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/690/690 
           3295 sequences; 1,000,347 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|134093875|ref|YP_001098950.1| 16S rRNA-processing protein Rim...   239   8e-65

>gi|134093875|ref|YP_001098950.1| 16S rRNA-processing protein RimM
           [Herminiimonas arsenicoxydans]
          Length = 177

 Score =  239 bits (610), Expect = 8e-65,   Method: Compositional matrix adjust.
 Identities = 122/191 (63%), Positives = 143/191 (74%), Gaps = 17/191 (8%)

Query: 12  PDDLVTVGHVTGAYGIQGWIRVRPYSSEAEALLNAKTWWLEKSGQPKQDVDVMQSKGHSG 71
           P+DLV VG+++GAYG+ GW+RVRPYS++A+ALLNAKTWWL+K     +DV +MQSK HSG
Sbjct: 4   PEDLVLVGYISGAYGLNGWVRVRPYSADADALLNAKTWWLDKP--EFRDVAMMQSKIHSG 61

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

Query: 132 DMMDNGAHPILKVTAPVQETAPEATAEAKPKKGAKEKSAAAPEMLIPFVDQFVKTVQQSE 191
           DMMDNGAHPIL+V  P        T+EA PK        AA E+LIPFV+QFV T+ Q+ 
Sbjct: 122 DMMDNGAHPILRVAVP-------QTSEADPK--------AAQELLIPFVEQFVITIDQTA 166

Query: 192 KKIIVDWDKDY 202
           KKI VDW  DY
Sbjct: 167 KKITVDWGLDY 177


  Database: BlastDatabases/690/690
    Posted date:  Apr 9, 2011  4:48 AM
  Number of letters in database: 1,000,347
  Number of sequences in database:  3295
  
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: 3295
Number of Hits to DB: 336,880
Number of extensions: 11283
Number of successful extensions: 33
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 31
Number of HSP's successfully gapped: 1
Length of query: 202
Length of database: 1,000,347
Length adjustment: 77
Effective length of query: 125
Effective length of database: 746,632
Effective search space: 93329000
Effective search space used: 93329000
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: 126 (53.1 bits)