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= 011059
         (494 letters)

Database: pdbaa 
           62,578 sequences; 14,973,337 total letters

Searching..................................................done



>pdb|3AQL|A Chain A, Structure Of Bacterial Protein (Apo Form Ii)
 pdb|3AQL|B Chain B, Structure Of Bacterial Protein (Apo Form Ii)
 pdb|3AQN|A Chain A, Complex Structure Of Bacterial Protein (Apo Form Ii)
 pdb|3AQN|B Chain B, Complex Structure Of Bacterial Protein (Apo Form Ii)
          Length = 415

 Score = 29.6 bits (65), Expect = 4.5,   Method: Compositional matrix adjust.
 Identities = 20/74 (27%), Positives = 35/74 (47%), Gaps = 9/74 (12%)

Query: 78  VRIAQCGYEYE------QSYAFLPLLPAFTHLLSRSVLAPLIGVIGY---RAVLGLAGYI 128
           +++ Q GY YE      + + F PL P  T   + +  +P+  +I          +   +
Sbjct: 224 LKLLQAGYGYETYKLLCEYHLFQPLFPTITRYFTENGDSPMERIIEQVLKNTDTRIHNDM 283

Query: 129 VSNVAFLFAAVYFY 142
             N AFLFAA+++Y
Sbjct: 284 RVNPAFLFAAMFWY 297


>pdb|3AQK|A Chain A, Structure Of Bacterial Protein (Apo Form I)
          Length = 414

 Score = 29.6 bits (65), Expect = 4.5,   Method: Compositional matrix adjust.
 Identities = 20/74 (27%), Positives = 35/74 (47%), Gaps = 9/74 (12%)

Query: 78  VRIAQCGYEYE------QSYAFLPLLPAFTHLLSRSVLAPLIGVIGY---RAVLGLAGYI 128
           +++ Q GY YE      + + F PL P  T   + +  +P+  +I          +   +
Sbjct: 223 LKLLQAGYGYETYKLLCEYHLFQPLFPTITRYFTENGDSPMERIIEQVLKNTDTRIHNDM 282

Query: 129 VSNVAFLFAAVYFY 142
             N AFLFAA+++Y
Sbjct: 283 RVNPAFLFAAMFWY 296


>pdb|3AQM|A Chain A, Structure Of Bacterial Protein (Form Ii)
 pdb|3AQM|B Chain B, Structure Of Bacterial Protein (Form Ii)
          Length = 415

 Score = 29.3 bits (64), Expect = 4.6,   Method: Compositional matrix adjust.
 Identities = 20/74 (27%), Positives = 35/74 (47%), Gaps = 9/74 (12%)

Query: 78  VRIAQCGYEYE------QSYAFLPLLPAFTHLLSRSVLAPLIGVIGY---RAVLGLAGYI 128
           +++ Q GY YE      + + F PL P  T   + +  +P+  +I          +   +
Sbjct: 224 LKLLQAGYGYETYKLLCEYHLFQPLFPTITRYFTENGDSPMERIIEQVLKNTDTRIHNDM 283

Query: 129 VSNVAFLFAAVYFY 142
             N AFLFAA+++Y
Sbjct: 284 RVNPAFLFAAMFWY 297


>pdb|1QO0|A Chain A, Amide Receptor Of The Amidase Operon Of Pseudomonas
           Aeruginosa (Amic) Complexed With The Positive Regulator
           Amir.
 pdb|1QO0|B Chain B, Amide Receptor Of The Amidase Operon Of Pseudomonas
           Aeruginosa (Amic) Complexed With The Positive Regulator
           Amir.
 pdb|1PEA|A Chain A, Amide ReceptorNEGATIVE REGULATOR OF THE AMIDASE OPERON OF
           Pseudomonas Aeruginosa (Amic) Complexed With Acetamide
          Length = 385

 Score = 28.5 bits (62), Expect = 9.6,   Method: Compositional matrix adjust.
 Identities = 13/24 (54%), Positives = 15/24 (62%)

Query: 350 EGKEYAPVFFSSGAAPKSNSAPVA 373
           EG EY+P     G AP  NSAP+A
Sbjct: 109 EGFEYSPNIVYGGPAPNQNSAPLA 132


>pdb|1QNL|A Chain A, Amide ReceptorNEGATIVE REGULATOR OF THE AMIDASE OPERON OF
           Pseudomonas Aeruginosa (Amic) Complexed With Butyramide
          Length = 385

 Score = 28.5 bits (62), Expect = 9.7,   Method: Compositional matrix adjust.
 Identities = 13/24 (54%), Positives = 15/24 (62%)

Query: 350 EGKEYAPVFFSSGAAPKSNSAPVA 373
           EG EY+P     G AP  NSAP+A
Sbjct: 109 EGFEYSPNIVYGGPAPNQNSAPLA 132


  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
   0.328    0.140    0.451 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,868,502
Number of Sequences: 62578
Number of extensions: 539359
Number of successful extensions: 1361
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1359
Number of HSP's gapped (non-prelim): 5
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: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 53 (25.0 bits)