSNASCTTNCLA-PLAKVIHDKF----GI 161
K+VI+ + ++ + V+ + + + I + L L + KF
Sbjct: 132 KEVILGDKTNNSSLLVIKAILDRGIDWDKKIFPYN--LKDELKTALKSSVLPKFNRLQDR 189
Query: 162 VEGLMTTVHSITATQKTVD 180
GL TVH I ATQ T+D
Sbjct: 190 FNGLGITVHDIYATQITID 208
>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|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 = 1.9
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|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 = 29.0 bits (66), 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|181041 PRK07574, PRK07574, formate dehydrogenase; Provisional.
Length = 385
Score = 29.3 bits (66), Expect = 2.0
Identities = 9/16 (56%), Positives = 10/16 (62%)
Query: 5 KIGINGFGRIGRLVAR 20
+GI G GRIG V R
Sbjct: 194 TVGIVGAGRIGLAVLR 209
>gnl|CDD|237436 PRK13581, PRK13581, D-3-phosphoglycerate dehydrogenase;
Provisional.
Length = 526
Score = 29.3 bits (67), Expect = 2.0
Identities = 11/19 (57%), Positives = 13/19 (68%), Gaps = 1/19 (5%)
Query: 2 GKVKIGINGFGRIGRLVAR 20
GK +GI G GRIG VA+
Sbjct: 140 GKT-LGIIGLGRIGSEVAK 157
>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 = 2.2
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 = 28.8 bits (65), Expect = 2.7
Identities = 8/26 (30%), Positives = 16/26 (61%)
Query: 6 IGINGFGRIGRLVARVILQRDDVELV 31
+ I G G +G+ VA ++ + D+E+
Sbjct: 1 VLIIGAGGVGQGVAPLLARHGDLEIT 26
>gnl|CDD|235287 PRK04342, PRK04342, DNA topoisomerase VI subunit A; Provisional.
Length = 367
Score = 28.7 bits (65), Expect = 2.9
Identities = 14/45 (31%), Positives = 20/45 (44%), Gaps = 11/45 (24%)
Query: 72 NPEEIPWAETGAEYV--VESTGV--------FTDKDKAA-AHLKG 105
N + I + + A++V VE G+ F K A HLKG
Sbjct: 179 NVDNIEFVDVDADFVLAVEKGGMFQRLVEEGFWKKYNAILVHLKG 223
>gnl|CDD|223189 COG0111, SerA, Phosphoglycerate dehydrogenase and related
dehydrogenases [Amino acid transport and metabolism].
Length = 324
Score = 28.8 bits (65), Expect = 2.9
Identities = 12/21 (57%), Positives = 14/21 (66%), Gaps = 1/21 (4%)
Query: 1 MGKVKIGINGFGRIGRLVARV 21
GK +GI G GRIGR VA+
Sbjct: 141 AGK-TVGIIGLGRIGRAVAKR 160
>gnl|CDD|215144 PLN02256, PLN02256, arogenate dehydrogenase.
Length = 304
Score = 28.5 bits (64), Expect = 3.0
Identities = 10/25 (40%), Positives = 17/25 (68%)
Query: 1 MGKVKIGINGFGRIGRLVARVILQR 25
K+KIGI GFG G+ +A+ +++
Sbjct: 34 SRKLKIGIVGFGNFGQFLAKTFVKQ 58
>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 = 28.5 bits (64), Expect = 3.1
Identities = 17/49 (34%), Positives = 24/49 (48%), Gaps = 16/49 (32%)
Query: 35 MFKYDSVHGQWKHHELKVKDDKTLLFGEK--PVTVFGV-----RNPEEI 76
+++Y S G W+ L F E+ P+TVFGV RNPE +
Sbjct: 70 LYEYGSRAGFWRLLRL---------FTERGLPLTVFGVAMALARNPEAV 109
>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 = 3.3
Identities = 9/16 (56%), Positives = 12/16 (75%)
Query: 5 KIGINGFGRIGRLVAR 20
+GI G GRIG+ VA+
Sbjct: 142 TVGIVGLGRIGQRVAK 157
>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 = 3.4
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|183914 PRK13243, PRK13243, glyoxylate reductase; Reviewed.
Length = 333
Score = 28.2 bits (63), Expect = 4.3
Identities = 12/15 (80%), Positives = 13/15 (86%)
Query: 6 IGINGFGRIGRLVAR 20
IGI GFGRIG+ VAR
Sbjct: 153 IGIIGFGRIGQAVAR 167
>gnl|CDD|235763 PRK06270, PRK06270, homoserine dehydrogenase; Provisional.
Length = 341
Score = 28.3 bits (64), Expect = 4.6
Identities = 8/25 (32%), Positives = 18/25 (72%)
Query: 3 KVKIGINGFGRIGRLVARVILQRDD 27
++KI + GFG +G+ VA ++ ++ +
Sbjct: 2 EMKIALIGFGGVGQGVAELLAEKRE 26
>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 = 27.9 bits (63), Expect = 4.9
Identities = 10/29 (34%), Positives = 13/29 (44%), Gaps = 1/29 (3%)
Query: 33 TYMFKYDSVHGQWKHHEL-KVKDDKTLLF 60
TY++ D G W L D +LLF
Sbjct: 99 TYIYTADDPEGPWTKTALDGGYHDPSLLF 127
>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 = 5.1
Identities = 8/20 (40%), Positives = 12/20 (60%)
Query: 1 MGKVKIGINGFGRIGRLVAR 20
+ + +GI G GRIG A+
Sbjct: 143 IRDLTVGIIGTGRIGSAAAK 162
>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 = 5.4
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|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 = 6.3
Identities = 9/17 (52%), Positives = 13/17 (76%)
Query: 5 KIGINGFGRIGRLVARV 21
++GI G+G IGR AR+
Sbjct: 135 RVGILGYGSIGRQTARL 151
>gnl|CDD|218170 pfam04607, RelA_SpoT, Region found in RelA / SpoT proteins. This
region of unknown function is found in RelA and SpoT of
Escherichia coli, and their homologues in plants and in
other eubacteria. RelA is a guanosine
3',5'-bis-pyrophosphate (ppGpp) synthetase (EC:2.7.6.5)
while SpoT is thought to be a bifunctional enzyme
catalyzing both ppGpp synthesis and degradation (ppGpp
3'-pyrophosphohydrolase, (EC:3.1.7.2)). This region is
often found in association with HD (pfam01966), a
metal-dependent phosphohydrolase, TGS (pfam02824) which
is a possible nucleotide-binding region, and the ACT
regulatory domain (pfam01842).
Length = 116
Score = 26.4 bits (59), Expect = 6.8
Identities = 10/36 (27%), Positives = 14/36 (38%), Gaps = 7/36 (19%)
Query: 20 RVILQ-RDDVELVATYMFKYDSVHGQWKHHELKVKD 54
R+I+Q DD V +H W + KD
Sbjct: 33 RIIVQFVDDCYRV------LGIIHTLWDPIPGRFKD 62
>gnl|CDD|235783 PRK06349, PRK06349, homoserine dehydrogenase; Provisional.
Length = 426
Score = 27.3 bits (62), Expect = 7.7
Identities = 8/27 (29%), Positives = 16/27 (59%)
Query: 1 MGKVKIGINGFGRIGRLVARVILQRDD 27
M +K+G+ G G +G V R++ + +
Sbjct: 1 MKPLKVGLLGLGTVGSGVVRILEENAE 27
>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 = 27.1 bits (61), Expect = 8.8
Identities = 11/20 (55%), Positives = 13/20 (65%), Gaps = 1/20 (5%)
Query: 1 MGKVKIGINGFGRIGRLVAR 20
GK +G+ G G IGRLVA
Sbjct: 134 RGK-TLGVIGLGNIGRLVAN 152
>gnl|CDD|224459 COG1542, COG1542, Uncharacterized conserved protein [Function
unknown].
Length = 593
Score = 27.5 bits (61), Expect = 9.0
Identities = 29/109 (26%), Positives = 38/109 (34%), Gaps = 37/109 (33%)
Query: 51 KVKDDKTLLFGEKPVTVFGVR-----------NPEEIPWAETGAEYVVESTGVFTDKDKA 99
KV +D EK VT GV+ N E W E E + S G T+K +
Sbjct: 358 KVLED-----LEKSVTADGVKAITYTEEFDAPNAE---WYEQAKEEGLVSRGAITEKGRL 409
Query: 100 AA----------HLKGGAKKVIISAPSK--DAPMFV------VGVNENE 130
A +L KV+I P K + VG +E E
Sbjct: 410 YAKLSKTIKRKPYLTKYEIKVLIKIPRKYIKRGELIEDIQGHVGGDEEE 458
>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 = 26.9 bits (60), Expect = 9.7
Identities = 10/43 (23%), Positives = 21/43 (48%)
Query: 82 GAEYVVESTGVFTDKDKAAAHLKGGAKKVIISAPSKDAPMFVV 124
GA+ V+++ G +A L+ G + V++ S P+ +
Sbjct: 201 GADVVIDAVGGPETLAQALRLLRPGGRIVVVGGTSGGPPLDDL 243
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 0.134 0.387
Gapped
Lambda K H
0.267 0.0796 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,914,802
Number of extensions: 1218351
Number of successful extensions: 1246
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1171
Number of HSP's successfully gapped: 98
Length of query: 254
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 159
Effective length of database: 6,723,972
Effective search space: 1069111548
Effective search space used: 1069111548
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)