RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13946
(90 letters)
>gnl|CDD|227455 COG5126, FRQ1, Ca2+-binding protein (EF-Hand superfamily) [Signal
transduction mechanisms / Cytoskeleton / Cell division
and chromosome partitioning / General function
prediction only].
Length = 160
Score = 40.0 bits (94), Expect = 2e-05
Identities = 12/43 (27%), Positives = 22/43 (51%)
Query: 7 PQSEDENTPQKRVDKIFDQMDKNHDDRLTLEEFREGSKADPRI 49
+S E + V+K+ + D++ D + EEF++ K P I
Sbjct: 118 LKSLGERLSDEEVEKLLKEYDEDGDGEIDYEEFKKLIKDSPTI 160
>gnl|CDD|238008 cd00051, EFh, EF-hand, calcium binding motif; A diverse
superfamily of calcium sensors and calcium signal
modulators; most examples in this alignment model have
2 active canonical EF hands. Ca2+ binding induces a
conformational change in the EF-hand motif, leading to
the activation or inactivation of target proteins.
EF-hands tend to occur in pairs or higher copy numbers.
Length = 63
Score = 35.2 bits (82), Expect = 3e-04
Identities = 10/35 (28%), Positives = 21/35 (60%)
Query: 8 QSEDENTPQKRVDKIFDQMDKNHDDRLTLEEFREG 42
+S E ++ +D++ ++DK+ D ++ EEF E
Sbjct: 27 KSLGEGLSEEEIDEMIREVDKDGDGKIDFEEFLEL 61
Score = 26.7 bits (60), Expect = 0.61
Identities = 5/24 (20%), Positives = 12/24 (50%)
Query: 18 RVDKIFDQMDKNHDDRLTLEEFRE 41
+ + F DK+ D ++ +E +
Sbjct: 1 ELREAFRLFDKDGDGTISADELKA 24
>gnl|CDD|222177 pfam13499, EF_hand_5, EF-hand domain pair.
Length = 60
Score = 33.1 bits (76), Expect = 0.002
Identities = 9/23 (39%), Positives = 17/23 (73%)
Query: 19 VDKIFDQMDKNHDDRLTLEEFRE 41
++ F+++DK+ D R++ EEF E
Sbjct: 36 IEADFNEIDKDGDGRISFEEFLE 58
Score = 25.8 bits (57), Expect = 1.4
Identities = 6/18 (33%), Positives = 11/18 (61%)
Query: 24 DQMDKNHDDRLTLEEFRE 41
+DK+ D + +EE R+
Sbjct: 1 KLLDKDGDGYIDVEELRK 18
>gnl|CDD|200946 pfam00036, efhand, EF hand. The EF-hands can be divided into two
classes: signaling proteins and buffering/transport
proteins. The first group is the largest and includes
the most well-known members of the family such as
calmodulin, troponin C and S100B. These proteins
typically undergo a calcium-dependent conformational
change which opens a target binding site. The latter
group is represented by calbindin D9k and do not
undergo calcium dependent conformational changes.
Length = 29
Score = 32.0 bits (74), Expect = 0.003
Identities = 8/24 (33%), Positives = 16/24 (66%)
Query: 18 RVDKIFDQMDKNHDDRLTLEEFRE 41
+ + F + DK+ D +++ EEF+E
Sbjct: 1 ELKEAFKEFDKDGDGKISFEEFKE 24
>gnl|CDD|205583 pfam13405, EF_hand_4, EF-hand domain.
Length = 30
Score = 31.8 bits (73), Expect = 0.004
Identities = 7/24 (29%), Positives = 13/24 (54%)
Query: 18 RVDKIFDQMDKNHDDRLTLEEFRE 41
+ + F DK+ D ++ EE R+
Sbjct: 1 ELREAFKLFDKDGDGYISAEELRK 24
>gnl|CDD|197492 smart00054, EFh, EF-hand, calcium binding motif. EF-hands are
calcium-binding motifs that occur at least in pairs.
Links between disease states and genes encoding
EF-hands, particularly the S100 subclass, are emerging.
Each motif consists of a 12 residue loop flanked on
either side by a 12 residue alpha-helix. EF-hands
undergo a conformational change unpon binding calcium
ions.
Length = 29
Score = 30.8 bits (71), Expect = 0.007
Identities = 9/27 (33%), Positives = 16/27 (59%)
Query: 19 VDKIFDQMDKNHDDRLTLEEFREGSKA 45
+ + F DK+ D ++ EEF++ KA
Sbjct: 2 LKEAFRLFDKDGDGKIDFEEFKDLLKA 28
>gnl|CDD|183426 PRK12309, PRK12309, transaldolase/EF-hand domain-containing
protein; Provisional.
Length = 391
Score = 32.4 bits (74), Expect = 0.017
Identities = 12/23 (52%), Positives = 16/23 (69%)
Query: 20 DKIFDQMDKNHDDRLTLEEFREG 42
D +FD +D NHD ++T EE R G
Sbjct: 360 DAVFDALDLNHDGKITPEEMRAG 382
>gnl|CDD|238131 cd00213, S-100, S-100: S-100 domain, which represents the largest
family within the superfamily of proteins carrying the
Ca-binding EF-hand motif. Note that this S-100
hierarchy contains only S-100 EF-hand domains, other
EF-hands have been modeled separately. S100 proteins
are expressed exclusively in vertebrates, and are
implicated in intracellular and extracellular
regulatory activities. Intracellularly, S100 proteins
act as Ca-signaling or Ca-buffering proteins. The most
unusual characteristic of certain S100 proteins is
their occurrence in extracellular space, where they act
in a cytokine-like manner through RAGE, the receptor
for advanced glycation products. Structural data
suggest that many S100 members exist within cells as
homo- or heterodimers and even oligomers;
oligomerization contributes to their functional
diversification. Upon binding calcium, most S100
proteins change conformation to a more open structure
exposing a hydrophobic cleft. This hydrophobic surface
represents the interaction site of S100 proteins with
their target proteins. There is experimental evidence
showing that many S100 proteins have multiple binding
partners with diverse mode of interaction with
different targets. In addition to S100 proteins (such
as S100A1,-3,-4,-6,-7,-10,-11,and -13), this group
includes the ''fused'' gene family, a group of calcium
binding S100-related proteins. The ''fused'' gene
family includes multifunctional epidermal
differentiation proteins - profilaggrin, trichohyalin,
repetin, hornerin, and cornulin; functionally these
proteins are associated with keratin intermediate
filaments and partially crosslinked to the cell
envelope. These ''fused'' gene proteins contain
N-terminal sequence with two Ca-binding EF-hands motif,
which may be associated with calcium signaling in
epidermal cells and autoprocessing in a
calcium-dependent manner. In contrast to S100 proteins,
"fused" gene family proteins contain an extraordinary
high number of almost perfect peptide repeats with
regular array of polar and charged residues similar to
many known cell envelope proteins.
Length = 88
Score = 30.5 bits (70), Expect = 0.035
Identities = 9/24 (37%), Positives = 14/24 (58%)
Query: 16 QKRVDKIFDQMDKNHDDRLTLEEF 39
+ VDKI +D N D ++ +EF
Sbjct: 50 PEAVDKIMKDLDVNKDGKVDFQEF 73
>gnl|CDD|205383 pfam13202, EF_hand_3, EF hand.
Length = 25
Score = 28.8 bits (66), Expect = 0.051
Identities = 7/23 (30%), Positives = 13/23 (56%)
Query: 19 VDKIFDQMDKNHDDRLTLEEFRE 41
+ +F Q D N D +++ EE +
Sbjct: 1 LKDLFRQFDTNGDGKISKEELKR 23
>gnl|CDD|238009 cd00052, EH, Eps15 homology domain; found in proteins implicated
in endocytosis, vesicle transport, and signal
transduction. The alignment contains a pair of EF-hand
motifs, typically one of them is canonical and binds to
Ca2+, while the other may not bind to Ca2+. A
hydrophobic binding pocket is formed by residues from
both EF-hand motifs. The EH domain binds to proteins
containing NPF (class I), [WF]W or SWG (class II), or
H[TS]F (class III) sequence motifs.
Length = 67
Score = 28.7 bits (65), Expect = 0.12
Identities = 9/27 (33%), Positives = 15/27 (55%)
Query: 13 NTPQKRVDKIFDQMDKNHDDRLTLEEF 39
P+ + +I+D D + D +L EEF
Sbjct: 29 GLPRSVLAQIWDLADTDKDGKLDKEEF 55
>gnl|CDD|240156 cd05030, calgranulins, Calgranulins: S-100 domain found in
proteins belonging to the Calgranulin subgroup of the
S100 family of EF-hand calcium-modulated proteins,
including S100A8, S100A9, and S100A12 . Note that the
S-100 hierarchy, to which this Calgranulin group
belongs, contains only S-100 EF-hand domains, other
EF-hands have been modeled separately. These proteins
are expressed mainly in granulocytes, and are involved
in inflammation, allergy, and neuritogenesis, as well
as in host-parasite response. Calgranulins are
modulated not only by calcium, but also by other metals
such as zinc and copper. Structural data suggested that
calgranulins may exist in multiple structural forms,
homodimers, as well as hetero-oligomers. For example,
the S100A8/S100A9 complex called calprotectin plays
important roles in the regulation of inflammatory
processes, wound repair, and regulating zinc-dependent
enzymes as well as microbial growth.
Length = 88
Score = 28.9 bits (65), Expect = 0.14
Identities = 14/39 (35%), Positives = 23/39 (58%)
Query: 1 MFKGQQPQSEDENTPQKRVDKIFDQMDKNHDDRLTLEEF 39
+ + + P + QK +DKIF+ +D N D +L+ EEF
Sbjct: 35 LVEKELPNFLKKEKNQKAIDKIFEDLDTNQDGQLSFEEF 73
>gnl|CDD|225308 COG2510, COG2510, Predicted membrane protein [Function unknown].
Length = 140
Score = 28.4 bits (64), Expect = 0.28
Identities = 13/32 (40%), Positives = 15/32 (46%), Gaps = 2/32 (6%)
Query: 52 ALSLGDSSNVAP-SGSSPASASAASPLVL-ER 81
AL G +S V P +S A S L L ER
Sbjct: 87 ALKKGKASRVVPLDKTSVVLAVLLSILFLGER 118
>gnl|CDD|226160 COG3634, AhpF, Alkyl hydroperoxide reductase, large subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 520
Score = 29.0 bits (65), Expect = 0.32
Identities = 15/47 (31%), Positives = 22/47 (46%), Gaps = 2/47 (4%)
Query: 30 HDDRLTLEEFRE--GSKADPRIVQALSLGDSSNVAPSGSSPASASAA 74
R+TLEE + A R + + D+ +V G PA A+AA
Sbjct: 181 GQGRMTLEEILAKIDTGAAKRDAEEFNAKDAYDVLVVGGGPAGAAAA 227
>gnl|CDD|240157 cd05031, S-100A10_like, S-100A10_like: S-100A10 domain found in
proteins similar to S100A10. S100A10 is a member of the
S100 family of EF-hand superfamily of calcium-binding
proteins. Note that the S-100 hierarchy, to which this
S-100A1_like group belongs, contains only S-100 EF-hand
domains, other EF-hands have been modeled separately.
S100 proteins are expressed exclusively in vertebrates,
and are implicated in intracellular and extracellular
regulatory activities. A unique feature of S100A10 is
that it contains mutation in both of the calcium
binding sites, making it calcium insensitive. S100A10
has been detected in brain, heart, gastrointestinal
tract, kidney, liver, lung, spleen, testes, epidermis,
aorta, and thymus. Structural data supports the homo-
and hetero-dimeric as well as hetero-tetrameric nature
of the protein. S100A10 has multiple binding partners
in its calcium free state and is therefore involved in
many diverse biological functions.
Length = 94
Score = 27.0 bits (60), Expect = 0.63
Identities = 11/30 (36%), Positives = 18/30 (60%), Gaps = 1/30 (3%)
Query: 10 EDENTPQKRVDKIFDQMDKNHDDRLTLEEF 39
+++ P VDKI +D+N D ++ EEF
Sbjct: 45 KNQKDP-MAVDKIMKDLDQNRDGKVNFEEF 73
>gnl|CDD|222407 pfam13833, EF_hand_6, EF-hand domain pair.
Length = 53
Score = 26.3 bits (59), Expect = 0.67
Identities = 8/21 (38%), Positives = 14/21 (66%)
Query: 19 VDKIFDQMDKNHDDRLTLEEF 39
VD +F + D + D +++ EEF
Sbjct: 26 VDILFREFDTDGDGKISFEEF 46
>gnl|CDD|237515 PRK13805, PRK13805, bifunctional acetaldehyde-CoA/alcohol
dehydrogenase; Provisional.
Length = 862
Score = 26.3 bits (59), Expect = 2.5
Identities = 8/24 (33%), Positives = 12/24 (50%)
Query: 3 KGQQPQSEDENTPQKRVDKIFDQM 26
K ++ Q E Q++VDKI
Sbjct: 20 KAKKAQEEFATFTQEQVDKIVRAA 43
>gnl|CDD|171495 PRK12434, PRK12434, tRNA pseudouridine synthase A; Reviewed.
Length = 245
Score = 25.9 bits (57), Expect = 3.2
Identities = 7/25 (28%), Positives = 15/25 (60%)
Query: 2 FKGQQPQSEDENTPQKRVDKIFDQM 26
+KG Q ++NT Q +++ + +M
Sbjct: 15 YKGWQKLGNNDNTIQGKIESVLSEM 39
>gnl|CDD|219506 pfam07669, Eco57I, Eco57I restriction-modification methylase.
Homologues of the Escherichia coli Eco57I
restriction-modification methylase are found in several
phylogenetically diverse bacteria. The structure of
TaqI has been solved.
Length = 106
Score = 25.3 bits (56), Expect = 3.2
Identities = 9/30 (30%), Positives = 16/30 (53%)
Query: 35 TLEEFREGSKADPRIVQALSLGDSSNVAPS 64
L++FRE D + + + DS +V P+
Sbjct: 61 GLKKFREKMLNDKHLRELIDFPDSKDVFPN 90
>gnl|CDD|182002 PRK09627, oorA, 2-oxoglutarate-acceptor oxidoreductase subunit
OorA; Reviewed.
Length = 375
Score = 25.4 bits (56), Expect = 3.9
Identities = 8/31 (25%), Positives = 19/31 (61%)
Query: 9 SEDENTPQKRVDKIFDQMDKNHDDRLTLEEF 39
+ED K +D++F++++ + D+ EE+
Sbjct: 240 TEDAKICGKLIDRLFNKIESHQDEIEEYEEY 270
>gnl|CDD|240149 cd05022, S-100A13, S-100A13: S-100A13 domain found in proteins
similar to S100A13. S100A13 is a calcium-binding
protein belonging to a large S100 vertebrate-specific
protein family within the EF-hand superfamily of
calcium-binding proteins. Note that the S-100
hierarchy, to which this S-100A13 group belongs,
contains only S-100 EF-hand domains, other EF-hands
have been modeled separately. S100A13 is involved in
the cellular export of interleukin-1 (IL-1) and of
fibroblast growth factor-1 (FGF-1), which plays an
important role in angiogenesis and tissue regeneration.
Export is based on the CuII-dependent formation of
multiprotein complexes containing the S100A13 protein.
Assembly of these complexes occurs near the inner
surface of the plasma membrane. Binding of two Ca(II)
ions per monomer triggers key conformational changes
leading to the creation of two identical and
symmetrical Cu(II)-binding sites on the surface of the
protein, close to the interface between the two
monomers. These Cu(II)-binding sites are unique among
the S100 proteins, which are reported to bind Cu(II) or
Zn(II) ions in addition to Ca(II) ions. In addition,
the three-dimensional structure of S100A13 differs
significantly from those of other S100 proteins; the
hydrophobic pocket that largely contributes to
protein-protein interactions in other S100 proteins is
absent in S100A13. The structure of S100A13 contains a
large patch of negatively charged residues flanked by
dense cationic clusters, formed mostly from positively
charged residues from the C-terminal end, which plays
major role in binding FGF-1.
Length = 89
Score = 24.6 bits (54), Expect = 4.6
Identities = 7/24 (29%), Positives = 14/24 (58%)
Query: 16 QKRVDKIFDQMDKNHDDRLTLEEF 39
+ +++ +D N D +L+ EEF
Sbjct: 46 VEGLEEKMKNLDVNQDSKLSFEEF 69
>gnl|CDD|107389 cd06394, PBP1_iGluR_Kainate_KA1_2, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the KA1 and KA2 subunits of Kainate receptor.
N-terminal leucine/isoleucine/valine-binding protein
(LIVBP)-like domain of the KA1 and KA2 subunits of
Kainate receptor. While this N-terminal domain belongs
to the periplasmic-binding fold type I superfamily, the
glutamate-binding domain of the iGluR is structurally
homologous to the periplasmic-binding fold type II. The
LIVBP-like domain of iGluRs is thought to play a role in
the initial assembly of iGluR subunits, but it is not
well understood how this domain is arranged and
functions in intact iGluR. There are five types of
kainate receptors, GluR5, GluR6, GluR7, KA1, and KA2,
which are structurally similar to AMPA and NMDA subunits
of ionotropic glutamate receptors. KA1 and KA2 subunits
can only form functional receptors with one of the
GluR5-7 subunits. Moreover, GluR5-7 can also form
functional homomeric receptor channels activated by
kainate and glutamate when expressed in heterologous
systems. Kainate receptors are involved in excitatory
neurotransmission by activating postsynaptic receptors
and in inhibitory neurotransmission by modulating
release of the inhibitory neurotransmitter GABA through
a presynaptic mechanism. Kainate receptors are closely
related to AMPA receptors. In contrast of AMPA
receptors, kainate receptors play only a minor role in
signaling at synapses and their function is not well
defined.
Length = 333
Score = 25.2 bits (55), Expect = 5.4
Identities = 19/45 (42%), Positives = 24/45 (53%), Gaps = 6/45 (13%)
Query: 51 QALSLGDSSNVAPSGSSPASASAASPLVLERDI-----MAERTPK 90
Q L G S + PS SSPAS+S S + E++I E TPK
Sbjct: 60 QILPKGVVSVLGPS-SSPASSSIVSHICGEKEIPHFKVGPEETPK 103
>gnl|CDD|219670 pfam07967, zf-C3HC, C3HC zinc finger-like. This zinc-finger like
domain is distributed throughout the eukaryotic kingdom
in NIPA (Nuclear interacting partner of ALK) proteins.
NIPA is implicate to perform some sort of antiapoptotic
role in nucleophosmin-anaplastic lymphoma kinase (ALK)
mediated signaling events. The domain is often
repeated, with the second domain usually containing a
large insert (approximately 90 residues) after the
first three cysteine residues. The Schizosaccharomyces
pombe the protein containing this domain is involved in
mRNA export from the nucleus.
Length = 132
Score = 24.7 bits (54), Expect = 7.0
Identities = 6/31 (19%), Positives = 14/31 (45%)
Query: 2 FKGQQPQSEDENTPQKRVDKIFDQMDKNHDD 32
+K DE+ +K V++ + H++
Sbjct: 55 YKLPNIVKLDESVYKKLVEEYSKLLVTGHEE 85
>gnl|CDD|237942 PRK15317, PRK15317, alkyl hydroperoxide reductase subunit F;
Provisional.
Length = 517
Score = 24.3 bits (54), Expect = 9.6
Identities = 16/44 (36%), Positives = 22/44 (50%), Gaps = 2/44 (4%)
Query: 33 RLTLEEFRE--GSKADPRIVQALSLGDSSNVAPSGSSPASASAA 74
R+TLEE + A R + L+ D +V G PA A+AA
Sbjct: 184 RMTLEEILAKLDTGAAARAAEELNAKDPYDVLVVGGGPAGAAAA 227
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
0.307 0.125 0.336
Gapped
Lambda K H
0.267 0.0908 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,356,806
Number of extensions: 339071
Number of successful extensions: 373
Number of sequences better than 10.0: 1
Number of HSP's gapped: 373
Number of HSP's successfully gapped: 39
Length of query: 90
Length of database: 10,937,602
Length adjustment: 58
Effective length of query: 32
Effective length of database: 8,365,070
Effective search space: 267682240
Effective search space used: 267682240
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.6 bits)
S2: 53 (23.9 bits)