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= 041344
         (236 letters)

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

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



>pdb|1U5E|A Chain A, Crystal Structure Of A N-Terminal Fragment Of Skap-Hom
           Containing Both The Helical Dimerization Domain And The
           Ph Domain
 pdb|1U5E|B Chain B, Crystal Structure Of A N-Terminal Fragment Of Skap-Hom
           Containing Both The Helical Dimerization Domain And The
           Ph Domain
 pdb|2OTX|A Chain A, Crystal Structure Of A N-Terminal Fragment Of Skap-Hom
           Containing Both The Helical Dimerization Domain And The
           Ph Domain
 pdb|2OTX|B Chain B, Crystal Structure Of A N-Terminal Fragment Of Skap-Hom
           Containing Both The Helical Dimerization Domain And The
           Ph Domain
          Length = 211

 Score = 30.8 bits (68), Expect = 0.59,   Method: Compositional matrix adjust.
 Identities = 13/30 (43%), Positives = 15/30 (50%)

Query: 36  CCFYIGTPQKKDYFLCAETPGAARAWVSTL 65
           CCF I  P K+ Y   A +P  A  WV  L
Sbjct: 174 CCFEICAPDKRIYQFTAASPKDAEEWVQQL 203


>pdb|1U5F|A Chain A, Crystal Structure Of The Ph Domain Of Skap-Hom With 8
           Vector-Derived N-Terminal Residues
          Length = 148

 Score = 30.4 bits (67), Expect = 0.92,   Method: Compositional matrix adjust.
 Identities = 13/30 (43%), Positives = 15/30 (50%)

Query: 36  CCFYIGTPQKKDYFLCAETPGAARAWVSTL 65
           CCF I  P K+ Y   A +P  A  WV  L
Sbjct: 85  CCFEICAPDKRIYQFTAASPKDAEEWVQQL 114


>pdb|1U5G|A Chain A, Crystal Structure Of The Ph Domain Of Skap-Hom
 pdb|1U5G|B Chain B, Crystal Structure Of The Ph Domain Of Skap-Hom
 pdb|1U5G|C Chain C, Crystal Structure Of The Ph Domain Of Skap-Hom
 pdb|1U5G|D Chain D, Crystal Structure Of The Ph Domain Of Skap-Hom
          Length = 122

 Score = 29.6 bits (65), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 13/30 (43%), Positives = 15/30 (50%)

Query: 36  CCFYIGTPQKKDYFLCAETPGAARAWVSTL 65
           CCF I  P K+ Y   A +P  A  WV  L
Sbjct: 85  CCFEICAPDKRIYQFTAASPKDAEEWVQQL 114


>pdb|3U2H|A Chain A, Crystal Structure Of The C-Terminal Duf1608 Domain Of The
           Methanosarcina Acetivorans S-Layer (Ma0829) Protein
          Length = 286

 Score = 28.9 bits (63), Expect = 2.9,   Method: Compositional matrix adjust.
 Identities = 17/49 (34%), Positives = 28/49 (57%), Gaps = 1/49 (2%)

Query: 110 EIEAAMQISLRNALGTMTNRITDGPMDDLSIMKETLRVKDEELQNLARD 158
           +IE    I   NA+ T+ +    G +DD+SI  +TL++ +E+   L RD
Sbjct: 199 QIEGLWLIDYANAM-TIESDDEFGNLDDVSIDGDTLKISNEDTFTLTRD 246


>pdb|1XYN|A Chain A, Structural Comparison Of Two Major Endo-1,4-Beta-Xylanases
           From Trichodrema Reesei
          Length = 178

 Score = 28.5 bits (62), Expect = 3.7,   Method: Compositional matrix adjust.
 Identities = 11/24 (45%), Positives = 18/24 (75%)

Query: 1   TRRNEPTVKGTITFDENSTIAISP 24
           TR NEP+++GT TF++  ++  SP
Sbjct: 108 TRVNEPSIQGTATFNQYISVRNSP 131


>pdb|3U2G|A Chain A, Crystal Structure Of The C-Terminal Duf1608 Domain Of The
           Methanosarcina Acetivorans S-Layer (Ma0829) Protein
          Length = 286

 Score = 27.7 bits (60), Expect = 5.1,   Method: Compositional matrix adjust.
 Identities = 17/49 (34%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 110 EIEAAMQISLRNALGTMTNRITDGPMDDLSIMKETLRVKDEELQNLARD 158
           +IE    I   NA  T+ +    G +DD+SI  +TL++ +E+   L RD
Sbjct: 199 QIEGLWLIDYANAX-TIESDDEFGNLDDVSIDGDTLKISNEDTFTLTRD 246


  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
   0.318    0.132    0.384 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,703,652
Number of Sequences: 62578
Number of extensions: 186386
Number of successful extensions: 406
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 402
Number of HSP's gapped (non-prelim): 6
length of query: 236
length of database: 14,973,337
effective HSP length: 96
effective length of query: 140
effective length of database: 8,965,849
effective search space: 1255218860
effective search space used: 1255218860
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)