RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 012104
(471 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 = 841 bits (2175), Expect = 0.0
Identities = 271/461 (58%), Positives = 330/461 (71%), Gaps = 7/461 (1%)
Query: 9 NSSLETVDPEIHDLIEKEKRRQCRGIELIASENFTSFAVIEALGSALTNKYSEGMPGNRY 68
L+ D E++D+I+KE RQ G+ELIASENF S AV+EALGS L NKYS G PG RY
Sbjct: 22 AQPLKDSDAEVYDIIKKESNRQRVGLELIASENFASRAVLEALGSCLNNKYSLGYPGQRY 81
Query: 69 YGGNEFIDEIENLCRSRALQTFHLDPTQWGVNVQPYSGSPANFAAYTAVLEPHDRIMGLD 128
YGG E IDE+E LC+ RALQ + LDP WGVNVQPYSGSPANFA YTA++EPH RIMGLD
Sbjct: 82 YGGTEHIDELETLCQKRALQAYGLDPQCWGVNVQPYSGSPANFAVYTALVEPHGRIMGLD 141
Query: 129 LPSGGHLTHGYYTSGGKKISATSIYFESLPYKVNSSTGYIDYDKLEEKALDFRPKLIICG 188
LP GGHLTHG+ T KKISATSI+FES+ YKVN TGYIDYD+LEE A F PKLII G
Sbjct: 142 LPDGGHLTHGFMTDK-KKISATSIFFESMAYKVNPDTGYIDYDRLEENARLFHPKLIIAG 200
Query: 189 GSAYPRDWDYARFRAVADKCGALLLCDMAHISGLVAAQEAANPFEYCHIVTTTTHKSLRG 248
S Y R+ DY R R +AD+ GA L+ DMAHISGLV A +PFE+CH+VTTTTHK+LRG
Sbjct: 201 TSCYSRNLDYGRLRKIADENGAYLMADMAHISGLVVAGVVPSPFEHCHVVTTTTHKTLRG 260
Query: 249 PRAGMIFYRKGPKPPKKGQPEGAVYDFEDKINFAVFPSLQGGPHNHQIGALAVALKQAST 308
RAGMIFYR+G + + +Y+ E IN AVFP LQGGPHNH I +AVALKQA T
Sbjct: 261 CRAGMIFYRRGVRSVDPKTGKEILYNLESLINSAVFPGLQGGPHNHAIAGVAVALKQAMT 320
Query: 309 PAFKAYAKQVKANAVALGNYLTGKGYSLVTGGTENHLVLWDLRPLGLTGNKVEKLCDLCN 368
P FK Y +QV AN AL L GY +VTGG++NHL+L DLR G G + EK+ + C+
Sbjct: 321 PEFKEYQRQVVANCRALSAALVELGYKIVTGGSDNHLILVDLRSKGTDGGRAEKVLEACS 380
Query: 369 ITVNKNAVFGDSSALAPGGVRIGTPAMTSRGLLEKDFEQIGEFLHRAVTLTLEIQKEYG- 427
I NKN GD SAL P G+R+GTPA+TSRGLLEKDF+++ F+HR + LT++IQ + G
Sbjct: 381 IACNKNTCPGDKSALRPSGLRLGTPALTSRGLLEKDFQKVAHFIHRGIELTVQIQDDTGP 440
Query: 428 -KLLKDFNKGLVNN----KDIEALKADVEKFASSFDMPGFK 463
LK+F + L + + + AL+ +VE FA+ F +PG
Sbjct: 441 RATLKEFKEKLAGDEKHQRAVRALRQEVESFAALFPLPGLP 481
>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 = 838 bits (2168), Expect = 0.0
Identities = 273/460 (59%), Positives = 335/460 (72%), Gaps = 6/460 (1%)
Query: 7 WGNSSLETVDPEIHDLIEKEKRRQCRGIELIASENFTSFAVIEALGSALTNKYSEGMPGN 66
G SL DPE+ +L+++EK RQCRG+ELIASENF S A +EALGS L NKYSEG PG
Sbjct: 30 TGQESLSDSDPEMWELLQREKDRQCRGLELIASENFCSRAALEALGSCLNNKYSEGYPGK 89
Query: 67 RYYGGNEFIDEIENLCRSRALQTFHLDPTQWGVNVQPYSGSPANFAAYTAVLEPHDRIMG 126
RYYGG E +DEIE LC+ RAL+ F LDP QWGVNVQPYSGSPAN A YTA+L+PHDRIMG
Sbjct: 90 RYYGGAEVVDEIELLCQRRALEAFDLDPAQWGVNVQPYSGSPANLAVYTALLQPHDRIMG 149
Query: 127 LDLPSGGHLTHGYYTSGGKKISATSIYFESLPYKVNSSTGYIDYDKLEEKALDFRPKLII 186
LDLP GGHLTHGY + K+ISATSI+FES+PYK+N TG IDY++L A FRP+LII
Sbjct: 150 LDLPDGGHLTHGYMSDV-KRISATSIFFESMPYKLNPKTGLIDYNQLALTARLFRPRLII 208
Query: 187 CGGSAYPRDWDYARFRAVADKCGALLLCDMAHISGLVAAQEAANPFEYCHIVTTTTHKSL 246
G SAY R DYAR R V D+ A LL DMAHISGLVAA+ +PF++ IVTTTTHK+L
Sbjct: 209 AGTSAYARLIDYARMREVCDEVKAHLLADMAHISGLVAAKVIPSPFKHADIVTTTTHKTL 268
Query: 247 RGPRAGMIFYRKGPKPPKKGQPEGAVYDFEDKINFAVFPSLQGGPHNHQIGALAVALKQA 306
RG R+G+IFYRKG K Y FED+INFAVFPSLQGGPHNH I A+AVALKQA
Sbjct: 269 RGARSGLIFYRKGVKAVDPKTGREIPYTFEDRINFAVFPSLQGGPHNHAIAAVAVALKQA 328
Query: 307 STPAFKAYAKQVKANAVALGNYLTGKGYSLVTGGTENHLVLWDLRPLGLTGNKVEKLCDL 366
TP F+ Y+ QV NA A+ + L +GYSLV+GGT+NHLVL DLRP GL G + E++ +L
Sbjct: 329 CTPMFREYSLQVLKNARAMADALLERGYSLVSGGTDNHLVLVDLRPKGLDGARAERVLEL 388
Query: 367 CNITVNKNAVFGDSSALAPGGVRIGTPAMTSRGLLEKDFEQIGEFLHRAVTLTLEIQKEY 426
+IT NKN GD SA+ PGG+R+G PA+TSR E DF ++ +F+ V + LE++ +
Sbjct: 389 VSITANKNTCPGDRSAITPGGLRLGAPALTSRQFREDDFRRVVDFIDEGVNIGLEVKSKT 448
Query: 427 GKLLKDFNKGLV----NNKDIEALKADVEKFASSFDMPGF 462
K L+DF L+ ++ + L+ VE+FA +F MPGF
Sbjct: 449 AK-LQDFKSFLLKDSETSQRLANLRQRVEQFARAFPMPGF 487
>2dkj_A Serine hydroxymethyltransferase; PLP dependent enzyme, structural
genomics; HET: PLP; 1.15A {Thermus thermophilus}
Length = 407
Score = 549 bits (1417), Expect = 0.0
Identities = 193/452 (42%), Positives = 256/452 (56%), Gaps = 47/452 (10%)
Query: 10 SSLETVDPEIHDLIEKEKRRQCRGIELIASENFTSFAVIEALGSALTNKYSEGMPGNRYY 69
S D + +LI E++RQ G+ELIASENF S V EA+GS LTNKY+EG PG RYY
Sbjct: 2 VSTLKRDEALFELIALEEKRQREGLELIASENFVSKQVREAVGSVLTNKYAEGYPGARYY 61
Query: 70 GGNEFIDEIENLCRSRALQTFHLDPTQWGVNVQPYSGSPANFAAYTAVLEPHDRIMGLDL 129
GG E ID +E+L RA F NVQP+SGS AN A Y A++EP D +MG+DL
Sbjct: 62 GGCEVIDRVESLAIERAKALFGAA----WANVQPHSGSQANMAVYMALMEPGDTLMGMDL 117
Query: 130 PSGGHLTHGYYTSGGKKISATSIYFESLPYKVNSSTGYIDYDKLEEKALDFRPKLIICGG 189
+GGHLTHG +++ + ++ + Y V T ID +++ AL+ RPK+I+ G
Sbjct: 118 AAGGHLTHG------SRVNFSGKLYKVVSYGVRPDTELIDLEEVRRLALEHRPKVIVAGA 171
Query: 190 SAYPRDWDYARFRAVADKCGALLLCDMAHISGLVAAQEAANPFEYCHIVTTTTHKSLRGP 249
SAYPR WD+ FR +AD+ GA L+ DMAH +GLVAA NP Y H+VT+TTHK+LRGP
Sbjct: 172 SAYPRFWDFKAFREIADEVGAYLVVDMAHFAGLVAAGLHPNPLPYAHVVTSTTHKTLRGP 231
Query: 250 RAGMIFYRKGPKPPKKGQPEGAVYDFEDKINFAVFPSLQGGPHNHQIGALAVALKQASTP 309
R G+I + +I+ +FP +QGGP H I AVA +A P
Sbjct: 232 RGGLILSNDP--------------ELGKRIDKLIFPGIQGGPLEHVIAGKAVAFFEALQP 277
Query: 310 AFKAYAKQVKANAVALGNYLTGKGYSLVTGGTENHLVLWDLRPLGLTGNKVEKLCDLCNI 369
FK Y++ V NA L L +GY +VTGGT+NHL L DLRP GLTG + E+ D I
Sbjct: 278 EFKEYSRLVVENAKRLAEELARRGYRIVTGGTDNHLFLVDLRPKGLTGKEAEERLDAVGI 337
Query: 370 TVNKNAV-FGDSSALAPGGVRIGTPAMTSRGLLEKDFEQIGEFLHRAVTLTLEIQKEYGK 428
TVNKNA+ F G+RIGTPA+T+RG ++ + E + RA
Sbjct: 338 TVNKNAIPFDPKPPRVTSGIRIGTPAITTRGFTPEEMPLVAELIDRA------------- 384
Query: 429 LLKDFNKGLVNNKDIEALKADVEKFASSFDMP 460
+ EAL+ +V + A + MP
Sbjct: 385 ---------LLEGPSEALREEVRRLALAHPMP 407
>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 = 547 bits (1412), Expect = 0.0
Identities = 191/409 (46%), Positives = 252/409 (61%), Gaps = 26/409 (6%)
Query: 10 SSLETVDPEIHDLIEKEKRRQCRGIELIASENFTSFAVIEALGSALTNKYSEGMPGNRYY 69
L DP++ IE+E++RQ IELIASENF S AV+EA GS LTNKY+EG PG RYY
Sbjct: 2 KYLPQQDPQVFAAIEQERKRQHAKIELIASENFVSRAVMEAQGSVLTNKYAEGYPGRRYY 61
Query: 70 GGNEFIDEIENLCRSRALQTFHLDPTQWGVNVQPYSGSPANFAAYTAVLEPHDRIMGLDL 129
GG E++D +E L R RA Q F + NVQP+SG+ AN A Y VLE D ++G++L
Sbjct: 62 GGCEYVDIVEELARERAKQLFGAE----HANVQPHSGAQANMAVYFTVLEHGDTVLGMNL 117
Query: 130 PSGGHLTHGYYTSGGKKISATSIYFESLPYKVNSSTGYIDYDKLEEKALDFRPKLIICGG 189
GGHLTHG ++ + + + + Y V+ T IDYD + EKA RPKLI+
Sbjct: 118 SHGGHLTHG------SPVNFSGVQYNFVAYGVDPETHVIDYDDVREKARLHRPKLIVAAA 171
Query: 190 SAYPRDWDYARFRAVADKCGALLLCDMAHISGLVAAQEAANPFEYCHIVTTTTHKSLRGP 249
+AYPR D+A+FR +AD+ GA L+ DMAHI+GLVAA NP Y H VTTTTHK+LRGP
Sbjct: 172 AAYPRIIDFAKFREIADEVGAYLMVDMAHIAGLVAAGLHPNPVPYAHFVTTTTHKTLRGP 231
Query: 250 RAGMIFYRKGPKPPKKGQPEGAVYDFEDKINFAVFPSLQGGPHNHQIGALAVALKQASTP 309
R GMI ++ F +I+ A+FP +QGGP H I A AVA +A
Sbjct: 232 RGGMILCQE---------------QFAKQIDKAIFPGIQGGPLMHVIAAKAVAFGEALQD 276
Query: 310 AFKAYAKQVKANAVALGNYLTGKGYSLVTGGTENHLVLWDLRPLGLTGNKVEKLCDLCNI 369
FKAYAK+V NA L + L +G++LV+GGT+NHL+L DLRP LTG EK+ D I
Sbjct: 277 DFKAYAKRVVDNAKRLASALQNEGFTLVSGGTDNHLLLVDLRPQQLTGKTAEKVLDEVGI 336
Query: 370 TVNKNAV-FGDSSALAPGGVRIGTPAMTSRGLLEKDFEQIGEFLHRAVT 417
TVNKN + + S G+RIGT A+T+RG ++ ++I + +
Sbjct: 337 TVNKNTIPYDPESPFVTSGIRIGTAAVTTRGFGLEEMDEIAAIIGLVLK 385
>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 = 547 bits (1412), Expect = 0.0
Identities = 187/450 (41%), Positives = 258/450 (57%), Gaps = 42/450 (9%)
Query: 9 NSSLETVDPEIHDLIEKEKRRQCRGIELIASENFTSFAVIEALGSALTNKYSEGMPGNRY 68
++ D E+ +E+EK RQ IELIASEN+TS V++A GS LTNKY+EG PG RY
Sbjct: 8 EMNIADYDAELWQAMEQEKVRQEEHIELIASENYTSPRVMQAQGSQLTNKYAEGYPGKRY 67
Query: 69 YGGNEFIDEIENLCRSRALQTFHLDPTQWGVNVQPYSGSPANFAAYTAVLEPHDRIMGLD 128
YGG E++D +E L RA + F D NVQP+SGS ANFA YTA+L+P D ++G++
Sbjct: 68 YGGCEYVDVVEQLAIDRAKELFGAD----YANVQPHSGSQANFAVYTALLQPGDTVLGMN 123
Query: 129 LPSGGHLTHGYYTSGGKKISATSIYFESLPYKVNSSTGYIDYDKLEEKALDFRPKLIICG 188
L GGHLTHG ++ + + +PY ++ +G IDYD++ + A + +PK+II G
Sbjct: 124 LAQGGHLTHG------SPVNFSGKLYNIVPYGIDE-SGKIDYDEMAKLAKEHKPKMIIGG 176
Query: 189 GSAYPRDWDYARFRAVADKCGALLLCDMAHISGLVAAQEAANPFEYCHIVTTTTHKSLRG 248
SAY D+A+ R +AD GA L DMAH++GL+AA NP + H+VTTTTHK+L G
Sbjct: 177 FSAYSGVVDWAKMREIADSIGAYLFVDMAHVAGLIAAGVYPNPVPHAHVVTTTTHKTLAG 236
Query: 249 PRAGMIFYRKGPKPPKKGQPEGAVYDFEDKINFAVFPSLQGGPHNHQIGALAVALKQAST 308
PR G+I + G + + K+N AVFPS QGGP H I AVALK+A
Sbjct: 237 PRGGLILAKGGDE------------ELYKKLNSAVFPSAQGGPLMHVIAGKAVALKEAME 284
Query: 309 PAFKAYAKQVKANAVALGNYLTGKGYSLVTGGTENHLVLWDLRPLGLTGNKVEKLCDLCN 368
P FK Y +QV NA A+ +GY +V+GGTENHL L DL LTG + + N
Sbjct: 285 PEFKVYQQQVAKNAKAMVEVFLNRGYKVVSGGTENHLFLLDLVDKNLTGKEADAALGRAN 344
Query: 369 ITVNKNAV-FGDSSALAPGGVRIGTPAMTSRGLLEKDFEQIGEFLHRAVTLTLEIQKEYG 427
ITVNKN+V S G+RIG+PA+T RG E + +++ ++ +
Sbjct: 345 ITVNKNSVPNDPKSPFVTSGIRIGSPAVTRRGFKEAEVKELAGWMCDVL----------- 393
Query: 428 KLLKDFNKGLVNNKDIEALKADVEKFASSF 457
+ + IE +KA V + F
Sbjct: 394 -------DNINDEATIERVKAKVLDICARF 416
>3n0l_A Serine hydroxymethyltransferase; alpha beta class, 3-layer(ABA)
sandwich, CSGI transferase, structural genomics; HET:
MSE; 1.80A {Campylobacter jejuni}
Length = 417
Score = 543 bits (1402), Expect = 0.0
Identities = 194/450 (43%), Positives = 254/450 (56%), Gaps = 44/450 (9%)
Query: 9 NSSLETVDPEIHDLIEKEKRRQCRGIELIASENFTSFAVIEALGSALTNKYSEGMPGNRY 68
SLE D EI DL KE RQC G+E+IASENFT V+E +GS LTNKY+EG PG RY
Sbjct: 3 AMSLEMFDKEIFDLTNKELERQCEGLEMIASENFTLPEVMEVMGSILTNKYAEGYPGKRY 62
Query: 69 YGGNEFIDEIENLCRSRALQTFHLDPTQWGVNVQPYSGSPANFAAYTAVLEPHDRIMGLD 128
YGG EF+DEIE L R + F+ NVQP SGS AN Y A++ P D+I+G+D
Sbjct: 63 YGGCEFVDEIETLAIERCKKLFNCK----FANVQPNSGSQANQGVYAALINPGDKILGMD 118
Query: 129 LPSGGHLTHGYYTSGGKKISATSIYFESLPYKVNSSTGYIDYDKLEEKALDFRPKLIICG 188
L GGHLTHG K+S++ +ES Y V G IDY+K+ E A +PKLI+CG
Sbjct: 119 LSHGGHLTHG------AKVSSSGKMYESCFYGVEL-DGRIDYEKVREIAKKEKPKLIVCG 171
Query: 189 GSAYPRDWDYARFRAVADKCGALLLCDMAHISGLVAAQEAANPFEYCHIVTTTTHKSLRG 248
SAY R D+A+FR +AD+ GA L D+AHI+GLV A E +PF Y H+V++TTHK+LRG
Sbjct: 172 ASAYARVIDFAKFREIADEIGAYLFADIAHIAGLVVAGEHPSPFPYAHVVSSTTHKTLRG 231
Query: 249 PRAGMIFYRKGPKPPKKGQPEGAVYDFEDKINFAVFPSLQGGPHNHQIGALAVALKQAST 308
PR G+I + KIN A+FP +QGGP H I A AV K +
Sbjct: 232 PRGGIIMTNDE--------------ELAKKINSAIFPGIQGGPLMHVIAAKAVGFKFNLS 277
Query: 309 PAFKAYAKQVKANAVALGNYLTGKGYSLVTGGTENHLVLWDLRPLGLTGNKVEKLCDLCN 368
+K YAKQV+ NA L N L + + LV+ GT+NHLVL +G +
Sbjct: 278 DEWKVYAKQVRTNAQVLANVLMDRKFKLVSDGTDNHLVLMSFLDREFSGKDADLALGNAG 337
Query: 369 ITVNKNAV-FGDSSALAPGGVRIGTPAMTSRGLLEKDFEQIGEFLHRAVTLTLEIQKEYG 427
IT NKN V S G+R+GTPA+T+RG EK+ E + ++ +
Sbjct: 338 ITANKNTVPGEIRSPFITSGLRLGTPALTARGFKEKEMEIVSNYIADIL----------- 386
Query: 428 KLLKDFNKGLVNNKDIEALKADVEKFASSF 457
+ N K E +K +++K AS+F
Sbjct: 387 -------DDVNNEKLQENIKQELKKLASNF 409
>3ecd_A Serine hydroxymethyltransferase 2; ssgcid, decode, bupsa00008A,
one-carbon metabolism, pyridoxa phosphate, structural
genomics; 1.60A {Burkholderia pseudomallei}
Length = 425
Score = 543 bits (1402), Expect = 0.0
Identities = 193/459 (42%), Positives = 253/459 (55%), Gaps = 40/459 (8%)
Query: 1 MDPVNEWGNSSLETVDPEIHDLIEKEKRRQCRGIELIASENFTSFAVIEALGSALTNKYS 60
M N + + SL D + I KE RQ +ELIASEN S AV++A GS LTNKY+
Sbjct: 2 MSNANPFFSQSLAERDASVRGAILKELERQQSQVELIASENIVSRAVLDAQGSVLTNKYA 61
Query: 61 EGMPGNRYYGGNEFIDEIENLCRSRALQTFHLDPTQWGVNVQPYSGSPANFAAYTAVLEP 120
EG PG RYYGG EF DE+E L R + F+ NVQP+SG+ AN A A+ +P
Sbjct: 62 EGYPGKRYYGGCEFADEVEALAIERVKRLFNAG----HANVQPHSGAQANGAVMLALAKP 117
Query: 121 HDRIMGLDLPSGGHLTHGYYTSGGKKISATSIYFESLPYKVNSSTGYIDYDKLEEKALDF 180
D ++G+ L +GGHLTHG K + + +F +L Y V+ T IDYD++E A
Sbjct: 118 GDTVLGMSLDAGGHLTHG------AKPALSGKWFNALQYGVSRDTMLIDYDQVEALAQQH 171
Query: 181 RPKLIICGGSAYPRDWDYARFRAVADKCGALLLCDMAHISGLVAAQEAANPFEYCHIVTT 240
+P LII G SAYPR D+ARFRA+AD GA L+ DMAHI+G++AA ANP E+ H+VT+
Sbjct: 172 KPSLIIAGFSAYPRKLDFARFRAIADSVGAKLMVDMAHIAGVIAAGRHANPVEHAHVVTS 231
Query: 241 TTHKSLRGPRAGMIFYRKGPKPPKKGQPEGAVYDFEDKINFAVFPSLQGGPHNHQIGALA 300
TTHK+LRGPR G + + KIN AVFP LQGGP H I A
Sbjct: 232 TTHKTLRGPRGGFVLTNDE--------------EIAKKINSAVFPGLQGGPLMHVIAGKA 277
Query: 301 VALKQASTPAFKAYAKQVKANAVALGNYLTGKGYSLVTGGTENHLVLWDLRPLGLTGNKV 360
VA +A T FK Y +V ANA ALG+ L G LVTGGT+NHL+L DLRP GL G +V
Sbjct: 278 VAFGEALTDDFKTYIDRVLANAQALGDVLKAGGVDLVTGGTDNHLLLVDLRPKGLKGAQV 337
Query: 361 EKLCDLCNITVNKNAV-FGDSSALAPGGVRIGTPAMTSRGLLEKDFEQIGEFLHRAVTLT 419
E+ + IT NKN + F G+R+GTPA T+RG +F ++G +
Sbjct: 338 EQALERAGITCNKNGIPFDPEKPTITSGIRLGTPAGTTRGFGAAEFREVGRLILEV---- 393
Query: 420 LEIQKEYGKLLKDFNKGLVNNKDIEA-LKADVEKFASSF 457
+ + E ++ ++ F
Sbjct: 394 ----------FEALRTNPEGDHATEQRVRREIFALCERF 422
>3h7f_A Serine hydroxymethyltransferase 1; cytoplasm, one-carbon
metabolism, pyridoxal phosphate, structural genomics;
HET: LLP; 1.50A {Mycobacterium tuberculosis}
Length = 447
Score = 538 bits (1389), Expect = 0.0
Identities = 184/455 (40%), Positives = 257/455 (56%), Gaps = 50/455 (10%)
Query: 9 NSSLETVDPEIHDLIEKEKRRQCRGIELIASENFTSFAVIEALGSALTNKYSEGMPGNRY 68
++ L VDP+I +L+ KE RQ +E+IASENF AV++A GS LTNKY+EG+PG RY
Sbjct: 23 SAPLAEVDPDIAELLAKELGRQRDTLEMIASENFVPRAVLQAQGSVLTNKYAEGLPGRRY 82
Query: 69 YGGNEFIDEIENLCRSRALQTFHLDPTQWGVNVQPYSGSPANFAAYTAVLEPHDRIMGLD 128
YGG E +D +ENL R RA F + NVQP+SG+ AN A A++ P +R++GLD
Sbjct: 83 YGGCEHVDVVENLARDRAKALFGAE----FANVQPHSGAQANAAVLHALMSPGERLLGLD 138
Query: 129 LPSGGHLTHGYYTSGGKKISATSIYFESLPYKVNSSTGYIDYDKLEEKALDFRPKLIICG 188
L +GGHLTHG +++ + +E+ Y V+ +T ID D + AL+FRPK+II G
Sbjct: 139 LANGGHLTHG------MRLNFSGKLYENGFYGVDPATHLIDMDAVRATALEFRPKVIIAG 192
Query: 189 GSAYPRDWDYARFRAVADKCGALLLCDMAHISGLVAAQEAANPFEYCHIVTTTTHKSLRG 248
SAYPR D+A FR++AD+ GA LL DMAH +GLVAA +P + +V+TT HK+L G
Sbjct: 193 WSAYPRVLDFAAFRSIADEVGAKLLVDMAHFAGLVAAGLHPSPVPHADVVSTTVHKTLGG 252
Query: 249 PRAGMIFYRKGPKPPKKGQPEGAVYDFEDKINFAVFPSLQGGPHNHQIGALAVALKQAST 308
R+G+I ++ + IN AVFP QGGP H I AVALK A+T
Sbjct: 253 GRSGLIVGKQ---------------QYAKAINSAVFPGQQGGPLMHVIAGKAVALKIAAT 297
Query: 309 PAFKAYAKQVKANAVALGNYLTG-----KGYSLVTGGTENHLVLWDLRPLGLTGNKVEKL 363
P F ++ + A + + L G S+V+GGT+ HLVL DLR L G E L
Sbjct: 298 PEFADRQRRTLSGARIIADRLMAPDVAKAGVSVVSGGTDVHLVLVDLRDSPLDGQAAEDL 357
Query: 364 CDLCNITVNKNAV-FGDSSALAPGGVRIGTPAMTSRGLLEKDFEQIGEFLHRAVTLTLEI 422
ITVN+NAV + G+RIGTPA+ +RG + +F ++ + + A
Sbjct: 358 LHEVGITVNRNAVPNDPRPPMVTSGLRIGTPALATRGFGDTEFTEVADIIATA------- 410
Query: 423 QKEYGKLLKDFNKGLVNNKDIEALKADVEKFASSF 457
L ++ D+ ALK + A +F
Sbjct: 411 -------LAT-----GSSVDVSALKDRATRLARAF 433
>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 = 67.8 bits (165), Expect = 2e-12
Identities = 48/330 (14%), Positives = 84/330 (25%), Gaps = 63/330 (19%)
Query: 52 GSALTNKYSEGMPGNRYYGGNEFIDEIENLCRSRALQTFHLDPTQWGVN--VQPYSGSPA 109
+ +++ M G+ Y G+E +E + +G V + G A
Sbjct: 54 NAMSDKQWAGMMMGDEAYAGSENFYHLERTVQEL-----------FGFKHIVPTHQGRGA 102
Query: 110 NFAAYTAVLEPHDRIMGLDLPSGGHLTHGYYTSGGKKISATSIYFESLPYKVNSSTGYID 169
++P + G T + G + G ID
Sbjct: 103 ENLLSQLAIKPGQYVAG---NMYFTTTRYHQEKNGAVFVDIVRDEAHDAGLNIAFKGDID 159
Query: 170 YDKLEEKALDFRPKLI----------ICGGSAYPRDWDYARFRAVADKCGALLLCDMAHI 219
KL++ + + I + GG + R + + G + D
Sbjct: 160 LKKLQKLIDEKGAENIAYICLAVTVNLAGGQPVSMA-NMRAVRELTEAHGIKVFYDATRC 218
Query: 220 SG--------------LVAAQEAANPFEYCHIVTTTTHKSLRGPRAGMIFYRKGPKPPKK 265
A+ F Y T + K G +
Sbjct: 219 VENAYFIKEQEQGFENKSIAEIVHEMFSYADGCTMSGKKDCLVNIGGFLCMND------- 271
Query: 266 GQPEGAVYDFEDKINFAVFPSL----QGGPHNHQIGALAVALKQASTPAFKAYAKQVKAN 321
+ V GG + A+A+ L++A Y +
Sbjct: 272 -------DEMFSSAKELVVVYEGMPSYGGLAGRDMEAMAIGLREAMQY---EYIEHRVKQ 321
Query: 322 AVALGNYLTGKGYSLVTGGTENHLVLWDLR 351
LG+ L G +V H V D R
Sbjct: 322 VRYLGDKLKAAGVPIVE-PVGGHAVFLDAR 350
>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 = 46.7 bits (110), Expect = 1e-05
Identities = 27/224 (12%), Positives = 62/224 (27%), Gaps = 39/224 (17%)
Query: 63 MPGNRYYGGNEFIDEIENLCRSRALQTFHLDPTQWGVNVQPYSGSPANFAAYTAVLEPHD 122
+ G+ Y G+ ++++ + ++ P G A + +L+
Sbjct: 66 ITGDEAYAGSRNYYDLKDKAKEL-FNYDYIIPAH--------QGRGAENILFPVLLKYKQ 116
Query: 123 RIMGLDLPSGGHLTHGYYTSGGKK----ISATSIYFESL-PYKVNSSTGYIDYDKLEEKA 177
+ P H T+ + + + ++ + G D KL+E
Sbjct: 117 KEGKAKNPVFISNFHFDTTAAHVELNGCKAINIVTEKAFDSETYDDWKGDFDIKKLKENI 176
Query: 178 LDFRPKLI----------ICGGSAYPRDWDYARFRAVADKCGALLLCDMAHI-------- 219
I GG + +A + G ++ D A
Sbjct: 177 AQHGADNIVAIVSTVTCNSAGGQPVSMS-NLKEVYEIAKQHGIFVVMDSARFCENAYFIK 235
Query: 220 ------SGLVAAQEAANPFEYCHIVTTTTHKSLRGPRAGMIFYR 257
+ + ++Y +T + K G++ R
Sbjct: 236 ARDPKYKNATIKEVIFDMYKYADALTMSAKKDPLLNIGGLVAIR 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 = 41.4 bits (96), Expect = 6e-04
Identities = 62/478 (12%), Positives = 123/478 (25%), Gaps = 162/478 (33%)
Query: 6 EWGNSSL--ETVDPE-IHDLIEKEKRRQCRGIELIASENFTSFAVIEALGSALTNKYSE- 61
++ S + E P + + +++ R ++ A N + L AL
Sbjct: 92 KFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAK 151
Query: 62 -----GMPGNRYYGGNEFIDEIENLCRSRALQTFHLDPTQWGVNVQPYSGSPANFAAYTA 116
G+ G G ++ C S +Q W N
Sbjct: 152 NVLIDGVLG---SGKTWVALDV---CLSYKVQCKMDFKIFW-----------LNLKNCN- 193
Query: 117 VLEPHDRIMGL-DLPSGGHLTHGYYTSGGKKISATSIYFESLPYKVNSSTGYIDYDKLEE 175
P + L L ++ S + ++ +++S
Sbjct: 194 --SPETVLEMLQKL----------LYQIDPNWTSRSDHSSNIKLRIHS------------ 229
Query: 176 KALDFRPKLIICGGSAYPRDWDYARFRAVADKCGALL-LCDMAHISGLVAAQEAANPFEY 234
+ + ++ + Y LL L + V +A N F
Sbjct: 230 --IQAELRRLL-------KSKPYEN---------CLLVLLN-------VQNAKAWNAFNL 264
Query: 235 -CHIVTTTTHKS----LRGPRAGMIFYRKGPKPPKKGQPEGAVYDFEDKINFAVF--PS- 286
C I+ TT K L I + + ++ P
Sbjct: 265 SCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSL---LLKYLDCRPQDLPRE 321
Query: 287 -LQGGPHNHQIGALAVALKQASTPAFKA---YAKQVKANAVALGNYLTGKGYSLVTGGTE 342
L P +++ S A K V + + T SL
Sbjct: 322 VLTTNP-------RRLSIIAESIRDGLATWDNWKHVNCDKLT-----TIIESSL------ 363
Query: 343 NHLVLWDLRPLGLTGNKVEKLCDLCNITVNKNAVFGDSSALAPGGVRIGTPAMT------ 396
N L + R + ++L +VF P I P +
Sbjct: 364 NVLEPAEYRKM------FDRL-----------SVF-------PPSAHI--PTILLSLIWF 397
Query: 397 ---------------SRGLLEKDFEQIGEFLHRAVTLTLEIQKEYGKLLKDFNKGLVN 439
L+EK ++ + ++ LE++ + + ++ +V+
Sbjct: 398 DVIKSDVMVVVNKLHKYSLVEKQPKESTISIP---SIYLELKVK-LENEYALHRSIVD 451
Score = 29.8 bits (66), Expect = 2.4
Identities = 16/59 (27%), Positives = 24/59 (40%), Gaps = 10/59 (16%)
Query: 413 HRAVTLTLEIQKEYGKLLKDFNKGLVNNKDIEALKADVEKFASSFDMPGFKMSEMKYKD 471
H T E Q +Y +L F V+N D + DV+ DMP +S+ +
Sbjct: 5 HHMDFETGEHQYQYKDILSVFEDAFVDNFDCK----DVQ------DMPKSILSKEEIDH 53
>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 = 36.4 bits (85), Expect = 0.016
Identities = 15/62 (24%), Positives = 26/62 (41%), Gaps = 10/62 (16%)
Query: 161 VNSSTGYIDYDKLEEKALDFRPKLII----CGGSAYPRDWDYARFRAVADKCGALLLCDM 216
V+ T + + +E A+ + K II G A D A+ ++ G ++ D
Sbjct: 108 VDRDTLMVTPEHIEA-AITPQTKAIIPVHYAGAPA-----DLDAIYALGERYGIPVIEDA 161
Query: 217 AH 218
AH
Sbjct: 162 AH 163
>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 = 36.6 bits (84), Expect = 0.022
Identities = 55/326 (16%), Positives = 93/326 (28%), Gaps = 99/326 (30%)
Query: 189 GSAYP---RDWDYARF---RAVADKCGALLLCDMAH-ISGLVAAQEAANPFEYCHIVTTT 241
GS D Y + V ++ I +V NP
Sbjct: 1625 GSQEQGMGMD-LYKTSKAAQDVWNRADNHFKDTYGFSILDIVIN----NPVNLTIHFGGE 1679
Query: 242 THKSLRGPRAGMIFYRKGPKPPKKGQPEGAVYDFEDKINFAVFPSLQGGPHNHQIGALA- 300
K +R + MIF + G+ + +KI + + G L+
Sbjct: 1680 KGKRIRENYSAMIF-----ETIVDGKLK------TEKIFKEINEHSTSYTFRSEKGLLSA 1728
Query: 301 -----VALKQASTPAFKAYAKQ--VKANAVALGNYLTGKG-YS-LV-TGGTENHLVLWDL 350
AL AF+ + + A+A G+ L G Y+ L V+
Sbjct: 1729 TQFTQPALTLMEKAAFEDLKSKGLIPADATFAGHSL---GEYAALASLAD-----VM--- 1777
Query: 351 RPLGLTGNKVEKLCDLCNITVNK------NAVFGDSS--------ALAPGGVRIGTPAMT 396
+E L ++ V AV D A+ PG V
Sbjct: 1778 --------SIESLVEV----VFYRGMTMQVAVPRDELGRSNYGMIAINPGRVAASFSQEA 1825
Query: 397 SRGLLEKDFEQIGEFLHRAVTLTLEI--------QKEY---GKL--LKDFNKGLVNNKDI 443
+ ++E+ ++ G +EI Q Y G L L L I
Sbjct: 1826 LQYVVERVGKRTGWL--------VEIVNYNVENQQ--YVAAGDLRALDTVTNVL---NFI 1872
Query: 444 EALKADVEKFASSFDMPGFKMSEMKY 469
+ K D+ + S + ++ +
Sbjct: 1873 KLQKIDIIELQKSLSLE--EVEGHLF 1896
Score = 35.4 bits (81), Expect = 0.042
Identities = 46/310 (14%), Positives = 84/310 (27%), Gaps = 119/310 (38%)
Query: 125 MGLDL----PS--------GGHLTHGYYTS----------------GGKKISATSIYFES 156
MG+DL + H Y S GG+K + +
Sbjct: 1631 MGMDLYKTSKAAQDVWNRADNHFKDTYGFSILDIVINNPVNLTIHFGGEKGKRIRENYSA 1690
Query: 157 LPYKVNSSTGYIDYDKLEEKALDFRPKLIICGGSAYPRD--------------WDYARFR 202
+ ++ G + +K+ K ++ + + A F
Sbjct: 1691 MIFE-TIVDGKLKTEKI-FKEINEHSTSYTFRS---EKGLLSATQFTQPALTLMEKAAFE 1745
Query: 203 AVADKCGALLLCDMA-H----ISGLVAAQEAAN--PFE-YCHIVTTTTHKSLRGPRAGMI 254
+ K A H + L + A+ E +V
Sbjct: 1746 DLKSKGLIPADATFAGHSLGEYAALAS---LADVMSIESLVEVV---------------- 1786
Query: 255 FYRKGPKPPKKGQPEGAVYDFEDKINFAVFPSLQGGPHNHQIGAL-----AVALKQASTP 309
FYR G + AV P + G N+ + A+ A + Q
Sbjct: 1787 FYR--------GM----------TMQVAV-PRDELGRSNYGMIAINPGRVAASFSQE--- 1824
Query: 310 AFKAYAKQVKANA-----VALGNY-LTGKGYSLVTGGTENHLVLWDLRPLG--LTGNKVE 361
A + ++V + NY + + Y V G L + L K++
Sbjct: 1825 ALQYVVERVGKRTGWLVEIV--NYNVENQQY--VAAGDLR-----ALDTVTNVLNFIKLQ 1875
Query: 362 KLCDLCNITV 371
K+ D+ +
Sbjct: 1876 KI-DIIELQK 1884
Score = 33.1 bits (75), Expect = 0.23
Identities = 82/516 (15%), Positives = 139/516 (26%), Gaps = 197/516 (38%)
Query: 34 IELIASENFTSF-----------AVIEALGSALTNKYSEGMPGNRYYGGNE---FIDEIE 79
EL+ F + + L L E N Y GN+ ++
Sbjct: 58 AELVGK--FLGYVSSLVEPSKVGQFDQVLNLCL--TEFE----NCYLEGNDIHALAAKLL 109
Query: 80 NLCRSRALQTFHLDPTQWGVNVQPYSGSPANFAAYTAVLEPHDRIMGLDLPSGGHLTHGY 139
+ ++T L ++ Y A P D+ S L
Sbjct: 110 QENDTTLVKTKEL--------IKNY------ITARIMAKRPFDK------KSNSALFRAV 149
Query: 140 YTSGGKKISA-------TSIYFESL-----PYK------VNSSTGYI--------DYDKL 173
G ++ A T YFE L Y + S + D +K+
Sbjct: 150 -GEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKV 208
Query: 174 EEKALDFRPKLIICGGSAYPRDWDYARFRAVADKCGALLLCDMAHISGLVAAQEAA-NPF 232
+ L+ L S P D DY ++ C + + +AH +V A+ P
Sbjct: 209 FTQGLNILEWLE--NPSNTP-DKDYLLSIPIS--CPLIGVIQLAHY--VVTAKLLGFTPG 261
Query: 233 EYC-HIVTTTTHKSLRGPRAGMIFYRKGPKPPKKGQPEGAVY--------DFEDKINFAV 283
E ++ T H G++ AV F + A+
Sbjct: 262 ELRSYLKGATGHS------QGLV---------------TAVAIAETDSWESFFVSVRKAI 300
Query: 284 ---FPSLQGGPHNHQIGALAVALKQASTPAFKAYAKQVKANAVALGNYLTGKGYSLVTGG 340
F IG + P ++ ++ G
Sbjct: 301 TVLF----------FIGVRC----YEAYPNTSLPPSILED-SLENNE------------G 333
Query: 341 TENHLVLWDLRPLGLTGNKVEKLCDLCN----------IT-VN--KNAVF-GDSSAL--- 383
+ + L LT +V+ + N I+ VN KN V G +L
Sbjct: 334 VPSPM----LSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGL 389
Query: 384 --------APGGV---RIG----TPAMTSRGL----------LEKDFEQIGEFLHRAVTL 418
AP G+ RI ++R L L + I + L +
Sbjct: 390 NLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKN--- 446
Query: 419 TLEIQKEYGKLLK----DFNKGLVNNKDIEALKADV 450
+ + ++ D G D+ L +
Sbjct: 447 NVSFNAKD---IQIPVYDTFDG----SDLRVLSGSI 475
Score = 30.8 bits (69), Expect = 1.2
Identities = 23/117 (19%), Positives = 42/117 (35%), Gaps = 30/117 (25%)
Query: 348 WDLRPLGLTGNKVEKLCDLCNITVNKNAVFGDS------SALAPGGVRIGTPAMTSRGLL 401
+ RPL L+ +E + V + F S + + P P + G
Sbjct: 4 YSTRPLTLSHGSLE-----HVLLVPTASFFIASQLQEQFNKILP------EP---TEGFA 49
Query: 402 EKD-----FEQIGEFL-HRAVTLTLEIQKEYGKLLK----DFNKGLVNNKDIEALKA 448
D E +G+FL + + + ++ ++L +F + DI AL A
Sbjct: 50 ADDEPTTPAELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAA 106
>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 = 35.6 bits (83), Expect = 0.030
Identities = 14/58 (24%), Positives = 22/58 (37%), Gaps = 10/58 (17%)
Query: 165 TGYIDYDKLEEKALDFRPKLII----CGGSAYPRDWDYARFRAVADKCGALLLCDMAH 218
G ID LE+ ++ R K I+ G S + + + K L D +H
Sbjct: 106 DGNIDELALEKL-INERTKAIVSVDYAGKSV-----EVESVQKLCKKHSLSFLSDSSH 157
>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 = 34.6 bits (79), Expect = 0.062
Identities = 23/185 (12%), Positives = 50/185 (27%), Gaps = 32/185 (17%)
Query: 105 SGSPANFAAYTAVLEPHDRIMGLDLPSGGHLTHGYYTSGGKKISATSIYFESLPYK---- 160
G A +++ ++ GLD ++ ++ + ++ K
Sbjct: 97 QGRGAEQIYIPVLIKKREQEKGLDRSKMVAFSNYFFDTTQGHSQINGCTVRNVYIKEAFD 156
Query: 161 ---VNSSTGYIDYDKLEEKALDFRP---KLII-------CGGSAYPRDWDYARFRAVADK 207
G D + LE + P I+ GG ++A K
Sbjct: 157 TGVRYDFKGNFDLEGLERGIEEVGPNNVPYIVATITSNSAGGQPVSLAN-LKAMYSIAKK 215
Query: 208 CGALLLCDMAHI--------------SGLVAAQEAANPFEYCHIVTTTTHKSLRGPRAGM 253
++ D A Q ++Y ++ + K P G+
Sbjct: 216 YDIPVVMDSARFAENAYFIKQREAEYKDWTIEQITRETYKYADMLAMSAKKDAMVPMGGL 275
Query: 254 IFYRK 258
+ +
Sbjct: 276 LCMKD 280
>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 = 32.7 bits (74), Expect = 0.28
Identities = 30/208 (14%), Positives = 48/208 (23%), Gaps = 33/208 (15%)
Query: 75 IDEIENLCRSRALQTFHLDPTQWGVNVQPYSGSPANFAAYTAVLEPHDRIMGLDLPSGGH 134
E E + F+ D + N S AN I+ + H
Sbjct: 197 HKEAEQY----IARVFNADRSYMVTN----GTSTANKIVGMYSAPAGSTIL---IDRNCH 245
Query: 135 --LTHGYYTSGGK------KISATSIYFESLPYKVNSSTGYIDYDKLEEKALDFRPKLII 186
LTH S +A I + +++E P +
Sbjct: 246 KSLTHLMMMSDVTPIYFRPTRNAYGIL---GGIPQSEFQHATIAKRVKETPNATWPVHAV 302
Query: 187 CGGSAYPRDWDYARFRAVADKCGAL-LLCDMAHISGLV--------AAQEAANPFEYCHI 237
S Y D + + D A +
Sbjct: 303 ITNSTY--DGLLYNTDFIKKTLDVKSIHFDSAWVPYTNFSPIYEGKCGMSGGRVEGKVIY 360
Query: 238 VTTTTHKSLRGPRAGMIFYRKGPKPPKK 265
T +THK L + + KG +
Sbjct: 361 ETQSTHKLLAAFSQASMIHVKGDVNEET 388
>2gt1_A Lipopolysaccharide heptosyltransferase-1; GT-B fold; 1.90A
{Escherichia coli UTI89} PDB: 2h1f_A* 2h1h_A*
Length = 326
Score = 31.8 bits (73), Expect = 0.48
Identities = 9/56 (16%), Positives = 16/56 (28%), Gaps = 3/56 (5%)
Query: 155 ESLPYKVNSSTGY--IDYDKLEEKALDFRPKLIICGGSAYP-RDWDYARFRAVADK 207
+SL Y + G I L D + + + W +R +
Sbjct: 150 KSLGYSKPQTQGDYAIAQHFLTNLPTDAGEYAVFLHATTRDDKHWPEEHWRELIGL 205
>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 = 31.9 bits (72), Expect = 0.49
Identities = 27/191 (14%), Positives = 52/191 (27%), Gaps = 19/191 (9%)
Query: 127 LDLPSGGHLTHGYYTSGGKKISATSIYFESLPYKVNSSTGYIDYDKLEEKALDFRPKLII 186
PS + G I + P + + D ++ EK D +I+
Sbjct: 163 KAFPSDHYAIESQLQLHGLNIEESMR--MIKPREGEETLRIEDILEVIEKEGD-SIAVIL 219
Query: 187 CGGSAYP--RDWDYARFRAVADKCGALLLCDMAHISGLVAAQEAANPFEYCHIVTTTTHK 244
G + + ++ G + D+AH G V ++K
Sbjct: 220 FSGVHFYTGQHFNIPAITKAGQAKGCYVGFDLAHAVGNVELYLHDWG---VDFACWCSYK 276
Query: 245 SLRGPRAGMIFYRKGPKPPKKGQPEGAVY-------DFEDKINFAVFPS----LQGGPHN 293
L G+ K +P + F+ + P P
Sbjct: 277 YLNAGAGGIAGAFIHEKHAHTIKPALVGWFGHELSTRFKMDNKLQLIPGVCGFRISNPPI 336
Query: 294 HQIGALAVALK 304
+ +L +L+
Sbjct: 337 LLVCSLHASLE 347
>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 = 31.8 bits (73), Expect = 0.52
Identities = 25/155 (16%), Positives = 43/155 (27%), Gaps = 36/155 (23%)
Query: 105 SGSPANFAAYTAVLEPHDRIMGLDLPSGGHLTH-----GYYTSGGKKISATSIYFESLPY 159
SG AN + +P+ + +D H G + + P+
Sbjct: 127 SGWNANVGLLQTICQPNTNVY-ID-----FFAHMSLWEGARYANAQAH----------PF 170
Query: 160 KVNSSTGYIDYDKLEEKALDFRPKLIICGGSAYPRDWDYARFR---AVADKCGALLLCDM 216
N + D L P +I+ Y A ++ + G LL D
Sbjct: 171 MHN------NCDHLRMLIQRHGPGIIVVDS-IYSTLGTIAPLAELVNISKEFGCALLVDE 223
Query: 217 AHISGLVAAQ-----EAANPFEYCHIVTTTTHKSL 246
+H G H +T + K+
Sbjct: 224 SHSLGTHGPNGAGLLAELGLTREVHFMTASLAKTF 258
>2bwn_A 5-aminolevulinate synthase; tetrapyrrole biosynthesis, heme
biosynthesis, pyridoxal PHOS dependent, transferase,
acyltransferase; HET: LLP; 2.1A {Rhodobacter capsulatus}
SCOP: c.67.1.4 PDB: 2bwo_A* 2bwp_A*
Length = 401
Score = 30.7 bits (70), Expect = 0.96
Identities = 17/61 (27%), Positives = 23/61 (37%), Gaps = 7/61 (11%)
Query: 169 DYDKLEEK---ALDFRPKLIICGGSAYPRDWDYARFRA---VADKCGALLLCDMAHISGL 222
D L E PKLI Y D D+ + +A++ GAL D H G+
Sbjct: 163 DVAHLRELIAADDPAAPKLIAFES-VYSMDGDFGPIKEICDIAEEFGALTYIDEVHAVGM 221
Query: 223 V 223
Sbjct: 222 Y 222
>1svv_A Threonine aldolase; structural genomics, structural genomics of
pathogenic proto SGPP, protein structure initiative,
PSI; 2.10A {Leishmania major} SCOP: c.67.1.1
Length = 359
Score = 30.7 bits (70), Expect = 1.0
Identities = 24/150 (16%), Positives = 46/150 (30%), Gaps = 32/150 (21%)
Query: 105 SGSPANFAAYTAVLEPHDRIMGLDLPSGGHL-TH---GYYTSGGKKISATSIYFESLPYK 160
G+ N A + L P + ++ GH+ TH +G K ++
Sbjct: 74 GGTQTNLIACSLALRPWEAVI---ATQLGHISTHETGAIEATGHKVVT------------ 118
Query: 161 VNSSTGYIDYDKLEEKALDF------RPKLI-----ICGGSAYPRDWDYARFRAVADKCG 209
G + +E + PKL+ G+ Y + + A + G
Sbjct: 119 APCPDGKLRVADIESALHENRSEHMVIPKLVYISNTTEVGTQYTKQ-ELEDISASCKEHG 177
Query: 210 ALLLCDMAHIS-GLVAAQEAANPFEYCHIV 238
L D A ++ L + + +
Sbjct: 178 LYLFLDGARLASALSSPVNDLTLADIARLT 207
>1weh_A Conserved hypothetical protein TT1887; rossman fold, structural
genomics, riken structural genomics/proteomics
initiative, RSGI; 1.80A {Thermus thermophilus} SCOP:
c.129.1.1
Length = 171
Score = 29.9 bits (68), Expect = 1.1
Identities = 7/35 (20%), Positives = 11/35 (31%), Gaps = 4/35 (11%)
Query: 306 ASTPAFKAYAKQVKANAVALGNYLTGKGYSLVTGG 340
+ + V G L +G+ L GG
Sbjct: 10 SRLSPEDPLYAR----WVRYGEVLAEEGFGLACGG 40
>1wek_A Hypothetical protein TT1465; rossman fold, structural genomics,
riken structural genomics/proteomics initiative, RSGI,
unknown function; 2.20A {Thermus thermophilus} SCOP:
c.129.1.1
Length = 217
Score = 29.9 bits (68), Expect = 1.2
Identities = 9/35 (25%), Positives = 12/35 (34%), Gaps = 4/35 (11%)
Query: 306 ASTPAFKAYAKQVKANAVALGNYLTGKGYSLVTGG 340
A + LG L G+ +VTGG
Sbjct: 46 ARFGEGHPAYEA----GYRLGRALAEAGFGVVTGG 76
>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 = 30.5 bits (69), Expect = 1.4
Identities = 28/149 (18%), Positives = 49/149 (32%), Gaps = 16/149 (10%)
Query: 168 IDYDKLEEKALDFRPKLIICGGSAYP--RDWDYARFRAVADKCGALLLCDMAHISGLVAA 225
+D + +A+D +++ Y D A++ +CGAL + D+AH +G V
Sbjct: 152 VDSPEELPQAIDQDTAVVMLTHVNYKTGYMHDMQALTALSHECGALAIWDLAHSAGAVPV 211
Query: 226 QEAANPFEYCHIVTTTTHKSLR-GPRAGMIFY-----RKGPKPPKKGQPEGAVYDFEDKI 279
+Y T+K L GP + + P G G F +
Sbjct: 212 DLHQAGADYA---IGCTYKYLNGGPGSQAFVWVSPQLCDLVPQPLSG-WFGHSRQFAMEP 267
Query: 280 NFAVFPS----LQGGPHNHQIGALAVALK 304
+ L G + + L
Sbjct: 268 RYEPSNGIARYLCGTQPITSLAMVECGLD 296
>2w8t_A SPT, serine palmitoyltransferase; HET: LLP; 1.25A {Sphingomonas
paucimobilis} PDB: 2w8u_A* 2w8w_A* 2xbn_A* 2w8j_A*
2w8v_A* 2jg2_A* 2jgt_A 2x8u_A*
Length = 427
Score = 29.9 bits (68), Expect = 2.0
Identities = 24/89 (26%), Positives = 33/89 (37%), Gaps = 12/89 (13%)
Query: 169 DYDKLEEK---ALDFRPKLIICGGSAYPRDWDYA---RFRAVADKCGALLLCDMAHISGL 222
+ L+++ KL++ G Y D A AVA K GA++L D AH G
Sbjct: 179 SVEDLDKRLGRLPKEPAKLVVLEG-VYSMLGDIAPLKEMVAVAKKHGAMVLVDEAHSMGF 237
Query: 223 VAAQ-----EAANPFEYCHIVTTTTHKSL 246
EA V T KS+
Sbjct: 238 FGPNGRGVYEAQGLEGQIDFVVGTFSKSV 266
>3tqx_A 2-amino-3-ketobutyrate coenzyme A ligase; energy metabolism,
transferase; HET: PLP; 2.30A {Coxiella burnetii}
Length = 399
Score = 29.9 bits (68), Expect = 2.1
Identities = 25/93 (26%), Positives = 34/93 (36%), Gaps = 14/93 (15%)
Query: 169 DYDKLEEK-----ALDFRPKLIICGGSAYPRDWDYA---RFRAVADKCGALLLCDMAHIS 220
LE K R KLI G + D A +ADK AL++ D +H
Sbjct: 158 AMGDLEAKLKEADEKGARFKLIATDG-VFSMDGIIADLKSICDLADKYNALVMVDDSHAV 216
Query: 221 GLVAAQ-----EAANPFEYCHIVTTTTHKSLRG 248
G + E + I+T T K+L G
Sbjct: 217 GFIGENGRGTPEYCGVADRVDILTGTLGKALGG 249
>1fc4_A 2-amino-3-ketobutyrate conenzyme A ligase; 2-amino-3-ketobutyrate
COA ligase, pyridoxal phosphate, COEN transferase,
structural genomics; HET: PLP; 2.00A {Escherichia coli}
SCOP: c.67.1.4
Length = 401
Score = 29.5 bits (67), Expect = 2.5
Identities = 25/93 (26%), Positives = 35/93 (37%), Gaps = 14/93 (15%)
Query: 169 DYDKLEEK-----ALDFRPKLIICGGSAYPRDWDYA---RFRAVADKCGALLLCDMAHIS 220
D +LE + R LI G + D A +ADK AL++ D +H
Sbjct: 160 DMQELEARLKEAREAGARHVLIATDG-VFSMDGVIANLKGVCDLADKYDALVMVDDSHAV 218
Query: 221 GLVAAQ-----EAANPFEYCHIVTTTTHKSLRG 248
G V E + I+T T K+L G
Sbjct: 219 GFVGENGRGSHEYCDVMGRVDIITGTLGKALGG 251
>2iz6_A Molybdenum cofactor carrier protein; metal transport; 1.60A
{Chlamydomonas reinhardtii} PDB: 2iz5_A 2iz7_A
Length = 176
Score = 28.8 bits (65), Expect = 2.7
Identities = 11/55 (20%), Positives = 18/55 (32%), Gaps = 10/55 (18%)
Query: 292 HNHQIGALAVALKQ------ASTPAFKAYAKQVKANAVALGNYLTGKGYSLVTGG 340
H+H G ++ + A LG + G+ L+TGG
Sbjct: 2 HHHHHGCMSGRKPIIGVMGPGKADTAENQLVM----ANELGKQIATHGWILLTGG 52
>1vyb_A ORF2 contains A reverse transcriptase domain; endonuclease, APE-1
type, retrotransposition, retrotransposon, transferase;
1.8A {Homo sapiens} SCOP: d.151.1.1 PDB: 2v0s_A 2v0r_A
Length = 238
Score = 29.1 bits (66), Expect = 2.7
Identities = 17/109 (15%), Positives = 31/109 (28%), Gaps = 22/109 (20%)
Query: 88 QTFHLDPTQWGVNVQP-----YSGSPANFAAYTAVL---EPHDRIMGLDLPSGGHLTHGY 139
T L W Q +G A+L + + + GH
Sbjct: 50 DTHRLKIKGWRKIYQANGKQKKAG--------VAILVSDKTDFKPTKIKRDKEGHYIMVK 101
Query: 140 YTSGGKKISATSIYFESLPYKVNSSTGYIDYDKLEEKALDFRPKLIICG 188
+ ++++ +IY P N+ L + D +I G
Sbjct: 102 GSIQQEELTILNIYA---P---NTGAPRFIKQVLSDLQRDLDSHTLIMG 144
>3laa_A Haemagluttinin family protein; niaid, seattle structural genomics
center for infectious DIS ssgcid, melioidosis; 1.35A
{Burkholderia pseudomallei} PDB: 3la9_A
Length = 200
Score = 28.5 bits (63), Expect = 3.2
Identities = 11/55 (20%), Positives = 17/55 (30%), Gaps = 1/55 (1%)
Query: 289 GGPHNHQIGALAVALKQASTPAFKAYAKQVKANAVALGNYLTGKGYSLVTGGTEN 343
H + +VA S A A +VA+G+ T V +
Sbjct: 93 KYFHANSTDPDSVATGTNSV-AIGPNAVANVDYSVAIGSGATTSAAVPVASASVG 146
>3fdb_A Beta C-S lyase, putative PLP-dependent beta-cystathionase;
PLP-dependent transferase-like fold, structural
genomics; HET: LLP; 1.99A {Corynebacterium diphtheriae}
Length = 377
Score = 29.0 bits (66), Expect = 3.2
Identities = 15/67 (22%), Positives = 28/67 (41%), Gaps = 10/67 (14%)
Query: 347 LW-DLRPLGLTGNKVEKLCDLCNITVNKNAVFGDSSALAPGGVR--IGTPAMTSRGLLEK 403
+W D R + G+ E + + +N A FG+ G R T R +LE+
Sbjct: 312 MWIDFRDTTIEGSPSEFFIEKAKVAMNDGAWFGED---GTGFCRLNFATS----REVLEE 364
Query: 404 DFEQIGE 410
+++ +
Sbjct: 365 AIDRMAK 371
>3bw2_A 2-nitropropane dioxygenase; TIM barrel, oxidoreductase; HET: FMN;
2.10A {Streptomyces ansochromogenes} PDB: 3bw4_A*
3bw3_A*
Length = 369
Score = 29.2 bits (66), Expect = 3.3
Identities = 10/46 (21%), Positives = 11/46 (23%), Gaps = 3/46 (6%)
Query: 98 GVNV---QPYSGSPANFAAYTAVLEPHDRIMGLDLPSGGHLTHGYY 140
GVNV QP Y L +L Y
Sbjct: 66 GVNVFMPQPELAESGAVEVYAHQLAGEAAWYETELGDPDGGRDDGY 111
>3a2b_A Serine palmitoyltransferase; vitamin B6-dependent enzyme fold type
I, acyltransferase, PY phosphate; HET: PLP; 2.30A
{Sphingobacterium multivorum}
Length = 398
Score = 29.1 bits (66), Expect = 3.8
Identities = 17/89 (19%), Positives = 34/89 (38%), Gaps = 12/89 (13%)
Query: 169 DYDKLEEK---ALDFRPKLIICGGSAYPRDWDYA---RFRAVADKCGALLLCDMAHISGL 222
+ + L K + KLI G + + D ++A++ A ++ D AH G+
Sbjct: 158 NMEDLRAKLSRLPEDSAKLICTDG-IFSMEGDIVNLPELTSIANEFDAAVMVDDAHSLGV 216
Query: 223 VAAQ-----EAANPFEYCHIVTTTTHKSL 246
+ + + ++ T KSL
Sbjct: 217 IGHKGAGTASHFGLNDDVDLIMGTFSKSL 245
>3tov_A Glycosyl transferase family 9; structural genomics, PSI-BIOL
protein structure initiative, midwest center for
structural genomics, MCSG; 2.98A {Veillonella parvula}
Length = 349
Score = 28.4 bits (64), Expect = 5.1
Identities = 13/40 (32%), Positives = 15/40 (37%), Gaps = 2/40 (5%)
Query: 171 DKLEEKALDFRPKLI-ICGGSAYP-RDWDYARFRAVADKC 208
+ L LI GSA P + W RF VAD
Sbjct: 174 EFYSSHGLTDTDILIGFNIGSAVPEKRWPAERFAHVADYF 213
>1c7n_A Cystalysin; transferase, aminotransferase, pyridoxal phosphate;
HET: PLP; 1.90A {Treponema denticola} SCOP: c.67.1.3
PDB: 1c7o_A*
Length = 399
Score = 27.9 bits (63), Expect = 8.4
Identities = 7/20 (35%), Positives = 12/20 (60%)
Query: 167 YIDYDKLEEKALDFRPKLII 186
ID+ KLE+ + D K ++
Sbjct: 150 TIDFQKLEKLSKDKNNKALL 169
>3b1d_A Betac-S lyase; HET: PLP PLS EPE; 1.66A {Streptococcus anginosus}
PDB: 3b1c_A* 3b1e_A*
Length = 392
Score = 27.9 bits (63), Expect = 8.6
Identities = 16/93 (17%), Positives = 33/93 (35%), Gaps = 28/93 (30%)
Query: 168 IDYDKLEEKALDFRPKLII-C-----GGSAYPRDWDYARFRAVADKC---GALLL----- 213
ID+++LE ++ KL + C GG R W+ + C +L+
Sbjct: 151 IDFEQLENDIVENDVKLYLLCNPHNPGG----RVWEREVLEQIGHLCQKHHVILVSDEIH 206
Query: 214 CDMA-----HISGLVAAQEAANPFEYCHIVTTT 241
D+ H+S + + + + +
Sbjct: 207 QDLTLFGHEHVSFNTVSPDFKD-----FALVLS 234
>3dzz_A Putative pyridoxal 5'-phosphate-dependent C-S LYA; putative
PLP-dependent aminotransferase; HET: MSE LLP PG4; 1.61A
{Lactobacillus delbrueckii subsp}
Length = 391
Score = 27.8 bits (63), Expect = 9.2
Identities = 15/93 (16%), Positives = 30/93 (32%), Gaps = 28/93 (30%)
Query: 168 IDYDKLEEKALDFRPKLII-C-----GGSAYPRDWDYARFRAVADKC---GALLL----- 213
+++ LEEK ++++ C G W + +A+ C LL+
Sbjct: 147 VNWADLEEKLATPSVRMMVFCNPHNPIG----YAWSEEEVKRIAELCAKHQVLLISDEIH 202
Query: 214 CDMA-----HISGLVAAQEAANPFEYCHIVTTT 241
D+ +A N +V+
Sbjct: 203 GDLVLTDEDITPAFTVDWDAKN-----WVVSLI 230
>3l8a_A METC, putative aminotransferase, probable beta-cystathi;
beta-cystathionase, lyase; HET: PLP; 1.54A
{Streptococcus mutans}
Length = 421
Score = 27.5 bits (62), Expect = 9.6
Identities = 6/19 (31%), Positives = 13/19 (68%)
Query: 168 IDYDKLEEKALDFRPKLII 186
ID+++LE+ +D K+ +
Sbjct: 181 IDFEQLEKDIIDNNVKIYL 199
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
0.317 0.136 0.408
Gapped
Lambda K H
0.267 0.0793 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 7,490,129
Number of extensions: 470868
Number of successful extensions: 1255
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1214
Number of HSP's successfully gapped: 62
Length of query: 471
Length of database: 6,701,793
Length adjustment: 97
Effective length of query: 374
Effective length of database: 3,993,456
Effective search space: 1493552544
Effective search space used: 1493552544
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: 59 (26.4 bits)