RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3180
(346 letters)
>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 = 34.8 bits (81), Expect = 0.004
Identities = 15/59 (25%), Positives = 31/59 (52%), Gaps = 1/59 (1%)
Query: 103 KRRWDVADIDGDRALTREEFASFLHPEETAHMRDLVVVETMEDIDKDKDGKVSLREYIE 161
+ + + D DGD ++ +E + L + + + E + ++DKD DGK+ E++E
Sbjct: 3 REAFRLFDKDGDGTISADELKAAL-KSLGEGLSEEEIDEMIREVDKDGDGKIDFEEFLE 60
Score = 34.8 bits (81), Expect = 0.005
Identities = 19/64 (29%), Positives = 27/64 (42%), Gaps = 8/64 (12%)
Query: 226 EDIDKDKDGKVSLREYIGDMFRGGDTDGDEELPDWVKNEKEQFAMYRDKNGDGFMDEEEV 285
DKD DG +S E + G+ +EE+ E DK+GDG +D EE
Sbjct: 7 RLFDKDGDGTISADELKAALKSLGEGLSEEEI-------DEMIREV-DKDGDGKIDFEEF 58
Query: 286 KNWI 289
+
Sbjct: 59 LELM 62
Score = 34.4 bits (80), Expect = 0.007
Identities = 14/58 (24%), Positives = 30/58 (51%), Gaps = 1/58 (1%)
Query: 185 KRRWDVADIDGDRALTREEFASFLHPEETAHMRDLVVVETMEDIDKDKDGKVSLREYI 242
+ + + D DGD ++ +E + L + + + E + ++DKD DGK+ E++
Sbjct: 3 REAFRLFDKDGDGTISADELKAAL-KSLGEGLSEEEIDEMIREVDKDGDGKIDFEEFL 59
Score = 26.7 bits (60), Expect = 3.2
Identities = 9/21 (42%), Positives = 13/21 (61%)
Query: 18 DKIDKDKDGFVSKEELKEWIQ 38
DKD DG +S +ELK ++
Sbjct: 7 RLFDKDGDGTISADELKAALK 27
Score = 26.7 bits (60), Expect = 3.7
Identities = 15/61 (24%), Positives = 20/61 (32%), Gaps = 24/61 (39%)
Query: 2 RLIVDKIDKDKDGLI------------------------VDKIDKDKDGFVSKEELKEWI 37
R DKD DG I + ++DKD DG + EE E +
Sbjct: 3 REAFRLFDKDGDGTISADELKAALKSLGEGLSEEEIDEMIREVDKDGDGKIDFEEFLELM 62
Query: 38 Q 38
Sbjct: 63 A 63
>gnl|CDD|185504 PTZ00184, PTZ00184, calmodulin; Provisional.
Length = 149
Score = 36.3 bits (84), Expect = 0.007
Identities = 37/135 (27%), Positives = 70/135 (51%), Gaps = 20/135 (14%)
Query: 192 DIDGDRALTREEFASFL-----HPEETAHMRDLVVVETMEDIDKDKDGKVSLREYIGDMF 246
D DGD +T +E + + +P E A ++D++ ++D D +G + E++ M
Sbjct: 21 DKDGDGTITTKELGTVMRSLGQNPTE-AELQDMI-----NEVDADGNGTIDFPEFLTLMA 74
Query: 247 RG-GDTDGDEELPDWVKNEKEQFAMYRDKNGDGFMDEEEVKNWILPPDFDHSDAEARHLI 305
R DTD +EE+ KE F ++ D++G+GF+ E+++ + +D E +I
Sbjct: 75 RKMKDTDSEEEI-------KEAFKVF-DRDGNGFISAAELRHVMTNLGEKLTDEEVDEMI 126
Query: 306 YESDSDADQKLTKDE 320
E+D D D ++ +E
Sbjct: 127 READVDGDGQINYEE 141
>gnl|CDD|222177 pfam13499, EF_hand_5, EF-hand domain pair.
Length = 60
Score = 33.1 bits (76), Expect = 0.017
Identities = 17/58 (29%), Positives = 28/58 (48%), Gaps = 3/58 (5%)
Query: 107 DVADIDGDRALTREEFASFLHP---EETAHMRDLVVVETMEDIDKDKDGKVSLREYIE 161
+ D DGD + EE L + T + ++ +IDKD DG++S E++E
Sbjct: 1 KLLDKDGDGYIDVEELRKLLKALGLKLTDEEVEELIEADFNEIDKDGDGRISFEEFLE 58
Score = 32.7 bits (75), Expect = 0.026
Identities = 16/57 (28%), Positives = 27/57 (47%), Gaps = 3/57 (5%)
Query: 189 DVADIDGDRALTREEFASFLHP---EETAHMRDLVVVETMEDIDKDKDGKVSLREYI 242
+ D DGD + EE L + T + ++ +IDKD DG++S E++
Sbjct: 1 KLLDKDGDGYIDVEELRKLLKALGLKLTDEEVEELIEADFNEIDKDGDGRISFEEFL 57
Score = 28.9 bits (65), Expect = 0.49
Identities = 15/55 (27%), Positives = 27/55 (49%), Gaps = 4/55 (7%)
Query: 273 DKNGDGFMDEEEVKNWI----LPPDFDHSDAEARHLIYESDSDADQKLTKDEILA 323
DK+GDG++D EE++ + L + + E D D D +++ +E L
Sbjct: 4 DKDGDGYIDVEELRKLLKALGLKLTDEEVEELIEADFNEIDKDGDGRISFEEFLE 58
Score = 28.5 bits (64), Expect = 0.79
Identities = 13/58 (22%), Positives = 29/58 (50%), Gaps = 4/58 (6%)
Query: 18 DKIDKDKDGFVSKEELKEWIQFTQKRYIHNDVESQWRTH----NPEDKEKITWDEYRE 71
+DKD DG++ EEL++ ++ + +VE + + +I+++E+ E
Sbjct: 1 KLLDKDGDGYIDVEELRKLLKALGLKLTDEEVEELIEADFNEIDKDGDGRISFEEFLE 58
Score = 27.7 bits (62), Expect = 1.6
Identities = 17/62 (27%), Positives = 30/62 (48%), Gaps = 4/62 (6%)
Query: 228 IDKDKDGKVSLREYIGDMFRGGDTDGDEELPDWVKNEKEQFAMYRDKNGDGFMDEEEVKN 287
+DKD DG + + E + G DEE+ + ++ + + DK+GDG + EE
Sbjct: 3 LDKDGDGYIDVEELRKLLKALGLKLTDEEVEELIEADFNEI----DKDGDGRISFEEFLE 58
Query: 288 WI 289
+
Sbjct: 59 AM 60
>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 = 33.4 bits (77), Expect = 0.074
Identities = 35/151 (23%), Positives = 56/151 (37%), Gaps = 23/151 (15%)
Query: 179 NMLNRDKRRWDVA----DIDGDRALTREEFASFLH----PEETAHMRDLVVVETMEDIDK 230
+ + A D D D + R E L A + L E+ID
Sbjct: 13 QLTEEQIQELKEAFQLFDRDSDGLIDRNELGKILRSLGFNPSEAEINKL-----FEEIDA 67
Query: 231 DKDGKVSLREYIGDMFRG-GDTDGDEELPDWVKNEKEQFAMYRDKNGDGFMDEEEVKNWI 289
V E++ M D +EEL +E F ++ DK+ DG++ E++ +
Sbjct: 68 GN-ETVDFPEFLTVMSVKLKRGDKEEEL-------REAFKLF-DKDHDGYISIGELRRVL 118
Query: 290 LPPDFDHSDAEARHLIYESDSDADQKLTKDE 320
SD E L+ E D D D ++ +E
Sbjct: 119 KSLGERLSDEEVEKLLKEYDEDGDGEIDYEE 149
>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 = 30.7 bits (70), Expect = 0.15
Identities = 22/68 (32%), Positives = 29/68 (42%), Gaps = 15/68 (22%)
Query: 144 EDIDKDKDGKVSLREYIEVDAAELAKDEDQGFSYKNMLNRD--KRRWDVADIDGDRALTR 201
+D D DG +S E F K+ L R + WD+AD D D L +
Sbjct: 6 RSLDPDGDGLIS--------GDEARP-----FLGKSGLPRSVLAQIWDLADTDKDGKLDK 52
Query: 202 EEFASFLH 209
EEFA +H
Sbjct: 53 EEFAIAMH 60
Score = 30.7 bits (70), Expect = 0.16
Identities = 12/22 (54%), Positives = 15/22 (68%)
Query: 106 WDVADIDGDRALTREEFASFLH 127
WD+AD D D L +EEFA +H
Sbjct: 39 WDLADTDKDGKLDKEEFAIAMH 60
>gnl|CDD|240155 cd05029, S-100A6, S-100A6: S-100A6 domain found in proteins similar
to S100A6. S100A6 is a member of the S100 domain family
within EF-hand Ca2+-binding proteins superfamily. Note
that the S-100 hierarchy, to which this S-100A6 group
belongs, contains only S-100 EF-hand domains, other
EF-hands have been modeled separately. S100 proteins
exhibit unique patterns of tissue- and cell
type-specific expression and have been implicated in the
Ca2+-dependent regulation of diverse physiological
processes, including cell cycle regulation,
differentiation, growth, and metabolic control . S100A6
is normally expressed in the G1 phase of the cell cycle
in neuronal cells. The function of S100A6 remains
unclear, but evidence suggests that it is involved in
cell cycle regulation and exocytosis. S100A6 may also be
involved in tumorigenesis; the protein is overexpressed
in several tumors. Ca2+ binding to S100A6 leads to a
conformational change in the protein, which exposes a
hydrophobic surface for interaction with target
proteins. Several such proteins have been identified:
glyceraldehyde-3-phosphate dehydrogenase , annexins 2,
6 and 11 and Calcyclin-Binding Protein (CacyBP).
Length = 88
Score = 31.0 bits (70), Expect = 0.20
Identities = 16/52 (30%), Positives = 34/52 (65%), Gaps = 3/52 (5%)
Query: 112 DGDR-ALTREEFASFLHPEET--AHMRDLVVVETMEDIDKDKDGKVSLREYI 160
+GD+ L+++E + E T + ++D + + MED+D++KD +V+ +EY+
Sbjct: 23 EGDKNTLSKKELKELIQKELTIGSKLQDAEIAKLMEDLDRNKDQEVNFQEYV 74
Score = 31.0 bits (70), Expect = 0.20
Identities = 16/52 (30%), Positives = 34/52 (65%), Gaps = 3/52 (5%)
Query: 194 DGDR-ALTREEFASFLHPEET--AHMRDLVVVETMEDIDKDKDGKVSLREYI 242
+GD+ L+++E + E T + ++D + + MED+D++KD +V+ +EY+
Sbjct: 23 EGDKNTLSKKELKELIQKELTIGSKLQDAEIAKLMEDLDRNKDQEVNFQEYV 74
>gnl|CDD|222184 pfam13507, GATase_5, CobB/CobQ-like glutamine amidotransferase
domain. This family captures members that are not found
in pfam00310, pfam07685 and pfam13230.
Length = 259
Score = 32.8 bits (76), Expect = 0.22
Identities = 24/93 (25%), Positives = 34/93 (36%), Gaps = 28/93 (30%)
Query: 197 RALTREEFASFLHPEETAHMRDLVVVETMEDIDKDKDGKVSLREYIGDMFRGGDTDGDEE 256
A R F + HM DL+ G+VSL ++ G + GG + GD
Sbjct: 20 AAFERAGFDA-----VDVHMSDLL------------SGRVSLDDFQGLVAPGGFSYGDVL 62
Query: 257 LPD--WVK----NEK--EQF-AMYRDKNGDGFM 280
W K N K + F A + + D F
Sbjct: 63 GSGKGWAKSILFNPKLRDAFEAFFNRR--DTFS 93
>gnl|CDD|234293 TIGR03648, Na_symport_lg, probable sodium:solute symporter, VC_2705
subfamily. This family belongs to a larger family of
transporters of the sodium:solute symporter superfamily,
TC 2.A.21. Members of this strictly bacterial protein
subfamily are found almost invariably immediately
downstream from a member of family TIGR03647.
Occasionally, the two genes are fused.
Length = 552
Score = 33.0 bits (76), Expect = 0.23
Identities = 14/27 (51%), Positives = 16/27 (59%), Gaps = 1/27 (3%)
Query: 255 EELPDWVKN-EKEQFAMYRDKNGDGFM 280
ELP WV N EK + DKNGDG +
Sbjct: 310 AELPGWVANWEKTGLLKFEDKNGDGIL 336
>gnl|CDD|205383 pfam13202, EF_hand_3, EF hand.
Length = 25
Score = 28.4 bits (65), Expect = 0.36
Identities = 9/18 (50%), Positives = 12/18 (66%)
Query: 18 DKIDKDKDGFVSKEELKE 35
+ D + DG +SKEELK
Sbjct: 6 RQFDTNGDGKISKEELKR 23
Score = 24.5 bits (55), Expect = 7.7
Identities = 6/24 (25%), Positives = 11/24 (45%)
Query: 139 VVETMEDIDKDKDGKVSLREYIEV 162
+ + D + DGK+S E +
Sbjct: 1 LKDLFRQFDTNGDGKISKEELKRL 24
>gnl|CDD|211937 TIGR04214, CSLREA_Nterm, CSLREA domain. This model describes an
N-terminal region, with a motif CSLREA, shared by tandem
genes in Acinetobacter that both have the GlyGly-CTERM
putative protein-sorting domain. Many proteins with this
domain are putative outer membrane proteins (OMPs) with
predicted beta strand-forming repeats.
Length = 27
Score = 28.3 bits (64), Expect = 0.39
Identities = 12/24 (50%), Positives = 14/24 (58%)
Query: 138 VVVETMEDIDKDKDGKVSLREYIE 161
+VV T D D D G SLRE I+
Sbjct: 1 IVVTTTADEDDDNCGTCSLREAIQ 24
Score = 27.9 bits (63), Expect = 0.66
Identities = 12/23 (52%), Positives = 13/23 (56%)
Query: 220 VVVETMEDIDKDKDGKVSLREYI 242
+VV T D D D G SLRE I
Sbjct: 1 IVVTTTADEDDDNCGTCSLREAI 23
>gnl|CDD|197477 smart00027, EH, Eps15 homology domain. Pair of EF hand motifs that
recognise proteins containing Asn-Pro-Phe (NPF)
sequences.
Length = 96
Score = 29.9 bits (68), Expect = 0.50
Identities = 11/22 (50%), Positives = 16/22 (72%)
Query: 106 WDVADIDGDRALTREEFASFLH 127
W++ADID D L ++EFA +H
Sbjct: 50 WNLADIDNDGELDKDEFALAMH 71
Score = 29.9 bits (68), Expect = 0.50
Identities = 11/22 (50%), Positives = 16/22 (72%)
Query: 188 WDVADIDGDRALTREEFASFLH 209
W++ADID D L ++EFA +H
Sbjct: 50 WNLADIDNDGELDKDEFALAMH 71
>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 = 27.8 bits (63), Expect = 0.77
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 16 IVDKIDKDKDGFVSKEELKEWIQ 38
+ DKD DG +S EE KE ++
Sbjct: 5 AFKEFDKDGDGKISFEEFKELLK 27
>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 = 27.0 bits (61), Expect = 1.3
Identities = 8/21 (38%), Positives = 12/21 (57%)
Query: 18 DKIDKDKDGFVSKEELKEWIQ 38
DKD DG + EE K+ ++
Sbjct: 7 RLFDKDGDGKIDFEEFKDLLK 27
Score = 26.2 bits (59), Expect = 2.8
Identities = 8/22 (36%), Positives = 12/22 (54%)
Query: 141 ETMEDIDKDKDGKVSLREYIEV 162
E DKD DGK+ E+ ++
Sbjct: 4 EAFRLFDKDGDGKIDFEEFKDL 25
Score = 24.6 bits (55), Expect = 7.8
Identities = 8/20 (40%), Positives = 10/20 (50%)
Query: 223 ETMEDIDKDKDGKVSLREYI 242
E DKD DGK+ E+
Sbjct: 4 EAFRLFDKDGDGKIDFEEFK 23
>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 = 28.6 bits (65), Expect = 1.3
Identities = 14/46 (30%), Positives = 25/46 (54%), Gaps = 4/46 (8%)
Query: 115 RALTREEFASFLHPEETAHMRDLVVVETMEDIDKDKDGKVSLREYI 160
+ L E +FL ++ V + M+D+D +KDGKV +E++
Sbjct: 33 KELLETELPNFLKNQKDPE----AVDKIMKDLDVNKDGKVDFQEFL 74
Score = 28.6 bits (65), Expect = 1.3
Identities = 14/46 (30%), Positives = 25/46 (54%), Gaps = 4/46 (8%)
Query: 197 RALTREEFASFLHPEETAHMRDLVVVETMEDIDKDKDGKVSLREYI 242
+ L E +FL ++ V + M+D+D +KDGKV +E++
Sbjct: 33 KELLETELPNFLKNQKDPE----AVDKIMKDLDVNKDGKVDFQEFL 74
>gnl|CDD|233466 TIGR01553, formate-DH-alph, formate dehydrogenase, alpha subunit,
proteobacterial-type. This model describes a subset of
formate dehydrogenase alpha chains found mainly in
proteobacteria but also in Aquifex. The alpha chain
contains domains for molybdopterin dinucleotide binding
and molybdopterin oxidoreductase (pfam01568 and
pfam00384, respectively). The holo-enzyme also contains
beta and gamma subunits of 32 and 20 kDa. The enzyme
catalyzes the oxidation of formate (produced from
pyruvate during anaerobic growth) to carbon dioxide with
the concomitant release of two electrons and two
protons. The electrons are utilized mainly in the
nitrate respiration by nitrate reductase. In E. coli and
Salmonella, there are two forms of the formate
dehydrogenase, one induced by nitrate which is strictly
anaerobic (fdn), and one incuced during the transition
from aerobic to anaerobic growth (fdo). This subunit is
one of only three proteins in E. coli which contain
selenocysteine. This model is well-defined, with a
large, unpopulated trusted/noise gap [Energy metabolism,
Anaerobic, Energy metabolism, Electron transport].
Length = 1009
Score = 30.6 bits (69), Expect = 1.4
Identities = 15/70 (21%), Positives = 25/70 (35%), Gaps = 8/70 (11%)
Query: 52 QWRTHNPEDKEKITWDEYREKVYGFLDEVDAAELAKDEDQGFSYKNMLNRDKRRWDVADI 111
+R + E+I+WD + + A + D F K+ + R D
Sbjct: 111 LYRAPGSDQWEEISWDWAIDTI--------ARRVKDTRDATFVTKDAKGQVVNRCDGIAS 162
Query: 112 DGDRALTREE 121
G A+ EE
Sbjct: 163 VGSSAMDNEE 172
>gnl|CDD|205583 pfam13405, EF_hand_4, EF-hand domain.
Length = 30
Score = 26.8 bits (60), Expect = 1.5
Identities = 9/21 (42%), Positives = 15/21 (71%)
Query: 18 DKIDKDKDGFVSKEELKEWIQ 38
DKD DG++S EEL++ ++
Sbjct: 7 KLFDKDGDGYISAEELRKALR 27
Score = 24.9 bits (55), Expect = 8.9
Identities = 9/25 (36%), Positives = 18/25 (72%), Gaps = 1/25 (4%)
Query: 265 KEQFAMYRDKNGDGFMDEEEVKNWI 289
+E F ++ DK+GDG++ EE++ +
Sbjct: 3 REAFKLF-DKDGDGYISAEELRKAL 26
>gnl|CDD|143992 pfam00241, Cofilin_ADF, Cofilin/tropomyosin-type actin-binding
protein. Severs actin filaments and binds to actin
monomers.
Length = 127
Score = 28.9 bits (65), Expect = 1.7
Identities = 21/63 (33%), Positives = 32/63 (50%), Gaps = 6/63 (9%)
Query: 2 RLIVDKIDKDKDGLIVDKIDKDKDGFVSKEELKEWIQFTQKRYIHNDVESQWRTHNPEDK 61
I+ KIDKDKD ++V+++ D + +E E + + RY DVE T + K
Sbjct: 17 NYIIFKIDKDKDQIVVEQVGDTGDSY---DEFVEELPERECRYAVYDVEY---TTDGSKK 70
Query: 62 EKI 64
KI
Sbjct: 71 SKI 73
>gnl|CDD|200439 cd11283, ADF_GMF-beta_like, ADF-homology domain of glia
maturation factor beta and related proteins. Actin
depolymerization factor/cofilin-like domains (ADF
domains) are present in a family of essential
eukaryotic actin regulatory proteins. Most of these
proteins enhance the turnover rate of actin and
interact with actin monomers as well as actin
filaments. The glia maturation factor (GMF), however,
does not bind actin but interacts with the Arp2/3
complex (which contains actin-related proteins, amongst
others) and suppresses Arp2/3 activity, inducing the
dissociation of branched daughter filaments from their
mother filaments. This family includes both mammalian
GMF isoforms, GMF-beta and GMF-gamma. GMF-beta
regulates cellular growth, fission, differentiation and
apoptosis. GMF-gamma is important in myeloid cell
development and is an important regulator for cell
migration and polarity in neutrophils.
Length = 122
Score = 28.4 bits (64), Expect = 2.2
Identities = 14/42 (33%), Positives = 25/42 (59%), Gaps = 4/42 (9%)
Query: 4 IVDKIDKDKDGLIVDKIDKDKDGFVSKEELKEWIQFTQKRYI 45
++ KIDK+K ++VD+ +D +S EEL E + R++
Sbjct: 24 LILKIDKEKQEIVVDEELED----ISIEELAEELPEHSPRFV 61
>gnl|CDD|113924 pfam05172, Nup35_RRM, Nup53/35/40-type RNA recognition motif.
Members of this family belong to the nucleor pore
complex, NPC, the only gateway between the nucleus and
the cytoplasm. The NPC consists of several subcomplexes
each one of which is made up of multiple copies of
several individual Nup, Nic or Sec protein subunits. In
yeast, this Nup or nucleoporin subunit is numbered
Nup53, Nup40 in Schizo. pombe and in vertebrates as
Nup35. This subunit forms part of the inner ring within
the membrane and interacts directly with Nup-Ndc1,
considered to be an anchor for the NPC in the pore
membrane. This region of the Nup is the RNA-recognition
region.
Length = 87
Score = 27.7 bits (62), Expect = 2.2
Identities = 10/28 (35%), Positives = 16/28 (57%)
Query: 303 HLIYESDSDADQKLTKDEILAKYDLFVG 330
HL Y+S S A + L+K+ + + VG
Sbjct: 47 HLTYQSPSSARKALSKNGTIINGSVMVG 74
>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 = 27.8 bits (62), Expect = 2.4
Identities = 14/47 (29%), Positives = 29/47 (61%), Gaps = 6/47 (12%)
Query: 115 RALTREEFASFLHPEETAHMRDLVVVET-MEDIDKDKDGKVSLREYI 160
+ L +E + FL + +D + V+ M+D+D+++DGKV+ E++
Sbjct: 33 KKLMEKELSEFL-----KNQKDPMAVDKIMKDLDQNRDGKVNFEEFV 74
Score = 27.8 bits (62), Expect = 2.4
Identities = 14/47 (29%), Positives = 29/47 (61%), Gaps = 6/47 (12%)
Query: 197 RALTREEFASFLHPEETAHMRDLVVVET-MEDIDKDKDGKVSLREYI 242
+ L +E + FL + +D + V+ M+D+D+++DGKV+ E++
Sbjct: 33 KKLMEKELSEFL-----KNQKDPMAVDKIMKDLDQNRDGKVNFEEFV 74
>gnl|CDD|193239 pfam12763, efhand_3, Cytoskeletal-regulatory complex EF hand. This
is an efhand family from the N-terminal of actin
cytoskeleton-regulatory complex END3 and similar
proteins from fungi and closely related species.
Length = 104
Score = 27.7 bits (62), Expect = 3.9
Identities = 11/18 (61%), Positives = 12/18 (66%)
Query: 106 WDVADIDGDRALTREEFA 123
WD+ADID D L EEF
Sbjct: 49 WDLADIDSDGKLDFEEFC 66
Score = 27.7 bits (62), Expect = 3.9
Identities = 11/18 (61%), Positives = 12/18 (66%)
Query: 188 WDVADIDGDRALTREEFA 205
WD+ADID D L EEF
Sbjct: 49 WDLADIDSDGKLDFEEFC 66
>gnl|CDD|234502 TIGR04212, GlyGly_RbtA, Acinetobacter rhombotarget A. Members of
this protein family are found, so far, exclusively in
the genus Acinetobacter. Members average just over 600
amino acids in length, including a 22-amino acid
C-terminal putative protein sorting recognition
sequence, GlyGly-CTERM (TIGR03501). The GlyGly-CTERM
signal always co-occurs with a subfamily of the rhomboid
family intramembrane serine proteases called
rhombosortase (TIGR03902). Members occur paired with a
second rhombosortase target, with which it also shares
an N-terminal motif CSLREA. This protein is designated
Acinetobacter rhombotarget A (rbtA).
Length = 605
Score = 29.0 bits (65), Expect = 4.6
Identities = 12/24 (50%), Positives = 14/24 (58%), Gaps = 1/24 (4%)
Query: 138 VVVETMEDIDKDKDGKVSLREYIE 161
+ V T D DKD D SLRE +E
Sbjct: 22 IQVTTTVDEDKD-DTVCSLREAVE 44
>gnl|CDD|240151 cd05024, S-100A10, S-100A10: A subgroup of the 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-100A10 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 = 91
Score = 27.1 bits (60), Expect = 4.7
Identities = 20/69 (28%), Positives = 32/69 (46%), Gaps = 14/69 (20%)
Query: 96 KNMLNRDKRRWDVADIDGDRALTREEFASFLHPEETAHMRDLVVVETMEDIDKDKDGKVS 155
KN LNRD + L +EF+ FL + + V + M+D+D +DGKV
Sbjct: 21 KNYLNRDDLQ----------KLMEKEFSEFLKNQNDP----MAVDKIMKDLDDCRDGKVG 66
Query: 156 LREYIEVDA 164
+ + + A
Sbjct: 67 FQSFFSLIA 75
Score = 27.1 bits (60), Expect = 5.3
Identities = 19/64 (29%), Positives = 30/64 (46%), Gaps = 14/64 (21%)
Query: 178 KNMLNRDKRRWDVADIDGDRALTREEFASFLHPEETAHMRDLVVVETMEDIDKDKDGKVS 237
KN LNRD + L +EF+ FL + + V + M+D+D +DGKV
Sbjct: 21 KNYLNRDDLQ----------KLMEKEFSEFLKNQNDP----MAVDKIMKDLDDCRDGKVG 66
Query: 238 LREY 241
+ +
Sbjct: 67 FQSF 70
>gnl|CDD|150280 pfam09551, Spore_II_R, Stage II sporulation protein R (spore_II_R).
SpoIIR is designated stage II sporulation protein R. A
comparative genome analysis of all sequenced genomes of
Firmicutes shows that the proteins are strictly
conserved among the sub-set of endospore-forming
species. SpoIIR is a signalling protein that links the
activation of sigma E to the transcriptional activity of
sigma F during sporulation.
Length = 132
Score = 27.5 bits (62), Expect = 5.4
Identities = 10/24 (41%), Positives = 14/24 (58%), Gaps = 3/24 (12%)
Query: 303 HLIYESDSDADQKL---TKDEILA 323
H++ SDS DQ L +DE+L
Sbjct: 9 HVLANSDSPEDQALKLKVRDEVLE 32
>gnl|CDD|179793 PRK04220, PRK04220, 2-phosphoglycerate kinase; Provisional.
Length = 301
Score = 28.0 bits (63), Expect = 7.0
Identities = 12/29 (41%), Positives = 18/29 (62%)
Query: 59 EDKEKITWDEYREKVYGFLDEVDAAELAK 87
E ++IT +E R +VY L E D E+A+
Sbjct: 50 EGIKEITKEELRRRVYYKLIEKDYEEVAE 78
>gnl|CDD|240152 cd05025, S-100A1, S-100A1: S-100A1 domain found in proteins similar
to S100A1. S100A1 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-100A1 group belongs, contains only S-100 EF-hand
domains, other EF-hands have been modeled separately. As
is the case with many other members of S100 protein
family, S100A1 is implicated in intracellular and
extracellular regulatory activities, including
interaction with myosin-associated twitchin kinase,
actin-capping protein CapZ, sinapsin I, and tubulin.
Structural data suggests that S100A1 proteins exist
within cells as antiparallel homodimers, while
heterodimers with S100A4 and S100B also has been
reported. Upon binding calcium S100A1 changes
conformation to expose a hydrophobic cleft which is the
interaction site of S100A1 with its more that 20 known
target proteins.
Length = 92
Score = 26.4 bits (58), Expect = 8.3
Identities = 14/51 (27%), Positives = 30/51 (58%), Gaps = 4/51 (7%)
Query: 115 RALTREEFASFLHPEETAHMRDLVVVETMEDIDKDKDGKVSLREYIEVDAA 165
+ L + E + FL ++ A D + M+++D++ DG+V +E++ + AA
Sbjct: 34 KDLLQTELSDFLDAQKDADAVDKI----MKELDENGDGEVDFQEFVVLVAA 80
>gnl|CDD|236970 PRK11756, PRK11756, exonuclease III; Provisional.
Length = 268
Score = 27.6 bits (62), Expect = 9.7
Identities = 10/27 (37%), Positives = 16/27 (59%), Gaps = 2/27 (7%)
Query: 53 WRTHNPEDKEKITWDEYREKVYGFLDE 79
+R NP+ ++ +W +YR K GF D
Sbjct: 199 FRQLNPDVNDRFSWFDYRSK--GFDDN 223
>gnl|CDD|193526 cd05649, M20_ArgE_DapE_like4, M20 Peptidases with similarity to
acetylornithine deacetylases and
succinyl-diaminopimelate desuccinylases. Peptidase M20
family, Uncharacterized protein subfamily with
similarity to acetylornithine
deacetylase/succinyl-diaminopimelate desuccinylase
(ArgE/DapE) subfamily. This group includes the
hypothetical protein ygeY from Escherichia coli, a
putative deacetylase, but many in this subfamily are
classified as unassigned peptidases. ArgE/DapE enzymes
catalyze analogous reactions and share a common
activator, the metal ion (usually Co2+ or Zn2+). ArgE
catalyzes a broad range of substrates, including
N-acetylornithine, alpha-N-acetylmethionine and
alpha-N-formylmethionine, while DapE catalyzes the
hydrolysis of N-succinyl-L,L-diaminopimelate (L,L-SDAP)
to L,L-diaminopimelate and succinate. Proteins in this
subfamily are mostly bacterial and archaeal, and have
been inferred by homology as being related to both ArgE
and DapE.
Length = 376
Score = 27.6 bits (62), Expect = 9.9
Identities = 14/63 (22%), Positives = 23/63 (36%), Gaps = 9/63 (14%)
Query: 217 RDLVVVETMEDI---------DKDKDGKVSLREYIGDMFRGGDTDGDEELPDWVKNEKEQ 267
R L+V ET E + K + KVS+ + G + + P W+ E +
Sbjct: 242 RRLLVGETRESVLAQIRDLKAVKGLEAKVSVATGKEPSYTGEVIEAERYFPAWLNEEDHE 301
Query: 268 FAM 270
Sbjct: 302 LVK 304
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 0.136 0.397
Gapped
Lambda K H
0.267 0.0709 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 19,189,380
Number of extensions: 1988203
Number of successful extensions: 1731
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1701
Number of HSP's successfully gapped: 114
Length of query: 346
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 248
Effective length of database: 6,590,910
Effective search space: 1634545680
Effective search space used: 1634545680
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: 42 (22.0 bits)
S2: 59 (26.5 bits)