RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddB 
           21,608 sequences; 5,994,473 total letters

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

Query= gi|254780906|ref|YP_003065319.1| hypothetical protein
CLIBASIA_04025 [Candidatus Liberibacter asiaticus str. psy62]
         (96 letters)



>gnl|CDD|173058 PRK14594, rimM, 16S rRNA-processing protein RimM; Provisional.
          Length = 166

 Score = 25.5 bits (56), Expect = 3.2
 Identities = 18/57 (31%), Positives = 27/57 (47%), Gaps = 8/57 (14%)

Query: 12 FITGMILSSCGDTLSDSKQHNKINNTKNHLDLLFPIDDSHNQKPTEKKPNTSSIKIK 68
          F+ G+ILSS G        + K+ +  N+        +  N K   KK N SSI++K
Sbjct: 2  FVKGIILSSYG-----INGYAKVKSISNNFCDFI---NLKNNKLVLKKSNCSSIEVK 50


>gnl|CDD|132636 TIGR03597, GTPase_YqeH, ribosome biogenesis GTPase YqeH.  This
           family describes YqeH, a member of a larger family of
           GTPases involved in ribosome biogenesis. Like YqlF, it
           shows a cyclical permutation relative to GTPases EngA
           (in which the GTPase domain is duplicated), Era, and
           others. Members of this protein family are found in a
           relatively small number of bacterial species, including
           Bacillus subtilis but not Escherichia coli.
          Length = 360

 Score = 25.3 bits (56), Expect = 3.5
 Identities = 13/45 (28%), Positives = 18/45 (40%), Gaps = 1/45 (2%)

Query: 28  SKQHNKINNTKNHL-DLLFPIDDSHNQKPTEKKPNTSSIKIKNNI 71
           +K  N       HL +LL P          E   +T +IK K +I
Sbjct: 282 TKLENADELYNKHLGNLLSPPCLDDKFNLPELVFHTFTIKEKTDI 326


>gnl|CDD|150837 pfam10225, DUF2215, Uncharacterized conserved protein (DUF2215). 
          This entry is the central 200 residues of a family of
          proteins conserved from worms to humans. The function
          is unknown.
          Length = 247

 Score = 24.3 bits (53), Expect = 6.4
 Identities = 5/20 (25%), Positives = 9/20 (45%)

Query: 9  ILFFITGMILSSCGDTLSDS 28
          +   + G++L      LS S
Sbjct: 14 VFVLVLGIVLFLLAPLLSRS 33


>gnl|CDD|131606 TIGR02555, OrgA_MxiK, type III secretion apparatus protein
           OrgA/MxiK.  This gene is found in type III secretion
           operons and has been shown to be essential for the
           invasion phenotype in Salmonella and a component of the
           secretion apparatus. The protein is known as OrgA in
           Salmonella due to its oxygen-dependent expression
           pattern in which low-oxygen levels up-regulate the gene.
           In Shigella the ghene is called MxiK and has been shown
           to be sessential for the proper assembly of the
           secretion needle complex.
          Length = 185

 Score = 24.4 bits (53), Expect = 6.5
 Identities = 6/17 (35%), Positives = 7/17 (41%)

Query: 41  LDLLFPIDDSHNQKPTE 57
           L+LLFP        P  
Sbjct: 143 LNLLFPDFLEGLLTPLP 159


>gnl|CDD|183230 PRK11613, folP, dihydropteroate synthase; Provisional.
          Length = 282

 Score = 23.9 bits (52), Expect = 8.4
 Identities = 9/28 (32%), Positives = 15/28 (53%)

Query: 17 ILSSCGDTLSDSKQHNKINNTKNHLDLL 44
          IL+   D+ SD   HN + +   H +L+
Sbjct: 20 ILNVTPDSFSDGGTHNSLIDAVKHANLM 47


  Database: CddB
    Posted date:  Feb 4, 2011  9:54 PM
  Number of letters in database: 5,994,473
  Number of sequences in database:  21,608
  
Lambda     K      H
   0.313    0.132    0.406 

Gapped
Lambda     K      H
   0.267   0.0768    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 1,509,879
Number of extensions: 74898
Number of successful extensions: 95
Number of sequences better than 10.0: 1
Number of HSP's gapped: 95
Number of HSP's successfully gapped: 14
Length of query: 96
Length of database: 5,994,473
Length adjustment: 64
Effective length of query: 32
Effective length of database: 4,611,561
Effective search space: 147569952
Effective search space used: 147569952
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: 50 (23.0 bits)