RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17325
(461 letters)
>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 = 56.8 bits (138), Expect = 7e-11
Identities = 21/41 (51%), Positives = 27/41 (65%)
Query: 143 IVVSGLDLVEGLAYDWIGGHIYWLDSRLNRIEVCDENGTNR 183
++ SGL GLA DWI G +YW D L+ IEV + +GTNR
Sbjct: 3 LLSSGLGHPNGLAVDWIEGRLYWTDWGLDVIEVANLDGTNR 43
Score = 54.5 bits (132), Expect = 4e-10
Identities = 18/42 (42%), Positives = 26/42 (61%)
Query: 361 TIISTKIYWPNGLTLDIATRRVYFADSKLDFIDFCNYDGTGR 402
T++S+ + PNGL +D R+Y+ D LD I+ N DGT R
Sbjct: 2 TLLSSGLGHPNGLAVDWIEGRLYWTDWGLDVIEVANLDGTNR 43
Score = 46.4 bits (111), Expect = 3e-07
Identities = 16/45 (35%), Positives = 22/45 (48%), Gaps = 3/45 (6%)
Query: 185 VLAKDNITQPRGMMLDPSPGTRWLFWTDWGENPRIERIGMDGSNR 229
L + P G+ +D L+WTDWG IE +DG+NR
Sbjct: 2 TLLSSGLGHPNGLAVDWI--EGRLYWTDWG-LDVIEVANLDGTNR 43
Score = 43.4 bits (103), Expect = 4e-06
Identities = 13/34 (38%), Positives = 21/34 (61%)
Query: 231 TIISTKIYWPNGLTLDIATRRVYFADSKLDFIDC 264
T++S+ + PNGL +D R+Y+ D LD I+
Sbjct: 2 TLLSSGLGHPNGLAVDWIEGRLYWTDWGLDVIEV 35
Score = 39.9 bits (94), Expect = 7e-05
Identities = 20/54 (37%), Positives = 24/54 (44%), Gaps = 14/54 (25%)
Query: 308 ILVSGQLY--EALALDLENGMLYYSTLKCTRWLFWTDWGENPRIERIGMDGSNR 359
L+S L LA+D G LY WTDWG IE +DG+NR
Sbjct: 2 TLLSSGLGHPNGLAVDWIEGRLY-----------WTDWG-LDVIEVANLDGTNR 43
>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 = 54.9 bits (133), Expect = 3e-10
Identities = 15/40 (37%), Positives = 23/40 (57%)
Query: 208 LFWTDWGENPRIERIGMDGSNRSTIISTKIYWPNGLTLDI 247
L+WTD I ++GS+R T+ S + WPNG+ +D
Sbjct: 3 LYWTDSSLRASISVADLNGSDRRTLFSEDLQWPNGIAVDP 42
Score = 54.9 bits (133), Expect = 3e-10
Identities = 15/40 (37%), Positives = 23/40 (57%)
Query: 338 LFWTDWGENPRIERIGMDGSNRSTIISTKIYWPNGLTLDI 377
L+WTD I ++GS+R T+ S + WPNG+ +D
Sbjct: 3 LYWTDSSLRASISVADLNGSDRRTLFSEDLQWPNGIAVDP 42
Score = 37.9 bits (89), Expect = 3e-04
Identities = 17/42 (40%), Positives = 25/42 (59%), Gaps = 1/42 (2%)
Query: 161 GHIYWLDSRL-NRIEVCDENGTNRIVLAKDNITQPRGMMLDP 201
G +YW DS L I V D NG++R L +++ P G+ +DP
Sbjct: 1 GRLYWTDSSLRASISVADLNGSDRRTLFSEDLQWPNGIAVDP 42
Score = 34.8 bits (81), Expect = 0.003
Identities = 13/44 (29%), Positives = 22/44 (50%), Gaps = 5/44 (11%)
Query: 280 RKLYWIDEGGNGVPLKIGKANMDGSNASILVSGQLY--EALALD 321
+LYW D + + I A+++GS+ L S L +A+D
Sbjct: 1 GRLYWTD---SSLRASISVADLNGSDRRTLFSEDLQWPNGIAVD 41
>gnl|CDD|214542 smart00179, EGF_CA, Calcium-binding EGF-like domain.
Length = 39
Score = 45.7 bits (109), Expect = 5e-07
Identities = 16/42 (38%), Positives = 19/42 (45%), Gaps = 5/42 (11%)
Query: 70 DMNECEQPGYCSQ--MCTNTKGSYICSCNEGYVLEYDNHTCK 109
D++EC C C NT GSY C C GY D C+
Sbjct: 1 DIDECASGNPCQNGGTCVNTVGSYRCECPPGY---TDGRNCE 39
Score = 28.4 bits (64), Expect = 0.69
Identities = 12/29 (41%), Positives = 12/29 (41%), Gaps = 3/29 (10%)
Query: 32 ECKHKFGLCSN--TCHPTPLGALCTCPPG 58
EC C N TC T C CPPG
Sbjct: 4 ECASG-NPCQNGGTCVNTVGSYRCECPPG 31
>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 = 43.4 bits (103), Expect = 3e-06
Identities = 15/34 (44%), Positives = 17/34 (50%), Gaps = 2/34 (5%)
Query: 70 DMNECEQPGYCS--QMCTNTKGSYICSCNEGYVL 101
D++EC C C NT GSY CSC GY
Sbjct: 1 DIDECASGNPCQNGGTCVNTVGSYRCSCPPGYTG 34
Score = 27.2 bits (61), Expect = 1.7
Identities = 13/32 (40%), Positives = 15/32 (46%), Gaps = 3/32 (9%)
Query: 29 DLAECKHKFGLCSN--TCHPTPLGALCTCPPG 58
D+ EC C N TC T C+CPPG
Sbjct: 1 DIDECAS-GNPCQNGGTCVNTVGSYRCSCPPG 31
>gnl|CDD|219496 pfam07645, EGF_CA, Calcium-binding EGF domain.
Length = 42
Score = 41.2 bits (97), Expect = 2e-05
Identities = 15/42 (35%), Positives = 20/42 (47%), Gaps = 3/42 (7%)
Query: 70 DMNECEQPGY-CSQM--CTNTKGSYICSCNEGYVLEYDNHTC 108
D++EC + C C NT GS+ C C +GY D C
Sbjct: 1 DVDECADGTHNCPANTVCVNTIGSFECVCPDGYENNEDGTNC 42
>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 = 44.3 bits (105), Expect = 5e-05
Identities = 18/41 (43%), Positives = 23/41 (56%), Gaps = 1/41 (2%)
Query: 68 CQDMNEC-EQPGYCSQMCTNTKGSYICSCNEGYVLEYDNHT 107
C + C C Q+C +T GSY+C+C EGY L DN T
Sbjct: 184 CVVPDLCATLSHVCQQVCISTPGSYLCACTEGYALLEDNKT 224
>gnl|CDD|214544 smart00181, EGF, Epidermal growth factor-like domain.
Length = 35
Score = 39.8 bits (93), Expect = 6e-05
Identities = 17/38 (44%), Positives = 19/38 (50%), Gaps = 4/38 (10%)
Query: 73 ECEQPGYCSQ-MCTNTKGSYICSCNEGYVLEYDNHTCK 109
EC G CS C NT GSY CSC GY + C+
Sbjct: 1 ECASGGPCSNGTCINTPGSYTCSCPPGYTG---DKRCE 35
Score = 29.0 bits (65), Expect = 0.35
Identities = 15/28 (53%), Positives = 16/28 (57%), Gaps = 2/28 (7%)
Query: 32 ECKHKFGLCSN-TCHPTPLGALCTCPPG 58
EC G CSN TC TP C+CPPG
Sbjct: 1 ECASG-GPCSNGTCINTPGSYTCSCPPG 27
>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 = 37.8 bits (89), Expect = 2e-04
Identities = 12/23 (52%), Positives = 14/23 (60%)
Query: 90 SYICSCNEGYVLEYDNHTCKAIN 112
SY CSC GY L D TC+ I+
Sbjct: 1 SYTCSCPPGYQLSGDGRTCEDID 23
Score = 32.4 bits (75), Expect = 0.018
Identities = 12/21 (57%), Positives = 16/21 (76%)
Query: 53 CTCPPGEILSNDSVTCQDMNE 73
C+CPPG LS D TC+D++E
Sbjct: 4 CSCPPGYQLSGDGRTCEDIDE 24
>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 = 37.8 bits (88), Expect = 3e-04
Identities = 15/38 (39%), Positives = 17/38 (44%), Gaps = 5/38 (13%)
Query: 73 ECEQPGYCS--QMCTNTKGSYICSCNEGYVLEYDNHTC 108
EC CS C NT GSY C C GY + +C
Sbjct: 1 ECAASNPCSNGGTCVNTPGSYRCVCPPGYTG---DRSC 35
Score = 28.2 bits (63), Expect = 0.67
Identities = 14/29 (48%), Positives = 14/29 (48%), Gaps = 3/29 (10%)
Query: 32 ECKHKFGLCSN--TCHPTPLGALCTCPPG 58
EC CSN TC TP C CPPG
Sbjct: 1 ECAA-SNPCSNGGTCVNTPGSYRCVCPPG 28
>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 = 37.5 bits (88), Expect = 4e-04
Identities = 13/25 (52%), Positives = 15/25 (60%), Gaps = 2/25 (8%)
Query: 84 CTNTKGSYICSCNEGYVLEYDNHTC 108
CTNT GS+ C+C GY D TC
Sbjct: 14 CTNTGGSFTCTCKSGY--TGDGVTC 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 = 36.1 bits (84), Expect = 0.001
Identities = 11/21 (52%), Positives = 15/21 (71%)
Query: 4 RCVNLTKVCDGKTDCPNGADE 24
RC+ + VCDG DC +G+DE
Sbjct: 13 RCIPSSWVCDGVDDCGDGSDE 33
>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 = 35.3 bits (82), Expect = 0.002
Identities = 11/21 (52%), Positives = 16/21 (76%)
Query: 4 RCVNLTKVCDGKTDCPNGADE 24
RC+ + VCDG+ DC +G+DE
Sbjct: 12 RCIPSSWVCDGEDDCGDGSDE 32
>gnl|CDD|200964 pfam00057, Ldl_recept_a, Low-density lipoprotein receptor domain
class A.
Length = 37
Score = 34.6 bits (80), Expect = 0.004
Identities = 10/21 (47%), Positives = 15/21 (71%)
Query: 4 RCVNLTKVCDGKTDCPNGADE 24
C+ ++ VCDG DC +G+DE
Sbjct: 14 ECIPMSWVCDGDPDCEDGSDE 34
>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 = 0.30
Identities = 12/28 (42%), Positives = 13/28 (46%), Gaps = 2/28 (7%)
Query: 74 CEQPGYCS--QMCTNTKGSYICSCNEGY 99
C CS C +T G Y C C EGY
Sbjct: 1 CSPNNPCSNGGTCVDTPGGYTCECPEGY 28
Score = 26.2 bits (58), Expect = 4.0
Identities = 12/21 (57%), Positives = 12/21 (57%), Gaps = 2/21 (9%)
Query: 40 CSN--TCHPTPLGALCTCPPG 58
CSN TC TP G C CP G
Sbjct: 7 CSNGGTCVDTPGGYTCECPEG 27
>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 = 31.6 bits (72), Expect = 0.56
Identities = 16/68 (23%), Positives = 27/68 (39%), Gaps = 14/68 (20%)
Query: 53 CTCPPGEILSNDSVTCQDMNECEQP----------GYC-SQMCTNTKGSYICSCNEGYVL 101
C C G +L N++ TC++ +C++ C +Q + + C C GY L
Sbjct: 22 CKCNEGYVLKNEN-TCEEKVKCDKLENVNKVCGEYATCINQANKAEEKALKCGCINGYTL 80
Query: 102 EYDNHTCK 109
C
Sbjct: 81 --SQGVCV 86
Score = 27.8 bits (62), Expect = 9.9
Identities = 15/36 (41%), Positives = 19/36 (52%), Gaps = 5/36 (13%)
Query: 78 GYCSQMCTNTKGSYICSCNEGYVLEYDNHTCKAINH 113
GY QM + C CNEGYVL+ +N TC+
Sbjct: 11 GYLIQM----SNHFECKCNEGYVLKNEN-TCEEKVK 41
>gnl|CDD|190848 pfam04056, Ssl1, Ssl1-like. Ssl1-like proteins are 40kDa subunits
of the Transcription factor II H complex.
Length = 193
Score = 31.6 bits (72), Expect = 0.57
Identities = 14/48 (29%), Positives = 23/48 (47%), Gaps = 6/48 (12%)
Query: 50 GALCTCPPGEI------LSNDSVTCQDMNECEQPGYCSQMCTNTKGSY 91
G+L TC PG+I L + + C + + C ++C T G+Y
Sbjct: 109 GSLSTCDPGDIYSTIDTLKKEKIRCSVIGLSAEVFICKELCKATNGTY 156
>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 = 31.4 bits (72), Expect = 0.78
Identities = 32/153 (20%), Positives = 50/153 (32%), Gaps = 39/153 (25%)
Query: 118 LIISNRHSILV-----------ADLEEKGKDHRAQDIVVSGL------DLVEGLAYDWIG 160
LI++ + + + ADLE +R D V + +A
Sbjct: 54 LIVALKRGLALLDLDTGELTTLADLEPDEPLNRFNDGKVDPDGRFWFGTMGFDIAPGGEP 113
Query: 161 GHIYWLDSRLNRIEVCDENGTNRIVLAKDNITQPRGMMLDPSPGTRWLFWTDWGENPRIE 220
G +Y LD ++ D IT G+ SP + L++ D RI
Sbjct: 114 GALYRLD------------PDGKVERVLDGITISNGLAW--SPDGKTLYFADSPTR-RIW 158
Query: 221 RI-----GMDGSNRSTIISTKIY--WPNGLTLD 246
G SNR K P+G+ +D
Sbjct: 159 AFDYDADGGLISNRRVFADFKDGDGEPDGMAVD 191
Score = 29.1 bits (66), Expect = 4.0
Identities = 37/203 (18%), Positives = 54/203 (26%), Gaps = 49/203 (24%)
Query: 203 PGTRWLFWTDWGENPRIERIGMDGSNRSTIISTKIYWPNGLTLDIATRRVYFADSK---- 258
L+W D RI R+ + P G R+ A +
Sbjct: 9 EEEGALYWVDI-LGGRIHRLDPATGKETVWDLPG---PVGAIALRDDGRLIVALKRGLAL 64
Query: 259 LDFIDCKSLEIKTNVNYSTIFRKLYWIDEGGNGVPLKIGKANMDGSNASILVSGQLYEAL 318
LD + L ++ GK + DG G + +
Sbjct: 65 LDL-------------DTGELTTLADLEPDEPLNRFNDGKVDPDGR----FWFGTMGFDI 107
Query: 319 ALDLENGMLYYSTLKCTRWLFWTDWGENPRIERIGMDGSNRSTIISTKIYWPNGLTLDIA 378
A E G LY +D + + I NGL
Sbjct: 108 APGGEPGALYR------------------------LDPDGKVERVLDGITISNGLAWSPD 143
Query: 379 TRRVYFADSKLDFIDFCNYDGTG 401
+ +YFADS I +YD G
Sbjct: 144 GKTLYFADSPTRRIWAFDYDADG 166
>gnl|CDD|213205 cd03238, ABC_UvrA, ATP-binding cassette domain of the excision
repair protein UvrA. Nucleotide excision repair in
eubacteria is a process that repairs DNA damage by the
removal of a 12-13-mer oligonucleotide containing the
lesion. Recognition and cleavage of the damaged DNA is a
multistep ATP-dependent reaction that requires the UvrA,
UvrB, and UvrC proteins. Both UvrA and UvrB are ATPases,
with UvrA having two ATP binding sites, which have the
characteristic signature of the family of ABC proteins,
and UvrB having one ATP binding site that is
structurally related to that of helicases.
Length = 176
Score = 30.4 bits (69), Expect = 1.1
Identities = 18/60 (30%), Positives = 30/60 (50%), Gaps = 2/60 (3%)
Query: 223 GMDGSNRSTIISTKIYWPNGLTLDIATRRVYFADSKLDFIDCKSLEIKTNVNYSTIFRKL 282
G+ GS +ST+++ +Y L + F+ +KL FID I + Y T+ +KL
Sbjct: 28 GVSGSGKSTLVNEGLYASGKARLISFLPK--FSRNKLIFIDQLQFLIDVGLGYLTLGQKL 85
>gnl|CDD|201923 pfam01683, EB, EB module. This domain has no known function. It is
found in several C. elegans proteins. The domain
contains 8 conserved cysteines that probably form four
disulphide bridges. This domain is found associated with
kunitz domains pfam00014.
Length = 52
Score = 27.8 bits (62), Expect = 1.8
Identities = 14/62 (22%), Positives = 21/62 (33%), Gaps = 18/62 (29%)
Query: 55 CPPGEILSNDS--------VTCQDMNECEQPGYCSQMCTNTKGSYICSCNEGYVLEYDNH 106
CP G++L N +C+ +C+ C C C EG+ L
Sbjct: 1 CPSGQVLVNGECLPKVLPGESCEYDEQCQGGSVCING--------TCQCPEGFTL--VGG 50
Query: 107 TC 108
C
Sbjct: 51 RC 52
>gnl|CDD|215497 PLN02919, PLN02919, haloacid dehalogenase-like hydrolase family
protein.
Length = 1057
Score = 30.6 bits (69), Expect = 2.3
Identities = 20/53 (37%), Positives = 26/53 (49%), Gaps = 4/53 (7%)
Query: 133 EKGKDHRAQDIVVSGLDLVEGLAYDWIGGHIYWLDSRLNRIEVCDENGTNRIV 185
EK D R ++ S L LA D + ++ DS NRI V D +G N IV
Sbjct: 555 EKDNDPR---LLTSPLKFPGKLAIDLLNNRLFISDSNHNRIVVTDLDG-NFIV 603
>gnl|CDD|216726 pfam01826, TIL, Trypsin Inhibitor like cysteine rich domain. This
family contains trypsin inhibitors as well as a domain
found in many extracellular proteins. The domain
typically contains ten cysteine residues that form five
disulphide bonds. The cysteine residues that form the
disulphide bonds are 1-7, 2-6, 3-5, 4-10 and 8-9.
Length = 55
Score = 27.3 bits (61), Expect = 2.6
Identities = 16/57 (28%), Positives = 20/57 (35%), Gaps = 11/57 (19%)
Query: 55 CPPGEILSNDSVTCQDMNECEQ---PGYCSQMCTNTKGSYICSCNEGYVLEYDNHTC 108
CPP E+ S C C P C C C C GYV + ++ C
Sbjct: 1 CPPNEVYSECGSACPP--TCANLSTPPPCPLPCVEG-----CVCPPGYVRD-NDGKC 49
>gnl|CDD|212108 cd10796, GH57N_APU, N-terminal catalytic domain of thermoactive
amylopullulanases; glycoside hydrolase family 57 (GH57).
Pullulanases (EC 3.2.1.41) are capable of hydrolyzing
the alpha-1,6 glucosidic bonds of pullulan, producing
maltotriose. Amylopullulanases (APU, E.C 3.2.1.1/41)
are type II pullulanases which can also degrade both the
alpha-1,6 and alpha-1,4 glucosidic bonds of starch,
producing oligosaccharides. This subfamily includes GH57
archaeal thermoactive APUs, which show both
pullulanolytic and amylolytic activities. They have an
acid pH optimum and the presence of Ca2+ might increase
their activity, thermostability, and substrate affinity.
Besides GH57 thermoactive APUs, all mesophilic and some
thermoactive APUs belong to glycoside hydrolase family
13 with catalytic features distinct from GH57. This
subfamily also includes many uncharacterized proteins
found in bacteria and archaea.
Length = 313
Score = 29.5 bits (67), Expect = 3.4
Identities = 20/71 (28%), Positives = 29/71 (40%), Gaps = 4/71 (5%)
Query: 381 RVYFADSKL-DFIDFCNYDGTGRQQVI--LIDLMVEFTNDLMGDNGVPALALDLENGMLY 437
V+F D +L D I F Y + I + + GV +ALD EN +
Sbjct: 197 YVFFRDHELSDLIGF-TYSFWPAEDAARDFIHRLKSIREQIYNPGGVVTIALDGENAWEF 255
Query: 438 YSTEGAEFLKT 448
Y G +FL+
Sbjct: 256 YPNNGYDFLEA 266
>gnl|CDD|238730 cd01453, vWA_transcription_factor_IIH_type, Transcription factors
IIH type: TFIIH is a multiprotein complex that is one of
the five general transcription factors that binds RNA
polymerase II holoenzyme. Orthologues of these genes are
found in all completed eukaryotic genomes and all these
proteins contain a VWA domain. The p44 subunit of TFIIH
functions as a DNA helicase in RNA polymerase II
transcription initiation and DNA repair, and its
transcriptional activity is dependent on its C-terminal
Zn-binding domains. The function of the vWA domain is
unclear, but may be involved in complex assembly. The
MIDAS motif is not conserved in this sub-group.
Length = 183
Score = 28.8 bits (65), Expect = 4.4
Identities = 12/48 (25%), Positives = 21/48 (43%), Gaps = 6/48 (12%)
Query: 50 GALCTCPPGEI------LSNDSVTCQDMNECEQPGYCSQMCTNTKGSY 91
+L TC PG I L +++ + + C ++C T G+Y
Sbjct: 115 SSLSTCDPGNIYETIDKLKKENIRVSVIGLSAEMHICKEICKATNGTY 162
>gnl|CDD|183740 PRK12779, PRK12779, putative bifunctional glutamate synthase
subunit beta/2-polyprenylphenol hydroxylase;
Provisional.
Length = 944
Score = 29.4 bits (66), Expect = 5.5
Identities = 30/113 (26%), Positives = 47/113 (41%), Gaps = 14/113 (12%)
Query: 320 LDLENGMLYYSTLKCTRWLFWTDWGENPRIERIGMDGSNRSTIISTKIYWPNGLTLDIAT 379
L L N + S + +LFWT E R+ ++ + ++ +I T T D +
Sbjct: 773 LRLGNHVTLISGFRAKEFLFWTGDDE--RVGKLKAEFGDQLDVIYT--------TNDGSF 822
Query: 380 RRVYFADSKLDFIDFCNYDGTGRQ--QVILID--LMVEFTNDLMGDNGVPALA 428
F L+ + N G GR +VI I LM+ +DL GV +A
Sbjct: 823 GVKGFVTGPLEEMLKANQQGKGRTIAEVIAIGPPLMMRAVSDLTKPYGVKTVA 875
>gnl|CDD|215784 pfam00200, Disintegrin, Disintegrin.
Length = 76
Score = 26.8 bits (60), Expect = 5.6
Identities = 20/76 (26%), Positives = 25/76 (32%), Gaps = 25/76 (32%)
Query: 12 CDGKTDCPNGADEGPGCDLAECKHK------FGLCSNTCHPTPLGALCTCPPGEILSNDS 65
C +C N P CD CK K G C + C P G +C
Sbjct: 8 CGSPEECQN-----PCCDATTCKLKPGAQCATGPCCDQCKFKPAGTVCR----------- 51
Query: 66 VTCQDMNECEQPGYCS 81
EC+ P YC+
Sbjct: 52 ---PASGECDLPEYCT 64
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
0.321 0.139 0.448
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: 23,351,192
Number of extensions: 2239606
Number of successful extensions: 1634
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1620
Number of HSP's successfully gapped: 54
Length of query: 461
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 361
Effective length of database: 6,502,202
Effective search space: 2347294922
Effective search space used: 2347294922
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)