RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy778
         (75 letters)



>gnl|CDD|132707 TIGR03668, Rv0121_F420, PPOX class probable F420-dependent
          enzyme, Rv0121 family.  A Genome Properties metabolic
          reconstruction for F420 biosynthesis shows that
          slightly over 10 percent of all prokaryotes with fully
          sequenced genomes, including about two thirds of the
          Actinomycetales, make F420. A variant of the Partial
          Phylogenetic Profiling algorithm, SIMBAL, shows that
          this protein likely binds F420 in a cleft similar to
          that in which the homologous enzyme pyridoxamine
          phosphate oxidase (PPOX) binds FMN [Unknown function,
          Enzymes of unknown specificity].
          Length = 141

 Score = 26.0 bits (57), Expect = 1.7
 Identities = 11/37 (29%), Positives = 14/37 (37%)

Query: 36 RPKLMPPLNERVMLYVRQESDEIYTPLHVSPPTTQGL 72
           P L+P +       V      IYT +   P TT  L
Sbjct: 25 EPHLVPVVFAVGAGAVAAGDAVIYTAVDAKPKTTPRL 61


>gnl|CDD|176484 cd08366, APC10, APC10 subunit of the anaphase-promoting complex
          (APC) that mediates substrate ubiquitination.  This
          model represents the single domain protein APC10, a
          subunit of the anaphase-promoting complex (APC), which
          is a multi-subunit E3 ubiquitin ligase. E3 ubiquitin
          ligases mediate substrate ubiquitination (or
          ubiquitylation), a vital component of the ubiquitin-26S
          proteasome pathway for selective proteolytic
          degradation. The APC (also known as the cyclosome), is
          a cell cycle-regulated E3 ubiquitin ligase that
          controls important transitions in mitosis and the G1
          phase by ubiquitinating regulatory proteins, thereby
          targeting them for degradation. In mitosis, the APC
          initiates sister chromatid separation by ubiquitinating
          the anaphase inhibitor securin and triggers exit from
          mitosis by ubiquitinating cyclin B. The C-terminus of
          APC10 binds to CDC27/APC3, an APC subunit that contains
          multiple tetratrico peptide repeats. APC10 domains are
          homologous to the DOC1 domains present in the HECT
          (Homologous to the E6-AP Carboxyl Terminus) E3
          ubiquitin ligase protein, and the Cullin-RING (Really
          Interesting New Gene) E3 ubiquitin ligase complex. The
          APC10/DOC1 domain forms a beta-sandwich structure that
          is related in architecture to the galactose-binding
          domain-like fold; their sequences are quite dissimilar,
          however, and are not included here.
          Length = 139

 Score = 25.2 bits (56), Expect = 2.5
 Identities = 10/29 (34%), Positives = 13/29 (44%), Gaps = 2/29 (6%)

Query: 37 PKLMPPLNERVMLYVRQESDEIYTPLHVS 65
           K        V LY+  + DE YTP  +S
Sbjct: 47 SKKTDI--SAVALYLDYKLDESYTPSKIS 73


>gnl|CDD|215283 PLN02518, PLN02518, pheophorbide a oxygenase.
          Length = 539

 Score = 24.4 bits (53), Expect = 7.5
 Identities = 13/49 (26%), Positives = 20/49 (40%)

Query: 23 TTDGTVFSSLPLKRPKLMPPLNERVMLYVRQESDEIYTPLHVSPPTTQG 71
              T+ SS P   P  +P      +   R    +I+TPL V+ P +  
Sbjct: 9  CNSLTLTSSTPKSTPFFIPARTIPFVSSSRPRRGKIFTPLRVAAPPSVP 57


>gnl|CDD|173692 cd05601, STKc_CRIK, Catalytic domain of the Protein
           Serine/Threonine Kinase, Citron Rho-interacting kinase. 
           Serine/Threonine Kinases (STKs), Citron Rho-interacting
           kinase (CRIK) subfamily, catalytic (c) domain. STKs
           catalyze the transfer of the gamma-phosphoryl group from
           ATP to serine/threonine residues on protein substrates.
           The CRIK subfamily is part of a larger superfamily that
           includes the catalytic domains of other protein STKs,
           protein tyrosine kinases, RIO kinases, aminoglycoside
           phosphotransferase, choline kinase, and phosphoinositide
           3-kinase. CRIK is also called citron kinase. It contains
           a catalytic domain, a central coiled-coil domain, and a
           C-terminal region containing a Rho-binding domain (RBD),
           a zinc finger, and a pleckstrin homology (PH) domain, in
           addition to other motifs. CRIK, an effector of the small
           GTPase Rho, plays an important function during
           cytokinesis and affects its contractile process.
           CRIK-deficient mice show severe ataxia and epilepsy as a
           result of abnormal cytokinesis and massive apoptosis in
           neuronal precursors. A Down syndrome critical region
           protein TTC3 interacts with CRIK and inhibits
           CRIK-dependent neuronal differentiation and neurite
           extension.
          Length = 330

 Score = 24.4 bits (53), Expect = 7.7
 Identities = 8/21 (38%), Positives = 11/21 (52%)

Query: 22  LTTDGTVFSSLPLKRPKLMPP 42
           LT +  V S LP+  P  + P
Sbjct: 152 LTANKMVNSKLPVGTPDYIAP 172


  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
   0.317    0.135    0.400 

Gapped
Lambda     K      H
   0.267   0.0802    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,854,942
Number of extensions: 287511
Number of successful extensions: 203
Number of sequences better than 10.0: 1
Number of HSP's gapped: 203
Number of HSP's successfully gapped: 4
Length of query: 75
Length of database: 10,937,602
Length adjustment: 45
Effective length of query: 30
Effective length of database: 8,941,672
Effective search space: 268250160
Effective search space used: 268250160
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (24.1 bits)