RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11469
(267 letters)
>gnl|CDD|214587 smart00255, TIR, Toll - interleukin 1 - resistance.
Length = 140
Score = 45.4 bits (108), Expect = 3e-06
Identities = 23/96 (23%), Positives = 36/96 (37%), Gaps = 3/96 (3%)
Query: 136 CQAYVIYSLKDEPFVKQILLPGLAFKDPAVKLRVHHRDLNPNLISTADFVTNSIERSEKV 195
++ YS E + L L K L V D P + + +IE+S
Sbjct: 2 YDVFISYS-GKEDVRNE-FLSHLLEKLRGYGLCVFIDDFEPG-GGDLEEIDEAIEKSRIA 58
Query: 196 IMVLSRAFIYGDWSRPEFKSALNGSLMRHRKPLFII 231
I+VLS + +W E +AL +L + I
Sbjct: 59 IVVLSPNYAESEWCLDELVAALENALEEGGLRVIPI 94
>gnl|CDD|216585 pfam01582, TIR, TIR domain. The Toll/interleukin-1 receptor (TIR)
homology domain is an intracellular signalling domain
found in MyD88, interleukin 1 receptor and the Toll
receptor. It contains three highly-conserved regions,
and mediates protein-protein interactions between the
Toll-like receptors (TLRs) and signal-transduction
components. TIR-like motifs are also found in plant
proteins thought to be involved in resistance to
disease. When activated, TIR domains recruit cytoplasmic
adaptor proteins MyD88 and TOLLIP (Toll interacting
protein). In turn, these associate with various kinases
to set off signalling cascades.
Length = 135
Score = 38.0 bits (89), Expect = 0.001
Identities = 25/121 (20%), Positives = 47/121 (38%), Gaps = 9/121 (7%)
Query: 138 AYVIYS-LKDEPFVKQILLPGLAFKDPAVKLRVHHRDLNPNLISTADFVTNSIERSEKVI 196
+V +S D LL L ++ +KL + RD P S + + +IE+S + I
Sbjct: 1 VFVSFSGKDDRDTFVSHLLKEL--EEKGIKLCIDDRDELPGE-SILENLFEAIEKSRRAI 57
Query: 197 MVLSRAFIYGDWSRPEFKSALNGSLMRHRKPLFIIMLPPHSNILV--IMPMSIYHLSVLL 254
++ S + +W E + +L ++LP + + P S L
Sbjct: 58 VIFSSNYASSEWCLDELVEIVKCAL---EGGGKKVILPIFYKVDPSDVRPQSGKFGKAFL 114
Query: 255 Q 255
+
Sbjct: 115 K 115
>gnl|CDD|222311 pfam13676, TIR_2, TIR domain. This is a family of bacterial
Toll-like receptors.
Length = 102
Score = 34.5 bits (80), Expect = 0.009
Identities = 21/103 (20%), Positives = 41/103 (39%), Gaps = 22/103 (21%)
Query: 139 YVIYSLKDEPFVKQILLPGLAFKDPAVKL-----RVHH-RDLNPNLISTADFVTNSIERS 192
++ Y+ D + + + A L RV D+ P D + ++ +
Sbjct: 2 FISYASADREWAEWL----------ADALEAAGIRVWLDWDIPPG-EDWRDEIEEALRSA 50
Query: 193 EKVIMVLSRAFIYGDWSRPEFKSALNGSLMRHRKPLFIIMLPP 235
+ V+++LS A++ W R E+ +AL K L + L
Sbjct: 51 DVVLVLLSPAYLASPWCRAEWGAAL-----ERGKRLIPVRLED 88
>gnl|CDD|188093 TIGR00864, PCC, polycystin cation channel protein. The
Polycystin Cation Channel (PCC) Family (TC 1.A.5)
Polycystin is a huge protein of 4303aas. Its repeated
leucine-rich (LRR) segment is found in many proteins.
It contains 16 polycystic kidney disease (PKD) domains,
one LDL-receptor class A domain, one C-type lectin
family domain, and 16-18 putative TMSs in positions
between residues 2200 and 4100. Polycystin-L has been
shown to be a cation (Na+, K+ and Ca2+) channel that is
activated by Ca2+. Two members of the PCC family
(polycystin 1 and 2) are mutated in autosomal dominant
polycystic kidney disease, and polycystin-L is deleted
in mice with renal and retinal defects. Note: this
model is restricted to the amino half for technical
reasons.
Length = 2740
Score = 33.1 bits (75), Expect = 0.17
Identities = 10/17 (58%), Positives = 11/17 (64%)
Query: 6 LGENPFECDCKMEWLQR 22
L NPFECDC + L R
Sbjct: 26 LSGNPFECDCGLARLPR 42
>gnl|CDD|214507 smart00082, LRRCT, Leucine rich repeat C-terminal domain.
Length = 51
Score = 29.3 bits (66), Expect = 0.27
Identities = 9/14 (64%), Positives = 11/14 (78%)
Query: 9 NPFECDCKMEWLQR 22
NPF CDC++ WL R
Sbjct: 1 NPFICDCELRWLLR 14
>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 = 30.4 bits (69), Expect = 0.37
Identities = 14/32 (43%), Positives = 18/32 (56%), Gaps = 7/32 (21%)
Query: 147 EPFVKQILLPGLAFKDPAVKL--RVHHRDLNP 176
+PFVK LLP D KL +V ++LNP
Sbjct: 38 DPFVKIYLLP-----DKKHKLETKVKRKNLNP 64
>gnl|CDD|214470 smart00013, LRRNT, Leucine rich repeat N-terminal domain.
Length = 33
Score = 27.7 bits (62), Expect = 0.59
Identities = 14/37 (37%), Positives = 16/37 (43%), Gaps = 6/37 (16%)
Query: 91 CPFNCTCYNDQAWTTNIVDCSNSQYNHVPLFVPMDAT 127
CP C C + VDCS VPL +P D T
Sbjct: 2 CPAPCNC------SGTAVDCSGRGLTEVPLDLPPDTT 32
>gnl|CDD|239499 cd03405, Band_7_HflC, Band_7_HflC: The band 7 domain of flotillin
(reggie) like proteins. This group includes proteins
similar to prokaryotic HlfC (High frequency of
lysogenization C). Although many members of the band 7
family are lipid raft associated, prokaryote plasma
membranes lack cholesterol and are unlikely to have
lipid raft domains. Individual proteins of this band 7
domain family may cluster to form membrane microdomains
which may in turn recruit multiprotein complexes.
Escherichia coli HflC is an integral membrane protein
which may localize to the plasma membrane. HflC
associates with another band 7 family member (HflK) to
form an HflKC complex. HflKC interacts with FtsH in a
large complex termed the FtsH holo-enzyme. FtsH is an
AAA ATP-dependent protease which exerts progressive
proteolysis against membrane-embedded and soluble
substrate proteins. HflKC can modulate the activity of
FtsH. HflKC plays a role in the decision between
lysogenic and lytic cycle growth during lambda phage
infection.
Length = 242
Score = 28.7 bits (65), Expect = 2.7
Identities = 12/40 (30%), Positives = 18/40 (45%), Gaps = 6/40 (15%)
Query: 150 VKQILLPGLAFKDPAV------KLRVHHRDLNPNLISTAD 183
V+ + PGL FK P + R+ D +P + T D
Sbjct: 19 VRVVTEPGLHFKLPFIQQVKKFDKRILTLDSDPQRVLTKD 58
>gnl|CDD|215583 PLN03112, PLN03112, cytochrome P450 family protein; Provisional.
Length = 514
Score = 29.0 bits (65), Expect = 2.7
Identities = 17/52 (32%), Positives = 22/52 (42%), Gaps = 10/52 (19%)
Query: 195 VIMVLSRAFIYGDWSRPEFKSALN-------GSLMRHRKPLFIIM---LPPH 236
V+M L+R F DWS P+ + G M KPL + L PH
Sbjct: 460 VLMALARLFHCFDWSPPDGLRPEDIDTQEVYGMTMPKAKPLRAVATPRLAPH 511
>gnl|CDD|221751 pfam12749, Metallothio_Euk, Eukaryotic metallothionein. This is
a family of eukaryotic metallothioneins.
Length = 70
Score = 26.7 bits (58), Expect = 3.5
Identities = 8/25 (32%), Positives = 12/25 (48%)
Query: 73 CFSLCRCCEYGACDCRMSCPFNCTC 97
C C+C DC+ + P +C C
Sbjct: 43 CKCGCKCSSSAVDDCKCTGPTSCKC 67
>gnl|CDD|188459 TIGR03944, dehyd_SbnB_fam, 2,3-diaminopropionate biosynthesis
protein SbnB. Members of this protein family are
probable NAD-dependent dehydrogenases related to the
alanine dehydrogenase of Archaeoglobus fulgidus (see
TIGR02371, PDB structure 1OMO and PMID:15313611) and
more distantly to ornithine cyclodeaminase. Members
include the staphylobactin biosynthesis protein SbnB and
tend to occur in contexts suggesting non-ribosomal
peptide synthesis, always adjacent to (occasionally
fused with) a pyridoxal phosphate-dependent enzyme,
SbnA. The pair appears to provide 2,3-diaminopropionate
for biosynthesis of siderophores or other secondary
metabolites [Cellular processes, Biosynthesis of natural
products].
Length = 327
Score = 28.0 bits (63), Expect = 4.8
Identities = 22/101 (21%), Positives = 34/101 (33%), Gaps = 23/101 (22%)
Query: 172 RDLNPNLISTADFVTNSIE---RSEKVI--MVL---SRAFIYGDWSRPEFKSALNGSLMR 223
RDL P +I AD + + E R+ + R FI L G +
Sbjct: 231 RDLAPEVILKADNIVDDWEHVCRANTSLHLAEQEGGHREFITA-----TLGEILTGEVPG 285
Query: 224 HRKPLFIIMLPPHSNILVIMPMSIYHLSV---LLQDNQASG 261
I+ P + I L+V + + QA+G
Sbjct: 286 REDDDEPIIFSP-------FGLGILDLAVARWVYEQAQAAG 319
>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 = 26.8 bits (60), Expect = 6.3
Identities = 14/30 (46%), Positives = 16/30 (53%), Gaps = 1/30 (3%)
Query: 148 PFVKQILLPGLAFKD-PAVKLRVHHRDLNP 176
PFVK LLP F D P K +V + L P
Sbjct: 39 PFVKVELLPRHLFPDVPTPKTQVKKKTLFP 68
>gnl|CDD|223714 COG0641, AslB, Arylsulfatase regulator (Fe-S oxidoreductase)
[General function prediction only].
Length = 378
Score = 27.8 bits (62), Expect = 7.3
Identities = 10/54 (18%), Positives = 19/54 (35%), Gaps = 4/54 (7%)
Query: 50 NLITYDNIFIADSSK---FLCDYEEHCFSLCRCCEYGACDCRMSCPFNCTCYND 100
N+ + S + F D ++ + C+ CE+ C CP +
Sbjct: 284 NIHETSLAQMLASPQQQQFGADKQKGLSAKCQRCEWLFL-CHGGCPKHRIVQGG 336
>gnl|CDD|179825 PRK04326, PRK04326, methionine synthase; Provisional.
Length = 330
Score = 27.6 bits (62), Expect = 7.6
Identities = 12/37 (32%), Positives = 19/37 (51%), Gaps = 4/37 (10%)
Query: 16 KMEWLQRAHEIHKDGIYPEIADLESLY---CRMVYEE 49
K +WL+ A +HK G E DL + R+V ++
Sbjct: 19 KPKWLREAIRLHKAGKISE-EDLHEAFDDAVRLVVKD 54
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
0.326 0.140 0.456
Gapped
Lambda K H
0.267 0.0723 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,430,317
Number of extensions: 1240855
Number of successful extensions: 1254
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1251
Number of HSP's successfully gapped: 26
Length of query: 267
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 172
Effective length of database: 6,723,972
Effective search space: 1156523184
Effective search space used: 1156523184
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 58 (26.1 bits)