RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy3276
         (62 letters)



>gnl|CDD|206037 pfam13866, zf-SAP30, SAP30 zinc-finger.  SAP30 is a subunit of
          the histone deacetylase complex, and this domain is a
          zinc-finger. Solution of the structure shows a novel
          fold comprising two beta-strands and two alpha-helices
          with the zinc organising centre showing remote
          resemblance to the treble clef motif. In silico
          analysis of the structure revealed a highly conserved
          surface dominated by basic residues. NMR-based analysis
          of potential ligands for the SAP30 zn-finger motif
          indicated a strong preference for nucleic acid
          substrates. The zinc-finger of SAP3 probably functions
          as a double-stranded DNA-binding motif, thereby
          expanding the known functions of both SAP30 and the
          mammalian Sin3 co-repressor complex.
          Length = 68

 Score = 56.9 bits (137), Expect = 4e-13
 Identities = 24/39 (61%), Positives = 31/39 (79%)

Query: 19 QICCLVDDGVRCPRPIGNASYSKRIQQIVTQKRLKLHLD 57
          Q CCL + G RC RP GNAS+SKRIQ+ ++QK+LK+ LD
Sbjct: 2  QCCCLREGGERCGRPAGNASFSKRIQKSISQKKLKIDLD 40


>gnl|CDD|237261 PRK12928, PRK12928, lipoyl synthase; Provisional.
          Length = 290

 Score = 26.8 bits (60), Expect = 0.53
 Identities = 10/24 (41%), Positives = 16/24 (66%), Gaps = 2/24 (8%)

Query: 32 RPIGNASYSKRIQQIVTQKRLKLH 55
           PIG AS  + +Q++V  K+ +LH
Sbjct: 20 APIGKASELETVQRLV--KQRRLH 41


>gnl|CDD|178323 PLN02721, PLN02721, threonine aldolase.
          Length = 353

 Score = 27.0 bits (60), Expect = 0.57
 Identities = 14/53 (26%), Positives = 26/53 (49%), Gaps = 2/53 (3%)

Query: 8   EEDSHGPTDLQQICCLVDDGVRCPRPIGNASYSKRIQQIVTQKRLKLHLDNFR 60
           + D H PT   ++ CL +    C     +  Y+ ++ ++  +  LKLH+D  R
Sbjct: 130 KGDDHFPT--TRLICLENTHANCGGRCLSVEYTDKVGELAKRHGLKLHIDGAR 180


>gnl|CDD|177589 PHA03348, PHA03348, tegument protein UL21; Provisional.
          Length = 526

 Score = 26.1 bits (58), Expect = 1.2
 Identities = 12/33 (36%), Positives = 17/33 (51%), Gaps = 4/33 (12%)

Query: 23  LVD---DGVRCPRPIGNA-SYSKRIQQIVTQKR 51
           LV+   DG+  PRP  +     +R   I+T KR
Sbjct: 188 LVEGLFDGIPVPRPPLSGDERPRRTDVIITGKR 220


>gnl|CDD|99748 cd06502, TA_like, Low-specificity threonine aldolase (TA). This
           family belongs to pyridoxal phosphate (PLP)-dependent
           aspartate aminotransferase superfamily (fold I).  TA
           catalyzes the conversion of L-threonine or
           L-allo-threonine to glycine and acetaldehyde in a
           secondary glycine biosynthetic pathway.
          Length = 338

 Score = 25.4 bits (56), Expect = 1.8
 Identities = 8/20 (40%), Positives = 10/20 (50%)

Query: 41  KRIQQIVTQKRLKLHLDNFR 60
           K I  +  +  L LHLD  R
Sbjct: 149 KAISALAKENGLPLHLDGAR 168


>gnl|CDD|220456 pfam09886, DUF2113, Uncharacterized protein conserved in archaea
          (DUF2113).  This domain, found in various hypothetical
          archaeal proteins, has no known function.
          Length = 189

 Score = 25.0 bits (55), Expect = 2.5
 Identities = 11/37 (29%), Positives = 17/37 (45%), Gaps = 7/37 (18%)

Query: 28 VRCPRPIGNASYSKRIQQIVTQ-------KRLKLHLD 57
          V C   +G   Y K IQ ++          RLK+++D
Sbjct: 3  VECTDEVGAEIYEKIIQDVLQDLNLGRAIGRLKVYID 39


>gnl|CDD|232933 TIGR00348, hsdR, type I site-specific deoxyribonuclease, HsdR
           family.  This gene is part of the type I restriction and
           modification system which is composed of three
           polypeptides R (restriction endonuclease), M
           (modification) and S (specificity). This group of
           enzymes recognize specific short DNA sequences and have
           an absolute requirement for ATP (or dATP) and
           S-adenosyl-L-methionine. They also catalyse the
           reactions of EC 2.1.1.72 and EC 2.1.1.73, with similar
           site specificity.(J. Mol. Biol. 271 (3), 342-348
           (1997)). Members of this family are assumed to differ
           from each other in DNA site specificity [DNA metabolism,
           Restriction/modification].
          Length = 667

 Score = 24.7 bits (54), Expect = 3.6
 Identities = 6/22 (27%), Positives = 12/22 (54%)

Query: 8   EEDSHGPTDLQQICCLVDDGVR 29
           EE+   P D +++  + D+  R
Sbjct: 355 EEEEKFPVDRKEVVVIFDEAHR 376


>gnl|CDD|227820 COG5533, UBP5, Ubiquitin C-terminal hydrolase [Posttranslational
           modification, protein turnover, chaperones].
          Length = 415

 Score = 23.8 bits (51), Expect = 6.9
 Identities = 11/36 (30%), Positives = 17/36 (47%)

Query: 24  VDDGVRCPRPIGNASYSKRIQQIVTQKRLKLHLDNF 59
             D  RCP+     S  KR++ +V    L +H+  F
Sbjct: 281 GKDAWRCPKCGRKESSRKRMEILVLPDVLIIHISRF 316


  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
   0.322    0.140    0.431 

Gapped
Lambda     K      H
   0.267   0.0585    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,053,080
Number of extensions: 203700
Number of successful extensions: 156
Number of sequences better than 10.0: 1
Number of HSP's gapped: 156
Number of HSP's successfully gapped: 8
Length of query: 62
Length of database: 10,937,602
Length adjustment: 33
Effective length of query: 29
Effective length of database: 9,473,920
Effective search space: 274743680
Effective search space used: 274743680
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 (21.9 bits)
S2: 53 (24.5 bits)