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= 0011.0148.p
         (360 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...   688   0.0  
gi|300312358|ref|YP_003776450.1| hypothetical protein Hsero_3054...    74   3e-14
gi|300309868|ref|YP_003773960.1| membrane transport protein [Her...    59   8e-10

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

 Score =  688 bits (1775), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 360/360 (100%), Positives = 360/360 (100%)

Query: 1   MPFSLSEEQKQNLVWLIVGFLLLALLIALGPMLSPFVAAGIIGYALNPGVDWIASRRLGP 60
           MPFSLSEEQKQNLVWLIVGFLLLALLIALGPMLSPFVAAGIIGYALNPGVDWIASRRLGP
Sbjct: 1   MPFSLSEEQKQNLVWLIVGFLLLALLIALGPMLSPFVAAGIIGYALNPGVDWIASRRLGP 60

Query: 61  VRVPRFVAVTIMVLLLILAGLALVLIVVPLVLRQIPLLQAQVPPLLDKLNAFVSPRLHQL 120
           VRVPRFVAVTIMVLLLILAGLALVLIVVPLVLRQIPLLQAQVPPLLDKLNAFVSPRLHQL
Sbjct: 61  VRVPRFVAVTIMVLLLILAGLALVLIVVPLVLRQIPLLQAQVPPLLDKLNAFVSPRLHQL 120

Query: 121 GIDVRLDLAGIKSLLTQQISTSSDEVWTSVLASAKVGGTALLTWLANLLFVPMVLFYLLQ 180
           GIDVRLDLAGIKSLLTQQISTSSDEVWTSVLASAKVGGTALLTWLANLLFVPMVLFYLLQ
Sbjct: 121 GIDVRLDLAGIKSLLTQQISTSSDEVWTSVLASAKVGGTALLTWLANLLFVPMVLFYLLQ 180

Query: 181 DWHQFIKRMQILIPRRWAGRINTMAAEVDGLLGQYLRGQLLVMLVLAVYYSVALTAAGFD 240
           DWHQFIKRMQILIPRRWAGRINTMAAEVDGLLGQYLRGQLLVMLVLAVYYSVALTAAGFD
Sbjct: 181 DWHQFIKRMQILIPRRWAGRINTMAAEVDGLLGQYLRGQLLVMLVLAVYYSVALTAAGFD 240

Query: 241 SALPVGVLTGLLVFIPYVGFGLGLVLAILAAILQFDGAIGLLWVALIYGVGQVLESFILT 300
           SALPVGVLTGLLVFIPYVGFGLGLVLAILAAILQFDGAIGLLWVALIYGVGQVLESFILT
Sbjct: 241 SALPVGVLTGLLVFIPYVGFGLGLVLAILAAILQFDGAIGLLWVALIYGVGQVLESFILT 300

Query: 301 PKLVGERIGLHPLVVIFALLAFGQLFGFVGVLLALPASAIVSVIALHVRREYLASNFYNR 360
           PKLVGERIGLHPLVVIFALLAFGQLFGFVGVLLALPASAIVSVIALHVRREYLASNFYNR
Sbjct: 301 PKLVGERIGLHPLVVIFALLAFGQLFGFVGVLLALPASAIVSVIALHVRREYLASNFYNR 360


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

 Score = 73.6 bits (179), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 85/311 (27%), Positives = 146/311 (46%), Gaps = 26/311 (8%)

Query: 43  GYALNPGVDWIASRRLGPVRVPRFVAVTIMVLLLILAGLALVLIVVPLVLRQIPL-LQAQ 101
            Y + P V+ I   R+ P RVPR V++  +V +L +A +A V  +    +++  L L  Q
Sbjct: 42  SYLVYPLVELI--ERVRPPRVPRTVSIA-LVFVLAIAIVATVATIFGARIQEEALRLSEQ 98

Query: 102 VPPLLDKLNAFVSPRLHQLGIDVRLDLAGIKSLLTQQISTSSDEVWTSVLASAKVGGTAL 161
           +P LL   +A     L      +R   A I   +  Q++  +D+     +  AK  G  +
Sbjct: 99  LPALLRSNDAVSRLPLPGFAEPLR---ARILGFVRDQLAAGTDQA----MPLAKQFGVGV 151

Query: 162 LTWLANLLF---VPMVLFYLLQDWHQFIKRMQILIPRRWAGRINT-----MAAEVDGLLG 213
           +   +NL++   VP++ F L+++     + M       W  R N      +  ++D LL 
Sbjct: 152 MHAASNLIYLVLVPVISFLLIKEAPAMREEML-----SWMSRANRKLWDGIVTDLDVLLS 206

Query: 214 QYLRGQLLVMLVLAVYYSVALTAAGFDSALPVGVLTGLLVFIPYVGFGLGLVLAILAAIL 273
           +Y+R  L + +   V YS+A +  G   A+ +  L  +L FIP+ G       A    + 
Sbjct: 207 RYVRALLFLSVATFVAYSIAFSLMGVPYAMLLAGLAAVLEFIPFAG--PLAASAAALVVA 264

Query: 274 QFDGAIGLLWVALIYGVGQVLESFILTPKLVGERIGLHPLVVIFALLAFGQLFGFVGVLL 333
            F     LLW+       +V + ++L P L+ E + + PL+VI  LLA  QL G  G+ L
Sbjct: 265 GFSAYDHLLWLVGFIVAYRVFQDYVLNPYLMSEGVEVSPLMVILGLLAGDQLGGVAGIFL 324

Query: 334 ALPASAIVSVI 344
           ++P  A + +I
Sbjct: 325 SVPVMAALKII 335


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

 Score = 58.5 bits (140), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 49/150 (32%), Positives = 77/150 (51%), Gaps = 4/150 (2%)

Query: 202 NTMAAEVDGLLG--QYLRGQLLVMLVLAVYYSVALTAAGFDSALPVGVLTGLLVFIPYVG 259
            TM A  D   G  ++   Q LV L   +     L A G   A+  G L G+L F+PY+G
Sbjct: 212 RTMQALGDAAEGVSRFFFSQFLVNLAFGLIMGAVLAAGGVPHAVLWGTLAGVLRFVPYLG 271

Query: 260 -FGLGLVLAILAAILQFDGAIGLLWVALIYGVGQVLESFILTPKLVGERIGLHPLVVIFA 318
               G+++AI  A +     + L ++A  YG  +V+ +  + P++ G   GL PL VI +
Sbjct: 272 ALASGVMIAIFIAAIDPGWWLALSFLAF-YGCLEVIVANFIEPRIYGHSSGLSPLAVIVS 330

Query: 319 LLAFGQLFGFVGVLLALPASAIVSVIALHV 348
            L +G L+G +G+LL+ P +  + V   HV
Sbjct: 331 ALFWGSLWGPIGLLLSTPLTLCLVVAGRHV 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
   0.330    0.146    0.435 

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: 825,029
Number of extensions: 25607
Number of successful extensions: 152
Number of sequences better than 1.0e-08: 3
Number of HSP's gapped: 149
Number of HSP's successfully gapped: 3
Length of query: 360
Length of database: 1,619,870
Length adjustment: 86
Effective length of query: 274
Effective length of database: 1,212,660
Effective search space: 332268840
Effective search space used: 332268840
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 131 (55.1 bits)