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= 041774
         (382 letters)

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

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



>pdb|1JM1|A Chain A, Crystal Structure Of The Soluble Domain Of The Rieske
           Protein Ii (Soxf) From Sulfolobus Acidocaldarius
          Length = 204

 Score = 29.3 bits (64), Expect = 4.1,   Method: Compositional matrix adjust.
 Identities = 13/37 (35%), Positives = 19/37 (51%)

Query: 97  HSKIKASKDGWVLFSKANINPSPFLFISYNSSPSSLF 133
           H  I A KDG V+ S     P P + + Y+SS   ++
Sbjct: 127 HGSIYALKDGGVVVSGPAPRPLPIVILDYDSSTGDIY 163


>pdb|2WSX|A Chain A, Crystal Structure Of Carnitine Transporter From
           Escherichia Coli
 pdb|2WSX|B Chain B, Crystal Structure Of Carnitine Transporter From
           Escherichia Coli
 pdb|2WSX|C Chain C, Crystal Structure Of Carnitine Transporter From
           Escherichia Coli
          Length = 504

 Score = 28.1 bits (61), Expect = 8.9,   Method: Compositional matrix adjust.
 Identities = 21/78 (26%), Positives = 36/78 (46%), Gaps = 4/78 (5%)

Query: 62  EINLQPWLF----SCHSISHLFDTTHKLKYTIKTDPRVLHSKIKASKDGWVLFSKANINP 117
           E +   W+F    SC S + LF  + ++ Y I T P  L      +K+  + +S  +  P
Sbjct: 85  EFSTASWIFMMFASCTSAAVLFWGSIEIYYYISTPPFGLEPNSTGAKELGLAYSLFHWGP 144

Query: 118 SPFLFISYNSSPSSLFFY 135
            P+   S+ S   + FF+
Sbjct: 145 LPWATYSFLSVAFAYFFF 162


>pdb|3HFX|A Chain A, Crystal Structure Of Carnitine Transporter
          Length = 504

 Score = 28.1 bits (61), Expect = 8.9,   Method: Compositional matrix adjust.
 Identities = 21/78 (26%), Positives = 36/78 (46%), Gaps = 4/78 (5%)

Query: 62  EINLQPWLF----SCHSISHLFDTTHKLKYTIKTDPRVLHSKIKASKDGWVLFSKANINP 117
           E +   W+F    SC S + LF  + ++ Y I T P  L      +K+  + +S  +  P
Sbjct: 85  EFSTASWIFMMFASCTSAAVLFWGSIEIYYYISTPPFGLEPNSTGAKELGLAYSLFHWGP 144

Query: 118 SPFLFISYNSSPSSLFFY 135
            P+   S+ S   + FF+
Sbjct: 145 LPWATYSFLSVAFAYFFF 162


  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    0.136    0.438 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,247,639
Number of Sequences: 62578
Number of extensions: 499511
Number of successful extensions: 929
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 928
Number of HSP's gapped (non-prelim): 3
length of query: 382
length of database: 14,973,337
effective HSP length: 101
effective length of query: 281
effective length of database: 8,652,959
effective search space: 2431481479
effective search space used: 2431481479
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 52 (24.6 bits)