RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11297
(132 letters)
>gnl|CDD|238058 cd00110, LamG, Laminin G domain; Laminin G-like domains are usually
Ca++ mediated receptors that can have binding sites for
steroids, beta1 integrins, heparin, sulfatides,
fibulin-1, and alpha-dystroglycans. Proteins that
contain LamG domains serve a variety of purposes
including signal transduction via cell-surface steroid
receptors, adhesion, migration and differentiation
through mediation of cell adhesion molecules.
Length = 151
Score = 48.6 bits (116), Expect = 3e-08
Identities = 20/54 (37%), Positives = 32/54 (59%), Gaps = 3/54 (5%)
Query: 80 FNGSSHIVMKTLKA-YNKLSIEIEFKTNKNDGILLYNQQNLDGTGDFVSLAIVN 132
F+GSS++ + TL A +LSI F+T +G+LLY GDF++L + +
Sbjct: 4 FSGSSYVRLPTLPAPRTRLSISFSFRTTSPNGLLLYAGS--QNGGDFLALELED 55
>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 = 40.3 bits (95), Expect = 6e-06
Identities = 15/34 (44%), Positives = 19/34 (55%), Gaps = 2/34 (5%)
Query: 34 CLS-HPCQNGATCQDEEDGLFECLCSPEFTGYLC 66
C S +PCQNG TC + + C C P +TG C
Sbjct: 5 CASGNPCQNGGTCVNTVGS-YRCSCPPGYTGRNC 37
>gnl|CDD|214598 smart00282, LamG, Laminin G domain.
Length = 132
Score = 38.5 bits (90), Expect = 2e-04
Identities = 12/35 (34%), Positives = 20/35 (57%), Gaps = 2/35 (5%)
Query: 98 SIEIEFKTNKNDGILLYNQQNLDGTGDFVSLAIVN 132
SI F+T +G+LLY G GD+++L + +
Sbjct: 1 SISFSFRTTSPNGLLLYAGSK--GGGDYLALELRD 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 = 36.7 bits (85), Expect = 2e-04
Identities = 13/32 (40%), Positives = 18/32 (56%), Gaps = 2/32 (6%)
Query: 33 PC-LSHPCQNGATCQDEEDGLFECLCSPEFTG 63
C S+PC NG TC + + C+C P +TG
Sbjct: 1 ECAASNPCSNGGTCVNTPGS-YRCVCPPGYTG 31
>gnl|CDD|214542 smart00179, EGF_CA, Calcium-binding EGF-like domain.
Length = 39
Score = 36.1 bits (84), Expect = 2e-04
Identities = 13/30 (43%), Positives = 17/30 (56%), Gaps = 2/30 (6%)
Query: 34 CLS-HPCQNGATCQDEEDGLFECLCSPEFT 62
C S +PCQNG TC + + C C P +T
Sbjct: 5 CASGNPCQNGGTCVNTVGS-YRCECPPGYT 33
>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 = 33.2 bits (76), Expect = 0.003
Identities = 12/27 (44%), Positives = 15/27 (55%), Gaps = 1/27 (3%)
Query: 37 HPCQNGATCQDEEDGLFECLCSPEFTG 63
+PC NG TC D G + C C +TG
Sbjct: 5 NPCSNGGTCVDTPGG-YTCECPEGYTG 30
>gnl|CDD|130127 TIGR01055, parE_Gneg, DNA topoisomerase IV, B subunit,
proteobacterial. Operationally, topoisomerase IV is a
type II topoisomerase required for the decatenation of
chromosome segregation. Not every bacterium has both a
topo II and a topo IV. The topo IV families of the
Gram-positive bacteria and the Gram-negative bacteria
appear not to represent a single clade among the type II
topoisomerases, and are represented by separate models
for this reason. This protein is active as an
alpha(2)beta(2) heterotetramer [DNA metabolism, DNA
replication, recombination, and repair].
Length = 625
Score = 33.0 bits (75), Expect = 0.035
Identities = 22/74 (29%), Positives = 35/74 (47%), Gaps = 2/74 (2%)
Query: 57 CSPEFTGYLCHTRAPPKLYDTPAFNGSSHIVMKTLKAYNKLSIEIEFKTNKNDGILLYNQ 116
C TG H P+++D+ F+ S + KA +EIEF+ N+ L+N
Sbjct: 155 CGKRLTGTSVHFTPDPEIFDSLHFSVSRLYHILRAKAVLCRGVEIEFEDEVNNTKALWNY 214
Query: 117 QNLDGTGDFVSLAI 130
DG D++S A+
Sbjct: 215 P--DGLKDYLSEAV 226
>gnl|CDD|214544 smart00181, EGF, Epidermal growth factor-like domain.
Length = 35
Score = 29.4 bits (66), Expect = 0.077
Identities = 13/32 (40%), Positives = 16/32 (50%), Gaps = 3/32 (9%)
Query: 33 PCLS-HPCQNGATCQDEEDGLFECLCSPEFTG 63
C S PC NG TC + + C C P +TG
Sbjct: 1 ECASGGPCSNG-TCINTPGS-YTCSCPPGYTG 30
>gnl|CDD|238649 cd01328, FSL_SPARC, Follistatin-like SPARC (secreted protein,
acidic, and rich in cysteines) domain;
SPARC/BM-40/osteonectin is a multifunctional
glycoprotein which modulates cellular interaction with
the extracellular matrix by its binding to structural
matrix proteins such as collagen and vitronectin. The
protein it composed of an N-terminal acidic region, a
follistatin (FS) domain and an EF-hand calcium binding
domain. The FS domain consists of an N-terminal beta
hairpin (FOLN/EGF-like domain) and a small hydrophobic
core of alpha/beta structure (Kazal domain) and has
five disulfide bonds and a conserved N-glycosylation
site. The FSL_SPARC domain is a member of the
superfamily of kazal-like proteinase inhibitors and
follistatin-like proteins.
Length = 86
Score = 29.4 bits (66), Expect = 0.17
Identities = 8/28 (28%), Positives = 15/28 (53%)
Query: 33 PCLSHPCQNGATCQDEEDGLFECLCSPE 60
PC +H C G C+ +++ +C+C
Sbjct: 1 PCENHHCGAGKVCEVDDENTPKCVCIDP 28
>gnl|CDD|216930 pfam02210, Laminin_G_2, Laminin G domain. This family includes the
Thrombospondin N-terminal-like domain, a Laminin G
subfamily.
Length = 124
Score = 29.7 bits (67), Expect = 0.21
Identities = 9/30 (30%), Positives = 17/30 (56%), Gaps = 2/30 (6%)
Query: 103 FKTNKNDGILLYNQQNLDGTGDFVSLAIVN 132
F+T + +G+LLY DF++L + +
Sbjct: 1 FRTTQPNGLLLYAGGE--DGLDFLALELED 28
>gnl|CDD|215681 pfam00054, Laminin_G_1, Laminin G domain.
Length = 131
Score = 29.2 bits (66), Expect = 0.36
Identities = 10/30 (33%), Positives = 18/30 (60%), Gaps = 2/30 (6%)
Query: 103 FKTNKNDGILLYNQQNLDGTGDFVSLAIVN 132
F+T + G+LLYN + DF++L + +
Sbjct: 1 FRTTEPSGLLLYNGTQTE--RDFLALELRD 28
>gnl|CDD|219496 pfam07645, EGF_CA, Calcium-binding EGF domain.
Length = 42
Score = 25.8 bits (57), Expect = 1.8
Identities = 8/24 (33%), Positives = 11/24 (45%), Gaps = 1/24 (4%)
Query: 36 SHPCQNGATCQDEEDGLFECLCSP 59
+H C C + G FEC+C
Sbjct: 9 THNCPANTVCVNT-IGSFECVCPD 31
>gnl|CDD|226981 COG4634, COG4634, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 113
Score = 26.6 bits (59), Expect = 2.8
Identities = 13/61 (21%), Positives = 25/61 (40%), Gaps = 6/61 (9%)
Query: 71 PPKLYDTPAFNGSSHIVMKTLKAYNKLSIEIEFKTNKNDGILLYNQQNLDGTGDFVSLAI 130
PP+L D G + + L + IEI + + + ++ + + DF LA+
Sbjct: 10 PPRLADWLPMAGIEAVHWRDLGLRDATDIEI-WAYARRNNRIIVTKDS-----DFADLAL 63
Query: 131 V 131
Sbjct: 64 T 64
>gnl|CDD|201944 pfam01735, PLA2_B, Lysophospholipase catalytic domain. This family
consists of Lysophospholipase / phospholipase B
EC:3.1.1.5 and cytosolic phospholipase A2 EC:3.1.4 which
also has a C2 domain pfam00168. Phospholipase B enzymes
catalyze the release of fatty acids from
lysophsopholipids and are capable in vitro of
hydrolysing all phospholipids extractable form yeast
cells. Cytosolic phospholipase A2 associates with
natural membranes in response to physiological increases
in Ca2+ and selectively hydrolyses arachidonyl
phospholipids, the aligned region corresponds the the
carboxy-terminal Ca2+-independent catalytic domain of
the protein as discussed in.
Length = 490
Score = 26.9 bits (60), Expect = 3.9
Identities = 9/35 (25%), Positives = 17/35 (48%), Gaps = 2/35 (5%)
Query: 10 MGCLSASVVQSSQASPNLRL--EESPCLSHPCQNG 42
C++ ++++ N+ L E S C + C NG
Sbjct: 454 AHCVACAIIRRKLERLNITLPSECSQCFENYCWNG 488
>gnl|CDD|219723 pfam08126, Propeptide_C25, Propeptide_C25. This is found at the N
terminal end of some of the members of the C25 peptidase
family (PF01364). Little is known about the function of
this motif.
Length = 202
Score = 26.4 bits (58), Expect = 4.6
Identities = 6/26 (23%), Positives = 11/26 (42%)
Query: 87 VMKTLKAYNKLSIEIEFKTNKNDGIL 112
V KTL+ Y ++ + + F
Sbjct: 158 VTKTLRIYTEIEVAVSFTGEDGVNTQ 183
>gnl|CDD|241350 cd13196, FERM_C_JAK, Janus kinase (JAK) FERM domain C-lobe. JAK
(also called Just Another Kinase) is a family of
intracellular, non-receptor tyrosine kinases that
transduce cytokine-mediated signals via the JAK-STAT
pathway. The JAK family in mammals consists of 4
members: JAK1, JAK2, JAK3 and TYK2. JAKs are composed of
seven JAK homology (JH) domains (JH1-JH7) . The
C-terminal JH1 domain is the main catalytic domain,
followed by JH2, which is often referred to as a
pseudokinase domain, followed by JH3-JH4 which is
homologous to the SH2 domain, and lastly JH5-JH7 which
is a FERM domain. Named after Janus, the two-faced
Roman god of doorways, JAKs possess two near-identical
phosphate-transferring domains; one which displays the
kinase activity (JH1), while the other negatively
regulates the kinase activity of the first (JH2). The
FERM domain has a cloverleaf tripart structure (FERM_N,
FERM_M, FERM_C/N, alpha-, and C-lobe/A-lobe,A-lobe,
B-lobe, C-lobe/F1, F2, F3). The C-lobe/F3 within the
FERM domain is part of the PH domain family. The FERM
domain is found in the cytoskeletal-associated proteins
such as ezrin, moesin, radixin, 4.1R, and merlin. These
proteins provide a link between the membrane and
cytoskeleton and are involved in signal transduction
pathways. The FERM domain is also found in protein
tyrosine phosphatases (PTPs) , the tyrosine kinases FAK
and JAK, in addition to other proteins involved in
signaling. This domain is structurally similar to the PH
and PTB domains and consequently is capable of binding
to both peptides and phospholipids at different sites.
Length = 148
Score = 25.8 bits (57), Expect = 6.0
Identities = 9/25 (36%), Positives = 10/25 (40%), Gaps = 2/25 (8%)
Query: 50 DGLFECLCSPEFTGYLCHTRAPPKL 74
DG + YLC APP L
Sbjct: 114 DGYYRLTVDWTH--YLCKDVAPPSL 136
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
0.318 0.134 0.405
Gapped
Lambda K H
0.267 0.0715 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,249,489
Number of extensions: 507106
Number of successful extensions: 305
Number of sequences better than 10.0: 1
Number of HSP's gapped: 301
Number of HSP's successfully gapped: 27
Length of query: 132
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 46
Effective length of database: 7,123,158
Effective search space: 327665268
Effective search space used: 327665268
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (24.2 bits)