RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10559
(418 letters)
>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 = 33.8 bits (78), Expect = 0.007
Identities = 12/31 (38%), Positives = 17/31 (54%), Gaps = 1/31 (3%)
Query: 42 PNSCSNHGQCRVNSDSQWECKCSDGWDGKDC 72
N C N G C VN+ + C C G+ G++C
Sbjct: 8 GNPCQNGGTC-VNTVGSYRCSCPPGYTGRNC 37
Score = 30.3 bits (69), Expect = 0.12
Identities = 9/28 (32%), Positives = 12/28 (42%), Gaps = 4/28 (14%)
Query: 14 CNEHGQCKNG----TCLCVTGWNGKHCT 37
C G C N C C G+ G++C
Sbjct: 11 CQNGGTCVNTVGSYRCSCPPGYTGRNCE 38
>gnl|CDD|113629 pfam04863, EGF_alliinase, Alliinase EGF-like domain. Allicin is
a thiosulphinate that gives rise to dithiines, allyl
sulphides and ajoenes, the three groups of active
compounds in Allium species. Allicin is synthesised
from sulfoxide cysteine derivatives by alliinase
(EC:4.4.1.4), whose C-S lyase activity cleaves
C(beta)-S(gamma) bonds. It is thought that this enzyme
forms part of a primitive plant defence system. This
family represents the N-terminal EGF-like domain.
Length = 56
Score = 33.6 bits (77), Expect = 0.014
Identities = 16/40 (40%), Positives = 24/40 (60%), Gaps = 4/40 (10%)
Query: 44 SCSNHGQCRVN---SDSQWECKCSDGWDGKDCSVLLEQNC 80
+CS HG+ ++ SD C+C+ + G DCSVL+ NC
Sbjct: 18 NCSGHGRAFLDGIISDGSPICECNTCYTGPDCSVLI-PNC 56
>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 = 32.4 bits (74), Expect = 0.020
Identities = 12/28 (42%), Positives = 18/28 (64%), Gaps = 1/28 (3%)
Query: 43 NSCSNHGQCRVNSDSQWECKCSDGWDGK 70
N CSN G C V++ + C+C +G+ GK
Sbjct: 5 NPCSNGGTC-VDTPGGYTCECPEGYTGK 31
Score = 27.0 bits (60), Expect = 1.7
Identities = 9/27 (33%), Positives = 12/27 (44%), Gaps = 4/27 (14%)
Query: 13 WCNEHGQCKNG----TCLCVTGWNGKH 35
C+ G C + TC C G+ GK
Sbjct: 6 PCSNGGTCVDTPGGYTCECPEGYTGKR 32
>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 = 31.7 bits (72), Expect = 0.045
Identities = 12/29 (41%), Positives = 15/29 (51%), Gaps = 1/29 (3%)
Query: 42 PNSCSNHGQCRVNSDSQWECKCSDGWDGK 70
N CSN G C VN+ + C C G+ G
Sbjct: 5 SNPCSNGGTC-VNTPGSYRCVCPPGYTGD 32
Score = 25.5 bits (56), Expect = 6.3
Identities = 9/29 (31%), Positives = 13/29 (44%), Gaps = 5/29 (17%)
Query: 14 CNEHGQCKNG----TCLCVTGWNG-KHCT 37
C+ G C N C+C G+ G + C
Sbjct: 8 CSNGGTCVNTPGSYRCVCPPGYTGDRSCE 36
>gnl|CDD|214542 smart00179, EGF_CA, Calcium-binding EGF-like domain.
Length = 39
Score = 31.4 bits (72), Expect = 0.052
Identities = 13/32 (40%), Positives = 19/32 (59%), Gaps = 2/32 (6%)
Query: 42 PNSCSNHGQCRVNSDSQWECKCSDGW-DGKDC 72
N C N G C VN+ + C+C G+ DG++C
Sbjct: 8 GNPCQNGGTC-VNTVGSYRCECPPGYTDGRNC 38
>gnl|CDD|219677 pfam07974, EGF_2, EGF-like domain. This family contains EGF
domains found in a variety of extracellular proteins.
Length = 31
Score = 31.3 bits (71), Expect = 0.060
Identities = 8/31 (25%), Positives = 11/31 (35%), Gaps = 3/31 (9%)
Query: 42 PNSCSNHGQCRVNSDSQWECKCSDGWDGKDC 72
C+ G C +C C G+ G C
Sbjct: 4 SGICNGRGTCV---RPCGKCVCDSGYQGATC 31
Score = 30.1 bits (68), Expect = 0.15
Identities = 10/25 (40%), Positives = 13/25 (52%), Gaps = 2/25 (8%)
Query: 14 CNEHGQC--KNGTCLCVTGWNGKHC 36
CN G C G C+C +G+ G C
Sbjct: 7 CNGRGTCVRPCGKCVCDSGYQGATC 31
>gnl|CDD|222268 pfam13620, CarboxypepD_reg, Carboxypeptidase regulatory-like
domain.
Length = 81
Score = 30.7 bits (70), Expect = 0.22
Identities = 21/82 (25%), Positives = 29/82 (35%), Gaps = 5/82 (6%)
Query: 162 VVRGRVVTSMGMGLVGVRVS---TSTPLEGFTLTRDDGWFDLLVNGGGAVTLQFGRSPFK 218
+ G V + G + G V+ T T T DG F L G TL +K
Sbjct: 1 TISGTVTDASGAPIPGATVTLTNADTGTVRGTTTDADGRFSLTGLPPGTYTLTVSAPGYK 60
Query: 219 PHNH-IVHVPWNEVVIIDTITM 239
V V + +D IT+
Sbjct: 61 SQTVKDVTVTAGQTTTLD-ITL 81
>gnl|CDD|220751 pfam10433, MMS1_N, Mono-functional DNA-alkylating methyl
methanesulfonate N-term. MMS1 is a protein that
protects against replication-dependent DNA damage in
Saccharomyces cerevisiae. MMS1 belongs to the DDB1
family of cullin 4 adaptors and the two proteins are
homologous. MMS1 bridges the interaction of MMS22 and
Crt10 with Cul8/Rtt101. Cul8/Rtt101 is a cullin protein
involved in the regulation of DNA replication subsequent
to DNA damage. The N-terminal region of MMS1 and the
C-terminal of MMS22 are required for the the MMS1-MMS22
interaction. The human HIV-1 virion-associated protein
Vpr assembles with DDB1 through interaction with DCAF1
(chromatin assembly factor) to form an E3 ubiquitin
ligase that targets cellular substrates for
proteasome-mediated degradation and subsequent G2
arrest.
Length = 513
Score = 32.7 bits (75), Expect = 0.35
Identities = 13/50 (26%), Positives = 17/50 (34%)
Query: 306 TSASIFYQIGRLWQVTLKGKGLVKLLRMGRKYLTPSSNISCASSNPPQVV 355
T A+ G + QVT L L I+ AS N V+
Sbjct: 422 TLAAGNTSDGVIIQVTENSIRLSDLELGKITDEWSDEIITAASVNGSLVL 471
>gnl|CDD|221873 pfam12955, DUF3844, Domain of unknown function (DUF3844). This
presumed domain is found in fungal species. It contains
8 largely conserved cysteine residues. This domain is
found in proteins that are thought to be found in the
endoplasmic reticulum.
Length = 103
Score = 30.7 bits (70), Expect = 0.39
Identities = 15/48 (31%), Positives = 17/48 (35%), Gaps = 17/48 (35%)
Query: 43 NSCSNHGQCRVNSDSQ----WECKCSD-------------GWDGKDCS 73
NSCS HG C S S+ + CKC W G C
Sbjct: 13 NSCSGHGSCVKKSKSKGGDCYACKCKPTVVRTGSDKGKTTRWGGPACQ 60
>gnl|CDD|216650 pfam01696, Adeno_E1B_55K, Adenovirus EB1 55K protein / large
t-antigen. This family consists of adenovirus E1B 55K
protein or large t-antigen. E1B 55K binds p53 the tumour
suppressor protein converting it from a transcriptional
activator which responds to damaged DNA in to an
unregulated repressor of genes with a p53 binding site.
This protects the virus against p53 induced host
antiviral responses and prevents apoptosis as induced by
the adenovirus E1A protein. The E1B region of adenovirus
encodes two proteins E1B 55K the large t-antigen as
found in this family and E1B 19K pfam01691 the small
t-antigen which is not found in this family; both of
these proteins inhibit E1A induced apoptosis. This
family shows distant similarities to the pectate lyase
superfamily.
Length = 387
Score = 31.1 bits (71), Expect = 1.0
Identities = 16/91 (17%), Positives = 26/91 (28%), Gaps = 22/91 (24%)
Query: 34 KHCTLEGCPNSCSNHGQCRVNSDSQWECKCSDGWDGKDCSVLLEQ----------NCNDG 83
K C E C + G R+ S+ C VLL+ +
Sbjct: 194 KKCVFEKCVLGIISEGDARIRH-----NAASE----TGCFVLLKGTGSIKHNSICGPSTL 244
Query: 84 KDNDKDGLVDCEDPEC---CSNHICRSSQLC 111
D+ ++ C D + HI +
Sbjct: 245 PDSMDFQMLTCADGNVHPLKTVHIVSHPRKK 275
>gnl|CDD|188502 TIGR03987, TIGR03987, TIGR03987 family protein. Conserved
hypothetical protein.
Length = 120
Score = 29.6 bits (67), Expect = 1.1
Identities = 13/40 (32%), Positives = 16/40 (40%), Gaps = 10/40 (25%)
Query: 299 IMPTVLITSASIFYQIG----------RLWQVTLKGKGLV 328
I + IT A +FY IG + W V GLV
Sbjct: 2 IFAIIFITLALVFYTIGVFSERKSGTLKKWHVIFFWLGLV 41
>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 = 26.0 bits (58), Expect = 4.1
Identities = 9/30 (30%), Positives = 12/30 (40%), Gaps = 3/30 (10%)
Query: 45 CSNHGQCRVNSDSQWECKCSDG--WDGKDC 72
C + C N+ + C C G DG C
Sbjct: 8 CHPNATCT-NTGGSFTCTCKSGYTGDGVTC 36
>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 = 28.6 bits (64), Expect = 4.3
Identities = 22/102 (21%), Positives = 37/102 (36%), Gaps = 20/102 (19%)
Query: 14 CNEHGQCKNG---------TCLCVTGW--NGKHCTLEGCPNSCSNHGQCRVNSDSQWECK 62
C E+ C N C C+ G+ + C C N G+C V+ +
Sbjct: 52 CGEYATCINQANKAEEKALKCGCINGYTLSQGVCVPNKCNNKVCGSGKCIVDPANPNNTT 111
Query: 63 CSDGWDGKDCSV--LLEQNCNDGKDNDKDGLVDCEDPECCSN 102
CS C++ + +QN K + + C++ E C
Sbjct: 112 CS-------CNIGKVPDQNGKCTKTGETKCSLKCKENEECKL 146
>gnl|CDD|224883 COG1972, NupC, Nucleoside permease [Nucleotide transport and
metabolism].
Length = 404
Score = 29.1 bits (66), Expect = 5.1
Identities = 14/42 (33%), Positives = 21/42 (50%), Gaps = 3/42 (7%)
Query: 297 LAIMPTVLITSA--SIFYQIGRL-WQVTLKGKGLVKLLRMGR 335
++P ++ SA SI Y IG L + + G GL K L +
Sbjct: 92 FRVLPPIIFISALISILYYIGILPLVIRIIGGGLQKALGTSK 133
>gnl|CDD|219496 pfam07645, EGF_CA, Calcium-binding EGF domain.
Length = 42
Score = 25.8 bits (57), Expect = 6.5
Identities = 12/35 (34%), Positives = 19/35 (54%), Gaps = 5/35 (14%)
Query: 42 PNSCSNHGQCRVNSDSQWECKCSDGW----DGKDC 72
++C + C VN+ +EC C DG+ DG +C
Sbjct: 9 THNCPANTVC-VNTIGSFECVCPDGYENNEDGTNC 42
>gnl|CDD|173909 cd00818, IleRS_core, catalytic core domain of isoleucyl-tRNA
synthetases. Isoleucine amino-acyl tRNA synthetases
(IleRS) catalytic core domain . This class I enzyme is a
monomer which aminoacylates the 2'-OH of the nucleotide
at the 3' of the appropriate tRNA. The core domain is
based on the Rossman fold and is responsible for the
ATP-dependent formation of the enzyme bound
aminoacyl-adenylate. It contains the characteristic
class I HIGH and KMSKS motifs, which are involved in ATP
binding. IleRS has an insertion in the core domain,
which is subject to both deletions and rearrangements.
This editing region hydrolyzes mischarged cognate tRNAs
and thus prevents the incorporation of chemically
similar amino acids.
Length = 338
Score = 28.4 bits (64), Expect = 8.4
Identities = 19/41 (46%), Positives = 23/41 (56%), Gaps = 9/41 (21%)
Query: 186 LEGFTLTRDDGWF-DLLVNGGGAVTLQFGRSPFKPHNHIVH 225
LEG TR GWF LL+ T FG++P+K N IVH
Sbjct: 257 LEGSDQTR--GWFYSLLLLS----TALFGKAPYK--NVIVH 289
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 0.135 0.431
Gapped
Lambda K H
0.267 0.0632 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 20,294,865
Number of extensions: 1865775
Number of successful extensions: 1365
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1356
Number of HSP's successfully gapped: 32
Length of query: 418
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 319
Effective length of database: 6,546,556
Effective search space: 2088351364
Effective search space used: 2088351364
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: 60 (27.1 bits)