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= 038023
(256 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1OLA|A Chain A, The Structural Basis Of Multispecificity In The
Oligopeptide-binding Protein Oppa
pdb|2OLB|A Chain A, Oligopeptide Binding Protein (Oppa) Complexed With Tri-
Lysine
pdb|1OLC|A Chain A, Oligo-Peptide Binding Protein (Oppa) Complexed With
Lys-Lys- Lys-Ala
pdb|1JEV|A Chain A, Oligo-peptide Binding Protein (oppa) Complexed With Kwk
pdb|1JET|A Chain A, Oligo-Peptide Binding Protein (Oppa) Complexed With Kak
pdb|1JEU|A Chain A, Oligo-Peptide Binding Protein (Oppa) Complexed With Kek
pdb|2RKM|A Chain A, Structure Of Oppa Complexed With Lys-Lys
pdb|1B32|A Chain A, Oligo-Peptide Binding Protein (Oppa) Complexed With Kmk
pdb|1B3F|A Chain A, Oligo-Peptide Binding Protein (Oppa) Complexed With Khk
pdb|1B3G|A Chain A, Oligo-Peptide Binding Protein (Oppa) Complexed With Kik
pdb|1B3L|A Chain A, Oligo-Peptide Binding Protein (Oppa) Complexed With Kgk
pdb|1B3L|C Chain C, Oligo-Peptide Binding Protein (Oppa) Complexed With Kgk
pdb|1B7H|A Chain A, Oligo-Peptide Binding Protein Complexed With Lysyl-
Norleucyl-Lysine
pdb|1B0H|A Chain A, Oligo-Peptide Binding Protein Complexed With Lysyl-
Napthylalanyl-Lysine
pdb|1B1H|A Chain A, Oligo-Peptide Binding ProteinTRIPEPTIDE (LYS HPE LYS)
Complex
pdb|1B2H|A Chain A, Oligo-Peptide Binding Protein Complexed With
Lysyl-Ornithyl-Lysine
pdb|1B3H|A Chain A, Oligo-Peptide Binding Protein Complexed With Lysyl-
Cyclohexylalanyl-Lysine
pdb|1B4H|A Chain A, Oligo-Peptide Binding Protein Complexed With Lysyl-
Diaminobutyric Acid-Lysine
pdb|1B5H|A Chain A, Oligo-Peptide Binding Protein Complexed With
Lysyl-Diaminopropanoic Acid-Lysine
pdb|1B6H|A Chain A, Oligo-Peptide Binding Protein Complexed With
Lysyl-Norvalyl- Lysine
pdb|1B52|A Chain A, Oligo-Peptide Binding Protein (Oppa) Complexed With Ktk
pdb|1B51|A Chain A, Oligo-Peptide Binding Protein (Oppa) Complexed With Ksk
pdb|1B5I|A Chain A, Oligo-Peptide Binding Protein (Oppa) Complexed With Knk
pdb|1B5J|A Chain A, Oligo-Peptide Binding Protein (Oppa) Complexed With Kqk
pdb|1B46|A Chain A, Oligo-Peptide Binding Protein (Oppa) Complexed With Kpk
pdb|1B9J|A Chain A, Oligo-Peptide Binding Protein (Oppa) Complexed With Klk
pdb|1QKA|A Chain A, Oligo-Peptide Binding Protein (Oppa) Complexed With Krk
pdb|1QKB|A Chain A, Oligo-Peptide Binding Protein (Oppa) Complexed With Kvk
pdb|1B4Z|A Chain A, Oligo-Peptide Binding Protein (Oppa) Complexed With Kdk
pdb|1B58|A Chain A, Oligo-Peptide Binding Protein (Oppa) Complexed With Kyk
pdb|1B40|A Chain A, Oligo-Peptide Binding Protein (Oppa) Complexed With Kfk
pdb|1B05|A Chain A, Structure Of Oligo-Peptide Binding Protein Complexed With
Lys-Cys-Lys
pdb|1RKM|A Chain A, Structure Of Oppa
Length = 517
Score = 28.5 bits (62), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 33/77 (42%), Gaps = 19/77 (24%)
Query: 32 GSDLIKSELSAYGDKLLGSGSAFIGRYFSNPRYYFQVNDQYVQNKLKGHWMRATETVKGK 91
D +SEL A ++ L SA + P YY YV +L W+ G
Sbjct: 457 ADDTQRSELYAKAEQQLDKDSAIV------PVYY------YVNARLVKPWV-------GG 497
Query: 92 FCYKPPIDDINAPNLYI 108
+ K P+D+I NLYI
Sbjct: 498 YTGKDPLDNIYVKNLYI 514
>pdb|1T9T|A Chain A, Structural Basis Of Multidrug Transport By The Acrb
Multidrug Efflux Pump
pdb|1T9U|A Chain A, Structural Basis Of Multidrug Transport By The Acrb
Multidrug Efflux Pump
pdb|1T9V|A Chain A, Structural Basis Of Multidrug Transport By The Acrb
Multidrug Efflux Pump
pdb|1T9W|A Chain A, Structural Basis Of Multidrug Transport By The Acrb
Multidrug Efflux Pump
pdb|1T9X|A Chain A, Structural Basis Of Multidrug Transport By The Acrb
Multidrug Efflux Pump
pdb|1T9Y|A Chain A, Structural Basis Of Multidrug Transport By The Acrb
Multidrug Efflux Pump
Length = 1049
Score = 27.7 bits (60), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 11/24 (45%), Positives = 15/24 (62%)
Query: 104 PNLYIPLMAFGTFVVLAGFFLGIN 127
P + +P++ GTF VLA F IN
Sbjct: 368 PTIAVPVVLLGTFAVLAAFGFSIN 391
>pdb|4DX6|A Chain A, Transport Of Drugs By The Multidrug Transporter Acrb
Involves An Access And A Deep Binding Pocket That Are
Separated By A Switch-Loop
pdb|4DX6|B Chain B, Transport Of Drugs By The Multidrug Transporter Acrb
Involves An Access And A Deep Binding Pocket That Are
Separated By A Switch-Loop
pdb|4DX6|C Chain C, Transport Of Drugs By The Multidrug Transporter Acrb
Involves An Access And A Deep Binding Pocket That Are
Separated By A Switch-Loop
Length = 1057
Score = 27.7 bits (60), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 11/24 (45%), Positives = 15/24 (62%)
Query: 104 PNLYIPLMAFGTFVVLAGFFLGIN 127
P + +P++ GTF VLA F IN
Sbjct: 368 PTIAVPVVLLGTFAVLAAFGFSIN 391
>pdb|2J8S|A Chain A, Drug Export Pathway Of Multidrug Exporter Acrb Revealed By
Darpin Inhibitors
pdb|2J8S|B Chain B, Drug Export Pathway Of Multidrug Exporter Acrb Revealed By
Darpin Inhibitors
pdb|2J8S|C Chain C, Drug Export Pathway Of Multidrug Exporter Acrb Revealed By
Darpin Inhibitors
Length = 1055
Score = 27.7 bits (60), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 11/24 (45%), Positives = 15/24 (62%)
Query: 104 PNLYIPLMAFGTFVVLAGFFLGIN 127
P + +P++ GTF VLA F IN
Sbjct: 368 PTIAVPVVLLGTFAVLAAFGFSIN 391
>pdb|2GIF|A Chain A, Asymmetric Structure Of Trimeric Acrb From Escherichia
Coli
pdb|2GIF|B Chain B, Asymmetric Structure Of Trimeric Acrb From Escherichia
Coli
pdb|2GIF|C Chain C, Asymmetric Structure Of Trimeric Acrb From Escherichia
Coli
pdb|2HRT|A Chain A, Asymmetric Structure Of Trimeric Acrb From Escherichia
Coli
pdb|2HRT|B Chain B, Asymmetric Structure Of Trimeric Acrb From Escherichia
Coli
pdb|2HRT|C Chain C, Asymmetric Structure Of Trimeric Acrb From Escherichia
Coli
pdb|2HRT|D Chain D, Asymmetric Structure Of Trimeric Acrb From Escherichia
Coli
pdb|2HRT|E Chain E, Asymmetric Structure Of Trimeric Acrb From Escherichia
Coli
pdb|2HRT|F Chain F, Asymmetric Structure Of Trimeric Acrb From Escherichia
Coli
pdb|4DX5|A Chain A, Transport Of Drugs By The Multidrug Transporter Acrb
Involves An Access And A Deep Binding Pocket That Are
Separated By A Switch-Loop
pdb|4DX5|B Chain B, Transport Of Drugs By The Multidrug Transporter Acrb
Involves An Access And A Deep Binding Pocket That Are
Separated By A Switch-Loop
pdb|4DX5|C Chain C, Transport Of Drugs By The Multidrug Transporter Acrb
Involves An Access And A Deep Binding Pocket That Are
Separated By A Switch-Loop
pdb|4DX7|A Chain A, Transport Of Drugs By The Multidrug Transporter Acrb
Involves An Access And A Deep Binding Pocket That Are
Separated By A Switch-Loop
pdb|4DX7|B Chain B, Transport Of Drugs By The Multidrug Transporter Acrb
Involves An Access And A Deep Binding Pocket That Are
Separated By A Switch-Loop
pdb|4DX7|C Chain C, Transport Of Drugs By The Multidrug Transporter Acrb
Involves An Access And A Deep Binding Pocket That Are
Separated By A Switch-Loop
Length = 1057
Score = 27.7 bits (60), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 11/24 (45%), Positives = 15/24 (62%)
Query: 104 PNLYIPLMAFGTFVVLAGFFLGIN 127
P + +P++ GTF VLA F IN
Sbjct: 368 PTIAVPVVLLGTFAVLAAFGFSIN 391
>pdb|3NOC|A Chain A, Designed Ankyrin Repeat Protein (Darpin) Binders To Acrb:
Plasticity Of The Interface
pdb|3NOC|B Chain B, Designed Ankyrin Repeat Protein (Darpin) Binders To Acrb:
Plasticity Of The Interface
pdb|3NOC|C Chain C, Designed Ankyrin Repeat Protein (Darpin) Binders To Acrb:
Plasticity Of The Interface
pdb|3NOG|A Chain A, Designed Ankyrin Repeat Protein (Darpin) Binders To Acrb:
Plasticity Of The Interface
pdb|3NOG|B Chain B, Designed Ankyrin Repeat Protein (Darpin) Binders To Acrb:
Plasticity Of The Interface
pdb|3NOG|C Chain C, Designed Ankyrin Repeat Protein (Darpin) Binders To Acrb:
Plasticity Of The Interface
Length = 1049
Score = 27.7 bits (60), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 11/24 (45%), Positives = 15/24 (62%)
Query: 104 PNLYIPLMAFGTFVVLAGFFLGIN 127
P + +P++ GTF VLA F IN
Sbjct: 368 PTIAVPVVLLGTFAVLAAFGFSIN 391
>pdb|1OY6|A Chain A, Structural Basis Of The Multiple Binding Capacity Of The
Acrb Multidrug Efflux Pump
pdb|1OY8|A Chain A, Structural Basis Of Multiple Drug Binding Capacity Of The
Acrb Multidrug Efflux Pump
pdb|1OY9|A Chain A, Structural Basis Of Multiple Drug Binding Capacity Of The
Acrb Multidrug Efflux Pump
pdb|1OYD|A Chain A, Structural Basis Of Multiple Binding Capacity Of The Acrb
Multidrug Efflux Pump
pdb|1OYE|A Chain A, Structural Basis Of Multiple Binding Capacity Of The Acrb
Multidrug Efflux Pump
pdb|2I6W|A Chain A, Crystal Structure Of The Multidrug Efflux Transporter Acrb
pdb|2RDD|A Chain A, X-Ray Crystal Structure Of Acrb In Complex With A Novel
Transmembrane Helix.
pdb|3D9B|A Chain A, Symmetric Structure Of E. Coli Acrb
pdb|2W1B|A Chain A, The Structure Of The Efflux Pump Acrb In Complex With Bile
Acid
Length = 1049
Score = 27.7 bits (60), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 11/24 (45%), Positives = 15/24 (62%)
Query: 104 PNLYIPLMAFGTFVVLAGFFLGIN 127
P + +P++ GTF VLA F IN
Sbjct: 368 PTIAVPVVLLGTFAVLAAFGFSIN 391
>pdb|1IWG|A Chain A, Crystal Structure Of Bacterial Multidrug Efflux
Transporter Acrb
pdb|2DHH|A Chain A, Crystal Structure Of A Multidrug Transporter Reveal A
Functionally Rotating Mechanism
pdb|2DHH|B Chain B, Crystal Structure Of A Multidrug Transporter Reveal A
Functionally Rotating Mechanism
pdb|2DHH|C Chain C, Crystal Structure Of A Multidrug Transporter Reveal A
Functionally Rotating Mechanism
pdb|2DR6|A Chain A, Crystal Structure Of A Multidrug Transporter Reveal A
Functionally Rotating Mechanism
pdb|2DR6|B Chain B, Crystal Structure Of A Multidrug Transporter Reveal A
Functionally Rotating Mechanism
pdb|2DR6|C Chain C, Crystal Structure Of A Multidrug Transporter Reveal A
Functionally Rotating Mechanism
pdb|2DRD|A Chain A, Crystal Structure Of A Multidrug Transporter Reveal A
Functionally Rotating Mechanism
pdb|2DRD|B Chain B, Crystal Structure Of A Multidrug Transporter Reveal A
Functionally Rotating Mechanism
pdb|2DRD|C Chain C, Crystal Structure Of A Multidrug Transporter Reveal A
Functionally Rotating Mechanism
pdb|3AOA|A Chain A, Structures Of The Multidrug Exporter Acrb Reveal A
Proximal Multisite Drug-Binding Pocket
pdb|3AOA|B Chain B, Structures Of The Multidrug Exporter Acrb Reveal A
Proximal Multisite Drug-Binding Pocket
pdb|3AOA|C Chain C, Structures Of The Multidrug Exporter Acrb Reveal A
Proximal Multisite Drug-Binding Pocket
pdb|3AOB|A Chain A, Structures Of The Multidrug Exporter Acrb Reveal A
Proximal Multisite Drug-Binding Pocket
pdb|3AOB|B Chain B, Structures Of The Multidrug Exporter Acrb Reveal A
Proximal Multisite Drug-Binding Pocket
pdb|3AOB|C Chain C, Structures Of The Multidrug Exporter Acrb Reveal A
Proximal Multisite Drug-Binding Pocket
pdb|3AOC|A Chain A, Structures Of The Multidrug Exporter Acrb Reveal A
Proximal Multisite Drug-Binding Pocket
pdb|3AOC|B Chain B, Structures Of The Multidrug Exporter Acrb Reveal A
Proximal Multisite Drug-Binding Pocket
pdb|3AOC|C Chain C, Structures Of The Multidrug Exporter Acrb Reveal A
Proximal Multisite Drug-Binding Pocket
pdb|3AOD|A Chain A, Structures Of The Multidrug Exporter Acrb Reveal A
Proximal Multisite Drug-Binding Pocket
pdb|3AOD|B Chain B, Structures Of The Multidrug Exporter Acrb Reveal A
Proximal Multisite Drug-Binding Pocket
pdb|3AOD|C Chain C, Structures Of The Multidrug Exporter Acrb Reveal A
Proximal Multisite Drug-Binding Pocket
Length = 1053
Score = 27.7 bits (60), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 11/24 (45%), Positives = 15/24 (62%)
Query: 104 PNLYIPLMAFGTFVVLAGFFLGIN 127
P + +P++ GTF VLA F IN
Sbjct: 368 PTIAVPVVLLGTFAVLAAFGFSIN 391
>pdb|2HQD|A Chain A, Conformation Of The Acrb Multidrug Efflux Pump In Mutants
Of The Putative Proton Relay Pathway
Length = 1053
Score = 27.7 bits (60), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 11/24 (45%), Positives = 15/24 (62%)
Query: 104 PNLYIPLMAFGTFVVLAGFFLGIN 127
P + +P++ GTF VLA F IN
Sbjct: 368 PTIAVPVVLLGTFAVLAAFGFSIN 391
>pdb|2HQF|A Chain A, Conformation Of The Acrb Multidrug Efflux Pump In Mutants
Of The Putative Proton Relay Pathway
Length = 1053
Score = 27.7 bits (60), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 11/24 (45%), Positives = 15/24 (62%)
Query: 104 PNLYIPLMAFGTFVVLAGFFLGIN 127
P + +P++ GTF VLA F IN
Sbjct: 368 PTIAVPVVLLGTFAVLAAFGFSIN 391
>pdb|2HQC|A Chain A, Conformation Of The Acrb Multidrug Efflux Pump In Mutants
Of The Putative Proton Relay Pathway
Length = 1053
Score = 27.7 bits (60), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 11/24 (45%), Positives = 15/24 (62%)
Query: 104 PNLYIPLMAFGTFVVLAGFFLGIN 127
P + +P++ GTF VLA F IN
Sbjct: 368 PTIAVPVVLLGTFAVLAAFGFSIN 391
>pdb|2HQG|A Chain A, Conformation Of The Acrb Multidrug Efflux Pump In Mutants
Of The Putative Proton Relay Pathway
Length = 1053
Score = 27.7 bits (60), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 11/24 (45%), Positives = 15/24 (62%)
Query: 104 PNLYIPLMAFGTFVVLAGFFLGIN 127
P + +P++ GTF VLA F IN
Sbjct: 368 PTIAVPVVLLGTFAVLAAFGFSIN 391
>pdb|1EI1|A Chain A, Dimerization Of E. Coli Dna Gyrase B Provides A Structural
Mechanism For Activating The Atpase Catalytic Center
pdb|1EI1|B Chain B, Dimerization Of E. Coli Dna Gyrase B Provides A Structural
Mechanism For Activating The Atpase Catalytic Center
Length = 391
Score = 27.7 bits (60), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 20/97 (20%), Positives = 39/97 (40%), Gaps = 5/97 (5%)
Query: 3 QSGGTHAQIFQQTSTEQYKKQFGEALYGAGSDLIKSELSAYGDKLLGSGSAFIGRYFSNP 62
+ GGTH F+ T + Y K+++SA GD A + +P
Sbjct: 275 RDGGTHLAGFRAAMTRTLNAYMDKEGYSK-----KAKVSATGDDAREGLIAVVSVKVPDP 329
Query: 63 RYYFQVNDQYVQNKLKGHWMRATETVKGKFCYKPPID 99
++ Q D+ V +++K + + ++ + P D
Sbjct: 330 KFSSQTKDKLVSSEVKSAVEQQMNELLAEYLLENPTD 366
>pdb|3NRE|A Chain A, Crystal Structure Of A Putative Aldose 1-Epimerase (B2544)
From Escherichia Coli K12 At 1.59 A Resolution
pdb|3NRE|B Chain B, Crystal Structure Of A Putative Aldose 1-Epimerase (B2544)
From Escherichia Coli K12 At 1.59 A Resolution
pdb|3NRE|C Chain C, Crystal Structure Of A Putative Aldose 1-Epimerase (B2544)
From Escherichia Coli K12 At 1.59 A Resolution
pdb|3NRE|D Chain D, Crystal Structure Of A Putative Aldose 1-Epimerase (B2544)
From Escherichia Coli K12 At 1.59 A Resolution
Length = 291
Score = 27.3 bits (59), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 24/42 (57%), Gaps = 2/42 (4%)
Query: 65 YFQVNDQ-YVQNKLKGHWMRATETVKGKFCYKPPID-DINAP 104
YF ++ Q +Q + G+W+ + + G+FC + P + D N P
Sbjct: 151 YFPLSPQTRIQAQASGYWLEREQWLAGEFCEQLPQELDFNQP 192
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
0.326 0.141 0.439
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,473,964
Number of Sequences: 62578
Number of extensions: 313611
Number of successful extensions: 616
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 605
Number of HSP's gapped (non-prelim): 16
length of query: 256
length of database: 14,973,337
effective HSP length: 97
effective length of query: 159
effective length of database: 8,903,271
effective search space: 1415620089
effective search space used: 1415620089
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: 50 (23.9 bits)