RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12096
(173 letters)
>gnl|CDD|176031 cd08385, C2A_Synaptotagmin-1-5-6-9-10, C2A domain first repeat
present in Synaptotagmins 1, 5, 6, 9, and 10.
Synaptotagmin is a membrane-trafficking protein
characterized by a N-terminal transmembrane region, a
linker, and 2 C-terminal C2 domains. Synaptotagmin 1, a
member of class 1 synaptotagmins, is located in the
brain and endocranium and localized to the synaptic
vesicles and secretory granules. It functions as a Ca2+
sensor for fast exocytosis as do synaptotagmins 5, 6,
and 10. It is distinguished from the other
synaptotagmins by having an N-glycosylated N-terminus.
Synaptotagmins 5, 6, and 10, members of class 3
synaptotagmins, are located primarily in the brain and
localized to the active zone and plasma membrane. They
is distinguished from the other synaptotagmins by having
disulfide bonds at its N-terminus. Synaptotagmin 6 also
regulates the acrosome reaction, a unique Ca2+-regulated
exocytosis, in sperm. Synaptotagmin 9, a class 5
synaptotagmins, is located in the brain and localized to
the synaptic vesicles. It is thought to be a
Ca2+-sensor for dense-core vesicle exocytosis.
Previously all synaptotagmins were thought to be calcium
sensors in the regulation of neurotransmitter release
and hormone secretion, but it has been shown that not
all of them bind calcium. Of the 17 identified
synaptotagmins only 8 bind calcium (1-3, 5-7, 9, 10).
The function of the two C2 domains that bind calcium
are: regulating the fusion step of synaptic vesicle
exocytosis (C2A) and binding to
phosphatidyl-inositol-3,4,5-triphosphate (PIP3) in the
absence of calcium ions and to phosphatidylinositol
bisphosphate (PIP2) in their presence (C2B). C2B also
regulates also the recycling step of synaptic vesicles.
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-I topology.
Length = 124
Score = 93.1 bits (232), Expect = 5e-25
Identities = 32/51 (62%), Positives = 41/51 (80%)
Query: 112 VPYADAMNKTLVFAIFDFDRFSKHDQIGEVKVALCQIDLAQTIEEWRELQS 162
VPY++ NKTLVF+++DFDRFSKHD IGEV+V L +DL EEWR+L+S
Sbjct: 74 VPYSELGNKTLVFSVYDFDRFSKHDLIGEVRVPLLTVDLGHVTEEWRDLES 124
>gnl|CDD|176032 cd08386, C2A_Synaptotagmin-7, C2A domain first repeat present in
Synaptotagmin 7. Synaptotagmin is a
membrane-trafficking protein characterized by a
N-terminal transmembrane region, a linker, and 2
C-terminal C2 domains. Synaptotagmin 7, a member of
class 2 synaptotagmins, is located in presynaptic plasma
membranes in neurons, dense-core vesicles in endocrine
cells, and lysosomes in fibroblasts. It has been shown
to play a role in regulation of Ca2+-dependent lysosomal
exocytosis in fibroblasts and may also function as a
vesicular Ca2+-sensor. It is distinguished from the
other synaptotagmins by having over 12 splice forms.
Previously all synaptotagmins were thought to be calcium
sensors in the regulation of neurotransmitter release
and hormone secretion, but it has been shown that not
all of them bind calcium. Of the 17 identified
synaptotagmins only 8 bind calcium (1-3, 5-7, 9, 10).
The function of the two C2 domains that bind calcium
are: regulating the fusion step of synaptic vesicle
exocytosis (C2A) and binding to
phosphatidyl-inositol-3,4,5-triphosphate (PIP3) in the
absence of calcium ions and to phosphatidylinositol
bisphosphate (PIP2) in their presence (C2B). C2B also
regulates also the recycling step of synaptic vesicles.
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-I topology.
Length = 125
Score = 63.1 bits (154), Expect = 2e-13
Identities = 20/52 (38%), Positives = 32/52 (61%)
Query: 110 EGVPYADAMNKTLVFAIFDFDRFSKHDQIGEVKVALCQIDLAQTIEEWRELQ 161
EG PY + L + D+DRFS++D IGEV + L ++DL + W++L+
Sbjct: 73 EGFPYEKLQQRVLYLQVLDYDRFSRNDPIGEVSLPLNKVDLTEEQTFWKDLK 124
>gnl|CDD|176036 cd08390, C2A_Synaptotagmin-15-17, C2A domain first repeat present
in Synaptotagmins 15 and 17. Synaptotagmin is a
membrane-trafficking protein characterized by a
N-terminal transmembrane region, a linker, and 2
C-terminal C2 domains. It is thought to be involved in
the trafficking and exocytosis of secretory vesicles in
non-neuronal tissues and is Ca2+ independent. Human
synaptotagmin 15 has 2 alternatively spliced forms that
encode proteins with different C-termini. The larger,
SYT15a, contains a N-terminal TM region, a putative
fatty-acylation site, and 2 tandem C terminal C2
domains. The smaller, SYT15b, lacks the C-terminal
portion of the second C2 domain. Unlike most other
synaptotagmins it is nearly absent in the brain and
rather is found in the heart, lungs, skeletal muscle,
and testis. Synaptotagmin 17 is located in the brain,
kidney, and prostate and is thought to be a peripheral
membrane protein. Previously all synaptotagmins were
thought to be calcium sensors in the regulation of
neurotransmitter release and hormone secretion, but it
has been shown that not all of them bind calcium. Of
the 17 identified synaptotagmins only 8 bind calcium
(1-3, 5-7, 9, 10). The function of the two C2 domains
that bind calcium are: regulating the fusion step of
synaptic vesicle exocytosis (C2A) and binding to
phosphatidyl-inositol-3,4,5-triphosphate (PIP3) in the
absence of calcium ions and to phosphatidylinositol
bisphosphate (PIP2) in their presence (C2B). C2B also
regulates also the recycling step of synaptic vesicles.
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-I topology.
Length = 123
Score = 49.6 bits (119), Expect = 2e-08
Identities = 18/50 (36%), Positives = 29/50 (58%)
Query: 112 VPYADAMNKTLVFAIFDFDRFSKHDQIGEVKVALCQIDLAQTIEEWRELQ 161
V + + +TL +++D DRFS+H IG V L +DL + WR+L+
Sbjct: 73 VSFKELQRRTLRLSVYDVDRFSRHCIIGHVLFPLKDLDLVKGGVVWRDLE 122
>gnl|CDD|176033 cd08387, C2A_Synaptotagmin-8, C2A domain first repeat present in
Synaptotagmin 8. Synaptotagmin is a
membrane-trafficking protein characterized by a
N-terminal transmembrane region, a linker, and 2
C-terminal C2 domains. Previously all synaptotagmins
were thought to be calcium sensors in the regulation of
neurotransmitter release and hormone secretion, but it
has been shown that not all of them bind calcium. Of
the 17 identified synaptotagmins only 8 bind calcium
(1-3, 5-7, 9, 10). The function of the two C2 domains
that bind calcium are: regulating the fusion step of
synaptic vesicle exocytosis (C2A) and binding to
phosphatidyl-inositol-3,4,5-triphosphate (PIP3) in the
absence of calcium ions and to phosphatidylinositol
bisphosphate (PIP2) in their presence (C2B). C2B also
regulates also the recycling step of synaptic vesicles.
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-I topology.
Length = 124
Score = 48.6 bits (116), Expect = 5e-08
Identities = 19/52 (36%), Positives = 36/52 (69%)
Query: 111 GVPYADAMNKTLVFAIFDFDRFSKHDQIGEVKVALCQIDLAQTIEEWRELQS 162
VP + +TL ++DFD+FS+ + IG V++ L ++DL++ ++ WR++QS
Sbjct: 73 EVPPQELPKRTLEVLLYDFDQFSRDECIGVVELPLAEVDLSEKLDLWRKIQS 124
>gnl|CDD|176034 cd08388, C2A_Synaptotagmin-4-11, C2A domain first repeat present in
Synaptotagmins 4 and 11. Synaptotagmin is a
membrane-trafficking protein characterized by a
N-terminal transmembrane region, a linker, and 2
C-terminal C2 domains. Synaptotagmins 4 and 11, class 4
synaptotagmins, are located in the brain. Their
functions are unknown. They are distinguished from the
other synaptotagmins by having and Asp to Ser
substitution in their C2A domains. Previously all
synaptotagmins were thought to be calcium sensors in the
regulation of neurotransmitter release and hormone
secretion, but it has been shown that not all of them
bind calcium. Of the 17 identified synaptotagmins only
8 bind calcium (1-3, 5-7, 9, 10). The function of the
two C2 domains that bind calcium are: regulating the
fusion step of synaptic vesicle exocytosis (C2A) and
binding to phosphatidyl-inositol-3,4,5-triphosphate
(PIP3) in the absence of calcium ions and to
phosphatidylinositol bisphosphate (PIP2) in their
presence (C2B). C2B also regulates also the recycling
step of synaptic vesicles. 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-I topology.
Length = 128
Score = 44.6 bits (106), Expect = 2e-06
Identities = 21/54 (38%), Positives = 29/54 (53%), Gaps = 2/54 (3%)
Query: 111 GVPYADAMNKTLVFAIFDFDRFSKHDQIGEVKVALCQIDLAQ--TIEEWRELQS 162
G+PY + +L FA+ FDR+S+ D IGEV L DL + RE+Q
Sbjct: 75 GIPYNQLQDLSLHFAVLSFDRYSRDDVIGEVVCPLAGADLLNEGELLVSREIQP 128
>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 = 39.7 bits (93), Expect = 7e-05
Identities = 19/49 (38%), Positives = 28/49 (57%), Gaps = 1/49 (2%)
Query: 113 PYADAMNKTLVFAIFDFDRFSKHDQIGEVKVALCQI-DLAQTIEEWREL 160
P D + TL ++D DRFSK D +GEV++ L ++ D + E W L
Sbjct: 54 PVLDPESDTLTVEVWDKDRFSKDDFLGEVEIPLSELLDSGKEGELWLPL 102
>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 = 37.1 bits (86), Expect = 6e-04
Identities = 12/46 (26%), Positives = 19/46 (41%)
Query: 112 VPYADAMNKTLVFAIFDFDRFSKHDQIGEVKVALCQIDLAQTIEEW 157
L ++D DRF + D IG+V + L + L E+
Sbjct: 56 FEVPPPELAELEIEVYDKDRFGRDDFIGQVTIPLSDLLLGGRHEKL 101
>gnl|CDD|175995 cd04029, C2A_SLP-4_5, C2 domain first repeat present in
Synaptotagmin-like proteins 4 and 5. All Slp members
basically share an N-terminal Slp homology domain (SHD)
and C-terminal tandem C2 domains (named the C2A domain
and the C2B domain) with the SHD and C2 domains being
separated by a linker sequence of various length. SHD of
Slp (except for the Slp4-SHD) function as a specific
Rab27A/B-binding domain. In addition to Slp, rabphilin,
Noc2, and Munc13-4 also function as Rab27-binding
proteins. It has been demonstrated that Slp4/granuphilin
promotes dense-core vesicle exocytosis. The C2A domain
of Slp4 is Ca2+ dependent. Slp5 mRNA has been shown to
be restricted to human placenta and liver suggesting a
role in Rab27A-dependent membrane trafficking in
specific tissues. 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-I topology.
Length = 125
Score = 36.6 bits (85), Expect = 0.001
Identities = 12/50 (24%), Positives = 26/50 (52%)
Query: 112 VPYADAMNKTLVFAIFDFDRFSKHDQIGEVKVALCQIDLAQTIEEWRELQ 161
+ ++ +TL +++ +DRF ++ +GEV++ L + EE L
Sbjct: 76 ISHSQLETRTLQLSVWHYDRFGRNTFLGEVEIPLDSWNFDSQHEECLPLH 125
>gnl|CDD|176000 cd04035, C2A_Rabphilin_Doc2, C2 domain first repeat present in
Rabphilin and Double C2 domain. Rabphilin is found
neurons and in neuroendrocrine cells, while Doc2 is
found not only in the brain but in tissues, including
mast cells, chromaffin cells, and osteoblasts.
Rabphilin and Doc2s share highly homologous tandem C2
domains, although their N-terminal structures are
completely different: rabphilin contains an N-terminal
Rab-binding domain (RBD),7 whereas Doc2 contains an
N-terminal Munc13-1-interacting domain (MID). 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-I topology.
Length = 123
Score = 35.0 bits (81), Expect = 0.005
Identities = 17/52 (32%), Positives = 25/52 (48%), Gaps = 1/52 (1%)
Query: 102 IFIERQILEGVPYADAMNKTLVFAIFDFDRFSKHDQIGEVKVALCQIDLAQT 153
F E G+ D KTL + D DRF +D +GE ++ L ++ QT
Sbjct: 66 EFNETLTYYGITEEDIQRKTLRLLVLDEDRFG-NDFLGETRIPLKKLKPNQT 116
>gnl|CDD|176004 cd04039, C2_PSD, C2 domain present in Phosphatidylserine
decarboxylase (PSD). PSD is involved in the
biosynthesis of aminophospholipid by converting
phosphatidylserine (PtdSer) to phosphatidylethanolamine
(PtdEtn). There is a single C2 domain present and it is
thought to confer PtdSer binding motif that is common to
PKC and synaptotagmin. 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 = 108
Score = 34.5 bits (80), Expect = 0.005
Identities = 17/82 (20%), Positives = 34/82 (41%), Gaps = 20/82 (24%)
Query: 94 MPPWVVVS-----------------IFIERQILEGVPYADAMNKTLVFAIFDFDRFSKHD 136
M P+V++S +F ER E P+ N + F + D D+FS +D
Sbjct: 26 MDPFVIISFGRRVFRTSWRRHTLNPVFNERLAFEVYPHE--KNFDIQFKVLDKDKFSFND 83
Query: 137 QIGEVKVALCQ-IDLAQTIEEW 157
+ +++ + ++ A +
Sbjct: 84 YVATGSLSVQELLNAAPQPDPE 105
>gnl|CDD|175997 cd04031, C2A_RIM1alpha, C2 domain first repeat contained in
Rab3-interacting molecule (RIM) proteins. RIMs are
believed to organize specialized sites of the plasma
membrane called active zones. They also play a role in
controlling neurotransmitter release, plasticity
processes, as well as memory and learning. RIM contains
an N-terminal zinc finger domain, a PDZ domain, and two
C-terminal C2 domains (C2A, C2B). 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. Members here have a type-I
topology and do not bind Ca2+.
Length = 125
Score = 34.5 bits (80), Expect = 0.007
Identities = 22/81 (27%), Positives = 32/81 (39%), Gaps = 19/81 (23%)
Query: 87 KVAEETGMPPWVVVSIFIERQILE--GVPYADAMNKTLVFAIFDFDRFSKHDQIGEVKVA 144
K ++T P W Q E V +TL ++D+DR ++D +GE
Sbjct: 58 KTVKKTLNPEW--------NQTFEYSNVRRETLKERTLEVTVWDYDRDGENDFLGE---- 105
Query: 145 LCQIDLAQTI----EEWRELQ 161
IDLA + W LQ
Sbjct: 106 -VVIDLADALLDDEPHWYPLQ 125
>gnl|CDD|176012 cd04047, C2B_Copine, C2 domain second repeat in Copine. There are
2 copies of the C2 domain present in copine, a protein
involved in membrane trafficking, protein-protein
interactions, and perhaps even cell division and growth.
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 second C2
repeat, C2B, and has a type-I topology.
Length = 110
Score = 33.3 bits (77), Expect = 0.014
Identities = 11/40 (27%), Positives = 22/40 (55%), Gaps = 1/40 (2%)
Query: 118 MNKTLVFAIFDFDRFSKHDQIGEVKVALCQIDLAQTIEEW 157
++ + ++D+D KHD IGE + L ++ L + E+
Sbjct: 68 YDRPIKIEVYDYDSSGKHDLIGEFETTLDEL-LKSSPLEF 106
>gnl|CDD|176029 cd08383, C2A_RasGAP, C2 domain (first repeat) of Ras GTPase
activating proteins (GAPs). RasGAPs suppress Ras
function by enhancing the GTPase activity of Ras
proteins resulting in the inactive GDP-bound form of
Ras. In this way it can control cellular proliferation
and differentiation. The proteins here all contain
either a single C2 domain or two tandem C2 domains, a
Ras-GAP domain, and a pleckstrin homology (PH)-like
domain. 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. Members here have a type-I topology.
Length = 117
Score = 33.0 bits (76), Expect = 0.023
Identities = 16/47 (34%), Positives = 24/47 (51%)
Query: 126 IFDFDRFSKHDQIGEVKVALCQIDLAQTIEEWRELQSVEGEGGQIGK 172
++ D+ SK I KVAL ++DL Q +EW L V+ + G
Sbjct: 64 FYNKDKRSKDRDIVIGKVALSKLDLGQGKDEWFPLTPVDPDSEVQGS 110
>gnl|CDD|175996 cd04030, C2C_KIAA1228, C2 domain third repeat present in
uncharacterized human KIAA1228-like proteins. KIAA
proteins are uncharacterized human proteins. They were
compiled by the Kazusa mammalian cDNA project which
identified more than 2000 human genes. They are
identified by 4 digit codes that precede the KIAA
designation. Many KIAA genes are still functionally
uncharacterized including KIAA1228. 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 = 127
Score = 33.0 bits (76), Expect = 0.028
Identities = 12/52 (23%), Positives = 24/52 (46%), Gaps = 2/52 (3%)
Query: 112 VPYADAMNKTLVFAI-FDFDRFSKH-DQIGEVKVALCQIDLAQTIEEWRELQ 161
V + +TL A+ S+ +G+V + L +DL++ +W +L
Sbjct: 76 VSLEELKRRTLDVAVKNSKSFLSREKKLLGQVLIDLSDLDLSKGFTQWYDLT 127
>gnl|CDD|176056 cd08521, C2A_SLP, C2 domain first repeat present in
Synaptotagmin-like proteins. All Slp members basically
share an N-terminal Slp homology domain (SHD) and
C-terminal tandem C2 domains (named the C2A domain and
the C2B domain) with the SHD and C2 domains being
separated by a linker sequence of various length.
Slp1/JFC1 and Slp2/exophilin 4 promote granule docking
to the plasma membrane. Additionally, their C2A domains
are both Ca2+ independent, unlike the case in Slp3 and
Slp4/granuphilin in which their C2A domains are Ca2+
dependent. It is thought that SHD (except for the
Slp4-SHD) functions as a specific Rab27A/B-binding
domain. In addition to Slps, rabphilin, Noc2, and
Munc13-4 also function as Rab27-binding proteins. It has
been demonstrated that Slp3 and Slp4/granuphilin promote
dense-core vesicle exocytosis. Slp5 mRNA has been shown
to be restricted to human placenta and liver suggesting
a role in Rab27A-dependent membrane trafficking in
specific tissues. 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-I topology.
Length = 123
Score = 32.6 bits (75), Expect = 0.037
Identities = 13/46 (28%), Positives = 24/46 (52%)
Query: 112 VPYADAMNKTLVFAIFDFDRFSKHDQIGEVKVALCQIDLAQTIEEW 157
+ + +TL +++ DRF ++ +GEV++ L DL EW
Sbjct: 75 ISKSQLETRTLQLSVWHHDRFGRNTFLGEVEIPLDSWDLDSQQSEW 120
>gnl|CDD|215765 pfam00168, C2, C2 domain.
Length = 85
Score = 31.1 bits (71), Expect = 0.066
Identities = 11/21 (52%), Positives = 14/21 (66%)
Query: 122 LVFAIFDFDRFSKHDQIGEVK 142
L ++D+DRF K D IGEV
Sbjct: 65 LRIEVYDYDRFGKDDFIGEVT 85
>gnl|CDD|175990 cd04024, C2A_Synaptotagmin-like, C2 domain first repeat present in
Synaptotagmin-like proteins. Synaptotagmin is a
membrane-trafficking protein characterized by a
N-terminal transmembrane region, a linker, and 2
C-terminal C2 domains. Previously all synaptotagmins
were thought to be calcium sensors in the regulation of
neurotransmitter release and hormone secretion, but it
has been shown that not all of them bind calcium. Of
the 17 identified synaptotagmins only 8 bind calcium
(1-3, 5-7, 9, 10). The function of the two C2 domains
that bind calcium are: regulating the fusion step of
synaptic vesicle exocytosis (C2A) and binding to
phosphatidyl-inositol-3,4,5-triphosphate (PIP3) in the
absence of calcium ions and to phosphatidylinositol
bisphosphate (PIP2) in their presence (C2B). C2B also
regulates also the recycling step of synaptic vesicles.
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-I topology.
Length = 128
Score = 31.6 bits (72), Expect = 0.091
Identities = 16/55 (29%), Positives = 26/55 (47%), Gaps = 3/55 (5%)
Query: 112 VPYADAMNKTLVFAIFDFDRFSKHDQIGEVKVALCQIDLAQTIEE---WRELQSV 163
P A N+ L ++D DRF+ D +GE +AL ++ + W L+S
Sbjct: 56 FPIFSAQNQLLKLILWDKDRFAGKDYLGEFDIALEEVFADGKTGQSDKWITLKST 110
>gnl|CDD|176047 cd08402, C2B_Synaptotagmin-1, C2 domain second repeat present in
Synaptotagmin 1. Synaptotagmin is a
membrane-trafficking protein characterized by a
N-terminal transmembrane region, a linker, and 2
C-terminal C2 domains. Synaptotagmin 1, a member of the
class 1 synaptotagmins, is located in the brain and
endocranium and localized to the synaptic vesicles and
secretory granules. It functions as a Ca2+ sensor for
fast exocytosis. It, like synaptotagmin-2, has an
N-glycosylated N-terminus. Synaptotagmin 4, a member of
class 4 synaptotagmins, is located in the brain. It
functions are unknown. It, like synaptotagmin-11, has an
Asp to Ser substitution in its C2A domain. Previously
all synaptotagmins were thought to be calcium sensors in
the regulation of neurotransmitter release and hormone
secretion, but it has been shown that not all of them
bind calcium. Of the 17 identified synaptotagmins only
8 bind calcium (1-3, 5-7, 9, 10). The function of the
two C2 domains that bind calcium are: regulating the
fusion step of synaptic vesicle exocytosis (C2A) and
binding to phosphatidyl-inositol-3,4,5-triphosphate
(PIP3) in the absence of calcium ions and to
phosphatidylinositol bisphosphate (PIP2) in their
presence (C2B). C2B also regulates also the recycling
step of synaptic vesicles. 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 second C2
repeat, C2B, and has a type-I topology.
Length = 136
Score = 30.8 bits (70), Expect = 0.19
Identities = 11/32 (34%), Positives = 18/32 (56%)
Query: 112 VPYADAMNKTLVFAIFDFDRFSKHDQIGEVKV 143
VP+ L+ + D+DR K+D IG+V +
Sbjct: 75 VPFEQIQKVHLIVTVLDYDRIGKNDPIGKVVL 106
>gnl|CDD|176002 cd04037, C2E_Ferlin, C2 domain fifth 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 fifth C2
repeat, C2E, and has a type-II topology.
Length = 124
Score = 29.8 bits (68), Expect = 0.34
Identities = 11/33 (33%), Positives = 14/33 (42%), Gaps = 5/33 (15%)
Query: 118 MNKTLVFAIFDFDRFSKHDQIGEVKVALCQIDL 150
N L ++ D+D D IGE IDL
Sbjct: 61 GNSILKISVMDYDLLGSDDLIGETV-----IDL 88
>gnl|CDD|176007 cd04042, C2A_MCTP_PRT, C2 domain first repeat found in Multiple C2
domain and Transmembrane region Proteins (MCTP). MCTPs
are involved in Ca2+ signaling at the membrane. MCTP is
composed of a variable N-terminal sequence, three C2
domains, two transmembrane regions (TMRs), and a short
C-terminal sequence. It is one of four protein classes
that are anchored to membranes via a transmembrane
region; the others being synaptotagmins, extended
synaptotagmins, and ferlins. MCTPs are the only
membrane-bound C2 domain proteins that contain two
functional TMRs. MCTPs are unique in that they bind Ca2+
but not phospholipids. 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 = 121
Score = 29.6 bits (67), Expect = 0.41
Identities = 11/36 (30%), Positives = 18/36 (50%)
Query: 120 KTLVFAIFDFDRFSKHDQIGEVKVALCQIDLAQTIE 155
+ L +FD+DR D +G V L ++L + E
Sbjct: 61 QPLYIKVFDYDRGLTDDFMGSAFVDLSTLELNKPTE 96
>gnl|CDD|99869 cd06116, CaCS_like, Chloroflexus aurantiacus (Ca) citrate synthase
(CS)_like. CS catalyzes the condensation of acetyl
coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate
and coenzyme A (CoA), the first step in the citric acid
cycle (TCA or Krebs cycle). This group is similar to
gram-negative Escherichia coli (Ec) CS (type II, gltA)
and Arabidopsis thaliana (Ath) peroxisomal (Per) CS.
However EcCS and AthPerCS are not found in this group.
The overall CS reaction is thought to proceed through
three partial reactions and involves both closed and
open conformational forms of the enzyme: a) the
carbanion or equivalent is generated from AcCoA by base
abstraction of a proton, b) the nucleophilic attack of
this carbanion on OAA to generate citryl-CoA, and c) the
hydrolysis of citryl-CoA to produce citrate and CoA.
There are two types of CSs: type I CS and type II CSs.
Type I CSs are found in eukarya, gram-positive bacteria,
archaea, and in some gram-negative bacteria and are
homodimers with both subunits participating in the
active site. Type II CSs are unique to gram-negative
bacteria and are homohexamers of identical subunits
(approximated as a trimer of dimers). Some type II CSs
are strongly and specifically inhibited by NADH through
an allosteric mechanism. C. aurantiacus is a
gram-negative thermophilic green gliding bacterium, its
CS belonging to this group may be a type I CS; it is not
inhibited by NADH or 2-oxoglutarate and is inhibited by
ATP. Both gram-positive and gram-negative bacteria are
found in this group.
Length = 384
Score = 30.2 bits (68), Expect = 0.50
Identities = 12/28 (42%), Positives = 19/28 (67%)
Query: 83 KIADKVAEETGMPPWVVVSIFIERQILE 110
KIAD+V E TG P + +++ +E+ LE
Sbjct: 281 KIADEVFEATGRNPLLDIAVELEKIALE 308
>gnl|CDD|226068 COG3538, COG3538, Uncharacterized conserved protein [Function
unknown].
Length = 434
Score = 30.1 bits (68), Expect = 0.58
Identities = 16/51 (31%), Positives = 22/51 (43%), Gaps = 6/51 (11%)
Query: 113 PYADAMNKTLVFAIFDFDRFSKHDQIGEVKV---ALCQ-IDLAQTIEEWRE 159
PYA+A N+T A D + + E K +LC I LA W+
Sbjct: 102 PYANAFNETANGAGHQTDHTEMNPWVWERKYEIDSLCYPIQLAYLY--WKA 150
>gnl|CDD|218797 pfam05890, Ebp2, Eukaryotic rRNA processing protein EBP2. This
family consists of several Eukaryotic rRNA processing
protein EBP2 sequences. Ebp2p is required for the
maturation of 25S rRNA and 60S subunit assembly. Ebp2p
may be one of the target proteins of Rrs1p for
executing the signal to regulate ribosome biogenesis.
This family also plays a role in chromosome
segregation.
Length = 270
Score = 29.6 bits (67), Expect = 0.66
Identities = 13/50 (26%), Positives = 23/50 (46%)
Query: 49 EEEDLEMTEAFEDVSEELSSTVASIKKEIANESMKIADKVAEETGMPPWV 98
++ D+E+ EAF D + V +K+ N + + K+ PWV
Sbjct: 1 DDSDVELQEAFADGELKPGLNVVPHQKKTINNTAALKAKLERIKLPLPWV 50
>gnl|CDD|130038 TIGR00965, dapD, 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate
N-succinyltransferase. This enzyme is part of the
diaminopimelate pathway of lysine biosynthesis.
Alternate name: tetrahydrodipicolinate
N-succinyltransferase. The closely related TabB protein
of Pseudomonas syringae (pv. tabaci) appears to act in
the biosynthesis of tabtoxin rather than lysine. The
trusted cutoff is set high enough to exclude this gene.
Sequences below trusted also include a version of this
enzyme which apparently utilize acetate rather than
succinate (EC: 2.3.1.89) [Amino acid biosynthesis,
Aspartate family].
Length = 269
Score = 29.5 bits (66), Expect = 0.81
Identities = 20/94 (21%), Positives = 41/94 (43%), Gaps = 13/94 (13%)
Query: 54 EMTEAFEDVSEELSSTVASIKKEIANES--------MKIADKVAEETGMPPWVVVSIFIE 105
+ AFE +E + ++ KE NE +++A+K+ + + W+ ++ +
Sbjct: 5 IIETAFERRAEITPANADTVTKEAVNEVIALLDSGALRVAEKIDGQWKVNEWLKKAVLLS 64
Query: 106 RQILEGVPYADAMNK-----TLVFAIFDFDRFSK 134
+I + A N+ + FA +D RF K
Sbjct: 65 FRINDNQVINGAENRYFDKVPMKFADYDEARFKK 98
>gnl|CDD|176039 cd08393, C2A_SLP-1_2, C2 domain first repeat present in
Synaptotagmin-like proteins 1 and 2. All Slp members
basically share an N-terminal Slp homology domain (SHD)
and C-terminal tandem C2 domains (named the C2A domain
and the C2B domain) with the SHD and C2 domains being
separated by a linker sequence of various length.
Slp1/JFC1 and Slp2/exophilin 4 promote granule docking
to the plasma membrane. Additionally, their C2A domains
are both Ca2+ independent, unlike Slp3 and
Slp4/granuphilin which are Ca2+ dependent. It is
thought that SHD (except for the Slp4-SHD) functions as
a specific Rab27A/B-binding domain. In addition to
Slps, rabphilin, Noc2, and Munc13-4 also function as
Rab27-binding 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 first C2
repeat, C2A, and has a type-I topology.
Length = 125
Score = 28.6 bits (64), Expect = 0.99
Identities = 13/50 (26%), Positives = 23/50 (46%)
Query: 112 VPYADAMNKTLVFAIFDFDRFSKHDQIGEVKVALCQIDLAQTIEEWRELQ 161
V + + L +++ D ++ +GEV+V L D + T W LQ
Sbjct: 76 VEREELPTRVLNLSVWHRDSLGRNSFLGEVEVDLGSWDWSNTQPTWYPLQ 125
>gnl|CDD|175987 cd04020, C2B_SLP_1-2-3-4, C2 domain second repeat present in
Synaptotagmin-like proteins 1-4. All Slp members
basically share an N-terminal Slp homology domain (SHD)
and C-terminal tandem C2 domains (named the C2A domain
and the C2B domain) with the SHD and C2 domains being
separated by a linker sequence of various length.
Slp1/JFC1 and Slp2/exophilin 4 promote granule docking
to the plasma membrane. Additionally, their C2A domains
are both Ca2+ independent, unlike the case in Slp3 and
Slp4/granuphilin in which their C2A domains are Ca2+
dependent. It is thought that SHD (except for the
Slp4-SHD) functions as a specific Rab27A/B-binding
domain. In addition to Slps, rabphilin, Noc2, and
Munc13-4 also function as Rab27-binding proteins. It has
been demonstrated that Slp3 and Slp4/granuphilin promote
dense-core vesicle exocytosis. 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 second
C2 repeat, C2B, and has a type-I topology.
Length = 162
Score = 28.8 bits (65), Expect = 1.0
Identities = 13/55 (23%), Positives = 23/55 (41%)
Query: 110 EGVPYADAMNKTLVFAIFDFDRFSKHDQIGEVKVALCQIDLAQTIEEWRELQSVE 164
+GV D L ++D D+ S +D +G V++ L +W + E
Sbjct: 86 DGVSPEDLSQACLELTVWDHDKLSSNDFLGGVRLGLGTGKSYGQAVDWMDSTGEE 140
>gnl|CDD|176014 cd04049, C2_putative_Elicitor-responsive_gene, C2 domain present in
the putative elicitor-responsive gene. In plants
elicitor-responsive proteins are triggered in response
to specific elicitor molecules such as glycolproteins,
peptides, carbohydrates and lipids. A host of defensive
responses are also triggered resulting in localized cell
death. Antimicrobial secondary metabolites, such as
phytoalexins, or defense-related proteins, including
pathogenesis-related (PR) proteins are also produced.
There is a single C2 domain present here. 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. Members have a type-II
topology.
Length = 124
Score = 28.5 bits (64), Expect = 1.1
Identities = 18/49 (36%), Positives = 19/49 (38%), Gaps = 6/49 (12%)
Query: 112 VPYADAMNKT-LVFAIFDFDRFSKHDQIGEVKVALCQIDLAQTIEEWRE 159
V Y T L+ I D D FS D IGE I L EE E
Sbjct: 57 VEYPGWGGDTKLILRIMDKDNFSDDDFIGEAT-----IHLKGLFEEGVE 100
>gnl|CDD|176059 cd08677, C2A_Synaptotagmin-13, C2 domain. Synaptotagmin is a
membrane-trafficking protein characterized by a
N-terminal transmembrane region, a linker, and 2
C-terminal C2 domains. Synaptotagmin 13, a member of
class 6 synaptotagmins, is located in the brain. It
functions are unknown. It, like synaptotagmins 8 and 12,
does not have any consensus Ca2+ binding sites.
Previously all synaptotagmins were thought to be calcium
sensors in the regulation of neurotransmitter release
and hormone secretion, but it has been shown that not
all of them bind calcium. Of the 17 identified
synaptotagmins only 8 bind calcium (1-3, 5-7, 9, 10).
The function of the two C2 domains that bind calcium
are: regulating the fusion step of synaptic vesicle
exocytosis (C2A) and binding to
phosphatidyl-inositol-3,4,5-triphosphate (PIP3) in the
absence of calcium ions and to phosphatidylinositol
bisphosphate (PIP2) in their presence (C2B). C2B also
regulates also the recycling step of synaptic vesicles.
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-I topology.
Length = 118
Score = 27.6 bits (61), Expect = 1.8
Identities = 12/40 (30%), Positives = 22/40 (55%)
Query: 121 TLVFAIFDFDRFSKHDQIGEVKVALCQIDLAQTIEEWREL 160
TL + DRFS+H +GE+++ L + + +W +L
Sbjct: 79 TLTLTLRCCDRFSRHSTLGELRLKLADVSMMLGAAQWVDL 118
>gnl|CDD|176037 cd08391, C2A_C2C_Synaptotagmin_like, C2 domain first and third
repeat in Synaptotagmin-like proteins. Synaptotagmin is
a membrane-trafficking protein characterized by a
N-terminal transmembrane region, a linker, and 2
C-terminal C2 domains. Previously all synaptotagmins
were thought to be calcium sensors in the regulation of
neurotransmitter release and hormone secretion, but it
has been shown that not all of them bind calcium. Of
the 17 identified synaptotagmins only 8 bind calcium
(1-3, 5-7, 9, 10). The function of the two C2 domains
that bind calcium are: regulating the fusion step of
synaptic vesicle exocytosis (C2A) and binding to
phosphatidyl-inositol-3,4,5-triphosphate (PIP3) in the
absence of calcium ions and to phosphatidylinositol
bisphosphate (PIP2) in their presence (C2B). C2B also
regulates also the recycling step of synaptic vesicles.
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 either the
first or third repeat in Synaptotagmin-like proteins
with a type-I topology.
Length = 121
Score = 27.3 bits (61), Expect = 2.3
Identities = 13/46 (28%), Positives = 23/46 (50%), Gaps = 1/46 (2%)
Query: 119 NKTLVFAIFDFDRFSKHDQIGEVKVALCQIDLAQTIEEWRELQSVE 164
+ L +FD D K D +G + + L ++ I+EW L+ V+
Sbjct: 67 GQELEIELFDEDP-DKDDFLGRLSIDLGSVEKKGFIDEWLPLEDVK 111
>gnl|CDD|176050 cd08405, C2B_Synaptotagmin-7, C2 domain second repeat present in
Synaptotagmin 7. Synaptotagmin is a
membrane-trafficking protein characterized by a
N-terminal transmembrane region, a linker, and 2
C-terminal C2 domains. Synaptotagmin 7, a member of
class 2 synaptotagmins, is located in presynaptic plasma
membranes in neurons, dense-core vesicles in endocrine
cells, and lysosomes in fibroblasts. It has been shown
to play a role in regulation of Ca2+-dependent lysosomal
exocytosis in fibroblasts and may also function as a
vesicular Ca2+-sensor. It is distinguished from the
other synaptotagmins by having over 12 splice forms.
Previously all synaptotagmins were thought to be calcium
sensors in the regulation of neurotransmitter release
and hormone secretion, but it has been shown that not
all of them bind calcium. Of the 17 identified
synaptotagmins only 8 bind calcium (1-3, 5-7, 9, 10).
The function of the two C2 domains that bind calcium
are: regulating the fusion step of synaptic vesicle
exocytosis (C2A) and binding to
phosphatidyl-inositol-3,4,5-triphosphate (PIP3) in the
absence of calcium ions and to phosphatidylinositol
bisphosphate (PIP2) in their presence (C2B). C2B also
regulates also the recycling step of synaptic vesicles.
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 second C2
repeat, C2B, and has a type-I topology.
Length = 136
Score = 27.0 bits (60), Expect = 3.0
Identities = 9/21 (42%), Positives = 15/21 (71%)
Query: 121 TLVFAIFDFDRFSKHDQIGEV 141
TL+ + D DR S++D IG++
Sbjct: 84 TLIITVMDKDRLSRNDLIGKI 104
>gnl|CDD|236278 PRK08506, PRK08506, replicative DNA helicase; Provisional.
Length = 472
Score = 27.7 bits (62), Expect = 3.8
Identities = 17/62 (27%), Positives = 29/62 (46%), Gaps = 5/62 (8%)
Query: 31 SIKRKTQATTTTTPLPEDEEEDLEMTEAFEDVSEELSSTVASIKKEIANESMKIADKVAE 90
SIKR+ + T P E+ +E + D+ +E+ + SI +E K + +V E
Sbjct: 101 SIKRELLSLANTIP-----EQAVEEDQKSSDILDEVERELYSITNGSNSEDFKDSKEVIE 155
Query: 91 ET 92
T
Sbjct: 156 ST 157
>gnl|CDD|222915 PHA02670, PHA02670, ORF112 putative chemokine-binding protein;
Provisional.
Length = 287
Score = 27.3 bits (60), Expect = 4.4
Identities = 9/28 (32%), Positives = 14/28 (50%)
Query: 35 KTQATTTTTPLPEDEEEDLEMTEAFEDV 62
K + T +TTP P E L++T+
Sbjct: 177 KPEPTPSTTPGPTLLETTLDLTDEPTTT 204
>gnl|CDD|176005 cd04040, C2D_Tricalbin-like, C2 domain fourth repeat present in
Tricalbin-like proteins. 5 to 6 copies of the C2 domain
are present in Tricalbin, a yeast homolog of
Synaptotagmin, which is involved in membrane trafficking
and sorting. 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 fifth C2
repeat, C2E, and has a type-II topology.
Length = 115
Score = 26.4 bits (59), Expect = 4.4
Identities = 14/50 (28%), Positives = 25/50 (50%), Gaps = 3/50 (6%)
Query: 119 NKTLVFAIFDFDRFSKHDQIGEVKVALCQIDLAQTIEEWRELQSVEGEGG 168
L ++D+DR K D +G + L ++ +T E L ++G+GG
Sbjct: 60 RAVLKVEVYDWDRGGKDDLLGSAYIDLSDLEPEETTE--LTLP-LDGQGG 106
>gnl|CDD|213841 TIGR03635, S17_bact, 30S ribosomal protein S17. This model
describes the bacterial ribosomal small subunit protein
S17, while excluding cytosolic eukaryotic homologs and
archaeal homologs. The model finds many, but not,
chloroplast and mitochondrial counterparts to bacterial
S17 [Protein synthesis, Ribosomal proteins: synthesis
and modification].
Length = 71
Score = 25.6 bits (57), Expect = 4.5
Identities = 12/30 (40%), Positives = 19/30 (63%), Gaps = 3/30 (10%)
Query: 106 RQILEGVPYADAMNKTLVFAIFDFDRFSKH 135
R+ L+GV +D M+KT+V + +R KH
Sbjct: 1 RKTLQGVVVSDKMDKTIVVLV---ERRVKH 27
>gnl|CDD|148209 pfam06466, PCAF_N, PCAF (P300/CBP-associated factor) N-terminal
domain. This region is spliced out of human histone
acetyltranfersase KAT2A isoform 2. It is predicted to be
of a mixed alpha/beta fold - though predominantly
helical.
Length = 252
Score = 27.2 bits (60), Expect = 5.0
Identities = 10/25 (40%), Positives = 14/25 (56%)
Query: 2 PPFDKREVVQEVLNVISFNASTLPP 26
PPF+K + Q VLN + + S L
Sbjct: 139 PPFEKPCIEQGVLNFVQYKFSHLST 163
>gnl|CDD|176027 cd08381, C2B_PI3K_class_II, C2 domain second repeat present in
class II phosphatidylinositol 3-kinases (PI3Ks). There
are 3 classes of PI3Ks based on structure, regulation,
and specificity. All classes contain a N-terminal C2
domain, a PIK domain, and a kinase catalytic domain.
Unlike class I and class III, class II PI3Ks have
additionally a PX domain and a C-terminal C2 domain
containing a nuclear localization signal both of which
bind phospholipids though in a slightly different
fashion. PI3Ks (AKA phosphatidylinositol (PtdIns)
3-kinases) regulate cell processes such as cell growth,
differentiation, proliferation, and motility. PI3Ks work
on phosphorylation of phosphatidylinositol,
phosphatidylinositide (4)P (PtdIns (4)P),2 or
PtdIns(4,5)P2. Specifically they phosphorylate the D3
hydroxyl group of phosphoinositol lipids on the inositol
ring. 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 second C2 repeat, C2B, and
has a type-I topology.
Length = 122
Score = 26.1 bits (58), Expect = 5.8
Identities = 19/71 (26%), Positives = 36/71 (50%), Gaps = 6/71 (8%)
Query: 87 KVAEETGMPPWVVVSIFIERQILEGVPYADAMNKTLVFAIFDFDRFSKHDQIGEVKVALC 146
KV +T P F E + +G+P D + L +++ D +++ +G V + L
Sbjct: 54 KVVRKTRNP------TFNEMLVYDGLPVEDLQQRVLQVSVWSHDSLVENEFLGGVCIPLK 107
Query: 147 QIDLAQTIEEW 157
++DL+Q E+W
Sbjct: 108 KLDLSQETEKW 118
>gnl|CDD|185268 PRK15370, PRK15370, E3 ubiquitin-protein ligase SlrP; Provisional.
Length = 754
Score = 27.0 bits (59), Expect = 5.9
Identities = 24/102 (23%), Positives = 41/102 (40%), Gaps = 4/102 (3%)
Query: 12 EVLNVISFNASTLPPLVADSIKRKTQATTTTTPLPEDEEEDLEMTEAFEDVSEELSSTVA 71
L+V + TLP + I + + T LPE L+ EA E+ L+S A
Sbjct: 286 RYLSVYDNSIRTLPAHLPSGITHLNVQSNSLTALPETLPPGLKTLEAGENA---LTSLPA 342
Query: 72 SIKKEIANESMKIADKVAEETGMPPWVVVSIFIERQILEGVP 113
S+ E+ + +PP + ++ + R L +P
Sbjct: 343 SLPPELQVLDVSKNQITVLPETLPP-TITTLDVSRNALTNLP 383
>gnl|CDD|175976 cd04009, C2B_Munc13-like, C2 domain second repeat in Munc13
(mammalian uncoordinated)-like 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 = 133
Score = 26.4 bits (59), Expect = 6.1
Identities = 9/30 (30%), Positives = 14/30 (46%)
Query: 119 NKTLVFAIFDFDRFSKHDQIGEVKVALCQI 148
L+F + D+D +D GE + L I
Sbjct: 87 GALLLFTVKDYDLLGSNDFEGEAFLPLNDI 116
>gnl|CDD|226683 COG4230, COG4230, Delta 1-pyrroline-5-carboxylate dehydrogenase
[Energy production and conversion].
Length = 769
Score = 27.0 bits (60), Expect = 6.1
Identities = 7/25 (28%), Positives = 13/25 (52%)
Query: 6 KREVVQEVLNVISFNASTLPPLVAD 30
+REV VL+V+ + L ++
Sbjct: 476 QREVFGPVLHVVRYKRDELDEVIDQ 500
>gnl|CDD|216973 pfam02324, Glyco_hydro_70, Glycosyl hydrolase family 70. Members
of this family belong to glycosyl hydrolase family 70
Glucosyltransferases or sucrose 6-glycosyl transferases
(GTF-S) catalyze the transfer of D-glucopyramnosyl units
from sucrose onto acceptor molecules, EC:2.4.1.5. This
family roughly corresponds to the N-terminal catalytic
domain of the enzyme. Members of this family also
contain the Putative cell wall binding domain pfam01473,
which corresponds with the C-terminal glucan-binding
domain.
Length = 808
Score = 27.0 bits (60), Expect = 6.3
Identities = 11/37 (29%), Positives = 20/37 (54%), Gaps = 2/37 (5%)
Query: 61 DVSEELSSTVASIKK--EIANESMKIADKVAEETGMP 95
++ L+ T+ +K+ +I NE M ADK + +P
Sbjct: 313 PKTDGLTFTLDELKQAFKIYNEDMLKADKKYTQYNIP 349
>gnl|CDD|176003 cd04038, C2_ArfGAP, C2 domain present in Arf GTPase Activating
Proteins (GAP). ArfGAP is a GTPase activating protein
which regulates the ADP ribosylation factor Arf, a
member of the Ras superfamily of GTP-binding proteins.
The GTP-bound form of Arf is involved in Golgi
morphology and is involved in recruiting coat proteins.
ArfGAP is responsible for the GDP-bound form of Arf
which is necessary for uncoating the membrane and
allowing the Golgi to fuse with an acceptor compartment.
These proteins contain an N-terminal ArfGAP domain
containing the characteristic zinc finger motif
(Cys-x2-Cys-x(16,17)-x2-Cys) and C-terminal C2 domain.
C2 domains were first identified in Protein Kinase C
(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 = 145
Score = 26.1 bits (58), Expect = 6.4
Identities = 11/28 (39%), Positives = 15/28 (53%)
Query: 118 MNKTLVFAIFDFDRFSKHDQIGEVKVAL 145
L +FD D FSK D +GE ++ L
Sbjct: 59 PMAPLKLEVFDKDTFSKDDSMGEAEIDL 86
>gnl|CDD|237018 PRK11905, PRK11905, bifunctional proline
dehydrogenase/pyrroline-5-carboxylate dehydrogenase;
Reviewed.
Length = 1208
Score = 26.8 bits (60), Expect = 7.0
Identities = 10/25 (40%), Positives = 15/25 (60%)
Query: 6 KREVVQEVLNVISFNASTLPPLVAD 30
+REV VL+V+ F A L ++ D
Sbjct: 916 EREVFGPVLHVVRFKADELDRVIDD 940
>gnl|CDD|176030 cd08384, C2B_Rabphilin_Doc2, C2 domain second repeat present in
Rabphilin and Double C2 domain. Rabphilin is found
neurons and in neuroendrocrine cells, while Doc2 is
found not only in the brain but in tissues, including
mast cells, chromaffin cells, and osteoblasts.
Rabphilin and Doc2s share highly homologous tandem C2
domains, although their N-terminal structures are
completely different: rabphilin contains an N-terminal
Rab-binding domain (RBD),7 whereas Doc2 contains an
N-terminal Munc13-1-interacting domain (MID). 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 second C2
repeat, C2B, and has a type-I topology.
Length = 133
Score = 26.2 bits (58), Expect = 7.1
Identities = 9/30 (30%), Positives = 16/30 (53%)
Query: 112 VPYADAMNKTLVFAIFDFDRFSKHDQIGEV 141
+ ++D KTL ++D D +D IG +
Sbjct: 73 IKHSDLAKKTLEITVWDKDIGKSNDYIGGL 102
>gnl|CDD|225352 COG2747, FlgM, Negative regulator of flagellin synthesis
(anti-sigma28 factor) [Transcription / Cell motility
and secretion / Intracellular trafficking and
secretion].
Length = 93
Score = 25.4 bits (56), Expect = 7.5
Identities = 15/64 (23%), Positives = 29/64 (45%), Gaps = 10/64 (15%)
Query: 33 KRKTQATTTTTPLPEDEEEDLEMTEAFEDVSEELSSTVASIKKEIAN-----ESMKIADK 87
+KT ++ L + + ++ D+ EE V +K+ I N ++ KIADK
Sbjct: 31 AKKTDSSNVEVSLSAQQAKLMQPGS--SDIREEK---VEELKQAIENGEYKVDTEKIADK 85
Query: 88 VAEE 91
+ +
Sbjct: 86 LLDF 89
>gnl|CDD|176049 cd08404, C2B_Synaptotagmin-4, C2 domain second repeat present in
Synaptotagmin 4. Synaptotagmin is a
membrane-trafficking protein characterized by a
N-terminal transmembrane region, a linker, and 2
C-terminal C2 domains. Synaptotagmin 4, a member of
class 4 synaptotagmins, is located in the brain. It
functions are unknown. It, like synaptotagmin-11, has an
Asp to Ser substitution in its C2A domain. Previously
all synaptotagmins were thought to be calcium sensors in
the regulation of neurotransmitter release and hormone
secretion, but it has been shown that not all of them
bind calcium. Of the 17 identified synaptotagmins only
8 bind calcium (1-3, 5-7, 9, 10). The function of the
two C2 domains that bind calcium are: regulating the
fusion step of synaptic vesicle exocytosis (C2A) and
binding to phosphatidyl-inositol-3,4,5-triphosphate
(PIP3) in the absence of calcium ions and to
phosphatidylinositol bisphosphate (PIP2) in their
presence (C2B). C2B also regulates also the recycling
step of synaptic vesicles. 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 second C2
repeat, C2B, and has a type-I topology.
Length = 136
Score = 25.9 bits (57), Expect = 7.9
Identities = 13/61 (21%), Positives = 27/61 (44%), Gaps = 4/61 (6%)
Query: 112 VPYADAMNKTLVFAIFDFDRFSKHDQIGEVKVALCQIDLAQTIEEWRELQSVEGEGGQIG 171
+P + + ++ F + D DR +K++ IG ++ L W+E+ QI
Sbjct: 75 IPSEELEDISVEFLVLDSDRVTKNEVIG--RLVLGPKASGSGGHHWKEVC--NPPRRQIA 130
Query: 172 K 172
+
Sbjct: 131 E 131
>gnl|CDD|176045 cd08400, C2_Ras_p21A1, C2 domain present in RAS p21 protein
activator 1 (RasA1). RasA1 is a GAP1 (GTPase activating
protein 1), a Ras-specific GAP member, which suppresses
Ras function by enhancing the GTPase activity of Ras
proteins resulting in the inactive GDP-bound form of
Ras. In this way it can control cellular proliferation
and differentiation. RasA1 contains a C2 domain, a
Ras-GAP domain, a pleckstrin homology (PH)-like domain,
a SH3 domain, and 2 SH2 domains. 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. Members here have a type-I
topology.
Length = 126
Score = 25.8 bits (57), Expect = 8.1
Identities = 12/30 (40%), Positives = 16/30 (53%)
Query: 133 SKHDQIGEVKVALCQIDLAQTIEEWRELQS 162
SK +I EV V L ++ Q +EW L S
Sbjct: 75 SKDSEIAEVTVQLSKLQNGQETDEWYPLSS 104
>gnl|CDD|200586 cd10964, CE4_PgaB_5s, N-terminal putative catalytic polysaccharide
deacetylase domain of bacterial
poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB,
and similar proteins. This family is represented by an
outer membrane lipoprotein,
poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase
(PgaB, EC 3.5.1.-), encoded by Escherichia coli pgaB
gene from the pgaABCD (formerly ycdSRQP) operon, which
affects biofilm development by promoting abiotic surface
binding and intercellular adhesion. PgaB catalyzes the
N-deacetylation of poly-beta-1,6-N-acetyl-D-glucosamine
(PGA), a biofilm adhesin polysaccharide that stabilizes
biofilms of E. coli and other bacteria. PgaB contains an
N-terminal NodB homology domain with a 5-stranded
beta/alpha barrel, and a C-terminal carbohydrate binding
domain required for PGA N-deacetylation, which may be
involved in binding to unmodified poly-beta-1,6-GlcNAc
and assisting catalysis by the deacetylase domain. This
family also includes several orthologs of PgaB, such as
the hemin storage system HmsF protein, encoded by
Yersinia pestis hmsF gene from the hmsHFRS operon, which
is essential for Y. pestis biofilm formation. Like PgaB,
HmsF is an outer membrane protein with an N-terminal
NodB homology domain, which is likely involved in the
modification of the exopolysaccharide (EPS) component of
the biofilm. HmsF also has a conserved but
uncharacterized C-terminal domain that is present in
other HmsF-like proteins in Gram-negative bacteria. This
alignment model corresponds to the N-terminal NodB
homology domain.
Length = 193
Score = 26.2 bits (58), Expect = 8.2
Identities = 10/32 (31%), Positives = 17/32 (53%)
Query: 69 TVASIKKEIANESMKIADKVAEETGMPPWVVV 100
T A ++ I N+ K + + + TG P V+V
Sbjct: 115 TDAEYRQRIRNDLKKSSALIKKHTGRAPRVMV 146
>gnl|CDD|220369 pfam09731, Mitofilin, Mitochondrial inner membrane protein.
Mitofilin controls mitochondrial cristae morphology.
Mitofilin is enriched in the narrow space between the
inner boundary and the outer membranes, where it forms a
homotypic interaction and assembles into a large
multimeric protein complex. The first 78 amino acids
contain a typical amino-terminal-cleavable mitochondrial
presequence rich in positive-charged and hydroxylated
residues and a membrane anchor domain. In addition, it
has three centrally located coiled coil domains.
Length = 493
Score = 26.5 bits (59), Expect = 8.6
Identities = 17/80 (21%), Positives = 33/80 (41%), Gaps = 9/80 (11%)
Query: 21 ASTLPPLVADSIKRKTQATTTTTPLPEDEEEDLEMTEAFEDV---------SEELSSTVA 71
+T P + + ++ + + E+ F D+ ++L S +A
Sbjct: 107 EATTPKSIQELVEALEELLEELLKETASDPVVQELVSIFNDLIDSIKEDNLKDDLESLIA 166
Query: 72 SIKKEIANESMKIADKVAEE 91
S K+E+ S K+A+ AEE
Sbjct: 167 SAKEELDQLSKKLAELKAEE 186
>gnl|CDD|176395 cd01800, SF3a120_C, Ubiquitin-like domain of Mammalian splicing
factor SF3a_120. SF3a120_C Mammalian splicing factor
SF3a consists of three subunits of 60, 66, and 120 kDa
and functions early during pre-mRNA splicing by
converting the U2 snRNP to its active form. The 120kDa
subunit (SF3a120) has a carboxy-terminal ubiquitin-like
domain and two SWAP (suppressor-of-white-apricot)
domains, referred to collectively as the SURP module,
at its amino-terminus.
Length = 76
Score = 25.1 bits (55), Expect = 9.3
Identities = 11/37 (29%), Positives = 17/37 (45%), Gaps = 11/37 (29%)
Query: 60 EDVSEELSSTVASIKKEIANESMKIADKVAEETGMPP 96
+ + +LS V+ +K K+ EETGMP
Sbjct: 10 LNFTLQLSDPVSVLKV-----------KIHEETGMPA 35
>gnl|CDD|222923 PHA02738, PHA02738, hypothetical protein; Provisional.
Length = 320
Score = 26.4 bits (58), Expect = 9.7
Identities = 14/43 (32%), Positives = 23/43 (53%), Gaps = 6/43 (13%)
Query: 60 EDVSEELSS--TVASIKKEIANESMKIADKVAEETGMPPWVVV 100
++ SE L+ V +KE+A ES++I + PP +VV
Sbjct: 194 KNTSEFLNFVLEVRQCQKELAQESLQIGHNRLQ----PPPIVV 232
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
0.313 0.130 0.358
Gapped
Lambda K H
0.267 0.0857 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,858,517
Number of extensions: 817234
Number of successful extensions: 1109
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1107
Number of HSP's successfully gapped: 114
Length of query: 173
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 83
Effective length of database: 6,945,742
Effective search space: 576496586
Effective search space used: 576496586
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 55 (24.7 bits)