RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12905
(611 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 = 216 bits (553), Expect = 2e-66
Identities = 82/142 (57%), Positives = 111/142 (78%), Gaps = 1/142 (0%)
Query: 470 IHLRQEEQLIISVGRNGGIETFELHGLLTLRISDEKYGRIKVLLANKDTRGIQMQTHPNV 529
+H+ EE++ ++ R+GG+E+ E+ G L+LRI+DE+ +IK+ LAN D +G Q +THPNV
Sbjct: 3 VHITVEEKISATLSRDGGLESLEVKGTLSLRINDEELAKIKIQLANNDDKGFQFKTHPNV 62
Query: 530 DKELFKSKTEIGLKNPSKPFPLNNDIGVLKWRFTSTDESCLPLSINCWPSDNGSGGCDVN 589
DK+LF S + +GLK+PSKPFP+N+ +GVLKWR S DES LPL+INCWPS++G GG DV
Sbjct: 63 DKKLFTSDSVLGLKDPSKPFPVNDPVGVLKWRLQSKDESLLPLTINCWPSESG-GGTDVT 121
Query: 590 IEYELEHEEKELNQVTISIPLP 611
IEYEL ++ ELN V ISIPLP
Sbjct: 122 IEYELNRDDLELNDVVISIPLP 143
>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 = 87.1 bits (216), Expect = 3e-19
Identities = 36/146 (24%), Positives = 66/146 (45%), Gaps = 11/146 (7%)
Query: 469 QIHLRQEEQLIISVGRNGGIETFELHGLLTLRISDEKYGRIKVLLANKDT--RGIQMQTH 526
++ L E++ + + ++G + E+ G + L+ I++ L N D + + H
Sbjct: 1 EVFLDVIEKVNLLISKDGSLLNSEVVGEIALKSFLSGMPEIRLGLNNPDVGIKLDDVSFH 60
Query: 527 PNVDKELFKSKTEIGLKNPSKPFPLNNDIGVLKWRFTSTDESCLPLSINCWPSDNGSGGC 586
P V + F+S+ I P F L + VL+ E LP++I S+ G G
Sbjct: 61 PCVRLKRFESERIISFIPPDGEFELMSYRTVLE-------EPILPITIFPVVSEEG-GRL 112
Query: 587 DVNIEYEL-EHEEKELNQVTISIPLP 611
+V ++ +L E + V + IPLP
Sbjct: 113 EVTVKLKLSESLQLTAENVEVHIPLP 138
>gnl|CDD|216199 pfam00928, Adap_comp_sub, Adaptor complexes medium subunit family.
This family also contains members which are coatomer
subunits.
Length = 228
Score = 42.4 bits (100), Expect = 3e-04
Identities = 33/149 (22%), Positives = 54/149 (36%), Gaps = 32/149 (21%)
Query: 469 QIHLRQEEQLIISVGRNGGIETFELHG------------LLTLRISDEKYGRIKVLLANK 516
++ L E++ + V ++GGI E+ G LTL ++D
Sbjct: 14 EVFLDVIERVSVIVDKDGGILNSEIQGTIDCKCYLSGMPELTLGLNDPLNIGK----IAS 69
Query: 517 DTRGIQM---QTHPNVDKELFKSKTEIGLKNPSKPFPLNNDIGVLKWRFTSTDESCLPLS 573
GI++ HP V F+S+ I P F L + +R + LP
Sbjct: 70 SGNGIELDDVSFHPCVRLSRFESERVISFIPPDGEFTL------MSYR--ISSNVPLPFK 121
Query: 574 INCWPSDNGSGGCDVNIEYELEHEEKELN 602
+N P S G + + + EE L
Sbjct: 122 VNPSPVLTVSDG-----KAKYDPEENALE 145
>gnl|CDD|220373 pfam09738, DUF2051, Double stranded RNA binding protein (DUF2051).
This is a novel protein identified as interacting with
the leucine-rich repeat domain of human flightless-I,
FliI protein.
Length = 294
Score = 34.5 bits (79), Expect = 0.14
Identities = 29/99 (29%), Positives = 46/99 (46%), Gaps = 10/99 (10%)
Query: 207 KREAENKMRE-KAKELKRQRMESAKKFPKM--------GSGVGVGSNPYFGSSSYSSSPV 257
KR+A + RE + KEL+RQ+ E ++ + S V + +N GSSS SS
Sbjct: 8 KRQARAEAREIRMKELERQQKELEERADRDFDRKDSSSTSAVSIATNSLGGSSSRRSSGD 67
Query: 258 TPVLESADISIRSSYIAQTVQREKKFRDIRIGRKSLENE 296
T + SIR ++ E+K + + L+NE
Sbjct: 68 TSSSVDTEASIR-ELKDSLIEVEEKVKKAMVSNAQLDNE 105
>gnl|CDD|234225 TIGR03480, HpnN, hopanoid biosynthesis associated RND transporter
like protein HpnN. The genomes containing members of
this family share the machinery for the biosynthesis of
hopanoid lipids. Furthermore, the genes of this family
are usually located proximal to other components of this
biological process. The proteins appear to be related to
the RND family of export proteins, particularly the
hydrophobe/amphiphile efflux-3 (HAE3) family represented
by TIGR00921.
Length = 862
Score = 30.4 bits (69), Expect = 3.7
Identities = 12/39 (30%), Positives = 15/39 (38%)
Query: 465 GHRLQIHLRQEEQLIISVGRNGGIETFELHGLLTLRISD 503
RL L + V GG F +GLL L + D
Sbjct: 85 AERLAEKLAADRTHFEDVYFPGGGPFFRRNGLLFLPLED 123
>gnl|CDD|215533 PLN02983, PLN02983, biotin carboxyl carrier protein of acetyl-CoA
carboxylase.
Length = 274
Score = 29.0 bits (65), Expect = 7.1
Identities = 16/107 (14%), Positives = 37/107 (34%), Gaps = 7/107 (6%)
Query: 250 SSYSSSPVTPVLESADISIRSSYIAQTVQREKKFRDIRIGRKSLENESYPLRIKIAQAIL 309
+S S +A++ R S + +Q + G + ++ ++ + +
Sbjct: 2 ASLSVPCAKTAAAAANVGSRLSRSSFRLQPKPNISFPSKGPNPKRSAVPKVKAQLNEVAV 61
Query: 310 WKPAVSAKAMKLGSKSHDVESFVDQLKSEGEKVISGPALSKVSTLSS 356
+ SA KS D +S V + + E + + + S
Sbjct: 62 DGSSNSA-------KSDDPKSEVAPSEPKDEPPSNSSSKPNLPDEES 101
>gnl|CDD|237683 PRK14344, PRK14344, lipoate-protein ligase B; Provisional.
Length = 223
Score = 28.9 bits (65), Expect = 7.3
Identities = 16/44 (36%), Positives = 25/44 (56%)
Query: 468 LQIHLRQEEQLIISVGRNGGIETFELHGLLTLRISDEKYGRIKV 511
L +LRQ EQ++I V + GI+ L GL + I ++K I +
Sbjct: 116 LNWYLRQLEQVLIDVLADLGIDGERLDGLTGVWIGNKKVASIGI 159
>gnl|CDD|213282 cd05914, FACL_like_3, Uncharacterized subfamily of fatty acid CoA
ligase (FACL). Fatty acyl-CoA ligases catalyze the
ATP-dependent activation of fatty acids in a two-step
reaction. The carboxylate substrate first reacts with
ATP to form an acyl-adenylate intermediate, which then
reacts with CoA to produce an acyl-CoA ester. This is a
required step before free fatty acids can participate in
most catabolic and anabolic reactions.
Length = 448
Score = 29.2 bits (66), Expect = 7.6
Identities = 13/29 (44%), Positives = 17/29 (58%), Gaps = 5/29 (17%)
Query: 462 GDLGHR-----LQIHLRQEEQLIISVGRN 485
GDLGH L I+ R++ +I S GRN
Sbjct: 331 GDLGHLDEEGYLYINGRKKNLIITSFGRN 359
>gnl|CDD|110234 pfam01217, Clat_adaptor_s, Clathrin adaptor complex small chain.
Length = 142
Score = 28.1 bits (63), Expect = 8.2
Identities = 21/93 (22%), Positives = 39/93 (41%)
Query: 102 KQHTFVETDSVRYVYQPLEKLYMLLITTKTSNILEDLETLRLFSRVIPEYCRTLDENEVT 161
K F+E + ++ +Y+ LY ++I N L LE + F + Y + E ++
Sbjct: 45 KMSNFIEFNDLKVIYKRYATLYFVVIVDDQDNELIILELIHRFVESLDRYFGNVCELDLI 104
Query: 162 DNAFSLIFAFDEIVALGYRESVNLAQVRTFVEM 194
N + DE+V G + +V V +
Sbjct: 105 FNFEKVYLILDEMVMGGEILETSKNEVLHRVAL 137
>gnl|CDD|222447 pfam13904, DUF4207, Domain of unknown function (DUF4207). This
family is found in eukaryotes; it has several conserved
tryptophan residues. The function is not known.
Length = 261
Score = 28.5 bits (64), Expect = 8.6
Identities = 11/37 (29%), Positives = 23/37 (62%), Gaps = 1/37 (2%)
Query: 199 EKVYQAVRKREAE-NKMREKAKELKRQRMESAKKFPK 234
+K+ Q +KRE E K R+K +E + ++ ++ + + K
Sbjct: 190 KKLKQQQQKREEERRKQRKKQQEEEERKQKAEEAWQK 226
>gnl|CDD|219572 pfam07780, Spb1_C, Spb1 C-terminal domain. This presumed domain is
found at the C-terminus of a family of FtsJ-like
methyltransferases. Members of this family are involved
in 60S ribosomal biogenesis.
Length = 212
Score = 28.4 bits (64), Expect = 9.2
Identities = 13/25 (52%), Positives = 17/25 (68%), Gaps = 2/25 (8%)
Query: 207 KREAENKMREKAKELKRQRMESAKK 231
K+ AE K R+K + LK R+E AKK
Sbjct: 111 KKVAEAKARKKMRALK--RLEKAKK 133
>gnl|CDD|214353 CHL00073, chlN, photochlorophyllide reductase subunit N.
Length = 457
Score = 28.8 bits (65), Expect = 9.9
Identities = 13/31 (41%), Positives = 18/31 (58%)
Query: 101 GKQHTFVETDSVRYVYQPLEKLYMLLITTKT 131
G HTF V ++YQ +E + L+I TKT
Sbjct: 16 GNYHTFCPISCVAWLYQKIEDSFFLVIGTKT 46
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 0.134 0.378
Gapped
Lambda K H
0.267 0.0820 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 30,597,824
Number of extensions: 3002726
Number of successful extensions: 2949
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2940
Number of HSP's successfully gapped: 32
Length of query: 611
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 508
Effective length of database: 6,369,140
Effective search space: 3235523120
Effective search space used: 3235523120
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 (27.5 bits)