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= 0029.0028.p
         (184 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300313854|ref|YP_003777946.1| LysR family transcription regul...   270   4e-74
gi|300313153|ref|YP_003777245.1| transcription regulator protein...   174   6e-45

>gi|300313854|ref|YP_003777946.1| LysR family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 310

 Score =  270 bits (691), Expect = 4e-74,   Method: Compositional matrix adjust.
 Identities = 136/182 (74%), Positives = 154/182 (84%)

Query: 1   VHDAVMALVERHCDLLICYHHPQQGIDLDSERYAMLSLGKEPLRPYVKAIGKGVPKYTLP 60
           VHDAVMALVER+CDLL+CY H QQGI LD+ERY +LSLGKEPLRPYVK +  G+PKY LP
Sbjct: 129 VHDAVMALVERNCDLLLCYDHRQQGIALDTERYDVLSLGKEPLRPYVKTLPNGLPKYVLP 188

Query: 61  GTASEPVPFLSYSSYSSLSRIVEKQLSASPRPVHVFRRFESDLAEGLKSMVLEGHGVAWL 120
           G  ++P PFLSYS YSSLSRIVEK L +SPR VH+FRRFE+DLAEGLKSM +EGHG+AWL
Sbjct: 189 GAPNDPQPFLSYSPYSSLSRIVEKALHSSPRQVHLFRRFETDLAEGLKSMAVEGHGIAWL 248

Query: 121 PASAVTREVAEGKLTLAIAPNDNEALSTGLWSDEMDIRLYRRIDDARSDLDRIWACLKAA 180
           PASAV RE+AEGKLTLAIAP D+EAL  GLW DEMDIR+YRR+D A  D+DRIW  LKA 
Sbjct: 249 PASAVAREIAEGKLTLAIAPTDSEALEQGLWCDEMDIRVYRRLDGANPDIDRIWNYLKAE 308

Query: 181 HA 182
           H 
Sbjct: 309 HG 310


>gi|300313153|ref|YP_003777245.1| transcription regulator protein
           [Herbaspirillum seropedicae SmR1]
          Length = 331

 Score =  174 bits (440), Expect = 6e-45,   Method: Compositional matrix adjust.
 Identities = 89/188 (47%), Positives = 119/188 (63%), Gaps = 11/188 (5%)

Query: 1   VHDAVMALVERHCDLLICYHHPQQGIDLDSERYAMLSLGKEPLRPYVKAIGKGVPKYTLP 60
           VHDAVM +VE  CDLL+CYHHP+Q + LDS RY ML++G E LRPY +    G P Y  P
Sbjct: 129 VHDAVMTIVEGGCDLLLCYHHPRQPVQLDSSRYDMLTMGTETLRPYSRCDRNGKPDYVFP 188

Query: 61  GTASEPVPFLSYSSYSSLSRIVEKQLSASPRPVHVFRRFESDLAEGLKSMVLEGHGVAWL 120
           G+A  PVPFLSY+S + L R+VE  ++ + RP+H+ + +E+D++E LK M LEGHGVA+L
Sbjct: 189 GSAKAPVPFLSYTSNAYLGRMVELMMADTKRPLHLDKHYETDMSESLKMMALEGHGVAFL 248

Query: 121 PASAVTREVAEGKLTLAIAPNDNEALSTGLWSDEMDIRLYRRIDDA----RSDLDRIWAC 176
           P S+V REV   +L     P       +G W  EM+IRLYR    A    ++ + R+W  
Sbjct: 249 PESSVVREVRNRQLARTDVP-------SGEWEVEMEIRLYRERPTAQRAGKALVARLWEY 301

Query: 177 LKAAHAVR 184
           L    A R
Sbjct: 302 LVELDAQR 309


  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    0.135    0.405 

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: 556,963
Number of extensions: 20608
Number of successful extensions: 80
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 79
Number of HSP's successfully gapped: 2
Length of query: 184
Length of database: 1,619,870
Length adjustment: 80
Effective length of query: 104
Effective length of database: 1,241,070
Effective search space: 129071280
Effective search space used: 129071280
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)