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= 047158
         (212 letters)

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

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



>pdb|1NZE|A Chain A, Crystal Structure Of Psbq Polypeptide Of Photosystem Ii
           From Higher Plants
 pdb|1VYK|A Chain A, Crystal Structure Of Psbq Protein Of Photosystem Ii From
           Higher Plants
          Length = 149

 Score = 30.0 bits (66), Expect = 0.97,   Method: Compositional matrix adjust.
 Identities = 15/46 (32%), Positives = 25/46 (54%), Gaps = 4/46 (8%)

Query: 19  LHRRVFVVLDNLDHIDQLKPLAGENKWFGSGSRIIITNRNEHLLKV 64
           L  ++F  +DNLDH  ++K      K++G      ++N NE L K+
Sbjct: 107 LTSKLFSSIDNLDHAAKIKSPTEAEKYYGQ----TVSNINEVLAKL 148


>pdb|4AKF|A Chain A, Crystal Structure Of Vipd From Legionella Pneumophila
          Length = 577

 Score = 28.5 bits (62), Expect = 2.7,   Method: Compositional matrix adjust.
 Identities = 22/92 (23%), Positives = 42/92 (45%), Gaps = 11/92 (11%)

Query: 3   DMESIDRGLNMMSSRLLHRR------VFVVLDNLDHIDQLKPLAGENKWFGSGSRIIITN 56
           D+E +D+ LN + + L   +        + L +L  + +L P   ENK       +++TN
Sbjct: 187 DLEKLDKALNSIPTELKGAKGEQLENPRLTLGDLGRLRELLP--EENKHLIKNLSVVVTN 244

Query: 57  RNEHLLKVFEVDGVCTVPRLCLGKSFQLFSWH 88
           + +H L+ +  D   T P+  + +  Q    H
Sbjct: 245 QTKHELERYSED---TTPQQSIAQVVQWSGAH 273


>pdb|3BF0|A Chain A, Crystal Structure Of Escherichia Coli Signal Peptide
           Peptidase (Sppa), Native Crystals
 pdb|3BF0|B Chain B, Crystal Structure Of Escherichia Coli Signal Peptide
           Peptidase (Sppa), Native Crystals
 pdb|3BF0|C Chain C, Crystal Structure Of Escherichia Coli Signal Peptide
           Peptidase (Sppa), Native Crystals
 pdb|3BF0|D Chain D, Crystal Structure Of Escherichia Coli Signal Peptide
           Peptidase (Sppa), Native Crystals
          Length = 593

 Score = 28.1 bits (61), Expect = 4.1,   Method: Compositional matrix adjust.
 Identities = 29/92 (31%), Positives = 46/92 (50%), Gaps = 14/92 (15%)

Query: 93  DKP--PQRFMKLSRELLRCAEGLPLEEKLKRIPNEEILNKLRVSFDVLNDDEEKNVFMDI 150
           DKP   QRF KLSR+LL  +      ++L+     +I+N +R + D   D     + MD+
Sbjct: 44  DKPDSSQRFSKLSRQLLGAS-----SDRLQENSLFDIVNTIRQAKD---DRNITGIVMDL 95

Query: 151 AHLFVGMDK---DYVLKILQGCGFSSEIVFFV 179
            + F G D+    Y+ K L+    S + V+ V
Sbjct: 96  KN-FAGGDQPSMQYIGKALKEFRDSGKPVYAV 126


>pdb|1Q98|A Chain A, Structure Of A Thiol Peroxidase From Haemophilus
           Influenzae Rd
 pdb|1Q98|B Chain B, Structure Of A Thiol Peroxidase From Haemophilus
           Influenzae Rd
          Length = 165

 Score = 27.3 bits (59), Expect = 7.1,   Method: Compositional matrix adjust.
 Identities = 11/27 (40%), Positives = 18/27 (66%)

Query: 180 LTQRCLIVIDEDNRLKMHDLIRDMKEK 206
           LT R +IV+DE N +    L+ ++KE+
Sbjct: 128 LTSRAVIVLDEQNNVLHSQLVEEIKEE 154


  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
   0.326    0.143    0.429 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,069,670
Number of Sequences: 62578
Number of extensions: 252397
Number of successful extensions: 864
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 863
Number of HSP's gapped (non-prelim): 7
length of query: 212
length of database: 14,973,337
effective HSP length: 95
effective length of query: 117
effective length of database: 9,028,427
effective search space: 1056325959
effective search space used: 1056325959
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 49 (23.5 bits)