RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 015609
(403 letters)
>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 = 520 bits (1341), Expect = 0.0
Identities = 160/310 (51%), Positives = 202/310 (65%), Gaps = 25/310 (8%)
Query: 106 PFTKRFAVEPGLESRRAGVRAW-GNQSLPLADPEIFDIMEKEKQRQFKGIELIASENFVC 164
+ R W G +SL +DPE+++++++EK RQ +G+ELIASENF
Sbjct: 8 MAIRAQHSNAAQTQTGEANRGWTGQESLSDSDPEMWELLQREKDRQCRGLELIASENFCS 67
Query: 165 RAVMEALGSHLTNKYSEGYPGARYYTGNQYIDQIENLCFERALKAFDLDSDNWGVNVQPY 224
RA +EALGS L NKYSEGYPG RYY G + +D+IE LC RAL+AFDLD WGVNVQPY
Sbjct: 68 RAALEALGSCLNNKYSEGYPGKRYYGGAEVVDEIELLCQRRALEAFDLDPAQWGVNVQPY 127
Query: 225 SCTSANFAVYTGLLLPGDRIMGLDSPSGGHLSHGYHTPGGKKVSAASIFFESFPYKVNPQ 284
S + AN AVYT LL P DRIMGLD P GGHL+HGY + K++SA SIFFES PYK+NP+
Sbjct: 128 SGSPANLAVYTALLQPHDRIMGLDLPDGGHLTHGYMSD-VKRISATSIFFESMPYKLNPK 186
Query: 285 TGYIDYEKLEEKAMDYRPKILICGGSSYPREWDYGRFRQIADKCGAVLMCDMAHISGLIA 344
TG IDY +L A +RP+++I G S+Y R DY R R++ D+ A L+ DMAHISGL+A
Sbjct: 187 TGLIDYNQLALTARLFRPRLIIAGTSAYARLIDYARMREVCDEVKAHLLADMAHISGLVA 246
Query: 345 AKELASPFDYCDIVTSTTHKSLRGPRGGIIFFRRGKKPRK-------------------- 384
AK + SPF + DIVT+TTHK+LRG R G+IF+R+G K
Sbjct: 247 AKVIPSPFKHADIVTTTTHKTLRGARSGLIFYRKGVKAVDPKTGREIPYTFEDRINFAVF 306
Query: 385 ---QGIPLNH 391
QG P NH
Sbjct: 307 PSLQGGPHNH 316
>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 = 518 bits (1337), Expect = 0.0
Identities = 162/293 (55%), Positives = 199/293 (67%), Gaps = 24/293 (8%)
Query: 122 AGVRAWGNQSLPLADPEIFDIMEKEKQRQFKGIELIASENFVCRAVMEALGSHLTNKYSE 181
+ Q L +D E++DI++KE RQ G+ELIASENF RAV+EALGS L NKYS
Sbjct: 15 SSHEQMLAQPLKDSDAEVYDIIKKESNRQRVGLELIASENFASRAVLEALGSCLNNKYSL 74
Query: 182 GYPGARYYTGNQYIDQIENLCFERALKAFDLDSDNWGVNVQPYSCTSANFAVYTGLLLPG 241
GYPG RYY G ++ID++E LC +RAL+A+ LD WGVNVQPYS + ANFAVYT L+ P
Sbjct: 75 GYPGQRYYGGTEHIDELETLCQKRALQAYGLDPQCWGVNVQPYSGSPANFAVYTALVEPH 134
Query: 242 DRIMGLDSPSGGHLSHGYHTPGGKKVSAASIFFESFPYKVNPQTGYIDYEKLEEKAMDYR 301
RIMGLD P GGHL+HG+ T KK+SA SIFFES YKVNP TGYIDY++LEE A +
Sbjct: 135 GRIMGLDLPDGGHLTHGFMTD-KKKISATSIFFESMAYKVNPDTGYIDYDRLEENARLFH 193
Query: 302 PKILICGGSSYPREWDYGRFRQIADKCGAVLMCDMAHISGLIAAKELASPFDYCDIVTST 361
PK++I G S Y R DYGR R+IAD+ GA LM DMAHISGL+ A + SPF++C +VT+T
Sbjct: 194 PKLIIAGTSCYSRNLDYGRLRKIADENGAYLMADMAHISGLVVAGVVPSPFEHCHVVTTT 253
Query: 362 THKSLRGPRGGIIFFRRGKK-----------------------PRKQGIPLNH 391
THK+LRG R G+IF+RRG + P QG P NH
Sbjct: 254 THKTLRGCRAGMIFYRRGVRSVDPKTGKEILYNLESLINSAVFPGLQGGPHNH 306
>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 = 374 bits (962), Expect = e-128
Identities = 128/270 (47%), Positives = 174/270 (64%), Gaps = 18/270 (6%)
Query: 130 QSLPLADPEIFDIMEKEKQRQFKGIELIASENFVCRAVMEALGSHLTNKYSEGYPGARYY 189
+ LP DP++F +E+E++RQ IELIASENFV RAVMEA GS LTNKY+EGYPG RYY
Sbjct: 2 KYLPQQDPQVFAAIEQERKRQHAKIELIASENFVSRAVMEAQGSVLTNKYAEGYPGRRYY 61
Query: 190 TGNQYIDQIENLCFERALKAFDLDSDNWGVNVQPYSCTSANFAVYTGLLLPGDRIMGLDS 249
G +Y+D +E L ERA + F + NVQP+S AN AVY +L GD ++G++
Sbjct: 62 GGCEYVDIVEELARERAKQLFGAEH----ANVQPHSGAQANMAVYFTVLEHGDTVLGMNL 117
Query: 250 PSGGHLSHGYHTPGGKKVSAASIFFESFPYKVNPQTGYIDYEKLEEKAMDYRPKILICGG 309
GGHL+HG V+ + + + Y V+P+T IDY+ + EKA +RPK+++
Sbjct: 118 SHGGHLTHG------SPVNFSGVQYNFVAYGVDPETHVIDYDDVREKARLHRPKLIVAAA 171
Query: 310 SSYPREWDYGRFRQIADKCGAVLMCDMAHISGLIAAKELASPFDYCDIVTSTTHKSLRGP 369
++YPR D+ +FR+IAD+ GA LM DMAHI+GL+AA +P Y VT+TTHK+LRGP
Sbjct: 172 AAYPRIIDFAKFREIADEVGAYLMVDMAHIAGLVAAGLHPNPVPYAHFVTTTTHKTLRGP 231
Query: 370 RGGIIFFRR--GKK------PRKQGIPLNH 391
RGG+I + K+ P QG PL H
Sbjct: 232 RGGMILCQEQFAKQIDKAIFPGIQGGPLMH 261
>2dkj_A Serine hydroxymethyltransferase; PLP dependent enzyme, structural
genomics; HET: PLP; 1.15A {Thermus thermophilus}
Length = 407
Score = 371 bits (954), Expect = e-127
Identities = 127/271 (46%), Positives = 174/271 (64%), Gaps = 19/271 (7%)
Query: 130 QSLPLADPEIFDIMEKEKQRQFKGIELIASENFVCRAVMEALGSHLTNKYSEGYPGARYY 189
S D +F+++ E++RQ +G+ELIASENFV + V EA+GS LTNKY+EGYPGARYY
Sbjct: 2 VSTLKRDEALFELIALEEKRQREGLELIASENFVSKQVREAVGSVLTNKYAEGYPGARYY 61
Query: 190 TGNQYIDQIENLCFERALKAFDLDSDNWGVNVQPYSCTSANFAVYTGLLLPGDRIMGLDS 249
G + ID++E+L ERA F NVQP+S + AN AVY L+ PGD +MG+D
Sbjct: 62 GGCEVIDRVESLAIERAKALFGAAW----ANVQPHSGSQANMAVYMALMEPGDTLMGMDL 117
Query: 250 PSGGHLSHGYHTPGGKKVSAASIFFESFPYKVNPQTGYIDYEKLEEKAMDYRPKILICGG 309
+GGHL+HG +V+ + ++ Y V P T ID E++ A+++RPK+++ G
Sbjct: 118 AAGGHLTHG------SRVNFSGKLYKVVSYGVRPDTELIDLEEVRRLALEHRPKVIVAGA 171
Query: 310 SSYPREWDYGRFRQIADKCGAVLMCDMAHISGLIAAKELASPFDYCDIVTSTTHKSLRGP 369
S+YPR WD+ FR+IAD+ GA L+ DMAH +GL+AA +P Y +VTSTTHK+LRGP
Sbjct: 172 SAYPRFWDFKAFREIADEVGAYLVVDMAHFAGLVAAGLHPNPLPYAHVVTSTTHKTLRGP 231
Query: 370 RGGIIFFRR---GKK------PRKQGIPLNH 391
RGG+I GK+ P QG PL H
Sbjct: 232 RGGLILSNDPELGKRIDKLIFPGIQGGPLEH 262
>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 = 369 bits (951), Expect = e-126
Identities = 120/274 (43%), Positives = 170/274 (62%), Gaps = 22/274 (8%)
Query: 129 NQSLPLADPEIFDIMEKEKQRQFKGIELIASENFVCRAVMEALGSHLTNKYSEGYPGARY 188
++ D E++ ME+EK RQ + IELIASEN+ VM+A GS LTNKY+EGYPG RY
Sbjct: 8 EMNIADYDAELWQAMEQEKVRQEEHIELIASENYTSPRVMQAQGSQLTNKYAEGYPGKRY 67
Query: 189 YTGNQYIDQIENLCFERALKAFDLDSDNWGVNVQPYSCTSANFAVYTGLLLPGDRIMGLD 248
Y G +Y+D +E L +RA + F D NVQP+S + ANFAVYT LL PGD ++G++
Sbjct: 68 YGGCEYVDVVEQLAIDRAKELFGADY----ANVQPHSGSQANFAVYTALLQPGDTVLGMN 123
Query: 249 SPSGGHLSHGYHTPGGKKVSAASIFFESFPYKVNPQTGYIDYEKLEEKAMDYRPKILICG 308
GGHL+HG V+ + + PY ++ ++G IDY+++ + A +++PK++I G
Sbjct: 124 LAQGGHLTHG------SPVNFSGKLYNIVPYGID-ESGKIDYDEMAKLAKEHKPKMIIGG 176
Query: 309 GSSYPREWDYGRFRQIADKCGAVLMCDMAHISGLIAAKELASPFDYCDIVTSTTHKSLRG 368
S+Y D+ + R+IAD GA L DMAH++GLIAA +P + +VT+TTHK+L G
Sbjct: 177 FSAYSGVVDWAKMREIADSIGAYLFVDMAHVAGLIAAGVYPNPVPHAHVVTTTTHKTLAG 236
Query: 369 PRGGIIFFRR-----GKK------PRKQGIPLNH 391
PRGG+I + KK P QG PL H
Sbjct: 237 PRGGLILAKGGDEELYKKLNSAVFPSAQGGPLMH 270
>3n0l_A Serine hydroxymethyltransferase; alpha beta class, 3-layer(ABA)
sandwich, CSGI transferase, structural genomics; HET:
MSE; 1.80A {Campylobacter jejuni}
Length = 417
Score = 369 bits (951), Expect = e-126
Identities = 134/272 (49%), Positives = 172/272 (63%), Gaps = 20/272 (7%)
Query: 129 NQSLPLADPEIFDIMEKEKQRQFKGIELIASENFVCRAVMEALGSHLTNKYSEGYPGARY 188
SL + D EIFD+ KE +RQ +G+E+IASENF VME +GS LTNKY+EGYPG RY
Sbjct: 3 AMSLEMFDKEIFDLTNKELERQCEGLEMIASENFTLPEVMEVMGSILTNKYAEGYPGKRY 62
Query: 189 YTGNQYIDQIENLCFERALKAFDLDSDNWGVNVQPYSCTSANFAVYTGLLLPGDRIMGLD 248
Y G +++D+IE L ER K F+ NVQP S + AN VY L+ PGD+I+G+D
Sbjct: 63 YGGCEFVDEIETLAIERCKKLFNCKF----ANVQPNSGSQANQGVYAALINPGDKILGMD 118
Query: 249 SPSGGHLSHGYHTPGGKKVSAASIFFESFPYKVNPQTGYIDYEKLEEKAMDYRPKILICG 308
GGHL+HG KVS++ +ES Y V G IDYEK+ E A +PK+++CG
Sbjct: 119 LSHGGHLTHG------AKVSSSGKMYESCFYGVELD-GRIDYEKVREIAKKEKPKLIVCG 171
Query: 309 GSSYPREWDYGRFRQIADKCGAVLMCDMAHISGLIAAKELASPFDYCDIVTSTTHKSLRG 368
S+Y R D+ +FR+IAD+ GA L D+AHI+GL+ A E SPF Y +V+STTHK+LRG
Sbjct: 172 ASAYARVIDFAKFREIADEIGAYLFADIAHIAGLVVAGEHPSPFPYAHVVSSTTHKTLRG 231
Query: 369 PRGGIIFFRR---GKK------PRKQGIPLNH 391
PRGGII KK P QG PL H
Sbjct: 232 PRGGIIMTNDEELAKKINSAIFPGIQGGPLMH 263
>3ecd_A Serine hydroxymethyltransferase 2; ssgcid, decode, bupsa00008A,
one-carbon metabolism, pyridoxa phosphate, structural
genomics; 1.60A {Burkholderia pseudomallei}
Length = 425
Score = 369 bits (949), Expect = e-126
Identities = 123/272 (45%), Positives = 166/272 (61%), Gaps = 19/272 (6%)
Query: 129 NQSLPLADPEIFDIMEKEKQRQFKGIELIASENFVCRAVMEALGSHLTNKYSEGYPGARY 188
+QSL D + + KE +RQ +ELIASEN V RAV++A GS LTNKY+EGYPG RY
Sbjct: 10 SQSLAERDASVRGAILKELERQQSQVELIASENIVSRAVLDAQGSVLTNKYAEGYPGKRY 69
Query: 189 YTGNQYIDQIENLCFERALKAFDLDSDNWGVNVQPYSCTSANFAVYTGLLLPGDRIMGLD 248
Y G ++ D++E L ER + F+ NVQP+S AN AV L PGD ++G+
Sbjct: 70 YGGCEFADEVEALAIERVKRLFNAGH----ANVQPHSGAQANGAVMLALAKPGDTVLGMS 125
Query: 249 SPSGGHLSHGYHTPGGKKVSAASIFFESFPYKVNPQTGYIDYEKLEEKAMDYRPKILICG 308
+GGHL+HG K + + +F + Y V+ T IDY+++E A ++P ++I G
Sbjct: 126 LDAGGHLTHG------AKPALSGKWFNALQYGVSRDTMLIDYDQVEALAQQHKPSLIIAG 179
Query: 309 GSSYPREWDYGRFRQIADKCGAVLMCDMAHISGLIAAKELASPFDYCDIVTSTTHKSLRG 368
S+YPR+ D+ RFR IAD GA LM DMAHI+G+IAA A+P ++ +VTSTTHK+LRG
Sbjct: 180 FSAYPRKLDFARFRAIADSVGAKLMVDMAHIAGVIAAGRHANPVEHAHVVTSTTHKTLRG 239
Query: 369 PRGGIIFFRR---GKK------PRKQGIPLNH 391
PRGG + KK P QG PL H
Sbjct: 240 PRGGFVLTNDEEIAKKINSAVFPGLQGGPLMH 271
>3h7f_A Serine hydroxymethyltransferase 1; cytoplasm, one-carbon
metabolism, pyridoxal phosphate, structural genomics;
HET: LLP; 1.50A {Mycobacterium tuberculosis}
Length = 447
Score = 368 bits (947), Expect = e-125
Identities = 117/271 (43%), Positives = 169/271 (62%), Gaps = 18/271 (6%)
Query: 129 NQSLPLADPEIFDIMEKEKQRQFKGIELIASENFVCRAVMEALGSHLTNKYSEGYPGARY 188
+ L DP+I +++ KE RQ +E+IASENFV RAV++A GS LTNKY+EG PG RY
Sbjct: 23 SAPLAEVDPDIAELLAKELGRQRDTLEMIASENFVPRAVLQAQGSVLTNKYAEGLPGRRY 82
Query: 189 YTGNQYIDQIENLCFERALKAFDLDSDNWGVNVQPYSCTSANFAVYTGLLLPGDRIMGLD 248
Y G +++D +ENL +RA F + NVQP+S AN AV L+ PG+R++GLD
Sbjct: 83 YGGCEHVDVVENLARDRAKALFGAEF----ANVQPHSGAQANAAVLHALMSPGERLLGLD 138
Query: 249 SPSGGHLSHGYHTPGGKKVSAASIFFESFPYKVNPQTGYIDYEKLEEKAMDYRPKILICG 308
+GGHL+HG +++ + +E+ Y V+P T ID + + A+++RPK++I G
Sbjct: 139 LANGGHLTHG------MRLNFSGKLYENGFYGVDPATHLIDMDAVRATALEFRPKVIIAG 192
Query: 309 GSSYPREWDYGRFRQIADKCGAVLMCDMAHISGLIAAKELASPFDYCDIVTSTTHKSLRG 368
S+YPR D+ FR IAD+ GA L+ DMAH +GL+AA SP + D+V++T HK+L G
Sbjct: 193 WSAYPRVLDFAAFRSIADEVGAKLLVDMAHFAGLVAAGLHPSPVPHADVVSTTVHKTLGG 252
Query: 369 PRGGIIFFRR--GKK------PRKQGIPLNH 391
R G+I ++ K P +QG PL H
Sbjct: 253 GRSGLIVGKQQYAKAINSAVFPGQQGGPLMH 283
>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 = 69.4 bits (169), Expect = 5e-13
Identities = 35/251 (13%), Positives = 66/251 (26%), Gaps = 49/251 (19%)
Query: 176 TNKYSEGYPGARYYTGNQYIDQIENLCFERALKAFDLDSDNWGVN--VQPYSCTSANFAV 233
+++ G Y G++ ER ++ +G V + A +
Sbjct: 58 DKQWAGMMMGDEAYAGSENFYH-----LERTVQEL------FGFKHIVPTHQGRGAENLL 106
Query: 234 YTGLLLPGDRIMGLDSPSGGHLSHGYHTPGGKKVSAASIFFESFPYKVNPQTGYIDYEKL 293
+ PG + + + G G ID +KL
Sbjct: 107 SQLAIKPGQYVA---GNMYFTTTRYHQEKNGAVFVDIVRDEAHDAGLNIAFKGDIDLKKL 163
Query: 294 EEKAMDYRPKI--LIC--------GGSSYPREWDYGRFRQIADKCGAVLMCDMAHISG-- 341
++ + + IC GG + R++ + G + D
Sbjct: 164 QKLIDEKGAENIAYICLAVTVNLAGGQPVSMA-NMRAVRELTEAHGIKVFYDATRCVENA 222
Query: 342 -LIAAKE-----------LASPFDYCDIVTSTTHKSLRGPRGGIIFFR--------RGKK 381
I +E + F Y D T + K GG + +
Sbjct: 223 YFIKEQEQGFENKSIAEIVHEMFSYADGCTMSGKKDCLVNIGGFLCMNDDEMFSSAKELV 282
Query: 382 PRKQGIPLNHG 392
+G+P G
Sbjct: 283 VVYEGMPSYGG 293
>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 = 50.6 bits (120), Expect = 5e-07
Identities = 30/210 (14%), Positives = 61/210 (29%), Gaps = 34/210 (16%)
Query: 225 SCTSANFAVYTGLLLPGDRIMGLDSPSGGHLSHGYHTPGGKKVSAASIFF----ESF-PY 279
A ++ LL + +P H T +++ ++F
Sbjct: 99 QGRGAENILFPVLLKYKQKEGKAKNPVFISNFHFDTTAAHVELNGCKAINIVTEKAFDSE 158
Query: 280 KVNPQTGYIDYEKLE----EKAMDYRPKILIC------GGSSYPREWDYGRFRQIADKCG 329
+ G D +KL+ + D I+ GG + +IA + G
Sbjct: 159 TYDDWKGDFDIKKLKENIAQHGADNIVAIVSTVTCNSAGGQPVSMS-NLKEVYEIAKQHG 217
Query: 330 AVLMCDMAHI--------------SGLIAAKELASPFDYCDIVTSTTHKSLRGPRGGIIF 375
++ D A + + + Y D +T + K GG++
Sbjct: 218 IFVVMDSARFCENAYFIKARDPKYKNATIKEVIFDMYKYADALTMSAKKDPLLNIGGLVA 277
Query: 376 FR----RGKKPRKQGIPLNHGDVVVIMISR 401
R R++ +P+ + R
Sbjct: 278 IRDNEEIFTLARQRCVPMEGFVTYGGLAGR 307
>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 = 45.2 bits (106), Expect = 3e-05
Identities = 63/441 (14%), Positives = 110/441 (24%), Gaps = 146/441 (33%)
Query: 26 TPPKTMIADDSISLQIDSSYCHSPNPMPSKPLQLLEERTE-----KLHSGNN-------- 72
+P + + QID ++ + + L++ + E K N
Sbjct: 194 SPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNV 253
Query: 73 -DERV---------------DK------------------------DDEQEEVEFSILGH 92
+ + K DE + + L
Sbjct: 254 QNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDC 313
Query: 93 PM-CLKRQRDCQSLPFT-KRFAVEPGLESRRAGVRAWGN--------------QSLPLAD 136
L R+ + P A ES R G+ W N SL + +
Sbjct: 314 RPQDLPRE-VLTTNPRRLSIIA-----ESIRDGLATWDNWKHVNCDKLTTIIESSLNVLE 367
Query: 137 PE----------IF----DIMEKEKQRQFKGIELI--ASENFVCRAVMEALGSH-LTNKY 179
P +F I + LI V+ L + L K
Sbjct: 368 PAEYRKMFDRLSVFPPSAHIPTIL-------LSLIWFDVIKSDVMVVVNKLHKYSLVEKQ 420
Query: 180 SEGYPGARYYTGNQYID---QIENLCFERALKAFDLDSDNWGVNVQPYSCTSANFAVYTG 236
+ + Y++ ++EN E AL +D N
Sbjct: 421 PKES---TISIPSIYLELKVKLEN---EYALHRSIVDHYNIPKTFDSDDLIPPY------ 468
Query: 237 LLLPGDRIMGLDSPSGGHLSHGYHTPGGKKVSAASIFFESFPYKVNPQTGYIDYEKLEEK 296
LD H+ G+H K + F ++D+ LE+K
Sbjct: 469 ----------LDQYFYSHI--GHHL---KNIEHPER-MTLFRMV------FLDFRFLEQK 506
Query: 297 AMDYRPKILICGGSSYPREWDYGRFRQ-IADKCGAV--LMCDMAHISGLIAAKELASPFD 353
+ + GS ++ I D L+ + I + S
Sbjct: 507 -IRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFLPKIEENLICSK-- 563
Query: 354 YCDIVTSTTHKSLRGPRGGII 374
Y D++ +L I
Sbjct: 564 YTDLL----RIALMAEDEAIF 580
Score = 41.0 bits (95), Expect = 8e-04
Identities = 42/287 (14%), Positives = 81/287 (28%), Gaps = 78/287 (27%)
Query: 141 DIMEKEKQRQFKGIELIASENFV----CRAVMEALGSHLTNK-----YSEGYPGARYYTG 191
D E Q Q+K I + + FV C+ V + S L+ + +
Sbjct: 8 DFETGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTL-- 65
Query: 192 NQYIDQIENLCF--ERALKAF--DLDSDNWG--------VNVQPYSCTSANFAVYTGLLL 239
+ L E ++ F ++ N+ QP S + + L
Sbjct: 66 --RL--FWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQP-SMMTRMYIEQRDRLY 120
Query: 240 PGDRIM----------------GL--DSPSGGHLSHGYHTPG-GKKVSAASI-----FFE 275
+++ L P+ L G G GK A +
Sbjct: 121 NDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDG--VLGSGKTWVALDVCLSYKVQC 178
Query: 276 SFPYKV------NPQTGYIDYEKLEE--KAMDYRPKILICGGSSYPR--EWDYGRFRQIA 325
+K+ N + E L++ +D S+ R+
Sbjct: 179 KMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRR-- 236
Query: 326 DKCGAVLMCDMAHISGLI-----AAKELASPFDY-CDIVTSTTHKSL 366
L+ + + L+ + + F+ C I+ +T K +
Sbjct: 237 ------LLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQV 277
Score = 37.5 bits (86), Expect = 0.008
Identities = 49/328 (14%), Positives = 94/328 (28%), Gaps = 97/328 (29%)
Query: 38 SLQIDSSYCHSP----NPMPSKPLQLLEERTEKLHSGN------NDERVDKDDE------ 81
L+I+ + SP PS ++ E+ ++L++ N N R+ +
Sbjct: 86 VLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALL 145
Query: 82 QEEVEFSILGHPM------CLKRQRDCQSLPFTKRFAVEPGLESRRAGVRAW---GNQSL 132
+ ++L + + C S + + W N +
Sbjct: 146 ELRPAKNVLIDGVLGSGKTWVALDV-CLSYKVQCKM---DF------KI-FWLNLKNCNS 194
Query: 133 PLADPEI-----FDIMEKEKQRQFKGIELIASENFVCRAVMEALGSHLTNKYSEGYPGAR 187
P E+ + I R + + ++ L L +K Y
Sbjct: 195 PETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIH----SIQAELRRLLKSK---PYE--- 244
Query: 188 YYTGNQYIDQIENLCFERALKAFDLDSDNWGVNVQPYSC----TSANFAVYTGLLLPGDR 243
N + + N+ +A AF+L SC T+ V L
Sbjct: 245 ----NCLLV-LLNVQNAKAWNAFNL------------SCKILLTTRFKQVTDFLSAATTT 287
Query: 244 IMGLDSPSGGHLSHGYHTPGGKKVSAASIFFESFPYKVNPQTGYIDYEKLEEKAMDYRPK 303
+ LD H S K + + ++ + L + + P+
Sbjct: 288 HISLD-----HHSMTLTPDEVKSL------LLKY---LD-----CRPQDLPREVLTTNPR 328
Query: 304 IL-ICGGS--SYPREWDYGRFRQI-ADK 327
L I S WD ++ + DK
Sbjct: 329 RLSIIAESIRDGLATWDN--WKHVNCDK 354
>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 = 44.6 bits (105), Expect = 3e-05
Identities = 30/217 (13%), Positives = 51/217 (23%), Gaps = 44/217 (20%)
Query: 225 SCTSANFAVYTGLLLPGDRIMGLDSPSGGHLSHGYHTPGGKKVSAASIFFESFPYK---- 280
A L+ ++ GLD S+ + + K
Sbjct: 97 QGRGAEQIYIPVLIKKREQEKGLDRSKMVAFSNYFFDTTQGHSQINGCTVRNVYIKEAFD 156
Query: 281 ---VNPQTGYIDYEKLEEKAMDY-RPKI-LIC--------GGSSYPREWDYGRFRQIADK 327
G D E LE + + I GG IA K
Sbjct: 157 TGVRYDFKGNFDLEGLERGIEEVGPNNVPYIVATITSNSAGGQPVSLAN-LKAMYSIAKK 215
Query: 328 CGAVLMCDMA-----------------HISGLIAAKELASPFDYCDIVTSTTHKSLRGPR 370
++ D A + +E + Y D++ + K P
Sbjct: 216 YDIPVVMDSARFAENAYFIKQREAEYKDWTIEQITRET---YKYADMLAMSAKKDAMVPM 272
Query: 371 GGII------FFRRGKKPRKQGIPLNHGDVVVIMISR 401
GG++ FF + R + +
Sbjct: 273 GGLLCMKDDSFFDVYTECRTLCVVQEGFPTYGGLEGG 309
>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 = 40.0 bits (93), Expect = 0.001
Identities = 73/491 (14%), Positives = 129/491 (26%), Gaps = 188/491 (38%)
Query: 3 LSSHTQSGLSLSFHSTNSSPPSPTPPKTMIADDSISLQIDSSYCHSPNPMPSKPLQLLEE 62
+ +++ L+LS S PT +S+ + QL E+
Sbjct: 1 MDAYSTRPLTLSHGSLEHVLLVPT----------------ASFFIA--------SQLQEQ 36
Query: 63 RTEKLHSGNNDERVDKDDEQE-EVE----FSILGHPMCLKRQRDCQSLP----------- 106
+ L E DDE E F LG+ + + +
Sbjct: 37 FNKILPE--PTEGFAADDEPTTPAELVGKF--LGY---VSSLVEPSKVGQFDQVLNLCLT 89
Query: 107 -FTKRFAVEPGLESRRAGVRAWGNQSLPLADPEI----FDIMEKEKQRQFKGIELI---- 157
F + L +I ++++ K ELI
Sbjct: 90 EFENCY----------------------LEGNDIHALAAKLLQENDTTLVKTKELIKNYI 127
Query: 158 ASENFVCRAVMEALGSHLTNKYSEGYPGARYYT-----GN--QYIDQIENL--------- 201
+ R + S L EG A+ GN Y +++ +L
Sbjct: 128 TARIMAKRPFDKKSNSALFRAVGEG--NAQLVAIFGGQGNTDDYFEELRDLYQTYHVLVG 185
Query: 202 -CFERALKAFD----------------LDSDNWGVNVQ-----------PYSC-----TS 228
+ + + L+ W N P SC
Sbjct: 186 DLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLIGVIQ 245
Query: 229 -ANFAVYTGLLLPGDRIMGLDSPSGGHLSHGYHTPGGKKVSAASI--------------- 272
A++ V +++G G V+A +I
Sbjct: 246 LAHYVVTA-------KLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRK 298
Query: 273 -----FF------ESFPYKVNPQTGYIDYEKLEEKAMDYRPKILICGGSSYPREWDYGRF 321
FF E++P P + D + E P + I +E +
Sbjct: 299 AITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVP--SPMLSISN---LTQE----QV 349
Query: 322 RQIADKCGAVLMCDMAHISGLIAAKELA-SPFDYCDIVTSTTHKSLRGPRGGIIFFRRGK 380
+ +K + L + I+ L + +V+ +SL G + R+ K
Sbjct: 350 QDYVNKTNSHLPAG-KQVE--IS---LVNGAKNL--VVSGPP-QSLYGLN---LTLRKAK 397
Query: 381 KPRK--QG-IP 388
P Q IP
Sbjct: 398 APSGLDQSRIP 408
>2gt1_A Lipopolysaccharide heptosyltransferase-1; GT-B fold; 1.90A
{Escherichia coli UTI89} PDB: 2h1f_A* 2h1h_A*
Length = 326
Score = 36.8 bits (86), Expect = 0.010
Identities = 15/107 (14%), Positives = 30/107 (28%), Gaps = 12/107 (11%)
Query: 232 AVYTGLLLPGDRIMGLDSPSGGHL------SHGYHTPGGKKV--SAASIFFESFPYKVNP 283
A L G + G+D + + +H + +F +S Y
Sbjct: 100 AALVTRLAHGVKH-GMDWQTAREPLASLFYNRKHHIAKQQHAVERTRELFAKSLGYSKPQ 158
Query: 284 QTGY--IDYEKLEEKAMDYRPKILICGGSSYP-REWDYGRFRQIADK 327
G I L D + ++ + W +R++
Sbjct: 159 TQGDYAIAQHFLTNLPTDAGEYAVFLHATTRDDKHWPEEHWRELIGL 205
>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 = 35.7 bits (83), Expect = 0.022
Identities = 24/165 (14%), Positives = 48/165 (29%), Gaps = 41/165 (24%)
Query: 225 SCTSANFAVYTGLLLPGDRIMGLDSPSGGHLSHGYHTPGGKKVSAASI-------FFESF 277
S +AN + + P + +D +H S+ ++
Sbjct: 127 SGWNANVGLLQTICQPNTNVY-IDF-----FAH------------MSLWEGARYANAQAH 168
Query: 278 PYKVNPQTGYIDYEKLEEKAMDYRPKILICGGSSYPREWDYGRFRQI---ADKCGAVLMC 334
P+ N + + L + P +I S Y ++ + + G L+
Sbjct: 169 PFMHN------NCDHLRMLIQRHGPG-IIVVDSIYSTLGTIAPLAELVNISKEFGCALLV 221
Query: 335 DMAHISGLIAAK-----ELASPFDYCDIVTSTTHKSLRGPRGGII 374
D +H G +T++ K+ R G I
Sbjct: 222 DESHSLGTHGPNGAGLLAELGLTREVHFMTASLAKTF-AYRAGAI 265
>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 = 35.6 bits (83), Expect = 0.026
Identities = 13/61 (21%), Positives = 25/61 (40%), Gaps = 8/61 (13%)
Query: 281 VNPQTGYIDYEKLEEKAMDYRPKILIC---GGSSYPREWDYGRFRQIADKCGAVLMCDMA 337
V+ T + E +E A+ + K +I G+ D + ++ G ++ D A
Sbjct: 108 VDRDTLMVTPEHIEA-AITPQTKAIIPVHYAGAPA----DLDAIYALGERYGIPVIEDAA 162
Query: 338 H 338
H
Sbjct: 163 H 163
>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 = 34.5 bits (80), Expect = 0.055
Identities = 44/165 (26%), Positives = 58/165 (35%), Gaps = 36/165 (21%)
Query: 225 SCTSANFAVYTGL--LLPGDRIMGLDSPSGGHLS--HGYHTPGGKKVSAASIFFESFPYK 280
S +AN A + L L PG I S S H S G G K ++
Sbjct: 114 SAYNANDATLSTLRVLFPGLIIY---SDSLNHASMIEGIKRNAGPK----------RIFR 160
Query: 281 VNPQTGYIDYEKLEEK---AMDYRPKILICGGSSYPREWDYGRFRQI---ADKCGAVLMC 334
N D L E PK LI S Y + D+G ++I A++ GA+
Sbjct: 161 HN------DVAHLRELIAADDPAAPK-LIAFESVYSMDGDFGPIKEICDIAEEFGALTYI 213
Query: 335 DMAHISGLIAAK-----ELASPFDYCDIVTSTTHKSLRGPRGGII 374
D H G+ + E DI T K+ G GG I
Sbjct: 214 DEVHAVGMYGPRGAGVAERDGLMHRIDIFNGTLAKAY-GVFGGYI 257
>3a2b_A Serine palmitoyltransferase; vitamin B6-dependent enzyme fold type
I, acyltransferase, PY phosphate; HET: PLP; 2.30A
{Sphingobacterium multivorum}
Length = 398
Score = 34.5 bits (80), Expect = 0.057
Identities = 52/234 (22%), Positives = 79/234 (33%), Gaps = 65/234 (27%)
Query: 163 VCRAVMEALGSHLTNKYSEGYPGARYYTGNQYIDQIENLCFERALKAFDLDSDNWGVNVQ 222
+ +A +AL KY G G+R+ G D L E L A+ V +
Sbjct: 62 IIKAAQDAL-----EKYGTGCAGSRFLNGTL--DIHVEL--EEKLSAY--------VGKE 104
Query: 223 P----YSCTSANFAVYTGLLLPGDRIMGLDSPSGGHLSHGYHTPGGKKVSAASI------ 272
+ +N + L+ D I+ LD H ASI
Sbjct: 105 AAILFSTGFQSNLGPLSCLMGRNDYIL-LDE-----RDH------------ASIIDGSRL 146
Query: 273 -FFESFPYKVNPQTGYIDYEKLEEK---AMDYRPKILICGGSSYPREWDYGRFRQI---A 325
F + Y N + E L K + K++ G + E D ++ A
Sbjct: 147 SFSKVIKYGHN------NMEDLRAKLSRLPEDSAKLICTDG-IFSMEGDIVNLPELTSIA 199
Query: 326 DKCGAVLMCDMAHISGLIAAK-----ELASPFDYCDIVTSTTHKSLRGPRGGII 374
++ A +M D AH G+I K D D++ T KSL GG +
Sbjct: 200 NEFDAAVMVDDAHSLGVIGHKGAGTASHFGLNDDVDLIMGTFSKSL-ASLGGFV 252
>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 = 34.3 bits (78), Expect = 0.075
Identities = 22/129 (17%), Positives = 43/129 (33%), Gaps = 13/129 (10%)
Query: 269 AASIF---FESFPYKVNPQTGYIDYEKLEEK-AMDYRPKILICGGSSYPREWDYGRF--- 321
A S ++ Y+ E +E + C S+ +
Sbjct: 192 AVSFVGMNMRLVETVLDGDRVYVPVEDIENAIKKEIELGNRPCVLSTLTF-FPPRNSDDI 250
Query: 322 ---RQIADKCGAVLMCDMAH-ISGLIAAKELASPFDY-CDIVTSTTHKSLRGPRGGIIFF 376
+I + + + A+ I ++L F Y D V S++ K+L P GG + +
Sbjct: 251 VEIAKICENYDIPHIINGAYAIQNNYYLEKLKKAFKYRVDAVVSSSDKNLLTPIGGGLVY 310
Query: 377 RRGKKPRKQ 385
+ K+
Sbjct: 311 STDAEFIKE 319
>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 = 34.2 bits (78), Expect = 0.084
Identities = 26/202 (12%), Positives = 48/202 (23%), Gaps = 37/202 (18%)
Query: 204 ERALKAFDLDSDNWGVNVQPYSCTSANFAVYTGLLLPGDRIMGLDSPSGGHLSHGYHTPG 263
+ + F+ D N ++AN V G I+ H S H
Sbjct: 202 QYIARVFNADRSYMVTN----GTSTANKIVGMYSAPAGSTIL---IDRNCHKSL-TH--- 250
Query: 264 GKKVSAASIFF-------ESFPYKVNPQ--TGYIDYEKLEEKAMDYRPKILICGGSSYPR 314
+S + + + ++++E P + S+Y
Sbjct: 251 LMMMSDVTPIYFRPTRNAYGILGGIPQSEFQHATIAKRVKETPNATWPVHAVITNSTY-- 308
Query: 315 EWDYGRF---RQIADKCGA-VLMCDMAHISGLI--------AAKELASPFDYCDIVTSTT 362
G I + D A + T +T
Sbjct: 309 ---DGLLYNTDFIKKTLDVKSIHFDSAWVPYTNFSPIYEGKCGMSGGRVEGKVIYETQST 365
Query: 363 HKSLRGPRGGIIFFRRGKKPRK 384
HK L + +G +
Sbjct: 366 HKLLAAFSQASMIHVKGDVNEE 387
>3tqx_A 2-amino-3-ketobutyrate coenzyme A ligase; energy metabolism,
transferase; HET: PLP; 2.30A {Coxiella burnetii}
Length = 399
Score = 33.7 bits (78), Expect = 0.085
Identities = 20/57 (35%), Positives = 26/57 (45%), Gaps = 5/57 (8%)
Query: 323 QIADKCGAVLMCDMAHISGLIAAK-----ELASPFDYCDIVTSTTHKSLRGPRGGII 374
+ADK A++M D +H G I E D DI+T T K+L G GG
Sbjct: 199 DLADKYNALVMVDDSHAVGFIGENGRGTPEYCGVADRVDILTGTLGKALGGASGGYT 255
>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 = 33.3 bits (77), Expect = 0.11
Identities = 36/168 (21%), Positives = 57/168 (33%), Gaps = 44/168 (26%)
Query: 225 SCTSANFAVYTGLLLPGDRIMGLDSPSGGHLSHGYHTPGGKKVSAASI-------FFESF 277
+ AN + + L G+ ++ LD+ SH ASI E
Sbjct: 132 TGYMANLGIISTLAGKGEYVI-LDA-----DSH------------ASIYDGCQQGNAEIV 173
Query: 278 PYKVNPQTGYIDYEKLEEK---AMDYRPKILICGGSSYPREWDYGRFRQI---ADKCGAV 331
++ N E L+++ K L+ Y D +++ A K GA+
Sbjct: 174 RFRHN------SVEDLDKRLGRLPKEPAK-LVVLEGVYSMLGDIAPLKEMVAVAKKHGAM 226
Query: 332 LMCDMAHISGLIAAK-----ELASPFDYCDIVTSTTHKSLRGPRGGII 374
++ D AH G E D V T KS+ G GG +
Sbjct: 227 VLVDEAHSMGFFGPNGRGVYEAQGLEGQIDFVVGTFSKSV-GTVGGFV 273
>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 = 32.9 bits (76), Expect = 0.18
Identities = 18/57 (31%), Positives = 25/57 (43%), Gaps = 5/57 (8%)
Query: 323 QIADKCGAVLMCDMAHISGLIAAK-----ELASPFDYCDIVTSTTHKSLRGPRGGII 374
+ADK A++M D +H G + E DI+T T K+L G GG
Sbjct: 201 DLADKYDALVMVDDSHAVGFVGENGRGSHEYCDVMGRVDIITGTLGKALGGASGGYT 257
>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 = 32.1 bits (74), Expect = 0.28
Identities = 12/61 (19%), Positives = 24/61 (39%), Gaps = 9/61 (14%)
Query: 281 VNPQTGYIDYEKLEEKAMDYRPKILIC---GGSSYPREWDYGRFRQIADKCGAVLMCDMA 337
+ G ID LE+ ++ R K ++ G S + +++ K + D +
Sbjct: 103 IKN-DGNIDELALEKL-INERTKAIVSVDYAGKSV----EVESVQKLCKKHSLSFLSDSS 156
Query: 338 H 338
H
Sbjct: 157 H 157
>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 = 32.1 bits (73), Expect = 0.31
Identities = 28/158 (17%), Positives = 51/158 (32%), Gaps = 31/158 (19%)
Query: 232 AVYTGL--LLPGDRIMGLDSPSGGHLSHGYHTPGGKKVSAASIFFESFPYKVNPQTGYID 289
A+ + L P I L PG + + Y +
Sbjct: 88 AILATILALKPKKVIHYLPE-----------LPGHPSIERSCKIVN---------AKYFE 127
Query: 290 YEKLE--EKAMDYRPKILICGG-SSYPRE--WDYGRFRQIADKCGAVLMCDMAHISGLIA 344
+K+ +D ++I G ++ + A A++ D A + +
Sbjct: 128 SDKVGEILNKIDKDTLVIITGSTMDLKVIELENFKKVINTAKNKEAIVFVDDASGARVRL 187
Query: 345 AKELASPFDY-CDIVTSTTHKSLRGPRGGIIFFRRGKK 381
D+V ++T K + GPRGG++ GKK
Sbjct: 188 LFNQPPALKLGADLVVTSTDKLMEGPRGGLLA---GKK 222
>3hl2_A O-phosphoseryl-tRNA(SEC) selenium transferase; selenocysteine,
sepsecs, protein-RNA complex, alternative splicing,
cytoplasm, protein biosynthesis, pyridoxal phosphate,
selenium; HET: PLR SEP; 2.81A {Homo sapiens}
Length = 501
Score = 32.0 bits (72), Expect = 0.36
Identities = 20/114 (17%), Positives = 36/114 (31%), Gaps = 12/114 (10%)
Query: 278 PYKVNPQTGYIDYEKLEEKAMDYRPKILICGGSSY----PREWDYGRFRQIADKC---GA 330
+ D + +E K + P ++C S+ PR D R ++A C
Sbjct: 190 ENVLEGDELRTDLKAVEAKVQELGPDCILCIHSTTSCFAPRVPD--RLEELAVICANYDI 247
Query: 331 VLMCDMA---HISGLIAAKELASPFDYCDIVTSTTHKSLRGPRGGIIFFRRGKK 381
+ + A S + + + D + K+ P GG I
Sbjct: 248 PHIVNNAYGVQSSKCMHLIQQGARVGRIDAFVQSLDKNFMVPVGGAIIAGFNDS 301
>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 = 32.0 bits (72), Expect = 0.42
Identities = 27/223 (12%), Positives = 59/223 (26%), Gaps = 49/223 (21%)
Query: 204 ERALKAFDLDSDNWGVNVQPYSCTSANFAVYTGLLLPGDRIMGLDSPSGGHLSHGYHTPG 263
+ A + ++ D + + ++AN V + L+ GD ++ H S Y+
Sbjct: 180 KHAARVYNADKTYFVLG----GSSNANNTVTSALVSNGDLVL---FDRNNHKS-VYN--S 229
Query: 264 GKKVSAASIFFESFPYKVNPQTGY----------------IDYEKLEEKAMDYRPKILIC 307
++ + NP E ++ +
Sbjct: 230 ALAMAGGRPVY--LQTNRNPYGFIGGIYDSDFDEKKIRELAAKVDPERAKWKRPFRLAVI 287
Query: 308 GGSSYPREWDYGRF---RQIADKCGA---VLMCDMAHISGLIAAKELASPF--------- 352
+Y G ++ + G + D A + + +
Sbjct: 288 QLGTY-----DGTIYNAHEVVKRIGHLCDYIEFDSAWVGYEQFIPMMRNSSPLLIDDLGP 342
Query: 353 -DYCDIVTSTTHKSLRGPRGGIIFFRRGKKPRKQGIPLNHGDV 394
D IV + HK G ++ + Q +H
Sbjct: 343 EDPGIIVVQSVHKQQAGFSQTSQIHKKDSHIKGQLRYCDHKHF 385
>3bc8_A O-phosphoseryl-tRNA(SEC) selenium transferase; disorder-order
transition, phosphate-loop, pyridoxal phospha
selenocysteine synthase (SECS, sepsecs); HET: LLP; 1.65A
{Mus musculus} SCOP: c.67.1.9 PDB: 3bca_A* 3bcb_A*
Length = 450
Score = 31.5 bits (71), Expect = 0.49
Identities = 20/114 (17%), Positives = 38/114 (33%), Gaps = 12/114 (10%)
Query: 278 PYKVNPQTGYIDYEKLEEKAMDYRPKILICGGSSY----PREWDYGRFRQIADKC---GA 330
+ D + +E K + P+ ++C S+ PR D R ++A C
Sbjct: 172 ENVLEGDELRTDLKAVEAKIQELGPEHILCLHSTTACFAPRVPD--RLEELAVICANYDI 229
Query: 331 VLMCDMA---HISGLIAAKELASPFDYCDIVTSTTHKSLRGPRGGIIFFRRGKK 381
+ + A S + + + D + K+ P GG I +
Sbjct: 230 PHVVNNAYGLQSSKCMHLIQQGARVGRIDAFVQSLDKNFMVPVGGAIIAGFNEP 283
>2vyc_A Biodegradative arginine decarboxylase; pyridoxal phosphate,
PLP-dependent E lyase, acid resistance; HET: LLP; 2.4A
{Escherichia coli}
Length = 755
Score = 31.6 bits (71), Expect = 0.53
Identities = 27/201 (13%), Positives = 47/201 (23%), Gaps = 50/201 (24%)
Query: 204 ERALKAFDLDSDNWGVNVQPYSCTSANFAVYTGLLLPGDRIMGLDSPSGGHLSHGYHTPG 263
+ A + F D V + +N + + D ++ H S
Sbjct: 212 KYAARVFGADRSWSVVV----GTSGSNRTIMQACMTDNDVVV---VDRNCHKSI-EQ--- 260
Query: 264 GKKVSAASIFFESFPYKVNPQTGY-------IDYEKLEEK---------AMDYRPKILIC 307
G ++ A + N + E L++K +P +
Sbjct: 261 GLMLTGAKPVY--MVPSRNRYGIIGPIYPQEMQPETLQKKISESPLTKDKAGQKPSYCVV 318
Query: 308 GGSSYPREWDYGRF---RQIADKCGA---VLMCDMAHISGLIAAKELAS----------P 351
+Y G ++ D L D A A
Sbjct: 319 TNCTY-----DGVCYNAKEAQDLLEKTSDRLHFDEAWYGYARFNPIYADHYAMRGEPGDH 373
Query: 352 FDYCDIVTSTTHKSLRGPRGG 372
T +THK L
Sbjct: 374 NGPTVFATHSTHKLLNALSQA 394
>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 = 31.3 bits (71), Expect = 0.59
Identities = 20/97 (20%), Positives = 38/97 (39%), Gaps = 5/97 (5%)
Query: 282 NPQTGYIDYEKLEEKAMDYRPKILICGGSSYP--REWDYGRFRQIADKCGAVLMCDMAHI 339
+D + +A+D +++ +Y D ++ +CGA+ + D+AH
Sbjct: 146 GYTLRLVDSPEELPQAIDQDTAVVMLTHVNYKTGYMHDMQALTALSHECGALAIWDLAHS 205
Query: 340 SGLIAAKELASPFDYCDIVTSTTHKSLRGPRGGIIFF 376
+G + + DY T+K L G G F
Sbjct: 206 AGAVPVDLHQAGADYA---IGCTYKYLNGGPGSQAFV 239
>2x3l_A ORN/Lys/Arg decarboxylase family protein; lyase; HET: LLP; 2.00A
{Staphylococcus aureus}
Length = 446
Score = 31.3 bits (71), Expect = 0.63
Identities = 28/166 (16%), Positives = 53/166 (31%), Gaps = 18/166 (10%)
Query: 227 TSANFAVYTGLLLPGDRIMGLDSPSGGHLSHGYHTPGGKKVSAASIFFESFPYKVNPQTG 286
TS +V I+ H S H +S F +P T
Sbjct: 82 TSGILSVIQSFSQKKGDILM---ARNVHKSV-LH---ALDISQQEGHF--IETHQSPLTN 132
Query: 287 ---YIDYEKLEEKAMDYRPKILICGGSSYPRE-WDYGRFRQIADKCGAVLMCDMAHISGL 342
++ +L K+++ +Y E ++ + + ++ D AH +
Sbjct: 133 HYNKVNLSRLNND----GHKLVVLTYPNYYGETFNVEEVIKSLHQLNIPVLIDEAHGAHF 188
Query: 343 IAAKELASPFDY-CDIVTSTTHKSLRGPRGGIIFFRRGKKPRKQGI 387
S +Y D V + HK+L G + + P ++ I
Sbjct: 189 GLQGFPDSTLNYQADYVVQSFHKTLPALTMGSVLYIHKNAPYRENI 234
>3ht4_A Aluminum resistance protein; lyase, putative cystathionine
BEAT-lyase, aluminium resistance protein, Q81A77_baccr,
NESG, BCR213; 2.90A {Bacillus cereus atcc 14579}
Length = 431
Score = 30.5 bits (69), Expect = 1.1
Identities = 29/166 (17%), Positives = 51/166 (30%), Gaps = 19/166 (11%)
Query: 144 EKEKQRQFKGIELIASENFVCRAVMEALGSHLTNKYSEGYPGARYY--TGNQYIDQIENL 201
E + K + + N V+E+ G H + Y G ++++
Sbjct: 19 ESQITEVHKRADEVIESNQ--FRVLESFGKHKISDSHFIPTTGYGYDDIGRDTLEKVYAD 76
Query: 202 CF--ERALKAFDLDSDNWGVNVQPYSCTSANFAVYTGLLLPGDRIMGLDSPSGGHLSHGY 259
F E L + S G T A G+L PGD ++ + L
Sbjct: 77 VFGAEAGLVRPQIIS---G--------THAISTALFGILRPGDELLYITGKPYDTLEEIV 125
Query: 260 HTPGGKKVSAASIFFESFPYKVNPQTGYIDYEKLEEKAMDYRPKIL 305
G S + G +D+E + A+ K++
Sbjct: 126 GVRGKGVGSFKEYNIGYNAVPLTE-GGLVDFEAV-AAAIHSNTKMI 169
>3lk7_A UDP-N-acetylmuramoylalanine--D-glutamate ligase; agalacitae, PSI,
MCSG, structural genomics, midwest center for structural
genomics; HET: MSE; 1.50A {Streptococcus agalactiae}
Length = 451
Score = 30.2 bits (69), Expect = 1.4
Identities = 8/39 (20%), Positives = 12/39 (30%), Gaps = 3/39 (7%)
Query: 296 KAMDYRPKILICGGSSYPREWDYGRFRQIADKC-GAVLM 333
D ILI GG R ++ V++
Sbjct: 342 SGFDNTKVILIAGG--LDRGNEFDELIPDITGLKHMVVL 378
>3p3b_A Mandelate racemase/muconate lactonizing protein; enolase
superfamily fold, galacturonate dehydratase, D-tartr
galacturonate, lyase; HET: TAR; 1.65A {Geobacillus SP}
PDB: 3ops_A* 3n4f_A* 3qpe_A*
Length = 392
Score = 30.0 bits (68), Expect = 1.5
Identities = 11/73 (15%), Positives = 16/73 (21%), Gaps = 13/73 (17%)
Query: 287 YIDYEKLEEKAMDYRPKILICGGSSYPREWDYGR--FRQIADKCGAVLMCDMAH--ISGL 342
YE L+E +LI G E VL D+ +
Sbjct: 240 EALYEDLKEWLGQRGQNVLIADG-----EGLASPHLIEWATRGRVDVLQYDIIWPGFTHW 294
Query: 343 --IAAKELASPFD 353
+
Sbjct: 295 MELGE--KLDAHG 305
>1c7n_A Cystalysin; transferase, aminotransferase, pyridoxal phosphate;
HET: PLP; 1.90A {Treponema denticola} SCOP: c.67.1.3
PDB: 1c7o_A*
Length = 399
Score = 29.8 bits (68), Expect = 1.7
Identities = 8/20 (40%), Positives = 13/20 (65%)
Query: 287 YIDYEKLEEKAMDYRPKILI 306
ID++KLE+ + D K L+
Sbjct: 150 TIDFQKLEKLSKDKNNKALL 169
>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 = 29.8 bits (68), Expect = 1.7
Identities = 4/19 (21%), Positives = 11/19 (57%)
Query: 288 IDYEKLEEKAMDYRPKILI 306
+++ LEEK ++++
Sbjct: 147 VNWADLEEKLATPSVRMMV 165
>3l8a_A METC, putative aminotransferase, probable beta-cystathi;
beta-cystathionase, lyase; HET: PLP; 1.54A
{Streptococcus mutans}
Length = 421
Score = 29.4 bits (67), Expect = 2.0
Identities = 8/19 (42%), Positives = 13/19 (68%)
Query: 288 IDYEKLEEKAMDYRPKILI 306
ID+E+LE+ +D KI +
Sbjct: 181 IDFEQLEKDIIDNNVKIYL 199
>4eef_G F-HB80.4, designed hemagglutinin binding protein; immunoglobulin,
fusion of virus membrane with membrane, membrane fusion,
sialic acid, virion; HET: NAG BMA; 2.70A {Artificial
gene}
Length = 74
Score = 27.1 bits (60), Expect = 2.1
Identities = 9/20 (45%), Positives = 11/20 (55%), Gaps = 1/20 (5%)
Query: 199 ENLCFERALKAFDLD-SDNW 217
EN+ FE AL + D D W
Sbjct: 27 ENIAFEIALSFTNKDTPDRW 46
>3b1d_A Betac-S lyase; HET: PLP PLS EPE; 1.66A {Streptococcus anginosus}
PDB: 3b1c_A* 3b1e_A*
Length = 392
Score = 29.4 bits (67), Expect = 2.3
Identities = 6/19 (31%), Positives = 12/19 (63%)
Query: 288 IDYEKLEEKAMDYRPKILI 306
ID+E+LE ++ K+ +
Sbjct: 151 IDFEQLENDIVENDVKLYL 169
>1d2f_A MALY protein; aminotransferase fold, large PLP-binding domain,
small C-TER domain, open alpha-beta structure.,
transferase; HET: PLP; 2.50A {Escherichia coli} SCOP:
c.67.1.3
Length = 390
Score = 29.4 bits (67), Expect = 2.5
Identities = 6/20 (30%), Positives = 9/20 (45%)
Query: 287 YIDYEKLEEKAMDYRPKILI 306
+ D KLE KI++
Sbjct: 148 FCDMGKLEAVLAKPECKIML 167
>1f4p_A Flavodoxin; electron transport, flavoprotein, FMN, 3D-STRCTURE,
anisotropic refinement, redox protein; HET: FMN; 1.30A
{Desulfovibrio vulgaris} SCOP: c.23.5.1 PDB: 1bu5_A*
1c7f_A* 1c7e_A* 1akr_A* 1fx1_A* 1akt_A* 1akq_A* 1aku_A*
1akv_A* 1azl_A* 1j8q_A* 2fx2_A* 3fx2_A* 4fx2_A* 5fx2_A*
1akw_A* 1i1o_A* 1wsw_A* 1wsb_A* 1xyv_A* ...
Length = 147
Score = 28.4 bits (64), Expect = 2.5
Identities = 17/69 (24%), Positives = 20/69 (28%), Gaps = 18/69 (26%)
Query: 302 PKILICGGSSYPREWDYGRFRQIADKCGAVL--------MCDMAHISGLIAAKELASPFD 353
PK LI GS G A+ L D A + A L FD
Sbjct: 1 PKALIVYGS------TTGNTEYTAETIARELADAGYEVDSRDAASVE----AGGLFEGFD 50
Query: 354 YCDIVTSTT 362
+ ST
Sbjct: 51 LVLLGCSTW 59
>2cjj_A Radialis; plant development, DNA-binding protein, MYB transcription
FA DNA-binding, nuclear protein, floral asymmetry; 1.9A
{Antirrhinum majus} SCOP: a.4.1.3
Length = 93
Score = 27.1 bits (60), Expect = 3.8
Identities = 11/20 (55%), Positives = 13/20 (65%), Gaps = 1/20 (5%)
Query: 199 ENLCFERALKAFDLDS-DNW 217
EN FERAL +D D+ D W
Sbjct: 15 ENKAFERALAVYDKDTPDRW 34
>2uuu_A Alkyldihydroxyacetonephosphate synthase; transferase, lavoprotein,
lipid synthesis, peroxisomal disor; HET: FAD PL3; 1.95A
{Dictyostelium discoideum} PDB: 2uuv_A*
Length = 584
Score = 28.5 bits (64), Expect = 3.9
Identities = 15/65 (23%), Positives = 23/65 (35%), Gaps = 11/65 (16%)
Query: 246 GLDSPSGGHLSHGYHTPGGKKVSAASIFFESFPYKVNPQTGYIDYEKLEEKAMDYRPKIL 305
G+ + H+SH Y ++F F K N Y + ++ D I
Sbjct: 485 GIPAWICAHISHTYTNG-------VCLYF-IFASKQNENKDMAQYIEAKKLMTD---IIF 533
Query: 306 ICGGS 310
GGS
Sbjct: 534 KYGGS 538
>3lws_A Aromatic amino acid beta-eliminating lyase/threonine aldolase;
structural genomics, joint center for structural
genomics, JCSG; HET: LLP MSE; 2.00A {Exiguobacterium
sibiricum}
Length = 357
Score = 28.4 bits (64), Expect = 4.0
Identities = 27/185 (14%), Positives = 46/185 (24%), Gaps = 46/185 (24%)
Query: 225 SCTSANFAVYTGLLLPGD-RIMGLDSPSGGHLSHGYHTPGGKKVSAASIFFESFPYKVNP 283
S T A D R + L H V
Sbjct: 70 SGTMAQQVALRIWSDETDNRTVAYH-----PLCHLEIHEQD----GLKELHPIETILVGA 120
Query: 284 QTGYIDYEKLEEKAMDYRPKI-LIC--------GGSSYPREWDY-GRFRQIADKCGAVLM 333
+ ++++ P I + GG + + + + G L
Sbjct: 121 ADRLMTLDEIK-----ALPDIACLLLELPQREIGGVAPA--FSELETISRYCRERGIRLH 173
Query: 334 CD-----MAHISGLIAAKELASPFDYCDIVTSTT---HKSLRGPRGGII-----FFRRGK 380
D A E+A FD S +K L G G I+ F + +
Sbjct: 174 LDGARLFEMLPYYEKTAAEIAGLFD------SIYISFYKGLGGIAGAILAGPAAFCQTAR 227
Query: 381 KPRKQ 385
+++
Sbjct: 228 IWKRR 232
>3hvy_A Cystathionine beta-lyase family protein, YNBB B.S ortholog;
NP_348457.1, putative cystathionine beta-lyase involved
in A resistance; HET: LLP MSE; 2.00A {Clostridium
acetobutylicum}
Length = 427
Score = 28.2 bits (63), Expect = 4.6
Identities = 33/171 (19%), Positives = 60/171 (35%), Gaps = 27/171 (15%)
Query: 136 DPEIFDIMEKEKQR---QFKGIELIASENFVCRAVMEALGSHLTNKYSEGYPG--ARY-Y 189
+ + ++ E+ +FK + I N V++A + SE + + Y Y
Sbjct: 17 NERVLELYERALNDVEKEFKYYDEIREYNQ--LKVLKAF---QEERISESHFTNSSGYGY 71
Query: 190 T--GNQYIDQIENLCF--ERALKAFDLDSDNWGVNVQPYSCTSANFAVYTGLLLPGDRIM 245
G +D++ F E A + G T A A G L P D +M
Sbjct: 72 NDIGRDSLDRVYANIFNTESAFVRPHFVN---G--------THAIGAALFGNLRPNDTMM 120
Query: 246 GLDSPSGGHLSHGYHTPGGKKVSAASIFFESFPYKVNPQTGYIDYEKLEEK 296
+ L KKV + + + V+ + G +D ++E+
Sbjct: 121 SICGMPYDTLHDIIGMDDSKKVGSLREYGVKYKM-VDLKDGKVDINTVKEE 170
>3bb8_A CDP-4-keto-6-deoxy-D-glucose-3-dehydrase; aspartate
aminotransferase fold, oxidoreductase; HET: PLP; 2.35A
{Yersinia pseudotuberculosis} PDB: 3bcx_A
Length = 437
Score = 28.0 bits (63), Expect = 5.7
Identities = 12/62 (19%), Positives = 23/62 (37%), Gaps = 10/62 (16%)
Query: 281 VNPQTGYIDYEKLEEKAMDYRPKILI----CGGSSYPREWDYGRFRQIADKCGAVLMCDM 336
V+ T ++ +E D + K ++ G + R++ADK L+ D
Sbjct: 139 VDIPTYNVNASLIEAAVSD-KTKAIMIAHTLG---NLFDLA--EVRRVADKYNLWLIEDC 192
Query: 337 AH 338
Sbjct: 193 CD 194
>3jzl_A Putative cystathionine beta-lyase involved in ALU resistance;
putative cystathionine beta-lyase involved in aluminum
resis structural genomics; HET: LLP; 1.91A {Listeria
monocytogenes str} PDB: 3fd0_A*
Length = 409
Score = 27.8 bits (62), Expect = 6.5
Identities = 46/253 (18%), Positives = 78/253 (30%), Gaps = 47/253 (18%)
Query: 144 EKEKQRQFKGIELIASENFVCRAVMEAL------GSHLTNKYSEGYPGARYYTGNQYIDQ 197
E + + IA N V++A H GY G +++
Sbjct: 13 ETQIDDLQNKTDEIAEFNQ--AKVLDAFQENKVSDFHFHPSTGYGY--DD--EGRDTLER 66
Query: 198 IENLCF--ERALKAFDLDSDNWGVNVQPYSCTSANFAVYTGLLLPGDRIMGLDSPSGGHL 255
+ F E AL Q S T A V G+L P D ++ + L
Sbjct: 67 VYATVFKTEAALVRP-----------QIISGTHAISTVLFGILRPDDELLYITGQPYDTL 115
Query: 256 SHGYHTPGGKKVSAAS--IFFESFPYKVNPQTGYIDYEKLEEKAMDYRPKILICGGSSYP 313
+ S I + S P N G +D+ ++ K M + K++ S
Sbjct: 116 EEIVGIRKQGQGSLKDFHIGYSSVPLLEN---GDVDFPRI-AKKMTPKTKMIGIQRSRGY 171
Query: 314 REWDYGRFRQIADKC--------GAVLMCDMAHISGLIAAKELASPFDY-CDIVTSTTHK 364
+ +I + ++ D + + E P + DI+ + K
Sbjct: 172 ADRPSFTIEKIKEMIVFVKNINPEVIVFVDNCYGEFV----EYQEPPEVGADIIAGSLIK 227
Query: 365 SLRG---PRGGII 374
+ G GG I
Sbjct: 228 NPGGGLAKTGGYI 240
>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB,
transcription factor, DNA-binding, DNA-directed RNA
polymerase; 4.30A {Saccharomyces cerevisiae}
Length = 197
Score = 27.3 bits (60), Expect = 7.9
Identities = 9/48 (18%), Positives = 16/48 (33%), Gaps = 6/48 (12%)
Query: 291 EKLEEKAMDYRPKILI------CGGSSYPREWDYGRFRQIADKCGAVL 332
E ++++A P + I C + + CG VL
Sbjct: 5 ESIDKRAGRRGPNLNIVLTCPECKVYPPKIVERFSEGDVVCALCGLVL 52
>2q62_A ARSH; alpha/beta, flavoprotein; 1.80A {Sinorhizobium meliloti}
Length = 247
Score = 27.2 bits (60), Expect = 8.5
Identities = 11/38 (28%), Positives = 13/38 (34%)
Query: 273 FFESFPYKVNPQTGYIDYEKLEEKAMDYRPKILICGGS 310
P Q D L +RP+ILI GS
Sbjct: 6 SSHDLPAANLQQLRLPDSASLRPAFSTHRPRILILYGS 43
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 0.136 0.414
Gapped
Lambda K H
0.267 0.0610 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 6,391,310
Number of extensions: 391133
Number of successful extensions: 995
Number of sequences better than 10.0: 1
Number of HSP's gapped: 966
Number of HSP's successfully gapped: 60
Length of query: 403
Length of database: 6,701,793
Length adjustment: 96
Effective length of query: 307
Effective length of database: 4,021,377
Effective search space: 1234562739
Effective search space used: 1234562739
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: 58 (26.4 bits)