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= 0028.0007.p
         (309 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300311238|ref|YP_003775330.1| LacI family transcription regul...   127   1e-30
gi|300310488|ref|YP_003774580.1| LacI family transcription regul...   117   1e-27
gi|300310423|ref|YP_003774515.1| GntR family transcription regul...   100   1e-22

>gi|300311238|ref|YP_003775330.1| LacI family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 340

 Score =  127 bits (318), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 68/176 (38%), Positives = 100/176 (56%), Gaps = 10/176 (5%)

Query: 1   VSLYLRNPEAVSPRLSPRIKRAIDTLGYVPNKLAGSLAARRDRALAGQRLLHRXIGVIVP 60
           VS  + +PE VSP    R++  I ++GY+PN LAG LA+RR R +A           IVP
Sbjct: 31  VSRVINSPEKVSPATRERVEAFIASMGYIPNLLAGGLASRRTRIVAA----------IVP 80

Query: 61  SLANAFFTDTVAALQKEFDRHDYQLLLGATEYDLERETELVRTFLSWSPTALVVTGCCHN 120
           +++++ F +T+  L ++     YQLLLG T Y  E ET LV  F+      LV+TG  H+
Sbjct: 81  TISHSIFAETLRGLSEQLCMQGYQLLLGQTNYSEEAETGLVEVFIGRRVDGLVLTGVQHS 140

Query: 121 EATRTLLRMADTPVAEMWEIGEEPFHLQVGFSHVAVGEVLAAHLHQQGATRIAFVG 176
             TR  L+ A  PV E W++ + P  +  GF + A G  +  +L+Q+G  R+AFVG
Sbjct: 141 PMTRQRLKAAGIPVVETWDLTDTPIDMLAGFDNHAAGRAMGDYLYQKGYRRMAFVG 196


>gi|300310488|ref|YP_003774580.1| LacI family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 365

 Score =  117 bits (293), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 61/180 (33%), Positives = 97/180 (53%), Gaps = 10/180 (5%)

Query: 5   LRNPEAVSPRLSPRIKRAIDTLGYVPNKLAGSLAARRDRALAGQRLLHRXIGVIVPSLAN 64
           L  P AVSP++  +++ A++  GYVPN LAG LA+ + R +A          V+VP++  
Sbjct: 56  LNTPSAVSPKVLQKVREAVEKTGYVPNLLAGGLASNKSRLVA----------VVVPTVIG 105

Query: 65  AFFTDTVAALQKEFDRHDYQLLLGATEYDLERETELVRTFLSWSPTALVVTGCCHNEATR 124
             F + V  L +      YQ++LG + Y+  RE  L+   +   P  +V+TG   +   R
Sbjct: 106 PVFQEIVHTLTETLAAAGYQVMLGQSGYENSREDALLEAIIGRRPDGVVLTGIMRSAEAR 165

Query: 125 TLLRMADTPVAEMWEIGEEPFHLQVGFSHVAVGEVLAAHLHQQGATRIAFVGARMQADRR 184
             L  +  PV E W++   P  + VGFSH A+G  +A +LHQ+G  ++A VG R +  +R
Sbjct: 166 KRLLASGIPVVETWDLTPTPIDMLVGFSHEAIGREVARYLHQRGRKKVAVVGGRDERSQR 225


>gi|300310423|ref|YP_003774515.1| GntR family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 352

 Score =  100 bits (250), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 59/179 (32%), Positives = 94/179 (52%), Gaps = 10/179 (5%)

Query: 1   VSLYLRNPEAVSPRLSPRIKRAIDTLGYVPNKLAGSLAARRDRALAGQRLLHRXIGVIVP 60
           VS  L+ P  V  +   RI  AID LGYVPN+ A +LA+ R + +A          V+VP
Sbjct: 42  VSRALKTPALVQEQSRQRILEAIDKLGYVPNQAAATLASARSQVVA----------VLVP 91

Query: 61  SLANAFFTDTVAALQKEFDRHDYQLLLGATEYDLERETELVRTFLSWSPTALVVTGCCHN 120
           SL NA F +T++ ++       YQ L+G T YD  +E EL+ T+L+ +P   +++    +
Sbjct: 92  SLTNAVFIETLSGIRDYLASVGYQFLIGETGYDRHKEEELIATYLAHAPAGFLLSSSQQH 151

Query: 121 EATRTLLRMADTPVAEMWEIGEEPFHLQVGFSHVAVGEVLAAHLHQQGATRIAFVGARM 179
           +  ++       P   M+++G       VGFS    G  +A HL ++G  R AF+ A++
Sbjct: 152 DILQSRPASRAIPAVRMFDLGRSQQDYSVGFSQTRAGHAVARHLAERGYRRPAFLAAQL 210


  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
   0.325    0.136    0.413 

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: 655,605
Number of extensions: 22994
Number of successful extensions: 107
Number of sequences better than 1.0e-08: 4
Number of HSP's gapped: 105
Number of HSP's successfully gapped: 4
Length of query: 309
Length of database: 1,619,870
Length adjustment: 85
Effective length of query: 224
Effective length of database: 1,217,395
Effective search space: 272696480
Effective search space used: 272696480
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 130 (54.7 bits)