RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy918
(504 letters)
>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 = 540 bits (1394), Expect = 0.0
Identities = 237/256 (92%), Positives = 246/256 (96%)
Query: 249 VTNAVSWRSEGIKYRKNEVFLDVIESVNLLANSNGNVLRSEIVGAIKMRVYLSGMPELRL 308
VTNAVSWRSEGIKYRKNEVFLDVIESVNLL ++NGNVLRSEIVG+IKMRVYLSGMPELRL
Sbjct: 1 VTNAVSWRSEGIKYRKNEVFLDVIESVNLLVSANGNVLRSEIVGSIKMRVYLSGMPELRL 60
Query: 309 GLNDKVLFESTGRGKSKSVELEDVKFHQCVRLSRFENDRTISFIPPDGEFELMSYRLNTH 368
GLNDKVLFE+TGRGKSKSVELEDVKFHQCVRLSRFENDRTISFIPPDGEFELMSYRLNTH
Sbjct: 61 GLNDKVLFENTGRGKSKSVELEDVKFHQCVRLSRFENDRTISFIPPDGEFELMSYRLNTH 120
Query: 369 VKPLIWIESVIERFVHSRVEYMIKAKSQFKRRSTANNVEIVIPVPADADSPKFKTTIGSV 428
VKPLIWIESVIER HSRVEYMIKAKSQFKRRSTANNVEI IPVP DADSPKFKTT+GSV
Sbjct: 121 VKPLIWIESVIERHSHSRVEYMIKAKSQFKRRSTANNVEIHIPVPNDADSPKFKTTVGSV 180
Query: 429 KYTPEQSAITWTIKSFPGGKEYLMRAHFGLPSVENEDAEGKPPIQVKFEIPYFTTSGIQV 488
KY PE SAI W+IKSFPGGKEYLMRAHFGLPSVE+E+ EG+PPI VKFEIPYFTTSGIQV
Sbjct: 181 KYVPENSAIVWSIKSFPGGKEYLMRAHFGLPSVESEEKEGRPPISVKFEIPYFTTSGIQV 240
Query: 489 RYLKIIEKSGYQALPW 504
RYLKIIEKSGYQALPW
Sbjct: 241 RYLKIIEKSGYQALPW 256
>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 = 504 bits (1300), Expect = e-180
Identities = 206/259 (79%), Positives = 225/259 (86%), Gaps = 4/259 (1%)
Query: 250 TNAVSWRSEGIKYRKNEVFLDVIESVNLLANSNGNVLRSEIVGAIKMRVYLSGMPELRLG 309
TNAVSWR EGIKY+KNEVFLDVIESVNLL + NG VLRSEIVG IKMR YLSGMPEL+LG
Sbjct: 1 TNAVSWRPEGIKYKKNEVFLDVIESVNLLVDLNGQVLRSEIVGTIKMRSYLSGMPELKLG 60
Query: 310 LNDKVLFESTGRG-KSKSVELEDVKFHQCVRLSRFENDRTISFIPPDGEFELMSYRLNTH 368
LNDKVLFE+TGR K K+VELEDVKFHQCVRLSRFENDRTISFIPPDGEFELMSYRL+T
Sbjct: 61 LNDKVLFEATGRSSKGKAVELEDVKFHQCVRLSRFENDRTISFIPPDGEFELMSYRLSTQ 120
Query: 369 VKPLIWIESVIERFVHSRVEYMIKAKSQFKRRSTANNVEIVIPVPADADSPKFKTTIGSV 428
VKPLIW+E +ER SRVE M+KAK+QFKRRSTANNVEI IPVP DADSP+FK + GSV
Sbjct: 121 VKPLIWVEPTVERHSRSRVEIMVKAKTQFKRRSTANNVEIRIPVPPDADSPRFKCSAGSV 180
Query: 429 KYTPEQSAITWTIKSFPGGKEYLMRAHFGLPSVENEDA---EGKPPIQVKFEIPYFTTSG 485
Y PE+ A+ W IKSFPGGKE+ MRA FGLPS+E+E+ E K PIQVKFEIPYFT SG
Sbjct: 181 VYAPEKDALLWKIKSFPGGKEFSMRAEFGLPSIESEEEQGTEKKAPIQVKFEIPYFTVSG 240
Query: 486 IQVRYLKIIEKSGYQALPW 504
+QVRYLKIIEKSGYQALPW
Sbjct: 241 LQVRYLKIIEKSGYQALPW 259
>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 = 475 bits (1223), Expect = e-168
Identities = 213/255 (83%), Positives = 238/255 (93%)
Query: 250 TNAVSWRSEGIKYRKNEVFLDVIESVNLLANSNGNVLRSEIVGAIKMRVYLSGMPELRLG 309
TNAVSWRSEGIKY+KNEVF+DVIESVNLL N+NG+VLRSEIVGAIK++V+LSGMPELRLG
Sbjct: 1 TNAVSWRSEGIKYKKNEVFIDVIESVNLLVNANGSVLRSEIVGAIKLKVFLSGMPELRLG 60
Query: 310 LNDKVLFESTGRGKSKSVELEDVKFHQCVRLSRFENDRTISFIPPDGEFELMSYRLNTHV 369
LND+VLFE TGR K+K+VELEDVKFHQCVRLSRFENDRTISFIPPDGE ELMSYRLNT V
Sbjct: 61 LNDRVLFELTGREKNKTVELEDVKFHQCVRLSRFENDRTISFIPPDGESELMSYRLNTQV 120
Query: 370 KPLIWIESVIERFVHSRVEYMIKAKSQFKRRSTANNVEIVIPVPADADSPKFKTTIGSVK 429
KPLIWIESVIE+F HSRVE M+KAK QFK++S ANNVEI++PVP+DADSPKFKT+ GS K
Sbjct: 121 KPLIWIESVIEKFSHSRVEIMVKAKGQFKKQSVANNVEILVPVPSDADSPKFKTSTGSAK 180
Query: 430 YTPEQSAITWTIKSFPGGKEYLMRAHFGLPSVENEDAEGKPPIQVKFEIPYFTTSGIQVR 489
Y PE++ + W+IKSFPGGKEYLMRAHFGLPSVE+E+ EGKPPI VKFEIPYFT SGIQVR
Sbjct: 181 YVPEKNVVVWSIKSFPGGKEYLMRAHFGLPSVESEELEGKPPITVKFEIPYFTVSGIQVR 240
Query: 490 YLKIIEKSGYQALPW 504
Y+KIIEKSGYQALPW
Sbjct: 241 YMKIIEKSGYQALPW 255
>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 = 311 bits (800), Expect = e-104
Identities = 121/250 (48%), Positives = 165/250 (66%), Gaps = 7/250 (2%)
Query: 262 YRKNEVFLDVIESVNLLANSNGNVLRSEIVGAIKMRVYLSGMPELRLGLNDKVLFESTGR 321
YRKNEVFLDV+ESVNLL +S G VLR+++ G I M+ +LSGMPE + GLNDK++ E G+
Sbjct: 1 YRKNEVFLDVVESVNLLMSSTGTVLRADVDGVIVMKAFLSGMPECKFGLNDKLVLEKEGK 60
Query: 322 GKS------KSVELEDVKFHQCVRLSRFENDRTISFIPPDGEFELMSYRLNTHVKPLIWI 375
KS SVEL+D KFHQCVRLS+F+++RTISFIPPDGEFELM YR+ ++ +
Sbjct: 61 AKSGDKAAKGSVELDDCKFHQCVRLSKFDSERTISFIPPDGEFELMRYRITENINLPFKV 120
Query: 376 ESVIERFVHSRVEYMIKAKSQFKRRSTANNVEIVIPVPADADSPKFKTTIGSVKYTPEQS 435
+++ +++EY +K KS F + A NV + IP P + + G KY PE++
Sbjct: 121 LPLVKEVGRTKLEYKVKIKSNFPPKLFATNVVVKIPTPKNTAKVTVSVSKGKAKYDPEEN 180
Query: 436 AITWTIKSFPGGKEYLMRAHFGLPSVENEDAE-GKPPIQVKFEIPYFTTSGIQVRYLKII 494
AI W IK FPG E + A L S +E + +PPI + FE+P FT SG++VRYLK+
Sbjct: 181 AIVWKIKKFPGMTESTLSAEVELLSTTSELKKWSRPPISMDFEVPMFTASGLRVRYLKVF 240
Query: 495 EKSGYQALPW 504
EKS Y+ + W
Sbjct: 241 EKSNYKTVKW 250
>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 = 265 bits (678), Expect = 4e-86
Identities = 110/243 (45%), Positives = 149/243 (61%), Gaps = 15/243 (6%)
Query: 266 EVFLDVIESVNLLANSNGNVLRSEIVGAIKMRVYLSGMPELRLGLNDKVLFESTGRGKSK 325
EVFLDVIE VNLL + +G++L SE+VG I ++ +LSGMPE+RLGLN+ +
Sbjct: 1 EVFLDVIEKVNLLISKDGSLLNSEVVGEIALKSFLSGMPEIRLGLNNPDV---------- 50
Query: 326 SVELEDVKFHQCVRLSRFENDRTISFIPPDGEFELMSYRLN-THVKPLIWIESVIERFVH 384
++L+DV FH CVRL RFE++R ISFIPPDGEFELMSYR I I V+
Sbjct: 51 GIKLDDVSFHPCVRLKRFESERIISFIPPDGEFELMSYRTVLEEPILPITIFPVV-SEEG 109
Query: 385 SRVEYMIKAKSQFKRRSTANNVEIVIPVPADADSPKFKTTIGSVKYTPEQSAITWTIKSF 444
R+E +K K + TA NVE+ IP+P+ S K + G K+ PE++A+ W IK
Sbjct: 110 GRLEVTVKLKLSESLQLTAENVEVHIPLPSGVTSLSSKPSDGQAKFDPEKNALVWRIKRI 169
Query: 445 P-GGKEYLMRAHFGLPSVENEDAEGKPPIQVKFEIPYFTTSGIQVRYLKIIEKS--GYQA 501
P GGKE + A F L + +E E PP+ + FEIP T SGIQVR L++ ++ G+
Sbjct: 170 PVGGKEQSLSATFELGGLAHECPEEAPPVSLSFEIPETTGSGIQVRSLQVFDEKNPGHDP 229
Query: 502 LPW 504
+ W
Sbjct: 230 IKW 232
>gnl|CDD|216199 pfam00928, Adap_comp_sub, Adaptor complexes medium subunit family.
This family also contains members which are coatomer
subunits.
Length = 228
Score = 256 bits (655), Expect = 6e-83
Identities = 108/255 (42%), Positives = 136/255 (53%), Gaps = 44/255 (17%)
Query: 253 VSWRSEGIKYRKNEVFLDVIESVNLLANSNGNVLRSEIVGAIKMRVYLSGMPELRLGLND 312
V WR GIKY+KNEVFLDVIE V+++ + +G +L SEI G I + YLSGMPEL LGLND
Sbjct: 1 VPWRPSGIKYKKNEVFLDVIERVSVIVDKDGGILNSEIQGTIDCKCYLSGMPELTLGLND 60
Query: 313 KVLFESTGRGKSKSVELEDVKFHQCVRLSRFENDRTISFIPPDGEFELMSYRLNTHVKPL 372
+ +EL+DV FH CVRLSRFE++R ISFIPPDGEF LMSYR++++V
Sbjct: 61 PLNIGKIASSG-NGIELDDVSFHPCVRLSRFESERVISFIPPDGEFTLMSYRISSNVPLP 119
Query: 373 IWIESVIERFVHSRVEYMIKAKSQFKRRSTANNVEIVIPVPADADSPKFKTTIGSVKYTP 432
+ SP + G KY P
Sbjct: 120 FKVNP----------------------------------------SPVLTVSDGKAKYDP 139
Query: 433 EQSAITWTIKSFPGGKEYLMRAHFGLPSVENEDA--EGKPPIQVKFEIPYFTTSGIQVRY 490
E++A+ WTI PGGKE + L S + PPI V+F IP FT SG++VR
Sbjct: 140 EENALEWTIGKIPGGKEPTLSGELELSSTSESPSKDWSFPPISVEFSIPGFTASGLKVRS 199
Query: 491 LKIIE-KSGYQALPW 504
LKI E KS Y+ W
Sbjct: 200 LKISEPKSNYKPYKW 214
>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 = 220 bits (562), Expect = 2e-68
Identities = 98/249 (39%), Positives = 150/249 (60%), Gaps = 6/249 (2%)
Query: 256 RSEGIKYRKNEVFLDVIESVNLLANSNGNVLRSEIVGAIKMRVYLSGMPELRLGLNDKVL 315
+ + +KNE+F+DV+E ++++ ++NG VL SEI G+I+M+ YLSG PELRL LN+ ++
Sbjct: 2 KPRSSQDKKNEIFVDVLERLSVVFSANGQVLNSEIDGSIQMKSYLSGNPELRLALNEDLV 61
Query: 316 F-ESTGRGKSKSVELEDVKFHQCVRLSRFENDRTISFIPPDGEFELMSYRLNTHVKPLIW 374
+ R S +V L+D FH+CV L FE+DRT+S PPDGEF LM+YR++ KP
Sbjct: 62 IGKRENRAYSSAVVLDDCNFHECVDLEEFESDRTLSLTPPDGEFTLMNYRISGEFKPPFR 121
Query: 375 IESVIERFVHSRVEYMIKAKSQFKRRSTANNVEIVIPVPADADSPKFKTTIG----SVKY 430
+ +E ++E ++K ++ F + TA NV + IP+P S + + G S +Y
Sbjct: 122 VFPSVEETSPYKLELVLKLRADFPPKVTATNVVVRIPLPKGTSSASCELSSGASGQSAEY 181
Query: 431 TPEQSAITWTIKSFPGGKEYLMRAHFGLPSVENEDAEGK-PPIQVKFEIPYFTTSGIQVR 489
++ + W IK FPGG E+ +R L S + PI + FEIP + SG+QV+
Sbjct: 182 KEKEKRVVWNIKKFPGGTEHSLRIKITLSSPIPSAVRKEIGPISLTFEIPMYNVSGLQVK 241
Query: 490 YLKIIEKSG 498
YL+I EKS
Sbjct: 242 YLRISEKSS 250
>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 = 166 bits (422), Expect = 4e-48
Identities = 84/245 (34%), Positives = 125/245 (51%), Gaps = 19/245 (7%)
Query: 253 VSWRSEGIKYRKNEVFLDVIESVNLLANSNGNVLRSEIVGAIKMRVYLSGMPELRLGLND 312
V WR G+KY NE+++DV+E ++ + + +G + E+ G+I LSGMP+L L LN+
Sbjct: 1 VPWRRAGVKYTNNEIYVDVVEEIDAIVDKSGKPVSGEVSGSIDCNSRLSGMPDLTLSLNN 60
Query: 313 KVLFESTGRGKSKSVELEDVKFHQCVRLSRFENDRTISFIPPDGEFELMSYR--LNTHVK 370
L L+D FH CVRLSR+E+DR +SFIPPDG+F LMSYR LN+ V+
Sbjct: 61 PGL-------------LDDPSFHPCVRLSRWESDRVLSFIPPDGKFTLMSYRVDLNSLVQ 107
Query: 371 PLIWIESVIE-RFVHSRVEYMIKAKSQFKRRSTANNVEIVIPVPADADSPKFKTTIGSVK 429
++++ I R E + + T NV + IP+P S + + G+
Sbjct: 108 LPVYVKPQISLGKGGGRFEISVGPRG--NLGKTIENVVVEIPLPKGVKSLRLTASHGTFS 165
Query: 430 YTPEQSAITWTIKSFPGGKEYLMRAHFGLPSVENEDAEGKPPIQVKFEIPYFTTSGIQVR 489
+ + W+I GK +R L S E P I V F+IP + SG++V
Sbjct: 166 FDSSTKTLVWSIGKLTPGKTPTLRGSISLES-GEEAPSEPPSISVSFKIPGYLPSGLKVD 224
Query: 490 YLKII 494
L I
Sbjct: 225 SLDIY 229
>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 = 114 bits (287), Expect = 2e-28
Identities = 71/291 (24%), Positives = 111/291 (38%), Gaps = 53/291 (18%)
Query: 256 RSEGIKYRKNEVFLDVIESVNLLANSNGNVLRSEIVGAIKMRVYLSGMPELRLGLNDKVL 315
R G+ YR++E+ +DV++ G +L+ + I +++GMPE LGLND
Sbjct: 2 RDRGLTYREDEITVDVVDEFRGKVTKEGEILKQAVRVRIFCLAFVTGMPECELGLNDIQR 61
Query: 316 F--ESTGRG------KSKSVELEDVKFHQCVRLSRFENDRTISFIPPDG-EFELMSYRLN 366
E R + ++LE+V+FH CV FE R I F P D FELM +R+
Sbjct: 62 KGREVVRRQDIIPVSTEEWIKLENVEFHSCVNKDEFEQSRVIKFHPLDACRFELMRFRVR 121
Query: 367 THVK---PLIW--IESVIERFVHSRVEYMIKAKSQFKRRS--TANNVEIVIPVP------ 413
+ PL + SV V R + ++ + N+ I PVP
Sbjct: 122 PPRERELPLTVKSVVSVKGAHVELRADLLVPGYTSRNPLGQVPCENIMIRFPVPEEWVYL 181
Query: 414 --------------------------ADADSPKFKTTIGSVKYTPEQSAITWTIKSFPG- 446
P + ++G+ KY AI W I P
Sbjct: 182 FRVEKHFRYKSLKSKKKRPGKIKSARELLSPPLIEVSVGTAKYEHAYRAIVWRIPRLPEK 241
Query: 447 ----GKEYLMRAHFGLPSVENEDAEGKPPIQVKFEIPYFTTSGIQVRYLKI 493
+L+ L S + + P +V+F +P T S VR + +
Sbjct: 242 NSAAYTPHLLSCRLELASDDEIPSSFYPHAEVEFTMPSTTASKTTVRSISV 292
>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 = 107 bits (269), Expect = 1e-26
Identities = 69/246 (28%), Positives = 118/246 (47%), Gaps = 21/246 (8%)
Query: 253 VSWRSEGIKYRKNEVFLDVIESVNLLANSNGNVLRSEIVGAIKMRVYLSGMPELRLGLND 312
+ WR G+KY NE + DV+E ++ + + +G+ + +EI G I + LSGMP+L L +
Sbjct: 1 IPWRRAGVKYTNNEAYFDVVEEIDAIIDKSGSTVFAEIQGVIDACIKLSGMPDLSLSFMN 60
Query: 313 KVLFESTGRGKSKSVELEDVKFHQCVRLSRFENDRTISFIPPDGEFELMSYRLNTH--VK 370
L L+DV FH C+R R+E++R +SFIPPDG F L+SYR+++ V
Sbjct: 61 PRL-------------LDDVSFHPCIRFKRWESERVLSFIPPDGNFRLISYRVSSQNLVA 107
Query: 371 PLIWIE---SVIERFVHSRVEYMIKAKSQFKRRSTANNVEIVIPVPADADSPKFKTTIGS 427
++++ S E R + I K + T + + + +P + T GS
Sbjct: 108 IPVYVKHLISFKENSSCGRFDITIGPKQNMGK--TIEGITVTVHMPKVVLNMNLTPTQGS 165
Query: 428 VKYTPEQSAITWTIKSFPGGKEYLMRAHFGLPSVENEDAEGKPPIQVKFEIPYFTTSGIQ 487
+ P + W + K ++ L S + E P + ++F+I SG++
Sbjct: 166 YTFDPVTKVLAWDVGKITPQKLPSLKGLVNLQSGAPKPEE-NPSLNIQFKIQQLAISGLK 224
Query: 488 VRYLKI 493
V L +
Sbjct: 225 VNRLDM 230
>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 = 104 bits (261), Expect = 2e-25
Identities = 70/246 (28%), Positives = 117/246 (47%), Gaps = 21/246 (8%)
Query: 253 VSWRSEGIKYRKNEVFLDVIESVNLLANSNGNVLRSEIVGAIKMRVYLSGMPELRLGLND 312
V WR G+KY NE + DVIE ++ + + +G+ + +EI G I V L+GMP+L L +
Sbjct: 1 VPWRRTGVKYTNNEAYFDVIEEIDAIIDKSGSTITAEIQGVIDACVKLTGMPDLTLSFMN 60
Query: 313 KVLFESTGRGKSKSVELEDVKFHQCVRLSRFENDRTISFIPPDGEFELMSYRLNTH--VK 370
L L+DV FH CVR R+E++R +SFIPPDG F L+SY ++ V
Sbjct: 61 PRL-------------LDDVSFHPCVRFKRWESERILSFIPPDGNFRLLSYHVSAQNLVA 107
Query: 371 PLIWIESVI---ERFVHSRVEYMIKAKSQFKRRSTANNVEIVIPVPADADSPKFKTTIGS 427
++++ I E R E + K + T V + +P + + G+
Sbjct: 108 IPVYVKHNISFREGSSLGRFEITLGPKQTMGK--TVEGVTVTSQMPKGVLNMSLTPSQGT 165
Query: 428 VKYTPEQSAITWTIKSFPGGKEYLMRAHFGLPSVENEDAEGKPPIQVKFEIPYFTTSGIQ 487
+ P ++W + K ++ L + ++ E P I ++F+I SG++
Sbjct: 166 YTFDPVTKLLSWDVGKINPQKLPSLKGSMSLQAGASKPDE-NPTINLQFKIQQLAISGLK 224
Query: 488 VRYLKI 493
V L +
Sbjct: 225 VNRLDM 230
>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 = 77.9 bits (192), Expect = 8e-16
Identities = 67/284 (23%), Positives = 107/284 (37%), Gaps = 53/284 (18%)
Query: 262 YRKNEVFLDVIESVNLLANSNGNVLRSEIVGAIKMRVYLSGMPELRLGLNDKVL------ 315
Y + E+ L++++ + G V+ S ++ I +++ E L LND L
Sbjct: 8 YEEQELSLEIVDHFWGRVDKEGKVMESSVITQIHCLCFVNAPAECFLTLNDLELQKRDED 67
Query: 316 FESTGRGKSKSVELEDVKFHQCVRLSRFENDRTISFIPPDG-EFELMSYR--LNTHVKPL 372
+ GK +E+ D FH+CV F R I F PPD FELM ++ N P
Sbjct: 68 YFEKEAGK-LWIEILDYHFHKCVNAQEFHQSRLIKFCPPDACRFELMRFKTRYNGGDLPF 126
Query: 373 IWIESVIERFVHSRVEYMIKAKSQFKRRSTAN------NVEIVIPVPA------------ 414
V+ + + ++ + F A NVEI PVPA
Sbjct: 127 SVKAMVVVQGAYVELQAFLNMAPTFPTFGVAGSLPYCENVEIRFPVPAQWVKALWTMSLQ 186
Query: 415 -------------------DADS-PKFKTTIGSVKYTPEQSAITWTIKSFPGGKEYLMRA 454
+A+S P + ++G+ KY A+ W I P +
Sbjct: 187 RQRSLKAKMNRRACLGSALEAESEPVIQVSVGTAKYENAYRAVVWKIDRLPDKNSAVDHP 246
Query: 455 H-----FGLPSVENEDAEGKPPIQVKFEIPYFTTSGIQVRYLKI 493
H L S + ++ P V+FE+ SG +V+ L I
Sbjct: 247 HSLSCKLELGSDQEIPSDWYPFATVEFEVEDTCASGTRVKSLGI 290
>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 = 72.3 bits (177), Expect = 7e-14
Identities = 69/295 (23%), Positives = 118/295 (40%), Gaps = 55/295 (18%)
Query: 259 GIKYRKNEVFLDVIESVN-LLANSNGNVLRSEIVGAIKMRVYLSGMPELRLGLNDKVL-- 315
G+ Y + E+ +DV + + +L+ + +L+ ++ I + +LSG+ E RLGLND ++
Sbjct: 5 GLNYTEEEITVDVRDEFHGILSKGDSRILQHSVLTRIYILSFLSGLAECRLGLNDILIKG 64
Query: 316 FESTGRG------KSKSVELEDVKFHQCVRLSRFENDRTISFIPPDG-EFELMSYRLNTH 368
E R +K ++L + +FH+CV F N R I F P D FELM +R
Sbjct: 65 NEVVARQDIMPTTTTKWIQLHECRFHECVDEDMFNNSRAILFNPLDACRFELMRFRTVFA 124
Query: 369 VKPLIWIESVIERFVHSRVE---YMIKAKSQFKRRST-----ANNVEIVIPVPAD----- 415
K L + + VE +++ + R NV I PVP +
Sbjct: 125 EKTLPFTLRTAACVNGAEVEVQSWLVMSTGFSSNRDPLTQVPCENVMIRYPVPEEWVKNF 184
Query: 416 ---------------------------ADSPKFKTTIGSVKYTPEQSAITWTIKSFPG-- 446
P + T+G+ KY +++ W I P
Sbjct: 185 RRESVLGEKSLKAKVNKGASFGSTSLSGSEPAMRVTLGTAKYEHAFNSVVWRINRLPDKN 244
Query: 447 ---GKEYLMRAHFGLPSVENEDAEGKPPIQVKFEIPYFTTSGIQVRYLKIIEKSG 498
G + H L S + ++V+F++P + S VR L + +K+
Sbjct: 245 SASGHPHCFFCHLELGSDREVPSSFVCHVEVEFDMPTASASKAAVRSLSVEDKTD 299
>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 = 52.4 bits (126), Expect = 1e-07
Identities = 45/218 (20%), Positives = 87/218 (39%), Gaps = 32/218 (14%)
Query: 289 EIVGAIKMRVYLSGMPELRLGLNDKVLFESTGRGKSKSVELEDVKFHQCVR-----LSRF 343
+ G++ + L G+P++ + L+ + L+++ H CV+ + F
Sbjct: 37 SVFGSVTCKAELEGLPDVTVSLS----------LPANGSPLQNIIVHPCVQSVDTGMLAF 86
Query: 344 ENDRTISFIPPDGEFELMSYR-LNTHVKPLIWIESVIERFVHSRVEYMIKAKSQFKRRST 402
+ F PP G F+L Y + P+ + H ++ +K + K ++
Sbjct: 87 SGPYKLRFSPPLGNFQLCHYTSQSVPEPPIKGFYQMKGEENHVKILIQLKLHEKVK--NS 144
Query: 403 ANNVEIVIPVPADADSPKFKTT--IGSVKYTPEQSAITWTI-KSFPGGKEYLMRA--HFG 457
E+ IP + T +G VK + ++ + W I + FP E + +FG
Sbjct: 145 FEYCEVHIPFFNRGLIVHVEATPSVGQVKVSKDKRLLVWNIGQKFPKSLEATLSGTVNFG 204
Query: 458 LPSVENEDAEGKPP-------IQVKFEIPYFTTSGIQV 488
S +NE P +++ F+I FT SG +
Sbjct: 205 --SEQNEADVEDPFCTGLNAYVKLSFKISDFTLSGCSI 240
>gnl|CDD|110234 pfam01217, Clat_adaptor_s, Clathrin adaptor complex small chain.
Length = 142
Score = 36.9 bits (86), Expect = 0.006
Identities = 26/136 (19%), Positives = 59/136 (43%), Gaps = 5/136 (3%)
Query: 102 ALYILDVKGKVLISRNY---RGDVEMGVIEKFMPLLMEKEEEGMLTPLLQTSDCTFAYIK 158
A+ I + +GK +++ Y + +IE+ L+ ++ + ++ ++ +D Y +
Sbjct: 4 AILIFNRQGKPRLAKWYTPYSDPEQQKLIEQIYALISARKPK--MSNFIEFNDLKVIYKR 61
Query: 159 YNNLFIVSTTKKNANIALVFVFLNKIVRVFTEYFKEIEEESIRDNFVVIYELLDELIDFG 218
Y L+ V N ++ +++ V YF + E + NF +Y +LDE++ G
Sbjct: 62 YATLYFVVIVDDQDNELIILELIHRFVESLDRYFGNVCELDLIFNFEKVYLILDEMVMGG 121
Query: 219 YPQTTDSKILQEYITQ 234
T + +
Sbjct: 122 EILETSKNEVLHRVAL 137
>gnl|CDD|211365 cd09254, AP_delta-COPI_MHD, Mu homology domain (MHD) of adaptor
protein (AP) coat protein I (COPI) delta subunit. COPI
complex-coated vesicles function in the early secretory
pathway. They mediate the retrograde transport from the
Golgi to the ER, and intra-Golgi transport. COPI
complex-coated vesicles consist of a small GTPase,
ADP-ribosylation factor 1 (ARF1) and a heteroheptameric
coatomer composed of two subcomplexes, F-COPI and
B-COPI. ARF1 regulates COPI vesicle formation by
recruiting the coatomer onto Golgi membranes to initiate
its coat function. Coatomer complexes then bind cargo
molecules and self-assemble to form spherical cages that
yield COPI-coated vesicles. The heterotetrameric F-COPI
subcomplex contains beta-, gamma-, delta-, and zeta-COP
subunits, where beta- and gamma-COP subunits are related
to the large AP subunits, and delta- and zeta-COP
subunits are related to the medium and small AP
subunits, respectively. Due to the sequence similarity
to the AP complexes, the F-COPI subcomplex might play a
role in the cargo-binding. The heterotrimeric B-COPI
contains alpha-, beta-, and epsilon-COP subunits, which
are not related to the adaptins. This subcomplex is
thought to participate in the cage-forming and might
serve a function similar to that of clathrin. This
family corresponds to the mu homology domain of
delta-subunit of COPI complex (delta-COP), which is
distantly related to the C-terminal domain of mu chains
among AP complexes. The delta-COP subunit appears
tightly associated with the beta-COP subunit to confer
its interaction with ARF1. In addition, both delta- and
beta-COP subunits contribute to a common binding site
for arginine (R)-based signals, which are sorting motifs
conferring transient endoplasmic reticulum (ER)
localization to unassembled subunits of multimeric
membrane proteins.
Length = 232
Score = 33.4 bits (77), Expect = 0.18
Identities = 34/187 (18%), Positives = 70/187 (37%), Gaps = 31/187 (16%)
Query: 267 VFLDVIESVNLLANSNGNVLRSEIVGAIKMRVYLSGMPELRLGLNDKVLFESTGRGKSKS 326
V + V E ++ + +G + E+ G + +R+ + ++++ L + K
Sbjct: 3 VHITVEEKISATLSRDGGLESLEVKGTLSLRINDEELAKIKIQLAN---------NDDKG 53
Query: 327 VELEDVKFHQCVRLSRFENDRTISFIPPDGEF------ELMSYRLNTHVKPLI------W 374
+ K H V F +D + P F ++ +RL + + L+ W
Sbjct: 54 FQF---KTHPNVDKKLFTSDSVLGLKDPSKPFPVNDPVGVLKWRLQSKDESLLPLTINCW 110
Query: 375 IESVIERFVHSRVEYMIKAKSQFKRRSTANNVEIVIPVPADADSPKFKTTIGSVKYTPEQ 434
S +EY + N+V I IP+P+ +P + G +Y +
Sbjct: 111 P-SESGGGTDVTIEYELNRDDL-----ELNDVVISIPLPS-GSAPVVNSDDGEYEYDGRK 163
Query: 435 SAITWTI 441
+ + W I
Sbjct: 164 NGLIWKI 170
>gnl|CDD|215653 pfam00009, GTP_EFTU, Elongation factor Tu GTP binding domain. This
domain contains a P-loop motif, also found in several
other families such as pfam00071, pfam00025 and
pfam00063. Elongation factor Tu consists of three
structural domains, this plus two C-terminal beta barrel
domains.
Length = 184
Score = 30.2 bits (69), Expect = 1.8
Identities = 15/55 (27%), Positives = 25/55 (45%), Gaps = 6/55 (10%)
Query: 168 TKKNANIAL-----VFVFLNKIVRVFTEYFKEIEEESIRDNFVVIYELLDELIDF 217
T+++ +A + VF+NKI RV +E+ EE I + Y E +
Sbjct: 107 TREHLLLAKTLGVPIIVFINKIDRVDDAELEEVVEE-ISRELLEKYGFGGETVPV 160
>gnl|CDD|227363 COG5030, APS2, Clathrin adaptor complex, small subunit
[Intracellular trafficking and secretion].
Length = 152
Score = 29.3 bits (66), Expect = 2.5
Identities = 17/88 (19%), Positives = 38/88 (43%)
Query: 146 LLQTSDCTFAYIKYNNLFIVSTTKKNANIALVFVFLNKIVRVFTEYFKEIEEESIRDNFV 205
++ + Y +Y L+ V + N ++ ++ V + +F + E + NF
Sbjct: 49 FIEGKNEKIVYRRYATLYFVFGVDNDDNELIILELIHNFVEILDRFFGNVCELDLIFNFQ 108
Query: 206 VIYELLDELIDFGYPQTTDSKILQEYIT 233
+Y +LDE+I G + + E++
Sbjct: 109 KVYAILDEMILGGEIIESSKNEVLEHVY 136
>gnl|CDD|226132 COG3604, FhlA, Transcriptional regulator containing GAF, AAA-type
ATPase, and DNA binding domains [Transcription / Signal
transduction mechanisms].
Length = 550
Score = 30.4 bits (69), Expect = 2.8
Identities = 39/206 (18%), Positives = 74/206 (35%), Gaps = 32/206 (15%)
Query: 95 LFIMSASALYILDVKGKVLISRNYRGDVEMGVIEKFMPLLMEKEEEGMLTPLLQT----- 149
LF ASAL LD K + ++ + +G ++F+ E +L +L+
Sbjct: 63 LFGCDASALLRLDSKNLIPLATDGLSKDHLGREQRFV-----VEGHPLLEQILKAGRPLV 117
Query: 150 ---SDCTFAYIKYNNLFIVSTTKKNANIALVFVFLNKIV------RVFTEYFKEIEEESI 200
+D F L KK+A I + +K++ + F E +E +
Sbjct: 118 FHPADSLFPDPYDGLLPDTEGNKKHACIGVPLKSGDKLIGALTLDHTEPDQFDEDLDEEL 177
Query: 201 RDNFVVIYELLDELIDFGYPQTTDSKILQEYITQEGHKLEIQPRIPMAVTNAVSWRSEGI 260
R L L + +L ++ +LE + + V GI
Sbjct: 178 R--------FLAALAAL----AVANALLHRELSSLKERLEEENLALEEQLSEVVLEVGGI 225
Query: 261 KYRKNEVFLDVIESVNLLANSNGNVL 286
R + +++ + ++A S+ VL
Sbjct: 226 IGR-SPAMRQLLKEIEVVAKSDSTVL 250
>gnl|CDD|220677 pfam10291, muHD, Muniscin C-terminal mu homology domain. The
muniscins are a family of endocytic adaptors that is
conserved from yeast to humans.This C-terminal domain is
structurally similar to mu homology domains, and is the
region of the muniscin proteins involved in the
interactions with the endocytic adaptor-scaffold
proteins Ede1-eps15. This interaction influences
muniscin localisation. The muniscins provide a combined
adaptor-membrane-tubulation activity that is important
for regulating endocytosis.
Length = 251
Score = 29.2 bits (66), Expect = 4.6
Identities = 30/131 (22%), Positives = 52/131 (39%), Gaps = 14/131 (10%)
Query: 363 YRLNTHVKPLIWIESV--IERFVHS-RVEYMIKAKSQFKRRSTANNVEIVIPV-PADADS 418
Y++++ PLI + V E S ++Y + N+ + + + + S
Sbjct: 98 YQVHSASCPLI-LHPVWKCEPHQTSLILDYKLNPSPASSSSLVLLNLVVSVNLDGSRVTS 156
Query: 419 PKFKTTIGSVKYTPEQSAITWTIKSF---PGGKEYLMRAHFGLPSVENEDAEGKPPIQVK 475
+ K + E++ ITW + G E + A F E +E +QVK
Sbjct: 157 AQSKP---QGTFNKEKNRITWRLPEPLVLSDGGEGKLIARF---MTEGGGSEKPGGVQVK 210
Query: 476 FEIPYFTTSGI 486
FEI T SG+
Sbjct: 211 FEIEGPTLSGL 221
>gnl|CDD|235212 PRK04043, tolB, translocation protein TolB; Provisional.
Length = 419
Score = 29.2 bits (66), Expect = 5.5
Identities = 18/52 (34%), Positives = 24/52 (46%), Gaps = 12/52 (23%)
Query: 389 YMIKAKSQFKRRSTANNVEIVIPVPADADSPKFKTTIGSV---KYTPEQSAI 437
Y+I S + RR TAN V P+F + GS+ KY QSA+
Sbjct: 352 YLISTNSDYIRRLTANGVNQF---------PRFSSDGGSIMFIKYLGNQSAL 394
>gnl|CDD|206647 cd00881, GTP_translation_factor, GTP translation factor family
primarily contains translation initiation, elongation
and release factors. The GTP translation factor family
consists primarily of translation initiation,
elongation, and release factors, which play specific
roles in protein translation. In addition, the family
includes Snu114p, a component of the U5 small nuclear
riboprotein particle which is a component of the
spliceosome and is involved in excision of introns,
TetM, a tetracycline resistance gene that protects the
ribosome from tetracycline binding, and the unusual
subfamily CysN/ATPS, which has an unrelated function
(ATP sulfurylase) acquired through lateral transfer of
the EF1-alpha gene and development of a new function.
Length = 183
Score = 28.4 bits (64), Expect = 6.4
Identities = 15/41 (36%), Positives = 22/41 (53%), Gaps = 5/41 (12%)
Query: 163 FIVSTTKKNANIAL-----VFVFLNKIVRVFTEYFKEIEEE 198
+ T+++ NIAL + V +NKI RV E F E+ E
Sbjct: 98 GVEPQTREHLNIALAGGLPIIVAVNKIDRVGEEDFDEVLRE 138
>gnl|CDD|205203 pfam13022, HTH_Tnp_1_2, Helix-turn-helix of insertion element
transposase. This is a family of largely phage proteins
which are likely to be a helix-turn-helix insertion
elements.
Length = 139
Score = 27.9 bits (62), Expect = 7.4
Identities = 29/108 (26%), Positives = 47/108 (43%), Gaps = 24/108 (22%)
Query: 233 TQEGHKLEIQPRIPMAVTNAVSWRSEGIKYRKNEVFLDVIESVNLLANSNGNVLRSEIVG 292
TQE E+ + + WR+ +N+ F I N LA+S + RSE+
Sbjct: 36 TQE----ELANELGINRMTLYEWRT------QNQDF---IAYKNELADSFLSEKRSEVYS 82
Query: 293 AIKMRVYLSGMPEL--------RLGL--NDKVLFESTGRGKSKSVELE 330
+ MR+ L P + R GL + KV+ ++TG + E+E
Sbjct: 83 QL-MRLILGPQPSVKAIDLFMRRYGLLTDKKVIEDNTGTATKTNAEIE 129
>gnl|CDD|114268 pfam05537, DUF759, Borrelia burgdorferi protein of unknown function
(DUF759). This family consists of several
uncharacterized proteins from the Lyme disease
spirochete Borrelia burgdorferi.
Length = 439
Score = 28.9 bits (64), Expect = 7.5
Identities = 23/84 (27%), Positives = 40/84 (47%), Gaps = 3/84 (3%)
Query: 207 IYELLDELIDFGYPQTTDSKILQEYITQEGHKLEIQPRIPMAVTNAVSWRSEGIKYRKNE 266
++LL ++ FG +K+ E +TQEG KL++ P I ++S GI + N+
Sbjct: 278 AFDLLKKIDGFGDKYIEAAKMALELLTQEGAKLDLDPEITKIADLFKDFKSFGIMGKSND 337
Query: 267 VFL---DVIESVNLLANSNGNVLR 287
D+ ++ L + NVL
Sbjct: 338 AEQAEDDLADAEQTLKDLTNNVLD 361
>gnl|CDD|153083 cd00576, RNR_PFL, Ribonucleotide reductase and Pyruvate formate
lyase. Ribonucleotide reductase (RNR) and pyruvate
formate lyase (PFL) are believed to have diverged from a
common ancestor. They have a structurally similar
ten-stranded alpha-beta barrel domain that hosts the
active site, and are radical enzymes. RNRs are found in
all organisms and provide the only mechanism by which
nucleotides are converted to deoxynucleotides. RNRs are
separated into three classes based on their
metallocofactor usage. Class I RNRs use a diiron-tyrosyl
radical while Class II RNRs use coenzyme B12
(adenosylcobalamin, AdoCbl). Class III RNRs use an FeS
cluster and S-adenosylmethionine to generate a glycyl
radical. PFL, an essential enzyme in anaerobic bacteria,
catalyzes the conversion of pyruvate and CoA to
acteylCoA and formate in a mechanism that uses a glycyl
radical.
Length = 401
Score = 28.7 bits (64), Expect = 7.8
Identities = 23/135 (17%), Positives = 43/135 (31%), Gaps = 22/135 (16%)
Query: 101 SALYILDVKGKVLISRNYRGDVEMG------------VIEKFMPLLMEKEEEGMLTPLLQ 148
A ++ K + N R G + ++F+ L + EG+
Sbjct: 100 EAADAFNLALKEVGQGNGRTGAATGFIGGVHKGKGDKISQEFLNLALANGGEGIPLNFPN 159
Query: 149 TS---DCTFAYIKYNNL----FIVSTTKKNANIALVFVFLNKIVRVFTEYFKEIEEESIR 201
S I + I +K + + L +V + I E++I
Sbjct: 160 LSVRVSSDKPGILVKAVELKQLIAEEARKTGSPGIFNDELCNLVSLN---LARIMEKAIN 216
Query: 202 DNFVVIYELLDELID 216
+ V+ E L+EL
Sbjct: 217 GSMDVVLEELEELAF 231
>gnl|CDD|211377 cd09266, SGIP1_MHD, mu-homology domain (MHD) of Scr homology 3
(SH3)-domain growth factor receptor-bound 2 (GRB2)-like
(endophilin) interacting protein 1 (also known as
endophilin-3-interacting protein, SGIP1) and similar
proteins. This family corresponds to the MHD found in
mammalian neuronal-specific transcript SGIP1 and similar
proteins. Unlike other members in this family, SGIP1
does not contain EFC/F-BAR domain, but does have a
proline-rich domain (PRD) and a C-terminal MHD. It is an
endophilin-interacting protein that plays an obligatory
role in the regulation of energy homeostasis, and is
also involved in clathrin-mediated endocytosis by
interacting with phospholipids and eps15.
Length = 261
Score = 28.5 bits (63), Expect = 7.9
Identities = 27/90 (30%), Positives = 39/90 (43%), Gaps = 12/90 (13%)
Query: 404 NNVEIVIPVPADADSPKFKTTIGSVKYTPEQSAITWTI-----KSFPGGKEYLMRAHFGL 458
NNV+ ++PV D K + + + EQ I W I KS GG L+ A F L
Sbjct: 161 NNVQFLVPV--DGGVTKLQAVLPPAVWNAEQQRILWKIPDISQKSENGGVGSLL-ARFQL 217
Query: 459 PSVENEDAEGKPPIQVKFEIPYFTTSGIQV 488
++ A P+ V+F T SG +
Sbjct: 218 SEGPSKPA----PLAVQFTSEGSTLSGCDI 243
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 0.136 0.392
Gapped
Lambda K H
0.267 0.0630 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 25,832,817
Number of extensions: 2548346
Number of successful extensions: 1974
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1948
Number of HSP's successfully gapped: 37
Length of query: 504
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 403
Effective length of database: 6,457,848
Effective search space: 2602512744
Effective search space used: 2602512744
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: 61 (27.5 bits)