RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy2512
         (115 letters)



>gnl|CDD|193472 pfam12999, PRKCSH-like, Glucosidase II beta subunit-like.  The
          sequences found in this family are similar to a region
          found in the beta-subunit of glucosidase II, which is
          also known as protein kinase C substrate 80K-H
          (PRKCSH). The enzyme catalyzes the sequential removal
          of two alpha-1,3-linked glucose residues in the second
          step of N-linked oligosaccharide processing. The beta
          subunit is required for the solubility and stability of
          the heterodimeric enzyme, and is involved in retaining
          the enzyme within the endoplasmic reticulum.
          Length = 176

 Score = 77.1 bits (190), Expect = 5e-19
 Identities = 33/79 (41%), Positives = 44/79 (55%), Gaps = 4/79 (5%)

Query: 5  VTLGVLFSSIWLTSSDVLRPRGVSLMRASLYQPASE--FTCF-DGSLTIPFSYVNDDYCD 61
          +   +L  S+ L +  + + RGVS     LYQP     + C     + + F  VNDDYCD
Sbjct: 1  LLQPLLAISL-LVAIALGKLRGVSPDNLHLYQPDENGNWKCLNHSEIKLSFDQVNDDYCD 59

Query: 62 CQDSSDEPGTSACPNGTFH 80
          C D SDEPGT+AC NG F+
Sbjct: 60 CPDGSDEPGTNACSNGKFY 78



 Score = 27.1 bits (60), Expect = 2.2
 Identities = 14/30 (46%), Positives = 15/30 (50%), Gaps = 4/30 (13%)

Query: 50  IPFSYVNDDYCD---CQDSSDEPGTSACPN 76
           IP   V+D  CD   C D SDE     CPN
Sbjct: 89  IPSFKVDDGVCDYDICCDGSDEA-LGKCPN 117


>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 = 34.1 bits (79), Expect = 0.001
 Identities = 16/32 (50%), Positives = 18/32 (56%), Gaps = 1/32 (3%)

Query: 37 PASEFTCFDGSLTIPFSYVNDDYCDCQDSSDE 68
          P  EF C +G   IP S+V D   DC D SDE
Sbjct: 3  PPGEFQCDNGR-CIPSSWVCDGVDDCGDGSDE 33


>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 = 31.4 bits (72), Expect = 0.010
 Identities = 16/34 (47%), Positives = 19/34 (55%), Gaps = 1/34 (2%)

Query: 37 PASEFTCFDGSLTIPFSYVNDDYCDCQDSSDEPG 70
          P +EF C +G   IP S+V D   DC D SDE  
Sbjct: 2  PPNEFRCANGR-CIPSSWVCDGEDDCGDGSDEEN 34


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

 Score = 28.0 bits (63), Expect = 0.21
 Identities = 15/33 (45%), Positives = 17/33 (51%), Gaps = 1/33 (3%)

Query: 38 ASEFTCFDGSLTIPFSYVNDDYCDCQDSSDEPG 70
            EF C  G   IP S+V D   DC+D SDE  
Sbjct: 5  PDEFQCGSGE-CIPMSWVCDGDPDCEDGSDEKN 36


>gnl|CDD|131358 TIGR02305, HpaG-N-term, 4-hydroxyphenylacetate degradation
           bifunctional isomerase/decarboxylase, N-terminal
           subunit.  This model represents one of two
           subunits/domains of the bifunctional
           isomerase/decarboxylase involved in
           4-hydroxyphenylacetate degradation. In E. coli and some
           other species this enzyme is encoded by a single
           polypeptide containing both this domain and the closely
           related C-terminal domain (TIGR02303). In other species
           such as Pasteurella multocida these domains are found as
           two separate proteins (usually as tandem genes).
           Together, these domains carry out the decarboxylation of
           5-oxopent-3-ene-1,2,5-tricarboxylic acid (OPET) to
           2-hydroxy-2,4-diene-1,7-dioate (HHDD) and the subsequent
           isomerization to 2-oxohept-3-ene-1,7-dioate (OHED).
          Length = 205

 Score = 27.4 bits (61), Expect = 1.5
 Identities = 11/24 (45%), Positives = 13/24 (54%)

Query: 27  VSLMRASLYQPASEFTCFDGSLTI 50
           VSL   S Y+PA +  C DG   I
Sbjct: 94  VSLPEDSYYRPAIKAKCRDGFCPI 117


>gnl|CDD|147175 pfam04875, DUF645, Protein of unknown function, DUF645.  This
          family includes several uncharacterized proteins from
          Vibrio cholerae.
          Length = 59

 Score = 25.2 bits (55), Expect = 3.0
 Identities = 14/48 (29%), Positives = 22/48 (45%)

Query: 6  TLGVLFSSIWLTSSDVLRPRGVSLMRASLYQPASEFTCFDGSLTIPFS 53
          T G + + I L+ S  L    ++L R   +QP S+    D  L   F+
Sbjct: 12 TKGCIIAVIVLSLSRTLNRGQLNLDRFEFWQPTSQLLVLDVCLFDAFA 59


>gnl|CDD|115715 pfam07079, DUF1347, Protein of unknown function (DUF1347).  This
           family consists of several hypothetical bacterial
           proteins of around 610 residues in length. Members of
           this family are highly conserved and seem to be specific
           to Chlamydia species. The function of this family is
           unknown.
          Length = 550

 Score = 25.9 bits (57), Expect = 6.0
 Identities = 11/37 (29%), Positives = 15/37 (40%), Gaps = 4/37 (10%)

Query: 11  FSSIWLT----SSDVLRPRGVSLMRASLYQPASEFTC 43
             S+WLT    S    R  G+ L+    Y  A E+  
Sbjct: 483 LYSLWLTKVAPSPLAYRLLGLCLLENKEYLEAWEYLH 519


>gnl|CDD|215268 PLN02487, PLN02487, zeta-carotene desaturase.
          Length = 569

 Score = 25.5 bits (56), Expect = 8.9
 Identities = 17/47 (36%), Positives = 24/47 (51%), Gaps = 9/47 (19%)

Query: 15  WLTS-SDVLRPRGVSLMRAS-----LYQPASEFTCF-DGSLTIPFSY 54
           W+T   D+   R   L RA+     LY   ++F+CF D +LT P  Y
Sbjct: 396 WVTEMQDLELSR--QLRRAAGLDNLLYSADADFSCFADLALTSPEDY 440


  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
   0.319    0.132    0.421 

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: 5,525,889
Number of extensions: 422353
Number of successful extensions: 303
Number of sequences better than 10.0: 1
Number of HSP's gapped: 302
Number of HSP's successfully gapped: 13
Length of query: 115
Length of database: 10,937,602
Length adjustment: 79
Effective length of query: 36
Effective length of database: 7,433,636
Effective search space: 267610896
Effective search space used: 267610896
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)