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= 0002.0003.p
         (429 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300309727|ref|YP_003773819.1| transmembrane protein [Herbaspi...   475   e-135

>gi|300309727|ref|YP_003773819.1| transmembrane protein
           [Herbaspirillum seropedicae SmR1]
          Length = 429

 Score =  475 bits (1222), Expect = e-135,   Method: Compositional matrix adjust.
 Identities = 274/440 (62%), Positives = 321/440 (72%), Gaps = 22/440 (5%)

Query: 1   MALATQCPHCLTIFRVASDQLKLRGGLVRCGNCRQVFNGNEYLVEASVADGHYQPAPGSK 60
           MALATQCPHCLTIFRV SDQLKLRGGLVRCG+CRQVFNGN+YLVEASVADGHYQPAPGSK
Sbjct: 1   MALATQCPHCLTIFRVVSDQLKLRGGLVRCGSCRQVFNGNDYLVEASVADGHYQPAPGSK 60

Query: 61  AQAGMATPVFAPAASSSSVPTPPANSPYERTGAPLTAQQPPFVPPAQTPVPEVNVPA-PQ 119
           AQAG+ TP  A A ++ +    P  +    T  P  A QP        PV  + V +   
Sbjct: 61  AQAGVMTPSAAAAPATPTPAPSPVPASPMATRGP--APQP------SAPVHAIPVSSGTA 112

Query: 120 PMSAAAPVQAAASAPLPAAIPVIAEPKVFRSPTSPGYLPDLGASFKPAVPVDKTSPEDEA 179
           P+SA  P      AP+PAAIPVIAEPKVFRSPTSPGY+PDLGA  K    VDK   ++  
Sbjct: 113 PVSAEPPPPVQVPAPVPAAIPVIAEPKVFRSPTSPGYIPDLGAPLKSPAAVDKDKRDEAD 172

Query: 180 SSPTLPEED----GPDSGA-LLRRSSAESDEIAAPPEVAAVF-----RIDDEPVLHDVAD 229
           + P  P  D     P  GA LLRRSS+  DEI +  ++ A F     R+D+E V H    
Sbjct: 173 ALPPFPVADEIPTAPAGGAALLRRSSSTDDEIVSAADIDAAFGPATSRLDEEDVHH--LR 230

Query: 230 AKDGVPGDGEKSDAQEAEAEDDEAADEPGFVKRAERRARISQAMKMVMMVLAGVMVPVLL 289
             +  P     +D   A+  +D+A + PGFV+R ERR R  + +K++MM+LAGVMVPVLL
Sbjct: 231 GHEDEPDQLSAADHSAADDSEDDA-ELPGFVRRVERRERAGRVLKVIMMILAGVMVPVLL 289

Query: 290 LQSLYYWRNPLAASVPQLRPMLNGMCVAFHCTVGLPTEIERLSLESNELQVVPPNQNVYA 349
           LQ+LYYWRNPLA ++P +RPMLNGMCVA HC+VGLP EI+RLSLE+NELQVVPPNQNVYA
Sbjct: 290 LQALYYWRNPLAEALPPVRPMLNGMCVALHCSVGLPAEIDRLSLEANELQVVPPNQNVYA 349

Query: 350 LSLVMRNRGTSAQAWPHIELTLNNDDEKAVVRRVFRPRDYLADPAQVDRGIGPESEQQIK 409
           L++VMRNRG  AQAWPH+ELTLNNDDEKAVVRRVFRPRDYL +  Q+DRGI  +SEQQIK
Sbjct: 350 LTVVMRNRGPGAQAWPHLELTLNNDDEKAVVRRVFRPRDYLPNARQIDRGIAADSEQQIK 409

Query: 410 LNFELKDALVSGYRIYLFYP 429
           LNFELKDALVSGYR+YLFYP
Sbjct: 410 LNFELKDALVSGYRVYLFYP 429


  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
   0.315    0.132    0.388 

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: 1,109,322
Number of extensions: 41808
Number of successful extensions: 115
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 113
Number of HSP's successfully gapped: 1
Length of query: 429
Length of database: 1,619,870
Length adjustment: 88
Effective length of query: 341
Effective length of database: 1,203,190
Effective search space: 410287790
Effective search space used: 410287790
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 132 (55.5 bits)