RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17615
(459 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 = 374 bits (962), Expect = e-129
Identities = 172/277 (62%), Positives = 213/277 (76%), Gaps = 30/277 (10%)
Query: 187 VPWRRTGVKYTNNEAYFDVIEEVDAIIDKTGSTIFSEIQGYIDCCIKLSGMPDLTLSFMN 246
VPWRRTGVKYTNNEAYFDVIEE+DAIIDK+GSTI +EIQG ID C+KL+GMPDLTLSFMN
Sbjct: 1 VPWRRTGVKYTNNEAYFDVIEEIDAIIDKSGSTITAEIQGVIDACVKLTGMPDLTLSFMN 60
Query: 247 PRLFDDVSFHPCVRFKRWEAERILSFIPPDGNFRLMSYHINTQNLVAIPLYINHNINFK- 305
PRL DDVSFHPCVRFKRWE+ERILSFIPPDGNFRL+SYH++ QNLVAIP+Y+ HNI+F+
Sbjct: 61 PRLLDDVSFHPCVRFKRWESERILSFIPPDGNFRLLSYHVSAQNLVAIPVYVKHNISFRE 120
Query: 306 ---QNKIDMTIGPKQTIGRTIENIVIEIPMPSVVLNCTLLQNQGKYTFDPIKKILTWDLH 362
+ ++T+GPKQT+G+T+E + + MP VLN +L
Sbjct: 121 GSSLGRFEITLGPKQTMGKTVEGVTVTSQMPKGVLNMSL--------------------- 159
Query: 363 STERSGDQGKYTFDPIKKILTWDVGRIDIENKLPNIRGSFTVQSGQENHNFNLTINVKFT 422
+ QG YTFDP+ K+L+WDVG+I+ + KLP+++GS ++Q+G + N TIN++F
Sbjct: 160 ----TPSQGTYTFDPVTKLLSWDVGKINPQ-KLPSLKGSMSLQAGASKPDENPTINLQFK 214
Query: 423 INQLAISGLKVNRLDMYGEKYKPFKGVKYITTGGTFQ 459
I QLAISGLKVNRLDMYGEKYKPFKG+KY+T G FQ
Sbjct: 215 IQQLAISGLKVNRLDMYGEKYKPFKGIKYMTKAGKFQ 251
>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 = 360 bits (925), Expect = e-124
Identities = 172/277 (62%), Positives = 208/277 (75%), Gaps = 30/277 (10%)
Query: 187 VPWRRTGVKYTNNEAYFDVIEEVDAIIDKTGSTIFSEIQGYIDCCIKLSGMPDLTLSFMN 246
+PWRR GVKYTNNEAYFDV+EE+DAIIDK+GST+F+EIQG ID CIKLSGMPDL+LSFMN
Sbjct: 1 IPWRRAGVKYTNNEAYFDVVEEIDAIIDKSGSTVFAEIQGVIDACIKLSGMPDLSLSFMN 60
Query: 247 PRLFDDVSFHPCVRFKRWEAERILSFIPPDGNFRLMSYHINTQNLVAIPLYINHNINFKQ 306
PRL DDVSFHPC+RFKRWE+ER+LSFIPPDGNFRL+SY +++QNLVAIP+Y+ H I+FK+
Sbjct: 61 PRLLDDVSFHPCIRFKRWESERVLSFIPPDGNFRLISYRVSSQNLVAIPVYVKHLISFKE 120
Query: 307 N----KIDMTIGPKQTIGRTIENIVIEIPMPSVVLNCTLLQNQGKYTFDPIKKILTWDLH 362
N + D+TIGPKQ +G+TIE I + + MP VVLN L
Sbjct: 121 NSSCGRFDITIGPKQNMGKTIEGITVTVHMPKVVLNMNL--------------------- 159
Query: 363 STERSGDQGKYTFDPIKKILTWDVGRIDIENKLPNIRGSFTVQSGQENHNFNLTINVKFT 422
+ QG YTFDP+ K+L WDVG+I KLP+++G +QSG N ++N++F
Sbjct: 160 ----TPTQGSYTFDPVTKVLAWDVGKI-TPQKLPSLKGLVNLQSGAPKPEENPSLNIQFK 214
Query: 423 INQLAISGLKVNRLDMYGEKYKPFKGVKYITTGGTFQ 459
I QLAISGLKVNRLDMYGEKYKPFKGVKYIT G FQ
Sbjct: 215 IQQLAISGLKVNRLDMYGEKYKPFKGVKYITKAGKFQ 251
>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 = 344 bits (885), Expect = e-118
Identities = 128/274 (46%), Positives = 174/274 (63%), Gaps = 28/274 (10%)
Query: 187 VPWRRTGVKYTNNEAYFDVIEEVDAIIDKTGSTIFSEIQGYIDCCIKLSGMPDLTLSFMN 246
VPWRR GVKYTNNE Y DV+EE+DAI+DK+G + E+ G IDC +LSGMPDLTLS N
Sbjct: 1 VPWRRAGVKYTNNEIYVDVVEEIDAIVDKSGKPVSGEVSGSIDCNSRLSGMPDLTLSLNN 60
Query: 247 PRLFDDVSFHPCVRFKRWEAERILSFIPPDGNFRLMSYHINTQNLVAIPLYINHNINFKQ 306
P L DD SFHPCVR RWE++R+LSFIPPDG F LMSY ++ +LV +P+Y+ I+ +
Sbjct: 61 PGLLDDPSFHPCVRLSRWESDRVLSFIPPDGKFTLMSYRVDLNSLVQLPVYVKPQISLGK 120
Query: 307 NK--IDMTIGPKQTIGRTIENIVIEIPMPSVVLNCTLLQNQGKYTFDPIKKILTWDLHST 364
++++GP+ +G+TIEN+V+EIP+P V + L
Sbjct: 121 GGGRFEISVGPRGNLGKTIENVVVEIPLPKGVKSLRL----------------------- 157
Query: 365 ERSGDQGKYTFDPIKKILTWDVGRIDIENKLPNIRGSFTVQSGQENHNFNLTINVKFTIN 424
+ G ++FD K L W +G++ K P +RGS +++SG+E + +I+V F I
Sbjct: 158 --TASHGTFSFDSSTKTLVWSIGKLT-PGKTPTLRGSISLESGEEAPSEPPSISVSFKIP 214
Query: 425 QLAISGLKVNRLDMYGEKYKPFKGVKYITTGGTF 458
SGLKV+ LD+Y EKYKPFKGVKYIT G +
Sbjct: 215 GYLPSGLKVDSLDIYNEKYKPFKGVKYITKAGKY 248
>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 = 214 bits (548), Expect = 3e-67
Identities = 87/264 (32%), Positives = 132/264 (50%), Gaps = 35/264 (13%)
Query: 200 EAYFDVIEEVDAIIDKTGSTIFSEIQGYIDCCIKLSGMPDLTLSFMNP---RLFDDVSFH 256
E + DVIE+V+ +I K GS + SE+ G I LSGMP++ L NP DDVSFH
Sbjct: 1 EVFLDVIEKVNLLISKDGSLLNSEVVGEIALKSFLSGMPEIRLGLNNPDVGIKLDDVSFH 60
Query: 257 PCVRFKRWEAERILSFIPPDGNFRLMSYHINTQNLVAIPLYINHNINFKQNKIDMTIGPK 316
PCVR KR+E+ERI+SFIPPDG F LMSY +P+ I ++ + ++++T+ K
Sbjct: 61 PCVRLKRFESERIISFIPPDGEFELMSYRTVL-EEPILPITIFPVVSEEGGRLEVTVKLK 119
Query: 317 QTIGR--TIENIVIEIPMPSVVLNCTLLQNQGKYTFDPIKKILTWDLHSTERSGDQGKYT 374
+ T EN+ + IP+PS V + + + G+
Sbjct: 120 LSESLQLTAENVEVHIPLPSGVTSLSSKPS-------------------------DGQAK 154
Query: 375 FDPIKKILTWDVGRIDIENKLPNIRGSFTVQSG-QENHNFNLTINVKFTINQLAISGLKV 433
FDP K L W + RI + K ++ +F + E +++ F I + SG++V
Sbjct: 155 FDPEKNALVWRIKRIPVGGKEQSLSATFELGGLAHECPEEAPPVSLSFEIPETTGSGIQV 214
Query: 434 NRLDMYGEK---YKPFKGVKYITT 454
L ++ EK + P K V+Y T
Sbjct: 215 RSLQVFDEKNPGHDPIKWVRYSTH 238
>gnl|CDD|216199 pfam00928, Adap_comp_sub, Adaptor complexes medium subunit family.
This family also contains members which are coatomer
subunits.
Length = 228
Score = 207 bits (528), Expect = 2e-64
Identities = 98/290 (33%), Positives = 129/290 (44%), Gaps = 82/290 (28%)
Query: 187 VPWRRTGVKYTNNEAYFDVIEEVDAIIDKTGSTIFSEIQGYIDCCIKLSGMPDLTLSFMN 246
VPWR +G+KY NE + DVIE V I+DK G + SEIQG IDC LSGMP+LTL +
Sbjct: 1 VPWRPSGIKYKKNEVFLDVIERVSVIVDKDGGILNSEIQGTIDCKCYLSGMPELTLGLND 60
Query: 247 PRLF------------DDVSFHPCVRFKRWEAERILSFIPPDGNFRLMSYHINTQNLVAI 294
P DDVSFHPCVR R+E+ER++SFIPPDG F LMSY I++ V +
Sbjct: 61 PLNIGKIASSGNGIELDDVSFHPCVRLSRFESERVISFIPPDGEFTLMSYRISSN--VPL 118
Query: 295 PLYINHNINFKQNKIDMTIGPKQTIGRTIENIVIEIPMPSVVLNCTLLQNQGKYTFDPIK 354
P +N + L + GK +DP +
Sbjct: 119 PFKVN-------------------------------------PSPVLTVSDGKAKYDPEE 141
Query: 355 KILTWDLHSTERSGDQGKYTFDPIKKILTWDVGRIDIENKLPNIRGSFTVQSGQE---NH 411
L W + G+I K P + G + S E
Sbjct: 142 NALEWTI-------------------------GKIP-GGKEPTLSGELELSSTSESPSKD 175
Query: 412 NFNLTINVKFTINQLAISGLKVNRLDMYG--EKYKPFKGVKYITTGGTFQ 459
I+V+F+I SGLKV L + YKP+K V+Y+T G +Q
Sbjct: 176 WSFPPISVEFSIPGFTASGLKVRSLKISEPKSNYKPYKWVRYVTKSGKYQ 225
>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 = 151 bits (385), Expect = 7e-43
Identities = 92/294 (31%), Positives = 133/294 (45%), Gaps = 48/294 (16%)
Query: 185 SSVPWRRTGVKYTNNEAYFDVIEEVDAIIDKTGSTIFSEIQGYIDCCIKLSGMPDLTLSF 244
++V WR G+KY NE + DVIE V+ ++D G + SEI G I LSGMP+L L
Sbjct: 2 NAVSWRPEGIKYKKNEVFLDVIESVNLLVDLNGQVLRSEIVGTIKMRSYLSGMPELKLGL 61
Query: 245 MNPRL---------------FDDVSFHPCVRFKRWEAERILSFIPPDGNFRLMSYHINTQ 289
N ++ +DV FH CVR R+E +R +SFIPPDG F LMSY ++TQ
Sbjct: 62 -NDKVLFEATGRSSKGKAVELEDVKFHQCVRLSRFENDRTISFIPPDGEFELMSYRLSTQ 120
Query: 290 N--LVAI-PLYINHNINFKQNKIDMTIGPKQTIGR--TIENIVIEIPMPSVVLNCTLLQN 344
L+ + P H ++++++ + K R T N+ I IP+P + +
Sbjct: 121 VKPLIWVEPTVERH----SRSRVEIMVKAKTQFKRRSTANNVEIRIPVPPDADSPRFKCS 176
Query: 345 QGKYTFDPIKKILTWDLHSTERSGDQGKYTFDPIKKILTWDVGRIDIENKLPNIRGSFTV 404
G + P K L W + S G F + E LP+I
Sbjct: 177 AGSVVYAPEKDALLWKIKSF-----PGGKEF------------SMRAEFGLPSIE----S 215
Query: 405 QSGQENHNFNLTINVKFTINQLAISGLKVNRLDMYGE-KYKPFKGVKYITTGGT 457
+ Q I VKF I +SGL+V L + + Y+ V+YIT G
Sbjct: 216 EEEQGTEKKAP-IQVKFEIPYFTVSGLQVRYLKIIEKSGYQALPWVRYITQSGD 268
>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 = 139 bits (352), Expect = 3e-38
Identities = 80/293 (27%), Positives = 129/293 (44%), Gaps = 61/293 (20%)
Query: 196 YTNNEAYFDVIEEVDAIIDKTGSTIFSEIQGYIDCCIKLSGMPDLTLSFMNPRL------ 249
Y NE + DV+E V+ ++ TG+ + +++ G I LSGMP+ +N +L
Sbjct: 1 YRKNEVFLDVVESVNLLMSSTGTVLRADVDGVIVMKAFLSGMPECKFG-LNDKLVLEKEG 59
Query: 250 --------------FDDVSFHPCVRFKRWEAERILSFIPPDGNFRLMSYHINTQNLVAIP 295
DD FH CVR ++++ER +SFIPPDG F LM Y I T+N + +P
Sbjct: 60 KAKSGDKAAKGSVELDDCKFHQCVRLSKFDSERTISFIPPDGEFELMRYRI-TEN-INLP 117
Query: 296 LYINHNIN-FKQNKIDMTIGPKQTIGRTI--ENIVIEIPMPSVVLNCTLLQNQGKYTFDP 352
+ + + K++ + K + N+V++IP P T+ ++GK +DP
Sbjct: 118 FKVLPLVKEVGRTKLEYKVKIKSNFPPKLFATNVVVKIPTPKNTAKVTVSVSKGKAKYDP 177
Query: 353 IKKILTWDLHSTERSGDQGKYTFDPIKKILTWDVGRIDIENKLPNIRGSFTVQSGQENHN 412
+ + W IKK G E+ L S V+
Sbjct: 178 EENAIVWK-----------------IKKF----PG--MTESTL-----SAEVELLSTTSE 209
Query: 413 FNLT----INVKFTINQLAISGLKVNRLDMYGEK--YKPFKGVKYITTGGTFQ 459
I++ F + SGL+V L ++ EK YK K V+YIT G+++
Sbjct: 210 LKKWSRPPISMDFEVPMFTASGLRVRYLKVF-EKSNYKTVKWVRYITRAGSYE 261
>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 = 125 bits (315), Expect = 6e-33
Identities = 93/295 (31%), Positives = 134/295 (45%), Gaps = 50/295 (16%)
Query: 185 SSVPWRRTGVKYTNNEAYFDVIEEVDAIIDKTGSTIFSEIQGYIDCCIKLSGMPDLTLSF 244
++V WR G+KY NE + DVIE V+ ++ G+ + SEI G I + LSGMP+L L
Sbjct: 3 NAVSWRSEGIKYRKNEVFLDVIESVNLLVSANGNVLRSEIVGSIKMRVYLSGMPELRLGL 62
Query: 245 MNPRLFD-------------DVSFHPCVRFKRWEAERILSFIPPDGNFRLMSYHINTQ-- 289
+ LF+ DV FH CVR R+E +R +SFIPPDG F LMSY +NT
Sbjct: 63 NDKVLFENTGRGKSKSVELEDVKFHQCVRLSRFENDRTISFIPPDGEFELMSYRLNTHVK 122
Query: 290 NLVAIPLYINHNINFKQNKIDMTIGPKQTIGR--TIENIVIEIPMPSVVLNCTLLQNQGK 347
L+ I I + ++++ I K R T N+ I IP+P+ + G
Sbjct: 123 PLIWIESVIERH---SHSRVEYMIKAKSQFKRRSTANNVEIHIPVPNDADSPKFKTTVGS 179
Query: 348 YTFDPIKKILTWDLHSTERSGDQGKYTFDPIKKILTWDVGRIDIENKLPNIRGSFTVQSG 407
+ P + W + S F K+ L +R F + S
Sbjct: 180 VKYVPENSAIVWSIKS-----------FPGGKEYL---------------MRAHFGLPSV 213
Query: 408 Q-ENHNFNLTINVKFTINQLAISGLKVNRLDMYGEK--YKPFKGVKYITTGGTFQ 459
+ E I+VKF I SG++V L + EK Y+ V+YIT G +Q
Sbjct: 214 ESEEKEGRPPISVKFEIPYFTTSGIQVRYLKII-EKSGYQALPWVRYITQNGDYQ 267
>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 = 124 bits (312), Expect = 1e-32
Identities = 87/289 (30%), Positives = 133/289 (46%), Gaps = 44/289 (15%)
Query: 185 SSVPWRRTGVKYTNNEAYFDVIEEVDAIIDKTGSTIFSEIQGYIDCCIKLSGMPDLTLSF 244
++V WR G+KY NE + DVIE V+ +++ GS + SEI G I + LSGMP+L L
Sbjct: 2 NAVSWRSEGIKYKKNEVFIDVIESVNLLVNANGSVLRSEIVGAIKLKVFLSGMPELRLGL 61
Query: 245 MNPRLF-------------DDVSFHPCVRFKRWEAERILSFIPPDGNFRLMSYHINTQNL 291
+ LF +DV FH CVR R+E +R +SFIPPDG LMSY +NTQ
Sbjct: 62 NDRVLFELTGREKNKTVELEDVKFHQCVRLSRFENDRTISFIPPDGESELMSYRLNTQ-- 119
Query: 292 VAIPLYINHNI-NFKQNKIDMTIGPKQTIGR--TIENIVIEIPMPSVVLNCTLLQNQGKY 348
V ++I I F +++++ + K + N+ I +P+PS + + G
Sbjct: 120 VKPLIWIESVIEKFSHSRVEIMVKAKGQFKKQSVANNVEILVPVPSDADSPKFKTSTGSA 179
Query: 349 TFDPIKKILTWDLHSTERSGDQGKYTFDPIKKILTWDVGRIDIENKLPNIRGSFTVQSGQ 408
+ P K ++ W + S G + V ++E K P
Sbjct: 180 KYVPEKNVVVWSIKSFP-----GGKEYLMRAHFGLPSVESEELEGKPP------------ 222
Query: 409 ENHNFNLTINVKFTINQLAISGLKVNRLDMYGEK-YKPFKGVKYITTGG 456
I VKF I +SG++V + + + Y+ V+YIT G
Sbjct: 223 --------ITVKFEIPYFTVSGIQVRYMKIIEKSGYQALPWVRYITQSG 263
>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 = 103 bits (260), Expect = 4e-25
Identities = 65/283 (22%), Positives = 113/283 (39%), Gaps = 57/283 (20%)
Query: 198 NNEAYFDVIEEVDAIIDKTGSTIFSEIQGYIDCCIK--LSGMPDLTLSFMNPRLF----- 250
NE + DV+E + + G + SEI G I +K LSG P+L L+ +
Sbjct: 10 KNEIFVDVLERLSVVFSANGQVLNSEIDGSIQ--MKSYLSGNPELRLALNEDLVIGKREN 67
Query: 251 ---------DDVSFHPCVRFKRWEAERILSFIPPDGNFRLMSYHINTQNLVAIPLYINHN 301
DD +FH CV + +E++R LS PPDG F LM+Y I + P + +
Sbjct: 68 RAYSSAVVLDDCNFHECVDLEEFESDRTLSLTPPDGEFTLMNYRI-SGEF-KPPFRVFPS 125
Query: 302 I-NFKQNKIDMTIGPKQTI--GRTIENIVIEIPMPSVVLNCTLLQNQGKYTFDPIKKILT 358
+ K+++ + + T N+V+ IP+P + +
Sbjct: 126 VEETSPYKLELVLKLRADFPPKVTATNVVVRIPLPKGTSSAS------------------ 167
Query: 359 WDLHSTERSGDQGKYTFDPIKKILTWDVGRI--DIENKLPNIRGSFTVQSGQENHNFNLT 416
+ +K + W++ + E+ ++R T+ S +
Sbjct: 168 ---CELSSGASGQSAEYKEKEKRVVWNIKKFPGGTEH---SLRIKITLSS--PIPSAVRK 219
Query: 417 ----INVKFTINQLAISGLKVNRLDMYGE--KYKPFKGVKYIT 453
I++ F I +SGL+V L + + Y P + V+YIT
Sbjct: 220 EIGPISLTFEIPMYNVSGLQVKYLRISEKSSSYNPHRWVRYIT 262
>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 = 63.1 bits (154), Expect = 6e-11
Identities = 37/175 (21%), Positives = 66/175 (37%), Gaps = 30/175 (17%)
Query: 190 RRTGVKYTNNEAYFDVIEEVDAIIDKTGSTIFSEIQGYIDCCIKLSGMPDLTLSFMNPRL 249
R G+ Y +E DV++E + K G + ++ I C ++GMP+ L + +
Sbjct: 2 RDRGLTYREDEITVDVVDEFRGKVTKEGEILKQAVRVRIFCLAFVTGMPECELGLNDIQR 61
Query: 250 ---------------------FDDVSFHPCVRFKRWEAERILSFIPPDGN-FRLMSYHIN 287
++V FH CV +E R++ F P D F LM + +
Sbjct: 62 KGREVVRRQDIIPVSTEEWIKLENVEFHSCVNKDEFEQSRVIKFHPLDACRFELMRFRVR 121
Query: 288 TQNLVAIPLYINHNINFKQNKIDM--------TIGPKQTIGRTIENIVIEIPMPS 334
+PL + ++ K +++ ENI+I P+P
Sbjct: 122 PPRERELPLTVKSVVSVKGAHVELRADLLVPGYTSRNPLGQVPCENIMIRFPVPE 176
>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 = 47.7 bits (114), Expect = 5e-06
Identities = 30/104 (28%), Positives = 46/104 (44%), Gaps = 11/104 (10%)
Query: 202 YFDVIEEVDAII-DKTGSTIFSEIQGYIDCCIKLSGMPDLTLSFMNP---RLFDDVSFHP 257
F + E V A DK + G + C +L G+PD+T+S P ++ HP
Sbjct: 15 DFKITETVKAAQYDKDDIPDVWSVFGSVTCKAELEGLPDVTVSLSLPANGSPLQNIIVHP 74
Query: 258 CVR-----FKRWEAERILSFIPPDGNFRLMSYHINTQNLVAIPL 296
CV+ + L F PP GNF+L Y +Q++ P+
Sbjct: 75 CVQSVDTGMLAFSGPYKLRFSPPLGNFQLCHY--TSQSVPEPPI 116
>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 = 42.5 bits (100), Expect = 3e-04
Identities = 35/174 (20%), Positives = 62/174 (35%), Gaps = 42/174 (24%)
Query: 196 YTNNEAYFDVIEEVDAIIDKTGSTIFSEIQGYIDCCIKLSG-------MPDLTLSFMNPR 248
Y E ++++ +DK G + S + I C ++ + DL L +
Sbjct: 8 YEEQELSLEIVDHFWGRVDKEGKVMESSVITQIHCLCFVNAPAECFLTLNDLELQKRDED 67
Query: 249 LFD-----------DVSFHPCVRFKRWEAERILSFIPPDG-NFRLMSY--HINTQNL--- 291
F+ D FH CV + + R++ F PPD F LM + N +L
Sbjct: 68 YFEKEAGKLWIEILDYHFHKCVNAQEFHQSRLIKFCPPDACRFELMRFKTRYNGGDLPFS 127
Query: 292 -----------VAIPLYINHNINFKQNKIDMTIGPKQTIGRTIENIVIEIPMPS 334
V + ++N F + ++ EN+ I P+P+
Sbjct: 128 VKAMVVVQGAYVELQAFLNMAPTFPTFGVAGSL-------PYCENVEIRFPVPA 174
>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 = 39.5 bits (93), Expect = 0.002
Identities = 49/247 (19%), Positives = 92/247 (37%), Gaps = 59/247 (23%)
Query: 205 VIEEVDAIIDKTGSTIFSEIQGYI--------DCCIKLSGMPDLTLSFMNPRLFDDVSF- 255
V E++ A + + G E++G + IK+ + F
Sbjct: 7 VEEKISATLSRDGGLESLEVKGTLSLRINDEELAKIKIQ---------LANNDDKGFQFK 57
Query: 256 -HPCVRFKRWEAERILSFIPPDGNFR------LMSYHINTQNLVAIPLYINHNINFKQNK 308
HP V K + ++ +L P F ++ + + +++ +PL IN +
Sbjct: 58 THPNVDKKLFTSDSVLGLKDPSKPFPVNDPVGVLKWRLQSKDESLLPLTINCWPSESGGG 117
Query: 309 IDMTI--GPKQTIGRTIENIVIEIPMPSVVLNCTLLQNQGKYTFDPIKKILTWDLHSTER 366
D+TI + + ++VI IP+PS +
Sbjct: 118 TDVTIEYELNRDDL-ELNDVVISIPLPSG--------------------------SAPVV 150
Query: 367 SGDQGKYTFDPIKKILTWDVGRIDIENKLPNIRGSFTVQSGQENHNFNLTINVKFTINQL 426
+ D G+Y +D K L W + ID N ++ F++ + E+ F I+V FT ++
Sbjct: 151 NSDDGEYEYDGRKNGLIWKIPLIDASNSSGSL--EFSIAASDEDDFF--PISVSFTSSKT 206
Query: 427 AISGLKV 433
G+KV
Sbjct: 207 -FCGVKV 212
>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 = 34.5 bits (79), Expect = 0.088
Identities = 29/118 (24%), Positives = 42/118 (35%), Gaps = 29/118 (24%)
Query: 193 GVKYTNNEAYFDVIEEVDAIIDKTGSTI-----------FSEIQGYIDCCIKLSG----- 236
G+ YT E DV +E I+ K S I S + G +C + L+
Sbjct: 5 GLNYTEEEITVDVRDEFHGILSKGDSRILQHSVLTRIYILSFLSGLAECRLGLNDILIKG 64
Query: 237 ---------MPDLTLSFMNPRLFDDVSFHPCVRFKRWEAERILSFIPPDG-NFRLMSY 284
MP T ++ + FH CV + R + F P D F LM +
Sbjct: 65 NEVVARQDIMPTTTTKWIQLH---ECRFHECVDEDMFNNSRAILFNPLDACRFELMRF 119
>gnl|CDD|227363 COG5030, APS2, Clathrin adaptor complex, small subunit
[Intracellular trafficking and secretion].
Length = 152
Score = 33.2 bits (76), Expect = 0.12
Identities = 20/64 (31%), Positives = 32/64 (50%), Gaps = 2/64 (3%)
Query: 59 VYRK--GVFFVAVTMSEVPPLFVIEFLDRVVTTFHDYFNDCSESVLKDNYVVVYEILDEM 116
VYR+ ++FV ++ L ++E + V +F + E L N+ VY ILDEM
Sbjct: 58 VYRRYATLYFVFGVDNDDNELIILELIHNFVEILDRFFGNVCELDLIFNFQKVYAILDEM 117
Query: 117 LDNG 120
+ G
Sbjct: 118 ILGG 121
>gnl|CDD|183698 PRK12715, flgK, flagellar hook-associated protein FlgK;
Provisional.
Length = 649
Score = 34.3 bits (78), Expect = 0.14
Identities = 29/104 (27%), Positives = 50/104 (48%), Gaps = 11/104 (10%)
Query: 143 IANTMTGGSNVSSILPSGQLSSVPWRRTGGS------NVSSILPS-GQLSSVPWRRTGVK 195
IAN T G + SI Q + + R GS +VSSI + Q ++ R T
Sbjct: 25 IANFKTRGYSRQSI----QFTPIASNRYAGSYIGAGVSVSSIYRNVDQFANAQVRSTLSY 80
Query: 196 YTNNEAYFDVIEEVDAIIDKTGSTIFSEIQGYIDCCIKLSGMPD 239
T +A+++ ++D ++ + GS+I +Q + D +L+ PD
Sbjct: 81 RTQYDAFYNQAIQIDKLLSQDGSSISVPLQTFFDSIGQLNSTPD 124
>gnl|CDD|110234 pfam01217, Clat_adaptor_s, Clathrin adaptor complex small chain.
Length = 142
Score = 32.3 bits (74), Expect = 0.22
Identities = 34/148 (22%), Positives = 59/148 (39%), Gaps = 28/148 (18%)
Query: 1 MIHSLFIINSTSDIILEKHWKRIISRSVCDYFFEAQNSVAKP---EDIPPIITTPHHYLI 57
MI ++ I N L K ++ + + E I +I+ +
Sbjct: 1 MIKAILIFNRQGKPRLAK-------------WYTPYSDPEQQKLIEQIYALISARKPKMS 47
Query: 58 S---------VYRK--GVFFVAVTMSEVPPLFVIEFLDRVVTTFHDYFNDCSESVLKDNY 106
+ +Y++ ++FV + + L ++E + R V + YF + E L N+
Sbjct: 48 NFIEFNDLKVIYKRYATLYFVVIVDDQDNELIILELIHRFVESLDRYFGNVCELDLIFNF 107
Query: 107 VVVYEILDEMLDNGFPLATESN-VLKEL 133
VY ILDEM+ G L T N VL +
Sbjct: 108 EKVYLILDEMVMGGEILETSKNEVLHRV 135
>gnl|CDD|224579 COG1665, COG1665, Predicted nucleotidyltransferase [General
function prediction only].
Length = 315
Score = 32.8 bits (75), Expect = 0.30
Identities = 18/81 (22%), Positives = 35/81 (43%), Gaps = 3/81 (3%)
Query: 100 SVLKDNYVVVYEILDEMLDNGFPLATESNVLKELIKPPNILRTIANTMTGGSNVSSILPS 159
S+ K + + E E L + + S+V + +++P L I + + S +I+
Sbjct: 55 SLFKIAFRFLEESHPEYLRSVVHVVPLSDV-ERILRPEERLEEILESPSSESKARAIVEF 113
Query: 160 GQLSSVPWRRTGGSNVSSILP 180
+ + VP G + SIL
Sbjct: 114 LEDAGVPVNSMGVT--GSILL 132
>gnl|CDD|227828 COG5541, RET3, Vesicle coat complex COPI, zeta subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 187
Score = 32.2 bits (73), Expect = 0.31
Identities = 18/77 (23%), Positives = 34/77 (44%), Gaps = 2/77 (2%)
Query: 64 VFFVAVTMSEVPPLFVIEFLDRVVTTFHDYFNDCS-ESVLKDNYVVVYEILDEMLDNGFP 122
V V+ E F+ + D + + + + +NY + ++DE +D G
Sbjct: 79 VLLYIVSPMEENEPFLGQVFDEIRAALILIVKTPTDKRNVWENYDQIVLLVDETIDEGVI 138
Query: 123 LATESN-VLKELIKPPN 138
L T+S+ + + KPPN
Sbjct: 139 LETKSDEIADRVPKPPN 155
>gnl|CDD|203973 pfam08542, Rep_fac_C, Replication factor C C-terminal domain. This
is the C-terminal domain of RFC (replication factor-C)
protein of the clamp loader complex which binds to the
DNA sliding clamp (proliferating cell nuclear antigen,
PCNA). The five modules of RFC assemble into a
right-handed spiral, which results in only three of the
five RFC subunits (RFC-A, RFC-B and RFC-C) making
contact with PCNA, leaving a wedge-shaped gap between
RFC-E and the PCNA clamp-loader complex. The C-terminal
is vital for the correct orientation of RFC-E with
respect to RFC-A.
Length = 89
Score = 29.4 bits (67), Expect = 1.0
Identities = 11/35 (31%), Positives = 18/35 (51%), Gaps = 3/35 (8%)
Query: 99 ESVLKDNYVVVYEILDEMLDNGFPLATESNVLKEL 133
+S+LK ++ E L E+L G +LK+L
Sbjct: 13 DSILKGDFDEARETLYELLVEGISAED---ILKQL 44
>gnl|CDD|218871 pfam06046, Sec6, Exocyst complex component Sec6. Sec6 is a
component of the multiprotein exocyst complex. Sec6
interacts with Sec8, Sec10 and Exo70.These exocyst
proteins localise to regions of active exocytosis-at the
growing ends of interphase cells and in the medial
region of cells undergoing cytokinesis-in an
F-actin-dependent and exocytosis- independent manner.
Length = 557
Score = 30.4 bits (69), Expect = 2.5
Identities = 9/31 (29%), Positives = 16/31 (51%)
Query: 83 LDRVVTTFHDYFNDCSESVLKDNYVVVYEIL 113
++++V T DY ND E + + + E L
Sbjct: 391 MEQIVETIEDYLNDYQEYLHPPLFQELLEEL 421
>gnl|CDD|226086 COG3556, COG3556, Predicted membrane protein [Function unknown].
Length = 150
Score = 28.6 bits (64), Expect = 3.8
Identities = 11/35 (31%), Positives = 20/35 (57%), Gaps = 2/35 (5%)
Query: 155 SILPSGQLSSVPWRRTGGSNVSSILPSGQLSSVPW 189
SI+P+ + + W R +N S ++ G+L+SV
Sbjct: 93 SIIPT--VRFLSWNRQLKANPSFVVTPGELASVRT 125
>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 = 29.3 bits (66), Expect = 4.5
Identities = 12/40 (30%), Positives = 19/40 (47%)
Query: 207 EEVDAIIDKTGSTIFSEIQGYIDCCIKLSGMPDLTLSFMN 246
DAI+ G+ + S GY C +PD+T +F+
Sbjct: 219 SVYDAILKALGAAVSSSDGGYGVDCSPCDTLPDITFTFLW 258
>gnl|CDD|213365 cd12831, TmCorA-like_u2, Uncharacterized bacterial subfamily of the
Thermotoga maritima CorA-like family. This subfamily
belongs to the Thermotoga maritima CorA (TmCorA)-like
family of the MIT superfamily of essential membrane
proteins involved in transporting divalent cations
(uptake or efflux) across membranes. Members of the
TmCorA-like family are found in all three kingdoms of
life. It is a functionally diverse family which includes
the CorA Co2+ transporter from the hyperthermophilic
Thermotoga maritima, and three Saccharomyces cerevisiae
proteins: two located in the plasma membrane: the Mg2+
transporter Alr1p/Swc3p and the putative Mg2+
transporter, Alr2p, and the vacuole membrane protein
Mnr2p, a putative Mg2+ transporter. Thermotoga maritima
CorA forms funnel-shaped homopentamers, the tip of the
funnel is formed from two C-terminal transmembrane (TM)
helices from each monomer, and the large opening of the
funnel from the N-terminal cytoplasmic domains. The GMN
signature motif of the MIT superfamily occurs just after
TM1, mutation within this motif is known to abolish Mg2+
transport by a related protein, Saccharomyces cerevisiae
Alr1p. Natural variants in this signature sequence may
be associated with the transport of different divalent
cations. The functional diversity of the MIT superfamily
may also be due to minor structural differences
regulating gating, substrate selection, and transport.
Length = 287
Score = 28.3 bits (64), Expect = 8.9
Identities = 15/57 (26%), Positives = 25/57 (43%), Gaps = 13/57 (22%)
Query: 77 LFVIEFLDRVVTTFH----DYFNDCSESVL------KDNYVVVYEILDEMLDNGFPL 123
LFV E + TFH N+ E + + Y I+D+++D+ FP+
Sbjct: 67 LFVGE---NYIVTFHKEPIREINEVWEKLKEKKDKKLGTLYIAYMIIDKIVDDYFPI 120
>gnl|CDD|218533 pfam05277, DUF726, Protein of unknown function (DUF726). This
family consists of several uncharacterized eukaryotic
proteins.
Length = 345
Score = 28.2 bits (63), Expect = 9.4
Identities = 18/67 (26%), Positives = 32/67 (47%), Gaps = 1/67 (1%)
Query: 113 LDEMLDNGFPLATESNVLKELIKPPNILRTIANTMTGGSNVSSILPSGQLSSVPWRRTGG 172
LD +L + + L E +LKEL + IL + A +M+ + + + +S++ W
Sbjct: 125 LDPVLGDLYSLRWEPEMLKELGQALTILASAAFSMSLQQILGYTILASLVSALQW-PLAL 183
Query: 173 SNVSSIL 179
V IL
Sbjct: 184 LKVGYIL 190
>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 = 27.2 bits (61), Expect = 9.4
Identities = 7/19 (36%), Positives = 12/19 (63%)
Query: 196 YTNNEAYFDVIEEVDAIID 214
Y+ AYF+ + E+ I+D
Sbjct: 36 YSPEIAYFETLHELKLIVD 54
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
0.321 0.139 0.418
Gapped
Lambda K H
0.267 0.0713 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 23,874,877
Number of extensions: 2363774
Number of successful extensions: 1982
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1947
Number of HSP's successfully gapped: 44
Length of query: 459
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 359
Effective length of database: 6,502,202
Effective search space: 2334290518
Effective search space used: 2334290518
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 (27.3 bits)