RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12307
(106 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 = 32.2 bits (74), Expect = 0.004
Identities = 11/22 (50%), Positives = 13/22 (59%)
Query: 33 RCIDDHVLCDGFIDCPTGEDED 54
RCI +CDG DC G DE+
Sbjct: 12 RCIPSSWVCDGEDDCGDGSDEE 33
>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 = 31.8 bits (73), Expect = 0.006
Identities = 11/21 (52%), Positives = 12/21 (57%)
Query: 33 RCIDDHVLCDGFIDCPTGEDE 53
RCI +CDG DC G DE
Sbjct: 13 RCIPSSWVCDGVDDCGDGSDE 33
>gnl|CDD|200964 pfam00057, Ldl_recept_a, Low-density lipoprotein receptor domain
class A.
Length = 37
Score = 28.4 bits (64), Expect = 0.12
Identities = 10/22 (45%), Positives = 11/22 (50%)
Query: 33 RCIDDHVLCDGFIDCPTGEDED 54
CI +CDG DC G DE
Sbjct: 14 ECIPMSWVCDGDPDCEDGSDEK 35
>gnl|CDD|183118 PRK11402, PRK11402, DNA-binding transcriptional regulator FrlR;
Provisional.
Length = 241
Score = 27.5 bits (61), Expect = 1.2
Identities = 16/40 (40%), Positives = 23/40 (57%), Gaps = 7/40 (17%)
Query: 61 ENELCWGLSIYKALDKSTGLRSILNWSDLVNLGLRIKWQG 100
ENELC + Y + + T ++I DLV G+ I+WQG
Sbjct: 36 ENELC---TQYN-VSRITIRKAIS---DLVADGVLIRWQG 68
>gnl|CDD|176257 cd08297, CAD3, Cinnamyl alcohol dehydrogenases (CAD). These
alcohol dehydrogenases are related to the cinnamyl
alcohol dehydrogenases (CAD), members of the medium
chain dehydrogenase/reductase family.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. Cinnamyl alcohol dehydrogenases
(CAD) reduce cinnamaldehydes to cinnamyl alcohols in the
last step of monolignal metabolism in plant cells walls.
CAD binds 2 zinc ions and is NADPH- dependent. CAD
family members are also found in non-plant species, e.g.
in yeast where they have an aldehyde reductase activity.
The medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 341
Score = 25.2 bits (56), Expect = 7.6
Identities = 10/18 (55%), Positives = 14/18 (77%), Gaps = 1/18 (5%)
Query: 64 LCWGLSIYKALDKSTGLR 81
LC G+++YKAL K GL+
Sbjct: 148 LCAGVTVYKAL-KKAGLK 164
>gnl|CDD|205511 pfam13331, DUF4093, Domain of unknown function (DUF4093). This
domain lies at the C-terminus of primase proteins
carrying the TOPRIM, pfam01751, domain. The exact
function of the domain is not known.
Length = 87
Score = 24.3 bits (54), Expect = 7.9
Identities = 9/31 (29%), Positives = 14/31 (45%), Gaps = 5/31 (16%)
Query: 69 SIYKALDK-----STGLRSILNWSDLVNLGL 94
+I +AL+ + W DL+ LGL
Sbjct: 11 AIREALENVRTEEEDEKSEEITWEDLIELGL 41
>gnl|CDD|173544 PTZ00351, PTZ00351, adenylosuccinate synthetase; Provisional.
Length = 710
Score = 25.0 bits (54), Expect = 9.4
Identities = 15/46 (32%), Positives = 19/46 (41%)
Query: 24 PTPDHMGRYRCIDDHVLCDGFIDCPTGEDEDRQNFLLENELCWGLS 69
P P Y C L DG+ D P + R+N L +C LS
Sbjct: 638 PVPSEPALYHCHPIVKLIDGWRDNPIAAAKRRRNAPLPRGVCELLS 683
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 0.142 0.476
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: 5,396,358
Number of extensions: 450277
Number of successful extensions: 312
Number of sequences better than 10.0: 1
Number of HSP's gapped: 312
Number of HSP's successfully gapped: 10
Length of query: 106
Length of database: 10,937,602
Length adjustment: 71
Effective length of query: 35
Effective length of database: 7,788,468
Effective search space: 272596380
Effective search space used: 272596380
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 (21.9 bits)
S2: 53 (24.1 bits)