RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy4969
(66 letters)
>3tsy_A Fusion protein 4-coumarate--COA ligase 1, resvera synthase;
transferase; 3.10A {Arabidospis thaliana}
Length = 979
Score = 89.3 bits (222), Expect = 4e-23
Identities = 27/62 (43%), Positives = 35/62 (56%), Gaps = 1/62 (1%)
Query: 5 IIDPVTSVQLPDGKTGELCLKGD-VFLGYRNKVEATKEMLDDDGWLHTGDLAYRLPDGTH 63
I+DP T L + GE+C++G + GY N AT E +D DGWLHTGD+ D
Sbjct: 415 IVDPDTGDSLSRNQPGEICIRGHQIMKGYLNNPAATAETIDKDGWLHTGDIGLIDDDDEL 474
Query: 64 FI 65
FI
Sbjct: 475 FI 476
>3ni2_A 4-coumarate:COA ligase; 4CL, phenylpropanoid biosynthesis; HET: AYL
EPE; 1.90A {Populus tomentosa} PDB: 3a9v_A* 3a9u_A*
Length = 536
Score = 89.2 bits (222), Expect = 4e-23
Identities = 29/62 (46%), Positives = 38/62 (61%), Gaps = 1/62 (1%)
Query: 5 IIDPVTSVQLPDGKTGELCLKGD-VFLGYRNKVEATKEMLDDDGWLHTGDLAYRLPDGTH 63
I+DP T LP + GE+C++GD + GY N EAT +D +GWLHTGD+ Y D
Sbjct: 368 IVDPETGASLPRNQPGEICIRGDQIMKGYLNDPEATSRTIDKEGWLHTGDIGYIDDDDEL 427
Query: 64 FI 65
FI
Sbjct: 428 FI 429
>2d1s_A Luciferase, luciferin 4-monooxygenase; alpha/beta, beta barrel,
alpha+beta, riken structural genomics/proteomics
initiative, RSGI; HET: SLU; 1.30A {Luciola cruciata}
PDB: 2d1q_A* 2d1r_A* 2d1t_A*
Length = 548
Score = 87.7 bits (218), Expect = 1e-22
Identities = 28/62 (45%), Positives = 39/62 (62%), Gaps = 1/62 (1%)
Query: 5 IIDPVTSVQLPDGKTGELCLKGD-VFLGYRNKVEATKEMLDDDGWLHTGDLAYRLPDGTH 63
+ID T L + GE+C+KG + GY N EATKE++D++GWLHTGD+ Y +
Sbjct: 375 VIDLDTKKSLGPNRRGEVCVKGPMLMKGYVNNPEATKELIDEEGWLHTGDIGYYDEEKHF 434
Query: 64 FI 65
FI
Sbjct: 435 FI 436
>3rix_A Luciferase, luciferin 4-monooxygenase; oxidoreductase,
photoprotein, luminescence, aspulvinone, natural product
extracts; HET: 923; 1.70A {Photinus pyralis} PDB: 1ba3_A
1lci_A* 3ies_A* 3iep_A* 3ier_A* 3qya_A
Length = 550
Score = 87.3 bits (217), Expect = 2e-22
Identities = 27/62 (43%), Positives = 37/62 (59%), Gaps = 1/62 (1%)
Query: 5 IIDPVTSVQLPDGKTGELCLKGD-VFLGYRNKVEATKEMLDDDGWLHTGDLAYRLPDGTH 63
++D T L + GELC++G + GY N EAT ++D DGWLH+GD+AY D
Sbjct: 373 VVDLDTGKTLGVNQRGELCVRGPMIMSGYVNNPEATNALIDKDGWLHSGDIAYWDEDEHF 432
Query: 64 FI 65
FI
Sbjct: 433 FI 434
>3g7s_A Long-chain-fatty-acid--COA ligase (FADD-1); protein structure
initiative, PSI-II, NYSGXRC, 11193J, structural
genomics; 2.15A {Archaeoglobus fulgidus dsm 4304}
Length = 549
Score = 79.6 bits (197), Expect = 1e-19
Identities = 14/66 (21%), Positives = 29/66 (43%), Gaps = 5/66 (7%)
Query: 5 IIDPVTSVQLPDGKTGELCLKGD-VFLGYRNKVEATKEML----DDDGWLHTGDLAYRLP 59
+I +L G++GE+ ++G +F GY + + +E + TGD+ +
Sbjct: 369 VISLEDGRELGVGESGEIVIRGPNIFKGYWKREKENQECWWYDEKGRKFFRTGDVGFIDE 428
Query: 60 DGTHFI 65
+G
Sbjct: 429 EGFLHF 434
>4fuq_A Malonyl COA synthetase; ANL superfamily, methylma malonate, ligase;
HET: MSE; 1.70A {Rhodopseudomonas palustris} PDB:
4fut_A*
Length = 503
Score = 78.4 bits (194), Expect = 3e-19
Identities = 25/62 (40%), Positives = 30/62 (48%), Gaps = 1/62 (1%)
Query: 5 IIDPVTSVQLPDGKTGELCLKGD-VFLGYRNKVEATKEMLDDDGWLHTGDLAYRLPDGTH 63
+ DP T +LP G G + +KG VF GY E TK DDG+ TGDL G
Sbjct: 333 VTDPETGKELPRGDIGMIEVKGPNVFKGYWRMPEKTKSEFRDDGFFITGDLGKIDERGYV 392
Query: 64 FI 65
I
Sbjct: 393 HI 394
>3nyq_A Malonyl-COA ligase; A/B topology ababa sandwich beta-barrel
adenylate-forming EN fold; HET: MCA AMP; 1.43A
{Streptomyces coelicolor} PDB: 3nyr_A*
Length = 505
Score = 74.6 bits (184), Expect = 6e-18
Identities = 20/64 (31%), Positives = 33/64 (51%), Gaps = 3/64 (4%)
Query: 5 IIDPVTS--VQLPDGKTGELCLKGD-VFLGYRNKVEATKEMLDDDGWLHTGDLAYRLPDG 61
+++ + L GE+ ++G +F Y N+ +AT +DG+ TGD+A R PDG
Sbjct: 337 LVEEDGTPIAALDGESVGEIQVRGPNLFTEYLNRPDATAAAFTEDGFFRTGDMAVRDPDG 396
Query: 62 THFI 65
I
Sbjct: 397 YVRI 400
>3o83_A Peptide arylation enzyme; ligase, adenylation of
2,3-dihydroxybenzoate and transfer to pantetheine
cofactor of BASF; HET: IXN; 1.90A {Acinetobacter
baumannii} PDB: 3o82_A* 3o84_A*
Length = 544
Score = 73.0 bits (180), Expect = 2e-17
Identities = 20/58 (34%), Positives = 31/58 (53%), Gaps = 2/58 (3%)
Query: 5 IIDPVTSVQLPDGKTGELCLKG-DVFLGYRNKVEATKEMLDDDGWLHTGDLAYRLPDG 61
I+D +P+G+ G L +G F GY E ++ D+D + ++GDL R PDG
Sbjct: 374 IVDEQYRE-VPEGEIGMLATRGPYTFCGYYQSPEHNSQVFDEDNYYYSGDLVQRTPDG 430
>1mdb_A 2,3-dihydroxybenzoate-AMP ligase; adenylation domain, peptide
synthetase, antibiotic biosynthesis, siderophore
formation; HET: AMP DBH; 2.15A {Bacillus subtilis} SCOP:
e.23.1.1 PDB: 1md9_A* 1mdf_A
Length = 539
Score = 71.8 bits (177), Expect = 5e-17
Identities = 16/58 (27%), Positives = 23/58 (39%), Gaps = 2/58 (3%)
Query: 5 IIDPVTSVQLPDGKTGELCLKG-DVFLGYRNKVEATKEMLDDDGWLHTGDLAYRLPDG 61
+ D + G+TG L +G GY E +DG+ TGD+ DG
Sbjct: 365 VWDDHDRD-VKPGETGHLLTRGPYTIRGYYKAEEHNAASFTEDGFYRTGDIVRLTRDG 421
>3rg2_A Enterobactin synthase component E (ENTE), 2,3-DIH dihydroxybenzoate
synthetase, isochroismatase...; adenylate-forming
enzymes, ANL superfamily; HET: SVS PNS; 3.10A
{Escherichia coli}
Length = 617
Score = 70.7 bits (174), Expect = 1e-16
Identities = 17/58 (29%), Positives = 25/58 (43%), Gaps = 2/58 (3%)
Query: 5 IIDPVTSVQLPDGKTGELCLKG-DVFLGYRNKVEATKEMLDDDGWLHTGDLAYRLPDG 61
+ D LP G+ G L +G F GY + D +G+ +GDL P+G
Sbjct: 369 VADA-EGNPLPQGEVGRLMTRGPYTFRGYYKSPQHNASAFDANGFYCSGDLISIDPEG 425
>1t5h_X 4-chlorobenzoyl COA ligase; adenylate-forming coenzyme A ligase
domain alternation confo change; 2.00A {Alcaligenes SP}
SCOP: e.23.1.1 PDB: 1t5d_X 3cw9_A* 3cw8_X* 2qvz_X*
2qw0_X* 3dlp_X* 2qvx_X* 2qvy_X*
Length = 504
Score = 69.1 bits (170), Expect = 4e-16
Identities = 24/65 (36%), Positives = 34/65 (52%), Gaps = 5/65 (7%)
Query: 5 IIDPVTSVQ--LPDGKTGELCLKG--DVFLGYRNKVEATKEMLDDDGWLHTGDLAYRLPD 60
I+ V + +G+ GEL + F+GY N+ +AT E L D GW T D+A P+
Sbjct: 334 IVRIGGGVDEIVANGEEGELIVAASDSAFVGYLNQPQATAEKLQD-GWYRTSDVAVWTPE 392
Query: 61 GTHFI 65
GT I
Sbjct: 393 GTVRI 397
>3ivr_A Putative long-chain-fatty-acid COA ligase; structural genomics,
PSI-2, protein S initiative, fatty acid synthesis; HET:
GOL; 2.00A {Rhodopseudomonas palustris}
Length = 509
Score = 65.3 bits (160), Expect = 1e-14
Identities = 24/62 (38%), Positives = 32/62 (51%), Gaps = 3/62 (4%)
Query: 5 IIDPVTSVQLPDGKTGELCLKGD-VFLGYRNKVEATKEMLDDDGWLHTGDLAYRLPDGTH 63
++D LP G+ GE+ L+G VF GY N AT+ + GW HTGD+ DG
Sbjct: 334 VVDA-EDRPLPPGEVGEIVLRGPTVFKGYWNNAAATQHAFRN-GWHHTGDMGRFDADGYL 391
Query: 64 FI 65
F
Sbjct: 392 FY 393
>2v7b_A Benzoate-coenzyme A ligase; benzoate oxidation, benzoate COA
ligase; 1.84A {Burkholderia xenovorans}
Length = 529
Score = 62.2 bits (152), Expect = 1e-13
Identities = 18/62 (29%), Positives = 30/62 (48%), Gaps = 3/62 (4%)
Query: 5 IIDPVTSVQLPDGKTGELCLKG-DVFLGYRNKVEATKEMLDDDGWLHTGDLAYRLPDGTH 63
+ D +PDG+ G+L +KG + Y N E ++ W+ +GD RLP+G +
Sbjct: 365 LRDE-AGHAVPDGEVGDLYIKGPSAAVMYWNNREKSRATFLG-EWIRSGDKYCRLPNGCY 422
Query: 64 FI 65
Sbjct: 423 VY 424
>3r44_A Fatty acyl COA synthetase FADD13 (fatty-acyl-COA synthetase);
ligase; HET: HIS; 1.80A {Mycobacterium tuberculosis}
PDB: 3t5c_A 3t5b_A
Length = 517
Score = 62.2 bits (152), Expect = 1e-13
Identities = 19/62 (30%), Positives = 30/62 (48%), Gaps = 4/62 (6%)
Query: 5 IIDPVTSVQLPDGKTGELCLKGD-VFLGYRNKVEATKEMLDDDGWLHTGDLAYRLPDGTH 63
+ V G GE+ +K D + Y N+ EAT++ D+ GW TGD+ +G
Sbjct: 350 VRGD-DGVIREHG-EGEVVIKSDILLKEYWNRPEATRDAFDN-GWFRTGDIGEIDDEGYL 406
Query: 64 FI 65
+I
Sbjct: 407 YI 408
>3gqw_A Fatty acid AMP ligase; FAAL, E. coli, ATP-dependent binding enzyme
family,, structural genomics, PSI-2, protein structure
initiative; HET: ZZ9; 3.00A {Escherichia coli O6} PDB:
3pbk_A*
Length = 576
Score = 61.9 bits (151), Expect = 1e-13
Identities = 18/62 (29%), Positives = 28/62 (45%), Gaps = 3/62 (4%)
Query: 5 IIDPVTSVQLPDGKTGELCLKGD-VFLGYRNKVEATKEMLDDDGWLHTGDLAYRLPDGTH 63
I + + + G +C+ G + GY + E + GWL TGDL Y L DG
Sbjct: 397 EIRNEAGMPVAERVVGHICISGPSLMSGYFGDQVSQDE-IAATGWLDTGDLGY-LLDGYL 454
Query: 64 FI 65
++
Sbjct: 455 YV 456
>3t5a_A Long-chain-fatty-acid--AMP ligase FADD28; acetyl-COA synthetase
like fold, AMP-binding; 2.05A {Mycobacterium
tuberculosis} PDB: 3e53_A
Length = 480
Score = 60.5 bits (147), Expect = 5e-13
Identities = 21/69 (30%), Positives = 32/69 (46%), Gaps = 13/69 (18%)
Query: 5 IIDPVTSVQLPDGKTGELCLKGD-VFLGYRNKVEATKEML-----------DDDGWLHTG 52
I+D T ++ PDG GE+ + GD V GY K + ++ + WL TG
Sbjct: 406 IVDSDTCIECPDGTVGEIWVHGDNVANGYWQKPDESERTFGGKIVTPSPGTPEGPWLRTG 465
Query: 53 DLAYRLPDG 61
D + + DG
Sbjct: 466 DSGF-VTDG 473
>3kxw_A Saframycin MX1 synthetase B; fatty acid AMP ligase, SGX, acyl
adenylate, structural genom 2, protein structure
initiative; HET: 1ZZ; 1.85A {Legionella pneumophila
subsp} PDB: 3lnv_A*
Length = 590
Score = 60.4 bits (147), Expect = 5e-13
Identities = 19/70 (27%), Positives = 32/70 (45%), Gaps = 10/70 (14%)
Query: 5 IIDPVTSVQLPDGKTGELCLKGD-VFLGYRNKVEATKEML--------DDDGWLHTGDLA 55
IIDP T + + GE+ ++ + V GY N+ E T+ +L TGDL
Sbjct: 385 IIDPDTLIPCDFDQVGEIWVQSNSVAKGYWNQPEETRHAFAGKIKDDERSAIYLRTGDLG 444
Query: 56 YRLPDGTHFI 65
+ L + ++
Sbjct: 445 F-LHENELYV 453
>3ipl_A 2-succinylbenzoate--COA ligase; structural genomics, acyl-protein
synthetase, PSI-2, protein structure initiative; 2.30A
{Staphylococcus aureus subsp}
Length = 501
Score = 59.9 bits (146), Expect = 8e-13
Identities = 17/58 (29%), Positives = 26/58 (44%), Gaps = 9/58 (15%)
Query: 5 IIDPVTSVQLPDGKTGELCLKGD-VFLGYRNKVEATKEMLDDDGWLHTGDLAYRLPDG 61
I +P GEL +KG V GY + T ++G+ +TGD+A +G
Sbjct: 340 IKNP------NKEGHGELMIKGANVMNGYLYPTDLTGTF--ENGYFNTGDIAEIDHEG 389
>1v25_A Long-chain-fatty-acid-COA synthetase; ligase, structural genomics,
riken structural genomics/proteomics initiative, RSGI;
HET: ANP; 2.30A {Thermus thermophilus} SCOP: e.23.1.1
PDB: 1ult_A* 1v26_A*
Length = 541
Score = 57.9 bits (141), Expect = 4e-12
Identities = 22/60 (36%), Positives = 29/60 (48%), Gaps = 2/60 (3%)
Query: 4 TIIDPVTSVQLPDGKT-GELCLKGD-VFLGYRNKVEATKEMLDDDGWLHTGDLAYRLPDG 61
+ D DGK GE+ LKG + GY EAT+ L DG+ TGD+A +G
Sbjct: 367 RVADEEGRPVPKDGKALGEVQLKGPWITGGYYGNEEATRSALTPDGFFRTGDIAVWDEEG 426
>3c5e_A Acyl-coenzyme A synthetase ACSM2A, mitochondrial; middle-chain
acyl-COA synthetase, xenobiotic/medium-chain FA COA
ligase; HET: ATP; 1.60A {Homo sapiens} PDB: 2vze_A
3b7w_A* 3day_A* 3eq6_A* 3eyn_A* 3gpc_A* 2wd9_A*
Length = 570
Score = 51.5 bits (124), Expect = 7e-10
Identities = 16/69 (23%), Positives = 28/69 (40%), Gaps = 10/69 (14%)
Query: 4 TIIDPVTSVQLPDGKTGELCLKGD------VFLGYRNKVEATKEMLDDDGWLHTGDLAYR 57
IID +V LP G G++ ++ +F GY + + T + + GD +
Sbjct: 386 QIIDDKGNV-LPPGTEGDIGIRVKPIRPIGIFSGYVDNPDKTAANIRG-DFWLLGDRGIK 443
Query: 58 LPDGTHFIW 66
DG +
Sbjct: 444 DEDG--YFQ 450
>3etc_A AMP-binding protein; adenylate-forming acyl-COA synthetase ligase,
ligase; HET: PGE 1PE EPE; 2.10A {Methanosarcina
acetivorans}
Length = 580
Score = 49.1 bits (118), Expect = 5e-09
Identities = 19/68 (27%), Positives = 33/68 (48%), Gaps = 10/68 (14%)
Query: 5 IIDPVTSVQLPDGKTGELCLKGD------VFLGYRNKVEATKEMLDDDGWLHTGDLAYRL 58
++D + G+ GE+ + +F+ Y E T+E D G+ HTGD+A+
Sbjct: 406 LMDRDGRL-CEVGEEGEIVINTMEGKPVGLFVHYGKDPERTEETWHD-GYYHTGDMAWMD 463
Query: 59 PDGTHFIW 66
DG ++W
Sbjct: 464 EDG--YLW 469
>3l8c_A D-alanine--poly(phosphoribitol) ligase subunit 1; structural
genomics, DLTA, ATP-binding, cytoplasm,
nucleotide-binding; 2.41A {Streptococcus pyogenes
serotype M6} PDB: 3lgx_A*
Length = 521
Score = 40.2 bits (95), Expect = 7e-06
Identities = 18/53 (33%), Positives = 22/53 (41%), Gaps = 4/53 (7%)
Query: 14 LPDGKTGELCLKGD-VFLGYRNKVEATKEM-LDDDG-WL-HTGDLAYRLPDGT 62
L G+ GE+ + G V GY N E T E G HTGD+ D
Sbjct: 343 LSSGEQGEIIVTGPAVSKGYLNNPEKTAEAFFTFKGQPAYHTGDIGSLTEDNI 395
>3ite_A SIDN siderophore synthetase; ligase, non-ribosomal peptide
synthesis, NRPS, sidna3, fungal, endophyte; HET: MSE;
2.00A {Neotyphodium lolii}
Length = 562
Score = 39.9 bits (94), Expect = 1e-05
Identities = 14/50 (28%), Positives = 23/50 (46%), Gaps = 2/50 (4%)
Query: 15 PDGKTGELCLKGD-VFLGYRNKVEATKEMLDDDGWLH-TGDLAYRLPDGT 62
G GEL ++G V GY N+ +A + ++ TGD+ D +
Sbjct: 370 KKGMAGELVIEGSLVANGYLNRPDAKGFCDINGRKMYRTGDIVRMDADSS 419
>1amu_A GRSA, gramicidin synthetase 1; peptide synthetase, adenylate
forming; HET: PHE AMP; 1.90A {Brevibacillus brevis}
SCOP: e.23.1.1
Length = 563
Score = 36.7 bits (86), Expect = 1e-04
Identities = 18/56 (32%), Positives = 24/56 (42%), Gaps = 7/56 (12%)
Query: 14 LPDGKTGELCLKGD-VFLGYRNKVEATKEM-----LDDDGWL-HTGDLAYRLPDGT 62
G+ GELC+ G+ + GY + E T + L TGD A L DG
Sbjct: 367 KSVGEAGELCIGGEGLARGYWKRPELTSQKFVDNPFVPGEKLYKTGDQARWLSDGN 422
>2vsq_A Surfactin synthetase subunit 3; ligase, peptidyl carrier protein,
ligase phosphoprotein, TER module, phosphopantetheine;
2.60A {Bacillus subtilis}
Length = 1304
Score = 34.1 bits (79), Expect = 0.001
Identities = 24/56 (42%), Positives = 30/56 (53%), Gaps = 7/56 (12%)
Query: 14 LPDGKTGELCLKGD-VFLGYRNKVEATKEMLDDDGWLH------TGDLAYRLPDGT 62
P G GELC+ G V GY N+ + TKE ++ + TGDLA LPDGT
Sbjct: 798 QPFGAVGELCISGMGVSKGYVNRADLTKEKFIENPFKPGETLYRTGDLARWLPDGT 853
>3e7w_A D-alanine--poly(phosphoribitol) ligase subunit 1; DLTA,
non-ribosomal peptide synthetase, NRPS, adenylation
domain, D-alanylation; HET: AMP; 2.28A {Bacillus
subtilis} PDB: 3e7x_A*
Length = 511
Score = 34.0 bits (79), Expect = 0.001
Identities = 17/53 (32%), Positives = 27/53 (50%), Gaps = 5/53 (9%)
Query: 14 LPDGKTGELCLKGD-VFLGYRNKVEATKE--MLDDDGWL-HTGDLAYRLPDGT 62
LP+G+ GE+ + G V GY + E T++ + W TGD + + DG
Sbjct: 339 LPEGEKGEIVIAGPSVSRGYLGEPELTEKAFFSHEGQWAYRTGDAGF-IQDGQ 390
>3fce_A D-alanine--poly(phosphoribitol) ligase subunit 1; DLTA, AMP-forming
domain, adenylation, D-alanine protein ligase, ATP
complex; HET: ATP; 1.90A {Bacillus cereus} PDB: 3fcc_A*
3dhv_A*
Length = 512
Score = 34.0 bits (79), Expect = 0.001
Identities = 17/53 (32%), Positives = 27/53 (50%), Gaps = 5/53 (9%)
Query: 14 LPDGKTGELCLKGD-VFLGYRNKVEATKE--MLDDDGWLH-TGDLAYRLPDGT 62
PDG+ GE+ + G V +GY E T++ + D + TGD Y + +G
Sbjct: 340 APDGEKGEIVIVGPSVSVGYLGSPELTEKAFTMIDGERAYKTGDAGY-VENGL 391
>3hgu_A EHPF; phenazine, antibiotic, biosynthetic protein; 1.95A {Pantoea
agglomerans} PDB: 3hgv_A 3l2k_A*
Length = 369
Score = 32.8 bits (74), Expect = 0.003
Identities = 10/62 (16%), Positives = 20/62 (32%), Gaps = 13/62 (20%)
Query: 5 IIDPVTSVQLPDGKTGELCLKGDVFLGYRNKVEATKEMLDDDGWLHTGDLAYRLPDGTHF 64
++D +T+ + G+ G + + + D A RLP + F
Sbjct: 299 VVDSITAQTVEYGERGNVIVT-----------HLSPWAFYPRVA--ERDTAIRLPGVSGF 345
Query: 65 IW 66
Sbjct: 346 AG 347
>4dg8_A PA1221; ANL superfamily, adenylation domain, peptidyl carrier
protei ribosomal peptide synthetase, NRPS, valine
adenylation, LIG; HET: AMP; 2.15A {Pseudomonas
aeruginosa} PDB: 4dg9_A*
Length = 620
Score = 32.5 bits (75), Expect = 0.004
Identities = 14/59 (23%), Positives = 20/59 (33%), Gaps = 9/59 (15%)
Query: 12 VQLPDGKTGELCLKGD-VFLGYRNKVEATKE------MLDDDGWLH-TGDLAYRLPDGT 62
+ P + GE+ G + GYRN T+ + TGD A G
Sbjct: 354 IAEP-DRAGEIVAFGAGLAQGYRNDAARTRASFVELPYRGRLLRAYRTGDRARYDEQGR 411
>3qov_A Phenylacetate-coenzyme A ligase; acetyl-COA synthetase-like,
structural genomics, joint cente structural genomics,
JCSG; HET: MSE ADP COA; 2.20A {Bacteroides
thetaiotaomicron} PDB: 3s89_A*
Length = 436
Score = 30.3 bits (69), Expect = 0.023
Identities = 11/20 (55%), Positives = 14/20 (70%)
Query: 5 IIDPVTSVQLPDGKTGELCL 24
IIDP T +P+G+ GEL L
Sbjct: 269 IIDPETGEPVPEGEIGELVL 288
>2y27_A Phenylacetate-coenzyme A ligase; phenylacetic acid degradation
pathway; HET: MSE PG4 ATP; 1.60A {Burkholderia
cenocepacia} PDB: 2y4n_A*
Length = 437
Score = 30.0 bits (68), Expect = 0.030
Identities = 12/20 (60%), Positives = 13/20 (65%)
Query: 5 IIDPVTSVQLPDGKTGELCL 24
IIDP T LPDG+ GEL
Sbjct: 274 IIDPETGEVLPDGELGELVF 293
>2y4o_A Phenylacetate-coenzyme A ligase; phenylacetic acid degradation
pathway; HET: DLL; 1.90A {Burkholderia cenocepacia}
Length = 443
Score = 30.0 bits (68), Expect = 0.032
Identities = 13/20 (65%), Positives = 13/20 (65%)
Query: 5 IIDPVTSVQLPDGKTGELCL 24
IIDPVT LPDG GEL
Sbjct: 276 IIDPVTGEVLPDGSQGELVF 295
>3f8d_A Thioredoxin reductase (TRXB-3); redox protein, nucleotide binding,
FAD, flavoprotein, oxidoreductase; HET: FAD; 1.40A
{Sulfolobus solfataricus} PDB: 3f8p_A* 3f8r_A*
Length = 323
Score = 25.9 bits (58), Expect = 0.86
Identities = 11/54 (20%), Positives = 23/54 (42%), Gaps = 7/54 (12%)
Query: 7 DPVTSVQLPDGKTGELC-LKGD---VFLGYRNKVEATKEM---LDDDGWLHTGD 53
V V + + KTGE+ L + + +G+ + K D +G++ +
Sbjct: 220 KVVKQVVVENLKTGEIKELNVNGVFIEIGFDPPTDFAKSNGIETDTNGYIKVDE 273
>2o7i_A Oligopeptide ABC transporter, periplasmic oligopeptide-binding
protein; periplasmic binding protein, cellulose,
thermophilic proteins; HET: CBI; 1.50A {Thermotoga
maritima} PDB: 2o7j_A* 3i5o_A*
Length = 592
Score = 25.9 bits (57), Expect = 0.97
Identities = 8/34 (23%), Positives = 14/34 (41%)
Query: 31 GYRNKVEATKEMLDDDGWLHTGDLAYRLPDGTHF 64
++ ++LD+ G+ D PDGT
Sbjct: 339 RIPFDLDMANKILDEAGYKKGPDGVRVGPDGTKL 372
>2z4i_A Copper homeostasis protein CUTF; outer memblane lipoprotein, beta
barrel, OB-fold, 3D domain swapping, signaling protein
activator; HET: P6G; 2.60A {Escherichia coli} PDB:
2z4h_A*
Length = 233
Score = 25.5 bits (55), Expect = 1.1
Identities = 7/18 (38%), Positives = 8/18 (44%)
Query: 41 EMLDDDGWLHTGDLAYRL 58
EMLD +G Y L
Sbjct: 98 EMLDREGNPIESQFNYTL 115
>2q0l_A TRXR, thioredoxin reductase; bacterial thiredoxin reductase, NADP+
B reduced izoalloxazine bending, oxidoreductase; HET:
FAD NAP; 1.45A {Helicobacter pylori} PDB: 2q0k_A*
3ish_A*
Length = 311
Score = 24.8 bits (55), Expect = 2.0
Identities = 11/57 (19%), Positives = 22/57 (38%), Gaps = 13/57 (22%)
Query: 9 VTSVQLPDGKTGE---LCLKGDVFL--GY-------RNKVEATKEMLDDDGWLHTGD 53
V+S+ + + T E L + G F+ GY + + + D+ G +
Sbjct: 212 VSSLSIKNTATNEKRELVVPG-FFIFVGYDVNNAVLKQEDNSMLCKCDEYGSIVVDF 267
>1zu0_A Chitin oligosaccharide binding protein; alpha helix/beta sheet,
sugar binding protein, signaling protein; HET: CBS;
2.20A {Vibrio cholerae} PDB: 1zty_A*
Length = 529
Score = 24.3 bits (53), Expect = 3.2
Identities = 10/30 (33%), Positives = 14/30 (46%), Gaps = 1/30 (3%)
Query: 36 VEATKEMLDDDGW-LHTGDLAYRLPDGTHF 64
VE +K++L G+ GD P G F
Sbjct: 323 VEGSKKLLAKAGFKDVNGDGFVETPSGKSF 352
>2kpm_A Uncharacterized protein; methods development, structural
genomics, PSI-2, protein structure initiative; NMR
{Nitrosomonas europaea}
Length = 105
Score = 23.8 bits (51), Expect = 3.5
Identities = 7/22 (31%), Positives = 11/22 (50%)
Query: 37 EATKEMLDDDGWLHTGDLAYRL 58
A ++ DD GW + G+ L
Sbjct: 28 AALEQSSDDAGWANLGNFGNYL 49
>3drf_A Oligopeptide-binding protein OPPA; oligo-peptide binding,
voluminous binding cavity, venus FLY- trap, peptide
binding protein; 1.30A {Lactococcus lactis} PDB: 3drg_A
3drh_A 3dri_A 3drj_A 3drk_A 3fto_A 3rya_A 3ryb_A
Length = 590
Score = 24.4 bits (53), Expect = 3.7
Identities = 9/29 (31%), Positives = 14/29 (48%)
Query: 36 VEATKEMLDDDGWLHTGDLAYRLPDGTHF 64
++ ++LD+DGW YR DG
Sbjct: 381 LDKANKLLDEDGWKLNKSTGYREKDGKEL 409
>2kzv_A Uncharacterized protein; structural genomics, PSI-2, protein
structure initiative, no structural genomics
consortium, NESG; NMR {Chromobacterium violaceum}
Length = 92
Score = 23.7 bits (51), Expect = 4.1
Identities = 5/22 (22%), Positives = 8/22 (36%)
Query: 37 EATKEMLDDDGWLHTGDLAYRL 58
A + + D GW + L
Sbjct: 15 SAIEAVARDSGWAELSAVGSYL 36
>1xzw_A Purple acid phosphatase; hydrolase; HET: NAG FUC MAN; 2.50A
{Ipomoea batatas} SCOP: b.1.12.1 d.159.1.1
Length = 426
Score = 24.3 bits (52), Expect = 4.2
Identities = 6/26 (23%), Positives = 8/26 (30%)
Query: 38 ATKEMLDDDGWLHTGDLAYRLPDGTH 63
+ L GDL+Y H
Sbjct: 148 YEQNSAKGQAVLFMGDLSYSNRWPNH 173
>1hyu_A AHPF, alkyl hydroperoxide reductase subunit F; thiol-thiolate
hydrogen bond, nucleotide binding fold, thior reductase,
thioredoxin; HET: FAD; 2.00A {Salmonella typhimurium}
SCOP: c.3.1.5 c.3.1.5 c.47.1.2 c.47.1.2 PDB: 1zyn_A
1zyp_A
Length = 521
Score = 24.2 bits (53), Expect = 4.2
Identities = 6/51 (11%), Positives = 16/51 (31%), Gaps = 6/51 (11%)
Query: 9 VTSVQLPDGKTGEL-CLKGD---VFLGYRNKVEATKEM--LDDDGWLHTGD 53
V ++ D +G++ + V +G + + G +
Sbjct: 424 VVGLEYRDRVSGDIHSVALAGIFVQIGLLPNTHWLEGALERNRMGEIIIDA 474
>2q1z_B Anti-sigma factor CHRR, transcriptional activator; ECF sigma
factor, cupin fold, zinc bindin transcription factor;
2.40A {Rhodobacter sphaeroides} PDB: 2z2s_B
Length = 195
Score = 23.9 bits (50), Expect = 4.4
Identities = 4/23 (17%), Positives = 7/23 (30%)
Query: 41 EMLDDDGWLHTGDLAYRLPDGTH 63
D+ GD+ + H
Sbjct: 155 AFRDETDRFGAGDIEIADQELEH 177
>3ry3_A Putative solute-binding protein; structural genomics, IDP00509,
center for structural genomic infectious diseases,
csgid, transport prote; 2.43A {Yersinia pestis}
Length = 528
Score = 23.9 bits (52), Expect = 4.4
Identities = 6/33 (18%), Positives = 12/33 (36%), Gaps = 1/33 (3%)
Query: 32 YRNKVEATKEMLDDDGWLHTGDLAYRLPDGTHF 64
++ K++L+ GW R +G
Sbjct: 329 KDGDIDKAKQILEQAGWQLNSQ-GTREKNGLPA 360
>1vr5_A Oligopeptide ABC transporter, periplasmic oligope binding protein;
TM1223, periplasmic oligopepti binding, structural
genomics; HET: EPE; 1.73A {Thermotoga maritima} SCOP:
c.94.1.1
Length = 547
Score = 23.9 bits (52), Expect = 5.0
Identities = 10/35 (28%), Positives = 17/35 (48%), Gaps = 1/35 (2%)
Query: 31 GYRNKVEATKEMLDDDGW-LHTGDLAYRLPDGTHF 64
G++ E K++LD+ G+ D P+G F
Sbjct: 333 GFKYDPEMAKKILDELGFKDVNKDGFREDPNGKPF 367
>3ewi_A N-acylneuraminate cytidylyltransferase; beta barrel, HAD-like,
rossmannoid fold, nucleotidyltransferase, nucleus; 1.90A
{Mus musculus}
Length = 168
Score = 23.6 bits (52), Expect = 5.3
Identities = 7/33 (21%), Positives = 13/33 (39%), Gaps = 1/33 (3%)
Query: 24 LKGDVFLGYRNKVEATKEMLDDDGWLHTGDLAY 56
L + +K+ E + G L ++AY
Sbjct: 73 LDCKTEVSVSDKLATVDEWRKEMG-LCWKEVAY 104
>1gr0_A Inositol-3-phosphate synthase; isomerase, oxidoreductase, PSI,
protein structure initiative, TB structural genomics
consortium, TB; HET: NAD; 1.95A {Mycobacterium
tuberculosis} SCOP: c.2.1.3 d.81.1.3
Length = 367
Score = 23.5 bits (50), Expect = 5.7
Identities = 12/40 (30%), Positives = 16/40 (40%), Gaps = 1/40 (2%)
Query: 6 IDPVTSVQ-LPDGKTGELCLKGDVFLGYRNKVEATKEMLD 44
I P V L D K + L+G F +E E+ D
Sbjct: 271 IGPSDHVGWLDDRKWAYVRLEGRAFGDVPLNLEYKLEVWD 310
>3cty_A Thioredoxin reductase; FAD, oxidoreductase, flavin, flavoprotein;
HET: FAD; 2.35A {Thermoplasma acidophilum}
Length = 319
Score = 23.6 bits (52), Expect = 5.7
Identities = 13/52 (25%), Positives = 24/52 (46%), Gaps = 7/52 (13%)
Query: 9 VTSVQLPDGKTGELC-LKGD---VFLGYRNKVEATKEM---LDDDGWLHTGD 53
VT V+ D TGE ++ D +++G + K+ LD+ G++
Sbjct: 223 VTGVKYKDRTTGEEKLIETDGVFIYVGLIPQTSFLKDSGVKLDERGYIVVDS 274
>2ecf_A Dipeptidyl peptidase IV; prolyl oligopeptidase family, peptidase
family S9, hydrolase; 2.80A {Stenotrophomonas
maltophilia}
Length = 741
Score = 23.5 bits (51), Expect = 6.4
Identities = 5/22 (22%), Positives = 9/22 (40%), Gaps = 1/22 (4%)
Query: 45 DDGWLHTGDLAYRLPDGTHFIW 66
W+ + L DG+ +W
Sbjct: 332 SPTWVPLHNSLRFLDDGS-ILW 352
>1xoc_A Oligopeptide-binding protein APPA; oligopeptide, APPA, transport,
transport protein; 1.55A {Bacillus subtilis} SCOP:
c.94.1.1
Length = 520
Score = 23.4 bits (51), Expect = 8.0
Identities = 9/29 (31%), Positives = 12/29 (41%)
Query: 36 VEATKEMLDDDGWLHTGDLAYRLPDGTHF 64
+ K+ML + GW T DG F
Sbjct: 332 EKKAKQMLAEAGWKDTNGDGILDKDGKKF 360
>1l6s_A Porphobilinogen synthase; dehydratase, lyase; HET: CME DSB; 1.70A
{Escherichia coli} SCOP: c.1.10.3 PDB: 1i8j_A* 1l6y_A*
1b4e_A
Length = 323
Score = 23.2 bits (51), Expect = 8.3
Identities = 7/21 (33%), Positives = 13/21 (61%)
Query: 36 VEATKEMLDDDGWLHTGDLAY 56
V+A ++ LD G+ T ++Y
Sbjct: 171 VQAIRQALDAAGFKDTAIMSY 191
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
0.320 0.142 0.456
Gapped
Lambda K H
0.267 0.0789 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,113,386
Number of extensions: 52804
Number of successful extensions: 195
Number of sequences better than 10.0: 1
Number of HSP's gapped: 165
Number of HSP's successfully gapped: 62
Length of query: 66
Length of database: 6,701,793
Length adjustment: 37
Effective length of query: 29
Effective length of database: 5,668,716
Effective search space: 164392764
Effective search space used: 164392764
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 (21.8 bits)
S2: 51 (23.3 bits)