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= 0007.0012.p
         (108 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300311849|ref|YP_003775941.1| LysR family transcription regul...    70   3e-14
gi|300311868|ref|YP_003775960.1| LysR family transcription regul...    67   4e-13
gi|300310278|ref|YP_003774370.1| transcription regulator protein...    62   1e-11
gi|300313187|ref|YP_003777279.1| transcription regulator protein...    62   1e-11
gi|300312835|ref|YP_003776927.1| LysR family transcription regul...    59   6e-11

>gi|300311849|ref|YP_003775941.1| LysR family transcription
          regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 309

 Score = 70.5 bits (171), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 48/88 (54%), Positives = 60/88 (68%), Gaps = 1/88 (1%)

Query: 3  SLDALLMFIEAANLGSFSAAARKLGKQQSSVSEAIANLEIDLGVTLFDRSTRKPTLTEHG 62
          SLD L +F++ A+ GSF AAARKL + QS+VS AIA+LE  LG+ LFDRS  +P LT  G
Sbjct: 7  SLDQLRVFVQVADSGSFLAAARKLARAQSAVSYAIASLEEQLGLLLFDRSGYRPQLTAPG 66

Query: 63 HALLTHARQLLDANDKLS-RADTIPTGR 89
           ALL  ARQ+LD  D L  RA +   G+
Sbjct: 67 EALLADARQVLDHVDSLQVRASSYARGQ 94


>gi|300311868|ref|YP_003775960.1| LysR family transcription
          regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 307

 Score = 66.6 bits (161), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 38/79 (48%), Positives = 46/79 (58%)

Query: 1  MHSLDALLMFIEAANLGSFSAAARKLGKQQSSVSEAIANLEIDLGVTLFDRSTRKPTLTE 60
          MH LD L +F   A L SFS AAR+LG   +SVS AI  LE  LG  L  R+TR+  LT 
Sbjct: 1  MHQLDTLRIFQRVAELASFSGAARQLGLPNASVSLAIQQLEQMLGTRLLQRTTRRVQLTA 60

Query: 61 HGHALLTHARQLLDANDKL 79
           G A    +R+LLD  + L
Sbjct: 61 DGEAFYRRSRELLDEFESL 79


>gi|300310278|ref|YP_003774370.1| transcription regulator protein
          [Herbaspirillum seropedicae SmR1]
          Length = 313

 Score = 61.6 bits (148), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 33/74 (44%), Positives = 47/74 (63%)

Query: 1  MHSLDALLMFIEAANLGSFSAAARKLGKQQSSVSEAIANLEIDLGVTLFDRSTRKPTLTE 60
          M  L  +++F     LG+FS AAR+LG   SSVS+ I+ LE  LG TL  R+TRK +LTE
Sbjct: 6  MDYLPRMVIFSRVVELGAFSKAARELGLTSSSVSQHISALEAMLGTTLLHRTTRKLSLTE 65

Query: 61 HGHALLTHARQLLD 74
           GH+   +  +++D
Sbjct: 66 AGHSFYANCSRIVD 79


>gi|300313187|ref|YP_003777279.1| transcription regulator protein
          [Herbaspirillum seropedicae SmR1]
          Length = 308

 Score = 61.6 bits (148), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 33/66 (50%), Positives = 45/66 (68%)

Query: 1  MHSLDALLMFIEAANLGSFSAAARKLGKQQSSVSEAIANLEIDLGVTLFDRSTRKPTLTE 60
          M ++ ++  F+ AA+ GSFSAAAR+LG   ++V + +A LE  LGV LF RSTRK +LTE
Sbjct: 1  METMTSIECFVAAAHAGSFSAAARQLGLTSAAVGKNVARLESSLGVRLFHRSTRKLSLTE 60

Query: 61 HGHALL 66
           G   L
Sbjct: 61 AGERFL 66


>gi|300312835|ref|YP_003776927.1| LysR family transcription
          regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 283

 Score = 59.3 bits (142), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 37/88 (42%), Positives = 49/88 (55%), Gaps = 2/88 (2%)

Query: 4  LDALLMFIEAANLGSFSAAARKLGKQQSSVSEAIANLEIDLGVTLFDRSTRKPTLTEHGH 63
          LD L M +  A+ G+FS AA  + + QS+VS  I  LE+ LG  LF R  R    T+ G 
Sbjct: 6  LDVLAMIVAVADTGNFSRAAELVHRTQSAVSMQIKTLELALGKPLFLRKPRSVVPTQDGE 65

Query: 64 ALLTHARQLLDANDKLSRADTIP--TGR 89
           LLT+AR++L   D+   A   P  TGR
Sbjct: 66 VLLTYARRMLTLRDEAWAAVVRPDVTGR 93


  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
   0.320    0.132    0.373 

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: 315,033
Number of extensions: 10739
Number of successful extensions: 111
Number of sequences better than 1.0e-08: 25
Number of HSP's gapped: 111
Number of HSP's successfully gapped: 25
Length of query: 108
Length of database: 1,619,870
Length adjustment: 72
Effective length of query: 36
Effective length of database: 1,278,950
Effective search space: 46042200
Effective search space used: 46042200
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 (21.9 bits)
S2: 124 (52.4 bits)