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= 0012.0165.p
         (258 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300313239|ref|YP_003777331.1| transcription regulator protein...   112   3e-26
gi|300311600|ref|YP_003775692.1| transcription regulator protein...    64   2e-11

>gi|300313239|ref|YP_003777331.1| transcription regulator protein
           [Herbaspirillum seropedicae SmR1]
          Length = 244

 Score =  112 bits (280), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 73/213 (34%), Positives = 115/213 (53%), Gaps = 7/213 (3%)

Query: 5   RSLSVLRLFTLETPAWTVEQIARTLEVSMSTAYRYVLALEEVGLVASSGGGYYILGPAIL 64
           R L VL LF    P   +E I   L  + ++AYRYV  L   GL+     GY + GP ++
Sbjct: 6   RMLEVLTLFKPSQPVIDIELICAQLGYTPASAYRYVRELGNAGLLVKMPRGYAV-GPKVI 64

Query: 65  QLDRQIQLTDPLLLSARPVMNRLAGYAPDGSVVLLCRAFADTVLCIHQVHTRGPQSLISY 124
           +LDR +   DPLL ++R ++  L   A  G  +L+   +  TV+ I Q  +    + +++
Sbjct: 65  ELDRHMTQFDPLLSASRDIVGDLV--AQTGLELLISELYGSTVITILQ-ESGSNDARLNF 121

Query: 125 ERGRPMPLLRGATSRIILAHEPTRRLKRLYE-RHQEELRSSGMADSWEQFRSQQSQLRKT 183
            RG PM L   AT+R+ILA+   R+L++ ++    EELR  G   +W  F     ++RK 
Sbjct: 122 GRGTPMDLFHSATARVILAYLLPRQLRKHFDGASAEELRLVG--SNWRDFSKVMLKIRKD 179

Query: 184 GYAVSFGEIDPDRIGIAVALLGEARQPIGSLSF 216
           GY VS GE+D  + GIA  +  E ++ +GS++ 
Sbjct: 180 GYCVSEGELDAGKTGIAAPIFDEKQRILGSITL 212


>gi|300311600|ref|YP_003775692.1| transcription regulator protein
           [Herbaspirillum seropedicae SmR1]
          Length = 292

 Score = 63.5 bits (153), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 59/221 (26%), Positives = 108/221 (48%), Gaps = 15/221 (6%)

Query: 3   TDRSLSVLRLFTLETPAWTVEQIARTLEVSMSTAYRYVLALEEVGLVASS-GGGYYILGP 61
            DR L VL          + +QIA  ++  +ST YR++ +L++ GL+      G +  GP
Sbjct: 57  VDRVLHVLAGVARAGKPVSAKQIAAMVQQPVSTVYRHLASLKKWGLLQEHMNSGTFEPGP 116

Query: 62  AILQLDRQIQLTDPLLLSARPVMNRLAGYAPDGSVVLLCRAFADTVLCIHQVHTRGPQSL 121
             +QL         L+  +R  ++ L   +  G  V L  A    ++CI    +  P   
Sbjct: 117 TGVQLAWGFDQNSNLVSQSREEISSLVQRS--GESVGLLVAINGQMVCIAMEESDQPLR- 173

Query: 122 ISYERGRPMPLLRGATSRIILAHEPTRRLKRLYERHQEELRSSGMADSWEQFRSQQSQL- 180
            S+ +GR  PLL+GA+++ +LA  P R+L       Q++L +  + D  E+  + ++QL 
Sbjct: 174 CSFTKGRAHPLLKGASAKSLLAFMP-RKL-------QQKLLTDQLGDKPEELAALETQLE 225

Query: 181 --RKTGYAVSFGEIDPDRIGIAVALLGEARQPIGSLSFVLP 219
             R+ GY +S  E+D    G++V ++    +  G+++ + P
Sbjct: 226 EIRRRGYCISESEVDLGVWGVSVPIMTSNGRLEGTITLMAP 266


  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
   0.320    0.135    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: 840,930
Number of extensions: 36145
Number of successful extensions: 140
Number of sequences better than 1.0e-08: 3
Number of HSP's gapped: 138
Number of HSP's successfully gapped: 3
Length of query: 258
Length of database: 1,619,870
Length adjustment: 83
Effective length of query: 175
Effective length of database: 1,226,865
Effective search space: 214701375
Effective search space used: 214701375
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: 129 (54.3 bits)