RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy9332
(148 letters)
>3tig_A TTL protein; ATP-grAsp, ligase, tubulin; 2.50A {Silurana} PDB:
3tii_A* 3tin_A*
Length = 380
Score = 80.0 bits (197), Expect = 9e-19
Identities = 21/93 (22%), Positives = 41/93 (44%), Gaps = 5/93 (5%)
Query: 17 RGKDITNKLFTNISWLIVHSLKSVSYIMANDK---HCFECYGYDIIIDNQLKPWLIEVNA 73
++ N + I +I L + ++ H F+ +G+D ++D LK WLIEVN
Sbjct: 278 LNINLENSILCQIKEIIRVCLSCLEPAISTKYLPYHSFQLFGFDFMVDKNLKVWLIEVNG 337
Query: 74 SPSLTCTTVNDRILKYKLIDNILNIVMWNKYKK 106
+P+ + L ++D ++ V +
Sbjct: 338 APACAQKLYAE--LCKGIVDLAISSVFPLNEEN 368
>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 = 34.6 bits (79), Expect = 0.008
Identities = 21/101 (20%), Positives = 35/101 (34%), Gaps = 33/101 (32%)
Query: 47 DKHCFECYGY---DIIIDNQLKPWLIEVNASP-----------SLTCTTVNDRILKYKLI 92
D H + YG+ DI+I+N P + ++ ++ T+ D LK + I
Sbjct: 1650 DNHFKDTYGFSILDIVINN---PVNLTIHFGGEKGKRIRENYSAMIFETIVDGKLKTEKI 1706
Query: 93 DNILNI----VMWNKYKKADGGAAGGEALNLGNF-Q--LLL 126
+N + G L+ F Q L L
Sbjct: 1707 FKEINEHSTSYTFR-------SEKG--LLSATQFTQPALTL 1738
Score = 28.5 bits (63), Expect = 1.00
Identities = 7/33 (21%), Positives = 15/33 (45%), Gaps = 10/33 (30%)
Query: 3 LLKQIISHS---SQVYPRGKDITNKLFTNISWL 32
L ++I + +V+ +G +I + WL
Sbjct: 194 TLSELIRTTLDAEKVFTQGLNI-------LEWL 219
>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 = 33.2 bits (76), Expect = 0.019
Identities = 10/42 (23%), Positives = 15/42 (35%), Gaps = 7/42 (16%)
Query: 54 YGYDIIIDNQLKPWLIEVNASPSL----TCTTVN--DRILKY 89
D+ + + EVN + T V+ ILKY
Sbjct: 234 VAVDLFESER-GLLVNEVNHTMEFKNSVHTTGVDIPGEILKY 274
>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 = 32.1 bits (74), Expect = 0.041
Identities = 10/29 (34%), Positives = 19/29 (65%), Gaps = 3/29 (10%)
Query: 53 CYGY---DIIIDNQLKPWLIEVNASPSLT 78
C G+ D+++D+ + +L+E N SP +T
Sbjct: 250 CKGWGRIDVMLDSDGQFYLLEANTSPGMT 278
>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 = 32.1 bits (74), Expect = 0.048
Identities = 8/29 (27%), Positives = 15/29 (51%), Gaps = 3/29 (10%)
Query: 53 CYGY---DIIIDNQLKPWLIEVNASPSLT 78
C + D ++D + +EVN +P +T
Sbjct: 259 CTDWGRADFMLDAAGNAYFLEVNTAPGMT 287
>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 = 31.0 bits (69), Expect = 0.15
Identities = 19/166 (11%), Positives = 49/166 (29%), Gaps = 37/166 (22%)
Query: 1 MRLLKQIISHSSQVYPRGKDITNKLFTNISWLIVHSLKSVSYIMANDKHCFECYGYDIII 60
+ +L++++ + D ++ + I + + ++ + + C +++
Sbjct: 199 LEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQ----AELRRLLKSKPYE-NCL---LVL 250
Query: 61 DNQLKPWLIEV-NASPSLTCTTVNDRIL---KYKLIDNILNIVMWNKY--KKADGGAAGG 114
N N L+C +IL ++K + + L+
Sbjct: 251 LNVQNAKAWNAFN----LSC-----KILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPD 301
Query: 115 EALNLGNFQLLLDEEYDE--NNVKQN----IS------KHNPNRWK 148
E +L LD + V +S + W
Sbjct: 302 EVKSL--LLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWD 345
>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 = 30.1 bits (69), Expect = 0.24
Identities = 9/29 (31%), Positives = 17/29 (58%), Gaps = 4/29 (13%)
Query: 53 CYGY---DIIIDNQLKPWLIEVNASPSLT 78
C Y D+++ + P+++EVN P +T
Sbjct: 244 CSVYARVDMMVKDG-IPYVMEVNTLPGMT 271
>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 = 29.7 bits (66), Expect = 0.35
Identities = 11/24 (45%), Positives = 17/24 (70%), Gaps = 1/24 (4%)
Query: 54 YGYDIIIDNQL-KPWLIEVNASPS 76
+G DIII+NQ + +I++NA P
Sbjct: 289 FGIDIIINNQTGQHAVIDINAFPG 312
>3ln6_A Glutathione biosynthesis bifunctional protein GSH; gamma-glutamyl
cysteine ligase domain, ATP-grAsp domain, HYB enzyme;
2.95A {Streptococcus agalactiae serogroup V}
Length = 750
Score = 28.7 bits (64), Expect = 0.74
Identities = 9/31 (29%), Positives = 15/31 (48%), Gaps = 8/31 (25%)
Query: 55 GYDIIIDNQLKPWL--------IEVNASPSL 77
G D+II N + + IE+N +P +
Sbjct: 694 GVDLIIPNATQAYSKDKKNATCIELNFNPLM 724
>3ln7_A Glutathione biosynthesis bifunctional protein GSH;
gamma-glutamylcysteine ligase domain, ATP-grAsp domain,
HYBR enzyme, ATP-binding; 3.20A {Pasteurella multocida}
Length = 757
Score = 28.7 bits (64), Expect = 0.83
Identities = 9/31 (29%), Positives = 14/31 (45%), Gaps = 8/31 (25%)
Query: 55 GYDIIIDNQLKPWL--------IEVNASPSL 77
G D+II + +P IE N +P +
Sbjct: 700 GVDLIIPDLKQPATPNLTSWGVIEANFNPMM 730
>3vmm_A Alanine-anticapsin ligase BACD; ATP-grAsp domain, amino acid
ligase, ATP binding; HET: ADP P0D; 2.50A {Bacillus
subtilis}
Length = 474
Score = 28.0 bits (62), Expect = 1.4
Identities = 6/17 (35%), Positives = 9/17 (52%)
Query: 57 DIIIDNQLKPWLIEVNA 73
+I + +P LIE A
Sbjct: 313 EIKLMKNREPGLIESAA 329
>3se7_A VANA; alpha-beta structure, D-alanine-D-lactate ligase, ligase;
HET: ATP; 3.07A {}
Length = 346
Score = 27.5 bits (62), Expect = 1.5
Identities = 10/30 (33%), Positives = 13/30 (43%), Gaps = 3/30 (10%)
Query: 52 ECYGY---DIIIDNQLKPWLIEVNASPSLT 78
C G D+ + K L EVN P +T
Sbjct: 284 GCRGLSRVDLFLTEDGKVVLNEVNTFPGMT 313
>2kcq_A MOV34/MPN/PAD-1 family; NESG, structure, structural genomics,
PSI-2, protein structure initiative; NMR {Salinibacter
ruber dsm 13855}
Length = 153
Score = 27.0 bits (59), Expect = 2.1
Identities = 11/51 (21%), Positives = 21/51 (41%), Gaps = 8/51 (15%)
Query: 9 SH-SSQVYPRGKDITNKLFTNISWLIVHSLKS------VSYIMANDKHCFE 52
SH P D+ F +++IV S++ ++ +A D+ F
Sbjct: 84 SHPDHPARPSATDLEEATFPGFTYVIV-SVRDGAPEALTAWALAPDRSEFH 133
>2dyq_A Amyloid beta A4 precursor protein-binding family 3;
phosphotyrosine-interaction domain (PTB/PID alzheimer'S
disease, structural genomics, NPPSFA; 3.10A {Homo
sapiens}
Length = 144
Score = 26.8 bits (59), Expect = 2.3
Identities = 4/28 (14%), Positives = 11/28 (39%), Gaps = 1/28 (3%)
Query: 28 NISWLIVHS-LKSVSYIMANDKHCFECY 54
++++ V + I + F+C
Sbjct: 88 LVTFIGVGRDPHTFGLIADLGRQSFQCA 115
>3dxe_A Amyloid beta A4 protein-binding family B member 1; alzheimer'S
disease, APP, AICD, Fe65, PTB domain, alternative
splicing, polymorphism, alzheimer disease, apoptosis;
2.00A {Homo sapiens} PDB: 3dxd_A 3dxc_A
Length = 140
Score = 26.4 bits (58), Expect = 2.9
Identities = 8/28 (28%), Positives = 15/28 (53%), Gaps = 1/28 (3%)
Query: 28 NISWLIVHS-LKSVSYIMANDKHCFECY 54
+S+L V + + ++IMA F C+
Sbjct: 75 FLSFLAVGRDVHTFAFIMAAGPASFCCH 102
>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 = 26.8 bits (60), Expect = 3.2
Identities = 7/30 (23%), Positives = 12/30 (40%), Gaps = 3/30 (10%)
Query: 52 ECYGY---DIIIDNQLKPWLIEVNASPSLT 78
C G D+ + + + E+N P T
Sbjct: 294 GCAGMARVDVFLTADNEVVINEINTLPGFT 323
>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 = 26.4 bits (59), Expect = 3.5
Identities = 9/30 (30%), Positives = 13/30 (43%), Gaps = 3/30 (10%)
Query: 52 ECYGY---DIIIDNQLKPWLIEVNASPSLT 78
C G D+ + + + L EVN P T
Sbjct: 284 GCRGLARVDMFLQDNGRIVLNEVNTLPGFT 313
>2ysz_A Amyloid beta A4 precursor protein-binding family B member 2 and
amyloid beta A4 protein...; chimera, Fe65L, PID domain,
amyloid precursor protein; NMR {Mus musculus}
Length = 185
Score = 26.3 bits (57), Expect = 3.9
Identities = 7/30 (23%), Positives = 16/30 (53%), Gaps = 1/30 (3%)
Query: 28 NISWLIVHS-LKSVSYIMANDKHCFECYGY 56
+S++ V + + ++IM FEC+ +
Sbjct: 84 FLSFMGVGKDVHTFAFIMDTGNQRFECHVF 113
>3cb4_D GTP-binding protein LEPA; GTPase, OB-fold, membrane,
nucleotide-binding, translation; 2.80A {Escherichia
coli} PDB: 3deg_C*
Length = 599
Score = 26.3 bits (59), Expect = 5.1
Identities = 5/19 (26%), Positives = 11/19 (57%)
Query: 7 IISHSSQVYPRGKDITNKL 25
+I+H RG+++ K+
Sbjct: 497 LITHRDNSQNRGRELVEKM 515
>3e5n_A D-alanine-D-alanine ligase A; bacterial blight; 2.00A {Xanthomonas
oryzae PV} PDB: 3r5f_A* 3rfc_A*
Length = 386
Score = 26.0 bits (58), Expect = 5.9
Identities = 8/30 (26%), Positives = 12/30 (40%), Gaps = 3/30 (10%)
Query: 52 ECYGY---DIIIDNQLKPWLIEVNASPSLT 78
C G D+ + + + EVN P T
Sbjct: 313 GCAGMARVDVFLCADGRIVINEVNTLPGFT 342
>2ywe_A GTP-binding protein LEPA; G domain, beta-barrel, ferredoxin-like
domain, structural GE NPPSFA; 2.05A {Aquifex aeolicus}
PDB: 2ywf_A* 2ywg_A* 2ywh_A*
Length = 600
Score = 25.9 bits (58), Expect = 6.5
Identities = 4/19 (21%), Positives = 8/19 (42%)
Query: 7 IISHSSQVYPRGKDITNKL 25
I H+ + + + KL
Sbjct: 502 FIVHADRAQKFARRVAEKL 520
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 0.416
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: 2,259,784
Number of extensions: 121748
Number of successful extensions: 196
Number of sequences better than 10.0: 1
Number of HSP's gapped: 194
Number of HSP's successfully gapped: 28
Length of query: 148
Length of database: 6,701,793
Length adjustment: 85
Effective length of query: 63
Effective length of database: 4,328,508
Effective search space: 272696004
Effective search space used: 272696004
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: 53 (24.0 bits)