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= 0004.0057.p
         (111 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300312341|ref|YP_003776433.1| XRE family transcription regula...   181   2e-47
gi|300312342|ref|YP_003776434.1| XRE family transcription regula...    90   4e-20
gi|300310419|ref|YP_003774511.1| Cro/CI family transcription reg...    79   1e-16

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

 Score =  181 bits (458), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 87/108 (80%), Positives = 98/108 (90%)

Query: 1   MFSEEIGGRIKEIRLAHGLSQRELGQRLNTSTGHISWLEAGKAMPGGELLLQLYREFAVD 60
           MFSEEIGGRIKE+RLA+GLSQRELGQRL+TSTGHISWLEAGKAMPGGELLLQL+REF+VD
Sbjct: 1   MFSEEIGGRIKEVRLANGLSQRELGQRLDTSTGHISWLEAGKAMPGGELLLQLHREFSVD 60

Query: 61  LNWLLTGSEPDVLPQESDSDVRLLVDHYCRTDVQGREIIRTLASYAGR 108
           LNWLLTG E +    E+D +VR LVDHYCR D+QGREI+R+LASY GR
Sbjct: 61  LNWLLTGEEGEPGVMETDEEVRQLVDHYCRVDLQGREILRSLASYVGR 108


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

 Score = 89.7 bits (221), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 47/102 (46%), Positives = 61/102 (59%), Gaps = 1/102 (0%)

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

Query: 64  LLTGSEPDVLPQESDSDVRLLVDHYCRTDVQGREIIRTLASY 105
           LLTG EP  LP      VR LV  Y      GR +I  +ASY
Sbjct: 78  LLTGQEPS-LPPRYGLHVRSLVSDYGGASQAGRSLIMAVASY 118


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

 Score = 78.6 bits (192), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 38/101 (37%), Positives = 56/101 (55%)

Query: 4   EEIGGRIKEIRLAHGLSQRELGQRLNTSTGHISWLEAGKAMPGGELLLQLYREFAVDLNW 63
           + +G RIK  RLA G SQR+    L T   HI  +E G+ MPG  LL  ++ +F +D+NW
Sbjct: 22  KAVGQRIKRARLAIGFSQRKFATVLGTLPNHICQIEQGRCMPGSRLLHGMHVQFNIDINW 81

Query: 64  LLTGSEPDVLPQESDSDVRLLVDHYCRTDVQGREIIRTLAS 104
           LLTG          +  +R+L+ HY R D  G+ ++ + A 
Sbjct: 82  LLTGQHQPFRLNSQEMGLRMLLHHYTRADETGKHLLCSAAC 122


  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
   0.318    0.136    0.400 

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: 383,032
Number of extensions: 15281
Number of successful extensions: 52
Number of sequences better than 1.0e-08: 3
Number of HSP's gapped: 51
Number of HSP's successfully gapped: 3
Length of query: 111
Length of database: 1,619,870
Length adjustment: 73
Effective length of query: 38
Effective length of database: 1,274,215
Effective search space: 48420170
Effective search space used: 48420170
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 124 (52.4 bits)