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= 0001.0305.p
         (486 letters)

Database: BlastDatabases/707/707 
           3697 sequences; 1,221,021 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|152980017|ref|YP_001354709.1| UDP-N-acetylmuramoylalanyl-D-gl...   553   e-159

>gi|152980017|ref|YP_001354709.1|
           UDP-N-acetylmuramoylalanyl-D-glutamyl-2,
           6-diaminopimelate--D-alanyl- D-alanine ligase
           [Janthinobacterium sp. Marseille]
          Length = 455

 Score =  553 bits (1425), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 297/449 (66%), Positives = 345/449 (76%), Gaps = 16/449 (3%)

Query: 38  LNDVVTDSRAVKPGNVFVALRGERFDAHDFLDAVAAQGAAAVVVERVPAGLSLPAIVVPD 97
            + V TDSR V  GN+FVALRGERFDAHDFL  VA +  AA+V E VP GL++PA++V D
Sbjct: 23  FDGVSTDSRTVGAGNLFVALRGERFDAHDFLPQVAERNVAAIVAETVPDGLTVPALIVQD 82

Query: 98  SRAALGQIAHGWRVQRQIPVIGVTGSNGKTTVKEMIAAILAAAFGEDGYLGTRGNFNNEI 157
           +R ALGQIAH WR Q ++P+IGVTGSNGKTTVKEMIAAIL AA G D YL TRGNFNN+I
Sbjct: 83  TRVALGQIAHYWRRQFKMPLIGVTGSNGKTTVKEMIAAILEAACGVDNYLATRGNFNNDI 142

Query: 158 GVPLTLFRLRAQHQAAVIEMGMNHPGEIAVLSRIAAPTLGLVNNAQREHQEFMASVEAVA 217
           GVPLTL RL+   +AAVIE+GMNHPGEIAVLS IA PT+GLVNNAQREHQEFMASVEAVA
Sbjct: 143 GVPLTLMRLQKTCKAAVIELGMNHPGEIAVLSAIAEPTVGLVNNAQREHQEFMASVEAVA 202

Query: 218 RENGAVIRHLPADGVAVFPADDDFTALWREEAGARRVLTFGLNAQADVSASYQATAFGST 277
           +ENGAV+  LPADG+AVFPADD+FT LWR+ A  R+VLTFG +  ADV  SY A AFGS 
Sbjct: 203 QENGAVLAGLPADGIAVFPADDEFTPLWRQLAAQRKVLTFGFSDDADVRCSYSANAFGSD 262

Query: 278 LQVTAKGLAVPPAQFKVELAAVGEHNVRNALAATACALGAGIAVDAVVRGLQSFAPVNGR 337
           ++++A        QF V L+A G HNVRNALAA ACAL  GIA DA+ RGLQ+FAPV+GR
Sbjct: 263 MEISAG-----RQQFTVALSAAGVHNVRNALAAIACALAIGIATDAIARGLQAFAPVSGR 317

Query: 338 LQRKQAKSGALVIDDTYNANPDSVRAAIDVLASIAGPRVLVLGDMGEVGDQGPQFHAEIG 397
           LQRK A +GALVIDDTYNANPDSVRAAIDVLA ++ PR+LVLG+MGEVG+ G Q+H EIG
Sbjct: 318 LQRKLAANGALVIDDTYNANPDSVRAAIDVLAQMSAPRILVLGEMGEVGNDGRQYHEEIG 377

Query: 398 AYARSRCIPLFFGLGELTKHAVAAYGAPLQGVAQAMHCDDIATLNAAVEQAAPQGATVLV 457
           AYAR++ I     LG+LT++A +A+GA       A H D +  LN A+       ATVLV
Sbjct: 378 AYARAKSIEYVLTLGDLTRYAASAFGAG------ANHYDSVEELNDALAGIFTADATVLV 431

Query: 458 KGSRFMKMERVVQHLVNVESLTQHQQETH 486
           KGSRFMKMERVVQHL     L Q  QE H
Sbjct: 432 KGSRFMKMERVVQHL-----LGQQTQEAH 455


  Database: BlastDatabases/707/707
    Posted date:  Apr 13, 2011 12:58 PM
  Number of letters in database: 1,221,021
  Number of sequences in database:  3697
  
Lambda     K      H
   0.320    0.133    0.381 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 3697
Number of Hits to DB: 1,092,086
Number of extensions: 44912
Number of successful extensions: 195
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 194
Number of HSP's successfully gapped: 2
Length of query: 486
Length of database: 1,221,021
Length adjustment: 87
Effective length of query: 399
Effective length of database: 899,382
Effective search space: 358853418
Effective search space used: 358853418
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 131 (55.1 bits)