RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11797
(249 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 = 44.2 bits (105), Expect = 9e-07
Identities = 19/46 (41%), Positives = 27/46 (58%), Gaps = 4/46 (8%)
Query: 169 GRCVLPTGPALLMEVTRMDCCCTMGMAWGPQCQLCPTRGSQEYTDL 214
GRC P VT+ +CCC++G AWG C+ CP +G+ E+ L
Sbjct: 1 GRCSNPLPGN----VTKSECCCSLGRAWGTPCEPCPVQGTAEFRQL 42
>gnl|CDD|219496 pfam07645, EGF_CA, Calcium-binding EGF domain.
Length = 42
Score = 41.6 bits (98), Expect = 9e-06
Identities = 18/42 (42%), Positives = 24/42 (57%), Gaps = 1/42 (2%)
Query: 89 DVNECELNLDSC-ANGRCVNLEGSYRCECERGFKLSLDGKQC 129
DV+EC +C AN CVN GS+ C C G++ + DG C
Sbjct: 1 DVDECADGTHNCPANTVCVNTIGSFECVCPDGYENNEDGTNC 42
Score = 39.6 bits (93), Expect = 4e-05
Identities = 16/34 (47%), Positives = 19/34 (55%), Gaps = 2/34 (5%)
Query: 30 DVDECRTPANTC--KFSCKNLIGSYMCTCPPGYQ 61
DVDEC + C C N IGS+ C CP GY+
Sbjct: 1 DVDECADGTHNCPANTVCVNTIGSFECVCPDGYE 34
>gnl|CDD|214542 smart00179, EGF_CA, Calcium-binding EGF-like domain.
Length = 39
Score = 41.1 bits (97), Expect = 1e-05
Identities = 20/42 (47%), Positives = 25/42 (59%), Gaps = 5/42 (11%)
Query: 89 DVNECELNLDSCANG-RCVNLEGSYRCECERGFKLSLDGKQC 129
D++EC + C NG CVN GSYRCEC G+ DG+ C
Sbjct: 1 DIDECASG-NPCQNGGTCVNTVGSYRCECPPGYT---DGRNC 38
Score = 37.6 bits (88), Expect = 2e-04
Identities = 17/34 (50%), Positives = 22/34 (64%), Gaps = 3/34 (8%)
Query: 30 DVDECRTPANTCK--FSCKNLIGSYMCTCPPGYQ 61
D+DEC + N C+ +C N +GSY C CPPGY
Sbjct: 1 DIDECASG-NPCQNGGTCVNTVGSYRCECPPGYT 33
>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 = 38.8 bits (91), Expect = 7e-05
Identities = 14/34 (41%), Positives = 17/34 (50%)
Query: 89 DVNECELNLDSCANGRCVNLEGSYRCECERGFKL 122
D++EC G CVN GSYRC C G+
Sbjct: 1 DIDECASGNPCQNGGTCVNTVGSYRCSCPPGYTG 34
Score = 36.8 bits (86), Expect = 4e-04
Identities = 17/34 (50%), Positives = 22/34 (64%), Gaps = 3/34 (8%)
Query: 30 DVDECRTPANTCKFS--CKNLIGSYMCTCPPGYQ 61
D+DEC + N C+ C N +GSY C+CPPGY
Sbjct: 1 DIDECASG-NPCQNGGTCVNTVGSYRCSCPPGYT 33
>gnl|CDD|214544 smart00181, EGF, Epidermal growth factor-like domain.
Length = 35
Score = 33.6 bits (77), Expect = 0.005
Identities = 13/32 (40%), Positives = 16/32 (50%), Gaps = 1/32 (3%)
Query: 92 ECELNLDSCANGRCVNLEGSYRCECERGFKLS 123
EC C+NG C+N GSY C C G+
Sbjct: 1 ECASG-GPCSNGTCINTPGSYTCSCPPGYTGD 31
Score = 27.5 bits (61), Expect = 0.72
Identities = 11/17 (64%), Positives = 12/17 (70%)
Query: 45 CKNLIGSYMCTCPPGYQ 61
C N GSY C+CPPGY
Sbjct: 13 CINTPGSYTCSCPPGYT 29
>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 = 32.4 bits (75), Expect = 0.012
Identities = 10/19 (52%), Positives = 13/19 (68%)
Query: 111 SYRCECERGFKLSLDGKQC 129
SY C C G++LS DG+ C
Sbjct: 1 SYTCSCPPGYQLSGDGRTC 19
Score = 27.4 bits (62), Expect = 0.59
Identities = 15/42 (35%), Positives = 19/42 (45%), Gaps = 18/42 (42%)
Query: 51 SYMCTCPPGYQQVTHSTVAIATTDTRTAESGGKSHECVDVNE 92
SY C+CPPGYQ + D RT C D++E
Sbjct: 1 SYTCSCPPGYQL---------SGDGRT---------CEDIDE 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 = 30.5 bits (69), Expect = 0.069
Identities = 15/38 (39%), Positives = 16/38 (42%), Gaps = 6/38 (15%)
Query: 86 ECVDVNECELNLDSCANGRCVNLEGSYRCECERGFKLS 123
EC N C G CVN GSYRC C G+
Sbjct: 1 ECAASNPCS------NGGTCVNTPGSYRCVCPPGYTGD 32
Score = 28.6 bits (64), Expect = 0.33
Identities = 11/21 (52%), Positives = 11/21 (52%)
Query: 45 CKNLIGSYMCTCPPGYQQVTH 65
C N GSY C CPPGY
Sbjct: 14 CVNTPGSYRCVCPPGYTGDRS 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 = 32.7 bits (75), Expect = 0.13
Identities = 14/41 (34%), Positives = 18/41 (43%), Gaps = 1/41 (2%)
Query: 87 CVDVNECELNLDSCANGRCVNLEGSYRCECERGFKLSLDGK 127
CV + C C C++ GSY C C G+ L D K
Sbjct: 184 CVVPDLCATLSHVCQQV-CISTPGSYLCACTEGYALLEDNK 223
Score = 28.5 bits (64), Expect = 2.7
Identities = 15/39 (38%), Positives = 21/39 (53%)
Query: 22 KFSCKNLIDVDECRTPANTCKFSCKNLIGSYMCTCPPGY 60
KF K + D C T ++ C+ C + GSY+C C GY
Sbjct: 178 KFQGKICVVPDLCATLSHVCQQVCISTPGSYLCACTEGY 216
>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 = 29.0 bits (66), Expect = 0.18
Identities = 14/38 (36%), Positives = 17/38 (44%), Gaps = 3/38 (7%)
Query: 93 CELNLDSC-ANGRCVNLEGSYRCECERGFKLSLDGKQC 129
C N C N C N GS+ C C+ G+ DG C
Sbjct: 1 CAENNGGCHPNATCTNTGGSFTCTCKSGYT--GDGVTC 36
Score = 27.1 bits (61), Expect = 0.93
Identities = 9/18 (50%), Positives = 11/18 (61%)
Query: 44 SCKNLIGSYMCTCPPGYQ 61
+C N GS+ CTC GY
Sbjct: 13 TCTNTGGSFTCTCKSGYT 30
>gnl|CDD|225249 COG2374, COG2374, Predicted extracellular nuclease [General
function prediction only].
Length = 798
Score = 30.2 bits (68), Expect = 1.1
Identities = 14/59 (23%), Positives = 19/59 (32%), Gaps = 1/59 (1%)
Query: 24 SCKNLIDVDECRTPANTCKFSCKNLIGSYMCTCPPGYQQVTHSTVAIATTDTRTAESGG 82
S K ++ +E TP+ IG T V S I R+ GG
Sbjct: 157 SVKESVNFEETATPSTYPG-LSHVNIGELSTTQYGNEALVLTSIGQIQGEGHRSGPLGG 214
>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 = 26.2 bits (58), Expect = 2.0
Identities = 11/29 (37%), Positives = 13/29 (44%)
Query: 93 CELNLDSCANGRCVNLEGSYRCECERGFK 121
C N G CV+ G Y CEC G+
Sbjct: 1 CSPNNPCSNGGTCVDTPGGYTCECPEGYT 29
>gnl|CDD|199858 cd06234, M14_Nna1_like_1, Peptidase M14-like domain of ATP/GTP
binding proteins and cytosolic carboxypeptidases;
uncharacterized bacterial subgroup. A bacterial
subgroup of the Peptidase M14-like domain of Nna-1
(Nervous system Nuclear protein induced by Axotomy),
also known as ATP/GTP binding protein (AGTPBP-1) and
cytosolic carboxypeptidase (CCP)-like proteins. The
Peptidase M14 family of metallocarboxypeptidases are
zinc-binding carboxypeptidases (CPs) which hydrolyze
single, C-terminal amino acids from polypeptide chains,
and have a recognition site for the free C-terminal
carboxyl group, which is a key determinant of
specificity. Nna1-like proteins are active
metallopeptidases that are thought to act on cytosolic
proteins (such as alpha-tubulin in eukaryotes) to remove
a C-terminal tyrosine. Nna1-like proteins from the
different phyla are highly diverse, but they all contain
a unique N-terminal conserved domain right before the CP
domain. It has been suggested that this N-terminal
domain might act as a folding domain.
Length = 263
Score = 28.0 bits (63), Expect = 4.2
Identities = 10/23 (43%), Positives = 12/23 (52%), Gaps = 1/23 (4%)
Query: 219 GLTVDGRDIDECVTIPAVESSKL 241
G TV GRDID +T+ K
Sbjct: 35 GQTVQGRDID-LLTVGTPGPGKK 56
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
0.322 0.135 0.437
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: 11,306,910
Number of extensions: 941393
Number of successful extensions: 614
Number of sequences better than 10.0: 1
Number of HSP's gapped: 605
Number of HSP's successfully gapped: 33
Length of query: 249
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 155
Effective length of database: 6,768,326
Effective search space: 1049090530
Effective search space used: 1049090530
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 (21.9 bits)
S2: 58 (26.3 bits)