RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254781182|ref|YP_003065595.1| hypothetical protein
CLIBASIA_05445 [Candidatus Liberibacter asiaticus str. psy62]
         (94 letters)



>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 = 25.4 bits (56), Expect = 3.4
 Identities = 9/27 (33%), Positives = 11/27 (40%)

Query: 11  FEKCGMLSDRTRYLKQHNLIIEEIFEW 37
           ++ C  L   T   K   L IEE   W
Sbjct: 214 YKDCSGLVSFTHLCKVTGLSIEEAITW 240


>gnl|CDD|133358 cd04158, ARD1, ARD1 subfamily.  ARD1 (ADP-ribosylation factor
           domain protein 1) is an unusual member of the Arf
           family.  In addition to the C-terminal Arf domain, ARD1
           has an additional 46-kDa N-terminal domain that contains
           a RING finger domain, two predicted B-Boxes, and a
           coiled-coil protein interaction motif.  This domain
           belongs to the TRIM (tripartite motif) or RBCC (RING,
           B-Box, coiled-coil) family.  Like most Arfs, the ARD1
           Arf domain lacks detectable GTPase activity.  However,
           unlike most Arfs, the full-length ARD1 protein has
           significant GTPase activity due to the GAP
           (GTPase-activating protein) activity exhibited by the
           46-kDa N-terminal domain.  The GAP domain of ARD1 is
           specific for its own Arf domain and does not bind other
           Arfs.  The rate of GDP dissociation from the ARD1 Arf
           domain is slowed by the adjacent 15 amino acids, which
           act as a GDI (GDP-dissociation inhibitor) domain.  ARD1
           is ubiquitously expressed in cells and localizes to the
           Golgi and to the lysosomal membrane.  Two Tyr-based
           motifs in the Arf domain are responsible for Golgi
           localization, while the GAP domain controls lysosomal
           localization.
          Length = 169

 Score = 24.9 bits (54), Expect = 5.6
 Identities = 17/57 (29%), Positives = 24/57 (42%), Gaps = 5/57 (8%)

Query: 18  SDRTRYLKQHN----LIIEEIFEWSNFVRIEGNKAVHEGQSSIEESDECLEFVNLFC 70
           S R R  + H+    L+ E+    +  + I  NK    G  S+EE  E L    L C
Sbjct: 77  SHRDRVSEAHSELAKLLTEKELRDALLL-IFANKQDVAGALSVEEMTELLSLHKLCC 132


>gnl|CDD|31738 COG1549, COG1549, Queuine tRNA-ribosyltransferases, contain PUA
          domain [Translation, ribosomal structure and
          biogenesis].
          Length = 519

 Score = 24.5 bits (53), Expect = 7.4
 Identities = 13/56 (23%), Positives = 21/56 (37%), Gaps = 2/56 (3%)

Query: 31 IEEIFEWSNF--VRIEGNKAVHEGQSSIEESDECLEFVNLFCDIVFTLPALIKEKK 84
           +E+F +S         + AV     S  E DE +E            PA+ K+ +
Sbjct: 4  DQELFGYSRPGEFPEYDSPAVTVLPESYVEVDEIIEKAGKRIPRQLYFPAVKKQSE 59


  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
   0.319    0.136    0.402 

Gapped
Lambda     K      H
   0.267   0.0822    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,127,968
Number of extensions: 48204
Number of successful extensions: 108
Number of sequences better than 10.0: 1
Number of HSP's gapped: 108
Number of HSP's successfully gapped: 5
Length of query: 94
Length of database: 6,263,737
Length adjustment: 62
Effective length of query: 32
Effective length of database: 4,923,979
Effective search space: 157567328
Effective search space used: 157567328
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (23.2 bits)