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= 0003.0006.p
         (176 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300310906|ref|YP_003774998.1| LysR family transcription regul...    86   2e-18
gi|300312894|ref|YP_003776986.1| LysR family transcription regul...    83   2e-17
gi|300313964|ref|YP_003778056.1| LysR family transcription regul...    79   1e-16
gi|300312645|ref|YP_003776737.1| LysR family transcription regul...    78   5e-16
gi|300309845|ref|YP_003773937.1| LysR family transcription regul...    77   9e-16

>gi|300310906|ref|YP_003774998.1| LysR family transcription
          regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 300

 Score = 85.9 bits (211), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 49/95 (51%), Positives = 66/95 (69%), Gaps = 2/95 (2%)

Query: 1  MTARTLPSLNALRAFEAAARHQSFTLAAQELHVTQGAVSHQVKALEEELGVPLFERLSNQ 60
          M   TLP LNA+RAF AAARHQSFTLAA EL+VT GA+S Q+K LE  LG+PLFER + Q
Sbjct: 1  MADLTLP-LNAIRAFLAAARHQSFTLAAHELNVTHGAISRQIKNLEGYLGMPLFERRTRQ 59

Query: 61 LRLTAAGQRYLVVAGEAFDRIESGTRQLL-ERPQR 94
          + LT  G+++   A  A + + +  R+++ + P R
Sbjct: 60 VLLTERGRQFFEEASPALEILANAARRVMRDAPTR 94


>gi|300312894|ref|YP_003776986.1| LysR family transcription
          regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 299

 Score = 82.8 bits (203), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 43/89 (48%), Positives = 61/89 (68%)

Query: 4  RTLPSLNALRAFEAAARHQSFTLAAQELHVTQGAVSHQVKALEEELGVPLFERLSNQLRL 63
          R +PS ++L AFEAAARH SF  AA+EL +T+GA+S Q+  LE  LGV LFER+ N++RL
Sbjct: 3  RRIPSNSSLMAFEAAARHGSFARAAEELALTEGAISRQISRLEGFLGVTLFERIGNRVRL 62

Query: 64 TAAGQRYLVVAGEAFDRIESGTRQLLERP 92
             GQRY     E  +R++  ++ L+ +P
Sbjct: 63 LPHGQRYASHVRETLERLDRDSQHLMSQP 91


>gi|300313964|ref|YP_003778056.1| LysR family transcription
          regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 314

 Score = 79.3 bits (194), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 49/89 (55%), Positives = 56/89 (62%)

Query: 6  LPSLNALRAFEAAARHQSFTLAAQELHVTQGAVSHQVKALEEELGVPLFERLSNQLRLTA 65
          LP L ALRAFEA AR  SFT AA ELHVTQ AVS QV+ LE  L   LF RL+ ++ LT 
Sbjct: 4  LPPLTALRAFEATARLLSFTAAADELHVTQSAVSRQVRILEAHLEQKLFVRLTRRIELTR 63

Query: 66 AGQRYLVVAGEAFDRIESGTRQLLERPQR 94
          AG  Y     +AF+RI +   QL  R QR
Sbjct: 64 AGAAYFQQIRQAFERICAAGEQLHARRQR 92


>gi|300312645|ref|YP_003776737.1| LysR family transcription
          regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 287

 Score = 77.8 bits (190), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 45/73 (61%), Positives = 50/73 (68%)

Query: 9  LNALRAFEAAARHQSFTLAAQELHVTQGAVSHQVKALEEELGVPLFERLSNQLRLTAAGQ 68
          LNALRAFE +ARH SFT AA+EL VTQ AVS QVK LE+ LGV LF RL   L LT  G 
Sbjct: 5  LNALRAFEVSARHLSFTRAAEELSVTQTAVSMQVKNLEQRLGVALFRRLPRGLALTDEGL 64

Query: 69 RYLVVAGEAFDRI 81
            L V  ++F RI
Sbjct: 65 ALLPVVAQSFGRI 77


>gi|300309845|ref|YP_003773937.1| LysR family transcription
          regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 294

 Score = 77.0 bits (188), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 43/83 (51%), Positives = 52/83 (62%)

Query: 6  LPSLNALRAFEAAARHQSFTLAAQELHVTQGAVSHQVKALEEELGVPLFERLSNQLRLTA 65
          +P L +L AFEA AR +SF LAA ELH+T  A+SHQV  LE+ LG+ LFER +  + LT 
Sbjct: 2  IPPLTSLMAFEAIARRKSFNLAAAELHLTPSAISHQVARLEKLLGLRLFERSTKGVELTP 61

Query: 66 AGQRYLVVAGEAFDRIESGTRQL 88
          AGQ YL     A   I S T  L
Sbjct: 62 AGQSYLNRVAGALGAINSATDDL 84


  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    0.131    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: 464,150
Number of extensions: 15479
Number of successful extensions: 174
Number of sequences better than 1.0e-08: 28
Number of HSP's gapped: 175
Number of HSP's successfully gapped: 28
Length of query: 176
Length of database: 1,619,870
Length adjustment: 79
Effective length of query: 97
Effective length of database: 1,245,805
Effective search space: 120843085
Effective search space used: 120843085
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: 127 (53.5 bits)