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= psy12800
         (134 letters)

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

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



>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 = 1.4,   Method: Composition-based stats.
 Identities = 25/84 (29%), Positives = 39/84 (46%), Gaps = 11/84 (13%)

Query: 36  QHFPNLQ-----LTKSKSGDTSKHTLSADSLDSKGQSPEMHR---RSFVGFNAGNGTRSY 87
           Q FP  Q     LTK+  GDT+K+ L    +D+   S E+ +   + F         R+ 
Sbjct: 228 QVFPGAQGLLEGLTKT-GGDTAKYALENKLVDALASSAEIEKALTKEFGWSKTDKNYRAI 286

Query: 88  EYYPYSQRSTIR--DLVGRGWANG 109
            YY Y+ ++     D +G  +ANG
Sbjct: 287 SYYDYALKTPADTGDSIGVVFANG 310


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

 Score = 27.7 bits (60), Expect = 1.9,   Method: Composition-based stats.
 Identities = 25/84 (29%), Positives = 39/84 (46%), Gaps = 11/84 (13%)

Query: 36  QHFPNLQ-----LTKSKSGDTSKHTLSADSLDSKGQSPEMHR---RSFVGFNAGNGTRSY 87
           Q FP  Q     LTK+  GDT+K+ L    +D+   S E+ +   + F         R+ 
Sbjct: 228 QVFPGAQGLLEGLTKT-GGDTAKYALENKLVDALASSAEIEKALTKEFGWSKTDKNYRAI 286

Query: 88  EYYPYSQRSTIR--DLVGRGWANG 109
            YY Y+ ++     D +G  +ANG
Sbjct: 287 SYYDYALKTPADTGDSIGVVFANG 310


>pdb|2YX0|A Chain A, Crystal Structure Of P. Horikoshii Tyw1
          Length = 342

 Score = 26.6 bits (57), Expect = 4.5,   Method: Compositional matrix adjust.
 Identities = 20/74 (27%), Positives = 31/74 (41%), Gaps = 8/74 (10%)

Query: 19  PSFISGRSFASASRILNQHFPNLQLTKSKSGDTSKHTLSADSLDSKGQ--------SPEM 70
           P+FI   S  +  ++L  +  N ++ K K  +    T +A SL  +            E 
Sbjct: 107 PAFIVEESIKAQRKLLIGYKGNPKVDKKKFEEAWNPTHAAISLSGEPMLYPYMGDLVEEF 166

Query: 71  HRRSFVGFNAGNGT 84
           H+R F  F   NGT
Sbjct: 167 HKRGFTTFIVTNGT 180


>pdb|1FH5|H Chain H, Crystal Structure Of The Fab Fragment Of The Monoclonal
           Antibody Mak33
          Length = 198

 Score = 25.8 bits (55), Expect = 8.1,   Method: Compositional matrix adjust.
 Identities = 17/63 (26%), Positives = 29/63 (46%), Gaps = 2/63 (3%)

Query: 4   ESNESLESSGKKSRRPSFISGRSFASASRILNQHFPNLQLTKSKSGDTSKHTLSADSLDS 63
           E   ++   G  +  P  + GR   S     N  +  LQ++  KS DT+ +  + D++D 
Sbjct: 40  EWVATISDGGSYTYYPDSVKGRFTISRDNAKNNLY--LQMSSLKSEDTAMYYCARDAMDY 97

Query: 64  KGQ 66
            GQ
Sbjct: 98  WGQ 100


  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
   0.314    0.131    0.376 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,988,813
Number of Sequences: 62578
Number of extensions: 157369
Number of successful extensions: 264
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 259
Number of HSP's gapped (non-prelim): 11
length of query: 134
length of database: 14,973,337
effective HSP length: 88
effective length of query: 46
effective length of database: 9,466,473
effective search space: 435457758
effective search space used: 435457758
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 46 (22.3 bits)