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= 0034.0036.p
         (130 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300312482|ref|YP_003776574.1| LysR family transcription regul...   205   1e-54
gi|300313657|ref|YP_003777749.1| LysR family transcription regul...   100   6e-23
gi|300313689|ref|YP_003777781.1| LysR family transcription regul...    99   1e-22

>gi|300312482|ref|YP_003776574.1| LysR family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 303

 Score =  205 bits (521), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 93/130 (71%), Positives = 113/130 (86%)

Query: 1   MRNGHPLSKFKSVTLSQLRPYPLALPDPDTTLRQLFDLACSRQQLVFEPVLTSNYIQTLH 60
           MR  HPL++F+ +++ QL+PYP+ALPDP TTLRQLFD+ACSRQQ+V EPV+TSNYIQ+LH
Sbjct: 174 MRKDHPLARFRQISVGQLKPYPMALPDPTTTLRQLFDIACSRQQVVIEPVMTSNYIQSLH 233

Query: 61  NYLLEGDALSITGAVTVRYRIAKGEFTMVPIHDRALDGRYVEVQTLSGRTLPRIVEIFLD 120
           NY+L+ DALSITG VTVRYRIA GE TM PI D   DGR+VEVQTL+GRTLPR VEIFLD
Sbjct: 234 NYVLDNDALSITGEVTVRYRIATGELTMRPIRDCPADGRFVEVQTLAGRTLPRSVEIFLD 293

Query: 121 YLLGELNEDI 130
           YL+ EL++D+
Sbjct: 294 YLVAELSKDL 303


>gi|300313657|ref|YP_003777749.1| LysR family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 333

 Score =  100 bits (248), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 44/124 (35%), Positives = 75/124 (60%)

Query: 1   MRNGHPLSKFKSVTLSQLRPYPLALPDPDTTLRQLFDLACSRQQLVFEPVLTSNYIQTLH 60
           M   H L+  K V+LS+L PYPLA+P    T+R+L D  CSR+ ++ EP L ++ I  L 
Sbjct: 204 MHPAHELAHRKQVSLSELAPYPLAMPKKTITMRRLIDACCSRRNVLLEPTLAADSISALL 263

Query: 61  NYLLEGDALSITGAVTVRYRIAKGEFTMVPIHDRALDGRYVEVQTLSGRTLPRIVEIFLD 120
            +++ G  +  + A+ +R  + +G+   +PI D+ ++   +E+Q+L+GRTLP     FL+
Sbjct: 264 CFVMAGQGIGFSAALPIRKLVREGKLAALPIRDKDMNTLQLEIQSLAGRTLPDAARAFLN 323

Query: 121 YLLG 124
            L+ 
Sbjct: 324 ALIA 327


>gi|300313689|ref|YP_003777781.1| LysR family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 307

 Score = 98.6 bits (244), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 51/129 (39%), Positives = 78/129 (60%), Gaps = 1/129 (0%)

Query: 1   MRNGHPLSKFKSVTLSQLRPYPLALPDPDTTLRQLFDLACSRQQLVFEPVLTSNYIQTLH 60
           M+  HPL+    + LS L PYPLALP+  TT+RQLFD+ACS + L+F PV TS+ +  ++
Sbjct: 169 MKRDHPLASRTLLALSDLSPYPLALPEVGTTVRQLFDIACSMRGLLFSPVFTSHSLGAVY 228

Query: 61  NYLLEG-DALSITGAVTVRYRIAKGEFTMVPIHDRALDGRYVEVQTLSGRTLPRIVEIFL 119
            +     D +++ G +TV  R  +    +V + +  L  R V+VQT++GR LP  V  F 
Sbjct: 229 RFTTRSPDTVALGGFLTVHERAEEDGMILVAMAESELHQRTVQVQTMAGRKLPPAVAAFS 288

Query: 120 DYLLGELNE 128
           D+L+  L +
Sbjct: 289 DFLIAALRQ 297


  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
   0.323    0.141    0.408 

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: 396,947
Number of extensions: 14342
Number of successful extensions: 32
Number of sequences better than 1.0e-08: 3
Number of HSP's gapped: 31
Number of HSP's successfully gapped: 3
Length of query: 130
Length of database: 1,619,870
Length adjustment: 75
Effective length of query: 55
Effective length of database: 1,264,745
Effective search space: 69560975
Effective search space used: 69560975
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 125 (52.8 bits)