RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy11983
         (66 letters)



>gnl|CDD|182541 PRK10551, PRK10551, phage resistance protein; Provisional.
          Length = 518

 Score = 27.6 bits (62), Expect = 0.35
 Identities = 9/39 (23%), Positives = 20/39 (51%), Gaps = 4/39 (10%)

Query: 19  EMTDIGIKIDDVANTVWDNRLVKLNQ----DFKEVTVRG 53
           +   I + I + A + + +RL+ +N+      +E T+ G
Sbjct: 181 DFDGIALIIGNTALSTFSSRLMNVNELPDMPLRETTIPG 219


>gnl|CDD|185742 cd09001, GH43_XYL_2, Glycosyl hydrolase family 43,
           beta-D-xylosidase.  This glycosyl hydrolase family 43
           (GH43) includes mostly enzymes that have been
           characterized to have beta-1,4-xylosidase
           (beta-D-xylosidase;xylan 1,4-beta-xylosidase; EC
           3.2.1.37) activity. They are part of an array of
           hemicellulases that are involved in the final breakdown
           of plant cell-wall whereby they degrade xylan. They
           hydrolyze beta-1,4 glycosidic bonds between two xylose
           units in short xylooligosaccharides. These are inverting
           enzymes (i.e. they invert the stereochemistry of the
           anomeric carbon atom of the substrate) that have an
           aspartate as the catalytic general base, a glutamate as
           the catalytic general acid and another aspartate that is
           responsible for pKa modulation and orienting the
           catalytic acid. A common structural feature of GH43
           enzymes is a 5-bladed beta-propeller domain that
           contains the catalytic acid and catalytic base. A long
           V-shaped groove, partially enclosed at one end, forms a
           single extended substrate-binding surface across the
           face of the propeller.
          Length = 269

 Score = 27.5 bits (62), Expect = 0.41
 Identities = 14/56 (25%), Positives = 20/56 (35%), Gaps = 5/56 (8%)

Query: 11  WAYIRYSGEMTDIGIKIDD-----VANTVWDNRLVKLNQDFKEVTVRGQVEINDQP 61
           W      G   D  +  DD     +       RLV+L+ D   V  + QV I+   
Sbjct: 111 WTKTALDGGYHDPSLLFDDDGTAYLVYGGGTIRLVELSPDLTGVGGKDQVIIDAGE 166


>gnl|CDD|189013 cd09606, M3B_PepF_1, Peptidase family M3B Oligopeptidase F
          (PepF).  Peptidase family M3B Oligopeptidase F (PepF;
          Pz-peptidase B; EC 3.4.24.-) is mostly bacterial and
          includes oligoendopeptidase F from Lactococcus lactis.
          This enzyme hydrolyzes peptides containing between 7
          and 17 amino acids with fairly broad specificity. The
          PepF gene is duplicated in L. lactis on the plasmid
          that bears it, while a shortened second copy is found
          in Bacillus subtilis. Most bacterial PepFs are
          cytoplasmic endopeptidases; however, the PepF Bacillus
          amyloliquefaciens oligopeptidase is a secreted protein
          and may facilitate the process of sporulation.
          Specifically, the yjbG gene encoding the homolog of the
          PepF1 and PepF2 oligoendopeptidases of Lactococcus
          lactis has been identified in Bacillus subtilis as an
          inhibitor of sporulation initiation when over expressed
          from a multicopy plasmid.
          Length = 546

 Score = 25.6 bits (57), Expect = 1.8
 Identities = 12/47 (25%), Positives = 20/47 (42%), Gaps = 6/47 (12%)

Query: 5  LLTLITWAYIRYSGEMTDIGIKIDDVANTVWDN---RLVKLNQDFKE 48
          L  + T AYIR++ + TD   +        +D     L +L  +  E
Sbjct: 43 LDEMATLAYIRHTIDTTDEFYE---KEYDYFDEIEPLLKELENELYE 86


>gnl|CDD|222740 pfam14412, AHH, A nuclease family of the HNH/ENDO VII superfamily
          with conserved AHH.  AHH is a predicted nuclease of the
          HNH/ENDO VII superfamily of the treble clef fold. The
          name is derived from the conserved motif, AHH. It is
          found in bacterial polymorphic toxin systems and
          functions as a toxin module. Like WHH and LHH, the AHH
          nuclease contains 4 conserved histidines of which, the
          first one is predicted to bind a metal-ion and the
          other three ones are involved in activation of a water
          molecule for hydrolysis.
          Length = 107

 Score = 25.4 bits (56), Expect = 1.9
 Identities = 8/32 (25%), Positives = 13/32 (40%), Gaps = 4/32 (12%)

Query: 8  LITWAYIRYSGEMTDI----GIKIDDVANTVW 35
          ++       + E   I    GI ++D  N VW
Sbjct: 22 IVPKKNFSRTPEARKILKKYGIDLNDAENGVW 53


>gnl|CDD|236701 PRK10490, PRK10490, sensor protein KdpD; Provisional.
          Length = 895

 Score = 25.0 bits (55), Expect = 3.3
 Identities = 9/28 (32%), Positives = 13/28 (46%), Gaps = 4/28 (14%)

Query: 14  IRYSGEMTDIGIKIDDVANT----VWDN 37
           ++Y+G   +IGI            VWDN
Sbjct: 791 VKYAGAQAEIGIDAHVEGERLQLDVWDN 818


>gnl|CDD|99737 cd00613, GDC-P, Glycine cleavage system P-protein, alpha- and
           beta-subunits. This family consists of Glycine cleavage
           system P-proteins EC:1.4.4.2 from bacterial, mammalian
           and plant sources. The P protein is part of the glycine
           decarboxylase multienzyme complex EC:2.1.2.10 (GDC) also
           annotated as glycine cleavage system or glycine
           synthase. GDC consists of four proteins P, H, L and T.
           The reaction catalysed by this protein is: Glycine +
           lipoylprotein <=> S-aminomethyldihydrolipoylprotein +
           CO2. Alpha-beta-type dimers associate to form an
           alpha(2)beta(2) tetramer, where the alpha- and
           beta-subunits are structurally similar and appear to
           have arisen by gene duplication and subsequent
           divergence with a loss of one active site. The members
           of this CD are widely dispersed among all three forms of
           cellular life.
          Length = 398

 Score = 24.5 bits (54), Expect = 4.5
 Identities = 8/15 (53%), Positives = 9/15 (60%)

Query: 4   ALLTLITWAYIRYSG 18
           ALL L+   YI Y G
Sbjct: 288 ALLALMAAMYIVYLG 302


>gnl|CDD|165216 PHA02889, PHA02889, hypothetical protein; Provisional.
          Length = 241

 Score = 24.2 bits (52), Expect = 6.7
 Identities = 13/43 (30%), Positives = 21/43 (48%), Gaps = 1/43 (2%)

Query: 3   CALLTLITWAYIRYSGEMTDIGIKIDDVANTVWDNRLVKLNQD 45
           C L+ +I   YI    +      KID + + + D  L+KL+ D
Sbjct: 182 CTLIIIIIVCYISCKHKTCFFKKKIDKIDD-IEDFILIKLHPD 223


>gnl|CDD|182797 PRK10872, relA, (p)ppGpp synthetase I/GTP pyrophosphokinase;
           Provisional.
          Length = 743

 Score = 24.0 bits (52), Expect = 7.1
 Identities = 13/35 (37%), Positives = 19/35 (54%), Gaps = 5/35 (14%)

Query: 5   LLTLITWAYIRYSGEMTDIGIKIDDVANTVWDNRL 39
           L  LI W       EM D G  +D+V + V+D+R+
Sbjct: 377 LRKLIAW-----QEEMADSGEMLDEVRSQVFDDRV 406


  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    0.412 

Gapped
Lambda     K      H
   0.267   0.0681    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,231,747
Number of extensions: 226769
Number of successful extensions: 207
Number of sequences better than 10.0: 1
Number of HSP's gapped: 207
Number of HSP's successfully gapped: 11
Length of query: 66
Length of database: 10,937,602
Length adjustment: 37
Effective length of query: 29
Effective length of database: 9,296,504
Effective search space: 269598616
Effective search space used: 269598616
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: 53 (24.3 bits)