RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17618
(164 letters)
>gnl|CDD|211372 cd09261, AP-3_Mu3B_Cterm, C-terminal domain of medium Mu3B subunit
in neuron-specific adaptor protein (AP) complex AP-3.
AP complexes participate in the formation of
intracellular coated transport vesicles and select cargo
molecules for incorporation into the coated vesicles in
the late secretory and endocytic pathways. There are
four AP complexes, AP-1, AP-2, AP-3, and AP-4, described
in various eukaryotic organisms. Each AP complex
consists of four subunits: two large chains (one each of
gamma/alpha/delta/epsilon and beta1-4, respectively), a
medium mu chain (mu1-4), and a small sigma chain
(sigma1-4). Each of the four subunits from the different
AP complexes exhibits similarity with each other. This
subfamily corresponds to the C-terminal domain of
heterotetrameric adaptor protein complex 3 (AP-3) medium
mu3B subunit encoded by ap3m2 gene. Mu3B is specifically
expressed in neurons and neuroendocrine cells.
Neuron-specific AP-3 appears to be involved in synaptic
vesicle biogenesis from endosomes in neurons and plays
an important role in synaptic transmission in the
central nervous system. Unlike AP-1 and AP-2, which
function in conjunction with clathrin which is a
scaffolding protein participating in the formation of
coated vesicles, the nature of the outer shell of
neuron-specific AP-3 containing coats remains to be
elucidated. Membrane-anchored cargo molecules interact
with adaptors through short sorting signals in their
cytosolic segments. Tyrosine-based endocytotic signals
are one of the most important sorting signals. They are
of the form Y-X-X-Phi, where Y is tyrosine, X is any
amino acid and Phi is a bulky hydrophobic residue that
can be Leu, Ile, Met, Phe, or Val. These kinds of
sorting signals can be recognized by the C-terminal
domain of AP-3 mu3B subunit, also known as Y-X-X-Phi
signal-binding domain that contains two hydrophobic
pockets, one for the tyrosine-binding and one for the
bulky hydrophobic residue-binding.
Length = 254
Score = 208 bits (530), Expect = 1e-68
Identities = 91/106 (85%), Positives = 98/106 (92%), Gaps = 2/106 (1%)
Query: 18 VPWRRTGVKYTNNEAYFDVIEEVDAIIDKTGSTIFSEIQGYIDCCIKLSGMPDLTLSFMN 77
VPWRRTGVKYTNNEAYFDVIEE+DAIIDK+GSTI +EIQG ID C+KL+GMPDLTLSFMN
Sbjct: 1 VPWRRTGVKYTNNEAYFDVIEEIDAIIDKSGSTITAEIQGVIDACVKLTGMPDLTLSFMN 60
Query: 78 PRLFDDVSFHPCVRFKRWEAERILSFIPPDGNFRLMSYHTRVSGSN 123
PRL DDVSFHPCVRFKRWE+ERILSFIPPDGNFRL+SYH VS N
Sbjct: 61 PRLLDDVSFHPCVRFKRWESERILSFIPPDGNFRLLSYH--VSAQN 104
>gnl|CDD|211363 cd09252, AP-3_Mu3_Cterm, C-terminal domain of medium Mu3 subunit in
adaptor protein (AP) complex AP-3. AP complexes
participate in the formation of intracellular coated
transport vesicles and select cargo molecules for
incorporation into the coated vesicles in the late
secretory and endocytic pathways. There are four AP
complexes, AP-1, AP-2, AP-3, and AP-4, described in
various eukaryotic organisms. Each AP complex consists
of four subunits: two large chains (one each of
gamma/alpha/delta/epsilon and beta1-4, respectively), a
medium mu chain (mu1-4), and a small sigma chain
(sigma1-4). Each of the four subunits from the different
AP complexes exhibits similarity with each other. This
family corresponds to the C-terminal domain of
heterotetrameric adaptor protein complex 3 (AP-3) medium
mu3 subunit, which includes two closely related
homologs, mu3A (P47A, encoded by ap3m1) and mu1B (P47B,
encoded by ap3m2). Mu3A is ubiquitously expressed, but
mu3B is specifically expressed in neurons and
neuroendocrine cells. AP-3 is particularly important for
targeting integral membrane proteins to lysosomes and
lysome-related organelles at trans-Golgi network (TGN)
and/or endosomes, such as the yeast vacuole, fly pigment
granules and mammalian melanosomes, platelet dense
bodies and the secretory lysosomes of cytotoxic T
lymphocytes. Unlike AP-1 and AP-2, which function in
conjunction with clathrin which is a scaffolding protein
participating in the formation of coated vesicles, the
nature of the outer shell of AP-3 containing coats
remains to be elucidated. Membrane-anchored cargo
molecules interact with adaptors through short sorting
signals in their cytosolic segments. Tyrosine-based
endocytotic signals are one of the most important
sorting signals. They are of the form Y-X-X-Phi, where Y
is tyrosine, X is any amino acid and Phi is a bulky
hydrophobic residue that can be Leu, Ile, Met, Phe, or
Val. These kinds of sorting signals can be recognized by
the C-terminal domain of AP-3 mu3 subunit, also known as
Y-X-X-Phi signal-binding domain that contains two
hydrophobic pockets, one for the tyrosine-binding and
one for the bulky hydrophobic residue-binding.
Length = 248
Score = 203 bits (520), Expect = 4e-67
Identities = 68/106 (64%), Positives = 80/106 (75%)
Query: 18 VPWRRTGVKYTNNEAYFDVIEEVDAIIDKTGSTIFSEIQGYIDCCIKLSGMPDLTLSFMN 77
VPWRR GVKYTNNE Y DV+EE+DAI+DK+G + E+ G IDC +LSGMPDLTLS N
Sbjct: 1 VPWRRAGVKYTNNEIYVDVVEEIDAIVDKSGKPVSGEVSGSIDCNSRLSGMPDLTLSLNN 60
Query: 78 PRLFDDVSFHPCVRFKRWEAERILSFIPPDGNFRLMSYHTRVSGSN 123
P L DD SFHPCVR RWE++R+LSFIPPDG F LMSY ++
Sbjct: 61 PGLLDDPSFHPCVRLSRWESDRVLSFIPPDGKFTLMSYRVDLNSLV 106
>gnl|CDD|211371 cd09260, AP-3_Mu3A_Cterm, C-terminal domain of medium Mu3A subunit
in ubiquitously expressed adaptor protein (AP) complex
AP-3. AP complexes participate in the formation of
intracellular coated transport vesicles and select cargo
molecules for incorporation into the coated vesicles in
the late secretory and endocytic pathways. There are
four AP complexes, AP-1, AP-2, AP-3, and AP-4, described
in various eukaryotic organisms. Each AP complex
consists of four subunits: two large chains (one each of
gamma/alpha/delta/epsilon and beta1-4, respectively), a
medium mu chain (mu1-4), and a small sigma chain
(sigma1-4). Each of the four subunits from the different
AP complexes exhibits similarity with each other. This
subfamily corresponds to the C-terminal domain of
heterotetrameric adaptor protein complex 3 (AP-3) medium
mu3A subunit encoded by ap3m1gene. Mu3A is ubiquitously
expressed in all mammalian tissues and cells. It appears
to be localized to the trans-Golgi network (TGN) and/or
endosomes and participates in trafficking to the
vacuole/lysosome in yeast, flies, and mammals. Unlike
AP-1 and AP-2, which function in conjunction with
clathrin which is a scaffolding protein participating in
the formation of coated vesicles, the nature of the
outer shell of ubiquitous AP-3 containing coats remains
to be elucidated. Membrane-anchored cargo molecules
interact with adaptors through short sorting signals in
their cytosolic segments. Tyrosine-based endocytotic
signals are one of the most important sorting signals.
They are of the form Y-X-X-Phi, where Y is tyrosine, X
is any amino acid and Phi is a bulky hydrophobic residue
that can be Leu, Ile, Met, Phe, or Val. These kinds of
sorting signals can be recognized by the C-terminal
domain of AP-3 mu3A subunit, also known as Y-X-X-Phi
signal-binding domain that contains two hydrophobic
pockets, one for the tyrosine-binding and one for the
bulky hydrophobic residue-binding.
Length = 254
Score = 198 bits (504), Expect = 9e-65
Identities = 87/106 (82%), Positives = 98/106 (92%), Gaps = 2/106 (1%)
Query: 18 VPWRRTGVKYTNNEAYFDVIEEVDAIIDKTGSTIFSEIQGYIDCCIKLSGMPDLTLSFMN 77
+PWRR GVKYTNNEAYFDV+EE+DAIIDK+GST+F+EIQG ID CIKLSGMPDL+LSFMN
Sbjct: 1 IPWRRAGVKYTNNEAYFDVVEEIDAIIDKSGSTVFAEIQGVIDACIKLSGMPDLSLSFMN 60
Query: 78 PRLFDDVSFHPCVRFKRWEAERILSFIPPDGNFRLMSYHTRVSGSN 123
PRL DDVSFHPC+RFKRWE+ER+LSFIPPDGNFRL+SY RVS N
Sbjct: 61 PRLLDDVSFHPCIRFKRWESERVLSFIPPDGNFRLISY--RVSSQN 104
>gnl|CDD|216199 pfam00928, Adap_comp_sub, Adaptor complexes medium subunit family.
This family also contains members which are coatomer
subunits.
Length = 228
Score = 154 bits (391), Expect = 6e-48
Identities = 61/112 (54%), Positives = 72/112 (64%), Gaps = 12/112 (10%)
Query: 18 VPWRRTGVKYTNNEAYFDVIEEVDAIIDKTGSTIFSEIQGYIDCCIKLSGMPDLTLSFMN 77
VPWR +G+KY NE + DVIE V I+DK G + SEIQG IDC LSGMP+LTL +
Sbjct: 1 VPWRPSGIKYKKNEVFLDVIERVSVIVDKDGGILNSEIQGTIDCKCYLSGMPELTLGLND 60
Query: 78 PRLF------------DDVSFHPCVRFKRWEAERILSFIPPDGNFRLMSYHT 117
P DDVSFHPCVR R+E+ER++SFIPPDG F LMSY
Sbjct: 61 PLNIGKIASSGNGIELDDVSFHPCVRLSRFESERVISFIPPDGEFTLMSYRI 112
>gnl|CDD|211360 cd07954, AP_MHD_Cterm, C-terminal domain of adaptor protein (AP)
complexes medium mu subunits and its homologs (MHD).
This family corresponds to the C-terminal domain of
heterotetrameric AP complexes medium mu subunits and its
homologs existing in monomeric stonins, delta-subunit of
the heteroheptameric coat protein I (delta-COPI), a
protein encoded by a pro-death gene referred as MuD
(also known as MUDENG, mu-2 related death-inducing
gene), an endocytic adaptor syp1, the mammalian FCH
domain only proteins (FCHo1/2), SH3-containing GRB2-like
protein 3-interacting protein 1 (SGIP1), and related
proteins. AP complexes participate in the formation of
intracellular coated transport vesicles and select cargo
molecules for incorporation into the coated vesicles in
the late secretory and endocytic pathways. Stonins have
been characterized as clathrin-dependent AP-2 mu chain
related factors and may act as cargo-specific sorting
adaptors in endocytosis. Coat protein complex I
(COPI)-coated vesicles function in the early secretory
pathway. They mediate the retrograde transport from the
Golgi to the ER, and intra-Golgi transport. MuD is
distantly related to the C-terminal domain of mu2
subunit of AP-2. It is able to induce cell death by
itself and plays an important role in cell death in
various tissues. Syp1 represents a novel type of
endocytic adaptor protein that participates in
endocytosis, promotes vesicle tabulation, and
contributes to cell polarity and stress responses. It
shares the same domain architecture with its two
ubiquitously expressed mammalian counterparts, FCHo1/2,
which represent key initial proteins ultimately
controlling cellular nutrient uptake, receptor
regulation, and synaptic vesicle retrieval. They bind
specifically to the plasma membrane and recruit the
scaffold proteins eps15 and intersectin, which
subsequently engage the adaptor complex AP2 and
clathrin, leading to coated vesicle formation. Another
mammalian neuronal-specific protein SGIP1 does have a
C-terminal MHD and has been classified into this family
as well. It is an endophilin-interacting protein that
plays an obligatory role in the regulation of energy
homeostasis. It is also involved in clathrin-mediated
endocytosis by interacting with phospholipids and eps15.
Length = 239
Score = 124 bits (314), Expect = 3e-36
Identities = 51/90 (56%), Positives = 62/90 (68%), Gaps = 3/90 (3%)
Query: 31 EAYFDVIEEVDAIIDKTGSTIFSEIQGYIDCCIKLSGMPDLTLSFMNP---RLFDDVSFH 87
E + DVIE+V+ +I K GS + SE+ G I LSGMP++ L NP DDVSFH
Sbjct: 1 EVFLDVIEKVNLLISKDGSLLNSEVVGEIALKSFLSGMPEIRLGLNNPDVGIKLDDVSFH 60
Query: 88 PCVRFKRWEAERILSFIPPDGNFRLMSYHT 117
PCVR KR+E+ERI+SFIPPDG F LMSY T
Sbjct: 61 PCVRLKRFESERIISFIPPDGEFELMSYRT 90
>gnl|CDD|211361 cd09250, AP-1_Mu1_Cterm, C-terminal domain of medium Mu1 subunit in
clathrin-associated adaptor protein (AP) complex AP-1.
AP complexes participate in the formation of
intracellular coated transport vesicles and select cargo
molecules for incorporation into the coated vesicles in
the late secretory and endocytic pathways. There are
four AP complexes, AP-1, AP-2, AP-3, and AP-4, described
in various eukaryotic organisms. Each AP complex
consists of four subunits: two large chains (one each of
gamma/alpha/delta/epsilon and beta1-4, respectively), a
medium mu chain (mu1-4), and a small sigma chain
(sigma1-4). Each of the four subunits from the different
AP complexes exhibits similarity with each other. This
family corresponds to the C-terminal domain of
heterotetrameric clathrin-associated adaptor protein
complex 1 (AP-1) medium mu1 subunit, which includes two
closely related homologs, mu1A (encoded by ap1m1) and
mu1B (encoded by ap1m2). Mu1A is ubiquitously expressed,
but mu1B is expressed exclusively in polarized
epithelial cells. AP-1 has been implicated in
bi-directional transport between the trans-Golgi network
(TGN) and endosomes. It plays an essential role in the
formation of clathrin-coated vesicles (CCVs) from the
trans-Golgi network (TGN). Epithelial cell-specific AP-1
is also involved in sorting to the basolateral surface
of polarized epithelial cells. Recruitment of AP-1 to
the TGN membrane is regulated by a small GTPase,
ADP-ribosylation factor 1 (ARF1).
Phosphorylation/dephosphorylation events can also
regulate the function of AP-1. The membrane-anchored
cargo molecules can be linked to the outer lattice of
CCVs by AP-1. Those cargo molecules interact with
adaptors through short sorting signals in their
cytosolic segments. Tyrosine-based endocytotic signals
are one of the most important sorting signals. They are
of the form Y-X-X-Phi, where Y is tyrosine, X is any
amino acid and Phi is a bulky hydrophobic residue that
can be Leu, Ile, Met, Phe, or Val. These kinds of
sorting signals can be recognized by the C-terminal
domain of AP-1 mu1 subunit, also known as Y-X-X-Phi
signal-binding domain that contains two hydrophobic
pockets, one for the tyrosine-binding and one for the
bulky hydrophobic residue-binding.
Length = 268
Score = 120 bits (302), Expect = 4e-34
Identities = 50/115 (43%), Positives = 65/115 (56%), Gaps = 16/115 (13%)
Query: 16 SSVPWRRTGVKYTNNEAYFDVIEEVDAIIDKTGSTIFSEIQGYIDCCIKLSGMPDLTLSF 75
++V WR G+KY NE + DVIE V+ ++D G + SEI G I LSGMP+L L
Sbjct: 2 NAVSWRPEGIKYKKNEVFLDVIESVNLLVDLNGQVLRSEIVGTIKMRSYLSGMPELKLGL 61
Query: 76 MNPRL---------------FDDVSFHPCVRFKRWEAERILSFIPPDGNFRLMSY 115
N ++ +DV FH CVR R+E +R +SFIPPDG F LMSY
Sbjct: 62 -NDKVLFEATGRSSKGKAVELEDVKFHQCVRLSRFENDRTISFIPPDGEFELMSY 115
>gnl|CDD|211369 cd09258, AP-1_Mu1A_Cterm, C-terminal domain of medium Mu1A subunit
in ubiquitously expressed clathrin-associated adaptor
protein (AP) complex AP-1. AP complexes participate in
the formation of intracellular coated transport vesicles
and select cargo molecules for incorporation into the
coated vesicles in the late secretory and endocytic
pathways. There are four AP complexes, AP-1, AP-2, AP-3,
and AP-4, described in various eukaryotic organisms.
Each AP complex consists of four subunits: two large
chains (one each of gamma/alpha/delta/epsilon and
beta1-4, respectively), a medium mu chain (mu1-4), and a
small sigma chain (sigma1-4). Each of the four subunits
from the different AP complexes exhibits similarity with
each other. This subfamily corresponds to the C-terminal
domain of heterotetrameric clathrin-associated adaptor
protein complex 1 (AP-1) medium mu1A subunit encoded by
ap1m1 gene, which is ubiquitously expressed in all
mammalian tissues and cells. AP-1 has been implicated in
bidirectional transport between the trans-Golgi network
(TGN) and endosomes. It is involved in the formation of
clathrin-coated vesicles (CCVs) from the trans-Golgi
network (TGN). The ubiquitous AP-1 is recruited to the
TGN membrane, as well as to immature secretory granules.
Recruitment of AP-1 to the TGN membrane is regulated by
a small GTPase, ADP-ribosylation factor 1 (ARF1).
Phosphorylation/dephosphorylation events can also
regulate the function of AP-1. The membrane-anchored
cargo molecules can be linked to the outer lattice of
CCVs by AP-1. Those cargo molecules interact with
adaptors through short sorting signals in their
cytosolic segments. Tyrosine-based endocytotic signals
are one of the most important sorting signals. They are
of the form Y-X-X-Phi, where Y is tyrosine, X is any
amino acid and Phi is a bulky hydrophobic residue that
can be Leu, Ile, Met, Phe, or Val. These kinds of
sorting signals can be recognized by the C-terminal
domain of AP-1 mu1A subunit, also known as Y-X-X-Phi
signal-binding domain that contains two hydrophobic
pockets, one for the tyrosine-binding and one for the
bulky hydrophobic residue-binding.
Length = 270
Score = 104 bits (262), Expect = 3e-28
Identities = 50/113 (44%), Positives = 66/113 (58%), Gaps = 13/113 (11%)
Query: 16 SSVPWRRTGVKYTNNEAYFDVIEEVDAIIDKTGSTIFSEIQGYIDCCIKLSGMPDLTLSF 75
++V WR G+KY NE + DVIE V+ ++ G+ + SEI G I + LSGMP+L L
Sbjct: 3 NAVSWRSEGIKYRKNEVFLDVIESVNLLVSANGNVLRSEIVGSIKMRVYLSGMPELRLGL 62
Query: 76 MNPRLFD-------------DVSFHPCVRFKRWEAERILSFIPPDGNFRLMSY 115
+ LF+ DV FH CVR R+E +R +SFIPPDG F LMSY
Sbjct: 63 NDKVLFENTGRGKSKSVELEDVKFHQCVRLSRFENDRTISFIPPDGEFELMSY 115
>gnl|CDD|211362 cd09251, AP-2_Mu2_Cterm, C-terminal domain of medium Mu2 subunit in
ubiquitously expressed clathrin-associated adaptor
protein (AP) complex AP-2. AP complexes participate in
the formation of intracellular coated transport vesicles
and select cargo molecules for incorporation into the
coated vesicles in the late secretory and endocytic
pathways. There are four AP complexes, AP-1, -2, -3, and
-4, described in various eukaryotic organisms. Each AP
complex consists of four subunits: two large chains (one
each of gamma/alpha/delta/epsilon and beta1-4,
respectively), a medium mu chain (mu1-4), and a small
sigma chain (sigma1-4). Each of the four subunits from
the different AP complexes exhibits similarity with each
other. This family corresponds to the C-terminal domain
of heterotetrameric clathrin-associated adaptor protein
complex 2 (AP-2) medium mu2 subunit. Mu2 is ubiquitously
expressed in mammals. In higher eukaryotes, AP-2 plays a
critical role in clathrin-mediated endocytosis from the
plasma membrane in different cells. The
membrane-anchored cargo molecules can be linked to the
outer lattice of CCVs by AP-2. Those cargo molecules
interact with adaptors through short sorting signals in
their cytosolic segments. Tyrosine-based endocytotic
signals are one of the most important sorting signals.
They are of the form Y-X-X-Phi, where Y is tyrosine, X
is any amino acid and Phi is a bulky hydrophobic residue
that can be Leu, Ile, Met, Phe, or Val. These kinds of
sorting signals can be recognized by the C-terminal
domain of AP-2 mu2 subunit, also known as Y-X-X-Phi
signal-binding domain that contains two hydrophobic
pockets, one for the tyrosine-binding and one for the
bulky hydrophobic residue-binding. Since the Y-X-X-Phi
binding site is buried in the core structure of AP-2, a
phosphorylation induced conformational change is
required when the cargo molecules binds to AP-2. In
addition, the C-terminal domain of mu2 subunit has been
shown to bind other molecules. For instance, it can bind
phosphoinositides, in particular PI[4,5]P2, which might
be involved in the recognition process of the
tyrosine-based signals. It can also interact with
synaptotagmins, a family of important modulators of
calcium-dependent neurosecretion within the synaptic
vesicle (SV) membrane. Since many of the other endocytic
adaptors responsible for biogenesis of synaptic vesicles
exist, in the absence of AP-2, clathrin-mediated
endocytosis can still occur. However, the cells may not
survive in the complete absence of clathrin as well as
AP-2.
Length = 263
Score = 104 bits (261), Expect = 5e-28
Identities = 38/112 (33%), Positives = 56/112 (50%), Gaps = 21/112 (18%)
Query: 27 YTNNEAYFDVIEEVDAIIDKTGSTIFSEIQGYIDCCIKLSGMPDLTLSFMNPRL------ 80
Y NE + DV+E V+ ++ TG+ + +++ G I LSGMP+ +N +L
Sbjct: 1 YRKNEVFLDVVESVNLLMSSTGTVLRADVDGVIVMKAFLSGMPECKFG-LNDKLVLEKEG 59
Query: 81 --------------FDDVSFHPCVRFKRWEAERILSFIPPDGNFRLMSYHTR 118
DD FH CVR ++++ER +SFIPPDG F LM Y
Sbjct: 60 KAKSGDKAAKGSVELDDCKFHQCVRLSKFDSERTISFIPPDGEFELMRYRIT 111
>gnl|CDD|211370 cd09259, AP-1_Mu1B_Cterm, C-terminal domain of medium Mu1B subunit
in epithelial cell-specific clathrin-associated adaptor
protein (AP) complex AP-1. AP complexes participate in
the formation of intracellular coated transport vesicles
and select cargo molecules for incorporation into the
coated vesicles in the late secretory and endocytic
pathways. There are four AP complexes, AP-1, AP-2, AP-3,
and AP-4, described in various eukaryotic organisms.
Each AP complex consists of four subunits: two large
chains (one each of gamma/alpha/delta/epsilon and
beta1-4, respectively), a medium mu chain (mu1-4), and a
small sigma chain (sigma1-4). Each of the four subunits
from different AP complexes exhibits similarity with
each other. This subfamily corresponds to the C-terminal
domain of heterotetrameric clathrin-associated adaptor
protein complex 1 (AP-1) medium mu1B subunit encoded by
ap1m2 gene exclusively expressed in polarized epithelial
cells. Epithelial cell-specific AP-1 is used to sort
proteins to the basolateral plasma membrane, which
involves the formation of clathrin-coated vesicles
(CCVs) from the trans-Golgi network (TGN). Recruitment
of AP-1 to the TGN membrane is regulated by a small
GTPase, ADP-ribosylation factor 1 (ARF1). The
phosphorylation/dephosphorylation events can also
regulate the function of AP-1. The membrane-anchored
cargo molecules can be linked to the outer lattice of
CCVs by AP-1. Those cargo molecules interact with
adaptors through short sorting signals in their
cytosolic segments. Tyrosine-based endocytotic signals
are one of the most important sorting signals. They are
of the form Y-X-X-Phi, where Y is tyrosine, X is any
amino acid and Phi is a bulky hydrophobic residue that
can be Leu, Ile, Met, Phe, or Val. These kinds of
sorting signals can be recognized by the C-terminal
domain of AP-1 mu1B subunit, also known as Y-X-X-Phi
signal-binding domain that contains two hydrophobic
pockets, one for the tyrosine-binding and one for the
bulky hydrophobic reside-binding. Besides, AP-1 mu1B
subunit mediates the basolateral recycling of
low-density lipoprotein receptor (LDLR) and transferrin
receptor (TfR) from the sorting endosomes, where the
basolateral sorting signal does not belong to the
tyrosine-based signals. Thus, the binding site in mu1B
subunit of AP-1 for the signals of LDLR and TfR might be
distinct from that for YXXPhi signals.
Length = 264
Score = 103 bits (258), Expect = 1e-27
Identities = 50/113 (44%), Positives = 66/113 (58%), Gaps = 13/113 (11%)
Query: 16 SSVPWRRTGVKYTNNEAYFDVIEEVDAIIDKTGSTIFSEIQGYIDCCIKLSGMPDLTLSF 75
++V WR G+KY NE + DVIE V+ +++ GS + SEI G I + LSGMP+L L
Sbjct: 2 NAVSWRSEGIKYKKNEVFIDVIESVNLLVNANGSVLRSEIVGAIKLKVFLSGMPELRLGL 61
Query: 76 MNPRLF-------------DDVSFHPCVRFKRWEAERILSFIPPDGNFRLMSY 115
+ LF +DV FH CVR R+E +R +SFIPPDG LMSY
Sbjct: 62 NDRVLFELTGREKNKTVELEDVKFHQCVRLSRFENDRTISFIPPDGESELMSY 114
>gnl|CDD|211364 cd09253, AP-4_Mu4_Cterm, C-terminal domain of medium Mu4 subunit in
adaptor protein (AP) complex AP-4. AP complexes
participate in the formation of intracellular coated
transport vesicles and select cargo molecules for
incorporation into the coated vesicles in the late
secretory and endocytic pathways. There are four AP
complexes, AP-1, AP-2, AP-3, and AP-4, described in
various eukaryotic organisms. Each AP complex consists
of four subunits: two large chains (one each of
gamma/alpha/delta/epsilon and beta1-4, respectively), a
medium mu chain (mu1-4), and a small sigma chain
(sigma1-4). Each of the four subunits from the different
AP complexes exhibits similarity with each other. This
family corresponds to the C-terminal domain of
heterotetrameric adaptor protein complex 4 (AP-4) medium
mu4 subunit. AP-4 plays a role in signal-mediated
trafficking of integral membrane proteins in mammalian
cells. Unlike other AP complexes, AP-4 is found only in
mammals and plants. It is believed to be part of a
nonclathrin coat, since it might function independently
of clathrin, a scaffolding protein participating in the
formation of coated vesicles. Recruitment of AP-4 to the
trans-Golgi network (TGN) membrane is regulated by a
small GTPase, ADP-ribosylation factor 1 (ARF1) or a
related protein. Membrane-anchored cargo molecules
interact with adaptors through short sorting signals in
their cytosolic segments. One of the most important
sorting signals binding to mu subunits of AP complexes
are tyrosine-based endocytotic signals, which are of the
form Y-X-X-Phi, where Y is tyrosine, X is any amino acid
and Phi is a bulky hydrophobic residue that can be Leu,
Ile, Met, Phe, or Val. However, AP-4 does not bind most
canonical tyrosine-based signals except for two
naturally occurring ones from the lysosomal membrane
proteins CD63 and LAMP-2a. It binds YX [FYL][FL]E motif,
where X can be any residue, from the cytosolic tails of
amyloid precursor protein (APP) family members in a
distinct way.
Length = 271
Score = 74.2 bits (183), Expect = 1e-16
Identities = 36/105 (34%), Positives = 51/105 (48%), Gaps = 18/105 (17%)
Query: 29 NNEAYFDVIEEVDAIIDKTGSTIFSEIQGYIDCCIK--LSGMPDLTLSFMNPRLF----- 81
NE + DV+E + + G + SEI G I +K LSG P+L L+ +
Sbjct: 10 KNEIFVDVLERLSVVFSANGQVLNSEIDGSIQ--MKSYLSGNPELRLALNEDLVIGKREN 67
Query: 82 ---------DDVSFHPCVRFKRWEAERILSFIPPDGNFRLMSYHT 117
DD +FH CV + +E++R LS PPDG F LM+Y
Sbjct: 68 RAYSSAVVLDDCNFHECVDLEEFESDRTLSLTPPDGEFTLMNYRI 112
>gnl|CDD|211366 cd09255, AP-like_stonins_MHD, Mu homology domain (MHD) of
adaptor-like proteins (AP-like), stonins. A small
family of proteins named stonins has been characterized
as clathrin-dependent AP-2 mu2 chain related factors,
which may act as cargo-specific sorting adaptors in
endocytosis. Stonins include stonin 1 and stonin 2,
which are only mammalian homologs of Drosophila stoned
B, a presynaptic protein implicated in neurotransmission
and synaptic vesicle (SV) recycling. They are conserved
from C. elegans to humans, but are not found in
prokaryotes or yeasts. This family corresponds to the mu
homology domain of stonins, which is distantly related
to the C-terminal domain of mu chains among AP
complexes. Due to the low degree of sequence
conservation of the corresponding binding site, the mu
homology domain of stonins is unable to recognize
tyrosine-based endocytic sorting signals. To data,
little is known about the localization and function of
stonin 1. Stonin 2, also known as stoned B, acts as an
AP-2-dependent synaptotagmin-specific sorting adaptors
for SV endocytosis. Stoned A is not a stonin. It is
structurally unrelated to the adaptins and does not
appear to have mammalian homologs. It is not included in
this family.
Length = 308
Score = 54.6 bits (132), Expect = 2e-09
Identities = 29/120 (24%), Positives = 48/120 (40%), Gaps = 22/120 (18%)
Query: 21 RRTGVKYTNNEAYFDVIEEVDAIIDKTGSTIFSEIQGYIDCCIKLSGMPDLTLSFMNPRL 80
R G+ Y +E DV++E + K G + ++ I C ++GMP+ L + +
Sbjct: 2 RDRGLTYREDEITVDVVDEFRGKVTKEGEILKQAVRVRIFCLAFVTGMPECELGLNDIQR 61
Query: 81 ---------------------FDDVSFHPCVRFKRWEAERILSFIPPDGN-FRLMSYHTR 118
++V FH CV +E R++ F P D F LM + R
Sbjct: 62 KGREVVRRQDIIPVSTEEWIKLENVEFHSCVNKDEFEQSRVIKFHPLDACRFELMRFRVR 121
>gnl|CDD|211367 cd09256, AP_MuD_MHD, Mu-homology domain (MHD) of a adaptor protein
(AP) encoded by mu-2 related death-inducing gene, MuD
(also known as MUDENG). This family corresponds to the
MHD found in a protein encoded by MuD, which is
distantly related to the C-terminal domain of the mu2
subunit of AP complexes that participates in
clathrin-mediated endocytosis. MuD is evolutionary
conserved from mammals to amphibians. It is able to
induce cell death by itself and plays an important role
in cell death in various tissues.
Length = 271
Score = 47.4 bits (113), Expect = 6e-07
Identities = 28/92 (30%), Positives = 40/92 (43%), Gaps = 9/92 (9%)
Query: 33 YFDVIEEVDAII-DKTGSTIFSEIQGYIDCCIKLSGMPDLTLSFMNP---RLFDDVSFHP 88
F + E V A DK + G + C +L G+PD+T+S P ++ HP
Sbjct: 15 DFKITETVKAAQYDKDDIPDVWSVFGSVTCKAELEGLPDVTVSLSLPANGSPLQNIIVHP 74
Query: 89 CVR-----FKRWEAERILSFIPPDGNFRLMSY 115
CV+ + L F PP GNF+L Y
Sbjct: 75 CVQSVDTGMLAFSGPYKLRFSPPLGNFQLCHY 106
>gnl|CDD|211373 cd09262, AP_stonin-1_MHD, Mu homology domain (MHD) of adaptor-like
protein (AP-like), stonin-1 (also called Stoned B-like
factor). A small family of proteins named stonins has
been characterized as clathrin-dependent AP-2 mu2 chain
related factors, which may act as cargo-specific sorting
adaptors in endocytosis. Stonins include stonin 1 and
stonin 2, which are the only mammalian homologs of
Drosophila stoned B, a presynaptic protein implicated in
neurotransmission and synaptic vesicle (SV) recycling.
They are conserved from C. elegans to humans, but are
not found in prokaryotes or yeasts. This family
corresponds to the mu homology domain of stonin 1, which
is distantly related to the C-terminal domain of mu
chains among AP complexes. Due to the low degree of
sequence conservation of the corresponding binding site,
the mu homology domain of stonin-1 is unable to
recognize tyrosine-based endocytic sorting signals. To
data, little is known about the localization and
function of stonin-1.
Length = 309
Score = 43.3 bits (102), Expect = 2e-05
Identities = 28/116 (24%), Positives = 47/116 (40%), Gaps = 19/116 (16%)
Query: 27 YTNNEAYFDVIEEVDAIIDKTGSTIFSEIQGYIDCCIKLSG-------MPDLTLSFMNPR 79
Y E ++++ +DK G + S + I C ++ + DL L +
Sbjct: 8 YEEQELSLEIVDHFWGRVDKEGKVMESSVITQIHCLCFVNAPAECFLTLNDLELQKRDED 67
Query: 80 LFD-----------DVSFHPCVRFKRWEAERILSFIPPDG-NFRLMSYHTRVSGSN 123
F+ D FH CV + + R++ F PPD F LM + TR +G +
Sbjct: 68 YFEKEAGKLWIEILDYHFHKCVNAQEFHQSRLIKFCPPDACRFELMRFKTRYNGGD 123
>gnl|CDD|211374 cd09263, AP_stonin-2_MHD, Mu homology domain (MHD) of adaptor-like
protein (AP-like), stonin-2. A small family of proteins
named stonins has been characterized as
clathrin-dependent AP-2 mu2 chain related factors, which
may act as cargo-specific sorting adaptors in
endocytosis. Stonins include stonin 1 and stonin 2,
which are the only mammalian homologs of Drosophila
stoned B, a presynaptic protein implicated in
neurotransmission and synaptic vesicle (SV) recycling.
They are conserved from C. elegans to humans, but are
not found in prokaryotes or yeasts. This family
corresponds to the mu homology domain of stonin 2, which
is distantly related to the C-terminal domain of mu
chains among AP complexes. Due to the low degree of
sequence conservation of the corresponding binding site,
the mu homology domain of stonin-2 is unable to
recognize tyrosine-based endocytic sorting signals. It
acts as an AP-2-dependent synaptotagmin-specific sorting
adaptor for SV endocytosis.
Length = 314
Score = 35.3 bits (81), Expect = 0.009
Identities = 30/120 (25%), Positives = 43/120 (35%), Gaps = 29/120 (24%)
Query: 24 GVKYTNNEAYFDVIEEVDAIIDKTGSTI-----------FSEIQGYIDCCIKLSG----- 67
G+ YT E DV +E I+ K S I S + G +C + L+
Sbjct: 5 GLNYTEEEITVDVRDEFHGILSKGDSRILQHSVLTRIYILSFLSGLAECRLGLNDILIKG 64
Query: 68 ---------MPDLTLSFMNPRLFDDVSFHPCVRFKRWEAERILSFIPPDG-NFRLMSYHT 117
MP T ++ + FH CV + R + F P D F LM + T
Sbjct: 65 NEVVARQDIMPTTTTKWIQLH---ECRFHECVDEDMFNNSRAILFNPLDACRFELMRFRT 121
>gnl|CDD|183698 PRK12715, flgK, flagellar hook-associated protein FlgK;
Provisional.
Length = 649
Score = 31.6 bits (71), Expect = 0.17
Identities = 19/68 (27%), Positives = 36/68 (52%), Gaps = 1/68 (1%)
Query: 4 VYVSSILPS-GQLSSVPWRRTGVKYTNNEAYFDVIEEVDAIIDKTGSTIFSEIQGYIDCC 62
V VSSI + Q ++ R T T +A+++ ++D ++ + GS+I +Q + D
Sbjct: 57 VSVSSIYRNVDQFANAQVRSTLSYRTQYDAFYNQAIQIDKLLSQDGSSISVPLQTFFDSI 116
Query: 63 IKLSGMPD 70
+L+ PD
Sbjct: 117 GQLNSTPD 124
>gnl|CDD|133138 cd05471, pepsin_like, Pepsin-like aspartic proteases, bilobal
enzymes that cleave bonds in peptides at acidic pH.
Pepsin-like aspartic proteases are found in mammals,
plants, fungi and bacteria. These well known and
extensively characterized enzymes include pepsins,
chymosin, renin, cathepsins, and fungal aspartic
proteases. Several have long been known to be medically
(renin, cathepsin D and E, pepsin) or commercially
(chymosin) important. Structurally, aspartic proteases
are bilobal enzymes, each lobe contributing a catalytic
Aspartate residue, with an extended active site cleft
localized between the two lobes of the molecule. The N-
and C-terminal domains, although structurally related by
a 2-fold axis, have only limited sequence homology
except the vicinity of the active site. This suggests
that the enzymes evolved by an ancient duplication
event. Most members of the pepsin family specifically
cleave bonds in peptides that are at least six residues
in length, with hydrophobic residues in both the P1 and
P1' positions. The active site is located at the groove
formed by the two lobes, with an extended loop
projecting over the cleft to form an 11-residue flap,
which encloses substrates and inhibitors in the active
site. Specificity is determined by nearest-neighbor
hydrophobic residues surrounding the catalytic
aspartates, and by three residues in the flap.The
enzymes are mostly secreted from cells as inactive
proenzymes that activate autocatalytically at acidic pH.
This family of aspartate proteases is classified by
MEROPS as the peptidase family A1 (pepsin A, clan AA).
Length = 283
Score = 29.7 bits (67), Expect = 0.53
Identities = 12/40 (30%), Positives = 19/40 (47%)
Query: 38 EEVDAIIDKTGSTIFSEIQGYIDCCIKLSGMPDLTLSFMN 77
DAI+ G+ + S GY C +PD+T +F+
Sbjct: 219 SVYDAILKALGAAVSSSDGGYGVDCSPCDTLPDITFTFLW 258
>gnl|CDD|238196 cd00319, Ribosomal_S12_like, Ribosomal protein S12-like family;
composed of prokaryotic 30S ribosomal protein S12,
eukaryotic 40S ribosomal protein S23 and similar
proteins. S12 and S23 are located at the interface of
the large and small ribosomal subunits, adjacent to the
decoding center. They play an important role in
translocation during the peptide elongation step of
protein synthesis. They are also involved in important
RNA and protein interactions. Ribosomal protein S12 is
essential for maintenance of a pretranslocation state
and, together with S13, functions as a control element
for the rRNA- and tRNA-driven movements of
translocation. S23 interacts with domain III of the
eukaryotic elongation factor 2 (eEF2), which catalyzes
translocation. Mutations in S12 and S23 have been found
to affect translational accuracy. Antibiotics such as
streptomycin may also bind S12/S23 and cause the
ribosome to misread the genetic code.
Length = 95
Score = 27.7 bits (61), Expect = 1.1
Identities = 3/22 (13%), Positives = 10/22 (45%)
Query: 89 CVRFKRWEAERILSFIPPDGNF 110
+ + + ++IP +G+
Sbjct: 37 VAKVRLTSGYEVTAYIPGEGHN 58
>gnl|CDD|216510 pfam01450, IlvC, Acetohydroxy acid isomeroreductase, catalytic
domain. Acetohydroxy acid isomeroreductase catalyzes
the conversion of acetohydroxy acids into dihydroxy
valerates. This reaction is the second in the synthetic
pathway of the essential branched side chain amino
acids valine and isoleucine.
Length = 146
Score = 28.0 bits (63), Expect = 1.6
Identities = 7/19 (36%), Positives = 12/19 (63%)
Query: 27 YTNNEAYFDVIEEVDAIID 45
Y+ AYF+ + E+ I+D
Sbjct: 36 YSPEIAYFETLHELKLIVD 54
>gnl|CDD|227751 COG5464, COG5464, Uncharacterized conserved protein [Function
unknown].
Length = 289
Score = 28.1 bits (63), Expect = 2.0
Identities = 13/40 (32%), Positives = 17/40 (42%), Gaps = 2/40 (5%)
Query: 45 DKTGSTIFSEIQGYIDCCIKLSGMPDLTLSF--MNPRLFD 82
D S E QGYI I+ MPD ++F M +
Sbjct: 56 DVLWSLKTQEGQGYIYVVIEHQSMPDKHMAFRLMRYAIAA 95
>gnl|CDD|237892 PRK15062, PRK15062, hydrogenase isoenzymes formation protein
HypD; Provisional.
Length = 364
Score = 27.4 bits (62), Expect = 3.4
Identities = 7/18 (38%), Positives = 10/18 (55%)
Query: 56 QGYIDCCIKLSGMPDLTL 73
G ID I+L+ P + L
Sbjct: 69 MGRIDAAIELASRPGVIL 86
>gnl|CDD|235095 PRK02983, lysS, lysyl-tRNA synthetase; Provisional.
Length = 1094
Score = 27.6 bits (62), Expect = 3.6
Identities = 10/28 (35%), Positives = 13/28 (46%), Gaps = 4/28 (14%)
Query: 2 RSVYVSSILPSGQ----LSSVPWRRTGV 25
+ V + GQ LS VPW R G+
Sbjct: 419 DCLLVEAHDADGQVVALLSFVPWGRRGL 446
>gnl|CDD|213349 cd12789, RasGAP_plexin_C1, Ras-GTPase Activating Domain of
plexin-C1. Plexins form a conserved family of
transmembrane receptors for semaphorins and may be the
ancestors of semaphorins. Plexins are divided into four
types (A-D) according to sequence similarity. Plexin-C1
has been identified as the receptor of semaphorin 7A,
which plays regulatory roles in both the immune and
nervous systems. Unlike other semaphorins which act as
repulsive guidance cues, Sema7A enhances central and
peripheral axon growth and is required for proper axon
tract formation during embryonic development. Plexin-C1
is a potential tumor suppressor for melanoma
progression. The expression of Plexin-C1 is diminished
or absent in human melanoma cell lines. Cofilin, an
actin-binding protein involved in cell migration, is a
downstream target of Sema7A and Plexin-C1 signaling.
Melanoma invasion and metastasis may be promoted through
the loss of Plexin-C1 inhibitory signaling on cofilin
activation. Plexins contain a C-terminal RasGAP domain,
which functions as an enhancer of the hydrolysis of GTP
that is bound to Ras-GTPases. Plexins display GAP
activity towards the Ras homolog Rap. Although the Rho
(Ras homolog) GTPases are most closely related to
members of the Ras family, RhoGAP and RasGAP show no
sequence homology at their amino acid level. RasGTPases
function as molecular switches in a large number of of
signaling pathways. When bound to GTP they are in the on
state and when bound to GDP they are in the off state.
The RasGAP domain speeds up the hydrolysis of GTP in
Ras-like proteins acting as a negative regulator.
Length = 393
Score = 26.8 bits (59), Expect = 6.1
Identities = 15/63 (23%), Positives = 26/63 (41%), Gaps = 2/63 (3%)
Query: 102 SFIPPDGNFRLMSYHTRVSGSNGGRPNASCPSFHRMVTSASCLTIRIRKVKKDKNRSISV 161
+F P G F + + + S + +++ + S L I ++K KN SV
Sbjct: 16 TFFPESGGFTHIFTRDDPHDRDQTDKDESLTALDKLICNKSFLVTLIHTLEKQKN--FSV 73
Query: 162 TDR 164
DR
Sbjct: 74 KDR 76
>gnl|CDD|220495 pfam09971, DUF2206, Predicted membrane protein (DUF2206). This
domain, found in various hypothetical archaeal proteins,
has no known function.
Length = 367
Score = 26.6 bits (59), Expect = 6.2
Identities = 9/28 (32%), Positives = 16/28 (57%)
Query: 25 VKYTNNEAYFDVIEEVDAIIDKTGSTIF 52
VK N ++++E++ I D GS I+
Sbjct: 339 VKKFNISDNKELLDEINKIYDNGGSQIY 366
>gnl|CDD|169599 PRK08955, PRK08955, glyceraldehyde-3-phosphate dehydrogenase;
Validated.
Length = 334
Score = 26.6 bits (59), Expect = 6.3
Identities = 8/14 (57%), Positives = 11/14 (78%)
Query: 132 PSFHRMVTSASCLT 145
P+ H +VT+ASC T
Sbjct: 141 PAIHPIVTAASCTT 154
>gnl|CDD|99942 cd05510, Bromo_SPT7_like, Bromodomain; SPT7_like subfamily. SPT7 is
a yeast protein that functions as a component of the
transcription regulatory histone acetylation (HAT)
complexes SAGA, SALSA, and SLIK. SAGA is involved in the
RNA polymerase II-dependent transcriptional regulation
of about 10% of all yeast genes. The SPT7 bromodomain
has been shown to weakly interact with acetylated
histone H3, but not H4. The human representative of this
subfamily is cat eye syndrome critical region protein 2
(CECR2). Bromodomains are 110 amino acid long domains,
that are found in many chromatin associated proteins.
Bromodomains can interact specifically with acetylated
lysine.
Length = 112
Score = 25.9 bits (57), Expect = 6.3
Identities = 13/39 (33%), Positives = 19/39 (48%), Gaps = 3/39 (7%)
Query: 70 DLTLSFMNPRLFDDVSFHP---CVRFKRWEAERILSFIP 105
DL L + N L++ HP F + +AE +L IP
Sbjct: 72 DLNLIWKNCLLYNSDPSHPLRRHANFMKKKAEHLLKLIP 110
>gnl|CDD|133141 cd05474, SAP_like, SAPs, pepsin-like proteinases secreted from
pathogens to degrade host proteins. SAPs (Secreted
aspartic proteinases) are secreted from a group of
pathogenic fungi, predominantly Candida species. They
are secreted from the pathogen to degrade host proteins.
SAP is one of the most significant extracellular
hydrolytic enzymes produced by C. albicans. SAP
proteins, encoded by a family of 10 SAP genes. All 10
SAP genes of C. albicans encode preproenzymes,
approximately 60 amino acid longer than the mature
enzyme, which are processed when transported via the
secretory pathway. The mature enzymes contain sequence
motifs typical for all aspartyl proteinases, including
the two conserved aspartate residues other active site
and conserved cysteine residues implicated in the
maintenance of the three-dimensional structure. Most Sap
proteins contain putative N-glycosylation sites, but it
remains to be determined which Sap proteins are
glycosylated. This family of aspartate proteases is
classified by MEROPS as the peptidase family A1 (pepsin
A, clan AA). The overall structure of Sap protein
conforms to the classical aspartic proteinase fold
typified by pepsin. SAP is a bilobal enzyme, each lobe
contributing a catalytic Asp residue, with an extended
active site cleft localized between the two lobes of the
molecule. One lobe may be evolved from the other through
ancient gene-duplication event. More recently evolved
enzymes have similar three-dimensional structures,
however their amino acid sequences are more divergent
except for the conserved catalytic site motif. This
family of aspartate proteases is classified by MEROPS as
the peptidase family A1 (pepsin A, clan AA).
Length = 295
Score = 26.4 bits (59), Expect = 7.3
Identities = 13/39 (33%), Positives = 20/39 (51%), Gaps = 5/39 (12%)
Query: 38 EEVDAIIDKTGSTIFSEIQGY-IDCCIKLSGMPDLTLSF 75
+ VDAI + G+T S+ Y +DC D +L+F
Sbjct: 195 DIVDAIAKQLGATYDSDEGLYVVDC----DAKDDGSLTF 229
>gnl|CDD|177256 MTH00213, ND6, NADH dehydrogenase subunit 6; Provisional.
Length = 239
Score = 26.4 bits (58), Expect = 8.3
Identities = 14/66 (21%), Positives = 27/66 (40%)
Query: 6 VSSILPSGQLSSVPWRRTGVKYTNNEAYFDVIEEVDAIIDKTGSTIFSEIQGYIDCCIKL 65
++S +P L++ R +Y D V +++ +I + IQ I +
Sbjct: 118 LASAVPDSFLNNPSGRGGAERYELTNILSDRNRGVSSLLGSDKESITTGIQNNIYMRVGA 177
Query: 66 SGMPDL 71
+G P L
Sbjct: 178 TGAPYL 183
>gnl|CDD|184448 PRK14010, PRK14010, potassium-transporting ATPase subunit B;
Provisional.
Length = 673
Score = 26.2 bits (57), Expect = 9.6
Identities = 15/64 (23%), Positives = 25/64 (39%), Gaps = 4/64 (6%)
Query: 10 LPSGQLSSVPW----RRTGVKYTNNEAYFDVIEEVDAIIDKTGSTIFSEIQGYIDCCIKL 65
LP +P+ R +GVK+T E Y + + + G I ++ + K
Sbjct: 360 LPQEVGEYIPFTAETRMSGVKFTTREVYKGAPNSMVKRVKEAGGHIPVDLDALVKGVSKK 419
Query: 66 SGMP 69
G P
Sbjct: 420 GGTP 423
>gnl|CDD|215658 pfam00017, SH2, SH2 domain.
Length = 77
Score = 24.8 bits (55), Expect = 9.6
Identities = 10/17 (58%), Positives = 11/17 (64%)
Query: 94 RWEAERILSFIPPDGNF 110
R EAER+L PDG F
Sbjct: 8 REEAERLLLNPKPDGTF 24
>gnl|CDD|241312 cd13158, PTB_APPL, Adaptor protein containing PH domain, PTB
domain, and Leucine zipper motif (APPL; also called
DCC-interacting protein (DIP)-13alpha)
Phosphotyrosine-binding (PTB) domain. APPL interacts
with oncoprotein serine/threonine kinase AKT2, tumor
suppressor protein DCC (deleted in colorectal cancer),
Rab5, GIPC (GAIP-interacting protein, C terminus), human
follicle-stimulating hormone receptor (FSHR), and the
adiponectin receptors AdipoR1 and AdipoR2. There are two
isoforms of human APPL: APPL1 and APPL2, which share
about 50% sequence identity. APPL has a BAR and a PH
domain near its N terminus, and the two domains are
thought to function as a unit (BAR-PH domain).
C-terminal to this is a PTB domain. Lipid binding assays
show that the BAR, PH, and PTB domains can bind
phospholipids. PTB domains have a common PH-like fold
and are found in various eukaryotic signaling molecules.
This domain was initially shown to binds peptides with a
NPXY motif with differing requirements for
phosphorylation of the tyrosine, although more recent
studies have found that some types of PTB domains can
bind to peptides lack tyrosine residues altogether. In
contrast to SH2 domains, which recognize phosphotyrosine
and adjacent carboxy-terminal residues, PTB-domain
binding specificity is conferred by residues
amino-terminal to the phosphotyrosine. PTB domains are
classified into three groups: phosphotyrosine-dependent
Shc-like, phosphotyrosine-dependent IRS-like, and
phosphotyrosine-independent Dab-like PTB domains.
Length = 135
Score = 25.8 bits (57), Expect = 9.8
Identities = 11/23 (47%), Positives = 14/23 (60%)
Query: 109 NFRLMSYHTRVSGSNGGRPNASC 131
N RL + R G +GGRP+ SC
Sbjct: 91 NKRLFGFVVRSRGGDGGRPSYSC 113
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
0.323 0.136 0.418
Gapped
Lambda K H
0.267 0.0696 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,354,833
Number of extensions: 759069
Number of successful extensions: 661
Number of sequences better than 10.0: 1
Number of HSP's gapped: 651
Number of HSP's successfully gapped: 35
Length of query: 164
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 74
Effective length of database: 6,945,742
Effective search space: 513984908
Effective search space used: 513984908
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 (22.0 bits)
S2: 55 (25.0 bits)