RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy17336
         (28 letters)



>gnl|CDD|202224 pfam02373, JmjC, JmjC domain, hydroxylase.  The JmjC domain
          belongs to the Cupin superfamily. JmjC-domain proteins
          may be protein hydroxylases that catalyze a novel
          histone modification. This is confirmed to be a
          hydroxylase: the human JmjC protein named Tyw5p
          unexpectedly acts in the biosynthesis of a
          hypermodified nucleoside, hydroxy-wybutosine, in
          tRNA-Phe by catalyzing hydroxylation.
          Length = 114

 Score = 26.1 bits (58), Expect = 0.22
 Identities = 11/28 (39%), Positives = 14/28 (50%)

Query: 1  MLFSACCWYRDPHGLPWIEYLHSGASKI 28
          M  S   W+ +  GL  I YLH G  K+
Sbjct: 6  MPGSTTPWHIEDQGLYSINYLHFGGPKV 33


>gnl|CDD|133201 cd05070, PTKc_Fyn_Yrk, Catalytic domain of the Protein Tyrosine
           Kinases, Fyn and Yrk.  Protein Tyrosine Kinase (PTK)
           family; Fyn and Yrk kinases; catalytic (c) domain. The
           PTKc family is part of a larger superfamily that
           includes the catalytic domains of other kinases such as
           protein serine/threonine kinases, RIO kinases, and
           phosphoinositide 3-kinase (PI3K). PTKs catalyze the
           transfer of the gamma-phosphoryl group from ATP to
           tyrosine (tyr) residues in protein substrates. Fyn and
           Yrk are members of the Src subfamily of proteins, which
           are cytoplasmic (or non-receptor) tyr kinases. Src
           kinases contain an N-terminal SH4 domain with a
           myristoylation site, followed by SH3 and SH2 domains, a
           tyr kinase domain, and a regulatory C-terminal region
           containing a conserved tyr. They are activated by
           autophosphorylation at the tyr kinase domain, but are
           negatively regulated by phosphorylation at the
           C-terminal tyr by Csk (C-terminal Src Kinase). Src
           proteins are involved in signaling pathways that
           regulate cytokine and growth factor responses,
           cytoskeleton dynamics, cell proliferation, survival, and
           differentiation. Fyn, together with Lck, plays a
           critical role in T-cell signal transduction by
           phosphorylating ITAM (immunoreceptor tyr activation
           motif) sequences on T-cell receptors, ultimately leading
           to the proliferation and differentiation of T-cells. In
           addition, Fyn is involved in the myelination of neurons,
           and is implicated in Alzheimer's and Parkinson's
           diseases. Yrk has been detected only in chickens. It is
           primarily found in neuronal and epithelial cells and in
           macrophages. It may play a role in inflammation and in
           response to injury.
          Length = 260

 Score = 25.7 bits (56), Expect = 0.35
 Identities = 9/17 (52%), Positives = 10/17 (58%)

Query: 7   CWYRDPHGLPWIEYLHS 23
           CW +DP   P  EYL S
Sbjct: 239 CWKKDPEERPTFEYLQS 255


>gnl|CDD|162284 TIGR01282, nifD, nitrogenase molybdenum-iron protein alpha chain.
           Nitrogenase consists of alpha (NifD) and beta (NifK)
           subunits of the molybdenum-iron protein and an
           ATP-binding iron-sulfur protein (NifH). This model
           describes a large clade of NifD proteins, but excludes a
           lineage that contains putative NifD and NifD homologs
           from species with vanadium-dependent nitrogenases
           [Central intermediary metabolism, Nitrogen fixation].
          Length = 466

 Score = 24.6 bits (54), Expect = 0.77
 Identities = 8/16 (50%), Positives = 12/16 (75%)

Query: 13  HGLPWIEYLHSGASKI 28
           +G+PW+EY   G +KI
Sbjct: 277 YGIPWMEYNFFGPTKI 292


>gnl|CDD|238935 cd01976, Nitrogenase_MoFe_alpha, Nitrogenase_MoFe_alpha_II:
           Nitrogenase MoFe protein, beta subunit. A group of
           proteins similar to the alpha subunit of the MoFe
           protein of the molybdenum (Mo-) nitrogenase. The
           nitrogenase enzyme catalyzes the ATP-dependent reduction
           of dinitrogen to ammonia. The Mo-nitrogenase is the most
           widespread and best characterized of these systems.
           Mo-nitrogenase consists of the MoFe protein (component
           1) and the Fe protein (component 2).  MoFe is an
           alpha2beta2 tetramer. Each alphabeta pair of MoFe
           contains one P-cluster (at the alphabeta interface) and,
           one molecule of iron molybdenum cofactor (FeMoco)
           contained within the alpha subunit. The Fe protein
           contains a single [4Fe-4S] cluster.  Electrons are
           transferred from the [4Fe-4S] cluster of the Fe protein
           to the P-cluster of the MoFe and in turn to FeMoCo, the
           site of substrate reduction.
          Length = 421

 Score = 24.2 bits (53), Expect = 1.00
 Identities = 8/16 (50%), Positives = 12/16 (75%)

Query: 13  HGLPWIEYLHSGASKI 28
           +G+PW+EY   G +KI
Sbjct: 242 YGIPWMEYNFFGPTKI 257


  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
   0.329    0.143    0.566 

Gapped
Lambda     K      H
   0.267   0.0737    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 1,381,941
Number of extensions: 42972
Number of successful extensions: 119
Number of sequences better than 10.0: 1
Number of HSP's gapped: 119
Number of HSP's successfully gapped: 4
Length of query: 28
Length of database: 10,937,602
Length adjustment: 3
Effective length of query: 25
Effective length of database: 10,804,540
Effective search space: 270113500
Effective search space used: 270113500
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 53 (24.2 bits)