RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 022564
(295 letters)
>1rv3_A Serine hydroxymethyltransferase, cytosolic; one-carbon metabolism;
HET: GLY PLP; 2.40A {Oryctolagus cuniculus} SCOP:
c.67.1.4 PDB: 1rv4_A* 1rvu_A* 1rvy_A* 1ls3_A* 1cj0_A*
1bj4_A* 1eji_A*
Length = 483
Score = 533 bits (1376), Expect = 0.0
Identities = 166/280 (59%), Positives = 211/280 (75%), Gaps = 3/280 (1%)
Query: 7 EAVYEKEKNGVTWP---KQLNAPLEVVDPEIADIIEHEKARQWKGLELIPSENFTSVSVM 63
AV ++ W + L PL+ D E+ DII+ E RQ GLELI SENF S +V+
Sbjct: 2 TAVNGAPRDAALWSSHEQMLAQPLKDSDAEVYDIIKKESNRQRVGLELIASENFASRAVL 61
Query: 64 QAVGSVMTNKYSEGYPGARYYGGNEYIDMAESLCQKRALEAFRLDPEKWGVNVQSLSGSP 123
+A+GS + NKYS GYPG RYYGG E+ID E+LCQKRAL+A+ LDP+ WGVNVQ SGSP
Sbjct: 62 EALGSCLNNKYSLGYPGQRYYGGTEHIDELETLCQKRALQAYGLDPQCWGVNVQPYSGSP 121
Query: 124 SNFQVYTALLKPHDRIMALDLPHGGHLSHGYQTDTKKISAVSIFFETMPYRLNESTGYID 183
+NF VYTAL++PH RIM LDLP GGHL+HG+ TD KKISA SIFFE+M Y++N TGYID
Sbjct: 122 ANFAVYTALVEPHGRIMGLDLPDGGHLTHGFMTDKKKISATSIFFESMAYKVNPDTGYID 181
Query: 184 YDQLEKSATLFRPKLIVAGASAYARLYDYERIRKVCNKQKAIMLADMAHISGLVAAGVIP 243
YD+LE++A LF PKLI+AG S Y+R DY R+RK+ ++ A ++ADMAHISGLV AGV+P
Sbjct: 182 YDRLEENARLFHPKLIIAGTSCYSRNLDYGRLRKIADENGAYLMADMAHISGLVVAGVVP 241
Query: 244 SPFEYADVVTTTTHKSLRGPRGAMIFFRKGVKEINKQGKE 283
SPFE+ VVTTTTHK+LRG R MIF+R+GV+ ++ + +
Sbjct: 242 SPFEHCHVVTTTTHKTLRGCRAGMIFYRRGVRSVDPKTGK 281
>2a7v_A Serine hydroxymethyltransferase; structural genomics, structural
genomics consortium, SGC; 2.04A {Homo sapiens} SCOP:
c.67.1.4 PDB: 3ou5_A
Length = 490
Score = 526 bits (1358), Expect = 0.0
Identities = 171/282 (60%), Positives = 213/282 (75%), Gaps = 2/282 (0%)
Query: 2 SSLPNEAVYEKEKNGVTWPKQLNAPLEVVDPEIADIIEHEKARQWKGLELIPSENFTSVS 61
+ N A + + W L DPE+ ++++ EK RQ +GLELI SENF S +
Sbjct: 12 AQHSNAAQTQTGEANRGWTG--QESLSDSDPEMWELLQREKDRQCRGLELIASENFCSRA 69
Query: 62 VMQAVGSVMTNKYSEGYPGARYYGGNEYIDMAESLCQKRALEAFRLDPEKWGVNVQSLSG 121
++A+GS + NKYSEGYPG RYYGG E +D E LCQ+RALEAF LDP +WGVNVQ SG
Sbjct: 70 ALEALGSCLNNKYSEGYPGKRYYGGAEVVDEIELLCQRRALEAFDLDPAQWGVNVQPYSG 129
Query: 122 SPSNFQVYTALLKPHDRIMALDLPHGGHLSHGYQTDTKKISAVSIFFETMPYRLNESTGY 181
SP+N VYTALL+PHDRIM LDLP GGHL+HGY +D K+ISA SIFFE+MPY+LN TG
Sbjct: 130 SPANLAVYTALLQPHDRIMGLDLPDGGHLTHGYMSDVKRISATSIFFESMPYKLNPKTGL 189
Query: 182 IDYDQLEKSATLFRPKLIVAGASAYARLYDYERIRKVCNKQKAIMLADMAHISGLVAAGV 241
IDY+QL +A LFRP+LI+AG SAYARL DY R+R+VC++ KA +LADMAHISGLVAA V
Sbjct: 190 IDYNQLALTARLFRPRLIIAGTSAYARLIDYARMREVCDEVKAHLLADMAHISGLVAAKV 249
Query: 242 IPSPFEYADVVTTTTHKSLRGPRGAMIFFRKGVKEINKQGKE 283
IPSPF++AD+VTTTTHK+LRG R +IF+RKGVK ++ +
Sbjct: 250 IPSPFKHADIVTTTTHKTLRGARSGLIFYRKGVKAVDPKTGR 291
>2vi8_A Serine hydroxymethyltransferase; SHMT, E53Q, FTHF, enzyme memory,
pyridoxal phosphate, one-carbon metabolism,
PLP-dependent enzymes; HET: PLP; 1.67A {Bacillus
stearothermophilus} PDB: 2vi9_A* 2via_A* 2vib_A* 1kkj_A*
1kkp_A* 1kl1_A* 1kl2_A* 1yjs_A* 2w7f_A* 2w7d_A* 2w7e_A*
2w7g_A* 2w7h_A* 1yjz_A* 1yjy_A* 2vgu_A* 2vgs_A* 2vgt_A*
2vgv_A* 2vgw_A* ...
Length = 405
Score = 348 bits (895), Expect = e-120
Identities = 119/257 (46%), Positives = 167/257 (64%), Gaps = 16/257 (6%)
Query: 27 LEVVDPEIADIIEHEKARQWKGLELIPSENFTSVSVMQAVGSVMTNKYSEGYPGARYYGG 86
L DP++ IE E+ RQ +ELI SENF S +VM+A GSV+TNKY+EGYPG RYYGG
Sbjct: 4 LPQQDPQVFAAIEQERKRQHAKIELIASENFVSRAVMEAQGSVLTNKYAEGYPGRRYYGG 63
Query: 87 NEYIDMAESLCQKRALEAFRLDPEKWGVNVQSLSGSPSNFQVYTALLKPHDRIMALDLPH 146
EY+D+ E L ++RA + F + NVQ SG+ +N VY +L+ D ++ ++L H
Sbjct: 64 CEYVDIVEELARERAKQLFGAE----HANVQPHSGAQANMAVYFTVLEHGDTVLGMNLSH 119
Query: 147 GGHLSHGYQTDTKKISAVSI---FFETMPYRLNESTGYIDYDQLEKSATLFRPKLIVAGA 203
GGHL+HG S V+ + + Y ++ T IDYD + + A L RPKLIVA A
Sbjct: 120 GGHLTHG--------SPVNFSGVQYNFVAYGVDPETHVIDYDDVREKARLHRPKLIVAAA 171
Query: 204 SAYARLYDYERIRKVCNKQKAIMLADMAHISGLVAAGVIPSPFEYADVVTTTTHKSLRGP 263
+AY R+ D+ + R++ ++ A ++ DMAHI+GLVAAG+ P+P YA VTTTTHK+LRGP
Sbjct: 172 AAYPRIIDFAKFREIADEVGAYLMVDMAHIAGLVAAGLHPNPVPYAHFVTTTTHKTLRGP 231
Query: 264 RGAMIFFRKGV-KEINK 279
RG MI ++ K+I+K
Sbjct: 232 RGGMILCQEQFAKQIDK 248
>3gbx_A Serine hydroxymethyltransferase; structural genomics, IDP01011,
serine hydroxymethyltransfera salmonella typhimurium.;
HET: MSE; 1.80A {Salmonella typhimurium} PDB: 1dfo_A*
3g8m_A* 1eqb_A*
Length = 420
Score = 348 bits (895), Expect = e-119
Identities = 120/260 (46%), Positives = 168/260 (64%), Gaps = 16/260 (6%)
Query: 24 NAPLEVVDPEIADIIEHEKARQWKGLELIPSENFTSVSVMQAVGSVMTNKYSEGYPGARY 83
+ D E+ +E EK RQ + +ELI SEN+TS VMQA GS +TNKY+EGYPG RY
Sbjct: 8 EMNIADYDAELWQAMEQEKVRQEEHIELIASENYTSPRVMQAQGSQLTNKYAEGYPGKRY 67
Query: 84 YGGNEYIDMAESLCQKRALEAFRLDPEKWGVNVQSLSGSPSNFQVYTALLKPHDRIMALD 143
YGG EY+D+ E L RA E F D NVQ SGS +NF VYTALL+P D ++ ++
Sbjct: 68 YGGCEYVDVVEQLAIDRAKELFGAD----YANVQPHSGSQANFAVYTALLQPGDTVLGMN 123
Query: 144 LPHGGHLSHGYQTDTKKISAVSI---FFETMPYRLNESTGYIDYDQLEKSATLFRPKLIV 200
L GGHL+HG S V+ + +PY ++E +G IDYD++ K A +PK+I+
Sbjct: 124 LAQGGHLTHG--------SPVNFSGKLYNIVPYGIDE-SGKIDYDEMAKLAKEHKPKMII 174
Query: 201 AGASAYARLYDYERIRKVCNKQKAIMLADMAHISGLVAAGVIPSPFEYADVVTTTTHKSL 260
G SAY+ + D+ ++R++ + A + DMAH++GL+AAGV P+P +A VVTTTTHK+L
Sbjct: 175 GGFSAYSGVVDWAKMREIADSIGAYLFVDMAHVAGLIAAGVYPNPVPHAHVVTTTTHKTL 234
Query: 261 RGPRGAMIFFRKGVKEINKQ 280
GPRG +I + G +E+ K+
Sbjct: 235 AGPRGGLILAKGGDEELYKK 254
>3h7f_A Serine hydroxymethyltransferase 1; cytoplasm, one-carbon
metabolism, pyridoxal phosphate, structural genomics;
HET: LLP; 1.50A {Mycobacterium tuberculosis}
Length = 447
Score = 347 bits (892), Expect = e-118
Identities = 115/278 (41%), Positives = 166/278 (59%), Gaps = 16/278 (5%)
Query: 6 NEAVYEKEKNGVTWPKQLNAPLEVVDPEIADIIEHEKARQWKGLELIPSENFTSVSVMQA 65
+ + P ++APL VDP+IA+++ E RQ LE+I SENF +V+QA
Sbjct: 5 HHHHMGTLEAQTQGPGSMSAPLAEVDPDIAELLAKELGRQRDTLEMIASENFVPRAVLQA 64
Query: 66 VGSVMTNKYSEGYPGARYYGGNEYIDMAESLCQKRALEAFRLDPEKWGVNVQSLSGSPSN 125
GSV+TNKY+EG PG RYYGG E++D+ E+L + RA F + NVQ SG+ +N
Sbjct: 65 QGSVLTNKYAEGLPGRRYYGGCEHVDVVENLARDRAKALFGAE----FANVQPHSGAQAN 120
Query: 126 FQVYTALLKPHDRIMALDLPHGGHLSHGYQTDTKKISAVSI---FFETMPYRLNESTGYI 182
V AL+ P +R++ LDL +GGHL+HG ++ +E Y ++ +T I
Sbjct: 121 AAVLHALMSPGERLLGLDLANGGHLTHG--------MRLNFSGKLYENGFYGVDPATHLI 172
Query: 183 DYDQLEKSATLFRPKLIVAGASAYARLYDYERIRKVCNKQKAIMLADMAHISGLVAAGVI 242
D D + +A FRPK+I+AG SAY R+ D+ R + ++ A +L DMAH +GLVAAG+
Sbjct: 173 DMDAVRATALEFRPKVIIAGWSAYPRVLDFAAFRSIADEVGAKLLVDMAHFAGLVAAGLH 232
Query: 243 PSPFEYADVVTTTTHKSLRGPRGAMIFFRKGV-KEINK 279
PSP +ADVV+TT HK+L G R +I ++ K IN
Sbjct: 233 PSPVPHADVVSTTVHKTLGGGRSGLIVGKQQYAKAINS 270
>2dkj_A Serine hydroxymethyltransferase; PLP dependent enzyme, structural
genomics; HET: PLP; 1.15A {Thermus thermophilus}
Length = 407
Score = 344 bits (886), Expect = e-118
Identities = 120/258 (46%), Positives = 161/258 (62%), Gaps = 17/258 (6%)
Query: 27 LEVVDPEIADIIEHEKARQWKGLELIPSENFTSVSVMQAVGSVMTNKYSEGYPGARYYGG 86
D + ++I E+ RQ +GLELI SENF S V +AVGSV+TNKY+EGYPGARYYGG
Sbjct: 4 TLKRDEALFELIALEEKRQREGLELIASENFVSKQVREAVGSVLTNKYAEGYPGARYYGG 63
Query: 87 NEYIDMAESLCQKRALEAFRLDPEKWGVNVQSLSGSPSNFQVYTALLKPHDRIMALDLPH 146
E ID ESL +RA F NVQ SGS +N VY AL++P D +M +DL
Sbjct: 64 CEVIDRVESLAIERAKALFGAA----WANVQPHSGSQANMAVYMALMEPGDTLMGMDLAA 119
Query: 147 GGHLSHGYQTDTKKISAVSI---FFETMPYRLNESTGYIDYDQLEKSATLFRPKLIVAGA 203
GGHL+HG S V+ ++ + Y + T ID +++ + A RPK+IVAGA
Sbjct: 120 GGHLTHG--------SRVNFSGKLYKVVSYGVRPDTELIDLEEVRRLALEHRPKVIVAGA 171
Query: 204 SAYARLYDYERIRKVCNKQKAIMLADMAHISGLVAAGVIPSPFEYADVVTTTTHKSLRGP 263
SAY R +D++ R++ ++ A ++ DMAH +GLVAAG+ P+P YA VVT+TTHK+LRGP
Sbjct: 172 SAYPRFWDFKAFREIADEVGAYLVVDMAHFAGLVAAGLHPNPLPYAHVVTSTTHKTLRGP 231
Query: 264 RGAMIFFRKG--VKEINK 279
RG +I K I+K
Sbjct: 232 RGGLILSNDPELGKRIDK 249
>3ecd_A Serine hydroxymethyltransferase 2; ssgcid, decode, bupsa00008A,
one-carbon metabolism, pyridoxa phosphate, structural
genomics; 1.60A {Burkholderia pseudomallei}
Length = 425
Score = 345 bits (887), Expect = e-118
Identities = 108/262 (41%), Positives = 148/262 (56%), Gaps = 17/262 (6%)
Query: 23 LNAPLEVVDPEIADIIEHEKARQWKGLELIPSENFTSVSVMQAVGSVMTNKYSEGYPGAR 82
+ L D + I E RQ +ELI SEN S +V+ A GSV+TNKY+EGYPG R
Sbjct: 9 FSQSLAERDASVRGAILKELERQQSQVELIASENIVSRAVLDAQGSVLTNKYAEGYPGKR 68
Query: 83 YYGGNEYIDMAESLCQKRALEAFRLDPEKWGVNVQSLSGSPSNFQVYTALLKPHDRIMAL 142
YYGG E+ D E+L +R F NVQ SG+ +N V AL KP D ++ +
Sbjct: 69 YYGGCEFADEVEALAIERVKRLFNAG----HANVQPHSGAQANGAVMLALAKPGDTVLGM 124
Query: 143 DLPHGGHLSHGYQTDTKKISAVSI---FFETMPYRLNESTGYIDYDQLEKSATLFRPKLI 199
L GGHL+HG + ++ +F + Y ++ T IDYDQ+E A +P LI
Sbjct: 125 SLDAGGHLTHG--------AKPALSGKWFNALQYGVSRDTMLIDYDQVEALAQQHKPSLI 176
Query: 200 VAGASAYARLYDYERIRKVCNKQKAIMLADMAHISGLVAAGVIPSPFEYADVVTTTTHKS 259
+AG SAY R D+ R R + + A ++ DMAHI+G++AAG +P E+A VVT+TTHK+
Sbjct: 177 IAGFSAYPRKLDFARFRAIADSVGAKLMVDMAHIAGVIAAGRHANPVEHAHVVTSTTHKT 236
Query: 260 LRGPRGAMIFFRKG--VKEINK 279
LRGPRG + K+IN
Sbjct: 237 LRGPRGGFVLTNDEEIAKKINS 258
>3n0l_A Serine hydroxymethyltransferase; alpha beta class, 3-layer(ABA)
sandwich, CSGI transferase, structural genomics; HET:
MSE; 1.80A {Campylobacter jejuni}
Length = 417
Score = 340 bits (875), Expect = e-116
Identities = 121/261 (46%), Positives = 165/261 (63%), Gaps = 18/261 (6%)
Query: 24 NAPLEVVDPEIADIIEHEKARQWKGLELIPSENFTSVSVMQAVGSVMTNKYSEGYPGARY 83
LE+ D EI D+ E RQ +GLE+I SENFT VM+ +GS++TNKY+EGYPG RY
Sbjct: 3 AMSLEMFDKEIFDLTNKELERQCEGLEMIASENFTLPEVMEVMGSILTNKYAEGYPGKRY 62
Query: 84 YGGNEYIDMAESLCQKRALEAFRLDPEKWGVNVQSLSGSPSNFQVYTALLKPHDRIMALD 143
YGG E++D E+L +R + F NVQ SGS +N VY AL+ P D+I+ +D
Sbjct: 63 YGGCEFVDEIETLAIERCKKLFNCK----FANVQPNSGSQANQGVYAALINPGDKILGMD 118
Query: 144 LPHGGHLSHGYQTDTKKISAVSI---FFETMPYRLNESTGYIDYDQLEKSATLFRPKLIV 200
L HGGHL+HG + VS +E+ Y + G IDY+++ + A +PKLIV
Sbjct: 119 LSHGGHLTHG--------AKVSSSGKMYESCFYGVEL-DGRIDYEKVREIAKKEKPKLIV 169
Query: 201 AGASAYARLYDYERIRKVCNKQKAIMLADMAHISGLVAAGVIPSPFEYADVVTTTTHKSL 260
GASAYAR+ D+ + R++ ++ A + AD+AHI+GLV AG PSPF YA VV++TTHK+L
Sbjct: 170 CGASAYARVIDFAKFREIADEIGAYLFADIAHIAGLVVAGEHPSPFPYAHVVSSTTHKTL 229
Query: 261 RGPRGAMIFFRKGV--KEINK 279
RGPRG +I K+IN
Sbjct: 230 RGPRGGIIMTNDEELAKKINS 250
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 43.1 bits (101), Expect = 8e-05
Identities = 22/167 (13%), Positives = 45/167 (26%), Gaps = 65/167 (38%)
Query: 174 RLNESTGYIDYDQLEKSATLFRPKLIVAGASAYARLYDYERIRKVCNK----QKAIMLAD 229
R+ E+ + ++ + I + ++ Y + + + + Q A+ L +
Sbjct: 1683 RIRENYSAMIFETIVDGKLKTEK--IFKEINEHSTSYTFRSEKGLLSATQFTQPALTLME 1740
Query: 230 MA-------------------H----ISGLVA-AGVIPSPFEYADVVTTTTHKSLRG--- 262
A H + L + A V+ E +V RG
Sbjct: 1741 KAAFEDLKSKGLIPADATFAGHSLGEYAALASLADVM--SIE--SLVEVV---FYRGMTM 1793
Query: 263 ----PRG-------AMI--------------FFRKGVKEINKQGKEF 284
PR MI + V+ + K+
Sbjct: 1794 QVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVVERVGKRTGWL 1840
>2ez2_A Beta-tyrosinase, tyrosine phenol-lyase; PLP-dependent enzyme,
pyridoxal-5'-phosphate, domain lyase; 1.85A {Citrobacter
freundii} PDB: 2ez1_A 2vlf_A* 2vlh_A* 2yct_A* 1tpl_A
2tpl_A* 2ycn_A* 2yhk_A* 2ycp_A* 1c7g_A*
Length = 456
Score = 42.4 bits (99), Expect = 1e-04
Identities = 33/261 (12%), Positives = 68/261 (26%), Gaps = 50/261 (19%)
Query: 42 KARQWKGLELIPSENFTSVSVMQAVGSVMTNKYSEGYPGARYYGGNEYIDMAESLCQKRA 101
+ + L + + + ++ +++ G Y G+E E
Sbjct: 29 QEAGYNTFLLNSKDIYIDLLTDSGTNAMSDKQWAGMMMGDEAYAGSENFYHLE------- 81
Query: 102 LEAFRLDPEKWGVN--VQSLSGSPSNFQVYTALLKPHDRIMA---LDLPHGGHLSHGYQT 156
+ E +G V + G + + +KP + +G
Sbjct: 82 -RTVQ---ELFGFKHIVPTHQGRGAENLLSQLAIKPGQYVAGNMYFTTTRYHQEKNG--- 134
Query: 157 DTKKISAVSIFFETM--PYRLNESTGYIDYDQLEKSATLFRPKLI----------VAGAS 204
V I + G ID +L+K + I +AG
Sbjct: 135 ----AVFVDIVRDEAHDAGLNIAFKGDIDLKKLQKLIDEKGAENIAYICLAVTVNLAGGQ 190
Query: 205 AYARLYDYERIRKVCNKQKAIMLADMAHISG--------------LVAAGVIPSPFEYAD 250
+ + + +R++ + D A ++ F YAD
Sbjct: 191 PVS-MANMRAVRELTEAHGIKVFYDATRCVENAYFIKEQEQGFENKSIAEIVHEMFSYAD 249
Query: 251 VVTTTTHKSLRGPRGAMIFFR 271
T + K G +
Sbjct: 250 GCTMSGKKDCLVNIGGFLCMN 270
>1ax4_A Tryptophanase; tryptophan biosynthesis, tryptophan indole-lyase,
pyridoxal 5'-phosphate, monovalent cation binding site;
HET: LLP; 2.10A {Proteus vulgaris} SCOP: c.67.1.2
Length = 467
Score = 39.4 bits (91), Expect = 0.001
Identities = 26/181 (14%), Positives = 54/181 (29%), Gaps = 29/181 (16%)
Query: 120 SGSPSNFQVYTALLKPHDRIMALDLPHGGHLSHGYQTDTKKI----SAVSIFFETM--PY 173
G + ++ LLK + P H T A++I E
Sbjct: 99 QGRGAENILFPVLLKYKQKEGKAKNPVFISNFHFDTTAAHVELNGCKAINIVTEKAFDSE 158
Query: 174 RLNESTGYIDYDQLE---KSATLFRPKLIVAGASAYAR------LYDYERIRKVCNKQKA 224
++ G D +L+ IV+ + + + + + + ++ +
Sbjct: 159 TYDDWKGDFDIKKLKENIAQHGADNIVAIVSTVTCNSAGGQPVSMSNLKEVYEIAKQHGI 218
Query: 225 IMLADMAHI--------------SGLVAAGVIPSPFEYADVVTTTTHKSLRGPRGAMIFF 270
++ D A VI ++YAD +T + K G ++
Sbjct: 219 FVVMDSARFCENAYFIKARDPKYKNATIKEVIFDMYKYADALTMSAKKDPLLNIGGLVAI 278
Query: 271 R 271
R
Sbjct: 279 R 279
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 39.5 bits (91), Expect = 0.001
Identities = 52/369 (14%), Positives = 107/369 (28%), Gaps = 115/369 (31%)
Query: 5 PNEAVYEKEKNGVTWPKQLNAPLEVVDPEIADIIEHEKARQWKGLELIPSENFTSVSV-- 62
+Y ++++ + Q+ A V + + K RQ LEL P++N V +
Sbjct: 107 MMTRMYIEQRDRLYNDNQVFAKYNVSRLQ-----PYLKLRQAL-LELRPAKN---VLIDG 157
Query: 63 MQAVG-SVMTN------KYSEGYPGARYY--GGN-----EYIDMAESLCQKRALEAFRLD 108
+ G + + K ++ N ++M + L +++D
Sbjct: 158 VLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLL-------YQID 210
Query: 109 PEKWGVNVQSLSGSPSNFQVYTALLKPHDRIMALDLPHGGHL---------------SHG 153
P N S S SN ++ ++ R + P+ L +
Sbjct: 211 P-----NWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLS 265
Query: 154 YQT-------------DTKKISAVSIFFETMPYRLNESTGY------IDYDQLEKSATLF 194
+ + +S+ +M +E L +
Sbjct: 266 CKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTT 325
Query: 195 RPKLI-VAGASAYARLYDYERIRKV-CNKQKAIMLADMAHIS-----------GLVAAGV 241
P+ + + S L ++ + V C+K I+ + + + +
Sbjct: 326 NPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSA 385
Query: 242 -IPS-----------PFEYADVVTTTTHKSLRGPRGAMIFFRKGVKEINKQGKEFTCR-- 287
IP+ + VV SL + KQ KE T
Sbjct: 386 HIPTILLSLIWFDVIKSDVMVVVNKLHKYSL----------------VEKQPKESTISIP 429
Query: 288 -CFMIMKKK 295
++ +K K
Sbjct: 430 SIYLELKVK 438
>2x3l_A ORN/Lys/Arg decarboxylase family protein; lyase; HET: LLP; 2.00A
{Staphylococcus aureus}
Length = 446
Score = 37.5 bits (87), Expect = 0.004
Identities = 18/70 (25%), Positives = 31/70 (44%), Gaps = 2/70 (2%)
Query: 206 YARLYDYERIRKVCNKQKAIMLADMAHISGLVAAGVIPSPFEY-ADVVTTTTHKSLRGPR 264
Y ++ E + K ++ +L D AH + G S Y AD V + HK+L
Sbjct: 158 YGETFNVEEVIKSLHQLNIPVLIDEAHGAHFGLQGFPDSTLNYQADYVVQSFHKTLPALT 217
Query: 265 -GAMIFFRKG 273
G++++ K
Sbjct: 218 MGSVLYIHKN 227
>2vyc_A Biodegradative arginine decarboxylase; pyridoxal phosphate,
PLP-dependent E lyase, acid resistance; HET: LLP; 2.4A
{Escherichia coli}
Length = 755
Score = 37.4 bits (86), Expect = 0.004
Identities = 38/204 (18%), Positives = 58/204 (28%), Gaps = 30/204 (14%)
Query: 98 QKRALEAFRLDPEKWGVNVQSLSGSPSNFQVYTALLKPHDRIMALDLPHGGHLS--HG-Y 154
+K A F D V S SN + A + +D ++ + H S G
Sbjct: 211 EKYAARVFGADRSWSVVV----GTSGSNRTIMQACMTDNDVVV---VDRNCHKSIEQGLM 263
Query: 155 QTDTK------KISAVSIFFETMPYRLNEST--GYIDYDQLEKSATLFRPKLIVAGASAY 206
T K + I P + T I L K +P V Y
Sbjct: 264 LTGAKPVYMVPSRNRYGIIGPIYPQEMQPETLQKKISESPLTKDKAGQKPSYCVVTNCTY 323
Query: 207 ARL-YDYERIRKVCNKQKAIMLADMAHISGLVAAGVIPS----------PFEYADVVTTT 255
+ Y+ + + + K + D A + T +
Sbjct: 324 DGVCYNAKEAQDLLEKTSDRLHFDEAWYGYARFNPIYADHYAMRGEPGDHNGPTVFATHS 383
Query: 256 THKSLRGPR-GAMIFFRKGVKEIN 278
THK L + I R+G IN
Sbjct: 384 THKLLNALSQASYIHVREGRGAIN 407
>2fnu_A Aminotransferase; protein-product complex, structural genomics,
montreal-kings bacterial structural genomics initiative,
BSGI; HET: PMP UD1; 1.50A {Helicobacter pylori} SCOP:
c.67.1.4 PDB: 2fni_A* 2fn6_A*
Length = 375
Score = 36.0 bits (84), Expect = 0.010
Identities = 20/60 (33%), Positives = 28/60 (46%), Gaps = 10/60 (16%)
Query: 177 ESTGYIDYDQLEKSATLFRPKLIV----AGASAYARLYDYERIRKVCNKQKAIMLADMAH 232
++ G ID LEK R K IV AG S + E ++K+C K L+D +H
Sbjct: 104 KNDGNIDELALEKLIN-ERTKAIVSVDYAGKSV-----EVESVQKLCKKHSLSFLSDSSH 157
>1mdo_A ARNB aminotransferase; type 1 aminotransferase fold; HET: MSE PMP;
1.70A {Salmonella typhimurium} SCOP: c.67.1.4 PDB:
1mdx_A* 1mdz_A*
Length = 393
Score = 33.7 bits (78), Expect = 0.071
Identities = 14/61 (22%), Positives = 26/61 (42%), Gaps = 10/61 (16%)
Query: 176 NESTGYIDYDQLEKSATLFRPKLIV----AGASAYARLYDYERIRKVCNKQKAIMLADMA 231
+ T + + +E + T + K I+ AGA A D + I + + ++ D A
Sbjct: 109 DRDTLMVTPEHIEAAIT-PQTKAIIPVHYAGAPA-----DLDAIYALGERYGIPVIEDAA 162
Query: 232 H 232
H
Sbjct: 163 H 163
>3f0h_A Aminotransferase; RER070207000802, structural genomics, JOIN for
structural genomics, JCSG; HET: MSE LLP; 1.70A
{Eubacterium rectale}
Length = 376
Score = 32.6 bits (75), Expect = 0.12
Identities = 20/77 (25%), Positives = 29/77 (37%), Gaps = 8/77 (10%)
Query: 209 LYDYERIRKVCNKQKAIMLADMAHISGLVAAGVIPSPFE--YADVVTTTTHKSLRGPRG- 265
LYD I + C K + D +S P ADV+ T + K L P G
Sbjct: 160 LYDTMMIGEFCKKNNMFFVCDC--VSAF---LADPFNMNECGADVMITGSQKVLACPPGI 214
Query: 266 AMIFFRKGVKEINKQGK 282
++I E ++ K
Sbjct: 215 SVIVLAPRGVERVEKSK 231
>3n75_A LDC, lysine decarboxylase, inducible; pyridoxal-5'-phosphate
dependent decarboxylase, acid stress stringent response;
HET: LLP G4P P6G; 2.00A {Escherichia coli} PDB: 3q16_A*
Length = 715
Score = 33.1 bits (75), Expect = 0.13
Identities = 33/200 (16%), Positives = 58/200 (29%), Gaps = 35/200 (17%)
Query: 98 QKRALEAFRLDPEKWGVNVQSLSGSPSNFQVYTALLKPHDRIMALDLPHGGHLS--HG-Y 154
++ F D N S +N V I+ + H S H
Sbjct: 201 EQYIARVFNADRSYMVTN----GTSTANKIVGMYSAPAGSTIL---IDRNCHKSLTHLMM 253
Query: 155 QTDTKKISAVSIFFET--------MPYRLNESTGYIDYDQLEKSATLFRPKLIVAGASAY 206
+D I+F +E +++++ P V S Y
Sbjct: 254 MSD-----VTPIYFRPTRNAYGILGGIPQSEFQHATIAKRVKETPNATWPVHAVITNSTY 308
Query: 207 ARL-YDYERIRKVCNKQKAIMLADMAHISGLVAAGVIPS--------PFEYADVVTTTTH 257
L Y+ + I+K + + + D A + + + T +TH
Sbjct: 309 DGLLYNTDFIKKTLDVKS--IHFDSAWVPYTNFSPIYEGKCGMSGGRVEGKVIYETQSTH 366
Query: 258 KSLRGPR-GAMIFFRKGVKE 276
K L +MI + V E
Sbjct: 367 KLLAAFSQASMIHVKGDVNE 386
>1c4k_A Protein (ornithine decarboxylase); lyase; HET: PLP GTP; 2.70A
{Lactobacillus SP} SCOP: c.23.1.4 c.67.1.5 d.125.1.1
PDB: 1ord_A*
Length = 730
Score = 32.8 bits (74), Expect = 0.13
Identities = 13/104 (12%), Positives = 28/104 (26%), Gaps = 12/104 (11%)
Query: 182 IDYDQLEKSATLFRPKLIVAGASAYARL-YDYERIRKVCNKQKAIMLADMAHISGLVAAG 240
E++ +L V Y Y+ + K + D A +
Sbjct: 268 AAKVDPERAKWKRPFRLAVIQLGTYDGTIYNAHEVVKRIGHLCDYIEFDSAWVGYEQFIP 327
Query: 241 VIPSPF----------EYADVVTTTTHKSLRGPR-GAMIFFRKG 273
++ + + +V + HK G + I +
Sbjct: 328 MMRNSSPLLIDDLGPEDPGIIVVQSVHKQQAGFSQTSQIHKKDS 371
>2z67_A O-phosphoseryl-tRNA(SEC) selenium transferase; selenocysteine
biosynthesis, seven-stranded BETE-strand, PYR
5'-phosphate; HET: PLP; 2.50A {Methanococcus
maripaludis} SCOP: c.67.1.9
Length = 456
Score = 32.3 bits (73), Expect = 0.17
Identities = 16/92 (17%), Positives = 35/92 (38%), Gaps = 4/92 (4%)
Query: 185 DQLEKSATLFRPKLIVAGASAYA-RLYD-YERIRKVCNKQKAIMLADMAH-ISGLVAAGV 241
+ ++K L +++ + + R D I K+C + + A+ I
Sbjct: 221 NAIKKEIELGNRPCVLSTLTFFPPRNSDDIVEIAKICENYDIPHIINGAYAIQNNYYLEK 280
Query: 242 IPSPF-EYADVVTTTTHKSLRGPRGAMIFFRK 272
+ F D V +++ K+L P G + +
Sbjct: 281 LKKAFKYRVDAVVSSSDKNLLTPIGGGLVYST 312
>1qz9_A Kynureninase; kynurenine, tryptophan, PLP, vitamin B6,
pyridoxal-5'-phosph hydrolase; HET: PLP P3G; 1.85A
{Pseudomonas fluorescens} SCOP: c.67.1.3
Length = 416
Score = 31.6 bits (72), Expect = 0.26
Identities = 15/63 (23%), Positives = 30/63 (47%), Gaps = 3/63 (4%)
Query: 208 RLYDYERIRKVCNKQKAIMLADMAHISGLVAAGVIPSPFEYADVVTTTTHKSLRGPRGAM 267
++D + + + ++ A+ + D+AH +G V + + AD T+K L G G+
Sbjct: 180 YMHDMQALTALSHECGALAIWDLAHSAGAVPVDLHQAG---ADYAIGCTYKYLNGGPGSQ 236
Query: 268 IFF 270
F
Sbjct: 237 AFV 239
>3e9k_A Kynureninase; kynurenine-L-hydrolase, kynurenine hydrolase,
pyridoxal-5'-phosphate, inhibitor complex, 3-hydroxy
hippur hydroxyhippuric acid, PLP; HET: PLP 3XH; 1.70A
{Homo sapiens} PDB: 2hzp_A*
Length = 465
Score = 31.5 bits (71), Expect = 0.35
Identities = 21/152 (13%), Positives = 46/152 (30%), Gaps = 10/152 (6%)
Query: 126 FQVYTALLKPHDRIMALDLPHGGHLSHGY----QTDTKKISAVSIFFETMPYRLNESTGY 181
+ + KP + + L S Y Q ++ P E+
Sbjct: 142 HLLMLSFFKPTPKRYKILLEAKAFPSDHYAIESQLQLHGLNIEESMRMIKPREGEETLRI 201
Query: 182 IDYDQLEKSATLFRPKLIVAGASAYA--RLYDYERIRKVCNKQKAIMLADMAHISGLVAA 239
D ++ + +I+ + + ++ I K + + D+AH G V
Sbjct: 202 EDILEVIEKEGD-SIAVILFSGVHFYTGQHFNIPAITKAGQAKGCYVGFDLAHAVGNVEL 260
Query: 240 GVIPSPFEYADVVTTTTHKSLRGPRGAMIFFR 271
+ ++A ++K L G +
Sbjct: 261 YLHDWGVDFA---CWCSYKYLNAGAGGIAGAF 289
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna;
HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 29.5 bits (65), Expect = 0.87
Identities = 7/23 (30%), Positives = 12/23 (52%), Gaps = 3/23 (13%)
Query: 13 EKNGVTWPKQLNAPLEVVDPEIA 35
EK + K+L A L++ + A
Sbjct: 18 EKQAL---KKLQASLKLYADDSA 37
>3kki_A CAI-1 autoinducer synthase; quorum sensing, CQSA, P virulence,
acyltransferase, aminotransferase, pyridoxal PHO
transferase; HET: PLP; 1.80A {Vibrio cholerae} PDB:
3hqt_A* 2wk9_A* 2wk8_A* 2wka_A* 2wk7_A
Length = 409
Score = 29.5 bits (67), Expect = 1.4
Identities = 24/170 (14%), Positives = 45/170 (26%), Gaps = 52/170 (30%)
Query: 120 SGSPSNFQVYTALLKPHDRIMALDLPH-----GGHLSHGYQTDTKKISAVSIFFETMPYR 174
SG +N + + +P+ + H G ++ + P+
Sbjct: 127 SGWNANVGLLQTICQPNTNVYIDFFAHMSLWEGARYANA---------------QAHPFM 171
Query: 175 LNESTGYIDYDQLEKSATLFRPKLIVA-------GASAYARLYDYERIRKVCNKQKAIML 227
N + D L P +IV G A + + + +L
Sbjct: 172 HN------NCDHLRMLIQRHGPGIIVVDSIYSTLGTIA-----PLAELVNISKEFGCALL 220
Query: 228 ADMAHISGLV---------AAGVIPSPFEYADVVTTTTHKSLRGPRGAMI 268
D +H G G+ +T + K+ R I
Sbjct: 221 VDESHSLGTHGPNGAGLLAELGLTREV----HFMTASLAKTF-AYRAGAI 265
>2aeu_A Hypothetical protein MJ0158; selenocysteine synthase, PLP,
pyridoxal phosphate, HOMO- oligomerization, unknown
function; 1.70A {Methanocaldococcus jannaschii} SCOP:
c.67.1.8 PDB: 2aev_A*
Length = 374
Score = 29.0 bits (65), Expect = 1.7
Identities = 20/80 (25%), Positives = 40/80 (50%), Gaps = 2/80 (2%)
Query: 211 DYERIRKVCNKQKAIMLADMAHISGLVAAGVIPSPFEY-ADVVTTTTHKSLRGPRGAMIF 269
+++++ ++AI+ D A + + P + AD+V T+T K + GPRG ++
Sbjct: 160 NFKKVINTAKNKEAIVFVDDASGARVRLLFNQPPALKLGADLVVTSTDKLMEGPRGGLLA 219
Query: 270 FRKG-VKEINKQGKEFTCRC 288
+K V +I +G +F
Sbjct: 220 GKKELVDKIYIEGTKFGLEA 239
>2e7j_A SEP-tRNA:Cys-tRNA synthase; seven-stranded BETE-strand, lyase,
structural genomics; HET: PLP; 2.40A {Archaeoglobus
fulgidus} SCOP: c.67.1.9 PDB: 2e7i_A*
Length = 371
Score = 28.5 bits (64), Expect = 2.5
Identities = 19/97 (19%), Positives = 35/97 (36%), Gaps = 14/97 (14%)
Query: 177 ESTGYIDYDQLEK---SATLFRPKLIVA---GASAYARLYDYERIRKVCNKQKAIMLADM 230
I + + ++ Y L D ++I KVC++ +L +
Sbjct: 125 YPDYAITPENFAQTIEETKKRGEVVLALITYPDGNYGNLPDVKKIAKVCSEYDVPLLVNG 184
Query: 231 AHISGLVAAGVIPSPFEY--ADVVTTTTHKSLRGPRG 265
A+ A G +P + AD + + HKS+ G
Sbjct: 185 AY-----AIGRMPVSLKEIGADFIVGSGHKSM-AASG 215
>1omo_A Alanine dehydrogenase; two-domain, beta-sandwich-dimer,
rossmann-fold NAD domain, human MU crystallin homolog;
HET: NAD; 2.32A {Archaeoglobus fulgidus} SCOP: c.2.1.13
PDB: 1vll_A
Length = 322
Score = 28.4 bits (64), Expect = 2.8
Identities = 11/54 (20%), Positives = 20/54 (37%), Gaps = 3/54 (5%)
Query: 205 AYARLYDYERIRKVC--NKQKAIMLADMAHISGLVAAGVIPSPFEYADVVTTTT 256
A R++D ++ ++ A G+ A+ DV+ TTT
Sbjct: 143 ALRRVFDIGEVK-AYDVREKAAKKFVSYCEDRGISASVQPAEEASRCDVLVTTT 195
>3b8x_A WBDK, pyridoxamine 5-phosphate-dependent dehydrase; aspartate
aminotransferase, colitose, perosamine, O-antigen,
pyridoxal phosphate,; HET: G4M; 1.70A {Escherichia coli}
PDB: 2gms_A* 2gmu_A* 2r0t_A* 3gr9_A*
Length = 390
Score = 28.3 bits (64), Expect = 3.4
Identities = 12/57 (21%), Positives = 26/57 (45%), Gaps = 2/57 (3%)
Query: 176 NESTGYIDYDQLEKSATLFRPKLIVAGASAYARLYDYERIRKVCNKQKAIMLADMAH 232
+ +T ID + L+++ T K I+ + +++ I K+ + I+L D
Sbjct: 110 DINTLNIDIESLKEAVTD-STKAILT-VNLLGNPNNFDEINKIIGGRDIILLEDNCE 164
>3hdj_A Probable ornithine cyclodeaminase; APC62486, bordetella pertussis
TOH structural genomics, PSI-2, protein structure
initiative; 1.70A {Bordetella pertussis}
Length = 313
Score = 28.0 bits (63), Expect = 4.2
Identities = 12/56 (21%), Positives = 23/56 (41%), Gaps = 7/56 (12%)
Query: 205 AYARLYDYERIRKVCNKQKAI-MLADMAHISGLVAAGVIPSPFEY---ADVVTTTT 256
+ + E I V + + +L + G+ A + +P + AD+V T T
Sbjct: 139 QLSARFALEAIL-VHDPYASPEILERIGRRCGVPA--RMAAPADIAAQADIVVTAT 191
>2vty_A Protein F1, F1L; BCL-2, apoptosis; 2.10A {Vaccinia virus}
Length = 182
Score = 27.5 bits (60), Expect = 4.4
Identities = 24/110 (21%), Positives = 38/110 (34%), Gaps = 8/110 (7%)
Query: 169 ETMPYRLNESTGYIDYDQLEKSATLFRPKLIVAGA---SAYARLYDYER-----IRKVCN 220
E M YR ++ST +DY E+ + + ++ Y +L R I C+
Sbjct: 35 ENMVYRFDKSTNILDYLSTERDHVMMAVRYYMSKQRLDDLYRQLPTKTRSYIDIINIYCD 94
Query: 221 KQKAIMLADMAHISGLVAAGVIPSPFEYADVVTTTTHKSLRGPRGAMIFF 270
K DM + + + +V T G R A I F
Sbjct: 95 KVSNDYNRDMNIMYDMASTKSFTVYDINNEVNTIMLDNKGLGVRLATISF 144
>1o69_A Aminotransferase; structural genomics, unknown function; HET: X04;
1.84A {Campylobacter jejuni} SCOP: c.67.1.4 PDB: 1o62_A
1o61_A*
Length = 394
Score = 27.2 bits (61), Expect = 6.3
Identities = 13/62 (20%), Positives = 27/62 (43%), Gaps = 11/62 (17%)
Query: 177 ESTGYIDYDQLEKSATLF--RPKLIVA----GASAYARLYDYERIRKVCNKQKAIMLADM 230
+ T ID D L+ + +PK ++ G +A + I ++C + +++ D
Sbjct: 102 DETYNIDVDLLKLAIKECEKKPKALILTHLYGNAA-----KMDEIVEICKENDIVLIEDA 156
Query: 231 AH 232
A
Sbjct: 157 AE 158
>1x7d_A Ornithine cyclodeaminase; binds NAD+, binds L-ornithine, binds
L-proline, 2 bundle, beta barrel, rossmann fold, lyase;
HET: NAD ORN MES; 1.60A {Pseudomonas putida} SCOP:
c.2.1.13 PDB: 1u7h_A*
Length = 350
Score = 27.3 bits (61), Expect = 6.4
Identities = 14/77 (18%), Positives = 25/77 (32%), Gaps = 10/77 (12%)
Query: 205 AYARLYDYERIRKVCN--KQKAIMLA-DMAHISGL--VAAGVIPSPFEYADVVTTTTHKS 259
A+ + E I + L ++ SGL A + + D++TT T
Sbjct: 147 AFHKHLGIEEIV-AYDTDPLATAKLIANLKEYSGLTIRRASSVAEAVKGVDIITTVTADK 205
Query: 260 LRGP--RGAMIFFRKGV 274
M+ G+
Sbjct: 206 AYATIITPDML--EPGM 220
>2oqx_A Tryptophanase; lyase, pyridoxal phosphate, tryptophan catabolism;
HET: CME EPE; 1.90A {Escherichia coli} SCOP: c.67.1.2
PDB: 2c44_A 2v1p_A* 2v0y_A*
Length = 467
Score = 27.3 bits (60), Expect = 7.6
Identities = 25/185 (13%), Positives = 55/185 (29%), Gaps = 33/185 (17%)
Query: 120 SGSPSNFQVYTALLKPHDRIMALDLPHGGHLSHGYQTDTK------KISAVSIFFE--TM 171
G + L+K ++ LD S+ + T+ + +++ +
Sbjct: 97 QGRGAEQIYIPVLIKKREQEKGLDRSKMVAFSNYFFDTTQGHSQINGCTVRNVYIKEAFD 156
Query: 172 PYRLNESTGYIDYDQLE---KSATLFRPKLIV-------AGASAYARLYDYERIRKVCNK 221
+ G D + LE + IV AG + L + + + + K
Sbjct: 157 TGVRYDFKGNFDLEGLERGIEEVGPNNVPYIVATITSNSAGGQPVS-LANLKAMYSIAKK 215
Query: 222 -------------QKAIMLADMAHISGLVAAGVIPSP-FEYADVVTTTTHKSLRGPRGAM 267
+ A + I ++YAD++ + K P G +
Sbjct: 216 YDIPVVMDSARFAENAYFIKQREAEYKDWTIEQITRETYKYADMLAMSAKKDAMVPMGGL 275
Query: 268 IFFRK 272
+ +
Sbjct: 276 LCMKD 280
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.318 0.133 0.394
Gapped
Lambda K H
0.267 0.0543 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,670,994
Number of extensions: 277868
Number of successful extensions: 609
Number of sequences better than 10.0: 1
Number of HSP's gapped: 591
Number of HSP's successfully gapped: 41
Length of query: 295
Length of database: 6,701,793
Length adjustment: 93
Effective length of query: 202
Effective length of database: 4,105,140
Effective search space: 829238280
Effective search space used: 829238280
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: 57 (26.2 bits)