RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 018401
(356 letters)
>gnl|CDD|215639 PLN03226, PLN03226, serine hydroxymethyltransferase; Provisional.
Length = 475
Score = 670 bits (1732), Expect = 0.0
Identities = 235/309 (76%), Positives = 258/309 (83%), Gaps = 3/309 (0%)
Query: 13 EKNGVTWPKQLNAPLEVVDPEIADIIEHEKARQWKGLELIPSENFTSVSVMQAVGSVMTN 72
EK+ V+ PK NAPLE VDPEIADIIE EK RQWKGLELI SENFTS +VM+A+GS +TN
Sbjct: 1 EKSMVSVPKWGNAPLEEVDPEIADIIEKEKRRQWKGLELIASENFTSRAVMEALGSCLTN 60
Query: 73 KYSEGYPGARYYGGNEYIDMAESLCQKRALEAFRLDPEKWGG---SLSGSPSNFQVYTAL 129
KYSEG PGARYYGGNEYID E+LCQKRALEAFRLDPEKWG LSGSP+NF VYTAL
Sbjct: 61 KYSEGLPGARYYGGNEYIDQIETLCQKRALEAFRLDPEKWGVNVQPLSGSPANFAVYTAL 120
Query: 130 LKPHDRIMALDLPHGGHLSHGYQTDTKKISAVSIFFETMPYRLNESTGYIDYDQLEKSAT 189
L+PHDRIM LDLPHGGHLSHGYQTD KKISA SI+FE+MPYRL+ESTG IDYD+LEK A
Sbjct: 121 LQPHDRIMGLDLPHGGHLSHGYQTDGKKISATSIYFESMPYRLDESTGLIDYDKLEKKAM 180
Query: 190 LFRPKLIVAGASAYARLYDYERIRKVCNKQKAIMLADMAHISGLVAAGVIPSPFEYADVV 249
LFRPKLI+AGASAY R +DY R+RK+ +K A+++ DMAHISGLVAA SPFEY DVV
Sbjct: 181 LFRPKLIIAGASAYPRDWDYARMRKIADKVGALLMCDMAHISGLVAAQEAASPFEYCDVV 240
Query: 250 TTTTHKSLRGPRGAMIFFRKGVKEINKQGKEVFYDYEEKINQAVFPGLQGGPHNHTITGL 309
TTTTHKSLRGPRG MIFFRKG K QG+ YDYE+KIN AVFPGLQGGPHNHTI L
Sbjct: 241 TTTTHKSLRGPRGGMIFFRKGPKPPKGQGEGAVYDYEDKINFAVFPGLQGGPHNHTIAAL 300
Query: 310 AVALKQVCT 318
AVALKQ T
Sbjct: 301 AVALKQAMT 309
>gnl|CDD|240264 PTZ00094, PTZ00094, serine hydroxymethyltransferase; Provisional.
Length = 452
Score = 535 bits (1381), Expect = 0.0
Identities = 190/299 (63%), Positives = 231/299 (77%), Gaps = 14/299 (4%)
Query: 23 LNAPLEVVDPEIADIIEHEKARQWKGLELIPSENFTSVSVMQAVGSVMTNKYSEGYPGAR 82
LN L+ DPE+ ++IE EK RQ +GLELI SENFTS +V++ +GS TNKY+EG PG R
Sbjct: 11 LNQSLKEADPELYELIEKEKERQIEGLELIASENFTSRAVLECLGSCFTNKYAEGLPGNR 70
Query: 83 YYGGNEYIDMAESLCQKRALEAFRLDPEKWGGS---LSGSPSNFQVYTALLKPHDRIMAL 139
YYGGNE +D E+LCQKRALEAF LDPE+WG + SGSP+NF VYTALL+PHDRIM L
Sbjct: 71 YYGGNEVVDKIENLCQKRALEAFGLDPEEWGVNVQPYSGSPANFAVYTALLQPHDRIMGL 130
Query: 140 DLPHGGHLSHGYQTDTKKISAVSIFFETMPYRLNESTGYIDYDQLEKSATLFRPKLIVAG 199
DLP GGHL+HG+ T KK+SA SI+FE++PY++NE G IDYD+LE+ A FRPKLI+AG
Sbjct: 131 DLPSGGHLTHGFYTAKKKVSATSIYFESLPYQVNE-KGLIDYDKLEELAKAFRPKLIIAG 189
Query: 200 ASAYARLYDYERIRKVCNKQKAIMLADMAHISGLVAAGVIPSPFEYADVVTTTTHKSLRG 259
ASAY R DY+R R++C+ A ++AD+AH SGLVAAGV+PSPF YADVVTTTTHKSLRG
Sbjct: 190 ASAYPRDIDYKRFREICDSVGAYLMADIAHTSGLVAAGVLPSPFPYADVVTTTTHKSLRG 249
Query: 260 PRGAMIFFRKGVKEINKQGKEVFYDYEEKINQAVFPGLQGGPHNHTITGLAVALKQVCT 318
PR +IF+RK VK D E KIN+AVFPGLQGGPHNH I +AV LK+V +
Sbjct: 250 PRSGLIFYRKKVKP----------DIENKINEAVFPGLQGGPHNHQIAAIAVQLKEVQS 298
>gnl|CDD|189558 pfam00464, SHMT, Serine hydroxymethyltransferase.
Length = 380
Score = 494 bits (1273), Expect = e-176
Identities = 183/297 (61%), Positives = 213/297 (71%), Gaps = 27/297 (9%)
Query: 27 LEVVDPEIADIIEHEKARQWKGLELIPSENFTSVSVMQAVGSVMTNKYSEGYPGARYYGG 86
L DPEI DII+ EK RQ +G+ELI SENFTS +VM+A+GSV+TNKY+EGYPG RYYGG
Sbjct: 1 LSDSDPEIFDIIKKEKERQREGIELIASENFTSRAVMEALGSVLTNKYAEGYPGKRYYGG 60
Query: 87 NEYIDMAESLCQKRALEAFRLD-----PEKWGGSLSGSPSNFQVYTALLKPHDRIMALDL 141
EY+D E+L Q RA E F LD P LSGS +N VYTALL P DRIM LDL
Sbjct: 61 CEYVDEVETLAQDRAKELFGLDGVNVQP------LSGSQANLAVYTALLNPGDRIMGLDL 114
Query: 142 PHGGHLSHGYQTDTKKISAVSIFFETMPYRLNESTGYIDYDQLEKSATLFRPKLIVAGAS 201
PHGGHL+HGY + FFE+MPY ++ TG IDYDQLEK+A LF+PKLIVAG S
Sbjct: 115 PHGGHLTHGYPVNF-----SGKFFESMPYGVDPDTGLIDYDQLEKNAKLFKPKLIVAGTS 169
Query: 202 AYARLYDYERIRKVCNKQKAIMLADMAHISGLVAAGVIPSPFEYADVVTTTTHKSLRGPR 261
AY+RL DY R R++ ++ A ++ DMAHI+GLVAAGVIPSPF YA VVTTTTHK+LRGPR
Sbjct: 170 AYSRLIDYARFREIADEVGAYLMVDMAHIAGLVAAGVIPSPFPYAHVVTTTTHKTLRGPR 229
Query: 262 GAMIFFRKGVKEINKQGKEVFYDYEEKINQAVFPGLQGGPHNHTITGLAVALKQVCT 318
G MIFFR E+ Y+ E+KIN AVFPGLQGGP NH I AVALKQ T
Sbjct: 230 GGMIFFR-----------EILYELEKKINSAVFPGLQGGPLNHVIAAKAVALKQALT 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 = 446 bits (1149), Expect = e-157
Identities = 161/291 (55%), Positives = 197/291 (67%), Gaps = 27/291 (9%)
Query: 30 VDPEIADIIEHEKARQWKGLELIPSENFTSVSVMQAVGSVMTNKYSEGYPGARYYGGNEY 89
VDPEIA+II+ E RQ + LELI SENFTS +VM+A+GS +TNKY+EGYPG RYYGG EY
Sbjct: 3 VDPEIAEIIKKENERQRETLELIASENFTSPAVMEAMGSDLTNKYAEGYPGKRYYGGCEY 62
Query: 90 IDMAESLCQKRALEAFRLD-----PEKWGGSLSGSPSNFQVYTALLKPHDRIMALDLPHG 144
+D E L +RA + F + P SGS +N VY ALL+P D IM LDL HG
Sbjct: 63 VDEIEDLAIERAKKLFGAEYANVQP------HSGSQANLAVYFALLEPGDTIMGLDLSHG 116
Query: 145 GHLSHGYQTDTKKISAVSIFFETMPYRLNESTGYIDYDQLEKSATLFRPKLIVAGASAYA 204
GHL+HG T K+SA FE++PY ++ TG IDYD LEK A F+PKLIVAGASAY
Sbjct: 117 GHLTHGSFT---KVSASGKLFESVPYGVDPETGLIDYDALEKMALEFKPKLIVAGASAYP 173
Query: 205 RLYDYERIRKVCNKQKAIMLADMAHISGLVAAGVIPSPFEYADVVTTTTHKSLRGPRGAM 264
R D++R R++ ++ A +L DMAH++GLVA GV P+P ADVVTTTTHK+LRGPRG +
Sbjct: 174 RPIDFKRFREIADEVGAYLLVDMAHVAGLVAGGVFPNPLPGADVVTTTTHKTLRGPRGGL 233
Query: 265 IFFRKGVKEINKQGKEVFYDYEEKINQAVFPGLQGGPHNHTITGLAVALKQ 315
I RKG + +KIN AVFPGLQGGPH H I AVALK+
Sbjct: 234 ILTRKG-------------ELAKKINSAVFPGLQGGPHLHVIAAKAVALKE 271
>gnl|CDD|215153 PLN02271, PLN02271, serine hydroxymethyltransferase.
Length = 586
Score = 425 bits (1095), Expect = e-146
Identities = 180/306 (58%), Positives = 226/306 (73%), Gaps = 12/306 (3%)
Query: 24 NAPLEVVDPEIADIIEHEKARQWKGLELIPSENFTSVSVMQAVGSVMTNKYSEGYPGARY 83
N PL DP+I +++E EK RQ+KG+ELI SENF +VM+A+GS +TNKYSEG PGARY
Sbjct: 126 NQPLPEADPDIHELMEKEKQRQFKGIELIASENFVCRAVMEALGSHLTNKYSEGMPGARY 185
Query: 84 YGGNEYIDMAESLCQKRALEAFRLDPEKWGGSL---SGSPSNFQVYTALLKPHDRIMALD 140
Y GN+YID E LC +RAL AF LD EKWG ++ S + +NF VYT LL P DRIM LD
Sbjct: 186 YTGNQYIDQIERLCCERALAAFGLDSEKWGVNVQPYSCTSANFAVYTGLLLPGDRIMGLD 245
Query: 141 LPHGGHLSHGYQTDT-KKISAVSIFFETMPYRLNESTGYIDYDQLEKSATLFRPKLIVAG 199
P GGH+SHGY T KK+S SIFFE++PY++N TGYIDYD+LE+ A FRPK+++ G
Sbjct: 246 SPSGGHMSHGYYTPGGKKVSGASIFFESLPYKVNPQTGYIDYDKLEEKALDFRPKILICG 305
Query: 200 ASAYARLYDYERIRKVCNKQKAIMLADMAHISGLVAAGVIPSPFEYADVVTTTTHKSLRG 259
S+Y R +DY R R++ +K A+++ DMAHISGLVAA +PF+Y D+VT+TTHKSLRG
Sbjct: 306 GSSYPREWDYARFRQIADKCGAVLMCDMAHISGLVAAKECVNPFDYCDIVTSTTHKSLRG 365
Query: 260 PRGAMIFFRKGVKEINKQGKEV-------FYDYEEKINQAVFPGLQGGPHNHTITGLAVA 312
PRG +IF+RKG K + KQG + YD+EEKIN AVFP LQGGPHN+ I LA+A
Sbjct: 366 PRGGIIFYRKGPK-LRKQGMLLSHGDDNSHYDFEEKINFAVFPSLQGGPHNNHIAALAIA 424
Query: 313 LKQVCT 318
LKQV T
Sbjct: 425 LKQVAT 430
>gnl|CDD|223190 COG0112, GlyA, Glycine/serine hydroxymethyltransferase [Amino acid
transport and metabolism].
Length = 413
Score = 397 bits (1022), Expect = e-137
Identities = 142/296 (47%), Positives = 185/296 (62%), Gaps = 29/296 (9%)
Query: 25 APLEVVDPEIADIIEHEKARQWKGLELIPSENFTSVSVMQAVGSVMTNKYSEGYPGARYY 84
A L DPEI + I+ E RQ + +ELI SENFTS +VM+A GS +TNKY+EGYPG RYY
Sbjct: 5 ASLADYDPEIFEAIQQELERQREHIELIASENFTSPAVMEAQGSDLTNKYAEGYPGKRYY 64
Query: 85 GGNEYIDMAESLCQKRALEAFRLD-----PEKWGGSLSGSPSNFQVYTALLKPHDRIMAL 139
GG EY+D E L +RA + F + P SGS +N VY ALL+P D IM L
Sbjct: 65 GGCEYVDEVEELAIERAKKLFGAEYANVQP------HSGSQANQAVYLALLQPGDTIMGL 118
Query: 140 DLPHGGHLSHGYQTDTKKISAVSIFFETMPYRLNESTGYIDYDQLEKSATLFRPKLIVAG 199
DL HGGHL+HG ++ F + Y ++ TG IDYD++EK A +PKLI+AG
Sbjct: 119 DLSHGGHLTHGS-----PVNFSGKLFNVVSYGVDPETGLIDYDEVEKLAKEVKPKLIIAG 173
Query: 200 ASAYARLYDYERIRKVCNKQKAIMLADMAHISGLVAAGVIPSPFEYADVVTTTTHKSLRG 259
SAY+R D++R R++ ++ A ++ DMAH++GL+A GV P+P +ADVVTTTTHK+LRG
Sbjct: 174 GSAYSRPIDFKRFREIADEVGAYLMVDMAHVAGLIAGGVHPNPLPHADVVTTTTHKTLRG 233
Query: 260 PRGAMIFFRKGVKEINKQGKEVFYDYEEKINQAVFPGLQGGPHNHTITGLAVALKQ 315
PRG +I + +KIN AVFPGLQGGP H I AVA K+
Sbjct: 234 PRGGIILTND-------------EELAKKINSAVFPGLQGGPLMHVIAAKAVAFKE 276
>gnl|CDD|234571 PRK00011, glyA, serine hydroxymethyltransferase; Reviewed.
Length = 416
Score = 389 bits (1002), Expect = e-134
Identities = 148/298 (49%), Positives = 187/298 (62%), Gaps = 29/298 (9%)
Query: 22 QLNAPLEVVDPEIADIIEHEKARQWKGLELIPSENFTSVSVMQAVGSVMTNKYSEGYPGA 81
L DPEIAD IE E RQ + +ELI SENF S +VM+A GSV+TNKY+EGYPG
Sbjct: 1 FFMDNLAEYDPEIADAIEQELKRQEEHIELIASENFVSPAVMEAQGSVLTNKYAEGYPGK 60
Query: 82 RYYGGNEYIDMAESLCQKRALEAFRLD-----PEKWGGSLSGSPSNFQVYTALLKPHDRI 136
RYYGG EY+D+ E L RA E F + P SGS +N VY ALLKP D I
Sbjct: 61 RYYGGCEYVDVVEQLAIDRAKELFGAEYANVQP------HSGSQANAAVYFALLKPGDTI 114
Query: 137 MALDLPHGGHLSHGYQTDTKKISAVSIFFETMPYRLNESTGYIDYDQLEKSATLFRPKLI 196
+ +DL HGGHL+HG ++ + + Y ++E TG IDYD++EK A +PKLI
Sbjct: 115 LGMDLAHGGHLTHG-----SPVNFSGKLYNVVSYGVDEETGLIDYDEVEKLALEHKPKLI 169
Query: 197 VAGASAYARLYDYERIRKVCNKQKAIMLADMAHISGLVAAGVIPSPFEYADVVTTTTHKS 256
+AGASAY+R D++R R++ ++ A ++ DMAHI+GLVAAGV PSP +ADVVTTTTHK+
Sbjct: 170 IAGASAYSRPIDFKRFREIADEVGAYLMVDMAHIAGLVAAGVHPSPVPHADVVTTTTHKT 229
Query: 257 LRGPRGAMIFFRKGVKEINKQGKEVFYDYEEKINQAVFPGLQGGPHNHTITGLAVALK 314
LRGPRG +I + +KIN AVFPG+QGGP H I AVA K
Sbjct: 230 LRGPRGGLILTNDE-------------ELAKKINSAVFPGIQGGPLMHVIAAKAVAFK 274
>gnl|CDD|237280 PRK13034, PRK13034, serine hydroxymethyltransferase; Reviewed.
Length = 416
Score = 335 bits (861), Expect = e-113
Identities = 145/297 (48%), Positives = 185/297 (62%), Gaps = 29/297 (9%)
Query: 24 NAPLEVVDPEIADIIEHEKARQWKGLELIPSENFTSVSVMQAVGSVMTNKYSEGYPGARY 83
+ LE D E+ I E RQ LELI SENFTS +VM+A GSV+TNKY+EGYPG RY
Sbjct: 6 SDSLEEYDDEVFAAINKELERQQDHLELIASENFTSPAVMEAQGSVLTNKYAEGYPGKRY 65
Query: 84 YGGNEYIDMAESLCQKRALEAFRLD-----PEKWGGSLSGSPSNFQVYTALLKPHDRIMA 138
YGG E++D E+L +RA + F D P SGS +N VY ALLKP D I+
Sbjct: 66 YGGCEFVDEVEALAIERAKQLFGCDYANVQPH------SGSQANGAVYLALLKPGDTILG 119
Query: 139 LDLPHGGHLSHGYQTDTKKISAVSIFFETMPYRLNESTGYIDYDQLEKSATLFRPKLIVA 198
+ L HGGHL+HG K+S ++ + Y ++ TG IDYD++E+ A +PKLI+A
Sbjct: 120 MSLSHGGHLTHG-----AKVSLSGKWYNAVQYGVDRLTGLIDYDEVEELAKEHKPKLIIA 174
Query: 199 GASAYARLYDYERIRKVCNKQKAIMLADMAHISGLVAAGVIPSPFEYADVVTTTTHKSLR 258
G SAY R D+ R R++ ++ A+++ DMAHI+GLVAAG P+PF +A VVTTTTHK+LR
Sbjct: 175 GFSAYPRELDFARFREIADEVGALLMVDMAHIAGLVAAGEHPNPFPHAHVVTTTTHKTLR 234
Query: 259 GPRGAMIFFRKGVKEINKQGKEVFYDYEEKINQAVFPGLQGGPHNHTITGLAVALKQ 315
GPRG MI +EI K KIN AVFPGLQGGP H I AVA +
Sbjct: 235 GPRGGMILTND--EEIAK-----------KINSAVFPGLQGGPLMHVIAAKAVAFGE 278
>gnl|CDD|184161 PRK13580, PRK13580, serine hydroxymethyltransferase; Provisional.
Length = 493
Score = 207 bits (529), Expect = 8e-63
Identities = 104/328 (31%), Positives = 168/328 (51%), Gaps = 65/328 (19%)
Query: 27 LEVVDPEIADIIEHEKARQWKGLELIPSENFTSVSVMQAVGSVMTNKYSEGYPGARYYGG 86
+ V+P IA+ I E A Q L+LI SEN++S++V A+G+++T+KY+EG PG R+Y G
Sbjct: 30 ILHVEPRIAEAIRQELADQRSSLKLIASENYSSLAVQLAMGNLLTDKYAEGTPGHRFYAG 89
Query: 87 NEYIDMAESLCQKRALEAFRLD-----PEKWGGSLSGSPSNFQVYTALLKPH-------- 133
+ +D E + A E F + P SG+ +N + A+L
Sbjct: 90 CQNVDTVEWEAAEHAKELFGAEHAYVQPH------SGADANLVAFWAILAHKVESPALEK 143
Query: 134 -----------------------DRIMALDLPHGGHLSHGYQTDTKKISAVSIFFETMPY 170
R++ + L GGHL+HG++ + IS F Y
Sbjct: 144 LGAKTVNDLTEEDWEALRAELGNQRLLGMSLDSGGHLTHGFRPN---IS--GKMFHQRSY 198
Query: 171 RLNESTGYIDYDQLEKSATLFRPKLIVAGASAYARLYDYERIRKVCNKQKAIMLADMAHI 230
++ TG +DYD++ A F+P ++VAG SAY R ++ ++R++ ++ A+++ DMAH
Sbjct: 199 GVDPDTGLLDYDEIAALAREFKPLILVAGYSAYPRRVNFAKLREIADEVGAVLMVDMAHF 258
Query: 231 SGLVAAGVIP---SPFEYADVVTTTTHKSLRGPRGAMIFFRKGVKEINKQGKEVFYDYEE 287
+GLVA V P +AD+VTTTTHK+LRGPRG ++ +K +Y +
Sbjct: 259 AGLVAGKVFTGDEDPVPHADIVTTTTHKTLRGPRGGLVLAKK--------------EYAD 304
Query: 288 KINQAVFPGLQGGPHNHTITGLAVALKQ 315
+++ P + GGP H + AVAL +
Sbjct: 305 AVDKGC-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 = 104 bits (260), Expect = 7e-27
Identities = 39/175 (22%), Positives = 70/175 (40%), Gaps = 12/175 (6%)
Query: 97 CQKRALEAFRLDPEKWGGSLSGSPSNFQVYTALLKPHDRIMALDLPHGGHLSHGYQTDTK 156
+++ + +K SG+ +N ALL P D ++ HG
Sbjct: 5 LEEKLARLLQPGNDKAVFVPSGTGANEAALLALLGPGDEVIVDANGHGSRYWV------- 57
Query: 157 KISAVSIFFETMPYRLNESTGY-IDYDQLEKSATLFRPKLIVAGASAYAR--LYDYERIR 213
+A + +P ++++ +D LE+ LIV + + L + IR
Sbjct: 58 --AAELAGAKPVPVPVDDAGYGGLDVAILEELKAKPNVALIVITPNTTSGGVLVPLKEIR 115
Query: 214 KVCNKQKAIMLADMAHISGLVAAGVIPSPFEYADVVTTTTHKSLRGPRGAMIFFR 268
K+ + ++L D A G A + P ADVVT + HK+L G G ++ +
Sbjct: 116 KIAKEYGILLLVDAASAGGASPAPGVLIPEGGADVVTFSLHKNLGGEGGGVVIVK 170
>gnl|CDD|223594 COG0520, csdA, Selenocysteine lyase/Cysteine desulfurase
[Posttranslational modification, protein turnover,
chaperones].
Length = 405
Score = 40.4 bits (95), Expect = 0.001
Identities = 16/57 (28%), Positives = 27/57 (47%), Gaps = 7/57 (12%)
Query: 208 DYERIRKVCNKQKAIMLADMAHISGLVAAGVIPSPFE--YADVVTTTTHKSLRGPRG 262
+ 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 = 38.0 bits (89), Expect = 0.005
Identities = 36/169 (21%), Positives = 61/169 (36%), Gaps = 26/169 (15%)
Query: 117 SGSPSNFQVYTALLKPHDRIMALDLPHGGHLSHGYQTDTKKISAVS-IFFETMPYRLNES 175
SG+ +N A + D ++ G +H Y +T + + +P
Sbjct: 55 SGTMANQLALMAHCRRGDEVIC------GEPAHIYFDETGGHAELGGAQPVPLP---GAE 105
Query: 176 TGYIDYDQLEKSATLF------RPKLIV-------AGASAYARLYDYERIRKVCNKQKAI 222
G +D + LE + LI AG + L + IR + +
Sbjct: 106 AGKLDLEDLEAAIRPVGDIHFPPTGLISLENTHNSAGGQVVS-LEELREIRAIAREHGIP 164
Query: 223 MLADMAHIS-GLVAAGVIPSP-FEYADVVTTTTHKSLRGPRGAMIFFRK 269
+ D A ++ VA GVI YAD V+ + K L P G+++
Sbjct: 165 LHLDGARLANAAVALGVIVKEITSYADSVSMSLSKGLGAPVGSVLAGSD 213
>gnl|CDD|215756 pfam00155, Aminotran_1_2, Aminotransferase class I and II.
Length = 357
Score = 35.0 bits (81), Expect = 0.047
Identities = 28/153 (18%), Positives = 54/153 (35%), Gaps = 26/153 (16%)
Query: 116 LSGSPSNFQVYTALLK--PHDRIMALDLPHGGHLSHGYQTDTKKISAVSIFFETMPYRLN 173
SG+ +N + LL+ P D I+ + + E + Y L
Sbjct: 71 GSGAGANIEALIFLLRLNPGDAILVPAPTYPSY----------IRIFRLAGGEVVRYPLY 120
Query: 174 ESTGY-IDYDQLE---KSATLFRPKLIVAGAS----AYARLYDYERIRKVCNKQKAIMLA 225
S + +D+D LE K AT ++ A L + E++ + + ++L
Sbjct: 121 SSNDFHLDFDALEAALKEATEGNKVVLHTSPHNPTGTVATLEELEKLLDLAKEHNILLLV 180
Query: 226 DMAHISGLVAAGVIPSPF-----EYADVVTTTT 253
D A+ G V + E +++ +
Sbjct: 181 DEAYA-GFVFGSLDAVATRALLAEGPNLLVVGS 212
>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 = 34.5 bits (80), Expect = 0.064
Identities = 36/158 (22%), Positives = 63/158 (39%), Gaps = 12/158 (7%)
Query: 119 SPSNFQVYTALLKPHDRIMALDLPHGGHLSHGYQTDTKKISAVSIFFETMPYRLNESTGY 178
S SN V A+ P D+I+ + H S AV ++ + G
Sbjct: 85 SSSNKAVILAVCGPGDKIL---IDRNCHKSVINGLVLSG--AVPVYLKPERNPYYGIAGG 139
Query: 179 IDYDQLEKSATLFRPK---LIVAGASAYARLYDYERIRKVCNKQKAIMLADMAHISGLVA 235
I + +K A + P ++ + Y Y+ +I + + + +L D AH +
Sbjct: 140 IPPETFKK-ALIEHPDAKAAVITNPTYYGICYNLRKIVEEAHHRGLPVLVDEAHGAHFRF 198
Query: 236 AGVIPS--PFEYADVVTTTTHKSLRGPR-GAMIFFRKG 270
++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 = 33.4 bits (77), Expect = 0.14
Identities = 29/136 (21%), Positives = 46/136 (33%), Gaps = 24/136 (17%)
Query: 196 IVAGASAYARLYDYERIRKVCNKQKAIMLADMAHISGLVAAGVIPSPFEYA----DVVTT 251
+ ++ L E I + K A+++ D +S L PF DV T
Sbjct: 130 LTHNETSTGVLNPLEGIGALAKKHDALLIVDA--VSSLGGE-----PFRMDEWGVDVAYT 182
Query: 252 TTHKSLRGPRGAMI--FFRKGVKEI-NKQGKEVFY-DYEEKINQAVFPGLQGGPHNHTIT 307
+ K+L P G F + ++ I K + FY D + + G HT
Sbjct: 183 GSQKALGAPPGLGPIAFSERALERIKKKTKPKGFYFDLLLLLK---YWGEGYSYP-HTPP 238
Query: 308 -----GLAVALKQVCT 318
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 = 30.9 bits (70), Expect = 0.24
Identities = 16/65 (24%), Positives = 29/65 (44%), Gaps = 5/65 (7%)
Query: 221 AIMLADMAHISGLVAAGVIPSPFEYADVVTTTTHKSLRGPRGAMIF-FRKGVKEINKQGK 279
+ + ++ AG +PF+ +V TH GP GA F ++G++E K+
Sbjct: 23 ENLKKTLLDLAKKAGAGEKLTPFDREMLVQGLTH----GPEGAAAFVVKQGIREAIKEML 78
Query: 280 EVFYD 284
+ D
Sbjct: 79 SEYSD 83
>gnl|CDD|133889 PHA00440, PHA00440, host protein H-NS-interacting protein.
Length = 98
Score = 30.6 bits (69), Expect = 0.34
Identities = 21/74 (28%), Positives = 36/74 (48%), Gaps = 5/74 (6%)
Query: 214 KVCNKQKAIMLADMAHISGLVAAGVIPSPFEYADVVTTTTHKSLRGPRGAMIF-FRKGVK 272
K+ ++ +AI+ D+ ++ AG +P + +V TH GP GA F R+G++
Sbjct: 16 KMDSETEAILEEDILDLAKQAGAGEEVNPKDKELLVQALTH----GPEGAAAFAVRQGIR 71
Query: 273 EINKQGKEVFYDYE 286
E K E D +
Sbjct: 72 EAIKDMHEESTDKD 85
>gnl|CDD|189002 cd09595, M1, Peptidase M1 family contains aminopeptidase N and
leukotriene A4 hydrolase. M1 Peptidase family includes
aminopeptidase N (APN) and leukotriene A4 hydrolase
(LTA4H). All peptidases in this family bind a single
catalytic zinc ion which is tetrahedrally co-ordinated
by three amino acid ligands and a water molecule that
forms the nucleophile on activation during catalysis.
APN consists of a small N-terminal cytoplasmic domain, a
single transmembrane domain and a large extracellular
ectodomain that contains the active site. It
preferentially cleaves neutral amino acids from the
N-terminus of oligopeptides and is present in a variety
of human tissues and cell types. APN expression is
dysregulated in many inflammatory diseases and is
enhanced in numerous tumor cells, making it a lead
target in the development of anti-cancer and
anti-inflammatory drugs. LTA4H is a bifunctional enzyme,
possessing an aminopeptidase as well as an epoxide
hydrolase activity. The two activities occupy different,
but overlapping sites. The activity and physiological
relevance of the aminopeptidase in LTA4H is as yet
unknown while the epoxide hydrolase converts leukotriene
A4 (LTA4) into leukotriene B4 (LTB4), a potent
chemotaxin that is fundamental to the inflammatory
response of mammals.
Length = 407
Score = 32.0 bits (73), Expect = 0.40
Identities = 17/115 (14%), Positives = 32/115 (27%), Gaps = 4/115 (3%)
Query: 20 PKQLNAPLEVVDPEIADIIEHEKARQWKGLELIPSENFTSVSVMQAVGSVMTNKYSEGYP 79
L A ++ D + ++I HE A QW G + + + + + + + + E
Sbjct: 254 QSLLLAMIDAGDELLENVIAHELAHQWFGNLVTG-ARWNDLWLNEGFATYLEGLWMEATF 312
Query: 80 GARYYGGNEYIDMAESLCQKRALEAFRLDPEKWGGSLSG-SPSNFQVYTALLKPH 133
G ++ L P PS K
Sbjct: 313 GTSAREAYRLEG--TRGLRRWRKLQDELPPAPPVMGKHPDDPSVEFDGVFYEKGA 365
>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 = 31.5 bits (72), Expect = 0.63
Identities = 22/67 (32%), Positives = 30/67 (44%), Gaps = 5/67 (7%)
Query: 184 LEKSATLFR-PKLIVAGASAYARLYDYERIRKVCNKQKAIMLA-DMAHISGLV--AAGVI 239
LE+ LF P +I +A LYD ERIR + K ++ D +S L A G I
Sbjct: 146 LEQFLELFEIPNVIGVKFTA-TDLYDLERIRAASPEDKLVLNGFDEMLLSALALGADGAI 204
Query: 240 PSPFEYA 246
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 = 0.79
Identities = 13/42 (30%), Positives = 22/42 (52%), Gaps = 4/42 (9%)
Query: 272 KEINKQGKEVFYDYEEKINQAVF----PGLQGGPHNHTITGL 309
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 = 0.95
Identities = 15/65 (23%), Positives = 25/65 (38%), Gaps = 2/65 (3%)
Query: 173 NESTGYIDYDQLEKSATLFRPKLIVAGASAYARLYDYERIRKVCNKQKAIMLADMAHISG 232
+ T ID D +E + T R K I+ + D + I + + ++ D A G
Sbjct: 104 DPDTLNIDPDLIEAAITP-RTKAIIP-VHLAGQPCDMDAIMALAKRHGLPVIEDAAQAHG 161
Query: 233 LVAAG 237
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 = 1.4
Identities = 13/35 (37%), Positives = 20/35 (57%), Gaps = 4/35 (11%)
Query: 281 VFYDYEEKINQAV--FPGLQGGPHNHTITGLAVAL 313
+ +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 = 30.2 bits (69), Expect = 1.5
Identities = 24/103 (23%), Positives = 35/103 (33%), Gaps = 18/103 (17%)
Query: 183 QLEKSATLFRPKLIVA-------GASAYARLYDYERIRKVCNKQKAIMLADMAHISGLV- 234
L ++ + KLIV G A + + K AI+ D AH G+
Sbjct: 123 LLREARRPYGKKLIVTEGVYSMDGDIA-----PLPELVDLAKKYGAILFVDEAHSVGVYG 177
Query: 235 --AAGVIPSPFEYADV--VTTTTHKSLRGPRGAMIFFRKGVKE 273
GV DV + T K+ G G I K + +
Sbjct: 178 PHGRGVEEFGGLTDDVDIIMGTLGKAF-GAVGGYIAGSKELID 219
>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 = 3.4
Identities = 15/35 (42%), Positives = 20/35 (57%), Gaps = 1/35 (2%)
Query: 116 LSGSPSNFQVYTALLKPHDRIMALDLP-HGGHLSH 149
GS +++Q LL PH R +A+DLP HG S
Sbjct: 11 FLGSGADWQALIELLGPHFRCLAIDLPGHGSSQSP 45
>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 = 29.0 bits (66), Expect = 4.1
Identities = 14/61 (22%), Positives = 24/61 (39%), Gaps = 10/61 (16%)
Query: 173 NESTGYIDYDQLEKSATLFRPKLIV----AGASAYARLYDYERIRKVCNKQKAIMLADMA 228
+ T ID + +E + T R K I+ G A D + I + + ++ D A
Sbjct: 88 DPDTYNIDPELIEAAITP-RTKAIIPVHLYGNPA-----DMDAIMAIAKRHGLPVIEDAA 141
Query: 229 H 229
Sbjct: 142 Q 142
>gnl|CDD|224893 COG1982, LdcC, Arginine/lysine/ornithine decarboxylases [Amino acid
transport and metabolism].
Length = 557
Score = 28.8 bits (65), Expect = 4.4
Identities = 32/143 (22%), Positives = 55/143 (38%), Gaps = 25/143 (17%)
Query: 160 AVSIFFETMPYRLNESTGY---IDYDQLEKSATLFRPK----LIVAGASAYARLYDYERI 212
A ++ E P R N G I + ++ A L P ++ + Y+ +I
Sbjct: 132 ATPVYLE--PSR-NPLYGIIGGIPLETFKE-ALLAHPDAEKLAVITNPTYDGVCYNLRKI 187
Query: 213 RKVCNKQKAIMLADMAHIS--GLVAAGVIPSPFEYADVVTTTTHKSLRGPR-GAMIFFRK 269
++ + A +L D AH + + AD VT +THK L +MI +
Sbjct: 188 VELLHHYGAWVLYDEAHPAHFDFSPMLPESALNGGADFVTQSTHKLLAALSQASMIHVKD 247
Query: 270 GVKEINKQGKEVFYDYEEKINQA 292
G + +N E+ N+A
Sbjct: 248 G-RAVN----------HERFNEA 259
>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 = 28.8 bits (65), Expect = 4.4
Identities = 20/75 (26%), Positives = 33/75 (44%), Gaps = 6/75 (8%)
Query: 174 ESTGYIDYDQ-LEK-SATLFRPKLIV---AGASAYARLYDYERIRKVCNKQKAIMLADMA 228
E +G D L+K + L+V +G Y +L+ +R V + + D
Sbjct: 147 EESGSYDLPAYLDKLKERIGNVDLVVCLDSGCGNYEQLWLTTSLRGVLGGDLTVQVLDEG 206
Query: 229 HISGLVAAGVIPSPF 243
SG A+G++PS F
Sbjct: 207 VHSG-DASGIVPSSF 220
>gnl|CDD|226509 COG4022, COG4022, Uncharacterized protein conserved in archaea
[Function unknown].
Length = 286
Score = 28.6 bits (64), Expect = 4.5
Identities = 24/91 (26%), Positives = 47/91 (51%), Gaps = 13/91 (14%)
Query: 172 LNESTGYID-YDQLEKSATLFRPKLIVAGASAYARLYDYERIRKVCNKQKAIMLADMAHI 230
L+ T ID + ++K+A L K+ V A A +R+RK+ + +++ + H+
Sbjct: 147 LDPKTATIDQVEGVKKAAELGYKKVAVTVADAE----TAKRLRKLEADELDLLVIAV-HV 201
Query: 231 SGLV---AAGVIPSPFEYADVVTTTTHKSLR 258
+G+ A G++ E +D+VT+ K +R
Sbjct: 202 TGIDEEEAQGLV----ENSDIVTSCASKYIR 228
>gnl|CDD|224832 COG1921, SelA, Selenocysteine synthase [seryl-tRNASer selenium
transferase] [Amino acid transport and metabolism].
Length = 395
Score = 28.9 bits (65), Expect = 4.6
Identities = 23/108 (21%), Positives = 36/108 (33%), Gaps = 34/108 (31%)
Query: 193 PKLIVAGASAYARLYDYERIRKVCNKQ-KAIM-----------------LADMAHISGLV 234
KL+ G + L DY N+ ++ L ++AH GL
Sbjct: 133 AKLVEVGTTNRTHLKDY---ELAINENTALLLKVHSSNYGFTGMLSEEELVEIAHEKGLP 189
Query: 235 ----AAGVIPSPFEY---------ADVVTTTTHKSLRGPRGAMIFFRK 269
A E AD+V+ + K L GP+ +I +K
Sbjct: 190 VIVDLASGALVDKEPDLREALALGADLVSFSGDKLLGGPQAGIIVGKK 237
>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 = 28.8 bits (65), Expect = 4.9
Identities = 41/166 (24%), Positives = 59/166 (35%), Gaps = 44/166 (26%)
Query: 117 SGSPSNFQVYTALLKPHDRIMALDLPH-----GGHLSHGYQTDTKKISAVSIFFETMPYR 171
SG +N V +AL+ D I++ L H G LS YR
Sbjct: 84 SGYLANVGVISALVGKGDLILSDALNHASLIDGCRLSGA---------------RVRRYR 128
Query: 172 LNESTGYIDYDQLE---KSATLFRPKLIVAGA--SAYARLYDYERIRKVCNKQKAIMLAD 226
N D + LE + R KLIV S + ++ + + A ++ D
Sbjct: 129 HN------DVEHLERLLEKNRGERRKLIVTDGVFSMDGDIAPLPQLVALAERYGAWLMVD 182
Query: 227 MAHISG---------LVAAGVIPSPFEYADVVTTTTHKSLRGPRGA 263
AH +G L G+ P P D+ T K+L G GA
Sbjct: 183 DAHGTGVLGEDGRGTLEHFGLKPEP---VDIQVGTLSKAL-GSYGA 224
>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 = 28.5 bits (64), Expect = 5.2
Identities = 27/98 (27%), Positives = 40/98 (40%), Gaps = 10/98 (10%)
Query: 174 ESTGYIDYDQLEKSATLFRPKLIVAG-ASAYARLY-DYERIRKVCNKQKAIMLADMAHIS 231
++ G I +++ K A KLIV AS E I ++ + + D A
Sbjct: 120 DNEGLISPERI-KRAIKTNTKLIVVSHASNVTGTILPIEEIGELAQENGIFFILDAAQ-- 176
Query: 232 GLVAAGVIPSPFEYA--DVVTTTTHKSLRGPRGAMIFF 267
AGVIP D++ T HK L GP+G +
Sbjct: 177 ---TAGVIPIDMTELAIDMLAFTGHKGLLGPQGTGGLY 211
>gnl|CDD|225280 COG2423, COG2423, Predicted ornithine cyclodeaminase, mu-crystallin
homolog [Amino acid transport and metabolism].
Length = 330
Score = 28.4 bits (64), Expect = 5.5
Identities = 20/69 (28%), Positives = 25/69 (36%), Gaps = 10/69 (14%)
Query: 195 LIVAGASAY------ARLYDYERIRKVC-NKQKAIMLADMAHISGLVAAGVIPSP---FE 244
+I AGA A + D IR + + A A G A G S E
Sbjct: 135 IIGAGAQARTQLEALKAVRDIREIRVYSRDPEAAEAFAARLRKRGGEAVGAADSAEEAVE 194
Query: 245 YADVVTTTT 253
AD+V T T
Sbjct: 195 GADIVVTAT 203
>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 = 28.6 bits (64), Expect = 5.7
Identities = 32/119 (26%), Positives = 55/119 (46%), Gaps = 14/119 (11%)
Query: 175 STGYIDYDQLEKSATLFRPKL-IVAGASAYARLYDYERIRKVCNKQK---AIMLADMAHI 230
Y + D+L + + L ++ G++ ++ E +++V + K AI+L D A
Sbjct: 119 GAEYFESDELSELKKIDGTSLVVITGSTMDLKVVSEEDLKRVIKQAKSKEAIVLVDDA-- 176
Query: 231 SGL---VAAGVIPSPFEYADVVTTTTHKSLRGPRGAMIFFRK----GVK-EINKQGKEV 281
SG G P+ AD+V T+T K + GPRG ++ RK +K + G E
Sbjct: 177 SGARVRRLYGQPPALDLGADLVVTSTDKLMDGPRGGLLAGRKELVDKIKSVGEQFGLEA 235
>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 = 6.7
Identities = 24/106 (22%), Positives = 42/106 (39%), Gaps = 15/106 (14%)
Query: 217 NKQKAIMLADMAHISGL--VAAGVIPSPFEYADVVTTTTHKSLR---GPRGAMIFFRKGV 271
+ ++ D +S + + AG I E +V T L+ P G + K +
Sbjct: 55 HYEEVGFDFDTDRVSSIDSIPAGYIDKELEL--IVGMQTSAPLKRNFMPFGGIRMAEKSL 112
Query: 272 KE----INKQGKEVFYDYEEKINQAVF----PGLQGGPHNHTITGL 309
KE ++ ++F Y + NQ VF ++ H +TGL
Sbjct: 113 KEYGLSVDPGLHDIFTQYRKTHNQGVFDAYTSAIRKARHAGVLTGL 158
>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 = 6.8
Identities = 20/107 (18%), Positives = 35/107 (32%), Gaps = 18/107 (16%)
Query: 179 IDYDQLEKSATLFRPKLIV---AGASAYARLYDYERIRKVCNKQKAIMLADMAHISGLVA 235
ID D LE++ +V AG + + D E + + + + H+
Sbjct: 193 IDVDALEEAIDENTIGGVVVGTAGTTDTGSIDDIEELADIAEEYGIWL-----HVDAAFG 247
Query: 236 AGVIPSPFEY---------ADVVTTTTHKSLRGPRGA-MIFFRKGVK 272
++P D +T HK P G ++ FR
Sbjct: 248 GFLLPFLEPDGRWDFGLEGVDSITVDGHKYGLAPIGCGVVLFRDEEA 294
>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 = 28.3 bits (64), Expect = 6.9
Identities = 28/130 (21%), Positives = 52/130 (40%), Gaps = 25/130 (19%)
Query: 125 VYTALLKPHDRIMALDLPHGGHLSHGYQTDTKKISAVSIFFETMPYRLNESTGYIDYDQL 184
V ALLK D ++A D +GG +F +P +L ++D D
Sbjct: 71 VLLALLKAGDHVVASDDLYGG--------------TYRLFERLLP-KLGIEVTFVDPDDP 115
Query: 185 EKSATLFRPK----LIVAGASAYARLYDYERIRKVCNKQKAIMLADMAHISGLVAAGVIP 240
E +P+ + + + ++ D E I ++ ++ A+++ D A +
Sbjct: 116 EALEAAIKPETKLVYVESPTNPTLKVVDIEAIAELAHEHGALLVVD-----NTFATPYLQ 170
Query: 241 SPFEY-ADVV 249
P E AD+V
Sbjct: 171 RPLELGADIV 180
>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 = 7.2
Identities = 29/123 (23%), Positives = 53/123 (43%), Gaps = 10/123 (8%)
Query: 172 LNESTGYID-YDQLEKSATLFRPKLIVAGASAYARLYDYERIRKVCNKQKAIMLADMAHI 230
L+ T ID +EK+ L K+ V A A D + IR++ ++ ++ H
Sbjct: 142 LDPDTATIDQIKGVEKAIELGYKKIAVTVADAE----DAKAIRELESESGIDIIIFAVHT 197
Query: 231 SGLVAAGVIPSPFEYADVVTTTTHKSLRGPRGAMIFFRKG----VKEINKQGKEVFYDYE 286
+G+ +YAD+VT+ K++R + G V + +GKE+ +
Sbjct: 198 TGIDREDA-EEVVQYADIVTSCASKNIREIAKPRALLQVGSAVPVYALTDKGKELLLERA 256
Query: 287 EKI 289
+ I
Sbjct: 257 KDI 259
>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 = 9.1
Identities = 11/25 (44%), Positives = 18/25 (72%)
Query: 328 FSLHVYPAFVSNQNNSENIEEDKGR 352
F LH+ P+ ++NQN +E +E+ K R
Sbjct: 338 FKLHISPSNMTNQNTNEYLEKIKQR 362
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
0.317 0.134 0.397
Gapped
Lambda K H
0.267 0.0730 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 18,475,464
Number of extensions: 1786579
Number of successful extensions: 1564
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1534
Number of HSP's successfully gapped: 49
Length of query: 356
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 258
Effective length of database: 6,590,910
Effective search space: 1700454780
Effective search space used: 1700454780
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 60 (26.9 bits)