RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy14743
         (86 letters)



>gnl|CDD|197516 smart00100, cNMP, Cyclic nucleotide-monophosphate binding domain.
           Catabolite gene activator protein (CAP) is a
          prokaryotic homologue of eukaryotic cNMP-binding
          domains, present in ion channels, and cNMP-dependent
          kinases.
          Length = 120

 Score = 53.2 bits (128), Expect = 1e-10
 Identities = 20/45 (44%), Positives = 30/45 (66%), Gaps = 1/45 (2%)

Query: 8  FMKNLDMTQIREIVDCMYPVEYIAGSIIIKEGDVGSIVY-VMEGK 51
            KNLD  ++RE+ D + PV Y AG +II++GDVG   Y ++ G+
Sbjct: 1  LFKNLDAEELRELADALEPVRYPAGEVIIRQGDVGDSFYIIVSGE 45


>gnl|CDD|237999 cd00038, CAP_ED, effector domain of the CAP family of
          transcription factors; members include CAP (or cAMP
          receptor protein (CRP)), which binds cAMP, FNR
          (fumarate and nitrate reduction), which uses an
          iron-sulfur cluster to sense oxygen) and CooA, a heme
          containing CO sensor. In all cases binding of the
          effector leads to conformational changes and the
          ability to activate transcription. Cyclic
          nucleotide-binding domain similar to CAP are also
          present in cAMP- and cGMP-dependent protein kinases
          (cAPK and cGPK) and vertebrate cyclic nucleotide-gated
          ion-channels.  Cyclic nucleotide-monophosphate binding
          domain; proteins that bind cyclic nucleotides (cAMP or
          cGMP) share a structural domain of about 120 residues;
          the best studied is the prokaryotic catabolite gene
          activator, CAP, where such a domain is known to be
          composed of three alpha-helices and a distinctive
          eight-stranded, antiparallel beta-barrel structure;
          three conserved glycine residues are thought to be
          essential for maintenance of the structural integrity
          of the beta-barrel; CooA is a homodimeric transcription
          factor that belongs to CAP family; cAMP- and
          cGMP-dependent protein kinases (cAPK and cGPK) contain
          two tandem copies of the cyclic nucleotide-binding
          domain; cAPK's are composed of two different subunits,
          a catalytic chain and a regulatory chain, which
          contains both copies of the domain; cGPK's are single
          chain enzymes that include the two copies of the domain
          in their N-terminal section; also found in vertebrate
          cyclic nucleotide-gated ion-channels.
          Length = 115

 Score = 45.0 bits (107), Expect = 1e-07
 Identities = 13/45 (28%), Positives = 23/45 (51%), Gaps = 1/45 (2%)

Query: 8  FMKNLDMTQIREIVDCMYPVEYIAGSIIIKEGDVGSIVY-VMEGK 51
              LD  ++ E+ D +    + AG +II++GD    +Y V+ G 
Sbjct: 1  LFSGLDDEELEELADALEERRFPAGEVIIRQGDPADSLYIVLSGS 45


>gnl|CDD|238788 cd01530, Cdc25, Cdc25 phosphatases are members of the Rhodanese
          Homology Domain superfamily. They activate the cell
          division kinases throughout the cell cycle progression.
          Cdc25 phosphatases dephosphorylate phosphotyrosine and
          phosphothreonine residues, in order to activate their
          Cdk/cyclin substrates. Cdc25A phosphatase functions to
          regulate S phase entry and Cdc25B is required for G2/M
          phase transition of the cell cycle. The Cdc25 domain
          binds oxyanions at the catalytic site and has the
          signature motif (H/YCxxxxxR).
          Length = 121

 Score = 30.3 bits (69), Expect = 0.049
 Identities = 9/34 (26%), Positives = 14/34 (41%), Gaps = 3/34 (8%)

Query: 2  AILDNDFMKNLDMTQIREIVDCMYPVEYIAGSII 35
           +L   +    +      I+DC +P EY  G I 
Sbjct: 11 RLLQGKY---DNFFDKYIIIDCRFPYEYNGGHIK 41


>gnl|CDD|219570 pfam07778, CENP-I, Mis6.  Mis6 is an essential centromere connector
           protein acting during G1-S phase of the cell cycle. Mis6
           is thought to be required for recruiting CENP-A, the
           centromere- specific histone H3 variant, an important
           event for centromere function and chromosome segregation
           during mitosis.
          Length = 470

 Score = 29.1 bits (65), Expect = 0.22
 Identities = 8/28 (28%), Positives = 14/28 (50%)

Query: 10  KNLDMTQIREIVDCMYPVEYIAGSIIIK 37
           K+ D      I+ C+YP   I+   ++K
Sbjct: 83  KHFDNAVNTRIIKCLYPATKISEDSVVK 110


>gnl|CDD|227436 COG5105, MIH1, Mitotic inducer, protein phosphatase [Cell division
           and chromosome partitioning].
          Length = 427

 Score = 27.7 bits (61), Expect = 0.72
 Identities = 9/33 (27%), Positives = 15/33 (45%), Gaps = 3/33 (9%)

Query: 3   ILDNDFMKNLDMTQIREIVDCMYPVEYIAGSII 35
           +L+  +  +     I   +DC +  EY  G II
Sbjct: 252 VLEGMYNIDFLKCII---IDCRFEYEYRGGHII 281


>gnl|CDD|178459 PLN02868, PLN02868, acyl-CoA thioesterase family protein.
          Length = 413

 Score = 27.0 bits (60), Expect = 1.0
 Identities = 9/41 (21%), Positives = 23/41 (56%)

Query: 8  FMKNLDMTQIREIVDCMYPVEYIAGSIIIKEGDVGSIVYVM 48
           ++ L  + +++I + + P  Y  G  +++EG+ G  +Y +
Sbjct: 15 LLQRLPSSSLKKIAEVVVPKRYGKGEYVVREGEPGDGLYFI 55


>gnl|CDD|215664 pfam00027, cNMP_binding, Cyclic nucleotide-binding domain. 
          Length = 91

 Score = 26.5 bits (59), Expect = 1.1
 Identities = 9/27 (33%), Positives = 14/27 (51%), Gaps = 1/27 (3%)

Query: 26 PVEYIAGSIIIKEGDVG-SIVYVMEGK 51
             +  G +I +EGD   S+  V+ GK
Sbjct: 1  LRSFKKGEVIFREGDPADSLYIVLSGK 27


>gnl|CDD|226234 COG3711, BglG, Transcriptional antiterminator [Transcription].
          Length = 491

 Score = 26.6 bits (59), Expect = 1.8
 Identities = 10/36 (27%), Positives = 15/36 (41%)

Query: 3   ILDNDFMKNLDMTQIREIVDCMYPVEYIAGSIIIKE 38
           IL +  +   +  Q+ + V   YP  YI    I K 
Sbjct: 425 ILISPILDEENDEQLLKQVKKKYPKAYIDVEKIDKL 460


>gnl|CDD|143599 cd07575, Xc-1258_like, Xanthomonas campestris XC1258 and related
          proteins, members of the nitrilase superfamily
          (putative class 13 nitrilases).  Uncharacterized
          subgroup belonging to a larger nitrilase superfamily
          comprised of nitrile- or amide-hydrolyzing enzymes and
          amide-condensing enzymes, which depend on a Glu-Lys-Cys
          catalytic triad. This superfamily has been classified
          in the literature based on global and structure based
          sequence analysis into thirteen different enzyme
          classes (referred to as 1-13), class 13 represents
          proteins that at the time were difficult to place in a
          distinct similarity group; this subgroup either
          represents a new class or one that was included
          previously in class 13. Members of this superfamily
          generally form homomeric complexes, the basic building
          block of which is a homodimer. XC1258 is a
          homotetramer.
          Length = 252

 Score = 24.8 bits (55), Expect = 5.6
 Identities = 8/11 (72%), Positives = 9/11 (81%)

Query: 30 IAGSIIIKEGD 40
          I GS+IIKEG 
Sbjct: 76 ITGSLIIKEGG 86


  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
   0.319    0.139    0.403 

Gapped
Lambda     K      H
   0.267   0.0685    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,366,994
Number of extensions: 352272
Number of successful extensions: 250
Number of sequences better than 10.0: 1
Number of HSP's gapped: 250
Number of HSP's successfully gapped: 10
Length of query: 86
Length of database: 10,937,602
Length adjustment: 54
Effective length of query: 32
Effective length of database: 8,542,486
Effective search space: 273359552
Effective search space used: 273359552
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 (21.7 bits)
S2: 53 (24.3 bits)