RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2523
(691 letters)
>gnl|CDD|211362 cd09251, AP-2_Mu2_Cterm, C-terminal domain of medium Mu2 subunit in
ubiquitously expressed clathrin-associated adaptor
protein (AP) complex AP-2. AP complexes participate in
the formation of intracellular coated transport vesicles
and select cargo molecules for incorporation into the
coated vesicles in the late secretory and endocytic
pathways. There are four AP complexes, AP-1, -2, -3, and
-4, described in various eukaryotic organisms. Each AP
complex consists of four subunits: two large chains (one
each of gamma/alpha/delta/epsilon and beta1-4,
respectively), a medium mu chain (mu1-4), and a small
sigma chain (sigma1-4). Each of the four subunits from
the different AP complexes exhibits similarity with each
other. This family corresponds to the C-terminal domain
of heterotetrameric clathrin-associated adaptor protein
complex 2 (AP-2) medium mu2 subunit. Mu2 is ubiquitously
expressed in mammals. In higher eukaryotes, AP-2 plays a
critical role in clathrin-mediated endocytosis from the
plasma membrane in different cells. The
membrane-anchored cargo molecules can be linked to the
outer lattice of CCVs by AP-2. Those cargo molecules
interact with adaptors through short sorting signals in
their cytosolic segments. Tyrosine-based endocytotic
signals are one of the most important sorting signals.
They are of the form Y-X-X-Phi, where Y is tyrosine, X
is any amino acid and Phi is a bulky hydrophobic residue
that can be Leu, Ile, Met, Phe, or Val. These kinds of
sorting signals can be recognized by the C-terminal
domain of AP-2 mu2 subunit, also known as Y-X-X-Phi
signal-binding domain that contains two hydrophobic
pockets, one for the tyrosine-binding and one for the
bulky hydrophobic residue-binding. Since the Y-X-X-Phi
binding site is buried in the core structure of AP-2, a
phosphorylation induced conformational change is
required when the cargo molecules binds to AP-2. In
addition, the C-terminal domain of mu2 subunit has been
shown to bind other molecules. For instance, it can bind
phosphoinositides, in particular PI[4,5]P2, which might
be involved in the recognition process of the
tyrosine-based signals. It can also interact with
synaptotagmins, a family of important modulators of
calcium-dependent neurosecretion within the synaptic
vesicle (SV) membrane. Since many of the other endocytic
adaptors responsible for biogenesis of synaptic vesicles
exist, in the absence of AP-2, clathrin-mediated
endocytosis can still occur. However, the cells may not
survive in the complete absence of clathrin as well as
AP-2.
Length = 263
Score = 451 bits (1163), Expect = e-156
Identities = 159/279 (56%), Positives = 198/279 (70%), Gaps = 18/279 (6%)
Query: 227 YRRNELFLDVLEYVNLLMSPQGQTLSAHVAGKVVMKSYLSGMPECKFGINDKIVMEAKGG 286
YR+NE+FLDV+E VNLLMS G L A V G +VMK++LSGMPECKFG+NDK+V+E +G
Sbjct: 1 YRKNEVFLDVVESVNLLMSSTGTVLRADVDGVIVMKAFLSGMPECKFGLNDKLVLEKEGK 60
Query: 287 SSAKSSGLTVAGGDDVGRSGKPVVVIDDCQFHQCVKLSKFETEHSISFIPPDGEFELMRY 346
+ + K V +DDC+FHQCV+LSKF++E +ISFIPPDGEFELMRY
Sbjct: 61 AKSGDKA------------AKGSVELDDCKFHQCVRLSKFDSERTISFIPPDGEFELMRY 108
Query: 347 RTTKDIALPFRVIPLVREATRTKMEVKVVLKSQFKASLLGQKIEVRIPTPLNTSGVQLIC 406
R T++I LPF+V+PLV+E RTK+E KV +KS F L + V+IPTP NT+ V +
Sbjct: 109 RITENINLPFKVLPLVKEVGRTKLEYKVKIKSNFPPKLFATNVVVKIPTPKNTAKVTVSV 168
Query: 407 LKGKAKYKASENAIVWKIKRMAGMKETQLSAEIELLETDT-KKKWTRPPISMNFEVP-FA 464
KGKAKY ENAIVWKIK+ GM E+ LSAE+ELL T + KKW+RPPISM+FEVP F
Sbjct: 169 SKGKAKYDPEENAIVWKIKKFPGMTESTLSAEVELLSTTSELKKWSRPPISMDFEVPMFT 228
Query: 465 PSGFKVRYLKVFEPKLNYSDHDVIKWVRYIGRSGLYETR 503
SG +VRYLKVFE + +KWVRYI R+G YE R
Sbjct: 229 ASGLRVRYLKVFEKSN----YKTVKWVRYITRAGSYEIR 263
Score = 201 bits (514), Expect = 7e-60
Identities = 68/119 (57%), Positives = 86/119 (72%), Gaps = 12/119 (10%)
Query: 573 YRRNELFLDVLEYVNLLMSPQGQTLSAHVAGKVVMKSYLSGMPECKFGINDKIVMEAKGG 632
YR+NE+FLDV+E VNLLMS G L A V G +VMK++LSGMPECKFG+NDK+V+E +G
Sbjct: 1 YRKNEVFLDVVESVNLLMSSTGTVLRADVDGVIVMKAFLSGMPECKFGLNDKLVLEKEGK 60
Query: 633 SSAKSSGLTVAGGDDVGRSGKPVVVIDDCQFHQCVKLSKFETEHSISFIPPDGEFELMR 691
+ + K V +DDC+FHQCV+LSKF++E +ISFIPPDGEFELMR
Sbjct: 61 AKSGDKA------------AKGSVELDDCKFHQCVRLSKFDSERTISFIPPDGEFELMR 107
>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 = 281 bits (722), Expect = 4e-90
Identities = 119/288 (41%), Positives = 166/288 (57%), Gaps = 25/288 (8%)
Query: 215 TGQIGWRREGIKYRRNELFLDVLEYVNLLMSPQGQTLSAHVAGKVVMKSYLSGMPECKFG 274
T + WR EGIKY++NE+FLDV+E VNLL+ GQ L + + G + M+SYLSGMPE K G
Sbjct: 1 TNAVSWRPEGIKYKKNEVFLDVIESVNLLVDLNGQVLRSEIVGTIKMRSYLSGMPELKLG 60
Query: 275 INDKIVMEAKGGSSAKSSGLTVAGGDDVGRSGKPVVVIDDCQFHQCVKLSKFETEHSISF 334
+NDK++ EA G SS + V ++D +FHQCV+LS+FE + +ISF
Sbjct: 61 LNDKVLFEATGRSSKGKA-----------------VELEDVKFHQCVRLSRFENDRTISF 103
Query: 335 IPPDGEFELMRYRTTKDIALPFRVIPLVREATRTKMEVKVVLKSQFKASLLGQKIEVRIP 394
IPPDGEFELM YR + + V P V +R+++E+ V K+QFK +E+RIP
Sbjct: 104 IPPDGEFELMSYRLSTQVKPLIWVEPTVERHSRSRVEIMVKAKTQFKRRSTANNVEIRIP 163
Query: 395 TPLNTSGVQLICLKGKAKYKASENAIVWKIKRMAGMKETQLSAEIEL---LETDTKKKWT 451
P + + C G Y ++A++WKIK G KE + AE L + +
Sbjct: 164 VPPDADSPRFKCSAGSVVYAPEKDALLWKIKSFPGGKEFSMRAEFGLPSIESEEEQGTEK 223
Query: 452 RPPISMNFEVP-FAPSGFKVRYLKVFEPKLNYSDHDVIKWVRYIGRSG 498
+ PI + FE+P F SG +VRYLK+ E Y + WVRYI +SG
Sbjct: 224 KAPIQVKFEIPYFTVSGLQVRYLKIIEKS-GYQ---ALPWVRYITQSG 267
Score = 167 bits (424), Expect = 5e-47
Identities = 66/130 (50%), Positives = 87/130 (66%), Gaps = 17/130 (13%)
Query: 561 TGQIGWRREGIKYRRNELFLDVLEYVNLLMSPQGQTLSAHVAGKVVMKSYLSGMPECKFG 620
T + WR EGIKY++NE+FLDV+E VNLL+ GQ L + + G + M+SYLSGMPE K G
Sbjct: 1 TNAVSWRPEGIKYKKNEVFLDVIESVNLLVDLNGQVLRSEIVGTIKMRSYLSGMPELKLG 60
Query: 621 INDKIVMEAKGGSSAKSSGLTVAGGDDVGRSGKPVVVIDDCQFHQCVKLSKFETEHSISF 680
+NDK++ EA G SS + V ++D +FHQCV+LS+FE + +ISF
Sbjct: 61 LNDKVLFEATGRSSKGKA-----------------VELEDVKFHQCVRLSRFENDRTISF 103
Query: 681 IPPDGEFELM 690
IPPDGEFELM
Sbjct: 104 IPPDGEFELM 113
>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 = 250 bits (640), Expect = 1e-78
Identities = 109/270 (40%), Positives = 150/270 (55%), Gaps = 34/270 (12%)
Query: 231 ELFLDVLEYVNLLMSPQGQTLSAHVAGKVVMKSYLSGMPECKFGINDKIVMEAKGGSSAK 290
E+FLDV+E VNLL+S G L++ V G++ +KS+LSGMPE + G+N+ V K
Sbjct: 1 EVFLDVIEKVNLLISKDGSLLNSEVVGEIALKSFLSGMPEIRLGLNNPDV-------GIK 53
Query: 291 SSGLTVAGGDDVGRSGKPVVVIDDCQFHQCVKLSKFETEHSISFIPPDGEFELMRYRTT- 349
+DD FH CV+L +FE+E ISFIPPDGEFELM YRT
Sbjct: 54 ---------------------LDDVSFHPCVRLKRFESERIISFIPPDGEFELMSYRTVL 92
Query: 350 KDIALPFRVIPLVREATRTKMEVKVVLKSQFKASLLGQKIEVRIPTPLNTSGVQLICLKG 409
++ LP + P+V E ++EV V LK L + +EV IP P + + G
Sbjct: 93 EEPILPITIFPVVSE-EGGRLEVTVKLKLSESLQLTAENVEVHIPLPSGVTSLSSKPSDG 151
Query: 410 KAKYKASENAIVWKIKRM-AGMKETQLSAEIELLETDTKKKWTRPPISMNFEVP-FAPSG 467
+AK+ +NA+VW+IKR+ G KE LSA EL + PP+S++FE+P SG
Sbjct: 152 QAKFDPEKNALVWRIKRIPVGGKEQSLSATFELGGLAHECPEEAPPVSLSFEIPETTGSG 211
Query: 468 FKVRYLKVFEPKLNYSDHDVIKWVRYIGRS 497
+VR L+VF+ K HD IKWVRY +
Sbjct: 212 IQVRSLQVFDEKNP--GHDPIKWVRYSTHT 239
Score = 111 bits (279), Expect = 1e-27
Identities = 50/115 (43%), Positives = 66/115 (57%), Gaps = 28/115 (24%)
Query: 577 ELFLDVLEYVNLLMSPQGQTLSAHVAGKVVMKSYLSGMPECKFGINDKIVMEAKGGSSAK 636
E+FLDV+E VNLL+S G L++ V G++ +KS+LSGMPE + G+N+ V K
Sbjct: 1 EVFLDVIEKVNLLISKDGSLLNSEVVGEIALKSFLSGMPEIRLGLNNPDV-------GIK 53
Query: 637 SSGLTVAGGDDVGRSGKPVVVIDDCQFHQCVKLSKFETEHSISFIPPDGEFELMR 691
+DD FH CV+L +FE+E ISFIPPDGEFELM
Sbjct: 54 ---------------------LDDVSFHPCVRLKRFESERIISFIPPDGEFELMS 87
>gnl|CDD|216199 pfam00928, Adap_comp_sub, Adaptor complexes medium subunit family.
This family also contains members which are coatomer
subunits.
Length = 228
Score = 248 bits (635), Expect = 5e-78
Identities = 109/290 (37%), Positives = 145/290 (50%), Gaps = 65/290 (22%)
Query: 218 IGWRREGIKYRRNELFLDVLEYVNLLMSPQGQTLSAHVAGKVVMKSYLSGMPECKFGIND 277
+ WR GIKY++NE+FLDV+E V++++ G L++ + G + K YLSGMPE G+ND
Sbjct: 1 VPWRPSGIKYKKNEVFLDVIERVSVIVDKDGGILNSEIQGTIDCKCYLSGMPELTLGLND 60
Query: 278 KIVMEAKGGSSAKSSGLTVAGGDDVGRSGKPVVVIDDCQFHQCVKLSKFETEHSISFIPP 337
+ + S + +DD FH CV+LS+FE+E ISFIPP
Sbjct: 61 PLNIGKIA-------------------SSGNGIELDDVSFHPCVRLSRFESERVISFIPP 101
Query: 338 DGEFELMRYRTTKDIALPFRVIPLVREATRTKMEVKVVLKSQFKASLLGQKIEVRIPTPL 397
DGEF LM YR + ++ LPF+V P
Sbjct: 102 DGEFTLMSYRISSNVPLPFKVNP------------------------------------- 124
Query: 398 NTSGVQLICLKGKAKYKASENAIVWKIKRMAGMKETQLSAEIELLET--DTKKKWTRPPI 455
L GKAKY ENA+ W I ++ G KE LS E+EL T K W+ PPI
Sbjct: 125 ---SPVLTVSDGKAKYDPEENALEWTIGKIPGGKEPTLSGELELSSTSESPSKDWSFPPI 181
Query: 456 SMNFEVP-FAPSGFKVRYLKVFEPKLNYSDHDVIKWVRYIGRSGLYETRK 504
S+ F +P F SG KVR LK+ EPK NY KWVRY+ +SG Y+ R
Sbjct: 182 SVEFSIPGFTASGLKVRSLKISEPKSNYK---PYKWVRYVTKSGKYQVRI 228
Score = 150 bits (380), Expect = 2e-41
Identities = 52/128 (40%), Positives = 73/128 (57%), Gaps = 19/128 (14%)
Query: 564 IGWRREGIKYRRNELFLDVLEYVNLLMSPQGQTLSAHVAGKVVMKSYLSGMPECKFGIND 623
+ WR GIKY++NE+FLDV+E V++++ G L++ + G + K YLSGMPE G+ND
Sbjct: 1 VPWRPSGIKYKKNEVFLDVIERVSVIVDKDGGILNSEIQGTIDCKCYLSGMPELTLGLND 60
Query: 624 KIVMEAKGGSSAKSSGLTVAGGDDVGRSGKPVVVIDDCQFHQCVKLSKFETEHSISFIPP 683
+ + S + +DD FH CV+LS+FE+E ISFIPP
Sbjct: 61 PLNIGKIA-------------------SSGNGIELDDVSFHPCVRLSRFESERVISFIPP 101
Query: 684 DGEFELMR 691
DGEF LM
Sbjct: 102 DGEFTLMS 109
>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 = 232 bits (594), Expect = 2e-71
Identities = 118/291 (40%), Positives = 167/291 (57%), Gaps = 23/291 (7%)
Query: 214 VTGQIGWRREGIKYRRNELFLDVLEYVNLLMSPQGQTLSAHVAGKVVMKSYLSGMPECKF 273
VT + WR EGIKYR+NE+FLDV+E VNLL+S G L + + G + M+ YLSGMPE +
Sbjct: 1 VTNAVSWRSEGIKYRKNEVFLDVIESVNLLVSANGNVLRSEIVGSIKMRVYLSGMPELRL 60
Query: 274 GINDKIVMEAKGGSSAKSSGLTVAGGDDVGRSGKPVVVIDDCQFHQCVKLSKFETEHSIS 333
G+NDK++ E G +KS V ++D +FHQCV+LS+FE + +IS
Sbjct: 61 GLNDKVLFENTGRGKSKS------------------VELEDVKFHQCVRLSRFENDRTIS 102
Query: 334 FIPPDGEFELMRYRTTKDIALPFRVIPLVREATRTKMEVKVVLKSQFKASLLGQKIEVRI 393
FIPPDGEFELM YR + + ++ + +++E + KSQFK +E+ I
Sbjct: 103 FIPPDGEFELMSYRLNTHVKPLIWIESVIERHSHSRVEYMIKAKSQFKRRSTANNVEIHI 162
Query: 394 PTPLNTSGVQLICLKGKAKYKASENAIVWKIKRMAGMKETQLSAEIELLETDTKKKWTRP 453
P P + + G KY +AIVW IK G KE + A L ++++K RP
Sbjct: 163 PVPNDADSPKFKTTVGSVKYVPENSAIVWSIKSFPGGKEYLMRAHFGLPSVESEEKEGRP 222
Query: 454 PISMNFEVP-FAPSGFKVRYLKVFEPKLNYSDHDVIKWVRYIGRSGLYETR 503
PIS+ FE+P F SG +VRYLK+ E S + + WVRYI ++G Y+ R
Sbjct: 223 PISVKFEIPYFTTSGIQVRYLKIIEK----SGYQALPWVRYITQNGDYQLR 269
Score = 143 bits (363), Expect = 1e-38
Identities = 65/131 (49%), Positives = 86/131 (65%), Gaps = 18/131 (13%)
Query: 560 VTGQIGWRREGIKYRRNELFLDVLEYVNLLMSPQGQTLSAHVAGKVVMKSYLSGMPECKF 619
VT + WR EGIKYR+NE+FLDV+E VNLL+S G L + + G + M+ YLSGMPE +
Sbjct: 1 VTNAVSWRSEGIKYRKNEVFLDVIESVNLLVSANGNVLRSEIVGSIKMRVYLSGMPELRL 60
Query: 620 GINDKIVMEAKGGSSAKSSGLTVAGGDDVGRSGKPVVVIDDCQFHQCVKLSKFETEHSIS 679
G+NDK++ E G +KS V ++D +FHQCV+LS+FE + +IS
Sbjct: 61 GLNDKVLFENTGRGKSKS------------------VELEDVKFHQCVRLSRFENDRTIS 102
Query: 680 FIPPDGEFELM 690
FIPPDGEFELM
Sbjct: 103 FIPPDGEFELM 113
>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 = 229 bits (587), Expect = 3e-70
Identities = 103/284 (36%), Positives = 155/284 (54%), Gaps = 30/284 (10%)
Query: 228 RRNELFLDVLEYVNLLMSPQGQTLSAHVAGKVVMKSYLSGMPECKFGINDKIVMEAKGGS 287
++NE+F+DVLE ++++ S GQ L++ + G + MKSYLSG PE + +N+ +V+
Sbjct: 9 KKNEIFVDVLERLSVVFSANGQVLNSEIDGSIQMKSYLSGNPELRLALNEDLVI------ 62
Query: 288 SAKSSGLTVAGGDDVGRSGKPVVVIDDCQFHQCVKLSKFETEHSISFIPPDGEFELMRYR 347
G R+ VV+DDC FH+CV L +FE++ ++S PPDGEF LM YR
Sbjct: 63 -----------GKRENRAYSSAVVLDDCNFHECVDLEEFESDRTLSLTPPDGEFTLMNYR 111
Query: 348 TTKDIALPFRVIPLVREATRTKMEVKVVLKSQFKASLLGQKIEVRIPTPLNTSGVQLICL 407
+ + PFRV P V E + K+E+ + L++ F + + VRIP P TS
Sbjct: 112 ISGEFKPPFRVFPSVEETSPYKLELVLKLRADFPPKVTATNVVVRIPLPKGTSSASCELS 171
Query: 408 KG----KAKYKASENAIVWKIKRMAGMKETQLSAEIELLETDT---KKKWTRPPISMNFE 460
G A+YK E +VW IK+ G E L +I L +K+ PIS+ FE
Sbjct: 172 SGASGQSAEYKEKEKRVVWNIKKFPGGTEHSLRIKITLSSPIPSAVRKEIG--PISLTFE 229
Query: 461 VP-FAPSGFKVRYLKVFEPKLNYSDHDVIKWVRYIGRSGLYETR 503
+P + SG +V+YL++ E +Y+ H +WVRYI +S Y R
Sbjct: 230 IPMYNVSGLQVKYLRISEKSSSYNPH---RWVRYITQSSSYVCR 270
Score = 120 bits (304), Expect = 1e-30
Identities = 46/118 (38%), Positives = 71/118 (60%), Gaps = 17/118 (14%)
Query: 574 RRNELFLDVLEYVNLLMSPQGQTLSAHVAGKVVMKSYLSGMPECKFGINDKIVMEAKGGS 633
++NE+F+DVLE ++++ S GQ L++ + G + MKSYLSG PE + +N+ +V+
Sbjct: 9 KKNEIFVDVLERLSVVFSANGQVLNSEIDGSIQMKSYLSGNPELRLALNEDLVI------ 62
Query: 634 SAKSSGLTVAGGDDVGRSGKPVVVIDDCQFHQCVKLSKFETEHSISFIPPDGEFELMR 691
G R+ VV+DDC FH+CV L +FE++ ++S PPDGEF LM
Sbjct: 63 -----------GKRENRAYSSAVVLDDCNFHECVDLEEFESDRTLSLTPPDGEFTLMN 109
>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 = 218 bits (556), Expect = 5e-66
Identities = 103/285 (36%), Positives = 163/285 (57%), Gaps = 23/285 (8%)
Query: 215 TGQIGWRREGIKYRRNELFLDVLEYVNLLMSPQGQTLSAHVAGKVVMKSYLSGMPECKFG 274
T + WR EGIKY++NE+F+DV+E VNLL++ G L + + G + +K +LSGMPE + G
Sbjct: 1 TNAVSWRSEGIKYKKNEVFIDVIESVNLLVNANGSVLRSEIVGAIKLKVFLSGMPELRLG 60
Query: 275 INDKIVMEAKGGSSAKSSGLTVAGGDDVGRSGKPVVVIDDCQFHQCVKLSKFETEHSISF 334
+ND+++ E G K+ V ++D +FHQCV+LS+FE + +ISF
Sbjct: 61 LNDRVLFELTGREKNKT------------------VELEDVKFHQCVRLSRFENDRTISF 102
Query: 335 IPPDGEFELMRYRTTKDIALPFRVIPLVREATRTKMEVKVVLKSQFKASLLGQKIEVRIP 394
IPPDGE ELM YR + + ++ + + +++E+ V K QFK + +E+ +P
Sbjct: 103 IPPDGESELMSYRLNTQVKPLIWIESVIEKFSHSRVEIMVKAKGQFKKQSVANNVEILVP 162
Query: 395 TPLNTSGVQLICLKGKAKYKASENAIVWKIKRMAGMKETQLSAEIELLETDTKKKWTRPP 454
P + + G AKY +N +VW IK G KE + A L ++++ +PP
Sbjct: 163 VPSDADSPKFKTSTGSAKYVPEKNVVVWSIKSFPGGKEYLMRAHFGLPSVESEELEGKPP 222
Query: 455 ISMNFEVPFAP-SGFKVRYLKVFEPKLNYSDHDVIKWVRYIGRSG 498
I++ FE+P+ SG +VRY+K+ E S + + WVRYI +SG
Sbjct: 223 ITVKFEIPYFTVSGIQVRYMKIIEK----SGYQALPWVRYITQSG 263
Score = 131 bits (330), Expect = 3e-34
Identities = 57/130 (43%), Positives = 83/130 (63%), Gaps = 18/130 (13%)
Query: 561 TGQIGWRREGIKYRRNELFLDVLEYVNLLMSPQGQTLSAHVAGKVVMKSYLSGMPECKFG 620
T + WR EGIKY++NE+F+DV+E VNLL++ G L + + G + +K +LSGMPE + G
Sbjct: 1 TNAVSWRSEGIKYKKNEVFIDVIESVNLLVNANGSVLRSEIVGAIKLKVFLSGMPELRLG 60
Query: 621 INDKIVMEAKGGSSAKSSGLTVAGGDDVGRSGKPVVVIDDCQFHQCVKLSKFETEHSISF 680
+ND+++ E G K+ V ++D +FHQCV+LS+FE + +ISF
Sbjct: 61 LNDRVLFELTGREKNKT------------------VELEDVKFHQCVRLSRFENDRTISF 102
Query: 681 IPPDGEFELM 690
IPPDGE ELM
Sbjct: 103 IPPDGESELM 112
>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 = 155 bits (394), Expect = 5e-43
Identities = 81/286 (28%), Positives = 135/286 (47%), Gaps = 45/286 (15%)
Query: 220 WRREGIKYRRNELFLDVLEYVNLLMSPQGQTLSAHVAGKVVMKSYLSGMPECKFGINDKI 279
WRR G+KY NE+++DV+E ++ ++ G+ +S V+G + S LSGMP+ +N+
Sbjct: 3 WRRAGVKYTNNEIYVDVVEEIDAIVDKSGKPVSGEVSGSIDCNSRLSGMPDLTLSLNNPG 62
Query: 280 VMEAKGGSSAKSSGLTVAGGDDVGRSGKPVVVIDDCQFHQCVKLSKFETEHSISFIPPDG 339
+ +DD FH CV+LS++E++ +SFIPPDG
Sbjct: 63 L-------------------------------LDDPSFHPCVRLSRWESDRVLSFIPPDG 91
Query: 340 EFELMRYRTTKD--IALPFRVIP-LVREATRTKMEVKVVLKSQFKASLLGQKIEVRIPTP 396
+F LM YR + + LP V P + + E+ V + ++ + + V IP P
Sbjct: 92 KFTLMSYRVDLNSLVQLPVYVKPQISLGKGGGRFEISVGPRGNLGKTI--ENVVVEIPLP 149
Query: 397 LNTSGVQLICLKGKAKYKASENAIVWKIKRMAGMKETQLSAEIELLETDTKKKWTRPPIS 456
++L G + +S +VW I ++ K L I L + P IS
Sbjct: 150 KGVKSLRLTASHGTFSFDSSTKTLVWSIGKLTPGKTPTLRGSISLESGEEAPS-EPPSIS 208
Query: 457 MNFEVP-FAPSGFKVRYLKVFEPKLN-YSDHDVIKWVRYIGRSGLY 500
++F++P + PSG KV L ++ K + K V+YI ++G Y
Sbjct: 209 VSFKIPGYLPSGLKVDSLDIYNEKYKPF------KGVKYITKAGKY 248
Score = 112 bits (283), Expect = 5e-28
Identities = 41/126 (32%), Positives = 66/126 (52%), Gaps = 31/126 (24%)
Query: 566 WRREGIKYRRNELFLDVLEYVNLLMSPQGQTLSAHVAGKVVMKSYLSGMPECKFGINDKI 625
WRR G+KY NE+++DV+E ++ ++ G+ +S V+G + S LSGMP+ +N+
Sbjct: 3 WRRAGVKYTNNEIYVDVVEEIDAIVDKSGKPVSGEVSGSIDCNSRLSGMPDLTLSLNNPG 62
Query: 626 VMEAKGGSSAKSSGLTVAGGDDVGRSGKPVVVIDDCQFHQCVKLSKFETEHSISFIPPDG 685
++DD FH CV+LS++E++ +SFIPPDG
Sbjct: 63 -------------------------------LLDDPSFHPCVRLSRWESDRVLSFIPPDG 91
Query: 686 EFELMR 691
+F LM
Sbjct: 92 KFTLMS 97
>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 = 101 bits (254), Expect = 1e-23
Identities = 76/326 (23%), Positives = 128/326 (39%), Gaps = 76/326 (23%)
Query: 221 RREGIKYRRNELFLDVLEYVNLLMSPQGQTLSAHVAGKVVMKSYLSGMPECKFGINDKIV 280
R G+ YR +E+ +DV++ ++ +G+ L V ++ ++++GMPEC+ G+ND
Sbjct: 2 RDRGLTYREDEITVDVVDEFRGKVTKEGEILKQAVRVRIFCLAFVTGMPECELGLNDI-- 59
Query: 281 MEAKGGSSAKSSGLTVAGGDDVGRSG-KPVVV-----IDDCQFHQCVKLSKFETEHSISF 334
G + V R PV +++ +FH CV +FE I F
Sbjct: 60 --------------QRKGREVVRRQDIIPVSTEEWIKLENVEFHSCVNKDEFEQSRVIKF 105
Query: 335 IPPDG-EFELMRYRTT----KDIALPFRVIPLVREATRTKMEVKVVLKSQFKASLLGQ-- 387
P D FELMR+R +++ L + + V+ A ++ +++ + LGQ
Sbjct: 106 HPLDACRFELMRFRVRPPRERELPLTVKSVVSVKGA-HVELRADLLVPGYTSRNPLGQVP 164
Query: 388 --KIEVRIPTP------LNTSGVQLI-----------CLK---------------GKAKY 413
I +R P P +K G AKY
Sbjct: 165 CENIMIRFPVPEEWVYLFRVEKHFRYKSLKSKKKRPGKIKSARELLSPPLIEVSVGTAKY 224
Query: 414 KASENAIVWKIKRM----AGMKETQ-LSAEIELLETDTKKKWTRPPISMNFEVPFAP-SG 467
+ + AIVW+I R+ + LS +EL D P + F +P S
Sbjct: 225 EHAYRAIVWRIPRLPEKNSAAYTPHLLSCRLELASDDEIPSSFYPHAEVEFTMPSTTASK 284
Query: 468 FKVRYLKVFEPKLNYSDHDVIKWVRY 493
VR + V +++ K+VRY
Sbjct: 285 TTVRSISV------SNENIPEKFVRY 304
Score = 76.2 bits (188), Expect = 5e-15
Identities = 38/132 (28%), Positives = 62/132 (46%), Gaps = 23/132 (17%)
Query: 567 RREGIKYRRNELFLDVLEYVNLLMSPQGQTLSAHVAGKVVMKSYLSGMPECKFGINDKIV 626
R G+ YR +E+ +DV++ ++ +G+ L V ++ ++++GMPEC+ G+ND
Sbjct: 2 RDRGLTYREDEITVDVVDEFRGKVTKEGEILKQAVRVRIFCLAFVTGMPECELGLNDI-- 59
Query: 627 MEAKGGSSAKSSGLTVAGGDDVGRSG-KPVVV-----IDDCQFHQCVKLSKFETEHSISF 680
G + V R PV +++ +FH CV +FE I F
Sbjct: 60 --------------QRKGREVVRRQDIIPVSTEEWIKLENVEFHSCVNKDEFEQSRVIKF 105
Query: 681 IPPDG-EFELMR 691
P D FELMR
Sbjct: 106 HPLDACRFELMR 117
>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 = 97.1 bits (241), Expect = 2e-22
Identities = 71/292 (24%), Positives = 128/292 (43%), Gaps = 45/292 (15%)
Query: 218 IGWRREGIKYRRNELFLDVLEYVNLLMSPQGQTLSAHVAGKVVMKSYLSGMPECKFGIND 277
I WRR G+KY NE + DV+E ++ ++ G T+ A + G + LSGMP
Sbjct: 1 IPWRRAGVKYTNNEAYFDVVEEIDAIIDKSGSTVFAEIQGVIDACIKLSGMP-------- 52
Query: 278 KIVMEAKGGSSAKSSGLTVAGGDDVGRSGKPVVVIDDCQFHQCVKLSKFETEHSISFIPP 337
D+ S ++DD FH C++ ++E+E +SFIPP
Sbjct: 53 -----------------------DLSLSFMNPRLLDDVSFHPCIRFKRWESERVLSFIPP 89
Query: 338 DGEFELMRYRTTKD--IALPFRV---IPLVREATRTKMEVKVVLKSQFKASLLGQKIEVR 392
DG F L+ YR + +A+P V I ++ + ++ + K ++ G + V
Sbjct: 90 DGNFRLISYRVSSQNLVAIPVYVKHLISFKENSSCGRFDITIGPKQNMGKTIEGITVTVH 149
Query: 393 IPTPLNTSGVQLICLKGKAKYKASENAIVWKIKRMAGMKETQLSAEIELLETDTKKKWTR 452
+P + + L +G + + W + ++ K L + L++ K
Sbjct: 150 MPKVV--LNMNLTPTQGSYTFDPVTKVLAWDVGKITPQKLPSLKGLVN-LQSGAPKPEEN 206
Query: 453 PPISMNFEV-PFAPSGFKVRYLKVFEPKLNYSDHDVIKWVRYIGRSGLYETR 503
P +++ F++ A SG KV L ++ K + K V+YI ++G ++ R
Sbjct: 207 PSLNIQFKIQQLAISGLKVNRLDMYGEK-----YKPFKGVKYITKAGKFQVR 253
Score = 70.9 bits (173), Expect = 1e-13
Identities = 39/127 (30%), Positives = 59/127 (46%), Gaps = 31/127 (24%)
Query: 564 IGWRREGIKYRRNELFLDVLEYVNLLMSPQGQTLSAHVAGKVVMKSYLSGMPECKFGIND 623
I WRR G+KY NE + DV+E ++ ++ G T+ A + G + LSGMP
Sbjct: 1 IPWRRAGVKYTNNEAYFDVVEEIDAIIDKSGSTVFAEIQGVIDACIKLSGMP-------- 52
Query: 624 KIVMEAKGGSSAKSSGLTVAGGDDVGRSGKPVVVIDDCQFHQCVKLSKFETEHSISFIPP 683
D+ S ++DD FH C++ ++E+E +SFIPP
Sbjct: 53 -----------------------DLSLSFMNPRLLDDVSFHPCIRFKRWESERVLSFIPP 89
Query: 684 DGEFELM 690
DG F L+
Sbjct: 90 DGNFRLI 96
>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 = 89.3 bits (221), Expect = 7e-20
Identities = 70/293 (23%), Positives = 128/293 (43%), Gaps = 47/293 (16%)
Query: 218 IGWRREGIKYRRNELFLDVLEYVNLLMSPQGQTLSAHVAGKVVMKSYLSGMPECKFGIND 277
+ WRR G+KY NE + DV+E ++ ++ G T++A + G + L+GMP+
Sbjct: 1 VPWRRTGVKYTNNEAYFDVIEEIDAIIDKSGSTITAEIQGVIDACVKLTGMPDLTLSF-- 58
Query: 278 KIVMEAKGGSSAKSSGLTVAGGDDVGRSGKPVVVIDDCQFHQCVKLSKFETEHSISFIPP 337
M + ++DD FH CV+ ++E+E +SFIPP
Sbjct: 59 ---MNPR--------------------------LLDDVSFHPCVRFKRWESERILSFIPP 89
Query: 338 DGEFELMRYRTTKD--IALPFRV---IPLVREATRTKMEVKVVLKSQFKASLLGQKIEVR 392
DG F L+ Y + +A+P V I ++ + E+ + K ++ G + +
Sbjct: 90 DGNFRLLSYHVSAQNLVAIPVYVKHNISFREGSSLGRFEITLGPKQTMGKTVEGVTVTSQ 149
Query: 393 IPTP-LNTSGVQLICLKGKAKYKASENAIVWKIKRMAGMKETQLSAEIELLETDTKKKWT 451
+P LN S L +G + + W + ++ K L + L+ K
Sbjct: 150 MPKGVLNMS---LTPSQGTYTFDPVTKLLSWDVGKINPQKLPSLKGSMS-LQAGASKPDE 205
Query: 452 RPPISMNFEV-PFAPSGFKVRYLKVFEPKLNYSDHDVIKWVRYIGRSGLYETR 503
P I++ F++ A SG KV L ++ K + K ++Y+ ++G ++ R
Sbjct: 206 NPTINLQFKIQQLAISGLKVNRLDMYGEK-----YKPFKGIKYMTKAGKFQVR 253
Score = 72.4 bits (177), Expect = 4e-14
Identities = 37/127 (29%), Positives = 60/127 (47%), Gaps = 31/127 (24%)
Query: 564 IGWRREGIKYRRNELFLDVLEYVNLLMSPQGQTLSAHVAGKVVMKSYLSGMPECKFGIND 623
+ WRR G+KY NE + DV+E ++ ++ G T++A + G + L+GMP+
Sbjct: 1 VPWRRTGVKYTNNEAYFDVIEEIDAIIDKSGSTITAEIQGVIDACVKLTGMPDLTLSF-- 58
Query: 624 KIVMEAKGGSSAKSSGLTVAGGDDVGRSGKPVVVIDDCQFHQCVKLSKFETEHSISFIPP 683
M + ++DD FH CV+ ++E+E +SFIPP
Sbjct: 59 ---MNPR--------------------------LLDDVSFHPCVRFKRWESERILSFIPP 89
Query: 684 DGEFELM 690
DG F L+
Sbjct: 90 DGNFRLL 96
>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 = 79.6 bits (196), Expect = 4e-16
Identities = 79/319 (24%), Positives = 131/319 (41%), Gaps = 66/319 (20%)
Query: 224 GIKYRRNELFLDVL-EYVNLLMSPQGQTLSAHVAGKVVMKSYLSGMPECKFGINDKIVME 282
G+ Y E+ +DV E+ +L + L V ++ + S+LSG+ EC+ G+ND ++
Sbjct: 5 GLNYTEEEITVDVRDEFHGILSKGDSRILQHSVLTRIYILSFLSGLAECRLGLNDILI-- 62
Query: 283 AKGGSSAKSSGLTVAGGDDVGRSGKPVVVIDDCQFHQCVKLSKFETEHSISFIPPDG-EF 341
KG VA D + + + + +C+FH+CV F +I F P D F
Sbjct: 63 -KGNE-------VVARQDIMPTTTTKWIQLHECRFHECVDEDMFNNSRAILFNPLDACRF 114
Query: 342 ELMRYRTT-KDIALPF--RVIPLVREATRTKMEVKVVLKSQFKA---------------- 382
ELMR+RT + LPF R V A +++ +V+ + F +
Sbjct: 115 ELMRFRTVFAEKTLPFTLRTAACVNGA-EVEVQSWLVMSTGFSSNRDPLTQVPCENVMIR 173
Query: 383 --------------SLLGQK-IEVRI-------PTPLNTSGVQLICLKGKAKYKASENAI 420
S+LG+K ++ ++ T L+ S + G AKY+ + N++
Sbjct: 174 YPVPEEWVKNFRRESVLGEKSLKAKVNKGASFGSTSLSGSEPAMRVTLGTAKYEHAFNSV 233
Query: 421 VWKIKRMAGMKETQLSAEIELLETDTKKKWTRPP-----ISMNFEVPFAP-SGFKVRYLK 474
VW+I R+ + P + + F++P A S VR L
Sbjct: 234 VWRINRLPDKNSASGHPHCFFCHLELGSDREVPSSFVCHVEVEFDMPTASASKAAVRSLS 293
Query: 475 VFEPKLNYSDHDVIKWVRY 493
V + DV KWV Y
Sbjct: 294 VED------KTDVKKWVNY 306
Score = 63.0 bits (153), Expect = 1e-10
Identities = 38/124 (30%), Positives = 61/124 (49%), Gaps = 12/124 (9%)
Query: 570 GIKYRRNELFLDVL-EYVNLLMSPQGQTLSAHVAGKVVMKSYLSGMPECKFGINDKIVME 628
G+ Y E+ +DV E+ +L + L V ++ + S+LSG+ EC+ G+ND ++
Sbjct: 5 GLNYTEEEITVDVRDEFHGILSKGDSRILQHSVLTRIYILSFLSGLAECRLGLNDILI-- 62
Query: 629 AKGGSSAKSSGLTVAGGDDVGRSGKPVVVIDDCQFHQCVKLSKFETEHSISFIPPDG-EF 687
KG VA D + + + + +C+FH+CV F +I F P D F
Sbjct: 63 -KGNE-------VVARQDIMPTTTTKWIQLHECRFHECVDEDMFNNSRAILFNPLDACRF 114
Query: 688 ELMR 691
ELMR
Sbjct: 115 ELMR 118
>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 = 69.5 bits (170), Expect = 7e-13
Identities = 61/238 (25%), Positives = 94/238 (39%), Gaps = 53/238 (22%)
Query: 305 SGKPVVVIDDCQFHQCVKLSKFETEHSISFIPPDG-EFELMRYRTTKDIA-LPFRV-IPL 361
+GK + I D FH+CV +F I F PPD FELMR++T + LPF V +
Sbjct: 73 AGKLWIEILDYHFHKCVNAQEFHQSRLIKFCPPDACRFELMRFKTRYNGGDLPFSVKAMV 132
Query: 362 VREATRTKMEVKVVLKSQFKASL------LGQKIEVRIPTPLN----TSGVQLI------ 405
V + +++ + + F + +E+R P P + L
Sbjct: 133 VVQGAYVELQAFLNMAPTFPTFGVAGSLPYCENVEIRFPVPAQWVKALWTMSLQRQRSLK 192
Query: 406 -------CLK---------------GKAKYKASENAIVWKIKRMAGMKETQ------LSA 437
CL G AKY+ + A+VWKI R+ K + LS
Sbjct: 193 AKMNRRACLGSALEAESEPVIQVSVGTAKYENAYRAVVWKIDRLPD-KNSAVDHPHSLSC 251
Query: 438 EIEL-LETDTKKKWTRPPISMNFEVPFA-PSGFKVRYLKVFEPKLNYSDHDVIKWVRY 493
++EL + + W P ++ FEV SG +V+ L + E + H V Y
Sbjct: 252 KLELGSDQEIPSDW-YPFATVEFEVEDTCASGTRVKSLGI-ESDMQPQKH-VTSRACY 306
Score = 48.7 bits (116), Expect = 5e-06
Identities = 19/42 (45%), Positives = 23/42 (54%), Gaps = 1/42 (2%)
Query: 651 SGKPVVVIDDCQFHQCVKLSKFETEHSISFIPPDG-EFELMR 691
+GK + I D FH+CV +F I F PPD FELMR
Sbjct: 73 AGKLWIEILDYHFHKCVNAQEFHQSRLIKFCPPDACRFELMR 114
>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 = 38.1 bits (89), Expect = 0.010
Identities = 29/145 (20%), Positives = 52/145 (35%), Gaps = 25/145 (17%)
Query: 311 VIDDCQFHQCVK-----LSKFETEHSISFIPPDGEFELMRYRTTKDIALPFRVIPLVREA 365
+ + H CV+ + F + + F PP G F+L Y + P + ++
Sbjct: 66 PLQNIIVHPCVQSVDTGMLAFSGPYKLRFSPPLGNFQLCHYTSQSVPEPPIKGFYQMKGE 125
Query: 366 -TRTKMEVKVVLKSQFKASLLGQKIEVRIPTPLNTSGVQLICLKGKAKYKAS-------- 416
K+ +++ L + K S + EV IP N L + S
Sbjct: 126 ENHVKILIQLKLHEKVKNSF--EYCEVHIPFF-NRG------LIVHVEATPSVGQVKVSK 176
Query: 417 -ENAIVWKI-KRMAGMKETQLSAEI 439
+ +VW I ++ E LS +
Sbjct: 177 DKRLLVWNIGQKFPKSLEATLSGTV 201
>gnl|CDD|227363 COG5030, APS2, Clathrin adaptor complex, small subunit
[Intracellular trafficking and secretion].
Length = 152
Score = 31.6 bits (72), Expect = 0.65
Identities = 25/138 (18%), Positives = 57/138 (41%), Gaps = 6/138 (4%)
Query: 1 MIGGLFVYNHKGEVLISRVYR--DDIGRNAVDAFRVNVIHARQQVRSPVTNIARTSFFHI 58
MI + ++N +G+ + + Y D + + A +I AR+ S +
Sbjct: 1 MIKFVLIFNRQGKPRLVKWYTPVSDPEQAKLIADIYELISARKPKESNFIEGKNEKIVYR 60
Query: 59 KRANIWLAAVTKQNVNAAMVFEFLLKFIDVMQSYFGKISEENIKNNFF--IDVMQSYF-- 114
+ A ++ + N ++ E + F++++ +FG + E ++ NF ++
Sbjct: 61 RYATLYFVFGVDNDDNELIILELIHNFVEILDRFFGNVCELDLIFNFQKVYAILDEMILG 120
Query: 115 GKISEENIKNNFVLIYEL 132
G+I E + +Y L
Sbjct: 121 GEIIESSKNEVLEHVYAL 138
Score = 28.9 bits (65), Expect = 5.6
Identities = 11/36 (30%), Positives = 23/36 (63%)
Query: 104 NFFIDVMQSYFGKISEENIKNNFVLIYELLDDRYLG 139
+ F++++ +FG + E ++ NF +Y +LD+ LG
Sbjct: 85 HNFVEILDRFFGNVCELDLIFNFQKVYAILDEMILG 120
>gnl|CDD|198191 cd09938, SH2_N-SH2_Zap70_Syk_like, N-terminal Src homology 2 (SH2)
domain found in Zeta-chain-associated protein kinase 70
(ZAP-70) and Spleen tyrosine kinase (Syk) proteins.
ZAP-70 and Syk comprise a family of hematopoietic cell
specific protein tyrosine kinases (PTKs) that are
required for antigen and antibody receptor function.
ZAP-70 is expressed in T and natural killer (NK) cells
and Syk is expressed in B cells, mast cells,
polymorphonuclear leukocytes, platelets, macrophages,
and immature T cells. They are required for the proper
development of T and B cells, immune receptors, and
activating NK cells. They consist of two N-terminal Src
homology 2 (SH2) domains and a C-terminal kinase domain
separated from the SH2 domains by a linker or hinge
region. Phosphorylation of both tyrosine residues within
the Immunoreceptor Tyrosine-based Activation Motifs
(ITAM; consensus sequence Yxx[LI]x(7,8)Yxx[LI]) by the
Src-family PTKs is required for efficient interaction of
ZAP-70 and Syk with the receptor subunits and for
receptor function. ZAP-70 forms two phosphotyrosine
binding pockets, one of which is shared by both SH2
domains. In Syk the two SH2 domains do not form such a
phosphotyrosine-binding site. The SH2 domains here are
believed to function independently. In addition, the two
SH2 domains of Syk display flexibility in their relative
orientation, allowing Syk to accommodate a greater
variety of spacing sequences between the ITAM
phosphotyrosines and singly phosphorylated non-classical
ITAM ligands. This model contains the N-terminus SH2
domains of both Syk and Zap70. In general SH2 domains
are involved in signal transduction. They typically bind
pTyr-containing ligands via two surface pockets, a pTyr
and hydrophobic binding pocket, allowing proteins with
SH2 domains to localize to tyrosine phosphorylated
sites.
Length = 104
Score = 30.4 bits (69), Expect = 0.91
Identities = 20/103 (19%), Positives = 41/103 (39%), Gaps = 15/103 (14%)
Query: 113 YFGKISEENIKNNFVLIYELLDDRYLGMESERGRASYILKIVHDRK----------ENTY 162
++G I+ E ++ + + D +L +S R Y+L + H RK TY
Sbjct: 4 FYGSITRE-EAEEYLKLAGMSDGLFLLRQSLRSLGGYVLSVCHGRKFHHYTIERQLNGTY 62
Query: 163 KSFNPSSFPSPSEILDFGYPQNSD---TGVLKTFILQQGVKSQ 202
+ P+E+ ++ + + D + K GV+ +
Sbjct: 63 AIAGGKAHCGPAELCEY-HSTDLDGLVCLLRKPCNRPPGVEPK 104
>gnl|CDD|201673 pfam01229, Glyco_hydro_39, Glycosyl hydrolases family 39.
Length = 486
Score = 31.0 bits (70), Expect = 2.3
Identities = 18/64 (28%), Positives = 21/64 (32%), Gaps = 13/64 (20%)
Query: 452 RPPISMNFEVPFAPSGFKVRYLKVFEPKLNYSD-HDVIKWV--------RYIGRSGLYET 502
P I + F SG VF K N + +W YI R GL E
Sbjct: 99 LPFIELGFMPMGLASGTFT----VFHDKGNITPPKQYEEWKDLVSLLARHYISRYGLNEV 154
Query: 503 RKEN 506
K N
Sbjct: 155 SKWN 158
>gnl|CDD|183266 PRK11663, PRK11663, regulatory protein UhpC; Provisional.
Length = 434
Score = 30.8 bits (70), Expect = 2.4
Identities = 21/59 (35%), Positives = 27/59 (45%), Gaps = 10/59 (16%)
Query: 488 IKWVRYIGRSGLYETRKENTYKSFNPSSFPSPSEILDFGYPQNSDTGVLKT-FILQQGV 545
I Y+G + Y TR KSFN P + D G + SD G+L T F + GV
Sbjct: 24 ILITMYLGYALFYFTR-----KSFN---AAMPEMLADLGLSR-SDIGLLATLFYITYGV 73
>gnl|CDD|182043 PRK09716, PRK09716, hypothetical protein; Provisional.
Length = 395
Score = 30.8 bits (69), Expect = 2.5
Identities = 20/63 (31%), Positives = 32/63 (50%), Gaps = 3/63 (4%)
Query: 61 ANIWLAAVTKQNVNAAMVFEFLLKFIDVMQSYFGKISEENIKNNFFIDVMQSYFGKISEE 120
AN++ NA + +++LLK V+ S SEE IK F++ + G I+EE
Sbjct: 191 ANMFQVNFVSSTQNATISWDYLLKITPVLTSISDMYSEEKIK---FVESCLNELGDITEE 247
Query: 121 NIK 123
+K
Sbjct: 248 QLK 250
>gnl|CDD|183464 PRK12352, PRK12352, putative carbamate kinase; Reviewed.
Length = 316
Score = 30.5 bits (69), Expect = 3.1
Identities = 18/69 (26%), Positives = 33/69 (47%), Gaps = 3/69 (4%)
Query: 359 IPLVREATRTKMEVKVVLKSQFKASLLGQKIEVRIPTPLNTSGVQLICLK-GKAKYKASE 417
IP+VR V V+ +LL ++I I + T+GV+ +C+ GK + +A +
Sbjct: 197 IPVVRTDAGDYQSVDAVIDKDLSTALLAREIHADI--LVITTGVEKVCIHFGKPQQQALD 254
Query: 418 NAIVWKIKR 426
+ + R
Sbjct: 255 RVDIATMTR 263
>gnl|CDD|149804 pfam08859, DGC, DGC domain. This domain appears to be a zinc
binding domain from the conservation of four potential
chelating cysteines. The domain is named after a
conserved central motif. The function of this domain is
unknown.
Length = 110
Score = 28.8 bits (65), Expect = 3.2
Identities = 12/31 (38%), Positives = 17/31 (54%), Gaps = 5/31 (16%)
Query: 296 VAGGD----DVGRSGKPVVVIDDCQFHQCVK 322
V GG + RSG+P++ ID C + C K
Sbjct: 37 VGGGVEGLVKLARSGRPIIAIDGCPLN-CAK 66
Score = 28.8 bits (65), Expect = 3.2
Identities = 12/31 (38%), Positives = 17/31 (54%), Gaps = 5/31 (16%)
Query: 642 VAGGD----DVGRSGKPVVVIDDCQFHQCVK 668
V GG + RSG+P++ ID C + C K
Sbjct: 37 VGGGVEGLVKLARSGRPIIAIDGCPLN-CAK 66
>gnl|CDD|235951 PRK07165, PRK07165, F0F1 ATP synthase subunit alpha; Validated.
Length = 507
Score = 30.3 bits (69), Expect = 4.0
Identities = 11/39 (28%), Positives = 18/39 (46%), Gaps = 4/39 (10%)
Query: 78 VFEFLLKFIDVMQSYFGKISEENIKNNFFID--VMQSYF 114
+F+ I+ K IKNN +D +M++YF
Sbjct: 430 ALDFIDYLIEN--DPDAKKIFNKIKNNEDVDDELMKNYF 466
>gnl|CDD|115806 pfam07176, DUF1400, Alpha/beta hydrolase of unknown function
(DUF1400). This family contains a number of
hypothetical proteins of unknown function that seem to
be specific to cyanobacteria. Members of this family
have an alpha/beta hydrolase fold.
Length = 127
Score = 28.5 bits (64), Expect = 5.5
Identities = 11/41 (26%), Positives = 21/41 (51%)
Query: 363 REATRTKMEVKVVLKSQFKASLLGQKIEVRIPTPLNTSGVQ 403
RE + ++ + V SQF S +G+ I ++ ++T Q
Sbjct: 50 REFLQMRLPLNPVTLSQFLNSPIGKDILAQLSQIIHTPSDQ 90
>gnl|CDD|226723 COG4273, COG4273, Uncharacterized conserved protein [Function
unknown].
Length = 135
Score = 28.6 bits (64), Expect = 5.6
Identities = 14/51 (27%), Positives = 19/51 (37%), Gaps = 5/51 (9%)
Query: 276 NDKIVMEAKGGSSAKSSGLTVAGG----DDVGRSGKPVVVIDDCQFHQCVK 322
N V K G + S V G D RSG+ ++ +D C C
Sbjct: 33 NQLAVALDKAGPAELSCTAGVGAGVPALVDAARSGRRILALDGCPLR-CAT 82
Score = 28.6 bits (64), Expect = 5.6
Identities = 14/51 (27%), Positives = 19/51 (37%), Gaps = 5/51 (9%)
Query: 622 NDKIVMEAKGGSSAKSSGLTVAGG----DDVGRSGKPVVVIDDCQFHQCVK 668
N V K G + S V G D RSG+ ++ +D C C
Sbjct: 33 NQLAVALDKAGPAELSCTAGVGAGVPALVDAARSGRRILALDGCPLR-CAT 82
>gnl|CDD|107289 cd06294, PBP1_ycjW_transcription_regulator_like, Ligand-binding
domain of uncharacterized transcription regulator ycjW
which is a member of the LacI-GalR family repressors.
This group includes the ligand-binding domain of
uncharacterized transcription regulator ycjW which is a
member of the LacI-GalR family repressors that are
composed of two functional domains: an N-terminal HTH
(helix-turn-helix) domain, which is responsible for the
DNA-binding specificity, and a C-terminal ligand-binding
domain, which is homologous to the sugar-binding domain
of ABC-type transport systems that contain the type I
periplasmic binding protein-like fold. As also observed
in the periplasmic binding proteins, the C-terminal
domain of the bacterial transcription repressor
undergoes a conformational change upon ligand binding
which in turn changes the DNA binding affinity of the
repressor.
Length = 270
Score = 29.1 bits (66), Expect = 6.4
Identities = 9/34 (26%), Positives = 18/34 (52%), Gaps = 4/34 (11%)
Query: 97 SEENIKNNFFIDVMQSYFGKISEENIKNNFVLIY 130
++E +N FFI+V++ IS +N + +
Sbjct: 10 ADEAFQNPFFIEVLRG----ISAVANENGYDISL 39
>gnl|CDD|227141 COG4804, COG4804, Predicted nuclease of restriction
endonuclease-like fold [General function prediction
only].
Length = 159
Score = 28.6 bits (64), Expect = 7.2
Identities = 13/83 (15%), Positives = 33/83 (39%), Gaps = 8/83 (9%)
Query: 38 HARQQVRSPVTNI-ARTSFFHIKRANIWLAAVTKQNVNAAMVFE--FLLKFIDVMQSYFG 94
RQ R + + RT H K + + ++ + ++L+F+ + ++Y
Sbjct: 29 SVRQLERQIASQLYERTLLSHDKEKVKQQSLQIEDDLTPEQIIMDPYVLEFLSLKRNYLE 88
Query: 95 KISEENIKNNFFIDVMQSYFGKI 117
E + I ++Q + ++
Sbjct: 89 FDLEYAL-----IQILQQFLLEL 106
>gnl|CDD|184516 PRK14115, gpmA, phosphoglyceromutase; Provisional.
Length = 247
Score = 29.1 bits (66), Expect = 7.8
Identities = 15/46 (32%), Positives = 19/46 (41%), Gaps = 11/46 (23%)
Query: 113 YFGKISEE-----NIKNNFVLIYELLDD------RYLGMESERGRA 147
Y IS+E NI L+YEL ++ YLG E A
Sbjct: 191 YLDNISDEEILELNIPTGVPLVYELDENLKPIKHYYLGDADEIAAA 236
>gnl|CDD|180975 PRK07429, PRK07429, phosphoribulokinase; Provisional.
Length = 327
Score = 29.2 bits (66), Expect = 8.2
Identities = 18/37 (48%), Positives = 21/37 (56%), Gaps = 4/37 (10%)
Query: 420 IVWKIKR-MA--GMKETQLSAEIELLETDTKKKWTRP 453
I WKIKR MA G Q+ AEIE E D + + RP
Sbjct: 139 IAWKIKRDMAKRGHTYEQVLAEIEAREPDF-EAYIRP 174
>gnl|CDD|211789 TIGR03137, AhpC, peroxiredoxin. This peroxiredoxin (AhpC,
alkylhydroperoxide reductase subunit C) is one subunit
of a two-subunit complex with subunit F(TIGR03140).
Usually these are found as an apparent operon. The gene
has been characterized in Bacteroides fragilis where it
is important in oxidative stress defense. This gene
contains two invariant cysteine residues, one near the
N-terminus and one near the C-terminus, each followed
immediately by a proline residue [Cellular processes,
Detoxification, Cellular processes, Adaptations to
atypical conditions].
Length = 187
Score = 28.5 bits (64), Expect = 9.0
Identities = 13/42 (30%), Positives = 22/42 (52%), Gaps = 2/42 (4%)
Query: 4 GLFVYNHKGEVLISRVYRDDIGRNAVDAFRVNVIHARQQVRS 45
G FV + +G + ++ + IGR+A + R I A Q V +
Sbjct: 121 GTFVIDPEGVIQAVEIHDNGIGRDASELLR--KIKAAQYVAA 160
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
0.318 0.135 0.389
Gapped
Lambda K H
0.267 0.0714 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 34,829,791
Number of extensions: 3409201
Number of successful extensions: 2618
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2567
Number of HSP's successfully gapped: 69
Length of query: 691
Length of database: 10,937,602
Length adjustment: 104
Effective length of query: 587
Effective length of database: 6,324,786
Effective search space: 3712649382
Effective search space used: 3712649382
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 62 (27.7 bits)