RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780160|ref|YP_003064573.1| hypothetical protein
CLIBASIA_00215 [Candidatus Liberibacter asiaticus str. psy62]
         (298 letters)



>gnl|CDD|35683 KOG0462, KOG0462, KOG0462, Elongation factor-type GTP-binding
           protein [Translation, ribosomal structure and
           biogenesis].
          Length = 650

 Score = 29.9 bits (67), Expect = 0.97
 Identities = 14/59 (23%), Positives = 26/59 (44%), Gaps = 1/59 (1%)

Query: 240 GESANASPSMVLSEGDYTVIARNKERNYSREFSVLTGKSTIVEVLMRQ-KRMDKNGQHN 297
             S ++ PS  +   ++++      RN+S    V  GKST+ + L+     +D N    
Sbjct: 36  LFSEDSKPSAAVGLPEFSLDPVENIRNFSIIAHVDHGKSTLADRLLELTGTIDNNIGQE 94


>gnl|CDD|146080 pfam03266, DUF265, Protein of unknown function, DUF265. 
          Length = 168

 Score = 28.3 bits (64), Expect = 2.5
 Identities = 8/30 (26%), Positives = 13/30 (43%)

Query: 178 TSHYGKYNAIVSTVVKVEPGKIIDVTIQNR 207
             H    + +V  + +    KI  VT +NR
Sbjct: 131 VVHRRSDSPLVERIRRRPDVKIFVVTEENR 160


>gnl|CDD|143644 cd07884, RHD-n_Relish, N-terminal sub-domain of the Rel homology
           domain (RHD) of the arthropod protein Relish.  Proteins
           containing the Rel homology domain (RHD) are metazoan
           transcription factors. The RHD is composed of two
           structural sub-domains; this model characterizes the
           N-terminal RHD sub-domain of the arthropod Relish
           protein, in which the RHD domain co-occurs with
           C-terminal ankyrin repeats. Family members are sometimes
           referred to as p110 or p68 (proteolytically processed
           form). Relish is an NF-kappa B-like transcription
           factor, which plays a role in mediating innate immunity
           in Drosophila. It is activated via the Imd (immune
           deficiency) pathway, which triggers phosphorylation of
           Relish. IKK-dependent proteolytic cleavage of Relish
           (which involves Dredd) results in a smaller active form
           (without the C-terminal ankyrin repeats), which is
           transported into the nucleus and functions as a
           transactivator.
          Length = 159

 Score = 27.8 bits (62), Expect = 3.4
 Identities = 13/43 (30%), Positives = 19/43 (44%), Gaps = 4/43 (9%)

Query: 255 DYTVIARNKERNYSREFSVL----TGKSTIVEVLMRQKRMDKN 293
           D   I  + E +Y   F  +    T K  I E L ++K M+ N
Sbjct: 84  DPHDIEVSPEGDYVAMFQNMGIIHTAKKNIPEELYKKKNMNLN 126


>gnl|CDD|133157 cd05490, Cathepsin_D2, Cathepsin_D2, pepsin family of proteinases. 
           Cathepsin D is the major aspartic proteinase of the
           lysosomal compartment where it functions in protein
           catabolism. It is a member of the pepsin family of
           proteinases. This enzyme is distinguished from other
           members of the pepsin family by two features that are
           characteristic of lysosomal hydrolases. First, mature
           Cathepsin D is found predominantly in a two-chain form
           due to a posttranslational cleavage event. Second, it
           contains phosphorylated, N-linked oligosaccharides that
           target the enzyme to lysosomes via mannose-6-phosphate
           receptors. Cathepsin D preferentially attacks peptide
           bonds flanked by bulky hydrophobic amino acids and its
           pH optimum is between pH 2.8 and 4.0. Two active site
           aspartic acid residues are essential for the catalytic
           activity of aspartic proteinases. Like other aspartic
           proteinases, Cathepsin D is a bilobed molecule; the two
           evolutionary related lobes are mostly made up of
           beta-sheets and flank a deep active site cleft. Each of
           the two related lobes contributes one active site
           aspartic acid residue and contains a single carbohydrate
           group. Cathepsin D is an essential enzyme. Mice
           deficient for proteinase cathepsin D, generated by gene
           targeting, develop normally during the first 2 weeks,
           stop thriving in the third week and die in a state of
           anorexia in the fourth week. The mice develop atrophy of
           ileal mucosa followed by other degradation of intestinal
           organs. In these knockout mice, lysosomal proteolysis
           was normal. These results suggest that vital functions
           of cathepsin D are exerted by limited proteolysis of
           proteins regulating cell growth and/or tissue
           homeostasis, while its contribution to bulk proteolysis
           in lysosomes appears to be non-critical. This family of
           aspartate proteases is classified by MEROPS as the
           peptidase family A1 (pepsin A, clan AA).
          Length = 325

 Score = 27.8 bits (62), Expect = 3.5
 Identities = 12/39 (30%), Positives = 21/39 (53%)

Query: 220 GGEAVADTAWSILTASGDTVGESANASPSMVLSEGDYTV 258
           G EA+ DT  S++T   + V     A  ++ L +G+Y +
Sbjct: 206 GCEAIVDTGTSLITGPVEEVRALQKAIGAVPLIQGEYMI 244


>gnl|CDD|35345 KOG0123, KOG0123, KOG0123, Polyadenylate-binding protein (RRM
           superfamily) [RNA processing and modification,
           Translation, ribosomal structure and biogenesis].
          Length = 369

 Score = 27.6 bits (61), Expect = 3.9
 Identities = 24/88 (27%), Positives = 39/88 (44%), Gaps = 11/88 (12%)

Query: 3   ISFSSYAKAENMHTTSTLLNNNISKGKGKRVVDAQRITCEARLTENSTSIDSGVSWHIFD 62
           ++F   A AE    T   +N ++ KGK  R++ +QR      +     SID+     ++D
Sbjct: 42  VNFQQPADAERALDT---MNFDVLKGKPIRIMWSQRDPSLVFIKNLDESIDNK---SLYD 95

Query: 63  SISNKKNTLS----TTKKIIGGK-VSFD 85
           + S   N LS    T +    G  V F+
Sbjct: 96  TFSEFGNILSCKVATDENGSKGYFVQFE 123


>gnl|CDD|33903 COG4152, COG4152, ABC-type uncharacterized transport system, ATPase
           component [General function prediction only].
          Length = 300

 Score = 27.2 bits (60), Expect = 5.5
 Identities = 11/36 (30%), Positives = 18/36 (50%)

Query: 177 ITSHYGKYNAIVSTVVKVEPGKIIDVTIQNRAAKIT 212
           +T  +G   A+ +   +V PG+I  +   N A K T
Sbjct: 8   VTKSFGDKKAVDNISFEVPPGEIFGLLGPNGAGKTT 43


>gnl|CDD|112512 pfam03702, UPF0075, Uncharacterized protein family (UPF0075).  The
           proteins is this family are about 370 amino acids long
           and have no known function.
          Length = 363

 Score = 27.3 bits (61), Expect = 5.8
 Identities = 10/20 (50%), Positives = 15/20 (75%)

Query: 120 ILNAGGIRLYSIYKPGSPIV 139
           +LN GGI   S+ KPG+P++
Sbjct: 162 VLNIGGIANVSVLKPGAPVL 181


>gnl|CDD|176956 CHL00013, rpoA, RNA polymerase alpha subunit.
          Length = 327

 Score = 26.5 bits (59), Expect = 9.6
 Identities = 15/51 (29%), Positives = 26/51 (50%), Gaps = 4/51 (7%)

Query: 236 GDTVGESANASPSMVLSEGDYTVIARNKERNYSREFSVLTG-KSTIVEVLM 285
            DT+G    A    +L E + T I R K      E+S + G + +++E+L+
Sbjct: 34  ADTIG---IALRRALLGEIEGTCITRAKIEGVPHEYSTIPGIRESVLEILL 81


  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
   0.313    0.129    0.353 

Gapped
Lambda     K      H
   0.267   0.0708    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 3,206,058
Number of extensions: 160176
Number of successful extensions: 310
Number of sequences better than 10.0: 1
Number of HSP's gapped: 310
Number of HSP's successfully gapped: 15
Length of query: 298
Length of database: 6,263,737
Length adjustment: 93
Effective length of query: 205
Effective length of database: 4,254,100
Effective search space: 872090500
Effective search space used: 872090500
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: 57 (25.8 bits)