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= psy17613
         (287 letters)

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

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



>pdb|1SR4|B Chain B, Crystal Structure Of The Haemophilus Ducreyi Cytolethal
           Distending Toxin
          Length = 261

 Score = 33.1 bits (74), Expect = 0.17,   Method: Compositional matrix adjust.
 Identities = 35/146 (23%), Positives = 59/146 (40%), Gaps = 31/146 (21%)

Query: 149 LGTCINPNILYFWYKWLDKAFTGKSAQIVVKKVLIDQFCM--------TPPLYAI----- 195
           LGT   PN++Y +Y  LD      +  IV ++   + F +        + P   I     
Sbjct: 73  LGTRSRPNMVYIYYSRLDVGANRVNLAIVSRRQADEAFIVHSDSSVLQSRPAVGIRIGTD 132

Query: 196 -FYTSMSLMEGKDDIFAELREKFLPTFQTSCIFWLPAQTINFFFLPPAARV---IFVGTC 251
            F+T  +L  G  D  + +R  F  TF +S               PP  RV   + VG  
Sbjct: 133 VFFTVHALATGGSDAVSLIRNIFT-TFNSSS-------------SPPERRVYSWMVVGDF 178

Query: 252 SFVWINILCWLKRSDLNAESSLAVAP 277
           +    N+   L++    +E+++ +AP
Sbjct: 179 NRAPANLEVALRQEPAVSENTIIIAP 204


>pdb|3TTG|A Chain A, Crystal Structure Of Putative Aminomethyltransferase From
           Leptospirillum Rubarum
          Length = 355

 Score = 31.2 bits (69), Expect = 0.74,   Method: Compositional matrix adjust.
 Identities = 25/97 (25%), Positives = 42/97 (43%), Gaps = 26/97 (26%)

Query: 193 YAIFYTSMS----LMEGKDDIFAELREKFLPTFQTSCIFWLPAQTINF-FFLPPAARVIF 247
           + +FY S+S     +EG+D      R+ FL    +  I     +++++ FFL P AR++F
Sbjct: 36  FGLFYPSVSRPSIFVEGED------RKNFLQGIASQDILKQDEKSLSYSFFLNPKARILF 89

Query: 248 VGTCSFVWINILCWLKRSDLNAESSLAVAPGVAVKEE 284
              C                N E  +A+ P    +EE
Sbjct: 90  DAWCG---------------NFEDKIALFPPAGTREE 111


  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
   0.325    0.136    0.425 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,379,999
Number of Sequences: 62578
Number of extensions: 276620
Number of successful extensions: 647
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 646
Number of HSP's gapped (non-prelim): 13
length of query: 287
length of database: 14,973,337
effective HSP length: 98
effective length of query: 189
effective length of database: 8,840,693
effective search space: 1670890977
effective search space used: 1670890977
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 51 (24.3 bits)