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= 0001.3514.p
         (626 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300309978|ref|YP_003774070.1| membrane transport protein [Her...    95   2e-20

>gi|300309978|ref|YP_003774070.1| membrane transport protein
           [Herbaspirillum seropedicae SmR1]
          Length = 683

 Score = 94.7 bits (234), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 60/177 (33%), Positives = 99/177 (55%), Gaps = 9/177 (5%)

Query: 59  RNKTATDFYTAGGGIGPIRNGLAIAGDYLSAAAFLGVSGLIALYGYDGIAYLIGFFVAFI 118
           R     ++Y AG  + P+ NG+A A D++SAA F+ ++G + L G+DG+AY++G+   + 
Sbjct: 62  RTSDVPEYYVAGRRVPPLFNGMATAADWISAATFISLAGGLYLQGFDGLAYILGWTGGYC 121

Query: 119 PVLLLVAEPCRNLGKYTLGDVLAFRNSFRS-------TKIAAAVSSIIVAVFYMVPQIVG 171
            V LL+A   R  G+YT+ D LA R   R         +I A  ++I+++  Y+V QI G
Sbjct: 122 LVALLIAPYLRKFGQYTIADFLAARYPGRPGSQGVNVIRILAVAATILISFTYVVAQIYG 181

Query: 172 GAVIIRALIGIPYEVSVLAVGLLMLTYVVF-GGMRATTSVQVIKAVLLISSCFILVI 227
             +I     GI + + +  +GL  +    F GGMRA T  QV + ++++ +  I VI
Sbjct: 182 VGLITSRFTGIDFSIGIF-LGLASILVCSFLGGMRAITWTQVAQYIIILLAYLIPVI 237



 Score = 76.3 bits (186), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 73/256 (28%), Positives = 127/256 (49%), Gaps = 51/256 (19%)

Query: 288 VSLGLALVLGTAAMPHILMRFFTVPDAKSARSSVLWAMLAIGVCHLLIV----------- 336
           ++L   L+LGTAA+PHILMR++T P    AR+SV W +  I + +L +            
Sbjct: 381 LALVFCLMLGTAALPHILMRYYTTPTVAGARTSVFWTLFFIMLIYLTVPALTVLVKYDIY 440

Query: 337 --VIGFAAAH-----YVGAK--------AITLLDKGG--------------NLAAPMLAQ 367
             ++G + +H     Y  A         +IT L++ G               LA P +A 
Sbjct: 441 TSLVGSSYSHLPDWVYYWANMDKLNPLVSITDLNRDGLVQLGEISMDGDIIVLAMPEIAG 500

Query: 368 FLGGGTDSLLGNFMLAFVAAVSFATIVAVVAGLTLAAASALAHDVYVGAIKNGKATEQEQ 427
                    L  F+   VAA   A  ++   GL L  ++AL+HDVY   + +  A+ Q++
Sbjct: 501 ---------LPYFVSGLVAAGGLAAALSTADGLLLTISNALSHDVYYKVV-DPSASTQKR 550

Query: 428 VRAARVATLMMSVICVACGILAKGQNVAHLVGLGYAVAASANLPALMLTLYWKRCSTAGV 487
           V  +++  L+++++      L  G ++  +VG  +++AAS   PAL+L ++WKR + AG 
Sbjct: 551 VTISKLLLLVVALLAAYAASLKPG-DILSMVGAAFSLAASTLFPALVLGVFWKRANQAGA 609

Query: 488 LAGVIGGTFLAIALVL 503
           +AG++ G  + +  +L
Sbjct: 610 IAGILCGFLMCVYYML 625


  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
   0.326    0.138    0.396 

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: 1,715,003
Number of extensions: 68764
Number of successful extensions: 377
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 375
Number of HSP's successfully gapped: 2
Length of query: 626
Length of database: 1,619,870
Length adjustment: 91
Effective length of query: 535
Effective length of database: 1,188,985
Effective search space: 636106975
Effective search space used: 636106975
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 133 (55.8 bits)