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= 0001.1015.p
         (621 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300309387|ref|YP_003773479.1| membrane protein [Herbaspirillu...    97   3e-21

>gi|300309387|ref|YP_003773479.1| membrane protein [Herbaspirillum
           seropedicae SmR1]
          Length = 711

 Score = 97.1 bits (240), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 176/607 (28%), Positives = 272/607 (44%), Gaps = 69/607 (11%)

Query: 13  LASDARRIARRLEL--RSFPLLQEQFSAAEGLRAGVAIALPLAAAMLSGQRWL-----AW 65
           L S  RR   R+E     FPL     S  EGLRA  +     AAAML    WL     +W
Sbjct: 20  LLSHCRRCRTRVERWRAQFPLRHANLS--EGLRAACS-----AAAMLLLGEWLGNPLFSW 72

Query: 66  AVFSAFWTCLCDAPGPHRQRRQLLAGFALAGTVVAFVGSWTSSWTPHAALLTAPLMVWAT 125
           A   AF TCL D+ G +R R   + GFALA T+   V +  +S +     LT  +M  A 
Sbjct: 73  AAIGAFLTCLADSAGSNRARLASMGGFALASTLGGMVAASAASLSVELGWLT--IMACAG 130

Query: 126 VTLTGLIPYAALLGTLLAVVAVVAAGFPHGPA----LAALQAASFLAGAAWAWILINLAW 181
           V     I Y A  G +L + A V+A     P     L+      +  G  WA +L    W
Sbjct: 131 VAGFSRI-YGAAAGLVLMLAAGVSAIMADAPVILWPLSQSHVLIYFGGCLWALLLGLTVW 189

Query: 182 RIDESAALRQAASAALLRMVDMGS------------ALLAAPEGQHREQNWHPEHGEHRR 229
           RI      RQA + A   + ++ S            A+ AA    H  ++   +    RR
Sbjct: 190 RIHPFGPARQAVARAYGTLAELASIAAANGLDDPAYAMHAADLAAHARRHARFDIAAARR 249

Query: 230 AVR-LALERLRAMLQRHADGSGSGAAPSARLLESCEMIFSALIALEHAAIQQLATPRQRR 288
           A++ +A+ER  +  +R  D      A +  LL+   +    L+ L+    Q+   PR R+
Sbjct: 250 ALQAVAVERTES--RRLYDNLLVRLARADDLLDGVTL----LVDLQLTHYQE---PRARQ 300

Query: 289 RAAR-LACVVLLRAHRRLAHAKGDATGADHRHRLPLRPPAPLCDPVMDGCQWSLLQADTL 347
           R  R LA +       + A ++G+A  AD   R+  R    L   +  G    L Q  T 
Sbjct: 301 RTTRVLAGIARQLQAMQAAMSQGEAIAADEDARIMARL-RQLVARLPSGTGRLLQQVHTP 359

Query: 348 LLSDPDWAIREAAIASAETADNVPPQAWSVRLLKSLQQGGRQAAGVAAVFYAA------- 400
           L    D       +A +       P     R+    ++    AA  +A ++ A       
Sbjct: 360 LAVGSDDPAGLKLMARSAAPAPALPAILLHRVRAWWRKAASHAATGSAEWHHAWRCAAAA 419

Query: 401 -------EAFHLGYPYWATMAVVVVLQGAARQTWTRCVERILGSLLGGALALTLLQLTQG 453
                      L + YWATMA ++V+Q +  ++W+R +ER +GS++GG LA+ L  +   
Sbjct: 420 GATYLIVHLLELPFGYWATMATMLVMQPSIAESWSRSMERAVGSVVGGVLAVVLCLVVH- 478

Query: 454 LEPV-LPMIAVLLAGLAIALRLVNYTVFVVFLTMLFICVTEM-LQPGVGIASA--RALDN 509
             P+ L ++   L  L +AL+ V+Y ++  FLT +F+ V ++   P   +A+A  RA +N
Sbjct: 479 -SPLALALLVFPLTVLTMALKPVSYGLYATFLTPVFVLVADVGGDPAHELANAALRAGNN 537

Query: 510 LIGSAAALLAALALWPDLG-ASPRQRIADGLKANRAYL-EAVVTHQAP--AALRRLQRQA 565
           +IG+  A+LA+   WP      P+ ++    + N AYL EA+ T  AP  A L   +R A
Sbjct: 538 VIGAVVAVLASYLFWPRRHPEDPQAQLQRMAQLNLAYLIEALATPAAPPMATLHAHRRAA 597

Query: 566 GLASIDA 572
            +A+++A
Sbjct: 598 CVANVEA 604


  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
   0.324    0.133    0.408 

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: 1,237,713
Number of extensions: 33155
Number of successful extensions: 246
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 243
Number of HSP's successfully gapped: 1
Length of query: 621
Length of database: 1,619,870
Length adjustment: 91
Effective length of query: 530
Effective length of database: 1,188,985
Effective search space: 630162050
Effective search space used: 630162050
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)