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= 048106
         (694 letters)

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

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



>pdb|3QE7|A Chain A, Crystal Structure Of Uracil Transporter--Uraa
          Length = 429

 Score = 34.7 bits (78), Expect = 0.17,   Method: Compositional matrix adjust.
 Identities = 85/407 (20%), Positives = 154/407 (37%), Gaps = 68/407 (16%)

Query: 194 FQHYLSMLGSLILIPLVIVPAMGGSHEDTSNVVSTVLFVSGVTTLLHTFF-GSRLPLIQG 252
            QH  +M G+ +L+P++        H +     +TVL  +G+ TLL+ F    ++P   G
Sbjct: 22  LQHLFAMFGATVLVPVLF-------HINP----ATVLLFNGIGTLLYLFICKGKIPAYLG 70

Query: 253 SSFNFKHIM---------KELQGAIIIGSVF--QAFLGYSGLMSLLLRLINPVVVAPTIA 301
           SSF F   +           L G I+ G +F   +F+        L  L  P  +   +A
Sbjct: 71  SSFAFISPVLLLLPLGYEVALGGFIMCGVLFCLVSFIVKKAGTGWLDVLFPPAAMGAIVA 130

Query: 302 AVGLSFYSYGFPLVGTCLEIGVVQILLVILFSLYLRKISVIGHRIF----LIYAVPLGLA 357
            +GL        + G     G       I+ S+    ++V+G  +F     I  + +G+ 
Sbjct: 131 VIGLELAGVAAGMAGLLPAEGQTPDSKTIIISITTLAVTVLGSVLFRGFLAIIPILIGVL 190

Query: 358 ITWAAAFLLTETGAYNYKECDVNVPVSNIISEHCRKHVSRMKQCRVDSSHALKSSPWFRF 417
           + +A +F +              V  + II+ H                       WF  
Sbjct: 191 VGYALSFAMGI------------VDTTPIINAH-----------------------WFAL 215

Query: 418 PYPLQWGTPVFHWKXXXXXXXXXXXXXXDSVGSYHASSLLVASRPPTPGVVSRAIGLEGL 477
           P      TP F W               + VG    ++ +V         + R++   GL
Sbjct: 216 P---TLYTPRFEWFAILTILPAALVVIAEHVGHLVVTANIVKKDLLRDPGLHRSMFANGL 272

Query: 478 CSVXXXXXXXXXXXXXXXENVHTIAVTKMGSRRAVEIGAGILIVLSLIGKVGGFIASIPQ 537
            +V               EN+  +A+T++ S   +   A   I+LS +GK+   I  IP 
Sbjct: 273 STV-ISGFFGSTPNTTYGENIGVMAITRVYSTWVIGGAAIFAILLSCVGKLAAAIQMIPL 331

Query: 538 VMVAGLLCFMWAMLAALGLSNLRYSEA--GSSRNIIIVGLSLFFSLS 582
            ++ G+   ++ ++ A G+  L  S+     ++N+I+  + L   +S
Sbjct: 332 PVMGGVSLLLYGVIGASGIRVLIESKVDYNKAQNLILTSVILIIGVS 378


>pdb|3C30|A Chain A, Crystal Structure Of The Vibrio Cholerae Luxq Periplasmic
           Domain (Semet)
          Length = 270

 Score = 32.0 bits (71), Expect = 1.0,   Method: Compositional matrix adjust.
 Identities = 19/65 (29%), Positives = 30/65 (46%), Gaps = 7/65 (10%)

Query: 561 YSEAGSSRNIIIVGLSLFFSLSIPAYFQQYGISPNTNL-------SVPSYFQPYSVASHG 613
           +S   + R+  IVG +     S+P Y   Y I  N N+       SVP+Y   YS+ ++ 
Sbjct: 206 HSAKDAXRDSFIVGQTFLEVESVPTYLCVYSIQTNQNVLTLRDNESVPTYLCVYSIQTNQ 265

Query: 614 PFRSK 618
             R +
Sbjct: 266 NVRHQ 270


>pdb|3C38|A Chain A, Crystal Structure Of The Periplasmic Domain Of Vibrio
           Cholerae Luxq
          Length = 270

 Score = 32.0 bits (71), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 19/65 (29%), Positives = 30/65 (46%), Gaps = 7/65 (10%)

Query: 561 YSEAGSSRNIIIVGLSLFFSLSIPAYFQQYGISPNTNL-------SVPSYFQPYSVASHG 613
           +S   + R+  IVG +     S+P Y   Y I  N N+       SVP+Y   YS+ ++ 
Sbjct: 206 HSAKDAMRDSFIVGQTFLEVESVPTYLCVYSIQTNQNVLTLRDNESVPTYLCVYSIQTNQ 265

Query: 614 PFRSK 618
             R +
Sbjct: 266 NVRHQ 270


  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    0.137    0.416 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,817,317
Number of Sequences: 62578
Number of extensions: 593059
Number of successful extensions: 813
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 809
Number of HSP's gapped (non-prelim): 5
length of query: 694
length of database: 14,973,337
effective HSP length: 106
effective length of query: 588
effective length of database: 8,340,069
effective search space: 4903960572
effective search space used: 4903960572
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: 55 (25.8 bits)