RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15816
(171 letters)
>gnl|CDD|129972 TIGR00894, 2A0114euk, Na(+)-dependent inorganic phosphate
cotransporter. [Transport and binding proteins,
Anions].
Length = 465
Score = 63.6 bits (155), Expect = 2e-12
Identities = 33/112 (29%), Positives = 51/112 (45%), Gaps = 5/112 (4%)
Query: 41 APNFSEDPIFAVAMFTLALTFNGAVTAGYLGNGLDIAPNFSGTIFGLANTLSSFGGFVSS 100
P S + + TLA + AG L N LD+AP F G I G+ GG ++S
Sbjct: 354 LPYLSAAFYLTIIILTLANAVSSGPLAGVLINSLDLAPRFLGFIKGITGLPGFIGGLIAS 413
Query: 101 HIVG-VLTDGDKVRHFRPWQYVFMVLTTTYTVGAIVFLIFGTGQLQPWNTPK 151
+ G +L+ K W VF+++ + I +LIFG+ + Q W +
Sbjct: 414 TLAGNILSQDSK----NVWLIVFLIMAFVNILCVIFYLIFGSAERQDWAKEE 461
>gnl|CDD|119392 cd06174, MFS, The Major Facilitator Superfamily (MFS) is a large
and diverse group of secondary transporters that
includes uniporters, symporters, and antiporters. MFS
proteins facilitate the transport across cytoplasmic or
internal membranes of a variety of substrates including
ions, sugar phosphates, drugs, neurotransmitters,
nucleosides, amino acids, and peptides. They do so using
the electrochemical potential of the transported
substrates. Uniporters transport a single substrate,
while symporters and antiporters transport two
substrates in the same or in opposite directions,
respectively, across membranes. MFS proteins are
typically 400 to 600 amino acids in length, and the
majority contain 12 transmembrane alpha helices (TMs)
connected by hydrophilic loops. The N- and C-terminal
halves of these proteins display weak similarity and may
be the result of a gene duplication/fusion event. Based
on kinetic studies and the structures of a few bacterial
superfamily members, GlpT (glycerol-3-phosphate
transporter), LacY (lactose permease), and EmrD
(multidrug transporter), MFS proteins are thought to
function through a single substrate binding site,
alternating-access mechanism involving a rocker-switch
type of movement. Bacterial members function primarily
for nutrient uptake, and as drug-efflux pumps to confer
antibiotic resistance. Some MFS proteins have medical
significance in humans such as the glucose transporter
Glut4, which is impaired in type II diabetes, and
glucose-6-phosphate transporter (G6PT), which causes
glycogen storage disease when mutated.
Length = 352
Score = 32.7 bits (75), Expect = 0.083
Identities = 23/92 (25%), Positives = 35/92 (38%), Gaps = 6/92 (6%)
Query: 48 PIFAVAMFTLALTFNGAVTAGYLGNGLDIAPNFSGTIFGLANTLSSFGGFVSSHIVGVLT 107
+ VA+ L A A P GT GL NT S GG + + G+L
Sbjct: 266 ALLLVALLLLGFGLGFAFPALLTLASELAPPEARGTASGLFNTFGSLGGALGPLLAGLLL 325
Query: 108 DGDKVRHFRPWQYVFMVLTTTYTVGAIVFLIF 139
D + VF++L + A++ L+
Sbjct: 326 DTGG------YGGVFLILAALALLAALLLLLL 351
>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 = 28.3 bits (64), Expect = 1.7
Identities = 11/27 (40%), Positives = 16/27 (59%)
Query: 127 TTYTVGAIVFLIFGTGQLQPWNTPKIS 153
T T+ A V L+ T +L+ W+ P IS
Sbjct: 193 TESTLSAEVELLSTTSELKKWSRPPIS 219
>gnl|CDD|130673 TIGR01612, 235kDa-fam, reticulocyte binding/rhoptry protein. This
model represents a group of paralogous families in
plasmodium species alternately annotated as reticulocyte
binding protein, 235-kDa family protein and rhoptry
protein. Rhoptry protein is localized on the cell
surface and is extremely large (although apparently
lacking in repeat structure) and is important for the
process of invasion of the RBCs by the parasite. These
proteins are found in P. falciparum, P. vivax and P.
yoelii.
Length = 2757
Score = 28.1 bits (62), Expect = 2.9
Identities = 10/23 (43%), Positives = 11/23 (47%), Gaps = 1/23 (4%)
Query: 146 PWNTPK-ISDDVELAKKEAEPLK 167
N K I D+ KE EPLK
Sbjct: 191 ILNKLKQIDKDIIAIIKECEPLK 213
>gnl|CDD|219907 pfam08566, Pam17, Mitochondrial import protein Pam17. The
presequence translocase-associated motor (PAM) drives
the completion of preprotein translocation into the
mitochondrial matrix. The Pam17 subunit is required for
formation of a stable complex between cochaperones Pam16
and Pam18 and promotes the association of Pam16-Pam18
with the presequence translocase. Mitochondria lacking
Pam17 are selectively impaired in the import of matrix
proteins.
Length = 174
Score = 27.3 bits (61), Expect = 3.0
Identities = 13/66 (19%), Positives = 20/66 (30%), Gaps = 13/66 (19%)
Query: 27 GAVTAGYLGNG-LD--IAPNFSEDPIFAVAMFTLALTFNGAVTAGYLGNGLDIAPNFSGT 83
YL +D DP + + T+A G+L + P
Sbjct: 53 AFAGLAYLSTLEIDSPTQQIMGLDPFMVLGLATIACGA-----LGWL-----LGPFIGNA 102
Query: 84 IFGLAN 89
+F L N
Sbjct: 103 VFRLLN 108
>gnl|CDD|233247 TIGR01047, nspC, carboxynorspermidine decarboxylase. This protein
is related to diaminopimelate decarboxylase. It is the
last enzyme in norspermidine biosynthesis by an unusual
pathway shown in Vibrio alginolyticus [Central
intermediary metabolism, Polyamine biosynthesis].
Length = 380
Score = 27.1 bits (60), Expect = 5.7
Identities = 24/90 (26%), Positives = 32/90 (35%), Gaps = 17/90 (18%)
Query: 41 APNFSEDPIFAVAMFTLALTFN-------------GAVTAGYLGNGLDIAPNFSGTIFGL 87
+P + ED I + + FN G +A L GL I P +S L
Sbjct: 77 SPAYKEDDIPEIIPLADHIVFNSLAQWHRYRHKVQGKNSAVKL--GLRINPEYSEVPTDL 134
Query: 88 ANTLSSFG--GFVSSHIVGVLTDGDKVRHF 115
N F G + VL DG + HF
Sbjct: 135 YNPCGRFSRLGVQAKDFEEVLLDGIEGLHF 164
>gnl|CDD|232942 TIGR00366, TIGR00366, TIGR00366 family protein. [Hypothetical
proteins, Conserved].
Length = 438
Score = 26.3 bits (58), Expect = 8.6
Identities = 18/53 (33%), Positives = 23/53 (43%)
Query: 119 QYVFMVLTTTYTVGAIVFLIFGTGQLQPWNTPKISDDVELAKKEAEPLKKISS 171
+ +F T IVFL F T + P S D +L KKE E KK+
Sbjct: 183 ETIFSGYNLIITAIIIVFLPFITYMMMPKRGELKSIDPKLLKKEKEEEKKLKK 235
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
0.323 0.140 0.423
Gapped
Lambda K H
0.267 0.0667 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,953,085
Number of extensions: 860871
Number of successful extensions: 996
Number of sequences better than 10.0: 1
Number of HSP's gapped: 988
Number of HSP's successfully gapped: 68
Length of query: 171
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 81
Effective length of database: 6,945,742
Effective search space: 562605102
Effective search space used: 562605102
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 55 (25.1 bits)