BLASTP 2.2.18 [Mar-02-2008]


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= 0001.3279.p
         (463 letters)

Database: BlastDatabases/689/689 
           4735 sequences; 1,619,870 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300312611|ref|YP_003776703.1| TRAP-type uncharacterized trans...   855   0.0  

>gi|300312611|ref|YP_003776703.1| TRAP-type uncharacterized
           transport system periplasmic protein [Herbaspirillum
           seropedicae SmR1]
          Length = 463

 Score =  855 bits (2209), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 426/463 (92%), Positives = 446/463 (96%)

Query: 1   MLKDKKLSAYAPSATRIRARFVAISWRDLAVSFGPIILLILVGAWLVIWLIRPAPPSSIT 60
           MLKDKKLSAYAPSATRIRARFVAISWRDLAVSFGPIILLILVGAWLVIWLIRPAPPSSIT
Sbjct: 1   MLKDKKLSAYAPSATRIRARFVAISWRDLAVSFGPIILLILVGAWLVIWLIRPAPPSSIT 60

Query: 61  IAAGPKDSNFWRVAERYKTLLARDGIRLDIVETGGSLDNLKRLADPDQDIDVGFVQGGLA 120
           IAAGPKDSNFWRVAERYKT+LARDGI+LDIVETGGSLDNLKRL D DQDIDVGFVQGGLA
Sbjct: 61  IAAGPKDSNFWRVAERYKTILARDGIKLDIVETGGSLDNLKRLVDSDQDIDVGFVQGGLA 120

Query: 121 SAVPAEALESLVSLGSISYVPVSVYYRAPPPREDGRPVPPLRQLSELAGKRIAIGGQGSG 180
            AVPA+A+ SLVSLGSISYVPVSVYYR+     +G+P+PPLRQLSELAGKRIAIGGQGSG
Sbjct: 121 GAVPADAMGSLVSLGSISYVPVSVYYRSASINAEGKPIPPLRQLSELAGKRIAIGGQGSG 180

Query: 181 SSVLAATLLKANGVENGGATQLLNIGGDEAAHALTSGKIDAAFLMGDSVSVATMGKLLRA 240
           SSVLAATLLKANGVE GGATQLLNIGGDEAA ALTSGKIDAAFLMGDSVSVATMGKLLRA
Sbjct: 181 SSVLAATLLKANGVEAGGATQLLNIGGDEAAQALTSGKIDAAFLMGDSVSVATMGKLLRA 240

Query: 241 PGIRLLDFSQADAYVRRFRYLNTLKMPMGVFDLAHNLPARDTLLIAPTAELVARDDLHPA 300
           PG+RLLDFSQA+AYVRRFRYLNTLKMPMGVFDLA NLPARDT LIAPTAELVAR+DLHPA
Sbjct: 241 PGVRLLDFSQAEAYVRRFRYLNTLKMPMGVFDLARNLPARDTQLIAPTAELVAREDLHPA 300

Query: 301 LSDLLIAAAREVHGKANVLQKAGEFPAPLEHEYPISDDAARYYKSGKTFFYRTLPFWMAS 360
           LSDLLI AA EVHGKANV+QKAGEFPAPLEHEY ISDDAARYYKSGKTFFYRTLPFW+AS
Sbjct: 301 LSDLLIEAAHEVHGKANVMQKAGEFPAPLEHEYRISDDAARYYKSGKTFFYRTLPFWLAS 360

Query: 361 LLDRAVVIVLPVILLLIPGIRLVPMLYGWRVRSRIYRWYGELIALERGLTRDSPEQQAEM 420
           LLDRAVVIVLPVILLLIPGIRLVPMLYGWRVRSRIYRWYGELIALERG++RDSP++QA++
Sbjct: 361 LLDRAVVIVLPVILLLIPGIRLVPMLYGWRVRSRIYRWYGELIALERGISRDSPQEQADI 420

Query: 421 LKRLDEIEIAVNRMKMPLAFADQFYVLREHIGFVRARLAGGVA 463
           LKRLDEIE+AVNRMKMPLAFADQFYVLREHIGFVRARLA GVA
Sbjct: 421 LKRLDEIEMAVNRMKMPLAFADQFYVLREHIGFVRARLAAGVA 463


  Database: BlastDatabases/689/689
    Posted date:  Apr 10, 2011 12:15 AM
  Number of letters in database: 1,619,870
  Number of sequences in database:  4735
  
Lambda     K      H
   0.322    0.139    0.411 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 4735
Number of Hits to DB: 1,424,679
Number of extensions: 59678
Number of successful extensions: 252
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 252
Number of HSP's successfully gapped: 1
Length of query: 463
Length of database: 1,619,870
Length adjustment: 89
Effective length of query: 374
Effective length of database: 1,198,455
Effective search space: 448222170
Effective search space used: 448222170
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 132 (55.5 bits)