RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 006864
(628 letters)
>gnl|CDD|237436 PRK13581, PRK13581, D-3-phosphoglycerate dehydrogenase;
Provisional.
Length = 526
Score = 635 bits (1642), Expect = 0.0
Identities = 257/535 (48%), Positives = 342/535 (63%), Gaps = 24/535 (4%)
Query: 91 PTILVSEKLGEAGLAILRSFGNVECLY--DLSPEALCEKISQCDALIVRSGTKVTRSVFE 148
+LVS+ + AGL IL+ VE L E L E I DALIVRS TKVT V E
Sbjct: 1 MKVLVSDPISPAGLEILKDAPGVEVDVKTGLDKEELLEIIGDYDALIVRSATKVTAEVLE 60
Query: 149 AANGKLKVVGRAGVGIDNVDLQAATEFGCLVVNAPIANTVAAAEHGIALLASMARNVSQA 208
AA LKV+GRAGVG+DNVD+ AAT G +VVNAP NT++AAEH IAL+ ++ARN+ QA
Sbjct: 61 AA-KNLKVIGRAGVGVDNVDVPAATRRGIIVVNAPTGNTISAAEHTIALMLALARNIPQA 119
Query: 209 DASIKAGKWLRSKYVGVSLVGKTLAVMGFGKVGSEVARRAKGLGMNVIAHDPYAPADKAR 268
AS+KAGKW R K++GV L GKTL ++G G++GSEVA+RAK GM VIA+DPY ++A
Sbjct: 120 HASLKAGKWERKKFMGVELYGKTLGIIGLGRIGSEVAKRAKAFGMKVIAYDPYISPERAA 179
Query: 269 AVGVELVSFDQALATADFISLHMPLNPTTSKIFNDETFAKMKKGVRIVNVARGGVIDEEA 328
+GVELVS D+ LA ADFI+LH PL P T + E AKMK GVRI+N ARGG+IDE A
Sbjct: 180 QLGVELVSLDELLARADFITLHTPLTPETRGLIGAEELAKMKPGVRIINCARGGIIDEAA 239
Query: 329 LVRALDSGVVAQAALDVFTEEPPAKDSKLVQHENVTVTPHLGASTKEAQEGVAIEIAEAV 388
L AL SG VA AALDVF +EPP DS L + NV VTPHLGAST EAQE VAI++AE V
Sbjct: 240 LAEALKSGKVAGAALDVFEKEPP-TDSPLFELPNVVVTPHLGASTAEAQENVAIQVAEQV 298
Query: 389 VGALRGELSATAINAPMVPSEVLSELAPYVVLAKKLGRLAVQLVSGGSGIKSVKLIYRSA 448
+ ALRG A+N P + +E +L PY+ LA+KLG LA QL IKSV++ YR
Sbjct: 299 IDALRGGPVPNAVNLPSITAEEAEKLKPYLDLAEKLGSLAAQLA--DGPIKSVEITYRG- 355
Query: 449 RDPDDLDTRILRAMITKGIIEPISASFINLVNADFTAKQKGLRISEERVVADSSPEFPID 508
+ + DT L A KG++ P+ +N VNA AK++G+ + E + ++ SP++ +
Sbjct: 356 -ELAEEDTEPLTAAALKGLLSPVLGERVNYVNAPLLAKERGIEVEESK--SEESPDYS-N 411
Query: 509 SIQVQLSNVDSKFAAAVSENGEISIEGKVKFG--IPHLTRVGSFGVDASLEGNLILCRQV 566
I V +++GE S+ G V FG P + + + VDA EG++++ R
Sbjct: 412 LITVT----------VTTDDGERSVAGTV-FGDGEPRIVEIDGYRVDAKPEGHMLIIRNR 460
Query: 567 DQPGMIGKVGNILGEHNVNVNFMSVGRTFRRNHGIMAIGVDEEPNQDSLKEIGKV 621
D+PG+IGKVG +LGE +N+ M +GR +M + VD+ ++ L+E+ +
Sbjct: 461 DRPGVIGKVGTLLGEAGINIAGMQLGRREAGGEALMVLSVDDPVPEEVLEELRAL 515
>gnl|CDD|233358 TIGR01327, PGDH, D-3-phosphoglycerate dehydrogenase. This model
represents a long form of D-3-phosphoglycerate
dehydrogenase, the serA gene of one pathway of serine
biosynthesis. Shorter forms, scoring between trusted and
noise cutoff, include SerA from E. coli [Amino acid
biosynthesis, Serine family].
Length = 525
Score = 518 bits (1335), Expect = e-179
Identities = 236/533 (44%), Positives = 340/533 (63%), Gaps = 24/533 (4%)
Query: 93 ILVSEKLGEAGLAILRSFG-NVECLYDLSPEALCEKISQCDALIVRSGTKVTRSVFEAAN 151
+L+++ + G+ IL G V+ LS E L E I DALIVRS TKVT V AA
Sbjct: 2 VLIADPISPDGIDILEDVGVEVDVQTGLSREELLEIIPDYDALIVRSATKVTEEVIAAAP 61
Query: 152 GKLKVVGRAGVGIDNVDLQAATEFGCLVVNAPIANTVAAAEHGIALLASMARNVSQADAS 211
KLKV+GRAGVG+DN+D++AAT G LVVNAP NT++AAEH +A+L + ARN+ QADAS
Sbjct: 62 -KLKVIGRAGVGVDNIDIEAATARGILVVNAPTGNTISAAEHALAMLLAAARNIPQADAS 120
Query: 212 IKAGKWLRSKYVGVSLVGKTLAVMGFGKVGSEVARRAKGLGMNVIAHDPYAPADKARAVG 271
+K G+W R ++G L GKTL V+G G++GS VA+RAK GM V+A+DPY ++A +G
Sbjct: 121 LKEGEWDRKAFMGTELYGKTLGVIGLGRIGSIVAKRAKAFGMKVLAYDPYISPERAEQLG 180
Query: 272 VELV-SFDQALATADFISLHMPLNPTTSKIFNDETFAKMKKGVRIVNVARGGVIDEEALV 330
VELV D+ LA ADFI++H PL P T + E AKMKKGV IVN ARGG+IDE AL
Sbjct: 181 VELVDDLDELLARADFITVHTPLTPETRGLIGAEELAKMKKGVIIVNCARGGIIDEAALY 240
Query: 331 RALDSGVVAQAALDVFTEEPPAKDSKLVQHENVTVTPHLGASTKEAQEGVAIEIAEAVVG 390
AL+ G V AALDVF +EPP D+ L +NV TPHLGAST+EAQE VA ++AE V+
Sbjct: 241 EALEEGHVRAAALDVFEKEPP-TDNPLFDLDNVIATPHLGASTREAQENVATQVAEQVLD 299
Query: 391 ALRGELSATAINAPMVPSEVLSELAPYVVLAKKLGRLAVQLVSGGSGIKSVKLIYRSARD 450
AL+G A+NAP + ++V+ +L PY+ LA+KLG+LA QL+ G ++SV++ YR +
Sbjct: 300 ALKGLPVPNAVNAPGIDADVMEKLKPYLDLAEKLGKLAGQLLDG--AVQSVEVTYRG--E 355
Query: 451 PDDLDTRILRAMITKGIIEPISASFINLVNADFTAKQKGLRISEERVVADSSPEFPIDSI 510
++ L KG++ P+ +N+VNA AK++G+ + E + ++SSP++ + +
Sbjct: 356 LATENSEPLTRAALKGLLSPVLDDEVNMVNAPAVAKERGITVEESK--SESSPDYK-NYL 412
Query: 511 QVQLSNVDSKFAAAVSENGEISIEGKVKFG--IPHLTRVGSFGVDASLEGNLILCRQVDQ 568
V ++ ++G +S+ G V FG P + + F VD EG +++ +D+
Sbjct: 413 SVTVTG----------DSGTVSVAGTV-FGGFSPRIVEIDGFHVDLEPEGIMLIILHLDK 461
Query: 569 PGMIGKVGNILGEHNVNVNFMSVGRTFRRNHGIMAIGVDEEPNQDSLKEIGKV 621
PG+IGKVG +LG +N+ M +GR + +M + +D+ + L+EI +
Sbjct: 462 PGVIGKVGTLLGTAGINIASMQLGRKEKGGEALMLLSLDQPVPDEVLEEIKAI 514
>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 = 474 bits (1222), Expect = e-165
Identities = 175/304 (57%), Positives = 221/304 (72%), Gaps = 2/304 (0%)
Query: 93 ILVSEKLGEAGLAILRSFG-NVECLYDLSPEALCEKISQCDALIVRSGTKVTRSVFEAAN 151
+LV++ + E GL +LR G V+ LS E L I+ DALIVRS TKVT V EAA
Sbjct: 2 VLVTDPIDEEGLELLREAGIEVDVAPGLSEEELLAIIADADALIVRSATKVTAEVIEAA- 60
Query: 152 GKLKVVGRAGVGIDNVDLQAATEFGCLVVNAPIANTVAAAEHGIALLASMARNVSQADAS 211
+LKV+GRAGVG+DN+D++AAT G LVVNAP ANT++ AEH IAL+ ++ARN+ QADAS
Sbjct: 61 PRLKVIGRAGVGVDNIDVEAATARGILVVNAPGANTISVAEHTIALMLALARNIPQADAS 120
Query: 212 IKAGKWLRSKYVGVSLVGKTLAVMGFGKVGSEVARRAKGLGMNVIAHDPYAPADKARAVG 271
++AGKW R K++GV L GKTL ++G G++G EVARRA+ GM V+A+DPY A++A A G
Sbjct: 121 LRAGKWDRKKFMGVELRGKTLGIVGLGRIGREVARRARAFGMKVLAYDPYISAERAAAGG 180
Query: 272 VELVSFDQALATADFISLHMPLNPTTSKIFNDETFAKMKKGVRIVNVARGGVIDEEALVR 331
VELVS D+ LA ADFISLH PL P T + N E AKMK G ++N ARGG++DE AL
Sbjct: 181 VELVSLDELLAEADFISLHTPLTPETRGLINAEELAKMKPGAILINTARGGIVDEAALAD 240
Query: 332 ALDSGVVAQAALDVFTEEPPAKDSKLVQHENVTVTPHLGASTKEAQEGVAIEIAEAVVGA 391
AL SG +A AALDVF +EPP DS L+ NV +TPHLGAST+EAQE VA++ AE V+
Sbjct: 241 ALKSGKIAGAALDVFEQEPPPADSPLLGLPNVILTPHLGASTEEAQERVAVDAAEQVLAV 300
Query: 392 LRGE 395
L GE
Sbjct: 301 LAGE 304
>gnl|CDD|223189 COG0111, SerA, Phosphoglycerate dehydrogenase and related
dehydrogenases [Amino acid transport and metabolism].
Length = 324
Score = 349 bits (898), Expect = e-116
Identities = 155/327 (47%), Positives = 201/327 (61%), Gaps = 7/327 (2%)
Query: 88 TPKPTILVSEKLGEAGLAILRSFGNVECL--YDLSPEALCEKISQCDALIVRSGTKVTRS 145
+LV++ L L L + +VE DL E L E ++ DALIV S T VT
Sbjct: 1 KMMIKVLVTDPLAPDALEELLAAYDVEVPDGPDLDEEELLEALADADALIV-SVTPVTEE 59
Query: 146 VFEAANGKLKVVGRAGVGIDNVDLQAATEFGCLVVNAPIANTVAAAEHGIALLASMARNV 205
V AA LK +GRAG G+DN+DL+AAT+ G LVVNAP N ++ AE +ALL ++AR +
Sbjct: 60 VLAAAP-NLKAIGRAGAGVDNIDLEAATKRGILVVNAPGGNAISVAELVLALLLALARRI 118
Query: 206 SQADASIKAGKWLRSKYVGVSLVGKTLAVMGFGKVGSEVARRAKGLGMNVIAHDPYAPAD 265
ADAS + G+W R + G L GKT+ ++G G++G VA+R K GM VI +DPY+P +
Sbjct: 119 PDADASQRRGEWDRKAFRGTELAGKTVGIIGLGRIGRAVAKRLKAFGMKVIGYDPYSPRE 178
Query: 266 KARAVGVELV-SFDQALATADFISLHMPLNPTTSKIFNDETFAKMKKGVRIVNVARGGVI 324
+A GV V S D+ LA AD ++LH+PL P T + N E AKMK G ++N ARGGV+
Sbjct: 179 RAGVDGVVGVDSLDELLAEADILTLHLPLTPETRGLINAEELAKMKPGAILINAARGGVV 238
Query: 325 DEEALVRALDSGVVAQAALDVFTEEPPAKDSKLVQHENVTVTPHLGASTKEAQEGVAIEI 384
DE+AL+ ALDSG +A AALDVF EEP DS L NV +TPH+G ST EAQE VA +
Sbjct: 239 DEDALLAALDSGKIAGAALDVFEEEPLPADSPLWDLPNVILTPHIGGSTDEAQERVAEIV 298
Query: 385 AEAVVGALRGELSATAINAPMVPSEVL 411
AE +V L G NAP V E
Sbjct: 299 AENIVRYLAGG--PVVNNAPEVDLERG 323
>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 = 346 bits (890), Expect = e-115
Identities = 144/301 (47%), Positives = 203/301 (67%), Gaps = 3/301 (0%)
Query: 93 ILVSEKLGEAGLAILRSFG-NVECLYDLSPEALCEKISQCDALIVRSGTKVTRSVFEAAN 151
IL+++ + E + L G V+ ++ E L EKI D LIVRS TKVT+ V +AA
Sbjct: 3 ILITDGIDEIAIEKLEEAGFEVDYEPLIAKEELLEKIKDYDVLIVRSRTKVTKEVIDAA- 61
Query: 152 GKLKVVGRAGVGIDNVDLQAATEFGCLVVNAPIANTVAAAEHGIALLASMARNVSQADAS 211
LK++ RAGVG+DN+D++ A + G V+N P A++ + AE I L+ S+AR + +A+
Sbjct: 62 KNLKIIARAGVGLDNIDVEYAKKKGIKVINTPGASSNSVAELVIGLMLSLARFIHRANRE 121
Query: 212 IKAGKWLRSKYVGVSLVGKTLAVMGFGKVGSEVARRAKGLGMNVIAHDPYAPADKARAVG 271
+K GKW + KY G+ L GKTL ++GFG++G EVA+ A+ LGMNVIA+DPY ++A +G
Sbjct: 122 MKLGKWNKKKYKGIELRGKTLGIIGFGRIGREVAKIARALGMNVIAYDPYPKDEQAVELG 181
Query: 272 VELVSFDQALATADFISLHMPLNPTTSKIFNDETFAKMKKGVRIVNVARGGVIDEEALVR 331
V+ VS ++ L +DFISLH+PL P T + N + MK G I+N +RGGVIDEEAL+
Sbjct: 182 VKTVSLEELLKNSDFISLHVPLTPETKHMINKKELELMKDGAIIINTSRGGVIDEEALLE 241
Query: 332 ALDSGVVAQAALDVFTEEPPAKDSKLVQHENVTVTPHLGASTKEAQEGVAIEIAEAVVGA 391
AL SG +A AALDVF EPP SKL++ NV++TPH+GASTKEAQE + E+A ++
Sbjct: 242 ALKSGKLAGAALDVFENEPP-PGSKLLELPNVSLTPHIGASTKEAQERIGEELANKIIEF 300
Query: 392 L 392
L
Sbjct: 301 L 301
>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 = 337 bits (866), Expect = e-112
Identities = 137/313 (43%), Positives = 184/313 (58%), Gaps = 14/313 (4%)
Query: 86 AVTPKPTILVSEKLGEAGLAILRSFG-NVECL---YDLSPEALCEKISQCDALIVRSGT- 140
VTP+ K E +L + G V L+ E L E + D +I G
Sbjct: 3 LVTPRSF----SKYSEEAKELLEAAGFEVVLNPLGRPLTEEELIELLKDADGVIA--GLD 56
Query: 141 KVTRSVFEAANGKLKVVGRAGVGIDNVDLQAATEFGCLVVNAPIANTVAAAEHGIALLAS 200
+T V AA +LKV+ R GVG DN+DL+AA + G +V N P AN+ + AE I L+ +
Sbjct: 57 PITEEVLAAAP-RLKVISRYGVGYDNIDLEAAKKRGIVVTNTPGANSNSVAELTIGLMLA 115
Query: 201 MARNVSQADASIKAGKWLRSKYVGVSLVGKTLAVMGFGKVGSEVARRAKGLGMNVIAHDP 260
+AR + QAD ++AG W + VG L GKTL ++G G++G VARR G GM V+A+DP
Sbjct: 116 LARQIPQADREVRAGGW--DRPVGTELYGKTLGIIGLGRIGKAVARRLSGFGMKVLAYDP 173
Query: 261 YAPADKARAVGVELVSFDQALATADFISLHMPLNPTTSKIFNDETFAKMKKGVRIVNVAR 320
Y + A+ GVE VS ++ L +DFISLH+PL P T + N A MK G ++N AR
Sbjct: 174 YPDEEFAKEHGVEFVSLEELLKESDFISLHLPLTPETRHLINAAELALMKPGAILINTAR 233
Query: 321 GGVIDEEALVRALDSGVVAQAALDVFTEEPPAKDSKLVQHENVTVTPHLGASTKEAQEGV 380
GG++DEEAL AL SG +A AALDVF EEPP DS L++ NV +TPH+GASTKEA +
Sbjct: 234 GGLVDEEALYEALKSGRIAGAALDVFEEEPPPADSPLLELPNVILTPHIGASTKEAVLRM 293
Query: 381 AIEIAEAVVGALR 393
A+ V+ L
Sbjct: 294 GTMAAQNVIDVLA 306
>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 = 302 bits (775), Expect = 3e-98
Identities = 124/301 (41%), Positives = 175/301 (58%), Gaps = 4/301 (1%)
Query: 92 TILVSEKLGE-AGLAILRSFG-NVECLYDLSPEALCEKISQCDALIVRSGTKVTRSVFEA 149
+LV E L L L + G V DL + L ++ DALIV S T VT V
Sbjct: 1 KVLVLEPLFPPEALEALEATGFEVIVADDLLADELEALLADADALIVSSTTPVTAEVLAK 60
Query: 150 ANGKLKVVGRAGVGIDNVDLQAATEFGCLVVNAPIANTVAAAEHGIALLASMARNVSQAD 209
A KLK + AG G+DN+DL AA + G V N P AN A AEH + LL ++ R + +AD
Sbjct: 61 AP-KLKFIQVAGAGVDNIDLDAAKKRGITVTNVPGANAEAVAEHALGLLLALLRRLPRAD 119
Query: 210 ASIKAGK-WLRSKYVGVSLVGKTLAVMGFGKVGSEVARRAKGLGMNVIAHDPYAPADKAR 268
A+++ G WL + + G L GKT+ ++G G++G VA+R + GM V+ +D +
Sbjct: 120 AAVRRGWGWLWAGFPGYELEGKTVGIVGLGRIGQRVAKRLQAFGMKVLYYDRTRKPEPEE 179
Query: 269 AVGVELVSFDQALATADFISLHMPLNPTTSKIFNDETFAKMKKGVRIVNVARGGVIDEEA 328
+G +VS D+ LA +D + LH+PL P T + N+E A MK G +VN ARGG++DE+A
Sbjct: 180 DLGFRVVSLDELLAQSDVVVLHLPLTPETRHLINEEELALMKPGAVLVNTARGGLVDEDA 239
Query: 329 LVRALDSGVVAQAALDVFTEEPPAKDSKLVQHENVTVTPHLGASTKEAQEGVAIEIAEAV 388
L+RAL SG +A AALDVF EP D L++ NV +TPH+ T+EA+E +A E +
Sbjct: 240 LLRALKSGKIAGAALDVFEPEPLPADHPLLELPNVILTPHIAGYTEEARERMAEIAVENL 299
Query: 389 V 389
Sbjct: 300 E 300
>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 = 301 bits (774), Expect = 5e-98
Identities = 135/314 (42%), Positives = 184/314 (58%), Gaps = 6/314 (1%)
Query: 93 ILVSEKLGEAGLAILRSFGNVECLYDLSPEALCEKISQCDALIVRSGTKVTRSVFEAANG 152
+L+++ L L +L+ G VE +L E L E DALIVRS T VT V EAA
Sbjct: 1 VLITDPLRPEELELLKEGGEVEVHDELLTEELLEAAKDADALIVRSTTPVTAEVLEAAP- 59
Query: 153 KLKVVGRAGVGIDNVDLQAATEFGCLVVNAPIANTVAAAEHGIALLASMARNVSQADASI 212
LKV+ R GVG+DN+DL AATE G LV N P +T + AE + L+ ++AR + +ADAS+
Sbjct: 60 GLKVIARRGVGVDNIDLDAATERGILVTNVPGYSTESVAELTVGLILALARRIPEADASV 119
Query: 213 KAGKWLRSKYVGVSLVGKTLAVMGFGKVGSEVARRAKGLGMNVIAHDPYAPADKARAVGV 272
+AG W + +G+ L GKTL V+G G +G A AK LGM V+A+DPY ++A GV
Sbjct: 120 RAGDWKKGGPIGLELYGKTLGVIGGGGIGGIGAAIAKALGMGVVAYDPYPNPERAEEGGV 179
Query: 273 ELVSFDQAL----ATADFISLHMPLNPTTSKIFNDETFAKMKKGVRIVNVARGGVIDEEA 328
E++ D L + D I+L P T I +E +K V I N GGVI+E A
Sbjct: 180 EVLLLDLLLLDLKESDDLINLAPPTTMKTGHIIINEARGMLKDAVAINNARGGGVIEEAA 239
Query: 329 LVRALDSGVVAQAALDVFTEEPPAKDSKLVQHENVTVTPHLGASTKEAQEGVAIEIAEAV 388
L L+ G+ A AALDV EEPP +S L+ NV +TPH+ +T+EAQE +A E AE +
Sbjct: 240 LDALLEEGIAA-AALDVVEEEPPPVNSPLLDLPNVILTPHIAGATEEAQENMAEEAAENL 298
Query: 389 VGALRGELSATAIN 402
+ L+G A+N
Sbjct: 299 LAFLKGGTPPNAVN 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 = 298 bits (765), Expect = 1e-96
Identities = 122/311 (39%), Positives = 172/311 (55%), Gaps = 9/311 (2%)
Query: 91 PTILVSEKLGEAGLAILRSFGNVECLYD----LSPEALCEKISQCDALIVRSGTKVTRSV 146
P +LV+ +L E LA+LR VE ++D L E L E D L+ K+ +
Sbjct: 1 PKVLVTRRLPEEALALLREGFEVE-VWDEDRPLPREELLEAAKGADGLLCTLTDKIDAEL 59
Query: 147 FEAANGKLKVVGRAGVGIDNVDLQAATEFGCLVVNAPIANTVAAAEHGIALLASMARNVS 206
+AA LKV+ VG D++D+ AA G V N P T A A+ ALL + AR V
Sbjct: 60 LDAA-PPLKVIANYSVGYDHIDVDAAKARGIPVTNTPDVLTDATADLAFALLLAAARRVV 118
Query: 207 QADASIKAGKWLR---SKYVGVSLVGKTLAVMGFGKVGSEVARRAKGLGMNVIAHDPYAP 263
+ D ++AG+W + +G L GKTL ++G G++G VARRAKG GM ++ H+
Sbjct: 119 EGDRFVRAGEWKGWSPTLLLGTDLHGKTLGIVGMGRIGQAVARRAKGFGMKILYHNRSRK 178
Query: 264 ADKARAVGVELVSFDQALATADFISLHMPLNPTTSKIFNDETFAKMKKGVRIVNVARGGV 323
+ +G VS D+ LA +DF+SLH PL P T + N E A MK ++N ARGGV
Sbjct: 179 PEAEEELGARYVSLDELLAESDFVSLHCPLTPETRHLINAERLALMKPTAILINTARGGV 238
Query: 324 IDEEALVRALDSGVVAQAALDVFTEEPPAKDSKLVQHENVTVTPHLGASTKEAQEGVAIE 383
+DE+ALV AL SG +A A LDVF EP D L+ NV + PH+G++T E + +A
Sbjct: 239 VDEDALVEALKSGKIAGAGLDVFEPEPLPADHPLLTLPNVVLLPHIGSATVETRTAMAEL 298
Query: 384 IAEAVVGALRG 394
A+ ++ L G
Sbjct: 299 AADNLLAVLAG 309
>gnl|CDD|240624 cd05299, CtBP_dh, C-terminal binding protein (CtBP),
D-isomer-specific 2-hydroxyacid dehydrogenases related
repressor. The transcriptional corepressor CtBP is a
dehydrogenase with sequence and structural similarity to
the d2-hydroxyacid dehydrogenase family. CtBP was
initially identified as a protein that bound the PXDLS
sequence at the adenovirus E1A C terminus, causing the
loss of CR-1-mediated transactivation. CtBP binds NAD(H)
within a deep cleft, undergoes a conformational change
upon NAD binding, and has NAD-dependent dehydrogenase
activity.
Length = 312
Score = 294 bits (754), Expect = 5e-95
Identities = 129/298 (43%), Positives = 175/298 (58%), Gaps = 10/298 (3%)
Query: 99 LGEAGLAILRSFGNVECLYDLSPEALCEKISQCDALIVRSGTKVTRSVFEAANGKLKVVG 158
L EAG+ ++ + + L E + DAL+V+ VT V EA +LKV+
Sbjct: 20 LEEAGVELVD-------AQSRTEDELIEAAADADALLVQY-APVTAEVIEALP-RLKVIV 70
Query: 159 RAGVGIDNVDLQAATEFGCLVVNAPIANTVAAAEHGIALLASMARNVSQADASIKAGKWL 218
R GVG+DNVD+ AATE G V N P T A+H +AL+ ++AR + D +++AG W
Sbjct: 71 RYGVGVDNVDVAAATERGIPVCNVPDYCTEEVADHALALILALARKLPFLDRAVRAGGWD 130
Query: 219 RSKYVGV-SLVGKTLAVMGFGKVGSEVARRAKGLGMNVIAHDPYAPADKARAVGVELVSF 277
+ + L G TL ++GFG++G VA+RAK G VIA+DPY P A GV +VS
Sbjct: 131 WTVGGPIRRLRGLTLGLVGFGRIGRAVAKRAKAFGFRVIAYDPYVPDGVAALGGVRVVSL 190
Query: 278 DQALATADFISLHMPLNPTTSKIFNDETFAKMKKGVRIVNVARGGVIDEEALVRALDSGV 337
D+ LA +D +SLH PL P T + + E A MK G +VN ARGG++DE AL RAL SG
Sbjct: 191 DELLARSDVVSLHCPLTPETRHLIDAEALALMKPGAFLVNTARGGLVDEAALARALKSGR 250
Query: 338 VAQAALDVFTEEPPAKDSKLVQHENVTVTPHLGASTKEAQEGVAIEIAEAVVGALRGE 395
+A AALDV EEPP DS L+ NV +TPH ++E+ + + AE VV LRGE
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 = 286 bits (734), Expect = 7e-92
Identities = 121/323 (37%), Positives = 170/323 (52%), Gaps = 10/323 (3%)
Query: 90 KPTILVSEKLGEAGLAILRSFGNVECLYDLSPEA--LCEKISQCDALIVRSGTKVTRSVF 147
K +L + KL L L+ VE D L E++ DA+I ++ V
Sbjct: 2 KIVVLSTRKLPPEVLERLKEKFEVERYEDDLTPDTELAERLKDADAVITFVNDRIDAEVL 61
Query: 148 EAANGKLKVVGRAGVGIDNVDLQAATEFGCLVVNAPIANTVAAAEHGIALLASMARNVSQ 207
E G LK++ G DNVDL+AA E G V N P +T A AEH +AL+ ++AR + +
Sbjct: 62 EKLPG-LKLIATRSAGYDNVDLEAAKERGITVTNVPGYSTEAVAEHAVALILALARRIHE 120
Query: 208 ADASIKAGKWLRSKYV----GVSLVGKTLAVMGFGKVGSEVARRAKGLGMNVIAHDPYAP 263
D ++ G W S G L GKTL ++G G++G VARR KG GM V+ +D
Sbjct: 121 GDRRVREGNWSLSGGPDPLLGFDLRGKTLGIIGLGRIGQAVARRLKGFGMKVLYYDRSPN 180
Query: 264 ADKARAVGVELVSFDQALATADFISLHMPLNPTTSKIFNDETFAKMKKGVRIVNVARGGV 323
+ + +G V D+ LA +D ISLH PL P T + N E AKMK G +VN ARGG+
Sbjct: 181 PEAEKELGARYVDLDELLAESDIISLHCPLTPETRHLINAEELAKMKPGAILVNTARGGL 240
Query: 324 IDEEALVRALDSGVVAQAALDVFTEEPPAKDSKL---VQHENVTVTPHLGASTKEAQEGV 380
+DE+AL+ AL SG +A A LDVF EP D L NV +TPH+ ++T+EA++ +
Sbjct: 241 VDEQALIDALKSGKIAGAGLDVFENEPALFDHPLLRLDNFPNVVLTPHIASATEEARKAM 300
Query: 381 AIEIAEAVVGALRGELSATAINA 403
A E + G + +N
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 = 285 bits (732), Expect = 1e-91
Identities = 109/311 (35%), Positives = 170/311 (54%), Gaps = 7/311 (2%)
Query: 92 TILVSEKLGEAGLAILRS----FGNVECLYDLSPEALCEKISQCDALIVRSGTKVTRSVF 147
+L +LR+ VE + + ++ D L+ + +
Sbjct: 1 KVLFLGPEFPDAEELLRALLPPAPGVEVVTAAELDEEAALLADADVLVPGMRKVIDAEL- 59
Query: 148 EAANGKLKVVGRAGVGIDNVDLQAATEFGCLVVNAPIANTVAAAEHGIALLASMARNVSQ 207
AA +L+++ + GVG+D VDL+AAT G V N P N + AEH + L+ ++ R + +
Sbjct: 60 LAAAPRLRLIQQPGVGLDGVDLEAATARGIPVANIPGGNAESVAEHAVMLMLALLRRLPE 119
Query: 208 ADASIKAGKWLRSKY-VGVSLVGKTLAVMGFGKVGSEVARRAKGLGMNVIAHDPYAPADK 266
AD ++AG+W R + L GKT+ ++G G +G VARR +G G+ VI +D + +
Sbjct: 120 ADRELRAGRWGRPEGRPSRELSGKTVGIVGLGNIGRAVARRLRGFGVEVIYYDRFRDPEA 179
Query: 267 A-RAVGVELVSFDQALATADFISLHMPLNPTTSKIFNDETFAKMKKGVRIVNVARGGVID 325
+ +GV V D+ LA +D +SLH+PL P T + E A MK G ++N ARGG++D
Sbjct: 180 EEKDLGVRYVELDELLAESDVVSLHVPLTPETRHLIGAEELAAMKPGAILINTARGGLVD 239
Query: 326 EEALVRALDSGVVAQAALDVFTEEPPAKDSKLVQHENVTVTPHLGASTKEAQEGVAIEIA 385
EEAL+ AL SG +A A LDVF +EP D L++ +NV +TPH+ T E+ + +A +A
Sbjct: 240 EEALLAALRSGHLAGAGLDVFWQEPLPPDDPLLRLDNVILTPHIAGVTDESYQRMAAIVA 299
Query: 386 EAVVGALRGEL 396
E + LRGE
Sbjct: 300 ENIARLLRGEP 310
>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 = 272 bits (699), Expect = 9e-87
Identities = 108/262 (41%), Positives = 155/262 (59%), Gaps = 10/262 (3%)
Query: 121 PEALCEKISQCDALIVRSGTKVTRSVFEAANGKLKVVG--RAGVGIDNVDLQAATEFGCL 178
E L E + D LI VT+ V EAA KLK++G R G +NVD++AATE G
Sbjct: 37 EEELLEALKDADILITHFAP-VTKKVIEAAP-KLKLIGVCRGGP--ENVDVEAATERGIP 92
Query: 179 VVNAPIANTVAAAEHGIALLASMARNVSQADASIKAGKWLRSKY----VGVSLVGKTLAV 234
V+N P N A AE + L+ + RN+++A A++K G+W + Y G L GKT+ +
Sbjct: 93 VLNTPGRNAEAVAEFTVGLMLAETRNIARAHAALKDGEWRKDYYNYDGYGPELRGKTVGI 152
Query: 235 MGFGKVGSEVARRAKGLGMNVIAHDPYAPADKARAVGVELVSFDQALATADFISLHMPLN 294
+GFG +G VA+R K G V+ +DPY +K A GV+ VS ++ L +D +SLH L
Sbjct: 153 VGFGAIGRRVAKRLKAFGAEVLVYDPYVDPEKIEADGVKKVSLEELLKRSDVVSLHARLT 212
Query: 295 PTTSKIFNDETFAKMKKGVRIVNVARGGVIDEEALVRALDSGVVAQAALDVFTEEPPAKD 354
P T + E FA MK +N AR G++DE+AL+ AL+ G + AALDVF EEP D
Sbjct: 213 PETRGMIGAEEFALMKPTAYFINTARAGLVDEDALIEALEEGKIGGAALDVFPEEPLPAD 272
Query: 355 SKLVQHENVTVTPHLGASTKEA 376
L++ +NVT+TPH+ +T++
Sbjct: 273 HPLLKLDNVTLTPHIAGATRDV 294
>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 = 266 bits (683), Expect = 3e-84
Identities = 121/289 (41%), Positives = 175/289 (60%), Gaps = 4/289 (1%)
Query: 117 YDLSPEALCEKISQCDALIVRSGTKVTRSVFEAANGKLKVVGRAGVGIDNVDLQAATEFG 176
D+S +AL EK+ D +I + FE +G LK++ R G+G DNVDL+AATE G
Sbjct: 34 PDISGKALAEKLKGYDIIIASVTPNFDKEFFEYNDG-LKLIARHGIGYDNVDLKAATEHG 92
Query: 177 CLVVNAP-IANTVAAAEHGIALLASMARNVSQADASIKAGKW-LRSKYVGVSLVGKTLAV 234
+V P A AEH +AL+ ++ R ++QA ++K GKW R+ +VG L GKT+ +
Sbjct: 93 VIVTRVPGAVERDAVAEHAVALILTVLRKINQASEAVKEGKWTERANFVGHELSGKTVGI 152
Query: 235 MGFGKVGSEVARRAK-GLGMNVIAHDPYAPADKARAVGVELVSFDQALATADFISLHMPL 293
+G+G +GS VA K G V+A+DPY + + G + VS ++ LA +D ISLH PL
Sbjct: 153 IGYGNIGSRVAEILKEGFNAKVLAYDPYVSEEVIKKKGAKPVSLEELLAESDIISLHAPL 212
Query: 294 NPTTSKIFNDETFAKMKKGVRIVNVARGGVIDEEALVRALDSGVVAQAALDVFTEEPPAK 353
T + N++ F+KMKKGV +VN ARG +IDEEAL+ AL SG +A A LDV EEP
Sbjct: 213 TEETYHMINEKAFSKMKKGVILVNTARGELIDEEALIEALKSGKIAGAGLDVLEEEPIKA 272
Query: 354 DSKLVQHENVTVTPHLGASTKEAQEGVAIEIAEAVVGALRGELSATAIN 402
D L+ +ENV +TPH+GA T E+ G+ ++ + + L G+ +N
Sbjct: 273 DHPLLHYENVVITPHIGAYTYESLYGMGEKVVDDIEDFLAGKEPKGILN 321
>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 = 262 bits (671), Expect = 1e-82
Identities = 109/311 (35%), Positives = 172/311 (55%), Gaps = 9/311 (2%)
Query: 92 TILVSEKLGEAGLAILRSFGNVEC---LYDLSPEALCEKISQCDALIVRSGTKVTRSVFE 148
+LV+ + + L L V L +S E L E+I+ DALI T V + + +
Sbjct: 2 KVLVTGWIPKEALEELEENFEVTYYDGLGLISKEELLERIADYDALITPLSTPVDKEIID 61
Query: 149 AANGKLKVVGRAGVGIDNVDLQAATEFGCLVVNAPIANTVAAAEHGIALLASMARNVSQA 208
AA LK++ G G DN+D+ A E G V N P +T AE L+ ++AR +++
Sbjct: 62 AAK-NLKIIANYGAGFDNIDVDYAKEKGIPVTNTPAVSTEPTAELTFGLILALARRIAEG 120
Query: 209 DASIKAGKWL---RSKYVGVSLVGKTLAVMGFGKVGSEVARRAKGLGMNVIAHDPY-APA 264
D ++ G +L ++G L GKTL ++G G++G VARRAK GM ++ ++ +
Sbjct: 121 DRLMRRGGFLGWAPLFFLGHELAGKTLGIIGMGRIGQAVARRAKAFGMKILYYNRHRLSE 180
Query: 265 DKARAVGVELVSFDQALATADFISLHMPLNPTTSKIFNDETFAKMKKGVRIVNVARGGVI 324
+ + +G V D+ L +DF+SLH P P T + + F MK ++N ARG ++
Sbjct: 181 ETEKELGATYVDLDELLKESDFVSLHAPYTPETHHLIDAAAFKLMKPTAYLINAARGPLV 240
Query: 325 DEEALVRALDSGVVAQAALDVFTEEPPAKDSKLVQHENVTVTPHLGASTKEAQEGVAIEI 384
DE+ALV AL +G +A AALDVF EP +L + +NV +TPH+G +T EA++ +A E
Sbjct: 241 DEKALVDALKTGEIAGAALDVFEFEPEVSP-ELKKLDNVILTPHIGNATVEARDAMAKEA 299
Query: 385 AEAVVGALRGE 395
A+ ++ L G+
Sbjct: 300 ADNIISFLEGK 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 = 257 bits (658), Expect = 7e-81
Identities = 120/307 (39%), Positives = 170/307 (55%), Gaps = 31/307 (10%)
Query: 92 TILVSEKLGEAGLAILRSFGNVECLYDLSPEALCEKISQCDALIVRSGTKVTRSVFEAAN 151
IL + K+ + GL + + Y++ +AL DALIVRS K+ + A
Sbjct: 2 KILTANKISKKGLERFK-----KDKYEVKEDAL----EDPDALIVRS-DKLH--DMDFAP 49
Query: 152 GKLKVVGRAGVGIDNVDLQAATEFGCLVVNAPIANTVAAAEHGIALLASMARNVSQA--- 208
LK + RAG G++N+D+ AA++ G +V N P AN A AE IA++ +++RN+ QA
Sbjct: 50 S-LKAIARAGAGVNNIDVDAASKRGIVVFNTPGANANAVAELVIAMMLALSRNIIQAIKW 108
Query: 209 ------DASIKAGKWLRSKYVGVSLVGKTLAVMGFGKVGSEVARRAKGLGMNVIAHDPYA 262
D K + + ++VG L GKTL V+G G +G VA A LGM VI +DPY
Sbjct: 109 VTNGDGDDISKGVEKGKKQFVGTELRGKTLGVIGLGNIGRLVANAALALGMKVIGYDPYL 168
Query: 263 PADKARAVGVELV---SFDQALATADFISLHMPLNPTTSKIFNDETFAKMKKGVRIVNVA 319
+ A + VE+ S ++ LATAD+I+LH+PL T + N E AKMK G ++N A
Sbjct: 169 SVEAAWKLSVEVQRVTSLEELLATADYITLHVPLTDETRGLINAELLAKMKPGAILLNFA 228
Query: 320 RGGVIDEEALVRALDSGVVAQAALDVFTEEPPAKDSKLVQHENVTVTPHLGASTKEAQEG 379
RG ++DEEAL+ ALD G + + F E PA NV TPHLGAST+EA+E
Sbjct: 229 RGEIVDEEALLEALDEGKL-GGYVTDFPE--PALLGH---LPNVIATPHLGASTEEAEEN 282
Query: 380 VAIEIAE 386
A+ A
Sbjct: 283 CAVMAAR 289
>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 = 247 bits (634), Expect = 3e-79
Identities = 82/176 (46%), Positives = 115/176 (65%), Gaps = 1/176 (0%)
Query: 195 IALLASMARNVSQADASIKAGKWLRSKYVGVSLVGKTLAVMGFGKVGSEVARRAKGLGMN 254
+ALL ++AR + +AD ++AG+W +G L GKT+ ++G G++G VARR K GM
Sbjct: 1 LALLLALARRIPEADRQVRAGRWRPDALLGRELSGKTVGIIGLGRIGRAVARRLKAFGMK 60
Query: 255 VIAHDPYAPADKARAVGVELVSFDQALATADFISLHMPLNPTTSKIFNDETFAKMKKGVR 314
VIA+D Y P +A A+G VS D+ LA +D +SLH+PL P T + N E A MK G
Sbjct: 61 VIAYDRY-PKAEAEALGARYVSLDELLAESDVVSLHLPLTPETRHLINAERLALMKPGAI 119
Query: 315 IVNVARGGVIDEEALVRALDSGVVAQAALDVFTEEPPAKDSKLVQHENVTVTPHLG 370
++N ARGG++DE+AL+ AL SG +A AALDVF EP D L++ NV +TPH+
Sbjct: 120 LINTARGGLVDEDALIAALKSGRIAGAALDVFEPEPLPPDHPLLELPNVILTPHIA 175
>gnl|CDD|240639 cd12162, 2-Hacid_dh_4, Putative D-isomer specific 2-hydroxyacid
dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine yydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 307
Score = 250 bits (642), Expect = 2e-78
Identities = 107/283 (37%), Positives = 158/283 (55%), Gaps = 15/283 (5%)
Query: 104 LAILRSFGNVECLYDL-SPEALCEKISQCDALIVRSGTKVTRSVFEAANGKLKVVGRAGV 162
L G + YD SPE + E+I D +I + + V LK++G
Sbjct: 18 WDPLEFLGELTV-YDRTSPEEVVERIKDADIVIT-NKVVLDAEVLAQLP-NLKLIGVLAT 74
Query: 163 GIDNVDLQAATEFGCLVVNAPIANTVAAAEHGIALLASMARNVSQADASIKAGKWLRS-- 220
G +NVDL AA E G V N P +T + A+H ALL ++AR V+ + +KAG+W +S
Sbjct: 75 GYNNVDLAAAKERGITVTNVPGYSTDSVAQHTFALLLALARLVAYHNDVVKAGEWQKSPD 134
Query: 221 ----KYVGVSLVGKTLAVMGFGKVGSEVARRAKGLGMNVIAHDPYAPADKARAVGVELVS 276
Y + L GKTL ++G+G +G VAR A+ GM V+ + + VS
Sbjct: 135 FCFWDYPIIELAGKTLGIIGYGNIGQAVARIARAFGMKVLFAERKGAPP----LREGYVS 190
Query: 277 FDQALATADFISLHMPLNPTTSKIFNDETFAKMKKGVRIVNVARGGVIDEEALVRALDSG 336
D+ LA +D ISLH PL P T + N E AKMK G ++N ARGG++DE+AL AL+SG
Sbjct: 191 LDELLAQSDVISLHCPLTPETRNLINAEELAKMKPGAILINTARGGLVDEQALADALNSG 250
Query: 337 VVAQAALDVFTEEPPAKDSKLVQ-HENVTVTPHLGASTKEAQE 378
+A A LDV ++EPP D+ L++ N+ +TPH+ +++EA++
Sbjct: 251 KIAGAGLDVLSQEPPRADNPLLKAAPNLIITPHIAWASREARQ 293
>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 = 241 bits (617), Expect = 9e-75
Identities = 112/292 (38%), Positives = 168/292 (57%), Gaps = 13/292 (4%)
Query: 106 ILRSFG-NVECLYD-LSPEALCEKISQCDALIVRSGTKVTRSVFEAANGKLKVVGRAGVG 163
+ R+ G VE L L + L E + L +RS T++T V EAA KL +G +G
Sbjct: 16 LFRAGGIEVERLKGALDEDELIEALKDVHLLGIRSKTQLTEEVLEAAP-KLLAIGCFCIG 74
Query: 164 IDNVDLQAATEFGCLVVNAPIANTVAAAEHGIALLASMARNVSQADASIKAGKWLRSKYV 223
+ VDL AA + G V NAP +NT + AE I + +AR + +A+ G W +S
Sbjct: 75 TNQVDLDAAAKRGIPVFNAPFSNTRSVAELVIGEIIMLARRLPDRNAAAHRGIWNKSATG 134
Query: 224 GVSLVGKTLAVMGFGKVGSEVARRAKGLGMNVIAHDPYAPADKARAVG--VELVSFDQAL 281
+ GKTL ++G+G +GS+++ A+ LGM VI +D + +G ++ S ++ L
Sbjct: 135 SHEVRGKTLGIIGYGHIGSQLSVLAEALGMRVIFYD----IAEKLPLGNARQVSSLEELL 190
Query: 282 ATADFISLHMPLNPTTSKIFNDETFAKMKKGVRIVNVARGGVIDEEALVRALDSGVVAQA 341
A ADF++LH+P P+T + E A+MKKG ++N +RG V+D +AL AL SG +A A
Sbjct: 191 AEADFVTLHVPATPSTKNMIGAEEIAQMKKGAILINASRGTVVDIDALAEALRSGHLAGA 250
Query: 342 ALDVFTEEPPAKD----SKLVQHENVTVTPHLGASTKEAQEGVAIEIAEAVV 389
A+DVF EEP + S L NV +TPH+G ST+EAQE + +E+A +V
Sbjct: 251 AVDVFPEEPASNGEPFSSPLQGLPNVILTPHIGGSTEEAQENIGLEVAGKLV 302
>gnl|CDD|183914 PRK13243, PRK13243, glyoxylate reductase; Reviewed.
Length = 333
Score = 238 bits (608), Expect = 3e-73
Identities = 120/327 (36%), Positives = 186/327 (56%), Gaps = 12/327 (3%)
Query: 90 KPTILVSEKLGEAGLAILRSFGNVECLYDLSP---EALCEKISQCDALIVRSGTKVTRSV 146
KP + ++ ++ E G+ +L VE D E L EK+ DAL+ ++ V
Sbjct: 2 KPKVFITREIPENGIEMLEEHFEVEVWEDEREIPREVLLEKVRDVDALVTMLSERIDCEV 61
Query: 147 FEAANGKLKVVGRAGVGIDNVDLQAATEFGCLVVNAPIANTVAAAEHGIALLASMARNVS 206
FEAA +L++V VG DN+D++ AT G V N P T A A+ ALL + AR +
Sbjct: 62 FEAAP-RLRIVANYAVGYDNIDVEEATRRGIYVTNTPGVLTEATADFAWALLLATARRLV 120
Query: 207 QADASIKAGKWLRSK-------YVGVSLVGKTLAVMGFGKVGSEVARRAKGLGMNVIAHD 259
+AD +++G+W R ++G + GKT+ ++GFG++G VARRAKG GM ++ +
Sbjct: 121 EADHFVRSGEWKRRGVAWHPLMFLGYDVYGKTIGIIGFGRIGQAVARRAKGFGMRILYYS 180
Query: 260 PYAPADKARAVGVELVSFDQALATADFISLHMPLNPTTSKIFNDETFAKMKKGVRIVNVA 319
+ + +G E ++ L +DF+SLH+PL T + N+E MK +VN A
Sbjct: 181 RTRKPEAEKELGAEYRPLEELLRESDFVSLHVPLTKETYHMINEERLKLMKPTAILVNTA 240
Query: 320 RGGVIDEEALVRALDSGVVAQAALDVFTEEPPAKDSKLVQHENVTVTPHLGASTKEAQEG 379
RG V+D +ALV+AL G +A A LDVF EE P + +L +NV + PH+G++T EA+EG
Sbjct: 241 RGKVVDTKALVKALKEGWIAGAGLDVFEEE-PYYNEELFSLKNVVLAPHIGSATFEAREG 299
Query: 380 VAIEIAEAVVGALRGELSATAINAPMV 406
+A +AE ++ RGE+ T +N +V
Sbjct: 300 MAELVAENLIAFKRGEVPPTLVNREVV 326
>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 = 235 bits (602), Expect = 2e-72
Identities = 107/295 (36%), Positives = 162/295 (54%), Gaps = 10/295 (3%)
Query: 102 AGLAILRSFGNVECLYDLSPEALCEKISQCDALIV-RSGTKVTRSVFEAANGKLKVVGRA 160
A + F + + L +AL E+++ DA+++ R T ++ E LK++
Sbjct: 22 DDRAEVTVFND----HLLDEDALAERLAPFDAIVLMRERTPFPAALLER-LPNLKLLVTT 76
Query: 161 GVGIDNVDLQAATEFGCLVVNAPIANTVAAAEHGIALLASMARNVSQADASIKAGKWLRS 220
G+ ++DL AA E G +V A AE AL+ ++ARN+ + DA+++AG W +
Sbjct: 77 GMRNASIDLAAAKERGIVVCGTG-GGPTATAELTWALILALARNLPEEDAALRAGGWQTT 135
Query: 221 KYVGVSLVGKTLAVMGFGKVGSEVARRAKGLGMNVIAHDPYAPADKARAVGVEL-VSFDQ 279
+G L GKTL ++G G++G+ VAR + GM VIA A++A A GVE VS ++
Sbjct: 136 --LGTGLAGKTLGIVGLGRIGARVARIGQAFGMRVIAWSSNLTAERAAAAGVEAAVSKEE 193
Query: 280 ALATADFISLHMPLNPTTSKIFNDETFAKMKKGVRIVNVARGGVIDEEALVRALDSGVVA 339
AT+D +SLH+ L+ T + E A MK +VN +RG ++DE AL+ AL +G +A
Sbjct: 194 LFATSDVVSLHLVLSDRTRGLVGAEDLALMKPTALLVNTSRGPLVDEGALLAALRAGRIA 253
Query: 340 QAALDVFTEEPPAKDSKLVQHENVTVTPHLGASTKEAQEGVAIEIAEAVVGALRG 394
AALDVF EP D L NV +TPH+G T+EA EG + E + L G
Sbjct: 254 GAALDVFDVEPLPADHPLRGLPNVLLTPHIGYVTEEAYEGFYGQAVENIAAWLAG 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 = 233 bits (597), Expect = 1e-71
Identities = 101/242 (41%), Positives = 139/242 (57%), Gaps = 7/242 (2%)
Query: 154 LKVVGRAGVGIDNVDLQAATEFGCLVVNAPIANTVAAAEHGIALLASMARNVSQADASIK 213
LK++ AG G D +D+ A T+ G V N P A A A+ + L+ RN S+A+ S +
Sbjct: 77 LKIIAHAGAGYDQIDVDALTKRGIQVSNTPGAVDEATADTALFLILGALRNFSRAERSAR 136
Query: 214 AGKWLRSK--YVGVSLVGKTLAVMGFGKVGSEVARRAKGLGMNVIAHDPY-APADKARAV 270
AGKW + GKTL ++G G +G +AR+A GM +I H+ P + +A+
Sbjct: 137 AGKWRGFLDLTLAHDPRGKTLGILGLGGIGKAIARKAAAFGMKIIYHNRSRLPEELEKAL 196
Query: 271 GVELVSFDQALATADFISLHMPLNPTTSKIFNDETFAKMKKGVRIVNVARGGVIDEEALV 330
VS D+ LA +D +SL+ PL T + N + FAKMK GV IVN ARG VIDE+ALV
Sbjct: 197 ATYYVSLDELLAQSDVVSLNCPLTAATRHLINKKEFAKMKDGVIIVNTARGAVIDEDALV 256
Query: 331 RALDSGVVAQAALDVFTEEPPAKDSKLVQHENVTVTPHLGASTKEAQ---EGVAIEIAEA 387
AL+SG VA A LDVF EP + L++ NVT+ PH+G T E Q E + +E EA
Sbjct: 257 DALESGKVASAGLDVFENEPEV-NPGLLKMPNVTLLPHMGTLTVETQEKMEELVLENIEA 315
Query: 388 VV 389
+
Sbjct: 316 FL 317
>gnl|CDD|240620 cd01619, LDH_like, D-Lactate and related Dehydrogenases,
NAD-binding and catalytic domains. D-Lactate
dehydrogenase (LDH) catalyzes the interconversion of
pyruvate and lactate, and is a member of the
2-hydroxyacid dehydrogenase family. LDH is homologous to
D-2-Hydroxyisocaproic acid dehydrogenase (D-HicDH) and
shares the 2 domain structure of formate dehydrogenase.
D-HicDH is a NAD-dependent member of the
hydroxycarboxylate dehydrogenase family, and shares the
Rossmann fold typical of many NAD binding proteins.
D-HicDH from Lactobacillus casei forms a monomer and
catalyzes the reaction R-CO-COO(-) + NADH + H+ to
R-COH-COO(-) + NAD+. Similar to the structurally
distinct L-HicDH, D-HicDH exhibits low side-chain R
specificity, accepting a wide range of 2-oxocarboxylic
acid side chains. (R)-2-hydroxyglutarate dehydrogenase
(HGDH) catalyzes the NAD-dependent reduction of
2-oxoglutarate to (R)-2-hydroxyglutarate.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain.
Length = 323
Score = 229 bits (586), Expect = 4e-70
Identities = 112/307 (36%), Positives = 159/307 (51%), Gaps = 17/307 (5%)
Query: 105 AILRSFG-NVEC-LYDLSPEALCEKISQCDALIVRSGTKVTRSVFEAANGKLKVVGRAGV 162
IL++ G +VE Y L+ + E DA++ K+ + + A G LK +
Sbjct: 18 EILKAGGVDVEIVTYLLNDDETAELAKGADAILTAFTDKIDAELLDKAPG-LKFISLRAT 76
Query: 163 GIDNVDLQAATEFGCLVVNAPIANTVAAAEHGIALLASMARNVSQADASIKAGKWLRSKY 222
G DN+DL A E G V N P + A AEH IAL+ ++ RN D K +
Sbjct: 77 GYDNIDLDYAKELGIGVTNVPEYSPNAVAEHTIALILALLRNRKYIDERDKNQDLQDAGV 136
Query: 223 VGVSLVGKTLAVMGFGKVGSEVARRAKGLGMNVIAHDPYAPADKARAVGVELVSFDQALA 282
+G L +T+ V+G GK+G VA+RAKG GM VIA+DP+ + GV+ VS ++
Sbjct: 137 IGRELEDQTVGVVGTGKIGRAVAQRAKGFGMKVIAYDPFRNPELE-DKGVKYVSLEELFK 195
Query: 283 TADFISLHMPLNPTTSKIFNDETFAKMKKGVRIVNVARGGVIDEEALVRALDSGVVAQAA 342
+D ISLH+PL P + N+E F MKKGV I+N ARG ++D EAL+ ALDSG + A
Sbjct: 196 NSDIISLHVPLTPENHHMINEEAFKLMKKGVIIINTARGSLVDTEALIEALDSGKIFGAG 255
Query: 343 LDVFTEEPP-------------AKDSKLVQHENVTVTPHLGASTKEAQEGVAIEIAEAVV 389
LDV +E P A ++ L + NV +TPH T +A + + E +V
Sbjct: 256 LDVLEDETPDLLKDLEGEIFKDALNALLGRRPNVIITPHTAFYTDDALKNMVEISCENIV 315
Query: 390 GALRGEL 396
L GE
Sbjct: 316 DFLEGEE 322
>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 = 217 bits (554), Expect = 3e-65
Identities = 97/281 (34%), Positives = 145/281 (51%), Gaps = 8/281 (2%)
Query: 99 LGEAGLAILRSFGNV---ECLYDLSPEALCEKISQCDALIVRSGT-KVTRSVFEAANGKL 154
G A LA L + V D + E L ++ + L+ GT + + A +L
Sbjct: 15 FGPAALARLAALAEVLPPTPDADFAAEELRALLAGVEVLVTGWGTPPLDAELLARA-PRL 73
Query: 155 KVVGRAGVGIDNVDLQAATEFGCLVVNAPIANTVAAAEHGIALLASMARNVSQADASIKA 214
+ V A + + A E G LV +A AN AE +A + R + + A+ +A
Sbjct: 74 RAVVHAAGSVRGLVTDAVWERGILVTSAADANAEPVAEFTLAAILLALRRIPRFAAAYRA 133
Query: 215 GKWL--RSKYVGVSLVGKTLAVMGFGKVGSEVARRAKGLGMNVIAHDPYAPADKARAVGV 272
G+ ++ G L G+T+ ++GFG++G V + G+ V+ +DPY PA +A A+GV
Sbjct: 134 GRDWGWPTRRGGRGLYGRTVGIVGFGRIGRAVVELLRPFGLRVLVYDPYLPAAEAAALGV 193
Query: 273 ELVSFDQALATADFISLHMPLNPTTSKIFNDETFAKMKKGVRIVNVARGGVIDEEALVRA 332
ELVS D+ LA +D +SLH PL P T + + A M+ G +N ARG ++DE AL+
Sbjct: 194 ELVSLDELLARSDVVSLHAPLTPETRGMIDARLLALMRDGATFINTARGALVDEAALLAE 253
Query: 333 LDSGVVAQAALDVFTEEPPAKDSKLVQHENVTVTPHLGAST 373
L SG + +AALDV EP DS L NV +TPH+ ST
Sbjct: 254 LRSGRL-RAALDVTDPEPLPPDSPLRTLPNVLLTPHIAGST 293
>gnl|CDD|236985 PRK11790, PRK11790, D-3-phosphoglycerate dehydrogenase;
Provisional.
Length = 409
Score = 219 bits (560), Expect = 4e-65
Identities = 117/329 (35%), Positives = 179/329 (54%), Gaps = 20/329 (6%)
Query: 90 KPTILVSEKLGEAGLAILRS--FGNVECLYD-LSPEALCEKISQCDALIVRSGTKVTRSV 146
K L+ E + ++ + +LR+ + N+E L E L E I + +RS T++T V
Sbjct: 10 KIKFLLLEGVHQSAVEVLRAAGYTNIEYHKGALDEEELIEAIKDAHFIGIRSRTQLTEEV 69
Query: 147 FEAANGKLKVVGRAGVGIDNVDLQAATEFGCLVVNAPIANTVAAAEHGIALLASMARNVS 206
AA KL +G +G + VDL AA + G V NAP +NT + AE I + + R +
Sbjct: 70 LAAAE-KLVAIGCFCIGTNQVDLDAAAKRGIPVFNAPFSNTRSVAELVIGEIILLLRGIP 128
Query: 207 QADASIKAGKWLRSKYVGVSLVGKTLAVMGFGKVGSEVARRAKGLGMNVIAHDPYAPADK 266
+ +A G W +S + GKTL ++G+G +G++++ A+ LGM V +D DK
Sbjct: 129 EKNAKAHRGGWNKSAAGSFEVRGKTLGIVGYGHIGTQLSVLAESLGMRVYFYDI---EDK 185
Query: 267 -----ARAVGVELVSFDQALATADFISLHMPLNPTTSKIFNDETFAKMKKGVRIVNVARG 321
AR VG S ++ LA +D +SLH+P P+T + E A MK G ++N +RG
Sbjct: 186 LPLGNARQVG----SLEELLAQSDVVSLHVPETPSTKNMIGAEELALMKPGAILINASRG 241
Query: 322 GVIDEEALVRALDSGVVAQAALDVFTEEPPAKD----SKLVQHENVTVTPHLGASTKEAQ 377
V+D +AL AL SG +A AA+DVF EP + S L +NV +TPH+G ST+EAQ
Sbjct: 242 TVVDIDALADALKSGHLAGAAIDVFPVEPKSNGDPFESPLRGLDNVILTPHIGGSTQEAQ 301
Query: 378 EGVAIEIAEAVVGALRGELSATAINAPMV 406
E + +E+A +V + +A+N P V
Sbjct: 302 ENIGLEVAGKLVKYSDNGSTLSAVNFPEV 330
>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 = 209 bits (533), Expect = 3e-62
Identities = 97/259 (37%), Positives = 139/259 (53%), Gaps = 25/259 (9%)
Query: 140 TKVTRSVFEAANGKLKVVGRAGVGIDNVDLQAATEFGCLVVNAPI--ANTVAAAEHGIAL 197
+++ V E +LK++ G D++DL+A E G V N P TVA EH AL
Sbjct: 51 SRLDAEVLEKLP-RLKLIATRSTGFDHIDLEACRERGIAVCNVPDYGEATVA--EHAFAL 107
Query: 198 LASMARNVSQADASIKAGKWLRSKYVGVSLVGKTLAVMGFGKVGSEVARRAKGLGMNVIA 257
L +++R + +A + G + ++ G L GKTL V+G G++G VAR A+G GM V+A
Sbjct: 108 LLALSRKLREAIERTRRGDFSQAGLRGFELAGKTLGVVGTGRIGRRVARIARGFGMKVLA 167
Query: 258 HDPYAPADKARAVGVELVSFDQALATADFISLHMPLNPTTSKIFNDETFAKMKKGVRIVN 317
+D + A +G VS ++ L +D ISLH+P P T + N E FA MK G ++N
Sbjct: 168 YDVVPDEELAERLGFRYVSLEELLQESDIISLHVPYTPQTHHLINRENFALMKPGAVLIN 227
Query: 318 VARGGVIDEEALVRALDSGVVAQAALDVFTEEP-------------PAKDSK-------L 357
ARG V+D EALVRAL G +A A LDV +E +D K L
Sbjct: 228 TARGAVVDTEALVRALKEGKLAGAGLDVLEQEEVLREEAELFREDVSPEDLKKLLADHAL 287
Query: 358 VQHENVTVTPHLGASTKEA 376
++ NV +TPH+ +TKEA
Sbjct: 288 LRKPNVIITPHVAYNTKEA 306
>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 = 205 bits (525), Expect = 2e-61
Identities = 102/305 (33%), Positives = 154/305 (50%), Gaps = 16/305 (5%)
Query: 93 ILVSEKLGEAGLAILRSFG-NVECLYDLSPEALCEKISQCDALIVRSGTKVTRSVFEAAN 151
IL+ +K + +L + G V+ +S E + I Q D LI+RS + + E A
Sbjct: 2 ILIIDKNHPSLTELLEALGFEVDYDPTISREEILAIIPQYDGLIIRSRFPIDKEFIEKAT 61
Query: 152 GKLKVVGRAGVGIDNVDLQAATEFGCLVVNAPIANTVAAAEHGIALLASMARNVSQADAS 211
LK + RAG G++N+DL+ A E G + NAP N A EH + +L ++ +++AD
Sbjct: 62 -NLKFIARAGAGLENIDLEYAKEKGIELFNAPEGNRDAVGEHALGMLLALFNKLNRADQE 120
Query: 212 IKAGKWLRSKYVGVSLVGKTLAVMGFGKVGSEVARRAKGLGMNVIAHDPY-APADKARAV 270
++ G W R GV L+GKT+ ++G+G +G A+R G G VIA+D Y D
Sbjct: 121 VRNGIWDREGNRGVELMGKTVGIIGYGNMGKAFAKRLSGFGCKVIAYDKYKNFGDA---- 176
Query: 271 GVELVSFDQALATADFISLHMPLNPTTSKIFNDETFAKMKKGVRIVNVARGGVIDEEALV 330
E VS + AD +SLH+PL P T + N E + KK +N ARG V+ + LV
Sbjct: 177 YAEQVSLETLFKEADILSLHIPLTPETRGMVNKEFISSFKKPFYFINTARGKVVVTKDLV 236
Query: 331 RALDSGVVAQAALDVF---------TEEPPAKDSKLVQHENVTVTPHLGASTKEAQEGVA 381
+AL SG + A LDV P L++ V +TPH+ T E+ E +A
Sbjct: 237 KALKSGKILGACLDVLEYEKASFESIFNQPEAFEYLIKSPKVILTPHIAGWTFESYEKIA 296
Query: 382 IEIAE 386
+ +
Sbjct: 297 EVLVD 301
>gnl|CDD|240634 cd12157, PTDH, Thermostable Phosphite Dehydrogenase. Phosphite
dehydrogenase (PTDH), a member of the D-specific
2-hydroxyacid dehydrogenase family, catalyzes the
NAD-dependent formation of phosphate from phosphite
(hydrogen phosphonate). PTDH has been suggested as a
potential enzyme for cofactor regeneration systems. The
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD-binding
domain.
Length = 318
Score = 204 bits (522), Expect = 9e-61
Identities = 102/319 (31%), Positives = 161/319 (50%), Gaps = 15/319 (4%)
Query: 90 KPTILVSEKLGEAGLAILRSFGNVEC-LYD--LSPEALCEKISQCDALIVRSGTKVTRSV 146
KP ++++ K+ L +L+ V D LS E L + D L+ ++
Sbjct: 1 KPKVVITHKVHPEVLELLKPHCEVISNQTDEPLSREELLRRCKDADGLMAFMPDRIDADF 60
Query: 147 FEAANGKLKVVGRAGVGIDNVDLQAATEFGCLVVNAPIANTVAAAEHGIALLASMARNVS 206
+A +LK++ A G DN D++A T G V P T AE I LL + R++
Sbjct: 61 LDACP-RLKIIACALKGYDNFDVEACTARGIWVTIVPDLLTEPTAELTIGLLIGLGRHIL 119
Query: 207 QADASIKAGK--WLRSKYVGVSLVGKTLAVMGFGKVGSEVARRAKGLGMNVIAHDPYA-P 263
D +++GK R K+ G L GKT+ ++G G +G +ARR G G ++ +DP+
Sbjct: 120 AGDRFVRSGKFGGWRPKFYGTGLDGKTVGILGMGALGRAIARRLSGFGATLLYYDPHPLD 179
Query: 264 ADKARAVGVELVSFDQALATADFISLHMPLNPTTSKIFNDETFAKMKKGVRIVNVARGGV 323
+ +A+ + V D+ L ++DF+ L +PL P T + N E AKMK G +VN RG V
Sbjct: 180 QAEEQALNLRRVELDELLESSDFLVLALPLTPDTLHLINAEALAKMKPGALLVNPCRGSV 239
Query: 324 IDEEALVRALDSGVVAQAALDVFTEEPPAKDSK--------LVQHENVTVTPHLGASTKE 375
+DE A+ AL SG + A DVF E A+ + L QH+ TPH+G++ E
Sbjct: 240 VDEAAVAEALKSGHLGGYAADVFEMEDWARPDRPRSIPQELLDQHDRTVFTPHIGSAVDE 299
Query: 376 AQEGVAIEIAEAVVGALRG 394
+ + +E A ++ AL+G
Sbjct: 300 VRLEIELEAALNILQALQG 318
>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 = 199 bits (508), Expect = 1e-58
Identities = 106/271 (39%), Positives = 146/271 (53%), Gaps = 21/271 (7%)
Query: 131 CDALIVRSGTKVTRSVFE--AANGKLKVVGRAGVGIDNVDLQAATEFGCLVVNAPIANTV 188
DA+ V + V E A G +K++ G +NVDL+AA E G VV P +
Sbjct: 45 FDAVCVFVNDDLDAPVLEKLAELG-VKLIALRCAGFNNVDLKAAKELGITVVRVPAYSPY 103
Query: 189 AAAEHGIALLASMARNVSQADASIKAGKWLRSKYVGVSLVGKTLAVMGFGKVGSEVARRA 248
A AEH +ALL ++ R + +A ++ G + +G L GKT+ V+G GK+G AR
Sbjct: 104 AVAEHAVALLLALNRKIHRAYNRVREGNFSLDGLLGFDLHGKTVGVIGTGKIGQAFARIL 163
Query: 249 KGLGMNVIAHDPYAPADKARAVGVELVSFDQALATADFISLHMPLNPTTSKIFNDETFAK 308
KG G V+A+DPY P + +GVE V D+ LA +D ISLH PL P T + N ET AK
Sbjct: 164 KGFGCRVLAYDPY-PNPELAKLGVEYVDLDELLAESDIISLHCPLTPETHHLINAETIAK 222
Query: 309 MKKGVRIVNVARGGVIDEEALVRALDSGVVAQAALDVFTEEPPA--KD-----------S 355
MK GV ++N +RGG+ID +AL+ AL SG + LDV+ EE +D +
Sbjct: 223 MKDGVMLINTSRGGLIDTKALIEALKSGKIGGLGLDVYEEEAGLFFEDHSDEIIQDDVLA 282
Query: 356 KLVQHENVTVTPHLGASTKEAQEGVAIEIAE 386
+L+ NV +T H TKEA IAE
Sbjct: 283 RLLSFPNVLITGHQAFFTKEALT----NIAE 309
>gnl|CDD|240638 cd12161, GDH_like_1, Putative glycerate dehydrogenase and related
proteins of the D-specific 2-hydroxy dehydrogenase
family. This group contains a variety of proteins
variously identified as glycerate dehydrogenase (GDH,
aka Hydroxypyruvate Reductase) and other enzymes of the
2-hydroxyacid dehydrogenase family. GDH catalyzes the
reversible reaction of (R)-glycerate + NAD+ to
hydroxypyruvate + NADH + H+. 2-hydroxyacid
dehydrogenases catalyze the conversion of a wide variety
of D-2-hydroxy acids to their corresponding keto acids.
The general mechanism is (R)-lactate + acceptor to
pyruvate + reduced acceptor. Formate/glycerate and
related dehydrogenases of the D-specific 2-hydroxyacid
dehydrogenase superfamily include groups such as formate
dehydrogenase, glycerate dehydrogenase, L-alanine
dehydrogenase, and S-adenosylhomocysteine hydrolase.
Despite often low sequence identity, these proteins
typically have a characteristic arrangement of 2 similar
subdomains of the alpha/beta Rossmann-fold NAD+ binding
form. The NAD+ binding domain is inserted within the
linear sequence of the mostly N-terminal catalytic
domain, which has a similar domain structure to the
internal NAD binding domain. Structurally, these domains
are connected by extended alpha helices and create a
cleft in which NAD is bound, primarily to the C-terminal
portion of the 2nd (internal) domain. Some related
proteins have similar structural subdomain but with a
tandem arrangement of the catalytic and NAD-binding
subdomains in the linear sequence. While many members of
this family are dimeric, alanine DH is hexameric and
phosphoglycerate DH is tetrameric.
Length = 315
Score = 198 bits (506), Expect = 2e-58
Identities = 98/259 (37%), Positives = 146/259 (56%), Gaps = 5/259 (1%)
Query: 121 PEALCEKISQCDALIVRSGTKVTRSVFEAANGKLKVVGRAGVGIDNVDLQAATEFGCLVV 180
L E+ D +++ + + V EA LK++ A G+D+VDL+A E G V
Sbjct: 39 TAELIERSKDADIVMI-ANMPLPGEVIEACK-NLKMISVAFTGVDHVDLEACKERGITVS 96
Query: 181 NAPIANTVAAAEHGIALLASMARNVSQADASIKAGKWLRSKYVGVSLVGKTLAVMGFGKV 240
NA +T A AE I L + RN+ DA+++AG ++ +G L GKT+ ++G G +
Sbjct: 97 NAAGYSTEAVAELTIGLAIDLLRNIVPCDAAVRAGG-TKAGLIGRELAGKTVGIVGTGAI 155
Query: 241 GSEVARRAKGLGMNVIAHDPYAPADKARAVGVELVSFDQALATADFISLHMPLNPTTSKI 300
G VAR K G V+A+ ++A+A+G+E VS D+ LA +D +SLH+PLN T +
Sbjct: 156 GLRVARLFKAFGCKVLAYSRS-EKEEAKALGIEYVSLDELLAESDIVSLHLPLNDETKGL 214
Query: 301 FNDETFAKMKKGVRIVNVARGGVIDEEALVRALDSGVVAQAALDVFTEEPP-AKDSKLVQ 359
E A MK+ ++N ARG V+D EAL AL+ G +A A +DVF EPP D L+
Sbjct: 215 IGKEKLALMKESAILINTARGPVVDNEALADALNEGKIAGAGIDVFDMEPPLPADYPLLH 274
Query: 360 HENVTVTPHLGASTKEAQE 378
N +TPH+ +T+EA E
Sbjct: 275 APNTILTPHVAFATEEAME 293
>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 = 197 bits (504), Expect = 3e-58
Identities = 97/294 (32%), Positives = 142/294 (48%), Gaps = 10/294 (3%)
Query: 91 PTILVSEKLGEAGLAILRSFGNVECLYDLSPEALCEKISQCDALIVRSGTKVTRSVFEAA 150
ILV L + L LR+ L ++ E L E+++ D L+ G + AA
Sbjct: 1 MKILVLSPLDDEHLERLRAAAPGAELRVVTAEELTEELADADVLL---GNPPLPELLPAA 57
Query: 151 NGKLKVVGRAGVGIDNVDLQAATEFGCLVVNAPIANTVAAAEHGIALLASMARNVSQADA 210
+L+ + G+D + E ++ NA AE+ + + + AR + +
Sbjct: 58 -PRLRWIQSTSAGVDALLFPELLERDVVLTNARGIFGPPIAEYVLGYMLAFARKLPRYAR 116
Query: 211 SIKAGKWLRSKYVGVSLVGKTLAVMGFGKVGSEVARRAKGLGMNVIA---HDPYAPADKA 267
+ +W R V L GKT+ ++G G +G E+ARRAK GM VI AP
Sbjct: 117 NQAERRWQRRGPVR-ELAGKTVLIVGLGDIGREIARRAKAFGMRVIGVRRSGRPAPPVVD 175
Query: 268 RAVGVELVSFDQALATADFISLHMPLNPTTSKIFNDETFAKMKKGVRIVNVARGGVIDEE 327
+ D+ L AD++ +PL P T +FN E FA MK G ++NV RG V+DE+
Sbjct: 176 EVYTPD--ELDELLPEADYVVNALPLTPETRGLFNAERFAAMKPGAVLINVGRGSVVDED 233
Query: 328 ALVRALDSGVVAQAALDVFTEEPPAKDSKLVQHENVTVTPHLGASTKEAQEGVA 381
AL+ AL+SG +A AALDVF EEP DS L NV +TPH+ + E V
Sbjct: 234 ALIEALESGRIAGAALDVFEEEPLPADSPLWDLPNVIITPHISGDSPSYPERVV 287
>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 = 198 bits (505), Expect = 4e-58
Identities = 89/278 (32%), Positives = 134/278 (48%), Gaps = 25/278 (8%)
Query: 118 DLSPEALCEKISQCDALIVRSGTKVTRSVFEA-ANGKLKVVGRAGVGIDNVDLQAATEFG 176
L+PE + + D ++V+ V+E A +K + G+D +DL A E G
Sbjct: 33 LLTPETV-DLAKGYDGVVVQQTLPYDEEVYEKLAEYGIKQIALRSAGVDMIDLDLAKENG 91
Query: 177 CLVVNAPIANTVAAAEHGIALLASMARNVSQADASIKAGKWLRSKYVGVSLVGK-----T 231
+ N P + A AE + ++ RN + D + G + + L+G+ T
Sbjct: 92 LKITNVPAYSPRAIAEFAVTQALNLLRNTPEIDRRVAKGDFRWAP----GLIGREIRDLT 147
Query: 232 LAVMGFGKVGSEVARRAKGLGMNVIAHDPYAPADKARAVGVELVSFDQALATADFISLHM 291
+ ++G G++GS A+ KG G VIA+DPY P + + S + L AD ISLH+
Sbjct: 148 VGIIGTGRIGSAAAKIFKGFGAKVIAYDPY-PNPELEKFLLYYDSLEDLLKQADIISLHV 206
Query: 292 PLNPTTSKIFNDETFAKMKKGVRIVNVARGGVIDEEALVRALDSGVVAQAALDVFTEE-- 349
PL + N E FAKMK G +VN ARGG++D +AL+ ALDSG +A AALD + E
Sbjct: 207 PLTKENHHLINAEAFAKMKDGAILVNAARGGLVDTKALIDALDSGKIAGAALDTYENETG 266
Query: 350 -----------PPAKDSKLVQHENVTVTPHLGASTKEA 376
+L+ NV +TPH+ T A
Sbjct: 267 YFNKDWSGKEIEDEVLKELIAMPNVLITPHIAFYTDTA 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 (446), Expect = 6e-50
Identities = 89/295 (30%), Positives = 134/295 (45%), Gaps = 26/295 (8%)
Query: 116 LYDLSPEALCEKISQCDALIVRSGTKVTRSVFEAANGKLKVVGRAGVGIDNVDLQAATEF 175
+ +L EA E + D L+ G ++T+ AA +LK++ G+D++ L+ E
Sbjct: 26 VPELPDEAAEEALEDADVLV---GGRLTKEEALAALKRLKLIQVPSAGVDHLPLERLPE- 81
Query: 176 GCLVVNAPIANT----VAAAEHGIALLASMARNVSQADASIKAGKWLRSKYVGV---SLV 228
+AN A AEH +AL+ ++A+ + + D ++ G W L
Sbjct: 82 -----GVVVANNHGNSPAVAEHALALILALAKRIVEYDNDLRRGIWHGRAGEEPESKELR 136
Query: 229 GKTLAVMGFGKVGSEVARRAKGLGMNVIA--HDPYAPADKARAVGVELVSFDQALATADF 286
GKT+ ++G+G +G E+AR K GM VI P + D+AL AD
Sbjct: 137 GKTVGILGYGHIGREIARLLKAFGMRVIGVSRSPKEDEGADFVGTLS--DLDEALEQADV 194
Query: 287 ISLHMPLNPTTSKIFNDETFAKMKKGVRIVNVARGGVIDEEALVRALDSGVVAQAALDVF 346
+ + +PL T + A MK G +VNV RG V+DEEAL AL +A AA+DV+
Sbjct: 195 VVVALPLTKQTRGLIGAAELAAMKPGAILVNVGRGPVVDEEALYEALKERPIAGAAIDVW 254
Query: 347 TEEPPAKDSKLVQH------ENVTVTPHLGASTKEAQEGVAIEIAEAVVGALRGE 395
P D NV ++PH T+E E AE + LRGE
Sbjct: 255 WRYPSRGDPVAPSRYPFHELPNVIMSPHNAGWTEETFRRRIDEAAENIRRYLRGE 309
>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 = 174 bits (445), Expect = 8e-50
Identities = 90/297 (30%), Positives = 143/297 (48%), Gaps = 24/297 (8%)
Query: 91 PTILVSEKLGEAGLAILRSFGNVECLYDLS--PEALCEKISQCDALIVRSGTKVTRSVFE 148
P +L L LA L + V L++ + L E + A++ T ++ ++
Sbjct: 1 PDVLQLGPLPPELLAELEARFTVHRLWEAADPAALLAEHGGRIRAVVTNGETGLSAALIA 60
Query: 149 AANGKLKVVGRAGVGIDNVDLQAATEFGCLVVNAPIANTVAAAEHGIALLASMARNVSQA 208
A L+++ GVG D +DL AA G V N P T A+ + LL ++ R + A
Sbjct: 61 ALP-ALELIASFGVGYDGIDLDAARARGIRVTNTPGVLTDDVADLAVGLLLAVLRRIPAA 119
Query: 209 DASIKAGKWLRSKY-VGVSLVGKTLAVMGFGKVGSEVARRAKGLGMNVIAHD-------P 260
D ++AG+W + + + + GK + ++G G++G +ARR + GM + H P
Sbjct: 120 DRFVRAGRWPKGAFPLTRKVSGKRVGIVGLGRIGRAIARRLEAFGMEIAYHGRRPKPDVP 179
Query: 261 YAPADKARAVGVELVSFDQALATADFISLHMPLNPTTSKIFNDETFAKM-KKGVRIVNVA 319
Y +EL A +D + + P P T + N E + GV +VNVA
Sbjct: 180 YRYYASL----LELA------AESDVLVVACPGGPATRHLVNAEVLEALGPDGV-LVNVA 228
Query: 320 RGGVIDEEALVRALDSGVVAQAALDVFTEEPPAKDSKLVQHENVTVTPHLGASTKEA 376
RG V+DE AL+ AL G +A A LDVF E P + L+ +NV +TPH+ ++T E
Sbjct: 229 RGSVVDEAALIAALQEGRIAGAGLDVFENE-PNVPAALLDLDNVVLTPHIASATVET 284
>gnl|CDD|180588 PRK06487, PRK06487, glycerate dehydrogenase; Provisional.
Length = 317
Score = 173 bits (440), Expect = 5e-49
Identities = 100/307 (32%), Positives = 152/307 (49%), Gaps = 18/307 (5%)
Query: 99 LGEAGLAILRSFGNVECLYDLS-PEALCEKISQCDALIVRSGTKVTRSVFEAANGKLKVV 157
LG+ L+ L + L+D + PE + E++ I + + AA +LK++
Sbjct: 13 LGDLDLSPLEQAFDELQLHDATTPEQVAERLRGAQVAISNK-VALDAAAL-AAAPQLKLI 70
Query: 158 GRAGVGIDNVDLQAATEFGCLVVNAPIANTVAAAEHGIALLASMARNVSQADASIKAGKW 217
A G +NVDL AA E G V N T + A+H +ALL ++A + ++ AG+W
Sbjct: 71 LVAATGTNNVDLAAARERGITVCNCQGYGTPSVAQHTLALLLALATRLPDYQQAVAAGRW 130
Query: 218 LRSKYVG------VSLVGKTLAVMGFGKVGSEVARRAKGLGMNV-IAHDPYAPADKARAV 270
+S V L GKTL ++G G++G VAR A+ GM V I P PA R
Sbjct: 131 QQSSQFCLLDFPIVELEGKTLGLLGHGELGGAVARLAEAFGMRVLIGQLPGRPARPDR-- 188
Query: 271 GVELVSFDQALATADFISLHMPLNPTTSKIFNDETFAKMKKGVRIVNVARGGVIDEEALV 330
+ D+ L D ++LH PL T + A MK G ++N ARGG++DE+AL
Sbjct: 189 ----LPLDELLPQVDALTLHCPLTEHTRHLIGARELALMKPGALLINTARGGLVDEQALA 244
Query: 331 RALDSGVVAQAALDVFTEEPPAKDSKLVQ--HENVTVTPHLGASTKEAQEGVAIEIAEAV 388
AL SG + AA DV + EPP + L+ + VTPH ++EA++ + ++AE
Sbjct: 245 DALRSGHLGGAATDVLSVEPPVNGNPLLAPDIPRLIVTPHSAWGSREARQRIVGQLAENA 304
Query: 389 VGALRGE 395
G+
Sbjct: 305 RAFFAGK 311
>gnl|CDD|185307 PRK15409, PRK15409, bifunctional glyoxylate/hydroxypyruvate
reductase B; Provisional.
Length = 323
Score = 169 bits (430), Expect = 1e-47
Identities = 99/320 (30%), Positives = 160/320 (50%), Gaps = 9/320 (2%)
Query: 90 KPTILVSEKLGEAGLAILRSFGNVECLYDLSPE---ALCEKISQCDALIVRSGTKVTRSV 146
KP++++ + L + L L V + +LSPE ++ + L+ SG KV ++
Sbjct: 2 KPSVILYKALPDDLLQRLEEHFTVTQVANLSPETVEQHAAAFAEAEGLL-GSGEKVDAAL 60
Query: 147 FEAANGKLKVVGRAGVGIDNVDLQAATEFGCLVVNAPIANTVAAAEHGIALLASMARNVS 206
E KL+ VG DN D+ A T L+++ P T A+ +AL+ S AR V
Sbjct: 61 LEKMP-KLRAASTISVGYDNFDVDALTARKILLMHTPTVLTETVADTLMALVLSTARRVV 119
Query: 207 QADASIKAGKWLRS---KYVGVSLVGKTLAVMGFGKVGSEVARRAK-GLGMNVIAHDPYA 262
+ +KAG+W S + G + KTL ++G G++G +A+RA G M ++ +
Sbjct: 120 EVAERVKAGEWTASIGPDWFGTDVHHKTLGIVGMGRIGMALAQRAHFGFNMPILYNARRH 179
Query: 263 PADKARAVGVELVSFDQALATADFISLHMPLNPTTSKIFNDETFAKMKKGVRIVNVARGG 322
+ D L +DF+ + +PL T +F E FAKMK +N RG
Sbjct: 180 HKEAEERFNARYCDLDTLLQESDFVCIILPLTDETHHLFGAEQFAKMKSSAIFINAGRGP 239
Query: 323 VIDEEALVRALDSGVVAQAALDVFTEEPPAKDSKLVQHENVTVTPHLGASTKEAQEGVAI 382
V+DE AL+ AL G + A LDVF +EP + DS L+ NV PH+G++T E + +A
Sbjct: 240 VVDENALIAALQKGEIHAAGLDVFEQEPLSVDSPLLSLPNVVAVPHIGSATHETRYNMAA 299
Query: 383 EIAEAVVGALRGELSATAIN 402
+ ++ AL+G++ +N
Sbjct: 300 CAVDNLIDALQGKVEKNCVN 319
>gnl|CDD|235890 PRK06932, PRK06932, glycerate dehydrogenase; Provisional.
Length = 314
Score = 168 bits (426), Expect = 3e-47
Identities = 87/260 (33%), Positives = 130/260 (50%), Gaps = 16/260 (6%)
Query: 120 SPEALCEKISQCDALIVRSGTKVTRSVFEAANGKLKVVGRAGVGIDNVDLQAATEFGCLV 179
S E E+ D +++ S TR KLK++ G +NVDL AA E G V
Sbjct: 34 SAEQTIERAKDAD-IVITSKVLFTRETLAQLP-KLKLIAITATGTNNVDLVAAKELGIAV 91
Query: 180 VNAPIANTVAAAEHGIALLASMARNVSQADASIKAGKWLRSK------YVGVSLVGKTLA 233
N ++ EH + ++ ++ ++ + +W K Y + G TL
Sbjct: 92 KNVTGYSSTTVPEHVLGMIFALKHSLMGWYRDQLSDRWATCKQFCYFDYPITDVRGSTLG 151
Query: 234 VMGFGKVGSEVARRAKGLGMNVIAHDPYAPADKARAVGVELVSFDQALATADFISLHMPL 293
V G G +G+EV R A+ LGM V+ YA A F++ L AD ++LH PL
Sbjct: 152 VFGKGCLGTEVGRLAQALGMKVL----YAEHKGASVCREGYTPFEEVLKQADIVTLHCPL 207
Query: 294 NPTTSKIFNDETFAKMKKGVRIVNVARGGVIDEEALVRALDSGVVAQAALDVFTEEPPAK 353
TT + N ET A MK ++N RG ++DE+AL+ AL++G +A AALDV +EPP K
Sbjct: 208 TETTQNLINAETLALMKPTAFLINTGRGPLVDEQALLDALENGKIAGAALDVLVKEPPEK 267
Query: 354 DSKLVQHE----NVTVTPHL 369
D+ L+Q N+ +TPH+
Sbjct: 268 DNPLIQAAKRLPNLLITPHI 287
>gnl|CDD|181414 PRK08410, PRK08410, 2-hydroxyacid dehydrogenase; Provisional.
Length = 311
Score = 167 bits (425), Expect = 5e-47
Identities = 92/316 (29%), Positives = 166/316 (52%), Gaps = 17/316 (5%)
Query: 90 KPTILVSEKLGEAGLAILRSFGNVECLYDL-SPEALCEKISQCDALIVRSGTKVTRSVFE 148
K IL ++ LG+ L++ FG+ + +Y SPE + E+I + +I+ + + + V
Sbjct: 2 KIVILDAKTLGDKDLSVFEEFGDFQ-IYPTTSPEEVIERIKDAN-IIITNKVVIDKEVLS 59
Query: 149 AANGKLKVVGRAGVGIDNVDLQAATEFGCLVVNAPIANTVAAAEHGIALLASMARNVSQA 208
LK++ G +NVD++ A + G V N +T + A+H A+L S+ ++
Sbjct: 60 QLP-NLKLICITATGTNNVDIEYAKKKGIAVKNVAGYSTESVAQHTFAMLLSLLGRINYY 118
Query: 209 DASIKAGKWLRSK-YVGVS-----LVGKTLAVMGFGKVGSEVARRAKGLGMNVIAHDPYA 262
D +K+G++ S + +S + GK ++G G +G VA+ A+ G V+ Y+
Sbjct: 119 DRYVKSGEYSESPIFTHISRPLGEIKGKKWGIIGLGTIGKRVAKIAQAFGAKVVY---YS 175
Query: 263 PADKARAVGVELVSFDQALATADFISLHMPLNPTTSKIFNDETFAKMKKGVRIVNVARGG 322
+ K + E VS ++ L T+D IS+H PLN T + + +K G ++NV RGG
Sbjct: 176 TSGKNKNEEYERVSLEELLKTSDIISIHAPLNEKTKNLIAYKELKLLKDGAILINVGRGG 235
Query: 323 VIDEEALVRALDSGVVAQAALDVFTEEPPAKDSKLVQ---HENVTVTPHLGASTKEAQEG 379
+++E+ L +ALD + A LDV +EP K+ L+ E + +TPH+ ++KEA++
Sbjct: 236 IVNEKDLAKALDEKDIY-AGLDVLEKEPMEKNHPLLSIKNKEKLLITPHIAWASKEARKT 294
Query: 380 VAIEIAEAVVGALRGE 395
+ ++ E + L G
Sbjct: 295 LIEKVKENIKDFLEGG 310
>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 (423), Expect = 2e-46
Identities = 89/271 (32%), Positives = 131/271 (48%), Gaps = 37/271 (13%)
Query: 105 AILRSFGNVECL--YDLSPEALCEKISQCDALIVRSGTKVTRSVFEAANGKLKVVGRAGV 162
+ G V L +++ E L D L+VRS TKV ++ E + K+K VG A +
Sbjct: 13 ELFSPLGEVTYLPGREITAEDL----KDADVLLVRSVTKVNEALLEGS--KVKFVGTATI 66
Query: 163 GIDNVDLQAATEFGCLVVNAPIANTVAAAEHGIALLASMARNVSQADASIKAGKWLRSKY 222
G D++D E G NAP N + AE+ ++ L +A +
Sbjct: 67 GTDHIDTDYLKERGIGFANAPGCNANSVAEYVLSALLVLA------------------QR 108
Query: 223 VGVSLVGKTLAVMGFGKVGSEVARRAKGLGMNVIAHDPYAPADKARAVGVELVSFDQALA 282
G SL GKT+ ++G G VGS +ARR + LGMNV+ DP VS ++ LA
Sbjct: 109 QGFSLKGKTVGIVGVGNVGSRLARRLEALGMNVLLCDPPR---AEAEGDPGFVSLEELLA 165
Query: 283 TADFISLHMPLNPT----TSKIFNDETFAKMKKGVRIVNVARGGVIDEEALVRALDSGVV 338
AD I+LH+PL T + +++ A +K G ++N +RG VID +AL+ L G
Sbjct: 166 EADIITLHVPLTRDGEHPTYHLLDEDFLAALKPGQILINASRGAVIDNQALLALLQRGKD 225
Query: 339 AQAALDVFTEEPPAKDSKLVQHENVT-VTPH 368
+ LDV+ EP D +L+ V TPH
Sbjct: 226 LRVVLDVWENEPEI-DLELLDK--VDIATPH 253
>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 = 162 bits (412), Expect = 6e-45
Identities = 90/293 (30%), Positives = 138/293 (47%), Gaps = 43/293 (14%)
Query: 112 NVECLYDLSPEALCEKISQ----CDALIVRSGTKVTRSVFEA-ANGKLKVVGRAGVGIDN 166
NVE L+ E L + + D + + +K++ + E +K + +G D+
Sbjct: 24 NVE--VTLTKEPLTLENAHLAEGYDGISILGKSKISAELLEKLKEAGVKYISTRSIGYDH 81
Query: 167 VDLQAATEFGCLVVNAPIA-NTVAAAEHGIALLASMARNVSQA-------DASIKA--GK 216
+DL AA E G V N + N+VA ++ + L+ R Q D S+ G+
Sbjct: 82 IDLDAAKELGIKVSNVTYSPNSVA--DYTVMLMLMALRKYKQIMKRAEVNDYSLGGLQGR 139
Query: 217 WLRSKYVGVSLVGKTLAVMGFGKVGSEVARRAKGLGMNVIAHDPYAPADKARAVGVELVS 276
LR+ VGV +G G++G V + G G ++A+DPY P ++ + E V
Sbjct: 140 ELRNLTVGV---------IGTGRIGQAVIKNLSGFGCKILAYDPY-PNEEVKK-YAEYVD 188
Query: 277 FDQALATADFISLHMPLNPTTSKIFNDETFAKMKKGVRIVNVARGGVIDEEALVRALDSG 336
D +D I+LH PL T + N E+ AKMK GV I+N ARG +ID EAL+ L+SG
Sbjct: 189 LDTLYKESDIITLHTPLTEETYHLINKESIAKMKDGVIIINTARGELIDTEALIEGLESG 248
Query: 337 VVAQAALDVFTEEP------------PAKD-SKLVQHENVTVTPHLGASTKEA 376
+ AALDV E ++ + L NV +TPH+ T +A
Sbjct: 249 KIGGAALDVIEGEDGIYYNDRKGDILSNRELAILRSFPNVILTPHMAFYTDQA 301
>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 = 160 bits (407), Expect = 2e-44
Identities = 71/230 (30%), Positives = 111/230 (48%), Gaps = 29/230 (12%)
Query: 153 KLKVVGRAGVGIDNVDLQAATEFGCLVVNAPIANTVAAAEHGIALLASMARNVSQADASI 212
LK + G+D + L+ + G L+ N +++ AE + + + + + +A +
Sbjct: 60 NLKWIQLYSAGVDYLPLEYIKKKGILLTNNSGIHSIPIAEWIVGYILEIYKGLKKAYKNQ 119
Query: 213 KAGKWLRSKYVGVSLVGKTLAVMGFGKVGSEVARRAKGLGMNVIAHDPYAPADKARAVGV 272
K KW + + L GKT+ +G G +G E+A+R K GM VI GV
Sbjct: 120 KEKKW-KMDSSLLELYGKTILFLGTGSIGQEIAKRLKAFGMKVI--------------GV 164
Query: 273 -----------ELVSFDQ---ALATADFISLHMPLNPTTSKIFNDETFAKMKKGVRIVNV 318
+ ++ L AD + +PL T +F++ F +MKKG +NV
Sbjct: 165 NTSGRDVEYFDKCYPLEELDEVLKEADIVVNVLPLTEETHHLFDEAFFEQMKKGALFINV 224
Query: 319 ARGGVIDEEALVRALDSGVVAQAALDVFTEEPPAKDSKLVQHENVTVTPH 368
RG +DE+AL+ AL + + AALDVF EEP KDS L +NV +TPH
Sbjct: 225 GRGPSVDEDALIEALKNKQIRGAALDVFEEEPLPKDSPLWDLDNVLITPH 274
>gnl|CDD|240627 cd05302, FDH, NAD-dependent Formate Dehydrogenase (FDH).
NAD-dependent formate dehydrogenase (FDH) catalyzes the
NAD+-dependent oxidation of a formate anion to carbon
dioxide coupled with the reduction of NAD+ to NADH.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxy acid dehydrogenase family have 2
highly similar subdomains of the alpha/beta form, with
NAD binding occurring in the cleft between subdomains.
NAD contacts are primarily to the Rossmann-fold
NAD-binding domain which is inserted within the linear
sequence of the more diverse flavodoxin-like catalytic
subdomain. Some related proteins have similar structural
subdomain but with a tandem arrangement of the catalytic
and NAD-binding subdomains in the linear sequence. FDHs
of this family contain no metal ions or prosthetic
groups. Catalysis occurs though direct transfer of the
hydride ion to NAD+ without the stages of acid-base
catalysis typically found in related dehydrogenases.
FDHs are found in all methylotrophic microorganisms in
energy production from C1 compounds such as methanol,
and in the stress responses of plants. NAD-dependent FDH
is useful in cofactor regeneration in asymmetrical
biocatalytic reduction processes, where FDH irreversibly
oxidizes formate to carbon dioxide, while reducing the
oxidized form of the cofactor to the reduced form.
Length = 348
Score = 161 bits (409), Expect = 2e-44
Identities = 80/244 (32%), Positives = 128/244 (52%), Gaps = 5/244 (2%)
Query: 142 VTRSVFEAANGKLKVVGRAGVGIDNVDLQAATEFGCLVVNAPIANTVAAAEHGIALLASM 201
+T A LK+ AG+G D+VDLQAA + G V +N V+ AEH + ++ +
Sbjct: 74 MTAERIAKAK-NLKLALTAGIGSDHVDLQAANDRGITVAEVTGSNVVSVAEHVVMMILIL 132
Query: 202 ARNVSQADASIKAGKWLRSKYVGVS--LVGKTLAVMGFGKVGSEVARRAKGLGMNVIAHD 259
RN G W + V + L GKT+ +G G++G V RR K ++++ +D
Sbjct: 133 VRNYVPGHEQAIEGGWNVADVVKRAYDLEGKTVGTVGAGRIGLRVLRRLKPFDVHLLYYD 192
Query: 260 PYA-PADKARAVGVELV-SFDQALATADFISLHMPLNPTTSKIFNDETFAKMKKGVRIVN 317
+ P + + +G+ + ++ D ++++ PL+P T +FN E +KMKKG +VN
Sbjct: 193 RHRLPEEVEKELGLTRHADLEDMVSKCDVVTINCPLHPETEGLFNKELLSKMKKGAYLVN 252
Query: 318 VARGGVIDEEALVRALDSGVVAQAALDVFTEEPPAKDSKLVQHENVTVTPHLGASTKEAQ 377
ARG + D EA+ AL+SG +A A DV+ +P KD N +TPH+ +T +AQ
Sbjct: 253 TARGKICDREAVAEALESGHLAGYAGDVWFPQPAPKDHPWRTMPNNAMTPHISGTTLDAQ 312
Query: 378 EGVA 381
A
Sbjct: 313 ARYA 316
>gnl|CDD|215501 PLN02928, PLN02928, oxidoreductase family protein.
Length = 347
Score = 156 bits (396), Expect = 2e-42
Identities = 77/268 (28%), Positives = 138/268 (51%), Gaps = 20/268 (7%)
Query: 122 EALCEKISQCDALIVRSGTKVTRSVFEAANGKLKVVGRAGVGIDNVDLQAATEFGCLVVN 181
E + + I+ D + + ++ + A+ ++K++ + GVG++ VD+ AAT+ G V
Sbjct: 53 EDVPDVIANYDICVPKM-MRLDADIIARAS-QMKLIMQFGVGLEGVDVDAATKHGIKVAR 110
Query: 182 APIANT---VAAAEHGIALLASMARNVSQADASIKAGKWLRSKYVGVSLVGKTLAVMGFG 238
P T + AE I L+ + R ++ S+KA + + +G +L GKT+ ++G+G
Sbjct: 111 IPSEGTGNAASCAEMAIYLMLGLLRKQNEMQISLKARRL--GEPIGDTLFGKTVFILGYG 168
Query: 239 KVGSEVARRAKGLGMNVIAHDPYAPADKARAVGVELVSFDQA-------------LATAD 285
+G E+A+R + G+ ++A ++ + + D AD
Sbjct: 169 AIGIELAKRLRPFGVKLLATRRSWTSEPEDGLLIPNGDVDDLVDEKGGHEDIYEFAGEAD 228
Query: 286 FISLHMPLNPTTSKIFNDETFAKMKKGVRIVNVARGGVIDEEALVRALDSGVVAQAALDV 345
+ L L T+ I NDE + MKKG +VN+ARGG++D +A++ AL+SG + A+DV
Sbjct: 229 IVVLCCTLTKETAGIVNDEFLSSMKKGALLVNIARGGLLDYDAVLAALESGHLGGLAIDV 288
Query: 346 FTEEPPAKDSKLVQHENVTVTPHLGAST 373
EP D +++H NV +TPH+ T
Sbjct: 289 AWSEPFDPDDPILKHPNVIITPHVAGVT 316
>gnl|CDD|181041 PRK07574, PRK07574, formate dehydrogenase; Provisional.
Length = 385
Score = 154 bits (391), Expect = 2e-41
Identities = 77/229 (33%), Positives = 128/229 (55%), Gaps = 4/229 (1%)
Query: 153 KLKVVGRAGVGIDNVDLQAATEFGCLVVNAPIANTVAAAEHGIALLASMARNVSQADASI 212
LK+ AG+G D+VDLQAA+E G V +N+++ AEH + ++ ++ RN +
Sbjct: 114 NLKLAITAGIGSDHVDLQAASEHGITVAEVTGSNSISVAEHVVMMILALVRNYEPSHRQA 173
Query: 213 KAGKWLRSKYVGVS--LVGKTLAVMGFGKVGSEVARRAKGLGMNVIAHDPY-APADKARA 269
G W + V S L G T+ ++G G++G V RR K + + D + P + +
Sbjct: 174 VEGGWNIADCVSRSYDLEGMTVGIVGAGRIGLAVLRRLKPFDVKLHYTDRHRLPEEVEQE 233
Query: 270 VGVEL-VSFDQALATADFISLHMPLNPTTSKIFNDETFAKMKKGVRIVNVARGGVIDEEA 328
+G+ VSFD ++ D +++H PL+P T +F+ + ++MK+G +VN ARG ++D +A
Sbjct: 234 LGLTYHVSFDSLVSVCDVVTIHCPLHPETEHLFDADVLSRMKRGSYLVNTARGKIVDRDA 293
Query: 329 LVRALDSGVVAQAALDVFTEEPPAKDSKLVQHENVTVTPHLGASTKEAQ 377
+VRAL+SG +A A DV+ +P D +TPH+ +T AQ
Sbjct: 294 VVRALESGHLAGYAGDVWFPQPAPADHPWRTMPRNGMTPHISGTTLSAQ 342
>gnl|CDD|177941 PLN02306, PLN02306, hydroxypyruvate reductase.
Length = 386
Score = 148 bits (375), Expect = 2e-39
Identities = 111/324 (34%), Positives = 163/324 (50%), Gaps = 31/324 (9%)
Query: 129 SQCDALIVRSGTKVTRSVFEAANGKLKVVGRA----GVGIDNVDLQAATEFGCLVVNAPI 184
+CD +I + ++F A + K G+A VG +NVD++AA ++G V N P
Sbjct: 61 DKCDGVIGQLTEDWGETLFSALS---KAGGKAFSNMAVGYNNVDVEAANKYGIAVGNTPG 117
Query: 185 ANTVAAAEHGIALLASMARNVSQADASIKAGK---WLRSKYVGVSLVGKTLAVMGFGKVG 241
T AE +L + AR + +AD ++AG WL +VG L G+T+ V+G G++G
Sbjct: 118 VLTETTAELAASLSLAAARRIVEADEFMRAGLYEGWLPHLFVGNLLKGQTVGVIGAGRIG 177
Query: 242 SEVARR-AKGLGMNVIAHDPY----------APADKARAVGVELV------SFDQALATA 284
S AR +G MN+I +D Y A +A G + V S ++ L A
Sbjct: 178 SAYARMMVEGFKMNLIYYDLYQSTRLEKFVTAYGQFLKANGEQPVTWKRASSMEEVLREA 237
Query: 285 DFISLHMPLNPTTSKIFNDETFAKMKKGVRIVNVARGGVIDEEALVRALDSGVVAQAALD 344
D ISLH L+ TT + N E A MKK +VN +RG VIDE ALV L + + + LD
Sbjct: 238 DVISLHPVLDKTTYHLINKERLALMKKEAVLVNASRGPVIDEVALVEHLKANPMFRVGLD 297
Query: 345 VFTEEPPAKDSKLVQHENVTVTPHLGASTKEAQEGVAIEIAEAVVGALRGELSATAIN-- 402
VF +EP K L +N V PH+ +++K +EG+A A V+G L+G N
Sbjct: 298 VFEDEPYMKPG-LADMKNAVVVPHIASASKWTREGMATLAALNVLGKLKGYPVWGDPNRV 356
Query: 403 APMV-PSEVLSELAPYVVLAKKLG 425
P + + +P +V AK LG
Sbjct: 357 EPFLNENAPPPAASPSIVNAKALG 380
>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 = 146 bits (370), Expect = 5e-39
Identities = 94/287 (32%), Positives = 139/287 (48%), Gaps = 33/287 (11%)
Query: 117 YDLS--PEAL----CEKISQCDALIVRSGTKVTRSVFEAANGK-LKVVGRAGVGIDNVDL 169
YDL+ E L DA+IVR + E +K V VG +++DL
Sbjct: 25 YDLTLVEEYLNDENVHLAKGHDAVIVRGNCFADKENLEIYKEYGIKYVFTRTVGFNHIDL 84
Query: 170 QAATEFGCLVVNAPIANTVAAAEHGIALLASMARNVS-----QADASIKAGKWLRSKYVG 224
+AA E G + P + A AE L +++R+ + A+ + K ++ SK +
Sbjct: 85 EAAKELGFKMARVPSYSPNAIAELAFTLAMTLSRHTAYTASRTANKNFKVDPFMFSKEIR 144
Query: 225 VSLVGKTLAVMGFGKVGSEVARRAKGLGMNVIAHDPYAPADKARAVGVELVSFDQALATA 284
S VG ++G G++G A+ KGLG VI +D Y P+D A+ V V VS D+ L +
Sbjct: 145 NSTVG----IIGTGRIGLTAAKLFKGLGAKVIGYDIY-PSDAAKDV-VTFVSLDELLKKS 198
Query: 285 DFISLHMPLNP-TTSKIFNDETFAKMKKGVRIVNVARGGVIDEEALVRALDSGVVAQAAL 343
D ISLH+P K+ N E +KMK G ++N ARG + DEEA++ AL+SG +A
Sbjct: 199 DIISLHVPYIKGKNDKLINKEFISKMKDGAILINTARGELQDEEAILEALESGKLAGFGT 258
Query: 344 DVFTEE-------------PPAKDSKLVQ-HENVTVTPHLGASTKEA 376
DV E KL+ + V +TPH+G+ T EA
Sbjct: 259 DVLNNEKEIFFKDFDGDKIEDPVVEKLLDLYPRVLLTPHIGSYTDEA 305
>gnl|CDD|240641 cd12164, GDH_like_2, Putative glycerate dehydrogenase and related
proteins of the D-specific 2-hydroxy dehydrogenase
family. This group contains a variety of proteins
variously identified as glycerate dehydrogenase (GDH,
also known as hydroxypyruvate reductase) and other
enzymes of the 2-hydroxyacid dehydrogenase family. GDH
catalyzes the reversible reaction of (R)-glycerate +
NAD+ to hydroxypyruvate + NADH + H+. 2-hydroxyacid
dehydrogenases catalyze the conversion of a wide variety
of D-2-hydroxy acids to their corresponding keto acids.
The general mechanism is (R)-lactate + acceptor to
pyruvate + reduced acceptor. Formate/glycerate and
related dehydrogenases of the D-specific 2-hydroxyacid
dehydrogenase superfamily include groups such as formate
dehydrogenase, glycerate dehydrogenase, L-alanine
dehydrogenase, and S-adenosylhomocysteine hydrolase.
Despite often low sequence identity, these proteins
typically have a characteristic arrangement of 2 similar
subdomains of the alpha/beta Rossmann-fold NAD+ binding
form. The NAD+ binding domain is inserted within the
linear sequence of the mostly N-terminal catalytic
domain, which has a similar domain structure to the
internal NAD binding domain. Structurally, these domains
are connected by extended alpha helices and create a
cleft in which NAD is bound, primarily to the C-terminal
portion of the 2nd (internal) domain. Some related
proteins have similar structural subdomain but with a
tandem arrangement of the catalytic and NAD-binding
subdomains in the linear sequence. While many members of
this family are dimeric, alanine DH is hexameric and
phosphoglycerate DH is tetrameric.
Length = 306
Score = 140 bits (356), Expect = 2e-37
Identities = 77/256 (30%), Positives = 115/256 (44%), Gaps = 30/256 (11%)
Query: 153 KLKVVGRAGVGIDNVDLQAATEFGCLVVNAPIANTVAA------AEHGIALLASMA--RN 204
LK + G G+D++ + PI V AE+ L A + R+
Sbjct: 58 NLKAIFSLGAGVDHLLADPDLP------DVPIVRLVDPGLAQGMAEY--VLAAVLRLHRD 109
Query: 205 VSQADASIKAGKWLRSKYVGVSLVGKTLAVMGFGKVGSEVARRAKGLGMNVIAHDPYAPA 264
+ + A + G W + + V+G G++G+ VARR LG V ++ +
Sbjct: 110 MDRYAAQQRRGVWKPLPQRPAAER--RVGVLGLGELGAAVARRLAALGFPVSG---WSRS 164
Query: 265 DKARAVGVELVS----FDQALATADF-ISLHMPLNPTTSKIFNDETFAKMKKGVRIVNVA 319
K GV D LA D + L +PL P T I N E A++ +G ++NV
Sbjct: 165 PKDIE-GVTCFHGEEGLDAFLAQTDILVCL-LPLTPETRGILNAELLARLPRGAALINVG 222
Query: 320 RGGVIDEEALVRALDSGVVAQAALDVFTEEPPAKDSKLVQHENVTVTPHLGASTKEAQEG 379
RG + E L+ ALDSG ++ A LDVF +EP D L +H VTVTPH+ A+ +
Sbjct: 223 RGPHLVEADLLAALDSGHLSGAVLDVFEQEPLPADHPLWRHPRVTVTPHI-AAITDPDSA 281
Query: 380 VAIEIAEAVVGALRGE 395
A +AE + GE
Sbjct: 282 AAQ-VAENIRRLEAGE 296
>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 = 139 bits (351), Expect = 9e-37
Identities = 71/205 (34%), Positives = 109/205 (53%), Gaps = 10/205 (4%)
Query: 185 ANTVAAAEHGIALLASMARNVSQADASIK-AGKWLRSKYVGVSLVGKTLAVMGFGKVGSE 243
A AE +A + + A+ + + +K A +W R SL G TL ++GFG +G
Sbjct: 94 VAAEAIAEFVLAAILAAAKRL--PEIWVKGAEQWRREP--LGSLAGSTLGIVGFGAIGQA 149
Query: 244 VARRAKGLGMNVIA-HDPYAPADKARAVGVELVS-FDQALATADFISLHMPLNPTTSKIF 301
+ARRA LGM V+A P+D GVE + + A +D + L PL P T +
Sbjct: 150 LARRALALGMRVLALRRSGRPSD---VPGVEAAADLAELFARSDHLVLAAPLTPETRHLI 206
Query: 302 NDETFAKMKKGVRIVNVARGGVIDEEALVRALDSGVVAQAALDVFTEEPPAKDSKLVQHE 361
N + A+ K G+ ++N+ARGG++D+EAL+ ALDSG ++ A+LDV EP + L H
Sbjct: 207 NADVLAQAKPGLHLINIARGGLVDQEALLEALDSGRISLASLDVTDPEPLPEGHPLYTHP 266
Query: 362 NVTVTPHLGASTKEAQEGVAIEIAE 386
V ++PH A + + +A E
Sbjct: 267 RVRLSPHTSAIAPDGRRNLADRFLE 291
>gnl|CDD|166874 PRK00257, PRK00257, erythronate-4-phosphate dehydrogenase;
Validated.
Length = 381
Score = 134 bits (338), Expect = 2e-34
Identities = 87/304 (28%), Positives = 137/304 (45%), Gaps = 39/304 (12%)
Query: 118 DLSPEALCEKISQCDALIVRSGTKVTRSVFEAANGKLKVVGRAGVGIDNVDLQAATEFGC 177
A + D L+VRS T+V R++ E + +++ VG +G D++DL E G
Sbjct: 29 AFDRAA----VRDADVLLVRSVTRVDRALLEGS--RVRFVGTCTIGTDHLDLDYFAEAGI 82
Query: 178 LVVNAPIANTVAAAEHGIALLASMARNVSQADASIKAGKWLRSKYVGVSLVGKTLAVMGF 237
+AP N ++ + L ++A GV L +T V+G
Sbjct: 83 TWSSAPGCNARGVVDYVLGSLLTLAE--------------RE----GVDLAERTYGVVGA 124
Query: 238 GKVGSEVARRAKGLGMNVIAHDPYAPADKARAVGVELVSFDQALATADFISLHMPLNPT- 296
G VG + R +GLG V+ DP P +A G + VS ++ L D ISLH PL
Sbjct: 125 GHVGGRLVRVLRGLGWKVLVCDP--PRQEAEGDG-DFVSLERILEECDVISLHTPLTKEG 181
Query: 297 ---TSKIFNDETFAKMKKGVRIVNVARGGVIDEEALVRALDSGVVAQAALDVFTEEPPAK 353
T + ++ A ++ G ++N +RG V+D +AL AL SG A LDV+ EP
Sbjct: 182 EHPTRHLLDEAFLASLRPGAWLINASRGAVVDNQALREALLSGEDLDAVLDVWEGEPQI- 240
Query: 354 DSKLVQHENVTV-TPHL-GASTKEAQEGVAIEIAEAVVGALRGELSATAINAPMVPSEVL 411
D +L T+ TPH+ G S G A +I +A+ + A ++P L
Sbjct: 241 DLELADL--CTIATPHIAGYSLDGKARGTA-QIYQALCRFFG--IPARVSLTDLLPPPWL 295
Query: 412 SELA 415
+++
Sbjct: 296 AQID 299
>gnl|CDD|178684 PLN03139, PLN03139, formate dehydrogenase; Provisional.
Length = 386
Score = 128 bits (322), Expect = 4e-32
Identities = 72/228 (31%), Positives = 113/228 (49%), Gaps = 4/228 (1%)
Query: 154 LKVVGRAGVGIDNVDLQAATEFGCLVVNAPIANTVAAAEHGIALLASMARNVSQADASIK 213
L+++ AG+G D++DL AA G V +N V+ AE + + + RN +
Sbjct: 122 LELLLTAGIGSDHIDLPAAAAAGLTVAEVTGSNVVSVAEDELMRILILLRNFLPGYHQVV 181
Query: 214 AGKWLRSK--YVGVSLVGKTLAVMGFGKVGSEVARRAKGLGMNVIAHDPYA-PADKARAV 270
+G+W + Y L GKT+ +G G++G + +R K N++ HD + +
Sbjct: 182 SGEWNVAGIAYRAYDLEGKTVGTVGAGRIGRLLLQRLKPFNCNLLYHDRLKMDPELEKET 241
Query: 271 GVELVS-FDQALATADFISLHMPLNPTTSKIFNDETFAKMKKGVRIVNVARGGVIDEEAL 329
G + D L D + ++ PL T +FN E AKMKKGV IVN ARG ++D +A+
Sbjct: 242 GAKFEEDLDAMLPKCDVVVINTPLTEKTRGMFNKERIAKMKKGVLIVNNARGAIMDTQAV 301
Query: 330 VRALDSGVVAQAALDVFTEEPPAKDSKLVQHENVTVTPHLGASTKEAQ 377
A SG + DV+ +P KD N +TPH+ +T +AQ
Sbjct: 302 ADACSSGHIGGYGGDVWYPQPAPKDHPWRYMPNHAMTPHISGTTIDAQ 349
>gnl|CDD|181499 PRK08605, PRK08605, D-lactate dehydrogenase; Validated.
Length = 332
Score = 123 bits (311), Expect = 4e-31
Identities = 77/268 (28%), Positives = 137/268 (51%), Gaps = 24/268 (8%)
Query: 154 LKVVGRAGVGIDNVDLQAATEFGCLVVNAPIANTVAAAEHGIALLASMARNVSQADASIK 213
+K + + G D DL+ AT++ ++ N P + + AE + ++ R+ +Q ++
Sbjct: 70 IKQIAQRSAGFDTYDLELATKYNLIISNVPSYSPESIAEFTVTQAINLVRHFNQIQTKVR 129
Query: 214 AG--KW---LRSKYVGVSLVGKTLAVMGFGKVGSEVAR-RAKGLGMNVIAHDPYAPADKA 267
+W + S+ S+ +AV+G G++G VA+ AKG G +V+A+DP+ P KA
Sbjct: 130 EHDFRWEPPILSR----SIKDLKVAVIGTGRIGLAVAKIFAKGYGSDVVAYDPF-PNAKA 184
Query: 268 RAVGVELVSFDQALATADFISLHMPLNPTTSKIFNDETFAKMKKGVRIVNVARGGVIDEE 327
+ ++A+ AD ++LHMP +FN + F KKG VN ARG ++D +
Sbjct: 185 ATYVDYKDTIEEAVEGADIVTLHMPATKYNHYLFNADLFKHFKKGAVFVNCARGSLVDTK 244
Query: 328 ALVRALDSGVVAQAALDVFTEEPP--AKDSK-----------LVQHENVTVTPHLGASTK 374
AL+ ALD+G++ AALD + E P D + L+ E+V +TPH+ T
Sbjct: 245 ALLDALDNGLIKGAALDTYEFERPLFPSDQRGQTINDPLLESLINREDVILTPHIAFYTD 304
Query: 375 EAQEGVAIEIAEAVVGALRGELSATAIN 402
A + + ++ +A + L+ + +N
Sbjct: 305 AAVKNLIVDALDATLEVLQTGTTRLRVN 332
>gnl|CDD|240636 cd12159, 2-Hacid_dh_2, Putative D-isomer specific 2-hydroxyacid
dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 303
Score = 120 bits (304), Expect = 2e-30
Identities = 72/216 (33%), Positives = 99/216 (45%), Gaps = 13/216 (6%)
Query: 185 ANTVAAAEHGIALLASMARNVSQADASIKAGKWLRSKYVGVSLV----GKTLAVMGFGKV 240
A TVA EH +ALL + R + A +A W LV G T+A++G G +
Sbjct: 84 AETVA--EHALALLLAGLRQLP---ARARATTW--DPAEEDDLVTLLRGSTVAIVGAGGI 136
Query: 241 GSEVARRAKGLGMNVIAHDPYA-PADKARAVGVELVSFDQALATADFISLHMPLNPTTSK 299
G + G VIA + P + A V D+ AD + L PL P T
Sbjct: 137 GRALIPLLAPFGAKVIAVNRSGRPVEGADET-VPADRLDEVWPDADHVVLAAPLTPETRH 195
Query: 300 IFNDETFAKMKKGVRIVNVARGGVIDEEALVRALDSGVVAQAALDVFTEEPPAKDSKLVQ 359
+ + A MK +VNVARG ++D +ALV AL SG +A AALDV EP L
Sbjct: 196 LVDAAALAAMKPHAWLVNVARGPLVDTDALVDALRSGEIAGAALDVTDPEPLPDGHPLWS 255
Query: 360 HENVTVTPHLGASTKEAQEGVAIEIAEAVVGALRGE 395
N +TPH+ + + + +A +AE V GE
Sbjct: 256 LPNALITPHVANTPEVIRPLLAERVAENVRAFAAGE 291
>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 = 120 bits (302), Expect = 5e-30
Identities = 78/289 (26%), Positives = 125/289 (43%), Gaps = 22/289 (7%)
Query: 92 TILVSEKLGEAGLAILRSFGNVEC-LYDLSPEALCEKISQCDALIVR--SGTKVTRSVFE 148
T+LV + A L L VE ++D + + + ++ + V ++
Sbjct: 1 TVLVPDPELVAALGPLPP--GVEVVVWDGE-GPPPDAAADVEFVVPPYMAAPPVLEALRA 57
Query: 149 AANGKLKVVGRAGVGIDNVDLQAATEFGCLVVNAPIANTVAAAEHGIALLASMARNVSQA 208
L+VV G D V G + NA + + AE +AL+ + R + +
Sbjct: 58 LPR--LRVVQTLSAGYDGVLPLLPE--GVTLCNARGVHDASTAELAVALILASLRGLPRF 113
Query: 209 DASIKAGKWLRSKYVGVSLVGKTLAVMGFGKVGSEVARRAKGLGMNVIAHDPYAPADKAR 268
+ G+W SL + + ++G+G +G + RR + V A AR
Sbjct: 114 VRAQARGRWEPR--RTPSLADRRVLIVGYGSIGRAIERRLAPFEVRVTR-----VARTAR 166
Query: 269 AVGVELVSFDQA---LATADFISLHMPLNPTTSKIFNDETFAKMKKGVRIVNVARGGVID 325
G ++ D+ L AD + L +PL T + + E A+M G +VNVARG V+D
Sbjct: 167 P-GEQVHGIDELPALLPEADVVVLIVPLTDETRGLVDAEFLARMPDGALLVNVARGPVVD 225
Query: 326 EEALVRALDSGVVAQAALDVFTEEPPAKDSKLVQHENVTVTPHLGASTK 374
+ALV L SG + +AALDV EP L V +TPH+G +T
Sbjct: 226 TDALVAELASGRL-RAALDVTDPEPLPPGHPLWSAPGVLITPHVGGATP 273
>gnl|CDD|235800 PRK06436, PRK06436, glycerate dehydrogenase; Provisional.
Length = 303
Score = 113 bits (284), Expect = 9e-28
Identities = 62/233 (26%), Positives = 115/233 (49%), Gaps = 9/233 (3%)
Query: 153 KLKVVGRAGVGIDNVDLQAATEFGCLVVNAPIANTVAAAEHGIALLASMARNVSQADASI 212
K K++ G+D++D+ E L NA A +++ AEH ALL + A+N+ + + ++
Sbjct: 49 KTKMIQSLSAGVDHIDVSGIPENVVLCSNAG-AYSISVAEHAFALLLAWAKNICENNYNM 107
Query: 213 KAGKWLRSKYVGVSLVGKTLAVMGFGKVGSEVARRAKGLGMNVIAHDPYAPADKARAVGV 272
K G + +S L K+L ++G+G +G VA AK GMN+ A Y + +
Sbjct: 108 KNGNFKQSPTK--LLYNKSLGILGYGGIGRRVALLAKAFGMNIYA---YTRSYVNDGISS 162
Query: 273 ELVSFDQALATADFISLHMPLNPTTSKIFNDETFAKMKKGVRIVNVARGGVIDEEALVRA 332
+ + + +DF+ + +PL T + N + + +KG+ I+NVAR V+D+ ++
Sbjct: 163 IYMEPEDIMKKSDFVLISLPLTDETRGMINSKMLSLFRKGLAIINVARADVVDKNDMLNF 222
Query: 333 LDSGVVAQAALDVFTEEPPAKDSKLVQHENVTVTPHLGASTKEAQEGVAIEIA 385
L + DV+ EP ++ +NV ++PH+ A+ +A
Sbjct: 223 LRNHNDKYYLSDVWWNEPIITETNP---DNVILSPHVAGGMSGEIMQPAVALA 272
>gnl|CDD|183550 PRK12480, PRK12480, D-lactate dehydrogenase; Provisional.
Length = 330
Score = 113 bits (285), Expect = 1e-27
Identities = 65/238 (27%), Positives = 117/238 (49%), Gaps = 18/238 (7%)
Query: 154 LKVVGRAGVGIDNVDLQAATEFGCLVVNAPIANTVAAAEHGIALLASMARNVSQADASIK 213
+K + + G D DL A + ++ N P + AE+ +++ + R + ++
Sbjct: 70 IKQIAQRTAGFDMYDLDLAKKHNIVISNVPSYSPETIAEYSVSIALQLVRRFPDIERRVQ 129
Query: 214 AG--KWLRSKYVGVSLVGKTLAVMGFGKVGSEVARRAKGLGMNVIAHDPYAPADKARAVG 271
A W +++ + + T+A++G G++G+ A+ G G + A+D Y P +
Sbjct: 130 AHDFTW-QAEIMSKPVKNMTVAIIGTGRIGAATAKIYAGFGATITAYDAY-PNKDLDFLT 187
Query: 272 VELVSFDQALATADFISLHMPLNPTTSKIFNDETFAKMKKGVRIVNVARGGVIDEEALVR 331
+ S +A+ AD ISLH+P N + +F+ F +KKG +VN ARG VI+ L+
Sbjct: 188 YK-DSVKEAIKDADIISLHVPANKESYHLFDKAMFDHVKKGAILVNAARGAVINTPDLIA 246
Query: 332 ALDSGVVAQAALDVFTEEPP-------AKD------SKLVQHENVTVTPHLGASTKEA 376
A++ G + AA+D + E KD +L++HE + VTPH+ + EA
Sbjct: 247 AVNDGTLLGAAIDTYENEAAYFTNDWTNKDIDDKTLLELIEHERILVTPHIAFFSDEA 304
>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 = 108 bits (272), Expect = 8e-26
Identities = 65/246 (26%), Positives = 100/246 (40%), Gaps = 51/246 (20%)
Query: 178 LVVNAPIANTVAAAEHGIAL--------LASMARNVSQADASIKAGKWLRSKYV--GVSL 227
L + + A+ HG + L + + K W R +
Sbjct: 73 LYKDPEVPLCTASGIHGPQIAEWVIGTWLVLSHHFLQYIELQ-KEQTWGRRQEAYSVEDS 131
Query: 228 VGKTLAVMGFGKVGSEVARRAKGLGMNVIAH----------------------DP----- 260
VGK + ++G+G +G + AR A+ LGM V A+ DP
Sbjct: 132 VGKRVGILGYGSIGRQTARLAQALGMEVYAYTRSPRPTPESRKDDGYIVPGTGDPDGSIP 191
Query: 261 ---YAPADKARAVGVELVSFDQALATA-DFISLHMPLNPTTSKIFNDETFAKM-KKGVRI 315
++ DKA S + L D + + +PL P T + E F + K+ +
Sbjct: 192 SAWFSGTDKA--------SLHEFLRQDLDLLVVSLPLTPATKHLLGAEEFEILAKRKTFV 243
Query: 316 VNVARGGVIDEEALVRALDSGVVAQAALDVFTEEPPAKDSKLVQHENVTVTPHLGASTKE 375
N+ARG ++D +ALV AL+SG + AALDV EP D L NV +TPH+ T+E
Sbjct: 244 SNIARGSLVDTDALVAALESGQIRGAALDVTDPEPLPADHPLWSAPNVIITPHVSWQTQE 303
Query: 376 AQEGVA 381
+
Sbjct: 304 YFDRAL 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 = 104 bits (261), Expect = 1e-24
Identities = 65/214 (30%), Positives = 102/214 (47%), Gaps = 17/214 (7%)
Query: 191 AEHGIALLASMARNVSQADASIKAGKW---------LRSKYVGVSLVGKTLAVMGFGKVG 241
AEH +AL+ + R + + + + +W LR +L+G + + GFG +G
Sbjct: 96 AEHTLALILAAVRRLDEMREAQREHRWAGELGGLQPLRPAGRLTTLLGARVLIWGFGSIG 155
Query: 242 SEVARRAKGLGMNVIAHDPYAPADKARAVGVELVSFDQ---ALATADFISLHMPLNPTTS 298
+A LG V A + RA G +V+ D+ L D + + +P P+T+
Sbjct: 156 QRLAPLLTALGARVT---GVARSAGERA-GFPVVAEDELPELLPETDVLVMILPATPSTA 211
Query: 299 KIFNDETFAKMKKGVRIVNVARGGVIDEEALVRALDSGVVAQAALDVFTEEPPAKDSKLV 358
+ E A + K +VNV RG +DE+ALV AL+SG + AALDV EP S L
Sbjct: 212 HALDAEVLAALPKHAWVVNVGRGATVDEDALVAALESGRLGGAALDVTATEPLPASSPLW 271
Query: 359 QHENVTVTPHL-GASTKEAQEGVAIEIAEAVVGA 391
N+ +TPH G + A+E +A + + G
Sbjct: 272 DAPNLILTPHAAGGRPQGAEELIAENLRAFLAGG 305
>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 = 93.4 bits (232), Expect = 7e-21
Identities = 59/264 (22%), Positives = 88/264 (33%), Gaps = 28/264 (10%)
Query: 127 KISQCDALIVRSGTKVTRSVFEAANGKLKVVGRAGVGIDNVDL-QAATEFGCLVVNAP-- 183
+ D ++ +++ +G D+ DL +A G +
Sbjct: 61 ALWSLDVVLKVKEPLTNAEYALIQKLGDRLLFTYTIGADHRDLTEALARAGLTAIAVEGV 120
Query: 184 -----IANTVAAAEHGIALLASMARNVSQADASIKAGKWLRSKYVGVSLVGKTLAVMGFG 238
+N++ A E + +A + GKT+ V+G G
Sbjct: 121 ELPLLTSNSIGAGELSVQFIARFLEVQQPGRLGGAPD-----------VAGKTVVVVGAG 169
Query: 239 KVGSEVARRAKGLGMNVIAHD--PYAPADKARAVGVELVSFDQALATADFISLHMPLNPT 296
VG E A+ +GLG V+ D A G + ++ALA AD I L
Sbjct: 170 VVGKEAAQMLRGLGAQVLITDINVEALEQLEELGGKNVEELEEALAEADVIVTTTLLPGK 229
Query: 297 TSKIFNDET-FAKMKKGVRIVNVARGGVIDEEALVR-ALDSGVVAQAALDVFTEEPPAKD 354
+ I E +MK G IVNVA G V +AL L+ G DV P
Sbjct: 230 RAGILVPEELVEQMKPGSVIVNVAVGAVGCVQALHTQLLEEGHGVVHYGDVNMPGPGC-- 287
Query: 355 SKLVQHENVTVTPHLGASTKEAQE 378
T L A+T A
Sbjct: 288 ---AMGVPWDATLRLAANTLPALV 308
>gnl|CDD|185335 PRK15438, PRK15438, erythronate-4-phosphate dehydrogenase PdxB;
Provisional.
Length = 378
Score = 89.6 bits (222), Expect = 3e-19
Identities = 76/267 (28%), Positives = 118/267 (44%), Gaps = 31/267 (11%)
Query: 126 EKISQCDALIVRSGTKVTRSVFEAANGKLKVVGRAGVGIDNVDLQAATEFGCLVVNAPIA 185
+++ DAL+VRS TKV S+ A +K VG A G D+VD + G AP
Sbjct: 33 AQLADADALMVRSVTKVNESLL--AGKPIKFVGTATAGTDHVDEAWLKQAGIGFSAAPGC 90
Query: 186 NTVAAAEHGIALLASMARNVSQADASIKAGKWLRSKYVGVSLVGKTLAVMGFGKVGSEVA 245
N +A E+ + L +A + D G SL +T+ ++G G VG +
Sbjct: 91 NAIAVVEYVFSSLLMLA----ERD--------------GFSLHDRTVGIVGVGNVGRRLQ 132
Query: 246 RRAKGLGMNVIAHDPYAPADKARAVGVELVSFDQALATADFISLHMPL---NPTTSKIFN 302
R + LG+ + DP R + S D+ + AD ++ H PL P +
Sbjct: 133 ARLEALGIKTLLCDP---PRADRGDEGDFRSLDELVQEADILTFHTPLFKDGPYKTLHLA 189
Query: 303 DETF-AKMKKGVRIVNVARGGVIDEEALVRALDSGVVAQAALDVFTEEPPAKDSKLVQHE 361
DE +K G ++N RG V+D AL+ L+ G LDV+ EP + + +
Sbjct: 190 DEKLIRSLKPGAILINACRGAVVDNTALLTCLNEGQKLSVVLDVWEGEP---ELNVELLK 246
Query: 362 NVTV-TPHLGASTKEAQEGVAIEIAEA 387
V + TPH+ T E + ++ EA
Sbjct: 247 KVDIGTPHIAGYTLEGKARGTTQVFEA 273
>gnl|CDD|153174 cd04902, ACT_3PGDH-xct, C-terminal ACT (regulatory) domain of
D-3-phosphoglycerate dehydrogenase (3PGDH). The
C-terminal ACT (regulatory) domain of
D-3-phosphoglycerate dehydrogenase (3PGDH), with an
extended C-terminal (xct) region from bacteria, archaea,
fungi, and plants. 3PGDH is an enzyme that belongs to
the D-isomer specific, 2-hydroxyacid dehydrogenase
family and catalyzes the oxidation of
D-3-phosphoglycerate to 3- phosphohydroxypyruvate, which
is the first step in the biosynthesis of L-serine, using
NAD+ as the oxidizing agent. In bacteria, 3PGDH is
feedback-controlled by the end product L-serine in an
allosteric manner. Some 3PGDH enzymes have an additional
domain formed by an extended C-terminal region. This
additional domain introduces significant asymmetry to
the homotetramer. Adjacent ACT (regulatory) domains
interact, creating two serine-binding sites, however,
this asymmetric arrangement results in the formation of
two different and distinct domain interfaces between
identical domains in the asymmetric unit. How this
asymmetry influences the mechanism of effector
inhibition is still unknown. Members of this CD belong
to the superfamily of ACT regulatory domains.
Length = 73
Score = 81.0 bits (201), Expect = 6e-19
Identities = 24/62 (38%), Positives = 37/62 (59%)
Query: 560 LILCRQVDQPGMIGKVGNILGEHNVNVNFMSVGRTFRRNHGIMAIGVDEEPNQDSLKEIG 619
+++ R D+PG+IGKVG ILGE +N+ M VGR +M + VDE + L+E+
Sbjct: 1 MLVVRNTDRPGVIGKVGTILGEAGINIAGMQVGRDEPGGEALMVLSVDEPVPDEVLEELR 60
Query: 620 KV 621
+
Sbjct: 61 AL 62
>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 = 74.8 bits (185), Expect = 8e-17
Identities = 24/62 (38%), Positives = 35/62 (56%)
Query: 560 LILCRQVDQPGMIGKVGNILGEHNVNVNFMSVGRTFRRNHGIMAIGVDEEPNQDSLKEIG 619
+L D PG+IGKVG ILGEH +N+ M VGR + M + VD ++ L+E+
Sbjct: 1 RLLIVHKDVPGVIGKVGTILGEHGINIAAMQVGRKEKGGIAYMVLDVDSPVPEEVLEELK 60
Query: 620 KV 621
+
Sbjct: 61 AL 62
>gnl|CDD|185366 PRK15469, ghrA, bifunctional glyoxylate/hydroxypyruvate reductase
A; Provisional.
Length = 312
Score = 79.8 bits (197), Expect = 2e-16
Identities = 57/169 (33%), Positives = 89/169 (52%), Gaps = 10/169 (5%)
Query: 231 TLAVMGFGKVGSEVARRAKGLGMNVIAHD---PYAPADKARAVGVELVSFDQALATADFI 287
T+ ++G G +GS+VA+ + G + P ++ A EL +F T I
Sbjct: 138 TIGILGAGVLGSKVAQSLQTWGFPLRCWSRSRKSWPGVQSFAGREELSAFLSQ--TRVLI 195
Query: 288 SLHMPLNPTTSKIFNDETFAKMKKGVRIVNVARGGVIDEEALVRALDSGVVAQAALDVFT 347
+L +P P T I N + ++ G ++N+ARG + E+ L+ ALDSG V A LDVF+
Sbjct: 196 NL-LPNTPETVGIINQQLLEQLPDGAYLLNLARGVHVVEDDLLAALDSGKVKGAMLDVFS 254
Query: 348 EEPPAKDSKLVQHENVTVTPHLGASTKEAQEGVAIE-IAEAVVGALRGE 395
EP +S L QH V +TPH+ A T+ A+ A+E I+ + +GE
Sbjct: 255 REPLPPESPLWQHPRVAITPHVAAVTRPAE---AVEYISRTIAQLEKGE 300
>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 = 59.5 bits (145), Expect = 2e-11
Identities = 23/64 (35%), Positives = 39/64 (60%), Gaps = 3/64 (4%)
Query: 567 DQPGMIGKVGNILGEHNVNVNFMSVGRTFRRNHGIMAIGVDEEPNQDSLKEIGK---VHF 623
D+PG I KV ++L +H +N+ FM V R + + +M I VD+ +++ ++EI K +H
Sbjct: 8 DKPGAIAKVTSVLADHEINIAFMRVSRKEKGDQALMVIEVDQPIDEEVIEEIKKIPNIHQ 67
Query: 624 VARI 627
V I
Sbjct: 68 VILI 71
>gnl|CDD|198065 smart00997, AdoHcyase_NAD, S-adenosyl-L-homocysteine hydrolase, NAD
binding domain.
Length = 162
Score = 55.1 bits (134), Expect = 5e-09
Identities = 33/103 (32%), Positives = 46/103 (44%), Gaps = 19/103 (18%)
Query: 224 GVSLVGKTLAVMGFGKVGSEVARRAKGLGMNVIAHDPYAPADKARAV-----GVELVSFD 278
V L GK + V G+G VG VA R +GLG VI + D RA+ G E++ +
Sbjct: 18 NVLLAGKNVVVAGYGDVGKGVAARLRGLGARVIVTE----IDPIRALEAAMDGFEVMKME 73
Query: 279 QALATAD-FISLHMPLNPTT--SKIFNDETFAKMKKGVRIVNV 318
+A AD F++ T + E F MK G + N
Sbjct: 74 EAAKRADIFVT-------ATGNKDVITREHFRAMKDGAILANA 109
>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 = 54.2 bits (131), Expect = 6e-08
Identities = 67/290 (23%), Positives = 107/290 (36%), Gaps = 29/290 (10%)
Query: 98 KLGEAGLAILRSFGNVECLYDLSP---EALCEKISQCDALIVRSGTKVTRSVFEAANGKL 154
L E L+ + YD P E + E+I D ++V T++ V EA +
Sbjct: 11 GLNEEAEEELKKYAEEVVFYDDIPESDEEIIERIGDADCVLVSYTTQIDEEVLEACP-NI 69
Query: 155 KVVGRAGVGID----NVDLQAATEFGCLVVNAPIANTVAAAEHGIALLASMARNVSQADA 210
K +G NVD+ AA E G V E+ I+ L +
Sbjct: 70 KYIGMCCSLYSEESANVDIAAARENGITVTGIRDYGDEGVVEYVISELIRLLHGFGGK-- 127
Query: 211 SIKAGKWLRSKYVGVSLVGKTLAVMGFGKVGSEVARRAKGLGMNVIAHDPYAPADK--AR 268
+W K L G + ++G G G +A G +V Y+ K A
Sbjct: 128 -----QW---KEEPRELTGLKVGIIGLGTTGQMIADALSFFGADVYY---YSRTRKPDAE 176
Query: 269 AVGVELVSFDQALATADFISLHMPLNPTTSKIFNDETFAKMKKGVRIVNVARGGVIDEEA 328
A G+ + ++ L T D I +P N + +E F + G + N + G + EA
Sbjct: 177 AKGIRYLPLNELLKTVDVICTCLPKN---VILLGEEEFELLGDGKILFNTSLGPSFEVEA 233
Query: 329 LVRALDSGVVAQAALDVFTEEPPAKDSKLVQHENVTVTPHLGASTKEAQE 378
L + L + D D +L+++ NV T T++A E
Sbjct: 234 LKKWLKASGYNIFDCD---TAGALGDEELLRYPNVICTNKSAGWTRQAFE 280
>gnl|CDD|235488 PRK05476, PRK05476, S-adenosyl-L-homocysteine hydrolase;
Provisional.
Length = 425
Score = 50.9 bits (123), Expect = 1e-06
Identities = 29/97 (29%), Positives = 44/97 (45%), Gaps = 14/97 (14%)
Query: 225 VSLVGKTLAVMGFGKVGSEVARRAKGLGMNVIAH--DPYAPADKARAVGVELVSFDQALA 282
V + GK + V G+G VG A+R +GLG VI DP A +A G +++ ++A
Sbjct: 208 VLIAGKVVVVAGYGDVGKGCAQRLRGLGARVIVTEVDPIC-ALQAAMDGFRVMTMEEAAE 266
Query: 283 TAD-FISLHMPLNPTTS--KIFNDETFAKMKKGVRIV 316
D F++ T + E MK G I+
Sbjct: 267 LGDIFVT-------ATGNKDVITAEHMEAMKDGA-IL 295
>gnl|CDD|223573 COG0499, SAM1, S-adenosylhomocysteine hydrolase [Coenzyme
metabolism].
Length = 420
Score = 50.3 bits (121), Expect = 2e-06
Identities = 32/99 (32%), Positives = 47/99 (47%), Gaps = 15/99 (15%)
Query: 225 VSLVGKTLAVMGFGKVGSEVARRAKGLGMNVIAH--DPYAPADKARAVGVELVSFDQALA 282
V L GK + V G+G VG +A R +G+G VI DP A +A G +++ ++A
Sbjct: 205 VLLAGKNVVVAGYGWVGRGIAMRLRGMGARVIVTEVDP-IRALEAAMDGFRVMTMEEAAK 263
Query: 283 TAD-FISLHMPLNPTTS---KIFNDETFAKMKKGVRIVN 317
T D F+ T + + E F KMK G + N
Sbjct: 264 TGDIFV--------TATGNKDVIRKEHFEKMKDGAILAN 294
>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 = 43.0 bits (102), Expect = 1e-05
Identities = 13/51 (25%), Positives = 26/51 (50%)
Query: 567 DQPGMIGKVGNILGEHNVNVNFMSVGRTFRRNHGIMAIGVDEEPNQDSLKE 617
D+PG++ KV ++L E +N+ + + + I VD + + + L E
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 = 47.5 bits (114), Expect = 1e-05
Identities = 33/98 (33%), Positives = 46/98 (46%), Gaps = 13/98 (13%)
Query: 225 VSLVGKTLAVMGFGKVGSEVARRAKGLGMNVIAH--DPYAPADKARAVGVELVSFDQALA 282
V + GK + V G+G VG A RA+GLG VI DP A +A G E++ ++A
Sbjct: 191 VLIAGKVVVVAGYGWVGKGCAMRARGLGARVIVTEVDPIC-ALQAAMDGFEVMPMEEAAK 249
Query: 283 TAD-FISLHMPLNPTT--SKIFNDETFAKMKKGVRIVN 317
D F++ T + E F KMK G + N
Sbjct: 250 IGDIFVT-------ATGNKDVIRGEHFEKMKDGAILCN 280
>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 = 46.6 bits (111), Expect = 2e-05
Identities = 35/109 (32%), Positives = 52/109 (47%), Gaps = 14/109 (12%)
Query: 227 LVGKTLAVMGFGKVGSEVARRAKGLGMNVIAH--DPYAPADKARAVGVELVSFDQALATA 284
+ GKT+ V G+G G +A RA+G+G VI DP A +A G +++ ++A
Sbjct: 194 IAGKTVVVAGYGWCGKGIAMRARGMGARVIVTEVDP-IRALEAAMDGFRVMTMEEAAKIG 252
Query: 285 D-FISLHMPLNPTTS--KIFNDETFAKMKKGVRIVNVARGGV-IDEEAL 329
D FI+ T + E F MK G + N+ V ID +AL
Sbjct: 253 DIFIT-------ATGNKDVIRGEHFENMKDGAIVANIGHFDVEIDVKAL 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 = 39.7 bits (93), Expect = 2e-04
Identities = 13/64 (20%), Positives = 32/64 (50%), Gaps = 1/64 (1%)
Query: 561 ILCRQVDQPGMIGKVGNILGEHNVNVNFMSVGRTFRRNHGI-MAIGVDEEPNQDSLKEIG 619
+ D+PG++ +V L + +N+ +S + + + + + VDEE + +L+ +
Sbjct: 3 LEVGVPDRPGLLAEVFGALADRGINIESISQSTSGDKAGIVFIVVVVDEEDLEAALEALK 62
Query: 620 KVHF 623
K+
Sbjct: 63 KLLG 66
>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 = 39.8 bits (93), Expect = 0.002
Identities = 35/130 (26%), Positives = 54/130 (41%), Gaps = 11/130 (8%)
Query: 221 KYVGVSLVGKTLAVMGFGKVGSEVARRAKGLGMNVIA-HDPYAPADKARAVGVELVSFDQ 279
K++G SL G T+AV G G VG +A++ G V+A DP EL+++
Sbjct: 15 KHLGDSLEGLTVAVQGLGNVGWGLAKKLAEEGGKVLAVSDPDGYIYDPGITTEELINYAV 74
Query: 280 ALATADFISLHMPLNPTTSKIFNDETFAKMKKGVRIVNVARGGVIDEEALVRALDSGVVA 339
AL + + + + A G VID E + L + VVA
Sbjct: 75 ALGGSA-------RVKVQDYFPGEAIL-GLDVDI-FAPCALGNVIDLEN-AKKLKAKVVA 124
Query: 340 QAALDVFTEE 349
+ A + T+E
Sbjct: 125 EGANNPTTDE 134
>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 = 39.8 bits (94), Expect = 0.002
Identities = 16/37 (43%), Positives = 21/37 (56%)
Query: 221 KYVGVSLVGKTLAVMGFGKVGSEVARRAKGLGMNVIA 257
K +G+ L G +A+ GFG VGS AR G V+A
Sbjct: 23 KKLGIGLAGARVAIQGFGNVGSHAARFLHEAGAKVVA 59
>gnl|CDD|240258 PTZ00075, PTZ00075, Adenosylhomocysteinase; Provisional.
Length = 476
Score = 39.6 bits (93), Expect = 0.005
Identities = 34/114 (29%), Positives = 51/114 (44%), Gaps = 16/114 (14%)
Query: 225 VSLVGKTLAVMGFGKVGSEVARRAKGLGMNVIAH--DPYAPADKARAVGVELVSFDQALA 282
V + GKT+ V G+G VG A+ +G G V+ DP A +A G ++V+ + +
Sbjct: 250 VMIAGKTVVVCGYGDVGKGCAQALRGFGARVVVTEIDPIC-ALQAAMEGYQVVTLEDVVE 308
Query: 283 TAD-FISLHMPLNPTTS--KIFNDETFAKMKKGVRIVNVARGGVIDEEALVRAL 333
TAD F++ T I E +MK + N+ G D E V L
Sbjct: 309 TADIFVT-------ATGNKDIITLEHMRRMKNNAIVGNI---GHFDNEIQVAEL 352
>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 = 38.8 bits (91), Expect = 0.005
Identities = 34/162 (20%), Positives = 60/162 (37%), Gaps = 22/162 (13%)
Query: 223 VGVSLVGKTLAVMGFGKVGSEVARRAKGLGMNVIAHDPYAP-ADKARAVGVELVSFDQAL 281
GV G T+ V+G G VG A+ AK G VI D + A+ +G + V
Sbjct: 129 AGVLKPGDTVLVLGAGGVGLLAAQLAKAAGARVIVTDRSDEKLELAKELGADHV------ 182
Query: 282 ATADFISLHMPLNPTTSKIFNDETFAKMKKGVRIVNVARGGVIDEEALVRALDS-GVVAQ 340
++ + +E G +V A GG +R L G +
Sbjct: 183 -----------IDYKE-EDLEEELRLTGGGGADVVIDAVGGPETLAQALRLLRPGGRIVV 230
Query: 341 AALDVFTEEPPAKDSKLVQHENVTVTPHLGASTKEAQEGVAI 382
+ PP D + + + +T+ G + ++ +E + +
Sbjct: 231 VG--GTSGGPPLDDLRRLLFKELTIIGSTGGTREDFEEALDL 270
>gnl|CDD|218507 pfam05221, AdoHcyase, S-adenosyl-L-homocysteine hydrolase.
Length = 430
Score = 39.3 bits (92), Expect = 0.005
Identities = 27/96 (28%), Positives = 39/96 (40%), Gaps = 7/96 (7%)
Query: 225 VSLVGKTLAVMGFGKVGSEVARRAKGLGMNVIAH--DPYAPADKARAVGVELVSFDQALA 282
V + GK V G+G VG A +G G VI DP A +A G ++V+ ++ +
Sbjct: 206 VMIAGKVAVVCGYGDVGKGCAASLRGQGARVIVTEIDPIC-ALQAAMEGYQVVTLEEVVK 264
Query: 283 TADFISLHMPLNPTTSKIFNDETFAKMKKGVRIVNV 318
AD I F MKK + N+
Sbjct: 265 DADIFV----TTTGCVDIIVGRHFMNMKKDAIVCNI 296
>gnl|CDD|106361 PRK13403, PRK13403, ketol-acid reductoisomerase; Provisional.
Length = 335
Score = 39.0 bits (90), Expect = 0.005
Identities = 24/87 (27%), Positives = 47/87 (54%), Gaps = 2/87 (2%)
Query: 227 LVGKTLAVMGFGKVGSEVARRAKGLGMNVIAH-DPYAPADKARAVGVELVSFDQALATAD 285
L GKT+AV+G+G G A+ + G+ V+ P + A+A G E++S +A+ TA
Sbjct: 14 LQGKTVAVIGYGSQGHAQAQNLRDSGVEVVVGVRPGKSFEVAKADGFEVMSVSEAVRTAQ 73
Query: 286 FISLHMPLNPTTSKIFNDETFAKMKKG 312
+ + +P + + ++ E +++G
Sbjct: 74 VVQMLLP-DEQQAHVYKAEVEENLREG 99
>gnl|CDD|215789 pfam00208, ELFV_dehydrog, Glutamate/Leucine/Phenylalanine/Valine
dehydrogenase.
Length = 237
Score = 38.3 bits (90), Expect = 0.007
Identities = 18/32 (56%), Positives = 21/32 (65%)
Query: 226 SLVGKTLAVMGFGKVGSEVARRAKGLGMNVIA 257
SL GKT+AV GFG VGS A + LG V+A
Sbjct: 29 SLEGKTVAVQGFGNVGSYAAEKLLELGAKVVA 60
>gnl|CDD|240621 cd01620, Ala_dh_like, Alanine dehydrogenase and related
dehydrogenases. Alanine dehydrogenase/Transhydrogenase,
such as the hexameric L-alanine dehydrogenase of
Phormidium lapideum, contain 2 Rossmann fold-like
domains linked by an alpha helical region. Related
proteins include Saccharopine Dehydrogenase (SDH),
bifunctional lysine ketoglutarate reductase
/saccharopine dehydrogenase enzyme,
N(5)-(carboxyethyl)ornithine synthase, and Rubrum
transdehydrogenase. Alanine dehydrogenase (L-AlaDH)
catalyzes the NAD-dependent conversion of pyrucate to
L-alanine via reductive amination. Transhydrogenases
found in bacterial and inner mitochondrial membranes
link NAD(P)(H)-dependent redox reactions to proton
translocation. The energy of the proton electrochemical
gradient (delta-p), generated by the respiratory
electron transport chain, is consumed by
transhydrogenase in NAD(P)+ reduction. Transhydrogenase
is likely involved in the regulation of the citric acid
cycle. Rubrum transhydrogenase has 3 components, dI,
dII, and dIII. dII spans the membrane while dI and dIII
protrude on the cytoplasmic/matirx side. DI contains 2
domains with Rossmann folds, linked by a long alpha
helix, and contains a NAD binding site. Two dI
polypeptides (represented in this sub-family)
spontaneously form a heterotrimer with one dIII in the
absence of dII. In the heterotrimer, both dI chains may
bind NAD, but only one is well-ordered. dIII also binds
a well-ordered NADP, but in a different orientation than
classical Rossmann domains.
Length = 317
Score = 38.2 bits (89), Expect = 0.010
Identities = 28/108 (25%), Positives = 46/108 (42%), Gaps = 14/108 (12%)
Query: 231 TLAVMGFGKVGSEVARRAKGLGMNVIAHDPYAPADKARAVGVELVSFD---------QAL 281
+ ++G G VG A+ AK LG NV+ +D +K + V S + L
Sbjct: 164 KVLIIGAGVVGLGAAKIAKKLGANVLVYD--IKEEKLKGVETLGGSRLRYSQKEELEKEL 221
Query: 282 ATAD-FISLHMPLNPTTSKIFNDETFAKMKKGVRIVNVA--RGGVIDE 326
D I+ + P + +E MK+G IV++A +GG +
Sbjct: 222 KQTDILINAILVDGPRAPILIMEELVGPMKRGAVIVDLAADQGGNDET 269
>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 = 0.014
Identities = 32/139 (23%), Positives = 55/139 (39%), Gaps = 23/139 (16%)
Query: 485 AKQKGLRISEERVVADSSPEFPIDSIQVQLSNVDSKFAAAVSENGE------ISIEGKVK 538
A+ G+ I E D+ +S ++ S+ E GE ISI G
Sbjct: 85 AEAAGIDI--EFRTEDAGDNVHPNSAKITFSD----------EKGEEEELIGISIGG--- 129
Query: 539 FGIPHLTRVGSFGVDASLEGNLILCRQVDQPGMIGKVGNILGEHNVNVNFMSVGRTFRRN 598
G +T + F ++ E IL D+ G I V N+L +N+ + + N
Sbjct: 130 -GAIEITEINGFAIEFRGEHPAILLEHNDKFGTIAGVANLLAGFEINIEHLETAKKDIGN 188
Query: 599 HGIMAIGVDEEPNQDSLKE 617
++ I +D + D +K+
Sbjct: 189 IALLTIEID-KNIDDHIKD 206
>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 = 36.3 bits (85), Expect = 0.014
Identities = 32/104 (30%), Positives = 41/104 (39%), Gaps = 12/104 (11%)
Query: 233 AVMGFGKVGSEVARRAKGLGMNVIAHDPYAPADKA-----RAVGVELVS----FDQALAT 283
V+G G VG A AKGLG V D + A L S ++A+
Sbjct: 24 VVIGAGVVGLGAAATAKGLGAEVTVLDVRPARLRQLESLLGARFTTLYSQAELLEEAVKE 83
Query: 284 AD-FISLHMPLNPTTSKIFNDETFAKMKKGVRIVNVA--RGGVI 324
AD I + K+ E MK G IV+VA +GG I
Sbjct: 84 ADLVIGAVLIPGAKAPKLVTREMVKSMKPGSVIVDVAADQGGCI 127
>gnl|CDD|109716 pfam00670, AdoHcyase_NAD, S-adenosyl-L-homocysteine hydrolase, NAD
binding domain.
Length = 162
Score = 36.5 bits (85), Expect = 0.015
Identities = 36/112 (32%), Positives = 49/112 (43%), Gaps = 12/112 (10%)
Query: 225 VSLVGKTLAVMGFGKVGSEVARRAKGLGMNVIAH--DPYAPADKARAVGVELVSFDQALA 282
V + GK V G+G VG A KG G VI DP A +A G ++V+ ++ +
Sbjct: 19 VMIAGKVAVVCGYGDVGKGCAASLKGQGARVIVTEIDPIC-ALQAAMEGFQVVTLEEVVK 77
Query: 283 TADFISLHMPLNPTTSK-IFNDETFAKMKKGVRIVNVARGGVIDEEALVRAL 333
AD + T +K I E AKMK + N+ G D E V L
Sbjct: 78 KADIF-----VTTTGNKDIITGEHMAKMKNDAIVCNI---GHFDNEIDVAWL 121
>gnl|CDD|181371 PRK08306, PRK08306, dipicolinate synthase subunit A; Reviewed.
Length = 296
Score = 37.1 bits (87), Expect = 0.018
Identities = 28/104 (26%), Positives = 42/104 (40%), Gaps = 17/104 (16%)
Query: 229 GKTLAVMGFGKVGSEVARRAKGLGMN--VIAHDPYAPADKARA--VGVELVSFDQ---AL 281
G + V+GFG+ G +AR K LG N V A A AR +G+ + +
Sbjct: 152 GSNVLVLGFGRTGMTLARTLKALGANVTVGARK---SAHLARITEMGLSPFHLSELAEEV 208
Query: 282 ATADFISLHMPLNPTTSKIFNDETFAKMKKGVRIVNVAR--GGV 323
D I N + + E +KM I+++A GG
Sbjct: 209 GKIDII-----FNTIPALVLTKEVLSKMPPEALIIDLASKPGGT 247
>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 = 34.1 bits (79), Expect = 0.018
Identities = 14/52 (26%), Positives = 28/52 (53%)
Query: 567 DQPGMIGKVGNILGEHNVNVNFMSVGRTFRRNHGIMAIGVDEEPNQDSLKEI 618
D+PG+I +V ILG+ +++ + + GI+ I + +++ KEI
Sbjct: 10 DEPGVIAEVTQILGDAGISIKNIEILEIREGIGGILRISFKTQEDRERAKEI 61
>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 = 33.2 bits (77), Expect = 0.022
Identities = 12/41 (29%), Positives = 22/41 (53%), Gaps = 1/41 (2%)
Query: 567 DQPGMIGKVGNILGEHNVNVNFMSVGRTFRRNHGIMAIGVD 607
++PG + +V IL E +N+ +S+ T R GI+ +
Sbjct: 7 NKPGRLAEVTEILAEAGINIKAISIAET-RGEFGILRLIFS 46
>gnl|CDD|153173 cd04901, ACT_3PGDH, C-terminal ACT (regulatory) domain of
D-3-Phosphoglycerate Dehydrogenase (3PGDH) found in
fungi and bacteria. The C-terminal ACT (regulatory)
domain of D-3-Phosphoglycerate Dehydrogenase (3PGDH)
found in fungi and bacteria. 3PGDH is an enzyme that
belongs to the D-isomer specific, 2-hydroxyacid
dehydrogenase family and catalyzes the oxidation of
D-3-phosphoglycerate to 3- phosphohydroxypyruvate, which
is the first step in the biosynthesis of L-serine, using
NAD+ as the oxidizing agent. In Escherichia coli, the
SerA 3PGDH is feedback-controlled by the end product
L-serine in an allosteric manner. In the homotetrameric
enzyme, the interface at adjacent ACT (regulatory)
domains couples to create an extended beta-sheet. Each
regulatory interface forms two serine-binding sites. The
mechanism by which serine transmits inhibition to the
active site is postulated to involve the tethering of
the regulatory domains together to create a rigid
quaternary structure with a solvent-exposed active site
cleft. Members of this CD belong to the superfamily of
ACT regulatory domains.
Length = 69
Score = 33.6 bits (78), Expect = 0.023
Identities = 16/67 (23%), Positives = 34/67 (50%), Gaps = 10/67 (14%)
Query: 567 DQPGMIGKVGNILGEHNVNVNFMSVGRTFRRNHGIMA---IGVDEEPNQDSLKEIGKVHF 623
+ PG++G++ IL EHN+N+ + + G + I +D E +++ L+ + +
Sbjct: 8 NVPGVLGQINTILAEHNINIAAQ-----YLQTRGEIGYVVIDIDSEVSEELLEALRAIPG 62
Query: 624 V--ARIL 628
R+L
Sbjct: 63 TIRVRLL 69
>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 = 33.6 bits (78), Expect = 0.047
Identities = 10/43 (23%), Positives = 18/43 (41%)
Query: 243 EVARRAKGLGMNVIAHDPYAPADKARAVGVELVSFDQALATAD 285
++ G V+ +DPYA + + ++AL AD
Sbjct: 21 DIIEELLEAGAEVVVYDPYAMEEAREYGLTYVSDLEEALKGAD 63
>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 = 34.3 bits (80), Expect = 0.052
Identities = 27/106 (25%), Positives = 37/106 (34%), Gaps = 25/106 (23%)
Query: 232 LAVMGFGKVGSEVARRAKGLGMNVIAHDPYAPADKARAVGVELVSFDQALATADFISLHM 291
L + G G V +AR A LG V DP A V + FD L +
Sbjct: 1 LVIFGAGHVAQALARLAALLGFRVTVVDP-REERFPGADEVICLPFDDLLE-------AL 52
Query: 292 PLNPTTSKIFNDETFAKMKKGVRIVNVARGGVIDEEALVRALDSGV 337
++P T+ +V + +D EAL AL S
Sbjct: 53 AIDPRTA----------------VV-MTHDHKLDLEALEAALRSPA 81
>gnl|CDD|223411 COG0334, GdhA, Glutamate dehydrogenase/leucine dehydrogenase [Amino
acid transport and metabolism].
Length = 411
Score = 35.7 bits (83), Expect = 0.062
Identities = 16/37 (43%), Positives = 20/37 (54%)
Query: 221 KYVGVSLVGKTLAVMGFGKVGSEVARRAKGLGMNVIA 257
K +G L G +AV GFG VG A + LG V+A
Sbjct: 199 KALGDDLEGARVAVQGFGNVGQYAAEKLHELGAKVVA 235
>gnl|CDD|223992 COG1064, AdhP, Zn-dependent alcohol dehydrogenases [General
function prediction only].
Length = 339
Score = 35.6 bits (83), Expect = 0.073
Identities = 32/168 (19%), Positives = 59/168 (35%), Gaps = 34/168 (20%)
Query: 229 GKTLAVMGFGKVGSEVARRAKGLGMNVIAHD-PYAPADKARAVGVELVSFDQALATADFI 287
GK +AV+G G +G + AK +G VIA + A+ +G + V + ++D
Sbjct: 167 GKWVAVVGAGGLGHMAVQYAKAMGAEVIAITRSEEKLELAKKLGADHV-----INSSD-- 219
Query: 288 SLHMPLNPTTSKIFNDETFAKMKKGVRIVNVARGGVIDEEALVRALDS-GVVAQAALDVF 346
+ +K+ + G E ++AL G + L
Sbjct: 220 ---------------SDALEAVKEIADAIIDTVGP-ATLEPSLKALRRGGTLVLVGLPGG 263
Query: 347 TEEPPAKDSKLVQHENVTVTPHLGASTKEAQE--------GVAIEIAE 386
P L+ E +++ L + + +E + EI E
Sbjct: 264 GPIPLLPAFLLILKE-ISIVGSLVGTRADLEEALDFAAEGKIKPEILE 310
>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 = 34.9 bits (81), Expect = 0.074
Identities = 33/120 (27%), Positives = 49/120 (40%), Gaps = 32/120 (26%)
Query: 226 SLVGKTLAVMGFGKVGSEVARRAKGLGMNVIAHD--PYAPADKARAVGVELVSFDQALAT 283
SL GKT+AV G GKVG ++A G +I D A A A G +V+ ++ +
Sbjct: 25 SLEGKTVAVQGLGKVGYKLAEHLLEEGAKLIVADINEEAVARAAELFGATVVAPEEIYSV 84
Query: 284 -ADFISLHMPLNPTTSKIFNDETFAKMKKGVRIVNVARGGVIDEEALVRALDSGVVAQAA 342
AD +F A GGVI+++ + L + +A AA
Sbjct: 85 DAD--------------VF--------------APCALGGVINDDT-IPQLKAKAIAGAA 115
>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 = 33.7 bits (78), Expect = 0.11
Identities = 29/102 (28%), Positives = 43/102 (42%), Gaps = 13/102 (12%)
Query: 230 KTLAVMGFGKVGSEVARRAKGLGMNVIAHDP-YAPADKARAVGVELV---------SFDQ 279
+ V+G G VG A AKGLG V D ++ ++ E V +
Sbjct: 21 AKVVVIGGGVVGLGAAATAKGLGAPVTILDVRPERLEQLDSLFAEFVETDIFSNCEYLAE 80
Query: 280 ALATADFI--SLHMPLNPTTSKIFNDETFAKMKKGVRIVNVA 319
A+A AD + ++ +P K+ E MK G IV+VA
Sbjct: 81 AIAEADLVIGTVLIPGARAP-KLVTREMVKTMKPGSVIVDVA 121
>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 = 34.9 bits (81), Expect = 0.11
Identities = 29/134 (21%), Positives = 56/134 (41%), Gaps = 24/134 (17%)
Query: 197 LLASMARNVSQADASIKAGKWLRSKYVGVSLVGKTLAVMGFG-KVGS---------EVAR 246
+ A+ N SQ D ++ + K + +L GKT+ ++G K + ++
Sbjct: 284 IEAAREINDSQPDYVVE-----KIKDLLGALKGKTVLILGLAFKPNTDDVRESPALDIIE 338
Query: 247 RAKGLGMNVIAHDPYAPADKARAVGVELVSFDQALATADFISL---HMPLNPTTSKIFND 303
K G V A+DP P ++ + + + ++AL AD + + H K +
Sbjct: 339 LLKEKGAKVKAYDPLVPEEEVKGLPS-IDDLEEALKGADALVILTDHSEF-----KDLDL 392
Query: 304 ETFAKMKKGVRIVN 317
E + KG +V+
Sbjct: 393 EKIKDLMKGKVVVD 406
>gnl|CDD|129609 TIGR00518, alaDH, alanine dehydrogenase. The family of known
L-alanine dehydrogenases includes representatives from
the Proteobacteria, Firmicutes, and Cyanobacteria, all
with about 50 % identity or better. An outlier to this
group in both sequence and gap pattern is the homolog
from Helicobacter pylori, an epsilon division
Proteobacteria, which must be considered a putative
alanine dehydrogenase. Related proteins include
saccharopine dehydrogenase and the N-terminal half of
the NAD(P) transhydrogenase alpha subunit. All of these
related proteins bind NAD and/or NADP [Energy
metabolism, Amino acids and amines].
Length = 370
Score = 34.9 bits (80), Expect = 0.12
Identities = 43/167 (25%), Positives = 67/167 (40%), Gaps = 25/167 (14%)
Query: 187 TVAAAEHGIALLASMARNVSQADASIKAGKWLRSKY-VGVSLVG------KTLAVMGFGK 239
TV A+ + LLA M+ + A + A +++ GV L G + ++G G
Sbjct: 118 TVQTADGALPLLAPMSEVAGRLAAQVGAYHLEKTQGGRGVLLGGVPGVEPGDVTIIGGGV 177
Query: 240 VGSEVARRAKGLGMNVIAHDPYAPADKARAVGVEL-----------VSFDQALATADF-I 287
VG+ A+ A GLG V D D+ R + E + A+ AD I
Sbjct: 178 VGTNAAKMANGLGATVTILD--INIDRLRQLDAEFGGRIHTRYSNAYEIEDAVKRADLLI 235
Query: 288 SLHMPLNPTTSKIFNDETFAKMKKGVRIVNVARGGVIDEEALVRALD 334
+ K+ ++ A+MK G IV+VA ID+ V
Sbjct: 236 GAVLIPGAKAPKLVSNSLVAQMKPGAVIVDVA----IDQGGCVETSR 278
>gnl|CDD|235824 PRK06545, PRK06545, prephenate dehydrogenase; Validated.
Length = 359
Score = 34.9 bits (81), Expect = 0.12
Identities = 14/52 (26%), Positives = 28/52 (53%)
Query: 567 DQPGMIGKVGNILGEHNVNVNFMSVGRTFRRNHGIMAIGVDEEPNQDSLKEI 618
D+PG+I +V ILGE +++ + + HG++ I E +++ K +
Sbjct: 299 DEPGVIARVTAILGEEGISIENLRILEAREDIHGVLQISFKNEEDRERAKAL 350
>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 = 33.3 bits (77), Expect = 0.17
Identities = 24/88 (27%), Positives = 45/88 (51%), Gaps = 3/88 (3%)
Query: 227 LVGKTLAVMGFGKVGSEVARRAKGLGMNVIA--HDPYAPADKARAVGVELVSFDQALATA 284
L GK +AV+G+G G A + G+NVI +KA+ G E+ + +A+ A
Sbjct: 2 LKGKKIAVIGYGSQGHAHALNLRDSGVNVIVGLRPGSKSWEKAKKDGFEVYTVAEAVKKA 61
Query: 285 DFISLHMPLNPTTSKIFNDETFAKMKKG 312
D + + +P + ++++ E +K+G
Sbjct: 62 DVVMILLP-DEVQAEVYEKEIAPNLKEG 88
>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 = 31.3 bits (72), Expect = 0.19
Identities = 8/24 (33%), Positives = 16/24 (66%)
Query: 566 VDQPGMIGKVGNILGEHNVNVNFM 589
D+PG++ K+ IL EH +++ +
Sbjct: 8 KDKPGVLAKITGILAEHGISIESV 31
>gnl|CDD|223137 COG0059, IlvC, Ketol-acid reductoisomerase [Amino acid transport
and metabolism / Coenzyme metabolism].
Length = 338
Score = 33.7 bits (78), Expect = 0.23
Identities = 25/95 (26%), Positives = 44/95 (46%), Gaps = 17/95 (17%)
Query: 227 LVGKTLAVMGFGKVGSEVARRAKGL-----GMNVIA--HDPYAPADKARAVGVELVSFDQ 279
L GK +A++G+G G A+ L G+NVI + KA+ G ++ + ++
Sbjct: 16 LKGKKVAIIGYGSQG-----HAQALNLRDSGLNVIIGLRKGSSSWKKAKEDGFKVYTVEE 70
Query: 280 ALATADFISLHMPLNPTT--SKIFNDETFAKMKKG 312
A AD + M L P +++ E +K+G
Sbjct: 71 AAKRADVV---MILLPDEQQKEVYEKEIAPNLKEG 102
>gnl|CDD|217691 pfam03720, UDPG_MGDP_dh_C, UDP-glucose/GDP-mannose dehydrogenase
family, UDP binding domain. The UDP-glucose/GDP-mannose
dehydrogenaseses are a small group of enzymes which
possesses the ability to catalyze the NAD-dependent
2-fold oxidation of an alcohol to an acid without the
release of an aldehyde intermediate.
Length = 103
Score = 31.8 bits (73), Expect = 0.27
Identities = 15/47 (31%), Positives = 23/47 (48%), Gaps = 4/47 (8%)
Query: 243 EVARRAKGLGMNVIAHDPYAPADKARAV---GVELV-SFDQALATAD 285
++ G V+ +DPY P + A+ GV LV ++AL AD
Sbjct: 21 DIIEELLEEGAEVVVYDPYVPEEAIEALGEDGVTLVDDLEEALKGAD 67
>gnl|CDD|184463 PRK14030, PRK14030, glutamate dehydrogenase; Provisional.
Length = 445
Score = 33.7 bits (77), Expect = 0.28
Identities = 14/33 (42%), Positives = 20/33 (60%)
Query: 224 GVSLVGKTLAVMGFGKVGSEVARRAKGLGMNVI 256
G+ + GKT+A+ GFG V A +A LG V+
Sbjct: 223 GIDIKGKTVAISGFGNVAWGAATKATELGAKVV 255
>gnl|CDD|224674 COG1760, SdaA, L-serine deaminase [Amino acid transport and
metabolism].
Length = 262
Score = 32.6 bits (75), Expect = 0.49
Identities = 16/62 (25%), Positives = 23/62 (37%), Gaps = 4/62 (6%)
Query: 568 QPGMI-GKVGNILGEHNVNVNFMSVGRTFRRNHGIMAIGVDEEPNQDSL---KEIGKVHF 623
G+ V ++ +N N M R MAI VD+ P + + E GK
Sbjct: 189 NLGLTCDPVAGLVQVPCINRNAMGAVRAINGAKAAMAIEVDQRPLDEVIETMYETGKDMN 248
Query: 624 VA 625
V
Sbjct: 249 VK 250
>gnl|CDD|236034 PRK07502, PRK07502, cyclohexadienyl dehydrogenase; Validated.
Length = 307
Score = 32.6 bits (75), Expect = 0.51
Identities = 20/70 (28%), Positives = 34/70 (48%), Gaps = 8/70 (11%)
Query: 230 KTLAVMGFGKVGSEVAR--RAKGLGMNVIAHDPYAPADKARAVGVELVSF-----DQALA 282
+A++G G +GS +AR R GL ++ D + +ARA + L +A+
Sbjct: 7 DRVALIGIGLIGSSLARAIRRLGLAGEIVGADR-SAETRARARELGLGDRVTTSAAEAVK 65
Query: 283 TADFISLHMP 292
AD + L +P
Sbjct: 66 GADLVILCVP 75
>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 = 30.7 bits (70), Expect = 0.52
Identities = 8/21 (38%), Positives = 12/21 (57%)
Query: 567 DQPGMIGKVGNILGEHNVNVN 587
D+ G++ V L E NVN+
Sbjct: 10 DRVGIVAGVSTKLAELNVNIL 30
>gnl|CDD|214963 smart00996, AdoHcyase, S-adenosyl-L-homocysteine hydrolase.
Length = 426
Score = 32.5 bits (75), Expect = 0.59
Identities = 30/100 (30%), Positives = 44/100 (44%), Gaps = 15/100 (15%)
Query: 225 VSLVGKTLAVMGFGKVGSEVARRAKGLGMNVIAH--DPYAPADKARAVGVELVSFDQALA 282
V + GK V G+G VG A+ +G G VI DP A +A G E+V+ ++
Sbjct: 203 VMIAGKVAVVCGYGDVGKGCAQSLRGQGARVIVTEIDPIC-ALQAAMDGFEVVTMEEVAP 261
Query: 283 TAD-FISLHMPLNPTTS---KIFNDETFAKMKKGVRIVNV 318
AD F+ TT+ + E MK G + N+
Sbjct: 262 QADIFV--------TTTGNKDVITREHMRAMKDGAIVCNI 293
>gnl|CDD|235707 PRK06130, PRK06130, 3-hydroxybutyryl-CoA dehydrogenase; Validated.
Length = 311
Score = 32.4 bits (74), Expect = 0.62
Identities = 15/43 (34%), Positives = 22/43 (51%), Gaps = 1/43 (2%)
Query: 230 KTLAVMGFGKVGSEVARRAKGLGMNVIAHDPYAPADKARAVGV 272
+ LA++G G +GS +A G+ V+ D A RA GV
Sbjct: 5 QNLAIIGAGTMGSGIAALFARKGLQVVLIDVMEGA-LERARGV 46
>gnl|CDD|222146 pfam13460, NAD_binding_10, NADH(P)-binding.
Length = 182
Score = 31.9 bits (73), Expect = 0.64
Identities = 23/96 (23%), Positives = 30/96 (31%), Gaps = 23/96 (23%)
Query: 238 GKVGSEVARRAKGLGMNVIAHDPYAPADKARAVGVELVSFDQALATADFISLHMPLNPTT 297
GK G + + G V A KA A GV V D
Sbjct: 8 GKTGRRLVKELLARGHQVTALSR--NPSKAPAPGVTPVQKD------------------- 46
Query: 298 SKIFNDETFAKMKKGVRIVNVARGGVIDEEALVRAL 333
+F+ A+ GV V A G D+ V+ L
Sbjct: 47 --LFDLADLAEALAGVDAVVDAFGARPDDSDGVKHL 80
>gnl|CDD|223758 COG0686, Ald, Alanine dehydrogenase [Amino acid transport and
metabolism].
Length = 371
Score = 32.3 bits (74), Expect = 0.66
Identities = 38/158 (24%), Positives = 61/158 (38%), Gaps = 19/158 (12%)
Query: 187 TVAAAEHGIALLASMARNVSQADASIKAGKWLRSK------YVGVSLV-GKTLAVMGFGK 239
TV + + LLA M+ + A A ++ GV V + V+G G
Sbjct: 119 TVQLPDGNLPLLAPMSEVAGRLAAQAGAYYLEKTNGGKGVLLGGVPGVLPAKVVVLGGGV 178
Query: 240 VGSEVARRAKGLGMNVIAHD---------PYAPADKARAVGVELVSFDQALATAD-FISL 289
VG+ A+ A GLG +V D + + + ++A+ AD I
Sbjct: 179 VGTNAAKIAIGLGADVTILDLNIDRLRQLDDLFGGRVHTLYSTPSNIEEAVKKADLVIGA 238
Query: 290 HMPLNPTTSKIFNDETFAKMKKGVRIVNVA--RGGVID 325
+ K+ E +MK G IV+VA +GG +
Sbjct: 239 VLIPGAKAPKLVTREMVKQMKPGSVIVDVAIDQGGCFE 276
>gnl|CDD|235491 PRK05479, PRK05479, ketol-acid reductoisomerase; Provisional.
Length = 330
Score = 32.0 bits (74), Expect = 0.77
Identities = 25/93 (26%), Positives = 44/93 (47%), Gaps = 17/93 (18%)
Query: 229 GKTLAVMGFGKVGSEVARRAKGL-----GMNVIA--HDPYAPADKARAVGVELVSFDQAL 281
GK +A++G+G G A L G++V+ + KA A G E+++ +A
Sbjct: 17 GKKVAIIGYGSQG-----HAHALNLRDSGVDVVVGLREGSKSWKKAEADGFEVLTVAEAA 71
Query: 282 ATADFISLHMPLNPTT--SKIFNDETFAKMKKG 312
AD I M L P ++++ +E +K+G
Sbjct: 72 KWADVI---MILLPDEVQAEVYEEEIEPNLKEG 101
>gnl|CDD|184511 PRK14106, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 450
Score = 32.3 bits (74), Expect = 0.78
Identities = 18/55 (32%), Positives = 25/55 (45%), Gaps = 6/55 (10%)
Query: 227 LVGKTLAVMGFGKVGSEVARRAKGLGMNVIAHDPYAPAD------KARAVGVELV 275
L GK + V+G G G +A+ K LG VI D + +G+ELV
Sbjct: 3 LKGKKVLVVGAGVSGLALAKFLKKLGAKVILTDEKEEDQLKEALEELGELGIELV 57
>gnl|CDD|223643 COG0569, TrkA, K+ transport systems, NAD-binding component
[Inorganic ion transport and metabolism].
Length = 225
Score = 31.9 bits (73), Expect = 0.87
Identities = 10/28 (35%), Positives = 15/28 (53%)
Query: 230 KTLAVMGFGKVGSEVARRAKGLGMNVIA 257
+ ++G G+VG VAR G NV+
Sbjct: 1 MKIIIIGAGRVGRSVARELSEEGHNVVL 28
>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 = 31.8 bits (73), Expect = 0.88
Identities = 12/37 (32%), Positives = 17/37 (45%)
Query: 221 KYVGVSLVGKTLAVMGFGKVGSEVARRAKGLGMNVIA 257
K +L GK +A+ G G V A + LG V+
Sbjct: 30 KDRNETLKGKRVAISGSGNVAQYAAEKLLELGAKVVT 66
>gnl|CDD|168796 PRK07066, PRK07066, 3-hydroxybutyryl-CoA dehydrogenase; Validated.
Length = 321
Score = 32.1 bits (73), Expect = 0.90
Identities = 16/38 (42%), Positives = 22/38 (57%)
Query: 230 KTLAVMGFGKVGSEVARRAKGLGMNVIAHDPYAPADKA 267
KT A +G G +GS RA G++V+A DP A+ A
Sbjct: 8 KTFAAIGSGVIGSGWVARALAHGLDVVAWDPAPGAEAA 45
>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 = 31.6 bits (72), Expect = 1.1
Identities = 26/104 (25%), Positives = 45/104 (43%), Gaps = 17/104 (16%)
Query: 229 GKTLAVMGFGKVGSEVARRAKGLG--MNVIAHDPYAPADKARA-----VGVELVSFDQAL 281
G + V+GFG+ G +AR LG + V A AD AR + L ++ +
Sbjct: 151 GSNVMVLGFGRTGMTIARTFSALGARVFVGARS---SADLARITEMGLIPFPLNKLEEKV 207
Query: 282 ATADFISLHMPLNPTTSKIFNDETFAKMKKGVRIVNVAR--GGV 323
A D + +N + + + +K+ K I+++A GG
Sbjct: 208 AEIDIV-----INTIPALVLTADVLSKLPKHAVIIDLASKPGGT 246
>gnl|CDD|145358 pfam02155, GCR, Glucocorticoid receptor.
Length = 370
Score = 31.4 bits (71), Expect = 1.3
Identities = 15/90 (16%), Positives = 31/90 (34%), Gaps = 5/90 (5%)
Query: 18 RSKSSNSSKSSLLSFLHNTKPKPISLKFSSHNSNYTTPPSFTISNSLQTALETSELHVSK 77
+ S S + ++ ++ +P+ + N T P + + SL L E
Sbjct: 13 SVQVSASVAPTSVASQSGSRQQPVLGDSPNGLVNNVTQPDLSKAVSLSMGLYMGETETKV 72
Query: 78 FQDDLNVQAVTPKPTILVSEKLGEAGLAIL 107
+D+ + LGE ++L
Sbjct: 73 MGNDIRFP---QQG--QTGISLGETDFSLL 97
>gnl|CDD|166227 PLN02586, PLN02586, probable cinnamyl alcohol dehydrogenase.
Length = 360
Score = 31.4 bits (71), Expect = 1.3
Identities = 24/76 (31%), Positives = 36/76 (47%), Gaps = 9/76 (11%)
Query: 221 KYVGVSLVGKTLAVMGFGKVGSEVAR--RAKGLGMNVIAHDPYAPADKARAVGVE--LVS 276
KY G++ GK L V G G +G + +A GL + VI+ + +G + LVS
Sbjct: 176 KYYGMTEPGKHLGVAGLGGLGHVAVKIGKAFGLKVTVISSSSNKEDEAINRLGADSFLVS 235
Query: 277 FD-----QALATADFI 287
D A+ T D+I
Sbjct: 236 TDPEKMKAAIGTMDYI 251
>gnl|CDD|130212 TIGR01142, purT, phosphoribosylglycinamide formyltransferase 2.
This enzyme is an alternative to PurN (TIGR00639)
[Purines, pyrimidines, nucleosides, and nucleotides,
Purine ribonucleotide biosynthesis].
Length = 380
Score = 31.6 bits (72), Expect = 1.4
Identities = 31/92 (33%), Positives = 44/92 (47%), Gaps = 9/92 (9%)
Query: 235 MGFGKVGSEVARRAKGLGMNVIAHDPY--APADKA--RAVGVELVSFDQALATADFISLH 290
+G G++G EVA A+ LG+ VIA D Y APA + R+ + ++ D A I
Sbjct: 5 LGSGELGKEVAIEAQRLGVEVIAVDRYANAPAMQVAHRSYVINMLDGDALRAV---IERE 61
Query: 291 MP--LNPTTSKIFNDETFAKMKKGVRIVNVAR 320
P + P I D F K+G +V AR
Sbjct: 62 KPDYIVPEIEAIATDALFELEKEGYFVVPNAR 93
>gnl|CDD|178135 PLN02520, PLN02520, bifunctional 3-dehydroquinate
dehydratase/shikimate dehydrogenase.
Length = 529
Score = 31.3 bits (71), Expect = 1.7
Identities = 32/82 (39%), Positives = 37/82 (45%), Gaps = 12/82 (14%)
Query: 223 VGVSLVGKTLAVMGFGKVGSEVARRAKGLGMN-VIAHDPYAPA-DKARAVGVELVSFDQA 280
G L GK V+G G G +A AK G VIA+ Y A + A AVG QA
Sbjct: 373 SGSPLAGKLFVVIGAGGAGKALAYGAKEKGARVVIANRTYERAKELADAVG------GQA 426
Query: 281 LATADFISLH----MPLNPTTS 298
L AD + H M L TTS
Sbjct: 427 LTLADLENFHPEEGMILANTTS 448
>gnl|CDD|178923 PRK00194, PRK00194, hypothetical protein; Validated.
Length = 90
Score = 29.0 bits (66), Expect = 1.7
Identities = 9/20 (45%), Positives = 13/20 (65%)
Query: 567 DQPGMIGKVGNILGEHNVNV 586
D+ G+I V +L E NVN+
Sbjct: 12 DKVGIIAGVSTVLAELNVNI 31
>gnl|CDD|223106 COG0027, PurT, Formate-dependent phosphoribosylglycinamide
formyltransferase (GAR transformylase) [Nucleotide
transport and metabolism].
Length = 394
Score = 30.8 bits (70), Expect = 2.1
Identities = 17/37 (45%), Positives = 24/37 (64%), Gaps = 2/37 (5%)
Query: 230 KTLAVMGFGKVGSEVARRAKGLGMNVIAHDPY--APA 264
+ ++G G++G EVA A+ LG+ VIA D Y APA
Sbjct: 13 TKVMLLGSGELGKEVAIEAQRLGVEVIAVDRYANAPA 49
>gnl|CDD|234950 PRK01390, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 460
Score = 30.6 bits (70), Expect = 2.4
Identities = 23/62 (37%), Positives = 27/62 (43%), Gaps = 5/62 (8%)
Query: 226 SLVGKTLAVMGFGKVGSEVARRAKGLGMNVIAHDPYAPA-DKARAVGVELVSFDQALATA 284
GKT+AV G G G AR G VIA D + KA A G+ L TA
Sbjct: 6 GFAGKTVAVFGLGGSGLATARALVAGGAEVIAWDDNPASRAKAAAAGITTAD----LRTA 61
Query: 285 DF 286
D+
Sbjct: 62 DW 63
>gnl|CDD|176207 cd08245, CAD, Cinnamyl alcohol dehydrogenases (CAD) and related
proteins. Cinnamyl alcohol dehydrogenases (CAD),
members of the medium chain dehydrogenase/reductase
family, reduce cinnamaldehydes to cinnamyl alcohols in
the last step of monolignal metabolism in plant cells
walls. CAD binds 2 zinc ions and is NADPH- dependent.
CAD family members are also found in non-plant species,
e.g. in yeast where they have an aldehyde reductase
activity. The medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes, or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 330
Score = 30.4 bits (69), Expect = 2.7
Identities = 23/95 (24%), Positives = 40/95 (42%), Gaps = 5/95 (5%)
Query: 229 GKTLAVMGFGKVGSEVARRAKGLGMNVIA--HDPYAPADKARAVGVELV--SFDQALATA 284
G+ +AV+G G +G + A+ +G +A P + AR +G + V S + A
Sbjct: 163 GERVAVLGIGGLGHLAVQYARAMGFETVAITRSP-DKRELARKLGADEVVDSGAELDEQA 221
Query: 285 DFISLHMPLNPTTSKIFNDETFAKMKKGVRIVNVA 319
+ L S + +++G RIV V
Sbjct: 222 AAGGADVILVTVVSGAAAEAALGGLRRGGRIVLVG 256
>gnl|CDD|223936 COG1004, Ugd, Predicted UDP-glucose 6-dehydrogenase [Cell envelope
biogenesis, outer membrane].
Length = 414
Score = 30.6 bits (70), Expect = 2.9
Identities = 26/73 (35%), Positives = 37/73 (50%), Gaps = 12/73 (16%)
Query: 227 LVGKTLAVMGFG-KVGS---------EVARRAKGLGMNVIAHDPYAPADKAR-AVGVELV 275
L GKT+AV+G K + ++ +R + G VIA+DP A + R VEL
Sbjct: 308 LKGKTIAVLGLAFKPNTDDMRESPALDIIKRLQEKGAEVIAYDPVAMENAFRNFPDVELE 367
Query: 276 S-FDQALATADFI 287
S ++AL AD I
Sbjct: 368 SDAEEALKGADAI 380
>gnl|CDD|237220 PRK12828, PRK12828, short chain dehydrogenase; Provisional.
Length = 239
Score = 29.8 bits (67), Expect = 3.4
Identities = 23/70 (32%), Positives = 28/70 (40%), Gaps = 12/70 (17%)
Query: 226 SLVGKTLAVMG-FGKVGSEVARRAKGLGMNVI----------AHDPYAPADKARAVGVEL 274
SL GK +A+ G FG +G A G V P PAD R G++L
Sbjct: 4 SLQGKVVAITGGFGGLGRATAAWLAARGARVALIGRGAAPLSQTLPGVPADALRIGGIDL 63
Query: 275 VSFDQALATA 284
V QA A
Sbjct: 64 VD-PQAARRA 72
>gnl|CDD|216949 pfam02254, TrkA_N, TrkA-N domain. This domain is found in a wide
variety of proteins. These protein include potassium
channels, phosphoesterases, and various other
transporters. This domain binds to NAD.
Length = 116
Score = 28.3 bits (64), Expect = 4.3
Identities = 13/45 (28%), Positives = 24/45 (53%), Gaps = 3/45 (6%)
Query: 233 AVMGFGKVGSEVARRAKGLGMNVIA--HDPYAPADKARAVGVELV 275
++G+G+VG +A + G +V+ DP ++ R GV +V
Sbjct: 2 IIIGYGRVGRSLAEELREGGPDVVVIDKDP-ERVEELREEGVPVV 45
>gnl|CDD|215418 PLN02782, PLN02782, Branched-chain amino acid aminotransferase.
Length = 403
Score = 29.8 bits (67), Expect = 4.3
Identities = 30/111 (27%), Positives = 45/111 (40%), Gaps = 13/111 (11%)
Query: 22 SNSSKSSLLSFLHNTK-PKPISLKFSSHNSNYTTPPSFTISNSL---QTALETSELHVSK 77
S + + L S P P SL NS+ ++ P + + SL +S V++
Sbjct: 7 SRAFSTRLHSSSRRLNFPPPSSLSLRHSNSSVSSNPISSKAISLTRCDAVSSSSYTEVTE 66
Query: 78 FQD-DLNVQAVTPKPT----ILVSEKLGEAGLAILRSFGNVECLYDLSPEA 123
D D + PT I+ + GE L+ FGN+E LSP A
Sbjct: 67 LADIDWDNLGFGLVPTDYMYIMKCNRDGEFSKGELQRFGNIE----LSPSA 113
>gnl|CDD|223842 COG0771, MurD, UDP-N-acetylmuramoylalanine-D-glutamate ligase [Cell
envelope biogenesis, outer membrane].
Length = 448
Score = 29.9 bits (68), Expect = 4.6
Identities = 13/35 (37%), Positives = 15/35 (42%)
Query: 225 VSLVGKTLAVMGFGKVGSEVARRAKGLGMNVIAHD 259
GK + V+G GK G AR LG V D
Sbjct: 3 EDFQGKKVLVLGLGKSGLAAARFLLKLGAEVTVSD 37
>gnl|CDD|235783 PRK06349, PRK06349, homoserine dehydrogenase; Provisional.
Length = 426
Score = 29.7 bits (68), Expect = 4.8
Identities = 6/21 (28%), Positives = 14/21 (66%)
Query: 566 VDQPGMIGKVGNILGEHNVNV 586
D+PG++ K+ I E+ +++
Sbjct: 356 ADKPGVLAKIAAIFAENGISI 376
>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 = 29.7 bits (67), Expect = 4.8
Identities = 25/68 (36%), Positives = 38/68 (55%), Gaps = 6/68 (8%)
Query: 226 SLVGKTLAVMGFGKVGSEVAR--RAKGLGMNVIAHDPYAPADK-ARAVGVELVSFDQ--- 279
SL GK ++G G++G VA+ KG+G +IA+ Y A+ A+ +G E V F+
Sbjct: 177 SLKGKKALLIGAGEMGELVAKHLLRKGVGKILIANRTYERAEDLAKELGGEAVKFEDLEE 236
Query: 280 ALATADFI 287
LA AD +
Sbjct: 237 YLAEADIV 244
>gnl|CDD|240630 cd05305, L-AlaDH, Alanine dehydrogenase NAD-binding and catalytic
domains. Alanine dehydrogenase (L-AlaDH) catalyzes the
NAD-dependent conversion of pyruvate to L-alanine via
reductive amination. Like formate dehydrogenase and
related enzymes, L-AlaDH is comprised of 2 domains
connected by a long alpha helical stretch, each
resembling a Rossmann fold NAD-binding domain. The
NAD-binding domain is inserted within the linear
sequence of the more divergent catalytic domain. Ligand
binding and active site residues are found in the cleft
between the subdomains. L-AlaDH is typically hexameric
and is critical in carbon and nitrogen metabolism in
micro-organisms.
Length = 359
Score = 29.7 bits (68), Expect = 4.9
Identities = 29/104 (27%), Positives = 44/104 (42%), Gaps = 14/104 (13%)
Query: 234 VMGFGKVGSEVARRAKGLGMNV--IAHDPY--APADKARAVGVELVSFD-----QALATA 284
++G G VG AR A GLG V + + D V + + +AL A
Sbjct: 173 ILGAGVVGENAARVALGLGAEVTVLDINLERLRYLDDIFGGRVTTLYSNPANLEEALKEA 232
Query: 285 DFI--SLHMPLNPTTSKIFNDETFAKMKKGVRIVNVA--RGGVI 324
D + ++ +P K+ +E MK G IV+VA +GG
Sbjct: 233 DLVIGAVLIPGA-KAPKLVTEEMVKTMKPGSVIVDVAIDQGGCF 275
>gnl|CDD|215300 PLN02545, PLN02545, 3-hydroxybutyryl-CoA dehydrogenase.
Length = 295
Score = 29.7 bits (67), Expect = 5.1
Identities = 12/31 (38%), Positives = 19/31 (61%)
Query: 230 KTLAVMGFGKVGSEVARRAKGLGMNVIAHDP 260
K + V+G G++GS +A+ A GM+V D
Sbjct: 5 KKVGVVGAGQMGSGIAQLAAAAGMDVWLLDS 35
>gnl|CDD|218696 pfam05692, Myco_haema, Mycoplasma haemagglutinin. This family
consists of several haemagglutinin sequences from
Mycoplasma synoviae and Mycoplasma gallisepticum. The
major plasma membrane proteins, pMGAs, of Mycoplasma
gallisepticum are cell adhesin (hemagglutinin)
molecules. It has been shown that the genetic
determinants that code for the haemagglutinins are
organised into a large family of genes and that only one
of these genes is predominately expressed in any given
strain.
Length = 437
Score = 29.6 bits (67), Expect = 5.6
Identities = 23/69 (33%), Positives = 37/69 (53%)
Query: 20 KSSNSSKSSLLSFLHNTKPKPISLKFSSHNSNYTTPPSFTISNSLQTALETSELHVSKFQ 79
KSS+S+ L L+N PK I ++ S + S S++ +TA ET+ ++ +
Sbjct: 132 KSSDSNNVGLQYKLNNGNPKAIEFNSTTTASASSDRSSSEESSADETATETNTMNPTPTV 191
Query: 80 DDLNVQAVT 88
DD+NV VT
Sbjct: 192 DDINVAKVT 200
>gnl|CDD|180458 PRK06194, PRK06194, hypothetical protein; Provisional.
Length = 287
Score = 29.2 bits (66), Expect = 5.6
Identities = 18/52 (34%), Positives = 23/52 (44%), Gaps = 8/52 (15%)
Query: 231 TLAVMGFGKVGSEVARRAKGLGMNVIAHDPYAPA-DKA----RAVGVELVSF 277
T A GFG AR LGM ++ D A D+A RA G E++
Sbjct: 12 TGAASGFGL---AFARIGAALGMKLVLADVQQDALDRAVAELRAQGAEVLGV 60
>gnl|CDD|153142 cd04870, ACT_PSP_1, CT domains found N-terminal of phosphoserine
phosphatase (PSP, SerB). The ACT_PSP_1 CD includes the
first of the two ACT domains found N-terminal of
phosphoserine phosphatase (PSP, SerB). PSPs belong to
the L-2-haloacid dehalogenase-like protein superfamily.
PSP is involved in serine metabolism; serine is
synthesized from phosphoglycerate through sequential
reactions catalyzed by 3-phosphoglycerate dehydrogenase
(SerA), 3-phosphoserine aminotransferase (SerC), and
SerB. Members of this CD belong to the superfamily of
ACT regulatory domains.
Length = 75
Score = 27.2 bits (61), Expect = 5.8
Identities = 15/62 (24%), Positives = 26/62 (41%), Gaps = 2/62 (3%)
Query: 567 DQPGMIGKVGNILGEHNVNVNFMSVGRTFRRNHGIMAIGVDEEPNQDSLKEIGKVHFVAR 626
D+PG+ + +L H V + + VG+ + I V + DS + + F A
Sbjct: 8 DRPGLTSALTEVLAAHGVRI--LDVGQAVIHGRLSLGILVQIPDSADSEALLKDLLFKAH 65
Query: 627 IL 628
L
Sbjct: 66 EL 67
>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 = 29.2 bits (66), Expect = 6.0
Identities = 17/41 (41%), Positives = 22/41 (53%), Gaps = 2/41 (4%)
Query: 221 KYVGVSLVGKTLAVMGFGKVGSEVARRAKGLGM-NVIAHDP 260
+ VGVS T+ V+G G VG A+ LG +VI DP
Sbjct: 157 RRVGVSGRD-TVLVVGAGPVGLGALMLARALGAEDVIGVDP 196
>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 = 29.3 bits (66), Expect = 6.0
Identities = 24/88 (27%), Positives = 44/88 (50%), Gaps = 3/88 (3%)
Query: 227 LVGKTLAVMGFGKVGSEVARRAKGLGMNVIAHDPYAPADKARAV--GVELVSFDQALATA 284
L GKT+A++G+G G A + G+NVI A +A G ++ + ++A+ A
Sbjct: 1 LKGKTVAIIGYGSQGHAQALNLRDSGLNVIVGLRKGGASWKKATEDGFKVGTVEEAIPQA 60
Query: 285 DFISLHMPLNPTTSKIFNDETFAKMKKG 312
D I +P + +++ E +K+G
Sbjct: 61 DLIMNLLP-DEVQHEVYEAEIQPLLKEG 87
>gnl|CDD|178111 PLN02494, PLN02494, adenosylhomocysteinase.
Length = 477
Score = 29.4 bits (66), Expect = 6.4
Identities = 27/99 (27%), Positives = 43/99 (43%), Gaps = 13/99 (13%)
Query: 225 VSLVGKTLAVMGFGKVGSEVARRAKGLGMNVIAH--DPYAPADKARAVGVELVSFDQALA 282
V + GK + G+G VG A K G VI DP A +A G ++++ + ++
Sbjct: 250 VMIAGKVAVICGYGDVGKGCAAAMKAAGARVIVTEIDPIC-ALQALMEGYQVLTLEDVVS 308
Query: 283 TAD-FISLHMPLNPTTSK--IFNDETFAKMKKGVRIVNV 318
AD F++ TT I + KMK + N+
Sbjct: 309 EADIFVT-------TTGNKDIIMVDHMRKMKNNAIVCNI 340
>gnl|CDD|223528 COG0451, WcaG, Nucleoside-diphosphate-sugar epimerases [Cell
envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 314
Score = 29.1 bits (65), Expect = 6.5
Identities = 12/41 (29%), Positives = 15/41 (36%)
Query: 238 GKVGSEVARRAKGLGMNVIAHDPYAPADKARAVGVELVSFD 278
G +GS + R G +V D GVE V D
Sbjct: 10 GFIGSHLVERLLAAGHDVRGLDRLRDGLDPLLSGVEFVVLD 50
>gnl|CDD|224995 COG2084, MmsB, 3-hydroxyisobutyrate dehydrogenase and related
beta-hydroxyacid dehydrogenases [Lipid metabolism].
Length = 286
Score = 29.1 bits (66), Expect = 6.9
Identities = 17/61 (27%), Positives = 26/61 (42%), Gaps = 3/61 (4%)
Query: 230 KTLAVMGFGKVGSEVARR--AKGLGMNVIAHDPYAPADKARAVGVELV-SFDQALATADF 286
+A +G G +GS +A G + V P A+ A G + S +A A AD
Sbjct: 1 MKIAFIGLGIMGSPMAANLLKAGHEVTVYNRTPEKAAELLAAAGATVAASPAEAAAEADV 60
Query: 287 I 287
+
Sbjct: 61 V 61
>gnl|CDD|220707 pfam10347, Fmp27_GFWDK, RNA pol II promoter Fmp27 protein domain.
Fmp27_GFWDK is a conserved domain of a family of
proteins involved in RNA polymerase II transcription
initiation. It contains characteristic GFWDK sequence
motifs. Some members are associated with domain Fmp27_SW
(pfam10305) towards the N terminus.
Length = 154
Score = 28.4 bits (64), Expect = 7.5
Identities = 15/52 (28%), Positives = 21/52 (40%)
Query: 255 VIAHDPYAPADKARAVGVELVSFDQALATADFISLHMPLNPTTSKIFNDETF 306
VIA + R + V LV A F S+ +P T K ++D F
Sbjct: 26 VIAEQLVQSPESLRTIFVPLVPSVTAENGDSFYSVTVPRTLTPVKFYSDLNF 77
>gnl|CDD|213993 cd07438, PHP_HisPPase_AMP, Polymerase and Histidinol Phosphatase
domain of Histidinol phosphate phosphatase (HisPPase)
AMP bound. The PHP domain of this HisPPase family has
an unknown function. It has a second domain inserted in
the middle that binds adenosine 5-monophosphate (AMP).
The PHP (also called histidinol phosphatase-2/HIS2)
domain is associated with several types of DNA
polymerases, such as PolIIIA and family X DNA
polymerases, stand alone histidinol phosphate
phosphatases (HisPPases), and a number of
uncharacterized protein families. HisPPase catalyzes the
eighth step of histidine biosynthesis, in which
L-histidinol phosphate undergoes dephosphorylation to
give histidinol. The PHP domain has four conserved
sequence motifs and contains an invariant histidine that
is involved in metal ion coordination. The PHP domain of
HisPPase is structurally homologous to the other members
of the PHP family that have a distorted (beta/alpha)7
barrel fold with a trinuclear metal site on the
C-terminal side of the barrel.
Length = 155
Score = 28.1 bits (64), Expect = 7.9
Identities = 13/42 (30%), Positives = 20/42 (47%), Gaps = 7/42 (16%)
Query: 242 SEVARRAKGLGMNVIA---HD---PYAPA-DKARAVGVELVS 276
E+ AK G+ V+A HD A A+ +G+EL+
Sbjct: 17 EELVELAKEAGLKVLAITDHDTVAGLEEALAAAKELGIELIP 58
>gnl|CDD|153158 cd04886, ACT_ThrD-II-like, C-terminal ACT domain of biodegradative
(catabolic) threonine dehydratase II (ThrD-II) and other
related ACT domains. This CD includes the C-terminal
ACT domain of biodegradative (catabolic) threonine
dehydratase II (ThrD-II) and other related ACT domains.
The Escherichia coli tdcB gene product, ThrD-II,
anaerobically catalyzes the pyridoxal
phosphate-dependent dehydration of L-threonine and
L-serine to ammonia and to alpha-ketobutyrate and
pyruvate, respectively. Tetrameric ThrD-II is subject to
allosteric activation by AMP, inhibition by alpha-keto
acids, and catabolite inactivation by several
metabolites of glycolysis and the citric acid cycle.
Also included in this CD are N-terminal ACT domains
present in smaller (~170 a.a.) archaeal proteins of
unknown function. Members of this CD belong to the
superfamily of ACT regulatory domains.
Length = 73
Score = 26.7 bits (60), Expect = 9.2
Identities = 6/20 (30%), Positives = 12/20 (60%)
Query: 567 DQPGMIGKVGNILGEHNVNV 586
D+PG + K+ ++ E N+
Sbjct: 7 DRPGQLAKLLAVIAEAGANI 26
>gnl|CDD|218484 pfam05185, PRMT5, PRMT5 arginine-N-methyltransferase. The human
homologue of yeast Skb1 (Shk1 kinase-binding protein 1)
is PRMT5, an arginine-N-methyltransferase. These
proteins appear to be key mitotic regulators. They play
a role in Jak signalling in higher eukaryotes.
Length = 445
Score = 28.8 bits (65), Expect = 9.5
Identities = 17/35 (48%), Positives = 18/35 (51%), Gaps = 12/35 (34%)
Query: 90 KPTILVSEKLGEAGLAILRSFGNVECLYDLSPEAL 124
K ILVSE LG SFG+ E LSPE L
Sbjct: 258 KADILVSELLG--------SFGDNE----LSPECL 280
>gnl|CDD|236454 PRK09288, purT, phosphoribosylglycinamide formyltransferase 2;
Validated.
Length = 395
Score = 28.6 bits (65), Expect = 9.8
Identities = 19/35 (54%), Positives = 23/35 (65%), Gaps = 4/35 (11%)
Query: 234 VM--GFGKVGSEVARRAKGLGMNVIAHDPY--APA 264
VM G G++G EVA A+ LG+ VIA D Y APA
Sbjct: 15 VMLLGSGELGKEVAIEAQRLGVEVIAVDRYANAPA 49
>gnl|CDD|226138 COG3611, DnaB, Replication initiation/membrane attachment protein
[DNA replication, recombination, and repair].
Length = 417
Score = 28.9 bits (65), Expect = 9.8
Identities = 19/75 (25%), Positives = 37/75 (49%), Gaps = 7/75 (9%)
Query: 442 KLIYRSARDPDDLDTRILRAMITKGI-IE----PISASFINLVNADFTAKQKGLRISEER 496
LI S + D++DT LR ++++ E P ++ N DFT + L ++
Sbjct: 214 NLIKNSLVNNDEIDTEELRKLLSQIYKNEHNTKPTLSTKSN--PEDFTEANQNLNTESKK 271
Query: 497 VVADSSPEFPIDSIQ 511
V++D FP++ ++
Sbjct: 272 VISDLELTFPLEKLK 286
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
0.315 0.131 0.358
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: 31,112,851
Number of extensions: 3129708
Number of successful extensions: 3617
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3420
Number of HSP's successfully gapped: 191
Length of query: 628
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 525
Effective length of database: 6,369,140
Effective search space: 3343798500
Effective search space used: 3343798500
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)