RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780913|ref|YP_003065326.1| cold shock protein [Candidatus
Liberibacter asiaticus str. psy62]
         (78 letters)



>gnl|CDD|31469 COG1278, CspC, Cold shock proteins [Transcription].
          Length = 67

 Score = 73.2 bits (180), Expect = 2e-14
 Identities = 30/70 (42%), Positives = 41/70 (58%), Gaps = 5/70 (7%)

Query: 4  RGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANG 63
           G++KW+N  KG+GFITPE     G DVF+H SA+  AG   L EGQ V ++  Q     
Sbjct: 3  TGTVKWFNATKGFGFITPED---GGKDVFVHISAIQRAGFRTLREGQKVEFEVEQGR--K 57

Query: 64 KYSAENLKLV 73
            SA N++ +
Sbjct: 58 GPSAANVRAL 67


>gnl|CDD|88424 cd04458, CSP_CDS, Cold-Shock Protein (CSP) contains an S1-like
          cold-shock domain (CSD) that is found in eukaryotes,
          prokaryotes, and archaea.  CSP's include the major
          cold-shock proteins CspA and CspB in bacteria and the
          eukaryotic gene regulatory factor Y-box protein. CSP
          expression is up-regulated by an abrupt drop in growth
          temperature. CSP's are also expressed under normal
          condition at lower level. The function of cold-shock
          proteins is not fully understood. They preferentially
          bind poly-pyrimidine region of single-stranded RNA and
          DNA.  CSP's are thought to bind mRNA and regulate
          ribosomal translation, mRNA degradation, and  the rate
          of transcription termination. The human Y-box protein,
          which contains a CSD, regulates transcription and
          translation of genes that contain the Y-box sequence in
          their promoters. This specific ssDNA-binding properties
          of CSD are required for the binding of Y-box protein to
          the promoter's Y-box sequence, thereby regulating
          transcription..
          Length = 65

 Score = 71.0 bits (174), Expect = 7e-14
 Identities = 26/69 (37%), Positives = 43/69 (62%), Gaps = 5/69 (7%)

Query: 4  RGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANG 63
           G++KW++ +KG+GFITP+   + G+DVF+H SA+   G  +L EG  V ++  + D   
Sbjct: 2  TGTVKWFDDEKGFGFITPD---DGGEDVFVHISALEGDGFRSLEEGDRVEFELEEGD--K 56

Query: 64 KYSAENLKL 72
             A N++L
Sbjct: 57 GPQAVNVRL 65


>gnl|CDD|144050 pfam00313, CSD, 'Cold-shock' DNA-binding domain. 
          Length = 66

 Score = 67.2 bits (165), Expect = 8e-13
 Identities = 29/70 (41%), Positives = 40/70 (57%), Gaps = 5/70 (7%)

Query: 4  RGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANG 63
           G++KW+N  KG+GFITPE       DVF+H SA+   G  +L EGQ V +D V+     
Sbjct: 2  TGTVKWFNAKKGFGFITPED---GDKDVFVHFSAIQGDGFRSLQEGQRVEFDIVEG--TK 56

Query: 64 KYSAENLKLV 73
             A N+ L+
Sbjct: 57 GPQAANVTLL 66


>gnl|CDD|38280 KOG3070, KOG3070, KOG3070, Predicted RNA-binding protein containing
           PIN domain and invovled in translation or RNA processing
           [Translation, ribosomal structure and biogenesis].
          Length = 235

 Score = 43.6 bits (102), Expect = 1e-05
 Identities = 23/58 (39%), Positives = 35/58 (60%), Gaps = 7/58 (12%)

Query: 5   GSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASA----GLFNLTEGQLVTYDYVQ 58
           G++KW+N  KGYGFIT     +  +DVF+H+SA+       G  +L EG+ V +D  +
Sbjct: 59  GTVKWFNVGKGYGFITR---DDGPEDVFVHQSAITKYTPSEGFRSLKEGEAVPFDIQE 113


  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
   0.312    0.131    0.386 

Gapped
Lambda     K      H
   0.267   0.0780    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 898,549
Number of extensions: 35355
Number of successful extensions: 48
Number of sequences better than 10.0: 1
Number of HSP's gapped: 44
Number of HSP's successfully gapped: 5
Length of query: 78
Length of database: 6,263,737
Length adjustment: 48
Effective length of query: 30
Effective length of database: 5,226,505
Effective search space: 156795150
Effective search space used: 156795150
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 (21.8 bits)
S2: 51 (23.3 bits)