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= 0001.0479.p
         (209 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300309825|ref|YP_003773917.1| TetR family transcription regul...   352   2e-98
gi|300310688|ref|YP_003774780.1| transcription regulator protein...    65   3e-12
gi|300311794|ref|YP_003775886.1| TetR family transcription regul...    54   7e-09

>gi|300309825|ref|YP_003773917.1| TetR family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 209

 Score =  352 bits (902), Expect = 2e-98,   Method: Compositional matrix adjust.
 Identities = 168/209 (80%), Positives = 190/209 (90%)

Query: 1   MSALAKEPRWERRKQDRPQELLAAALELFVERGYAATRLEDVASRAGVSKGTLYLYFDGK 60
           MSA AKEPRWERRKQDRPQELLAAAL+LFVERGYAATRLEDVA++AGVSKGTLYLYFD K
Sbjct: 1   MSASAKEPRWERRKQDRPQELLAAALQLFVERGYAATRLEDVAAQAGVSKGTLYLYFDSK 60

Query: 61  ESLFKSVVRTNMLPLLDQAEARIEGHAGSSAELLRDLLMHWWQAASHSGVMGIAKLMVAE 120
           ESLFKSVVR +MLPLLD+AEAR++ H G +A+LLR+L++ WWQ AS SG+ GIAKLM+AE
Sbjct: 61  ESLFKSVVRAHMLPLLDEAEARVDSHDGHTADLLRELILGWWQGASRSGLKGIAKLMLAE 120

Query: 121 SGNFPELARFYHEEITVRGDATMVRVLERGMARGEFRRVDVDVMKKVIVAPIVMLMLWDQ 180
           SGNFPELARFYHEEIT RGDAT+VRVLERGMARGEFR +D   +KKVI API+MLMLWDQ
Sbjct: 121 SGNFPELARFYHEEITSRGDATLVRVLERGMARGEFRPLDAHALKKVIAAPIMMLMLWDQ 180

Query: 181 SLAPCAVAPIDPLAYLDNMIDLCLHGLKA 209
           SLAPCA+APID  AYL ++IDLC+HGLKA
Sbjct: 181 SLAPCAIAPIDSAAYLASLIDLCVHGLKA 209


>gi|300310688|ref|YP_003774780.1| transcription regulator protein
           [Herbaspirillum seropedicae SmR1]
          Length = 201

 Score = 65.5 bits (158), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 46/148 (31%), Positives = 73/148 (49%), Gaps = 7/148 (4%)

Query: 16  DRPQELLAAALELFVERGYAATRLEDVASRAGVSKGTLYLYFDGKESLFKSVVRTNMLPL 75
           +R   +LAAA E+F+E G+    +  +++R G SKGTLY YF  KE LF +V        
Sbjct: 7   ERRDAILAAAAEVFLEEGFEGASMAGISARIGGSKGTLYSYFKSKEELFVAVTHEQAKKQ 66

Query: 76  LDQAEARIEGHAGSSAELLRDLLMHWWQAAS---HSGVMGIAKLMVAESGNFPELARFYH 132
           ++ A A +E   G   +L + L +   +A S       +   +++VAESG   ++ R +H
Sbjct: 67  MEPALAALEKDTG---DLQKTLQVFGEKAVSFLCQESTLQTHRMIVAESGR-SDIGRRFH 122

Query: 133 EEITVRGDATMVRVLERGMARGEFRRVD 160
           E     G   +   L R M  G  ++ D
Sbjct: 123 ESGPKLGMERIAAFLSRQMQAGRLKQAD 150


>gi|300311794|ref|YP_003775886.1| TetR family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 239

 Score = 54.3 bits (129), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 52/175 (29%), Positives = 84/175 (48%), Gaps = 18/175 (10%)

Query: 12  RRKQDRPQELLAAALELFVERGYAATRLEDVASRAGVSKGTLYLYFDGKESL-FKSVVRT 70
           RR       +L A   +  E G+    LE VA+RAGV K T+Y ++  K +L  ++++R 
Sbjct: 50  RRNAVSHDAILDATYVMLEEIGFDKLSLEGVAARAGVGKATIYRWWPNKSALAMEALLRA 109

Query: 71  --NMLPLLDQAEAR--IEGHAGSSAELLRDLLMHWWQAASHSGVMGIAKLMVAESGNFPE 126
              M P+ D   +R  IE H    ++LLR            SG   + + M+A +   PE
Sbjct: 110 VEPMPPIGDSGSSRTDIELHMLQLSQLLR----------GKSG--RVVREMIALAQFEPE 157

Query: 127 LARFYHEEITVRGDATMVRVLERGMARGEFRR-VDVDVMKKVIVAPIVMLMLWDQ 180
             R +++         +V VL RG  RGEFR   D+ ++  ++ AP++  +L  Q
Sbjct: 158 SKRIFNDNYLEPRRLALVSVLRRGAQRGEFREDADLSLVFDLLYAPLLQRLLTGQ 212


  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    0.136    0.401 

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: 589,910
Number of extensions: 22335
Number of successful extensions: 82
Number of sequences better than 1.0e-08: 4
Number of HSP's gapped: 86
Number of HSP's successfully gapped: 4
Length of query: 209
Length of database: 1,619,870
Length adjustment: 81
Effective length of query: 128
Effective length of database: 1,236,335
Effective search space: 158250880
Effective search space used: 158250880
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: 128 (53.9 bits)