RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254781099|ref|YP_003065512.1|
UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase [Candidatus
Liberibacter asiaticus str. psy62]
(468 letters)
>gnl|CDD|31114 COG0771, MurD, UDP-N-acetylmuramoylalanine-D-glutamate ligase [Cell
envelope biogenesis, outer membrane].
Length = 448
Score = 350 bits (900), Expect = 4e-97
Identities = 166/464 (35%), Positives = 233/464 (50%), Gaps = 28/464 (6%)
Query: 2 KLSSFRNHSIAVFGLGRSGLSAACALKDSGVHVIAWDDHP----CAVKQAKDMGIEVID- 56
+ F+ + V GLG+SGL+AA L G V DD P A + GIEV
Sbjct: 1 MMEDFQGKKVLVLGLGKSGLAAARFLLKLGAEVTVSDDRPAPEGLAAQPLLLEGIEVELG 60
Query: 57 -FREIPWSIISFLVLSPGIALTGENAHWCVKLANQFNVEIIGDIELFVRERRFSSLQSPF 115
+ + +V SPGI T H V+ A +EIIGDIELF R ++P
Sbjct: 61 SHDDEDLAEFDLVVKSPGIPPT----HPLVEAAKAAGIEIIGDIELFYRLSG----EAPI 112
Query: 116 IAVTGTNGKSSTVALISHVLRKNGYDVQLGGNIGLPILNL-EYFSPNRFYVIECSSYQIE 174
+A+TGTNGK++T +LI+H+L+ G D LGGNIG P L L E P YV+E SS+Q+E
Sbjct: 113 VAITGTNGKTTTTSLIAHLLKAAGLDALLGGNIGTPALELLEQAEPADVYVLELSSFQLE 172
Query: 175 LTPTIDPSIGVLLNISPDHLDRHHTLENYVNIKKKIVT-MSKHAIICINDHQCEKIAYDM 233
T ++ P I V+LNIS DHLDRH ++ENY K +I+ ++ A+I +D + +A
Sbjct: 173 TTSSLRPEIAVILNISEDHLDRHGSMENYAAAKLRILEGQTEVAVINADDAYLKTLA--D 230
Query: 234 NFIGHSISRISSQSLQSDSDLYIDESFLKCSATSEVIFDFSQET--KKHNIQNLVTSAVV 291
+ S +D D D K E + + HN++N + + +
Sbjct: 231 EATKARVIWFSFGEPLADGDYIYDG---KLVFKGEKLLPADELKLPGAHNLENALAALAL 287
Query: 292 CMQLGLKVEEIKRALLSCGGLTHRLQTIARLGHVIFINDSKATNLHSVIHAFLNEKRRIY 351
LG+ E I AL S GL HRL+ + V+FINDSKATN+ + + A +
Sbjct: 288 ARALGVPPEAILEALSSFTGLPHRLEFVGEKDGVLFINDSKATNVDATLAALSGFDGPVI 347
Query: 352 WIAGGLSKSDDFSTLFPFISK-IAKAYFIGNSAMLFFHHFGGK-INSTLSKTLDQALKSV 409
IAGG K DFS L ++K I K IG A + + +TL++A++
Sbjct: 348 LIAGGDDKGADFSPLAEILAKVIKKLVLIGEDAEKIAAALKEAGPSLVICETLEEAVQLA 407
Query: 410 VRDVENVQLPSIVLFSPGCASFDQYNNFRERGFSFMSQVSEIPG 453
+ +VL SP CASFDQ+ NF ERG F VSE+ G
Sbjct: 408 RELAQP---GDVVLLSPACASFDQFKNFEERGEEFKELVSELGG 448
>gnl|CDD|31113 COG0770, MurF, UDP-N-acetylmuramyl pentapeptide synthase [Cell
envelope biogenesis, outer membrane].
Length = 451
Score = 99.6 bits (248), Expect = 1e-21
Identities = 61/266 (22%), Positives = 104/266 (39%), Gaps = 25/266 (9%)
Query: 94 EIIGDIELFVRERRFSSLQSPFIAVTGTNGKSSTVALISHVLRKNGYDVQLGGN----IG 149
E +G + R++ + IA+TG+NGK++T +++ +L G GN IG
Sbjct: 88 EALGKLAKAYRQK----FNAKVIAITGSNGKTTTKEMLAAILSTKGKVHATPGNFNNEIG 143
Query: 150 LPILNLEYFSPNRFYVIECSSYQI----ELTPTIDPSIGVLLNISPDHLDRHHTLENYVN 205
LP+ L + + V+E EL+ P I V+ NI HL+ + E
Sbjct: 144 LPLTLLRLPADTEYAVLEMGMNHPGEIAELSEIARPDIAVITNIGEAHLEGFGSREGIAE 203
Query: 206 IKKKIVT-MSKHAIICINDHQCEKIAYDMNFIGHSISRISSQSLQSDSDLYIDESFLKCS 264
K +I+ + I +N + +++ S L + D +
Sbjct: 204 AKAEILAGLRPEGIAILNA---DNPLLKNWAAKIGNAKVLSFGLNNGGDFRA-TNIHLDE 259
Query: 265 ATSEVIFDFSQETK--------KHNIQNLVTSAVVCMQLGLKVEEIKRALLSCGGLTHRL 316
S D +HN+ N + +A + ++LGL +EEI L + RL
Sbjct: 260 EGSSFTLDIEGGEAEFELPLPGRHNVTNALAAAALALELGLDLEEIAAGLKELKPVKGRL 319
Query: 317 QTIARLGHVIFINDSKATNLHSVIHA 342
+ I I+DS N S+ A
Sbjct: 320 EVILLANGKTLIDDSYNANPDSMRAA 345
>gnl|CDD|31116 COG0773, MurC, UDP-N-acetylmuramate-alanine ligase [Cell envelope
biogenesis, outer membrane].
Length = 459
Score = 87.9 bits (218), Expect = 5e-18
Identities = 74/343 (21%), Positives = 127/343 (37%), Gaps = 44/343 (12%)
Query: 9 HSIAVFGLGRSGLSAACALKDSGVHVIAWDDHPCAV-KQAKDMGIEVID-FREIPWSIIS 66
H I + G+G SGL A L + G V D + ++ + +GIE+
Sbjct: 11 HFIGIGGIGMSGL--AEILLNLGYKVSGSDLAESPMTQRLEALGIEIFIGHDAENILDAD 68
Query: 67 FLVLSPGIALTGENAHWCVKLANQFNVEIIGDIELFVR--ERRFSSLQSPFIAVTGTNGK 124
+V+S A+ +N + A + + +I E+ R S IAV GT+GK
Sbjct: 69 VVVVSN--AIKEDNP--EIVAALERGIPVISRAEMLAELMRFRTS------IAVAGTHGK 118
Query: 125 SSTVALISHVLRKNGYD--VQLGGNIGLPILNLEYFSPNRFYVIECSSYQIELTPTIDPS 182
++T ++++ VL G D +GG + N ++V E +P
Sbjct: 119 TTTTSMLAWVLEAAGLDPTFLIGGILKNFGTNA-RLGSGDYFVAEADESDSSFLH-YNPR 176
Query: 183 IGVLLNISPDHLDRHHTLENYVNIKKKI---VTMSKHAIICIND----------HQCEKI 229
+ ++ NI DHLD + LE V A++C +D +
Sbjct: 177 VAIVTNIEFDHLDYYGDLEAIKQAFHHFVRNVPFYGRAVVCGDDPNLRELLSRGCWSPVV 236
Query: 230 AYDMNFIGH-SISRISSQSLQSDSDLYIDESFLKCSATSEVIFDFS-QETKKHNIQNLVT 287
Y + I + D+ E + + +HN+ N +
Sbjct: 237 TYGFDDEADWRAENIRQDGSGTTFDVLFR---------GEELGEVKLPLPGRHNVLNALA 287
Query: 288 SAVVCMQLGLKVEEIKRALLSCGGLTHRLQTIARLGHVIFIND 330
+ V +LG+ E I AL S G+ R + + V I+D
Sbjct: 288 AIAVARELGIDPEAIAEALASFQGVKRRFELKGEVNGVTVIDD 330
>gnl|CDD|31112 COG0769, MurE, UDP-N-acetylmuramyl tripeptide synthase [Cell
envelope biogenesis, outer membrane].
Length = 475
Score = 84.6 bits (209), Expect = 5e-17
Identities = 49/250 (19%), Positives = 94/250 (37%), Gaps = 37/250 (14%)
Query: 114 PFIAVTGTNGKSSTVALISHVLRKNGYDVQLGGNIG----------------LPILNLEY 157
I VTGTNGK++T +L++ +L+K G L G G +
Sbjct: 92 KVIGVTGTNGKTTTTSLLAQILKKLGKKTALIGTEGDELSPGILEPTGLTTPEALDLQNL 151
Query: 158 FSPNR-----FYVIECSSYQIELTPTIDPS--IGVLLNISPDHLDRHHTLENYVNIKKKI 210
V+E SS+ + + +GV N+S DHLD H T+E Y K +
Sbjct: 152 LRDLLDRGAEIAVMEVSSHGLVQGRVEGVTFDVGVFTNLSRDHLDYHGTMEYYGAAKAVL 211
Query: 211 ---VTMSKHAIICINDHQCEKIAYDMNFIGHSISRISSQSLQSDSDLYIDESFLKCSATS 267
+ S A+I + +++ + + S+ S
Sbjct: 212 FESLPHSGEAVINP---DDGHGLDYKERLKNALGDYITYGCDFKRPDLDYRGIEESSSGS 268
Query: 268 EVIFDFSQETKK--------HNIQNLVTSAVVCMQLGLKVEEIKRALLSCGGLTHRLQTI 319
+ +F+ S + N+ N + + + LG+ +E+I L + + R++ +
Sbjct: 269 DFVFEPSGGIGEYELPLPGLFNVYNALAAVAAALALGVDLEDILAGLETLKPVPGRMELV 328
Query: 320 ARLGHVIFIN 329
G ++ ++
Sbjct: 329 NIGGKLVIVD 338
>gnl|CDD|30633 COG0285, FolC, Folylpolyglutamate synthase [Coenzyme metabolism].
Length = 427
Score = 53.4 bits (128), Expect = 1e-07
Identities = 72/375 (19%), Positives = 122/375 (32%), Gaps = 71/375 (18%)
Query: 114 PFIAVTGTNGKSSTVALISHVLRKNGYDVQL----------------GGNIGLPIL---- 153
P I V GTNGK ST A + +LR+ GY V + G I L
Sbjct: 45 PVIHVAGTNGKGSTCAFLESILREAGYKVGVYTSPHLLSFNERIRINGEPISDEELAAAF 104
Query: 154 --------NLEYFSPNRFYVIECSSYQ-----------IEL--------TPTIDPSIGVL 186
+L+ S F V+ ++ +E+ T I+P + V+
Sbjct: 105 ERVEEAAGSLDLISLTYFEVLTAMAFLYFAEAKVDVAILEVGLGGRLDATNVIEPDVSVI 164
Query: 187 LNISPDHLDR-HHTLENYVNIKKKIVTMSKHAIICINDHQC--EKIAYDMNFIGHSISRI 243
+I DH TLE+ K I+ K A+I IA +G + +
Sbjct: 165 TSIGLDHTAFLGDTLESIAREKAGIIKAGKPAVIGEQQPPEALNVIAERAEELGAPLFVL 224
Query: 244 SSQSLQSDSDLYIDESFLKCSATSEVIFDFSQETKKHNIQNLVTSAVVCMQLGLKV--EE 301
+ H I+N + LG ++ E
Sbjct: 225 GPDFQVLEEGNGFSFQGGGGLLD----LPLPLLGGHHQIENAALAIAALEALGKEISEEA 280
Query: 302 IKRALLSCGGLTHRLQTIARLGHVIFI----NDSKATNLHSVIHAFLNEKRRIYWIAGGL 357
I++ L + RL+ ++ +I + N A L + N++ R+ + G L
Sbjct: 281 IRKGLANV-DWPGRLERLSE-NPLILLDGAHNPHAARALAETLKTLFNDRPRLTLVFGML 338
Query: 358 SKSDDFSTLFPFISKIAKAYF---------IGNSAMLFFHHFGGKINSTLSKTLDQALKS 408
D L + + + Y + F GG +++ L+ AL+
Sbjct: 339 KDKDIAGMLAALLPIVDEIYTTPLPWPRALDAEELLAFAGERGGVELDDVAEALELALEK 398
Query: 409 VVRDVENVQLPSIVL 423
D + S+ L
Sbjct: 399 ADEDDLVLVTGSLYL 413
>gnl|CDD|176243 cd08283, FDH_like_1, Glutathione-dependent formaldehyde
dehydrogenase related proteins, child 1. Members
identified as glutathione-dependent formaldehyde
dehydrogenase(FDH), a member of the
zinc-dependent/medium chain alcohol dehydrogenase
family. FDH converts formaldehyde and NAD(P) to formate
and NAD(P)H. The initial step in this process the
spontaneous formation of a S-(hydroxymethyl)glutathione
adduct from formaldehyde and glutathione, followed by
FDH-mediated oxidation (and detoxification) of the
adduct to S-formylglutathione. MDH family uses NAD(H)
as a cofactor in the interconversion of alcohols and
aldehydes, or ketones. Like many zinc-dependent alcohol
dehydrogenases (ADH) of the medium chain alcohol
dehydrogenase/reductase family (MDR), these FDHs form
dimers, with 4 zinc ions per dimer. The medium chain
alcohol dehydrogenase family (MDR) has a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The N-terminal region typically has an
all-beta catalytic domain. These proteins typically form
dimers (typically higher plants, mammals) or tetramers
(yeast, bacteria), and have 2 tightly bound zinc atoms
per subunit.
Length = 386
Score = 41.4 bits (98), Expect = 5e-04
Identities = 20/53 (37%), Positives = 28/53 (52%), Gaps = 2/53 (3%)
Query: 11 IAVFGLGRSGLSAA-CALKDSGVHVIAWDDHPCAVKQAKD-MGIEVIDFREIP 61
+AV+G G GL AA A VIA D P ++ A+ +G E I+F E+
Sbjct: 188 VAVWGCGPVGLFAARSAKLLGAERVIAIDRVPERLEMARSHLGAETINFEEVD 240
>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 = 40.0 bits (94), Expect = 0.002
Identities = 16/51 (31%), Positives = 23/51 (45%), Gaps = 2/51 (3%)
Query: 8 NHSIAVFGLGRSGLSAACALKDSGVH-VIAWDDHPCAVKQAKDMGI-EVID 56
++ V G G GL A + G VI D P ++ AK +G VI+
Sbjct: 164 RDTVLVVGAGPVGLGALMLARALGAEDVIGVDPSPERLELAKALGADFVIN 214
>gnl|CDD|35291 KOG0068, KOG0068, KOG0068, D-3-phosphoglycerate dehydrogenase,
D-isomer-specific 2-hydroxy acid dehydrogenase
superfamily [Amino acid transport and metabolism].
Length = 406
Score = 37.6 bits (87), Expect = 0.007
Identities = 20/66 (30%), Positives = 30/66 (45%), Gaps = 2/66 (3%)
Query: 5 SFRNHSIAVFGLGRSGLSAACALKDSGVHVIAWDDHPCAVKQAKDMGIEVIDFREIPWSI 64
R ++ V GLGR G A K G+HVI +D A+ G++++ EI
Sbjct: 143 ELRGKTLGVLGLGRIGSEVAVRAKAMGMHVIGYDPITPM-ALAEAFGVQLVSLEEI-LPK 200
Query: 65 ISFLVL 70
F+ L
Sbjct: 201 ADFITL 206
>gnl|CDD|145824 pfam02875, Mur_ligase_C, Mur ligase family, glutamate ligase
domain. This family contains a number of related ligase
enzymes which have EC numbers 6.3.2.*. This family
includes: MurC, MurD, MurE, MurF, Mpl and FolC. MurC,
MurD, Mure and MurF catalyse consecutive steps in the
synthesis of peptidoglycan. Peptidoglycan consists of a
sheet of two sugar derivatives, with one of these
N-acetylmuramic acid attaching to a small pentapeptide.
The pentapeptide is is made of L-alanine, D-glutamic
acid, Meso-diaminopimelic acid and D-alanyl alanine. The
peptide moiety is synthesized by successively adding
these amino acids to UDP-N-acetylmuramic acid. MurC
transfers the L-alanine, MurD transfers the D-glutamate,
MurE transfers the diaminopimelic acid, and MurF
transfers the D-alanyl alanine. This family also
includes Folylpolyglutamate synthase that transfers
glutamate to folylpolyglutamate.
Length = 87
Score = 37.3 bits (87), Expect = 0.010
Identities = 15/80 (18%), Positives = 28/80 (35%), Gaps = 13/80 (16%)
Query: 314 HRLQTIARLGHVIFINDSKATNLHS---VIHAFLNE-KRRIYWIAG-GLSKSDDFSTLFP 368
RL+ + V+ I+D A N + + A R+ + G G + +F L
Sbjct: 3 GRLEVVGENNGVLVIDD-YAHNPDALEAALQALKELFDGRLILVFGAGGDRDAEFHALLG 61
Query: 369 FISKIAKAYFIGNSAMLFFH 388
+A A ++
Sbjct: 62 ---ALAAALA----DVVILT 74
>gnl|CDD|176241 cd08281, liver_ADH_like1, Zinc-dependent alcohol dehydrogenases
(ADH) and class III ADG (AKA formaldehyde
dehydrogenase). NAD(P)(H)-dependent oxidoreductases are
the major enzymes in the interconversion of alcohols and
aldehydes or ketones. This group contains members
identified as zinc dependent alcohol dehydrogenases
(ADH), and class III ADG (aka formaldehyde
dehydrogenase, FDH). Alcohol dehydrogenase in the liver
converts ethanol and NAD+ to acetaldehyde and NADH,
while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. NAD(P)(H)-dependent
oxidoreductases are the major enzymes in the
interconversion of alcohols and aldehydes or ketones.
Alcohol dehydrogenase in the liver converts ethanol and
NAD+ to acetaldehyde and NADH, while in yeast and some
other microorganisms ADH catalyzes the conversion
acetaldehyde to ethanol in alcoholic fermentation.
Class III ADH are also know as glutathione-dependent
formaldehyde dehydrogenase (FDH), which convert
aldehydes to the corresponding carboxylic acid and
alcohol. ADH is a member of the medium chain alcohol
dehydrogenase family (MDR), which have a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES. These
proteins typically form dimers (typically higher plants,
mammals) or tetramers (yeast, bacteria), and 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. NAD(H) binding occurs in the
cleft between the catalytic and coenzyme-binding domains
at the active site, and coenzyme binding induces a
conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
In human ADH catalysis, the zinc ion helps coordinate
the alcohol, followed by deprotonation of a histidine,
the ribose of NAD, a serine, then the alcohol, which
allows the transfer of a hydride to NAD+, creating NADH
and a zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 371
Score = 36.6 bits (85), Expect = 0.015
Identities = 16/43 (37%), Positives = 24/43 (55%), Gaps = 1/43 (2%)
Query: 10 SIAVFGLGRSGLSAACALKDSGVH-VIAWDDHPCAVKQAKDMG 51
S+AV GLG GLSA +G V+A D + + A+++G
Sbjct: 194 SVAVVGLGGVGLSALLGAVAAGASQVVAVDLNEDKLALARELG 236
>gnl|CDD|176245 cd08285, NADP_ADH, NADP(H)-dependent alcohol dehydrogenases. This
group is predominated by atypical alcohol
dehydrogenases; they exist as tetramers and exhibit
specificity for NADP(H) as a cofactor in the
interconversion of alcohols and aldehydes, or ketones.
Like other zinc-dependent alcohol dehydrogenases (ADH)
of the medium chain alcohol dehydrogenase/reductase
family (MDR), tetrameric ADHs have a catalytic zinc that
resides between the catalytic and NAD(H)binding domains;
however, they do not have and a structural zinc in a
lobe of the catalytic domain. The medium chain alcohol
dehydrogenase family (MDR) has a NAD(P)(H)-binding
domain in a Rossmann fold of a beta-alpha form. The
N-terminal region typically has an all-beta catalytic
domain. These proteins typically form dimers (typically
higher plants, mammals) or tetramers (yeast, bacteria),
and have 2 tightly bound zinc atoms per subunit.
Length = 351
Score = 36.5 bits (85), Expect = 0.017
Identities = 18/54 (33%), Positives = 31/54 (57%), Gaps = 4/54 (7%)
Query: 9 HSIAVFGLGRSGLSA--ACALKDSGVHVIAWDDHPCAVKQAKDMGI-EVIDFRE 59
++AVFG+G GL A L+ +G +IA P V+ AK+ G +++D++
Sbjct: 168 DTVAVFGIGPVGLMAVAGARLRGAG-RIIAVGSRPNRVELAKEYGATDIVDYKN 220
>gnl|CDD|31226 COG1023, Gnd, Predicted 6-phosphogluconate dehydrogenase
[Carbohydrate transport and metabolism].
Length = 300
Score = 36.0 bits (83), Expect = 0.022
Identities = 16/46 (34%), Positives = 23/46 (50%)
Query: 11 IAVFGLGRSGLSAACALKDSGVHVIAWDDHPCAVKQAKDMGIEVID 56
I + GLGR G + L D G V+ +D + AV++ KD G
Sbjct: 3 IGMIGLGRMGANLVRRLLDGGHDVVGYDVNQTAVEELKDEGATGAA 48
>gnl|CDD|30408 COG0059, IlvC, Ketol-acid reductoisomerase [Amino acid transport
and metabolism / Coenzyme metabolism].
Length = 338
Score = 35.9 bits (83), Expect = 0.025
Identities = 19/71 (26%), Positives = 34/71 (47%), Gaps = 3/71 (4%)
Query: 2 KLSSFRNHSIAVFGLGRSGLSAACALKDSGVHV-IAWDDHPCAVKQAKDMGIEVIDFRE- 59
L + +A+ G G G + A L+DSG++V I + K+AK+ G +V E
Sbjct: 12 DLDLLKGKKVAIIGYGSQGHAQALNLRDSGLNVIIGLRKGSSSWKKAKEDGFKVYTVEEA 71
Query: 60 IPWS-IISFLV 69
+ ++ L+
Sbjct: 72 AKRADVVMILL 82
>gnl|CDD|176239 cd08278, benzyl_alcohol_DH, Benzyl alcohol dehydrogenase. Benzyl
alcohol dehydrogenase is similar to liver alcohol
dehydrogenase, but has some amino acid substitutions
near the active site, which may determine the enzyme's
specificity of oxidizing aromatic substrates. Also
known as aryl-alcohol dehydrogenases, they catalyze the
conversion of an aromatic alcohol + NAD+ to an aromatic
aldehyde + NADH + H+. NAD(P)(H)-dependent
oxidoreductases are the major enzymes in the
interconversion of alcohols and aldehydes, or ketones.
Alcohol dehydrogenase in the liver converts ethanol and
NAD+ to acetaldehyde and NADH, while in yeast and some
other microorganisms ADH catalyzes the conversion
acetaldehyde to ethanol in alcoholic fermentation. ADH
is a member of the medium chain alcohol dehydrogenase
family (MDR), which has a NAD(P)(H)-binding domain in a
Rossmann fold of a beta-alpha form. The NAD(H)-binding
region is comprised of 2 structurally similar halves,
each of which contacts a mononucleotide. A GxGxxG motif
after the first mononucleotide contact half allows the
close contact of the coenzyme with the ADH backbone.
The N-terminal catalytic domain has a distant homology
to GroES. These proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and 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.
NAD(H) binding occurs in the cleft between the catalytic
and coenzyme-binding domains at the active site, and
coenzyme binding induces a conformational closing of
this cleft. Coenzyme binding typically precedes and
contributes to substrate binding. In human ADH
catalysis, the zinc ion helps coordinate the alcohol,
followed by deprotonation of a histidine, the ribose of
NAD, a serine, then the alcohol, which allows the
transfer of a hydride to NAD+, creating NADH and a
zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 365
Score = 34.8 bits (81), Expect = 0.054
Identities = 19/43 (44%), Positives = 26/43 (60%), Gaps = 1/43 (2%)
Query: 10 SIAVFGLGRSGLSAACALKDSGV-HVIAWDDHPCAVKQAKDMG 51
SIAVFG G GL+A A K +G +IA D ++ AK++G
Sbjct: 189 SIAVFGAGAVGLAAVMAAKIAGCTTIIAVDIVDSRLELAKELG 231
>gnl|CDD|145796 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 = 176
Score = 34.4 bits (80), Expect = 0.069
Identities = 23/78 (29%), Positives = 38/78 (48%), Gaps = 9/78 (11%)
Query: 7 RNHSIAVFGLGRSGLSAACALKDSGVHVIAWDDHPCAVKQAKDMGIEVIDFREI-PWS-I 64
++ + GLGR G + A LK G+ VIA+D +P +A+ +G + E+ S +
Sbjct: 35 SGKTVGIIGLGRIGRAVARRLKAFGMKVIAYDRYP--KAEAEALGARYVSLDELLAESDV 92
Query: 65 ISFLVLSPGIALTGENAH 82
+S + LT E H
Sbjct: 93 VSLHL-----PLTPETRH 105
>gnl|CDD|37736 KOG2525, KOG2525, KOG2525, Folylpolyglutamate synthase [Coenzyme
transport and metabolism].
Length = 496
Score = 34.1 bits (78), Expect = 0.079
Identities = 12/26 (46%), Positives = 14/26 (53%)
Query: 115 FIAVTGTNGKSSTVALISHVLRKNGY 140
I V GT GK ST A +LR+ G
Sbjct: 74 IIHVAGTKGKGSTCAFTESILRQQGL 99
>gnl|CDD|31021 COG0677, WecC, UDP-N-acetyl-D-mannosaminuronate dehydrogenase
[Cell envelope biogenesis, outer membrane].
Length = 436
Score = 34.1 bits (78), Expect = 0.096
Identities = 14/36 (38%), Positives = 17/36 (47%)
Query: 11 IAVFGLGRSGLSAACALKDSGVHVIAWDDHPCAVKQ 46
I V GLG GL A A +G VI D + V +
Sbjct: 12 IGVIGLGYVGLPLAAAFASAGFKVIGVDINQKKVDK 47
>gnl|CDD|176242 cd08282, PFDH_like, Pseudomonas putida aldehyde-dismutating
formaldehyde dehydrogenase (PFDH). Formaldehyde
dehydrogenase (FDH) is a member of the
zinc-dependent/medium chain alcohol dehydrogenase
family. Unlike typical FDH, Pseudomonas putida
aldehyde-dismutating FDH (PFDH) is
glutathione-independent. PFDH converts 2 molecules of
aldehydes to corresponding carboxylic acid and alcohol.
MDH family uses NAD(H) as a cofactor in the
interconversion of alcohols and aldehydes, or ketones.
Like the zinc-dependent alcohol dehydrogenases (ADH) of
the medium chain alcohol dehydrogenase/reductase family
(MDR), these tetrameric FDHs have a catalytic zinc that
resides between the catalytic and NAD(H)binding domains
and a structural zinc in a lobe of the catalytic domain.
Unlike ADH, where NAD(P)(H) acts as a cofactor, NADH in
FDH is a tightly bound redox cofactor (similar to
nicotinamide proteins). The medium chain alcohol
dehydrogenase family (MDR) has 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. These proteins typically form dimers (typically
higher plants, mammals) or tetramers (yeast, bacteria),
and have 2 tightly bound zinc atoms per subunit.
Length = 375
Score = 33.7 bits (78), Expect = 0.12
Identities = 18/52 (34%), Positives = 27/52 (51%), Gaps = 3/52 (5%)
Query: 10 SIAVFGLGRSGL-SAACA-LKDSGVHVIAWDDHPCAVKQAKDMGIEVIDFRE 59
++AVFG G GL +A A L+ + V D P + A+ +G IDF +
Sbjct: 179 TVAVFGAGPVGLMAAYSAILRGASR-VYVVDHVPERLDLAESIGAIPIDFSD 229
>gnl|CDD|32383 COG2201, CheB, Chemotaxis response regulator containing a CheY-like
receiver domain and a methylesterase domain [Cell
motility and secretion / Signal transduction
mechanisms].
Length = 350
Score = 33.3 bits (76), Expect = 0.13
Identities = 20/71 (28%), Positives = 34/71 (47%), Gaps = 8/71 (11%)
Query: 6 FRNHSIAVF--GLGRSGLSAACALKDSGVHVIAWDDHPCAV----KQAKDMG--IEVIDF 57
+ ++++ V G+G G + A+K +G IA D+ C V K A + G EV+
Sbjct: 273 YGSNALGVILTGMGSDGAAGLRAIKKAGGITIAQDEASCVVYGMPKAAIEAGLVDEVLPL 332
Query: 58 REIPWSIISFL 68
EI I+ +
Sbjct: 333 EEIAEEIVKIV 343
>gnl|CDD|176223 cd08262, Zn_ADH8, Alcohol dehydrogenases of the MDR family. The
medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P)-binding Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. 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 = 341
Score = 32.7 bits (75), Expect = 0.21
Identities = 18/49 (36%), Positives = 23/49 (46%), Gaps = 2/49 (4%)
Query: 13 VFGLGRSGLSAACALKDSGVH-VIAWDDHPCAVKQAKDMGIE-VIDFRE 59
V G G GL+ ALK GV ++A D P A MG + V+D
Sbjct: 167 VIGCGPIGLAVIAALKARGVGPIVASDFSPERRALALAMGADIVVDPAA 215
>gnl|CDD|176193 cd08231, MDR_TM0436_like, Hypothetical enzyme TM0436 resembles the
zinc-dependent alcohol dehydrogenases (ADH). This group
contains the hypothetical TM0436 alcohol dehydrogenase
from Thermotoga maritima, proteins annotated as
5-exo-alcohol dehydrogenase, and other members of the
medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
MDR, which contains the zinc-dependent alcohol
dehydrogenase (ADH-Zn) and related proteins, is a
diverse group of proteins related to the first
identified member, class I mammalian ADH. MDRs display
a broad range of activities and are distinguished from
the smaller short chain dehydrogenases (~ 250 amino
acids vs. the ~ 350 amino acids of the MDR). The MDR
proteins have 2 domains: a C-terminal NAD(P)
binding-Rossmann fold domain of a beta-alpha form and an
N-terminal catalytic domain with distant homology to
GroES. The MDR group contains a host of activities,
including the founding alcohol dehydrogenase (ADH),
quinone reductase, sorbitol dehydrogenase, formaldehyde
dehydrogenase, butanediol DH, ketose reductase, cinnamyl
reductase, and numerous others. The zinc-dependent
alcohol dehydrogenases (ADHs) catalyze the
NAD(P)(H)-dependent interconversion of alcohols to
aldehydes or ketones. Active site zinc has a catalytic
role, while structural zinc aids in stability.
Length = 361
Score = 32.6 bits (75), Expect = 0.23
Identities = 19/59 (32%), Positives = 28/59 (47%), Gaps = 2/59 (3%)
Query: 5 SFRNHSIAVFGLGRSGLSAACALKDSG-VHVIAWDDHPCAVKQAKDMGIE-VIDFREIP 61
++ V G G GL A A K +G VI D P ++ A++ G + ID E+P
Sbjct: 175 VGAGDTVVVQGAGPLGLYAVAAAKLAGARRVIVIDGSPERLELAREFGADATIDIDELP 233
>gnl|CDD|31262 COG1062, AdhC, Zn-dependent alcohol dehydrogenases, class III
[Energy production and conversion].
Length = 366
Score = 32.5 bits (74), Expect = 0.26
Identities = 18/43 (41%), Positives = 26/43 (60%), Gaps = 1/43 (2%)
Query: 10 SIAVFGLGRSGLSAACALKDSG-VHVIAWDDHPCAVKQAKDMG 51
++AVFGLG GL+A K +G +IA D +P ++ AK G
Sbjct: 188 TVAVFGLGGVGLAAIQGAKAAGAGRIIAVDINPEKLELAKKFG 230
>gnl|CDD|32267 COG2084, MmsB, 3-hydroxyisobutyrate dehydrogenase and related
beta-hydroxyacid dehydrogenases [Lipid metabolism].
Length = 286
Score = 32.1 bits (73), Expect = 0.33
Identities = 14/48 (29%), Positives = 18/48 (37%), Gaps = 1/48 (2%)
Query: 10 SIAVFGLGRSGLSAACALKDSGVHVIAWDDHP-CAVKQAKDMGIEVID 56
IA GLG G A L +G V ++ P A + G V
Sbjct: 2 KIAFIGLGIMGSPMAANLLKAGHEVTVYNRTPEKAAELLAAAGATVAA 49
>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 = 31.9 bits (73), Expect = 0.39
Identities = 19/56 (33%), Positives = 28/56 (50%), Gaps = 1/56 (1%)
Query: 8 NHSIAVFGLGRSGLSAACALKDSGVHVIAWDDHPCAVKQAKDMG-IEVIDFREIPW 62
++ V G G GL AA K +G VI D ++ AK++G VID++E
Sbjct: 135 GDTVLVLGAGGVGLLAAQLAKAAGARVIVTDRSDEKLELAKELGADHVIDYKEEDL 190
>gnl|CDD|176261 cd08301, alcohol_DH_plants, Plant alcohol dehydrogenase.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and aldehydes
or ketones. Alcohol dehydrogenase in the liver converts
ethanol and NAD+ to acetaldehyde and NADH, while in
yeast and some other microorganisms ADH catalyzes the
conversion acetaldehyde to ethanol in alcoholic
fermentation. There are 7 vertebrate ADH 7 classes, 6
of which have been identified in humans. Class III,
glutathione-dependent formaldehyde dehydrogenase, has
been identified as the primordial form and exists in
diverse species, including plants, micro-organisms,
vertebrates, and invertebrates. Class I, typified by
liver dehydrogenase, is an evolving form. Gene
duplication and functional specialization of ADH into
ADH classes and subclasses created numerous forms in
vertebrates. For example, the A, B and C (formerly
alpha, beta, gamma) human class I subunits have high
overall structural similarity, but differ in the
substrate binding pocket and therefore in substrate
specificity. In human ADH catalysis, the zinc ion helps
coordinate the alcohol, followed by deprotonation of a
histidine (His-51), the ribose of NAD, a serine
(Ser-48) , then the alcohol, which allows the transfer
of a hydride to NAD+, creating NADH and a zinc-bound
aldehyde or ketone. In yeast and some bacteria, the
active site zinc binds an aldehyde, polarizing it, and
leading to the reverse reaction. ADH is a member of the
medium chain alcohol dehydrogenase family (MDR), which
has a NAD(P)(H)-binding domain in a Rossmann fold of an
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES.
These proteins typically form dimers (typically higher
plants, mammals) or tetramers (yeast, bacteria), and
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. NAD(H) binding occurs in the
cleft between the catalytic and coenzyme-binding
domains at the active site, and coenzyme binding induces
a conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
Length = 369
Score = 31.9 bits (73), Expect = 0.40
Identities = 18/49 (36%), Positives = 27/49 (55%), Gaps = 3/49 (6%)
Query: 10 SIAVFGLGRSGLSAACALKDSGV-HVIAWDDHPCAVKQAKDMGIEVIDF 57
++A+FGLG GL+ A + G +I D +P +QAK G V +F
Sbjct: 190 TVAIFGLGAVGLAVAEGARIRGASRIIGVDLNPSKFEQAKKFG--VTEF 236
>gnl|CDD|31252 COG1052, LdhA, Lactate dehydrogenase and related dehydrogenases
[Energy production and conversion / Coenzyme metabolism
/ General function prediction only].
Length = 324
Score = 31.8 bits (72), Expect = 0.44
Identities = 24/77 (31%), Positives = 36/77 (46%), Gaps = 6/77 (7%)
Query: 7 RNHSIAVFGLGRSGLSAACALKDSGVHVIAWDDHPCAVKQAKDMGIEVIDFRE-IPWSII 65
R ++ + GLGR G + A LK G+ V+ +D P + K++G +D E + S I
Sbjct: 145 RGKTLGIIGLGRIGQAVARRLKGFGMKVLYYDRSPNP-EAEKELGARYVDLDELLAESDI 203
Query: 66 SFLVLSPGIALTGENAH 82
L LT E H
Sbjct: 204 ISLHC----PLTPETRH 216
>gnl|CDD|176221 cd08260, Zn_ADH6, Alcohol dehydrogenases of the MDR family.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. This group has the characteristic
catalytic and structural zinc sites of the
zinc-dependent alcohol dehydrogenases. Alcohol
dehydrogenase in the liver converts ethanol and NAD+ to
acetaldehyde and NADH, while in yeast and some other
microorganisms ADH catalyzes the conversion acetaldehyde
to ethanol in alcoholic fermentation. ADH is a member of
the medium chain alcohol dehydrogenase family (MDR),
which has a NAD(P)(H)-binding domain in a Rossmann fold
of a beta-alpha form. The NAD(H)-binding region is
comprised of 2 structurally similar halves, each of
which contacts a mononucleotide. A GxGxxG motif after
the first mononucleotide contact half allows the close
contact of the coenzyme with the ADH backbone. The
N-terminal catalytic domain has a distant homology to
GroES. These proteins typically form dimers (typically
higher plants, mammals) or tetramers (yeast, bacteria),
and 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. NAD(H)-binding occurs
in the cleft between the catalytic and coenzyme-binding
domains at the active site, and coenzyme binding induces
a conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
In human ADH catalysis, the zinc ion helps coordinate
the alcohol, followed by deprotonation of a histidine,
the ribose of NAD, a serine, then the alcohol, which
allows the transfer of a hydride to NAD+, creating NADH
and a zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 345
Score = 31.8 bits (73), Expect = 0.44
Identities = 19/55 (34%), Positives = 29/55 (52%), Gaps = 7/55 (12%)
Query: 11 IAVFGLGRSGLSA---ACALKDSGVHVIAWDDHPCAVKQAKDMG-IEVIDFREIP 61
+AV G G GLSA A AL G VIA D ++ A+++G + ++ E+
Sbjct: 169 VAVHGCGGVGLSAVMIASAL---GARVIAVDIDDDKLELARELGAVATVNASEVE 220
>gnl|CDD|146202 pfam03446, NAD_binding_2, NAD binding domain of
6-phosphogluconate dehydrogenase. The NAD binding
domain of 6-phosphogluconate dehydrogenase adopts a
Rossmann fold.
Length = 163
Score = 31.7 bits (73), Expect = 0.48
Identities = 12/45 (26%), Positives = 17/45 (37%)
Query: 10 SIAVFGLGRSGLSAACALKDSGVHVIAWDDHPCAVKQAKDMGIEV 54
I GLG G A L +G V ++ P V++ G
Sbjct: 3 KIGFIGLGVMGSPMALNLLKAGYTVTVYNRTPEKVEELVAEGAVA 47
>gnl|CDD|30989 COG0644, FixC, Dehydrogenases (flavoproteins) [Energy production
and conversion].
Length = 396
Score = 31.2 bits (70), Expect = 0.56
Identities = 9/31 (29%), Positives = 16/31 (51%)
Query: 11 IAVFGLGRSGLSAACALKDSGVHVIAWDDHP 41
+ + G G +G SAA L +G+ V+ +
Sbjct: 6 VVIVGAGPAGSSAARRLAKAGLDVLVLEKGS 36
>gnl|CDD|176238 cd08277, liver_alcohol_DH_like, Liver alcohol dehydrogenase.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. There are 7 vertebrate ADH 7
classes, 6 of which have been identified in humans.
Class III, glutathione-dependent formaldehyde
dehydrogenase, has been identified as the primordial
form and exists in diverse species, including plants,
micro-organisms, vertebrates, and invertebrates. Class
I, typified by liver dehydrogenase, is an evolving
form. Gene duplication and functional specialization of
ADH into ADH classes and subclasses created numerous
forms in vertebrates. For example, the A, B and C
(formerly alpha, beta, gamma) human class I subunits
have high overall structural similarity, but differ in
the substrate binding pocket and therefore in substrate
specificity. In human ADH catalysis, the zinc ion helps
coordinate the alcohol, followed by deprotonation of a
histidine (His-51), the ribose of NAD, a serine
(Ser-48) , then the alcohol, which allows the transfer
of a hydride to NAD+, creating NADH and a zinc-bound
aldehyde or ketone. In yeast and some bacteria, the
active site zinc binds an aldehyde, polarizing it, and
leading to the reverse reaction. ADH is a member of the
medium chain alcohol dehydrogenase family (MDR), which
has a NAD(P)(H)-binding domain in a Rossmann fold of an
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES.
These proteins typically form dimers (typically higher
plants, mammals) or tetramers (yeast, bacteria), and
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. NAD(H) binding occurs in the
cleft between the catalytic and coenzyme-binding
domains at the active site, and coenzyme binding induces
a conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
Length = 365
Score = 31.2 bits (71), Expect = 0.58
Identities = 18/57 (31%), Positives = 31/57 (54%), Gaps = 2/57 (3%)
Query: 10 SIAVFGLGRSGLSAACALKDSGV-HVIAWDDHPCAVKQAKDMGI-EVIDFREIPWSI 64
++AVFGLG GLSA K +G +I D + ++AK+ G + I+ ++ +
Sbjct: 187 TVAVFGLGAVGLSAIMGAKIAGASRIIGVDINEDKFEKAKEFGATDFINPKDSDKPV 243
>gnl|CDD|35245 KOG0022, KOG0022, KOG0022, Alcohol dehydrogenase, class III
[Secondary metabolites biosynthesis, transport and
catabolism].
Length = 375
Score = 31.0 bits (70), Expect = 0.69
Identities = 25/95 (26%), Positives = 43/95 (45%), Gaps = 15/95 (15%)
Query: 10 SIAVFGLGRSGLSAACALKDSGV-HVIAWDDHPCAVKQAKDMGI-EVIDFREIPWSIISF 67
++AVFGLG GL+ A K +G +I D +P ++AK+ G E I+ +++ I
Sbjct: 195 TVAVFGLGGVGLAVAMGAKAAGASRIIGVDINPDKFEKAKEFGATEFINPKDLKKPIQEV 254
Query: 68 LVLSPGIALTGENAHWCVKLANQFNVEIIGDIELF 102
+ I +T + E IG++
Sbjct: 255 I-----IEMTDGGVDYS--------FECIGNVSTM 276
>gnl|CDD|31009 COG0665, DadA, Glycine/D-amino acid oxidases (deaminating) [Amino
acid transport and metabolism].
Length = 387
Score = 30.7 bits (68), Expect = 0.85
Identities = 14/67 (20%), Positives = 25/67 (37%), Gaps = 1/67 (1%)
Query: 11 IAVFGLGRSGLSAACALKDSGVHVIAWDDHPCAVKQA-KDMGIEVIDFREIPWSIISFLV 69
+ + G G GLSAA L + G V + A ++ G + + + +
Sbjct: 7 VVIIGGGIVGLSAAYYLAERGADVTVLEAGEAGGGAAGRNAGGILAPWASPGGELEVRPL 66
Query: 70 LSPGIAL 76
+AL
Sbjct: 67 ADLSLAL 73
>gnl|CDD|176244 cd08284, FDH_like_2, Glutathione-dependent formaldehyde
dehydrogenase related proteins, child 2.
Glutathione-dependent formaldehyde dehydrogenases (FDHs)
are members of the zinc-dependent/medium chain alcohol
dehydrogenase family. Formaldehyde dehydrogenase (FDH)
is a member of the zinc-dependent/medium chain alcohol
dehydrogenase family. FDH converts formaldehyde and NAD
to formate and NADH. The initial step in this process
the spontaneous formation of a
S-(hydroxymethyl)glutathione adduct from formaldehyde
and glutathione, followed by FDH-mediated oxidation (and
detoxification) of the adduct to S-formylglutathione.
These tetrameric FDHs have a catalytic zinc that resides
between the catalytic and NAD(H)binding domains and a
structural zinc in a lobe of the catalytic domain. The
medium chain alcohol dehydrogenase family (MDR) has a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The N-terminal region typically has an
all-beta catalytic domain. These proteins typically form
dimers (typically higher plants, mammals) or tetramers
(yeast, bacteria), and have 2 tightly bound zinc atoms
per subunit.
Length = 344
Score = 30.7 bits (70), Expect = 0.92
Identities = 17/49 (34%), Positives = 26/49 (53%), Gaps = 1/49 (2%)
Query: 10 SIAVFGLGRSGLSAACALKDSGVH-VIAWDDHPCAVKQAKDMGIEVIDF 57
++AV G G GL A + + G V A D P +++A +G E I+F
Sbjct: 170 TVAVIGCGPVGLCAVLSAQVLGAARVFAVDPVPERLERAAALGAEPINF 218
>gnl|CDD|176260 cd08300, alcohol_DH_class_III, class III alcohol dehydrogenases.
Members identified as glutathione-dependent formaldehyde
dehydrogenase(FDH), a member of the zinc
dependent/medium chain alcohol dehydrogenase family.
FDH converts formaldehyde and NAD(P) to formate and
NAD(P)H. The initial step in this process the
spontaneous formation of a S-(hydroxymethyl)glutathione
adduct from formaldehyde and glutathione, followed by
FDH-mediated oxidation (and detoxification) of the
adduct to S-formylglutathione. MDH family uses NAD(H)
as a cofactor in the interconversion of alcohols and
aldehydes or ketones. Like many zinc-dependent alcohol
dehydrogenases (ADH) of the medium chain alcohol
dehydrogenase/reductase family (MDR), these FDHs form
dimers, with 4 zinc ions per dimer. The medium chain
alcohol dehydrogenase family (MDR) have a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The N-terminal region typically has an
all-beta catalytic domain. These proteins typically form
dimers (typically higher plants, mammals) or tetramers
(yeast, bacteria), and have 2 tightly bound zinc atoms
per subunit. Alcohol dehydrogenase in the liver
converts ethanol and NAD+ to acetaldehyde and NADH,
while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which have a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES.
These proteins typically form dimers (typically higher
plants, mammals) or tetramers (yeast, bacteria), and
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. NAD(H) binding occurs in the
cleft between the catalytic and coenzyme-binding
domains at the active site, and coenzyme binding induces
a conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
Length = 368
Score = 30.3 bits (69), Expect = 1.2
Identities = 19/62 (30%), Positives = 31/62 (50%), Gaps = 2/62 (3%)
Query: 10 SIAVFGLGRSGLSAACALKDSGV-HVIAWDDHPCAVKQAKDMGI-EVIDFREIPWSIISF 67
++AVFGLG GL+ K +G +I D +P + AK G + ++ ++ I
Sbjct: 189 TVAVFGLGAVGLAVIQGAKAAGASRIIGIDINPDKFELAKKFGATDCVNPKDHDKPIQQV 248
Query: 68 LV 69
LV
Sbjct: 249 LV 250
>gnl|CDD|176182 cd05279, Zn_ADH1, Liver alcohol dehydrogenase and related
zinc-dependent alcohol dehydrogenases.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. There are 7 vertebrate ADH 7
classes, 6 of which have been identified in humans.
Class III, glutathione-dependent formaldehyde
dehydrogenase, has been identified as the primordial
form and exists in diverse species, including plants,
micro-organisms, vertebrates, and invertebrates. Class
I, typified by liver dehydrogenase, is an evolving
form. Gene duplication and functional specialization of
ADH into ADH classes and subclasses created numerous
forms in vertebrates. For example, the A, B and C
(formerly alpha, beta, gamma) human class I subunits
have high overall structural similarity, but differ in
the substrate binding pocket and therefore in substrate
specificity. In human ADH catalysis, the zinc ion helps
coordinate the alcohol, followed by deprotonation of a
histidine (His-51), the ribose of NAD, a serine
(Ser-48), then the alcohol, which allows the transfer of
a hydride to NAD+, creating NADH and a zinc-bound
aldehyde or ketone. In yeast and some bacteria, the
active site zinc binds an aldehyde, polarizing it, and
leading to the reverse reaction. ADH is a member of the
medium chain alcohol dehydrogenase family (MDR), which
has a NAD(P)(H)-binding domain in a Rossmann fold of an
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES.
These proteins typically form dimers (typically higher
plants, mammals) or tetramers (yeast, bacteria), and
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. NAD(H) binding occurs in the
cleft between the catalytic and coenzyme-binding domains
at the active site, and coenzyme binding induces a
conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
Length = 365
Score = 30.1 bits (68), Expect = 1.3
Identities = 20/52 (38%), Positives = 29/52 (55%), Gaps = 2/52 (3%)
Query: 10 SIAVFGLGRSGLSAACALKDSGVH-VIAWDDHPCAVKQAKDMG-IEVIDFRE 59
+ AVFGLG GLS K +G +IA D + ++AK +G E I+ R+
Sbjct: 186 TCAVFGLGGVGLSVIMGCKAAGASRIIAVDINKDKFEKAKQLGATECINPRD 237
>gnl|CDD|163675 cd07937, DRE_TIM_PC_TC_5S, Pyruvate carboxylase and
Transcarboxylase 5S, carboxyltransferase domain. This
family includes the carboxyltransferase domains of
pyruvate carboxylase (PC) and the transcarboxylase (TC)
5S subunit. Transcarboxylase 5S is a cobalt-dependent
metalloenzyme subunit of the biotin-dependent
transcarboxylase multienzyme complex. Transcarboxylase
5S transfers carbon dioxide from the 1.3S biotin to
pyruvate in the second of two carboxylation reactions
catalyzed by TC. The first reaction involves the
transfer of carbon dioxide from methylmalonyl-CoA to the
1.3S biotin, and is catalyzed by the 12S subunit. These
two steps allow a carboxylate group to be transferred
from oxaloacetate to propionyl-CoA to yield pyruvate and
methylmalonyl-CoA. The catalytic domain of
transcarboxylase 5S has a canonical TIM-barrel fold with
a large C-terminal extension that forms a funnel leading
to the active site. Transcarboxylase 5S forms a
homodimer and there are six dimers per complex. In
addition to the catalytic domain, transcarboxylase 5S
has several other domains including a
carbamoyl-phosphate synthase domain, a biotin
carboxylase domain, a carboxyltransferase domain, and an
ATP-grasp domain. Pyruvate carboxylase, like TC, is a
biotin-dependent enzyme that catalyzes the carboxylation
of pyruvate to produce oxaloacetate. In mammals, PC has
critical roles in gluconeogenesis, lipogenesis,
glyceroneogenesis, and insulin secretion. Inherited PC
deficiencies are linked to serious diseases in humans
such as lactic acidemia, hypoglycemia, psychomotor
retardation, and death. PC is a single-chain enzyme and
is active only in its homotetrameric form. PC has three
domains, an N-terminal biotin carboxylase domain, a
carboxyltransferase domain (this alignment model), and a
C-terminal biotin-carboxyl carrier protein domain. This
family belongs to the DRE-TIM metallolyase superfamily.
DRE-TIM metallolyases include 2-isopropylmalate synthase
(IPMS), alpha-isopropylmalate synthase (LeuA),
3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate
synthase, citramalate synthase, 4-hydroxy-2-oxovalerate
aldolase, re-citrate synthase, transcarboxylase 5S,
pyruvate carboxylase, AksA, and FrbC. These members all
share a conserved triose-phosphate isomerase (TIM)
barrel domain consisting of a core beta(8)-alpha(8)
motif with the eight parallel beta strands forming an
enclosed barrel surrounded by eight alpha helices. The
domain has a catalytic center containing a divalent
cation-binding site formed by a cluster of invariant
residues that cap the core of the barrel. In addition,
the catalytic site includes three invariant residues -
an aspartate (D), an arginine (R), and a glutamate (E) -
which is the basis for the domain name "DRE-TIM".
Length = 275
Score = 30.1 bits (69), Expect = 1.4
Identities = 12/27 (44%), Positives = 15/27 (55%), Gaps = 1/27 (3%)
Query: 198 HTLENYVNIKKKIVTMSKHAIICINDH 224
HTLE YV + K++ M ICI D
Sbjct: 146 HTLEYYVKLAKELEDMGAD-SICIKDM 171
>gnl|CDD|30999 COG0654, UbiH, 2-polyprenyl-6-methoxyphenol hydroxylase and
related FAD-dependent oxidoreductases [Coenzyme
metabolism / Energy production and conversion].
Length = 387
Score = 30.0 bits (67), Expect = 1.4
Identities = 10/26 (38%), Positives = 16/26 (61%)
Query: 9 HSIAVFGLGRSGLSAACALKDSGVHV 34
+A+ G G +GL+ A AL +G+ V
Sbjct: 3 LDVAIVGAGPAGLALALALARAGLDV 28
>gnl|CDD|31264 COG1064, AdhP, Zn-dependent alcohol dehydrogenases [General
function prediction only].
Length = 339
Score = 30.2 bits (68), Expect = 1.4
Identities = 16/50 (32%), Positives = 22/50 (44%), Gaps = 1/50 (2%)
Query: 11 IAVFGLGRSGLSAACALKDSGVHVIAWDDHPCAVKQAKDMGI-EVIDFRE 59
+AV G G G A K G VIA ++ AK +G VI+ +
Sbjct: 170 VAVVGAGGLGHMAVQYAKAMGAEVIAITRSEEKLELAKKLGADHVINSSD 219
>gnl|CDD|31263 COG1063, Tdh, Threonine dehydrogenase and related Zn-dependent
dehydrogenases [Amino acid transport and metabolism /
General function prediction only].
Length = 350
Score = 30.0 bits (67), Expect = 1.6
Identities = 16/52 (30%), Positives = 23/52 (44%), Gaps = 2/52 (3%)
Query: 10 SIAVFGLGRSGLSAACALKDSGV-HVIAWDDHPCAVKQAKD-MGIEVIDFRE 59
++ V G G GL A K G VI D P ++ AK+ G +V+
Sbjct: 171 TVVVVGAGPIGLLAIALAKLLGASVVIVVDRSPERLELAKEAGGADVVVNPS 222
>gnl|CDD|176259 cd08299, alcohol_DH_class_I_II_IV, class I, II, IV alcohol
dehydrogenases. NAD(P)(H)-dependent oxidoreductases are
the major enzymes in the interconversion of alcohols and
aldehydes or ketones. This group includes alcohol
dehydrogenases corresponding to mammalian classes I, II,
IV. Alcohol dehydrogenase in the liver converts ethanol
and NAD+ to acetaldehyde and NADH, while in yeast and
some other microorganisms ADH catalyzes the conversion
acetaldehyde to ethanol in alcoholic fermentation. ADH
is a member of the medium chain alcohol dehydrogenase
family (MDR), which have a NAD(P)(H)-binding domain in a
Rossmann fold of a beta-alpha form. The NAD(H)-binding
region is comprised of 2 structurally similar halves,
each of which contacts a mononucleotide. A GxGxxG motif
after the first mononucleotide contact half allows the
close contact of the coenzyme with the ADH backbone.
The N-terminal catalytic domain has a distant homology
to GroES. These proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and 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.
NAD(H) binding occurs in the cleft between the catalytic
and coenzyme-binding domains at the active site, and
coenzyme binding induces a conformational closing of
this cleft. Coenzyme binding typically precedes and
contributes to substrate binding. In human ADH
catalysis, the zinc ion helps coordinate the alcohol,
followed by deprotonation of a histidine (His-51), the
ribose of NAD, a serine (Ser-48) , then the alcohol,
which allows the transfer of a hydride to NAD+, creating
NADH and a zinc-bound aldehyde or ketone. In yeast and
some bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 373
Score = 29.6 bits (67), Expect = 1.7
Identities = 18/41 (43%), Positives = 24/41 (58%), Gaps = 1/41 (2%)
Query: 12 AVFGLGRSGLSAACALKDSGV-HVIAWDDHPCAVKQAKDMG 51
AVFGLG GLSA K +G +IA D + +AK++G
Sbjct: 195 AVFGLGGVGLSAIMGCKAAGASRIIAVDINKDKFAKAKELG 235
>gnl|CDD|30898 COG0552, FtsY, Signal recognition particle GTPase [Intracellular
trafficking and secretion].
Length = 340
Score = 29.4 bits (66), Expect = 2.0
Identities = 15/56 (26%), Positives = 27/56 (48%), Gaps = 3/56 (5%)
Query: 93 VEIIGDIELFVRERRFSSLQSPF-IAVTGTNG--KSSTVALISHVLRKNGYDVQLG 145
+EI+ ++ + PF I G NG K++T+A ++ L++ G V L
Sbjct: 118 IEILRPVDKVDLPLEIPKEKKPFVILFVGVNGVGKTTTIAKLAKYLKQQGKSVLLA 173
>gnl|CDD|30190 cd01672, TMPK, Thymidine monophosphate kinase (TMPK), also known as
thymidylate kinase, catalyzes the phosphorylation of
thymidine monophosphate (TMP) to thymidine diphosphate
(TDP) utilizing ATP as its preferred phophoryl donor.
TMPK represents the rate-limiting step in either de novo
or salvage biosynthesis of thymidine triphosphate
(TTP)..
Length = 200
Score = 29.5 bits (66), Expect = 2.0
Identities = 10/30 (33%), Positives = 17/30 (56%), Gaps = 2/30 (6%)
Query: 115 FIAVTGTN--GKSSTVALISHVLRKNGYDV 142
FI G + GK++ + L++ L GY+V
Sbjct: 2 FIVFEGIDGAGKTTLIELLAERLEARGYEV 31
>gnl|CDD|30460 COG0111, SerA, Phosphoglycerate dehydrogenase and related
dehydrogenases [Amino acid transport and metabolism].
Length = 324
Score = 29.5 bits (66), Expect = 2.1
Identities = 15/54 (27%), Positives = 25/54 (46%)
Query: 7 RNHSIAVFGLGRSGLSAACALKDSGVHVIAWDDHPCAVKQAKDMGIEVIDFREI 60
++ + GLGR G + A LK G+ VI +D + + D + V E+
Sbjct: 141 AGKTVGIIGLGRIGRAVAKRLKAFGMKVIGYDPYSPRERAGVDGVVGVDSLDEL 194
>gnl|CDD|110228 pfam01210, NAD_Gly3P_dh_N, NAD-dependent glycerol-3-phosphate
dehydrogenase N-terminus. NAD-dependent
glycerol-3-phosphate dehydrogenase (GPDH) catalyses the
interconversion of dihydroxyacetone phosphate and
L-glycerol-3-phosphate. This family represents the
N-terminal NAD-binding domain.
Length = 159
Score = 28.7 bits (65), Expect = 3.1
Identities = 11/41 (26%), Positives = 17/41 (41%), Gaps = 3/41 (7%)
Query: 10 SIAVFGLGRSGLSAACALKDSGVHVIAWDDHPCAVKQAKDM 50
IAV G G G + A L +G V W + +++
Sbjct: 2 KIAVLGAGSWGTALAKVLARNGHEVRLWGRDE---ELIEEI 39
>gnl|CDD|145298 pfam02046, COX6A, Cytochrome c oxidase subunit VIa.
Length = 116
Score = 28.9 bits (65), Expect = 3.3
Identities = 9/28 (32%), Positives = 11/28 (39%), Gaps = 6/28 (21%)
Query: 62 WSIISFLVLSPGIALTG------ENAHW 83
W +S+ V P IAL E H
Sbjct: 45 WKKLSYYVAIPAIALCAINAYFLEAEHA 72
>gnl|CDD|176226 cd08265, Zn_ADH3, Alcohol dehydrogenases of the MDR family. This
group resembles the zinc-dependent alcohol dehydrogenase
and has the catalytic and structural zinc-binding sites
characteristic of this group. 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. Other MDR members have only a catalytic zinc,
and some contain no coordinated zinc.
Length = 384
Score = 28.6 bits (64), Expect = 3.3
Identities = 15/46 (32%), Positives = 24/46 (52%), Gaps = 1/46 (2%)
Query: 11 IAVFGLGRSGLSAACALKDSGV-HVIAWDDHPCAVKQAKDMGIEVI 55
+ V+G G GL+A K +G VIA++ AK+MG + +
Sbjct: 207 VVVYGAGPIGLAAIALAKAAGASKVIAFEISEERRNLAKEMGADYV 252
>gnl|CDD|34183 COG4536, CorB, Putative Mg2+ and Co2+ transporter CorB [Inorganic
ion transport and metabolism].
Length = 423
Score = 28.6 bits (64), Expect = 3.7
Identities = 12/54 (22%), Positives = 19/54 (35%), Gaps = 3/54 (5%)
Query: 297 LKVEEIKRALLSCGGLTHRLQTIARLGHVIFINDSKATNLHSVIHAFLNEKRRI 350
L V ++ R L T + F+ + T L + AF K+ I
Sbjct: 250 LHVRDLLRLLNEKNEFTK-EDILRAADEPYFVPEG--TPLSDQLVAFQRNKKHI 300
>gnl|CDD|30474 COG0125, Tmk, Thymidylate kinase [Nucleotide transport and
metabolism].
Length = 208
Score = 28.7 bits (64), Expect = 3.7
Identities = 14/45 (31%), Positives = 20/45 (44%), Gaps = 7/45 (15%)
Query: 115 FIAVTGTN--GKSSTVALISHVLRKNGYDVQL-----GGNIGLPI 152
FI + G + GK++ L+ L + G V L G IG I
Sbjct: 5 FIVIEGIDGAGKTTQAELLKERLEERGIKVVLTREPGGTPIGEKI 49
>gnl|CDD|32255 COG2072, TrkA, Predicted flavoprotein involved in K+ transport
[Inorganic ion transport and metabolism].
Length = 443
Score = 28.5 bits (63), Expect = 3.9
Identities = 13/22 (59%), Positives = 18/22 (81%)
Query: 11 IAVFGLGRSGLSAACALKDSGV 32
+A+ G G+SGL+AA ALK +GV
Sbjct: 11 VAIIGAGQSGLAAAYALKQAGV 32
>gnl|CDD|35252 KOG0029, KOG0029, KOG0029, Amine oxidase [Secondary metabolites
biosynthesis, transport and catabolism].
Length = 501
Score = 28.4 bits (63), Expect = 4.1
Identities = 12/26 (46%), Positives = 16/26 (61%)
Query: 10 SIAVFGLGRSGLSAACALKDSGVHVI 35
+ V G G +GLSAA L+D G V+
Sbjct: 17 KVIVIGAGLAGLSAARQLQDFGFDVL 42
>gnl|CDD|34621 COG5016, COG5016, Pyruvate/oxaloacetate carboxyltransferase [Energy
production and conversion].
Length = 472
Score = 28.3 bits (63), Expect = 4.4
Identities = 12/26 (46%), Positives = 17/26 (65%), Gaps = 1/26 (3%)
Query: 198 HTLENYVNIKKKIVTMSKHAIICIND 223
HTLE YV + K+++ M + ICI D
Sbjct: 153 HTLEYYVELAKELLEMGVDS-ICIKD 177
>gnl|CDD|36107 KOG0889, KOG0889, KOG0889, Histone acetyltransferase SAGA, TRRAP/TRA1
component, PI-3 kinase superfamily [Signal transduction
mechanisms, Chromatin structure and dynamics,
Replication, recombination and repair, Cell cycle
control, cell division, chromosome partitioning].
Length = 3550
Score = 28.3 bits (63), Expect = 4.9
Identities = 23/164 (14%), Positives = 49/164 (29%), Gaps = 20/164 (12%)
Query: 157 YFSPNRFYVIECSSYQIELTPTIDPSIGVLLNISPDHLDRHH----TLENYVNIKKKIVT 212
Y + + I+ + P I ++ + L L ++ +
Sbjct: 1488 LDPEISSYTVPNMASDIQ--FQMVPLISTMVKNDDEWLLSSQFIVLALRRIWKLESILER 1545
Query: 213 MSKHAIICINDHQ------CEKIAYDMNFIGHSISRISSQSLQSDSDLYIDESFLKCSAT 266
+ +C+N YD+ + +S ID +FLK
Sbjct: 1546 LFLEDRLCLNSIVKCLLEYLSLNKYDLELLLQILSFFEGNDN-------IDLTFLKEFLE 1598
Query: 267 SEVIFDFSQETKKHNIQNLVTSAV-VCMQLGLKVEEIKRALLSC 309
EVI +S K++ + + K + ++ + C
Sbjct: 1599 HEVIKSYSYNMKRNLFLVFLNLFGDKDLGADHKAQVLQGLINPC 1642
>gnl|CDD|73299 cd02036, MinD, Bacterial cell division requires the formation of a
septum at mid-cell. The site is determined by the min
operon products MinC, MinD and MinE. MinC is a
nonspecific inhibitor of the septum protein FtsZ. MinE
is the supressor of MinC. MinD plays a pivotal role,
selecting the mid-cell over other sites through the
activation and regulation of MinC and MinE. MinD is a
membrane-associated ATPase, related to nitrogenase iron
protein. More distantly related proteins include
flagellar biosynthesis proteins and ParA chromosome
partitioning proteins. MinD is a monomer..
Length = 179
Score = 28.2 bits (63), Expect = 5.3
Identities = 19/51 (37%), Positives = 26/51 (50%), Gaps = 4/51 (7%)
Query: 116 IAVT---GTNGKSSTVALISHVLRKNGYDVQL-GGNIGLPILNLEYFSPNR 162
I VT G GK++T A + L + GY V L ++GL L+L NR
Sbjct: 2 IVVTSGKGGVGKTTTTANLGTALAQLGYKVVLIDADLGLRNLDLILGLENR 52
>gnl|CDD|32539 COG2403, COG2403, Predicted GTPase [General function prediction
only].
Length = 449
Score = 28.0 bits (62), Expect = 5.5
Identities = 15/35 (42%), Positives = 21/35 (60%), Gaps = 3/35 (8%)
Query: 111 LQSPFIAVTGTN---GKSSTVALISHVLRKNGYDV 142
L+ P IAVT T GKS+ ++ +LR+ GY V
Sbjct: 124 LEKPVIAVTATRTGVGKSAVSRYVARLLRERGYRV 158
>gnl|CDD|176216 cd08254, hydroxyacyl_CoA_DH, 6-hydroxycyclohex-1-ene-1-carboxyl-CoA
dehydrogenase, N-benzyl-3-pyrrolidinol dehydrogenase,
and other MDR family members. This group contains
enzymes of the zinc-dependent alcohol dehydrogenase
family, including members (aka MDR) identified as
6-hydroxycyclohex-1-ene-1-carboxyl-CoA dehydrogenase and
N-benzyl-3-pyrrolidinol dehydrogenase.
6-hydroxycyclohex-1-ene-1-carboxyl-CoA dehydrogenase
catalyzes the conversion of
6-Hydroxycyclohex-1-enecarbonyl-CoA and NAD+ to
6-Ketoxycyclohex-1-ene-1-carboxyl-CoA,NADH, and H+. This
group displays the characteristic catalytic and
structural zinc sites of the zinc-dependent alcohol
dehydrogenases. NAD(P)(H)-dependent oxidoreductases are
the major enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which have a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES. These
proteins typically form dimers (typically higher plants,
mammals) or tetramers (yeast, bacteria), and 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. NAD(H)-binding occurs in the cleft
between the catalytic and coenzyme-binding domains at
the active site, and coenzyme binding induces a
conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
In human ADH catalysis, the zinc ion helps coordinate
the alcohol, followed by deprotonation of a histidine,
the ribose of NAD, a serine, then the alcohol, which
allows the transfer of a hydride to NAD+, creating NADH
and a zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 338
Score = 28.0 bits (63), Expect = 6.7
Identities = 16/44 (36%), Positives = 23/44 (52%)
Query: 8 NHSIAVFGLGRSGLSAACALKDSGVHVIAWDDHPCAVKQAKDMG 51
++ V GLG GL+A K G VIA D ++ AK++G
Sbjct: 166 GETVLVIGLGGLGLNAVQIAKAMGAAVIAVDIKEEKLELAKELG 209
>gnl|CDD|146385 pfam03721, UDPG_MGDP_dh_N, UDP-glucose/GDP-mannose dehydrogenase
family, NAD binding domain. The
UDP-glucose/GDP-mannose dehydrogenaseses 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 = 185
Score = 27.6 bits (62), Expect = 7.0
Identities = 13/30 (43%), Positives = 15/30 (50%)
Query: 9 HSIAVFGLGRSGLSAACALKDSGVHVIAWD 38
IAV GLG GL A L + G V+ D
Sbjct: 1 MRIAVIGLGYVGLPTAVCLAEIGHDVVGVD 30
>gnl|CDD|30915 COG0569, TrkA, K+ transport systems, NAD-binding component
[Inorganic ion transport and metabolism].
Length = 225
Score = 27.5 bits (61), Expect = 7.3
Identities = 12/44 (27%), Positives = 20/44 (45%)
Query: 11 IAVFGLGRSGLSAACALKDSGVHVIAWDDHPCAVKQAKDMGIEV 54
I + G GR G S A L + G +V+ D V++ ++
Sbjct: 3 IIIIGAGRVGRSVARELSEEGHNVVLIDRDEERVEEFLADELDT 46
>gnl|CDD|35875 KOG0656, KOG0656, KOG0656, G1/S-specific cyclin D [Cell cycle
control, cell division, chromosome partitioning].
Length = 335
Score = 27.6 bits (61), Expect = 7.5
Identities = 17/56 (30%), Positives = 23/56 (41%), Gaps = 5/56 (8%)
Query: 271 FDFSQETKKHNIQNLVTSAVVCMQLGLKVEEIKRALLS---CGGLTH--RLQTIAR 321
F SQ+ K L AV C+ L K+EE LL+ + +TI R
Sbjct: 109 FLSSQKLPKDKPWMLQLLAVACLSLASKMEETDVPLLADLQVEYTDNVFEAKTIQR 164
>gnl|CDD|145418 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 = 115
Score = 27.5 bits (62), Expect = 8.0
Identities = 15/45 (33%), Positives = 25/45 (55%), Gaps = 1/45 (2%)
Query: 11 IAVFGLGRSGLSAACALKDSGVHVIAWDDHPCAVKQAKDMGIEVI 55
I + G GR G S A L++ G V+ D P V++ ++ G+ V+
Sbjct: 1 IIIIGYGRVGRSLAEELREGG-PVVVIDKDPERVEELREEGVPVV 44
>gnl|CDD|31342 COG1148, HdrA, Heterodisulfide reductase, subunit A and related
polyferredoxins [Energy production and conversion].
Length = 622
Score = 27.6 bits (61), Expect = 8.5
Identities = 11/28 (39%), Positives = 16/28 (57%)
Query: 8 NHSIAVFGLGRSGLSAACALKDSGVHVI 35
+ S+ V G G +G++AA L D G V
Sbjct: 124 SKSVLVIGGGVAGITAALELADMGFKVY 151
>gnl|CDD|146960 pfam04572, Gb3_synth, Alpha 1,4-glycosyltransferase conserved
region. The glycosphingolipids (GSL) form part of
eukaryotic cell membranes. They consist of a hydrophilic
carbohydrate moiety linked to a hydrophobic ceramide
tail embedded within the lipid bilayer of the membrane.
Lactosylceramide, Gal1,4Glc1Cer (LacCer), is the common
synthetic precursor to the majority of GSL found in
vertebrates. Alpha 1.4-glycosyltransferases utilize UDP
donors and transfer the sugar to a beta-linked acceptor.
This region appears to be confined to higher eukaryotes.
No function has been yet assigned to this region.
Length = 135
Score = 27.3 bits (61), Expect = 8.8
Identities = 27/117 (23%), Positives = 38/117 (32%), Gaps = 29/117 (24%)
Query: 120 GTNGKSSTVALISHVLRK--NGYDVQLGGNIGLPILNLEYFSPNRFYVIECSSYQ----- 172
G NG L++ VLRK N D G L P+ FY I ++
Sbjct: 27 GHNGP----GLVTRVLRKWCNTGDFA--GMTRLRCGGFTVLPPDAFYPIPWPQWKKFFEE 80
Query: 173 IELTPT---IDPSIGVLLNISPDHLDRHHTLENYVNIKKKIVTMSKHAIICINDHQC 226
L T + S V H L N + K+ S+ A + + C
Sbjct: 81 PRLEETMNWVKESYAV-------H------LWNKASKGLKVEEGSRVAYGTLAEQHC 124
>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 = 27.6 bits (62), Expect = 8.8
Identities = 19/60 (31%), Positives = 28/60 (46%), Gaps = 1/60 (1%)
Query: 2 KLSSFRNHSIAVFGLGRSGLSAACALKDSGVHVIAWDDHPCAVKQAKD-MGIEVIDFREI 60
S ++AV GLG+ G A L + G +I D + AV +A + G V+ EI
Sbjct: 22 GTDSLEGKTVAVQGLGKVGYKLAEHLLEEGAKLIVADINEEAVARAAELFGATVVAPEEI 81
>gnl|CDD|73297 cd02034, CooC, The accessory protein CooC, which contains a
nucleotide-binding domain (P-loop) near the N-terminus,
participates in the maturation of the nickel center of
carbon monoxide dehydrogenase (CODH). CODH from
Rhodospirillum rubrum catalyzes the reversible oxidation
of CO to CO2. CODH contains a nickel-iron-sulfur cluster
(C-center) and an iron-sulfur cluster (B-center). CO
oxidation occurs at the C-center. Three accessory
proteins encoded by cooCTJ genes are involved in nickel
incorporation into a nickel site. CooC functions as a
nickel insertase that mobilizes nickel to apoCODH using
energy released from ATP hydrolysis. CooC is a homodimer
and has NTPase activities. Mutation at the P-loop
abolishs its function..
Length = 116
Score = 27.1 bits (60), Expect = 9.4
Identities = 11/29 (37%), Positives = 17/29 (58%), Gaps = 2/29 (6%)
Query: 116 IAVTGTNG--KSSTVALISHVLRKNGYDV 142
IA+TG G K++ AL++ L + G V
Sbjct: 2 IAITGKGGVGKTTIAALLARYLAEKGKPV 30
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.322 0.137 0.405
Gapped
Lambda K H
0.267 0.0721 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 5,642,516
Number of extensions: 304675
Number of successful extensions: 876
Number of sequences better than 10.0: 1
Number of HSP's gapped: 860
Number of HSP's successfully gapped: 75
Length of query: 468
Length of database: 6,263,737
Length adjustment: 97
Effective length of query: 371
Effective length of database: 4,167,664
Effective search space: 1546203344
Effective search space used: 1546203344
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 59 (26.5 bits)