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= 0057.0012.p
         (139 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300310464|ref|YP_003774556.1| dipeptide/oligopeptide/nickel A...    74   3e-15
gi|300312480|ref|YP_003776572.1| dipeptide/oligopeptide/nickel A...    72   2e-14
gi|300310893|ref|YP_003774985.1| dipeptide/oligopeptide/nickel A...    57   7e-10

>gi|300310464|ref|YP_003774556.1| dipeptide/oligopeptide/nickel ABC
           transporter permease [Herbaspirillum seropedicae SmR1]
          Length = 318

 Score = 74.3 bits (181), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 43/99 (43%), Positives = 58/99 (58%), Gaps = 4/99 (4%)

Query: 18  VSMVIFSLLAILPGDPVTAILGLEATPEAAAALRAQLGLDDPLYVQYGRWLWNVLHGDLG 77
           VS  +F +  +LPGD     LG  ATPE  AALR Q GLD P  ++Y  WL N+L G+ G
Sbjct: 23  VSAGVFFITNLLPGDAAQTALGQAATPETVAALRLQYGLDLPAPLRYAHWLGNLLSGNPG 82

Query: 78  RSFIDRTPVIDVLMQRLPVTIELAIGSFAVGILIAVPXA 116
            S ++  PV  ++  RLP ++ LA    AV  L++VP A
Sbjct: 83  MSLVNNVPVAQMIGGRLPASLMLA----AVTALVSVPLA 117


>gi|300312480|ref|YP_003776572.1| dipeptide/oligopeptide/nickel ABC
           transporter permease [Herbaspirillum seropedicae SmR1]
          Length = 305

 Score = 72.0 bits (175), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 38/111 (34%), Positives = 66/111 (59%), Gaps = 1/111 (0%)

Query: 4   LIKRILLVIPTLLLVSMVIFSLLAILPGDPVTAILGLEATPEAAAALRAQLGLDDPLYVQ 63
           +++R+ + +   + VS+V F+LL  + GD   +I G EAT     ++R Q GLD P+  Q
Sbjct: 5   ILRRLAIALCVAVTVSVVSFTLLH-MSGDLAVSIAGPEATAAQVESVRTQFGLDRPMATQ 63

Query: 64  YGRWLWNVLHGDLGRSFIDRTPVIDVLMQRLPVTIELAIGSFAVGILIAVP 114
           Y  WL   +  D G+SF  + PV++++ +RLP+T +L   +  + +L A+P
Sbjct: 64  YLDWLGRAVQLDFGKSFYFQGPVMEMIAERLPITFKLGGSALLLAVLTAIP 114


>gi|300310893|ref|YP_003774985.1| dipeptide/oligopeptide/nickel
          ABC transporter permease [Herbaspirillum seropedicae
          SmR1]
          Length = 324

 Score = 56.6 bits (135), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 32/81 (39%), Positives = 47/81 (58%), Gaps = 2/81 (2%)

Query: 15 LLLVSMVIFSLLAILPGDPVTAILGLEATPEAAAALRAQLGLDDPLYVQYGRWLWNVLHG 74
          LL+  +V F L  I  G+PV  ++G +        +  +LGLD P++ QY  +L   LHG
Sbjct: 17 LLMTVIVFFGLHMI--GNPVDILIGQDVDQVDRLRIIQELGLDQPVWRQYLAFLNGALHG 74

Query: 75 DLGRSFIDRTPVIDVLMQRLP 95
          +LG SF+  TP I ++ QRLP
Sbjct: 75 NLGNSFVYNTPAILLIFQRLP 95


  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
   0.327    0.142    0.456 

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: 393,193
Number of extensions: 13424
Number of successful extensions: 85
Number of sequences better than 1.0e-08: 6
Number of HSP's gapped: 83
Number of HSP's successfully gapped: 6
Length of query: 139
Length of database: 1,619,870
Length adjustment: 76
Effective length of query: 63
Effective length of database: 1,260,010
Effective search space: 79380630
Effective search space used: 79380630
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 (21.7 bits)
S2: 126 (53.1 bits)