RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy15072
         (97 letters)



>gnl|CDD|110592 pfam01599, Ribosomal_S27, Ribosomal protein S27a.  This family of
          ribosomal proteins consists mainly of the 40S ribosomal
          protein S27a which is synthesised as a C-terminal
          extension of ubiquitin (CEP). The S27a domain
          compromises the C-terminal half of the protein. The
          synthesis of ribosomal proteins as extensions of
          ubiquitin promotes their incorporation into nascent
          ribosomes by a transient metabolic stabilisation and is
          required for efficient ribosome biogenesis. The
          ribosomal extension protein S27a contains a basic
          region that is proposed to form a zinc finger; its
          fusion gene is proposed as a mechanism to maintain a
          fixed ratio between ubiquitin necessary for degrading
          proteins and ribosomes a source of proteins.
          Length = 47

 Score = 73.3 bits (180), Expect = 4e-19
 Identities = 23/36 (63%), Positives = 26/36 (72%)

Query: 9  NVDENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCG 44
           VD  GK+ RLRREC + +CGAGVFMA   DR YCG
Sbjct: 7  KVDGEGKVVRLRRECPNPRCGAGVFMAEHKDRQYCG 42


>gnl|CDD|224909 COG1998, RPS31, Ribosomal protein S27AE [Translation, ribosomal
          structure and biogenesis].
          Length = 51

 Score = 42.8 bits (101), Expect = 4e-07
 Identities = 15/34 (44%), Positives = 19/34 (55%), Gaps = 2/34 (5%)

Query: 11 DENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCG 44
           ++ K+ R  R C   +CG GVFMA   DR  CG
Sbjct: 10 VDDEKVKRKNRFCP--RCGPGVFMADHKDRWACG 41


>gnl|CDD|234760 PRK00432, PRK00432, 30S ribosomal protein S27ae; Validated.
          Length = 50

 Score = 31.5 bits (72), Expect = 0.008
 Identities = 14/34 (41%), Positives = 20/34 (58%), Gaps = 3/34 (8%)

Query: 11 DENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCG 44
           + GK+ R  + C   +CG+G FMA   DR +CG
Sbjct: 11 VDGGKVKRKNKFCP--RCGSG-FMAEHLDRWHCG 41


>gnl|CDD|237754 PRK14554, PRK14554, putative pseudouridylate synthase; Provisional.
          Length = 422

 Score = 28.4 bits (64), Expect = 0.48
 Identities = 10/34 (29%), Positives = 15/34 (44%), Gaps = 3/34 (8%)

Query: 43  CGNKFSSLSVELKSARSQVRFPPGANFLTFVLGT 76
           CG  F  +    + A   +    G  F TF++GT
Sbjct: 91  CGGIFDEIDEFAEKAAEALS---GYEFDTFLVGT 121


>gnl|CDD|185167 PRK15255, PRK15255, fimbrial outer membrane usher protein StdB;
           Provisional.
          Length = 829

 Score = 25.5 bits (55), Expect = 5.8
 Identities = 12/26 (46%), Positives = 17/26 (65%)

Query: 52  VELKSARSQVRFPPGANFLTFVLGTA 77
           +EL+SA SQVR+      LTF++  A
Sbjct: 115 LELRSADSQVRYSAENQRLTFIIPQA 140


>gnl|CDD|153280 cd07596, BAR_SNX, The Bin/Amphiphysin/Rvs (BAR) domain of Sorting
           Nexins.  BAR domains are dimerization, lipid binding and
           curvature sensing modules found in many different
           proteins with diverse functions. Sorting nexins (SNXs)
           are Phox homology (PX) domain containing proteins that
           are involved in regulating membrane traffic and protein
           sorting in the endosomal system. SNXs differ from each
           other in their lipid-binding specificity, subcellular
           localization and specific function in the endocytic
           pathway. A subset of SNXs also contain BAR domains. The
           PX-BAR structural unit determines the specific membrane
           targeting of SNXs. BAR domains form dimers that bind to
           membranes, induce membrane bending and curvature, and
           may also be involved in protein-protein interactions.
          Length = 218

 Score = 25.0 bits (55), Expect = 7.6
 Identities = 7/32 (21%), Positives = 12/32 (37%)

Query: 30  AGVFMAAMSDRHYCGNKFSSLSVELKSARSQV 61
                  + DR        SL  +L S ++Q+
Sbjct: 102 CQAVKETLDDRADALLTLQSLKKDLASKKAQL 133


>gnl|CDD|211353 cd07263, Glo_EDI_BRP_like_16, This conserved domain belongs to a
          superfamily including the bleomycin resistance protein,
          glyoxalase I, and type I ring-cleaving dioxygenases.
          This protein family belongs to a conserved domain
          superfamily that is found in a variety of structurally
          related metalloproteins, including the bleomycin
          resistance protein, glyoxalase I, and type I
          ring-cleaving dioxygenases. A bound metal ion is
          required for protein activities for the members of this
          superfamily. A variety of metal ions have been found in
          the catalytic centers of these proteins including
          Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein
          superfamily contains members with or without domain
          swapping.
          Length = 120

 Score = 24.5 bits (54), Expect = 9.1
 Identities = 8/34 (23%), Positives = 13/34 (38%)

Query: 64 PPGANFLTFVLGTASFLVSYPVLLFDSDFTFLIL 97
          PPG+   + VL   +   +    L       L+L
Sbjct: 41 PPGSPETSLVLAPPANPAAMASGLQPGGTPGLVL 74


  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
   0.326    0.137    0.422 

Gapped
Lambda     K      H
   0.267   0.0668    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,807,277
Number of extensions: 371524
Number of successful extensions: 392
Number of sequences better than 10.0: 1
Number of HSP's gapped: 392
Number of HSP's successfully gapped: 12
Length of query: 97
Length of database: 10,937,602
Length adjustment: 64
Effective length of query: 33
Effective length of database: 8,098,946
Effective search space: 267265218
Effective search space used: 267265218
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 53 (24.3 bits)