RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780409|ref|YP_003064822.1| ribose-phosphate pyrophosphokinase [Candidatus Liberibacter asiaticus str. psy62] (310 letters) >gnl|CDD|30810 COG0462, PrsA, Phosphoribosylpyrophosphate synthetase [Nucleotide transport and metabolism / Amino acid transport and metabolism]. Length = 314 Score = 410 bits (1056), Expect = e-115 Identities = 182/311 (58%), Positives = 231/311 (74%), Gaps = 2/311 (0%) Query: 1 MKIFAGNSNRNLAQEICDYLHTSLGKASVTYFSDREVFVEIGENVRGEDVFIVQSTSCPA 60 MKIF+G+SN LA++I L LGK V F D E++V I E+VRG+DVFI+QSTS P Sbjct: 5 MKIFSGSSNPELAEKIAKRLGIPLGKVEVKRFPDGEIYVRIEESVRGKDVFIIQSTSPPV 64 Query: 61 NDYLMELLIMIDAVRRSSARRITGVIPYFGYCRQDRKPSPRTPISAKLVANLITQAGADR 120 ND LMELLIMIDA++R+SA+RIT VIPYFGY RQD+ PR PISAKLVANL+ AGADR Sbjct: 65 NDNLMELLIMIDALKRASAKRITAVIPYFGYARQDKAFKPREPISAKLVANLLETAGADR 124 Query: 121 VIMLDLHAGQVQGFFDIPTDNLYALPILERDIKERNDISNLMVVSPDVGGVVRARALAKR 180 V+ +DLHA Q+QGFFDIP DNLYA P+L I+E+ D+ + +VVSPD GGV RARALA R Sbjct: 125 VLTVDLHAPQIQGFFDIPVDNLYAAPLLAEYIREKYDLDDPVVVSPDKGGVKRARALADR 184 Query: 181 LGCLLAIVDKRR-EHPGKIEVMNIIGKVEGKDCILIDDIVDTGGTLCGAADALYEQGALS 239 LG LAI+DKRR P +EVMN+IG VEGKD +++DDI+DTGGT+ AA AL E+GA Sbjct: 185 LGAPLAIIDKRRDSSPNVVEVMNLIGDVEGKDVVIVDDIIDTGGTIAKAAKALKERGAKK 244 Query: 240 VTAYITHGVLSSSSIERIEKSKMKELVITDSIQPTDLVKSSAKIRILTIAQLMGEAINRT 299 V A THGV S +++ER+E S + E+++TD+I P K K+ ++++A L+ EAI R Sbjct: 245 VYAAATHGVFSGAALERLEASAIDEVIVTDTI-PLPEKKKIPKVSVISVAPLIAEAIRRI 303 Query: 300 FEERSISSLFD 310 S+SSLFD Sbjct: 304 HNGESVSSLFD 314 >gnl|CDD|36661 KOG1448, KOG1448, KOG1448, Ribose-phosphate pyrophosphokinase [Nucleotide transport and metabolism, Amino acid transport and metabolism]. Length = 316 Score = 319 bits (818), Expect = 8e-88 Identities = 155/312 (49%), Positives = 205/312 (65%), Gaps = 3/312 (0%) Query: 1 MKIFAGNSNRNLAQEICDYLHTSLGKASVTYFSDREVFVEIGENVRGEDVFIVQSTSCPA 60 +K+F+G+S+ LA+ I L LGK ++ FS+ E V+IGE+VRGEDV+I+QS S P Sbjct: 4 IKLFSGDSHPELAERIAARLGIELGKVNLKKFSNGETSVQIGESVRGEDVYIIQSGSGPI 63 Query: 61 NDYLMELLIMIDAVRRSSARRITGVIPYFGYCRQDRKPSPRTPISAKLVANLITQAGADR 120 ND LMELLIMI+A +R+SA R+T VIPYF Y RQD+K R PI AKLVANL++ AGAD Sbjct: 64 NDNLMELLIMINACKRASASRVTAVIPYFPYARQDKKDKSRAPILAKLVANLLSSAGADH 123 Query: 121 VIMLDLHAGQVQGFFDIPTDNLYALPILERDIKERN-DISNLMVVSPDVGGVVRARALAK 179 VI +DLHA Q+QGFFDIP DNLYA P + I+E D N ++VSPD GG R +LA Sbjct: 124 VITMDLHASQIQGFFDIPVDNLYAEPAVLNYIRENIPDSENAVIVSPDAGGAKRVTSLAD 183 Query: 180 RLGCLLA-IVDKRREHPGKIEVMNIIGKVEGKDCILIDDIVDTGGTLCGAADALYEQGAL 238 RL A I +RR+ M ++G V+GK IL+DD+ DT GTL AAD L E GA Sbjct: 184 RLNLDFALIHKERRKANEVDIRMVLVGDVKGKVAILVDDMADTCGTLIKAADKLLEHGAK 243 Query: 239 SVTAYITHGVLSSSSIERIEKSKMKELVITDSIQPTDLVKSSAKIRILTIAQLMGEAINR 298 V A +THGV S +IER+ +S + +V+T++I P D K+ + ++ ++ EAI R Sbjct: 244 KVYAIVTHGVFSGPAIERLNESALDRVVVTNTI-PIDDSCLEPKLTTIDVSPVLAEAIRR 302 Query: 299 TFEERSISSLFD 310 T S+S LF Sbjct: 303 THNGESVSYLFS 314 >gnl|CDD|36716 KOG1503, KOG1503, KOG1503, Phosphoribosylpyrophosphate synthetase-associated protein [Amino acid transport and metabolism, Nucleotide transport and metabolism]. Length = 354 Score = 207 bits (527), Expect = 4e-54 Identities = 123/341 (36%), Positives = 192/341 (56%), Gaps = 34/341 (9%) Query: 1 MKIFAGNSNRNLAQEICDYLHTSLGKASVTYFSDREVFVEIGENVRGEDVFIVQSTSCPA 60 M +F+GNS+ LA+ + + L LGKA+V ++RE VEI E+VRG+DVFI+Q+ S Sbjct: 9 MVLFSGNSHPELAKMVAERLGIELGKATVYQKTNRETRVEIKESVRGKDVFIIQTGSKDV 68 Query: 61 NDYLMELLIMIDAVRRSSARRITGVIPYFGYCRQDRKPSPRTPISAKLVANLITQAGADR 120 N+ +MELLIM A + S A+ I GVIPY Y +Q + R I +KL+A+++ +AG Sbjct: 69 NNDVMELLIMAYACKTSCAKSIIGVIPYLPYSKQCKM-RKRGSIVSKLLASMMCKAGLTH 127 Query: 121 VIMLDLHAGQVQGFFDIPTDNLYALPILERDIKER-NDISNLMVVSPDVGGVVRARALAK 179 +I +DLH ++QGFF IP DNL A P L + I+E D N ++V+ G +A++ A+ Sbjct: 128 LITMDLHQKEIQGFFSIPVDNLRASPFLLQYIQEEIPDYRNAVIVAKSPGVAKKAQSYAE 187 Query: 180 RLGCLLAI------------VDKRREHPGKIEV------------------MNIIGKVEG 209 RL LA+ VD R P + + ++G V G Sbjct: 188 RLRLGLAVIHGEQKDTESDLVDGRHSPPPVVTATTHPSLELPAQISKEKPPLTVVGDVGG 247 Query: 210 KDCILIDDIVDTGGTLCGAADALYEQGALSVTAYITHGVLSSSSIERIEKSKMKELVITD 269 + I++DDI+D + AA+ L E+GA + THG+LSS + +E+S + E+V+T+ Sbjct: 248 RIAIMVDDIIDDVQSFVAAAEVLKERGAYKIYVMATHGLLSSDAPRLLEESPIDEVVVTN 307 Query: 270 SIQPTDLVK-SSAKIRILTIAQLMGEAINRTFEERSISSLF 309 ++ P ++ K KI+ + I+ ++ EAI R S+S LF Sbjct: 308 TV-PHEVQKLQCHKIKTVDISLIISEAIRRIHNGESMSYLF 347 >gnl|CDD|143924 pfam00156, Pribosyltran, Phosphoribosyl transferase domain. This family includes a range of diverse phosphoribosyl transferase enzymes. This family includes: Adenine phosphoribosyltransferase EC:2.4.2.7. Hypoxanthine-guanine-xanthine phosphoribosyltransferase. Hypoxanthine phosphoribosyltransferase EC:2.4.2.8. Ribose-phosphate pyrophosphokinase i EC:2.7.6.1. Amidophosphoribosyltransferase EC:2.4.2.14. Orotate phosphoribosyltransferase EC:2.4.2.10. Uracil phosphoribosyltransferase EC:2.4.2.9. Xanthine-guanine phosphoribosyltransferase EC:2.4.2.22. In Arabidopsis, At the very N-terminus of this domain is the ATP-GTP-binding domain. Length = 123 Score = 66.2 bits (162), Expect = 1e-11 Identities = 33/109 (30%), Positives = 51/109 (46%), Gaps = 10/109 (9%) Query: 147 ILERDIKERNDISNLMVVSPDVGGVVRARALAKRLGCLLAIVDKRREHP---------GK 197 L I+E I ++V GG+ A ALA+ LG L +V KR P Sbjct: 16 ALAEKIREEG-IDPDVIVGIARGGIPLATALARELGIPLVLVRKRISLPSSIKSRGGESV 74 Query: 198 IEVMNIIGKVEGKDCILIDDIVDTGGTLCGAADALYEQGALSVTAYITH 246 + + ++GK +++DD++DTGGTL A + L + GA V + Sbjct: 75 TLLSRLPELLKGKRVLIVDDVLDTGGTLRAAVELLKKAGAKVVGVAVLV 123 >gnl|CDD|31242 COG1040, ComFC, Predicted amidophosphoribosyltransferases [General function prediction only]. Length = 225 Score = 45.8 bits (108), Expect = 2e-05 Identities = 28/85 (32%), Positives = 39/85 (45%), Gaps = 18/85 (21%) Query: 174 ARALAKRLGCLLAIV--------------DKRREHPGKIEVMNIIGKVEG-KDCILIDDI 218 ARALA+RLG +A+ ++RR G + +E K+ +L+DD+ Sbjct: 137 ARALARRLGKPIALRRVKDTSPQQGLKALERRRNLKGAFRL---KKGIEEPKNVLLVDDV 193 Query: 219 VDTGGTLCGAADALYEQGALSVTAY 243 TG TL AA L E GA V Sbjct: 194 YTTGATLKEAAKLLREAGAKRVFVL 218 >gnl|CDD|30849 COG0503, Apt, Adenine/guanine phosphoribosyltransferases and related PRPP-binding proteins [Nucleotide transport and metabolism]. Length = 179 Score = 44.9 bits (106), Expect = 3e-05 Identities = 28/120 (23%), Positives = 49/120 (40%), Gaps = 16/120 (13%) Query: 134 FFDIPT--DNLYALPILERDIKERNDISNL-MVVSPDVGGVVRARALAKRLGCLLAIVDK 190 F DI + L L ++ ER + +V+ + G+ A A+A LG V K Sbjct: 25 FVDITLLLGDPELLAKLIDELAERYKDDGIDKIVTIEARGIPLAAAVALELGVPFVPVRK 84 Query: 191 RREHPGK-----------IEVMNIIGKV--EGKDCILIDDIVDTGGTLCGAADALYEQGA 237 + + P + E + + G +++DD++ TGGT + L + GA Sbjct: 85 KGKLPEESVVETYYLEYGSETLELHKDALKPGDRVLIVDDLLATGGTALALIELLEQAGA 144 >gnl|CDD|30809 COG0461, PyrE, Orotate phosphoribosyltransferase [Nucleotide transport and metabolism]. Length = 201 Score = 41.8 bits (98), Expect = 3e-04 Identities = 26/84 (30%), Positives = 43/84 (51%), Gaps = 1/84 (1%) Query: 162 MVVSPDVGGVVRARALAKRLGCLLAIVDKRREHPGKIEVMNIIGK-VEGKDCILIDDIVD 220 +V P +GG+ A A A L L + R+E I G V+G+ ++++D++ Sbjct: 64 VVAGPALGGIPLAAATALALAHLPPMAYVRKEAKDHGTGGLIEGGEVKGEKVVVVEDVIT 123 Query: 221 TGGTLCGAADALYEQGALSVTAYI 244 TGG++ A +AL E GA V + Sbjct: 124 TGGSILEAVEALREAGAEVVGVAV 147 >gnl|CDD|31197 COG0856, COG0856, Orotate phosphoribosyltransferase homologs [Nucleotide transport and metabolism]. Length = 203 Score = 41.5 bits (97), Expect = 3e-04 Identities = 29/87 (33%), Positives = 43/87 (49%), Gaps = 5/87 (5%) Query: 163 VVSPDVGGVVRARALAKRLGCLLAIVDKRR----EHPGKIEVMNI-IGKVEGKDCILIDD 217 VV + GV A +A LG LAI R+ E GK ++ VEGK C+++DD Sbjct: 90 VVGIAISGVPLATMVAYELGKELAIYHPRKHRKDEGAGKGGSISSNFASVEGKRCVIVDD 149 Query: 218 IVDTGGTLCGAADALYEQGALSVTAYI 244 ++ TG T+ + L E+G V + Sbjct: 150 VITTGSTIKETIEQLKEEGGKPVLVVV 176 >gnl|CDD|30979 COG0634, Hpt, Hypoxanthine-guanine phosphoribosyltransferase [Nucleotide transport and metabolism]. Length = 178 Score = 38.5 bits (90), Expect = 0.002 Identities = 24/102 (23%), Positives = 43/102 (42%), Gaps = 8/102 (7%) Query: 148 LERDIKERNDISNLMVVSPDVGGVVRARALAKRLGCLLAI--VDKRREHPGKIE------ 199 L I E + +VV G L + + L + + G Sbjct: 24 LAAQITEDYGGKDPLVVGVLKGSFPFMADLIRAIDFPLEVDFMHVSSYGGGTSSSGEVKI 83 Query: 200 VMNIIGKVEGKDCILIDDIVDTGGTLCGAADALYEQGALSVT 241 + ++ ++G+D ++++DI+D+G TL D L E+GA SV Sbjct: 84 LKDLDEDIKGRDVLIVEDIIDSGLTLSKVRDLLKERGAKSVR 125 >gnl|CDD|32417 COG2236, COG2236, Predicted phosphoribosyltransferases [General function prediction only]. Length = 192 Score = 37.3 bits (86), Expect = 0.005 Identities = 29/93 (31%), Positives = 45/93 (48%), Gaps = 9/93 (9%) Query: 148 LERDIKERNDISNLMVVSPDVGGVVRARALAKRLGC--LLAIVDKR----REHPGKIEVM 201 L I+ +++V GG++ AR L+ LG L +I + E G+ +V Sbjct: 19 LAEKIRASGFKPDVIVAIAR-GGLIPARILSDFLGVKPLYSIKVEHYDETAERDGEAKVK 77 Query: 202 NII--GKVEGKDCILIDDIVDTGGTLCGAADAL 232 I + GK +++DDIVDTG TL A + L Sbjct: 78 YPITIDPLSGKKVLIVDDIVDTGETLELALEEL 110 >gnl|CDD|32248 COG2065, PyrR, Pyrimidine operon attenuation protein/uracil phosphoribosyltransferase [Nucleotide transport and metabolism]. Length = 179 Score = 36.7 bits (85), Expect = 0.008 Identities = 31/102 (30%), Positives = 47/102 (46%), Gaps = 18/102 (17%) Query: 152 IKERN-DISNLMVVSPDVGGVVRARALAKRLGCL------LAIVD----------KRREH 194 I ERN + NL++V GV A LA+R+ L + +D K Sbjct: 23 IIERNKGLDNLVLVGIKTRGVPLAERLAERIEELEGIEVPVGELDITLYRDDLTQKGPLR 82 Query: 195 PGKIEVMNIIGKVEGKDCILIDDIVDTGGTLCGAADALYEQG 236 P + + + + GK IL+DD++ TG T+ A DAL + G Sbjct: 83 P-QAKTTILPFDITGKRVILVDDVLYTGRTIRAALDALVDYG 123 >gnl|CDD|36924 KOG1712, KOG1712, KOG1712, Adenine phosphoribosyl transferases [Nucleotide transport and metabolism]. Length = 183 Score = 34.1 bits (78), Expect = 0.045 Identities = 19/74 (25%), Positives = 35/74 (47%), Gaps = 13/74 (17%) Query: 177 LAKRLGCLLAIVDKRREHPGKI-----------EVMNI-IGKVE-GKDCILIDDIVDTGG 223 +A LG + K + PG++ + + G ++ G+ +++DD++ TGG Sbjct: 77 IALALGAGFVPIRKPGKLPGEVISESYELEYGEDRFEMQKGAIKPGQRVVVVDDLLATGG 136 Query: 224 TLCGAADALYEQGA 237 TL A + L GA Sbjct: 137 TLAAATELLERVGA 150 >gnl|CDD|143409 cd07090, ALDH_F9_TMBADH, NAD+-dependent 4-trimethylaminobutyraldehyde dehydrogenase, ALDH family 9A1. NAD+-dependent, 4-trimethylaminobutyraldehyde dehydrogenase (TMABADH, EC=1.2.1.47), also known as aldehyde dehydrogenase family 9 member A1 (ALDH9A1) in humans, is a cytosolic tetramer which catalyzes the oxidation of gamma-aminobutyraldehyde involved in 4-aminobutyric acid (GABA) biosynthesis and also oxidizes betaine aldehyde (gamma-trimethylaminobutyraldehyde) which is involved in carnitine biosynthesis. Length = 457 Score = 31.9 bits (73), Expect = 0.24 Identities = 12/21 (57%), Positives = 18/21 (85%) Query: 97 KPSPRTPISAKLVANLITQAG 117 KPSP TP++A L+A ++T+AG Sbjct: 150 KPSPFTPLTALLLAEILTEAG 170 >gnl|CDD|143395 cd06534, ALDH-SF, NAD(P)+-dependent aldehyde dehydrogenase superfamily. The aldehyde dehydrogenase superfamily (ALDH-SF) of NAD(P)+-dependent enzymes, in general, oxidize a wide range of endogenous and exogenous aliphatic and aromatic aldehydes to their corresponding carboxylic acids and play an important role in detoxification. Besides aldehyde detoxification, many ALDH isozymes possess multiple additional catalytic and non-catalytic functions such as participating in metabolic pathways, or as binding proteins, or osmoregulants, to mention a few. The enzyme has three domains, a NAD(P)+ cofactor-binding domain, a catalytic domain, and a bridging domain; and the active enzyme is generally either homodimeric or homotetrameric. The catalytic mechanism is proposed to involve cofactor binding, resulting in a conformational change and activation of an invariant catalytic cysteine nucleophile. The cysteine and aldehyde substrate form an oxyanion thiohemiacetal intermediate resulting in hydride transfer to the cofactor and formation of a thioacylenzyme intermediate. Hydrolysis of the thioacylenzyme and release of the carboxylic acid product occurs, and in most cases, the reduced cofactor dissociates from the enzyme. The evolutionary phylogenetic tree of ALDHs appears to have an initial bifurcation between what has been characterized as the classical aldehyde dehydrogenases, the ALDH family (ALDH) and extended family members or aldehyde dehydrogenase-like (ALDH-L) proteins. The ALDH proteins are represented by enzymes which share a number of highly conserved residues necessary for catalysis and cofactor binding and they include such proteins as retinal dehydrogenase, 10-formyltetrahydrofolate dehydrogenase, non-phosphorylating glyceraldehyde 3-phosphate dehydrogenase, delta(1)-pyrroline-5-carboxylate dehydrogenases, alpha-ketoglutaric semialdehyde dehydrogenase, alpha-aminoadipic semialdehyde dehydrogenase, coniferyl aldehyde dehydrogenase and succinate-semialdehyde dehydrogenase. Included in this larger group are all human, Arabidopsis, Tortula, fungal, protozoan, and Drosophila ALDHs identified in families ALDH1 through ALDH22 with the exception of families ALDH18, ALDH19, and ALDH20 which are present in the ALDH-like group. The ALDH-like group is represented by such proteins as gamma-glutamyl phosphate reductase, LuxC-like acyl-CoA reductase, and coenzyme A acylating aldehyde dehydrogenase. All of these proteins have a conserved cysteine that aligns with the catalytic cysteine of the ALDH group. Length = 367 Score = 31.4 bits (72), Expect = 0.30 Identities = 10/23 (43%), Positives = 15/23 (65%) Query: 97 KPSPRTPISAKLVANLITQAGAD 119 KPS TP++A +A L+ +AG Sbjct: 126 KPSELTPLTALALAELLQEAGLP 148 >gnl|CDD|143397 cd07078, ALDH, NAD(P)+ dependent aldehyde dehydrogenase family. The aldehyde dehydrogenase family (ALDH) of NAD(P)+ dependent enzymes, in general, oxidize a wide range of endogenous and exogenous aliphatic and aromatic aldehydes to their corresponding carboxylic acids and play an important role in detoxification. Besides aldehyde detoxification, many ALDH isozymes possess multiple additional catalytic and non-catalytic functions such as participating in metabolic pathways, or as binding proteins, or as osmoregulants, to mention a few. The enzyme has three domains, a NAD(P)+ cofactor-binding domain, a catalytic domain, and a bridging domain; and the active enzyme is generally either homodimeric or homotetrameric. The catalytic mechanism is proposed to involve cofactor binding, resulting in a conformational change and activation of an invariant catalytic cysteine nucleophile. The cysteine and aldehyde substrate form an oxyanion thiohemiacetal intermediate resulting in hydride transfer to the cofactor and formation of a thioacylenzyme intermediate. Hydrolysis of the thioacylenzyme and release of the carboxylic acid product occurs, and in most cases, the reduced cofactor dissociates from the enzyme. The evolutionary phylogenetic tree of ALDHs appears to have an initial bifurcation between what has been characterized as the classical aldehyde dehydrogenases, the ALDH family (ALDH) and extended family members or aldehyde dehydrogenase-like (ALDH-like) proteins. The ALDH proteins are represented by enzymes which share a number of highly conserved residues necessary for catalysis and cofactor binding and they include such proteins as retinal dehydrogenase, 10-formyltetrahydrofolate dehydrogenase, non-phosphorylating glyceraldehyde 3-phosphate dehydrogenase, delta(1)-pyrroline-5-carboxylate dehydrogenases, alpha-ketoglutaric semialdehyde dehydrogenase, alpha-aminoadipic semialdehyde dehydrogenase, coniferyl aldehyde dehydrogenase and succinate-semialdehyde dehydrogenase. Included in this larger group are all human, Arabidopsis, Tortula, fungal, protozoan, and Drosophila ALDHs identified in families ALDH1 through ALDH22 with the exception of families ALDH18, ALDH19, and ALDH20 which are present in the ALDH-like group. Length = 432 Score = 30.3 bits (69), Expect = 0.82 Identities = 11/23 (47%), Positives = 16/23 (69%) Query: 97 KPSPRTPISAKLVANLITQAGAD 119 KPS TP++A L+A L+ +AG Sbjct: 130 KPSELTPLTALLLAELLAEAGLP 152 >gnl|CDD|143404 cd07085, ALDH_F6_MMSDH, Methylmalonate semialdehyde dehydrogenase and ALDH family members 6A1 and 6B2. Methylmalonate semialdehyde dehydrogenase (MMSDH, EC=1.2.1.27) [acylating] from Bacillus subtilis is involved in valine metabolism and catalyses the NAD+- and CoA-dependent oxidation of methylmalonate semialdehyde into propionyl-CoA. Mitochondrial human MMSDH ALDH6A1 and Arabidopsis MMSDH ALDH6B2 are also present in this CD. Length = 478 Score = 29.4 bits (67), Expect = 1.2 Identities = 10/21 (47%), Positives = 14/21 (66%) Query: 97 KPSPRTPISAKLVANLITQAG 117 KPS R P +A +A L+ +AG Sbjct: 170 KPSERVPGAAMRLAELLQEAG 190 >gnl|CDD|143465 cd07147, ALDH_F21_RNP123, Aldehyde dehydrogenase family 21A1-like. Aldehyde dehydrogenase ALDH21A1 (gene name RNP123) was first described in the moss Tortula ruralis and is believed to play an important role in the detoxification of aldehydes generated in response to desiccation- and salinity-stress, and ALDH21A1 expression represents a unique stress tolerance mechanism. So far, of plants, only the bryophyte sequence has been observed, but similar protein sequences from bacteria and archaea are also present in this CD. Length = 452 Score = 29.1 bits (66), Expect = 1.7 Identities = 8/21 (38%), Positives = 15/21 (71%) Query: 97 KPSPRTPISAKLVANLITQAG 117 KP+ RTP+SA ++ ++ + G Sbjct: 157 KPASRTPLSALILGEVLAETG 177 >gnl|CDD|143457 cd07139, ALDH_AldA-Rv0768, Mycobacterium tuberculosis aldehyde dehydrogenase AldA-like. The Mycobacterium tuberculosis NAD+-dependent, aldehyde dehydrogenase PDB structure, 3B4W, and the Mycobacterium tuberculosis H37Rv aldehyde dehydrogenase AldA (locus Rv0768) sequence, as well as the Rhodococcus rhodochrous ALDH involved in haloalkane catabolism, and other similar sequences, are included in this CD. Length = 471 Score = 28.7 bits (65), Expect = 1.9 Identities = 11/21 (52%), Positives = 14/21 (66%) Query: 97 KPSPRTPISAKLVANLITQAG 117 KPSP TP+ A L+A +AG Sbjct: 171 KPSPETPLDAYLLAEAAEEAG 191 >gnl|CDD|37661 KOG2450, KOG2450, KOG2450, Aldehyde dehydrogenase [Energy production and conversion]. Length = 501 Score = 28.7 bits (64), Expect = 2.3 Identities = 9/21 (42%), Positives = 16/21 (76%) Query: 97 KPSPRTPISAKLVANLITQAG 117 KP+ +TP++A +A+L +AG Sbjct: 192 KPAEQTPLTALYLASLCKEAG 212 >gnl|CDD|143467 cd07149, ALDH_y4uC, Uncharacterized ALDH (y4uC) with similarity to Tortula ruralis aldehyde dehydrogenase ALDH21A1. Uncharacterized aldehyde dehydrogenase (ORF name y4uC) with sequence similarity to the moss Tortula ruralis aldehyde dehydrogenase ALDH21A1 (RNP123) believed to play an important role in the detoxification of aldehydes generated in response to desiccation- and salinity-stress, and similar sequences are included in this CD. Length = 453 Score = 28.3 bits (64), Expect = 2.5 Identities = 10/21 (47%), Positives = 16/21 (76%) Query: 97 KPSPRTPISAKLVANLITQAG 117 KP+ +TP+SA +A L+ +AG Sbjct: 157 KPASQTPLSALKLAELLLEAG 177 >gnl|CDD|32109 COG1926, COG1926, Predicted phosphoribosyltransferases [General function prediction only]. Length = 220 Score = 28.3 bits (63), Expect = 2.5 Identities = 15/51 (29%), Positives = 23/51 (45%), Gaps = 2/51 (3%) Query: 209 GKDCILIDDIVDTGGTLCGAADALYEQGALSVTAYITHGVLSSSSIERIEK 259 G+ IL+DD + TG T+ A AL +G + I V + +E Sbjct: 124 GRTVILVDDGIATGATMKAAVRALRAKGPKEI--VIAVPVAPEDAAAELES 172 >gnl|CDD|143464 cd07146, ALDH_PhpJ, Streptomyces putative phosphonoformaldehyde dehydrogenase PhpJ-like. Putative phosphonoformaldehyde dehydrogenase (PhpJ), an aldehyde dehydrogenase homolog reportedly involved in the biosynthesis of phosphinothricin tripeptides in Streptomyces viridochromogenes DSM 40736, and similar sequences are included in this CD. Length = 451 Score = 28.1 bits (63), Expect = 3.2 Identities = 11/21 (52%), Positives = 17/21 (80%) Query: 97 KPSPRTPISAKLVANLITQAG 117 KPS +TP+SA +A+L+ +AG Sbjct: 154 KPSEKTPLSAIYLADLLYEAG 174 >gnl|CDD|143443 cd07125, ALDH_PutA-P5CDH, Delta(1)-pyrroline-5-carboxylate dehydrogenase, PutA. The proline catabolic enzymes of the aldehyde dehydrogenase (ALDH) protein superfamily, proline dehydrogenase and Delta(1)-pyrroline-5-carboxylate dehydrogenase (P5CDH, (EC=1.5.1.12 )), catalyze the two-step oxidation of proline to glutamate; P5CDH catalyzes the oxidation of glutamate semialdehyde, utilizing NAD+ as the electron acceptor. In some bacteria, the two enzymes are fused into the bifunctional flavoenzyme, proline utilization A (PutA) These enzymes play important roles in cellular redox control, superoxide generation, and apoptosis. In certain prokaryotes such as Escherichia coli, PutA is also a transcriptional repressor of the proline utilization genes. Length = 518 Score = 27.9 bits (63), Expect = 3.4 Identities = 24/102 (23%), Positives = 40/102 (39%), Gaps = 35/102 (34%) Query: 97 KPSPRTPISAKLVANLITQAGADRVIMLDLHAGQVQGFFDIPTDNLYALPILERDIKERN 156 KP+ +TP+ A L+ +AG +P D L +P + Sbjct: 201 KPAEQTPLIAARAVELLHEAG-------------------VPRDVLQLVP------GDGE 235 Query: 157 DISNLMVVSPDVGGVVR----------ARALAKRLGCLLAIV 188 +I +V P + GV+ RALA+R G +L ++ Sbjct: 236 EIGEALVAHPRIDGVIFTGSTETAKLINRALAERDGPILPLI 277 >gnl|CDD|143421 cd07103, ALDH_F5_SSADH_GabD, Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like. Succinate-semialdehyde dehydrogenase, mitochondrial (SSADH, GabD, EC=1.2.1.24) catalyzes the NAD+-dependent oxidation of succinate semialdehyde (SSA) to succinate. This group includes the human aldehyde dehydrogenase family 5 member A1 (ALDH5A1) which is a mitochondrial homotetramer that converts SSA to succinate in the last step of 4-aminobutyric acid (GABA) catabolism. This CD also includes the Arabidopsis SSADH gene product ALDH5F1. Mutations in this gene result in the accumulation of H2O2, suggesting a role in plant defense against the environmental stress of elevated reactive oxygen species. Length = 451 Score = 28.2 bits (64), Expect = 3.5 Identities = 10/21 (47%), Positives = 14/21 (66%) Query: 97 KPSPRTPISAKLVANLITQAG 117 KP+ TP+SA +A L +AG Sbjct: 151 KPAEETPLSALALAELAEEAG 171 >gnl|CDD|143410 cd07091, ALDH_F1-2_Ald2-like, ALDH subfamily: ALDH families 1and 2, including 10-formyltetrahydrofolate dehydrogenase, NAD+-dependent retinal dehydrogenase 1 and related proteins. ALDH subfamily which includes the NAD+-dependent retinal dehydrogenase 1 (RALDH 1, ALDH1, EC=1.2.1.36), also known as aldehyde dehydrogenase family 1 member A1 (ALDH1A1), in humans, a homotetrameric, cytosolic enzyme that catalyzes the oxidation of retinaldehyde to retinoic acid. Human ALDH1B1 and ALDH2 are also in this cluster; both are mitochrondrial homotetramers which play important roles in acetaldehyde oxidation; ALDH1B1 in response to UV light exposure and ALDH2 during ethanol metabolism. 10-formyltetrahydrofolate dehydrogenase (FTHFDH, EC=1.5.1.6), also known as aldehyde dehydrogenase family 1 member L1 (ALDH1L1), in humans, a multi-domain homotetramer with an N-terminal formyl transferase domain and a C-terminal ALDH domain. FTHFDH catalyzes an NADP+-dependent dehydrogenase reaction resulting in the conversion of 10-formyltetrahydrofolate to tetrahydrofolate and CO2. Also included in this subfamily is the Arabidosis aldehyde dehydrogenase family 2 members B4 and B7 (EC=1.2.1.3), which are mitochondrial, homotetramers that oxidize acetaldehyde and glycolaldehyde, as well as, the Arabidosis cytosolic, homotetramer ALDH2C4 (EC=1.2.1.3), an enzyme involved in the oxidation of sinapalehyde and coniferaldehyde. Also included is the AldA aldehyde dehydrogenase of Aspergillus nidulans (locus AN0554), the aldehyde dehydrogenase 2 (YMR170c, ALD5, EC=1.2.1.5) of Saccharomyces cerevisiae, and other similar sequences. Length = 476 Score = 27.9 bits (63), Expect = 3.6 Identities = 11/21 (52%), Positives = 16/21 (76%) Query: 97 KPSPRTPISAKLVANLITQAG 117 KP+ +TP+SA +A LI +AG Sbjct: 175 KPAEQTPLSALYLAELIKEAG 195 >gnl|CDD|143408 cd07089, ALDH_CddD-AldA-like, Rhodococcus ruber 6-oxolauric acid dehydrogenase-like and related proteins. The 6-oxolauric acid dehydrogenase (CddD) from Rhodococcus ruber SC1 which converts 6-oxolauric acid to dodecanedioic acid; and the aldehyde dehydrogenase (locus SSP0762) from Staphylococcus saprophyticus subsp. saprophyticus ATCC 15305 and also, the Mycobacterium tuberculosis H37Rv ALDH AldA (locus Rv0768) sequence; and other similar sequences, are included in this CD. Length = 459 Score = 28.0 bits (63), Expect = 4.0 Identities = 9/21 (42%), Positives = 14/21 (66%) Query: 97 KPSPRTPISAKLVANLITQAG 117 KP+P TP+SA L+ +I + Sbjct: 157 KPAPDTPLSALLLGEIIAETD 177 >gnl|CDD|143459 cd07141, ALDH_F1AB_F2_RALDH1, NAD+-dependent retinal dehydrogenase 1, ALDH families 1A, 1B, and 2-like. NAD+-dependent retinal dehydrogenase 1 (RALDH 1, ALDH1, EC=1.2.1.36) also known as aldehyde dehydrogenase family 1 member A1 (ALDH1A1) in humans, is a homotetrameric, cytosolic enzyme that catalyzes the oxidation of retinaldehyde to retinoic acid. Human ALDH1B1 and ALDH2 are also in this cluster; both are mitochrondrial homotetramers which play important roles in acetaldehyde oxidation; ALDH1B1 in response to UV light exposure and ALDH2 during ethanol metabolism. Length = 481 Score = 27.7 bits (62), Expect = 4.6 Identities = 10/21 (47%), Positives = 17/21 (80%) Query: 97 KPSPRTPISAKLVANLITQAG 117 KP+ +TP++A +A+LI +AG Sbjct: 179 KPAEQTPLTALYLASLIKEAG 199 >gnl|CDD|143412 cd07093, ALDH_F8_HMSADH, Human aldehyde dehydrogenase family 8 member A1-like. In humans, the aldehyde dehydrogenase family 8 member A1 (ALDH8A1) protein functions to convert 9-cis-retinal to 9-cis-retinoic acid and has a preference for NAD+. Also included in this CD is the 2-hydroxymuconic semialdehyde dehydrogenase (HMSADH) which catalyzes the conversion of 2-hydroxymuconic semialdehyde to 4-oxalocrotonate, a step in the meta cleavage pathway of aromatic hydrocarbons in bacteria. Such HMSADHs seen here are: XylG of the TOL plasmid pWW0 of Pseudomonas putida, TomC of Burkholderia cepacia G4, and AphC of Comamonas testosterone. Length = 455 Score = 27.5 bits (62), Expect = 4.8 Identities = 11/21 (52%), Positives = 15/21 (71%) Query: 97 KPSPRTPISAKLVANLITQAG 117 KPS TP++A L+A L +AG Sbjct: 151 KPSEWTPLTAWLLAELANEAG 171 >gnl|CDD|143442 cd07124, ALDH_PutA-P5CDH-RocA, Delta(1)-pyrroline-5-carboxylate dehydrogenase, RocA. Delta(1)-pyrroline-5-carboxylate dehydrogenase (EC=1.5.1.12 ), RocA: a proline catabolic enzyme of the aldehyde dehydrogenase (ALDH) protein superfamily. The proline catabolic enzymes, proline dehydrogenase and Delta(1)-pyrroline-5-carboxylate dehydrogenase (P5CDH), catalyze the two-step oxidation of proline to glutamate; P5CDH catalyzes the oxidation of glutamate semialdehyde, utilizing NAD+ as the electron acceptor. In some bacteria, the two enzymes are fused into the bifunctional flavoenzyme, proline utilization A (PutA). In this CD, monofunctional enzyme sequences such as seen in the Bacillus subtilis RocA P5CDH are also present. These enzymes play important roles in cellular redox control, superoxide generation, and apoptosis. Length = 512 Score = 27.2 bits (61), Expect = 6.3 Identities = 7/21 (33%), Positives = 13/21 (61%) Query: 97 KPSPRTPISAKLVANLITQAG 117 KP+ TP+ A + ++ +AG Sbjct: 200 KPAEDTPVIAAKLVEILEEAG 220 >gnl|CDD|144841 pfam01398, Mov34, Mov34/MPN/PAD-1 family. Members of this family are found in proteasome regulatory subunits, eukaryotic initiation factor 3 (eIF3) subunits and regulators of transcription factors. This family is also known as the MPN domain and PAD-1-like domain. It has been shown that this domain occurs in prokaryotes. Length = 117 Score = 27.0 bits (60), Expect = 6.4 Identities = 15/37 (40%), Positives = 20/37 (54%), Gaps = 2/37 (5%) Query: 184 LLAIVDK-RREHPGKIEVMNI-IGKVEGKDCILIDDI 218 LL IVD RR K EVM + +G +EG I + + Sbjct: 12 LLKIVDHARRGGKSKEEVMGVLLGTLEGDRVIEVTNS 48 >gnl|CDD|38577 KOG3367, KOG3367, KOG3367, Hypoxanthine-guanine phosphoribosyltransferase [Nucleotide transport and metabolism]. Length = 216 Score = 27.1 bits (59), Expect = 6.8 Identities = 11/32 (34%), Positives = 17/32 (53%) Query: 209 GKDCILIDDIVDTGGTLCGAADALYEQGALSV 240 GK+ ++++DIVDTG TL + V Sbjct: 125 GKNVLIVEDIVDTGRTLSTLLSHMKAYKPSMV 156 >gnl|CDD|34675 COG5071, RPN5, 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]. Length = 439 Score = 26.9 bits (59), Expect = 7.1 Identities = 11/52 (21%), Positives = 23/52 (44%) Query: 141 NLYALPILERDIKERNDISNLMVVSPDVGGVVRARALAKRLGCLLAIVDKRR 192 NL L I E+ +++ +D S V + ++ + + L L + K+ Sbjct: 31 NLEKLLIFEKKVRQASDTSTNTKVLIYIADLLFSAGDFQGLNEQLVSLFKKH 82 >gnl|CDD|143938 pfam00171, Aldedh, Aldehyde dehydrogenase family. This family of dehydrogenases act on aldehyde substrates. Members use NADP as a cofactor. The family includes the following members: The prototypical members are the aldehyde dehydrogenases EC:1.2.1.3. Succinate-semialdehyde dehydrogenase EC:1.2.1.16. Lactaldehyde dehydrogenase EC:1.2.1.22. Benzaldehyde dehydrogenase EC:1.2.1.28. Methylmalonate-semialdehyde dehydrogenase EC:1.2.1.27. Glyceraldehyde-3-phosphate dehydrogenase EC:1.2.1.9. Delta-1-pyrroline-5-carboxylate dehydrogenase EC: 1.5.1.12. Acetaldehyde dehydrogenase EC:1.2.1.10. Glutamate-5-semialdehyde dehydrogenase EC:1.2.1.41. This family also includes omega crystallin, an eye lens protein from squid and octopus that has little aldehyde dehydrogenase activity. Length = 459 Score = 26.7 bits (60), Expect = 7.4 Identities = 11/21 (52%), Positives = 15/21 (71%) Query: 97 KPSPRTPISAKLVANLITQAG 117 KPS TP++A L+A L +AG Sbjct: 160 KPSELTPLTALLLAELFEEAG 180 >gnl|CDD|30384 COG0035, Upp, Uracil phosphoribosyltransferase [Nucleotide transport and metabolism]. Length = 210 Score = 26.7 bits (59), Expect = 8.1 Identities = 15/68 (22%), Positives = 32/68 (47%), Gaps = 1/68 (1%) Query: 207 VEGKDCILIDDIVDTGGTLCGAADALYEQGALSVTAYITHGVLSSSSIERIEKSKMKELV 266 ++ + I++D ++ TGG+ A D L ++G + V + I+ +EK+ + Sbjct: 122 IDERTVIVLDPMLATGGSAIAAIDLLKKRGGPKNI-KVVSLVAAPEGIKAVEKAHPDVEI 180 Query: 267 ITDSIQPT 274 T +I Sbjct: 181 YTAAIDEG 188 >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 = 26.6 bits (59), Expect = 8.7 Identities = 13/47 (27%), Positives = 22/47 (46%), Gaps = 5/47 (10%) Query: 219 VDTGGTLCGAADALYEQGA-----LSVTAYITHGVLSSSSIERIEKS 260 + GTL L +G L V+A+ + V+S S+ +I+K Sbjct: 117 ANGAGTLLSGGRRLRLRGGEINHHLGVSAFAEYAVVSRRSVVKIDKD 163 >gnl|CDD|143462 cd07144, ALDH_ALD2-YMR170C, Saccharomyces cerevisiae aldehyde dehydrogenase 2 (YMR170c)-like. NAD(P)+-dependent Saccharomyces cerevisiae aldehyde dehydrogenase 2 (YMR170c, ALD5, EC=1.2.1.5) and other similar sequences, are present in this CD. Length = 484 Score = 26.6 bits (59), Expect = 9.7 Identities = 10/21 (47%), Positives = 14/21 (66%) Query: 97 KPSPRTPISAKLVANLITQAG 117 KP+ TP+S ANL+ +AG Sbjct: 178 KPAENTPLSLLYFANLVKEAG 198 >gnl|CDD|176187 cd05284, arabinose_DH_like, D-arabinose dehydrogenase. This group contains arabinose dehydrogenase (AraDH) and related alcohol dehydrogenases. AraDH is a member of the medium chain dehydrogenase/reductase family and catalyzes the NAD(P)-dependent oxidation of D-arabinose and other pentoses, the initial step in the metabolism of d-arabinose into 2-oxoglutarate. Like the alcohol dehydrogenases, AraDH binds a zinc in the catalytic cleft as well as a distal structural zinc. AraDH forms homotetramers as a dimer of dimers. AraDH replaces a conserved catalytic His with replace with Arg, compared to the canonical ADH site. 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 = 340 Score = 26.4 bits (59), Expect = 9.8 Identities = 35/132 (26%), Positives = 55/132 (41%), Gaps = 12/132 (9%) Query: 174 ARALAKRLGC--LLAIVDKRREHPGKIEVMNIIGKVEGKDCILIDDIVDTGGTLCGAADA 231 A LA+RLG +L D E EV + G G D ++ D V + TL AA Sbjct: 204 ALKLAERLGADHVLNASDDVVE-----EVRELTGGR-GADAVI--DFVGSDETLALAAKL 255 Query: 232 LYEQGALSVTAYITHGVLSSSSIERIEKSKMKELVITDSIQPTDLVKSSAKIRI-LTIAQ 290 L + G + Y HG L +S + E S + L T + ++V + ++ + I + Sbjct: 256 LAKGGRYVIVGYGGHGRLPTSDLVPTEISVIGSLWGTRAEL-VEVVALAESGKVKVEITK 314 Query: 291 LMGEAINRTFEE 302 E N + Sbjct: 315 FPLEDANEALDR 326 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 0.321 0.137 0.385 Gapped Lambda K H 0.267 0.0727 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 3,570,517 Number of extensions: 188402 Number of successful extensions: 573 Number of sequences better than 10.0: 1 Number of HSP's gapped: 563 Number of HSP's successfully gapped: 57 Length of query: 310 Length of database: 6,263,737 Length adjustment: 94 Effective length of query: 216 Effective length of database: 4,232,491 Effective search space: 914218056 Effective search space used: 914218056 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 (21.8 bits) S2: 57 (25.7 bits)