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= 0101.0003.p
         (94 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300309668|ref|YP_003773760.1| HU histone family DNA-binding p...   178   7e-47
gi|300311300|ref|YP_003775392.1| integration host factor alpha-s...    65   1e-12
gi|300312982|ref|YP_003777074.1| integration host factor subunit...    59   1e-10

>gi|300309668|ref|YP_003773760.1| HU histone family DNA-binding
           protein [Herbaspirillum seropedicae SmR1]
          Length = 115

 Score =  178 bits (452), Expect = 7e-47,   Method: Compositional matrix adjust.
 Identities = 91/94 (96%), Positives = 93/94 (98%)

Query: 1   VNKSELVDAIAADTEISKAAAQRALDSVVENIIKAVTKGDTVQLVGFGSFSTGKRAARTG 60
           VNKSELVD IAADTEISKAAAQRALDSV+ENIIKAVTKGDTVQLVGFGSFSTGKRAARTG
Sbjct: 22  VNKSELVDVIAADTEISKAAAQRALDSVIENIIKAVTKGDTVQLVGFGSFSTGKRAARTG 81

Query: 61  RNPQTGEEIKIAAATTVKFSAGKSFKEAVNKKKK 94
           RNPQTGEEIKIAAATTVKFSAGK+FKEAVNKKKK
Sbjct: 82  RNPQTGEEIKIAAATTVKFSAGKAFKEAVNKKKK 115


>gi|300311300|ref|YP_003775392.1| integration host factor
          alpha-subunit [Herbaspirillum seropedicae SmR1]
          Length = 104

 Score = 65.1 bits (157), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 32/89 (35%), Positives = 51/89 (57%)

Query: 1  VNKSELVDAIAADTEISKAAAQRALDSVVENIIKAVTKGDTVQLVGFGSFSTGKRAARTG 60
          + K+EL + +     ++K  A+  +++  + I  A+ +G+ V+L GFG+F    +  R G
Sbjct: 4  LTKAELAELLFEQVGLNKREAKDMVETFFDEIRNALERGEAVKLSGFGNFQLRDKPQRPG 63

Query: 61 RNPQTGEEIKIAAATTVKFSAGKSFKEAV 89
          RNP+TGEEI I A   V F A +  KE V
Sbjct: 64 RNPKTGEEIPITARRVVTFHASQKLKEMV 92


>gi|300312982|ref|YP_003777074.1| integration host factor subunit
          beta [Herbaspirillum seropedicae SmR1]
          Length = 101

 Score = 58.5 bits (140), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 26/91 (28%), Positives = 52/91 (57%), Gaps = 1/91 (1%)

Query: 1  VNKSELVDAIAAD-TEISKAAAQRALDSVVENIIKAVTKGDTVQLVGFGSFSTGKRAART 59
          + KSEL+  +A    ++    A  A+ ++++ ++ A+  G  +++ GFGSF+  +R  R 
Sbjct: 1  MTKSELIARLAERYPQLVAKDADYAVKTILDAMVDALATGQRIEIRGFGSFALNRRPPRI 60

Query: 60 GRNPQTGEEIKIAAATTVKFSAGKSFKEAVN 90
          GRNP++G+++ +       F  GK  +E V+
Sbjct: 61 GRNPKSGDKVMVPEKRVPHFKPGKELRERVD 91


  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
   0.308    0.123    0.310 

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: 230,850
Number of extensions: 7415
Number of successful extensions: 34
Number of sequences better than 1.0e-08: 3
Number of HSP's gapped: 34
Number of HSP's successfully gapped: 3
Length of query: 94
Length of database: 1,619,870
Length adjustment: 63
Effective length of query: 31
Effective length of database: 1,321,565
Effective search space: 40968515
Effective search space used: 40968515
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 123 (52.0 bits)