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= psy9205
         (220 letters)

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

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



>pdb|3GI8|C Chain C, Crystal Structure Of Apct K158a Transporter Bound To 7f11
           Monoclonal Fab Fragment
          Length = 444

 Score = 32.3 bits (72), Expect = 0.20,   Method: Compositional matrix adjust.
 Identities = 25/94 (26%), Positives = 47/94 (50%), Gaps = 2/94 (2%)

Query: 12  NLPRAIWIAMPIVTLVYVCANVAYFTVLTKEEMLTSPAVAVTFGGKIY-KELVW-IIPIL 69
           N+PRAI+I++ IV  VYV   ++    L  +E++ +   A+    K +   L + +I I 
Sbjct: 220 NVPRAIFISILIVMFVYVGVAISAIGNLPIDELIKASENALAVAAKPFLGNLGFLLISIG 279

Query: 70  VAMSTFGGVNGILFTSARLFLTGSQEGHLPPLFS 103
              S    +N  ++  A +  + +++G LP  F 
Sbjct: 280 ALFSISSAMNATIYGGANVAYSLAKDGELPEFFE 313


>pdb|3GI9|C Chain C, Crystal Structure Of Apct Transporter Bound To 7f11
           Monoclonal Fab Fragment
 pdb|3GIA|A Chain A, Crystal Structure Of Apct Transporter
          Length = 444

 Score = 32.3 bits (72), Expect = 0.20,   Method: Compositional matrix adjust.
 Identities = 25/94 (26%), Positives = 47/94 (50%), Gaps = 2/94 (2%)

Query: 12  NLPRAIWIAMPIVTLVYVCANVAYFTVLTKEEMLTSPAVAVTFGGKIY-KELVW-IIPIL 69
           N+PRAI+I++ IV  VYV   ++    L  +E++ +   A+    K +   L + +I I 
Sbjct: 220 NVPRAIFISILIVMFVYVGVAISAIGNLPIDELIKASENALAVAAKPFLGNLGFLLISIG 279

Query: 70  VAMSTFGGVNGILFTSARLFLTGSQEGHLPPLFS 103
              S    +N  ++  A +  + +++G LP  F 
Sbjct: 280 ALFSISSAMNATIYGGANVAYSLAKDGELPEFFE 313


>pdb|3V67|A Chain A, Periplasmic Domain Of Vibrio Parahaemolyticus Cpxa
 pdb|3V67|B Chain B, Periplasmic Domain Of Vibrio Parahaemolyticus Cpxa
          Length = 138

 Score = 30.4 bits (67), Expect = 0.80,   Method: Compositional matrix adjust.
 Identities = 16/59 (27%), Positives = 25/59 (42%), Gaps = 8/59 (13%)

Query: 170 ACCIFLVVVPTIREPMNTVISLFIIASGVPV--------YYVCVKWKSKPALLLEMHEH 220
           A   F+  +    +P   +   ++IA  VP+         YV  KW   P LLL + +H
Sbjct: 80  AMQNFVTSIEDYNKPKQRLYGRYMIAGPVPIVLADSELLMYVGFKWNEPPPLLLRLFDH 138


>pdb|3RKO|L Chain L, Crystal Structure Of The Membrane Domain Of Respiratory
           Complex I From E. Coli At 3.0 Angstrom Resolution
 pdb|3RKO|B Chain B, Crystal Structure Of The Membrane Domain Of Respiratory
           Complex I From E. Coli At 3.0 Angstrom Resolution
          Length = 613

 Score = 27.3 bits (59), Expect = 7.0,   Method: Compositional matrix adjust.
 Identities = 25/85 (29%), Positives = 41/85 (48%), Gaps = 8/85 (9%)

Query: 69  LVAMSTFGGVNGILFTSARLFLTGSQEGHLPPLFSYIHIKICLMSVLMLVTSDVFALINY 128
           L  +S   GV  ++   A  ++ G +EG+    F+Y ++ I  M VL+L  +    L+ Y
Sbjct: 86  LTMLSVVTGVGFLIHMYASWYMRG-EEGY-SRFFAYTNLFIASMVVLVLADN---LLLMY 140

Query: 129 MSVALWLSVGACTAGLISLRFTQPD 153
           +    W  VG C+  LI   +T P 
Sbjct: 141 LG---WEGVGLCSYLLIGFYYTDPK 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
   0.330    0.142    0.442 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,075,148
Number of Sequences: 62578
Number of extensions: 214921
Number of successful extensions: 439
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 437
Number of HSP's gapped (non-prelim): 4
length of query: 220
length of database: 14,973,337
effective HSP length: 95
effective length of query: 125
effective length of database: 9,028,427
effective search space: 1128553375
effective search space used: 1128553375
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 49 (23.5 bits)