RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy13853
         (108 letters)



>gnl|CDD|173789 cd04059, Peptidases_S8_Protein_convertases_Kexins_Furin-like,
           Peptidase S8 family domain in Protein convertases.
           Protein convertases, whose members include furins and
           kexins, are members of the peptidase S8 or Subtilase
           clan of proteases. They have an Asp/His/Ser catalytic
           triad that is not homologous to trypsin. Kexins are
           involved in the activation of peptide hormones, growth
           factors, and viral proteins.  Furin cleaves cell surface
           vasoactive peptides and proteins involved in
           cardiovascular tissue remodeling in the TGN, at cell
           surface, or in endosomes but rarely in the ER.  Furin
           also plays a key role in blood pressure regulation
           though the activation of transforming growth factor
           (TGF)-beta. High specificity is seen for cleavage after
           dibasic (Lys-Arg or Arg-Arg) or multiple basic residues
           in protein convertases.  There is also strong sequence
           conservation.
          Length = 297

 Score = 90.3 bits (225), Expect = 2e-23
 Identities = 35/60 (58%), Positives = 41/60 (68%), Gaps = 1/60 (1%)

Query: 48  IRMLDQPYMTDLIEANSMGHEPNLIDIYSASWGPTDDGKTVDGPRNATMRAIVRGVNETR 107
           IRMLD   +TD++EA S+G  P+ IDIYS SWGP DDGKTVDGP     RA+  GV   R
Sbjct: 116 IRMLDGD-VTDVVEAESLGLNPDYIDIYSNSWGPDDDGKTVDGPGPLAQRALENGVTNGR 174


>gnl|CDD|215701 pfam00082, Peptidase_S8, Subtilase family.  Subtilases are a family
           of serine proteases. They appear to have independently
           and convergently evolved an Asp/Ser/His catalytic triad,
           like that found in the trypsin serine proteases (see
           pfam00089). Structure is an alpha/beta fold containing a
           7-stranded parallel beta sheet, order 2314567.
          Length = 277

 Score = 35.0 bits (81), Expect = 0.003
 Identities = 14/64 (21%), Positives = 23/64 (35%), Gaps = 9/64 (14%)

Query: 48  IRMLDQPYMTDLIEANSMG---HEPNLIDIYSASWGPTDDGKTVDGPRNATMRAIVRGVN 104
           +++L     TD   A ++      PN I + + S GP D       P ++   AI     
Sbjct: 77  VKVLPGSGGTDSELAGAIEWAAERPNDIRVINMSLGPVDG------PPSSWSSAIDELAV 130

Query: 105 ETRT 108
               
Sbjct: 131 NGAD 134


>gnl|CDD|197314 cd09080, TDP2, Phosphodiesterase domain of human TDP2, a 5'-tyrosyl
           DNA phosphodiesterase, and related domains.  Human TDP2,
           also known as TTRAP (TRAF/TNFR-associated factors, and
           tumor necrosis factor receptor/TNFR-associated protein),
           is a 5'-tyrosyl DNA phosphodiesterase. It is required
           for the efficient repair of topoisomerase II-induced DNA
           double strand breaks. The topoisomerase is covalently
           linked by a phosphotyrosyl bond to the 5'-terminus of
           the break. TDP2 cleaves the DNA 5'-phosphodiester bond
           and restores 5'-phosphate termini, needed for subsequent
           DNA ligation, and hence repair of the break. TDP2 and
           3'-tyrosyl DNA phosphodiesterase (TDP1) are
           complementary activities; together, they allow cells to
           remove trapped topoisomerase from both 3'- and 5'-DNA
           termini. TTRAP has been reported as being involved in
           apoptosis, embryonic development, and transcriptional
           regulation, and it may inhibit the activation of nuclear
           factor-kB. This family belongs to the large EEP
           (exonuclease/endonuclease/phosphatase) superfamily that
           contains functionally diverse enzymes that share a
           common catalytic mechanism of cleaving phosphodiester
           bonds.
          Length = 248

 Score = 29.2 bits (66), Expect = 0.27
 Identities = 9/39 (23%), Positives = 15/39 (38%)

Query: 64  SMGHEPNLIDIYSASWGPTDDGKTVDGPRNATMRAIVRG 102
           + G     +D +     P + G T D  +N  +R    G
Sbjct: 163 TGGLPNGFVDAWEELGPPGEPGYTWDTQKNPMLRKGEAG 201


>gnl|CDD|130895 TIGR01836, PHA_synth_III_C, poly(R)-hydroxyalkanoic acid synthase,
           class III, PhaC subunit.  This model represents the PhaC
           subunit of a heterodimeric form of polyhydroxyalkanoic
           acid (PHA) synthase. Excepting the PhaC of Bacillus
           megaterium (which needs PhaR), all members require PhaE
           (TIGR01834) for activity and are designated class III.
           This enzyme builds ester polymers for carbon and energy
           storage that accumulate in inclusions, and both this
           enzyme and the depolymerase associate with the
           inclusions. Class III enzymes polymerize
           short-chain-length hydroxyalkanoates [Fatty acid and
           phospholipid metabolism, Biosynthesis].
          Length = 350

 Score = 27.8 bits (62), Expect = 1.2
 Identities = 13/38 (34%), Positives = 19/38 (50%), Gaps = 6/38 (15%)

Query: 50  MLDQPYMTDLIEANSMGHEPNL----IDIYSASWGPTD 83
           ++++PYM DL E  S+     L     D+Y   WG  D
Sbjct: 71  LVNRPYMLDLQEDRSLVR--GLLERGQDVYLIDWGYPD 106


>gnl|CDD|239213 cd02862, NorE_like, NorE_like subfamily of heme-copper oxidase
           subunit III.  Heme-copper oxidases include cytochrome c
           and ubiquinol oxidases.  Alcaligenes faecalis norE is
           found in a gene cluster containing norCB. norCB encodes
           the cytochrome c and cytochrome b subunits of nitric
           oxide reductase (NOR). Based on this and on its
           similarity to subunit III of cytochrome c oxidase (CcO)
           and ubiquinol oxidase, NorE has been speculated to be a
           subunit of NOR.
          Length = 186

 Score = 26.4 bits (59), Expect = 2.4
 Identities = 9/24 (37%), Positives = 12/24 (50%)

Query: 21  AQNPHLGSFRVLSFVVTTLHSRHV 44
             +P  G F  L F++T  H  HV
Sbjct: 112 GIDPDAGLFFTLYFLLTGFHLLHV 135


>gnl|CDD|218006 pfam04286, DUF445, Protein of unknown function (DUF445).  Predicted
           to be a membrane protein.
          Length = 366

 Score = 25.7 bits (57), Expect = 5.5
 Identities = 6/38 (15%), Positives = 13/38 (34%), Gaps = 3/38 (7%)

Query: 30  RVLSFVVTTLHS---RHVSSRIRMLDQPYMTDLIEANS 64
                ++   H    + +S  +   D   + +LIE   
Sbjct: 300 DAAERILERYHLEIGQLISETVNRWDAEELEELIELIV 337


>gnl|CDD|182485 PRK10472, PRK10472, low affinity gluconate transporter;
           Provisional.
          Length = 445

 Score = 25.9 bits (57), Expect = 5.7
 Identities = 11/30 (36%), Positives = 14/30 (46%)

Query: 5   WASVYHYLTVLEIPLDAQNPHLGSFRVLSF 34
           W +       L IP D   PHLG  ++ SF
Sbjct: 197 WGNFISRYVELHIPDDISEPHLGEGKMPSF 226


  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    0.133    0.402 

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: 5,380,446
Number of extensions: 439178
Number of successful extensions: 300
Number of sequences better than 10.0: 1
Number of HSP's gapped: 300
Number of HSP's successfully gapped: 17
Length of query: 108
Length of database: 10,937,602
Length adjustment: 73
Effective length of query: 35
Effective length of database: 7,699,760
Effective search space: 269491600
Effective search space used: 269491600
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 (24.1 bits)