RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6634
(90 letters)
>gnl|CDD|239655 cd03683, ClC_1_like, ClC-1-like chloride channel proteins. This CD
includes isoforms ClC-0, ClC-1, ClC-2 and ClC_K. ClC-1
is expressed in skeletal muscle and its mutation leads
to both recessively and dominantly-inherited forms of
muscle stiffness or myotonia. ClC-K is exclusively
expressed in kidney. Similarly, mutation of ClC-K leads
to nephrogenic diabetes insipidus in mice and Bartter's
syndrome in human. These proteins belong to the ClC
superfamily of chloride ion channels, which share the
unique double-barreled architecture and
voltage-dependent gating mechanism. The gating is
conferred by the permeating anion itself, acting as the
gating charge. This domain is found in the eukaryotic
halogen ion (Cl-, Br- and I-) channel proteins, that
perform a variety of functions including cell volume
regulation, regulation of intracelluar chloride
concentration, membrane potential stabilization, charge
compensation necessary for the acidification of
intracellular organelles and transepithelial chloride
transport.
Length = 426
Score = 88.5 bits (220), Expect = 3e-22
Identities = 39/45 (86%), Positives = 40/45 (88%)
Query: 24 GSGIPEMKTILRGVALKEYLTFNTLVAKIIGLTATLGSGLPLGKE 68
GSGIPEMKTILRGV L EYLTF TLVAK+IGLT LGSGLPLGKE
Sbjct: 72 GSGIPEMKTILRGVVLPEYLTFKTLVAKVIGLTCALGSGLPLGKE 116
>gnl|CDD|238507 cd01036, ClC_euk, Chloride channel, ClC. These domains are found
in the eukaryotic halogen ion (Cl-, Br- and I-) channel
proteins that perform a variety of functions including
cell volume regulation, membrane potential
stabilization, charge compensation necessary for the
acidification of intracellular organelles, signal
transduction and transepithelial transport. They are
also involved in many pathophysiological processes and
are responsible for a number of human diseases. These
proteins belong to the ClC superfamily of chloride ion
channels, which share the unique double-barreled
architecture and voltage-dependent gating mechanism.
The gating is conferred by the permeating anion itself,
acting as the gating charge. Some proteins possess long
C-terminal cytoplasmic regions containing two CBS
(cystathionine beta synthase) domains of putative
regulatory function.
Length = 416
Score = 67.4 bits (165), Expect = 8e-15
Identities = 25/46 (54%), Positives = 30/46 (65%)
Query: 23 SGSGIPEMKTILRGVALKEYLTFNTLVAKIIGLTATLGSGLPLGKE 68
+GSGIPE+ L GV L YL+ TL+AK I + SGLPLGKE
Sbjct: 63 AGSGIPEVMAYLNGVHLPMYLSIRTLIAKTISCICAVASGLPLGKE 108
>gnl|CDD|239656 cd03684, ClC_3_like, ClC-3-like chloride channel proteins. This
CD includes ClC-3, ClC-4, ClC-5 and ClC-Y1. ClC-3 was
initially cloned from rat kidney. Expression of ClC-3
produces outwardly-rectifying Cl currents that are
inhibited by protein kinase C activation. It has been
suggested that ClC-3 may be a ubiquitous
swelling-activated Cl channel that has very similar
characteristics to those of native volume-regulated Cl
currents. The function of ClC-4 is unclear. Studies of
human ClC-4 have revealed that it gives rise to Cl
currents that rapidly activate at positive voltages,
and are sensitive to extracellular pH, with currents
decreasing when pH falls below 6.5. ClC-4 is broadly
distributed, especially in brain and heart. ClC-5 is
predominantly expressed in the kidney, but can be found
in the brain and liver. Mutations in the ClC-5 gene
cause certain hereditary diseases, including Dent's
disease, an X-chromosome linked syndrome characterised
by proteinuria, hypercalciuria, and kidney stones
(nephrolithiasis), leading to progressive renal
failure. These proteins belong to the ClC superfamily
of chloride ion channels, which share the unique
double-barreled architecture and voltage-dependent
gating mechanism. The gating is conferred by the
permeating anion itself, acting as the gating charge.
This domain is found in the eukaryotic halogen ion (Cl-
and I-) channel proteins, that perform a variety of
functions including cell volume regulation, the
membrane potential stabilization, transepithelial
chloride transport and charge compensation necessary
for the acidification of intracellular organelles.
Length = 445
Score = 57.2 bits (139), Expect = 3e-11
Identities = 25/48 (52%), Positives = 33/48 (68%)
Query: 21 YLSGSGIPEMKTILRGVALKEYLTFNTLVAKIIGLTATLGSGLPLGKE 68
Y +GSGIPE+KTIL G ++ +L TL+ K +GL + SGL LGKE
Sbjct: 52 YAAGSGIPEIKTILSGFIIRGFLGKWTLLIKSVGLVLAVASGLSLGKE 99
>gnl|CDD|239657 cd03685, ClC_6_like, ClC-6-like chloride channel proteins. This CD
includes ClC-6, ClC-7 and ClC-B, C, D in plants.
Proteins in this family are ubiquitous in eukarotes and
their functions are unclear. They are expressed in
intracellular organelles membranes. This family belongs
to the ClC superfamily of chloride ion channels, which
share the unique double-barreled architecture and
voltage-dependent gating mechanism. The gating is
conferred by the permeating anion itself, acting as the
gating charge. ClC chloride ion channel superfamily
perform a variety of functions including cellular
excitability regulation, cell volume regulation,
membrane potential stabilization, acidification of
intracellular organelles, signal transduction, and
transepithelial transport in animals.
Length = 466
Score = 51.5 bits (124), Expect = 3e-09
Identities = 25/55 (45%), Positives = 34/55 (61%), Gaps = 1/55 (1%)
Query: 23 SGSGIPEMKTILRGVALKEYLTFNTLVAKIIGLTATLGSGLPLGKE-PISVSGHC 76
+GSGIPE+K L GV + L TL+ KI+G+ ++ GL LGKE P+ G C
Sbjct: 104 AGSGIPEVKGYLNGVKIPHILRLKTLLVKIVGVILSVSGGLALGKEGPMIHIGAC 158
>gnl|CDD|216046 pfam00654, Voltage_CLC, Voltage gated chloride channel. This
family of ion channels contains 10 or 12 transmembrane
helices. Each protein forms a single pore. It has been
shown that some members of this family form homodimers.
In terms of primary structure, they are unrelated to
known cation channels or other types of anion channels.
Three ClC subfamilies are found in animals. ClC-1 is
involved in setting and restoring the resting membrane
potential of skeletal muscle, while other channels play
important parts in solute concentration mechanisms in
the kidney. These proteins contain two pfam00571
domains.
Length = 345
Score = 43.3 bits (103), Expect = 2e-06
Identities = 22/46 (47%), Positives = 27/46 (58%), Gaps = 2/46 (4%)
Query: 23 SGSGIPEMKTILRGVALKEYLTFNTLVAKIIGLTATLGSGLPLGKE 68
+GSGIPE+ L GV K L L+ K +G TLGSG LG+E
Sbjct: 17 AGSGIPEVIAALHGV--KGPLPLRVLLVKFLGTLLTLGSGGSLGRE 60
Score = 25.6 bits (57), Expect = 3.4
Identities = 14/46 (30%), Positives = 22/46 (47%)
Query: 21 YLSGSGIPEMKTILRGVALKEYLTFNTLVAKIIGLTATLGSGLPLG 66
+ G G ++ +L G L L L+ K++ +LGSG P G
Sbjct: 217 EVLGGGYGLIQLLLNGSTLSLLLLLLLLLLKLLATALSLGSGAPGG 262
>gnl|CDD|238504 cd01031, EriC, ClC chloride channel EriC. This domain is found in
the EriC chloride transporters that mediate the extreme
acid resistance response in eubacteria and archaea. This
response allows bacteria to survive in the acidic
environments by decarboxylation-linked proton
utilization. As shown for Escherichia coli EriC, these
channels can counterbalance the electric current
produced by the outwardly directed virtual proton pump
linked to amino acid decarboxylation. The EriC proteins
belong to the ClC superfamily of chloride ion channels,
which share a unique double-barreled architecture and
voltage-dependent gating mechanism. The
voltage-dependent gating is conferred by the permeating
anion itself, acting as the gating charge. In
Escherichia coli EriC, a glutamate residue that
protrudes into the pore is thought to participate in
gating by binding to a Cl- ion site within the
selectivity filter.
Length = 402
Score = 41.8 bits (99), Expect = 7e-06
Identities = 21/50 (42%), Positives = 28/50 (56%), Gaps = 2/50 (4%)
Query: 23 SGSGIPEMKTILRGVALKEYLTFNTLVAKIIGLTATLGSGLPLGKEPISV 72
GSGIP+++ +L G L + L K +G LGSGL LG+E SV
Sbjct: 63 KGSGIPQVEGVLAG--LLPPNWWRVLPVKFVGGVLALGSGLSLGREGPSV 110
>gnl|CDD|223116 COG0038, EriC, Chloride channel protein EriC [Inorganic ion
transport and metabolism].
Length = 443
Score = 32.7 bits (75), Expect = 0.015
Identities = 18/50 (36%), Positives = 26/50 (52%), Gaps = 2/50 (4%)
Query: 23 SGSGIPEMKTILRGVALKEYLTFNTLVAKIIGLTATLGSGLPLGKEPISV 72
GSGIP+ L G + ++ L K++ T+GSG LG+E SV
Sbjct: 90 RGSGIPQAIEALHGRKGR--ISPRVLPVKLVATLLTIGSGASLGREGPSV 137
>gnl|CDD|238506 cd01034, EriC_like, ClC chloride channel family. These protein
sequences, closely related to the ClC Eric family, are
putative halogen ion (Cl-, Br- and I-) transport
proteins found in eubacteria. They belong to the ClC
superfamily of chloride ion channels, which share a
unique double-barreled architecture and
voltage-dependent gating mechanism. This superfamily
lacks any structural or sequence similarity to other
known ion channels and exhibit unique properties of ion
permeation and gating. The voltage-dependent gating is
conferred by the permeating anion itself, acting as the
gating charge.
Length = 390
Score = 30.7 bits (70), Expect = 0.066
Identities = 18/54 (33%), Positives = 26/54 (48%), Gaps = 3/54 (5%)
Query: 23 SGSGIPEMKTILR---GVALKEYLTFNTLVAKIIGLTATLGSGLPLGKEPISVS 73
+GSGIP++ L A + L+ T V KI+ L G +G+E SV
Sbjct: 52 AGSGIPQVIAALELPSAAARRRLLSLRTAVGKILLTLLGLLGGASVGREGPSVQ 105
>gnl|CDD|235385 PRK05277, PRK05277, chloride channel protein; Provisional.
Length = 438
Score = 30.2 bits (69), Expect = 0.087
Identities = 20/46 (43%), Positives = 26/46 (56%), Gaps = 2/46 (4%)
Query: 23 SGSGIPEMKTILRGVALKEYLTFNTLVAKIIGLTATLGSGLPLGKE 68
GSGIPE++ L G L+ + L K G TLGSG+ LG+E
Sbjct: 70 GGSGIPEIEGALEG--LRPVRWWRVLPVKFFGGLGTLGSGMVLGRE 113
>gnl|CDD|225538 COG2991, COG2991, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 77
Score = 27.1 bits (60), Expect = 0.53
Identities = 13/42 (30%), Positives = 19/42 (45%), Gaps = 6/42 (14%)
Query: 43 LTFNTLVAKIIGLTATLGSGLPLGKEPISVSGHCGPISNFGI 84
LTF + I G++ G ++ I G CG I+ GI
Sbjct: 6 LTFGIFLLVIAGMSI----GYIFKRKSIK--GSCGGIAALGI 41
>gnl|CDD|130176 TIGR01106, ATPase-IIC_X-K, sodium or proton efflux -- potassium
uptake antiporter, P-type ATPase, alpha subunit. This
model describes the P-type ATPases responsible for the
exchange of either protons or sodium ions for potassium
ions across the plasma membranes of eukaryotes. Unlike
most other P-type ATPases, members of this subfamily
require a beta subunit for activity. This model
encompasses eukaryotes and consists of two functional
types, a Na/K antiporter found widely distributed in
eukaryotes and a H/K antiporter found only in
vertebrates. The Na+ or H+/K+ antiporter P-type ATPases
have been characterized as Type IIC based on a published
phylogenetic analysis. Sequences from Blastocladiella
emersonii (GP|6636502, GP|6636502 and PIR|T43025), C.
elegans (GP|2315419, GP|6671808 and PIR|T31763) and
Drosophila melanogaster (GP|7291424) score below trusted
cutoff, apparently due to long branch length (excessive
divergence from the last common ancestor) as evidenced
by a phylogenetic tree. Experimental evidence is needed
to determine whether these sequences represent ATPases
with conserved function. Aside from fragments, other
sequences between trusted and noise appear to be
bacterial ATPases of unclear lineage, but most likely
calcium pumps [Energy metabolism, ATP-proton motive
force interconversion].
Length = 997
Score = 26.7 bits (59), Expect = 1.9
Identities = 10/21 (47%), Positives = 15/21 (71%)
Query: 52 IIGLTATLGSGLPLGKEPISV 72
++G A+L SGL GK PI++
Sbjct: 240 VMGRIASLASGLENGKTPIAI 260
>gnl|CDD|129582 TIGR00491, aIF-2, translation initiation factor aIF-2/yIF-2. This
model describes archaeal and eukaryotic orthologs of
bacterial IF-2. Like IF-2, it helps convey the initiator
tRNA to the ribosome, although the initiator is
N-formyl-Met in bacteria and Met here. This protein is
not closely related to the subunits of eIF-2 of
eukaryotes, which is also involved in the initiation of
translation. The aIF-2 of Methanococcus jannaschii
contains a large intein interrupting a region of very
strongly conserved sequence very near the amino end; the
alignment generated by This model does not correctly
align the sequences from Methanococcus jannaschii and
Pyrococcus horikoshii in this region [Protein synthesis,
Translation factors].
Length = 590
Score = 26.7 bits (59), Expect = 2.0
Identities = 12/28 (42%), Positives = 18/28 (64%), Gaps = 3/28 (10%)
Query: 22 LSGSGIPEMKTILRGVA---LKEYLTFN 46
++G GIPE+ T+L G+A L+E L
Sbjct: 199 ITGEGIPELLTMLAGLAQQYLEEQLKLE 226
>gnl|CDD|238233 cd00400, Voltage_gated_ClC, CLC voltage-gated chloride channel. The
ClC chloride channels catalyse the selective flow of Cl-
ions across cell membranes, thereby regulating
electrical excitation in skeletal muscle and the flow of
salt and water across epithelial barriers. This domain
is found in the halogen ions (Cl-, Br- and I-) transport
proteins of the ClC family. The ClC channels are found
in all three kingdoms of life and perform a variety of
functions including cellular excitability regulation,
cell volume regulation, membrane potential
stabilization, acidification of intracellular
organelles, signal transduction, transepithelial
transport in animals, and the extreme acid resistance
response in eubacteria. They lack any structural or
sequence similarity to other known ion channels and
exhibit unique properties of ion permeation and gating.
Unlike cation-selective ion channels, which form
oligomers containing a single pore along the axis of
symmetry, the ClC channels form two-pore homodimers with
one pore per subunit without axial symmetry. Although
lacking the typical voltage-sensor found in cation
channels, all studied ClC channels are gated (opened and
closed) by transmembrane voltage. The gating is
conferred by the permeating ion itself, acting as the
gating charge. In addition, eukaryotic and some
prokaryotic ClC channels have two additional C-terminal
CBS (cystathionine beta synthase) domains of putative
regulatory function.
Length = 383
Score = 26.0 bits (58), Expect = 2.7
Identities = 17/64 (26%), Positives = 27/64 (42%), Gaps = 2/64 (3%)
Query: 13 LIGGSNQVYLSGSGIPEMKTILRGVALKE-YLTFNTLVAKIIGLTATLGSGLPLGKE-PI 70
L+ G L + + ++ +AL L + K + TLGSG +G+E PI
Sbjct: 49 LLVGLLVRLLGPARGHGIPEVIEAIALGGGRLPLRVALVKFLASALTLGSGGSVGREGPI 108
Query: 71 SVSG 74
G
Sbjct: 109 VQIG 112
>gnl|CDD|222905 PHA02603, nrdC.11, hypothetical protein; Provisional.
Length = 330
Score = 25.5 bits (56), Expect = 4.1
Identities = 6/18 (33%), Positives = 8/18 (44%)
Query: 27 IPEMKTILRGVALKEYLT 44
+P + IL G A K
Sbjct: 30 LPHPRDILLGNAKKHMSK 47
>gnl|CDD|173111 PRK14648, PRK14648, UDP-N-acetylenolpyruvoylglucosamine reductase;
Provisional.
Length = 354
Score = 25.5 bits (55), Expect = 4.8
Identities = 13/56 (23%), Positives = 29/56 (51%), Gaps = 5/56 (8%)
Query: 11 VDLIGGSNQVYLSGSGIPEMKTILRGVALKEYLTFNTLVAKIIGLTATLGSGLPLG 66
+ LIGG + V ++ G+P + ++L+ + + +T + + G+GLP+
Sbjct: 56 LSLIGGGSNVLIADEGVPGLM-----LSLRRFRSLHTQTQRDGSVLVHAGAGLPVA 106
>gnl|CDD|215235 PLN02426, PLN02426, cytochrome P450, family 94, subfamily C
protein.
Length = 502
Score = 25.4 bits (56), Expect = 5.4
Identities = 15/46 (32%), Positives = 20/46 (43%), Gaps = 12/46 (26%)
Query: 27 IPEMKTILRGVALKEYLTFNTLVAK--------IIGLTATLGSGLP 64
+ EMK+ VA+ F+ V GLTAT+ GLP
Sbjct: 452 LMEMKS----VAVAVVRRFDIEVVGRSNRAPRFAPGLTATVRGGLP 493
>gnl|CDD|226220 COG3696, COG3696, Putative silver efflux pump [Inorganic ion
transport and metabolism].
Length = 1027
Score = 24.9 bits (55), Expect = 7.6
Identities = 14/49 (28%), Positives = 22/49 (44%), Gaps = 6/49 (12%)
Query: 42 YLTFNTL-VAKIIGLT---ATLGS--GLPLGKEPISVSGHCGPISNFGI 84
Y F ++ A +I A +G L L +SV+ G I+ FG+
Sbjct: 879 YFAFKSVGEALLIFSNLPFALIGGVIALALRGFNLSVAAAVGFIALFGV 927
>gnl|CDD|237309 PRK13211, PRK13211, N-acetylglucosamine-binding protein A;
Reviewed.
Length = 478
Score = 24.6 bits (54), Expect = 8.8
Identities = 12/27 (44%), Positives = 18/27 (66%), Gaps = 1/27 (3%)
Query: 2 AGDLNTHDQVDLIGGSNQVYL-SGSGI 27
AG LN Q++ + G N +YL +GSG+
Sbjct: 269 AGQLNADGQIEPVYGKNPIYLKAGSGL 295
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
0.316 0.137 0.414
Gapped
Lambda K H
0.267 0.0643 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,545,066
Number of extensions: 374516
Number of successful extensions: 312
Number of sequences better than 10.0: 1
Number of HSP's gapped: 309
Number of HSP's successfully gapped: 26
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 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (24.4 bits)