RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780924|ref|YP_003065337.1| potassium-efflux system
protein [Candidatus Liberibacter asiaticus str. psy62]
(609 letters)
>gnl|CDD|34270 COG4651, RosB, Kef-type K+ transport system, predicted NAD-binding
component [Inorganic ion transport and metabolism].
Length = 408
Score = 440 bits (1134), Expect = e-124
Identities = 237/412 (57%), Positives = 309/412 (75%), Gaps = 15/412 (3%)
Query: 1 MTTIIWGFVLAFIFGAIANRCRLPTLIGYLVAGILVGPRTPGFVASQSLVPALAEIGIIL 60
+TTI+ G VLAF+ GA+ANR RL L+GYL+AG+L GP TPGFVA Q+L P LAE+G+IL
Sbjct: 8 ITTIVGGLVLAFLLGALANRLRLSPLVGYLLAGVLAGPFTPGFVADQTLAPELAELGVIL 67
Query: 61 LMFGVGLHFSVKDLISVRGIALPGALIQIILGTALGALMGMVMGWSLGGSVVFGLALSIA 120
LMFGVGLHFS+KDL++V+ IA+PGAL QI L T LG + ++GWS G +VFGLALS+A
Sbjct: 68 LMFGVGLHFSLKDLLAVKAIAIPGALAQIALATLLGMGLSSLLGWSFGTGIVFGLALSVA 127
Query: 121 STVVLLKALQENRILETDRGKIAVGWLIVEDLIIVLALVLIPAAATNYSAEPSSMTHPWT 180
STVVLL+AL+E ++++T RG+IA+GWLIVEDL +VLALVL+PA A
Sbjct: 128 STVVLLRALEERQLIDTQRGRIAIGWLIVEDLAMVLALVLLPALA--------------- 172
Query: 181 SFITQQMGFEVGMPGLIMITLLKVVAFIGVMLIFGRRVIPWILHMIFYTGSRELFRLGVL 240
+ Q + + ITL KV AFI +ML+ GRR+IPWIL + TGSRELF L VL
Sbjct: 173 GVLGQGDVGFATLLVDLGITLGKVAAFIAIMLVVGRRLIPWILERVAATGSRELFTLAVL 232
Query: 241 AIALGFAYGSSKLFGVSLSLGAFFAGMILAESELSQSAAQESLPLRDAFSVLFFISVGMM 300
AIALG A+G+++LFGVS +LGAFFAGM+LAESELS AA++SLPLRDAF+VLFF+SVGM+
Sbjct: 233 AIALGVAFGAAELFGVSFALGAFFAGMVLAESELSHRAAEDSLPLRDAFAVLFFVSVGML 292
Query: 301 FNPDILISNPILLMMAVIIVIIGKALIAFIVVIAFGRSVATALTIAASLSQIGEFSFILA 360
F+P ILI P+ ++ ++I++ GK++ AF +V AFG V TALTI+ASL+QIGEFSFILA
Sbjct: 293 FDPMILIQQPLAVLATLLIILFGKSVAAFFIVRAFGHPVRTALTISASLAQIGEFSFILA 352
Query: 361 NLGVELGILPDQARDLILASSIISIILNPLVFVLAEFLQSFLVLRFARVTSS 412
LG++L +LP+ RDL+LA +I+SI+LNPL+F L + Q + S
Sbjct: 353 GLGIKLNLLPEAGRDLVLAGAILSILLNPLLFALLDRYQRSAEWLKEQAAES 404
>gnl|CDD|144551 pfam00999, Na_H_Exchanger, Sodium/hydrogen exchanger family. Na/H
antiporters are key transporters in maintaining the pH
of actively metabolising cells. The molecular mechanisms
of antiport are unclear. These antiporters contain 10-12
transmembrane regions (M) at the amino-terminus and a
large cytoplasmic region at the carboxyl terminus. The
transmembrane regions M3-M12 share identity with other
members of the family. The M6 and M7 regions are highly
conserved. Thus, this is thought to be the region that
is involved in the transport of sodium and hydrogen
ions. The cytoplasmic region has little similarity
throughout the family.
Length = 371
Score = 187 bits (477), Expect = 7e-48
Identities = 111/396 (28%), Positives = 193/396 (48%), Gaps = 33/396 (8%)
Query: 4 IIWGFVLAFIFGAIANRCRLPTLIGYLVAGILVGPRTPGFVASQSLVP-ALAEIGIILLM 62
+ +LA + G +A R LP ++G ++AGIL+GP G V L LAE+G+ L+
Sbjct: 1 AVLLILLALLAGLLARRLGLPPVVGLILAGILLGPSGLGLVEPDELDLEVLAELGLPFLL 60
Query: 63 FGVGLHFSVKDLISVRGIALPGALIQIILGTALGAL---MGMVMGWSLGGSVVFGLALSI 119
F GL +++L L AL+ ++L L L + +G L +++FG ALS
Sbjct: 61 FLAGLELDLRELRKNGKSILLLALLGVLLPFLLIGLLLALLGGLGIPLLEALLFGAALSA 120
Query: 120 ASTVVLLKALQENRILETDRGKIAVGWLIVEDLIIVLALVLIPAAATNYSAEPSSMTHPW 179
S VV+L L+E L T G + +G ++ D + V+ L ++ A A
Sbjct: 121 TSPVVVLAILKERGRLNTRLGTLILGESVLNDAVAVVLLAVLLALAGVGG---------- 170
Query: 180 TSFITQQMGFEVGMPGLIMITLLKVVAFIGVMLIFGRRVIPWI--LHMIFYTGSRELFRL 237
+ LL + + + + V W+ L F +G REL L
Sbjct: 171 ---------------LSDLGLLLLIFLVVALGGLLLGLVFGWLLRLITRFTSGDRELEVL 215
Query: 238 GVLAIALGFAYGSSKLFGVSLSLGAFFAGMILAESELSQSAAQESLPLRDAFS-VLFFIS 296
VLA+AL A ++L G+S LGAF AG++L+ + +++ P LFF+
Sbjct: 216 LVLALALL-AALLAELLGLSGILGAFLAGLVLSNYAFANELSEKLEPFGYGLFLPLFFVL 274
Query: 297 VGMMFNPDILISNPILLMMAVIIVIIGKALIAFIVVIAFGRSVATALTIAASLSQIGEFS 356
VG+ + +L+S +L+++ ++ +++GK L F++ G S+ AL + Q G S
Sbjct: 275 VGLSLDLSLLLSLLLLVLLLLVAILLGKLLGVFLLARLLGLSLREALIVGFGGLQRGAVS 334
Query: 357 FILANLGVELGILPDQARDLILASSIISIILNPLVF 392
LA +G++LG++ + L++A +++ +L PL+
Sbjct: 335 LALAAIGLQLGLIDRELYTLLVAVVLLTTLLKPLLK 370
>gnl|CDD|30823 COG0475, KefB, Kef-type K+ transport systems, membrane components
[Inorganic ion transport and metabolism].
Length = 397
Score = 157 bits (398), Expect = 8e-39
Identities = 134/399 (33%), Positives = 219/399 (54%), Gaps = 32/399 (8%)
Query: 9 VLAFIFGAIANRCRLPTLIGYLVAGILVGPRTPGFV-ASQSLVPALAEIGIILLMFGVGL 67
++A I G + R LP ++GYL+AGI++GP + S ++ LAE+G++ L+F +GL
Sbjct: 16 LVAVILGPLFKRLGLPPVLGYLLAGIILGPWGLLLIIESSEIIELLAELGVVFLLFLIGL 75
Query: 68 HFSVKDLISVRG-IALPGALIQIILGTALGALMG-MVMGWSLGGSVVFGLALSIASTVVL 125
F ++ L V + L A + + LG L+ ++G SL ++ G AL+++ST ++
Sbjct: 76 EFDLERLKKVGRSVGLGVAQVGLTAPFLLGLLLLLGILGLSLIAALFLGAALALSSTAIV 135
Query: 126 LKALQENRILETDRGKIAVGWLIVEDLIIVLALVLIPAAATNYSAEPSSMTHPWTSFITQ 185
LK L E +L+T G++ +G L+ +D+ +L L ++PA A S
Sbjct: 136 LKILMELGLLKTREGQLILGALVFDDIAAILLLAIVPALAGGGS---------------- 179
Query: 186 QMGFEVGMPGLIMITLLKVVAFIGVMLIFGRRVIPWILHMIFYTGSRELFRLGVLAIALG 245
G G I+ LL ++AF+ ++L+ GR ++P + + T S ELF L VL + LG
Sbjct: 180 ------GSVGFILGLLLAILAFLALLLLLGRYLLPPLFRRVAKTESSELFILFVLLLVLG 233
Query: 246 FAYGSSKLFGVSLSLGAFFAGMILAESELSQSAAQESL-PLRDAFSV-LFFISVGMMFNP 303
AY + L G+S+ LGAF AG++L+ESE + +E + P D + LFFISVGM +
Sbjct: 234 AAYLAE-LLGLSMILGAFLAGLLLSESEYRKHELEEKIEPFGDGLFIPLFFISVGMSLDL 292
Query: 304 DILISNPILLMMAVIIVIIGKALIAFIVVIAFGRSVATALTIAASLSQIGEFSFILANLG 363
+L+ N +L+++ V + I+GK L A++ G S AL I L Q GEF+F+LA +
Sbjct: 293 GVLLENLLLILLLVALAILGKILGAYLAARLLGFSKRLALGIGLLLRQGGEFAFVLAGIA 352
Query: 364 VELGILPDQARDLILASSIISIILNPLVFVLAEFLQSFL 402
+ I L+ A I+S+I P++ +L L L
Sbjct: 353 LGSAISE----ALLTAVVILSMITTPILPLLTPILLKRL 387
>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 = 96.5 bits (241), Expect = 2e-20
Identities = 41/115 (35%), Positives = 66/115 (57%), Gaps = 1/115 (0%)
Query: 451 VILVGYGRIGKVIVQNLKAAGIALLVIEDSEKKIEELRSLGIDVIYGNATITKILLMANI 510
+I++GYGR+G+ + + L+ G ++VI+ +++EELR G+ V+ G+AT ++L A I
Sbjct: 1 IIIIGYGRVGRSLAEELREGGP-VVVIDKDPERVEELREEGVPVVVGDATDEEVLEEAGI 59
Query: 511 EKARSLVVSISTAFEAAYITQEARNSNPSILIIALADSDSEVEHLTRYGADTVVM 565
E A ++V + I AR NP+ IIA A+ E L R GAD V+
Sbjct: 60 EDADAVVAATGDDEANILIVLLARELNPAKKIIARANDPEHAELLRRLGADEVIS 114
>gnl|CDD|36863 KOG1650, KOG1650, KOG1650, Predicted K+/H+-antiporter [Inorganic
ion transport and metabolism].
Length = 769
Score = 70.0 bits (171), Expect = 2e-12
Identities = 84/428 (19%), Positives = 158/428 (36%), Gaps = 50/428 (11%)
Query: 4 IIWGFVLAFIFGAIANRCRLPTLIGYLVAGILVGP----------RTPGFVASQSLVPAL 53
II VL+ + + P +I ++AGI++GP T +S ++ L
Sbjct: 28 IILIIVLSRLLHILLKPLGQPRVISEILAGIILGPSLLGRIPSYMNTIFPKSSMIVLELL 87
Query: 54 AEIGIILLMFGVGL---------HFSVKDLISVRGIALPGALIQIILGTALGALMGMVMG 104
A +G + +F +GL +I++ + LP L + G
Sbjct: 88 ANLGFLFFLFLMGLEIDLRVIRRTGKKAIVIAIASVVLPFGLGFGLAFLLSDTKADKEDG 147
Query: 105 --WSLGGSVVFGLALSIASTVVLLKALQENRILETDRGKIAVGWLIVEDLIIVLALVLIP 162
+ + A SI S VL + L E ++L ++ G++A+ +V D+ + L L
Sbjct: 148 ALFLPFEILFILSAQSITSFPVLARILAELKLLNSELGRLALSAAVVNDVAGWILLALAL 207
Query: 163 AAATNYSAEPSSMTHPWTSFITQQMGFEVGMPGLIMITLLKVVAFIGVMLIFGRRVIPWI 222
A ++ P + L+ V+ F+ + R ++ WI
Sbjct: 208 AFSSE----------------------LKLSPLRSVWDLVLVIGFVLFLFFVVRPLMKWI 245
Query: 223 LHMIFYTGSRELFRLGV-LAIALGFAYGSSKLFGVSLSLGAFFAGMILAESELSQSAAQE 281
+ + V L L A+ + + G+ GAF G+ + SA E
Sbjct: 246 IKRTPEGKPVSDAYICVTLLGVLASAFLTDLIGGIHSIFGAFILGLAIPHGPPLGSALIE 305
Query: 282 SL--PLRDAFSVLFFISVGMMFNPDILISNPILLMMAVI-IVIIGKALIAFIVVIAFGRS 338
L + L+F G+ DI N ++ I I K L +
Sbjct: 306 KLEDLVSGLLLPLYFAISGLKT--DISRINKWGALIRTILIFGAVKLLSTLGTSLYCKLP 363
Query: 339 VATALTIAASLSQIGEFSFILANLGVELGILPDQA-RDLILASSIISIILNPLVFVLAEF 397
+ +L + +S G I+ N G++ IL D+ ++L + + + I PL+ L +
Sbjct: 364 LRDSLALGLLMSTKGLVELIVLNTGLDRKILSDEGFTVMVLMALVSTFITPPLLMFLYDP 423
Query: 398 LQSFLVLR 405
+ + +
Sbjct: 424 TRKYHGYK 431
>gnl|CDD|31419 COG1226, Kch, Kef-type K+ transport systems, predicted NAD-binding
component [Inorganic ion transport and metabolism].
Length = 212
Score = 68.6 bits (166), Expect = 4e-12
Identities = 54/134 (40%), Positives = 82/134 (61%), Gaps = 1/134 (0%)
Query: 446 DLCDHVILVGYGRIGKVIVQNLKAAGIALLVIEDSEKKIEELRSLGIDVIYGNATITKIL 505
L HVI+VG+GR+G+++ + L A+GI ++VI+ E ++E LR LG+ V+ G+AT ++L
Sbjct: 19 RLKRHVIIVGFGRVGQIVARALLASGIPVVVIDSDEDRVELLRELGLLVVLGDATREEVL 78
Query: 506 LMANIEKARSLVVSISTAFEAAYITQEARNSNPSILIIALADS-DSEVEHLTRYGADTVV 564
A IE+AR+++V++S +I AR NP + I+A A D VE LT GAD VV
Sbjct: 79 EAAGIERARAVIVTLSDDATNVFIVLLARAINPELEILARARDLDEAVETLTTVGADEVV 138
Query: 565 MSAREIALGMLDRL 578
E AL +
Sbjct: 139 PPTFESALLLARAA 152
>gnl|CDD|30915 COG0569, TrkA, K+ transport systems, NAD-binding component
[Inorganic ion transport and metabolism].
Length = 225
Score = 62.2 bits (151), Expect = 5e-10
Identities = 30/132 (22%), Positives = 64/132 (48%), Gaps = 2/132 (1%)
Query: 451 VILVGYGRIGKVIVQNLKAAGIALLVIEDSEKKIEELRSLGID--VIYGNATITKILLMA 508
+I++G GR+G+ + + L G +++I+ E+++EE + +D V+ G+AT +L A
Sbjct: 3 IIIIGAGRVGRSVARELSEEGHNVVLIDRDEERVEEFLADELDTHVVIGDATDEDVLEEA 62
Query: 509 NIEKARSLVVSISTAFEAAYITQEARNSNPSILIIALADSDSEVEHLTRYGADTVVMSAR 568
I+ A ++V + + + A +IA A + + L + GAD ++ +
Sbjct: 63 GIDDADAVVAATGNDEVNSVLALLALKEFGVPRVIARARNPEHEKVLEKLGADVIISPEK 122
Query: 569 EIALGMLDRLNQ 580
A + +
Sbjct: 123 LAAKRLARLIVT 134
>gnl|CDD|37228 KOG2017, KOG2017, KOG2017, Molybdopterin synthase sulfurylase
[Coenzyme transport and metabolism].
Length = 427
Score = 38.4 bits (89), Expect = 0.006
Identities = 41/166 (24%), Positives = 70/166 (42%), Gaps = 18/166 (10%)
Query: 434 ILEQQEVTIQKTDLCDHVILVGYGRIGKVIVQNLKAAGIALLVIEDSEKKIEELRSLGID 493
IL + V Q + V++VG G +G Q L AAG+ L I D + EL +L
Sbjct: 52 ILPEFGVHGQLSLKNSSVLVVGAGGLGCPAAQYLAAAGVGRLGIVDYDVV--ELSNLHRQ 109
Query: 494 VIYGNATITKILLMANIEKARSLVVSISTAFEAAYITQEARNSNPSILI----IALADSD 549
V++ A + M E A + + +++ E + +SN +I + L +D
Sbjct: 110 VLHTEARVG----MHKAESAAAFLRRLNSHVEVQTYNEFLSSSNAFDIIKQYDVVLDCTD 165
Query: 550 SEVEHLTRYG-ADTVVMSAREI----ALGMLDRLNQVHHEKVTCDR 590
+ TRY +D V+ + + AL +L ++ C R
Sbjct: 166 NV---PTRYLISDVCVLLGKPLVSGSALRWEGQLTVYNYNNGPCYR 208
>gnl|CDD|30375 COG0025, NhaP, NhaP-type Na+/H+ and K+/H+ antiporters [Inorganic
ion transport and metabolism].
Length = 429
Score = 37.6 bits (87), Expect = 0.010
Identities = 60/334 (17%), Positives = 128/334 (38%), Gaps = 33/334 (9%)
Query: 1 MTTIIWGFVLAFIFGAIANRCRLPTLIGYLVAGILVGPRTPGFVASQSLV--PALAEIGI 58
+ ++ +L + +A R LP + L+ G+L GP ++ + + +
Sbjct: 8 LFLLLLILLLGLLVSVLAGRLLLPEIPLLLLLGLLGGPPGLNLISPDLELDPELFLVLFL 67
Query: 59 ILLMFGVGLHFSVKDLISVRGIALPGALIQIILGTAL--GALMGMVMGWSLGGSVVFGLA 116
+L+F GL +++L V L AL +++ ++ G L + + G
Sbjct: 68 AILLFAGGLELDLRELRRVWRSILVLALPLVLITALGIGLLAHWLLPGIPLAAAFLLGAI 127
Query: 117 LSIASTVVLLKALQENRILETDRGKIAVGWLIVEDLIIVLALVLIPAAATNYSAEPSSMT 176
LS V + + R+ + R + L+ + + IVL V +
Sbjct: 128 LSPTDPVAVSPIFKRVRVPKRIRTILEGESLLNDGVGIVLFKVAL--------------- 172
Query: 177 HPWTSFITQQMGFEVGMPGLIMITLLKVVAFIGVMLIFGRRVIPWILHMIFYTGSRELFR 236
+ + F +G L+ + +G++L + + L +T S L
Sbjct: 173 ----AALLGTGAFSLGWALLLFLIEALGGILLGLLLGYLLGRLLRRLDRRGWT-SPLLET 227
Query: 237 LGVLAIALGFAYGSSKLFGVSLSLGAFFAGMILAESELSQSAAQESLPLRDAF------- 289
L L +A AY ++ GVS L AG++L E+ + + +F
Sbjct: 228 LLTLLLAFA-AYLLAEALGVSGILAVVVAGLVLGEAVRINLSPASARLRLSSFWEVLDFL 286
Query: 290 -SVLFFISVGMMFNPDILISNPILLMMAVIIVII 322
+ L F+ +G +L++ +L ++ ++ ++
Sbjct: 287 LNGLLFVLLGAQLPLSLLLALGLLGLLVALVAVL 320
>gnl|CDD|176207 cd08245, CAD, Cinnamyl alcohol dehydrogenases (CAD) and related
proteins. Cinnamyl alcohol dehydrogenases (CAD),
members of the medium chain dehydrogenase/reductase
family, reduce cinnamaldehydes to cinnamyl alcohols in
the last step of monolignal metabolism in plant cells
walls. CAD binds 2 zinc ions and is NADPH- dependent.
CAD family members are also found in non-plant species,
e.g. in yeast where they have an aldehyde reductase
activity. The medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes, or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 330
Score = 36.5 bits (85), Expect = 0.022
Identities = 16/46 (34%), Positives = 23/46 (50%)
Query: 449 DHVILVGYGRIGKVIVQNLKAAGIALLVIEDSEKKIEELRSLGIDV 494
+ V ++G G +G + VQ +A G + I S K E R LG D
Sbjct: 164 ERVAVLGIGGLGHLAVQYARAMGFETVAITRSPDKRELARKLGADE 209
>gnl|CDD|176198 cd08236, sugar_DH, NAD(P)-dependent sugar dehydrogenases. This
group contains proteins identified as sorbitol
dehydrogenases and other sugar dehydrogenases of the
medium-chain dehydrogenase/reductase family (MDR), which
includes zinc-dependent alcohol dehydrogenase and
related proteins. Sorbitol and aldose reductase are
NAD(+) binding proteins of the polyol pathway, which
interconverts glucose and fructose. Sorbitol
dehydrogenase is tetrameric and has a single catalytic
zinc per subunit. NAD(P)(H)-dependent oxidoreductases
are the major enzymes in the interconversion of alcohols
and aldehydes, or ketones. Related proteins include
threonine dehydrogenase, formaldehyde dehydrogenase, and
butanediol dehydrogenase. 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. Horse
liver alcohol dehydrogenase is a dimeric enzyme and each
subunit has two domains. The NAD binding domain is in a
Rossmann fold and the catalytic domain contains a zinc
ion to which substrates bind. There is a cleft between
the domains that closes upon formation of the ternary
complex.
Length = 343
Score = 36.4 bits (85), Expect = 0.023
Identities = 15/49 (30%), Positives = 27/49 (55%), Gaps = 1/49 (2%)
Query: 449 DHVILVGYGRIGKVIVQNLKAAGIA-LLVIEDSEKKIEELRSLGIDVIY 496
D V+++G G IG + +Q LK G ++ ++ ++K+ R LG D
Sbjct: 161 DTVVVIGAGTIGLLAIQWLKILGAKRVIAVDIDDEKLAVARELGADDTI 209
>gnl|CDD|176204 cd08242, MDR_like, Medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
This group contains members identified as related to
zinc-dependent alcohol dehydrogenase and other members
of the MDR family, including threonine dehydrogenase.
The medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group includes
various activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has a
catalytic role, while structural zinc aids in stability.
ADH-like proteins typically form dimers (typically
higher plants, mammals) or tetramers (yeast, bacteria),
and generally have 2 tightly bound zinc atoms per
subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 319
Score = 35.7 bits (83), Expect = 0.035
Identities = 18/62 (29%), Positives = 33/62 (53%), Gaps = 5/62 (8%)
Query: 434 ILEQQEVTIQKTDLCDHVILVGYGRIGKVIVQNLKAAGIALLVIEDSEKKIEELRSLGID 493
ILEQ +T D V ++G G++G +I Q L G ++++ +K+ R LG++
Sbjct: 147 ILEQVPITPG-----DKVAVLGDGKLGLLIAQVLALTGPDVVLVGRHSEKLALARRLGVE 201
Query: 494 VI 495
+
Sbjct: 202 TV 203
>gnl|CDD|30635 COG0287, TyrA, Prephenate dehydrogenase [Amino acid transport and
metabolism].
Length = 279
Score = 34.6 bits (79), Expect = 0.082
Identities = 23/117 (19%), Positives = 46/117 (39%), Gaps = 4/117 (3%)
Query: 448 CDHVILVGYGRIGKVIVQNLKAAGIALLVIEDSEKKIEELRSLGIDVIYGNATITKILLM 507
V +VG G +G + + LK AG+ + +I +L + VI +T L
Sbjct: 3 SMKVGIVGLGLMGGSLARALKEAGLVVRIIGRDRSAATLKAALELGVID---ELTVAGLA 59
Query: 508 ANIEKARSLVVSISTAFEAAYITQEARNSNPSILIIALADSDSEV-EHLTRYGADTV 563
+A ++V++ + + A + ++ + S V E + +Y V
Sbjct: 60 EAAAEADLVIVAVPIEATEEVLKELAPHLKKGAIVTDVGSVKSSVVEAMEKYLPGDV 116
>gnl|CDD|35246 KOG0023, KOG0023, KOG0023, Alcohol dehydrogenase, class V
[Secondary metabolites biosynthesis, transport and
catabolism].
Length = 360
Score = 34.1 bits (78), Expect = 0.11
Identities = 22/47 (46%), Positives = 29/47 (61%), Gaps = 1/47 (2%)
Query: 449 DHVILVGYGRIGKVIVQNLKAAGIALLVIEDSEKKIEE-LRSLGIDV 494
V +VG G +G + VQ KA G+ + VI S KK EE ++SLG DV
Sbjct: 183 KWVGIVGLGGLGHMAVQYAKAMGMRVTVISTSSKKKEEAIKSLGADV 229
>gnl|CDD|31264 COG1064, AdhP, Zn-dependent alcohol dehydrogenases [General
function prediction only].
Length = 339
Score = 33.6 bits (77), Expect = 0.15
Identities = 18/48 (37%), Positives = 27/48 (56%)
Query: 449 DHVILVGYGRIGKVIVQNLKAAGIALLVIEDSEKKIEELRSLGIDVIY 496
V +VG G +G + VQ KA G ++ I SE+K+E + LG D +
Sbjct: 168 KWVAVVGAGGLGHMAVQYAKAMGAEVIAITRSEEKLELAKKLGADHVI 215
>gnl|CDD|73271 cd01492, Aos1_SUMO, Ubiquitin activating enzyme (E1) subunit Aos1.
Aos1 is part of the heterodimeric activating enzyme
(E1), specific for the SUMO family of ubiquitin-like
proteins (Ubls). E1 enzymes are part of a conjugation
cascade to attach Ub or Ubls, covalently to substrate
proteins consisting of activating (E1), conjugating
(E2), and/or ligating (E3) enzymes. E1 activates
ubiquitin by C-terminal adenylation, and subsequently
forms a highly reactive thioester bond between its
catalytic cysteine and Ubls C-terminus. The E1 also
associates with E2 and promotes ubiquitin transfer to
the E2's catalytic cysteine. Post-translational
modification by SUMO family of ubiquitin-like proteins
(Ublps) is involved in cell division, nuclear transport,
the stress response and signal transduction. Aos1
contains part of the adenylation domain..
Length = 197
Score = 30.9 bits (70), Expect = 0.93
Identities = 22/91 (24%), Positives = 41/91 (45%), Gaps = 2/91 (2%)
Query: 443 QKTDLCDHVILVGYGRIGKVIVQNLKAAGIALLVIEDSEKKIEELRSLGIDVIYGNATIT 502
QK ++L+G +G I +NL +GI L I D EE LG + +
Sbjct: 16 QKRLRSARILLIGLKGLGAEIAKNLVLSGIGSLTILDDRTVTEE--DLGAQFLIPAEDLG 73
Query: 503 KILLMANIEKARSLVVSISTAFEAAYITQEA 533
+ A++E+ R+L + + + I+++
Sbjct: 74 QNRAEASLERLRALNPRVKVSVDTDDISEKP 104
>gnl|CDD|176196 cd08234, threonine_DH_like, L-threonine dehydrogenase. L-threonine
dehydrogenase (TDH) catalyzes the zinc-dependent
formation of 2-amino-3-ketobutyrate from L-threonine,
via NAD(H)-dependent oxidation. THD is a member of the
zinc-requiring, medium chain NAD(H)-dependent alcohol
dehydrogenase family (MDR). MDRs have a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. NAD(P)(H)-dependent oxidoreductases are
the major enzymes in the interconversion of alcohols and
aldehydes, or ketones. 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. Sorbitol and aldose
reductase are NAD(+) binding proteins of the polyol
pathway, which interconverts glucose and fructose.
Length = 334
Score = 31.0 bits (71), Expect = 0.99
Identities = 17/49 (34%), Positives = 27/49 (55%), Gaps = 1/49 (2%)
Query: 449 DHVILVGYGRIGKVIVQNLKAAGIA-LLVIEDSEKKIEELRSLGIDVIY 496
D V++ G G IG ++ Q LK G + + V E +E+K+E + LG
Sbjct: 161 DSVLVFGAGPIGLLLAQLLKLNGASRVTVAEPNEEKLELAKKLGATETV 209
>gnl|CDD|34564 COG4956, COG4956, Integral membrane protein (PIN domain
superfamily) [General function prediction only].
Length = 356
Score = 31.0 bits (70), Expect = 1.0
Identities = 22/124 (17%), Positives = 52/124 (41%), Gaps = 7/124 (5%)
Query: 289 FSVLFFISVGMMFNPDIL----ISNPILLMMAVIIVIIGKALIAFIVVIAFGRSVATALT 344
++ +G P++L I + L + +IG A+I F++ FG+ V L
Sbjct: 9 LFIIIGAVLGFAVIPELLADLGIQDTAFLNNEYVDALIG-AIIFFLISFWFGKYVLNWLK 67
Query: 345 -IAASLSQIGEFSFILANLGVELGILPDQARDLILASSIISIILNPLVFVLAEFLQSFLV 403
+ + ++ + + +G+ +G+L L I I + ++ V+ + ++
Sbjct: 68 RLEEQIRKLPVTTILFGTIGLIIGLLIAVLLSSPLFLLPIPFI-STIIPVILTIILAYFG 126
Query: 404 LRFA 407
+ A
Sbjct: 127 FQLA 130
>gnl|CDD|31366 COG1173, DppC, ABC-type dipeptide/oligopeptide/nickel transport
systems, permease components [Amino acid transport and
metabolism / Inorganic ion transport and metabolism].
Length = 289
Score = 30.2 bits (68), Expect = 1.7
Identities = 14/62 (22%), Positives = 30/62 (48%)
Query: 299 MMFNPDILISNPILLMMAVIIVIIGKALIAFIVVIAFGRSVATALTIAASLSQIGEFSFI 358
+M DI ++ P LL+ +++ I+G L+ I+ +A A + + + E ++
Sbjct: 121 LMRITDIFLAFPSLLLAILLVAILGPGLLNLILALALVGWPGYARIVRGQVLSLREREYV 180
Query: 359 LA 360
A
Sbjct: 181 EA 182
>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 = 29.5 bits (67), Expect = 2.5
Identities = 19/77 (24%), Positives = 34/77 (44%), Gaps = 5/77 (6%)
Query: 451 VILVGYGRIGKVIVQNLKAAGIALLVIEDSEKKIEELRSLGIDVIYGNATITKILLMANI 510
V+++G G +G VQ KA G A++ ++ E+K+E + LG D + + + A
Sbjct: 169 VLVIGLGGLGLNAVQIAKAMGAAVIAVDIKEEKLELAKELGADEVLNSLDDSPKDKKAA- 227
Query: 511 EKARSLVVSISTAFEAA 527
L F+
Sbjct: 228 ----GLGGGFDVIFDFV 240
>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 = 29.6 bits (67), Expect = 2.8
Identities = 17/45 (37%), Positives = 29/45 (64%)
Query: 449 DHVILVGYGRIGKVIVQNLKAAGIALLVIEDSEKKIEELRSLGID 493
D V+++G G +G + Q KAAG ++V + S++K+E + LG D
Sbjct: 136 DTVLVLGAGGVGLLAAQLAKAAGARVIVTDRSDEKLELAKELGAD 180
>gnl|CDD|107344 cd06349, PBP1_ABC_ligand_binding_like_14, Type I periplasmic
ligand-binding domain of uncharacterized ABC (Atpase
Binding Cassette)-type active transport systems. This
subgroup includes the type I periplasmic ligand-binding
domain of uncharacterized ABC (Atpase Binding
Cassette)-type active transport systems that are
predicted to be involved in the uptake of amino acids,
peptides, or inorganic ions. This subgroup has high
sequence similarity to members of the family of
hydrophobic amino acid transporters (HAAT), such as
leucine/isoleucine/valine binding protein (LIVBP);
however its ligand specificity has not been determined
experimentally.
Length = 340
Score = 29.3 bits (66), Expect = 3.2
Identities = 23/83 (27%), Positives = 36/83 (43%), Gaps = 4/83 (4%)
Query: 449 DHVILVGYGRIGKVIVQNLKAAGIALLVIEDSEKKIEELRSLGIDVIYGNATITKILLMA 508
D +IL+ Y G I + +A G+ + V+ S + LG D + G T T
Sbjct: 192 DAIILISYYNDGAPIARQARAVGLDIPVVASSSVYSPKFIELGGDAVEGVYTPTAFFPGD 251
Query: 509 NIEKARSLVVSISTAFEAAYITQ 531
+ +S V +A+EA Y Q
Sbjct: 252 PRPEVQSFV----SAYEAKYGAQ 270
>gnl|CDD|30949 COG0604, Qor, NADPH:quinone reductase and related Zn-dependent
oxidoreductases [Energy production and conversion /
General function prediction only].
Length = 326
Score = 29.2 bits (65), Expect = 3.3
Identities = 13/45 (28%), Positives = 24/45 (53%)
Query: 451 VILVGYGRIGKVIVQNLKAAGIALLVIEDSEKKIEELRSLGIDVI 495
++ G +G +Q KA G ++ + S +K+E L+ LG D +
Sbjct: 147 LVHGAAGGVGSAAIQLAKALGATVVAVVSSSEKLELLKELGADHV 191
>gnl|CDD|35574 KOG0353, KOG0353, KOG0353, ATP-dependent DNA helicase [General
function prediction only].
Length = 695
Score = 29.0 bits (64), Expect = 3.5
Identities = 32/144 (22%), Positives = 54/144 (37%), Gaps = 12/144 (8%)
Query: 426 KQEVPVESILEQQEVTIQKTDLCDHVILVGYGRIGKVIVQNLKAA---GIALLV---IED 479
K++ +E Q I T + L+ GK + L A G AL++ I
Sbjct: 87 KEQFHLEKFRPLQLAAINATMAGEDAFLILPTGGGKSLCYQLPALCADGFALVICPLISL 146
Query: 480 SEKKIEELRSLGIDVIYGNATITKILLMANIEKARSLVVSISTAFEAAYITQEARNSNPS 539
E +I +L+ LGID NA +K ++ + + + + F+ Y+T E S
Sbjct: 147 MEDQILQLKQLGIDASMLNANSSK----EEAKRVEAAITNKDSEFKLIYVTPEKIAK--S 200
Query: 540 ILIIALADSDSEVEHLTRYGADTV 563
+ + E D V
Sbjct: 201 KKFMNKLEKALEAGFFKLIAIDEV 224
>gnl|CDD|176195 cd08233, butanediol_DH_like, (2R,3R)-2,3-butanediol dehydrogenase.
(2R,3R)-2,3-butanediol dehydrogenase, a zinc-dependent
medium chain alcohol dehydrogenase, catalyzes the
NAD(+)-dependent oxidation of (2R,3R)-2,3-butanediol and
meso-butanediol to acetoin. BDH functions as a
homodimer. NAD(P)(H)-dependent oxidoreductases are the
major enzymes in the interconversion of alcohols and
aldehydes, or ketones. 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.
Sorbitol and aldose reductase are NAD(+) binding
proteins of the polyol pathway, which interconverts
glucose and fructose. Sorbitol dehydrogenase is
tetrameric and has a single catalytic zinc per subunit.
Length = 351
Score = 28.7 bits (65), Expect = 5.3
Identities = 17/49 (34%), Positives = 28/49 (57%), Gaps = 1/49 (2%)
Query: 449 DHVILVGYGRIGKVIVQNLKAAGIA-LLVIEDSEKKIEELRSLGIDVIY 496
D +++G G IG + + LKAAG + ++V E SE + E LG ++
Sbjct: 174 DTALVLGAGPIGLLTILALKAAGASKIIVSEPSEARRELAEELGATIVL 222
>gnl|CDD|31311 COG1114, BrnQ, Branched-chain amino acid permeases [Amino acid
transport and metabolism].
Length = 431
Score = 28.6 bits (64), Expect = 5.6
Identities = 45/188 (23%), Positives = 75/188 (39%), Gaps = 17/188 (9%)
Query: 3 TIIWGFVL-AFIFGAIANRCRLPTLIGYLVAGILVGPRTPGFVASQSLVPALAEIGIILL 61
I GF+L A FGA P ++G AG V P GF+ + +P L GII +
Sbjct: 7 IIALGFMLFALFFGA--GNLIFPPMLGLH-AGEHVWPAILGFLLTGVGLPLL---GIIAV 60
Query: 62 MFGVGLHFSVKDLISVR-GIALPGALIQII---LGTALGALMGMVMGWSLGGSVVFGLAL 117
G S+ I G+ A+ I + +G S +L
Sbjct: 61 ALYGGGVESLATRIGPWFGVLFAIAIYLSIGPFFAIPRTGAVSFEVGISPLLGDSSLPSL 120
Query: 118 SIAST----VVLLKALQENRILETDRGKIAVGWLIVEDLIIVLALVLIPAAATNYSAEPS 173
I S + L +L +++++ GK L+V L+I++ +IP A +A +
Sbjct: 121 FIFSVIFFAIAYLFSLNPSKLIDR-VGKFLTPILLVL-LLILVIAAIIPPAGPISAASGA 178
Query: 174 SMTHPWTS 181
+ P++
Sbjct: 179 YQSQPFSK 186
>gnl|CDD|30111 cd00757, ThiF_MoeB_HesA_family, ThiF_MoeB_HesA. Family of E1-like
enzymes involved in molybdopterin and thiamine
biosynthesis family. The common reaction mechanism
catalyzed by MoeB and ThiF, like other E1 enzymes,
begins with a nucleophilic attack of the C-terminal
carboxylate of MoaD and ThiS, respectively, on the
alpha-phosphate of an ATP molecule bound at the active
site of the activating enzymes, leading to the formation
of a high-energy acyladenylate intermediate and
subsequently to the formation of a thiocarboxylate at
the C termini of MoaD and ThiS. MoeB, as the MPT
synthase (MoaE/MoaD complex) sulfurase, is involved in
the biosynthesis of the molybdenum cofactor, a
derivative of the tricyclic pterin, molybdopterin (MPT).
ThiF catalyzes the adenylation of ThiS, as part of the
biosynthesis pathway of thiamin pyrophosphate (vitamin
B1). .
Length = 228
Score = 28.5 bits (64), Expect = 5.6
Identities = 15/52 (28%), Positives = 28/52 (53%), Gaps = 2/52 (3%)
Query: 450 HVILVGYGRIGKVIVQNLKAAGIALLVIEDSEKKIEELRSLGIDVIYGNATI 501
V++VG G +G + L AAG+ L + D + + EL +L +++ A +
Sbjct: 23 RVLVVGAGGLGSPAAEYLAAAGVGKLGLVDDD--VVELSNLQRQILHTEADV 72
>gnl|CDD|31226 COG1023, Gnd, Predicted 6-phosphogluconate dehydrogenase
[Carbohydrate transport and metabolism].
Length = 300
Score = 28.3 bits (63), Expect = 5.8
Identities = 11/40 (27%), Positives = 23/40 (57%)
Query: 453 LVGYGRIGKVIVQNLKAAGIALLVIEDSEKKIEELRSLGI 492
++G GR+G +V+ L G ++ + ++ +EEL+ G
Sbjct: 5 MIGLGRMGANLVRRLLDGGHDVVGYDVNQTAVEELKDEGA 44
>gnl|CDD|144461 pfam00875, DNA_photolyase, DNA photolyase. This domain binds a
light harvesting cofactor.
Length = 164
Score = 28.3 bits (64), Expect = 5.8
Identities = 12/36 (33%), Positives = 19/36 (52%), Gaps = 2/36 (5%)
Query: 465 QNLKAAGIALLVIE-DSEKKIEEL-RSLGIDVIYGN 498
++L GI L+V D + + EL + LG +Y N
Sbjct: 60 ESLAKLGIPLIVRRGDPAEVLPELAKELGASAVYWN 95
>gnl|CDD|35292 KOG0069, KOG0069, KOG0069, Glyoxylate/hydroxypyruvate reductase
(D-isomer-specific 2-hydroxy acid dehydrogenase
superfamily) [Energy production and conversion].
Length = 336
Score = 28.4 bits (63), Expect = 6.1
Identities = 14/44 (31%), Positives = 21/44 (47%)
Query: 451 VILVGYGRIGKVIVQNLKAAGIALLVIEDSEKKIEELRSLGIDV 494
V ++G GRIGK I + LK G +L ++ EE +
Sbjct: 165 VGILGLGRIGKAIAKRLKPFGCVILYHSRTQLPPEEAYEYYAEF 208
>gnl|CDD|176220 cd08259, Zn_ADH5, 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 contains proteins that
share the characteristic catalytic and structural
zinc-binding sites of the zinc-dependent alcohol
dehydrogenase family. 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 = 332
Score = 28.4 bits (64), Expect = 6.6
Identities = 12/45 (26%), Positives = 24/45 (53%)
Query: 451 VILVGYGRIGKVIVQNLKAAGIALLVIEDSEKKIEELRSLGIDVI 495
++ G +G +Q KA G ++ + S +K++ L+ LG D +
Sbjct: 167 LVTGAGGGVGIHAIQLAKALGARVIAVTRSPEKLKILKELGADYV 211
>gnl|CDD|144913 pfam01496, V_ATPase_I, V-type ATPase 116kDa subunit family. This
family consists of the 116kDa V-type ATPase (vacuolar
(H+)-ATPases) subunits, as well as V-type ATP synthase
subunit i. The V-type ATPases family are proton pumps
that acidify intracellular compartments in eukaryotic
cells for example yeast central vacuoles,
clathrin-coated and synaptic vesicles. They have
important roles in membrane trafficking processes. The
116kDa subunit (subunit a) in the V-type ATPase is part
of the V0 functional domain responsible for proton
transport. The a subunit is a transmembrane glycoprotein
with multiple putative transmembrane helices it has a
hydrophilic amino terminal and a hydrophobic carboxy
terminal. It has roles in proton transport and assembly
of the V-type ATPase complex. This subunit is encoded by
two homologous gene in yeast VPH1 and STV1.
Length = 707
Score = 28.1 bits (63), Expect = 7.2
Identities = 35/177 (19%), Positives = 67/177 (37%), Gaps = 19/177 (10%)
Query: 234 LFRLGVLAIALGFAYGSSKLFGVSLSLGAFFAGMILAESELSQSAAQESLPL-RDAFSVL 292
L +GV +I GF Y FG SL++ F +G + S + F +
Sbjct: 404 LLLMGVFSIYTGFIYND--CFGKSLNI--FGSGWLWPVMIKSGETLTLAPHEGPYPFGID 459
Query: 293 FFISVGMMFNPDILISNPILLMMAVIIVIIGKA---LIAFIVVIAFGRSVATALTIAASL 349
+ +L N + +++I+ +I + F + F + A +
Sbjct: 460 PEWNGV---ENKLLFLNSYKMKLSIILGVIHMTFGLFLGFFNHVKFKSKID---IKDAFI 513
Query: 350 SQIGEFSFILANLG-VELGILPDQARDLILASSIISIILNPLVFV-LAEFLQSFLVL 404
Q+ S+++ G + + I+ D S +L L+ + L +Q FLV+
Sbjct: 514 PQL---SWLIIIFGYLVILIIYKWLVDWAKTSKPAPSLLIGLINMFLFPGVQVFLVV 567
>gnl|CDD|32044 COG1859, KptA, RNA:NAD 2'-phosphotransferase [Translation,
ribosomal structure and biogenesis].
Length = 211
Score = 27.9 bits (62), Expect = 7.4
Identities = 22/117 (18%), Positives = 37/117 (31%), Gaps = 27/117 (23%)
Query: 455 GYGRIGKVIVQNLKA---AGIALL--VIEDSEKKIEELRSLGIDVIYG----------NA 499
G+ I +++ KA LL V+ +K EL+ I YG A
Sbjct: 58 GWADIDELLEGLRKAGRWLTRELLLAVVATDDKGRFELKEGKIRARYGHSIPVDLRLPEA 117
Query: 500 TITKILLMANIEKARSLV------------VSISTAFEAAYITQEARNSNPSILIIA 544
+L + + V +S +E A + +P +L I
Sbjct: 118 EPPAVLYHGTSPEFLPSILEEGLKPMKRRHVHLSADYETAKQVGLRHSGSPVVLEID 174
>gnl|CDD|30845 COG0499, SAM1, S-adenosylhomocysteine hydrolase [Coenzyme
metabolism].
Length = 420
Score = 27.9 bits (62), Expect = 7.9
Identities = 13/44 (29%), Positives = 21/44 (47%)
Query: 451 VILVGYGRIGKVIVQNLKAAGIALLVIEDSEKKIEELRSLGIDV 494
V++ GYG +G+ I L+ G ++V E + E G V
Sbjct: 212 VVVAGYGWVGRGIAMRLRGMGARVIVTEVDPIRALEAAMDGFRV 255
>gnl|CDD|36584 KOG1370, KOG1370, KOG1370, S-adenosylhomocysteine hydrolase
[Coenzyme transport and metabolism].
Length = 434
Score = 28.0 bits (62), Expect = 8.6
Identities = 11/28 (39%), Positives = 16/28 (57%)
Query: 451 VILVGYGRIGKVIVQNLKAAGIALLVIE 478
++ GYG +GK Q LK G ++V E
Sbjct: 217 AVVCGYGDVGKGCAQALKGFGARVIVTE 244
>gnl|CDD|32775 COG2954, COG2954, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 156
Score = 27.6 bits (61), Expect = 9.8
Identities = 13/33 (39%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 252 KLFGVSLSLGAFFAGMILAESELSQSAAQESLP 284
L+ V + LG AG+++AE EL A LP
Sbjct: 97 FLWEVDVFLGDN-AGLVVAEVELPDENADFDLP 128
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
0.326 0.140 0.392
Gapped
Lambda K H
0.267 0.0779 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 7,001,269
Number of extensions: 405656
Number of successful extensions: 2627
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2497
Number of HSP's successfully gapped: 395
Length of query: 609
Length of database: 6,263,737
Length adjustment: 99
Effective length of query: 510
Effective length of database: 4,124,446
Effective search space: 2103467460
Effective search space used: 2103467460
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 60 (26.8 bits)