RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy16375
         (89 letters)



>gnl|CDD|192997 pfam12349, Sterol-sensing, Sterol-sensing domain of SREBP
           cleavage-activation.  Sterol regulatory element-binding
           proteins (SREBPs) are membrane-bound transcription
           factors that promote lipid synthesis in animal cells.
           They are embedded in the membranes of the endoplasmic
           reticulum (ER) in a helical hairpin orientation and are
           released from the ER by a two-step proteolytic process.
           Proteolysis begins when the SREBPs are cleaved at
           Site-1, which is located at a leucine residue in the
           middle of the hydrophobic loop in the lumen of the ER.
           Upon proteolytic processing SREBP can activate the
           expression of genes involved in cholesterol biosynthesis
           and uptake. SCAP stimulates cleavage of SREBPs via
           fusion of the their two C-termini. This domain is the
           transmembrane region that traverses the membrane eight
           times and is the sterol-sensing domain of the cleavage
           protein. WD40 domains are found towards the C-terminus.
          Length = 153

 Score = 64.1 bits (157), Expect = 1e-14
 Identities = 24/72 (33%), Positives = 38/72 (52%)

Query: 18  IIIVLPYFIIIVGLENILVLTKSIISIPSHLDSKIRIAQGLSKEGWSITKNFFLELTVLT 77
              V+P+ ++ VG++N+ +L  ++   P  LD + RIA+ L + G SIT     EL    
Sbjct: 38  PGEVIPFLVLAVGVDNMFLLVHAVQRTPRSLDVEERIAEALGEVGPSITLTSLTELLAFL 97

Query: 78  AGLLTFFPVIQI 89
            G LT  P +Q 
Sbjct: 98  IGALTPMPAVQE 109


>gnl|CDD|233186 TIGR00920, 2A060605, 3-hydroxy-3-methylglutaryl-coenzyme A
           reductase.  [Transport and binding proteins,
           Carbohydrates, organic alcohols, and acids].
          Length = 889

 Score = 30.2 bits (68), Expect = 0.084
 Identities = 17/61 (27%), Positives = 34/61 (55%)

Query: 22  LPYFIIIVGLENILVLTKSIISIPSHLDSKIRIAQGLSKEGWSITKNFFLELTVLTAGLL 81
           LP+F++++ L     L K  +S  S  + +  IA+G++  G +IT +  +E  V+  G +
Sbjct: 125 LPFFLLLIDLSKASALAKFALSSNSQDEVRDNIARGMAILGPTITLDTVVETLVIGVGTM 184

Query: 82  T 82
           +
Sbjct: 185 S 185


>gnl|CDD|222629 pfam14257, DUF4349, Domain of unknown function (DUF4349).  This
           family of proteins is found in bacteria and archaea.
           Proteins in this family are typically between 282 and
           353 amino acids in length. There is a single completely
           conserved residue D that may be functionally important.
          Length = 262

 Score = 26.0 bits (58), Expect = 2.5
 Identities = 10/35 (28%), Positives = 13/35 (37%), Gaps = 1/35 (2%)

Query: 53  RIAQGLSKEGWSITKNFFLELTVLTAGLLTFFPVI 87
                L  EGW     F   L V    LL + P++
Sbjct: 217 GFGDALR-EGWDALVAFLAGLLVFLGALLPWLPLL 250


>gnl|CDD|217050 pfam02460, Patched, Patched family.  The transmembrane protein
           Patched is a receptor for the morphogene Sonic Hedgehog.
           This protein associates with the smoothened protein to
           transduce hedgehog signals.
          Length = 801

 Score = 25.8 bits (57), Expect = 3.7
 Identities = 19/76 (25%), Positives = 37/76 (48%), Gaps = 1/76 (1%)

Query: 15  PYF-IIIVLPYFIIIVGLENILVLTKSIISIPSHLDSKIRIAQGLSKEGWSITKNFFLEL 73
           P+  I+ V P+ ++ +G++++ ++  +       L  K R+ + LS+ G SIT      +
Sbjct: 277 PFNSIVCVTPFLVLAIGVDDMFLMVHAWQRTTKTLSVKKRMGETLSEAGPSITITSLTNV 336

Query: 74  TVLTAGLLTFFPVIQI 89
                G  T  P IQ+
Sbjct: 337 LSFGIGTYTPTPAIQL 352


>gnl|CDD|233184 TIGR00917, 2A060601, Niemann-Pick C type protein family.  The model
           describes Niemann-Pick C type protein in eukaryotes. The
           defective protein has been associated with Niemann-Pick
           disease which is described in humans as autosomal
           recessive lipidosis. It is characterized by the
           lysosomal accumulation of unestrified cholesterol. It is
           an integral membrane protein, which indicates that this
           protein is most likely involved in cholesterol transport
           or acts as some component of cholesterol homeostasis
           [Transport and binding proteins, Other].
          Length = 1204

 Score = 25.6 bits (56), Expect = 4.5
 Identities = 18/82 (21%), Positives = 39/82 (47%), Gaps = 11/82 (13%)

Query: 18  IIIVLPYFIIIVGLENILVLTKSIISI-----PSHLDSKI------RIAQGLSKEGWSIT 66
           I+ V+P+ ++ VG++NI +L ++   +        +D++       ++ + L + G SIT
Sbjct: 637 IMEVIPFLVLAVGVDNIFILVQTYQRLERFYREVGVDNEQELTLEQQLGRALGEVGPSIT 696

Query: 67  KNFFLELTVLTAGLLTFFPVIQ 88
                E      G L+  P ++
Sbjct: 697 LASLSESLAFFLGALSKMPAVR 718


>gnl|CDD|237791 PRK14701, PRK14701, reverse gyrase; Provisional.
          Length = 1638

 Score = 24.5 bits (53), Expect = 9.8
 Identities = 12/36 (33%), Positives = 17/36 (47%)

Query: 49   DSKIRIAQGLSKEGWSITKNFFLELTVLTAGLLTFF 84
            DSK+ IAQ   K+  SI ++    L    +G    F
Sbjct: 1103 DSKVAIAQTPLKDVKSILEDILPFLRTWESGNQVGF 1138


  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
   0.330    0.147    0.427 

Gapped
Lambda     K      H
   0.267   0.0777    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,649,356
Number of extensions: 393860
Number of successful extensions: 643
Number of sequences better than 10.0: 1
Number of HSP's gapped: 639
Number of HSP's successfully gapped: 45
Length of query: 89
Length of database: 10,937,602
Length adjustment: 57
Effective length of query: 32
Effective length of database: 8,409,424
Effective search space: 269101568
Effective search space used: 269101568
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 53 (24.1 bits)