RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 022463
(297 letters)
>gnl|CDD|215639 PLN03226, PLN03226, serine hydroxymethyltransferase; Provisional.
Length = 475
Score = 593 bits (1531), Expect = 0.0
Identities = 201/259 (77%), Positives = 221/259 (85%)
Query: 1 MQAVGSVMTNKYSEGYPGARYYGGNEYIDMAESLCQKRALEAFRLDPEKWGVNVQSLSGS 60
M+A+GS +TNKYSEG PGARYYGGNEYID E+LCQKRALEAFRLDPEKWGVNVQ LSGS
Sbjct: 51 MEALGSCLTNKYSEGLPGARYYGGNEYIDQIETLCQKRALEAFRLDPEKWGVNVQPLSGS 110
Query: 61 PSNFQVYTALLKPHDRIMALDLPHGGHLSHGYQTDTKKISAVSIFFETMPYRLNESTGYI 120
P+NF VYTALL+PHDRIM LDLPHGGHLSHGYQTD KKISA SI+FE+MPYRL+ESTG I
Sbjct: 111 PANFAVYTALLQPHDRIMGLDLPHGGHLSHGYQTDGKKISATSIYFESMPYRLDESTGLI 170
Query: 121 DYDQLEKSATLFRPKLIVAGASAYARLYDYERIRKVCNKQKAIMLADMAHISGLVAAGVI 180
DYD+LEK A LFRPKLI+AGASAY R +DY R+RK+ +K A+++ DMAHISGLVAA
Sbjct: 171 DYDKLEKKAMLFRPKLIIAGASAYPRDWDYARMRKIADKVGALLMCDMAHISGLVAAQEA 230
Query: 181 PSPFEYADVVTTTTHKSLRGPRGAMIFFRKGVKEINKQGKEVFYDYEEKINQAVFPGLQG 240
SPFEY DVVTTTTHKSLRGPRG MIFFRKG K QG+ YDYE+KIN AVFPGLQG
Sbjct: 231 ASPFEYCDVVTTTTHKSLRGPRGGMIFFRKGPKPPKGQGEGAVYDYEDKINFAVFPGLQG 290
Query: 241 GPHNHTITGLAVALKQVCT 259
GPHNHTI LAVALKQ T
Sbjct: 291 GPHNHTIAALAVALKQAMT 309
>gnl|CDD|240264 PTZ00094, PTZ00094, serine hydroxymethyltransferase; Provisional.
Length = 452
Score = 491 bits (1265), Expect = e-175
Identities = 170/259 (65%), Positives = 204/259 (78%), Gaps = 11/259 (4%)
Query: 1 MQAVGSVMTNKYSEGYPGARYYGGNEYIDMAESLCQKRALEAFRLDPEKWGVNVQSLSGS 60
++ +GS TNKY+EG PG RYYGGNE +D E+LCQKRALEAF LDPE+WGVNVQ SGS
Sbjct: 51 LECLGSCFTNKYAEGLPGNRYYGGNEVVDKIENLCQKRALEAFGLDPEEWGVNVQPYSGS 110
Query: 61 PSNFQVYTALLKPHDRIMALDLPHGGHLSHGYQTDTKKISAVSIFFETMPYRLNESTGYI 120
P+NF VYTALL+PHDRIM LDLP GGHL+HG+ T KK+SA SI+FE++PY++NE G I
Sbjct: 111 PANFAVYTALLQPHDRIMGLDLPSGGHLTHGFYTAKKKVSATSIYFESLPYQVNE-KGLI 169
Query: 121 DYDQLEKSATLFRPKLIVAGASAYARLYDYERIRKVCNKQKAIMLADMAHISGLVAAGVI 180
DYD+LE+ A FRPKLI+AGASAY R DY+R R++C+ A ++AD+AH SGLVAAGV+
Sbjct: 170 DYDKLEELAKAFRPKLIIAGASAYPRDIDYKRFREICDSVGAYLMADIAHTSGLVAAGVL 229
Query: 181 PSPFEYADVVTTTTHKSLRGPRGAMIFFRKGVKEINKQGKEVFYDYEEKINQAVFPGLQG 240
PSPF YADVVTTTTHKSLRGPR +IF+RK VK D E KIN+AVFPGLQG
Sbjct: 230 PSPFPYADVVTTTTHKSLRGPRSGLIFYRKKVKP----------DIENKINEAVFPGLQG 279
Query: 241 GPHNHTITGLAVALKQVCT 259
GPHNH I +AV LK+V +
Sbjct: 280 GPHNHQIAAIAVQLKEVQS 298
>gnl|CDD|189558 pfam00464, SHMT, Serine hydroxymethyltransferase.
Length = 380
Score = 451 bits (1163), Expect = e-160
Identities = 164/259 (63%), Positives = 190/259 (73%), Gaps = 20/259 (7%)
Query: 1 MQAVGSVMTNKYSEGYPGARYYGGNEYIDMAESLCQKRALEAFRLDPEKWGVNVQSLSGS 60
M+A+GSV+TNKY+EGYPG RYYGG EY+D E+L Q RA E F LD GVNVQ LSGS
Sbjct: 37 MEALGSVLTNKYAEGYPGKRYYGGCEYVDEVETLAQDRAKELFGLD----GVNVQPLSGS 92
Query: 61 PSNFQVYTALLKPHDRIMALDLPHGGHLSHGYQTDTKKISAVSIFFETMPYRLNESTGYI 120
+N VYTALL P DRIM LDLPHGGHL+HGY + FFE+MPY ++ TG I
Sbjct: 93 QANLAVYTALLNPGDRIMGLDLPHGGHLTHGYPVNF-----SGKFFESMPYGVDPDTGLI 147
Query: 121 DYDQLEKSATLFRPKLIVAGASAYARLYDYERIRKVCNKQKAIMLADMAHISGLVAAGVI 180
DYDQLEK+A LF+PKLIVAG SAY+RL DY R R++ ++ A ++ DMAHI+GLVAAGVI
Sbjct: 148 DYDQLEKNAKLFKPKLIVAGTSAYSRLIDYARFREIADEVGAYLMVDMAHIAGLVAAGVI 207
Query: 181 PSPFEYADVVTTTTHKSLRGPRGAMIFFRKGVKEINKQGKEVFYDYEEKINQAVFPGLQG 240
PSPF YA VVTTTTHK+LRGPRG MIFFR E+ Y+ E+KIN AVFPGLQG
Sbjct: 208 PSPFPYAHVVTTTTHKTLRGPRGGMIFFR-----------EILYELEKKINSAVFPGLQG 256
Query: 241 GPHNHTITGLAVALKQVCT 259
GP NH I AVALKQ T
Sbjct: 257 GPLNHVIAAKAVALKQALT 275
>gnl|CDD|99733 cd00378, SHMT, Serine-glycine hydroxymethyltransferase (SHMT). This
family belongs to pyridoxal phosphate (PLP)-dependent
aspartate aminotransferase superfamily (fold I). SHMT
carries out interconversion of serine and glycine; it
catalyzes the transfer of hydroxymethyl group of N5,
N10-methylene tetrahydrofolate to glycine resulting in
the formation of serine and tetrahydrofolate. Both
eukaryotic and prokaryotic SHMT enzymes form tight
obligate homodimers; the mammalian enzyme forms a
homotetramer comprising four pyridoxal phosphate-bound
active sites.
Length = 402
Score = 405 bits (1043), Expect = e-142
Identities = 141/256 (55%), Positives = 173/256 (67%), Gaps = 20/256 (7%)
Query: 1 MQAVGSVMTNKYSEGYPGARYYGGNEYIDMAESLCQKRALEAFRLDPEKWGVNVQSLSGS 60
M+A+GS +TNKY+EGYPG RYYGG EY+D E L +RA + F + NVQ SGS
Sbjct: 36 MEAMGSDLTNKYAEGYPGKRYYGGCEYVDEIEDLAIERAKKLFGAE----YANVQPHSGS 91
Query: 61 PSNFQVYTALLKPHDRIMALDLPHGGHLSHGYQTDTKKISAVSIFFETMPYRLNESTGYI 120
+N VY ALL+P D IM LDL HGGHL+HG T K+SA FE++PY ++ TG I
Sbjct: 92 QANLAVYFALLEPGDTIMGLDLSHGGHLTHGSFT---KVSASGKLFESVPYGVDPETGLI 148
Query: 121 DYDQLEKSATLFRPKLIVAGASAYARLYDYERIRKVCNKQKAIMLADMAHISGLVAAGVI 180
DYD LEK A F+PKLIVAGASAY R D++R R++ ++ A +L DMAH++GLVA GV
Sbjct: 149 DYDALEKMALEFKPKLIVAGASAYPRPIDFKRFREIADEVGAYLLVDMAHVAGLVAGGVF 208
Query: 181 PSPFEYADVVTTTTHKSLRGPRGAMIFFRKGVKEINKQGKEVFYDYEEKINQAVFPGLQG 240
P+P ADVVTTTTHK+LRGPRG +I RKG + +KIN AVFPGLQG
Sbjct: 209 PNPLPGADVVTTTTHKTLRGPRGGLILTRKG-------------ELAKKINSAVFPGLQG 255
Query: 241 GPHNHTITGLAVALKQ 256
GPH H I AVALK+
Sbjct: 256 GPHLHVIAAKAVALKE 271
>gnl|CDD|215153 PLN02271, PLN02271, serine hydroxymethyltransferase.
Length = 586
Score = 390 bits (1004), Expect = e-133
Identities = 163/267 (61%), Positives = 200/267 (74%), Gaps = 9/267 (3%)
Query: 1 MQAVGSVMTNKYSEGYPGARYYGGNEYIDMAESLCQKRALEAFRLDPEKWGVNVQSLSGS 60
M+A+GS +TNKYSEG PGARYY GN+YID E LC +RAL AF LD EKWGVNVQ S +
Sbjct: 165 MEALGSHLTNKYSEGMPGARYYTGNQYIDQIERLCCERALAAFGLDSEKWGVNVQPYSCT 224
Query: 61 PSNFQVYTALLKPHDRIMALDLPHGGHLSHGYQTDT-KKISAVSIFFETMPYRLNESTGY 119
+NF VYT LL P DRIM LD P GGH+SHGY T KK+S SIFFE++PY++N TGY
Sbjct: 225 SANFAVYTGLLLPGDRIMGLDSPSGGHMSHGYYTPGGKKVSGASIFFESLPYKVNPQTGY 284
Query: 120 IDYDQLEKSATLFRPKLIVAGASAYARLYDYERIRKVCNKQKAIMLADMAHISGLVAAGV 179
IDYD+LE+ A FRPK+++ G S+Y R +DY R R++ +K A+++ DMAHISGLVAA
Sbjct: 285 IDYDKLEEKALDFRPKILICGGSSYPREWDYARFRQIADKCGAVLMCDMAHISGLVAAKE 344
Query: 180 IPSPFEYADVVTTTTHKSLRGPRGAMIFFRKGVKEINKQGKEV-------FYDYEEKINQ 232
+PF+Y D+VT+TTHKSLRGPRG +IF+RKG K + KQG + YD+EEKIN
Sbjct: 345 CVNPFDYCDIVTSTTHKSLRGPRGGIIFYRKGPK-LRKQGMLLSHGDDNSHYDFEEKINF 403
Query: 233 AVFPGLQGGPHNHTITGLAVALKQVCT 259
AVFP LQGGPHN+ I LA+ALKQV T
Sbjct: 404 AVFPSLQGGPHNNHIAALAIALKQVAT 430
>gnl|CDD|223190 COG0112, GlyA, Glycine/serine hydroxymethyltransferase [Amino acid
transport and metabolism].
Length = 413
Score = 358 bits (922), Expect = e-123
Identities = 124/256 (48%), Positives = 162/256 (63%), Gaps = 22/256 (8%)
Query: 1 MQAVGSVMTNKYSEGYPGARYYGGNEYIDMAESLCQKRALEAFRLDPEKWGVNVQSLSGS 60
M+A GS +TNKY+EGYPG RYYGG EY+D E L +RA + F + NVQ SGS
Sbjct: 43 MEAQGSDLTNKYAEGYPGKRYYGGCEYVDEVEELAIERAKKLFGAE----YANVQPHSGS 98
Query: 61 PSNFQVYTALLKPHDRIMALDLPHGGHLSHGYQTDTKKISAVSIFFETMPYRLNESTGYI 120
+N VY ALL+P D IM LDL HGGHL+HG ++ F + Y ++ TG I
Sbjct: 99 QANQAVYLALLQPGDTIMGLDLSHGGHLTHGS-----PVNFSGKLFNVVSYGVDPETGLI 153
Query: 121 DYDQLEKSATLFRPKLIVAGASAYARLYDYERIRKVCNKQKAIMLADMAHISGLVAAGVI 180
DYD++EK A +PKLI+AG SAY+R D++R R++ ++ A ++ DMAH++GL+A GV
Sbjct: 154 DYDEVEKLAKEVKPKLIIAGGSAYSRPIDFKRFREIADEVGAYLMVDMAHVAGLIAGGVH 213
Query: 181 PSPFEYADVVTTTTHKSLRGPRGAMIFFRKGVKEINKQGKEVFYDYEEKINQAVFPGLQG 240
P+P +ADVVTTTTHK+LRGPRG +I + +KIN AVFPGLQG
Sbjct: 214 PNPLPHADVVTTTTHKTLRGPRGGIILTND-------------EELAKKINSAVFPGLQG 260
Query: 241 GPHNHTITGLAVALKQ 256
GP H I AVA K+
Sbjct: 261 GPLMHVIAAKAVAFKE 276
>gnl|CDD|234571 PRK00011, glyA, serine hydroxymethyltransferase; Reviewed.
Length = 416
Score = 343 bits (882), Expect = e-117
Identities = 129/255 (50%), Positives = 165/255 (64%), Gaps = 22/255 (8%)
Query: 1 MQAVGSVMTNKYSEGYPGARYYGGNEYIDMAESLCQKRALEAFRLDPEKWGVNVQSLSGS 60
M+A GSV+TNKY+EGYPG RYYGG EY+D+ E L RA E F + NVQ SGS
Sbjct: 42 MEAQGSVLTNKYAEGYPGKRYYGGCEYVDVVEQLAIDRAKELFGAE----YANVQPHSGS 97
Query: 61 PSNFQVYTALLKPHDRIMALDLPHGGHLSHGYQTDTKKISAVSIFFETMPYRLNESTGYI 120
+N VY ALLKP D I+ +DL HGGHL+HG ++ + + Y ++E TG I
Sbjct: 98 QANAAVYFALLKPGDTILGMDLAHGGHLTHG-----SPVNFSGKLYNVVSYGVDEETGLI 152
Query: 121 DYDQLEKSATLFRPKLIVAGASAYARLYDYERIRKVCNKQKAIMLADMAHISGLVAAGVI 180
DYD++EK A +PKLI+AGASAY+R D++R R++ ++ A ++ DMAHI+GLVAAGV
Sbjct: 153 DYDEVEKLALEHKPKLIIAGASAYSRPIDFKRFREIADEVGAYLMVDMAHIAGLVAAGVH 212
Query: 181 PSPFEYADVVTTTTHKSLRGPRGAMIFFRKGVKEINKQGKEVFYDYEEKINQAVFPGLQG 240
PSP +ADVVTTTTHK+LRGPRG +I + +KIN AVFPG+QG
Sbjct: 213 PSPVPHADVVTTTTHKTLRGPRGGLILTNDE-------------ELAKKINSAVFPGIQG 259
Query: 241 GPHNHTITGLAVALK 255
GP H I AVA K
Sbjct: 260 GPLMHVIAAKAVAFK 274
>gnl|CDD|237280 PRK13034, PRK13034, serine hydroxymethyltransferase; Reviewed.
Length = 416
Score = 299 bits (768), Expect = e-100
Identities = 128/256 (50%), Positives = 165/256 (64%), Gaps = 22/256 (8%)
Query: 1 MQAVGSVMTNKYSEGYPGARYYGGNEYIDMAESLCQKRALEAFRLDPEKWGVNVQSLSGS 60
M+A GSV+TNKY+EGYPG RYYGG E++D E+L +RA + F D NVQ SGS
Sbjct: 45 MEAQGSVLTNKYAEGYPGKRYYGGCEFVDEVEALAIERAKQLFGCD----YANVQPHSGS 100
Query: 61 PSNFQVYTALLKPHDRIMALDLPHGGHLSHGYQTDTKKISAVSIFFETMPYRLNESTGYI 120
+N VY ALLKP D I+ + L HGGHL+HG K+S ++ + Y ++ TG I
Sbjct: 101 QANGAVYLALLKPGDTILGMSLSHGGHLTHG-----AKVSLSGKWYNAVQYGVDRLTGLI 155
Query: 121 DYDQLEKSATLFRPKLIVAGASAYARLYDYERIRKVCNKQKAIMLADMAHISGLVAAGVI 180
DYD++E+ A +PKLI+AG SAY R D+ R R++ ++ A+++ DMAHI+GLVAAG
Sbjct: 156 DYDEVEELAKEHKPKLIIAGFSAYPRELDFARFREIADEVGALLMVDMAHIAGLVAAGEH 215
Query: 181 PSPFEYADVVTTTTHKSLRGPRGAMIFFRKGVKEINKQGKEVFYDYEEKINQAVFPGLQG 240
P+PF +A VVTTTTHK+LRGPRG MI +EI K KIN AVFPGLQG
Sbjct: 216 PNPFPHAHVVTTTTHKTLRGPRGGMILTND--EEIAK-----------KINSAVFPGLQG 262
Query: 241 GPHNHTITGLAVALKQ 256
GP H I AVA +
Sbjct: 263 GPLMHVIAAKAVAFGE 278
>gnl|CDD|184161 PRK13580, PRK13580, serine hydroxymethyltransferase; Provisional.
Length = 493
Score = 178 bits (454), Expect = 1e-52
Identities = 89/289 (30%), Positives = 145/289 (50%), Gaps = 58/289 (20%)
Query: 2 QAVGSVMTNKYSEGYPGARYYGGNEYIDMAESLCQKRALEAFRLDPEKWGVNVQSLSGSP 61
A+G+++T+KY+EG PG R+Y G + +D E + A E F + VQ SG+
Sbjct: 67 LAMGNLLTDKYAEGTPGHRFYAGCQNVDTVEWEAAEHAKELFGAE----HAYVQPHSGAD 122
Query: 62 SNFQVYTALLKPH-------------------------------DRIMALDLPHGGHLSH 90
+N + A+L R++ + L GGHL+H
Sbjct: 123 ANLVAFWAILAHKVESPALEKLGAKTVNDLTEEDWEALRAELGNQRLLGMSLDSGGHLTH 182
Query: 91 GYQTDTKKISAVSIFFETMPYRLNESTGYIDYDQLEKSATLFRPKLIVAGASAYARLYDY 150
G++ + IS F Y ++ TG +DYD++ A F+P ++VAG SAY R ++
Sbjct: 183 GFRPN---IS--GKMFHQRSYGVDPDTGLLDYDEIAALAREFKPLILVAGYSAYPRRVNF 237
Query: 151 ERIRKVCNKQKAIMLADMAHISGLVAAGVIP---SPFEYADVVTTTTHKSLRGPRGAMIF 207
++R++ ++ A+++ DMAH +GLVA V P +AD+VTTTTHK+LRGPRG ++
Sbjct: 238 AKLREIADEVGAVLMVDMAHFAGLVAGKVFTGDEDPVPHADIVTTTTHKTLRGPRGGLVL 297
Query: 208 FRKGVKEINKQGKEVFYDYEEKINQAVFPGLQGGPHNHTITGLAVALKQ 256
+K +Y + +++ P + GGP H + AVAL +
Sbjct: 298 AKK--------------EYADAVDKGC-PLVLGGPLPHVMAAKAVALAE 331
>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 = 105 bits (264), Expect = 7e-28
Identities = 39/178 (21%), Positives = 69/178 (38%), Gaps = 15/178 (8%)
Query: 35 CQKRALEAFRLDPEKWGVNVQSLSGSPSNFQVYTALLKPHDRIMALDLPHGGHLSHGYQT 94
+++ + P SG+ +N ALL P D ++ HG
Sbjct: 5 LEEKLARLLQ--PGNDKAVFVP-SGTGANEAALLALLGPGDEVIVDANGHGSRYWV---- 57
Query: 95 DTKKISAVSIFFETMPYRLNESTGY-IDYDQLEKSATLFRPKLIVAGASAYAR--LYDYE 151
+A + +P ++++ +D LE+ LIV + + L +
Sbjct: 58 -----AAELAGAKPVPVPVDDAGYGGLDVAILEELKAKPNVALIVITPNTTSGGVLVPLK 112
Query: 152 RIRKVCNKQKAIMLADMAHISGLVAAGVIPSPFEYADVVTTTTHKSLRGPRGAMIFFR 209
IRK+ + ++L D A G A + P ADVVT + HK+L G G ++ +
Sbjct: 113 EIRKIAKEYGILLLVDAASAGGASPAPGVLIPEGGADVVTFSLHKNLGGEGGGVVIVK 170
>gnl|CDD|215756 pfam00155, Aminotran_1_2, Aminotransferase class I and II.
Length = 357
Score = 41.5 bits (98), Expect = 3e-04
Identities = 34/189 (17%), Positives = 61/189 (32%), Gaps = 30/189 (15%)
Query: 25 NEYIDMAESLCQKRALEAFRLDPEKWG----VNVQSLSGSPSNFQVYTALLK--PHDRIM 78
N Y + AL F V SG+ +N + LL+ P D I+
Sbjct: 35 NLYGPTDGLPELREALAKFLGRSPVLKLDREAAVVFGSGAGANIEALIFLLRLNPGDAIL 94
Query: 79 ALDLPHGGHLSHGYQTDTKKISAVSIFFETMPYRLNESTGY-IDYDQLE---KSATLFRP 134
+ + E + Y L S + +D+D LE K AT
Sbjct: 95 VPAPTYPSY----------IRIFRLAGGEVVRYPLYSSNDFHLDFDALEAALKEATEGNK 144
Query: 135 KLIVAGAS----AYARLYDYERIRKVCNKQKAIMLADMAHISGLVAAGVIPSPF-----E 185
++ A L + E++ + + ++L D A+ G V + E
Sbjct: 145 VVLHTSPHNPTGTVATLEELEKLLDLAKEHNILLLVDEAYA-GFVFGSLDAVATRALLAE 203
Query: 186 YADVVTTTT 194
+++ +
Sbjct: 204 GPNLLVVGS 212
>gnl|CDD|223594 COG0520, csdA, Selenocysteine lyase/Cysteine desulfurase
[Posttranslational modification, protein turnover,
chaperones].
Length = 405
Score = 40.0 bits (94), Expect = 9e-04
Identities = 16/57 (28%), Positives = 27/57 (47%), Gaps = 7/57 (12%)
Query: 149 DYERIRKVCNKQKAIMLADMAHISGLVAAGVIPSPFE--YADVVTTTTHKSLRGPRG 203
+ I ++ ++ A++L D A AAG +P + D + + HK L GP G
Sbjct: 180 PVKEIAELAHEHGALVLVDAAQ-----AAGHLPIDVQELGCDFLAFSGHKWLLGPTG 231
>gnl|CDD|216367 pfam01212, Beta_elim_lyase, Beta-eliminating lyase.
Length = 288
Score = 37.2 bits (87), Expect = 0.006
Identities = 36/169 (21%), Positives = 61/169 (36%), Gaps = 26/169 (15%)
Query: 58 SGSPSNFQVYTALLKPHDRIMALDLPHGGHLSHGYQTDTKKISAVS-IFFETMPYRLNES 116
SG+ +N A + D ++ G +H Y +T + + +P
Sbjct: 55 SGTMANQLALMAHCRRGDEVIC------GEPAHIYFDETGGHAELGGAQPVPLP---GAE 105
Query: 117 TGYIDYDQLEKSATLF------RPKLIV-------AGASAYARLYDYERIRKVCNKQKAI 163
G +D + LE + LI AG + L + IR + +
Sbjct: 106 AGKLDLEDLEAAIRPVGDIHFPPTGLISLENTHNSAGGQVVS-LEELREIRAIAREHGIP 164
Query: 164 MLADMAHIS-GLVAAGVIPSP-FEYADVVTTTTHKSLRGPRGAMIFFRK 210
+ D A ++ VA GVI YAD V+ + K L P G+++
Sbjct: 165 LHLDGARLANAAVALGVIVKEITSYADSVSMSLSKGLGAPVGSVLAGSD 213
>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 = 0.069
Identities = 36/158 (22%), Positives = 63/158 (39%), Gaps = 12/158 (7%)
Query: 60 SPSNFQVYTALLKPHDRIMALDLPHGGHLSHGYQTDTKKISAVSIFFETMPYRLNESTGY 119
S SN V A+ P D+I+ + H S AV ++ + G
Sbjct: 85 SSSNKAVILAVCGPGDKIL---IDRNCHKSVINGLVLSG--AVPVYLKPERNPYYGIAGG 139
Query: 120 IDYDQLEKSATLFRPK---LIVAGASAYARLYDYERIRKVCNKQKAIMLADMAHISGLVA 176
I + +K A + P ++ + Y Y+ +I + + + +L D AH +
Sbjct: 140 IPPETFKK-ALIEHPDAKAAVITNPTYYGICYNLRKIVEEAHHRGLPVLVDEAHGAHFRF 198
Query: 177 AGVIPS--PFEYADVVTTTTHKSLRGPR-GAMIFFRKG 211
++PS AD+V +THK+L G+MI +
Sbjct: 199 HPILPSSAAMAGADIVVQSTHKTLPALTQGSMIHVKGD 236
>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 = 33.8 bits (78), Expect = 0.091
Identities = 29/136 (21%), Positives = 46/136 (33%), Gaps = 24/136 (17%)
Query: 137 IVAGASAYARLYDYERIRKVCNKQKAIMLADMAHISGLVAAGVIPSPFEYA----DVVTT 192
+ ++ L E I + K A+++ D +S L PF DV T
Sbjct: 130 LTHNETSTGVLNPLEGIGALAKKHDALLIVDA--VSSLGGE-----PFRMDEWGVDVAYT 182
Query: 193 TTHKSLRGPRGAMI--FFRKGVKEI-NKQGKEVFY-DYEEKINQAVFPGLQGGPHNHTIT 248
+ K+L P G F + ++ I K + FY D + + G HT
Sbjct: 183 GSQKALGAPPGLGPIAFSERALERIKKKTKPKGFYFDLLLLLK---YWGEGYSYP-HTPP 238
Query: 249 -----GLAVALKQVCT 259
L AL +
Sbjct: 239 VNLLYALREALDLILE 254
>gnl|CDD|151689 pfam11247, DUF2675, Protein of unknown function (DUF2675). Members
in this family of proteins are annotated as Gene protein
5.5. Currently no function is known.
Length = 98
Score = 31.3 bits (71), Expect = 0.15
Identities = 16/65 (24%), Positives = 29/65 (44%), Gaps = 5/65 (7%)
Query: 162 AIMLADMAHISGLVAAGVIPSPFEYADVVTTTTHKSLRGPRGAMIF-FRKGVKEINKQGK 220
+ + ++ AG +PF+ +V TH GP GA F ++G++E K+
Sbjct: 23 ENLKKTLLDLAKKAGAGEKLTPFDREMLVQGLTH----GPEGAAAFVVKQGIREAIKEML 78
Query: 221 EVFYD 225
+ D
Sbjct: 79 SEYSD 83
>gnl|CDD|133889 PHA00440, PHA00440, host protein H-NS-interacting protein.
Length = 98
Score = 30.6 bits (69), Expect = 0.23
Identities = 21/74 (28%), Positives = 36/74 (48%), Gaps = 5/74 (6%)
Query: 155 KVCNKQKAIMLADMAHISGLVAAGVIPSPFEYADVVTTTTHKSLRGPRGAMIF-FRKGVK 213
K+ ++ +AI+ D+ ++ AG +P + +V TH GP GA F R+G++
Sbjct: 16 KMDSETEAILEEDILDLAKQAGAGEEVNPKDKELLVQALTH----GPEGAAAFAVRQGIR 71
Query: 214 EINKQGKEVFYDYE 227
E K E D +
Sbjct: 72 EAIKDMHEESTDKD 85
>gnl|CDD|188641 cd00954, NAL, N-Acetylneuraminic acid aldolase, also called
N-acetylneuraminate lyase (NAL). N-Acetylneuraminic
acid aldolase, also called N-acetylneuraminate lyase
(NAL), which catalyses the reversible aldol reaction of
N-acetyl-D-mannosamine and pyruvate to give
N-acetyl-D-neuraminic acid (D-sialic acid). It has a
widespread application as biocatalyst for the synthesis
of sialic acid and its derivatives. This enzyme has been
shown to be quite specific for pyruvate as the donor,
but flexible to a variety of D- and, to some extent,
L-hexoses and pentoses as acceptor substrates. NAL is
member of dihydrodipicolinate synthase family that
comprises several pyruvate-dependent class I aldolases.
Length = 288
Score = 31.1 bits (71), Expect = 0.56
Identities = 22/67 (32%), Positives = 30/67 (44%), Gaps = 5/67 (7%)
Query: 125 LEKSATLFR-PKLIVAGASAYARLYDYERIRKVCNKQKAIMLA-DMAHISGLV--AAGVI 180
LE+ LF P +I +A LYD ERIR + K ++ D +S L A G I
Sbjct: 146 LEQFLELFEIPNVIGVKFTA-TDLYDLERIRAASPEDKLVLNGFDEMLLSALALGADGAI 204
Query: 181 PSPFEYA 187
S +
Sbjct: 205 GSTYNVN 211
>gnl|CDD|153087 cd01678, PFL1, Pyruvate formate lyase 1. Pyruvate formate lyase
catalyzes a key step in anaerobic glycolysis, the
conversion of pyruvate and CoenzymeA to formate and
acetylCoA. The PFL mechanism involves an unusual radical
cleavage of pyruvate in which two cysteines and one
glycine form radicals that are required for catalysis.
PFL has a ten-stranded alpha/beta barrel domain that is
structurally similar to those of all three
ribonucleotide reductase (RNR) classes as well as
benzylsuccinate synthase and B12-independent glycerol
dehydratase.
Length = 738
Score = 31.6 bits (72), Expect = 0.63
Identities = 13/42 (30%), Positives = 22/42 (52%), Gaps = 4/42 (9%)
Query: 213 KEINKQGKEVFYDYEEKINQAVF----PGLQGGPHNHTITGL 250
E++ + K++F Y + N VF P ++ H+ ITGL
Sbjct: 118 YELDPELKKIFTKYRKTHNDGVFDAYTPEIRRARHSGIITGL 159
>gnl|CDD|223476 COG0399, WecE, Predicted pyridoxal phosphate-dependent enzyme
apparently involved in regulation of cell wall
biogenesis [Cell envelope biogenesis, outer membrane].
Length = 374
Score = 31.1 bits (71), Expect = 0.74
Identities = 15/65 (23%), Positives = 25/65 (38%), Gaps = 2/65 (3%)
Query: 114 NESTGYIDYDQLEKSATLFRPKLIVAGASAYARLYDYERIRKVCNKQKAIMLADMAHISG 173
+ T ID D +E + T R K I+ + D + I + + ++ D A G
Sbjct: 104 DPDTLNIDPDLIEAAITP-RTKAIIP-VHLAGQPCDMDAIMALAKRHGLPVIEDAAQAHG 161
Query: 174 LVAAG 178
G
Sbjct: 162 ATYKG 166
>gnl|CDD|219349 pfam07250, Glyoxal_oxid_N, Glyoxal oxidase N-terminus. This family
represents the N-terminus (approximately 300 residues)
of a number of plant and fungal glyoxal oxidase enzymes.
Glyoxal oxidase catalyzes the oxidation of aldehydes to
carboxylic acids, coupled with reduction of dioxygen to
hydrogen peroxide. It is an essential component of the
extracellular lignin degradation pathways of the
wood-rot fungus Phanerochaete chrysosporium.
Length = 243
Score = 30.1 bits (68), Expect = 1.1
Identities = 13/35 (37%), Positives = 20/35 (57%), Gaps = 4/35 (11%)
Query: 222 VFYDYEEKINQAV--FPGLQGGPHNHTITGLAVAL 254
+ +DY + N V FP + GGP N+ +G +V L
Sbjct: 192 ILFDY--RKNTVVKEFPQIPGGPRNYPSSGSSVLL 224
>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 = 29.8 bits (68), Expect = 1.5
Identities = 24/103 (23%), Positives = 35/103 (33%), Gaps = 18/103 (17%)
Query: 124 QLEKSATLFRPKLIVA-------GASAYARLYDYERIRKVCNKQKAIMLADMAHISGLV- 175
L ++ + KLIV G A + + K AI+ D AH G+
Sbjct: 123 LLREARRPYGKKLIVTEGVYSMDGDIA-----PLPELVDLAKKYGAILFVDEAHSVGVYG 177
Query: 176 --AAGVIPSPFEYADV--VTTTTHKSLRGPRGAMIFFRKGVKE 214
GV DV + T K+ G G I K + +
Sbjct: 178 PHGRGVEEFGGLTDDVDIIMGTLGKAF-GAVGGYIAGSKELID 219
>gnl|CDD|226509 COG4022, COG4022, Uncharacterized protein conserved in archaea
[Function unknown].
Length = 286
Score = 29.4 bits (66), Expect = 2.5
Identities = 24/91 (26%), Positives = 47/91 (51%), Gaps = 13/91 (14%)
Query: 113 LNESTGYID-YDQLEKSATLFRPKLIVAGASAYARLYDYERIRKVCNKQKAIMLADMAHI 171
L+ T ID + ++K+A L K+ V A A +R+RK+ + +++ + H+
Sbjct: 147 LDPKTATIDQVEGVKKAAELGYKKVAVTVADAE----TAKRLRKLEADELDLLVIAV-HV 201
Query: 172 SGLV---AAGVIPSPFEYADVVTTTTHKSLR 199
+G+ A G++ E +D+VT+ K +R
Sbjct: 202 TGIDEEEAQGLV----ENSDIVTSCASKYIR 228
>gnl|CDD|234315 TIGR03695, menH_SHCHC,
2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate
synthase. This protein catalyzes the formation of
SHCHC, or (1 R,6
R)-2-succinyl-6-hydroxy-2,
4-cyclohexadiene-1-carboxylate, by elmination of
pyruvate from
2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-
carboxylate (SEPHCHC). Note that SHCHC synthase
activity previously was attributed to MenD, which in
fact is SEPHCHC synthase [Biosynthesis of cofactors,
prosthetic groups, and carriers, Menaquinone and
ubiquinone].
Length = 252
Score = 29.1 bits (66), Expect = 2.7
Identities = 15/35 (42%), Positives = 20/35 (57%), Gaps = 1/35 (2%)
Query: 57 LSGSPSNFQVYTALLKPHDRIMALDLP-HGGHLSH 90
GS +++Q LL PH R +A+DLP HG S
Sbjct: 11 FLGSGADWQALIELLGPHFRCLAIDLPGHGSSQSP 45
>gnl|CDD|193557 cd05682, M20_dipept_like_5, Uncharacterized M20 Dipeptidases.
Peptidase M20 family, unknown dipeptidase-like subfamily
3 (inferred by homology to be dipeptidases). M20
dipeptidases include a large variety of bacterial
enzymes including cytosolic nonspecific dipeptidase
(CNDP), Xaa-methyl-His dipeptidase (anserinase),and
canosinase. These dipeptidases have been shown to act on
a wide range of dipeptides, but not larger peptides. For
example, anserinase mainly catalyzes the hydrolysis of
N-alpha-acetylhistidine while carnosinase degrades
beta-alanyl-L-histidine.
Length = 451
Score = 29.2 bits (66), Expect = 2.8
Identities = 20/75 (26%), Positives = 33/75 (44%), Gaps = 6/75 (8%)
Query: 115 ESTGYIDYDQ-LEK-SATLFRPKLIV---AGASAYARLYDYERIRKVCNKQKAIMLADMA 169
E +G D L+K + L+V +G Y +L+ +R V + + D
Sbjct: 147 EESGSYDLPAYLDKLKERIGNVDLVVCLDSGCGNYEQLWLTTSLRGVLGGDLTVQVLDEG 206
Query: 170 HISGLVAAGVIPSPF 184
SG A+G++PS F
Sbjct: 207 VHSG-DASGIVPSSF 220
>gnl|CDD|224832 COG1921, SelA, Selenocysteine synthase [seryl-tRNASer selenium
transferase] [Amino acid transport and metabolism].
Length = 395
Score = 29.3 bits (66), Expect = 2.8
Identities = 23/108 (21%), Positives = 36/108 (33%), Gaps = 34/108 (31%)
Query: 134 PKLIVAGASAYARLYDYERIRKVCNKQ-KAIM-----------------LADMAHISGLV 175
KL+ G + L DY N+ ++ L ++AH GL
Sbjct: 133 AKLVEVGTTNRTHLKDY---ELAINENTALLLKVHSSNYGFTGMLSEEELVEIAHEKGLP 189
Query: 176 ----AAGVIPSPFEY---------ADVVTTTTHKSLRGPRGAMIFFRK 210
A E AD+V+ + K L GP+ +I +K
Sbjct: 190 VIVDLASGALVDKEPDLREALALGADLVSFSGDKLLGGPQAGIIVGKK 237
>gnl|CDD|213830 TIGR03576, pyridox_MJ0158, pyridoxal phosphate enzyme, MJ0158
family. Members of this archaeal protein family are
pyridoxal phosphate enzymes of unknown function.
Sequence similarity to SelA, a bacterial enzyme of
selenocysteine biosynthesis, has led to some members
being misannotated as functionally equivalent, but
selenocysteine is made on tRNA in Archaea by a two-step
process that does not involve a SelA homolog [Unknown
function, Enzymes of unknown specificity].
Length = 346
Score = 29.0 bits (65), Expect = 3.3
Identities = 32/119 (26%), Positives = 55/119 (46%), Gaps = 14/119 (11%)
Query: 116 STGYIDYDQLEKSATLFRPKL-IVAGASAYARLYDYERIRKVCNKQK---AIMLADMAHI 171
Y + D+L + + L ++ G++ ++ E +++V + K AI+L D A
Sbjct: 119 GAEYFESDELSELKKIDGTSLVVITGSTMDLKVVSEEDLKRVIKQAKSKEAIVLVDDA-- 176
Query: 172 SGL---VAAGVIPSPFEYADVVTTTTHKSLRGPRGAMIFFRK----GVK-EINKQGKEV 222
SG G P+ AD+V T+T K + GPRG ++ RK +K + G E
Sbjct: 177 SGARVRRLYGQPPALDLGADLVVTSTDKLMDGPRGGLLAGRKELVDKIKSVGEQFGLEA 235
>gnl|CDD|99740 cd00616, AHBA_syn, 3-amino-5-hydroxybenzoic acid synthase family
(AHBA_syn). AHBA_syn family belongs to pyridoxal
phosphate (PLP)-dependent aspartate aminotransferase
superfamily (fold I). The members of this CD are
involved in various biosynthetic pathways for secondary
metabolites. Some well studied proteins in this CD are
AHBA_synthase, protein product of pleiotropic regulatory
gene degT, Arnb aminotransferase and pilin
glycosylation protein. The prototype of this family, the
AHBA_synthase, is a dimeric PLP dependent enzyme.
AHBA_syn is the terminal enzyme of
3-amino-5-hydroxybenzoic acid (AHBA) formation which is
involved in the biosynthesis of ansamycin antibiotics,
including rifamycin B. Some members of this CD are
involved in 4-amino-6-deoxy-monosaccharide D-perosamine
synthesis. Perosamine is an important element in the
glycosylation of several cell products, such as
antibiotics and lipopolysaccharides of gram-positive and
gram-negative bacteria. The pilin glycosylation protein
encoded by gene pglA, is a galactosyltransferase
involved in pilin glycosylation. Additionally, this CD
consists of ArnB (PmrH) aminotransferase, a
4-amino-4-deoxy-L-arabinose lipopolysaccharide-modifying
enzyme. This CD also consists of several predicted
pyridoxal phosphate-dependent enzymes apparently
involved in regulation of cell wall biogenesis. The
catalytic lysine which is present in all characterized
PLP dependent enzymes is replaced by histidine in some
members of this CD.
Length = 352
Score = 28.7 bits (65), Expect = 3.4
Identities = 14/61 (22%), Positives = 24/61 (39%), Gaps = 10/61 (16%)
Query: 114 NESTGYIDYDQLEKSATLFRPKLIV----AGASAYARLYDYERIRKVCNKQKAIMLADMA 169
+ T ID + +E + T R K I+ G A D + I + + ++ D A
Sbjct: 88 DPDTYNIDPELIEAAITP-RTKAIIPVHLYGNPA-----DMDAIMAIAKRHGLPVIEDAA 141
Query: 170 H 170
Sbjct: 142 Q 142
>gnl|CDD|131032 TIGR01977, am_tr_V_EF2568, cysteine desulfurase family protein.
This model describes a subfamily of probable pyridoxal
phosphate-dependent enzymes in the aminotransferase
class V family. Related families contain members active
as cysteine desulfurases, selenocysteine lyases, or
both. The members of this family form a distinct clade
and all are shorter at the N-terminus. The function of
this subfamily is unknown [Unknown function, Enzymes of
unknown specificity].
Length = 376
Score = 28.9 bits (65), Expect = 3.8
Identities = 27/98 (27%), Positives = 40/98 (40%), Gaps = 10/98 (10%)
Query: 115 ESTGYIDYDQLEKSATLFRPKLIVAG-ASAYARLY-DYERIRKVCNKQKAIMLADMAHIS 172
++ G I +++ K A KLIV AS E I ++ + + D A
Sbjct: 120 DNEGLISPERI-KRAIKTNTKLIVVSHASNVTGTILPIEEIGELAQENGIFFILDAAQ-- 176
Query: 173 GLVAAGVIPSPFEYA--DVVTTTTHKSLRGPRGAMIFF 208
AGVIP D++ T HK L GP+G +
Sbjct: 177 ---TAGVIPIDMTELAIDMLAFTGHKGLLGPQGTGGLY 211
>gnl|CDD|224893 COG1982, LdcC, Arginine/lysine/ornithine decarboxylases [Amino acid
transport and metabolism].
Length = 557
Score = 28.8 bits (65), Expect = 4.0
Identities = 32/143 (22%), Positives = 55/143 (38%), Gaps = 25/143 (17%)
Query: 101 AVSIFFETMPYRLNESTGY---IDYDQLEKSATLFRPK----LIVAGASAYARLYDYERI 153
A ++ E P R N G I + ++ A L P ++ + Y+ +I
Sbjct: 132 ATPVYLE--PSR-NPLYGIIGGIPLETFKE-ALLAHPDAEKLAVITNPTYDGVCYNLRKI 187
Query: 154 RKVCNKQKAIMLADMAHIS--GLVAAGVIPSPFEYADVVTTTTHKSLRGPR-GAMIFFRK 210
++ + A +L D AH + + AD VT +THK L +MI +
Sbjct: 188 VELLHHYGAWVLYDEAHPAHFDFSPMLPESALNGGADFVTQSTHKLLAALSQASMIHVKD 247
Query: 211 GVKEINKQGKEVFYDYEEKINQA 233
G + +N E+ N+A
Sbjct: 248 G-RAVN----------HERFNEA 259
>gnl|CDD|225280 COG2423, COG2423, Predicted ornithine cyclodeaminase, mu-crystallin
homolog [Amino acid transport and metabolism].
Length = 330
Score = 28.4 bits (64), Expect = 4.3
Identities = 20/69 (28%), Positives = 25/69 (36%), Gaps = 10/69 (14%)
Query: 136 LIVAGASAY------ARLYDYERIRKVC-NKQKAIMLADMAHISGLVAAGVIPSP---FE 185
+I AGA A + D IR + + A A G A G S E
Sbjct: 135 IIGAGAQARTQLEALKAVRDIREIRVYSRDPEAAEAFAARLRKRGGEAVGAADSAEEAVE 194
Query: 186 YADVVTTTT 194
AD+V T T
Sbjct: 195 GADIVVTAT 203
>gnl|CDD|132318 TIGR03275, methan_mark_8, putative methanogenesis marker protein 8.
Members of this protein family, to date, are found in a
completed prokaryotic genome if and only if the species
is one of the archaeal methanogens. The exact function
is unknown, but likely is linked to methanogenesis or a
process closely connected to it.
Length = 259
Score = 28.1 bits (63), Expect = 4.7
Identities = 29/123 (23%), Positives = 53/123 (43%), Gaps = 10/123 (8%)
Query: 113 LNESTGYID-YDQLEKSATLFRPKLIVAGASAYARLYDYERIRKVCNKQKAIMLADMAHI 171
L+ T ID +EK+ L K+ V A A D + IR++ ++ ++ H
Sbjct: 142 LDPDTATIDQIKGVEKAIELGYKKIAVTVADAE----DAKAIRELESESGIDIIIFAVHT 197
Query: 172 SGLVAAGVIPSPFEYADVVTTTTHKSLRGPRGAMIFFRKG----VKEINKQGKEVFYDYE 227
+G+ +YAD+VT+ K++R + G V + +GKE+ +
Sbjct: 198 TGIDREDA-EEVVQYADIVTSCASKNIREIAKPRALLQVGSAVPVYALTDKGKELLLERA 256
Query: 228 EKI 230
+ I
Sbjct: 257 KDI 259
>gnl|CDD|129937 TIGR00858, bioF, 8-amino-7-oxononanoate synthase.
7-keto-8-aminopelargonic acid synthetase is an alternate
name. This model represents 8-amino-7-oxononanoate
synthase, the BioF protein of biotin biosynthesis. This
model is based on a careful phylogenetic analysis to
separate members of this family from
2-amino-3-ketobutyrate and other related pyridoxal
phosphate-dependent enzymes. In several species,
including Staphylococcus and Coxiella, a candidate
8-amino-7-oxononanoate synthase is confirmed by location
in the midst of a biotin biosynthesis operon but scores
below the trusted cutoff of this model [Biosynthesis of
cofactors, prosthetic groups, and carriers, Biotin].
Length = 360
Score = 28.4 bits (64), Expect = 5.0
Identities = 41/166 (24%), Positives = 59/166 (35%), Gaps = 44/166 (26%)
Query: 58 SGSPSNFQVYTALLKPHDRIMALDLPH-----GGHLSHGYQTDTKKISAVSIFFETMPYR 112
SG +N V +AL+ D I++ L H G LS YR
Sbjct: 84 SGYLANVGVISALVGKGDLILSDALNHASLIDGCRLSGA---------------RVRRYR 128
Query: 113 LNESTGYIDYDQLE---KSATLFRPKLIVAGA--SAYARLYDYERIRKVCNKQKAIMLAD 167
N D + LE + R KLIV S + ++ + + A ++ D
Sbjct: 129 HN------DVEHLERLLEKNRGERRKLIVTDGVFSMDGDIAPLPQLVALAERYGAWLMVD 182
Query: 168 MAHISG---------LVAAGVIPSPFEYADVVTTTTHKSLRGPRGA 204
AH +G L G+ P P D+ T K+L G GA
Sbjct: 183 DAHGTGVLGEDGRGTLEHFGLKPEP---VDIQVGTLSKAL-GSYGA 224
>gnl|CDD|223154 COG0076, GadB, Glutamate decarboxylase and related PLP-dependent
proteins [Amino acid transport and metabolism].
Length = 460
Score = 28.5 bits (64), Expect = 5.2
Identities = 20/107 (18%), Positives = 35/107 (32%), Gaps = 18/107 (16%)
Query: 120 IDYDQLEKSATLFRPKLIV---AGASAYARLYDYERIRKVCNKQKAIMLADMAHISGLVA 176
ID D LE++ +V AG + + D E + + + + H+
Sbjct: 193 IDVDALEEAIDENTIGGVVVGTAGTTDTGSIDDIEELADIAEEYGIWL-----HVDAAFG 247
Query: 177 AGVIPSPFEY---------ADVVTTTTHKSLRGPRGA-MIFFRKGVK 213
++P D +T HK P G ++ FR
Sbjct: 248 GFLLPFLEPDGRWDFGLEGVDSITVDGHKYGLAPIGCGVVLFRDEEA 294
>gnl|CDD|233331 TIGR01255, pyr_form_ly_1, formate acetyltransferase 1. Alternate
names: pyruvate formate-lyase; formate
C-acetyltransferase This enzyme converts formate +
acetyl-CoA into pyruvate + CoA. This model describes
formate acetyltransferase 1. More distantly related
putative formate acetyltransferases have also been
identified, including formate acetyltransferase 2 from
E. coli, which is excluded from this model [Energy
metabolism, Fermentation].
Length = 744
Score = 28.3 bits (63), Expect = 5.3
Identities = 24/106 (22%), Positives = 42/106 (39%), Gaps = 15/106 (14%)
Query: 158 NKQKAIMLADMAHISGL--VAAGVIPSPFEYADVVTTTTHKSLR---GPRGAMIFFRKGV 212
+ ++ D +S + + AG I E +V T L+ P G + K +
Sbjct: 55 HYEEVGFDFDTDRVSSIDSIPAGYIDKELEL--IVGMQTSAPLKRNFMPFGGIRMAEKSL 112
Query: 213 KE----INKQGKEVFYDYEEKINQAVF----PGLQGGPHNHTITGL 250
KE ++ ++F Y + NQ VF ++ H +TGL
Sbjct: 113 KEYGLSVDPGLHDIFTQYRKTHNQGVFDAYTSAIRKARHAGVLTGL 158
>gnl|CDD|99738 cd00614, CGS_like, CGS_like: Cystathionine gamma-synthase is a PLP
dependent enzyme and catalyzes the committed step of
methionine biosynthesis. This pathway is unique to
microorganisms and plants, rendering the enzyme an
attractive target for the development of antimicrobials
and herbicides. This subgroup also includes
cystathionine gamma-lyases (CGL), O-acetylhomoserine
sulfhydrylases and O-acetylhomoserine thiol lyases.
CGL's are very similar to CGS's. Members of this group
are widely distributed among all three forms of life.
Length = 369
Score = 27.9 bits (63), Expect = 6.0
Identities = 28/130 (21%), Positives = 52/130 (40%), Gaps = 25/130 (19%)
Query: 66 VYTALLKPHDRIMALDLPHGGHLSHGYQTDTKKISAVSIFFETMPYRLNESTGYIDYDQL 125
V ALLK D ++A D +GG +F +P +L ++D D
Sbjct: 71 VLLALLKAGDHVVASDDLYGG--------------TYRLFERLLP-KLGIEVTFVDPDDP 115
Query: 126 EKSATLFRPK----LIVAGASAYARLYDYERIRKVCNKQKAIMLADMAHISGLVAAGVIP 181
E +P+ + + + ++ D E I ++ ++ A+++ D A +
Sbjct: 116 EALEAAIKPETKLVYVESPTNPTLKVVDIEAIAELAHEHGALLVVD-----NTFATPYLQ 170
Query: 182 SPFEY-ADVV 190
P E AD+V
Sbjct: 171 RPLELGADIV 180
>gnl|CDD|182007 PRK09634, nusB, transcription antitermination protein NusB;
Provisional.
Length = 207
Score = 27.5 bits (62), Expect = 7.1
Identities = 13/36 (36%), Positives = 16/36 (44%)
Query: 128 SATLFRPKLIVAGASAYARLYDYERIRKVCNKQKAI 163
SA L P+L+ R Y ERI V +K I
Sbjct: 95 SAALELPELLQLADQEEVREYALERIGAVIRNRKEI 130
>gnl|CDD|212534 cd10010, HDAC1, Histone deacetylase 1 (HDAC1). Histone deacetylase
1 (HDAC1) is a Zn-dependent class I enzyme that
catalyzes hydrolysis of N(6)-acetyl-lysine residue of a
histone to yield a deacetylated histone (EC 3.5.1.98).
Histone acetylation/deacetylation process is important
for mediation of transcriptional regulation of many
genes. HDAC1 is involved in regulation through
association with DNA binding proteins to target specific
chromatin regions. In particular, HDAC1 appears to play
a major role in pre-implantation embryogenesis in
establishing a repressive chromatin state. Its
interaction with retinoblastoma tumor-suppressor protein
is essential in the control of cell proliferation and
differentiation. Together with metastasis-associated
protein-2 (MTA2), it deacetylates p53, thereby
modulating its effect on cell growth and apoptosis. It
participates in DNA-damage response, along with HDAC2;
together, they promote DNA non-homologous end-joining.
HDAC1 is also involved in tumorogenesis; its
overexpression modulates cancer progression. Specific
inhibitors of HDAC1 are currently used in cancer
therapy.
Length = 371
Score = 27.7 bits (61), Expect = 8.1
Identities = 11/25 (44%), Positives = 18/25 (72%)
Query: 269 FSLHVYPAFVSNQNNSENIEEDKGR 293
F LH+ P+ ++NQN +E +E+ K R
Sbjct: 338 FKLHISPSNMTNQNTNEYLEKIKQR 362
>gnl|CDD|216267 pfam01053, Cys_Met_Meta_PP, Cys/Met metabolism PLP-dependent
enzyme. This family includes enzymes involved in
cysteine and methionine metabolism. The following are
members: Cystathionine gamma-lyase, Cystathionine
gamma-synthase, Cystathionine beta-lyase, Methionine
gamma-lyase, OAH/OAS sulfhydrylase, O-succinylhomoserine
sulfhydrylase All of these members participate is
slightly different reactions. All these enzymes use PLP
(pyridoxal-5'-phosphate) as a cofactor.
Length = 382
Score = 27.6 bits (62), Expect = 9.6
Identities = 33/148 (22%), Positives = 55/148 (37%), Gaps = 25/148 (16%)
Query: 58 SGSPSNFQVYTALLKPHDRIMALDLPHGGHLSHGYQTDTKKISAVSIFFETMPYRLNEST 117
SG + F ALLK D ++A D +GG FE + R
Sbjct: 75 SGMAAIFAALLALLKAGDHVVATDDLYGG---------------TYRLFEKVLPRFGIEV 119
Query: 118 GYIDYDQLEKSATLFRPK----LIVAGASAYARLYDYERIRKVCNKQKAIMLADMAHISG 173
++D L+ +P + + ++ D E I K+ K A+++ D
Sbjct: 120 TFVDPSDLDALEAAIKPNTKAVFLETPTNPLLKVVDIEAIAKIAKKHGALVVVD-----N 174
Query: 174 LVAAGVIPSPFEY-ADVVTTTTHKSLRG 200
A+ + P E AD+V + K + G
Sbjct: 175 TFASPYLQRPLELGADIVVHSATKYIGG 202
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.319 0.135 0.400
Gapped
Lambda K H
0.267 0.0637 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,327,341
Number of extensions: 1460561
Number of successful extensions: 1283
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1256
Number of HSP's successfully gapped: 44
Length of query: 297
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 201
Effective length of database: 6,679,618
Effective search space: 1342603218
Effective search space used: 1342603218
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: 59 (26.7 bits)