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= 0001.0639.p
         (243 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300310012|ref|YP_003774104.1| outer membrane W protein [Herba...   304   4e-84
gi|300312492|ref|YP_003776584.1| outer membrane W protein [Herba...    74   1e-14

>gi|300310012|ref|YP_003774104.1| outer membrane W protein
           [Herbaspirillum seropedicae SmR1]
          Length = 245

 Score =  304 bits (779), Expect = 4e-84,   Method: Compositional matrix adjust.
 Identities = 162/253 (64%), Positives = 184/253 (72%), Gaps = 18/253 (7%)

Query: 1   MQKQFSFLPKLAALSVMAAFAAPAMAQSAGSNVVNVGWFHLAPQDSSDPLQTPAGP---- 56
           MQKQFSFLPK+AALSVMAAFAAP MAQ+AGSN+VNVGWFHL PQDSS  L    GP    
Sbjct: 1   MQKQFSFLPKIAALSVMAAFAAPVMAQTAGSNIVNVGWFHLQPQDSSSGLTKLNGPQAGF 60

Query: 57  LPGSGASVGTADTLGLAFTHFFTDNFALTTDLGIPPTFHLNGTGSLSGVGEIGKAKQWSP 116
            P S ++V  ADTLG+AFTHFFTDNFA+T DLGIPP F L GTG L  +GE+GKAKQWSP
Sbjct: 61  FPNSTSTVSNADTLGIAFTHFFTDNFAVTADLGIPPEFKLKGTGDLQALGELGKAKQWSP 120

Query: 117 AVVAKWFFGDANSQFRPFVGAGVSYVWYDSIQLSNTFQQAISMRYTGNRSAASPSTAALS 176
           A+VAKW+FG A   FRPFVGAGV+YVWY  + LS  FQ   S+   G       +TA LS
Sbjct: 121 AIVAKWYFGGAQDAFRPFVGAGVTYVWYSDVSLSQAFQNRASLNSGGT------ATANLS 174

Query: 177 SSWAPVVSLGANYNFDKNWSLGFSVSYIPLKTDADITTTLPTGT------QVHSTTSLKI 230
           SSWAPV++ GA Y F+  WS  FSVSYIPLKTDADIT   P G       Q + TT + +
Sbjct: 175 SSWAPVLTGGATYAFNDRWSASFSVSYIPLKTDADITAN-PAGAFAGLGPQRYKTT-ITL 232

Query: 231 NPIVTFLSVGYKF 243
           +PIVTFLSVGYKF
Sbjct: 233 DPIVTFLSVGYKF 245


>gi|300312492|ref|YP_003776584.1| outer membrane W protein
           [Herbaspirillum seropedicae SmR1]
          Length = 207

 Score = 73.9 bits (180), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 61/226 (26%), Positives = 103/226 (45%), Gaps = 44/226 (19%)

Query: 23  PAMAQSAGSN-VVNVGWFHLAPQDSSDPLQTPAGPLPGSGAS----VGTADTLGLAFTHF 77
           P  AQ A S  +V V   HL+P++ SDP+        G GAS    + +     +  ++F
Sbjct: 21  PVFAQEAQSPWLVRVRAVHLSPENKSDPIN-------GQGASDLITINSKTIPEVDISYF 73

Query: 78  FTDNFALTTDLGIPPTFHLNGTGSLSGVGEIGKAKQWSPAVVAKWFFGDANSQFRPFVGA 137
           FT N A    L  P    +   GS     +IG  K   P+++ ++ F   +S F P+VGA
Sbjct: 74  FTKNIAAELVLTYPQEQDVRLNGS-----KIGTFKHLPPSLLVQYHFM-PDSAFSPYVGA 127

Query: 138 GVSYVWYDSIQLSNTFQQAISMRYTGNRSAASPSTAALSSSWAPVVSLGANYNFDKNWSL 197
           G++Y    S+ +S   Q                     +SS+   + +GA+Y  +KNW +
Sbjct: 128 GINYTRISSVNISGGLQLD-------------------NSSFGGALQIGADYKINKNWLI 168

Query: 198 GFSVSYIPLKTDADITTTLPTGTQVHSTTSLKINPIVTFLSVGYKF 243
            F +  + + +D         G ++   +S+KI+P +  + VGY+F
Sbjct: 169 NFDIKKVQISSDVKTA----AGAKI---SSVKIDPWLIGVGVGYRF 207


  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
   0.317    0.130    0.397 

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: 719,263
Number of extensions: 30416
Number of successful extensions: 90
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 84
Number of HSP's successfully gapped: 2
Length of query: 243
Length of database: 1,619,870
Length adjustment: 83
Effective length of query: 160
Effective length of database: 1,226,865
Effective search space: 196298400
Effective search space used: 196298400
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: 41 (21.7 bits)
S2: 129 (54.3 bits)