RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254781126|ref|YP_003065539.1| hypothetical protein
CLIBASIA_05140 [Candidatus Liberibacter asiaticus str. psy62]
         (85 letters)



>gnl|CDD|132757 cd07072, NR_LBD_DHR38_like, Ligand binding domain of  DHR38_like
           proteins, members of the nuclear receptor superfamily.
           The ligand binding domain of nuclear receptor DHR38_like
           proteins:  DHR38 is a member of the steroid receptor
           superfamily in Drosophila. DHR38 interacts with the USP
           component of the ecdysone receptor complex, suggesting
           that DHR38 might modulate ecdysone-triggered signals in
           the fly, in addition to the ECR/USP pathway. At least
           four differentially expressed mRNA isoforms have been
           detected during development. Like other members of the
           nuclear receptor (NR) superfamily of ligand-activated
           transcription factors, DHR38 has  a central well
           conserved DNA binding domain (DBD), a variable
           N-terminal domain, a flexible hinge and a C-terminal
           ligand binding domain (LBD).
          Length = 239

 Score = 26.7 bits (59), Expect = 1.5
 Identities = 14/52 (26%), Positives = 25/52 (48%)

Query: 1   MNIFVRDISCLRALVFVITRGVARLPKDQKKAFFRHEKKVADHLNYNAGDRK 52
           M+I +   +CL AL  +  R   + P   ++   +    + DH+ YNA  +K
Sbjct: 137 MDIDISAFACLCALTLITERHGLKEPHKVEQLQMKIISSLRDHVTYNAEAQK 188


>gnl|CDD|35265 KOG0042, KOG0042, KOG0042, Glycerol-3-phosphate dehydrogenase
           [Energy production and conversion].
          Length = 680

 Score = 24.9 bits (54), Expect = 4.5
 Identities = 10/24 (41%), Positives = 13/24 (54%)

Query: 37  EKKVADHLNYNAGDRKSNIDKLYK 60
           E  VA HL+   GDR   + K+ K
Sbjct: 486 ESDVAQHLSQTYGDRAFRVAKMAK 509


>gnl|CDD|144517 pfam00945, Rhabdo_ncap, Rhabdovirus nucleocapsid protein.  The
           Nucleocapsid (N) Protein is said to have a "tight"
           structure. The carboxyl end of the N-terminal domain
           possesses an RNA binding domain. Sequence alignments
           show 2 regions of reasonable conservation, approx.
           64-103 and 201-329. A whole functional protein is
           required for encapsidation to take place.
          Length = 406

 Score = 24.3 bits (53), Expect = 8.7
 Identities = 14/61 (22%), Positives = 25/61 (40%), Gaps = 9/61 (14%)

Query: 7   DISCLRALVFVITRGVARLPKDQKKAFFRHEKKVADH-----LNYNAGDRKSNIDKLYKA 61
           +++    L+       A L    ++ FFR EKK  ++      N +A       D+  K+
Sbjct: 318 ELTVAALLLSYAFGSKATL----EQRFFRDEKKYTEYRDDDGDNTDAPLADDGDDEAPKS 373

Query: 62  R 62
           R
Sbjct: 374 R 374


  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
   0.325    0.136    0.389 

Gapped
Lambda     K      H
   0.267   0.0732    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 941,102
Number of extensions: 38785
Number of successful extensions: 105
Number of sequences better than 10.0: 1
Number of HSP's gapped: 105
Number of HSP's successfully gapped: 8
Length of query: 85
Length of database: 6,263,737
Length adjustment: 54
Effective length of query: 31
Effective length of database: 5,096,851
Effective search space: 158002381
Effective search space used: 158002381
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 51 (23.4 bits)