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)