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= 013381
(444 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 = 192 bits (489), Expect = 2e-49, Method: Compositional matrix adjust.
Identities = 95/200 (47%), Positives = 124/200 (62%), Gaps = 1/200 (0%)
Query: 8 FILQYCRWVNAPPCDGCSNETVGQGMGT-PLPSEIQYGAARVELFRCKVCSKITRFPRYN 66
F ++ RWVN C C ET + P E+++GA VE C C RFPRYN
Sbjct: 71 FKEEFFRWVNNIVCSKCGGETRSRDEALLPNDDELKWGAKNVENHYCDACQLSNRFPRYN 130
Query: 67 DPLKLVETKRGRCGEWANCFTLYCRAFGYESRLILDFTDHVWTECFSQSLGRWMHLDPCE 126
+P KL+ET+ GRCGEWANCFTL CRA G+E+R + D+TDHVWTE +S S RW+H D CE
Sbjct: 131 NPEKLLETRCGRCGEWANCFTLCCRALGFEARYVWDYTDHVWTEVYSPSQQRWLHCDACE 190
Query: 127 GIYDRPLLYEKGWNKKLNYVIAISKDGVFDVTKRYTRKWHEVLSRRNIATEQTVSAVLAK 186
+ D+PLLYE GW KKL+Y+IA SKD V DVT RY+ K EV+SRR E+ + +
Sbjct: 191 DVCDKPLLYEIGWGKKLSYIIAFSKDEVVDVTWRYSCKHDEVMSRRTKVKEELLRETING 250
Query: 187 MTRECRRSFASETLSTLEDR 206
+ ++ + S + L R
Sbjct: 251 LNKQRQLSLSESRRKELLQR 270
>pdb|1X3Z|A Chain A, Structure Of A Peptide:n-Glycanase-Rad23 Complex
Length = 335
Score = 171 bits (434), Expect = 5e-43, Method: Compositional matrix adjust.
Identities = 87/212 (41%), Positives = 122/212 (57%), Gaps = 9/212 (4%)
Query: 8 FILQYCRWVNAPPCDGCSNETVGQ----GMGTPLPSEIQYGAARVELFRCKVCSKITRFP 63
F + +W N P C+ C T G P E ++ VE+++C C ITRFP
Sbjct: 109 FKQDFFKWCNKPDCNHCGQNTSENMTPLGSQGPNGEESKFNCGTVEIYKCNRCGNITRFP 168
Query: 64 RYNDPLKLVETKRGRCGEWANCFTLYCRAFGYESRLILDFTDHVWTECFSQSLGRWMHLD 123
RYNDP+KL+ET++GRCGEW N FTL ++FG + R + + DHVW E FS L RW+H+D
Sbjct: 169 RYNDPIKLLETRKGRCGEWCNLFTLILKSFGLDVRYVWNREDHVWCEYFSNFLNRWVHVD 228
Query: 124 PCEGIYDRPLLYEKGWNKKLNYVIAISKDGVFDVTKRYTRKWHEVLSRRNIATEQTVSAV 183
CE +D+P +Y WNKK++Y IA KDGV DV+KRY + L R I E+ + +
Sbjct: 229 SCEQSFDQPYIYSINWNKKMSYCIAFGKDGVVDVSKRYILQ--NELPRDQIK-EEDLKFL 285
Query: 184 LAKMTRECRRSFASETLSTLEDRDKCEREAME 215
+T+ R S + + L RD E+E +E
Sbjct: 286 CQFITKRLRYSLNDDEIYQLACRD--EQEQIE 315
>pdb|1X3W|A Chain A, Structure Of A Peptide:n-Glycanase-Rad23 Complex
Length = 335
Score = 170 bits (431), Expect = 1e-42, Method: Compositional matrix adjust.
Identities = 87/212 (41%), Positives = 121/212 (57%), Gaps = 9/212 (4%)
Query: 8 FILQYCRWVNAPPCDGCSNETVGQ----GMGTPLPSEIQYGAARVELFRCKVCSKITRFP 63
F + +W N P C+ C T G P E ++ VE+++C C ITRFP
Sbjct: 109 FKQDFFKWCNKPDCNHCGQNTSENXTPLGSQGPNGEESKFNCGTVEIYKCNRCGNITRFP 168
Query: 64 RYNDPLKLVETKRGRCGEWANCFTLYCRAFGYESRLILDFTDHVWTECFSQSLGRWMHLD 123
RYNDP+KL+ET++GRCGEW N FTL ++FG + R + + DHVW E FS L RW+H+D
Sbjct: 169 RYNDPIKLLETRKGRCGEWCNLFTLILKSFGLDVRYVWNREDHVWCEYFSNFLNRWVHVD 228
Query: 124 PCEGIYDRPLLYEKGWNKKLNYVIAISKDGVFDVTKRYTRKWHEVLSRRNIATEQTVSAV 183
CE +D+P +Y WNKK +Y IA KDGV DV+KRY + L R I E+ + +
Sbjct: 229 SCEQSFDQPYIYSINWNKKXSYCIAFGKDGVVDVSKRYILQ--NELPRDQIK-EEDLKFL 285
Query: 184 LAKMTRECRRSFASETLSTLEDRDKCEREAME 215
+T+ R S + + L RD E+E +E
Sbjct: 286 CQFITKRLRYSLNDDEIYQLACRD--EQEQIE 315
>pdb|3ESW|A Chain A, Complex Of Yeast Pngase With Glcnac2-Iac
Length = 355
Score = 168 bits (425), Expect = 7e-42, Method: Compositional matrix adjust.
Identities = 85/213 (39%), Positives = 121/213 (56%), Gaps = 7/213 (3%)
Query: 8 FILQYCRWVNAPPCDGCSNETVGQ----GMGTPLPSEIQYGAARVELFRCKVCSKITRFP 63
F + +W N P C+ C T G P E ++ VE+++C C ITRFP
Sbjct: 130 FKQDFFKWCNKPDCNHCGQNTSENMTPLGSQGPNGEESKFNCGTVEIYKCNRCGNITRFP 189
Query: 64 RYNDPLKLVETKRGRCGEWANCFTLYCRAFGYESRLILDFTDHVWTECFSQSLGRWMHLD 123
RYNDP+KL+ET++GR GEW N FTL ++FG + R + + DHVW E FS L RW+H+D
Sbjct: 190 RYNDPIKLLETRKGRXGEWCNLFTLILKSFGLDVRYVWNREDHVWCEYFSNFLNRWVHVD 249
Query: 124 PCEGIYDRPLLYEKGWNKKLNYVIAISKDGVFDVTKRYTRKWHEVLSRRNIATEQTVSAV 183
CE +D+P +Y WNKK++Y IA KDGV DV+KRY + L R I E+ + +
Sbjct: 250 SCEQSFDQPYIYSINWNKKMSYCIAFGKDGVVDVSKRYILQ--NELPRDQIK-EEDLKFL 306
Query: 184 LAKMTRECRRSFASETLSTLEDRDKCEREAMER 216
+T+ R S + + L RD+ E+ + R
Sbjct: 307 CQFITKRLRYSLNDDEIYQLACRDEQEQIELIR 339
>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 = 1.9, Method: Compositional matrix adjust.
Identities = 21/81 (25%), Positives = 37/81 (45%), Gaps = 11/81 (13%)
Query: 132 PLLYEKGWNKKLNYVIAISKDGVFDVTKRYTRKWHEVLSRRNIATEQTVSAVLAKMTREC 191
PLL+EKGW +L+ G V + V +R ++ E+ ++ A+ E
Sbjct: 114 PLLFEKGWEGRLH--------GTLLVAAPLEERVRRVXARSGLSREEVLARERAQXPEEE 165
Query: 192 RRSFAS---ETLSTLEDRDKC 209
+R A+ E +LED ++
Sbjct: 166 KRKRATWVLENTGSLEDLERA 186
>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 = 2.0, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 22/36 (61%)
Query: 174 IATEQTVSAVLAKMTRECRRSFASETLSTLEDRDKC 209
I E+T+ ++ K RE ++ FA+ LS+LED K
Sbjct: 453 IGDERTMYNLMKKELREVKKKFATPRLSSLEDTAKA 488
>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 = 6.9, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 19/35 (54%)
Query: 405 IHSGSVLASGEEFPFGIVTSAFDGIRPSKWEDLMA 439
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
0.321 0.137 0.428
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,883,396
Number of Sequences: 62578
Number of extensions: 505807
Number of successful extensions: 891
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: 882
Number of HSP's gapped (non-prelim): 7
length of query: 444
length of database: 14,973,337
effective HSP length: 102
effective length of query: 342
effective length of database: 8,590,381
effective search space: 2937910302
effective search space used: 2937910302
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (25.0 bits)