RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 009673
(529 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 = 821 bits (2123), Expect = 0.0
Identities = 272/463 (58%), Positives = 334/463 (72%), Gaps = 9/463 (1%)
Query: 76 SSFVDYSLGEADPEVCEIITKEKERQFKSLELIASENFTSRAVMEAVGSCLTNKYSEGLP 135
+ L ++D EV +II KE RQ LELIASENF SRAV+EA+GSCL NKYS G P
Sbjct: 18 EQMLAQPLKDSDAEVYDIIKKESNRQRVGLELIASENFASRAVLEALGSCLNNKYSLGYP 77
Query: 136 GKRYYGGNEYIDELETLCQKRALAAFNLDENKWGVNVQPLSGSPANFEVYTAILKPHDRI 195
G+RYYGG E+IDELETLCQKRAL A+ LD WGVNVQP SGSPANF VYTA+++PH RI
Sbjct: 78 GQRYYGGTEHIDELETLCQKRALQAYGLDPQCWGVNVQPYSGSPANFAVYTALVEPHGRI 137
Query: 196 MGLDLPHGGHLSHGFMTPKRRVSGTSIYFESMPYRLDESTGLVDYDMLEKTAILFRPKLI 255
MGLDLP GGHL+HGFMT K+++S TSI+FESM Y+++ TG +DYD LE+ A LF PKLI
Sbjct: 138 MGLDLPDGGHLTHGFMTDKKKISATSIFFESMAYKVNPDTGYIDYDRLEENARLFHPKLI 197
Query: 256 IAGASAYPRDFDYPRMRQIADAVGALLMMDMAHISGLVAASVVADPFKYCDVVTTTTHKS 315
IAG S Y R+ DY R+R+IAD GA LM DMAHISGLV A VV PF++C VVTTTTHK+
Sbjct: 198 IAGTSCYSRNLDYGRLRKIADENGAYLMADMAHISGLVVAGVVPSPFEHCHVVTTTTHKT 257
Query: 316 LRGPRGGMIFFKKDP---------VLGVELESAINNAVFPGLQGGPHNHTIGGLAVCLKH 366
LRG R GMIF+++ + LES IN+AVFPGLQGGPHNH I G+AV LK
Sbjct: 258 LRGCRAGMIFYRRGVRSVDPKTGKEILYNLESLINSAVFPGLQGGPHNHAIAGVAVALKQ 317
Query: 367 AQSPEFKVYQNKVVSNCRALASRLVELGYKLVSGGSDNHLVLVDLRPMGIDGARVEKILD 426
A +PEFK YQ +VV+NCRAL++ LVELGYK+V+GGSDNHL+LVDLR G DG R EK+L+
Sbjct: 318 AMTPEFKEYQRQVVANCRALSAALVELGYKIVTGGSDNHLILVDLRSKGTDGGRAEKVLE 377
Query: 427 MASITLNKNSVPGDKSALVPGGIRIGSPAMTTRGFSEKEFVAIADFIHEGVEITLEAKKL 486
SI NKN+ PGDKSAL P G+R+G+PA+T+RG EK+F +A FIH G+E+T++ +
Sbjct: 378 ACSIACNKNTCPGDKSALRPSGLRLGTPALTSRGLLEKDFQKVAHFIHRGIELTVQIQDD 437
Query: 487 VQGSKLQDFMNFVTSPNFSLMNNVADLRGRVEALTTQFPIPGV 529
+ + V LR VE+ FP+PG+
Sbjct: 438 TGPRATLKEFKEKLAGDEKHQRAVRALRQEVESFAALFPLPGL 480
>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 = 818 bits (2114), Expect = 0.0
Identities = 272/479 (56%), Positives = 344/479 (71%), Gaps = 12/479 (2%)
Query: 59 RPPSSVSVPIPEIGGDGSSFVDYSLGEADPEVCEIITKEKERQFKSLELIASENFTSRAV 118
R S + + SL ++DPE+ E++ +EK+RQ + LELIASENF SRA
Sbjct: 11 RAQHSNAAQTQTGEANRGWTGQESLSDSDPEMWELLQREKDRQCRGLELIASENFCSRAA 70
Query: 119 MEAVGSCLTNKYSEGLPGKRYYGGNEYIDELETLCQKRALAAFNLDENKWGVNVQPLSGS 178
+EA+GSCL NKYSEG PGKRYYGG E +DE+E LCQ+RAL AF+LD +WGVNVQP SGS
Sbjct: 71 LEALGSCLNNKYSEGYPGKRYYGGAEVVDEIELLCQRRALEAFDLDPAQWGVNVQPYSGS 130
Query: 179 PANFEVYTAILKPHDRIMGLDLPHGGHLSHGFMTPKRRVSGTSIYFESMPYRLDESTGLV 238
PAN VYTA+L+PHDRIMGLDLP GGHL+HG+M+ +R+S TSI+FESMPY+L+ TGL+
Sbjct: 131 PANLAVYTALLQPHDRIMGLDLPDGGHLTHGYMSDVKRISATSIFFESMPYKLNPKTGLI 190
Query: 239 DYDMLEKTAILFRPKLIIAGASAYPRDFDYPRMRQIADAVGALLMMDMAHISGLVAASVV 298
DY+ L TA LFRP+LIIAG SAY R DY RMR++ D V A L+ DMAHISGLVAA V+
Sbjct: 191 DYNQLALTARLFRPRLIIAGTSAYARLIDYARMREVCDEVKAHLLADMAHISGLVAAKVI 250
Query: 299 ADPFKYCDVVTTTTHKSLRGPRGGMIFFKKDP---------VLGVELESAINNAVFPGLQ 349
PFK+ D+VTTTTHK+LRG R G+IF++K + E IN AVFP LQ
Sbjct: 251 PSPFKHADIVTTTTHKTLRGARSGLIFYRKGVKAVDPKTGREIPYTFEDRINFAVFPSLQ 310
Query: 350 GGPHNHTIGGLAVCLKHAQSPEFKVYQNKVVSNCRALASRLVELGYKLVSGGSDNHLVLV 409
GGPHNH I +AV LK A +P F+ Y +V+ N RA+A L+E GY LVSGG+DNHLVLV
Sbjct: 311 GGPHNHAIAAVAVALKQACTPMFREYSLQVLKNARAMADALLERGYSLVSGGTDNHLVLV 370
Query: 410 DLRPMGIDGARVEKILDMASITLNKNSVPGDKSALVPGGIRIGSPAMTTRGFSEKEFVAI 469
DLRP G+DGAR E++L++ SIT NKN+ PGD+SA+ PGG+R+G+PA+T+R F E +F +
Sbjct: 371 DLRPKGLDGARAERVLELVSITANKNTCPGDRSAITPGGLRLGAPALTSRQFREDDFRRV 430
Query: 470 ADFIHEGVEITLEAKKLVQGSKLQDFMNFVTSPNFSLMNNVADLRGRVEALTTQFPIPG 528
DFI EGV I LE K + +KLQDF +F+ + +A+LR RVE FP+PG
Sbjct: 431 VDFIDEGVNIGLEVKS--KTAKLQDFKSFLLK-DSETSQRLANLRQRVEQFARAFPMPG 486
>2dkj_A Serine hydroxymethyltransferase; PLP dependent enzyme, structural
genomics; HET: PLP; 1.15A {Thermus thermophilus}
Length = 407
Score = 581 bits (1500), Expect = 0.0
Identities = 202/447 (45%), Positives = 262/447 (58%), Gaps = 43/447 (9%)
Query: 82 SLGEADPEVCEIITKEKERQFKSLELIASENFTSRAVMEAVGSCLTNKYSEGLPGKRYYG 141
S + D + E+I E++RQ + LELIASENF S+ V EAVGS LTNKY+EG PG RYYG
Sbjct: 3 STLKRDEALFELIALEEKRQREGLELIASENFVSKQVREAVGSVLTNKYAEGYPGARYYG 62
Query: 142 GNEYIDELETLCQKRALAAFNLDENKWGVNVQPLSGSPANFEVYTAILKPHDRIMGLDLP 201
G E ID +E+L +RA A F NVQP SGS AN VY A+++P D +MG+DL
Sbjct: 63 GCEVIDRVESLAIERAKALFGAAW----ANVQPHSGSQANMAVYMALMEPGDTLMGMDLA 118
Query: 202 HGGHLSHGFMTPKRRVSGTSIYFESMPYRLDESTGLVDYDMLEKTAILFRPKLIIAGASA 261
GGHL+HG + SG ++ + Y + T L+D + + + A+ RPK+I+AGASA
Sbjct: 119 AGGHLTHGS---RVNFSG--KLYKVVSYGVRPDTELIDLEEVRRLALEHRPKVIVAGASA 173
Query: 262 YPRDFDYPRMRQIADAVGALLMMDMAHISGLVAASVVADPFKYCDVVTTTTHKSLRGPRG 321
YPR +D+ R+IAD VGA L++DMAH +GLVAA + +P Y VVT+TTHK+LRGPRG
Sbjct: 174 YPRFWDFKAFREIADEVGAYLVVDMAHFAGLVAAGLHPNPLPYAHVVTSTTHKTLRGPRG 233
Query: 322 GMIFFKKDPVLGVELESAINNAVFPGLQGGPHNHTIGGLAVCLKHAQSPEFKVYQNKVVS 381
G+I EL I+ +FPG+QGGP H I G AV A PEFK Y VV
Sbjct: 234 GLILSNDP-----ELGKRIDKLIFPGIQGGPLEHVIAGKAVAFFEALQPEFKEYSRLVVE 288
Query: 382 NCRALASRLVELGYKLVSGGSDNHLVLVDLRPMGIDGARVEKILDMASITLNKNSVPGD- 440
N + LA L GY++V+GG+DNHL LVDLRP G+ G E+ LD IT+NKN++P D
Sbjct: 289 NAKRLAEELARRGYRIVTGGTDNHLFLVDLRPKGLTGKEAEERLDAVGITVNKNAIPFDP 348
Query: 441 KSALVPGGIRIGSPAMTTRGFSEKEFVAIADFIHEGVEITLEAKKLVQGSKLQDFMNFVT 500
K V GIRIG+PA+TTRGF+ +E +A+ I L
Sbjct: 349 KPPRVTSGIRIGTPAITTRGFTPEEMPLVAELIDR----ALLEG---------------- 388
Query: 501 SPNFSLMNNVADLRGRVEALTTQFPIP 527
LR V L P+P
Sbjct: 389 --------PSEALREEVRRLALAHPMP 407
>3ecd_A Serine hydroxymethyltransferase 2; ssgcid, decode, bupsa00008A,
one-carbon metabolism, pyridoxa phosphate, structural
genomics; 1.60A {Burkholderia pseudomallei}
Length = 425
Score = 581 bits (1499), Expect = 0.0
Identities = 207/454 (45%), Positives = 269/454 (59%), Gaps = 34/454 (7%)
Query: 74 DGSSFVDYSLGEADPEVCEIITKEKERQFKSLELIASENFTSRAVMEAVGSCLTNKYSEG 133
+ + F SL E D V I KE ERQ +ELIASEN SRAV++A GS LTNKY+EG
Sbjct: 4 NANPFFSQSLAERDASVRGAILKELERQQSQVELIASENIVSRAVLDAQGSVLTNKYAEG 63
Query: 134 LPGKRYYGGNEYIDELETLCQKRALAAFNLDENKWGVNVQPLSGSPANFEVYTAILKPHD 193
PGKRYYGG E+ DE+E L +R FN NVQP SG+ AN V A+ KP D
Sbjct: 64 YPGKRYYGGCEFADEVEALAIERVKRLFNAGH----ANVQPHSGAQANGAVMLALAKPGD 119
Query: 194 RIMGLDLPHGGHLSHGFMTPKRRVSGTSIYFESMPYRLDESTGLVDYDMLEKTAILFRPK 253
++G+ L GGHL+HG K +SG +F ++ Y + T L+DYD +E A +P
Sbjct: 120 TVLGMSLDAGGHLTHGA---KPALSG--KWFNALQYGVSRDTMLIDYDQVEALAQQHKPS 174
Query: 254 LIIAGASAYPRDFDYPRMRQIADAVGALLMMDMAHISGLVAASVVADPFKYCDVVTTTTH 313
LIIAG SAYPR D+ R R IAD+VGA LM+DMAHI+G++AA A+P ++ VVT+TTH
Sbjct: 175 LIIAGFSAYPRKLDFARFRAIADSVGAKLMVDMAHIAGVIAAGRHANPVEHAHVVTSTTH 234
Query: 314 KSLRGPRGGMIFFKKDPVLGVELESAINNAVFPGLQGGPHNHTIGGLAVCLKHAQSPEFK 373
K+LRGPRGG + + E+ IN+AVFPGLQGGP H I G AV A + +FK
Sbjct: 235 KTLRGPRGGFVLTNDE-----EIAKKINSAVFPGLQGGPLMHVIAGKAVAFGEALTDDFK 289
Query: 374 VYQNKVVSNCRALASRLVELGYKLVSGGSDNHLVLVDLRPMGIDGARVEKILDMASITLN 433
Y ++V++N +AL L G LV+GG+DNHL+LVDLRP G+ GA+VE+ L+ A IT N
Sbjct: 290 TYIDRVLANAQALGDVLKAGGVDLVTGGTDNHLLLVDLRPKGLKGAQVEQALERAGITCN 349
Query: 434 KNSVPGD-KSALVPGGIRIGSPAMTTRGFSEKEFVAIADFIHEGVEITLEAKKLVQGSKL 492
KN +P D + + GIR+G+PA TTRGF EF + I E EA +
Sbjct: 350 KNGIPFDPEKPTITSGIRLGTPAGTTRGFGAAEFREVGRLILE----VFEALRTNPEGDH 405
Query: 493 QDFMNFVTSPNFSLMNNVADLRGRVEALTTQFPI 526
+R + AL +FPI
Sbjct: 406 A---------------TEQRVRREIFALCERFPI 424
>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 = 581 bits (1499), Expect = 0.0
Identities = 200/450 (44%), Positives = 272/450 (60%), Gaps = 38/450 (8%)
Query: 80 DYSLGEADPEVCEIITKEKERQFKSLELIASENFTSRAVMEAVGSCLTNKYSEGLPGKRY 139
+ ++ + D E+ + + +EK RQ + +ELIASEN+TS VM+A GS LTNKY+EG PGKRY
Sbjct: 8 EMNIADYDAELWQAMEQEKVRQEEHIELIASENYTSPRVMQAQGSQLTNKYAEGYPGKRY 67
Query: 140 YGGNEYIDELETLCQKRALAAFNLDENKWGVNVQPLSGSPANFEVYTAILKPHDRIMGLD 199
YGG EY+D +E L RA F D NVQP SGS ANF VYTA+L+P D ++G++
Sbjct: 68 YGGCEYVDVVEQLAIDRAKELFGADY----ANVQPHSGSQANFAVYTALLQPGDTVLGMN 123
Query: 200 LPHGGHLSHGFMTPKRRVSGTSIYFESMPYRLDESTGLVDYDMLEKTAILFRPKLIIAGA 259
L GGHL+HG SG + +PY +DE +G +DYD + K A +PK+II G
Sbjct: 124 LAQGGHLTHG---SPVNFSG--KLYNIVPYGIDE-SGKIDYDEMAKLAKEHKPKMIIGGF 177
Query: 260 SAYPRDFDYPRMRQIADAVGALLMMDMAHISGLVAASVVADPFKYCDVVTTTTHKSLRGP 319
SAY D+ +MR+IAD++GA L +DMAH++GL+AA V +P + VVTTTTHK+L GP
Sbjct: 178 SAYSGVVDWAKMREIADSIGAYLFVDMAHVAGLIAAGVYPNPVPHAHVVTTTTHKTLAGP 237
Query: 320 RGGMIFFKKDPVLGVELESAINNAVFPGLQGGPHNHTIGGLAVCLKHAQSPEFKVYQNKV 379
RGG+I K EL +N+AVFP QGGP H I G AV LK A PEFKVYQ +V
Sbjct: 238 RGGLILAKGG---DEELYKKLNSAVFPSAQGGPLMHVIAGKAVALKEAMEPEFKVYQQQV 294
Query: 380 VSNCRALASRLVELGYKLVSGGSDNHLVLVDLRPMGIDGARVEKILDMASITLNKNSVPG 439
N +A+ + GYK+VSGG++NHL L+DL + G + L A+IT+NKNSVP
Sbjct: 295 AKNAKAMVEVFLNRGYKVVSGGTENHLFLLDLVDKNLTGKEADAALGRANITVNKNSVPN 354
Query: 440 D-KSALVPGGIRIGSPAMTTRGFSEKEFVAIADFIHEGVEITLEAKKLVQGSKLQDFMNF 498
D KS V GIRIGSPA+T RGF E E +A ++ + ++
Sbjct: 355 DPKSPFVTSGIRIGSPAVTRRGFKEAEVKELAGWMCDVLD-------------------- 394
Query: 499 VTSPNFSLMNNVADLRGRVEALTTQFPIPG 528
N + + ++ +V + +FP+
Sbjct: 395 ----NINDEATIERVKAKVLDICARFPVYA 420
>3n0l_A Serine hydroxymethyltransferase; alpha beta class, 3-layer(ABA)
sandwich, CSGI transferase, structural genomics; HET:
MSE; 1.80A {Campylobacter jejuni}
Length = 417
Score = 578 bits (1491), Expect = 0.0
Identities = 191/446 (42%), Positives = 265/446 (59%), Gaps = 40/446 (8%)
Query: 82 SLGEADPEVCEIITKEKERQFKSLELIASENFTSRAVMEAVGSCLTNKYSEGLPGKRYYG 141
SL D E+ ++ KE ERQ + LE+IASENFT VME +GS LTNKY+EG PGKRYYG
Sbjct: 5 SLEMFDKEIFDLTNKELERQCEGLEMIASENFTLPEVMEVMGSILTNKYAEGYPGKRYYG 64
Query: 142 GNEYIDELETLCQKRALAAFNLDENKWGVNVQPLSGSPANFEVYTAILKPHDRIMGLDLP 201
G E++DE+ETL +R FN NVQP SGS AN VY A++ P D+I+G+DL
Sbjct: 65 GCEFVDEIETLAIERCKKLFNCKF----ANVQPNSGSQANQGVYAALINPGDKILGMDLS 120
Query: 202 HGGHLSHGFMTPKRRVSGTSIYFESMPYRLDESTGLVDYDMLEKTAILFRPKLIIAGASA 261
HGGHL+HG K SG +ES Y ++ G +DY+ + + A +PKLI+ GASA
Sbjct: 121 HGGHLTHG---AKVSSSG--KMYESCFYGVEL-DGRIDYEKVREIAKKEKPKLIVCGASA 174
Query: 262 YPRDFDYPRMRQIADAVGALLMMDMAHISGLVAASVVADPFKYCDVVTTTTHKSLRGPRG 321
Y R D+ + R+IAD +GA L D+AHI+GLV A PF Y VV++TTHK+LRGPRG
Sbjct: 175 YARVIDFAKFREIADEIGAYLFADIAHIAGLVVAGEHPSPFPYAHVVSSTTHKTLRGPRG 234
Query: 322 GMIFFKKDPVLGVELESAINNAVFPGLQGGPHNHTIGGLAVCLKHAQSPEFKVYQNKVVS 381
G+I + EL IN+A+FPG+QGGP H I AV K S E+KVY +V +
Sbjct: 235 GIIMTNDE-----ELAKKINSAIFPGIQGGPLMHVIAAKAVGFKFNLSDEWKVYAKQVRT 289
Query: 382 NCRALASRLVELGYKLVSGGSDNHLVLVDLRPMGIDGARVEKILDMASITLNKNSVPGD- 440
N + LA+ L++ +KLVS G+DNHLVL+ G + L A IT NKN+VPG+
Sbjct: 290 NAQVLANVLMDRKFKLVSDGTDNHLVLMSFLDREFSGKDADLALGNAGITANKNTVPGEI 349
Query: 441 KSALVPGGIRIGSPAMTTRGFSEKEFVAIADFIHEGVEITLEAKKLVQGSKLQDFMNFVT 500
+S + G+R+G+PA+T RGF EKE ++++I + ++
Sbjct: 350 RSPFITSGLRLGTPALTARGFKEKEMEIVSNYIADILD---------------------- 387
Query: 501 SPNFSLMNNVADLRGRVEALTTQFPI 526
+ + +++ ++ L + F I
Sbjct: 388 --DVNNEKLQENIKQELKKLASNFII 411
>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 = 576 bits (1488), Expect = 0.0
Identities = 195/395 (49%), Positives = 257/395 (65%), Gaps = 16/395 (4%)
Query: 82 SLGEADPEVCEIITKEKERQFKSLELIASENFTSRAVMEAVGSCLTNKYSEGLPGKRYYG 141
L + DP+V I +E++RQ +ELIASENF SRAVMEA GS LTNKY+EG PG+RYYG
Sbjct: 3 YLPQQDPQVFAAIEQERKRQHAKIELIASENFVSRAVMEAQGSVLTNKYAEGYPGRRYYG 62
Query: 142 GNEYIDELETLCQKRALAAFNLDENKWGVNVQPLSGSPANFEVYTAILKPHDRIMGLDLP 201
G EY+D +E L ++RA F + NVQP SG+ AN VY +L+ D ++G++L
Sbjct: 63 GCEYVDIVEELARERAKQLFGAEH----ANVQPHSGAQANMAVYFTVLEHGDTVLGMNLS 118
Query: 202 HGGHLSHGFMTPKRRVSGTSIYFESMPYRLDESTGLVDYDMLEKTAILFRPKLIIAGASA 261
HGGHL+HG V+ + + + + Y +D T ++DYD + + A L RPKLI+A A+A
Sbjct: 119 HGGHLTHGS-----PVNFSGVQYNFVAYGVDPETHVIDYDDVREKARLHRPKLIVAAAAA 173
Query: 262 YPRDFDYPRMRQIADAVGALLMMDMAHISGLVAASVVADPFKYCDVVTTTTHKSLRGPRG 321
YPR D+ + R+IAD VGA LM+DMAHI+GLVAA + +P Y VTTTTHK+LRGPRG
Sbjct: 174 YPRIIDFAKFREIADEVGAYLMVDMAHIAGLVAAGLHPNPVPYAHFVTTTTHKTLRGPRG 233
Query: 322 GMIFFKKDPVLGVELESAINNAVFPGLQGGPHNHTIGGLAVCLKHAQSPEFKVYQNKVVS 381
GMI ++ + I+ A+FPG+QGGP H I AV A +FK Y +VV
Sbjct: 234 GMILCQE------QFAKQIDKAIFPGIQGGPLMHVIAAKAVAFGEALQDDFKAYAKRVVD 287
Query: 382 NCRALASRLVELGYKLVSGGSDNHLVLVDLRPMGIDGARVEKILDMASITLNKNSVPGD- 440
N + LAS L G+ LVSGG+DNHL+LVDLRP + G EK+LD IT+NKN++P D
Sbjct: 288 NAKRLASALQNEGFTLVSGGTDNHLLLVDLRPQQLTGKTAEKVLDEVGITVNKNTIPYDP 347
Query: 441 KSALVPGGIRIGSPAMTTRGFSEKEFVAIADFIHE 475
+S V GIRIG+ A+TTRGF +E IA I
Sbjct: 348 ESPFVTSGIRIGTAAVTTRGFGLEEMDEIAAIIGL 382
>3h7f_A Serine hydroxymethyltransferase 1; cytoplasm, one-carbon
metabolism, pyridoxal phosphate, structural genomics;
HET: LLP; 1.50A {Mycobacterium tuberculosis}
Length = 447
Score = 578 bits (1491), Expect = 0.0
Identities = 201/459 (43%), Positives = 270/459 (58%), Gaps = 46/459 (10%)
Query: 74 DGSSFVDYSLGEADPEVCEIITKEKERQFKSLELIASENFTSRAVMEAVGSCLTNKYSEG 133
G + L E DP++ E++ KE RQ +LE+IASENF RAV++A GS LTNKY+EG
Sbjct: 17 QGPGSMSAPLAEVDPDIAELLAKELGRQRDTLEMIASENFVPRAVLQAQGSVLTNKYAEG 76
Query: 134 LPGKRYYGGNEYIDELETLCQKRALAAFNLDENKWGVNVQPLSGSPANFEVYTAILKPHD 193
LPG+RYYGG E++D +E L + RA A F + NVQP SG+ AN V A++ P +
Sbjct: 77 LPGRRYYGGCEHVDVVENLARDRAKALFGAEF----ANVQPHSGAQANAAVLHALMSPGE 132
Query: 194 RIMGLDLPHGGHLSHGFMTPKRRVSGTSIYFESMPYRLDESTGLVDYDMLEKTAILFRPK 253
R++GLDL +GGHL+HG + SG +E+ Y +D +T L+D D + TA+ FRPK
Sbjct: 133 RLLGLDLANGGHLTHGM---RLNFSGK--LYENGFYGVDPATHLIDMDAVRATALEFRPK 187
Query: 254 LIIAGASAYPRDFDYPRMRQIADAVGALLMMDMAHISGLVAASVVADPFKYCDVVTTTTH 313
+IIAG SAYPR D+ R IAD VGA L++DMAH +GLVAA + P + DVV+TT H
Sbjct: 188 VIIAGWSAYPRVLDFAAFRSIADEVGAKLLVDMAHFAGLVAAGLHPSPVPHADVVSTTVH 247
Query: 314 KSLRGPRGGMIFFKKDPVLGVELESAINNAVFPGLQGGPHNHTIGGLAVCLKHAQSPEFK 373
K+L G R G+I K+ + AIN+AVFPG QGGP H I G AV LK A +PEF
Sbjct: 248 KTLGGGRSGLIVGKQ------QYAKAINSAVFPGQQGGPLMHVIAGKAVALKIAATPEFA 301
Query: 374 VYQNKVVSNCRALASRLV-----ELGYKLVSGGSDNHLVLVDLRPMGIDGARVEKILDMA 428
Q + +S R +A RL+ + G +VSGG+D HLVLVDLR +DG E +L
Sbjct: 302 DRQRRTLSGARIIADRLMAPDVAKAGVSVVSGGTDVHLVLVDLRDSPLDGQAAEDLLHEV 361
Query: 429 SITLNKNSVPGD-KSALVPGGIRIGSPAMTTRGFSEKEFVAIADFIHEGVEITLEAKKLV 487
IT+N+N+VP D + +V G+RIG+PA+ TRGF + EF +AD I +
Sbjct: 362 GITVNRNAVPNDPRPPMVTSGLRIGTPALATRGFGDTEFTEVADIIATALATGSSVD--- 418
Query: 488 QGSKLQDFMNFVTSPNFSLMNNVADLRGRVEALTTQFPI 526
V+ L+ R L FP+
Sbjct: 419 ----------------------VSALKDRATRLARAFPL 435
>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 = 72.5 bits (177), Expect = 9e-14
Identities = 56/346 (16%), Positives = 99/346 (28%), Gaps = 55/346 (15%)
Query: 98 KERQFKSLELIASENFTSRAVMEAVGSCLTNKYSEGLPGKRYYGGNEYIDELETLCQKRA 157
+E + + L + + + + +++ + G Y G+E LE R
Sbjct: 29 QEAGYNTFLLNSKDIYIDLLTDSGTNAMSDKQWAGMMMGDEAYAGSENFYHLE-----RT 83
Query: 158 LAAFNLDENKWGVNVQPLSGSPANFEVYTAILKPHDRIMG---LDLPHGGHLSHGFMTPK 214
+ ++ + G A + +KP + G +G
Sbjct: 84 VQELFGFKHIVPTH----QGRGAENLLSQLAIKPGQYVAGNMYFTTTRYHQEKNGA---- 135
Query: 215 RRVSGTSIYFESMPYRLDESTGLVDYDMLEKTAILFRPKLI----------IAGASAYPR 264
G +D L+K + I +AG
Sbjct: 136 -VFVDIVRDEAHDAGLNIAFKGDIDLKKLQKLIDEKGAENIAYICLAVTVNLAGGQPVSM 194
Query: 265 DFDYPRMRQIADAVGALLMMDMAHISG--------------LVAASVVADPFKYCDVVTT 310
+ +R++ +A G + D A +V + F Y D T
Sbjct: 195 A-NMRAVRELTEAHGIKVFYDATRCVENAYFIKEQEQGFENKSIAEIVHEMFSYADGCTM 253
Query: 311 TTHKSLRGPRGGMIFFKKDPVLGVELESAINNAVFPGL----QGGPHNHTIGGLAVCLKH 366
+ K GG + D E+ S+ V GG + +A+ L+
Sbjct: 254 SGKKDCLVNIGGFLCMNDD-----EMFSSAKELVVVYEGMPSYGGLAGRDMEAMAIGLRE 308
Query: 367 AQSPEFKVYQNKVVSNCRALASRLVELGYKLVSGGSDNHLVLVDLR 412
A E Y V R L +L G +V H V +D R
Sbjct: 309 AMQYE---YIEHRVKQVRYLGDKLKAAGVPIVE-PVGGHAVFLDAR 350
>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 = 64.3 bits (156), Expect = 7e-11
Identities = 101/556 (18%), Positives = 177/556 (31%), Gaps = 188/556 (33%)
Query: 60 PPSSVSVPIPEIGGDGSSFVDYSLGEADP-------EVCEIITKEKERQF---------- 102
P++ E+ G F+ Y +P +V + E E +
Sbjct: 53 EPTTP----AELVG---KFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALA 105
Query: 103 ------------KSLELI----ASENFTSRAVMEAVGSCLTNKYSEGLPGKRYY---GG- 142
K+ ELI + R + S L EG + GG
Sbjct: 106 AKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEG--NAQLVAIFGGQ 163
Query: 143 ---NEYIDELETLCQK-RALAAFNLDENKWGVNVQPLSGSPANFE-VYTAILKPHDRIMG 197
++Y +EL L Q L + + + L + + E V+T G
Sbjct: 164 GNTDDYFEELRDLYQTYHVLVGDLIKFS--AETLSELIRTTLDAEKVFTQ---------G 212
Query: 198 LDLPHGGHLSHGFMTPKRRVSGTSIYFESMPYRLDES------TGLVDYDMLEKTAILFR 251
L++ ++ Y S+P S L Y + +
Sbjct: 213 LNI-------LEWLENPSNTPDKD-YLLSIPI----SCPLIGVIQLAHY------VVTAK 254
Query: 252 PKLIIAGASAYPRDFDYPRMRQIADAVGALLMMDMAHISGLVAASVVA-----DPFKYCD 306
+ G + P + ++ GA H GLV A +A + F
Sbjct: 255 ----LLGFT--PGEL-RSYLK------GAT-----GHSQGLVTAVAIAETDSWESF---- 292
Query: 307 VVTTTTHKSLRGPRGGMIFFKKDPVLGVE-LESAINNAVFPGLQGGPHNHTIGG----LA 361
+ K++ ++FF +GV E+ N ++ P + + G L+
Sbjct: 293 --FVSVRKAIT-----VLFF-----IGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLS 340
Query: 362 VC-LKHAQSPEFKVYQNKV-VSNCRALASRLVELGYKLVSGGSDNHLVL----VDLRPMG 415
+ L Q Q+ V +N A + VE+ LV+G +LV+ L G
Sbjct: 341 ISNLTQEQV------QDYVNKTNSHLPAGKQVEIS--LVNG--AKNLVVSGPPQSLY--G 388
Query: 416 IDGARVEKILDMASITLNKNSVPGDKSALVPGG--IRIGSPAMTTRGFSEKEFVAIADFI 473
++ + K A L+++ +P + L + + SP F V +D I
Sbjct: 389 LN-LTLRKA--KAPSGLDQSRIPFSERKLKFSNRFLPVASP------FHSHLLVPASDLI 439
Query: 474 HE---GVEITLEAKKL-------VQGSKLQDFMNFVTSPNFSLMNNVAD--LRGRV--EA 519
++ ++ AK + GS L+ + S+ + D +R V E
Sbjct: 440 NKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVL-------SGSISERIVDCIIRLPVKWET 492
Query: 520 LTTQFPI-------PG 528
TTQF PG
Sbjct: 493 -TTQFKATHILDFGPG 507
Score = 37.0 bits (85), Expect = 0.017
Identities = 43/309 (13%), Positives = 90/309 (29%), Gaps = 121/309 (39%)
Query: 196 MGLDLPHGGHLSHGFMTPK--RRVSGTSIYFESMPYRLDESTGLVDYDMLEKTAILFRPK 253
MG+DL + T K + V + ++ G D++ P
Sbjct: 1631 MGMDL---------YKTSKAAQDV------WNRADNHFKDTYGFSILDIVIN-----NPV 1670
Query: 254 LIIAGASAYPRDFDYPRMRQIADAVGALLMMDMAHISGLVAASVVADPFKYCDVVTTTTH 313
+ F + ++I + M + + FK ++ +T
Sbjct: 1671 NLTI-------HFGGEKGKRIRE-----NYSAMIFETIVDGKLKTEKIFK--EINEHSTS 1716
Query: 314 KSLRGPRGGM---------IFFKKDPVLGV----ELESA---INNAVFPGLQGGPHNHTI 357
+ R +G + + ++ +L+S +A F G H++
Sbjct: 1717 YTFRSEKGLLSATQFTQPALT-----LMEKAAFEDLKSKGLIPADATFAG-------HSL 1764
Query: 358 GGLAVCLKHAQSPEFKVYQNKVVSNCRALASRLVELGYKLVSGGS---DNHLVLVDLRPM 414
G E+ + ALAS ++ + +V R
Sbjct: 1765 G------------EY--------A---ALAS----------LADVMSIESLVEVVFYR-- 1789
Query: 415 GIDGARVEKILDMASITLNKNSVPGDKSALVPGGIRIGSPAMTTRGFSEKEFVAIADFIH 474
G+ + +VP D+ G+ +P FS++ + + +
Sbjct: 1790 GM---------------TMQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVVERVG 1834
Query: 475 EG----VEI 479
+ VEI
Sbjct: 1835 KRTGWLVEI 1843
Score = 36.6 bits (84), Expect = 0.028
Identities = 23/154 (14%), Positives = 49/154 (31%), Gaps = 47/154 (30%)
Query: 82 SLGE-------AD----PEVCEIITKEKER-QFKSLELIASENFTSRAVMEAVGSCLTNK 129
SLGE AD + E++ R + + E S M A+
Sbjct: 1763 SLGEYAALASLADVMSIESLVEVV---FYRGMTMQVAVPRDELGRSNYGMIAIN------ 1813
Query: 130 YSEGLPGKRYYGGNEYIDELETLCQKRA--------LAAFNLDENKWGVNVQP-LSGSPA 180
PG+ ++ + L+ + ++ + +N++ N Q +G
Sbjct: 1814 -----PGRVAASFSQ--EALQYVVERVGKRTGWLVEIVNYNVE------NQQYVAAGDLR 1860
Query: 181 NFEVYTAILKPHDRIMGLDLPHGGHLSHGFMTPK 214
+ T +L ++ +D+ L +
Sbjct: 1861 ALDTVTNVLN-FIKLQKIDI---IELQKSLSLEE 1890
>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 = 52.5 bits (125), Expect = 3e-07
Identities = 58/413 (14%), Positives = 115/413 (27%), Gaps = 123/413 (29%)
Query: 80 DYSLGEADPEVCEIITKEKERQFKSLELIAS-ENFTSRAVMEAVGSCLTNKYSEGLPGKR 138
D E + I K+ +L L + + V + V L Y
Sbjct: 40 DMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINY-------- 91
Query: 139 YYGGNEYI-DELETLCQKRAL--AAFNLDENKWGVNVQPLSGSPAN---FEVYTAI---- 188
+++ ++T ++ ++ + ++ + Q + N + Y +
Sbjct: 92 -----KFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFA--KYNVSRLQPYLKLRQAL 144
Query: 189 --LKPHDRI----MG------------LDLPHGGHLSHG-F-MTPKRRVSGTSI--YFES 226
L+P + + L + F + K S ++ +
Sbjct: 145 LELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQK 204
Query: 227 MPYRLDES-TGLVDYDMLEKTAILFRPKLIIAGASAYPRDF----DYPRMRQIADAVGAL 281
+ Y++D + T D+ KL I A R Y L
Sbjct: 205 LLYQIDPNWTSRSDHS--------SNIKLRIHSIQAELRRLLKSKPYEN---------CL 247
Query: 282 LMMDMAHISGLVAASVVADPFKY-CDVVTTT--------------THKSLRGPRGGMIFF 326
L++ + V + + F C ++ TT TH SL
Sbjct: 248 LVLL--N----VQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMT---L 298
Query: 327 KKDPVLGVELESAINNAVF--P--GLQGGPHNHTIGGLAVCLKHAQSPEFKV-YQNKVVS 381
D V + L ++ P L P + + + + N
Sbjct: 299 TPDEVKSL-LLKYLDCRPQDLPREVLTTNP-------RRLSIIAESIRDGLATWDNWKHV 350
Query: 382 NCRALASRLVELGYKLVSGGSDNHLVLVDLRPM----GI--DGARV-EKILDM 427
NC L + ++E N L + R M + A + +L +
Sbjct: 351 NCDKL-TTIIESSL--------NVLEPAEYRKMFDRLSVFPPSAHIPTILLSL 394
>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 = 51.7 bits (123), Expect = 4e-07
Identities = 46/269 (17%), Positives = 78/269 (28%), Gaps = 35/269 (13%)
Query: 176 SGSPANFEVYTAILKPHDRIMGLDLPHGGHLSHGFMTPKR-RVSGTSIYFESMPYRLDES 234
G A ++ +LK + P H T ++G D
Sbjct: 99 QGRGAENILFPVLLKYKQKEGKAKNPVFISNFHFDTTAAHVELNGCKAINIVTEKAFDSE 158
Query: 235 T-----GLVDYDMLEKTAILFRPKLIIA---------GASAYPRDFDYPR-MRQIADAVG 279
T G D L++ I I A P + + +IA G
Sbjct: 159 TYDDWKGDFDIKKLKE-NIAQHGADNIVAIVSTVTCNSAGGQPVSMSNLKEVYEIAKQHG 217
Query: 280 ALLMMDMAHI--------------SGLVAASVVADPFKYCDVVTTTTHKSLRGPRGGMIF 325
++MD A V+ D +KY D +T + K GG++
Sbjct: 218 IFVVMDSARFCENAYFIKARDPKYKNATIKEVIFDMYKYADALTMSAKKDPLLNIGGLVA 277
Query: 326 FKKDPVLGVELESAINNAVFPGLQGGPHNHTIGGLAVCLKHAQSPEFKVYQNKVVSNCRA 385
+ + + GG + + L+ E Y + + +
Sbjct: 278 IRDNEEIFTLARQRCVPMEGFVTYGGLAGRDMAAMVQGLEEGTEEE---YLHYRIGQVKY 334
Query: 386 LASRLVELGYKLVSGGSDNHLVLVDLRPM 414
L RL E G + + H V VD + +
Sbjct: 335 LGDRLREAGIPIQY-PTGGHAVFVDCKKL 362
>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 = 38.9 bits (90), Expect = 0.003
Identities = 45/278 (16%), Positives = 79/278 (28%), Gaps = 50/278 (17%)
Query: 176 SGSPANFEVYTAILKPHDRIMGLDLPHGGHLSHGFMTPKR---RVSGTSIYFESMPYRLD 232
G A ++K ++ GLD S+ F + +++G ++ + D
Sbjct: 97 QGRGAEQIYIPVLIKKREQEKGLDRSKMVAFSNYFFDTTQGHSQINGCTVRNVYIKEAFD 156
Query: 233 EST-----GLVDYDMLEKTAI----LFRPKLII-------AGASAYPRDFDYPR-MRQIA 275
G D + LE+ I I+ AG + M IA
Sbjct: 157 TGVRYDFKGNFDLEGLER-GIEEVGPNNVPYIVATITSNSAGGQPVS--LANLKAMYSIA 213
Query: 276 DAVGALLMMDMAHI--------------SGLVAASVVADPFKYCDVVTTTTHKSLRGPRG 321
++MD A + + +KY D++ + K P G
Sbjct: 214 KKYDIPVVMDSARFAENAYFIKQREAEYKDWTIEQITRETYKYADMLAMSAKKDAMVPMG 273
Query: 322 GMIFFKKDPVLGVELESAINNAVFPGLQGGPHNHTIGGLAVCLKHAQSPEFKV-----YQ 376
G++ K D + T GGL + +
Sbjct: 274 GLLCMKDDSFF------DVYTECRTLCVVQEGFPTYGGLEGGAMERLAVGLYDGMNLDWL 327
Query: 377 NKVVSNCRALASRLVELGYKLVSGGSDNHLVLVDLRPM 414
++ + L L E+G G H VD +
Sbjct: 328 AYRIAQVQYLVDGLEEIGVVCQQAGG--HAAFVDAGKL 363
>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 = 37.7 bits (87), Expect = 0.007
Identities = 37/224 (16%), Positives = 71/224 (31%), Gaps = 30/224 (13%)
Query: 225 ESMPYRLDESTGLVDYDMLEKTAILFRPK----LIIAGASAYP-RDFD-YPRMRQIADAV 278
+ LD V + +E +++ + +P R+ D + +I +
Sbjct: 201 RLVETVLDGDRVYVPVEDIENAIKKEIELGNRPCVLSTLTFFPPRNSDDIVEIAKICENY 260
Query: 279 GALLMMDMAH-ISGLVAASVVADPFKY-CDVVTTTTHKSLRGPRGGMIFFKKDPVLGVEL 336
+++ A+ I + FKY D V +++ K+L P GG + + D
Sbjct: 261 DIPHIINGAYAIQNNYYLEKLKKAFKYRVDAVVSSSDKNLLTPIGGGLVYSTDA------ 314
Query: 337 ESAINNAVFPGLQGGPHNHTIGGLAVCLKHAQSPEFKVYQNKVVSNCRALASRLVELGYK 396
+ G + V L S + ++ + L L +L K
Sbjct: 315 --EFIKEISLSYPGRASATPVVNTLVSLLSMGSKNYLELVKNQKNSKKLLDELLNDLSKK 372
Query: 397 --------------LVSGGSDNHLVLVDLRPMGIDGARVEKILD 426
+S SD + L + + G R K D
Sbjct: 373 TGGKFLDVESPIASCISVNSDPVEIAAKLYNLRVTGPRGIKKTD 416
>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 = 36.7 bits (86), Expect = 0.015
Identities = 18/61 (29%), Positives = 27/61 (44%), Gaps = 10/61 (16%)
Query: 232 DESTGLVDYDMLEKTAILFRPKLII----AGASAYPRDFDYPRMRQIADAVGALLMMDMA 287
D T +V + +E AI + K II AGA A D + + + G ++ D A
Sbjct: 109 DRDTLMVTPEHIEA-AITPQTKAIIPVHYAGAPA-----DLDAIYALGERYGIPVIEDAA 162
Query: 288 H 288
H
Sbjct: 163 H 163
>2vyc_A Biodegradative arginine decarboxylase; pyridoxal phosphate,
PLP-dependent E lyase, acid resistance; HET: LLP; 2.4A
{Escherichia coli}
Length = 755
Score = 35.9 bits (82), Expect = 0.034
Identities = 40/275 (14%), Positives = 70/275 (25%), Gaps = 38/275 (13%)
Query: 154 QKRALAAFNLDENKWGVNVQPLSGSPANFEVYTAILKPHDRIMGLDLPHGGHLS--HG-- 209
+K A F D + V S +N + A + +D ++ + H S G
Sbjct: 211 EKYAARVFGADRSWSVVV----GTSGSNRTIMQACMTDNDVVV---VDRNCHKSIEQGLM 263
Query: 210 -------FMTPKRRVSGTSIYFESMPYRLDEST--GLVDYDMLEKTAILFRPKLIIAGAS 260
+M P R + I P + T + L K +P +
Sbjct: 264 LTGAKPVYMVPSR--NRYGIIGPIYPQEMQPETLQKKISESPLTKDKAGQKPSYCVVTNC 321
Query: 261 AYPRD---FDYPRMRQIADAVGALLMMDMAHISGLV----------AASVVADPFKYCDV 307
Y D ++ + + + L D A D
Sbjct: 322 TY--DGVCYNAKEAQDLLEKTSDRLHFDEAWYGYARFNPIYADHYAMRGEPGDHNGPTVF 379
Query: 308 VTTTTHKSLRGPRGGMIFFKKDPVLGVELESAINNAVFPGLQGGPHNHTIGGLAVCLKHA 367
T +THK L ++ + N A P V +
Sbjct: 380 ATHSTHKLLNALSQASYIHVREGRGAINFS-RFNQAYMMHATTSPLYAICASNDVAVSMM 438
Query: 368 QSPEFKVYQNKVVSNCRALASRLVELGYKLVSGGS 402
+V+ + L + + GS
Sbjct: 439 DGNSGLSLTQEVIDEAVDFRQAMARLYKEFTADGS 473
>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 = 35.5 bits (82), Expect = 0.036
Identities = 16/61 (26%), Positives = 24/61 (39%), Gaps = 3/61 (4%)
Query: 266 FDYPRMRQIADAVGALLMMDMAHISGLVAASVVADPFKYCDVVTTTTHKSLRGPRGGMIF 325
D + ++ GAL + D+AH +G V + D T+K L G G F
Sbjct: 182 HDMQALTALSHECGALAIWDLAHSAGAVPVDLHQAG---ADYAIGCTYKYLNGGPGSQAF 238
Query: 326 F 326
Sbjct: 239 V 239
>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 = 35.0 bits (80), Expect = 0.064
Identities = 34/258 (13%), Positives = 57/258 (22%), Gaps = 34/258 (13%)
Query: 154 QKRALAAFNLDENKWGVNVQPLSGSPANFEVYTAILKPHDRIMGLDLPHGGHLS--HG-- 209
++ FN D + N S AN V I+ + H S H
Sbjct: 201 EQYIARVFNADRSYMVTN----GTSTANKIVGMYSAPAGSTIL---IDRNCHKSLTHLMM 253
Query: 210 -------FMTPKRRVSGTSIYFESMPYRLDESTGLVDYDMLEKTAILFRPKLIIAGASAY 262
+ P R + I E +++T P + S Y
Sbjct: 254 MSDVTPIYFRPTR--NAYGIL---GGIPQSEFQHATIAKRVKETPNATWPVHAVITNSTY 308
Query: 263 PR-DFDYPRMRQIADAVGALLMMDMAHISGLV------AASVVADPFKYCDVVTTTTHKS 315
++ +++ D + T +THK
Sbjct: 309 DGLLYNTDFIKKTLDVKSIHFDSAWVPYTNFSPIYEGKCGMSGGRVEGKVIYETQSTHKL 368
Query: 316 LRGPRGGMIFFKKDPVLGVELESAINNAVFPGLQGGPHNHTIGGLAVCLKHAQSPEFKVY 375
L + K V A PH + + K
Sbjct: 369 LAAFSQASMIHVKGDVNEETFNEAYMMHT----TTSPHYGIVASTETAAAMMKGNAGKRL 424
Query: 376 QNKVVSNCRALASRLVEL 393
N + + L
Sbjct: 425 INGSIERAIKFRKEIKRL 442
>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 = 33.2 bits (76), Expect = 0.18
Identities = 28/149 (18%), Positives = 54/149 (36%), Gaps = 11/149 (7%)
Query: 273 QIADAVGALLMMDMAHISGLVAASVVA-DPFKYCDVVTTTTHKSLRGPRG--GMIFFKKD 329
++ L+++ A+ G + S+ D + + HKS+ G G++ K++
Sbjct: 171 KVCSEYDVPLLVNGAYAIGRMPVSLKEIG----ADFIVGSGHKSM-AASGPIGVMGMKEE 225
Query: 330 PVLGVELESAINNAVFPGLQGG-PHNHTIGGLAVCLKHAQSPEFKVYQNKVVSNCRALAS 388
V S L G TI L H + E ++ V R A+
Sbjct: 226 WAEIVLRRSEKYKNKEVELLGCTARGATIITLMASFPHVR--ERIKRWDEEVEKARRFAA 283
Query: 389 RLVELGYKLVSGGSDNHLVLVDLRPMGID 417
+ +LG K + NH ++ + +
Sbjct: 284 EMEKLGIKQLGDNPHNHDLMFFHAEVLYE 312
>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 = 0.62
Identities = 13/61 (21%), Positives = 23/61 (37%), Gaps = 3/61 (4%)
Query: 266 FDYPRMRQIADAVGALLMMDMAHISGLVAASVVADPFKYCDVVTTTTHKSLRGPRGGMIF 325
F+ P + + A G + D+AH G V + + ++K L GG+
Sbjct: 231 FNIPAITKAGQAKGCYVGFDLAHAVGNVELYLHDWGVDFA---CWCSYKYLNAGAGGIAG 287
Query: 326 F 326
Sbjct: 288 A 288
>3fed_A Glutamate carboxypeptidase III; metallopeptidase, bimetallic active
site, N-glycosylation, C cation, chloride anion, zinc
IONS, dipept glycoprotein; HET: NAG BIX; 1.29A {Homo
sapiens} PDB: 3fec_A* 3fee_A* 3ff3_A* 2c6c_A* 2c6g_A*
2c6p_A* 2cij_A* 2jbj_A* 2jbk_A* 3rbu_A* 3bi1_A* 2oot_A*
2pvv_A* 2pvw_A* 2xei_A* 2or4_A* 3bi0_A* 3bhx_A* 3d7d_A*
3d7f_A* ...
Length = 707
Score = 31.5 bits (70), Expect = 0.77
Identities = 11/55 (20%), Positives = 24/55 (43%)
Query: 139 YYGGNEYIDELETLCQKRALAAFNLDENKWGVNVQPLSGSPANFEVYTAILKPHD 193
G E+ +E + Q+R++A N D + G + +P +++ + K
Sbjct: 385 LLGSTEWAEENVKILQERSIAYINSDSSIEGNYTLRVDCTPLLYQLVYKLTKEIP 439
>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 = 31.1 bits (70), Expect = 0.86
Identities = 24/178 (13%), Positives = 49/178 (27%), Gaps = 16/178 (8%)
Query: 227 MPYRLDESTGLVDYDMLEKTAILFRPKLIIAGASAY----PRDFD-YPRMRQIADAVGAL 281
+ L+ D +E P+ I+ S PR D + I
Sbjct: 171 IENVLEGDELRTDLKAVEAKIQELGPEHILCLHSTTACFAPRVPDRLEELAVICANYDIP 230
Query: 282 LMMDMA---HISGLVAASVVADPFKYCDVVTTTTHKSLRGPRGGMIFFKKDPVLGVELES 338
+++ A S + D + K+ P GG I + ++
Sbjct: 231 HVVNNAYGLQSSKCMHLIQQGARVGRIDAFVQSLDKNFMVPVGGAIIAGFNEPFIQDISK 290
Query: 339 AINNAVFPGLQGGPHNHTIGGLAVCLKHAQSPEFKVYQNKVVSNCRALASRLVELGYK 396
+PG + + L ++ + L+++L +L
Sbjct: 291 M-----YPGRASA---SPSLDVLITLLSLGCSGYRKLLKERKEMFVYLSTQLKKLAEA 340
>2x3l_A ORN/Lys/Arg decarboxylase family protein; lyase; HET: LLP; 2.00A
{Staphylococcus aureus}
Length = 446
Score = 31.3 bits (71), Expect = 0.91
Identities = 26/172 (15%), Positives = 62/172 (36%), Gaps = 15/172 (8%)
Query: 266 FDYPRMRQIADAVGALLMMDMAHISGLVAASVVADPFKY-CDVVTTTTHKSLRGPR-GGM 323
F+ + + + +++D AH + Y D V + HK+L G +
Sbjct: 162 FNVEEVIKSLHQLNIPVLIDEAHGAHFGLQGFPDSTLNYQADYVVQSFHKTLPALTMGSV 221
Query: 324 IFFKKDPVLGVELESAINNAVFPGLQG-GPHNHTIGGLAVCLKHAQSPEFKVYQNKVVSN 382
++ K+ + ++ Q P + L + ++ + ++ K
Sbjct: 222 LYIHKNAPYRENIIEYLS-----YFQTSSPSYLIMASLESAAQFYKTYDSTLFFAKRAQL 276
Query: 383 CRALASRLVELGYKLVSGGSDNHLVLVDLRPMGIDGARVEKILDMASITLNK 434
L ++ G++++ D+ L L+ ++ G G ++ A I L
Sbjct: 277 IECLENK----GFEML--QVDDPLKLL-IKYEGFTGHDIQNWFMNAHIYLEL 321
>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 = 30.8 bits (69), Expect = 1.3
Identities = 35/270 (12%), Positives = 75/270 (27%), Gaps = 38/270 (14%)
Query: 154 QKRALAAFNLDENKWGVNVQPLSGSPANFEVYTAILKPHDRIMGLDLPHGGHLS--HG-- 209
+K A +N D+ + + S AN V +A++ D ++ H S +
Sbjct: 179 EKHAARVYNADKTYFVLG----GSSNANNTVTSALVSNGDLVL---FDRNNHKSVYNSAL 231
Query: 210 --------FMTPKRRVSGTSIYFESMPYRLDEST--GLVDYDMLEKTAILFRPKLIIAGA 259
++ R + DE L E+ +L +
Sbjct: 232 AMAGGRPVYLQTNR--NPYGFIGGIYDSDFDEKKIRELAAKVDPERAKWKRPFRLAVIQL 289
Query: 260 SAYPRD-FDYPRMRQIADAVGALLMMDMAHISGLVAASVVADPF----------KYCDVV 308
Y ++ + + + + D A + ++ + +V
Sbjct: 290 GTYDGTIYNAHEVVKRIGHLCDYIEFDSAWVGYEQFIPMMRNSSPLLIDDLGPEDPGIIV 349
Query: 309 TTTTHKSLRGPRGGMIFFKKDPVLGVELESAINNAV---FPGLQG-GPHNHTIGGLAVCL 364
+ HK G KKD + +L + F P L V
Sbjct: 350 VQSVHKQQAGFSQTSQIHKKDSHIKGQLRYCDHKHFNNSFNLFMSTSPFYPMYAALDVNA 409
Query: 365 KHAQSPEFKVYQNKVVSNCRALASRLVELG 394
+ + + ++ +L++ G
Sbjct: 410 AMQEGEAGRKLWHDLLITTIEARKKLIKAG 439
>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 = 30.6 bits (69), Expect = 1.3
Identities = 19/66 (28%), Positives = 33/66 (50%), Gaps = 5/66 (7%)
Query: 267 DYPRMRQIADAVGALLMMDMAHISGLVAASVVADPFKY---CDVVTTTTHKSLRGPRGGM 323
++ ++ A A++ +D A SG + P D+V T+T K + GPRGG+
Sbjct: 160 NFKKVINTAKNKEAIVFVDDA--SGARVRLLFNQPPALKLGADLVVTSTDKLMEGPRGGL 217
Query: 324 IFFKKD 329
+ KK+
Sbjct: 218 LAGKKE 223
>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 = 30.7 bits (70), Expect = 1.3
Identities = 24/165 (14%), Positives = 45/165 (27%), Gaps = 47/165 (28%)
Query: 141 GGNEYIDELETLCQKRALAAFNLDENKWGVNVQPLSGSPANFEVYTAILKPHDRIMGLDL 200
+ +E + LA F + SG AN + I +P+ +
Sbjct: 101 QNDYDKPMIE-----KRLAKFTGFDECLLSQ----SGWNANVGLLQTICQPNTNVYIDFF 151
Query: 201 PH-----GGHLSHGFMTPKRRVSGTSIYFESMPYRLDESTGLVDYDMLEKTAILFRPKLI 255
H G ++ + + + + D L P +I
Sbjct: 152 AHMSLWEGARYANA----QAHP-----------FMHN------NCDHLRMLIQRHGPGII 190
Query: 256 IA-------GASAYPRDFDYPRMRQIADAVGALLMMDMAHISGLV 293
+ G A + I+ G L++D +H G
Sbjct: 191 VVDSIYSTLGTIA-----PLAELVNISKEFGCALLVDESHSLGTH 230
>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 = 2.2
Identities = 19/64 (29%), Positives = 27/64 (42%), Gaps = 11/64 (17%)
Query: 269 PRMRQIADAVGALLMMDMAHIS--------GLVAASVVADPFKYCDVVTTTTHKSLRGPR 320
+ +AD AL+M+D +H G VAD D++T T K+L G
Sbjct: 195 KSICDLADKYNALVMVDDSHAVGFIGENGRGTPEYCGVADR---VDILTGTLGKALGGAS 251
Query: 321 GGMI 324
GG
Sbjct: 252 GGYT 255
>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 = 29.8 bits (68), Expect = 2.4
Identities = 17/64 (26%), Positives = 25/64 (39%), Gaps = 11/64 (17%)
Query: 269 PRMRQIADAVGALLMMDMAHISG--------LVAASVVADPFKYCDVVTTTTHKSLRGPR 320
+ +AD AL+M+D +H G V D++T T K+L G
Sbjct: 197 KGVCDLADKYDALVMVDDSHAVGFVGENGRGSHEYCDVMGR---VDIITGTLGKALGGAS 253
Query: 321 GGMI 324
GG
Sbjct: 254 GGYT 257
>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 = 29.3 bits (65), Expect = 3.5
Identities = 18/114 (15%), Positives = 30/114 (26%), Gaps = 8/114 (7%)
Query: 227 MPYRLDESTGLVDYDMLEKTAILFRPKLIIAGASAY----PRDFD-YPRMRQIADAVGAL 281
+ L+ D +E P I+ S PR D + I
Sbjct: 189 IENVLEGDELRTDLKAVEAKVQELGPDCILCIHSTTSCFAPRVPDRLEELAVICANYDIP 248
Query: 282 LMMDMA---HISGLVAASVVADPFKYCDVVTTTTHKSLRGPRGGMIFFKKDPVL 332
+++ A S + D + K+ P GG I +
Sbjct: 249 HIVNNAYGVQSSKCMHLIQQGARVGRIDAFVQSLDKNFMVPVGGAIIAGFNDSF 302
>1af7_A Chemotaxis receptor methyltransferase CHER; chemotaxis receptor
methylation; HET: SAH; 2.00A {Salmonella typhimurium}
SCOP: a.58.1.1 c.66.1.8 PDB: 1bc5_A*
Length = 274
Score = 28.3 bits (64), Expect = 5.7
Identities = 15/71 (21%), Positives = 28/71 (39%), Gaps = 10/71 (14%)
Query: 461 FSEKEFVAIADFIHEGVEITLEAKK--LVQGSKLQDFMNFVTSPNFS-LMNNVADLRGRV 517
S+ F I I++ I L K +V ++L + + +F ++ + +
Sbjct: 12 LSDAHFRRICQLIYQRAGIVLADHKRDMVY-NRLVRRLRALGLDDFGRYLSMLEANQNSA 70
Query: 518 E------ALTT 522
E ALTT
Sbjct: 71 EWQAFINALTT 81
>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 = 28.0 bits (63), Expect = 7.6
Identities = 41/178 (23%), Positives = 66/178 (37%), Gaps = 24/178 (13%)
Query: 239 DYDMLE---KTAILFRPKLIIAGASAYPRDFDYPRMRQI---ADAVGALLMMDMAHISGL 292
D L PKLI A S Y D D+ +++I A+ GAL +D H G+
Sbjct: 163 DVAHLRELIAADDPAAPKLI-AFESVYSMDGDFGPIKEICDIAEEFGALTYIDEVHAVGM 221
Query: 293 VAASV--VADPFKY---CDVVTTTTHKSLRGPRGGMIFFKKDPVLGVELESA---INNAV 344
VA+ D+ T K+ G GG I V V + + ++
Sbjct: 222 YGPRGAGVAERDGLMHRIDIFNGTLAKAY-GVFGGYIAASARMVDAVRSYAPGFIFSTSL 280
Query: 345 FPGLQGGPHNHTIGGLAVCLKHAQSPEFKVYQNKVVSNCRALASRLVELGYKLVSGGS 402
P + G A + ++ E + ++ + + L RL LG ++ GS
Sbjct: 281 PPAIAA-------GAQAS-IAFLKTAEGQKLRDAQQMHAKVLKMRLKALGMPIIDHGS 330
>3kas_A Transferrin receptor protein 1; transferrin receptor 1, arenavirus,
cell MEMB disulfide bond, endocytosis, HOST-virus inter
receptor, secreted, transmembrane; HET: NAG FUC BMA MAN;
2.40A {Homo sapiens} PDB: 1de4_C* 3s9l_A* 3s9m_A*
3s9n_A* 1cx8_A* 1suv_A 2nsu_A
Length = 640
Score = 27.8 bits (61), Expect = 9.5
Identities = 10/50 (20%), Positives = 22/50 (44%)
Query: 141 GGNEYIDELETLCQKRALAAFNLDENKWGVNVQPLSGSPANFEVYTAILK 190
G E+++ + +A NLD+ G + +S SP + + ++
Sbjct: 342 GATEWLEGYLSSLHLKAFTYINLDKAVLGTSNFKVSASPLLYTLIEKTMQ 391
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
0.319 0.136 0.401
Gapped
Lambda K H
0.267 0.0770 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 8,247,053
Number of extensions: 516857
Number of successful extensions: 1176
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1134
Number of HSP's successfully gapped: 42
Length of query: 529
Length of database: 6,701,793
Length adjustment: 98
Effective length of query: 431
Effective length of database: 3,965,535
Effective search space: 1709145585
Effective search space used: 1709145585
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 60 (26.8 bits)