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= 0001.1347.p
         (202 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|152980656|ref|YP_001352282.1| 16S rRNA processing protein Rim...   234   3e-63

>gi|152980656|ref|YP_001352282.1| 16S rRNA processing protein RimM
           [Janthinobacterium sp. Marseille]
          Length = 179

 Score =  234 bits (596), Expect = 3e-63,   Method: Compositional matrix adjust.
 Identities = 119/191 (62%), Positives = 141/191 (73%), Gaps = 15/191 (7%)

Query: 12  PDDLVTVGHVTGAYGIQGWIRVRPYSSEAEALLNAKTWWLEKSGQPKQDVDVMQSKGHSG 71
           P+DLV VG+++GAYG+ GW+RVRPYS++A+ALL AKTWWL+K      DV++MQSK H+G
Sbjct: 4   PEDLVLVGYISGAYGLNGWVRVRPYSADADALLTAKTWWLDKP--EFHDVEMMQSKIHTG 61

Query: 72  DVVARLTGVADRNAAEAMKGTVVSISRKHFPALDDNEFYWVDLIGSAVENLQGETLGVVS 131
           DVVA+L GVA R+AAEA+KG  V I R HFPAL DNEFYWVDLIG  VENLQGE LG VS
Sbjct: 62  DVVAKLMGVAGRDAAEALKGATVQIPRSHFPALSDNEFYWVDLIGLEVENLQGEHLGQVS 121

Query: 132 DMMDNGAHPILKVTAPVQETAPEATAEAKPKKGAKEKSAAAPEMLIPFVDQFVKTVQQSE 191
           DMMDNGAHPIL+V        P+A     PK       AA  E+LIPFV+QFV TV ++ 
Sbjct: 122 DMMDNGAHPILRV------AVPQAAETTDPK-------AAPQELLIPFVEQFVITVDRTA 168

Query: 192 KKIIVDWDKDY 202
           KKI VDW  DY
Sbjct: 169 KKITVDWGLDY 179


  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
   0.313    0.129    0.380 

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: 411,902
Number of extensions: 14028
Number of successful extensions: 32
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 30
Number of HSP's successfully gapped: 1
Length of query: 202
Length of database: 1,221,021
Length adjustment: 79
Effective length of query: 123
Effective length of database: 928,958
Effective search space: 114261834
Effective search space used: 114261834
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: 127 (53.5 bits)