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= 0003.0021.p
         (135 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300312626|ref|YP_003776718.1| GntR family transcription regul...    89   2e-19
gi|300312613|ref|YP_003776705.1| transcription regulator protein...    77   5e-16
gi|300309587|ref|YP_003773679.1| GntR family transcription regul...    69   1e-13

>gi|300312626|ref|YP_003776718.1| GntR family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 256

 Score = 88.6 bits (218), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 52/124 (41%), Positives = 75/124 (60%)

Query: 1   MRARWVIESEVAALAAQNRTDADIDRIYAQLAAMGRNFNDKLANEADDRLFHIRIAEASG 60
           +RAR +IE EVA  AAQ+ +   I  +    A M  N    +     DRLFHIR+AEA+G
Sbjct: 96  IRAREMIEGEVAYAAAQHGSKQQIAAVEEAYALMISNAQAGIDPLEADRLFHIRLAEATG 155

Query: 61  NSVMAQVVTALWDQLRGVLWKKLEEHFHTPQLREASLEEHQKVFDALVARDPVAARDAMR 120
           NSV+  +VT L+D   G L+K+L  HF   ++ + +++EH  V +AL  R+P  AR AMR
Sbjct: 156 NSVLVGLVTQLFDARLGPLFKRLHSHFDGTRVWQEAIDEHALVMEALRQRNPEQARAAMR 215

Query: 121 EHLE 124
            H++
Sbjct: 216 RHMD 219


>gi|300312613|ref|YP_003776705.1| transcription regulator protein
           [Herbaspirillum seropedicae SmR1]
          Length = 239

 Score = 77.0 bits (188), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 51/134 (38%), Positives = 73/134 (54%), Gaps = 6/134 (4%)

Query: 3   ARWVIESEVAALAAQNRTDADIDRIYAQLAAMGRNFNDKLANEADDRLFHIRIAEASGNS 62
           AR +IE+ VAALAA +  DA++DR+   +    R  +D  A  A D  FH  I EA  N 
Sbjct: 103 ARLIIETGVAALAATHIEDAELDRLARNVEDEARLLSDPAAFAAADVEFHEAIIEACNNP 162

Query: 63  VMAQVVTALWDQLRGVLWKKLEE-HFHTPQLREASLEEHQKVFDALVARDPVAARDAMRE 121
            +  +  +L+     +L KK        P   E SL++H+++ DAL ARDP  A +AMR 
Sbjct: 163 FLQSIAGSLY-----MLGKKSRSITSRIPATLERSLQDHRQILDALKARDPQKASEAMRH 217

Query: 122 HLERVMNEFKKAWR 135
           HL RV + ++ A R
Sbjct: 218 HLMRVRDAYRSAGR 231


>gi|300309587|ref|YP_003773679.1| GntR family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 249

 Score = 69.3 bits (168), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 43/124 (34%), Positives = 65/124 (52%)

Query: 1   MRARWVIESEVAALAAQNRTDADIDRIYAQLAAMGRNFNDKLANEADDRLFHIRIAEASG 60
           M AR + E  + AL A      DI  + A    M R      +  A DR FHIRIA  +G
Sbjct: 111 MGARAIFEGAIVALVAPLAKPRDIKALRAIYDTMERECQAGQSPAATDRDFHIRIARMTG 170

Query: 61  NSVMAQVVTALWDQLRGVLWKKLEEHFHTPQLREASLEEHQKVFDALVARDPVAARDAMR 120
           N V+ Q V  L+D+ +  +  KL +H+        +L EH+++ +A+ ARD + A+ AM+
Sbjct: 171 NDVLVQTVARLYDERQDPISAKLLDHYEPEDSWLTALHEHREILEAIEARDAIQAQAAMQ 230

Query: 121 EHLE 124
            HL+
Sbjct: 231 RHLK 234


  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
   0.321    0.130    0.384 

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: 409,784
Number of extensions: 14542
Number of successful extensions: 86
Number of sequences better than 1.0e-08: 5
Number of HSP's gapped: 90
Number of HSP's successfully gapped: 5
Length of query: 135
Length of database: 1,619,870
Length adjustment: 76
Effective length of query: 59
Effective length of database: 1,260,010
Effective search space: 74340590
Effective search space used: 74340590
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)