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= 011513
         (484 letters)

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

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



>pdb|2XUT|A Chain A, Crystal Structure Of A Proton Dependent Oligopeptide (Pot)
           Family Transporter.
 pdb|2XUT|B Chain B, Crystal Structure Of A Proton Dependent Oligopeptide (Pot)
           Family Transporter.
 pdb|2XUT|C Chain C, Crystal Structure Of A Proton Dependent Oligopeptide (Pot)
           Family Transporter
          Length = 524

 Score = 72.8 bits (177), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 85/356 (23%), Positives = 155/356 (43%), Gaps = 32/356 (8%)

Query: 37  LFTGLGLMVIGAGGIRPCNLAFGADQFNPNTESGKQGITSFFNWYYFTFTFAMMISLTVI 96
            +TGL L+ +G+GGI+P   +F  DQF+ + +S  Q     F+ +YFT  F    +   +
Sbjct: 112 FYTGLFLIALGSGGIKPLVSSFMGDQFDQSNKSLAQ---KAFDMFYFTINFGSFFASLSM 168

Query: 97  VYVQSDVSWAWGLGIPAFMMFLSCAMFFLGSRLYAKVKPE-GSPLASTVQVFVAAIKKRH 155
             +  +   A   GIP  +MF++   F+LG + Y  + PE   P      +  A + K  
Sbjct: 169 PLLLKNFGAAVAFGIPGVLMFVATVFFWLGRKRYIHMPPEPKDPHGFLPVIRSALLTKVE 228

Query: 156 LKLPEEPWLTLHNHIPKNCINSKLPHTGQFRCLDKAAIMTPEDQIKSDGSAINPWRLSSM 215
            K      L L   +        +P  G    L  A ++         G+++   R    
Sbjct: 229 GKGNIGLVLALIGGVSAAYALVNIPTLGIVAGLCCAMVLV--MGFVGAGASLQLERARKS 286

Query: 216 Q---KVEEVKVLIRVIPIWASAIVYYVALVQQQTYVVFQALQSDRRVGNTHFKIPAASYA 272
                V+ V+ ++R++ ++A    ++    Q+ +  +   LQ++  V    F+ PA   A
Sbjct: 287 HPDAAVDGVRSVLRILVLFALVTPFWSLFDQKASTWI---LQANDMVKPQWFE-PAMMQA 342

Query: 273 IFSMLGLTIWIPIYDRIIVPRLQRLTKKEGGITILQRMAIGMILAIFTMIISGIIEDKRR 332
           +  +L + + IP  + ++ P ++R+  K   +T L++M  G+ +   + I+ G I+    
Sbjct: 343 LNPLL-VMLLIPFNNFVLYPAIERMGVK---LTALRKMGAGIAITGLSWIVVGTIQ---- 394

Query: 333 SLALSRPVGLEQRRGAISSLSGLWLIPQLSLIGFSEAFTIIAEVEFYYKQFPENMR 388
                    L    G  S+LS  W I   +L+ F E       +EF Y Q P+ M+
Sbjct: 395 ---------LMMDGG--SALSIFWQILPYALLTFGEVLVSATGLEFAYSQAPKAMK 439


>pdb|3QPT|A Chain A, Crystal Structure Of The Salmonella Transcriptional
           Regulator Slya
          Length = 147

 Score = 32.0 bits (71), Expect = 0.73,   Method: Composition-based stats.
 Identities = 30/109 (27%), Positives = 49/109 (44%), Gaps = 14/109 (12%)

Query: 131 AKVKPEGSPLASTVQVFVAAIKKR--HLKLPEEPWLTLHNHIPKNCINSKLPHTGQFRCL 188
           A   P GS LA  V+++ A I  R   L+L +  W+TLHN      I+   P   Q +  
Sbjct: 3   AXESPLGSDLARLVRIWRALIDHRLKPLELTQTHWVTLHN------IHQLPPDQSQIQLA 56

Query: 189 DKAAIMTPE-----DQIKSDGSAINPWRLSSMQKVEEVKVLIRVIPIWA 232
               I  P      DQ++  G  I+    +S ++ + +K+  +  P+ A
Sbjct: 57  KAIGIEQPSLVRTLDQLEDKG-LISRQTCASDRRAKRIKLTEKAEPLIA 104


>pdb|3Q5F|A Chain A, Crystal Structure Of The Salmonella Transcriptional
           Regulator Slya In Complex With Dna
 pdb|3Q5F|B Chain B, Crystal Structure Of The Salmonella Transcriptional
           Regulator Slya In Complex With Dna
          Length = 147

 Score = 31.6 bits (70), Expect = 0.92,   Method: Composition-based stats.
 Identities = 29/105 (27%), Positives = 48/105 (45%), Gaps = 14/105 (13%)

Query: 135 PEGSPLASTVQVFVAAIKKR--HLKLPEEPWLTLHNHIPKNCINSKLPHTGQFRCLDKAA 192
           P GS LA  V+++ A I  R   L+L +  W+TLHN      I+   P   Q +      
Sbjct: 7   PLGSDLARLVRIWRALIDHRLKPLELTQTHWVTLHN------IHQLPPDQSQIQLAKAIG 60

Query: 193 IMTPE-----DQIKSDGSAINPWRLSSMQKVEEVKVLIRVIPIWA 232
           I  P      DQ++  G  I+    +S ++ + +K+  +  P+ A
Sbjct: 61  IEQPSLVRTLDQLEDKG-LISRQTCASDRRAKRIKLTEKAEPLIA 104


>pdb|3CTD|A Chain A, Crystal Structure Of A Putative Aaa Family Atpase From
           Prochlorococcus Marinus Subsp. Pastoris
 pdb|3CTD|B Chain B, Crystal Structure Of A Putative Aaa Family Atpase From
           Prochlorococcus Marinus Subsp. Pastoris
          Length = 213

 Score = 28.5 bits (62), Expect = 9.2,   Method: Compositional matrix adjust.
 Identities = 33/110 (30%), Positives = 46/110 (41%), Gaps = 18/110 (16%)

Query: 94  TVIVYVQSDVSWAWGLGIPAFMMFLSCAMFFLGSRLYAKVKPEGSPLASTVQVFVA--AI 151
             IV VQS       +G P  + FLS A       LY  + P+ +   ST  +F A  AI
Sbjct: 89  NAIVVVQSCCDAFDRVGFPEGLFFLSQA------SLYLAISPKSN---STKSIFKAMEAI 139

Query: 152 KKRHLKLPEEPWLTLHNHIPKNCINSKLPHTGQFRCLDKAAIMTPEDQIK 201
           K  ++ L       + NH+  N  N   PH  Q + L +  + T    IK
Sbjct: 140 KATNVSL-------VPNHLKNNASNYLNPHNYQGKWLQQEYLPTDLQGIK 182


  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
   0.324    0.139    0.432 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,110,884
Number of Sequences: 62578
Number of extensions: 563991
Number of successful extensions: 1160
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1157
Number of HSP's gapped (non-prelim): 6
length of query: 484
length of database: 14,973,337
effective HSP length: 103
effective length of query: 381
effective length of database: 8,527,803
effective search space: 3249092943
effective search space used: 3249092943
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: 53 (25.0 bits)