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= 039000
         (262 letters)

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

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



>pdb|1WPK|A Chain A, Methylated Form Of N-terminal Transcriptional Regulator
           Domain Of Escherichia Coli Ada Protein
          Length = 146

 Score = 33.1 bits (74), Expect = 0.17,   Method: Compositional matrix adjust.
 Identities = 27/94 (28%), Positives = 36/94 (38%), Gaps = 7/94 (7%)

Query: 175 RETVSKYADTSNPNKSDMRELDEIQPEPLTVQQQLLDDETRALQ-------VELTSLLDA 227
           RE VS YA+ S    +  R     QPE    QQ  LD  T A +       V L +L D 
Sbjct: 49  RENVSFYANASEALAAGFRPCKRCQPEKANAQQHRLDKITHACRLLEQETPVTLEALADQ 108

Query: 228 VQQTETKMVEMSALNHLMSTHILHQAKQIEHLYE 261
           V  +   +  +      M+     QA +   L E
Sbjct: 109 VAMSPFHLHRLFKATTGMTPKAWQQAWRARRLRE 142


>pdb|4ABN|A Chain A, Crystal Structure Of Full Length Mouse Strap (Ttc5)
 pdb|4ABN|B Chain B, Crystal Structure Of Full Length Mouse Strap (Ttc5)
          Length = 474

 Score = 32.0 bits (71), Expect = 0.31,   Method: Compositional matrix adjust.
 Identities = 28/84 (33%), Positives = 41/84 (48%), Gaps = 9/84 (10%)

Query: 169 PRRKLKRETVSKYADTSNP---NKSDMRELDEIQPEPLTVQQQLLDDETRALQVELTSLL 225
           P   L R T+ KY ++        S    LD   PEP   +QQLL+  +R     LTSLL
Sbjct: 258 PDLHLNRATLHKYEESYGEALEGFSQAAALDPAWPEPQQREQQLLEFLSR-----LTSLL 312

Query: 226 DAVQQTETKMVEMSALNHLMSTHI 249
           ++  +T+ K ++ S L  L   H+
Sbjct: 313 ESKGKTKPKKLQ-SMLGSLRPAHL 335


>pdb|4DDQ|A Chain A, Structural Plasticity Of The Bacillus Subtilis Gyra
           Homodimer
 pdb|4DDQ|B Chain B, Structural Plasticity Of The Bacillus Subtilis Gyra
           Homodimer
 pdb|4DDQ|C Chain C, Structural Plasticity Of The Bacillus Subtilis Gyra
           Homodimer
 pdb|4DDQ|D Chain D, Structural Plasticity Of The Bacillus Subtilis Gyra
           Homodimer
 pdb|4DDQ|E Chain E, Structural Plasticity Of The Bacillus Subtilis Gyra
           Homodimer
 pdb|4DDQ|F Chain F, Structural Plasticity Of The Bacillus Subtilis Gyra
           Homodimer
          Length = 502

 Score = 27.7 bits (60), Expect = 6.4,   Method: Compositional matrix adjust.
 Identities = 17/52 (32%), Positives = 26/52 (50%), Gaps = 4/52 (7%)

Query: 59  GALEQFILNHRKDY----VEMHRTSEQERDSIEHEVTAFIKTCKEKIDILQN 106
           G +EQF L  ++      + + R +  ER+ IE E  + +K   E  DIL N
Sbjct: 409 GLIEQFSLTEKQAQAILDMRLQRLTGLEREKIEEEYQSLVKLIAELKDILAN 460


  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
   0.316    0.128    0.347 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,515,478
Number of Sequences: 62578
Number of extensions: 224275
Number of successful extensions: 691
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 688
Number of HSP's gapped (non-prelim): 12
length of query: 262
length of database: 14,973,337
effective HSP length: 97
effective length of query: 165
effective length of database: 8,903,271
effective search space: 1469039715
effective search space used: 1469039715
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 bits)