RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8460
(86 letters)
>gnl|CDD|222177 pfam13499, EF_hand_5, EF-hand domain pair.
Length = 60
Score = 36.2 bits (84), Expect = 1e-04
Identities = 14/40 (35%), Positives = 24/40 (60%)
Query: 15 LISHPQDEDPDEGVRDLVELALRKMDYDKDGKISFQDFQQ 54
L+ + DE V +L+E ++D D DG+ISF++F +
Sbjct: 19 LLKALGLKLTDEEVEELIEADFNEIDKDGDGRISFEEFLE 58
>gnl|CDD|215520 PLN02964, PLN02964, phosphatidylserine decarboxylase.
Length = 644
Score = 33.7 bits (77), Expect = 0.006
Identities = 18/46 (39%), Positives = 25/46 (54%), Gaps = 7/46 (15%)
Query: 22 EDPDEGVRDLVELALRKMDYDKDGKISFQDFQQSVTDEPLLLEAFG 67
EDP E R L +DYD+DG++SF +F L++AFG
Sbjct: 171 EDPVETERSFARRILAIVDYDEDGQLSFSEFSD-------LIKAFG 209
>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 = 31.0 bits (71), Expect = 0.012
Identities = 9/27 (33%), Positives = 18/27 (66%)
Query: 28 VRDLVELALRKMDYDKDGKISFQDFQQ 54
+ ++ +R++D D DGKI F++F +
Sbjct: 34 SEEEIDEMIREVDKDGDGKIDFEEFLE 60
Score = 26.0 bits (58), Expect = 1.1
Identities = 8/23 (34%), Positives = 11/23 (47%)
Query: 32 VELALRKMDYDKDGKISFQDFQQ 54
+ A R D D DG IS + +
Sbjct: 2 LREAFRLFDKDGDGTISADELKA 24
>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 = 29.7 bits (68), Expect = 0.022
Identities = 10/23 (43%), Positives = 18/23 (78%)
Query: 32 VELALRKMDYDKDGKISFQDFQQ 54
++ A ++ D D DGKISF++F++
Sbjct: 2 LKEAFKEFDKDGDGKISFEEFKE 24
>gnl|CDD|205383 pfam13202, EF_hand_3, EF hand.
Length = 25
Score = 29.6 bits (68), Expect = 0.022
Identities = 7/20 (35%), Positives = 13/20 (65%)
Query: 35 ALRKMDYDKDGKISFQDFQQ 54
R+ D + DGKIS ++ ++
Sbjct: 4 LFRQFDTNGDGKISKEELKR 23
>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 = 29.3 bits (67), Expect = 0.025
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 35 ALRKMDYDKDGKISFQDFQQ 54
A R D D DGKI F++F+
Sbjct: 5 AFRLFDKDGDGKIDFEEFKD 24
>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 = 30.0 bits (68), Expect = 0.074
Identities = 13/42 (30%), Positives = 24/42 (57%), Gaps = 4/42 (9%)
Query: 21 DEDPDEGVRDLVELALRKMDYDKDGKISFQDFQQSVTDEPLL 62
+ DE V L L++ D D DG+I +++F++ + D P +
Sbjct: 123 ERLSDEEVEKL----LKEYDEDGDGEIDYEEFKKLIKDSPTI 160
>gnl|CDD|238255 cd00453, FTBP_aldolase_II, Fructose/tagarose-bisphosphate aldolase
class II. This family includes fructose-1,6-bisphosphate
(FBP) and tagarose 1,6-bisphosphate (TBP) aldolases.
FBP-aldolase is homodimeric and used in gluconeogenesis
and glycolysis; the enzyme controls the condensation of
dihydroxyacetone phosphate with
glyceraldehyde-3-phosphate to yield
fructose-1,6-bisphosphate. TBP-aldolase is tetrameric
and produces tagarose-1,6-bisphosphate. There is an
absolute requirement for a divalent metal ion, usually
zinc, and in addition the enzymes are activated by
monovalent cations such as Na+. Although structurally
similar, the class I aldolases use a different mechanism
and are believed to have an independent evolutionary
origin.
Length = 340
Score = 30.2 bits (67), Expect = 0.088
Identities = 7/35 (20%), Positives = 15/35 (42%)
Query: 15 LISHPQDEDPDEGVRDLVELALRKMDYDKDGKISF 49
+ H + ++D V + KM+ D D + +
Sbjct: 245 FVFHGGSGSTAQEIKDSVSYGVVKMNIDTDTQWAT 279
>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 = 0.14
Identities = 9/24 (37%), Positives = 17/24 (70%)
Query: 29 RDLVELALRKMDYDKDGKISFQDF 52
+ V+ ++ +D +KDGK+ FQ+F
Sbjct: 50 PEAVDKIMKDLDVNKDGKVDFQEF 73
>gnl|CDD|150423 pfam09748, Med10, Transcription factor subunit Med10 of Mediator
complex. Med10 is one of the protein subunits of the
Mediator complex, tethered to Rgr1 protein. The Mediator
complex is required for the transcription of most RNA
polymerase II (Pol II)-transcribed genes. Med10
specifically mediates basal-level HIS4 transcription via
Gcn4, and, additionally, there is a putative requirement
for Med10 in Bas2-mediated transcription. Med10 is part
of the middle region of Mediator.
Length = 120
Score = 29.1 bits (66), Expect = 0.15
Identities = 19/58 (32%), Positives = 26/58 (44%), Gaps = 8/58 (13%)
Query: 20 QDEDPDEGVRDLVELALRKMDYDKDGKI-SFQDFQQSVTDEPLLLEAFGQCLPSDAAR 76
+PD R+ VEL LRK Y K GK+ +F+ F+ L E + P A
Sbjct: 66 DGRNPDLYTREFVELVLRKNQYVK-GKMHAFKKFRDV------LAEELSEAFPELVAE 116
>gnl|CDD|183711 PRK12738, kbaY, tagatose-bisphosphate aldolase; Reviewed.
Length = 286
Score = 27.7 bits (61), Expect = 0.58
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 15 LISHPQDEDPDEGVRDLVELALRKMDYDKDGKISFQD 51
L+ H + PDE VR +EL + K++ + KI+F
Sbjct: 205 LVLHGASDVPDEFVRRTIELGVTKVNVATELKIAFAG 241
>gnl|CDD|205583 pfam13405, EF_hand_4, EF-hand domain.
Length = 30
Score = 25.6 bits (57), Expect = 0.74
Identities = 7/20 (35%), Positives = 12/20 (60%)
Query: 35 ALRKMDYDKDGKISFQDFQQ 54
A + D D DG IS ++ ++
Sbjct: 5 AFKLFDKDGDGYISAEELRK 24
>gnl|CDD|236397 PRK09182, PRK09182, DNA polymerase III subunit epsilon;
Validated.
Length = 294
Score = 27.2 bits (61), Expect = 0.79
Identities = 11/43 (25%), Positives = 19/43 (44%), Gaps = 13/43 (30%)
Query: 17 SHPQDEDPDEGVRDLVELALRKMDYDKDGKI-----SFQDFQQ 54
+DE ++E+ + +YD DG+I +F QQ
Sbjct: 50 DPRKDE--------IIEIGMVAFEYDDDGRIGDVLDTFGGLQQ 84
>gnl|CDD|185219 PRK15319, PRK15319, AIDA autotransporter-like protein ShdA;
Provisional.
Length = 2039
Score = 27.0 bits (59), Expect = 1.4
Identities = 13/41 (31%), Positives = 19/41 (46%)
Query: 35 ALRKMDYDKDGKISFQDFQQSVTDEPLLLEAFGQCLPSDAA 75
+ + MD D D F ++TD+P L G P DA+
Sbjct: 1368 SFKLMDMDSDISGDFTSLTMNLTDQPDYLTVTGTINPEDAS 1408
>gnl|CDD|130917 TIGR01858, tag_bisphos_ald, class II aldolase, tagatose
bisphosphate family. This model describes
tagatose-1,6-bisphosphate aldolases, and perhaps other
closely related class II aldolases. This tetrameric,
Zn2+-dependent enzyme is related to the class II
fructose bisphosphate aldolase; fructose
1,6-bisphosphate and tagatose 1,6 bisphosphate differ
only in chirality at C4.
Length = 282
Score = 26.4 bits (58), Expect = 1.6
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 15 LISHPQDEDPDEGVRDLVELALRKMDYDKDGKISFQD 51
L+ H + PDE VR +EL + K++ + KI+F
Sbjct: 203 LVLHGASDVPDEDVRRTIELGICKVNVATELKIAFSG 239
>gnl|CDD|222407 pfam13833, EF_hand_6, EF-hand domain pair.
Length = 53
Score = 25.2 bits (56), Expect = 1.7
Identities = 11/30 (36%), Positives = 18/30 (60%)
Query: 30 DLVELALRKMDYDKDGKISFQDFQQSVTDE 59
+ V++ R+ D D DGKISF++F +
Sbjct: 24 EEVDILFREFDTDGDGKISFEEFCVLLQRL 53
>gnl|CDD|237235 PRK12857, PRK12857, fructose-1,6-bisphosphate aldolase; Reviewed.
Length = 284
Score = 26.6 bits (59), Expect = 1.7
Identities = 9/26 (34%), Positives = 17/26 (65%)
Query: 24 PDEGVRDLVELALRKMDYDKDGKISF 49
PDE +R + L +RK++ D + + +F
Sbjct: 214 PDEAIRKAISLGVRKVNIDTNIREAF 239
>gnl|CDD|150503 pfam09840, DUF2067, Uncharacterized protein conserved in archaea
(DUF2067). This domain, found in various archaeal
proteins, has no known function.
Length = 190
Score = 26.1 bits (58), Expect = 2.3
Identities = 12/34 (35%), Positives = 19/34 (55%), Gaps = 2/34 (5%)
Query: 15 LISHPQDEDPDEGVRDLVELALRKMDYDKDGKIS 48
S+ +DPD+ + +LVE L + +DGKI
Sbjct: 147 AASYATGKDPDDAIEELVEKGL--LREGEDGKIE 178
>gnl|CDD|237860 PRK14939, gyrB, DNA gyrase subunit B; Provisional.
Length = 756
Score = 26.2 bits (59), Expect = 2.4
Identities = 9/19 (47%), Positives = 12/19 (63%)
Query: 43 KDGKISFQDFQQSVTDEPL 61
+DGKI Q+F+ V PL
Sbjct: 138 RDGKIHEQEFEHGVPVAPL 156
>gnl|CDD|227087 COG4744, COG4744, Uncharacterized conserved protein [Function
unknown].
Length = 121
Score = 25.6 bits (56), Expect = 2.4
Identities = 9/25 (36%), Positives = 15/25 (60%)
Query: 12 RNSLISHPQDEDPDEGVRDLVELAL 36
R + P+D+DP GV +L + A+
Sbjct: 9 RMRFLEDPEDDDPMTGVANLFDAAM 33
>gnl|CDD|185503 PTZ00183, PTZ00183, centrin; Provisional.
Length = 158
Score = 25.8 bits (57), Expect = 2.7
Identities = 10/38 (26%), Positives = 22/38 (57%), Gaps = 4/38 (10%)
Query: 25 DEGVRDLVELALRKMDYDKDGKISFQDFQQSVTDEPLL 62
DE ++++++ A D + DG+IS ++F + + L
Sbjct: 125 DEELQEMIDEA----DRNGDGEISEEEFYRIMKKTNLF 158
>gnl|CDD|235035 PRK02406, PRK02406, DNA polymerase IV; Validated.
Length = 343
Score = 25.5 bits (57), Expect = 3.3
Identities = 13/43 (30%), Positives = 17/43 (39%), Gaps = 8/43 (18%)
Query: 32 VELALRKMDYDKDG-----KISFQDFQQ---SVTDEPLLLEAF 66
+E L + DK K+ F DFQQ T +PL
Sbjct: 262 LERRLERAKPDKRIKTVGVKLKFADFQQTTKEHTADPLDKADL 304
>gnl|CDD|232957 TIGR00398, metG, methionyl-tRNA synthetase. The methionyl-tRNA
synthetase (metG) is a class I amino acyl-tRNA ligase.
This model appears to recognize the methionyl-tRNA
synthetase of every species, including eukaryotic
cytosolic and mitochondrial forms. The UPGMA difference
tree calculated after search and alignment according to
This model shows an unusual deep split between two
families of MetG. One family contains forms from the
Archaea, yeast cytosol, spirochetes, and E. coli, among
others. The other family includes forms from yeast
mitochondrion, Synechocystis sp., Bacillus subtilis, the
Mycoplasmas, Aquifex aeolicus, and Helicobacter pylori.
The E. coli enzyme is homodimeric, although monomeric
forms can be prepared that are fully active. Activity of
this enzyme in bacteria includes aminoacylation of
fMet-tRNA with Met; subsequent formylation of the Met to
fMet is catalyzed by a separate enzyme. Note that the
protein from Aquifex aeolicus is split into an alpha
(large) and beta (small) subunit; this model does not
include the C-terminal region corresponding to the beta
chain [Protein synthesis, tRNA aminoacylation].
Length = 530
Score = 25.8 bits (57), Expect = 3.5
Identities = 8/24 (33%), Positives = 14/24 (58%)
Query: 36 LRKMDYDKDGKISFQDFQQSVTDE 59
L++ KDG S++DF + V +
Sbjct: 355 LKERPLGKDGDFSWEDFVERVNAD 378
>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 = 24.8 bits (54), Expect = 3.9
Identities = 8/23 (34%), Positives = 17/23 (73%)
Query: 30 DLVELALRKMDYDKDGKISFQDF 52
D V+ ++++D + DG++ FQ+F
Sbjct: 52 DAVDKIMKELDENGDGEVDFQEF 74
>gnl|CDD|226021 COG3490, COG3490, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 366
Score = 25.5 bits (56), Expect = 4.2
Identities = 10/35 (28%), Positives = 19/35 (54%), Gaps = 1/35 (2%)
Query: 30 DLVELALRKMDYDKDGKISF-QDFQQSVTDEPLLL 63
L +L++R +D +DG + F ++ D P L+
Sbjct: 222 SLRQLSIRHLDIGRDGTVWFGCQYRGPRNDLPPLV 256
>gnl|CDD|233960 TIGR02642, phage_xxxx, uncharacterized phage protein. This
uncharacterized protein is found in prophage regions of
Shewanella oneidensis MR-1, Vibrio vulnificus YJ016,
Yersinia pseudotuberculosis IP 32953, and Aeromonas
hydrophila ATCC7966. It appears to have regions of
sequence similarity to phage lambda antitermination
protein Q [Mobile and extrachromosomal element
functions, Prophage functions].
Length = 186
Score = 25.2 bits (55), Expect = 4.9
Identities = 12/48 (25%), Positives = 14/48 (29%), Gaps = 4/48 (8%)
Query: 15 LISHPQDEDPDEG----VRDLVELALRKMDYDKDGKISFQDFQQSVTD 58
LI Q E R VE L+ D I +D V
Sbjct: 110 LIQRRQRECDTCAGTGRFRPTVEDLLKSFGVDSGAAIVLKDNWPQVVT 157
>gnl|CDD|239498 cd03404, Band_7_HflK, Band_7_HflK: The band 7 domain of flotillin
(reggie) like proteins. This group includes proteins
similar to prokaryotic HlfK (High frequency of
lysogenization K). 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 HflK is an integral membrane protein
which may localize to the plasma membrane. HflK
associates with another band 7 family member (HflC) 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 = 266
Score = 25.2 bits (56), Expect = 5.0
Identities = 10/27 (37%), Positives = 13/27 (48%), Gaps = 5/27 (18%)
Query: 16 ISHPQD-----EDPDEGVRDLVELALR 37
IS P D DP+ +R E A+R
Sbjct: 98 ISDPYDYLFNVRDPEGTLRQAAESAMR 124
>gnl|CDD|238477 cd00947, TBP_aldolase_IIB, Tagatose-1,6-bisphosphate (TBP) aldolase
and related Type B Class II aldolases. TBP aldolase is a
tetrameric class II aldolase that catalyzes the
reversible condensation of dihydroxyacetone phosphate
with glyceraldehyde 3-phsophate to produce tagatose
1,6-bisphosphate. There is an absolute requirement for a
divalent metal ion, usually zinc, and in addition the
enzymes are activated by monovalent cations such as Na+.
The type A and type B Class II FBPA's differ in the
presence and absence of distinct indels in the sequence
that result in differing loop lengths in the structures.
Length = 276
Score = 25.2 bits (56), Expect = 5.2
Identities = 8/28 (28%), Positives = 18/28 (64%)
Query: 24 PDEGVRDLVELALRKMDYDKDGKISFQD 51
PDE +R ++L + K++ + D +++F
Sbjct: 208 PDEQIRKAIKLGVCKININTDLRLAFTA 235
>gnl|CDD|227482 COG5153, CVT17, Putative lipase essential for disintegration of
autophagic bodies inside the vacuole [Intracellular
trafficking and secretion / Lipid metabolism].
Length = 425
Score = 24.9 bits (54), Expect = 6.5
Identities = 11/40 (27%), Positives = 15/40 (37%)
Query: 6 SLMYLGRNSLISHPQDEDPDEGVRDLVELALRKMDYDKDG 45
SL+ + N+ S P D D E +D DG
Sbjct: 137 SLIEMSSNAYHSIPLDGDWRNVTEPWNETVPETFGWDGDG 176
>gnl|CDD|213369 cd12835, EcCorA-like_1, Escherichia coli Mg2+ transporter CorA_like
subgroup. A bacterial subgroup of the Escherichia coli
CorA-Salmonella typhimurium ZntB_like (EcCorA_ZntB-like)
family of the MIT superfamily of essential membrane
proteins involved in transporting divalent cations
(uptake or efflux) across membranes. This subgroup
includes the Mg2+ transporters Escherichia coli CorA and
Salmonella typhimurium CorA (which can also transport
Co2+, and Ni2+). Structures of the intracellular domain
of Vibrio parahaemolyticus and Salmonella typhimurium
ZntB form funnel-shaped homopentamers, the tip of the
funnel is formed from two C-terminal transmembrane (TM)
helices from each monomer, and the large opening of the
funnel from the N-terminal cytoplasmic domains. The GMN
signature motif of the MIT superfamily occurs just after
TM1, mutation within this motif is known to abolish Mg2+
transport through Salmonella typhimurium CorA, and
Mrs2p. Natural variants such as GVN and GIN, such as
occur in some ZntB family proteins, may be associated
with the transport of different divalent cations, such
as zinc and cadmium. The functional diversity of MIT
transporters may also be due to minor structural
differences regulating gating, substrate selection, and
transport.
Length = 287
Score = 24.5 bits (54), Expect = 7.0
Identities = 12/31 (38%), Positives = 18/31 (58%)
Query: 1 MGQKRSLMYLGRNSLISHPQDEDPDEGVRDL 31
M +R+L +L R +S Q ED E +RD+
Sbjct: 164 MDTQRALSFLLRTRRLSDEQLEDAREILRDI 194
>gnl|CDD|153299 cd07615, BAR_Endophilin_A3, The Bin/Amphiphysin/Rvs (BAR) domain of
Endophilin-A3. BAR domains are dimerization, lipid
binding and curvature sensing modules found in many
different proteins with diverse functions. Endophilins
are accessory proteins localized at synapses that
interacts with the endocytic proteins, dynamin and
synaptojanin. They are essential for synaptic vesicle
formation from the plasma membrane. They interact with
voltage-gated calcium channels, thus linking vesicle
endocytosis to calcium regulation. They also play roles
in virus budding, mitochondrial morphology maintenance,
receptor-mediated endocytosis inhibition, and endosomal
sorting. Endophilins contain an N-terminal N-BAR domain
(BAR domain with an additional N-terminal amphipathic
helix), followed by a variable region containing proline
clusters, and a C-terminal SH3 domain. They are
classified into two types, A and B. Endophilin-A
proteins are enriched in the brain and play multiple
roles in receptor-mediated endocytosis. Endophilin-A3
(or endophilin-3) is also referred to as SH3P13 (SH3
domain containing protein 13) or SH3GL3 (SH3 domain
containing Grb2-like protein 3). It regulates
Arp2/3-dependent actin filament assembly during
endocytosis. It binds N-WASP through its SH3 domain and
enhances the ability of N-WASP to activate the Arp2/3
complex. Endophilin-A3 co-localizes with the vesicular
glutamate transporter 1 (VGLUT1), and may play an
important role in the synaptic release of glutamate.
Length = 223
Score = 24.6 bits (53), Expect = 8.0
Identities = 14/41 (34%), Positives = 24/41 (58%), Gaps = 4/41 (9%)
Query: 20 QDEDPDEGVRDLVELALRKMDYD----KDGKISFQDFQQSV 56
QD+D E L +L R++D+D + GKI ++ +Q+V
Sbjct: 123 QDKDLKEIGHHLKKLEGRRLDFDYKKKRQGKIPDEEIRQAV 163
>gnl|CDD|132954 cd06623, PKc_MAPKK_plant_like, Catalytic domain of Plant
dual-specificity MAP kinase kinases and similar
proteins. Protein kinases (PKs), MAP kinase kinase
(MAPKK) subfamily, Plant MAPKKs and similar proteins,
catalytic (c) domain. PKs catalyze the transfer of the
gamma-phosphoryl group from ATP to serine/threonine or
tyrosine residues on protein substrates. The MAPKK
subfamily is part of a larger superfamily that includes
the catalytic domains of other protein serine/threonine
kinases, protein tyrosine kinases, RIO kinases,
aminoglycoside phosphotransferase, choline kinase, and
phosphoinositide 3-kinase. The mitogen-activated protein
(MAP) kinase signaling pathways are important mediators
of cellular responses to extracellular signals. The
pathways involve a triple kinase core cascade comprising
of the MAP kinase (MAPK), which is phosphorylated and
activated by a MAPK kinase (MAPKK or MKK), which itself
is phosphorylated and activated by a MAPK kinase kinase
(MAPKKK or MKKK). Members of this group include MAPKKs
from plants, kinetoplastids, alveolates, and mycetozoa.
The MAPKK, LmxPK4, from Leishmania mexicana, is
important in differentiation and virulence.
Dictyostelium discoideum MEK1 is required for proper
chemotaxis. MEK1 null mutants display severe defects in
cell polarization and directional movement. Plants
contain multiple MAPKKs like other eukaryotes. The
Arabidopsis genome encodes for 10 MAPKKs while poplar
and rice contain 13 MAPKKs each. The functions of these
proteins have not been fully elucidated. There is
evidence to suggest that MAPK cascades are involved in
plant stress responses. In Arabidopsis, MKK3 plays a
role in pathogen signaling, MKK2 is involved in cold and
salt stress signaling, MKK4/MKK5 participates in innate
immunity, and MKK7 regulates basal and systemic acquired
resistance.
Length = 264
Score = 24.5 bits (54), Expect = 8.2
Identities = 16/56 (28%), Positives = 25/56 (44%), Gaps = 6/56 (10%)
Query: 31 LVELALRKMDYDKDGKISFQDFQQSVTDEPLLLEAFGQCLPSDAARQSFLSTLQAC 86
L+E AL K + G+ SF + Q++ D P LP++ F + AC
Sbjct: 190 LLECALGKFPFLPPGQPSFFELMQAICDGPPPS------LPAEEFSPEFRDFISAC 239
>gnl|CDD|238083 cd00143, PP2Cc, Serine/threonine phosphatases, family 2C, catalytic
domain; The protein architecture and deduced catalytic
mechanism of PP2C phosphatases are similar to the PP1,
PP2A, PP2B family of protein Ser/Thr phosphatases, with
which PP2C shares no sequence similarity.
Length = 254
Score = 24.2 bits (53), Expect = 9.2
Identities = 10/24 (41%), Positives = 15/24 (62%)
Query: 15 LISHPQDEDPDEGVRDLVELALRK 38
+ S ED E ++LV+LALR+
Sbjct: 218 VRSELAKEDLQEAAQELVDLALRR 241
>gnl|CDD|107266 cd06271, PBP1_AglR_RafR_like, Ligand-binding domain of DNA
transcription repressors specific for raffinose (RafR)
and alpha-glucosides (AglR) which are members of the
LacI-GalR family of bacterial transcription regulators.
Ligand-binding domain of DNA transcription repressors
specific for raffinose (RafR) and alpha-glucosides
(AglR) which are members of the LacI-GalR family of
bacterial transcription regulators. The LacI-GalR
family repressors are composed of two functional
domains: an N-terminal HTH (helix-turn-helix) domain,
which is responsible for the DNA-binding specificity,
and a C-terminal ligand-binding domain, which is
homologous to the sugar-binding domain of ABC-type
transport systems that contain the type I periplasmic
binding protein-like fold. As also observed in the
periplasmic binding proteins, the C-terminal domain of
the bacterial transcription repressor undergoes a
conformational change upon ligand binding which in turn
changes the DNA binding affinity of the repressor.
Length = 268
Score = 24.5 bits (54), Expect = 9.5
Identities = 10/20 (50%), Positives = 11/20 (55%)
Query: 14 SLISHPQDEDPDEGVRDLVE 33
L+ DEDP E R LVE
Sbjct: 37 VLLPVDPDEDPLEVYRRLVE 56
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
0.318 0.135 0.387
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: 4,384,413
Number of extensions: 357671
Number of successful extensions: 424
Number of sequences better than 10.0: 1
Number of HSP's gapped: 424
Number of HSP's successfully gapped: 42
Length of query: 86
Length of database: 10,937,602
Length adjustment: 54
Effective length of query: 32
Effective length of database: 8,542,486
Effective search space: 273359552
Effective search space used: 273359552
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 (21.7 bits)
S2: 53 (23.9 bits)