RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddA 
           21,609 sequences; 6,263,737 total letters

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

Query= gi|254780878|ref|YP_003065291.1| hypothetical protein
CLIBASIA_03875 [Candidatus Liberibacter asiaticus str. psy62]
         (51 letters)



>gnl|CDD|144198 pfam00517, GP41, Retroviral envelope protein.  This family includes
           envelope protein from a variety of retroviruses. It
           includes the GP41 subunit of the envelope protein
           complex from human and simian immunodeficiency viruses
           (HIV and SIV) which mediate membrane fusion during viral
           entry. The family also includes bovine immunodeficiency
           virus, feline immunodeficiency virus and Equine
           infectious anaemia (EIAV). The family also includes the
           Gp36 protein from mouse mammary tumour virus (MMTV) and
           human endogenous retroviruses (HERVs).
          Length = 204

 Score = 24.3 bits (53), Expect = 7.9
 Identities = 13/41 (31%), Positives = 19/41 (46%), Gaps = 1/41 (2%)

Query: 6   WVSRIQIFFIALLIVFSLSWFVFTLLYLIGDVRLRTCDFQM 46
           W+S I+I  + LLI+  L   +  +L     VR      QM
Sbjct: 153 WISYIKIGILILLIIIVLR-ILPGVLRNCRRVRQGYSPLQM 192


  Database: CddA
    Posted date:  Feb 4, 2011  9:38 PM
  Number of letters in database: 6,263,737
  Number of sequences in database:  21,609
  
Lambda     K      H
   0.350    0.155    0.548 

Gapped
Lambda     K      H
   0.267   0.0775    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 699,760
Number of extensions: 27419
Number of successful extensions: 507
Number of sequences better than 10.0: 1
Number of HSP's gapped: 504
Number of HSP's successfully gapped: 55
Length of query: 51
Length of database: 6,263,737
Length adjustment: 24
Effective length of query: 27
Effective length of database: 5,745,121
Effective search space: 155118267
Effective search space used: 155118267
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 14 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 38 (21.9 bits)
S2: 51 (23.3 bits)