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= 009800
(525 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 = 218 bits (555), Expect = 7e-57, Method: Compositional matrix adjust.
Identities = 114/242 (47%), Positives = 146/242 (60%), Gaps = 3/242 (1%)
Query: 31 ISKVLMYEDPIRQEAAKKTVPVERLEEKSLVSLAREGNFKPSKTEQDHAFLLQLL-FWFK 89
I V +YE+P+ QE A +PV L+ K+ L R D FLL L WFK
Sbjct: 13 IQHVQLYENPVLQEKALTCIPVSELKRKAQEKLFRARKLDKGTNVSDEDFLLLELLHWFK 72
Query: 90 QTF-RWVNAPPCDGCSNETVGQGMGT-PLPSEIQYGAARVELFRCKVCSKITRFPRYNDP 147
+ F RWVN C C ET + P E+++GA VE C C RFPRYN+P
Sbjct: 73 EEFFRWVNNIVCSKCGGETRSRDEALLPNDDELKWGAKNVENHYCDACQLSNRFPRYNNP 132
Query: 148 LKLVETKRGRCGEWANCFTLYCRAFGYESRLILDFTDHVWTECFSQSLGRWMHLDPCEGI 207
KL+ET+ GRCGEWANCFTL CRA G+E+R + D+TDHVWTE +S S RW+H D CE +
Sbjct: 133 EKLLETRCGRCGEWANCFTLCCRALGFEARYVWDYTDHVWTEVYSPSQQRWLHCDACEDV 192
Query: 208 YDRPLLYEKGWNKKLNYVIAISKDGVFDVTKRYTRKWHEVLSRRNIATEQTVSAVLAKMT 267
D+PLLYE GW KKL+Y+IA SKD V DVT RY+ K EV+SRR E+ + + +
Sbjct: 193 CDKPLLYEIGWGKKLSYIIAFSKDEVVDVTWRYSCKHDEVMSRRTKVKEELLRETINGLN 252
Query: 268 RE 269
++
Sbjct: 253 KQ 254
>pdb|1X3Z|A Chain A, Structure Of A Peptide:n-Glycanase-Rad23 Complex
Length = 335
Score = 184 bits (466), Expect = 1e-46, Method: Compositional matrix adjust.
Identities = 98/264 (37%), Positives = 149/264 (56%), Gaps = 11/264 (4%)
Query: 36 MYEDPIRQEAAKKTVPVERLEEKSLVSLAREGNFKPSKTEQDHAFLLQLLFWFKQTF-RW 94
+Y++P +T+ ++ + + A++G+ + D+ + +LL +FKQ F +W
Sbjct: 58 VYDNPSWHSIVLETLDLDLIYKNVDKEFAKDGHAEGENIYTDY-LVKELLRYFKQDFFKW 116
Query: 95 VNAPPCDGCSNETVGQ----GMGTPLPSEIQYGAARVELFRCKVCSKITRFPRYNDPLKL 150
N P C+ C T G P E ++ VE+++C C ITRFPRYNDP+KL
Sbjct: 117 CNKPDCNHCGQNTSENMTPLGSQGPNGEESKFNCGTVEIYKCNRCGNITRFPRYNDPIKL 176
Query: 151 VETKRGRCGEWANCFTLYCRAFGYESRLILDFTDHVWTECFSQSLGRWMHLDPCEGIYDR 210
+ET++GRCGEW N FTL ++FG + R + + DHVW E FS L RW+H+D CE +D+
Sbjct: 177 LETRKGRCGEWCNLFTLILKSFGLDVRYVWNREDHVWCEYFSNFLNRWVHVDSCEQSFDQ 236
Query: 211 PLLYEKGWNKKLNYVIAISKDGVFDVTKRYTRKWHEVLSRRNIATEQTVSAVLAKMTREC 270
P +Y WNKK++Y IA KDGV DV+KRY + L R I E+ + + +T+
Sbjct: 237 PYIYSINWNKKMSYCIAFGKDGVVDVSKRYILQ--NELPRDQIK-EEDLKFLCQFITKRL 293
Query: 271 RRSFASETLSTLEDRDKCEREAME 294
R S + + L RD E+E +E
Sbjct: 294 RYSLNDDEIYQLACRD--EQEQIE 315
>pdb|1X3W|A Chain A, Structure Of A Peptide:n-Glycanase-Rad23 Complex
Length = 335
Score = 182 bits (462), Expect = 4e-46, Method: Compositional matrix adjust.
Identities = 98/264 (37%), Positives = 148/264 (56%), Gaps = 11/264 (4%)
Query: 36 MYEDPIRQEAAKKTVPVERLEEKSLVSLAREGNFKPSKTEQDHAFLLQLLFWFKQTF-RW 94
+Y++P +T+ ++ + + A++G+ + D+ + +LL +FKQ F +W
Sbjct: 58 VYDNPSWHSIVLETLDLDLIYKNVDKEFAKDGHAEGENIYTDY-LVKELLRYFKQDFFKW 116
Query: 95 VNAPPCDGCSNETVGQ----GMGTPLPSEIQYGAARVELFRCKVCSKITRFPRYNDPLKL 150
N P C+ C T G P E ++ VE+++C C ITRFPRYNDP+KL
Sbjct: 117 CNKPDCNHCGQNTSENXTPLGSQGPNGEESKFNCGTVEIYKCNRCGNITRFPRYNDPIKL 176
Query: 151 VETKRGRCGEWANCFTLYCRAFGYESRLILDFTDHVWTECFSQSLGRWMHLDPCEGIYDR 210
+ET++GRCGEW N FTL ++FG + R + + DHVW E FS L RW+H+D CE +D+
Sbjct: 177 LETRKGRCGEWCNLFTLILKSFGLDVRYVWNREDHVWCEYFSNFLNRWVHVDSCEQSFDQ 236
Query: 211 PLLYEKGWNKKLNYVIAISKDGVFDVTKRYTRKWHEVLSRRNIATEQTVSAVLAKMTREC 270
P +Y WNKK +Y IA KDGV DV+KRY + L R I E+ + + +T+
Sbjct: 237 PYIYSINWNKKXSYCIAFGKDGVVDVSKRYILQ--NELPRDQIK-EEDLKFLCQFITKRL 293
Query: 271 RRSFASETLSTLEDRDKCEREAME 294
R S + + L RD E+E +E
Sbjct: 294 RYSLNDDEIYQLACRD--EQEQIE 315
>pdb|3ESW|A Chain A, Complex Of Yeast Pngase With Glcnac2-Iac
Length = 355
Score = 179 bits (455), Expect = 3e-45, Method: Compositional matrix adjust.
Identities = 97/264 (36%), Positives = 148/264 (56%), Gaps = 11/264 (4%)
Query: 36 MYEDPIRQEAAKKTVPVERLEEKSLVSLAREGNFKPSKTEQDHAFLLQLLFWFKQTF-RW 94
+Y++P +T+ ++ + + A++G+ + D+ + +LL +FKQ F +W
Sbjct: 79 VYDNPSWHSIVLETLDLDLIYKNVDKEFAKDGHAEGENIYTDY-LVKELLRYFKQDFFKW 137
Query: 95 VNAPPCDGCSNETVGQ----GMGTPLPSEIQYGAARVELFRCKVCSKITRFPRYNDPLKL 150
N P C+ C T G P E ++ VE+++C C ITRFPRYNDP+KL
Sbjct: 138 CNKPDCNHCGQNTSENMTPLGSQGPNGEESKFNCGTVEIYKCNRCGNITRFPRYNDPIKL 197
Query: 151 VETKRGRCGEWANCFTLYCRAFGYESRLILDFTDHVWTECFSQSLGRWMHLDPCEGIYDR 210
+ET++GR GEW N FTL ++FG + R + + DHVW E FS L RW+H+D CE +D+
Sbjct: 198 LETRKGRXGEWCNLFTLILKSFGLDVRYVWNREDHVWCEYFSNFLNRWVHVDSCEQSFDQ 257
Query: 211 PLLYEKGWNKKLNYVIAISKDGVFDVTKRYTRKWHEVLSRRNIATEQTVSAVLAKMTREC 270
P +Y WNKK++Y IA KDGV DV+KRY + L R I E+ + + +T+
Sbjct: 258 PYIYSINWNKKMSYCIAFGKDGVVDVSKRYILQ--NELPRDQIK-EEDLKFLCQFITKRL 314
Query: 271 RRSFASETLSTLEDRDKCEREAME 294
R S + + L RD E+E +E
Sbjct: 315 RYSLNDDEIYQLACRD--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 = 2.8, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 22/36 (61%)
Query: 253 IATEQTVSAVLAKMTRECRRSFASETLSTLEDRDKC 288
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 = 30.0 bits (66), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 21/81 (25%), Positives = 37/81 (45%), Gaps = 11/81 (13%)
Query: 211 PLLYEKGWNKKLNYVIAISKDGVFDVTKRYTRKWHEVLSRRNIATEQTVSAVLAKMTREC 270
PLL+EKGW +L+ G V + V +R ++ E+ ++ A+ E
Sbjct: 114 PLLFEKGWEGRLH--------GTLLVAAPLEERVRRVXARSGLSREEVLARERAQXPEEE 165
Query: 271 RRSFAS---ETLSTLEDRDKC 288
+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 = 28.9 bits (63), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 19/35 (54%)
Query: 484 IHSGSVLASGEEFPFGIVTSAFDGIRPSKWEDLMA 518
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
0.319 0.135 0.414
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,060,987
Number of Sequences: 62578
Number of extensions: 597571
Number of successful extensions: 1175
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 1164
Number of HSP's gapped (non-prelim): 7
length of query: 525
length of database: 14,973,337
effective HSP length: 103
effective length of query: 422
effective length of database: 8,527,803
effective search space: 3598732866
effective search space used: 3598732866
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: 54 (25.4 bits)