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= 0001.2617.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...    96   4e-22
gi|300311300|ref|YP_003775392.1| integration host factor alpha-s...    59   7e-11
gi|300312982|ref|YP_003777074.1| integration host factor subunit...    56   6e-10

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

 Score = 96.3 bits (238), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 51/89 (57%), Positives = 62/89 (69%)

Query: 1   VNKGELVEHIAGAADISKVAAGRAVDAFIGAVTTTLKKNGTVTLVGFGTFAVGKRAARAG 60
           VNK ELV+ IA   +ISK AA RA+D+ I  +   + K  TV LVGFG+F+ GKRAAR G
Sbjct: 22  VNKSELVDVIAADTEISKAAAQRALDSVIENIIKAVTKGDTVQLVGFGSFSTGKRAARTG 81

Query: 61  RNPQTGAAIKIKASKVPKFKAGKALKDAI 89
           RNPQTG  IKI A+   KF AGKA K+A+
Sbjct: 82  RNPQTGEEIKIAAATTVKFSAGKAFKEAV 110


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

 Score = 58.9 bits (141), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 30/90 (33%), Positives = 46/90 (51%)

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

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


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

 Score = 55.8 bits (133), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 28/90 (31%), Positives = 47/90 (52%), Gaps = 1/90 (1%)

Query: 1  VNKGELVEHIAG-AADISKVAAGRAVDAFIGAVTTTLKKNGTVTLVGFGTFAVGKRAARA 59
          + K EL+  +A     +    A  AV   + A+   L     + + GFG+FA+ +R  R 
Sbjct: 1  MTKSELIARLAERYPQLVAKDADYAVKTILDAMVDALATGQRIEIRGFGSFALNRRPPRI 60

Query: 60 GRNPQTGAAIKIKASKVPKFKAGKALKDAI 89
          GRNP++G  + +   +VP FK GK L++ +
Sbjct: 61 GRNPKSGDKVMVPEKRVPHFKPGKELRERV 90


  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
   0.315    0.131    0.353 

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: 259,165
Number of extensions: 9118
Number of successful extensions: 44
Number of sequences better than 1.0e-08: 3
Number of HSP's gapped: 44
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 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 123 (52.0 bits)