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= 0248.0026.p
         (347 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300309680|ref|YP_003773772.1| D-alanine-D-alanine ligase B pr...   548   e-157

>gi|300309680|ref|YP_003773772.1| D-alanine-D-alanine ligase B
           protein [Herbaspirillum seropedicae SmR1]
          Length = 334

 Score =  548 bits (1412), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 265/340 (77%), Positives = 298/340 (87%), Gaps = 8/340 (2%)

Query: 1   MMNQINQAAGFGKVGVLFGGRSAEREVSLMSGAGVLKALRSKGVDAHPFDPAERSLAELA 60
           M++Q +Q   FG+VGVLFGGRSAEREVS+MSG GVL+ALRSKGVDAHPFDPAERSL EL 
Sbjct: 1   MISQ-DQIKAFGRVGVLFGGRSAEREVSMMSGNGVLQALRSKGVDAHPFDPAERSLGELQ 59

Query: 61  AEKFDRVFIALHGRYGEDGTLQGALEQLGIPYTGPGVMASSIAMDKVMTKRIWLGYDLPT 120
           AE+FDRVFIALHGRYGEDGTLQGALEQ+G+PYTGPGVM+SSIAMDKVMTKRIWL + LPT
Sbjct: 60  AEQFDRVFIALHGRYGEDGTLQGALEQMGLPYTGPGVMSSSIAMDKVMTKRIWLSHGLPT 119

Query: 121 PRFVVLDSAATPREELRQVPDVLGLPLMLKAPHEGSTIGIAKVAGYSDMQEGFDLCAQYD 180
           PRF+ LD+ AT RE+LR VPD LGLPLMLKAPHEGSTIGIAKV GYSDMQEGFDLCA+YD
Sbjct: 120 PRFLTLDAQATTREQLRLVPDTLGLPLMLKAPHEGSTIGIAKVNGYSDMQEGFDLCARYD 179

Query: 181 AVVLAEEFVTGRELTVPVMGKGTSGDNKAKAFPVIEIRAPEGNYDYQHKYFTDDTKYLCP 240
            VVLAEEF+ GRELTVPV+G G++    A+A PVIEIRAPEGNYDYQ+KYFTDDTKYLCP
Sbjct: 180 KVVLAEEFIRGRELTVPVLGTGSA----ARALPVIEIRAPEGNYDYQNKYFTDDTKYLCP 235

Query: 241 APLDEALTQRVQELAVKAYNALGCRGWSRVDFMLRASDN--EPFLLEINTSPGMTGHSLV 298
           APLDE LT+ +Q LAV+A+NALGCRGWSRVDFMLR  D   EP+LLEINTSPGMTGHSLV
Sbjct: 236 APLDEELTRHLQNLAVQAFNALGCRGWSRVDFMLREVDGKAEPYLLEINTSPGMTGHSLV 295

Query: 299 PMSARQAGMTYEDLCYEILKFAALDLKPSDAWKSPAAANA 338
           PM+A+  GM+YEDLC EIL+ AALD+ PS  W +P A  +
Sbjct: 296 PMAAKAVGMSYEDLCCEILQMAALDMTPSKDW-TPQAGQS 334


  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
   0.318    0.135    0.399 

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: 1,175,804
Number of extensions: 51556
Number of successful extensions: 151
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 149
Number of HSP's successfully gapped: 1
Length of query: 347
Length of database: 1,619,870
Length adjustment: 86
Effective length of query: 261
Effective length of database: 1,212,660
Effective search space: 316504260
Effective search space used: 316504260
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: 131 (55.1 bits)