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= 0001.3005.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...   174   2e-45
gi|300312341|ref|YP_003776433.1| XRE family transcription regula...    85   1e-18
gi|300310419|ref|YP_003774511.1| Cro/CI family transcription reg...    82   1e-17

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

 Score =  174 bits (441), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 81/123 (65%), Positives = 97/123 (78%)

Query: 1   MNDTIAPASAAASDFGKQAIGERLKGVRMMSGLNQRDFAARLGTSGAYISCVELGHSMPG 60
           M   I  +  +     K AIGERLK VR+++G+NQRDFAARL TSGAYISCVELGHSMPG
Sbjct: 1   MGKHIGKSDTSGMRISKDAIGERLKSVRLLAGMNQRDFAARLKTSGAYISCVELGHSMPG 60

Query: 61  GRFLRTLHREFDVNINWLLTGLQAELPPRHGFHVKVLIGDYVRASERGKSLVMAVASFLV 120
           GRFLR+LH EFDVN+NWLLTG +  LPPR+G HV+ L+ DY  AS+ G+SL+MAVAS+LV
Sbjct: 61  GRFLRSLHHEFDVNVNWLLTGQEPSLPPRYGLHVRSLVSDYGGASQAGRSLIMAVASYLV 120

Query: 121 AQG 123
            QG
Sbjct: 121 GQG 123


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

 Score = 85.1 bits (209), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 44/105 (41%), Positives = 66/105 (62%), Gaps = 5/105 (4%)

Query: 18  QAIGERLKGVRMMSGLNQRDFAARLGTSGAYISCVELGHSMPGGRFLRTLHREFDVNINW 77
           + IG R+K VR+ +GL+QR+   RL TS  +IS +E G +MPGG  L  LHREF V++NW
Sbjct: 4   EEIGGRIKEVRLANGLSQRELGQRLDTSTGHISWLEAGKAMPGGELLLQLHREFSVDLNW 63

Query: 78  LLTGLQAELPP---RHGFHVKVLIGDYVRASERGKSLVMAVASFL 119
           LLTG + E  P        V+ L+  Y R   +G+ ++ ++AS++
Sbjct: 64  LLTGEEGE--PGVMETDEEVRQLVDHYCRVDLQGREILRSLASYV 106


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

 Score = 82.4 bits (202), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 45/117 (38%), Positives = 65/117 (55%), Gaps = 5/117 (4%)

Query: 8   ASAAASDFGKQAIGERLKGVRMMSGLNQRDFAARLGTSGAYISCVELGHSMPGGRFLRTL 67
            S  A +  K+A+G+R+K  R+  G +QR FA  LGT   +I  +E G  MPG R L  +
Sbjct: 12  TSQPAMNASKKAVGQRIKRARLAIGFSQRKFATVLGTLPNHICQIEQGRCMPGSRLLHGM 71

Query: 68  HREFDVNINWLLTGLQAELPPR---HGFHVKVLIGDYVRASERGKSLVMAVASFLVA 121
           H +F+++INWLLTG     P R       +++L+  Y RA E GK L+ + A  L  
Sbjct: 72  HVQFNIDINWLLTGQHQ--PFRLNSQEMGLRMLLHHYTRADETGKHLLCSAACLLAT 126


  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
   0.322    0.137    0.405 

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: 405,570
Number of extensions: 15825
Number of successful extensions: 49
Number of sequences better than 1.0e-08: 3
Number of HSP's gapped: 48
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 (21.9 bits)
S2: 125 (52.8 bits)