RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12064
(148 letters)
>gnl|CDD|220800 pfam10540, Membr_traf_MHD, Munc13 (mammalian uncoordinated)
homology domain. Munc13 proteins constitute a family of
three highly homologous molecules (Munc13-1, Munc13-2
and Munc13-3) with homology to Caenorhabditis elegans
unc-13p. Munc13 proteins contain a phorbol ester-binding
C1 domain and two C2 domains, which are
Ca2+/phospholipid binding domains. Sequence analyses
have uncovered two regions called Munc13 homology
domains 1 (MHD1) and 2 (MHD2) that are arranged between
two flanking C2 domains. MHD1 and MHD2 domains are
present in a wide variety of proteins from Arabidopsis
thaliana, C. elegans, Drosophila melanogaster, mouse,
rat and human, some of which may function in a
Munc13-like manner to regulate membrane trafficking. The
MHD1 and MHD2 domains are predicted to be alpha-helical.
Length = 119
Score = 90.8 bits (226), Expect = 2e-24
Identities = 40/62 (64%), Positives = 50/62 (80%)
Query: 2 EKSLSPKQCALLDASLDSIKNYFHAAGNGLKKTYLDKSPELASLRYALSLYTQTTDALIK 61
EK LSP+QCA L +L ++K +FHA GNGLKK +L+KSPE SL+YALSLYTQ+TD LI+
Sbjct: 58 EKPLSPRQCARLYVALQTLKQFFHAEGNGLKKEFLEKSPEFQSLKYALSLYTQSTDELIE 117
Query: 62 TF 63
F
Sbjct: 118 KF 119
>gnl|CDD|176041 cd08395, C2C_Munc13, C2 domain third repeat in Munc13 (mammalian
uncoordinated) proteins. C2-like domains are thought to
be involved in phospholipid binding in a Ca2+
independent manner in both Unc13 and Munc13.
Caenorabditis elegans Unc13 has a central domain with
sequence similarity to PKC, which includes C1 and
C2-related domains. Unc13 binds phorbol esters and DAG
with high affinity in a phospholipid manner. Mutations
in Unc13 results in abnormal neuronal connections and
impairment in cholinergic neurotransmission in the
nematode. Munc13 is the mammalian homolog which are
expressed in the brain. There are 3 isoforms (Munc13-1,
-2, -3) and are thought to play a role in
neurotransmitter release and are hypothesized to be
high-affinity receptors for phorbol esters. Unc13 and
Munc13 contain both C1 and C2 domains. There are two C2
related domains present, one central and one at the
carboxyl end. Munc13-1 contains a third C2-like domain.
Munc13 interacts with syntaxin, synaptobrevin, and
synaptotagmin suggesting a role for these as scaffolding
proteins.C2 domains fold into an 8-standed beta-sandwich
that can adopt 2 structural arrangements: Type I and
Type II, distinguished by a circular permutation
involving their N- and C-terminal beta strands. Many C2
domains are Ca2+-dependent membrane-targeting modules
that bind a wide variety of substances including bind
phospholipids, inositol polyphosphates, and
intracellular proteins. Most C2 domain proteins are
either signal transduction enzymes that contain a single
C2 domain, such as protein kinase C, or membrane
trafficking proteins which contain at least two C2
domains, such as synaptotagmin 1. However, there are a
few exceptions to this including RIM isoforms and some
splice variants of piccolo/aczonin and intersectin which
only have a single C2 domain. C2 domains with a calcium
binding region have negatively charged residues,
primarily aspartates, that serve as ligands for calcium
ions. This cd contains the third C2 repeat, C2C, and
has a type-II topology.
Length = 120
Score = 85.9 bits (213), Expect = 2e-22
Identities = 30/41 (73%), Positives = 35/41 (85%)
Query: 75 IGNEEQLEFFELHICVKDYCFARDDRLVGVAVLQLKDIVEQ 115
+GNE+ E +ELHICVKDYCFARDDRLVGV VLQL+DI +
Sbjct: 61 LGNEDDPESYELHICVKDYCFARDDRLVGVTVLQLRDIAQA 101
>gnl|CDD|214577 smart00239, C2, Protein kinase C conserved region 2 (CalB).
Ca2+-binding motif present in phospholipases, protein
kinases C, and synaptotagmins (among others). Some do
not appear to contain Ca2+-binding sites. Particular C2s
appear to bind phospholipids, inositol polyphosphates,
and intracellular proteins. Unusual occurrence in
perforin. Synaptotagmin and PLC C2s are permuted in
sequence with respect to N- and C-terminal beta strands.
SMART detects C2 domains using one or both of two
profiles.
Length = 101
Score = 30.9 bits (70), Expect = 0.094
Identities = 10/37 (27%), Positives = 16/37 (43%)
Query: 85 ELHICVKDYCFARDDRLVGVAVLQLKDIVEQVKHQIC 121
EL I V D D +G + L D++ +H+
Sbjct: 65 ELEIEVYDKDRFGRDDFIGQVTIPLSDLLLGGRHEKL 101
Score = 25.5 bits (56), Expect = 6.4
Identities = 7/29 (24%), Positives = 12/29 (41%)
Query: 119 QICVKDYCFARDDRLVGVAVLQLKDIVEQ 147
+I V D D +G + L D++
Sbjct: 67 EIEVYDKDRFGRDDFIGQVTIPLSDLLLG 95
>gnl|CDD|176019 cd08373, C2A_Ferlin, C2 domain first repeat in Ferlin. Ferlins are
involved in vesicle fusion events. Ferlins and other
proteins, such as Synaptotagmins, are implicated in
facilitating the fusion process when cell membranes fuse
together. There are six known human Ferlins: Dysferlin
(Fer1L1), Otoferlin (Fer1L2), Myoferlin (Fer1L3),
Fer1L4, Fer1L5, and Fer1L6. Defects in these genes can
lead to a wide range of diseases including muscular
dystrophy (dysferlin), deafness (otoferlin), and
infertility (fer-1, fertilization factor-1).
Structurally they have 6 tandem C2 domains, designated
as (C2A-C2F) and a single C-terminal transmembrane
domain, though there is a new study that disputes this
and claims that there are actually 7 tandem C2 domains
with another C2 domain inserted between C2D and C2E.
In a subset of them (Dysferlin, Myoferlin, and Fer1)
there is an additional conserved domain called DysF. C2
domains fold into an 8-standed beta-sandwich that can
adopt 2 structural arrangements: Type I and Type II,
distinguished by a circular permutation involving their
N- and C-terminal beta strands. Many C2 domains are
Ca2+-dependent membrane-targeting modules that bind a
wide variety of substances including bind phospholipids,
inositol polyphosphates, and intracellular proteins.
Most C2 domain proteins are either signal transduction
enzymes that contain a single C2 domain, such as protein
kinase C, or membrane trafficking proteins which contain
at least two C2 domains, such as synaptotagmin 1.
However, there are a few exceptions to this including
RIM isoforms and some splice variants of piccolo/aczonin
and intersectin which only have a single C2 domain. C2
domains with a calcium binding region have negatively
charged residues, primarily aspartates, that serve as
ligands for calcium ions. This cd contains the first C2
repeat, C2A, and has a type-II topology.
Length = 127
Score = 27.2 bits (61), Expect = 2.2
Identities = 13/30 (43%), Positives = 18/30 (60%)
Query: 85 ELHICVKDYCFARDDRLVGVAVLQLKDIVE 114
L I VKDY +RL+G A + L+D+V
Sbjct: 58 SLEIVVKDYEKVGRNRLIGSATVSLQDLVS 87
>gnl|CDD|215170 PLN02301, PLN02301, pectinesterase/pectinesterase inhibitor.
Length = 548
Score = 27.5 bits (61), Expect = 3.1
Identities = 20/64 (31%), Positives = 30/64 (46%), Gaps = 3/64 (4%)
Query: 12 LLDASLDSIKNYFHAAGNGLKKTYLDKSPELASLRYALSLYTQTTDALIKTFVQSQCNEG 71
L+D S D IK+ A GN K++ D L+S+ L+ + D + QS
Sbjct: 127 LMDLSKDRIKDSVEALGNVTSKSHADAHTWLSSV---LTNHVTCLDGINGPSRQSMKPGL 183
Query: 72 RDLI 75
+DLI
Sbjct: 184 KDLI 187
>gnl|CDD|181884 PRK09469, glnA, glutamine synthetase; Provisional.
Length = 469
Score = 27.0 bits (60), Expect = 4.0
Identities = 16/34 (47%), Positives = 18/34 (52%), Gaps = 1/34 (2%)
Query: 11 ALLDASLDSIKNYFHAAGNGLKKTYLDKSPELAS 44
ALL A LD IKN H G + K D PE A+
Sbjct: 374 ALLMAGLDGIKNKIH-PGEAMDKNLYDLPPEEAA 406
>gnl|CDD|175973 cd00030, C2, C2 domain. The C2 domain was first identified in PKC.
C2 domains fold into an 8-standed beta-sandwich that can
adopt 2 structural arrangements: Type I and Type II,
distinguished by a circular permutation involving their
N- and C-terminal beta strands. Many C2 domains are
Ca2+-dependent membrane-targeting modules that bind a
wide variety of substances including bind phospholipids,
inositol polyphosphates, and intracellular proteins.
Most C2 domain proteins are either signal transduction
enzymes that contain a single C2 domain, such as protein
kinase C, or membrane trafficking proteins which contain
at least two C2 domains, such as synaptotagmin 1.
However, there are a few exceptions to this including
RIM isoforms and some splice variants of piccolo/aczonin
and intersectin which only have a single C2 domain. C2
domains with a calcium binding region have negatively
charged residues, primarily aspartates, that serve as
ligands for calcium ions.
Length = 102
Score = 25.9 bits (57), Expect = 4.4
Identities = 7/33 (21%), Positives = 14/33 (42%)
Query: 85 ELHICVKDYCFARDDRLVGVAVLQLKDIVEQVK 117
L + V D D +G + L ++++ K
Sbjct: 62 TLTVEVWDKDRFSKDDFLGEVEIPLSELLDSGK 94
>gnl|CDD|226960 COG4597, BatB, ABC-type amino acid transport system, permease
component [Amino acid transport and metabolism].
Length = 397
Score = 26.7 bits (59), Expect = 5.7
Identities = 9/15 (60%), Positives = 10/15 (66%)
Query: 39 SPELASLRYALSLYT 53
PE A+L ALS YT
Sbjct: 263 IPEFAALFLALSFYT 277
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
0.322 0.137 0.395
Gapped
Lambda K H
0.267 0.0645 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,352,031
Number of extensions: 652516
Number of successful extensions: 455
Number of sequences better than 10.0: 1
Number of HSP's gapped: 455
Number of HSP's successfully gapped: 22
Length of query: 148
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 60
Effective length of database: 7,034,450
Effective search space: 422067000
Effective search space used: 422067000
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 54 (24.8 bits)