RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 018231
(359 letters)
>gnl|CDD|215639 PLN03226, PLN03226, serine hydroxymethyltransferase; Provisional.
Length = 475
Score = 688 bits (1777), Expect = 0.0
Identities = 239/309 (77%), Positives = 262/309 (84%)
Query: 13 EKNGVTWPKQLNAPLEVVDPEIADIIEHEKARQWKGLELIPSENFTSVSVMQAVGSVMTN 72
EK+ V+ PK NAPLE VDPEIADIIE EK RQWKGLELI SENFTS +VM+A+GS +TN
Sbjct: 1 EKSMVSVPKWGNAPLEEVDPEIADIIEKEKRRQWKGLELIASENFTSRAVMEALGSCLTN 60
Query: 73 KYSEGYPGARYYGGNEYIDMAESLCQKRALEAFRLDPEKWGVNVQSLSGSPSNFQVYTAL 132
KYSEG PGARYYGGNEYID E+LCQKRALEAFRLDPEKWGVNVQ LSGSP+NF VYTAL
Sbjct: 61 KYSEGLPGARYYGGNEYIDQIETLCQKRALEAFRLDPEKWGVNVQPLSGSPANFAVYTAL 120
Query: 133 LKPHDRIMALDLPHGGHLSHGYQTDTKKISAVSIFFETMPYRLNESTGYIDYDQLEKSAT 192
L+PHDRIM LDLPHGGHLSHGYQTD KKISA SI+FE+MPYRL+ESTG IDYD+LEK A
Sbjct: 121 LQPHDRIMGLDLPHGGHLSHGYQTDGKKISATSIYFESMPYRLDESTGLIDYDKLEKKAM 180
Query: 193 LFRPKLIVAGASAYARLYDYERIRKVCNKQKAIMLADMAHISGLVAAGVIPSPFEYADVV 252
LFRPKLI+AGASAY R +DY R+RK+ +K A+++ DMAHISGLVAA SPFEY DVV
Sbjct: 181 LFRPKLIIAGASAYPRDWDYARMRKIADKVGALLMCDMAHISGLVAAQEAASPFEYCDVV 240
Query: 253 TTTTHKSLRGPRGAMIFFRKGVKEINKQGKEVFYDYEEKINQAVFPGLQGGPHNHTITGL 312
TTTTHKSLRGPRG MIFFRKG K QG+ YDYE+KIN AVFPGLQGGPHNHTI L
Sbjct: 241 TTTTHKSLRGPRGGMIFFRKGPKPPKGQGEGAVYDYEDKINFAVFPGLQGGPHNHTIAAL 300
Query: 313 AVALKQVCT 321
AVALKQ T
Sbjct: 301 AVALKQAMT 309
>gnl|CDD|240264 PTZ00094, PTZ00094, serine hydroxymethyltransferase; Provisional.
Length = 452
Score = 552 bits (1425), Expect = 0.0
Identities = 194/299 (64%), Positives = 234/299 (78%), Gaps = 11/299 (3%)
Query: 23 LNAPLEVVDPEIADIIEHEKARQWKGLELIPSENFTSVSVMQAVGSVMTNKYSEGYPGAR 82
LN L+ DPE+ ++IE EK RQ +GLELI SENFTS +V++ +GS TNKY+EG PG R
Sbjct: 11 LNQSLKEADPELYELIEKEKERQIEGLELIASENFTSRAVLECLGSCFTNKYAEGLPGNR 70
Query: 83 YYGGNEYIDMAESLCQKRALEAFRLDPEKWGVNVQSLSGSPSNFQVYTALLKPHDRIMAL 142
YYGGNE +D E+LCQKRALEAF LDPE+WGVNVQ SGSP+NF VYTALL+PHDRIM L
Sbjct: 71 YYGGNEVVDKIENLCQKRALEAFGLDPEEWGVNVQPYSGSPANFAVYTALLQPHDRIMGL 130
Query: 143 DLPHGGHLSHGYQTDTKKISAVSIFFETMPYRLNESTGYIDYDQLEKSATLFRPKLIVAG 202
DLP GGHL+HG+ T KK+SA SI+FE++PY++NE G IDYD+LE+ A FRPKLI+AG
Sbjct: 131 DLPSGGHLTHGFYTAKKKVSATSIYFESLPYQVNE-KGLIDYDKLEELAKAFRPKLIIAG 189
Query: 203 ASAYARLYDYERIRKVCNKQKAIMLADMAHISGLVAAGVIPSPFEYADVVTTTTHKSLRG 262
ASAY R DY+R R++C+ A ++AD+AH SGLVAAGV+PSPF YADVVTTTTHKSLRG
Sbjct: 190 ASAYPRDIDYKRFREICDSVGAYLMADIAHTSGLVAAGVLPSPFPYADVVTTTTHKSLRG 249
Query: 263 PRGAMIFFRKGVKEINKQGKEVFYDYEEKINQAVFPGLQGGPHNHTITGLAVALKQVCT 321
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 = 510 bits (1314), Expect = 0.0
Identities = 187/295 (63%), Positives = 217/295 (73%), Gaps = 20/295 (6%)
Query: 27 LEVVDPEIADIIEHEKARQWKGLELIPSENFTSVSVMQAVGSVMTNKYSEGYPGARYYGG 86
L DPEI DII+ EK RQ +G+ELI SENFTS +VM+A+GSV+TNKY+EGYPG RYYGG
Sbjct: 1 LSDSDPEIFDIIKKEKERQREGIELIASENFTSRAVMEALGSVLTNKYAEGYPGKRYYGG 60
Query: 87 NEYIDMAESLCQKRALEAFRLDPEKWGVNVQSLSGSPSNFQVYTALLKPHDRIMALDLPH 146
EY+D E+L Q RA E F LD GVNVQ LSGS +N VYTALL P DRIM LDLPH
Sbjct: 61 CEYVDEVETLAQDRAKELFGLD----GVNVQPLSGSQANLAVYTALLNPGDRIMGLDLPH 116
Query: 147 GGHLSHGYQTDTKKISAVSIFFETMPYRLNESTGYIDYDQLEKSATLFRPKLIVAGASAY 206
GGHL+HGY + FFE+MPY ++ TG IDYDQLEK+A LF+PKLIVAG SAY
Sbjct: 117 GGHLTHGYPVNF-----SGKFFESMPYGVDPDTGLIDYDQLEKNAKLFKPKLIVAGTSAY 171
Query: 207 ARLYDYERIRKVCNKQKAIMLADMAHISGLVAAGVIPSPFEYADVVTTTTHKSLRGPRGA 266
+RL DY R R++ ++ A ++ DMAHI+GLVAAGVIPSPF YA VVTTTTHK+LRGPRG
Sbjct: 172 SRLIDYARFREIADEVGAYLMVDMAHIAGLVAAGVIPSPFPYAHVVTTTTHKTLRGPRGG 231
Query: 267 MIFFRKGVKEINKQGKEVFYDYEEKINQAVFPGLQGGPHNHTITGLAVALKQVCT 321
MIFFR E+ Y+ E+KIN AVFPGLQGGP NH I AVALKQ T
Sbjct: 232 MIFFR-----------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 = 461 bits (1188), Expect = e-163
Identities = 163/289 (56%), Positives = 199/289 (68%), Gaps = 20/289 (6%)
Query: 30 VDPEIADIIEHEKARQWKGLELIPSENFTSVSVMQAVGSVMTNKYSEGYPGARYYGGNEY 89
VDPEIA+II+ E RQ + LELI SENFTS +VM+A+GS +TNKY+EGYPG RYYGG EY
Sbjct: 3 VDPEIAEIIKKENERQRETLELIASENFTSPAVMEAMGSDLTNKYAEGYPGKRYYGGCEY 62
Query: 90 IDMAESLCQKRALEAFRLDPEKWGVNVQSLSGSPSNFQVYTALLKPHDRIMALDLPHGGH 149
+D E L +RA + F + NVQ SGS +N VY ALL+P D IM LDL HGGH
Sbjct: 63 VDEIEDLAIERAKKLFGAE----YANVQPHSGSQANLAVYFALLEPGDTIMGLDLSHGGH 118
Query: 150 LSHGYQTDTKKISAVSIFFETMPYRLNESTGYIDYDQLEKSATLFRPKLIVAGASAYARL 209
L+HG T K+SA FE++PY ++ TG IDYD LEK A F+PKLIVAGASAY R
Sbjct: 119 LTHGSFT---KVSASGKLFESVPYGVDPETGLIDYDALEKMALEFKPKLIVAGASAYPRP 175
Query: 210 YDYERIRKVCNKQKAIMLADMAHISGLVAAGVIPSPFEYADVVTTTTHKSLRGPRGAMIF 269
D++R R++ ++ A +L DMAH++GLVA GV P+P ADVVTTTTHK+LRGPRG +I
Sbjct: 176 IDFKRFREIADEVGAYLLVDMAHVAGLVAGGVFPNPLPGADVVTTTTHKTLRGPRGGLIL 235
Query: 270 FRKGVKEINKQGKEVFYDYEEKINQAVFPGLQGGPHNHTITGLAVALKQ 318
RKG + +KIN AVFPGLQGGPH H I AVALK+
Sbjct: 236 TRKG-------------ELAKKINSAVFPGLQGGPHLHVIAAKAVALKE 271
>gnl|CDD|215153 PLN02271, PLN02271, serine hydroxymethyltransferase.
Length = 586
Score = 441 bits (1137), Expect = e-152
Identities = 184/306 (60%), Positives = 228/306 (74%), Gaps = 9/306 (2%)
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 YGGNEYIDMAESLCQKRALEAFRLDPEKWGVNVQSLSGSPSNFQVYTALLKPHDRIMALD 143
Y GN+YID E LC +RAL AF LD EKWGVNVQ S + +NF VYT LL P DRIM LD
Sbjct: 186 YTGNQYIDQIERLCCERALAAFGLDSEKWGVNVQPYSCTSANFAVYTGLLLPGDRIMGLD 245
Query: 144 LPHGGHLSHGYQTDT-KKISAVSIFFETMPYRLNESTGYIDYDQLEKSATLFRPKLIVAG 202
P GGH+SHGY T KK+S SIFFE++PY++N TGYIDYD+LE+ A FRPK+++ G
Sbjct: 246 SPSGGHMSHGYYTPGGKKVSGASIFFESLPYKVNPQTGYIDYDKLEEKALDFRPKILICG 305
Query: 203 ASAYARLYDYERIRKVCNKQKAIMLADMAHISGLVAAGVIPSPFEYADVVTTTTHKSLRG 262
S+Y R +DY R R++ +K A+++ DMAHISGLVAA +PF+Y D+VT+TTHKSLRG
Sbjct: 306 GSSYPREWDYARFRQIADKCGAVLMCDMAHISGLVAAKECVNPFDYCDIVTSTTHKSLRG 365
Query: 263 PRGAMIFFRKGVKEINKQGKEV-------FYDYEEKINQAVFPGLQGGPHNHTITGLAVA 315
PRG +IF+RKG K + KQG + YD+EEKIN AVFP LQGGPHN+ I LA+A
Sbjct: 366 PRGGIIFYRKGPK-LRKQGMLLSHGDDNSHYDFEEKINFAVFPSLQGGPHNNHIAALAIA 424
Query: 316 LKQVCT 321
LKQV T
Sbjct: 425 LKQVAT 430
>gnl|CDD|223190 COG0112, GlyA, Glycine/serine hydroxymethyltransferase [Amino acid
transport and metabolism].
Length = 413
Score = 409 bits (1054), Expect = e-142
Identities = 144/294 (48%), Positives = 187/294 (63%), Gaps = 22/294 (7%)
Query: 25 APLEVVDPEIADIIEHEKARQWKGLELIPSENFTSVSVMQAVGSVMTNKYSEGYPGARYY 84
A L DPEI + I+ E RQ + +ELI SENFTS +VM+A GS +TNKY+EGYPG RYY
Sbjct: 5 ASLADYDPEIFEAIQQELERQREHIELIASENFTSPAVMEAQGSDLTNKYAEGYPGKRYY 64
Query: 85 GGNEYIDMAESLCQKRALEAFRLDPEKWGVNVQSLSGSPSNFQVYTALLKPHDRIMALDL 144
GG EY+D E L +RA + F + NVQ SGS +N VY ALL+P D IM LDL
Sbjct: 65 GGCEYVDEVEELAIERAKKLFGAE----YANVQPHSGSQANQAVYLALLQPGDTIMGLDL 120
Query: 145 PHGGHLSHGYQTDTKKISAVSIFFETMPYRLNESTGYIDYDQLEKSATLFRPKLIVAGAS 204
HGGHL+HG ++ F + Y ++ TG IDYD++EK A +PKLI+AG S
Sbjct: 121 SHGGHLTHGS-----PVNFSGKLFNVVSYGVDPETGLIDYDEVEKLAKEVKPKLIIAGGS 175
Query: 205 AYARLYDYERIRKVCNKQKAIMLADMAHISGLVAAGVIPSPFEYADVVTTTTHKSLRGPR 264
AY+R D++R R++ ++ A ++ DMAH++GL+A GV P+P +ADVVTTTTHK+LRGPR
Sbjct: 176 AYSRPIDFKRFREIADEVGAYLMVDMAHVAGLIAGGVHPNPLPHADVVTTTTHKTLRGPR 235
Query: 265 GAMIFFRKGVKEINKQGKEVFYDYEEKINQAVFPGLQGGPHNHTITGLAVALKQ 318
G +I + +KIN AVFPGLQGGP H I AVA K+
Sbjct: 236 GGIILTND-------------EELAKKINSAVFPGLQGGPLMHVIAAKAVAFKE 276
>gnl|CDD|234571 PRK00011, glyA, serine hydroxymethyltransferase; Reviewed.
Length = 416
Score = 399 bits (1028), Expect = e-138
Identities = 150/296 (50%), Positives = 189/296 (63%), Gaps = 22/296 (7%)
Query: 22 QLNAPLEVVDPEIADIIEHEKARQWKGLELIPSENFTSVSVMQAVGSVMTNKYSEGYPGA 81
L DPEIAD IE E RQ + +ELI SENF S +VM+A GSV+TNKY+EGYPG
Sbjct: 1 FFMDNLAEYDPEIADAIEQELKRQEEHIELIASENFVSPAVMEAQGSVLTNKYAEGYPGK 60
Query: 82 RYYGGNEYIDMAESLCQKRALEAFRLDPEKWGVNVQSLSGSPSNFQVYTALLKPHDRIMA 141
RYYGG EY+D+ E L RA E F + NVQ SGS +N VY ALLKP D I+
Sbjct: 61 RYYGGCEYVDVVEQLAIDRAKELFGAE----YANVQPHSGSQANAAVYFALLKPGDTILG 116
Query: 142 LDLPHGGHLSHGYQTDTKKISAVSIFFETMPYRLNESTGYIDYDQLEKSATLFRPKLIVA 201
+DL HGGHL+HG ++ + + Y ++E TG IDYD++EK A +PKLI+A
Sbjct: 117 MDLAHGGHLTHG-----SPVNFSGKLYNVVSYGVDEETGLIDYDEVEKLALEHKPKLIIA 171
Query: 202 GASAYARLYDYERIRKVCNKQKAIMLADMAHISGLVAAGVIPSPFEYADVVTTTTHKSLR 261
GASAY+R D++R R++ ++ A ++ DMAHI+GLVAAGV PSP +ADVVTTTTHK+LR
Sbjct: 172 GASAYSRPIDFKRFREIADEVGAYLMVDMAHIAGLVAAGVHPSPVPHADVVTTTTHKTLR 231
Query: 262 GPRGAMIFFRKGVKEINKQGKEVFYDYEEKINQAVFPGLQGGPHNHTITGLAVALK 317
GPRG +I + +KIN AVFPG+QGGP H I AVA K
Sbjct: 232 GPRGGLILTNDE-------------ELAKKINSAVFPGIQGGPLMHVIAAKAVAFK 274
>gnl|CDD|237280 PRK13034, PRK13034, serine hydroxymethyltransferase; Reviewed.
Length = 416
Score = 345 bits (886), Expect = e-117
Identities = 147/295 (49%), Positives = 187/295 (63%), Gaps = 22/295 (7%)
Query: 24 NAPLEVVDPEIADIIEHEKARQWKGLELIPSENFTSVSVMQAVGSVMTNKYSEGYPGARY 83
+ LE D E+ I E RQ LELI SENFTS +VM+A GSV+TNKY+EGYPG RY
Sbjct: 6 SDSLEEYDDEVFAAINKELERQQDHLELIASENFTSPAVMEAQGSVLTNKYAEGYPGKRY 65
Query: 84 YGGNEYIDMAESLCQKRALEAFRLDPEKWGVNVQSLSGSPSNFQVYTALLKPHDRIMALD 143
YGG E++D E+L +RA + F D NVQ SGS +N VY ALLKP D I+ +
Sbjct: 66 YGGCEFVDEVEALAIERAKQLFGCD----YANVQPHSGSQANGAVYLALLKPGDTILGMS 121
Query: 144 LPHGGHLSHGYQTDTKKISAVSIFFETMPYRLNESTGYIDYDQLEKSATLFRPKLIVAGA 203
L HGGHL+HG K+S ++ + Y ++ TG IDYD++E+ A +PKLI+AG
Sbjct: 122 LSHGGHLTHG-----AKVSLSGKWYNAVQYGVDRLTGLIDYDEVEELAKEHKPKLIIAGF 176
Query: 204 SAYARLYDYERIRKVCNKQKAIMLADMAHISGLVAAGVIPSPFEYADVVTTTTHKSLRGP 263
SAY R D+ R R++ ++ A+++ DMAHI+GLVAAG P+PF +A VVTTTTHK+LRGP
Sbjct: 177 SAYPRELDFARFREIADEVGALLMVDMAHIAGLVAAGEHPNPFPHAHVVTTTTHKTLRGP 236
Query: 264 RGAMIFFRKGVKEINKQGKEVFYDYEEKINQAVFPGLQGGPHNHTITGLAVALKQ 318
RG MI +EI K KIN AVFPGLQGGP H I AVA +
Sbjct: 237 RGGMILTND--EEIAK-----------KINSAVFPGLQGGPLMHVIAAKAVAFGE 278
>gnl|CDD|184161 PRK13580, PRK13580, serine hydroxymethyltransferase; Provisional.
Length = 493
Score = 211 bits (540), Expect = 3e-64
Identities = 105/326 (32%), Positives = 169/326 (51%), Gaps = 58/326 (17%)
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 NEYIDMAESLCQKRALEAFRLDPEKWGVNVQSLSGSPSNFQVYTALLKPH---------- 136
+ +D E + A E F + VQ SG+ +N + A+L
Sbjct: 90 CQNVDTVEWEAAEHAKELFGAE----HAYVQPHSGADANLVAFWAILAHKVESPALEKLG 145
Query: 137 ---------------------DRIMALDLPHGGHLSHGYQTDTKKISAVSIFFETMPYRL 175
R++ + L GGHL+HG++ + IS F Y +
Sbjct: 146 AKTVNDLTEEDWEALRAELGNQRLLGMSLDSGGHLTHGFRPN---IS--GKMFHQRSYGV 200
Query: 176 NESTGYIDYDQLEKSATLFRPKLIVAGASAYARLYDYERIRKVCNKQKAIMLADMAHISG 235
+ TG +DYD++ A F+P ++VAG SAY R ++ ++R++ ++ A+++ DMAH +G
Sbjct: 201 DPDTGLLDYDEIAALAREFKPLILVAGYSAYPRRVNFAKLREIADEVGAVLMVDMAHFAG 260
Query: 236 LVAAGVIP---SPFEYADVVTTTTHKSLRGPRGAMIFFRKGVKEINKQGKEVFYDYEEKI 292
LVA V P +AD+VTTTTHK+LRGPRG ++ +K +Y + +
Sbjct: 261 LVAGKVFTGDEDPVPHADIVTTTTHKTLRGPRGGLVLAKK--------------EYADAV 306
Query: 293 NQAVFPGLQGGPHNHTITGLAVALKQ 318
++ P + GGP H + AVAL +
Sbjct: 307 DKGC-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 = 106 bits (267), Expect = 9e-28
Identities = 39/178 (21%), Positives = 69/178 (38%), Gaps = 15/178 (8%)
Query: 97 CQKRALEAFRLDPEKWGVNVQSLSGSPSNFQVYTALLKPHDRIMALDLPHGGHLSHGYQT 156
+++ + P SG+ +N ALL P D ++ HG
Sbjct: 5 LEEKLARLLQ--PGNDKAVFVP-SGTGANEAALLALLGPGDEVIVDANGHGSRYWV---- 57
Query: 157 DTKKISAVSIFFETMPYRLNESTGY-IDYDQLEKSATLFRPKLIVAGASAYAR--LYDYE 213
+A + +P ++++ +D LE+ LIV + + L +
Sbjct: 58 -----AAELAGAKPVPVPVDDAGYGGLDVAILEELKAKPNVALIVITPNTTSGGVLVPLK 112
Query: 214 RIRKVCNKQKAIMLADMAHISGLVAAGVIPSPFEYADVVTTTTHKSLRGPRGAMIFFR 271
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 = 41.9 bits (99), Expect = 3e-04
Identities = 34/189 (17%), Positives = 61/189 (32%), Gaps = 30/189 (15%)
Query: 87 NEYIDMAESLCQKRALEAFRLDPEKWG----VNVQSLSGSPSNFQVYTALLK--PHDRIM 140
N Y + AL F V SG+ +N + LL+ P D I+
Sbjct: 35 NLYGPTDGLPELREALAKFLGRSPVLKLDREAAVVFGSGAGANIEALIFLLRLNPGDAIL 94
Query: 141 ALDLPHGGHLSHGYQTDTKKISAVSIFFETMPYRLNESTGY-IDYDQLE---KSATLFRP 196
+ + E + Y L S + +D+D LE K AT
Sbjct: 95 VPAPTYPSY----------IRIFRLAGGEVVRYPLYSSNDFHLDFDALEAALKEATEGNK 144
Query: 197 KLIVAGAS----AYARLYDYERIRKVCNKQKAIMLADMAHISGLVAAGVIPSPF-----E 247
++ A L + E++ + + ++L D A+ G V + E
Sbjct: 145 VVLHTSPHNPTGTVATLEELEKLLDLAKEHNILLLVDEAYA-GFVFGSLDAVATRALLAE 203
Query: 248 YADVVTTTT 256
+++ +
Sbjct: 204 GPNLLVVGS 212
>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: 211 DYERIRKVCNKQKAIMLADMAHISGLVAAGVIPSPFE--YADVVTTTTHKSLRGPRG 265
+ 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 = 38.4 bits (90), Expect = 0.004
Identities = 36/169 (21%), Positives = 61/169 (36%), Gaps = 26/169 (15%)
Query: 120 SGSPSNFQVYTALLKPHDRIMALDLPHGGHLSHGYQTDTKKISAVS-IFFETMPYRLNES 178
SG+ +N A + D ++ G +H Y +T + + +P
Sbjct: 55 SGTMANQLALMAHCRRGDEVIC------GEPAHIYFDETGGHAELGGAQPVPLP---GAE 105
Query: 179 TGYIDYDQLEKSATLF------RPKLIV-------AGASAYARLYDYERIRKVCNKQKAI 225
G +D + LE + LI AG + L + IR + +
Sbjct: 106 AGKLDLEDLEAAIRPVGDIHFPPTGLISLENTHNSAGGQVVS-LEELREIRAIAREHGIP 164
Query: 226 MLADMAHIS-GLVAAGVIPSP-FEYADVVTTTTHKSLRGPRGAMIFFRK 272
+ 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 = 34.5 bits (80), Expect = 0.063
Identities = 36/158 (22%), Positives = 63/158 (39%), Gaps = 12/158 (7%)
Query: 122 SPSNFQVYTALLKPHDRIMALDLPHGGHLSHGYQTDTKKISAVSIFFETMPYRLNESTGY 181
S SN V A+ P D+I+ + H S AV ++ + G
Sbjct: 85 SSSNKAVILAVCGPGDKIL---IDRNCHKSVINGLVLSG--AVPVYLKPERNPYYGIAGG 139
Query: 182 IDYDQLEKSATLFRPK---LIVAGASAYARLYDYERIRKVCNKQKAIMLADMAHISGLVA 238
I + +K A + P ++ + Y Y+ +I + + + +L D AH +
Sbjct: 140 IPPETFKK-ALIEHPDAKAAVITNPTYYGICYNLRKIVEEAHHRGLPVLVDEAHGAHFRF 198
Query: 239 AGVIPS--PFEYADVVTTTTHKSLRGPR-GAMIFFRKG 273
++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 = 0.13
Identities = 29/136 (21%), Positives = 46/136 (33%), Gaps = 24/136 (17%)
Query: 199 IVAGASAYARLYDYERIRKVCNKQKAIMLADMAHISGLVAAGVIPSPFEYA----DVVTT 254
+ ++ L E I + K A+++ D +S L PF DV T
Sbjct: 130 LTHNETSTGVLNPLEGIGALAKKHDALLIVDA--VSSLGGE-----PFRMDEWGVDVAYT 182
Query: 255 TTHKSLRGPRGAMI--FFRKGVKEI-NKQGKEVFY-DYEEKINQAVFPGLQGGPHNHTIT 310
+ K+L P G F + ++ I K + FY D + + G HT
Sbjct: 183 GSQKALGAPPGLGPIAFSERALERIKKKTKPKGFYFDLLLLLK---YWGEGYSYP-HTPP 238
Query: 311 -----GLAVALKQVCT 321
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: 224 AIMLADMAHISGLVAAGVIPSPFEYADVVTTTTHKSLRGPRGAMIF-FRKGVKEINKQGK 282
+ + ++ AG +PF+ +V TH GP GA F ++G++E K+
Sbjct: 23 ENLKKTLLDLAKKAGAGEKLTPFDREMLVQGLTH----GPEGAAAFVVKQGIREAIKEML 78
Query: 283 EVFYD 287
+ D
Sbjct: 79 SEYSD 83
>gnl|CDD|133889 PHA00440, PHA00440, host protein H-NS-interacting protein.
Length = 98
Score = 30.6 bits (69), Expect = 0.35
Identities = 21/74 (28%), Positives = 36/74 (48%), Gaps = 5/74 (6%)
Query: 217 KVCNKQKAIMLADMAHISGLVAAGVIPSPFEYADVVTTTTHKSLRGPRGAMIF-FRKGVK 275
K+ ++ +AI+ D+ ++ AG +P + +V TH GP GA F R+G++
Sbjct: 16 KMDSETEAILEEDILDLAKQAGAGEEVNPKDKELLVQALTH----GPEGAAAFAVRQGIR 71
Query: 276 EINKQGKEVFYDYE 289
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 = 31.5 bits (72), Expect = 0.65
Identities = 22/67 (32%), Positives = 30/67 (44%), Gaps = 5/67 (7%)
Query: 187 LEKSATLFR-PKLIVAGASAYARLYDYERIRKVCNKQKAIMLA-DMAHISGLV--AAGVI 242
LE+ LF P +I +A LYD ERIR + K ++ D +S L A G I
Sbjct: 146 LEQFLELFEIPNVIGVKFTA-TDLYDLERIRAASPEDKLVLNGFDEMLLSALALGADGAI 204
Query: 243 PSPFEYA 249
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: 275 KEINKQGKEVFYDYEEKINQAVF----PGLQGGPHNHTITGL 312
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 = 0.96
Identities = 15/65 (23%), Positives = 25/65 (38%), Gaps = 2/65 (3%)
Query: 176 NESTGYIDYDQLEKSATLFRPKLIVAGASAYARLYDYERIRKVCNKQKAIMLADMAHISG 235
+ T ID D +E + T R K I+ + D + I + + ++ D A G
Sbjct: 104 DPDTLNIDPDLIEAAITP-RTKAIIP-VHLAGQPCDMDAIMALAKRHGLPVIEDAAQAHG 161
Query: 236 LVAAG 240
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: 284 VFYDYEEKINQAV--FPGLQGGPHNHTITGLAVAL 316
+ +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 = 1.4
Identities = 24/103 (23%), Positives = 35/103 (33%), Gaps = 18/103 (17%)
Query: 186 QLEKSATLFRPKLIVA-------GASAYARLYDYERIRKVCNKQKAIMLADMAHISGLV- 237
L ++ + KLIV G A + + K AI+ D AH G+
Sbjct: 123 LLREARRPYGKKLIVTEGVYSMDGDIA-----PLPELVDLAKKYGAILFVDEAHSVGVYG 177
Query: 238 --AAGVIPSPFEYADV--VTTTTHKSLRGPRGAMIFFRKGVKE 276
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: 119 LSGSPSNFQVYTALLKPHDRIMALDLP-HGGHLSH 152
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 = 4.0
Identities = 14/61 (22%), Positives = 24/61 (39%), Gaps = 10/61 (16%)
Query: 176 NESTGYIDYDQLEKSATLFRPKLIV----AGASAYARLYDYERIRKVCNKQKAIMLADMA 231
+ T ID + +E + T R K I+ G A D + I + + ++ D A
Sbjct: 88 DPDTYNIDPELIEAAITP-RTKAIIPVHLYGNPA-----DMDAIMAIAKRHGLPVIEDAA 141
Query: 232 H 232
Sbjct: 142 Q 142
>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 = 4.2
Identities = 20/75 (26%), Positives = 33/75 (44%), Gaps = 6/75 (8%)
Query: 177 ESTGYIDYDQ-LEK-SATLFRPKLIV---AGASAYARLYDYERIRKVCNKQKAIMLADMA 231
E +G D L+K + L+V +G Y +L+ +R V + + D
Sbjct: 147 EESGSYDLPAYLDKLKERIGNVDLVVCLDSGCGNYEQLWLTTSLRGVLGGDLTVQVLDEG 206
Query: 232 HISGLVAAGVIPSPF 246
SG A+G++PS F
Sbjct: 207 VHSG-DASGIVPSSF 220
>gnl|CDD|224893 COG1982, LdcC, Arginine/lysine/ornithine decarboxylases [Amino acid
transport and metabolism].
Length = 557
Score = 29.2 bits (66), Expect = 4.3
Identities = 32/143 (22%), Positives = 55/143 (38%), Gaps = 25/143 (17%)
Query: 163 AVSIFFETMPYRLNESTGY---IDYDQLEKSATLFRPK----LIVAGASAYARLYDYERI 215
A ++ E P R N G I + ++ A L P ++ + Y+ +I
Sbjct: 132 ATPVYLE--PSR-NPLYGIIGGIPLETFKE-ALLAHPDAEKLAVITNPTYDGVCYNLRKI 187
Query: 216 RKVCNKQKAIMLADMAHIS--GLVAAGVIPSPFEYADVVTTTTHKSLRGPR-GAMIFFRK 272
++ + A +L D AH + + AD VT +THK L +MI +
Sbjct: 188 VELLHHYGAWVLYDEAHPAHFDFSPMLPESALNGGADFVTQSTHKLLAALSQASMIHVKD 247
Query: 273 GVKEINKQGKEVFYDYEEKINQA 295
G + +N E+ N+A
Sbjct: 248 G-RAVN----------HERFNEA 259
>gnl|CDD|224832 COG1921, SelA, Selenocysteine synthase [seryl-tRNASer selenium
transferase] [Amino acid transport and metabolism].
Length = 395
Score = 28.9 bits (65), Expect = 4.4
Identities = 23/108 (21%), Positives = 36/108 (33%), Gaps = 34/108 (31%)
Query: 196 PKLIVAGASAYARLYDYERIRKVCNKQ-KAIM-----------------LADMAHISGLV 237
KL+ G + L DY N+ ++ L ++AH GL
Sbjct: 133 AKLVEVGTTNRTHLKDY---ELAINENTALLLKVHSSNYGFTGMLSEEELVEIAHEKGLP 189
Query: 238 ----AAGVIPSPFEY---------ADVVTTTTHKSLRGPRGAMIFFRK 272
A E AD+V+ + K L GP+ +I +K
Sbjct: 190 VIVDLASGALVDKEPDLREALALGADLVSFSGDKLLGGPQAGIIVGKK 237
>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: 175 LNESTGYID-YDQLEKSATLFRPKLIVAGASAYARLYDYERIRKVCNKQKAIMLADMAHI 233
L+ T ID + ++K+A L K+ V A A +R+RK+ + +++ + H+
Sbjct: 147 LDPKTATIDQVEGVKKAAELGYKKVAVTVADAE----TAKRLRKLEADELDLLVIAV-HV 201
Query: 234 SGLV---AAGVIPSPFEYADVVTTTTHKSLR 261
+G+ A G++ E +D+VT+ K +R
Sbjct: 202 TGIDEEEAQGLV----ENSDIVTSCASKYIR 228
>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 = 4.6
Identities = 41/166 (24%), Positives = 59/166 (35%), Gaps = 44/166 (26%)
Query: 120 SGSPSNFQVYTALLKPHDRIMALDLPH-----GGHLSHGYQTDTKKISAVSIFFETMPYR 174
SG +N V +AL+ D I++ L H G LS YR
Sbjct: 84 SGYLANVGVISALVGKGDLILSDALNHASLIDGCRLSGA---------------RVRRYR 128
Query: 175 LNESTGYIDYDQLE---KSATLFRPKLIVAGA--SAYARLYDYERIRKVCNKQKAIMLAD 229
N D + LE + R KLIV S + ++ + + A ++ D
Sbjct: 129 HN------DVEHLERLLEKNRGERRKLIVTDGVFSMDGDIAPLPQLVALAERYGAWLMVD 182
Query: 230 MAHISG---------LVAAGVIPSPFEYADVVTTTTHKSLRGPRGA 266
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 = 5.1
Identities = 27/98 (27%), Positives = 40/98 (40%), Gaps = 10/98 (10%)
Query: 177 ESTGYIDYDQLEKSATLFRPKLIVAG-ASAYARLY-DYERIRKVCNKQKAIMLADMAHIS 234
++ G I +++ K A KLIV AS E I ++ + + D A
Sbjct: 120 DNEGLISPERI-KRAIKTNTKLIVVSHASNVTGTILPIEEIGELAQENGIFFILDAAQ-- 176
Query: 235 GLVAAGVIPSPFEYA--DVVTTTTHKSLRGPRGAMIFF 270
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 = 5.4
Identities = 20/69 (28%), Positives = 25/69 (36%), Gaps = 10/69 (14%)
Query: 198 LIVAGASAY------ARLYDYERIRKVC-NKQKAIMLADMAHISGLVAAGVIPSP---FE 247
+I AGA A + D IR + + A A G A G S E
Sbjct: 135 IIGAGAQARTQLEALKAVRDIREIRVYSRDPEAAEAFAARLRKRGGEAVGAADSAEEAVE 194
Query: 248 YADVVTTTT 256
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 = 5.5
Identities = 32/119 (26%), Positives = 55/119 (46%), Gaps = 14/119 (11%)
Query: 178 STGYIDYDQLEKSATLFRPKL-IVAGASAYARLYDYERIRKVCNKQK---AIMLADMAHI 233
Y + D+L + + L ++ G++ ++ E +++V + K AI+L D A
Sbjct: 119 GAEYFESDELSELKKIDGTSLVVITGSTMDLKVVSEEDLKRVIKQAKSKEAIVLVDDA-- 176
Query: 234 SGL---VAAGVIPSPFEYADVVTTTTHKSLRGPRGAMIFFRK----GVK-EINKQGKEV 284
SG G P+ AD+V T+T K + GPRG ++ RK +K + G E
Sbjct: 177 SGARVRRLYGQPPALDLGADLVVTSTDKLMDGPRGGLLAGRKELVDKIKSVGEQFGLEA 235
>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 = 28.6 bits (64), Expect = 6.3
Identities = 14/92 (15%), Positives = 29/92 (31%), Gaps = 3/92 (3%)
Query: 20 PKQLNAPLEVVDPEIADIIEHEKARQWKGLELIPSENFTSVSVMQAVGSVMTNKYSEGYP 79
L A ++ D + ++I HE A QW G + + + + + + + + E
Sbjct: 254 QSLLLAMIDAGDELLENVIAHELAHQWFGNLVTG-ARWNDLWLNEGFATYLEGLWMEATF 312
Query: 80 GARYYGGNEYIDMAESLCQKRALEAFRLDPEK 111
G ++ L P
Sbjct: 313 GTSAREAYRLEG--TRGLRRWRKLQDELPPAP 342
>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 = 6.6
Identities = 20/107 (18%), Positives = 35/107 (32%), Gaps = 18/107 (16%)
Query: 182 IDYDQLEKSATLFRPKLIV---AGASAYARLYDYERIRKVCNKQKAIMLADMAHISGLVA 238
ID D LE++ +V AG + + D E + + + + H+
Sbjct: 193 IDVDALEEAIDENTIGGVVVGTAGTTDTGSIDDIEELADIAEEYGIWL-----HVDAAFG 247
Query: 239 AGVIPSPFEY---------ADVVTTTTHKSLRGPRGA-MIFFRKGVK 275
++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 = 6.7
Identities = 28/130 (21%), Positives = 52/130 (40%), Gaps = 25/130 (19%)
Query: 128 VYTALLKPHDRIMALDLPHGGHLSHGYQTDTKKISAVSIFFETMPYRLNESTGYIDYDQL 187
V ALLK D ++A D +GG +F +P +L ++D D
Sbjct: 71 VLLALLKAGDHVVASDDLYGG--------------TYRLFERLLP-KLGIEVTFVDPDDP 115
Query: 188 EKSATLFRPK----LIVAGASAYARLYDYERIRKVCNKQKAIMLADMAHISGLVAAGVIP 243
E +P+ + + + ++ D E I ++ ++ A+++ D A +
Sbjct: 116 EALEAAIKPETKLVYVESPTNPTLKVVDIEAIAELAHEHGALLVVD-----NTFATPYLQ 170
Query: 244 SPFEY-ADVV 252
P E AD+V
Sbjct: 171 RPLELGADIV 180
>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: 220 NKQKAIMLADMAHISGL--VAAGVIPSPFEYADVVTTTTHKSLR---GPRGAMIFFRKGV 274
+ ++ D +S + + AG I E +V T L+ P G + K +
Sbjct: 55 HYEEVGFDFDTDRVSSIDSIPAGYIDKELEL--IVGMQTSAPLKRNFMPFGGIRMAEKSL 112
Query: 275 KE----INKQGKEVFYDYEEKINQAVF----PGLQGGPHNHTITGL 312
KE ++ ++F Y + NQ VF ++ H +TGL
Sbjct: 113 KEYGLSVDPGLHDIFTQYRKTHNQGVFDAYTSAIRKARHAGVLTGL 158
>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: 175 LNESTGYID-YDQLEKSATLFRPKLIVAGASAYARLYDYERIRKVCNKQKAIMLADMAHI 233
L+ T ID +EK+ L K+ V A A D + IR++ ++ ++ H
Sbjct: 142 LDPDTATIDQIKGVEKAIELGYKKIAVTVADAE----DAKAIRELESESGIDIIIFAVHT 197
Query: 234 SGLVAAGVIPSPFEYADVVTTTTHKSLRGPRGAMIFFRKG----VKEINKQGKEVFYDYE 289
+G+ +YAD+VT+ K++R + G V + +GKE+ +
Sbjct: 198 TGIDREDA-EEVVQYADIVTSCASKNIREIAKPRALLQVGSAVPVYALTDKGKELLLERA 256
Query: 290 EKI 292
+ 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 = 9.0
Identities = 11/25 (44%), Positives = 18/25 (72%)
Query: 331 FSLHVYPAFVSNQNNSENIEEDKGR 355
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 0.395
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: 18,557,143
Number of extensions: 1787873
Number of successful extensions: 1572
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1545
Number of HSP's successfully gapped: 48
Length of query: 359
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 261
Effective length of database: 6,590,910
Effective search space: 1720227510
Effective search space used: 1720227510
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)