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= 0001.0272.p
         (135 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300309635|ref|YP_003773727.1| biopolymer transport ExbD/TolR ...   256   5e-70
gi|300311921|ref|YP_003776013.1| biopolymer transport ExbD/TolR ...    80   4e-17
gi|300310551|ref|YP_003774643.1| biopolymer transport ExbD/TolR ...    59   2e-10

>gi|300309635|ref|YP_003773727.1| biopolymer transport ExbD/TolR
           protein [Herbaspirillum seropedicae SmR1]
          Length = 135

 Score =  256 bits (654), Expect = 5e-70,   Method: Compositional matrix adjust.
 Identities = 128/134 (95%), Positives = 130/134 (97%)

Query: 1   MRSWDEPKKRKARVEIIPMIDVMMFLLVFFVLISLNVIPALGLKTQLPSSSTAQDLKPQT 60
           MRSWDEPKKRKARVEIIPMIDVMMFLLVFFVLISLNVIPALGLKTQLPSSSTAQDLKPQT
Sbjct: 1   MRSWDEPKKRKARVEIIPMIDVMMFLLVFFVLISLNVIPALGLKTQLPSSSTAQDLKPQT 60

Query: 61  KAIITIAKDDVIQVDGENTNLDGLTAHLDKLRKEGEKLNLIINSDRGVEVQRLVDVMDTL 120
           KA+ITIAKD+VIQVDGENT LD LTA LDKLR EGEKLNLIINSDRGVEVQRLVDVMDTL
Sbjct: 61  KAVITIAKDEVIQVDGENTTLDALTARLDKLRHEGEKLNLIINSDRGVEVQRLVDVMDTL 120

Query: 121 KKGGFDSISIATRK 134
           KKGGFDSISIATRK
Sbjct: 121 KKGGFDSISIATRK 134


>gi|300311921|ref|YP_003776013.1| biopolymer transport ExbD/TolR
           protein [Herbaspirillum seropedicae SmR1]
          Length = 132

 Score = 80.5 bits (197), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 47/130 (36%), Positives = 72/130 (55%), Gaps = 7/130 (5%)

Query: 5   DEPKKRKARVEIIPMIDVMMFLLVFFVLISLNVIPALGLKTQLPSSSTAQDLKPQTKAII 64
           DEP      +EIIPMID+MMFLL+FF++  L +I   GLK  +P +++A  L P     I
Sbjct: 10  DEP-----HIEIIPMIDIMMFLLIFFMVTMLKMIDVSGLKINVPQAASAATL-PSKSLTI 63

Query: 65  TIAKDDVIQVDGENTNLDGLTAHLDKLRKEGEKLNLIINSDRGVEVQRLVDVMDTLKKGG 124
            + K   +  +G+    D L A L K R +  KL +++  D+ V ++ L+ VMD  +  G
Sbjct: 64  VVDKTGAMFFEGKPLEHDALVAQL-KERAQTAKLEVLVAGDKEVSLENLLHVMDVARAAG 122

Query: 125 FDSISIATRK 134
            + I IA + 
Sbjct: 123 IEDIGIAAKH 132


>gi|300310551|ref|YP_003774643.1| biopolymer transport ExbD/TolR
           protein [Herbaspirillum seropedicae SmR1]
          Length = 144

 Score = 58.5 bits (140), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 40/134 (29%), Positives = 68/134 (50%), Gaps = 7/134 (5%)

Query: 7   PKKRKARVEIIPMIDVMMFLLVFFVLI------SLNVIPALGLKTQLPSSSTAQDLKPQT 60
           P+K K+ + ++P IDVM+ LL+ F++       S+  +P  G  TQ PS      LKP +
Sbjct: 11  PRKFKSEINVVPYIDVMLVLLIIFMVATPITNPSVINLPTAGKSTQPPSDYIEIALKPNS 70

Query: 61  KAIITIAKDDVIQVDGEN-TNLDGLTAHLDKLRKEGEKLNLIINSDRGVEVQRLVDVMDT 119
           +A I I          E  T    L+  L KL  +  +L ++I++D+ ++   +V V+  
Sbjct: 71  QATIRINGPKSGGKKAETVTGKTDLSERLRKLHDDNPELAVMISADKDIKYDEVVQVISE 130

Query: 120 LKKGGFDSISIATR 133
            KK G   + +AT+
Sbjct: 131 AKKQGIARVGLATK 144


  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
   0.319    0.136    0.372 

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: 376,060
Number of extensions: 13719
Number of successful extensions: 61
Number of sequences better than 1.0e-08: 3
Number of HSP's gapped: 62
Number of HSP's successfully gapped: 3
Length of query: 135
Length of database: 1,619,870
Length adjustment: 76
Effective length of query: 59
Effective length of database: 1,260,010
Effective search space: 74340590
Effective search space used: 74340590
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 125 (52.8 bits)