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= 0031.0062.p
         (90 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...   100   2e-23
gi|300312982|ref|YP_003777074.1| integration host factor subunit...    59   7e-11
gi|300311300|ref|YP_003775392.1| integration host factor alpha-s...    54   2e-09

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

 Score =  100 bits (250), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 52/90 (57%), Positives = 65/90 (72%)

Query: 1   VNKTELIDHIAKQADISKAASARALEAVISAVKTTLKKNGSVTLVGFGTFSVGKRAARTG 60
           VNK+EL+D IA   +ISKAA+ RAL++VI  +   + K  +V LVGFG+FS GKRAARTG
Sbjct: 22  VNKSELVDVIAADTEISKAAAQRALDSVIENIIKAVTKGDTVQLVGFGSFSTGKRAARTG 81

Query: 61  RNPRTGAAIKIKAAKVPKFKPGKGLKDALN 90
           RNP+TG  IKI AA   KF  GK  K+A+N
Sbjct: 82  RNPQTGEEIKIAAATTVKFSAGKAFKEAVN 111


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

 Score = 58.9 bits (141), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 29/91 (31%), Positives = 54/91 (59%), Gaps = 1/91 (1%)

Query: 1  VNKTELIDHIAKQADISKAASA-RALEAVISAVKTTLKKNGSVTLVGFGTFSVGKRAART 59
          + K+ELI  +A++     A  A  A++ ++ A+   L     + + GFG+F++ +R  R 
Sbjct: 1  MTKSELIARLAERYPQLVAKDADYAVKTILDAMVDALATGQRIEIRGFGSFALNRRPPRI 60

Query: 60 GRNPRTGAAIKIKAAKVPKFKPGKGLKDALN 90
          GRNP++G  + +   +VP FKPGK L++ ++
Sbjct: 61 GRNPKSGDKVMVPEKRVPHFKPGKELRERVD 91


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

 Score = 54.3 bits (129), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 27/90 (30%), Positives = 47/90 (52%)

Query: 1  VNKTELIDHIAKQADISKAASARALEAVISAVKTTLKKNGSVTLVGFGTFSVGKRAARTG 60
          + K EL + + +Q  ++K  +   +E     ++  L++  +V L GFG F +  +  R G
Sbjct: 4  LTKAELAELLFEQVGLNKREAKDMVETFFDEIRNALERGEAVKLSGFGNFQLRDKPQRPG 63

Query: 61 RNPRTGAAIKIKAAKVPKFKPGKGLKDALN 90
          RNP+TG  I I A +V  F   + LK+ + 
Sbjct: 64 RNPKTGEEIPITARRVVTFHASQKLKEMVE 93


  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
   0.313    0.128    0.340 

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: 216,217
Number of extensions: 6060
Number of successful extensions: 28
Number of sequences better than 1.0e-08: 3
Number of HSP's gapped: 28
Number of HSP's successfully gapped: 3
Length of query: 90
Length of database: 1,619,870
Length adjustment: 60
Effective length of query: 30
Effective length of database: 1,335,770
Effective search space: 40073100
Effective search space used: 40073100
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 123 (52.0 bits)