RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11356
(70 letters)
>gnl|CDD|219472 pfam07575, Nucleopor_Nup85, Nup85 Nucleoporin. A family of
nucleoporins conserved from yeast to human. THe nuclear
pore complex is a large assembly composed of two
essential complexes: the heptameric Nup84 complex and
the heteromeric Nic96-containing complex. The Nup84
complex is composed of one copy each of Nup84, Nup85,
Nup120, Nup133, Nup145C, Sec13, and Seh1. The structure
of a complex of Nup85 and Seh1 was solved. The
N-terminus of Nup85 is inserted and forms a
three-stranded blade that completes the Seh1 6-bladed
beta-propeller in trans. Following its N-terminal
insertion blade, Nup85 forms a compact cuboid structure
composed of 20 helices, with two distinct modules,
referred to as crown and trunk.
Length = 564
Score = 27.3 bits (61), Expect = 0.58
Identities = 7/49 (14%), Positives = 17/49 (34%), Gaps = 5/49 (10%)
Query: 4 SIVTKELLTECLTFETQMDYKTYLDFVLSLENKHEPQALQYLFRFLDIK 52
++ + L+ L+F Y +F +A + L ++
Sbjct: 480 NLGSGMFLSPRLSF-----LAKYREFFRLYREGDFLKAAELLVSLIEFP 523
>gnl|CDD|149409 pfam08337, Plexin_cytopl, Plexin cytoplasmic RasGAP domain. This
family features the C-terminal regions of various
plexins. Plexins are receptors for semaphorins, and
plexin signalling is important in path finding and
patterning of both neurons and developing blood vessels.
The cytoplasmic region, which has been called a SEX
domain in some members of this family, is involved in
downstream signalling pathways, by interaction with
proteins such as Rac1, RhoD, Rnd1 and other plexins.
This domain acts as a RasGAP domain.
Length = 538
Score = 25.0 bits (55), Expect = 3.6
Identities = 9/21 (42%), Positives = 12/21 (57%)
Query: 30 VLSLENKHEPQALQYLFRFLD 50
+LS P A++Y F FLD
Sbjct: 375 ILSTAGSALPLAVKYFFDFLD 395
>gnl|CDD|204733 pfam11753, DUF3310, Protein of unknwon function (DUF3310). This
is a family of conserved bacteriophage proteins of
unknown function.
Length = 60
Score = 24.2 bits (53), Expect = 3.7
Identities = 11/36 (30%), Positives = 16/36 (44%), Gaps = 7/36 (19%)
Query: 13 ECLTFETQMDYKTYLDFVLSLENKHEPQALQYLFRF 48
EC+ F + Y+ L F L A++YL R
Sbjct: 14 ECIDFIESVTYEQALGFCLG-------NAIKYLSRA 42
>gnl|CDD|140297 PTZ00271, PTZ00271, hypoxanthine-guanine phosphoribosyltransferase;
Provisional.
Length = 211
Score = 25.0 bits (54), Expect = 3.8
Identities = 18/55 (32%), Positives = 22/55 (40%), Gaps = 9/55 (16%)
Query: 18 ETQMDYKTYLDFVLSLENKH---------EPQALQYLFRFLDIKHQGYLDTFTLF 63
ET + LD S+EN+H LQYL RF+ K L T L
Sbjct: 101 ETSGQVRMLLDVRDSVENRHILIVEDIVDSAITLQYLMRFMLAKKPASLKTVVLL 155
>gnl|CDD|213344 cd12205, RasGAP_plexin, Ras-GTPase Activating Domain of plexins.
Plexins form a conserved family of transmembrane
receptors for semaphorins and may be the ancestors of
semaphorins. Ligand binding activates signal
transduction pathways controlling axon guidance in the
nervous system and other developmental processes,
including cell migration and morphogenesis, immune
function, and tumor progression. Plexins are divided
into four types (A-D) according to sequence similarity.
In vertebrates, type A Plexins serve as the co-receptors
for neuropilins to mediate the signaling of class 3
semaphorins except Sema3E, which signals through Plexin
D1. Plexins serve as direct receptors for several other
members of the semaphorin family: class 6 semaphorins
signal through type A plexins and class 4 semaphorins
through type B. Plexin C1 serves as the receptor of
Sema7A and plays regulation roles in both immune and
nervous systems. Plexins contain a C-terminal RasGAP
domain, which functions as an enhancer of the hydrolysis
of GTP that is bound to Ras-GTPases. Plexins display GAP
activity towards the Ras homolog Rap. Other proteins
having a RasGAP domain include p120GAP, IQGAP,
Rab5-activating protein 6, and Neurofibromin. Although
the Rho (Ras homolog) GTPases are most closely related
to members of the Ras family, RhoGAP and RasGAP show no
sequence homology at their amino acid level. RasGTPases
function as molecular switches in a large number of of
signaling pathways. When bound to GTP they are in the on
state and when bound to GDP they are in the off state.
The RasGAP domain speeds up the hydrolysis of GTP in
Ras-like proteins acting as a negative regulator.
Length = 382
Score = 24.1 bits (53), Expect = 6.2
Identities = 14/41 (34%), Positives = 23/41 (56%), Gaps = 2/41 (4%)
Query: 10 LLTECLTFETQMDYKTYLDFVLSLENKHEPQALQYLFRFLD 50
LL+ T + +D + +LS+ + P A++YLF FLD
Sbjct: 177 LLSTKGTLQKFVD--DLFESILSVPQRSLPPAIKYLFDFLD 215
>gnl|CDD|240150 cd05023, S-100A11, S-100A11: S-100A11 domain found in proteins
similar to S100A11. S100A11 is a member of the S-100
domain family within EF-hand Ca2+-binding proteins
superfamily. Note that the S-100 hierarchy, to which
this S-100A11 group belongs, contains only S-100
EF-hand domains, other EF-hands have been modeled
separately. S100 proteins exhibit unique patterns of
tissue- and cell type-specific expression and have been
implicated in the Ca2+-dependent regulation of diverse
physiological processes, including cell cycle
regulation, differentiation, growth, and metabolic
control . S100 proteins have also been associated with
a variety of pathological events, including neoplastic
transformation and neurodegenerative diseases such as
Alzheimer's, usually via over expression of the
protein. S100A11 is expressed in smooth muscle and
other tissues and involves in calcium-dependent
membrane aggregation, which is important for cell
vesiculation . As is the case for many other S100
proteins, S100A11 is homodimer, which is able to form a
heterodimer with S100B through subunit exchange. Ca2+
binding to S100A11 results in a conformational change
in the protein, exposing a hydrophobic surface that
interacts with target proteins. In addition to binding
to annexin A1 and A6 S100A11 also interacts with actin
and transglutaminase.
Length = 89
Score = 23.6 bits (51), Expect = 8.0
Identities = 11/45 (24%), Positives = 21/45 (46%), Gaps = 5/45 (11%)
Query: 19 TQMDYKTYLDFVLS-----LENKHEPQALQYLFRFLDIKHQGYLD 58
Q+ +L F+ + +N+ +P L + + LD+ G LD
Sbjct: 26 YQLSKTEFLSFMNTELASFTKNQKDPGVLDRMMKKLDLNSDGQLD 70
>gnl|CDD|227455 COG5126, FRQ1, Ca2+-binding protein (EF-Hand superfamily) [Signal
transduction mechanisms / Cytoskeleton / Cell division
and chromosome partitioning / General function
prediction only].
Length = 160
Score = 23.8 bits (52), Expect = 8.4
Identities = 10/46 (21%), Positives = 21/46 (45%), Gaps = 1/46 (2%)
Query: 20 QMDYKTYLDFV-LSLENKHEPQALQYLFRFLDIKHQGYLDTFTLFY 64
+D+ +L + + L+ + + L+ F+ D H GY+ L
Sbjct: 71 TVDFPEFLTVMSVKLKRGDKEEELREAFKLFDKDHDGYISIGELRR 116
>gnl|CDD|193336 pfam12862, Apc5, Anaphase-promoting complex subunit 5. Apc5 is a
subunit of the anaphase-promoting complex/cyclosome
(APC/C) which is a multisubunit ubiquitin ligase that
mediates the proteolysis of cell cycle proteins in
mitosis and G1. Apc5, although it does not harbour a
classical RNA binding domain, Apc5 binds the poly(A)
binding protein (PABP), which directly binds the
internal ribosome entry site (IRES) of growth factor 2
mRNA. PABP was found to enhance IRES-mediated
translation, whereas Apc5 over-expression counteracted
this effect. In addition to its association with the
APC/C complex, Apc5 binds much heavier complexes and
co-sediments with the ribosomal fraction. The
N-terminus of Afi1 serves to stabilise the union
between Apc4 and Apc5, both of which lie towards the
bottom-front of the APC. This region of the Apc5 member
proteins carries a TPR-like motif.
Length = 91
Score = 23.3 bits (51), Expect = 9.4
Identities = 8/25 (32%), Positives = 12/25 (48%)
Query: 26 YLDFVLSLENKHEPQALQYLFRFLD 50
YL ++ +L AL L R+ D
Sbjct: 2 YLSYLNALRVGDYQGALDSLHRYFD 26
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
0.330 0.143 0.430
Gapped
Lambda K H
0.267 0.0780 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,461,864
Number of extensions: 252435
Number of successful extensions: 263
Number of sequences better than 10.0: 1
Number of HSP's gapped: 263
Number of HSP's successfully gapped: 13
Length of query: 70
Length of database: 10,937,602
Length adjustment: 40
Effective length of query: 30
Effective length of database: 9,163,442
Effective search space: 274903260
Effective search space used: 274903260
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 53 (24.1 bits)