RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 046427
(595 letters)
>gnl|CDD|237436 PRK13581, PRK13581, D-3-phosphoglycerate dehydrogenase;
Provisional.
Length = 526
Score = 628 bits (1622), Expect = 0.0
Identities = 263/546 (48%), Positives = 346/546 (63%), Gaps = 24/546 (4%)
Query: 54 PTVLVAEKLGEAGLDVLKNFA--NVDCSYNLSPEELCTKISLCDALIVRSGTKVTREVFE 111
VLV++ + AGL++LK+ VD L EEL I DALIVRS TKVT EV E
Sbjct: 1 MKVLVSDPISPAGLEILKDAPGVEVDVKTGLDKEELLEIIGDYDALIVRSATKVTAEVLE 60
Query: 112 SSAGRLKVVGRAGVGIDNVDLSAATEHGCLVVNAPTANTIAAAEHGIALLTAMARNIAQA 171
+ A LKV+GRAGVG+DNVD+ AAT G +VVNAPT NTI+AAEH IAL+ A+ARNI QA
Sbjct: 61 A-AKNLKVIGRAGVGVDNVDVPAATRRGIIVVNAPTGNTISAAEHTIALMLALARNIPQA 119
Query: 172 DASVKAGKWQRNKYVGVSLVGKTLAVMGFGKVGTEVARRAKGLGMNVIAHDPYAQADRAR 231
AS+KAGKW+R K++GV L GKTL ++G G++G+EVA+RAK GM VIA+DPY +RA
Sbjct: 120 HASLKAGKWERKKFMGVELYGKTLGIIGLGRIGSEVAKRAKAFGMKVIAYDPYISPERAA 179
Query: 232 ATGVGLVSFEEAISTADFISLHMPLTPATSKMFNDEAFFKMKKGVRIVNVARGGVVDEEA 291
GV LVS +E ++ ADFI+LH PLTP T + E KMK GVRI+N ARGG++DE A
Sbjct: 180 QLGVELVSLDELLARADFITLHTPLTPETRGLIGAEELAKMKPGVRIINCARGGIIDEAA 239
Query: 292 LVRALDSGIISQAALDVFTEEPPAKDSKLVLHENVTVTPHLGASTTEAQEGVAIEIAEAV 351
L AL SG ++ AALDVF +EPP DS L NV VTPHLGAST EAQE VAI++AE V
Sbjct: 240 LAEALKSGKVAGAALDVFEKEPP-TDSPLFELPNVVVTPHLGASTAEAQENVAIQVAEQV 298
Query: 352 IGALKGELAATAVNAPMVPAEVISELAPFVTLAEKLGGLAVQLVAGGSGVKSVKVSYASA 411
I AL+G AVN P + AE +L P++ LAEKLG LA QL +KSV+++Y
Sbjct: 299 IDALRGGPVPNAVNLPSITAEEAEKLKPYLDLAEKLGSLAAQLA--DGPIKSVEITY--- 353
Query: 412 RGP-DDLDTRLLRAMITKGIIEPISSVFVNLVNADFIAKQRGLRVTEERIVLDGSPENPL 470
RG + DT L A KG++ P+ VN VNA +AK+RG+ V E + N
Sbjct: 354 RGELAEEDTEPLTAAALKGLLSPVLGERVNYVNAPLLAKERGIEVEESKSEESPDYSN-- 411
Query: 471 EFIQVQIANVESKFGSAISDIGDIRVEGRV-KDGKPHLTKVGSFGVDVSLEGSIILCRQV 529
I V + +D G+ V G V DG+P + ++ + VD EG +++ R
Sbjct: 412 -LITV----------TVTTDDGERSVAGTVFGDGEPRIVEIDGYRVDAKPEGHMLIIRNR 460
Query: 530 DQPGIIGKVGSLLGDNNVNVNFMSVGRIAPQKQAVMTIGVDEEPSREVLKKIGETPAIEE 589
D+PG+IGKVG+LLG+ +N+ M +GR +A+M + VD+ EVL+++ P I
Sbjct: 461 DRPGVIGKVGTLLGEAGINIAGMQLGRREAGGEALMVLSVDDPVPEEVLEELRALPGILS 520
Query: 590 FVFLKL 595
++L
Sbjct: 521 AKAVEL 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 = 517 bits (1333), Expect = e-179
Identities = 247/549 (44%), Positives = 338/549 (61%), Gaps = 34/549 (6%)
Query: 56 VLVAEKLGEAGLDVLKN-FANVDCSYNLSPEELCTKISLCDALIVRSGTKVTREVFESSA 114
VL+A+ + G+D+L++ VD LS EEL I DALIVRS TKVT EV + A
Sbjct: 2 VLIADPISPDGIDILEDVGVEVDVQTGLSREELLEIIPDYDALIVRSATKVTEEVIAA-A 60
Query: 115 GRLKVVGRAGVGIDNVDLSAATEHGCLVVNAPTANTIAAAEHGIALLTAMARNIAQADAS 174
+LKV+GRAGVG+DN+D+ AAT G LVVNAPT NTI+AAEH +A+L A ARNI QADAS
Sbjct: 61 PKLKVIGRAGVGVDNIDIEAATARGILVVNAPTGNTISAAEHALAMLLAAARNIPQADAS 120
Query: 175 VKAGKWQRNKYVGVSLVGKTLAVMGFGKVGTEVARRAKGLGMNVIAHDPYAQADRARATG 234
+K G+W R ++G L GKTL V+G G++G+ VA+RAK GM V+A+DPY +RA G
Sbjct: 121 LKEGEWDRKAFMGTELYGKTLGVIGLGRIGSIVAKRAKAFGMKVLAYDPYISPERAEQLG 180
Query: 235 VGLV-SFEEAISTADFISLHMPLTPATSKMFNDEAFFKMKKGVRIVNVARGGVVDEEALV 293
V LV +E ++ ADFI++H PLTP T + E KMKKGV IVN ARGG++DE AL
Sbjct: 181 VELVDDLDELLARADFITVHTPLTPETRGLIGAEELAKMKKGVIIVNCARGGIIDEAALY 240
Query: 294 RALDSGIISQAALDVFTEEPPAKDSKLVLHENVTVTPHLGASTTEAQEGVAIEIAEAVIG 353
AL+ G + AALDVF +EPP D+ L +NV TPHLGAST EAQE VA ++AE V+
Sbjct: 241 EALEEGHVRAAALDVFEKEPP-TDNPLFDLDNVIATPHLGASTREAQENVATQVAEQVLD 299
Query: 354 ALKGELAATAVNAPMVPAEVISELAPFVTLAEKLGGLAVQLVAGGSGVKSVKVSYASARG 413
ALKG AVNAP + A+V+ +L P++ LAEKLG LA QL+ G V+SV+V+Y RG
Sbjct: 300 ALKGLPVPNAVNAPGIDADVMEKLKPYLDLAEKLGKLAGQLLDG--AVQSVEVTY---RG 354
Query: 414 P-DDLDTRLLRAMITKGIIEPISSVFVNLVNADFIAKQRGLRVTEERIVLDGSPENPLEF 472
++ L KG++ P+ VN+VNA +AK+RG+ V E +
Sbjct: 355 ELATENSEPLTRAALKGLLSPVLDDEVNMVNAPAVAKERGITVEESK------------- 401
Query: 473 IQVQIANVESKFGSAIS-----DIGDIRVEGRV-KDGKPHLTKVGSFGVDVSLEGSIILC 526
+ + + +S D G + V G V P + ++ F VD+ EG +++
Sbjct: 402 -----SESSPDYKNYLSVTVTGDSGTVSVAGTVFGGFSPRIVEIDGFHVDLEPEGIMLII 456
Query: 527 RQVDQPGIIGKVGSLLGDNNVNVNFMSVGRIAPQKQAVMTIGVDEEPSREVLKKIGETPA 586
+D+PG+IGKVG+LLG +N+ M +GR +A+M + +D+ EVL++I P
Sbjct: 457 LHLDKPGVIGKVGTLLGTAGINIASMQLGRKEKGGEALMLLSLDQPVPDEVLEEIKAIPD 516
Query: 587 IEEFVFLKL 595
I + L
Sbjct: 517 ILSVFVVDL 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 = 452 bits (1166), Expect = e-157
Identities = 179/304 (58%), Positives = 220/304 (72%), Gaps = 2/304 (0%)
Query: 56 VLVAEKLGEAGLDVLKNF-ANVDCSYNLSPEELCTKISLCDALIVRSGTKVTREVFESSA 114
VLV + + E GL++L+ VD + LS EEL I+ DALIVRS TKVT EV E+ A
Sbjct: 2 VLVTDPIDEEGLELLREAGIEVDVAPGLSEEELLAIIADADALIVRSATKVTAEVIEA-A 60
Query: 115 GRLKVVGRAGVGIDNVDLSAATEHGCLVVNAPTANTIAAAEHGIALLTAMARNIAQADAS 174
RLKV+GRAGVG+DN+D+ AAT G LVVNAP ANTI+ AEH IAL+ A+ARNI QADAS
Sbjct: 61 PRLKVIGRAGVGVDNIDVEAATARGILVVNAPGANTISVAEHTIALMLALARNIPQADAS 120
Query: 175 VKAGKWQRNKYVGVSLVGKTLAVMGFGKVGTEVARRAKGLGMNVIAHDPYAQADRARATG 234
++AGKW R K++GV L GKTL ++G G++G EVARRA+ GM V+A+DPY A+RA A G
Sbjct: 121 LRAGKWDRKKFMGVELRGKTLGIVGLGRIGREVARRARAFGMKVLAYDPYISAERAAAGG 180
Query: 235 VGLVSFEEAISTADFISLHMPLTPATSKMFNDEAFFKMKKGVRIVNVARGGVVDEEALVR 294
V LVS +E ++ ADFISLH PLTP T + N E KMK G ++N ARGG+VDE AL
Sbjct: 181 VELVSLDELLAEADFISLHTPLTPETRGLINAEELAKMKPGAILINTARGGIVDEAALAD 240
Query: 295 ALDSGIISQAALDVFTEEPPAKDSKLVLHENVTVTPHLGASTTEAQEGVAIEIAEAVIGA 354
AL SG I+ AALDVF +EPP DS L+ NV +TPHLGAST EAQE VA++ AE V+
Sbjct: 241 ALKSGKIAGAALDVFEQEPPPADSPLLGLPNVILTPHLGASTEEAQERVAVDAAEQVLAV 300
Query: 355 LKGE 358
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 = 341 bits (878), Expect = e-114
Identities = 144/301 (47%), Positives = 201/301 (66%), Gaps = 3/301 (0%)
Query: 56 VLVAEKLGEAGLDVLKNFA-NVDCSYNLSPEELCTKISLCDALIVRSGTKVTREVFESSA 114
+L+ + + E ++ L+ VD ++ EEL KI D LIVRS TKVT+EV ++ A
Sbjct: 3 ILITDGIDEIAIEKLEEAGFEVDYEPLIAKEELLEKIKDYDVLIVRSRTKVTKEVIDA-A 61
Query: 115 GRLKVVGRAGVGIDNVDLSAATEHGCLVVNAPTANTIAAAEHGIALLTAMARNIAQADAS 174
LK++ RAGVG+DN+D+ A + G V+N P A++ + AE I L+ ++AR I +A+
Sbjct: 62 KNLKIIARAGVGLDNIDVEYAKKKGIKVINTPGASSNSVAELVIGLMLSLARFIHRANRE 121
Query: 175 VKAGKWQRNKYVGVSLVGKTLAVMGFGKVGTEVARRAKGLGMNVIAHDPYAQADRARATG 234
+K GKW + KY G+ L GKTL ++GFG++G EVA+ A+ LGMNVIA+DPY + ++A G
Sbjct: 122 MKLGKWNKKKYKGIELRGKTLGIIGFGRIGREVAKIARALGMNVIAYDPYPKDEQAVELG 181
Query: 235 VGLVSFEEAISTADFISLHMPLTPATSKMFNDEAFFKMKKGVRIVNVARGGVVDEEALVR 294
V VS EE + +DFISLH+PLTP T M N + MK G I+N +RGGV+DEEAL+
Sbjct: 182 VKTVSLEELLKNSDFISLHVPLTPETKHMINKKELELMKDGAIIINTSRGGVIDEEALLE 241
Query: 295 ALDSGIISQAALDVFTEEPPAKDSKLVLHENVTVTPHLGASTTEAQEGVAIEIAEAVIGA 354
AL SG ++ AALDVF EPP SKL+ NV++TPH+GAST EAQE + E+A +I
Sbjct: 242 ALKSGKLAGAALDVFENEPP-PGSKLLELPNVSLTPHIGASTKEAQERIGEELANKIIEF 300
Query: 355 L 355
L
Sbjct: 301 L 301
>gnl|CDD|223189 COG0111, SerA, Phosphoglycerate dehydrogenase and related
dehydrogenases [Amino acid transport and metabolism].
Length = 324
Score = 335 bits (862), Expect = e-111
Identities = 155/325 (47%), Positives = 200/325 (61%), Gaps = 7/325 (2%)
Query: 51 TSKPTVLVAEKLGEAGLDVLKNFANVDCS--YNLSPEELCTKISLCDALIVRSGTKVTRE 108
VLV + L L+ L +V+ +L EEL ++ DALIV S T VT E
Sbjct: 1 KMMIKVLVTDPLAPDALEELLAAYDVEVPDGPDLDEEELLEALADADALIV-SVTPVTEE 59
Query: 109 VFESSAGRLKVVGRAGVGIDNVDLSAATEHGCLVVNAPTANTIAAAEHGIALLTAMARNI 168
V + A LK +GRAG G+DN+DL AAT+ G LVVNAP N I+ AE +ALL A+AR I
Sbjct: 60 VLAA-APNLKAIGRAGAGVDNIDLEAATKRGILVVNAPGGNAISVAELVLALLLALARRI 118
Query: 169 AQADASVKAGKWQRNKYVGVSLVGKTLAVMGFGKVGTEVARRAKGLGMNVIAHDPYAQAD 228
ADAS + G+W R + G L GKT+ ++G G++G VA+R K GM VI +DPY+ +
Sbjct: 119 PDADASQRRGEWDRKAFRGTELAGKTVGIIGLGRIGRAVAKRLKAFGMKVIGYDPYSPRE 178
Query: 229 RARATGV-GLVSFEEAISTADFISLHMPLTPATSKMFNDEAFFKMKKGVRIVNVARGGVV 287
RA GV G+ S +E ++ AD ++LH+PLTP T + N E KMK G ++N ARGGVV
Sbjct: 179 RAGVDGVVGVDSLDELLAEADILTLHLPLTPETRGLINAEELAKMKPGAILINAARGGVV 238
Query: 288 DEEALVRALDSGIISQAALDVFTEEPPAKDSKLVLHENVTVTPHLGASTTEAQEGVAIEI 347
DE+AL+ ALDSG I+ AALDVF EEP DS L NV +TPH+G ST EAQE VA +
Sbjct: 239 DEDALLAALDSGKIAGAALDVFEEEPLPADSPLWDLPNVILTPHIGGSTDEAQERVAEIV 298
Query: 348 AEAVIGALKGELAATAVNAPMVPAE 372
AE ++ L G NAP V E
Sbjct: 299 AENIVRYLAGG--PVVNNAPEVDLE 321
>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 = 326 bits (838), Expect = e-108
Identities = 140/298 (46%), Positives = 179/298 (60%), Gaps = 10/298 (3%)
Query: 60 EKLGEAGLDVLKNFANVDCSYNLSPEELCTKISLCDALIVRSGT-KVTREVFESSAGRLK 118
E L AG +V+ N L+ EEL + D +I G +T EV + A RLK
Sbjct: 18 ELLEAAGFEVVLN----PLGRPLTEEELIELLKDADGVIA--GLDPITEEVLAA-APRLK 70
Query: 119 VVGRAGVGIDNVDLSAATEHGCLVVNAPTANTIAAAEHGIALLTAMARNIAQADASVKAG 178
V+ R GVG DN+DL AA + G +V N P AN+ + AE I L+ A+AR I QAD V+AG
Sbjct: 71 VISRYGVGYDNIDLEAAKKRGIVVTNTPGANSNSVAELTIGLMLALARQIPQADREVRAG 130
Query: 179 KWQRNKYVGVSLVGKTLAVMGFGKVGTEVARRAKGLGMNVIAHDPYAQADRARATGVGLV 238
W ++ VG L GKTL ++G G++G VARR G GM V+A+DPY + A+ GV V
Sbjct: 131 GW--DRPVGTELYGKTLGIIGLGRIGKAVARRLSGFGMKVLAYDPYPDEEFAKEHGVEFV 188
Query: 239 SFEEAISTADFISLHMPLTPATSKMFNDEAFFKMKKGVRIVNVARGGVVDEEALVRALDS 298
S EE + +DFISLH+PLTP T + N MK G ++N ARGG+VDEEAL AL S
Sbjct: 189 SLEELLKESDFISLHLPLTPETRHLINAAELALMKPGAILINTARGGLVDEEALYEALKS 248
Query: 299 GIISQAALDVFTEEPPAKDSKLVLHENVTVTPHLGASTTEAQEGVAIEIAEAVIGALK 356
G I+ AALDVF EEPP DS L+ NV +TPH+GAST EA + A+ VI L
Sbjct: 249 GRIAGAALDVFEEEPPPADSPLLELPNVILTPHIGASTKEAVLRMGTMAAQNVIDVLA 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 = 299 bits (768), Expect = 2e-97
Identities = 134/313 (42%), Positives = 177/313 (56%), Gaps = 4/313 (1%)
Query: 56 VLVAEKLGEAGLDVLKNFANVDCSYNLSPEELCTKISLCDALIVRSGTKVTREVFESSAG 115
VL+ + L L++LK V+ L EEL DALIVRS T VT EV E+ A
Sbjct: 1 VLITDPLRPEELELLKEGGEVEVHDELLTEELLEAAKDADALIVRSTTPVTAEVLEA-AP 59
Query: 116 RLKVVGRAGVGIDNVDLSAATEHGCLVVNAPTANTIAAAEHGIALLTAMARNIAQADASV 175
LKV+ R GVG+DN+DL AATE G LV N P +T + AE + L+ A+AR I +ADASV
Sbjct: 60 GLKVIARRGVGVDNIDLDAATERGILVTNVPGYSTESVAELTVGLILALARRIPEADASV 119
Query: 176 KAGKWQRNKYVGVSLVGKTLAVMGFGKVGTEVARRAKGLGMNVIAHDPYAQADRARATGV 235
+AG W++ +G+ L GKTL V+G G +G A AK LGM V+A+DPY +RA GV
Sbjct: 120 RAGDWKKGGPIGLELYGKTLGVIGGGGIGGIGAAIAKALGMGVVAYDPYPNPERAEEGGV 179
Query: 236 GLVSFEEAIST---ADFISLHMPLTPATSKMFNDEAFFKMKKGVRIVNVARGGVVDEEAL 292
++ + + +D + P T + M K +N ARGG V EEA
Sbjct: 180 EVLLLDLLLLDLKESDDLINLAPPTTMKTGHIIINEARGMLKDAVAINNARGGGVIEEAA 239
Query: 293 VRALDSGIISQAALDVFTEEPPAKDSKLVLHENVTVTPHLGASTTEAQEGVAIEIAEAVI 352
+ AL I+ AALDV EEPP +S L+ NV +TPH+ +T EAQE +A E AE ++
Sbjct: 240 LDALLEEGIAAAALDVVEEEPPPVNSPLLDLPNVILTPHIAGATEEAQENMAEEAAENLL 299
Query: 353 GALKGELAATAVN 365
LKG AVN
Sbjct: 300 AFLKGGTPPNAVN 312
>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 = 290 bits (744), Expect = 7e-94
Identities = 120/310 (38%), Positives = 168/310 (54%), Gaps = 7/310 (2%)
Query: 54 PTVLVAEKLGEAGLDVLKNFANV---DCSYNLSPEELCTKISLCDALIVRSGTKVTREVF 110
P VLV +L E L +L+ V D L EEL D L+ K+ E+
Sbjct: 1 PKVLVTRRLPEEALALLREGFEVEVWDEDRPLPREELLEAAKGADGLLCTLTDKIDAELL 60
Query: 111 ESSAGRLKVVGRAGVGIDNVDLSAATEHGCLVVNAPTANTIAAAEHGIALLTAMARNIAQ 170
++ A LKV+ VG D++D+ AA G V N P T A A+ ALL A AR + +
Sbjct: 61 DA-APPLKVIANYSVGYDHIDVDAAKARGIPVTNTPDVLTDATADLAFALLLAAARRVVE 119
Query: 171 ADASVKAGKWQRNK---YVGVSLVGKTLAVMGFGKVGTEVARRAKGLGMNVIAHDPYAQA 227
D V+AG+W+ +G L GKTL ++G G++G VARRAKG GM ++ H+ +
Sbjct: 120 GDRFVRAGEWKGWSPTLLLGTDLHGKTLGIVGMGRIGQAVARRAKGFGMKILYHNRSRKP 179
Query: 228 DRARATGVGLVSFEEAISTADFISLHMPLTPATSKMFNDEAFFKMKKGVRIVNVARGGVV 287
+ G VS +E ++ +DF+SLH PLTP T + N E MK ++N ARGGVV
Sbjct: 180 EAEEELGARYVSLDELLAESDFVSLHCPLTPETRHLINAERLALMKPTAILINTARGGVV 239
Query: 288 DEEALVRALDSGIISQAALDVFTEEPPAKDSKLVLHENVTVTPHLGASTTEAQEGVAIEI 347
DE+ALV AL SG I+ A LDVF EP D L+ NV + PH+G++T E + +A
Sbjct: 240 DEDALVEALKSGKIAGAGLDVFEPEPLPADHPLLTLPNVVLLPHIGSATVETRTAMAELA 299
Query: 348 AEAVIGALKG 357
A+ ++ L G
Sbjct: 300 ADNLLAVLAG 309
>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 = 287 bits (738), Expect = 3e-93
Identities = 124/309 (40%), Positives = 174/309 (56%), Gaps = 11/309 (3%)
Query: 45 VLATFITSKPTVLVAEKLGEAGLDVLKNFANVDCSYNLSPEELCTKISLCDALIVRSGTK 104
VL P L E L G +V+ + +L +EL ++ DALIV S T
Sbjct: 2 VLVLEPLFPPEAL--EALEATGFEVI-------VADDLLADELEALLADADALIVSSTTP 52
Query: 105 VTREVFESSAGRLKVVGRAGVGIDNVDLSAATEHGCLVVNAPTANTIAAAEHGIALLTAM 164
VT EV A +LK + AG G+DN+DL AA + G V N P AN A AEH + LL A+
Sbjct: 53 VTAEVLAK-APKLKFIQVAGAGVDNIDLDAAKKRGITVTNVPGANAEAVAEHALGLLLAL 111
Query: 165 ARNIAQADASVKAGK-WQRNKYVGVSLVGKTLAVMGFGKVGTEVARRAKGLGMNVIAHDP 223
R + +ADA+V+ G W + G L GKT+ ++G G++G VA+R + GM V+ +D
Sbjct: 112 LRRLPRADAAVRRGWGWLWAGFPGYELEGKTVGIVGLGRIGQRVAKRLQAFGMKVLYYDR 171
Query: 224 YAQADRARATGVGLVSFEEAISTADFISLHMPLTPATSKMFNDEAFFKMKKGVRIVNVAR 283
+ + G +VS +E ++ +D + LH+PLTP T + N+E MK G +VN AR
Sbjct: 172 TRKPEPEEDLGFRVVSLDELLAQSDVVVLHLPLTPETRHLINEEELALMKPGAVLVNTAR 231
Query: 284 GGVVDEEALVRALDSGIISQAALDVFTEEPPAKDSKLVLHENVTVTPHLGASTTEAQEGV 343
GG+VDE+AL+RAL SG I+ AALDVF EP D L+ NV +TPH+ T EA+E +
Sbjct: 232 GGLVDEDALLRALKSGKIAGAALDVFEPEPLPADHPLLELPNVILTPHIAGYTEEARERM 291
Query: 344 AIEIAEAVI 352
A E +
Sbjct: 292 AEIAVENLE 300
>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 = 287 bits (738), Expect = 6e-93
Identities = 131/298 (43%), Positives = 177/298 (59%), Gaps = 10/298 (3%)
Query: 62 LGEAGLDVLKNFANVDCSYNLSPEELCTKISLCDALIVRSGTKVTREVFESSAGRLKVVG 121
L EAG+++ VD + +EL + DAL+V+ VT EV E+ RLKV+
Sbjct: 20 LEEAGVEL------VDAQSR-TEDELIEAAADADALLVQY-APVTAEVIEALP-RLKVIV 70
Query: 122 RAGVGIDNVDLSAATEHGCLVVNAPTANTIAAAEHGIALLTAMARNIAQADASVKAGKWQ 181
R GVG+DNVD++AATE G V N P T A+H +AL+ A+AR + D +V+AG W
Sbjct: 71 RYGVGVDNVDVAAATERGIPVCNVPDYCTEEVADHALALILALARKLPFLDRAVRAGGWD 130
Query: 182 RNKYVGV-SLVGKTLAVMGFGKVGTEVARRAKGLGMNVIAHDPYAQADRARATGVGLVSF 240
+ L G TL ++GFG++G VA+RAK G VIA+DPY A GV +VS
Sbjct: 131 WTVGGPIRRLRGLTLGLVGFGRIGRAVAKRAKAFGFRVIAYDPYVPDGVAALGGVRVVSL 190
Query: 241 EEAISTADFISLHMPLTPATSKMFNDEAFFKMKKGVRIVNVARGGVVDEEALVRALDSGI 300
+E ++ +D +SLH PLTP T + + EA MK G +VN ARGG+VDE AL RAL SG
Sbjct: 191 DELLARSDVVSLHCPLTPETRHLIDAEALALMKPGAFLVNTARGGLVDEAALARALKSGR 250
Query: 301 ISQAALDVFTEEPPAKDSKLVLHENVTVTPHLGASTTEAQEGVAIEIAEAVIGALKGE 358
I+ AALDV EEPP DS L+ NV +TPH + E+ + + AE V+ L+GE
Sbjct: 251 IAGAALDVLEEEPPPADSPLLSAPNVILTPHAAWYSEESLAELRRKAAEEVVRVLRGE 308
>gnl|CDD|223980 COG1052, LdhA, Lactate dehydrogenase and related dehydrogenases
[Energy production and conversion / Coenzyme metabolism
/ General function prediction only].
Length = 324
Score = 278 bits (713), Expect = 5e-89
Identities = 123/323 (38%), Positives = 167/323 (51%), Gaps = 10/323 (3%)
Query: 53 KPTVLVAEKLGEAGLDVLKNFANVDCSYNLSPE--ELCTKISLCDALIVRSGTKVTREVF 110
K VL KL L+ LK V+ + EL ++ DA+I ++ EV
Sbjct: 2 KIVVLSTRKLPPEVLERLKEKFEVERYEDDLTPDTELAERLKDADAVITFVNDRIDAEVL 61
Query: 111 ESSAGRLKVVGRAGVGIDNVDLSAATEHGCLVVNAPTANTIAAAEHGIALLTAMARNIAQ 170
E LK++ G DNVDL AA E G V N P +T A AEH +AL+ A+AR I +
Sbjct: 62 EK-LPGLKLIATRSAGYDNVDLEAAKERGITVTNVPGYSTEAVAEHAVALILALARRIHE 120
Query: 171 ADASVKAGKWQRNKYV----GVSLVGKTLAVMGFGKVGTEVARRAKGLGMNVIAHDPYAQ 226
D V+ G W + G L GKTL ++G G++G VARR KG GM V+ +D
Sbjct: 121 GDRRVREGNWSLSGGPDPLLGFDLRGKTLGIIGLGRIGQAVARRLKGFGMKVLYYDRSPN 180
Query: 227 ADRARATGVGLVSFEEAISTADFISLHMPLTPATSKMFNDEAFFKMKKGVRIVNVARGGV 286
+ + G V +E ++ +D ISLH PLTP T + N E KMK G +VN ARGG+
Sbjct: 181 PEAEKELGARYVDLDELLAESDIISLHCPLTPETRHLINAEELAKMKPGAILVNTARGGL 240
Query: 287 VDEEALVRALDSGIISQAALDVFTEEPPAKDSKL---VLHENVTVTPHLGASTTEAQEGV 343
VDE+AL+ AL SG I+ A LDVF EP D L NV +TPH+ ++T EA++ +
Sbjct: 241 VDEQALIDALKSGKIAGAGLDVFENEPALFDHPLLRLDNFPNVVLTPHIASATEEARKAM 300
Query: 344 AIEIAEAVIGALKGELAATAVNA 366
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 = 271 bits (696), Expect = 1e-86
Identities = 107/311 (34%), Positives = 168/311 (54%), Gaps = 7/311 (2%)
Query: 55 TVLVAEKLGEAGLDVLKNFANVDCSYNL----SPEELCTKISLCDALIVRSGTKVTREVF 110
VL ++L+ + +E ++ D L+ + E+
Sbjct: 1 KVLFLGPEFPDAEELLRALLPPAPGVEVVTAAELDEEAALLADADVLVPGMRKVIDAEL- 59
Query: 111 ESSAGRLKVVGRAGVGIDNVDLSAATEHGCLVVNAPTANTIAAAEHGIALLTAMARNIAQ 170
++A RL+++ + GVG+D VDL AAT G V N P N + AEH + L+ A+ R + +
Sbjct: 60 LAAAPRLRLIQQPGVGLDGVDLEAATARGIPVANIPGGNAESVAEHAVMLMLALLRRLPE 119
Query: 171 ADASVKAGKWQRNKY-VGVSLVGKTLAVMGFGKVGTEVARRAKGLGMNVIAHDPYAQAD- 228
AD ++AG+W R + L GKT+ ++G G +G VARR +G G+ VI +D + +
Sbjct: 120 ADRELRAGRWGRPEGRPSRELSGKTVGIVGLGNIGRAVARRLRGFGVEVIYYDRFRDPEA 179
Query: 229 RARATGVGLVSFEEAISTADFISLHMPLTPATSKMFNDEAFFKMKKGVRIVNVARGGVVD 288
+ GV V +E ++ +D +SLH+PLTP T + E MK G ++N ARGG+VD
Sbjct: 180 EEKDLGVRYVELDELLAESDVVSLHVPLTPETRHLIGAEELAAMKPGAILINTARGGLVD 239
Query: 289 EEALVRALDSGIISQAALDVFTEEPPAKDSKLVLHENVTVTPHLGASTTEAQEGVAIEIA 348
EEAL+ AL SG ++ A LDVF +EP D L+ +NV +TPH+ T E+ + +A +A
Sbjct: 240 EEALLAALRSGHLAGAGLDVFWQEPLPPDDPLLRLDNVILTPHIAGVTDESYQRMAAIVA 299
Query: 349 EAVIGALKGEL 359
E + L+GE
Sbjct: 300 ENIARLLRGEP 310
>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 = 264 bits (677), Expect = 6e-84
Identities = 126/323 (39%), Positives = 172/323 (53%), Gaps = 31/323 (9%)
Query: 55 TVLVAEKLGEAGLDVLKNFANVDCSYNLSPEELCTKISLCDALIVRSGTKVTREVFESSA 114
+L A K+ + GL+ K Y + E+ DALIVRS K+ F S
Sbjct: 2 KILTANKISKKGLERFK-----KDKYEVK-EDALED---PDALIVRS-DKLHDMDFAPS- 50
Query: 115 GRLKVVGRAGVGIDNVDLSAATEHGCLVVNAPTANTIAAAEHGIALLTAMARNIAQA--- 171
LK + RAG G++N+D+ AA++ G +V N P AN A AE IA++ A++RNI QA
Sbjct: 51 --LKAIARAGAGVNNIDVDAASKRGIVVFNTPGANANAVAELVIAMMLALSRNIIQAIKW 108
Query: 172 ------DASVKAGKWQRNKYVGVSLVGKTLAVMGFGKVGTEVARRAKGLGMNVIAHDPYA 225
D K + + ++VG L GKTL V+G G +G VA A LGM VI +DPY
Sbjct: 109 VTNGDGDDISKGVEKGKKQFVGTELRGKTLGVIGLGNIGRLVANAALALGMKVIGYDPYL 168
Query: 226 QADRARATGVGLV---SFEEAISTADFISLHMPLTPATSKMFNDEAFFKMKKGVRIVNVA 282
+ A V + S EE ++TAD+I+LH+PLT T + N E KMK G ++N A
Sbjct: 169 SVEAAWKLSVEVQRVTSLEELLATADYITLHVPLTDETRGLINAELLAKMKPGAILLNFA 228
Query: 283 RGGVVDEEALVRALDSGIISQAALDVFTEEPPAKDSKLVLHENVTVTPHLGASTTEAQEG 342
RG +VDEEAL+ ALD G + + F E PA NV TPHLGAST EA+E
Sbjct: 229 RGEIVDEEALLEALDEGKL-GGYVTDFPE--PALLGH---LPNVIATPHLGASTEEAEEN 282
Query: 343 VAIEIAEAVIGALKGELAATAVN 365
A+ A ++ L+ +VN
Sbjct: 283 CAVMAARQIMDFLETGNITNSVN 305
>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 = 264 bits (677), Expect = 6e-84
Identities = 112/262 (42%), Positives = 154/262 (58%), Gaps = 10/262 (3%)
Query: 84 PEELCTKISLCDALIVRSGTKVTREVFESSAGRLKVVG--RAGVGIDNVDLSAATEHGCL 141
EEL + D LI VT++V E+ A +LK++G R G +NVD+ AATE G
Sbjct: 37 EEELLEALKDADILITHFAP-VTKKVIEA-APKLKLIGVCRGGP--ENVDVEAATERGIP 92
Query: 142 VVNAPTANTIAAAEHGIALLTAMARNIAQADASVKAGKWQRNKY----VGVSLVGKTLAV 197
V+N P N A AE + L+ A RNIA+A A++K G+W+++ Y G L GKT+ +
Sbjct: 93 VLNTPGRNAEAVAEFTVGLMLAETRNIARAHAALKDGEWRKDYYNYDGYGPELRGKTVGI 152
Query: 198 MGFGKVGTEVARRAKGLGMNVIAHDPYAQADRARATGVGLVSFEEAISTADFISLHMPLT 257
+GFG +G VA+R K G V+ +DPY ++ A GV VS EE + +D +SLH LT
Sbjct: 153 VGFGAIGRRVAKRLKAFGAEVLVYDPYVDPEKIEADGVKKVSLEELLKRSDVVSLHARLT 212
Query: 258 PATSKMFNDEAFFKMKKGVRIVNVARGGVVDEEALVRALDSGIISQAALDVFTEEPPAKD 317
P T M E F MK +N AR G+VDE+AL+ AL+ G I AALDVF EEP D
Sbjct: 213 PETRGMIGAEEFALMKPTAYFINTARAGLVDEDALIEALEEGKIGGAALDVFPEEPLPAD 272
Query: 318 SKLVLHENVTVTPHLGASTTEA 339
L+ +NVT+TPH+ +T +
Sbjct: 273 HPLLKLDNVTLTPHIAGATRDV 294
>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 = 261 bits (669), Expect = 1e-82
Identities = 117/318 (36%), Positives = 175/318 (55%), Gaps = 9/318 (2%)
Query: 55 TVLVAEKLGEAGLDVLKNFANVDCS---YNLSPEELCTKISLCDALIVRSGTKVTREVFE 111
VLV + + L+ L+ V +S EEL +I+ DALI T V +E+ +
Sbjct: 2 KVLVTGWIPKEALEELEENFEVTYYDGLGLISKEELLERIADYDALITPLSTPVDKEIID 61
Query: 112 SSAGRLKVVGRAGVGIDNVDLSAATEHGCLVVNAPTANTIAAAEHGIALLTAMARNIAQA 171
+ A LK++ G G DN+D+ A E G V N P +T AE L+ A+AR IA+
Sbjct: 62 A-AKNLKIIANYGAGFDNIDVDYAKEKGIPVTNTPAVSTEPTAELTFGLILALARRIAEG 120
Query: 172 DASVKAGK---WQRNKYVGVSLVGKTLAVMGFGKVGTEVARRAKGLGMNVIAHDPY-AQA 227
D ++ G W ++G L GKTL ++G G++G VARRAK GM ++ ++ +
Sbjct: 121 DRLMRRGGFLGWAPLFFLGHELAGKTLGIIGMGRIGQAVARRAKAFGMKILYYNRHRLSE 180
Query: 228 DRARATGVGLVSFEEAISTADFISLHMPLTPATSKMFNDEAFFKMKKGVRIVNVARGGVV 287
+ + G V +E + +DF+SLH P TP T + + AF MK ++N ARG +V
Sbjct: 181 ETEKELGATYVDLDELLKESDFVSLHAPYTPETHHLIDAAAFKLMKPTAYLINAARGPLV 240
Query: 288 DEEALVRALDSGIISQAALDVFTEEPPAKDSKLVLHENVTVTPHLGASTTEAQEGVAIEI 347
DE+ALV AL +G I+ AALDVF EP +L +NV +TPH+G +T EA++ +A E
Sbjct: 241 DEKALVDALKTGEIAGAALDVFEFEPEVSP-ELKKLDNVILTPHIGNATVEARDAMAKEA 299
Query: 348 AEAVIGALKGELAATAVN 365
A+ +I L+G+ VN
Sbjct: 300 ADNIISFLEGKRPKNIVN 317
>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 = 4e-82
Identities = 126/309 (40%), Positives = 176/309 (56%), Gaps = 9/309 (2%)
Query: 60 EKLGEAGLDVLKNFANVDCSYNLSPEELCTKISLCDALIVRSGTKVTREVFESSAGRLKV 119
++L + G V ++S + L K+ D +I +E FE LK+
Sbjct: 19 QRLKKIGYVD---RFEVP--PDISGKALAEKLKGYDIIIASVTPNFDKEFFEY-NDGLKL 72
Query: 120 VGRAGVGIDNVDLSAATEHGCLVVNAPTA-NTIAAAEHGIALLTAMARNIAQADASVKAG 178
+ R G+G DNVDL AATEHG +V P A A AEH +AL+ + R I QA +VK G
Sbjct: 73 IARHGIGYDNVDLKAATEHGVIVTRVPGAVERDAVAEHAVALILTVLRKINQASEAVKEG 132
Query: 179 KWQ-RNKYVGVSLVGKTLAVMGFGKVGTEVARRAK-GLGMNVIAHDPYAQADRARATGVG 236
KW R +VG L GKT+ ++G+G +G+ VA K G V+A+DPY + + G
Sbjct: 133 KWTERANFVGHELSGKTVGIIGYGNIGSRVAEILKEGFNAKVLAYDPYVSEEVIKKKGAK 192
Query: 237 LVSFEEAISTADFISLHMPLTPATSKMFNDEAFFKMKKGVRIVNVARGGVVDEEALVRAL 296
VS EE ++ +D ISLH PLT T M N++AF KMKKGV +VN ARG ++DEEAL+ AL
Sbjct: 193 PVSLEELLAESDIISLHAPLTEETYHMINEKAFSKMKKGVILVNTARGELIDEEALIEAL 252
Query: 297 DSGIISQAALDVFTEEPPAKDSKLVLHENVTVTPHLGASTTEAQEGVAIEIAEAVIGALK 356
SG I+ A LDV EEP D L+ +ENV +TPH+GA T E+ G+ ++ + + L
Sbjct: 253 KSGKIAGAGLDVLEEEPIKADHPLLHYENVVITPHIGAYTYESLYGMGEKVVDDIEDFLA 312
Query: 357 GELAATAVN 365
G+ +N
Sbjct: 313 GKEPKGILN 321
>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 = 250 bits (641), Expect = 2e-78
Identities = 108/282 (38%), Positives = 158/282 (56%), Gaps = 13/282 (4%)
Query: 67 LDVLKNFANVDCSYNLSPEELCTKISLCDALIVRSGTKVTREVFESSAGRLKVVGRAGVG 126
D L+ + SPEE+ +I D +I + + EV LK++G G
Sbjct: 18 WDPLEFLGELTVYDRTSPEEVVERIKDADIVIT-NKVVLDAEVLAQ-LPNLKLIGVLATG 75
Query: 127 IDNVDLSAATEHGCLVVNAPTANTIAAAEHGIALLTAMARNIAQADASVKAGKWQRN--- 183
+NVDL+AA E G V N P +T + A+H ALL A+AR +A + VKAG+WQ++
Sbjct: 76 YNNVDLAAAKERGITVTNVPGYSTDSVAQHTFALLLALARLVAYHNDVVKAGEWQKSPDF 135
Query: 184 ---KYVGVSLVGKTLAVMGFGKVGTEVARRAKGLGMNVIAHDPYAQADRARATGVGLVSF 240
Y + L GKTL ++G+G +G VAR A+ GM V+ + G VS
Sbjct: 136 CFWDYPIIELAGKTLGIIGYGNIGQAVARIARAFGMKVLFAERKGAPPL----REGYVSL 191
Query: 241 EEAISTADFISLHMPLTPATSKMFNDEAFFKMKKGVRIVNVARGGVVDEEALVRALDSGI 300
+E ++ +D ISLH PLTP T + N E KMK G ++N ARGG+VDE+AL AL+SG
Sbjct: 192 DELLAQSDVISLHCPLTPETRNLINAEELAKMKPGAILINTARGGLVDEQALADALNSGK 251
Query: 301 ISQAALDVFTEEPPAKDSKLV-LHENVTVTPHLGASTTEAQE 341
I+ A LDV ++EPP D+ L+ N+ +TPH+ ++ EA++
Sbjct: 252 IAGAGLDVLSQEPPRADNPLLKAAPNLIITPHIAWASREARQ 293
>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 = 240 bits (615), Expect = 1e-76
Identities = 83/176 (47%), Positives = 114/176 (64%), Gaps = 1/176 (0%)
Query: 158 IALLTAMARNIAQADASVKAGKWQRNKYVGVSLVGKTLAVMGFGKVGTEVARRAKGLGMN 217
+ALL A+AR I +AD V+AG+W+ + +G L GKT+ ++G G++G VARR K GM
Sbjct: 1 LALLLALARRIPEADRQVRAGRWRPDALLGRELSGKTVGIIGLGRIGRAVARRLKAFGMK 60
Query: 218 VIAHDPYAQADRARATGVGLVSFEEAISTADFISLHMPLTPATSKMFNDEAFFKMKKGVR 277
VIA+D Y + A A G VS +E ++ +D +SLH+PLTP T + N E MK G
Sbjct: 61 VIAYDRYPK-AEAEALGARYVSLDELLAESDVVSLHLPLTPETRHLINAERLALMKPGAI 119
Query: 278 IVNVARGGVVDEEALVRALDSGIISQAALDVFTEEPPAKDSKLVLHENVTVTPHLG 333
++N ARGG+VDE+AL+ AL SG I+ AALDVF EP D L+ NV +TPH+
Sbjct: 120 LINTARGGLVDEDALIAALKSGRIAGAALDVFEPEPLPPDHPLLELPNVILTPHIA 175
>gnl|CDD|183914 PRK13243, PRK13243, glyoxylate reductase; Reviewed.
Length = 333
Score = 231 bits (591), Expect = 5e-71
Identities = 125/328 (38%), Positives = 187/328 (57%), Gaps = 12/328 (3%)
Query: 52 SKPTVLVAEKLGEAGLDVLKNFANVDCSYNLSP---EELCTKISLCDALIVRSGTKVTRE 108
KP V + ++ E G+++L+ V+ + E L K+ DAL+ ++ E
Sbjct: 1 MKPKVFITREIPENGIEMLEEHFEVEVWEDEREIPREVLLEKVRDVDALVTMLSERIDCE 60
Query: 109 VFESSAGRLKVVGRAGVGIDNVDLSAATEHGCLVVNAPTANTIAAAEHGIALLTAMARNI 168
VFE+ A RL++V VG DN+D+ AT G V N P T A A+ ALL A AR +
Sbjct: 61 VFEA-APRLRIVANYAVGYDNIDVEEATRRGIYVTNTPGVLTEATADFAWALLLATARRL 119
Query: 169 AQADASVKAGKWQRNK-------YVGVSLVGKTLAVMGFGKVGTEVARRAKGLGMNVIAH 221
+AD V++G+W+R ++G + GKT+ ++GFG++G VARRAKG GM ++ +
Sbjct: 120 VEADHFVRSGEWKRRGVAWHPLMFLGYDVYGKTIGIIGFGRIGQAVARRAKGFGMRILYY 179
Query: 222 DPYAQADRARATGVGLVSFEEAISTADFISLHMPLTPATSKMFNDEAFFKMKKGVRIVNV 281
+ + + G EE + +DF+SLH+PLT T M N+E MK +VN
Sbjct: 180 SRTRKPEAEKELGAEYRPLEELLRESDFVSLHVPLTKETYHMINEERLKLMKPTAILVNT 239
Query: 282 ARGGVVDEEALVRALDSGIISQAALDVFTEEPPAKDSKLVLHENVTVTPHLGASTTEAQE 341
ARG VVD +ALV+AL G I+ A LDVF EE P + +L +NV + PH+G++T EA+E
Sbjct: 240 ARGKVVDTKALVKALKEGWIAGAGLDVFEEE-PYYNEELFSLKNVVLAPHIGSATFEARE 298
Query: 342 GVAIEIAEAVIGALKGELAATAVNAPMV 369
G+A +AE +I +GE+ T VN +V
Sbjct: 299 GMAELVAENLIAFKRGEVPPTLVNREVV 326
>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 = 227 bits (581), Expect = 9e-70
Identities = 104/277 (37%), Positives = 158/277 (57%), Gaps = 11/277 (3%)
Query: 82 LSPEELCTKISLCDALIVRSGTKVTREVFESSAGRLKVVGRAGVGIDNVDLSAATEHGCL 141
L +EL + L +RS T++T EV E+ A +L +G +G + VDL AA + G
Sbjct: 31 LDEDELIEALKDVHLLGIRSKTQLTEEVLEA-APKLLAIGCFCIGTNQVDLDAAAKRGIP 89
Query: 142 VVNAPTANTIAAAEHGIALLTAMARNIAQADASVKAGKWQRNKYVGVSLVGKTLAVMGFG 201
V NAP +NT + AE I + +AR + +A+ G W ++ + GKTL ++G+G
Sbjct: 90 VFNAPFSNTRSVAELVIGEIIMLARRLPDRNAAAHRGIWNKSATGSHEVRGKTLGIIGYG 149
Query: 202 KVGTEVARRAKGLGMNVIAHDPYAQADRARATG--VGLVSFEEAISTADFISLHMPLTPA 259
+G++++ A+ LGM VI +D G + S EE ++ ADF++LH+P TP+
Sbjct: 150 HIGSQLSVLAEALGMRVIFYD----IAEKLPLGNARQVSSLEELLAEADFVTLHVPATPS 205
Query: 260 TSKMFNDEAFFKMKKGVRIVNVARGGVVDEEALVRALDSGIISQAALDVFTEEPPAKD-- 317
T M E +MKKG ++N +RG VVD +AL AL SG ++ AA+DVF EEP +
Sbjct: 206 TKNMIGAEEIAQMKKGAILINASRGTVVDIDALAEALRSGHLAGAAVDVFPEEPASNGEP 265
Query: 318 --SKLVLHENVTVTPHLGASTTEAQEGVAIEIAEAVI 352
S L NV +TPH+G ST EAQE + +E+A ++
Sbjct: 266 FSSPLQGLPNVILTPHIGGSTEEAQENIGLEVAGKLV 302
>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 = 227 bits (582), Expect = 1e-69
Identities = 115/295 (38%), Positives = 154/295 (52%), Gaps = 15/295 (5%)
Query: 78 CSYNLSPEELCTKISLCDALIVRSGTKVTREVFESSAGRLKVVGRAGVGIDNVDLSAATE 137
+Y L+ +E DA++ K+ E+ + + G LK + G DN+DL A E
Sbjct: 30 VTYLLNDDETAELAKGADAILTAFTDKIDAELLDKAPG-LKFISLRATGYDNIDLDYAKE 88
Query: 138 HGCLVVNAPTANTIAAAEHGIALLTAMARNIAQADASVKAGKWQRNKYVGVSLVGKTLAV 197
G V N P + A AEH IAL+ A+ RN D K Q +G L +T+ V
Sbjct: 89 LGIGVTNVPEYSPNAVAEHTIALILALLRNRKYIDERDKNQDLQDAGVIGRELEDQTVGV 148
Query: 198 MGFGKVGTEVARRAKGLGMNVIAHDPYAQADRARATGVGLVSFEEAISTADFISLHMPLT 257
+G GK+G VA+RAKG GM VIA+DP+ + GV VS EE +D ISLH+PLT
Sbjct: 149 VGTGKIGRAVAQRAKGFGMKVIAYDPFRNPELE-DKGVKYVSLEELFKNSDIISLHVPLT 207
Query: 258 PATSKMFNDEAFFKMKKGVRIVNVARGGVVDEEALVRALDSGIISQAALDVFTEEPP--- 314
P M N+EAF MKKGV I+N ARG +VD EAL+ ALDSG I A LDV +E P
Sbjct: 208 PENHHMINEEAFKLMKKGVIIINTARGSLVDTEALIEALDSGKIFGAGLDVLEDETPDLL 267
Query: 315 ----------AKDSKLVLHENVTVTPHLGASTTEAQEGVAIEIAEAVIGALKGEL 359
A ++ L NV +TPH T +A + + E ++ L+GE
Sbjct: 268 KDLEGEIFKDALNALLGRRPNVIITPHTAFYTDDALKNMVEISCENIVDFLEGEE 322
>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 = 225 bits (577), Expect = 4e-69
Identities = 107/278 (38%), Positives = 152/278 (54%), Gaps = 6/278 (2%)
Query: 82 LSPEELCTKISLCDALIV-RSGTKVTREVFESSAGRLKVVGRAGVGIDNVDLSAATEHGC 140
L + L +++ DA+++ R T + E LK++ G+ ++DL+AA E G
Sbjct: 35 LDEDALAERLAPFDAIVLMRERTPFPAALLER-LPNLKLLVTTGMRNASIDLAAAKERGI 93
Query: 141 LVVNAPTANTIAAAEHGIALLTAMARNIAQADASVKAGKWQRNKYVGVSLVGKTLAVMGF 200
+V T A AE AL+ A+ARN+ + DA+++AG WQ +G L GKTL ++G
Sbjct: 94 VVCGTGGGPT-ATAELTWALILALARNLPEEDAALRAGGWQTT--LGTGLAGKTLGIVGL 150
Query: 201 GKVGTEVARRAKGLGMNVIAHDPYAQADRARATGVGL-VSFEEAISTADFISLHMPLTPA 259
G++G VAR + GM VIA A+RA A GV VS EE +T+D +SLH+ L+
Sbjct: 151 GRIGARVARIGQAFGMRVIAWSSNLTAERAAAAGVEAAVSKEELFATSDVVSLHLVLSDR 210
Query: 260 TSKMFNDEAFFKMKKGVRIVNVARGGVVDEEALVRALDSGIISQAALDVFTEEPPAKDSK 319
T + E MK +VN +RG +VDE AL+ AL +G I+ AALDVF EP D
Sbjct: 211 TRGLVGAEDLALMKPTALLVNTSRGPLVDEGALLAALRAGRIAGAALDVFDVEPLPADHP 270
Query: 320 LVLHENVTVTPHLGASTTEAQEGVAIEIAEAVIGALKG 357
L NV +TPH+G T EA EG + E + L G
Sbjct: 271 LRGLPNVLLTPHIGYVTEEAYEGFYGQAVENIAAWLAG 308
>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 = 218 bits (558), Expect = 3e-66
Identities = 95/242 (39%), Positives = 138/242 (57%), Gaps = 7/242 (2%)
Query: 117 LKVVGRAGVGIDNVDLSAATEHGCLVVNAPTANTIAAAEHGIALLTAMARNIAQADASVK 176
LK++ AG G D +D+ A T+ G V N P A A A+ + L+ RN ++A+ S +
Sbjct: 77 LKIIAHAGAGYDQIDVDALTKRGIQVSNTPGAVDEATADTALFLILGALRNFSRAERSAR 136
Query: 177 AGKWQRNK--YVGVSLVGKTLAVMGFGKVGTEVARRAKGLGMNVIAHDPY-AQADRARAT 233
AGKW+ + GKTL ++G G +G +AR+A GM +I H+ + +A
Sbjct: 137 AGKWRGFLDLTLAHDPRGKTLGILGLGGIGKAIARKAAAFGMKIIYHNRSRLPEELEKAL 196
Query: 234 GVGLVSFEEAISTADFISLHMPLTPATSKMFNDEAFFKMKKGVRIVNVARGGVVDEEALV 293
VS +E ++ +D +SL+ PLT AT + N + F KMK GV IVN ARG V+DE+ALV
Sbjct: 197 ATYYVSLDELLAQSDVVSLNCPLTAATRHLINKKEFAKMKDGVIIVNTARGAVIDEDALV 256
Query: 294 RALDSGIISQAALDVFTEEPPAKDSKLVLHENVTVTPHLGASTTEAQ---EGVAIEIAEA 350
AL+SG ++ A LDVF EP + L+ NVT+ PH+G T E Q E + +E EA
Sbjct: 257 DALESGKVASAGLDVFENEPEV-NPGLLKMPNVTLLPHMGTLTVETQEKMEELVLENIEA 315
Query: 351 VI 352
+
Sbjct: 316 FL 317
>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 = 216 bits (553), Expect = 1e-65
Identities = 109/307 (35%), Positives = 153/307 (49%), Gaps = 14/307 (4%)
Query: 56 VLVAEKLGEAGLDVLKNFA-NVDCSYNLSPEELCTKISLCDALIVRSGTKVTREVFESSA 114
+L+ +K + ++L+ VD +S EE+ I D LI+RS + +E E A
Sbjct: 2 ILIIDKNHPSLTELLEALGFEVDYDPTISREEILAIIPQYDGLIIRSRFPIDKEFIEK-A 60
Query: 115 GRLKVVGRAGVGIDNVDLSAATEHGCLVVNAPTANTIAAAEHGIALLTAMARNIAQADAS 174
LK + RAG G++N+DL A E G + NAP N A EH + +L A+ + +AD
Sbjct: 61 TNLKFIARAGAGLENIDLEYAKEKGIELFNAPEGNRDAVGEHALGMLLALFNKLNRADQE 120
Query: 175 VKAGKWQRNKYVGVSLVGKTLAVMGFGKVGTEVARRAKGLGMNVIAHDPYAQADRARATG 234
V+ G W R GV L+GKT+ ++G+G +G A+R G G VIA+D Y A A
Sbjct: 121 VRNGIWDREGNRGVELMGKTVGIIGYGNMGKAFAKRLSGFGCKVIAYDKYKNFGDAYAEQ 180
Query: 235 VGLVSFEEAISTADFISLHMPLTPATSKMFNDEAFFKMKKGVRIVNVARGGVVDEEALVR 294
V L E AD +SLH+PLTP T M N E KK +N ARG VV + LV+
Sbjct: 181 VSL---ETLFKEADILSLHIPLTPETRGMVNKEFISSFKKPFYFINTARGKVVVTKDLVK 237
Query: 295 ALDSGIISQAALDVF---------TEEPPAKDSKLVLHENVTVTPHLGASTTEAQEGVAI 345
AL SG I A LDV P L+ V +TPH+ T E+ E +A
Sbjct: 238 ALKSGKILGACLDVLEYEKASFESIFNQPEAFEYLIKSPKVILTPHIAGWTFESYEKIAE 297
Query: 346 EIAEAVI 352
+ + +
Sbjct: 298 VLVDKIK 304
>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 = 210 bits (537), Expect = 5e-63
Identities = 98/257 (38%), Positives = 133/257 (51%), Gaps = 21/257 (8%)
Query: 103 TKVTREVFESSAGRLKVVGRAGVGIDNVDLSAATEHGCLVVNAPTANTIAAAEHGIALLT 162
+++ EV E RLK++ G D++DL A E G V N P AEH ALL
Sbjct: 51 SRLDAEVLEKLP-RLKLIATRSTGFDHIDLEACRERGIAVCNVPDYGEATVAEHAFALLL 109
Query: 163 AMARNIAQADASVKAGKWQRNKYVGVSLVGKTLAVMGFGKVGTEVARRAKGLGMNVIAHD 222
A++R + +A + G + + G L GKTL V+G G++G VAR A+G GM V+A+D
Sbjct: 110 ALSRKLREAIERTRRGDFSQAGLRGFELAGKTLGVVGTGRIGRRVARIARGFGMKVLAYD 169
Query: 223 PYAQADRARATGVGLVSFEEAISTADFISLHMPLTPATSKMFNDEAFFKMKKGVRIVNVA 282
+ A G VS EE + +D ISLH+P TP T + N E F MK G ++N A
Sbjct: 170 VVPDEELAERLGFRYVSLEELLQESDIISLHVPYTPQTHHLINRENFALMKPGAVLINTA 229
Query: 283 RGGVVDEEALVRALDSGIISQAALDVFTEEP-------------PAKDSKLVL------- 322
RG VVD EALVRAL G ++ A LDV +E +D K +L
Sbjct: 230 RGAVVDTEALVRALKEGKLAGAGLDVLEQEEVLREEAELFREDVSPEDLKKLLADHALLR 289
Query: 323 HENVTVTPHLGASTTEA 339
NV +TPH+ +T EA
Sbjct: 290 KPNVIITPHVAYNTKEA 306
>gnl|CDD|236985 PRK11790, PRK11790, D-3-phosphoglycerate dehydrogenase;
Provisional.
Length = 409
Score = 211 bits (540), Expect = 1e-62
Identities = 113/330 (34%), Positives = 175/330 (53%), Gaps = 20/330 (6%)
Query: 52 SKPTVLVAEKLGEAGLDVLKN--FANVDC-SYNLSPEELCTKISLCDALIVRSGTKVTRE 108
K L+ E + ++ ++VL+ + N++ L EEL I + +RS T++T E
Sbjct: 9 DKIKFLLLEGVHQSAVEVLRAAGYTNIEYHKGALDEEELIEAIKDAHFIGIRSRTQLTEE 68
Query: 109 VFESSAGRLKVVGRAGVGIDNVDLSAATEHGCLVVNAPTANTIAAAEHGIALLTAMARNI 168
V + A +L +G +G + VDL AA + G V NAP +NT + AE I + + R I
Sbjct: 69 VLAA-AEKLVAIGCFCIGTNQVDLDAAAKRGIPVFNAPFSNTRSVAELVIGEIILLLRGI 127
Query: 169 AQADASVKAGKWQRNKYVGVSLVGKTLAVMGFGKVGTEVARRAKGLGMNVIAHD-----P 223
+ +A G W ++ + GKTL ++G+G +GT+++ A+ LGM V +D P
Sbjct: 128 PEKNAKAHRGGWNKSAAGSFEVRGKTLGIVGYGHIGTQLSVLAESLGMRVYFYDIEDKLP 187
Query: 224 YAQADRARATGVGLVSFEEAISTADFISLHMPLTPATSKMFNDEAFFKMKKGVRIVNVAR 283
A + S EE ++ +D +SLH+P TP+T M E MK G ++N +R
Sbjct: 188 LGNARQVG-------SLEELLAQSDVVSLHVPETPSTKNMIGAEELALMKPGAILINASR 240
Query: 284 GGVVDEEALVRALDSGIISQAALDVFTEEPPAKD----SKLVLHENVTVTPHLGASTTEA 339
G VVD +AL AL SG ++ AA+DVF EP + S L +NV +TPH+G ST EA
Sbjct: 241 GTVVDIDALADALKSGHLAGAAIDVFPVEPKSNGDPFESPLRGLDNVILTPHIGGSTQEA 300
Query: 340 QEGVAIEIAEAVIGALKGELAATAVNAPMV 369
QE + +E+A ++ +AVN P V
Sbjct: 301 QENIGLEVAGKLVKYSDNGSTLSAVNFPEV 330
>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 = 205 bits (524), Expect = 2e-61
Identities = 106/319 (33%), Positives = 161/319 (50%), Gaps = 15/319 (4%)
Query: 53 KPTVLVAEKLGEAGLDVLKNFANVDCSYN---LSPEELCTKISLCDALIVRSGTKVTREV 109
KP V++ K+ L++LK V + LS EEL + D L+ ++ +
Sbjct: 1 KPKVVITHKVHPEVLELLKPHCEVISNQTDEPLSREELLRRCKDADGLMAFMPDRIDADF 60
Query: 110 FESSAGRLKVVGRAGVGIDNVDLSAATEHGCLVVNAPTANTIAAAEHGIALLTAMARNIA 169
++ RLK++ A G DN D+ A T G V P T AE I LL + R+I
Sbjct: 61 LDA-CPRLKIIACALKGYDNFDVEACTARGIWVTIVPDLLTEPTAELTIGLLIGLGRHIL 119
Query: 170 QADASVKAGKWQ--RNKYVGVSLVGKTLAVMGFGKVGTEVARRAKGLGMNVIAHDPYA-Q 226
D V++GK+ R K+ G L GKT+ ++G G +G +ARR G G ++ +DP+
Sbjct: 120 AGDRFVRSGKFGGWRPKFYGTGLDGKTVGILGMGALGRAIARRLSGFGATLLYYDPHPLD 179
Query: 227 ADRARATGVGLVSFEEAISTADFISLHMPLTPATSKMFNDEAFFKMKKGVRIVNVARGGV 286
+A + V +E + ++DF+ L +PLTP T + N EA KMK G +VN RG V
Sbjct: 180 QAEEQALNLRRVELDELLESSDFLVLALPLTPDTLHLINAEALAKMKPGALLVNPCRGSV 239
Query: 287 VDEEALVRALDSGIISQAALDVFTEEPPAKDSK--------LVLHENVTVTPHLGASTTE 338
VDE A+ AL SG + A DVF E A+ + L H+ TPH+G++ E
Sbjct: 240 VDEAAVAEALKSGHLGGYAADVFEMEDWARPDRPRSIPQELLDQHDRTVFTPHIGSAVDE 299
Query: 339 AQEGVAIEIAEAVIGALKG 357
+ + +E A ++ AL+G
Sbjct: 300 VRLEIELEAALNILQALQG 318
>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 = 204 bits (521), Expect = 9e-61
Identities = 93/262 (35%), Positives = 134/262 (51%), Gaps = 7/262 (2%)
Query: 82 LSPEELCTKISLCDALIVRSGT-KVTREVFESSAGRLKVVGRAGVGI-DNVDLSAATEHG 139
+ EEL ++ + L+ GT + E+ A RL+ V A + V A E G
Sbjct: 38 FAAEELRALLAGVEVLVTGWGTPPLDAELLAR-APRLRAVVHAAGSVRGLVTD-AVWERG 95
Query: 140 CLVVNAPTANTIAAAEHGIALLTAMARNIAQADASVKAGKWQ--RNKYVGVSLVGKTLAV 197
LV +A AN AE +A + R I + A+ +AG+ + G L G+T+ +
Sbjct: 96 ILVTSAADANAEPVAEFTLAAILLALRRIPRFAAAYRAGRDWGWPTRRGGRGLYGRTVGI 155
Query: 198 MGFGKVGTEVARRAKGLGMNVIAHDPYAQADRARATGVGLVSFEEAISTADFISLHMPLT 257
+GFG++G V + G+ V+ +DPY A A A GV LVS +E ++ +D +SLH PLT
Sbjct: 156 VGFGRIGRAVVELLRPFGLRVLVYDPYLPAAEAAALGVELVSLDELLARSDVVSLHAPLT 215
Query: 258 PATSKMFNDEAFFKMKKGVRIVNVARGGVVDEEALVRALDSGIISQAALDVFTEEPPAKD 317
P T M + M+ G +N ARG +VDE AL+ L SG + AALDV EP D
Sbjct: 216 PETRGMIDARLLALMRDGATFINTARGALVDEAALLAELRSGRLR-AALDVTDPEPLPPD 274
Query: 318 SKLVLHENVTVTPHLGASTTEA 339
S L NV +TPH+ ST +
Sbjct: 275 SPLRTLPNVLLTPHIAGSTGDE 296
>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 = 96/299 (32%), Positives = 142/299 (47%), Gaps = 20/299 (6%)
Query: 54 PTVLVAEKLGEAGLDVLKN-FANVDCSYNLSPEELCTKISLCDALIVRSGTKVTREVFES 112
+LV L + L+ L+ + ++ EEL +++ D L+ G E+ +
Sbjct: 1 MKILVLSPLDDEHLERLRAAAPGAELRV-VTAEELTEELADADVLL---GNPPLPELLPA 56
Query: 113 SAGRLKVVGRAGVGIDNVDLSAATEHGCLVVNAPTANTIAAAEHGIALLTAMARNIAQAD 172
A RL+ + G+D + E ++ NA AE+ + + A AR + +
Sbjct: 57 -APRLRWIQSTSAGVDALLFPELLERDVVLTNARGIFGPPIAEYVLGYMLAFARKLPRYA 115
Query: 173 ASVKAGKWQRNKYVGVSLVGKTLAVMGFGKVGTEVARRAKGLGMNVIA-------HDPYA 225
+ +WQR V L GKT+ ++G G +G E+ARRAK GM VI P
Sbjct: 116 RNQAERRWQRRGPVR-ELAGKTVLIVGLGDIGREIARRAKAFGMRVIGVRRSGRPAPPVV 174
Query: 226 QADRARATGVGLVSFEEAISTADFISLHMPLTPATSKMFNDEAFFKMKKGVRIVNVARGG 285
+E + AD++ +PLTP T +FN E F MK G ++NV RG
Sbjct: 175 DEVYTPD------ELDELLPEADYVVNALPLTPETRGLFNAERFAAMKPGAVLINVGRGS 228
Query: 286 VVDEEALVRALDSGIISQAALDVFTEEPPAKDSKLVLHENVTVTPHLGASTTEAQEGVA 344
VVDE+AL+ AL+SG I+ AALDVF EEP DS L NV +TPH+ + E V
Sbjct: 229 VVDEDALIEALESGRIAGAALDVFEEEPLPADSPLWDLPNVIITPHISGDSPSYPERVV 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 = 191 bits (488), Expect = 7e-56
Identities = 102/277 (36%), Positives = 142/277 (51%), Gaps = 19/277 (6%)
Query: 94 CDALIVRSGTKVTREVFES-SAGRLKVVGRAGVGIDNVDLSAATEHGCLVVNAPTANTIA 152
DA+ V + V E + +K++ G +NVDL AA E G VV P + A
Sbjct: 45 FDAVCVFVNDDLDAPVLEKLAELGVKLIALRCAGFNNVDLKAAKELGITVVRVPAYSPYA 104
Query: 153 AAEHGIALLTAMARNIAQADASVKAGKWQRNKYVGVSLVGKTLAVMGFGKVGTEVARRAK 212
AEH +ALL A+ R I +A V+ G + + +G L GKT+ V+G GK+G AR K
Sbjct: 105 VAEHAVALLLALNRKIHRAYNRVREGNFSLDGLLGFDLHGKTVGVIGTGKIGQAFARILK 164
Query: 213 GLGMNVIAHDPYAQADRARATGVGLVSFEEAISTADFISLHMPLTPATSKMFNDEAFFKM 272
G G V+A+DPY + GV V +E ++ +D ISLH PLTP T + N E KM
Sbjct: 165 GFGCRVLAYDPYPNPE-LAKLGVEYVDLDELLAESDIISLHCPLTPETHHLINAETIAKM 223
Query: 273 KKGVRIVNVARGGVVDEEALVRALDSGIISQAALDVFTEEPPA--KD-----------SK 319
K GV ++N +RGG++D +AL+ AL SG I LDV+ EE +D ++
Sbjct: 224 KDGVMLINTSRGGLIDTKALIEALKSGKIGGLGLDVYEEEAGLFFEDHSDEIIQDDVLAR 283
Query: 320 LVLHENVTVTPHLGASTTEAQEGVAIEIAEAVIGALK 356
L+ NV +T H T EA IAE + L
Sbjct: 284 LLSFPNVLITGHQAFFTKEALT----NIAETTLENLD 316
>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 = 190 bits (485), Expect = 1e-55
Identities = 96/259 (37%), Positives = 140/259 (54%), Gaps = 5/259 (1%)
Query: 84 PEELCTKISLCDALIVRSGTKVTREVFESSAGRLKVVGRAGVGIDNVDLSAATEHGCLVV 143
EL + D +++ + + EV E+ LK++ A G+D+VDL A E G V
Sbjct: 39 TAELIERSKDADIVMI-ANMPLPGEVIEA-CKNLKMISVAFTGVDHVDLEACKERGITVS 96
Query: 144 NAPTANTIAAAEHGIALLTAMARNIAQADASVKAGKWQRNKYVGVSLVGKTLAVMGFGKV 203
NA +T A AE I L + RNI DA+V+AG + +G L GKT+ ++G G +
Sbjct: 97 NAAGYSTEAVAELTIGLAIDLLRNIVPCDAAVRAGG-TKAGLIGRELAGKTVGIVGTGAI 155
Query: 204 GTEVARRAKGLGMNVIAHDPYAQADRARATGVGLVSFEEAISTADFISLHMPLTPATSKM 263
G VAR K G V+A+ + + A+A G+ VS +E ++ +D +SLH+PL T +
Sbjct: 156 GLRVARLFKAFGCKVLAYSRS-EKEEAKALGIEYVSLDELLAESDIVSLHLPLNDETKGL 214
Query: 264 FNDEAFFKMKKGVRIVNVARGGVVDEEALVRALDSGIISQAALDVFTEEPP-AKDSKLVL 322
E MK+ ++N ARG VVD EAL AL+ G I+ A +DVF EPP D L+
Sbjct: 215 IGKEKLALMKESAILINTARGPVVDNEALADALNEGKIAGAGIDVFDMEPPLPADYPLLH 274
Query: 323 HENVTVTPHLGASTTEAQE 341
N +TPH+ +T EA E
Sbjct: 275 APNTILTPHVAFATEEAME 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 = 189 bits (483), Expect = 3e-55
Identities = 87/265 (32%), Positives = 130/265 (49%), Gaps = 24/265 (9%)
Query: 94 CDALIVRSGTKVTREVFES-SAGRLKVVGRAGVGIDNVDLSAATEHGCLVVNAPTANTIA 152
D ++V+ EV+E + +K + G+D +DL A E+G + N P + A
Sbjct: 45 YDGVVVQQTLPYDEEVYEKLAEYGIKQIALRSAGVDMIDLDLAKENGLKITNVPAYSPRA 104
Query: 153 AAEHGIALLTAMARNIAQADASVKAGKWQRNKYVGVSLVGK-----TLAVMGFGKVGTEV 207
AE + + RN + D V G ++ L+G+ T+ ++G G++G+
Sbjct: 105 IAEFAVTQALNLLRNTPEIDRRVAKGDFRWAP----GLIGREIRDLTVGIIGTGRIGSAA 160
Query: 208 ARRAKGLGMNVIAHDPYAQADRARATGVGLVSFEEAISTADFISLHMPLTPATSKMFNDE 267
A+ KG G VIA+DPY + + S E+ + AD ISLH+PLT + N E
Sbjct: 161 AKIFKGFGAKVIAYDPYPNPE-LEKFLLYYDSLEDLLKQADIISLHVPLTKENHHLINAE 219
Query: 268 AFFKMKKGVRIVNVARGGVVDEEALVRALDSGIISQAALDVFTEE-------------PP 314
AF KMK G +VN ARGG+VD +AL+ ALDSG I+ AALD + E
Sbjct: 220 AFAKMKDGAILVNAARGGLVDTKALIDALDSGKIAGAALDTYENETGYFNKDWSGKEIED 279
Query: 315 AKDSKLVLHENVTVTPHLGASTTEA 339
+L+ NV +TPH+ T A
Sbjct: 280 EVLKELIAMPNVLITPHIAFYTDTA 304
>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 = 175 bits (445), Expect = 6e-50
Identities = 87/253 (34%), Positives = 123/253 (48%), Gaps = 13/253 (5%)
Query: 116 RLKVVGRAGVGIDNVDLSAATEHGCLVVNAPTA-NTIAAAEHGIALLTAMARNIAQADAS 174
RLK++ G+D++ L E VV A N+ A AEH +AL+ A+A+ I + D
Sbjct: 60 RLKLIQVPSAGVDHLPLERLPEG---VVVANNHGNSPAVAEHALALILALAKRIVEYDND 116
Query: 175 VKAGKWQR---NKYVGVSLVGKTLAVMGFGKVGTEVARRAKGLGMNVIAHDPYAQADRAR 231
++ G W + L GKT+ ++G+G +G E+AR K GM VI + D
Sbjct: 117 LRRGIWHGRAGEEPESKELRGKTVGILGYGHIGREIARLLKAFGMRVIGVSRSPKEDEGA 176
Query: 232 ATGVGLVSFEEAISTADFISLHMPLTPATSKMFNDEAFFKMKKGVRIVNVARGGVVDEEA 291
L +EA+ AD + + +PLT T + MK G +VNV RG VVDEEA
Sbjct: 177 DFVGTLSDLDEALEQADVVVVALPLTKQTRGLIGAAELAAMKPGAILVNVGRGPVVDEEA 236
Query: 292 LVRALDSGIISQAALDVFTEEPPAKD----SKLVLHE--NVTVTPHLGASTTEAQEGVAI 345
L AL I+ AA+DV+ P D S+ HE NV ++PH T E
Sbjct: 237 LYEALKERPIAGAAIDVWWRYPSRGDPVAPSRYPFHELPNVIMSPHNAGWTEETFRRRID 296
Query: 346 EIAEAVIGALKGE 358
E AE + L+GE
Sbjct: 297 EAAENIRRYLRGE 309
>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 = 165/325 (50%), Gaps = 19/325 (5%)
Query: 53 KPTVLVAEKLGEAGLDVLKNFANVDCSYNLSPEELCTKISLCDAL-----IVRSGTKVTR 107
KP+V++ + L + L L+ V NLSPE T A ++ SG KV
Sbjct: 2 KPSVILYKALPDDLLQRLEEHFTVTQVANLSPE---TVEQHAAAFAEAEGLLGSGEKVDA 58
Query: 108 EVFESSAGRLKVVGRAGVGIDNVDLSAATEHGCLVVNAPTANTIAAAEHGIALLTAMARN 167
+ E +L+ VG DN D+ A T L+++ PT T A+ +AL+ + AR
Sbjct: 59 ALLEK-MPKLRAASTISVGYDNFDVDALTARKILLMHTPTVLTETVADTLMALVLSTARR 117
Query: 168 IAQADASVKAGKWQRN---KYVGVSLVGKTLAVMGFGKVGTEVARRAK-GLGMNVI--AH 221
+ + VKAG+W + + G + KTL ++G G++G +A+RA G M ++ A
Sbjct: 118 VVEVAERVKAGEWTASIGPDWFGTDVHHKTLGIVGMGRIGMALAQRAHFGFNMPILYNAR 177
Query: 222 DPYAQAD-RARATGVGLVSFEEAISTADFISLHMPLTPATSKMFNDEAFFKMKKGVRIVN 280
+ +A+ R A L + + +DF+ + +PLT T +F E F KMK +N
Sbjct: 178 RHHKEAEERFNARYCDL---DTLLQESDFVCIILPLTDETHHLFGAEQFAKMKSSAIFIN 234
Query: 281 VARGGVVDEEALVRALDSGIISQAALDVFTEEPPAKDSKLVLHENVTVTPHLGASTTEAQ 340
RG VVDE AL+ AL G I A LDVF +EP + DS L+ NV PH+G++T E +
Sbjct: 235 AGRGPVVDENALIAALQKGEIHAAGLDVFEQEPLSVDSPLLSLPNVVAVPHIGSATHETR 294
Query: 341 EGVAIEIAEAVIGALKGELAATAVN 365
+A + +I AL+G++ VN
Sbjct: 295 YNMAACAVDNLIDALQGKVEKNCVN 319
>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 = 172 bits (438), Expect = 5e-49
Identities = 81/246 (32%), Positives = 125/246 (50%), Gaps = 8/246 (3%)
Query: 96 ALIVRSGTKVTREVFESSAGRLKVVGRAGVGIDNVDLSAATEHGCLVVNAPTANTIAAAE 155
A++ T ++ + + L+++ GVG D +DL AA G V N P T A+
Sbjct: 45 AVVTNGETGLSAALIAA-LPALELIASFGVGYDGIDLDAARARGIRVTNTPGVLTDDVAD 103
Query: 156 HGIALLTAMARNIAQADASVKAGKWQRNKY-VGVSLVGKTLAVMGFGKVGTEVARRAKGL 214
+ LL A+ R I AD V+AG+W + + + + GK + ++G G++G +ARR +
Sbjct: 104 LAVGLLLAVLRRIPAADRFVRAGRWPKGAFPLTRKVSGKRVGIVGLGRIGRAIARRLEAF 163
Query: 215 GMNVIAHDPYAQADRARATGVGLVSFEEAISTADFISLHMPLTPATSKMFNDEAFFKM-K 273
GM + H + D L+ +D + + P PAT + N E +
Sbjct: 164 GMEIAYHGRRPKPDVPYRYYASLLELAAE---SDVLVVACPGGPATRHLVNAEVLEALGP 220
Query: 274 KGVRIVNVARGGVVDEEALVRALDSGIISQAALDVFTEEPPAKDSKLVLHENVTVTPHLG 333
GV +VNVARG VVDE AL+ AL G I+ A LDVF E P + L+ +NV +TPH+
Sbjct: 221 DGV-LVNVARGSVVDEAALIAALQEGRIAGAGLDVFENE-PNVPAALLDLDNVVLTPHIA 278
Query: 334 ASTTEA 339
++T E
Sbjct: 279 SATVET 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 = 170 bits (434), Expect = 2e-48
Identities = 78/248 (31%), Positives = 118/248 (47%), Gaps = 23/248 (9%)
Query: 95 DALIVRSGTKVTREVFESSAGRLKVVGRAGVGIDNVDLSAATEHGCLVVNAPTANTIAAA 154
D I+ E+ + LK + G+D + L + G L+ N ++I A
Sbjct: 39 DIEILYGYNPDFDELDLAKMKNLKWIQLYSAGVDYLPLEYIKKKGILLTNNSGIHSIPIA 98
Query: 155 EHGIALLTAMARNIAQADASVKAGKWQRNKYVGVSLVGKTLAVMGFGKVGTEVARRAKGL 214
E + + + + + +A + K KW+ + + L GKT+ +G G +G E+A+R K
Sbjct: 99 EWIVGYILEIYKGLKKAYKNQKEKKWKMDS-SLLELYGKTILFLGTGSIGQEIAKRLKAF 157
Query: 215 GMNVIA-----HDP------YAQADRARATGVGLVSFEEAISTADFISLHMPLTPATSKM 263
GM VI D Y + +E + AD + +PLT T +
Sbjct: 158 GMKVIGVNTSGRDVEYFDKCYPLEEL-----------DEVLKEADIVVNVLPLTEETHHL 206
Query: 264 FNDEAFFKMKKGVRIVNVARGGVVDEEALVRALDSGIISQAALDVFTEEPPAKDSKLVLH 323
F++ F +MKKG +NV RG VDE+AL+ AL + I AALDVF EEP KDS L
Sbjct: 207 FDEAFFEQMKKGALFINVGRGPSVDEDALIEALKNKQIRGAALDVFEEEPLPKDSPLWDL 266
Query: 324 ENVTVTPH 331
+NV +TPH
Sbjct: 267 DNVLITPH 274
>gnl|CDD|180588 PRK06487, PRK06487, glycerate dehydrogenase; Provisional.
Length = 317
Score = 167 bits (424), Expect = 5e-47
Identities = 89/256 (34%), Positives = 132/256 (51%), Gaps = 15/256 (5%)
Query: 112 SSAGRLKVVGRAGVGIDNVDLSAATEHGCLVVNAPTANTIAAAEHGIALLTAMARNIAQA 171
++A +LK++ A G +NVDL+AA E G V N T + A+H +ALL A+A +
Sbjct: 62 AAAPQLKLILVAATGTNNVDLAAARERGITVCNCQGYGTPSVAQHTLALLLALATRLPDY 121
Query: 172 DASVKAGKWQRNKYVG------VSLVGKTLAVMGFGKVGTEVARRAKGLGMNV-IAHDPY 224
+V AG+WQ++ V L GKTL ++G G++G VAR A+ GM V I P
Sbjct: 122 QQAVAAGRWQQSSQFCLLDFPIVELEGKTLGLLGHGELGGAVARLAEAFGMRVLIGQLP- 180
Query: 225 AQADRARATGVGLVSFEEAISTADFISLHMPLTPATSKMFNDEAFFKMKKGVRIVNVARG 284
R + +E + D ++LH PLT T + MK G ++N ARG
Sbjct: 181 -----GRPARPDRLPLDELLPQVDALTLHCPLTEHTRHLIGARELALMKPGALLINTARG 235
Query: 285 GVVDEEALVRALDSGIISQAALDVFTEEPPAKDSKLVL--HENVTVTPHLGASTTEAQEG 342
G+VDE+AL AL SG + AA DV + EPP + L+ + VTPH + EA++
Sbjct: 236 GLVDEQALADALRSGHLGGAATDVLSVEPPVNGNPLLAPDIPRLIVTPHSAWGSREARQR 295
Query: 343 VAIEIAEAVIGALKGE 358
+ ++AE G+
Sbjct: 296 IVGQLAENARAFFAGK 311
>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 = 166 bits (424), Expect = 1e-46
Identities = 85/242 (35%), Positives = 124/242 (51%), Gaps = 31/242 (12%)
Query: 95 DALIVRSGTKVTREVFESSAGRLKVVGRAGVGIDNVDLSAATEHGCLVVNAPTANTIAAA 154
D L+VRS TKV + E S ++K VG A +G D++D E G NAP N + A
Sbjct: 38 DVLLVRSVTKVNEALLEGS--KVKFVGTATIGTDHIDTDYLKERGIGFANAPGCNANSVA 95
Query: 155 EHGIALLTAMARNIAQADASVKAGKWQRNKYVGVSLVGKTLAVMGFGKVGTEVARRAKGL 214
E+ ++ L +A QR G SL GKT+ ++G G VG+ +ARR + L
Sbjct: 96 EYVLSALLVLA---------------QRQ---GFSLKGKTVGIVGVGNVGSRLARRLEAL 137
Query: 215 GMNVIAHDPYAQADRARATGVGLVSFEEAISTADFISLHMPLTP----ATSKMFNDEAFF 270
GMNV+ DP G VS EE ++ AD I+LH+PLT T + +++
Sbjct: 138 GMNVLLCDPPRAE---AEGDPGFVSLEELLAEADIITLHVPLTRDGEHPTYHLLDEDFLA 194
Query: 271 KMKKGVRIVNVARGGVVDEEALVRALDSGIISQAALDVFTEEPPAKDSKLVLHENVT-VT 329
+K G ++N +RG V+D +AL+ L G + LDV+ EP D +L+ + V T
Sbjct: 195 ALKPGQILINASRGAVIDNQALLALLQRGKDLRVVLDVWENEPEI-DLELL--DKVDIAT 251
Query: 330 PH 331
PH
Sbjct: 252 PH 253
>gnl|CDD|181414 PRK08410, PRK08410, 2-hydroxyacid dehydrogenase; Provisional.
Length = 311
Score = 165 bits (419), Expect = 2e-46
Identities = 95/320 (29%), Positives = 160/320 (50%), Gaps = 25/320 (7%)
Query: 53 KPTVLVAEKLGEAGLDVLKNFANVDCSYNL-SPEELCTKISLCDA-LIVRSGTKVTREVF 110
K +L A+ LG+ L V + F + Y SPEE+ +I DA +I+ + + +EV
Sbjct: 2 KIVILDAKTLGDKDLSVFEEFGDFQ-IYPTTSPEEVIERIK--DANIIITNKVVIDKEVL 58
Query: 111 ESSAGRLKVVGRAGVGIDNVDLSAATEHGCLVVNAPTANTIAAAEHGIALLTAMARNIAQ 170
S LK++ G +NVD+ A + G V N +T + A+H A+L ++ I
Sbjct: 59 -SQLPNLKLICITATGTNNVDIEYAKKKGIAVKNVAGYSTESVAQHTFAMLLSLLGRINY 117
Query: 171 ADASVKAGKWQRNK-YVGVS-----LVGKTLAVMGFGKVGTEVARRAKGLGMNVIAHDPY 224
D VK+G++ + + +S + GK ++G G +G VA+ A+ G V+ +
Sbjct: 118 YDRYVKSGEYSESPIFTHISRPLGEIKGKKWGIIGLGTIGKRVAKIAQAFGAKVVYYSTS 177
Query: 225 A---QADRARATGVGLVSFEEAISTADFISLHMPLTPATSKMFNDEAFFKMKKGVRIVNV 281
+ R VS EE + T+D IS+H PL T + + +K G ++NV
Sbjct: 178 GKNKNEEYER------VSLEELLKTSDIISIHAPLNEKTKNLIAYKELKLLKDGAILINV 231
Query: 282 ARGGVVDEEALVRALDSGIISQAALDVFTEEPPAKDSKLV---LHENVTVTPHLGASTTE 338
RGG+V+E+ L +ALD I A LDV +EP K+ L+ E + +TPH+ ++ E
Sbjct: 232 GRGGIVNEKDLAKALDEKDIY-AGLDVLEKEPMEKNHPLLSIKNKEKLLITPHIAWASKE 290
Query: 339 AQEGVAIEIAEAVIGALKGE 358
A++ + ++ E + L+G
Sbjct: 291 ARKTLIEKVKENIKDFLEGG 310
>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 (415), Expect = 3e-45
Identities = 79/247 (31%), Positives = 124/247 (50%), Gaps = 11/247 (4%)
Query: 105 VTREVFESSAGRLKVVGRAGVGIDNVDLSAATEHGCLVVNAPTANTIAAAEHGIALLTAM 164
+T E A LK+ AG+G D+VDL AA + G V +N ++ AEH + ++ +
Sbjct: 74 MTAERIAK-AKNLKLALTAGIGSDHVDLQAANDRGITVAEVTGSNVVSVAEHVVMMILIL 132
Query: 165 ARNIAQADASVKAGKWQ-----RNKYVGVSLVGKTLAVMGFGKVGTEVARRAKGLGMNVI 219
RN G W + Y L GKT+ +G G++G V RR K ++++
Sbjct: 133 VRNYVPGHEQAIEGGWNVADVVKRAY---DLEGKTVGTVGAGRIGLRVLRRLKPFDVHLL 189
Query: 220 AHDPYAQ-ADRARATGVGLV-SFEEAISTADFISLHMPLTPATSKMFNDEAFFKMKKGVR 277
+D + + + G+ E+ +S D ++++ PL P T +FN E KMKKG
Sbjct: 190 YYDRHRLPEEVEKELGLTRHADLEDMVSKCDVVTINCPLHPETEGLFNKELLSKMKKGAY 249
Query: 278 IVNVARGGVVDEEALVRALDSGIISQAALDVFTEEPPAKDSKLVLHENVTVTPHLGASTT 337
+VN ARG + D EA+ AL+SG ++ A DV+ +P KD N +TPH+ +T
Sbjct: 250 LVNTARGKICDREAVAEALESGHLAGYAGDVWFPQPAPKDHPWRTMPNNAMTPHISGTTL 309
Query: 338 EAQEGVA 344
+AQ A
Sbjct: 310 DAQARYA 316
>gnl|CDD|181041 PRK07574, PRK07574, formate dehydrogenase; Provisional.
Length = 385
Score = 161 bits (409), Expect = 4e-44
Identities = 98/302 (32%), Positives = 149/302 (49%), Gaps = 13/302 (4%)
Query: 50 ITSKPTVLVAEKLGEAGL-DVLKNFAN--VDCSYNLSPEELCTKISLCDALIVRSG---- 102
I P L+ GE GL L+ + V S P+ K L DA +V S
Sbjct: 43 IDFTPGELLGSVSGELGLRKFLEERGHELVVTSDKDGPDSDFEK-ELPDADVVISQPFWP 101
Query: 103 TKVTREVFESSAGRLKVVGRAGVGIDNVDLSAATEHGCLVVNAPTANTIAAAEHGIALLT 162
+T E A LK+ AG+G D+VDL AA+EHG V +N+I+ AEH + ++
Sbjct: 102 AYLTAERIAK-APNLKLAITAGIGSDHVDLQAASEHGITVAEVTGSNSISVAEHVVMMIL 160
Query: 163 AMARNIAQADASVKAGKWQRNKYVGVS--LVGKTLAVMGFGKVGTEVARRAKGLGMNVIA 220
A+ RN + G W V S L G T+ ++G G++G V RR K + +
Sbjct: 161 ALVRNYEPSHRQAVEGGWNIADCVSRSYDLEGMTVGIVGAGRIGLAVLRRLKPFDVKLHY 220
Query: 221 HDPY-AQADRARATGVGL-VSFEEAISTADFISLHMPLTPATSKMFNDEAFFKMKKGVRI 278
D + + + G+ VSF+ +S D +++H PL P T +F+ + +MK+G +
Sbjct: 221 TDRHRLPEEVEQELGLTYHVSFDSLVSVCDVVTIHCPLHPETEHLFDADVLSRMKRGSYL 280
Query: 279 VNVARGGVVDEEALVRALDSGIISQAALDVFTEEPPAKDSKLVLHENVTVTPHLGASTTE 338
VN ARG +VD +A+VRAL+SG ++ A DV+ +P D +TPH+ +T
Sbjct: 281 VNTARGKIVDRDAVVRALESGHLAGYAGDVWFPQPAPADHPWRTMPRNGMTPHISGTTLS 340
Query: 339 AQ 340
AQ
Sbjct: 341 AQ 342
>gnl|CDD|235890 PRK06932, PRK06932, glycerate dehydrogenase; Provisional.
Length = 314
Score = 159 bits (403), Expect = 5e-44
Identities = 88/260 (33%), Positives = 131/260 (50%), Gaps = 16/260 (6%)
Query: 83 SPEELCTKISLCDALIVRSGTKVTREVFESSAGRLKVVGRAGVGIDNVDLSAATEHGCLV 142
S E+ + D +++ S TRE + +LK++ G +NVDL AA E G V
Sbjct: 34 SAEQTIERAKDAD-IVITSKVLFTRETL-AQLPKLKLIAITATGTNNVDLVAAKELGIAV 91
Query: 143 VNAPTANTIAAAEHGIALLTAMARNIAQADASVKAGKWQRNK------YVGVSLVGKTLA 196
N ++ EH + ++ A+ ++ + +W K Y + G TL
Sbjct: 92 KNVTGYSSTTVPEHVLGMIFALKHSLMGWYRDQLSDRWATCKQFCYFDYPITDVRGSTLG 151
Query: 197 VMGFGKVGTEVARRAKGLGMNVIAHDPYAQADRARATGVGLVSFEEAISTADFISLHMPL 256
V G G +GTEV R A+ LGM V+ YA+ A G FEE + AD ++LH PL
Sbjct: 152 VFGKGCLGTEVGRLAQALGMKVL----YAEHKGASVCREGYTPFEEVLKQADIVTLHCPL 207
Query: 257 TPATSKMFNDEAFFKMKKGVRIVNVARGGVVDEEALVRALDSGIISQAALDVFTEEPPAK 316
T T + N E MK ++N RG +VDE+AL+ AL++G I+ AALDV +EPP K
Sbjct: 208 TETTQNLINAETLALMKPTAFLINTGRGPLVDEQALLDALENGKIAGAALDVLVKEPPEK 267
Query: 317 DSKLVLHE----NVTVTPHL 332
D+ L+ N+ +TPH+
Sbjct: 268 DNPLIQAAKRLPNLLITPHI 287
>gnl|CDD|215501 PLN02928, PLN02928, oxidoreductase family protein.
Length = 347
Score = 150 bits (380), Expect = 2e-40
Identities = 82/278 (29%), Positives = 139/278 (50%), Gaps = 24/278 (8%)
Query: 76 VDCSYNLSPEELCTKISLCDALIVRSGTKVTREVFESSAGRLKVVGRAGVGIDNVDLSAA 135
+ P+ I+ D + + ++ ++ + A ++K++ + GVG++ VD+ AA
Sbjct: 48 DAVAREDVPDV----IANYDICVPKM-MRLDADII-ARASQMKLIMQFGVGLEGVDVDAA 101
Query: 136 TEHGCLVVNAP---TANTIAAAEHGIALLTAMARNIAQADASVKAGKWQRNKYVGVSLVG 192
T+HG V P T N + AE I L+ + R + S+KA + + +G +L G
Sbjct: 102 TKHGIKVARIPSEGTGNAASCAEMAIYLMLGLLRKQNEMQISLKARRL--GEPIGDTLFG 159
Query: 193 KTLAVMGFGKVGTEVARRAKGLGMNVIA------HDPYAQADRARATGVGLV-------S 239
KT+ ++G+G +G E+A+R + G+ ++A +P LV
Sbjct: 160 KTVFILGYGAIGIELAKRLRPFGVKLLATRRSWTSEPEDGLLIPNGDVDDLVDEKGGHED 219
Query: 240 FEEAISTADFISLHMPLTPATSKMFNDEAFFKMKKGVRIVNVARGGVVDEEALVRALDSG 299
E AD + L LT T+ + NDE MKKG +VN+ARGG++D +A++ AL+SG
Sbjct: 220 IYEFAGEADIVVLCCTLTKETAGIVNDEFLSSMKKGALLVNIARGGLLDYDAVLAALESG 279
Query: 300 IISQAALDVFTEEPPAKDSKLVLHENVTVTPHLGASTT 337
+ A+DV EP D ++ H NV +TPH+ T
Sbjct: 280 HLGGLAIDVAWSEPFDPDDPILKHPNVIITPHVAGVTE 317
>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 = 148 bits (375), Expect = 5e-40
Identities = 78/260 (30%), Positives = 120/260 (46%), Gaps = 17/260 (6%)
Query: 94 CDALIVRSGTKVTREVFES-SAGRLKVVGRAGVGIDNVDLSAATEHGCLVVNAPTANTIA 152
D + + +K++ E+ E +K + +G D++DL AA E G V N + +
Sbjct: 45 YDGISILGKSKISAELLEKLKEAGVKYISTRSIGYDHIDLDAAKELGIKVSNVTYSPN-S 103
Query: 153 AAEHGIALLTAMARNIAQADASVKAGKWQRNKYVGVSLVGKTLAVMGFGKVGTEVARRAK 212
A++ + L+ R Q + + G L T+ V+G G++G V +
Sbjct: 104 VADYTVMLMLMALRKYKQIMKRAEVNDYSLGGLQGRELRNLTVGVIGTGRIGQAVIKNLS 163
Query: 213 GLGMNVIAHDPYAQADRARATGVGLVSFEEAISTADFISLHMPLTPATSKMFNDEAFFKM 272
G G ++A+DPY + + V + +D I+LH PLT T + N E+ KM
Sbjct: 164 GFGCKILAYDPYPNEEVKK--YAEYVDLDTLYKESDIITLHTPLTEETYHLINKESIAKM 221
Query: 273 KKGVRIVNVARGGVVDEEALVRALDSGIISQAALDVFTEE-----PPAKDSKLVLHE--- 324
K GV I+N ARG ++D EAL+ L+SG I AALDV E K L E
Sbjct: 222 KDGVIIINTARGELIDTEALIEGLESGKIGGAALDVIEGEDGIYYNDRKGDILSNRELAI 281
Query: 325 -----NVTVTPHLGASTTEA 339
NV +TPH+ T +A
Sbjct: 282 LRSFPNVILTPHMAFYTDQA 301
>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 = 137 bits (348), Expect = 2e-36
Identities = 72/245 (29%), Positives = 115/245 (46%), Gaps = 22/245 (8%)
Query: 116 RLKVVGRAGVGIDNVDLSAATEHGCLV--VNAPTANTIAAAEHGIALLTAMARNIAQADA 173
LK + G G+D++ +V V+ A +A E+ +A + + R++ + A
Sbjct: 58 NLKAIFSLGAGVDHLLADPDLPDVPIVRLVDPGLAQGMA--EYVLAAVLRLHRDMDRYAA 115
Query: 174 SVKAGKWQRNKYVGVSLVGKTLAVMGFGKVGTEVARRAKGLGMNVIAHDPYAQADRARAT 233
+ G W+ + + V+G G++G VARR LG V R+
Sbjct: 116 QQRRGVWKPLPQRPAAER--RVGVLGLGELGAAVARRLAALGFPVSGWS------RSPKD 167
Query: 234 GVGLVSF------EEAISTADF-ISLHMPLTPATSKMFNDEAFFKMKKGVRIVNVARGGV 286
G+ F + ++ D + L +PLTP T + N E ++ +G ++NV RG
Sbjct: 168 IEGVTCFHGEEGLDAFLAQTDILVCL-LPLTPETRGILNAELLARLPRGAALINVGRGPH 226
Query: 287 VDEEALVRALDSGIISQAALDVFTEEPPAKDSKLVLHENVTVTPHLGASTTEAQEGVAIE 346
+ E L+ ALDSG +S A LDVF +EP D L H VTVTPH+ A+ T+ A
Sbjct: 227 LVEADLLAALDSGHLSGAVLDVFEQEPLPADHPLWRHPRVTVTPHI-AAITDPDSAAAQ- 284
Query: 347 IAEAV 351
+AE +
Sbjct: 285 VAENI 289
>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 = 137 bits (347), Expect = 5e-36
Identities = 82/263 (31%), Positives = 129/263 (49%), Gaps = 19/263 (7%)
Query: 94 CDALIVRSGTKVTREVFESSAGR-LKVVGRAGVGIDNVDLSAATEHGCLVVNAPTANTIA 152
DA+IVR +E E +K V VG +++DL AA E G + P+ + A
Sbjct: 45 HDAVIVRGNCFADKENLEIYKEYGIKYVFTRTVGFNHIDLEAAKELGFKMARVPSYSPNA 104
Query: 153 AAEHGIALLTAMARNIAQADASVKAGKWQRNKYV-GVSLVGKTLAVMGFGKVGTEVARRA 211
AE L ++R+ A + ++ + ++ + T+ ++G G++G A+
Sbjct: 105 IAELAFTLAMTLSRHTAYTASRTANKNFKVDPFMFSKEIRNSTVGIIGTGRIGLTAAKLF 164
Query: 212 KGLGMNVIAHDPYAQADRARATGVGLVSFEEAISTADFISLHMPLTPATS-KMFNDEAFF 270
KGLG VI +D Y +D A+ V VS +E + +D ISLH+P + K+ N E
Sbjct: 165 KGLGAKVIGYDIY-PSDAAKDV-VTFVSLDELLKKSDIISLHVPYIKGKNDKLINKEFIS 222
Query: 271 KMKKGVRIVNVARGGVVDEEALVRALDSGIISQAALDVFTEEP--------------PAK 316
KMK G ++N ARG + DEEA++ AL+SG ++ DV E P
Sbjct: 223 KMKDGAILINTARGELQDEEAILEALESGKLAGFGTDVLNNEKEIFFKDFDGDKIEDPVV 282
Query: 317 DSKLVLHENVTVTPHLGASTTEA 339
+ L L+ V +TPH+G+ T EA
Sbjct: 283 EKLLDLYPRVLLTPHIGSYTDEA 305
>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 = 136 bits (345), Expect = 6e-36
Identities = 85/240 (35%), Positives = 122/240 (50%), Gaps = 16/240 (6%)
Query: 115 GRLKVVGRAGVGIDNV--DLSAATEHGCLVVNAPTANTIAAAEHGIALLTAMARNIAQAD 172
GRL+ V GID L G +V A A AE +A + A A+ + +
Sbjct: 63 GRLRWVQLVSSGIDYYPDWLFE----GPVVTCARGVAAEAIAEFVLAAILAAAKRLP--E 116
Query: 173 ASVK-AGKWQRNKYVGVSLVGKTLAVMGFGKVGTEVARRAKGLGMNVIAHDPYAQADRAR 231
VK A +W+R SL G TL ++GFG +G +ARRA LGM V+A ++ R
Sbjct: 117 IWVKGAEQWRREP--LGSLAGSTLGIVGFGAIGQALARRALALGMRVLA---LRRSGRPS 171
Query: 232 -ATGVGLVS-FEEAISTADFISLHMPLTPATSKMFNDEAFFKMKKGVRIVNVARGGVVDE 289
GV + E + +D + L PLTP T + N + + K G+ ++N+ARGG+VD+
Sbjct: 172 DVPGVEAAADLAELFARSDHLVLAAPLTPETRHLINADVLAQAKPGLHLINIARGGLVDQ 231
Query: 290 EALVRALDSGIISQAALDVFTEEPPAKDSKLVLHENVTVTPHLGASTTEAQEGVAIEIAE 349
EAL+ ALDSG IS A+LDV EP + L H V ++PH A + + +A E
Sbjct: 232 EALLEALDSGRISLASLDVTDPEPLPEGHPLYTHPRVRLSPHTSAIAPDGRRNLADRFLE 291
>gnl|CDD|166874 PRK00257, PRK00257, erythronate-4-phosphate dehydrogenase;
Validated.
Length = 381
Score = 137 bits (348), Expect = 8e-36
Identities = 85/245 (34%), Positives = 115/245 (46%), Gaps = 35/245 (14%)
Query: 95 DALIVRSGTKVTREVFESSAGRLKVVGRAGVGIDNVDLSAATEHGCLVVNAPTANTIAAA 154
D L+VRS T+V R + E S R++ VG +G D++DL E G +AP N
Sbjct: 39 DVLLVRSVTRVDRALLEGS--RVRFVGTCTIGTDHLDLDYFAEAGITWSSAPGCNARGVV 96
Query: 155 EHGIALLTAMARNIAQADASVKAGKWQRNKYVGVSLVGKTLAVMGFGKVGTEVARRAKGL 214
++ + L +A GV L +T V+G G VG + R +GL
Sbjct: 97 DYVLGSLLTLAER------------------EGVDLAERTYGVVGAGHVGGRLVRVLRGL 138
Query: 215 GMNVIAHDPYAQADRARATGVG-LVSFEEAISTADFISLHMPLTP----ATSKMFNDEAF 269
G V+ DP R A G G VS E + D ISLH PLT T + DEAF
Sbjct: 139 GWKVLVCDP----PRQEAEGDGDFVSLERILEECDVISLHTPLTKEGEHPTRHLL-DEAF 193
Query: 270 F-KMKKGVRIVNVARGGVVDEEALVRALDSGIISQAALDVFTEEPPAKDSKLVLHENVTV 328
++ G ++N +RG VVD +AL AL SG A LDV+ EP L L + T+
Sbjct: 194 LASLRPGAWLINASRGAVVDNQALREALLSGEDLDAVLDVWEGEP---QIDLELADLCTI 250
Query: 329 -TPHL 332
TPH+
Sbjct: 251 ATPHI 255
>gnl|CDD|177941 PLN02306, PLN02306, hydroxypyruvate reductase.
Length = 386
Score = 136 bits (343), Expect = 4e-35
Identities = 94/254 (37%), Positives = 132/254 (51%), Gaps = 23/254 (9%)
Query: 125 VGIDNVDLSAATEHGCLVVNAPTANTIAAAEHGIALLTAMARNIAQADASVKAGK---WQ 181
VG +NVD+ AA ++G V N P T AE +L A AR I +AD ++AG W
Sbjct: 95 VGYNNVDVEAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYEGWL 154
Query: 182 RNKYVGVSLVGKTLAVMGFGKVGTEVARR-AKGLGMNVIAHDPYAQADRA---------- 230
+ +VG L G+T+ V+G G++G+ AR +G MN+I +D Y Q+ R
Sbjct: 155 PHLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLY-QSTRLEKFVTAYGQF 213
Query: 231 -RATGVGLV------SFEEAISTADFISLHMPLTPATSKMFNDEAFFKMKKGVRIVNVAR 283
+A G V S EE + AD ISLH L T + N E MKK +VN +R
Sbjct: 214 LKANGEQPVTWKRASSMEEVLREADVISLHPVLDKTTYHLINKERLALMKKEAVLVNASR 273
Query: 284 GGVVDEEALVRALDSGIISQAALDVFTEEPPAKDSKLVLHENVTVTPHLGASTTEAQEGV 343
G V+DE ALV L + + + LDVF +EP K L +N V PH+ +++ +EG+
Sbjct: 274 GPVIDEVALVEHLKANPMFRVGLDVFEDEPYMKPG-LADMKNAVVVPHIASASKWTREGM 332
Query: 344 AIEIAEAVIGALKG 357
A A V+G LKG
Sbjct: 333 ATLAALNVLGKLKG 346
>gnl|CDD|178684 PLN03139, PLN03139, formate dehydrogenase; Provisional.
Length = 386
Score = 130 bits (329), Expect = 4e-33
Identities = 81/252 (32%), Positives = 122/252 (48%), Gaps = 10/252 (3%)
Query: 114 AGRLKVVGRAGVGIDNVDLSAATEHGCLVVNAPTANTIAAAEHGIALLTAMARNIAQADA 173
A L+++ AG+G D++DL AA G V +N ++ AE + + + RN
Sbjct: 119 AKNLELLLTAGIGSDHIDLPAAAAAGLTVAEVTGSNVVSVAEDELMRILILLRNFLPGYH 178
Query: 174 SVKAGKWQRNK--YVGVSLVGKTLAVMGFGKVGTEVARRAKGLGMNVIAHDPYA-QADRA 230
V +G+W Y L GKT+ +G G++G + +R K N++ HD +
Sbjct: 179 QVVSGEWNVAGIAYRAYDLEGKTVGTVGAGRIGRLLLQRLKPFNCNLLYHDRLKMDPELE 238
Query: 231 RATGVGLVSFEEAIST----ADFISLHMPLTPATSKMFNDEAFFKMKKGVRIVNVARGGV 286
+ TG FEE + D + ++ PLT T MFN E KMKKGV IVN ARG +
Sbjct: 239 KETGA---KFEEDLDAMLPKCDVVVINTPLTEKTRGMFNKERIAKMKKGVLIVNNARGAI 295
Query: 287 VDEEALVRALDSGIISQAALDVFTEEPPAKDSKLVLHENVTVTPHLGASTTEAQEGVAIE 346
+D +A+ A SG I DV+ +P KD N +TPH+ +T +AQ A
Sbjct: 296 MDTQAVADACSSGHIGGYGGDVWYPQPAPKDHPWRYMPNHAMTPHISGTTIDAQLRYAAG 355
Query: 347 IAEAVIGALKGE 358
+ + + KGE
Sbjct: 356 VKDMLDRYFKGE 367
>gnl|CDD|181499 PRK08605, PRK08605, D-lactate dehydrogenase; Validated.
Length = 332
Score = 129 bits (325), Expect = 5e-33
Identities = 81/265 (30%), Positives = 133/265 (50%), Gaps = 18/265 (6%)
Query: 117 LKVVGRAGVGIDNVDLSAATEHGCLVVNAPTANTIAAAEHGIALLTAMARNIAQADASVK 176
+K + + G D DL AT++ ++ N P+ + + AE + + R+ Q V+
Sbjct: 70 IKQIAQRSAGFDTYDLELATKYNLIISNVPSYSPESIAEFTVTQAINLVRHFNQIQTKVR 129
Query: 177 AG--KWQRNKYVGVSLVGKTLAVMGFGKVGTEVAR-RAKGLGMNVIAHDPYAQADRARAT 233
+W+ + S+ +AV+G G++G VA+ AKG G +V+A+DP+ +A
Sbjct: 130 EHDFRWEPP-ILSRSIKDLKVAVIGTGRIGLAVAKIFAKGYGSDVVAYDPF-PNAKAATY 187
Query: 234 GVGLVSFEEAISTADFISLHMPLTPATSKMFNDEAFFKMKKGVRIVNVARGGVVDEEALV 293
+ EEA+ AD ++LHMP T +FN + F KKG VN ARG +VD +AL+
Sbjct: 188 VDYKDTIEEAVEGADIVTLHMPATKYNHYLFNADLFKHFKKGAVFVNCARGSLVDTKALL 247
Query: 294 RALDSGIISQAALDVFTEEPP--AKDSK-----------LVLHENVTVTPHLGASTTEAQ 340
ALD+G+I AALD + E P D + L+ E+V +TPH+ T A
Sbjct: 248 DALDNGLIKGAALDTYEFERPLFPSDQRGQTINDPLLESLINREDVILTPHIAFYTDAAV 307
Query: 341 EGVAIEIAEAVIGALKGELAATAVN 365
+ + ++ +A + L+ VN
Sbjct: 308 KNLIVDALDATLEVLQTGTTRLRVN 332
>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 = 121 bits (306), Expect = 9e-31
Identities = 72/225 (32%), Positives = 106/225 (47%), Gaps = 14/225 (6%)
Query: 116 RLKVVGRAGVGIDNVDLSAATEHGCLVVNAPTANTIAAAEHGIALLTAMARNIAQADASV 175
RL+VV G D V L E G + NA + + AE +AL+ A R + + +
Sbjct: 60 RLRVVQTLSAGYDGV-LPLLPE-GVTLCNARGVHDASTAELAVALILASLRGLPRFVRAQ 117
Query: 176 KAGKWQRNKYVGVSLVGKTLAVMGFGKVGTEVARRAKGLGMNVIAHDPYAQADRARATGV 235
G+W+ SL + + ++G+G +G + RR + V A AR G
Sbjct: 118 ARGRWEPR--RTPSLADRRVLIVGYGSIGRAIERRLAPFEVRVTR-----VARTAR-PGE 169
Query: 236 GLVSFEEA---ISTADFISLHMPLTPATSKMFNDEAFFKMKKGVRIVNVARGGVVDEEAL 292
+ +E + AD + L +PLT T + + E +M G +VNVARG VVD +AL
Sbjct: 170 QVHGIDELPALLPEADVVVLIVPLTDETRGLVDAEFLARMPDGALLVNVARGPVVDTDAL 229
Query: 293 VRALDSGIISQAALDVFTEEPPAKDSKLVLHENVTVTPHLGASTT 337
V L SG + +AALDV EP L V +TPH+G +T
Sbjct: 230 VAELASGRL-RAALDVTDPEPLPPGHPLWSAPGVLITPHVGGATP 273
>gnl|CDD|235800 PRK06436, PRK06436, glycerate dehydrogenase; Provisional.
Length = 303
Score = 120 bits (303), Expect = 2e-30
Identities = 68/233 (29%), Positives = 120/233 (51%), Gaps = 9/233 (3%)
Query: 116 RLKVVGRAGVGIDNVDLSAATEHGCLVVNAPTANTIAAAEHGIALLTAMARNIAQADASV 175
+ K++ G+D++D+S E+ L NA A +I+ AEH ALL A A+NI + + ++
Sbjct: 49 KTKMIQSLSAGVDHIDVSGIPENVVLCSNA-GAYSISVAEHAFALLLAWAKNICENNYNM 107
Query: 176 KAGKWQRNKYVGVSLVGKTLAVMGFGKVGTEVARRAKGLGMNVIAHDPYAQADRARATGV 235
K G ++++ L K+L ++G+G +G VA AK GMN+ A Y ++
Sbjct: 108 KNGNFKQSPTK--LLYNKSLGILGYGGIGRRVALLAKAFGMNIYA---YTRSYVNDGISS 162
Query: 236 GLVSFEEAISTADFISLHMPLTPATSKMFNDEAFFKMKKGVRIVNVARGGVVDEEALVRA 295
+ E+ + +DF+ + +PLT T M N + +KG+ I+NVAR VVD+ ++
Sbjct: 163 IYMEPEDIMKKSDFVLISLPLTDETRGMINSKMLSLFRKGLAIINVARADVVDKNDMLNF 222
Query: 296 LDSGIISQAALDVFTEEPPAKDSKLVLHENVTVTPHLGASTTEAQEGVAIEIA 348
L + DV+ EP ++ +NV ++PH+ + A+ +A
Sbjct: 223 LRNHNDKYYLSDVWWNEPIITETNP---DNVILSPHVAGGMSGEIMQPAVALA 272
>gnl|CDD|183550 PRK12480, PRK12480, D-lactate dehydrogenase; Provisional.
Length = 330
Score = 118 bits (296), Expect = 4e-29
Identities = 69/238 (28%), Positives = 115/238 (48%), Gaps = 18/238 (7%)
Query: 117 LKVVGRAGVGIDNVDLSAATEHGCLVVNAPTANTIAAAEHGIALLTAMARNIAQADASVK 176
+K + + G D DL A +H ++ N P+ + AE+ +++ + R + V+
Sbjct: 70 IKQIAQRTAGFDMYDLDLAKKHNIVISNVPSYSPETIAEYSVSIALQLVRRFPDIERRVQ 129
Query: 177 AG--KWQRNKYVGVSLVGKTLAVMGFGKVGTEVARRAKGLGMNVIAHDPYAQADRARATG 234
A WQ + + + T+A++G G++G A+ G G + A+D Y D T
Sbjct: 130 AHDFTWQ-AEIMSKPVKNMTVAIIGTGRIGAATAKIYAGFGATITAYDAYPNKDLDFLTY 188
Query: 235 VGLVSFEEAISTADFISLHMPLTPATSKMFNDEAFFKMKKGVRIVNVARGGVVDEEALVR 294
S +EAI AD ISLH+P + +F+ F +KKG +VN ARG V++ L+
Sbjct: 189 KD--SVKEAIKDADIISLHVPANKESYHLFDKAMFDHVKKGAILVNAARGAVINTPDLIA 246
Query: 295 ALDSGIISQAALDVFTEEPP-------AKD------SKLVLHENVTVTPHLGASTTEA 339
A++ G + AA+D + E KD +L+ HE + VTPH+ + EA
Sbjct: 247 AVNDGTLLGAAIDTYENEAAYFTNDWTNKDIDDKTLLELIEHERILVTPHIAFFSDEA 304
>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 = 116 bits (293), Expect = 7e-29
Identities = 74/221 (33%), Positives = 97/221 (43%), Gaps = 17/221 (7%)
Query: 154 AEHGIALLTAMARNIAQADASVKAGKWQRNKYVGVSLV----GKTLAVMGFGKVGTEVAR 209
AEH +ALL A R + A +A W LV G T+A++G G +G +
Sbjct: 88 AEHALALLLAGLRQLP---ARARATTWD--PAEEDDLVTLLRGSTVAIVGAGGIGRALIP 142
Query: 210 RAKGLGMNVIA----HDPYAQADRARATGVGLVSFEEAISTADFISLHMPLTPATSKMFN 265
G VIA P AD V +E AD + L PLTP T + +
Sbjct: 143 LLAPFGAKVIAVNRSGRPVEGADET----VPADRLDEVWPDADHVVLAAPLTPETRHLVD 198
Query: 266 DEAFFKMKKGVRIVNVARGGVVDEEALVRALDSGIISQAALDVFTEEPPAKDSKLVLHEN 325
A MK +VNVARG +VD +ALV AL SG I+ AALDV EP L N
Sbjct: 199 AAALAAMKPHAWLVNVARGPLVDTDALVDALRSGEIAGAALDVTDPEPLPDGHPLWSLPN 258
Query: 326 VTVTPHLGASTTEAQEGVAIEIAEAVIGALKGELAATAVNA 366
+TPH+ + + +A +AE V GE V+
Sbjct: 259 ALITPHVANTPEVIRPLLAERVAENVRAFAAGEPLLGVVDP 299
>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 = 113 bits (286), Expect = 1e-27
Identities = 66/196 (33%), Positives = 91/196 (46%), Gaps = 28/196 (14%)
Query: 176 KAGKWQRNKYV--GVSLVGKTLAVMGFGKVGTEVARRAKGLGMNVIAHD----PYAQADR 229
K W R + VGK + ++G+G +G + AR A+ LGM V A+ P ++ +
Sbjct: 115 KEQTWGRRQEAYSVEDSVGKRVGILGYGSIGRQTARLAQALGMEVYAYTRSPRPTPESRK 174
Query: 230 ARA-----TGVGLVSFEEA-ISTADFISLH-------------MPLTPATSKMFNDEAFF 270
TG S A S D SLH +PLTPAT + E F
Sbjct: 175 DDGYIVPGTGDPDGSIPSAWFSGTDKASLHEFLRQDLDLLVVSLPLTPATKHLLGAEEF- 233
Query: 271 KM--KKGVRIVNVARGGVVDEEALVRALDSGIISQAALDVFTEEPPAKDSKLVLHENVTV 328
++ K+ + N+ARG +VD +ALV AL+SG I AALDV EP D L NV +
Sbjct: 234 EILAKRKTFVSNIARGSLVDTDALVAALESGQIRGAALDVTDPEPLPADHPLWSAPNVII 293
Query: 329 TPHLGASTTEAQEGVA 344
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 = 96.3 bits (240), Expect = 6e-22
Identities = 60/190 (31%), Positives = 91/190 (47%), Gaps = 16/190 (8%)
Query: 154 AEHGIALLTAMARNIAQADASVKAGKWQ---------RNKYVGVSLVGKTLAVMGFGKVG 204
AEH +AL+ A R + + + + +W R +L+G + + GFG +G
Sbjct: 96 AEHTLALILAAVRRLDEMREAQREHRWAGELGGLQPLRPAGRLTTLLGARVLIWGFGSIG 155
Query: 205 TEVARRAKGLGMNVIAHDPYAQADRARATGVGLVS---FEEAISTADFISLHMPLTPATS 261
+A LG V A++ RA G +V+ E + D + + +P TP+T+
Sbjct: 156 QRLAPLLTALGARVT---GVARSAGERA-GFPVVAEDELPELLPETDVLVMILPATPSTA 211
Query: 262 KMFNDEAFFKMKKGVRIVNVARGGVVDEEALVRALDSGIISQAALDVFTEEPPAKDSKLV 321
+ E + K +VNV RG VDE+ALV AL+SG + AALDV EP S L
Sbjct: 212 HALDAEVLAALPKHAWVVNVGRGATVDEDALVAALESGRLGGAALDVTATEPLPASSPLW 271
Query: 322 LHENVTVTPH 331
N+ +TPH
Sbjct: 272 DAPNLILTPH 281
>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 = 87.5 bits (218), Expect = 2e-21
Identities = 28/72 (38%), Positives = 45/72 (62%)
Query: 524 ILCRQVDQPGIIGKVGSLLGDNNVNVNFMSVGRIAPQKQAVMTIGVDEEPSREVLKKIGE 583
++ R D+PG+IGKVG++LG+ +N+ M VGR P +A+M + VDE EVL+++
Sbjct: 2 LVVRNTDRPGVIGKVGTILGEAGINIAGMQVGRDEPGGEALMVLSVDEPVPDEVLEELRA 61
Query: 584 TPAIEEFVFLKL 595
P I ++L
Sbjct: 62 LPGILSAKVVEL 73
>gnl|CDD|185335 PRK15438, PRK15438, erythronate-4-phosphate dehydrogenase PdxB;
Provisional.
Length = 378
Score = 92.3 bits (229), Expect = 4e-20
Identities = 79/261 (30%), Positives = 118/261 (45%), Gaps = 31/261 (11%)
Query: 95 DALIVRSGTKVTREVFESSAGRLKVVGRAGVGIDNVDLSAATEHGCLVVNAPTANTIAAA 154
DAL+VRS TKV + +K VG A G D+VD + + G AP N IA
Sbjct: 39 DALMVRSVTKVNESLLAGKP--IKFVGTATAGTDHVDEAWLKQAGIGFSAAPGCNAIAVV 96
Query: 155 EHGIALLTAMARNIAQADASVKAGKWQRNKYVGVSLVGKTLAVMGFGKVGTEVARRAKGL 214
E+ + L +A +R+ G SL +T+ ++G G VG + R + L
Sbjct: 97 EYVFSSLLMLA---------------ERD---GFSLHDRTVGIVGVGNVGRRLQARLEAL 138
Query: 215 GMNVIAHDPYAQADRARATGVGLVSFEEAISTADFISLHMPL---TPATSKMFNDEAFF- 270
G+ + DP +ADR S +E + AD ++ H PL P + DE
Sbjct: 139 GIKTLLCDP-PRADRGDEGD--FRSLDELVQEADILTFHTPLFKDGPYKTLHLADEKLIR 195
Query: 271 KMKKGVRIVNVARGGVVDEEALVRALDSGIISQAALDVFTEEPPAKDSKLVLHENVTV-T 329
+K G ++N RG VVD AL+ L+ G LDV+ EP + + L + V + T
Sbjct: 196 SLKPGAILINACRGAVVDNTALLTCLNEGQKLSVVLDVWEGEP---ELNVELLKKVDIGT 252
Query: 330 PHLGASTTEAQEGVAIEIAEA 350
PH+ T E + ++ EA
Sbjct: 253 PHIAGYTLEGKARGTTQVFEA 273
>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 = 85.0 bits (210), Expect = 5e-18
Identities = 55/242 (22%), Positives = 83/242 (34%), Gaps = 23/242 (9%)
Query: 86 ELCTKISLCDALIVRSGTKVTREVFESSAGRLKVVGRAGVGIDNVDLS-AATEHGCLVVN 144
L + D ++ E +++ +G D+ DL+ A G +
Sbjct: 57 TLAKALWSLDVVLKVKEPLTNAEYALIQKLGDRLLFTYTIGADHRDLTEALARAGLTAIA 116
Query: 145 APTA-------NTIAAAEHGIALLTAMARNIAQADASVKAGKWQRNKYVGVSLVGKTLAV 197
N+I A E + + + GKT+ V
Sbjct: 117 VEGVELPLLTSNSIGAGELSVQFIARFLEVQQPGRLGGAPD-----------VAGKTVVV 165
Query: 198 MGFGKVGTEVARRAKGLGMNVIAHDPYAQADRARAT--GVGLVSFEEAISTADFISLHMP 255
+G G VG E A+ +GLG V+ D +A G + EEA++ AD I
Sbjct: 166 VGAGVVGKEAAQMLRGLGAQVLITDINVEALEQLEELGGKNVEELEEALAEADVIVTTTL 225
Query: 256 LTPATSKMFNDEAFF-KMKKGVRIVNVARGGVVDEEALVR-ALDSGIISQAALDVFTEEP 313
L + + E +MK G IVNVA G V +AL L+ G DV P
Sbjct: 226 LPGKRAGILVPEELVEQMKPGSVIVNVAVGAVGCVQALHTQLLEEGHGVVHYGDVNMPGP 285
Query: 314 PA 315
Sbjct: 286 GC 287
>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 = 76.0 bits (188), Expect = 3e-17
Identities = 25/70 (35%), Positives = 38/70 (54%)
Query: 524 ILCRQVDQPGIIGKVGSLLGDNNVNVNFMSVGRIAPQKQAVMTIGVDEEPSREVLKKIGE 583
+L D PG+IGKVG++LG++ +N+ M VGR A M + VD EVL+++
Sbjct: 2 LLIVHKDVPGVIGKVGTILGEHGINIAAMQVGRKEKGGIAYMVLDVDSPVPEEVLEELKA 61
Query: 584 TPAIEEFVFL 593
P I +
Sbjct: 62 LPGIIRVRLI 71
>gnl|CDD|185366 PRK15469, ghrA, bifunctional glyoxylate/hydroxypyruvate reductase
A; Provisional.
Length = 312
Score = 78.7 bits (194), Expect = 5e-16
Identities = 58/180 (32%), Positives = 91/180 (50%), Gaps = 18/180 (10%)
Query: 194 TLAVMGFGKVGTEVARRAKGLGMNVIAHDPYAQADRARATGVGLVSFEEAISTADF---- 249
T+ ++G G +G++VA+ + G P R+R + G+ SF + F
Sbjct: 138 TIGILGAGVLGSKVAQSLQTWGF------PLRCWSRSRKSWPGVQSFAGREELSAFLSQT 191
Query: 250 ---ISLHMPLTPATSKMFNDEAFFKMKKGVRIVNVARGGVVDEEALVRALDSGIISQAAL 306
I+L +P TP T + N + ++ G ++N+ARG V E+ L+ ALDSG + A L
Sbjct: 192 RVLINL-LPNTPETVGIINQQLLEQLPDGAYLLNLARGVHVVEDDLLAALDSGKVKGAML 250
Query: 307 DVFTEEPPAKDSKLVLHENVTVTPHLGASTTEAQEGVAIE-IAEAVIGALKGELAATAVN 365
DVF+ EP +S L H V +TPH+ A T A+ A+E I+ + KGE V+
Sbjct: 251 DVFSREPLPPESPLWQHPRVAITPHVAAVTRPAE---AVEYISRTIAQLEKGERVCGQVD 307
>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 = 61.4 bits (150), Expect = 5e-12
Identities = 25/59 (42%), Positives = 36/59 (61%)
Query: 530 DQPGIIGKVGSLLGDNNVNVNFMSVGRIAPQKQAVMTIGVDEEPSREVLKKIGETPAIE 588
D+PG I KV S+L D+ +N+ FM V R QA+M I VD+ EV+++I + P I
Sbjct: 8 DKPGAIAKVTSVLADHEINIAFMRVSRKEKGDQALMVIEVDQPIDEEVIEEIKKIPNIH 66
>gnl|CDD|198065 smart00997, AdoHcyase_NAD, S-adenosyl-L-homocysteine hydrolase, NAD
binding domain.
Length = 162
Score = 49.8 bits (120), Expect = 4e-07
Identities = 36/99 (36%), Positives = 45/99 (45%), Gaps = 11/99 (11%)
Query: 187 GVSLVGKTLAVMGFGKVGTEVARRAKGLGMNVIAH--DPYAQADRARATGVGLVSFEEAI 244
V L GK + V G+G VG VA R +GLG VI DP +A A G ++ EEA
Sbjct: 18 NVLLAGKNVVVAGYGDVGKGVAARLRGLGARVIVTEIDP-IRALEAAMDGFEVMKMEEAA 76
Query: 245 STADFISLHMPLTPAT--SKMFNDEAFFKMKKGVRIVNV 281
AD +T AT + E F MK G + N
Sbjct: 77 KRADIF-----VT-ATGNKDVITREHFRAMKDGAILANA 109
>gnl|CDD|223573 COG0499, SAM1, S-adenosylhomocysteine hydrolase [Coenzyme
metabolism].
Length = 420
Score = 48.8 bits (117), Expect = 5e-06
Identities = 33/96 (34%), Positives = 46/96 (47%), Gaps = 9/96 (9%)
Query: 188 VSLVGKTLAVMGFGKVGTEVARRAKGLGMNVIAH--DPYAQADRARATGVGLVSFEEAIS 245
V L GK + V G+G VG +A R +G+G VI DP +A A G +++ EEA
Sbjct: 205 VLLAGKNVVVAGYGWVGRGIAMRLRGMGARVIVTEVDP-IRALEAAMDGFRVMTMEEAAK 263
Query: 246 TAD-FISLHMPLTPATSKMFNDEAFFKMKKGVRIVN 280
T D F++ + E F KMK G + N
Sbjct: 264 TGDIFVT-----ATGNKDVIRKEHFEKMKDGAILAN 294
>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 = 42.3 bits (100), Expect = 2e-05
Identities = 13/61 (21%), Positives = 27/61 (44%), Gaps = 1/61 (1%)
Query: 522 SIILCRQVDQPGIIGKVGSLLGDNNVNVNFMSVGRI-APQKQAVMTIGVDEEPSREVLKK 580
+++ D+PG++ +V L D +N+ +S + + VDEE L+
Sbjct: 1 TVLEVGVPDRPGLLAEVFGALADRGINIESISQSTSGDKAGIVFIVVVVDEEDLEAALEA 60
Query: 581 I 581
+
Sbjct: 61 L 61
>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 = 41.1 bits (97), Expect = 5e-05
Identities = 14/51 (27%), Positives = 26/51 (50%)
Query: 530 DQPGIIGKVGSLLGDNNVNVNFMSVGRIAPQKQAVMTIGVDEEPSREVLKK 580
D+PG++ KV S+L + +N+ + +A + I VD + E L +
Sbjct: 7 DRPGLLAKVLSVLAEAGINITSIEQRTSGDGGEADIFIVVDGDGDLEKLLE 57
>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 = 44.8 bits (107), Expect = 9e-05
Identities = 25/64 (39%), Positives = 32/64 (50%), Gaps = 3/64 (4%)
Query: 188 VSLVGKTLAVMGFGKVGTEVARRAKGLGMNVIAH--DPYAQADRARATGVGLVSFEEAIS 245
V + GK + V G+G VG A RA+GLG VI DP A +A G ++ EEA
Sbjct: 191 VLIAGKVVVVAGYGWVGKGCAMRARGLGARVIVTEVDPI-CALQAAMDGFEVMPMEEAAK 249
Query: 246 TADF 249
D
Sbjct: 250 IGDI 253
>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 = 44.3 bits (105), Expect = 1e-04
Identities = 31/94 (32%), Positives = 44/94 (46%), Gaps = 9/94 (9%)
Query: 190 LVGKTLAVMGFGKVGTEVARRAKGLGMNVIAH--DPYAQADRARATGVGLVSFEEAISTA 247
+ GKT+ V G+G G +A RA+G+G VI DP +A A G +++ EEA
Sbjct: 194 IAGKTVVVAGYGWCGKGIAMRARGMGARVIVTEVDP-IRALEAAMDGFRVMTMEEAAKIG 252
Query: 248 D-FISLHMPLTPATSKMFNDEAFFKMKKGVRIVN 280
D FI+ + E F MK G + N
Sbjct: 253 DIFIT-----ATGNKDVIRGEHFENMKDGAIVAN 281
>gnl|CDD|235488 PRK05476, PRK05476, S-adenosyl-L-homocysteine hydrolase;
Provisional.
Length = 425
Score = 44.3 bits (106), Expect = 1e-04
Identities = 24/65 (36%), Positives = 33/65 (50%), Gaps = 3/65 (4%)
Query: 188 VSLVGKTLAVMGFGKVGTEVARRAKGLGMNVIAH--DPYAQADRARATGVGLVSFEEAIS 245
V + GK + V G+G VG A+R +GLG VI DP A +A G +++ EEA
Sbjct: 208 VLIAGKVVVVAGYGDVGKGCAQRLRGLGARVIVTEVDPIC-ALQAAMDGFRVMTMEEAAE 266
Query: 246 TADFI 250
D
Sbjct: 267 LGDIF 271
>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 = 41.1 bits (97), Expect = 0.001
Identities = 67/291 (23%), Positives = 108/291 (37%), Gaps = 31/291 (10%)
Query: 61 KLGEAGLDVLKNFANVDCSYNLSP---EELCTKISLCDALIVRSGTKVTREVFESSAGRL 117
L E + LK +A Y+ P EE+ +I D ++V T++ EV E+ +
Sbjct: 11 GLNEEAEEELKKYAEEVVFYDDIPESDEEIIERIGDADCVLVSYTTQIDEEVLEACP-NI 69
Query: 118 KVVGRAGVGID----NVDLSAATEHGCLVVNAPTANTIAAAEHGIALLTAMARNIAQADA 173
K +G NVD++AA E+G V E+ I+ L +
Sbjct: 70 KYIGMCCSLYSEESANVDIAAARENGITVTGIRDYGDEGVVEYVISELIRLLHGFGGK-- 127
Query: 174 SVKAGKWQRNKYVGVSLVGKTLAVMGFGKVGTEVARRAKGLGMNVIAHDPYAQADR---A 230
+W K L G + ++G G G +A G +V Y R A
Sbjct: 128 -----QW---KEEPRELTGLKVGIIGLGTTGQMIADALSFFGADVY----YYSRTRKPDA 175
Query: 231 RATGVGLVSFEEAISTADFISLHMPLTPATSKMFNDEAFFKMKKGVRIVNVARGGVVDEE 290
A G+ + E + T D I + P + +E F + G + N + G + E
Sbjct: 176 EAKGIRYLPLNELLKTVDVICTCL---PKNVILLGEEEFELLGDGKILFNTSLGPSFEVE 232
Query: 291 ALVRALDSGIISQAALDVFTEEPPAKDSKLVLHENVTVTPHLGASTTEAQE 341
AL + L + + D D +L+ + NV T T +A E
Sbjct: 233 ALKKWLKASGYNIFDCD---TAGALGDEELLRYPNVICTNKSAGWTRQAFE 280
>gnl|CDD|218507 pfam05221, AdoHcyase, S-adenosyl-L-homocysteine hydrolase.
Length = 430
Score = 40.5 bits (95), Expect = 0.002
Identities = 29/96 (30%), Positives = 39/96 (40%), Gaps = 7/96 (7%)
Query: 188 VSLVGKTLAVMGFGKVGTEVARRAKGLGMNVIAH--DPYAQADRARATGVGLVSFEEAIS 245
V + GK V G+G VG A +G G VI DP A +A G +V+ EE +
Sbjct: 206 VMIAGKVAVVCGYGDVGKGCAASLRGQGARVIVTEIDPIC-ALQAAMEGYQVVTLEEVVK 264
Query: 246 TADFISLHMPLTPATSKMFNDEAFFKMKKGVRIVNV 281
AD T + F MKK + N+
Sbjct: 265 DADIFV----TTTGCVDIIVGRHFMNMKKDAIVCNI 296
>gnl|CDD|181371 PRK08306, PRK08306, dipicolinate synthase subunit A; Reviewed.
Length = 296
Score = 39.4 bits (93), Expect = 0.003
Identities = 24/66 (36%), Positives = 30/66 (45%), Gaps = 10/66 (15%)
Query: 192 GKTLAVMGFGKVGTEVARRAKGLGMN--VIAHDPYAQADRARATGVGLVSF-----EEAI 244
G + V+GFG+ G +AR K LG N V A A AR T +GL F E +
Sbjct: 152 GSNVLVLGFGRTGMTLARTLKALGANVTVGARKS---AHLARITEMGLSPFHLSELAEEV 208
Query: 245 STADFI 250
D I
Sbjct: 209 GKIDII 214
>gnl|CDD|224674 COG1760, SdaA, L-serine deaminase [Amino acid transport and
metabolism].
Length = 262
Score = 38.0 bits (89), Expect = 0.008
Identities = 21/82 (25%), Positives = 32/82 (39%), Gaps = 3/82 (3%)
Query: 507 LTKVGSFGVDVSLEGSIILCRQVDQPGII-GKVGSLLGDNNVNVNFMSVGRIAPQKQAVM 565
LT++ + S I G+ V L+ +N N M R +A M
Sbjct: 167 LTELNGGSPEQSGNAPEIAM--EHNLGLTCDPVAGLVQVPCINRNAMGAVRAINGAKAAM 224
Query: 566 TIGVDEEPSREVLKKIGETPAI 587
I VD+ P EV++ + ET
Sbjct: 225 AIEVDQRPLDEVIETMYETGKD 246
>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 = 37.2 bits (86), Expect = 0.011
Identities = 18/79 (22%), Positives = 34/79 (43%)
Query: 503 GKPHLTKVGSFGVDVSLEGSIILCRQVDQPGIIGKVGSLLGDNNVNVNFMSVGRIAPQKQ 562
G +T++ F ++ E IL D+ G I V +LL +N+ + +
Sbjct: 130 GAIEITEINGFAIEFRGEHPAILLEHNDKFGTIAGVANLLAGFEINIEHLETAKKDIGNI 189
Query: 563 AVMTIGVDEEPSREVLKKI 581
A++TI +D+ + I
Sbjct: 190 ALLTIEIDKNIDDHIKDAI 208
>gnl|CDD|106361 PRK13403, PRK13403, ketol-acid reductoisomerase; Provisional.
Length = 335
Score = 37.8 bits (87), Expect = 0.011
Identities = 22/67 (32%), Positives = 37/67 (55%), Gaps = 1/67 (1%)
Query: 190 LVGKTLAVMGFGKVGTEVARRAKGLGMNVIAH-DPYAQADRARATGVGLVSFEEAISTAD 248
L GKT+AV+G+G G A+ + G+ V+ P + A+A G ++S EA+ TA
Sbjct: 14 LQGKTVAVIGYGSQGHAQAQNLRDSGVEVVVGVRPGKSFEVAKADGFEVMSVSEAVRTAQ 73
Query: 249 FISLHMP 255
+ + +P
Sbjct: 74 VVQMLLP 80
>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 = 37.5 bits (88), Expect = 0.011
Identities = 15/37 (40%), Positives = 21/37 (56%)
Query: 184 KYVGVSLVGKTLAVMGFGKVGTEVARRAKGLGMNVIA 220
K +G+ L G +A+ GFG VG+ AR G V+A
Sbjct: 23 KKLGIGLAGARVAIQGFGNVGSHAARFLHEAGAKVVA 59
>gnl|CDD|236034 PRK07502, PRK07502, cyclohexadienyl dehydrogenase; Validated.
Length = 307
Score = 36.5 bits (85), Expect = 0.028
Identities = 22/70 (31%), Positives = 35/70 (50%), Gaps = 8/70 (11%)
Query: 193 KTLAVMGFGKVGTEVAR--RAKGLGMNVIAHDPYAQADRARATGVGLVSF-----EEAIS 245
+A++G G +G+ +AR R GL ++ D + RARA +GL EA+
Sbjct: 7 DRVALIGIGLIGSSLARAIRRLGLAGEIVGADR-SAETRARARELGLGDRVTTSAAEAVK 65
Query: 246 TADFISLHMP 255
AD + L +P
Sbjct: 66 GADLVILCVP 75
>gnl|CDD|240258 PTZ00075, PTZ00075, Adenosylhomocysteinase; Provisional.
Length = 476
Score = 36.9 bits (86), Expect = 0.031
Identities = 32/112 (28%), Positives = 49/112 (43%), Gaps = 12/112 (10%)
Query: 188 VSLVGKTLAVMGFGKVGTEVARRAKGLGMNVIAH--DPYAQADRARATGVGLVSFEEAIS 245
V + GKT+ V G+G VG A+ +G G V+ DP A +A G +V+ E+ +
Sbjct: 250 VMIAGKTVVVCGYGDVGKGCAQALRGFGARVVVTEIDPIC-ALQAAMEGYQVVTLEDVVE 308
Query: 246 TAD-FISLHMPLTPATSKMFNDEAFFKMKKGVRIVNVARGGVVDEEALVRAL 296
TAD F++ + E +MK + N+ D E V L
Sbjct: 309 TADIFVT-----ATGNKDIITLEHMRRMKNNAIVGNIGHF---DNEIQVAEL 352
>gnl|CDD|215789 pfam00208, ELFV_dehydrog, Glutamate/Leucine/Phenylalanine/Valine
dehydrogenase.
Length = 237
Score = 35.6 bits (83), Expect = 0.049
Identities = 17/32 (53%), Positives = 21/32 (65%)
Query: 189 SLVGKTLAVMGFGKVGTEVARRAKGLGMNVIA 220
SL GKT+AV GFG VG+ A + LG V+A
Sbjct: 29 SLEGKTVAVQGFGNVGSYAAEKLLELGAKVVA 60
>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 = 35.8 bits (83), Expect = 0.052
Identities = 30/90 (33%), Positives = 43/90 (47%), Gaps = 7/90 (7%)
Query: 190 LVGKTLAVMGFGKVGTEVARRAKGLGMNVIAHDPYAQADRARATGVGLV--SFEEAISTA 247
L GKT+A++G+G G A + G+NVI A +AT G + EEAI A
Sbjct: 1 LKGKTVAIIGYGSQGHAQALNLRDSGLNVIVGLRKGGASWKKATEDGFKVGTVEEAIPQA 60
Query: 248 DFISLHMPLTP--ATSKMFNDEAFFKMKKG 275
D I M L P +++ E +K+G
Sbjct: 61 DLI---MNLLPDEVQHEVYEAEIQPLLKEG 87
>gnl|CDD|109716 pfam00670, AdoHcyase_NAD, S-adenosyl-L-homocysteine hydrolase, NAD
binding domain.
Length = 162
Score = 34.6 bits (80), Expect = 0.054
Identities = 24/65 (36%), Positives = 30/65 (46%), Gaps = 3/65 (4%)
Query: 188 VSLVGKTLAVMGFGKVGTEVARRAKGLGMNVIAH--DPYAQADRARATGVGLVSFEEAIS 245
V + GK V G+G VG A KG G VI DP A +A G +V+ EE +
Sbjct: 19 VMIAGKVAVVCGYGDVGKGCAASLKGQGARVIVTEIDPIC-ALQAAMEGFQVVTLEEVVK 77
Query: 246 TADFI 250
AD
Sbjct: 78 KADIF 82
>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 = 0.066
Identities = 22/71 (30%), Positives = 34/71 (47%), Gaps = 5/71 (7%)
Query: 190 LVGKTLAVMGFGKVGTEVARRAKGLGMNVIA--HDPYAQADRARATGVGLVSFEEAISTA 247
L GK +AV+G+G G A + G+NVI ++A+ G + + EA+ A
Sbjct: 2 LKGKKIAVIGYGSQGHAHALNLRDSGVNVIVGLRPGSKSWEKAKKDGFEVYTVAEAVKKA 61
Query: 248 DFISLHMPLTP 258
D + M L P
Sbjct: 62 DVV---MILLP 69
>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 = 34.8 bits (80), Expect = 0.086
Identities = 33/130 (25%), Positives = 56/130 (43%), Gaps = 11/130 (8%)
Query: 184 KYVGVSLVGKTLAVMGFGKVGTEVARRAKGLGMNVIA-HDPYAQADRARATGVGLVSFEE 242
K++G SL G T+AV G G VG +A++ G V+A DP T L+++
Sbjct: 15 KHLGDSLEGLTVAVQGLGNVGWGLAKKLAEEGGKVLAVSDPDGYIYDPGITTEELINYAV 74
Query: 243 AISTADFISLHMPLTPATSKMFNDEAFFKMKKGVRIVNVARGGVVDEEALVRALDSGIIS 302
A+ + F EA + + A G V+D E + L + +++
Sbjct: 75 ALGGSA--------RVKVQDYFPGEAILGLDVDI-FAPCALGNVIDLEN-AKKLKAKVVA 124
Query: 303 QAALDVFTEE 312
+ A + T+E
Sbjct: 125 EGANNPTTDE 134
>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 = 34.6 bits (80), Expect = 0.10
Identities = 36/162 (22%), Positives = 58/162 (35%), Gaps = 22/162 (13%)
Query: 186 VGVSLVGKTLAVMGFGKVGTEVARRAKGLGMNVIAHDPYAQ-ADRARATGVGLVSFEEAI 244
GV G T+ V+G G VG A+ AK G VI D + + A+ G + I
Sbjct: 129 AGVLKPGDTVLVLGAGGVGLLAAQLAKAAGARVIVTDRSDEKLELAKELGA-----DHVI 183
Query: 245 STADFISLHMPLTPATSKMFNDEAFFKMKKGVRIVNVARGGVVDEEALVRALDS-GIISQ 303
+ +E G +V A GG +R L G I
Sbjct: 184 DYKEED-------------LEEELRLTGGGGADVVIDAVGGPETLAQALRLLRPGGRIVV 230
Query: 304 AALDVFTEEPPAKDSKLVLHENVTVTPHLGASTTEAQEGVAI 345
+ PP D + +L + +T+ G + + +E + +
Sbjct: 231 VG--GTSGGPPLDDLRRLLFKELTIIGSTGGTREDFEEALDL 270
>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 = 32.3 bits (74), Expect = 0.13
Identities = 11/33 (33%), Positives = 19/33 (57%)
Query: 449 KQRGLRVTEERIVLDGSPENPLEFIQVQIANVE 481
++ G + E LDG +PLE ++ Q+A +E
Sbjct: 54 RRLGFSLREIGRALDGPDFDPLELLRRQLARLE 86
>gnl|CDD|223758 COG0686, Ald, Alanine dehydrogenase [Amino acid transport and
metabolism].
Length = 371
Score = 34.6 bits (80), Expect = 0.13
Identities = 41/159 (25%), Positives = 61/159 (38%), Gaps = 21/159 (13%)
Query: 150 TIAAAEHGIALLTAMARNIAQADASVKAGKWQRNK------YVGVSLV-GKTLAVMGFGK 202
T+ + + LL M+ + A A ++ GV V + V+G G
Sbjct: 119 TVQLPDGNLPLLAPMSEVAGRLAAQAGAYYLEKTNGGKGVLLGGVPGVLPAKVVVLGGGV 178
Query: 203 VGTEVARRAKGLGMNVIAHD---------PYAQADRARATGVGLVSFEEAISTADFISLH 253
VGT A+ A GLG +V D R + EEA+ AD + +
Sbjct: 179 VGTNAAKIAIGLGADVTILDLNIDRLRQLDDLFGGRVHTLYSTPSNIEEAVKKADLV-IG 237
Query: 254 MPLTP--ATSKMFNDEAFFKMKKGVRIVNVA--RGGVVD 288
L P K+ E +MK G IV+VA +GG +
Sbjct: 238 AVLIPGAKAPKLVTREMVKQMKPGSVIVDVAIDQGGCFE 276
>gnl|CDD|153153 cd04881, ACT_HSDH-Hom, ACT_HSDH_Hom CD includes the C-terminal ACT
domain of the NAD(P)H-dependent, homoserine
dehydrogenase (HSDH) and related domains. The
ACT_HSDH_Hom CD includes the C-terminal ACT domain of
the NAD(P)H-dependent, homoserine dehydrogenase (HSDH)
encoded by the hom gene of Bacillus subtilis and other
related sequences. HSDH reduces aspartate semi-aldehyde
to the amino acid homoserine, one that is required for
the biosynthesis of Met, Thr, and Ile from Asp. Neither
the enzyme nor the aspartate pathway is found in the
animal kingdom. This mostly bacterial HSDH group has a
C-terminal ACT domain and is believed to be involved in
enzyme regulation. A C-terminal deletion in the
Corynebacterium glutamicum HSDH abolished allosteric
inhibition by L-threonine. Members of this CD belong to
the superfamily of ACT regulatory domains.
Length = 79
Score = 31.7 bits (73), Expect = 0.14
Identities = 13/70 (18%), Positives = 30/70 (42%), Gaps = 15/70 (21%)
Query: 529 VDQPGIIGKVGSLLGDNNVNVNFMSVGRIAPQKQA---------VMTIGVDEEPSREVLK 579
D+PG++ K+ +L ++ +++ + QK+A ++T E L
Sbjct: 8 KDKPGVLAKITGILAEHGISIESVI------QKEADGGETAPVVIVTHETSEAALNAALA 61
Query: 580 KIGETPAIEE 589
+I A++
Sbjct: 62 EIEALDAVQG 71
>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 = 33.2 bits (77), Expect = 0.15
Identities = 29/98 (29%), Positives = 37/98 (37%), Gaps = 12/98 (12%)
Query: 196 AVMGFGKVGTEVARRAKGLGMNVIAHDPYAQADRARATGVGLVSFEEAISTADFISLHMP 255
V+G G VG A AKGLG V D R + +G F S A+ + +
Sbjct: 24 VVIGAGVVGLGAAATAKGLGAEVTVLDVRPARLRQLESLLGA-RFTTLYSQAELLEEAVK 82
Query: 256 ---------LTP--ATSKMFNDEAFFKMKKGVRIVNVA 282
L P K+ E MK G IV+VA
Sbjct: 83 EADLVIGAVLIPGAKAPKLVTREMVKSMKPGSVIVDVA 120
>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 = 33.7 bits (78), Expect = 0.16
Identities = 24/60 (40%), Positives = 30/60 (50%), Gaps = 2/60 (3%)
Query: 189 SLVGKTLAVMGFGKVGTEVARRAKGLGMNVIAHD--PYAQADRARATGVGLVSFEEAIST 246
SL GKT+AV G GKVG ++A G +I D A A A G +V+ EE S
Sbjct: 25 SLEGKTVAVQGLGKVGYKLAEHLLEEGAKLIVADINEEAVARAAELFGATVVAPEEIYSV 84
>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 = 32.1 bits (74), Expect = 0.17
Identities = 11/43 (25%), Positives = 18/43 (41%)
Query: 206 EVARRAKGLGMNVIAHDPYAQADRARATGVGLVSFEEAISTAD 248
++ G V+ +DPYA + + EEA+ AD
Sbjct: 21 DIIEELLEAGAEVVVYDPYAMEEAREYGLTYVSDLEEALKGAD 63
>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 = 31.0 bits (71), Expect = 0.19
Identities = 16/57 (28%), Positives = 31/57 (54%), Gaps = 4/57 (7%)
Query: 530 DQPGIIGKVGSLLGDNNVNVNFMSVGRIAPQKQAVMTIGV----DEEPSREVLKKIG 582
D+PG+I +V +LGD +++ + + I ++ I D E ++E+LK+ G
Sbjct: 10 DEPGVIAEVTQILGDAGISIKNIEILEIREGIGGILRISFKTQEDRERAKEILKEAG 66
>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 = 33.9 bits (78), Expect = 0.22
Identities = 29/125 (23%), Positives = 52/125 (41%), Gaps = 15/125 (12%)
Query: 178 GKWQRNKYVGVSLVGK-TLAVMGFGKVGTEVARRAKGLGMNVIAHDPYAQADRARATGVG 236
+ Q + G V + ++G G VG A+ AK LG NV+ +D + ++ +
Sbjct: 147 ARIQGGRMGGAGGVPPAKVLIIGAGVVGLGAAKIAKKLGANVLVYD--IKEEKLKGVETL 204
Query: 237 LVSF---------EEAISTAD-FISLHMPLTPATSKMFNDEAFFKMKKGVRIVNVA--RG 284
S E+ + D I+ + P + +E MK+G IV++A +G
Sbjct: 205 GGSRLRYSQKEELEKELKQTDILINAILVDGPRAPILIMEELVGPMKRGAVIVDLAADQG 264
Query: 285 GVVDE 289
G +
Sbjct: 265 GNDET 269
>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 = 33.7 bits (78), Expect = 0.27
Identities = 25/104 (24%), Positives = 43/104 (41%), Gaps = 15/104 (14%)
Query: 188 VSLVGKTLAVMGFG-KVGT---------EVARRAKGLGMNVIAHDPYAQADRARATGVGL 237
+L GKT+ ++G K T ++ K G V A+DP + + +
Sbjct: 307 GALKGKTVLILGLAFKPNTDDVRESPALDIIELLKEKGAKVKAYDPLVPEEEVKGLPS-I 365
Query: 238 VSFEEAISTADFISLHMPLTP-ATSKMFNDEAFFKMKKGVRIVN 280
EEA+ AD + + LT + K + E + KG +V+
Sbjct: 366 DDLEEALKGADALVI---LTDHSEFKDLDLEKIKDLMKGKVVVD 406
>gnl|CDD|184463 PRK14030, PRK14030, glutamate dehydrogenase; Provisional.
Length = 445
Score = 33.7 bits (77), Expect = 0.30
Identities = 14/33 (42%), Positives = 20/33 (60%)
Query: 187 GVSLVGKTLAVMGFGKVGTEVARRAKGLGMNVI 219
G+ + GKT+A+ GFG V A +A LG V+
Sbjct: 223 GIDIKGKTVAISGFGNVAWGAATKATELGAKVV 255
>gnl|CDD|223411 COG0334, GdhA, Glutamate dehydrogenase/leucine dehydrogenase [Amino
acid transport and metabolism].
Length = 411
Score = 33.4 bits (77), Expect = 0.30
Identities = 16/37 (43%), Positives = 20/37 (54%)
Query: 184 KYVGVSLVGKTLAVMGFGKVGTEVARRAKGLGMNVIA 220
K +G L G +AV GFG VG A + LG V+A
Sbjct: 199 KALGDDLEGARVAVQGFGNVGQYAAEKLHELGAKVVA 235
>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 = 33.1 bits (76), Expect = 0.32
Identities = 23/66 (34%), Positives = 33/66 (50%), Gaps = 10/66 (15%)
Query: 192 GKTLAVMGFGKVGTEVARRAKGLG--MNVIAHDPYAQADRARATGVGLVSF-----EEAI 244
G + V+GFG+ G +AR LG + V A AD AR T +GL+ F EE +
Sbjct: 151 GSNVMVLGFGRTGMTIARTFSALGARVFVGARSS---ADLARITEMGLIPFPLNKLEEKV 207
Query: 245 STADFI 250
+ D +
Sbjct: 208 AEIDIV 213
>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 = 33.3 bits (76), Expect = 0.37
Identities = 43/160 (26%), Positives = 68/160 (42%), Gaps = 23/160 (14%)
Query: 150 TIAAAEHGIALLTAMARNIAQADASVKAGKWQRNKY-VGVSLVG------KTLAVMGFGK 202
T+ A+ + LL M+ + A V A ++ + GV L G + ++G G
Sbjct: 118 TVQTADGALPLLAPMSEVAGRLAAQVGAYHLEKTQGGRGVLLGGVPGVEPGDVTIIGGGV 177
Query: 203 VGTEVARRAKGLGMNVIAHDPYAQADRARATGV-----------GLVSFEEAISTADFIS 251
VGT A+ A GLG V D DR R E+A+ AD +
Sbjct: 178 VGTNAAKMANGLGATVTILD--INIDRLRQLDAEFGGRIHTRYSNAYEIEDAVKRADLLI 235
Query: 252 LHMPLTPATS-KMFNDEAFFKMKKGVRIVNVA--RGGVVD 288
+ + A + K+ ++ +MK G IV+VA +GG V+
Sbjct: 236 GAVLIPGAKAPKLVSNSLVAQMKPGAVIVDVAIDQGGCVE 275
>gnl|CDD|223137 COG0059, IlvC, Ketol-acid reductoisomerase [Amino acid transport
and metabolism / Coenzyme metabolism].
Length = 338
Score = 33.0 bits (76), Expect = 0.41
Identities = 29/112 (25%), Positives = 47/112 (41%), Gaps = 22/112 (19%)
Query: 190 LVGKTLAVMGFGKVGTEVARRAKGL-----GMNVIAHDPYAQADRARATGVGLV--SFEE 242
L GK +A++G+G G A+ L G+NVI + +A G + EE
Sbjct: 16 LKGKKVAIIGYGSQG-----HAQALNLRDSGLNVIIGLRKGSSSWKKAKEDGFKVYTVEE 70
Query: 243 AISTADFISLHMPLTP--ATSKMFNDEAFFKMKKGVRIV-----NVARGGVV 287
A AD + M L P +++ E +K+G + N+ G +V
Sbjct: 71 AAKRADVV---MILLPDEQQKEVYEKEIAPNLKEGAALGFAHGFNIHFGLIV 119
>gnl|CDD|234950 PRK01390, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 460
Score = 33.3 bits (77), Expect = 0.42
Identities = 20/49 (40%), Positives = 23/49 (46%), Gaps = 1/49 (2%)
Query: 189 SLVGKTLAVMGFGKVGTEVARRAKGLGMNVIAHDPYAQADRARATGVGL 237
GKT+AV G G G AR G VIA D A RA+A G+
Sbjct: 6 GFAGKTVAVFGLGGSGLATARALVAGGAEVIAWDD-NPASRAKAAAAGI 53
>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 = 32.2 bits (74), Expect = 0.60
Identities = 12/37 (32%), Positives = 17/37 (45%)
Query: 184 KYVGVSLVGKTLAVMGFGKVGTEVARRAKGLGMNVIA 220
K +L GK +A+ G G V A + LG V+
Sbjct: 30 KDRNETLKGKRVAISGSGNVAQYAAEKLLELGAKVVT 66
>gnl|CDD|153144 cd04872, ACT_1ZPV, ACT domain proteins similar to the yet
uncharacterized Streptococcus pneumoniae ACT domain
protein. This CD, ACT_1ZPV, includes those single ACT
domain proteins similar to the yet uncharacterized
Streptococcus pneumoniae ACT domain protein (pdb
structure 1ZPV). Members of this CD belong to the
superfamily of ACT regulatory domains.
Length = 88
Score = 30.3 bits (69), Expect = 0.64
Identities = 8/21 (38%), Positives = 13/21 (61%)
Query: 530 DQPGIIGKVGSLLGDNNVNVN 550
D+ GI+ V + L + NVN+
Sbjct: 10 DRVGIVAGVSTKLAELNVNIL 30
>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 = 16/61 (26%), Positives = 33/61 (54%), Gaps = 8/61 (13%)
Query: 530 DQPGIIGKVGSLLGDNNVNVNFM---SVGRIAPQKQAVMTIGVDEEPSREVLKKIGETPA 586
+ PG++G++ ++L ++N+N+ + G I V+ I +D E S E+L+ + P
Sbjct: 8 NVPGVLGQINTILAEHNINIAAQYLQTRGEIG----YVV-IDIDSEVSEELLEALRAIPG 62
Query: 587 I 587
Sbjct: 63 T 63
>gnl|CDD|214963 smart00996, AdoHcyase, S-adenosyl-L-homocysteine hydrolase.
Length = 426
Score = 32.1 bits (74), Expect = 0.88
Identities = 23/65 (35%), Positives = 30/65 (46%), Gaps = 3/65 (4%)
Query: 188 VSLVGKTLAVMGFGKVGTEVARRAKGLGMNVIAH--DPYAQADRARATGVGLVSFEEAIS 245
V + GK V G+G VG A+ +G G VI DP A +A G +V+ EE
Sbjct: 203 VMIAGKVAVVCGYGDVGKGCAQSLRGQGARVIVTEIDPIC-ALQAAMDGFEVVTMEEVAP 261
Query: 246 TADFI 250
AD
Sbjct: 262 QADIF 266
>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 = 30.9 bits (71), Expect = 0.89
Identities = 25/106 (23%), Positives = 37/106 (34%), Gaps = 25/106 (23%)
Query: 195 LAVMGFGKVGTEVARRAKGLGMNVIAHDPYAQADRARATGVGLVSFEEAISTADFISLHM 254
L + G G V +AR A LG V DP A V + F++ + +
Sbjct: 1 LVIFGAGHVAQALARLAALLGFRVTVVDPRE-ERFPGADEVICLPFDDLLE-------AL 52
Query: 255 PLTPATSKMFNDEAFFKMKKGVRIVNVARGGVVDEEALVRALDSGI 300
+ P T+ +V + +D EAL AL S
Sbjct: 53 AIDPRTA----------------VV-MTHDHKLDLEALEAALRSPA 81
>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 = 30.2 bits (69), Expect = 0.91
Identities = 12/47 (25%), Positives = 19/47 (40%), Gaps = 4/47 (8%)
Query: 206 EVARRAKGLGMNVIAHDPYAQADRARATGVG----LVSFEEAISTAD 248
++ G V+ +DPY + A G + EEA+ AD
Sbjct: 21 DIIEELLEEGAEVVVYDPYVPEEAIEALGEDGVTLVDDLEEALKGAD 67
>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 = 30.6 bits (70), Expect = 0.99
Identities = 33/122 (27%), Positives = 45/122 (36%), Gaps = 27/122 (22%)
Query: 183 NKYVGVSLVG------KTLAVMGFGKVGTEVARRAKGLGMNVIAHDPYAQADRARATGVG 236
G+ L G + V+G G VG A AKGLG V D R +
Sbjct: 5 GGGFGMLLGGAGGVPPAKVVVIGGGVVGLGAAATAKGLGAPVTILDV----RPERLEQLD 60
Query: 237 LV--------------SFEEAISTADFI--SLHMPLTPATSKMFNDEAFFKMKKGVRIVN 280
+ EAI+ AD + ++ +P A K+ E MK G IV+
Sbjct: 61 SLFAEFVETDIFSNCEYLAEAIAEADLVIGTVLIPGARAP-KLVTREMVKTMKPGSVIVD 119
Query: 281 VA 282
VA
Sbjct: 120 VA 121
>gnl|CDD|184511 PRK14106, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 450
Score = 31.5 bits (72), Expect = 1.3
Identities = 14/33 (42%), Positives = 18/33 (54%)
Query: 190 LVGKTLAVMGFGKVGTEVARRAKGLGMNVIAHD 222
L GK + V+G G G +A+ K LG VI D
Sbjct: 3 LKGKKVLVVGAGVSGLALAKFLKKLGAKVILTD 35
>gnl|CDD|212099 cd10787, LamB_YcsF_like, LamB/YcsF family of lactam utilization
protein. The LamB/YbgL family includes the Aspergillus
nidulans protein LamB, and its homologs from all three
kingdoms of life. The lamb gene locates at the lam locus
of Aspergillus nidulans, consisting of two divergently
transcribed genes, lamA and lamB, needed for the
utilization of lactams such as 2-pyrrolidinone. Both
genes are under the control of the positive regulatory
gene amdR and are subject to carbon and nitrogen
metabolite repression. Although the exact molecular
function of LamB is unknown, it might be required for
conversion of exogenous 2-pyrrolidinone to endogenous
GABA.
Length = 238
Score = 30.9 bits (71), Expect = 1.4
Identities = 22/75 (29%), Positives = 32/75 (42%), Gaps = 16/75 (21%)
Query: 156 HGIALLTAMARNIAQADASVKAGKWQRNKYVGVSLVGKTLAVMGFGKVGTEVARRAKGLG 215
HG AL A++ A A +A V+ V L ++G G+ + R A+ G
Sbjct: 109 HG-ALYNMAAKDEELARAVARA----------VAAVDPDLILLGLA--GSALERAARAAG 155
Query: 216 MNVIAHDPYAQADRA 230
+ V A ADRA
Sbjct: 156 LRVAFE---AFADRA 167
>gnl|CDD|215300 PLN02545, PLN02545, 3-hydroxybutyryl-CoA dehydrogenase.
Length = 295
Score = 31.2 bits (71), Expect = 1.5
Identities = 13/41 (31%), Positives = 21/41 (51%), Gaps = 1/41 (2%)
Query: 193 KTLAVMGFGKVGTEVARRAKGLGMNVIAHDPYAQA-DRARA 232
K + V+G G++G+ +A+ A GM+V D A R
Sbjct: 5 KKVGVVGAGQMGSGIAQLAAAAGMDVWLLDSDPAALSRGLD 45
>gnl|CDD|235446 PRK05406, PRK05406, LamB/YcsF family protein; Provisional.
Length = 246
Score = 30.9 bits (71), Expect = 1.5
Identities = 23/75 (30%), Positives = 35/75 (46%), Gaps = 16/75 (21%)
Query: 156 HGIALLTAMARNIAQADASVKAGKWQRNKYVGVSLVGKTLAVMGFGKVGTEVARRAKGLG 215
HG AL A++ A ADA +A V+ V +L ++G G+E+ R A+ G
Sbjct: 112 HG-ALYNMAAKDPALADAVAEA----------VAAVDPSLILVGLA--GSELIRAAEEAG 158
Query: 216 MNVIAHDPYAQADRA 230
+ + ADRA
Sbjct: 159 LRTASE---VFADRA 170
>gnl|CDD|178923 PRK00194, PRK00194, hypothetical protein; Validated.
Length = 90
Score = 29.0 bits (66), Expect = 1.6
Identities = 9/20 (45%), Positives = 14/20 (70%)
Query: 530 DQPGIIGKVGSLLGDNNVNV 549
D+ GII V ++L + NVN+
Sbjct: 12 DKVGIIAGVSTVLAELNVNI 31
>gnl|CDD|178111 PLN02494, PLN02494, adenosylhomocysteinase.
Length = 477
Score = 31.4 bits (71), Expect = 1.7
Identities = 22/67 (32%), Positives = 33/67 (49%), Gaps = 4/67 (5%)
Query: 188 VSLVGKTLAVMGFGKVGTEVARRAKGLGMNVIAH--DPYAQADRARATGVGLVSFEEAIS 245
V + GK + G+G VG A K G VI DP A +A G +++ E+ +S
Sbjct: 250 VMIAGKVAVICGYGDVGKGCAAAMKAAGARVIVTEIDPIC-ALQALMEGYQVLTLEDVVS 308
Query: 246 TAD-FIS 251
AD F++
Sbjct: 309 EADIFVT 315
>gnl|CDD|223643 COG0569, TrkA, K+ transport systems, NAD-binding component
[Inorganic ion transport and metabolism].
Length = 225
Score = 30.7 bits (70), Expect = 1.9
Identities = 10/28 (35%), Positives = 15/28 (53%)
Query: 193 KTLAVMGFGKVGTEVARRAKGLGMNVIA 220
+ ++G G+VG VAR G NV+
Sbjct: 1 MKIIIIGAGRVGRSVARELSEEGHNVVL 28
>gnl|CDD|227376 COG5043, MRS6, Vacuolar protein sorting-associated protein
[Intracellular trafficking and secretion].
Length = 2552
Score = 31.0 bits (70), Expect = 2.3
Identities = 13/65 (20%), Positives = 22/65 (33%)
Query: 229 RARATGVGLVSFEEAISTADFISLHMPLTPATSKMFNDEAFFKMKKGVRIVNVARGGVVD 288
R + +V E ++ +L +P F+D F + K V + VD
Sbjct: 873 RVTSNSNDIVDKEFTYPSSLCDNLLSRSSPKPKNNFDDTVFIEYKSIDYDVLDSVYEEVD 932
Query: 289 EEALV 293
V
Sbjct: 933 TTIAV 937
>gnl|CDD|223842 COG0771, MurD, UDP-N-acetylmuramoylalanine-D-glutamate ligase [Cell
envelope biogenesis, outer membrane].
Length = 448
Score = 30.7 bits (70), Expect = 2.3
Identities = 13/35 (37%), Positives = 15/35 (42%)
Query: 188 VSLVGKTLAVMGFGKVGTEVARRAKGLGMNVIAHD 222
GK + V+G GK G AR LG V D
Sbjct: 3 EDFQGKKVLVLGLGKSGLAAARFLLKLGAEVTVSD 37
>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 = 30.4 bits (69), Expect = 2.4
Identities = 21/61 (34%), Positives = 30/61 (49%), Gaps = 3/61 (4%)
Query: 180 WQRNKYVGVSLVGKTLAVMGFGKVGTEVARRAKGLGM-NVIAHDPYAQ-ADRARATGVGL 237
+ + VGVS T+ V+G G VG A+ LG +VI DP + + A+A G
Sbjct: 153 YHALRRVGVSGRD-TVLVVGAGPVGLGALMLARALGAEDVIGVDPSPERLELAKALGADF 211
Query: 238 V 238
V
Sbjct: 212 V 212
>gnl|CDD|223936 COG1004, Ugd, Predicted UDP-glucose 6-dehydrogenase [Cell envelope
biogenesis, outer membrane].
Length = 414
Score = 30.6 bits (70), Expect = 2.8
Identities = 26/73 (35%), Positives = 35/73 (47%), Gaps = 12/73 (16%)
Query: 190 LVGKTLAVMGFG-KVGT---------EVARRAKGLGMNVIAHDPYA-QADRARATGVGLV 238
L GKT+AV+G K T ++ +R + G VIA+DP A + V L
Sbjct: 308 LKGKTIAVLGLAFKPNTDDMRESPALDIIKRLQEKGAEVIAYDPVAMENAFRNFPDVELE 367
Query: 239 S-FEEAISTADFI 250
S EEA+ AD I
Sbjct: 368 SDAEEALKGADAI 380
>gnl|CDD|223106 COG0027, PurT, Formate-dependent phosphoribosylglycinamide
formyltransferase (GAR transformylase) [Nucleotide
transport and metabolism].
Length = 394
Score = 30.4 bits (69), Expect = 2.8
Identities = 16/35 (45%), Positives = 23/35 (65%)
Query: 193 KTLAVMGFGKVGTEVARRAKGLGMNVIAHDPYAQA 227
+ ++G G++G EVA A+ LG+ VIA D YA A
Sbjct: 13 TKVMLLGSGELGKEVAIEAQRLGVEVIAVDRYANA 47
>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 = 30.5 bits (69), Expect = 2.9
Identities = 16/30 (53%), Positives = 21/30 (70%)
Query: 198 MGFGKVGTEVARRAKGLGMNVIAHDPYAQA 227
+G G++G EVA A+ LG+ VIA D YA A
Sbjct: 5 LGSGELGKEVAIEAQRLGVEVIAVDRYANA 34
>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 = 27.5 bits (62), Expect = 3.0
Identities = 6/25 (24%), Positives = 16/25 (64%)
Query: 530 DQPGIIGKVGSLLGDNNVNVNFMSV 554
++PG + +V +L + +N+ +S+
Sbjct: 7 NKPGRLAEVTEILAEAGINIKAISI 31
>gnl|CDD|235986 PRK07313, PRK07313, phosphopantothenoylcysteine decarboxylase;
Validated.
Length = 182
Score = 29.5 bits (67), Expect = 3.0
Identities = 26/98 (26%), Positives = 44/98 (44%), Gaps = 19/98 (19%)
Query: 71 KNFANVDCSYNLSPEELCTKISLCDALIVRSGTKVTREVFESSAGRLKVVGRAGVGIDNV 130
K V + + T ++L L S V +V + +L ++++
Sbjct: 26 KRGYQVTVLMTKAATKFITPLTL-QVL---SKNPVHLDVMDEHDPKL---------MNHI 72
Query: 131 DLSAATEHGCLVVNAP-TANTIAAAEHGIA--LLTAMA 165
+L+ + L + AP TANTIA HGIA L+T++A
Sbjct: 73 ELAKRAD---LFLVAPATANTIAKLAHGIADDLVTSVA 107
>gnl|CDD|237059 PRK12325, PRK12325, prolyl-tRNA synthetase; Provisional.
Length = 439
Score = 30.2 bits (69), Expect = 3.8
Identities = 20/55 (36%), Positives = 30/55 (54%), Gaps = 8/55 (14%)
Query: 484 FGSAISDIGDIRVEGRVKDGKPHLTKVGSFGVDVS-LEGSIILCRQV--DQPGII 535
FG+ S+ + +V+G DGK +GS+G+ VS L +II + D GII
Sbjct: 289 FGTKYSEPMNAKVQG--PDGKEVPVHMGSYGIGVSRLVAAII---EASHDDKGII 338
>gnl|CDD|233242 TIGR01035, hemA, glutamyl-tRNA reductase. This enzyme, together
with glutamate-1-semialdehyde-2,1-aminomutase
(TIGR00713), leads to the production of
delta-amino-levulinic acid from Glu-tRNA [Biosynthesis
of cofactors, prosthetic groups, and carriers, Heme,
porphyrin, and cobalamin].
Length = 417
Score = 30.0 bits (68), Expect = 4.1
Identities = 21/68 (30%), Positives = 33/68 (48%), Gaps = 6/68 (8%)
Query: 189 SLVGKTLAVMGFGKVGTEVAR--RAKGLGMNVIAHDPYAQ----ADRARATGVGLVSFEE 242
SL GK ++G G++G VA+ KG+G +IA+ Y + A V EE
Sbjct: 177 SLKGKKALLIGAGEMGELVAKHLLRKGVGKILIANRTYERAEDLAKELGGEAVKFEDLEE 236
Query: 243 AISTADFI 250
++ AD +
Sbjct: 237 YLAEADIV 244
>gnl|CDD|182236 PRK10093, PRK10093, primosomal replication protein N'';
Provisional.
Length = 171
Score = 29.1 bits (65), Expect = 4.5
Identities = 14/37 (37%), Positives = 18/37 (48%), Gaps = 6/37 (16%)
Query: 154 AEHGIALLTAMARNIA-----QAD-ASVKAGKWQRNK 184
AEH A L A+AR A + D A +WQR +
Sbjct: 72 AEHLAAQLEAIAREAAAWSLREWDSAPPGLARWQRKR 108
>gnl|CDD|217035 pfam02441, Flavoprotein, Flavoprotein. This family contains
diverse flavoprotein enzymes. This family includes
epidermin biosynthesis protein, EpiD, which has been
shown to be a flavoprotein that binds FMN. This enzyme
catalyzes the removal of two reducing equivalents from
the cysteine residue of the C-terminal meso-lanthionine
of epidermin to form a --C==C-- double bond. This family
also includes the B chain of dipicolinate synthase a
small polar molecule that accumulates to high
concentrations in bacterial endospores, and is thought
to play a role in spore heat resistance, or the
maintenance of heat resistance. dipicolinate synthase
catalyzes the formation of dipicolinic acid from
dihydroxydipicolinic acid. This family also includes
phenyl-acrylic acid decarboxylase (EC:4.1.1.-).
Length = 132
Score = 28.7 bits (65), Expect = 4.6
Identities = 16/29 (55%), Positives = 19/29 (65%), Gaps = 3/29 (10%)
Query: 141 LVVNAP-TANTIAAAEHGIA--LLTAMAR 166
L+V AP TANT+A +GIA LLT A
Sbjct: 79 LMVVAPATANTLAKIANGIADNLLTRAAL 107
>gnl|CDD|180326 PRK05954, PRK05954, precorrin-8X methylmutase; Provisional.
Length = 203
Score = 29.3 bits (66), Expect = 4.9
Identities = 17/37 (45%), Positives = 21/37 (56%), Gaps = 5/37 (13%)
Query: 469 PLEFIQVQIANVESKFGSAISDIGDIRVEGRVKDGKP 505
P+ F+ V VE+K A D+ IRVEGR K G P
Sbjct: 155 PVGFVSV----VEAKQALAQLDVPQIRVEGR-KGGSP 186
>gnl|CDD|176192 cd08230, glucose_DH, Glucose dehydrogenase. Glucose dehydrogenase
(GlcDH), a member of the medium chain
dehydrogenase/zinc-dependent alcohol dehydrogenase-like
family, catalyzes the NADP(+)-dependent oxidation of
glucose to gluconate, the first step in the
Entner-Doudoroff pathway, an alternative to or
substitute for glycolysis or the pentose phosphate
pathway. 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-Rossman 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 = 355
Score = 29.5 bits (67), Expect = 5.1
Identities = 21/64 (32%), Positives = 29/64 (45%), Gaps = 13/64 (20%)
Query: 273 KKGVRIVNVARGGVVDEEALVRAL-------DSGIISQAALDVFTEEPPAKDSKLVL-HE 324
K GVR+V++ E LVR L D I++ + PP +D LVL HE
Sbjct: 10 KPGVRVVDIPEPEPTPGEVLVRTLEVGVCGTDREIVA----GEYGTAPPGED-FLVLGHE 64
Query: 325 NVTV 328
+ V
Sbjct: 65 ALGV 68
>gnl|CDD|168796 PRK07066, PRK07066, 3-hydroxybutyryl-CoA dehydrogenase; Validated.
Length = 321
Score = 29.4 bits (66), Expect = 5.1
Identities = 24/85 (28%), Positives = 34/85 (40%), Gaps = 22/85 (25%)
Query: 193 KTLAVMGFGKVGTEVARRAKGLGMNVIAHDPYAQAD---RARATG-------VGLV---- 238
KT A +G G +G+ RA G++V+A DP A+ RA GL
Sbjct: 8 KTFAAIGSGVIGSGWVARALAHGLDVVAWDPAPGAEAALRANVANAWPALERQGLAPGAS 67
Query: 239 --------SFEEAISTADFISLHMP 255
+ E ++ ADFI P
Sbjct: 68 PARLRFVATIEACVADADFIQESAP 92
>gnl|CDD|235707 PRK06130, PRK06130, 3-hydroxybutyryl-CoA dehydrogenase; Validated.
Length = 311
Score = 29.4 bits (66), Expect = 5.2
Identities = 17/72 (23%), Positives = 30/72 (41%), Gaps = 17/72 (23%)
Query: 193 KTLAVMGFGKVGTEVARRAKGLGMNVIAHDPYAQA-DRARAT----------------GV 235
+ LA++G G +G+ +A G+ V+ D A +RAR G+
Sbjct: 5 QNLAIIGAGTMGSGIAALFARKGLQVVLIDVMEGALERARGVIERALGVYAPLGIASAGM 64
Query: 236 GLVSFEEAISTA 247
G + E ++ A
Sbjct: 65 GRIRMEAGLAAA 76
>gnl|CDD|233118 TIGR00761, argB, acetylglutamate kinase. This model describes
N-acetylglutamate kinases (ArgB) of many prokaryotes and
the N-acetylglutamate kinase domains of multifunctional
proteins from yeasts. This enzyme is the second step in
the "acetylated" ornithine biosynthesis pathway. A
related group of enzymes representing the first step of
the pathway contain a homologous domain and are excluded
from this model [Amino acid biosynthesis, Glutamate
family].
Length = 231
Score = 29.2 bits (66), Expect = 5.5
Identities = 20/79 (25%), Positives = 31/79 (39%), Gaps = 10/79 (12%)
Query: 380 FVTLAEKLGGLAVQLVAGGSGVKSVKVSYASARG----PDDLDTRLLRAMITKGIIEPIS 435
V L K G A+ L G + + + G ++ L+ A++ G I IS
Sbjct: 82 LVALLNKHGINAIGLTGGDGQLFTARYLDKEDLGYVGEIKKVNKALIEALLKAGYIPVIS 141
Query: 436 SVFVNL------VNADFIA 448
S+ + VNAD A
Sbjct: 142 SLALTAEGQALNVNADTAA 160
>gnl|CDD|130753 TIGR01692, HIBADH, 3-hydroxyisobutyrate dehydrogenase.
3-hydroxyisobutyrate dehydrogenase is an enzyme that
catalyzes the NAD+-dependent oxidation of
3-hydroxyisobutyrate to methylmalonate semialdehyde of
the valine catabolism pathway. In Pseudomonas
aeruginosa, 3-hydroxyisobutyrate dehydrogenase (mmsB) is
co-induced with methylmalonate-semialdehyde
dehydrogenase (mmsA) when grown on medium containing
valine as the sole carbon source. The positive
transcriptional regulator of this operon (mmsR) is
located upstream of these genes and has been identified
as a member of the XylS/AraC family of transcriptional
regulators. 3-hydroxyisobutyrate dehydrogenase shares
high sequence homology to the characterized
3-hydroxyisobutyrate dehydrogenase from rat liver with
conservation of proposed NAD+ binding residues at the
N-terminus (G-8,10,13,24 and D-31). This enzyme belongs
to the 3-hydroxyacid dehydrogenase family, sharing a
common evolutionary origin and enzymatic mechanism with
6-phosphogluconate. HIBADH exhibits sequence similarity
to the NAD binding domain of 6-phosphogluconate
dehydrogenase above trusted (pfam03446) [Energy
metabolism, Amino acids and amines].
Length = 288
Score = 29.4 bits (66), Expect = 5.6
Identities = 33/154 (21%), Positives = 55/154 (35%), Gaps = 33/154 (21%)
Query: 68 DVLKNFANVDCSYNLSPEELCTKISLCDALI--VRSGTKVTREVFESSAGRLKVVGRAGV 125
D ++ SP E D +I + +G V V+ G L V + +
Sbjct: 30 DAVEEAVAAGAQAAASPAEAAEGA---DRVITMLPAGQHV-ISVYSGDEGILPKVAKGSL 85
Query: 126 GID----NVDLS-----AATEHGCLVVNAPTANTIAAAEHGI----------------AL 160
ID + D + A HG + ++AP + + A G +
Sbjct: 86 LIDCSTIDPDSARKLAELAAAHGAVFMDAPVSGGVGGARAGTLTFMVGGVAEEFAAAEPV 145
Query: 161 LTAMARNI--AQADASVKAGKWQRNKYVGVSLVG 192
L M RNI + +A K N +G+S++G
Sbjct: 146 LGPMGRNIVHCGDHGAGQAAKICNNMLLGISMIG 179
>gnl|CDD|200414 TIGR04163, rSAM_cobopep, peptide-modifying radical SAM enzyme CbpB.
Members of this family are radical SAM enzymes that
modify a short peptide encoded by an upstream gene. A
role in metal chelation is suggested.
Length = 428
Score = 29.4 bits (66), Expect = 6.1
Identities = 16/44 (36%), Positives = 22/44 (50%), Gaps = 11/44 (25%)
Query: 75 NVDCSYNLSPEELCTKISLCDALIVRSGTKVTREVFESSAGRLK 118
N++CSY PEE + RSG ++ E E + GRLK
Sbjct: 75 NLNCSYCYIPEE-----------MRRSGKHMSPEELEEALGRLK 107
>gnl|CDD|233483 TIGR01587, cas3_core, CRISPR-associated helicase Cas3. This model
represents the highly conserved core region of an
alignment of Cas3, a protein found in association with
CRISPR repeat elements in a broad range of bacteria and
archaea. Cas3 appears to be a helicase, with regions
found by pfam00270 (DEAD/DEAH box helicase) and
pfam00271 (Helicase conserved C-terminal domain). Some
but not all members have an N-terminal HD domain region
(pfam01966) that is not included within this model
[Mobile and extrachromosomal element functions, Other].
Length = 358
Score = 29.3 bits (66), Expect = 6.4
Identities = 18/67 (26%), Positives = 29/67 (43%), Gaps = 15/67 (22%)
Query: 36 RRRKTKRFAVLATFITSKPTVLVAEKLGEAGLDVLKNFANVDCSYNLSPEELCTKISLCD 95
R +K +L ++ V+VA ++ EA LD+ S ++ EL D
Sbjct: 263 RAKKEAE--LLEEMKKNEKFVIVATQVIEASLDI---------SADVMITELAP----ID 307
Query: 96 ALIVRSG 102
+LI R G
Sbjct: 308 SLIQRLG 314
>gnl|CDD|235513 PRK05579, PRK05579, bifunctional phosphopantothenoylcysteine
decarboxylase/phosphopantothenate synthase; Validated.
Length = 399
Score = 29.3 bits (67), Expect = 6.4
Identities = 15/28 (53%), Positives = 17/28 (60%), Gaps = 3/28 (10%)
Query: 141 LVVNAP-TANTIAAAEHGIA--LLTAMA 165
LV+ AP TA+ IA HGIA LLT
Sbjct: 85 LVLIAPATADLIAKLAHGIADDLLTTTL 112
>gnl|CDD|224995 COG2084, MmsB, 3-hydroxyisobutyrate dehydrogenase and related
beta-hydroxyacid dehydrogenases [Lipid metabolism].
Length = 286
Score = 29.1 bits (66), Expect = 6.5
Identities = 18/70 (25%), Positives = 29/70 (41%), Gaps = 3/70 (4%)
Query: 193 KTLAVMGFGKVGTEVARR--AKGLGMNVIAHDPYAQADRARATGVGLV-SFEEAISTADF 249
+A +G G +G+ +A G + V P A+ A G + S EA + AD
Sbjct: 1 MKIAFIGLGIMGSPMAANLLKAGHEVTVYNRTPEKAAELLAAAGATVAASPAEAAAEADV 60
Query: 250 ISLHMPLTPA 259
+ +P A
Sbjct: 61 VITMLPDDAA 70
>gnl|CDD|237729 PRK14491, PRK14491, putative bifunctional molybdopterin-guanine
dinucleotide biosynthesis protein MobB/MoeA;
Provisional.
Length = 597
Score = 29.2 bits (66), Expect = 7.4
Identities = 21/56 (37%), Positives = 30/56 (53%), Gaps = 7/56 (12%)
Query: 103 TKVTREVFESSA-GRLKVV--GRAGVGIDNVDLSAATEHGCLVVNAPTANTIAAAE 155
T+ +R ++ A GRL V G+ G GI LS+ +E CL+ P A T+ A E
Sbjct: 535 TEFSRGIYHLGADGRLHVRTTGKQGSGI----LSSMSEANCLIEIGPAAETVNAGE 586
>gnl|CDD|201125 pfam00271, Helicase_C, Helicase conserved C-terminal domain. The
Prosite family is restricted to DEAD/H helicases,
whereas this domain family is found in a wide variety
of helicases and helicase related proteins. It may be
that this is not an autonomously folding unit, but an
integral part of the helicase.
Length = 78
Score = 26.7 bits (60), Expect = 7.5
Identities = 10/34 (29%), Positives = 16/34 (47%)
Query: 36 RRRKTKRFAVLATFITSKPTVLVAEKLGEAGLDV 69
+ +R +L F K VLVA + G+D+
Sbjct: 16 GLSQEEREEILEDFRNGKSKVLVATDVAGRGIDL 49
>gnl|CDD|187770 cd09639, Cas3_I, CRISPR/Cas system-associated protein Cas3. CRISPR
(Clustered Regularly Interspaced Short Palindromic
Repeats) and associated Cas proteins comprise a system
for heritable host defense by prokaryotic cells against
phage and other foreign DNA; DEAD/DEAH box helicase DNA
helicase cas3'; Often but not always is fused to HD
nuclease domain; signature gene for Type I.
Length = 353
Score = 28.9 bits (65), Expect = 7.8
Identities = 20/67 (29%), Positives = 29/67 (43%), Gaps = 15/67 (22%)
Query: 36 RRRKTKRFAVLATFITSKPTVLVAEKLGEAGLDVLKNFANVDCSYNLSPEELCTKISLCD 95
R +K L F S+ V+VA ++ EA LD+ S ++ EL D
Sbjct: 259 RAKKEAEL--LLEFKKSEKFVIVATQVIEASLDI---------SVDVMITELAP----ID 303
Query: 96 ALIVRSG 102
+LI R G
Sbjct: 304 SLIQRLG 310
>gnl|CDD|132039 TIGR02994, ectoine_eutE, ectoine utilization protein EutE. Members
of this family, part of the succinylglutamate
desuccinylase / aspartoacylase family (pfam04952),
belong to ectoine utilization operons, as found in
Sinorhizobium meliloti 1021 (where it the operon is
known to be induced by ectoine), Mesorhizobium loti,
Silicibacter pomeroyi, Agrobacterium tumefaciens, and
Pseudomonas putida.
Length = 325
Score = 29.0 bits (65), Expect = 7.9
Identities = 26/92 (28%), Positives = 43/92 (46%), Gaps = 6/92 (6%)
Query: 356 KGELAATAVNAP--MVPAEVISELAPFVTLAEKLGGLAVQLVAGGSGVKSVKVSYASARG 413
K A A AP M E I + + T AE++G + V GG G S + + RG
Sbjct: 168 KCFDAVAAFAAPYSMKMLE-IDSVGMYDTAAEEMGKVFVTTELGGGGTASARTIKIAKRG 226
Query: 414 PDDLDTRLLRAMITKGIIEPISSVFVNLVNAD 445
++ L A I KG +E ++++++ + D
Sbjct: 227 VRNV---LRHAGILKGELEIAPTIWLDMPSDD 255
>gnl|CDD|225186 COG2303, BetA, Choline dehydrogenase and related flavoproteins
[Amino acid transport and metabolism].
Length = 542
Score = 29.0 bits (65), Expect = 8.0
Identities = 37/183 (20%), Positives = 51/183 (27%), Gaps = 20/183 (10%)
Query: 96 ALIVRSGTKVTREVFESSAGRLKVVGRAGVGIDNVDLSAATEHGCLVVNAPTANTIAAAE 155
L + +G +V R + E G + VG D + VV A A I +
Sbjct: 217 NLTLLTGARVRRILLE---GD-RAVGVEVEIGDGGTI-ETAVAAREVVLA--AGAINSP- 268
Query: 156 HGIALLTAMARNIAQADASVKAGKWQ--RNKYVGVSLVGKTLAVMGFGKVGTEVARRAKG 213
LL + I AD ++ G R VG +L + F
Sbjct: 269 ---KLL--LLSGIGPADHLLEHGIDVVGRLPGVGQNLQDHLEIYVAFEATEPTNDSVLSL 323
Query: 214 LGMNVIAHDPYAQADR-ARATGVGLVSF---EEAISTADFISLHMPLTPATSKMFNDEAF 269
I D Y AT F A D H P + E
Sbjct: 324 FSKLGIGADRYLLTRDGPGATNHFEGGFVRSGPAGEYPD-GQYHFAPLPLAIRAAGAEHG 382
Query: 270 FKM 272
F +
Sbjct: 383 FTL 385
>gnl|CDD|236454 PRK09288, purT, phosphoribosylglycinamide formyltransferase 2;
Validated.
Length = 395
Score = 28.9 bits (66), Expect = 8.6
Identities = 18/33 (54%), Positives = 22/33 (66%), Gaps = 2/33 (6%)
Query: 197 VM--GFGKVGTEVARRAKGLGMNVIAHDPYAQA 227
VM G G++G EVA A+ LG+ VIA D YA A
Sbjct: 15 VMLLGSGELGKEVAIEAQRLGVEVIAVDRYANA 47
>gnl|CDD|235783 PRK06349, PRK06349, homoserine dehydrogenase; Provisional.
Length = 426
Score = 28.9 bits (66), Expect = 9.0
Identities = 12/66 (18%), Positives = 29/66 (43%), Gaps = 4/66 (6%)
Query: 529 VDQPGIIGKVGSLLGDNNVNVNFMSVGRIAPQKQA---VMTIGVDEEPSREVLKKIGETP 585
D+PG++ K+ ++ +N +++ + + + A + A ++T E R L I
Sbjct: 356 ADKPGVLAKIAAIFAENGISIESI-LQKGAGGEGAEIVIVTHETSEAALRAALAAIEALD 414
Query: 586 AIEEFV 591
+
Sbjct: 415 VVLGIP 420
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 0.133 0.365
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: 30,295,571
Number of extensions: 3104480
Number of successful extensions: 3695
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3497
Number of HSP's successfully gapped: 200
Length of query: 595
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 493
Effective length of database: 6,413,494
Effective search space: 3161852542
Effective search space used: 3161852542
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)