RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 010058
(519 letters)
>gnl|CDD|215639 PLN03226, PLN03226, serine hydroxymethyltransferase; Provisional.
Length = 475
Score = 965 bits (2496), Expect = 0.0
Identities = 334/477 (70%), Positives = 386/477 (80%), Gaps = 2/477 (0%)
Query: 43 EKAPAPWINQLNAPLEEIDPEIADIIELEKARQWKGLELIPSENFTSVSVMQAVGSVMTN 102
EK+ NAPLEE+DPEIADIIE EK RQWKGLELI SENFTS +VM+A+GS +TN
Sbjct: 1 EKSMVSVPKWGNAPLEEVDPEIADIIEKEKRRQWKGLELIASENFTSRAVMEALGSCLTN 60
Query: 103 KYSEGYPGARYYGGNEYIDMAESLCQKRALDAFQLDPAKWGVNVQSLSGSPANFQVYTAL 162
KYSEG PGARYYGGNEYID E+LCQKRAL+AF+LDP KWGVNVQ LSGSPANF VYTAL
Sbjct: 61 KYSEGLPGARYYGGNEYIDQIETLCQKRALEAFRLDPEKWGVNVQPLSGSPANFAVYTAL 120
Query: 163 LKPHERIMALDLPHGGHLSHGYQTDTKKISAVSIFFETMPYRLDESTGYIDYEQLEKSAA 222
L+PH+RIM LDLPHGGHLSHGYQTD KKISA SI+FE+MPYRLDESTG IDY++LEK A
Sbjct: 121 LQPHDRIMGLDLPHGGHLSHGYQTDGKKISATSIYFESMPYRLDESTGLIDYDKLEKKAM 180
Query: 223 LFRPKLIVAGASAYARLYDYARIRKVCDKQKAVMLADMAHISGLVAAGVIPSPFEYADVV 282
LFRPKLI+AGASAY R +DYAR+RK+ DK A+++ DMAHISGLVAA SPFEY DVV
Sbjct: 181 LFRPKLIIAGASAYPRDWDYARMRKIADKVGALLMCDMAHISGLVAAQEAASPFEYCDVV 240
Query: 283 TTTTHKSLRGPRGAMIFFRKGVKEINKQGQEVMYAYEDKINQAVFPGLQGGPHNHTISGL 342
TTTTHKSLRGPRG MIFFRKG K QG+ +Y YEDKIN AVFPGLQGGPHNHTI+ L
Sbjct: 241 TTTTHKSLRGPRGGMIFFRKGPKPPKGQGEGAVYDYEDKINFAVFPGLQGGPHNHTIAAL 300
Query: 343 AVALKQVKTPEYKAYQEQVLSNSSKFARSLLERGYDLVSGGTENHLVLVNLRNKGIDGSR 402
AVALKQ TPE+KAYQ+QV +N++ A L+ +GY LV+GGT+NHLVL +LR G+ GSR
Sbjct: 301 AVALKQAMTPEFKAYQKQVKANAAALANRLMSKGYKLVTGGTDNHLVLWDLRPLGLTGSR 360
Query: 403 VEKVLESVHIAANKNTVPGDVSAMVPGGIRMGTPALTSRGFVEEDFEKVAEFFDAAVKLA 462
VEKVL+ HI NKN VPGD SA+VPGG+R+GTPA+TSRG VE+DFEKVAEF AV +A
Sbjct: 361 VEKVLDLAHITLNKNAVPGDSSALVPGGVRIGTPAMTSRGLVEKDFEKVAEFLHRAVTIA 420
Query: 463 LKIKGDTKGTKLKDFVATLMSDESIQSEISNLRDKVEEYAKRFPTVGFEKETMKYKN 519
LKI+ + G KLKDF L S++ +I LR +VEE+A FP GF+KE+MKYK
Sbjct: 421 LKIQKEH-GKKLKDFKKGLESNDF-SKDIEALRAEVEEFATSFPMPGFDKESMKYKE 475
>gnl|CDD|240264 PTZ00094, PTZ00094, serine hydroxymethyltransferase; Provisional.
Length = 452
Score = 759 bits (1963), Expect = 0.0
Identities = 275/458 (60%), Positives = 349/458 (76%), Gaps = 16/458 (3%)
Query: 53 LNAPLEEIDPEIADIIELEKARQWKGLELIPSENFTSVSVMQAVGSVMTNKYSEGYPGAR 112
LN L+E DPE+ ++IE EK RQ +GLELI SENFTS +V++ +GS TNKY+EG PG R
Sbjct: 11 LNQSLKEADPELYELIEKEKERQIEGLELIASENFTSRAVLECLGSCFTNKYAEGLPGNR 70
Query: 113 YYGGNEYIDMAESLCQKRALDAFQLDPAKWGVNVQSLSGSPANFQVYTALLKPHERIMAL 172
YYGGNE +D E+LCQKRAL+AF LDP +WGVNVQ SGSPANF VYTALL+PH+RIM L
Sbjct: 71 YYGGNEVVDKIENLCQKRALEAFGLDPEEWGVNVQPYSGSPANFAVYTALLQPHDRIMGL 130
Query: 173 DLPHGGHLSHGYQTDTKKISAVSIFFETMPYRLDESTGYIDYEQLEKSAALFRPKLIVAG 232
DLP GGHL+HG+ T KK+SA SI+FE++PY+++E G IDY++LE+ A FRPKLI+AG
Sbjct: 131 DLPSGGHLTHGFYTAKKKVSATSIYFESLPYQVNE-KGLIDYDKLEELAKAFRPKLIIAG 189
Query: 233 ASAYARLYDYARIRKVCDKQKAVMLADMAHISGLVAAGVIPSPFEYADVVTTTTHKSLRG 292
ASAY R DY R R++CD A ++AD+AH SGLVAAGV+PSPF YADVVTTTTHKSLRG
Sbjct: 190 ASAYPRDIDYKRFREICDSVGAYLMADIAHTSGLVAAGVLPSPFPYADVVTTTTHKSLRG 249
Query: 293 PRGAMIFFRKGVKEINKQGQEVMYAYEDKINQAVFPGLQGGPHNHTISGLAVALKQVKTP 352
PR +IF+RK VK E+KIN+AVFPGLQGGPHNH I+ +AV LK+V++P
Sbjct: 250 PRSGLIFYRKKVKP----------DIENKINEAVFPGLQGGPHNHQIAAIAVQLKEVQSP 299
Query: 353 EYKAYQEQVLSNSSKFARSLLERGYDLVSGGTENHLVLVNLRNKGIDGSRVEKVLESVHI 412
E+K Y +QVL N+ A +L +RGYDLV+GGT+NHLVLV+LR GI GS++EK+L++V+I
Sbjct: 300 EWKEYAKQVLKNAKALAAALEKRGYDLVTGGTDNHLVLVDLRPFGITGSKMEKLLDAVNI 359
Query: 413 AANKNTVPGDVSAMVPGGIRMGTPALTSRGFVEEDFEKVAEFFDAAVKLALKIKGDTKGT 472
+ NKNT+PGD SA+ P G+R+GTPALT+RG E+DF+ VA+F D AVKLA +I+ G
Sbjct: 360 SVNKNTIPGDKSALNPSGVRLGTPALTTRGAKEKDFKFVADFLDRAVKLAQEIQKQ-VGK 418
Query: 473 KLKDFVATLMSDESIQSEISNLRDKVEEYAKRFPTVGF 510
KL DF L + +Q LR +V E+A +FP G
Sbjct: 419 KLVDFKKALEKNPELQ----KLRQEVVEFASQFPFPGI 452
>gnl|CDD|189558 pfam00464, SHMT, Serine hydroxymethyltransferase.
Length = 380
Score = 676 bits (1746), Expect = 0.0
Identities = 255/400 (63%), Positives = 299/400 (74%), Gaps = 21/400 (5%)
Query: 57 LEEIDPEIADIIELEKARQWKGLELIPSENFTSVSVMQAVGSVMTNKYSEGYPGARYYGG 116
L + DPEI DII+ EK RQ +G+ELI SENFTS +VM+A+GSV+TNKY+EGYPG RYYGG
Sbjct: 1 LSDSDPEIFDIIKKEKERQREGIELIASENFTSRAVMEALGSVLTNKYAEGYPGKRYYGG 60
Query: 117 NEYIDMAESLCQKRALDAFQLDPAKWGVNVQSLSGSPANFQVYTALLKPHERIMALDLPH 176
EY+D E+L Q RA + F LD GVNVQ LSGS AN VYTALL P +RIM LDLPH
Sbjct: 61 CEYVDEVETLAQDRAKELFGLD----GVNVQPLSGSQANLAVYTALLNPGDRIMGLDLPH 116
Query: 177 GGHLSHGYQTDTKKISAVSIFFETMPYRLDESTGYIDYEQLEKSAALFRPKLIVAGASAY 236
GGHL+HGY + FFE+MPY +D TG IDY+QLEK+A LF+PKLIVAG SAY
Sbjct: 117 GGHLTHGYPVNF-----SGKFFESMPYGVDPDTGLIDYDQLEKNAKLFKPKLIVAGTSAY 171
Query: 237 ARLYDYARIRKVCDKQKAVMLADMAHISGLVAAGVIPSPFEYADVVTTTTHKSLRGPRGA 296
+RL DYAR R++ D+ A ++ DMAHI+GLVAAGVIPSPF YA VVTTTTHK+LRGPRG
Sbjct: 172 SRLIDYARFREIADEVGAYLMVDMAHIAGLVAAGVIPSPFPYAHVVTTTTHKTLRGPRGG 231
Query: 297 MIFFRKGVKEINKQGQEVMYAYEDKINQAVFPGLQGGPHNHTISGLAVALKQVKTPEYKA 356
MIFFR E++Y E KIN AVFPGLQGGP NH I+ AVALKQ TPE+K
Sbjct: 232 MIFFR-----------EILYELEKKINSAVFPGLQGGPLNHVIAAKAVALKQALTPEFKV 280
Query: 357 YQEQVLSNSSKFARSLLERGYDLVSGGTENHLVLVNLRNKGIDGSRVEKVLESVHIAANK 416
YQ+QVL N+ A +L ERGY LVSGGT+NHLVLV+LR KG+DG R EK LE +I ANK
Sbjct: 281 YQQQVLKNAKALAEALKERGYKLVSGGTDNHLVLVDLRPKGLDGKRAEKALERANITANK 340
Query: 417 NTVPGD-VSAMVPGGIRMGTPALTSRGFVEEDFEKVAEFF 455
NT+PGD S V G+R+GTPALTSRGF E DFE+VA +
Sbjct: 341 NTIPGDPKSPFVTSGLRLGTPALTSRGFGEADFEEVAGYI 380
>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 = 628 bits (1623), Expect = 0.0
Identities = 227/425 (53%), Positives = 283/425 (66%), Gaps = 24/425 (5%)
Query: 58 EEIDPEIADIIELEKARQWKGLELIPSENFTSVSVMQAVGSVMTNKYSEGYPGARYYGGN 117
++DPEIA+II+ E RQ + LELI SENFTS +VM+A+GS +TNKY+EGYPG RYYGG
Sbjct: 1 ADVDPEIAEIIKKENERQRETLELIASENFTSPAVMEAMGSDLTNKYAEGYPGKRYYGGC 60
Query: 118 EYIDMAESLCQKRALDAFQLDPAKWGVNVQSLSGSPANFQVYTALLKPHERIMALDLPHG 177
EY+D E L +RA F + NVQ SGS AN VY ALL+P + IM LDL HG
Sbjct: 61 EYVDEIEDLAIERAKKLFGAE----YANVQPHSGSQANLAVYFALLEPGDTIMGLDLSHG 116
Query: 178 GHLSHGYQTDTKKISAVSIFFETMPYRLDESTGYIDYEQLEKSAALFRPKLIVAGASAYA 237
GHL+HG T K+SA FE++PY +D TG IDY+ LEK A F+PKLIVAGASAY
Sbjct: 117 GHLTHGSFT---KVSASGKLFESVPYGVDPETGLIDYDALEKMALEFKPKLIVAGASAYP 173
Query: 238 RLYDYARIRKVCDKQKAVMLADMAHISGLVAAGVIPSPFEYADVVTTTTHKSLRGPRGAM 297
R D+ R R++ D+ A +L DMAH++GLVA GV P+P ADVVTTTTHK+LRGPRG +
Sbjct: 174 RPIDFKRFREIADEVGAYLLVDMAHVAGLVAGGVFPNPLPGADVVTTTTHKTLRGPRGGL 233
Query: 298 IFFRKGVKEINKQGQEVMYAYEDKINQAVFPGLQGGPHNHTISGLAVALKQVKTPEYKAY 357
I RKG KIN AVFPGLQGGPH H I+ AVALK+ PE+KAY
Sbjct: 234 ILTRKG-------------ELAKKINSAVFPGLQGGPHLHVIAAKAVALKEALEPEFKAY 280
Query: 358 QEQVLSNSSKFARSLLERGYDLVSGGTENHLVLVNLRNKGIDGSRVEKVLESVHIAANKN 417
+QV+ N+ A +L ERG+ +VSGGT+NHLVLV+LR KGI G E LE I NKN
Sbjct: 281 AKQVVENAKALAEALKERGFKVVSGGTDNHLVLVDLRPKGITGKAAEDALEEAGITVNKN 340
Query: 418 TVPGDVS-AMVPGGIRMGTPALTSRGFVEEDFEKVAEFFDAAVKLALKIKGDTKGTKLKD 476
T+P D S VP GIR+GTPA+T+RG EE+ E++A+F A+K A + +++
Sbjct: 341 TLPWDPSSPFVPSGIRIGTPAMTTRGMGEEEMEEIADFIARALKDA---EDVAVAEEVRK 397
Query: 477 FVATL 481
VA L
Sbjct: 398 EVAEL 402
>gnl|CDD|215153 PLN02271, PLN02271, serine hydroxymethyltransferase.
Length = 586
Score = 579 bits (1495), Expect = 0.0
Identities = 253/471 (53%), Positives = 331/471 (70%), Gaps = 17/471 (3%)
Query: 49 WINQLNAPLEEIDPEIADIIELEKARQWKGLELIPSENFTSVSVMQAVGSVMTNKYSEGY 108
W NQ PL E DP+I +++E EK RQ+KG+ELI SENF +VM+A+GS +TNKYSEG
Sbjct: 124 WGNQ---PLPEADPDIHELMEKEKQRQFKGIELIASENFVCRAVMEALGSHLTNKYSEGM 180
Query: 109 PGARYYGGNEYIDMAESLCQKRALDAFQLDPAKWGVNVQSLSGSPANFQVYTALLKPHER 168
PGARYY GN+YID E LC +RAL AF LD KWGVNVQ S + ANF VYT LL P +R
Sbjct: 181 PGARYYTGNQYIDQIERLCCERALAAFGLDSEKWGVNVQPYSCTSANFAVYTGLLLPGDR 240
Query: 169 IMALDLPHGGHLSHGYQTDT-KKISAVSIFFETMPYRLDESTGYIDYEQLEKSAALFRPK 227
IM LD P GGH+SHGY T KK+S SIFFE++PY+++ TGYIDY++LE+ A FRPK
Sbjct: 241 IMGLDSPSGGHMSHGYYTPGGKKVSGASIFFESLPYKVNPQTGYIDYDKLEEKALDFRPK 300
Query: 228 LIVAGASAYARLYDYARIRKVCDKQKAVMLADMAHISGLVAAGVIPSPFEYADVVTTTTH 287
+++ G S+Y R +DYAR R++ DK AV++ DMAHISGLVAA +PF+Y D+VT+TTH
Sbjct: 301 ILICGGSSYPREWDYARFRQIADKCGAVLMCDMAHISGLVAAKECVNPFDYCDIVTSTTH 360
Query: 288 KSLRGPRGAMIFFRKGVKEINKQGQEV-------MYAYEDKINQAVFPGLQGGPHNHTIS 340
KSLRGPRG +IF+RKG K + KQG + Y +E+KIN AVFP LQGGPHN+ I+
Sbjct: 361 KSLRGPRGGIIFYRKGPK-LRKQGMLLSHGDDNSHYDFEEKINFAVFPSLQGGPHNNHIA 419
Query: 341 GLAVALKQVKTPEYKAYQEQVLSNSSKFARSLLERGYDLVSGGTENHLVLVNLRNKGIDG 400
LA+ALKQV TPEYKAY +QV N+ A +LL R LV+GGT+NHL+L +L G+ G
Sbjct: 420 ALAIALKQVATPEYKAYMQQVKKNAQALASALLRRKCRLVTGGTDNHLLLWDLTTLGLTG 479
Query: 401 SRVEKVLESVHIAANKNTVPGDVSAMVPGGIRMGTPALTSRGFVEEDFEKVAEFFDAAVK 460
EKV E HI NK + GD + PGG+R+GTPA+TSRG +E DFE +A+F A +
Sbjct: 480 KNYEKVCEMCHITLNKTAIFGDNGTISPGGVRIGTPAMTSRGCLESDFETIADFLLRAAQ 539
Query: 461 LALKIKGDTKGTKLKDFVATLMSDESIQSEISNLRDKVEEYAKRFPTVGFE 511
+A ++ + G K+F+ L +++ +I LR++VE +A +F GF+
Sbjct: 540 IASAVQRE-HGKLQKEFLKGLQNNK----DIVELRNRVEAFASQFAMPGFD 585
>gnl|CDD|234571 PRK00011, glyA, serine hydroxymethyltransferase; Reviewed.
Length = 416
Score = 571 bits (1474), Expect = 0.0
Identities = 215/460 (46%), Positives = 285/460 (61%), Gaps = 46/460 (10%)
Query: 52 QLNAPLEEIDPEIADIIELEKARQWKGLELIPSENFTSVSVMQAVGSVMTNKYSEGYPGA 111
L E DPEIAD IE E RQ + +ELI SENF S +VM+A GSV+TNKY+EGYPG
Sbjct: 1 FFMDNLAEYDPEIADAIEQELKRQEEHIELIASENFVSPAVMEAQGSVLTNKYAEGYPGK 60
Query: 112 RYYGGNEYIDMAESLCQKRALDAFQLDPAKWGVNVQSLSGSPANFQVYTALLKPHERIMA 171
RYYGG EY+D+ E L RA + F A++ NVQ SGS AN VY ALLKP + I+
Sbjct: 61 RYYGGCEYVDVVEQLAIDRAKELFG---AEY-ANVQPHSGSQANAAVYFALLKPGDTILG 116
Query: 172 LDLPHGGHLSHGYQTDTKKISAVSIFFETMPYRLDESTGYIDYEQLEKSAALFRPKLIVA 231
+DL HGGHL+HG ++ + + Y +DE TG IDY+++EK A +PKLI+A
Sbjct: 117 MDLAHGGHLTHG-----SPVNFSGKLYNVVSYGVDEETGLIDYDEVEKLALEHKPKLIIA 171
Query: 232 GASAYARLYDYARIRKVCDKQKAVMLADMAHISGLVAAGVIPSPFEYADVVTTTTHKSLR 291
GASAY+R D+ R R++ D+ A ++ DMAHI+GLVAAGV PSP +ADVVTTTTHK+LR
Sbjct: 172 GASAYSRPIDFKRFREIADEVGAYLMVDMAHIAGLVAAGVHPSPVPHADVVTTTTHKTLR 231
Query: 292 GPRGAMIFFRKGVKEINKQGQEVMYAYEDKINQAVFPGLQGGPHNHTISGLAVALKQVKT 351
GPRG +I +E+ K KIN AVFPG+QGGP H I+ AVA K+
Sbjct: 232 GPRGGLILTND--EELAK-----------KINSAVFPGIQGGPLMHVIAAKAVAFKEALE 278
Query: 352 PEYKAYQEQVLSNSSKFARSLLERGYDLVSGGTENHLVLVNLRNKGIDGSRVEKVLESVH 411
PE+K Y +QV+ N+ A +L ERG+ +VSGGT+NHLVLV+LR+KG+ G E LE +
Sbjct: 279 PEFKEYAQQVVKNAKALAEALAERGFRVVSGGTDNHLVLVDLRSKGLTGKEAEAALEEAN 338
Query: 412 IAANKNTVPGDV-SAMVPGGIRMGTPALTSRGFVEEDFEKVAEFFDAAVKLALKIKGDTK 470
I NKN VP D S V GIR+GTPA+T+RGF E + +++AE +
Sbjct: 339 ITVNKNAVPFDPRSPFVTSGIRIGTPAITTRGFKEAEMKEIAELIADVLD---------- 388
Query: 471 GTKLKDFVATLMSDESIQSEISNLRDKVEEYAKRFPTVGF 510
+ ++ I ++++V+E KRFP +
Sbjct: 389 -------------NPDDEAVIEEVKEEVKELCKRFPLYKY 415
>gnl|CDD|223190 COG0112, GlyA, Glycine/serine hydroxymethyltransferase [Amino acid
transport and metabolism].
Length = 413
Score = 567 bits (1464), Expect = 0.0
Identities = 203/456 (44%), Positives = 272/456 (59%), Gaps = 48/456 (10%)
Query: 55 APLEEIDPEIADIIELEKARQWKGLELIPSENFTSVSVMQAVGSVMTNKYSEGYPGARYY 114
A L + DPEI + I+ E RQ + +ELI SENFTS +VM+A GS +TNKY+EGYPG RYY
Sbjct: 5 ASLADYDPEIFEAIQQELERQREHIELIASENFTSPAVMEAQGSDLTNKYAEGYPGKRYY 64
Query: 115 GGNEYIDMAESLCQKRALDAFQLDPAKWGVNVQSLSGSPANFQVYTALLKPHERIMALDL 174
GG EY+D E L +RA F + NVQ SGS AN VY ALL+P + IM LDL
Sbjct: 65 GGCEYVDEVEELAIERAKKLFGAE----YANVQPHSGSQANQAVYLALLQPGDTIMGLDL 120
Query: 175 PHGGHLSHGYQTDTKKISAVSIFFETMPYRLDESTGYIDYEQLEKSAALFRPKLIVAGAS 234
HGGHL+HG ++ F + Y +D TG IDY+++EK A +PKLI+AG S
Sbjct: 121 SHGGHLTHGS-----PVNFSGKLFNVVSYGVDPETGLIDYDEVEKLAKEVKPKLIIAGGS 175
Query: 235 AYARLYDYARIRKVCDKQKAVMLADMAHISGLVAAGVIPSPFEYADVVTTTTHKSLRGPR 294
AY+R D+ R R++ D+ A ++ DMAH++GL+A GV P+P +ADVVTTTTHK+LRGPR
Sbjct: 176 AYSRPIDFKRFREIADEVGAYLMVDMAHVAGLIAGGVHPNPLPHADVVTTTTHKTLRGPR 235
Query: 295 GAMIFFRKGVKEINKQGQEVMYAYEDKINQAVFPGLQGGPHNHTISGLAVALKQVKTPEY 354
G +I KIN AVFPGLQGGP H I+ AVA K+ PE+
Sbjct: 236 GGIILTND-------------EELAKKINSAVFPGLQGGPLMHVIAAKAVAFKEALEPEF 282
Query: 355 KAYQEQVLSNSSKFARSLLERGYDLVSGGTENHLVLVNLRNKGIDGSRVEKVLESVHIAA 414
K Y +QV+ N+ A +L ERG+ +VSGGT+NHLVLV+LR+KG+ G + E LE I
Sbjct: 283 KEYAKQVVKNAKALAEALKERGFKVVSGGTDNHLVLVDLRSKGLTGKKAEAALERAGITV 342
Query: 415 NKNTVPGD-VSAMVPGGIRMGTPALTSRGFVEEDFEKVAEFFDAAVKLALKIKGDTKGTK 473
NKN +P D S V GIR+GTPA+T+RGF E + E++A+ +
Sbjct: 343 NKNAIPFDPESPFVTSGIRIGTPAVTTRGFGEAEMEEIADLIADVLD------------- 389
Query: 474 LKDFVATLMSDESIQSEISNLRDKVEEYAKRFPTVG 509
++ + ++++V E +RFP
Sbjct: 390 ------------GLKDVPAEVKEEVAELCRRFPLYK 413
>gnl|CDD|237280 PRK13034, PRK13034, serine hydroxymethyltransferase; Reviewed.
Length = 416
Score = 485 bits (1250), Expect = e-169
Identities = 214/458 (46%), Positives = 276/458 (60%), Gaps = 54/458 (11%)
Query: 54 NAPLEEIDPEIADIIELEKARQWKGLELIPSENFTSVSVMQAVGSVMTNKYSEGYPGARY 113
+ LEE D E+ I E RQ LELI SENFTS +VM+A GSV+TNKY+EGYPG RY
Sbjct: 6 SDSLEEYDDEVFAAINKELERQQDHLELIASENFTSPAVMEAQGSVLTNKYAEGYPGKRY 65
Query: 114 YGGNEYIDMAESLCQKRALDAFQLDPAKWGVNVQSLSGSPANFQVYTALLKPHERIMALD 173
YGG E++D E+L +RA F D A NVQ SGS AN VY ALLKP + I+ +
Sbjct: 66 YGGCEFVDEVEALAIERAKQLFGCDYA----NVQPHSGSQANGAVYLALLKPGDTILGMS 121
Query: 174 LPHGGHLSHGYQTDTKKISAVSIFFETMPYRLDESTGYIDYEQLEKSAALFRPKLIVAGA 233
L HGGHL+HG K+S ++ + Y +D TG IDY+++E+ A +PKLI+AG
Sbjct: 122 LSHGGHLTHG-----AKVSLSGKWYNAVQYGVDRLTGLIDYDEVEELAKEHKPKLIIAGF 176
Query: 234 SAYARLYDYARIRKVCDKQKAVMLADMAHISGLVAAGVIPSPFEYADVVTTTTHKSLRGP 293
SAY R D+AR R++ D+ A+++ DMAHI+GLVAAG P+PF +A VVTTTTHK+LRGP
Sbjct: 177 SAYPRELDFARFREIADEVGALLMVDMAHIAGLVAAGEHPNPFPHAHVVTTTTHKTLRGP 236
Query: 294 RGAMIFFRKGVKEINKQGQEVMYAYEDKINQAVFPGLQGGPHNHTISGLAVALKQVKTPE 353
RG MI +EI K KIN AVFPGLQGGP H I+ AVA + PE
Sbjct: 237 RGGMILTND--EEIAK-----------KINSAVFPGLQGGPLMHVIAAKAVAFGEALQPE 283
Query: 354 YKAYQEQVLSNSSKFARSLLERGYDLVSGGTENHLVLVNLRNKGIDGSRVEKVLESVHIA 413
+K Y +QV++N+ A L ERGYDLVSGGT+NHL+LV+LR KG+ G E+ LE I
Sbjct: 284 FKTYAKQVIANAQALAEVLKERGYDLVSGGTDNHLLLVDLRPKGLSGKDAEQALERAGIT 343
Query: 414 ANKNTVPGDV-SAMVPGGIRMGTPALTSRGFVEEDFE----KVAEFFDAAVKLALKIKGD 468
NKNTVPGD S V GIR+GTPA T+RGF E +F + + D
Sbjct: 344 VNKNTVPGDTESPFVTSGIRIGTPAGTTRGFGEAEFREIANWILDVLDD----------- 392
Query: 469 TKGTKLKDFVATLMSDESIQSEISNLRDKVEEYAKRFP 506
+ + +++ + R +V+ RFP
Sbjct: 393 -------------LGNAALEQRV---RKEVKALCSRFP 414
>gnl|CDD|184161 PRK13580, PRK13580, serine hydroxymethyltransferase; Provisional.
Length = 493
Score = 320 bits (822), Expect = e-104
Identities = 165/485 (34%), Positives = 258/485 (53%), Gaps = 66/485 (13%)
Query: 57 LEEIDPEIADIIELEKARQWKGLELIPSENFTSVSVMQAVGSVMTNKYSEGYPGARYYGG 116
+ ++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: 117 NEYIDMAESLCQKRALDAFQLDPAKWGVNVQSLSGSPANFQVYTALLKPH---------- 166
+ +D E + A + F + A VQ SG+ AN + A+L
Sbjct: 90 CQNVDTVEWEAAEHAKELFGAEHAY----VQPHSGADANLVAFWAILAHKVESPALEKLG 145
Query: 167 ---------------------ERIMALDLPHGGHLSHGYQTDTKKISAVSIFFETMPYRL 205
+R++ + L GGHL+HG++ + IS F Y +
Sbjct: 146 AKTVNDLTEEDWEALRAELGNQRLLGMSLDSGGHLTHGFRPN---IS--GKMFHQRSYGV 200
Query: 206 DESTGYIDYEQLEKSAALFRPKLIVAGASAYARLYDYARIRKVCDKQKAVMLADMAHISG 265
D TG +DY+++ A F+P ++VAG SAY R ++A++R++ D+ AV++ DMAH +G
Sbjct: 201 DPDTGLLDYDEIAALAREFKPLILVAGYSAYPRRVNFAKLREIADEVGAVLMVDMAHFAG 260
Query: 266 LVAAGVIP---SPFEYADVVTTTTHKSLRGPRGAMIFFRKGVKEINKQGQEVMYAYEDKI 322
LVA V P +AD+VTTTTHK+LRGPRG ++ +K Y D +
Sbjct: 261 LVAGKVFTGDEDPVPHADIVTTTTHKTLRGPRGGLVLAKK--------------EYADAV 306
Query: 323 NQAVFPGLQGGPHNHTISGLAVALKQVKTPEYKAYQEQVLSNSSKFARSLLERGYDLVSG 382
++ P + GGP H ++ AVAL + +TPE++ Y +QV+ N+ A L+RG LV+G
Sbjct: 307 DKGC-PLVLGGPLPHVMAAKAVALAEARTPEFQKYAQQVVDNARALAEGFLKRGARLVTG 365
Query: 383 GTENHLVLVNLRNKGIDGSRVEKVLESVHIAANKNTVPGDVS-AMVPGGIRMGTPALTSR 441
GT+NHLVL+++ + G+ G + E L I N+N++P D + A GIR+GTPALT+
Sbjct: 366 GTDNHLVLIDVTSFGLTGRQAESALLDAGIVTNRNSIPSDPNGAWYTSGIRLGTPALTTL 425
Query: 442 GFVEEDFEKVAEFFDAAVKLALKIKGDTKGTKLKDFVATLMSDESIQSEISNLRDKVEEY 501
G ++ ++VAE + +G K A DE + E+ R +V E
Sbjct: 426 GMGSDEMDEVAELIVKVLS-NTTPGTTAEGAPSK---AKYELDEGVAQEV---RARVAEL 478
Query: 502 AKRFP 506
RFP
Sbjct: 479 LARFP 483
>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 = 111 bits (280), Expect = 9e-29
Identities = 42/178 (23%), Positives = 69/178 (38%), Gaps = 15/178 (8%)
Query: 127 CQKRALDAFQLDPAKWGVNVQSLSGSPANFQVYTALLKPHERIMALDLPHGGHLSHGYQT 186
+++ Q P SG+ AN ALL P + ++ HG
Sbjct: 5 LEEKLARLLQ--PGNDKAVFVP-SGTGANEAALLALLGPGDEVIVDANGHGSRYWV---- 57
Query: 187 DTKKISAVSIFFETMPYRLDESTGY-IDYEQLEKSAALFRPKLIVAGASAYAR--LYDYA 243
+A + +P +D++ +D LE+ A LIV + + L
Sbjct: 58 -----AAELAGAKPVPVPVDDAGYGGLDVAILEELKAKPNVALIVITPNTTSGGVLVPLK 112
Query: 244 RIRKVCDKQKAVMLADMAHISGLVAAGVIPSPFEYADVVTTTTHKSLRGPRGAMIFFR 301
IRK+ + ++L D A G A + P ADVVT + HK+L G G ++ +
Sbjct: 113 EIRKIAKEYGILLLVDAASAGGASPAPGVLIPEGGADVVTFSLHKNLGGEGGGVVIVK 170
>gnl|CDD|216367 pfam01212, Beta_elim_lyase, Beta-eliminating lyase.
Length = 288
Score = 39.9 bits (94), Expect = 0.002
Identities = 38/169 (22%), Positives = 60/169 (35%), Gaps = 26/169 (15%)
Query: 150 SGSPANFQVYTALLKPHERIMALDLPHGGHLSHGYQTDTKKISAVSIFFETMPYRLD-ES 208
SG+ AN A + + ++ G +H Y +T + P L
Sbjct: 55 SGTMANQLALMAHCRRGDEVIC------GEPAHIYFDETG---GHAELGGAQPVPLPGAE 105
Query: 209 TGYIDYEQLEKSAALF------RPKLIV-------AGASAYARLYDYARIRKVCDKQKAV 255
G +D E LE + LI AG + L + IR + +
Sbjct: 106 AGKLDLEDLEAAIRPVGDIHFPPTGLISLENTHNSAGGQVVS-LEELREIRAIAREHGIP 164
Query: 256 MLADMAHIS-GLVAAGVIPSP-FEYADVVTTTTHKSLRGPRGAMIFFRK 302
+ D A ++ VA GVI YAD V+ + K L P G+++
Sbjct: 165 LHLDGARLANAAVALGVIVKEITSYADSVSMSLSKGLGAPVGSVLAGSD 213
>gnl|CDD|223594 COG0520, csdA, Selenocysteine lyase/Cysteine desulfurase
[Posttranslational modification, protein turnover,
chaperones].
Length = 405
Score = 39.2 bits (92), Expect = 0.004
Identities = 43/193 (22%), Positives = 68/193 (35%), Gaps = 32/193 (16%)
Query: 241 DYARIRKVCDKQKAVMLADMAHISGLVAAGVIPSPFE--YADVVTTTTHKSLRGPRG-AM 297
I ++ + A++L D A AAG +P + D + + HK L GP G +
Sbjct: 180 PVKEIAELAHEHGALVLVDAAQ-----AAGHLPIDVQELGCDFLAFSGHKWLLGPTGIGV 234
Query: 298 IFFRKGVKEINKQ----GQEVMYAYEDKINQAVFPGL--QGGPHNHT-ISGLAVALKQVK 350
++ RK + E + G + Y D+ L + G N GLA AL
Sbjct: 235 LYVRKELLEELEPFLGGGGMIEYVSRDEGVTLAELPLRFEAGTPNIAGAIGLAAAL---- 290
Query: 351 TPEYKAYQEQVLSNSSKFARSLLERGYDLVSG---------GTENHLVLVNLRNKGIDGS 401
E + R L E + +S + +V+ KGI
Sbjct: 291 ----DYLLEIGMEAIEAHERELTEYLLEGLSELPGVEIYGPPDADRGGIVSFNVKGIHPH 346
Query: 402 RVEKVLESVHIAA 414
V +L+ IA
Sbjct: 347 DVATLLDEKGIAV 359
>gnl|CDD|223154 COG0076, GadB, Glutamate decarboxylase and related PLP-dependent
proteins [Amino acid transport and metabolism].
Length = 460
Score = 38.9 bits (91), Expect = 0.006
Identities = 34/226 (15%), Positives = 67/226 (29%), Gaps = 39/226 (17%)
Query: 204 RLDESTGYIDYEQLEKSAALFRPKLIV---AGASAYARLYDYARIRKVCDKQKAVMLADM 260
+ ID + LE++ +V AG + + D + + ++ +
Sbjct: 185 PTVPTDYRIDVDALEEAIDENTIGGVVVGTAGTTDTGSIDDIEELADIAEEYGIWL---- 240
Query: 261 AHISGLVAAGVIPSPFEY---------ADVVTTTTHKSLRGPRGA-MIFFRKGVKEINKQ 310
H+ ++P D +T HK P G ++ FR
Sbjct: 241 -HVDAAFGGFLLPFLEPDGRWDFGLEGVDSITVDGHKYGLAPIGCGVVLFRDEEA----- 294
Query: 311 GQEVMYAYEDKINQAVFPGLQGGPHNHTISGLA-------VALKQVKTPEYKAYQEQVLS 363
PG S L+++ Y+ ++ L
Sbjct: 295 -----LRRILIFADYYLPGGGIPNFTILGSRPGRQALALYANLRRLGREGYRKLLDRTLE 349
Query: 364 NSSKFARSLLERG-YDLVSGGTENHLVLVNLRNKGIDGSRVEKVLE 408
+ A L + G ++LV+ E L +V R K + + +
Sbjct: 350 LARYLAEELEKLGDFELVN---EPELPIVAFRLKDDEDTLADLSER 392
>gnl|CDD|99734 cd00609, AAT_like, Aspartate aminotransferase family. This family
belongs to pyridoxal phosphate (PLP)-dependent aspartate
aminotransferase superfamily (fold I). Pyridoxal
phosphate combines with an alpha-amino acid to form a
compound called a Schiff base or aldimine intermediate,
which depending on the reaction, is the substrate in
four kinds of reactions (1) transamination (movement of
amino groups), (2) racemization (redistribution of
enantiomers), (3) decarboxylation (removing COOH
groups), and (4) various side-chain reactions depending
on the enzyme involved. Pyridoxal phosphate (PLP)
dependent enzymes were previously classified into alpha,
beta and gamma classes, based on the chemical
characteristics (carbon atom involved) of the reaction
they catalyzed. The availability of several structures
allowed a comprehensive analysis of the evolutionary
classification of PLP dependent enzymes, and it was
found that the functional classification did not always
agree with the evolutionary history of these enzymes.
The major groups in this CD corresponds to Aspartate
aminotransferase a, b and c, Tyrosine, Alanine,
Aromatic-amino-acid, Glutamine phenylpyruvate,
1-Aminocyclopropane-1-carboxylate synthase,
Histidinol-phosphate, gene products of malY and cobC,
Valine-pyruvate aminotransferase and Rhizopine
catabolism regulatory protein.
Length = 350
Score = 34.6 bits (80), Expect = 0.12
Identities = 45/271 (16%), Positives = 91/271 (33%), Gaps = 48/271 (17%)
Query: 202 PYRLDESTGYIDYEQLEKSAALFRPKLIV-------AGASAYARLYDYARIRKV---CDK 251
P LDE G++ +L ++A + KL+ G + + ++ K
Sbjct: 109 PVPLDEEGGFLLDLELLEAAKTPKTKLLYLNNPNNPTG-----AVLSEEELEELAELAKK 163
Query: 252 QKAVMLADMAHISGLVAAGVIPSPFEYAD-----VVTTTTHKSLRGP--RGAMIFFRKGV 304
++++D A+ + LV G P D +V + K+ P R +
Sbjct: 164 HGILIISDEAY-AELVYDGEPPPALALLDAYERVIVLRSFSKTFGLPGLRIGYLIAPP-- 220
Query: 305 KEINKQGQEVMYAYEDKINQAVFPGLQGGPHNHTISGLAVALKQVKTPEYKAYQEQVLSN 364
+E++ + + P GP + + A AL + +E+
Sbjct: 221 -------EELLERLKKLL-----PYTTSGPSTLSQAAAAAALDD-GEEHLEELRERYRRR 267
Query: 365 SSKFARSLLERGYDLVSGGTENHLVLVNLRNKGIDGSRVEKVLESVHIAANKNTVPGDVS 424
+L E G +V + + ++L +G D +E++L +
Sbjct: 268 RDALLEALKELGPLVVVKPSGGFFLWLDLP-EGDDEEFLERLLLEAGVVV---RPGSAFG 323
Query: 425 AMVPGGIRMGTPALTSRGFVEEDFEKVAEFF 455
G +R+ EE+ E+ E
Sbjct: 324 EGGEGFVRLSF------ATPEEELEEALERL 348
>gnl|CDD|215756 pfam00155, Aminotran_1_2, Aminotransferase class I and II.
Length = 357
Score = 33.5 bits (77), Expect = 0.23
Identities = 26/158 (16%), Positives = 53/158 (33%), Gaps = 26/158 (16%)
Query: 144 VNVQSLSGSPANFQVYTALLK--PHERIMALDLPHGGHLSHGYQTDTKKISAVSIFFETM 201
V SG+ AN + LL+ P + I+ + + E +
Sbjct: 66 AAVVFGSGAGANIEALIFLLRLNPGDAILVPAPTYPSY----------IRIFRLAGGEVV 115
Query: 202 PYRLDESTGY-IDYEQLE---KSAALFRPKLIVAGAS----AYARLYDYARIRKVCDKQK 253
Y L S + +D++ LE K A ++ A L + ++ + +
Sbjct: 116 RYPLYSSNDFHLDFDALEAALKEATEGNKVVLHTSPHNPTGTVATLEELEKLLDLAKEHN 175
Query: 254 AVMLADMAHISGLVAAGVIPSPF-----EYADVVTTTT 286
++L D A+ G V + E +++ +
Sbjct: 176 ILLLVDEAYA-GFVFGSLDAVATRALLAEGPNLLVVGS 212
>gnl|CDD|216899 pfam02142, MGS, MGS-like domain. This domain composes the whole
protein of methylglyoxal synthetase and the domain is
also found in Carbamoyl phosphate synthetase (CPS) where
it forms a regulatory domain that binds to the
allosteric effector ornithine. This family also includes
inosicase. The known structures in this family show a
common phosphate binding site.
Length = 92
Score = 30.1 bits (69), Expect = 0.55
Identities = 14/43 (32%), Positives = 21/43 (48%), Gaps = 6/43 (13%)
Query: 367 KFARSLLERGYDLVS-GGTENHLVLVNLRNKGIDGSRVEKVLE 408
+ A++L+E G+ L + GGT L+ GI V K E
Sbjct: 4 ELAKALVELGFKLYATGGTAKF-----LKEAGIPTEVVNKTGE 41
>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 = 31.8 bits (73), Expect = 0.69
Identities = 42/194 (21%), Positives = 71/194 (36%), Gaps = 14/194 (7%)
Query: 128 QKRALDAFQLDPAKWGVNVQSLSGSPANFQVYTALLKPHERIMALDLPHGGHLSHGYQTD 187
Q+ A AF + VN S S N V A+ P ++I+ + H S
Sbjct: 65 QELAARAFGAKHTFFLVNGTSSS----NKAVILAVCGPGDKIL---IDRNCHKSVINGLV 117
Query: 188 TKKISAVSIFFETMPYRLDESTGYIDYEQLEK-SAALFRPKLIVAGASAY-ARLYDYARI 245
AV ++ + G I E +K K V Y Y+ +I
Sbjct: 118 LSG--AVPVYLKPERNPYYGIAGGIPPETFKKALIEHPDAKAAVITNPTYYGICYNLRKI 175
Query: 246 RKVCDKQKAVMLADMAHISGLVAAGVIPS--PFEYADVVTTTTHKSLRGPR-GAMIFFRK 302
+ + +L D AH + ++PS AD+V +THK+L G+MI +
Sbjct: 176 VEEAHHRGLPVLVDEAHGAHFRFHPILPSSAAMAGADIVVQSTHKTLPALTQGSMIHVKG 235
Query: 303 GVKEINKQGQEVMY 316
+ ++ + +
Sbjct: 236 DLVNPDRVNEALNL 249
>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 = 31.8 bits (73), Expect = 0.77
Identities = 38/183 (20%), Positives = 71/183 (38%), Gaps = 27/183 (14%)
Query: 215 EQLEKSAALFRPKLIVAGASAYARLYDYARIRKVC---DKQKAVMLADMAHISGLV---A 268
+ L ++ + KLIV Y+ D A + ++ K A++ D AH G+
Sbjct: 122 KLLREARRPYGKKLIVT-EGVYSMDGDIAPLPELVDLAKKYGAILFVDEAHSVGVYGPHG 180
Query: 269 AGVIPSPFEYADV--VTTTTHKSLRGPRGAMIFFRKGVKEINKQGQEVMYAYEDKINQAV 326
GV DV + T K+ G G I K + + + YA + ++
Sbjct: 181 RGVEEFGGLTDDVDIIMGTLGKAF-GAVGGYIAGSKELIDYLRS-----YARGFIFSTSL 234
Query: 327 FPGLQGGPHNHTISGLAVALKQVKTPEYKAYQEQVLSNSSKFARSLLERGYDLVSGGTEN 386
P + AL+ ++ + +E++ N R L E G+ + GG+ +
Sbjct: 235 PP--------AVAAAALAALEVLQGGPER--RERLQENVRYLRRGLKELGFPV--GGSPS 282
Query: 387 HLV 389
H++
Sbjct: 283 HII 285
>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 = 31.4 bits (72), Expect = 1.1
Identities = 15/65 (23%), Positives = 23/65 (35%), Gaps = 2/65 (3%)
Query: 206 DESTGYIDYEQLEKSAALFRPKLIVAGASAYARLYDYARIRKVCDKQKAVMLADMAHISG 265
D T ID + +E A R K I+ + D I + + ++ D A G
Sbjct: 104 DPDTLNIDPDLIEA-AITPRTKAIIP-VHLAGQPCDMDAIMALAKRHGLPVIEDAAQAHG 161
Query: 266 LVAAG 270
G
Sbjct: 162 ATYKG 166
>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 = 29.4 bits (66), Expect = 1.3
Identities = 15/56 (26%), Positives = 26/56 (46%), Gaps = 5/56 (8%)
Query: 259 DMAHISGLVAAGVIPSPFEYADVVTTTTHKSLRGPRGAMIF-FRKGVKEINKQGQE 313
+ ++ AG +PF+ +V TH GP GA F ++G++E K+
Sbjct: 28 TLLDLAKKAGAGEKLTPFDREMLVQGLTH----GPEGAAAFVVKQGIREAIKEMLS 79
>gnl|CDD|206723 cd04158, ARD1, (ADP-ribosylation factor domain protein 1 (ARD1).
ARD1 (ADP-ribosylation factor domain protein 1) is an
unusual member of the Arf family. In addition to the
C-terminal Arf domain, ARD1 has an additional 46-kDa
N-terminal domain that contains a RING finger domain,
two predicted B-Boxes, and a coiled-coil protein
interaction motif. This domain belongs to the TRIM
(tripartite motif) or RBCC (RING, B-Box, coiled-coil)
family. Like most Arfs, the ARD1 Arf domain lacks
detectable GTPase activity. However, unlike most Arfs,
the full-length ARD1 protein has significant GTPase
activity due to the GAP (GTPase-activating protein)
activity exhibited by the 46-kDa N-terminal domain. The
GAP domain of ARD1 is specific for its own Arf domain
and does not bind other Arfs. The rate of GDP
dissociation from the ARD1 Arf domain is slowed by the
adjacent 15 amino acids, which act as a GDI
(GDP-dissociation inhibitor) domain. ARD1 is
ubiquitously expressed in cells and localizes to the
Golgi and to the lysosomal membrane. Two Tyr-based
motifs in the Arf domain are responsible for Golgi
localization, while the GAP domain controls lysosomal
localization.
Length = 169
Score = 30.4 bits (68), Expect = 1.6
Identities = 11/23 (47%), Positives = 17/23 (73%)
Query: 497 KVEEYAKRFPTVGFEKETMKYKN 519
K +E+ + PT+GF ET++YKN
Sbjct: 20 KQDEFMQPIPTIGFNVETVEYKN 42
>gnl|CDD|233587 TIGR01821, 5aminolev_synth, 5-aminolevulinic acid synthase. This
model represents 5-aminolevulinic acid synthase, an
enzyme for one of two routes to the heme precursor
5-aminolevulinate. The protein is a pyridoxal
phosphate-dependent enzyme related to
2-amino-3-ketobutyrate CoA tranferase and
8-amino-7-oxononanoate synthase. This enzyme appears
restricted to the alpha Proteobacteria and mitochondrial
derivatives [Biosynthesis of cofactors, prosthetic
groups, and carriers, Heme, porphyrin, and cobalamin].
Length = 402
Score = 30.9 bits (70), Expect = 1.6
Identities = 28/95 (29%), Positives = 36/95 (37%), Gaps = 28/95 (29%)
Query: 213 DYEQLEKSAALFRPKLIVAGASAYARLYDYARIRKVCD---KQKAVMLADMAHISGLVAA 269
E+L +S RPK+I A S Y+ D A I ++CD K A+ D H GL
Sbjct: 165 HLEKLLQSVDPNRPKII-AFESVYSMDGDIAPIEEICDLADKYGALTYLDEVHAVGLY-- 221
Query: 270 GVIPSPFEYADVVTTTTHKSLRGPRGAMIFFRKGV 304
GPRG I R G+
Sbjct: 222 ----------------------GPRGGGIAERDGL 234
>gnl|CDD|99748 cd06502, TA_like, Low-specificity threonine aldolase (TA). This
family belongs to pyridoxal phosphate (PLP)-dependent
aspartate aminotransferase superfamily (fold I). TA
catalyzes the conversion of L-threonine or
L-allo-threonine to glycine and acetaldehyde in a
secondary glycine biosynthetic pathway.
Length = 338
Score = 30.8 bits (70), Expect = 1.8
Identities = 30/164 (18%), Positives = 51/164 (31%), Gaps = 23/164 (14%)
Query: 150 SGSPANFQVYTALLKPHERIMALDLPHGGHLSHGYQTDTKKISAVSIFFETMPYRLDEST 209
SG+ AN A +P ++ +H Y T + A +
Sbjct: 55 SGTAANQLALAAHTQPGGSVIC------HETAHIY---TDEAGAPEFLSGVKLLPVPGEN 105
Query: 210 GYIDYEQLEKSAALF------RPKLIV----AGASAYARLYDYARIRKVCDKQKAVML-A 258
G + E LE + P L+ L + I + K+ + L
Sbjct: 106 GKLTPEDLEAAIRPRDDIHFPPPSLVSLENTTEGGTVYPLDELKAISALA-KENGLPLHL 164
Query: 259 DMAHISGLVAAGVIP--SPFEYADVVTTTTHKSLRGPRGAMIFF 300
D A ++ AA + + D V+ K P GA++
Sbjct: 165 DGARLANAAAALGVALKTYKSGVDSVSFCLSKGGGAPVGAVVVG 208
>gnl|CDD|224832 COG1921, SelA, Selenocysteine synthase [seryl-tRNASer selenium
transferase] [Amino acid transport and metabolism].
Length = 395
Score = 30.8 bits (70), Expect = 1.8
Identities = 50/278 (17%), Positives = 91/278 (32%), Gaps = 52/278 (18%)
Query: 226 PKLIVAGASAYARLYDY--------ARIRKV----CDKQKAVMLAD---MAHISGLV--- 267
KL+ G + L DY A + KV + + +AH GL
Sbjct: 133 AKLVEVGTTNRTHLKDYELAINENTALLLKVHSSNYGFTGMLSEEELVEIAHEKGLPVIV 192
Query: 268 -AAGVIPSPFEY---------ADVVTTTTHKSLRGPRGAMIFFRKGVKEINKQGQEVMYA 317
A E AD+V+ + K L GP+ +I G KE+ ++ Q
Sbjct: 193 DLASGALVDKEPDLREALALGADLVSFSGDKLLGGPQAGIIV---GKKELIEKLQSHPLK 249
Query: 318 YEDKINQAVFPGLQGGPHNHTISGLAVALKQVKTPEYKAYQEQVLSNSSKFARSLLER-- 375
++ T++ L AL+ PE + + L ++ A +LL +
Sbjct: 250 RALRV---------DKE---TLAALEAALELYLQPEILGERLRTLRLLTQPAEALLAQAG 297
Query: 376 --GYDLVSGGTENHLVLVNLRNKGI-DGSRVEKVLES--VHIAANKNTVPGDVSAMVPGG 430
+ + +V + I GS +++L S + I G + + P
Sbjct: 298 RLAVVELDPTGDRLVVKIVSSESQIGSGSLPDELLPSLALIITPKYGIRGGKLEGL-PRR 356
Query: 431 IRMGTPALTSRGFVEE-DFEKVAEFFDAAVKLALKIKG 467
+R + +R + + K L +
Sbjct: 357 LRTLRVPIIARIAERILWLDLRELIEEDLKKFLLTLNE 394
>gnl|CDD|234854 PRK00881, purH, bifunctional
phosphoribosylaminoimidazolecarboxamide
formyltransferase/IMP cyclohydrolase; Provisional.
Length = 513
Score = 30.8 bits (71), Expect = 2.1
Identities = 10/22 (45%), Positives = 16/22 (72%), Gaps = 1/22 (4%)
Query: 368 FARSLLERGYDLVS-GGTENHL 388
FA++L+E G +++S GGT L
Sbjct: 20 FAKALVELGVEILSTGGTAKLL 41
>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 = 30.3 bits (69), Expect = 2.1
Identities = 16/35 (45%), Positives = 20/35 (57%), Gaps = 1/35 (2%)
Query: 149 LSGSPANFQVYTALLKPHERIMALDLP-HGGHLSH 182
GS A++Q LL PH R +A+DLP HG S
Sbjct: 11 FLGSGADWQALIELLGPHFRCLAIDLPGHGSSQSP 45
>gnl|CDD|206716 cd04149, Arf6, ADP ribosylation factor 6 (Arf6). Arf6 subfamily.
Arf6 (ADP ribosylation factor 6) proteins localize to
the plasma membrane, where they perform a wide variety
of functions. In its active, GTP-bound form, Arf6 is
involved in cell spreading, Rac-induced formation of
plasma membrane ruffles, cell migration, wound healing,
and Fc-mediated phagocytosis. Arf6 appears to change the
actin structure at the plasma membrane by activating
Rac, a Rho family protein involved in membrane ruffling.
Arf6 is required for and enhances Rac formation of
ruffles. Arf6 can regulate dendritic branching in
hippocampal neurons, and in yeast it localizes to the
growing bud, where it plays a role in polarized growth
and bud site selection. In leukocytes, Arf6 is required
for chemokine-stimulated migration across endothelial
cells. Arf6 also plays a role in down-regulation of
beta2-adrenergic receptors and luteinizing hormone
receptors by facilitating the release of sequestered
arrestin to allow endocytosis. Arf6 is believed to
function at multiple sites on the plasma membrane
through interaction with a specific set of GEFs, GAPs,
and effectors. Arf6 has been implicated in breast cancer
and melanoma cell invasion, and in actin remodelling at
the invasion site of Chlamydia infection.
Length = 168
Score = 29.0 bits (65), Expect = 3.5
Identities = 10/14 (71%), Positives = 11/14 (78%)
Query: 506 PTVGFEKETMKYKN 519
PTVGF ET+ YKN
Sbjct: 39 PTVGFNVETVTYKN 52
>gnl|CDD|234269 TIGR03588, PseC, UDP-4-keto-6-deoxy-N-acetylglucosamine
4-aminotransferase. This family of enzymes are
aminotransferases of the pfam01041 family involved in
the biosynthesis of pseudaminic acid. They convert
UDP-4-keto-6-deoxy-N-acetylglucosamine into
UDP-4-amino-4,6-dideoxy-N-acetylgalactose. Pseudaminic
acid has a role in surface polysaccharide in Pseudomonas
as well as in the modification of flagellin in
Campylobacter and Helicobacter species.
Length = 380
Score = 29.6 bits (67), Expect = 4.1
Identities = 26/83 (31%), Positives = 32/83 (38%), Gaps = 12/83 (14%)
Query: 206 DESTGYIDYEQLEK---SAALFRPKLIV----AGASAYARLYDYARIRKVCDKQKAVMLA 258
D TG ID + LEK +A PK IV AG S D I + K ++
Sbjct: 99 DPDTGNIDEDALEKKLAAAKGKLPKAIVPVDFAGKSV-----DMQAIAALAKKHGLKIIE 153
Query: 259 DMAHISGLVAAGVIPSPFEYADV 281
D +H G G YAD
Sbjct: 154 DASHALGAEYGGKPVGNCRYADA 176
>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 = 29.5 bits (67), Expect = 4.2
Identities = 41/166 (24%), Positives = 60/166 (36%), Gaps = 44/166 (26%)
Query: 150 SGSPANFQVYTALLKPHERIMALDLPH-----GGHLSHGYQTDTKKISAVSIFFETMPYR 204
SG AN V +AL+ + I++ L H G LS YR
Sbjct: 84 SGYLANVGVISALVGKGDLILSDALNHASLIDGCRLSGA---------------RVRRYR 128
Query: 205 LDESTGYIDYEQLE---KSAALFRPKLIVAGA--SAYARLYDYARIRKVCDKQKAVMLAD 259
+ D E LE + R KLIV S + ++ + ++ A ++ D
Sbjct: 129 ------HNDVEHLERLLEKNRGERRKLIVTDGVFSMDGDIAPLPQLVALAERYGAWLMVD 182
Query: 260 MAHISG---------LVAAGVIPSPFEYADVVTTTTHKSLRGPRGA 296
AH +G L G+ P P D+ T K+L G GA
Sbjct: 183 DAHGTGVLGEDGRGTLEHFGLKPEP---VDIQVGTLSKAL-GSYGA 224
>gnl|CDD|214855 smart00851, MGS, MGS-like domain. This domain composes the whole
protein of methylglyoxal synthetase and the domain is
also found in Carbamoyl phosphate synthetase (CPS) where
it forms a regulatory domain that binds to the
allosteric effector ornithine. This family also includes
inosicase. The known structures in this family show a
common phosphate binding site.
Length = 91
Score = 27.8 bits (63), Expect = 4.2
Identities = 15/51 (29%), Positives = 22/51 (43%), Gaps = 9/51 (17%)
Query: 368 FARSLLERGYDLVS-GGTENHLVLVNLRNKGIDGSR--VEKVLE-SVHIAA 414
FA+ L E G++L++ GGT LR G+ + KV I
Sbjct: 5 FAKRLAELGFELLATGGTAKF-----LREAGLPVVKTLHPKVHGGIPQILD 50
>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 = 29.3 bits (66), Expect = 5.0
Identities = 49/215 (22%), Positives = 82/215 (38%), Gaps = 21/215 (9%)
Query: 207 ESTGYIDYEQLEKSAALFRPKLIVAG-ASAYARLY-DYARIRKVCDKQKAVMLADMAHIS 264
++ G I E++ K A KLIV AS I ++ + + D A
Sbjct: 120 DNEGLISPERI-KRAIKTNTKLIVVSHASNVTGTILPIEEIGELAQENGIFFILDAAQ-- 176
Query: 265 GLVAAGVIPSPFEYA--DVVTTTTHKSLRGPRGAMIFF---RKGVKEINKQGQEVMYAYE 319
AGVIP D++ T HK L GP+G + +K + G ++
Sbjct: 177 ---TAGVIPIDMTELAIDMLAFTGHKGLLGPQGTGGLYIREGIKLKPLKSGGTG---SHS 230
Query: 320 DKINQAVF-PG-LQGGPHN-HTISGLAVALKQVKTPEYKAYQEQVLSNSSKFARSLLERG 376
I+Q P + G N I+GL +K ++ ++ + K L E
Sbjct: 231 ALIDQPSELPDRFESGTLNTPGIAGLNAGIKFIEKIGIANIAKKECMLTEKLLNGLREIN 290
Query: 377 YDLVSGGTE--NHLVLVNLRNKGIDGSRVEKVLES 409
+ G + N + +V+ +GID V +L+
Sbjct: 291 KVKIYGPADPANRVGVVSFTVEGIDSEEVADILDE 325
>gnl|CDD|173423 PTZ00133, PTZ00133, ADP-ribosylation factor; Provisional.
Length = 182
Score = 28.3 bits (63), Expect = 6.7
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 497 KVEEYAKRFPTVGFEKETMKYKN 519
K+ E PT+GF ET++YKN
Sbjct: 38 KLGEVVTTIPTIGFNVETVEYKN 60
>gnl|CDD|165788 PLN00223, PLN00223, ADP-ribosylation factor; Provisional.
Length = 181
Score = 28.4 bits (63), Expect = 7.2
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 497 KVEEYAKRFPTVGFEKETMKYKN 519
K+ E PT+GF ET++YKN
Sbjct: 38 KLGEIVTTIPTIGFNVETVEYKN 60
>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 = 7.4
Identities = 23/86 (26%), Positives = 36/86 (41%), Gaps = 11/86 (12%)
Query: 196 IFFETMPYRLDESTGYIDYEQ-LEK-SAALFRPKLIV---AGASAYARLYDYARIRKVCD 250
+ ET E +G D L+K + L+V +G Y +L+ +R V
Sbjct: 141 VLIET-----CEESGSYDLPAYLDKLKERIGNVDLVVCLDSGCGNYEQLWLTTSLRGVLG 195
Query: 251 KQKAVMLADMAHISGLVAAGVIPSPF 276
V + D SG A+G++PS F
Sbjct: 196 GDLTVQVLDEGVHSG-DASGIVPSSF 220
>gnl|CDD|128474 smart00177, ARF, ARF-like small GTPases; ARF, ADP-ribosylation
factor. Ras homologues involved in vesicular transport.
Activator of phospholipase D isoforms. Unlike Ras
proteins they lack cysteine residues at their C-termini
and therefore are unlikely to be prenylated. ARFs are
N-terminally myristoylated. Contains ATP/GTP-binding
motif (P-loop).
Length = 175
Score = 28.3 bits (63), Expect = 7.5
Identities = 11/23 (47%), Positives = 14/23 (60%)
Query: 497 KVEEYAKRFPTVGFEKETMKYKN 519
K+ E PT+GF ET+ YKN
Sbjct: 34 KLGESVTTIPTIGFNVETVTYKN 56
>gnl|CDD|206717 cd04150, Arf1_5_like, ADP-ribosylation factor-1 (Arf1) and
ADP-ribosylation factor-5 (Arf5). The Arf1-Arf5-like
subfamily contains Arf1, Arf2, Arf3, Arf4, Arf5, and
related proteins. Arfs1-5 are soluble proteins that are
crucial for assembling coat proteins during vesicle
formation. Each contains an N-terminal myristoylated
amphipathic helix that is folded into the protein in the
GDP-bound state. GDP/GTP exchange exposes the helix,
which anchors to the membrane. Following GTP hydrolysis,
the helix dissociates from the membrane and folds back
into the protein. A general feature of Arf1-5 signaling
may be the cooperation of two Arfs at the same site.
Arfs1-5 are generally considered to be interchangeable
in function and location, but some specific functions
have been assigned. Arf1 localizes to the
early/cis-Golgi, where it is activated by GBF1 and
recruits the coat protein COPI. It also localizes to the
trans-Golgi network (TGN), where it is activated by
BIG1/BIG2 and recruits the AP1, AP3, AP4, and GGA
proteins. Humans, but not rodents and other lower
eukaryotes, lack Arf2. Human Arf3 shares 96% sequence
identity with Arf1 and is believed to generally function
interchangeably with Arf1. Human Arf4 in the activated
(GTP-bound) state has been shown to interact with the
cytoplasmic domain of epidermal growth factor receptor
(EGFR) and mediate the EGF-dependent activation of
phospholipase D2 (PLD2), leading to activation of the
activator protein 1 (AP-1) transcription factor. Arf4
has also been shown to recognize the C-terminal sorting
signal of rhodopsin and regulate its incorporation into
specialized post-Golgi rhodopsin transport carriers
(RTCs). There is some evidence that Arf5 functions at
the early-Golgi and the trans-Golgi to affect
Golgi-associated alpha-adaptin homology Arf-binding
proteins (GGAs).
Length = 159
Score = 28.1 bits (63), Expect = 7.6
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 497 KVEEYAKRFPTVGFEKETMKYKN 519
K+ E PT+GF ET++YKN
Sbjct: 21 KLGEIVTTIPTIGFNVETVEYKN 43
>gnl|CDD|236370 PRK09064, PRK09064, 5-aminolevulinate synthase; Validated.
Length = 407
Score = 28.7 bits (65), Expect = 7.9
Identities = 18/47 (38%), Positives = 23/47 (48%), Gaps = 7/47 (14%)
Query: 213 DYEQLEKSAALFRPKLIVAGASAYARLYDYARIRKVCDKQKAVMLAD 259
E+L +A RPKLI S Y+ D A I ++CD LAD
Sbjct: 166 HLEELLAAADPDRPKLIAF-ESVYSMDGDIAPIAEICD------LAD 205
>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 = 28.2 bits (63), Expect = 8.4
Identities = 12/31 (38%), Positives = 18/31 (58%), Gaps = 2/31 (6%)
Query: 318 YEDKINQAV--FPGLQGGPHNHTISGLAVAL 346
++ + N V FP + GGP N+ SG +V L
Sbjct: 194 FDYRKNTVVKEFPQIPGGPRNYPSSGSSVLL 224
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
0.315 0.132 0.376
Gapped
Lambda K H
0.267 0.0850 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 26,600,597
Number of extensions: 2628571
Number of successful extensions: 2802
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2762
Number of HSP's successfully gapped: 57
Length of query: 519
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 418
Effective length of database: 6,457,848
Effective search space: 2699380464
Effective search space used: 2699380464
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 (21.6 bits)
S2: 61 (27.1 bits)