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= 0001.1842.p
         (157 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300311300|ref|YP_003775392.1| integration host factor alpha-s...   212   1e-56
gi|300312982|ref|YP_003777074.1| integration host factor subunit...    67   7e-13
gi|300309668|ref|YP_003773760.1| HU histone family DNA-binding p...    65   3e-12

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

 Score =  212 bits (539), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 103/104 (99%), Positives = 104/104 (100%)

Query: 54  LPTLTKAELAELLFEQVGLNKREAKDMVETFFDEIRNALERGEAVKLSGFGNFQLRDKPQ 113
           +PTLTKAELAELLFEQVGLNKREAKDMVETFFDEIRNALERGEAVKLSGFGNFQLRDKPQ
Sbjct: 1   MPTLTKAELAELLFEQVGLNKREAKDMVETFFDEIRNALERGEAVKLSGFGNFQLRDKPQ 60

Query: 114 RPGRNPKTGEEIPITARRVVTFHASQKLKEMVELSSGSPVEMSV 157
           RPGRNPKTGEEIPITARRVVTFHASQKLKEMVELSSGSPVEMSV
Sbjct: 61  RPGRNPKTGEEIPITARRVVTFHASQKLKEMVELSSGSPVEMSV 104


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

 Score = 67.0 bits (162), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 35/98 (35%), Positives = 60/98 (61%), Gaps = 1/98 (1%)

Query: 57  LTKAELAELLFEQVG-LNKREAKDMVETFFDEIRNALERGEAVKLSGFGNFQLRDKPQRP 115
           +TK+EL   L E+   L  ++A   V+T  D + +AL  G+ +++ GFG+F L  +P R 
Sbjct: 1   MTKSELIARLAERYPQLVAKDADYAVKTILDAMVDALATGQRIEIRGFGSFALNRRPPRI 60

Query: 116 GRNPKTGEEIPITARRVVTFHASQKLKEMVELSSGSPV 153
           GRNPK+G+++ +  +RV  F   ++L+E V+   G P+
Sbjct: 61  GRNPKSGDKVMVPEKRVPHFKPGKELRERVDAMVGQPI 98


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

 Score = 65.1 bits (157), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 32/89 (35%), Positives = 52/89 (58%)

Query: 57  LTKAELAELLFEQVGLNKREAKDMVETFFDEIRNALERGEAVKLSGFGNFQLRDKPQRPG 116
           + K+EL +++     ++K  A+  +++  + I  A+ +G+ V+L GFG+F    +  R G
Sbjct: 22  VNKSELVDVIAADTEISKAAAQRALDSVIENIIKAVTKGDTVQLVGFGSFSTGKRAARTG 81

Query: 117 RNPKTGEEIPITARRVVTFHASQKLKEMV 145
           RNP+TGEEI I A   V F A +  KE V
Sbjct: 82  RNPQTGEEIKIAAATTVKFSAGKAFKEAV 110


  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
   0.311    0.127    0.335 

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: 416,346
Number of extensions: 15010
Number of successful extensions: 53
Number of sequences better than 1.0e-08: 3
Number of HSP's gapped: 53
Number of HSP's successfully gapped: 3
Length of query: 157
Length of database: 1,619,870
Length adjustment: 78
Effective length of query: 79
Effective length of database: 1,250,540
Effective search space: 98792660
Effective search space used: 98792660
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 (21.8 bits)
S2: 126 (53.1 bits)