BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 048704
(220 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1I7D|A Chain A, Noncovalent Complex Of E.Coli Dna Topoisomerase Iii With
An 8-Base Single-Stranded Dna Oligonucleotide
Length = 659
Score = 43.1 bits (100), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 54/195 (27%), Positives = 82/195 (42%), Gaps = 25/195 (12%)
Query: 7 LMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFP 66
L +AEKPS+A +IA VL RK DG + + VT +GH+ P
Sbjct: 3 LFIAEKPSLARAIADVLPKPH---RKG-------DGFIECGNGQV-VTWCIGHLLEQAQP 51
Query: 67 PAYQD----WNASNPLDLFQAPVHKAESNPKVHICRHLNQEAR---GCGHLVLWLDCDRE 119
AY WN + DL P K + P+ + + LN R +V D DRE
Sbjct: 52 DAYDSRYARWNLA---DLPIVP-EKWQLQPRPSVTKQLNVIKRFLHEASEIVHAGDPDRE 107
Query: 120 GENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNLVEPNRNEALAVD--ARQ 177
G+ + EV++ + R++V R + + + + +A+ L + L V AR
Sbjct: 108 GQLLVDEVLDYLQL-APEKRQQVQRCLINDLNPQAVERAIDRLRSNSEFVPLCVSALARA 166
Query: 178 EIDLKVGVAFTRFQT 192
D G+ TR T
Sbjct: 167 RADWLYGINMTRAYT 181
>pdb|2O19|A Chain A, Structure Of E. Coli Topoisomersae Iii In Complex With An
8- Base Single Stranded Oligonucleotide. Frozen In
Glycerol At Ph 5.5
pdb|2O19|B Chain B, Structure Of E. Coli Topoisomersae Iii In Complex With An
8- Base Single Stranded Oligonucleotide. Frozen In
Glycerol At Ph 5.5
pdb|2O54|A Chain A, Structure Of E. Coli Topoisomerase Iii In Complex With An
8- Base Single Stranded Oligonucleotide. Frozen In
Glycerol At Ph 7.0
pdb|2O54|B Chain B, Structure Of E. Coli Topoisomerase Iii In Complex With An
8- Base Single Stranded Oligonucleotide. Frozen In
Glycerol At Ph 7.0
pdb|2O59|A Chain A, Structure Of E. Coli Topoisomerase Iii In Complex With An
8- Base Single Stranded Oligonucleotide. Frozen In
Glycerol Ph 8.0
pdb|2O59|B Chain B, Structure Of E. Coli Topoisomerase Iii In Complex With An
8- Base Single Stranded Oligonucleotide. Frozen In
Glycerol Ph 8.0
pdb|2O5C|A Chain A, Structure Of E. Coli Topoisomerase Iii In Complex With An
8- Base Single Stranded Oligonucleotide. Frozen In
Glucose Ph 5.5
pdb|2O5C|B Chain B, Structure Of E. Coli Topoisomerase Iii In Complex With An
8- Base Single Stranded Oligonucleotide. Frozen In
Glucose Ph 5.5
pdb|2O5E|A Chain A, Structure Of E. Coli Topoisomerase Iii In Complex With An
8- Base Single Stranded Oligonucleotide. Frozen In
Glucose Ph 7.0
pdb|2O5E|B Chain B, Structure Of E. Coli Topoisomerase Iii In Complex With An
8- Base Single Stranded Oligonucleotide. Frozen In
Glucose Ph 7.0
Length = 659
Score = 43.1 bits (100), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 54/195 (27%), Positives = 82/195 (42%), Gaps = 25/195 (12%)
Query: 7 LMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFP 66
L +AEKPS+A +IA VL RK DG + + VT +GH+ P
Sbjct: 3 LFIAEKPSLARAIADVLPKPH---RKG-------DGFIECGNGQV-VTWCIGHLLEQAQP 51
Query: 67 PAYQD----WNASNPLDLFQAPVHKAESNPKVHICRHLNQEAR---GCGHLVLWLDCDRE 119
AY WN + DL P K + P+ + + LN R +V D DRE
Sbjct: 52 DAYDSRYARWNLA---DLPIVP-EKWQLQPRPSVTKQLNVIKRFLHEASEIVHAGDPDRE 107
Query: 120 GENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNLVEPNRNEALAVD--ARQ 177
G+ + EV++ + R++V R + + + + +A+ L + L V AR
Sbjct: 108 GQLLVDEVLDYLQL-APEKRQQVQRCLINDLNPQAVERAIDRLRSNSEFVPLCVSALARA 166
Query: 178 EIDLKVGVAFTRFQT 192
D G+ TR T
Sbjct: 167 RADWLYGINMTRAYT 181
>pdb|1D6M|A Chain A, Crystal Structure Of E. Coli Dna Topoisomerase Iii
Length = 653
Score = 43.1 bits (100), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 54/195 (27%), Positives = 82/195 (42%), Gaps = 25/195 (12%)
Query: 7 LMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFP 66
L +AEKPS+A +IA VL RK DG + + VT +GH+ P
Sbjct: 3 LFIAEKPSLARAIADVLPKPH---RKG-------DGFIECGNGQV-VTWCIGHLLEQAQP 51
Query: 67 PAYQD----WNASNPLDLFQAPVHKAESNPKVHICRHLNQEAR---GCGHLVLWLDCDRE 119
AY WN + DL P K + P+ + + LN R +V D DRE
Sbjct: 52 DAYDSRYARWNLA---DLPIVP-EKWQLQPRPSVTKQLNVIKRFLHEASEIVHAGDPDRE 107
Query: 120 GENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNLVEPNRNEALAVD--ARQ 177
G+ + EV++ + R++V R + + + + +A+ L + L V AR
Sbjct: 108 GQLLVDEVLDYLQL-APEKRQQVQRCLINDLNPQAVERAIDRLRSNSEFVPLCVSALARA 166
Query: 178 EIDLKVGVAFTRFQT 192
D G+ TR T
Sbjct: 167 RADWLYGINMTRAYT 181
>pdb|1ECL|A Chain A, Amino Terminal 67kda Domain Of Escherichia Coli Dna
Topoisomerase I (Residues 2-590 Of Mature Protein)
Cloning Artifact Adds Two Residues To The Amino-Terminus
Which Were Not Observed In The Experimental Electron
Density (Gly-2, Ser-1)
Length = 597
Score = 41.2 bits (95), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 31/92 (33%), Positives = 43/92 (46%), Gaps = 4/92 (4%)
Query: 93 KVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTE 152
K + L Q A H+ L D DREGE I + + E G +DAR R F+ +T+
Sbjct: 89 KEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGG--DDAR--YSRVVFNEITK 144
Query: 153 KDILKAMGNLVEPNRNEALAVDARQEIDLKVG 184
I +A E N + A AR+ +D VG
Sbjct: 145 NAIRQAFNKPGELNIDRVNAQQARRFMDRVVG 176
>pdb|1CY1|A Chain A, Complex Of E.Coli Dna Topoisomerase I With 5'ptptpt
pdb|1CY2|A Chain A, Complex Of E.Coli Dna Topoisomerase I With Tptptp3'
pdb|1CY6|A Chain A, Complex Of E.Coli Dna Topoisomerase I With 3' Thymidine
Monophosphate
pdb|1CY7|A Chain A, Complex Of E.coli Dna Topoisomerase I With 5'-thymidine
Monophosphate
pdb|1CY8|A Chain A, Complex Of E.Coli Dna Topoisomerase I With 5'-Thymidine
Monophosphate And 3'-Thymidine Monophosphate
pdb|1CY0|A Chain A, Complex Of E.Coli Dna Topoisomerase I With 3'-5'-Adenosine
Diphosphate
pdb|1CY4|A Chain A, Complex Of E.Coli Dna Topoisomerase I With 5'ptptptp3'
Length = 599
Score = 40.8 bits (94), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 31/92 (33%), Positives = 43/92 (46%), Gaps = 4/92 (4%)
Query: 93 KVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTE 152
K + L Q A H+ L D DREGE I + + E G +DAR R F+ +T+
Sbjct: 91 KEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGG--DDAR--YSRVVFNEITK 146
Query: 153 KDILKAMGNLVEPNRNEALAVDARQEIDLKVG 184
I +A E N + A AR+ +D VG
Sbjct: 147 NAIRQAFNKPGELNIDRVNAQQARRFMDRVVG 178
>pdb|1MW8|X Chain X, Crystal Structure Of A Complex Between H365r Mutant Of 67
Kda N-Terminal Fragment Of E. Coli Dna Topoisomerase I
And 5'-Acttcgggatg-3'
pdb|1MW9|X Chain X, Crystal Structure Of H365r Mutant Of 67 Kda N-Terminal
Fragment Of E. Coli Dna Topoisomerase I
Length = 592
Score = 40.8 bits (94), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 31/92 (33%), Positives = 43/92 (46%), Gaps = 4/92 (4%)
Query: 93 KVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTE 152
K + L Q A H+ L D DREGE I + + E G +DAR R F+ +T+
Sbjct: 89 KEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGG--DDAR--YSRVVFNEITK 144
Query: 153 KDILKAMGNLVEPNRNEALAVDARQEIDLKVG 184
I +A E N + A AR+ +D VG
Sbjct: 145 NAIRQAFNKPGELNIDRVNAQQARRFMDRVVG 176
>pdb|2GAI|A Chain A, Structure Of Full Length Topoisomerase I From Thermotoga
Maritima In Triclinic Crystal Form
pdb|2GAI|B Chain B, Structure Of Full Length Topoisomerase I From Thermotoga
Maritima In Triclinic Crystal Form
pdb|2GAJ|A Chain A, Structure Of Full Length Topoisomerase I From Thermotoga
Maritima In Monoclinic Crystal Form
pdb|2GAJ|B Chain B, Structure Of Full Length Topoisomerase I From Thermotoga
Maritima In Monoclinic Crystal Form
Length = 633
Score = 35.0 bits (79), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 27/81 (33%), Positives = 42/81 (51%), Gaps = 5/81 (6%)
Query: 108 GHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNLVEPNR 167
G L++ D DREGE I + + T N RK +R FS +T + I +A+ N E +
Sbjct: 77 GELLIASDMDREGEAIAWHIARVT----NTLGRK-NRIVFSEITPRVIREAVKNPREIDM 131
Query: 168 NEALAVDARQEIDLKVGVAFT 188
+ A AR+ +D VG + +
Sbjct: 132 KKVRAQLARRILDRIVGYSLS 152
>pdb|2NX9|A Chain A, Crystal Structure Of The Carboxyltransferase Domain Of The
Oxaloacetate Decarboxylase Na+ Pump From Vibrio Cholerae
pdb|2NX9|B Chain B, Crystal Structure Of The Carboxyltransferase Domain Of The
Oxaloacetate Decarboxylase Na+ Pump From Vibrio Cholerae
Length = 464
Score = 29.3 bits (64), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 24/52 (46%), Gaps = 1/52 (1%)
Query: 29 YTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAYQDWNASNPLDL 80
Y R + H F+GM GS A I V V G + + + NA + LDL
Sbjct: 273 YFRDVRKKYHAFEGMMKGSDARILVAQVPGGMLT-NMESQLKQQNALDKLDL 323
>pdb|2DW6|A Chain A, Crystal Structure Of The Mutant K184a Of D-Tartrate
Dehydratase From Bradyrhizobium Japonicum Complexed With
Mg++ And D-Tartrate
pdb|2DW6|B Chain B, Crystal Structure Of The Mutant K184a Of D-Tartrate
Dehydratase From Bradyrhizobium Japonicum Complexed With
Mg++ And D-Tartrate
pdb|2DW6|C Chain C, Crystal Structure Of The Mutant K184a Of D-Tartrate
Dehydratase From Bradyrhizobium Japonicum Complexed With
Mg++ And D-Tartrate
pdb|2DW6|D Chain D, Crystal Structure Of The Mutant K184a Of D-Tartrate
Dehydratase From Bradyrhizobium Japonicum Complexed With
Mg++ And D-Tartrate
Length = 389
Score = 28.1 bits (61), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 28/121 (23%), Positives = 49/121 (40%), Gaps = 15/121 (12%)
Query: 74 ASNPLDLFQAPVHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGF 133
A PL A H ++NP+V + A G + G+ + E G+
Sbjct: 128 AGKPLFRLLAERHGVKANPRVFVY------AAGGYYY--------PGKGLSMLRGEMRGY 173
Query: 134 QVNDARRKVHRARFSSVTEKDILKAMGNLVEPNRNEALAVDARQEIDLKVGVAFTRFQTT 193
++ V A + E+D ++ L E ++ LAVDA +L+ G+A+ +
Sbjct: 174 -LDRGYNVVKMAIGGAPIEEDRMRIEAVLEEIGKDAQLAVDANGRFNLETGIAYAKMLRD 232
Query: 194 Y 194
Y
Sbjct: 233 Y 233
>pdb|1TZZ|A Chain A, Crystal Structure Of The Protein L1841, Unknown Member Of
Enolase Superfamily From Bradyrhizobium Japonicum
pdb|1TZZ|B Chain B, Crystal Structure Of The Protein L1841, Unknown Member Of
Enolase Superfamily From Bradyrhizobium Japonicum
Length = 392
Score = 27.3 bits (59), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 13/43 (30%), Positives = 23/43 (53%)
Query: 152 EKDILKAMGNLVEPNRNEALAVDARQEIDLKVGVAFTRFQTTY 194
E+D ++ L E ++ LAVDA +L+ G+A+ + Y
Sbjct: 194 EEDRMRIEAVLEEIGKDAQLAVDANGRFNLETGIAYAKMLRDY 236
>pdb|2DW7|A Chain A, Crystal Structure Of D-Tartrate Dehydratase From
Bradyrhizobium Japonicum Complexed With Mg++ And Meso-
Tartrate
pdb|2DW7|B Chain B, Crystal Structure Of D-Tartrate Dehydratase From
Bradyrhizobium Japonicum Complexed With Mg++ And Meso-
Tartrate
pdb|2DW7|C Chain C, Crystal Structure Of D-Tartrate Dehydratase From
Bradyrhizobium Japonicum Complexed With Mg++ And Meso-
Tartrate
pdb|2DW7|D Chain D, Crystal Structure Of D-Tartrate Dehydratase From
Bradyrhizobium Japonicum Complexed With Mg++ And Meso-
Tartrate
pdb|2DW7|E Chain E, Crystal Structure Of D-Tartrate Dehydratase From
Bradyrhizobium Japonicum Complexed With Mg++ And Meso-
Tartrate
pdb|2DW7|F Chain F, Crystal Structure Of D-Tartrate Dehydratase From
Bradyrhizobium Japonicum Complexed With Mg++ And Meso-
Tartrate
pdb|2DW7|G Chain G, Crystal Structure Of D-Tartrate Dehydratase From
Bradyrhizobium Japonicum Complexed With Mg++ And Meso-
Tartrate
pdb|2DW7|H Chain H, Crystal Structure Of D-Tartrate Dehydratase From
Bradyrhizobium Japonicum Complexed With Mg++ And Meso-
Tartrate
pdb|2DW7|I Chain I, Crystal Structure Of D-Tartrate Dehydratase From
Bradyrhizobium Japonicum Complexed With Mg++ And Meso-
Tartrate
pdb|2DW7|J Chain J, Crystal Structure Of D-Tartrate Dehydratase From
Bradyrhizobium Japonicum Complexed With Mg++ And Meso-
Tartrate
pdb|2DW7|K Chain K, Crystal Structure Of D-Tartrate Dehydratase From
Bradyrhizobium Japonicum Complexed With Mg++ And Meso-
Tartrate
pdb|2DW7|L Chain L, Crystal Structure Of D-Tartrate Dehydratase From
Bradyrhizobium Japonicum Complexed With Mg++ And Meso-
Tartrate
pdb|2DW7|M Chain M, Crystal Structure Of D-Tartrate Dehydratase From
Bradyrhizobium Japonicum Complexed With Mg++ And Meso-
Tartrate
pdb|2DW7|N Chain N, Crystal Structure Of D-Tartrate Dehydratase From
Bradyrhizobium Japonicum Complexed With Mg++ And Meso-
Tartrate
pdb|2DW7|O Chain O, Crystal Structure Of D-Tartrate Dehydratase From
Bradyrhizobium Japonicum Complexed With Mg++ And Meso-
Tartrate
pdb|2DW7|P Chain P, Crystal Structure Of D-Tartrate Dehydratase From
Bradyrhizobium Japonicum Complexed With Mg++ And Meso-
Tartrate
Length = 389
Score = 27.3 bits (59), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 13/43 (30%), Positives = 23/43 (53%)
Query: 152 EKDILKAMGNLVEPNRNEALAVDARQEIDLKVGVAFTRFQTTY 194
E+D ++ L E ++ LAVDA +L+ G+A+ + Y
Sbjct: 191 EEDRMRIEAVLEEIGKDAQLAVDANGRFNLETGIAYAKMLRDY 233
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.324 0.138 0.420
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,251,027
Number of Sequences: 62578
Number of extensions: 247925
Number of successful extensions: 683
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 677
Number of HSP's gapped (non-prelim): 11
length of query: 220
length of database: 14,973,337
effective HSP length: 95
effective length of query: 125
effective length of database: 9,028,427
effective search space: 1128553375
effective search space used: 1128553375
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 49 (23.5 bits)