RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15906
(352 letters)
>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 = 208 bits (531), Expect = 3e-63
Identities = 71/126 (56%), Positives = 96/126 (76%), Gaps = 1/126 (0%)
Query: 59 SLSVFVVTYFLLSVWTYGVSVSGGVFIPCLLTGAAWGRLFSLFLQSIFPEATWIDPGKYA 118
+L +F V Y+ L+ WT+G++V G+FIP +L GAA+GRL + L S F T IDPG YA
Sbjct: 335 TLLIFFVLYYFLACWTFGIAVPSGLFIPMILIGAAYGRLVGILLGSYF-GFTSIDPGLYA 393
Query: 119 LIGAAAQLGGVVRMTISLTIILIEATGNISFGLPLMLTLITAKWIGDFFTEGLYDIHIQL 178
L+GAAA LGGV+RMT+SLT+IL+E T N+++ P+ML L+ AKW+GD+F EG+YDI IQL
Sbjct: 394 LLGAAAFLGGVMRMTVSLTVILLELTNNLTYLPPIMLVLMIAKWVGDYFNEGIYDIIIQL 453
Query: 179 SGIPLL 184
G+P L
Sbjct: 454 KGVPFL 459
>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 = 140 bits (354), Expect = 5e-38
Identities = 54/122 (44%), Positives = 75/122 (61%), Gaps = 7/122 (5%)
Query: 59 SLSVFVVTYFLLSVWTYGVSVSGGVFIPCLLTGAAWGRLFSLFLQSIFPE-------ATW 111
+L +F++ YF +S +G++V GG FIP L+ GAA GRL L + I W
Sbjct: 295 TLLLFLLIYFWMSALAFGIAVPGGTFIPSLVIGAAIGRLVGLLVHRIAVAGIGAESATLW 354
Query: 112 IDPGKYALIGAAAQLGGVVRMTISLTIILIEATGNISFGLPLMLTLITAKWIGDFFTEGL 171
DPG YALIGAAA LGG R+T S+ +I++E TG++ LPLM+ ++ AK + D F E L
Sbjct: 355 ADPGVYALIGAAAFLGGTTRLTFSICVIMMELTGDLHHLLPLMVAILIAKAVADAFCESL 414
Query: 172 YD 173
Y
Sbjct: 415 YH 416
>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 = 123 bits (310), Expect = 2e-31
Identities = 54/142 (38%), Positives = 92/142 (64%), Gaps = 14/142 (9%)
Query: 57 VFSLSVFVVTYFLLSVWTYGVSVSGGVFIPCLLTGAAWGRLFSLFLQSI---FPEATW-- 111
++SL + ++ LL+++T+G+ V G+F+P + GA +GR+ + ++ + +P++ +
Sbjct: 304 LWSLLLALIIKLLLTIFTFGIKVPAGIFVPSMAVGALFGRIVGILVEQLAYSYPDSIFFA 363
Query: 112 --------IDPGKYALIGAAAQLGGVVRMTISLTIILIEATGNISFGLPLMLTLITAKWI 163
I PG YA++GAAA LGGV RMT+SL +I+ E TG +++ LPLM+ ++ +KW+
Sbjct: 364 CCTAGPSCITPGLYAMVGAAAFLGGVTRMTVSLVVIMFELTGALNYILPLMIAVMVSKWV 423
Query: 164 GDFFT-EGLYDIHIQLSGIPLL 184
D EG+YD HI L+G P L
Sbjct: 424 ADAIGKEGIYDAHIHLNGYPFL 445
>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 = 113 bits (285), Expect = 1e-28
Identities = 40/123 (32%), Positives = 63/123 (51%), Gaps = 3/123 (2%)
Query: 44 VRTMLHDPKGAFGVFSLSVFVVTYFLLSVWTYGVSVSGGVFIPCLLTGAAWGRLFSLFLQ 103
++ +L+ + L + ++ L + + G GG+F P L GAA GRL L L
Sbjct: 226 IQLLLNG--STLSLLLLLLLLLLKLLATALSLGSGAPGGIFAPSLFIGAALGRLLGLLLP 283
Query: 104 SIFPEATWIDPGKYALIGAAAQLGGVVRMTISLTIILIEATGNISFGLPLMLTLITAKWI 163
+FP PG +AL+G AA L GV R ++ +++ E TG+ S LPLML ++ A +
Sbjct: 284 LLFPG-IAPSPGAFALLGMAAFLAGVTRAPLTAIVLVFELTGSYSLLLPLMLAVLIAYLV 342
Query: 164 GDF 166
Sbjct: 343 SRL 345
>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 = 101 bits (255), Expect = 4e-24
Identities = 46/136 (33%), Positives = 74/136 (54%), Gaps = 7/136 (5%)
Query: 55 FGVFSLSVFVVTYFLLSVWTYGVSVSGGVFIPCLLTGAAWGRLFSLFLQSIFPEATW--- 111
F +L +F+V F+L+ + V G+F+P + GAA GRL + +FPE
Sbjct: 290 FPFLTLFLFIVVKFVLTALAITLPVPAGIFMPVFVIGAALGRLVGEIMAVLFPEGIRGGI 349
Query: 112 ---IDPGKYALIGAAAQLGGVVRMTISLTIILIEATGNISFGLPLMLTLITAKWIGDFFT 168
I PG YA++GAAA G V T+S+ +I+ E TG IS LP+++ ++ + + F
Sbjct: 350 SNPIGPGGYAVVGAAAFSGAVTH-TVSVAVIIFELTGQISHLLPVLIAVLISNAVAQFLQ 408
Query: 169 EGLYDIHIQLSGIPLL 184
+YD I++ +P L
Sbjct: 409 PSIYDSIIKIKKLPYL 424
>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 = 79.9 bits (198), Expect = 1e-16
Identities = 42/115 (36%), Positives = 61/115 (53%), Gaps = 1/115 (0%)
Query: 46 TMLHDPKGAFGVFSLSVFVVTYFLLSVWTYGVSVSGGVFIPCLLTGAAWGRLFSLFLQSI 105
+L G + L + ++ L + T G GGVF P L GAA G F L L ++
Sbjct: 269 AILLALAGELSLLLLLLLLLLKLLATALTLGSGFPGGVFAPSLFIGAALGAAFGLLLPAL 328
Query: 106 FPEATWIDPGKYALIGAAAQLGGVVRMTISLTIILIEATGNISFGLPLMLTLITA 160
FP PG YAL+G AA L V+R ++ ++++E TG+ S LPLML ++ A
Sbjct: 329 FPGLV-ASPGAYALVGMAALLAAVLRAPLTAILLVLELTGDYSLLLPLMLAVVIA 382
>gnl|CDD|223116 COG0038, EriC, Chloride channel protein EriC [Inorganic ion
transport and metabolism].
Length = 443
Score = 78.5 bits (194), Expect = 4e-16
Identities = 39/131 (29%), Positives = 65/131 (49%), Gaps = 2/131 (1%)
Query: 55 FGVFSLSVFVVTYFLLSVWTYGVSVSGGVFIPCLLTGAAWGRLFSLFLQSIFPEATWIDP 114
G+ L + + L ++ +YG GG+F P L GAA G F L +FP + ++P
Sbjct: 307 GGLLVLLLLFLLKLLATLLSYGSGAPGGIFAPSLFIGAALGLAFGALLGLLFP-PSILEP 365
Query: 115 GKYALIGAAAQLGGVVRMTISLTIILIEATGNISFGLPLMLTLITAKWIGD-FFTEGLYD 173
G +AL+G AA L R ++ ++++E TGN LPL++ + A + +Y
Sbjct: 366 GLFALLGMAAFLAATTRAPLTAIVLVLEMTGNYQLLLPLLIACLIAYLVSRLLGGRPIYT 425
Query: 174 IHIQLSGIPLL 184
+ G P+L
Sbjct: 426 QLLARRGAPIL 436
>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 = 68.7 bits (169), Expect = 8e-13
Identities = 39/108 (36%), Positives = 56/108 (51%), Gaps = 4/108 (3%)
Query: 56 GVFSLSVFVVTYFLLSVWT---YGVSVSGGVFIPCLLTGAAWGRLFSLFLQSIFPEATWI 112
G FS+S+ ++ + L ++T YG GG+F P L GA G LF L + P
Sbjct: 278 GNFSISLLLLIFVLRFIFTMLSYGSGAPGGIFAPMLALGALLGLLFGTILVQLGPIPI-S 336
Query: 113 DPGKYALIGAAAQLGGVVRMTISLTIILIEATGNISFGLPLMLTLITA 160
P +A+ G AA VVR I+ I++ E TGN + LPLM+ + A
Sbjct: 337 APATFAIAGMAAFFAAVVRAPITAIILVTEMTGNFNLLLPLMVVCLVA 384
>gnl|CDD|235385 PRK05277, PRK05277, chloride channel protein; Provisional.
Length = 438
Score = 62.6 bits (153), Expect = 8e-11
Identities = 32/108 (29%), Positives = 55/108 (50%), Gaps = 4/108 (3%)
Query: 56 GVFSLSV---FVVTYFLLSVWTYGVSVSGGVFIPCLLTGAAWGRLFSLFLQSIFPEATWI 112
G FS+ + V F+ ++ +G GG+F P L G G F + ++FP+ I
Sbjct: 291 GNFSIGMLLFIFVARFITTLLCFGSGAPGGIFAPMLALGTLLGLAFGMVAAALFPQYH-I 349
Query: 113 DPGKYALIGAAAQLGGVVRMTISLTIILIEATGNISFGLPLMLTLITA 160
+PG +A+ G A VR ++ ++++E T N LPL++T + A
Sbjct: 350 EPGTFAIAGMGALFAATVRAPLTGIVLVLEMTDNYQLILPLIITCLGA 397
Score = 28.7 bits (65), Expect = 5.8
Identities = 25/107 (23%), Positives = 34/107 (31%), Gaps = 31/107 (28%)
Query: 53 GAFGV-FSLSVFVVTYFLLSVWTYGVSVSGGVFIPCLLTGAAWGRLFSLFLQSIFPEATW 111
G FGV F+ + + GG +L G A G L L L + P A
Sbjct: 228 GIFGVLFNKLLLRTQDLF-------DRLHGGNKKRWVLMGGAVGGLCGL-LGLLAPAAV- 278
Query: 112 IDPGKYALIGAAAQLGGVVRMTISLTIILIEATGNISFGLPLMLTLI 158
G + LI A GN S G+ L + +
Sbjct: 279 --GGGFNLIPIAL-------------------AGNFSIGMLLFIFVA 304
>gnl|CDD|234987 PRK01862, PRK01862, putative voltage-gated ClC-type chloride
channel ClcB; Provisional.
Length = 574
Score = 58.2 bits (141), Expect = 3e-09
Identities = 42/137 (30%), Positives = 65/137 (47%), Gaps = 15/137 (10%)
Query: 44 VRTMLHDPKGAFGVFSLSVFVVTYFLL--SVWTYGVSVSGGVFIPCLLTGAAWGRLFSLF 101
V T+LH P ++ V L + T G GGVF P L GA G LF L
Sbjct: 303 VNTILHAP-----WTWQALVAVLVAKLIATAATAGSGAVGGVFTPTLFVGAVVGSLFGLA 357
Query: 102 LQSIFPEATWIDPGKYALIGAAAQLGGVVRMTISLTIILIEATGNISFGLPLMLTLI--- 158
+ +++P T P YA++G A L G + + +++ E T + LPLM++ +
Sbjct: 358 MHALWPGHT-SAPFAYAMVGMGAFLAGATQAPLMAILMIFEMTLSYQVVLPLMVSCVVAY 416
Query: 159 -TAKWIGDFFTEGLYDI 174
TA+ +G T +Y+I
Sbjct: 417 FTARALG---TTSMYEI 430
>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 = 55.7 bits (135), Expect = 1e-08
Identities = 34/112 (30%), Positives = 53/112 (47%), Gaps = 8/112 (7%)
Query: 63 FVVTYFLLSVWTYGVSVSGGVFIPCLLTGAAWGRLFSLFLQSIFPEATWIDPGKYALIGA 122
F + FL ++ +Y + GG+F P L GA G L + L S+ G L+G
Sbjct: 286 FGLLKFLATLLSYWSGIPGGLFAPSLAVGAGLGSLLAALLGSV-------SQGALVLLGM 338
Query: 123 AAQLGGVVRMTISLTIILIEATGNISFGLPLMLTLITAKWIGDFF-TEGLYD 173
AA L GV + ++ +I++E TG+ LPL+ + A + E LY
Sbjct: 339 AAFLAGVTQAPLTAFVIVMEMTGDQQMLLPLLAAALLASGVSRLVCPEPLYH 390
>gnl|CDD|239964 cd04591, CBS_pair_EriC_assoc_euk_bac, This cd contains two tandem
repeats of the cystathionine beta-synthase (CBS pair)
domains in the EriC CIC-type chloride channels in
eukaryotes and bacteria. These ion channels are proteins
with a seemingly simple task of allowing the passive
flow of chloride ions across biological membranes.
CIC-type chloride channels come from all kingdoms of
life, have several gene families, and can be gated by
voltage. The members of the CIC-type chloride channel
are double-barreled: two proteins forming homodimers at
a broad interface formed by four helices from each
protein. The two pores are not found at this interface,
but are completely contained within each subunit, as
deduced from the mutational analyses, unlike many other
channels, in which four or five identical or
structurally related subunits jointly form one pore. CBS
is a small domain originally identified in cystathionine
beta-synthase and subsequently found in a wide range of
different proteins. CBS domains usually come in tandem
repeats, which associate to form a so-called Bateman
domain or a CBS pair which is reflected in this model.
The interface between the two CBS domains forms a cleft
that is a potential ligand binding site. The CBS pair
coexists with a variety of other functional domains. It
has been proposed that the CBS domain may play a
regulatory role, although its exact function is unknown.
Mutations of conserved residues within this domain in
CLC chloride channel family members have been associated
with classic Bartter syndrome, Osteopetrosis, Dent's
disease, idiopathic generalized epilepsy, and myotonia.
Length = 105
Score = 42.6 bits (101), Expect = 2e-05
Identities = 26/97 (26%), Positives = 36/97 (37%), Gaps = 40/97 (41%)
Query: 202 SHPVICLRPLETVGNIIDVLKATSHNGFPIVDVEPMTKHSSDGAEQSSAGSTDSHKGDTS 261
V+ L TV ++ +L TSHNGFP+VD
Sbjct: 1 VPLVVLLPEGMTVEDLESLLSTTSHNGFPVVD---------------------------- 32
Query: 262 HKRDSSHKGDASRKDSPGRLVGLILRSQLIILIKHKI 298
+ RLVG ILRSQL++ +K+ I
Sbjct: 33 ------------STEESPRLVGYILRSQLVVALKNYI 57
>gnl|CDD|238505 cd01033, ClC_like, Putative ClC chloride channel. Clc proteins are
putative halogen ion (Cl-, Br- and I-) transporters
found in eubacteria. They belong to the ClC superfamily
of halogen 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 = 388
Score = 38.8 bits (91), Expect = 0.003
Identities = 26/88 (29%), Positives = 42/88 (47%), Gaps = 4/88 (4%)
Query: 69 LLSVWTYGVSVSGGVFIPCLLTGAAWGRLFSLFLQSIFPEATWIDPGKYALIGAAAQLGG 128
+ ++ GG+ P L GA G L + ++ P + +ALIGAAA L
Sbjct: 290 VATLLALRAGAYGGLLTPSLALGALLGALLGIVWNALLPPLSI---AAFALIGAAAFLAA 346
Query: 129 VVRMTISLTIILIEATG-NISFGLPLML 155
+ ++ I+++E T N F +PLML
Sbjct: 347 TQKAPLTALILVLEFTRQNPLFLIPLML 374
>gnl|CDD|239983 cd04610, CBS_pair_ParBc_assoc, This cd contains two tandem repeats
of the cystathionine beta-synthase (CBS pair) domains
associated with a ParBc (ParB-like nuclease) domain
downstream. CBS is a small domain originally identified
in cystathionine beta-synthase and subsequently found in
a wide range of different proteins. CBS domains usually
come in tandem repeats, which associate to form a
so-called Bateman domain or a CBS pair which is
reflected in this model. The interface between the two
CBS domains forms a cleft that is a potential ligand
binding site. The CBS pair coexists with a variety of
other functional domains. It has been proposed that the
CBS domain may play a regulatory role, although its
exact function is unknown.
Length = 107
Score = 35.5 bits (82), Expect = 0.007
Identities = 14/29 (48%), Positives = 21/29 (72%)
Query: 205 VICLRPLETVGNIIDVLKATSHNGFPIVD 233
VI + P TV ++I ++K T H+GFP+VD
Sbjct: 4 VITVSPDNTVKDVIKLIKETGHDGFPVVD 32
>gnl|CDD|214522 smart00116, CBS, Domain in cystathionine beta-synthase and other
proteins. Domain present in all 3 forms of cellular
life. Present in two copies in inosine monophosphate
dehydrogenase, of which one is disordered in the crystal
structure. A number of disease states are associated
with CBS-containing proteins including homocystinuria,
Becker's and Thomsen disease.
Length = 49
Score = 32.5 bits (75), Expect = 0.023
Identities = 7/30 (23%), Positives = 15/30 (50%)
Query: 204 PVICLRPLETVGNIIDVLKATSHNGFPIVD 233
V+ + P T+ +++L+ P+VD
Sbjct: 1 DVVTVSPDTTLEEALELLRENGIRRLPVVD 30
>gnl|CDD|223445 COG0368, CobS, Cobalamin-5-phosphate synthase [Coenzyme
metabolism].
Length = 246
Score = 33.0 bits (76), Expect = 0.15
Identities = 18/115 (15%), Positives = 41/115 (35%), Gaps = 11/115 (9%)
Query: 53 GAFGVFSLSVFVVTYFLLSVWTYGVSVSGGVFIPCLLTGAAWGRLFSLFLQSIFPEATWI 112
GA GV +L + ++ L + G + L A + L ++ + +
Sbjct: 105 GAGGVAALILVLLLKVLAL---ASLLDLGAAALLAL---AEVLAKSRMLLVALLSKPPYA 158
Query: 113 DPGKYALIGAAAQLGGVVRMTISLTIILI----EATGNISFGLPLMLTLITAKWI 163
G A G++ + L ++L+ +G I+ + L+ + +
Sbjct: 159 GLGGLG-KEFADPRKGLIGALLLLVLLLLALLFGLSGAIAVAVALLAAALLGRLA 212
>gnl|CDD|234963 PRK01610, PRK01610, putative voltage-gated ClC-type chloride
channel ClcB; Provisional.
Length = 418
Score = 32.4 bits (74), Expect = 0.31
Identities = 23/70 (32%), Positives = 28/70 (40%), Gaps = 1/70 (1%)
Query: 76 GVSVSGGVFIPCLLTGAAWGRLFSLFLQSIFPEATWIDPGKYALIGAAAQLGGVVRMTIS 135
G GGVF P L G A G L+ L P+ I L G A L I
Sbjct: 314 GSGAPGGVFTPTLFVGLAIGMLYGRSLGLWLPDGEEI-TLLLGLTGMATLLAATTHAPIM 372
Query: 136 LTIILIEATG 145
T+++ E TG
Sbjct: 373 STLMICEMTG 382
>gnl|CDD|240531 cd13126, MATE_like_11, Uncharacterized subfamily of the multidrug
and toxic compound extrusion (MATE) proteins. This
family might function as a translocase for
lipopolysaccharides, such as O-antigen. The integral
membrane proteins from the MATE family are involved in
exporting metabolites across the cell membrane and are
responsible for multidrug resistance (MDR) in many
bacteria and animals. A number of family members are
involved in the synthesis of peptidoglycan components in
bacteria.
Length = 396
Score = 31.1 bits (71), Expect = 0.93
Identities = 24/77 (31%), Positives = 31/77 (40%), Gaps = 7/77 (9%)
Query: 54 AFGVFSLSVFVVTYFLLSVWTYGVSVSGGVFIPCLLTGAAWGRLFSLFLQSIFPEATWID 113
A G+ V + LL V+ GV +P LL AW R + F Q A D
Sbjct: 81 AVGLALGLVTALVGALLGGTVGSPLVALGVVLPGLLLQDAW-R-GAFFAQGRPGRAAAND 138
Query: 114 PGKYALIGAAAQLGGVV 130
L+ A AQL G +
Sbjct: 139 -----LVWAVAQLAGAM 150
>gnl|CDD|237640 PRK14209, PRK14209, camphor resistance protein CrcB; Provisional.
Length = 124
Score = 29.5 bits (66), Expect = 1.0
Identities = 25/82 (30%), Positives = 40/82 (48%), Gaps = 4/82 (4%)
Query: 54 AFGVFSLSVFVVTYFLLSVWTYGVSVSGGVFIPCLLTGAAWGRLFSLFLQSIFPEATWID 113
AF V ++ V VV FL+ V ++ G + P L+TG G F+ F T +
Sbjct: 33 AFPVGTMIVNVVGSFLMGVLVVVLAHKGNRYAPFLMTGMLGG--FTTFSAFSLDAVTLYE 90
Query: 114 PGKYALIGAAAQLGGVVRMTIS 135
G+ L AAA +G V ++++
Sbjct: 91 RGQAGL--AAAYVGLSVGLSLA 110
>gnl|CDD|201313 pfam00571, CBS, CBS domain. CBS domains are small intracellular
modules that pair together to form a stable globular
domain. This family represents a single CBS domain.
Pairs of these domains have been termed a Bateman
domain. CBS domains have been shown to bind ligands with
an adenosyl group such as AMP, ATP and S-AdoMet. CBS
domains are found attached to a wide range of other
protein domains suggesting that CBS domains may play a
regulatory role making proteins sensitive to adenosyl
carrying ligands. The region containing the CBS domains
in Cystathionine-beta synthase is involved in regulation
by S-AdoMet. CBS domain pairs from AMPK bind AMP or ATP.
The CBS domains from IMPDH and the chloride channel CLC2
bind ATP.
Length = 57
Score = 26.4 bits (59), Expect = 3.6
Identities = 5/32 (15%), Positives = 17/32 (53%)
Query: 202 SHPVICLRPLETVGNIIDVLKATSHNGFPIVD 233
+ V+ + P ++ +++++ + P+VD
Sbjct: 6 TPDVVTVPPDTSLEEALELMRENGISRLPVVD 37
>gnl|CDD|227714 COG5427, COG5427, Uncharacterized membrane protein [Function
unknown].
Length = 684
Score = 29.1 bits (65), Expect = 3.9
Identities = 17/58 (29%), Positives = 22/58 (37%), Gaps = 7/58 (12%)
Query: 52 KGAFGVFSLSVFVVTYF-LLSVWTYGVSVSGGVFIPCLLTGAAWGRLFSLFLQSIFPE 108
+GA LS+ VVT + YG V GGVF+ L A R +
Sbjct: 17 RGASVAMPLSLVVVTLATWVGQVAYGQLVVGGVFVAVLAAAAWLAR------GGVEIP 68
>gnl|CDD|236884 PRK11234, nfrB, bacteriophage N4 adsorption protein B; Provisional.
Length = 727
Score = 28.9 bits (65), Expect = 4.3
Identities = 12/54 (22%), Positives = 18/54 (33%), Gaps = 1/54 (1%)
Query: 49 HDPKGAFGVF-SLSVFVVTYFLLSVWTYGVSVSGGVFIPCLLTGAAWGRLFSLF 101
D KGA F S ++ LL + Y + +G+AW
Sbjct: 350 RDRKGAITNFVSFLAMLLMLQLLLLLLYESLWPDAWHFLSIFSGSAWLMTLLWL 403
>gnl|CDD|239067 cd02205, CBS_pair, The CBS domain, named after human CBS, is a
small domain originally identified in cystathionine
beta-synthase and is subsequently found in a wide range
of different proteins. CBS domains usually occur in
tandem repeats. They associate to form a so-called
Bateman domain or a CBS pair based on crystallographic
studies in bacteria. The CBS pair was used as a basis
for this cd hierarchy since the human CBS proteins can
adopt the typical core structure and form an
intramolecular CBS pair. The interface between the two
CBS domains forms a cleft that is a potential ligand
binding site. The CBS pair coexists with a variety of
other functional domains and this has been used to help
in its classification here. It has been proposed that
the CBS domain may play a regulatory role, although its
exact function is unknown. Mutations of conserved
residues within this domain are associated with a
variety of human hereditary diseases, including
congenital myotonia, idiopathic generalized epilepsy,
hypercalciuric nephrolithiasis, and classic Bartter
syndrome (CLC chloride channel family members),
Wolff-Parkinson-White syndrome (gamma 2 subunit of
AMP-activated protein kinase), retinitis pigmentosa (IMP
dehydrogenase-1), and homocystinuria (cystathionine
beta-synthase).
Length = 113
Score = 27.4 bits (61), Expect = 5.7
Identities = 8/31 (25%), Positives = 16/31 (51%)
Query: 203 HPVICLRPLETVGNIIDVLKATSHNGFPIVD 233
V+ + P +TV + ++ +G P+VD
Sbjct: 1 RDVVTVSPDDTVAEALRLMLEHGISGLPVVD 31
>gnl|CDD|239968 cd04595, CBS_pair_DHH_polyA_Pol_assoc, This cd contains two tandem
repeats of the cystathionine beta-synthase (CBS pair)
domains associated with an upstream DHH domain which
performs a phosphoesterase function and a downstream
polyA polymerase domain. CBS is a small domain
originally identified in cystathionine beta-synthase and
subsequently found in a wide range of different
proteins. CBS domains usually come in tandem repeats,
which associate to form a so-called Bateman domain or a
CBS pair which is reflected in this model. The interface
between the two CBS domains forms a cleft that is a
potential ligand binding site. The CBS pair coexists
with a variety of other functional domains. It has been
proposed that the CBS domain may play a regulatory role,
although its exact function is unknown.
Length = 110
Score = 27.2 bits (61), Expect = 6.2
Identities = 10/32 (31%), Positives = 16/32 (50%)
Query: 202 SHPVICLRPLETVGNIIDVLKATSHNGFPIVD 233
S PV +RP T+ ++L H P+V+
Sbjct: 1 SSPVKTVRPEATIEEARELLLRYGHTALPVVE 32
>gnl|CDD|234717 PRK00293, dipZ, thiol:disulfide interchange protein precursor;
Provisional.
Length = 571
Score = 28.3 bits (64), Expect = 6.7
Identities = 20/59 (33%), Positives = 24/59 (40%), Gaps = 8/59 (13%)
Query: 52 KGAFGV--FSLSVFVVTYFLLSVWT------YGVSVSGGVFIPCLLTGAAWGRLFSLFL 102
K AFG +L VF++ L VW GV+ G FI L W RL L
Sbjct: 364 KTAFGFVLLALPVFLLERVLPGVWGLRLWSLLGVAFFGWAFIQSLKAKRGWMRLLGQIL 422
>gnl|CDD|177781 PLN00187, PLN00187, photosystem II light-harvesting complex II
protein Lhcb4; Provisional.
Length = 286
Score = 28.2 bits (63), Expect = 7.2
Identities = 23/70 (32%), Positives = 32/70 (45%), Gaps = 5/70 (7%)
Query: 84 FIPCLLTGAAWGRLFSLFLQSI--FPEATWIDPGKYALIGAAAQLGGVVRMTISLTIILI 141
F C L W L +L S+ TW D GK L+ ++ LG + +I+ T+I I
Sbjct: 133 FRECELIHGRWAMLATLGALSVEALTGVTWQDAGKVELVDGSSYLGQPLPFSIT-TLIWI 191
Query: 142 EA--TGNISF 149
E G I F
Sbjct: 192 EVLVIGYIEF 201
>gnl|CDD|222207 pfam13536, EmrE, Multidrug resistance efflux transporter. This is
a membrane protein family acting as a multidrug
resistance efflux transporter.
Length = 112
Score = 26.8 bits (60), Expect = 8.4
Identities = 16/104 (15%), Positives = 33/104 (31%), Gaps = 10/104 (9%)
Query: 32 LAALWLQVPEKSVRTMLHDPKGAFGVFSLSVFVVTYFLLSVWTYGVSVSGGVFIPCLLTG 91
L + ++ V L + + + + + Y L + G +
Sbjct: 13 LLIVLIRGRLGDVFRALKTKPWLWLILAGLIGFLFYAL---LCLALQYGPGWVVAITALT 69
Query: 92 AAWGRLFSLFLQSIFPEATWIDPGKYALIGAAAQLGGVVRMTIS 135
+ L +F + K L+ +A L GVV M ++
Sbjct: 70 PVFAALLGRL---LFKQRLP----KRELLASAIILAGVVLMQVT 106
>gnl|CDD|239975 cd04602, CBS_pair_IMPDH_2, This cd contains two tandem repeats of
the cystathionine beta-synthase (CBS pair) domains in
the inosine 5' monophosphate dehydrogenase (IMPDH)
protein. IMPDH is an essential enzyme that catalyzes
the first step unique to GTP synthesis, playing a key
role in the regulation of cell proliferation and
differentiation. CBS is a small domain originally
identified in cystathionine beta-synthase and
subsequently found in a wide range of different
proteins. CBS domains usually come in tandem repeats,
which associate to form a so-called Bateman domain or a
CBS pair which is reflected in this model. The interface
between the two CBS domains forms a cleft that is a
potential ligand binding site. The CBS pair coexists
with a variety of other functional domains. It has been
proposed that the CBS domain may play a regulatory role,
although its exact function is unknown. Mutations of
conserved residues within this domain in IMPDH have been
associated with retinitis pigmentosa.
Length = 114
Score = 26.8 bits (60), Expect = 8.5
Identities = 6/29 (20%), Positives = 15/29 (51%)
Query: 206 ICLRPLETVGNIIDVLKATSHNGFPIVDV 234
L P TV +++++ + +G P+ +
Sbjct: 5 SVLSPDHTVADVLEIKEKKGFSGIPVTED 33
>gnl|CDD|226844 COG4420, COG4420, Predicted membrane protein [Function unknown].
Length = 191
Score = 27.4 bits (61), Expect = 9.0
Identities = 12/28 (42%), Positives = 14/28 (50%)
Query: 163 IGDFFTEGLYDIHIQLSGIPLLAWDPPP 190
I F L I + L +P LAWDP P
Sbjct: 61 ILTFTLLLLLWIVLNLFLVPGLAWDPYP 88
>gnl|CDD|237401 PRK13499, PRK13499, rhamnose-proton symporter; Provisional.
Length = 345
Score = 27.6 bits (62), Expect = 9.4
Identities = 16/46 (34%), Positives = 21/46 (45%), Gaps = 3/46 (6%)
Query: 53 GAFGVFSLSVF--VVTYFLL-SVWTYGVSVSGGVFIPCLLTGAAWG 95
G+FS + ++ LL W Y S SG +P L GA WG
Sbjct: 39 SVGGIFSWLILPWLIAALLLPDFWAYYSSFSGSTLLPVFLFGALWG 84
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
0.320 0.137 0.419
Gapped
Lambda K H
0.267 0.0828 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 17,961,978
Number of extensions: 1735508
Number of successful extensions: 1542
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1529
Number of HSP's successfully gapped: 69
Length of query: 352
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 254
Effective length of database: 6,590,910
Effective search space: 1674091140
Effective search space used: 1674091140
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 59 (26.3 bits)