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/690/690 
           3295 sequences; 1,000,347 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|134094955|ref|YP_001100030.1| DNA-binding protein HU-beta [He...   139   4e-35
gi|134095000|ref|YP_001100075.1| integration host factor subunit...    57   1e-10
gi|134095741|ref|YP_001100816.1| integration host factor subunit...    55   6e-10

>gi|134094955|ref|YP_001100030.1| DNA-binding protein HU-beta
          [Herminiimonas arsenicoxydans]
          Length = 90

 Score =  139 bits (349), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 71/89 (79%), Positives = 80/89 (89%)

Query: 1  VNKGELVEHIAGAADISKVAAGRAVDAFIGAVTTTLKKNGTVTLVGFGTFAVGKRAARAG 60
          +NK EL++HIAG+ADISK AA RA+DA I AV TTLKKNGTVTLVGFGTF+VGKRAAR G
Sbjct: 1  MNKTELIDHIAGSADISKAAATRALDAVIVAVKTTLKKNGTVTLVGFGTFSVGKRAARTG 60

Query: 61 RNPQTGAAIKIKASKVPKFKAGKALKDAI 89
          RNP+TG AIKIKA+KVPKFK GKALKDA+
Sbjct: 61 RNPRTGEAIKIKAAKVPKFKPGKALKDAV 89


>gi|134095000|ref|YP_001100075.1| integration host factor subunit
           alpha [Herminiimonas arsenicoxydans]
          Length = 151

 Score = 57.4 bits (137), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 30/90 (33%), Positives = 45/90 (50%)

Query: 1   VNKGELVEHIAGAADISKVAAGRAVDAFIGAVTTTLKKNGTVTLVGFGTFAVGKRAARAG 60
           + K EL E +     ++K  A   V+ F   +   L++   V L GFG F +  +  R G
Sbjct: 51  LTKAELAELLFEQVGLNKREAKDMVETFFDEIRNALERGEAVKLSGFGNFQLRDKPQRPG 110

Query: 61  RNPQTGAAIKIKASKVPKFKAGKALKDAIK 90
           RNP+TG  I I A +V  F A + LK  ++
Sbjct: 111 RNPKTGEEIPITARRVVTFHASQKLKSMVE 140


>gi|134095741|ref|YP_001100816.1| integration host factor subunit
          beta [Herminiimonas arsenicoxydans]
          Length = 101

 Score = 55.5 bits (132), 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  MTKSELIARLAERYPQLVAKDADYAVKTILDAMSDALATGQRIEIRGFGSFALNSRPPRI 60

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


  Database: BlastDatabases/690/690
    Posted date:  Apr 9, 2011  4:48 AM
  Number of letters in database: 1,000,347
  Number of sequences in database:  3295
  
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: 3295
Number of Hits to DB: 159,331
Number of extensions: 5615
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: 1,000,347
Length adjustment: 59
Effective length of query: 31
Effective length of database: 805,942
Effective search space: 24984202
Effective search space used: 24984202
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: 121 (51.2 bits)