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)