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= 0012.0006.p
         (191 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300311585|ref|YP_003775677.1| Ku domain-containing protein [H...   114   6e-27
gi|300311586|ref|YP_003775678.1| ATP-dependent DNA ligase [Herba...    81   5e-17

>gi|300311585|ref|YP_003775677.1| Ku domain-containing protein
           [Herbaspirillum seropedicae SmR1]
          Length = 349

 Score =  114 bits (284), Expect = 6e-27,   Method: Compositional matrix adjust.
 Identities = 62/114 (54%), Positives = 82/114 (71%), Gaps = 2/114 (1%)

Query: 64  DDLPVPDANPKKAGLSAKEVEMAQSLVESMSGEWDPESLRDTYRDDILAMVQKKIRSRQT 123
           DDLPVP    KKA ++ +EVEMA++LVE MS +W+PE   DTYRDD+LA++QKK +SRQT
Sbjct: 174 DDLPVPTRKSKKAAVTRQEVEMARALVEHMSAQWEPEQFHDTYRDDVLALIQKKTKSRQT 233

Query: 124 HEIAEPEADDDSKPRSSAKVIDLMALLKQSIDGKGKKPA-ASAAKXPRRARASR 176
           HE+AEP+        S AKV+DLMALLK S++G+G+  A A   K P+ A+  R
Sbjct: 234 HEVAEPDEAAAPAS-SGAKVVDLMALLKSSLEGRGRSSAKAGDDKAPQEAKEKR 286


>gi|300311586|ref|YP_003775678.1| ATP-dependent DNA ligase
           [Herbaspirillum seropedicae SmR1]
          Length = 856

 Score = 81.3 bits (199), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 34/52 (65%), Positives = 43/52 (82%)

Query: 1   MPAKLDVQLATLAEHAPDGDEWLSEMKFDGYRGLCRIEGGEARIFTREHLDW 52
           MPA++  QLATL + AP G++WL E+KFDGYRGLCRI+ G+A I+TRE LDW
Sbjct: 211 MPAQMQAQLATLVDRAPAGEQWLCELKFDGYRGLCRIDHGQAAIYTREGLDW 262


  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    0.130    0.372 

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: 550,304
Number of extensions: 19262
Number of successful extensions: 36
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 35
Number of HSP's successfully gapped: 2
Length of query: 191
Length of database: 1,619,870
Length adjustment: 80
Effective length of query: 111
Effective length of database: 1,241,070
Effective search space: 137758770
Effective search space used: 137758770
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: 128 (53.9 bits)