RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8875
(734 letters)
>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 = 62.6 bits (153), Expect = 9e-13
Identities = 15/39 (38%), Positives = 24/39 (61%)
Query: 604 MYWSDWGQNAKIERAGMDGSHRNMVIVSDIKWPNGLTLD 642
+YW+D A I A ++GS R + D++WPNG+ +D
Sbjct: 3 LYWTDSSLRASISVADLNGSDRRTLFSEDLQWPNGIAVD 41
Score = 35.6 bits (83), Expect = 0.003
Identities = 13/41 (31%), Positives = 24/41 (58%), Gaps = 1/41 (2%)
Query: 560 HIYWTDA-HKNTIELANFEGTMRKVLVRSYLDEPRSLALNP 599
+YWTD+ + +I +A+ G+ R+ L L P +A++P
Sbjct: 2 RLYWTDSSLRASISVADLNGSDRRTLFSEDLQWPNGIAVDP 42
Score = 33.7 bits (78), Expect = 0.015
Identities = 15/43 (34%), Positives = 24/43 (55%), Gaps = 2/43 (4%)
Query: 515 GMIFWSDIS-EKKIYKAPIDEGSERTVVIEEDKTIADGLAVDW 556
G ++W+D S I A ++ GS+R + ED +G+AVD
Sbjct: 1 GRLYWTDSSLRASISVADLN-GSDRRTLFSEDLQWPNGIAVDP 42
Score = 30.6 bits (70), Expect = 0.17
Identities = 16/40 (40%), Positives = 20/40 (50%), Gaps = 3/40 (7%)
Query: 646 RRLYWVDAKLNE-ISSCDYNGGNRRLVLYSPQTLSHPFSI 684
RLYW D+ L IS D NG +RR + + L P I
Sbjct: 1 GRLYWTDSSLRASISVADLNGSDRRTLF--SEDLQWPNGI 38
Score = 29.8 bits (68), Expect = 0.33
Identities = 6/19 (31%), Positives = 8/19 (42%)
Query: 691 LYWSDWQQKAIYKANKFTG 709
LYW+D +A G
Sbjct: 3 LYWTDSSLRASISVADLNG 21
>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 = 59.5 bits (145), Expect = 9e-12
Identities = 22/35 (62%), Positives = 27/35 (77%)
Query: 265 CRSDEFTCANGNCIQRIWLCDGDDDCKDGSDEKSC 299
C +EF CANG CI W+CDG+DDC DGSDE++C
Sbjct: 1 CPPNEFRCANGRCIPSSWVCDGEDDCGDGSDEENC 35
Score = 55.7 bits (135), Expect = 2e-10
Identities = 21/33 (63%), Positives = 24/33 (72%)
Query: 135 CQASEFRCGNNRCIPNHWQCDGEFDCSDKSDED 167
C +EFRC N RCIP+ W CDGE DC D SDE+
Sbjct: 1 CPPNEFRCANGRCIPSSWVCDGEDDCGDGSDEE 33
Score = 51.1 bits (123), Expect = 1e-08
Identities = 20/33 (60%), Positives = 24/33 (72%)
Query: 57 STMFRCTGGMCIPSTWVCDGQNDCPDGVDEKKC 89
FRC G CIPS+WVCDG++DC DG DE+ C
Sbjct: 3 PNEFRCANGRCIPSSWVCDGEDDCGDGSDEENC 35
Score = 51.1 bits (123), Expect = 1e-08
Identities = 20/33 (60%), Positives = 24/33 (72%)
Query: 229 STMFRCTGGMCIPSTWVCDGQNDCPDGVDEKKC 261
FRC G CIPS+WVCDG++DC DG DE+ C
Sbjct: 3 PNEFRCANGRCIPSSWVCDGEDDCGDGSDEENC 35
Score = 49.5 bits (119), Expect = 3e-08
Identities = 18/37 (48%), Positives = 24/37 (64%), Gaps = 2/37 (5%)
Query: 94 CGQEEFTCRSSPGECVPLTWMCDDNPDCSDGSDEKSC 130
C EF C + G C+P +W+CD DC DGSDE++C
Sbjct: 1 CPPNEFRCAN--GRCIPSSWVCDGEDDCGDGSDEENC 35
Score = 33.3 bits (77), Expect = 0.017
Identities = 12/24 (50%), Positives = 14/24 (58%), Gaps = 1/24 (4%)
Query: 304 CTAGQFTCQNLTACIPDKWVCDGD 327
C +F C N CIP WVCDG+
Sbjct: 1 CPPNEFRCANGR-CIPSSWVCDGE 23
>gnl|CDD|200964 pfam00057, Ldl_recept_a, Low-density lipoprotein receptor domain
class A.
Length = 37
Score = 58.5 bits (142), Expect = 3e-11
Identities = 23/36 (63%), Positives = 27/36 (75%)
Query: 264 TCRSDEFTCANGNCIQRIWLCDGDDDCKDGSDEKSC 299
TC DEF C +G CI W+CDGD DC+DGSDEK+C
Sbjct: 2 TCGPDEFQCGSGECIPMSWVCDGDPDCEDGSDEKNC 37
Score = 55.0 bits (133), Expect = 4e-10
Identities = 19/35 (54%), Positives = 22/35 (62%)
Query: 133 RTCQASEFRCGNNRCIPNHWQCDGEFDCSDKSDED 167
TC EF+CG+ CIP W CDG+ DC D SDE
Sbjct: 1 STCGPDEFQCGSGECIPMSWVCDGDPDCEDGSDEK 35
Score = 47.7 bits (114), Expect = 1e-07
Identities = 20/38 (52%), Positives = 22/38 (57%), Gaps = 1/38 (2%)
Query: 52 KPCRNSTMFRCTGGMCIPSTWVCDGQNDCPDGVDEKKC 89
C F+C G CIP +WVCDG DC DG DEK C
Sbjct: 1 STCGPDE-FQCGSGECIPMSWVCDGDPDCEDGSDEKNC 37
Score = 47.7 bits (114), Expect = 1e-07
Identities = 20/38 (52%), Positives = 22/38 (57%), Gaps = 1/38 (2%)
Query: 224 KPCRNSTMFRCTGGMCIPSTWVCDGQNDCPDGVDEKKC 261
C F+C G CIP +WVCDG DC DG DEK C
Sbjct: 1 STCGPDE-FQCGSGECIPMSWVCDGDPDCEDGSDEKNC 37
Score = 46.1 bits (110), Expect = 5e-07
Identities = 23/37 (62%), Positives = 30/37 (81%), Gaps = 2/37 (5%)
Query: 94 CGQEEFTCRSSPGECVPLTWMCDDNPDCSDGSDEKSC 130
CG +EF C S GEC+P++W+CD +PDC DGSDEK+C
Sbjct: 3 CGPDEFQCGS--GECIPMSWVCDGDPDCEDGSDEKNC 37
Score = 31.1 bits (71), Expect = 0.10
Identities = 12/26 (46%), Positives = 14/26 (53%), Gaps = 1/26 (3%)
Query: 302 VKCTAGQFTCQNLTACIPDKWVCDGD 327
C +F C + CIP WVCDGD
Sbjct: 1 STCGPDEFQCGS-GECIPMSWVCDGD 25
>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 = 58.4 bits (142), Expect = 3e-11
Identities = 19/44 (43%), Positives = 29/44 (65%), Gaps = 1/44 (2%)
Query: 582 KVLVRSYLDEPRSLALNPIDGWMYWSDWGQNAKIERAGMDGSHR 625
+ L+ S L P LA++ I+G +YW+DWG IE A +DG++R
Sbjct: 1 RTLLSSGLGHPNGLAVDWIEGRLYWTDWGL-DVIEVANLDGTNR 43
Score = 58.0 bits (141), Expect = 4e-11
Identities = 16/42 (38%), Positives = 25/42 (59%)
Query: 627 MVIVSDIKWPNGLTLDLVQRRLYWVDAKLNEISSCDYNGGNR 668
++ S + PNGL +D ++ RLYW D L+ I + +G NR
Sbjct: 2 TLLSSGLGHPNGLAVDWIEGRLYWTDWGLDVIEVANLDGTNR 43
Score = 53.0 bits (128), Expect = 3e-09
Identities = 18/42 (42%), Positives = 25/42 (59%)
Query: 540 VVIEEDKTIADGLAVDWIYSHIYWTDAHKNTIELANFEGTMR 581
++ +GLAVDWI +YWTD + IE+AN +GT R
Sbjct: 2 TLLSSGLGHPNGLAVDWIEGRLYWTDWGLDVIEVANLDGTNR 43
Score = 33.3 bits (77), Expect = 0.021
Identities = 12/36 (33%), Positives = 15/36 (41%), Gaps = 3/36 (8%)
Query: 678 LSHP--FSISTFEDWLYWSDWQQKAIYKANKFTGDN 711
L HP ++ E LYW+DW I G N
Sbjct: 8 LGHPNGLAVDWIEGRLYWTDWGLDVIE-VANLDGTN 42
Score = 28.7 bits (65), Expect = 0.81
Identities = 8/41 (19%), Positives = 17/41 (41%), Gaps = 1/41 (2%)
Query: 498 IVNSTKSATAIDFVFRTGMIFWSDISEKKIYKAPIDEGSER 538
+ + + + G ++W+D I A +D G+ R
Sbjct: 4 LSSGLGHPNGLAVDWIEGRLYWTDWGLDVIEVANLD-GTNR 43
>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 = 54.6 bits (132), Expect = 5e-10
Identities = 21/33 (63%), Positives = 22/33 (66%)
Query: 264 TCRSDEFTCANGNCIQRIWLCDGDDDCKDGSDE 296
TC EF C NG CI W+CDG DDC DGSDE
Sbjct: 1 TCPPGEFQCDNGRCIPSSWVCDGVDDCGDGSDE 33
Score = 54.2 bits (131), Expect = 6e-10
Identities = 20/33 (60%), Positives = 22/33 (66%)
Query: 134 TCQASEFRCGNNRCIPNHWQCDGEFDCSDKSDE 166
TC EF+C N RCIP+ W CDG DC D SDE
Sbjct: 1 TCPPGEFQCDNGRCIPSSWVCDGVDDCGDGSDE 33
Score = 46.9 bits (112), Expect = 3e-07
Identities = 18/31 (58%), Positives = 21/31 (67%)
Query: 56 NSTMFRCTGGMCIPSTWVCDGQNDCPDGVDE 86
F+C G CIPS+WVCDG +DC DG DE
Sbjct: 3 PPGEFQCDNGRCIPSSWVCDGVDDCGDGSDE 33
Score = 46.9 bits (112), Expect = 3e-07
Identities = 18/31 (58%), Positives = 21/31 (67%)
Query: 228 NSTMFRCTGGMCIPSTWVCDGQNDCPDGVDE 258
F+C G CIPS+WVCDG +DC DG DE
Sbjct: 3 PPGEFQCDNGRCIPSSWVCDGVDDCGDGSDE 33
Score = 44.5 bits (106), Expect = 2e-06
Identities = 17/34 (50%), Positives = 21/34 (61%), Gaps = 2/34 (5%)
Query: 94 CGQEEFTCRSSPGECVPLTWMCDDNPDCSDGSDE 127
C EF C + G C+P +W+CD DC DGSDE
Sbjct: 2 CPPGEFQCDN--GRCIPSSWVCDGVDDCGDGSDE 33
Score = 32.2 bits (74), Expect = 0.044
Identities = 13/25 (52%), Positives = 14/25 (56%), Gaps = 1/25 (4%)
Query: 303 KCTAGQFTCQNLTACIPDKWVCDGD 327
C G+F C N CIP WVCDG
Sbjct: 1 TCPPGEFQCDN-GRCIPSSWVCDGV 24
>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 = 42.4 bits (101), Expect = 8e-06
Identities = 13/24 (54%), Positives = 15/24 (62%)
Query: 409 GYMCECNEGYKLSSNRHTCIDIDE 432
Y C C GY+LS + TC DIDE
Sbjct: 1 SYTCSCPPGYQLSGDGRTCEDIDE 24
>gnl|CDD|214542 smart00179, EGF_CA, Calcium-binding EGF-like domain.
Length = 39
Score = 41.1 bits (97), Expect = 4e-05
Identities = 14/37 (37%), Positives = 19/37 (51%), Gaps = 2/37 (5%)
Query: 429 DIDECETPGSCSQ--ICLNEKGGFKCECVAGYIKDPH 463
DIDEC + C C+N G ++CEC GY +
Sbjct: 1 DIDECASGNPCQNGGTCVNTVGSYRCECPPGYTDGRN 37
Score = 32.6 bits (75), Expect = 0.033
Identities = 14/42 (33%), Positives = 19/42 (45%), Gaps = 6/42 (14%)
Query: 389 VDECAKDNGGCLH--KCVDLPVGYMCECNEGYKLSSNRHTCI 428
+DECA C + CV+ Y CEC GY ++ C
Sbjct: 2 IDECA-SGNPCQNGGTCVNTVGSYRCECPPGY---TDGRNCE 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 = 39.5 bits (93), Expect = 1e-04
Identities = 13/33 (39%), Positives = 17/33 (51%), Gaps = 2/33 (6%)
Query: 429 DIDECETPGSCS--QICLNEKGGFKCECVAGYI 459
DIDEC + C C+N G ++C C GY
Sbjct: 1 DIDECASGNPCQNGGTCVNTVGSYRCSCPPGYT 33
Score = 32.2 bits (74), Expect = 0.047
Identities = 12/34 (35%), Positives = 15/34 (44%), Gaps = 3/34 (8%)
Query: 389 VDECAKDNGGCLH--KCVDLPVGYMCECNEGYKL 420
+DECA C + CV+ Y C C GY
Sbjct: 2 IDECA-SGNPCQNGGTCVNTVGSYRCSCPPGYTG 34
>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 = 39.7 bits (93), Expect = 0.003
Identities = 13/36 (36%), Positives = 17/36 (47%)
Query: 388 GVDECAKDNGGCLHKCVDLPVGYMCECNEGYKLSSN 423
D CA + C C+ P Y+C C EGY L +
Sbjct: 186 VPDLCATLSHVCQQVCISTPGSYLCACTEGYALLED 221
Score = 33.1 bits (76), Expect = 0.39
Identities = 12/34 (35%), Positives = 17/34 (50%), Gaps = 1/34 (2%)
Query: 427 CIDIDECET-PGSCSQICLNEKGGFKCECVAGYI 459
C+ D C T C Q+C++ G + C C GY
Sbjct: 184 CVVPDLCATLSHVCQQVCISTPGSYLCACTEGYA 217
Score = 30.4 bits (69), Expect = 2.9
Identities = 14/45 (31%), Positives = 20/45 (44%), Gaps = 6/45 (13%)
Query: 170 MCNGVNHCAAVNGHCSHLCLPAPQINAHSPKISCACPEGLKLLPD 214
+C + CA ++ C +C+ P CAC EG LL D
Sbjct: 183 ICVVPDLCATLSHVCQQVCISTPG------SYLCACTEGYALLED 221
>gnl|CDD|219496 pfam07645, EGF_CA, Calcium-binding EGF domain.
Length = 42
Score = 35.4 bits (82), Expect = 0.003
Identities = 13/33 (39%), Positives = 18/33 (54%), Gaps = 3/33 (9%)
Query: 429 DIDECETPG-SCSQ--ICLNEKGGFKCECVAGY 458
D+DEC +C +C+N G F+C C GY
Sbjct: 1 DVDECADGTHNCPANTVCVNTIGSFECVCPDGY 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 = 32.4 bits (74), Expect = 0.043
Identities = 12/34 (35%), Positives = 15/34 (44%), Gaps = 2/34 (5%)
Query: 432 ECETPGSCS--QICLNEKGGFKCECVAGYIKDPH 463
EC CS C+N G ++C C GY D
Sbjct: 1 ECAASNPCSNGGTCVNTPGSYRCVCPPGYTGDRS 34
Score = 28.6 bits (64), Expect = 0.97
Identities = 12/35 (34%), Positives = 16/35 (45%), Gaps = 3/35 (8%)
Query: 391 ECAKDNGGCLH--KCVDLPVGYMCECNEGYKLSSN 423
ECA + C + CV+ P Y C C GY +
Sbjct: 1 ECA-ASNPCSNGGTCVNTPGSYRCVCPPGYTGDRS 34
>gnl|CDD|214544 smart00181, EGF, Epidermal growth factor-like domain.
Length = 35
Score = 32.1 bits (73), Expect = 0.055
Identities = 13/33 (39%), Positives = 16/33 (48%), Gaps = 1/33 (3%)
Query: 432 ECETPGSCSQ-ICLNEKGGFKCECVAGYIKDPH 463
EC + G CS C+N G + C C GY D
Sbjct: 1 ECASGGPCSNGTCINTPGSYTCSCPPGYTGDKR 33
Score = 29.0 bits (65), Expect = 0.63
Identities = 12/34 (35%), Positives = 15/34 (44%), Gaps = 2/34 (5%)
Query: 391 ECAKDNGGCLH-KCVDLPVGYMCECNEGYKLSSN 423
ECA G C + C++ P Y C C GY
Sbjct: 1 ECA-SGGPCSNGTCINTPGSYTCSCPPGYTGDKR 33
>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 = 35.1 bits (81), Expect = 0.059
Identities = 25/71 (35%), Positives = 28/71 (39%), Gaps = 13/71 (18%)
Query: 116 DDNPDCSDGSDEKSCKNRTCQASEFRCGNNRCIPNHWQ--------CDGEFDCSDKSDED 167
DD DC DGSDE C +F C N IP + CD + C D SDE
Sbjct: 55 DDYCDCPDGSDEPG--TNACSNGKFYCANEGFIPGYIPSFKVDDGVCDYDI-CCDGSDEA 111
Query: 168 PEMCNGVNHCA 178
C N C
Sbjct: 112 LGKCP--NKCG 120
Score = 32.5 bits (74), Expect = 0.41
Identities = 26/67 (38%), Positives = 30/67 (44%), Gaps = 11/67 (16%)
Query: 245 VCDGQNDCPDGVDEKKCHETCRSDEFTCAN----GNCIQRIWLCDG---DDDCKDGSDEK 297
V D DCPDG DE + C + +F CAN I + DG D C DGSDE
Sbjct: 53 VNDDYCDCPDGSDEPGTN-ACSNGKFYCANEGFIPGYIPSFKVDDGVCDYDICCDGSDEA 111
Query: 298 SCQPVKC 304
KC
Sbjct: 112 L---GKC 115
Score = 29.0 bits (65), Expect = 5.4
Identities = 27/83 (32%), Positives = 32/83 (38%), Gaps = 22/83 (26%)
Query: 73 VCDGQNDCPDGVDE---KKCQ--KRICGQEEF------TCRSSPGECVPLTWMCDDNPDC 121
V D DCPDG DE C K C E F + + G C D C
Sbjct: 53 VNDDYCDCPDGSDEPGTNACSNGKFYCANEGFIPGYIPSFKVDDGVC--------DYDIC 104
Query: 122 SDGSDEKS--CKNRTCQ-ASEFR 141
DGSDE C N+ + A +F
Sbjct: 105 CDGSDEALGKCPNKCGEIARQFE 127
>gnl|CDD|215652 pfam00008, EGF, EGF-like domain. There is no clear separation
between noise and signal. pfam00053 is very similar, but
has 8 instead of 6 conserved cysteines. Includes some
cytokine receptors. The EGF domain misses the N-terminus
regions of the Ca2+ binding EGF domains (this is the
main reason of discrepancy between swiss-prot domain
start/end and Pfam). The family is hard to model due to
many similar but different sub-types of EGF domains.
Pfam certainly misses a number of EGF domains.
Length = 32
Score = 29.3 bits (66), Expect = 0.40
Identities = 14/27 (51%), Positives = 15/27 (55%), Gaps = 2/27 (7%)
Query: 395 DNGGCLH--KCVDLPVGYMCECNEGYK 419
N C + CVD P GY CEC EGY
Sbjct: 3 PNNPCSNGGTCVDTPGGYTCECPEGYT 29
>gnl|CDD|218955 pfam06247, Plasmod_Pvs28, Plasmodium ookinete surface protein
Pvs28. This family consists of several ookinete surface
protein (Pvs28) from several species of Plasmodium.
Pvs25 and Pvs28 are expressed on the surface of
ookinetes. These proteins are potential candidates for
vaccine and induce antibodies that block the infectivity
of Plasmodium vivax in immunised animals.
Length = 196
Score = 31.3 bits (71), Expect = 1.4
Identities = 18/61 (29%), Positives = 30/61 (49%), Gaps = 12/61 (19%)
Query: 410 YMCECNEGYKLSSNRHTCIDIDECETPGSCSQIC-----------LNEKGGFKCECVAGY 458
+ C+CNEGY L N +TC + +C+ + +++C E+ KC C+ GY
Sbjct: 20 FECKCNEGYVLK-NENTCEEKVKCDKLENVNKVCGEYATCINQANKAEEKALKCGCINGY 78
Query: 459 I 459
Sbjct: 79 T 79
>gnl|CDD|166839 PRK00178, tolB, translocation protein TolB; Provisional.
Length = 430
Score = 31.2 bits (71), Expect = 2.0
Identities = 23/95 (24%), Positives = 39/95 (41%), Gaps = 21/95 (22%)
Query: 515 GMIFWSDISEK-KIYKAPIDEGSERTVVIEED-----KTIADGLAVDWIYS-----HIYW 563
+ F SD K +IYK ++ G V + + ADG + ++ H+
Sbjct: 300 TLYFTSDRGGKPQIYKVNVNGGRAERVTFVGNYNARPRLSADGKTLVMVHRQDGNFHVAA 359
Query: 564 TDAHKNTIELANFEGTMRKVLVRSYLDEPRSLALN 598
D + G++R +L + LDE S+A N
Sbjct: 360 QDLQR---------GSVR-ILTDTSLDESPSVAPN 384
>gnl|CDD|219847 pfam08450, SGL, SMP-30/Gluconolaconase/LRE-like region. This
family describes a region that is found in proteins
expressed by a variety of eukaryotic and prokaryotic
species. These proteins include various enzymes, such as
senescence marker protein 30 (SMP-30), gluconolactonase
and luciferin-regenerating enzyme (LRE). SMP-30 is known
to hydrolyse diisopropyl phosphorofluoridate in the
liver, and has been noted as having sequence similarity,
in the region described in this family, with PON1 and
LRE.
Length = 245
Score = 30.7 bits (70), Expect = 2.4
Identities = 14/58 (24%), Positives = 24/58 (41%), Gaps = 5/58 (8%)
Query: 620 MDGSHRNMVIVSDIKWPNGLTLDLVQRRLYWVDAKLNEISSCDYNG-----GNRRLVL 672
+D + ++ I NGL + LY+ D+ I + DY+ NRR+
Sbjct: 119 LDPDGKVERVLDGITISNGLAWSPDGKTLYFADSPTRRIWAFDYDADGGLISNRRVFA 176
>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 = 27.1 bits (61), Expect = 3.4
Identities = 12/31 (38%), Positives = 16/31 (51%), Gaps = 4/31 (12%)
Query: 392 CAKDNGGCLH---KCVDLPVGYMCECNEGYK 419
CA++NGGC H C + + C C GY
Sbjct: 1 CAENNGGC-HPNATCTNTGGSFTCTCKSGYT 30
>gnl|CDD|215497 PLN02919, PLN02919, haloacid dehalogenase-like hydrolase family
protein.
Length = 1057
Score = 30.2 bits (68), Expect = 4.7
Identities = 13/38 (34%), Positives = 22/38 (57%)
Query: 628 VIVSDIKWPNGLTLDLVQRRLYWVDAKLNEISSCDYNG 665
++ S +K+P L +DL+ RL+ D+ N I D +G
Sbjct: 562 LLTSPLKFPGKLAIDLLNNRLFISDSNHNRIVVTDLDG 599
>gnl|CDD|216666 pfam01728, FtsJ, FtsJ-like methyltransferase. This family consists
of FtsJ from various bacterial and archaeal sources FtsJ
is a methyltransferase, but actually has no effect on
cell division. FtsJ's substrate is the 23S rRNA. The 1.5
A crystal structure of FtsJ in complex with its cofactor
S-adenosylmethionine revealed that FtsJ has a
methyltransferase fold. This family also includes the N
terminus of flaviviral NS5 protein. It has been
hypothesised that the N-terminal domain of NS5 is a
methyltransferase involved in viral RNA capping.
Length = 177
Score = 29.1 bits (66), Expect = 5.0
Identities = 13/40 (32%), Positives = 20/40 (50%), Gaps = 4/40 (10%)
Query: 411 MCECNEGYKLSSNR-HTCIDIDECETPGSCSQICLNEKGG 449
+ E +E + L + T +D+ PG SQ L E+GG
Sbjct: 9 LLEIDERFGLKPGKGKTVLDL--GAAPGGFSQ-VLLERGG 45
>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 = 29.7 bits (67), Expect = 5.2
Identities = 16/51 (31%), Positives = 20/51 (39%), Gaps = 5/51 (9%)
Query: 121 CSDGSDEKSCKNRTCQASE-FRCGNNRCIPNHWQCDGEFDCSDKSDEDPEM 170
C +GSDE C Q S + C C + C G+ C D PE
Sbjct: 59 CLEGSDEGVCL----QWSVTYDCEQRVCSTTQYVCGGDVFCLDGDCLTPES 105
Score = 28.9 bits (65), Expect = 7.7
Identities = 15/66 (22%), Positives = 20/66 (30%), Gaps = 14/66 (21%)
Query: 243 TWVCDGQNDCPDGVDEKKC---HETCRSDE-----------FTCANGNCIQRIWLCDGDD 288
T+ C N C + C TC + C C ++C GD
Sbjct: 34 TYQCQSNNTCAALESQPGCSFTRSTCLEGSDEGVCLQWSVTYDCEQRVCSTTQYVCGGDV 93
Query: 289 DCKDGS 294
C DG
Sbjct: 94 FCLDGD 99
>gnl|CDD|183738 PRK12775, PRK12775, putative trifunctional 2-polyprenylphenol
hydroxylase/glutamate synthase subunit beta/ferritin
domain-containing protein; Provisional.
Length = 1006
Score = 29.5 bits (66), Expect = 8.1
Identities = 16/50 (32%), Positives = 22/50 (44%), Gaps = 10/50 (20%)
Query: 75 DGQNDCPDGVDEKKCQKRICGQEEFTCRSSPGECVPLTWMCDDNPDCSDG 124
G CP KC + + G EE+ C ++ L W CDD S+G
Sbjct: 794 TGVATCP------KCHRPLEGDEEYVCCATS----ELQWRCDDCGKVSEG 833
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 0.459
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: 35,949,762
Number of extensions: 3340189
Number of successful extensions: 2188
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2162
Number of HSP's successfully gapped: 78
Length of query: 734
Length of database: 10,937,602
Length adjustment: 104
Effective length of query: 630
Effective length of database: 6,324,786
Effective search space: 3984615180
Effective search space used: 3984615180
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: 63 (28.0 bits)