RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11343
(1150 letters)
>gnl|CDD|241267 cd01234, PH_CADPS, Ca2+-dependent activator protein (also called
CAPS) Pleckstrin homology (PH) domain. CADPS/CAPS
consists of two members, CAPS1 which regulates
catecholamine release from neuroendocrine cells and
CAPS2 which is involved in the release of two
neurotrophins, brain-derived neurotrophic factor (BDNF)
and neurotrophin-3 (NT-3) from cerebellar granule cells.
CADPS plays an important role in vesicle exocytosis in
neurons and endocrine cells where it functions to prime
the exocytic machinery for Ca2+-triggered fusion.
Priming involves the assembly of trans SNARE complexes.
The initial interaction of vesicles with target
membranes is mediated by diverse stage-specific
tethering factors or multi-subunit tethering complexes.
CADPS and Munc13 proteins are proposed to be the
functional homologs of the stage-specific tethering
factors that prime membrane fusion. Interestingly,
regions in the C-terminal half of CADPS are similar to
the C-terminal region of Munc13-1 that was reported to
bind syntaxin-1. CADPS has independent interactions with
each of the SNARE proteins (Q-SNARE and R-SNARE)
required for vesicle fusion. CADPS interacts with
Q-SNARE proteins syntaxin-1 (H3 SNARE) and SNAP-25 (SN1)
and might promote Q-SNARE heterodimer formation. Through
its N-terminal R-SNARE VAMP-2 interactions, CADPS bound
to heterodimeric Q-SNARE complexes could be involved in
catalyzing the zippering of VAMP-2 into recipient
complexes. It also contains a central PH domain that
binds to phosphoinositide 4,5 bisphosphate containing
liposomes. Membrane association may also be mediated by
binding to phosphatidlyserine via general electrostatic
interactions. PH domains have diverse functions, but in
general are involved in targeting proteins to the
appropriate cellular location or in the interaction with
a binding partner. They share little sequence
conservation, but all have a common fold, which is
electrostatically polarized. Less than 10% of PH domains
bind phosphoinositide phosphates (PIPs) with high
affinity and specificity. PH domains are distinguished
from other PIP-binding domains by their specific
high-affinity binding to PIPs with two vicinal phosphate
groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3
which results in targeting some PH domain proteins to
the plasma membrane. A few display strong specificity in
lipid binding. Any specificity is usually determined by
loop regions or insertions in the N-terminus of the
domain, which are not conserved across all PH domains.
PH domains are found in cellular signaling proteins such
as serine/threonine kinase, tyrosine kinases, regulators
of G-proteins, endocytotic GTPases, adaptors, as well as
cytoskeletal associated molecules and in lipid
associated enzymes.
Length = 122
Score = 164 bits (418), Expect = 2e-47
Identities = 56/72 (77%), Positives = 63/72 (87%)
Query: 145 RMEKPLNMKHCGYLFAYGKSTWRKWKKRYFVLVQVSQYTFAMCSFKEKKSDPSEFMQLDG 204
RM+KP NMKHCGYL+A GKS W+KWKKRYFVLVQVSQYTFAMCS++EKKS+P E MQLDG
Sbjct: 1 RMDKPQNMKHCGYLYALGKSVWKKWKKRYFVLVQVSQYTFAMCSYREKKSEPQEMMQLDG 60
Query: 205 YTVDYIEPASEK 216
YTVDY EP +
Sbjct: 61 YTVDYTEPQPDL 72
Score = 87.0 bits (216), Expect = 4e-20
Identities = 33/46 (71%), Positives = 39/46 (84%)
Query: 475 LEGGRYFFNAFKESESILYACDDENEYHLWVMAMYRATGQSHKPTP 520
LEGGR+FFNA KE +S+L+A DDEN+ LWV A+YRATGQSHKP P
Sbjct: 74 LEGGRFFFNAVKEGDSVLFASDDENDRQLWVQALYRATGQSHKPVP 119
Score = 34.3 bits (79), Expect = 0.086
Identities = 7/51 (13%), Positives = 11/51 (21%)
Query: 543 KHGMEEFISADPSKMEHSSLFKSLQSLTLEYRLNDPYCSMGWYSPGQLFVL 593
+ K S LF S + + Y + G
Sbjct: 72 LGLEGGRFFFNAVKEGDSVLFASDDENDRQLWVQALYRATGQSHKPVPPKQ 122
>gnl|CDD|218976 pfam06292, DUF1041, Domain of Unknown Function (DUF1041). This
family consists of several eukaryotic domains of unknown
function. Members of this family are often found in
tandem repeats and co-occur with pfam00168, pfam00130
and pfam00169 domains.
Length = 104
Score = 120 bits (302), Expect = 4e-32
Identities = 40/104 (38%), Positives = 58/104 (55%), Gaps = 9/104 (8%)
Query: 717 REVIKKCLETAALINYSKLSSEARVE------EDLTAEGGVSPSKKLEDLIHLGELCVDL 770
V++KCL+ AL+ Y++L + ++ ED + P+K+LE I L ELCV +
Sbjct: 1 SNVVRKCLKACALVTYTRLFNNCKILYNRQIQEDTGRDDQPPPAKRLEFWIRLIELCVSV 60
Query: 771 LQQNEEHYA---EAFAWYSDLLVEHAEIFWSLFAVDMDQVLAEQ 811
+Q+++EHY F +L E AE FWSLFAVDM L E
Sbjct: 61 IQEDKEHYTPVLNQFPQELNLGKESAETFWSLFAVDMKAALEEH 104
>gnl|CDD|214574 smart00233, PH, Pleckstrin homology domain. Domain commonly found
in eukaryotic signalling proteins. The domain family
possesses multiple functions including the abilities to
bind inositol phosphates, and various proteins. PH
domains have been found to possess inserted domains
(such as in PLC gamma, syntrophins) and to be inserted
within other domains. Mutations in Brutons tyrosine
kinase (Btk) within its PH domain cause X-linked
agammaglobulinaemia (XLA) in patients. Point mutations
cluster into the positively charged end of the molecule
around the predicted binding site for
phosphatidylinositol lipids.
Length = 102
Score = 40.2 bits (94), Expect = 5e-04
Identities = 19/73 (26%), Positives = 27/73 (36%), Gaps = 9/73 (12%)
Query: 152 MKHCGYLFAYGKSTWRKWKKRYFVLVQVSQYTFAMCSFKEKK----SDPSEFMQLDGYTV 207
+ G+L+ + WKKRYFVL + + +K KK P + L G TV
Sbjct: 1 VIKEGWLYKKSGGGKKSWKKRYFVL-----FNSTLLYYKSKKDKKSYKPKGSIDLSGCTV 55
Query: 208 DYIEPASEKVSPR 220
P
Sbjct: 56 REAPDPDSSKKPH 68
>gnl|CDD|215766 pfam00169, PH, PH domain. PH stands for pleckstrin homology.
Length = 101
Score = 39.0 bits (91), Expect = 0.001
Identities = 18/68 (26%), Positives = 29/68 (42%), Gaps = 8/68 (11%)
Query: 152 MKHCGYLFAYGKSTWRKWKKRYFVLVQVSQYTFAMCSFKEKK---SDPSEFMQLDGYTVD 208
+ G+L G + WKKRYFVL + + +K+ K S P + L G V
Sbjct: 1 VIKEGWLLKKGSGGRKSWKKRYFVL-----FDGVLLYYKDSKKSSSRPKGSIPLSGCQVT 55
Query: 209 YIEPASEK 216
+ + +
Sbjct: 56 KVPDSEDG 63
>gnl|CDD|176011 cd04046, C2_Calpain, C2 domain present in Calpain proteins. A
single C2 domain is found in calpains (EC 3.4.22.52, EC
3.4.22.53), calcium-dependent, non-lysosomal cysteine
proteases. Caplains are classified as belonging to Clan
CA by MEROPS and include six families: C1, C2, C10, C12,
C28, and C47. C2 domains fold into an 8-standed
beta-sandwich that can adopt 2 structural arrangements:
Type I and Type II, distinguished by a circular
permutation involving their N- and C-terminal beta
strands. Many C2 domains are Ca2+-dependent
membrane-targeting modules that bind a wide variety of
substances including bind phospholipids, inositol
polyphosphates, and intracellular proteins. Most C2
domain proteins are either signal transduction enzymes
that contain a single C2 domain, such as protein kinase
C, or membrane trafficking proteins which contain at
least two C2 domains, such as synaptotagmin 1. However,
there are a few exceptions to this including RIM
isoforms and some splice variants of piccolo/aczonin and
intersectin which only have a single C2 domain. C2
domains with a calcium binding region have negatively
charged residues, primarily aspartates, that serve as
ligands for calcium ions.
Length = 126
Score = 36.1 bits (84), Expect = 0.022
Identities = 26/95 (27%), Positives = 42/95 (44%), Gaps = 8/95 (8%)
Query: 32 VIVMEVKGLKSLAPNRI--VYCTMEVEGGEKLQTD-QAEASKPMWDTQADFSTNQPLPAI 88
V V +GL Y ++ EG E +++ Q + P +DTQA F +P I
Sbjct: 7 VHVHSAEGLSKQDSGGGADPYVIIKCEG-ESVRSPVQKDTLSPEFDTQAIFYRKKPRSPI 65
Query: 89 KVKLFTENPGMLALEDKELGKVILRPTPLSSKAPE 123
K++++ N L D+ LG+ L P S+
Sbjct: 66 KIQVWNSN----LLCDEFLGQATLSADPNDSQTLR 96
>gnl|CDD|241402 cd13248, PH_PEPP1_2_3, Phosphoinositol 3-phosphate binding proteins
1, 2, and 3 pleckstrin homology (PH) domain. PEPP1
(also called PLEKHA4/PH domain-containing family A
member 4 and RHOXF1/Rhox homeobox family member 1), and
related homologs PEPP2 (also called PLEKHA5/PH
domain-containing family A member 5) and PEPP3 (also
called PLEKHA6/PH domain-containing family A member 6),
have PH domains that interact specifically with
PtdIns(3,4)P3. Other proteins that bind PtdIns(3,4)P3
specifically are: TAPP1 (tandem PH-domain-containing
protein-1) and TAPP2], PtdIns3P AtPH1, and Ptd-
Ins(3,5)P2 (centaurin-beta2). All of these proteins
contain at least 5 of the 6 conserved amino acids that
make up the putative phosphatidylinositol 3,4,5-
trisphosphate-binding motif (PPBM) located at their
N-terminus. PH domains have diverse functions, but in
general are involved in targeting proteins to the
appropriate cellular location or in the interaction with
a binding partner. They share little sequence
conservation, but all have a common fold, which is
electrostatically polarized. Less than 10% of PH domains
bind phosphoinositide phosphates (PIPs) with high
affinity and specificity. PH domains are distinguished
from other PIP-binding domains by their specific
high-affinity binding to PIPs with two vicinal phosphate
groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3
which results in targeting some PH domain proteins to
the plasma membrane. A few display strong specificity in
lipid binding. Any specificity is usually determined by
loop regions or insertions in the N-terminus of the
domain, which are not conserved across all PH domains.
PH domains are found in cellular signaling proteins such
as serine/threonine kinase, tyrosine kinases, regulators
of G-proteins, endocytotic GTPases, adaptors, as well as
cytoskeletal associated molecules and in lipid
associated enzymes.
Length = 104
Score = 34.9 bits (81), Expect = 0.043
Identities = 11/24 (45%), Positives = 14/24 (58%)
Query: 155 CGYLFAYGKSTWRKWKKRYFVLVQ 178
G+L G S + WKKR+FVL
Sbjct: 10 SGWLHKQGGSGLKNWKKRWFVLKD 33
>gnl|CDD|241231 cd00821, PH, Pleckstrin homology (PH) domain. PH domains have
diverse functions, but in general are involved in
targeting proteins to the appropriate cellular location
or in the interaction with a binding partner. They share
little sequence conservation, but all have a common
fold, which is electrostatically polarized. Less than
10% of PH domains bind phosphoinositide phosphates
(PIPs) with high affinity and specificity. PH domains
are distinguished from other PIP-binding domains by
their specific high-affinity binding to PIPs with two
vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2
or PtdIns(3,4,5)P3 which results in targeting some PH
domain proteins to the plasma membrane. A few display
strong specificity in lipid binding. Any specificity is
usually determined by loop regions or insertions in the
N-terminus of the domain, which are not conserved across
all PH domains. PH domains are found in cellular
signaling proteins such as serine/threonine kinase,
tyrosine kinases, regulators of G-proteins, endocytotic
GTPases, adaptors, as well as cytoskeletal associated
molecules and in lipid associated enzymes.
Length = 92
Score = 33.1 bits (75), Expect = 0.14
Identities = 10/23 (43%), Positives = 13/23 (56%)
Query: 154 HCGYLFAYGKSTWRKWKKRYFVL 176
G+L G + WKKR+FVL
Sbjct: 1 KEGWLKKRGGKGLKSWKKRWFVL 23
>gnl|CDD|234170 TIGR03336, IOR_alpha, indolepyruvate ferredoxin oxidoreductase,
alpha subunit. Indolepyruvate ferredoxin oxidoreductase
(IOR) is an alpha 2/beta 2 tetramer related to ketoacid
oxidoreductases for pyruvate (1.2.7.1, POR),
2-ketoglutarate (1.2.7.3, KOR), and 2-oxoisovalerate
(1.2.7.7, VOR). These multi-subunit enzymes typically
are found in anaerobes and are inactiviated by oxygen.
IOR in Pyrococcus acts in fermentation of all three
aromatic amino acids, following removal of the amino
group by transamination. In Methanococcus maripaludis,
by contrast, IOR acts in the opposite direction, in
pathways of amino acid biosynthesis from phenylacetate,
indoleacetate, and p-hydroxyphenylacetate. In M.
maripaludis and many other species, iorA and iorB are
found next to an apparent phenylacetate-CoA ligase.
Length = 595
Score = 35.5 bits (82), Expect = 0.18
Identities = 18/60 (30%), Positives = 36/60 (60%), Gaps = 3/60 (5%)
Query: 661 FNVIKERLKELLIN-QITNFRYAFPFGRPEGILKSTLSLLERVLMKDSVTPVQPEEVREV 719
+N +KE L+ L ++ + + +P PEG+++ LS +E VL+ + + PV E+V+ +
Sbjct: 242 YNYVKEALERLGVDVSVLKIGFTYPV--PEGLVEEFLSGVEEVLVVEELEPVVEEQVKAL 299
>gnl|CDD|241430 cd13276, PH_AtPH1, Arabidopsis thaliana Pleckstrin homolog (PH) 1
(AtPH1) PH domain. AtPH1 is expressed in all plant
tissue and is proposed to be the plant homolog of human
pleckstrin. Pleckstrin consists of two PH domains
separated by a linker region, while AtPH has a single PH
domain with a short N-terminal extension. AtPH1 binds
PtdIns3P specifically and is thought to be an adaptor
molecule since it has no obvious catalytic functions. PH
domains have diverse functions, but in general are
involved in targeting proteins to the appropriate
cellular location or in the interaction with a binding
partner. They share little sequence conservation, but
all have a common fold, which is electrostatically
polarized. Less than 10% of PH domains bind
phosphoinositide phosphates (PIPs) with high affinity
and specificity. PH domains are distinguished from other
PIP-binding domains by their specific high-affinity
binding to PIPs with two vicinal phosphate groups:
PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which
results in targeting some PH domain proteins to the
plasma membrane. A few display strong specificity in
lipid binding. Any specificity is usually determined by
loop regions or insertions in the N-terminus of the
domain, which are not conserved across all PH domains.
PH domains are found in cellular signaling proteins such
as serine/threonine kinase, tyrosine kinases, regulators
of G-proteins, endocytotic GTPases, adaptors, as well as
cytoskeletal associated molecules and in lipid
associated enzymes.
Length = 117
Score = 32.3 bits (74), Expect = 0.38
Identities = 17/79 (21%), Positives = 33/79 (41%), Gaps = 8/79 (10%)
Query: 151 NMKHCGYLFAYGKSTWRKWKKRYFVLVQVSQYTFAMCSFKEKKSDPSEFMQLDGYTVDYI 210
+ + G+L G S + W++R+FVL Q + FK++ D +D +
Sbjct: 6 DPEKAGWLTKQGGSI-KTWRRRWFVL---KQGK--LFYFKDEDPDSEPRGVIDLSDCLTV 59
Query: 211 EPASEKVSPRDS--ISQAH 227
+ A E + + +S
Sbjct: 60 KSAEEATNKEFAFEVSTPE 78
>gnl|CDD|241417 cd13263, PH_RhoGap25-like, Rho GTPase activating protein 25 and
related proteins Pleckstrin homology (PH) domain.
RhoGAP25 (also called ArhGap25) like other RhoGaps are
involved in cell polarity, cell morphology and
cytoskeletal organization. They act as GTPase activators
for the Rac-type GTPases by converting them to an
inactive GDP-bound state and control actin remodeling by
inactivating Rac downstream of Rho leading to suppress
leading edge protrusion and promotes cell retraction to
achieve cellular polarity and are able to suppress RAC1
and CDC42 activity in vitro. Overexpression of these
proteins induces cell rounding with partial or complete
disruption of actin stress fibers and formation of
membrane ruffles, lamellipodia, and filopodia. This
hierarchy contains RhoGAP22, RhoGAP24, and RhoGAP25.
Members here contain an N-terminal PH domain followed by
a RhoGAP domain and either a BAR or TATA Binding Protein
(TBP) Associated Factor 4 (TAF4) domain. PH domains have
diverse functions, but in general are involved in
targeting proteins to the appropriate cellular location
or in the interaction with a binding partner. They share
little sequence conservation, but all have a common
fold, which is electrostatically polarized. Less than
10% of PH domains bind phosphoinositide phosphates
(PIPs) with high affinity and specificity. PH domains
are distinguished from other PIP-binding domains by
their specific high-affinity binding to PIPs with two
vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2
or PtdIns(3,4,5)P3 which results in targeting some PH
domain proteins to the plasma membrane. A few display
strong specificity in lipid binding. Any specificity is
usually determined by loop regions or insertions in the
N-terminus of the domain, which are not conserved across
all PH domains. PH domains are found in cellular
signaling proteins such as serine/threonine kinase,
tyrosine kinases, regulators of G-proteins, endocytotic
GTPases, adaptors, as well as cytoskeletal associated
molecules and in lipid associated enzymes.
Length = 114
Score = 31.9 bits (73), Expect = 0.43
Identities = 18/61 (29%), Positives = 27/61 (44%), Gaps = 8/61 (13%)
Query: 147 EKPLNMKHCGYLFAYGKSTWRKWKKRYFVLVQVSQYTFAMCSFKEKKSDPSEFMQLDGYT 206
EK + G+L G + W++R+FVL Y + E +S P + L G T
Sbjct: 1 EKVI---KSGWLKKQG-GIVKNWQRRWFVLRGDQLYYYK----DEDESKPQGCIPLPGNT 52
Query: 207 V 207
V
Sbjct: 53 V 53
>gnl|CDD|235223 PRK04132, PRK04132, replication factor C small subunit;
Provisional.
Length = 846
Score = 33.3 bits (76), Expect = 0.83
Identities = 33/128 (25%), Positives = 64/128 (50%), Gaps = 20/128 (15%)
Query: 316 IVFLLQA-FLRGDTQIMTDEAFQNAVQSYTDV--FLKS----DRVLNFVQSGACSLYDFR 368
I+FL +A L D Q +A + ++ ++ F+ S +++ +QS C+++ FR
Sbjct: 633 IIFLDEADALTQDAQ----QALRRTMEMFSSNVRFILSCNYSSKIIEPIQS-RCAIFRFR 687
Query: 369 EVFRKNIQKRVRSLPEIDGLS-KETVLSSWMAKFDCILKVGEEDLKRPNRALQQALNCEL 427
+ ++I KR+R + E +GL E L + IL + E D++R LQ A +
Sbjct: 688 PLRDEDIAKRLRYIAENEGLELTEEGLQA-------ILYIAEGDMRRAINILQAAAALDD 740
Query: 428 ILSKEQLY 435
++ E ++
Sbjct: 741 KITDENVF 748
>gnl|CDD|241462 cd13308, PH_3BP2, SH3 domain-binding protein 2 Pleckstrin homology
(PH) domain. SH3BP2 (the gene that encodes the adaptor
protein 3BP2), HD, ITU, IT10C3, and ADD1 are located
near the Huntington's Disease Gene on Human Chromosome
4pl6.3. SH3BP2 lies in a region that is often missing in
individuals with Wolf-Hirschhorn syndrome (WHS). Gain of
function mutations in SH3BP2 causes enhanced B-cell
antigen receptor (BCR)-mediated activation of nuclear
factor of activated T cells (NFAT), resulting in a rare,
genetic disorder called cherubism. This results in an
increase in the signaling complex formation with Syk,
phospholipase C-gamma2 (PLC-gamma2), and Vav1. It was
recently discovered that Tankyrase regulates 3BP2
stability through ADP-ribosylation and ubiquitylation by
the E3-ubiquitin ligase. Cherubism mutations uncouple
3BP2 from Tankyrase-mediated protein destruction, which
results in its stabilization and subsequent
hyperactivation of the Src, Syk, and Vav signaling
pathways. SH3BP2 is also a potential negative regulator
of the abl oncogene. PH domains have diverse functions,
but in general are involved in targeting proteins to the
appropriate cellular location or in the interaction with
a binding partner. They share little sequence
conservation, but all have a common fold, which is
electrostatically polarized. Less than 10% of PH domains
bind phosphoinositide phosphates (PIPs) with high
affinity and specificity. PH domains are distinguished
from other PIP-binding domains by their specific
high-affinity binding to PIPs with two vicinal phosphate
groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3
which results in targeting some PH domain proteins to
the plasma membrane. A few display strong specificity in
lipid binding. Any specificity is usually determined by
loop regions or insertions in the N-terminus of the
domain, which are not conserved across all PH domains.
PH domains are found in cellular signaling proteins such
as serine/threonine kinase, tyrosine kinases, regulators
of G-proteins, endocytotic GTPases, adaptors, as well as
cytoskeletal associated molecules and in lipid
associated enzymes.
Length = 113
Score = 31.2 bits (71), Expect = 0.86
Identities = 17/57 (29%), Positives = 24/57 (42%), Gaps = 8/57 (14%)
Query: 154 HCGYLFAYGKS--TWRKWKKRYFVLVQVSQYTFAMCSFKEKKSDPSEFM-QLDGYTV 207
H GYL G S KW RY ++ + Y FK +S + + L+GY
Sbjct: 11 HSGYLTKKGGSQKQLLKWPLRYVIIHKGCVYY-----FKNSQSAKPKGVFSLNGYNR 62
>gnl|CDD|177779 PLN00185, PLN00185, 60S ribosomal protein L4-1; Provisional.
Length = 405
Score = 32.9 bits (75), Expect = 1.0
Identities = 18/50 (36%), Positives = 26/50 (52%), Gaps = 5/50 (10%)
Query: 151 NMKHCGYLFAYGKSTWRKWKKRYFVLVQVSQYTFAMCSFKEKKSDPSEFM 200
NM G +FA K TWR+W ++ V V+Q +A+ S + PS M
Sbjct: 98 NMCRGGRMFAPTK-TWRRWHRK----VNVNQKRYAVVSALAASAVPSLVM 142
>gnl|CDD|233417 TIGR01447, recD, exodeoxyribonuclease V, alpha subunit. This
family describes the exodeoxyribonuclease V alpha
subunit, RecD. RecD is part of a RecBCD complex. A
related family in the Gram-positive bacteria separates
in a phylogenetic tree, has an additional N-terminal
extension of about 200 residues, and is not supported as
a member of a RecBCD complex by neighboring genes. The
related family is consequently described by a different
model [DNA metabolism, DNA replication, recombination,
and repair].
Length = 586
Score = 31.7 bits (72), Expect = 2.7
Identities = 36/187 (19%), Positives = 66/187 (35%), Gaps = 26/187 (13%)
Query: 276 IAYPFNSKQSTDMIRRHSKITRHLLEVIQSRFQVPMLHTSIVF--------LLQAFLRGD 327
I Y F S Q+ + ++ + TR+ L V L TS F L +A GD
Sbjct: 316 IGYLFQSAQAYALCKKINSKTRNPL-----SDNVCFLKTSHRFGKDSGIGQLAKAINSGD 370
Query: 328 TQIMTDEAFQNAVQSYTDVFLKSDRVLNFVQSGACSLYDFREVFRKNIQKRVRSLPEIDG 387
EA N ++S + + +L+ F + + ++
Sbjct: 371 I-----EAVLNNLRSGQLIEFEFLNSKEDAIERLKNLFVKYRTFLQKLAALSDIKEILET 425
Query: 388 LSKETVLSSWMAKFDCILKVGEEDLKRPNRALQQALNCELILSKEQLYDMFQQILVIKKF 447
+ +L L+ G + NR ++Q L + E+ + + + I+V +
Sbjct: 426 FDRLRLL--------TALRDGPFGVLGLNRRIEQELQEKYFDPDEEGWYIGRPIMVTEND 477
Query: 448 EHQLLFN 454
LFN
Sbjct: 478 YTLGLFN 484
>gnl|CDD|237089 PRK12398, PRK12398, pyruvoyl-dependent arginine decarboxylase;
Provisional.
Length = 162
Score = 30.1 bits (68), Expect = 3.5
Identities = 11/21 (52%), Positives = 14/21 (66%)
Query: 33 IVMEVKGLKSLAPNRIVYCTM 53
IV +GLK L+P IV+C M
Sbjct: 50 IVSREEGLKELSPGEIVFCVM 70
>gnl|CDD|241391 cd13237, PH2_FGD5_FGD6, FYVE, RhoGEF and PH domain
containing/faciogenital dysplasia proteins 5 and 6
pleckstrin homology (PH) domain, C-terminus. FGD5
regulates promotes angiogenesis of vascular endothelial
growth factor (VEGF) in vascular endothelial cells,
including network formation, permeability, directional
movement, and proliferation. The specific function of
FGD6 is unknown. In general, FGDs have a RhoGEF (DH)
domain, followed by a PH domain, a FYVE domain and a
C-terminal PH domain. All FGDs are guanine nucleotide
exchange factors that activate the Rho GTPase Cdc42, an
important regulator of membrane trafficking. The RhoGEF
domain is responsible for GEF catalytic activity, while
the PH domain is involved in intracellular targeting of
the DH domain. PH domains have diverse functions, but in
general are involved in targeting proteins to the
appropriate cellular location or in the interaction with
a binding partner. They share little sequence
conservation, but all have a common fold, which is
electrostatically polarized. Less than 10% of PH domains
bind phosphoinositide phosphates (PIPs) with high
affinity and specificity. PH domains are distinguished
from other PIP-binding domains by their specific
high-affinity binding to PIPs with two vicinal phosphate
groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3
which results in targeting some PH domain proteins to
the plasma membrane. A few display strong specificity in
lipid binding. Any specificity is usually determined by
loop regions or insertions in the N-terminus of the
domain, which are not conserved across all PH domains.
PH domains are found in cellular signaling proteins such
as serine/threonine kinase, tyrosine kinases, regulators
of G-proteins, endocytotic GTPases, adaptors, as well as
cytoskeletal associated molecules and in lipid
associated enzymes.
Length = 90
Score = 28.9 bits (65), Expect = 3.6
Identities = 24/82 (29%), Positives = 32/82 (39%), Gaps = 11/82 (13%)
Query: 156 GYLFAYGKSTWRKWKKRYFVLVQVSQYTFAMCSFKEKKSDPSEFMQLDGYTVDYIEPASE 215
GYL+ K + WK+ +FVL YT+ E E + L GYTV PA E
Sbjct: 3 GYLY-RRKRKKKSWKRLWFVLKDKVLYTYKA---SEDV-VALESIPLLGYTV---VPAKE 54
Query: 216 KVSPRDS--ISQAHIRNASPIT 235
+S H + P
Sbjct: 55 GFEGDESLVFQLLH-KGQLPYI 75
>gnl|CDD|132014 TIGR02969, mam_aldehyde_ox, aldehyde oxidase. Members of this
family are mammalian aldehyde oxidase (EC 1.2.3.1)
isozymes, closely related to xanthine
dehydrogenase/oxidase.
Length = 1330
Score = 31.5 bits (71), Expect = 3.7
Identities = 40/150 (26%), Positives = 64/150 (42%), Gaps = 13/150 (8%)
Query: 310 PMLHTSIVF--LLQAF-LRGDTQIMTDEAFQNAVQSYTDVFLKSDRVLNFVQSGACSLYD 366
H IV L +A L G I+T E Q+A T+ L +D+V Q C++
Sbjct: 614 SRAHAKIVSIDLSEALSLPGVVDIITAEHLQDANTFGTEKLLATDKVHCVGQL-VCAVIA 672
Query: 367 FREVFRKNIQKRVRSL-----PEIDGLSKETVLSSWMAKFDCILKVGEEDLKRPNRALQQ 421
EV K K V+ + P I L+ E + + F+ K+ ++ + + Q
Sbjct: 673 DSEVQAKQAAKHVKIVYRDLEPLI--LTIEEAIQH-KSFFEPERKLEYGNVDEAFKVVDQ 729
Query: 422 ALNCEL-ILSKEQLYDMFQQILVIKKFEHQ 450
L E+ + +E Y Q +LV+ K E Q
Sbjct: 730 ILEGEIHMGGQEHFYMETQSMLVVPKGEDQ 759
>gnl|CDD|241421 cd13267, PH_DOCK-D, Dedicator of cytokinesis-D subfamily Pleckstrin
homology (PH) domain. DOCK-D subfamily (also called
Zizimin subfamily) consists of Dock9/Zizimin1,
Dock10/Zizimin3, and Dock11/Zizimin2. DOCK-D has a
N-terminal DUF3398 domain, a PH-like domain, a Dock
Homology Region 1, DHR1 (also called CZH1), a C2 domain,
and a C-terminal DHR2 domain (also called CZH2).
Zizimin1 is enriched in the brain, lung, and kidney;
zizimin2 is found in B and T lymphocytes, and zizimin3
is enriched in brain, lung, spleen and thymus. Zizimin1
functions in autoinhibition and membrane targeting.
Zizimin2 is an immune-related and age-regulated guanine
nucleotide exchange factor, which facilitates filopodial
formation through activation of Cdc42, which results in
activation of cell migration. No function has been
determined for Zizimin3 to date. The N-terminal half of
zizimin1 binds to the GEF domain through three distinct
areas, including CZH1, to inhibit the interaction with
Cdc42. In addition its PH domain binds phosphoinositides
and mediates zizimin1 membrane targeting. DOCK is a
family of proteins involved in intracellular signalling
networks. They act as guanine nucleotide exchange
factors for small G proteins of the Rho family, such as
Rac and Cdc42. There are 4 subfamilies of DOCK family
proteins based on their sequence homology: A-D. PH
domains have diverse functions, but in general are
involved in targeting proteins to the appropriate
cellular location or in the interaction with a binding
partner. They share little sequence conservation, but
all have a common fold, which is electrostatically
polarized. Less than 10% of PH domains bind
phosphoinositide phosphates (PIPs) with high affinity
and specificity. PH domains are distinguished from other
PIP-binding domains by their specific high-affinity
binding to PIPs with two vicinal phosphate groups:
PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which
results in targeting some PH domain proteins to the
plasma membrane. A few display strong specificity in
lipid binding. Any specificity is usually determined by
loop regions or insertions in the N-terminus of the
domain, which are not conserved across all PH domains.
PH domains are found in cellular signaling proteins such
as serine/threonine kinase, tyrosine kinases, regulators
of G-proteins, endocytotic GTPases, adaptors, as well as
cytoskeletal associated molecules and in lipid
associated enzymes.
Length = 125
Score = 29.6 bits (67), Expect = 4.5
Identities = 10/38 (26%), Positives = 21/38 (55%), Gaps = 1/38 (2%)
Query: 167 RKWKKRYFVLVQVSQYTFAMCSFK-EKKSDPSEFMQLD 203
+ +K+R+F L Q+ ++ + +K EK + + LD
Sbjct: 28 KSFKRRFFHLKQLVDGSYILEFYKDEKSKEAKGTIYLD 65
>gnl|CDD|220248 pfam09455, Cas_DxTHG, CRISPR-associated (Cas) DxTHG family. CRISPR
is a term for Clustered Regularly Interspaced Short
Palidromic Repeats. A number of protein families appear
only in association with these repeats and are
designated Cas (CRISPR associated) proteins. The family
describes Cas proteins of about 400 residues that
include the motif [VIL]-D-x-[ST]-H-[GS]. The CRISPR and
associated proteins are thought to be involved in the
evolution of host resistance. The exact molecular
function of this family is currently unknown.
Length = 370
Score = 30.9 bits (70), Expect = 4.6
Identities = 20/116 (17%), Positives = 39/116 (33%), Gaps = 15/116 (12%)
Query: 655 QEEKNRFNV-IKERLKELLINQITNFRYAFPFGRPEGILKSTLSLLERVLMKDSVTPVQP 713
++ K + + E + + P RP + +S L E L+++++
Sbjct: 195 KKRKIKESRKKLPENLEKIAKLLKALSNGLPLVRPVELRESLEELKE--LLEEAIEVNNE 252
Query: 714 EEVREVIKKCLETAALINYSKLSSEARVEEDLTAEGGVSPSKKLEDLIHLGELCVD 769
E+ + K + A+ EE L EDL L E ++
Sbjct: 253 EDEEAIFAKPFYLLLEKIIERYKKFAKDEESL------------EDLEKLIEWYLE 296
>gnl|CDD|215581 PLN03109, PLN03109, ETHYLENE-INSENSITIVE3-like3 protein;
Provisional.
Length = 599
Score = 30.6 bits (69), Expect = 5.2
Identities = 19/65 (29%), Positives = 30/65 (46%), Gaps = 11/65 (16%)
Query: 203 DGYTVDYIEPASEKVSPRDSISQAHIRNASPIT--RQNSHTDNLDKEVMDPQDSQEKQEE 260
Y VD +E A VS +D RN P+ + + D ++ V D +EK ++
Sbjct: 321 SDYDVDGLEDAPGSVSSKDD-----RRNLQPVAQEPERARDDAPNQVVPD----KEKTKK 371
Query: 261 ERKRR 265
RKR+
Sbjct: 372 PRKRK 376
>gnl|CDD|183592 PRK12556, PRK12556, tryptophanyl-tRNA synthetase; Provisional.
Length = 332
Score = 30.5 bits (69), Expect = 5.4
Identities = 19/92 (20%), Positives = 36/92 (39%), Gaps = 19/92 (20%)
Query: 799 LFAVDMDQVLAEQPSDTWDSFPLFQILNEYLRADE---------------NLKNGRFHQH 843
+F + D L +P D ++ LF I E+ +E ++K F +
Sbjct: 224 IFKIKTDSSLPNEPKDP-ETSALFTIYKEFATEEEVQSMREKYETGIGWGDVKKELF-RV 281
Query: 844 LREYFAPLVVRYVDLME--SSIAQSIHKGFEK 873
+ A +Y M S + +++ KG E+
Sbjct: 282 VDRELAGPREKYAMYMNEPSLLDEALEKGAER 313
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
0.319 0.133 0.392
Gapped
Lambda K H
0.267 0.0618 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 57,563,418
Number of extensions: 5691209
Number of successful extensions: 4825
Number of sequences better than 10.0: 1
Number of HSP's gapped: 4820
Number of HSP's successfully gapped: 35
Length of query: 1150
Length of database: 10,937,602
Length adjustment: 107
Effective length of query: 1043
Effective length of database: 6,191,724
Effective search space: 6457968132
Effective search space used: 6457968132
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: 65 (29.1 bits)