RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy2507
(111 letters)
>3tig_A TTL protein; ATP-grAsp, ligase, tubulin; 2.50A {Silurana} PDB:
3tii_A* 3tin_A*
Length = 380
Score = 66.6 bits (162), Expect = 2e-14
Identities = 16/49 (32%), Positives = 29/49 (59%), Gaps = 2/49 (4%)
Query: 6 YELYGFDILIDSDLKPWLLEVNLSPSLGCDTPLDTRLKSAMLADTLTLV 54
++L+GFD ++D +LK WL+EVN +P+ L L ++ ++ V
Sbjct: 315 FQLFGFDFMVDKNLKVWLIEVNGAPACA--QKLYAELCKGIVDLAISSV 361
>1uc8_A LYSX, lysine biosynthesis enzyme; alpha-aminoadipate pathway, riken
structural genomics/proteomics initiative, RSGI,
structural genomics; 2.00A {Thermus thermophilus} SCOP:
c.30.1.6 d.142.1.7 PDB: 1uc9_A*
Length = 280
Score = 30.5 bits (69), Expect = 0.076
Identities = 4/26 (15%), Positives = 8/26 (30%), Gaps = 1/26 (3%)
Query: 7 ELYGFDILIDSDLKPWLLEVNLSPSL 32
+ D+ + EVN +
Sbjct: 232 GVVAVDLFESER-GLLVNEVNHTMEF 256
>1iow_A DD-ligase, DDLB, D-ALA\:D-Ala ligase; glycogen phosphorylase, cell
WALL, peptidoglycan synthesis, vancomycin, ADP binding;
HET: ADP PHY; 1.90A {Escherichia coli} SCOP: c.30.1.2
d.142.1.1 PDB: 1iov_A* 2dln_A* 3v4z_A*
Length = 306
Score = 30.2 bits (69), Expect = 0.11
Identities = 10/19 (52%), Positives = 15/19 (78%)
Query: 12 DILIDSDLKPWLLEVNLSP 30
D+++DSD + +LLE N SP
Sbjct: 257 DVMLDSDGQFYLLEANTSP 275
>4eg0_A D-alanine--D-alanine ligase; structural genomics, seattle
structural genomics center for infectious disease,
ssgcid; 1.65A {Burkholderia ambifaria} PDB: 4egq_A
Length = 317
Score = 29.8 bits (68), Expect = 0.12
Identities = 7/19 (36%), Positives = 12/19 (63%)
Query: 12 DILIDSDLKPWLLEVNLSP 30
D ++D+ + LEVN +P
Sbjct: 266 DFMLDAAGNAYFLEVNTAP 284
>2q7d_A Inositol-tetrakisphosphate 1-kinase; inositol kinase, ITPK1,
inositol 1,3,4-5/6 phosphate, inositol phosphate,
inositolphosphate; HET: ANP; 1.60A {Homo sapiens} PDB:
2qb5_A* 2odt_X
Length = 346
Score = 28.2 bits (62), Expect = 0.48
Identities = 7/25 (28%), Positives = 16/25 (64%), Gaps = 1/25 (4%)
Query: 8 LYGFDILIDSDL-KPWLLEVNLSPS 31
L+G DI+I++ + ++++N P
Sbjct: 288 LFGIDIIINNQTGQHAVIDINAFPG 312
>3vmm_A Alanine-anticapsin ligase BACD; ATP-grAsp domain, amino acid
ligase, ATP binding; HET: ADP P0D; 2.50A {Bacillus
subtilis}
Length = 474
Score = 27.6 bits (61), Expect = 1.0
Identities = 5/27 (18%), Positives = 11/27 (40%)
Query: 12 DILIDSDLKPWLLEVNLSPSLGCDTPL 38
+I + + +P L+E + P
Sbjct: 313 EIKLMKNREPGLIESAARFAGWNMIPN 339
>1z2n_X Inositol 1,3,4-trisphosphate 5/6-kinase; inositol phosphate kinase,
ATP-grAsp, transferase; HET: ADP; 1.20A {Entamoeba
histolytica} PDB: 1z2o_X* 1z2p_X*
Length = 324
Score = 27.1 bits (59), Expect = 1.4
Identities = 9/28 (32%), Positives = 18/28 (64%), Gaps = 1/28 (3%)
Query: 7 ELYGFDILIDSDL-KPWLLEVNLSPSLG 33
+L G D + +++ P +++VN+ PS G
Sbjct: 275 QLCGIDFIKENEQGNPLVVDVNVFPSYG 302
>3r5x_A D-alanine--D-alanine ligase; alpha-beta structure, cytosol,
structural genomics, for structural genomics of
infectious diseases, csgid; HET: MSE ATP; 2.00A
{Bacillus anthracis} PDB: 3r23_A*
Length = 307
Score = 26.7 bits (60), Expect = 1.9
Identities = 6/19 (31%), Positives = 12/19 (63%), Gaps = 1/19 (5%)
Query: 12 DILIDSDLKPWLLEVNLSP 30
D+++ P+++EVN P
Sbjct: 251 DMMVKDG-IPYVMEVNTLP 268
>3e5n_A D-alanine-D-alanine ligase A; bacterial blight; 2.00A {Xanthomonas
oryzae PV} PDB: 3r5f_A* 3rfc_A*
Length = 386
Score = 26.4 bits (59), Expect = 2.0
Identities = 6/19 (31%), Positives = 11/19 (57%)
Query: 12 DILIDSDLKPWLLEVNLSP 30
D+ + +D + + EVN P
Sbjct: 321 DVFLCADGRIVINEVNTLP 339
>1vlb_A Aldehyde oxidoreductase; iron-sulphur cluster; HET: PCD; 1.28A
{Desulfovibrio gigas} SCOP: a.56.1.1 d.15.4.2 d.41.1.1
d.133.1.1 PDB: 1sij_A* 1zcs_A* 3fah_A* 3fc4_A* 3l4p_A*
Length = 907
Score = 26.5 bits (59), Expect = 2.1
Identities = 7/46 (15%), Positives = 12/46 (26%), Gaps = 5/46 (10%)
Query: 33 GCDTPLDTRLKSAMLADTLTLVGIPALDPMLRHNSTKRSPFLSSSH 78
G D + L +G+ +T +P S
Sbjct: 656 GADIGC-----VGTAHEALRPMGVAPEKIKFTWPNTATTPNSGPSG 696
>3k3p_A D-alanine--D-alanine ligase; D-alanyl-alanine synthetase,
ATP-binding, cell shape, cell W biogenesis/degradation,
magnesium, manganese; 2.23A {Streptococcus mutans}
Length = 383
Score = 26.5 bits (59), Expect = 2.1
Identities = 7/19 (36%), Positives = 10/19 (52%)
Query: 12 DILIDSDLKPWLLEVNLSP 30
D + D K +L E+N P
Sbjct: 323 DFFLTEDGKVYLNELNTMP 341
>3se7_A VANA; alpha-beta structure, D-alanine-D-lactate ligase, ligase;
HET: ATP; 3.07A {}
Length = 346
Score = 26.0 bits (58), Expect = 2.5
Identities = 8/19 (42%), Positives = 10/19 (52%)
Query: 12 DILIDSDLKPWLLEVNLSP 30
D+ + D K L EVN P
Sbjct: 292 DLFLTEDGKVVLNEVNTFP 310
>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 = 26.2 bits (57), Expect = 3.4
Identities = 13/58 (22%), Positives = 23/58 (39%), Gaps = 13/58 (22%)
Query: 7 ELYGFDIL-IDSDLKPWLLEVNLSPSLG-----------CDTPLDTRLKSAMLADTLT 52
+ YGF IL I + P L ++ G +T +D +LK+ + +
Sbjct: 1655 DTYGFSILDIVIN-NPVNLTIHFGGEKGKRIRENYSAMIFETIVDGKLKTEKIFKEIN 1711
Score = 25.4 bits (55), Expect = 5.0
Identities = 14/57 (24%), Positives = 22/57 (38%), Gaps = 15/57 (26%)
Query: 3 SEKYELYGFDILIDSDLKPWLLEVNLSPSLGCDTPLDTRLKSAMLADTLTLVGIPAL 59
+EK G +IL WL + +TP L S ++ L+G+ L
Sbjct: 205 AEKVFTQGLNIL------EWLENPS-------NTPDKDYLLSIPIS--CPLIGVIQL 246
>3i12_A D-alanine-D-alanine ligase A; D-alanyl-alanine synthetase A, ADP
binding protein, csgid, A binding, cell shape; HET: ADP;
2.20A {Salmonella typhimurium} PDB: 3q1k_A*
Length = 364
Score = 25.6 bits (57), Expect = 3.5
Identities = 5/19 (26%), Positives = 11/19 (57%)
Query: 12 DILIDSDLKPWLLEVNLSP 30
D+ + +D + + E+N P
Sbjct: 302 DVFLTADNEVVINEINTLP 320
>1e4e_A Vancomycin/teicoplanin A-type resistance protein; ligase, cell
WALL, antibiotic resistance, membrane, peptidog
synthesis; HET: ADP PHY; 2.5A {Enterococcus faecium}
SCOP: c.30.1.2 d.142.1.1 PDB: 1e4e_B*
Length = 343
Score = 25.6 bits (57), Expect = 4.4
Identities = 6/19 (31%), Positives = 10/19 (52%)
Query: 12 DILIDSDLKPWLLEVNLSP 30
D+ + + + L EVN P
Sbjct: 292 DMFLQDNGRIVLNEVNTLP 310
>2i87_A D-alanine-D-alanine ligase; APO; 2.00A {Staphylococcus aureus
subsp} PDB: 2i8c_A* 3n8d_A* 2i80_A*
Length = 364
Score = 25.2 bits (56), Expect = 5.1
Identities = 5/19 (26%), Positives = 9/19 (47%)
Query: 12 DILIDSDLKPWLLEVNLSP 30
D + D + ++ E N P
Sbjct: 293 DFFVTEDNQIYINETNAMP 311
>1ehi_A LMDDL2, D-alanine:D-lactate ligase; ATP-binding. grAsp motif for
ATP.; HET: ADP PHY; 2.38A {Leuconostoc mesenteroides}
SCOP: c.30.1.2 d.142.1.1
Length = 377
Score = 24.5 bits (54), Expect = 8.5
Identities = 8/19 (42%), Positives = 11/19 (57%)
Query: 12 DILIDSDLKPWLLEVNLSP 30
D L+D + P+L E N P
Sbjct: 303 DFLLDENNVPYLGEPNTLP 321
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 0.134 0.395
Gapped
Lambda K H
0.267 0.0812 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,580,435
Number of extensions: 76961
Number of successful extensions: 107
Number of sequences better than 10.0: 1
Number of HSP's gapped: 106
Number of HSP's successfully gapped: 20
Length of query: 111
Length of database: 6,701,793
Length adjustment: 75
Effective length of query: 36
Effective length of database: 4,607,718
Effective search space: 165877848
Effective search space used: 165877848
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: 51 (23.3 bits)