RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy4547
(92 letters)
>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 = 100 bits (252), Expect = 8e-27
Identities = 29/88 (32%), Positives = 39/88 (44%), Gaps = 7/88 (7%)
Query: 2 GTPGDIYIGGPTLAIGYLNRPDLNKMRFISTPEHLRKTCGVRLYNTGDWGYALGDGTFEV 61
G G+I + GP ++ GYLN P+ F + G Y+TGD G D
Sbjct: 346 GEQGEIIVTGPAVSKGYLNNPEKTAEAFFTFK-------GQPAYHTGDIGSLTEDNILLY 398
Query: 62 IGRSDTMVKIRGYTIELQAIEVALRDYP 89
GR D +K GY IEL+ + L P
Sbjct: 399 GGRLDFQIKYAGYRIELEDVSQQLNQSP 426
>2vsq_A Surfactin synthetase subunit 3; ligase, peptidyl carrier protein,
ligase phosphoprotein, TER module, phosphopantetheine;
2.60A {Bacillus subtilis}
Length = 1304
Score = 100 bits (252), Expect = 1e-26
Identities = 41/88 (46%), Positives = 51/88 (57%), Gaps = 4/88 (4%)
Query: 2 GTPGDIYIGGPTLAIGYLNRPDLNKMRFISTPEHLRKTCGVRLYNTGDWGYALGDGTFEV 61
G G++ I G ++ GY+NR DL K +FI P G LY TGD L DGT E
Sbjct: 801 GAVGELCISGMGVSKGYVNRADLTKEKFIENPFKP----GETLYRTGDLARWLPDGTIEY 856
Query: 62 IGRSDTMVKIRGYTIELQAIEVALRDYP 89
GR D VKIRG+ IEL+ IE L++YP
Sbjct: 857 AGRIDDQVKIRGHRIELEEIEKQLQEYP 884
>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 = 100 bits (251), Expect = 1e-26
Identities = 32/88 (36%), Positives = 45/88 (51%), Gaps = 8/88 (9%)
Query: 2 GTPGDIYIGGPTLAIGYLNRPDLNKMRFISTPEHLRKTCGVRLYNTGDWGYALGDGTFEV 61
G G+I I GP+++ GYL P+L + F S G Y TGD G+ + DG
Sbjct: 342 GEKGEIVIAGPSVSRGYLGEPELTEKAFFSHE-------GQWAYRTGDAGF-IQDGQIFC 393
Query: 62 IGRSDTMVKIRGYTIELQAIEVALRDYP 89
GR D +K+ GY +EL+ IE +R
Sbjct: 394 QGRLDFQIKLHGYRMELEEIEFHVRQSQ 421
>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 = 99.9 bits (250), Expect = 2e-26
Identities = 33/88 (37%), Positives = 46/88 (52%), Gaps = 8/88 (9%)
Query: 2 GTPGDIYIGGPTLAIGYLNRPDLNKMRFISTPEHLRKTCGVRLYNTGDWGYALGDGTFEV 61
G G+I I GP++++GYL P+L + F G R Y TGD GY + +G
Sbjct: 343 GEKGEIVIVGPSVSVGYLGSPELTEKAFTMID-------GERAYKTGDAGY-VENGLLFY 394
Query: 62 IGRSDTMVKIRGYTIELQAIEVALRDYP 89
GR D +K+ GY +EL+ IE LR
Sbjct: 395 NGRLDFQIKLHGYRMELEEIEHHLRACS 422
>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 = 97.9 bits (245), Expect = 8e-26
Identities = 36/88 (40%), Positives = 48/88 (54%), Gaps = 4/88 (4%)
Query: 2 GTPGDIYIGGPTLAIGYLNRPDLNKMRFISTPEHLRKTCGVRLYNTGDWGYALGDGTFEV 61
G G++ IGG LA GY RP+L +F+ P G +LY TGD L DG E
Sbjct: 370 GEAGELCIGGEGLARGYWKRPELTSQKFVDNPFVP----GEKLYKTGDQARWLSDGNIEY 425
Query: 62 IGRSDTMVKIRGYTIELQAIEVALRDYP 89
+GR D VKIRG+ +EL+ +E L +
Sbjct: 426 LGRIDNQVKIRGHRVELEEVESILLKHM 453
>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 = 97.2 bits (243), Expect = 2e-25
Identities = 30/88 (34%), Positives = 38/88 (43%), Gaps = 3/88 (3%)
Query: 2 GTPGDIYIGGPTLAIGYLNRPDLNKMRFISTPEHLRKTCGVRLYNTGDWGYALGDGTFEV 61
G+I G LA GY N + F+ P R +R Y TGD G
Sbjct: 358 DRAGEIVAFGAGLAQGYRNDAARTRASFVELPYRGR---LLRAYRTGDRARYDEQGRLRF 414
Query: 62 IGRSDTMVKIRGYTIELQAIEVALRDYP 89
IGR D VK+ GY ++L A+E R P
Sbjct: 415 IGRGDGQVKLNGYRLDLPALEQRFRRQP 442
>3ite_A SIDN siderophore synthetase; ligase, non-ribosomal peptide
synthesis, NRPS, sidna3, fungal, endophyte; HET: MSE;
2.00A {Neotyphodium lolii}
Length = 562
Score = 95.8 bits (239), Expect = 5e-25
Identities = 29/88 (32%), Positives = 40/88 (45%), Gaps = 9/88 (10%)
Query: 2 GTPGDIYIGGPTLAIGYLNRPDLNKMRFISTPEHLRKTCGVRLYNTGDWGYALGDGTFEV 61
G G++ I G +A GYLNRPD F G ++Y TGD D +
Sbjct: 372 GMAGELVIEGSLVANGYLNRPDAK--GFCDIN-------GRKMYRTGDIVRMDADSSILF 422
Query: 62 IGRSDTMVKIRGYTIELQAIEVALRDYP 89
+GR D VK+RG +EL + +R
Sbjct: 423 LGRKDEQVKVRGQRLELGEVSEVIRSLS 450
>2v7b_A Benzoate-coenzyme A ligase; benzoate oxidation, benzoate COA
ligase; 1.84A {Burkholderia xenovorans}
Length = 529
Score = 51.0 bits (123), Expect = 3e-09
Identities = 22/75 (29%), Positives = 35/75 (46%), Gaps = 11/75 (14%)
Query: 2 GTPGDIYIGGPTLAIGYLNRPDLNKMRFISTPEHLRKTCGVRLYNTGDWGYALGDGTFEV 61
G GD+YI GP+ A+ Y N + ++ F+ +GD L +G +
Sbjct: 376 GEVGDLYIKGPSAAVMYWNNREKSRATFLG-----------EWIRSGDKYCRLPNGCYVY 424
Query: 62 IGRSDTMVKIRGYTI 76
GRSD M+K+ G +
Sbjct: 425 AGRSDDMLKVSGQYV 439
>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 = 47.3 bits (113), Expect = 6e-08
Identities = 22/86 (25%), Positives = 38/86 (44%), Gaps = 3/86 (3%)
Query: 2 GTPGDIYIGGPTLAIGYLNRPDLNKMRFISTPEHLRKTCGVRLYNTGDWGYALGDGTFEV 61
G+I++ ++A GY N+P+ + F + ++ TGD G+ L + V
Sbjct: 397 DQVGEIWVQSNSVAKGYWNQPEETRHAFAGKIKDDERSAIY--LRTGDLGF-LHENELYV 453
Query: 62 IGRSDTMVKIRGYTIELQAIEVALRD 87
GR ++ I G Q IE +L
Sbjct: 454 TGRIKDLIIIYGKNHYPQDIEFSLMH 479
>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 = 44.6 bits (106), Expect = 5e-07
Identities = 27/88 (30%), Positives = 31/88 (35%), Gaps = 12/88 (13%)
Query: 2 GTPGDIYIGGPTLAIGYLNRPDLNKMRFISTPEHLRKTCGVRLYNTGDWGYALGDGTFEV 61
G I I GP+L GY +TGD GY L DG V
Sbjct: 409 RVVGHICISGPSLMSGYFGDQVSQDEIA-----------ATGWLDTGDLGY-LLDGYLYV 456
Query: 62 IGRSDTMVKIRGYTIELQAIEVALRDYP 89
GR ++ IRG I Q IE P
Sbjct: 457 TGRIKDLIIIRGRNIWPQDIEYIAEQEP 484
>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 = 42.6 bits (101), Expect = 3e-06
Identities = 22/80 (27%), Positives = 31/80 (38%), Gaps = 16/80 (20%)
Query: 2 GTPGDIYIGGPT-----LAIGYLNRPDLNKMRFISTPEHLRKTCGVRLYNTGDWGYALGD 56
GT GDI I + GY++ PD + GD G D
Sbjct: 398 GTEGDIGIRVKPIRPIGIFSGYVDNPDKTAANIRG-----------DFWLLGDRGIKDED 446
Query: 57 GTFEVIGRSDTMVKIRGYTI 76
G F+ +GR+D ++ GY I
Sbjct: 447 GYFQFMGRADDIINSSGYRI 466
>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 = 42.4 bits (100), Expect = 3e-06
Identities = 20/64 (31%), Positives = 31/64 (48%), Gaps = 2/64 (3%)
Query: 2 GTPGDIYIGGPTLAIGYLNRPDLNKMRFISTPEHLRKTCGVRLY-NTGDWGYALGDGTFE 60
GT G+I++ G +A GY +PD ++ F + TGD G+ + DG
Sbjct: 418 GTVGEIWVHGDNVANGYWQKPDESERTFGGKIVTPSPGTPEGPWLRTGDSGF-VTDGKMF 476
Query: 61 VIGR 64
+IGR
Sbjct: 477 IIGR 480
>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 = 37.6 bits (88), Expect = 2e-04
Identities = 18/72 (25%), Positives = 22/72 (30%), Gaps = 11/72 (15%)
Query: 2 GTPGDIYIGGPTLAIGYLNRPDLNKMRFISTPEHLRKTCGVRLYNTGDWGYALGDGTFEV 61
G G + GP GY P N F Y +GD +G V
Sbjct: 380 GEVGRLMTRGPYTFRGYYKSPQHNASAF--DAN--------GFYCSGDLISIDPEGYITV 429
Query: 62 IGRSDTMVKIRG 73
GR + RG
Sbjct: 430 QGREKDQI-NRG 440
>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 = 36.8 bits (86), Expect = 3e-04
Identities = 20/84 (23%), Positives = 37/84 (44%), Gaps = 15/84 (17%)
Query: 2 GTPGDIYIGGPTLAIGYLNRPDLNKMRFISTPEH-LRKTCGVRLYNTGDWGYALGDGTFE 60
G++ + GP + GY+N P+ + L +GD Y D F
Sbjct: 385 NQRGELCVRGPMIMSGYVNNPEATNALI--DKDGWLH---------SGDIAYWDEDEHFF 433
Query: 61 VIGRSDTMVKIRGYTI---ELQAI 81
++ R +++K +GY + EL++I
Sbjct: 434 IVDRLKSLIKYKGYQVAPAELESI 457
>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 = 36.8 bits (86), Expect = 3e-04
Identities = 23/84 (27%), Positives = 39/84 (46%), Gaps = 15/84 (17%)
Query: 2 GTPGDIYIGGPTLAIGYLNRPDLNKMRFISTPEH-LRKTCGVRLYNTGDWGYALGDGTFE 60
G++ + GP L GY+N P+ K E L TGD GY + F
Sbjct: 387 NRRGEVCVKGPMLMKGYVNNPEATKELI--DEEGWLH---------TGDIGYYDEEKHFF 435
Query: 61 VIGRSDTMVKIRGYTI---ELQAI 81
++ R +++K +GY + EL+++
Sbjct: 436 IVDRLKSLIKYKGYQVPPAELESV 459
>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 = 36.4 bits (85), Expect = 5e-04
Identities = 19/72 (26%), Positives = 25/72 (34%), Gaps = 11/72 (15%)
Query: 2 GTPGDIYIGGPTLAIGYLNRPDLNKMRFISTPEHLRKTCGVRLYNTGDWGYALGDGTFEV 61
G G + GP GY P+ N F + Y +GD DG V
Sbjct: 385 GEIGMLATRGPYTFCGYYQSPEHNSQVF--DED--------NYYYSGDLVQRTPDGNLRV 434
Query: 62 IGRSDTMVKIRG 73
+GR + RG
Sbjct: 435 VGRIKDQI-NRG 445
>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 = 35.2 bits (82), Expect = 0.001
Identities = 20/72 (27%), Positives = 25/72 (34%), Gaps = 11/72 (15%)
Query: 2 GTPGDIYIGGPTLAIGYLNRPDLNKMRFISTPEHLRKTCGVRLYNTGDWGYALGDGTFEV 61
G G + GP GY + N F T + Y TGD DG V
Sbjct: 376 GETGHLLTRGPYTIRGYYKAEEHNAASF--TED--------GFYRTGDIVRLTRDGYIVV 425
Query: 62 IGRSDTMVKIRG 73
GR+ + RG
Sbjct: 426 EGRAKDQI-NRG 436
>3tsy_A Fusion protein 4-coumarate--COA ligase 1, resvera synthase;
transferase; 3.10A {Arabidospis thaliana}
Length = 979
Score = 35.0 bits (81), Expect = 0.001
Identities = 24/94 (25%), Positives = 37/94 (39%), Gaps = 22/94 (23%)
Query: 2 GTPGDIYIGGPTLAIGYLNRPDLNKMRFISTPE---HLRKTCGVRLYNTGDWGYALGDGT 58
PG+I I G + GYLN P + H TGD G D
Sbjct: 427 NQPGEICIRGHQIMKGYLNNPAATAETI--DKDGWLH-----------TGDIGLIDDDDE 473
Query: 59 FEVIGRSDTMVKIRGYTI---ELQAIEVALRDYP 89
++ R ++K +G+ + EL+A+ L +P
Sbjct: 474 LFIVDRLKELIKYKGFQVAPAELEAL---LIGHP 504
>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 = 34.5 bits (80), Expect = 0.002
Identities = 31/90 (34%), Positives = 41/90 (45%), Gaps = 13/90 (14%)
Query: 2 GTPGDIYIGGPTLAIGYLNRPDLNKMRFISTPEH-LRKTCGVRLYNTGDWGYALGDGTFE 60
+ G+I + GP L YLNRPD F T + R TGD DG
Sbjct: 351 ESVGEIQVRGPNLFTEYLNRPDATAAAF--TEDGFFR---------TGDMAVRDPDGYVR 399
Query: 61 VIGRSDT-MVKIRGYTIELQAIEVALRDYP 89
++GR T ++K GY I IE AL ++P
Sbjct: 400 IVGRKATDLIKSGGYKIGAGEIENALLEHP 429
>3etc_A AMP-binding protein; adenylate-forming acyl-COA synthetase ligase,
ligase; HET: PGE 1PE EPE; 2.10A {Methanosarcina
acetivorans}
Length = 580
Score = 34.1 bits (79), Expect = 0.003
Identities = 19/80 (23%), Positives = 31/80 (38%), Gaps = 16/80 (20%)
Query: 2 GTPGDIYIGGPT-----LAIGYLNRPDLNKMRFISTPEHLRKTCGVRLYNTGDWGYALGD 56
G G+I I L + Y P+ + + Y+TGD + D
Sbjct: 417 GEEGEIVINTMEGKPVGLFVHYGKDPERTEETWHD-----------GYYHTGDMAWMDED 465
Query: 57 GTFEVIGRSDTMVKIRGYTI 76
G +GR+D ++K GY +
Sbjct: 466 GYLWFVGRADDIIKTSGYKV 485
>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 = 33.3 bits (77), Expect = 0.004
Identities = 20/76 (26%), Positives = 30/76 (39%), Gaps = 12/76 (15%)
Query: 2 GTPGDIYIGGPTLAIGYLNRPDLNKMRFISTPEH---LRKTCGVRLYNTGDWGYALGDGT 58
G G+I I GP + GY R N+ + + R TGD G+ +G
Sbjct: 381 GESGEIVIRGPNIFKGYWKREKENQECWWYDEKGRKFFR---------TGDVGFIDEEGF 431
Query: 59 FEVIGRSDTMVKIRGY 74
R ++K +GY
Sbjct: 432 LHFQDRVKEVIKYKGY 447
>3ipl_A 2-succinylbenzoate--COA ligase; structural genomics, acyl-protein
synthetase, PSI-2, protein structure initiative; 2.30A
{Staphylococcus aureus subsp}
Length = 501
Score = 32.9 bits (76), Expect = 0.006
Identities = 18/92 (19%), Positives = 28/92 (30%), Gaps = 20/92 (21%)
Query: 2 GTPGDIYIGGPTLAIGYLNRPDLNKMRFISTPEHLRKTCGVRLYNTGDWGYALGDGTFEV 61
G++ I G + GYL D TGD +G +
Sbjct: 346 EGHGELMIKGANVMNGYLYPTD--------LTGTFE---NGYFN-TGDIAEIDHEGYVMI 393
Query: 62 IGRSDTMVKIRG----YTIELQAIEVALRDYP 89
R ++ I G Y + IE + +P
Sbjct: 394 YDRRKDLI-ISGGENIYPYQ---IETVAKQFP 421
>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 = 33.0 bits (76), Expect = 0.007
Identities = 11/29 (37%), Positives = 15/29 (51%)
Query: 61 VIGRSDTMVKIRGYTIELQAIEVALRDYP 89
+ GRSD M I+G I +E L +P
Sbjct: 326 IKGRSDDMFIIKGVNIFPMQVEKILVQFP 354
>2y27_A Phenylacetate-coenzyme A ligase; phenylacetic acid degradation
pathway; HET: MSE PG4 ATP; 1.60A {Burkholderia
cenocepacia} PDB: 2y4n_A*
Length = 437
Score = 33.0 bits (76), Expect = 0.007
Identities = 10/29 (34%), Positives = 14/29 (48%)
Query: 61 VIGRSDTMVKIRGYTIELQAIEVALRDYP 89
+ GRSD M+ +RG + IE L
Sbjct: 328 ITGRSDDMMIVRGVNVFPTQIEEQLLKQR 356
>2y4o_A Phenylacetate-coenzyme A ligase; phenylacetic acid degradation
pathway; HET: DLL; 1.90A {Burkholderia cenocepacia}
Length = 443
Score = 32.7 bits (75), Expect = 0.007
Identities = 10/29 (34%), Positives = 15/29 (51%)
Query: 61 VIGRSDTMVKIRGYTIELQAIEVALRDYP 89
+ GRSD M+ +RG + IE + P
Sbjct: 330 ITGRSDDMLIVRGVNVFPSQIEEIVVALP 358
>4fuq_A Malonyl COA synthetase; ANL superfamily, methylma malonate, ligase;
HET: MSE; 1.70A {Rhodopseudomonas palustris} PDB:
4fut_A*
Length = 503
Score = 32.6 bits (75), Expect = 0.008
Identities = 25/92 (27%), Positives = 33/92 (35%), Gaps = 18/92 (19%)
Query: 2 GTPGDIYIGGPTLAIGYLNRPDLNKMRFISTPEHLRKTCGVRLYNTGDWGYALGDGTFEV 61
G G I + GP + GY P+ T R + TGD G G +
Sbjct: 345 GDIGMIEVKGPNVFKGYWRMPE-------KTKSEFRDD---GFFITGDLGKIDERGYVHI 394
Query: 62 IGRSDTMVKIRG----YTIELQAIEVALRDYP 89
+GR +V I G Y E IE + P
Sbjct: 395 LGRGKDLV-ITGGFNVYPKE---IESEIDAMP 422
>3ni2_A 4-coumarate:COA ligase; 4CL, phenylpropanoid biosynthesis; HET: AYL
EPE; 1.90A {Populus tomentosa} PDB: 3a9v_A* 3a9u_A*
Length = 536
Score = 32.5 bits (75), Expect = 0.008
Identities = 24/86 (27%), Positives = 36/86 (41%), Gaps = 19/86 (22%)
Query: 2 GTPGDIYIGGPTLAIGYLNRPDLNKMRFISTPE---HLRKTCGVRLYNTGDWGYALGDGT 58
PG+I I G + GYLN P+ E H TGD GY D
Sbjct: 380 NQPGEICIRGDQIMKGYLNDPEATSRTI--DKEGWLH-----------TGDIGYIDDDDE 426
Query: 59 FEVIGRSDTMVKIRGYTI---ELQAI 81
++ R ++K +G+ + EL+A+
Sbjct: 427 LFIVDRLKELIKYKGFQVAPAELEAL 452
>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 = 30.8 bits (69), Expect = 0.046
Identities = 17/82 (20%), Positives = 29/82 (35%), Gaps = 25/82 (30%)
Query: 10 GGPT--LAIGYLNRPDLNKMRFIS-TPEHL--RKTCGVRLYNTGDWGYALGDGTFEVIGR 64
G P+ L+I L + + +++ T HL K + L N G
Sbjct: 333 GVPSPMLSISNLTQEQVQD--YVNKTNSHLPAGKQVEISLVN----------------GA 374
Query: 65 SDTMVKIRGYTIELQAIEVALR 86
+V + G L + + LR
Sbjct: 375 -KNLV-VSGPPQSLYGLNLTLR 394
>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 = 30.6 bits (70), Expect = 0.048
Identities = 26/94 (27%), Positives = 36/94 (38%), Gaps = 21/94 (22%)
Query: 2 GTPGDIYIGGPTLAIGYLNRPDLNKMRFISTPEHLRKTCGVRLYNTGDWGYALGDGTFEV 61
G G+I + GPT+ GY N T R + TGD G DG
Sbjct: 345 GEVGEIVLRGPTVFKGYWNNAAA-------TQHAFR---NGWHH-TGDMGRFDADGYLFY 393
Query: 62 IGRSDT--MVKIRG----YTIELQAIEVALRDYP 89
GR+ ++ G Y E +E AL+ +P
Sbjct: 394 AGRAPEKELI-KTGGENVYPAE---VEGALKQHP 423
>1m8p_A Sulfate adenylyltransferase; rossmann fold, phosphosulfate binding,
T-state; HET: PPS; 2.60A {Penicillium chrysogenum} SCOP:
b.122.1.3 c.26.1.5 c.37.1.15 PDB: 1i2d_A*
Length = 573
Score = 29.2 bits (65), Expect = 0.14
Identities = 14/40 (35%), Positives = 18/40 (45%), Gaps = 2/40 (5%)
Query: 1 MGTPGDIYIGGPTLAIGYLNRPDLNKMRFISTPEHLRKTC 40
T + YIGG A+ LN D +R+ TP LR
Sbjct: 148 NNTVKEFYIGGKIEAVNKLNHYDYVALRY--TPAELRVHF 185
>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 = 28.7 bits (65), Expect = 0.19
Identities = 27/93 (29%), Positives = 40/93 (43%), Gaps = 20/93 (21%)
Query: 2 GTPGDIYI-GGPTLAIGYLNRPDLNKMRFISTPEHLRKTCGVRLYNTGDWGYALGDGTFE 60
G G++ + + +GYLN+P +T E L+ G Y T D +GT
Sbjct: 348 GEEGELIVAASDSAFVGYLNQPQ-------ATAEKLQD--G--WYRTSDVAVWTPEGTVR 396
Query: 61 VIGRSDTMVKIRG----YTIELQAIEVALRDYP 89
++GR D M+ I G + E IE L P
Sbjct: 397 ILGRVDDMI-ISGGENIHPSE---IERVLGTAP 425
>3qio_A GAG-POL polyprotein; RNAse H, inhibitor, nuclease, transferase,
hydrolase- complex; HET: QID; 1.40A {Hiv-1 M} PDB:
3qin_A* 3hyf_A* 1o1w_A 3lp3_A* 1hrh_A 3k2p_A* 1rdh_A
Length = 150
Score = 28.3 bits (64), Expect = 0.23
Identities = 15/46 (32%), Positives = 20/46 (43%), Gaps = 12/46 (26%)
Query: 48 GDWGYALGDGTFEVIGRSDT----MVKIRGYTIELQAIEVALRDYP 89
G GY G +V+ +DT ELQAI +AL+D
Sbjct: 28 GKAGYVTNRGRQKVVTLTDTTNQKT--------ELQAIYLALQDSG 65
>2gks_A Bifunctional SAT/APS kinase; transferase, sulfurylase; HET: ADP;
2.31A {Aquifex aeolicus}
Length = 546
Score = 28.4 bits (63), Expect = 0.26
Identities = 13/68 (19%), Positives = 21/68 (30%), Gaps = 7/68 (10%)
Query: 5 GDIYIGGPTLAIGYLNRPDLNKMRFISTPEHLRKTCGVRLYNTGDWGYALGDGTFEVIGR 64
G+ YI G I D + R TP+ +R+ + T + R
Sbjct: 125 GEYYISGELKVIQLPKYYDFPEYRK--TPKQVREEIKSL-----GLDKIVAFQTRNPMHR 177
Query: 65 SDTMVKIR 72
+ R
Sbjct: 178 VHEELTKR 185
>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 = 28.3 bits (64), Expect = 0.33
Identities = 23/89 (25%), Positives = 32/89 (35%), Gaps = 19/89 (21%)
Query: 5 GDIYIGGPTLAIGYLNRPDLNKMRFISTPEHLRKTCGVRLYNTGDWGYALGDGTFEVIGR 64
G++ I L Y NRP+ T + G + TGD G +G + R
Sbjct: 363 GEVVIKSDILLKEYWNRPEA-------TRDAFDN--G--WFRTGDIGEIDDEGYLYIKDR 411
Query: 65 SDTMVKIRG----YTIELQAIEVALRDYP 89
M+ I G Y E IE + P
Sbjct: 412 LKDMI-ISGGENVYPAE---IESVIIGVP 436
>2nxp_A Transcription initiation factor TFIID subunit 5; transcription
factor, TAF5; 2.17A {Homo sapiens} SCOP: d.379.1.1
Length = 156
Score = 27.2 bits (60), Expect = 0.56
Identities = 8/68 (11%), Positives = 25/68 (36%), Gaps = 10/68 (14%)
Query: 7 IYIGGPTLAIGYLNR----------PDLNKMRFISTPEHLRKTCGVRLYNTGDWGYALGD 56
+Y A + + DL + ++ EH++ + + T + +
Sbjct: 65 VYNQHENEAKSFFEKFHGDQECYYQDDLRVLSSLTKKEHMKGNETMLDFRTSKFVLRISR 124
Query: 57 GTFEVIGR 64
+++++ R
Sbjct: 125 DSYQLLKR 132
>3gxs_A Phenylacetate-coenzyme A ligase; APC62324.1, structural genomics,
PSI-2, protein structure initiative; 1.43A {Bacteroides
vulgatus atcc 8482} PDB: 3lax_A
Length = 109
Score = 26.1 bits (58), Expect = 0.99
Identities = 7/26 (26%), Positives = 12/26 (46%)
Query: 64 RSDTMVKIRGYTIELQAIEVALRDYP 89
+D M+ ++G I IE L +
Sbjct: 2 NADDMIILKGVNIFPIQIETILLQFK 27
>2j4b_A TAF5, transcription initiation factor TFIID subunit 72/ kDa; WD
repeat; 2.5A {Encephalitozoon cuniculi} SCOP: d.379.1.1
Length = 138
Score = 26.0 bits (57), Expect = 1.5
Identities = 7/67 (10%), Positives = 22/67 (32%), Gaps = 9/67 (13%)
Query: 7 IYIGGPTLAIGYLNR---------PDLNKMRFISTPEHLRKTCGVRLYNTGDWGYALGDG 57
I A + + ++ + I T +H+ + + + ++G
Sbjct: 46 IQQNKTDEAKEFFEKYRGDHYNKSEEIKQFESIYTVQHIHENNFAYTFKNSKYHLSMGRY 105
Query: 58 TFEVIGR 64
F+++
Sbjct: 106 AFDLLIN 112
>3cr8_A Sulfate adenylyltranferase, adenylylsulfate kinase; APS kinase,
transferase, sulfate metabolism, nucleotide 2 kinase;
2.95A {Thiobacillus denitrificans}
Length = 552
Score = 26.4 bits (58), Expect = 1.7
Identities = 8/33 (24%), Positives = 11/33 (33%), Gaps = 2/33 (6%)
Query: 6 DIYIGGPTLAIGYLNRPDLNKMRFISTPEHLRK 38
++ G PD +R TP LR
Sbjct: 126 RWHLAGEVEGAALPPHPDFVSLRA--TPAELRA 156
>2kq2_A Ribonuclease H-related protein; PSI, NESG, protein structure, APO
enzyme, structural genomics, protein structure
initiative; NMR {Desulfitobacterium hafniense dcb-2}
PDB: 2kw4_A
Length = 147
Score = 25.8 bits (57), Expect = 2.0
Identities = 9/46 (19%), Positives = 14/46 (30%), Gaps = 5/46 (10%)
Query: 46 NTGDWGYAL---GDGTFEVIGRSD--TMVKIRGYTIELQAIEVALR 86
W YA G +E +R E+ A A++
Sbjct: 18 GQYAWAYAFVKDGKVHYEDADVGKNPAAATMRNVAGEIAAALYAVK 63
>2juh_A Telomere binding protein TBP1; helix, nucleus, nuclear protein;
NMR {Nicotiana glutinosa}
Length = 121
Score = 25.5 bits (55), Expect = 2.0
Identities = 9/43 (20%), Positives = 14/43 (32%), Gaps = 2/43 (4%)
Query: 34 EHLRKTCGVRLYNTGDWGYALGDGTFEVIGRSDTMVKIRGYTI 76
E L + V TG W R+ +K + T+
Sbjct: 26 EALVE--AVEHLGTGRWRDVKMRAFDNADHRTYVDLKDKWKTL 66
>2ckx_A NGTRF1, telomere binding protein TBP1; nuclear protein; 1.9A
{Nicotiana tabacum} SCOP: a.4.1.3 PDB: 2qhb_A
Length = 83
Score = 24.9 bits (54), Expect = 2.4
Identities = 9/43 (20%), Positives = 14/43 (32%), Gaps = 2/43 (4%)
Query: 34 EHLRKTCGVRLYNTGDWGYALGDGTFEVIGRSDTMVKIRGYTI 76
E L + V TG W R+ +K + T+
Sbjct: 9 EALVE--AVEHLGTGRWRDVKMRAFDNADHRTYVDLKDKWKTL 49
>2aje_A Telomere repeat-binding protein; DNA-binding, Trp, MYB motif, DNA
binding protein; NMR {Arabidopsis thaliana} SCOP:
a.4.1.3
Length = 105
Score = 25.4 bits (55), Expect = 2.4
Identities = 10/47 (21%), Positives = 16/47 (34%), Gaps = 2/47 (4%)
Query: 34 EHLRKTCGVRLYNTGDWGYALGDGTFEVIGRSDTMVKIRGYTIELQA 80
E L + V TG W + R+ +K + T+ A
Sbjct: 22 EALVQ--AVEKLGTGRWRDVKLCAFEDADHRTYVDLKDKWKTLVHTA 66
>2roh_A RTBP1, telomere binding protein-1; plant, nucleus, DNA binding
protein; NMR {Oryza sativa}
Length = 122
Score = 25.1 bits (54), Expect = 3.1
Identities = 9/39 (23%), Positives = 13/39 (33%), Gaps = 2/39 (5%)
Query: 34 EHLRKTCGVRLYNTGDWGYALGDGTFEVIGRSDTMVKIR 72
E L + V TG W V R+ +K +
Sbjct: 40 ELLVE--AVEHLGTGRWRDVKFRAFENVHHRTYVDLKDK 76
>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 = 25.2 bits (56), Expect = 4.0
Identities = 5/27 (18%), Positives = 11/27 (40%)
Query: 3 TPGDIYIGGPTLAIGYLNRPDLNKMRF 29
G++ + GP + GY + +
Sbjct: 382 ALGEVQLKGPWITGGYYGNEEATRSAL 408
>2j49_A Transcription initiation factor TFIID subunit 5; nuclear protein,
transcription regulation, TA TFIID, WD repeat; 2.3A
{Saccharomyces cerevisiae} SCOP: d.379.1.1
Length = 148
Score = 24.4 bits (53), Expect = 5.3
Identities = 6/65 (9%), Positives = 25/65 (38%), Gaps = 10/65 (15%)
Query: 6 DIYIGGPTLAIGYLNR----------PDLNKMRFISTPEHLRKTCGVRLYNTGDWGYALG 55
++ P A + +R ++N++ +++ +H+++ + + + +
Sbjct: 46 NLVAKNPVYARRFFDRFSPDFKDFHGSEINRLFSVNSIDHIKENEVASAFQSHKYRITMS 105
Query: 56 DGTFE 60
T
Sbjct: 106 KTTLN 110
>1i2k_A 4-amino-4-deoxychorismate lyase; pyridoxal phosphate, PABC; HET:
PLP; 1.79A {Escherichia coli} SCOP: e.17.1.1 PDB:
1et0_A* 1i2l_A*
Length = 269
Score = 24.4 bits (54), Expect = 6.7
Identities = 4/12 (33%), Positives = 4/12 (33%)
Query: 51 GYALGDGTFEVI 62
GDG F
Sbjct: 18 ATQFGDGCFTTA 29
>2xpf_A 4-amino-4-deoxychorismate lyase; para-aminobenzoic acid, folate
biosynthesis; HET: PLP PG4; 1.75A {Pseudomonas
aeruginosa} PDB: 2y4r_A* 2xpf_B*
Length = 292
Score = 24.1 bits (53), Expect = 9.7
Identities = 7/12 (58%), Positives = 8/12 (66%)
Query: 51 GYALGDGTFEVI 62
G A GDG FE +
Sbjct: 40 GLAYGDGLFETL 51
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
0.322 0.144 0.443
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: 1,570,184
Number of extensions: 84303
Number of successful extensions: 241
Number of sequences better than 10.0: 1
Number of HSP's gapped: 219
Number of HSP's successfully gapped: 52
Length of query: 92
Length of database: 6,701,793
Length adjustment: 59
Effective length of query: 33
Effective length of database: 5,054,454
Effective search space: 166796982
Effective search space used: 166796982
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)