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= psy10068
         (157 letters)

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

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



>pdb|2V0O|A Chain A, Fcho2 F-Bar Domain
 pdb|2V0O|B Chain B, Fcho2 F-Bar Domain
 pdb|2V0O|C Chain C, Fcho2 F-Bar Domain
          Length = 276

 Score = 32.3 bits (72), Expect = 0.13,   Method: Compositional matrix adjust.
 Identities = 14/26 (53%), Positives = 20/26 (76%)

Query: 27 ELQDYFRKRAEVELDYSKSLDKLARS 52
          EL D+ R+RA +E  YS+S+ KLA+S
Sbjct: 36 ELADFVRERATIEEAYSRSMTKLAKS 61


>pdb|3LIU|A Chain A, Crystal Structure Of Putative Cell Adhesion Protein
           (yp_001304840.1) From Parabacteroides Distasonis Atcc
           8503 At 2.05 A Resolution
 pdb|3LIU|B Chain B, Crystal Structure Of Putative Cell Adhesion Protein
           (yp_001304840.1) From Parabacteroides Distasonis Atcc
           8503 At 2.05 A Resolution
          Length = 402

 Score = 27.7 bits (60), Expect = 2.9,   Method: Compositional matrix adjust.
 Identities = 14/41 (34%), Positives = 20/41 (48%)

Query: 49  LARSLQLRHKEQKQNELDNNVNSLGYQYEVEDLSMKSTSGK 89
           L + L    K      + N  N +GY  EV D+++K  SGK
Sbjct: 121 LTKGLTXSSKVLDVTLVANTTNYIGYDDEVGDITVKDISGK 161


>pdb|3TB6|A Chain A, Structure Of The Effector-binding Domain Of Arabinose
           Repressor Arar From Bacillus Subtilis
 pdb|3TB6|B Chain B, Structure Of The Effector-binding Domain Of Arabinose
           Repressor Arar From Bacillus Subtilis
          Length = 298

 Score = 26.6 bits (57), Expect = 6.9,   Method: Compositional matrix adjust.
 Identities = 20/71 (28%), Positives = 37/71 (52%), Gaps = 7/71 (9%)

Query: 2   DIRLQLNEQLRCLDLRMETQTAVIGELQDYFRKRAEVELDYSKS----LDKLARSLQ--- 54
           +I L++ + LR +DL++    +++G    +F + +EV+L   K     L K A       
Sbjct: 211 EIALKVIDMLREMDLKVPEDMSIVGYDDSHFAQISEVKLTSVKHPKSVLGKAAAKYVIDC 270

Query: 55  LRHKEQKQNEL 65
           L HK+ KQ ++
Sbjct: 271 LEHKKPKQEDV 281


  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
   0.309    0.126    0.330 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,612,048
Number of Sequences: 62578
Number of extensions: 114212
Number of successful extensions: 254
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 250
Number of HSP's gapped (non-prelim): 9
length of query: 157
length of database: 14,973,337
effective HSP length: 91
effective length of query: 66
effective length of database: 9,278,739
effective search space: 612396774
effective search space used: 612396774
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 47 (22.7 bits)