RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4900
(485 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 = 53.4 bits (129), Expect = 1e-09
Identities = 22/35 (62%), Positives = 28/35 (80%)
Query: 307 CAPGEFQCASGRCVPSTFKCDAENDCGDYSDETGC 341
C P EF+CA+GRC+PS++ CD E+DCGD SDE C
Sbjct: 1 CPPNEFRCANGRCIPSSWVCDGEDDCGDGSDEENC 35
Score = 52.6 bits (127), Expect = 2e-09
Identities = 21/35 (60%), Positives = 24/35 (68%)
Query: 96 CHVGQFKCANSLCIPVSYHCDGYRDCIDGSDETNC 130
C +F+CAN CIP S+ CDG DC DGSDE NC
Sbjct: 1 CPPNEFRCANGRCIPSSWVCDGEDDCGDGSDEENC 35
Score = 51.4 bits (124), Expect = 4e-09
Identities = 21/34 (61%), Positives = 27/34 (79%)
Query: 346 CSLSQFACENGRCVPSTWKCDSENDCGDGSDEGD 379
C ++F C NGRC+PS+W CD E+DCGDGSDE +
Sbjct: 1 CPPNEFRCANGRCIPSSWVCDGEDDCGDGSDEEN 34
Score = 48.7 bits (117), Expect = 4e-08
Identities = 19/36 (52%), Positives = 25/36 (69%), Gaps = 1/36 (2%)
Query: 56 CDLDQFRCANGQKCIDAKLKCNYHNDCGDNSDEEKC 91
C ++FRCANG+ CI + C+ +DCGD SDEE C
Sbjct: 1 CPPNEFRCANGR-CIPSSWVCDGEDDCGDGSDEENC 35
Score = 41.4 bits (98), Expect = 1e-05
Identities = 17/37 (45%), Positives = 20/37 (54%), Gaps = 2/37 (5%)
Query: 12 CSPGDFECDPPHGICIPKDKRCDGYYDCRNRKDEEGC 48
C P +F C +G CIP CDG DC + DEE C
Sbjct: 1 CPPNEFRCA--NGRCIPSSWVCDGEDDCGDGSDEENC 35
Score = 40.3 bits (95), Expect = 3e-05
Identities = 19/39 (48%), Positives = 23/39 (58%), Gaps = 6/39 (15%)
Query: 135 CPNNKFLCPMGAAGGKPKCIPKAQVCDGRKDCEDNADEE 173
CP N+F C G +CIP + VCDG DC D +DEE
Sbjct: 1 CPPNEFRCANG------RCIPSSWVCDGEDDCGDGSDEE 33
>gnl|CDD|200964 pfam00057, Ldl_recept_a, Low-density lipoprotein receptor domain
class A.
Length = 37
Score = 52.3 bits (126), Expect = 2e-09
Identities = 20/37 (54%), Positives = 24/37 (64%)
Query: 305 PTCAPGEFQCASGRCVPSTFKCDAENDCGDYSDETGC 341
TC P EFQC SG C+P ++ CD + DC D SDE C
Sbjct: 1 STCGPDEFQCGSGECIPMSWVCDGDPDCEDGSDEKNC 37
Score = 48.4 bits (116), Expect = 5e-08
Identities = 17/34 (50%), Positives = 22/34 (64%)
Query: 344 VTCSLSQFACENGRCVPSTWKCDSENDCGDGSDE 377
TC +F C +G C+P +W CD + DC DGSDE
Sbjct: 1 STCGPDEFQCGSGECIPMSWVCDGDPDCEDGSDE 34
Score = 47.7 bits (114), Expect = 1e-07
Identities = 19/37 (51%), Positives = 25/37 (67%)
Query: 94 TACHVGQFKCANSLCIPVSYHCDGYRDCIDGSDETNC 130
+ C +F+C + CIP+S+ CDG DC DGSDE NC
Sbjct: 1 STCGPDEFQCGSGECIPMSWVCDGDPDCEDGSDEKNC 37
Score = 41.9 bits (99), Expect = 1e-05
Identities = 16/39 (41%), Positives = 20/39 (51%), Gaps = 2/39 (5%)
Query: 10 RKCSPGDFECDPPHGICIPKDKRCDGYYDCRNRKDEEGC 48
C P +F+C G CIP CDG DC + DE+ C
Sbjct: 1 STCGPDEFQCG--SGECIPMSWVCDGDPDCEDGSDEKNC 37
Score = 41.5 bits (98), Expect = 1e-05
Identities = 15/36 (41%), Positives = 21/36 (58%), Gaps = 1/36 (2%)
Query: 56 CDLDQFRCANGQKCIDAKLKCNYHNDCGDNSDEEKC 91
C D+F+C +G+ CI C+ DC D SDE+ C
Sbjct: 3 CGPDEFQCGSGE-CIPMSWVCDGDPDCEDGSDEKNC 37
Score = 33.0 bits (76), Expect = 0.017
Identities = 17/40 (42%), Positives = 23/40 (57%), Gaps = 6/40 (15%)
Query: 135 CPNNKFLCPMGAAGGKPKCIPKAQVCDGRKDCEDNADEET 174
C ++F C G +CIP + VCDG DCED +DE+
Sbjct: 3 CGPDEFQCGSG------ECIPMSWVCDGDPDCEDGSDEKN 36
>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 = 49.9 bits (120), Expect = 1e-08
Identities = 21/33 (63%), Positives = 26/33 (78%)
Query: 345 TCSLSQFACENGRCVPSTWKCDSENDCGDGSDE 377
TC +F C+NGRC+PS+W CD +DCGDGSDE
Sbjct: 1 TCPPGEFQCDNGRCIPSSWVCDGVDDCGDGSDE 33
Score = 48.4 bits (116), Expect = 6e-08
Identities = 22/33 (66%), Positives = 27/33 (81%)
Query: 306 TCAPGEFQCASGRCVPSTFKCDAENDCGDYSDE 338
TC PGEFQC +GRC+PS++ CD +DCGD SDE
Sbjct: 1 TCPPGEFQCDNGRCIPSSWVCDGVDDCGDGSDE 33
Score = 46.1 bits (110), Expect = 3e-07
Identities = 19/32 (59%), Positives = 22/32 (68%)
Query: 96 CHVGQFKCANSLCIPVSYHCDGYRDCIDGSDE 127
C G+F+C N CIP S+ CDG DC DGSDE
Sbjct: 2 CPPGEFQCDNGRCIPSSWVCDGVDDCGDGSDE 33
Score = 42.6 bits (101), Expect = 5e-06
Identities = 15/33 (45%), Positives = 21/33 (63%), Gaps = 1/33 (3%)
Query: 56 CDLDQFRCANGQKCIDAKLKCNYHNDCGDNSDE 88
C +F+C NG+ CI + C+ +DCGD SDE
Sbjct: 2 CPPGEFQCDNGR-CIPSSWVCDGVDDCGDGSDE 33
Score = 37.6 bits (88), Expect = 3e-04
Identities = 17/38 (44%), Positives = 21/38 (55%), Gaps = 6/38 (15%)
Query: 135 CPNNKFLCPMGAAGGKPKCIPKAQVCDGRKDCEDNADE 172
CP +F C G +CIP + VCDG DC D +DE
Sbjct: 2 CPPGEFQCDNG------RCIPSSWVCDGVDDCGDGSDE 33
Score = 36.8 bits (86), Expect = 7e-04
Identities = 17/35 (48%), Positives = 21/35 (60%), Gaps = 2/35 (5%)
Query: 11 KCSPGDFECDPPHGICIPKDKRCDGYYDCRNRKDE 45
C PG+F+CD +G CIP CDG DC + DE
Sbjct: 1 TCPPGEFQCD--NGRCIPSSWVCDGVDDCGDGSDE 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 = 44.5 bits (106), Expect = 2e-06
Identities = 15/41 (36%), Positives = 23/41 (56%)
Query: 436 IVSEAAYKASGVALDINAKRLFWCDNLLDYIETVDYEGKNR 476
++S +G+A+D RL+W D LD IE + +G NR
Sbjct: 3 LLSSGLGHPNGLAVDWIEGRLYWTDWGLDVIEVANLDGTNR 43
Score = 43.0 bits (102), Expect = 5e-06
Identities = 14/41 (34%), Positives = 20/41 (48%), Gaps = 2/41 (4%)
Query: 394 IVLGSNLTNPTDLALDPTSGLMFVADSNQ--ILRTNMDGTM 432
+L S L +P LA+D G ++ D I N+DGT
Sbjct: 2 TLLSSGLGHPNGLAVDWIEGRLYWTDWGLDVIEVANLDGTN 42
>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 = 42.5 bits (100), Expect = 1e-04
Identities = 34/84 (40%), Positives = 39/84 (46%), Gaps = 9/84 (10%)
Query: 99 GQFKCANSLCIPVSYH--CDGYRDCIDGSDETNCTSIACPNNKFLCPMGAAGGKPKCIPK 156
G +KC N I +S+ D Y DC DGSDE AC N KF C G P IP
Sbjct: 36 GNWKCLNHSEIKLSFDQVNDDYCDCPDGSDEPGTN--ACSNGKFYC--ANEGFIPGYIPS 91
Query: 157 AQVCDGRKD---CEDNADEETVCC 177
+V DG D C D +DE C
Sbjct: 92 FKVDDGVCDYDICCDGSDEALGKC 115
Score = 38.6 bits (90), Expect = 0.002
Identities = 29/66 (43%), Positives = 30/66 (45%), Gaps = 16/66 (24%)
Query: 81 DCGDNSDEEKCNFTACHVGQFKCANSLCIPVSY---------HCDGYRDCIDGSDETNCT 131
DC D SDE N AC G+F CAN IP Y CD Y C DGSDE
Sbjct: 59 DCPDGSDEPGTN--ACSNGKFYCANEGFIP-GYIPSFKVDDGVCD-YDICCDGSDE---A 111
Query: 132 SIACPN 137
CPN
Sbjct: 112 LGKCPN 117
Score = 28.6 bits (64), Expect = 5.9
Identities = 21/64 (32%), Positives = 24/64 (37%), Gaps = 9/64 (14%)
Query: 331 DCGDYSDETGCVNVTCSLSQFACENGRCVPSTWKCDSEND-------CGDGSDEGDFCSE 383
DC D SDE G CS +F C N +P +D C DGSDE
Sbjct: 59 DCPDGSDEPG--TNACSNGKFYCANEGFIPGYIPSFKVDDGVCDYDICCDGSDEALGKCP 116
Query: 384 KTCA 387
C
Sbjct: 117 NKCG 120
>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 = 32.4 bits (74), Expect = 0.40
Identities = 14/43 (32%), Positives = 20/43 (46%), Gaps = 5/43 (11%)
Query: 257 QSPNPCGSNNGGCEHMCIITRASGNALGYKCACDIGYRLSVNG 299
P+ C + + C+ +CI T S Y CAC GY L +
Sbjct: 185 VVPDLCATLSHVCQQVCISTPGS-----YLCACTEGYALLEDN 222
Score = 28.9 bits (65), Expect = 5.1
Identities = 10/35 (28%), Positives = 17/35 (48%)
Query: 177 CDCSLLNCEFTCQASPTGGVCQCPEGQKVANDSRT 211
C C+ C ++P +C C EG + D++T
Sbjct: 190 CATLSHVCQQVCISTPGSYLCACTEGYALLEDNKT 224
>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 = 27.0 bits (61), Expect = 1.6
Identities = 9/19 (47%), Positives = 12/19 (63%)
Query: 284 GYKCACDIGYRLSVNGNNC 302
Y C+C GY+LS +G C
Sbjct: 1 SYTCSCPPGYQLSGDGRTC 19
>gnl|CDD|215497 PLN02919, PLN02919, haloacid dehalogenase-like hydrolase family
protein.
Length = 1057
Score = 29.8 bits (67), Expect = 3.9
Identities = 17/49 (34%), Positives = 28/49 (57%), Gaps = 2/49 (4%)
Query: 395 VLGSNLTNPTDLALDPTSGLMFVADSN--QILRTNMDGTMAMSIVSEAA 441
+L S L P LA+D + +F++DSN +I+ T++DG + I S
Sbjct: 562 LLTSPLKFPGKLAIDLLNNRLFISDSNHNRIVVTDLDGNFIVQIGSTGE 610
>gnl|CDD|235553 PRK05672, dnaE2, error-prone DNA polymerase; Validated.
Length = 1046
Score = 29.4 bits (67), Expect = 4.8
Identities = 7/11 (63%), Positives = 7/11 (63%)
Query: 337 DETGCVNVTCS 347
DETG VNV
Sbjct: 981 DETGMVNVVVW 991
>gnl|CDD|219253 pfam06986, TraN, Type-1V conjugative transfer system mating pair
stabilisation. TraN is a large cysteine-rich outer
membrane protein involved in the mating-pair
stabilisation (adhesin) component of the F-type
conjugative plasmid transfer system. TraN is believed to
interact with the core type IV secretion system
apparatus through the TraV protein.
Length = 243
Score = 28.5 bits (64), Expect = 6.8
Identities = 15/66 (22%), Positives = 23/66 (34%), Gaps = 13/66 (19%)
Query: 323 TFKCDAENDCGDYSDETGC--VNVTCSLSQ-----------FACENGRCVPSTWKCDSEN 369
T++C + N C + GC TC + CE C + + C +
Sbjct: 34 TYQCQSNNTCAALESQPGCSFTRSTCLEGSDEGVCLQWSVTYDCEQRVCSTTQYVCGGDV 93
Query: 370 DCGDGS 375
C DG
Sbjct: 94 FCLDGD 99
>gnl|CDD|233730 TIGR02104, pulA_typeI, pullulanase, type I. Pullulan is an
unusual, industrially important polysaccharide in which
short alpha-1,4 chains (maltotriose) are connected in
alpha-1,6 linkages. Enzymes that cleave alpha-1,6
linkages in pullulan and release maltotriose are called
pullulanases although pullulan itself may not be the
natural substrate. This family consists of pullulanases
related to the subfamilies described in TIGR02102 and
TIGR02103 but having a different domain architecture
with shorter sequences. Members are called type I
pullulanases.
Length = 605
Score = 28.8 bits (65), Expect = 7.9
Identities = 8/18 (44%), Positives = 10/18 (55%)
Query: 330 NDCGDYSDETGCVNVTCS 347
N+ G S+ TG N T S
Sbjct: 274 NEDGTLSNGTGVGNDTAS 291
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 0.452
Gapped
Lambda K H
0.267 0.0702 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 22,464,103
Number of extensions: 1981157
Number of successful extensions: 1228
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1211
Number of HSP's successfully gapped: 53
Length of query: 485
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 384
Effective length of database: 6,457,848
Effective search space: 2479813632
Effective search space used: 2479813632
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 (27.3 bits)