RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy6537
         (66 letters)



>gnl|CDD|238060 cd00112, LDLa, Low Density Lipoprotein Receptor Class A domain, a
          cysteine-rich repeat that plays a central role in
          mammalian cholesterol metabolism; the receptor protein
          binds LDL and transports it into cells by endocytosis;
          7 successive cysteine-rich repeats of about 40 amino
          acids are present in the N-terminal of this multidomain
          membrane protein; other homologous domains occur in
          related receptors, including the very low-density
          lipoprotein receptor and the LDL receptor-related
          protein/alpha 2-macroglobulin receptor, and in proteins
          which are functionally unrelated, such as the C9
          component of complement; the binding of calcium is
          required for in vitro formation of the native disulfide
          isomer and is necessary in establishing and maintaining
          the modular structure.
          Length = 35

 Score = 43.0 bits (102), Expect = 6e-08
 Identities = 17/36 (47%), Positives = 22/36 (61%), Gaps = 1/36 (2%)

Query: 29 CAWSEFSCHDRLQCVPLSARCNGVSDCRDYSDEVNC 64
          C  +EF C +  +C+P S  C+G  DC D SDE NC
Sbjct: 1  CPPNEFRCANG-RCIPSSWVCDGEDDCGDGSDEENC 35


>gnl|CDD|200964 pfam00057, Ldl_recept_a, Low-density lipoprotein receptor domain
          class A. 
          Length = 37

 Score = 40.7 bits (96), Expect = 7e-07
 Identities = 17/36 (47%), Positives = 21/36 (58%), Gaps = 1/36 (2%)

Query: 29 CAWSEFSCHDRLQCVPLSARCNGVSDCRDYSDEVNC 64
          C   EF C    +C+P+S  C+G  DC D SDE NC
Sbjct: 3  CGPDEFQCGSG-ECIPMSWVCDGDPDCEDGSDEKNC 37


>gnl|CDD|197566 smart00192, LDLa, Low-density lipoprotein receptor domain class
          A.  Cysteine-rich repeat in the low-density lipoprotein
          (LDL) receptor that plays a central role in mammalian
          cholesterol metabolism. The N-terminal type A repeats
          in LDL receptor bind the lipoproteins. Other homologous
          domains occur in related receptors, including the very
          low-density lipoprotein receptor and the LDL
          receptor-related protein/alpha 2-macroglobulin
          receptor, and in proteins which are functionally
          unrelated, such as the C9 component of complement.
          Mutations in the LDL receptor gene cause familial
          hypercholesterolemia.
          Length = 33

 Score = 36.5 bits (85), Expect = 3e-05
 Identities = 16/33 (48%), Positives = 20/33 (60%), Gaps = 1/33 (3%)

Query: 29 CAWSEFSCHDRLQCVPLSARCNGVSDCRDYSDE 61
          C   EF C +  +C+P S  C+GV DC D SDE
Sbjct: 2  CPPGEFQCDNG-RCIPSSWVCDGVDDCGDGSDE 33


>gnl|CDD|235315 PRK04841, PRK04841, transcriptional regulator MalT; Provisional.
          Length = 903

 Score = 26.8 bits (60), Expect = 0.67
 Identities = 7/28 (25%), Positives = 12/28 (42%), Gaps = 6/28 (21%)

Query: 28  SCAW------SEFSCHDRLQCVPLSARC 49
            CA       S +    +LQC+ + A+ 
Sbjct: 594 QCARKGLEVLSNYQPQQQLQCLAMLAKI 621


>gnl|CDD|220421 pfam09817, DUF2352, Uncharacterized conserved protein (DUF2352).
           Members of this family of uncharacterized proteins have
           no known function.
          Length = 584

 Score = 26.3 bits (58), Expect = 1.0
 Identities = 10/42 (23%), Positives = 15/42 (35%), Gaps = 5/42 (11%)

Query: 26  TVSCAWSEFSCHDRLQCVPLSARC-----NGVSDCRDYSDEV 62
           T+  +W+  S    LQ   L+         G  DCR   +  
Sbjct: 208 TLDLSWNTVSELVILQHPDLALSATLNIKVGSGDCRSPLEYF 249


>gnl|CDD|215282 PLN02511, PLN02511, hydrolase.
          Length = 388

 Score = 24.7 bits (54), Expect = 3.4
 Identities = 10/18 (55%), Positives = 11/18 (61%), Gaps = 3/18 (16%)

Query: 7   CLGCATSYVPPVTTPAYY 24
             GCA S   PVTTP +Y
Sbjct: 137 SRGCADS---PVTTPQFY 151


  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
   0.324    0.136    0.484 

Gapped
Lambda     K      H
   0.267   0.0761    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,088,885
Number of extensions: 195534
Number of successful extensions: 171
Number of sequences better than 10.0: 1
Number of HSP's gapped: 171
Number of HSP's successfully gapped: 7
Length of query: 66
Length of database: 10,937,602
Length adjustment: 37
Effective length of query: 29
Effective length of database: 9,296,504
Effective search space: 269598616
Effective search space used: 269598616
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (24.1 bits)