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= 0013.0160.p
         (163 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300310441|ref|YP_003774533.1| TRAP-type C4-dicarboxylate tran...   249   1e-67
gi|300309847|ref|YP_003773939.1| TRAP-type C4-dicarboxylate tran...   246   5e-67
gi|300313112|ref|YP_003777204.1| TRAP-type C4-dicarboxylate tran...   133   6e-33

>gi|300310441|ref|YP_003774533.1| TRAP-type C4-dicarboxylate
           transport system periplasmic protein [Herbaspirillum
           seropedicae SmR1]
          Length = 348

 Score =  249 bits (635), Expect = 1e-67,   Method: Compositional matrix adjust.
 Identities = 116/135 (85%), Positives = 126/135 (93%)

Query: 8   KKNITRRQVLKIGAAATALPLFSIMTRPANAAEFTYKFATGQDPTHPVNKRAQEAIERIR 67
           K +++RRQ+LK GA   ALPLFSIM+RPANAAEF YKFATGQDP+HPVNKRAQ+AI+RIR
Sbjct: 10  KTSVSRRQLLKAGAVGAALPLFSIMSRPANAAEFNYKFATGQDPSHPVNKRAQQAIDRIR 69

Query: 68  NATNGRLEIKLFPANQLGSDTDLMSQIRNGGVEFFNQASVVLSTLVPAAGIVNTGFAFHD 127
            AT GRL+IKLFPANQLGSDTDLMSQIRNGGVEFFNQASVVLSTLVPAAGIVNTGFAFHD
Sbjct: 70  EATGGRLDIKLFPANQLGSDTDLMSQIRNGGVEFFNQASVVLSTLVPAAGIVNTGFAFHD 129

Query: 128 YKEVWAAMDGPLGAF 142
           YKEVW AMDGPLGA+
Sbjct: 130 YKEVWQAMDGPLGAY 144


>gi|300309847|ref|YP_003773939.1| TRAP-type C4-dicarboxylate
           transport system periplasmic protein [Herbaspirillum
           seropedicae SmR1]
          Length = 345

 Score =  246 bits (629), Expect = 5e-67,   Method: Compositional matrix adjust.
 Identities = 116/137 (84%), Positives = 126/137 (91%)

Query: 5   EDAKKNITRRQVLKIGAAATALPLFSIMTRPANAAEFTYKFATGQDPTHPVNKRAQEAIE 64
           E AKK +TRR +LK GA   ALPLFSI++RPA+AAEF+YKFATGQDP+HPVNKRAQEAI+
Sbjct: 4   ERAKKQVTRRNMLKAGAVGAALPLFSILSRPASAAEFSYKFATGQDPSHPVNKRAQEAID 63

Query: 65  RIRNATNGRLEIKLFPANQLGSDTDLMSQIRNGGVEFFNQASVVLSTLVPAAGIVNTGFA 124
           RIRNATNGRLEIKLFPANQLGSDTDLMSQ+RNGGVEFFNQA+ VLSTLVPAAGIVNTGFA
Sbjct: 64  RIRNATNGRLEIKLFPANQLGSDTDLMSQVRNGGVEFFNQANTVLSTLVPAAGIVNTGFA 123

Query: 125 FHDYKEVWAAMDGPLGA 141
           FHDY  VW AMDGPLGA
Sbjct: 124 FHDYGAVWKAMDGPLGA 140


>gi|300313112|ref|YP_003777204.1| TRAP-type C4-dicarboxylate
           transport system periplasmic protein [Herbaspirillum
           seropedicae SmR1]
          Length = 344

 Score =  133 bits (335), Expect = 6e-33,   Method: Compositional matrix adjust.
 Identities = 65/131 (49%), Positives = 90/131 (68%)

Query: 11  ITRRQVLKIGAAATALPLFSIMTRPANAAEFTYKFATGQDPTHPVNKRAQEAIERIRNAT 70
           ITRR  LK  + A+A     +++  A+AAEFT+K+A     THP+N RA+E    I   +
Sbjct: 8   ITRRNFLKTASVASAAAATGLVSTSAHAAEFTFKYANNLPVTHPMNARAKEMAAAIAEQS 67

Query: 71  NGRLEIKLFPANQLGSDTDLMSQIRNGGVEFFNQASVVLSTLVPAAGIVNTGFAFHDYKE 130
            GR+E++L+P NQLG+DTD++SQ+R G ++FF  + ++L TLVPAA I   GFAF DY +
Sbjct: 68  KGRIELQLYPNNQLGTDTDMLSQVRAGAIDFFTLSPLILGTLVPAAQISGIGFAFKDYSQ 127

Query: 131 VWAAMDGPLGA 141
           VW AMDG LGA
Sbjct: 128 VWPAMDGELGA 138


  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    0.133    0.385 

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: 506,869
Number of extensions: 20022
Number of successful extensions: 55
Number of sequences better than 1.0e-08: 3
Number of HSP's gapped: 55
Number of HSP's successfully gapped: 3
Length of query: 163
Length of database: 1,619,870
Length adjustment: 78
Effective length of query: 85
Effective length of database: 1,250,540
Effective search space: 106295900
Effective search space used: 106295900
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 (21.8 bits)
S2: 127 (53.5 bits)