RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy16337
         (104 letters)



>gnl|CDD|217080 pfam02517, Abi, CAAX protease self-immunity.  Members of this
          family are probably proteases (after a isoprenyl group
          is attached to the Cys residue in the C-terminal CAAX
          motif of a protein to attach it to the membrane, the
          AAX tripeptide being removed by one of the CAAX prenyl
          proteases). The family contains the CAAX prenyl
          protease. The proteins contain a highly conserved
          Glu-Glu motif at the amino end of the alignment. The
          alignment also contains two histidine residues that may
          be involved in zinc binding. While they are involved in
          membrane anchoring of proteins in eukaryotes, little is
          known about their function in prokaryotes. In some
          known bacteriocin loci, Abi genes have been found
          downstream of bacteriocin structural genes where they
          are probably involved in self-immunity. Investigation
          of the bacteriocin-like loci in the Gram positive
          bacteria locus from Lactobacillus sakei 23K confirmed
          that the bacteriocin-like genes (sak23Kalphabeta)
          exhibited antimicrobial activity when expressed in a
          heterologous host and that the associated Abi gene
          (sak23Ki) conferred immunity against the cognate
          bacteriocin. Interestingly, the immunity genes from
          three similar systems conferred a high degree of
          cross-immunity against each other's bacteriocins,
          suggesting the recognition of a common receptor.
          Site-directed mutagenesis demonstrated that the
          conserved motifs constituting the putative proteolytic
          active site of the Abi proteins are essential for the
          immunity function of Sak23Ki - thus a new concept in
          self-immunity.
          Length = 93

 Score = 27.5 bits (62), Expect = 0.54
 Identities = 12/34 (35%), Positives = 15/34 (44%)

Query: 19 FQFSYTSLFGGYSAFLFVRTGHFVAPFLAHAFCN 52
            F    L G    +L++RTG   A  L HA  N
Sbjct: 58 LAFLSAFLLGLVLGWLYLRTGSLWAAILLHALNN 91


>gnl|CDD|237835 PRK14850, PRK14850, penicillin-binding protein 1b; Provisional.
          Length = 764

 Score = 26.7 bits (59), Expect = 2.4
 Identities = 17/44 (38%), Positives = 21/44 (47%), Gaps = 3/44 (6%)

Query: 55  GFPDFEEIYAFGEPRRSAVL--CVCVVGLIGWAFLLGPMTSPAL 96
           GFP    IY FG P     L     +VG++  A L  P T+P L
Sbjct: 270 GFP-LASIYYFGRPINELNLDQYALLVGMVKGASLYNPWTNPNL 312


>gnl|CDD|234925 PRK01233, glyS, glycyl-tRNA synthetase subunit beta; Validated.
          Length = 682

 Score = 25.9 bits (58), Expect = 5.3
 Identities = 11/23 (47%), Positives = 11/23 (47%), Gaps = 3/23 (13%)

Query: 59 FEEIYAFGEPRRSAVLCVCVVGL 81
          F  I  F  PRR   L V V GL
Sbjct: 40 FGSIKVFATPRR---LAVLVEGL 59


>gnl|CDD|235170 PRK03881, PRK03881, hypothetical protein; Provisional.
          Length = 467

 Score = 25.6 bits (57), Expect = 5.4
 Identities = 8/20 (40%), Positives = 9/20 (45%)

Query: 54  MGFPDFEEIYAFGEPRRSAV 73
            G    EE+Y FG   R A 
Sbjct: 150 YGGLSPEELYKFGMAIREAA 169


>gnl|CDD|224155 COG1234, ElaC, Metal-dependent hydrolases of the beta-lactamase
           superfamily III [General function prediction only].
          Length = 292

 Score = 25.5 bits (56), Expect = 6.2
 Identities = 12/54 (22%), Positives = 15/54 (27%)

Query: 21  FSYTSLFGGYSAFLFVRTGHFVAPFLAHAFCNHMGFPDFEEIYAFGEPRRSAVL 74
           F  TSL   YS   +   GH +           +        Y   EP R    
Sbjct: 97  FVETSLRLSYSKLTYEIIGHEIEEDAFEVEALELDHGVPALGYRIEEPDRPGRF 150


>gnl|CDD|216871 pfam02092, tRNA_synt_2f, Glycyl-tRNA synthetase beta subunit. 
          Length = 549

 Score = 25.5 bits (57), Expect = 6.3
 Identities = 11/24 (45%), Positives = 12/24 (50%), Gaps = 3/24 (12%)

Query: 58 DFEEIYAFGEPRRSAVLCVCVVGL 81
           F E+  F  PRR   L V V GL
Sbjct: 36 SFGEVKVFATPRR---LAVLVEGL 56


>gnl|CDD|215734 pfam00124, Photo_RC, Photosynthetic reaction centre protein. 
          Length = 257

 Score = 25.3 bits (56), Expect = 6.6
 Identities = 6/23 (26%), Positives = 11/23 (47%)

Query: 81  LIGWAFLLGPMTSPALYSNNLWW 103
           +IG+        +P L+  N +W
Sbjct: 20  IIGFNAAASVTWNPLLFGRNFFW 42


>gnl|CDD|223822 COG0751, GlyS, Glycyl-tRNA synthetase, beta subunit [Translation,
          ribosomal structure and biogenesis].
          Length = 691

 Score = 25.3 bits (56), Expect = 7.9
 Identities = 10/23 (43%), Positives = 12/23 (52%), Gaps = 3/23 (13%)

Query: 59 FEEIYAFGEPRRSAVLCVCVVGL 81
          FE +  F  PRR   L + V GL
Sbjct: 42 FEGVEVFATPRR---LALLVKGL 61


>gnl|CDD|185304 PRK15406, PRK15406, oligopeptide ABC transporter permease OppC;
           Provisional.
          Length = 302

 Score = 25.2 bits (55), Expect = 8.4
 Identities = 12/33 (36%), Positives = 17/33 (51%)

Query: 70  RSAVLCVCVVGLIGWAFLLGPMTSPALYSNNLW 102
           R+AV  + V+ LI    +L PM S   Y +  W
Sbjct: 37  RAAVASLIVLVLIALFVILAPMLSQFAYDDTDW 69


  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
   0.333    0.143    0.508 

Gapped
Lambda     K      H
   0.267   0.0736    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,575,396
Number of extensions: 481268
Number of successful extensions: 669
Number of sequences better than 10.0: 1
Number of HSP's gapped: 667
Number of HSP's successfully gapped: 44
Length of query: 104
Length of database: 10,937,602
Length adjustment: 69
Effective length of query: 35
Effective length of database: 7,877,176
Effective search space: 275701160
Effective search space used: 275701160
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 (22.0 bits)
S2: 53 (24.2 bits)