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= 0012.0004.p
         (163 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300311586|ref|YP_003775678.1| ATP-dependent DNA ligase [Herba...   197   4e-52

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

 Score =  197 bits (501), Expect = 4e-52,   Method: Compositional matrix adjust.
 Identities = 100/159 (62%), Positives = 120/159 (75%), Gaps = 3/159 (1%)

Query: 1   VVDGARLVHGLLEEIGLRSFVKTSGGKGLHVVVPIVPEQDWDVVKEWSRSLATHMAEVLP 60
           VV+GA+LV GLL+EIGL  F+KTSGGKGLHV+VPI PE DW VVK+W+   A H+A  LP
Sbjct: 695 VVEGAQLVRGLLKEIGLDCFLKTSGGKGLHVMVPIRPEHDWAVVKDWAHRFAAHLARHLP 754

Query: 61  DYFTAKMAKVARNGKIYIDYLRNGIGATTVAAYSPRARPGAPVSVPLTWDELSA--RTKA 118
           D F AKM+K ARNGKI+IDYLRN  GATTV AYS RAR GAPVSVP+TW+EL      KA
Sbjct: 755 DRFIAKMSKAARNGKIFIDYLRNAPGATTVVAYSVRARDGAPVSVPITWEELEQGKGIKA 814

Query: 119 DSFNVATVPKRLASLKR-DPWHDYAGTKQRLTKKILSLF 156
           D F V+T+P R+ SL++ DPW  +    QRLTK +L+ F
Sbjct: 815 DHFRVSTMPARIRSLEQHDPWAHFGQAPQRLTKAMLAAF 853


  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
   0.317    0.133    0.397 

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: 535,539
Number of extensions: 21289
Number of successful extensions: 72
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 70
Number of HSP's successfully gapped: 1
Length of query: 163
Length of database: 1,619,870
Length adjustment: 78
Effective length of query: 85
Effective length of database: 1,250,540
Effective search space: 106295900
Effective search space used: 106295900
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 (21.7 bits)
S2: 127 (53.5 bits)