RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11795
(313 letters)
>gnl|CDD|201391 pfam00683, TB, TB domain. This domain is also known as the 8
cysteine domain. This family includes the hybrid
domains. This cysteine rich repeat is found in TGF
binding protein and fibrillin.
Length = 42
Score = 42.3 bits (100), Expect = 6e-06
Identities = 19/38 (50%), Positives = 22/38 (57%), Gaps = 1/38 (2%)
Query: 57 MCQGQLEGVVCTKQLCCATVGRAWGHPCEHCPAQLDCD 94
C L G V TK CC ++GRAWG PCE CP Q +
Sbjct: 2 RCSNPLPGNV-TKSECCCSLGRAWGTPCEPCPVQGTAE 38
Score = 30.8 bits (70), Expect = 0.062
Identities = 15/40 (37%), Positives = 22/40 (55%), Gaps = 2/40 (5%)
Query: 215 NQCKNKLPIRLSRKDCCCGKNMGKAWGDECLQCPMIGEDC 254
+C N LP +++ +CCC G+AWG C CP+ G
Sbjct: 1 GRCSNPLPGNVTKSECCCSL--GRAWGTPCEPCPVQGTAE 38
Score = 29.6 bits (67), Expect = 0.20
Identities = 14/35 (40%), Positives = 21/35 (60%), Gaps = 2/35 (5%)
Query: 276 NQCKNKLPIRLSRKDCCCGKNMGKAWGDECLQCPM 310
+C N LP +++ +CCC G+AWG C CP+
Sbjct: 1 GRCSNPLPGNVTKSECCCSL--GRAWGTPCEPCPV 33
>gnl|CDD|219496 pfam07645, EGF_CA, Calcium-binding EGF domain.
Length = 42
Score = 38.5 bits (90), Expect = 1e-04
Identities = 17/42 (40%), Positives = 24/42 (57%), Gaps = 1/42 (2%)
Query: 159 DRNECREEPNIC-ANGKCVNTDGGFYCICNPGFIPTQDRMSC 199
D +EC + + C AN CVNT G F C+C G+ +D +C
Sbjct: 1 DVDECADGTHNCPANTVCVNTIGSFECVCPDGYENNEDGTNC 42
Score = 33.1 bits (76), Expect = 0.011
Identities = 17/42 (40%), Positives = 19/42 (45%), Gaps = 1/42 (2%)
Query: 117 DIDECEAVPGLC-RGGRCINTPGSFTCECARGKSRNPDTNAC 157
D+DEC C C+NT GSF C C G N D C
Sbjct: 1 DVDECADGTHNCPANTVCVNTIGSFECVCPDGYENNEDGTNC 42
>gnl|CDD|214542 smart00179, EGF_CA, Calcium-binding EGF-like domain.
Length = 39
Score = 37.2 bits (87), Expect = 3e-04
Identities = 16/31 (51%), Positives = 19/31 (61%)
Query: 117 DIDECEAVPGLCRGGRCINTPGSFTCECARG 147
DIDEC + GG C+NT GS+ CEC G
Sbjct: 1 DIDECASGNPCQNGGTCVNTVGSYRCECPPG 31
Score = 36.1 bits (84), Expect = 8e-04
Identities = 16/33 (48%), Positives = 19/33 (57%), Gaps = 2/33 (6%)
Query: 159 DRNECREEPNICANG-KCVNTDGGFYCICNPGF 190
D +EC N C NG CVNT G + C C PG+
Sbjct: 1 DIDEC-ASGNPCQNGGTCVNTVGSYRCECPPGY 32
>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 = 35.7 bits (83), Expect = 0.001
Identities = 15/31 (48%), Positives = 18/31 (58%)
Query: 117 DIDECEAVPGLCRGGRCINTPGSFTCECARG 147
DIDEC + GG C+NT GS+ C C G
Sbjct: 1 DIDECASGNPCQNGGTCVNTVGSYRCSCPPG 31
Score = 35.7 bits (83), Expect = 0.001
Identities = 16/34 (47%), Positives = 19/34 (55%), Gaps = 2/34 (5%)
Query: 159 DRNECREEPNICAN-GKCVNTDGGFYCICNPGFI 191
D +EC N C N G CVNT G + C C PG+
Sbjct: 1 DIDEC-ASGNPCQNGGTCVNTVGSYRCSCPPGYT 33
>gnl|CDD|214544 smart00181, EGF, Epidermal growth factor-like domain.
Length = 35
Score = 32.9 bits (75), Expect = 0.011
Identities = 11/27 (40%), Positives = 15/27 (55%)
Query: 165 EEPNICANGKCVNTDGGFYCICNPGFI 191
C+NG C+NT G + C C PG+
Sbjct: 3 ASGGPCSNGTCINTPGSYTCSCPPGYT 29
Score = 29.4 bits (66), Expect = 0.19
Identities = 15/25 (60%), Positives = 16/25 (64%)
Query: 123 AVPGLCRGGRCINTPGSFTCECARG 147
A G C G CINTPGS+TC C G
Sbjct: 3 ASGGPCSNGTCINTPGSYTCSCPPG 27
>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 = 34.7 bits (80), Expect = 0.040
Identities = 10/39 (25%), Positives = 18/39 (46%), Gaps = 1/39 (2%)
Query: 157 CEDRNECREEPNICANGKCVNTDGGFYCICNPGFIPTQD 195
C + C ++C C++T G + C C G+ +D
Sbjct: 184 CVVPDLCATLSHVCQQV-CISTPGSYLCACTEGYALLED 221
Score = 32.7 bits (75), Expect = 0.15
Identities = 13/39 (33%), Positives = 19/39 (48%), Gaps = 1/39 (2%)
Query: 116 PDIDECEAVPGLCRGGRCINTPGSFTCECARGKSRNPDT 154
D C + +C+ CI+TPGS+ C C G + D
Sbjct: 185 VVPDLCATLSHVCQQV-CISTPGSYLCACTEGYALLEDN 222
>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 = 29.0 bits (65), Expect = 0.31
Identities = 13/28 (46%), Positives = 17/28 (60%), Gaps = 1/28 (3%)
Query: 165 EEPNICAN-GKCVNTDGGFYCICNPGFI 191
N C+N G CVNT G + C+C PG+
Sbjct: 3 AASNPCSNGGTCVNTPGSYRCVCPPGYT 30
Score = 26.7 bits (59), Expect = 2.0
Identities = 11/18 (61%), Positives = 13/18 (72%)
Query: 130 GGRCINTPGSFTCECARG 147
GG C+NTPGS+ C C G
Sbjct: 11 GGTCVNTPGSYRCVCPPG 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 = 28.3 bits (64), Expect = 0.45
Identities = 12/30 (40%), Positives = 13/30 (43%), Gaps = 1/30 (3%)
Query: 163 CREEPNIC-ANGKCVNTDGGFYCICNPGFI 191
C E C N C NT G F C C G+
Sbjct: 1 CAENNGGCHPNATCTNTGGSFTCTCKSGYT 30
>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 = 27.8 bits (63), Expect = 0.54
Identities = 7/21 (33%), Positives = 11/21 (52%)
Query: 181 GFYCICNPGFIPTQDRMSCID 201
+ C C PG+ + D +C D
Sbjct: 1 SYTCSCPPGYQLSGDGRTCED 21
Score = 27.0 bits (61), Expect = 1.1
Identities = 10/24 (41%), Positives = 13/24 (54%)
Query: 139 SFTCECARGKSRNPDTNACEDRNE 162
S+TC C G + D CED +E
Sbjct: 1 SYTCSCPPGYQLSGDGRTCEDIDE 24
>gnl|CDD|226810 COG4373, COG4373, Mu-like prophage FluMu protein gp28 [General
function prediction only].
Length = 509
Score = 29.9 bits (67), Expect = 1.8
Identities = 18/63 (28%), Positives = 25/63 (39%), Gaps = 8/63 (12%)
Query: 251 GEDCLFPLLISDARQG-SCYT--SLTSDNQCKNKLPIR---LSRKDCCCGKNMGKAWGDE 304
G D LF +I +ARQG Y+ S+T D+ + L R + R W E
Sbjct: 174 GVDNLFNQMIQEARQGRKKYSVHSITLDDAIADGLYERICNVDRPAWAPEVE--AKWLAE 231
Query: 305 CLQ 307
Sbjct: 232 LRA 234
>gnl|CDD|216334 pfam01153, Glypican, Glypican.
Length = 559
Score = 28.9 bits (65), Expect = 4.0
Identities = 14/50 (28%), Positives = 18/50 (36%), Gaps = 9/50 (18%)
Query: 98 LKNIHSGQCVD-IDECEAVPDIDECEAVPGLCRGGRCINTPGSFTCECAR 146
L+ +SG VD D DE G G C++ TCE
Sbjct: 468 LRAAYSGNDVDFQDAS------DESSGGSGS--GSGCVDKRLRITCEGGH 509
>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 = 25.5 bits (56), Expect = 4.0
Identities = 10/28 (35%), Positives = 13/28 (46%)
Query: 163 CREEPNICANGKCVNTDGGFYCICNPGF 190
C G CV+T GG+ C C G+
Sbjct: 1 CSPNNPCSNGGTCVDTPGGYTCECPEGY 28
Score = 24.7 bits (54), Expect = 7.8
Identities = 11/18 (61%), Positives = 14/18 (77%)
Query: 130 GGRCINTPGSFTCECARG 147
GG C++TPG +TCEC G
Sbjct: 10 GGTCVDTPGGYTCECPEG 27
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
0.324 0.140 0.498
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: 14,639,101
Number of extensions: 1251173
Number of successful extensions: 731
Number of sequences better than 10.0: 1
Number of HSP's gapped: 721
Number of HSP's successfully gapped: 37
Length of query: 313
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 216
Effective length of database: 6,635,264
Effective search space: 1433217024
Effective search space used: 1433217024
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 59 (26.7 bits)