RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17376
(227 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 = 50.3 bits (121), Expect = 4e-09
Identities = 18/35 (51%), Positives = 23/35 (65%)
Query: 118 CPVSHYKCSNDFCIPLDKVCNFIDDCGDNSDEMEC 152
CP + ++C+N CIP VC+ DDCGD SDE C
Sbjct: 1 CPPNEFRCANGRCIPSSWVCDGEDDCGDGSDEENC 35
Score = 44.9 bits (107), Expect = 4e-07
Identities = 18/35 (51%), Positives = 20/35 (57%), Gaps = 1/35 (2%)
Query: 80 CLPNEFRCSN-SCIDHLKRCDRTQDCELGEDEIDC 113
C PNEFRC+N CI CD DC G DE +C
Sbjct: 1 CPPNEFRCANGRCIPSSWVCDGEDDCGDGSDEENC 35
Score = 32.2 bits (74), Expect = 0.012
Identities = 11/27 (40%), Positives = 18/27 (66%)
Query: 34 FQCNQTQCILETSLCNGIPECGNGRDE 60
F+C +CI + +C+G +CG+G DE
Sbjct: 6 FRCANGRCIPSSWVCDGEDDCGDGSDE 32
>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 = 44.5 bits (106), Expect = 4e-07
Identities = 17/32 (53%), Positives = 21/32 (65%)
Query: 118 CPVSHYKCSNDFCIPLDKVCNFIDDCGDNSDE 149
CP ++C N CIP VC+ +DDCGD SDE
Sbjct: 2 CPPGEFQCDNGRCIPSSWVCDGVDDCGDGSDE 33
Score = 37.6 bits (88), Expect = 1e-04
Identities = 15/32 (46%), Positives = 16/32 (50%), Gaps = 1/32 (3%)
Query: 80 CLPNEFRCSNS-CIDHLKRCDRTQDCELGEDE 110
C P EF+C N CI CD DC G DE
Sbjct: 2 CPPGEFQCDNGRCIPSSWVCDGVDDCGDGSDE 33
Score = 31.1 bits (71), Expect = 0.033
Identities = 12/27 (44%), Positives = 20/27 (74%)
Query: 34 FQCNQTQCILETSLCNGIPECGNGRDE 60
FQC+ +CI + +C+G+ +CG+G DE
Sbjct: 7 FQCDNGRCIPSSWVCDGVDDCGDGSDE 33
>gnl|CDD|200964 pfam00057, Ldl_recept_a, Low-density lipoprotein receptor domain
class A.
Length = 37
Score = 42.3 bits (100), Expect = 3e-06
Identities = 16/35 (45%), Positives = 20/35 (57%), Gaps = 1/35 (2%)
Query: 80 CLPNEFRCSNS-CIDHLKRCDRTQDCELGEDEIDC 113
C P+EF+C + CI CD DCE G DE +C
Sbjct: 3 CGPDEFQCGSGECIPMSWVCDGDPDCEDGSDEKNC 37
Score = 38.0 bits (89), Expect = 1e-04
Identities = 14/35 (40%), Positives = 19/35 (54%)
Query: 118 CPVSHYKCSNDFCIPLDKVCNFIDDCGDNSDEMEC 152
C ++C + CIP+ VC+ DC D SDE C
Sbjct: 3 CGPDEFQCGSGECIPMSWVCDGDPDCEDGSDEKNC 37
Score = 31.1 bits (71), Expect = 0.039
Identities = 12/27 (44%), Positives = 18/27 (66%)
Query: 34 FQCNQTQCILETSLCNGIPECGNGRDE 60
FQC +CI + +C+G P+C +G DE
Sbjct: 8 FQCGSGECIPMSWVCDGDPDCEDGSDE 34
>gnl|CDD|220844 pfam10675, DUF2489, Protein of unknown function (DUF2489). This is
a bacterial family of uncharacterized proteins.
Length = 131
Score = 28.3 bits (64), Expect = 1.8
Identities = 6/20 (30%), Positives = 11/20 (55%)
Query: 7 HEVYHKVLDVPRTQARQKVS 26
+E+Y V +P AR+ +
Sbjct: 83 YELYEVVKHMPTHDARKALP 102
>gnl|CDD|152695 pfam12260, PIP49_C, Pancreatitis induced protein 49 C terminal.
This protein is found in bacteria and eukaryotes.
Proteins in this family are typically between 344 to 431
amino acids in length. This protein has a single
completely conserved residue C that may be functionally
important. PIP49 is a putative transmembrane protein
which is induced to express during pancreatitis.
Length = 205
Score = 28.5 bits (64), Expect = 2.0
Identities = 15/48 (31%), Positives = 23/48 (47%), Gaps = 5/48 (10%)
Query: 96 KRCDRTQDCELGEDEIDCKTYMCPVSHYKCSNDFCIP-LDKVCNFIDD 142
+ C+ DC G DC+T C +S +C+ + P L K C + D
Sbjct: 141 RHCESDSDCVYGA---DCRT-TCDLSMKRCTTEVIQPNLAKACELLKD 184
>gnl|CDD|182130 PRK09880, PRK09880, L-idonate 5-dehydrogenase; Provisional.
Length = 343
Score = 28.9 bits (65), Expect = 2.4
Identities = 14/43 (32%), Positives = 20/43 (46%), Gaps = 8/43 (18%)
Query: 7 HEVYHKVL--DVPRTQARQKVSCNSSRPIFQC------NQTQC 41
HEV K++ D + Q V+ N S+P C N+ QC
Sbjct: 65 HEVIGKIVHSDSSGLKEGQTVAINPSKPCGHCKYCLSHNENQC 107
>gnl|CDD|227382 COG5049, XRN1, 5'-3' exonuclease [DNA replication, recombination,
and repair / Cell division and chromosome partitioning /
Translation].
Length = 953
Score = 28.7 bits (64), Expect = 2.6
Identities = 15/40 (37%), Positives = 21/40 (52%), Gaps = 6/40 (15%)
Query: 148 DEMECSLFTFLSFRLNKKIPRKSISMT------SAKMNQQ 181
+EM ++F ++ L K PRK + M AKMNQQ
Sbjct: 56 EEMYKAVFEYIDHILLKIRPRKLLYMAVDGVAPRAKMNQQ 95
>gnl|CDD|235721 PRK06163, PRK06163, hypothetical protein; Provisional.
Length = 202
Score = 27.9 bits (62), Expect = 3.4
Identities = 9/11 (81%), Positives = 9/11 (81%)
Query: 186 GNENFDLWVAG 196
GN NFDLW AG
Sbjct: 37 GNTNFDLWAAG 47
>gnl|CDD|226140 COG3613, COG3613, Nucleoside 2-deoxyribosyltransferase
[Nucleotide transport and metabolism].
Length = 172
Score = 27.4 bits (61), Expect = 5.4
Identities = 8/27 (29%), Positives = 9/27 (33%)
Query: 58 RDESVAMCGEYNIRDLLPNPLGCLPNE 84
RDE A+ E L P E
Sbjct: 22 RDELKALLLEAGFEVLSPFDEAEPIAE 48
>gnl|CDD|130651 TIGR01590, yir-bir-cir_Pla, yir/bir/cir-family of variant antigens,
Plasmodium-specific. This model represents a large
paralogous family of variant antigens from several
Plasmodium species (P. yoelii, P. berghei and P.
chabaudi). The seed was generated from a list of ORF's
in P. yoelii containing a paralagous domain as defined
by an algorithm implemented at TIFR. The list was
aligned and reduced to six sequences approximating the
most divergent clades present in the data set. The model
only hits genes previously characterized as yir, bir, or
cir genes above the trusted cutoff. In between trusted
and noise is one gene from P. vivax (vir25) which has
been characterized as a distant relative of the
yir/bir/cir family. The vir family appears to be present
in 600-1000 copies per haploid genome and is
preferentially located in the sub-telomeric regions of
the chromosomes. The genomic data for yoelii is
consistent with this observation. It is not believed
that there are any orthologs of this family in P.
falciparum.
Length = 199
Score = 26.7 bits (59), Expect = 8.0
Identities = 13/58 (22%), Positives = 20/58 (34%), Gaps = 10/58 (17%)
Query: 118 CPVSHYKCSNDF------CIPLDKVCNFIDDCGDNSDEMECSLFTF----LSFRLNKK 165
CP + C ND C+ L I + + + LS+ LN+K
Sbjct: 21 CPKTGSNCDNDIDKINAGCLWLLNQLYGISKDFKYKNNNNKAFIEYIIIWLSYILNQK 78
>gnl|CDD|220690 pfam10321, 7TM_GPCR_Srt, Serpentine type 7TM GPCR chemoreceptor
Srt. Chemoreception is mediated in Caenorhabditis
elegans by members of the seven-transmembrane
G-protein-coupled receptor class (7TM GPCRs) of proteins
which are of the serpentine type. Srt is a member of the
Srg superfamily of chemoreceptors. Chemoperception is
one of the central senses of soil nematodes like C.
elegans which are otherwise 'blind' and 'deaf'.
Length = 313
Score = 26.8 bits (60), Expect = 9.4
Identities = 10/33 (30%), Positives = 14/33 (42%), Gaps = 1/33 (3%)
Query: 152 CSLFTFLSFRLNKKIPRKSISMTSAKMNQQALL 184
L+ +L + L KK S S K +Q L
Sbjct: 211 TFLYGYLCYLLIKKF-GYSTSSWLYKSKRQIFL 242
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
0.323 0.138 0.453
Gapped
Lambda K H
0.267 0.0704 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,822,980
Number of extensions: 927481
Number of successful extensions: 536
Number of sequences better than 10.0: 1
Number of HSP's gapped: 533
Number of HSP's successfully gapped: 23
Length of query: 227
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 134
Effective length of database: 6,812,680
Effective search space: 912899120
Effective search space used: 912899120
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 57 (25.8 bits)