RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy16699
         (231 letters)



>gnl|CDD|216929 pfam02207, zf-UBR, Putative zinc finger in N-recognin (UBR box).
           This region is found in E3 ubiquitin ligases that
           recognise N-recognins.
          Length = 71

 Score = 53.9 bits (130), Expect = 4e-10
 Identities = 27/75 (36%), Positives = 39/75 (52%), Gaps = 10/75 (13%)

Query: 34  KNCTYSQGYMKRQALYACLTCTPDICDPAGFCLAC-NYHCHEGHNIVELYTKR---CDCG 89
             C Y       Q +Y CLTC+ D       C  C +  CH+GH++VEL++KR   CDCG
Sbjct: 1   SVCGYVFK--SGQPVYRCLTCSLD--PTCVICYECFSISCHKGHDVVELFSKRGGCCDCG 56

Query: 90  NSKFGEKK--CNLEP 102
           + +  +K+  C L  
Sbjct: 57  DPEAWKKEGFCKLHK 71


>gnl|CDD|197698 smart00396, ZnF_UBR1, Putative zinc finger in N-recognin, a
           recognition component of the N-end rule pathway.  Domain
           is involved in recognition of N-end rule substrates in
           yeast Ubr1p.
          Length = 71

 Score = 37.0 bits (86), Expect = 5e-04
 Identities = 23/75 (30%), Positives = 27/75 (36%), Gaps = 12/75 (16%)

Query: 34  KNCTYSQGYMKRQALYACLTCTPDICDPAGFCLAC-NYHCHEGHNIVELYTKR----CDC 88
             C Y     +    Y C TC  D       C  C    CH+GH  V L T R    CDC
Sbjct: 1   DVCGYKFTGGEVI--YRCKTCGLDPT--CVLCSDCFRPSCHKGH-DVSLKTSRGSGICDC 55

Query: 89  GNS--KFGEKKCNLE 101
           G+      + KC   
Sbjct: 56  GDKEAWNEDLKCKAH 70


>gnl|CDD|237278 PRK13029, PRK13029, 2-oxoacid ferredoxin oxidoreductase;
           Provisional.
          Length = 1186

 Score = 30.9 bits (70), Expect = 0.72
 Identities = 13/26 (50%), Positives = 16/26 (61%)

Query: 6   GTVTLGDVLALQDHLEESAVAVLGAA 31
           G VT+G VL +  HLE   V+VL  A
Sbjct: 756 GVVTIGGVLGMAAHLEGKGVSVLDMA 781


>gnl|CDD|224193 COG1274, PckA, Phosphoenolpyruvate carboxykinase (GTP) [Energy
           production and conversion].
          Length = 608

 Score = 30.4 bits (69), Expect = 0.93
 Identities = 8/18 (44%), Positives = 13/18 (72%)

Query: 195 KDVSSIPPVTEAFFWQEG 212
           +  +++P VTEAF W+ G
Sbjct: 422 RRPTTVPLVTEAFDWEHG 439


>gnl|CDD|240447 cd13432, LDT_IgD_like_2, IgD-like repeat domain of mycobacterial
           L,D-transpeptidases.  Immunoglobulin-like domain found
           in actinobacterial L,D-transpeptidases, including
           Mycobacterium tuberculosis LdtMt2, which is a
           non-classical transpeptidase that generates 3->3
           transpeptide linkages. LdtMt2 is associated with
           virulence and resistance to amoxicillin. This domain may
           occur in a tandem-repeat arrangement and is found
           N-terminal to the catalytic L,D-transpeptidase domain;
           this model represents the  repeat adjacent to the
           catalytic domain.
          Length = 99

 Score = 28.3 bits (64), Expect = 1.3
 Identities = 8/26 (30%), Positives = 14/26 (53%), Gaps = 7/26 (26%)

Query: 191 PIKDKD-------VSSIPPVTEAFFW 209
           P+ D+        V++ PPV  A++W
Sbjct: 26  PVTDRAAVEKALKVTTSPPVEGAWYW 51


>gnl|CDD|235256 PRK04210, PRK04210, phosphoenolpyruvate carboxykinase; Provisional.
          Length = 601

 Score = 28.6 bits (65), Expect = 2.7
 Identities = 9/17 (52%), Positives = 11/17 (64%)

Query: 196 DVSSIPPVTEAFFWQEG 212
              ++P VTEAF WQ G
Sbjct: 415 RSDTVPLVTEAFDWQHG 431


>gnl|CDD|215859 pfam00326, Peptidase_S9, Prolyl oligopeptidase family. 
          Length = 212

 Score = 28.3 bits (64), Expect = 3.0
 Identities = 12/43 (27%), Positives = 18/43 (41%), Gaps = 3/43 (6%)

Query: 146 EDWFHSGHLGLDSPIPDGEDYSEMSCASCINMYPVLKLYPHLL 188
              F   ++   +P  + E Y  +S  S    Y  +K YP LL
Sbjct: 108 TSPFTERYMEWGNPWDNEEGYRYLSPYS---PYDNVKAYPPLL 147


>gnl|CDD|240432 PTZ00477, PTZ00477, rhoptry-associated protein; Provisional.
          Length = 524

 Score = 28.6 bits (64), Expect = 3.1
 Identities = 11/32 (34%), Positives = 14/32 (43%), Gaps = 6/32 (18%)

Query: 60  DPAGFCLACNYHCHEGHNIVELYTKRC---DC 88
           DP+ FC          H +V  Y +RC   DC
Sbjct: 73  DPSMFC---EGDLETCHTLVNRYVERCKAGDC 101


>gnl|CDD|214584 smart00249, PHD, PHD zinc finger.  The plant homeodomain (PHD)
           finger is a C4HC3 zinc-finger-like motif found in
           nuclear proteins thought to be involved in epigenetics
           and chromatin-mediated transcriptional regulation. The
           PHD finger binds two zinc ions using the so-called
           'cross-brace' motif and is thus structurally related to
           the RING finger and the FYVE finger. It is not yet known
           if PHD fingers have a common molecular function. Several
           reports suggest that it can function as a
           protein-protein interacton domain and it was recently
           demonstrated that the PHD finger of p300 can cooperate
           with the adjacent BROMO domain in nucleosome binding in
           vitro. Other reports suggesting that the PHD finger is a
           ubiquitin ligase have been refuted as these domains were
           RING fingers misidentified as PHD fingers.
          Length = 47

 Score = 24.9 bits (54), Expect = 8.0
 Identities = 12/38 (31%), Positives = 19/38 (50%), Gaps = 2/38 (5%)

Query: 137 DEMIQCALCEDWFHSGHLGLDSPIPDGEDYSEMSCASC 174
            E++QC  C+ W+H   LG   P+ + E   +  C  C
Sbjct: 12  GELLQCDGCDRWYHQTCLGP--PLLEEEPDGKWYCPKC 47


>gnl|CDD|201356 pfam00628, PHD, PHD-finger.  PHD folds into an interleaved type of
           Zn-finger chelating 2 Zn ions in a similar manner to
           that of the RING and FYVE domains. Several PHD fingers
           have been identified as binding modules of methylated
           histone H3.
          Length = 51

 Score = 24.8 bits (54), Expect = 8.6
 Identities = 8/29 (27%), Positives = 12/29 (41%), Gaps = 6/29 (20%)

Query: 122 CTCARPYPDEENPNCDEMIQCALCEDWFH 150
             C +   D E      ++ C  C+ WFH
Sbjct: 3   AVCGKVDDDGE------LLLCDGCDRWFH 25


>gnl|CDD|216136 pfam00821, PEPCK, Phosphoenolpyruvate carboxykinase.  catalyzes the
           formation of phosphoenolpyruvate by decarboxylation of
           oxaloacetate.
          Length = 586

 Score = 27.1 bits (61), Expect = 8.8
 Identities = 7/18 (38%), Positives = 11/18 (61%)

Query: 195 KDVSSIPPVTEAFFWQEG 212
           +   ++P V EAF W+ G
Sbjct: 400 RRPDTVPLVYEAFDWEHG 417


  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
   0.320    0.137    0.460 

Gapped
Lambda     K      H
   0.267   0.0666    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,315,762
Number of extensions: 984836
Number of successful extensions: 705
Number of sequences better than 10.0: 1
Number of HSP's gapped: 701
Number of HSP's successfully gapped: 20
Length of query: 231
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 137
Effective length of database: 6,768,326
Effective search space: 927260662
Effective search space used: 927260662
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 (21.8 bits)
S2: 57 (25.9 bits)