RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4487
(315 letters)
>gnl|CDD|238492 cd00992, PDZ_signaling, PDZ domain found in a variety of Eumetazoan
signaling molecules, often in tandem arrangements. May
be responsible for specific protein-protein
interactions, as most PDZ domains bind C-terminal
polypeptides, and binding to internal (non-C-terminal)
polypeptides and even to lipids has been demonstrated.
In this subfamily of PDZ domains an N-terminal
beta-strand forms the peptide-binding groove base, a
circular permutation with respect to PDZ domains found
in proteases.
Length = 82
Score = 64.5 bits (158), Expect = 2e-13
Identities = 27/91 (29%), Positives = 44/91 (48%), Gaps = 12/91 (13%)
Query: 98 HMILRKSGDRYPSASSTLGIKVIGGKLLEDGTRGAIIEKVKKGSPADLEGHLLAGDQVIE 157
+ LRK LG + GGK D G + +V+ G PA+ G L GD+++E
Sbjct: 3 TVTLRKDPGG------GLGFSLRGGK---DSGGGIFVSRVEPGGPAERGG-LRVGDRILE 52
Query: 158 WNGRSMRGKSFQDVEDIIAESRQEPQVELIV 188
NG S+ G + ++ +++ S +V L V
Sbjct: 53 VNGVSVEGLTHEEAVELLKNSG--DEVTLTV 81
>gnl|CDD|214570 smart00228, PDZ, Domain present in PSD-95, Dlg, and ZO-1/2. Also
called DHR (Dlg homologous region) or GLGF (relatively
well conserved tetrapeptide in these domains). Some PDZs
have been shown to bind C-terminal polypeptides; others
appear to bind internal (non-C-terminal) polypeptides.
Different PDZs possess different binding specificities.
Length = 85
Score = 58.5 bits (142), Expect = 3e-11
Identities = 26/77 (33%), Positives = 40/77 (51%), Gaps = 6/77 (7%)
Query: 115 LGIKVIGGKLLEDGTRGAIIEKVKKGSPADLEGHLLAGDQVIEWNGRSMRGKSFQDVEDI 174
LG ++GGK D G ++ V GSPA G L GD ++E NG S+ G + + D+
Sbjct: 14 LGFSLVGGK---DEGGGVVVSSVVPGSPAAKAG-LRVGDVILEVNGTSVEGLTHLEAVDL 69
Query: 175 IAESRQEPQVELIVSRR 191
+ ++ + V L V R
Sbjct: 70 LKKAGGK--VTLTVLRG 84
>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 = 58.0 bits (141), Expect = 1e-10
Identities = 20/44 (45%), Positives = 29/44 (65%)
Query: 272 SVKFYLDSGTLRLVVTLMCAASLVPRSNGQPRCPYAKIYLLPDR 315
++ + D T +L+VT++ A L PR +G R PY K+YLLPDR
Sbjct: 6 QIQLWYDKVTSQLIVTVLQARDLPPRDDGSLRNPYVKVYLLPDR 49
>gnl|CDD|238080 cd00136, PDZ, PDZ domain, also called DHR (Dlg homologous region)
or GLGF (after a conserved sequence motif). Many PDZ
domains bind C-terminal polypeptides, though binding to
internal (non-C-terminal) polypeptides and even to
lipids has been demonstrated. Heterodimerization through
PDZ-PDZ domain interactions adds to the domain's
versatility, and PDZ domain-mediated interactions may be
modulated dynamically through target phosphorylation.
Some PDZ domains play a role in scaffolding
supramolecular complexes. PDZ domains are found in
diverse signaling proteins in bacteria, archebacteria,
and eurkayotes. This CD contains two distinct structural
subgroups with either a N- or C-terminal beta-strand
forming the peptide-binding groove base. The circular
permutation placing the strand on the N-terminus appears
to be found in Eumetazoa only, while the C-terminal
variant is found in all three kingdoms of life, and
seems to co-occur with protease domains. PDZ domains
have been named after PSD95(post synaptic density
protein), DlgA (Drosophila disc large tumor suppressor),
and ZO1, a mammalian tight junction protein.
Length = 70
Score = 46.9 bits (112), Expect = 3e-07
Identities = 23/76 (30%), Positives = 38/76 (50%), Gaps = 7/76 (9%)
Query: 113 STLGIKVIGGKLLEDGTRGAIIEKVKKGSPADLEGHLLAGDQVIEWNGRSMRGKSFQDVE 172
LG + GG G ++ V+ GSPA+ G L AGD ++ NG ++ + +DV
Sbjct: 1 GGLGFSIRGG-----TEGGVVVLSVEPGSPAERAG-LQAGDVILAVNGTDVKNLTLEDVA 54
Query: 173 DIIAESRQEPQVELIV 188
+++ + E V L V
Sbjct: 55 ELLKKEVGEK-VTLTV 69
>gnl|CDD|238489 cd00989, PDZ_metalloprotease, PDZ domain of bacterial and plant
zinc metalloprotases, presumably membrane-associated or
integral membrane proteases, which may be involved in
signalling and regulatory mechanisms. May be responsible
for substrate recognition and/or binding, as most PDZ
domains bind C-terminal polypeptides, and binding to
internal (non-C-terminal) polypeptides and even to
lipids has been demonstrated. In this subfamily of
protease-associated PDZ domains a C-terminal beta-strand
forms the peptide-binding groove base, a circular
permutation with respect to PDZ domains found in
Eumetazoan signaling proteins.
Length = 79
Score = 46.1 bits (110), Expect = 7e-07
Identities = 25/78 (32%), Positives = 41/78 (52%), Gaps = 10/78 (12%)
Query: 113 STLGIKVIGGKLLEDGTRGAIIEKVKKGSPADLEGHLLAGDQVIEWNGRSMRGKSFQDVE 172
+ LG G + +I +V GSPA G L AGD+++ NG+ + KS++D+
Sbjct: 1 AILGFVPGGPPI------EPVIGEVVPGSPAAKAG-LKAGDRILAINGQKI--KSWEDLV 51
Query: 173 DIIAESRQEPQVELIVSR 190
D + E+ +P + L V R
Sbjct: 52 DAVQENPGKP-LTLTVER 68
>gnl|CDD|238487 cd00987, PDZ_serine_protease, PDZ domain of tryspin-like serine
proteases, such as DegP/HtrA, which are oligomeric
proteins involved in heat-shock response, chaperone
function, and apoptosis. May be responsible for
substrate recognition and/or binding, as most PDZ
domains bind C-terminal polypeptides, though binding to
internal (non-C-terminal) polypeptides and even to
lipids has been demonstrated. In this subfamily of
protease-associated PDZ domains a C-terminal beta-strand
forms the peptide-binding groove base, a circular
permutation with respect to PDZ domains found in
Eumetazoan signaling proteins.
Length = 90
Score = 43.4 bits (103), Expect = 7e-06
Identities = 26/82 (31%), Positives = 40/82 (48%), Gaps = 9/82 (10%)
Query: 115 LGIKV------IGGKLLEDGTRGAIIEKVKKGSPADLEGHLLAGDQVIEWNGRSMRGKSF 168
LG+ V + +L T+G ++ V GSPA G L GD ++ NG+ + KS
Sbjct: 3 LGVTVQDLTPDLAEELGLKDTKGVLVASVDPGSPAAKAG-LKPGDVILAVNGKPV--KSV 59
Query: 169 QDVEDIIAESRQEPQVELIVSR 190
D+ +AE + +V L V R
Sbjct: 60 ADLRRALAELKPGDKVTLTVLR 81
>gnl|CDD|201332 pfam00595, PDZ, PDZ domain (Also known as DHR or GLGF). PDZ
domains are found in diverse signaling proteins.
Length = 80
Score = 40.7 bits (96), Expect = 5e-05
Identities = 19/73 (26%), Positives = 34/73 (46%), Gaps = 4/73 (5%)
Query: 115 LGIKVIGGKLLEDGTRGAIIEKVKKGSPADLEGHLLAGDQVIEWNGRSMRGKSFQDVEDI 174
LG ++GG DG G + +V G A+ G L GD+++ NG+ + S +
Sbjct: 12 LGFSLVGG---SDGDPGIFVSEVLPGGAAEAGG-LQEGDRILSINGQDLENLSHDEAVLA 67
Query: 175 IAESRQEPQVELI 187
+ S E + ++
Sbjct: 68 LKGSGGEVTLTIL 80
>gnl|CDD|233695 TIGR02037, degP_htrA_DO, periplasmic serine protease, Do/DeqQ
family. This family consists of a set proteins various
designated DegP, heat shock protein HtrA, and protease
DO. The ortholog in Pseudomonas aeruginosa is designated
MucD and is found in an operon that controls mucoid
phenotype. This family also includes the DegQ (HhoA)
paralog in E. coli which can rescue a DegP mutant, but
not the smaller DegS paralog, which cannot. Members of
this family are located in the periplasm and have
separable functions as both protease and chaperone.
Members have a trypsin domain and two copies of a PDZ
domain. This protein protects bacteria from thermal and
other stresses and may be important for the survival of
bacterial pathogens.// The chaperone function is
dominant at low temperatures, whereas the proteolytic
activity is turned on at elevated temperatures [Protein
fate, Protein folding and stabilization, Protein fate,
Degradation of proteins, peptides, and glycopeptides].
Length = 428
Score = 39.9 bits (94), Expect = 0.001
Identities = 21/64 (32%), Positives = 34/64 (53%), Gaps = 3/64 (4%)
Query: 127 DGTRGAIIEKVKKGSPADLEGHLLAGDQVIEWNGRSMRGKSFQDVEDIIAESRQEPQVEL 186
+ RGA++ +V GSPA+ + L AGD + NG+ + SF D+ I + +V L
Sbjct: 254 EKQRGALVAQVLPGSPAE-KAGLKAGDVITSVNGKPI--SSFADLRRAIGTLKPGKKVTL 310
Query: 187 IVSR 190
+ R
Sbjct: 311 GILR 314
Score = 36.8 bits (86), Expect = 0.013
Identities = 18/66 (27%), Positives = 36/66 (54%), Gaps = 3/66 (4%)
Query: 125 LEDGTRGAIIEKVKKGSPADLEGHLLAGDQVIEWNGRSMRGKSFQDVEDIIAESRQEPQV 184
L+ +G ++ KV GSPA G L GD ++ N + + S ++ ++A +++ +V
Sbjct: 357 LKGDVKGVVVTKVVSGSPAARAG-LQPGDVILSVNQQPV--SSVAELRKVLARAKKGGRV 413
Query: 185 ELIVSR 190
L++ R
Sbjct: 414 ALLILR 419
>gnl|CDD|223343 COG0265, DegQ, Trypsin-like serine proteases, typically
periplasmic, contain C-terminal PDZ domain
[Posttranslational modification, protein turnover,
chaperones].
Length = 347
Score = 39.1 bits (91), Expect = 0.002
Identities = 20/69 (28%), Positives = 33/69 (47%), Gaps = 3/69 (4%)
Query: 127 DGTRGAIIEKVKKGSPADLEGHLLAGDQVIEWNGRSMRGKSFQDVEDIIAESRQEPQVEL 186
GA++ V GSPA G + AGD + NG+ + S D+ +A +R +V L
Sbjct: 267 PVAAGAVVLGVLPGSPAAKAG-IKAGDIITAVNGKPV--ASLSDLVAAVASNRPGDEVAL 323
Query: 187 IVSRRIQPK 195
+ R + +
Sbjct: 324 KLLRGGKER 332
>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 = 36.9 bits (86), Expect = 0.003
Identities = 13/33 (39%), Positives = 20/33 (60%), Gaps = 1/33 (3%)
Query: 283 RLVVTLMCAASLVPR-SNGQPRCPYAKIYLLPD 314
+L V+L+ A +L PR + P+ K+ LLPD
Sbjct: 15 QLTVSLIKARNLPPRTKDVAHCDPFVKVCLLPD 47
>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 = 36.5 bits (85), Expect = 0.004
Identities = 12/33 (36%), Positives = 20/33 (60%)
Query: 283 RLVVTLMCAASLVPRSNGQPRCPYAKIYLLPDR 315
+L+VT+ +L P + PY ++YLLPD+
Sbjct: 17 KLIVTVHKCRNLPPCDSSDIPDPYVRLYLLPDK 49
>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 = 35.7 bits (83), Expect = 0.007
Identities = 15/38 (39%), Positives = 21/38 (55%)
Query: 278 DSGTLRLVVTLMCAASLVPRSNGQPRCPYAKIYLLPDR 315
D + +L V ++ AA L G PY K+YLLPD+
Sbjct: 12 DFQSNQLTVGIIQAADLPAMDMGGTSDPYVKVYLLPDK 49
>gnl|CDD|223864 COG0793, Prc, Periplasmic protease [Cell envelope biogenesis, outer
membrane].
Length = 406
Score = 35.4 bits (82), Expect = 0.032
Identities = 16/61 (26%), Positives = 29/61 (47%), Gaps = 6/61 (9%)
Query: 137 VKKGSPADLEGHLLAGDQVIEWNGRSMRGKSFQDVEDIIAESRQEP--QVELIVSRRIQP 194
GSPA + GD +I+ +G+S+ G +++ + R +P +V L + R
Sbjct: 119 PIDGSPAAK-AGIKPGDVIIKIDGKSVGG---VSLDEAVKLIRGKPGTKVTLTILRAGGG 174
Query: 195 K 195
K
Sbjct: 175 K 175
>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 = 32.8 bits (75), Expect = 0.055
Identities = 11/33 (33%), Positives = 16/33 (48%)
Query: 283 RLVVTLMCAASLVPRSNGQPRCPYAKIYLLPDR 315
L V ++ A +L P+ G PY K+ L D
Sbjct: 1 TLTVKIISARNLPPKDKGGKSDPYVKVSLDGDP 33
>gnl|CDD|215765 pfam00168, C2, C2 domain.
Length = 85
Score = 31.5 bits (72), Expect = 0.095
Identities = 10/32 (31%), Positives = 16/32 (50%)
Query: 284 LVVTLMCAASLVPRSNGQPRCPYAKIYLLPDR 315
L VT++ A +L P+ PY K+ L +
Sbjct: 1 LRVTVISAKNLPPKDLNGKSDPYVKVSLGGQK 32
>gnl|CDD|238488 cd00988, PDZ_CTP_protease, PDZ domain of C-terminal processing-,
tail-specific-, and tricorn proteases, which function in
posttranslational protein processing, maturation, and
disassembly or degradation, in Bacteria, Archaea, and
plant chloroplasts. May be responsible for substrate
recognition and/or binding, as most PDZ domains bind
C-terminal polypeptides, and binding to internal
(non-C-terminal) polypeptides and even to lipids has
been demonstrated. In this subfamily of
protease-associated PDZ domains a C-terminal beta-strand
forms the peptide-binding groove base, a circular
permutation with respect to PDZ domains found in
Eumetazoan signaling proteins.
Length = 85
Score = 31.4 bits (72), Expect = 0.11
Identities = 20/62 (32%), Positives = 32/62 (51%), Gaps = 6/62 (9%)
Query: 131 GAIIEKVKKGSPADLEGHLLAGDQVIEWNGRSMRGKSFQDVEDIIAESRQEP--QVELIV 188
G +I V GSPA G + AGD ++ +G + G S +DV ++ R + +V L +
Sbjct: 14 GLVITSVLPGSPAAKAG-IKAGDIIVAIDGEPVDGLSLEDVVKLL---RGKAGTKVRLTL 69
Query: 189 SR 190
R
Sbjct: 70 KR 71
>gnl|CDD|221961 pfam13180, PDZ_2, PDZ domain.
Length = 81
Score = 30.3 bits (69), Expect = 0.27
Identities = 13/43 (30%), Positives = 25/43 (58%), Gaps = 1/43 (2%)
Query: 119 VIGGKLLEDGTRGAIIEKVKKGSPADLEGHLLAGDQVIEWNGR 161
IG +++++ G + VK+GSPA + L GD ++ +G+
Sbjct: 2 DIGVRVVQNEGTGVTVVSVKEGSPAA-KAGLKPGDIILSIDGK 43
>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 = 30.3 bits (69), Expect = 0.45
Identities = 16/48 (33%), Positives = 24/48 (50%), Gaps = 9/48 (18%)
Query: 272 SVKFYLDSGTLRLVV----TLMCAASLVPRSNGQPRCPYAKIYLLPDR 315
S+ + +G+L + + L A RSN PY K+YLLPD+
Sbjct: 6 SLSYNYKTGSLEVHIKECRNLAYADEKKKRSN-----PYVKVYLLPDK 48
>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 = 30.3 bits (69), Expect = 0.52
Identities = 16/45 (35%), Positives = 24/45 (53%), Gaps = 4/45 (8%)
Query: 272 SVKFYLDSGTLRLVVTLMCAASLVP-RSNGQPRC-PYAKIYLLPD 314
+VK Y + L V ++ A +L+P SNG P+ K+ LLP
Sbjct: 6 TVKAYYRASEQSLRVEILNARNLLPLDSNGS--SDPFVKVELLPR 48
>gnl|CDD|238491 cd00991, PDZ_archaeal_metalloprotease, PDZ domain of archaeal zinc
metalloprotases, presumably membrane-associated or
integral membrane proteases, which may be involved in
signalling and regulatory mechanisms. May be responsible
for substrate recognition and/or binding, as most PDZ
domains bind C-terminal polypeptides, and binding to
internal (non-C-terminal) polypeptides and even to
lipids has been demonstrated. In this subfamily of
protease-associated PDZ domains a C-terminal beta-strand
forms the peptide-binding groove base, a circular
permutation with respect to PDZ domains found in
Eumetazoan signaling proteins.
Length = 79
Score = 28.9 bits (65), Expect = 0.75
Identities = 14/60 (23%), Positives = 25/60 (41%), Gaps = 3/60 (5%)
Query: 131 GAIIEKVKKGSPADLEGHLLAGDQVIEWNGRSMRGKSFQDVEDIIAESRQEPQVELIVSR 190
G +I V GSPA+ L GD + NG + +D + + ++ + + V
Sbjct: 11 GVVIVGVIVGSPAENAV-LHTGDVIYSING--TPITTLEDFMEALKPTKPGEVITVTVLP 67
>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 = 29.6 bits (67), Expect = 0.96
Identities = 14/31 (45%), Positives = 17/31 (54%), Gaps = 1/31 (3%)
Query: 284 LVVTLMCAASLVPRSNGQPRCPYAKIYLLPD 314
L V +M A +L +G PY K YLLPD
Sbjct: 15 LFVMVMHAKNLPLL-DGSDPDPYVKTYLLPD 44
>gnl|CDD|182262 PRK10139, PRK10139, serine endoprotease; Provisional.
Length = 455
Score = 30.7 bits (69), Expect = 1.2
Identities = 17/32 (53%), Positives = 21/32 (65%), Gaps = 2/32 (6%)
Query: 125 LEDGTRGAIIEKVKKGSPADLEGHLLAGDQVI 156
L+DGT+G I++V KGSPA G L D VI
Sbjct: 385 LKDGTKGIKIDEVVKGSPAAQAG--LQKDDVI 414
>gnl|CDD|226541 COG4055, McrD, Methyl coenzyme M reductase, subunit D [Coenzyme
metabolism].
Length = 165
Score = 29.3 bits (66), Expect = 1.5
Identities = 19/88 (21%), Positives = 36/88 (40%), Gaps = 7/88 (7%)
Query: 182 PQVELIVSRRIQPKYAPTLSKDVYERVRDKPSVLVTSPGSPDIHSGRPGRPVPSHHTDHH 241
VE+ R ++ + L ++Y+ + V++ P P P R +P +H D
Sbjct: 9 IDVEIFPHRLLKAETTEKLLNELYD-LDGIVRVVIHGPRLPKRVPYGPARGLPVNHPDRR 67
Query: 242 PITNSSVGGRIQVKFYLDSGTLRLVVTL 269
PI V G + L R+++ +
Sbjct: 68 PIQ---VKG---EEIELKVKVGRIILEI 89
>gnl|CDD|214598 smart00282, LamG, Laminin G domain.
Length = 132
Score = 28.8 bits (65), Expect = 2.0
Identities = 11/46 (23%), Positives = 18/46 (39%), Gaps = 7/46 (15%)
Query: 248 VGGRIQVKFYLDSGTLRLVVTLI-------HSVKFYLDSGTLRLVV 286
GR+ +++ L SG RL H V + ++ L V
Sbjct: 32 RDGRLVLRYDLGSGPARLTSDPTPLNDGQWHRVAVERNGRSVTLSV 77
>gnl|CDD|239580 cd03500, SQR_TypeA_SdhD_like, Succinate:quinone oxidoreductase
(SQR) Type A subfamily, Succinate dehydrogenase D
(SdhD)-like subunit; SQR catalyzes the oxidation of
succinate to fumarate coupled to the reduction of
quinone to quinol. Members of this subfamily reduce low
potential quinones such as menaquinone and
thermoplasmaquinone. SQR is also called succinate
dehydrogenase or Complex II, and is part of the citric
acid cycle and the aerobic respiratory chain. SQR is
composed of a flavoprotein catalytic subunit, an
iron-sulfur protein and one or two hydrophobic
transmembrane subunits. Members of this subfamily are
similar to the Thermoplasma acidophilum SQR and are
classified as Type A because they contain two
transmembrane subunits as well as two heme groups.
Although there are no structures available for this
subfamily, the presence of two hemes has been proven
spectroscopically for T. acidophilum. The two membrane
anchor subunits are similar to the SdhD and SdhC
subunits of bacterial SQRs, which contain heme and
quinone binding sites. The two-electron oxidation of
succinate in the flavoprotein active site is coupled to
the two-electron reduction of quinone in the membrane
anchor subunits via electron transport through FAD and
three iron-sulfur centers. The reversible reduction of
quinone is an essential feature of respiration, allowing
transfer of electrons between respiratory complexes.
Length = 106
Score = 28.4 bits (64), Expect = 2.1
Identities = 12/65 (18%), Positives = 22/65 (33%), Gaps = 7/65 (10%)
Query: 238 TDHHPITNSSVGGRIQVKFYLDSGTLRLVVTLIH-------SVKFYLDSGTLRLVVTLMC 290
I + V R+ + L LV+ L+H + Y+ LR V +
Sbjct: 30 NGGDVIDFAFVANRLASPLWKVWDLLLLVLALLHGGNGLRNILLDYVRRPRLRRAVKGLL 89
Query: 291 AASLV 295
+ +
Sbjct: 90 YVAGL 94
>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 = 28.4 bits (64), Expect = 2.5
Identities = 14/44 (31%), Positives = 21/44 (47%), Gaps = 2/44 (4%)
Query: 272 SVKFYLDSGTLRLVVTLMCAASLVPRSNGQPRCPYAKIYLLPDR 315
SV + TL + ++ A L + P+ KIYLLPD+
Sbjct: 8 SVSYDFQESTL--TLKILKAVELPAKDFSGTSDPFVKIYLLPDK 49
>gnl|CDD|235564 PRK05691, PRK05691, peptide synthase; Validated.
Length = 4334
Score = 29.4 bits (66), Expect = 3.7
Identities = 13/31 (41%), Positives = 21/31 (67%), Gaps = 2/31 (6%)
Query: 271 HSVKFYLDSGTLRLVVTLMCAASLVPRSNGQ 301
+S+ F D+ + RL+V L+C A +V R+ GQ
Sbjct: 2381 YSINF--DAASERLLVPLLCGARVVLRAQGQ 2409
>gnl|CDD|240480 cd12900, SPRY_PRY_Btn_TRIMs, PRY/SPRY domain in butyrophilins and
butyrophilins-like proteins, pyrin, as well as
tripartite motif-containing proteins (TRIM4, 5, 6, 11,
21, 22, 27, 30, 34, 38, 58, 60, 68, 75). This domain,
consisting of the distinct N-terminal PRY subdomain
followed by the SPRY subdomain, is found at the
C-terminus of pyrin, several tripartite motif-containing
proteins (TRIMs), as well as butyrophilin (Btns) and
butyrophilin-like (Btnl) family members, with the
exception of Btnl2. Btn and Btnl family members are
novel regulators of immune responses, with many of the
genes located within the MHC. They are implicated in
T-cell inhibition and modulation of epithelial cell-T
cell interactions. Expression of TRIM4 (also known as
ring finger protein 87 or RNF87) genes, including that
of CHCHD2 and PKIB, differs significantly in
Huntington's disease (HD), a prototypical genetic
disorder with delayed clinical onset, despite ubiquitous
expression of the mutated gene during development.
TRIM5-alpha is a cytoplasmic protein that recognizes the
incoming capsid (CA) protein of retroviruses and
potently inhibits virus infection in a species-specific
manner; it recognizes and interacts directly with HIV
CA, thus disrupting the ordered process of viral
uncoating, and subsequent reverse transcription and
virus replication, while species-specific differences
are determined by sequence variations within the
C-terminal B30.2/PRYSPRY domain. TRIM6 regulates the
transcriptional activity of proto-oncogene product Myc
during the maintenance of ES cell pluripotency,
suggesting that TRIM6 functions as a novel regulator for
Myc-mediated transcription in ES cells. TRIM11 is
involved in the function and development of the nervous
system and is overexpressed in high-grade gliomas and
promotes proliferation, invasion, migration and glial
tumor growth. TRIM21 (also known as RO52, SSA1 or RNF81)
is a major autoantigen in autoimmune diseases such as
rheumatoid arthritis, systemic lupus erythematosus, and
Sjorgen's syndrome. TRIM21 interacts with connexin 43
(Cx43) providing mechanisms for down-regulation of gap
junction (GJ) intercellular communication thus impacting
a variety of physiological processes. Expression of the
TRIM34 gene is up-regulated by interferon and is mapped
to chromosome 11p15, where it resides within a TRIM gene
cluster. TRIM30 alpha negatively regulates Toll-like
receptor (TLR)-mediated NF-kappa B activation by
targeting degradation of adaptors TAB2 and TAB3 that are
in complex with kinase TAK1. TRIM5 gene's closest human
paralogs are TRIM6, TRIM22 and TRIM34. It has also been
shown that the RBCC domains of TRIM6, 21 and 34 can
functionally replace the corresponding domains of
TRIM5alpha with respect to inhibition of HIV-1 infection
through binding of the chimeras to HIV-1 capsid
complexes. TRIM27 (also known as Ret finger protein, RFP
or RNF76) negatively regulates CD4 T-cells by
ubiquitinating and inhibiting the class II
phosphatidylinositol 3 kinase C2beta (PI3K-C2beta), a
kinase critical for KCa3.1 channel activation. It is
also a specific binding partner for NOD2, the
nucleotide-binding domain and leucine-rich repeat
containing gene family (NLR) member 2 involved in
mediating antimicrobial responses. It negatively
regulates NOD2-mediated signaling by degrading NOD2, and
therefore a potential target for therapeutic
intervention in NOD2-associated diseases such as
early-onset sarcoidosis and Blau syndrome. TRIM38
negatively regulates Toll-like receptor 3
(TLR3)-mediated type I interferon signaling by targeting
TIR domain-containing adaptor inducing IFN-beta (TRIF).
TRIM60 (also known as RNF33 or ring finger protein 33)
interacts with kinesin-2 family members 3A (KIF3A) and
3B (KIF3B) motor proteins known to transport cargos
along the microtubule, possibly contributing to
kinesin-dependent mobilization of specific cargos along
the microtubule. TRIM68 regulates ligand-dependent
transcription of androgen receptor in prostate cancer
cells; its overexpression causes an increase in
prostate-specific antigen (PSA), a reliable diagnostic
marker for prostate cancer, making TRIM68 a likely novel
diagnostic tool and a potentially therapeutic target.
The PRY/SPRY domain of pyrin, which is mutated in
familial Mediterranean fever patients, interacts with
inflammasome components and inhibits proIL-1beta
processing.
Length = 173
Score = 28.2 bits (64), Expect = 4.2
Identities = 16/47 (34%), Positives = 19/47 (40%), Gaps = 7/47 (14%)
Query: 185 ELIVS---RRIQPKYAPTLSKDVYERVRDKPSVLVTSPGSPDIHSGR 228
LI+S R ++ D ER P VL GSP SGR
Sbjct: 15 NLILSEDRRSVRYGDTRQDLPDNPERFDSYPCVL----GSPGFTSGR 57
>gnl|CDD|162494 TIGR01696, deoB, phosphopentomutase. This protein is involved in
the purine and pyrimidine salvage pathway. It catalyzes
the conversion of D-ribose 1-phosphate to D-ribose
5-phosphate and the conversion of 2-deoxy-D-ribose
1-phosphate to 2-deoxy-D-ribose 5-phosphate. The seed
members of this protein are characterized deoB proteins
from E.Coli and Bacillus. This model matches pfam01676
for Metalloenzyme superfamily [Purines, pyrimidines,
nucleosides, and nucleotides, Other].
Length = 381
Score = 28.3 bits (63), Expect = 5.6
Identities = 41/181 (22%), Positives = 66/181 (36%), Gaps = 48/181 (26%)
Query: 91 DGKYMIGHMILR----------KSGDRY-----PSASSTL------GIKVIG-GKLLEDG 128
D KY IG +I R ++G+R+ P A + L G VI GK+ +
Sbjct: 181 DPKYNIGRIIARPFVGEPGNFQRTGNRHDYALKPFAPTVLQKLKDEGHDVISIGKIADIY 240
Query: 129 TRGAIIEKVKKGSPADLEGHLLAGDQVIEWNGRSMRGKSFQDVEDIIAESRQEPQVELIV 188
I +KV+ S D D I+ G SF ++ D A L
Sbjct: 241 DGEGITKKVRTTSNMDGM------DATIKEMKEDFTGISFTNLVDFDA---------LWG 285
Query: 189 SRRIQPKYAPTLSK------DVYERVRDKPSVLVTSPGSPDIHSGRPGRPVPSHHTDHHP 242
RR YA L +++ +R+ +++T+ H P H ++ P
Sbjct: 286 HRRDVAGYAAALELFDRRLPELFSLLREDDLLIITAD-----HGNDPTWTGTDHTREYIP 340
Query: 243 I 243
+
Sbjct: 341 V 341
>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 = 27.4 bits (61), Expect = 5.7
Identities = 15/32 (46%), Positives = 18/32 (56%)
Query: 284 LVVTLMCAASLVPRSNGQPRCPYAKIYLLPDR 315
L V L+ A +L PR PY K+ LLPDR
Sbjct: 18 LNVKLIQARNLQPRDFSGTADPYCKVRLLPDR 49
>gnl|CDD|232883 TIGR00225, prc, C-terminal peptidase (prc). A C-terminal peptidase
with different substrates in different species including
processing of D1 protein of the photosystem II reaction
center in higher plants and cleavage of a peptide of 11
residues from the precursor form of penicillin-binding
protein in E.coli E.coli and H influenza have the most
distal branch of the tree and their proteins have an
N-terminal 200 amino acids that show no homology to
other proteins in the database [Protein fate,
Degradation of proteins, peptides, and glycopeptides,
Protein fate, Protein modification and repair].
Length = 334
Score = 28.1 bits (63), Expect = 5.7
Identities = 15/37 (40%), Positives = 24/37 (64%), Gaps = 1/37 (2%)
Query: 139 KGSPADLEGHLLAGDQVIEWNGRSMRGKSFQDVEDII 175
+GSPA+ G + GD++I+ NG+S+ G S D +I
Sbjct: 71 EGSPAEKAG-IKPGDKIIKINGKSVAGMSLDDAVALI 106
>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 = 27.3 bits (61), Expect = 5.9
Identities = 10/41 (24%), Positives = 18/41 (43%), Gaps = 5/41 (12%)
Query: 278 DSGTLRLVVTLMCAASLVPRSNGQPRC---PYAKIYLLPDR 315
+S L+V ++ L + PY K+ LLP++
Sbjct: 12 NSEKKALLVNIIECRDLPAM--DEQSGTSDPYVKLQLLPEK 50
>gnl|CDD|175992 cd04026, C2_PKC_alpha_gamma, C2 domain in Protein Kinase C (PKC)
alpha and gamma. A single C2 domain is found in PKC
alpha and gamma. The PKC family of serine/threonine
kinases regulates apoptosis, proliferation, migration,
motility, chemo-resistance, and differentiation. There
are 3 groups: group 1(alpha, betaI, beta II, gamma)
which require phospholipids and calcium, group 2 (delta,
epsilon, theta, eta) which do not require calcium for
activation, and group 3 (xi, iota/lambda) which are
atypical and can be activated in the absence of
diacylglycerol and calcium. 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 = 131
Score = 27.2 bits (61), Expect = 5.9
Identities = 17/67 (25%), Positives = 25/67 (37%), Gaps = 23/67 (34%)
Query: 250 GRIQVKFYLDSGTLRLVVTLIHSVKFYLDSGTLRLVVTLMCAASLVPR-SNGQPRCPYAK 308
GRI +K + +L V + A +L+P NG PY K
Sbjct: 2 GRIYLKISVKDN---------------------KLTVEVREAKNLIPMDPNGLSD-PYVK 39
Query: 309 IYLLPDR 315
+ L+PD
Sbjct: 40 LKLIPDP 46
>gnl|CDD|215641 PLN03237, PLN03237, DNA topoisomerase 2; Provisional.
Length = 1465
Score = 28.3 bits (63), Expect = 6.5
Identities = 18/62 (29%), Positives = 29/62 (46%), Gaps = 14/62 (22%)
Query: 156 IEWNGRSMRGKSFQDVEDIIAESRQEPQVELIVSRRIQPKYAPTLSKDVYERVRDKPSVL 215
+E NG+ + KSF D D+ ES + +P+ P +YE+V D+ V
Sbjct: 254 VELNGKRIPVKSFSDYVDLYLESANKS----------RPENLPR----IYEKVNDRWEVC 299
Query: 216 VT 217
V+
Sbjct: 300 VS 301
>gnl|CDD|239210 cd02844, PAZ_CAF_like, PAZ domain, CAF_like subfamily. CAF (for
carpel factory) is a plant homolog of Dicer. CAF has
been implicated in flower morphogenesis and in early
Arabidopsis development and might function through
posttranscriptional regulation of specific mRNA
molecules. PAZ domains are named after the proteins
Piwi, Argonaut, and Zwille. PAZ is found in two families
of proteins that are essential components of
RNA-mediated gene-silencing pathways, including RNA
interference, the Piwi and Dicer families. PAZ functions
as a nucleic-acid binding domain, with a strong
preference for single-stranded nucleic acids (RNA or
DNA) or RNA duplexes with single-stranded 3' overhangs.
It has been suggested that the PAZ domain provides a
unique mode for the recognition of the two 3'-terminal
nucleotides in single-stranded nucleic acids and buries
the 3' OH group, and that it might recognize
characteristic 3' overhangs in siRNAs within RISC
(RNA-induced silencing) and other complexes.
Length = 135
Score = 27.4 bits (61), Expect = 6.6
Identities = 15/46 (32%), Positives = 21/46 (45%), Gaps = 5/46 (10%)
Query: 265 LVVTLIHSVKFYLDSGTLRLVVTLMCAASLVPRSNGQPRCPYAKIY 310
VVT H+ +FY+ SG L + A S P G YA+ +
Sbjct: 34 SVVTAPHNGRFYVISGILD-----LNANSSFPGKEGLGYATYAEYF 74
>gnl|CDD|240095 cd04747, OYE_like_5_FMN, Old yellow enzyme (OYE)-related FMN
binding domain, group 5. Each monomer of OYE contains
FMN as a non-covalently bound cofactor, uses NADPH as a
reducing agent with oxygens, quinones, and
alpha,beta-unsaturated aldehydes and ketones, and can
act as electron acceptors in the catalytic reaction.
Other members of OYE family include trimethylamine
dehydrogenase, 2,4-dienoyl-CoA reductase, enoate
reductase, pentaerythriol tetranitrate reductase,
xenobiotic reductase, and morphinone reductase.
Length = 361
Score = 27.7 bits (62), Expect = 7.9
Identities = 13/34 (38%), Positives = 18/34 (52%), Gaps = 6/34 (17%)
Query: 24 PSSDSGVDMRHSTARSRDEELRYYRGELEGSTGN 57
P D+GVD+ H + R R++ E EGS N
Sbjct: 243 PLVDAGVDIFHCSTR------RFWEPEFEGSELN 270
>gnl|CDD|182820 PRK10898, PRK10898, serine endoprotease; Provisional.
Length = 353
Score = 27.7 bits (62), Expect = 8.6
Identities = 15/61 (24%), Positives = 27/61 (44%), Gaps = 3/61 (4%)
Query: 130 RGAIIEKVKKGSPADLEGHLLAGDQVIEWNGRSMRGKSFQDVEDIIAESRQEPQVELIVS 189
+G ++ +V PA G + D +I N + S + D +AE R + ++V
Sbjct: 279 QGIVVNEVSPDGPAAKAG-IQVNDLIISVNNK--PAISALETMDQVAEIRPGSVIPVVVM 335
Query: 190 R 190
R
Sbjct: 336 R 336
>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 = 26.9 bits (60), Expect = 9.1
Identities = 9/31 (29%), Positives = 15/31 (48%)
Query: 284 LVVTLMCAASLVPRSNGQPRCPYAKIYLLPD 314
L+V ++ +L P+ K+YL PD
Sbjct: 15 LIVGIIRCVNLAAMDANGYSDPFVKLYLKPD 45
>gnl|CDD|191324 pfam05628, Borrelia_P13, Borrelia membrane protein P13. This
family consists of P13 proteins from Borrelia species.
P13 is a 13kDa integral membrane protein which is
post-translationally processed at both ends and modified
by an unknown mechanism.
Length = 133
Score = 26.6 bits (59), Expect = 9.5
Identities = 13/48 (27%), Positives = 22/48 (45%), Gaps = 4/48 (8%)
Query: 105 GDRYPSASSTLGIKVIGGKLLEDGTRGAIIEKVKKGSPADLEGHLLAG 152
GD Y + LG +++GG L+ G I+ + + G +L G
Sbjct: 32 GD-YIGGGAVLGFQLLGGILI---ITGYILGHTENKKADSITGKILMG 75
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
0.315 0.135 0.392
Gapped
Lambda K H
0.267 0.0715 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,354,347
Number of extensions: 1608063
Number of successful extensions: 1335
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1326
Number of HSP's successfully gapped: 49
Length of query: 315
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 218
Effective length of database: 6,635,264
Effective search space: 1446487552
Effective search space used: 1446487552
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 59 (26.5 bits)