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= 0001.3004.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...   177   2e-46
gi|300312342|ref|YP_003776434.1| XRE family transcription regula...    97   4e-22
gi|300310419|ref|YP_003774511.1| Cro/CI family transcription reg...    76   7e-16

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

 Score =  177 bits (448), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 84/111 (75%), Positives = 96/111 (86%)

Query: 1   MFSEEIGSRIREIRLSNGLSQRELGQRLQTSTGHISWLEAGKAMPGGELLLQLHREFAVD 60
           MFSEEIG RI+E+RL+NGLSQRELGQRL TSTGHISWLEAGKAMPGGELLLQLHREF+VD
Sbjct: 1   MFSEEIGGRIKEVRLANGLSQRELGQRLDTSTGHISWLEAGKAMPGGELLLQLHREFSVD 60

Query: 61  INWLLTGSEPESVPPEGEPDVRRLVDHYCRADMQAREIIRTLASYAGRTRS 111
           +NWLLTG E E    E + +VR+LVDHYCR D+Q REI+R+LASY GR + 
Sbjct: 61  LNWLLTGEEGEPGVMETDEEVRQLVDHYCRVDLQGREILRSLASYVGREKK 111


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

 Score = 96.7 bits (239), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 48/102 (47%), Positives = 64/102 (62%), Gaps = 1/102 (0%)

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

Query: 64  LLTGSEPESVPPEGEPDVRRLVDHYCRADMQAREIIRTLASY 105
           LLTG EP S+PP     VR LV  Y  A    R +I  +ASY
Sbjct: 78  LLTGQEP-SLPPRYGLHVRSLVSDYGGASQAGRSLIMAVASY 118


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

 Score = 75.9 bits (185), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 39/101 (38%), Positives = 55/101 (54%)

Query: 4   EEIGSRIREIRLSNGLSQRELGQRLQTSTGHISWLEAGKAMPGGELLLQLHREFAVDINW 63
           + +G RI+  RL+ G SQR+    L T   HI  +E G+ MPG  LL  +H +F +DINW
Sbjct: 22  KAVGQRIKRARLAIGFSQRKFATVLGTLPNHICQIEQGRCMPGSRLLHGMHVQFNIDINW 81

Query: 64  LLTGSEPESVPPEGEPDVRRLVDHYCRADMQAREIIRTLAS 104
           LLTG          E  +R L+ HY RAD   + ++ + 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    0.135    0.396 

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: 313,370
Number of extensions: 9980
Number of successful extensions: 35
Number of sequences better than 1.0e-08: 3
Number of HSP's gapped: 35
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)