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= 011061
(494 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2F4M|A Chain A, The Mouse Pngase-Hr23 Complex Reveals A Complete
Remodulation Of The Protein-Protein Interface Compared
To Its Yeast Orthologs
pdb|2F4O|A Chain A, The Mouse Pngase-Hr23 Complex Reveals A Complete
Remodulation Of The Protein-Protein Interface Compared
To Its Yeast Orthologs
Length = 295
Score = 198 bits (504), Expect = 5e-51, Method: Compositional matrix adjust.
Identities = 98/201 (48%), Positives = 126/201 (62%), Gaps = 2/201 (0%)
Query: 58 WFKQTF-RWVNAPPCDGCSNETVGQGMGT-PLPSEIQYGAARVELFRCKVCSKITRFPRY 115
WFK+ F RWVN C C ET + P E+++GA VE C C RFPRY
Sbjct: 70 WFKEEFFRWVNNIVCSKCGGETRSRDEALLPNDDELKWGAKNVENHYCDACQLSNRFPRY 129
Query: 116 NDPLKLVETKRGRCGEWANCFTLYCRAFGYESRLILDFTDHVWTECFSQSLGRWMHLDPC 175
N+P KL+ET+ GRCGEWANCFTL CRA G+E+R + D+TDHVWTE +S S RW+H D C
Sbjct: 130 NNPEKLLETRCGRCGEWANCFTLCCRALGFEARYVWDYTDHVWTEVYSPSQQRWLHCDAC 189
Query: 176 EGIYDRPLLYEKGWNKKLNYVIAISKDGVFDVTKRYTRKWHEVLSRRNIATEQTVSAVLA 235
E + D+PLLYE GW KKL+Y+IA SKD V DVT RY+ K EV+SRR E+ + +
Sbjct: 190 EDVCDKPLLYEIGWGKKLSYIIAFSKDEVVDVTWRYSCKHDEVMSRRTKVKEELLRETIN 249
Query: 236 KMTRECRRSFASETLSTLEDR 256
+ ++ + S + L R
Sbjct: 250 GLNKQRQLSLSESRRKELLQR 270
>pdb|1X3Z|A Chain A, Structure Of A Peptide:n-Glycanase-Rad23 Complex
Length = 335
Score = 179 bits (453), Expect = 4e-45, Method: Compositional matrix adjust.
Identities = 92/217 (42%), Positives = 128/217 (58%), Gaps = 10/217 (4%)
Query: 54 QLLFWFKQTF-RWVNAPPCDGCSNETVGQ----GMGTPLPSEIQYGAARVELFRCKVCSK 108
+LL +FKQ F +W N P C+ C T G P E ++ VE+++C C
Sbjct: 104 ELLRYFKQDFFKWCNKPDCNHCGQNTSENMTPLGSQGPNGEESKFNCGTVEIYKCNRCGN 163
Query: 109 ITRFPRYNDPLKLVETKRGRCGEWANCFTLYCRAFGYESRLILDFTDHVWTECFSQSLGR 168
ITRFPRYNDP+KL+ET++GRCGEW N FTL ++FG + R + + DHVW E FS L R
Sbjct: 164 ITRFPRYNDPIKLLETRKGRCGEWCNLFTLILKSFGLDVRYVWNREDHVWCEYFSNFLNR 223
Query: 169 WMHLDPCEGIYDRPLLYEKGWNKKLNYVIAISKDGVFDVTKRYTRKWHEVLSRRNIATEQ 228
W+H+D CE +D+P +Y WNKK++Y IA KDGV DV+KRY + L R I E+
Sbjct: 224 WVHVDSCEQSFDQPYIYSINWNKKMSYCIAFGKDGVVDVSKRYILQ--NELPRDQIK-EE 280
Query: 229 TVSAVLAKMTRECRRSFASETLSTLEDRDKCEREAME 265
+ + +T+ R S + + L RD E+E +E
Sbjct: 281 DLKFLCQFITKRLRYSLNDDEIYQLACRD--EQEQIE 315
>pdb|1X3W|A Chain A, Structure Of A Peptide:n-Glycanase-Rad23 Complex
Length = 335
Score = 177 bits (450), Expect = 1e-44, Method: Compositional matrix adjust.
Identities = 92/217 (42%), Positives = 127/217 (58%), Gaps = 10/217 (4%)
Query: 54 QLLFWFKQTF-RWVNAPPCDGCSNETVGQ----GMGTPLPSEIQYGAARVELFRCKVCSK 108
+LL +FKQ F +W N P C+ C T G P E ++ VE+++C C
Sbjct: 104 ELLRYFKQDFFKWCNKPDCNHCGQNTSENXTPLGSQGPNGEESKFNCGTVEIYKCNRCGN 163
Query: 109 ITRFPRYNDPLKLVETKRGRCGEWANCFTLYCRAFGYESRLILDFTDHVWTECFSQSLGR 168
ITRFPRYNDP+KL+ET++GRCGEW N FTL ++FG + R + + DHVW E FS L R
Sbjct: 164 ITRFPRYNDPIKLLETRKGRCGEWCNLFTLILKSFGLDVRYVWNREDHVWCEYFSNFLNR 223
Query: 169 WMHLDPCEGIYDRPLLYEKGWNKKLNYVIAISKDGVFDVTKRYTRKWHEVLSRRNIATEQ 228
W+H+D CE +D+P +Y WNKK +Y IA KDGV DV+KRY + L R I E+
Sbjct: 224 WVHVDSCEQSFDQPYIYSINWNKKXSYCIAFGKDGVVDVSKRYILQ--NELPRDQIK-EE 280
Query: 229 TVSAVLAKMTRECRRSFASETLSTLEDRDKCEREAME 265
+ + +T+ R S + + L RD E+E +E
Sbjct: 281 DLKFLCQFITKRLRYSLNDDEIYQLACRD--EQEQIE 315
>pdb|3ESW|A Chain A, Complex Of Yeast Pngase With Glcnac2-Iac
Length = 355
Score = 174 bits (442), Expect = 7e-44, Method: Compositional matrix adjust.
Identities = 91/217 (41%), Positives = 127/217 (58%), Gaps = 10/217 (4%)
Query: 54 QLLFWFKQTF-RWVNAPPCDGCSNETVGQ----GMGTPLPSEIQYGAARVELFRCKVCSK 108
+LL +FKQ F +W N P C+ C T G P E ++ VE+++C C
Sbjct: 125 ELLRYFKQDFFKWCNKPDCNHCGQNTSENMTPLGSQGPNGEESKFNCGTVEIYKCNRCGN 184
Query: 109 ITRFPRYNDPLKLVETKRGRCGEWANCFTLYCRAFGYESRLILDFTDHVWTECFSQSLGR 168
ITRFPRYNDP+KL+ET++GR GEW N FTL ++FG + R + + DHVW E FS L R
Sbjct: 185 ITRFPRYNDPIKLLETRKGRXGEWCNLFTLILKSFGLDVRYVWNREDHVWCEYFSNFLNR 244
Query: 169 WMHLDPCEGIYDRPLLYEKGWNKKLNYVIAISKDGVFDVTKRYTRKWHEVLSRRNIATEQ 228
W+H+D CE +D+P +Y WNKK++Y IA KDGV DV+KRY + L R I E+
Sbjct: 245 WVHVDSCEQSFDQPYIYSINWNKKMSYCIAFGKDGVVDVSKRYILQ--NELPRDQIK-EE 301
Query: 229 TVSAVLAKMTRECRRSFASETLSTLEDRDKCEREAME 265
+ + +T+ R S + + L RD E+E +E
Sbjct: 302 DLKFLCQFITKRLRYSLNDDEIYQLACRD--EQEQIE 336
>pdb|2NOV|A Chain A, Breakage-Reunion Domain Of S.Pneumoniae Topo Iv: Crystal
Structure Of A Gram-Positive Quinolone Target
pdb|2NOV|B Chain B, Breakage-Reunion Domain Of S.Pneumoniae Topo Iv: Crystal
Structure Of A Gram-Positive Quinolone Target
pdb|2NOV|C Chain C, Breakage-Reunion Domain Of S.Pneumoniae Topo Iv: Crystal
Structure Of A Gram-Positive Quinolone Target
pdb|2NOV|D Chain D, Breakage-Reunion Domain Of S.Pneumoniae Topo Iv: Crystal
Structure Of A Gram-Positive Quinolone Target
pdb|3FOE|A Chain A, Structural Insight Into The Quinolone-Dna Cleavage Complex
Of Type Iia Topoisomerases
pdb|3FOE|B Chain B, Structural Insight Into The Quinolone-Dna Cleavage Complex
Of Type Iia Topoisomerases
pdb|3FOF|A Chain A, Structural Insight Into The Quinolone-Dna Cleavage Complex
Of Type Iia Topoisomerases
pdb|3FOF|B Chain B, Structural Insight Into The Quinolone-Dna Cleavage Complex
Of Type Iia Topoisomerases
pdb|3K9F|A Chain A, Detailed Structural Insight Into The Quinolone-Dna
Cleavage Complex Of Type Iia Topoisomerases
pdb|3K9F|B Chain B, Detailed Structural Insight Into The Quinolone-Dna
Cleavage Complex Of Type Iia Topoisomerases
pdb|3KSA|A Chain A, Detailed Structural Insight Into The Dna Cleavage Complex
Of Type Iia Topoisomerases (Cleaved Form)
pdb|3KSA|B Chain B, Detailed Structural Insight Into The Dna Cleavage Complex
Of Type Iia Topoisomerases (Cleaved Form)
pdb|3KSB|A Chain A, Detailed Structural Insight Into The Dna Cleavage Complex
Of Type Iia Topoisomerases (Re-Sealed Form)
pdb|3KSB|B Chain B, Detailed Structural Insight Into The Dna Cleavage Complex
Of Type Iia Topoisomerases (Re-Sealed Form)
pdb|3LTN|A Chain A, Inhibitor-Stabilized Topoisomerase Iv-Dna Cleavage Complex
(S. Pneumoniae)
pdb|3LTN|B Chain B, Inhibitor-Stabilized Topoisomerase Iv-Dna Cleavage Complex
(S. Pneumoniae)
pdb|3RAF|A Chain A, Quinazolinedione-Dna Cleavage Complex Of Type Iv
Topoisomerase From S. Pneumoniae
pdb|3RAF|B Chain B, Quinazolinedione-Dna Cleavage Complex Of Type Iv
Topoisomerase From S. Pneumoniae
pdb|3RAD|A Chain A, Quinolone(Clinafloxacin)-Dna Cleavage Complex Of Type Iv
Topoisomerase From S. Pneumoniae
pdb|3RAD|B Chain B, Quinolone(Clinafloxacin)-Dna Cleavage Complex Of Type Iv
Topoisomerase From S. Pneumoniae
pdb|3RAE|A Chain A, Quinolone(Levofloxacin)-Dna Cleavage Complex Of Type Iv
Topoisomerase From S. Pneumoniae
pdb|3RAE|B Chain B, Quinolone(Levofloxacin)-Dna Cleavage Complex Of Type Iv
Topoisomerase From S. Pneumoniae
Length = 496
Score = 30.4 bits (67), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 22/36 (61%)
Query: 224 IATEQTVSAVLAKMTRECRRSFASETLSTLEDRDKC 259
I E+T+ ++ K RE ++ FA+ LS+LED K
Sbjct: 453 IGDERTMYNLMKKELREVKKKFATPRLSSLEDTAKA 488
>pdb|1UF9|A Chain A, Crystal Structure Of Tt1252 From Thermus Thermophilus
pdb|1UF9|B Chain B, Crystal Structure Of Tt1252 From Thermus Thermophilus
pdb|1UF9|C Chain C, Crystal Structure Of Tt1252 From Thermus Thermophilus
Length = 203
Score = 30.4 bits (67), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 21/81 (25%), Positives = 37/81 (45%), Gaps = 11/81 (13%)
Query: 182 PLLYEKGWNKKLNYVIAISKDGVFDVTKRYTRKWHEVLSRRNIATEQTVSAVLAKMTREC 241
PLL+EKGW +L+ G V + V +R ++ E+ ++ A+ E
Sbjct: 114 PLLFEKGWEGRLH--------GTLLVAAPLEERVRRVXARSGLSREEVLARERAQXPEEE 165
Query: 242 RRSFAS---ETLSTLEDRDKC 259
+R A+ E +LED ++
Sbjct: 166 KRKRATWVLENTGSLEDLERA 186
>pdb|1VPB|A Chain A, Crystal Structure Of A Putative Modulator Of Dna Gyrase
(Bt3649) From Bacteroides Thetaiotaomicron Vpi-5482 At
1.75 A Resolution
Length = 451
Score = 28.5 bits (62), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 19/35 (54%)
Query: 455 IHSGSVLASGEEFPFGIVTSAFDGIRPSKWEDLMA 489
I GS GE+F + ++++ F+G S W L A
Sbjct: 160 ISVGSSYGDGEDFAYRLISNGFEGETKSTWYSLSA 194
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
0.320 0.136 0.421
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,346,389
Number of Sequences: 62578
Number of extensions: 570145
Number of successful extensions: 1283
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1273
Number of HSP's gapped (non-prelim): 13
length of query: 494
length of database: 14,973,337
effective HSP length: 103
effective length of query: 391
effective length of database: 8,527,803
effective search space: 3334370973
effective search space used: 3334370973
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (25.0 bits)