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= 0035.0227.p
         (124 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300312342|ref|YP_003776434.1| XRE family transcription regula...   251   2e-68
gi|300312341|ref|YP_003776433.1| XRE family transcription regula...    87   4e-19
gi|300310419|ref|YP_003774511.1| Cro/CI family transcription reg...    81   2e-17

>gi|300312342|ref|YP_003776434.1| XRE family transcription regulator
           protein [Herbaspirillum seropedicae SmR1]
          Length = 124

 Score =  251 bits (640), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 123/124 (99%), Positives = 123/124 (99%)

Query: 1   MGKHIGKSDTSGMRISKDAIGERLKSVRLLAGMNQRDFAARLKTSGAYISCVELGHSMPG 60
           MGKHIGKSDTSGMRISKDAIGERLKSVRLLAGMNQRDFAARLKTSGAYISCVELGHSMPG
Sbjct: 1   MGKHIGKSDTSGMRISKDAIGERLKSVRLLAGMNQRDFAARLKTSGAYISCVELGHSMPG 60

Query: 61  GRFLRSLHHEFDVNVNWLLTGQEPSLPPRYGLHVRSLVSDYGGASQAGRSLIMAVASYLV 120
           GRFLRSLHHEFDVNVNWLLTGQEPSLPPRYGLHVRSLVSDYGGASQAGRSLIMAVASYLV
Sbjct: 61  GRFLRSLHHEFDVNVNWLLTGQEPSLPPRYGLHVRSLVSDYGGASQAGRSLIMAVASYLV 120

Query: 121 RQGA 124
            QGA
Sbjct: 121 GQGA 124


>gi|300312341|ref|YP_003776433.1| XRE family transcription regulator
           protein [Herbaspirillum seropedicae SmR1]
          Length = 115

 Score = 87.0 bits (214), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 47/107 (43%), Positives = 65/107 (60%), Gaps = 3/107 (2%)

Query: 18  DAIGERLKSVRLLAGMNQRDFAARLKTSGAYISCVELGHSMPGGRFLRSLHHEFDVNVNW 77
           + IG R+K VRL  G++QR+   RL TS  +IS +E G +MPGG  L  LH EF V++NW
Sbjct: 4   EEIGGRIKEVRLANGLSQRELGQRLDTSTGHISWLEAGKAMPGGELLLQLHREFSVDLNW 63

Query: 78  LLTGQ--EPSLPPRYGLHVRSLVSDYGGASQAGRSLIMAVASYLVRQ 122
           LLTG+  EP +       VR LV  Y      GR ++ ++ASY+ R+
Sbjct: 64  LLTGEEGEPGV-METDEEVRQLVDHYCRVDLQGREILRSLASYVGRE 109


>gi|300310419|ref|YP_003774511.1| Cro/CI family transcription
           regulator [Herbaspirillum seropedicae SmR1]
          Length = 152

 Score = 81.3 bits (199), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 43/116 (37%), Positives = 64/116 (55%), Gaps = 1/116 (0%)

Query: 6   GKSDTSGMRISKDAIGERLKSVRLLAGMNQRDFAARLKTSGAYISCVELGHSMPGGRFLR 65
           G +    M  SK A+G+R+K  RL  G +QR FA  L T   +I  +E G  MPG R L 
Sbjct: 10  GITSQPAMNASKKAVGQRIKRARLAIGFSQRKFATVLGTLPNHICQIEQGRCMPGSRLLH 69

Query: 66  SLHHEFDVNVNWLLTGQ-EPSLPPRYGLHVRSLVSDYGGASQAGRSLIMAVASYLV 120
            +H +F++++NWLLTGQ +P       + +R L+  Y  A + G+ L+ + A  L 
Sbjct: 70  GMHVQFNIDINWLLTGQHQPFRLNSQEMGLRMLLHHYTRADETGKHLLCSAACLLA 125


  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    0.135    0.398 

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: 403,307
Number of extensions: 15919
Number of successful extensions: 41
Number of sequences better than 1.0e-08: 3
Number of HSP's gapped: 40
Number of HSP's successfully gapped: 3
Length of query: 124
Length of database: 1,619,870
Length adjustment: 74
Effective length of query: 50
Effective length of database: 1,269,480
Effective search space: 63474000
Effective search space used: 63474000
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: 125 (52.8 bits)