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= 0002.0731.p
         (210 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300313616|ref|YP_003777708.1| TetR family transcription regul...   258   2e-70
gi|300311331|ref|YP_003775423.1| transcription regulator protein...    92   4e-20

>gi|300313616|ref|YP_003777708.1| TetR family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 210

 Score =  258 bits (660), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 123/210 (58%), Positives = 160/210 (76%), Gaps = 6/210 (2%)

Query: 1   MQQTRGRPRSFDRDEALRLAMQVFWNKGYEGTTMADLTAAIGVKAPSLYAAFGDKNALFR 60
           M +TRGRPRSFDRD+AL+ AMQVFW+KGYEGTTMADLT AIGVKAPSLYAAFGDK+ALFR
Sbjct: 1   MIRTRGRPRSFDRDQALQQAMQVFWSKGYEGTTMADLTEAIGVKAPSLYAAFGDKDALFR 60

Query: 61  EAIDFYSATTAIGPINALKEGKGMREDLHNMLQASVALYADPAN------GKGCMVVVSA 114
           E ++ Y+ T +  P+  L+ GKG+REDL  ML+ASV +Y+  +       GKGCMVV+SA
Sbjct: 61  EVVEVYARTVSAEPLRLLQAGKGIREDLQAMLRASVRMYSGKSTVPGLPAGKGCMVVISA 120

Query: 115 INCAPENAAHAEEMTVRRQKKRQELAKRFRKAQEQNELSADADIDGLADFYTAVLHGLSL 174
           INCAPEN+ H++ ++ RR K+R E+  R  +AQ + E+ ADAD+  L DFYT+ L+GL+L
Sbjct: 121 INCAPENSEHSDALSQRRHKRRNEIRARLLQAQREGEIRADADVTALGDFYTSFLNGLAL 180

Query: 175 SARDGVSCERLANTICHAMKALDAVLIAPK 204
            A+DGVS  RLA T+  AM  L++VL+  +
Sbjct: 181 GAKDGVSSARLAATLGPAMLPLESVLLGAR 210


>gi|300311331|ref|YP_003775423.1| transcription regulator protein
           [Herbaspirillum seropedicae SmR1]
          Length = 223

 Score = 91.7 bits (226), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 62/196 (31%), Positives = 98/196 (50%), Gaps = 8/196 (4%)

Query: 6   GRPRSFDRDEALRLAMQVFWNKGYEGTTMADLTAAIGVKAPSLYAAFGDKNALFREAIDF 65
           GRPR FD D+AL  A++VF  +GY G +++DL+ A+ +   SLY AF DK +LF  A++ 
Sbjct: 32  GRPREFDADQALDGAVRVFSERGYAGASISDLSEAMQLAQGSLYKAFRDKQSLFLAALER 91

Query: 66  YSATTAIGPINALKEGKGMREDLHNMLQASVALYADPANG----KGCMVVVSAINCAPEN 121
           Y    +     A+  G   RE L NML      YA+ A G    +GC+VV SA+      
Sbjct: 92  YRTQRSEKLRRAIDAGATGRERLRNML----LFYAESAQGAAGRQGCLVVSSAVAITGFE 147

Query: 122 AAHAEEMTVRRQKKRQELAKRFRKAQEQNELSADADIDGLADFYTAVLHGLSLSARDGVS 181
            + A ++     +    L +  R+ Q+   ++A AD    A     +  G+ +  + G S
Sbjct: 148 PSVATQIASTLARNEALLGELIRQGQQDGSVAAHADPPSTARLLLCLTQGMRVVGKAGRS 207

Query: 182 CERLANTICHAMKALD 197
            + +   +  A+K LD
Sbjct: 208 RKEMLALVEVALKVLD 223


  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
   0.319    0.130    0.372 

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: 596,793
Number of extensions: 22179
Number of successful extensions: 88
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 87
Number of HSP's successfully gapped: 2
Length of query: 210
Length of database: 1,619,870
Length adjustment: 81
Effective length of query: 129
Effective length of database: 1,236,335
Effective search space: 159487215
Effective search space used: 159487215
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 (21.8 bits)
S2: 128 (53.9 bits)