RPS-BLAST 2.2.26 [Sep-21-2011]

Database: CDD.v3.10 
           44,354 sequences; 10,937,602 total letters

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

Query= psy4412
         (39 letters)



>gnl|CDD|222150 pfam13465, zf-H2C2_2, Zinc-finger double domain. 
          Length = 26

 Score = 28.1 bits (63), Expect = 0.018
 Identities = 11/19 (57%), Positives = 15/19 (78%)

Query: 21 HMRDHIRRHTGEKPFVCPF 39
          ++R H+R HTGEKP+ CP 
Sbjct: 1  NLRRHMRTHTGEKPYKCPV 19


>gnl|CDD|224089 COG1167, ARO8, Transcriptional regulators containing a DNA-binding
           HTH domain and an aminotransferase domain (MocR family)
           and their eukaryotic orthologs [Transcription / Amino
           acid transport and metabolism].
          Length = 459

 Score = 25.8 bits (57), Expect = 0.58
 Identities = 7/15 (46%), Positives = 8/15 (53%)

Query: 14  YHTLNSGHMRDHIRR 28
              L SGH   H+RR
Sbjct: 340 AAFLLSGHYDRHLRR 354


>gnl|CDD|225210 COG2331, COG2331, Uncharacterized protein conserved in bacteria
          [Function unknown].
          Length = 82

 Score = 24.8 bits (54), Expect = 0.85
 Identities = 8/22 (36%), Positives = 8/22 (36%)

Query: 3  PTYLYACLWCDYHTLNSGHMRD 24
          PTY Y C  C         M D
Sbjct: 9  PTYSYECTECGNRFDVVQAMTD 30


>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger. 
          Length = 23

 Score = 23.6 bits (51), Expect = 1.1
 Identities = 7/23 (30%), Positives = 11/23 (47%)

Query: 7  YACLWCDYHTLNSGHMRDHIRRH 29
          Y C  C     +   +R+H+R H
Sbjct: 1  YRCPECGKVFKSKSALREHMRTH 23


>gnl|CDD|220356 pfam09709, Cas_Csd1, CRISPR-associated protein (Cas_Csd1).  CRISPR
           loci appear to be mobile elements with a wide host
           range. This entry represents proteins that tend to be
           found near CRISPR repeats. The species range, so far, is
           exclusively bacterial and mesophilic, although CRISPR
           loci are particularly common among the archaea and
           thermophilic bacteria. Clusters of short DNA repeats
           with nonhomologous spacers, which are found at regular
           intervals in the genomes of phylogenetically distinct
           prokaryotic species, comprise a family with recognisable
           features. This family is known as CRISPR (short for
           Clustered, Regularly Interspaced Short Palindromic
           Repeats). A number of protein families appear only in
           association with these repeats and are designated Cas
           (CRISPR-Associated) proteins.
          Length = 572

 Score = 24.5 bits (54), Expect = 1.2
 Identities = 3/17 (17%), Positives = 7/17 (41%)

Query: 13  DYHTLNSGHMRDHIRRH 29
            +  L  G   + + +H
Sbjct: 337 FWRELTVGEFLERLEQH 353


>gnl|CDD|187887 cd09757, Cas8c_I-C, CRISPR/Cas system-associated protein Cas8c.
           CRISPR (Clustered Regularly Interspaced Short
           Palindromic Repeats) and associated Cas proteins
           comprise a system for heritable host defense by
           prokaryotic cells against phage and other foreign DNA;
           Zn-finger domain containing protein, distant homologs of
           Cas8 proteins; signature gene for I-C subtype; also
           known as Csd1 family.
          Length = 569

 Score = 24.5 bits (54), Expect = 1.4
 Identities = 4/17 (23%), Positives = 7/17 (41%)

Query: 13  DYHTLNSGHMRDHIRRH 29
            +  L  G   + + RH
Sbjct: 336 FWRELTVGEFLERLERH 352


>gnl|CDD|227381 COG5048, COG5048, FOG: Zn-finger [General function prediction
          only].
          Length = 467

 Score = 24.3 bits (52), Expect = 1.8
 Identities = 11/19 (57%), Positives = 13/19 (68%)

Query: 21 HMRDHIRRHTGEKPFVCPF 39
          H+  HIR HTGEKP  C +
Sbjct: 48 HLTRHIRSHTGEKPSQCSY 66


  Database: CDD.v3.10
    Posted date:  Mar 20, 2013  7:55 AM
  Number of letters in database: 10,937,602
  Number of sequences in database:  44,354
  
Lambda     K      H
   0.331    0.145    0.557 

Gapped
Lambda     K      H
   0.267   0.0655    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 1,917,028
Number of extensions: 86524
Number of successful extensions: 143
Number of sequences better than 10.0: 1
Number of HSP's gapped: 143
Number of HSP's successfully gapped: 11
Length of query: 39
Length of database: 10,937,602
Length adjustment: 13
Effective length of query: 26
Effective length of database: 10,361,000
Effective search space: 269386000
Effective search space used: 269386000
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 53 (24.3 bits)