RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16332
(359 letters)
>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 = 230 bits (589), Expect = 9e-75
Identities = 90/156 (57%), Positives = 117/156 (75%), Gaps = 1/156 (0%)
Query: 129 THPNVDKELFKSKTEIGLKNPSKPFPLNNDIGVLKWRFTSTDESCLPLSINCWPSDNGSG 188
THPNVDK+LF S + +GLK+PSKPFP+N+ +GVLKWR S DES LPL+INCWPS++G G
Sbjct: 58 THPNVDKKLFTSDSVLGLKDPSKPFPVNDPVGVLKWRLQSKDESLLPLTINCWPSESG-G 116
Query: 189 GCDVNIEYELEHEEKELNQVTISIPLPLHCTPNVTECDGDYNYDARKNTLTWSLALIDSS 248
G DV IEYEL ++ ELN V ISIPLP P V DG+Y YD RKN L W + LID+S
Sbjct: 117 GTDVTIEYELNRDDLELNDVVISIPLPSGSAPVVNSDDGEYEYDGRKNGLIWKIPLIDAS 176
Query: 249 NKSGALEFSAPSASQSDFFPLQVSFSCNQSYANIKI 284
N SG+LEFS ++ + DFFP+ VSF+ ++++ +K+
Sbjct: 177 NSSGSLEFSIAASDEDDFFPISVSFTSSKTFCGVKV 212
Score = 86.5 bits (215), Expect = 9e-20
Identities = 31/64 (48%), Positives = 45/64 (70%)
Query: 296 PNVTECDGDYNYDARKNTLTWSLALIDSSNKSGALEFSAPSASQSDFFPLQVSFSCNQSY 355
P V DG+Y YD RKN L W + LID+SN SG+LEFS ++ + DFFP+ VSF+ ++++
Sbjct: 148 PVVNSDDGEYEYDGRKNGLIWKIPLIDASNSSGSLEFSIAASDEDDFFPISVSFTSSKTF 207
Query: 356 ANIK 359
+K
Sbjct: 208 CGVK 211
>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 = 89.8 bits (223), Expect = 7e-21
Identities = 41/164 (25%), Positives = 67/164 (40%), Gaps = 16/164 (9%)
Query: 129 THPNVDKELFKSKTEIGLKNPSKPFPLNNDIGVLKWRFTSTDESCLPLSINCWPSDNGSG 188
HP V + F+S+ I P F L + VL+ E LP++I S+ G G
Sbjct: 59 FHPCVRLKRFESERIISFIPPDGEFELMSYRTVLE-------EPILPITIFPVVSEEG-G 110
Query: 189 GCDVNIEYEL-EHEEKELNQVTISIPLPLHCT-PNVTECDGDYNYDARKNTLTWSLALID 246
+V ++ +L E + V + IPLP T + DG +D KN L W + I
Sbjct: 111 RLEVTVKLKLSESLQLTAENVEVHIPLPSGVTSLSSKPSDGQAKFDPEKNALVWRIKRIP 170
Query: 247 SSNKSGALEF-----SAPSASQSDFFPLQVSFSCNQ-SYANIKI 284
K +L + P+ +SF + + + I++
Sbjct: 171 VGGKEQSLSATFELGGLAHECPEEAPPVSLSFEIPETTGSGIQV 214
Score = 39.7 bits (93), Expect = 0.001
Identities = 13/60 (21%), Positives = 20/60 (33%), Gaps = 5/60 (8%)
Query: 296 PNVTECDGDYNYDARKNTLTWSLALIDSSNKSGALEF-----SAPSASQSDFFPLQVSFS 350
+ DG +D KN L W + I K +L + P+ +SF
Sbjct: 144 LSSKPSDGQAKFDPEKNALVWRIKRIPVGGKEQSLSATFELGGLAHECPEEAPPVSLSFE 203
>gnl|CDD|216199 pfam00928, Adap_comp_sub, Adaptor complexes medium subunit family.
This family also contains members which are coatomer
subunits.
Length = 228
Score = 47.8 bits (114), Expect = 2e-06
Identities = 25/76 (32%), Positives = 36/76 (47%), Gaps = 8/76 (10%)
Query: 207 QVTISIPLPLHCTPNVT--ECDGDYNYDARKNTLTWSLALIDSSN---KSGALEFSAPSA 261
+++ ++PLP P+ DG YD +N L W++ I SG LE S+ S
Sbjct: 111 RISSNVPLPFKVNPSPVLTVSDGKAKYDPEENALEWTIGKIPGGKEPTLSGELELSSTSE 170
Query: 262 SQS---DFFPLQVSFS 274
S S F P+ V FS
Sbjct: 171 SPSKDWSFPPISVEFS 186
Score = 44.7 bits (106), Expect = 2e-05
Identities = 24/67 (35%), Positives = 33/67 (49%), Gaps = 6/67 (8%)
Query: 290 FLLHCTPNVTECDGDYNYDARKNTLTWSLALIDSSN---KSGALEFSAPSASQS---DFF 343
F ++ +P +T DG YD +N L W++ I SG LE S+ S S S F
Sbjct: 120 FKVNPSPVLTVSDGKAKYDPEENALEWTIGKIPGGKEPTLSGELELSSTSESPSKDWSFP 179
Query: 344 PLQVSFS 350
P+ V FS
Sbjct: 180 PISVEFS 186
>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 = 43.3 bits (103), Expect = 7e-05
Identities = 19/87 (21%), Positives = 38/87 (43%), Gaps = 5/87 (5%)
Query: 203 KELNQVTISIPLPLHC-TPNVTECDGDYNYDARKNTLTWSLALIDSS---NKSGALEFSA 258
K + V + IPLP + +T G +++D+ TL WS+ + G++ +
Sbjct: 137 KTIENVVVEIPLPKGVKSLRLTASHGTFSFDSSTKTLVWSIGKLTPGKTPTLRGSISLES 196
Query: 259 PSASQSDFFPLQVSFSC-NQSYANIKI 284
+ S+ + VSF + +K+
Sbjct: 197 GEEAPSEPPSISVSFKIPGYLPSGLKV 223
Score = 35.6 bits (83), Expect = 0.022
Identities = 13/69 (18%), Positives = 29/69 (42%), Gaps = 4/69 (5%)
Query: 295 TPNVTECDGDYNYDARKNTLTWSLALIDSS---NKSGALEFSAPSASQSDFFPLQVSFSC 351
+ +T G +++D+ TL WS+ + G++ + + S+ + VSF
Sbjct: 154 SLRLTASHGTFSFDSSTKTLVWSIGKLTPGKTPTLRGSISLESGEEAPSEPPSISVSFKI 213
Query: 352 -NQSYANIK 359
+ +K
Sbjct: 214 PGYLPSGLK 222
>gnl|CDD|235865 PRK06814, PRK06814, acylglycerophosphoethanolamine acyltransferase;
Provisional.
Length = 1140
Score = 30.7 bits (70), Expect = 1.3
Identities = 23/102 (22%), Positives = 35/102 (34%), Gaps = 27/102 (26%)
Query: 47 KLKNIKIAIVSRQFVEMTRARIEGLLAAFPKLMSSGKQHTFVETDSVRYVYQPLEKLYML 106
K +K + SR F+E +AR+ L+ A + + VR +K+ L
Sbjct: 726 KAAQVKTVLTSRAFIE--KARLGPLIEAL------EFGIRIIYLEDVRAQIGLADKIKGL 777
Query: 107 LITTKTSNILEDLETLRLFSRVTHPNVDKE-----LFKSKTE 143
L F V N D + LF S +E
Sbjct: 778 LAGR--------------FPLVYFCNRDPDDPAVILFTSGSE 805
>gnl|CDD|211379 cd09268, FCHo1_MHD, mu-homology domain (MHD) of F-BAR
domain-containing Fer/Cip4 homology domain-only protein
1 (FCH domain only 1 or FCHo1, also known as KIAA0290)
and similar proteins. This family corresponds to the
MHD found in ubiquitously expressed mammalian
membrane-sculpting FCHo1 and similar proteins. FCHo1
represents a key initial protein that ultimately
controls cellular nutrient uptake, receptor regulation,
and synaptic vesicle retrieval. It is required for
plasma membrane clathrin-coated vesicle (CCV) budding
and marks sites of CCV formation. It binds specifically
to the plasma membrane and recruits the scaffold
proteins eps15 and intersectin, which subsequently
engage the adaptor complex AP2 and clathrin, leading to
coated vesicle formation. FCHo1 contains an N-terminal
EFC/F-BAR domain, a proline-rich domain (PRD) in the
middle region, and a C-terminal MHD. The crescent-shaped
EFC/F-BAR domain can form an antiparallel dimer
structure that binds PtdIns(4,5)P2-enriched membranes
and can polymerize into rings to generate membrane
tubules. The MHD is structurally related to the
cargo-binding mu2 subunit of adaptor complex 2 (AP-2)
and is responsible for the binding of eps15 and
intersectin. Unlike other F-BAR domain containing
proteins, FCHo1 has neither the Src homology 3 (SH3)
domain nor any other known domain for interaction with
dynamin and actin cytoskeleton. However, it can
periodically accumulate at the budding site of clathrin.
FCHo1 may utilize a unique action mode for vesicle
formation as compared with other F-BAR proteins.
Length = 259
Score = 29.9 bits (67), Expect = 1.9
Identities = 22/108 (20%), Positives = 44/108 (40%), Gaps = 7/108 (6%)
Query: 147 KNPSKPFPLNNDIGVLKWRFTSTDESCLPLSINC-WPSDNGSGGCDVNIEYELEHEEKEL 205
+NP + ++ +LK++ + + S PL ++ W G DV+++Y
Sbjct: 102 QNPQASY---YNVTLLKYQVSKSGPSAAPLYLSATWQC--GPTSTDVSLDYRQNPATAPA 156
Query: 206 NQVT-ISIPLPLHCTPNVTECDGDYNYDARKNTLTWSLALIDSSNKSG 252
+T + I LPL + ++A + L W L + N+
Sbjct: 157 TFLTDVQILLPLDEPFTNLQSQPPAAWNAEERRLHWQLPHESAGNEHD 204
>gnl|CDD|214353 CHL00073, chlN, photochlorophyllide reductase subunit N.
Length = 457
Score = 28.8 bits (65), Expect = 4.7
Identities = 13/31 (41%), Positives = 18/31 (58%)
Query: 82 GKQHTFVETDSVRYVYQPLEKLYMLLITTKT 112
G HTF V ++YQ +E + L+I TKT
Sbjct: 16 GNYHTFCPISCVAWLYQKIEDSFFLVIGTKT 46
>gnl|CDD|224169 COG1249, Lpd, Pyruvate/2-oxoglutarate dehydrogenase complex,
dihydrolipoamide dehydrogenase (E3) component, and
related enzymes [Energy production and conversion].
Length = 454
Score = 28.7 bits (65), Expect = 4.8
Identities = 15/67 (22%), Positives = 24/67 (35%), Gaps = 8/67 (11%)
Query: 22 IFAFDEIVALGYRESVNLAQEATKIKLKNIKIAIVSRQFVEMTRARIEGLLAAFPKLMSS 81
+F EI ++G E +EA + I + F RA G F KL+
Sbjct: 349 VFTDPEIASVGLTE-----EEAKE---AGIDYKVGKFPFAANGRAITMGETDGFVKLVVD 400
Query: 82 GKQHTFV 88
+ +
Sbjct: 401 KETGRIL 407
>gnl|CDD|183181 PRK11534, PRK11534, DNA-binding transcriptional regulator CsiR;
Provisional.
Length = 224
Score = 28.3 bits (63), Expect = 5.2
Identities = 10/27 (37%), Positives = 19/27 (70%)
Query: 85 HTFVETDSVRYVYQPLEKLYMLLITTK 111
+ +++ D +R +QP EKL M L+T++
Sbjct: 13 YRWLKNDIIRGNFQPDEKLRMSLLTSR 39
>gnl|CDD|224768 COG1855, COG1855, ATPase (PilT family) [General function prediction
only].
Length = 604
Score = 28.5 bits (64), Expect = 7.1
Identities = 16/59 (27%), Positives = 24/59 (40%), Gaps = 13/59 (22%)
Query: 12 NEVTDNAFSLIFAFDEIVALGYRESVNLAQEATKIKLKNIKIAIVSRQF---VEMTRAR 67
E+ + A +F EI G AT ++L+N +I I F E+T R
Sbjct: 191 REIIERAKRDPDSFIEIDRPG----------ATVVQLRNYRIVIARPPFSDRWEITAVR 239
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
0.317 0.132 0.387
Gapped
Lambda K H
0.267 0.0665 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 17,532,946
Number of extensions: 1634669
Number of successful extensions: 1165
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1162
Number of HSP's successfully gapped: 19
Length of query: 359
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 261
Effective length of database: 6,590,910
Effective search space: 1720227510
Effective search space used: 1720227510
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: 60 (27.0 bits)