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= 0001.0883.p
         (127 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300310419|ref|YP_003774511.1| Cro/CI family transcription reg...   119   7e-29
gi|300312342|ref|YP_003776434.1| XRE family transcription regula...    82   1e-17
gi|300312341|ref|YP_003776433.1| XRE family transcription regula...    78   2e-16

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

 Score =  119 bits (298), Expect = 7e-29,   Method: Compositional matrix adjust.
 Identities = 59/111 (53%), Positives = 72/111 (64%), Gaps = 1/111 (0%)

Query: 1   MNSDKLAIGQRIRLIRLKMGISQRLFARALETAPNHICQIERGRCVPGSKLLHGMRAQFG 60
           MN+ K A+GQRI+  RL +G SQR FA  L T PNHICQIE+GRC+PGS+LLHGM  QF 
Sbjct: 17  MNASKKAVGQRIKRARLAIGFSQRKFATVLGTLPNHICQIEQGRCMPGSRLLHGMHVQFN 76

Query: 61  IDLNWLLSGQS-ALTTTLLKREIKTLVADYQRADTDGKALLMYTASFLVEG 110
           ID+NWLL+GQ         +  ++ L+  Y RAD  GK LL   A  L  G
Sbjct: 77  IDINWLLTGQHQPFRLNSQEMGLRMLLHHYTRADETGKHLLCSAACLLATG 127


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

 Score = 82.4 bits (202), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 40/108 (37%), Positives = 66/108 (61%)

Query: 1   MNSDKLAIGQRIRLIRLKMGISQRLFARALETAPNHICQIERGRCVPGSKLLHGMRAQFG 60
           M   K AIG+R++ +RL  G++QR FA  L+T+  +I  +E G  +PG + L  +  +F 
Sbjct: 13  MRISKDAIGERLKSVRLLAGMNQRDFAARLKTSGAYISCVELGHSMPGGRFLRSLHHEFD 72

Query: 61  IDLNWLLSGQSALTTTLLKREIKTLVADYQRADTDGKALLMYTASFLV 108
           +++NWLL+GQ           +++LV+DY  A   G++L+M  AS+LV
Sbjct: 73  VNVNWLLTGQEPSLPPRYGLHVRSLVSDYGGASQAGRSLIMAVASYLV 120


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

 Score = 78.2 bits (191), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 41/108 (37%), Positives = 64/108 (59%), Gaps = 3/108 (2%)

Query: 8   IGQRIRLIRLKMGISQRLFARALETAPNHICQIERGRCVPGSKLLHGMRAQFGIDLNWLL 67
           IG RI+ +RL  G+SQR   + L+T+  HI  +E G+ +PG +LL  +  +F +DLNWLL
Sbjct: 6   IGGRIKEVRLANGLSQRELGQRLDTSTGHISWLEAGKAMPGGELLLQLHREFSVDLNWLL 65

Query: 68  SGQSALTTTL-LKREIKTLVADYQRADTDGKALLMYTASFLVEGREAR 114
           +G+      +    E++ LV  Y R D  G+ +L   AS++  GRE +
Sbjct: 66  TGEEGEPGVMETDEEVRQLVDHYCRVDLQGREILRSLASYV--GREKK 111


  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    0.135    0.385 

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: 358,743
Number of extensions: 12479
Number of successful extensions: 33
Number of sequences better than 1.0e-08: 3
Number of HSP's gapped: 32
Number of HSP's successfully gapped: 3
Length of query: 127
Length of database: 1,619,870
Length adjustment: 75
Effective length of query: 52
Effective length of database: 1,264,745
Effective search space: 65766740
Effective search space used: 65766740
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 (22.0 bits)
S2: 125 (52.8 bits)