RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17767
(64 letters)
>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 = 72.2 bits (178), Expect = 2e-17
Identities = 29/49 (59%), Positives = 36/49 (73%), Gaps = 2/49 (4%)
Query: 1 MAGMKETQLSAEIELLETDT-KKKWTRPPISMNFEVP-FAPSGFKVSHL 47
GM E+ LSAE+ELL T + KKW+RPPISM+FEVP F SG +V +L
Sbjct: 189 FPGMTESTLSAEVELLSTTSELKKWSRPPISMDFEVPMFTASGLRVRYL 237
>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 = 42.8 bits (101), Expect = 1e-06
Identities = 18/50 (36%), Positives = 24/50 (48%), Gaps = 1/50 (2%)
Query: 2 AGMKETQLSAEIELLETDTKKKWTRPPISMNFEVP-FAPSGFKVSHLSEI 50
G KE LSA EL + PP+S++FE+P SG +V L
Sbjct: 171 VGGKEQSLSATFELGGLAHECPEEAPPVSLSFEIPETTGSGIQVRSLQVF 220
>gnl|CDD|216199 pfam00928, Adap_comp_sub, Adaptor complexes medium subunit family.
This family also contains members which are coatomer
subunits.
Length = 228
Score = 41.3 bits (97), Expect = 4e-06
Identities = 22/47 (46%), Positives = 27/47 (57%), Gaps = 3/47 (6%)
Query: 1 MAGMKETQLSAEIELLET--DTKKKWTRPPISMNFEVP-FAPSGFKV 44
+ G KE LS E+EL T K W+ PPIS+ F +P F SG KV
Sbjct: 151 IPGGKEPTLSGELELSSTSESPSKDWSFPPISVEFSIPGFTASGLKV 197
>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 = 38.7 bits (91), Expect = 3e-05
Identities = 16/51 (31%), Positives = 24/51 (47%), Gaps = 4/51 (7%)
Query: 1 MAGMKETQLSAEIEL---LETDTKKKWTRPPISMNFEVP-FAPSGFKVSHL 47
G KE + AE L + + + PI + FE+P F SG +V +L
Sbjct: 196 FPGGKEFSMRAEFGLPSIESEEEQGTEKKAPIQVKFEIPYFTVSGLQVRYL 246
>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 = 33.7 bits (77), Expect = 0.002
Identities = 20/49 (40%), Positives = 29/49 (59%), Gaps = 1/49 (2%)
Query: 3 GMKETQLSAEIELLETDTKKKWTRPPISMNFEVP-FAPSGFKVSHLSEI 50
G KE + A L ++++K RPPIS+ FE+P F SG +V +L I
Sbjct: 198 GGKEYLMRAHFGLPSVESEEKEGRPPISVKFEIPYFTTSGIQVRYLKII 246
>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 = 30.4 bits (68), Expect = 0.031
Identities = 15/49 (30%), Positives = 28/49 (57%), Gaps = 1/49 (2%)
Query: 3 GMKETQLSAEIELLETDTKKKWTRPPISMNFEVPFAP-SGFKVSHLSEI 50
G KE + A L ++++ +PPI++ FE+P+ SG +V ++ I
Sbjct: 197 GGKEYLMRAHFGLPSVESEELEGKPPITVKFEIPYFTVSGIQVRYMKII 245
>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 = 28.3 bits (64), Expect = 0.20
Identities = 11/22 (50%), Positives = 16/22 (72%), Gaps = 1/22 (4%)
Query: 27 PPISMNFEVP-FAPSGFKVSHL 47
P IS++F++P + PSG KV L
Sbjct: 205 PSISVSFKIPGYLPSGLKVDSL 226
>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 = 27.9 bits (63), Expect = 0.22
Identities = 10/21 (47%), Positives = 15/21 (71%), Gaps = 1/21 (4%)
Query: 28 PISMNFEVP-FAPSGFKVSHL 47
PIS+ FE+P + SG +V +L
Sbjct: 223 PISLTFEIPMYNVSGLQVKYL 243
>gnl|CDD|130391 TIGR01324, cysta_beta_ly_B, cystathionine beta-lyase, bacterial.
This model represents cystathionine beta-lyase
(alternate name: beta-cystathionase), one of several
pyridoxal-dependent enzymes of cysteine, methionine, and
homocysteine metabolism. This enzyme is involved in the
biosynthesis of Met from Cys [Amino acid biosynthesis,
Aspartate family].
Length = 377
Score = 27.5 bits (61), Expect = 0.33
Identities = 11/40 (27%), Positives = 22/40 (55%)
Query: 15 LLETDTKKKWTRPPISMNFEVPFAPSGFKVSHLSEILILL 54
L++ +TK + P S+ FE+ P+ K + I+I++
Sbjct: 131 LIQPNTKVLFLEAPSSITFEIQDIPAIAKAARNPGIVIMI 170
>gnl|CDD|237042 PRK12291, PRK12291, apolipoprotein N-acyltransferase; Reviewed.
Length = 418
Score = 25.3 bits (56), Expect = 2.1
Identities = 12/24 (50%), Positives = 14/24 (58%)
Query: 31 MNFEVPFAPSGFKVSHLSEILILL 54
+N E+ F S F VS LS LI L
Sbjct: 134 LNPEIFFVYSYFDVSKLSLALIFL 157
>gnl|CDD|223150 COG0072, PheT, Phenylalanyl-tRNA synthetase beta subunit
[Translation, ribosomal structure and biogenesis].
Length = 650
Score = 24.5 bits (54), Expect = 4.0
Identities = 8/21 (38%), Positives = 10/21 (47%)
Query: 11 AEIELLETDTKKKWTRPPISM 31
EI+L +KK PIS
Sbjct: 539 FEIDLDALLKRKKPAYKPISK 559
>gnl|CDD|232989 TIGR00471, pheT_arch, phenylalanyl-tRNA synthetase, beta subunit.
Every known example of the phenylalanyl-tRNA synthetase,
except the monomeric form of mitochondrial, is an alpha
2 beta 2 heterotetramer. The beta subunits break into
two subfamilies that are considerably different in
sequence, length, and pattern of gaps. This model
represents the subfamily that includes the beta subunit
from eukaryotic cytosol, the Archaea, and spirochetes
[Protein synthesis, tRNA aminoacylation].
Length = 551
Score = 24.3 bits (53), Expect = 5.3
Identities = 8/18 (44%), Positives = 11/18 (61%)
Query: 27 PPISMNFEVPFAPSGFKV 44
P + NFE+ F S F+V
Sbjct: 528 PEVLTNFELEFPVSAFEV 545
>gnl|CDD|184977 PRK15016, PRK15016, isochorismate synthase EntC; Provisional.
Length = 391
Score = 23.7 bits (51), Expect = 8.8
Identities = 14/35 (40%), Positives = 17/35 (48%), Gaps = 3/35 (8%)
Query: 28 PISMNFEVPFAPSGFKVSHLSEILILLLSPEGPGF 62
P+S NF VP A G + E LLL +G F
Sbjct: 176 PVSYNFHVPLADGGVLLGASPE---LLLRKDGERF 207
>gnl|CDD|177688 PLN00057, PLN00057, proliferating cell nuclear antigen;
Provisional.
Length = 263
Score = 23.5 bits (51), Expect = 8.9
Identities = 12/33 (36%), Positives = 19/33 (57%)
Query: 28 PISMNFEVPFAPSGFKVSHLSEILILLLSPEGP 60
P+S+ F + + S K + LS+ + L LS E P
Sbjct: 202 PVSLTFALRYLNSFTKATPLSDTVTLSLSKELP 234
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
0.314 0.134 0.391
Gapped
Lambda K H
0.267 0.0665 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,235,361
Number of extensions: 220381
Number of successful extensions: 119
Number of sequences better than 10.0: 1
Number of HSP's gapped: 118
Number of HSP's successfully gapped: 15
Length of query: 64
Length of database: 10,937,602
Length adjustment: 35
Effective length of query: 29
Effective length of database: 9,385,212
Effective search space: 272171148
Effective search space used: 272171148
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: 42 (21.9 bits)
S2: 53 (24.3 bits)