RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 007512
(600 letters)
>gnl|CDD|237436 PRK13581, PRK13581, D-3-phosphoglycerate dehydrogenase;
Provisional.
Length = 526
Score = 632 bits (1633), Expect = 0.0
Identities = 260/550 (47%), Positives = 350/550 (63%), Gaps = 32/550 (5%)
Query: 59 PTVLIAEKLGQAGLDLLNEFA--NVDCAYNLSPEELCTKISLCDALIVRSGTKVNRDVFE 116
VL+++ + AGL++L + VD L EEL I DALIVRS TKV +V E
Sbjct: 1 MKVLVSDPISPAGLEILKDAPGVEVDVKTGLDKEELLEIIGDYDALIVRSATKVTAEVLE 60
Query: 117 SSAGRLKVVGRAGVGIDNVDLAAATEFGCLVVNAPTANTVAAAEHGIALLAAMARNVAQA 176
+ A LKV+GRAGVG+DNVD+ AAT G +VVNAPT NT++AAEH IAL+ A+ARN+ QA
Sbjct: 61 A-AKNLKVIGRAGVGVDNVDVPAATRRGIIVVNAPTGNTISAAEHTIALMLALARNIPQA 119
Query: 177 DASVKAGKWQRNKYVGVSLVGKTLAVLGFGKVGSEVARRAKGLGMHVIAHDPYAPADRAR 236
AS+KAGKW+R K++GV L GKTL ++G G++GSEVA+RAK GM VIA+DPY +RA
Sbjct: 120 HASLKAGKWERKKFMGVELYGKTLGIIGLGRIGSEVAKRAKAFGMKVIAYDPYISPERAA 179
Query: 237 AIGVDLVSFDEAIATADFISLHMPLTPATSKVLNDETFGKMKKGVRIINVARGGVIDEEA 296
+GV+LVS DE +A ADFI+LH PLTP T ++ E KMK GVRIIN ARGG+IDE A
Sbjct: 180 QLGVELVSLDELLARADFITLHTPLTPETRGLIGAEELAKMKPGVRIINCARGGIIDEAA 239
Query: 297 LVRALDSGRVAQAALDVFTEEPPPADSKLVQHERVTVTPHLGASTMEAQEGVAIEIAEAV 356
L AL SG+VA AALDVF +EPP DS L + V VTPHLGAST EAQE VAI++AE V
Sbjct: 240 LAEALKSGKVAGAALDVFEKEPPT-DSPLFELPNVVVTPHLGASTAEAQENVAIQVAEQV 298
Query: 357 VGALKGELAATAVNAPMVPAEVLTELKPFVELAEKLGRLAVQLVAGGSGVKTVKVSYASS 416
+ AL+G AVN P + AE +LKP+++LAEKLG LA QL +K+V+++Y
Sbjct: 299 IDALRGGPVPNAVNLPSITAEEAEKLKPYLDLAEKLGSLAAQLA--DGPIKSVEITYRGE 356
Query: 417 RAPDDLDTRLLRAMITKGLIEPISDVFVNLVNADYTAKQRGLRLTEERILLDGSPESPLE 476
A + DT L A KGL+ P+ VN VNA AK+RG+ + E + S ESP
Sbjct: 357 LA--EEDTEPLTAAALKGLLSPVLGERVNYVNAPLLAKERGIEVEESK-----SEESP-- 407
Query: 477 FIQVQIANVESKFASAI-----SESGEIKVEGRV-KDGVPHLTKVGSFEVDVSLEGSIIL 530
+++ I ++ GE V G V DG P + ++ + VD EG +++
Sbjct: 408 -----------DYSNLITVTVTTDDGERSVAGTVFGDGEPRIVEIDGYRVDAKPEGHMLI 456
Query: 531 CRQVDQPGMIGTVGSILGSENVNVSFMSVGRVAPRKHAVMAIGVDEQPRKETLKKIGDVP 590
R D+PG+IG VG++LG +N++ M +GR A+M + VD+ +E L+++ +P
Sbjct: 457 IRNRDRPGVIGKVGTLLGEAGINIAGMQLGRREAGGEALMVLSVDDPVPEEVLEELRALP 516
Query: 591 AIEEFVFLKL 600
I ++L
Sbjct: 517 GILSAKAVEL 526
>gnl|CDD|233358 TIGR01327, PGDH, D-3-phosphoglycerate dehydrogenase. This model
represents a long form of D-3-phosphoglycerate
dehydrogenase, the serA gene of one pathway of serine
biosynthesis. Shorter forms, scoring between trusted and
noise cutoff, include SerA from E. coli [Amino acid
biosynthesis, Serine family].
Length = 525
Score = 518 bits (1335), Expect = e-179
Identities = 244/548 (44%), Positives = 341/548 (62%), Gaps = 32/548 (5%)
Query: 61 VLIAEKLGQAGLDLL-NEFANVDCAYNLSPEELCTKISLCDALIVRSGTKVNRDVFESSA 119
VLIA+ + G+D+L + VD LS EEL I DALIVRS TKV +V + A
Sbjct: 2 VLIADPISPDGIDILEDVGVEVDVQTGLSREELLEIIPDYDALIVRSATKVTEEVIAA-A 60
Query: 120 GRLKVVGRAGVGIDNVDLAAATEFGCLVVNAPTANTVAAAEHGIALLAAMARNVAQADAS 179
+LKV+GRAGVG+DN+D+ AAT G LVVNAPT NT++AAEH +A+L A ARN+ QADAS
Sbjct: 61 PKLKVIGRAGVGVDNIDIEAATARGILVVNAPTGNTISAAEHALAMLLAAARNIPQADAS 120
Query: 180 VKAGKWQRNKYVGVSLVGKTLAVLGFGKVGSEVARRAKGLGMHVIAHDPYAPADRARAIG 239
+K G+W R ++G L GKTL V+G G++GS VA+RAK GM V+A+DPY +RA +G
Sbjct: 121 LKEGEWDRKAFMGTELYGKTLGVIGLGRIGSIVAKRAKAFGMKVLAYDPYISPERAEQLG 180
Query: 240 VDLV-SFDEAIATADFISLHMPLTPATSKVLNDETFGKMKKGVRIINVARGGVIDEEALV 298
V+LV DE +A ADFI++H PLTP T ++ E KMKKGV I+N ARGG+IDE AL
Sbjct: 181 VELVDDLDELLARADFITVHTPLTPETRGLIGAEELAKMKKGVIIVNCARGGIIDEAALY 240
Query: 299 RALDSGRVAQAALDVFTEEPPPADSKLVQHERVTVTPHLGASTMEAQEGVAIEIAEAVVG 358
AL+ G V AALDVF +EPP D+ L + V TPHLGAST EAQE VA ++AE V+
Sbjct: 241 EALEEGHVRAAALDVFEKEPPT-DNPLFDLDNVIATPHLGASTREAQENVATQVAEQVLD 299
Query: 359 ALKGELAATAVNAPMVPAEVLTELKPFVELAEKLGRLAVQLVAGGSGVKTVKVSYASSRA 418
ALKG AVNAP + A+V+ +LKP+++LAEKLG+LA QL+ G V++V+V+Y A
Sbjct: 300 ALKGLPVPNAVNAPGIDADVMEKLKPYLDLAEKLGKLAGQLLDG--AVQSVEVTYRGELA 357
Query: 419 PDDLDTRLLRAMITKGLIEPISDVFVNLVNADYTAKQRGLRLTEERILLDGSPESPLEFI 478
++ L KGL+ P+ D VN+VNA AK+RG+ + E +
Sbjct: 358 --TENSEPLTRAALKGLLSPVLDDEVNMVNAPAVAKERGITVEESK-------------- 401
Query: 479 QVQIANVESKFASAIS-----ESGEIKVEGRV-KDGVPHLTKVGSFEVDVSLEGSIILCR 532
+ + + +S +SG + V G V P + ++ F VD+ EG +++
Sbjct: 402 ----SESSPDYKNYLSVTVTGDSGTVSVAGTVFGGFSPRIVEIDGFHVDLEPEGIMLIIL 457
Query: 533 QVDQPGMIGTVGSILGSENVNVSFMSVGRVAPRKHAVMAIGVDEQPRKETLKKIGDVPAI 592
+D+PG+IG VG++LG+ +N++ M +GR A+M + +D+ E L++I +P I
Sbjct: 458 HLDKPGVIGKVGTLLGTAGINIASMQLGRKEKGGEALMLLSLDQPVPDEVLEEIKAIPDI 517
Query: 593 EEFVFLKL 600
+ L
Sbjct: 518 LSVFVVDL 525
>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 = 456 bits (1176), Expect = e-159
Identities = 179/304 (58%), Positives = 223/304 (73%), Gaps = 2/304 (0%)
Query: 61 VLIAEKLGQAGLDLLNEF-ANVDCAYNLSPEELCTKISLCDALIVRSGTKVNRDVFESSA 119
VL+ + + + GL+LL E VD A LS EEL I+ DALIVRS TKV +V E+ A
Sbjct: 2 VLVTDPIDEEGLELLREAGIEVDVAPGLSEEELLAIIADADALIVRSATKVTAEVIEA-A 60
Query: 120 GRLKVVGRAGVGIDNVDLAAATEFGCLVVNAPTANTVAAAEHGIALLAAMARNVAQADAS 179
RLKV+GRAGVG+DN+D+ AAT G LVVNAP ANT++ AEH IAL+ A+ARN+ QADAS
Sbjct: 61 PRLKVIGRAGVGVDNIDVEAATARGILVVNAPGANTISVAEHTIALMLALARNIPQADAS 120
Query: 180 VKAGKWQRNKYVGVSLVGKTLAVLGFGKVGSEVARRAKGLGMHVIAHDPYAPADRARAIG 239
++AGKW R K++GV L GKTL ++G G++G EVARRA+ GM V+A+DPY A+RA A G
Sbjct: 121 LRAGKWDRKKFMGVELRGKTLGIVGLGRIGREVARRARAFGMKVLAYDPYISAERAAAGG 180
Query: 240 VDLVSFDEAIATADFISLHMPLTPATSKVLNDETFGKMKKGVRIINVARGGVIDEEALVR 299
V+LVS DE +A ADFISLH PLTP T ++N E KMK G +IN ARGG++DE AL
Sbjct: 181 VELVSLDELLAEADFISLHTPLTPETRGLINAEELAKMKPGAILINTARGGIVDEAALAD 240
Query: 300 ALDSGRVAQAALDVFTEEPPPADSKLVQHERVTVTPHLGASTMEAQEGVAIEIAEAVVGA 359
AL SG++A AALDVF +EPPPADS L+ V +TPHLGAST EAQE VA++ AE V+
Sbjct: 241 ALKSGKIAGAALDVFEQEPPPADSPLLGLPNVILTPHLGASTEEAQERVAVDAAEQVLAV 300
Query: 360 LKGE 363
L GE
Sbjct: 301 LAGE 304
>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 = 345 bits (888), Expect = e-115
Identities = 141/301 (46%), Positives = 203/301 (67%), Gaps = 3/301 (0%)
Query: 61 VLIAEKLGQAGLDLLNEFA-NVDCAYNLSPEELCTKISLCDALIVRSGTKVNRDVFESSA 119
+LI + + + ++ L E VD ++ EEL KI D LIVRS TKV ++V ++ A
Sbjct: 3 ILITDGIDEIAIEKLEEAGFEVDYEPLIAKEELLEKIKDYDVLIVRSRTKVTKEVIDA-A 61
Query: 120 GRLKVVGRAGVGIDNVDLAAATEFGCLVVNAPTANTVAAAEHGIALLAAMARNVAQADAS 179
LK++ RAGVG+DN+D+ A + G V+N P A++ + AE I L+ ++AR + +A+
Sbjct: 62 KNLKIIARAGVGLDNIDVEYAKKKGIKVINTPGASSNSVAELVIGLMLSLARFIHRANRE 121
Query: 180 VKAGKWQRNKYVGVSLVGKTLAVLGFGKVGSEVARRAKGLGMHVIAHDPYAPADRARAIG 239
+K GKW + KY G+ L GKTL ++GFG++G EVA+ A+ LGM+VIA+DPY ++A +G
Sbjct: 122 MKLGKWNKKKYKGIELRGKTLGIIGFGRIGREVAKIARALGMNVIAYDPYPKDEQAVELG 181
Query: 240 VDLVSFDEAIATADFISLHMPLTPATSKVLNDETFGKMKKGVRIINVARGGVIDEEALVR 299
V VS +E + +DFISLH+PLTP T ++N + MK G IIN +RGGVIDEEAL+
Sbjct: 182 VKTVSLEELLKNSDFISLHVPLTPETKHMINKKELELMKDGAIIINTSRGGVIDEEALLE 241
Query: 300 ALDSGRVAQAALDVFTEEPPPADSKLVQHERVTVTPHLGASTMEAQEGVAIEIAEAVVGA 359
AL SG++A AALDVF EPPP SKL++ V++TPH+GAST EAQE + E+A ++
Sbjct: 242 ALKSGKLAGAALDVFENEPPPG-SKLLELPNVSLTPHIGASTKEAQERIGEELANKIIEF 300
Query: 360 L 360
L
Sbjct: 301 L 301
>gnl|CDD|223189 COG0111, SerA, Phosphoglycerate dehydrogenase and related
dehydrogenases [Amino acid transport and metabolism].
Length = 324
Score = 332 bits (854), Expect = e-110
Identities = 155/327 (47%), Positives = 202/327 (61%), Gaps = 7/327 (2%)
Query: 56 SSKPTVLIAEKLGQAGLDLLNEFANVDC--AYNLSPEELCTKISLCDALIVRSGTKVNRD 113
VL+ + L L+ L +V+ +L EEL ++ DALIV S T V +
Sbjct: 1 KMMIKVLVTDPLAPDALEELLAAYDVEVPDGPDLDEEELLEALADADALIV-SVTPVTEE 59
Query: 114 VFESSAGRLKVVGRAGVGIDNVDLAAATEFGCLVVNAPTANTVAAAEHGIALLAAMARNV 173
V + A LK +GRAG G+DN+DL AAT+ G LVVNAP N ++ AE +ALL A+AR +
Sbjct: 60 VLAA-APNLKAIGRAGAGVDNIDLEAATKRGILVVNAPGGNAISVAELVLALLLALARRI 118
Query: 174 AQADASVKAGKWQRNKYVGVSLVGKTLAVLGFGKVGSEVARRAKGLGMHVIAHDPYAPAD 233
ADAS + G+W R + G L GKT+ ++G G++G VA+R K GM VI +DPY+P +
Sbjct: 119 PDADASQRRGEWDRKAFRGTELAGKTVGIIGLGRIGRAVAKRLKAFGMKVIGYDPYSPRE 178
Query: 234 RARAIGVDLV-SFDEAIATADFISLHMPLTPATSKVLNDETFGKMKKGVRIINVARGGVI 292
RA GV V S DE +A AD ++LH+PLTP T ++N E KMK G +IN ARGGV+
Sbjct: 179 RAGVDGVVGVDSLDELLAEADILTLHLPLTPETRGLINAEELAKMKPGAILINAARGGVV 238
Query: 293 DEEALVRALDSGRVAQAALDVFTEEPPPADSKLVQHERVTVTPHLGASTMEAQEGVAIEI 352
DE+AL+ ALDSG++A AALDVF EEP PADS L V +TPH+G ST EAQE VA +
Sbjct: 239 DEDALLAALDSGKIAGAALDVFEEEPLPADSPLWDLPNVILTPHIGGSTDEAQERVAEIV 298
Query: 353 AEAVVGALKGELAATAVNAPMVPAEVL 379
AE +V L G NAP V E
Sbjct: 299 AENIVRYLAGG--PVVNNAPEVDLERG 323
>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 = 322 bits (827), Expect = e-106
Identities = 135/301 (44%), Positives = 181/301 (60%), Gaps = 10/301 (3%)
Query: 66 KLGQAGLDLLNEF-ANVDCA---YNLSPEELCTKISLCDALIVRSGT-KVNRDVFESSAG 120
K + +LL V L+ EEL + D +I G + +V + A
Sbjct: 11 KYSEEAKELLEAAGFEVVLNPLGRPLTEEELIELLKDADGVIA--GLDPITEEVLAA-AP 67
Query: 121 RLKVVGRAGVGIDNVDLAAATEFGCLVVNAPTANTVAAAEHGIALLAAMARNVAQADASV 180
RLKV+ R GVG DN+DL AA + G +V N P AN+ + AE I L+ A+AR + QAD V
Sbjct: 68 RLKVISRYGVGYDNIDLEAAKKRGIVVTNTPGANSNSVAELTIGLMLALARQIPQADREV 127
Query: 181 KAGKWQRNKYVGVSLVGKTLAVLGFGKVGSEVARRAKGLGMHVIAHDPYAPADRARAIGV 240
+AG W ++ VG L GKTL ++G G++G VARR G GM V+A+DPY + A+ GV
Sbjct: 128 RAGGW--DRPVGTELYGKTLGIIGLGRIGKAVARRLSGFGMKVLAYDPYPDEEFAKEHGV 185
Query: 241 DLVSFDEAIATADFISLHMPLTPATSKVLNDETFGKMKKGVRIINVARGGVIDEEALVRA 300
+ VS +E + +DFISLH+PLTP T ++N MK G +IN ARGG++DEEAL A
Sbjct: 186 EFVSLEELLKESDFISLHLPLTPETRHLINAAELALMKPGAILINTARGGLVDEEALYEA 245
Query: 301 LDSGRVAQAALDVFTEEPPPADSKLVQHERVTVTPHLGASTMEAQEGVAIEIAEAVVGAL 360
L SGR+A AALDVF EEPPPADS L++ V +TPH+GAST EA + A+ V+ L
Sbjct: 246 LKSGRIAGAALDVFEEEPPPADSPLLELPNVILTPHIGASTKEAVLRMGTMAAQNVIDVL 305
Query: 361 K 361
Sbjct: 306 A 306
>gnl|CDD|215893 pfam00389, 2-Hacid_dh, D-isomer specific 2-hydroxyacid
dehydrogenase, catalytic domain. This family represents
the largest portion of the catalytic domain of
2-hydroxyacid dehydrogenases as the NAD binding domain
is inserted within the structural domain.
Length = 312
Score = 296 bits (760), Expect = 3e-96
Identities = 134/313 (42%), Positives = 178/313 (56%), Gaps = 4/313 (1%)
Query: 61 VLIAEKLGQAGLDLLNEFANVDCAYNLSPEELCTKISLCDALIVRSGTKVNRDVFESSAG 120
VLI + L L+LL E V+ L EEL DALIVRS T V +V E+ A
Sbjct: 1 VLITDPLRPEELELLKEGGEVEVHDELLTEELLEAAKDADALIVRSTTPVTAEVLEA-AP 59
Query: 121 RLKVVGRAGVGIDNVDLAAATEFGCLVVNAPTANTVAAAEHGIALLAAMARNVAQADASV 180
LKV+ R GVG+DN+DL AATE G LV N P +T + AE + L+ A+AR + +ADASV
Sbjct: 60 GLKVIARRGVGVDNIDLDAATERGILVTNVPGYSTESVAELTVGLILALARRIPEADASV 119
Query: 181 KAGKWQRNKYVGVSLVGKTLAVLGFGKVGSEVARRAKGLGMHVIAHDPYAPADRARAIGV 240
+AG W++ +G+ L GKTL V+G G +G A AK LGM V+A+DPY +RA GV
Sbjct: 120 RAGDWKKGGPIGLELYGKTLGVIGGGGIGGIGAAIAKALGMGVVAYDPYPNPERAEEGGV 179
Query: 241 DLVSFDEAI---ATADFISLHMPLTPATSKVLNDETFGKMKKGVRIINVARGGVIDEEAL 297
+++ D + +D + P T + + M K IN ARGG + EEA
Sbjct: 180 EVLLLDLLLLDLKESDDLINLAPPTTMKTGHIIINEARGMLKDAVAINNARGGGVIEEAA 239
Query: 298 VRALDSGRVAQAALDVFTEEPPPADSKLVQHERVTVTPHLGASTMEAQEGVAIEIAEAVV 357
+ AL +A AALDV EEPPP +S L+ V +TPH+ +T EAQE +A E AE ++
Sbjct: 240 LDALLEEGIAAAALDVVEEEPPPVNSPLLDLPNVILTPHIAGATEEAQENMAEEAAENLL 299
Query: 358 GALKGELAATAVN 370
LKG AVN
Sbjct: 300 AFLKGGTPPNAVN 312
>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 = 288 bits (739), Expect = 3e-93
Identities = 117/278 (42%), Positives = 168/278 (60%), Gaps = 2/278 (0%)
Query: 81 VDCAYNLSPEELCTKISLCDALIVRSGTKVNRDVFESSAGRLKVVGRAGVGIDNVDLAAA 140
V A +L +EL ++ DALIV S T V +V A +LK + AG G+DN+DL AA
Sbjct: 24 VIVADDLLADELEALLADADALIVSSTTPVTAEVLAK-APKLKFIQVAGAGVDNIDLDAA 82
Query: 141 TEFGCLVVNAPTANTVAAAEHGIALLAAMARNVAQADASVKAGK-WQRNKYVGVSLVGKT 199
+ G V N P AN A AEH + LL A+ R + +ADA+V+ G W + G L GKT
Sbjct: 83 KKRGITVTNVPGANAEAVAEHALGLLLALLRRLPRADAAVRRGWGWLWAGFPGYELEGKT 142
Query: 200 LAVLGFGKVGSEVARRAKGLGMHVIAHDPYAPADRARAIGVDLVSFDEAIATADFISLHM 259
+ ++G G++G VA+R + GM V+ +D + +G +VS DE +A +D + LH+
Sbjct: 143 VGIVGLGRIGQRVAKRLQAFGMKVLYYDRTRKPEPEEDLGFRVVSLDELLAQSDVVVLHL 202
Query: 260 PLTPATSKVLNDETFGKMKKGVRIINVARGGVIDEEALVRALDSGRVAQAALDVFTEEPP 319
PLTP T ++N+E MK G ++N ARGG++DE+AL+RAL SG++A AALDVF EP
Sbjct: 203 PLTPETRHLINEEELALMKPGAVLVNTARGGLVDEDALLRALKSGKIAGAALDVFEPEPL 262
Query: 320 PADSKLVQHERVTVTPHLGASTMEAQEGVAIEIAEAVV 357
PAD L++ V +TPH+ T EA+E +A E +
Sbjct: 263 PADHPLLELPNVILTPHIAGYTEEARERMAEIAVENLE 300
>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 = 285 bits (732), Expect = 5e-92
Identities = 122/310 (39%), Positives = 173/310 (55%), Gaps = 7/310 (2%)
Query: 59 PTVLIAEKLGQAGLDLLNEFANVDCA---YNLSPEELCTKISLCDALIVRSGTKVNRDVF 115
P VL+ +L + L LL E V+ L EEL D L+ K++ ++
Sbjct: 1 PKVLVTRRLPEEALALLREGFEVEVWDEDRPLPREELLEAAKGADGLLCTLTDKIDAELL 60
Query: 116 ESSAGRLKVVGRAGVGIDNVDLAAATEFGCLVVNAPTANTVAAAEHGIALLAAMARNVAQ 175
++ A LKV+ VG D++D+ AA G V N P T A A+ ALL A AR V +
Sbjct: 61 DA-APPLKVIANYSVGYDHIDVDAAKARGIPVTNTPDVLTDATADLAFALLLAAARRVVE 119
Query: 176 ADASVKAGKWQRNK---YVGVSLVGKTLAVLGFGKVGSEVARRAKGLGMHVIAHDPYAPA 232
D V+AG+W+ +G L GKTL ++G G++G VARRAKG GM ++ H+
Sbjct: 120 GDRFVRAGEWKGWSPTLLLGTDLHGKTLGIVGMGRIGQAVARRAKGFGMKILYHNRSRKP 179
Query: 233 DRARAIGVDLVSFDEAIATADFISLHMPLTPATSKVLNDETFGKMKKGVRIINVARGGVI 292
+ +G VS DE +A +DF+SLH PLTP T ++N E MK +IN ARGGV+
Sbjct: 180 EAEEELGARYVSLDELLAESDFVSLHCPLTPETRHLINAERLALMKPTAILINTARGGVV 239
Query: 293 DEEALVRALDSGRVAQAALDVFTEEPPPADSKLVQHERVTVTPHLGASTMEAQEGVAIEI 352
DE+ALV AL SG++A A LDVF EP PAD L+ V + PH+G++T+E + +A
Sbjct: 240 DEDALVEALKSGKIAGAGLDVFEPEPLPADHPLLTLPNVVLLPHIGSATVETRTAMAELA 299
Query: 353 AEAVVGALKG 362
A+ ++ L G
Sbjct: 300 ADNLLAVLAG 309
>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 = 283 bits (726), Expect = 5e-91
Identities = 124/276 (44%), Positives = 165/276 (59%), Gaps = 7/276 (2%)
Query: 88 SPEELCTKISLCDALIVRSGTKVNRDVFESSAGRLKVVGRAGVGIDNVDLAAATEFGCLV 147
+ +EL + DAL+V+ V +V E+ RLKV+ R GVG+DNVD+AAATE G V
Sbjct: 34 TEDELIEAAADADALLVQY-APVTAEVIEALP-RLKVIVRYGVGVDNVDVAAATERGIPV 91
Query: 148 VNAPTANTVAAAEHGIALLAAMARNVAQADASVKAGKWQRNKYVGV-SLVGKTLAVLGFG 206
N P T A+H +AL+ A+AR + D +V+AG W + L G TL ++GFG
Sbjct: 92 CNVPDYCTEEVADHALALILALARKLPFLDRAVRAGGWDWTVGGPIRRLRGLTLGLVGFG 151
Query: 207 KVGSEVARRAKGLGMHVIAHDPYAPADRARAIGVDLVSFDEAIATADFISLHMPLTPATS 266
++G VA+RAK G VIA+DPY P A GV +VS DE +A +D +SLH PLTP T
Sbjct: 152 RIGRAVAKRAKAFGFRVIAYDPYVPDGVAALGGVRVVSLDELLARSDVVSLHCPLTPETR 211
Query: 267 KVLNDETFGKMKKGVRIINVARGGVIDEEALVRALDSGRVAQAALDVFTEEPPPADSKLV 326
+++ E MK G ++N ARGG++DE AL RAL SGR+A AALDV EEPPPADS L+
Sbjct: 212 HLIDAEALALMKPGAFLVNTARGGLVDEAALARALKSGRIAGAALDVLEEEPPPADSPLL 271
Query: 327 QHERVTVTPHLG----ASTMEAQEGVAIEIAEAVVG 358
V +TPH S E + A E+ + G
Sbjct: 272 SAPNVILTPHAAWYSEESLAELRRKAAEEVVRVLRG 307
>gnl|CDD|223980 COG1052, LdhA, Lactate dehydrogenase and related dehydrogenases
[Energy production and conversion / Coenzyme metabolism
/ General function prediction only].
Length = 324
Score = 279 bits (716), Expect = 2e-89
Identities = 120/323 (37%), Positives = 170/323 (52%), Gaps = 10/323 (3%)
Query: 58 KPTVLIAEKLGQAGLDLLNEFANVDCAYNLSPE--ELCTKISLCDALIVRSGTKVNRDVF 115
K VL KL L+ L E V+ + EL ++ DA+I +++ +V
Sbjct: 2 KIVVLSTRKLPPEVLERLKEKFEVERYEDDLTPDTELAERLKDADAVITFVNDRIDAEVL 61
Query: 116 ESSAGRLKVVGRAGVGIDNVDLAAATEFGCLVVNAPTANTVAAAEHGIALLAAMARNVAQ 175
E LK++ G DNVDL AA E G V N P +T A AEH +AL+ A+AR + +
Sbjct: 62 EK-LPGLKLIATRSAGYDNVDLEAAKERGITVTNVPGYSTEAVAEHAVALILALARRIHE 120
Query: 176 ADASVKAGKWQRNKYV----GVSLVGKTLAVLGFGKVGSEVARRAKGLGMHVIAHDPYAP 231
D V+ G W + G L GKTL ++G G++G VARR KG GM V+ +D
Sbjct: 121 GDRRVREGNWSLSGGPDPLLGFDLRGKTLGIIGLGRIGQAVARRLKGFGMKVLYYDRSPN 180
Query: 232 ADRARAIGVDLVSFDEAIATADFISLHMPLTPATSKVLNDETFGKMKKGVRIINVARGGV 291
+ + +G V DE +A +D ISLH PLTP T ++N E KMK G ++N ARGG+
Sbjct: 181 PEAEKELGARYVDLDELLAESDIISLHCPLTPETRHLINAEELAKMKPGAILVNTARGGL 240
Query: 292 IDEEALVRALDSGRVAQAALDVFTEEPPPADSKL---VQHERVTVTPHLGASTMEAQEGV 348
+DE+AL+ AL SG++A A LDVF EP D L V +TPH+ ++T EA++ +
Sbjct: 241 VDEQALIDALKSGKIAGAGLDVFENEPALFDHPLLRLDNFPNVVLTPHIASATEEARKAM 300
Query: 349 AIEIAEAVVGALKGELAATAVNA 371
A E + G + VN
Sbjct: 301 AELALENLEAFFDGGVPPNEVNP 323
>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 = 276 bits (709), Expect = 1e-88
Identities = 112/311 (36%), Positives = 172/311 (55%), Gaps = 7/311 (2%)
Query: 60 TVLIAEKLGQAGLD----LLNEFANVDCAYNLSPEELCTKISLCDALIVRSGTKVNRDVF 115
VL + LL V+ +E ++ D L+ ++ ++
Sbjct: 1 KVLFLGPEFPDAEELLRALLPPAPGVEVVTAAELDEEAALLADADVLVPGMRKVIDAEL- 59
Query: 116 ESSAGRLKVVGRAGVGIDNVDLAAATEFGCLVVNAPTANTVAAAEHGIALLAAMARNVAQ 175
++A RL+++ + GVG+D VDL AAT G V N P N + AEH + L+ A+ R + +
Sbjct: 60 LAAAPRLRLIQQPGVGLDGVDLEAATARGIPVANIPGGNAESVAEHAVMLMLALLRRLPE 119
Query: 176 ADASVKAGKWQRNKY-VGVSLVGKTLAVLGFGKVGSEVARRAKGLGMHVIAHDPYA-PAD 233
AD ++AG+W R + L GKT+ ++G G +G VARR +G G+ VI +D + P
Sbjct: 120 ADRELRAGRWGRPEGRPSRELSGKTVGIVGLGNIGRAVARRLRGFGVEVIYYDRFRDPEA 179
Query: 234 RARAIGVDLVSFDEAIATADFISLHMPLTPATSKVLNDETFGKMKKGVRIINVARGGVID 293
+ +GV V DE +A +D +SLH+PLTP T ++ E MK G +IN ARGG++D
Sbjct: 180 EEKDLGVRYVELDELLAESDVVSLHVPLTPETRHLIGAEELAAMKPGAILINTARGGLVD 239
Query: 294 EEALVRALDSGRVAQAALDVFTEEPPPADSKLVQHERVTVTPHLGASTMEAQEGVAIEIA 353
EEAL+ AL SG +A A LDVF +EP P D L++ + V +TPH+ T E+ + +A +A
Sbjct: 240 EEALLAALRSGHLAGAGLDVFWQEPLPPDDPLLRLDNVILTPHIAGVTDESYQRMAAIVA 299
Query: 354 EAVVGALKGEL 364
E + L+GE
Sbjct: 300 ENIARLLRGEP 310
>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 = 268 bits (687), Expect = 2e-85
Identities = 113/318 (35%), Positives = 179/318 (56%), Gaps = 9/318 (2%)
Query: 60 TVLIAEKLGQAGLDLLNEFANVDCA---YNLSPEELCTKISLCDALIVRSGTKVNRDVFE 116
VL+ + + L+ L E V +S EEL +I+ DALI T V++++ +
Sbjct: 2 KVLVTGWIPKEALEELEENFEVTYYDGLGLISKEELLERIADYDALITPLSTPVDKEIID 61
Query: 117 SSAGRLKVVGRAGVGIDNVDLAAATEFGCLVVNAPTANTVAAAEHGIALLAAMARNVAQA 176
+ A LK++ G G DN+D+ A E G V N P +T AE L+ A+AR +A+
Sbjct: 62 A-AKNLKIIANYGAGFDNIDVDYAKEKGIPVTNTPAVSTEPTAELTFGLILALARRIAEG 120
Query: 177 DASVKAGK---WQRNKYVGVSLVGKTLAVLGFGKVGSEVARRAKGLGMHVIAHDPY-APA 232
D ++ G W ++G L GKTL ++G G++G VARRAK GM ++ ++ +
Sbjct: 121 DRLMRRGGFLGWAPLFFLGHELAGKTLGIIGMGRIGQAVARRAKAFGMKILYYNRHRLSE 180
Query: 233 DRARAIGVDLVSFDEAIATADFISLHMPLTPATSKVLNDETFGKMKKGVRIINVARGGVI 292
+ + +G V DE + +DF+SLH P TP T +++ F MK +IN ARG ++
Sbjct: 181 ETEKELGATYVDLDELLKESDFVSLHAPYTPETHHLIDAAAFKLMKPTAYLINAARGPLV 240
Query: 293 DEEALVRALDSGRVAQAALDVFTEEPPPADSKLVQHERVTVTPHLGASTMEAQEGVAIEI 352
DE+ALV AL +G +A AALDVF EP + +L + + V +TPH+G +T+EA++ +A E
Sbjct: 241 DEKALVDALKTGEIAGAALDVFEFEPEVSP-ELKKLDNVILTPHIGNATVEARDAMAKEA 299
Query: 353 AEAVVGALKGELAATAVN 370
A+ ++ L+G+ VN
Sbjct: 300 ADNIISFLEGKRPKNIVN 317
>gnl|CDD|240651 cd12174, PGDH_like_3, Putative D-3-Phosphoglycerate Dehydrogenases,
NAD-binding and catalytic domains. Phosphoglycerate
dehydrogenases (PGDHs) catalyze the initial step in the
biosynthesis of L-serine from D-3-phosphoglycerate.
PGDHs come in 3 distinct structural forms, with this
first group being related to 2-hydroxy acid
dehydrogenases, sharing structural similarity to formate
and glycerate dehydrogenases of the D-specific
2-hydroxyacid dehydrogenase superfamily, which also
include groups such as L-alanine dehydrogenase and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. Many, not all, members of this family are
dimeric.
Length = 305
Score = 262 bits (673), Expect = 2e-83
Identities = 118/323 (36%), Positives = 171/323 (52%), Gaps = 31/323 (9%)
Query: 60 TVLIAEKLGQAGLDLLNEFANVDCAYNLSPEELCTKISLCDALIVRSGTKVNRDVFESSA 119
+L A K+ + GL+ Y + E+ DALIVRS + +
Sbjct: 2 KILTANKISKKGLERFK-----KDKYEVK-EDALED---PDALIVRSD---KLHDMDFAP 49
Query: 120 GRLKVVGRAGVGIDNVDLAAATEFGCLVVNAPTANTVAAAEHGIALLAAMARNVAQA--- 176
LK + RAG G++N+D+ AA++ G +V N P AN A AE IA++ A++RN+ QA
Sbjct: 50 S-LKAIARAGAGVNNIDVDAASKRGIVVFNTPGANANAVAELVIAMMLALSRNIIQAIKW 108
Query: 177 ------DASVKAGKWQRNKYVGVSLVGKTLAVLGFGKVGSEVARRAKGLGMHVIAHDPYA 230
D K + + ++VG L GKTL V+G G +G VA A LGM VI +DPY
Sbjct: 109 VTNGDGDDISKGVEKGKKQFVGTELRGKTLGVIGLGNIGRLVANAALALGMKVIGYDPYL 168
Query: 231 PADRARAIGVDLV---SFDEAIATADFISLHMPLTPATSKVLNDETFGKMKKGVRIINVA 287
+ A + V++ S +E +ATAD+I+LH+PLT T ++N E KMK G ++N A
Sbjct: 169 SVEAAWKLSVEVQRVTSLEELLATADYITLHVPLTDETRGLINAELLAKMKPGAILLNFA 228
Query: 288 RGGVIDEEALVRALDSGRVAQAALDVFTEEPPPADSKLVQHERVTVTPHLGASTMEAQEG 347
RG ++DEEAL+ ALD G++ D P + L V TPHLGAST EA+E
Sbjct: 229 RGEIVDEEALLEALDEGKLGGYVTDF------PEPALLGHLPNVIATPHLGASTEEAEEN 282
Query: 348 VAIEIAEAVVGALKGELAATAVN 370
A+ A ++ L+ +VN
Sbjct: 283 CAVMAARQIMDFLETGNITNSVN 305
>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 = 259 bits (665), Expect = 6e-82
Identities = 122/309 (39%), Positives = 178/309 (57%), Gaps = 9/309 (2%)
Query: 65 EKLGQAGLDLLNEFANVDCAYNLSPEELCTKISLCDALIVRSGTKVNRDVFESSAGRLKV 124
++L + G + V ++S + L K+ D +I +++ FE LK+
Sbjct: 19 QRLKKIGYV---DRFEVP--PDISGKALAEKLKGYDIIIASVTPNFDKEFFEY-NDGLKL 72
Query: 125 VGRAGVGIDNVDLAAATEFGCLVVNAPTA-NTVAAAEHGIALLAAMARNVAQADASVKAG 183
+ R G+G DNVDL AATE G +V P A A AEH +AL+ + R + QA +VK G
Sbjct: 73 IARHGIGYDNVDLKAATEHGVIVTRVPGAVERDAVAEHAVALILTVLRKINQASEAVKEG 132
Query: 184 KWQ-RNKYVGVSLVGKTLAVLGFGKVGSEVARRAK-GLGMHVIAHDPYAPADRARAIGVD 241
KW R +VG L GKT+ ++G+G +GS VA K G V+A+DPY + + G
Sbjct: 133 KWTERANFVGHELSGKTVGIIGYGNIGSRVAEILKEGFNAKVLAYDPYVSEEVIKKKGAK 192
Query: 242 LVSFDEAIATADFISLHMPLTPATSKVLNDETFGKMKKGVRIINVARGGVIDEEALVRAL 301
VS +E +A +D ISLH PLT T ++N++ F KMKKGV ++N ARG +IDEEAL+ AL
Sbjct: 193 PVSLEELLAESDIISLHAPLTEETYHMINEKAFSKMKKGVILVNTARGELIDEEALIEAL 252
Query: 302 DSGRVAQAALDVFTEEPPPADSKLVQHERVTVTPHLGASTMEAQEGVAIEIAEAVVGALK 361
SG++A A LDV EEP AD L+ +E V +TPH+GA T E+ G+ ++ + + L
Sbjct: 253 KSGKIAGAGLDVLEEEPIKADHPLLHYENVVITPHIGAYTYESLYGMGEKVVDDIEDFLA 312
Query: 362 GELAATAVN 370
G+ +N
Sbjct: 313 GKEPKGILN 321
>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 = 256 bits (656), Expect = 1e-80
Identities = 108/262 (41%), Positives = 156/262 (59%), Gaps = 10/262 (3%)
Query: 89 PEELCTKISLCDALIVRSGTKVNRDVFESSAGRLKVVG--RAGVGIDNVDLAAATEFGCL 146
EEL + D LI V + V E+ A +LK++G R G +NVD+ AATE G
Sbjct: 37 EEELLEALKDADILITHFAP-VTKKVIEA-APKLKLIGVCRGGP--ENVDVEAATERGIP 92
Query: 147 VVNAPTANTVAAAEHGIALLAAMARNVAQADASVKAGKWQRNKY----VGVSLVGKTLAV 202
V+N P N A AE + L+ A RN+A+A A++K G+W+++ Y G L GKT+ +
Sbjct: 93 VLNTPGRNAEAVAEFTVGLMLAETRNIARAHAALKDGEWRKDYYNYDGYGPELRGKTVGI 152
Query: 203 LGFGKVGSEVARRAKGLGMHVIAHDPYAPADRARAIGVDLVSFDEAIATADFISLHMPLT 262
+GFG +G VA+R K G V+ +DPY ++ A GV VS +E + +D +SLH LT
Sbjct: 153 VGFGAIGRRVAKRLKAFGAEVLVYDPYVDPEKIEADGVKKVSLEELLKRSDVVSLHARLT 212
Query: 263 PATSKVLNDETFGKMKKGVRIINVARGGVIDEEALVRALDSGRVAQAALDVFTEEPPPAD 322
P T ++ E F MK IN AR G++DE+AL+ AL+ G++ AALDVF EEP PAD
Sbjct: 213 PETRGMIGAEEFALMKPTAYFINTARAGLVDEDALIEALEEGKIGGAALDVFPEEPLPAD 272
Query: 323 SKLVQHERVTVTPHLGASTMEA 344
L++ + VT+TPH+ +T +
Sbjct: 273 HPLLKLDNVTLTPHIAGATRDV 294
>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 = 245 bits (627), Expect = 2e-78
Identities = 86/176 (48%), Positives = 118/176 (67%), Gaps = 1/176 (0%)
Query: 163 IALLAAMARNVAQADASVKAGKWQRNKYVGVSLVGKTLAVLGFGKVGSEVARRAKGLGMH 222
+ALL A+AR + +AD V+AG+W+ + +G L GKT+ ++G G++G VARR K GM
Sbjct: 1 LALLLALARRIPEADRQVRAGRWRPDALLGRELSGKTVGIIGLGRIGRAVARRLKAFGMK 60
Query: 223 VIAHDPYAPADRARAIGVDLVSFDEAIATADFISLHMPLTPATSKVLNDETFGKMKKGVR 282
VIA+D Y P A A+G VS DE +A +D +SLH+PLTP T ++N E MK G
Sbjct: 61 VIAYDRY-PKAEAEALGARYVSLDELLAESDVVSLHLPLTPETRHLINAERLALMKPGAI 119
Query: 283 IINVARGGVIDEEALVRALDSGRVAQAALDVFTEEPPPADSKLVQHERVTVTPHLG 338
+IN ARGG++DE+AL+ AL SGR+A AALDVF EP P D L++ V +TPH+
Sbjct: 120 LINTARGGLVDEDALIAALKSGRIAGAALDVFEPEPLPPDHPLLELPNVILTPHIA 175
>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 = 248 bits (637), Expect = 7e-78
Identities = 110/282 (39%), Positives = 160/282 (56%), Gaps = 13/282 (4%)
Query: 72 LDLLNEFANVDCAYNLSPEELCTKISLCDALIVRSGTKVNRDVFESSAGRLKVVGRAGVG 131
D L + SPEE+ +I D +I + ++ +V LK++G G
Sbjct: 18 WDPLEFLGELTVYDRTSPEEVVERIKDADIVIT-NKVVLDAEVLAQ-LPNLKLIGVLATG 75
Query: 132 IDNVDLAAATEFGCLVVNAPTANTVAAAEHGIALLAAMARNVAQADASVKAGKWQRN--- 188
+NVDLAAA E G V N P +T + A+H ALL A+AR VA + VKAG+WQ++
Sbjct: 76 YNNVDLAAAKERGITVTNVPGYSTDSVAQHTFALLLALARLVAYHNDVVKAGEWQKSPDF 135
Query: 189 ---KYVGVSLVGKTLAVLGFGKVGSEVARRAKGLGMHVIAHDPYAPADRARAIGVDLVSF 245
Y + L GKTL ++G+G +G VAR A+ GM V+ + VS
Sbjct: 136 CFWDYPIIELAGKTLGIIGYGNIGQAVARIARAFGMKVLFAERKGAPPL----REGYVSL 191
Query: 246 DEAIATADFISLHMPLTPATSKVLNDETFGKMKKGVRIINVARGGVIDEEALVRALDSGR 305
DE +A +D ISLH PLTP T ++N E KMK G +IN ARGG++DE+AL AL+SG+
Sbjct: 192 DELLAQSDVISLHCPLTPETRNLINAEELAKMKPGAILINTARGGLVDEQALADALNSGK 251
Query: 306 VAQAALDVFTEEPPPADSKLVQ-HERVTVTPHLGASTMEAQE 346
+A A LDV ++EPP AD+ L++ + +TPH+ ++ EA++
Sbjct: 252 IAGAGLDVLSQEPPRADNPLLKAAPNLIITPHIAWASREARQ 293
>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 = 233 bits (598), Expect = 3e-72
Identities = 107/278 (38%), Positives = 156/278 (56%), Gaps = 6/278 (2%)
Query: 87 LSPEELCTKISLCDALIV-RSGTKVNRDVFESSAGRLKVVGRAGVGIDNVDLAAATEFGC 145
L + L +++ DA+++ R T + E LK++ G+ ++DLAAA E G
Sbjct: 35 LDEDALAERLAPFDAIVLMRERTPFPAALLER-LPNLKLLVTTGMRNASIDLAAAKERGI 93
Query: 146 LVVNAPTANTVAAAEHGIALLAAMARNVAQADASVKAGKWQRNKYVGVSLVGKTLAVLGF 205
+V A AE AL+ A+ARN+ + DA+++AG WQ +G L GKTL ++G
Sbjct: 94 VVCGTG-GGPTATAELTWALILALARNLPEEDAALRAGGWQTT--LGTGLAGKTLGIVGL 150
Query: 206 GKVGSEVARRAKGLGMHVIAHDPYAPADRARAIGVDL-VSFDEAIATADFISLHMPLTPA 264
G++G+ VAR + GM VIA A+RA A GV+ VS +E AT+D +SLH+ L+
Sbjct: 151 GRIGARVARIGQAFGMRVIAWSSNLTAERAAAAGVEAAVSKEELFATSDVVSLHLVLSDR 210
Query: 265 TSKVLNDETFGKMKKGVRIINVARGGVIDEEALVRALDSGRVAQAALDVFTEEPPPADSK 324
T ++ E MK ++N +RG ++DE AL+ AL +GR+A AALDVF EP PAD
Sbjct: 211 TRGLVGAEDLALMKPTALLVNTSRGPLVDEGALLAALRAGRIAGAALDVFDVEPLPADHP 270
Query: 325 LVQHERVTVTPHLGASTMEAQEGVAIEIAEAVVGALKG 362
L V +TPH+G T EA EG + E + L G
Sbjct: 271 LRGLPNVLLTPHIGYVTEEAYEGFYGQAVENIAAWLAG 308
>gnl|CDD|183914 PRK13243, PRK13243, glyoxylate reductase; Reviewed.
Length = 333
Score = 232 bits (593), Expect = 3e-71
Identities = 119/328 (36%), Positives = 189/328 (57%), Gaps = 12/328 (3%)
Query: 57 SKPTVLIAEKLGQAGLDLLNEFANVDCAYNLSP---EELCTKISLCDALIVRSGTKVNRD 113
KP V I ++ + G+++L E V+ + E L K+ DAL+ +++ +
Sbjct: 1 MKPKVFITREIPENGIEMLEEHFEVEVWEDEREIPREVLLEKVRDVDALVTMLSERIDCE 60
Query: 114 VFESSAGRLKVVGRAGVGIDNVDLAAATEFGCLVVNAPTANTVAAAEHGIALLAAMARNV 173
VFE+ A RL++V VG DN+D+ AT G V N P T A A+ ALL A AR +
Sbjct: 61 VFEA-APRLRIVANYAVGYDNIDVEEATRRGIYVTNTPGVLTEATADFAWALLLATARRL 119
Query: 174 AQADASVKAGKWQRNK-------YVGVSLVGKTLAVLGFGKVGSEVARRAKGLGMHVIAH 226
+AD V++G+W+R ++G + GKT+ ++GFG++G VARRAKG GM ++ +
Sbjct: 120 VEADHFVRSGEWKRRGVAWHPLMFLGYDVYGKTIGIIGFGRIGQAVARRAKGFGMRILYY 179
Query: 227 DPYAPADRARAIGVDLVSFDEAIATADFISLHMPLTPATSKVLNDETFGKMKKGVRIINV 286
+ + +G + +E + +DF+SLH+PLT T ++N+E MK ++N
Sbjct: 180 SRTRKPEAEKELGAEYRPLEELLRESDFVSLHVPLTKETYHMINEERLKLMKPTAILVNT 239
Query: 287 ARGGVIDEEALVRALDSGRVAQAALDVFTEEPPPADSKLVQHERVTVTPHLGASTMEAQE 346
ARG V+D +ALV+AL G +A A LDVF EEP + +L + V + PH+G++T EA+E
Sbjct: 240 ARGKVVDTKALVKALKEGWIAGAGLDVFEEEPYY-NEELFSLKNVVLAPHIGSATFEARE 298
Query: 347 GVAIEIAEAVVGALKGELAATAVNAPMV 374
G+A +AE ++ +GE+ T VN +V
Sbjct: 299 GMAELVAENLIAFKRGEVPPTLVNREVV 326
>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 = 229 bits (587), Expect = 2e-70
Identities = 102/243 (41%), Positives = 145/243 (59%), Gaps = 9/243 (3%)
Query: 122 LKVVGRAGVGIDNVDLAAATEFGCLVVNAPTANTVAAAEHGIAL-LAAMARNVAQADASV 180
LK++ AG G D +D+ A T+ G V N P A A A+ + L L A+ RN ++A+ S
Sbjct: 77 LKIIAHAGAGYDQIDVDALTKRGIQVSNTPGAVDEATADTALFLILGAL-RNFSRAERSA 135
Query: 181 KAGKWQRNK--YVGVSLVGKTLAVLGFGKVGSEVARRAKGLGMHVIAHDPY-APADRARA 237
+AGKW+ + GKTL +LG G +G +AR+A GM +I H+ P + +A
Sbjct: 136 RAGKWRGFLDLTLAHDPRGKTLGILGLGGIGKAIARKAAAFGMKIIYHNRSRLPEELEKA 195
Query: 238 IGVDLVSFDEAIATADFISLHMPLTPATSKVLNDETFGKMKKGVRIINVARGGVIDEEAL 297
+ VS DE +A +D +SL+ PLT AT ++N + F KMK GV I+N ARG VIDE+AL
Sbjct: 196 LATYYVSLDELLAQSDVVSLNCPLTAATRHLINKKEFAKMKDGVIIVNTARGAVIDEDAL 255
Query: 298 VRALDSGRVAQAALDVFTEEPPPADSKLVQHERVTVTPHLGASTMEAQ---EGVAIEIAE 354
V AL+SG+VA A LDVF EP + L++ VT+ PH+G T+E Q E + +E E
Sbjct: 256 VDALESGKVASAGLDVFENEPEV-NPGLLKMPNVTLLPHMGTLTVETQEKMEELVLENIE 314
Query: 355 AVV 357
A +
Sbjct: 315 AFL 317
>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 = 226 bits (578), Expect = 4e-69
Identities = 109/295 (36%), Positives = 154/295 (52%), Gaps = 15/295 (5%)
Query: 83 CAYNLSPEELCTKISLCDALIVRSGTKVNRDVFESSAGRLKVVGRAGVGIDNVDLAAATE 142
Y L+ +E DA++ K++ ++ + + G LK + G DN+DL A E
Sbjct: 30 VTYLLNDDETAELAKGADAILTAFTDKIDAELLDKAPG-LKFISLRATGYDNIDLDYAKE 88
Query: 143 FGCLVVNAPTANTVAAAEHGIALLAAMARNVAQADASVKAGKWQRNKYVGVSLVGKTLAV 202
G V N P + A AEH IAL+ A+ RN D K Q +G L +T+ V
Sbjct: 89 LGIGVTNVPEYSPNAVAEHTIALILALLRNRKYIDERDKNQDLQDAGVIGRELEDQTVGV 148
Query: 203 LGFGKVGSEVARRAKGLGMHVIAHDPYAPADRARAIGVDLVSFDEAIATADFISLHMPLT 262
+G GK+G VA+RAKG GM VIA+DP+ + GV VS +E +D ISLH+PLT
Sbjct: 149 VGTGKIGRAVAQRAKGFGMKVIAYDPFRNPELE-DKGVKYVSLEELFKNSDIISLHVPLT 207
Query: 263 PATSKVLNDETFGKMKKGVRIINVARGGVIDEEALVRALDSGRVAQAALDVFTEEPP--- 319
P ++N+E F MKKGV IIN ARG ++D EAL+ ALDSG++ A LDV +E P
Sbjct: 208 PENHHMINEEAFKLMKKGVIIINTARGSLVDTEALIEALDSGKIFGAGLDVLEDETPDLL 267
Query: 320 ----------PADSKLVQHERVTVTPHLGASTMEAQEGVAIEIAEAVVGALKGEL 364
++ L + V +TPH T +A + + E +V L+GE
Sbjct: 268 KDLEGEIFKDALNALLGRRPNVIITPHTAFYTDDALKNMVEISCENIVDFLEGEE 322
>gnl|CDD|240653 cd12176, PGDH_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. 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 = 221 bits (566), Expect = 2e-67
Identities = 108/305 (35%), Positives = 168/305 (55%), Gaps = 13/305 (4%)
Query: 61 VLIAEKLGQAGLDLLNE-FANVDCAYN-LSPEELCTKISLCDALIVRSGTKVNRDVFESS 118
+L+ E + + +L V+ L +EL + L +RS T++ +V E+
Sbjct: 3 ILLLENIHPSADELFRAGGIEVERLKGALDEDELIEALKDVHLLGIRSKTQLTEEVLEA- 61
Query: 119 AGRLKVVGRAGVGIDNVDLAAATEFGCLVVNAPTANTVAAAEHGIALLAAMARNVAQADA 178
A +L +G +G + VDL AA + G V NAP +NT + AE I + +AR + +A
Sbjct: 62 APKLLAIGCFCIGTNQVDLDAAAKRGIPVFNAPFSNTRSVAELVIGEIIMLARRLPDRNA 121
Query: 179 SVKAGKWQRNKYVGVSLVGKTLAVLGFGKVGSEVARRAKGLGMHVIAHDPYAPADRARAI 238
+ G W ++ + GKTL ++G+G +GS+++ A+ LGM VI +D +
Sbjct: 122 AAHRGIWNKSATGSHEVRGKTLGIIGYGHIGSQLSVLAEALGMRVIFYD----IAEKLPL 177
Query: 239 G--VDLVSFDEAIATADFISLHMPLTPATSKVLNDETFGKMKKGVRIINVARGGVIDEEA 296
G + S +E +A ADF++LH+P TP+T ++ E +MKKG +IN +RG V+D +A
Sbjct: 178 GNARQVSSLEELLAEADFVTLHVPATPSTKNMIGAEEIAQMKKGAILINASRGTVVDIDA 237
Query: 297 LVRALDSGRVAQAALDVFTEEP----PPADSKLVQHERVTVTPHLGASTMEAQEGVAIEI 352
L AL SG +A AA+DVF EEP P S L V +TPH+G ST EAQE + +E+
Sbjct: 238 LAEALRSGHLAGAAVDVFPEEPASNGEPFSSPLQGLPNVILTPHIGGSTEEAQENIGLEV 297
Query: 353 AEAVV 357
A +V
Sbjct: 298 AGKLV 302
>gnl|CDD|240656 cd12179, 2-Hacid_dh_14, 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 = 306
Score = 215 bits (550), Expect = 3e-65
Identities = 107/304 (35%), Positives = 157/304 (51%), Gaps = 14/304 (4%)
Query: 61 VLIAEKLGQAGLDLLNEFA-NVDCAYNLSPEELCTKISLCDALIVRSGTKVNRDVFESSA 119
+LI +K + +LL VD +S EE+ I D LI+RS ++++ E A
Sbjct: 2 ILIIDKNHPSLTELLEALGFEVDYDPTISREEILAIIPQYDGLIIRSRFPIDKEFIEK-A 60
Query: 120 GRLKVVGRAGVGIDNVDLAAATEFGCLVVNAPTANTVAAAEHGIALLAAMARNVAQADAS 179
LK + RAG G++N+DL A E G + NAP N A EH + +L A+ + +AD
Sbjct: 61 TNLKFIARAGAGLENIDLEYAKEKGIELFNAPEGNRDAVGEHALGMLLALFNKLNRADQE 120
Query: 180 VKAGKWQRNKYVGVSLVGKTLAVLGFGKVGSEVARRAKGLGMHVIAHDPYAPADRARAIG 239
V+ G W R GV L+GKT+ ++G+G +G A+R G G VIA+D Y A A
Sbjct: 121 VRNGIWDREGNRGVELMGKTVGIIGYGNMGKAFAKRLSGFGCKVIAYDKYKNFGDAYAEQ 180
Query: 240 VDLVSFDEAIATADFISLHMPLTPATSKVLNDETFGKMKKGVRIINVARGGVIDEEALVR 299
V L + AD +SLH+PLTP T ++N E KK IN ARG V+ + LV+
Sbjct: 181 VSL---ETLFKEADILSLHIPLTPETRGMVNKEFISSFKKPFYFINTARGKVVVTKDLVK 237
Query: 300 ALDSGRVAQAALDVF--------TEEPPPAD-SKLVQHERVTVTPHLGASTMEAQEGVAI 350
AL SG++ A LDV + P L++ +V +TPH+ T E+ E +A
Sbjct: 238 ALKSGKILGACLDVLEYEKASFESIFNQPEAFEYLIKSPKVILTPHIAGWTFESYEKIAE 297
Query: 351 EIAE 354
+ +
Sbjct: 298 VLVD 301
>gnl|CDD|240634 cd12157, PTDH, Thermostable Phosphite Dehydrogenase. Phosphite
dehydrogenase (PTDH), a member of the D-specific
2-hydroxyacid dehydrogenase family, catalyzes the
NAD-dependent formation of phosphate from phosphite
(hydrogen phosphonate). PTDH has been suggested as a
potential enzyme for cofactor regeneration systems. 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.
Length = 318
Score = 208 bits (532), Expect = 2e-62
Identities = 108/319 (33%), Positives = 162/319 (50%), Gaps = 15/319 (4%)
Query: 58 KPTVLIAEKLGQAGLDLLNEFANVDCAYN---LSPEELCTKISLCDALIVRSGTKVNRDV 114
KP V+I K+ L+LL V LS EEL + D L+ +++ D
Sbjct: 1 KPKVVITHKVHPEVLELLKPHCEVISNQTDEPLSREELLRRCKDADGLMAFMPDRIDADF 60
Query: 115 FESSAGRLKVVGRAGVGIDNVDLAAATEFGCLVVNAPTANTVAAAEHGIALLAAMARNVA 174
++ RLK++ A G DN D+ A T G V P T AE I LL + R++
Sbjct: 61 LDA-CPRLKIIACALKGYDNFDVEACTARGIWVTIVPDLLTEPTAELTIGLLIGLGRHIL 119
Query: 175 QADASVKAGKWQ--RNKYVGVSLVGKTLAVLGFGKVGSEVARRAKGLGMHVIAHDPYA-P 231
D V++GK+ R K+ G L GKT+ +LG G +G +ARR G G ++ +DP+
Sbjct: 120 AGDRFVRSGKFGGWRPKFYGTGLDGKTVGILGMGALGRAIARRLSGFGATLLYYDPHPLD 179
Query: 232 ADRARAIGVDLVSFDEAIATADFISLHMPLTPATSKVLNDETFGKMKKGVRIINVARGGV 291
+A+ + V DE + ++DF+ L +PLTP T ++N E KMK G ++N RG V
Sbjct: 180 QAEEQALNLRRVELDELLESSDFLVLALPLTPDTLHLINAEALAKMKPGALLVNPCRGSV 239
Query: 292 IDEEALVRALDSGRVAQAALDVFTEEP------PPA--DSKLVQHERVTVTPHLGASTME 343
+DE A+ AL SG + A DVF E P + L QH+R TPH+G++ E
Sbjct: 240 VDEAAVAEALKSGHLGGYAADVFEMEDWARPDRPRSIPQELLDQHDRTVFTPHIGSAVDE 299
Query: 344 AQEGVAIEIAEAVVGALKG 362
+ + +E A ++ AL+G
Sbjct: 300 VRLEIELEAALNILQALQG 318
>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 = 208 bits (531), Expect = 3e-62
Identities = 97/257 (37%), Positives = 137/257 (53%), Gaps = 21/257 (8%)
Query: 108 TKVNRDVFESSAGRLKVVGRAGVGIDNVDLAAATEFGCLVVNAPTANTVAAAEHGIALLA 167
++++ +V E RLK++ G D++DL A E G V N P AEH ALL
Sbjct: 51 SRLDAEVLEKLP-RLKLIATRSTGFDHIDLEACRERGIAVCNVPDYGEATVAEHAFALLL 109
Query: 168 AMARNVAQADASVKAGKWQRNKYVGVSLVGKTLAVLGFGKVGSEVARRAKGLGMHVIAHD 227
A++R + +A + G + + G L GKTL V+G G++G VAR A+G GM V+A+D
Sbjct: 110 ALSRKLREAIERTRRGDFSQAGLRGFELAGKTLGVVGTGRIGRRVARIARGFGMKVLAYD 169
Query: 228 PYAPADRARAIGVDLVSFDEAIATADFISLHMPLTPATSKVLNDETFGKMKKGVRIINVA 287
+ A +G VS +E + +D ISLH+P TP T ++N E F MK G +IN A
Sbjct: 170 VVPDEELAERLGFRYVSLEELLQESDIISLHVPYTPQTHHLINRENFALMKPGAVLINTA 229
Query: 288 RGGVIDEEALVRALDSGRVAQAALDVFTEEP-------------PP-------ADSKLVQ 327
RG V+D EALVRAL G++A A LDV +E P AD L++
Sbjct: 230 RGAVVDTEALVRALKEGKLAGAGLDVLEQEEVLREEAELFREDVSPEDLKKLLADHALLR 289
Query: 328 HERVTVTPHLGASTMEA 344
V +TPH+ +T EA
Sbjct: 290 KPNVIITPHVAYNTKEA 306
>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 = 201 bits (514), Expect = 1e-59
Identities = 97/275 (35%), Positives = 142/275 (51%), Gaps = 6/275 (2%)
Query: 72 LDLLNEFANV---DCAYNLSPEELCTKISLCDALIVRSGTKVNRDVFESSAGRLKVVGRA 128
L L A V + + EEL ++ + L+ GT + A RL+ V A
Sbjct: 20 LARLAALAEVLPPTPDADFAAEELRALLAGVEVLVTGWGTPPLDAELLARAPRLRAVVHA 79
Query: 129 GVGIDNVDLAAATEFGCLVVNAPTANTVAAAEHGIALLAAMARNVAQADASVKAGKWQ-- 186
+ + A E G LV +A AN AE +A + R + + A+ +AG+
Sbjct: 80 AGSVRGLVTDAVWERGILVTSAADANAEPVAEFTLAAILLALRRIPRFAAAYRAGRDWGW 139
Query: 187 RNKYVGVSLVGKTLAVLGFGKVGSEVARRAKGLGMHVIAHDPYAPADRARAIGVDLVSFD 246
+ G L G+T+ ++GFG++G V + G+ V+ +DPY PA A A+GV+LVS D
Sbjct: 140 PTRRGGRGLYGRTVGIVGFGRIGRAVVELLRPFGLRVLVYDPYLPAAEAAALGVELVSLD 199
Query: 247 EAIATADFISLHMPLTPATSKVLNDETFGKMKKGVRIINVARGGVIDEEALVRALDSGRV 306
E +A +D +SLH PLTP T +++ M+ G IN ARG ++DE AL+ L SGR+
Sbjct: 200 ELLARSDVVSLHAPLTPETRGMIDARLLALMRDGATFINTARGALVDEAALLAELRSGRL 259
Query: 307 AQAALDVFTEEPPPADSKLVQHERVTVTPHLGAST 341
+AALDV EP P DS L V +TPH+ ST
Sbjct: 260 -RAALDVTDPEPLPPDSPLRTLPNVLLTPHIAGST 293
>gnl|CDD|236985 PRK11790, PRK11790, D-3-phosphoglycerate dehydrogenase;
Provisional.
Length = 409
Score = 203 bits (518), Expect = 2e-59
Identities = 111/327 (33%), Positives = 174/327 (53%), Gaps = 14/327 (4%)
Query: 57 SKPTVLIAEKLGQAGLDLLNE--FANVDC-AYNLSPEELCTKISLCDALIVRSGTKVNRD 113
K L+ E + Q+ +++L + N++ L EEL I + +RS T++ +
Sbjct: 9 DKIKFLLLEGVHQSAVEVLRAAGYTNIEYHKGALDEEELIEAIKDAHFIGIRSRTQLTEE 68
Query: 114 VFESSAGRLKVVGRAGVGIDNVDLAAATEFGCLVVNAPTANTVAAAEHGIALLAAMARNV 173
V + A +L +G +G + VDL AA + G V NAP +NT + AE I + + R +
Sbjct: 69 VLAA-AEKLVAIGCFCIGTNQVDLDAAAKRGIPVFNAPFSNTRSVAELVIGEIILLLRGI 127
Query: 174 AQADASVKAGKWQRNKYVGVSLVGKTLAVLGFGKVGSEVARRAKGLGMHVIAHDPYA--P 231
+ +A G W ++ + GKTL ++G+G +G++++ A+ LGM V +D P
Sbjct: 128 PEKNAKAHRGGWNKSAAGSFEVRGKTLGIVGYGHIGTQLSVLAESLGMRVYFYDIEDKLP 187
Query: 232 ADRARAIGVDLVSFDEAIATADFISLHMPLTPATSKVLNDETFGKMKKGVRIINVARGGV 291
AR +G S +E +A +D +SLH+P TP+T ++ E MK G +IN +RG V
Sbjct: 188 LGNARQVG----SLEELLAQSDVVSLHVPETPSTKNMIGAEELALMKPGAILINASRGTV 243
Query: 292 IDEEALVRALDSGRVAQAALDVFTEEPPPAD----SKLVQHERVTVTPHLGASTMEAQEG 347
+D +AL AL SG +A AA+DVF EP S L + V +TPH+G ST EAQE
Sbjct: 244 VDIDALADALKSGHLAGAAIDVFPVEPKSNGDPFESPLRGLDNVILTPHIGGSTQEAQEN 303
Query: 348 VAIEIAEAVVGALKGELAATAVNAPMV 374
+ +E+A +V +AVN P V
Sbjct: 304 IGLEVAGKLVKYSDNGSTLSAVNFPEV 330
>gnl|CDD|240625 cd05300, 2-Hacid_dh_1, Putative D-isomer specific 2-hydroxyacid
dehydrogenase. 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 subdomains 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. 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 the
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.
Length = 313
Score = 199 bits (509), Expect = 4e-59
Identities = 99/294 (33%), Positives = 143/294 (48%), Gaps = 10/294 (3%)
Query: 59 PTVLIAEKLGQAGLDLLNEFANVDCAYNLSPEELCTKISLCDALIVRSGTKVNRDVFESS 118
+L+ L L+ L A ++ EEL +++ D L+ G ++ +
Sbjct: 1 MKILVLSPLDDEHLERLRAAAPGAELRVVTAEELTEELADADVLL---GNPPLPELLPA- 56
Query: 119 AGRLKVVGRAGVGIDNVDLAAATEFGCLVVNAPTANTVAAAEHGIALLAAMARNVAQADA 178
A RL+ + G+D + E ++ NA AE+ + + A AR + +
Sbjct: 57 APRLRWIQSTSAGVDALLFPELLERDVVLTNARGIFGPPIAEYVLGYMLAFARKLPRYAR 116
Query: 179 SVKAGKWQRNKYVGVSLVGKTLAVLGFGKVGSEVARRAKGLGMHVIA---HDPYAPADRA 235
+ +WQR V L GKT+ ++G G +G E+ARRAK GM VI AP
Sbjct: 117 NQAERRWQRRGPVR-ELAGKTVLIVGLGDIGREIARRAKAFGMRVIGVRRSGRPAPPVVD 175
Query: 236 RAIGVDLVSFDEAIATADFISLHMPLTPATSKVLNDETFGKMKKGVRIINVARGGVIDEE 295
D DE + AD++ +PLTP T + N E F MK G +INV RG V+DE+
Sbjct: 176 EVYTPD--ELDELLPEADYVVNALPLTPETRGLFNAERFAAMKPGAVLINVGRGSVVDED 233
Query: 296 ALVRALDSGRVAQAALDVFTEEPPPADSKLVQHERVTVTPHLGASTMEAQEGVA 349
AL+ AL+SGR+A AALDVF EEP PADS L V +TPH+ + E V
Sbjct: 234 ALIEALESGRIAGAALDVFEEEPLPADSPLWDLPNVIITPHISGDSPSYPERVV 287
>gnl|CDD|240659 cd12183, LDH_like_2, 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-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 = 328
Score = 195 bits (499), Expect = 2e-57
Identities = 104/270 (38%), Positives = 144/270 (53%), Gaps = 19/270 (7%)
Query: 99 CDALIVRSGTKVNRDVFES-SAGRLKVVGRAGVGIDNVDLAAATEFGCLVVNAPTANTVA 157
DA+ V ++ V E + +K++ G +NVDL AA E G VV P + A
Sbjct: 45 FDAVCVFVNDDLDAPVLEKLAELGVKLIALRCAGFNNVDLKAAKELGITVVRVPAYSPYA 104
Query: 158 AAEHGIALLAAMARNVAQADASVKAGKWQRNKYVGVSLVGKTLAVLGFGKVGSEVARRAK 217
AEH +ALL A+ R + +A V+ G + + +G L GKT+ V+G GK+G AR K
Sbjct: 105 VAEHAVALLLALNRKIHRAYNRVREGNFSLDGLLGFDLHGKTVGVIGTGKIGQAFARILK 164
Query: 218 GLGMHVIAHDPYAPADRARAIGVDLVSFDEAIATADFISLHMPLTPATSKVLNDETFGKM 277
G G V+A+DPY P +GV+ V DE +A +D ISLH PLTP T ++N ET KM
Sbjct: 165 GFGCRVLAYDPY-PNPELAKLGVEYVDLDELLAESDIISLHCPLTPETHHLINAETIAKM 223
Query: 278 KKGVRIINVARGGVIDEEALVRALDSGRVAQAALDVFTEE-----------PPPAD--SK 324
K GV +IN +RGG+ID +AL+ AL SG++ LDV+ EE D ++
Sbjct: 224 KDGVMLINTSRGGLIDTKALIEALKSGKIGGLGLDVYEEEAGLFFEDHSDEIIQDDVLAR 283
Query: 325 LVQHERVTVTPHLGASTMEAQEGVAIEIAE 354
L+ V +T H T EA IAE
Sbjct: 284 LLSFPNVLITGHQAFFTKEALT----NIAE 309
>gnl|CDD|240638 cd12161, GDH_like_1, Putative glycerate dehydrogenase and related
proteins of the D-specific 2-hydroxy dehydrogenase
family. This group contains a variety of proteins
variously identified as glycerate dehydrogenase (GDH,
aka Hydroxypyruvate Reductase) and other enzymes of the
2-hydroxyacid dehydrogenase family. GDH catalyzes the
reversible reaction of (R)-glycerate + NAD+ to
hydroxypyruvate + NADH + H+. 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 = 315
Score = 193 bits (494), Expect = 6e-57
Identities = 103/288 (35%), Positives = 154/288 (53%), Gaps = 16/288 (5%)
Query: 63 IAEKLGQAGLDLLNEFANVDCAYN---LSPEELCTKISLCDALIVRSGTKVNRDVFESSA 119
+A L + G +EF Y+ EL + D +++ + + +V E+
Sbjct: 18 LAAPLEEQG----HEFV----YYDTKTTDTAELIERSKDADIVMI-ANMPLPGEVIEA-C 67
Query: 120 GRLKVVGRAGVGIDNVDLAAATEFGCLVVNAPTANTVAAAEHGIALLAAMARNVAQADAS 179
LK++ A G+D+VDL A E G V NA +T A AE I L + RN+ DA+
Sbjct: 68 KNLKMISVAFTGVDHVDLEACKERGITVSNAAGYSTEAVAELTIGLAIDLLRNIVPCDAA 127
Query: 180 VKAGKWQRNKYVGVSLVGKTLAVLGFGKVGSEVARRAKGLGMHVIAHDPYAPADRARAIG 239
V+AG + +G L GKT+ ++G G +G VAR K G V+A+ + A+A+G
Sbjct: 128 VRAGG-TKAGLIGRELAGKTVGIVGTGAIGLRVARLFKAFGCKVLAYSRS-EKEEAKALG 185
Query: 240 VDLVSFDEAIATADFISLHMPLTPATSKVLNDETFGKMKKGVRIINVARGGVIDEEALVR 299
++ VS DE +A +D +SLH+PL T ++ E MK+ +IN ARG V+D EAL
Sbjct: 186 IEYVSLDELLAESDIVSLHLPLNDETKGLIGKEKLALMKESAILINTARGPVVDNEALAD 245
Query: 300 ALDSGRVAQAALDVFTEEPP-PADSKLVQHERVTVTPHLGASTMEAQE 346
AL+ G++A A +DVF EPP PAD L+ +TPH+ +T EA E
Sbjct: 246 ALNEGKIAGAGIDVFDMEPPLPADYPLLHAPNTILTPHVAFATEEAME 293
>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 = 188 bits (479), Expect = 1e-54
Identities = 83/265 (31%), Positives = 130/265 (49%), Gaps = 24/265 (9%)
Query: 99 CDALIVRSGTKVNRDVFES-SAGRLKVVGRAGVGIDNVDLAAATEFGCLVVNAPTANTVA 157
D ++V+ + +V+E + +K + G+D +DL A E G + N P + A
Sbjct: 45 YDGVVVQQTLPYDEEVYEKLAEYGIKQIALRSAGVDMIDLDLAKENGLKITNVPAYSPRA 104
Query: 158 AAEHGIALLAAMARNVAQADASVKAGKWQRNKYVGVSLVGK-----TLAVLGFGKVGSEV 212
AE + + RN + D V G ++ L+G+ T+ ++G G++GS
Sbjct: 105 IAEFAVTQALNLLRNTPEIDRRVAKGDFRWAP----GLIGREIRDLTVGIIGTGRIGSAA 160
Query: 213 ARRAKGLGMHVIAHDPYAPADRARAIGVDLVSFDEAIATADFISLHMPLTPATSKVLNDE 272
A+ KG G VIA+DPY P + S ++ + AD ISLH+PLT ++N E
Sbjct: 161 AKIFKGFGAKVIAYDPY-PNPELEKFLLYYDSLEDLLKQADIISLHVPLTKENHHLINAE 219
Query: 273 TFGKMKKGVRIINVARGGVIDEEALVRALDSGRVAQAALDVFTEE-------------PP 319
F KMK G ++N ARGG++D +AL+ ALDSG++A AALD + E
Sbjct: 220 AFAKMKDGAILVNAARGGLVDTKALIDALDSGKIAGAALDTYENETGYFNKDWSGKEIED 279
Query: 320 PADSKLVQHERVTVTPHLGASTMEA 344
+L+ V +TPH+ T A
Sbjct: 280 EVLKELIAMPNVLITPHIAFYTDTA 304
>gnl|CDD|180588 PRK06487, PRK06487, glycerate dehydrogenase; Provisional.
Length = 317
Score = 173 bits (441), Expect = 2e-49
Identities = 94/256 (36%), Positives = 135/256 (52%), Gaps = 15/256 (5%)
Query: 117 SSAGRLKVVGRAGVGIDNVDLAAATEFGCLVVNAPTANTVAAAEHGIALLAAMARNVAQA 176
++A +LK++ A G +NVDLAAA E G V N T + A+H +ALL A+A +
Sbjct: 62 AAAPQLKLILVAATGTNNVDLAAARERGITVCNCQGYGTPSVAQHTLALLLALATRLPDY 121
Query: 177 DASVKAGKWQRNKYVG------VSLVGKTLAVLGFGKVGSEVARRAKGLGMHV-IAHDPY 229
+V AG+WQ++ V L GKTL +LG G++G VAR A+ GM V I P
Sbjct: 122 QQAVAAGRWQQSSQFCLLDFPIVELEGKTLGLLGHGELGGAVARLAEAFGMRVLIGQLP- 180
Query: 230 APADRARAIGVDLVSFDEAIATADFISLHMPLTPATSKVLNDETFGKMKKGVRIINVARG 289
R D + DE + D ++LH PLT T ++ MK G +IN ARG
Sbjct: 181 -----GRPARPDRLPLDELLPQVDALTLHCPLTEHTRHLIGARELALMKPGALLINTARG 235
Query: 290 GVIDEEALVRALDSGRVAQAALDVFTEEPPPADSKLVQ--HERVTVTPHLGASTMEAQEG 347
G++DE+AL AL SG + AA DV + EPP + L+ R+ VTPH + EA++
Sbjct: 236 GLVDEQALADALRSGHLGGAATDVLSVEPPVNGNPLLAPDIPRLIVTPHSAWGSREARQR 295
Query: 348 VAIEIAEAVVGALKGE 363
+ ++AE G+
Sbjct: 296 IVGQLAENARAFFAGK 311
>gnl|CDD|185307 PRK15409, PRK15409, bifunctional glyoxylate/hydroxypyruvate
reductase B; Provisional.
Length = 323
Score = 173 bits (440), Expect = 3e-49
Identities = 107/325 (32%), Positives = 162/325 (49%), Gaps = 19/325 (5%)
Query: 58 KPTVLIAEKLGQAGLDLLNEFANVDCAYNLSPEELCTKISLCDAL-----IVRSGTKVNR 112
KP+V++ + L L L E V NLSPE T A ++ SG KV+
Sbjct: 2 KPSVILYKALPDDLLQRLEEHFTVTQVANLSPE---TVEQHAAAFAEAEGLLGSGEKVDA 58
Query: 113 DVFESSAGRLKVVGRAGVGIDNVDLAAATEFGCLVVNAPTANTVAAAEHGIALLAAMARN 172
+ E +L+ VG DN D+ A T L+++ PT T A+ +AL+ + AR
Sbjct: 59 ALLEK-MPKLRAASTISVGYDNFDVDALTARKILLMHTPTVLTETVADTLMALVLSTARR 117
Query: 173 VAQADASVKAGKWQRN---KYVGVSLVGKTLAVLGFGKVGSEVARRAK-GLGMHVI--AH 226
V + VKAG+W + + G + KTL ++G G++G +A+RA G M ++ A
Sbjct: 118 VVEVAERVKAGEWTASIGPDWFGTDVHHKTLGIVGMGRIGMALAQRAHFGFNMPILYNAR 177
Query: 227 DPYAPAD-RARAIGVDLVSFDEAIATADFISLHMPLTPATSKVLNDETFGKMKKGVRIIN 285
+ A+ R A DL D + +DF+ + +PLT T + E F KMK IN
Sbjct: 178 RHHKEAEERFNARYCDL---DTLLQESDFVCIILPLTDETHHLFGAEQFAKMKSSAIFIN 234
Query: 286 VARGGVIDEEALVRALDSGRVAQAALDVFTEEPPPADSKLVQHERVTVTPHLGASTMEAQ 345
RG V+DE AL+ AL G + A LDVF +EP DS L+ V PH+G++T E +
Sbjct: 235 AGRGPVVDENALIAALQKGEIHAAGLDVFEQEPLSVDSPLLSLPNVVAVPHIGSATHETR 294
Query: 346 EGVAIEIAEAVVGALKGELAATAVN 370
+A + ++ AL+G++ VN
Sbjct: 295 YNMAACAVDNLIDALQGKVEKNCVN 319
>gnl|CDD|240642 cd12165, 2-Hacid_dh_6, Putative D-isomer specific 2-hydroxyacid
dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 314
Score = 170 bits (432), Expect = 5e-48
Identities = 81/254 (31%), Positives = 119/254 (46%), Gaps = 15/254 (5%)
Query: 121 RLKVVGRAGVGIDNVDLAAATEFGCLVVNAPTANTVAAAEHGIALLAAMARNVAQADASV 180
RLK++ G+D++ L E G +V N N+ A AEH +AL+ A+A+ + + D +
Sbjct: 60 RLKLIQVPSAGVDHLPLERLPE-GVVVANNH-GNSPAVAEHALALILALAKRIVEYDNDL 117
Query: 181 KAGKWQR---NKYVGVSLVGKTLAVLGFGKVGSEVARRAKGLGMHVIA--HDPYAPADRA 235
+ G W + L GKT+ +LG+G +G E+AR K GM VI P
Sbjct: 118 RRGIWHGRAGEEPESKELRGKTVGILGYGHIGREIARLLKAFGMRVIGVSRSPKEDEGAD 177
Query: 236 RAIGVDLVSFDEAIATADFISLHMPLTPATSKVLNDETFGKMKKGVRIINVARGGVIDEE 295
+ DEA+ AD + + +PLT T ++ MK G ++NV RG V+DEE
Sbjct: 178 FVGTLS--DLDEALEQADVVVVALPLTKQTRGLIGAAELAAMKPGAILVNVGRGPVVDEE 235
Query: 296 ALVRALDSGRVAQAALDVFTEEPPPADSKLVQH------ERVTVTPHLGASTMEAQEGVA 349
AL AL +A AA+DV+ P D V ++PH T E
Sbjct: 236 ALYEALKERPIAGAAIDVWWRYPSRGDPVAPSRYPFHELPNVIMSPHNAGWTEETFRRRI 295
Query: 350 IEIAEAVVGALKGE 363
E AE + L+GE
Sbjct: 296 DEAAENIRRYLRGE 309
>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 = 170 bits (434), Expect = 5e-48
Identities = 88/242 (36%), Positives = 127/242 (52%), Gaps = 31/242 (12%)
Query: 100 DALIVRSGTKVNRDVFESSAGRLKVVGRAGVGIDNVDLAAATEFGCLVVNAPTANTVAAA 159
D L+VRS TKVN + E S ++K VG A +G D++D E G NAP N + A
Sbjct: 38 DVLLVRSVTKVNEALLEGS--KVKFVGTATIGTDHIDTDYLKERGIGFANAPGCNANSVA 95
Query: 160 EHGIALLAAMARNVAQADASVKAGKWQRNKYVGVSLVGKTLAVLGFGKVGSEVARRAKGL 219
E+ ++ L +A QR G SL GKT+ ++G G VGS +ARR + L
Sbjct: 96 EYVLSALLVLA---------------QRQ---GFSLKGKTVGIVGVGNVGSRLARRLEAL 137
Query: 220 GMHVIAHDPYAPADRARAIGVDLVSFDEAIATADFISLHMPLTP----ATSKVLNDETFG 275
GM+V+ DP VS +E +A AD I+LH+PLT T +L+++
Sbjct: 138 GMNVLLCDPPRAE---AEGDPGFVSLEELLAEADIITLHVPLTRDGEHPTYHLLDEDFLA 194
Query: 276 KMKKGVRIINVARGGVIDEEALVRALDSGRVAQAALDVFTEEPPPADSKLVQHERVT-VT 334
+K G +IN +RG VID +AL+ L G+ + LDV+ EP D +L+ ++V T
Sbjct: 195 ALKPGQILINASRGAVIDNQALLALLQRGKDLRVVLDVWENEPEI-DLELL--DKVDIAT 251
Query: 335 PH 336
PH
Sbjct: 252 PH 253
>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 = 169 bits (430), Expect = 6e-48
Identities = 80/248 (32%), Positives = 127/248 (51%), Gaps = 12/248 (4%)
Query: 101 ALIVRSGTKVNRDVFESSAGRLKVVGRAGVGIDNVDLAAATEFGCLVVNAPTANTVAAAE 160
A++ T ++ + + L+++ GVG D +DL AA G V N P T A+
Sbjct: 45 AVVTNGETGLSAALIAA-LPALELIASFGVGYDGIDLDAARARGIRVTNTPGVLTDDVAD 103
Query: 161 HGIALLAAMARNVAQADASVKAGKWQRNKY-VGVSLVGKTLAVLGFGKVGSEVARRAKGL 219
+ LL A+ R + AD V+AG+W + + + + GK + ++G G++G +ARR +
Sbjct: 104 LAVGLLLAVLRRIPAADRFVRAGRWPKGAFPLTRKVSGKRVGIVGLGRIGRAIARRLEAF 163
Query: 220 GMHVIAHDPYAPADRARAIGVDLVSFDEAIATADFISLHMPLTPATSKVLNDETFGKM-K 278
GM + H D L+ +D + + P PAT ++N E +
Sbjct: 164 GMEIAYHGRRPKPDVPYRYYASLLELAAE---SDVLVVACPGGPATRHLVNAEVLEALGP 220
Query: 279 KGVRIINVARGGVIDEEALVRALDSGRVAQAALDVFTEEP--PPADSKLVQHERVTVTPH 336
GV ++NVARG V+DE AL+ AL GR+A A LDVF EP P A L+ + V +TPH
Sbjct: 221 DGV-LVNVARGSVVDEAALIAALQEGRIAGAGLDVFENEPNVPAA---LLDLDNVVLTPH 276
Query: 337 LGASTMEA 344
+ ++T+E
Sbjct: 277 IASATVET 284
>gnl|CDD|240632 cd12155, PGDH_1, Phosphoglycerate Dehydrogenase, 2-hydroxyacid
dehydrogenase family. Phosphoglycerate Dehydrogenase
(PGDH) catalyzes the NAD-dependent conversion of
3-phosphoglycerate into 3-phosphohydroxypyruvate, which
is the first step in serine biosynthesis.
Over-expression of PGDH has been implicated as
supporting proliferation of certain breast cancers,
while PGDH deficiency is linked to defects in mammalian
central nervous system development. PGDH is a member of
the 2-hydroxyacid dehydrogenase family, 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. Formate/glycerate and related
dehydrogenases of the D-specific 2-hydroxyacid
dehydrogenase superfamily include groups such as formate
dehydrogenase, glycerate dehydrogenase, L-alanine
dehydrogenase, and S-Adenosylhomocysteine Hydrolase.
Despite often low sequence identity, these proteins
typically have a characteristic arrangement of 2 similar
subdomains of the alpha/beta Rossmann-fold NAD+ binding
form. The NAD+ binding domain is inserted within the
linear sequence of the mostly N-terminal catalytic
domain, which has a similar domain structure to the
internal NAD binding domain. Structurally, these domains
are connected by extended alpha helices and create a
cleft in which NAD is bound, primarily to the C-terminal
portion of the 2nd (internal) domain. Some related
proteins have similar structural subdomain but with a
tandem arrangement of the catalytic and NAD-binding
subdomains in the linear sequence. While many members of
this family are dimeric, alanine DH is hexameric and
phosphoglycerate DH is tetrameric.
Length = 314
Score = 168 bits (428), Expect = 2e-47
Identities = 75/229 (32%), Positives = 117/229 (51%), Gaps = 13/229 (5%)
Query: 114 VFESSAGRLKVVGRAGVGIDNVDLAAATEFGCLVVNAPTANTVAAAEHGIALLAAMARNV 173
+ + LK + G+D + L + G L+ N +++ AE + + + + +
Sbjct: 53 LDLAKMKNLKWIQLYSAGVDYLPLEYIKKKGILLTNNSGIHSIPIAEWIVGYILEIYKGL 112
Query: 174 AQADASVKAGKWQRNKYVGVSLVGKTLAVLGFGKVGSEVARRAKGLGMHVIA-----HD- 227
+A + K KW+ + + L GKT+ LG G +G E+A+R K GM VI D
Sbjct: 113 KKAYKNQKEKKWKMDS-SLLELYGKTILFLGTGSIGQEIAKRLKAFGMKVIGVNTSGRDV 171
Query: 228 PYAPADRARAIGVDLVSFDEAIATADFISLHMPLTPATSKVLNDETFGKMKKGVRIINVA 287
Y D+ + +L DE + AD + +PLT T + ++ F +MKKG INV
Sbjct: 172 EYF--DKCYPLE-EL---DEVLKEADIVVNVLPLTEETHHLFDEAFFEQMKKGALFINVG 225
Query: 288 RGGVIDEEALVRALDSGRVAQAALDVFTEEPPPADSKLVQHERVTVTPH 336
RG +DE+AL+ AL + ++ AALDVF EEP P DS L + V +TPH
Sbjct: 226 RGPSVDEDALIEALKNKQIRGAALDVFEEEPLPKDSPLWDLDNVLITPH 274
>gnl|CDD|240627 cd05302, FDH, NAD-dependent Formate Dehydrogenase (FDH).
NAD-dependent formate dehydrogenase (FDH) catalyzes the
NAD+-dependent oxidation of a formate anion to carbon
dioxide coupled with the reduction of NAD+ to NADH.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxy acid dehydrogenase family have 2
highly similar subdomains of the alpha/beta form, with
NAD binding occurring in the cleft between subdomains.
NAD contacts are primarily to the Rossmann-fold
NAD-binding domain which is inserted within the linear
sequence of the more diverse flavodoxin-like catalytic
subdomain. Some related proteins have similar structural
subdomain but with a tandem arrangement of the catalytic
and NAD-binding subdomains in the linear sequence. FDHs
of this family contain no metal ions or prosthetic
groups. Catalysis occurs though direct transfer of the
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 from C1 compounds such as methanol,
and in the stress responses of plants. NAD-dependent FDH
is useful in cofactor regeneration in asymmetrical
biocatalytic reduction processes, where FDH irreversibly
oxidizes formate to carbon dioxide, while reducing the
oxidized form of the cofactor to the reduced form.
Length = 348
Score = 163 bits (414), Expect = 3e-45
Identities = 76/240 (31%), Positives = 123/240 (51%), Gaps = 10/240 (4%)
Query: 117 SSAGRLKVVGRAGVGIDNVDLAAATEFGCLVVNAPTANTVAAAEHGIALLAAMARNVAQA 176
+ A LK+ AG+G D+VDL AA + G V +N V+ AEH + ++ + RN
Sbjct: 80 AKAKNLKLALTAGIGSDHVDLQAANDRGITVAEVTGSNVVSVAEHVVMMILILVRNYVPG 139
Query: 177 DASVKAGKWQ-----RNKYVGVSLVGKTLAVLGFGKVGSEVARRAKGLGMHVIAHDPYA- 230
G W + Y L GKT+ +G G++G V RR K +H++ +D +
Sbjct: 140 HEQAIEGGWNVADVVKRAY---DLEGKTVGTVGAGRIGLRVLRRLKPFDVHLLYYDRHRL 196
Query: 231 PADRARAIGVDLV-SFDEAIATADFISLHMPLTPATSKVLNDETFGKMKKGVRIINVARG 289
P + + +G+ ++ ++ D ++++ PL P T + N E KMKKG ++N ARG
Sbjct: 197 PEEVEKELGLTRHADLEDMVSKCDVVTINCPLHPETEGLFNKELLSKMKKGAYLVNTARG 256
Query: 290 GVIDEEALVRALDSGRVAQAALDVFTEEPPPADSKLVQHERVTVTPHLGASTMEAQEGVA 349
+ D EA+ AL+SG +A A DV+ +P P D +TPH+ +T++AQ A
Sbjct: 257 KICDREAVAEALESGHLAGYAGDVWFPQPAPKDHPWRTMPNNAMTPHISGTTLDAQARYA 316
>gnl|CDD|181414 PRK08410, PRK08410, 2-hydroxyacid dehydrogenase; Provisional.
Length = 311
Score = 160 bits (406), Expect = 2e-44
Identities = 90/317 (28%), Positives = 164/317 (51%), Gaps = 19/317 (5%)
Query: 58 KPTVLIAEKLGQAGLDLLNEFANVDCAYNL-SPEELCTKISLCDA-LIVRSGTKVNRDVF 115
K +L A+ LG L + EF + Y SPEE+ +I DA +I+ + ++++V
Sbjct: 2 KIVILDAKTLGDKDLSVFEEFGDFQ-IYPTTSPEEVIERIK--DANIIITNKVVIDKEVL 58
Query: 116 ESSAGRLKVVGRAGVGIDNVDLAAATEFGCLVVNAPTANTVAAAEHGIALLAAMARNVAQ 175
S LK++ G +NVD+ A + G V N +T + A+H A+L ++ +
Sbjct: 59 -SQLPNLKLICITATGTNNVDIEYAKKKGIAVKNVAGYSTESVAQHTFAMLLSLLGRINY 117
Query: 176 ADASVKAGKWQRNK-YVGVS-----LVGKTLAVLGFGKVGSEVARRAKGLGMHVIAHDPY 229
D VK+G++ + + +S + GK ++G G +G VA+ A+ G V+ Y
Sbjct: 118 YDRYVKSGEYSESPIFTHISRPLGEIKGKKWGIIGLGTIGKRVAKIAQAFGAKVVY---Y 174
Query: 230 APADRARAIGVDLVSFDEAIATADFISLHMPLTPATSKVLNDETFGKMKKGVRIINVARG 289
+ + + + + VS +E + T+D IS+H PL T ++ + +K G +INV RG
Sbjct: 175 STSGKNKNEEYERVSLEELLKTSDIISIHAPLNEKTKNLIAYKELKLLKDGAILINVGRG 234
Query: 290 GVIDEEALVRALDSGRVAQAALDVFTEEPPPADSKLVQ---HERVTVTPHLGASTMEAQE 346
G+++E+ L +ALD + A LDV +EP + L+ E++ +TPH+ ++ EA++
Sbjct: 235 GIVNEKDLAKALDEKDIY-AGLDVLEKEPMEKNHPLLSIKNKEKLLITPHIAWASKEARK 293
Query: 347 GVAIEIAEAVVGALKGE 363
+ ++ E + L+G
Sbjct: 294 TLIEKVKENIKDFLEGG 310
>gnl|CDD|240661 cd12185, HGDH_LDH_like, Putative Lactate dehydrogenase and
(R)-2-Hydroxyglutarate Dehydrogenase-like proteins,
NAD-binding and catalytic domains. This group contains
various putative dehydrogenases related to D-lactate
dehydrogenase (LDH), (R)-2-hydroxyglutarate
dehydrogenase (HGDH), and related enzymes, members of
the 2-hydroxyacid dehydrogenases family. LDH catalyzes
the interconversion of pyruvate and lactate, and HGDH
catalyzes the NAD-dependent reduction of 2-oxoglutarate
to (R)-2-hydroxyglutarate. Despite often low sequence
identity within this 2-hydroxyacid dehydrogenase family,
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 = 322
Score = 158 bits (403), Expect = 7e-44
Identities = 79/261 (30%), Positives = 124/261 (47%), Gaps = 19/261 (7%)
Query: 99 CDALIVRSGTKVNRDVFES-SAGRLKVVGRAGVGIDNVDLAAATEFGCLVVNAPTA-NTV 156
D + + +K++ ++ E +K + +G D++DL AA E G V N + N+V
Sbjct: 45 YDGISILGKSKISAELLEKLKEAGVKYISTRSIGYDHIDLDAAKELGIKVSNVTYSPNSV 104
Query: 157 AAAEHGIALLAAMARNVAQADASVKAGKWQRNKYVGVSLVGKTLAVLGFGKVGSEVARRA 216
A ++ + L+ R Q + + G L T+ V+G G++G V +
Sbjct: 105 A--DYTVMLMLMALRKYKQIMKRAEVNDYSLGGLQGRELRNLTVGVIGTGRIGQAVIKNL 162
Query: 217 KGLGMHVIAHDPYAPADRARAIGVDLVSFDEAIATADFISLHMPLTPATSKVLNDETFGK 276
G G ++A+DPY P + + + V D +D I+LH PLT T ++N E+ K
Sbjct: 163 SGFGCKILAYDPY-PNEEVK-KYAEYVDLDTLYKESDIITLHTPLTEETYHLINKESIAK 220
Query: 277 MKKGVRIINVARGGVIDEEALVRALDSGRVAQAALDVFTEE-------------PPPADS 323
MK GV IIN ARG +ID EAL+ L+SG++ AALDV E +
Sbjct: 221 MKDGVIIINTARGELIDTEALIEGLESGKIGGAALDVIEGEDGIYYNDRKGDILSNRELA 280
Query: 324 KLVQHERVTVTPHLGASTMEA 344
L V +TPH+ T +A
Sbjct: 281 ILRSFPNVILTPHMAFYTDQA 301
>gnl|CDD|235890 PRK06932, PRK06932, glycerate dehydrogenase; Provisional.
Length = 314
Score = 158 bits (400), Expect = 1e-43
Identities = 83/260 (31%), Positives = 131/260 (50%), Gaps = 16/260 (6%)
Query: 88 SPEELCTKISLCDALIVRSGTKVNRDVFESSAGRLKVVGRAGVGIDNVDLAAATEFGCLV 147
S E+ + D +++ S R+ + +LK++ G +NVDL AA E G V
Sbjct: 34 SAEQTIERAKDAD-IVITSKVLFTRETL-AQLPKLKLIAITATGTNNVDLVAAKELGIAV 91
Query: 148 VNAPTANTVAAAEHGIALLAAMARNVAQADASVKAGKWQRNK------YVGVSLVGKTLA 201
N ++ EH + ++ A+ ++ + +W K Y + G TL
Sbjct: 92 KNVTGYSSTTVPEHVLGMIFALKHSLMGWYRDQLSDRWATCKQFCYFDYPITDVRGSTLG 151
Query: 202 VLGFGKVGSEVARRAKGLGMHVIAHDPYAPADRARAIGVDLVSFDEAIATADFISLHMPL 261
V G G +G+EV R A+ LGM V+ YA A F+E + AD ++LH PL
Sbjct: 152 VFGKGCLGTEVGRLAQALGMKVL----YAEHKGASVCREGYTPFEEVLKQADIVTLHCPL 207
Query: 262 TPATSKVLNDETFGKMKKGVRIINVARGGVIDEEALVRALDSGRVAQAALDVFTEEPPPA 321
T T ++N ET MK +IN RG ++DE+AL+ AL++G++A AALDV +EPP
Sbjct: 208 TETTQNLINAETLALMKPTAFLINTGRGPLVDEQALLDALENGKIAGAALDVLVKEPPEK 267
Query: 322 DSKLVQHER----VTVTPHL 337
D+ L+Q + + +TPH+
Sbjct: 268 DNPLIQAAKRLPNLLITPHI 287
>gnl|CDD|215501 PLN02928, PLN02928, oxidoreductase family protein.
Length = 347
Score = 157 bits (400), Expect = 3e-43
Identities = 80/277 (28%), Positives = 141/277 (50%), Gaps = 24/277 (8%)
Query: 81 VDCAYNLSPEELCTKISLCDALIVRSGTKVNRDVFESSAGRLKVVGRAGVGIDNVDLAAA 140
A P+ I+ D + + +++ D+ + A ++K++ + GVG++ VD+ AA
Sbjct: 48 DAVAREDVPDV----IANYDICVPKM-MRLDADII-ARASQMKLIMQFGVGLEGVDVDAA 101
Query: 141 TEFGCLVVNAP---TANTVAAAEHGIALLAAMARNVAQADASVKAGKWQRNKYVGVSLVG 197
T+ G V P T N + AE I L+ + R + S+KA + + +G +L G
Sbjct: 102 TKHGIKVARIPSEGTGNAASCAEMAIYLMLGLLRKQNEMQISLKARRL--GEPIGDTLFG 159
Query: 198 KTLAVLGFGKVGSEVARRAKGLGMHVIAHDPYAPADRARAIGVDLVSFD----------- 246
KT+ +LG+G +G E+A+R + G+ ++A ++ + + D
Sbjct: 160 KTVFILGYGAIGIELAKRLRPFGVKLLATRRSWTSEPEDGLLIPNGDVDDLVDEKGGHED 219
Query: 247 --EAIATADFISLHMPLTPATSKVLNDETFGKMKKGVRIINVARGGVIDEEALVRALDSG 304
E AD + L LT T+ ++NDE MKKG ++N+ARGG++D +A++ AL+SG
Sbjct: 220 IYEFAGEADIVVLCCTLTKETAGIVNDEFLSSMKKGALLVNIARGGLLDYDAVLAALESG 279
Query: 305 RVAQAALDVFTEEPPPADSKLVQHERVTVTPHLGAST 341
+ A+DV EP D +++H V +TPH+ T
Sbjct: 280 HLGGLAIDVAWSEPFDPDDPILKHPNVIITPHVAGVT 316
>gnl|CDD|181041 PRK07574, PRK07574, formate dehydrogenase; Provisional.
Length = 385
Score = 157 bits (400), Expect = 8e-43
Identities = 79/231 (34%), Positives = 128/231 (55%), Gaps = 4/231 (1%)
Query: 119 AGRLKVVGRAGVGIDNVDLAAATEFGCLVVNAPTANTVAAAEHGIALLAAMARNVAQADA 178
A LK+ AG+G D+VDL AA+E G V +N+++ AEH + ++ A+ RN +
Sbjct: 112 APNLKLAITAGIGSDHVDLQAASEHGITVAEVTGSNSISVAEHVVMMILALVRNYEPSHR 171
Query: 179 SVKAGKWQRNKYVGVS--LVGKTLAVLGFGKVGSEVARRAKGLGMHVIAHDPY-APADRA 235
G W V S L G T+ ++G G++G V RR K + + D + P +
Sbjct: 172 QAVEGGWNIADCVSRSYDLEGMTVGIVGAGRIGLAVLRRLKPFDVKLHYTDRHRLPEEVE 231
Query: 236 RAIGVDL-VSFDEAIATADFISLHMPLTPATSKVLNDETFGKMKKGVRIINVARGGVIDE 294
+ +G+ VSFD ++ D +++H PL P T + + + +MK+G ++N ARG ++D
Sbjct: 232 QELGLTYHVSFDSLVSVCDVVTIHCPLHPETEHLFDADVLSRMKRGSYLVNTARGKIVDR 291
Query: 295 EALVRALDSGRVAQAALDVFTEEPPPADSKLVQHERVTVTPHLGASTMEAQ 345
+A+VRAL+SG +A A DV+ +P PAD R +TPH+ +T+ AQ
Sbjct: 292 DAVVRALESGHLAGYAGDVWFPQPAPADHPWRTMPRNGMTPHISGTTLSAQ 342
>gnl|CDD|240657 cd12180, 2-Hacid_dh_15, Putative D-isomer specific 2-hydroxyacid
dehydrogenases, NAD-binding and catalytic domains.
2-Hydroxyacid dehydrogenases catalyze the conversion of
a wide variety of D-2-hydroxy acids to their
corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 308
Score = 150 bits (380), Expect = 8e-41
Identities = 87/242 (35%), Positives = 122/242 (50%), Gaps = 20/242 (8%)
Query: 120 GRLKVVGRAGVGIDNV--DLAAATEFGCLVVNAPTANTVAAAEHGIALLAAMARNVAQAD 177
GRL+ V GID L G +V A A AE +A + A A+ + +
Sbjct: 63 GRLRWVQLVSSGIDYYPDWLFE----GPVVTCARGVAAEAIAEFVLAAILAAAKRLP--E 116
Query: 178 ASVK-AGKWQRNKYVGVSLVGKTLAVLGFGKVGSEVARRAKGLGMHVIAHDPYAPADRAR 236
VK A +W+R SL G TL ++GFG +G +ARRA LGM V+A R
Sbjct: 117 IWVKGAEQWRREP--LGSLAGSTLGIVGFGAIGQALARRALALGMRVLA-----LRRSGR 169
Query: 237 AIGVDLVS----FDEAIATADFISLHMPLTPATSKVLNDETFGKMKKGVRIINVARGGVI 292
V V E A +D + L PLTP T ++N + + K G+ +IN+ARGG++
Sbjct: 170 PSDVPGVEAAADLAELFARSDHLVLAAPLTPETRHLINADVLAQAKPGLHLINIARGGLV 229
Query: 293 DEEALVRALDSGRVAQAALDVFTEEPPPADSKLVQHERVTVTPHLGASTMEAQEGVAIEI 352
D+EAL+ ALDSGR++ A+LDV EP P L H RV ++PH A + + +A
Sbjct: 230 DQEALLEALDSGRISLASLDVTDPEPLPEGHPLYTHPRVRLSPHTSAIAPDGRRNLADRF 289
Query: 353 AE 354
E
Sbjct: 290 LE 291
>gnl|CDD|240660 cd12184, HGDH_like, (R)-2-Hydroxyglutarate Dehydrogenase and
related dehydrogenases, NAD-binding and catalytic
domains. (R)-2-hydroxyglutarate dehydrogenase (HGDH)
catalyzes the NAD-dependent reduction of 2-oxoglutarate
to (R)-2-hydroxyglutarate. HGDH is a member of the
D-2-hydroxyacid NAD(+)-dependent dehydrogenase family;
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 = 330
Score = 149 bits (378), Expect = 3e-40
Identities = 92/272 (33%), Positives = 132/272 (48%), Gaps = 37/272 (13%)
Query: 99 CDALIVRSGTKVNRDVFESSAGR-LKVVGRAGVGIDNVDLAAATEFGCLVVNAPTANTVA 157
DA+IVR +++ E +K V VG +++DL AA E G + P+ + A
Sbjct: 45 HDAVIVRGNCFADKENLEIYKEYGIKYVFTRTVGFNHIDLEAAKELGFKMARVPSYSPNA 104
Query: 158 AAE----HGIALL---AAMARNVAQADASVKA---GKWQRNKYVGVSLVGKTLAVLGFGK 207
AE + L A A A + V K RN VG+ +G G+
Sbjct: 105 IAELAFTLAMTLSRHTAYTASRTANKNFKVDPFMFSKEIRNSTVGI---------IGTGR 155
Query: 208 VGSEVARRAKGLGMHVIAHDPYAPADRARAIGVDLVSFDEAIATADFISLHMPLTPATS- 266
+G A+ KGLG VI +D Y P+D A+ + V VS DE + +D ISLH+P +
Sbjct: 156 IGLTAAKLFKGLGAKVIGYDIY-PSDAAKDV-VTFVSLDELLKKSDIISLHVPYIKGKND 213
Query: 267 KVLNDETFGKMKKGVRIINVARGGVIDEEALVRALDSGRVAQAALDVFTEE--------- 317
K++N E KMK G +IN ARG + DEEA++ AL+SG++A DV E
Sbjct: 214 KLINKEFISKMKDGAILINTARGELQDEEAILEALESGKLAGFGTDVLNNEKEIFFKDFD 273
Query: 318 ----PPPADSKLVQ-HERVTVTPHLGASTMEA 344
P KL+ + RV +TPH+G+ T EA
Sbjct: 274 GDKIEDPVVEKLLDLYPRVLLTPHIGSYTDEA 305
>gnl|CDD|240641 cd12164, GDH_like_2, Putative glycerate dehydrogenase and related
proteins of the D-specific 2-hydroxy dehydrogenase
family. This group contains a variety of proteins
variously identified as glycerate dehydrogenase (GDH,
also known as hydroxypyruvate reductase) and other
enzymes of the 2-hydroxyacid dehydrogenase family. GDH
catalyzes the reversible reaction of (R)-glycerate +
NAD+ to hydroxypyruvate + NADH + H+. 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 = 306
Score = 138 bits (349), Expect = 2e-36
Identities = 81/254 (31%), Positives = 120/254 (47%), Gaps = 26/254 (10%)
Query: 121 RLKVVGRAGVGIDNVDLAAATEFG---CLVVNAPTANTVAAAEHGIALLAAMA--RNVAQ 175
LK + G G+D++ LA +V+ A +A L A + R++ +
Sbjct: 58 NLKAIFSLGAGVDHL-LADPDLPDVPIVRLVDPGLAQGMAEY----VLAAVLRLHRDMDR 112
Query: 176 ADASVKAGKWQRNKYVGVSLVGKTLAVLGFGKVGSEVARRAKGLGMHVIAHDPYAPADRA 235
A + G W+ + + VLG G++G+ VARR LG V +
Sbjct: 113 YAAQQRRGVWKPLPQRPAAER--RVGVLGLGELGAAVARRLAALGFPVSGW-----SRSP 165
Query: 236 RAI-GVDLVS----FDEAIATADF-ISLHMPLTPATSKVLNDETFGKMKKGVRIINVARG 289
+ I GV D +A D + L +PLTP T +LN E ++ +G +INV RG
Sbjct: 166 KDIEGVTCFHGEEGLDAFLAQTDILVCL-LPLTPETRGILNAELLARLPRGAALINVGRG 224
Query: 290 GVIDEEALVRALDSGRVAQAALDVFTEEPPPADSKLVQHERVTVTPHLGASTMEAQEGVA 349
+ E L+ ALDSG ++ A LDVF +EP PAD L +H RVTVTPH+ A+ + A
Sbjct: 225 PHLVEADLLAALDSGHLSGAVLDVFEQEPLPADHPLWRHPRVTVTPHI-AAITDPDSAAA 283
Query: 350 IEIAEAVVGALKGE 363
+AE + GE
Sbjct: 284 Q-VAENIRRLEAGE 296
>gnl|CDD|166874 PRK00257, PRK00257, erythronate-4-phosphate dehydrogenase;
Validated.
Length = 381
Score = 131 bits (331), Expect = 2e-33
Identities = 93/303 (30%), Positives = 135/303 (44%), Gaps = 35/303 (11%)
Query: 100 DALIVRSGTKVNRDVFESSAGRLKVVGRAGVGIDNVDLAAATEFGCLVVNAPTANTVAAA 159
D L+VRS T+V+R + E S R++ VG +G D++DL E G +AP N
Sbjct: 39 DVLLVRSVTRVDRALLEGS--RVRFVGTCTIGTDHLDLDYFAEAGITWSSAPGCNARGVV 96
Query: 160 EHGIALLAAMARNVAQADASVKAGKWQRNKYVGVSLVGKTLAVLGFGKVGSEVARRAKGL 219
++ + L +A GV L +T V+G G VG + R +GL
Sbjct: 97 DYVLGSLLTLAERE------------------GVDLAERTYGVVGAGHVGGRLVRVLRGL 138
Query: 220 GMHVIAHDPYAPADRARAIGVDLVSFDEAIATADFISLHMPLTP----ATSKVLNDETFG 275
G V+ DP P A G D VS + + D ISLH PLT T +L++
Sbjct: 139 GWKVLVCDP--PRQEAEGDG-DFVSLERILEECDVISLHTPLTKEGEHPTRHLLDEAFLA 195
Query: 276 KMKKGVRIINVARGGVIDEEALVRALDSGRVAQAALDVFTEEPPPADSKLVQHERVTVTP 335
++ G +IN +RG V+D +AL AL SG A LDV+ E P D +L + TP
Sbjct: 196 SLRPGAWLINASRGAVVDNQALREALLSGEDLDAVLDVWEGE-PQIDLELADLCTIA-TP 253
Query: 336 HL-GASTMEAQEGVAIEIAEAVVGALKGELAATAVNAPMVPAEVL--TELKPFVELAEKL 392
H+ G S G A +I +A+ + A ++P L +L + A L
Sbjct: 254 HIAGYSLDGKARGTA-QIYQALCRFFG--IPARVSLTDLLPPPWLAQIDLDASADPAWAL 310
Query: 393 GRL 395
L
Sbjct: 311 ATL 313
>gnl|CDD|181499 PRK08605, PRK08605, D-lactate dehydrogenase; Validated.
Length = 332
Score = 129 bits (325), Expect = 4e-33
Identities = 78/265 (29%), Positives = 132/265 (49%), Gaps = 18/265 (6%)
Query: 122 LKVVGRAGVGIDNVDLAAATEFGCLVVNAPTANTVAAAEHGIALLAAMARNVAQADASVK 181
+K + + G D DL AT++ ++ N P+ + + AE + + R+ Q V+
Sbjct: 70 IKQIAQRSAGFDTYDLELATKYNLIISNVPSYSPESIAEFTVTQAINLVRHFNQIQTKVR 129
Query: 182 AG--KWQRNKYVGVSLVGKTLAVLGFGKVGSEVAR-RAKGLGMHVIAHDPYAPADRARAI 238
+W+ + S+ +AV+G G++G VA+ AKG G V+A+DP+ P +A
Sbjct: 130 EHDFRWEPP-ILSRSIKDLKVAVIGTGRIGLAVAKIFAKGYGSDVVAYDPF-PNAKAATY 187
Query: 239 GVDLVSFDEAIATADFISLHMPLTPATSKVLNDETFGKMKKGVRIINVARGGVIDEEALV 298
+ +EA+ AD ++LHMP T + N + F KKG +N ARG ++D +AL+
Sbjct: 188 VDYKDTIEEAVEGADIVTLHMPATKYNHYLFNADLFKHFKKGAVFVNCARGSLVDTKALL 247
Query: 299 RALDSGRVAQAALDVFTEEPP--PADSK-----------LVQHERVTVTPHLGASTMEAQ 345
ALD+G + AALD + E P P+D + L+ E V +TPH+ T A
Sbjct: 248 DALDNGLIKGAALDTYEFERPLFPSDQRGQTINDPLLESLINREDVILTPHIAFYTDAAV 307
Query: 346 EGVAIEIAEAVVGALKGELAATAVN 370
+ + ++ +A + L+ VN
Sbjct: 308 KNLIVDALDATLEVLQTGTTRLRVN 332
>gnl|CDD|177941 PLN02306, PLN02306, hydroxypyruvate reductase.
Length = 386
Score = 128 bits (322), Expect = 4e-32
Identities = 89/254 (35%), Positives = 129/254 (50%), Gaps = 23/254 (9%)
Query: 130 VGIDNVDLAAATEFGCLVVNAPTANTVAAAEHGIALLAAMARNVAQADASVKAGK---WQ 186
VG +NVD+ AA ++G V N P T AE +L A AR + +AD ++AG W
Sbjct: 95 VGYNNVDVEAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYEGWL 154
Query: 187 RNKYVGVSLVGKTLAVLGFGKVGSEVARR-AKGLGMHVIAHDPYAPADR----ARAIGVD 241
+ +VG L G+T+ V+G G++GS AR +G M++I +D Y + R A G
Sbjct: 155 PHLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLY-QSTRLEKFVTAYGQF 213
Query: 242 L-------------VSFDEAIATADFISLHMPLTPATSKVLNDETFGKMKKGVRIINVAR 288
L S +E + AD ISLH L T ++N E MKK ++N +R
Sbjct: 214 LKANGEQPVTWKRASSMEEVLREADVISLHPVLDKTTYHLINKERLALMKKEAVLVNASR 273
Query: 289 GGVIDEEALVRALDSGRVAQAALDVFTEEPPPADSKLVQHERVTVTPHLGASTMEAQEGV 348
G VIDE ALV L + + + LDVF +E P L + V PH+ +++ +EG+
Sbjct: 274 GPVIDEVALVEHLKANPMFRVGLDVFEDE-PYMKPGLADMKNAVVVPHIASASKWTREGM 332
Query: 349 AIEIAEAVVGALKG 362
A A V+G LKG
Sbjct: 333 ATLAALNVLGKLKG 346
>gnl|CDD|178684 PLN03139, PLN03139, formate dehydrogenase; Provisional.
Length = 386
Score = 126 bits (318), Expect = 1e-31
Identities = 73/249 (29%), Positives = 118/249 (47%), Gaps = 4/249 (1%)
Query: 119 AGRLKVVGRAGVGIDNVDLAAATEFGCLVVNAPTANTVAAAEHGIALLAAMARNVAQADA 178
A L+++ AG+G D++DL AA G V +N V+ AE + + + RN
Sbjct: 119 AKNLELLLTAGIGSDHIDLPAAAAAGLTVAEVTGSNVVSVAEDELMRILILLRNFLPGYH 178
Query: 179 SVKAGKWQRNK--YVGVSLVGKTLAVLGFGKVGSEVARRAKGLGMHVIAHDPYA-PADRA 235
V +G+W Y L GKT+ +G G++G + +R K +++ HD +
Sbjct: 179 QVVSGEWNVAGIAYRAYDLEGKTVGTVGAGRIGRLLLQRLKPFNCNLLYHDRLKMDPELE 238
Query: 236 RAIGVDLVS-FDEAIATADFISLHMPLTPATSKVLNDETFGKMKKGVRIINVARGGVIDE 294
+ G D + D + ++ PLT T + N E KMKKGV I+N ARG ++D
Sbjct: 239 KETGAKFEEDLDAMLPKCDVVVINTPLTEKTRGMFNKERIAKMKKGVLIVNNARGAIMDT 298
Query: 295 EALVRALDSGRVAQAALDVFTEEPPPADSKLVQHERVTVTPHLGASTMEAQEGVAIEIAE 354
+A+ A SG + DV+ +P P D +TPH+ +T++AQ A + +
Sbjct: 299 QAVADACSSGHIGGYGGDVWYPQPAPKDHPWRYMPNHAMTPHISGTTIDAQLRYAAGVKD 358
Query: 355 AVVGALKGE 363
+ KGE
Sbjct: 359 MLDRYFKGE 367
>gnl|CDD|240643 cd12166, 2-Hacid_dh_7, 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 = 300
Score = 123 bits (311), Expect = 2e-31
Identities = 73/224 (32%), Positives = 109/224 (48%), Gaps = 14/224 (6%)
Query: 121 RLKVVGRAGVGIDNVDLAAATEFGCLVVNAPTANTVAAAEHGIALLAAMARNVAQADASV 180
RL+VV G D V L E G + NA + + AE +AL+ A R + + +
Sbjct: 60 RLRVVQTLSAGYDGV-LPLLPE-GVTLCNARGVHDASTAELAVALILASLRGLPRFVRAQ 117
Query: 181 KAGKWQRNKYVGVSLVGKTLAVLGFGKVGSEVARRAKGLGMHVIAHDPYAPADRARAIGV 240
G+W+ SL + + ++G+G +G + RR + V A AR G
Sbjct: 118 ARGRWEPR--RTPSLADRRVLIVGYGSIGRAIERRLAPFEVRVTR-----VARTARP-GE 169
Query: 241 DLVSFDEA---IATADFISLHMPLTPATSKVLNDETFGKMKKGVRIINVARGGVIDEEAL 297
+ DE + AD + L +PLT T +++ E +M G ++NVARG V+D +AL
Sbjct: 170 QVHGIDELPALLPEADVVVLIVPLTDETRGLVDAEFLARMPDGALLVNVARGPVVDTDAL 229
Query: 298 VRALDSGRVAQAALDVFTEEPPPADSKLVQHERVTVTPHLGAST 341
V L SGR+ +AALDV EP P L V +TPH+G +T
Sbjct: 230 VAELASGRL-RAALDVTDPEPLPPGHPLWSAPGVLITPHVGGAT 272
>gnl|CDD|240636 cd12159, 2-Hacid_dh_2, 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 = 303
Score = 120 bits (303), Expect = 3e-30
Identities = 75/225 (33%), Positives = 100/225 (44%), Gaps = 15/225 (6%)
Query: 153 ANTVAAAEHGIALLAAMARNVAQADASVKAGKWQRNKYV--GVSLVGKTLAVLGFGKVGS 210
A TVA EH +ALL A R Q A +A W + L G T+A++G G +G
Sbjct: 84 AETVA--EHALALLLAGLR---QLPARARATTWDPAEEDDLVTLLRGSTVAIVGAGGIGR 138
Query: 211 EVARRAKGLGMHVIA----HDPYAPADRARAIGVDLVSFDEAIATADFISLHMPLTPATS 266
+ G VIA P AD V DE AD + L PLTP T
Sbjct: 139 ALIPLLAPFGAKVIAVNRSGRPVEGADET----VPADRLDEVWPDADHVVLAAPLTPETR 194
Query: 267 KVLNDETFGKMKKGVRIINVARGGVIDEEALVRALDSGRVAQAALDVFTEEPPPADSKLV 326
+++ MK ++NVARG ++D +ALV AL SG +A AALDV EP P L
Sbjct: 195 HLVDAAALAAMKPHAWLVNVARGPLVDTDALVDALRSGEIAGAALDVTDPEPLPDGHPLW 254
Query: 327 QHERVTVTPHLGASTMEAQEGVAIEIAEAVVGALKGELAATAVNA 371
+TPH+ + + +A +AE V GE V+
Sbjct: 255 SLPNALITPHVANTPEVIRPLLAERVAENVRAFAAGEPLLGVVDP 299
>gnl|CDD|183550 PRK12480, PRK12480, D-lactate dehydrogenase; Provisional.
Length = 330
Score = 112 bits (281), Expect = 4e-27
Identities = 66/242 (27%), Positives = 115/242 (47%), Gaps = 26/242 (10%)
Query: 122 LKVVGRAGVGIDNVDLAAATEFGCLVVNAPTANTVAAAEHGIALLAAMARNVAQADASVK 181
+K + + G D DL A + ++ N P+ + AE+ +++ + R + V+
Sbjct: 70 IKQIAQRTAGFDMYDLDLAKKHNIVISNVPSYSPETIAEYSVSIALQLVRRFPDIERRVQ 129
Query: 182 AG--KWQRNKYVGVSLVGKTLAVLGFGKVGSEVARRAKGLGMHVIAHDPYAPADRARAIG 239
A WQ + + + T+A++G G++G+ A+ G G + A+D Y P
Sbjct: 130 AHDFTWQ-AEIMSKPVKNMTVAIIGTGRIGAATAKIYAGFGATITAYDAY-PNK-----D 182
Query: 240 VDLV----SFDEAIATADFISLHMPLTPATSKVLNDETFGKMKKGVRIINVARGGVIDEE 295
+D + S EAI AD ISLH+P + + + F +KKG ++N ARG VI+
Sbjct: 183 LDFLTYKDSVKEAIKDADIISLHVPANKESYHLFDKAMFDHVKKGAILVNAARGAVINTP 242
Query: 296 ALVRALDSGRVAQAALDVFTEEPP-------------PADSKLVQHERVTVTPHLGASTM 342
L+ A++ G + AA+D + E +L++HER+ VTPH+ +
Sbjct: 243 DLIAAVNDGTLLGAAIDTYENEAAYFTNDWTNKDIDDKTLLELIEHERILVTPHIAFFSD 302
Query: 343 EA 344
EA
Sbjct: 303 EA 304
>gnl|CDD|235800 PRK06436, PRK06436, glycerate dehydrogenase; Provisional.
Length = 303
Score = 109 bits (275), Expect = 1e-26
Identities = 63/233 (27%), Positives = 118/233 (50%), Gaps = 9/233 (3%)
Query: 121 RLKVVGRAGVGIDNVDLAAATEFGCLVVNAPTANTVAAAEHGIALLAAMARNVAQADASV 180
+ K++ G+D++D++ E L NA A +++ AEH ALL A A+N+ + + ++
Sbjct: 49 KTKMIQSLSAGVDHIDVSGIPENVVLCSNA-GAYSISVAEHAFALLLAWAKNICENNYNM 107
Query: 181 KAGKWQRNKYVGVSLVGKTLAVLGFGKVGSEVARRAKGLGMHVIAHDPYAPADRARAIGV 240
K G ++++ L K+L +LG+G +G VA AK GM++ A Y + I
Sbjct: 108 KNGNFKQSPTK--LLYNKSLGILGYGGIGRRVALLAKAFGMNIYA---YTRSYVNDGISS 162
Query: 241 DLVSFDEAIATADFISLHMPLTPATSKVLNDETFGKMKKGVRIINVARGGVIDEEALVRA 300
+ ++ + +DF+ + +PLT T ++N + +KG+ IINVAR V+D+ ++
Sbjct: 163 IYMEPEDIMKKSDFVLISLPLTDETRGMINSKMLSLFRKGLAIINVARADVVDKNDMLNF 222
Query: 301 LDSGRVAQAALDVFTEEPPPADSKLVQHERVTVTPHLGASTMEAQEGVAIEIA 353
L + DV+ EP ++ + V ++PH+ A+ +A
Sbjct: 223 LRNHNDKYYLSDVWWNEPIITETNP---DNVILSPHVAGGMSGEIMQPAVALA 272
>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 = 110 bits (277), Expect = 2e-26
Identities = 64/196 (32%), Positives = 93/196 (47%), Gaps = 28/196 (14%)
Query: 181 KAGKWQRNKYV--GVSLVGKTLAVLGFGKVGSEVARRAKGLGMHVIAH------DPYAPA 232
K W R + VGK + +LG+G +G + AR A+ LGM V A+ P +
Sbjct: 115 KEQTWGRRQEAYSVEDSVGKRVGILGYGSIGRQTARLAQALGMEVYAYTRSPRPTPESRK 174
Query: 233 DRARAI----------------GVDLVSFDEAIATA-DFISLHMPLTPATSKVLNDETFG 275
D + G D S E + D + + +PLTPAT +L E F
Sbjct: 175 DDGYIVPGTGDPDGSIPSAWFSGTDKASLHEFLRQDLDLLVVSLPLTPATKHLLGAEEF- 233
Query: 276 KM--KKGVRIINVARGGVIDEEALVRALDSGRVAQAALDVFTEEPPPADSKLVQHERVTV 333
++ K+ + N+ARG ++D +ALV AL+SG++ AALDV EP PAD L V +
Sbjct: 234 EILAKRKTFVSNIARGSLVDTDALVAALESGQIRGAALDVTDPEPLPADHPLWSAPNVII 293
Query: 334 TPHLGASTMEAQEGVA 349
TPH+ T E +
Sbjct: 294 TPHVSWQTQEYFDRAL 309
>gnl|CDD|240637 cd12160, 2-Hacid_dh_3, 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 = 103 bits (259), Expect = 2e-24
Identities = 61/190 (32%), Positives = 93/190 (48%), Gaps = 16/190 (8%)
Query: 159 AEHGIALLAAMARNVAQADASVKAGKWQ---------RNKYVGVSLVGKTLAVLGFGKVG 209
AEH +AL+ A R + + + + +W R +L+G + + GFG +G
Sbjct: 96 AEHTLALILAAVRRLDEMREAQREHRWAGELGGLQPLRPAGRLTTLLGARVLIWGFGSIG 155
Query: 210 SEVARRAKGLGMHVIAHDPYAPADRARAIGVDLVS---FDEAIATADFISLHMPLTPATS 266
+A LG V A + RA G +V+ E + D + + +P TP+T+
Sbjct: 156 QRLAPLLTALGARVT---GVARSAGERA-GFPVVAEDELPELLPETDVLVMILPATPSTA 211
Query: 267 KVLNDETFGKMKKGVRIINVARGGVIDEEALVRALDSGRVAQAALDVFTEEPPPADSKLV 326
L+ E + K ++NV RG +DE+ALV AL+SGR+ AALDV EP PA S L
Sbjct: 212 HALDAEVLAALPKHAWVVNVGRGATVDEDALVAALESGRLGGAALDVTATEPLPASSPLW 271
Query: 327 QHERVTVTPH 336
+ +TPH
Sbjct: 272 DAPNLILTPH 281
>gnl|CDD|185335 PRK15438, PRK15438, erythronate-4-phosphate dehydrogenase PdxB;
Provisional.
Length = 378
Score = 102 bits (256), Expect = 1e-23
Identities = 82/261 (31%), Positives = 122/261 (46%), Gaps = 31/261 (11%)
Query: 100 DALIVRSGTKVNRDVFESSAGRLKVVGRAGVGIDNVDLAAATEFGCLVVNAPTANTVAAA 159
DAL+VRS TKVN + +K VG A G D+VD A + G AP N +A
Sbjct: 39 DALMVRSVTKVNESLLAGKP--IKFVGTATAGTDHVDEAWLKQAGIGFSAAPGCNAIAVV 96
Query: 160 EHGIALLAAMARNVAQADASVKAGKWQRNKYVGVSLVGKTLAVLGFGKVGSEVARRAKGL 219
E+ + L +A +R+ G SL +T+ ++G G VG + R + L
Sbjct: 97 EYVFSSLLMLA---------------ERD---GFSLHDRTVGIVGVGNVGRRLQARLEAL 138
Query: 220 GMHVIAHDPYAPADRARAIGVDLVSFDEAIATADFISLHMPL---TPATSKVLNDETF-G 275
G+ + DP ADR D S DE + AD ++ H PL P + L DE
Sbjct: 139 GIKTLLCDP-PRADRGDE--GDFRSLDELVQEADILTFHTPLFKDGPYKTLHLADEKLIR 195
Query: 276 KMKKGVRIINVARGGVIDEEALVRALDSGRVAQAALDVFTEEPPPADSKLVQHERVTV-T 334
+K G +IN RG V+D AL+ L+ G+ LDV+ EP + + ++V + T
Sbjct: 196 SLKPGAILINACRGAVVDNTALLTCLNEGQKLSVVLDVWEGEP---ELNVELLKKVDIGT 252
Query: 335 PHLGASTMEAQEGVAIEIAEA 355
PH+ T+E + ++ EA
Sbjct: 253 PHIAGYTLEGKARGTTQVFEA 273
>gnl|CDD|153174 cd04902, ACT_3PGDH-xct, C-terminal ACT (regulatory) domain of
D-3-phosphoglycerate dehydrogenase (3PGDH). The
C-terminal ACT (regulatory) domain of
D-3-phosphoglycerate dehydrogenase (3PGDH), with an
extended C-terminal (xct) region from bacteria, archaea,
fungi, and plants. 3PGDH is an enzyme that belongs to
the D-isomer specific, 2-hydroxyacid dehydrogenase
family and catalyzes the oxidation of
D-3-phosphoglycerate to 3- phosphohydroxypyruvate, which
is the first step in the biosynthesis of L-serine, using
NAD+ as the oxidizing agent. In bacteria, 3PGDH is
feedback-controlled by the end product L-serine in an
allosteric manner. Some 3PGDH enzymes have an additional
domain formed by an extended C-terminal region. This
additional domain introduces significant asymmetry to
the homotetramer. Adjacent ACT (regulatory) domains
interact, creating two serine-binding sites, however,
this asymmetric arrangement results in the formation of
two different and distinct domain interfaces between
identical domains in the asymmetric unit. How this
asymmetry influences the mechanism of effector
inhibition is still unknown. Members of this CD belong
to the superfamily of ACT regulatory domains.
Length = 73
Score = 82.5 bits (205), Expect = 2e-19
Identities = 27/72 (37%), Positives = 43/72 (59%)
Query: 529 ILCRQVDQPGMIGTVGSILGSENVNVSFMSVGRVAPRKHAVMAIGVDEQPRKETLKKIGD 588
++ R D+PG+IG VG+ILG +N++ M VGR P A+M + VDE E L+++
Sbjct: 2 LVVRNTDRPGVIGKVGTILGEAGINIAGMQVGRDEPGGEALMVLSVDEPVPDEVLEELRA 61
Query: 589 VPAIEEFVFLKL 600
+P I ++L
Sbjct: 62 LPGILSAKVVEL 73
>gnl|CDD|185366 PRK15469, ghrA, bifunctional glyoxylate/hydroxypyruvate reductase
A; Provisional.
Length = 312
Score = 87.2 bits (216), Expect = 9e-19
Identities = 64/180 (35%), Positives = 96/180 (53%), Gaps = 18/180 (10%)
Query: 199 TLAVLGFGKVGSEVARRAKGLGMHVIAHDPYAPADRARAIGVDLVSF---DEAIA----T 251
T+ +LG G +GS+VA+ + G P R+R + SF +E A T
Sbjct: 138 TIGILGAGVLGSKVAQSLQTWGF------PLRCWSRSRKSWPGVQSFAGREELSAFLSQT 191
Query: 252 ADFISLHMPLTPATSKVLNDETFGKMKKGVRIINVARGGVIDEEALVRALDSGRVAQAAL 311
I+L +P TP T ++N + ++ G ++N+ARG + E+ L+ ALDSG+V A L
Sbjct: 192 RVLINL-LPNTPETVGIINQQLLEQLPDGAYLLNLARGVHVVEDDLLAALDSGKVKGAML 250
Query: 312 DVFTEEPPPADSKLVQHERVTVTPHLGASTMEAQEGVAIE-IAEAVVGALKGELAATAVN 370
DVF+ EP P +S L QH RV +TPH+ A T A+ A+E I+ + KGE V+
Sbjct: 251 DVFSREPLPPESPLWQHPRVAITPHVAAVTRPAE---AVEYISRTIAQLEKGERVCGQVD 307
>gnl|CDD|240631 cd12154, FDH_GDH_like, Formate/glycerate dehydrogenases, D-specific
2-hydroxy acid dehydrogenases and related
dehydrogenases. The formate/glycerate dehydrogenase
like family contains a diverse group of enzymes such as
formate dehydrogenase (FDH), glycerate dehydrogenase
(GDH), D-lactate dehydrogenase, L-alanine dehydrogenase,
and S-Adenosylhomocysteine hydrolase, that share a
common 2-domain structure. Despite often low sequence
identity, these proteins typically have a characteristic
arrangement of 2 similar domains of the alpha/beta
Rossmann fold NAD+ binding form. The NAD(P) binding
domain is inserted within the linear sequence of the
mostly N-terminal catalytic domain. Structurally, these
domains are connected by extended alpha helices and
create a cleft in which NAD(P) is bound, primarily to
the C-terminal portion of the 2nd (internal) domain.
While many members of this family are dimeric, alanine
DH is hexameric and phosphoglycerate DH is tetrameric.
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.
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 a hydride ion
to NAD+ without the stages of acid-base catalysis
typically found in related dehydrogenases.
Length = 310
Score = 83.8 bits (207), Expect = 1e-17
Identities = 56/243 (23%), Positives = 86/243 (35%), Gaps = 23/243 (9%)
Query: 91 ELCTKISLCDALIVRSGTKVNRDVFESSAGRLKVVGRAGVGIDNVDLA-AATEFGCLVVN 149
L + D ++ N + +++ +G D+ DL A G +
Sbjct: 57 TLAKALWSLDVVLKVKEPLTNAEYALIQKLGDRLLFTYTIGADHRDLTEALARAGLTAIA 116
Query: 150 APTA-------NTVAAAEHGIALLAAMARNVAQADASVKAGKWQRNKYVGVSLVGKTLAV 202
N++ A E + +A + GKT+ V
Sbjct: 117 VEGVELPLLTSNSIGAGELSVQFIARFLEVQQPGRLGGAPD-----------VAGKTVVV 165
Query: 203 LGFGKVGSEVARRAKGLGMHVIAHD--PYAPADRARAIGVDLVSFDEAIATADFISLHMP 260
+G G VG E A+ +GLG V+ D A G ++ +EA+A AD I
Sbjct: 166 VGAGVVGKEAAQMLRGLGAQVLITDINVEALEQLEELGGKNVEELEEALAEADVIVTTTL 225
Query: 261 LTPATSKVLNDET-FGKMKKGVRIINVARGGVIDEEALVR-ALDSGRVAQAALDVFTEEP 318
L + +L E +MK G I+NVA G V +AL L+ G DV P
Sbjct: 226 LPGKRAGILVPEELVEQMKPGSVIVNVAVGAVGCVQALHTQLLEEGHGVVHYGDVNMPGP 285
Query: 319 PPA 321
A
Sbjct: 286 GCA 288
>gnl|CDD|153151 cd04879, ACT_3PGDH-like, ACT_3PGDH-like CD includes the C-terminal
ACT (regulatory) domain of D-3-phosphoglycerate
dehydrogenase (3PGDH). ACT_3PGDH-like: The
ACT_3PGDH-like CD includes the C-terminal ACT
(regulatory) domain of D-3-phosphoglycerate
dehydrogenase (3PGDH), with or without an extended
C-terminal (xct) region found in various bacteria,
archaea, fungi, and plants. 3PGDH is an enzyme that
belongs to the D-isomer specific, 2-hydroxyacid
dehydrogenase family and catalyzes the oxidation of
D-3-phosphoglycerate to 3- phosphohydroxypyruvate, which
is the first step in the biosynthesis of L-serine, using
NAD+ as the oxidizing agent. In bacteria, 3PGDH is
feedback controlled by the end product L-serine in an
allosteric manner. In the Escherichia coli
homotetrameric enzyme, the interface at adjacent ACT
(regulatory) domains couples to create an extended
beta-sheet. Each regulatory interface forms two
serine-binding sites. The mechanism by which serine
transmits inhibition to the active site is postulated to
involve the tethering of the regulatory domains together
to create a rigid quaternary structure with a
solvent-exposed active site cleft. This CD also includes
the C-terminal ACT domain of the L-serine dehydratase
(LSD), iron-sulfur-dependent, beta subunit, found in
various bacterial anaerobes such as Clostridium,
Bacillus, and Treponema species. LSD enzymes catalyze
the deamination of L-serine, producing pyruvate and
ammonia. Unlike the eukaryotic L-serine dehydratase,
which requires the pyridoxal-5'-phosphate (PLP)
cofactor, the prokaryotic L-serine dehydratase contains
an [4Fe-4S] cluster instead of a PLP active site. The
LSD alpha and beta subunits of the 'clostridial' enzyme
are encoded by the sdhA and sdhB genes. The single
subunit bacterial homologs of L-serine dehydratase
(LSD1, LSD2, TdcG) present in E. coli, and other
Enterobacteriales, lack the ACT domain described here.
Members of this CD belong to the superfamily of ACT
regulatory domains.
Length = 71
Score = 71.7 bits (177), Expect = 1e-15
Identities = 24/70 (34%), Positives = 37/70 (52%)
Query: 529 ILCRQVDQPGMIGTVGSILGSENVNVSFMSVGRVAPRKHAVMAIGVDEQPRKETLKKIGD 588
+L D PG+IG VG+ILG +N++ M VGR A M + VD +E L+++
Sbjct: 2 LLIVHKDVPGVIGKVGTILGEHGINIAAMQVGRKEKGGIAYMVLDVDSPVPEEVLEELKA 61
Query: 589 VPAIEEFVFL 598
+P I +
Sbjct: 62 LPGIIRVRLI 71
>gnl|CDD|153175 cd04903, ACT_LSD, C-terminal ACT domain of the L-serine dehydratase
(LSD), iron-sulfur-dependent, beta subunit. The
C-terminal ACT domain of the L-serine dehydratase (LSD),
iron-sulfur-dependent, beta subunit, found in various
bacterial anaerobes such as Clostridium, Bacillis, and
Treponema species. These enzymes catalyze the
deamination of L-serine, producing pyruvate and ammonia.
Unlike the eukaryotic L-serine dehydratase, which
requires the pyridoxal-5'-phosphate (PLP) cofactor, the
prokaryotic L-serine dehydratase contains an [4Fe-4S]
cluster instead of a PLP active site. The LSD alpha and
beta subunits of the 'clostridial' enzyme are encoded by
the sdhA and sdhB genes. The single subunit bacterial
homologs of L-serine dehydratase (LSD1, LSD2, TdcG)
present in Escherichia coli, and other enterobacterials,
lack the ACT domain described here. Members of this CD
belong to the superfamily of ACT regulatory domains.
Length = 71
Score = 56.0 bits (136), Expect = 3e-10
Identities = 21/59 (35%), Positives = 33/59 (55%)
Query: 535 DQPGMIGTVGSILGSENVNVSFMSVGRVAPRKHAVMAIGVDEQPRKETLKKIGDVPAIE 593
D+PG I V S+L +N++FM V R A+M I VD+ +E +++I +P I
Sbjct: 8 DKPGAIAKVTSVLADHEINIAFMRVSRKEKGDQALMVIEVDQPIDEEVIEEIKKIPNIH 66
>gnl|CDD|198065 smart00997, AdoHcyase_NAD, S-adenosyl-L-homocysteine hydrolase, NAD
binding domain.
Length = 162
Score = 56.7 bits (138), Expect = 1e-09
Identities = 35/102 (34%), Positives = 47/102 (46%), Gaps = 17/102 (16%)
Query: 192 GVSLVGKTLAVLGFGKVGSEVARRAKGLGMHVIAHDPYAPADRARAI-----GVDLVSFD 246
V L GK + V G+G VG VA R +GLG VI + D RA+ G +++ +
Sbjct: 18 NVLLAGKNVVVAGYGDVGKGVAARLRGLGARVIVTE----IDPIRALEAAMDGFEVMKME 73
Query: 247 EAIATADFISLHMPLTPAT--SKVLNDETFGKMKKGVRIINV 286
EA AD +T AT V+ E F MK G + N
Sbjct: 74 EAAKRADIF-----VT-ATGNKDVITREHFRAMKDGAILANA 109
>gnl|CDD|223573 COG0499, SAM1, S-adenosylhomocysteine hydrolase [Coenzyme
metabolism].
Length = 420
Score = 51.5 bits (124), Expect = 7e-07
Identities = 33/96 (34%), Positives = 46/96 (47%), Gaps = 9/96 (9%)
Query: 193 VSLVGKTLAVLGFGKVGSEVARRAKGLGMHVIAH--DPYAPADRARAIGVDLVSFDEAIA 250
V L GK + V G+G VG +A R +G+G VI DP A A G +++ +EA
Sbjct: 205 VLLAGKNVVVAGYGWVGRGIAMRLRGMGARVIVTEVDP-IRALEAAMDGFRVMTMEEAAK 263
Query: 251 TAD-FISLHMPLTPATSKVLNDETFGKMKKGVRIIN 285
T D F++ V+ E F KMK G + N
Sbjct: 264 TGDIFVT-----ATGNKDVIRKEHFEKMKDGAILAN 294
>gnl|CDD|213572 TIGR00936, ahcY, adenosylhomocysteinase. This enzyme hydrolyzes
adenosylhomocysteine as part of a cycle for the
regeneration of the methyl donor S-adenosylmethionine.
Species that lack this enzyme are likely to have
adenosylhomocysteine nucleosidase (EC 3.2.2.9), an
enzyme which also acts as 5'-methyladenosine
nucleosidase (see TIGR01704) [Energy metabolism, Amino
acids and amines].
Length = 407
Score = 48.2 bits (115), Expect = 8e-06
Identities = 36/107 (33%), Positives = 51/107 (47%), Gaps = 10/107 (9%)
Query: 195 LVGKTLAVLGFGKVGSEVARRAKGLGMHVIAH--DPYAPADRARAIGVDLVSFDEAIATA 252
+ GKT+ V G+G G +A RA+G+G VI DP A A G +++ +EA
Sbjct: 194 IAGKTVVVAGYGWCGKGIAMRARGMGARVIVTEVDP-IRALEAAMDGFRVMTMEEAAKIG 252
Query: 253 D-FISLHMPLTPATSKVLNDETFGKMKKGVRIINVARGGV-IDEEAL 297
D FI+ V+ E F MK G + N+ V ID +AL
Sbjct: 253 DIFIT-----ATGNKDVIRGEHFENMKDGAIVANIGHFDVEIDVKAL 294
>gnl|CDD|240619 cd00401, SAHH, S-Adenosylhomocysteine Hydrolase, NAD-binding and
catalytic domains. S-adenosyl-L-homocysteine hydrolase
(SAHH, AdoHycase) catalyzes the hydrolysis of
S-adenosyl-L-homocysteine (AdoHyc) to form adenosine
(Ado) and homocysteine (Hcy). The equilibrium lies far
on the side of AdoHyc synthesis, but in nature the
removal of Ado and Hyc is sufficiently fast, so that the
net reaction is in the direction of hydrolysis. Since
AdoHyc is a potent inhibitor of S-adenosyl-L-methionine
dependent methyltransferases, AdoHycase plays a critical
role in the modulation of the activity of various
methyltransferases. The enzyme forms homotetramers, with
each monomer binding one molecule of NAD+.
Length = 402
Score = 47.5 bits (114), Expect = 1e-05
Identities = 34/94 (36%), Positives = 46/94 (48%), Gaps = 13/94 (13%)
Query: 193 VSLVGKTLAVLGFGKVGSEVARRAKGLGMHVIAH--DPYAPADRARAIGVDLVSFDEAIA 250
V + GK + V G+G VG A RA+GLG VI DP A +A G +++ +EA
Sbjct: 191 VLIAGKVVVVAGYGWVGKGCAMRARGLGARVIVTEVDPIC-ALQAAMDGFEVMPMEEAAK 249
Query: 251 TAD-FISLHMPLTPAT--SKVLNDETFGKMKKGV 281
D F++ AT V+ E F KMK G
Sbjct: 250 IGDIFVT-------ATGNKDVIRGEHFEKMKDGA 276
>gnl|CDD|235488 PRK05476, PRK05476, S-adenosyl-L-homocysteine hydrolase;
Provisional.
Length = 425
Score = 47.4 bits (114), Expect = 1e-05
Identities = 31/94 (32%), Positives = 44/94 (46%), Gaps = 13/94 (13%)
Query: 193 VSLVGKTLAVLGFGKVGSEVARRAKGLGMHVIAH--DPYAPADRARAIGVDLVSFDEAIA 250
V + GK + V G+G VG A+R +GLG VI DP A +A G +++ +EA
Sbjct: 208 VLIAGKVVVVAGYGDVGKGCAQRLRGLGARVIVTEVDPIC-ALQAAMDGFRVMTMEEAAE 266
Query: 251 TAD-FISLHMPLTPATS--KVLNDETFGKMKKGV 281
D F++ AT V+ E MK G
Sbjct: 267 LGDIFVT-------ATGNKDVITAEHMEAMKDGA 293
>gnl|CDD|181371 PRK08306, PRK08306, dipicolinate synthase subunit A; Reviewed.
Length = 296
Score = 43.7 bits (104), Expect = 2e-04
Identities = 32/104 (30%), Positives = 43/104 (41%), Gaps = 17/104 (16%)
Query: 197 GKTLAVLGFGKVGSEVARRAKGLGMH--VIAHDPYAPADRARA--IGVDLVSFD---EAI 249
G + VLGFG+ G +AR K LG + V A A AR +G+ E +
Sbjct: 152 GSNVLVLGFGRTGMTLARTLKALGANVTVGARK---SAHLARITEMGLSPFHLSELAEEV 208
Query: 250 ATADFISLHMPLTPATSKVLNDETFGKMKKGVRIINVAR--GGV 291
D I +P + VL E KM II++A GG
Sbjct: 209 GKIDIIFNTIP-----ALVLTKEVLSKMPPEALIIDLASKPGGT 247
>gnl|CDD|153139 cd02116, ACT, ACT domains are commonly involved in specifically
binding an amino acid or other small ligand leading to
regulation of the enzyme. Members of this CD belong to
the superfamily of ACT regulatory domains. Pairs of ACT
domains are commonly involved in specifically binding an
amino acid or other small ligand leading to regulation
of the enzyme. The ACT domain has been detected in a
number of diverse proteins; some of these proteins are
involved in amino acid and purine biosynthesis,
phenylalanine hydroxylation, regulation of bacterial
metabolism and transcription, and many remain to be
characterized. ACT domain-containing enzymes involved in
amino acid and purine synthesis are in many cases
allosteric enzymes with complex regulation enforced by
the binding of ligands. The ACT domain is commonly
involved in the binding of a small regulatory molecule,
such as the amino acids L-Ser and L-Phe in the case of
D-3-phosphoglycerate dehydrogenase and the bifunctional
chorismate mutase-prephenate dehydratase enzyme
(P-protein), respectively. Aspartokinases typically
consist of two C-terminal ACT domains in a tandem
repeat, but the second ACT domain is inserted within
the first, resulting in, what is normally the terminal
beta strand of ACT2, formed from a region N-terminal of
ACT1. ACT domain repeats have been shown to have
nonequivalent ligand-binding sites with complex
regulatory patterns such as those seen in the
bifunctional enzyme, aspartokinase-homoserine
dehydrogenase (ThrA). In other enzymes, such as
phenylalanine hydroxylases, the ACT domain appears to
function as a flexible small module providing allosteric
regulation via transmission of conformational changes,
these conformational changes are not necessarily
initiated by regulatory ligand binding at the ACT domain
itself. ACT domains are present either singularly, N- or
C-terminal, or in pairs present C-terminal or between
two catalytic domains. Unique to cyanobacteria are four
ACT domains C-terminal to an aspartokinase domain. A few
proteins are composed almost entirely of ACT domain
repeats as seen in the four ACT domain protein, the ACR
protein, found in higher plants; and the two ACT domain
protein, the glycine cleavage system transcriptional
repressor (GcvR) protein, found in some bacteria. Also
seen are single ACT domain proteins similar to the
Streptococcus pneumoniae ACT domain protein
(uncharacterized pdb structure 1ZPV) found in both
bacteria and archaea. Purportedly, the ACT domain is an
evolutionarily mobile ligand binding regulatory module
that has been fused to different enzymes at various
times.
Length = 60
Score = 37.7 bits (88), Expect = 7e-04
Identities = 13/51 (25%), Positives = 23/51 (45%)
Query: 535 DQPGMIGTVGSILGSENVNVSFMSVGRVAPRKHAVMAIGVDEQPRKETLKK 585
D+PG++ V S+L +N++ + A + I VD E L +
Sbjct: 7 DRPGLLAKVLSVLAEAGINITSIEQRTSGDGGEADIFIVVDGDGDLEKLLE 57
>gnl|CDD|240258 PTZ00075, PTZ00075, Adenosylhomocysteinase; Provisional.
Length = 476
Score = 40.8 bits (96), Expect = 0.002
Identities = 32/112 (28%), Positives = 51/112 (45%), Gaps = 12/112 (10%)
Query: 193 VSLVGKTLAVLGFGKVGSEVARRAKGLGMHVIAH--DPYAPADRARAIGVDLVSFDEAIA 250
V + GKT+ V G+G VG A+ +G G V+ DP A +A G +V+ ++ +
Sbjct: 250 VMIAGKTVVVCGYGDVGKGCAQALRGFGARVVVTEIDPIC-ALQAAMEGYQVVTLEDVVE 308
Query: 251 TAD-FISLHMPLTPATSKVLNDETFGKMKKGVRIINVARGGVIDEEALVRAL 301
TAD F++ ++ E +MK + N+ G D E V L
Sbjct: 309 TADIFVT-----ATGNKDIITLEHMRRMKNNAIVGNI---GHFDNEIQVAEL 352
>gnl|CDD|234094 TIGR03026, NDP-sugDHase, nucleotide sugar dehydrogenase. Enzymes
in this family catalyze the NAD-dependent
alcohol-to-acid oxidation of nucleotide-linked sugars.
Examples include UDP-glucose 6-dehydrogenase (1.1.1.22)
, GDP-mannose 6-dehydrogenase (1.1.1.132) ,
UDP-N-acetylglucosamine 6-dehydrogenase (1.1.1.136),
UDP-N-acetyl-D-galactosaminuronic acid dehydrogenase and
UDP-N-acetyl-D-mannosaminuronic acid dehydrogenase.
These enzymes are most often involved in the
biosynthesis of polysaccharides and are often found in
operons devoted to that purpose. All of these enzymes
contain three Pfam domains, pfam03721, pfam00984, and
pfam03720 for the N-terminal, central, and C-terminal
regions respectively.
Length = 409
Score = 40.7 bits (96), Expect = 0.002
Identities = 25/104 (24%), Positives = 46/104 (44%), Gaps = 15/104 (14%)
Query: 193 VSLVGKTLAVLGFG-KVGS---------EVARRAKGLGMHVIAHDPYAPADRARAIGVDL 242
+L GKT+ +LG K + ++ K G V A+DP P + + + +
Sbjct: 307 GALKGKTVLILGLAFKPNTDDVRESPALDIIELLKEKGAKVKAYDPLVPEEEVKGLP-SI 365
Query: 243 VSFDEAIATADFISLHMPLTP-ATSKVLNDETFGKMKKGVRIIN 285
+EA+ AD + + LT + K L+ E + KG +++
Sbjct: 366 DDLEEALKGADALVI---LTDHSEFKDLDLEKIKDLMKGKVVVD 406
>gnl|CDD|190133 pfam01842, ACT, ACT domain. This family of domains generally have
a regulatory role. ACT domains are linked to a wide
range of metabolic enzymes that are regulated by amino
acid concentration. Pairs of ACT domains bind
specifically to a particular amino acid leading to
regulation of the linked enzyme. The ACT domain is found
in: D-3-phosphoglycerate dehydrogenase EC:1.1.1.95,
which is inhibited by serine. Aspartokinase EC:2.7.2.4,
which is regulated by lysine. Acetolactate synthase
small regulatory subunit, which is inhibited by valine.
Phenylalanine-4-hydroxylase EC:1.14.16.1, which is
regulated by phenylalanine. Prephenate dehydrogenase
EC:4.2.1.51. formyltetrahydrofolate deformylase
EC:3.5.1.10, which is activated by methionine and
inhibited by glycine. GTP pyrophosphokinase EC:2.7.6.5.
Length = 66
Score = 36.2 bits (84), Expect = 0.003
Identities = 11/66 (16%), Positives = 28/66 (42%), Gaps = 1/66 (1%)
Query: 527 SIILCRQVDQPGMIGTVGSILGSENVNVSFMSVGRVAPRKH-AVMAIGVDEQPRKETLKK 585
+++ D+PG++ V L +N+ +S + + + VDE+ + L+
Sbjct: 1 TVLEVGVPDRPGLLAEVFGALADRGINIESISQSTSGDKAGIVFIVVVVDEEDLEAALEA 60
Query: 586 IGDVPA 591
+ +
Sbjct: 61 LKKLLG 66
>gnl|CDD|218507 pfam05221, AdoHcyase, S-adenosyl-L-homocysteine hydrolase.
Length = 430
Score = 39.7 bits (93), Expect = 0.004
Identities = 28/96 (29%), Positives = 40/96 (41%), Gaps = 7/96 (7%)
Query: 193 VSLVGKTLAVLGFGKVGSEVARRAKGLGMHVIAH--DPYAPADRARAIGVDLVSFDEAIA 250
V + GK V G+G VG A +G G VI DP A +A G +V+ +E +
Sbjct: 206 VMIAGKVAVVCGYGDVGKGCAASLRGQGARVIVTEIDPIC-ALQAAMEGYQVVTLEEVVK 264
Query: 251 TADFISLHMPLTPATSKVLNDETFGKMKKGVRIINV 286
AD T ++ F MKK + N+
Sbjct: 265 DADIFV----TTTGCVDIIVGRHFMNMKKDAIVCNI 296
>gnl|CDD|240647 cd12170, 2-Hacid_dh_9, 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 = 294
Score = 39.2 bits (92), Expect = 0.004
Identities = 36/157 (22%), Positives = 58/157 (36%), Gaps = 13/157 (8%)
Query: 193 VSLVGKTLAVLGFGKVGSEVARRAKGLGMHVIAHDPYAPADR---ARAIGVDLVSFDEAI 249
L G + ++G G G +A G V Y R A A G+ + +E +
Sbjct: 134 RELTGLKVGIIGLGTTGQMIADALSFFGADVY----YYSRTRKPDAEAKGIRYLPLNELL 189
Query: 250 ATADFISLHMPLTPATSKVLNDETFGKMKKGVRIINVARGGVIDEEALVRALDSGRVAQA 309
T D I + P +L +E F + G + N + G + EAL + L +
Sbjct: 190 KTVDVICTCL---PKNVILLGEEEFELLGDGKILFNTSLGPSFEVEALKKWLKASGYNIF 246
Query: 310 ALDVFTEEPPPADSKLVQHERVTVTPHLGASTMEAQE 346
D D +L+++ V T T +A E
Sbjct: 247 DCDTAGALG---DEELLRYPNVICTNKSAGWTRQAFE 280
>gnl|CDD|236034 PRK07502, PRK07502, cyclohexadienyl dehydrogenase; Validated.
Length = 307
Score = 39.2 bits (92), Expect = 0.005
Identities = 24/69 (34%), Positives = 36/69 (52%), Gaps = 6/69 (8%)
Query: 198 KTLAVLGFGKVGSEVAR--RAKGLGMHVIAHDPYAPA-DRARAIG-VDLVSFD--EAIAT 251
+A++G G +GS +AR R GL ++ D A RAR +G D V+ EA+
Sbjct: 7 DRVALIGIGLIGSSLARAIRRLGLAGEIVGADRSAETRARARELGLGDRVTTSAAEAVKG 66
Query: 252 ADFISLHMP 260
AD + L +P
Sbjct: 67 ADLVILCVP 75
>gnl|CDD|240621 cd01620, Ala_dh_like, Alanine dehydrogenase and related
dehydrogenases. Alanine dehydrogenase/Transhydrogenase,
such as the hexameric L-alanine dehydrogenase of
Phormidium lapideum, contain 2 Rossmann fold-like
domains linked by an alpha helical region. Related
proteins include Saccharopine Dehydrogenase (SDH),
bifunctional lysine ketoglutarate reductase
/saccharopine dehydrogenase enzyme,
N(5)-(carboxyethyl)ornithine synthase, and Rubrum
transdehydrogenase. Alanine dehydrogenase (L-AlaDH)
catalyzes the NAD-dependent conversion of pyrucate to
L-alanine via reductive amination. Transhydrogenases
found in bacterial and inner mitochondrial membranes
link NAD(P)(H)-dependent redox reactions to proton
translocation. The energy of the proton electrochemical
gradient (delta-p), generated by the respiratory
electron transport chain, is consumed by
transhydrogenase in NAD(P)+ reduction. Transhydrogenase
is likely involved in the regulation of the citric acid
cycle. Rubrum transhydrogenase has 3 components, dI,
dII, and dIII. dII spans the membrane while dI and dIII
protrude on the cytoplasmic/matirx side. DI contains 2
domains with Rossmann folds, linked by a long alpha
helix, and contains a NAD binding site. Two dI
polypeptides (represented in this sub-family)
spontaneously form a heterotrimer with one dIII in the
absence of dII. In the heterotrimer, both dI chains may
bind NAD, but only one is well-ordered. dIII also binds
a well-ordered NADP, but in a different orientation than
classical Rossmann domains.
Length = 317
Score = 38.9 bits (91), Expect = 0.006
Identities = 27/125 (21%), Positives = 53/125 (42%), Gaps = 15/125 (12%)
Query: 183 GKWQRNKYVGVSLVGK-TLAVLGFGKVGSEVARRAKGLGMHVIAHDPYAPADRARAIGVD 241
+ Q + G V + ++G G VG A+ AK LG +V+ +D ++ + +
Sbjct: 147 ARIQGGRMGGAGGVPPAKVLIIGAGVVGLGAAKIAKKLGANVLVYD--IKEEKLKGVETL 204
Query: 242 LVSFD---------EAIATAD-FISLHMPLTPATSKVLNDETFGKMKKGVRIINVA--RG 289
S + + D I+ + P ++ +E G MK+G I+++A +G
Sbjct: 205 GGSRLRYSQKEELEKELKQTDILINAILVDGPRAPILIMEELVGPMKRGAVIVDLAADQG 264
Query: 290 GVIDE 294
G +
Sbjct: 265 GNDET 269
>gnl|CDD|133415 cd04788, HTH_NolA-AlbR, Helix-Turn-Helix DNA binding domain of the
transcription regulators NolA and AlbR.
Helix-turn-helix (HTH) transcription regulators NolA and
AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp.
NC92, NolA is required for efficient nodulation of host
plants. In Xanthomonas albilineans, AlbR regulates the
expression of the pathotoxin, albicidin. These proteins
are putatively comprised of distinct domains that harbor
the regulatory (effector-binding) site and the active
(DNA-binding) site. Their conserved N-terminal domains
contain predicted winged HTH motifs that mediate DNA
binding, while the C-terminal domains are often
unrelated and bind specific coactivator molecules. They
share the N-terminal DNA binding domain with other
transcription regulators of the MerR superfamily that
promote transcription by reconfiguring the spacer
between the -35 and -10 promoter elements.
Length = 96
Score = 35.8 bits (83), Expect = 0.007
Identities = 13/39 (33%), Positives = 20/39 (51%)
Query: 454 KQRGLRLTEERILLDGSPESPLEFIQVQIANVESKFASA 492
++ G L E LDG PLE ++ Q+A +E + A
Sbjct: 54 RRLGFSLREIGRALDGPDFDPLELLRRQLARLEEQLELA 92
>gnl|CDD|133445 cd01076, NAD_bind_1_Glu_DH, NAD(P) binding domain of glutamate
dehydrogenase, subgroup 1. Amino acid dehydrogenase
(DH) is a widely distributed family of enzymes that
catalyzes the oxidative deamination of an amino acid to
its keto acid and ammonia with concomitant reduction of
NADP+. Glutamate DH is a multidomain enzyme that
catalyzes the reaction from glutamate to 2-oxyoglutarate
and ammonia in the presence of NAD or NADP. It is
present in all organisms. Enzymes involved in ammonia
assimilation are typically NADP+-dependent, while those
involved in glutamate catabolism are generally
NAD+-dependent. Amino acid DH-like NAD(P)-binding
domains are members of the Rossmann fold superfamily and
include glutamate, leucine, and phenylalanine DHs,
methylene tetrahydrofolate DH,
methylene-tetrahydromethanopterin DH,
methylene-tetrahydropholate DH/cyclohydrolase, Shikimate
DH-like proteins, malate oxidoreductases, and glutamyl
tRNA reductase. Amino acid DHs catalyze the deamination
of amino acids to keto acids with NAD(P)+ as a cofactor.
The NAD(P)-binding Rossmann fold superfamily includes a
wide variety of protein families including NAD(P)-
binding domains of alcohol DHs, tyrosine-dependent
oxidoreductases, glyceraldehyde-3-phosphate DH,
lactate/malate DHs, formate/glycerate DHs, siroheme
synthases, 6-phosphogluconate DH, amino acid DHs,
repressor rex, NAD-binding potassium channel domain,
CoA-binding, and ornithine cyclodeaminase-like domains.
These domains have an alpha -beta-alpha configuration.
NAD binding involves numerous hydrogen and van der Waals
contacts.
Length = 227
Score = 37.9 bits (89), Expect = 0.007
Identities = 16/37 (43%), Positives = 21/37 (56%)
Query: 189 KYVGVSLVGKTLAVLGFGKVGSEVARRAKGLGMHVIA 225
K +G+ L G +A+ GFG VGS AR G V+A
Sbjct: 23 KKLGIGLAGARVAIQGFGNVGSHAARFLHEAGAKVVA 59
>gnl|CDD|106361 PRK13403, PRK13403, ketol-acid reductoisomerase; Provisional.
Length = 335
Score = 38.6 bits (89), Expect = 0.008
Identities = 22/67 (32%), Positives = 38/67 (56%), Gaps = 1/67 (1%)
Query: 195 LVGKTLAVLGFGKVGSEVARRAKGLGMHVIAH-DPYAPADRARAIGVDLVSFDEAIATAD 253
L GKT+AV+G+G G A+ + G+ V+ P + A+A G +++S EA+ TA
Sbjct: 14 LQGKTVAVIGYGSQGHAQAQNLRDSGVEVVVGVRPGKSFEVAKADGFEVMSVSEAVRTAQ 73
Query: 254 FISLHMP 260
+ + +P
Sbjct: 74 VVQMLLP 80
>gnl|CDD|223992 COG1064, AdhP, Zn-dependent alcohol dehydrogenases [General
function prediction only].
Length = 339
Score = 38.0 bits (89), Expect = 0.011
Identities = 35/168 (20%), Positives = 58/168 (34%), Gaps = 34/168 (20%)
Query: 197 GKTLAVLGFGKVGSEVARRAKGLGMHVIAHD-PYAPADRARAIGVDLVSFDEAIATADFI 255
GK +AV+G G +G + AK +G VIA + A+ +G D V I ++D
Sbjct: 167 GKWVAVVGAGGLGHMAVQYAKAMGAEVIAITRSEEKLELAKKLGADHV-----INSSD-- 219
Query: 256 SLHMPLTPATSKVLNDETFGKMKKGVRIINVARGGVIDEEALVRALDS-GRVAQAALDVF 314
+ +K+ I G E ++AL G + L
Sbjct: 220 ---------------SDALEAVKEIADAIIDTVGP-ATLEPSLKALRRGGTLVLVGLPGG 263
Query: 315 TEEPPPADSKLVQHERVTVTPHLGASTMEAQE--------GVAIEIAE 354
P L+ E ++ L + + +E + EI E
Sbjct: 264 GPIPLLPAFLLILKEI-SIVGSLVGTRADLEEALDFAAEGKIKPEILE 310
>gnl|CDD|215789 pfam00208, ELFV_dehydrog, Glutamate/Leucine/Phenylalanine/Valine
dehydrogenase.
Length = 237
Score = 36.7 bits (86), Expect = 0.018
Identities = 18/32 (56%), Positives = 21/32 (65%)
Query: 194 SLVGKTLAVLGFGKVGSEVARRAKGLGMHVIA 225
SL GKT+AV GFG VGS A + LG V+A
Sbjct: 29 SLEGKTVAVQGFGNVGSYAAEKLLELGAKVVA 60
>gnl|CDD|235824 PRK06545, PRK06545, prephenate dehydrogenase; Validated.
Length = 359
Score = 37.2 bits (87), Expect = 0.020
Identities = 31/108 (28%), Positives = 57/108 (52%), Gaps = 11/108 (10%)
Query: 198 KTLAVLGFGKVGSEVAR--RAKGLGMHVIAHDPYAPADRARAIGVDLV-----SFDEAIA 250
+T+ ++G G +G +A +A G + +I +DP + A ARA+G ++ A A
Sbjct: 1 RTVLIVGLGLIGGSLALAIKAAGPDVFIIGYDP-SAAQLARALGFGVIDELAADLQRAAA 59
Query: 251 TADFISLHMPLTPATSKVLNDETFGKMKKGVRIINVA--RGGVIDEEA 296
AD I L +P+ AT+ +L + ++K GV + +V +G ++ E
Sbjct: 60 EADLIVLAVPV-DATAALLAELADLELKPGVIVTDVGSVKGAILAEAE 106
>gnl|CDD|214966 smart01002, AlaDh_PNT_C, Alanine dehydrogenase/PNT, C-terminal
domain. Alanine dehydrogenase catalyzes the
NAD-dependent reversible reductive amination of pyruvate
into alanine.
Length = 149
Score = 35.6 bits (83), Expect = 0.021
Identities = 33/104 (31%), Positives = 42/104 (40%), Gaps = 12/104 (11%)
Query: 201 AVLGFGKVGSEVARRAKGLGMHVIAHDPYAPADRA-----RAIGVDLVS----FDEAIAT 251
V+G G VG A AKGLG V D R A L S +EA+
Sbjct: 24 VVIGAGVVGLGAAATAKGLGAEVTVLDVRPARLRQLESLLGARFTTLYSQAELLEEAVKE 83
Query: 252 AD-FISLHMPLTPATSKVLNDETFGKMKKGVRIINVA--RGGVI 292
AD I + K++ E MK G I++VA +GG I
Sbjct: 84 ADLVIGAVLIPGAKAPKLVTREMVKSMKPGSVIVDVAADQGGCI 127
>gnl|CDD|222162 pfam13478, XdhC_C, XdhC Rossmann domain. This entry is the
rossmann domain found in the Xanthine dehydrogenase
accessory protein.
Length = 137
Score = 35.1 bits (82), Expect = 0.026
Identities = 26/105 (24%), Positives = 36/105 (34%), Gaps = 25/105 (23%)
Query: 200 LAVLGFGKVGSEVARRAKGLGMHVIAHDPYAPADRARAIGVDLVSFDEAIATADFISLHM 259
L + G G V +AR A LG V DP A V + FD+ + +
Sbjct: 1 LVIFGAGHVAQALARLAALLGFRVTVVDP-REERFPGADEVICLPFDDLLE-------AL 52
Query: 260 PLTPATSKVLNDETFGKMKKGVRIINVARGGVIDEEALVRALDSG 304
+ P T+ V+ +D EAL AL S
Sbjct: 53 AIDPRTAVVM-----------------THDHKLDLEALEAALRSP 80
>gnl|CDD|109716 pfam00670, AdoHcyase_NAD, S-adenosyl-L-homocysteine hydrolase, NAD
binding domain.
Length = 162
Score = 35.4 bits (82), Expect = 0.028
Identities = 30/97 (30%), Positives = 43/97 (44%), Gaps = 9/97 (9%)
Query: 193 VSLVGKTLAVLGFGKVGSEVARRAKGLGMHVIAH--DPYAPADRARAIGVDLVSFDEAIA 250
V + GK V G+G VG A KG G VI DP A +A G +V+ +E +
Sbjct: 19 VMIAGKVAVVCGYGDVGKGCAASLKGQGARVIVTEIDPIC-ALQAAMEGFQVVTLEEVVK 77
Query: 251 TAD-FISLHMPLTPATSKVLNDETFGKMKKGVRIINV 286
AD F++ T ++ E KMK + N+
Sbjct: 78 KADIFVT-----TTGNKDIITGEHMAKMKNDAIVCNI 109
>gnl|CDD|224995 COG2084, MmsB, 3-hydroxyisobutyrate dehydrogenase and related
beta-hydroxyacid dehydrogenases [Lipid metabolism].
Length = 286
Score = 36.4 bits (85), Expect = 0.030
Identities = 26/93 (27%), Positives = 38/93 (40%), Gaps = 5/93 (5%)
Query: 198 KTLAVLGFGKVGSEVARR--AKGLGMHVIAHDPYAPADRARAIGVDLV-SFDEAIATADF 254
+A +G G +GS +A G + V P A+ A G + S EA A AD
Sbjct: 1 MKIAFIGLGIMGSPMAANLLKAGHEVTVYNRTPEKAAELLAAAGATVAASPAEAAAEADV 60
Query: 255 ISLHMPLTPATSKVLNDET--FGKMKKGVRIIN 285
+ +P A VL E +K G +I+
Sbjct: 61 VITMLPDDAAVRAVLFGENGLLEGLKPGAIVID 93
>gnl|CDD|131900 TIGR02853, spore_dpaA, dipicolinic acid synthetase, A subunit.
This predicted Rossman fold-containing protein is the A
subunit of dipicolinic acid synthetase as found in most,
though not all, endospore-forming low-GC Gram-positive
bacteria; it is absent in Clostridium. The B subunit is
represented by TIGR02852. This protein is also known as
SpoVFA [Cellular processes, Sporulation and
germination].
Length = 287
Score = 36.2 bits (84), Expect = 0.032
Identities = 32/104 (30%), Positives = 44/104 (42%), Gaps = 17/104 (16%)
Query: 197 GKTLAVLGFGKVGSEVARRAKGLGMHVI--AHDPYAPADRARA-----IGVDLVSFDEAI 249
G + VLGFG+ G +AR LG V A AD AR I L +E +
Sbjct: 151 GSNVMVLGFGRTGMTIARTFSALGARVFVGARS---SADLARITEMGLIPFPLNKLEEKV 207
Query: 250 ATADFISLHMPLTPATSKVLNDETFGKMKKGVRIINVAR--GGV 291
A D + +P + VL + K+ K II++A GG
Sbjct: 208 AEIDIVINTIP-----ALVLTADVLSKLPKHAVIIDLASKPGGT 246
>gnl|CDD|176207 cd08245, CAD, Cinnamyl alcohol dehydrogenases (CAD) and related
proteins. Cinnamyl alcohol dehydrogenases (CAD),
members of the medium chain dehydrogenase/reductase
family, reduce cinnamaldehydes to cinnamyl alcohols in
the last step of monolignal metabolism in plant cells
walls. CAD binds 2 zinc ions and is NADPH- dependent.
CAD family members are also found in non-plant species,
e.g. in yeast where they have an aldehyde reductase
activity. The medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes, or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. 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.
Length = 330
Score = 36.5 bits (85), Expect = 0.033
Identities = 26/95 (27%), Positives = 41/95 (43%), Gaps = 5/95 (5%)
Query: 197 GKTLAVLGFGKVGSEVARRAKGLGMHVIA--HDPYAPADRARAIGVDLV--SFDEAIATA 252
G+ +AVLG G +G + A+ +G +A P + AR +G D V S E A
Sbjct: 163 GERVAVLGIGGLGHLAVQYARAMGFETVAITRSP-DKRELARKLGADEVVDSGAELDEQA 221
Query: 253 DFISLHMPLTPATSKVLNDETFGKMKKGVRIINVA 287
+ L S + G +++G RI+ V
Sbjct: 222 AAGGADVILVTVVSGAAAEAALGGLRRGGRIVLVG 256
>gnl|CDD|216396 pfam01262, AlaDh_PNT_C, Alanine dehydrogenase/PNT, C-terminal
domain. This family now also contains the lysine
2-oxoglutarate reductases.
Length = 150
Score = 34.8 bits (81), Expect = 0.037
Identities = 35/118 (29%), Positives = 49/118 (41%), Gaps = 19/118 (16%)
Query: 188 NKYVGVSLVG------KTLAVLGFGKVGSEVARRAKGLGMHVIAHDP------YAPADRA 235
G+ L G + V+G G VG A AKGLG V D + A
Sbjct: 5 GGGFGMLLGGAGGVPPAKVVVIGGGVVGLGAAATAKGLGAPVTILDVRPERLEQLDSLFA 64
Query: 236 RAIGVDLVS----FDEAIATADFI--SLHMPLTPATSKVLNDETFGKMKKGVRIINVA 287
+ D+ S EAIA AD + ++ +P A K++ E MK G I++VA
Sbjct: 65 EFVETDIFSNCEYLAEAIAEADLVIGTVLIPGARAP-KLVTREMVKTMKPGSVIVDVA 121
>gnl|CDD|223137 COG0059, IlvC, Ketol-acid reductoisomerase [Amino acid transport
and metabolism / Coenzyme metabolism].
Length = 338
Score = 36.0 bits (84), Expect = 0.044
Identities = 23/95 (24%), Positives = 41/95 (43%), Gaps = 17/95 (17%)
Query: 195 LVGKTLAVLGFGKVGSEVARRAKGLGMH------VIAHDPYAPA-DRARAIGVDLVSFDE 247
L GK +A++G+G G A+ L + +I + + +A+ G + + +E
Sbjct: 16 LKGKKVAIIGYGSQG-----HAQALNLRDSGLNVIIGLRKGSSSWKKAKEDGFKVYTVEE 70
Query: 248 AIATADFISLHMPLTP--ATSKVLNDETFGKMKKG 280
A AD + M L P +V E +K+G
Sbjct: 71 AAKRADVV---MILLPDEQQKEVYEKEIAPNLKEG 102
>gnl|CDD|217691 pfam03720, UDPG_MGDP_dh_C, UDP-glucose/GDP-mannose dehydrogenase
family, UDP binding domain. The UDP-glucose/GDP-mannose
dehydrogenaseses are a small group of enzymes which
possesses the ability to catalyze the NAD-dependent
2-fold oxidation of an alcohol to an acid without the
release of an aldehyde intermediate.
Length = 103
Score = 33.7 bits (78), Expect = 0.049
Identities = 13/47 (27%), Positives = 22/47 (46%), Gaps = 4/47 (8%)
Query: 211 EVARRAKGLGMHVIAHDPYAPADRARAIGVD----LVSFDEAIATAD 253
++ G V+ +DPY P + A+G D + +EA+ AD
Sbjct: 21 DIIEELLEEGAEVVVYDPYVPEEAIEALGEDGVTLVDDLEEALKGAD 67
>gnl|CDD|129802 TIGR00719, sda_beta, L-serine dehydratase, iron-sulfur-dependent,
beta subunit. This enzyme is also called serine
deaminase. This model describes the beta chain of an
iron-sulfur-dependent L-serine dehydratase, as in
Bacillus subtilis. A fairly deep split in a UPGMA tree
separates members of this family of beta chains from the
homologous region of single chain forms such as found in
E. coli. This family of enzymes is not homologous to the
pyridoxal phosphate-dependent threonine deaminases and
eukaryotic serine deaminases [Energy metabolism, Amino
acids and amines, Energy metabolism,
Glycolysis/gluconeogenesis].
Length = 208
Score = 35.3 bits (81), Expect = 0.051
Identities = 16/77 (20%), Positives = 34/77 (44%), Gaps = 1/77 (1%)
Query: 508 GVPHLTKVGSFEVDVSLEGSIILCRQVDQPGMIGTVGSILGSENVNVSFMSVGRVAPRKH 567
G +T++ F ++ E IL D+ G I V ++L +N+ + +
Sbjct: 130 GAIEITEINGFAIEFRGEHPAILLEHNDKFGTIAGVANLLAGFEINIEHLETAKKDIGNI 189
Query: 568 AVMAIGVDEQPRKETLK 584
A++ I +D + + +K
Sbjct: 190 ALLTIEID-KNIDDHIK 205
>gnl|CDD|223758 COG0686, Ald, Alanine dehydrogenase [Amino acid transport and
metabolism].
Length = 371
Score = 35.8 bits (83), Expect = 0.052
Identities = 41/159 (25%), Positives = 63/159 (39%), Gaps = 21/159 (13%)
Query: 155 TVAAAEHGIALLAAMARNVAQADASVKAGKWQRNK------YVGVSLV-GKTLAVLGFGK 207
TV + + LLA M+ + A A ++ GV V + VLG G
Sbjct: 119 TVQLPDGNLPLLAPMSEVAGRLAAQAGAYYLEKTNGGKGVLLGGVPGVLPAKVVVLGGGV 178
Query: 208 VGSEVARRAKGLGMHVIAHD---------PYAPADRARAIGVDLVSFDEAIATADFISLH 258
VG+ A+ A GLG V D R + + +EA+ AD + +
Sbjct: 179 VGTNAAKIAIGLGADVTILDLNIDRLRQLDDLFGGRVHTLYSTPSNIEEAVKKADLV-IG 237
Query: 259 MPLTP--ATSKVLNDETFGKMKKGVRIINVA--RGGVID 293
L P K++ E +MK G I++VA +GG +
Sbjct: 238 AVLIPGAKAPKLVTREMVKQMKPGSVIVDVAIDQGGCFE 276
>gnl|CDD|133444 cd01075, NAD_bind_Leu_Phe_Val_DH, NAD(P) binding domain of leucine
dehydrogenase, phenylalanine dehydrogenase, and valine
dehydrogenase. Amino acid dehydrogenase (DH) is a
widely distributed family of enzymes that catalyzes the
oxidative deamination of an amino acid to its keto acid
and ammonia with concomitant reduction of NADP+. For
example, leucine DH catalyzes the reversible oxidative
deamination of L-leucine and several other straight or
branched chain amino acids to the corresponding
2-oxoacid derivative. Amino acid DH -like NAD(P)-binding
domains are members of the Rossmann fold superfamily and
include glutamate, leucine, and phenylalanine DHs,
methylene tetrahydrofolate DH,
methylene-tetrahydromethanopterin DH,
methylene-tetrahydropholate DH/cyclohydrolase, Shikimate
DH-like proteins, malate oxidoreductases, and glutamyl
tRNA reductase. Amino acid DHs catalyze the deamination
of amino acids to keto acids with NAD(P)+ as a cofactor.
The NAD(P)-binding Rossmann fold superfamily includes a
wide variety of protein families including NAD(P)-
binding domains of alcohol DHs, tyrosine-dependent
oxidoreductases, glyceraldehyde-3-phosphate DH,
lactate/malate DHs, formate/glycerate DHs, siroheme
synthases, 6-phosphogluconate DH, amino acid DHs,
repressor rex, NAD-binding potassium channel domain,
CoA-binding, and ornithine cyclodeaminase-like domains.
These domains have an alpha-beta-alpha configuration.
NAD binding involves numerous hydrogen and van der Waals
contacts.
Length = 200
Score = 35.3 bits (82), Expect = 0.056
Identities = 32/95 (33%), Positives = 46/95 (48%), Gaps = 12/95 (12%)
Query: 194 SLVGKTLAVLGFGKVGSEVARRAKGLGMHVIAHD--PYAPADRARAIGVDLVSFDEAIAT 251
SL GKT+AV G GKVG ++A G +I D A A A G +V+ +E +
Sbjct: 25 SLEGKTVAVQGLGKVGYKLAEHLLEEGAKLIVADINEEAVARAAELFGATVVAPEEIYSV 84
Query: 252 -ADFISLHMPLTP-ATSKVLNDETFGKMKKGVRII 284
AD + P A V+ND+T ++K + I
Sbjct: 85 DADVFA------PCALGGVINDDTIPQLK--AKAI 111
>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 = 35.4 bits (82), Expect = 0.063
Identities = 38/162 (23%), Positives = 60/162 (37%), Gaps = 22/162 (13%)
Query: 191 VGVSLVGKTLAVLGFGKVGSEVARRAKGLGMHVIAHDPYAP-ADRARAIGVDLVSFDEAI 249
GV G T+ VLG G VG A+ AK G VI D + A+ +G D V D
Sbjct: 129 AGVLKPGDTVLVLGAGGVGLLAAQLAKAAGARVIVTDRSDEKLELAKELGADHV-IDY-- 185
Query: 250 ATADFISLHMPLTPATSKVLNDETFGKMKKGVRIINVARGGVIDEEALVRALDS-GRVAQ 308
+ L +E G ++ A GG +R L GR+
Sbjct: 186 ---------------KEEDLEEELRLTGGGGADVVIDAVGGPETLAQALRLLRPGGRIVV 230
Query: 309 AALDVFTEEPPPADSKLVQHERVTVTPHLGASTMEAQEGVAI 350
+ PP D + + + +T+ G + + +E + +
Sbjct: 231 VG--GTSGGPPLDDLRRLLFKELTIIGSTGGTREDFEEALDL 270
>gnl|CDD|116601 pfam07991, IlvN, Acetohydroxy acid isomeroreductase, catalytic
domain. Acetohydroxy acid isomeroreductase catalyzes
the conversion of acetohydroxy acids into dihydroxy
valerates. This reaction is the second in the synthetic
pathway of the essential branched side chain amino acids
valine and isoleucine.
Length = 165
Score = 34.4 bits (80), Expect = 0.064
Identities = 21/71 (29%), Positives = 35/71 (49%), Gaps = 5/71 (7%)
Query: 195 LVGKTLAVLGFGKVGSEVARRAKGLGMHVIA--HDPYAPADRARAIGVDLVSFDEAIATA 252
L GK +AV+G+G G A + G++VI ++A+ G ++ + EA+ A
Sbjct: 2 LKGKKIAVIGYGSQGHAHALNLRDSGVNVIVGLRPGSKSWEKAKKDGFEVYTVAEAVKKA 61
Query: 253 DFISLHMPLTP 263
D + M L P
Sbjct: 62 DVV---MILLP 69
>gnl|CDD|223411 COG0334, GdhA, Glutamate dehydrogenase/leucine dehydrogenase [Amino
acid transport and metabolism].
Length = 411
Score = 35.3 bits (82), Expect = 0.088
Identities = 16/37 (43%), Positives = 20/37 (54%)
Query: 189 KYVGVSLVGKTLAVLGFGKVGSEVARRAKGLGMHVIA 225
K +G L G +AV GFG VG A + LG V+A
Sbjct: 199 KALGDDLEGARVAVQGFGNVGQYAAEKLHELGAKVVA 235
>gnl|CDD|223364 COG0287, TyrA, Prephenate dehydrogenase [Amino acid transport and
metabolism].
Length = 279
Score = 35.0 bits (81), Expect = 0.091
Identities = 27/98 (27%), Positives = 47/98 (47%), Gaps = 11/98 (11%)
Query: 198 KTLAVLGFGKVGSEVAR--RAKGLGMHVIAHDPYAPADRARAIGVDLV------SFDEAI 249
+ ++G G +G +AR + GL + +I D A A A+ + ++ EA
Sbjct: 4 MKVGIVGLGLMGGSLARALKEAGLVVRIIGRDRSA-ATLKAALELGVIDELTVAGLAEAA 62
Query: 250 ATADFISLHMPLTPATSKVLNDETFGKMKKGVRIINVA 287
A AD + + +P+ AT +VL E +KKG + +V
Sbjct: 63 AEADLVIVAVPI-EATEEVL-KELAPHLKKGAIVTDVG 98
>gnl|CDD|214954 smart00984, UDPG_MGDP_dh_C, UDP binding domain. The
UDP-glucose/GDP-mannose dehydrogenases are a small group
of enzymes which possesses the ability to catalyse the
NAD-dependent 2-fold oxidation of an alcohol to an acid
without the release of an aldehyde intermediate.
Length = 99
Score = 32.9 bits (76), Expect = 0.094
Identities = 14/44 (31%), Positives = 22/44 (50%), Gaps = 2/44 (4%)
Query: 211 EVARRAKGLGMHVIAHDPYAPADRARAIGVDLV-SFDEAIATAD 253
++ G V+ +DPYA + AR G+ V +EA+ AD
Sbjct: 21 DIIEELLEAGAEVVVYDPYA-MEEAREYGLTYVSDLEEALKGAD 63
>gnl|CDD|129557 TIGR00465, ilvC, ketol-acid reductoisomerase. This is the second
enzyme in the parallel isoleucine-valine biosynthetic
pathway [Amino acid biosynthesis, Pyruvate family].
Length = 314
Score = 34.3 bits (79), Expect = 0.16
Identities = 28/90 (31%), Positives = 42/90 (46%), Gaps = 7/90 (7%)
Query: 195 LVGKTLAVLGFGKVGSEVARRAKGLGMHVIAHDPYAPADRARAI--GVDLVSFDEAIATA 252
L GKT+A++G+G G A + G++VI A +A G + + +EAI A
Sbjct: 1 LKGKTVAIIGYGSQGHAQALNLRDSGLNVIVGLRKGGASWKKATEDGFKVGTVEEAIPQA 60
Query: 253 DFISLHMPLTP--ATSKVLNDETFGKMKKG 280
D I M L P +V E +K+G
Sbjct: 61 DLI---MNLLPDEVQHEVYEAEIQPLLKEG 87
>gnl|CDD|133450 cd05211, NAD_bind_Glu_Leu_Phe_Val, NAD(P) binding domain of
glutamate dehydrogenase, leucine dehydrogenase,
phenylalanine dehydrogenase, and valine dehydrogenase.
Amino acid dehydrogenase (DH) is a widely distributed
family of enzymes that catalyzes the oxidative
deamination of an amino acid to its keto acid and
ammonia with concomitant reduction of NAD(P)+. This
subfamily includes glutamate, leucine, phenylalanine,
and valine DHs. Glutamate DH is a multi-domain enzyme
that catalyzes the reaction from glutamate to
2-oxyoglutarate and ammonia in the presence of NAD or
NADP. It is present in all organisms. Enzymes involved
in ammonia assimilation are typically NADP+-dependent,
while those involved in glutamate catabolism are
generally NAD+-dependent. As in other NAD+-dependent
DHs, monomers in this family have 2 domains separated by
a deep cleft. Here the c-terminal domain contains a
modified NAD-binding Rossmann fold with 7 rather than
the usual 6 beta strands and one strand anti-parrallel
to the others. Amino acid DH-like NAD(P)-binding domains
are members of the Rossmann fold superfamily and include
glutamate, leucine, and phenylalanine DHs, methylene
tetrahydrofolate DH, methylene-tetrahydromethanopterin
DH, methylene-tetrahydropholate DH/cyclohydrolase,
Shikimate DH-like proteins, malate oxidoreductases, and
glutamyl tRNA reductase. Amino acid DHs catalyze the
deamination of amino acids to keto acids with NAD(P)+ as
a cofactor. The NAD(P)-binding Rossmann fold superfamily
includes a wide variety of protein families including
NAD(P)- binding domains of alcohol DHs,
tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate DH, lactate/malate DHs,
formate/glycerate DHs, siroheme synthases,
6-phosphogluconate DH, amino acid DHs, repressor rex,
NAD-binding potassium channel domain, CoA-binding, and
ornithine cyclodeaminase-like domains. These domains
have an alpha-beta-alpha configuration. NAD binding
involves numerous hydrogen and van der Waals contacts.
Length = 217
Score = 33.7 bits (77), Expect = 0.16
Identities = 29/121 (23%), Positives = 48/121 (39%), Gaps = 16/121 (13%)
Query: 189 KYVGVSLVGKTLAVLGFGKVGSEVARRAKGLGMHVIA-HDPYAPADRARAIGVDLVSFDE 247
K++G SL G T+AV G G VG +A++ G V+A DP +L+++
Sbjct: 15 KHLGDSLEGLTVAVQGLGNVGWGLAKKLAEEGGKVLAVSDPDGYIYDPGITTEELINYAV 74
Query: 248 AIATADFISLHMPLTP--------------ATSKVLNDETFGKMKKGVRIINVARGGVID 293
A+ + + + A V++ E K+K V + A D
Sbjct: 75 ALGGSARVKVQDYFPGEAILGLDVDIFAPCALGNVIDLENAKKLKAKV-VAEGANNPTTD 133
Query: 294 E 294
E
Sbjct: 134 E 134
>gnl|CDD|129609 TIGR00518, alaDH, alanine dehydrogenase. The family of known
L-alanine dehydrogenases includes representatives from
the Proteobacteria, Firmicutes, and Cyanobacteria, all
with about 50 % identity or better. An outlier to this
group in both sequence and gap pattern is the homolog
from Helicobacter pylori, an epsilon division
Proteobacteria, which must be considered a putative
alanine dehydrogenase. Related proteins include
saccharopine dehydrogenase and the N-terminal half of
the NAD(P) transhydrogenase alpha subunit. All of these
related proteins bind NAD and/or NADP [Energy
metabolism, Amino acids and amines].
Length = 370
Score = 34.5 bits (79), Expect = 0.17
Identities = 42/167 (25%), Positives = 69/167 (41%), Gaps = 25/167 (14%)
Query: 155 TVAAAEHGIALLAAMARNVAQADASVKAGKWQRNKY-VGVSLVG------KTLAVLGFGK 207
TV A+ + LLA M+ + A V A ++ + GV L G + ++G G
Sbjct: 118 TVQTADGALPLLAPMSEVAGRLAAQVGAYHLEKTQGGRGVLLGGVPGVEPGDVTIIGGGV 177
Query: 208 VGSEVARRAKGLGMHVIAHDPYAPADRARAIG------VDL-----VSFDEAIATADFIS 256
VG+ A+ A GLG V D DR R + + ++A+ AD +
Sbjct: 178 VGTNAAKMANGLGATVTILD--INIDRLRQLDAEFGGRIHTRYSNAYEIEDAVKRADLLI 235
Query: 257 LHMPLTPATSKVL-NDETFGKMKKGVRIINVARGGVIDEEALVRALD 302
+ + A + L ++ +MK G I++VA ID+ V
Sbjct: 236 GAVLIPGAKAPKLVSNSLVAQMKPGAVIVDVA----IDQGGCVETSR 278
>gnl|CDD|236454 PRK09288, purT, phosphoribosylglycinamide formyltransferase 2;
Validated.
Length = 395
Score = 34.0 bits (79), Expect = 0.20
Identities = 20/42 (47%), Positives = 25/42 (59%), Gaps = 6/42 (14%)
Query: 203 LGFGKVGSEVARRAKGLGMHVIAHDPY--AP----ADRARAI 238
LG G++G EVA A+ LG+ VIA D Y AP A R+ I
Sbjct: 18 LGSGELGKEVAIEAQRLGVEVIAVDRYANAPAMQVAHRSHVI 59
>gnl|CDD|234950 PRK01390, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 460
Score = 34.0 bits (79), Expect = 0.21
Identities = 24/60 (40%), Positives = 26/60 (43%), Gaps = 8/60 (13%)
Query: 194 SLVGKTLAVLGFGKVGSEVARRAKGLGMHVIAHDPYAPADRARAIGVDLVSFDEAIATAD 253
GKT+AV G G G AR G VIA D PA RA+A I TAD
Sbjct: 6 GFAGKTVAVFGLGGSGLATARALVAGGAEVIAWDD-NPASRAKA-------AAAGITTAD 57
>gnl|CDD|133455 cd05313, NAD_bind_2_Glu_DH, NAD(P) binding domain of glutamate
dehydrogenase, subgroup 2. Amino acid dehydrogenase
(DH) is a widely distributed family of enzymes that
catalyzes the oxidative deamination of an amino acid to
its keto acid and ammonia with concomitant reduction of
NADP+. Glutamate DH is a multidomain enzyme that
catalyzes the reaction from glutamate to 2-oxyoglutarate
and ammonia in the presence of NAD or NADP. It is
present in all organisms. Enzymes involved in ammonia
asimilation are typically NADP+-dependent, while those
involved in glutamate catabolism are generally
NAD+-dependent. Amino acid DH-like NAD(P)-binding
domains are members of the Rossmann fold superfamily and
include glutamate, leucine, and phenylalanine DHs,
methylene tetrahydrofolate DH,
methylene-tetrahydromethanopterin DH,
methylene-tetrahydropholate DH/cyclohydrolase, Shikimate
DH-like proteins, malate oxidoreductases, and glutamyl
tRNA reductase. Amino acid DHs catalyze the deamination
of amino acids to keto acids with NAD(P)+ as a cofactor.
The NAD(P)-binding Rossmann fold superfamily includes a
wide variety of protein families including NAD(P)-
binding domains of alcohol DHs, tyrosine-dependent
oxidoreductases, glyceraldehyde-3-phosphate DH,
lactate/malate DHs, formate/glycerate DHs, siroheme
synthases, 6-phosphogluconate DH, amino acid DHs,
repressor rex, NAD-binding potassium channel domain,
CoA-binding, and ornithine cyclodeaminase-like domains.
These domains have an alpha -beta-alpha configuration.
NAD binding involves numerous hydrogen and van der Waals
contacts.
Length = 254
Score = 33.4 bits (77), Expect = 0.27
Identities = 12/37 (32%), Positives = 17/37 (45%)
Query: 189 KYVGVSLVGKTLAVLGFGKVGSEVARRAKGLGMHVIA 225
K +L GK +A+ G G V A + LG V+
Sbjct: 30 KDRNETLKGKRVAISGSGNVAQYAAEKLLELGAKVVT 66
>gnl|CDD|217311 pfam02995, DUF229, Protein of unknown function (DUF229). Members
of this family are uncharacterized. They are 500-1200
amino acids in length and share a long region
conservation that probably corresponds to several
domains. The Go annotation for the protein indicates
that it is involved in nematode larval development and
has a positive regulation on growth rate.
Length = 492
Score = 33.5 bits (77), Expect = 0.36
Identities = 19/112 (16%), Positives = 33/112 (29%), Gaps = 15/112 (13%)
Query: 478 IQVQIANVESKFASAISESG-----EIKVEGRVKDGVPHLTKVGSF---------EVDVS 523
N++++ A E + R +D H + F EV +
Sbjct: 23 FGTLRLNIDAELAKPRLNRLENLNCEYREIKRKRDSENHYSYSKLFPLRLLTQSVEVKIG 82
Query: 524 LEGSIILCRQVDQPGMIGTVGSILGSENVNVSFMSVGRVAPRKHAVMAIGVD 575
E I C + V + L S K +V+ +G+D
Sbjct: 83 AEFLITECWEDFGKIYQKDVFNFLHDRIPPKKLSSTPADV-DKPSVLILGID 133
>gnl|CDD|223936 COG1004, Ugd, Predicted UDP-glucose 6-dehydrogenase [Cell envelope
biogenesis, outer membrane].
Length = 414
Score = 32.9 bits (76), Expect = 0.44
Identities = 32/115 (27%), Positives = 48/115 (41%), Gaps = 23/115 (20%)
Query: 157 AAAEHGIA---LLAAMARNVAQADASVKAGKWQRNKYVGVSLVGKTLAVLGFG-KVGS-- 210
A E G L A + N + D + ++G L GKT+AVLG K +
Sbjct: 273 NAEELGYDPNLLEAVVEVNERRKDKLAEKIL----NHLG--LKGKTIAVLGLAFKPNTDD 326
Query: 211 -------EVARRAKGLGMHVIAHDPYAPADRARAIGVDLV---SFDEAIATADFI 255
++ +R + G VIA+DP A + A D+ +EA+ AD I
Sbjct: 327 MRESPALDIIKRLQEKGAEVIAYDPVA-MENAFRNFPDVELESDAEEALKGADAI 380
>gnl|CDD|184463 PRK14030, PRK14030, glutamate dehydrogenase; Provisional.
Length = 445
Score = 32.9 bits (75), Expect = 0.44
Identities = 14/33 (42%), Positives = 20/33 (60%)
Query: 192 GVSLVGKTLAVLGFGKVGSEVARRAKGLGMHVI 224
G+ + GKT+A+ GFG V A +A LG V+
Sbjct: 223 GIDIKGKTVAISGFGNVAWGAATKATELGAKVV 255
>gnl|CDD|166227 PLN02586, PLN02586, probable cinnamyl alcohol dehydrogenase.
Length = 360
Score = 32.9 bits (75), Expect = 0.47
Identities = 26/76 (34%), Positives = 36/76 (47%), Gaps = 9/76 (11%)
Query: 189 KYVGVSLVGKTLAVLGFGKVGSEVAR--RAKGLGMHVIAHDPYAPADRARAIGVD--LVS 244
KY G++ GK L V G G +G + +A GL + VI+ + +G D LVS
Sbjct: 176 KYYGMTEPGKHLGVAGLGGLGHVAVKIGKAFGLKVTVISSSSNKEDEAINRLGADSFLVS 235
Query: 245 FD-----EAIATADFI 255
D AI T D+I
Sbjct: 236 TDPEKMKAAIGTMDYI 251
>gnl|CDD|240630 cd05305, L-AlaDH, Alanine dehydrogenase NAD-binding and catalytic
domains. Alanine dehydrogenase (L-AlaDH) catalyzes the
NAD-dependent conversion of pyruvate to L-alanine via
reductive amination. Like formate dehydrogenase and
related enzymes, L-AlaDH is comprised of 2 domains
connected by a long alpha helical stretch, each
resembling a Rossmann fold NAD-binding domain. The
NAD-binding domain is inserted within the linear
sequence of the more divergent catalytic domain. Ligand
binding and active site residues are found in the cleft
between the subdomains. L-AlaDH is typically hexameric
and is critical in carbon and nitrogen metabolism in
micro-organisms.
Length = 359
Score = 32.4 bits (75), Expect = 0.57
Identities = 30/108 (27%), Positives = 48/108 (44%), Gaps = 22/108 (20%)
Query: 202 VLGFGKVGSEVARRAKGLGMHV--IAHDPYAPADRARAI------GVDLVSFD-----EA 248
+LG G VG AR A GLG V + + +R R + V + + EA
Sbjct: 173 ILGAGVVGENAARVALGLGAEVTVLDINL----ERLRYLDDIFGGRVTTLYSNPANLEEA 228
Query: 249 IATADFI--SLHMPLTPATSKVLNDETFGKMKKGVRIINVA--RGGVI 292
+ AD + ++ +P K++ +E MK G I++VA +GG
Sbjct: 229 LKEADLVIGAVLIPGA-KAPKLVTEEMVKTMKPGSVIVDVAIDQGGCF 275
>gnl|CDD|235707 PRK06130, PRK06130, 3-hydroxybutyryl-CoA dehydrogenase; Validated.
Length = 311
Score = 32.4 bits (74), Expect = 0.58
Identities = 14/42 (33%), Positives = 23/42 (54%), Gaps = 1/42 (2%)
Query: 198 KTLAVLGFGKVGSEVARRAKGLGMHVIAHDPYAPA-DRARAI 238
+ LA++G G +GS +A G+ V+ D A +RAR +
Sbjct: 5 QNLAIIGAGTMGSGIAALFARKGLQVVLIDVMEGALERARGV 46
>gnl|CDD|153173 cd04901, ACT_3PGDH, C-terminal ACT (regulatory) domain of
D-3-Phosphoglycerate Dehydrogenase (3PGDH) found in
fungi and bacteria. The C-terminal ACT (regulatory)
domain of D-3-Phosphoglycerate Dehydrogenase (3PGDH)
found in fungi and bacteria. 3PGDH is an enzyme that
belongs to the D-isomer specific, 2-hydroxyacid
dehydrogenase family and catalyzes the oxidation of
D-3-phosphoglycerate to 3- phosphohydroxypyruvate, which
is the first step in the biosynthesis of L-serine, using
NAD+ as the oxidizing agent. In Escherichia coli, the
SerA 3PGDH is feedback-controlled by the end product
L-serine in an allosteric manner. In the homotetrameric
enzyme, the interface at adjacent ACT (regulatory)
domains couples to create an extended beta-sheet. Each
regulatory interface forms two serine-binding sites. The
mechanism by which serine transmits inhibition to the
active site is postulated to involve the tethering of
the regulatory domains together to create a rigid
quaternary structure with a solvent-exposed active site
cleft. Members of this CD belong to the superfamily of
ACT regulatory domains.
Length = 69
Score = 29.8 bits (68), Expect = 0.65
Identities = 14/61 (22%), Positives = 31/61 (50%), Gaps = 8/61 (13%)
Query: 535 DQPGMIGTVGSILGSENVNVSFM---SVGRVAPRKHAVMAIGVDEQPRKETLKKIGDVPA 591
+ PG++G + +IL N+N++ + G + V+ I +D + +E L+ + +P
Sbjct: 8 NVPGVLGQINTILAEHNINIAAQYLQTRGEIG----YVV-IDIDSEVSEELLEALRAIPG 62
Query: 592 I 592
Sbjct: 63 T 63
>gnl|CDD|176201 cd08239, THR_DH_like, L-threonine dehydrogenase (TDH)-like.
MDR/AHD-like proteins, including a protein annotated as
a threonine dehydrogenase. L-threonine dehydrogenase
(TDH) catalyzes the zinc-dependent formation of
2-amino-3-ketobutyrate from L-threonine via
NAD(H)-dependent oxidation. The zinc-dependent alcohol
dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent
interconversion of alcohols to aldehydes or ketones.
Zinc-dependent ADHs are medium chain
dehydrogenase/reductase type proteins (MDRs) and have a
NAD(P)(H)-binding domain in a Rossmann fold of an
beta-alpha form. The N-terminal region typically has an
all-beta catalytic domain. In addition to alcohol
dehydrogenases, this group includes quinone reductase,
sorbitol dehydrogenase, formaldehyde dehydrogenase,
butanediol DH, ketose reductase, cinnamyl reductase, and
numerous others. These proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. 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.
Length = 339
Score = 32.3 bits (74), Expect = 0.69
Identities = 22/61 (36%), Positives = 30/61 (49%), Gaps = 3/61 (4%)
Query: 185 WQRNKYVGVSLVGKTLAVLGFGKVGSEVARRAKGLGMH-VIAHDPYAP-ADRARAIGVDL 242
+ + VGVS T+ V+G G VG A+ LG VI DP + A+A+G D
Sbjct: 153 YHALRRVGVSGRD-TVLVVGAGPVGLGALMLARALGAEDVIGVDPSPERLELAKALGADF 211
Query: 243 V 243
V
Sbjct: 212 V 212
>gnl|CDD|214963 smart00996, AdoHcyase, S-adenosyl-L-homocysteine hydrolase.
Length = 426
Score = 32.1 bits (74), Expect = 0.81
Identities = 22/65 (33%), Positives = 31/65 (47%), Gaps = 3/65 (4%)
Query: 193 VSLVGKTLAVLGFGKVGSEVARRAKGLGMHVIAH--DPYAPADRARAIGVDLVSFDEAIA 250
V + GK V G+G VG A+ +G G VI DP A +A G ++V+ +E
Sbjct: 203 VMIAGKVAVVCGYGDVGKGCAQSLRGQGARVIVTEIDPIC-ALQAAMDGFEVVTMEEVAP 261
Query: 251 TADFI 255
AD
Sbjct: 262 QADIF 266
>gnl|CDD|223106 COG0027, PurT, Formate-dependent phosphoribosylglycinamide
formyltransferase (GAR transformylase) [Nucleotide
transport and metabolism].
Length = 394
Score = 31.9 bits (73), Expect = 0.92
Identities = 18/37 (48%), Positives = 24/37 (64%), Gaps = 2/37 (5%)
Query: 198 KTLAVLGFGKVGSEVARRAKGLGMHVIAHDPY--APA 232
+ +LG G++G EVA A+ LG+ VIA D Y APA
Sbjct: 13 TKVMLLGSGELGKEVAIEAQRLGVEVIAVDRYANAPA 49
>gnl|CDD|130212 TIGR01142, purT, phosphoribosylglycinamide formyltransferase 2.
This enzyme is an alternative to PurN (TIGR00639)
[Purines, pyrimidines, nucleosides, and nucleotides,
Purine ribonucleotide biosynthesis].
Length = 380
Score = 31.6 bits (72), Expect = 1.1
Identities = 28/90 (31%), Positives = 44/90 (48%), Gaps = 5/90 (5%)
Query: 203 LGFGKVGSEVARRAKGLGMHVIAHDPY--APADRA--RAIGVDLVSFDEAIATADFISLH 258
LG G++G EVA A+ LG+ VIA D Y APA + R+ ++++ D A +
Sbjct: 5 LGSGELGKEVAIEAQRLGVEVIAVDRYANAPAMQVAHRSYVINMLDGDALRAVIEREKPD 64
Query: 259 MPLTPATSKVLNDETFGKMKKGVRIINVAR 288
+ P + D F K+G ++ AR
Sbjct: 65 Y-IVPEIEAIATDALFELEKEGYFVVPNAR 93
>gnl|CDD|237220 PRK12828, PRK12828, short chain dehydrogenase; Provisional.
Length = 239
Score = 31.3 bits (71), Expect = 1.3
Identities = 23/71 (32%), Positives = 27/71 (38%), Gaps = 11/71 (15%)
Query: 194 SLVGKTLAVLG-FGKVGSEVARRAKGLGMHVI----------AHDPYAPADRARAIGVDL 242
SL GK +A+ G FG +G A G V P PAD R G+DL
Sbjct: 4 SLQGKVVAITGGFGGLGRATAAWLAARGARVALIGRGAAPLSQTLPGVPADALRIGGIDL 63
Query: 243 VSFDEAIATAD 253
V A D
Sbjct: 64 VDPQAARRAVD 74
>gnl|CDD|184433 PRK13978, PRK13978, ribose-5-phosphate isomerase A; Provisional.
Length = 228
Score = 30.9 bits (70), Expect = 1.6
Identities = 13/39 (33%), Positives = 19/39 (48%)
Query: 490 ASAISESGEIKVEGRVKDGVPHLTKVGSFEVDVSLEGSI 528
I +IKVE RV + V +T G++ +D L I
Sbjct: 149 LRKIESYADIKVERRVNEDVAFITDNGNYILDCKLPKGI 187
>gnl|CDD|224674 COG1760, SdaA, L-serine deaminase [Amino acid transport and
metabolism].
Length = 262
Score = 30.7 bits (70), Expect = 1.9
Identities = 17/82 (20%), Positives = 31/82 (37%), Gaps = 3/82 (3%)
Query: 512 LTKVGSFEVDVSLEGSIILCRQVDQPGMI-GTVGSILGSENVNVSFMSVGRVAPRKHAVM 570
LT++ + S I G+ V ++ +N + M R A M
Sbjct: 167 LTELNGGSPEQSGNAPEIAM--EHNLGLTCDPVAGLVQVPCINRNAMGAVRAINGAKAAM 224
Query: 571 AIGVDEQPRKETLKKIGDVPAI 592
AI VD++P E ++ + +
Sbjct: 225 AIEVDQRPLDEVIETMYETGKD 246
>gnl|CDD|235491 PRK05479, PRK05479, ketol-acid reductoisomerase; Provisional.
Length = 330
Score = 30.4 bits (70), Expect = 2.4
Identities = 24/88 (27%), Positives = 42/88 (47%), Gaps = 7/88 (7%)
Query: 197 GKTLAVLGFGKVGSEVARRAKGLGMHVIA--HDPYAPADRARAIGVDLVSFDEAIATADF 254
GK +A++G+G G A + G+ V+ + +A A G ++++ EA AD
Sbjct: 17 GKKVAIIGYGSQGHAHALNLRDSGVDVVVGLREGSKSWKKAEADGFEVLTVAEAAKWADV 76
Query: 255 ISLHMPLTP--ATSKVLNDETFGKMKKG 280
I M L P ++V +E +K+G
Sbjct: 77 I---MILLPDEVQAEVYEEEIEPNLKEG 101
>gnl|CDD|224996 COG2085, COG2085, Predicted dinucleotide-binding enzymes [General
function prediction only].
Length = 211
Score = 30.0 bits (68), Expect = 2.5
Identities = 25/86 (29%), Positives = 35/86 (40%), Gaps = 7/86 (8%)
Query: 198 KTLAVLGFGKVGSEVARRAKGLGMHVI-----AHDPYAPADRARAIGVDLVSFDEAIATA 252
+A++G G +GS +A R G VI A A A + S ++A A A
Sbjct: 2 MIIAIIGTGNIGSALALRLAKAGHEVIIGSSRGPKALAAAAAALGPLITGGSNEDAAALA 61
Query: 253 DFISLHMPLT--PATSKVLNDETFGK 276
D + L +P P L D GK
Sbjct: 62 DVVVLAVPFEAIPDVLAELRDALGGK 87
>gnl|CDD|184511 PRK14106, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 450
Score = 30.7 bits (70), Expect = 2.5
Identities = 15/44 (34%), Positives = 20/44 (45%)
Query: 195 LVGKTLAVLGFGKVGSEVARRAKGLGMHVIAHDPYAPADRARAI 238
L GK + V+G G G +A+ K LG VI D A+
Sbjct: 3 LKGKKVLVVGAGVSGLALAKFLKKLGAKVILTDEKEEDQLKEAL 46
>gnl|CDD|153181 cd04909, ACT_PDH-BS, C-terminal ACT domain of the monofunctional,
NAD dependent, prephenate dehydrogenase (PDH). The
C-terminal ACT domain of the monofunctional, NAD
dependent, prephenate dehydrogenase (PDH) enzyme that
catalyzes the formation of 4-hydroxyphenylpyruvate from
prephenate, found in Bacillus subtilis (BS) and other
Firmicutes, Deinococci, and Bacteroidetes. PDH is the
first enzyme in the aromatic amino acid pathway specific
for the biosynthesis of tyrosine. This enzyme is
feedback-inhibited by tyrosine in B. subtilis and other
microorganisms. Both phenylalanine and tryptophan have
been shown to be inhibitors of this activity in B.
subtilis. Bifunctional chorismate mutase-PDH (TyrA)
enzymes such as those seen in Escherichia coli do not
contain an ACT domain. Members of this CD belong to the
superfamily of ACT regulatory domains.
Length = 69
Score = 28.0 bits (63), Expect = 2.5
Identities = 8/20 (40%), Positives = 13/20 (65%)
Query: 535 DQPGMIGTVGSILGSENVNV 554
D+PG+I V ILG +++
Sbjct: 10 DEPGVIAEVTQILGDAGISI 29
>gnl|CDD|178111 PLN02494, PLN02494, adenosylhomocysteinase.
Length = 477
Score = 30.6 bits (69), Expect = 2.8
Identities = 25/97 (25%), Positives = 43/97 (44%), Gaps = 9/97 (9%)
Query: 193 VSLVGKTLAVLGFGKVGSEVARRAKGLGMHVIAH--DPYAPADRARAIGVDLVSFDEAIA 250
V + GK + G+G VG A K G VI DP A +A G +++ ++ ++
Sbjct: 250 VMIAGKVAVICGYGDVGKGCAAAMKAAGARVIVTEIDPIC-ALQALMEGYQVLTLEDVVS 308
Query: 251 TAD-FISLHMPLTPATSKVLNDETFGKMKKGVRIINV 286
AD F++ T ++ + KMK + N+
Sbjct: 309 EADIFVT-----TTGNKDIIMVDHMRKMKNNAIVCNI 340
>gnl|CDD|168796 PRK07066, PRK07066, 3-hydroxybutyryl-CoA dehydrogenase; Validated.
Length = 321
Score = 30.2 bits (68), Expect = 3.0
Identities = 16/38 (42%), Positives = 21/38 (55%)
Query: 198 KTLAVLGFGKVGSEVARRAKGLGMHVIAHDPYAPADRA 235
KT A +G G +GS RA G+ V+A DP A+ A
Sbjct: 8 KTFAAIGSGVIGSGWVARALAHGLDVVAWDPAPGAEAA 45
>gnl|CDD|153161 cd04889, ACT_PDH-BS-like, C-terminal ACT domain of the
monofunctional, NAD dependent, prephenate dehydrogenase
(PDH) enzyme that catalyzes the formation of
4-hydroxyphenylpyruvate from prephenate. Included in
this CD is the C-terminal ACT domain of the
monofunctional, NAD dependent, prephenate dehydrogenase
(PDH) enzyme that catalyzes the formation of
4-hydroxyphenylpyruvate from prephenate, found in
Bacillus subtilis (BS) and other Firmicutes, Deinococci,
and Bacteroidetes. PDH is the first enzyme in the
aromatic amino acid pathway specific for the
biosynthesis of tyrosine. This enzyme is feedback
inhibited by tyrosine in B. subtilis and other
microorganisms. Both phenylalanine and tryptophan have
been shown to be inhibitors of this activity in B.
subtilis. Bifunctional chorismate mutase-PDH (TyrA)
enzymes such as those seen in Escherichia coli do not
contain an ACT domain. Also included in this CD is the
N-terminal ACT domain of a novel protein composed almost
entirely of two tandem ACT domains as seen in the
uncharacterized structure (pdb 2F06) of the Bt0572
protein from Bacteroides thetaiotaomicron and related
ACT domains. Members of this CD belong to the
superfamily of ACT regulatory domains.
Length = 56
Score = 27.1 bits (61), Expect = 4.2
Identities = 7/25 (28%), Positives = 14/25 (56%)
Query: 535 DQPGMIGTVGSILGSENVNVSFMSV 559
++PG + V IL +N+ +S+
Sbjct: 7 NKPGRLAEVTEILAEAGINIKAISI 31
>gnl|CDD|202773 pfam03807, F420_oxidored, NADP oxidoreductase coenzyme
F420-dependent.
Length = 93
Score = 27.9 bits (63), Expect = 4.7
Identities = 17/67 (25%), Positives = 30/67 (44%), Gaps = 5/67 (7%)
Query: 199 TLAVLGFGKVGSEVARRAKGLGMHVI---AHDPYAPADRARAIGVDLVSFD--EAIATAD 253
+ ++G G +G +AR G V+ + +P A A +GV + EA+ AD
Sbjct: 1 KIGIIGAGNMGEALARGLAAAGHEVVIANSRNPEKAAALAEELGVKATAVSNEEAVEEAD 60
Query: 254 FISLHMP 260
+ L +
Sbjct: 61 VVFLAVK 67
>gnl|CDD|176230 cd08269, Zn_ADH9, Alcohol dehydrogenases of the MDR family. The
medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P)-binding Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability.
Length = 312
Score = 29.2 bits (66), Expect = 5.4
Identities = 21/59 (35%), Positives = 29/59 (49%), Gaps = 2/59 (3%)
Query: 197 GKTLAVLGFGKVGSEVARRAKGLGMH-VIAHDPY-APADRARAIGVDLVSFDEAIATAD 253
GKT+AV+G G +G + A G VIA D A AR +G V D++ A +
Sbjct: 130 GKTVAVIGAGFIGLLFLQLAAAAGARRVIAIDRRPARLALARELGATEVVTDDSEAIVE 188
>gnl|CDD|235446 PRK05406, PRK05406, LamB/YcsF family protein; Provisional.
Length = 246
Score = 29.3 bits (67), Expect = 5.6
Identities = 24/75 (32%), Positives = 35/75 (46%), Gaps = 16/75 (21%)
Query: 161 HGIALLAAMARNVAQADASVKAGKWQRNKYVGVSLVGKTLAVLGFGKVGSEVARRAKGLG 220
HG AL A++ A ADA +A V+ V +L ++G GSE+ R A+ G
Sbjct: 112 HG-ALYNMAAKDPALADAVAEA----------VAAVDPSLILVGLA--GSELIRAAEEAG 158
Query: 221 MHVIAHDPYAPADRA 235
+ + ADRA
Sbjct: 159 LRTASE---VFADRA 170
>gnl|CDD|216949 pfam02254, TrkA_N, TrkA-N domain. This domain is found in a wide
variety of proteins. These protein include potassium
channels, phosphoesterases, and various other
transporters. This domain binds to NAD.
Length = 116
Score = 27.9 bits (63), Expect = 5.7
Identities = 13/45 (28%), Positives = 22/45 (48%), Gaps = 3/45 (6%)
Query: 201 AVLGFGKVGSEVARRAKGLGMHVIA--HDPYAPADRARAIGVDLV 243
++G+G+VG +A + G V+ DP + R GV +V
Sbjct: 2 IIIGYGRVGRSLAEELREGGPDVVVIDKDP-ERVEELREEGVPVV 45
>gnl|CDD|176222 cd08261, Zn_ADH7, Alcohol dehydrogenases of the MDR family. This
group contains members identified as related to
zinc-dependent alcohol dehydrogenase and other members
of the MDR family. The medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, which contains the
zinc-dependent alcohol dehydrogenase (ADH-Zn) and
related proteins, is a diverse group of proteins related
to the first identified member, class I mammalian ADH.
MDRs display a broad range of activities and are
distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P)-binding Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group includes
various activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has a
catalytic role, while structural zinc aids in stability.
ADH-like proteins typically form dimers (typically
higher plants, mammals) or tetramers (yeast, bacteria),
and generally have 2 tightly bound zinc atoms per
subunit. 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.
Length = 337
Score = 29.1 bits (66), Expect = 6.1
Identities = 17/48 (35%), Positives = 23/48 (47%), Gaps = 1/48 (2%)
Query: 197 GKTLAVLGFGKVGSEVARRAKGLGMHVIAHDPYAP-ADRARAIGVDLV 243
G T+ V+G G +G V + AK G VI D + AR +G D
Sbjct: 160 GDTVLVVGAGPIGLGVIQVAKARGARVIVVDIDDERLEFARELGADDT 207
>gnl|CDD|215300 PLN02545, PLN02545, 3-hydroxybutyryl-CoA dehydrogenase.
Length = 295
Score = 28.9 bits (65), Expect = 7.0
Identities = 14/41 (34%), Positives = 20/41 (48%), Gaps = 1/41 (2%)
Query: 198 KTLAVLGFGKVGSEVARRAKGLGMHVIAHDPYAPA-DRARA 237
K + V+G G++GS +A+ A GM V D A R
Sbjct: 5 KKVGVVGAGQMGSGIAQLAAAAGMDVWLLDSDPAALSRGLD 45
>gnl|CDD|236582 PRK09599, PRK09599, 6-phosphogluconate dehydrogenase-like protein;
Reviewed.
Length = 301
Score = 28.9 bits (66), Expect = 7.3
Identities = 11/42 (26%), Positives = 19/42 (45%), Gaps = 1/42 (2%)
Query: 200 LAVLGFGKVGSEVARRAKGLGMHVIAHDPY-APADRARAIGV 240
L ++G G++G +ARR G V+ +D + G
Sbjct: 3 LGMIGLGRMGGNMARRLLRGGHEVVGYDRNPEAVEALAEEGA 44
>gnl|CDD|235986 PRK07313, PRK07313, phosphopantothenoylcysteine decarboxylase;
Validated.
Length = 182
Score = 28.4 bits (64), Expect = 8.0
Identities = 26/112 (23%), Positives = 46/112 (41%), Gaps = 24/112 (21%)
Query: 54 GISSKPTVLIAEKLGQAGLDLLNEFANVDCAYNLSPEELCTKISLCDALIVRSGTKVNRD 113
I++ + +L + G V + + T ++L L S V+ D
Sbjct: 11 SIAAYKAADLTSQLTKRG-------YQVTVLMTKAATKFITPLTL-QVL---SKNPVHLD 59
Query: 114 VFESSAGRLKVVGRAGVGIDNVDLAAATEFGCLVVNAP-TANTVAAAEHGIA 164
V + +L +++++LA + L + AP TANT+A HGIA
Sbjct: 60 VMDEHDPKL---------MNHIELAKRAD---LFLVAPATANTIAKLAHGIA 99
>gnl|CDD|222146 pfam13460, NAD_binding_10, NADH(P)-binding.
Length = 182
Score = 28.4 bits (64), Expect = 8.1
Identities = 18/61 (29%), Positives = 25/61 (40%), Gaps = 7/61 (11%)
Query: 200 LAVLG-FGKVGSEVARRAKGLGMHVIA---HDPYAPADRARAIGVD---LVSFDEAIATA 252
+AV+G GK G + + G V A + APA + D L EA+A
Sbjct: 1 IAVIGATGKTGRRLVKELLARGHQVTALSRNPSKAPAPGVTPVQKDLFDLADLAEALAGV 60
Query: 253 D 253
D
Sbjct: 61 D 61
>gnl|CDD|223954 COG1023, Gnd, Predicted 6-phosphogluconate dehydrogenase
[Carbohydrate transport and metabolism].
Length = 300
Score = 28.9 bits (65), Expect = 8.3
Identities = 20/93 (21%), Positives = 38/93 (40%), Gaps = 6/93 (6%)
Query: 198 KTLAVLGFGKVGSEVARRAKGLGMHVIAHD--PYAPADRARAIGVDLVSFDEAIA---TA 252
+ ++G G++G+ + RR G V+ +D A + S DE +A
Sbjct: 1 MQIGMIGLGRMGANLVRRLLDGGHDVVGYDVNQTAVEELKDEGATGAASLDELVAKLSAP 60
Query: 253 DFISLHMPLTPATSKVLNDETFGKMKKGVRIIN 285
+ L +P T V+ D+ + G +I+
Sbjct: 61 RIVWLMVPAGDITDAVI-DDLAPLLSAGDIVID 92
>gnl|CDD|223643 COG0569, TrkA, K+ transport systems, NAD-binding component
[Inorganic ion transport and metabolism].
Length = 225
Score = 28.4 bits (64), Expect = 8.8
Identities = 9/28 (32%), Positives = 15/28 (53%)
Query: 198 KTLAVLGFGKVGSEVARRAKGLGMHVIA 225
+ ++G G+VG VAR G +V+
Sbjct: 1 MKIIIIGAGRVGRSVARELSEEGHNVVL 28
>gnl|CDD|223842 COG0771, MurD, UDP-N-acetylmuramoylalanine-D-glutamate ligase [Cell
envelope biogenesis, outer membrane].
Length = 448
Score = 28.8 bits (65), Expect = 9.1
Identities = 14/35 (40%), Positives = 15/35 (42%)
Query: 193 VSLVGKTLAVLGFGKVGSEVARRAKGLGMHVIAHD 227
GK + VLG GK G AR LG V D
Sbjct: 3 EDFQGKKVLVLGLGKSGLAAARFLLKLGAEVTVSD 37
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 0.132 0.363
Gapped
Lambda K H
0.267 0.0831 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 30,488,177
Number of extensions: 3139088
Number of successful extensions: 3860
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3666
Number of HSP's successfully gapped: 201
Length of query: 600
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 498
Effective length of database: 6,413,494
Effective search space: 3193920012
Effective search space used: 3193920012
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: 62 (27.5 bits)