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= 046614
         (142 letters)

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

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



>pdb|3T7V|A Chain A, Crystal Structure Of Methylornithine Synthase (Pylb)
          Length = 350

 Score = 27.3 bits (59), Expect = 3.3,   Method: Compositional matrix adjust.
 Identities = 15/38 (39%), Positives = 20/38 (52%), Gaps = 4/38 (10%)

Query: 43  HFVVYTTDEKRFTVPLEYLSRNVFIELLRMSEEEFGLP 80
           H V  T  E     P  Y   N F+EL+++ +EE GLP
Sbjct: 109 HMVDLTMGED----PYYYEDPNRFVELVQIVKEELGLP 142


>pdb|1FRG|H Chain H, Crystal Structure, Sequence, And Epitope Mapping Of A
          Peptide Complex Of An Anti-Influenza Ha Peptide
          Antibody Fab 26(Slash)9: Fine-Tuning Antibody
          Specificity
          Length = 220

 Score = 26.9 bits (58), Expect = 3.7,   Method: Compositional matrix adjust.
 Identities = 12/45 (26%), Positives = 24/45 (53%), Gaps = 1/45 (2%)

Query: 36 SSVANKGHFVVYTTDEK-RFTVPLEYLSRNVFIELLRMSEEEFGL 79
          ++++N G +  Y    K RFT+  +     +F+E+  +  E+ GL
Sbjct: 49 ATISNGGGYTYYQDSVKGRFTISRDNAKNTLFLEMTSLKSEDAGL 93


>pdb|2G9H|D Chain D, Crystal Structure Of Staphylococcal Enterotoxin I (Sei) In
           Complex With A Human Mhc Class Ii Molecule
          Length = 218

 Score = 26.2 bits (56), Expect = 6.1,   Method: Compositional matrix adjust.
 Identities = 12/36 (33%), Positives = 19/36 (52%)

Query: 40  NKGHFVVYTTDEKRFTVPLEYLSRNVFIELLRMSEE 75
           NKG  + +  DEK F+  L Y    V +  L++ E+
Sbjct: 162 NKGKVLFHLNDEKSFSYDLFYTGDGVPVSFLKIYED 197


>pdb|1EWF|A Chain A, The 1.7 Angstrom Crystal Structure Of Bpi
          Length = 456

 Score = 25.8 bits (55), Expect = 9.5,   Method: Compositional matrix adjust.
 Identities = 16/61 (26%), Positives = 31/61 (50%), Gaps = 3/61 (4%)

Query: 4  SKRLIELARKWQKMATIKR--RRISFPRRAASQNSSVANKGHFVVYTTDEKRFTVPLEYL 61
          S++ ++ A + Q  A +++  +RI  P  + S       KGH+  Y+ D + F +P   +
Sbjct: 10 SQKGLDYASQ-QGTAALQKELKRIKIPDYSDSFKIKHLGKGHYSFYSMDIREFQLPSSQI 68

Query: 62 S 62
          S
Sbjct: 69 S 69


>pdb|1BP1|A Chain A, Crystal Structure Of Bpi, The Human Bactericidal
          Permeability-Increasing Protein
          Length = 456

 Score = 25.4 bits (54), Expect = 10.0,   Method: Compositional matrix adjust.
 Identities = 16/61 (26%), Positives = 31/61 (50%), Gaps = 3/61 (4%)

Query: 4  SKRLIELARKWQKMATIKR--RRISFPRRAASQNSSVANKGHFVVYTTDEKRFTVPLEYL 61
          S++ ++ A + Q  A +++  +RI  P  + S       KGH+  Y+ D + F +P   +
Sbjct: 10 SQKGLDYASQ-QGTAALQKELKRIKIPDYSDSFKIKHLGKGHYSFYSMDIREFQLPSSQI 68

Query: 62 S 62
          S
Sbjct: 69 S 69


  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
   0.322    0.134    0.385 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,730,484
Number of Sequences: 62578
Number of extensions: 132475
Number of successful extensions: 255
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 251
Number of HSP's gapped (non-prelim): 5
length of query: 142
length of database: 14,973,337
effective HSP length: 89
effective length of query: 53
effective length of database: 9,403,895
effective search space: 498406435
effective search space used: 498406435
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 46 (22.3 bits)