RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254781091|ref|YP_003065504.1| putative pyridoxal-phosphate-dependent aminotransferase protein [Candidatus Liberibacter asiaticus str. psy62] (383 letters) >gnl|CDD|31301 COG1104, NifS, Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]. Length = 386 Score = 381 bits (980), Expect = e-106 Identities = 156/382 (40%), Positives = 227/382 (59%), Gaps = 12/382 (3%) Query: 3 KRVYLDWNATAPLLEVVRQSFVKSLD-FYGNPSSVHKEGQKTRLYIEESRRIIADFCGAK 61 +YLD AT P+ V ++ + L +GNPSS+H G++ R +EE+R IA GA Sbjct: 1 MMIYLDNAATTPVDPEVLEAMLPYLTEVFGNPSSLHSFGREARKAVEEAREQIAKLLGAD 60 Query: 62 PDHVVFTSSATEAANWVLTPHFYQGSHKISIDSLYISAIEHPAVYAGGHFPSH---KIHK 118 P+ ++FTS ATE+ N + + + SAIEHPAV + ++ Sbjct: 61 PEEIIFTSGATESNNLAIKGAALAYRNAQKGKHIITSAIEHPAVLNTCRYLERQGFEVTY 120 Query: 119 IPVLSKGIVDIQALTDFLEQRNSTCGIPMIAVMFVNNETGVIQPIKEIAQIVKEYQGILV 178 +PV S G+VD++ L + L ++++M NNETG IQPI EI +I KE + Sbjct: 121 LPVDSNGLVDLEQLEEALRPDT-----ILVSIMHANNETGTIQPIAEIGEICKERGILFH 175 Query: 179 VDAVQAAGRIPLSIEEIKADFLIISSHKLGAPVGAGALVFREDILLPSPLLRGGDQEKGQ 238 VDAVQA G+IP+ +EE+ D L S+HK G P G GAL R + L PL+ GG QE+G Sbjct: 176 VDAVQAVGKIPIDLEELGVDLLSFSAHKFGGPKGIGALYVRPGVRL-EPLIHGGGQERGL 234 Query: 239 RAGTENYAVIGGFAVAAQQMVKDIQKRSSRVFAIRDYLEQELKKLIPNIIIYGKDAERIS 298 R+GTEN I GF AA+ V+++++ ++R+ +RD LE L ++IP++ + G D R+ Sbjct: 235 RSGTENVPGIVGFGKAAEIAVEELEEENARLRKLRDRLEDGLLEIIPDVYLNGDDEPRLP 294 Query: 299 NTCCFSIPFLKAEVLQIALDLEGIAVSAGSACSSGKIKKNHVLAAMGFD--TSQGAVRVS 356 N FS P ++ E L +ALDL GIAVS GSACSSG ++ +HVL AMG + G++R S Sbjct: 295 NILNFSFPGVEGESLLLALDLAGIAVSTGSACSSGSLEPSHVLRAMGISEELAHGSIRFS 354 Query: 357 CGDSTTQEDIDIFLNALQKIIR 378 G TT+E+ID AL++II+ Sbjct: 355 LGRFTTEEEIDAAAEALKEIIK 376 >gnl|CDD|144011 pfam00266, Aminotran_5, Aminotransferase class-V. This domain is found in amino transferases, and other enzymes including cysteine desulphurase EC:4.4.1.-. Length = 371 Score = 216 bits (552), Expect = 9e-57 Identities = 115/393 (29%), Positives = 169/393 (43%), Gaps = 50/393 (12%) Query: 5 VYLDWNATAPLLEVVRQSFVK-SLDFYGNP-SSVHKEGQKTRLYIEESRRIIADFCGAKP 62 +YLD AT + V + + D+ GN VH G++ EE+R +A+F A Sbjct: 1 IYLDSAATTQKPQAVLDALQEYYTDYNGNVHRGVHHLGKEATQAYEEAREKVAEFINAPS 60 Query: 63 DH-VVFTSSATEAANWV---LTPHFYQGSHKISIDSLYISAIEH-----PAVYAGGHFPS 113 D ++FTS TEA N V L G D + ++ +EH P + Sbjct: 61 DEEIIFTSGTTEAINLVAISLGRRLKPG------DEILVTEMEHHANLVPWQELAKRTGA 114 Query: 114 HKIHKIPVLSKGIVDIQALTDFLEQRNSTCGIPMIAVMFVNNETGVIQPIKEIAQIVKEY 173 + IPV G++D+ AL L R T ++A+ V+N TG + P++EI ++ EY Sbjct: 115 -TVRVIPVDPNGLLDLDALEKLLTPR--TK---LVAITHVSNVTGTVNPVEEIGKLAHEY 168 Query: 174 QGILVVDAVQAAGRIPLSIEEIKADFLIISSHKLGAPVGAGALVFREDIL--LPSPLLRG 231 ++VVDA QA G P+ ++ + DFL S HKL P G G L R D+L LP G Sbjct: 169 GALVVVDAAQAVGHRPIDVQALGVDFLAFSGHKLYGPTGIGVLYGRRDLLEKLPPWKGGG 228 Query: 232 G-------DQEKGQ-------RAGTENYAVIGGFAVAAQQMVK-DIQKRSSRVFAIRDYL 276 G QE AGT N A I G A + + ++ + YL Sbjct: 229 GMIDLVSLLQETTFADAPSKFEAGTPNIAGIIGLGAALDYLAEIGLEAIEKHERELAAYL 288 Query: 277 EQELKKLIPNIIIYGKDAERISNTCCFSIPFLKAEVLQIALDLEGIAVSAGSACSSGKIK 336 + L IP I + AER + F+ P + + LD GIAV +G C+ Sbjct: 289 YERLLA-IPGIRLVPAVAERRPSIISFNFPGVHPHDVATLLDERGIAVRSGHHCAQP--- 344 Query: 337 KNHVLAAMGFDTSQGAVRVSCGDSTTQEDIDIF 369 M G +R S T+E++D Sbjct: 345 ------LMERLGVHGTLRASLYFYNTEEEVDRL 371 >gnl|CDD|36762 KOG1549, KOG1549, KOG1549, Cysteine desulfurase NFS1 [Amino acid transport and metabolism]. Length = 428 Score = 208 bits (530), Expect = 2e-54 Identities = 130/383 (33%), Positives = 204/383 (53%), Gaps = 21/383 (5%) Query: 3 KRVYLDWNATAPLLEVVRQSFVKSLD-FYGNPSSVHKEGQKTRLYIEESRRIIADFCGAK 61 + VYLD AT P+ V + + L + GNP S G K +E +R +A A Sbjct: 43 RPVYLDNQATGPMDPRVLDAMLPYLLEYLGNPHS-RSYGWKAEDAVEAAREQVAKLINAD 101 Query: 62 PDHVVFTSSATEAANWVL--TPHFYQGSHKISIDSLYISAIEHPAVYAGGHF---PSHKI 116 P +VFTS ATE+ N VL F+ K I +L EHP V ++ Sbjct: 102 PSDIVFTSGATESNNLVLKGVARFFGDKTKKHIITL---QTEHPCVLDSCRALQEEGLEV 158 Query: 117 HKIPVLSKGIVDIQALTDFLEQRNSTCGIPMIAVMFVNNETGVIQPIKEIAQIVKEYQGI 176 +PV G+VDI L + + + T ++++M VNNE GV+QP+KEI +I +E Sbjct: 159 TYLPVEDSGLVDISKLREAIRSK--TR---LVSIMHVNNEIGVLQPVKEIVKICREEGVQ 213 Query: 177 LVVDAVQAAGRIPLSIEEIKADFLIISSHKLGAPVGAGALVFREDILLP--SPLLRGGDQ 234 + VDA QA G+IP+ ++E+ ADFL IS+HK+ P G GAL R P L GG Q Sbjct: 214 VHVDAAQAVGKIPVDVQELNADFLSISAHKIYGPPGIGALYVRRKRPRLRVEPPLSGGGQ 273 Query: 235 EKGQRAGTENYAVIGGFAVAAQQMVKDIQKRSSRVFAIRDYLEQELKKLIPNIIIYGKDA 294 E+G R+GT + G AA+ + K++ + + + + L + + +P + + G Sbjct: 274 ERGLRSGTVATPLAVGLGSAAEFVNKEMAYDEAIIKRLSEKLLMGIGQSLPEVTLNGSGK 333 Query: 295 ERISNTCCFSIPFLKAEVLQIALDLEGIAVSAGSACSSGKIKKNHVLAAMG--FDTSQGA 352 R S P+++ E L +DL+ +A+S+GSAC+S ++ ++VL A+G D + + Sbjct: 334 SRYPGLVSLSFPYVEGESL--LMDLKDVALSSGSACTSASLEPSYVLRAIGVDEDLAHSS 391 Query: 353 VRVSCGDSTTQEDIDIFLNALQK 375 +R+S G TT+EDID ++A++K Sbjct: 392 IRISIGRYTTEEDIDYLVDAIKK 414 >gnl|CDD|30866 COG0520, CsdB, Selenocysteine lyase [Amino acid transport and metabolism]. Length = 405 Score = 203 bits (517), Expect = 7e-53 Identities = 112/402 (27%), Positives = 179/402 (44%), Gaps = 49/402 (12%) Query: 5 VYLDWNATAPLLEVVRQSFVKSL-DFYGNP-SSVHKEGQKTRLYIEESRRIIADFCGAKP 62 VYLD AT+ + V + + + N H ++ E +R +A F A Sbjct: 24 VYLDNAATSQKPQAVLDAVAEYYRRYNANVHRGAHTLAEEATDLYEAAREAVARFLNADS 83 Query: 63 -DHVVFTSSATEAANWV---LTPHFYQGSHKISIDSLYISAIEHPAVYAGGHFPSH---- 114 D +VFT TEA N V L G D + +S +EH + + Sbjct: 84 SDEIVFTRGTTEALNLVARGLGRSLKPG------DEIVVSDLEHHSNIVPWQELAKRTGA 137 Query: 115 KIHKIPVLSKGIVDIQALTDFLEQRNSTCGIPMIAVMFVNNETGVIQPIKEIAQIVKEYQ 174 K+ IP+ G++D+ AL + + ++A+ V+N TG + P+KEIA++ E+ Sbjct: 138 KVRVIPLDDDGLLDLDALEKLITPKT-----KLVALSHVSNVTGTVNPVKEIAELAHEHG 192 Query: 175 GILVVDAVQAAGRIPLSIEEIKADFLIISSHK-LGAPVGAGALVFREDIL--LPSPLLRG 231 +++VDA QAAG +P+ ++E+ DFL S HK L P G G L R+++L L L G Sbjct: 193 ALVLVDAAQAAGHLPIDVQELGCDFLAFSGHKWLLGPTGIGVLYVRKELLEELEPFLGGG 252 Query: 232 GDQEKGQR--------------AGTENYAVIGGFAVAAQQMVK-DIQKRSSRVFAIRDYL 276 G E R AGT N A G A A +++ ++ + + +YL Sbjct: 253 GMIEYVSRDEGVTLAELPLRFEAGTPNIAGAIGLAAALDYLLEIGMEAIEAHERELTEYL 312 Query: 277 EQELKKLIPNIIIYGKDAERISNTCCFSIPFLKAEVLQIALDLEGIAVSAGSACSSGKIK 336 + L + +P + IYG F++ + + LD +GIAV AG C+ Sbjct: 313 LEGLSE-LPGVEIYGPPDADRGGIVSFNVKGIHPHDVATLLDEKGIAVRAGHHCAQ---- 367 Query: 337 KNHVLAAMGFDTSQGAVRVSCGDSTTQEDIDIFLNALQKIIR 378 + +G D +R S T+ED+D L AL+K + Sbjct: 368 --PLHRLLGVD---ATIRASLHLYNTEEDVDRLLEALKKALA 404 >gnl|CDD|99746 cd06453, SufS_like, Cysteine desulfurase (SufS)-like. This family belongs to the pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to cysteine desulfurase (SufS) and selenocysteine lyase. SufS catalyzes the removal of elemental sulfur and selenium atoms from L-cysteine, L-cystine, L-selenocysteine, and L-selenocystine to produce L-alanine; and selenocysteine lyase catalyzes the decomposition of L-selenocysteine.. Length = 373 Score = 164 bits (417), Expect = 4e-41 Identities = 118/412 (28%), Positives = 180/412 (43%), Gaps = 82/412 (19%) Query: 5 VYLDWNATA----PLLEVVRQSFVKSLDFYGNPS-SVHKEGQK-TRLYIEESRRIIADFC 58 VYLD AT+ P+++ + + + N VH+ + T Y E +R +A F Sbjct: 1 VYLDNAATSQKPQPVIDAIVDYYRH---YNANVHRGVHELSARATDAY-EAAREKVARFI 56 Query: 59 GAK-PDHVVFTSSATEAANWV---LTPHFYQGSHKISIDSLYISAIEHPAVYAGGHFPSH 114 A PD ++FT + TEA N V L G + S +EH + P Sbjct: 57 NAPSPDEIIFTRNTTEAINLVAYGLGRANKPGDEIV------TSVMEHHSN----IVPWQ 106 Query: 115 --------KIHKIPVLSKGIVDIQALTDFLEQRNSTCGIPMIAVMFVNNETGVIQPIKEI 166 K+ +PV G +D++AL L +R ++AV V+N G I P+KEI Sbjct: 107 QLAERTGAKLKVVPVDDDGQLDLEALEKLLTER-----TKLVAVTHVSNVLGTINPVKEI 161 Query: 167 AQIVKEYQGILVVDAVQAAGRIPLSIEEIKADFLIISSHKLGAPVGAGALVFREDILLPS 226 +I E ++VD Q+AG +P+ ++++ DFL S HK+ P G G L +E++L Sbjct: 162 GEIAHEAGVPVLVDGAQSAGHMPVDVQDLGCDFLAFSGHKMLGPTGIGVLYGKEELLEEM 221 Query: 227 PLLRGG-------DQEKGQ--------RAGTENYAVIGGFAVAAQQMVKDIQKRSSRVFA 271 P GG E+ AGT N A G AA ++ I A Sbjct: 222 PPYGGGGEMIEEVSFEETTYADLPHKFEAGTPNIAGAIGLG-AAIDYLEKIGME-----A 275 Query: 272 IRDYLEQEL-----KKL--IPNIIIYGKDAER---ISNTCCFSIPFLKAEVLQIALDLEG 321 I + E EL ++L IP + +YG +R +S F++ + + LD G Sbjct: 276 IAAH-EHELTAYALERLSEIPGVRVYGDAEDRAGVVS----FNLEGIHPHDVATILDQYG 330 Query: 322 IAVSAGSACSSGKIKKNHVLAAMGFDTSQGAVRVSCGDSTTQEDIDIFLNAL 373 IAV AG C+ ++ +G G VR S G T+E+ID + AL Sbjct: 331 IAVRAGHHCAQ------PLMRRLGV---PGTVRASFGLYNTEEEIDALVEAL 373 >gnl|CDD|30424 COG0075, COG0075, Serine-pyruvate aminotransferase/archaeal aspartate aminotransferase [Amino acid transport and metabolism]. Length = 383 Score = 81.0 bits (200), Expect = 4e-16 Identities = 63/268 (23%), Positives = 107/268 (39%), Gaps = 38/268 (14%) Query: 127 VDIQALTDFLEQRNSTCGIPMIAVMFVNNETGVIQPIKEIAQIVKEYQGILVVDAVQAAG 186 VD + + + L++ I +AV+ TGV+ P+KEIA+ KE+ +L+VDAV + G Sbjct: 117 VDPEEVEEALDKDP---DIKAVAVVHNETSTGVLNPLKEIAKAAKEHGALLIVDAVSSLG 173 Query: 187 RIPLSIEEIKADFLIISSHK-LGAPVGAGALVFREDIL------------LPSPLLRGGD 233 PL ++E D I S K LGAP G + E L L Sbjct: 174 GEPLKVDEWGIDVAITGSQKALGAPPGLAFVAVSERALEAIEERKHPSFYLDLKKWLKYM 233 Query: 234 QEKGQRAGTENYAVIGGFAVAAQQMVKD-IQKRSSRVFAIRDYLEQELKKLIPNIIIYGK 292 ++KG T +I A ++++ ++ R +R + + L L+ L + ++ Sbjct: 234 EKKGSTPYTPPVNLIYALREALDLILEEGLEARIARHRRLAEALRAGLEAL--GLELFAD 291 Query: 293 DAERISNTCCFSIP--FLKAEVLQIALDLEGIAVSAGSACSSGKIKKNHVLAAMGFDTSQ 350 R +P +V + L G+ ++ G GKI Sbjct: 292 PERRSPTVTAIKVPEGVDDKKVRRALLKEYGVEIAGGQGPLKGKI--------------- 336 Query: 351 GAVRVSCGDSTTQEDIDIFLNALQKIIR 378 R+ + ED+ L AL+ +R Sbjct: 337 --FRIGHMGNVRPEDVLAALAALEAALR 362 >gnl|CDD|99742 cd01494, AAT_I, Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V).. Length = 170 Score = 70.1 bits (172), Expect = 9e-13 Identities = 51/180 (28%), Positives = 72/180 (40%), Gaps = 18/180 (10%) Query: 47 IEESRRIIADFCGAKPDHVVFTSSATEAANWVLTPHFYQGSHKISIDSLYISAIEHPAVY 106 +EE +A D VF S T A L G I + + S A Sbjct: 2 LEELEEKLARLLQPGNDKAVFVPSGTGANEAALLALLGPGDEVIVDANGHGSRYWVAAEL 61 Query: 107 AGGHFPSHKIHKIPVL--SKGIVDIQALTDFLEQRNSTCGIPMIAVMFVNNET--GVIQP 162 AG K +PV G +D+ L + + N ++ N T GV+ P Sbjct: 62 AGA-----KPVPVPVDDAGYGGLDVAILEELKAKPNVA------LIVITPNTTSGGVLVP 110 Query: 163 IKEIAQIVKEYQGILVVDAVQAAGRIP---LSIEEIKADFLIISSHKLGAPVGAGALVFR 219 +KEI +I KEY +L+VDA A G P + I E AD + S HK G G ++ + Sbjct: 111 LKEIRKIAKEYGILLLVDAASAGGASPAPGVLIPEGGADVVTFSLHKNLGGEGGGVVIVK 170 >gnl|CDD|99744 cd06451, AGAT_like, Alanine-glyoxylate aminotransferase (AGAT) family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to alanine-glyoxylate aminotransferase (AGAT), serine-glyoxylate aminotransferase (SGAT), and 3-hydroxykynurenine transaminase (HKT). AGAT is a homodimeric protein, which catalyses the transamination of glyoxylate to glycine, and SGAT converts serine and glyoxylate to hydroxypyruvate and glycine. HKT catalyzes the PLP-dependent transamination of 3-hydroxykynurenine, a potentially toxic metabolite of the kynurenine pathway.. Length = 356 Score = 65.8 bits (161), Expect = 2e-11 Identities = 33/97 (34%), Positives = 50/97 (51%), Gaps = 9/97 (9%) Query: 127 VDIQALTDFLEQRNSTCGIPMIAVMFVNNE--TGVIQPIKEIAQIVKEYQGILVVDAVQA 184 V + + + LEQ + AV +NE TGV+ P++ I + K++ +L+VDAV + Sbjct: 111 VSPEEIAEALEQHDIK------AVTLTHNETSTGVLNPLEGIGALAKKHDALLIVDAVSS 164 Query: 185 AGRIPLSIEEIKADFLIISSHK-LGAPVGAGALVFRE 220 G P ++E D S K LGAP G G + F E Sbjct: 165 LGGEPFRMDEWGVDVAYTGSQKALGAPPGLGPIAFSE 201 >gnl|CDD|30425 COG0076, GadB, Glutamate decarboxylase and related PLP-dependent proteins [Amino acid transport and metabolism]. Length = 460 Score = 65.4 bits (159), Expect = 3e-11 Identities = 61/290 (21%), Positives = 106/290 (36%), Gaps = 39/290 (13%) Query: 66 VFTSSATEA--------ANWVLTPHFYQGSHKISIDSLYISAIEHPAVYAGGHFPSHKIH 117 FTS TEA + ++ S H + + + Sbjct: 123 TFTSGGTEANLLALLAARERWRKRALAESGKPGGKPNIVCSETAHFSFEKAARYLGLGLR 182 Query: 118 KIP-VLSKGIVDIQALTDFLEQRNSTCGIPMIAVMFVNNETGVIQPIKEIAQIVKEYQGI 176 ++P V + +D+ AL + +++ + + +TG I I+E+A I +EY Sbjct: 183 RVPTVPTDYRIDVDALEEAIDENTIGGVV--VGTAG-TTDTGSIDDIEELADIAEEYGIW 239 Query: 177 LVVDAVQAAGRIPLSIEEIKADFLI-------ISSHKLG-APVGAGALVFREDILLP--- 225 L VDA +P + + DF + + HK G AP+G G ++FR++ L Sbjct: 240 LHVDAAFGGFLLPFLEPDGRWDFGLEGVDSITVDGHKYGLAPIGCGVVLFRDEEALRRIL 299 Query: 226 ---SPLLRGGD----QEKGQRAGTENYAVIGGFAVAAQQMVKDIQKRSSRVFAIRDYLEQ 278 L GG G R G + +A + + +K R + YL + Sbjct: 300 IFADYYLPGGGIPNFTILGSRPGR---QALALYANLRRLGREGYRKLLDRTLELARYLAE 356 Query: 279 ELKKLIPNIIIYGKDAERISNTCCFSIPFLKAEVLQI--ALDLEGIAVSA 326 EL+KL ++ E F + + + + LD G V A Sbjct: 357 ELEKLGDFELV----NEPELPIVAFRLKDDEDTLADLSERLDRRGWQVPA 402 >gnl|CDD|38073 KOG2862, KOG2862, KOG2862, Alanine-glyoxylate aminotransferase AGT1 [General function prediction only]. Length = 385 Score = 51.5 bits (123), Expect = 3e-07 Identities = 25/106 (23%), Positives = 48/106 (45%), Gaps = 6/106 (5%) Query: 115 KIHKIPVLSKGIVDIQALTDFLEQRNSTCGIPMIAVMFVNNETGVIQPIKEIAQ-IVKEY 173 ++ + V ++ +T+ L Q + V ++ TGV+Q + I+ + ++ Sbjct: 117 EVDVVEADIGQAVPLEEITEKLSQHK----PKAVFVTHGDSSTGVLQDLLAISGELCHKH 172 Query: 174 QGILVVDAVQAAGRIPLSIEEIKADFLIISSHK-LGAPVGAGALVF 218 + +L+VD V + G ++E D S K LGAP G + F Sbjct: 173 EALLLVDTVASLGGTEFEMDEWGVDVAYTGSQKALGAPAGLSIISF 218 >gnl|CDD|99734 cd00609, AAT_like, Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. The major groups in this CD corresponds to Aspartate aminotransferase a, b and c, Tyrosine, Alanine, Aromatic-amino-acid, Glutamine phenylpyruvate, 1-Aminocyclopropane-1-carboxylate synthase, Histidinol-phosphate, gene products of malY and cobC, Valine-pyruvate aminotransferase and Rhizopine catabolism regulatory protein.. Length = 350 Score = 51.6 bits (124), Expect = 4e-07 Identities = 66/350 (18%), Positives = 129/350 (36%), Gaps = 66/350 (18%) Query: 51 RRIIADFCG------AKPDHVVFTSSATEAANWVLTPHFYQGSHKISIDSLYISAIEHPA 104 R IA++ G P+ +V T+ A EA + +L G ++ + E A Sbjct: 42 REAIAEWLGRRGGVDVPPEEIVVTNGAQEALSLLLRALLNPGD-EVLVPDPTYPGYEAAA 100 Query: 105 VYAGGHFPSHKIHKIPVLSKGIVDIQALTDFLEQRNSTCGIPMIAVMFVNNETGVIQP-- 162 AG ++ +P+ +G L L + T ++ + NN TG + Sbjct: 101 RLAGA-----EVVPVPLDEEGGFL---LDLELLEAAKTPKTKLLYLNNPNNPTGAVLSEE 152 Query: 163 -IKEIAQIVKEYQGILVVDAV------QAAGRIPLSIEEIKADFLIISSH-K-LGAP--- 210 ++E+A++ K++ +++ D L++ + +++ S K G P Sbjct: 153 ELEELAELAKKHGILIISDEAYAELVYDGEPPPALALLDAYERVIVLRSFSKTFGLPGLR 212 Query: 211 VGAGALVFREDILLPSPLLRGGDQEKGQRAGTENYAVIGGFAVAAQQMVKD----IQKRS 266 +G ++ P L ++ T + + AA + D +++ Sbjct: 213 IGY--------LIAPPEELLERLKKL-LPYTTSGPSTLS--QAAAAAALDDGEEHLEELR 261 Query: 267 SRVFAIRDYLEQELKKLIPNIIIYGKDAERISNTCCFSIP-FLKAEVLQIALDLEGIAVS 325 R RD L + LK+L P +++ +P E L+ L G+ V Sbjct: 262 ERYRRRRDALLEALKELGPLVVVKPSGG----FFLWLDLPEGDDEEFLERLLLEAGVVVR 317 Query: 326 AGSACSSGKIKKNHVLAAMGFDTSQGAVRVSCGDSTTQEDIDIFLNALQK 375 GSA + +G VR+S T +E+++ L L + Sbjct: 318 PGSAF---------------GEGGEGFVRLSFA--TPEEELEEALERLAE 350 >gnl|CDD|99743 cd06450, DOPA_deC_like, DOPA decarboxylase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to DOPA/tyrosine decarboxylase (DDC), histidine decarboxylase (HDC), and glutamate decarboxylase (GDC). DDC is active as a dimer and catalyzes the decarboxylation of tyrosine. GDC catalyzes the decarboxylation of glutamate and HDC catalyzes the decarboxylation of histidine.. Length = 345 Score = 51.0 bits (123), Expect = 5e-07 Identities = 49/184 (26%), Positives = 73/184 (39%), Gaps = 26/184 (14%) Query: 54 IADFCGAKPDHVVFTSSATE-------AANWVLTPHFYQGSHKISIDSL--YISAIEHPA 104 D G VFTS +E AA G + ID L S H + Sbjct: 55 SEDADG------VFTSGGSESNLLALLAARDRARKRLKAGGGRG-IDKLVIVCSDQAHVS 107 Query: 105 VYAGGHFPSHKIHKIPVLSKGIVDIQALTDFLEQRNSTCGIP-MIAVMFVNNETGVIQPI 163 V + K+ +PV G +D +AL +++ + P M+ +TG I P+ Sbjct: 108 VEKAAAYLDVKVRLVPVDEDGRMDPEALEAAIDEDKAEGLNPIMVVATAGTTDTGAIDPL 167 Query: 164 KEIAQIVKEYQGILVVDAVQAAGRIPLSIEEIKADFLI-------ISSHKLG-APVGAGA 215 +EIA + ++Y L VDA +P E DF I + HK G P+G A Sbjct: 168 EEIADLAEKYDLWLHVDAAYGGFLLP-FPEPRHLDFGIERVDSISVDPHKYGLVPLGCSA 226 Query: 216 LVFR 219 ++ R Sbjct: 227 VLVR 230 >gnl|CDD|31300 COG1103, COG1103, Archaea-specific pyridoxal phosphate-dependent enzymes [General function prediction only]. Length = 382 Score = 49.5 bits (118), Expect = 1e-06 Identities = 28/98 (28%), Positives = 50/98 (51%), Gaps = 3/98 (3%) Query: 127 VDIQALTDFLEQRNSTCGIP--MIAVMFVNNETGVIQPIKEIAQIVKEYQGILVVDAVQA 184 + + + +E+ G P + + V+ E G + K++A+I +EY L+++ Sbjct: 137 ITPEGYAEVIEEVKDEGGDPPALALLTHVDGEYGNLADAKKVAKICREYGVPLLLNCAYT 196 Query: 185 AGRIPLSIEEIKADFLIISSHKLGAPVG-AGALVFRED 221 GR+P+S +EI ADF++ S HK A G L E+ Sbjct: 197 VGRMPVSGKEIGADFIVGSGHKSMAASAPIGVLAMSEE 234 >gnl|CDD|30509 COG0160, GabT, 4-aminobutyrate aminotransferase and related aminotransferases [Amino acid transport and metabolism]. Length = 447 Score = 48.7 bits (116), Expect = 3e-06 Identities = 54/280 (19%), Positives = 102/280 (36%), Gaps = 56/280 (20%) Query: 43 TRLYIEESRRIIADFCGAKPDHVVFTSSATEA-------------ANWVLTPHFYQGSHK 89 Y+E + ++ A G+ V F +S EA V+ F H Sbjct: 98 YEPYVELAEKLTALAPGSGLKKVFFGNSGAEAVEAAIKIARAYTGRPGVIA--FDGAFHG 155 Query: 90 ISIDSLYISAIEHPAVYAGGHFPSHKIH-----------KIPVLSKGIVDIQALTDFLEQ 138 ++ +L ++ + P G P H I G ++ + L Sbjct: 156 RTLGALSLTGSKPPYKAGFGPLPPGVYHVPYPNPYRCPFGIGGEECGDDALEYIERALFD 215 Query: 139 RNSTCGIPMIAVMF---VNNETGVIQP----IKEIAQIVKEYQGILVVDAVQA-AGRIP- 189 G +A + + E G+I P +K + ++ +E+ +L+ D VQ GR Sbjct: 216 LEV--GPEEVAAIIIEPIQGEGGIIVPPKGFLKALRKLCREHGILLIADEVQTGFGRTGK 273 Query: 190 -LSIE--EIKADFLIISSHKLGAPVGAGALVFREDILLPSPLLRGGDQEKGQRAGT---E 243 + E ++ D ++ + LG + A+V R +I+ P G GT Sbjct: 274 MFAFEHFGVEPD-IVTLAKSLGGGLPLSAVVGRAEIMDWPP---------GGHGGTFGGN 323 Query: 244 NYAVIGGFAVAAQQMVKDIQKRSSRVFAIRDYLEQELKKL 283 A AV +++ +R++ + +YL L++L Sbjct: 324 PVACAAALAVLDVIEEENLLERAAEL---GEYLRDRLEEL 360 >gnl|CDD|99745 cd06452, SepCysS, Sep-tRNA:Cys-tRNA synthase. This family belongs to the pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Cys-tRNA(Cys) is produced by O-phosphoseryl-tRNA synthetase which ligates O-phosphoserine (Sep) to tRNA(Cys), and Sep-tRNA:Cys-tRNA synthase (SepCysS) converts Sep-tRNA(Cys) to Cys-tRNA(Cys), in methanogenic archaea. SepCysS forms a dimer, each monomer is composed of a large and small domain; the larger, a typical pyridoxal 5'-phosphate (PLP)-dependent-like enzyme fold. In the active site of each monomer, PLP is covalently bound to a conserved Lys residue near the dimer interface.. Length = 361 Score = 46.2 bits (110), Expect = 2e-05 Identities = 23/77 (29%), Positives = 41/77 (53%), Gaps = 1/77 (1%) Query: 146 PMIAVMFVNNETGVIQPIKEIAQIVKEYQGILVVDAVQAAGRIPLSIEEIKADFLIISSH 205 + + V+ G + K+IA++ EY L+++ GR+P+S +E+ ADF++ S H Sbjct: 141 ALALLTHVDGNYGNLHDAKKIAKVCHEYGVPLLLNGAYTVGRMPVSGKELGADFIVGSGH 200 Query: 206 K-LGAPVGAGALVFRED 221 K + A G L E+ Sbjct: 201 KSMAASAPIGVLATTEE 217 >gnl|CDD|99737 cd00613, GDC-P, Glycine cleavage system P-protein, alpha- and beta-subunits. This family consists of Glycine cleavage system P-proteins EC:1.4.4.2 from bacterial, mammalian and plant sources. The P protein is part of the glycine decarboxylase multienzyme complex EC:2.1.2.10 (GDC) also annotated as glycine cleavage system or glycine synthase. GDC consists of four proteins P, H, L and T. The reaction catalysed by this protein is: Glycine + lipoylprotein <=> S-aminomethyldihydrolipoylprotein + CO2. Alpha-beta-type dimers associate to form an alpha(2)beta(2) tetramer, where the alpha- and beta-subunits are structurally similar and appear to have arisen by gene duplication and subsequent divergence with a loss of one active site. The members of this CD are widely dispersed among all three forms of cellular life.. Length = 398 Score = 41.8 bits (99), Expect = 3e-04 Identities = 40/154 (25%), Positives = 65/154 (42%), Gaps = 21/154 (13%) Query: 101 EHPAVYA-GGHFPSHKIHKIPVLSKGIVDIQALTDFLEQRNSTCGIPMIAVMFVN-NETG 158 +PAV G ++ ++P G VD++AL + + + + A+M N G Sbjct: 120 TNPAVARTRGEPLGIEVVEVPSDEGGTVDLEALKEEVSEEVA-------ALMVQYPNTLG 172 Query: 159 VI-QPIKEIAQIVKEYQGILVVDA--VQAAGRIPLSIEEIKADFLIISSHKLGAPVG--- 212 V IKEIA I ++ VD + G P E AD ++ + K G P G Sbjct: 173 VFEDLIKEIADIAHSAGALVYVDGDNLNLTGLKPPG--EYGADIVVGNLQKTGVPHGGGG 230 Query: 213 --AGALVFREDIL--LPSPLLRGGDQEKGQRAGT 242 AG +++++ LP L+ +G RA Sbjct: 231 PGAGFFAVKKELVRFLPGRLVGVTKDAEGNRAFR 264 >gnl|CDD|143923 pfam00155, Aminotran_1_2, Aminotransferase class I and II. Length = 351 Score = 41.9 bits (99), Expect = 3e-04 Identities = 65/372 (17%), Positives = 123/372 (33%), Gaps = 85/372 (22%) Query: 39 EGQKTRLY-----IEESRRIIADFCGA------KPDHVVFTSSATEAANWVLTPHFYQGS 87 G LY + E R +A F G + V S A L Sbjct: 28 AGGTRNLYGPTDGLPELREALAKFLGRSPVLKLDREAAVVFGSGAGANIEALIFLLANPG 87 Query: 88 HKISIDSLYISAIEHPAVYAGGHFPSHKIHKIPVLSKGI--VDIQALTDFLEQRNSTCGI 145 I + + ++ A AGG ++ + P+ +D AL L+++ Sbjct: 88 DAILVPAPTYASYIRIARLAGG-----EVVRYPLYDSNDFHLDFDALEAALKEKPK---- 138 Query: 146 PMIAVMFVNNETGVIQP---IKEIAQIVKEYQGILVVD------AVQAAGRIPLSIEEIK 196 ++ +N TG + P ++++ + KE+ +L+VD + + + Sbjct: 139 -VVLHESPHNPTGTVAPLEELEKLLDLAKEHNILLLVDEAYAGFVFGSPDAVATRALLAE 197 Query: 197 ADFLIIS---SHKLGAP---VGAGALVFREDILLPSPLLRGGDQEKGQRAGTENYAVIGG 250 L++ S G VG IL + ++ K R + Sbjct: 198 GPNLLVVGSFSKAFGLAGWRVGY--------ILGNAAVISQ--LRKLARPF--YSSTHLQ 245 Query: 251 FAVAA-----QQMVKDIQKRSSRVFAIRDYLEQELKKLIPNIIIYGKDAERISNTCCFSI 305 A AA + ++++ R+ RDYL L+ + + S F + Sbjct: 246 AAAAAALSDPLLVASELEEMRQRIKERRDYLRDGLEAA--GLSVL------PSQAGFFLL 297 Query: 306 PFLKAEV---LQIAL-DLEGIAVSAGSACSSGKIKKNHVLAAMGFDTSQGAVRVSCGDST 361 L E L L + G+ V+ GS+ G +R++ Sbjct: 298 TGLDPETAKELAQVLLEEVGVYVTPGSSP-----------------GVPGWLRITVA-GG 339 Query: 362 TQEDIDIFLNAL 373 T+E+++ L A+ Sbjct: 340 TEEELEELLEAI 351 >gnl|CDD|33635 COG3844, COG3844, Kynureninase [Amino acid transport and metabolism]. Length = 407 Score = 41.5 bits (97), Expect = 4e-04 Identities = 37/174 (21%), Positives = 70/174 (40%), Gaps = 26/174 (14%) Query: 54 IADFCGAKPDHVVFTSSATEAANWVLTPHFYQGSHKISIDSLYISAIEHPAVYAGGHFPS 113 +A GA+ VV T + + VL +L V G +FP+ Sbjct: 85 LAPLIGARAGEVVVTDTTSINLFKVL------------AAALRPQEGRRVIVSEGDNFPT 132 Query: 114 H--------KIHKIPVLSKGIVDIQALTDFLEQRNSTCGIPMIAVMFVNNETGVIQPIKE 165 + I +G++ +AL + + + ++ + VN +TG + ++ Sbjct: 133 DLYIAEGLADLLGIGYDLEGVIAPRALEEAITDD-----VAVVLLSHVNYKTGQLLDMRA 187 Query: 166 IAQIVKEYQGILVVDAVQAAGRIPLSIEEIKADFLIISSHK-LGAPVGAGALVF 218 I + ++ ++ D +AG +P+ + ADF I S+K L GA A +F Sbjct: 188 ITALAHQHGALVGWDLAHSAGAVPVDLHAAGADFAIGCSYKYLNGGPGAPAGLF 241 >gnl|CDD|144709 pfam01212, Beta_elim_lyase, Beta-eliminating lyase. Length = 288 Score = 41.4 bits (98), Expect = 4e-04 Identities = 43/185 (23%), Positives = 74/185 (40%), Gaps = 24/185 (12%) Query: 54 IADFCGAKPDHVVFTSSATEAANWVLTPHFYQGSHKISIDSLYISAIEHPAVY-AGGH-- 110 +A+ G + +F S T AN + +H D + H GGH Sbjct: 41 VAELFGK--EAALFVPSGT-MANQLALM-----AHCRRGDEVICGEPAHIYFDETGGHAE 92 Query: 111 FPSHKIHKIPVLSKGIVDIQALTDFLEQRNST--CGIPMIAVMFVNNETG--VIQP--IK 164 + +P G +D++ L + +I++ +N G V+ ++ Sbjct: 93 LGGAQPVPLPGAEAGKLDLEDLEAAIRPVGDIHFPPTGLISLENTHNSAGGQVVSLEELR 152 Query: 165 EIAQIVKEYQGILVVDA---VQAAGRIPLSIEEIK--ADFLIISSHK-LGAPVGAGALVF 218 EI I +E+ L +D AA + + ++EI AD + +S K LGAPVG L Sbjct: 153 EIRAIAREHGIPLHLDGARLANAAVALGVIVKEITSYADSVSMSLSKGLGAPVG-SVLAG 211 Query: 219 REDIL 223 +D + Sbjct: 212 SDDFI 216 >gnl|CDD|99735 cd00610, OAT_like, Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase, alanine-glyoxylate aminotransferase, dialkylglycine decarboxylase, 4-aminobutyrate aminotransferase, beta-alanine-pyruvate aminotransferase, adenosylmethionine-8-amino-7-oxononanoate aminotransferase, and glutamate-1-semialdehyde 2,1-aminomutase. All the enzymes belonging to this family act on basic amino acids and their derivatives are involved in transamination or decarboxylation.. Length = 413 Score = 39.5 bits (93), Expect = 0.002 Identities = 47/260 (18%), Positives = 95/260 (36%), Gaps = 59/260 (22%) Query: 4 RVYLD----WNATA------PLLEVVRQSFVKSLDFYGNPSSVHKEGQKTRLYIEESRRI 53 YLD ++E + + + L + +E + + Sbjct: 36 NRYLDFLSGIGVLNLGHNHPEVVEAL-KEQLAKLTHFSLG------FFYNEPAVELAELL 88 Query: 54 IADFCGAKPDHVVFTSS---ATEAA----------NWVLTPHFYQGSHKISIDSLYISAI 100 +A D V F +S A EAA +++ F H ++ +L ++ Sbjct: 89 LALT-PEGLDKVFFVNSGTEAVEAALKLARAYTGRKKIIS--FEGAYHGRTLGALSLTG- 144 Query: 101 EHPAVYAGGHFPSHKIHKIP------VLSKGIVDIQALTDFLEQRNSTCGIPMIAVMF-- 152 G + +P ++ D++AL + LE+ +A + Sbjct: 145 -SKKYRGGFGPLLPGVLHVPYPYRYRPPAELADDLEALEEALEEHPEE-----VAAVIVE 198 Query: 153 -VNNETGVIQP----IKEIAQIVKEYQGILVVDAVQA-AGRI--PLSIE--EIKADFLII 202 + E GVI P +K + ++ +++ +L+ D VQ GR + E ++ D ++ Sbjct: 199 PIQGEGGVIVPPPGYLKALRELCRKHGILLIADEVQTGFGRTGKMFAFEHFGVEPD-IVT 257 Query: 203 SSHKLGAPVGAGALVFREDI 222 LG + GA++ RE+I Sbjct: 258 LGKGLGGGLPLGAVLGREEI 277 >gnl|CDD|30505 COG0156, BioF, 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]. Length = 388 Score = 38.7 bits (90), Expect = 0.003 Identities = 47/254 (18%), Positives = 88/254 (34%), Gaps = 45/254 (17%) Query: 19 VRQSFVKSLDFYGNPS-SVHKEGQKTRLYIEESRRIIADFCGAKPDHVVFTSSATEAANW 77 + ++ ++ YG + + L++E + ADF G ++F+S AN Sbjct: 58 LIEAAKAAIRRYGVGAGGSRLISGTSDLHVELEEEL-ADFLG-AEAALLFSSGFV--ANL 113 Query: 78 VLTPHFYQGSHKISIDSLYISAIEHPAVYAGGHFPSHKIHKIPVLSKGIVDIQALTDFLE 137 L + I D L H ++ G ++ + D+ L LE Sbjct: 114 GLLSALLKKGDLIFSDELN-----HASIIDGIRLSRAEVRRFKHN-----DLDHLEALLE 163 Query: 138 Q-RNSTCGIPMIAVMFVNNETGVIQPIKEIAQIVKEYQGILVVDAVQAAGRIPLSIEEIK 196 + R + +I V + G I P+ E+ ++ ++Y +L VD A G Sbjct: 164 EARENGARRKLIVTEGVFSMDGDIAPLPELVELAEKYGALLYVDEAHAVG---------- 213 Query: 197 ADFLIISSHKLGAPVGAGALVFREDILLPSPLLRGGDQEKGQRAGTENYAVIGGFAVAAQ 256 ++ + G G DI++ G K GG+ +A Sbjct: 214 ----VLGPNGRGLAEHFGLEPEEVDIIV-------GTLGKA-------LGSSGGY-IAGS 254 Query: 257 QMVKDIQKRSSRVF 270 + D + +R F Sbjct: 255 AALIDYLRNRARPF 268 >gnl|CDD|99741 cd00617, Tnase_like, Tryptophanase family (Tnase). This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to tryptophanase (Tnase) and tyrosine phenol-lyase (TPL). Tnase and TPL are active as tetramers and catalyze beta-elimination reactions. Tnase catalyzes degradation of L-tryptophan to yield indole, pyruvate and ammonia and TPL catalyzes degradation of L-tyrosine to yield phenol, pyruvate and ammonia.. Length = 431 Score = 35.4 bits (82), Expect = 0.028 Identities = 16/66 (24%), Positives = 33/66 (50%), Gaps = 5/66 (7%) Query: 124 KGIVDIQALTDFLEQRNSTCGIPMIAVMFVNNETG----VIQPIKEIAQIVKEYQGILVV 179 KG +D+ L +++ + IP I + NN G + ++E+ ++ +Y +V+ Sbjct: 133 KGNIDVAKLEKLIDEVGAE-NIPYIVLTITNNTAGGQPVSMANLREVRELAHKYGIPVVL 191 Query: 180 DAVQAA 185 DA + A Sbjct: 192 DAARFA 197 >gnl|CDD|109343 pfam00282, Pyridoxal_deC, Pyridoxal-dependent decarboxylase conserved domain. Length = 370 Score = 34.7 bits (80), Expect = 0.050 Identities = 48/275 (17%), Positives = 80/275 (29%), Gaps = 47/275 (17%) Query: 66 VFTSSATE-------AANWVLTPHFYQGSHKISIDSLYISAIEHPAVYAGGHFPSHKIHK 118 V ++E AA + Y S H ++ ++ + Sbjct: 107 VLQGGSSESNLLALLAARTKWIRRMKAAGKPLGKLVAYTSDQAHSSIEKAALIAGVELRE 166 Query: 119 IPVLSKGIVDIQALTDFLEQRNSTCGIPM-IAVMFVNNETGVIQPIKEIAQIVKEYQGIL 177 IP G + L +E+ IP + +G P++E+ I +Y L Sbjct: 167 IPTDENGKMRGMDLEKAIEEDKENGLIPFFVCATLGTTGSGAFDPLQELGDICNKYDLWL 226 Query: 178 VVDAVQAAG------------RIPLSIEEIKADFLIISSHKLG-APVGAGALVFREDILL 224 VDA A I AD + HK + AL R+ L Sbjct: 227 HVDAAYAGSAFICPEFRHWLFGIER------ADSFSFNPHKWMLVLLDCSALWVRDKGAL 280 Query: 225 PSPL------LRGGDQEKGQRAGTENYAVIGGFAVAAQQM--------VKDIQKRSSRVF 270 L L D ++ + ++ V+ +Q + R Sbjct: 281 QQALQFNPEYLGHTD--SDVAVDYGDWQIPLSRRFRILKLWFVLRSYGVEGLQNQIRRHV 338 Query: 271 AIRDYLEQELKKLIPNIIIYGKDAERISNTCCFSI 305 + Y E ++K I AER CF + Sbjct: 339 ELAKYFEALVRKDSRFEIC----AERGLGLVCFRL 369 >gnl|CDD|99739 cd00615, Orn_deC_like, Ornithine decarboxylase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD corresponds to ornithine decarboxylase (ODC), arginine decarboxylase (ADC) and lysine decarboxylase (LDC). ODC is a dodecamer composed of six homodimers and catalyzes the decarboxylation of tryptophan. ADC catalyzes the decarboxylation of arginine and LDC catalyzes the decarboxylation of lysine. Members of this family are widely found in all three forms of life.. Length = 294 Score = 34.1 bits (79), Expect = 0.058 Identities = 37/206 (17%), Positives = 63/206 (30%), Gaps = 50/206 (24%) Query: 24 VKSLDFYGNPSSVHKEGQKTRLYIEESRRIIADFCGAKPDHVVFTSSATEAAN-----WV 78 + LD +P+ KE Q+ + A GA H F + T ++N V Sbjct: 48 LTGLDDLLDPTGPIKEAQE----------LAARAFGA--KHTFFLVNGTSSSNKAVILAV 95 Query: 79 LTPH----FYQGSHKISIDSLYISAIE----HPAVYAGGHFPSHKIHKIPVLSKGIVDIQ 130 P + HK I+ L +S P G + + Sbjct: 96 CGPGDKILIDRNCHKSVINGLVLSGAVPVYLKPERNPYYGIA------------GGIPPE 143 Query: 131 ALTDFLEQRNSTCGIPMIAVMFVNNET--GVIQPIKEIAQIVKEYQGILVVDAVQAA--- 185 L + + N T G+ +++I + ++VD A Sbjct: 144 TFKKALIEHPDAKAA------VITNPTYYGICYNLRKIVEEAHHRGLPVLVDEAHGAHFR 197 Query: 186 --GRIPLSIEEIKADFLIISSHKLGA 209 +P S AD ++ S+HK Sbjct: 198 FHPILPSSAAMAGADIVVQSTHKTLP 223 >gnl|CDD|30752 COG0403, GcvP, Glycine cleavage system protein P (pyridoxal-binding), N-terminal domain [Amino acid transport and metabolism]. Length = 450 Score = 33.3 bits (76), Expect = 0.12 Identities = 51/287 (17%), Positives = 104/287 (36%), Gaps = 67/287 (23%) Query: 126 IVDIQALTDFLEQRNSTCGIPMIAVMFVNNETGVIQPIKEIAQIVKEYQGILVVDAVQAA 185 +VD L D + + + V + N V + ++ + + +++V AA Sbjct: 194 VVDADDLDDLESADDG--DVFGVLVQYPNTFGIVEEDLRALIEAAHSAGALVIV----AA 247 Query: 186 GRIPLSI----EEIKADFLIISSHKLGAPVG-----AGALVFREDIL--LPSPLLRGGDQ 234 + L + E AD ++ S+ + G P+G AG +++ +P L+ Sbjct: 248 DPLALGLLKPPGEFGADIVVGSAQRFGVPMGFGGPHAGYFAVKDEFKRQMPGRLVGVSVD 307 Query: 235 EKGQRA----------------GTEN-------YAVIGGFAVAAQQMVKD-IQKRSSRVF 270 G+RA T N A+ ++ A +++ + R+ Sbjct: 308 AAGKRAFRLALQTREQHIRREKATSNICTNQALLALA--ASMYAVYHGPQGLKEIAERIH 365 Query: 271 AIRDYLEQELKKLIPNIIIYGKDAERISNTCCFSIPFLKAEVLQIALDLEGIAVSAGSAC 330 + YL LK++ + + + +T +P AE L A GI + Sbjct: 366 RLAAYLAAGLKEIGAGVELVF---DHFFDTFTVRVPEEVAEALLAAAIAGGINL------ 416 Query: 331 SSGKIKKNHVLAAMGFDTSQGAVRVSCGDSTTQEDIDIFLNALQKII 377 ++ + VL ++ ++TT+EDID + A + Sbjct: 417 --RRVDADTVL-------------IALTETTTKEDIDALVAAFGGVN 448 >gnl|CDD|30748 COG0399, WecE, Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]. Length = 374 Score = 32.5 bits (74), Expect = 0.19 Identities = 30/146 (20%), Positives = 50/146 (34%), Gaps = 24/146 (16%) Query: 46 YIEESRRIIADFCGAKPDHVVFTSSATEAANWVLTPHFYQGSHKISIDSLYISAIEHPAV 105 ++ + A++ G K + V SS T A + L ++ + S A + + Sbjct: 35 FVRRFEQAFAEYLGVK--YAVAVSSGTAALHLALLALAIGPGDEVIVPSFTFVATANAVL 92 Query: 106 YAGGHFPSHKIHKIPVLSKGIVDIQALT-----DFLEQRNSTCGIPMIAVMFVNNETGVI 160 G PV VDI T D +E + +I V G Sbjct: 93 LVGA---------KPVF----VDIDPDTLNIDPDLIEAAITPRTKAIIPVHLA----GQP 135 Query: 161 QPIKEIAQIVKEYQGILVVDAVQAAG 186 + I + K + ++ DA QA G Sbjct: 136 CDMDAIMALAKRHGLPVIEDAAQAHG 161 >gnl|CDD|99747 cd06454, KBL_like, KBL_like; this family belongs to the pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD corresponds to serine palmitoyltransferase (SPT), 5-aminolevulinate synthase (ALAS), 8-amino-7-oxononanoate synthase (AONS), and 2-amino-3-ketobutyrate CoA ligase (KBL). SPT is responsible for the condensation of L-serine with palmitoyl-CoA to produce 3-ketodihydrospingosine, the reaction of the first step in sphingolipid biosynthesis. ALAS is involved in heme biosynthesis; it catalyzes the synthesis of 5-aminolevulinic acid from glycine and succinyl-coenzyme A. AONS catalyses the decarboxylative condensation of l-alanine and pimeloyl-CoA in the first committed step of biotin biosynthesis. KBL catalyzes the second reaction step of the metabolic degradation pathway for threonine converting 2-amino-3-ketobutyrate, to glycine and acetyl-CoA. The members of this CD are widely found in all three forms of life.. Length = 349 Score = 32.1 bits (74), Expect = 0.23 Identities = 11/30 (36%), Positives = 16/30 (53%) Query: 157 TGVIQPIKEIAQIVKEYQGILVVDAVQAAG 186 G I P+ E+ + K+Y IL VD + G Sbjct: 145 DGDIAPLPELVDLAKKYGAILFVDEAHSVG 174 >gnl|CDD|36574 KOG1360, KOG1360, KOG1360, 5-aminolevulinate synthase [Coenzyme transport and metabolism]. Length = 570 Score = 32.3 bits (73), Expect = 0.24 Identities = 15/60 (25%), Positives = 30/60 (50%), Gaps = 3/60 (5%) Query: 128 DIQALTDFLEQRNSTCGIP-MIAVMFVNNETGVIQPIKEIAQIVKEYQGILVVDAVQAAG 186 D+ L L+ + +P ++A V++ G + P++E+ + +Y I +D V A G Sbjct: 288 DLDHLEQLLQSSPKS--VPKIVAFETVHSMDGAVCPLEELCDVAHKYGAITFLDEVHAVG 345 >gnl|CDD|30785 COG0436, COG0436, Aspartate/tyrosine/aromatic aminotransferase [Amino acid transport and metabolism]. Length = 393 Score = 31.8 bits (72), Expect = 0.32 Identities = 28/146 (19%), Positives = 52/146 (35%), Gaps = 18/146 (12%) Query: 47 IEESRRIIADFCGAK-------PDHVVFTSSATEAANWVLTPHFYQGSHKISIDSLYISA 99 I E R IA+ + + ++ T+ A EA G + D Y S Sbjct: 67 IPELREAIAEKYKRRYGLDVDPEEEIIVTAGAKEALFLAFLALLNPGDEVLIPDPGYPSY 126 Query: 100 IEHPAVYAGGHFPSHKIHKIPVLSKGIVDIQALTDFLEQRNSTCGIPMIAVMFVNNETGV 159 + AGG + + D++ L + + I + NN TG Sbjct: 127 EAAVKL-AGGK--PVPVPLDEEENGFKPDLEDLEAAITPK-----TKAIILNSPNNPTGA 178 Query: 160 IQP---IKEIAQIVKEYQGILVVDAV 182 + +K I ++ +E+ I++ D + Sbjct: 179 VYSKEELKAIVELAREHDIIIISDEI 204 >gnl|CDD|35848 KOG0629, KOG0629, KOG0629, Glutamate decarboxylase and related proteins [Amino acid transport and metabolism]. Length = 510 Score = 31.8 bits (72), Expect = 0.33 Identities = 35/147 (23%), Positives = 60/147 (40%), Gaps = 23/147 (15%) Query: 95 LYISAIEHPAVYAGGHF---PSHKIHKIPVLSKGIVDIQALTDFLEQRNSTCGIPMIAVM 151 L+ S H ++ F + K+ +G + L + + + G+P Sbjct: 200 LFTSEESHYSIKKAAAFLGLGTDHCIKVKTDERGKMIPDDLEKKILEAKAKGGVP----- 254 Query: 152 FVNNET------GVIQPIKEIAQIVKEYQGILVVDAVQAAG-------RIPLSIEEIKAD 198 F N T G + IA I ++++ + VDA G R L+ E +A+ Sbjct: 255 FFVNATAGTTVLGAFDDLNGIADICEKHKLWMHVDAAWGGGLLMSRKHRHKLTGIE-RAN 313 Query: 199 FLIISSHKL-GAPVGAGALVFREDILL 224 + + HKL GAP+ A + RE+ LL Sbjct: 314 SVTWNPHKLMGAPLQCSAFLTREEGLL 340 >gnl|CDD|99872 cd00518, H2MP, Hydrogenase specific C-terminal endopeptidases, also called Hydrogen Maturation Proteases (H2MP). These enzymes belong to the peptidase family M52. Maturation of [FeNi] hydrogenases includes formation of the nickel metallocenter, proteolytic processing and assembly with other subunits. Hydrogenase maturation endopeptidases are responsible for the proteolytic processing, liberating a short C-terminal peptide by cleaving after a His or an Arg residue, e.g., HycI (E. coli) is involved in processing of HypE, the large subunit of hydrogenase 3. This cleavage is nickel dependent. This CD also includes such hydrogenase-processing proteins as HydD, HupW, and HoxW, as well as, proteins of the F420-reducing hydrogenase of methanogens (e.g., FrcD). Also included, is the Pyrococcus furiosus FrxA protein, a bifunctional endopeptidase/ sulfhydrogenase found in NADP-reducing hyperthermophiles.The Pyrococcus FrxA is not related to those found in Helicobacter pylori.. Length = 139 Score = 30.6 bits (70), Expect = 0.69 Identities = 14/48 (29%), Positives = 26/48 (54%), Gaps = 4/48 (8%) Query: 165 EIAQIVKEYQGILVVDAVQ---AAGRI-PLSIEEIKADFLIISSHKLG 208 E+ +++ +++VDAV G + L EE+ A +S+H+LG Sbjct: 43 ELLDLLEGADRVIIVDAVDSGGEPGTVRRLEPEELPAYLSALSTHQLG 90 >gnl|CDD|39050 KOG3846, KOG3846, KOG3846, L-kynurenine hydrolase [Amino acid transport and metabolism]. Length = 465 Score = 29.2 bits (65), Expect = 1.9 Identities = 51/223 (22%), Positives = 95/223 (42%), Gaps = 17/223 (7%) Query: 5 VYLDWNATAPLLEVVRQSFVKSLDFYGNPSSV-HKEGQKTRLYIEES-RRIIADFCGAKP 62 +YL N+ + + R S LD + + H +G+ + I+E ++A GA+ Sbjct: 69 IYLCGNSLGLMPKSTRNSINAELDKWAKCAVEGHFKGKVPWVSIDEPILPLLAPIVGAQE 128 Query: 63 DHVVFTSSATEAANWVLTPHFYQGS---HKISIDSLYISAIEHPAVYAG----GHFPSHK 115 + V +S T + +L FY+ + KI ++ + +H A+ + G P + Sbjct: 129 NEVAVMNSLTVNLHSLLIS-FYKPTEKRFKILLEKKAFPS-DHYAIESQCKLHGISPENS 186 Query: 116 IHKI-PVLSKGIVDIQALTDFLEQRNSTCGIPMIAVMFVNNETGVIQPIKEIAQIVKEYQ 174 + +I P + + + + D +E+ I ++ V TG I I +++ Sbjct: 187 MIQIEPREGEETLRTEDILDTIEKNGDE--IALVCFSGVQYYTGQYFDIGAITF-AGQFK 243 Query: 175 GILV-VDAVQAAGRIPLSIEEIKADFLIISSHKLGAPVGAGAL 216 G LV D A G +PL + + DF S+K GAG + Sbjct: 244 GCLVGFDLAHAVGNVPLQLHDWGVDFACWCSYKYLN-AGAGGI 285 >gnl|CDD|32165 COG1982, LdcC, Arginine/lysine/ornithine decarboxylases [Amino acid transport and metabolism]. Length = 557 Score = 28.7 bits (64), Expect = 2.7 Identities = 41/195 (21%), Positives = 70/195 (35%), Gaps = 31/195 (15%) Query: 26 SLDFYGNPSSVHKEGQKTRLYIEESRRIIADFCGAKPDHVVFTSSATEAANWVLTPHFYQ 85 LD +P KE Q+ + A GA DH F + T AN + Sbjct: 61 ELDSLLDPEGPIKEAQE----------LAARVFGA--DHTYFVVNGTSTANKAVINAVLT 108 Query: 86 GSHKISIDSLYISAIEHPAVYAGGH---FPSHKIHKIPVLSKGIVDIQALT-DFLEQRNS 141 K+ +D +I H + AG + ++ G + ++ L ++ Sbjct: 109 PGDKVLVDRNCHKSIHHGLILAGATPVYLEPSRNPLYGII--GGIPLETFKEALLAHPDA 166 Query: 142 TCGIPMIAVMFVNNET--GVIQPIKEIAQIVKEYQGILVVDAVQAA-----GRIPLSIEE 194 + N T GV +++I +++ Y ++ D A +P S Sbjct: 167 EKLA------VITNPTYDGVCYNLRKIVELLHHYGAWVLYDEAHPAHFDFSPMLPESALN 220 Query: 195 IKADFLIISSHKLGA 209 ADF+ S+HKL A Sbjct: 221 GGADFVTQSTHKLLA 235 >gnl|CDD|73216 cd00578, L-fuc_L-ara-isomerases, L-fucose isomerase (FucIase) and L-arabinose isomerase (AI) family; composed of FucIase, AI and similar proteins. FucIase converts L-fucose, an aldohexose, to its ketose form, which prepares it for aldol cleavage (similar to the isomerization of glucose in glycolysis). L-fucose (or 6-deoxy-L-galactose) is found in various oligo- and polysaccharides in mammals, bacteria and plants. AI catalyzes the isomerization of L-arabinose to L-ribulose, the first reaction in its conversion to D-xylulose-5-phosphate, an intermediate in the pentose phosphate pathway, which allows L-arabinose to be used as a carbon source. AI can also convert D-galactose to D-tagatose at elevated temperatures in the presence of divalent metal ions. D-tagatose, rarely found in nature, is of commercial interest as a low-calorie sugar substitute.. Length = 452 Score = 28.3 bits (63), Expect = 3.4 Identities = 22/129 (17%), Positives = 39/129 (30%), Gaps = 10/129 (7%) Query: 33 PSSVHKEGQKTRLYIEESRRIIADFCGAKPDHVVFTSSATEAANWVLTPHFYQGSHKISI 92 S H G++ +EE R +AD P VV T + + + + Sbjct: 7 TGSQHLYGEELLEQVEEYAREVADLLNELPVEVVDKPEVTGTP-----DEARKAAEEFNE 61 Query: 93 DSLYISAIEHPAVYAGGHF--PSHKIHKIPVLSKGIVDIQALTDFLEQRNSTCGIPMIAV 150 + I + + PVL + + DF+ S CG + Sbjct: 62 ANC-DGLIVWMHTFGPAKMWIAGLSELRKPVLLLATQFNREIPDFMNLNQSACG--LREF 118 Query: 151 MFVNNETGV 159 + G+ Sbjct: 119 GNILARLGI 127 >gnl|CDD|34597 COG4992, ArgD, Ornithine/acetylornithine aminotransferase [Amino acid transport and metabolism]. Length = 404 Score = 27.8 bits (62), Expect = 4.9 Identities = 23/86 (26%), Positives = 40/86 (46%), Gaps = 14/86 (16%) Query: 149 AVMF--VNNETGVIQP----IKEIAQIVKEYQGILVVDAVQAA-GR----IPLSIEEIKA 197 AV+ + E GVI +K + ++ E+ +L++D VQ GR ++ Sbjct: 187 AVIVEPIQGEGGVIPAPPEFLKALRELCDEHGALLILDEVQTGLGRTGKLFAYEHYGVEP 246 Query: 198 DFLIISSHK-LGAPVGAGALVFREDI 222 D I++ K LG GA++ E+I Sbjct: 247 D--ILTLAKALGGGFPIGAMLATEEI 270 >gnl|CDD|34444 COG4835, COG4835, Uncharacterized protein conserved in bacteria [Function unknown]. Length = 124 Score = 27.6 bits (61), Expect = 6.3 Identities = 17/61 (27%), Positives = 29/61 (47%), Gaps = 6/61 (9%) Query: 262 IQKRSSRVFAIRDYLEQELKKLIPNIIIYGKDAERISNTCCFSIPFLKAEVLQIALDLEG 321 I R S++ I+D + +E +L ++ E ++ + L EV +IALD G Sbjct: 66 ISGRISQINQIKDRIVKEPSEL------EQEEVEGLAAPLLDMLKRLTYEVTEIALDEPG 119 Query: 322 I 322 I Sbjct: 120 I 120 >gnl|CDD|35478 KOG0257, KOG0257, KOG0257, Kynurenine aminotransferase, glutamine transaminase K [Amino acid transport and metabolism]. Length = 420 Score = 27.6 bits (61), Expect = 6.9 Identities = 31/141 (21%), Positives = 53/141 (37%), Gaps = 15/141 (10%) Query: 51 RRIIADFCGA---KPDHVVFTSSATEAANWVLTPHFYQGSHKISIDSLYISAIEHPAVYA 107 + ++F G D V+ T+ A EA + L G I + + I V A Sbjct: 79 AKAYSEFYGGLLDPDDEVLVTAGANEAISSALLGLLNPGDEVIVFEPFFDCYIPQ-VVMA 137 Query: 108 GG--HFPSHKIHKIPVLSKGIVDIQALTDFLEQRNSTCGIP-MIAVMFVNNETGVIQP-- 162 GG F K + V S D E + I + +N TG + Sbjct: 138 GGTPVFVPLKPKEGNVSSS-----DWTLDPEELESKITEKTKAIILNTPHNPTGKVFSRE 192 Query: 163 -IKEIAQIVKEYQGILVVDAV 182 ++ IA++ K++ +++ D V Sbjct: 193 ELERIAELCKKHGLLVISDEV 213 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 0.136 0.391 Gapped Lambda K H 0.267 0.0807 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 4,562,498 Number of extensions: 245271 Number of successful extensions: 690 Number of sequences better than 10.0: 1 Number of HSP's gapped: 652 Number of HSP's successfully gapped: 56 Length of query: 383 Length of database: 6,263,737 Length adjustment: 96 Effective length of query: 287 Effective length of database: 4,189,273 Effective search space: 1202321351 Effective search space used: 1202321351 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: 58 (26.0 bits)