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= 020408
         (326 letters)

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

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



>pdb|1GCC|A Chain A, Solution Nmr Structure Of The Complex Of Gcc-Box Binding
           Domain Of Aterf1 And Gcc-Box Dna, Minimized Average
           Structure
          Length = 63

 Score = 72.8 bits (177), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 33/59 (55%), Positives = 38/59 (64%), Gaps = 1/59 (1%)

Query: 50  QYRGIRQRPWGKWAAEIRDPTK-GVRVWLGTFNTXXXXXXXXXXXXXXIRGKKAKVNFP 107
            YRG+RQRPWGK+AAEIRDP K G RVWLGTF T              +RG +A +NFP
Sbjct: 2   HYRGVRQRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLNFP 60


>pdb|2GCC|A Chain A, Solution Structure Of The Gcc-Box Binding Domain, Nmr,
           Minimized Mean Structure
 pdb|3GCC|A Chain A, Solution Structure Of The Gcc-Box Binding Domain, Nmr, 46
           Structures
          Length = 70

 Score = 72.4 bits (176), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 33/62 (53%), Positives = 39/62 (62%), Gaps = 1/62 (1%)

Query: 47  RKNQYRGIRQRPWGKWAAEIRDPTK-GVRVWLGTFNTXXXXXXXXXXXXXXIRGKKAKVN 105
           +   YRG+RQRPWGK+AAEIRDP K G RVWLGTF T              +RG +A +N
Sbjct: 2   KGKHYRGVRQRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLN 61

Query: 106 FP 107
           FP
Sbjct: 62  FP 63


>pdb|1SJX|A Chain A, Three-Dimensional Structure Of A Llama Vhh Domain Oe7
           Binding The Cell Wall Protein Malf1
          Length = 122

 Score = 32.0 bits (71), Expect = 0.48,   Method: Compositional matrix adjust.
 Identities = 18/60 (30%), Positives = 29/60 (48%), Gaps = 2/60 (3%)

Query: 204 NSFDCSDFGWGEQAPKTPEISSVLEATPEVDESQFVDAVANPMKKLKSNSENAVPVQDNN 263
           N F  +D GW  QAP T     ++ A      +++ D+V       K N++N V +Q N+
Sbjct: 27  NIFRINDMGWYRQAPGTQR--ELVAAITSGGSTKYADSVKGRFTISKDNAKNTVYLQMNS 84


>pdb|2XA3|A Chain A, Crystal Structure Of The Broadly Neutralizing Llama Vhh D7
           And Its Mode Of Hiv-1 Gp120 Interaction
          Length = 127

 Score = 28.5 bits (62), Expect = 5.2,   Method: Compositional matrix adjust.
 Identities = 22/78 (28%), Positives = 36/78 (46%), Gaps = 3/78 (3%)

Query: 210 DFGWGEQAPKTPEISSVLEATPEVDESQFVDAVANPMKKLKSNSENAVPVQDNNGKSLSD 269
           D GW  QAP   E   V   +     + +VD+V       K N++NAV +Q N+ K   +
Sbjct: 33  DMGWFRQAPG-KEREFVAAISWSGGTTNYVDSVKGRFDISKDNAKNAVYLQMNSLK--PE 89

Query: 270 ELLAFDNQVKFLPMPYPE 287
           +   +    K+ P+ Y +
Sbjct: 90  DTAVYYCAAKWRPLRYSD 107


  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
   0.313    0.132    0.397 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,455,554
Number of Sequences: 62578
Number of extensions: 456140
Number of successful extensions: 708
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 703
Number of HSP's gapped (non-prelim): 6
length of query: 326
length of database: 14,973,337
effective HSP length: 99
effective length of query: 227
effective length of database: 8,778,115
effective search space: 1992632105
effective search space used: 1992632105
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 51 (24.3 bits)