RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14262
(482 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 = 1e-08
Identities = 21/35 (60%), Positives = 23/35 (65%), Gaps = 1/35 (2%)
Query: 205 CTPGQFSCGMGKCIPESWKCDGFVDCLEDGSDEPN 239
C P +F C G+CIP SW CDG DC DGSDE N
Sbjct: 1 CPPNEFRCANGRCIPSSWVCDGEDDC-GDGSDEEN 34
Score = 39.1 bits (92), Expect = 1e-04
Identities = 16/33 (48%), Positives = 21/33 (63%), Gaps = 1/33 (3%)
Query: 165 CHPNELRCGSSNQCVALSKFCDGKPDCSNGEDE 197
C PNE RC + +C+ S CDG+ DC +G DE
Sbjct: 1 CPPNEFRCANG-RCIPSSWVCDGEDDCGDGSDE 32
Score = 39.1 bits (92), Expect = 1e-04
Identities = 16/33 (48%), Positives = 21/33 (63%), Gaps = 1/33 (3%)
Query: 340 CHPNELRCGSSNQCVALSKFCDGKPDCSNGEDE 372
C PNE RC + +C+ S CDG+ DC +G DE
Sbjct: 1 CPPNEFRCANG-RCIPSSWVCDGEDDCGDGSDE 32
Score = 29.9 bits (68), Expect = 0.19
Identities = 15/39 (38%), Positives = 23/39 (58%), Gaps = 6/39 (15%)
Query: 5 CFNGQVQCALSKKCIPHNWLCDEEMDCSTDDIVDNTDED 43
C + +CA + +CIP +W+CD E DC D +DE+
Sbjct: 1 CPPNEFRCA-NGRCIPSSWVCDGEDDCG-----DGSDEE 33
Score = 29.9 bits (68), Expect = 0.19
Identities = 15/39 (38%), Positives = 23/39 (58%), Gaps = 6/39 (15%)
Query: 245 CFNGQVQCALSKKCIPHNWLCDEEMDCSTDDIVDNTDED 283
C + +CA + +CIP +W+CD E DC D +DE+
Sbjct: 1 CPPNEFRCA-NGRCIPSSWVCDGEDDCG-----DGSDEE 33
Score = 29.9 bits (68), Expect = 0.19
Identities = 15/39 (38%), Positives = 23/39 (58%), Gaps = 6/39 (15%)
Query: 290 CFNGQVQCALSKKCIPHNWLCDEEMDCSTDDIVDNTDED 328
C + +CA + +CIP +W+CD E DC D +DE+
Sbjct: 1 CPPNEFRCA-NGRCIPSSWVCDGEDDCG-----DGSDEE 33
>gnl|CDD|214531 smart00135, LY, Low-density lipoprotein-receptor YWTD domain. Type
"B" repeats in low-density lipoprotein (LDL) receptor
that plays a central role in mammalian cholesterol
metabolism. Also present in a variety of molecules
similar to gp300/megalin.
Length = 43
Score = 48.0 bits (115), Expect = 8e-08
Identities = 12/40 (30%), Positives = 24/40 (60%)
Query: 121 LVTKNIQWPSSLVIDYNQDILYWCDSHLNTVESVRVDGSH 160
L++ + P+ L +D+ + LYW D L+ +E +DG++
Sbjct: 3 LLSSGLGHPNGLAVDWIEGRLYWTDWGLDVIEVANLDGTN 42
>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 = 46.9 bits (112), Expect = 2e-07
Identities = 21/34 (61%), Positives = 23/34 (67%), Gaps = 1/34 (2%)
Query: 204 ECTPGQFSCGMGKCIPESWKCDGFVDCLEDGSDE 237
C PG+F C G+CIP SW CDG DC DGSDE
Sbjct: 1 TCPPGEFQCDNGRCIPSSWVCDGVDDC-GDGSDE 33
Score = 38.0 bits (89), Expect = 3e-04
Identities = 14/33 (42%), Positives = 19/33 (57%), Gaps = 1/33 (3%)
Query: 165 CHPNELRCGSSNQCVALSKFCDGKPDCSNGEDE 197
C P E +C + +C+ S CDG DC +G DE
Sbjct: 2 CPPGEFQCDNG-RCIPSSWVCDGVDDCGDGSDE 33
Score = 38.0 bits (89), Expect = 3e-04
Identities = 14/33 (42%), Positives = 19/33 (57%), Gaps = 1/33 (3%)
Query: 340 CHPNELRCGSSNQCVALSKFCDGKPDCSNGEDE 372
C P E +C + +C+ S CDG DC +G DE
Sbjct: 2 CPPGEFQCDNG-RCIPSSWVCDGVDDCGDGSDE 33
Score = 28.4 bits (64), Expect = 0.64
Identities = 15/39 (38%), Positives = 21/39 (53%), Gaps = 6/39 (15%)
Query: 4 QCFNGQVQCALSKKCIPHNWLCDEEMDCSTDDIVDNTDE 42
C G+ QC + +CIP +W+CD DC D +DE
Sbjct: 1 TCPPGEFQCD-NGRCIPSSWVCDGVDDCG-----DGSDE 33
Score = 28.4 bits (64), Expect = 0.64
Identities = 15/39 (38%), Positives = 21/39 (53%), Gaps = 6/39 (15%)
Query: 244 QCFNGQVQCALSKKCIPHNWLCDEEMDCSTDDIVDNTDE 282
C G+ QC + +CIP +W+CD DC D +DE
Sbjct: 1 TCPPGEFQCD-NGRCIPSSWVCDGVDDCG-----DGSDE 33
Score = 28.4 bits (64), Expect = 0.64
Identities = 15/39 (38%), Positives = 21/39 (53%), Gaps = 6/39 (15%)
Query: 289 QCFNGQVQCALSKKCIPHNWLCDEEMDCSTDDIVDNTDE 327
C G+ QC + +CIP +W+CD DC D +DE
Sbjct: 1 TCPPGEFQCD-NGRCIPSSWVCDGVDDCG-----DGSDE 33
>gnl|CDD|200964 pfam00057, Ldl_recept_a, Low-density lipoprotein receptor domain
class A.
Length = 37
Score = 45.0 bits (107), Expect = 9e-07
Identities = 23/35 (65%), Positives = 25/35 (71%), Gaps = 1/35 (2%)
Query: 205 CTPGQFSCGMGKCIPESWKCDGFVDCLEDGSDEPN 239
C P +F CG G+CIP SW CDG DC EDGSDE N
Sbjct: 3 CGPDEFQCGSGECIPMSWVCDGDPDC-EDGSDEKN 36
Score = 37.3 bits (87), Expect = 4e-04
Identities = 17/33 (51%), Positives = 23/33 (69%), Gaps = 1/33 (3%)
Query: 165 CHPNELRCGSSNQCVALSKFCDGKPDCSNGEDE 197
C P+E +CGS +C+ +S CDG PDC +G DE
Sbjct: 3 CGPDEFQCGSG-ECIPMSWVCDGDPDCEDGSDE 34
Score = 37.3 bits (87), Expect = 4e-04
Identities = 17/33 (51%), Positives = 23/33 (69%), Gaps = 1/33 (3%)
Query: 340 CHPNELRCGSSNQCVALSKFCDGKPDCSNGEDE 372
C P+E +CGS +C+ +S CDG PDC +G DE
Sbjct: 3 CGPDEFQCGSG-ECIPMSWVCDGDPDCEDGSDE 34
Score = 25.7 bits (57), Expect = 6.6
Identities = 15/41 (36%), Positives = 21/41 (51%), Gaps = 6/41 (14%)
Query: 4 QCFNGQVQCALSKKCIPHNWLCDEEMDCSTDDIVDNTDEDW 44
C + QC S +CIP +W+CD + DC D +DE
Sbjct: 2 TCGPDEFQCG-SGECIPMSWVCDGDPDC-----EDGSDEKN 36
Score = 25.7 bits (57), Expect = 6.6
Identities = 15/41 (36%), Positives = 21/41 (51%), Gaps = 6/41 (14%)
Query: 244 QCFNGQVQCALSKKCIPHNWLCDEEMDCSTDDIVDNTDEDW 284
C + QC S +CIP +W+CD + DC D +DE
Sbjct: 2 TCGPDEFQCG-SGECIPMSWVCDGDPDC-----EDGSDEKN 36
Score = 25.7 bits (57), Expect = 6.6
Identities = 15/41 (36%), Positives = 21/41 (51%), Gaps = 6/41 (14%)
Query: 289 QCFNGQVQCALSKKCIPHNWLCDEEMDCSTDDIVDNTDEDW 329
C + QC S +CIP +W+CD + DC D +DE
Sbjct: 2 TCGPDEFQCG-SGECIPMSWVCDGDPDC-----EDGSDEKN 36
>gnl|CDD|238752 cd01475, vWA_Matrilin, VWA_Matrilin: In cartilaginous plate,
extracellular matrix molecules mediate cell-matrix and
matrix-matrix interactions thereby providing tissue
integrity. Some members of the matrilin family are
expressed specifically in developing cartilage
rudiments. The matrilin family consists of at least four
members. All the members of the matrilin family contain
VWA domains, EGF-like domains and a heptad repeat
coiled-coiled domain at the carboxy terminus which is
responsible for the oligomerization of the matrilins.
The VWA domains have been shown to be essential for
matrilin network formation by interacting with matrix
ligands.
Length = 224
Score = 46.6 bits (111), Expect = 8e-06
Identities = 19/41 (46%), Positives = 24/41 (58%), Gaps = 1/41 (2%)
Query: 413 CVDADEC-LIDGSCDQTCTNTHLSYVCSCTEGYTLRPDGKS 452
CV D C + C Q C +T SY+C+CTEGY L D K+
Sbjct: 184 CVVPDLCATLSHVCQQVCISTPGSYLCACTEGYALLEDNKT 224
>gnl|CDD|215683 pfam00058, Ldl_recept_b, Low-density lipoprotein receptor repeat
class B. This domain is also known as the YWTD motif
after the most conserved region of the repeat. The YWTD
repeat is found in multiple tandem repeats and has been
predicted to form a beta-propeller structure.
Length = 42
Score = 36.4 bits (85), Expect = 0.001
Identities = 9/33 (27%), Positives = 20/33 (60%)
Query: 104 LDERLEKAGMHGENRSPLVTKNIQWPSSLVIDY 136
L + A ++G +R L ++++QWP+ + +D
Sbjct: 10 LRASISVADLNGSDRRTLFSEDLQWPNGIAVDP 42
>gnl|CDD|221695 pfam12662, cEGF, Complement Clr-like EGF-like. cEGF, or complement
Clr-like EGF, domains have six conserved cysteine
residues disulfide-bonded into the characteristic
pattern 'ababcc'. They are found in blood coagulation
proteins such as fibrillin, Clr and Cls, thrombomodulin,
and the LDL receptor. The core fold of the EGF domain
consists of two small beta-hairpins packed against each
other. Two major structural variants have been
identified based on the structural context of the
C-terminal cysteine residue of disulfide 'c' in the
C-terminal hairpin: hEGFs and cEGFs. In cEGFs the
C-terminal thiol resides on the C-terminal beta-sheet,
resulting in long loop-lengths between the cysteine
residues of disulfide 'c', typically C[10+]XC. These
longer loop-lengths may have arisen by selective
cysteine loss from a four-disulfide EGF template such as
laminin or integrin. Tandem cEGF domains have five
linking residues between terminal cysteines of adjacent
domains. cEGF domains may or may not bind calcium in the
linker region. cEGF domains with the consensus motif
CXN4X[F,Y]XCXC are hydroxylated exclusively on the
asparagine residue.
Length = 24
Score = 35.5 bits (83), Expect = 0.001
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 435 SYVCSCTEGYTLRPDGKSCTAVN 457
SY CSC GY L DG++C ++
Sbjct: 1 SYTCSCPPGYQLSGDGRTCEDID 23
>gnl|CDD|214542 smart00179, EGF_CA, Calcium-binding EGF-like domain.
Length = 39
Score = 35.7 bits (83), Expect = 0.002
Identities = 19/42 (45%), Positives = 21/42 (50%), Gaps = 5/42 (11%)
Query: 415 DADECLIDGSCDQ--TCTNTHLSYVCSCTEGYTLRPDGKSCT 454
D DEC C TC NT SY C C GYT DG++C
Sbjct: 1 DIDECASGNPCQNGGTCVNTVGSYRCECPPGYT---DGRNCE 39
>gnl|CDD|238011 cd00054, EGF_CA, Calcium-binding EGF-like domain, present in a
large number of membrane-bound and extracellular (mostly
animal) proteins. Many of these proteins require calcium
for their biological function and calcium-binding sites
have been found to be located at the N-terminus of
particular EGF-like domains; calcium-binding may be
crucial for numerous protein-protein interactions. Six
conserved core cysteines form three disulfide bridges as
in non calcium-binding EGF domains, whose structures are
very similar. EGF_CA can be found in tandem repeat
arrangements.
Length = 38
Score = 34.5 bits (80), Expect = 0.005
Identities = 18/35 (51%), Positives = 18/35 (51%), Gaps = 2/35 (5%)
Query: 415 DADECLIDGSC--DQTCTNTHLSYVCSCTEGYTLR 447
D DEC C TC NT SY CSC GYT R
Sbjct: 1 DIDECASGNPCQNGGTCVNTVGSYRCSCPPGYTGR 35
>gnl|CDD|219496 pfam07645, EGF_CA, Calcium-binding EGF domain.
Length = 42
Score = 30.4 bits (69), Expect = 0.16
Identities = 16/42 (38%), Positives = 20/42 (47%), Gaps = 3/42 (7%)
Query: 415 DADECLIDG-SCDQ--TCTNTHLSYVCSCTEGYTLRPDGKSC 453
D DEC +C C NT S+ C C +GY DG +C
Sbjct: 1 DVDECADGTHNCPANTVCVNTIGSFECVCPDGYENNEDGTNC 42
>gnl|CDD|205157 pfam12947, EGF_3, EGF domain. This family includes a variety of
EGF-like domain homologues. This family includes the
C-terminal domain of the malaria parasite MSP1 protein.
Length = 36
Score = 29.8 bits (68), Expect = 0.24
Identities = 16/33 (48%), Positives = 19/33 (57%), Gaps = 4/33 (12%)
Query: 423 GSCDQ--TCTNTHLSYVCSCTEGYTLRPDGKSC 453
G C TCTNT S+ C+C GYT DG +C
Sbjct: 6 GGCHPNATCTNTGGSFTCTCKSGYTG--DGVTC 36
>gnl|CDD|214544 smart00181, EGF, Epidermal growth factor-like domain.
Length = 35
Score = 29.0 bits (65), Expect = 0.39
Identities = 16/33 (48%), Positives = 16/33 (48%), Gaps = 1/33 (3%)
Query: 418 ECLIDGSCDQ-TCTNTHLSYVCSCTEGYTLRPD 449
EC G C TC NT SY CSC GYT
Sbjct: 1 ECASGGPCSNGTCINTPGSYTCSCPPGYTGDKR 33
>gnl|CDD|238010 cd00053, EGF, Epidermal growth factor domain, found in epidermal
growth factor (EGF) presents in a large number of
proteins, mostly animal; the list of proteins currently
known to contain one or more copies of an EGF-like
pattern is large and varied; the functional significance
of EGF-like domains in what appear to be unrelated
proteins is not yet clear; a common feature is that
these repeats are found in the extracellular domain of
membrane-bound proteins or in proteins known to be
secreted (exception: prostaglandin G/H synthase); the
domain includes six cysteine residues which have been
shown to be involved in disulfide bonds; the main
structure is a two-stranded beta-sheet followed by a
loop to a C-terminal short two-stranded sheet;
Subdomains between the conserved cysteines vary in
length; the region between the 5th and 6th cysteine
contains two conserved glycines of which at least one
is present in most EGF-like domains; a subset of
these bind calcium.
Length = 36
Score = 28.6 bits (64), Expect = 0.59
Identities = 14/32 (43%), Positives = 14/32 (43%), Gaps = 2/32 (6%)
Query: 418 ECLIDGSCD--QTCTNTHLSYVCSCTEGYTLR 447
EC C TC NT SY C C GYT
Sbjct: 1 ECAASNPCSNGGTCVNTPGSYRCVCPPGYTGD 32
>gnl|CDD|225590 COG3048, DsdA, D-serine dehydratase [Amino acid transport and
metabolism].
Length = 443
Score = 31.3 bits (71), Expect = 1.3
Identities = 27/81 (33%), Positives = 33/81 (40%), Gaps = 15/81 (18%)
Query: 98 AP---EIFPLDERLEKAGMHGENRSPLV-TKNIQWPSSLVIDYNQDI----LYWCDSHLN 149
AP + FP E A G SPLV +Q L +Y Q I L DSHL
Sbjct: 60 APYIAKAFP-----ETAATGGIIESPLVEIPAMQ--KRLEKEYQQPIPGRLLLKKDSHLP 112
Query: 150 TVESVRVDGSHNAVLCHPNEL 170
S++ G VL H +L
Sbjct: 113 ISGSIKARGGIYEVLKHAEKL 133
>gnl|CDD|161785 TIGR00239, 2oxo_dh_E1, 2-oxoglutarate dehydrogenase, E1 component.
The 2-oxoglutarate dehydrogenase complex consists of
this thiamine pyrophosphate-binding subunit (E1),
dihydrolipoamide succinyltransferase (E2), and lipoamide
dehydrogenase (E3). The E1 ortholog from Corynebacterium
glutamicum is unusual in having an N-terminal extension
that resembles the dihydrolipoamide succinyltransferase
(E2) component of 2-oxoglutarate dehydrogenase [Energy
metabolism, TCA cycle].
Length = 929
Score = 31.0 bits (70), Expect = 1.6
Identities = 16/93 (17%), Positives = 22/93 (23%), Gaps = 26/93 (27%)
Query: 38 DNTDEDWDKYFKRILNGTHTLALEF--------------NHRNQSLCFIQQQNVSSVR-- 81
D+ D W F + L G +F R NVS V+
Sbjct: 22 DSVDASWRSTFDQ-LPGPGPAPDQFHSPTRSYFRRLAKDASRGSVTISDPDTNVSQVKVL 80
Query: 82 --LRCAQIN-------DLLNSWDLPAPEIFPLD 105
+R + D L L
Sbjct: 81 QLIRAYRFRGHLHANLDPLGLKQQDKVPELDLS 113
>gnl|CDD|182241 PRK10100, PRK10100, DNA-binding transcriptional regulator CsgD;
Provisional.
Length = 216
Score = 29.5 bits (66), Expect = 3.2
Identities = 13/35 (37%), Positives = 20/35 (57%), Gaps = 5/35 (14%)
Query: 155 RVDGSHNAVLCHP-----NELRCGSSNQCVALSKF 184
R + + +A+L H N+LR G+SN +A S F
Sbjct: 147 RYNSTESALLTHREKEILNKLRIGASNNEIARSLF 181
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
0.320 0.136 0.465
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: 23,105,666
Number of extensions: 2085992
Number of successful extensions: 1563
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1547
Number of HSP's successfully gapped: 52
Length of query: 482
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 381
Effective length of database: 6,457,848
Effective search space: 2460440088
Effective search space used: 2460440088
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: 61 (27.2 bits)