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= 0001.3856.p
         (120 letters)

Database: BlastDatabases/690/690 
           3295 sequences; 1,000,347 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|134096265|ref|YP_001101340.1| putative sigma(54) modulation p...   172   4e-45

>gi|134096265|ref|YP_001101340.1| putative sigma(54) modulation
           protein RpoX [Herminiimonas arsenicoxydans]
          Length = 117

 Score =  172 bits (437), Expect = 4e-45,   Method: Compositional matrix adjust.
 Identities = 87/119 (73%), Positives = 103/119 (86%), Gaps = 3/119 (2%)

Query: 1   MNLTISGHHLELTPAIREYVQSKLSRIKRHFDNVIDVSVILSVDKLTEKEKRQKAEINVH 60
           MNLTISGHHLELTPAIREYVQ KL RIKRHFD+VID++VIL+VD L EKEKRQ+AEIN+ 
Sbjct: 1   MNLTISGHHLELTPAIREYVQGKLERIKRHFDHVIDIAVILTVDNLPEKEKRQRAEINLR 60

Query: 61  IKGKDLHAESIAHDLYAAIDALIDKLDRQVIKHKDRLQEH-HSMAKRLPDETPADAVAG 118
           ++GKD+H ESIA++LYAAID L+DKLDRQVIK+K + Q+H H   KRLPDE+  DAVA 
Sbjct: 61  VRGKDIHVESIANNLYAAIDTLVDKLDRQVIKYKTKQQDHQHDAIKRLPDES--DAVAS 117


  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
   0.317    0.132    0.361 

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: 213,508
Number of extensions: 7336
Number of successful extensions: 24
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 23
Number of HSP's successfully gapped: 1
Length of query: 120
Length of database: 1,000,347
Length adjustment: 71
Effective length of query: 49
Effective length of database: 766,402
Effective search space: 37553698
Effective search space used: 37553698
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: 123 (52.0 bits)