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= 0009.0161.p
         (331 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300309967|ref|YP_003774059.1| permease [Herbaspirillum serope...   458   e-130
gi|300312358|ref|YP_003776450.1| hypothetical protein Hsero_3054...    75   7e-15
gi|300309868|ref|YP_003773960.1| membrane transport protein [Her...    55   6e-09

>gi|300309967|ref|YP_003774059.1| permease [Herbaspirillum
           seropedicae SmR1]
          Length = 360

 Score =  458 bits (1179), Expect = e-130,   Method: Compositional matrix adjust.
 Identities = 244/328 (74%), Positives = 289/328 (88%)

Query: 1   MLTPFVTAAILAYALNPGVDWLARRRIGPFLLPRVLAVLIVVLLLLLAGLALVLVVVPVL 60
           ML+PFV A I+ YALNPGVDW+A RR+GP  +PR +AV I+VLLL+LAGLALVL+VVP++
Sbjct: 32  MLSPFVAAGIIGYALNPGVDWIASRRLGPVRVPRFVAVTIMVLLLILAGLALVLIVVPLV 91

Query: 61  VKEIPLLQQQIPNFLDKLNAKVAPRLSEFGIHVRLDITGIKRILTQQLATSGDEIWASVL 120
           +++IPLLQ Q+P  LDKLNA V+PRL + GI VRLD+ GIK +LTQQ++TS DE+W SVL
Sbjct: 92  LRQIPLLQAQVPPLLDKLNAFVSPRLHQLGIDVRLDLAGIKSLLTQQISTSSDEVWTSVL 151

Query: 121 ASAKIGGTALLTWAANLLFIPMVLFYLLQDWHPFIKRLRGMIPRRWVGKISAMTEEVDDL 180
           ASAK+GGTALLTW ANLLF+PMVLFYLLQDWH FIKR++ +IPRRW G+I+ M  EVD L
Sbjct: 152 ASAKVGGTALLTWLANLLFVPMVLFYLLQDWHQFIKRMQILIPRRWAGRINTMAAEVDGL 211

Query: 181 LAQYLRGQLLVMLILATYYSVALAIAGFDIALPVGILTGLLVFIPYVGFGLGLVLALIAA 240
           L QYLRGQLLVML+LA YYSVAL  AGFD ALPVG+LTGLLVFIPYVGFGLGLVLA++AA
Sbjct: 212 LGQYLRGQLLVMLVLAVYYSVALTAAGFDSALPVGVLTGLLVFIPYVGFGLGLVLAILAA 271

Query: 241 VLQFTGLYGLVAVAIIYGIGQVLESFILTPQLVGERIGLHPLMVIFALLAFGQLFGFVGV 300
           +LQF G  GL+ VA+IYG+GQVLESFILTP+LVGERIGLHPL+VIFALLAFGQLFGFVGV
Sbjct: 272 ILQFDGAIGLLWVALIYGVGQVLESFILTPKLVGERIGLHPLVVIFALLAFGQLFGFVGV 331

Query: 301 LLALPASAIMSVVVRHLRQHYLSSSFYN 328
           LLALPASAI+SV+  H+R+ YL+S+FYN
Sbjct: 332 LLALPASAIVSVIALHVRREYLASNFYN 359


>gi|300312358|ref|YP_003776450.1| hypothetical protein Hsero_3054
           [Herbaspirillum seropedicae SmR1]
          Length = 374

 Score = 75.1 bits (183), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 86/313 (27%), Positives = 152/313 (48%), Gaps = 18/313 (5%)

Query: 6   VTAAILAYALNPGVDWLARRRIGPFLLPRVLAVLIVVLLLLLAGLALVLVVVPVLVKEIP 65
           V A   +Y + P V+ + R R  P  +PR +++ +V  +L +A +A V  +    ++E  
Sbjct: 36  VFAVFFSYLVYPLVELIERVR--PPRVPRTVSIALV-FVLAIAIVATVATIFGARIQEEA 92

Query: 66  L-LQQQIPNFLDKLNAKVAPRLSEFGIHVRLDITGIKRILTQQLATSGDEIWASVLASAK 124
           L L +Q+P  L   +A     L  F   +R  I G  R    QLA   D+     +  AK
Sbjct: 93  LRLSEQLPALLRSNDAVSRLPLPGFAEPLRARILGFVR---DQLAAGTDQ----AMPLAK 145

Query: 125 IGGTALLTWAANLLF---IPMVLFYLLQDWHPFIKRLRGMIPRRWVGKISAMTEEVDDLL 181
             G  ++  A+NL++   +P++ F L+++     + +   + R        +  ++D LL
Sbjct: 146 QFGVGVMHAASNLIYLVLVPVISFLLIKEAPAMREEMLSWMSRANRKLWDGIVTDLDVLL 205

Query: 182 AQYLRGQLLVMLILATYYSVALAIAGFDIALPVGILTGLLVFIPYVGFGLGLVLALIAAV 241
           ++Y+R  L + +     YS+A ++ G   A+ +  L  +L FIP+ G       AL+ A 
Sbjct: 206 SRYVRALLFLSVATFVAYSIAFSLMGVPYAMLLAGLAAVLEFIPFAGPLAASAAALVVAG 265

Query: 242 LQ-FTGLYGLVAVAIIYGIGQVLESFILTPQLVGERIGLHPLMVIFALLAFGQLFGFVGV 300
              +  L  LV   + Y   +V + ++L P L+ E + + PLMVI  LLA  QL G  G+
Sbjct: 266 FSAYDHLLWLVGFIVAY---RVFQDYVLNPYLMSEGVEVSPLMVILGLLAGDQLGGVAGI 322

Query: 301 LLALPASAIMSVV 313
            L++P  A + ++
Sbjct: 323 FLSVPVMAALKII 335


>gi|300309868|ref|YP_003773960.1| membrane transport protein
           [Herbaspirillum seropedicae SmR1]
          Length = 626

 Score = 55.5 bits (132), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 42/138 (30%), Positives = 73/138 (52%), Gaps = 2/138 (1%)

Query: 181 LAQYLRGQLLVMLILATYYSVALAIAGFDIALPVGILTGLLVFIPYVG-FGLGLVLALIA 239
           ++++   Q LV L         LA  G   A+  G L G+L F+PY+G    G+++A+  
Sbjct: 224 VSRFFFSQFLVNLAFGLIMGAVLAAGGVPHAVLWGTLAGVLRFVPYLGALASGVMIAIFI 283

Query: 240 AVLQFTGLYGLVAVAIIYGIGQVLESFILTPQLVGERIGLHPLMVIFALLAFGQLFGFVG 299
           A +   G +  ++    YG  +V+ +  + P++ G   GL PL VI + L +G L+G +G
Sbjct: 284 AAID-PGWWLALSFLAFYGCLEVIVANFIEPRIYGHSSGLSPLAVIVSALFWGSLWGPIG 342

Query: 300 VLLALPASAIMSVVVRHL 317
           +LL+ P +  + V  RH+
Sbjct: 343 LLLSTPLTLCLVVAGRHV 360


  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
   0.331    0.147    0.432 

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: 793,128
Number of extensions: 26638
Number of successful extensions: 159
Number of sequences better than 1.0e-08: 3
Number of HSP's gapped: 158
Number of HSP's successfully gapped: 3
Length of query: 331
Length of database: 1,619,870
Length adjustment: 86
Effective length of query: 245
Effective length of database: 1,212,660
Effective search space: 297101700
Effective search space used: 297101700
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 131 (55.1 bits)