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= 0012.0060.p
         (118 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300309921|ref|YP_003774013.1| LysR family transcription regul...    87   5e-19
gi|300313187|ref|YP_003777279.1| transcription regulator protein...    86   8e-19
gi|300310802|ref|YP_003774894.1| LysR family transcription regul...    82   9e-18
gi|300312244|ref|YP_003776336.1| LysR family transcription regul...    72   1e-14
gi|300311424|ref|YP_003775516.1| LysR family transcription regul...    70   5e-14

>gi|300309921|ref|YP_003774013.1| LysR family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 299

 Score = 86.7 bits (213), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 48/101 (47%), Positives = 63/101 (62%)

Query: 6   RVRAIISFVQAADSGSFAGAGRTLGISSAAVSQNVAGLETALGVRLMNRTTRSLNLTEEG 65
           ++R I  F+  AD GSF  A   LGIS AAVS+ V  LE  LG RLM RTTR L+LTE G
Sbjct: 3   KLREIECFIAVADLGSFVKAAEALGISKAAVSRTVLELEARLGSRLMQRTTRRLSLTEAG 62

Query: 66  SAFLRQARIALDALEQATDDVVAARATPTGRVRISTSAAFG 106
           + +L + +  + ALE+A D + +  A PTG +RI+    FG
Sbjct: 63  ALYLERCKQIVAALEEADDLLSSGSAKPTGLLRINAPLTFG 103


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

 Score = 85.9 bits (211), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 45/95 (47%), Positives = 64/95 (67%)

Query: 13  FVQAADSGSFAGAGRTLGISSAAVSQNVAGLETALGVRLMNRTTRSLNLTEEGSAFLRQA 72
           FV AA +GSF+ A R LG++SAAV +NVA LE++LGVRL +R+TR L+LTE G  FL++ 
Sbjct: 10  FVAAAHAGSFSAAARQLGLTSAAVGKNVARLESSLGVRLFHRSTRKLSLTEAGERFLQEV 69

Query: 73  RIALDALEQATDDVVAARATPTGRVRISTSAAFGR 107
              L A+  A  ++ +A   P G +++S    FGR
Sbjct: 70  GGGLQAIRSAVANLASAGGQPAGTLKVSMGTGFGR 104


>gi|300310802|ref|YP_003774894.1| LysR family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 304

 Score = 82.4 bits (202), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 45/95 (47%), Positives = 59/95 (62%)

Query: 13  FVQAADSGSFAGAGRTLGISSAAVSQNVAGLETALGVRLMNRTTRSLNLTEEGSAFLRQA 72
           F   A   SFAG+ R +G S A +S+ +A LE ALGVRL +RTTRS+ +TEEG      A
Sbjct: 13  FCVVARHSSFAGSAREVGASPAYISKRIALLEQALGVRLFHRTTRSVVMTEEGGNVHEWA 72

Query: 73  RIALDALEQATDDVVAARATPTGRVRISTSAAFGR 107
           R  LD +EQ  + V +A+  P G ++ISTS   GR
Sbjct: 73  RRILDDVEQMMETVSSAKRVPRGLLKISTSFGLGR 107


>gi|300312244|ref|YP_003776336.1| LysR family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 293

 Score = 72.4 bits (176), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 38/94 (40%), Positives = 56/94 (59%)

Query: 12  SFVQAADSGSFAGAGRTLGISSAAVSQNVAGLETALGVRLMNRTTRSLNLTEEGSAFLRQ 71
           +FV   ++G+ + A   L  +++ VS+ ++ LE  LG  L+ RTTR + LTEEG AFL Q
Sbjct: 10  TFVAVVEAGTLSAAAELLAQTTSGVSRALSRLEDKLGASLLTRTTRRMELTEEGRAFLEQ 69

Query: 72  ARIALDALEQATDDVVAARATPTGRVRISTSAAF 105
           AR  L A+E A D +      P G++R+  SA F
Sbjct: 70  ARAILAAMESAQDSIRLRTRKPVGKLRVDASAPF 103


>gi|300311424|ref|YP_003775516.1| LysR family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 327

 Score = 69.7 bits (169), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 42/107 (39%), Positives = 65/107 (60%), Gaps = 3/107 (2%)

Query: 1   MDTSQRVRAIISFVQAADSGSFAGAGRTLGISSAAVSQNVAGLETALGVRLMNRTTRSLN 60
           MDT Q +R    F +  ++GSF  A + +G+++A VS+ VA LE  L  RLMNRTTR + 
Sbjct: 2   MDTLQNMRV---FARVVEAGSFTQAAQQMGLTTAHVSRAVADLERHLRTRLMNRTTRRIA 58

Query: 61  LTEEGSAFLRQARIALDALEQATDDVVAARATPTGRVRISTSAAFGR 107
           LTE G  +L + +  +  +++A  +  AA   P+GR+RI    +FG+
Sbjct: 59  LTEAGERYLLRCQQIMSYVDEAEAEASAAYVKPSGRLRIHAMTSFGQ 105


  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    0.128    0.353 

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: 272,430
Number of extensions: 9131
Number of successful extensions: 134
Number of sequences better than 1.0e-08: 37
Number of HSP's gapped: 135
Number of HSP's successfully gapped: 37
Length of query: 118
Length of database: 1,619,870
Length adjustment: 74
Effective length of query: 44
Effective length of database: 1,269,480
Effective search space: 55857120
Effective search space used: 55857120
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)